title: L1_D6_H3K27ac

status: Public on Jul 20 2025

city: Akita

first: Yoshihiro

last: Matsumura

state: Akita

address: Hondo 1-1-1

department: Biochemistry and Metabolic Science

institute: Akita University Graduate School of Medicine

data_processing:
RNA-seq reads were aligned to the mouse mm9 genome using STAR2.
The FPKM tables of RNA-seq were assessed using GFOLD with the GENCODE comprehensive gene annotation set M1 release.
As for ChIP-seq, all bound DNA fragments were mapped UCSC build mm9 assembly of the mouse genome by the mapping program Bowtie2 based on the 5'-side 36-bp sequences.
Signals of ChIP-seq occupancy are presented as counts per million mapped reads (CPM) by using deepTools bamCoverage.
SICER2 program was used for H3K27ac and H3K27me3 under the following parameters: window size 200 bp; gap size 400 bp ; E-value threshold, 100. The FindPeaks function of HOMER was used for H3K9me2 and JMJD1A with histone mode. MACS3 program was used for NFIC with default setting.
Assembly: mm9
Supplementary files format and content: tab files (RNA-seq)
Supplementary files format and content: bigwig and txt files (ChIP-seq)

growth_protocol: 3T3-L1 preadipocytes were maintained in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum at 37 °C. Immortalized stromal vascular fraction (imSVF) cells were maintained in Dulbecco's modified Eagle's medium/F12 supplemented with 10% fetal bovine serum at 37 °C. For adipocyte differentiation, two days after reaching confluence (day 0), 3T3-L1 preadipocytes were treated with differentiation medium containing insulin (1 g/ml), 0.25 M dexamethasone, and 0.5 mM isobutylmethylxanthine (MDI cocktail).

extract_protocol:
Total RNA was isolated using ISOGEN (Nippongene) following manufacturer's protocol. Sonicated nuclear fraction was incubated with each antibody and protein-DNA complexes were isolated.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Duplexes of each small interfering RNA (siRNA) against Jmjd1a and control siRNA were transfected into cells using the Lipofectamine RNAi MAX reagent (Thrmo Fisher Scientific).

tag: time

value: Day 6

tag: chip antibody


title: L1_D0_H3K27ac

type: SRA

country: Japan

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell line

value: Day 0


title: Hep3B_shACADS_biol rep 3

city: Shanghai

first: Yibin

last: Che

state: shanghai

country: China

institute: shanghai jiaotong university

library_source: transcriptomic

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Assembly: hg18
Supplementary files format and content: tab-delimited text files include counts values for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: Hep3B cells were maintained in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum, 100 units/ml penicillin, and 100 μg/ml streptomycin (all reagents from HyClone Europe). Cells were grown in a humidified environment at 37°C and 5% CO2.

extract_protocol:
We extracted total RNA using Rneasy microkit Qiagen according to the manufacturer's instructions.The quality of all RNA samples was examined by the Agilent 2100 Bioanalyzer.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

treatment_protocol:
HCC cell line Hep3B was stably transfected with ACADS shRNA. Cells were consecutively grown for 1 week in selection medium containing 2 μg/mL puromycin (Wisent, Canada) to isolate stable clones. Cells were also mock-transfected, and stably transfected clones were isolated as controls. Cells were treated with 2.5mM sodium butyrate for 24h in sodium butyrate treatment group.
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

tag: cell type

value: hepatocellular carcinoma

tag: genotype

value: ACADS knockdown

tag: treatment


title: B6_PBS_02

status: Public on Jul 21 2025

type: RNA

city: Manchester

first: James

middle: Edward

last: Parkinson

state: Greater Manchester

address: Oxford Road

department: DIIIRM

country: United Kingdom

institute: University of Manchester

description: Whole lung RNA was extracted and run as per manufacturers instructions on the Nanostring Innate Immune Response Panel

hyb_protocol: 20µl of 5ng/µl total RNA was loaded onto the Nanostring innate immune panel as per manufacturers recommendations

scan_protocol: Extracted RNA were quantified using a Qubit™ RNA BR Assay Kit (Thermofisher) kit and subsequently diluted to 20 ng/μl in RNase-free water. Sample were run on a Nanostring nCounter® FLEX system using the Myeloid Innate Immunity v2 panel (XT-CSO-MMII2-12) as per manufacturer’s instructions.

data_processing: Raw data were loaded into nSolver version 4.0 using default settings and non-normalized counts extracted and subsequent analyses performed in R (version 4.2.0) using RStudio Version 2023.03.0 Build 386 – © 2009–2023 RStudio, Inc. Internal housekeeping as well as positive and negative control probes were used to ensure data integrity and set thresholds for minimum expression. Data were normalized using the edgeR package and differential expression calculated using the limma package with the function voomwithqualityscores().

source_name: Allergic mouse lung

extract_protocol: The post-caudal lung lobe was stored in RNAlater (Thermo) prior to homogenization in Trizol reagent (Thermo). RNA was prepared according to manufacturer’s instructions using phenol-chloroform extraction and stored at −70°C.

treatment_protocol: WT or Chil4 KD mice were treated intranasally with PBS or DRA allergens twice weekly for eight weeks.

tag: tissue

value: Whole Lung


title: Hep3B_shACADS_biol rep 2


title: liver, infected dead2

city: HONGKONG

first: JINGYAO

last: WANG

address: Hong Kong Kowloon Tat Chee Avenue

institute: CITYU

description: Library name: PL23_L1

data_processing:
The quality of raw libraries was assessed using FastQC v0.11.8 (Babraham Bioinformatics, UK).
Raw data were trimmed with Trimmomatic v0.39 to remove adaptors and low-quality bases (Q-value ≤ 20)
The filtered reads were aligned to the reference genome (GenBank assembly accession: GCA_016699485.1) using TopHat2 (version 2.1.1)
Differential gene expression analysis was performed using the edgeR package, with normalization conducted via the trimmed mean of M-values (TMM) method
Assembly: GCA_016699485.1
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

molecule: polyA RNA

organism: Gallus

source_name: liver

growth_protocol: Specific pathogen-free (SPF) embryonated chicken eggs were randomly assigned to either treatment or control groups and incubated at 37 °C with 65% relative humidity

extract_protocol:
Yolk sac and embryonic liver tissues were collected and immediately placed in 1 mL of TRIzol reagent (Invitrogen, CA, USA). Tissue homogenization was performed using the Precellys® Evolution Touch homogenizer (Bertin Technologies, France) with ceramic beads at 8000 rpm for two cycles of 30 seconds each, separated by a 15-second pause. RNA extraction was carried out using the phenol: chloroform: isoamyl alcohol method (25:24:1), followed by isopropanol precipitation.
Non-strand-specific cDNA libraries were constructed according to the manufacturer’s protocol for the NEBNext® Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, MA, USA).

treatment_protocol: On day 12 of incubation, twenty-four SPF eggs in the treatment group were inoculated with 100 µL of E. coli suspension containing approximately 5 × 10³ colony-forming units (CFU)/ml via the allantoic sac. In parallel, sixteen SPF eggs in the control group were injected with 100 µL of sterile PBS.

value: liver

tag: group

value: APEC infection


title: Hep3B_shACADS_biol rep 1


title: Hep3B_biol rep 1

value: WT

value: control


title: Hep3B_biol rep 3


title: Hep3B_sodium butyrate treatment_biol rep 2

value: sodium butyrate treatment


title: IP_MC38_TUM_ATAC-Seq_Rep_4

city: Neuherberg

first: Peter

last: Weber

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Zentrum München

description:
Library name: MUC6458_IP_MC38_TUM_9638
IP'ed nuclei from HEP-INTACT mice

data_processing:
Sequence tags from ATAC-seq libraries were aligned to the mm10 using the BWA aligner (version 0.7.5a-r405) (Li and Durbin, 2009).
Post-alignment processing of reads was performed with Samtools (0.1.19-44428cd) (Li et al., 2009) by removing duplicate reads and filtering for high quality reads using Samtools view using the following settings ”-b -h -f 1 -F 4 -F 8 -F 256 -F 2048 -q 30”. Furthermore, only reads with a fragment length<100bp was used corresponding to the reads located in nucleosome-free regions.
ATAC seq peaks were identified, annotated and tags in peaks were counted using HOMER (Heinz et al., 2010). Tag directories from conditions with technical duplicates were combined into one before further analyses. Peaks were called in each library with HOMER findPeaks using the following settings: ‘peaks’, ‘-fragLength 70’, ‘-style factor’, ‘-minDist 140’, ‘-size 70’.
For all peak files, overlapping peaks were merged and collected in one master peak file. Tags were then counted in a 200bp window around the peak centers for each individual library in the resulting master peak file.
Assembly: mm10
Supplementary files format and content: mergedPeaks_All_400ann.txt

source_name: hepatocyte nuclei

extract_protocol:
Approximately 25,000 bead-bound nuclei from INTACT reactions were transposed in a 50 μL volume of 1X TTBL buffer and 3.5 μL TTE Mix V50 (from TruePrep™ DNA Library Prep Kit V2 for Illumina, Vazyme TD501) for 30 minutes at 37°C. Fragmented genomic DNA was recovered using Buffer ERC coupled with MinElute spin column purification (Qiagen).
Transposed genomic DNA was amplified by 12 cycles of quantitative PCR. Amplified DNA was purified and size-selected on AMPure XP beads (Beckman A63881), analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 4000 platform.

tag: mouse strain

value: hepatocyte nuclei

value: CAG-Sun1/sfGFP, Albumin-Cre

tag: animal id

tag: replicate


title: B6_PBS_01


title: liver, negative control3

description: Library name: N10_L1

value: Negative control

value: PBS


title: IP_MC38_PBS_ATAC-Seq_Rep_4

description:
Library name: MUC6457_IP_MC38_PBS_9635
IP'ed nuclei from HEP-INTACT mice


title: IP_MC38_TUM_ATAC-Seq_Rep_3

description:
Library name: MUC6454_IP_MC38_TUM_9591
IP'ed nuclei from HEP-INTACT mice


title: WT_control RNAi rep2

city: kennesaw

first: Brandon

middle: Scott

last: Carpenter

state: GA

address: 370 Paulding Avenue, Room 119

department: Molecular and Cellular Biology

country: USA

institute: Kennesaw State University

description: Library name: Sample 2

data_processing:
Raw RNAseq reads were checked for quality using FastQC (Andrews 2010), filtered using Trimmomatic (Bolger et al. 2014)
Trimmed reads emapped to the C. elegans transcriptome (ce11, WBcel235) using HISAT2 (Kim et al., 2015b)
Read count by gene was obtained by FeatureCounts (Yang liao et al 2014)
Differentially expressed transcripts were determined using DESEQ2 (v.2.11.40.2) (Love et al 2014)
Assembly: ce11
Supplementary files format and content: FeatureCounts files are in tabular format and include Read count by gene
Supplementary files format and content: Processed files from DESEQ2 analysis are in tabular format and contain a list of differentially expressed genes compared to WT (N2 strain on control RNAi)

organism: Caenorhabditis elegans

source_name: whole animal L1 Larvae

growth_protocol: Animals were cultured with OP50 on 10-cm NGM agar plates at 20C.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) from 500-1000 starved L1 larvae born at 20°C overnight on unseeded NGM plates. Total RNA was sent to Georgia Genomics and Bioinformatics Core (University of Georgia, Athens, Georgia) for standard Poly-A RNA-seq services (Illumina Nextseq, 50bp paired-end reads)
Libraries were prepared by HAIB-GSL (for HiSeq).

treatment_protocol: Feeding experiments were performed on RNAi plates (NGM plates containing 100 ug/ml ampicillin, 0.4mM IPTG, and 12.5ug/ml tetracycline). F0 worms were placed on RNAi plates as L2 larvae and then moved to fresh RNAi plates 48hrs later where they were allowed to lay embryos for 2-4 hrs. F0 worms were then removed from plates and sacrificed or placed on unseeded RNAi plates overnight so that starved L1 progeny could be isolated for RNAseq experiments. F1 progeny were scored 72hrs after the synchronized lay for L1 larval arrest. For each RNAi experiment, pos-1 RNAi was used as a positive control. Each RNAi experiment reported here pos-1 RNAi resulted in >95% embryonic lethality, indicating that RNAi plates were optimal.

value: whole animal L1 Larvae


title: IP_NC26_PBS_ATAC-Seq_Rep_3

description:
Library name: MUC6451_IP_NC26_PBS_9034
IP'ed nuclei from HEP-INTACT mice

value: BALB/c


title: guidedNOMe-seq in ADNP PxVxL mutant mESC, replicate 2

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
Library name: ADNPpxvxl_gNOMe-seq_r2
MiSeq v3 600bp paired-end

data_processing:
Barcoded samples were pooled and sequenced on an Illumina MiSeq instrument.
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
umi_tools (version 1.0.1) were used to remove reads that contain identical UMIs, then reads were aligned using bisulfite aware mapping by Biscuit (v 0.3.16, opions: with the options -b 1 -f 0 -K NAGATCGGAAGAGCACACGTCTGAACTCCAGTCA -J NAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).Methylation call extraction was performed using nomeR get_data_matrix_from_bins. This matrix was converted to a single cell experiment object upon import into dinoR for further analysis.
Assembly: mm10
Supplementary files format and content: The processed data file contains methylation call matrices from nomeR saved as .rds files (R Data Serialization). Sample replicates have been averaged and the .rds file can be imported to dinoR for visulaization and analysis. The matix also contains ADNP wt and ko data from GSE249661 used for analysis.

growth_protocol: Mouse embryonic stem cells were grown under standard conditions in medium containing serum, LIF and 2i.

extract_protocol:
0.8*10e6 cells were harvested at the indicated time-points, washed and nuclei were treated with M.CviPI for methylation foot-printing. Then cells were lysed and DNA was isolated. 120ng DNA was dephosphorylated with rSAP and digested by Cas9 loaded with an in vitro transcribed guideRNA pool for the regions of interest. The digested DNA was used to generate an NGS library. For a detailed protocol, please see Schwaiger et al, 2024.
Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit and xGen Methyl UDI-UMI (IDT) premethylated adapters. The library was bisulfite treated with the EZ DNA Methylation-Direct Kit, amplified using the KAPA HiFi Uracil+ (Roche) Kit, size selected with Ampure beads (targeting 300-600bp) and sequenced on an Illumina MISeq instrument in 600bp paired-end mode. For a detailed protocol, please see Schwaiger et al, 2024.

treatment_protocol: dTAG-13 was added to the culture medium at a final concentration of 0.5 uM.

tag: genetic background

value: hybrid 129-C57BL/6

value: embryonic stem cells (ESC)


title: IP_8025_CX_ATAC-Seq_Rep_4

description:
Library name: MUC6449_IP_8025_CX_9194
IP'ed nuclei from HEP-INTACT mice


title: IP_8025_CX_ATAC-Seq_Rep_2

description:
Library name: MUC6443_IP_8025_CX_9144
IP'ed nuclei from HEP-INTACT mice


title: IP_8025_CX_ATAC-Seq_Rep_3

description:
Library name: MUC6446_IP_8025_CX_9178
IP'ed nuclei from HEP-INTACT mice


title: IP_NC26_PBS_ATAC-Seq_Rep_4

description:
Library name: MUC6455_IP_NC26_PBS_8899
IP'ed nuclei from HEP-INTACT mice


title: IP_8025_PBS_ATAC-Seq_Rep_4

description:
Library name: MUC6448_IP_8025_PBS_9179
IP'ed nuclei from HEP-INTACT mice


title: Hep3B_sodium butyrate treatment_biol rep 3


title: IP_8025_PBS_ATAC-Seq_Rep_2

description:
Library name: MUC6442_IP_8025_PBS_9004
IP'ed nuclei from HEP-INTACT mice


title: IP_MC38_TUM_ATAC-Seq_Rep_2

description:
Library name: MUC5969_IP_MC38_TUM_9590
IP'ed nuclei from HEP-INTACT mice


title: IP_8025_PBS_ATAC-Seq_Rep_1

description:
Library name: MUC6439_IP_8025_PBS_9002
IP'ed nuclei from HEP-INTACT mice


title: IP_NC26_TUM_ATAC-Seq_Rep_3

description:
Library name: MUC6452_IP_NC26_TUM_9036
IP'ed nuclei from HEP-INTACT mice


title: Hep3B_sodium butyrate treatment_biol rep 1


title: IP_NC26_PBS_ATAC-Seq_Rep_2

description:
Library name: MUC5966_IP_NC26_PBS_9370
IP'ed nuclei from HEP-INTACT mice


title: IP_8025_CX_ATAC-Seq_Rep_1

description:
Library name: MUC6441_IP_8025_CX_9143
IP'ed nuclei from HEP-INTACT mice


title: Hep3B_biol rep 2


title: IP_NC26_TUM_ATAC-Seq_Rep_2

description:
Library name: MUC5967_IP_NC26_TUM_9027
IP'ed nuclei from HEP-INTACT mice


title: IP_NC26_PBS_ATAC-Seq_Rep_1

description:
Library name: MUC5962_IP_NC26_PBS_9367
IP'ed nuclei from HEP-INTACT mice


title: IP_NC26_TUM_ATAC-Seq_Rep_1

description:
Library name: MUC5963_IP_NC26_TUM_8898
IP'ed nuclei from HEP-INTACT mice


title: IP_MC38_TUM_ATAC-Seq_Rep_1

description:
Library name: MUC5965_IP_MC38_TUM_9222
IP'ed nuclei from HEP-INTACT mice


title: IP_C26_PRE_ATAC-Seq_Rep_4

description:
Library name: MUC5960_IP_C26_PRE_8273
IP'ed nuclei from HEP-INTACT mice


title: IP_C26_PBS_ATAC-Seq_Rep_4

description:
Library name: MUC5959_IP_C26_PBS_8271
IP'ed nuclei from HEP-INTACT mice


title: IP_NC26_TUM_ATAC-Seq_Rep_4

description:
Library name: MUC6456_IP_NC26_TUM_9366
IP'ed nuclei from HEP-INTACT mice


title: IP_MC38_PBS_ATAC-Seq_Rep_1

description:
Library name: MUC5964_IP_MC38_PBS_9588
IP'ed nuclei from HEP-INTACT mice


title: IP_MC38_PBS_ATAC-Seq_Rep_3

description:
Library name: MUC6453_IP_MC38_PBS_9219
IP'ed nuclei from HEP-INTACT mice


title: IP_C26_PBS_ATAC-Seq_Rep_3

description:
Library name: MUC5956_IP_C26_PBS_8270
IP'ed nuclei from HEP-INTACT mice


title: IP_C26_PRE_ATAC-Seq_Rep_3

description:
Library name: MUC5957_IP_C26_PRE_8272
IP'ed nuclei from HEP-INTACT mice


title: IP_C26_CX_ATAC-Seq_Rep_3

description:
Library name: MUC5958_IP_C26_CX_8073
IP'ed nuclei from HEP-INTACT mice


title: IP_C26_CX_ATAC-Seq_Rep_2

description:
Library name: MUC5955_IP_C26_CX_8147
IP'ed nuclei from HEP-INTACT mice


title: IP_C26_PRE_ATAC-Seq_Rep_2

description:
Library name: MUC5954_IP_C26_PRE_8146
IP'ed nuclei from HEP-INTACT mice


title: IP_MC38_PBS_ATAC-Seq_Rep_2

description:
Library name: MUC5968_IP_MC38_PBS_9589
IP'ed nuclei from HEP-INTACT mice


title: IP_C26_PBS_ATAC-Seq_Rep_2

description:
Library name: MUC5953_IP_C26_PBS_8143
IP'ed nuclei from HEP-INTACT mice


title: IP_C26_PRE_ATAC-Seq_Rep_1

description:
Library name: MUC5951_IP_C26_PRE_8072
IP'ed nuclei from HEP-INTACT mice


title: IP_C26_CX_ATAC-Seq_Rep_1

description:
Library name: MUC5952_IP_C26_CX_8222
IP'ed nuclei from HEP-INTACT mice


title: IP_MC38_P_Rep_3

description:
Library name: MUC6528_IP_MC38_P_9219
IP'ed nuclei from HEP-INTACT mice

data_processing:
The STAR aligner (v 2.4.2a) (Dobin et al., 2013) with modified parameter settings (--twopassMode=Basic) was used for split-read alignment against the mouse genome assembly mm10 and UCSC knownGene annotation.
Quantification of the number of mapped reads of each gene was performed using iRNA-seq (v 1.1) specifying the "-count gene" option (Madsen et al., 2015)
Differential expression was determined using DESeq2 (v 1.24.0) (Love et al., 2014)
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing unnormalized counts (output from iRNA-seq)

extract_protocol:
Whole liver nuclei as well as bead-bound and supernatant nuclei prepared from INTACT mice were directly resuspended in Trizol. RNA purification was performed using EconoSpin columns (Epoch) with on-column DNase digestion (Qiagen).
Total RNA (50-100ng) was prepared for sequencing using VAHTS Stranded mRNA-seq Library Kit for Illumina (Vazyme NR602) following manufacturer’s recommendations, except that no selection for poly-adenylated RNA was used. Prepared PCR products were purified and size-selected on AMPure XP beads (Beckman A63881), and library quality was assessed on the Agilent Bioanalyzer 2100 system. RNA libraries were sequenced as 50 bp paired-end runs on a HiSeq 4000 platform (Illumina, San Diego, USA).


title: IP_MC38_P_Rep_4

description:
Library name: MUC6530_IP_MC38_P_9635
IP'ed nuclei from HEP-INTACT mice


title: IP_MC38_T_Rep_1

description:
Library name: MUC6525_IP_MC38_T_9222
IP'ed nuclei from HEP-INTACT mice


title: IP_MC38_T_Rep_4

description:
Library name: MUC6531_IP_MC38_T_9638
IP'ed nuclei from HEP-INTACT mice


title: IP_MC38_P_Rep_2

description:
Library name: MUC6526_IP_MC38_P_9589
IP'ed nuclei from HEP-INTACT mice


title: IP_MC38_T_Rep_2

description:
Library name: MUC6527_IP_MC38_T_9590
IP'ed nuclei from HEP-INTACT mice


title: IP_C26_PBS_ATAC-Seq_Rep_1

description:
Library name: MUC5950_IP_C26_PBS_8079
IP'ed nuclei from HEP-INTACT mice


title: IN_MC38_TUM_Rep_2

description:
Library name: MUC6519_IN_MC38_TUM_9590
Whole liver nuclei from HEP-INTACT mice

source_name: whole liver nuclei

value: whole liver nuclei


title: IN_MC38_TUM_Rep_3

description:
Library name: MUC6521_IN_MC38_TUM_9591
Whole liver nuclei from HEP-INTACT mice


title: IP_MC38_T_Rep_3

description:
Library name: MUC6529_IP_MC38_T_9591
IP'ed nuclei from HEP-INTACT mice


title: IN_MC38_TUM_Rep_1

description:
Library name: MUC6517_IN_MC38_TUM_9222
Whole liver nuclei from HEP-INTACT mice


title: IP_MC38_P_Rep_1

description:
Library name: MUC6524_IP_MC38_P_9588
IP'ed nuclei from HEP-INTACT mice


title: IP_C26_CX_ATAC-Seq_Rep_4

description:
Library name: MUC5961_IP_C26_CX_8074
IP'ed nuclei from HEP-INTACT mice


title: IN_MC38_PBS_Rep_4

description:
Library name: MUC6522_IN_MC38_PBS_9635
Whole liver nuclei from HEP-INTACT mice


title: IN_MC38_PBS_Rep_1

description:
Library name: MUC6516_IN_MC38_PBS_9588
Whole liver nuclei from HEP-INTACT mice


title: IP_NC26_PBS_Rep_4

description:
Library name: MUC6514_IP_NC26_PBS_8899
IP'ed nuclei from HEP-INTACT mice


title: IP_NC26_TUM_Rep_4

description:
Library name: MUC6515_IP_NC26_TUM_9366
IP'ed nuclei from HEP-INTACT mice


title: IP_NC26_TUM_Rep_2

description:
Library name: MUC6511_IP_NC26_TUM_9027
IP'ed nuclei from HEP-INTACT mice


title: IP_NC26_PBS_Rep_3

description:
Library name: MUC6512_IP_NC26_PBS_9034
IP'ed nuclei from HEP-INTACT mice


title: IP_NC26_TUM_Rep_3

description:
Library name: MUC6513_IP_NC26_TUM_9036
IP'ed nuclei from HEP-INTACT mice


title: IP_NC26_PBS_Rep_2

description:
Library name: MUC6510_IP_NC26_PBS_9370
IP'ed nuclei from HEP-INTACT mice


title: IP_NC26_PBS_Rep_1

description:
Library name: MUC6508_IP_NC26_PBS_9367
IP'ed nuclei from HEP-INTACT mice


title: IN_MC38_TUM_Rep_4

description:
Library name: MUC6523_IN_MC38_TUM_9638
Whole liver nuclei from HEP-INTACT mice


title: IN_NC26_TUM_Rep_4

description:
Library name: MUC6507_IN_NC26_TUM_9366
Whole liver nuclei from HEP-INTACT mice


title: IN_NC26_PBS_Rep_3

description:
Library name: MUC6504_IN_NC26_PBS_9034
Whole liver nuclei from HEP-INTACT mice


title: IN_NC26_TUM_Rep_3

description:
Library name: MUC6505_IN_NC26_TUM_9036
Whole liver nuclei from HEP-INTACT mice


title: IN_NC26_PBS_Rep_4

description:
Library name: MUC6506_IN_NC26_PBS_8899
Whole liver nuclei from HEP-INTACT mice


title: IP_NC26_TUM_Rep_1

description:
Library name: MUC6509_IP_NC26_TUM_8898
IP'ed nuclei from HEP-INTACT mice


title: IN_NC26_TUM_Rep_1

description:
Library name: MUC6501_IN_NC26_TUM_8898
Whole liver nuclei from HEP-INTACT mice


title: E-3

city: Lanzhou City

first: Lan

middle: Lan

last: Yu

state: Anning District

address: Northwest Normal University, Shi Street, Anning District, Lanzhou City, Gansu Province, China

department: College of Life Sciences

institute: Northwest Normal University

description: Oudemansiella raphanipes grown at different development stages:Matured fruiting body

data_processing:
The longest transcript was choose as a unigene based the similarity and length of a sequence for subsequent analysis.
Assembly: De novo RNA-seq
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

organism: Hymenopellis raphanipes

source_name: Matured fruiting body

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated NanoDrop 2000 spectrophotometer (Thermo Scientific,USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
Libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina according to the manufacturer’s instructions. The libraries were finally sequenced using the Illumina Novaseq 6000 platform. 150 bp paired-end reads were generated. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China)

value: Matured fruiting body


title: IN_NC26_PBS_Rep_2

description:
Library name: MUC6502_IN_NC26_PBS_9370
Whole liver nuclei from HEP-INTACT mice


title: IN_MC38_PBS_Rep_2

description:
Library name: MUC6518_IN_MC38_PBS_9589
Whole liver nuclei from HEP-INTACT mice


title: E-2


title: E-1


title: IP_8025_CX_Rep_4

description:
Library name: MUC6437_IP_8025_CX_9194
IP'ed nuclei from HEP-INTACT mice


title: D-3

description: Oudemansiella raphanipes grown at different development stages:Unmatured fruiting body

source_name: Unmatured fruiting body

value: Unmatured fruiting body


title: D-2


title: IP_8025_CX_Rep_3

description:
Library name: MUC6434_IP_8025_CX_9178
IP'ed nuclei from HEP-INTACT mice


title: IP_8025_PBS_Rep_4

description:
Library name: MUC6436_IP_8025_PBS_9179
IP'ed nuclei from HEP-INTACT mice


title: IN_MC38_PBS_Rep_3

description:
Library name: MUC6520_IN_MC38_PBS_9219
Whole liver nuclei from HEP-INTACT mice


title: D-1


title: IP_8025_PBS_Rep_3

description:
Library name: MUC6433_IP_8025_PBS_9177
IP'ed nuclei from HEP-INTACT mice


title: C-3

description: Oudemansiella raphanipes grown at different development stages:Primordia stage

source_name: Primordia stage

value: Primordia stage


title: IP_8025_CX_Rep_2

description:
Library name: MUC6431_IP_8025_CX_9144
IP'ed nuclei from HEP-INTACT mice


title: C-2


title: C-1


title: IP_8025_CX_Rep_1

description:
Library name: MUC6429_IP_8025_CX_9143
IP'ed nuclei from HEP-INTACT mice


title: IP_8025_PBS_Rep_2

description:
Library name: MUC6430_IP_8025_PBS_9004
IP'ed nuclei from HEP-INTACT mice


title: IP_8025_PBS_Rep_1

description:
Library name: MUC6427_IP_8025_PBS_9002
IP'ed nuclei from HEP-INTACT mice


title: IN_NC26_TUM_Rep_2

description:
Library name: MUC6503_IN_NC26_TUM_9027
Whole liver nuclei from HEP-INTACT mice


title: B-2

description: Oudemansiella raphanipes grown at different development stages:Mycelial stage

source_name: Mycelial stage

value: Mycelial stage


title: IN_8025_CX_Rep_4

description:
Library name: MUC6425_IN_8025_CX_9194
Whole liver nuclei from HEP-INTACT mice


title: IN_8025_CX_Rep_3

description:
Library name: MUC6422_IN_8025_CX_9178
Whole liver nuclei from HEP-INTACT mice


title: B-1


title: IN_8025_PBS_Rep_4

description:
Library name: MUC6424_IN_8025_PBS_9179
Whole liver nuclei from HEP-INTACT mice


title: IN_NC26_PBS_Rep_1

description:
Library name: MUC6500_IN_NC26_PBS_9367
Whole liver nuclei from HEP-INTACT mice


title: IN_8025_PBS_Rep_3

description:
Library name: MUC6421_IN_8025_PBS_9177
Whole liver nuclei from HEP-INTACT mice


title: A-1

description: Oudemansiella raphanipes grown at different development stages:Spores

source_name: Spores

value: Spores


title: IN_8025_CX_Rep_2

description:
Library name: MUC6419_IN_8025_CX_9144
Whole liver nuclei from HEP-INTACT mice


title: IN_8025_PBS_Rep_2

description:
Library name: MUC6418_IN_8025_PBS_9004
Whole liver nuclei from HEP-INTACT mice


title: IN_8025_CX_Rep_1

description:
Library name: MUC6417_IN_8025_CX_9143
Whole liver nuclei from HEP-INTACT mice


title: IP_C26_CX_Rep_4

description:
Library name: MUC6414_IP_C26_CX_8074
IP'ed nuclei from HEP-INTACT mice


title: IN_8025_PBS_Rep_1

description:
Library name: MUC6415_IN_8025_PBS_9002
Whole liver nuclei from HEP-INTACT mice


title: IP_C26_PRE_Rep_4

description:
Library name: MUC6413_IP_C26_PRE_8273
IP'ed nuclei from HEP-INTACT mice


title: IP_C26_PBS_Rep_4

description:
Library name: MUC6412_IP_C26_PBS_8271
IP'ed nuclei from HEP-INTACT mice


title: IP_C26_CX_Rep_3

description:
Library name: MUC6411_IP_C26_CX_8073
IP'ed nuclei from HEP-INTACT mice


title: B-3

value: WT


title: IP_C26_PRE_Rep_3

description:
Library name: MUC6410_IP_C26_PRE_8272
IP'ed nuclei from HEP-INTACT mice


title: KO_Ex_5

city: Boston

first: Sumeet

middle: Anand

last: Khetarpal

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description: Library name: G4-5

data_processing:
RNA-seq Data Processing and Analysis
Total RNA quality was assessed, and libraries were prepared and sequenced on an Illumina platform to generate paired-end reads. Raw reads were quality-filtered using in-house scripts to remove adapters, poly-N sequences, and low-quality reads. Clean reads were assessed for Q20/Q30 scores and GC content.
Reads were aligned to the mouse reference genome (mm10) using HISAT2 v2.0.5, incorporating known splice junctions from the gene annotation file. Gene-level read counts were quantified using featureCounts v1.5.0-p3, and expression levels were normalized as FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Differential expression analysis between conditions was performed using DESeq2 (v1.20.0), which models count data using a negative binomial distribution. P-values were adjusted for multiple testing using the Benjamini-Hochberg method. Genes with an adjusted p-value ≤ 0.05 were considered significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: tab delimited text file contains FPKM for each sample

source_name: Heart

extract_protocol:
Total RNA was extracted from approximately 15-20 mg of heart tissue  using TRIzol (Thermo Fisher Scientific), purified with RNeasy Mini spin columns (Qiagen). RNA was eluted using Rnase-free water.
Libraries were constructed from polyA-selected RNA using a NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) using manufacturer protocols and sequenced on Illumina HiSeq2500 instrument.

value: Heart

tag: Sex

value: male

tag: age

value: 14-16 weeks

value: knockout

value: exercised

tag: batch


title: KO_Ex_4

description: Library name: G4-4


title: A-3


title: KO_Ex_3

description: Library name: G4-3


title: IP_C26_PBS_Rep_3

description:
Library name: MUC6409_IP_C26_PBS_8270
IP'ed nuclei from HEP-INTACT mice

value: hepatocyte nuclei

value: CAG-Sun1/sfGFP, Albumin-Cre


title: IP_C26_PRE_Rep_2

description:
Library name: MUC6407_IP_C26_PRE_8146
IP'ed nuclei from HEP-INTACT mice

value: BALB/c


title: A-2


title: KO_Ex_2

description: Library name: G4-2


title: IP_C26_CX_Rep_2

description:
Library name: MUC6408_IP_C26_CX_8147
IP'ed nuclei from HEP-INTACT mice


title: IP_C26_CX_Rep_1

description:
Library name: MUC6405_IP_C26_CX_8222
IP'ed nuclei from HEP-INTACT mice


title: L1_si-Idh3b-1_D8

description: Gene expression in 3T3-L1 cells transfected with si-Idh3b #1

hyb_protocol: Biotinylated cRNA was hybridized  according to the standard Affymetrix protocol.

scan_protocol: Scanned by Affymetrix GeneChip scanner 3000 (Affymetrix).

data_processing: GeneChip Analysis Suite software program version 5.0 was (Affymetrix) was used.

label: Biotin

source_name: 3T3-L1 cells transfected with si-Idh3b #1 on day 8 of differentiation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: 3T3-L1 preadipocytes were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum at 37 °C. 3T3-L1 preadipocytes were transfected with si-Ctr or si-Idh3b.

extract_protocol: Total RNA was extracted using ISOGEN (Nippongene) following manufacturer's protocol.

treatment_protocol: Two days after reaching confluent (day 0), 3T3-L1 preadipocytes were treated with differentiation medium containing insulin (1 μg/ml), 0.25 μM dexamethasone (DEX), and 0.5 mM isobutylmethylxanthine (MDI mixture) for 48 h followed by treatment with insulin (1 μg/ml) alone with medium replacement every 2 days. Under glucose restricction, glucose in the medium was reduced from 25 to 1 mM.

tag: glucose

value: 25 mM glucose

tag: si-rna

value: si-Idh3b #1

tag: day

value: Day 8


title: IP_C26_PBS_Rep_2

description:
Library name: MUC6406_IP_C26_PBS_8143
IP'ed nuclei from HEP-INTACT mice


title: KO_Ex_1

description: Library name: G4-1


title: L1_1mM_Gluc_D8

description: Gene expression in 3T3-L1 cells differentiated under 1 mM glucose

source_name: 3T3-L1 cells differentiated under 1 mM glucose on day 8

value: 1 mM glucose


title: L1_25mM_Gluc_D4

description: Gene expression in 3T3-L1 cells differentiated under 25 mM glucose

source_name: 3T3-L1 cells differentiated under 25 mM glucose on day 4

value: Day 4


title: L1_si-Idh3b-2_D8

description: Gene expression in 3T3-L1 cells transfected with si-Idh3b #2

source_name: 3T3-L1 cells transfected with si-Idh3b #2 on day 8 of differentiation

value: si-Idh3b #2


title: WT_Ex_4

description: Library name: G3-4

value: wild-type


title: L1_1mM_Gluc_D4

source_name: 3T3-L1 cells differentiated under 1 mM glucose on day 4


title: IP_C26_PBS_Rep_1

description:
Library name: MUC6403_IP_C26_PBS_8079
IP'ed nuclei from HEP-INTACT mice


title: L1_25mM_Gluc_D8

source_name: 3T3-L1 cells differentiated under 25 mM glucose on day 8


title: WT_Ex_5

description: Library name: G3-5


title: L1_25mM_Gluc_D0

source_name: 3T3-L1 cells before differentiation

value: Day 0


title: IP_C26_PRE_Rep_1

description:
Library name: MUC6404_IP_C26_PRE_8072
IP'ed nuclei from HEP-INTACT mice


title: IN_C26_CX_Rep_4

description:
Library name: MUC6402_IN_C26_CX_8074
Whole liver nuclei from HEP-INTACT mice

value: whole liver nuclei


title: WT_Ex_3

description: Library name: G3-3

value: Heart


title: WT_Ex_2

description: Library name: G3-2

value: male


title: L1_si-Ctr_D8

description: Gene expression in 3T3-L1 cells transfected with si-Ctr

source_name: 3T3-L1 cells transfected with si-ctr on day 8 of differentiation

value: s-Ctr


title: WT_Ex_1

description: Library name: G3-1

value: 14-16 weeks


title: IN_C26_PRE_Rep_4

description:
Library name: MUC6401_IN_C26_PRE_8273
Whole liver nuclei from HEP-INTACT mice


title: KO_Sed_5

description: Library name: G2-5

value: knockout

value: sedentary


title: IN_C26_PBS_Rep_4

description:
Library name: MUC6400_IN_C26_PBS_8271
Whole liver nuclei from HEP-INTACT mice

value: CAG-Sun1/sfGFP, Albumin-Cre


title: IN_C26_CX_Rep_3

description:
Library name: MUC6399_IN_C26_CX_8073
Whole liver nuclei from HEP-INTACT mice

value: BALB/c


title: KO_Sed_4

description: Library name: G2-4


title: IN_C26_PRE_Rep_3

description:
Library name: MUC6398_IN_C26_PRE_8272
Whole liver nuclei from HEP-INTACT mice


title: KO_Sed_3

description: Library name: G2-3


title: KO_Sed_2

description: Library name: G2-2


title: IN_C26_CX_Rep_2

description:
Library name: MUC6396_IN_C26_CX_8147
Whole liver nuclei from HEP-INTACT mice


title: IN_C26_PBS_Rep_3

description:
Library name: MUC6397_IN_C26_PBS_8270
Whole liver nuclei from HEP-INTACT mice


title: KO_Sed_1

description: Library name: G2-1


title: WT_Sed_4

description: Library name: G1-4


title: IN_C26_PRE_Rep_1

description:
Library name: MUC6392_IN_C26_PRE_8072
Whole liver nuclei from HEP-INTACT mice


title: WT_Sed_5

description: Library name: G1-5


title: IN_C26_PBS_Rep_1

description:
Library name: MUC6391_IN_C26_PBS_8079
Whole liver nuclei from HEP-INTACT mice


title: WT_Sed_1

description: Library name: G1-1


title: WT_Sed_2

description: Library name: G1-2


title: IN_C26_PRE_Rep_2

description:
Library name: MUC6395_IN_C26_PRE_8146
Whole liver nuclei from HEP-INTACT mice


title: IN_C26_PBS_Rep_2

description:
Library name: MUC6394_IN_C26_PBS_8143
Whole liver nuclei from HEP-INTACT mice


title: 360

city: Princeton

first: Ian

middle: Michael

last: Traniello

state: NJ

address: Princeton University

department: Lewis-Sigler Insitute for Genomic Biology

institute: Princeton University

data_processing:
Adaptors have been trimmed from the 3'-end of the reads. Sequence of adaptors used to make the libraries (used the first 33nt for adaptor trimming).
fastq.gz files were aligned to the honey bee genome (vHAv3.1) with STAR v2.7.3a
count files were generated using the "featureCounts" function in Subread v2.0.0
Assembly: HAv3.1
Supplementary files format and content: featureCounts output files: gene names in column 1, gene counts in column 7

organism: Apis mellifera

source_name: Mushroom bodies (brain region)

growth_protocol: Honey bees were flash frozen in liquid nitrogen and stored at -80C until processing

extract_protocol:
RNA was extracted with the RNeasy Mini Kit (Qiagen) and assessed on a Nanodrop, Qubit, and Bioanalyzer
The RNAseq libraries were prepared with the Kapa Hyper Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand. The libraries were pooled; quantitated by qPCR and sequenced on one S4 lane for 151 cycles from both ends of the fragments on a NovaSeq 6000.  Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).

treatment_protocol: Heads were chipped, incubated in RNA-laterICE for ~16 hr, and the mushroom body was dissected.

value: Mushroom bodies (brain region)

tag: input reads

tag: mapped reads

tag: assigned reads

tag: reads aligned_to_dwv_genome

tag: reads aligned_to_vdv_genome

tag: replicate (note

value: Nurse


title: C26_REV-ERBa_Rep_10

description: Library name: CR39

source_name: heart

extract_protocol:
For RNA isolation from tissue, ~200 mg heart tissue was lysed in TRIzol using the TissueLyser II (Qiagen, #85300) followed by RNA purification using EconoSpin columns (Epoch). RNA concentrations were determined using the Nanodrop 2000 (Thermo Fisher).
Total RNA (50-100ng) was prepared for sequencing using VAHTS Stranded mRNA-seq Library Kit for Illumina (Vazyme NR602) following manufacturer’s recommendations, except that no selection for poly-adenylated RNA was used. Prepared PCR products were purified and size-selected on AMPure XP beads (Beckman A63881), and library quality was assessed on the Agilent Bioanalyzer 2100 system. RNA libraries were sequenced as 50 bp paired-end runs on a HiSeq 4000 platform (Illumina, San Diego, USA).

value: mus musculus, BALB/c

tag: tissue

value: heart

tag: genotype

value: wildtype

tag: treatment

value: Tbg_AAV_REVERB + C26


title: WT_Sed_3

description: Library name: G1-3

value: wild-type


title: C26_REV-ERBa_Rep_8

description: Library name: CR37

tag: mouse strain

tag: animal id

tag: replicate


title: C26_REV-ERBa_Rep_9

description: Library name: CR38


title: 384


title: 281

value: Non-Responder


title: 329


title: 306


title: C26_REV-ERBa_Rep_5

description: Library name: CR33


title: 357


title: C26_REV-ERBa_Rep_4

description: Library name: CR32


title: C26_REV-ERBa_Rep_2

description: Library name: CR30


title: 346

value: Generalist


title: 361


title: C26_REV-ERBa_Rep_3

description: Library name: CR31


title: 312

value: Guard


title: C26_REV-ERBa_Rep_6

description: Library name: CR34


title: C26_REV-ERBa_Rep_1

description: Library name: CR29


title: IN_C26_CX_Rep_1

description:
Library name: MUC6393_IN_C26_CX_8222
Whole liver nuclei from HEP-INTACT mice

source_name: whole liver nuclei

value: whole liver nuclei


title: 259


title: C26_GFP_Rep_9

description: Library name: CG26

value: Tbg_AAV_GFP + C26


title: C26_GFP_Rep_10

description: Library name: CG28


title: 288


title: 249


title: C26_GFP_Rep_8

description: Library name: CG25


title: 388


title: C26_REV-ERBa_Rep_7

description: Library name: CR35


title: C26_GFP_Rep_7

description: Library name: CG24


title: 285


title: 385


title: C26_GFP_Rep_6

description: Library name: CG23


title: C26_GFP_Rep_5

description: Library name: CG21


title: C26_GFP_Rep_4

description: Library name: CG20


title: 383

value: Forager


title: 316


title: 343


title: 252


title: C26_GFP_Rep_1

description: Library name: CG17


title: C26_GFP_Rep_2

description: Library name: CG18


title: 387


title: PBS_REV-ERBa_Rep_4

description: Library name: PR15

value: Tbg_AAV_REVERBa + PBS


title: PBS_REV-ERBa_Rep_2

description: Library name: PR13


title: 356


title: PBS_REV-ERBa_Rep_5

description: Library name: PR16


title: PBS_REV-ERBa_Rep_1

description: Library name: PR12


title: 325


title: 284


title: 355


title: PBS_GFP_Rep_2

description: Library name: PG8

value: Tbg_AAV_GFP + PBS


title: C26_GFP_Rep_3

description: Library name: CG19


title: 332


title: PBS_GFP_Rep_1

description: Library name: PG7


title: 331


title: 301


title: PBS_GFP_Rep_3

description: Library name: PG10


title: PBS_GFP_Rep_4

description: Library name: PG11


title: 260


title: 271


title: 390


title: Healthy_pos_5

city: Hamburg

first: Marcel

middle: Seungsu

last: Woo

state: Hamburg

address: Falkenried 94

department: Neurology

institute: UKE

data_processing:
STAR v.2.4 alignment to genome
featurCounts v.1.5.1 for gene loci counting
DESeq2 for differential expression analysis
Assembly: GRCm39 - mm10
Supplementary files format and content: tab-delimited text file including raw gene counts of every sample

source_name: Spinal cord

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using poly A enrichment withTruSeq RNA Sample Prep Kit Kit from Illumina according to manufacturers protocol.

treatment_protocol: Neuronal nuclei were sorted from spinal cords of healthy and EAE mice 15 days after active immunization.

value: Spinal cord

tag: cell type

value: Nuclei


title: Healthy_neg_5


title: 265

value: Mushroom bodies (brain region)


title: Healthy_pos_4


title: Healthy_neg_4


title: Healthy_pos_3


title: 263

value: Nurse


title: 365


title: PBS_REV-ERBa_Rep_3

description: Library name: PR14

value: mus musculus, BALB/c


title: Healthy_neg_3


title: Healthy_neg_2


title: 380


title: 354


title: 333


title: 246


title: Healthy_pos_1


title: 292


title: EAE_neg_5


title: 344


title: EAE_pos_5


title: EAE_pos_4


title: 275


title: EAE_neg_4


title: 379


title: 314


title: EAE_neg_3


title: 247


title: EAE_pos_3


title: EAE_neg_2


title: 376


title: EAE_pos_1


title: 353


title: 293


title: EAE_pos_2


title: EAE_neg_1


title: Healthy_pos_2


title: 264


title: 295


title: AdCD4; Biol Rep-4

city: Los Angeles

first: Yajing

last: Gao

state: CA

address: 675 Charles E Young Dr S

department: Pathology and Laboratory Medicine

institute: University of California, Los Angeles

data_processing:
Raw fastq data was processed in UCLA Hoffman2 cluster.
Adapter and quality trimming of raw FASTQ files was performed using Trimmomatic. FastQC was used to perform quality control of the FASTQ files before and after trimming.
Trimmed FASTQ files were aligned to GRCm38/mm10 using STAR package.
HTSeq-count was used to extract gene counts.
Gene expression analysis was performed using DESeq2 package implemented in R.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: xlsx file containing compiled normalized counts from DESeq analysis

source_name: Small Intestine Lamina Propria

extract_protocol:
Total RNA was extracted using TRIzol and the miRNeasy Mini Kit with on-column DNase I digestion (Qiagen).
RNA library preparations and sequencing reactions were conducted at GENEWIZ, LLC. RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions.

treatment_protocol: Mice were fasted for 16 h and gavaged with olive oil for 2 h. Small intestinal lamina propria mononuclear cells were isolated and FACS sorted for CD4 T cells (CD45+/CD90+/CD3+/CD4+).

value: Small Intestine Lamina Propria

tag: cell line

value: CD4 T lymphocyte

value: CD4-Cre; Aster-A F/F

value: 2 h Olive Oil gavage


title: 369


title: 326


title: AdCD4; Biol Rep-2


title: AdCD4; Biol Rep-3


title: 337


title: Healthy_neg_1


title: AdCD4; Biol Rep-1


title: WT; Biol Rep-3

value: Aster-A F/F


title: 297

value: Generalist


title: WT; Biol Rep-2


title: 334


title: 299


title: 283


title: RNA_LPS_8h_R2_2

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Base calling was performed by Illumina Real Time Analysis (2.7.7) software and the base calls were converted to short reads using the IlluminaBasecallsToSam tool from the Picard toolkit (2.19.2).
Sequencing reads were mapped, and gene counts were generated with STAR (2.7.8a) using the GRCm38 (mm10) assembly of the mouse genome and respective Ensembl annotations using a publicly available Snakemake workflow (10.5281/zenodo.4737358).
Assembly: mm10
Supplementary files format and content: RNA_raw_counts.csv: comma-separated read count file of the RNA-seq data

source_name: bone marrow-derived macrophages

growth_protocol: Femur and tibia were obtained from 8-12 week old female Cas9-mice (Jackson Laboratory cat. No. 024858) and washed with PBS. The bones were crushed in PBS with a sterile mortar and pestle and the bone marrow containing supernatant was filtered through a 100 µm and subsequently a 45 µm filter. The cells were counted, centrifuged at 4 °C for 5 min at 400 rcf and resuspended in DMEM-GlutaMAX (Gibco cat. No. 31966047) with 40% FBS. The cell suspension was mixed with an equal volume of DMEM GlutaMAX with 40% FBS and 30% DMSO (Sigma cat. No. 1019001000) and frozen in 50 million/ml aliquots and stored at -80 °C (short-term) or in liquid nitrogen (long-term storage). Bone marrow aliquots were thawed, once washed with media to remove excess DMSO, and seeded on three 15 cm dishes (non-cell culture treated, VWR cat. No. 734-2797) in 20 ml standard media (DMEM-GlutaMAX (Gibco cat. No. 31966047) with 10% FBS and 1x penicillin-streptomycin (Gibco cat. No. 15140122)) supplemented with 200 ng/ml murine-mCSF (Peprotech cat. No. 315-02). After four days, 5 ml of the media was exchanged with fresh media supplemented with murine-mCSF to reach a total concentration of 100 ng/ml in the dish, and the media substitution was repeated after an additional 3 days

extract_protocol:
For RNA-seq, 300,000 to 500,000 cells were centrifuged for 5 minutes at 4 °C at 500 rcf, resuspended in 150 µl RLT buffer (from RNeasy kit (Qiagen cat. No. 74181)) with β-mercaptoethanol, vortexed for 1 minute, and frozen at -80 °C. RNA was extracted using the RNeasy kit (Qiagen cat. No. 74181) following the manufacturer’s recommendations. RNA was eluted in two rounds, with 45 µl and 20 µl RNase-free water, respectively
5 µl eluted RNA was processed with the QuantSeq 3’ mRNA-Seq library kit (Lexogen cat. No. 015.96) according to the manufacturer’s recommendations, using 16 PCR cycles for the amplification.

treatment_protocol: On day 9, cells were scraped, counted, and seeded into 6 well plates (non-cell culture treated, Fischer Scientific cat. No. 10284901) with fresh standard media (without penicillin-streptomycin antibiotic) plus 100 ng/ml mCSF, at 1-2 million cells per well. The following day, wells were treated in a staggered manner by adding the respective stimulus for the stated duration, such that all treatments (except the 24 hour timepoint) could be stopped and harvested at the same time to minimize technical variability. UV-killed Candida albi-cans SC5314 were added at a multiplicity of infection (MOI) of 2, LCMV Cl13 at an MOI of 3, Listeria monocytogenes LO28 at an MOI of 20, LPS (Merck cat. No. L4641) at a final concentration of 10 ng/ml, IFN-β (Pbl Assay Science cat. No. 12401-1) at a final concentration of 500 U/ml, and IFN-γ (Peprotech cat. No. 315-05) at a final concentration of 240 U/ml. 50 µg/ml Gentamicin (MP Biomedicals cat. No. 1676045) was added to Listeria monocytogenes LO28 treated wells after one hour. Two hours after infection, the media was exchanged to standard media without antibiotics supplemented with 100 ng/ml mCSF and 5 µg/ml gentamicin.

value: bone marrow-derived macrophages

tag: protocol

value: Quant-seq

tag: timepoint after_thawing

tag: stimulus

value: LPS

tag: time point

tag: Sex

value: female

tag: bio-replicate

tag: batch


title: RNA_LPS_4h_R2_1


title: RNA_LPS_24h_R2_2


title: 308

tag: input reads

tag: mapped reads

tag: assigned reads

tag: reads aligned_to_dwv_genome

tag: reads aligned_to_vdv_genome


title: 319

tag: tissue

tag: replicate (note

tag: genotype

tag: treatment

value: Forager


title: 255

value: Guard


title: 389


title: 364


title: WT; Biol Rep-1

tag: cell line

tag: cell type


title: RNA_Listeria_6h_R2_1

tag: protocol

tag: timepoint after_thawing

value: Listeria


title: 307


title: RNA_LPS_2h_R2_1

tag: stimulus

tag: time point


title: 311


title: 280


title: RNA_LPS_6h_R2_1

tag: Sex

tag: bio-replicate


title: RNA_Listeria_4h_R2_1

tag: batch


title: RNA_Listeria_8h_R2_2


title: 286

tag: input reads

tag: mapped reads


title: RNA_Listeria_24h_R2_2


title: RNA_Listeria_2h_R2_1


title: 378

tag: assigned reads

tag: reads aligned_to_dwv_genome


title: 340

tag: tissue

tag: reads aligned_to_vdv_genome


title: RNA_LCMV_8h_R2_2

value: LCMV


title: RNA_LCMV_6h_R2_1


title: 362

value: Mushroom bodies (brain region)

tag: replicate (note

tag: genotype

value: Non-Responder


title: 309

tag: treatment


title: RNA_LCMV_4h_R2_1

tag: cell type


title: RNA_LCMV_24h_R2_2

tag: protocol


title: 375


title: 219


title: RNA_IFNgamma_8h_R2_2

tag: timepoint after_thawing

value: IFNgamma


title: 95


title: RNA_IFNgamma_6h_R2_1

tag: stimulus


title: 65


title: RNA_IFNgamma_4h_R2_1

tag: time point


title: 160

value: Nurse


title: 53


title: RNA_IFNgamma_24h_R2_2

tag: Sex


title: RNA_IFNbeta_6h_R2_1

value: IFNbeta

tag: bio-replicate


title: 127


title: RNA_IFNgamma_2h_R2_1

tag: batch


title: RNA_IFNbeta_8h_R2_2


title: RNA_IFNbeta_4h_R2_1


title: 107

tag: input reads


title: RNA_IFNbeta_24h_R2_2


title: RNA_IFNbeta_2h_R2_1


title: 145

tag: mapped reads


title: RNA_untreated_8h_R2_2

value: untreated


title: 49

tag: assigned reads


title: 74

tag: reads aligned_to_dwv_genome


title: RNA_untreated_0h_R2_1


title: 173

tag: tissue


title: RNA_Candida_8h_R2_2

value: Candida


title: RNA_LCMV_2h_R2_1


title: 56

tag: reads aligned_to_vdv_genome


title: 136

tag: replicate (note


title: RNA_Candida_4h_R2_1


title: 169

tag: genotype


title: 185

tag: treatment


title: RNA_Candida_6h_R2_1

tag: cell type


title: 22


title: 26


title: 225


title: RNA_LPS_8h_R1_2

tag: protocol


title: RNA_Candida_24h_R2_2

tag: timepoint after_thawing


title: 133


title: 141


title: RNA_LPS_4h_R1_1

tag: stimulus


title: 181


title: RNA_Listeria_8h_R1_2

tag: time point


title: RNA_LPS_2h_R1_1

tag: Sex


title: 202


title: RNA_untreated_24h_R2_2

tag: bio-replicate


title: 158


title: RNA_Listeria_6h_R1_1

tag: batch


title: 211

tag: input reads


title: RNA_Listeria_24h_R1_2


title: RNA_Listeria_4h_R1_1


title: 16

tag: mapped reads


title: 189

tag: assigned reads


title: RNA_Listeria_2h_R1_1


title: RNA_Candida_2h_R2_1


title: 226

tag: reads aligned_to_dwv_genome


title: RNA_LCMV_6h_R1_1


title: 201

tag: tissue


title: 131

tag: reads aligned_to_vdv_genome


title: RNA_LCMV_4h_R1_1


title: RNA_LCMV_24h_R1_2


title: RNA_LPS_6h_R1_1


title: 123

tag: replicate (note


title: RNA_LCMV_2h_R1_1


title: 194

tag: genotype


title: 80

tag: treatment


title: 230


title: RNA_IFNgamma_8h_R1_2

tag: cell type


title: 193


title: RNA_IFNgamma_6h_R1_1

tag: protocol


title: 177


title: primary mouse chondrocytes from Tiki2 fl/fl Col2a1-Cre/ERT mice, rep1

city: Chengdu

first: Hengye

last: Zhang

state: Sichuan

address: No.4,Section 2,North Jianshe Road

institute: University of Electronic Science and Technology of China

description: Library name: iMAC-cre-1

data_processing:
The reads processed in the RNA-seq analysis were aligned to the Reads were first trimmed and quality checked with Trim Galore (Version 0.6.7) and FastQC (Version 0.11.9), respectively. Reads were aligned to the mouse genome version (UCSC mm10) applying HISAT2 (Version 2.2.1).
Mapped reads from each sample were assembled using StringTie (Version 2.1.7). StringTie was utilized to estimate the expression of all transcripts and generate the count table.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: primary mouse chondrocytes

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent and purified using the RNeasy Mini Kit (Qiagen). RNA integrity was verified using the Agilent 4200 TapeStation.
Poly(A) mRNA was enriched with oligo(dT) beads, fragmented, and reverse-transcribed with random primers and M-MuLV. After second-strand synthesis (RNase H / DNA Pol I), ds-cDNA was end-repaired, A-tailed, ligated to Illumina adapters, size-selected (~200 bp) with AMPure XP beads, PCR-amplified, and purified to yield the final RNA-seq library.

value: primary mouse chondrocytes

value: Tiki2 fl/fl; Col2a-CreERT2


title: 12 hours post fertilization

first: Juan

middle: Daniel

last: Montenegro

state: Vienna

address: Djerassiplatz 1

department: Department of neurobiology and developmental biology

institute: University of Vienna

description: Library name: 89085

library_source: transcriptomic single cell

data_processing:
cellranger pipeline using default parameters with forced recovery of 10000 cells for each library
Assembly: PRJNA667495 from Zimmerman et al 2023 doi:10.1038/s41467-023-44080-7
Supplementary files format and content: Seurat object as an RDS file

organism: Nematostella vectensis

source_name: embryo

extract_protocol:
Whole embryos were dissociated with cysteine treatment (8 and 10hpf) or tripleE (12hpf).  Mechanical force was used to disrupt the tissues and obtain single-cell suspensions. Cell suspensions were washed with 0.1% BSA (bovine serum albumin), and cell viability and counts were assayed with a Cellometer X2 (Nexcelom). Cell suspensions were diluted to 1000 cells/ microliter and loaded into a 10x Genomics single cell platform using vs3 reagents (8 and 10hpf) or vs2 reagents (12hpf).
10X Genomics Chromium v2/v3 chemistry according to manufacturer protocols

value: embryo

value: wt


title: primary mouse chondrocytes from Tiki2 fl/fl mice, rep2

description: Library name: iMAC-con-2

value: Tiki2 fl/fl


title: 8 hours post fertilization

description: Library name: 8hr-SCI7T008-SCI5T008


title: primary mouse chondrocytes from Tiki2 fl/fl Col2a1-Cre/ERT mice, rep2

description: Library name: iMAC-cre-2


title: primary mouse chondrocytes from Tiki2 fl/fl mice, rep1

description: Library name: iMAC-con-1


title: RNA_LCMV_8h_R1_2

value: bone marrow-derived macrophages

value: Quant-seq

tag: timepoint after_thawing

value: female


title: HiC_WT

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

description: Library name: WT

data_processing:
Hi-C sequencing data were processed using HiC-Pro as previously described to generate high-resolution chromatin contact maps (Servant, N. el Al. Genome Biol 2015). Briefly, raw paired-end reads of fastq from the NovaSeq 6000 platform were aligned to the mm10 mouse reference genome using Bowtie2 with default end-to-end alignment settings. Only uniquely mapped, valid read pairs were retained, while unligated ends, self-circles, and duplicate reads were filtered out by HiC-Pro. Valid interaction pairs were binned into genome-wide contact matrices at multiple resolutions (5kb, 10 kb, 25kb, 50 kb, 100 kb), and ICE normalization was applied to correct for systematic biases. Normalized contact matrices were exported in .hic format.
Assembly: mm10
Supplementary files format and content: hic file; file contents: contact matrices, normalization vector, metadata, master index

source_name: Spleen

extract_protocol:
Hi-C libraries were prepared using a modified three-enzyme Hi-C (3e Hi-C) protocol (Ren, G. el al. Mol Cell 2017). Wild-type (WT) and CD8CreSatb1fl/fl (KO) mice were infected with LCMV Clone 13 and sacrificed at day 21 post-infection. Antigen-specific CD8⁺ T cells were sorted, and 300,000 to 500,000 cells per sample were collected for Hi-C. Cells were crosslinked with 1% formaldehyde for 10 minutes at 25 °C and quenched with 2.5 M glycine.
Cells were crosslinked with 1% formaldehyde for 10 minutes at 25 °C and quenched with 2.5 M glycine. Fixed cells were lysed in 10 mL of ice-cold lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% NP-40) supplemented with protease inhibitors and incubated at 4 °C for 1 hour. Nuclei were pelleted and permeabilized in 0.1% SDS in CutSmart buffer (NEB) at 65 °C for 10 minutes, followed by quenching with Triton X-100 to a final concentration of 1%. Chromatin was digested with the restriction enzymes FatI, CviQI, and BfaI (New England Biolabs) at 37 °C for 20 minutes. Digestion was stopped by two washes with buffer containing 10 mM NaCl, 1 mM EDTA, and 0.1% Triton X-100. DNA ends were filled in using Klenow enzyme in the presence of dCTP, dGTP, dTTP, and biotin-14-dATP to label ligation junctions. Proximity ligation was performed using T4 DNA ligase under dilute conditions to promote intranuclear ligation. After reverse crosslinking, DNA was sheared to 200–700 bp fragments using a Diagenode Bioruptor. Fragmented DNA was end-repaired, and biotinylated ligation products were purified using Dynabeads MyOne Streptavidin C1 beads (Invitrogen). Sequencing libraries were constructed by ligating Illumina-compatible paired-end adapters and performing PCR amplification. Size selection (200–700 bp) was performed using E-gel electrophoresis, and libraries were sequenced on an Illumina NovaSeq 6000 platform with 50 bp paired-end reads.

treatment_protocol: WT (Satb1+/+ CD8Cre) and KO (Satb1 fl/fl CD8Cre) mice were infected with LCMV Cl13 for 21 days, then antigen-specific CD8+ T cell were isoloated from spleens via FACs-sorting

value: Spleen

value: CD8+ T cell

value: Satb1 +/+ CD8Cre

value: wild-type, without Satb1 delection


title: HiC_KO

description: Library name: KO

value: Satb1 fl/fl CD8Cre

value: knock-out, with Satb1 deletion


title: RNA_IFNgamma_24h_R1_2

tag: stimulus

value: IFNgamma


title: RNA_IFNgamma_2h_R1_1

tag: time point


title: 85

value: Mushroom bodies (brain region)

value: Generalist


title: BMDM, hWDFY3KI/KI, replicate 5

city: New York

first: Hanrui

state: United States

address: 630 West 168th Street

institute: Columbia University Irving Medical Center

description:
Library name: XH010
hWDFY3_BMDM_5

data_processing:
Raw sequencing reads were mapped to the mouse genome version GRCm39 (M28) using Salmon (version 1.6.0) to obtain transcript abundance counts. MultiQC was used to generate quality control reports based on Salmon read mapping results.
The transcript-level count information was summarized to the gene level using tximport (version 1.20.0).
Differential expression was assessed using DESeq2 (version 1.34.0). Genes with an absolute fold change > 1.5 and false discovery rate (FDR) < 0.05 were considered as differentially expressed (DE).
Assembly: mm10
Supplementary files format and content: tab-delimited text file for salmon counts
Supplementary files format and content: tab-delimited text file for DESeq2 normalized counts by rld

source_name: BMDM

growth_protocol: Bone marrow (BM) cells from 6-8 week old mice were isolated by flushing femurs and tibia with DMEM basal medium using 10 mL syringes with 22G needles (day 0). The isolated BM cells were cultured at 37°C, 5% CO2 on non-tissue-culture-treated vessels for 7-10 days in BMDM culture medium containing DMEM supplemented with 10% (vol/vol) heat-activated fetal bovine serum (HI-FBS), 20% (vol/vol) L-929 fibroblast conditioned medium, and 2 mM L-Glutamine. During differentiation, the growth medium was replaced with fresh medium 96 h after seeding and then every 2-3 days. BMDMs were harvested at day 7 for RNA extraction.

extract_protocol:
Total RNAs were extracted from BMDMs (6-8 weeks old male mice: 5 Ctrl and 5 hWDFY3KI/KI) using the Quick-RNA miniprep plus kit (Zymo).
With ~1 µg input RNA, strand-specific, poly(A)+ libraries were prepared and sequenced at 20 million 100-bp paired-end reads per sample.

value: BMDM

value: Human WDFY3 overexpression

tag: Sex

value: Male

tag: age

value: 6-8 weeks


title: BMDM, hWDFY3KI/KI, replicate 2

description:
Library name: XH007
hWDFY3_BMDM_2


title: BMDM, hWDFY3KI/KI, replicate 4

description:
Library name: XH009
hWDFY3_BMDM_4


title: 84

value: Guard


title: 62


title: BMDM, hWDFY3KI/KI, replicate 3

description:
Library name: XH008
hWDFY3_BMDM_3


title: RNA_IFNbeta_8h_R1_2

value: bone marrow-derived macrophages

value: IFNbeta

tag: bio-replicate

tag: batch


title: 10 hours post fertilization

description: Library name: 10hr-SCI7T007-SCI5T007

value: embryo

value: wt


title: 41

tag: input reads

tag: mapped reads


title: BMDM, Ctrl, replicate 5

description:
Library name: XH005
CTRL_BMDM_5

value: Wild-type control


title: BMDM, Ctrl, replicate 4

description:
Library name: XH004
CTRL_BMDM_4


title: RNA_IFNbeta_6h_R1_1

value: Quant-seq

value: female


title: BMDM, hWDFY3KI/KI, replicate 1

description:
Library name: XH006
hWDFY3_BMDM_1


title: 79

tag: assigned reads

tag: reads aligned_to_dwv_genome

value: Forager


title: BMDM, Ctrl, replicate 3

description:
Library name: XH003
CTRL_BMDM_3


title: BMDM, Ctrl, replicate 2

description:
Library name: XH002
CTRL_BMDM_2


title: BMDM, Ctrl, replicate 1

description:
Library name: XH001
CTRL_BMDM_1


title: 227

tag: tissue

tag: reads aligned_to_vdv_genome


title: RNA_untreated_24h_R1_2

value: untreated


title: Control_6

source_name: Cortex

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using poly A enrichment with NovaSeq6000 kit according to manufacturers protocol.

treatment_protocol: Neuronal cultures were transduced at 7 d.i.v. with a lentiviral Ifng overexpression construct and were harvested after an additional 10 d.i.v.

value: Cortex

value: Neuronal culture

value: Control


title: RNA_IFNbeta_24h_R1_2


title: RNA_IFNbeta_2h_R1_1


title: 149

value: Mushroom bodies (brain region)

tag: replicate (note

tag: genotype

value: Non-Responder


title: 88

tag: treatment

value: Generalist


title: IFNG_4

tag: cell type

value: IFNy


title: 10


title: Control_4


title: 105


title: IFNG_3


title: RNA_Candida_8h_R1_2

tag: protocol

tag: timepoint after_thawing

value: Candida


title: RNA_untreated_0h_R1_1

value: bone marrow-derived macrophages

tag: stimulus

tag: time point


title: RNA_Candida_6h_R1_1

tag: Sex


title: IFNG_5


title: IFNG_2


title: Control_1


title: IFNG_6


title: 148

value: Guard


title: Control_3


title: RNA_IFNgamma_4h_R1_1

value: IFNgamma

tag: bio-replicate


title: RNA_IFNbeta_4h_R1_1

value: IFNbeta

tag: batch


title: 28

tag: input reads


title: RNA_Candida_4h_R1_1


title: Psmb8_6

value: Psmb8 overexpression


title: Control_5


title: 130

tag: mapped reads


title: Psmb8_4


title: Psmb8_5


title: RNA_Candida_24h_R1_2

value: Quant-seq


title: IFNG_1


title: 59

tag: assigned reads


title: Control_2


title: 175

tag: reads aligned_to_dwv_genome


title: Psmb8_2

tag: tissue


title: RNA_Candida_2h_R1_1

value: female


title: Psmb5_6

value: Psmb5 overexpression


title: 71

tag: reads aligned_to_vdv_genome


title: Psmb8_1


title: 83

tag: replicate (note

value: Forager


title: ATAC_untreated_24h_R2_2

data_processing:
Base calling was performed by Illumina Real Time Analysis (2.7.7) software and the base calls were converted to short reads using the IlluminaBasecallsToSam tool from the Picard toolkit (2.19.2). Sequencing adapters were removed using the software fastp (0.20.1). Bowtie2 (2.4.4) was used for the alignment of the short reads (representing locations of transposition events) to the GRCm38 (mm10) assembly of the mouse genome using the “–very-sensitive” parameter. PCR duplicates were marked using samblaster (0.1.24). Aligned BAM files were then sorted, filtered using ENCODE blacklisted regions, and indexed using samtools (1.12).
To detect the open chromatin regions, peak calling was performed using MACS2 (2.2.7.1) using the “–nomodel”, “–keep-dup auto” and “–extsize 147” options on each sample. A consensus region set was generated by merging the identified peak summits, extended by 250 bp on both sides using the slop function from bedtools (2.27.1) and pybedtools (0.8.1), across all samples while again discarding peaks overlapping blacklisted features as defined by the ENCODE project. A total of 142,831 genomic regions were obtained and were annotated using the annotatePeaks function from Homer (4.11).
The consensus region set was used to quantify the chromatin accessibility in each sample by summing the number of reads overlapping each consensus region. The consensus region set, and sample-wise quantification of accessibility was performed using bedtools (2.27.1) and pybedtools (0.8.1). The data processing was performed using a Snakemake workflow publicly shared on GitHub (https://github.com/epigen/atacseq_pipeline).
Assembly: mm10
Supplementary files format and content: ATAC_raw_counts.csv: comma-separated read count file of the ATAC-seq data
Supplementary files format and content: ATAC_region_annotation.csv: comma-separated annotation on the genomic location and HOMER gene annotation of each consensus region in the ATAC-seq data

extract_protocol:
At the end of the treatment period, cells were washed with PBS and then scraped in 0.5 ml PBS per million cells. 50,000 cells were directly used for ATAC-seq. Cells were centrifuged at 4 °C and 500 rcf for 5 minutes. The supernatant was removed, and cells were lysed and tagmented at 37 °C for 30 minutes in the following mixture (per sample): 9.75 µl water, 2x transposase buffer (Illumina cat. No. 20034197), 0.5 µl PIC (Roche cat. No. 11873580001), 2 µl TDE1 DNA Enzyme (Illumina cat. No. 20034197), and 0.25 µl 1% Digitonin (Promega cat. No. G9441). The DNA was cleaned using the Qiagen MinElute kit (Qiagen cat. No. 28006) according to the manufacturer’s recommendations and eluted in 12 µl EB buffer.
To estimate the enrichment cycle number, a qPCR was set up using 2.9 µl water, 0.5 µl index primer 1 noMX and Index primer 2.1 barcode, respectively, 0.1 µl 100x SYBR green (Invitrogen cat. No. S7563), 5 µl NEBnext HF 2x MM (NEB cat. No. M0541L), and 1 µl eluted sample, and run as follows: 5 min at 72 °C, 30 seconds at 98 °C, 25x cycles of (10 sec at 98 °C, 30 sec at 63 °C and 1 min at 72 °C). The cycle number was determined based on the amplification entering the early exponential phase. Subsequently, an enrichment PCR was set up with 10 µl water, 2.5 µl Index primer 1 noMX and Index primer 2 barcode, respectively, 25 µl NEBnext HF 2x MM (NEB cat. No. M0541L), and 10 µl eluted sample (see Buenrostro et al. 2013 for primer sequences https://doi.org/10.1038/nmeth.2688). A left-sided 1.6x clean-up was performed using AMPure XP beads (Beckman Coulter cat. No. A63881). To that end, 80 µl beads were added and the sample incubated for 10 minutes at room temperature, followed by 10 minutes on a magnetic rack at room temperature. The beads were washed twice with 80% EtOH, air-dried for 2 minutes and the DNA eluted in 50 µl EB buffer. A second 0.5/1.4 double-sided clean-up was performed. 25 µl beads were added and the sample incubated 10 minutes at room temperature followed by 10 minutes on a magnetic rack as before. The supernatant was transferred to a new well and mixed with additional 45 µl beads, and the left-sided clean-up continued as described above. The DNA was eluted in 15 µl EB buffer

value: ATAC-seq

value: untreated


title: Psmb5_3

value: Cortex

value: Neuronal culture


title: 61

value: Mushroom bodies (brain region)

tag: genotype


title: Psmb5_4

tag: treatment


title: Psmb5_5

tag: cell type


title: Psmb5_2


title: 110


title: Psmb5_1


title: ATAC_LPS_8h_R2_2

tag: protocol

value: LPS


title: ATAC_LPS_24h_R2_2

tag: timepoint after_thawing


title: mSc_6

value: mSc overexpression


title: mSc_5


title: 106

value: Generalist


title: mSc_4


title: ATAC_Listeria_8h_R2_2

value: bone marrow-derived macrophages

tag: stimulus

value: Listeria


title: Psmb8_3


title: ATAC_Listeria_24h_R2_2

tag: time point


title: mSc_3


title: mSc_1


title: 76


title: 45


title: mSc_2


title: ATAC_LCMV_8h_R2_2

value: LCMV

tag: Sex


title: L1_si-Jmjd1a_D8_RNA-seq

first: Yoshihiro

institute: Akita University Graduate School of Medicine

data_processing:
RNA-seq reads were aligned to the mouse mm9 genome using STAR2.
The FPKM tables of RNA-seq were assessed using GFOLD with the GENCODE comprehensive gene annotation set M1 release.
As for ChIP-seq, all bound DNA fragments were mapped UCSC build mm9 assembly of the mouse genome by the mapping program Bowtie2 based on the 5'-side 36-bp sequences.
Signals of ChIP-seq occupancy are presented as counts per million mapped reads (CPM) by using deepTools bamCoverage.
SICER2 program was used for H3K27ac and H3K27me3 under the following parameters: window size 200 bp; gap size 400 bp ; E-value threshold, 100. The FindPeaks function of HOMER was used for H3K9me2 and JMJD1A with histone mode. MACS3 program was used for NFIC with default setting.
Assembly: mm9
Supplementary files format and content: tab files (RNA-seq)
Supplementary files format and content: bigwig and txt files (ChIP-seq)

extract_protocol:
Total RNA was isolated using ISOGEN (Nippongene) following manufacturer's protocol. Sonicated nuclear fraction was incubated with each antibody and protein-DNA complexes were isolated.
Libraries were prepared according to Illumina's instructions.

tag: cell line

tag: time

value: Day 8


title: ATAC_LCMV_24h_R2_2

tag: bio-replicate

tag: batch


title: WT, scRNA-Seq

description: 10X Genomics

data_processing:
Raw reads were aligned to mouse mm10 genome using CellRanger (v7.2.0).
Counts from ambient RNA was removed using CellBender (v0.3.0) and doublets were removed using scDblFinder (v1.18.0).
Preprocessing was performed using Seurat (v5.0.1).
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: Not applicable, primary tissue/cells

extract_protocol:
Libraries were prepared using a 10X Genomics 3’GEX Kits following the manufacturer's protocols.
Libraries were then sequenced on an Illumina NovaSeq S2 using 2x50bp paired end sequencing with a targeted depth of 50,000 read pairs per cell.

treatment_protocol: Mice were fasted for 16 h and gavaged with olive oil for 2 h. Small intestine lamina propria mononuclear cells were isolated using the method described in the bulk mRNA sequencing section. Single Live EPCAM- Ter119- CD31- CD45+ cells were sorted from 10- to 12-week-old female littermates (n = 3 /genotype) on a BD Aria FACS sorter. 100,000 cells were sorted from each mouse and pooled together before loading to a Chromium Single Cell Controller (10X Genomics).

value: Small Intestine Lamina Propria

value: mononuclear immune cells

value: Aster-A F/F

value: 2 h Olive Oil gavage


title: AdCD4, scRNA-Seq

description: 10X Genomics

value: CD4-Cre; Aster-A F/F


title: 161

tag: input reads

tag: mapped reads

tag: assigned reads

value: Non-Responder


title: 102

tag: tissue

tag: reads aligned_to_dwv_genome

tag: reads aligned_to_vdv_genome

value: Forager


title: L1_si-Ctr_D8_RNA-seq

tag: treatment

value: si-Ctr


title: ATAC_IFNgamma_24h_R2_2

tag: cell type

value: ATAC-seq

value: IFNgamma

value: female


title: ATAC_IFNgamma_8h_R2_2

tag: protocol


title: CROPseq_KO150_C3_GEX

description:
polyA RNA
CROPseq_KO150_C3_raw_feature_bc_matrix.h5
CROPseq_KO150_C3_filtered_feature_bc_matrix.h5

data_processing:
Raw basecalls from the sequencer were demultiplexed and converted to FASTQ format using the 10x Genomics' Cell Ranger (3.0.2) command “mkfastq”.
FASTQ files were then aligned to the mouse reference genome assembly GRCm38 (mm10), and count matrices were generated for each sample based on genome annotation v93 using the Cell Ranger command “count”.
Assembly: mm10
Supplementary files format and content: raw and filtered feature barcode matrices: .h5 archives of CellRanger output
Supplementary files format and content: feature_reference.csv: comma-separated feature reference file for ADT, HTO, GDO quantification and annotation
Library strategy: CROP-seq

growth_protocol: RAW264.7-Cas9 (transduced with vector from Addgene #52962) cell lines were cultivated in standard media (DMEM-GlutaMAX (Gibco cat. No. 31966047) with 10% FBS and 1x penicillin-streptomycin (Gibco cat. No. 15140122)) supplemented with 20 µg/ml blasticidin (InvivoGen cat. No. ant-bl-1). The cell line was split every 3-4 days after detachment with 0.05x Trypsin-EDTA (Gibco cat. No. 25300054) and kept at low passage number. All cells were grown at 37 °C, 5% CO2 and regularly tested for potential contamination with mycoplasma (Lonza cat. No. LT07-318)

extract_protocol:
Cells were washed with ice cold FACS buffer, scraped without trypsin, and centrifuged at 4 °C for 5 min at 500 rcf. The cells were resuspended in 100 µl FACS buffer with 1 µg TrueStain FcX PLUS (Biozym cat. No. 156604) per 1 million cells and incubated on ice for 10 minutes. Afterward, 100 µl FACS buffer containing CITE-seq antibodies (see Table S6; 1 µl per antibody per 10 million cells for KO15; 0.33 µl per 10 million cells for KO150) as well as TotalSeq-C hashing antibodies (BioLegend; 1 µl antibody per per 10 million cells) were added, and the incubation continued at 4 °C for 30 minutes. Cells were washed twice with FACS buffer and resuspended in fresh FACS buffer with Zombie NIR viability staining (BioLegend cat. No. 423105) at a 1:1000 dilution. Cells were sorted on a FACS Aria by selecting NIR negative (live) cells that were mCherry positive. The replicates of the same condition for the KO150 library were sorted, with 50,000 cells each going into three tubes. Superfluous supernatant was reduced using the VRNxT machine and processed according to the Chromium Next GEM Single Cell 5’ v2 Dual Indexing kit with Feature Barcoding (10x Genomics cat. No. 1000263), with the following modifications. At the GEM generation, step 1.1, an additional 0.5 µl of a 10 µM stock CROPseq-3P5P_gRNA_RT primer (5'-AAGCAGTGGTATCAACGCAGAGTACCAAGTTGTTAACGGTCTAGCC-3') were added to the master mix.  To limit technical bias/batch effects we sorted each of the three RAW264.7 thaws (individually hashtagged) together (1:1:1) for a total of three tubes per treatment (3 tubes x 3 treatments = 9 samples). One tube per treatment was processed on a 10x chip resulting in a total of 3 chips being used. The treatment is indicated by the letter in the library name, the chip/tube number is indicated by the number (e.g. "_A1_").
The cDNA amplification was performed for 11 cycles, and during the SPRI select clean-up, the remaining 80 µl supernatant were mixed with 30 µl beads to perform a 1.2x clean-up, otherwise following the 2.3B Cell Surface Protein protocol. 5 µl of the guide RNA fraction were amplified with the following PCR mix: 3 µl of a 10 µM fwd/rev CROPseq-3P5P i7/i5 primer mix (see Table S6), 2x Kapa HIFI MM (Roche cat. No. 7958935001), 0.5 µl SYBR green (Life Technologies cat. No. S7563) and 16.5 µl water. The PCR was run for 30 sec at 98 °C, 7 to 8 cycles of (10 sec at 98 °C, 30 sec at 70 °C and 20 sec at 72 °C), followed by 1 min at 72 °C. The amount of amplification cycles was determined by inspecting the fluorescence signal. The reaction was stopped once the amplification has reached the early exponential phase. A left-sided 0.9x SPRI bead clean-up was performed, and the DNA was eluted in 15 µl EB buffer. Correct amplification was determined using a Bioanalyzer HS chip, confirming a peak around 272 bp for the guide RNA library. For the KO15 and KO150 experiments, cell surface and guide RNA libraries were added to the gene expression library at 10% and 15% of the final concentration, respectively.

treatment_protocol: 12 million RAW264.7 cells were seeded per 10 cm dish in triplicates at least three hours before transduction start. For the scaled-up screen (KO150) we used cells from three independent frozen vials thawed at different days. To transduce the cells, 8 µg/ml polybrene (Sigma Aldrich, cat. No. H9268-5G) and virus dilutions were added to achieve an MOI of 0.1. After 24 hours, the cells were detached, and 95% of these cells were seeded in fresh media without polybrene on 15 cm dishes. The remaining 5% of cells were seeded in a 6-well plate and kept for MOI assessment via FACS after three days, for which cells were scraped in FACS buffer with 1x DAPI stain (BioLegend, cat. No. 422801). mCherry signal (i.e., guide RNA positive) among DAPI negative cells (live gate) was measured to confirm MOI. Five days after transduction, the cells were detached and single-cell filtered through a 45 µm filter, and 25-30 million cells per treatment condition were seeded in standard media without antibiotics (no penicillin/streptomycin and blasticidin). Three hours after cell seeding, Listeria monocytogenes LO28 were added for the 24 hour time point with an MOI of 20, while the other time points were started the next day, in order to finish at a single shared time point. All treatments were harvested at the same time at 6 days after transduction. Gentamicin addition was added to Listeria monocytogenes LO28 treated wells after 1 hour. Two hours later, the media was exchanged to standard media without antibiotics supplemented with 5 µg/ml gentamicin.

value: Listeria 24h

tag: library type

value: mRNA


title: 86

value: Mushroom bodies (brain region)

tag: replicate (note

tag: genotype


title: CROPseq_KO150_C3_ADT_HTO

description:
Antibody-derived oligonucleotide (ADT) for surface protein measurements and Hashtag-derived oligonucleotides (HTO) for multiplexing
CROPseq_KO150_C3_raw_feature_bc_matrix.h5
CROPseq_KO150_C3_filtered_feature_bc_matrix.h5

library_source: other

molecule: protein


title: CROPseq_KO150_C3_GDO

description:
Guide-derived oligonucleotide (GDO)
CROPseq_KO150_C3_raw_feature_bc_matrix.h5
CROPseq_KO150_C3_filtered_feature_bc_matrix.h5

molecule: other

value: GDO


title: 239


title: ATAC_IFNbeta_8h_R2_2

value: bone marrow-derived macrophages

tag: timepoint after_thawing

tag: stimulus

value: IFNbeta

tag: time point

tag: Sex


title: CROPseq_KO150_C2_GDO

description:
Guide-derived oligonucleotide (GDO)
CROPseq_KO150_C2_raw_feature_bc_matrix.h5
CROPseq_KO150_C2_filtered_feature_bc_matrix.h5

tag: cell line


title: CROPseq_KO150_C2_GEX

description:
polyA RNA
CROPseq_KO150_C2_raw_feature_bc_matrix.h5
CROPseq_KO150_C2_filtered_feature_bc_matrix.h5


title: CROPseq_KO150_C2_ADT_HTO

description:
Antibody-derived oligonucleotide (ADT) for surface protein measurements and Hashtag-derived oligonucleotides (HTO) for multiplexing
CROPseq_KO150_C2_raw_feature_bc_matrix.h5
CROPseq_KO150_C2_filtered_feature_bc_matrix.h5


title: ATAC_IFNbeta_24h_R2_2

tag: bio-replicate

tag: batch


title: CROPseq_KO150_C1_GEX

description:
polyA RNA
CROPseq_KO150_C1_raw_feature_bc_matrix.h5
CROPseq_KO150_C1_filtered_feature_bc_matrix.h5


title: 198

tag: input reads

tag: mapped reads

tag: assigned reads

value: Guard


title: ATAC_Candida_8h_R2_2

value: Candida


title: CROPseq_KO150_C1_ADT_HTO

description:
Antibody-derived oligonucleotide (ADT) for surface protein measurements and Hashtag-derived oligonucleotides (HTO) for multiplexing
CROPseq_KO150_C1_raw_feature_bc_matrix.h5
CROPseq_KO150_C1_filtered_feature_bc_matrix.h5


title: CROPseq_KO150_B3_GEX

description:
polyA RNA
CROPseq_KO150_B3_raw_feature_bc_matrix.h5
CROPseq_KO150_B3_filtered_feature_bc_matrix.h5

value: Listeria 6h


title: 156

tag: tissue

tag: reads aligned_to_dwv_genome

tag: reads aligned_to_vdv_genome


title: CROPseq_KO150_C1_GDO

description:
Guide-derived oligonucleotide (GDO)
CROPseq_KO150_C1_raw_feature_bc_matrix.h5
CROPseq_KO150_C1_filtered_feature_bc_matrix.h5

tag: treatment


title: ATAC_Candida_24h_R2_2

tag: cell type

tag: protocol


title: CROPseq_KO150_B3_GDO

description:
Guide-derived oligonucleotide (GDO)
CROPseq_KO150_B3_raw_feature_bc_matrix.h5
CROPseq_KO150_B3_filtered_feature_bc_matrix.h5

tag: library type


title: CROPseq_KO150_B3_ADT_HTO

description:
Antibody-derived oligonucleotide (ADT) for surface protein measurements and Hashtag-derived oligonucleotides (HTO) for multiplexing
CROPseq_KO150_B3_raw_feature_bc_matrix.h5
CROPseq_KO150_B3_filtered_feature_bc_matrix.h5


title: ATAC_untreated_8h_R1_2

tag: timepoint after_thawing

value: untreated


title: 192

tag: replicate (note

tag: genotype


title: 92

value: Generalist


title: CROPseq_KO150_B2_GDO

description:
Guide-derived oligonucleotide (GDO)
CROPseq_KO150_B2_raw_feature_bc_matrix.h5
CROPseq_KO150_B2_filtered_feature_bc_matrix.h5


title: ATAC_untreated_24h_R1_2

tag: stimulus

tag: time point

tag: Sex


title: ATAC_LPS_8h_R1_2

value: LPS

tag: bio-replicate

tag: batch


title: CROPseq_KO150_B1_GDO

description:
Guide-derived oligonucleotide (GDO)
CROPseq_KO150_B1_raw_feature_bc_matrix.h5
CROPseq_KO150_B1_filtered_feature_bc_matrix.h5

tag: cell line


title: 13

tag: input reads

tag: mapped reads

tag: assigned reads

value: Non-Responder


title: CROPseq_KO150_B2_ADT_HTO

description:
Antibody-derived oligonucleotide (ADT) for surface protein measurements and Hashtag-derived oligonucleotides (HTO) for multiplexing
CROPseq_KO150_B2_raw_feature_bc_matrix.h5
CROPseq_KO150_B2_filtered_feature_bc_matrix.h5


title: 68

tag: tissue

tag: reads aligned_to_dwv_genome

tag: reads aligned_to_vdv_genome


title: CROPseq_KO150_A3_GEX

description:
polyA RNA
CROPseq_KO150_A3_raw_feature_bc_matrix.h5
CROPseq_KO150_A3_filtered_feature_bc_matrix.h5

tag: treatment


title: CROPseq_KO150_B1_ADT_HTO

description:
Antibody-derived oligonucleotide (ADT) for surface protein measurements and Hashtag-derived oligonucleotides (HTO) for multiplexing
CROPseq_KO150_B1_raw_feature_bc_matrix.h5
CROPseq_KO150_B1_filtered_feature_bc_matrix.h5

tag: library type


title: 75

value: Forager


title: CROPseq_KO150_A3_GDO

description:
Guide-derived oligonucleotide (GDO)
CROPseq_KO150_A3_raw_feature_bc_matrix.h5
CROPseq_KO150_A3_filtered_feature_bc_matrix.h5


title: ATAC_LPS_24h_R1_2

tag: cell type

tag: protocol

value: ATAC-seq

tag: timepoint after_thawing


title: 94

tag: replicate (note

tag: genotype


title: CROPseq_KO150_A3_ADT_HTO

description:
Antibody-derived oligonucleotide (ADT) for surface protein measurements and Hashtag-derived oligonucleotides (HTO) for multiplexing
CROPseq_KO150_A3_raw_feature_bc_matrix.h5
CROPseq_KO150_A3_filtered_feature_bc_matrix.h5


title: 77


title: CROPseq_KO150_A2_GEX

description:
polyA RNA
CROPseq_KO150_A2_raw_feature_bc_matrix.h5
CROPseq_KO150_A2_filtered_feature_bc_matrix.h5


title: CROPseq_KO150_A2_GDO

description:
Guide-derived oligonucleotide (GDO)
CROPseq_KO150_A2_raw_feature_bc_matrix.h5
CROPseq_KO150_A2_filtered_feature_bc_matrix.h5


title: ATAC_Listeria_24h_R1_2

tag: stimulus

value: Listeria

tag: time point

tag: Sex


title: CROPseq_KO150_A2_ADT_HTO

description:
Antibody-derived oligonucleotide (ADT) for surface protein measurements and Hashtag-derived oligonucleotides (HTO) for multiplexing
CROPseq_KO150_A2_raw_feature_bc_matrix.h5
CROPseq_KO150_A2_filtered_feature_bc_matrix.h5

tag: cell line


title: CROPseq_KO150_B2_GEX

description:
polyA RNA
CROPseq_KO150_B2_raw_feature_bc_matrix.h5
CROPseq_KO150_B2_filtered_feature_bc_matrix.h5


title: 51

tag: input reads


title: CROPseq_KO150_A1_GEX

description:
polyA RNA
CROPseq_KO150_A1_raw_feature_bc_matrix.h5
CROPseq_KO150_A1_filtered_feature_bc_matrix.h5


title: ATAC_LCMV_8h_R1_2

value: LCMV

value: female

tag: bio-replicate

tag: batch


title: CROPseq_KO150_A1_GDO

description:
Guide-derived oligonucleotide (GDO)
CROPseq_KO150_A1_raw_feature_bc_matrix.h5
CROPseq_KO150_A1_filtered_feature_bc_matrix.h5


title: 66

tag: tissue

tag: mapped reads

tag: assigned reads

value: Nurse


title: ATAC_LCMV_24h_R1_2


title: 91

value: Mushroom bodies (brain region)

tag: reads aligned_to_dwv_genome

tag: reads aligned_to_vdv_genome

tag: treatment


title: CROPseq_KO15_2_GEX

description:
polyA RNA
CROPseq_KO15_2_raw_feature_bc_matrix.h5
CROPseq_KO15_2_filtered_feature_bc_matrix.h5

extract_protocol:
Cells were washed with ice cold FACS buffer, scraped without trypsin, and centrifuged at 4 °C for 5 min at 500 rcf. The cells were resuspended in 100 µl FACS buffer with 1 µg TrueStain FcX PLUS (Biozym cat. No. 156604) per 1 million cells and incubated on ice for 10 minutes. Afterward, 100 µl FACS buffer containing CITE-seq antibodies (see Table S6; 1 µl per antibody per 10 million cells for KO15; 0.33 µl per 10 million cells for KO150) as well as TotalSeq-C hashing antibodies (BioLegend; 1 µl antibody per per 10 million cells) were added, and the incubation continued at 4 °C for 30 minutes. Cells were washed twice with FACS buffer and resuspended in fresh FACS buffer with Zombie NIR viability staining (BioLegend cat. No. 423105) at a 1:1000 dilution. Cells were sorted on a FACS Aria by selecting NIR negative (live) cells that were mCherry positive. For the KO15 transduced cells, two tubes with 50,000 cells per condition were sorted. Superfluous supernatant was reduced using the VRNxT machine and processed according to the Chromium Next GEM Single Cell 5’ v2 Dual Indexing kit with Feature Barcoding (10x Genomics cat. No. 1000263), with the following modifications. At the GEM generation, step 1.1, an additional 0.5 µl of a 10 µM stock CROPseq-3P5P_gRNA_RT primer (5'-AAGCAGTGGTATCAACGCAGAGTACCAAGTTGTTAACGGTCTAGCC-3') were added to the master mix.
The cDNA amplification was performed for 11 cycles, and during the SPRI select clean-up, the remaining 80 µl supernatant were mixed with 30 µl beads to perform a 1.2x clean-up, otherwise following the 2.3B Cell Surface Protein protocol. 5 µl of the guide RNA fraction were amplified with the following PCR mix: 3 µl of a 10 µM fwd/rev CROPseq-3P5P i7/i5 primer mix (see Table S6), 2x Kapa HIFI MM (Roche cat. No. 7958935001), 0.5 µl SYBR green (Life Technologies cat. No. S7563) and 16.5 µl water. The PCR was run for 30 sec at 98 °C, 7 to 8 cycles of (10 sec at 98 °C, 30 sec at 70 °C and 20 sec at 72 °C), followed by 1 min at 72 °C. The amount of amplification cycles was determined by inspecting the fluorescence signal. The reaction was stopped once the amplification has reached the early exponential phase. A left-sided 0.9x SPRI bead clean-up was performed, and the DNA was eluted in 15 µl EB buffer. Correct amplification was deter-mined using a Bioanalyzer HS chip, confirming a peak around 272 bp for the guide RNA library. For the KO15 and KO150 experiments, cell surface and guide RNA libraries were added to the gene expression library at 10% and 15% of the final concentration, respectively.

treatment_protocol: 12 million RAW264.7 cells were seeded per 10 cm dish in triplicates at least three hours before transduction start. To transduce the cells, 8 µg/ml polybrene (Sigma Aldrich, cat. No. H9268-5G) and virus dilutions were added to achieve an MOI of 0.1. After 24 hours, the cells were detached, and 95% of these cells were seeded in fresh media without polybrene on 15 cm dishes. The remaining 5% of cells were seeded in a 6-well plate and kept for MOI assessment via FACS after three days, for which cells were scraped in FACS buffer with 1x DAPI stain (BioLegend, cat. No. 422801). mCherry signal (i.e., guide RNA positive) among DAPI negative cells (live gate) was measured to confirm MOI. For the KO15 library, we selected plates with 10% mCherry positive cells, counted and expanded them, and exchanged media. Five days after transduction, the cells were detached and single-cell filtered through a 45 µm filter, and 25-30 million cells per treatment condition were seeded in standard media without antibiotics (no penicillin/streptomycin and blasticidin). Three hours after cell seeding, Listeria monocytogenes LO28 were added for the 24 hour time point with an MOI of 20, while the other time points were started the next day, in order to finish at a single shared time point. All treatments were harvested at the same time at 6 days after transduction. Gentamicin addition was added to Listeria monocytogenes LO28 treated wells after 1 hour. Two hours later, the media was exchanged to standard media without antibiotics supplemented with 5 µg/ml gentamicin.

value: mixed sample (untreated, Listeria 2h, Listeria 6h)

tag: library type

value: mRNA


title: ATAC_IFNgamma_8h_R1_2

tag: cell type

value: bone marrow-derived macrophages

tag: protocol

tag: timepoint after_thawing

value: IFNgamma


title: 166

tag: replicate (note

tag: genotype


title: CROPseq_KO15_2_GDO

description:
Guide-derived oligonucleotide (GDO)
CROPseq_KO15_2_raw_feature_bc_matrix.h5
CROPseq_KO15_2_filtered_feature_bc_matrix.h5

value: GDO


title: 70


title: CROPseq_KO15_2_ADT_HTO

description:
Antibody-derived oligonucleotide (ADT) for surface protein measurements and Hashtag-derived oligonucleotides (HTO) for treatment multiplexing
CROPseq_KO15_2_raw_feature_bc_matrix.h5
CROPseq_KO15_2_filtered_feature_bc_matrix.h5


title: ATAC_Listeria_8h_R1_2

tag: stimulus

tag: time point

tag: Sex


title: CROPseq_KO15_1_ADT_HTO

description:
Antibody-derived oligonucleotide (ADT) for surface protein measurements and Hashtag-derived oligonucleotides (HTO) for treatment multiplexing
CROPseq_KO15_1_raw_feature_bc_matrix.h5
CROPseq_KO15_1_filtered_feature_bc_matrix.h5

tag: cell line


title: ATAC_IFNbeta_8h_R1_2

value: IFNbeta

tag: bio-replicate

tag: batch


title: ATAC_IFNgamma_24h_R1_2


title: 32

tag: tissue

tag: input reads

tag: mapped reads

value: Guard


title: ATAC_IFNbeta_24h_R1_2


title: CROPseq_KO15_1_GDO

description:
Guide-derived oligonucleotide (GDO)
CROPseq_KO15_1_raw_feature_bc_matrix.h5
CROPseq_KO15_1_filtered_feature_bc_matrix.h5


title: ATAC_Candida_8h_R1_2

value: Candida


title: Small intestine_YP147_2

city: Nanjing

first: Mangge

last: Zou

address: No.6 Building, Life Science TechTown, 568 Longmian Avenue Jiangning District

institute: Legend Biotech

data_processing:
Sequencing reads were mapped to mouse genome (mm10) using STAR and aligned reads to annotated genes were quantified with htseq-count.
Calculated read counts were further processed with DESeq2 for quantiﬁcation of differential gene expression. Raw read counts were converted to RPKM (reads per kilobase of exon length per million mapped reads) values.
Assembly: mm10
Supplementary files format and content: Comma-separated values (.csv) file of DESeq2 results.

source_name: Small intestine

extract_protocol:
Dendritic cells were FACS sorted into RLT+ lysis buffer (Qiagen) which contained 10 µl/ml β-mercaptoethanol (Roth). In the following, the total RNA was extracted with the RNeasy Plus Micro kit (Qiagen) according to manufacturer`s instructions.
RNA libcDNA conversion was carried out using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech Laboratories) according to manufacturer’s instructions, followed by PCR product purification with Agencourt AMPure XP magnetic beads (Beckman Coulter). Libraries were prepared with the Nextera XT DNA Library Prep Kit (Illumina) employing enzymatic tagmentation and simultaneous adapter ligation before subsequent indexing and fragment amplification. PCR product clean-up and size selection was performed with the Agencourt AMPure XP magnetic beads. RNA and cDNA quality and content as well as the correct sizing of cDNA library fragments was verified using the Agilent Technologies 2100 Bioanalyzer profiles and Qubit measurements after each step.raries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
Sequencing of libraries was carried out at the sequencing facility on Illumina NovaSeq6000 using 50 bp single-end reads and quality of sequenced libraries was verified with FastQC.

value: Small intestine

value: ex vivo isolated dendritic cells

tag: strain

value: BALB/c

value: Yersinia

tag: infection time

value: Less than 24-hour-old newborns


title: Small intestine_YP147_3

tag: treatment


title: Small intestine_YP147_1

tag: cell type


title: 213

tag: assigned reads

tag: reads aligned_to_dwv_genome

tag: reads aligned_to_vdv_genome


title: Small intestine_PBS_4

value: PBS


title: CROPseq_KO150_A1_ADT_HTO

description:
Antibody-derived oligonucleotide (ADT) for surface protein measurements and Hashtag-derived oligonucleotides (HTO) for multiplexing
CROPseq_KO150_A1_raw_feature_bc_matrix.h5
CROPseq_KO150_A1_filtered_feature_bc_matrix.h5

value: untreated

tag: library type


title: ATAC_Candida_24h_R1_2

tag: protocol

value: ATAC-seq

tag: timepoint after_thawing

tag: stimulus

value: female


title: Small intestine_PBS_3


title: 47

value: Mushroom bodies (brain region)

tag: replicate (note

tag: genotype

value: Non-Responder


title: Small intestine_PBS_2


title: ATAC_LPS_8h_R2_1

value: bone marrow-derived macrophages

value: LPS

tag: time point

tag: Sex

tag: bio-replicate

tag: batch


title: Small intestine_PBS_1

tag: tissue

tag: strain


title: 31

tag: input reads

tag: mapped reads

tag: treatment


title: Pancreas_YP147_4

source_name: Pancreas

value: Pancreas

tag: cell type

tag: infection time


title: ATAC_LPS_6h_R2_1


title: Small intestine_YP147_4


title: Pancreas_YP147_2


title: Pancreas_YP147_3


title: ATAC_LPS_4h_R2_1


title: CROPseq_KO15_1_GEX

description:
polyA RNA
CROPseq_KO15_1_raw_feature_bc_matrix.h5
CROPseq_KO15_1_filtered_feature_bc_matrix.h5

tag: cell line

value: mixed sample (untreated, Listeria 2h, Listeria 6h)

tag: library type

value: mRNA


title: Pancreas_YP147_1


title: 67

tag: assigned reads

tag: reads aligned_to_dwv_genome

tag: reads aligned_to_vdv_genome

value: Forager


title: 204

tag: replicate (note

tag: genotype

value: Guard


title: Pancreas_PBS_4

value: ex vivo isolated dendritic cells


title: ATAC_LPS_2h_R2_1

tag: protocol

tag: timepoint after_thawing

tag: stimulus

tag: time point

tag: Sex


title: Pancreas_PBS_2

tag: tissue

tag: strain

value: BALB/c


title: ATAC_Listeria_8h_R2_1

value: Listeria

tag: bio-replicate

tag: batch


title: 82

tag: input reads

tag: mapped reads

tag: treatment


title: Pancreas_PBS_1

tag: cell type

tag: infection time

value: Less than 24-hour-old newborns


title: ATAC_untreated_8h_R2_2


title: 208

tag: assigned reads

tag: reads aligned_to_dwv_genome

tag: reads aligned_to_vdv_genome


title: Liver_YP147_4

source_name: Liver

value: Liver

value: Yersinia


title: ATAC_Listeria_6h_R2_1

tag: protocol

value: ATAC-seq


title: Liver_YP147_2


title: Liver_YP147_3


title: ATAC_Listeria_4h_R2_1

tag: timepoint after_thawing

value: female


title: 58

value: Mushroom bodies (brain region)

tag: replicate (note

tag: genotype


title: Liver_YP147_1


title: 104


title: Liver_PBS_4

value: PBS


title: ATAC_Listeria_2h_R2_1

value: bone marrow-derived macrophages

tag: stimulus

tag: time point

tag: Sex


title: Liver_PBS_3

tag: tissue

tag: strain


title: 63

tag: input reads


title: Liver_PBS_2


title: ATAC_LCMV_8h_R2_1

value: LCMV

tag: bio-replicate

tag: batch


title: Liver_PBS_1

tag: cell type

tag: treatment


title: 36

tag: mapped reads

tag: assigned reads

value: Non-Responder


title: drsh-1(cdb328) I; mir-80(cdb530) III, , replicate 2

city: Chevy Chase

first: Katherine

last: McJunkin

state: Maryland

address: 3714 Cardiff Court

institute: NIH/NIDDK Intramural Research Program

description:
Library name: sBY408
bias_minimized_processed_2.xlsx

data_processing:
Adapters were removed using fastq. Bowtiew was used to map reads to the WS235 genome. htseq was used to count reads using gff files from mirGeneDB.
Assembly: WS280
Supplementary files format and content: raw counts from htseq

source_name: whole worm

growth_protocol: C. elegans strains grown at 20 degrees.

extract_protocol:
Total RNA was extracted form whole worms using Trizol.
bias-minimized small RNA cloning protocol with adaptors containing degenerate bases for unbiased ligations

value: whole worm

value: drsh-1(cdb328) I; mir-80(cdb530) III


title: Pancreas_PBS_3

value: Pancreas

tag: infection time


title: drsh-1(cdb328) I; mir-80(cdb530) III, , replicate 1

description:
Library name: sBY407
bias_minimized_processed_2.xlsx


title: ATAC_LCMV_6h_R2_1

tag: protocol


title: mir-80(cdb530) III, , replicate 3

description:
Library name: sBY403
bias_minimized_processed_2.xlsx

value: mir-80(cdb530) III