title: col3_080

tag: tissue

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: nurse


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

status: Public on Jun 26 2023

type: SRA

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:
Cell Hashing library
Hashtag-derived oligonucleotide (HTO)

library_source: other

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

molecule: protein

organism: Mus musculus

source_name: liver

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.

value: liver

tag: cell type

value: CD4+ T cells

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: AlfpCre_P300wtwt_P0_Epcam_2_3

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

library_source: transcriptomic

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).

molecule: total RNA

source_name: Liver

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.

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).

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

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

value: EpCAM+

tag: genotype/treatment


title: E17.5_6, scRNA-seq

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)

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: hepatocyte

tag: genotype

value: Alb-Cre; Rosa-tdTomato

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: col3_079

city: Lausanne

first: Tomas

last: Kay

state: Vaud

address: Biophore building

country: Switzerland

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

tag: tissue

value: Brain

tag: colony

tag: bodylength

tag: headwidth

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: E17.5_5, scRNA-seq

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

tag: cell type

tag: genotype

tag: age

tag: ploidy


title: col3_078

tag: tissue

tag: colony

tag: age (months)

tag: nurse


title: AlfpCre_P300wtwt_P0_Epcam_2_2

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E17.5_4, scRNA-seq

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

tag: treatment

tag: zonation


title: col3_077

tag: bodylength

tag: headwidth

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

tag: tissue

tag: cell type

tag: library type

tag: antibodies/tags

value: Anti CD45 + Anti MHC classI:9238M/TotalSeq-C0304; 8702F/TotalSeq-C0305; 8704M/TotalSeq-C0306;  8637F/TotalSeq-C0307


title: AlfpCre_P300wtwt_P0_Epcam_3_10

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E17.5_3, scRNA-seq

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

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: E17.5_2, scRNA-seq

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


title: col3_076

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: nurse


title: Hnf4ctrl.Hnf4dTEC.Pdpn-CD104-.mTEClo.rep#1-7.GEX

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

description:
7 samples (3 Hnf4ctrl, 4 Hnf4dTEC) were hashed together into a single 10X scRNA-seq run
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
metadata.txt

library_source: transcriptomic single cell

data_processing:
Sequenced reads were demultiplexed, aligned, assigned to cells, and output as transcript-by-cell matrices using Cell Ranger (v6.1.0, 10X Genomics).
Hash-by-cell matrices were computed using CITE-seq-count (v1.4.3).
Cells with no or multiple hashes, high mitochondrial content, or lineage markers of contaminants (i.e., T, endothelial cells) were filtered out in Seurat (v4.0.2)
Assembly: mm10
Supplementary files format and content: The tsv files for barcodes, features and counts for gene expression and hash matrices, and txt files indicating retained cells with their hash assignment.

source_name: Thymus

extract_protocol:
mTEC were prepared by digesting thymi with collagenase and dispase, magnetically depleting CD45+ cells, staining with fluorescent antibodies, hashing with TotalSeq antibodies against H2-Kb, and flow sorting mTECs into DMEM/10%FCS.
Purified cells were sent to the Broad Institute Genomics Platform, which performed encapsulation and RNA and hash library preparation following 10X Genomics protocols (3' v3.1 chemistry)
scRNA-seq

tag: strain

tag: genotype

value: Foxn1(cre/+) Hnf4a(fl/+) Hnf4g(+/-) and Foxn1(cre/+) Hnf4a(fl/fl) Hnf4g(-/-)

tag: cell type

value: mTEClo

tag: hashid

value: HT1-ACCCACCAGTAAGAC (hnf4ctrl_r1); HT2-GGTCGAGAGCATTCA (hnf4ctrl_r2); HT3-CTTGCCGCATGTCAT (hnf4ctrl_r3); HT5-CTTTGTCTTTGTGAG (hnf4dtec_r1); HT6-TATGCTGCCACGGTA (hnf4dtec_r2); HT8-TATAGAACGCCAGGC (hnf4dtec_r3); HT9-TGCCTATGAAACAAG (hnf4dtec_r4)

tag: library type

value: total RNA


title: Hnf4ctrl.Hnf4dTEC.Pdpn-CD104-.mTEClo.rep#1-7.FBC

value: ADT oligo


title: AlfpCre_P300wtwt_P0_Epcam_2_18

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: AlfpCre_P300wtwt_P0_Epcam_2_17


title: AlfpCre_P300wtwt_P0_Epcam_2_16


title: AlfpCre_P300wtwt_P0_Epcam_2_15


title: col3_075

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: maturity


title: col3_073

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: nurse

value: forage ratio:NA


title: col3_072


title: Hnf4dTEC.mTEC.IgG.rep#2

description:
CUT&RUN
Hnf4_IgG.merged.CPM.bigwig

library_source: genomic

data_processing:
Fastq data were trimmed using TrimGalore
Reads were aligned to mm10 reference genome using bowtie2 v.2.3.4.3 with parameters --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 1000
Non-unique, duplicated and ChrM reads were removed using SAMTools view and Picard MarkDuplicates.
Bam files were converted bigWig using deepTools 3.5.0 with the following parameters --binSize 1 --normalizeUsing CPM --effectiveGenomeSize 2407883318
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

molecule: genomic DNA

extract_protocol:
CUT&RUN protocol for genomic DNA extraction
CUTANA CUT&RUN Library Prep Kit

treatment_protocol: mTEC were prepared by digesting thymi with collagenase and dispase, magnetically depleting CD45+ cells, staining with fluorescent antibodies, fixing cells for 1 minute at RT in 0.1% PFA, flow sorting mTECs into PBS, extracting nuclei and freezing at -80C

value: Thymus

tag: strain

tag: genotype

tag: cell type

value: mTEC

tag: antibody

value: IgG


title: E17.5_1, scRNA-seq

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

tag: tissue

value: liver

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: col3_074

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding


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

value: CD4+ T cells

tag: library type

value: HTO

tag: antibodies/tags


title: 2021_Prostate_Pb-ERG, Trp53pc-/- -Rep3

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (GRCm38/mm10) using STAR (2.5.2b)
RseQC was used to calculate gene expression
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: processed data file is in TSV format: chrom:TSS:TES:Symbol:mRNA_size:strand <TAB>   FPKM

source_name: Prostate

extract_protocol:
Prostate tissues were removed, flash frozen on dry ice, and RNA was extracted using RNeasy Mini Kit (Cat No.74104, QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: prostate

value: 15 months

tag: genotyping

value: Pb-ERG, Trp53pc-/-


title: Hnf4ctrl.mTEC.IgG.rep#2

description:
CUT&RUN
WT_IgG.merged.CPM.bigwig

tag: tissue

tag: genotype

tag: cell type

tag: antibody


title: AlfpCre_P300wtwt_P0_Epcam_2_13

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

value: EpCAM+

tag: genotype/treatment


title: 2021_Prostate_Pb-ERG, Trp53pc-/- -Rep2

tag: age


title: AlfpCre_P300wtwt_P0_Epcam_2_14


title: col3_071

value: Brain

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: maturity

tag: nurse

value: forage ratio:0


title: 2021_Prostate_Pb-ERG, Trp53pc-/- -Rep1

tag: strain

tag: tissue

tag: genotyping


title: Hnf4dTEC.mTEC.IgG.rep#1

description:
CUT&RUN
Hnf4_IgG.merged.CPM.bigwig

tag: genotype

tag: cell type

tag: antibody


title: AlfpCre_P300wtwt_P0_Epcam_2_12

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: AlfpCre_P300wtwt_P0_Epcam_2_11


title: Hnf4dTEC.mTEC.CTCF.rep#2

description:
CUT&RUN
Hnf4_CTCF.merged.CPM.bigwig

value: CTCF


title: col3_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: 2021_Prostate_Trp53pc-/- -Rep2

tag: strain

tag: tissue

tag: age

tag: genotyping


title: Hnf4dTEC.mTEC.CTCF.rep#1

description:
CUT&RUN
Hnf4_CTCF.merged.CPM.bigwig

tag: genotype

tag: cell type

tag: antibody


title: col3_067

tag: colony

tag: bodylength

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: AlfpCre_P300wtwt_P0_Epcam_2_1

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col3_069

tag: tissue

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: Hnf4ctrl.mTEC.IgG.rep#1

description:
CUT&RUN
WT_IgG.merged.CPM.bigwig

tag: strain

tag: genotype

tag: cell type

tag: antibody


title: 2021_Prostate_Pb-ERG-Rep3

tag: age

tag: genotyping

value: Pb-ERG


title: AlfpCre_P300wtwt_P0_Epcam_1_8

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: Hnf4dTEC.mTEC.H33.rep#2

description:
CUT&RUN
Hnf4_H33.merged.CPM.bigwig

tag: tissue


title: AlfpCre_P300wtwt_P0_Epcam_2_10


title: 2021_Prostate_Trp53pc-/- -Rep1


title: col3_066

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: col3_062

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: col3_065


title: AlfpCre_P300wtwt_P0_Epcam_1_9

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: Hnf4ctrl.mTEC.H33.rep#2

description:
CUT&RUN
WT_H33.merged.CPM.bigwig

tag: tissue

tag: strain

tag: genotype

tag: cell type

tag: antibody


title: Hnf4ctrl.mTEC.CTCF.rep#2

description:
CUT&RUN
WT_CTCF.merged.CPM.bigwig


title: 2021_Prostate_Pb-ERG-Rep1

tag: age

tag: genotyping


title: 2021_Prostate_WT-Rep2

value: WT


title: Hnf4dTEC.mTEC.H33.rep#1

description:
CUT&RUN
Hnf4_H33.merged.CPM.bigwig


title: AlfpCre_P300wtwt_P0_Epcam_1_6


title: 2021_Prostate_Pb-ERG-Rep2


title: 2021_Prostate_WT-Rep3


title: 2021_Prostate_Trp53pc-/- -Rep3


title: AlfpCre_P300wtwt_P0_Epcam_1_7


title: col3_064

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: Hnf4ctrl.mTEC.CTCF.rep#1

description:
CUT&RUN
WT_CTCF.merged.CPM.bigwig

tag: tissue

tag: strain

tag: genotype


title: Hnf4ctrl.mTEC.H33.rep#1

description:
CUT&RUN
WT_H33.merged.CPM.bigwig

tag: cell type

tag: antibody


title: 2021_Prostate_WT-Rep1

tag: age

tag: genotyping


title: Hnf4dTEC.mTEC.H3K36me3.rep#2

description:
CUT&RUN
Hnf4_H3K36me3.merged.CPM.bigwig


title: col3_060

tag: colony

tag: bodylength

tag: headwidth

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: 2018_Prostate_Pb-ERG, Trp53pcR172H/- -Rep3

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (GRCm38/mm10) using STAR (2.5.2b)
RseQC was used to calculate gene expression
Genome_build: GRChm38/mm10
Supplementary_files_format_and_content: processed data file is in TSV format: Chrom:TSS:TES:Symbol <tab> FPKM

value: Pb-ERG, Trp53pcR172H/-


title: AlfpCre_P300wtwt_P0_Epcam_1_4

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: Hnf4dTEC.mTEC.H3K36me3.rep#1

description:
CUT&RUN
Hnf4_H3K36me3.merged.CPM.bigwig

tag: tissue

tag: strain

tag: genotype


title: AlfpCre_P300wtwt_P0_Epcam_1_3


title: col3_059

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: 2018_Prostate_Trp53pcR172H/- -Rep2

tag: age

tag: genotyping


title: Hnf4ctrl.mTEC.H3K36me3.rep#2

description:
CUT&RUN
WT_H3K36me3.merged.CPM.bigwig

tag: cell type

tag: antibody


title: AlfpCre_P300wtwt_P0_Epcam_1_2

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col3_052

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


title: col3_051

tag: broodcare

tag: guarding

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: 2018_Prostate_Trp53pcR172H/- -Rep1

tag: strain

tag: age

tag: genotyping


title: col3_054

tag: tissue

tag: colony

tag: bodylength


title: 2018_Prostate_Pb-ERG-Rep3


title: col3_056

tag: headwidth

tag: age (months)

tag: cleaning nest


title: AlfpCre_P300wtwt_P0_Epcam_1_12

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: Hnf4ctrl.mTEC.H3K4me3.rep#2

description:
CUT&RUN
WT_H3K4me3.merged.CPM.bigwig

tag: genotype

tag: cell type

tag: antibody


title: Hnf4dTEC.mTEC.H3K4me3.rep#2

description:
CUT&RUN
Hnf4_H3K4me3.merged.CPM.bigwig

tag: strain


title: AlfpCre_P300wtwt_P0_Epcam_1_5


title: AlfpCre_P300wtwt_P0_Epcam_1_1


title: 2018_Prostate_Pb-ERG, Trp53pcR172H/- -Rep1

tag: age

tag: genotyping


title: AlfpCre_P300wtwt_P0_Epcam_1_10


title: Hnf4ctrl.mTEC.H3K36me3.rep#1

description:
CUT&RUN
WT_H3K36me3.merged.CPM.bigwig

tag: tissue


title: Hnf4dTEC.mTEC.H3K4me3.rep#1

description:
CUT&RUN
Hnf4_H3K4me3.merged.CPM.bigwig


title: AlfpCre_P300wtwt_P0_Epcam_1_11


title: col3_061

tag: colony

tag: bodylength

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_050

tag: headwidth

tag: age (months)

tag: cleaning nest


title: 2018_Prostate_Pb-ERG, Trp53pcR172H/- -Rep2

tag: strain

tag: age

tag: genotyping


title: 2018_Prostate_Pb-ERG-Rep2

tag: tissue


title: col3_049

tag: colony

tag: bodylength

tag: trophallaxis nest


title: 2018_Prostate_Pb-ERG-Rep1


title: Hnf4dTEC.mTEC.H3K4me1.rep#2

description:
CUT&RUN
Hnf4_H3K4me1.merged.CPM.bigwig

tag: genotype

tag: cell type

tag: antibody


title: AlfpCre_P300wtwt_P0_Dlk_3_9

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

value: DLK+

tag: genotype/treatment


title: AlfpCre_P300wtwt_P0_Dlk_3_8


title: col3_048

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: 2018_Prostate_WT-Rep2

tag: strain

tag: tissue

tag: age

tag: genotyping


title: col3_046

tag: colony

tag: bodylength

tag: trophallaxis nest


title: 2018_Prostate_WT-Rep1


title: AlfpCre_P300wtwt_P0_Dlk_3_7

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: 2018_Prostate_WT-Rep3


title: col3_045

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: Hnf4dTEC.mTEC.H3K4me1.rep#1

description:
CUT&RUN
Hnf4_H3K4me1.merged.CPM.bigwig

tag: tissue

value: Thymus

tag: strain

tag: genotype

tag: cell type

tag: antibody


title: col3_047

tag: colony

tag: bodylength

tag: trophallaxis nest

tag: grooming forage

tag: maturity

tag: nurse


title: Hnf4ctrl.mTEC.H3K4me3.rep#1

description:
CUT&RUN
WT_H3K4me3.merged.CPM.bigwig

value: mTEC


title: Hnf4dTEC.mTEC.H3K27me3.rep#1

description:
CUT&RUN
Hnf4_H3K27me3.merged.CPM.bigwig


title: Hnf4ctrl.mTEC.H3K4me1.rep#1

description:
CUT&RUN
WT_H3K4me1.merged.CPM.bigwig


title: E17.5CC-RNAseq_1

tag: Stage

tag: protocol

value: bulk cell RNA-seq

tag: culture

tag: batch

tag: sort

value: tdTomato

tag: genotype/treatment


title: Hnf4dTEC.mTEC.H3K27me3.rep#2

description:
CUT&RUN
Hnf4_H3K27me3.merged.CPM.bigwig

tag: tissue


title: E17.5CC-RNAseq_2


title: AlfpCre_P300wtwt_P0_Dlk_3_3


title: E17.5HC-RNAseq_2


title: AlfpCre_P300wtwt_P0_Dlk_3_5


title: AlfpCre_P300wtwt_P0_Dlk_3_2


title: col3_043

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: Hnf4ctrl.mTEC.H3K27me3.rep#2

description:
CUT&RUN
WT_H3K27me3.merged.CPM.bigwig

tag: strain

tag: genotype

tag: cell type

tag: antibody


title: AlfpCre_P300wtwt_P0_Dlk_3_13

tag: Stage

tag: protocol

tag: culture

tag: batch


title: col3_040

tag: tissue

tag: colony

tag: bodylength

tag: headwidth

tag: trophallaxis nest

tag: grooming forage

tag: maturity

tag: nurse


title: Hnf4ctrl.mTEC.H3K27me3.rep#1

description:
CUT&RUN
WT_H3K27me3.merged.CPM.bigwig


title: AlfpCre_P300wtwt_P0_Dlk_3_6

tag: sort

tag: genotype/treatment


title: Hnf4ctrl.mTEC.H3K4me1.rep#2

description:
CUT&RUN
WT_H3K4me1.merged.CPM.bigwig

tag: strain

tag: genotype


title: col3_039

tag: age (months)

tag: cleaning nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: col3_044

tag: tissue

tag: colony

tag: bodylength

tag: headwidth


title: Hnf4dTEC.mTEC.H3K27ac.rep#1

description:
CUT&RUN
Hnf4_H3K27ac.merged.CPM.bigwig

tag: cell type

tag: antibody


title: Hnf4dTEC.mTEC.H3K27ac.rep#2

description:
CUT&RUN
Hnf4_H3K27ac.merged.CPM.bigwig


title: AlfpCre_P300wtwt_P0_Dlk_3_11

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: AlfpCre_P300wtwt_P0_Dlk_3_4


title: E17.5HC-RNAseq_1


title: col3_038

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming forage

tag: maturity

tag: nurse


title: Hnf4ctrl.mTEC.H3K27ac.rep#2

description:
CUT&RUN
WT_H3K27ac.merged.CPM.bigwig

tag: tissue

tag: strain

tag: genotype


title: AlfpCre_P300wtwt_P0_Dlk_3_10

tag: Stage


title: col3_036

tag: colony

tag: bodylength

tag: headwidth

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: AlfpCre_P300wtwt_P0_Dlk_3_1

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: E17.5CC-EZH2_1

data_processing:
Library strategy: CUT&RUN
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).

value: CUT&RUN


title: Hnf4ctrl.mTEC.H3K27ac.rep#1

description:
CUT&RUN
WT_H3K27ac.merged.CPM.bigwig

tag: cell type

tag: antibody


title: col3_037

tag: tissue

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming forage

tag: maturity

tag: nurse


title: E17.5HC-EZH2_2

tag: Stage


title: E12.5HB-EZH2_2

tag: protocol


title: col3_033

tag: colony

tag: bodylength

tag: headwidth

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: E12.5HB-EZH2_1

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col3_031

tag: tissue

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding


title: AlfpCre_P300wtwt_P0_Dlk_3_12

tag: Stage

tag: protocol


title: AlfpCre_P300wtwt_P0_Dlk_1_7


title: AlfpCre_P300wtwt_P0_Dlk_1_8


title: E17.5HC-EZH2_1


title: col3_029

tag: colony

tag: bodylength

tag: headwidth

tag: grooming forage

tag: maturity

tag: nurse


title: KO-3

city: shanghai

first: Zhenyu

last: Shao

state: --- Select a state ---

address: Yueyang Road 320

department: Center for Excellence in Molecular Cell Science

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Raw data were trimmed by Trim Galore with default settings.
The clean data were mapped to mouse reference genome mm9 using bowtie2 (v2.2.5) with default parameters.
Duplicates were removed using Picard (v2.22.4).
Assembly: mm9
Library strategy: CUT&Tag

source_name: GV oocytes

extract_protocol:
The CUT&Tag assay was conducted following the protocol of Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) Briefly, 250 GV oocytes were collected and washed once with 500 μl wash buffer before they were bound to activated ConA beads for 10 min at room temperature. After that, cells were incubated with 1 μg anti-H3K9me3 antibody (Active Motif, # 39161) at 4°C overnight. Anti-rabbit IgG was added and incubated for 1 h at 25°C the next day. Then cells were washed three times with DIG wash buffer and incubated with 0.04 μM pA/G–Tnp for 1 h at 25°C. Similarly, cells were washed three times with DIG 300 buffer, resuspended in tagmentation buffer and incubated at 37°C for 1 h. Tagmentation was stopped by adding proteinase K, buffer LB and DNA extract beads. After incubation at 55°C for 10 min, cells were plated on a magnet and unbound liquid was removed. Beads were gently rinsed twice with 80% ethanol and DNA was eluted with double-distilled water.
15 μl of purifed DNA was mixed with 25 μl of 2× CAM, along with 5 μl of uniquely barcoded i5 and i7 primers from the TruePrep Index Kit V2 for Illumina (Vazyme Biotech, # TD202). A total volume of 50 μl of sample was placed in the Mastercycler® nexus (Eppendorf, #6331000076) using the following program: 72°C for 3 min; 98°C for 3 min; 18 cycles of 98°C for 10 s, 60°C for 5 s, and 72°C for 1 min; and holding at 12°C. To purify the PCR products, 2× volumes of VAHTS DNA Clean Beads (Vazyme Biotech, #N411) were added and incubated at room temperature for 5 min. The beads were washed twice with 200 μl fresh 80% ethanol and eluted in 22 μl ddH2O. All CUT&Tag libraries were sequenced using the Illumina NovaSeq 6000 platform in PE150 mode.

tag: cell type

value: GV oocytes

tag: genotype

value: Tet3 LCDf/f; Zp3-Cre

tag: antibody


title: Treated_JD6

city: Austin

first: Anna

last: Battenhouse

state: TX

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

institute: The University of Texas at Austin

data_processing:
Paired-end pseudo alignment was performed using kallisto (ver. 0.45.0) with the --bias option, against the human transcriptome (GENCODE v39 transcript sequences).
Downstream analysis of kallisto estimated counts was performed in R (ver. 4.0.3).
The tximport package (v1.18.0) was used to roll up transcript-level counts into gene-level counts provided to the DESeq2 package (ver. 1.30.0).
Before DESeq2 analysis, count data matrices were filtered to remove genes with fewer than 1 read across all included samples.
The DGE model analyzed was Treated vs Control
Assembly: GENCODE v39 transcriptome (transcript sequences and main gene annotation set)
Supplementary files format and content: Tab-delimited kallisto_counts.tsv text files provide kallisto per-transcript estimated counts and transcripts per million values for each sample. Full DESeq2 DGE and GO analysis details can be found in the Supplementary zip file.

organism: Homo sapiens

source_name: cultured A375 cells, hMGL treated 24h

growth_protocol: A375 melanoma cells from ATCC were cultured in Dulbecco's modified Eagle's medium, supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Life Technologies), in an incubator at 37°C in 95% air and 5% CO2.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (QIAGEN) with DNase treatment. The NanoDrop was used to quantify RNA amount and the Agilent Bioanalyzer was used to ensure RNA quality.
Standard library preparation for Illumina RNA-seq sequencing was performed by MD Anderson Research Park in Smithville TX, before the move of this facility to the main MDA complex in Houston. The MDA Science Park sequencing run was MDACCSPNGS-SC-937.

treatment_protocol: Treatment with hMGL was applied for 24 hours to half the A375 cell culture dishes; the other half remained untreated. hMGL, a high-catalytic activity human methioninase (methionine-degrading) enzyme, was created using protein engineering and was shown to exert a strong antitumor effect in prostate cancer preclinical models.

tag: cell line

tag: treatment

value: hMGL treated 24h

value: melanoma


title: KO-2


title: col3_034

tag: tissue

tag: age (months)

tag: cleaning nest

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: DKO-2

value: Dnmt3af/f, Tet3 LCDf/f; Zp3-Cre


title: AlfpCre_P300wtwt_P0_Dlk_1_6

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: DKO-1

tag: cell type

tag: genotype


title: E17.5CC-EZH2_2


title: col3_028

value: Brain

tag: colony

tag: bodylength

tag: headwidth

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming forage

tag: maturity

tag: nurse


title: KO-1

tag: antibody


title: AlfpCre_P300wtwt_P0_Dlk_1_9

tag: Stage

tag: protocol


title: col3_025

tag: tissue

tag: age (months)

tag: cleaning nest

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

value: forage ratio:0


title: Treated_JD5

tag: cell line

tag: treatment

tag: cell type


title: AlfpCre_P300wtwt_P0_Dlk_1_5

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: WT-3

tag: genotype

value: Tet3 LCDf/f

tag: antibody


title: AlfpCre_P300wtwt_P0_Dlk_1_4

tag: Stage

tag: protocol


title: Control_JD3

source_name: cultured A375 cells, untreated

value: untreated


title: col3_024

tag: tissue

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming forage

tag: maturity

tag: nurse


title: Control_JD2

tag: cell line

tag: treatment

tag: cell type


title: WT-2

tag: genotype

tag: antibody


title: AlfpCre_P300wtwt_P0_Dlk_1_3

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col3_023

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: WT-1

tag: cell type

tag: genotype

tag: antibody


title: Control_JD1

tag: cell line

tag: treatment


title: AlfpCre_P300wtwt_P0_Dlk_1_2

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: mouse oligodendroglia Sox9_tg, biological replicate 4

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

country: Germany

data_processing:
RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA)
Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).
The sequencing libraries were multiplexed and loaded on the flow cell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
DESeq2 was used for differential gene expression analysis.
Assembly: GRCm38
Supplementary files format and content: tab-delmited text files containing counts and DESeq results

source_name: mouse oligodendroglia derived from brain

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit according to QIAGEN protocol.

tag: tissue

value: mouse oligodendroglia


title: col3_022

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: Treated_JD4

tag: cell line

tag: treatment

tag: cell type


title: col3_020

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: AlfpCre_P300wtwt_P0_Dlk_1_12

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: AlfpCre_P300wtwt_P0_Dlk_1_11


title: RKO_LY_2

first: Nadine

last: Fournier

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Reads were trimmed of their adapters with bcl2fastq v2.20 (Illumina) and quality-controlled with FastQC v0.11.9.
Reads were aligned to the human genome build hg38 using HISAT2 (2.2.1).
Transcript-level counts and tpm were estimated using Salmon (1.4.0).
Counts were then summarized at the gene level with the tximport R package (1.20.0).
Assembly: hg38
Supplementary files format and content: tab separated, raw and normalized counts

source_name: RPMI-8402 PIK3R1 KO + GSI 24hrs

growth_protocol: Cells were cultured in growth media RPMI 1640 GlutaMAX (GIBCO, Cat# 61870010) supplemented with 10% FBS, and treated with DMSO or CB-103 or GSI for 24hrs.

extract_protocol:
Cells were collected, RNA was extracted from cell lines using RNeasy Mini Kit (QIAGEN, Cat#74104). RNA quality was assessed on a Fragment Analyzer (Agilent) or TapeStation 4200 (Agilent) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA) to proceed to the polyA-based stranded mRNA library prep method (scores >7.2).
Libraries for mRNA-seq were prepared with the Stranded mRNA Ligation method (Illumina) starting from 1µg RNA, according to manufacturer’s instructions.
Libraries, all bearing unique dual indices, were subsequently loaded at 250pM in a HiSeq 4000 instrument (Illumina) and sequenced according to manufacturer’s instructions, yielding paired-end reads of 75 nucleotides.

treatment_protocol: PIK3R1 knockout and control RPMI-8402 cells were treated with DMSO or CB-103 or GSI for 24hrs.

value: RPMI-8402 cell line

tag: genotyope

value: PIK3R1 knockout

value: GSI 24hrs

tag: group

tag: replicate


title: mouse oligodendroglia Sox9_tg, biological replicate 3

tag: tissue

value: mouse oligodendroglia derived from brain

tag: genotype


title: AlfpCre_P300wtwt_P0_Dlk_1_10

value: DLK+


title: mouse oligodendroglia Sox9_tg, biological replicate 2


title: RKO_LY_1

tag: cell line

tag: treatment


title: col3_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: AlfpCre_P300wtwt_P0_Dlk_1_1

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: col3_019

tag: tissue

tag: colony

tag: bodylength

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: mouse oligodendroglia Sox9_tg, biological replicate 1

tag: cell type

tag: genotype


title: AlfpCre_P300flfl_P0_Epcam_4_9

value: EpCAM+


title: RKO_CB103_1

source_name: RPMI-8402 PIK3R1 KO + CB-103 24hrs

tag: cell line

tag: genotyope

tag: treatment

tag: group

tag: replicate


title: RKO_DMSO_3

source_name: RPMI-8402 PIK3R1 KO + DMSO 24hrs

value: DMSO 24hrs


title: mouse oligodendroglia Sox9_ctrl, biological replicate 3


title: RKO_LY_3


title: AlfpCre_P300flfl_P0_Epcam_4_8

tag: Stage

tag: protocol

tag: culture


title: mouse oligodendroglia Sox9_ctrl, biological replicate 1


title: AlfpCre_P300flfl_P0_Epcam_4_7

tag: batch

tag: sort

tag: genotype/treatment


title: col3_015

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: grooming forage

tag: maturity

tag: nurse


title: col3_014

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage


title: col3_013


title: RKO_CB103_3

tag: cell line

tag: genotyope

tag: treatment

tag: group

tag: replicate


title: col3_012

tag: tissue

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)


title: AlfpCre_P300flfl_P0_Epcam_4_6

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: 5177

city: Indianapolis

first: Steven

last: Rhodes

state: IN

address: 1044 W. Walnut St.; Bldg R4, Rm 325

institute: Indiana University

data_processing:
The sequencing data was next assessed using FastQC (Babraham Bioinfomatics, Cambridge, UK) and then mapped to the mouse genome (UCSC mm10) using STAR RNA-seq aligner 2.7.0a (PMC3530905).
The data were further normalized using RPKM (Reads Per Kilobase Million).
Differential gene expression analysis was conducted by using DESeq2 method (25516281).
Pathway enrichment analyses were conducted by hypergeometric tests against mouse Gene Ontology and canonical pathways collected from MsigDB.
Assembly: UCSC mm10
Supplementary files format and content: Processed file (Veh_ERK_CDK_Combo_rawcounts.txt) contains raw counts of each sample, organized by gene ID.

molecule: polyA RNA

source_name: Nf1 flox/flox PostnCre+ sciatic nerve

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Plus Mini kit.
100ng total RNA and 15 cycles of amplification were used for libraries constructed with Roche KAPA RNA HyperPrep Kit and Qiagen QIAseq FastSelect rRNA removal kit.
library preparation kit:  Roche KAPA RNA HyperPrep Kit & Qiagen QIAseq FastSelect rRNA removal kit

value: abemaciclib (CDK4/6i) and LY3214996 (ERK1/2i) for 1 week

tag: tumor stage

value: plexiform neurofibroma

value: sciatic nerve

tag: genotype

value: Nf1 flox/flox PostnCre+


title: RKO_CB103_2

tag: cell line

tag: genotyope


title: RKO_DMSO_2

tag: treatment

tag: group


title: RKO_DMSO_1

tag: replicate


title: AlfpCre_P300flfl_P0_Epcam_4_5


title: col3_017

tag: tissue

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: mouse oligodendroglia Sox9_ctrl, biological replicate 2

tag: cell type

tag: genotype


title: col3_011

tag: bodylength

tag: headwidth

tag: age (months)


title: AlfpCre_P300flfl_P0_Epcam_4_40

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: 5173

tag: treatment

tag: tumor stage

tag: tissue


title: 5128


title: Rneg1_LY_3

source_name: RPMI-8402 non-targeting control + GSI 24hrs

tag: cell line

tag: genotyope

value: WT

tag: group

tag: replicate


title: 4885

tag: genotype


title: AlfpCre_P300flfl_P0_Epcam_4_4


title: Rneg1_LY_2


title: Rneg1_LY_1


title: col3_007

value: Brain

tag: colony

tag: bodylength

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_009

tag: tissue

tag: headwidth

tag: age (months)

value: forage ratio:0


title: AlfpCre_P300flfl_P0_Epcam_4_39

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: 4854

tag: treatment

tag: tumor stage

tag: genotype


title: AlfpCre_P300flfl_P0_Epcam_4_38


title: 4861


title: Rneg1_CB103_3

source_name: RPMI-8402 non-targeting control + CB-103 24hrs

tag: cell line

tag: genotyope

tag: group

tag: replicate


title: 5219

value: abemaciclib (CDK4/6i) for 1 week


title: col3_003

tag: colony

tag: bodylength

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: AlfpCre_P300flfl_P0_Epcam_4_37

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: 5181

tag: treatment

tag: tumor stage

tag: tissue

tag: genotype


title: Rneg1_CB103_1

tag: cell line

tag: genotyope

tag: group

tag: replicate


title: AlfpCre_P300flfl_P0_Epcam_4_36


title: AlfpCre_P300flfl_P0_Epcam_4_35


title: Rneg1_DMSO_3

source_name: RPMI-8402 non-targeting control + DMSO 24hrs


title: 5178


title: col3_002

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

value: forage ratio:NA


title: col3_010

tag: tissue

tag: maturity

tag: nurse


title: Rneg1_DMSO_2

tag: cell line

tag: genotyope

tag: treatment

tag: group

tag: replicate


title: 4936

tag: tumor stage

tag: genotype


title: col2_140

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare


title: col2_138

tag: tissue

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage


title: Rneg1_DMSO_1

tag: cell line

tag: genotyope

tag: treatment

tag: group

tag: replicate


title: AlfpCre_P300flfl_P0_Epcam_4_34

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

tag: genotype/treatment


title: 4852

tag: tumor stage

tag: tissue

tag: genotype


title: AlfpCre_P300flfl_P0_Epcam_4_33


title: col3_005

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: maturity

tag: nurse


title: col2_137

tag: cleaning forage

tag: grooming forage


title: Rneg1_CB103_2

tag: cell line

tag: genotyope

tag: treatment

tag: group

tag: replicate


title: 4788

tag: tumor stage

tag: tissue

tag: genotype


title: U2OS_iCLIP_IgG-(GAR1)_rep2

city: Solna

first: Federico

last: Agostini

state: Stockholm

address: Tomtebodavägen 23a

country: Sweden

institute: Science for Life Laboratories

data_processing:
Sequencing quality checks were performed on all experiments using FastQC (v0.11.9).
Adapter sequences were removed using Cutadapt and the following parameters: -q 20 -m 10 --times 1 --error-rate 0.1 -O 3.
Reads were mapped to the human reference genome (GRCh38/hg38) using GENCODE (v27) gene annotation as reference and STAR (v2.7.0e), with the following parameters: --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterType Normal --outFilterMismatchNmax 2 --alignEndsType EndToEnd --outSAMunmapped Within --outSAMattributes Standard.
Mapped reads were analysed with the iCount (v2.0.1.dev) software: the xlsites module (--group_by start --quant cDNA --mismatches 1 --mapq_th 0 --multimax 50 --gap_th 1000000 --ratio_th 0.001) was used to extract the cross-link sites; the bedgraph module was used to generate genomic coverage tracks; the peaks module (--group_by gene_id --half_window 3 --fdr 0.05 --perms 100 --rnd_seed 42) was used to identify the regions significantly enriched in protein binding events.
Assembly: GRCh38/hg38
Supplementary files format and content: BED files containing peaks composed of statistically significant cross-linked sites
Supplementary files format and content: BED files containing clusters of significant cross-linked sites

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37°C at 5% CO2.

extract_protocol:
Protein-RNA complexes were fixed by exposing cells to 1500 J/m^2 254 nm UV light and collected by scraping. After nuclear fractionation, the lysate was treated with 0.4 Units RNaseI and 4 Units TurboDNase (both from Thermo Fisher Scientific) per 1ml of cell lysate at 1mg/ml protein concentration. Beads coupled with mouse IgG, dyskerin (Abnova, H00001736-m04) or GAR1 (Proteintech, #11711-1-AP) antibodies were used to precipitate protein-RNA complexes. RNA was ligated to a pre-adenylated infra-red labeled IRL3 adaptor. Complexes were resolved through SDS-PAGE and cut from the nitrocellulose membrane. RNA was then released from the membrane with proteinase K digestion and recovered by precipitation.
RNA was retrotranscribed with Superscript IV Reverse Transcriptase (Thermo FIsher Scientific). The resulting cDNA was purified using AMPure XP beads (Beckman- Coulter), then circularised using CircLigase II (Epicentre), and purified again with AMPure XP beads. After PCR amplification, libraries were size-selected with Ampure XP beads and quality-controlled for sequencing.

tag: cell type

value: Human bone osteosarcoma

tag: molecule type

value: nuclear RNA


title: col2_136

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest


title: 5206

tag: treatment

value: LY3214996 (ERK1/2i) for 1 week


title: U2OS_iCLIP_IgG-(GAR1)_rep1

tag: cell line


title: U2OS_iCLIP_IgG-(Dyskerin)_rep2


title: 5191


title: col2_135

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: col2_134

tag: tissue

tag: colony


title: 4883

tag: tumor stage

tag: genotype


title: U2OS_iCLIP_IgG-(Dyskerin)_rep1

tag: cell type

tag: molecule type


title: U2OS_iCLIP_GAR1_rep2

tag: antibody

value: GAR1 (Proteintech, #11711-1-AP)


title: 4860


title: 4853


title: col2_132

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding


title: U2OS_iCLIP_dyskerin_rep2

tag: cell line

value: dyskerin (Abnova, H00001736-m04)


title: col2_130

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage

tag: maturity


title: U2OS_iCLIP_GAR1_rep1

tag: cell type


title: 4836

tag: treatment

tag: tumor stage

tag: tissue

tag: genotype


title: col2_128

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: nurse


title: U2OS_iCLIP_dyskerin_rep1

tag: cell line

tag: molecule type

tag: antibody


title: col2_127

tag: cleaning nest

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: Tumour 7 (T7)

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

country: France

institute: I.G.B.M.C. - Institut de génétique et de biologie moléculaire et cellulaire

data_processing:
Libraries were sequenced on an Illumina HiSeq 4000 platform as paired-end 2x100 bp reads and trimmed at 28+50 bp reads.
Image analysis and base calling were performed using RTA version 2.7.7 and Spaceranger 1.1.0 mkfastq.
Alignment to reference genome hg38 and gene quantification was done using SpaceRanger v1.3.1.
Data are imported into R and analyzed using the Seurat package v4.0.3.
Assembly: hg38
Supplementary files format and content: Raw and filtered barcode transcript counts in h5 format as well as the compressed (tar-gz) “spatial” folder output from SpaceRanger.

source_name: spatial transcriptomic

extract_protocol:
Spatial transcriptomics was performed on Formalin Fixed Paraffin Embedded (FFPE) tissue sections using the 10X Genomics Visium Spatial Gene Expression platform (10X Genomics, Pleasanton, CA, USA). Using a Leica RM2235 microtome (Leica, Germany), 5 µm tissue sections were cut from FFPE tissue blocks and placed within the etched frames of the capture areas on the active surface of the Visium Spatial Slide. Slide was dried in an oven overnight at 37°C then at 60°C during 25 minutes before dehydration in ethanol and Hematoxylin & Eosin (H&E) staining. Slide was finally transferred to water and mounted in 87% glycerol before image acquisition the same day. Image mosaic of each section was acquired at 5X and 20X magnification (Zeiss EC Plan-Neofluar 5x/0.16, Zeiss Plan-Apochromat 20x/0.8) with transmitted white light and a Zeiss colour camera Zeiss Axiocam Color on a Zeiss Axio Observer microscope to generate a brightfield image of each section including the fiducial markers frame. The final stitched mosaic was created with Zeiss ZEN Stitching module.
Stained FFPE tissue sections were strictly processed as outlined in the demonstrated protocol « Visium Spatial Gene Expression Reagent kits for FFPE, UserGuide » (Part number CG000407, RevC). Quantification and quality control of the final libraries were performed using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

tag: disease state

value: clear-cell renal cell carcinoma

tag: tissue

value: Kidney

tag: sample type

value: Tumour

tag: patient

value: Patient 7

tag: disease stage

value: Stage III

tag: tumour grade

tag: prior treatment

value: Naive


title: 5210

tag: treatment

value: Vehicle for 1 week

tag: tumor stage

value: plexiform neurofibroma

value: sciatic nerve

tag: genotype

value: Nf1 flox/flox PostnCre+


title: Tumour 1 (T1)

value: Patient 1

value: Stage IV

value: Nivolumab+Ipilimumab


title: 5194


title: col2_126

value: Brain

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: cleaning nest

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: 4839

tag: tissue


title: Tumour 2 (T2)

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment to reference genome hg19 and gene quantification for each cell was done using CellRanger v3.1.
Data are imported into R and analyzed using the Seurat package v3.1.4.
Assembly: hg19
Supplementary files format and content: TSV files containing raw UMI counts for cells used in Seurat analysis.

source_name: Captured single cell RNA

extract_protocol:
Tumor dissociation kit (Miltenyi, 130-095-929); Dead cell removal kit (Miltenyi, 130-090-101)
Single Cell 3ʹ Gene Expression libraries comprise standard Illumina paired-end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1, while 8 bp sample index sequences are incorporated as the i7 index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired-end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 12 bp UMI.

tag: disease state

tag: sample type

tag: patient

value: Patient 2


title: col2_125

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: col2_133

tag: colony

tag: bodylength

tag: headwidth

value: forage ratio:0


title: col2_124

tag: age (months)

tag: cleaning nest

tag: cleaning forage


title: col2_122

tag: grooming forage

tag: maturity

tag: nurse


title: col2_121

tag: tissue


title: Tumour 3 (T3)

tag: disease state

tag: sample type

tag: patient

value: Patient 3

tag: disease stage

tag: tumour grade

tag: prior treatment

value: Sunitinib


title: 4769

tag: treatment

tag: tumor stage

tag: genotype


title: Tnrc6a_Ago2KO_3_IP

city: Basel

first: Helge

last: Grosshans

address: Maulbeerstrasse 66

institute: Friedriche Miescher Institute for Biomedical Research (FMI)

description: Experiment 2

data_processing:
Base calling and quality scoring is performed using RTA software (v3.4.4), demultiplexing with  bcl2fastq2 v2.20.
Alignment was performed as follows: Samples were aligned against the GRCm38 mouse genome assembly from GENCODE (Frankish et al., 2021), primary assembly from release M24).(Rosenbloom et al., 2015) Alignments were performed using STAR version 2.7.3a with settings --outFilterType BySJout --outFilterMultimapNmax 20 --outMultimapperOrder Random --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMmultNmax 1(Gaidatzis et al., 2015). These settings follow ENCODE guidelines and report a single randomly selected alignment for reads that map to the genome no more than 20 times(Langmead et al., 2009) Gene annotations were also obtained from GENCODE release M24, transforming the gtf file into a Bioconductor TxDb object using the makeTxDbFromGFF function from the GenomicFeatures package (version 1.44.0, (Lawrence et al., 2013). Gene-level read counts were obtained by summing the counts from the union of all exons per gene, using the qCount function from the QuasR package (version 1.32.0, (Gaidatzis et al., 2015)) with the created TxDb and parameters orientation = “opposite”.
Assembly: mm10
Supplementary files format and content: csv: First column contains ENSEMBL transcript ID, second column contains ENSEMBL gene ID,  third column contains ENTREZ gene ID, fourth column contains gene symbol (Ensembl identifiers), fifth column contains gene nams (EMSENBL), sixth column contains summed width of exons per gene (quasr package),  columns named 'raw.count' contain raw counts of reads overlapping each gene for each sample, columns named 'rpkm' contain rpkm read counts overlapping each gene for each sample.

source_name: mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin) were cultured on gelatin-coated dishes in mES medium (DMEM [Gibco; 11995065]) supplemented with 15% fetal bovine serum [Gibco], 1 x non-essential amino acids [Gibco], 1mM sodium pyruvate [Gibco], 2mM L-glutamine [Gibco], 0.1 mM ß-mercaptoethanol [Sigma], 50 µg/ml penicillin, 80 µg/ml streptomycin, 1x MycoZap™ Prophylactic [Lonza; VZA-2032], 1x ESGRO® LIF [MerckMillipore; ESG1107]) at 37 °C in 5% CO2.

extract_protocol:
Norgen Single Cell RNA Purification Kit [Norgen; 51800] with on-column DNAse digestion [Norgen; 25710]
TruSeq Illumina Total RNA-seq (stranded - high input)

tag: cell type

value: mouse embryonic stem cells

value: IP RNA GFP_5xT71BS, HA-AVI-Tnrc6a, Ago2-/-


title: Tumour 1 (T1)

value: clear-cell renal cell carcinoma

value: Kidney

value: Tumour


title: col2_120

source_name: Brain

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: CS20-13503_snRNA_02

city: Farmington

first: Tara

middle: N.

last: Yankee

state: Connecticut

address: 400 Farmington Ave

institute: UConn Health

description:
cs20_R1R2_barcode_label.tsv
CS20_craniofacial_snRNA.rds

data_processing:
single cell Multiome-seq (ATAC & snRNA)
Gene counts per cell were imported into the R package Seurat (v3.1.2) using BUSpaRse (v.1.0.0)
Seurat (v.3.1.0) was used for filtering, merging of replicates, scaling, normalization, dimensionality reduction, and clustering.
Clusters were functionally annotated using GO enrichment analysis (clusterProfiler, v.3.14.3)from marker genes of each cluster.
Genome_build: hg38
Supplementary_files_format_and_content: The tab delimited file contains four columns, one for cell barcodes, two UMAP values and the cell type designation. The rds file is the R object of class Seurat containing 28470 features across 4233 samples for 1 snRNA assay.

source_name: Craniofacial Tissue

extract_protocol: Protocol from 10X Genomics followed for frozen embryonic tissue: Nuclei Isolation from Embryonic Mouse Brain for Single Cell Multiome ATAC + Gene Expression Sequencing, 2022

treatment_protocol: Samples flash frozen immediately after collection by HDBR

value: Primary Craniofacial Tissue

tag: developmental stage


title: CS20-13327_snRNA_01


title: col2_119

tag: tissue

tag: cleaning nest

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: Normal Adjacent Tissue 1 (N1)

tag: disease state

tag: sample type

value: Normal Adjacent Tissue

tag: patient

value: Pool of three samples

tag: disease stage

tag: tumour grade

tag: prior treatment


title: Tnrc6a_Ago2KO_1_IP

description: Experiment 2

tag: cell type

tag: treatment


title: 5224

value: Vehicle for 1 week

tag: tumor stage

value: plexiform neurofibroma

value: sciatic nerve

tag: genotype

value: Nf1 flox/flox PostnCre+


title: col2_118

value: Brain

tag: colony

tag: bodylength

tag: headwidth

tag: age (months)

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: Tnrc6a_Ago2KO_2_IP

description: Experiment 2


title: VCaP_Input

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 version 2.3.3.1 with the following configurations: bowtie2-align-s --wrapper basic-0 -k 2 -p 6
Data were filtered using the following specifications…
Peak calling was performed using MASC2 (v2.0.10) with pvalue cutoff = 1.0e-05.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bedGraph files were generated by MACS2. BedGraph files were converted into BigWig files using UCSC's "wigToBigWig" command.

source_name: Prostate

growth_protocol: Cells were cultivated at 37°C and 5% CO2 in DMEM containing 10% fetal bovine serum (FBS) (Gibco) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).

extract_protocol:
VCaP cell lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with indicated antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: prostate cancer

tag: cell line

value: VCaP

tag: chip antibody

value: untreated


title: VCaP_p53-Rep2

value: p53 (Santa Cruz Biotechnology, sc-126)


title: col2_117

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

tag: tissue

tag: cleaning nest

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse

value: forage ratio:0


title: col2_116

tag: colony

tag: bodylength


title: Tnrc6a_Trim71KO_2_IP

description: Experiment 2

tag: cell type

value: mouse embryonic stem cells

tag: treatment

value: IP RNA GFP_5xT71BS, HA-AVI-Tnrc6a, Trim71-/-


title: 5209

tag: tumor stage

tag: genotype


title: col2_115

tag: headwidth

tag: age (months)

tag: trophallaxis nest

tag: broodcare

tag: guarding

tag: grooming nest


title: VCaP_p53-Rep1

tag: cell line

tag: chip antibody


title: Tnrc6a_Trim71KO_1_IP

description: Experiment 2


title: VCaP_ERG-Rep2

value: ERG (Abcam, ab92513)


title: Tnrc6a_3_IP

description: Experiment 2

value: IP RNA GFP_5xT71BS, HA-AVI-Tnrc6a


title: col2_113

tag: tissue

tag: cleaning nest

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

tag: grooming forage


title: Tnrc6a_2_IP

description: Experiment 2

tag: cell type

tag: treatment


title: col2_111

tag: colony

tag: bodylength

tag: maturity

tag: nurse


title: RNCM_100nMET-1_n2

city: Montreal

first: Terence

last: Hébert

state: Quebec

address: 3655 Promenade Sir William Osler

department: Pharmacology and Therapeutics

institute: McGill University

description: RNCMs Day 5 post-isolation

data_processing:
Fastq files were trimmed with TrimGalore.
Quality control was performed with FastQC.
Reads were aligned to Ensembl rat genome Rnor_6.0.94 or human Homo_sapiens.GRCh38.104 using STAR.
Transcripts were assembled using StringTie.
Differential expression analysis was performed using DEseq2.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: neonatal primay cells

extract_protocol:
Qiagen RNeasy Mini Kit.
NEB rRNA-depleted (HMR) stranded library preparation

value: neonatal primay cells

value: Isolated rat neonatal cardiomyocytes

tag: genotype

value: Wildtype

value: 100 nM Endothelin-1


title: VCaP_ERG-Rep1


title: col2_110

tag: headwidth

tag: age (months)

tag: trophallaxis nest

tag: broodcare

tag: guarding

value: forage ratio:NA


title: Tnrc6a_Trim71KO_3_IP

description: Experiment 2


title: RNCM_100nMET-1_n1

description: RNCMs Day 5 post-isolation

tag: tissue

tag: cell line


title: Ctrl_1_IP

description: Experiment 2

value: IP RNA GFP_5xT71BS (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin)


title: RNCM_10uMSII_n2

description: RNCMs Day 5 post-isolation

value: 10 uM SII


title: col2_108

value: Brain

tag: cleaning nest

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: Ctrl_2_IP

description: Experiment 2

tag: cell type

tag: treatment


title: DAPT_3

data_processing:
Reads were trimmed of their adapters with bcl2fastq v2.19 (Illumina) and quality-controlled with fastQC v0.11.5.
MAGeCK (v.0.5.9.2) was used to quality control, read mapping on Human_GeCKOv2_Library_A and Human_GeCKOv2_Library_B, and analyse the data using RRA.
Assembly: Human_GeCKOv2_combined
Supplementary files format and content: tab separated; raw and normalized counts
Library strategy: CRISPR screen

source_name: DND-41 cells

growth_protocol: Cell isolation and growth protocol: Cells were cultured in growth media (RPMI 1640 GlutaMAX (GIBCO, Cat# 61870010) supplemented with 10% FBS) with corresponding treatments.

extract_protocol:
At endpoint, at least 3x10^7 cells per replicate were collected for genomic DNA extraction to ensure over 400-fold coverage of library using ZymoResearch Quick-gDNA MidiPrep Plus Kit (Zymo Research, Cat#ZYM-D4075-25TST).
sgRNA sequences were amplified in two rounds: first round by GeCKO-F1/R1 primers using Herculase II Fusion DNA polymerase (Agilent Technologies, Cat #600679); second round by NGS-Lib_Fwd/Rev 1-10 indexed using NEBNext® High-Fidelity 2X PCR Master Mix (Cat #M0544L). PCR products were purified (Qiagen gel purification kit, Cat #28706, and Qiagen PCR purification kit, Cat #28106), quantified by Qubit (Thermo Fisher Scientific), and profiled by Fragment Analyzer.
Samples were sequenced in one run on Illumina NextSeq 500 Instrument (Illumina) according to the manufacturer instructions, yeilding 20 to 48 mio single-end 75 nucleotide reads per sample.

treatment_protocol: sgRNA/Cas9+ DND-41 cells were treated with DMSO, CB-103 (5uM) or DAPT (10uM) for 21 days for sgRNA selection.

value: DND-41 cells

value: GSI 21 days

tag: group

value: GSI (DAPT)

tag: replicate


title: Tnrc6a_1_IP

description: Experiment 2


title: col2_109

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

tag: colony

tag: bodylength

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: Tnrc6a_Ago2KO_3_input

description: Experiment 2

value: Input RNA GFP_5xT71BS, HA-AVI-Tnrc6a, Ago2-/-


title: col2_107

tag: headwidth

tag: age (months)

tag: trophallaxis nest

tag: broodcare

tag: guarding

value: forage ratio:0


title: DAPT_2

tag: cell line


title: col2_106

tag: tissue

tag: cleaning nest

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: RNCM_1uMAngII_n2

description: RNCMs Day 5 post-isolation

tag: cell type

tag: genotype

tag: treatment

value: 1 uM Angiotensin II


title: Tnrc6a_Ago2KO_1_input

description: Experiment 2

value: mouse embryonic stem cells


title: RNCM_10uMSII_n1

description: RNCMs Day 5 post-isolation


title: DAPT_1

tag: group

tag: replicate


title: col2_112

tag: colony

tag: bodylength

tag: cleaning forage

tag: grooming forage

tag: maturity

tag: nurse


title: col2_105

tag: headwidth

tag: age (months)

tag: trophallaxis nest

tag: broodcare

tag: guarding


title: Tnrc6a_Trim71KO_3_input

description: Experiment 2

value: Input RNA GFP_5xT71BS, HA-AVI-Tnrc6a, Trim71-/-


title: RNCM_10uMPhenylephrine_n1

description: RNCMs Day 5 post-isolation

tag: tissue

tag: cell line

value: 10 uM Phenylephrine


title: RNCM_10uMPhenylephrine_n2

description: RNCMs Day 5 post-isolation

value: neonatal primay cells

tag: cell type

tag: genotype


title: col2_104

tag: cleaning nest

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: Ctrl_3_IP

description: Experiment 2

tag: treatment


title: RNCM_10uMNorepinephrine_n2

description: RNCMs Day 5 post-isolation

value: Isolated rat neonatal cardiomyocytes

value: 10 uM Norepinephrine


title: Tnrc6a_Trim71KO_2_input

description: Experiment 2


title: col2_103

tag: colony

tag: bodylength

tag: cleaning forage

tag: grooming forage


title: CB-103_2

value: CB-103 21 days

tag: group

tag: replicate


title: CB-103_1


title: col2_102

tag: headwidth

tag: age (months)

tag: trophallaxis nest

tag: broodcare

tag: maturity

tag: nurse


title: RNCM_10uMNorepinephrine_n1

description: RNCMs Day 5 post-isolation

tag: tissue

tag: cell line

tag: cell type

tag: genotype

value: Wildtype


title: Tnrc6a_Trim71KO_1_input

description: Experiment 2

tag: treatment


title: RNCM_10uMIsoproterenol_n2

description: RNCMs Day 5 post-isolation

value: 10 uM Isoproterenol


title: Tnrc6a_2_input

description: Experiment 2

value: Input RNA GFP_5xT71BS, HA-AVI-Tnrc6a


title: col2_100

value: Brain

tag: colony

tag: cleaning nest

tag: guarding

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: DMSO_2

value: DND-41 cells

value: DMSO 21 days

tag: group

value: DMSO

tag: replicate


title: CB-103_3


title: RNCM_AceticAcid_n2

description: RNCMs Day 5 post-isolation

value: Acetic Acid (vehicle)


title: DMSO_1


title: col2_101

tag: bodylength

tag: headwidth

tag: age (months)

tag: trophallaxis nest

tag: cleaning forage

tag: grooming forage

value: forage ratio:0


title: Ctrl_3_input

description: Experiment 2

tag: cell type

value: Input RNA GFP_5xT71BS (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin)


title: RNCM_10uMIsoproterenol_n1

description: RNCMs Day 5 post-isolation

tag: tissue

tag: cell line

tag: genotype


title: TimeZero

tag: treatment

value: TimerZero


title: col2_098

tag: colony

tag: cleaning nest

tag: broodcare

tag: guarding

tag: maturity

tag: nurse


title: Tnrc6a_1_input

description: Experiment 2

value: mouse embryonic stem cells


title: RNCM_AscorbicAcid_n2

description: RNCMs Day 5 post-isolation

value: Ascorbic Acid (vehicle)


title: Ctrl_2_input

description: Experiment 2


title: White_Hepatocytes_ATAC_Seq

city: Gainesville

first: Danxin

last: Wang

state: FL

address: 1345 Center Drive MSB PG-05B

department: Pharmacotherapy and Translational Research

institute: University of Florida

data_processing:
The paired-end reads were Illumina chastity-filtered and contain phred+33 scores. These raw fastq.gz files are provided. Reads were mapped to GrCH38.p13 (without alt contigs) (PMID: 28396521) using bowtie2 (PMID: 22388286) in end-to-end mode with the very-sensitive setting. The resulting sam-format alignment files were sorted and converted to bam files via Samtools (PMID: 19505943). The “ATACSeq_QC” R package (PMID: 29490630) was used to filter reads mapping to the mitochondrial genome, PCR duplicates, and to shift the alignments (+4 bp forward strand/-5 bp reverse strand) to account for sequence insertion by the Tn5 transposase during tagmentation. The “cleaned” bam alignments from both technical replicates were merged and are provided here. MACS2 (PMID: 18798982) was used to call peaks on the alignments using “bam-paired-end” mode and “keep-dup all”, all other settings were the default.
Assembly: GrCH38.p13 (without alt contigs)
Supplementary files format and content: wig, tab-delimited text-files containing MACS2 called peaks

source_name: Primary Hepatocytes

growth_protocol: Cryopreserved human primary hepatocytes were purchased from Lonza Biosciences. Three vials each from black and white donors were pooled prior to plating. Thawing, plating, and maintenance of the hepatocytes followed the protocol provided by Lonza using Lonza media: thawing (MCHT50), plating (MP100), and maintenance (CC-3198). Approximately 500,000 cells were plated into a single well of a 24-well collagen I coated plate (Gibco®). Cells were placed in an incubator at 37°C/5% CO2, with gentle agitation at 15, 30, and 45 minutes post-seeding to disperse the cells. After one hour, the medium was removed and replaced with fresh plating medium. Four hours post-seeding, the medium was replaced with maintenance medium. The following day, cells were collected following the ATAC-Seq sample preparation protocol from ActiveMotif®. The existing media was removed and the cells were washed with pre-warmed maintenance media once. Fresh pre-warmed maintenance media containing 2.5 mM MgCl2, 0.5 mM CaCl2, and 1000 units of DNase was added to the well and incubated for 30 mins at 37°C/5% CO2. The media was removed, the cells were washed with PBS, and cells were detached using pre-warmed 0.25% trypsin/EDTA (Gibco®) and a three-minute incubation at 37°C/5% CO2. Cells were collected in 5 ml maintenance medium, centrifuged at 500xg for 5 mins at 4°C, and resuspended in 5 mL of ice-cold PBS for cell counting. Approximately 200,000 cells were centrifuged at 500xg at 4°C for 5 mins, the PBS was aspirated, and the cells were resuspended in ice-cold 50% FBS/40% maintenance media/10% DMSO. The resuspended cells were transferred to a 1.5 mL cryotube, frozen in a Mr. Frosty™ (ThermoFisher), and shipped to ActiveMotif® on dry ice. Two technical replicates were generated for both the black and white samples.

extract_protocol:
ATAC-Seq sample preparation and sequencing was conducted by ActiveMotif® (Carlsbad, CA, USA). Their procedure is summarized here with their permission. Cryopreserved cells were thawed in a 37°C water bath, pelleted via centrifugation, washed with ice-cold PBS, and tagmented (following Buenrostro et al., 2013) with modifications (based on Corces et al., 2017). Cells were resuspended in lysis buffer, centrifuged to pellet the debris.
DNA was tagmented using the Nextera® Library Prep Kit (Illumina). The resulting DNA was purified via the MinElute™ PCR purification kit (Qiagen), amplified by PCR (ten cycles), and then re-purified with Agencourt AMPure SPRI beads (Beckman Coulter). The eluted samples were then quantified using the KAPA library quantification kit for Illumina (Roche) and sequenced via PE42 sequencing on a NextSeq® 500 sequencer (Illumina).

value: Primary Hepatocytes

tag: donor group

value: white donors


title: col2_097

tag: bodylength

tag: headwidth

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: Tnrc6a_3_input

description: Experiment 2

tag: cell type


title: RNCM_AceticAcid_n1

description: RNCMs Day 5 post-isolation

tag: tissue

value: neonatal primay cells

value: Isolated rat neonatal cardiomyocytes


title: Black_Hepatocytes_ATAC_Seq

value: black donors


title: col2_096

tag: age (months)

tag: trophallaxis nest

tag: cleaning forage

tag: grooming forage


title: Ctrl_1_input

description: Experiment 2

tag: treatment


title: HA-Tnrc6a_Trim71KO_IP_3

description: Experiment 1

value: IP RNA GFP_5xT71BS, HA-AVI-Tnrc6a, Trim71-/-


title: RNCM_H2O_n1

description: RNCMs Day 5 post-isolation

tag: cell line

tag: genotype

value: Wildtype

value: H2O (vehicle)


title: DMSO_3

value: DND-41 cells

tag: group

tag: replicate


title: col2_095

value: Brain

tag: colony

tag: cleaning nest

tag: broodcare

tag: guarding

tag: maturity

tag: nurse


title: RNCM_AscorbicAcid_n1

description: RNCMs Day 5 post-isolation

tag: cell type


title: RNCM_H2O_n2

description: RNCMs Day 5 post-isolation

tag: tissue


title: HA-Tnrc6a_Trim71KO_IP_2

description: Experiment 1


title: col2_094

tag: bodylength

tag: headwidth

tag: age (months)

tag: grooming nest

tag: queenattending

tag: trophallaxis forage


title: col2_099

tag: trophallaxis nest

tag: cleaning forage

tag: grooming forage


title: HA-Tnrc6a_Trim71KO_IP_1

description: Experiment 1

tag: treatment


title: col2_093

tag: colony

tag: cleaning nest


title: HA-Tnrc6a_IP_3

description: Experiment 1

value: IP RNA GFP_5xT71BS, HA-AVI-Tnrc6a


title: NIP_ACC

city: Hangzhou

first: lv

middle: yu

last: song

address: CNRRI

institute: CNRRI

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Oryza sativa v7_JGI (Rice)
Supplementary_files_format_and_content: excel files include FPKM values for all Samples.

organism: Oryza sativa

source_name: mesocotyl

extract_protocol:
Total RNA was extracted from mesocotyl tissue using the TRIzol reagent (Invitrogen, Waltham, MA, USA), following the supplier’s protocol. The resulting RNA preparations were quantified and their purity tested using, respectively, a Bioanalyzer 2100 device and an RNA 6000 Nano Lab Chip kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 μg of total RNA was treated with magnetic beads coated with poly-T (Invitrogen) to capture the poly (A) mRNA.
The RNA fragments were reverse-transcribed to create a cDNA library, following the protocol supplied with an Illumina mRNA-Seq sample preparation kit; the average insert size was 300±50bp. Paired-end sequencing was performed by LC-Bio (Hangzhou, China) using an Illumina Hiseq 2500 device

treatment_protocol: the sterile grains of pao5 and NIP were sowed on a 0.6% agar medium containing 10 μM ACC or 10 μM H2O2, and cultivated for 7 days under absolute darkness environment (at 30 ℃ and 75% humidity).

tag: genotype/variation

value: wild type NIP

tag: development stage

value: 7 days after sowing in the dark

value: mesocotyl

value: 10 μM ACC treatment of NIP under darkness for 7 days


title: NIP_H2O2

value: 10 μM H2O2 reatment of NIP under darkness for 7 days


title: pao5

value: pao5 mutant

value: pao5 mutant  sowed under darkness for 7 days


title: HA-Tnrc6a_IP_2

description: Experiment 1

value: mouse embryonic stem cells


title: col2_091

tag: broodcare

tag: guarding

tag: maturity

tag: nurse


title: HA-Tnrc6a_IP_1

description: Experiment 1

tag: cell type


title: Human bone marrow mononuclear cells H3K27me3 ChIP-seq Sample 09

first: Mrinal

middle: M.

last: Patnaik

address: 200 First Street SW

department: Division of Hematology

description:
ASXL1_MT_H3K27me3_Consensus_Peaks.bw
ASXL1_MT_ChromHMM_States.bw

data_processing:
FastQC (v0.11.8) pre-alignment quality and adapter trimming, Bowtie2 (v2.3.3.1) / BWA (v0.7.17) alignment, post-alignment quality control, MACS2 (v3.0.0a6), MSPC(v5.4.0), ChromHMM (v1.20)
Assembly: GRCh38 / hg38
Supplementary files format and content: Consensus peaks in BW file generated by subjecting the peaks called by MACS2 to a second selection step by MSPC; Chromatin states (7-state model) in BW file generated by ChromHMM

source_name: Bone marrow mononuclear cells

extract_protocol:
DNA
N-CHIP, MeDIP, ATAC

tag: tissue

value: Bone marrow

tag: cell selection

value: Ficoll-gradient selected mononuclear cells

tag: disease state

tag: antibody


title: NIP

value: wild type NIP sowed under darkness for 7 days (mock)


title: col2_086

tag: bodylength

tag: headwidth

tag: age (months)

tag: trophallaxis nest

tag: grooming nest

tag: queenattending

tag: trophallaxis forage

value: forage ratio:0


title: untagged control_IP_3

description: Experiment 1

tag: treatment

value: IP RNA GFP_5xT71BS (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin)


title: col2_085

tag: colony

tag: cleaning nest

tag: broodcare

tag: cleaning forage

tag: grooming forage


title: U2OS_ChIPseq_Input_flavopiridol_rep2

data_processing:
Sequencing quality checks were performed on all experiments using FastQC (v0.11.9). X
Adapter sequences were removed using TrimGalore (v0.6.4_dev) and reads shorter than 20 nt were discarded.
Reads were aligned to the human reference genome (GRCh38/hg38) using bwa-mem (v0.7.17-r1188) with default options.
Reads that failed to align and those with MAPQ ≤ 30 were filtered out, and PCR duplicates were discarded using the Picard MarkDuplicates (v2.18.11) module.
Genome coverage tracks in bigWig format were generated using the bamCoverage module from deeptools (v3.2.1) with --binSize 50 --normalizeUsing CPM options.
Assembly: GRCh38/hg38
Supplementary files format and content: bigWig, genomic coverage CPM-normalized

extract_protocol:
6 to 10 million cells were crosslinked for 5 minutes at room temperature with 16% methanol-free formaldehyde (Thermo Fisher Scientific) used at a final concentration of 1%. After quenching the reaction with 125 mM glycine final concentration, cells were washed twice in ice-cold PBS and collected by scraping. Pellets were resuspended in buffer A (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40 substitute) and incubated on ice for 10 minutes. After centrifugation (5000 rpm for 5 minutes at 4°C), the supernatants containing the cytoplasm were removed and the nuclei-containing pellets were washed in buffer A without detergent. Pellets were then resuspended in shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 0.1% SDS) and sonicated with a ME220 focused-ultrasonicator (Covaris). After clarification by centrifugation (13000 rpm for 10 minutes at 4°C), the supernatant was adjusted in composition to RIPA buffer and transferred to a new tube to be used for immunoprecipitation. Equal amounts of chromatin (as measured by DNA concentration) were incubated rotating overnight at 4°C with pre-conjugated beads (20 μl of Dynabeads and 3 μg antibody, dyskerin (Abnova, H00001736-m04) or RNAPII (MBL, MAB0601)) in RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 200 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS). Immunoprecipitates were washed once with each of the following: RIPA buffer, RIPA buffer high salt (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LCiCl, 0.5% NP-40 substitute, 0.5% sodium deoxycholate), and twice with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The beads were then resuspended in TE buffer with 0.5% SDS supplemented with proteinase K (New England Biolabs) and RNase A (Thermo Fisher Scientific) and incubated with shaking at 65°C for 4 hours. The DNA was recovered by phenol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation using standard procedures, and resuspended in TE buffer.
Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s instructions.

treatment_protocol: 250nM flavopiridol for 2 hours prior to cell harvest, added directly to culture medium.

tag: cell line

tag: cell type

value: Human bone osteosarcoma

value: Flavopiridol


title: col2_083

tag: tissue

value: Brain

tag: guarding

tag: maturity

tag: nurse


title: untagged control_IP_2

description: Experiment 1


title: Human bone marrow mononuclear cells H3K27ac ChIP-seq Sample 16

description:
ASXL1_MT_H3K27ac_Consensus_Peaks.bw
ASXL1_MT_ChromHMM_States.bw

tag: cell selection

tag: disease state

tag: antibody


title: untagged control_IP_1

description: Experiment 1


title: Human bone marrow mononuclear cells H3K4me3 ChIP-seq  Sample 07

description:
ASXL1_WT_H3K4me3_Consensus_Peaks.bw
ASXL1_WT_ChromHMM_States.bw


title: HA-Tnrc6a_Trim71KO_input_2

description: Experiment 1

value: Input RNA GFP_5xT71BS, HA-AVI-Tnrc6a, Trim71-/-


title: col2_082

tag: bodylength

tag: headwidth

tag: age (months)

tag: trophallaxis nest

tag: grooming nest

tag: queenattending


title: col2_092

tag: colony

tag: cleaning nest

tag: broodcare

tag: trophallaxis forage

tag: cleaning forage


title: col2_081

tag: tissue

tag: guarding

tag: grooming forage


title: HA-Tnrc6a_Trim71KO_input_3

description: Experiment 1

tag: cell type

tag: treatment


title: HA-Tnrc6a_Trim71KO_input_1

description: Experiment 1


title: U2OS_ChIPseq_Input_control_rep2

tag: cell line

value: Vehicle


title: U2OS_ChIPseq_Input_flavopiridol_rep1


title: U2OS_ChIPseq_Input_control_rep1


title: HA-Tnrc6a_input_3

description: Experiment 1

value: Input RNA GFP_5xT71BS, HA-AVI-Tnrc6a


title: col2_077

tag: bodylength

tag: maturity

tag: nurse


title: col2_090

tag: headwidth

tag: age (months)

tag: trophallaxis nest


title: col2_079

tag: colony

tag: grooming nest

tag: queenattending


title: HA-Tnrc6a_input_2

description: Experiment 1


title: col2_076

tag: cleaning nest

tag: broodcare

tag: trophallaxis forage


title: U2OS_ChIPseq_RNAPII_flavopiridol_rep2

tag: chip antibody

value: RNAPII (MBL, MAB0601)


title: U2OS_ChIPseq_RNAPII_flavopiridol_rep1


title: HA-Tnrc6a_input_1

description: Experiment 1


title: col2_075

tag: tissue

tag: guarding

tag: cleaning forage

tag: grooming forage


title: U2OS_ChIPseq_RNAPII_control_rep2

tag: cell line

tag: cell type

tag: treatment


title: untagged control_input_3

description: Experiment 1

value: Input RNA GFP_5xT71BS (mES [129S6/SvEvTac], yGlob [GFP_5xT71BS], stable transfection FLAG-Cas9::T2A::Blasticidin)


title: col2_073

tag: bodylength

tag: headwidth

tag: maturity

tag: nurse


title: U2OS_ChIPseq_RNAPII_control_rep1


title: untagged control_input_1

description: Experiment 1


title: untagged control_input_2

description: Experiment 1


title: U2OS_ChIPseq_Dyskerin_flavopiridol_rep1

value: dyskerin (Abnova, H00001736-m04)


title: col2_071

tag: colony

tag: age (months)

tag: trophallaxis nest

tag: grooming nest


title: Tumor

city: Shanghai

first: Zhigang

last: Lu

address: 130 Dongan Road, Shanghai

department: IBS

institute: Fudan University

data_processing: The read counts of each oligo in the sgRNA library were calculated with MAGeCK packages according to the protocol described in "Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute" (Nat Protoc, 2019).

source_name: tumor

extract_protocol:
CD45+ cells from tumor or BM were sorted for genomic DNA extraction with the kit (QIAGEN, Cat#56304).
sgRNA fragment in the genomic DNA was amplified by PCR reaction with primers (Lib-Rev 5' GACTGGAGTTCAGACGTGTGCTCTTCCGATCTATGCTGTTTCCAGCATAGCTCTTAAAC 3', Lib-Fwd 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCTTAAGTAGAggctttatatatcttgtggaaaggacgaaacacc 3'). Barcode was added by PCR reaction with primers (P5 5'AATGATACGGCGACCACCGAGATCTACACTATAGCCTACACTCTTTCCCTACACGACGCTCTTCCGATCT 3', P7 5' CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT 3').

value: CD45+ cells

tag: strain

tag: age

value: 8 weeks

tag: genotype

value: WT

value: tumor


title: U2OS_ChIPseq_Dyskerin_control_rep2

tag: chip antibody


title: col2_070

first: Tomas

last: Kay

address: Biophore building

tag: tissue

tag: cleaning nest

tag: broodcare

tag: guarding

tag: queenattending

tag: trophallaxis forage

tag: cleaning forage

value: forage ratio:NA


title: bone marrow

source_name: bone marrow

tag: cell type

value: bone marrow


title: col2_069

tag: bodylength

tag: headwidth

tag: grooming forage

tag: maturity

tag: nurse

value: forage ratio:0


title: PMN-MDSC-13

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9

source_name: neutrophils

extract_protocol:
PMN-MDSCs were solated and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: neutrophils

tag: strain

value: CD300ld KO


title: U2OS_ChIPseq_Dyskerin_control_rep1

tag: cell line

value: Human bone osteosarcoma

tag: treatment


title: col2_068

value: Brain

tag: colony

tag: age (months)

tag: trophallaxis nest

tag: grooming nest