title: vehicle_E12.5plus2d_Epcam_2_9

data_processing:
For scRNA-seq and bulk cell RNA-seq, sequencing reads were aligned to the Mus musculus reference genome (mm10) using TopHat (v2.1.0) with the parameters "-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq [input_fastq2]". HTSeq (v0.6.0) was used to quantify the reads that mapped to each gene with the parameters "-f bam -r pos -s no -a 30".
For N-ChIP, sequencing reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5)24 with default parameters. Reads with mapping quality ≥30 were retained for downstream analyses. PCR duplicate reads were removed using samtools (v1.3.1) with "samtools sort in_bam | samtools rmdup -s - out_bam". Reads from biological replicates were concatenated. TP10M (tags per 10 million) values were calculated and stored in the bedGraph format using Homer with the parameters "makeUCSCfile out_dir –o out.bdg –name sample_name -color track_color –fragLength 150 –avg -fsize 1e20". Highly enriched regions (peaks) of H3K4me1, H3K4me3 and H3K27ac were identified using MACS (v1.4.2) with default parameters. Peaks of H3K27me3 were identified using MACS2 (v2.1.0) with "—broad" mode. Peaks that overlapped with ENCODE blacklisted genomic regions were excluded.
For CUT&RUN ChIP, index, primer and daptor sequences were identified using FastQC (v0.11.3) with parameters "--extract --o out_dir -t 4 fastqc.file". Next, we trimmed the index, primer and adaptor sequences off from the paired-end reads using Trimmomatic (v0.38) 30 with parameters "java jar trimmoma 0.38.jar PE -phred33 fasq1.file fastq2.file ILLUMINACLIP:fasta.file:2:30:10 LEADING:3 TAILING:3 SLIDINGWINDOW:4:15 MINLEN:36". The trimmed reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5) with default parameters. Reads with mapping quality ≥30 were retained for the downstream analysis. Duplicate reads were removed from the PCR results using samtools (v1.3.1) with the command "samtools sort in_bam|samtools rmdup -s - out_bam". Reads generated from biological replicates were pooled. TP10M values were calculated and stored in bedGraph files using Homer with the command "makeUCSCfile out_dir -o out.bdg -name sample_name -avg -fsize 1e20". Peak calling was performed using MACS2 (v2.1.0) with ‘--broad’ mode and default parameters. Genome regions that overlapped with ENCODE blacklist regions (Encode Project Consortium, 2012) were excluded from peak regions.
Genome_build: mm10
Supplementary_files_format_and_content: For scRNA-seq and bulk cell RNA-seq, comma-Separated Values files (.csv) include read count for each sample. For N-ChIP and CUT&RUN ChIP, bedgraph files (.bdg) include scores representing read count per bp per 1 × 10e7 reads; BED files (.bed) include highly enriched regions (peaks).

source_name: Liver

extract_protocol:
For scRNA-seq, livers were dissociated into single cells by treatment with 0.25% trypsin at 37°C. The reaction was terminated by the addition of 0.4 volumes of FBS. The single-cell suspensions were centrifuged at 100 × g for 5 min at 4 °C, and the resulting pellets were re-suspended with PBS containing 1% FBS. Cells were incubated with the DLK-FITC antibody (MBL, D187-4, 1:100) and/or EpCAM-APC antibody (eBioscience, 17-5791-82, 1:50) at 4 °C for 20 min. After washing, cells were sorted with a BD FACS Aria SORP cell sorter (BD Bioscience). Dead cells were excluded by DAPI (Sigma, D9564, 0.5 µg/mL). The generation of cDNA were performed according to Smart-seq2 method.
For scRNA-seq, two nanograms of cDNA was used to prepare libraries using a TruePrep DNA Library Prep Kit (Vazyme, TD502). Four-cycle PCR using biotinylated index primers introduced a biotin tag to the 3’ end of the cDNA. After cDNA fragmentation using a Bioruptor Plus sonicator (Diagenode), the 3’ terminals of the cDNA were captured using Dynabeads MyOne Streptavidin C1 (Thermo Fisher, 65002). Thirty nanograms of cDNA was used to construct libraries using a Kapa Hyper Prep Kit (Kapa Biosystems, KK8505).
For N-ChIP and CUT&RUN ChIP, we collected approximately 20,000 cells for each ChIP-seq, and used antibodies against H3K4me3 (Abcam, ab8580, 1ng), H3K27me3 (Millipore, 07-449, 1ng), H3K4me1 (Millipore, 07-436, 1ng), H3K27ac (Active motif, 39133, 1ng) and EZH2 (Cell Signaling Technology, 5246, 1:100). N-ChIP was carried out following the protocol of Brind'Amour et al. (2015), and CUT&RUN ChIP-seq was performed following the protocol of Peter J Skene et al. (2018).
For N-ChIP and CUT&RUN ChIP, libraries of ChIP DNA were constructed with the Ultra DNA Library Prep Kit for Illumina (New England Biolabs, E7370) or the KAPA Hyper Prep Kit (Kapa Biosystems, KK8502). DNA purification was conducted with VAHTS DNA Clean Beads XP beads (Vazyme, N411-03). The quality of the libraries was assessed with an Advanced Analytical Fragment Analyzer (AATI).
For bulk cell RNA-seq, livers were dissociated into single cells by treatment with 0.25% trypsin at 37°C. The reaction was terminated by the addition of 0.4 volumes of FBS. The single-cell suspensions were centrifuged at 100 × g for 5 min at 4 °C, and the resulting pellets were re-suspended with PBS containing 1% FBS. Cells were incubated with the DLK-FITC antibody (MBL, D187-4, 1:100) at 4 °C for 20 min. After washing, cells were sorted with a BD FACS Aria SORP cell sorter (BD Bioscience). Dead cells were excluded by DAPI (Sigma, D9564, 0.5 µg/mL). Total RNA was extracted from approximately 50,000 cells using the RNeasy Micro Kit (Qiagen, 74004).
For bulk cell RNA-seq, libraries were constructed with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, #E7490) and the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, #E7420).

tag: Stage

tag: protocol

tag: culture

tag: sort

value: EpCAM+

tag: genotype/treatment

value: DMSO


title: female, 0mM (ctrl), 1h, replicate 1

status: Public on Jun 26 2023

type: SRA

city: Bloomington

first: Jason

middle: M

last: Tennessen

email: tennessenlab@gmail.com, tennlab@iu.edu, jtenness@iu.edu, tourigny@iu.edu

state: IN

address: 1001 E 3rd St

department: Biology

country: USA

institute: Indiana University

description: raw fastq files are coded with the schema "[NaAsO2 (soduium arsenite)]- [M/F (male or female)  0/1/2/4/8/24/48 (time of treatment in hours)  A/B/C (0, 0.25, or 1mM arsenite, respectively)]-[1/2/3/4 (replicate number)]

library_source: transcriptomic

data_processing:
Reads were quantified with Salmon psueodoaligner
Normalized counts were generated with DESeq2 using tximport and the Salmon quantification
Assembly: BDGP6.32
Supplementary files format and content: Salmon qunatification directories (including quant.sf, bootstrap, log files) as gzipped tar archives
Supplementary files format and content: supplemtental file contains ZIP of excel sheets containing sex-specific normalized log counts as output by vst() function of DESeq2

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: whole animal

growth_protocol: Flies were kept at 25°C, 60% humidity, 12h/12h light/dark cycle, on Bloomington food

extract_protocol:
Treated flies were frozen in bead tubes, followed by disruption and extraction in Trizol.  RNA was then cleaned with Qiagen RNeasy kit
Illumina Stranded mRNA prep, 96 index
Poly-A-selected total RNA prepared with TruSeq ligation for paired-end sequencing

treatment_protocol: 5-7 day old flies were anaesthetized with CO2 and sorted by sex into separate vials.  Two days later, flies were transferred to vials with sterile water and starved for 16h before transfer to exposure vials containing 0, 0.25, or 1mM sodium arseinite in liquid food (sucrose + yeast extract)  for 1h, 2h, 4h, 8h, 24h or 48h (see Holsopple et al doi:10.3791/65029 for treatment details)

tag: tissue

value: whole animal

tag: genotype

value: OregonR

tag: Sex

value: female

tag: treatment

value: 0mM (ctrl)

tag: time

tag: replicate


title: E19.5_87, scRNA-seq

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

description:
mSTRT-seq
readcount.mSTRT-seq.csv

data_processing:
For mSTRT-seq, libraries were sequenced as 150-bp paired-end reads on an Illumina HiSeq 4000 platform. Raw files (fastq format) were separated based on cell-specific barcode sequences. PolyA sequences were trimmed from R1 reads (3’ end of cDNA). Preprocessed R1 reads from each cell were then aligned to the Mus musculus reference genome GRCm38/mm10 with TopHat V2.1.0. Bam files were annotated to genes with featureCounts (v1.5.3). We used samtools (v1.3.1) to sort and index the output bam files. UMIs of each gene were counted with umi-tools (v0.5.0) with the “unique” method.
For Smart-seq 3, libraries were sequenced as 100-bp paired-end reads on an MGI-seq 2000 platform. We trimmed the index, primer and adaptor sequences from the paired-end reads using Trimmomatic v0.39. The trimmed reads were aligned to the M. musculus reference genome GRCm38/mm10 with HISAT v2.1.0. Bam files were annotated to genes with featureCounts (v2.0.0). Either 5’ fragments or internal fragments were used during alignment.
For snRNA-seq, libraries were sequenced as 150-bp paired-end reads on an Illumina HiSeq 4000 platform. The alignment processes of snRNA-seq were similar to those of mSTRT-seq. The specific parameter of featureCounts (v1.5.3) during snRNA-seq alignment was “-t transcript” to ensure that the intron of mRNA could be detected.
For RNA-seq, libraries were sequenced as 150-bp paired-end reads on an Illumina HiSeq 2500 platform. the sequencing reads were aligned to the M. musculus genome (mm10) using TopHat (v2.1.0; https://ccb.jhu.edu/software/tophat/index.shtml) with the parameters ‘-o out_dir -G gtf –transcriptome-index trans_index bowtie2_index input_fastq1 input_fastq2’. Reads aligned to genes were counted using HTSeq (v0.6.0; https://htseq.readthedocs.io/) with the parameters ‘htseq-count -f bam -r pos -s reverse -a 30 input_bam gtf’.
Assembly: mm10
Supplementary files format and content: Comma-Separated Values files (.csv)

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
For scRNA-seq, single cells were picked up into cell lysis buffer, and mRNA was reverse transcribed and amplified. For snRNA-seq, nucleus extraction was performed as previously reported(Krishnaswami et al., 2016). In brief, hepatocytes were collected through FACS sorting. Cell membranes were broken down with a homogenizer in homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris buffer (pH 8.0), 1 µM DTT, protease inhibitor, RNase inhibitor and 0.1% Triton X-100). After centrifugation (5 min, 500 g, 4° C), the nucleus was washed with PBS containing RNase inhibitor and stained with 0.5 ug/ml DAPI. The single nucleus was sorted into cell lysis. SnRNA-seq was performed using well-based mSTRT-seq just as scRNA-seq, but the cycles of cDNA amplification was 4 + 16. For bulk RNA-seq, total RNA was extracted using the RNAprep Pure Micro Kit. Poly(A) RNA was purified with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490).
For well-based mSTRT-seq(Li et al., 2017), barcoded DNA products were pooled and libraries were constructed with a Kapa Hyper Prep Kit (Kapa Biosystems, KK8505). For Smart-seq3(Hagemann-Jensen et al., 2022), the library of each cell was constructed separately with TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501).  For bulk RNA-seq, libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads (NEB, #E7765) according to the manufacturer’s instructions.

value: liver

tag: cell type

value: hepatocyte

value: Alb-Cre; Rosa-tdTomato

tag: age

tag: ploidy

tag: zonation


title: P12_40d_Nr2f2-KO_113, scRNA-seq

description:
MGI-seq 2000
Smart-seq3
readcount.Smartseq3.csv


title: female, 0mM (ctrl), 0h (ctrl), replicate 3

value: 0h (ctrl)


title: vehicle_E12.5plus2d_Epcam_2_8

growth_protocol: Liver lobes from E12.5 mouse livers were collected and cultured on Nuclepore Track-Etch Membranes (Whatman, 110414). 12-well plates filled with 2 mL RPMI 1640 medium (Invitrogen, 22400) supplemented with 10% FBS, 1 × ITS-X (Gibco, 51500), 50 ng/mL EGF and 1 × Penicillin-Streptomycin (Gibco, 15140) were used.

treatment_protocol: Cultured explants were treated for 2 days with DMSO (control), 2 µM GSKJ4 (Tocris Bioscience, 4594) or 1 µM GSK126.

tag: batch


title: P12_40d_Nr2f2-KO_112, scRNA-seq


title: E19.5_86, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: vehicle_E12.5plus2d_Epcam_2_7


title: female, 0mM (ctrl), 0h (ctrl), replicate 2


title: E19.5_85, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_111, scRNA-seq


title: female, 0mM (ctrl), 0h (ctrl), replicate 1


title: TAM_pos_1

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Illumina bcl2fastq 2.17 software was used for base calling.
Adapter sequences and low-quality ends were removed with cutadapt, trimming for TrueSeq and polyA sequences.
Reads were aligned to the mouse genome build mm10 using HISAT2 aligner (v2.1.0).
Raw counts per gene were calculated with featureCounts (v1.4.4).
Samples were normalized with TMM method (edgeR package) and log2 transformed with voom (limma package)
Genome_build: mm10
Supplementary_files_format_and_content: tab separated raw counts from featureCounts with Ensembl gene ID and gene symbol, tab separated log2 normalized counts with Ensembl gene ID and gene symbol.

source_name: TAMs

extract_protocol: RNA extraction, library preparation and sequencing were performed by Genewiz (South Plainfield, New Jersey, USA) on an Illumina HiSeq 2500 (Illumina).

value: TAMs

tag: gender

value: male

tag: group


title: female, 0mM (ctrl), 2h, replicate 1


title: vehicle_E12.5plus2d_Epcam_2_5

tag: Stage

tag: protocol


title: P12_40d_Nr2f2-KO_110, scRNA-seq


title: vehicle_E12.5plus2d_Epcam_2_6

tag: culture

tag: sort


title: E19.5_83, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue


title: E19.5_84, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: genotype


title: E19.5_82, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_108, scRNA-seq


title: vehicle_E12.5plus2d_Epcam_2_4

tag: genotype/treatment


title: vehicle_E12.5plus2d_Epcam_2_3


title: P12_40d_Nr2f2-KO_109, scRNA-seq

tag: treatment


title: female, 0.25mM, 8h, replicate 3

tag: Sex

value: 0.25mM arsenite

tag: time


title: female, 0.25mM, 8h, replicate 2

tag: replicate


title: E19.5_81, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: age


title: P12_40d_Nr2f2-KO_107, scRNA-seq

tag: ploidy

tag: zonation


title: female, 0.25mM, 8h, replicate 1


title: vehicle_E12.5plus2d_Epcam_2_2

tag: batch


title: female, 0.25mM, 4h, replicate 3


title: E19.5_80, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_106, scRNA-seq


title: female, 0.25mM, 4h, replicate 2


title: vehicle_E12.5plus2d_Epcam_2_12


title: E19.5_79, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_105, scRNA-seq


title: female, 0.25mM, 4h, replicate 1


title: E19.5_78, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_104, scRNA-seq


title: vehicle_E12.5plus2d_Epcam_2_10


title: female, 0.25mM, 48h, replicate 3


title: vehicle_E12.5plus2d_Epcam_2_11


title: E19.5_77, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: female, 0.25mM, 48h, replicate 2


title: P12_40d_Nr2f2-KO_103, scRNA-seq


title: female, 0.25mM, 48h, replicate 1


title: E19.5_75, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: E19.5_76, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_101, scRNA-seq


title: vehicle_E12.5plus2d_Epcam_1_9


title: vehicle_E12.5plus2d_Epcam_2_1


title: vehicle_E12.5plus2d_Epcam_1_8


title: vehicle_E12.5plus2d_Epcam_1_7


title: female, 0.25mM, 2h, replicate 2


title: E19.5_73, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: E19.5_74, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_100, scRNA-seq


title: P12_40d_Nr2f2-KO_99, scRNA-seq


title: vehicle_E12.5plus2d_Epcam_1_6


title: female, 0.25mM, 2h, replicate 1


title: E19.5_72, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: vehicle_E12.5plus2d_Epcam_1_5


title: female, 0.25mM, 24h, replicate 3


title: P12_40d_Nr2f2-KO_102, scRNA-seq


title: E19.5_71, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_97, scRNA-seq


title: vehicle_E12.5plus2d_Epcam_1_4


title: female, 0.25mM, 2h, replicate 3


title: female, 0.25mM, 24h, replicate 2


title: E19.5_70, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: female, 0.25mM, 24h, replicate 1


title: P12_40d_Nr2f2-KO_95, scRNA-seq


title: female, 0.25mM, 1h, replicate 3


title: vehicle_E12.5plus2d_Epcam_1_24


title: vehicle_E12.5plus2d_Epcam_1_3


title: E19.5_68, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_98, scRNA-seq


title: P12_40d_Nr2f2-KO_94, scRNA-seq


title: P12_40d_Nr2f2-KO_93, scRNA-seq


title: E19.5_66, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: female, 0.25mM, 1h, replicate 1


title: P12_40d_Nr2f2-KO_92, scRNA-seq


title: E19.5_67, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: female, 0.25mM, 1h, replicate 2


title: E19.5_65, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_137

first: Tomas

last: Kay

address: Biophore building

institute: University of Lausanne

data_processing:
Reads were mapped using STAR (to the reference genome and annotation), using default parameter settings
Reads were counted using FeatureCounts, using default parameter settings
Supplementary files format and content: csv file: unnormalised counts matrix

organism: Camponotus fellah

source_name: Brain

extract_protocol:
RNA was extracted using Tri reagent, following manufacturers protocol
RNA libraraies were prepared using the KAPA Stranded mRNASeq Library Preparation Kit, following manufacturers protocol

value: Brain

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse

value: forage ratio:0


title: vehicle_E12.5plus2d_Epcam_1_21

tag: Stage

tag: protocol

tag: culture

tag: sort

tag: genotype/treatment


title: vehicle_E12.5plus2d_Epcam_1_22

tag: batch


title: P12_40d_Nr2f2-KO_91, scRNA-seq

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_96, scRNA-seq


title: P12_40d_Nr2f2-KO_90, scRNA-seq


title: E19.5_69, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: E19.5_63, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_136

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: P12_40d_Nr2f2-KO_89, scRNA-seq

tag: tissue

tag: cell type

tag: genotype


title: E19.5_62, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: age

tag: ploidy

tag: treatment


title: E19.5_64, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: zonation


title: vehicle_E12.5plus2d_Epcam_1_23

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col4_134

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: grooming forage

tag: maturity

tag: nurse


title: col4_133

tag: tissue

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: col4_132


title: P12_40d_Nr2f2-KO_87, scRNA-seq

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: vehicle_E12.5plus2d_Epcam_1_2

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col4_131

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: grooming forage

tag: maturity

tag: nurse


title: E19.5_60, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: vehicle_E12.5plus2d_Epcam_1_17

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: vehicle_E12.5plus2d_Epcam_1_18


title: E19.5_61, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: vehicle_E12.5plus2d_Epcam_1_19


title: vehicle_E12.5plus2d_Epcam_1_16


title: P12_40d_Nr2f2-KO_88, scRNA-seq


title: E19.5_59, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_86, scRNA-seq


title: col4_129

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: P12_40d_Nr2f2-KO_85, scRNA-seq

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: vehicle_E12.5plus2d_Epcam_1_20

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: vehicle_E12.5plus2d_Epcam_1_15


title: P12_40d_Nr2f2-KO_84, scRNA-seq


title: E19.5_57, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_127

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: grooming forage

tag: maturity

tag: nurse

value: forage ratio:2.46E-06


title: P12_40d_Nr2f2-KO_83, scRNA-seq

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: col4_126

tag: colony

tag: bodylength

tag: headwidth

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: vehicle_E12.5plus2d_Epcam_1_13

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E19.5_56, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype


title: P12_40d_Nr2f2-KO_82, scRNA-seq

tag: age

tag: ploidy

tag: treatment


title: vehicle_E12.5plus2d_Epcam_1_12


title: P12_40d_Nr2f2-KO_81, scRNA-seq

tag: zonation


title: col4_125

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: grooming forage

tag: maturity

tag: nurse


title: col4_124

tag: tissue

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: P12_40d_Nr2f2-KO_80, scRNA-seq

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: col4_130

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest


title: E19.5_55, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: E19.5_53, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: E19.5_54, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: vehicle_E12.5plus2d_Epcam_1_11

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: vehicle_E12.5plus2d_Epcam_1_10


title: col4_123

tag: tissue

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: E19.5_58, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_79, scRNA-seq


title: vehicle_E12.5plus2d_Epcam_1_14

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col4_121

tag: tissue

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: P12_40d_Nr2f2-KO_78, scRNA-seq

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_77, scRNA-seq

tag: tissue


title: E19.5_52, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_122

tag: colony

tag: bodylength

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: E19.5_50, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_120

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding


title: col4_117

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: E19.5_49, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_75, scRNA-seq

tag: tissue


title: E19.5_48, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_116

tag: colony

tag: bodylength

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_6

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment

value: GSKJ4 2umol


title: P12_40d_Nr2f2-KO_74, scRNA-seq

tag: cell type

tag: genotype

tag: age


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_7

value: EpCAM+


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_8


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_5


title: vehicle_E12.5plus2d_Epcam_1_1

value: DMSO


title: col4_115

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_9

tag: Stage

tag: protocol


title: P12_40d_Nr2f2-KO_73, scRNA-seq

tag: tissue

tag: ploidy

tag: treatment

tag: zonation


title: col4_114

tag: colony

tag: bodylength

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: P12_40d_Nr2f2-KO_72, scRNA-seq

tag: cell type

tag: genotype

tag: age


title: col4_113

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending


title: P12_40d_Nr2f2-KO_76, scRNA-seq

tag: tissue

tag: ploidy

tag: treatment

tag: zonation


title: E19.5_51, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_24

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: P12_40d_Nr2f2-KO_71, scRNA-seq

tag: cell type

tag: genotype

tag: age


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_3


title: col4_112

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: E19.5_45, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_70, scRNA-seq

tag: cell type

tag: genotype

tag: age


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_23

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col4_109

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: E19.5_43, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: E19.5_47, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_69, scRNA-seq


title: E19.5_42, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_108

tag: colony

tag: bodylength

tag: headwidth

tag: grooming forage

tag: maturity

tag: nurse


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_22

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col4_106

tag: tissue

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_21


title: E19.5_40, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: E19.5_41, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_67, scRNA-seq


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_20

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E19.5_46, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue


title: E19.5_44, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_103

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: grooming forage

tag: maturity

tag: nurse


title: col4_104

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_4

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E19.5_39, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: col4_102

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: grooming forage

tag: maturity

tag: nurse


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_19

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: P12_40d_Nr2f2-KO_65, scRNA-seq

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_18


title: E19.5_38, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_2


title: col4_101

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: E19.5_37, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype


title: P12_40d_Nr2f2-KO_68, scRNA-seq

tag: age

tag: ploidy

tag: treatment


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_17

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: P12_40d_Nr2f2-KO_63, scRNA-seq

tag: zonation


title: col4_100

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: grooming forage

tag: maturity

tag: nurse


title: E19.5_35, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment


title: E19.5_36, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: zonation


title: P12_40d_Nr2f2-KO_66, scRNA-seq


title: P12_40d_Nr2f2-KO_61, scRNA-seq


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_15

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E19.5_34, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_096

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_14

tag: Stage

tag: protocol


title: col4_094

tag: tissue

tag: grooming forage

tag: maturity

tag: nurse


title: P12_40d_Nr2f2-KO_64, scRNA-seq

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_13

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E19.5_33, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_59, scRNA-seq


title: E19.5_32, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_58, scRNA-seq


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_12


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_11


title: P12_40d_Nr2f2-KO_57, scRNA-seq


title: P12_40d_Nr2f2-KO_62, scRNA-seq


title: col4_093

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

value: forage ratio:7.66E-06


title: col4_092

tag: tissue

tag: grooming forage

tag: maturity

tag: nurse


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_16

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col4_091

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest


title: E19.5_30, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_56, scRNA-seq

tag: tissue


title: col4_090

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: col4_097

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest


title: E19.5_29, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_55, scRNA-seq

tag: tissue


title: P12_40d_Nr2f2-KO_60, scRNA-seq


title: P12_40d_Nr2f2-KO_54, scRNA-seq


title: E19.5_28, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_1

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: GSKJ4_2umol_E12.5plus2d_Epcam_3_10


title: GSKJ4_2umol_E12.5plus2d_Epcam_2_24


title: col4_089

tag: colony

tag: bodylength

tag: headwidth

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: col4_087

tag: tissue

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest


title: E19.5_27, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_53, scRNA-seq


title: E19.5_31, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_086

tag: colony

tag: bodylength

tag: headwidth

tag: broodcare

tag: guarding

tag: grooming nest


title: GSKJ4_2umol_E12.5plus2d_Epcam_2_22

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: GSKJ4_2umol_E12.5plus2d_Epcam_2_23


title: E19.5_26, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype


title: E19.5_25, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: age

tag: ploidy

tag: treatment


title: GSKJ4_2umol_E12.5plus2d_Epcam_2_21


title: P12_40d_Nr2f2-KO_51, scRNA-seq

tag: zonation


title: col4_085

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: E19.5_23, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype


title: E19.5_24, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: age

tag: ploidy

tag: treatment


title: col4_084

tag: colony

tag: bodylength

tag: broodcare

tag: guarding

tag: grooming nest


title: col4_083

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: queenattending


title: P12_40d_Nr2f2-KO_49, scRNA-seq

tag: zonation


title: GSKJ4_2umol_E12.5plus2d_Epcam_2_20

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col4_081

tag: tissue

tag: colony

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: P12_40d_Nr2f2-KO_50, scRNA-seq

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment


title: GSKJ4_2umol_E12.5plus2d_Epcam_2_19

tag: Stage

tag: protocol


title: GSKJ4_2umol_E12.5plus2d_Epcam_2_18

tag: culture

tag: batch


title: col4_077

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending


title: P12_40d_Nr2f2-KO_48, scRNA-seq

tag: tissue

tag: cell type

tag: genotype

tag: zonation


title: P12_40d_Nr2f2-KO_47, scRNA-seq

tag: age

tag: ploidy

tag: treatment


title: E19.5_21, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: E19.5_20, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_46, scRNA-seq


title: GSKJ4_2umol_E12.5plus2d_Epcam_2_17

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E19.5_22, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: GSKJ4_2umol_E12.5plus2d_Epcam_2_16


title: P12_40d_Nr2f2-KO_52, scRNA-seq


title: col4_076

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: col4_075

tag: tissue

tag: guarding

tag: grooming nest

tag: queenattending


title: E19.5_19, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_45, scRNA-seq


title: col4_074

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest


title: E19.5_18, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_44, scRNA-seq


title: E19.5_17, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_43, scRNA-seq


title: col4_072

tag: broodcare

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: col4_073

tag: tissue

tag: guarding

tag: grooming nest

tag: queenattending


title: GSKJ4_2umol_E12.5plus2d_Epcam_2_14

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: GSKJ4_2umol_E12.5plus2d_Epcam_2_15


title: E19.5_16, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_42, scRNA-seq


title: col4_071

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: P12_40d_Nr2f2-KO_41, scRNA-seq

tag: tissue

tag: cell type

tag: genotype


title: E19.5_15, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: age

tag: ploidy

tag: treatment


title: GSKJ4_2umol_E12.5plus2d_Epcam_2_13

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col4_070

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: P12_40d_Nr2f2-KO_40, scRNA-seq

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: GSK126_1umol_E12.5plus2d_Epcam_2_7

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment

value: GSK126 1umol


title: P12_40d_Nr2f2-KO_39, scRNA-seq


title: col4_068

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: E19.5_13, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: col4_067

tag: colony

tag: bodylength

tag: headwidth

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: E19.5_12, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_38, scRNA-seq


title: E19.5_11, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_066

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: cleaning forage


title: P12_40d_Nr2f2-KO_37, scRNA-seq

tag: tissue

tag: cell type

tag: genotype


title: col4_064

tag: grooming forage

tag: maturity

tag: nurse

value: forage ratio:NA


title: GSK126_1umol_E12.5plus2d_Epcam_2_9

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E19.5_10, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: GSK126_1umol_E12.5plus2d_Epcam_2_8


title: P12_40d_Nr2f2-KO_36, scRNA-seq


title: E19.5_9, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_35, scRNA-seq


title: col4_063

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: col4_060

tag: tissue

tag: grooming forage

tag: maturity

tag: nurse


title: E19.5_8, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_34, scRNA-seq


title: E19.5_14, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_059

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest


title: E19.5_7, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_058

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: E19.5_6, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype


title: P12_40d_Nr2f2-KO_33, scRNA-seq

tag: age

tag: ploidy

tag: treatment


title: P12_40d_Nr2f2-KO_32, scRNA-seq

tag: zonation


title: col4_057

tag: colony

tag: bodylength

tag: headwidth

tag: grooming forage

tag: maturity

tag: nurse


title: GSK126_1umol_E12.5plus2d_Epcam_2_23

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: GSK126_1umol_E12.5plus2d_Epcam_2_24


title: GSK126_1umol_E12.5plus2d_Epcam_2_3


title: GSK126_1umol_E12.5plus2d_Epcam_2_6


title: GSK126_1umol_E12.5plus2d_Epcam_2_22


title: GSK126_1umol_E12.5plus2d_Epcam_2_4


title: GSK126_1umol_E12.5plus2d_Epcam_2_5


title: E19.5_5, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype


title: P12_40d_Nr2f2-KO_31, scRNA-seq

tag: age

tag: ploidy

tag: treatment


title: col4_056

tag: colony

tag: bodylength

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: E19.5_4, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: zonation


title: P12_40d_Nr2f2-KO_30, scRNA-seq

tag: cell type

tag: genotype


title: GSK126_1umol_E12.5plus2d_Epcam_2_2

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: GSK126_1umol_E12.5plus2d_Epcam_2_20


title: col4_055

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: grooming forage

tag: maturity

tag: nurse


title: E19.5_3, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_29, scRNA-seq

tag: genotype


title: E19.5_2, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_28, scRNA-seq


title: GSK126_1umol_E12.5plus2d_Epcam_2_19

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col4_054

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: GSK126_1umol_E12.5plus2d_Epcam_2_18

tag: Stage

tag: protocol


title: E19.5_1, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: col4_053

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: grooming forage

tag: maturity

tag: nurse


title: GSK126_1umol_E12.5plus2d_Epcam_2_21

tag: Stage

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: P12_40d_Nr2f2-KO_27, scRNA-seq

tag: tissue

tag: cell type

tag: genotype

tag: age


title: col4_051

tag: colony

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: GSK126_1umol_E12.5plus2d_Epcam_2_17

tag: Stage

tag: protocol


title: E17.5_89, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_26, scRNA-seq

tag: tissue


title: col4_050

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: grooming forage

tag: maturity

tag: nurse


title: E17.5_88, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age


title: GSK126_1umol_E12.5plus2d_Epcam_2_16

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E17.5_87, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: ploidy

tag: treatment


title: col4_048

tag: tissue

tag: colony

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: P12_40d_Nr2f2-KO_24, scRNA-seq

tag: cell type

tag: genotype

tag: zonation


title: P12_40d_Nr2f2-KO_25, scRNA-seq

tag: age


title: GSK126_1umol_E12.5plus2d_Epcam_2_14

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort


title: GSK126_1umol_E12.5plus2d_Epcam_2_15

tag: genotype/treatment


title: col4_046

tag: tissue

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: grooming forage

tag: maturity

tag: nurse


title: E17.5_86, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_23, scRNA-seq


title: E17.5_85, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_22, scRNA-seq


title: col4_042

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: P12_40d_Nr2f2-KO_21, scRNA-seq

tag: tissue


title: E17.5_84, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: GSK126_1umol_E12.5plus2d_Epcam_2_12

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: GSK126_1umol_E12.5plus2d_Epcam_2_13


title: col4_041

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: grooming forage

tag: maturity

tag: nurse


title: GSK126_1umol_E12.5plus2d_Epcam_2_11


title: E17.5_83, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_20, scRNA-seq

tag: tissue


title: col4_040

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

value: forage ratio:3.18E-05


title: GSK126_1umol_E12.5plus2d_Epcam_2_10

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: P12_40d_Nr2f2-KO_19, scRNA-seq

value: liver

tag: cell type

tag: genotype

tag: age


title: E17.5_82, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

value: hepatocyte

tag: ploidy

tag: treatment

tag: zonation


title: col4_039

tag: tissue

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming forage

tag: maturity

tag: nurse


title: GSK126_1umol_E12.5plus2d_Epcam_2_1

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E17.5_81, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

value: Alb-Cre; Rosa-tdTomato

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_18, scRNA-seq


title: col4_038

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: P12_40d_Nr2f2-KO_17, scRNA-seq

tag: tissue

tag: cell type

tag: genotype


title: GSK126_1umol_E12.5plus2d_Epcam_1_9

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E17.5_80, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: GSK126_1umol_E12.5plus2d_Epcam_1_8


title: col4_045

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: grooming forage

tag: maturity

tag: nurse


title: GSK126_1umol_E12.5plus2d_Epcam_1_7

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col4_034

tag: tissue

tag: colony

tag: bodylength

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: E17.5_78, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: col4_032

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: grooming forage

tag: maturity

tag: nurse


title: P12_40d_Nr2f2-KO_15, scRNA-seq

tag: tissue


title: E17.5_77, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type


title: GSK126_1umol_E12.5plus2d_Epcam_1_6

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: GSK126_1umol_E12.5plus2d_Epcam_1_5


title: P12_40d_Nr2f2-KO_14, scRNA-seq

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: E17.5_76, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_13, scRNA-seq


title: col4_031

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: col4_030

tag: tissue

tag: grooming forage

tag: maturity

tag: nurse


title: E17.5_75, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: GSK126_1umol_E12.5plus2d_Epcam_1_4

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: P12_40d_Nr2f2-KO_12, scRNA-seq


title: GSK126_1umol_E12.5plus2d_Epcam_1_3


title: col4_029

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: GSK126_1umol_E12.5plus2d_Epcam_1_2

tag: Stage

tag: protocol


title: col4_037

tag: tissue

tag: grooming forage

tag: maturity

tag: nurse


title: E17.5_79, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_16, scRNA-seq


title: E17.5_74, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: E17.5_73, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_10, scRNA-seq


title: GSK126_1umol_E12.5plus2d_Epcam_1_12

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col4_026

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: col4_025

tag: tissue

tag: grooming forage

tag: maturity

tag: nurse


title: E17.5_72, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_9, scRNA-seq


title: col4_024

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest


title: E17.5_71, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_8, scRNA-seq


title: col4_023

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: GSK126_1umol_E12.5plus2d_Epcam_1_10

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: P12_40d_Nr2f2-KO_7, scRNA-seq

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: E17.5_70, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_022

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: grooming forage

tag: maturity

tag: nurse


title: E17.5_69, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype


title: P12_40d_Nr2f2-KO_11, scRNA-seq

tag: age

tag: ploidy

tag: treatment


title: P12_40d_Nr2f2-KO_6, scRNA-seq

tag: zonation


title: GSK126_1umol_E12.5plus2d_Epcam_1_1

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: AlfpCre_P300wtwt_P0_Epcam_4_9


title: col4_021

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: col4_020

tag: tissue

tag: grooming forage

tag: maturity

tag: nurse


title: P12_40d_Nr2f2-KO_5, scRNA-seq

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: AlfpCre_P300wtwt_P0_Epcam_4_8

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: AlfpCre_P300wtwt_P0_Epcam_4_7


title: col4_019

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: E17.5_67, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Nr2f2-KO_4, scRNA-seq


title: E17.5_66, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: E17.5_65, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Nr2f2-KO_3, scRNA-seq


title: AlfpCre_P300wtwt_P0_Epcam_4_5

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: AlfpCre_P300wtwt_P0_Epcam_4_6


title: GSK126_1umol_E12.5plus2d_Epcam_1_11


title: P12_40d_Nr2f2-KO_2, scRNA-seq


title: P12_40d_Nr2f2-KO_1, scRNA-seq


title: col4_018

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: grooming forage

tag: maturity

tag: nurse


title: col4_016

tag: tissue

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: E17.5_63, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: E17.5_68, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_017

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest


title: E17.5_62, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col4_015

tag: broodcare

tag: guarding

tag: grooming nest

tag: grooming forage

tag: maturity

tag: nurse


title: E17.5_61, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype


title: KO2

city: beijing

first: Guo

last: Tianwei

address: No.167 North Lishi Road, Xicheng District, Beijing, China

institute: fuwai hospital

data_processing:
For Transcriptome resequencing, first of all, we filter out low quality reads, contaminated connectors, and high content of unknown base N to obtain clean reads. Then compare clean reads to the reference genome, and then conduct differential alternative splicing Genetic testing. Then calculate the gene expression level. Finally, for multiple samples, differential expression genes between different samples are detected according to requirements, and in-depth cluster analysis and functional enrichment analysis are conducted on the differentially expressed genes.
Assembly: hg38
Supplementary files format and content: xls file include gene_expression values for each sample

organism: Homo sapiens

extract_protocol:
Extracting total RNA using trizol.
Take a certain amount of Total RNA sample and use oligodT to obtain mRNA from the total RNA; MRNA interruption; Fragmented mRNA was added to random primers for cDNA strand synthesis; Synthesize cDNA double stranded; End repair, addition of "A" and splicing of double stranded cDNA; Connect the product for PCR reaction and purification recovery; Library quality inspection;

tag: cell line

value: human embryonic stem cell derived cardiomyocytes

value: KO-CMs


title: KO3


title: col4_014

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: AlfpCre_P300wtwt_P0_Epcam_4_4

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: KO1


title: AlfpCre_P300wtwt_P0_Epcam_4_40


title: col4_013

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest


title: E17.5_60, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: WT3

tag: cell line

value: WT-CMs


title: col4_011

tag: colony

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: AlfpCre_P300wtwt_P0_Epcam_4_38

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: WT2

tag: cell type

tag: genotype


title: AlfpCre_P300wtwt_P0_Epcam_4_37


title: E17.5_58, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: AlfpCre_P300wtwt_P0_Epcam_4_39


title: col4_010

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: E17.5_64, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype


title: WT1

tag: cell line


title: AlfpCre_P300wtwt_P0_Epcam_4_41

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: AlfpCre_P300wtwt_P0_Epcam_4_36


title: col4_008

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: grooming forage

tag: maturity

tag: nurse


title: col4_007

tag: tissue

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: E17.5_56, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: AlfpCre_P300wtwt_P0_Epcam_4_34

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col4_006

tag: tissue

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming forage

tag: maturity

tag: nurse


title: lin-39p::RFP wt MNs rep 1

city: Nashville

first: David

last: Miller

state: TN

address: 465 21st Avenue South

department: Cell and Developmental Biology

institute: Vanderbilt University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, read mapping and gene counting were performed using CellRanger v6.1.1
see Samples section
We distinguished cells from empty droplets using the emptydrops algorithm from the DropletUtils R package, then corrected for background RNA using SoupX. Quality control metrics were generated with the scater R package. These steps were performed on the gene by barcode matrix from CellRanger for each sample independently.
Background corrected datasets were converted into monocle3 cell_data_set objects and combined into one dataset in monocle3. Monocle3 was used for dimensionality reduction (PCA followed by UMAP) and plotting.
Assembly: Custom 3' UTR extended genome reference built from WS273, available as supplemental file.
Supplementary files format and content: Two sets of processed data files are provided. One set contains all the cells that passed quality control and doublet removal. The second set contains just the ventral cord motor neurons. For both sets, three files are provided: 1) Gene by barcode matrix, 2)tab-separated table featuring metadata for barcodes (including barcode, percent of UMIs from mitochondria, Size factor, number of genes expressed, UMAP coordinates, cluster, experiment ID, Cell type, strain, and anatomical class) and 3) a tab-separated table featuring metadata for genes (gene IDs, gene symbols, and number of cells in which gene was detected).

organism: Caenorhabditis elegans

source_name: Motor neurons

growth_protocol: Worms were grown on 8P plates seeded with NA22 bacteria.

extract_protocol:
KRA257 worms were collected and washed twice. 250 uL pellets of worms were incubated in 500 uL of SDS-DTT buffer (20 mM HEPES, 0.25% SDS, 200 mM DTT, 3% sucrose, pH 8.0) for 6 minutes, then washed 5 times in egg buffer (25 mM HEPES pH 7.3, 118 mM NaCl, 48 mM KCl, 2mM CaCl2, 2mM MgCl2). Worms were then incubated in 500 uL of cold active protease (10 mg/mL in egg buffer, Protease from Bacillus licheniformis, Sigma-Aldrich P4860, with DNAse I 35 U/mL) for 35 minutes at 4 C. During the protease incubations, solutions were triturated by pipetting through a P1000 pipette tip for four sets of 80 repetitions Digestions were quenched by addition of 750 uL of L-15 media supplemented with 10% FBS. Cells and worm debris were pelleted by centrifugation (530 rcf for 5 minutes at 4 C), and then resuspended in 1 mL L-15-10. Cells were separated from worm debris by centrifugation for 2 minutes at 100 rcf at 4 C. The supernatant was collected and filtered through the 35-micron strainer cap of a 5 mL FACS tube (Falcon 352235) The pellet was resuspended a second time in 1 mL of L-15-10, spun at 100 rcf for 2 min at 4 C, and the supernatant was collected and filtered into the same FACS tube to combine with the first extraction. Fluorescently labeled motor neurons were isolated using FACS on a BD FACSAria III equipped with a 70-micron nozzle. GFP+ cells were collected into L-15 media with 33% FBS.
see columns in Samples section
Libraries were constructed using manufacturer protocols for 10X Chromium 3' gene expression assay v3.0

value: Motor neurons

tag: strain

value: KRA257 kasIs2 [lin-39p::RFP  + pha-1(+)]

tag: genotype

value: wt

tag: age

value: young adult

tag: synchronization protocol

value: L1 arrest + mesh synchronization


title: lin-39p::RFP wt MNs rep 2

description: 10X Genomics


title: AlfpCre_P300wtwt_P0_Epcam_4_33

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

value: EpCAM+

tag: genotype/treatment


title: col4_005

tag: tissue

value: Brain

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

value: forage ratio:0


title: acr-2::GFP wt MNs rep 1

description: 10X Genomics

data_processing:
Demultiplexing, barcode processing, read mapping and gene counting were performed using CellRanger v6.0.2
see Samples section
We distinguished cells from empty droplets using the emptydrops algorithm from the DropletUtils R package, then corrected for background RNA using SoupX. Quality control metrics were generated with the scater R package. These steps were performed on the gene by barcode matrix from CellRanger for each sample independently.
Background corrected datasets were converted into monocle3 cell_data_set objects and combined into one dataset in monocle3. Monocle3 was used for dimensionality reduction (PCA followed by UMAP) and plotting.
Assembly: Custom 3' UTR extended genome reference built from WS273, available as supplemental file.
Supplementary files format and content: Two sets of processed data files are provided. One set contains all the cells that passed quality control and doublet removal. The second set contains just the ventral cord motor neurons. For both sets, three files are provided: 1) Gene by barcode matrix, 2)tab-separated table featuring metadata for barcodes (including barcode, percent of UMIs from mitochondria, Size factor, number of genes expressed, UMAP coordinates, cluster, experiment ID, Cell type, strain, and anatomical class) and 3) a tab-separated table featuring metadata for genes (gene IDs, gene symbols, and number of cells in which gene was detected).

extract_protocol:
CZ631 worms were collected and washed twice. 250 uL pellets of worms were incubated in 500 uL of SDS-DTT buffer (20 mM HEPES, 0.25% SDS, 200 mM DTT, 3% sucrose, pH 8.0) for 6 minutes, then washed 5 times in egg buffer (25 mM HEPES pH 7.3, 118 mM NaCl, 48 mM KCl, 2mM CaCl2, 2mM MgCl2). Worms were then incubated in 500 uL of pronase (15 mg/mL in egg buffer, Sigma-Aldrich P8811) for 23 minutes at room temperature. During the protease incubations, solutions were triturated by pipetting through a P1000 pipette tip for four sets of 80 repetitions Digestions were quenched by addition of 750 uL of L-15 media supplemented with 10% FBS. Cells and worm debris were pelleted by centrifugation (530 rcf for 5 minutes at 4 C), and then resuspended in 1 mL L-15-10. Cells were separated from worm debris by centrifugation for 2 minutes at 100 rcf at 4 C. The supernatant was collected and filtered through the 35-micron strainer cap of a 5 mL FACS tube (Falcon 352235) The pellet was resuspended a second time in 1 mL of L-15-10, spun at 100 rcf for 2 min at 4 C, and the supernatant was collected and filtered into the same FACS tube to combine with the first extraction. Fluorescently labeled motor neurons were isolated using FACS on a BD FACSAria III equipped with a 70-micron nozzle. GFP+ cells were collected into L-15 media with 33% FBS.
see columns in Samples section
Libraries were constructed using manufacturer protocols for 10X Chromium 3' gene expression assay v3.0

tag: strain

tag: genotype

tag: age

tag: synchronization protocol

value: L1 arrest


title: acr-2::GFP wt MNs rep 2

description: 10X Genomics


title: E17.5_59, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: ploidy

tag: treatment

tag: zonation


title: col4_004

tag: tissue

tag: colony

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming forage

tag: maturity

tag: nurse


title: AlfpCre_P300wtwt_P0_Epcam_4_32

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col4_003

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: AlfpCre_P300wtwt_P0_Epcam_4_31


title: u25_PA_2

city: Changsha

first: Xibin

last: Tian

address: Tianma Road

institute: Hunan University

data_processing:
Illumina Casava1.8 software used for basecalling.
The clean reads were mapped to the C. elegans genome sequence using Hisat2 v2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of three biological replicates per condition was performed using the DESeq R package (1.18.0).
Genome_build: WBcel2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Samples.

source_name: Caenorhabditis elegans

growth_protocol: Synchronized L1 worms were placed onto NGM plates seeded with OP50 and grown at 20oC till L4 stage.

extract_protocol:
Animals were washed off the plates with M9 solution and frozen in TRIzol (Transgen, ER501-01-01). Total RNA was obtained using the kit (Transgen, ER501-01) and 1 ug total RNA from each sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: L4 stage animals were collected and washed with M9 solution before being transferred to modified NGM plates containing OP50 or PA14 for 24 h at 25oC.

tag: strain

tag: treatment duration

value: L4 animal exposured for 24 h

tag: treatment

value: P. aeruginosa PA14


title: u25_PA_3


title: u25_PA_1


title: col4_002

tag: tissue

tag: colony

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming forage

tag: maturity

tag: nurse


title: E17.5_51, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

value: liver

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: zonation


title: E17.5_57, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

value: hepatocyte


title: E17.5_53, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

value: Alb-Cre; Rosa-tdTomato


title: AlfpCre_P300wtwt_P0_Epcam_4_35

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col4_001

tag: tissue

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: AlfpCre_P300wtwt_P0_Epcam_4_3

tag: Stage


title: u25_OP_3

tag: strain

tag: treatment duration

tag: treatment

value: E. coli OP50


title: col3_134

tag: broodcare

tag: guarding

tag: grooming forage

tag: maturity

tag: nurse


title: E17.5_54, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: zonation


title: E17.5_49, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: E17.5_55, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: AlfpCre_P300wtwt_P0_Epcam_4_28

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: u25_OP_2

tag: strain

tag: treatment duration

tag: treatment


title: WT_PA_3

value: wild-type (N2)


title: col3_131

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage


title: col3_133

tag: tissue

tag: maturity

tag: nurse


title: E17.5_47, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: AlfpCre_P300wtwt_P0_Epcam_4_30

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: AlfpCre_P300wtwt_P0_Epcam_4_27


title: E17.5_52, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: WT_PA_2

tag: strain

tag: treatment duration


title: E17.5_48, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue


title: AlfpCre_P300wtwt_P0_Epcam_4_26


title: col3_127

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity


title: E17.5_50, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: col3_123

tag: tissue

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: nurse


title: col3_122

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending


title: WT_OP_3

tag: strain

tag: treatment duration


title: E17.5_44, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy


title: E17.5_45, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: treatment

tag: zonation


title: AlfpCre_P300wtwt_P0_Epcam_4_24

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: AlfpCre_P300wtwt_P0_Epcam_4_25


title: WT_PA_1


title: AlfpCre_P300wtwt_P0_Epcam_4_29


title: AlfpCre_P300wtwt_P0_Epcam_4_23


title: u25_OP_1


title: AlfpCre_P300wtwt_P0_Epcam_4_22


title: E17.5_42, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col3_121

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: E17.5_43, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: E17.5_41, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: DBD-sfGFP, GFP IP, 2

city: Madison

first: Melissa

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

library_source: genomic

data_processing:
ChIP-seq data was aligned to the Drosophila melanogaster reference genome (version dm6) using bowtie 2 v2.3.5 with the following non-default parameters: -k 2, --very-sensitive.
ChIP-seq aligned reads with a mapping quality < 30 were discarded, as were reads aligning to scaffolds or the mitochondrial genome.
ChIP-seq peak calling was performed using MACS v2 with the following parameters: -g 1.2e8, --call-summits.
To focus analysis on robust, high-quality peaks, we used 100 bp up- and downstream of peak summits, and retained only peaks that were detected in both replicates and overlapped by at least 100 bp.
Assembly: dm6
Supplementary files format and content: Replicates were merged into a single bigWig file.
Supplementary files format and content: bed files containing peaks. Contains only peaks that were detected in both replicates.

molecule: genomic DNA

source_name: embryo

growth_protocol: All stocks were grown on molasses food at 25ºC.

extract_protocol:
ChIP was performed as described previously (Blythe and Wieschaus 2015) on hand selected 2-2.5 hr AEL embryos from: sfGFP-GAF/+ and sfGFP-GAFSDPQ/+ females, nos-degradFP/His2Av-RFP (II); sfGFP-GAF (N) (III) and His2Av-RFP (II); sfGFP-GAF (N) (III) females, and nos-DBD-sfGFP/+ females. Briefly, 200-400 embryos were collected, dechorionated in 50% bleach for 3 min, fixed for 15 min in 4% formaldehyde and then lysed in 1 mL of RIPA buffer (50 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 0.5% sodium deoxycholate, and 150 mM NaCl). The fixed chromatin was then sonicated for 20 s 11 times at 20% output and full duty cycle (Branson Sonifier 250). Chromatin was incubated with 6 μg of anti-GFP antibody (Abcam #ab290) or 10 μl anti-H3K9me3 antibody (Active Motif, # 39162) overnight at 4°C , and then bound to 50 μl of Protein A magnetic beads (Dynabeads Protein A, Thermo Scientific). The purified chromatin was then washed, eluted, and treated with 90 μg of RNaseA (37°C, for 30 min) and 100 μg of Proteinase K (65°C, overnight). The DNA was purified using phenol/chloroform extraction and concentrated by ethanol precipitation. Each sample was resuspended in 25 μl of water.
Sequencing libraries were made using the NEB Next Ultra II library kit. For sfGFP-GAFSDPQ ChIP-seq, libraries were sequenced on the Illumina NextSeq 500 using 75bp single-end reads at the Northwestern Sequencing Core (NUCore). For DBD-sfGFP ChIP-seq, libraries were sequenced on the Illumina HiSeq 4000 using 50bp single-end reads at the Northwestern Sequencing Core (NUCore). For H3K9me3 ChIP-seq, libraries were sequenced on the Illumina NovaSeq 6000 using 150bp paired-end reads at the UW Madison Biotechnology Center.

value: embryo

tag: developmental stage

value: 2-2.5 hr AEL

value: nos-DBD-sfGFP/+

tag: chip antibody

value: anti-GFP (Abcam #ab290)


title: col3_119

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: queenattending

value: forage ratio:NA


title: E17.5_40, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue


title: col3_118

tag: guarding

tag: grooming nest

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: AlfpCre_P300wtwt_P0_Epcam_4_20

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col3_116

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest


title: E17.5_46, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: AlfpCre_P300wtwt_P0_Epcam_4_21

tag: Stage

tag: protocol

tag: culture


title: DBD-sfGFP, GFP Input, 2

tag: developmental stage

tag: chip antibody

value: none (input)


title: E17.5_39, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col3_115

tag: colony

tag: bodylength

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: AlfpCre_P300wtwt_P0_Epcam_4_19

tag: batch

tag: sort

value: EpCAM+

tag: genotype/treatment


title: E17.5_37, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: WT_OP_2

tag: strain

tag: treatment duration


title: DBD-sfGFP, GFP Input, 1

tag: developmental stage

tag: chip antibody


title: E17.5_38, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col3_113

value: Brain

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage


title: col3_120

tag: tissue

tag: maturity

tag: nurse


title: col3_112

value: forage ratio:0


title: AlfpCre_P300wtwt_P0_Epcam_4_18

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: AlfpCre_P300wtwt_P0_Epcam_4_17


title: col3_111

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest


title: WT_OP_1

tag: strain

tag: treatment duration

tag: treatment


title: E17.5_36, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: zonation


title: AlfpCre_P300wtwt_P0_Epcam_4_16

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort


title: Trem2-KO transplanted Trem2-KO; 5XFAD 3

city: Stanford

first: Yongjin

last: Yoo

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

data_processing:
150 bp paired-end reads were generated producing a mean of 30.1 million reads per sample.
RNA-sequencing data were processed and interpreted using in-house bioinformatic analysis pipelines in Sherlock computing clusters of The Stanford Research Computing Center.
Briefly, raw sequencing reads were demultiplexed with bcl2fastq and aligned to mouse transcriptome (mm10; GRCm38.p6) using STAR (version 2.5.2b) with the default parameters.
The expression of Gencode-annotated was calculated using HTSeq-count, and FPKM/TPM values were calculated using RSEM with the default parameters.
Raw counts of each gene were normalized, and genes with low counts were removed using the mean of normalized counts as a filter statistic, performed principal component analysis, and conducted differential expression analysis using the DESeq2 package (3.17) in R with standard parameters.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including normalized counts for each sample

extract_protocol:
DAPI-negative CD45+CD11b+ cells were directly sorted in 400 μL TRIzol LS using a FACSAria II. Total RNA was extracted and then purified using a Qiagen RNeasy MinElute Cleanup Kit.
The SMART-Seq v4 Ultra Low Input RNA Kit was used to generate cDNA and libraries according to the manufacturer’s protocol. The libraries were synthesized, indexed libraries were pooled and sequenced on NovaSeq platform.

tag: cell line

value: Primary

value: Circulation-derived myeloid cells


title: Trem2-KO transplanted Trem2-KO; 5XFAD 4


title: AlfpCre_P300wtwt_P0_Epcam_4_15

tag: genotype/treatment


title: DBD-sfGFP, GFP IP, 1

tag: developmental stage

tag: chip antibody


title: AlfpCre_P300wtwt_P0_Epcam_4_2


title: Trem2-KO transplanted Trem2-KO; 5XFAD 2


title: E17.5_35, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col3_110

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: Trem2-KO transplanted Trem2-KO; 5XFAD 1

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: E17.5_34, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: age

tag: ploidy

tag: zonation


title: E17.5_33, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: Trem2-KO; 5XFAD 3

value: Microglia


title: AlfpCre_P300wtwt_P0_Epcam_4_13

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: AlfpCre_P300wtwt_P0_Epcam_4_14


title: Trem2-KO; 5XFAD 2


title: col3_108

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage


title: Trem2-KO; 5XFAD 1

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: E17.5_31, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

value: liver

tag: age

tag: ploidy

tag: zonation


title: E17.5_32, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

value: hepatocyte


title: col3_106

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: maturity

tag: nurse


title: AlfpCre_P300wtwt_P0_Epcam_4_11

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col3_107

tag: tissue

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage


title: AlfpCre_P300wtwt_P0_Epcam_4_12


title: AlfpCre_P300wtwt_P0_Epcam_4_10


title: col3_105

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: maturity


title: Trem2-WT; 5XFAD 2

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Trem2-WT; 5XFAD 3

tag: tissue


title: AlfpCre_P300wtwt_P0_Epcam_4_1

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col3_104

tag: colony

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: nurse


title: AlfpCre_P300wtwt_P0_Epcam_3_9


title: col3_103

tag: tissue

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: maturity


title: col3_109


title: E17.5_29, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

value: Alb-Cre; Rosa-tdTomato

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: E17.5_28, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: E17.5_27, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: Normal 3

tag: cell line

value: No 5xFAD wildtype


title: Trem2-WT; 5XFAD 1


title: AlfpCre_P300wtwt_P0_Epcam_3_8

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col3_101

tag: tissue

tag: colony

tag: bodylength

tag: headwidth

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: nurse


title: AlfpCre_P300wtwt_P0_Epcam_3_7

tag: Stage

tag: protocol

tag: culture


title: E17.5_26, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: E17.5_25, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue


title: col3_100

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: maturity


title: E17.5_30, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: AlfpCre_P300wtwt_P0_Epcam_3_6

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: Normal 1

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: col3_099

tag: tissue

tag: colony

tag: bodylength

tag: headwidth

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: nurse


title: E17.5_24, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: age

tag: ploidy

tag: zonation


title: Trem2-WT transplanted Trem2-KO; 5XFAD 4

tag: cell line


title: col3_098

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: maturity


title: E17.5_23, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: AlfpCre_P300wtwt_P0_Epcam_3_4

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: Trem2-WT transplanted Trem2-KO; 5XFAD 3

tag: cell line


title: AlfpCre_P300wtwt_P0_Epcam_3_5


title: Trem2-WT transplanted Trem2-KO; 5XFAD 2


title: AlfpCre_P300wtwt_P0_Epcam_3_3


title: E17.5_22, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: age

tag: ploidy

tag: zonation


title: col3_095

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: nurse


title: E17.5_21, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: AlfpCre_P300wtwt_P0_Epcam_3_2

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E17.5_20, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: age

tag: ploidy

tag: zonation


title: Trem2-WT transplanted Trem2-KO; 5XFAD 1

tag: cell line


title: col3_094

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: maturity


title: AlfpCre_P300wtwt_P0_Epcam_3_16

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: Normal 2

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: E17.5_19, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: age

tag: ploidy

tag: zonation


title: AlfpCre_P300wtwt_P0_Epcam_3_15


title: col3_092

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: grooming forage

tag: nurse


title: col3_091

tag: tissue

tag: cleaning forage

tag: maturity


title: E17.5_18, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: E17.5_17, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: WTT2_1

first: Dhanya

last: Nambiar

state: CA

address: 269 Campus Drive

description: 20M Paired Reads

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Supplementary files format and content: CSV files with normalised read count data

source_name: Mouse primary cells

extract_protocol:
2x10^6 sorted PMN-MDSCs from tumors or lungs 633 using a RNeasy micro Kit
Library preparation and RNA sequencing were performed by Novogene via Illumina platforms based on mechanism of SBS (Sequencing by synthesis).

tag: cell line

value: Mouse primary cells

value: PMN-MDSC

value: WT

value: Tumor


title: WTL2_1

description: 20M Paired Reads

value: Lung


title: WTT3_1

description: 20M Paired Reads


title: WTL3-1

description: 20M Paired Reads


title: AlfpCre_P300wtwt_P0_Epcam_3_13

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E17.5_16, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col3_090

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: grooming forage

tag: nurse


title: col3_089

tag: tissue

tag: cleaning forage

tag: maturity


title: WTL1_1

description: 20M Paired Reads

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: col3_097

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)


title: AlfpCre_P300wtwt_P0_Epcam_3_14

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E17.5_15, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: age

tag: ploidy

tag: zonation


title: AlfpCre_P300wtwt_P0_Epcam_3_12


title: AlfpCre_P300wtwt_P0_Epcam_3_11


title: Chat-GFP+CD4+ T cells from HCC liver [HG_TCR]

city: Toronto

first: Tak

last: Mak

state: ON

address: 610 University Ave

department: The Campbell Family Institute for Breast Cancer Research

country: Canada

institute: Princess Margaret Cancer Centre, University Health Network

description:
TCR V(D)J library
poly A RNA

data_processing:
library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
For single-cell RNA-seq data analysis, sequencing data were processed using Cell Ranger (version 7.0.0) and aligned to the annotated mouse genome (mm10). The Cell Ranger VDJ pipeline was used to call TCR sequences.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_feature_bc_matrix.h5

extract_protocol:
Hepatic MNCs were stained with antibodies for CD4, CD8, CD19, TCR-β, NK1.1, CD45 and CD1d tetramer, as well as with barcode antibodies (TotalSeq-C0304, C0305, C0306, or C0307) to hashtag cells from individual mice of the HCC or control group. CD45+DAPI-NK1.1-CD1dTetramer-CD19-TCR-β+CD4+CD8-GFP+ (Chat-GFP+ CD4 T cells) and CD45+DAPI-NK1.1-CD1dTetramer-CD19-TCR-β+CD4+CD8-GFP- (Chat-GFP- CD4 T cells) populations were sorted. The two CD4 T cell compartments were individually sorted from each mouse. The same CD4 T compartments from mice under the same treatment were pooled into 4 samples: control Chat-GFP+, control Chat-GFP-, HCC Chat-GFP+ and HCC Chat-GFP-.
The 4 samples were loaded on 10x Chromium Controller. Libraries were prepared using Chromium Next GEM Single Cell 5' HT Reagent Kits v2 (Dual Index) (10x Genomics). The libraries were sequenced on the Illumina NovaSeq 6000. The sequencing depths are GEX ~50,000 reads/cell, TCR ~5000 reads per cell, and cell hashing TotalSeq C ~2000 reads/cell.

tag: cell type

value: CD4+ T cells

tag: library type

value: mRNA

tag: antibodies/tags


title: col3_093

tag: colony

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: col3_088

tag: tissue

tag: bodylength

tag: headwidth

tag: age (months)


title: col3_087


title: col3_086


title: Chat-GFP+CD4+ T cells from healthy liver [CG_TCR]

description:
TCR V(D)J library
poly A RNA

tag: cell type

tag: library type

tag: antibodies/tags


title: E17.5_14, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: Chat-GFP-CD4+ T cells from HCC liver [HN_TCR]

description:
TCR V(D)J library
poly A RNA


title: E17.5_12, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col3_085

tag: colony

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: E17.5_11, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue


title: Chat-GFP-CD4+ T cells from healthy liver [CN_TCR]

description:
TCR V(D)J library
poly A RNA

tag: cell type


title: Chat-GFP+CD4+ T cells from HCC liver [HG_GEX]

description:
5' mRNA library
poly A RNA

tag: library type


title: col3_084

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: E17.5_10, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: E17.5_9, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: col3_082

tag: colony

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending


title: Chat-GFP-CD4+ T cells from HCC liver [HN_GEX]

description:
5' mRNA library
poly A RNA

tag: tissue

tag: cell type

tag: library type

tag: antibodies/tags


title: Chat-GFP-CD4+ T cells from healthy liver [CN_GEX]

description:
5' mRNA library
poly A RNA


title: AlfpCre_P300wtwt_P0_Epcam_3_1

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

value: EpCAM+

tag: genotype/treatment


title: AlfpCre_P300wtwt_P0_Epcam_2_7


title: AlfpCre_P300wtwt_P0_Epcam_2_9


title: Chat-GFP+CD4+ T cells from healthy liver [CG_GEX]

description:
5' mRNA library
poly A RNA


title: col3_081

value: Brain

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: E17.5_8, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: tissue

tag: cell type

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: AlfpCre_P300wtwt_P0_Epcam_2_5

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E17.5_7, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: AlfpCre_P300wtwt_P0_Epcam_2_6


title: AlfpCre_P300wtwt_P0_Epcam_2_8


title: E17.5_13, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: Chat-GFP+CD4+ T cells from HCC liver [HG_CITE]

description:
Cell Hashing library
Hashtag-derived oligonucleotide (HTO)

library_source: other

molecule: protein

tag: library type

value: HTO

tag: antibodies/tags

value: Anti CD45 + Anti MHC classI:9239M/TotalSeq-C0304; 8703F/TotalSeq-C0305; 8705M/TotalSeq-C0306;  8634F/TotalSeq-C0307


title: col3_083

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

value: forage ratio:0


title: AlfpCre_P300wtwt_P0_Epcam_2_4

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment