title: SUIT-2-ATM-siRNA-1

city: Singapore

first: Daisuke

last: Douchi

address: 14 Medical Drive

department: Centre for Translational Medicine

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
After filtering using SOAPnuke, the clean reads were mapped to the reference genome (GCF_000001405.38_GRCh38.p12) using Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT2).
After genome mapping, Bowtie2 was used to reconstruct transcripts and RSEM was used to calculate the gene expression level of each sample.
Assembly: GRCh38

extract_protocol:
RNA was extracted from cell lines using the Nucleospin RNA kit (Takara Biotechnology, Tokyo, Japan).
RNA were sent to Beijing Genomics Institute (BGI) for transcriptome library preparation and sequencing.

value: Pancreatic cancer cell line


title: SUIT-2-Control-siRNA

status: Public on Feb 13 2023

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type


title: SUIT-2-ATM-siRNA-2


title: Cx3cr1_Oil_3

city: Lisboa

first: Pedro

last: Sousa-Victor

address: Avenida Professor Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular (iMM)

description: macrophages, control, 3dpi

data_processing:
FPKM
Assembly: ensembl_mus_musculus_grcm38_p6_gca_000001635_8
Supplementary files format and content: excel file includes FPKM values for each Sample

organism: Mus musculus

source_name: Macrophages

extract_protocol: RNA was extracted with RNeasy Micro Kit

value: Macrophages

tag: genotype

value: Cx3cr1-CreER, Manffl/fl

tag: treatment

value: Oil


title: End1/E6E7 cells, Mock-infected rep3

city: Omaha

first: Rey

last: Carabeo

state: Nebraska

address: 985900 Nebraska Medical Center

department: Pathology and Microbiology

country: USA

institute: University of Nebraska Medical Center

description: UI R3

data_processing:
CLC Genomics Workbench version 10.1.1 used for all data processing steps.
Adaptor sequences and low-quality reads were trimmed using default parameters, then aligned to the hg19 reference genome.
Transcripts per million (TPM) were calculated using default parameters.
An initial ANOVA-like pass of differential expression testing was performed. Genes that did not significantly vary between any of the three treatments were culled from downstream analysis.
Differential expression testing was performed using default paramters to identify differentially expressed genes in either L2 or B-infected samples relative to the mock-infected control, accounting for variation between replicates.
Genome_build: hg19
Supplementary_files_format_and_content: CLC file containing raw counts, TPM, and FDRP values for every gene and sample.
Supplementary_files_format_and_content: Expression_Browser files (differential expression analysis)

molecule: polyA RNA

growth_protocol: Human endocervical epithelial HPV-16 E6/E7 transformed End1s (End1 E6/E7, ATCC CRL-2615) were cultured at 37C with 5% atmospheric CO2 in Keratinocyte Serum-Free Medium (KSFM, Thermo Fisher Scientific) supplemented with human recombinant epidermal growth factor, bovine pituitary extract, 5 ug/mL gentamicin, and 0.4 mM CaCl2. For all experiments, End1s were cultured between passages 3 and 15. Chlamydia trachomatis serovar L2/434/Bu and B/Jali was originally obtained from Dr. Ted Hackstadt (Rocky Mountain National Laboratory, NIAID).

extract_protocol:
End1s were harvested for Total RNA at 24 hpi using TRIzol (Thermo Fisher Scientific 15596026) and the DNA-free DNA removal kit (Thermo Fisher Scientific AM1906), according to manufacturers’ protocols. Extracted RNA was subsequently enriched for polyadenylated mRNA transcripts using the NucleoTrap mRNA enrichment kit (Macherey-Nagel), again according to the manufacturer’s protocol. For the comparison of Mock- and Ct serovar L2-infected transcriptomes, RNA samples were subsequently assayed for fragmentation using an Agilent 5200 Fragment Analyzer; intact samples were enriched for polyadenylated transcripts via the NucleoTrap kit a second time due to the high incidence of ribosomal RNA in the fragment analysis results.
cDNA library preparation was performed using the Ion Xpress Plus Fragment Library kit (Thermo Fisher Scientific 4471269), according to the manufacturer's protocol.

treatment_protocol: End1s cultured to 125% of confluence seeded on fibronectin-coated 6-well plates (Corning 354402) were washed with pre-warmed Hanks Buffered Saline Solution (HBSS) prior to inoculation with Chlamydia-containing KSFM at a multiplicity of infection (MOI) of 2. Tissue culture plates were centrifuged at 4C and 500 rcf (Eppendorf 5810 R tabletop centrifuge, A-4-81 rotor) for 15 minutes to synchronize infection. Inoculum was then aspirated, and cells were washed with chilled HBSS prior to the addition of pre-warmed KSFM. Infected cultures were then returned to the tissue culture incubator until 24 hours post-infection.

value: Endocervical epithelial cells

tag: cell line

tag: infection

value: Mock-infected

tag: infection time

value: 24 hpi


title: Cx3cr1_Oil_2

description: macrophages, control, 3dpi


title: End1/E6E7 cells, L2-infected rep1

description: L2 R1

value: Serovar L2/434/bu-infected


title: MeA_E2_CRE2

city: Albany

first: Shannon

last: Stephens

state: NY

address: 47 New Scotland Ave; MC-136

department: Neuroscience & Experimental Therapeutics

institute: Albany Medical College

description:
SS_MeA_IP_5_S5
20200521_MeAonly_GDXvsE2_AllGenesWithAvg.csv
20200109_rnaseq_voom_tmm_normed_logcpms_with_avgs_MeAonly.csv
multiqc_report.html

data_processing:
Samples were analyzed for quality control (Fastqc v0.11.8), read trimming (Trimmomatic 0.38), alignment (STAR v2.6.0a), and quantification (RSEMv1.3.0) of reads using GRChm38.p6/mm10 and Mus_musculus.GRCm38.98.gtf.
Assembly: mm10
Supplementary files format and content: 20200521_MeAonly_GDXvsE2_AllGenesWithAvg.csv
Supplementary files format and content: 20200109_rnaseq_voom_tmm_normed_logcpms_with_avgs_MeAonly.csv

source_name: brain: Medial amygdala

extract_protocol:
Brains from ovariectomized (OVX) or OVX + Estradiol (E2) treated Kiss1Cre+/Rpl22HA+/+ mice collected and flash frozen. The MeA was bilaterally micropunched from each brain and pooled (n=4 brains per pooled sample). Each pooled MeA sample was run through the Ribotag immunoprecipitation pulldown procedure (Sanz et al., Current Protocols in Neuroscience, 88:e77, 2019) to isolate HA-tagged ribosomes (specific to Kiss1 cells). RNA was extracted from these ribosomes using the Qiagen RNeasy Plus Micro Kit (#74034) per the kit instructions.  Unstranded mRNA library kits from Illumina that used polyA enrichment were used to create the library.
The library was created using unstranded mRNA library kits from Illumina that used polyA enrichment.

value: brain:Medial amygdala

value: OVX + Estradiol


title: MeA_E2_CRE3

description:
SS_MeA_IP_6_S6
20200521_MeAonly_GDXvsE2_AllGenesWithAvg.csv
20200109_rnaseq_voom_tmm_normed_logcpms_with_avgs_MeAonly.csv
multiqc_report.html


title: Cx3cr1_Oil_1

description: macrophages, control, 3dpi


title: MeA_E2_CRE1

description:
SS_MeA_IP_4_S4
20200521_MeAonly_GDXvsE2_AllGenesWithAvg.csv
20200109_rnaseq_voom_tmm_normed_logcpms_with_avgs_MeAonly.csv
multiqc_report.html


title: End1/E6E7 cells, Mock-infected rep2

description: UI R2


title: MeA_OVX_CRE3

description:
SS_MeA_IP_3_S3
20200521_MeAonly_GDXvsE2_AllGenesWithAvg.csv
20200109_rnaseq_voom_tmm_normed_logcpms_with_avgs_MeAonly.csv
multiqc_report.html

value: OVX


title: MIA-PaCa-2-ATM-siRNA-1


title: OldAnti3

description: pro-repair macrophages, old, 3dpi

value: wt

tag: condition

value: old


title: MIA-PaCa-2-Control-siRNA


title: End1/E6E7 cells, Mock-infected rep1

description: UI R1


title: OldAnti2

description: pro-repair macrophages, old, 3dpi


title: MeA_OVX_CRE2

description:
SS_MeA_IP_2_S2
20200521_MeAonly_GDXvsE2_AllGenesWithAvg.csv
20200109_rnaseq_voom_tmm_normed_logcpms_with_avgs_MeAonly.csv
multiqc_report.html


title: MN14-1539M

city: Grand Forks

first: Sergei

last: Nechaev

state: North Dakota

address: Columbia Hall Room 1733c, 501 North Columbia Road Stop 9061

department: Biomedical Sciences

institute: University of North Dakota

description: Single Molecule Real Time

library_source: genomic

data_processing:
Sequencing reads were processed for ROI Analysis and mapped to the published B. mayonii MN14-1539 genome (RefSeq numbers NZ_CP015796.1-NZ_CP015809.1) using SMRTLink version 10.1. Modified m6A sites and motifs were identified using the SMRTLink 10 software with the standard 10 pb_basemods workflow.
Assembly: B. mayonii MN14-1539 (NCBI RefSeq numbers NZ_CP015796.1-NZ_CP015809.1)
Supplementary files format and content: Tab-delimited text files (*m6A.gff) for called m6A modified bases with included sequence context, IPD ratio, coverage, modification QV, and applicable motif at each position.
Supplementary files format and content: Tab-delimited text files (*coverageSummary.gff) for binned sequencing coverage/concordance.

molecule: genomic DNA

organism: Borreliella mayonii

growth_protocol: All Borrelia mayonii clones were grown at 35°C under 5% CO2 in modified Barbour-Stoenner-Kelly medium (BSKII) supplemented with 6% rabbit serum. Cell densities and growth phase were monitored by visualization under dark-field microscopy and counting using a Petroff-Hausser counting chamber. Cells were harvested for nucleic acid isolation during mid-late log phase (~3X107 cells / ml).

extract_protocol:
DNA was isolated from a pool of three independent, late log-phase cultures (5 ml per culture) for each B. mayonii strain by standard phenol-chloroform extraction, concentrated by precipitation with isopropanol, and cleaned using Agencourt AMPure XP beads (Beckman Coulter).
Purified DNA was outsourced to The University of Massachusetts Chan Medical School PacBio Core Enterprise for sample quality control, library construction and validation, and NGS analysis. Briefly, DNA was sheared to 10-15Kb inserts using a Diagenode Bioruptor Pico. Template libraries were constructed and multiplexed using SMRTBell Express Kit v2.0 with Adapter Kit 8A.  Following DNA Fragment Analysis profiling and secondary QC analysis, the barcoded libraries were multiplexed (1:1) and loaded into one 8M SMRTCell for sequencing.

tag: strain

tag: clone

value: M

tag: plasmid missing

value: lp25, cp9

tag: source

value: Log-phase in vitro bacterial culture


title: OldAnti1

description: pro-repair macrophages, old, 3dpi


title: MeA_OVX_CRE1

description:
SS_MeA_IP_1_S1
20200521_MeAonly_GDXvsE2_AllGenesWithAvg.csv
20200109_rnaseq_voom_tmm_normed_logcpms_with_avgs_MeAonly.csv
multiqc_report.html


title: ZT12-KO-rep1.13015GP48

city: Philadelphia

first: Georgios

middle: K

last: Paschos

state: PA

address: 10-102 Translational Research Center, 3400 Civic Center Boulevard, Building 421

department: Pharmacology

institute: University of Pennsylvania, School of Medicine

data_processing:
CASAVA was used to demultiplex pooled samples and convert BCL to FASTQ.
Multiple fastq files were combined into one file for the forward reads and one file for the reverse reads.
RNA-Seq data were aligned to the mouse genome build mm9 by STAR_2.4.1d
Data were normalized at the gene-level, using a resampling strategy (PORT v0.7.3), the code is available at https://github.com/itmat/Normalization
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

source_name: ZT12-KO, liver

growth_protocol: Mice were housed in groups on a 12 hour light, 12 hour dark schedule. 1 day of constant darkness before sample collection. diet availability : ad libitum, fasted for 24 hours before sacrifice; water supply type : bottle; water type : tap

extract_protocol:
Liver totalRNA extracted at different time points: 0, 4, 8, 12, 16, and 20. Stored at -80C.
Library construction was carried out using TruSeq Stranded mRNA Sample Prep Kit Set A. In line controls were not used, and samples were barcoded using kit adapters. Library construction was carried out over three days. Selection strategy: polyA; PCR cycles: 13

value: KO

tag: Sex

value: female

tag: collection time

tag: age (weeks)

tag: weight (g)

value: liver


title: ZT8-KO-rep2.13015GP47

source_name: ZT8-KO, liver


title: MN14-1539J

description: Single Molecule Real Time

value: J


title: YgAnti3

description: pro-repair macrophages, young, 3dpi

value: Macrophages

value: young


title: MIA-PaCa-2-ATM-siRNA-2

value: Pancreatic cancer cell line


title: ZT4-KO-rep2.13015GP46

source_name: ZT4-KO, liver


title: SG_sgNK_B_6

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

data_processing:
BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14, v2.18.0,  or v2.20.0.422).
Paired-end reads were mapped and counted at the gene level with HISAT2 (v. 2.0.5) and Rsubread (v. 1.30.9) using exon regions from GENCODE vM13 annotation.
Assembly: mm10
Supplementary files format and content: Tab delimited text files are raw estimated gene-level counts (1 count = 1 read pair) as quantified by the featureCounts function from the Rsubread R package (v. 1.30.9). Row names indicate gene names.

source_name: SG

extract_protocol:
Phase separation in cells lysed in TRIzol Reagent (ThermoFisher catalog # 15596018) was induced with chloroform. RNA was precipitated with isopropanol and linear acrylamide and washed with 75% ethanol. The samples were resuspended in 13 µL nuclease-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 2 ng total RNA with RNA integrity numbers ranging from 1 to 9.7 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a PE50 run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 44 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 69% to 79%.

value: SG

tag: replicate

value: sgNK

value: B6 Eomes-GFP

tag: batch

value: B


title: ZT12-KO-rep2.13015GP45

tag: tissue


title: SG_sgNK_B_5

tag: cell type

tag: genotype


title: YgAnti2

description: pro-repair macrophages, young, 3dpi


title: MN14-1539HA

description: Single Molecule Real Time

value: HA


title: ZT8-WT-rep2.13015GP44

source_name: ZT8-WT, liver

value: WT


title: ZT16-WT-rep1.13015GP43

source_name: ZT16-WT, liver


title: YgAnti1

description: pro-repair macrophages, young, 3dpi

value: wt


title: SG_sgNK_B_4


title: ZT4-WT-rep3.13015GP41

source_name: ZT4-WT, liver


title: ZT0-WT-rep2.13015GP42

source_name: ZT0-WT, liver


title: SG_sgNK_A_2

value: A


title: SG_NK_B_6

value: NK


title: SG_sgNK_A_1


title: F2_KO

type: RNA

city: Riverside

first: Djurdjica

last: Coss

state: CA

address: 900 University Ave

institute: UC Riverside

description:
20200926_30102421270621-01_Sample05_05.RCC
NanoString technology is based on digital detection and direct molecular barcoding of target molecules through the use of a color coded probe pair. The probe pair consists of a Reporter Probe, which carries the signal on its 5’ end, and a Capture Probe which carries a biotin moiety on the 3’ end. The color codes carry six positions and each position can be one of four colors, thus allowing for a large diversity of tags that can be mixed together in a single well for direct hybridization to targets and yet still be individually resolved and identified during data collection.

hyb_protocol: RNA with integrity number RIN > 7 were used and hybridized with hybridization master mix at 65 degrees celcius for 16 hours.

scan_protocol: Samles were loaded onto a nCounter cartridge and ran on a nCounter SPRINT

data_processing: Analysis of data was performed using nSolver Analysis Software 4.0, including nCounter Advanced Analysis (version 2.0.115). Genes with the expression lower than the limit of detection after background subtraction, and compared to negative controls included in the panel, were excluded. Seven housekeeping control genes that are included in the panel, were used for normalization.

label: Biotin

source_name: Hypothalamus

label_protocol: Gene expression in 50 ng RNA per sample was analyzed using the nCounter instrument, according to manufacturer’s instruction, with the nCounter Mouse Neuroinflammation Panel (770 genes, gene list available at the manufacturer’s website). Panel was customized with an addition of 30 custom probes for hypothalamic neuropeptides and their receptors.

growth_protocol: Mice were maintained under a 12-h light, 12-h dark cycle and received food and water ad libitum.

extract_protocol: 8-week old female mice were perfused with ice cold PBS, brains rapidly removed and flash frozen in isopentane on dry ice. Coronal brain sections of 500 um were obtained using vibratome, hypothalamus dissected and analyzed for gene expression changes by Nanostring. RNA was isolated using the RNAqueous®-Micro Kit (Ambion) and quantified using Nanodrop.

treatment_protocol: Estrous cycle stage was determined with vaginal smears and females were collected in a specific Diestrus cycle stage.

value: Hypothalamus

value: Fermale

value: Fmr1 KO

tag: Stage

value: Diestrus


title: F3_KO

description:
20200926_30102421270621-01_Sample06_06.RCC
NanoString technology is based on digital detection and direct molecular barcoding of target molecules through the use of a color coded probe pair. The probe pair consists of a Reporter Probe, which carries the signal on its 5’ end, and a Capture Probe which carries a biotin moiety on the 3’ end. The color codes carry six positions and each position can be one of four colors, thus allowing for a large diversity of tags that can be mixed together in a single well for direct hybridization to targets and yet still be individually resolved and identified during data collection.


title: SG_sgNK_A_3


title: F3_FVB

description:
20200926_30102421270621-01_Sample03_03.RCC
NanoString technology is based on digital detection and direct molecular barcoding of target molecules through the use of a color coded probe pair. The probe pair consists of a Reporter Probe, which carries the signal on its 5’ end, and a Capture Probe which carries a biotin moiety on the 3’ end. The color codes carry six positions and each position can be one of four colors, thus allowing for a large diversity of tags that can be mixed together in a single well for direct hybridization to targets and yet still be individually resolved and identified during data collection.


title: F1_KO

description:
20200926_30102421270621-01_Sample04_04.RCC
NanoString technology is based on digital detection and direct molecular barcoding of target molecules through the use of a color coded probe pair. The probe pair consists of a Reporter Probe, which carries the signal on its 5’ end, and a Capture Probe which carries a biotin moiety on the 3’ end. The color codes carry six positions and each position can be one of four colors, thus allowing for a large diversity of tags that can be mixed together in a single well for direct hybridization to targets and yet still be individually resolved and identified during data collection.


title: ZT16-WT-rep5.13015GP39

value: female

value: liver


title: ZT12-WT-rep3.13015GP40

source_name: ZT12-WT, liver


title: F2_FVB

description:
20200926_30102421270621-01_Sample02_02.RCC
NanoString technology is based on digital detection and direct molecular barcoding of target molecules through the use of a color coded probe pair. The probe pair consists of a Reporter Probe, which carries the signal on its 5’ end, and a Capture Probe which carries a biotin moiety on the 3’ end. The color codes carry six positions and each position can be one of four colors, thus allowing for a large diversity of tags that can be mixed together in a single well for direct hybridization to targets and yet still be individually resolved and identified during data collection.


title: ZT0-KO-rep4.13015GP38

source_name: ZT0-KO, liver

value: KO


title: SG_NK_B_4


title: F1_FVB

description:
20200926_30102421270621-01_Sample01_01.RCC
NanoString technology is based on digital detection and direct molecular barcoding of target molecules through the use of a color coded probe pair. The probe pair consists of a Reporter Probe, which carries the signal on its 5’ end, and a Capture Probe which carries a biotin moiety on the 3’ end. The color codes carry six positions and each position can be one of four colors, thus allowing for a large diversity of tags that can be mixed together in a single well for direct hybridization to targets and yet still be individually resolved and identified during data collection.


title: LNAMcol5

city: Raleigh

first: Heike

last: Sederoff

state: NC

address: 851 Main Campus Dr

department: Plant & Microbial Biology

institute: North Carolina State University

data_processing:
QC metrics were obtained using FastQC and high-quality (Q>30) read pairs were mapped to RefSeq GCF_000188115.4 using HISAT2 with default parameter settings
Aligned reads were assigned genomic features according to Araport11 (arabidopsis) or Gifu v1.2 (lotus) annotations using featureCounts and read abundances quantified at the isoform level with default parameter settings
Raw counts were filtered for zero and low counts (<2) and library normalization was performed using DESeq2 size factor estimates
Assembly: Arabidopsis: TAIR10 INSDC Assembly GCA_000001735.1; Lotus: LotusBase Lotusjaponicus_Gifu_v1.2
Supplementary files format and content: Text files with counts for each sample by gene isoform

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Plants were grown in sterile conditions in a growth chamber on one of two media types, dependent upon treatment.

extract_protocol:
A PureLink RNA mini on-column kit with TRIzol with on-column DNAse treatment
The mRNA library was prepped by BGI Genomics Co., Ltd with polyA selection by an oligo dT library
Arabidopsis and lotus samples were multiplexed, pooled and loaded onto a DNBSEQ Technology Platform sequencer, separately by species

treatment_protocol: Plants were grown on either 1/2 MS medium or LN (low-nutrient) medium. +AM designated treatments were exposed to Rhizophagus AM fungi prior to root tissue sampling.

value: root

value: wildtype

tag: background ecotype

tag: media

value: low nutrient medium

tag: am presence

value: +AM

tag: treatment

value: LN| +AM|col-0


title: LNAMcol4


title: LNAMcol1


title: SG_NK_A_2

value: SG

value: B6 Eomes-GFP


title: ZT0-WT-rep1.13015GP37

value: WT

tag: strain


title: ZT4-WT-rep1.13015GP36


title: SG_ILC1_B_6

value: B


title: ZT0-KO-rep1.13015GP35


title: ZT20-KO-rep1.13015GP34

source_name: ZT20-KO, liver


title: SG_NK_A_3

value: NK

value: A


title: SG_NK_A_1


title: LNAM308.3

value: IPD3-min line 308


title: ZT4-KO-rep4.13015GP32


title: LNAMcol2


title: LNAM308.1


title: LNAMcol3


title: SG_ILC1_A_2


title: SG_ILC1_A_1


title: SG_ILC1_B_5


title: MSnoAMcol4

value: 1/2 MS medium

value: -AM


title: SG_ILC1_B_4


title: ZT12-WT-rep1.13015GP30

value: female


title: ZT20-KO-rep4.13015GP33

value: liver


title: ZT4-KO-rep3.13015GP31

value: KO


title: ZT20-KO-rep3.13015GP29


title: Wnt1Cre_E8.5, scRNAseq

city: Bronx

first: Christopher

last: De Bono

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (v6.0.1, from 10x Genomics) was used to align scRNA-seq reads to the mouse reference genome (assembly and annotation, mm10-2020-A) to generate gene-by-cell count matrices.
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Anterior half of the embryo

extract_protocol:
Embryos were collected and microdissected in 1x PBS at 4°C. Dissected tissues of interest were maintained in DMEM (Dulbecco’s Modified Eagle Medium, GIBCO 11885084) at 4°C. Then, tissues were incubated in 1ml of 0.25% Trypsin-EDTA (GIBCO, 25200056) containing 50U/ml of DNase I (Millipore, 260913-10MU), at room temperature for 7 minutes. Next, heat inactivated FBS (Fetal Bovine Serum, ATCC, 30-2021) was added to stop the reaction at a final concentration of 10%, at 4°C. Dissociated cells were centrifugated for 5 minutes at 300 x g at 4°C and the supernatant was removed. Cells were then resuspended in 1x PBS without Ca2+ and Mg2+ (Coming, 21-031-cv) containing 10% FBS at 4°C and filtered with a 100μm cell strainer. A total of 1μl DAPI (1mM) (Thermo Fisher Scientific, D3571) was added before FACS using a BD FACS Aria II system. EGFP positive, DAPI negative cells were then centrifuged at 4°C, 5 minutes at 300 x g and resuspended in 50μl of 1xPBS without Ca2+ and Mg2+ with 10% FBS.
Chromium Single Cell 3’ Library & Gel Bead kit v2.

value: Neural crest cells

value: Anterior half of the embryo

value: Swiss-Webster

tag: age

value: Embryonic day 8.5


title: MSnoAMcol3

value: root

value: wildtype


title: Tamoxifen-injected Gli1creERT/Hhipflo/flox

city: San Francisco

first: Tien

last: Peng

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

data_processing:
Data were processed according to the 10x Cellranger pipeline.
BAM files were generated with V5.0.1 10X Genomics Cellranger software using default parameters.
Gene-barcode matrices were generated from Cellranger cellranger-5.0.1 using default parameteres.
Assembly: GRCm38 mm10
Supplementary files format and content: Cellranger outputs a .mtx file with the gene-barcode matrix. This matrix contains the counts of molecules per cell (UMI/cell) as determined after filtering and counting by Cellranger. The matrix is in market exchange format while the row (gene names) and columns (cell barcodes) are provided as TSV files. File formats are documented in Cellranger software manual.

source_name: Fresh sorted  lung live CD45-postive-CD45IV-negative cells

extract_protocol:
For isolating resident lung immune cells, 3 min before euthanizing each mouse, 3 μg of anti-mouse fluorophore-conjugated CD45 antibody diluted in 150 μl of 1X DPBS was intravenously injected via the retro-orbital injections. A digestion cocktail of Liberase TM (100 μg/mL, Sigma) and Dnase (50 U/ml, Sigma) in HBSS was used to dissociate the lung. CD45+CD45IV- resident immune cells are sorted by FACS.
cDNA libraries were prepared for sequencing using standard protocol for the 10x Single Cell instrument, using Single Cell 3' v3 Chemistry

tag: developmental stage

value: adult

value: lung resident immune cells (CD45+ CD45IV-negative cells)

tag: condition


title: LIV_NK_B_6

source_name: LIV

value: LIV

value: B6 Eomes-GFP

value: B


title: LNAM308.2

value: IPD3-min line 308

value: low nutrient medium

value: +AM


title: ZT20-WT-rep4.13015GP28

source_name: ZT20-WT, liver

value: WT

tag: Sex

value: female

tag: collection time


title: MSnoAMcol2

value: 1/2 MS medium

value: -AM


title: Oil-injected Gli1creERT/Hhipflo/flox

source_name: Fresh sorted lung live CD45-postive-CD45IV-negative cells

value: Oil-injected Gli1creERT/Hhipflo/flox


title: KFCA-11mo

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: MI

address: 1500 E Medical Center Dr

institute: University of Michigan

data_processing:
Sample was run using paired-end 50 cycle reads on NovaSeq 6000 (Illumina) to a depth of 100,000 reads.
Raw Data was processed and aligned by the University of Michigan Advanced Genomics Core. Files were demulitplexed into FASTQ files using cellranger mkfastq v4.0.0.
FASTQ files were aligned, filtered, and counted by cellranger count v4.0.0 and formed into feature-barcode matrices.
Feature-barcode matrices were read into R using the package Seurat version 4.0.2 and package SeuratObject version 4.0.1 and were analyzed according to the Seurat pipeline, including normalizing, scaling, filtering based on read counts and mitochondrial gene percentage, and manually labeling cells according to gene expression profiles.
Assembly: mm10-2020-A
Supplementary files format and content: H5 files containing aligned single cell sequencing data output by CellRanger

source_name: Spontaneous pancreatic tumor

growth_protocol: Both KF and KFCA mice were aged to 11 months. Mice were euthanized and the tumor was harvested and processed to single cell for single cell RNA sequencing.

extract_protocol:
Spontaneous pancreatic tumor digested to single cell suspension and submitted for single cell RNA sequencing
Samples were mechanically and enzymatically digested (Collagenase V; 1 mg/mL in RPMI) under constant agitation. Single cell suspensions were obtained by filtering consecutively through 500 µm, 100 µm, and 40 µm cell strainers. Dead cells were removed using MACS Dead Cell Removal Kit (Miltenyi Biotec).
Single cell cDNA libraries were prepared and sequenced using the 10x Genomics platform at the University of Michigan Advanced Genomics Core.

tag: disease state

value: spontaneous pancreatic cancer model

value: pancreatic tumor

tag: number of mice pooled

value: myeloid cells


title: LIV_NK_B_4

tag: replicate

value: NK

tag: batch


title: MSnoAM308.4

tag: tissue

value: root


title: MSnoAMcol1

tag: genotype

value: wildtype


title: ZT20-KO-rep2.13015GP26

value: KO

tag: age (weeks)

tag: weight (g)

value: liver


title: MSnoAM308.3

tag: background ecotype

tag: media


title: LIV_ILC1_B_5

value: LIV

tag: cell type

value: B6 Eomes-GFP

value: B


title: ZT16-KO-rep2.13015GP24

source_name: ZT16-KO, liver

tag: strain


title: MSnoAM308.2

value: IPD3-min line 308

tag: am presence

tag: treatment


title: KF-11mo


title: ZT16-WT-rep4.13015GP25

value: WT


title: LIV_ILC1_B_4


title: WAGO-10

city: Hefei

first: Xiaolin

last: Wang

address: Huangshan Road

country: China

institute: USTC

data_processing:
Alignment with bowtie
After filtering out reads shorter than 17 nt, the remaining reads were mapped to C. elegans genome (ce11) with bowtie (-v 1).
For miRNAs, piRNAs and tRNAs, sense reads are counted. For mRNAs, lincRNAs, transposons, pseudogenes and risiRNAs, antisense reads are counted. For rRNA, sense and antisense reads are counted.
Assembly: ce11
Supplementary files format and content: bw for all samples

organism: Caenorhabditis elegans

source_name: whole worms

extract_protocol:
Immunoprecipitated RNA was extracted with TRIzol reagent according to the manufacturer’s instructions.
RNAs were treated with RNA 5’ polyphosphatase (Lucigen, Cat# RP8092H) and purified with RNA clean up kit (Zymo Research, Cat# R1015) for RNA libraries. Adaptor ligation, Unique Molecular Identifier (UMI)-mediated reverse transcription and library amplification were prepared according to manufacturer’s instructions

value: whole worms

tag: developmental stage

value: L4 stage

tag: antibody

value: GFP-Trap Agarose (ChromoTek, Gta-20)


title: ZT20-WT-rep3.13015GP23

tag: Sex

value: female

tag: collection time


title: WAGO-4

value: Young Adult stage


title: Wnt1Cre_Tbx1null_E10.5_R2, replicate2, scRNAseq

description: 10x Genomics

source_name: Pharyngeal apparatus below arches 1 with heart

extract_protocol:
Embryos were collected and microdissected in 1x PBS at 4°C. Dissected tissues of interest were maintained in DMEM (Dulbecco’s Modified Eagle Medium, GIBCO 11885084) at 4°C. Then, tissues were incubated in 1ml of 0.25% Trypsin-EDTA (GIBCO, 25200056) containing 50U/ml of DNase I (Millipore, 260913-10MU), at room temperature for 7 minutes. Next, heat inactivated FBS (Fetal Bovine Serum, ATCC, 30-2021) was added to stop the reaction at a final concentration of 10%, at 4°C. Dissociated cells were centrifugated for 5 minutes at 300 x g at 4°C and the supernatant was removed. Cells were then resuspended in 1x PBS without Ca2+ and Mg2+ (Coming, 21-031-cv) containing 10% FBS at 4°C and filtered with a 100μm cell strainer. A total of 1μl DAPI (1mM) (Thermo Fisher Scientific, D3571) was added before FACS using a BD FACS Aria II system. EGFP positive, DAPI negative cells were then centrifuged at 4°C, 5 minutes at 300 x g and resuspended in 50μl of 1xPBS without Ca2+ and Mg2+ with 10% FBS.
Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead kit v3.1.

value: Neural crest cells

value: Swiss-Webster

tag: age

value: Embryonic day 10.5


title: MSnoAM308.1

value: root

value: 1/2 MS medium

value: -AM


title: WAGO-1

value: wago-1(hzhCR183[gfp::3xflag::wago-1]) I


title: LIV_NK_B_5

value: LIV

tag: replicate

value: NK


title: ZT8-KO-rep3.13015GP27

source_name: ZT8-KO, liver

value: KO

value: liver


title: Wnt1Cre_Tbx1null_E10.5_R1, replicate1, scRNAseq

description: 10x Genomics

extract_protocol:
Embryos were collected and microdissected in 1x PBS at 4°C. Dissected tissues of interest were maintained in DMEM (Dulbecco’s Modified Eagle Medium, GIBCO 11885084) at 4°C. Then, tissues were incubated in 1ml of 0.25% Trypsin-EDTA (GIBCO, 25200056) containing 50U/ml of DNase I (Millipore, 260913-10MU), at room temperature for 7 minutes. Next, heat inactivated FBS (Fetal Bovine Serum, ATCC, 30-2021) was added to stop the reaction at a final concentration of 10%, at 4°C. Dissociated cells were centrifugated for 5 minutes at 300 x g at 4°C and the supernatant was removed. Cells were then resuspended in 1x PBS without Ca2+ and Mg2+ (Coming, 21-031-cv) containing 10% FBS at 4°C and filtered with a 100μm cell strainer. A total of 1μl DAPI (1mM) (Thermo Fisher Scientific, D3571) was added before FACS using a BD FACS Aria II system. EGFP positive, DAPI negative cells were then centrifuged at 4°C, 5 minutes at 300 x g and resuspended in 50μl of 1xPBS without Ca2+ and Mg2+ with 10% FBS.
Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead kit v3.

value: Pharyngeal apparatus below arches 1 with heart


title: MSnoAM310.3

value: IPD3-min line 310


title: ZT8-KO-rep1.13015GP21


title: SAGO-2

value: whole worms

value: sago-2(hzhCR181[gfp::3xflag::sago-2]) I


title: LIV_ILC1_B_6

value: B6 Eomes-GFP

tag: batch

value: B


title: MSnoAM310.2

tag: tissue


title: MSnoAM310.1

tag: genotype


title: ZT16-WT-rep2.13015GP20

source_name: ZT16-WT, liver

value: WT

value: female

tag: age (weeks)


title: Wnt1Cre_E10.5_R1, replicate 1, scRNAseq

description: 10x Genomics

source_name: Pharyngeal apparatus from arches 2 to 6 with heart

extract_protocol:
Embryos were collected and microdissected in 1x PBS at 4°C. Dissected tissues of interest were maintained in DMEM (Dulbecco’s Modified Eagle Medium, GIBCO 11885084) at 4°C. Then, tissues were incubated in 1ml of 0.25% Trypsin-EDTA (GIBCO, 25200056) containing 50U/ml of DNase I (Millipore, 260913-10MU), at room temperature for 7 minutes. Next, heat inactivated FBS (Fetal Bovine Serum, ATCC, 30-2021) was added to stop the reaction at a final concentration of 10%, at 4°C. Dissociated cells were centrifugated for 5 minutes at 300 x g at 4°C and the supernatant was removed. Cells were then resuspended in 1x PBS without Ca2+ and Mg2+ (Coming, 21-031-cv) containing 10% FBS at 4°C and filtered with a 100μm cell strainer. A total of 1μl DAPI (1mM) (Thermo Fisher Scientific, D3571) was added before FACS using a BD FACS Aria II system. EGFP positive, DAPI negative cells were then centrifuged at 4°C, 5 minutes at 300 x g and resuspended in 50μl of 1xPBS without Ca2+ and Mg2+ with 10% FBS.
Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead kit v3.1

value: Neural crest cells

value: Swiss-Webster

value: Embryonic day 10.5


title: ZT16-KO-rep3.13015GP19

tag: weight (g)


title: PPW-2

value: Young Adult stage

value: GFP-Trap Agarose (ChromoTek, Gta-20)

value: ppw-2(hzhCR187[gfp::3xflag::ppw-2]) I


title: PRG-1

value: prg-1(hzhCR195[gfp::3xflag::prg-1]) I


title: PPW-1

value: ppw-1(hzhCR182[ppw-1::3xflag::gfp]) I


title: MSAMcol4

value: root

value: wildtype

tag: background ecotype

value: 1/2 MS medium

value: +AM


title: MSAMcol2

tag: media


title: ZT0-KO-rep2.13015GP18

value: KO

value: liver


title: Wnt1Cre_E9.5, scRNAseq

description: 10x Genomics

source_name: Pharyngeal apparatus with heart

tag: cell type

value: Pharyngeal apparatus with heart

value: Embryonic day 9.5


title: ZT8-WT-rep3.13015GP16

source_name: ZT8-WT, liver

value: WT

tag: strain

value: female


title: RDE-1

value: whole worms

value: rde-1(hzhCR194[gfp::3xflag::rde-1]) V


title: ZT4-WT-rep2.13015GP22

source_name: ZT4-WT, liver


title: ZT20-WT-rep2.13015GP17


title: NRDE-3

value: Young Adult stage

value: nrde-3(hzhCR177[gfp::3xflag::nrde-3]) X


title: ZT0-KO-rep3.13015GP15

source_name: ZT0-KO, liver


title: E14 ESCs recovered, INPUT, biological replicate 1

city: Edinburgh

first: Iain

last: Williamson

address: Crewe Road

department: Chromosomes and Gene Expression

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

data_processing:
Calibrated ChIP-seq data analysis was performed using the Nextflow (version 22.04.0) pipeline chip_quant_analysis.nf (https://gitbio.ens-lyon.fr/LBMC/Bernard/quantitative-nucleosome-analysis, 295ce7f5838d8fe08ad465232bdd178773a5f2c3) with the reference genome M. musculus (GRCm38) and for internal calibration the H. sapiens (GRCh38) genome.
Fastq files were processed with fastp (0.20.1, options --qualified_quality_phred 20 --disable_length_filtering--detect_adapter_for_pe). The processed fastq files were mapped to a concatenated reference and calibration genome with bowtie2 (2.3.4.1, option --very-sensitive).
Bam files were split into reads mapping exclusively to either the reference genome, or the calibration genome, using samtools (1.11), and awk. Mapped reads were deduplicated using picard (2.18.11, options MarkDuplicates VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true).
The deduplicated bam files were converted to bigwig and bedgraph formats using deeptools (3.5.1). Normalization and generation of ratio coverage files were generated using software and scripts contained in the docker containers lbmc/chip_quant_r:0.0.6 and biocontainers/danpos:v2.2.2_cv3 as described in in the paper https://www.biorxiv.org/content/10.1101/2022.03.18.484892v1.
Assembly: mm10/hg38
Supplementary files format and content: bigWig

organism:
Homo sapiens
Mus musculus

source_name: human MCF-7 (mammary gland epithelial tumor cells)

growth_protocol: Feeder-free mouse embryonic stem cells (mESCs) E14tg2A (129/Ola; Ring1B+/+) and the derivative line (Ring1B−/−) (Illingworth et al. 2015) were cultured at 37°C on 0.1% gelatin-coated (Sigma G1890) Corning flasks in GMEM BHK-21 (Gibco 21710-025) supplemented with 10% fetal calf serum (FCS; Sigma F-7524), 1000 U/mL LIF, nonessential amino acids (Gibco 11140-035), sodium pyruvate (Gibco 11360-039), 50 μM2-β-mercaptoethanol (Gibco 31350-010), and L-glutamine.

extract_protocol:
Pellets were then thawed and combined with 1×10^6 formaldehyde-fixed human MCF-7 cells (for downstream calibration of ChIP-seq data). Following lysis, cells were sonicated using a cooled Bioruptor (50 cycles, 1 minute cycles of 30s on/30s off on “high” setting at 4°C). The sonicated extract was pre- cleared by centrifugation at 16,000g for 10 min at 4°C. The supernatant was transferred to a fresh tube and supplemented with BSA to a final concentration of 25 mg/mL. A sample of the chromatin was retained as an input reference.   Antibodies were precoupled to a 1/1 mixture of protein A (Life Technologies 10001D) and protein G (Life Technologies 1003D) Dynabeads at a ratio of 1 mg antibody per 30 mL of Dynabead suspension by rotation for 2 hours at 4°C. Cell equivalents (~6.5×10^6) of lysate were added to 7.5 microgrammes of anti-Ring1B (Cell Signaling D22F2), 5 microgrammes of anti-H3K27me3 (Cell Signaling C36B11), or 5 microgrammes Rabbit IgG (Cell Signaling) respectively, and incubated overnight on a rotating wheel at 4°C. Following incubation, bead-associated immune complexes were washed sequentially with ChIP dilution buffer, wash buffer A, and wash buffer B, each for 10 min at 4°C on a rotating wheel, followed by two washes in TE buffer at room temperature. Chromatin was released by incubating the beads in 100 µL of elution buffer (0.1M NaHCO3, 1% SDS) for 15 min at 37°C, followed by the addition of 20 µg of RNase A and 6 µL of 2 M Tris (pH 6.8) and incubation for 1 h at 37°C and finally by the addition of 20 µg proteinase K and incubation overnight at 65°C to degrade proteins and reverse the cross-links. Dynabeads were removed using a magnetic rack and the chromatin purified using PCR purification columns (Qiagen) according to the manufacturer’s instructions.
Libraries (Ring1B and corresponding input samples only) were constructed using the NEBNext Ultra II DNA library preparation kit for Illumina according to the manufacturer’s instructions (NEB E7645S). To determine the number of PCR cycles required for amplification, one aliquot of library preparation from each sample were supplemented with evagreen so that amplification could be monitored by quantitative PCR on a BioRad C1000 Touch Thermal Cycler. To allow for sample multiplexing, PCRs were performed using index primers (NEBNext multiplex oligos for Illumina, set 1, E7335 and amplified to linear phase). Size selection purifications following the ligation and amplification PCR steps were performed with 0.9× reaction volumes of Agencourt AMPure XP beads (Beckman Coulter A63880).
Purified libraries were combined as a 8-sample equimolar pool containing a combination of indexes from 1–12 and sequenced on an Illumina NextSeq on an Illumina NextSeq 2000 on a P2 flow cell (paired-end 75-bp reads).

treatment_protocol: Trypsinized untreated, 2,5-HD, 1,6-HD and recovered mESCs (~2 ×10^7) were washed twice in PBS.  After 10 minutes of formaldehyde (Calbiochem, cat. # 344198, final concentration 1%) fixation, stopped by 5 minutes incubation with 125 mM of glycine at room temperature, cells were washed in PBS, pelleted, and stored at -80°C.

tag: cell line

value: mouse E14 (embryonic stem cells)

value: E14 ESCs recovered

tag: chip antibody


title: E14 ESCs 1,6HD-treated, INPUT, biological replicate 2

value: human MCF-7 (mammary gland epithelial tumor cells)

tag: treatment

value: E14 ESCs 1,6HD-treated


title: SAGO-1

tag: developmental stage

tag: antibody

value: GFP-Trap Agarose (ChromoTek, Gta-20)

value: sago-1(hzhCR180[gfp::3xflag::sago-1]) V


title: HRDE-1


title: Wnt1Cre_Tbx1null_E9.5, scRNAseq

description: 10x Genomics

value: Neural crest cells

value: Swiss-Webster


title: ZT8-WT-rep4.13015GP14

tag: Sex

tag: collection time

value: liver


title: Wnt1Cre_E10.5_R1, replicate 2, scRNAseq

description: 10x Genomics

value: Pharyngeal apparatus from arches 2 to 6 with heart

tag: age

value: Embryonic day 10.5


title: MSAM308.3

source_name: root

value: root

value: IPD3-min line 308

value: 1/2 MS medium

tag: am presence

value: +AM


title: E14 ESCs recovered, INPUT, biological replicate 2


title: E14 ESCs 1,6HD-treated, INPUT, biological replicate 1


title: ERGO-1

tag: tissue

value: whole worms

value: Young Adult stage

value: ergo-1(hzhCR193[ergo-1::3xflag::gfp]) V


title: ZT20-WT-rep1.13015GP13

tag: genotype

value: WT

value: female


title: CSR-1

value: anti-FLAG (Sigma, Cat#F1804)

value: csr-1(hzhCR178[3xflag::csr-1]) IV


title: E14 ESCs 2,5HD-treated, INPUT, biological replicate 2

value: mouse E14 (embryonic stem cells)

value: human MCF-7 (mammary gland epithelial tumor cells)

value: E14 ESCs 2,5HD-treated


title: MSAM308.2


title: MSAM310.3

value: IPD3-min line 310


title: MSAM308.1


title: ZT8-KO-rep4.13015GP12

value: KO

tag: age (weeks)

value: liver


title: MSAM308.4

value: root


title: ALG-5

value: GFP-Trap Agarose (ChromoTek, Gta-20)

value: alg-5(hzhCR192[gfp::3xflag::alg-5]) I


title: E14 ESCs untreated, INPUT, biological replicate 2

value: E14 ESCs untreated


title: MSAM310.2

value: 1/2 MS medium

value: +AM


title: MSAMcol1

value: wildtype


title: C04F12.1

value: whole worms

value: L4 stage


title: E14 ESCs 2,5HD-treated, INPUT, biological replicate 1


title: ZT16-KO-rep1.13015GP09

value: female

tag: weight (g)


title: E14 ESCs untreated, INPUT, biological replicate 1


title: ALG-4

value: alg-4(hzhCR189[alg-4::3xflag::gfp]) III


title: ZT4-WT-rep4.13015GP10

value: WT


title: ALG-3

value: alg-3(hzhCR188[alg-3::3xflag::gfp]) IV


title: ZT4-KO-rep1.13015GP08

source_name: ZT4-KO, liver


title: MSAM310.1

tag: background ecotype


title: MSAMcol3

tag: media


title: E14 ESCs recovered, RING1B, Cell Signaling, biological replicate 2

value: mouse E14 (embryonic stem cells)

value: human MCF-7 (mammary gland epithelial tumor cells)

value: E14 ESCs recovered

value: anti-RING1B (Cell Signaling D22F2)


title: ALG-2

value: Young Adult stage

value: alg-2(hzhCR191[gfp::3xflag::alg-2]) II


title: E14 ESCs recovered, RING1B, Cell Signaling, biological replicate 1


title: ZT16-WT-rep3.13015GP11

value: liver


title: ALG-1

value: GFP-Trap Agarose (ChromoTek, Gta-20)

value: alg-1(hzhCR190[gfp::3xflag::alg-1]) X


title: E14 ESCs 1,6HD-treated, RING1B, Cell Signaling, biological replicate 2

value: E14 ESCs 1,6HD-treated


title: Input

value: wild-type


title: ZT12-WT-rep2.13015GP05

source_name: ZT12-WT, liver


title: E14 ESCs 1,6HD-treated, RING1B, Cell Signaling, biological replicate 1


title: E14 ESCs 2,5HD-treated, RING1B, Cell Signaling, biological replicate 2

value: E14 ESCs 2,5HD-treated


title: ZT12-WT-rep4.13015GP04


title: E14 ESCs untreated, RING1B, Cell Signaling, biological replicate 2

value: E14 ESCs untreated


title: RNA-Seq_MCF7_si-circPGR_DMSO

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

institute: xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4.
Reads were aligned to the hg19 genome assembly using Tophat version 2.1.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: circRNA-seq: Tab-delimited text files.
Supplementary_files_format_and_content: RNA-seq: bigWig files.

source_name: Human breast cancer MCF7 cells

growth_protocol: MCF7 cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq platform at RiboBio Co., Ltd. or Amogene Biotech Co., Ltd.

treatment_protocol: MCF7 cells were maintained in stripping medium (phenol red free) for three days before treating with or without estrogen (E2, 10-7 M) for 6h.

tag: cell type

value: Breast cancer cell line

value: DMSO

tag: sirna

value: si-circPGR


title: circRNA-Seq_MCF7_E2

tag: cell line


title: E14 ESCs 2,5HD-treated, RING1B, Cell Signaling, biological replicate 1

tag: chip antibody


title: ZT0-WT-rep3.13015GP02

source_name: ZT0-WT, liver

value: WT

tag: strain

value: female


title: ZT12-KO-rep3.13015GP03

source_name: ZT12-KO, liver

value: KO


title: ZT12-KO-rep4.13015GP01


title: ZT0-WT-rep4.13015GP07


title: RNA-Seq_MCF7_siCTL_DMSO

tag: treatment

value: siCTL


title: E14 ESCs untreated, RING1B, Cell Signaling, biological replicate 1

value: mouse E14 (embryonic stem cells)

value: human MCF-7 (mammary gland epithelial tumor cells)

value: anti-RING1B (Cell Signaling D22F2)


title: SG_NK_B_5

source_name: SG

value: SG

tag: replicate

value: NK

value: B6 Eomes-GFP

tag: batch

value: B


title: ZT8-WT-rep1.13015GP06

tag: Sex

tag: collection time

value: liver


title: WF4

status: Public on Feb 12 2023

city: New York

first: Aya

last: Osman

address: 109 east 102nd street, apartment 3c

department: Neurology

institute: Icahn School of Medicine Mount Sinai

data_processing:
The sequencing library was validated on the Agilent TapeStation, (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (ThermoFisher  Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The libraries were then multiplexed and sequenced on an Illumina HiSeq 4000 instrument using a 2x150bp Paired End (PE) configuration according to manufacturer’s instructions.
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.
The raw RNA-Seq reads (Fastq files) for each sample were aligned and read counts generated using the cloud-based BioJupies software package using the default settings [1]
Raw count matrices were then analyzed using the Network Analyst Software package with the variance filter set to 5% and the low abundance filter set to 2 [2,3]. Data were normalized to Log2 counts per million. Differential gene expression analysis was then performed using Deseq2. Statistical significance was set at a threshold of FDR-corrected p < 0.2 except as described.
Assembly: The raw RNA-Seq reads (Fastq files) for each sample were aligned and read counts generated using the cloud-based BioJupies software package using the default settings
Supplementary files format and content: tab-delimited text files including Raw Counts for each sample

source_name: Nucleus Accumbens

extract_protocol:
RNA was harvested using g RNeasy kits (Qiagen-#74106)
The RNA sequencing library was generated using NEBNext Ultra II RNA library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA).

value: Nucleus Accumbens

value: Bulk tissue

value: Wt

value: Male


title: circRNA-Seq_MCF7_DMSO

value: Breast cancer cell line

value: DMSO


title: WF3


title: Repl_BPT_Lowtype_Stress R2

city: Bangalore

first: Vidya

last: Niranjan

address: Mysuru Road, Kengeri

country: India

institute: R V College of Engineering

hyb_protocol: Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method

organism: Oryza sativa

source_name: Whole Seedling

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

extract_protocol: RNA Extraction was performed using Sigma-Spectrum RNA isolation kit as per the manufacturer's recommendations.

value: whole seedlings

value: stress

tag: type

value: low type


title: Repl_BPT_Lowtype_Control R2

tag: tissue

value: control


title: Repl_BPT_Lowtype_Stress R1


title: WE3

tag: genotype


title: Repl_BPT_Lowtype_Control R1


title: WE4


title: WF2


title: Hightype-Stress-R2

value: high type


title: Hightype-Stress-R1


title: WD1


title: Hightype-Control-R1


title: WA3


title: WE1


title: WD3


title: WE2


title: WC2


title: WC3


title: PF1


title: PE3


title: WB1


title: WB3


title: WB2


title: Hightype-Control-R2


title: PD3


title: PC4


title: PC3


title: PD4


title: WA2


title: PF4


title: PF3


title: PA2


title: PE4


title: PB2


title: PE2


title: WB4


title: MERVL-KD_8C_ATAC_rep2

city: Shinjuku-ku

first: Akihiko

last: Sakashita

state: Tokyo

address: 35 Shinanomachi

department: Department of Molecular Biology,

country: Japan

institute: Keio University School of Medicine

data_processing:
Basecalls performed using bcl2fastq version 2.20.0.
Raw paired-end RNA-seq reads were aligned to the indexed mouse genome (GRCm38/mm10) using STAR aligner (version 2.5.3a). with following options, --twopassMode Basic; --outSAMtype BAM SortedByCoordinate; --outFilterType BySJout; --outFilterMultimapNmax 1; --winAnchorMultimapNmax 50; --chimSegmentMin 12; --chimJunctionOverhangMin 8; --alignSJoverhangMin 8; --alignSJDBoverhangMin 10; --outFilterMismatchNmax 999; --outFilterMismatchNoverReadLmax 0.04; --alignSJstitchMismatchNmax 5 -1 5 5; --outSAMattrRGline ID:GRPundef; --alignIntronMin 20; --alignIntronMax 1000000; --alignMatesGapMax 1000000 for unique alignments. Raw paired-end ATAC-seq reads  were filtered by TrimGalore with defalt setting and aligned to indexed mouse genome (GRCm38/mm10) using bowtie2 with following options, -N 1; -L 25; --no-mixed; --no-discordant. Multiple aligned reads and PCR duplicates were removed using grep -v ‘XS:’ and MarkDuplicates function with REMOVE_DUPLICATES=true option, a part of Picard tools.
Aligned RNA-seq output file (.bam) was input to the featureCounts function, a part of the Subread package, to quantify uniquely aligned reads on respective annotated transcript loci (NCBI RefSeq transcripts). Read count output file (.txt) was input to the DESeq2 package version 1.16.1, to detect differentially expressed genes between two biological samples.
Based on aligned ATAC-seq output file (.bam), peak calling was performed using MACS2 (version 2.1.4) with default arguments; we used a cut-off of P < 10-5. For k-means clustering of ATAC-seq peaks, we firstly generated a set of regions that were called peaks with MACS2 in at least one of the samples, by merging ATAC-seq peak regions of all biological replicates using the mergeBed function from BEDTools (version 2.30.0). Using this merged peak file and ATAC-seq data from control embryos, we ran k-means clustering analysis using computeMatrix and plotHeatmap program as implemented in deepTools (version 3.1.3) and determined that k=5 was suitable for our data.
To visualize enrichment of RNA-seq and ATAC-seq reads over representative genomic loci, bigWig files (.bw) were created from sorted BAM files using the bamCoverage function as implemented in deepTools (version 3.1.3). Figures for continuous tag counts over selected genomic intervals were created in the IGV browser (Broad Institute).
Genome_build: mm10
Supplementary_files_format_and_content: Read count data (.txt) and read coverage data (.bw) from RNA-seq analysis. Read coverage data (.bw) from ATAC-seq analysis.

source_name: MERVL-KD 8-cell stage embryo

growth_protocol: Eight-weeks old female and male B6D2F1 (BDF1) mice were purchased from the Japan SLC, Inc. All animal experiments were reviewed and approved by the Institutional Animal Care and Use Committee (protocol no. 09105-(10) and 11045-(6)) at Keio University, where mice were maintained and fed ad libitum with standard diet and water in a temperature- and light-controlled room (23℃±3℃, 14 light/10 dark cycle).

extract_protocol:
Acidic Tyrode’s solution (Sigma) containing 0.2% PVA was used to remove the zona pellucida (ZP) from embryos before sample collection.
For preparation of RNA-seq library, 30 each ZP-free embryos were lysed in 1x Lysis Buffer containing RNase inhibitor (0.2 IU/µl, from SMART-Seq Stranded Kit, Clontech), directly. RNAs were randomly sheared by heating at 85℃ for 8 min and supplied to reverse transcription with random hexamers and PCR amplification. Ribosomal fragments were depleted from each cDNA sample with scZapR and scR-Probes. Indexed total RNA-seq libraries were enriched by second PCR amplification. For preparation of ATAC-seq library, 30 each ZP-free embryo was lysed in 6 µl of Lysis Buffer (10 mM Tris-HCl (pH7.4), 10 mM NaCl, 3 mM MgCl2 and 0.5% NP-40) for 10 min on ice. After cell lysis, 2 µl of ddH2O, 10 µl of 2x TD Buffer (from Nextera XT DNA Prep Kit, Illumina) and 2 µl of Tn5 Transposase (from Nextera XT DNA Prep Kit, Illumina) were added to the lysates, which were mixed by pipetting followed by incubated at 37℃ for 30 min. To stop transposase reaction, 5 µl of 0.5% SDS was added and incubated at RT for 5 min. After Tn5 tagmentation, 100 ng Carrier RNA (Yeast tRNA, Sigma) was added and then messed up samples to 130 µl with 1x TE Buffer (10 mM Tris-HCl (pH8.0) and 1mM EDTA). Tagmented DNA was purified by phenol-chloroform extraction and ethanol precipitation with 20 µg of glycogen as carrier and dissolved in 20 µl of ddH2O. Afterwards, PCR was performed to amplify and index libraries using the following conditions: 72℃ for 5 min and 98℃ for 30 sec, followed by 18 cycles each of 98℃ for 10 sec, 63℃ for 30 sec and 72℃ for 1 min, with NEBNext HiFi PCR Master Mix and specific index primer sets.

treatment_protocol: Female mice were superovulated by intraperitoneal administrations of 150 µl of CARD HyperOva (Kudo) followed 48 hrs. later with 7.5 IU of human chorionic gonadotropin (hCG, Asuka Pharmaceutical Co.). After injection of hCG, females were housed with male mice overnight for copulation. Following day, zygotes were collected from oviducts of superovulated/mated females. The microinjection was carried out under phase-contrast inverted microscope (IX73, Olympus) equipped with micromanipulation system (Narishige). Each 20 µM antisense oligonucleotide was microinjected into the male pronuclear of zygotes using FemtoJet 4i (Eppendorf). Embryos were cultured in KSOM (MR-101-D, Sigma) at 37℃ with 5% CO2.

tag: days post-coitum (dpc)

value: 2.5 dpc

tag: experimental conditions

value: MERVL-KD

tag: background strain


title: PC2


title: PB4


title: PC1


title: MERVL-KD_4C_ATAC_rep2

source_name: MERVL-KD 4-cell stage embryo


title: PA3


title: Ctrl_8C_ATAC_rep2

source_name: Control 8-cell stage embryo

value: Control


title: Ctrl_8C_ATAC_rep1


title: Input JMJ14 in TRB3-ZF

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Input JMJ14 in TRB3-ZF

data_processing:
All libraries were sequenced at a length of 50 bps with HiSeq 2500 or NovaSeq 6000 platforms following manufacturer’s instructions (Illumina). Raw reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie2 (v2.1.0)43, allowing only uniquely mapped reads with perfect matches. Duplicated reads were removed with Samtools (v1.9)44. Peaks were called using MACS2 (v2.1.1)45.
BS-sPCR reads were mapped to TAIR10 reference genome by bsmap (v2.90) with allowing 2 mismatches and 1 best hit (-v 2 -w 1)46. Reads with three or more consecutively methylated CHH sites were considered as non-converted reads and removed from the analyses. DNA methylation levels were calculated by #C/ (#C + #T). Differential Methylated Regions (DMRs) were called by methdiff function with every 100bp bin for where the difference in CG, CHG, and CHH methylation are at least 0.4, 0.2, and 0.1, respectively.
Assembly: tair10
Supplementary files format and content: bigWig, Wig, Peak

source_name: Arabidopsis leaf tissue

growth_protocol: Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown under green house condition (16 h light/8 h dark, 22C). Floral tissues were collected from 5-6 week plants

extract_protocol:
ChIP seq: Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer’s instructions. BS seeq: 300 ng of DNA was sheared to 200bp with a Covaris S2 (Covaris). Libraries were prepared with the Epitect Bisulfite Conversion kit (QIAGEN) and the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer’s instructions. RNA seq: 1 ug of total RNA was used for library preparation with TruSeq Stranded mRNA kit (Illumina). Libraries were sequenced on HiSeq 2500 or NovaSeq 6000 (Illumina).
ChIP-seq library preparation: 2-3 grams of inflorescence and meristem or leaf tissues were used for Flag and Myc ChIP-seq. ChIP were performed as described previously60 with anti-FLAG M2 (Sigma) and anti-Myc (Cell signaling)

value: leaf tissue

tag: developmental stage

value: 3-4 weeks

tag: target protein

value: input


title: Input JMJ14 in TRB2-ZF

description: Input JMJ14 in TRB2-ZF


title: Input JMJ14 in TRB1-ZF replicate1

description: Input JMJ14 in TRB1-ZF replicate1


title: Input JMJ14 in TRB1-ZF replicate2

description: Input JMJ14 in TRB1-ZF replicate2


title: Input Col-0

description: Input Col-0


title: 72 hours_3

city: Manchester

first: Juan

middle: Fernando

last: Quintana

address: 2.18c CTF, Grafton Street

department: Lydia Becker Institute of Immunology and Inflammation

institute: University of Manchester

description:
iPSC-derived human brain organoids 72h
BGI Technology

data_processing:
Upon sequencing, the data was filtered using the software SOAPnuke (BGI proprietary), incluiding adaptor removal, reads containing N values greater than 5%, and remove low-quality reads (base quality score <15%)
Reads were mapped against the Homo sapiens genome (GCF_000001405.38_GRCh38.p12) using HISAT to generate Fastq files
Assembly: Hg38
Supplementary files format and content: excel file containing include FPKM, TPM, and read counts for all the samples included in this project

source_name: Human brain organoids

extract_protocol:
Total RNA was purified using mRNeasy kit (Qiagen) and eluted in 50 uL of EB (Qiagen)
polyadenylated mRNAs were enriched using Oligo dT selection, followed by cDNA synthesis using random N6-primed reverse transcription and a second-strand cDNA synthesis with dUTP instead of dTTP. The synthesised cDNA was then subjected to end-repair and 3' adenylated, followed by adaptor ligation to both ends. The dUTP-marked strand was selectively degraded using Uracil-DNA-Glycosylase (UDG).
The remaining strand was amplified to generate a cDNA library suitable for sequencing prior to several cyclyes of PCR amplifcation.
The PCR products were heat-denatured and the single strand DNA was cyclised by splint oligos and DNA ligase, followed by DNA nanoball synthesis and sequencing on DNBSEQ platform (BGI)

value: Human brain organoids

tag: cell type

value: Induced pluripotent embryonic stem cells

value: WT

value: 72h co-culture with T. b. gambiense


title: 24 hours_3

description:
iPSC-derived human brain organoids 24h
BGI Technology

tag: cell line

value: 24h co-culture with T. b. gambiense


title: MERVL-KD_4C_ATAC_rep1


title: MERVL-KD_2C_ATAC_rep2

source_name: MERVL-KD 2-cell stage embryo

value: 1.5 dpc


title: 72 hours_1


title: Myc ChIPseq  results JMJ14 in TRB3-ZF

description: Myc ChIPseq JMJ14 in TRB3-ZF

tag: antibody

value: Anti-Myc(Cell signaling)

value: MYC


title: MERVL-KD_2C_ATAC_rep1


title: Ctrl_4C_ATAC_rep2

source_name: Control 4-cell stage embryo


title: FLAG ChIPseq results  TRB3 replicate 4

description: FLAG ChIPseq TRB3 replicate 4

source_name: Arabidopsis floral tissue

value: floral tissue

value: 5-6 weeks

tag: strain

value: Anti-flag (Abcam)

value: FLAG


title: Myc ChIPseq  results JMJ14 in TRB1-ZF replicate2

description: Myc ChIPseq JMJ14 in TRB1-ZF replicate2


title: Myc ChIPseq  results JMJ14 in TRB1-ZF replicate1

description: Myc ChIPseq JMJ14 in TRB1-ZF replicate1


title: MERVL-KD_8C_ATAC_rep1

value: 2.5 dpc

value: MERVL-KD


title: Ctrl_4C_ATAC_rep1

value: Control


title: 24 hours_2

tag: treatment


title: Myc ChIPseq  results JMJ14

description: Myc ChIPseq JMJ14

value: leaf tissue

value: 3-4 weeks


title: Myc ChIPseq  results Col-0

description: Myc ChIPseq Col-0


title: Myc ChIPseq  results JMJ14 in TRB2-ZF

description: Myc ChIPseq JMJ14 in TRB2-ZF


title: FLAG ChIPseq results  TRB3 replicate 3

description: FLAG ChIPseq TRB3 replicate 3


title: 72 hours_2

value: Human brain organoids


title: Untreated 3

description:
iPSC-derived human brain organoids untreated
BGI Technology

value: Induced pluripotent embryonic stem cells

value: untreated


title: Untreated 2

value: WT


title: 24 hours_1

value: 24h co-culture with T. b. gambiense


title: Ctrl_2C_ATAC_rep2

source_name: Control 2-cell stage embryo

value: 1.5 dpc


title: MERVL-KD_8C_RNA_rep2


title: FLAG ChIPseq results Col0 replicate 3

description: FLAG ChIPseq Col0 replicate 3


title: Untreated 1


title: FLAG ChIPseq results  Col0 replicate 4

description: FLAG ChIPseq Col0 replicate 4


title: FLAG ChIPseq results  TRB2 replicate 3

description: FLAG ChIPseq TRB2 replicate 3


title: Ctrl_2C_ATAC_rep1


title: FLAG ChIPseq results  TRB1 replicate 3

description: FLAG ChIPseq TRB1 replicate 3


title: BSPCR results for TRB3-ZF-Replicate2

description: BSPCR results for TRB3-ZF-Replicate2

data_processing:
All libraries were sequenced at a length of 50 bps with HiSeq 2500 or NovaSeq 6000 platforms following manufacturer’s instructions (Illumina). Raw reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie2 (v2.1.0)43, allowing only uniquely mapped reads with perfect matches. Duplicated reads were removed with Samtools (v1.9)44. Peaks were called using MACS2 (v2.1.1)45.
RNA-seq analysis: Cleaned short reads were aligned to reference genome tair10 by Bowtie2 (v2.1.0), and expression abundance was calculated by RSEM with default parameters68. Heatmaps were visualized with the R package pheatmap. To reduce false positive of differential expression, transcripts with less than 5 reads of all replicates in total were regarded as lowly expressed genes and have been removed in subsequent analysis. Differential expression analysis was conducted using edgeR. A threshold of p value < 0.05 and Fold Change > 2 were used to decide whether significant expression difference exists between samples.
ChIP-seq analysis: ChIP-seq fastq reads were aligned to the TAIR10 reference genome with Bowtie (v1.1.2)70, allowing only uniquely mapping reads with 0 mismatches. Duplicated reads were removed by Samtools. ChIP-seq peaks were called by MACS2 (v2.1.1) and annotated with ChIPseeker71. Differential peaks were called by bdgdiff function in MACS2. ChIP-seq data metaplots were plotted by deeptools (v2.5.1)72. For Pol II 5’ occupancy analysis, Pol II occupancy was calculated based normalized reads count (RPKM) on a TSS +/- 200 bp region and a TSS +500 bp to TTS gene body region by bedtools.
Whole genome bisulfite sequencing (BS-seq) analysis: Trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim adapters after filtering low quality reads. BS-seq reads were aligned to TAIR10 reference genome by Bismark (v0.18.2)73 with default settings. Reads with three or more consecutive CHH sites were considered as unconverted reads and filtered. DNA methylation levels were defined as #C/ (#C + #T). DMRs (Differentially Methylated Regions) were called by DMRcaller with p < 0.01 for where the differences in CG, CHG, and CHH methylation were at least 0.4, 0.2, and 0.1, respectively.
BS-PCR analysis: BS-PCR data were analyzed with a previously published pipeline. BS-PCR data were trimmed with primer sequences and mapped to TAIR10 reference genome with bsmap (v2.90) allowing 2 mismatches and 1 best hit (-v 2 -w 1).
BS-sPCR reads were mapped to TAIR10 reference genome by bsmap (v2.90) with allowing 2 mismatches and 1 best hit (-v 2 -w 1)46. Reads with three or more consecutively methylated CHH sites were considered as non-converted reads and removed from the analyses. DNA methylation levels were calculated by #C/ (#C + #T). Differential Methylated Regions (DMRs) were called by methdiff function with every 100bp bin for where the difference in CG, CHG, and CHH methylation are at least 0.4, 0.2, and 0.1, respectively.
Assembly: Tair10
Supplementary files format and content: bed, bigwig, wig

extract_protocol:
ChIP seq: Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer’s instructions. BS seq: 300 ng of DNA was sheared to 200bp with a Covaris S2 (Covaris). Libraries were prepared with the Epitect Bisulfite Conversion kit (QIAGEN) and the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer’s instructions. RNA seq: 1 ug of total RNA was used for library preparation with TruSeq Stranded mRNA kit (Illumina). Libraries were sequenced on HiSeq 2500 or NovaSeq 6000 (Illumina).
Plants total RNAs were extracted with TRIzol and Direct-zol RNA Miniprep kit (Zymo, R2050). Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina) following the manufacturer instructions.
RNA-seq library preparation: Plants total RNAs were extracted with TRIzol and Direct-zol RNA Miniprep kit (Zymo, R2050). Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina) following the manufacturer instructions.
ChIP-seq library preparation: 10 grams of inflorescence and meristem tissues were used for Flag, H3, H3K4me3, and H3K27me3 ChIP-seq. ChIP were performed as described previously60 with anti-FLAG M2 (Sigma), anti-H3 (Ab1791, Abcam), anti-H3K4me3 (Milipore Sigma 04-745),  andanti-H3K4me3 (Milipore Sigma 07-449) antibodies.
BS-PCR and McrBC assay for FWA tandem repeat: For BS-PCR of FWA tandem repeat, genomic DNA was extracted from leaf tissue of TRB-ZF T2 lines as well as fwa with CTAB-based method and converted using the Epitect Bisulfite kit kit (Qiagene research). Methylation level of FWA promoter region and several control regions have been amplified with primers described previously46. HiSeq 2500 (Illumina) sequencing libraries were made from purified PCR products using a Kapa Hyper DNA Library Prep kit. For McrBC of FWA tandem repeat, genomic DNA was extracted from leaf tissue with CTAB-based method, and treated with PureLink RNase (Invitrogen) and then with McrBC (NEB) for 4 hours at 37°C. FWA tandem repeat region was quantified by qPCR.

tag: ecotype


title: BSPCR results for TRB2-ZF-Replicate2

description: BSPCR results for TRB2-ZF-Replicate2


title: BSPCR results for fwa-Replicate2

description: BSPCR results for fwa-Replicate2


title: BSPCR results for fwa-Replicate1

description: BSPCR results for fwa-Replicate1


title: Acinar cells, p53 KO, biol.rep2

city: Saarbrücken

first: Fabian

last: Müller

address: Campus A 2.4

country: Germany

institute: Saarland University

data_processing:
FASTQ files were aligned to the mouse genome mm10 using bowtie. Alignments were processed to remove reads that did not align to the genome or aligned to the mitochondrial genome or sex chromosomes. PCR duplicates were removed using picard tools. Accessible regions of the genome were called using MACS2. ChrAccR (version 0.9.18) was used to process aligned and filtered reads from BAM files and to identify a consensus peak set and to summarize counts for genomic regions of interest. To assess differential accessibility, DESeq2 was applied using a model to account for mouse model, cell type, and batch.
Assembly: mm10
Supplementary files format and content: *_fragments.bed.gz' contain filtered ATAC-seq fragment files. Fragment end coordinates have been adjusted for Tn5 insertion center
Supplementary files format and content: consensusPeaks.bed' contains genomic coordinates of the consensus peak set from all samples. 'consPeaks_diffAcc_AciKO_vs_AciWT.tsv.gz' contains differential accessibility metrics comparing the Aci_KO vs ci_WT groups on the consensus peak set

source_name: Pancreas

extract_protocol:
The pancreata from mice were resected and dissociated. Briefly, dissociation was done through consecutive steps, starting with collagenase (2.5 mg/mL of collagenase D + 0.1 mg/mL DNAse I in HBSS) for 10 min at 37°C, warm Trypsin-EDTA solution (0.05%) for 5 min at 37°C, DNAse I (0.1 mg/mL in PBS) and warm dispase solution (2 U/mL of dispase + 0.1 mg/mL DNAse I in PBS). After dissociation, acinar cells were sorted using a surface marker for acinar cell identity (CD49F), as well as markers to exclude ductal-like cells (CD133), erythroid (TER-119) and immune cells (CD45).
50,000 acinar cells from single cell suspensions were washed in PBS and resuspended in lysis buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2, an 0.1% IGEPAL CA-630), followed by centrifugation and removal of supernatant. Transposition mix (1x TD from Illumina and 2.5 ul of Tn5 transposase in 50ul total) was added to the cell pellet and transposition proceeded at 37˚C for 30 minutes. At the end of the transposition reaction, DNA was purified with a Qiagen minElute column. To create sequencing libraries, transposed DNA was amplified and indexed with Illumina Nextera sequencing primers as previously described (Buenrostro et. al., Nat Meth 10, 1213-1218 (2013)).

value: Pancreas

value: Acinar cells


title: BSPCR results for TRB1-ZF-Replicate2

description: BSPCR results for TRB1-ZF-Replicate2


title: Acinar cells, p53 KO, biol.rep3


title: Ctrl_8C_RNA_rep2


title: Acinar cells, p53 KO, biol.rep4


title: Ctrl_8C_RNA_rep1


title: MERVL-KD_8C_RNA_rep1


title: Acinar cells, p53 KO, biol.rep1


title: BSPCR results for Col0-Replicate1

description: BSPCR results for Col0-Replicate1


title: FLAG ChIPseq results  TRB1 replicate 4

description: FLAG ChIPseq TRB1 replicate 4

value: floral tissue


title: BSPCR results for Col0-Replicate2

description: BSPCR results for Col0-Replicate2

value: 5-6 weeks


title: MERVL-KD_4C_RNA_rep2


title: BSPCR results for TRB3-ZF-Replicate1

description: BSPCR results for TRB3-ZF-Replicate1


title: Input JMJ14

description: Input JMJ14

value: input


title: Acinar cells, p53 wild-type, biol.rep3


title: BSPCR results for TRB1-ZF-Replicate1

description: BSPCR results for TRB1-ZF-Replicate1


title: MERVL-KD_4C_RNA_rep1


title: BSPCR results for TRB2-ZF-Replicate1

description: BSPCR results for TRB2-ZF-Replicate1


title: WGBS data of trb123 replicate 1

description: WGBS data of trb123 replicate 1

source_name: Arabidopsis seedling tissue

value: seedling tissue

value: 2-3 weeks


title: WGBS data of trb123 replicate 2

description: WGBS data of trb123 replicate 2


title: Acinar cells, p53 wild-type, biol.rep1


title: H3K4me3 ChIPseq TRB3 ZF replicate 1

description: H3K4me3 ChIPseq TRB3 ZF replicate 1

value: Anti-H3K4me3 (Millipore Sigma)


title: Ctrl_4C_RNA_rep2

value: 2.5 dpc

value: Control


title: WGBS data of Col0 replicate 1

description: WGBS data of Col0 replicate 1


title: MERVL-KD_2C_RNA_rep2

value: MERVL-KD


title: Ctrl_4C_RNA_rep1


title: CORT treated Hippocampus RNA ZT2_9381

city: Irvine

first: Matthew

last: Birnie

address: Health Sciences Road

institute: University of California-Irvine

data_processing:
Illumina Casava 1.8.2 software was used for basecalling
Sequenced reads were trimmed (to 100bp) for adaptor sequence, mapped to rn6 genome using tophat2 (version 2.0.10)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CuffDiff (version 2.2.0)
Assembly: rn6
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
Hippocampi were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Qiagen miRNeasy RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq stranded Illumina protocols

treatment_protocol: Vehicle (0.45% saline) or Corticosterone-2-hydroxypropyl-β-cyclodextrin (0.75mg/mL) infused for 30 minutes at ZT2.

value: Sprague-Dawley

value: Brain

tag: brain region

value: Hippocampus

tag: age

value: 3-4 months

tag: time


title: H3K4me3 ChIPseq TRB1 ZF replicate 3

description: H3K4me3 ChIPseq TRB1 ZF replicate 3


title: H3K4me3 ChIPseq TRB2 ZF replicate 1

description: H3K4me3 ChIPseq TRB2 ZF replicate 1


title: H3K4me3 ChIPseq TRB1 ZF replicate 1

description: H3K4me3 ChIPseq TRB1 ZF replicate 1


title: H3K27me3 ChIPseq TRB3 ZF replicate 1

description: H3K27me3 ChIPseq TRB3 ZF replicate 1

value: Anti-H3K27me3 (Millipore Sigma)


title: H3K4me3 ChIPseq fwa replicate 3

description: H3K4me3 ChIPseq fwa replicate 3


title: H3K27me3 ChIPseq TRB2 ZF replicate 1

description: H3K27me3 ChIPseq TRB2 ZF replicate 1


title: Ctrl_2C_RNA_rep2

value: 1.5 dpc


title: CORT treated Hippocampus RNA ZT2_9337


title: H3K4me3 ChIPseq fwa replicate 1

description: H3K4me3 ChIPseq fwa replicate 1


title: MERVL-KD_2C_RNA_rep1


title: H3K27me3 ChIPseq TRB1 ZF replicate 1

description: H3K27me3 ChIPseq TRB1 ZF replicate 1


title: H3K27me3 ChIPseq fwa replicate 1

description: H3K27me3 ChIPseq fwa replicate 1


title: WGBS data of Col0 replicate 2

description: WGBS data of Col0 replicate 2


title: Acinar cells, p53 wild-type, biol.rep2

value: Pancreas


title: CORT treated Hippocampus RNA ZT2_9336


title: Untreated Hippocampus RNA ZT2_9493

value: Vehicle (0.45% saline)


title: H3 TRB3 ZF

description: H3 TRB3 ZF

value: floral tissue

value: Anti-H3 (Abcam)


title: Untreated Hippocampus RNA ZT2_9491


title: H3 ChIPseq TRB1 ZF replicate 3

description: H3 ChIPseq TRB1 ZF replicate 3

value: 5-6 weeks


title: ALRM_Adult astrocytes_3

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl DM6.gtf none -d [TAG DIR] -count 3utr -condenseGenes -strand +
single end protocol R2 used for 7N barcode + 8N UMI concatenated to R1 headed
Genome_build: DM6
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

organism: Drosophila melanogaster

source_name: Adult astrocytes

growth_protocol: Flies were reared at 25°C under standard laboratory conditions on molasses-containing food.

extract_protocol:
Pools of 1000 DsRed+ positive cells were sorted using a 100μm nozzle and low pressure in BD FACSAria III (BD Bioscience) cell sorter directly into 100μl Pico-Pure RNA isolation kit extraction buffer (Life Technologies), followed by RNA extraction using the kit or stored in -80°C for later use. To minimize injury or stress responses, samples were kept on ice whenever possible.
To produce expression libraries, we used a derivation of MARS-seq (Jaitin et al., 2014). Briefly, mRNA was barcoded, converted into cDNA and linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into an Illumina sequencing-ready library through ligation, RT and PCR. Prior to sequencing, libraries were evaluated by Qubit fluorometer (ThermoFisher) and TapeStation (Agilent).
3' MARseq  Jaitin et al, 2014

treatment_protocol: Brain dissociation and sorting of astrocytes was done as described previously (Alyagor et al., 2018). Briefly, L3 or adult brains were dissected in ice cold Ringer’s solution, incubated at 29°C with collagenase/dispase (Roche, 15 min for larval brains and 30 min for adult brains), washed in dissociation solution (Sigma-Aldrich), mechanically dissociated by pipetting into single cells and transferred via a 35µm mesh (Falcon) to eliminate clusters and debris.

value: Adult

tag: selection marker

value: DsRed


title: ALRM_Adult astrocytes_4

tag: tissue


title: CORT treated Hippocampus RNA ZT2_9338


title: Untreated Hippocampus RNA ZT2_9375


title: H3 TRB2 ZF

description: H3 TRB2 ZF


title: FLAG ChIPseq results  TRB2 replicate 4

description: FLAG ChIPseq TRB2 replicate 4

value: Anti-flag (Abcam)

value: FLAG


title: H3 ChIPseq TRB1 ZF replicate 1

description: H3 ChIPseq TRB1 ZF replicate 1


title: H3 ChIPseq fwa replicate 3

description: H3 ChIPseq fwa replicate 3


title: ALRM_Adult astrocytes_1


title: Methylprednisolone Hippocampus RNA ZT22_4026

data_processing:
Illumina Casava 1.8.2 software was used for basecalling
Sequenced reads were trimmed (to 100bp) for adaptor sequence, mapped to rn6 genome using tophat2 (version 2.0.10)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CuffDiff (version 2.2.0)
Assembly: rn6
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Hippocampus

treatment_protocol: Vehicle (normal drinking water) or methylprednisolone (1mg/mL) in drinking water for 5 days, ad libitum

value: Methylprednisolone (20mg per day)

tag: timepoint


title: H3 ChIPseq fwa replicate 1

description: H3 ChIPseq fwa replicate 1


title: Untreated Hippocampus RNA ZT2_9373


title: ALRM_L3_2

source_name: Third instar larva (L3) astrocytes


title: ALRM_Adult astrocytes_2


title: H3K4me3 ChIPseq fwa replicate 2

description: H3K4me3 ChIPseq fwa replicate 2

value: Anti-H3K4me3 (Millipore Sigma)


title: Ctrl_2C_RNA_rep1

tag: days post-coitum (dpc)

value: Control


title: H3K4me3 ChIPseq TRB1 ZF replicate 2

description: H3K4me3 ChIPseq TRB1 ZF replicate 2


title: Methylprednisolone Hippocampus RNA ZT22_4025

value: Sprague-Dawley

value: Brain


title: H3K4me3 ChIPseq TRB3 ZF replicate 2

description: H3K4me3 ChIPseq TRB3 ZF replicate 2


title: Methylprednisolone Hippocampus RNA ZT22_4023

value: Hippocampus

value: 3-4 months


title: H3 ChIPseq TRB3 ZF replicate 2

description: H3 ChIPseq TRB3 ZF replicate 2


title: H3K27me3 ChIPseq fwa replicate 2

description: H3K27me3 ChIPseq fwa replicate 2

value: Anti-H3K27me3 (Millipore Sigma)


title: H3K4me3 ChIPseq TRB2 ZF replicate 2

description: H3K4me3 ChIPseq TRB2 ZF replicate 2


title: H3K27me3 ChIPseq TRB1 ZF replicate 2

description: H3K27me3 ChIPseq TRB1 ZF replicate 2


title: H3K27me3 ChIPseq TRB2 ZF replicate 2

description: H3K27me3 ChIPseq TRB2 ZF replicate 2


title: Methylprednisolone Hippocampus RNA ZT22_4024


title: Methylprednisolone Hippocampus RNA ZT10_4021


title: H3K27me3 ChIPseq TRB3 ZF replicate 2

description: H3K27me3 ChIPseq TRB3 ZF replicate 2


title: Methylprednisolone Hippocampus RNA ZT10_4022


title: H3 ChIPseq TRB2 ZF replicate 2

description: H3 ChIPseq TRB2 ZF replicate 2


title: Methylprednisolone Hippocampus RNA ZT10_4020


title: H3 ChIPseq TRB1 ZF replicate 2

description: H3 ChIPseq TRB1 ZF replicate 2


title: H3 ChIPseq fwa replicate 2

description: H3 ChIPseq fwa replicate 2


title: FLAG ChIPseq TRB3 replicate 2

description: FLAG ChIPseq TRB3 replicate 2

value: Flag


title: FLAG ChIPseq TRB2 replicate 2

description: FLAG ChIPseq TRB2 replicate 2


title: FLAG ChIPseq TRB2 replicate 1

description: FLAG ChIPseq TRB2 replicate 1


title: Methylprednisolone Hippocampus RNA ZT10_4019


title: OMVs@P2O-Ads biol rep1

city: Shenyang

first: li

last: bingwu

address: shenhe

institute: Shenyang Pharmaceutical University

data_processing:
Illumina NovaSeq 6000 reads were trimmed and clipped for quality control in trim_galore
Read quality was checked for each sample using FastQC
Trimmed sequence reads were mapped to GRCm39 using hisat2
Read count extraction by using  fearturecounts
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

source_name: TC-1 cells

extract_protocol:
Cell derived xenografts treated with OMVs@P2O-Ads or PBS were collected and then the total RNA was isolated using RNAiso Plus (TaKaRa).
After removal of the remaining genomic DNA,  mRNA was purified from total RNA using polyT and then fragmented with 10× RNA fragmentation buffer (100 mM Tris-HCl, 100 mM ZnCl2 in nuclease free H2O) and the RNA-seq library was constructed using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen) according to the manufacturer's protocol, and was sequenced using Illumina NovaSeq 6000.

treatment_protocol: TC-1 cells (1×106) were subcutaneously injected into the waist of female C57 mice, and tumor-bearing mice were divided into two groups. When the tumor reached the size of 100-150 mm3, the mice were intratumorally injected with PBS and OMVs@P2O-Ads. The drug was given every three days for four consecutive times, the tumor volume was measured with a vernier caliper, and mice were weighed daily.

value: TC-1 cells

value: adherent cell line

tag: genotype

value: WT


title: PBS biol rep2

value: PBS


title: PBS biol rep1


title: OMVs@P2O-Ads biol rep2


title: ALRM_L3_1


title: FLAG ChIPseq TRB3 replicate 1

description: FLAG ChIPseq TRB3 replicate 1

value: floral tissue

value: 5-6 weeks


title: FLAG ChIPseq TRB1 replicate 2

description: FLAG ChIPseq TRB1 replicate 2

value: Anti-flag (Abcam)


title: 3geneKOWTmale26

city: Iowa City

first: Yann

last: Vanrobaeys

state: IA

address: 169 Newton Road

department: Neuroscience and Pharmacology

institute: University of Iowa

data_processing:
Bulk RNA-seq raw files were processed with bcbio-nextgen-1.2.4.
Assembly: mm10
Supplementary files format and content: Raw count matrix from htseq-counts for the comparison between 16p11.2 del/+ and wild-type mice for males and females.
Supplementary files format and content: Raw count matrix from htseq-counts for the comparison between 3 genes hemodeletion knockout and wild-type mice for males and females.

source_name: Striatum

extract_protocol:
Bulk RNA-seq
Total RNA was extracted from sampled human brains using miRNeasy Mini Kite and homogenized in Qiazol using stainless steel beads. Chloroform was then used for phase separation. RNA containing an aqueous layer was further purified using the RNeasy MinElute spin column. RNA was finally eluted in RNase-free water.
For bulk RNA-seq librairies were prepared using Ribo-Zero gold sample preparation kit. Library concentrations were measured using KAPA Illumina Library Quantification Kit. Polled libraries were sequenced on Illumina NovaSeq6000 sequencer with 150-bp Paired-End chemistry.

value: Striatum

tag: Sex

value: Male

tag: condition

value: Wild-type


title: 3geneKOWTmale34


title: Methylprednisolone Hippocampus RNA ZT18_4018

value: Methylprednisolone (20mg per day)


title: 3geneKOWTmale24


title: Methylprednisolone Hippocampus RNA ZT18_4017

value: Sprague-Dawley


title: FLAG ChIPseq TRB1 replicate 1

description: FLAG ChIPseq TRB1 replicate 1

tag: developmental stage

tag: target protein


title: wt, 0.1xLB, pyruvate, rep 2

city: La Jolla

first: Cameron

last: Lamoureux

address: 9500 Gilman Drive

department: Bioengineering

institute: University of California San Diego

data_processing:
Raw read trimming was performed with Trim Galore using the default options, followed by FastQC on the trimmed reads.
Reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using bowtie with the following optional arguments: -X 1000, -3 3, -n 2
Read direction was inferred with RSEQC.
Read counts were generated with featureCounts with the following optional arguments: -p -B -C -P --fracOverlap 0.5
Quality control metrics were assembled with MultiQC and the final expression was reported in units of log2-transformed transcripts per million for each gene.
Assembly: NC_000913.3
Supplementary files format and content: tcs_log_tpm.csv contains log2[TPM] values for all samples and genes.
Supplementary files format and content: tcs_counts.csv contains raw read counts as computed by featureCounts for all samples and genes.

organism: Escherichia coli str. K-12 substr. MG1655

extract_protocol:
3 ml of cell broth (at an A600 ≈ 0.6) was immediately added to two volumes of Qiagen RNA-protect Bacteria Reagent (6 ml), vortexed for 5 s, incubated at room temperature for 5 min and immediately centrifuged for 10 min at 17,500 r.p.m. The supernatant was decanted, and the cell pellet was stored at −80 °C. Cell pellets were thawed and incubated with Ready-Lyse Lysozyme, SuperaseIn, protease K and 20% SDS for 20 min at 37 °C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase treatment was performed for 30 min at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA nano chip on a bioanalyser. The ribosomal RNA was removed using an Illumina Ribo-Zero rRNA removal kit for Gram-negative bacteria.
A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around 300 bp

tag: culture type

value: batch

tag: media

tag: supplement


title: wt, 0.1xLB, pyruvate, rep 1

tag: strain


title: 3geneKOWTmale17


title: Methylprednisolone Hippocampus RNA ZT18_4016

value: Brain

value: Hippocampus

tag: treatment


title: H3K27me3 ChIPseq trb123 replicate 2

description: H3K27me3 ChIPseq trb123 replicate 2

value: seedling tissue

value: 2-3 weeks

tag: ecotype

tag: antibody

value: Anti-H3K27me3 (Millipore Sigma)


title: wt, M9, LiCl, rep 2


title: 3geneKOWTfemale39

value: Female


title: H3K27me3 ChIPseq trb123 replicate 1

description: H3K27me3 ChIPseq trb123 replicate 1


title: Methylprednisolone Hippocampus RNA ZT18_4015

tag: age

value: 3-4 months


title: wt, M9, LiCl, rep 1


title: 3geneKOWTfemale35


title: wt, M9, LiCl/acetoacetate, rep 2


title: Methylprednisolone Hippocampus RNA ZT6_4013


title: 3geneKOWTfemale30


title: H3K27me3 ChIPseq Col0 replicate 2

description: H3K27me3 ChIPseq Col0 replicate 2


title: wt, M9, LiCl/acetoacetate, rep 1


title: wt, LB, CuSO4, rep 2

value: LB


title: H3 ChIPseq trb123 replicate 2-2

description: H3 ChIPseq trb123 replicate 2

value: Anti-H3 (Abcam)


title: Methylprednisolone Hippocampus RNA ZT6_4012


title: Methylprednisolone Hippocampus RNA ZT6_4011


title: wt, LB, CuSO4, rep 1


title: H3 ChIPseq trb123 replicate 1

description: H3 ChIPseq trb123 replicate 1


title: H3 ChIPseq Col0 replicate 2-2

description: H3 ChIPseq Col0 replicate 2


title: wt, 0.1xLB, rep 1


title: wt, 0.1xLB, rep 2


title: Methylprednisolone Hippocampus RNA ZT14_4010


title: Methylprednisolone Hippocampus RNA ZT14_4009


title: H3 ChIPseq Col0 replicate 1

description: H3 ChIPseq Col0 replicate 1


title: FLAG ChIPseq JMJ14 replicate 2

description: FLAG ChIPseq JMJ14 replicate 2

value: floral tissue

value: 5-6 weeks

value: Flag


title: Methylprednisolone Hippocampus RNA ZT14_4008


title: 3geneKOMutmale27

value: Striatum

value: Male

value: 3 genes hemideletion knockout


title: FLAG ChIPseq JMJ14 replicate 1

description: FLAG ChIPseq JMJ14 replicate 1

value: Anti-flag (Abcam)


title: Methylprednisolone Hippocampus RNA ZT6_4014

value: Sprague-Dawley

value: Methylprednisolone (20mg per day)


title: 3geneKOMutmale33


title: 3geneKOMutmale25


title: 3geneKOMutmale32


title: 3geneKOWTfemale29

value: Wild-type


title: Methylprednisolone Hippocampus RNA ZT14_4007

value: Brain

value: Hippocampus


title: 3geneKOMutfemale37


title: H3K27me3 ChIPseq Col0 replicate 1

description: H3K27me3 ChIPseq Col0 replicate 1

value: seedling tissue

value: 2-3 weeks

value: Anti-H3K27me3 (Millipore Sigma)


title: del rcsB, LB, rep 1

source_name: MG1655 del_rcsB

value: MG1655 del_rcsB

value: batch

value: LB


title: 3geneKOMutfemale36

value: Female


title: del rcsB, LB, ethanol, rep 2


title: FLAG ChIPseq Col0 replicate 2

description: FLAG ChIPseq Col0 replicate 2

value: floral tissue

value: 5-6 weeks

value: Flag


title: Methylprednisolone Hippocampus RNA ZT2_4006

value: 3-4 months


title: Methylprednisolone Hippocampus RNA ZT2_4005


title: del rcsB, LB, rep 2


title: del rcsB, LB, ethanol, rep 1


title: 3geneKOMutfemale28

value: Striatum

value: 3 genes hemideletion knockout


title: 3geneKOMutfemale31


title: H3K4me3 ChIPseq trb123 replicate 1

description: H3K4me3 ChIPseq trb123 replicate 1

value: Anti-H3K4me3 (Millipore Sigma)


title: Methylprednisolone Hippocampus RNA ZT2_4003

value: Sprague-Dawley

value: Methylprednisolone (20mg per day)


title: Methylprednisolone Hippocampus RNA ZT2_4004

value: Brain

value: Hippocampus


title: del cusR, LB, rep 2

source_name: MG1655 del_cusR

value: MG1655 del_cusR


title: H3K4me3 ChIPseq jmj14 replicate 1

description: H3K4me3 ChIPseq jmj14 replicate 1

value: seedling tissue

value: 2-3 weeks


title: del cusR, LB, rep 1

value: batch


title: 16pdelWT_male3

value: Male

value: Wild-type


title: Untreated Hippocampus RNA ZT22_3830

value: Vehicle


title: del cusR, LB, CuSO4, rep 2

value: LB


title: Untreated Hippocampus RNA ZT22_3828


title: Untreated Hippocampus RNA ZT22_3829


title: del cusR, LB, CuSO4, rep 1


title: del btsR, 0.1x LB, pyruvate, rep 2

source_name: MG1655 del_btsR

value: MG1655 del_btsR


title: 16pdelWT_male1


title: H3 ChIPseq jmj14 replicate 1

description: H3 ChIPseq jmj14 replicate 1

value: Anti-H3 (Abcam)


title: 16pdelWT_male2

value: Striatum


title: H3K4me3 ChIPseq Col0 replicate 2

description: H3K4me3 ChIPseq Col0 replicate 2


title: FLAG ChIPseq Col0 replicate 1

description: FLAG ChIPseq Col0 replicate 1

value: floral tissue

value: 5-6 weeks

value: Anti-flag (Abcam)

value: Flag


title: H3K4me3 ChIPseq trb123 replicate 2

description: H3K4me3 ChIPseq trb123 replicate 2

value: Anti-H3K4me3 (Millipore Sigma)


title: 16pdelWT_female4

value: Female


title: del btsR, 0.1x LB, pyruvate, rep 1


title: 16pdelWT_male4


title: del btsR, LB, rep 2


title: H3 ChIPseq trb123 replicate 2

description: H3 ChIPseq trb123 replicate 2


title: 16pdelWT_female2


title: H3 ChIPseq Col0 replicate 2

description: H3 ChIPseq Col0 replicate 2


title: del btsR, LB, rep 1


title: del btsR, 0.1x LB, rep 2


title: RNA seq data of trb123 replicate 3

description: RNA seq data of trb123 replicate 3


title: 16pdelhet_male4


title: H3K4me3 ChIPseq Col0 replicate 1

description: H3K4me3 ChIPseq Col0 replicate 1


title: RNA seq data of trb123 replicate 2

description: RNA seq data of trb123 replicate 2


title: del atoC, M9, rep2

source_name: MG1655 del_atoC

value: MG1655 del_atoC


title: del btsR, 0.1x LB, rep 1


title: 16pdelhet_male2


title: Untreated Hippocampus RNA ZT10_3825

value: Sprague-Dawley

value: Brain

value: Hippocampus

value: 3-4 months


title: 16pdelWT_female3

value: Wild-type


title: Untreated Hippocampus RNA ZT18_3822

value: Vehicle


title: Untreated Hippocampus RNA ZT22_3827


title: Untreated Hippocampus RNA ZT18_3821


title: Untreated Hippocampus RNA ZT10_3826


title: RNA seq data of trb123 replicate 1

description: RNA seq data of trb123 replicate 1

value: seedling tissue

value: 2-3 weeks


title: Untreated Hippocampus RNA ZT10_3823


title: RNA seq data of jmj14 replicate 3

description: RNA seq data of jmj14 replicate 3


title: RNA seq data of jmj14 replicate 2

description: RNA seq data of jmj14 replicate 2


title: Untreated Hippocampus RNA ZT18_3820


title: Untreated Hippocampus RNA ZT10_3824


title: 16pdelhet_male3

value: Male


title: del atoC, M9, LiCl, rep2

value: batch


title: RNA seq data of jmj14 replicate 1

description: RNA seq data of jmj14 replicate 1


title: 16pdelWT_female1

value: Striatum


title: del atoC, M9, LiCl, rep1


title: 16pdelhet_female4


title: 16pdelhet_female3


title: del atoC, M9, LiCl/acetoacetate, rep 2


title: Untreated Hippocampus RNA ZT6_3818


title: 16pdelhet_female2


title: 16pdelhet_female1


title: Untreated Hippocampus RNA ZT6_3817


title: 16pdelhet_male1


title: del atoC, M9, LiCl/acetoacetate, rep 1


title: Untreated Hippocampus RNA ZT6_3816


title: RNA seq data of Col0 replicate 1

description: RNA seq data of Col0 replicate 1


title: Untreated Hippocampus RNA ZT6_3815


title: RNA seq data of TRB3 ZF replicate 3

description: RNA seq data of TRB3 ZF replicate 3

source_name: Arabidopsis leaf tissue

value: leaf tissue

value: 5-6 weeks