title: M_Hippocamp_3_sequencingreplicate

data_processing:
Barcode extraction from sample fastq - see bitbucket repository for script. Requires flanking 14 bp around barcode to be identical to design, plus a 10bp sequence to be found in between the flanks. All 10bp sequences extracted from Fastqs into text file.
Tabulation of barcode counts for each sample using table() in R. Subsequently, merging to a metadata table on designed barcodes to drop sequences that were not a perfect match to a designed barcode.
Filtering for low read counts, poor barcode representation across replicates, etc. Described at length in Supplementary Methods.
Calculation of log2(cpm RNA barcode) / log2(cpm DNA barcode) for each retained barcode in each sample.
Subtract the within-sample mean of "basal" (minimal-promoter-only) barcode expression from all other barcode expression values --> REML linear mixed model: expression ~ allele + sex + sex:allele + (1|BC), where BC is the unique barcode identifier to control for effects of barcode sequence.
Genome_build: hg19-derived sequences (up to 126bp); see enclosed file "Reference-Barcode Sequences, their paired internal identifiers, and the corresponding sequence placed upstream of min promoter.txt" for each allele of each sequence and its paired reporter (RNA) barcodes
Supplementary_files_format_and_content: Tab-delimited text; barcode counts for each RNA sample and the DNA sample.

source_name: Hippocampus

extract_protocol:
Hippocampus dissected away from rest of brain, homogenized with power drill in glass pestle with RNAse inhibitors and translation inhibitor cycloheximide, spun 2,000g, supernatant mixed with 10% NPC and 10% DHPC 20min on ice, 20,000g spin, part of supernatant added to trizol for "input" (total hippocampal) RNA and remainder used for immunoprecipitation of GFP+ ribosomes (i.e. TRAP). See methods in paper for full details.
Reporter-specific cDNA synthesis using a reverse-complementary primer, followed by PCR, digestion, adapter ligation, and index PCR. DNA from plasmid was prepared simultaneously, starting with the first PCR step. Each step was followed by a cleanup using size-selection beads (brands Ampure XP and Magbind).

treatment_protocol: Stereotactic delivery of AAV9 to 1 hippocampal coordinate at 2 depths per side, 2µL of AAV9 per site (4 sites/mouse) 28 days prior to tissue collection.

tag: tissue (trap fraction)

value: Total hippocampus

tag: material

value: RNA


title: P0_A3

status: Public on Feb 10 2023

type: SRA

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: 660 S Euclid Ave, Campus Box 8232

department: Genetics

country: USA

institute: Washington University in St. Louis

library_source: transcriptomic

data_processing:
Barcode extraction from sample fastq - see bitbucket repository for script. Requires flanking 14 bp around barcode to be identical to design, plus a 10bp sequence to be found in between the flanks. All 10bp sequences extracted from Fastqs into text file.
Tabulation of barcode counts for each sample using table() in R. Subsequently, merging to a metadata table on designed barcodes to drop sequences that were not a perfect match to a designed barcode.
For samples prepared and sequenced multiple times (e.g., A8_p0p10coprep and A8_prep1, AAV DNAs), CPM values were calculated for each sample individually and then averaged to get a single CPM value per biological sample.
Filtering for low read counts, poor barcode representation across replicates, etc. Described at length in Supplementary Methods.
Calculation of log2(cpm RNA barcode) / log2(cpm DNA barcode) for each retained barcode in each sample.
Subtract the within-sample mean of "basal" (minimal-promoter-only) barcode expression from all other barcode expression values --> REML linear mixed model: expression ~ allele + sex + sex:allele + (1|BC), where BC is the unique barcode identifier to control for effects of barcode sequence.
Genome_build: hg19-derived sequences (up to 126bp); see enclosed file "Reference-Barcode Sequences, their paired internal identifiers, and the corresponding sequence placed upstream of min promoter.txt" for each allele of each sequence and its paired reporter (RNA) barcodes
Supplementary_files_format_and_content: Tab-delimited text; barcode counts for each RNA sample and the DNA sample.

molecule: total RNA

organism: Mus musculus

source_name: Whole brain

extract_protocol:
Brain dry frozen at -80°C overnight, lysed in 500µL (P0) or 1mL Trizol, the following day, returned to -80. At time of RNA prep,addition of 200uL chloroform and cleanup of the aqueous phase using the Zymo Clean and Concentrator 5 kit per manufacturer instructions. Turbo DNAse-free kit was used to remove incidental DNA
Reporter-specific cDNA synthesis using a reverse-complementary primer, followed by PCR, digestion, adapter ligation, and index PCR. DNA from plasmid was prepared simultaneously, starting with the first PCR step. Each step was followed by a cleanup using size-selection beads (brands Ampure XP and Magbind).

treatment_protocol: Intrauterine AAV9 into brain

tag: tissue

value: brain without cerebellum

tag: age

tag: sequencing prep and run

tag: Sex

value: F


title: P0_A4

value: M


title: LPB [1059]

city: Guelph

first: Samantha

last: Dixon

state: Ontario

address: 50 Stone Rd E

department: Animal Biosciences

country: Canada

institute: University of Guelph

description: DESeqControlvsLow

data_processing:
RNA-Seq analysis was performed using the CLC genomics workbench software, version 12 (CLC Bio, Aarhus, Denmark). Quality control analysis, including guanine-cytosine (GC) content, ambiguous base content, Phred score, base coverage, nucleotide contributions and over-represented sequences parameters, was performed on fastq files
Sequence reads were aligned to the annotated Oar_v3.1 ovine reference genome (release 95).
Counts per gene were transformed using a Log10 transformation and normalized to reads per kilo base per million mapped reads (RPKM) values
Assembly: Oar_v3.1
Supplementary files format and content: DESeq log2FoldChange

organism: Ovis aries

source_name: liver

extract_protocol:
A representative sample of tissue (30 mg) from the center of the right liver lobe was ground using a mortar and pestle with liquid nitrogen and homogenized using a hand-held homogenizer. Total RNA was extracted following the manufacturer’s instructions using Qiagen RNeasy Mini Prep Kit (Qiagen, Calif., USA).
The NEBNext Ultra RNA Library Prep kit for Illumina (New England Biolabs, Mass., USA) was used for library preparation with Poly-A selection, according to the manufacturer’s recommendations

value: liver

tag: treatment

value: GIN-exposed


title: M_Hippocamp_5

growth_protocol: Ad libitum feeding in single-sex group housing on 12 hour light/dark cycle.


title: M_Hippocamp_6


title: TBIE #2, day2 [TBIE2_2d_s110]

city: Kuopio

first: Mette

last: Heiskanen

address: Neulaniementie 2, P.O.B. 1627

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

data_processing:
Read quality of the raw data was assessed using FastQC v11.8 software produced by the Babraham Institute (Babraham, Cambridgeshire, UK) and the Trimmomatic v0.36 was used to filter low-quality base calls and any adapter contamination. Low-quality leading and trailing bases were removed from each read, and a sliding window trimming using a window of 4 and a phred33 score threshold of 15 was used to assess the quality of the read body. Any reads <17 nucleotides were discarded.
After quality control the replicates for each sample were merged and aligned to the rat reference genome (Rno6) using Bowtie2 using --very-sensitive-local settings. Using the featureCounts program from the Subread package, the number of reads aligned with the known rat miRNAs in accordance with miRBase22 was calculated.
Assembly: Rno6, miRBase22
Supplementary files format and content: compiled matrix table with raw counts for every miRNA in every sample

organism: Rattus norvegicus

source_name: plasma

extract_protocol:
Whole blood was drawn from the lateral tail vein into Microtainer K2 EDTA-tubes. To obtain plasma, tubes were centrifuged at 1300xg for 10 min at 4 °C within 1 hour after blood sampling. RNA was extracted from 200 μl plasma using miRNeasy Mini Kit (#217004, QIAGEN).
Small RNA library preparation was performed using the Illumina TruSeq Small RNA Sample Prep Kit. Briefly, small RNA was isolated from purified RNA by size selection after adapter ligation. The excised product was used for PCR amplification of the resulting product. The quality and yield after sample preparation were measured with a Fragment Analyzer. The size of the resulting products was consistent with the expected size of approximately 150 bp. Single-read sequencing with a read length of 51 nts was performed on a Illumina HiSeq 4000. To increase read depth each sample was sequenced on two flow-cells giving two replicates for each sample.

value: plasma

tag: strain

value: Sprague-Dawley

value: adult

value: male

tag: time

value: Day 2

tag: group

value: traumatic brain injury

tag: outcome

value: epilepsy


title: Low Parasite Burden (LPB) [1024]

description: DESeqControlvsLow


title: M_Hippocamp_4


title: TBIE #7, day2 [TBIE7_2d_s145]


title: TBIE #1, day2 [TBIE1_2d_s102]


title: M_Hippocamp_3


title: HPB [1017]

description: DESeqControlvsHigh


title: M_Hippocamp_2


title: P10_A32


title: High Parasite Burden (HPB) [1010]

description: DESeqControlvsHigh


title: sham #3, day9 [sham3_9d_s171]

value: Day 9

value: sham


title: P0_A2


title: AAV_Lysate6_Rep2

library_source: genomic

data_processing:
Barcode extraction from sample fastq - see bitbucket repository for script. Requires flanking 14 bp around barcode to be identical to design, plus a 10bp sequence to be found in between the flanks. All 10bp sequences extracted from Fastqs into text file.
Tabulation of barcode counts for each sample using table() in R. Subsequently, merging to a metadata table on designed barcodes to drop sequences that were not a perfect match to a designed barcode.
Filtering for low read counts, poor barcode representation across replicates, etc. Described at length in Supplementary Methods.
Calculation of log2(cpm RNA barcode) / log2(cpm DNA barcode) for each retained barcode in each sample.
Subtract the within-sample mean of "basal" (minimal-promoter-only) barcode expression from all other barcode expression values --> REML linear mixed model: expression ~ allele + sex + sex:allele + (1|BC), where BC is the unique barcode identifier to control for effects of barcode sequence.
Assembly: hg19-derived sequences (up to 126bp); see enclosed file "Reference-Barcode Sequences, their paired internal identifiers, and the corresponding sequence placed upstream of min promoter.txt" for each allele of each sequence and its paired reporter (RNA) barcodes
Supplementary files format and content: Tab-delimited text; barcode counts for each RNA sample and the DNA sample.

molecule: genomic DNA

organism: Adeno-associated virus 9

treatment_protocol: Stereotactic delivery of AAV9 to 1 hippocampal coordinate at 2 depths per side, 2µL of AAV9 per site (4 sites/mouse) 28 days prior to tissue collection. Females received either ovariectomy surgery or sham surgery prior to AAV delivery during the same surgical session.

value: Virus

value: DNA

tag: condition


title: HPB [1113]

description: DESeqControlvsHigh


title: F_Hippocamp_5

value: Total hippocampus

value: RNA


title: sham #2, day9 [sham2_9d_s164]


title: F_Hippocamp_4

value: F


title: AAV_Lysate6_Rep1


title: sham #1, day9 [sham1_9d_s157]


title: sham #4, day2 [sham4_2d_s125]


title: AAV_Lyaste5_Rep1


title: F_Hippocamp_2


title: F_Hippocamp_3


title: AAV_seqprep1_techrep3

value: viral DNA


title: AAV_Lyaste5_Rep2


title: F_Hippocamp_1


title: LC24_3   COS-sprayed after 24 hours of cold treament sample3

city: shenyang

first: jun

last: zhang

address: liaoning

country: China

institute: Shenyang Agricultural University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Cucumis sativus.Cucumber (Chinese Long) v3（http://cucurbitgenomics.org/ftp/genome/cucumber/Chinese_long/v3/）
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Cucumis sativus

source_name: leaves

growth_protocol: Cucumber seeds were immersed in 55℃ for 10-15 min water (hot water treatment, HWT), and placed in a moist petri dish for germination in the dark at 28℃. The sprouting seeds were transferred into seedling tray in an incubator with a temperature of 28℃/18℃ (day/night) and photoperiod of 12h/12h (day/night). At the first-true-leaf stage, the robust seedlings were placed to a 7 cm diameter nutrient bowl.

extract_protocol:
The samples of cucumber leaves under cold stress were collected and frozen in liquid nitrogen. The tatal RNA was extracted using Trizol reagent and checked its integrity. The qualified RNA was used to construct cDNA libraries.
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: seedlings at the third-true-leaf were pre-treated with the most effective exogenous substance, 50mg.L-1 COS, or distilled water under normal temperature (28℃/18℃, day/night) for 24h, and then exposed to cold stress (12℃/6℃, day/night) for 0, 3, 12, 24h. The cucumber seedlings were exposed to treatments as follows: LC0 (50mg.L-1 COS-sprayed group, of cold stress 0h), LC3 (50mg.L-1 COS-sprayed group, cold stress 3h), LC12 (50mg.L-1 COS-sprayed group, cold stress 12h), LC24 (50mg.L-1 COS-sprayed group, cold stress 24h), L0 (distilled water-sprayed group, cold stress 0h), L3 (distilled water-sprayed group, cold stress 3h), L12 (distilled water-sprayed group, cold stress 12h), and L24 (distilled water-sprayed group, cold stress 24h). The fully-expanded 2nd and 3rd leaves were sampled for cucumber seedling transcriptome analysis.

value: leaves

tag: cos treatment

value: COS-sprayed

value: cold stress


title: sham #3, day2 [sham3_2d_s117]

value: plasma

value: Sprague-Dawley


title: sham #4, day9 [sham4_9d_s178]

value: adult

value: male


title: sham #2, day2 [sham2_2d_s109]

value: Day 2


title: LC24_2   COS-sprayed after 24 hours of cold treament sample2


title: LC24_1    COS-sprayed after 24 hours of cold treament sample1


title: Male_Vglut1_6

value: Hippocampal Vglut1+

value: M


title: AAV_seqprep2_techrep3


title: sham #1, day2 [sham1_2d_s101]

value: sham


title: LC12_3   COS-sprayed after 12 hours of cold treament sample3


title: LC12_2   COS-sprayed after 12 hours of cold treament sample2


title: AAV_seqprep1_techrep2


title: Male_Vglut1_4


title: RPTi3

city: shanghai

first: daofang

last: ding

address: 1200 Cai Lun Road,Zhangjiang Hi-TechPark,Pudong New Area

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to rat genome assembly Rnor6 (ftp://ftp.ensembl.org/pub/release-89/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz)  using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ensembl.org/pub/release-89/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.89.gtf.gz.
Differential expression analysis of two conditions was performed using the DESeq2 R package (v1.26.0). Pvalue < 0.05 and absolute log2 (fold change) > 0.58 were set as the threshold for significantly differential expression.
Genome_build: Rnor6
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

source_name: cartilage

growth_protocol: Primary rat chonrocytes were routinely cultured with DMEM plus 10% FBS,chondrocytes at passage 1 or passage 2 were used for experiments.

extract_protocol:
Total RNA was extracted by using TRIzol (Invitrogen) according to the manufacturer's instructions.
A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. MRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The library preparations were sequenced on an Illumina HiSeq 4000 platform by Shanghai Life Genes Biotech Co. Ltd (Shanghai, China), and 150 bp paired-end reads were generated.

treatment_protocol: Rat chondrocytes were cultured with Rat Plasma (RP group), and Rat plasma plus thrombin group (RPT group), and Rat plasma plus thrombin and inhibitor group (RPTi group).

value: SD

tag: cell types

value: chondrocytes

value: treated with RPTi for 24 hours


title: RPTi2


title: AAV_seqprep2_techrep4


title: AAV_seqprep2_techrep2


title: Male_Vglut1_3

value: RNA


title: RPTi1


title: Male_Vglut1_2


title: LC12_1    COS-sprayed after 12 hours of cold treament sample1


title: LC3_3    COS-sprayed after 3 hours of cold treament sample3


title: RPT3

value: treated with RPT for 24 hours


title: AAV_seqprep1_techrep1

value: viral DNA


title: Male_Vglut1_1


title: AAV_seqprep2_techrep1


title: LC3_2      COS-sprayed after 3 hours of cold treament sample2

value: leaves


title: Female_Vglut1_6

value: F


title: Female_Vglut1_5


title: LC3_1       COS-sprayed after 3 hours of cold treament sample1

value: COS-sprayed

value: cold stress


title: RPT2


title: Female_Vglut1_4


title: RPT1


title: RP3

value: treated with RP for 24 hours


title: AAV9_Lysate_TechRep3

value: DNA


title: Female_Vglut1_3


title: LC0_2      COS-sprayed without cold treament sample2

value: without cold stress


title: LC0_3      COS-sprayed without cold treament sample3


title: AAV9_Lysate_TechRep2


title: LC0_1     COS-sprayed without cold treament sample1


title: AAV9_Lysate_TechRep1


title: RP2


title: Female_Vglut1_1


title: RP1


title: cDNA replicate 2

status: Public on Feb 09 2023

city: Cambridge

first: Terence

middle: D

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard Univserity

description:
GFP mRNA
covid_mpra_count_file_forDeseq.txt

data_processing:
Library strategy: MPRA
Barcodes were extracted from sequence files and matched to oligos using the attached covid_mpra_plasmid_seq_outfile_ALL_4_INDEXES.txt.gz file. The barcode is the first column and the oligos attached to it are in the last column. Any barcodes matched to duplicate oligos were excluded. Oligo sequences that match the oligo ids can be found in the attached covid_oligo_pool_just_oligos_and_names_10.14.20.txt (column 1 is the oligo sequence, column 2 is the oligo id).
Counts per oligo per replicate were determined by summing all barcode matches together for each replicate and a reported unnormalized in the included count file.
Supplementary_files_format_and_content: Counts per oligo per replicate were determined by summing all barcode matches together for each replicate and are reported unnormalized in the included count file.

organism: Homo sapiens

source_name: K562 cells

growth_protocol: K562 cells were grown with RPMI 1640 Complete Medium is supplemented with 2mM L-Glutamine + 10% FBS + 1% Penicillin-Streptomycin to a density of ~6*10^5 cells/ML

extract_protocol:
Twenty-four hours after transfection, cells were collected and snap frozen in liquid N2. Total RNA was extracted and GFP mRNA was isolatedand converted to cDNA Tewhey and colleagues 2016.
Following Tewhey et al. 2016, cDNA libraries were quanitified using qPCR including the plasmid pool used to transfect the cells. They were then diluted to be of equal concentration with the lowest library (20 cycles) and amplified using one fewer cycle than the lowest cycle threshold. An additional PCR was performed to add P7 indexing primers.

treatment_protocol: K562 cells 10 million cells per replicate were transfected with 40ug the MPRA library using electroporation with the Neon transfection system following the manufacturers protocol.

tag: cell type


title: Plasmid replicate 1

description:
MPRA Plasmid DNA
covid_mpra_count_file_forDeseq.txt

molecule: other

organism: synthetic construct

source_name: plasmid DNA

value: plasmid DNA


title: cDNA replicate 1


title: cDNA replicate 4


title: Plasmid replicate 3


title: Plasmid replicate 2


title: cDNA replicate 3


title: AAV9_Lysate_TechRep4


title: Plasmid replicate 4


title: PHH, HEV negative, treated with 200 nM baricitinib

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

country: Germany

institute: Ruhr University Bochum

data_processing:
Data generated from individual samples (>30 million read per sample, paired-end read 50-mers) were mapped separately against the hg38 human reference genome using CLC Workbench Genomics (Qiagen).
Gene expression was calculated for individual transcripts as reads per kilobase per million bases mapped (RPKM) using CLC Workbench Genomics (Qiagen).
Differentially expressed genes (DEGs) were identified by calculating fold changes in expression; p-values were corrected by taking false discovery rate (FDR) for multiple comparison into account using CLC Workbench Genomics (Qiagen).
Homo sapiens EBI Gene Ontology Annotation Database was used to execute Gene ontology (GO) Enrichment Analyses for biological processes. P-values for specific GO categories were generated after Bonferroni correction for multiple testing using CLC Workbench Genomics (Qiagen).
Assembly: hg38
Supplementary files format and content: csv with gene expression data

growth_protocol: PHHs were prepared from non-tumorous tissue obtained from freshly resected livers as previously described. PHHs were seeded into collagen I-coated culture plates and cultured in William’s E Medium supplemented with 5% (v/v) FCS, 1% (v/v) NEAAs , 100 U/mL penicillin, 100 µg/mL streptomycin, 2 mM L-alanyl-L-glutamine dipeptide (GlutaMax, Gibco, Cat.Nr. 35050), 2% (v/v) dimethyl sulfoxide (DMSO Hybri-Max, Sigma-Aldrich, Cat.Nr. D2650), 10 mM HEPES (Gibco, Cat. Nr.  15630), 5.4 µM hydrocortisone hemisuccinate (Sigma-Aldrich, Cat.Nr. 1319002), 5.5 ng/mL epidermal growth factor (EGF, human, Med Chem Express, HY-P7109 ), and 5 µg/mL insulin (Sigma-Aldrich, Cat.Nr. I9278). All cells were kept at 37 °C in a 5% (v/v) CO2 incubator.

extract_protocol:
NucleoSpin RNA kit (Macherey-Nagel)  according to the manufacturer’s instructions.
NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs)  according to the manufacturer’s instructions.

treatment_protocol: Plated PHH of one representative donor were inoculated with HEV-3 p6 (MOI=1) and treated with 200 nM or 2 uM baricitinib for 72h.

value: liver

tag: cell line

value: PHH

value: hepatocytes

value: HEV negative

value: 200 nM baricitinib


title: PHH, HEV positive, treated with 200 nM baricitinib

value: HEV positive


title: PHH, HEV negative, untreated

value: untreated


title: PHH, HEV negative, treated with 2 uM baricitinib

value: 2 uM baricitinib


title: PHH, HEV positive, untreated


title: PHH, HEV positive, treated with 2 uM baricitinib


title: adagrasib_30nM_BR3_TR2

city: Chilly Mazarin

first: Veeranagouda

last: Yaligara

address: Sanofi R&D

country: France

institute: Sanofi

description:
Biological replicate3_Technical replicate2
P4_B08_S296_R1_001

data_processing:
Raw read QC
First 5 and last 10 bases were trimmed and mapped to Reference Human.B38 with GeneModel RefGene20170606
Count data generated using GeneModel RefGene20170606
Normalization by DESeq using count data (Gene IDs having at least 10 count or reads in any three samples were kept).
Log2 conversion (0   replaced with 1) using DESeq data (Log2DESeq)
Assembly: Human.B38
Supplementary files format and content: Log2 DESeq

source_name: NCI-H2030 Lung cancer cell line

growth_protocol: NCI-H2030 cell line were seeded in 6-well plates in complete culture medium and cultured at densities allowing exponential growth: 50000 cells/well.

extract_protocol:
Total RNA was isolated from frozen cell pellet using RNEASY Plus Mini Kit (#74136, Qiagen).
HiCARSeq library was prepared as described in “Veeranagouda, Y., et al., High-Throughput Cellular RNA Sequencing (HiCAR-Seq): Cost-Effective, High-Throughput 3' mRNA-Seq Method Enabling Individual Sample Quality Control. Curr Protoc Mol Biol, 2020. 132(1): p. e123”

treatment_protocol: After 24 h, compounds were added (DMOS, adagrasib (30 nM), K-975 (100 nM) and adagrasib (30 nM) + K-975 (100 nM)) at a final percentage of 0.2% DMSO.

value: Lung cancer cell line


title: K-975_100nM_adagrasib_30nM_BR3_TR2

description:
Biological replicate3_Technical replicate2
P4_B12_S300_R1_001


title: K-975_100nM_adagrasib_30nM_BR2_TR1

description:
Biological replicate2_Technical replicate1
P4_B03_S291_R1_001


title: DMSO_BR3_TR2

description:
Biological replicate3_Technical replicate2
P4_B06_S294_R1_001

value: DMSO


title: DMSO_BR3_TR1

description:
Biological replicate3_Technical replicate1
P4_B05_S293_R1_001


title: K-975_100nM_BR2_TR1

description:
Biological replicate2_Technical replicate1
P4_B01_S289_R1_001


title: K-975_100nM_BR2_TR2

description:
Biological replicate2_Technical replicate2
P4_B02_S290_R1_001


title: adagrasib_30nM_BR2_TR2

description:
Biological replicate2_Technical replicate2
P4_A12_S288_R1_001


title: adagrasib_30nM_BR3_TR1

description:
Biological replicate3_Technical replicate1
P4_B07_S295_R1_001


title: K-975_100nM_BR3_TR2

description:
Biological replicate3_Technical replicate2
P4_B10_S298_R1_001


title: K-975_100nM_adagrasib_30nM_BR2_TR2

description:
Biological replicate2_Technical replicate2
P4_B04_S292_R1_001


title: K-975_100nM_adagrasib_30nM_BR3_TR1

description:
Biological replicate3_Technical replicate1
P4_B11_S299_R1_001


title: K-975_100nM_adagrasib_30nM_BR1_TR2

description:
Biological replicate1_Technical replicate2
P4_A08_S284_R1_001


title: DMSO_BR2_TR1

description:
Biological replicate2_Technical replicate1
P4_A09_S285_R1_001


title: DMSO_BR2_TR2

description:
Biological replicate2_Technical replicate2
P4_A10_S286_R1_001


title: K-975_100nM_adagrasib_30nM_BR1_TR1

description:
Biological replicate1_Technical replicate1
P4_A07_S283_R1_001


title: K-975_100nM_BR1_TR1

description:
Biological replicate1_Technical replicate1
P4_A05_S281_R1_001


title: K-975_100nM_BR1_TR2

description:
Biological replicate1_Technical replicate2
P4_A06_S282_R1_001


title: adagrasib_30nM_BR1_TR2

description:
Biological replicate1_Technical replicate2
P4_A04_S280_R1_001


title: adagrasib_30nM_BR1_TR1

description:
Biological replicate1_Technical replicate1
P4_A03_S279_R1_001


title: K-975_100nM_BR3_TR1

description:
Biological replicate3_Technical replicate1
P4_B09_S297_R1_001


title: DMSO_BR1_TR2

description:
Biological replicate1_Technical replicate2
P4_A02_S278_R1_001


title: DMSO_BR1_TR1

description:
Biological replicate1_Technical replicate1
P4_A01_S277_R1_001


title: NP_control_3

city: Guangzhou

first: Yanjiao

last: Wu

state: Guangdong

address: street address: No.1023,South Shatai Road, Baiyun District

institute: Southern Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
RNA-seq reads were aligned to the hg38 genome assembly using Hisat2 (Hierarchical Indexing for Spliced Alignment of  Transcripts, version 2.0.5).
Gene abundance was expressed as fragments per kilobase of exon per million  reads mapped (FPKM). Stringtie software was used to count the fragment within each gene,  and TMM algorithm was used for normalization
Differential expression analysis for RNA was performed using R package edgeR（3.4.3）.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: NP tissues

extract_protocol:
Total RNA was extracted from NP tissues using the RNeasy mini kit (Qiagen, Germany).  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Nucleus pulposus

tag: disease state

value: control


title: NP_degenerated_1

value: degenerated


title: NP_degenerated_3


title: NP_degenerated_2


title: NP_control_1


title: NP_control_2


title: Early gastrula (21 hours), RNA-seq

city: London

first: Ferdinand

last: Marlétaz

address: Gower Street

department: Genetics, Evolution & Environment

country: United Kingdom

institute: University College London

data_processing:
RNA-seq reads were aligned to the genome using STAR (v2.5.2b)
RNA-seq counts were obtained using featureCounts v1.6.1
RNA-seq: bigwig file for signal visualisation
RNA-seq: tab-delimited file containing raw counts

organism: Paracentrotus lividus

source_name: Whole embryo

extract_protocol:
RNA-seq: RNA was extracted using Trizol reagent (Invitrogen).
RNA-seq: Strand-specific RNA-seq libraries were prepared using the TruSeq RNA Library (Illumina) and sequenced in a 2x150bp layout.

value: Whole embryo

tag: Stage

value: Early gastrula

value: Whole organism

tag: genotype

value: WT

value: Normal embryonic development


title: Pluteus larva (48 hours, 4 arms-stage),RNA-seq

source_name: Whole larvae

tag: tissue

value: Whole larvae

value: Pluteus larva


title: Ovaries, RNA-seq

source_name: Ovaries

value: Ovaries

value: Adult


title: Late mesenchyme blastula (20 hours), RNA-seq

value: Late mesenchyme blastula


title: Gut, RNA-seq

source_name: Gut

value: Gut


title: Aristotle's lantern, RNA-seq

source_name: Aristotle's lantern

value: Aristotle's lantern


title: Prism (36 hours), RNA-seq

value: Prism


title: Blastula (7h30), RNA-seq

value: Blastula


title: Late gastrula (24 hours) , RNA-seq

value: Late gastrula


title: Bodywall, RNA-seq

source_name: Bodywall

value: Bodywall


title: Tubefeet, RNA-seq

source_name: Tubefeet

value: Tubefeet


title: Early mesenchyme blastula (18 hours), RNA-seq

value: Whole embryo

value: Early mesenchyme blastula


title: 64-cell stage blastula (5h30) , RNA-seq

value: 64-cell stage

value: Whole organism


title: 32-cell stage blastula (5 hours), RNA-seq

value: 32-cell stage

value: WT

value: Normal embryonic development


title: 128-cell stage blastula (6 hours), RNA-seq

value: 128-cell stage


title: 16-cell stage blastula (4h30), RNA-seq

value: 16-cell stage


title: 8 cell stage blastula (4 hours), RNA-seq

value: 8-cell stage


title: 2-cell stage blastula (2 hours), RNA-seq

value: 2-cell stage


title: 4-cell stage blastula (3 hours), RNA-seq

value: 4-cell stage


title: Eggs, 0 hours, RNA-seq

source_name: Eggs

value: Eggs

value: Egg


title: Tibetan

city: Yiwu

first: Jiafei

last: Shen

address: N1 Shangcheng Road

institute: International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine

description: SixRoosterMerged.sorted.bam.Sniffles.1read.vcf.txt.gz

data_processing:
Analyses were performed using piPipes v1.4. All data from the small RNA-seq, RNA sequencing, were analyzed using the latest mouse genome release galGal6 (GCA_000002315.5). Generally, one mismatch is allowed for genome mapping.
For RNA-seq reads, the expression per transcript was normalized to the top quartile of expressed transcripts per library calculated by Cuffdiff, and the tpm (transcripts per million) value was quantified using the Salmon software.
For small RNA-seq analysis, uniquely mapping reads excluding rRNA and miRNA  between 26 nt and 32 nt were selected for further analysis.
For ONT, the ONT Sequencing data collected in this experiment were obtained as fast5 files, and after conversion of electric signals into base calls via the guppy (Oxford Nanopore Technologies, UK), the reads with mean qScore greater or equal to 7 were kept to continue subsequent bioinformatic analysis. The filtered data were aligned with the chicken genome (galGal6) using NGMLR (v0.27). The SVs were detected using Sniffles (v1.0.8). We also independently used SVIM (v1.4.2 ) to call SVs with default settings.
Assembly: Gallus gallus: galGal6 (GCA_000002315.5)
Supplementary files format and content: For small RNA-seq, processed data files are unique genome alignment results in bigWig result format. RNAseq quantification results are .sf files output by Salmon software. For ONT, processed data files are performed a shuffling test in .txt format.

organism: Gallus gallus

source_name: testis

growth_protocol: Chickens were used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester.

extract_protocol:
Total RNAs were extracted using mirVana miRNA Isolation Kit (ThermoFisher, AM1560). Genomic DNA was size selected using the Pippin HT DNA Size Selection System (Sage Science, Beverly, MA, USA).
1, Strand-specific RNA-seq: libraries were constructed following the TruSeq RNA sample preparation protocol. rRNAs were depleted from total RNAs by Ribo-Zero Gold (Epicentre Biotechnologies, Madison, WI, USA).  2, Small RNA-seq: Testes samples were lysed and treated with sodium periodate for library constrution. The 3'-adapter is TGGAATTCTCGGGTGCCAAGG and has been trimmed in the raw data.
1, Strand-specific RNA-seq; 2, Small RNA-seq

value: whole testis

tag: breed

value: Tibetan

tag: age

value: adult

value: wildtype

tag: fraction

value: genomic DNA


title: Swimming blastula (12 hours), RNA-seq

value: Whole embryo

value: Swimming blastula

tag: treatment


title: RedJungleFowl

value: RedJungleFowl


title: Input

first: Philip

last: Wigge

address: 47 Bateman street

department: Sainsbury Laboratory

institute: Cambridge University

data_processing:
Adapters were trimmed off from raw reads with Trimmomatic with argument "ILLUMINACLIP:$FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15". Raw reads were mapped to the genome "TAIR10" with Bowtie2 under argument:"--no-mixed --no-discordant --no-unal -k2". Any read that mapped to more than one genomic location was discarded. Duplicate reads were removed with Picard using default setting.
Genomic binding profile was quantified in RPKM (Reads Per Kilobase per Million mapped reads) using a bin-size of 10bp. "deeptools.bamCoverage" is used.
For each treated ChIP-Seq library, peaks were called against a control 188CS11 using MACS2 with argument "--keep-dup 1 -p 0.1".
Assembly: Bd21-v3-1

organism: Brachypodium distachyon

growth_protocol: Seedlings were grown at 20C in SD for Week2 and harvested at ZT0. Seeds were sterilized and sown on Â½Â X Murashige and Skoog-agar (MS-agar) plates at pH 5.7.

extract_protocol:
3g seedlings for each set were fixed under vacuum for 20 min in 1xPBS  (10 mM PO43â, 137 mM NaCl, and 2.7 mM KCl) containing 1% Formaldehyde (F8775Â SIGMA). The reaction was quenched by adding glycine to a final concentration of 62 mM. Chromatin immunoprecipitation (ChIP) was performed as described (12), with the exception thatÂ 100 Âµl FLAG M2 agarose affinity gel antibody was used (A2220 SIGMA-Aldrich) per sample. Sequencing libraries were prepared usingÂ TruSeq ChIP Sample Preparation Kit (IlluminaÂ  IP-202-1024) and samples sequenced on NextSeq500 machine from Illumina using NextSeqÂ® 500/550 High Output Kit v2 (75 cycles) TG-160-2005. Sequence reads were analysed using in-house pipelines.
The efficiency of ChIP materials was assessed by qPCR prior to in-house library preparation. Sequencing libraries were prepared usingÂ TruSeq ChIP Sample Preparation Kit (IlluminaÂ  IP-202-1024) and samples sequenced on NextSeq500 machine from Illumina using NextSeqÂ® 500/550 High Output Kit v2 (75 cycles) TG-160-2005. Sequence reads were analysed using in-house pipelines. The libraries were sequenced at the Sainsbury Laboratory Cambridge University Services sequencing facility.

tag: photoperiod

value: SD

tag: chip antibody

tag: timepoint


title: adagrasib_30nM_BR2_TR1

description:
Biological replicate2_Technical replicate1
P4_A11_S287_R1_001

value: Lung cancer cell line


title: Cornell2


title: ACRB

value: ACRB


title: Luoyangwu

value: Luoyangwu


title: IV_E8_S152

city: Wurzburg

first: Regan

last: Hayward

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

library_source: transcriptomic single cell

data_processing:
Read trimming and quality control of MATQ-seq reads was executed using BBDuk. To efficiently remove primer and  adapter sequences located at both ends of a read, we ran BBDuk in a two-pass procedure using the default adapter sequence database augmented with MATQ-seq specific sequences. The first pass focused on the 5’ end, with parameters: minlen=18 qtrim=rl trimq=20 ktrim=l k=17 mink=11 hdist=1 trimpolya=30; while the second pass focused on the 3’ end with parameters: minlen=18 qtrim=rl trimq=20 ktrim=r k=17 mink=11 hdist=1.
Read alignment and counting was performed with Bowtie2 (Langmead & Salzberg 2012) and featureCounts (Liao et al. 2014), allowing a single mismatch and run-in --local mode. BigWig files were generated using deepTools (Ramírez et al. 2014), passing additional parameters: --binSize 5 --normalizeUsing BPM. We have employed the same gene detection method from the original MATQ-seq analyses (Imdahl et al. 2020), requiring a detected gene to have > 5 reads.
DESeq2 (Love et al. 2014) was used for normalization and differential expression analysis, using size factors calculated by the computeSumFactors function in Scran (Lun et al. 2016) and other recommended parameters for DESeq2 single cell analysis, which included using the likelihood ratio test (LRT), useT=TRUE, minmu=1e-6, and minReplicatesForReplace=Inf.
Assembly: NC_016810.1
Supplementary files format and content: Unprocessed count matrix from all samples
Supplementary files format and content: sc_counts.tsv

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: bacterial cell

extract_protocol:
Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer’s recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer’s recommendation using 100ng total RNA as input per sample.
cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer’s recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio

value: bacterial cell

tag: media

value: Lennox broth media

tag: od

value: ESP


title: IV_H9_S189

tag: condition


title: IV_H7_S187


title: IV_F7_S163


title: IV_H8_S188


title: IV_E9_S153


title: IV_G9_S177


title: IV_E7_S151


title: IV_F9_S165


title: IV_G8_S176


title: IV_D9_S141


title: IV_G7_S175


title: IV_D8_S140


title: IV_D7_S139


title: IV_F8_S164


title: genomic DNA from PMA-treated THP-1 shUHRF1_rep2

type: genomic

city: Seoul

first: Junyoung

last: Park

address: 84, Heukseok-ro

department: Department of Life Science

country: South Korea

institute: Chung-Ang University

description: modified THP-1 cell line

hyb_protocol: The whole-genome amplification process requires 250ng of input bisulfite-converted gDNA, MA1 and creates a sufficient quantity of DNA (1000X amplification) to be used on a single BeadChip in the infinium methylation assay (Illumina RPM and MSM). After amplification, the product is fragmented using a proprietary reagent (FMS), precipitated with 2-propanol (plus precipitating reagent; PM1), and resuspended in formamide-containing hybridization buffer (RA1). The DNA samples were denatured at 95 °C for 20 min, then placed in a humidified container for a minimum of 16 h at 48 °C allowing CpG loci to hybridize to the 50mer capture probes.

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles. Background intensity computed from a set of negative controls was subtracted from each analytical data point. The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100). The ß-value reflects the methylation level of each CpG site. A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

label: Cy5 and Cy3

source_name: THP-1 cell, shUHRF1_rep2, PMA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA (gDNA) was extracted from each sample using Promega Wizard® Genomic DNA Purification Kit. Quality of extracted gDNA was checked with NanoDrop® ND-2000 UV-Vis Spectrophotometer. Then samples were electrophoresed on agarose gels. Samples with intact gDNA showing no smearing on agarose gel electrophoresis were selected for experiment. Intact gDNA was diluted to 50 ng/㎕ concentration based on Quant-iT Picogreen (Invitrogen) quantitation. Concentrations were adjusted based on these results. All prepared samples were bisulfite-converted according to the Zymo EZ DNA methylation kit protocols.

tag: disease

value: Acute myeloid leukemia


title: IV_C9_S129

tag: cell type


title: Rooster1_Araucana


title: IV_C8_S128


title: IV_B7_S115


title: IV_B8_S116


title: IV_C7_S127


title: genomic DNA from DMSO-treated THP-1 shUHRF1_rep2

description: modified THP-1 cell line

source_name: THP-1 cell, shUHRF1_rep2, DMSO


title: IV_A9_S105


title: IV_A7_S103


title: IV_A8_S104


title: IV_B9_S117


title: III_H12_S96


title: III_H10_S94


title: III_G11_S83


title: III_G10_S82


title: III_F12_S72


title: III_H11_S95


title: III_F10_S70


title: III_E11_S59


title: III_G12_S84


title: III_E12_S60


title: III_D10_S46


title: III_D12_S48


title: III_E10_S58


title: III_C10_S34


title: III_B12_S24


title: III_C11_S35


title: III_D11_S47


title: III_B11_S23


title: III_C12_S36


title: III_B10_S22


title: III_A10_S10


title: III_A11_S11


title: II_H3_S375


title: II_H2_S374


title: II_H1_S373


title: II_G3_S363


title: III_F11_S71


title: Early blastula (6h30), RNA-seq

value: Early blastula

value: Whole organism

value: WT

value: Normal embryonic development


title: II_G2_S362


title: III_A12_S12


title: II_E3_S339


title: II_F2_S350


title: BVE-Ctnnb1null 3

city: Riyadh

first: yufei

last: shi

address: PO Box 3354

country: Saudi Arabia

institute: King Faisal Specialist Hospital and Research Centre

data_processing: The significant DEGs were selected based on the following criteria: Log2 fold change>2, false discovery rate (FDR) <0.001, and p-value from difference test<0.01.

source_name: thyroid epithelial cells

extract_protocol:
Thyroid tumors were collected aseptically from donor mice (BVE and BVE-Ctnnb1null) using blunt dissection, mechanically dissociated by mincing and passing through a 40-μM mesh sterile screen, and suspended in DMEM/F12 growth medium (10% fetal bovine serum, 100 units/ml penicillin, 100 ug/ml streptomycin). Cells were cultured in DMEM/F12 growth medium containing 4 mU/mL bovine TSH (Sigma-Aldrich). For establishment of immortalized cell lines, cells were cultured continually for more than 6 months and passaged weekly or bi-weekly at 1:3 ratio with 0.25% trypsin. BVE-Ctnnb1wt (BVE) and BVE-Ctnnb1null cell lines had about 25 and 20 passages, respectively before they were used for experiments.  Thyroid origin of the cell lines was confirmed by genotyping to rule out fibroblast contamination. Genotyping of the cell lines and expression of genes for thyroid hormone synthesis were verified every 6 months when the cells were in culture.
Libraries were constructed using an Illumina (San Diego, Ca, USA) TruSeq RNA Library Prep kit according to the manufacturer’s procedure.

value: thyroid epithelial cells

value: thyroid cancer with BRAFV600E and deletion of CTNNB1


title: II_E2_S338


title: II_D2_S326


title: II_D3_S327


title: BVE-Ctnnb1null 2


title: BVE, control 2

value: thyroid cancer with BRAFV600E


title: BVE-Ctnnb1null 1


title: II_C3_S315


title: II_C2_S314


title: BVE, control 1


title: II_C1_S313


title: II_B3_S303


title: HDP-006071

city: Lausanne

first: Giorgia

last: Benegiamo

state: Vaud

address: AI 1351 (Bâtiment AI), Station 15

country: Switzerland

institute: EPFL

data_processing:
The STAR reference genome was generated using STAR 2.7.1a using  Mus_musculus.GRCm38.dna.primary_assembly.fa and Mus_musculus.GRCm38.91.gtf as reference genomes and annotations. Command: STAR --runThreadN [#threads] --runMode genomeGenerate --genomeDir [stargenome_directory] --genomeFastaFiles Mus_musculus.GRCm38.dna.primary_assembly.fa --sjdbGTFfile Mus_musculus.GRCm38.91.gt --sjdbOverhang 99
Mapping for each sample was performed using this command: STAR --runThreadN [#threads] --genomeDir [stargenomedirectory] --quantMode GeneCounts TranscriptomeSAM --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --readFilesIn [raw fq.gz files] --outFileNamePrefix [sample_id]
Counts were extracted from the STAR ReadsPerGene output files using the first 2 columns.
Assembly: mm10
Supplementary files format and content: Comma-separated file with raw counts

source_name: Liver

growth_protocol: 6-8 domesticated (C57BL/6J, DBA/2J, A/J, 129S1/SvlmJ) or wild-derived (CAST/EiJ, PWK/PhJ, WSB/EiJ) inbred mouse strains were imported from Charles River and bred at the École Polytechnique Fédérale de Lausanne (EPFL) animal facility for more than two generations before incorporation into the study. Mice were housed at 2-5 animals per cage under 12 hours light/dark cycle, with ad libitum access to food and water at all times.

extract_protocol:
Livers were crushed in liquid nitrogen and then 10 mg of tissues were suspended in TRIzol (Invitrogen) and homogenized with stainless steel beads using a TissueLyser II (Qiagen) at 30 Hz for 2 min. RNA was extracted and purified using Direct-zol-96 RNA kits (Zymo Research). mRNA concentration was measured for all samples. All samples passed a quality check of purity (NanoDrop) and fragmentation (FragmentAnalyzer).
BGISEQ-500 library construction was performed by BGI

treatment_protocol: Starting from 6 weeks of age, all mice were housed at 30°C (thermoneutrality). From 7 weeks of age the mice were fed a “western-style” diet (WD, Research Diets D12079B 40% kCal from fat, 17% kCal from protein, and 43% kCal from carbohydrates), or a matched control diet (CD, Research Diets D16042904B (10% kCal from fat, 17% kCal from protein, and 73% kCal from carbohydrates).

tag: strain

value: WSB/EiJ

tag: diet

value: CD

tag: Sex

value: Male

tag: cohort

tag: rin


title: HDP-006070


title: HDP-006072

value: WD


title: HDP-006251


title: II_B2_S302


title: HDP-005615


title: II_B1_S301


title: II_G1_S361


title: II_F1_S349


title: II_F3_S351


title: HDP-005614


title: II_A3_S291


title: I_H6_S282


title: II_A1_S289


title: II_E1_S337


title: HDP-005607


title: HDP-005612


title: HDP-005613


title: II_A2_S290


title: I_H5_S281


title: HDP-005464


title: HDP-005463


title: I_G5_S269


title: I_G4_S268


title: II_D1_S325


title: HDP-005477


title: HDP-005435


title: I_F5_S257


title: I_F6_S258


title: I_H4_S280


title: I_F4_S256


title: I_E6_S246


title: HDP-005436


title: HDP-005433


title: HDP-005358


title: I_E5_S245


title: HDP-005476


title: HDP-005357


title: I_G6_S270


title: I_D6_S234


title: HDP-005462


title: I_D5_S233


title: HDP-005356


title: HDP-005434


title: I_D4_S232


title: HDP-005299


title: I_C6_S222


title: I_C5_S221


title: HDP-005296


title: HDP-005297


title: I_C4_S220


title: HDP-005108


title: HDP-005069

value: CAST/EiJ


title: HDP-005355


title: HDP-005070


title: I_A6_S198


title: HDP-005066


title: I_A5_S197


title: IV_H6_S186

value: LEP


title: I_A4_S196

value: bacterial cell


title: HDP-005065


title: HDP-005109


title: I_B6_S210

value: Lennox broth media


title: HDP-005062


title: I_B5_S209

value: ESP


title: I_B4_S208


title: HDP-005068


title: HDP-005067


title: HDP-005037


title: IV_G6_S174


title: IV_G5_S173


title: HDP-005036


title: HDP-003478

value: A/J


title: IV_G4_S172


title: HDP-005026


title: IV_F5_S161


title: IV_F4_S160


title: HDP-005041


title: HDP-003516


title: IV_E6_S150


title: HDP-003474


title: IV_E5_S149


title: IV_F6_S162


title: HDP-003473


title: HDP-005040


title: IV_H5_S185


title: IV_E4_S148


title: HDP-003464


title: HDP-003463


title: IV_D6_S138


title: HDP-003459


title: IV_H4_S184


title: IV_D4_S136


title: IV_D5_S137


title: HDP-003458


title: HDP-003421


title: IV_C6_S126


title: IV_C5_S125


title: IV_C4_S124


title: HDP-003417


title: IV_B6_S114


title: HDP-003420


title: HDP-003409


title: IV_B5_S113


title: HDP-003400


title: IV_B4_S112


title: IV_A6_S102


title: HDP-003404


title: HDP-003166


title: IV_A5_S101


title: HDP-003167


title: IV_A4_S100


title: I_E4_S244


title: III_H9_S93


title: HDP-003120


title: HDP-003165


title: III_H8_S92


title: HDP-003164


title: III_H7_S91


title: HDP-003408


title: III_G9_S81


title: HDP-003090


title: III_G8_S80


title: III_G7_S79


title: HDP-003088


title: III_F9_S69


title: III_F7_S67


title: HDP-003077

value: PWK/PhJ


title: HDP-003050


title: III_E9_S57


title: HDP-003040


title: HDP-003052


title: III_E8_S56


title: HDP-003033


title: HDP-003039


title: III_D9_S45


title: HDP-003119


title: HDP-003032


title: III_D8_S44


title: III_C8_S32


title: III_D7_S43


title: HDP-003030


title: III_C9_S33


title: HDP-003024


title: HDP-003023


title: HDP-002669


title: III_B9_S21


title: III_F8_S68


title: HDP-003022


title: III_C7_S31


title: III_B8_S20


title: III_B7_S19


title: HDP-003089


title: HDP-002662


title: HDP-002584


title: HDP-002583


title: III_A8_S8


title: III_A7_S7


title: III_E7_S55


title: HDP-002582


title: II_H11_S383


title: II_H12_S384


title: HDP-002580


title: HDP-002581


title: II_H10_S382


title: HDP-003031


title: HDP-002579


title: HDP-002578


title: II_G12_S372


title: II_G10_S370


title: HDP-002577


title: HDP-002546


title: II_F10_S358


title: II_G11_S371


title: II_F11_S359


title: HDP-002544


title: HDP-002536


title: HDP-002531


title: HDP-002520


title: II_E11_S347


title: II_E10_S346


title: III_A9_S9


title: HDP-002530


title: II_E12_S348


title: II_F12_S360


title: II_D11_S335


title: II_D12_S336


title: II_D10_S334


title: HDP-002600


title: II_C10_S322


title: II_C12_S324


title: meninges of young mouse R19296

city: Basel

first: Albert

last: Neutzner

state: BS

address: Hebelstrasse 20

department: Department of Biomedicine

institute: University Hospital Basel

description: meninges of young mouse

data_processing:
aligment using subread v2.0.0
features were counted using Bioconductor featureCounts - files provides as *.FC.out
Assembly: mm10

source_name: meninges

extract_protocol:
RNAeasy plus Mini Qiagen
RNA-Seq libraries were prepared by Novogen using their low input protocol

tag: tissue

value: meninges

tag: genotype

value: not aged


title: meninges of young mouse R19301

description: meninges of young mouse


title: meninges of young mouse R19297

description: meninges of young mouse


title: meninges of young mouse R19299

description: meninges of young mouse


title: HDP-002521


title: II_C11_S323


title: meninges of young mouse R19300

description: meninges of young mouse


title: II_B12_S312


title: meninges of aged mouse R2746

description: meninges of aged mouse

value: aging


title: meninges of aged mouse R2745

description: meninges of aged mouse


title: II_B11_S311


title: TriMix_3

type: RNA

city: Jette

first: Kirsten

last: De Ridder

state: Brussel

address: Laarbeeklaan 103

department: Laboratory for Molecular and Cellular Therapy, Department of Biomedical Sciences

country: Belgium

institute: Vrije Universiteit Brussel

hyb_protocol: Probes and target transcripts were hybridized overnight at 65°C for 20 hours as described in the manufacturer’s protocol.

scan_protocol: Samples are loaded onto the nCounter Prep Station for further purification and immobilization onto the sample cartridge. After transfer to the Digital Analyzer (MAX Analysis System, Brightcore, VUB) absolute counts are quantified.

data_processing: For quality control the nSolver_analysis_software_4.0 was used. Raw counts were processed in R and normalized using the RUVSeq method adjusted for NanoString analysis. The DESeq R-package was used for differential expression analysis.

label: Biotin

source_name: Monoctye derived denritic cells

label_protocol: After RNA was converted to cDNA and amplified using target-specific primers samples were mixed with a 3′ biotinylated capture probe and a 5′ reporter probe tagged with a fluorescent barcode from the nCounter Human PanCancer Immune Profiling Panel

growth_protocol: Monocyte dendritic cells were maintained in CellGenix media supplemented with 1% human serum albumin.

extract_protocol: Total RNA was extracted from monocyte derived dendritic cells using the RNeasy plus mini kit (Qiagen, 74134).  RNA recovery was quantified using fluorimetry (Qubit, LifeTechnologies) qualified for purity and integrity using Bioanalyzer Labchip (Agilent Technologies).

treatment_protocol: Monocyte dendritic cells were electroporated with a total concentration of 100 µg/ml mRNA and evaluated after 24hours.

tag: donor

value: DTP

tag: mrna

value: TriMix


title: eGFP_3

value: eGFP

tag: treatment

value: control


title: TetraMix_3

value: TetraMix


title: II_A12_S300


title: meninges of aged mouse R2660

description: meninges of aged mouse


title: eGFP_2

value: DLS


title: TetraMix_2


title: meninges of young mouse R19298

description: meninges of young mouse


title: TriMix_2


title: II_A11_S299


title: TriMix_1

value: DHA


title: eGFP_1


title: TetraMix_1


title: meninges of aged mouse R2606

description: meninges of aged mouse


title: Plasmid_Library

city: Berlin

first: Oriana

last: Genolet

address: Ihnestrasse 63

department: OWL Schulz

institute: Max Planck Institute for Molecular Genetics

description: Cloned sgRNA phosphatase library

data_processing:
Tab delimited text files with raw and normalized counts were generated on the public Galaxy server usegalaxy.eu (Afgan et al., 2016) with the MAGeCK CRISPR screen analysis tools (Li et al., 2014, 2015). Alignment and read counting was performed with MAGeCK_count and statistical analysis was performed with MAGeCK_mle.
Genome_build: GRCm38 mm10
Supplementary_files_format_and_content: Tab delimited text files include raw and normalized counts for each sample
Supplementary_files_format_and_content: Phosphatase sgRNA library (tab delimited text files provided)

source_name: Cloned sgRNA phosphatase library

growth_protocol: All mESC lines were grown without feeder cells on gelatin-coated flasks (Millipore, 0.1%) in serum-containing ES cell medium (DMEM (Sigma), 15% FBS (PanBiotech), 0.1 mM ß-Mercaptoethanol (Sigma), 1000 U/ml leukemia inhibitory factor (LIF, Merck)). mESCs were passaged every second day at a density of 4*104 cells/cm2 and medium was changed daily. For stable expression of the Cas9 endonuclease, cells were transduced with virus carrying Cas9 and selected for cells with stable integration. Cells were then transduced with the respective sgRNA library with a MOI (multiplicity of infection) of 0.3 and selected for stable sgRNA cassette integration. Cells were then grown for seven days prior to sorting.

extract_protocol:
Genomic DNA from frozen cell pellets was isolated via Phenol/Chloroform extraction due to higher yields. Briefly, cell pellets were thawed and resuspended in 250µl of Lysis buffer (1% SDS (Thermo Fisher Scientific), 0.2M NaCl and 5mM DTT (Roth) in TE Buffer) and incubated over night at 65°C. 200µg of RNAse A (Thermo Fisher Scientific) was added to the sample and incubated at 37°C for 1h. 100µg of Proteinase K (Sigma) were subsequently added followed by a 1h incubation at 50°C. Phenol/Chloroform/Isoamyl alcohol (Roth) was added to each sample in a 1:1 ratio, the mixture was vortexed at RT for 1 min and subsequently centrifuged at 16000 xg for 10 min at room temperature. The aqueous phase was transferred to a new tube, 1 ml 100% EtOH, 90 µl 5 M NaCl and 1µl Pellet Paint (Merck) was added to each sample, mixed, and incubated at -80°C for 1 hr. DNA was pelleted by centrifugation for 16000 xg for 15 min at 4°C, pellets were washed twice with 70% EtOH, air-dried and resuspended in 50µl H2O.
The PCR amplification of the sgRNA cassette was performed in two PCR steps as described previously with minor modifications (Shalem et al. 2014).

treatment_protocol: No treatment was carried out.

tag: gdna isolation

value: Phenol/Chloroform

tag: molecule

value: DNA PCR Amplicon


title: II_A10_S298

value: bacterial cell

tag: media

value: LEP


title: meninges of aged mouse R2605

description: meninges of aged mouse


title: I_H3_S279

value: Lennox broth media

tag: od


title: meninges of young mouse R3218

description: meninges of young mouse


title: II_B10_S310

tag: condition


title: ATACseq_R1NPC_1

city: NIJMEGEN

first: Hannah

last: Neikes

state: Gelderland

address: Geert Grooteplein Zuid 28

country: Netherlands

institute: Radboud University

data_processing:
Sequence data processing was performed automatically with automated processing pipeline seq2science, v 0.7.2. with the ATAC-seq workflow.
Read alignment to target and spike-in genome with bwa-mem2 v2.1, options -M
Filtering out MAPQ <30, multimapper and map to the ENCODE blacklist
Duplicates removed with PICARD v2.23.8
Peak calling with macs2 v2.2.7, options --keep-dup 1 --buffer-size 10000 --call-summits -BAMPE
Total read counts per sample determined with samtools v1.9
Read counts were determined with samtools at SP1 high confidence binding sites and analyzed for differential accessibility with DESeq2.
Assembly: mm10
Supplementary files format and content: Tab delimited .txt file containing DESeq2 restults for NPC vs. ESC.

extract_protocol:
Nuclei were isolated from cryopreserved cells. Per replicate, roughly 50,000 nuclei were tagmented for 5 minutes with in-house generated Tn5 while shaking at 37°C and DNA was purified using 2x SPRI beads (Ampure) purification.
DNA was subsequently PCR amplified by using KAPA HiFi Hotstart Ready Mix (KAPA Biosystems) and Nextera Index Kit (Illumina) primers followed by reverse phase 0.65 x SPRI beads purification and a column purification (Zymo). To remove large DNA fragments from the libraries, samples were subjected to another 0.5X SPRI beads purification, followed by a 1X purification.
Samples were analyzed for purity using a High Sensitivity DNA Chip on a Bioanalyzer 2100 system (Agilent). Libraries were paired-end sequenced on a Illumina NextSeq500.


title: I_H2_S278


title: ATACseq_R1NPC_2


title: I_H1_S277


title: ATACseq_R1NPC_3


title: ATACseq_R1mESC_2


title: meninges of young mouse R3215

description: meninges of young mouse


title: meninges of young mouse R3216

description: meninges of young mouse


title: R1NPC_FLAG_SP1_CUTaRUN_0300nM

description: R1_mESC_NPC_FLAG_SP1_CUTaRUN_relEnr_Kds.txt

data_processing:
Sequence data processing was performed automatically with automated processing pipeline seq2science, v 0.7.2
Read alignment to target and spike-in genome with bwa-mem2 v2.1, options -M
Filtering out MAPQ <30, multimapper and map to the ENCODE blacklist
Duplicates removed with PICARD v2.23.8
Peak calling with macs2 v2.2.7, options --keep-dup 1 --buffer-size 10000 --call-summits -BAMPE
Total read counts per sample determined with samtools v1.9
Read normalisation in R v4.0.3 to reads per million spike-in reads and to highest signal per binding site and experiment. Fit signal-over-concentration to hill equation at bound sites to determine genome-wide binding affinities (apparent Kds).
Assembly: mm10, hg38, CAST/EiJ, 129S1/SvImJ, dm6, E.coli_C142, S.cerevisiae-74-D694-2.0
Supplementary files format and content: Tab delimited .txt file containing relative signal per concentration as well as KdApps and additional values
Library strategy: CUT&Run

extract_protocol:
Isolated nuclei of MCF-7, R1 mESC, NPC or F121 cells were incubated with a titration series of FLAG-tagged transcription factor of interest, which was followed up by either ChIP-seq or CUT&RUN with anti-FLAG antibody, including heterologous spike-in DNA (dm6 or S.cerevisiae for ChIP-seq or CUT&RUN-based follow-up, resp.). Released DNA fragments were column purified and used for preparation of sequencing libraries.
Libraries were prepared using the Kapa Hyper Prep Kit (Kapa Biosystems) according to manufacturer’s protocol, with the following modifications. All input material was used to prepare libraries and 2.5 μl of the NEXTflex adapter stock (600nM, Bioo Scientific) was used for adapter ligation of each sample. Libraries were amplified with 12 PCR cycles and a double post-amplification clean-up was used to ensure proper removal of adapters.
Samples were analyzed for purity using a High Sensitivity DNA Chip on a Bioanalyzer 2100 system (Agilent). Libraries were paired-end sequenced on a Illumina NextSeq500.

tag: banc-seq follow up method

value: CUT&RUN

tag: spike in genome


title: ATACseq_R1mESC_1

tag: cell type

tag: strain


title: I_G3_S267


title: I_G2_S266


title: meninges of aged mouse R2416

description: meninges of aged mouse


title: R1NPC_FLAG_SP1_CUTaRUN_0500nM


title: meninges of aged mouse R2251

description: meninges of aged mouse


title: I_G1_S265


title: I_F3_S255


title: R1NPC_FLAG_SP1_CUTaRUN_0000nM


title: R1NPC_FLAG_SP1_CUTaRUN_0010nM


title: R1NPC_FLAG_SP1_CUTaRUN_0001nM


title: ATACseq_R1mESC_3


title: R1mESC_FLAG_SP1_CUTaRUN_0300nM


title: R1NPC_FLAG_SP1_CUTaRUN_0100nM


title: meninges of aged mouse R12498

description: meninges of aged mouse


title: meninges of aged mouse R2607

description: meninges of aged mouse


title: I_F2_S254


title: meninges of aged mouse R2418

description: meninges of aged mouse


title: meninges of aged mouse R12497

description: meninges of aged mouse


title: R1mESC_FLAG_SP1_CUTaRUN_0010nM


title: R1mESC_FLAG_SP1_CUTaRUN_0000nM


title: I_F1_S253


title: I_E3_S243


title: R1mESC_FLAG_SP1_CUTaRUN_0100nM


title: primEB cells, p53  NFIA-ETO2, differentiation medium, rep6

first: Jonathan

last: Seguin

address: Spitalstrasse 33

institute: UKBB-DBM

data_processing:
RNA-seq reads were mapped to the mouse genome assembly, version mm10, with STAR (versions 2.5.2) with default parameters except for using the multi-map settings (outFilterMultimapNmax=10 and outSAMmultNmax=1) and filtering reads without evidence in spliced junction table (outFilterType="BySJout").
The output was sorted and indexed with samtools (version 1.15).
The qCount function of QuasR was used to count the number of read (5'ends) overlapping with the exons of each gene assuming an exon union model.
Assembly: mm10
Supplementary files format and content: raw counts matrix with genes as rows and samples as columns

source_name: fetal liver

extract_protocol:
Total RNA was isolated using Nucleospin RNA Plus XS kit (Ref 740990.250, Macherey-Nagel).
Library preparation was performed, starting from 200ng total RNA, using the TruSeq Stranded mRNA Library Kit (Cat# 20020595, Illumina, San Diego, CA, USA) and the TruSeq RNA UD Indexes (Cat# 20022371, Illumina, San Diego, CA, USA) / and the TruSeq RNA CD Index Plate (Cat# 20019792, Illumina, San Diego, CA, USA). 15 cycles of PCR were performed.

treatment_protocol: Cells were transduced with viral supernatants, containing the vector to express NFIA-ETO2 gene fusion, in presence of 5ug/ml polybrene (Sigma Aldrich, Buchs, Switzerland) 90min, 1800 rpm at 30°C. Cells were incubated overnight with the cells, and washed with PBS and plated in their respective mediums. To induce differentiation, 105 cells were cultured in DMEM with 2%DMSO (sigma). After 2 days, cells were washed and counted, and cultured again in right volume of newly prepared medium. Differentiation was continued for 4 days in presence of DMSO.

value: fetal liver

value: primary erythroblasts

value: HUPKI

tag: age

value: differentiation medium


title: R1mESC_FLAG_SP1_CUTaRUN_0500nM


title: primEB cells, WT NFIA-ETO2, differentiation medium, rep6


title: Pancreas, mouse 1, replicate 2

city: München

first: Johannes

last: Wirth

address: Trogerstrasse 18

department: Institute of Pathology

institute: Technical University Munich

data_processing:
ReadsToCounts pipeline: Concerns all samples that are not marked as "cross-contamination experiment" in the title. This script takes two FASTQ files (Read 1 and Read 2) and barcode-coordinate information as input and processes them as follows: Read 1 sequences are trimmed and filtered using cutadapt v3.7 (Martin, 2011) and mapped against the mm10 (GRCm38.p6) mouse genome using STAR-2.7.4a (Dobin et al., 2013). Unique molecular identifiers (UMIs) and spatial barcodes are extracted from Read 2 using the Drop-seq tool TagBamWithReadSequenceExtended and a custom Python 3 pipeline assigns coordinates using barcode information provided in a CSV file. The DigitalExpression function is used to collaps the UMIs and generate a spot-count matrix. RNA metrics are calculated using CollectRnaSeqMetrics.
CountsToAnndata pipeline: Concerns all samples that are not marked as "cross-contamination experiment" in the title. In this stage the spot-count matrix and imaging data are aligned and integrated. In brief, the positions of the alignment marker vertices are extracted semi-automatically from the alignment images using napari (Sofroniew et al., 2022) and Squidpy (Palla et al., 2022). The coordinates of the vertices are used to register alignment image and xDBiT spots by performing an affine transformation using OpenCV (Bradski, 2000). In order to align the high-resolution images of the first imaging round with the xDBiT spots, the SIFT algorithm (Lowe, 2004) is used to extract common features between the alignment DAPI image and the high-resolution DAPI image. Based on the coordinates of these features an affine transformation matrix is determined which is used to align the xDBiT spots to the high-resolution image. The dataset is saved in the AnnData format (Virshup et al., 2021). In this study we included intronic reads (Supp. Fig. 2 C) into the analysis.
Cross-contamination experiment: This data processing description concerns only the samples which are marked with "Cross-contamination experiment" in their title (MUC28220-MUC28227). To calculate the percentage of spilled over reads, only read 2, containing the RevT barcodes and spatial barcodes was analyzed. For the analysis the ReadsToCounts script was modified to disregard read 1 and instead only run up to the barcode filtering steps to retrieve counts of the spatial barcodes and RevT primer barcodes. This script can be invoked using the `--spatial_only` flag. Further, to be able to catch information about reads from other wells, information about all 36 barcodes used in the experiment was added to the barcode legend file. Count values of the found barcodes were stored in the `recording_dictionary.json` file in the `rna_out` folder. This information was read, analyzed and plotted using Python 3.8.
Assembly: mm10 (GRCm38.p6)
Supplementary files format and content: gzipped tar archive containing gene expression matrix in txt.gz format and metadata file from ReadsToCounts pipeline
Supplementary files format and content: h5ad file containing anndata object with xDBiT spatial transcriptomic data and aligned images
Library strategy: xDBiT

molecule: polyA RNA

source_name: Pancreas

extract_protocol:
The amplified cDNA was purified using SPRIselectTM beads (Beckman Coulter) following a left sided size selection with a bead-to-sample ratio of 0.8X. In brief, 160 µL of sample were mixed with 128 µL of resuspended SPRIselect beads and incubated for 5 min at rt. Beads were washed two times in 85% ethanol and air-dried for 3 min. The cDNA was eluted in 20 µL ultrapure water by incubation at 37 °C for 10 min. The supernatants were transferred to a fresh tube resulting in 9 tubes of purified cDNA. The quality of the cDNA was analyzed using the Bioanalyzer High Sensitivity DNA chip (Agilent) and samples were stored at -20 °C.
The concentration of the cDNA was determined using a Qubit 1X dsDNA assay (Invitrogen) and the sequencing library was generated using the Nextera XT DNA Library Preparation Kit (Illumina). The quality of the library was assessed using the Bioanalyzer High Sensitivity DNA chip (Agilent). Samples were sequenced on a NovaSeq 6000 system (Illumina) at a sequencing depth of minimum 50,000 reads per spot using a 100 cycles kit in paired-end mode. Following read length configurations were used: R1: 7 cycles, i7: 6 cycles, R2: 58 cycles.

value: Pancreas

value: 3 months

tag: Sex

value: male

value: wild-type


title: R1mESC_FLAG_SP1_CUTaRUN_0001nM


title: meninges of aged mouse R11655

description: meninges of aged mouse

value: meninges

value: aging


title: primEB cells, p53  NFIA-ETO2, maintenance medium, rep6

value: maintenance medium


title: I_E1_S241


title: primEB cells, WT NHR4, differentiation medium, rep6


title: Pancreas, mouse 1, replicate 1


title: I_E2_S242


title: Cross-contamination experiment: Liver, mouse 4, replicate 4

value: Liver


title: I_D3_S231


title: Cross-contamination experiment: Liver, mouse 4, replicate 3


title: primEB cells, WT NHR4, maintenance medium, rep6


title: primEB cells, p53  NFIA-ETO2, maintenance medium, rep3


title: primEB cells, p53  NFIA-ETO2, differentiation medium, rep3


title: primEB cells, WT NFIA-ETO2, differentiation medium, rep3


title: primEB cells, WT NFIA-ETO2, maintenance medium, rep3


title: primEB cells, WT NHR4, differentiation medium, rep3


title: I_D2_S230


title: primEB cells, WT NFIA-ETO2, maintenance medium, rep6


title: I_D1_S229


title: I_C3_S219


title: Cross-contamination experiment: Liver, mouse 4, replicate 1


title: primEB cells, p53  NFIA-ETO2, differentiation medium, rep2


title: Cross-contamination experiment: Liver, mouse 3, replicate 4

value: 22 months


title: Cross-contamination experiment: Liver, mouse 3, replicate 3


title: I_C1_S217

value: bacterial cell


title: Cross-contamination experiment: Liver, mouse 3, replicate 2


title: primEB cells, WT NFIA-ETO2, differentiation medium, rep2


title: primEB cells, WT NHR4, differentiation medium, rep2


title: I_C2_S218

value: LEP


title: primEB cells, WT NFIA-ETO2, maintenance medium, rep2


title: I_B3_S207

value: Lennox broth media


title: primEB cells, p53  NFIA-ETO2, maintenance medium, rep1


title: primEB cells, WT NHR4, maintenance medium, rep2


title: primEB cells, WT NFIA-ETO2, differentiation medium, rep1


title: Cross-contamination experiment: Liver, mouse 4, replicate 2


title: I_B2_S206


title: Cross-contamination experiment: Liver, mouse 3, replicate 1


title: primEB cells, WT NFIA-ETO2, maintenance medium, rep1


title: primEB cells, WT NHR4, differentiation medium, rep1


title: primEB cells, WT NHR4, maintenance medium, rep3


title: I_A3_S195


title: MEL cells, NFIA-ETO2, rep4

data_processing:
RNA-seq reads were mapped to the mouse genome assembly, version mm10, with STAR (versions 2.7) with default parameters except for using the multi-map settings (outFilterMultimapNmax=10 and outSAMmultNmax=1) and filtering reads without evidence in spliced junction table (outFilterType="BySJout").
The output was sorted and indexed with samtools (version 1.15).
Coverage tracks per sample were generated by tiling the genome in 20bp windows, counting overlapping reads per window using the function bamCount from the bioconductor package bamsignals (bioconductor versions 3.13) and exporting these window counts in bigWig format using the export function of the bioconductor package rtracklayer.
The qCount function of QuasR was used to count the number of read (5'ends) overlapping with the exons of each gene assuming an exon union model.
Assembly: mm10
Supplementary files format and content: raw counts matrix with genes as rows and samples as columns
Supplementary files format and content: bigWig

source_name: murine erythroleukemia

growth_protocol: Murine erythroleukemia (MEL) cells were obtained from DSMZ (cultured in suspension in DMEM (Dulbecco's Modified Eagle Medium) (Gibco, Lubio, Thermo Fisher Scientific, Reinach, Switzerland), 5% FCS (Fetal Calf Serum), 1% P/S  (Penicillin-Streptomycin) (Reddy and Shen 1992).

value: murine erythroleukemia


title: MEL cells, CTRL, rep4

value: CTRL


title: I_A2_S194


title: primEB cells, p53  NFIA-ETO2, differentiation medium, rep1

value: fetal liver

value: primary erythroblasts


title: MEL cells, NFIA-ETO2, rep3


title: primEB cells, p53  NFIA-ETO2, maintenance medium, rep2

value: HUPKI


title: I_A1_S193


title: MEL cells, CTRL, rep2


title: s39, BMDM, AhR-KO, LPS (ATAC-seq)

city: Neuherberg

first: Caspar

last: Ohnmacht

address: Ingolstaedter Landstrasse 1

department: Center of Allergy and Environment

institute: Helmholtz Center Munich

data_processing:
[basecalling]  Basecalls were done with Illumina bcl2fastq version 2.20.0.
The nf-core/atacseq pipeline (version v1.2.1; Patel et al., 2020; 10.5281/zenodo.3965985) was used to perform the primary analysis of the samples. The command used was "nextflow run nf-core/atacseq --input samples.csv --genome mm10 --outdir results -with-singularity atacseq_latest.sif -r 1.2.1". All data was processed relative to the mouse genome mm10. Gene annotation files in GTF format were downloaded from Ensembl (v98). For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/atacseq).
Assembly: mm10
Supplementary files format and content: bfx1782.consensus_peaks.mLb.clN.featureCounts.txt.gz: Tab-separated file with the output from featureCounts. Each row represents a consensus peak (produced by combining the individual sample peaks) and the columns contain the consensus peak information followed by the sample counts.
Supplementary files format and content: bigWig files: Normalised bigWig files scaled to 1 million mapped reads.
Supplementary files format and content: narrowPeak files: Peak calling files produced by MACS2. BED format with the following columns: chromosome, start, end, name, score, strand, signalValue, pValue, qValue and peak.

source_name: BMDM

growth_protocol: AhR-KO and wildtype bone marrow was cultured in RPMI supplemented with 10 ng/ml GM-CSF, 2 ng/ml TGF-ß, 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Rneasy plus mini kit (Qiagen).
Tagmentation of genomic DNA and library preparation was done with the Nextera DNA Library Preparation Kit (Illumina).

treatment_protocol: On the 6th day of differentiation cells where stimulated with 97 EU/ml LPS. After 24 h of stimulation 5 µM Ca2+-ionophore A23187 was added for 10 min to ensure full release of lipid mediators.

value: BMDM

value: AhR-KO

value: LPS


title: MEL cells, CTRL, rep1


title: s36, BMDM, AhR-KO, unstimulated (ATAC-seq)

value: unstimulated


title: s35, BMDM, AhR-KO, unstimulated (ATAC-seq)


title: MEL cells, CTRL, rep3


title: IV_H3_S183

value: MEP


title: s37, BMDM, WT, LPS (ATAC-seq)

value: WT


title: IV_H2_S182


title: s34, BMDM, WT, unstimulated (ATAC-seq)


title: primEB cells, WT NHR4, maintenance medium, rep1

value: maintenance medium


title: s40, BMDM, AhR-KO, LPS (ATAC-seq)


title: F121_FLAG_YY1_CUTaRUN_0564nM

description: F121_FLAG_YY1_CUTaRUN_relEnr_Kds_noOutliers.txt

data_processing:
Sequence data processing was performed automatically with automated processing pipeline seq2science, v 0.5.4.
Read alignment to target and spike-in genome with bwa-mem2 v2.1, options -M
Filtering out MAPQ <30, multimapper and map to the ENCODE blacklist
Duplicates removed with PICARD v2.23.8
Peak calling with macs2 v2.2.7, options --keep-dup 1 --buffer-size 10000 --call-summits -BAMPE
Total read counts per sample determined with samtools v1.9
Read normalisation in R v4.0.3 to reads per million spike-in reads and to highest signal per binding site and experiment. Fit signal-over-concentration to hill equation at bound sites to determine genome-wide binding affinities (apparent Kds).
Genome_build: mm10, hg38, CAST/EiJ, 129S1/SvImJ, dm6, E.coli_C142, S.cerevisiae-74-D694-2.0
Supplementary_files_format_and_content: Tab delimited .txt file containing relative signal per concentration as well as KdApps and additional values

extract_protocol:
Isolated nuclei of MCF-7 or F121 cells were incubated with a titration series of FLAG-tagged transcription factor of interest, which was followed up by either ChIP-seq or CUT&RUN with anti-FLAG antibody, including heterologous spike-in DNA (dm6 or S.cerevisiae for ChIP-seq or CUT&RUN-based follow-up, resp.). Released DNA fragments were column purified and used for preparation of sequencing libraries.
Libraries were prepared using the Kapa Hyper Prep Kit (Kapa Biosystems) according to manufacturer’s protocol, with the following modifications. All input material was used to prepare libraries and 2.5 μl of the NEXTflex adapter stock (600nM, Bioo Scientific) was used for adapter ligation of each sample. Libraries were amplified with 12 PCR cycles and a double post-amplification clean-up was used to ensure proper removal of adapters.
Samples were analyzed for purity using a High Sensitivity DNA Chip on a Bioanalyzer 2100 system (Agilent). Libraries were paired-end sequenced on a Illumina NextSeq500.

value: CUT&RUN


title: MEL cells, NFIA-ETO2, rep2


title: F121_FLAG_YY1_CUTaRUN_0500nM


title: F121_FLAG_YY1_CUTaRUN_1000nM


title: I_B1_S205


title: F121_FLAG_YY1_CUTaRUN_0050nM


title: F121_FLAG_YY1_CUTaRUN_0250nM


title: IV_H1_S181


title: IV_G3_S171


title: s38, BMDM, WT, LPS (ATAC-seq)


title: s33, BMDM, WT, unstimulated (ATAC-seq)


title: F121_FLAG_YY1_CUTaRUN_0001nM


title: s32, BMDM, AhR-KO, LPS (ATAC-seq)


title: IV_G2_S170


title: F121_FLAG_YY1_CUTaRUN_0000nM


title: MEL cells, NFIA-ETO2, rep1


title: IV_G1_S169


title: s30, BMDM, WT, LPS (ATAC-seq)


title: IV_F3_S159


title: s28, BMDM, AhR-KO, unstimulated (ATAC-seq)


title: MCO_Mix_DAPT_rep2

city: Beijing

first: Jie

address: 30 Shuangqing Rd, Haidian District, Beijing, China

department: School of Medicine

institute: Tsinghua University

description:
Cells undergo CM differentiation by adding CHIR99021 and IWP2, followed by multi-lineage mini-cardiac organoid construction and DAPT treatment
MCO_Mix_DAPT_rep2

data_processing:
for single cell RAN-seq data, UMI count matrx was generated using cellranger (v2.0.1) software
for bulk RNA-seq data, adapter sequences were trimmed from raw fastq file using TrimGalore (v0.6.4), clean data were mapped to the human reference genome (GRCh38) using STAR (2.7.3a) with --quantMode GeneCounts option to output read count tables, differential gene expression analysis was performed using DESeq2 (v1.24.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: single cell UMI matrix files generated by cellranger, all three files are needed for downstream analysis
Supplementary_files_format_and_content: tab-delimited text files include read count values for all samples

source_name: CD46-iPS cells

growth_protocol: Human iPSCs were routinely maintained on Matrigel (BD Biosciences) - coated plates (Corning) in TeSR-E8 medium (STEMCELL Technologies). hiPSCs were passaged every 4 d using Accutase (Merck) and 10 uM ROCK inhibitor Y27632 (Selleck) was added for the first 24 h after passage.

extract_protocol:
SMART-seq2
100ng total RNA in each sample are used for SMART-seq2 library construction.
Total RNA are extracted using Trizol.

treatment_protocol: Cells undergo CM differentiation by adding CHIR99021 and IWP2.

tag: treatment protocol

value: bulk RNA-seq


title: IV_F2_S158

value: bacterial cell


title: s27, BMDM, AhR-KO, unstimulated (ATAC-seq)


title: IV_F1_S157


title: s26, BMDM, WT, unstimulated (ATAC-seq)


title: IV_E2_S146


title: MCO_Mix_DAPT_rep1

description:
Cells undergo CM differentiation by adding CHIR99021 and IWP2, followed by multi-lineage mini-cardiac organoid construction and DAPT treatment
MCO_Mix_DAPT_rep1

source_name: CD45-iPS cells


title: 2D_CM_rep2

description:
Cells undergo CM differentiation by adding CHIR99021 and IWP2
2D_CM_rep2

source_name: CD40-iPS cells


title: IV_E3_S147


title: s25, BMDM, WT, unstimulated (ATAC-seq)


title: 2D_CM_rep1

description:
Cells undergo CM differentiation by adding CHIR99021 and IWP2
2D_CM_rep1

source_name: CD39-iPS cells


title: 2D_CM_DLK1_rep2

description:
Cells undergo CM differentiation by adding CHIR99021 and IWP2, followed by sDLK1 treatment
2D_CM_DLK1_rep2

source_name: CD42-iPS cells


title: IV_E1_S145

source_name: bacterial cell


title: s24, BMDM, AhR-KO, LPS (ATAC-seq)


title: MMTV-Neu Mice Treated by Ricolinostat for 4 weeks Replicate 1

city: Memphis

first: Qingfei

last: Pan

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St. Jude Children's Research Hospital

description: SurePrint G3 Mouse Gene Expression v2 8x60K Microarray Kit

hyb_protocol: Labeled cRNA was hybridized using Gene Expression Hybridization Kit.

scan_protocol: Scanned on an Agilent G2600D scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1.1.1).

data_processing: The data normalization was performed by limma R package (v-3.42.2) with LOESS method within array and QUANTILE between arrays.

source_name: mammary tumor tissue

label_protocol: Sample labeling and array hybridization were performed according to the Two-Color Microarray-Based Gene Expression Analysis—Low Input Quick Amp Labeling—protocol (Agilent Technologies).

extract_protocol: Total RNA of three sensitive cell lines (MDA-MB-453, SK-BR-3 and SUM-149) and mouse model (MMTV- Neu) was extracted using the RNAeasy Kit (Qiagen). The samples with the optical density 260/280 ratio greater than 1.8 and the total RNA yield greater than 1 μg were considered qualified.

tag: agent

value: Ricolinostat

tag: time point

value: 4 weeks

tag: replicate

tag: subtype

value: Luminal

tag: response

value: Sensitive

source_name: Universal Mouse Reference RNA

tag: catalog#


title: s29, BMDM, WT, LPS (ATAC-seq)

tag: genotype

tag: treatment


title: P aerug Pgi ALE 2, endpoint, rep 2

city: La Jolla

first: Cameron

last: Lamoureux

state: CA

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: svns_pgi_log_tpm.csv contains log2[TPM] values for all samples and genes.
Supplementary files format and content: svns_pgi_counts.csv contains raw read counts as computed by featureCounts for all samples and genes.

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

source_name: MG1655, adapted

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: evolution stage

value: Endpoint

value: MG1655, adapted

tag: culture type

value: batch


title: s31, BMDM, AhR-KO, LPS (ATAC-seq)

value: BMDM


title: MMTV-Neu Mice Treated by Ricolinostat for 4 weeks Replicate 3


title: MCO_Mix

description: Cells undergo CM differentiation by adding CHIR99021 and IWP2, followed by multi-lineage mini-cardiac organoid construction

source_name: CD38-iPS cells

extract_protocol:
Single Cell 3' v2 chemistry (10X genomics)
Total RNA are extracted using Trizol.

value: single cell RNA-seq


title: MMTV-Neu Mice Treated by Ricolinostat for 4 weeks Replicate 2


title: IV_D3_S135

data_processing:
Read trimming and quality control of MATQ-seq reads was executed using BBDuk. To efficiently remove primer and  adapter sequences located at both ends of a read, we ran BBDuk in a two-pass procedure using the default adapter sequence database augmented with MATQ-seq specific sequences. The first pass focused on the 5’ end, with parameters: minlen=18 qtrim=rl trimq=20 ktrim=l k=17 mink=11 hdist=1 trimpolya=30; while the second pass focused on the 3’ end with parameters: minlen=18 qtrim=rl trimq=20 ktrim=r k=17 mink=11 hdist=1.
Read alignment and counting was performed with Bowtie2 (Langmead & Salzberg 2012) and featureCounts (Liao et al. 2014), allowing a single mismatch and run-in --local mode. BigWig files were generated using deepTools (Ramírez et al. 2014), passing additional parameters: --binSize 5 --normalizeUsing BPM. We have employed the same gene detection method from the original MATQ-seq analyses (Imdahl et al. 2020), requiring a detected gene to have > 5 reads.
DESeq2 (Love et al. 2014) was used for normalization and differential expression analysis, using size factors calculated by the computeSumFactors function in Scran (Lun et al. 2016) and other recommended parameters for DESeq2 single cell analysis, which included using the likelihood ratio test (LRT), useT=TRUE, minmu=1e-6, and minReplicatesForReplace=Inf.
Assembly: NC_016810.1
Supplementary files format and content: Unprocessed count matrix from all samples
Supplementary files format and content: sc_counts.tsv

extract_protocol:
Bacterial RNA was isolated from Salmonella strain SL1344. RNA extraction was performed with 1.8 ml of each in vitro culture using the TRIzol reagent (Invitrogen) according to the manufacturer’s recommendation. RNA quality was checked using Qubit RNA High Sensitivity Assay Kit (Invitrogen) and 2100 Bioanalyzer RNA 6000 Pico/ Nano kit (Agilent Technologies). Prior library preparation, DNAse treatment was performed using DNAse I kit (Thermo Fisher) followed by ribosomal RNA depletion. Ribosomal RNA (rRNA) was depleted using Lexogen's RiboCop META rRNA Depletion Kit protocol according to manufacturer’s recommendation using 100ng total RNA as input per sample.
cDNA obtained from single-cells after MATQseq was further processed for library preparation including ribosomal depletion protocol. Library preparation was done using the Nextera XT DNA Library Preparation Kit (Illumina) including DASH protocol (according to (Prezza et al. 2020) with several modifications). Tagmentation was performed with only ¼ of reaction and 0.5 ng cDNA input according to manufacturer’s recommendations. Index PCR was performed with 13 cycles using IDT for Illumina Nextera DNA Unique Dual Indexes (Illumina). Obtained libraries were purified with AMPure XP beads (Beckman Coulter) at a 1:1 v/v ratio to ensure capturing sRNA-derived cDNA. After QC, up to 12 samples were pooled equimolar for ribosomal depletion. sgRNA/Cas9 complex formation is followed by DASH using the appropriate ratio of cDNA : Cas9 : sgRNA. Cas9 enzyme was inactivated by Proteinase K (15 min at 37 °C). Afterwards, Proteinase K was inactivated by adding PMSF (1 mM final concentration). Depleted cDNA was purified by another round of AMPure XP bead clean-up and used as input for second PCR amplification. 0.5 ng depleted cDNA was used as input for Nextera XT reactions omitting the tagmentation steps. As primers i5 and i7 index-independent primers were used to amplify non-cleaved cDNA products. PCR was done with 13 cycles and clean-up was performed with AMPure XP beads at a 1:1 v/v ratio

tag: media

value: Lennox broth media

tag: od

tag: condition


title: P aerug Pgi ALE 2, endpoint, rep 1

tag: strain


title: MMTV-Neu Mice Treated by Vehicle Replicate 3

value: Vehicle


title: MMTV-Neu Mice Treated by Vehicle Replicate 2


title: MCO_Mix_rep1

description:
Cells undergo CM differentiation by adding CHIR99021 and IWP2, followed by multi-lineage mini-cardiac organoid construction
MCO_Mix_rep1

source_name: CD43-iPS cells


title: s23, BMDM, AhR-KO, LPS (ATAC-seq)

tag: cell type

value: AhR-KO

value: LPS


title: 2D_CM_DLK1_rep1

description:
Cells undergo CM differentiation by adding CHIR99021 and IWP2, followed by sDLK1 treatment
2D_CM_DLK1_rep1

source_name: CD41-iPS cells


title: s22, BMDM, WT, LPS (ATAC-seq)

value: WT


title: P aerug Pgi ALE 2, midpoint, rep 2

value: Midpoint


title: MCO_Mix_rep2

description:
Cells undergo CM differentiation by adding CHIR99021 and IWP2, followed by multi-lineage mini-cardiac organoid construction
MCO_Mix_rep2

source_name: CD44-iPS cells

value: bulk RNA-seq


title: MCO_CM

description: Cells undergo CM differentiation by adding CHIR99021 and IWP2, followed by mini-cardiac organoid construction

source_name: CD37-iPS cells


title: SMC

description: Cells undergo CM differentiation by adding CHIR99021 PDGF-BB and TGF-β1

source_name: CD36-iPS cells


title: P aerug Pgi ALE 2, midpoint, rep 1


title: MMTV-Neu Mice Treated by Vehicle Replicate 1


title: IV_D2_S134

value: bacterial cell

value: MEP


title: s21, BMDM, WT, LPS (ATAC-seq)


title: IV_C3_S123


title: IV_D1_S133


title: P aerug ALE 1, midpoint, rep 2


title: 2D_CM

description: Cells undergo CM differentiation by adding CHIR99021 and IWP2

source_name: CD34-iPS cells


title: IV_C1_S121


title: s17, BMDM, WT, unstimulated (ATAC-seq)

source_name: BMDM

value: unstimulated


title: R2

first: Wang

middle: Ya

last: ning

state: Beijing

address: Yong An Road

department: internation medical center

institute: Beijing Friendship Hospital

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

source_name: Neutrophils

extract_protocol:
CD45+CD11b+Ly6G+ neutrophils were sorted using FACS Aria II from mouse bone marrow, and then stimulated by LPS with or without resveratrol (25 μmol) for 6 hours. And then RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Neutrophils isolated from bone marrow were stimulated by LPS with or without resveratrol (25 μmol) for 6 hours.

value: Neutrophils

value: LPS and resveratrol co-stimulated

tag: time

value: 6 hours


title: P aerug Pgi ALE 1, midpoint, rep 1

value: MG1655, adapted


title: IV_B3_S111


title: IV_C2_S122


title: R1


title: IV_B2_S110


title: R3


title: s40, BMDM, AhR-KO, LPS

data_processing:
[basecalling]  Basecalls were done with Illumina bcl2fastq version 2.20.0.
[mapping]  Reads were aligned to the mouse reference genome mm10 using the aligner gsnap (v2020-12-16) with Ensembl 98 human splice sites as support (parameter: --gunzip -A sam -t 11 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -n 1 -m 0.6 -s EnsemblGene-92.ss.hg38.iit -N 0 --action-if-cigar-error noprint).
[counts per feature]  Uniquely mapped reads were compared based on their overlap to Ensembl 98 mouse gene annotations using featureCounts (v2.0.1) to create a table of fragments per mouse gene and sample (parameter: featureCounts -a EnsemblGene-98.mm10.TR.gtf -s 2 -p -o bfx1781.mm10.e98.txt -Q 1 -T 8).
Assembly: mm10
Supplementary files format and content: bfx1781.mm10.e98.txt.gz is a tab-separated file with the output from featureCounts. Each row represents a gene and the columns contain the gene information followed by the sample counts.

extract_protocol:
RNA was harvested using Rneasy plus mini kit (Qiagen).
mRNA enrichment,  reverse-transcription into cDNA and library preparation was done with the NEBNext Ultra II Directional RNA Lib Prep Kit for Illumina (NEB) following manufacturer's protocol.


title: EC

description: Cells undergo EC differentiation by adding CHIR99021, VEGF165 and FGF2

source_name: CD35-iPS cells

tag: treatment protocol


title: Bme Pgi ALE 2, endpoint, rep 2

value: Endpoint

value: batch


title: P aerug Pgi ALE 1, endpoint, rep 2


title: Bme Pgi ALE 2, endpoint, rep 1


title: IV_B1_S109


title: s39, BMDM, AhR-KO, LPS

value: BMDM


title: P aerug Pgi ALE 1, endpoint, rep 1


title: s20, BMDM, AhR-KO, unstimulated (ATAC-seq)


title: IV_A3_S99

value: Lennox broth media


title: Bme Pgi ALE 2, midpoint, rep 2


title: s18, BMDM, WT, unstimulated (ATAC-seq)


title: C2

value: LPS stimulated


title: s38, BMDM, WT, LPS


title: Bme Pgi ALE 2, midpoint, rep 1


title: C1


title: MCF7_FLAG_cMYCMAX_0500nM_HisMYC_0250nM_CUTaRUN_b

data_processing:
Sequence data processing was performed automatically with automated processing pipeline seq2science, v 0.7.2
Read alignment to target and spike-in genome with bwa-mem2 v2.1, options -M
Filtering out MAPQ <30, multimapper and map to the ENCODE blacklist
Duplicates removed with PICARD v2.23.8
Peak calling with macs2 v2.2.7, options --keep-dup 1 --buffer-size 10000 --call-summits -BAMPE
Total read counts per sample determined with samtools v1.9
Read normalisation in R v4.0.3 to reads per million spike-in reads and to highest signal per binding site and experiment. Fit signal-over-concentration to hill equation at bound sites to determine genome-wide binding affinities (apparent Kds).
Assembly: hg38, S.cerevisiae-74-D694-2.0
Library strategy: CUT&RUN

tag: banc-seq follow up method

value: CUT&RUN

tag: spike in genome


title: C3


title: IV_A1_S97


title: MCF7_FLAG_cMYCMAX_0100nM_HisMYC_0250nM_CUTaRUN_b


title: III_H6_S90


title: MCF7_FLAG_cMYCMAX_0250nM_HisMYC_0250nM_CUTaRUN_b


title: s36, BMDM, AhR-KO, unstimulated

value: AhR-KO


title: Bme Pgi ALE 1, endpoint, rep 1


title: Bme Pgi ALE 1, midpoint, rep 2


title: Bme Pgi ALE 1, midpoint, rep 1


title: s34, BMDM, WT, unstimulated

value: WT


title: MCF7_FLAG_cMYCMAX_0010nM_HisMYC_0250nM_CUTaRUN_b


title: III_H5_S89


title: III_H4_S88


title: MCF7_FLAG_cMYCMAX_0001nM_HisMYC_0250nM_CUTaRUN_b


title: MCF7_FLAG_cMYCMAX_0000nM_HisMYC_0250nM_CUTaRUN_b


title: III_G5_S77


title: III_G6_S78


title: s31, BMDM, AhR-KO, LPS

value: LPS


title: MCF7_FLAG_cMYCMAX_0500nM_HisMYC_0000nM_CUTaRUN_b


title: s37, BMDM, WT, LPS


title: Bme Pgi ALE 1, endpoint, rep 2