title: NANS-KO iPSCs-derived cerebral organoids, Day15, 3

description: Day15 NANS-KO cerebral organoids.txt


title: P12_40d_Usf1-KO_51, scRNA-seq

status: Public on Jun 26 2023

type: SRA

city: Beijing

first: Cheng-ran

last: Xu

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

department: School of Basic Medical Sciences

country: China

institute: Peking University

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

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: liver

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

tag: tissue

value: liver

tag: cell type

value: hepatocyte

tag: genotype

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: AlfpCre_Jmjd3flfl_P0_Dlk_2_7

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

source_name: Liver

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: DLK+

tag: genotype/treatment


title: P3_29, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: AlfpCre_Jmjd3flfl_P0_Dlk_2_6


title: NANS-KO iPSCs-derived cerebral organoids, Day15, 2

city: chengdu

first: Qian

last: Bu

state: Sichuan

address: 28 Gaopeng Street, High-tech District

institute: Chengdu  West China-Frontier PharmaTech Co.,Ltd

description: Day15 NANS-KO cerebral organoids.txt

data_processing:
library enrichment： PCR amplification of 15 cycles
recovery of target bands by 2% agarose gel
TBS380 (Picogreen) quantification, mixed on the machine in proportion to the data
bridge PCR amplification on cBot to generate clusters
sequencing on Illumina platform (PE library, read length 2×150bp）
Assembly: Homo_sapiens, GRCh38.p13
Supplementary files format and content: Excel of DEGs in 4 time points include TPM values, Fold change, P value for each Sample

organism: Homo sapiens

source_name: Cerebral organoids

growth_protocol: two hiPSCs were cultured and differentiated according to the protocol of STEMdiffTM Cerebral Organoid Kit (Stemcell Technologies, 08570)

extract_protocol:
RNA was harvested using miRneasy mini kit (Qiagen). The quantity of RNA samples was analyzed by NanoDrop 2000c (Thermo Scientific). The mRNA was extracted using an RNA sample preparation kit (Illumina).
A double-stranded cDNA synthesis kit (Invitrogen) was used to produce the cDNA and 200–300 bps sheared cDNA was inserted into the library.

value: Cerebral organoids

tag: cell line

value: hiPSCs (NCCSEDi001-A-1)

value: NANS homozygous knockout

value: brain differentiation


title: P3_27, scRNA-seq

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


title: NANS-KO iPSCs-derived cerebral organoids, Day15, 1

description: Day15 NANS-KO cerebral organoids.txt


title: P3_26, scRNA-seq

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


title: P12_40d_Usf1-KO_49, scRNA-seq


title: P12_40d_Usf1-KO_50, scRNA-seq


title: AlfpCre_Jmjd3flfl_P0_Dlk_2_5


title: WT iPSCs-derived cerebral organoids, Day15, 3

description: Day15 NANS-KO cerebral organoids.txt

value: hiPSCs (NCCSEDi001-A)

value: WT


title: AlfpCre_Jmjd3flfl_P0_Dlk_2_4


title: P3_25, scRNA-seq

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


title: P12_40d_Usf1-KO_48, scRNA-seq


title: AlfpCre_Jmjd3flfl_P0_Dlk_2_3


title: WT iPSCs-derived cerebral organoids, Day15, 2

description: Day15 NANS-KO cerebral organoids.txt


title: AlfpCre_Jmjd3flfl_P0_Epcam_1_8

value: EpCAM+


title: P3_24, scRNA-seq

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


title: WT iPSCs-derived cerebral organoids, Day15, 1

description: Day15 NANS-KO cerebral organoids.txt


title: P12_40d_Usf1-KO_47, scRNA-seq


title: P3_23, scRNA-seq

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


title: AlfpCre_Jmjd3flfl_P0_Dlk_2_12


title: NANS-KO iPSCs, Day0, 3

description: Day0 NANS-KO hiPSC.txt

source_name: NANS-KO iPSCs

value: NANS-KO iPSCs

value: human iPSCs


title: P3_28, scRNA-seq

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


title: P12_40d_WT_10, scRNA-seq


title: P12_40d_Usf1-KO_46, scRNA-seq


title: P12_40d_Usf1-KO_45, scRNA-seq


title: NANS-KO iPSCs, Day0, 2

description: Day0 NANS-KO hiPSC.txt


title: AlfpCre_Jmjd3flfl_P0_Dlk_2_11


title: P3_21, scRNA-seq

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


title: P12_40d_Usf1-KO_44, scRNA-seq


title: NANS-KO iPSCs, Day0, 1

description: Day0 NANS-KO hiPSC.txt


title: P12_40d_Usf1-KO_43, scRNA-seq


title: AlfpCre_Jmjd3flfl_P0_Dlk_2_10


title: P3_20, scRNA-seq

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


title: WT iPSCs, Day0, 3

description: Day0 NANS-KO hiPSC.txt

source_name: WT iPSCs

value: WT iPSCs


title: AlfpCre_Jmjd3flfl_P0_Dlk_2_1


title: P12_40d_Usf1-KO_42, scRNA-seq


title: AlfpCre_Jmjd3flfl_P0_Dlk_1_9


title: P3_18, scRNA-seq

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


title: AlfpCre_Jmjd3flfl_P0_Dlk_2_2


title: WT iPSCs, Day0, 2

description: Day0 NANS-KO hiPSC.txt


title: AlfpCre_Jmjd3flfl_P0_Dlk_1_8


title: P3_17, scRNA-seq

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


title: P3_19, scRNA-seq

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


title: Sample_12 KD

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

country: USA

institute: Joslin Diabetes Center

data_processing:
Reads were aligned to the human transcriptome (Ensembl version 94) using kallisto.
Transcript counts were converted to gene counts using tximport.
Assembly: GRCh38
Supplementary files format and content: CSV file includes gene counts for each Sample

source_name: hepatocytes

extract_protocol:
High-quality total RNA (>200nt) was extracted using standard Trizol reagent (Invitrogen) according to manufacturer instructions. The resultant aqueous phase was mixed (1:1) with 70% RNA-free ethanol and added to Qiagen Rneasy mini kit columns (Qiagen) and the kit protocol was followed.
RNA libraries for RNA-seq were prepared by Truseq Stranded mRNA Prep Kit following manufacturer's protocols.

value: hepatocytes

value: KD


title: P12_40d_Usf1-KO_39, scRNA-seq


title: AlfpCre_Jmjd3flfl_P0_Dlk_1_7


title: P12_40d_Usf1-KO_40, scRNA-seq


title: AlfpCre_Jmjd3flfl_P0_Dlk_1_6


title: Sample_11 KD


title: P3_15, scRNA-seq

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


title: P12_40d_Usf1-KO_38, scRNA-seq


title: Sample_10 KD


title: P3_14, scRNA-seq

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


title: WT iPSCs, Day0, 1

description: Day0 NANS-KO hiPSC.txt


title: P12_40d_Usf1-KO_37, scRNA-seq


title: P3_22, scRNA-seq

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


title: P12_40d_Usf1-KO_36, scRNA-seq


title: P3_13, scRNA-seq

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


title: AlfpCre_Jmjd3flfl_P0_Dlk_1_3


title: AlfpCre_Jmjd3flfl_P0_Dlk_1_4


title: Sample_9 CTRL

value: CTRL


title: P3_12, scRNA-seq

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

value: liver


title: Sample_8 CTRL


title: P3_11, scRNA-seq

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

value: hepatocyte


title: AlfpCre_Jmjd3flfl_P0_Dlk_1_2

value: DLK+


title: Sample_7 CTRL


title: P3_16, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: P12_40d_Usf1-KO_34, scRNA-seq


title: AlfpCre_Jmjd3flfl_P0_Dlk_1_12


title: P12_40d_Usf1-KO_35, scRNA-seq


title: P3_10, scRNA-seq

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


title: lymphatic tissue of patient 5

city: Jinan

first: Rui

last: Guan

state: Shandong

address: West Wenhua Road

institute: Shandong University

library_source: transcriptomic single cell

data_processing:
Basecalls performed using bcl2fastq V2.19.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Quantify gene expression using read2 by featureCounts software
Supplementary files format and content: matrix files

molecule: polyA RNA

source_name: lymph node

extract_protocol:
HSCC tissues, adjacent normal tissues and lymph node metastases from 5 HSCC patients were collected and stored at -20℃.Fresh tumor tissue was stored in GEXSCOPE® tissue preservation solution (Singleron) and shipped on ice to the Singleron laboratory as soon as possible.
Single cell suspension was loaded onto a microfluidic chip and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library Kit, Singleron Biotechnologies).

value: lymph node

tag: disease state

value: hypopharyngeal squamous cell carcinoma

value: untreated


title: AlfpCre_Jmjd3flfl_P0_Dlk_1_5


title: AlfpCre_Jmjd3flfl_P0_Dlk_1_11


title: lymphatic tissue of patient 4


title: P12_40d_Usf1-KO_33, scRNA-seq


title: P3_9, scRNA-seq

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


title: P3_8, scRNA-seq

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


title: P12_40d_Usf1-KO_32, scRNA-seq


title: AlfpCre_Jmjd3flfl_P0_Dlk_1_10


title: lymphatic tissue of patient 3


title: AlfpCre_Jmjd3flfl_P0_Dlk_1_1


title: lymphatic tissue of patient 2


title: P3_7, scRNA-seq

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


title: AlfpCre_Ezh2wtwt_P0_Epcam_2_9


title: AlfpCre_Ezh2wtwt_P0_Epcam_2_8


title: P3_6, scRNA-seq

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


title: hypopharynx tissue of patient 5

source_name: hypopharynx

value: hypopharynx


title: AlfpCre_Ezh2wtwt_P0_Epcam_2_7


title: P3_4, scRNA-seq

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


title: P12_40d_Usf1-KO_28, scRNA-seq


title: P12_40d_Usf1-KO_29, scRNA-seq


title: hypopharynx tissue of patient 4


title: AlfpCre_Ezh2wtwt_P0_Epcam_2_6


title: P12_40d_Usf1-KO_31, scRNA-seq


title: P12_40d_Usf1-KO_41, scRNA-seq


title: P12_40d_Usf1-KO_26, scRNA-seq


title: hypopharynx tissue of patient 2


title: hypopharynx tissue of patient 1


title: P12_40d_Usf1-KO_30, scRNA-seq


title: AlfpCre_Ezh2wtwt_P0_Epcam_2_4


title: P12_40d_Usf1-KO_24, scRNA-seq


title: P3_1, scRNA-seq

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


title: lymphatic tissue of patient 1


title: P3_2, scRNA-seq

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


title: P12_40d_Usf1-KO_25, scRNA-seq


title: P0_116, scRNA-seq

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


title: P3_5, scRNA-seq

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


title: AlfpCre_Ezh2wtwt_P0_Epcam_2_5


title: hypopharynx tissue of patient 3


title: P0_115, scRNA-seq

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


title: AIW002-2_hiPSC-CM_Day28_10uMPhenylephrine_n1

city: Montreal

first: Terence

last: Hébert

state: Quebec

address: 3655 Promenade Sir William Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

description: iPSC-CMs Day 28

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

source_name: hiPSC-derived cells

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

value: hiPSC-derived cells

value: iPSC-derived cardiomyocytes

value: Control

value: 10 uM Phenylephrine


title: P12_40d_Usf1-KO_27, scRNA-seq


title: P12_40d_Usf1-KO_22, scRNA-seq


title: P12_40d_Usf1-KO_23, scRNA-seq


title: AlfpCre_Ezh2wtwt_P0_Epcam_2_11

value: EpCAM+


title: P0_114, scRNA-seq

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


title: P3_3, scRNA-seq

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


title: P12_40d_Usf1-KO_21, scRNA-seq


title: AlfpCre_Ezh2wtwt_P0_Epcam_2_10


title: AIW002-2_hiPSC-CM_Day28_100nM_ET-1_n1

description: iPSC-CMs Day 28

value: 100 nM Endothelin-1


title: P0_113, scRNA-seq

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


title: P12_40d_Usf1-KO_20, scRNA-seq


title: AlfpCre_Ezh2wtwt_P0_Epcam_2_3


title: AlfpCre_Ezh2wtwt_P0_Epcam_2_1


title: P0_112, scRNA-seq

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


title: AIW002-2_hiPSC-CM_Day28_10uMSII_n2

description: iPSC-CMs Day 28

value: 10 uM SII


title: P12_40d_Usf1-KO_19, scRNA-seq


title: AIW002-2_hiPSC-CM_Day28_10uMPhenylephrine_n2

description: iPSC-CMs Day 28


title: AlfpCre_Ezh2wtwt_P0_Epcam_2_2


title: P0_111, scRNA-seq

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


title: P0_110, scRNA-seq

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


title: AlfpCre_Ezh2wtwt_P0_Epcam_1_8


title: AIW002-2_hiPSC-CM_Day28_1uMAngII_n2

description: iPSC-CMs Day 28

value: 1 uM Angiotensin II


title: AIW002-2_hiPSC-CM_Day28_10uMSII_n1

description: iPSC-CMs Day 28


title: AIW002-2_hiPSC-CM_Day28_1uMAngII_n1

description: iPSC-CMs Day 28


title: AIW002-2_hiPSC-CM_Day28_100nM_ET-1_n2

description: iPSC-CMs Day 28


title: AIW002-2_hiPSC-CM_Day28_10uMNorepinephrine_n2

description: iPSC-CMs Day 28

value: 10 uM Norepinephrine


title: AlfpCre_Ezh2wtwt_P0_Epcam_1_7


title: P0_109, scRNA-seq

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

value: liver


title: P12_40d_Usf1-KO_17, scRNA-seq

value: hepatocyte


title: P12_40d_Usf1-KO_16, scRNA-seq


title: AlfpCre_Ezh2wtwt_P0_Epcam_1_6


title: AlfpCre_Ezh2wtwt_P0_Epcam_1_5


title: AIW002-2_hiPSC-CM_Day28_10uMNorepinephrine_n1

description: iPSC-CMs Day 28


title: P0_107, scRNA-seq

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


title: P12_40d_Usf1-KO_15, scRNA-seq


title: P0_108, scRNA-seq

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


title: P12_40d_Usf1-KO_14, scRNA-seq


title: AIW002-2_hiPSC-CM_Day28_10uMIsoproterenol_n2

description: iPSC-CMs Day 28

value: 10 uM Isoproterenol


title: AlfpCre_Ezh2wtwt_P0_Epcam_1_9


title: AIW002-2_hiPSC-CM_Day28_10uMIsoproterenol_n1

description: iPSC-CMs Day 28


title: AlfpCre_Ezh2wtwt_P0_Epcam_1_4


title: P0_106, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: AlfpCre_Ezh2wtwt_P0_Epcam_1_3


title: P12_40d_Usf1-KO_18, scRNA-seq


title: P0_105, scRNA-seq

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


title: P12_40d_Usf1-KO_12, scRNA-seq


title: AIW002-2_hiPSC-CM_Day28_AceticAcid_n2

description: iPSC-CMs Day 28

value: Acetic Acid (vehicle)


title: P0_104, scRNA-seq

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


title: AlfpCre_Ezh2wtwt_P0_Epcam_1_13


title: AlfpCre_Ezh2wtwt_P0_Epcam_1_2


title: P12_40d_Usf1-KO_11, scRNA-seq


title: P12_40d_Usf1-KO_10, scRNA-seq


title: AIW002-2_hiPSC-CM_Day28_AscorbicAcid_n2

description: iPSC-CMs Day 28

value: Ascorbic Acid (vehicle)


title: AlfpCre_Ezh2wtwt_P0_Epcam_1_12


title: AlfpCre_Ezh2wtwt_P0_Epcam_1_11


title: AIW002-2_hiPSC-CM_Day28_AscorbicAcid_n1

description: iPSC-CMs Day 28


title: P12_40d_Usf1-KO_9, scRNA-seq


title: P12_40d_Usf1-KO_8, scRNA-seq


title: AIW002-2_hiPSC-CM_Day28_H2O_n2

description: iPSC-CMs Day 28

value: H2O (vehicle)


title: P0_101, scRNA-seq

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


title: P12_40d_Usf1-KO_13, scRNA-seq


title: P12_40d_Usf1-KO_7, scRNA-seq


title: AlfpCre_Ezh2wtwt_P0_Epcam_1_1


title: AIW002-2_hiPSC-CM_Day28_H2O_n1

description: iPSC-CMs Day 28


title: P0_100, scRNA-seq

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


title: P12_40d_Usf1-KO_6, scRNA-seq


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_9

value: DLK+


title: P0_98, scRNA-seq

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


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_8


title: P0_103, scRNA-seq

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


title: FR-B-2-15-3

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (GRCm39) by STAR (version 2.7.9a).
The number of fragments in each known gene from GENCODE (version vM28) was quantified using STAR QuantMode (GeneCounts) function.
The differential gene expression was analyzed by R/Bioconductor package DESeq2 (version 1.34.0).
Assembly: GRCm39
Supplementary files format and content: The first column represents gene symbol. The other columns are raw counts for all the samples.

source_name: Sorted T-cells

growth_protocol: FR-B 2/7 or FR-B 2/15 T cells (8.4 x 105/mouse, prepared in 200μl PBS) were adoptively transferred by IP injection into IE9-mp1-hFRa tumor-bearing mice and peritoneal washes collected from mice 5 days later following IP injection of 5ml PBS. Collected cells were washed and immediately stained for cell viability (Zombie UV, prepared in PBS) followed by Fc blocking and surface phenotyping using antibodies prepared in BD FACs Pre-Sort Buffer (BD Biosciences). Live CD45+CD11b-CD19-CD4- (Gated out using a PE-Cy7 Dump Channel) CD8+ GFP+ FR-B TALs were sorted using a BD FACSAria II Cell Sorter and collected directly into PCR tubes containing 2μl of Takara Plain Sorting Solution with a target collection of 500 cells/sample.  Sufficient cell input (359-500 cells) was achieved for downstream analysis using 5 unique biological samples (n=2 for FR-B 2/7 CD8+ TALs, n=3 for FR-B 2/15 CD8+ TALs).

extract_protocol:
Takara Bio USA, Inc. SMART-Seq® v4 PLUS Kit was used for library preparation.
Raw sequencing reads were aligned to the human genome (GRCm39) using STAR. Raw feature counts were normalized and differential expression analysis using DESeq2.

value: T-cell

tag: condition


title: P12_40d_Usf1-KO_5, scRNA-seq


title: AIW002-2_hiPSC-CM_Day28_AceticAcid_n1

description: iPSC-CMs Day 28

value: hiPSC-derived cells

value: iPSC-derived cardiomyocytes


title: P12_40d_Usf1-KO_4, scRNA-seq


title: FR-B-2-15-1


title: P0_97, scRNA-seq

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


title: FR-B-2-15-2


title: P0_96, scRNA-seq

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


title: P0_102, scRNA-seq

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


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_7


title: P12_40d_Usf1-KO_3, scRNA-seq


title: AlfpCre_Ezh2wtwt_P0_Epcam_1_10


title: FR-B-2-7-4


title: P0_95, scRNA-seq

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


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_6


title: FR-B-2-7-1


title: P0_94, scRNA-seq

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


title: P12_40d_Usf1-KO_1, scRNA-seq


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_4


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_5


title: P0_99, scRNA-seq

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


title: Donor_C_Restim_BG_DMI

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
Fastq files were assessed for quality using the FastQC package and no samples were excluded from analysis. Bowtie was used to map 100-bp paired end reads to the human transcriptome (Ensembl, GRCh37v70), and gene expression estimates were derived using the mmseq pipeline. DESeq2  was used to normalise count data and determine gene expression differences between treatments.
Assembly: hg19
Supplementary files format and content: .gene.mmseq.txt files contain counts per gene

source_name: Adult Human Peripheral Blood

growth_protocol: Monocytes were differentiated into resting macrophages by ex vivo culture in RPMI 1640 medium (Sigma Aldrich) with 10% Human Serum. Trained immunity was induced by exposing cells to BCG vaccines for 24 hours, while a tolerance control was induced by LPS for 24 hours.

extract_protocol:
Total RNA were extracted using the QIAGEN AllPrep DNA/RNA micro-kit according to manufacturer’s instructions.
Library preparation was performed using the Illumina TruSeq stranded mRNA kit with a starting input of 300ng and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 20 million reads per sample.

tag: individual

value: Monocyte

value: BG and DMI exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: P12_40d_Tef-KO_126, scRNA-seq

tag: tissue

value: Tef-KO


title: P0_93, scRNA-seq

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

tag: cell type


title: P0_92, scRNA-seq

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

tag: genotype


title: P12_40d_Tef-KO_125, scRNA-seq

tag: age


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_3


title: Donor_C_Restim_itaconate

value: Itaconate exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_21


title: P12_40d_Tef-KO_124, scRNA-seq

tag: ploidy


title: Donor_C_Restim_DMI

tag: treatment

value: DMI exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: P0_90, scRNA-seq

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

tag: zonation


title: Donor_C_Restim_BG

value: BG exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_20

tag: Stage


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_2

tag: protocol


title: P12_40d_Tef-KO_123, scRNA-seq

value: liver


title: P12_40d_Usf1-KO_2, scRNA-seq

value: hepatocyte


title: Donor_C_Restim_RPMI

value: RPMI media only for 6 days, then exposed to LPS for 4 hours


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_19

tag: culture


title: P12_40d_Tef-KO_122, scRNA-seq


title: P0_88, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: P0_89, scRNA-seq

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


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_18

tag: batch


title: Donor_C_d6_itaconate

value: Itaconate exposed for 24 hours, rested in media alone for 5 days


title: Donor_C_d6_BG_DMI

value: BG and DMI exposed for 24 hours, rested in media alone for 5 days


title: P0_86, scRNA-seq

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


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_17

tag: sort


title: P12_40d_Tef-KO_120, scRNA-seq


title: P0_91, scRNA-seq

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


title: Donor_C_d6_DMI

value: DMI exposed for 24 hours, rested in media alone for 5 days


title: Donor_C_d6_BG

value: BG exposed for 24 hours, rested in media alone for 5 days


title: P0_87, scRNA-seq

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


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_16

value: DLK+

tag: genotype/treatment


title: P0_84, scRNA-seq

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


title: P0_85, scRNA-seq

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


title: Donor_C_d6_RPMI

value: RPMI media only, collected at 6 days post culture


title: P12_40d_Tef-KO_118, scRNA-seq


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_14


title: P12_40d_Tef-KO_117, scRNA-seq


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_15


title: Donor_C_d1_BG_DMI

value: BG and DMI exposed, collected at 24 hours post exposure.


title: P0_83, scRNA-seq

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


title: P12_40d_Tef-KO_121, scRNA-seq


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_13


title: P12_40d_Tef-KO_116, scRNA-seq


title: P0_82, scRNA-seq

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


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_12


title: P12_40d_Tef-KO_115, scRNA-seq


title: Donor_C_d1_itaconate

value: Monocyte

value: Itaconate exposed, collected at 24 hours post exposure.


title: Donor_C_d1_LPS_DMI

value: LPS and DMI exposed, collected at 24 hours post exposure.


title: P12_40d_Tef-KO_119, scRNA-seq

value: Tef-KO


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_11


title: P0_81, scRNA-seq

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


title: Donor_C_d1_DMI

value: DMI exposed, collected at 24 hours post exposure.


title: P12_40d_Tef-KO_113, scRNA-seq


title: P0_80, scRNA-seq

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


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_10


title: P0_79, scRNA-seq

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


title: P12_40d_Tef-KO_112, scRNA-seq


title: Donor_C_d1_BG

value: BG exposed, collected at 24 hours post exposure.


title: AlfpCre_Ezh2wtwt_P0_Dlk_2_1


title: Donor_C_d1_LPS

value: LPS exposed, collected at 24 hours post exposure.


title: P0_78, scRNA-seq

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

value: liver

value: hepatocyte


title: Donor_C_d1_RPMI

value: RPMI media only, collected at 24 hours post culture


title: Donor_C_4h_BG_DMI

value: BG and DMI exposed, collected at 4 hours post exposure.


title: AlfpCre_Ezh2wtwt_P0_Dlk_1_5


title: P12_40d_Tef-KO_110, scRNA-seq


title: P12_40d_Tef-KO_109, scRNA-seq


title: P0_75, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: Donor_C_4h_LPS_DMI

value: LPS and DMI exposed, collected at 4 hours post exposure.


title: AlfpCre_Ezh2wtwt_P0_Dlk_1_6


title: AlfpCre_Ezh2wtwt_P0_Dlk_1_4


title: P12_40d_Tef-KO_111, scRNA-seq


title: P0_76, scRNA-seq

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


title: P12_40d_Tef-KO_114, scRNA-seq


title: Donor_C_4h_itaconate

value: Itaconate exposed, collected at 4 hours post exposure.


title: P0_74, scRNA-seq

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


title: P12_40d_Tef-KO_107, scRNA-seq


title: P0_77, scRNA-seq

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


title: AlfpCre_Ezh2wtwt_P0_Dlk_1_3

value: DLK+


title: AlfpCre_Ezh2wtwt_P0_Dlk_1_2


title: P0_73, scRNA-seq

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


title: Donor_C_4h_DMI

value: DMI exposed, collected at 4 hours post exposure.


title: P0_72, scRNA-seq

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


title: P12_40d_Tef-KO_106, scRNA-seq


title: AlfpCre_Ezh2wtwt_P0_Dlk_1_1


title: Donor_C_4h_BG

value: BG exposed, collected at 4 hours post exposure.


title: AlfpCre_Ezh2flfl_P0_Epcam_2_9

value: EpCAM+


title: P12_40d_Tef-KO_105, scRNA-seq


title: P0_71, scRNA-seq

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


title: AlfpCre_Ezh2flfl_P0_Epcam_2_8


title: P0_70, scRNA-seq

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


title: AlfpCre_Ezh2flfl_P0_Epcam_2_7


title: Donor_C_4h_LPS

value: Monocyte

value: LPS exposed, collected at 4 hours post exposure.


title: P0_69, scRNA-seq

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


title: P12_40d_Tef-KO_102, scRNA-seq

value: Tef-KO


title: P12_40d_Tef-KO_101, scRNA-seq


title: P12_40d_Tef-KO_104, scRNA-seq


title: Donor_C_4h_RPMI

value: RPMI media only, collected at 4 hours post culture


title: AlfpCre_Ezh2flfl_P0_Epcam_2_4


title: P12_40d_Tef-KO_100, scRNA-seq


title: P12_40d_Tef-KO_108, scRNA-seq


title: Donor_B_Restim_DMI

value: DMI exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: Donor_B_Restim_BG

value: BG exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: P12_40d_Tef-KO_103, scRNA-seq

value: liver


title: P0_66, scRNA-seq

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

value: hepatocyte


title: P0_65, scRNA-seq

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


title: AlfpCre_Ezh2flfl_P0_Epcam_2_2


title: P0_64, scRNA-seq

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


title: AlfpCre_Ezh2flfl_P0_Epcam_2_17


title: Donor_C_d0

value: Baseline monocyte, attached to dish for 1  hour


title: AlfpCre_Ezh2flfl_P0_Epcam_2_6


title: Donor_B_Restim_BG_DMI

value: BG and DMI exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: P0_63, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: Donor_B_Restim_itaconate

value: Itaconate exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: P0_68, scRNA-seq

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


title: P12_40d_Tef-KO_97, scRNA-seq


title: P12_40d_Tef-KO_96, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Epcam_2_16


title: AlfpCre_Ezh2flfl_P0_Epcam_2_5


title: AlfpCre_Ezh2flfl_P0_Epcam_2_15


title: P0_67, scRNA-seq

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


title: Donor_B_d6_itaconate

value: Itaconate exposed for 24 hours, rested in media alone for 5 days


title: P12_40d_Tef-KO_94, scRNA-seq


title: P12_40d_Tef-KO_99, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Epcam_2_3


title: AlfpCre_Ezh2flfl_P0_Epcam_2_13


title: P12_40d_Tef-KO_98, scRNA-seq


title: Donor_B_d6_BG

value: BG exposed for 24 hours, rested in media alone for 5 days


title: P0_60, scRNA-seq

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


title: Donor_B_d6_RPMI

value: RPMI media only, collected at 6 days post culture


title: Donor_B_Restim_RPMI

value: RPMI media only for 6 days, then exposed to LPS for 4 hours


title: Donor_B_d6_BG_DMI

value: BG and DMI exposed for 24 hours, rested in media alone for 5 days


title: P0_59, scRNA-seq

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


title: P12_40d_Tef-KO_92, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Epcam_2_11

value: EpCAM+


title: Donor_B_d1_BG_DMI

value: Monocyte

value: BG and DMI exposed, collected at 24 hours post exposure.


title: P12_40d_Tef-KO_91, scRNA-seq

value: Tef-KO


title: P12_40d_Tef-KO_90, scRNA-seq


title: P12_40d_Tef-KO_89, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Epcam_2_1


title: P0_54, scRNA-seq

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


title: P0_55, scRNA-seq

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


title: Donor_B_d1_BG

value: BG exposed, collected at 24 hours post exposure.


title: P0_62, scRNA-seq

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


title: P12_40d_Tef-KO_87, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Epcam_1_8


title: P0_53, scRNA-seq

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


title: P0_52, scRNA-seq

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


title: Donor_B_d6_DMI

value: DMI exposed for 24 hours, rested in media alone for 5 days


title: AlfpCre_Ezh2flfl_P0_Epcam_1_6


title: P0_61, scRNA-seq

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

value: liver


title: AlfpCre_Ezh2flfl_P0_Epcam_2_14


title: P12_40d_Tef-KO_93, scRNA-seq

value: hepatocyte


title: Donor_B_4h_BG_DMI

value: BG and DMI exposed, collected at 4 hours post exposure.


title: P0_50, scRNA-seq

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


title: AlfpCre_Ezh2flfl_P0_Epcam_2_12


title: P12_40d_Tef-KO_95, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Epcam_1_7


title: P0_58, scRNA-seq

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


title: P0_57, scRNA-seq

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


title: Donor_B_d1_itaconate

value: Itaconate exposed, collected at 24 hours post exposure.


title: P0_56, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: Donor_B_d1_DMI

value: DMI exposed, collected at 24 hours post exposure.


title: AlfpCre_Ezh2flfl_P0_Epcam_1_4


title: Donor_B_4h_itaconate

value: Itaconate exposed, collected at 4 hours post exposure.


title: P12_40d_Tef-KO_88, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Epcam_1_9


title: Donor_B_d1_LPS

value: LPS exposed, collected at 24 hours post exposure.


title: Donor_B_d1_RPMI

value: RPMI media only, collected at 24 hours post culture


title: Donor_B_d1_LPS_DMI

value: LPS and DMI exposed, collected at 24 hours post exposure.


title: P12_40d_Tef-KO_86, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Epcam_2_10


title: P12_40d_Tef-KO_85, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Epcam_1_3


title: P12_40d_Tef-KO_82, scRNA-seq


title: P12_40d_Tef-KO_80, scRNA-seq


title: P0_46, scRNA-seq

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


title: Donor_B_4h_LPS

value: LPS exposed, collected at 4 hours post exposure.


title: AlfpCre_Ezh2flfl_P0_Epcam_1_12

value: EpCAM+


title: Donor_A_Restim_BG_DMI

value: Monocyte

value: BG and DMI exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: P12_40d_Tef-KO_77, scRNA-seq

value: Tef-KO


title: P0_43, scRNA-seq

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


title: AlfpCre_Ezh2flfl_P0_Epcam_1_10


title: Donor_B_4h_RPMI

value: RPMI media only, collected at 4 hours post culture


title: P0_42, scRNA-seq

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


title: P0_41, scRNA-seq

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


title: P12_40d_Tef-KO_84, scRNA-seq


title: P0_51, scRNA-seq

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


title: AlfpCre_Ezh2flfl_P0_Epcam_1_5


title: Donor_A_Restim_BG

value: BG exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: Donor_A_Restim_DMI

value: DMI exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: Donor_B_4h_LPS_DMI

value: LPS and DMI exposed, collected at 4 hours post exposure.


title: P12_40d_Tef-KO_74, scRNA-seq

value: liver

value: hepatocyte


title: AlfpCre_Ezh2flfl_P0_Epcam_1_1


title: P12_40d_Tef-KO_83, scRNA-seq


title: P0_49, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: P12_40d_Tef-KO_72, scRNA-seq


title: Donor_A_d6_itaconate

value: Itaconate exposed for 24 hours, rested in media alone for 5 days


title: Donor_A_Restim_RPMI

value: RPMI media only for 6 days, then exposed to LPS for 4 hours


title: AlfpCre_Ezh2flfl_P0_Epcam_1_2


title: Donor_B_4h_BG

value: BG exposed, collected at 4 hours post exposure.


title: P0_47, scRNA-seq

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


title: Donor_B_4h_DMI

value: DMI exposed, collected at 4 hours post exposure.


title: AlfpCre_Ezh2flfl_P0_Epcam_1_14


title: P0_36, scRNA-seq

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


title: P12_40d_Tef-KO_79, scRNA-seq


title: P0_48, scRNA-seq

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


title: AlfpCre_Ezh2flfl_P0_Epcam_1_13


title: Donor_A_d6_DMI

value: DMI exposed for 24 hours, rested in media alone for 5 days


title: P12_40d_Tef-KO_81, scRNA-seq


title: P0_45, scRNA-seq

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


title: P12_40d_Tef-KO_78, scRNA-seq


title: Donor_B_d0

value: Baseline monocyte, attached to dish for 1  hour


title: P0_44, scRNA-seq

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


title: P12_40d_Tef-KO_68, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Epcam_1_11

value: EpCAM+


title: P12_40d_Tef-KO_76, scRNA-seq


title: Donor_A_d1_BG_DMI

value: Monocyte

value: BG and DMI exposed, collected at 24 hours post exposure.


title: P0_35, scRNA-seq

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


title: P0_33, scRNA-seq

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


title: P12_40d_Tef-KO_66, scRNA-seq

value: Tef-KO


title: Donor_A_Restim_itaconate

value: Itaconate exposed for 24 hours, rested in media alone for 5 days, then exposed to LPS for 4 hours


title: P0_32, scRNA-seq

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


title: P12_40d_Tef-KO_75, scRNA-seq


title: P12_40d_Tef-KO_65, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Dlk_2_9

value: DLK+


title: P0_40, scRNA-seq

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


title: P12_40d_Tef-KO_73, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Dlk_2_8


title: AlfpCre_Ezh2flfl_P0_Dlk_2_7


title: Donor_A_d6_BG_DMI

value: BG and DMI exposed for 24 hours, rested in media alone for 5 days


title: P0_38, scRNA-seq

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


title: P0_30, scRNA-seq

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


title: AlfpCre_Ezh2flfl_P0_Dlk_2_18


title: P12_40d_Tef-KO_71, scRNA-seq


title: P0_29, scRNA-seq

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


title: AlfpCre_Ezh2flfl_P0_Dlk_2_6


title: P0_39, scRNA-seq

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


title: P0_37, scRNA-seq

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


title: AlfpCre_Ezh2flfl_P0_Dlk_2_16


title: AlfpCre_Ezh2flfl_P0_Dlk_2_17


title: P12_40d_Tef-KO_62, scRNA-seq


title: Donor_A_d1_DMI

value: DMI exposed, collected at 24 hours post exposure.


title: P12_40d_Tef-KO_70, scRNA-seq

value: liver


title: AlfpCre_Ezh2flfl_P0_Dlk_2_19


title: Donor_A_d6_RPMI

value: RPMI media only, collected at 6 days post culture


title: P0_34, scRNA-seq

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

value: hepatocyte

value: Alb-Cre; Rosa-tdTomato


title: AlfpCre_Ezh2flfl_P0_Dlk_2_4


title: AlfpCre_Ezh2flfl_P0_Dlk_2_5


title: Donor_A_d6_BG

value: BG exposed for 24 hours, rested in media alone for 5 days


title: P12_40d_Tef-KO_69, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Dlk_2_3


title: P12_40d_Tef-KO_64, scRNA-seq


title: P12_40d_Tef-KO_61, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Dlk_2_2


title: P12_40d_Tef-KO_67, scRNA-seq


title: Donor_A_d1_LPS_DMI

value: LPS and DMI exposed, collected at 24 hours post exposure.


title: Donor_A_d1_itaconate

value: Itaconate exposed, collected at 24 hours post exposure.


title: P12_40d_Tef-KO_63, scRNA-seq


title: P0_31, scRNA-seq

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


title: P0_28, scRNA-seq

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


title: Donor_A_d1_BG

value: BG exposed, collected at 24 hours post exposure.


title: Donor_A_d1_RPMI

value: RPMI media only, collected at 24 hours post culture


title: AlfpCre_Ezh2flfl_P0_Dlk_2_15


title: P12_40d_Tef-KO_60, scRNA-seq


title: P0_27, scRNA-seq

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


title: Donor_A_4h_BG_DMI

value: BG and DMI exposed, collected at 4 hours post exposure.


title: AlfpCre_Ezh2flfl_P0_Dlk_2_20


title: AlfpCre_Ezh2flfl_P0_Dlk_2_14


title: Donor_A_4h_LPS_DMI

value: Monocyte

value: LPS and DMI exposed, collected at 4 hours post exposure.


title: AlfpCre_Ezh2flfl_P0_Dlk_2_13


title: Donor_A_d1_LPS

value: LPS exposed, collected at 24 hours post exposure.


title: P12_40d_Tef-KO_58, scRNA-seq

value: Tef-KO


title: P12_40d_Tef-KO_59, scRNA-seq


title: P12_40d_Tef-KO_57, scRNA-seq


title: P0_24, scRNA-seq

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


title: Donor_A_4h_DMI

value: DMI exposed, collected at 4 hours post exposure.


title: P0_23, scRNA-seq

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


title: Donor_A_4h_itaconate

value: Itaconate exposed, collected at 4 hours post exposure.


title: AlfpCre_Ezh2flfl_P0_Dlk_2_11

value: DLK+


title: P0_22, scRNA-seq

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

value: liver


title: AlfpCre_Ezh2flfl_P0_Dlk_2_12


title: Donor_A_4h_BG

value: BG exposed, collected at 4 hours post exposure.


title: AlfpCre_Ezh2flfl_P0_Dlk_2_1


title: AlfpCre_Ezh2flfl_P0_Dlk_2_10


title: P0_25, scRNA-seq

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

value: hepatocyte


title: Donor_A_4h_LPS

value: LPS exposed, collected at 4 hours post exposure.


title: P12_40d_Tef-KO_56, scRNA-seq


title: P0_26, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: AlfpCre_Ezh2flfl_P0_Dlk_1_9


title: P12_40d_Tef-KO_55, scRNA-seq


title: P12_40d_Tef-KO_54, scRNA-seq


title: P0_20, scRNA-seq

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


title: AlfpCre_Ezh2flfl_P0_Dlk_1_8


title: Donor_A_d0

value: Baseline monocyte, attached to dish for 1  hour


title: P0_19, scRNA-seq

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


title: AlfpCre_Ezh2flfl_P0_Dlk_1_7


title: Donor_A_4h_RPMI

value: RPMI media only, collected at 4 hours post culture


title: P12_40d_Tef-KO_52, scRNA-seq


title: P12_40d_Tef-KO_51, scRNA-seq


title: U2OS_RNAseq_siGAR1_rep1

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).
Adaptor sequences were removed using TrimGalore (v0.6.4_dev) with default parameters.
Reads were filtered against human rRNA and tRNA sequences obtained from the NCBI using Bowtie2 (v2.4.1) with the option --sensitive-local.
Reads that failed to align were used as input for STAR (v2.7.0e) and were mapped to the human reference genome (GRCh38/hg38) using GENCODE (v27) gene annotation  as reference, with the following parameters: --twopassMode Basic --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outFilterMultimapNmax 1 --outFilterType BySJout --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outSAMattributes All --outSAMtype BAM SortedByCoordinate --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000.
PCR duplicates were removed using Picard MarkDuplicates (v2.18.11) with default parameters.
Transcript expression quantification was carried out using Salmon (v1.2.0) in pseudo-alignment mode, with library type (-l ISR) and correction of sequence-specific (--seqBias) and position-specific (--posBias) biases, and the GENCODE (v27) annotation and corresponding transcriptome as references.
Assembly: GRCh38/hg38
Supplementary files format and content: Salmon quantification file, tab-separated file with a single header line

molecule: nuclear RNA

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

extract_protocol:
Cells were harvested and subjected to nuclear fractionation. Nuclear RNA was extracted using Trizol (Thermo Fisher Scientific) according to manufacturer’s instructions.
Libraries were generated using the RiboCop rRNA depletion kit followed by the CORALL Total RNA-Seq library preparation kit (both from Lexogen), following manufacturer’s instructions.

treatment_protocol: Cells were transfected for 48 hours with 15 nM siRNA using RNAiMAX (Thermo Fisher Scientific) according to manufacturer’s instructions.

tag: cell line

value: Human bone osteosarcoma


title: U2OS_RNAseq_siGAR1_rep3


title: P12_40d_Tef-KO_50, scRNA-seq


title: U2OS_RNAseq_siGAR1_rep2


title: P0_16, scRNA-seq

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


title: AlfpCre_Ezh2flfl_P0_Dlk_1_6


title: AlfpCre_Ezh2flfl_P0_Dlk_1_5


title: P0_21, scRNA-seq

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


title: P0_15, scRNA-seq

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


title: U2OS_RNAseq_siDyskerin_rep2

value: siDyskerin


title: AlfpCre_Ezh2flfl_P0_Dlk_1_4


title: P12_40d_Tef-KO_53, scRNA-seq


title: U2OS_RNAseq_siDyskerin_rep3


title: P12_40d_Tef-KO_48, scRNA-seq


title: P0_14, scRNA-seq

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


title: P0_17, scRNA-seq

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


title: U2OS_RNAseq_siDyskerin_rep1


title: AlfpCre_Ezh2flfl_P0_Dlk_1_2


title: P12_40d_Tef-KO_49, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Dlk_1_3


title: P0_18, scRNA-seq

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


title: AlfpCre_Ezh2flfl_P0_Dlk_1_10


title: P0_13, scRNA-seq

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


title: U2OS_RNAseq_siControl_rep3

value: siControl


title: P0_12, scRNA-seq

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


title: U2OS_RNAseq_siControl_rep2


title: P12_40d_Tef-KO_45, scRNA-seq


title: AlfpCre_Ezh2flfl_P0_Dlk_1_1


title: R3_DC_8HR_Apilimod

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

data_processing:
Reads were aligned with the Spliced Transcripts Alignment to a Reference (STAR) to the mouse reference genome.
Tables of read counts were then transformed into fragments per kilobase of transcript per million mapped reads using the Bioconductor edgeR package.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Primary dendritic cells

growth_protocol: Bone marrow cells collected from the femurs and tibias of mice.

extract_protocol:
Total RNA was extracted using the Qiagen miRNeasy mini kit with the inclusion of the genomic DNA digestion step with the RNase-free DNase Kit.
Depletion of rRNA using RiboErase selection kit from Kapa Biosystems was performed. RNA libraries were then generated using the KAPA RNA HyperPrep Kit from Roche according to manufacturer's protocols.

treatment_protocol: Dendritic cells were generated from bone marrow cells cultured with Flt3L in IMDM supplemented with 10% FBS and collected on Day 9.

value: Primary dendritic cells

value: Cultured dendritic cells

value: WT

value: 8 hours of treatment with Apilimod on culture Day 6


title: P0_11, scRNA-seq

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


title: P12_40d_Tef-KO_47, scRNA-seq

value: Tef-KO


title: P0_9, scRNA-seq

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


title: U2OS_RNAseq_siControl_rep1


title: Black Hepatocytes, 4C

city: Gainesville

first: Danxin

last: Wang

state: FL

address: 1345 Center Drive MSB PG-05B

department: Pharmacotherapy and Translational Research

institute: University of Florida

library_source: genomic

data_processing:
The paired-end reads were Illumina chastity-filtered and contain phred+33 scores. We used the pipeline in Krijger et. al (2020) (PMID: 31351925) to demultiplex the fastq files, trim adapter sequences, map the reads to GrCH38.p13 (without alt contigs) (PMID: 28396521), and calculate read counts per restriction ends. Both the raw fastq and wig files for each viewpoint are provided here.
Assembly: GrCH38.p13 (without alt contigs)
Supplementary files format and content: wig
Library strategy: 4C-Seq

molecule: genomic DNA

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 10,000,000 cells were plated into a single well of a 6-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.

extract_protocol:
Generation of the 4C templates followed the protocol outlined by Krijger et. al (2020) (PMID: 31351925) with modifications noted here. Cells were crosslinked using formaldehyde and chromatin was purified as follows. During cell lysis, the post-crosslinked cell pellet was resuspended in 1 mL cold lysis buffer and then transferred to a 1 mL Dounce homogenizer (Active Motif, Carlsbad, CA, USA) kept on ice. Lysis was facilitated by ten strokes with the loose pestle followed by strokes with the tight pestle. Cell nuclei were digested with primary restriction enzymes (RE), followed by proximal ligation after being diluted following the protocol. We then used phenol:chloroform extraction to purify the DNA, instead of beads. After secondary RE digestion and ligation we purified the 4C templates with the QIAquick PCR purification kit (Qiagen, Germantown, MD, USA). After the first round of PCR, samples were purified using High Pure PCR Product Purification (Roche, Madison, WI, USA). Two technical replicates were generated for both the black and white samples.
The resulting 4C libraries were size-selected to remove all sequences shorter than 150 bp and sequenced on an Illumina NovaSeq 6000 (Illumina, San Diego, CA, USA) at the University of Florida Interdisciplinary Center for Biotechnology Research (ICBR).
4C-Seq

value: Primary Hepatocytes

tag: donor group

value: Black donors


title: P12_40d_Tef-KO_44, scRNA-seq

value: liver


title: R1_DC_8HR_Apilimod


title: P12_40d_Tef-KO_42, scRNA-seq


title: Trabecular OVX+ERT 3

city: Rochester

first: Michael

middle: Justin

last: Emch

state: Minnesota

address: 200 1st Street SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

data_processing:
miRNA-seq analysis follows the CAP-miRseq pipeline (PMID: 24894665) Fastq file quality was assessed with FastQC (0.10.1 or higher) and reads were trimmed with Cutadapt as necessary. Alignment to mm10 was performed with miRDeep2 (2.0.0.5)  and Bowtie (0.12.7) for novel miR detection and total/variant detection, respectively. miRs are then compared to and identified using miRBase.
Assembly: mm10
Supplementary files format and content: .xlsx table of mature miR expression in counts following CAP-miRseq pipeline delineated by treatment type.
Supplementary files format and content: .xlsx table of mature miR expression in counts following CAP-miRseq pipeline

source_name: Femur

growth_protocol: Animals were housed in the Mayo Clinic Animal Facility in a temperature controlled (22 ± 2°C)  environment with a standard 12 hour light dark cycle. They had standard laboratory chow and unrestricted access to water

extract_protocol:
Muscle and connective tissue were removed from the femurs, followed by removal of the epiphyses. Marrow was removed by centrifugation. Trabecular bone was isolated using a 1mm biopsy punch and then submerged in trizol. Cortical bone was trimmed and each end and the mid diaphysis was placed in a separate trizol containing microcentrifuge tube. Bone tissues were then homogenized using an ULTRA-TURRAX homogenizer and RNA was was extracted using the Qiagen miRNeasy kit. Prior to sequencing, equal amounts of cortical or trabecular RNA from two individual mice were pooled to generate 3 replicate samples for each bone compartment and treatment group.
NEBNext Multiplex Small RNA Library Prep Kit

treatment_protocol: 18 8-week old C57BL/6 mice were randomized to sham+placebo, OVX+placebo, or OVX+ERT treatment groups. Sham and OVX surgeries were performed, and immediately following surgery a 1.88μg 17β-estradiol 30-day slow release pellet or placebo was implanted subcutaneously. 30 days post surgery the mice were sacrificed and the femurs were collected.

value: Femur

tag: tissue type

value: Trabecular

value: OVX+ERT


title: White Hepatocytes, 4C

value: White donors


title: R2_DC_8HR_Apilimod


title: P12_40d_Tef-KO_40, scRNA-seq

value: hepatocyte


title: P0_7, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: R3_DC_8HR_DMSO

value: 8 hours of treatment with DMSO on culture Day 6


title: Trabecular OVX+ERT 2


title: P0_6, scRNA-seq

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


title: P12_40d_Tef-KO_46, scRNA-seq


title: P12_40d_Tef-KO_41, scRNA-seq


title: R2_DC_8HR_DMSO


title: R1_DC_8HR_DMSO


title: P0_10, scRNA-seq

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


title: P12_40d_Tef-KO_43, scRNA-seq


title: R3_DC_3HR_Apilimod

value: 3 hours of treatment with Apilimod on culture Day 6


title: Trabecular OVX+ERT 1


title: P0_5, scRNA-seq

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


title: Trabecular OVX 3

value: OVX


title: P0_4, scRNA-seq

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


title: P0_8, scRNA-seq

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


title: P12_40d_Tef-KO_37, scRNA-seq


title: P12_40d_Tef-KO_38, scRNA-seq


title: R2_DC_3HR_Apilimod

value: Primary dendritic cells


title: P12_40d_Tef-KO_36, scRNA-seq


title: P0_2, scRNA-seq

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


title: Trabecular OVX 1


title: R3_DC_3HR_DMSO

value: Cultured dendritic cells

value: 3 hours of treatment with DMSO on culture Day 6


title: R1_DC_3HR_Apilimod

value: WT


title: Trabecular OVX 2


title: P12_40d_Tef-KO_33, scRNA-seq

value: Tef-KO


title: P12_40d_Tef-KO_35, scRNA-seq


title: R1_DC_3HR_DMSO


title: P0_3, scRNA-seq

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


title: E19.5_172, scRNA-seq

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


title: Trabecular Sham 1

value: Sham


title: R2_DC_3HR_DMSO


title: P12_40d_Tef-KO_39, scRNA-seq


title: Trabecular Sham 2


title: P12_40d_Tef-KO_34, scRNA-seq


title: Trabecular Sham 3


title: P12_40d_Tef-KO_32, scRNA-seq


title: E19.5_171, scRNA-seq

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


title: P12_40d_Tef-KO_31, scRNA-seq


title: E19.5_170, scRNA-seq

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


title: Cortical OVX+ERT 3

value: Cortical


title: Cortical OVX+ERT 2


title: P12_40d_Tef-KO_30, scRNA-seq

value: liver


title: P0_1, scRNA-seq

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


title: Cortical OVX+ERT 1

value: Femur


title: E19.5_169, scRNA-seq

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


title: E19.5_168, scRNA-seq

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


title: R2 DC Day9 Pikfyvef/f

value: Conventional dendritic cells


title: R3 DC Day9 Pikfyvef/f


title: R2 DC Day9 CD11cCre Pikfyvef/f

value: KO


title: R3 DC Day9 CD11cCre Pikfyvef/f


title: Cortical OVX 3


title: E19.5_167, scRNA-seq

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


title: R1 DC Day9 CD11cCre Pikfyvef/f


title: E19.5_166, scRNA-seq

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


title: R1 DC Day9 Pikfyvef/f


title: P12_40d_Tef-KO_27, scRNA-seq


title: P12_40d_Tef-KO_26, scRNA-seq


title: E19.5_165, scRNA-seq

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


title: Cortical OVX 1


title: Cortical OVX 2


title: P12_40d_Tef-KO_25, scRNA-seq


title: E19.5_164, scRNA-seq

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


title: E19.5_163, scRNA-seq

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


title: Cortical Sham 2


title: Small intestine ILC3, pellet of meRIP, rep1

city: New York

first: Yuefeng

last: Huang

address: 701 West 168th Street

department: Microbiology & Immunology

institute: Columbia University

data_processing:
Adapter sequences were trimmed using Cutadapt (v3.3) with default parameters. Reads were mapped to mouse transcriptome (genome build: GRCm38/mm10; gene annotation: Gencode m25) using STAR aligner (v2.7.9a) with parameter “--quantMode GeneCounts” to get the read counts of each gene. We filtered out low-count genes whose read count is less than 10 in more than half of samples and identified the differential genes by comparing the unbound and pellet fractions using DEseq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files of STAR read counts for each Sample

extract_protocol:
RNA was harvested from the IL-1 plus IL-23-induced ILC3 in small intestine using miRNeasy Micro Kit (Qiagen). Then m6A immunoprecipitation (meRIP) was performed to obtain the unbound and pellet fractions. RNA of unbound and pellet fractions were used for the construction of sequencing libraries.
cDNA libraries for RNA-seq were prepared using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: C57BL/6 mice were intraperitonially injected with recombinant mouse IL-1 plus IL-23 cytokine every day for three days. Then activated ILC3 were sorted from the small intestine on Day4.

value: Small intestine

value: IL-1 plus IL-23 intraperitonially (i.p.) injection

tag: time

value: Day 4


title: Small intestine ILC3, unbound fraction of meRIP, rep2

tag: tissue


title: Cortical Sham 3


title: P12_40d_Tef-KO_24, scRNA-seq

tag: cell type

value: hepatocyte


title: Small intestine ILC3, pellet of meRIP, rep2

tag: genotype


title: P12_40d_Tef-KO_23, scRNA-seq

tag: age


title: E19.5_162, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato

tag: ploidy


title: Cortical Sham 1

tag: treatment


title: P12_40d_Tef-KO_28, scRNA-seq

tag: zonation


title: P12_40d_Tef-KO_22, scRNA-seq


title: Small intestine ILC3, unbound fraction of meRIP, rep1

source_name: Small intestine ILC3, unbound fraction of methylated RNA immunoprecipitation (meRIP), rep1


title: P12_40d_Tef-KO_29, scRNA-seq


title: E19.5_161, scRNA-seq

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


title: P12_40d_Tef-KO_21, scRNA-seq


title: Small intestine ILC2 of Melttl3 Klrg1Cre mice, pellet of meRIP, rep2

data_processing:
Adapter sequences were trimmed using Cutadapt (v3.3) with default parameters. Reads were mapped to mouse transcriptome (genome build: GRCm38/mm10; gene annotation: Gencode m25) using STAR aligner (v2.7.9a) with parameter “--quantMode GeneCounts” to get the read counts of each gene. We filtered out low-count genes whose read count is less than 10 in more than half of samples and identified the differential genes by comparing the unbound and pellet fractions using DEseq2. For library size estimation, the size factor (N_i*r)/(10^6*R_i) was used, where N_i was the total number of mapped reads of sample i; R_i was the cDNA concentration of sample i; r was the average cDNA concentration of all samples
Assembly: mm10
Supplementary files format and content: tab-delimited text files of STAR read counts for each Sample

source_name: Small intestine

extract_protocol:
RNA was harvested from small intestine ILC2 of WT and Melttl3 Klrg1Cre mice using miRNeasy Micro Kit (Qiagen). Then m6A immunoprecipitation (meRIP) was performed to obtain the pellet fractions, which were used for the construction of sequencing libraries.
cDNA libraries for RNA-seq were prepared using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: ILC2 were sorted from small intestine of WT and Melttl3 Klrg1Cre mice

value: Mettl3 fl/fl; Klrg1-cre +/-

value: No

tag: cdna concentration


title: E19.5_160, scRNA-seq

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


title: male, 1mM, 8h, replicate 2

city: Bloomington

first: Jason

middle: M

last: Tennessen

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

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University

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

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

organism: Drosophila melanogaster

source_name: whole animal

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

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

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

value: whole animal

value: OregonR

tag: Sex

value: male

value: 1mM arsenite

tag: replicate


title: male, 1mM, 8h, replicate 3


title: Small intestine ILC2 of Melttl3 Klrg1Cre mice, pellet of meRIP, rep1


title: E19.5_159, scRNA-seq

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

source_name: liver


title: Small intestine ILC2 of WT mice, pellet of meRIP, rep2

value: Mettl3 fl/fl


title: E19.5_158, scRNA-seq

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


title: P12_40d_Tef-KO_19, scRNA-seq

value: Tef-KO


title: male, 1mM, 4h, replicate 3


title: P12_40d_Tef-KO_20, scRNA-seq

value: liver


title: male, 1mM, 8h, replicate 1


title: Small intestine ILC2 of WT mice, pellet of meRIP, rep1

description: Small intestine ILC2 of WT mice, pellet of methylated RNA immunoprecipitation (meRIP), rep1


title: P12_40d_Tef-KO_18, scRNA-seq


title: Liver ILC1, pellet of meRIP, rep2

data_processing:
Adapter sequences were trimmed using Cutadapt (v3.3) with default parameters. Reads were mapped to mouse transcriptome (genome build: GRCm38/mm10; gene annotation: Gencode m25) using STAR aligner (v2.7.9a) with parameter “--quantMode GeneCounts” to get the read counts of each gene. We filtered out low-count genes whose read count is less than 10 in more than half of samples and identified the differential genes by comparing the unbound and pellet fractions using DEseq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files of STRA read counts for each Sample

source_name: Liver ILC1, pellet of meRIP, rep2

extract_protocol:
RNA was harvested from the IL-12 plus IL-18-induced ILC1 in liver using miRNeasy Micro Kit (Qiagen). Then m6A immunoprecipitation (meRIP) was performed to obtain the unbound and pellet fractions. RNA of unbound and pellet fractions were used for the construction of sequencing libraries.
cDNA libraries for RNA-seq were prepared using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: C57BL/6 mice were intraperitonially injected with recombinant mouse IL-12 plus IL-18 cytokine every day for three days. Then activated ILC1 were sorted from the liver on Day4.

value: Liver

value: WT

value: IL-12 plus IL-18 intraperitonially (i.p.) injection


title: male, 1mM, 4h, replicate 2


title: male, 1mM, 2h, replicate 3


title: E19.5_156, scRNA-seq

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


title: male, 1mM, 4h, replicate 1


title: E19.5_155, scRNA-seq

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


title: E19.5_157, scRNA-seq

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


title: P12_40d_Tef-KO_16, scRNA-seq


title: P12_40d_Tef-KO_17, scRNA-seq


title: Liver ILC1, unbound fraction of meRIP, rep2


title: Liver ILC1, pellet of meRIP, rep1

source_name: Liver ILC1, pellet of meRIP, rep1


title: male, 1mM, 2h, replicate 2


title: P12_40d_Tef-KO_15, scRNA-seq


title: male, 1mM, 2h, replicate 1


title: male, 1mM, 1h, replicate 3


title: P12_40d_Tef-KO_14, scRNA-seq


title: P12_40d_Tef-KO_13, scRNA-seq


title: male, 1mM, 1h, replicate 2


title: mouse_ESC_Cas9_Blast_EGFP-unc-54_3_UTR_WelteFMI_12K_mCRISPR_g003_PF66-59NB_FACS_GFP_high_low_positive_8d

city: Basel

first: Helge

last: Grosshans

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedriche Miescher Institute for Biomedical Research (FMI)

data_processing:
Data processing as described in Hoepfner et al., 2019 (https://link.springer.com/protocol/10.1007/978-1-4939-8891-4_9)
Base calling and quality scoring is performed using RTA software (v3.4.4), demultiplexing with  bcl2fastq2 v2.20.
SgRNA counts were generated by aligning raw sequences to the reference libraries using Bowtie (Langmead et al., 2009), allowing for no mismatches.
Assembly: NA
Supplementary files format and content: Comma separated files with sgRNA sequence raw read counts for each sgRNA.

source_name: mouse ESCs

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:
DNA extracted by Phenol/Chloroform extraction.
Library preparation done as specified in Hoepfner et al., 2019 (https://link.springer.com/protocol/10.1007/978-1-4939-8891-4_9)
DNA-seq

treatment_protocol: Screen1: Genome-wide screen: Cells were transduced with two separate lentiviral sgRNA libraries (library 1: 52,000 unique sgRNAs (~5 per gene); library 2: 39,000 unique sgRNAs (~5 per gene); (Zeng et al., 2018). Cells were transduced at a multiplicity of infection (MOI) of 0.31 using 10 µg/ml polybrene at 700x coverage/sgRNA. Screen2: validation screen: Cells were transduced at an MOI of 0.1 using 10 µg/ml polybrene with a 500x coverage/sgRNA.

value: mouse ESCs

value: mouse ESC Cas9_Blast_EGFP-ctrl 3'UTR

value: day 8


title: mouse_ESC_Cas9_Blast_EGFP-unc-54-mab-10condensed_3_UTR_WelteFMI_12K_mCRISPR_g003_PF66-59NB_FACS_GFP_high_low_negative_8d

value: mouse ESC Cas9_Blast_EGFP-5xT71BS 3'UTR


title: E19.5_150, 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

value: Alb-Cre; Rosa-tdTomato


title: male, 1mM, 1h, replicate 1


title: P12_40d_Tef-KO_12, scRNA-seq


title: E19.5_151, scRNA-seq

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


title: mouse_ESC_Cas9_Blast_EGFP-unc-54_3_UTR_WelteFMI_12K_mCRISPR_g003_PF66-59NB_FACS_GFP_high_low_negative_8d


title: P12_40d_Tef-KO_11, scRNA-seq


title: male, 0mM (ctrl), 8h, replicate 3

value: 0mM (ctrl)


title: Cellecta_mCRISPR_v1_POOL2_EE-93-GP68_plasmid_pool

description: unsorted

value: PLASMID

value: Cellecta mCRISPR v1 POOL2


title: P12_40d_Tef-KO_9, scRNA-seq


title: E19.5_149, scRNA-seq

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


title: P12_40d_Tef-KO_8, scRNA-seq


title: E19.5_153, scRNA-seq

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


title: E19.5_147, scRNA-seq

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


title: male, 0mM (ctrl), 8h, replicate 1

value: whole animal

value: OregonR

value: male


title: male, 0mM (ctrl), 8h, replicate 2


title: Cellecta_mCRISPR_v1_POOL1_YC-86-OH04_plasmid_pool

description: unsorted

value: Cellecta mCRISPR v1 POOL1


title: male, 0mM (ctrl), 4h, replicate 3


title: E19.5_154, scRNA-seq

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

value: liver


title: E19.5_146, scRNA-seq

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


title: P12_40d_Tef-KO_7, scRNA-seq

value: Tef-KO


title: Cellecta_mCRISPR_v1_POOL1_DF38-64KB_mouse_ESC_Cas9_Blast_EGFP-unc-54_3_UTR_FACS_GFP_high_low_unsorted_8d

description: unsorted


title: P12_40d_Tef-KO_6, scRNA-seq


title: Cellecta_mCRISPR_v1_POOL2_TF39-69EB_mouse_ESC_Cas9_Blast_EGFP-unc-54_3_UTR_FACS_GFP_high_low_positive_8d


title: male, 0mM (ctrl), 4h, replicate 2


title: male, 0mM (ctrl), 4h, replicate 1


title: P12_40d_Tef-KO_5, scRNA-seq


title: Cellecta_mCRISPR_v1_POOL1_DF38-64KB_mouse_ESC_Cas9_Blast_EGFP-unc-54_3_UTR_FACS_GFP_high_low_positive_8d


title: E19.5_144, scRNA-seq

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


title: E19.5_145, scRNA-seq

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


title: P12_40d_Tef-KO_10, scRNA-seq


title: mouse_ESC_Cas9_Blast_EGFP-unc-54-mab-10condensed_3_UTR_WelteFMI_12K_mCRISPR_g003_PF66-59NB_FACS_GFP_high_low_positive_8d


title: E19.5_148, scRNA-seq

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


title: male, 0mM (ctrl), 2h, replicate 3


title: E19.5_143, scRNA-seq

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


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


title: P12_40d_Tef-KO_4, scRNA-seq


title: Cellecta_mCRISPR_v1_POOL2_TF39-69EB_mouse_ESC_Cas9_Blast_EGFP-unc-54-mab-10condensed_3_UTR_FACS_GFP_high_low_unsorted_4d

description: unsorted

value: day 4


title: E19.5_142, scRNA-seq

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


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


title: E19.5_141, scRNA-seq

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


title: male, 0mM (ctrl), 1h, replicate 3


title: E19.5_140, scRNA-seq

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


title: P12_40d_Tef-KO_2, scRNA-seq


title: Cellecta_mCRISPR_v1_POOL2_TF39-69EB_mouse_ESC_Cas9_Blast_EGFP-unc-54-mab-10condensed_3_UTR_FACS_GFP_high_low_unsorted_8d

description: unsorted


title: P12_40d_Tef-KO_3, scRNA-seq


title: Cellecta_mCRISPR_v1_POOL1_DF38-64KB_mouse_ESC_Cas9_Blast_EGFP-unc-54_3_UTR_FACS_GFP_high_low_negative_8d


title: P12_40d_Tef-KO_1, scRNA-seq


title: E19.5_139, scRNA-seq

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


title: Cellecta_mCRISPR_v1_POOL1_DF38-64KB_mouse_ESC_Cas9_Blast_EGFP-unc-54-mab-10condensed_3_UTR_FACS_GFP_high_low_unsorted_4d

description: unsorted


title: P12_40d_Nr2f2-KO_165, scRNA-seq


title: Cellecta_mCRISPR_v1_POOL2_TF39-69EB_mouse_ESC_Cas9_Blast_EGFP-unc-54-mab-10condensed_3_UTR_FACS_GFP_high_low_positive_8d


title: E19.5_138, scRNA-seq

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


title: E19.5_137, scRNA-seq

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


title: P12_40d_Nr2f2-KO_164, scRNA-seq


title: P12_40d_Nr2f2-KO_163, scRNA-seq


title: Cellecta_mCRISPR_v1_POOL2_TF39-69EB_mouse_ESC_Cas9_Blast_EGFP-unc-54_3_UTR_FACS_GFP_high_low_negative_8d


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

value: 0h (ctrl)


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


title: Cellecta_mCRISPR_v1_POOL1_DF38-64KB_mouse_ESC_Cas9_Blast_EGFP-unc-54-mab-10condensed_3_UTR_FACS_GFP_high_low_unsorted_8d

description: unsorted

value: mouse ESCs


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


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


title: E19.5_136, scRNA-seq

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


title: Cellecta_mCRISPR_v1_POOL2_TF39-69EB_mouse_ESC_Cas9_Blast_EGFP-unc-54-mab-10condensed_3_UTR_FACS_GFP_high_low_negative_8d


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


title: E19.5_135, scRNA-seq

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


title: P12_40d_Nr2f2-KO_161, scRNA-seq


title: Cellecta_mCRISPR_v1_POOL1_DF38-64KB_mouse_ESC_Cas9_Blast_EGFP-unc-54-mab-10condensed_3_UTR_FACS_GFP_high_low_positive_8d


title: Cellecta_mCRISPR_v1_POOL1_DF38-64KB_mouse_ESC_Cas9_Blast_EGFP-unc-54-mab-10condensed_3_UTR_FACS_GFP_high_low_negative_8d


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

value: 0.25mM arsenite


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


title: P12_40d_Nr2f2-KO_160, scRNA-seq


title: validation_screen_plasmid_pool

description: unsorted


title: Liver ILC1, unbound fraction of meRIP, rep1

source_name: Liver ILC1, unbound fraction of methylated RNA immunoprecipitation (meRIP), rep1

value: Liver

value: WT

value: IL-12 plus IL-18 intraperitonially (i.p.) injection

value: Day 4


title: P12_40d_Nr2f2-KO_159, scRNA-seq

value: hepatocyte


title: E19.5_133, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: Cellecta_mCRISPR_v1_POOL1_DF38-64KB_mouse_ESC_Cas9_Blast_EGFP-unc-54_3_UTR_FACS_GFP_high_low_unsorted_4d

description: unsorted

value: mouse ESC Cas9_Blast_EGFP-ctrl 3'UTR


title: P12_40d_Nr2f2-KO_157, scRNA-seq


title: E19.5_131, scRNA-seq

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


title: P12_40d_Nr2f2-KO_162, scRNA-seq


title: male, 0.25mM, 4h, replicate 4

value: whole animal


title: Cellecta_mCRISPR_v1_POOL2_TF39-69EB_mouse_ESC_Cas9_Blast_EGFP-unc-54_3_UTR_FACS_GFP_high_low_unsorted_8d

description: unsorted

value: Cellecta mCRISPR v1 POOL2

value: day 8


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

value: OregonR

value: male


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


title: E19.5_129, scRNA-seq

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

value: liver


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


title: MLN iILC2, pellet of meRIP, rep2

data_processing:
Adapter sequences were trimmed using Cutadapt (v3.3) with default parameters. Reads were mapped to mouse transcriptome (genome build: GRCm38/mm10; gene annotation: Gencode m25) using STAR aligner (v2.7.9a) with parameter “--quantMode GeneCounts” to get the read counts of each gene. We filtered out low-count genes whose read count is less than 10 in more than half of samples and identified the differentially methylated genes by comparing the supernatant and pellet read counts using DEseq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include DESeq2 normalized read counts for each Sample

source_name: Mesenteric lymph node (MLN)

extract_protocol:
RNA was harvested from the IL-25-induced iILC2 in MLN using miRNeasy Micro Kit (Qiagen). Then m6A immunoprecipitation (meRIP) was performed to obtain the input, unbound and pellet fractions. 30 ng of RNA of input, unbound or pellet fractions was used for the construction of sequencing libraries.
cDNA libraries for RNA-seq were prepared using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: C57BL/6 mice were intraperitonially injected with recombinant mouse IL-25 cytokine every day for three days. Then 200,000 IL-25-induced iILC2 were sorted from the MLN.

value: Mesenteric lymph node (MLN)

value: C57BL/6 WT

value: IL-25 intraperitonially (i.p.) injection


title: E19.5_128, scRNA-seq

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


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

value: 0.25mM arsenite


title: MLN iILC2, pellet of meRIP, rep1


title: P12_40d_Nr2f2-KO_154, scRNA-seq


title: Cellecta_mCRISPR_v1_POOL2_TF39-69EB_mouse_ESC_Cas9_Blast_EGFP-unc-54_3_UTR_FACS_GFP_high_low_unsorted_4d

description: unsorted

value: mouse ESCs

value: day 4


title: P12_40d_Nr2f2-KO_153, scRNA-seq


title: MLN iILC2, unbound fraction of meRIP, rep3


title: E19.5_127, scRNA-seq

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


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


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


title: E19.5_126, scRNA-seq

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


title: P12_40d_Nr2f2-KO_158, scRNA-seq


title: E19.5_132, scRNA-seq

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


title: E19.5_130, scRNA-seq

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


title: P12_40d_Nr2f2-KO_156, scRNA-seq


title: MLN iILC2, unbound fraction of meRIP, rep2


title: E19.5_125, scRNA-seq

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


title: MLN iILC2, pellet of meRIP, rep3


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


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


title: MLN iILC2, unbound fraction of meRIP, rep1


title: P12_40d_Nr2f2-KO_152, scRNA-seq


title: P12_40d_Nr2f2-KO_151, scRNA-seq


title: P12_40d_Nr2f2-KO_155, scRNA-seq


title: E19.5_124, scRNA-seq

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


title: MLN iILC2, input of meRIP, rep3


title: E19.5_123, scRNA-seq

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


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


title: P12_40d_Nr2f2-KO_149, scRNA-seq


title: MLN iILC2, input of meRIP, rep2


title: female, 1mM, 8h, replicate 3

value: female

value: 1mM arsenite


title: E19.5_122, scRNA-seq

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

value: hepatocyte


title: MLN iILC2, input of meRIP, rep1

value: Day 4


title: E19.5_121, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: Ago2KO_2

description: Experiment 2

data_processing:
Base calling and quality scoring is performed using RTA software (v1.18.64), demultiplexing with bcl2fastq2 v2.17.
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 7-27 contain raw counts of reads overlapping each gene for each sample, columns 28-48 contain rpkm read counts overlapping each gene for each sample.

source_name: mouse embryonic stem cells

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)

value: mouse embryonic stem cells

value: GFP_5xT71BS, Ago2-/-, transfection with empty plasmid


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

value: whole animal


title: Ago2KO_3

description: Experiment 2


title: P12_40d_Nr2f2-KO_148, scRNA-seq


title: P12_40d_Nr2f2-KO_147, scRNA-seq


title: P12_40d_Nr2f2-KO_146, scRNA-seq


title: P12_40d_Nr2f2-KO_145, scRNA-seq


title: E19.5_119, scRNA-seq

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


title: E19.5_120, scRNA-seq

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


title: P12_40d_Nr2f2-KO_150, scRNA-seq


title: E19.5_118, scRNA-seq

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


title: female, 1mM, 4h, replicate 3

value: OregonR


title: E19.5_117, scRNA-seq

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


title: Ago2KO_1

description: Experiment 2


title: P12_40d_Nr2f2-KO_144, scRNA-seq


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


title: female, 1mM, 4h, replicate 2


title: P12_40d_Nr2f2-KO_143, scRNA-seq


title: Trim71KO_2

description: Experiment 2

value: GFP_5xT71BS, Trim71-/-, transfection with empty plasmid


title: female, 1mM, 48h, replicate 4


title: female, 1mM, 8h, replicate 2


title: Trim71KO_1

description: Experiment 2


title: female, 1mM, 48h, replicate 3


title: P12_40d_Nr2f2-KO_141, scRNA-seq

value: liver


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


title: T6B_Mut_3

description: Experiment 2

value: GFP_5xT71BS, transfection with pCIP FH-T6B_MUT::mCherry


title: female, 1mM, 2h, replicate 3


title: Trim71KO_3

description: Experiment 2


title: P12_40d_Nr2f2-KO_140, scRNA-seq


title: E19.5_112, scRNA-seq

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


title: T6B_Mut_1

description: Experiment 2


title: T6B_Mut_2

description: Experiment 2


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


title: E19.5_113, scRNA-seq

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


title: P12_40d_Nr2f2-KO_138, scRNA-seq


title: P12_40d_Nr2f2-KO_139, scRNA-seq


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


title: P12_40d_Nr2f2-KO_137, scRNA-seq


title: E19.5_111, scRNA-seq

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


title: female, 1mM, 24h, replicate 3


title: E19.5_110, scRNA-seq

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


title: P12_40d_Nr2f2-KO_136, scRNA-seq


title: E19.5_152, scRNA-seq

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


title: E19.5_115, scRNA-seq

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


title: P12_40d_Nr2f2-KO_142, scRNA-seq


title: T6B_Wt_2

description: Experiment 2

value: GFP_5xT71BS, transfection with pCIP FH-T6B_WT::mCherry


title: E19.5_114, scRNA-seq

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


title: female, 1mM, 24h, replicate 2


title: E19.5_116, scRNA-seq

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


title: T6B_Wt_3

description: Experiment 2


title: Ago2KO3

description: Experiment 1

value: GFP_5xT71BS, Ago2-/-


title: T6B_Wt_1

description: Experiment 2


title: E19.5_109, scRNA-seq

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


title: E19.5_108, scRNA-seq

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


title: P12_40d_Nr2f2-KO_134, scRNA-seq


title: E19.5_107, scRNA-seq

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


title: P12_40d_Nr2f2-KO_135, scRNA-seq


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


title: Ago2KO1

description: Experiment 1


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


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


title: E19.5_106, scRNA-seq

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


title: E19.5_134, scRNA-seq

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


title: Trim71KO3

description: Experiment 1

value: GFP_5xT71BS, Trim71-/-


title: P12_40d_Nr2f2-KO_132, scRNA-seq


title: Ago2KO2

description: Experiment 1


title: E19.5_105, scRNA-seq

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


title: E19.5_104, scRNA-seq

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


title: female, 0mM (ctrl), 8h, replicate 3

value: 0mM (ctrl)


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


title: P12_40d_Nr2f2-KO_130, scRNA-seq


title: P12_40d_Nr2f2-KO_131, scRNA-seq


title: P12_40d_Nr2f2-KO_129, scRNA-seq


title: Trim71KO2

description: Experiment 1


title: W3

description: Experiment 1

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


title: Trim71KO1

description: Experiment 1


title: E19.5_102, scRNA-seq

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


title: E19.5_103, scRNA-seq

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


title: female, 0mM (ctrl), 8h, replicate 1

value: female


title: P12_40d_Nr2f2-KO_128, scRNA-seq


title: P12_40d_Nr2f2-KO_133, scRNA-seq


title: female, 0mM (ctrl), 4h, replicate 3


title: W2

description: Experiment 1


title: female, 0mM (ctrl), 8h, replicate 2


title: E19.5_101, scRNA-seq

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


title: W1

description: Experiment 1


title: female, 0mM (ctrl), 4h, replicate 2


title: E19.5_100, scRNA-seq

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


title: P12_40d_Nr2f2-KO_127, scRNA-seq


title: P12_40d_Nr2f2-KO_126, scRNA-seq


title: TAM_pos_6

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

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

source_name: TAMs

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

value: TAMs

tag: gender

tag: group

tag: batch


title: E19.5_99, scRNA-seq

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

value: hepatocyte


title: female, 0mM (ctrl), 4h, replicate 1


title: TAM_neg_6


title: female, 0mM (ctrl), 48h, replicate 3


title: P12_40d_Nr2f2-KO_125, scRNA-seq


title: E19.5_98, scRNA-seq

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


title: P12_40d_Nr2f2-KO_124, scRNA-seq


title: female, 0mM (ctrl), 48h, replicate 2


title: TAM_neg_5


title: TAM_pos_5


title: TAM_pos_4

value: male


title: E19.5_97, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: P12_40d_Nr2f2-KO_122, scRNA-seq


title: E19.5_96, scRNA-seq

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


title: P12_40d_Nr2f2-KO_121, scRNA-seq


title: female, 0mM (ctrl), 2h, replicate 3


title: E19.5_95, scRNA-seq

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


title: TAM_neg_4


title: TAM_pos_3


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


title: E19.5_94, scRNA-seq

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


title: P12_40d_Nr2f2-KO_119, scRNA-seq


title: E19.5_93, scRNA-seq

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


title: TAM_pos_2


title: P12_40d_Nr2f2-KO_118, scRNA-seq


title: P12_40d_Nr2f2-KO_117, scRNA-seq


title: female, 0mM (ctrl), 48h, replicate 1


title: female, 0mM (ctrl), 24h, replicate 2


title: E19.5_92, scRNA-seq

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


title: TAM_neg_3


title: P12_40d_Nr2f2-KO_123, scRNA-seq


title: E19.5_91, scRNA-seq

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


title: TAM_neg_2


title: female, 0mM (ctrl), 24h, replicate 3


title: P12_40d_Nr2f2-KO_116, scRNA-seq


title: E19.5_90, scRNA-seq

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


title: female, 0mM (ctrl), 24h, replicate 1


title: female, 0mM (ctrl), 1h, replicate 3


title: P12_40d_Nr2f2-KO_120, scRNA-seq


title: E19.5_89, scRNA-seq

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


title: P12_40d_Nr2f2-KO_115, scRNA-seq


title: TAM_neg_1


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


title: E19.5_88, scRNA-seq

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


title: P12_40d_Nr2f2-KO_114, scRNA-seq