title: RPL3L OE C2C12 Ribo-seq replicate 1

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt.
Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit.
Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCm38.p6) and human genome (mm10) also with the use of STAR.
Read counting was performed with the use of featureCounts.
Assembly: mm10
Supplementary files format and content: Counts per transcript
Library strategy: Ribo-seq

source_name: C2C12 cells

value: RPL3L OE


title: Wildtype 3 [WT_5]

status: Public on Mar 15 2023

type: SRA

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

country: USA

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
Sequencing reads were trimmed of adapters and filtered
STAR alignment was performed against mouse reference
Quantification of reads was determined by Novogene
DEG analysis was performed with DeSeq2
clusterProfiler was used to perform enrichment analyses
Assembly: mm10
Supplementary files format and content: Excel file containing results of DEG, raw counts, and FPKM counts

molecule: total RNA

organism: Mus musculus

source_name: Heart

growth_protocol: Mice were housed at animal facilities at the National Institutes of Health, Bethesda and Frederick, MD. Animal handling was conducted in accordance with the ACUC, under protocol number 21-018.

extract_protocol:
RNA isolation was performed with a Qiagen tissue RNA isolation kit, then tested via an Agilent BioAnalyzer analysis.
Illumina paired-end total RNA-seq

treatment_protocol: All mice were age matched (20-25 weeks).

tag: tissue

value: Heart

tag: strain

tag: age

value: 20-25 weeks

tag: genotype

value: WT


title: Wildtype 2 [WT_4]


title: Rpl3l KO heart disome-seq replicate 1-1

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

country: Japan

institute: Nagoya University

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt.
Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit.
Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCm38.p6) and human genome (mm10) also with the use of STAR.
Read counting was performed with the use of featureCounts.
Assembly: mm10
Supplementary files format and content: Counts per transcript
Library strategy: disome-seq

growth_protocol: C2C12 (CRL-1772) cells were obtained from American Type Culture Collection and were checked for mycoplasma contamination with the use of MycoAlert (Lonza). The cells were cultured under an atmosphere of 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Life Technologies) and antibiotics.

extract_protocol:
C2C12 cells were lysed with a lysis buffer [50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, 1 mM dithiothreitol, 1% Triton X-100, and EDTA-free protease inhibitor cocktail] supplemented with cycloheximide (100 μg/ml). The heart tissues were flash frozen in liquid nitrogen and lysed in a lysis buffer with the use of Multi beads shocker (YASUI KIKAI). The lysates were centrifuged at 20,380 × g for 10 min at 4°C, and the resulting supernatants were collected, assayed for RNA concentration with a Qubit RNA BR Assay Kit (Thermo Fisher Scientific), incubated with RNase I (20 U per 10 μg of RNA, Epicentre) for 45 min at 25°C, and placed on ice before the addition of SUPERase•In RNase inhibitor (Invitrogen). The samples were then loaded on a 1 M sucrose cushion [containing 20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, SUPERase•In (10 U/ml), 1 mM dithiothreitol, and cycloheximide (100 μg/ml)], and the gradients were centrifuged at 100,000 rpm (417,200 × g) for 1 h at 4°C in a Beckman TLA110 rotor. The resulting pellets were suspended in ribosome splitting buffer [20 mM Tris-HCl (pH 7.5), 300 mM NaCl, 5 mM EDTA, SUPERase•In (20 U/ml), 1 mM dithiothreitol, and 1% Triton X-100] and subjected to purification with the use of an Amicon Ultra filtration device (100-kDa cutoff, Millipore) to deplete rRNAs.
The purified RNA was subjected to selection on the basis of a size range of 17 to 34 nt for Ribo-seq and 50 to 80 nt for Disome-seq by electrophoresis through a 15% polyacrylamide and Tris-borate-EDTA (TBE)–urea gel (SuperSep RNA, Fujifilm). The footprint fragments were treated with T4 polynucleotide kinase (New England Biolabs) to repair the 2'-3' cyclic phosphates, a DNA linker including barcode sequences (NI-810 to NI-817) was ligated with the use of T4 RNA ligase 2, truncated K227Q (New England Biolabs), and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. Ribosomal RNAs were further depleted with the use of RiboZero Gold (Illumina). Reverse transcription (RT) was performed with the NI-802 primer, and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. The purified cDNAs were circularized with circLigase II (Lucigen), and index sequences were then added by amplification with the polymerase chain reaction (PCR) as performed with the common primer (NI-798) and primers including index sequences (NI-799 and NI-822 to NI-826). Products of the desired size were purified on a 15% polyacrylamide nondenaturing gel (SuperSep DNA, Fujifilm), and the libraries were sequenced with a NovaSeq 6000 system (Illumina).

value: Rpl3l KO


title: sample08

city: Lille

first: Vance

last: Gao

address: 1 Rue du Professeur Calmette

country: France

institute: Institut Pasteur de Lille

data_processing:
Libraries were aligned to the human genome (hg38) using STAR.
Low-quality reads (mapq<15) were excluded from downstream analysis.
Read counts per gene were obtained with HOMER2’s analyzeRepeats.pl script using default settings and reporting raw read counts.
Log counts normalized for sequencing depth were created using the "DESeq" and "rlog" functions in the DESeq2 R package.
Genome_build: hg38
Supplementary_files_format_and_content: "Counts RefSeq.txt" - Read counts of RefSeq sequences. Tab-delimited file
Supplementary_files_format_and_content: "Log counts Genes.txt" - Normalized, log counts generated by DESeq2. Collapsed to gene symbols by taking the highest RefSeq count for each gene. Tab-delimited file

organism: Homo sapiens

source_name: monocytes

growth_protocol: Monocytes in circulating blood of cardiopulmonary bypass surgery patients (median age 70), collected before surgery

extract_protocol:
Classical CD14++ CD16- monocytes were sorted from blood (PBMC). Total RNA was extracted using the Direct-Zol RNA Microprep kit with on-column DNaseI treatment (Zymo Research). Whole transcriptome amplification and cDNA synthesis were performed with the Ovation RNA-seq V2 kit (NuGEN) following the manufacturer’s instructions.
Sequencing libraries were prepared using the Ovation Ultralow V2 DNA-seq Library preparation kit. Libraries were pooled and sequenced on a HiSeq4000 (Illumina) to obtain 20 million single-end 50bp reads.

tag: ChIP

value: FALSE


title: GSC23_ctrl_2

city: Pittsburgh

first: Huairui

last: Yuan

state: PA

address: 4200 Fifth Ave

institute: University of Pittsburgh

data_processing:
For RNA-seq, raw FASTQ reads were trimmed using Trim Galore, followed by transcript mapping with Hisat2 to human reference genome (hg38). Samtools was used for sorting, indexing and format conversion from SAM files. Quantification and differential analysis were performed using FeatureCounts and DESeq2 with paired sample analysis.
Assembly: hg38
Supplementary files format and content: For RNA-seq, text files include gene count for each Sample.

source_name: Glioblastoma

extract_protocol:
Cellular total RNA was isolated using TRIzol (cat: 15596018; Life Technologies) followed by Direct-zol RNA Miniprep kit (cat: R2052; Zymo Research).
Total RNA was extracted and used for library construction using the Illumina TruSeq Stranded Total RNA Library Prep Kit, which was performed by Novogene.

value: Glioblastoma

tag: cell line

tag: cell type

value: Glioblastoma stem cells

tag: treatment

value: shCONT


title: siS17

city: St. Louis

first: Zhiyu

last: Dai

state: MO

address: 4960 Childrens Place

institute: Washington University in St. Louis

description: electroporation

data_processing:
raw reads were aligned with Hisat2
Per-gene expression was quantified and the differential expression, fold-changes between conditions using CuffDiff
Genome_build: GRCh38

source_name: Human lung microvascular endothelial cells

growth_protocol: HPMVECs were cultured in 0.2% gelatin (Sigma) precoated T75 flasks in EBM-2 medium supplemented with 10% FBS and EGM-2 MV singlequots (Lonza, #CC-3162), and incubated at 37 C in a humidified 5% CO2 atmosphere. Cells between passage 4 and 7 were used for experiments.

extract_protocol:
Total RNA was isolated from cells with Zymo Research Quick-RNA Miniprep Kits with DNase I digestion.
Library construction was carried out at the Novogene Corporation Inc.

treatment_protocol: HPMVECs were transfected into ECs using HMVEC-L Nucleofector kit (Lonza, # VPB-1003) with NucleofectorTM 2b device (Lonza, #AAB-1001) with program A-034.

tag: organ

value: lung primary endothelial cells

value: SOX17 siRNA

tag: source

value: Lonza, cat #CC-2527


title: sample03

value: TRUE


title: sample07


title: WT heart disome-seq replicate 4-1


title: RPL3 OE C2C12 Ribo-seq replicate 2

value: RPL3 OE


title: WT heart disome-seq replicate 3-1


title: RPL3 OE C2C12 Ribo-seq replicate 1


title: sample05


title: WT heart disome-seq replicate 1-1


title: sample04


title: GSC23_ctrl_1


title: Rbbp4-AID 0 h, scRNAseq

city: Guangzhou

first: Wang

middle: Fang

last: Ping

state: Guangdong

address: 190 Kaiyuan Avenue

department: Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description:
DNBelab C4
DNBSEQ-T7RS

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the DNBC4tools v2.0 (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

extract_protocol:
RNA was extracted according to the manufacturer’s manual for DNBelab C4's scRNA-seq.
Library was performed according to the manufacturer’s instructions.

value: embryonic stem cells

value: Rbbp4-AID, Tir1

value: auxin-induced degradation of RBBP4 0h


title: siCTL

description: electroporation

value: control siRNA


title: Control C2C12 Ribo-seq replicate 3

value: empty


title: Knockout 2 [KO_3]

value: Heart

value: 20-25 weeks

value: ARE-/-


title: RPL3L OE C2C12 Ribo-seq replicate 3

value: RPL3L OE


title: Knockout 1 [KO_2]


title: Rbbp4-AID 24 h, scRNAseq

description:
DNBelab C4
DNBSEQ-T7RS

value: auxin-induced degradation of RBBP4 24h


title: sample02


title: RPL3L OE C2C12 Ribo-seq replicate 2


title: RPL3 OE C2C12 Ribo-seq replicate 3


title: accession_9981_smallRNA-seq

city: Vienna

first: Aleksandra

last: Kornienko

state: Vienna

address: Dr. Bohrgasse 3

country: Austria

institute: Gregor Mendel Institute

description: 75bp SE

data_processing:
Raw data (fastq files) was trimmed with cutadapt. Command used: cutadapt -a AACTGTAGGCACCATCAAT --minimum-length 18 -o $fastq.trimmed.fastq $fastq.fastq
trimmed sequencing reads were aligned to the TAIR10 genome using STAR (v.2.9.6) adjusted for smallRNAseq, allowing 10 multimappers and 2 mismatches. STAR command used: STAR --runMode alignReads --runRNGseed 12345 --genomeDir $stargenomedir --readFilesIn $fastq.trimmed.fastq  --outFileNamePrefix $out --alignEndsType Extend5pOfRead1 --alignIntronMax 5000 --alignSJDBoverhangMin 1 --outReadsUnmapped Fastx --outSAMtype BAM Unsorted --outSAMmultNmax 100 --outSAMprimaryFlag AllBestScore --outSAMattributes NH HI AS nM NM MD jM jI XS --outFilterMultimapNmax 10 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0.66 --outFilterMismatchNmax 2 --outFilterMismatchNoverReadLmax 0.05 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --twopassMode None --quantMode GeneCounts
24nt-long reads were extracted
read coverage of each base in the genome was calculated using genomeCoverageBed from the bedtools package and normalized by dividing by the total number of reads in the sample
final 24nt smallRNA coverage was calculated by mapping read coverage per base over loci in the annotation and calculating the average
Assembly: TAIR10
Supplementary files format and content: flowers_14acc.24nt.new_annotation.coverage.perbase_calc.normalized.bed contains a table of normalized 24nt read coverage for genes in the annotation created in the paper. The gene annotation is submitted as supplementary file
Supplementary files format and content: flowers_14acc.24nt.Araport11.coverage.perbase_calc.normalized.bed contains a table of normalized 24nt read coverage for Araport11 annotated genes and transposable element fragments

organism: Arabidopsis thaliana

source_name: flowers and flower buds

growth_protocol: plants from 14 different A.thaliana accessions were grown at the growth chambers of GMI, Vienna, Austria. The growing conditions were 22 degrees Celcius, long-day (16-hour light, 8-hour dark).

extract_protocol:
NucleoSpin miRNA kit from Macherey-Nagel following the manufacturer's protocol
QIAseq miRNA Library Kit from Qiagen following the manufacturer's protocol

treatment_protocol: Accessions 1741, 6024, 6244, 9888 and 9905 were cold-treated at 10 degrees for ~ 4 weeks to induce flowering and then returned to 22 degrees.

value: flowers and flower buds


title: accession_9905_smallRNA-seq

description: 75bp SE


title: Wildtype 1 [WT_1]

value: WT


title: Control C2C12 Ribo-seq replicate 2


title: accession_9888_smallRNA-seq

description: 75bp SE


title: RPL3 OE C2C12 RNA-seq replicate 2

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt.
Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit.
Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCm38.p6) and human genome (mm10) also with the use of STAR.
Read counting was performed with the use of featureCounts.
Assembly: mm10
Supplementary files format and content: Counts per transcript


title: 8546278051_I: High Altitude Andean

type: RNA

city: Tampa

first: Derek

last: Wildman

state: FL

address: 3720 Spectrum Blvd

institute: University of South Florida

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normailzation and log2 transformation

label: biotin

source_name: Placenta

label_protocol: Not provided

extract_protocol: Not provided

tag: gender

value: F

tag: gestational age (wks)

tag: altitude

value: High

tag: ancestry

value: Andean

value: Placenta

tag: sample number

value: SAMPLE 5


title: accession_10024_smallRNA-seq

description: 75bp SE


title: accession_22005_smallRNA-seq

description: 75bp SE


title: RPL3 OE C2C12 RNA-seq replicate 1

value: RPL3 OE


title: Control C2C12 Ribo-seq replicate 1


title: 8546278051_E: High Altitude Andean

value: M

value: SAMPLE 22


title: accession_8236_smallRNA-seq

description: 75bp SE


title: RPL3L OE C2C12 RNA-seq replicate 3


title: 8546278051_C: High Altitude European

value: European

value: SAMPLE 9


title: accession_10015_smallRNA-seq

description: 75bp SE


title: accession_10002_smallRNA-seq

description: 75bp SE


title: 8546278051_H: High Altitude Andean

value: SAMPLE 19


title: RPL3L OE C2C12 RNA-seq replicate 2


title: 8546278051_G: High Altitude European

value: SAMPLE 23


title: Hela cell line after Arp5 knockdown

city: Changchun

first: Yong

last: Cai

address: Qianjin Street

institute: JiLin University

description: SAMPLE 1

data_processing: background normalization, using the signals of built-in negative controls, which are designed to be thermodynamically equivalent to the regular probes but lack a specific target in the transcriptome.

source_name: Hela cell

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: HeLa cells were cultured in 6-well tissue culture plates (~2x105 cells/well) in DMEM medium containing 10% fetal bovine serum.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The cells were transiently transfected with 10~20 pmol specific siRNAs using Lipofetamine RNAMAX transfection kit (Invitrogen, Cat.No-864425) following the manufacture’s instruction. 24 hours after transfection, cells were divided into new 6-well plates for western blot, RT-PCR, and DNA microarray analysis. 48 hours after siRNAs transfection, cells were harvested and lysed. Whole-cell extract (WCE) were prepared by adding 4 x SDS sample buffer, and total RNA was isolated using TRIzol® LS Reagent (Invitrogen). In addition, cells from 1 well of a 6-well plate were rinsed twice with warm PBS and harvested. Cells were then stored in an RNA hold solution (ER501-01, Beijing Transgen Biotech Co., Ltd.). After the knockdown efficiency was confirmed, cells in RNA hold solution were sent to EMTD Science and Technology Development Co., Ltd. (Beijing, China) for DNA microarray analysis.

value: HeLa

value: Knock-down


title: PBMC_PolyIC

city: Setagaya

first: Kenichiro

last: Motomura

state: Tokyo

department: Allergy and Clinical Immunology

institute: National Research Institute for Child Health and Development

hyb_protocol: Biotinylated cRNA was fragmented and hybridized to an Affymetrix  microarray according to the standard Affymetrix protocol.

scan_protocol: Slides were scanned on the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were normalized analyzed using Subio platform version 1.24.5853 (Subio Inc) with global normalization (75 percentale), low signal cutoff (1.0), log transfomation (base 2), and centering (Mean).

source_name: Human PBMC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Two-Cycle Target Labeling).

extract_protocol: The cells were lysed with QIAzol, and the total RNA was extracted using an RNeasy Mini Kit according to the manufacturer’s instructions.

treatment_protocol: Human peripheral blood mononuclear cells (PBMCs) were cultured with poly I:C (30 µg/mL) or its vehicle control (endotoxin-free water) for 3 h.

value: Poly I:C (1 µg/mL)


title: accession_6966_smallRNA-seq

description: 75bp SE

value: flowers and flower buds


title: Control C2C12 RNA-seq replicate 2

value: empty


title: 8546278051_A: Low Altitude European

value: F

value: Low

value: SAMPLE 11


title: RPL3L OE C2C12 RNA-seq replicate 1

value: RPL3L OE


title: PBMC_Control

value: peripheral blood mononuclear cells (PBMCs)

value: Vehicle


title: 8546278051_F: Low Altitude Andean

value: Andean

value: Placenta

value: SAMPLE 48


title: RPL3 OE C2C12 RNA-seq replicate 3

value: RPL3 OE


title: Control C2C12 RNA-seq replicate 1


title: accession_6909_smallRNA-seq

description: 75bp SE


title: Control C2C12 RNA-seq replicate 3


title: 8546278051_D: High Altitude Andean

value: High

value: SAMPLE 34


title: 8546278051_B: Low Altitude Andean

value: M

value: SAMPLE 24


title: Anti-PD1+ DLnano-Vax+ TA99-HL2-KOA1

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
The Cell Ranger Software Suite (Version 3.1.0, https://support.10xgenomics.com) was used to preprocess scRNA-seq data using mm10 genome version
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contain output from CellRanger

molecule: polyA RNA

source_name: CD45+ mouse tumor infiltrating lymphocytes

extract_protocol:
Viable single cells from each of the 3 mouse TIL samples were uniquely barcoded using the 10× chromium single-cell platform, and complementary DNA (cDNA) libraries were prepared for Next Generation Sequencing according to the manufacturer’s protocol (Chromium Next GEM Single Cell 3′ Reagent Kits v3.1, 10× Genomics, USA). Cell suspensions of each sample, reverse transcription master mix, and partitioning oil were loaded on a single-cell “G” chip with a targeted cell output of 6,000 cells per library and then run on the Chromium Controller.  A total of 3 lanes were used on the G chip, 1 lane/ sample.
Reverse transcription was performed within the droplets at 53°C for 45 min and newly synthesized cDNA was amplified for 11 cycles on a Veriti Thermal Cycler (Thermofisher, USA). cDNA size selection was performed using SPRIselect beads (Beckman Coulter, USA) at a ratio of SPRIselect reagent volume to sample volume of 0.6. cDNA was analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip (Agilent, USA) for qualitative and quantitative control purposes. cDNA was fragmented using the proprietary fragmentation enzyme blend for 5 min at 32°C, followed by end-repair and A-tailing at 65°C for 30 min. cDNA was double-sided size selected using SPRIselect beads. Sequencing adaptors were ligated to the cDNA at 20°C for 15 min. and after a round of post-ligation SPRIselect bead clean-up, cDNA was amplified for 15 cycles using a sample-specific index oligo as a primer. A final round of double-sided size selection using SPRIselect beads followed. Final library size and quantity was determined using an Agilent Bioanalyzer High Sensitivity DNA chip and a Qubit dsDNA High Sensitivity Assay kit (Thermofisher, USA), respectively

tag: treatement

value: Anti-PD1+ DLnano-Vax+ TA99-HL2-KOA1


title: Anti-PD1+ DLnano-Vax+ TA99

value: Anti-PD1+ DLnano-Vax+ TA99


title: accession_6244_smallRNA-seq

description: 75bp SE

value: flowers and flower buds


title: accession_9537_smallRNA-seq

description: 75bp SE


title: accession_6024_smallRNA-seq

description: 75bp SE


title: Anti-PD1 alone treatment

value: Anti-PD1 alone treatment


title: Rpl3l KO heart Ribo-seq replicate 1

value: Rpl3l KO


title: accession_1741_smallRNA-seq

description: 75bp SE


title: Rpl3l KO heart Ribo-seq replicate 4


title: Rpl3l KO heart Ribo-seq replicate 2


title: 8546278036_J: High Altitude European

value: F

value: European

value: SAMPLE 10


title: Glo2 -/- 6

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Assembly: GRCz11
Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.

organism: Danio rerio

extract_protocol:
Total RNA was extracted using TRIzol method
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

value: whole liver

tag: trained

value: no

value: KO


title: DNMT5_WT_rep1

city: Nantes

first: LEILA

last: TIRICHINE

address: 2, rue de la Houssinière, BP 92208, Nantes

department: BIOLOGY

institute: Nantes Universte, CNRS UMR 6286

data_processing:
A reference sequence for Phaeodactylum tricornutum is built with STAR 2.5.3a.
Reads were mapped on the Phatr3 genome.
Counting tables were obtained using HTseq v 0.7.2.
Genome_build: Phatr3 genome
Supplementary_files_format_and_content: tsv files containing Phaeodactylum tricornutum CDS IDs raw expression values.
Supplementary_files_format_and_content: TPM_counts_DNMT5_RNAseq.tsv: Tab-delimited text file containing TPM normalized (Transcripts Per Million) expression values of Phaeodactylum tricornutum CDS Ids in each condition.

organism: Phaeodactylum tricornutum

source_name: PT18.6 cell line

growth_protocol: Axenic Phaeodactylum tricornutum CCMP2561 clone Pt18.6 cultures were obtained from the culture collection of the Provasoli-Guillard National Center for Culture of Marine Phytoplankton (Bigelow Laboratory for Ocean Sciences, USA.). Cultures were grown in autoclaved and filtered (0.22 μM) Enhanced Sea Artificial Water (ESAW - https://biocyclopedia.com/index/algae/algal_culturing/esaw_medium_composition.php) medium supplemented with f/2 nutrients and vitamins without silica under constant shaking (100rpm). Cultures were maintained in flasks at exponential state in a controlled growth chamber at 19°C under cool white fluorescent lights at 100 μE m−2 s−1 with a 12h photoperiod. WT and DNMT5 mutant cultures were seeded in duplicate at 10.000 cells/ml and grown side by side in 250ml flasks until early-exponential at 1.000.000 cells/ml.

extract_protocol:
Trizol-Chloroform isolation of RNAs from PBS washed cell pellets.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: DNMT5 WT


title: 8546278036_H: High Altitude European

tag: tissue

value: Placenta

value: SAMPLE 18


title: DNMT5_KO_M25_rep2

value: DNMT5 KO (M25)


title: DNMT5_WT_rep2


title: 8546278036_K: High Altitude European

value: M

value: High

value: SAMPLE 46


title: 8546278036_G: Low Altitude Andean

value: Low

value: Andean

value: SAMPLE 35


title: 8546278036_I: Low Altitude Andean

value: SAMPLE 27


title: WT heart Ribo-seq replicate 4

value: WT


title: Glo2 -/- 5


title: Rpl3l KO heart Ribo-seq replicate 3

value: Rpl3l KO


title: WT heart Ribo-seq replicate 3


title: Glo2 +/+ 5


title: DNMT5_KO_M25_rep1


title: 8546278036_E: High Altitude Andean

value: F

value: SAMPLE 26


title: Glo2 +/+ 6

value: whole liver

value: no


title: WT heart Ribo-seq replicate 1


title: DNMT5_KO_M23_rep1

value: DNMT5 KO (M23)


title: DNMT5_KO_M23_rep2


title: Glo2 -/- 4

value: KO


title: 8546278036_F: Low Altitude Andean

value: Placenta

value: SAMPLE 13


title: WT heart Ribo-seq replicate 2


title: 8546278036_D: Low Altitude European

value: European

value: SAMPLE 28


title: DNMT5_M25

library_source: genomic

data_processing:
A reference sequence for Phaeodactylum tricornutum is built with Bowtie2.
Reads were mapped on the Phatr3 genome.
CHG, CHH and CpG methylation contexts were obtained using Bismark v0.18.1_dev.
Genome_build: Phatr3 genome
Supplementary_files_format_and_content: Bigwig files reporting CHG, CHH and CpG methylation levels in Phaeodactylum tricornutum (#methylated cytosines/#total cytosines sequenced), the negative values indicate methylation levels on the reverse strand. (H=A,T,C)

molecule: genomic DNA

extract_protocol:
DNA extraction was performed using the Invitrogen™ Easy-DNA™ gDNA Purification Kit following ‘Protocol #3’ instructions provided by the manufacturer.
Bisulfite-Seq libraries were prepared for sequencing using standard Illumina protocols.

value: DNMT5 KO (M25)


title: Glo2 +/+ 4


title: DNMT5_WT

value: DNMT5 WT


title: Rpl3l KO heart RNA-seq replicate 3


title: 8546278036_L: Low Altitude European

value: Low

value: SAMPLE 2


title: DNMT5_M23


title: Glo2 +/+ 3


title: Rpl3l KO heart RNA-seq replicate 2


title: Glo2 -/- 3


title: Rpl3l KO heart RNA-seq replicate 4


title: RD3_W34

city: Lake Alfred

first: Xiaokang

last: Zhuo

state: Florida

address: 700 Experiment Station Rd

department: Citrus Research and Education Center

institute: University of Florida

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to mapped to Citrus clementina genome v1.0 (JGI) using HISAT2 software
StringTie was used to assemble transcripts of each sample, merge transcripts to get a consensus transcriptome assembly, and compute the abundance of transcripts for each sample

organism: Citrus jambhiri

source_name: leaf midrib

extract_protocol:
Total RNA was extracted using TRIzol® Reagent and purified using an RNeasy Mini Kit following the manufacturer’s protocol
Ribosomal RNA was removed from the total RNA using a Ribo-Zero rRNA removal kit  for using plant seed/plant leaf following the manufacturer’s protocol. Subsequently, 50 ng of the purified RNA from each sample were used for library construction utilizing an Epicentre ScriptSeq v2 RNA-Seq library preparation kit according to the user’s guide.

value: leaf midrib

tag: infection

value: CLas infection

value: Week 34


title: Glo2 -/- 2


title: Rpl3l KO heart RNA-seq replicate 1

value: Rpl3l KO


title: Glo2 +/+ 2

value: WT


title: 8546278036_B: Low Altitude Andean

value: M

value: Andean

value: SAMPLE 20


title: Glo2 -/- 1

value: whole liver

value: no

value: KO


title: WT heart RNA-seq replicate 4


title: WT heart RNA-seq replicate 3


title: RD3_W17

value: Week 17


title: RD3_W7

value: Week 7


title: Glo2 +/+ 1


title: WT heart RNA-seq replicate 2


title: 8546278021_L: High Altitude European

value: High

value: European

value: Placenta

value: SAMPLE 3


title: 8546278036_A: High Altitude European

value: SAMPLE 1


title: 8546278021_H: Low Altitude European

value: Low

value: SAMPLE 33


title: RD3_W0

value: leaf midrib

value: CLas infection

value: Week 0


title: 8546278036_C: High Altitude European

value: F

value: SAMPLE 42


title: 8546278021_I: High Altitude Andean

value: M

value: Andean

value: SAMPLE 45


title: 8546278021_K: Low Altitude European

value: SAMPLE 8


title: 8546278021_J: High Altitude European

value: SAMPLE 43


title: RD2_W0


title: S31P

city: Chongqing

first: Peng

last: Xie

address: 1st, Youyi Street

institute: The first affiliated hospital of Chongqing medical university

data_processing:
Basecalls performed using CASAVA version 1.8
Read alignment and count summarization were performed using CellRanger
Nucleus expressing fewer than 200 genes and cells with a mitochondrial UMI rate higher than 20% were excluded. Mitochondrial genes were removed from the expression matrix but used for cell expression regression to avoid cell status effect in clustering analysis and marker analysis of each cluster.
Assembly: mm10_Ensembl92
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Prefrontal cortex

growth_protocol: GF and CGF mice were kept in a flexible film gnotobiotic isolators until experiment and behavioral tests. All mice were housed on a 12-h light/dark cycle and had food and water ad libitum, with controlled conditions of temperature 22-24°C and 50-60% humidity. All mice were harvested at 8 weeks old.

extract_protocol:
Sn protocol: the frozen tissue was homogenized in nuclei lysis buffer (NLB) containing 250mM sucrose, 10mM Tris-HCl, 3 mM MgAc2, 0.1mM EDTA, 0.1% Triton X-100 (Sigma-Aldrich, USA) and 0.2 U/μl RNase Inhibitor (Takara, Japan). Tissues were homogenized using a tissue grinder for 15-30 strokes at 2-8°C until they were lysed uniformly. Sucrose concentration was adjusted to purify the nucleus better. sc-RNA Seq sample concentration was adjusted to ~1000 nuclei/μl.single nucleus were collected using  the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3.1 Reagent Kits (10X Genomics, Pleasanton, USA) .
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: SPF

tag: tissue/cell type

value: Prefrontal cortex cells

tag: molecule subtype

value: single-cell nucleus RNA


title: RD2_W17

value: Week 17


title: 8546278021_G: High Altitude Andean

value: High

value: Placenta

value: SAMPLE 17


title: RD2_W7

value: leaf midrib

value: Week 7


title: S30P


title: RD1_W34

value: CLas infection

value: Week 34


title: 8546278021_E: Low Altitude European

value: Low

value: European

value: SAMPLE 30


title: 8546278021_F: High Altitude European

value: F

value: SAMPLE 7


title: WT heart RNA-seq replicate 1

tag: genotype

value: WT


title: G7P

value: GF


title: G5P

value: Prefrontal cortex cells


title: G6P

value: single-cell nucleus RNA


title: CLP_LV_rep5

city: Shanghai

first: hui

last: zhang

address: Kongjiang Road 1665

institute: Shanghai Jiao Tong University

description: gene expression of CLP mice exposed to 12h LV

hyb_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray.

scan_protocol: the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data.Genespring (version 14.8,Agilent Technologies) were employed to finish the basic analysis with the raw data.

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Lung tissues were collected from Sham mice;CLP mice (24h); LV mice(Sham mice exposed to low tidal volume ventilation for 12 h);CLP+LV mice ( CLP mice exposed to low tidal volume ventilation for 12 h)

value: lung tissue

value: male

tag: treatmant


title: RD2_W34

tag: treatment


title: CLP_LV_rep4

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray.


title: 8546278021_D: Low Altitude Andean

value: M

value: Andean

value: Placenta

value: SAMPLE 47


title: C19P

value: CGF


title: CLP_LV_rep2


title: RD1_W7

value: leaf midrib

value: CLas infection

value: Week 7


title: CLP_LV_rep1


title: RD1_W17

value: Week 17


title: C18P


title: C17P


title: 8546278021_B: Low Altitude European

value: F

value: Low

value: European

value: SAMPLE 14


title: RD1_W0

value: Week 0


title: RH3_W17

value: Mock-infection


title: 8546278021_A: High Altitude Andean

value: High

value: SAMPLE 16


title: RH3_W34

value: Week 34


title: CLP_LV_rep3

value: lung tissue

value: male


title: 8546278021_C: Low Altitude European

value: M

value: Placenta

value: SAMPLE 36


title: S32H

source_name: Hippocampus

value: SPF

value: Hippocampus cells

value: single-cell nucleus RNA


title: RH3_W7

value: leaf midrib

value: Week 7


title: CLP_rep5

description: gene expression of CLP mice


title: 8546278019_L: Low Altitude Andean

value: F

value: Low

value: Andean

value: SAMPLE 40


title: CLP_rep4

description: gene expression of CLP mice


title: CLP_rep3

description: gene expression of CLP mice


title: RH3_W0

value: Mock-infection

value: Week 0


title: CLP_rep2

description: gene expression of CLP mice


title: CLP_rep1

description: gene expression of CLP mice


title: S31H


title: 8546278019_K: High Altitude European

value: High

value: European

value: SAMPLE 39


title: G7H

value: GF


title: 8546278019_H: Low Altitude Andean

value: M

value: Placenta

value: SAMPLE 44


title: 8546278019_I: Low Altitude Andean

value: SAMPLE 25


title: 8546278019_J: Low Altitude European

value: SAMPLE 31


title: S30H

value: SPF

value: Hippocampus cells

value: single-cell nucleus RNA


title: RH2_W17

value: leaf midrib

value: Week 17


title: G6H


title: RH2_W7

value: Week 7


title: G5H


title: LV_rep5

description: gene expression of LV mice

value: lung tissue

value: male


title: RH2_W34

value: Mock-infection

value: Week 34


title: LV_rep3

description: gene expression of LV mice


title: LV_rep4

description: gene expression of LV mice


title: LV_rep2

description: gene expression of LV mice


title: 8546278019_F: Low Altitude European

value: F

value: Low

value: European

value: SAMPLE 29


title: 8546278019_G: High Altitude Andean

value: M

value: High

value: Andean

value: Placenta

value: SAMPLE 15


title: LV_rep1

description: gene expression of LV mice


title: 8546278019_E: Low Altitude Andean

value: SAMPLE 21


title: 8546278019_D: Low Altitude European

value: SAMPLE 38


title: RH1_W34

value: leaf midrib


title: RH2_W0

value: Week 0


title: C17H

value: CGF

value: Hippocampus cells

value: single-cell nucleus RNA


title: C19H


title: RH1_W7

value: Mock-infection

value: Week 7


title: RH1_W0


title: RH1_W17

value: Week 17


title: C18H


title: Sham_rep5

description: gene expression of Sham mice

value: lung tissue

value: male


title: S. cerevisiae tRNAGly(GCC) pus4Δ

city: Konstanz

first: Luisa

middle: Barbara

last: Huber

state: Baden-Württemberg

address: Universitätsstraße 10

department: Department of Chemistry

institute: Universität Konstanz

data_processing:
Sequencing data were processed by using the open source software KNIME 4.6.2
Quality and sequence are read from the FastQ files
Read1 and Read 2 were merged giving the expected size of transcript (RNA oligo samples 109 bp & tRNA samples 69 bp)
High quality data were filtered and aligned to the RNA reference of the oligonucleotide or tRNA sequences (http://gtrnadb.ucsc.edu).
Reads were sorted into unique molecular identifier (UMI) families and family read numbers were counted.
Error calculation are performed in each UMI family having more than 10 or 15 (tRNA data) reads.
If 90 % of the reads within each family carry the misincorporation, the error is set to 1 (otherwise 0).
Afterwards, the error is calculated over all UMI families at each position of the transcript and plotted using Microsoft excel software
Supplementary files format and content: excel-files include position, reference RNA sequence and error rates
Library strategy: DNA Amplicon-Seq

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: The S. cerevisiae strains were grown in standard YPD medium (20 g/L peptone, 20 g/L dextrose, 10 g/L yeast extract) at 30°C to exponential phase (0.6-0.7 OD600)

extract_protocol:
Total RNA from yeast cells was isolated using hot acid phenol. RNA concentration was measured on Nanodrop One and RNA quality was assessed by capillary electrophoresis using a PicoRNA Chip on Bioanalyzer 2100 (Agilent technologies). Yeast total tRNA fraction was enriched using NucleoBond RNA 80 kit (Macherey-Nagel). Briefly, 50-80 micrograms of total RNA were loaded onto AXR80 column previously equilibrated with RO buffer. The column was washed 4 times with R1 buffer and tRNA fraction was eluted using R2 buffer. The eluate was then precipitated with an equal volume of isopropanol and centrifuged. The pellet was washed with 80% ethanol, and dissolved with RNAse free water
For RNA oligo samples: RT-Reaction mix contained 225 nM RNA template (unmodified or modified oligonucleotide), 150 nM DNA reverse primer with overhang, 100 µM of each nucleotide and 2 nM RT-KTq variant in 1x RT-KTq reaction buffer (50 mM Tris-HCl (pH 9.2), 16 mM (NH4)2SO4, 25 mM MgCl2, 0.1% (v/v) Tween 20). After annealing of template/primer and heating the mixture to 55°C, 4 µL DNA polymerase in 1x RT-KTq reaction buffer was added to start reverse transcription (10 µL reaction volume). After 10 min reaction time, mixture was heated to 95°C for 5 min and annealing was allowed once again by cooling stepwise to 4°C. The reaction was heated to 55°C and 10 µL Superscript IV reaction mix (Invitrogen) was added to reach a final volume of 20 µL. Reactions contained finally 10 U/µL Superscript IV (Invitrogen), 300 µM dNTP each, 5 mM DTT and 1x Superscript IV RT buffer (Invitrogen). After primer elongation for 10 min at 55°C, the reaction was put on ice. For each DNA library, the described reverse transcription was performed three times and combined after reaction. 60 µL combined reaction mix was mixed with 240 µL Buffer NTC (Macherey-Nagel) and clean-up was conducted with NucleoSpin Gel and PCR clean-up kit (Macherey-Nagel) according to the manufacturer's specifications. Elution was achieved by adding 15 µL Milli-Q water and centrifugation for 1 min at 13.000 rpm. Then, RNA template was digested by addition of 0.05 U/µL RNase H (NEB) in 1x RNase H reaction buffer at 37°C for 20 min. Enzyme was inactivated by heat at 65°C for 20 min. Purification of DNA was performed by agarose gel electrophoresis (2.5 % agarose gel in 1x TAE buffer), excision of the respective bands and applying the NucleoSpin Gel and PCR clean-up kit (Macherey-Nagel). To achieve DNA binding to the columns, buffer NTC was added to the gel pieces (400 µL buffer per 100 mg gel) and incubated at 50°C until gel was dissolved. Elution was conducted in the same way as described above. Afterwards, DNA was repaired by using 0.1 µL PreCR Repair mix (NEB) with 100 µM of each dNTP, 1x NAD+ (provided by the manufacturer) and 1x ThermoPol reaction buffer (NEB) to reach 20 µL reaction volume. DNA repair was performed at 37°C for 20 min. Without any purification step, DNA was used as template for primer extension reaction with 0.02 U/µL Q5 Hot Start High-Fidelity DNA Polymerase (NEB), 200 µM of each dNTP, 300 nM DNA forward primer with overhang and 0.2x Q5 reaction buffer in 25 µL reaction volume. A one step cycling protocol was chosen where denaturation at 98°C for 1 min, annealing at 62°C for 45 s and finale extension at 72°C for 2 min were conducted. Reaction was analyzed and purified by agarose gel electrophoresis as described above. This time NTI buffer (Machery Nagel) was used for dissolving the gel pieces at 55°C. A second DNA repair with the PreCR mix (NEB) was conducted in the similar way as described above. UMI introduction was obtained by applying Q5 Hot Start High-Fidelity DNA Polymerase (NEB) in a three step PCR reaction. The reaction mixture contained 20 µL repair mix, 0.02 U/µL DNA polymerase, 200 nM forward and reverse primer and finally 0.2x Q5 reaction buffer to reach 25 µL reaction volume. After initial denaturation at 98°C for 2 min, two cycles with 98°C for 10 s, 62°C for 30 s and 72°C for 30 s were carried out followed by a final elongation step at 72°C for 2 min. Reaction was analyzed and purified by agarose gel electrophoresis as described above. Here, buffer NTI was diluted with Milli-Q in a ratio of 2:1 and afterwards used for dissolving gel pieces at 50°C. Concentration of the DNA was determined with a qPCR approach, where an oligonucleotide with the same length was applied as reference in different template concentrations. 1x NEBNext Ultra II Q5 Master Mix (NEB) was used for PCR with 400 nM fwd and rev primer, 1x sybr green I in 5 µL reaction volume. After a final denaturation step at 98°C for 1 min, a three step cycling protocol with 35 PCR cycles followed with 98°C 10 s, 60°C 30 s and 72°C for 30 s and finally an elongation step with 72°C for 2 min was conducted. Fluorescent intensity was measured at the end of each cycle and melting curves were determined at the end of the reaction. For analysis, Cq values of reactions with reference DNA were blotted against the decadic logarithm of the template concentrations and linear regression was created. DNA concentrations were calculated by using the linear predictor function. Results were multiplied by two since reference DNA was applied double stranded and target DNA in the analyzed samples was only present in the single stranded format. DNA was repaired once again by using 0.05 µL PreCR mix (NEB), 1x NAD+, 100 µM of each dNTP, 59.044 fM DNA and 1x ThermoPol reaction buffer (NEB) to reach 11.25 µL end volume. After reaction for 20 min at 37°C, DNA mix was directly used for Amplicon PCR. Here, 400 nM forward and reverse primer (equipped with Illumina Adapter Sequence and Indices), the entire repair mix (final DNA concentration 26.57 fM) and 1x NEBNext Ultra II Q5 Master Mix (NEB) was used for reaction in 25 µL end volume. After a final denaturation step at 98 °C for 5 min, a three step cycling protocol with 35 PCR cycles followed with 98°C 10 s, 70°C 30 s and 72°C for 30 s and finally an elongation step with 72°C for 2 min was conducted. Reaction was analyzed and purified by agarose gel electrophoresis as described above. To dissolve gel pieces, buffer NTI (Macherey Nagel) was diluted with Milli-Q water in ration 2:1 and 450 µL NTI mix was added to the gel pieces. After complete dissolving at 50°C, mixture was dilute once again with Milli‑Q water to reach a final volume of 1750 µL. DNA was loaded on the column and eluted with 20 µL Milli-Q water. After performing the repair reaction on the whole eluate as described above, DNA was purified by using the QIAEX II System (Qiagen). 2 µL particle slurry was used for each sample and elution of DNA was achieved by adding 18 µL Milli-Q to the dried beads, incubation for 5 min and taking 16 µL after centrifugation. The concentration of the final DNA library was determined by Quantus™ Fluorometer (Promega) and usually ranged between 20 and 85 nM. After quality control with Bioanalyzer 2100 (Agilent), DNA libraries were pooled and sequenced in paired-end mode (2*75 bp) on an IIlumina NextSeq2000 instrument. For tRNA samples: 300 ng RNA (isolated from S. cerevisiae) was annealed to 300 nM reverse primer (containing UMI sequence) in the similar way as described in the chapter above. Hybridized template/primer was added to the reaction mix containing 100 µM of d(G/C/T)TP (each) and 2 µM dATP in 1x RT-KTq reaction buffer (50 mM Tris-HCl (pH 9.2), 16 mM (NH4)2SO4, 25 mM MgCl2, 0.1% (v/v) Tween 20). After heating to 55°C, RT was started by adding 100 nM RT-KTq I614Y in 1x RT-KTq reaction buffer to reach a final reaction volume of 10 µL. After 1 h reaction time, mixture was heated to 95°C for 5 min and annealing was allowed once again by cooling to 4°C stepwise. The reaction was heated to 55°C and 10 µL Superscript IV reaction mix was added to reach a final volume of 20 µL. Reactions contained finally 10 U/µL Superscript IV (Invitrogen), 300 µM dNTP each, 5 mM DTT and 1x Superscript IV RT buffer (Invitrogen). After primer elongation for 10 min at 55°C, the reaction was put on ice. Reaction mix was mixed with 160 µL Buffer NTC (Macherey-Nagel) and clean-up was conducted with NucleoSpin Gel and PCR clean‑up XS kit (Macherey-Nagel) according to the manufacturer's specifications. Elution was achieved by adding 16 µL elution buffer (Machery-Nagel). DNA was used for second UMI Introduction with 0.02 U/µL Q5 Hot Start High-Fidelity DNA Polymerase (NEB), 200 µM of each dNTP, 200 nM DNA forward primer and 1x Q5 reaction buffer in 25 µL reaction volume. A one step cycling protocol was chosen where denaturation at 98°C for 1 min, annealing at 62°C for 45 s and finale extension at 72°C for 2 min were conducted. Buffer NTI (Macherey-Nagel) was mixed with water in ratio of 3:1 and 50 µL NTI-mix was added to the PCR reaction mix. The NucleoSpin Gel and PCR clean‑up XS kit (Macherey-Nagel) was used for purification and 16 µL elution buffer (Macherey-Nagel) was added for elution. Concentration of the DNA was determined with a qPCR approach described in the chapter above. DNA was repaired by using 0.05 µL PreCR mix (NEB), 1x NAD+, 100 µM of each dNTP, 56.008 fM DNA and 1x ThermoPol reaction buffer (NEB) to reach 11.25 µL end volume. After reaction for 20 min at 37°C, DNA mix was directly used for Amplicon PCR with NEBNext Ultra II Q5 Master Mix (NEB) as described in the chapter above (final DNA concentration 22 fM). Purification of DNA was performed by agarose gel electrophoresis (2.5 % agarose gel in 1x TAE buffer), excision of the respective bands and applying the NucleoSpin Gel and PCR clean-up XS kit (Macherey-Nagel). Here, buffer NTI (Macherey-Nagel) was diluted with Milli-Q water in ration 2:1 and 450 µL NTI mix was added to the gel pieces. After complete dissolving at 50°C, mixture was dilute once again with Milli‑Q water to reach a final volume of 1750 µL. DNA was loaded on the column and eluted with 20 µL elution buffer (Macherey-Nagel). DNA Repair on the whole eluate and purification with the QIAEX II system (Qiagen) was performed as described in the chapter above. The concentration of the final DNA library was determined by Quantus™ Fluorometer (Promega) and usually ranged between 6 and 46 nM. After quality control with Bioanalyzer 2100 (Agilent), DNA libraries were pooled and sequenced in paired-end mode (2*75 bp) on an IIlumina NextSeq2000 instrument.

tag: cell type

value: yeast cell

value: S. cerevisiae Y01152 (Pus4{delta})

value: BY4741; MATa; ura3{delta}0; leu2{delta}0; his3{delta}1; met15{delta}0; YNL292w::kanMX4

value: grown in standard YPD medium at 30°C

tag: protocol

value: U55; RT by RT-KTq I614Y, 100 µM d(G/C/T)TP & 2 µM dATP

tag: molecule type

value: enriched tRNA fractions from total RNA


title: F3_naive_rep3

status: Public on Mar 14 2023

city: Aveiro

first: Guilherme

middle: de Abreu

last: Jeremias

address: Campus Universitário de Santiago

department: Biology Department

country: Portugal

institute: University of Aveiro

data_processing:
Data was trimmed using Trim Galore! (version 0.6.5, Babraham Bioinformatics) by selecting the RRBS mode, trimming DNA bases with a Phred scale score below 30 and removing adapter sequences;
The mapping of the samples was performed using Bismark (version 0.22.3);
Extraction of methylated calls was performed using Bismark (version 0.22.3);
Statistical analysis were performed using DSS package, in RStudio (version 3.6.1).
Assembly: GenBank LRGB00000000
Supplementary files format and content: Processed .txt files were generated using RStudio version 3.6.1;  Information displayed in each line concerns, respectively, a specific gene code, its position in the genome, total coverage and number of methylated calls for the gene.

organism: Daphnia magna

source_name: Whole-body

extract_protocol:
DNA was extracted from frozen tissues at -80 °C by using the MasterPure Complete DNA and RNA Purification Kit (Epicenter, USA), according to the instructions of the manufacturer.
DNA was fragmented with the restriction enzyme MspI (New England BioLabs, USA) and purified using the GeneJET PCR purfication kit (Thermo Fisher Scientific, USA). After this, library preparation was achieved with the NEBNext Ultra II DNA library prep kit (New England Biolabs, USA) by using methylated adapters for Illumina sequencing.

treatment_protocol: Monoclonal cultures containing 70 neonates (aging less than 24 h) collected from 3rd brood bulk cultures were established in plastic buckets containing 4 L of test solution (57 mL per organism), under controlled conditions. Three replicates of these cultures were assigned to each of the three following experimental treatments: (i) control treatment composed of blank ASTM medium (0 g/L of Cu); (ii) naïve daphnids, i.e. organisms collected from bulk cultures acclimated in blank ASTM for three generations, were exposed to 0.021 mg/L Cu; (iii) non-naïve daphnids, i.e. organisms collected from bulk cultures acclimated in Cu-enriched ASTM (0.021 mg/L) for three generations, were exposed to 0.021 mg/L Cu. The exposure kept as described for one generation (F0), which corresponded to the growth of organisms until releasing of their 3rd brood neonates. These neonates were used to start the corresponding F1 generations, the same applying to establish F2 from F1 and F3 from F2, all (F1, F2, F3) reared in blank ASTM, regardless of the exposure treatment held at F0.

value: Whole-body

tag: clone

value: Beak

tag: Sex

value: female

tag: age

value: adult

value: blank ASTM


title: F3_naive_rep2


title: 8546278019_A: High Altitude Andean

tag: gender

value: M

tag: gestational age (wks)

tag: altitude

value: High

tag: ancestry

value: Andean

value: Placenta

tag: sample number

value: SAMPLE 4


title: Sham_rep4

description: gene expression of Sham mice

tag: tissue

value: lung tissue

value: male


title: Sham_rep2

description: gene expression of Sham mice


title: Sham_rep3

description: gene expression of Sham mice


title: S. cerevisiae tRNAGly(GCC) wt

value: yeast cell

tag: strain

value: S. cerevisiae Y00000 (BY4741)

value: MATa; ura3{delta}0; leu2{delta}0; his3{delta}1; met15{delta}0

value: Ψ55; RT by RT-KTq I614Y, 100 µM d(G/C/T)TP & 2 µM dATP


title: Sham_rep1

description: gene expression of Sham mice


title: F0_naive_rep1

value: EC20 of Copper (Cu)


title: F0_nonnaive_rep3

value: Whole-body


title: F0_naive_rep2

value: Beak


title: F3_nonnaive_rep3

value: female


title: F3_nonnaive_rep1

value: adult


title: F0_control_rep3

value: control:blank ASTM


title: F0_control_rep2


title: F0_nonnaive_rep2


title: F0_nonnaive_rep1


title: Visium result of patient 4

city: Suwon

first: Soon Sang

last: Park

address: Worldcup-Ro 206

country: South Korea

institute: Ajou University School of Medicine

data_processing:
For Visium, libraries were sequenced on a NextSeq (Illumina), with 28 bases from read 1 and 120 from read 2, and at a depth of 84-116 million reads per sample. Following demultiplexing of bcl files, the read 2 fastq files were trimmed using Cutadapt (Martin, 2011) (Martin, 2011) to remove full-length or truncated template switch oligo (TSO) sequences from the 5’ end and polyA homopolymers from the 3’ end. The TSO sequence ( AAGCAGTGGTATCAACGCAGAGTACATGGG) was used as a non-internal 5’ adapter with a minimum overlap of 5, meaning that partial matches (up to 5 base pairs) or intact TSO sequences were removed from the 5’ end of read 2. The error tolerance was set to 0.1 for the TSO trimming to allow for a maximum of 3 errors. For the 3’ homopolymer trimming, a sequence of 10 As was used as a regular 3’ adapter to remove potential polyA tail products regardless of its position in the read, also with a minimum overlap of 5 base pairs. The trimmed data was processed with the spaceranger pipeline (version 1.0.0, 10X Genomics) and mapped to the GRCH38 v93 genome assembly.
Genome_build: GRCh38 v86
Supplementary files format and content: barcodes.tsv, features.tsv, and matrix.mtx
Library strategy: Spatial transcriptomics

source_name: Primary colorectal cancer

growth_protocol: Colorectal cancer tissues were collected under the protocol of Review Board at Ajou University Hospital (AJOUIRB-OBS-2016-218).  Then the tissues were processed into formalin-fixed paraffin-embedded (FFPE) samples

extract_protocol: Two sections per patients were cut at 10 mm thickness. One is mounted onto Visium slide capture area, and the other is used for hematoxyllin & eosin staining. Sequencing libraries were prepared following the manufacturer's protocol. After tissue staining, bright-field images were taken as described in the Spatial Transcriptomics procedure. The Visium Spatial Gene Expression Slide & Reacgent kit (10X genomics) was used to make sequencing libraries.

value: Human colorectal cancer

value: Male

tag: t staging

tag: n staging

tag: m staging


title: F0_control_rep1

tag: treatment


title: F3_nonnaive_rep2

value: blank ASTM


title: Visium result of patient 1

value: Female


title: Visium result of patient 3


title: F3_naive_rep1


title: 8546278019_B: Low Altitude Andean

value: M

value: Low

value: Andean

value: Placenta

value: SAMPLE 32


title: Smarca5-KD-high-MNase-Rep3

first: David

last: Klein

address: 4249 Fifth Ave

department: Biological Sciences

description:
Smarca5_KD_high_MNase_merged_mono.bw
Smarca5_KD_high_MNase_merged_subnucleosome.bw

data_processing:
Barcode adapter sequences removed
Reads mapped to mm10 genome using bowtie2, allowing for 1 mismatch
Duplicates were removed using Picard
Reads were filtered for quality using SAMtools (MAPQ ≥ 10)
Reads were size-selected into overlapping dinucleosome (230-270 bp), mononucleosome (135-165 bp), and subnucleosome (100-130 bp)
Nucleosome-sized reads were processed in deepTools by using the bamCoverage command to generate bigwig files detailing coverage genome-wide in 1 bp bins with RPGC normalization
Assembly: mm10
Supplementary files format and content: bigwig

source_name: E14 mES cell line

growth_protocol: Murine embryonic stem cells were grown under feeder-free conditions in DMEM, supplemented with 10% Fetal Bovine Serum, 2 mM-Glutamine, 1X non-essential amino acids, 0.129mM 2-mercaptoethanol, and 1000U/mL Leukemia Inhibitory Factor (LIF). Cells were passaged every 48 hours using trypsin (Gibco) and split at a ratio of ~1:8 with fresh medium. Routine anti-mycoplasma cleaning was conducted (LookOut DNA Erase spray, Sigma) and cell lines were screened by PCR to confirm no mycoplasma presence.

extract_protocol:
Cells were trypsinized, quenched, pelleted, washed with cold PBS, and crosslinked with 1% formaldehyde for 15 minutes. Crosslinking was quenched with .5M glycine for 5 minutes. Fixed cells were pelleted and washed with cold PBS
Digested for 5 minutes at 37C with 60U micrococcal nuclease (TaKaRa)
Medium was aspirated and cells were washed with DPBS. DPBS was aspirated and cells were trypsinized. Cells were pelleted, washed with DPBS, crosslinked with 1% formaldehyde for 15 minutes at room temperature, and quenched with 0.5M glycine for five minutes. Crosslinked cells were pelleted, lysed in hypotonic buffer and pre-incubated with calcium, then digested with 10U or 60U MNase for five minutes and chelated with EDTA.

treatment_protocol:
Cells were incubated with 3.5 µg esiRNAs, 25 µL Lipofectamine 3000 in serum-free medium for 18 hours, then medium was replaced and cells were incubated for 30 more hours. Cells were incubated at 37 degrees Celsius with 5% CO2 for the duration of treatment.
After 48 hours of undisturbed growth on 10 cm plates, medium was aspirated and cells were washed with DPBS. DPBS was aspirated and fresh serum-free medium (Opti-MEM) was added, containing 3 µg of esiRNAs targeting EGFP (control), Smarca4, or Smarca5, along with 30 µL Lipofectamine 3000. Cells were incubated in 5% CO2 incubators for 18 hours to allow esiRNA transfection, then medium was aspirated and replaced with fresh DMEM. 48 hours after the initial esiRNA addition, cells were harvested as follows.

tag: cell line

value: E14 mES cell line

tag: extraction

value: unextracted

tag: genotype

value: Smarca5 KD

tag: mnase digestion condition

value: high MNase


title: F0_naive_rep3

value: Whole-body

tag: clone

value: Beak

tag: Sex

value: EC20 of Copper (Cu)


title: 8546278019_C: Low Altitude European

tag: gender

value: F

value: European

value: SAMPLE 6


title: Smarca5-KD-high-MNase-extracted-Rep3

description: Smarca5_KD_high_MNase_extracted_merged_OLDN.bw

value: Input DNA was gel-extracted between 200-300 bp to enrich for putative overlapping dinucleosomes


title: Smarca5-KD-high-MNase-Rep1


title: Smarca4-KD-high-MNase-Rep3

description:
Smarca4_KD_high_MNase_merged_mono.bw
Smarca4_KD_high_MNase_merged_subnucleosome.bw

value: Smarca4 KD


title: Smarca5-KD-high-MNase-extracted-Rep1


title: Smarca4-KD-high-MNase-Rep1


title: Smarca4-KD-high-MNase-Rep2


title: Smarca4-KD-high-MNase-extracted-Rep3

description: Smarca4_KD_high_MNase_extracted_merged_OLDN.bw


title: Visium result of patient 2

value: Human colorectal cancer

value: Female


title: S32P

value: SPF

tag: tissue/cell type

value: Prefrontal cortex cells

tag: molecule subtype

value: single-cell nucleus RNA


title: Control-high-MNase-Rep3

description:
Control_high_MNase_merged_mono.bw
Control_high_MNase_merged_subnucleosome.bw

value: E14 mES cell line

value: control


title: Control-high-MNase-Rep2

value: unextracted


title: Control-high-MNase-Rep1

value: high MNase


title: Smarca4-KD-high-MNase-extracted-Rep1


title: Control-high-MNase-extracted-Rep3

description: Control_high_MNase_extracted_merged_OLDN.bw


title: Control-high-MNase-extracted-Rep1


title: Smarca5-KD-low-MNase-Rep3

description:
Smarca5_KD_low_MNase_merged_mono.bw
Smarca5_KD_low_MNase_merged_subnucleosome.bw

extract_protocol:
Cells were trypsinized, quenched, pelleted, washed with cold PBS, and crosslinked with 1% formaldehyde for 15 minutes. Crosslinking was quenched with .5M glycine for 5 minutes. Fixed cells were pelleted and washed with cold PBS
Digested for 5 minutes at 37C with 10U micrococcal nuclease (TaKaRa)
Medium was aspirated and cells were washed with DPBS. DPBS was aspirated and cells were trypsinized. Cells were pelleted, washed with DPBS, crosslinked with 1% formaldehyde for 15 minutes at room temperature, and quenched with 0.5M glycine for five minutes. Crosslinked cells were pelleted, lysed in hypotonic buffer and pre-incubated with calcium, then digested with 10U or 60U MNase for five minutes and chelated with EDTA.

value: Smarca5 KD

value: low MNase


title: Smarca5-KD-low-MNase-extracted-Rep2

description: Smarca5_KD_low_MNase_extracted_merged_OLDN.bw


title: Smarca5-KD-low-MNase-Rep2


title: Smarca5-KD-low-MNase-Rep1


title: Smarca5-KD-low-MNase-extracted-Rep1


title: Smarca4-KD-high-MNase-extracted-Rep2


title: Smarca4-KD-low-MNase-Rep2

description:
Smarca4_KD_low_MNase_merged_mono.bw
Smarca4_KD_low_MNase_merged_subnucleosome.bw


title: Smarca5-KD-low-MNase-extracted-Rep3


title: Control-high-MNase-extracted-Rep2


title: Smarca4-KD-low-MNase-Rep3


title: Control-low-MNase-Rep3

description:
Control_low_MNase_merged_mono.bw
Control_low_MNase_merged_subnucleosome.bw


title: Smarca4-KD-low-MNase-extracted-Rep2

description: Smarca4_KD_low_MNase_extracted_merged_OLDN.bw


title: Smarca4-KD-low-MNase-Rep1


title: Control-low-MNase-extracted-Rep3

description: Control_low_MNase_extracted_merged_OLDN.bw


title: Control-low-MNase-Rep2


title: Control-low-MNase-extracted-Rep2


title: Control-low-MNase-Rep1


title: Control-low-MNase-extracted-Rep1


title: 10X_22_028, 10 days post single ablation

city: Stockholm

first: Olov

last: Andersson

state: Other (Non U.S.)

address: Biomedicum Quarter 5D, Tomtebodavagen 16

country: Sweden

institute: Karolinska Institute

data_processing:
The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 (10× Genomics) with the option ‘--expect-cells’ set to 7000 (all other options were used as per default).
Assembly: danRer11
Supplementary files format and content: matrix files

source_name: krt4 lineage traced cells in adult zebrafish pancreas

extract_protocol:
Droplet-based scRNA-seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 (10× Genomics) and Chromium Single Cell 3′ Chip G (10× Genomics). Approximately 8,000-10,000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription.
The 10× scRNA-Seq libraries were PCR amplified (13 cycles), pooled, denatured, and diluted in prior to paired-end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome (GRCz11) with addition of the mCherry sequence using Cell Ranger v5.0.1 (10× Genomics) to generate a gene-by-cell count matrix with default parameters.

treatment_protocol:
We selected 6-9 months old fish with 8-10 fish in each condition, We sacrificed the adult fish by putting each one into ice-cold Hanks' Balanced Salt Solution (HBSS, no calcium, no magnesium) for 10 minutes. Next, we used blunt forceps to carefully remove the skin, kidney, eggs (in females), liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then, we cut at the anterior region of the intestinal bulb and hindgut, and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile, we also removed the spleen (appearing in dark red), which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition, we pooled 4-8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ (Thermofisher) supplemented with 60 μL 100× Pluronic™ F68 (Thermofisher) at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. After removing the supernatant, we washed the pellets with 300 μL pre-cooled solution containing 1% BSA, 0.1% Pluronic F-68 and 0.1% DAPI, and used a Corning™ Falcon™ cell strainer (Corning™ 352235) to filter out not fully digested tissues.
During FACS, we selected single-cell populations based on forward scatter and side scatter signals. Next, we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly, we used the Cherry channel for the subsequent gating to collect all cells of the krt4-derived lineage in a new tube as the single-cell suspension.

value: WT

value: pancreas

tag: cell type

value: krt4 lineage traced cells

value: ablation

tag: time

value: 10 days post single ablation


title: 10X_22_023, 2 days after double ablation

tag: tissue

value: 2 days after double ablation


title: 10X_22_022, 2 days after double ablation


title: 10X_22_029, 10 days post single ablation


title: Smarca5-KD-high-MNase-extracted-Rep2

city: Pittsburgh

institute: University of Pittsburgh

value: Input DNA was gel-extracted between 200-300 bp to enrich for putative overlapping dinucleosomes


title: Smarca4-KD-low-MNase-extracted-Rep1

value: Smarca4 KD


title: 10X_22_019, no ablation

value: no ablation


title: 10X_22_018, no ablation


title: 10X_22_016, 5 days post double ablation

value: 5 days post double ablation


title: N1: Nevus skin 1

city: Irvine

first: Maksim

middle: V

last: Plikus

state: California

address: 845 Health Sciences Road

department: Developmental and Cell Biology

institute: University of California, Irvine

data_processing:
Pair-end RNA-seq reads were aligned using STAR/2.5.1b-static with parameters ‘–outFilterMismatchNmax10 outFilterMismatchNoverReadLmax 0.1–outFilter-MultimapNmax 10’ to the reference genome hg38. We used STAR to then convert to transcriptome-based mapping with gene annotation Gencode.v24.annotation.gtf. Gene expression was measured using RESM/1.2.22 with expression values normalized into FPKM.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

source_name: Whole skin

extract_protocol:
RNA from freshly removed facial skin was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: nevus skin from the facial region


title: C3: Control skin 3

value: normal skin from the facial region


title: C2: Control skin 2


title: N3: Nevus skin 3


title: C1: Control skin 1


title: N2: Nevus skin 2


title: WT2-female biol rep 2

city: Aachen

first: Sandro

last: Capellmnn

address: Pauwelsstrasse 30

department: Institute of Biochemistry and Molecular Immunology

institute: University Hospital RWTH Aachen

data_processing:
Samples were then processed using the nf-core/RNA-seq pipeline version 3.5 (Ewels et al. 2020) implemented in Nextflow 21.10.6 (Di Tommaso et al. 2017) using Docker 20.10.12 (Merkel 2014) with the minimal command. In brief, lane-level reads were trimmed using Trim Galore 0.6.7 (Krueger et al. 2021) and aligned to the mouse genome (GRCm39) using STAR 2.7.9a (Dobin et al. 2013). Gene-level and transcript-level quantification was done by Salmon v1.5.2 (Patro et al. 2017).
Assembly: Genome Reference Consortium Mouse Build 39 (mm39)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary cells

growth_protocol: Peritoneal mast cells were generated according to Meurer et al. PLOS ONE 2016; 11(6):e0158104. The PMC lines developed spontaneously by a combination of ageing and neglect.

extract_protocol: Sequencing libraries were generated from 1000 ng of total RNA using TruSeq Stranded Total RNA Library Preparation Kit (Illumina, San Diego, USA, #20020596).

treatment_protocol: PMCs were left untreated

tag: strain

value: Peritoneal mast cells (primary cells)

value: wild-type

value: female


title: WT5-male biol rep 2

value: male


title: WT6-male biol rep 3


title: WT1-female biol rep 1


title: PMC-306

source_name: cell line

value: Peritoneal mast cells (cell line)

value: not applicable


title: 10X_22_020, 2 days after single ablation

value: WT

value: pancreas

value: 2 days after single ablation


title: WT31-female biol rep 3


title: 10X_22_021, 2 days after single ablation

value: krt4 lineage traced cells

value: ablation


title: 10X_22_017, 5 days after single ablation

value: 5 days after single ablation


title: vH-PFC superficial mouse d

city: London

first: Andrew

middle: F

last: MacAskill

state: England

address: Gower St

department: Neuroscience, Physiology and Pharmacology

country: United Kingdom

institute: University College London

data_processing:
Fragments Per Kilobase Million (FPKM) scores were calculated from the raw data using TopHat (2.1.0) and Cufflinks (2.2.1) via Illumina Basespace software (1.1.0)
Assembly: Mus musculus (UCSC mm10)
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: brain

extract_protocol:
Neurons in vCA1 projecting to PFC were fluorescently labeled using retrobead injections into PFC. Slices of vCA1 were then manually dissected into superficial or deep layers. After trituration to create a single cell suspension, fluorescent neurons were isolated using FACS, and RNA harvested using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories, Inc.)
200pg of cDNA was then converted to sequencing library using the Nextera XT DNA protocol (Illumina, San Diego, US)

value: brain

tag: brain region

value: hippocampus

value: ventral CA1 neuron

tag: layer

value: superficial


title: vH-PFC deep mouse b

value: deep


title: vH-PFC deep mouse c


title: WT4-male biol rep 1

value: Peritoneal mast cells (primary cells)


title: vH-PFC superficial mouse b


title: vH-PFC superficial mouse c


title: vH-PFC superficial mouse a


title: WT, E10.5, rep 2 [27_S27]

city: Oklahoma City

first: Alla

last: Tsytsykova

state: OK

address: 1122 NE 13th Street

department: Neurosurgery

institute: OUHSC

description: WT_E10.5_S27 (biol rep 2)

data_processing:
Sequencing was done from Single-end 75bp on an Illumina NextSeq High Output.
Post-sequence reads were quality-filtered for length and contaminants and were trimmed for Illumina adapters using Trimmomatic v0.35.
Resulting reads were pseudo-aligned to coding regions of the mouse reference genome using STAR.
Assembly: Ensembl release 105
Supplementary files format and content: Excel file with raw counts of sequencing reads (the rows are features/genes and the columns are samples)

source_name: Mouse embryo

growth_protocol: Commd10_Het mice were bought from the Jackson Laboratory (B6.Cg-Commd10Tg(Vav1-icre)A2Kio/J, Stock # 008610). WT and Commd10_Null embryos were generated by interbreeding of Commd10_Het littermates.

extract_protocol:
WT and Commd10Null embryos at days E8.5, E9.5, and E10.5 were extracted from yolk sacs and immediately placed in Invitrogen™ RNAlater™ Stabilization Solution (Fisher Scientific, AM7023). Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN, 74034) and QIAshredder (QIAGEN, 79656) according to the manufacturer’s instructions.
3’-end RNA libraries were made using the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina.

value: Mouse embryo

tag: developmental stage


title: COMMD10_Null, E10.5, rep 3 [32_S32]

description: COMMD10_Null_E10.5_S32 (biol rep 3)


title: COMMD10_Null, E10.5, rep 1 [30_S30]

description: COMMD10_Null_E10.5_S30 (biol rep 1)


title: WT, E10.5, rep 3 [28_S28]

description: WT_E10.5_S28 (biol rep 3)


title: COMMD10_Null, E9.5, rep 2 [24_S24]

description: COMMD10_Null_E9.5_S24 (biol rep 2)


title: WT, E10.5, rep 1 [26_S26]

description: WT_E10.5_S26 (biol rep 1)


title: COMMD10_Null, E9.5, rep 1 [23_S23]

description: COMMD10_Null_E9.5_S23 (biol rep 1)


title: COMMD10_Null, E9.5, rep 3 [25_S25]

description: COMMD10_Null_E9.5_S25 (biol rep 3)


title: WT, E9.5, rep 8 [21_S21]

description: WT_E9.5_S21 (biol rep 8)


title: WT, E9.5, rep 9 [22_S22]

description: WT_E9.5_S22 (biol rep 9)


title: vH-PFC deep mouse d


title: WT, E9.5, rep 7 [20_S20]

description: WT_E9.5_S20 (biol rep 7)


title: PMC-303

value: wild-type


title: WT, E9.5, rep 4 [17_S17]

description: WT_E9.5_S17 (biol rep 4)


title: WT, E9.5, rep 2 [15_S15]

description: WT_E9.5_S15 (biol rep 2)


title: WT, E9.5, rep 6 [19_S19]

description: WT_E9.5_S19 (biol rep 6)


title: WT, E9.5, rep 3 [16_S16]

description: WT_E9.5_S16 (biol rep 3)


title: COMMD10_Null, E10.5, rep 2 [31_S31]

description: COMMD10_Null_E10.5_S31 (biol rep 2)


title: COMMD10_Null, E8.5, rep 2 [12_S12]

description: COMMD10_Null_E8.5_S12 (biol rep 2)


title: WT, E8.5, rep 9 [9_S9]

description: WT_E8.5_S9 (biol rep 9)


title: vH-PFC deep mouse a


title: WT, E8.5, rep 10 [10_S10]

description: WT_E8.5_S10 (biol rep 10)


title: COMMD10_Null, E8.5, rep 3 [13_S13]

description: COMMD10_Null_E8.5_S13 (biol rep 3)


title: WT, E10.5, rep 4 [29_S29]

description: WT_E10.5_S29 (biol rep 4)


title: WT, E9.5, rep 5 [18_S18]

description: WT_E9.5_S18 (biol rep 5)


title: WT, E8.5, rep 8 [8_S8]

description: WT_E8.5_S8 (biol rep 8)


title: COMMD10_Null, E8.5, rep 1 [11_S11]

description: COMMD10_Null_E8.5_S11 (biol rep 1)


title: WT, E8.5, rep 4 [4_S4]

description: WT_E8.5_S4 (biol rep 4)


title: WT, E8.5, rep 5 [5_S5]

description: WT_E8.5_S5 (biol rep 5)


title: WT, E8.5, rep 1 [1_S1]

description: WT_E8.5_S1 (biol rep 1)


title: Bulge WT P30 H12

description: Bulge_stem_cells_WT_P30_genelist_TPM.txt

data_processing:
Pair-end RNA-seq reads were aligned using STAR_2.4.2 with parameters ‘–outFilterMismatchNmax10–outFilterMismatchNoverReadLmax 0.1–outFilter-MultimapNmax 10’ to the reference genome GRCm38/mm10. We used STAR to then convert to transcriptome-based mapping with gene annotation Gencode v.M8. Gene expression was measured using RESM/1.2.25 with expression values normalized into TPM.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each sample

source_name: Bulge stem cells

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols. Smart-seq2 protocols.

value: Dorsal skin

tag: age

value: Postnatal day 30


title: WT, E8.5, rep 7 [7_S7]

description: WT_E8.5_S7 (biol rep 7)


title: Bulge WT P30 H7


title: Bulge WT P30 H9


title: Bulge WT P30 H10


title: Bulge WT P30 H8


title: WT, E9.5, rep 1 [14_S14]

description: WT_E9.5_S14 (biol rep 1)


title: Bulge WT P30 H5


title: Bulge WT P30 H6


title: Bulge WT P30 H4


title: Bulge WT P30 H3


title: Bulge WT P30 H1


title: Bulge WT P30 H2


title: Bulge WT P30 G12


title: Bulge WT P30 G8


title: Bulge WT P30 G6


title: Bulge WT P30 G7


title: Smarca4-KD-low-MNase-extracted-Rep3

tag: cell line

value: E14 mES cell line

value: Input DNA was gel-extracted between 200-300 bp to enrich for putative overlapping dinucleosomes

value: Smarca4 KD

value: low MNase


title: Bulge WT P30 G11


title: Bulge WT P30 H11


title: Bulge WT P30 G5


title: Bulge WT P30 G3


title: Bulge WT P30 G1


title: WT, E8.5, rep 3 [3_S3]

description: WT_E8.5_S3 (biol rep 3)

value: WT


title: WT, E8.5, rep 6 [6_S6]

description: WT_E8.5_S6 (biol rep 6)


title: WT, E8.5, rep 2 [2_S2]

description: WT_E8.5_S2 (biol rep 2)


title: Bulge WT P30 G2


title: Bulge WT P30 F10


title: Bulge WT P30 G10


title: Bulge WT P30 F8


title: Bulge WT P30 F11


title: Bulge WT P30 G9


title: Bulge WT P30 G4


title: Bulge WT P30 F5


title: Bulge WT P30 F6


title: Bulge WT P30 F3


title: Bulge WT P30 F7


title: Bulge WT P30 F2


title: Bulge WT P30 F1


title: Bulge WT P30 E11


title: Bulge WT P30 F4


title: Bulge WT P30 E10


title: Bulge WT P30 E9


title: Bulge WT P30 E7


title: Bulge WT P30 E5


title: Bulge WT P30 E6


title: Bulge WT P30 E8


title: Bulge WT P30 E2


title: Bulge WT P30 E4


title: Bulge WT P30 D12


title: Bulge WT P30 D10


title: Bulge WT P30 F12


title: Bulge WT P30 D11


title: Bulge WT P30 D5


title: Bulge WT P30 D3


title: Bulge WT P30 D7


title: Bulge WT P30 D6


title: Bulge WT P30 D8


title: Bulge WT P30 D9


title: Bulge WT P30 E1


title: Bulge WT P30 D4


title: Bulge WT P30 C11


title: Bulge WT P30 C4


title: Bulge WT P30 D1


title: Bulge WT P30 C12


title: Bulge WT P30 D2


title: Bulge WT P30 C9


title: Bulge WT P30 C2


title: Bulge WT P30 C10


title: Smarca5-KD-high-MNase-Rep2

tag: extraction

value: unextracted

value: Smarca5 KD

value: high MNase


title: Bulge WT P30 C1


title: Bulge WT P30 C7


title: Bulge WT P30 B11


title: Bulge WT P30 C3


title: Bulge WT P30 B8


title: Bulge WT P30 B10


title: Bulge WT P30 B12


title: Bulge WT P30 B7


title: Bulge WT P30 B6


title: Bulge WT P30 B5


title: Bulge WT P30 B2


title: Bulge WT P30 B4


title: Bulge WT P30 C8


title: Bulge WT P30 A12


title: Bulge WT P30 B1


title: Bulge WT P30 C5


title: Bulge WT P30 A10


title: Bulge WT P30 A11


title: Bulge WT P30 A8


title: Bulge WT P30 A9


title: Bulge WT P30 A6


title: Bulge WT P30 A5


title: Bulge WT P30 A7


title: Bulge WT P30 A2


title: Bulge WT P30 A3


title: Bulge WT P30 A1


title: Bulge WT P30 B3


title: Myeloid Mut P56 G10

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56G10

source_name: Myeloid Mut P56

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
Smart-seq2

value: Myeloid cells

tag: genotype

value: Mut

value: Postnatal day 56


title: Myeloid Mut P56 H11

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56H11


title: Myeloid Mut P56 H8

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56H8


title: Myeloid Mut P56 H6

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56H6


title: Myeloid Mut P56 H3

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56H3


title: Myeloid Mut P56 H9

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56H9


title: Myeloid Mut P56 H2

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56H2


title: Myeloid Mut P56 H7

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56H7


title: Myeloid Mut P56 G11

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56G11


title: Myeloid Mut P56 H10

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56H10


title: Bulge WT P30 C6


title: Myeloid Mut P56 G7

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56G7


title: Myeloid Mut P56 G4

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56G4


title: Myeloid Mut P56 G6

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56G6


title: Myeloid Mut P56 G2

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56G2


title: Myeloid Mut P56 G9

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56G9


title: Myeloid Mut P56 F10

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56F10


title: Myeloid Mut P56 F12

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56F12


title: Myeloid Mut P56 G1

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56G1


title: Myeloid Mut P56 F6

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56F6


title: Myeloid Mut P56 F8

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56F8


title: Myeloid Mut P56 F5

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56F5


title: Myeloid Mut P56 F11

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56F11


title: Myeloid Mut P56 F4

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56F4


title: Myeloid Mut P56 F1

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56F1


title: Myeloid Mut P56 E12

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56E12


title: Myeloid Mut P56 G5

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56G5


title: Myeloid Mut P56 E11

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56E11


title: Myeloid Mut P56 E5

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56E5


title: Myeloid Mut P56 D7

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56D7


title: Myeloid Mut P56 E8

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56E8


title: Myeloid Mut P56 E3

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56E3


title: Myeloid Mut P56 D10

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56D10


title: Myeloid Mut P56 D9

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56D9


title: Myeloid Mut P56 E10

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56E10


title: Myeloid Mut P56 E6

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56E6


title: Myeloid Mut P56 E2

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56E2


title: Myeloid Mut P56 E1

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56E1


title: Myeloid Mut P56 D11

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56D11


title: Myeloid Mut P56 D6

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56D6


title: Myeloid Mut P56 E4

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56E4


title: Myeloid Mut P56 D12

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56D12


title: Myeloid Mut P56 D3

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56D3


title: Myeloid Mut P56 C10

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56C10


title: Myeloid Mut P56 C9

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56C9


title: Myeloid Mut P56 D5

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56D5


title: Myeloid Mut P56 D4

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56D4


title: Myeloid Mut P56 C11

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56C11


title: Myeloid Mut P56 H1

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56H1


title: Myeloid Mut P56 F2

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56F2


title: Myeloid Mut P56 C7

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56C7


title: Myeloid Mut P56 C5

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56C5


title: Myeloid Mut P56 C6

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56C6


title: Myeloid Mut P56 C3

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56C3


title: Myeloid Mut P56 G8

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56G8


title: Myeloid Mut P56 C8

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56C8


title: Myeloid Mut P56 B1

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56B1


title: Myeloid Mut P56 B9

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56B9


title: Myeloid Mut P56 A10

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56A10


title: Myeloid Mut P56 A12

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56A12


title: Myeloid Mut P56 A6

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56A6


title: Myeloid WT P56 H9

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56H9

source_name: Myeloid WT P56


title: Myeloid WT P56 H10

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56H10


title: Myeloid Mut P56 C2

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56C2


title: Myeloid Mut P56 B6

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56B6


title: Myeloid Mut P56 B2

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56B2


title: Myeloid Mut P56 B10

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56B10


title: Myeloid Mut P56 B8

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56B8


title: Myeloid Mut P56 A7

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56A7


title: Myeloid Mut P56 A9

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56A9


title: Myeloid Mut P56 A2

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56A2


title: Myeloid WT P56 H7

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56H7


title: Myeloid Mut P56 C12

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56C12


title: Myeloid WT P56 H5

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56H5


title: Myeloid Mut P56 A5

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56A5


title: Myeloid WT P56 H4

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56H4


title: Myeloid Mut P56 A1

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56A1


title: Myeloid WT P56 H8

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56H8


title: Myeloid WT P56 H6

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56H6


title: Myeloid Mut P56 B12

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56B12


title: Myeloid Mut P56 A8

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56A8


title: Myeloid Mut P56 A4

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56A4


title: Myeloid Mut P56 A3

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56A3


title: Myeloid Mut P56 B5

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56B5


title: Myeloid WT P56 H3

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56H3


title: Myeloid WT P56 H1

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56H1


title: Myeloid Mut P56 B7

description:
Myeloid_cells_Mut_P56_genelist_TPM.txt
Myel Mut P56B7


title: Myeloid WT P56 G10

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56G10


title: Myeloid WT P56 G9

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56G9


title: Myeloid WT P56 H2

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56H2


title: Myeloid WT P56 G5

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56G5


title: Myeloid WT P56 G2

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56G2


title: Myeloid WT P56 G1

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56G1


title: Myeloid WT P56 G3

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56G3


title: Myeloid WT P56 F9

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56F9


title: Myeloid WT P56 F8

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56F8


title: Myeloid WT P56 F12

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56F12


title: Myeloid WT P56 F4

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56F4


title: Myeloid WT P56 F3

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56F3


title: Myeloid WT P56 F6

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56F6


title: Myeloid WT P56 F2

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56F2


title: Myeloid WT P56 E10

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56E10


title: Myeloid WT P56 E9

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56E9


title: Myeloid WT P56 E12

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56E12


title: Myeloid WT P56 E11

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56E11


title: Myeloid WT P56 E8

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56E8


title: Myeloid WT P56 E3

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56E3


title: Myeloid WT P56 E6

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56E6


title: Myeloid WT P56 E2

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56E2


title: Myeloid WT P56 E1

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56E1


title: Myeloid WT P56 D11

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56D11


title: Myeloid WT P56 D10

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56D10


title: Myeloid WT P56 D5

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56D5


title: Myeloid WT P56 D4

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56D4


title: Myeloid WT P56 D2

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56D2


title: Myeloid WT P56 D1

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56D1


title: Myeloid WT P56 F5

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56F5


title: Myeloid WT P56 C12

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56C12


title: Myeloid WT P56 D7

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56D7


title: Myeloid WT P56 C10

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56C10


title: Myeloid WT P56 C9

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56C9


title: Myeloid WT P56 C7

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56C7


title: Myeloid WT P56 C11

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56C11


title: Myeloid WT P56 C6

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56C6


title: Myeloid WT P56 C5

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56C5


title: Myeloid WT P56 C4

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56C4


title: Myeloid WT P56 F1

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56F1


title: Myeloid WT P56 C2

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56C2


title: Myeloid WT P56 B12

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56B12


title: Myeloid WT P56 C1

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56C1


title: Myeloid WT P56 E5

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56E5


title: Myeloid WT P56 C3

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56C3


title: Myeloid WT P56 B10

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56B10


title: Myeloid WT P56 B11

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56B11


title: Myeloid WT P56 B9

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56B9


title: Myeloid WT P56 B7

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56B7


title: Myeloid WT P56 B8

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56B8


title: Myeloid WT P56 D12

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56D12


title: Myeloid WT P56 D9

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56D9


title: Myeloid WT P56 B6

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56B6


title: Myeloid WT P56 B5

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56B5


title: Myeloid WT P56 B3

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56B3


title: Myeloid WT P56 B1

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56B1


title: Myeloid WT P56 A12

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56A12


title: Myeloid WT P56 A11

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56A11


title: Myeloid WT P56 B2

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56B2


title: Myeloid WT P56 C8

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56C8


title: Myeloid WT P56 B4

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56B4


title: Myeloid WT P56 A4

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56A4


title: Myeloid WT P56 A5

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56A5


title: Myeloid WT P56 A3

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56A3


title: Myeloid WT P56 A2

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56A2


title: Myeloid WT P56 A1

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56A1


title: Myeloid WT P56 A6

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56A6


title: Melanocyte Mut P56 H12

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56H12

source_name: Melanocyte Mut P56

value: Melanocytes


title: Melanocyte Mut P56 H9

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56H9


title: Melanocyte Mut P56 H8

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56H8


title: Melanocyte Mut P56 H4

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56H4


title: Melanocyte Mut P56 G12

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56G12


title: Melanocyte Mut P56 H6

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56H6


title: Melanocyte Mut P56 H1

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56H1


title: Melanocyte Mut P56 H7

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56H7


title: Melanocyte Mut P56 H11

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56H11


title: Melanocyte Mut P56 H2

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56H2


title: Melanocyte Mut P56 G10

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56G10


title: Myeloid WT P56 A7

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56A7


title: Melanocyte Mut P56 H3

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56H3


title: Myeloid WT P56 A10

description:
Myeloid_cells_WT_P56_genelist_TPM.txt
Myel WT P56A10


title: Melanocyte Mut P56 G9

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56G9


title: Melanocyte Mut P56 G5

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56G5


title: Melanocyte Mut P56 G4

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56G4


title: Melanocyte Mut P56 G2

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56G2


title: Melanocyte Mut P56 G3

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56G3


title: Melanocyte Mut P56 G6

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56G6


title: Melanocyte Mut P56 G1

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56G1


title: Melanocyte Mut P56 F12

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56F12


title: Melanocyte Mut P56 H10

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56H10


title: Melanocyte Mut P56 F10

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56F10


title: Melanocyte Mut P56 F9

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56F9


title: Melanocyte Mut P56 F6

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56F6


title: Melanocyte Mut P56 H5

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56H5


title: Melanocyte Mut P56 F5

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56F5


title: Melanocyte Mut P56 F4

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56F4


title: Melanocyte Mut P56 F3

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56F3


title: Melanocyte Mut P56 F1

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56F1


title: Melanocyte Mut P56 E9

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56E9


title: Melanocyte Mut P56 E10

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56E10


title: Melanocyte Mut P56 E11

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56E11


title: Melanocyte Mut P56 E8

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56E8


title: Melanocyte Mut P56 G7

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56G7


title: Melanocyte Mut P56 E4

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56E4


title: Melanocyte Mut P56 E2

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56E2


title: Melanocyte Mut P56 D11

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56D11


title: Melanocyte Mut P56 D10

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56D10


title: Melanocyte Mut P56 E1

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56E1


title: Melanocyte Mut P56 D7

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56D7


title: Melanocyte Mut P56 D8

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56D8


title: Melanocyte Mut P56 F11

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56F11


title: Melanocyte Mut P56 D6

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56D6


title: Melanocyte Mut P56 D5

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56D5


title: Melanocyte Mut P56 D1

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56D1


title: Melanocyte Mut P56 D2

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56D2


title: Melanocyte Mut P56 C12

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56C12


title: Melanocyte Mut P56 D3

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56D3


title: Melanocyte Mut P56 D4

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56D4


title: Melanocyte Mut P56 G8

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56G8


title: Melanocyte Mut P56 C9

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56C9


title: Melanocyte Mut P56 F2

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56F2


title: Melanocyte Mut P56 C8

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56C8


title: Melanocyte Mut P56 C10

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56C10


title: Melanocyte Mut P56 C7

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56C7


title: Melanocyte Mut P56 E3

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56E3


title: Melanocyte Mut P56 D12

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56D12


title: Melanocyte Mut P56 C5

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56C5


title: Melanocyte Mut P56 C2

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56C2


title: Melanocyte Mut P56 B12

description:
Melanocyte_SC_Mut_genelist_TPM.txt
Melan Mut P56B12