title: Tumor-49

type: RNA

city: ankara

first: nevin

last: belder

address: gumusdere

country: Turkey

institute: ankara university

description: Gene expression data from 49 colorectal cancer patients and paired normal FFPE tissues

hyb_protocol: Labeled products were hybridized onto the Affymetrix U133 X3P array according to the manufacturer’s specifications.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing:
The data were analyzed with Partek Genomics Suite Version 6.6
The Affymetrix CEL files were pre-processed with Genomics Suite v6.6 (Partek) using the robust multi-array analysis (RMA) algorithm.

label: biotin

source_name: colorectal cancer patient #49

label_protocol: 100 ng of input RNA was used to generate the amplified RiboSPIA product using the Ovation® FFPE WTA System (NuGEN) according to the manufacturer’s instructions. The fragmented and labeled samples (3.5 μg) were then hybridized to Affymetrix GeneChip® Human X3P Arrays.

extract_protocol: RNA was extracted using the Qiagen FFPE RNeasy kit.

value: FFPE

tag: tissue type

value: tumor

tag: gender

tag: tumor stage

value: Stage IIIB

tag: grade

value: Grade III

tag: localization

value: Right

tag: overall survival time

tag: overall_event (death from any cause)

value: no death


title: control Day4 siRNA 13

status: Public on Jul 21 2025

type: SRA

city: Stanford

first: Douglas

last: Porter

state: CA

address: 269 Campus Drive

department: Dermatology

country: USA

institute: Stanford

library_source: transcriptomic

data_processing:
Lexogen reads were processed according to the manufacturer’s recommendation, mapped with STAR (v. 2.7) to hg38 using “basic” tagged Gencode v.39 transcripts, and genes quantified with FeatureCounts (from Rsubread v.2.10.5). Quantifications were analyzed with DESeq2 (v.1.38.3), with apeGLM shrinkage.
Assembly: hg38
Supplementary files format and content: Featurecounts estimated raw reads per gene.

molecule: polyA RNA

organism: Homo sapiens

source_name: Primary keratinocytes

growth_protocol: Primary human keratinocytes were isolated from fresh surgically discarded newborn foreskin, and progenitor cells cultured in complete Keratinocyte-SFM (Life Technologies, #17005-142) and Medium 154 (Life Technologies #M-154-500). Cells were induced to differentiate by the addition of 1.2 mM calcium for 3 days at full confluence. Biological replicates were performed in all cases using primary cells from at least 2 independent, unrelated donors.

extract_protocol:
Total RNA was extracted using the RNeasy Plus kit (QIAGEN, 74136).
QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen, 191.96) following manufacturer’s protocol with UMI Second Strand Synthesis Module for QuantSeq FWD (Lexogen, 018.96)

tag: tissue

value: Primary keratinocytes

tag: genotype

tag: treatment

value: Progenitor


title: 11G_AZA_250620, RNA

city: Newcastle

first: Heather

last: Lee

state: NSW

address: University Drive, Callaghan

country: Australia

institute: The University of Newcastle

library_source: transcriptomic single cell

data_processing:
Following demultiplexing, multiple sequencing lanes per read were concatenated into single R1 and R2 fastq files, per sample using zcat and gzip.
Raw reads were trimmed in pair-end mode using Trim Galore (v0.6.5) and Cutadapt (v2.10), retaining unpaired reads.
Hisat2 (v2.1.0) was used to map and align trimmed and unpaired reads using default parameters (--phred33) to the human reference genome build (GRCh38), and samtools (v1.10) was used to sort by coordinate and generate bam files.
TEtranscripts (v2.2.1) was used to obtain raw gene and transposable element counts from unique and ambiguously aligned reads (bam files) using TEcount with the flags '--sortByPos --mode multi’. The GTF files used were generated as follows: 1) TEs (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz; USCS repeating element Repeat Masker; hg38; 2021-09-03) and 2) genes (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_30/gencode.v30.annotation.gtf.gz; gencode Release 30; GRCh38.p12; 2019-04-08). To ensure the GTF files worked with TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial genes in the chromosome column and removal of ‘Chr’ preceding each chromosome number. The TE GTF was generated from the repeat mask file  using the conversion tool from the TEtranscripts developers (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/makeTEgtf.pl.gz) ‘perl makeTEgtf.pl -c 6 -s 7 -e 8 -o 10 -t 11 -n hg38_rmsk -f 13 -C 12 -S 2 rmsk.txt >> hg38_rmsk_TE.gtf’ and removing ‘chr’ from chromosome names ‘sed 's/chr//' hg38_rmsk_TE.gtf > hg38_rmsk_TE_NoChr.gtf’.    TEtranscripts the gene GTF (from gencode) was updated by converting ‘M’ to ‘MT’ for mitochondrial
Individual sample counts from TEtranscripts were collated into a single count table (tab-deliminated) and updated with relevant gene information from the gene GTF file.
Assembly: GRCh38
Supplementary files format and content: Bismark output file: genome-wide CpG methylation reports (CpG.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>
Supplementary files format and content: Bismark output file: genome-wide GpC methylation reports (GpC.cov.gz) are tab-delimited, use 1-based genomic coordinates and are in the following format: <chromosome> <position> <methylation rate>
Supplementary files format and content: Count table (tab-deliminated) compiled from TEtranscripts results. First column contains gene (ensembl ID) and transposable element (TE) ID and column two contains hgnc symbol equiavelnt (gene IDs). Columns 3-7 contains TE information and columns 7-13  contains gene informations. Counts for individual samples are contained in column 14 onwards.

source_name: Peripheral blood

growth_protocol: AML cell line, HL-60 (ATCC #CCL-240), were maintained in tissue culture flasks (Greiner Bio-One) at 37°C, 5% CO2, and sub-cultured at 500,000 cells/mL every 2-3 days with fresh medium. HL-60 cells were maintained in Iscove′s Modified Dulbecco′s media (IMDM; Sigma-Aldrich) supplemented with 4mM GlutaMAX (Thermo Fisher Scientific) and 10% Fetal Bovine Serum (FBS; Sigma-Aldrich).

extract_protocol:
At 72 hours, viable (propidium iodide negative) single cells were isolated by Fluoresence activated cell sorting (FACS) and sorted into 2.5µL of RLT PLUS buffer (Qiagen) containing 2.5U SUPERas-In (Thermo Fisher Scientific) in LoBind 96-well full skirted plates (Eppendorf) using indexed sorting on a FACS Aria II (BD Biosciences). Plates were sealed and briefly centrifuged before storage at -80°C for sequencing analyses.
For scNMT-seq, matched scNOMe-seq and scRNA-seq libraries were prepared from sorted HL-60 single cells, as previously described (Clark, S. J. et al. scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nature Communications [2018]) with minor modifications described below and within the associated manuscript.
Cell lysates were incubated with magnetic Dynabeads conjugated to the Bio-dT30VN oligonucleotide (5’- AAG CAG TGG TAT CAA CGC AGA GTA CT30VN-3’). Poly-adenylated mRNA captured on the Dynabeads underwent reverse transcription and cDNA amplification (for scRNA-seq), while genomic DNA was transferred to a new multi-well plate for bisulphite conversion (for scNOMe-seq).
For reverse transcription, Dynabeads were resuspended in 10µL reaction mix containing: 100U SuperScript II reverse transcriptase (Thermofisher), 1X First-strand buffer (Thermofisher), 2.5mM DTT (Thermofisher), 1M Betaine (Sigma-Aldrich), 9mM MgCl2 (Thermofisher), 1μM Template switching oligo (5’AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’), 1mM dNTPs (New England Biolabs) and 5U SUPERase-In RNAse inhibitor (Thermofisher). First-strand synthesis and template switching was then performed by incubating at 42 °C for 60 min, 50 °C for 30 min and 60 °C for 10 min. Amplification of cDNA was performed by adding KAPA HiFi HotStart ReadyMix (final concentration 1x, Roche sequencing) and ISPCR primer (5’-AAGCAGTGGTATCAACGCAGAGT-3’, final concentration 0.11μM) to the reverse transcription mix and amplifying as follows: 98 °C for 3 min, 23 repeats of (98 °C for 20s, 67 °C for 15 s, 72 °C for 6 min) and 72 °C for 5 min. Amplified cDNA was stored at -20 °C for later scRNA-seq library preparation.
Genomic DNA was purified using a 0.8x volume of AMPure XP beads (Beckman Coulter), and bisulphite converted using the Zymo EZ-96 DNA Methylation-Direct MagPrep Kit (Zymo Research) with halved reaction volumes. Converted DNA was eluted in first-strand synthesis mix containing: 1X Blue Buffer, 0.4mM dNTPs, 0.4 μM oligo1 - 5’CTACACGACGCTCTTCCGATCTNNNNNN 3’. Samples were incubated at 65 °C for 3 min and rapidly cooled before addition of 50 U of Klenow 3’ -> 5’ exo– (Enzymatics). The final reaction volume was 40µL, and samples were incubated as follows: 4°C 5 min, +1°C/15 s to 37°C, 37°C 30 min. Samples were heated to 95°C for 45s and rapidly cooled before addition of 2.5µL containing: 1X Blue Buffer, 0.4mM dNTPs, 0.4 μM oligo1 and 25U of Klenow 3’ -> 5’ exo–. The first strand synthesis step was then repeated (4°C 5 min, +1°C/15 s to 37°C, 37°C 30 min). In total, 5 rounds of first-strand synthesis were performed with the final round having an extended incubation for strand extension (4°C 5 min, +1°C/15 s to 37°C, 37°C 90 min). Samples were then incubated with 40 U exonuclease I (New England Bio-labs) for 1 h at 37 °C before DNA was purified using a 0.65x volume of AMPure XP beads. Samples were eluted in second-strand synthesis mix containing: 1X Blue Buffer, 0.4mM dNTP mix, 0.4 μM oligo2 (5’-TGCTGAACCGCTCTTCCGATCTNNNNNN-3’. Samples were incubated at 95°C for 45s and rapidly cooled before addition of 50 U of Klenow 3’ -> 5’ exo–. The final reaction volume was 40µL, and samples were incubated as follows: 4 °C for 5 min, +1 °C/15 s to 37 °C, 37 °C for 90 min. DNA purification was carried out using a 0.65x volume of AMPure XP bead buffer. Beads were resuspended in 1X KAPA HiFi HotStart ReadyMix with 0.2μM of i5 and i7 indexed primers from the NEBNext Multiplex Oligos for Illumina Dual Index Primer Sets (New England Biolabs, USA). Libraries were then amplified by PCR as follows: 95 °C 2 min, 12–14 repeats of (94 °C for 80 s, 65 °C for 30 s, 72 °C for 30 s), 72 °C for 3 min and 4 °C hold. Amplified libraries were purified using a 0.65x volume of AMPure XP beads and eluted in nuclease free water.
Amplified cDNA samples were quantified using Qubit dsDNA HS Assay Kit (ThermoFisher Scientific) and normalised to 0.2 ng/μL with nuclease free water before proceeding with RNA-seq library preparation. The Nextera XT DNA library preparation kit (Illumina) was used according to the manufacturer’s guidelines, but with halved reaction volumes and one in five dilutions of i5 and i7 indexed primers.

treatment_protocol: HL-60 cells were treated in suspension culture, every 24h for 72h total, with 100nM decitabine (DAC; Selleckchem #S1200) or with 2000nM azacytidine (AZA; Selleckchem # S1782). Untreated cells (UNT) were given an equal volume of 0.1% DMSO in UltraPure™ DNase/RNase-Free Distilled Water (Thermo Fisher Scientific) and served as a negative control.

value: Peripheral blood

tag: cell line

tag: cell type

value: promyeloblast

tag: disease/cancer type

value: Acute promyelocytic leukemia

tag: Sex

value: Female

tag: age

tag: batch

value: azacytidine


title: 11F_AZA_250620, RNA


title: Thy, replicate 4, scTCR-seq

city: Seoul

first: Suyeong

last: Park

address: 1, Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description: 10x Genomics

data_processing:
FASTQ files were produced by converting BCL files with Illumina bcl2fastq.
The gene expression and TCR data from these FASTQ files were analyzed using Cell Ranger(v.6.1.2) for both gene expression and TCR data.
Assembly: GRCh38-2020-A
Supplementary files format and content: Barcodes.tsv.gv', 'features.tsv.gv' and 'matrix.mtx.gz' files are uploaded and prefixed with individual library name for gene expression analysis.
Supplementary files format and content: Specifically, for TCR analysis, the ‘filtered_contig_annotations.csv’ file was refined to include only high-confidence, complete, and productive contigs associated with either TCRα or TCRβ chains.

molecule: total RNA

source_name: NKT, MAIT and γδ T cells

extract_protocol:
Human thymus samples were obtained from cardiac patients who underwent cardiac surgery. Thymocytes were isolated by density gradient centrifugation using Ficoll-Paque (GE Healthcare Life Science). Single cell suspensions of thymocytes were stained with BV421 conjugated Anti-Human TCRγ/δ or PE conjugated CD1d and APC conjugated MR1 tetramers and enriched with anti-PE and anti-APC microbeads (Miltenyi) according to the manufacturer’s instructions. CD3+CD19- cells were identified within the single-cell-resolved lymphocyte gating. CD3+tet+ cells were then sorted and collected in RPMI-1640 with 50% FBS. The sorting purity exceeded 96%. Subsequently, iNKT, MAIT and γδ T cells were combined and processed simultaneously.
Single-cell libraries was constructed according to the manufacturer’s instructions (10x Genomics). Samples were processed using 10X genomics's Single Cell 5' R2-only chemistry, as per the manufacturer’s recommendations.

value: thymus

value: NKT, MAIT and delta-gamma T cells


title: Tumor-48

source_name: colorectal cancer patient #48

value: Stage IIA

value: Grade II

value: Left

value: death


title: 11E_AZA_250620, RNA


title: 11D_DAC_250620, RNA

value: decitabine


title: Thy, replicate 3, scTCR-seq

description: 10x Genomics


title: 1A_Neg_250620, RNA

value: control


title: COVID-19,Hospitalized,patient001,Visit4

city: Ulsan

first: Jong

last: Bhak

state: Ulju-gun/Eonyang-eup

address: 50 UNIST-gil,

department: Biomedical Engineering (BME)

institute: Korean Genomics Center (KOGIC)

description:
Library name: C19-C001-V4
sample_age:66,sample_sex:F,severity_scale:3,severity_class:Severe-Critical

data_processing:
Raw sequencing reads were processed using Fastp (v0.23.1) to remove adapters and low-quality bases, with the following parameters: --cut_front 1 --cut_right 0 --cut_tail 1 --detect_adapter_for_pe --trim_front1 15 --trim_front2 15 --trim_tail1 0 --trim_tail2 0 --cut_mean_quality 20 --n_base_limit 1 --average_qual 20 34. Read quality was assessed before and after filtering reads using FastQC (v0.11.9).
Filtered reads were aligned to the human reference genome (GRCh38.p13) using STAR (v2.7.10b), a splice-aware aligner, with default settings.
Gene-level quantification was performed using RSEM (v1.3.3) using default options, with gene annotations from GENCODE v42 (GFF3 format).
Raw expected gene counts were normalized using the DESeq2 R package (v1.38.3). A variance stabilizing transformation (VST) was subsequently applied to the normalized counts.
Assembly: GRCh38.p13 (GENCODE v42)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: Whole blood

extract_protocol:
Frozen whole blood samples collected in PAXgene® Blood RNA Tubes (PreAnalytiX, #762174) were used for total RNA extraction. RNA integrity and concentration were assessed using a Qubit 2.0 Fluorometer (Thermo Fisher Scientific, #Q32866) and the Qubit RNA HS Assay Kit (Thermo Fisher Scientific, #Q32854). For mRNA enrichment, 200 ng of total RNA per sample was processed using the Dynabeads mRNA Purification Kit (Thermo Fisher Scientific, #01152851), which depletes rRNA and isolates polyadenylated transcripts using oligo(dT) beads.
Library preparation was performed using the MGIEasy RNA Directional Library Prep Set (MGI, #MG1000006386), following the manufacturer’s protocol. Fragment size distribution was checked using 4150 TapeStation (Agilent, #G2992A) with the cDNA D1000 ScreenTape (Agilent, #5067-5582). Final libraries were quantitated using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific, Q32866). RNA sequencing was run on DNBSEQ-T7RS (MGI) platform, generating 150 bp paired-end reads.

value: Whole blood

tag: severity scale

tag: severity class

value: Severe-Critical

tag: visit number


title: Tumor-47

source_name: colorectal cancer patient #47

value: FFPE

tag: tissue type

value: tumor

tag: gender

tag: tumor stage

value: Grade III

value: Right

value: no death


title: 11C_DAC_250620, RNA

value: Peripheral blood

value: promyeloblast

value: Acute promyelocytic leukemia

value: Female


title: 12F_Unt_250620, RNA

value: untreated


title: Thy, replicate 2, scTCR-seq

description: 10x Genomics

value: thymus

value: NKT, MAIT and delta-gamma T cells


title: 11B_DAC_250620, RNA


title: 11A_DAC_250620, RNA


title: Tumor-46

source_name: colorectal cancer patient #46

value: Male

value: Stage IIIA

tag: grade

value: Grade II

tag: localization

value: Left

tag: overall survival time


title: 10H_AZA_250620, RNA

tag: tissue

value: azacytidine


title: control Day4 siRNA 19

value: Primary keratinocytes

tag: genotype

tag: treatment

value: Progenitor


title: Thy, replicate 1, scTCR-seq

description: 10x Genomics

tag: cell type


title: 10G_AZA_250620, RNA

tag: cell line

tag: disease/cancer type


title: Tumor-45

source_name: colorectal cancer patient #45

value: FFPE

value: tumor

value: Stage IIA

value: Grade III

tag: overall_event (death from any cause)


title: Tumor-44

source_name: colorectal cancer patient #44

value: Stage IIIB

value: no death


title: Thy, replicate 4, scRNA-seq

description: 10x Genomics


title: 10E_AZA_250620, RNA

value: Peripheral blood

value: promyeloblast

value: Acute promyelocytic leukemia

tag: Sex

value: Female

tag: age

tag: batch


title: 10D_DAC_250620, RNA

value: decitabine


title: Thy, replicate 3, scRNA-seq

description: 10x Genomics

value: thymus

value: NKT, MAIT and delta-gamma T cells


title: Tumor-43

source_name: colorectal cancer patient #43

value: Male

value: Left

value: death


title: 10C_DAC_250620, RNA


title: 10B_DAC_250620, RNA


title: Thy, replicate 2, scRNA-seq

description: 10x Genomics


title: Tumor-42

source_name: colorectal cancer patient #42

value: Grade II


title: 10A_DAC_250620, RNA


title: 9H_AZA_060320, RNA

value: azacytidine


title: 9G_AZA_060320, RNA


title: Tumor-41

source_name: colorectal cancer patient #41

value: FFPE

value: tumor

value: Stage IIIC

value: Right


title: Thy, replicate 1, scRNA-seq

description: 10x Genomics


title: 9F_AZA_060320, RNA


title: 9E_AZA_060320, RNA


title: Tumor-40

source_name: colorectal cancer patient #40

value: Grade III


title: 15q13_del_2_d125

city: New York

first: Ryan

last: Walsh

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: MSKCC

description: 10x Genomics

data_processing:
Cellranger v6.1.2 was used for demultiplexing and generation of a count matrix
Assembly: GRCh38
Supplementary files format and content: comma separated count matrix

source_name: Organoid

extract_protocol:
Organoids were dissociated with a papain dissociation system (Worthington) according to the manufacturer's protocol for 30min at 37C. The single cell suspension was washed, filtered and resuspended in 0.04% BSA/PBS + Ribolock RNase inhibitor for scRNAseq.
Libraries were constructed with the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics) according to the manufacturer's protocol. In brief, single cell suspensions were loaded onto a Chromium Next GEM Chip G for GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 7,000-15,000 cells. cDNA amplification included 11-12 cycles and 30-240 ng of the material were used to prepare sequencing libraries with 10-16 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/88 run using the NovaSeq 6000 S1 or S4 Reagent Kit (100 or 200 cycles) (Illumina).

value: Organoid

value: progenitors and neurons

value: 15q13.3 deletion


title: 9D_DAC_060320, RNA

value: Peripheral blood

value: promyeloblast

value: Acute promyelocytic leukemia

value: Female


title: 10F_AZA_250620, RNA


title: 9C_DAC_060320, RNA

value: decitabine


title: MEL1_Control_2_d125

description: 10x Genomics

value: WT


title: 9B_DAC_060320, RNA


title: 8H_AZA_060320, RNA


title: 9A_DAC_060320, RNA


title: 15q13_del_1_d125

description: 10x Genomics


title: Tumor-38

source_name: colorectal cancer patient #38

value: Stage IIIB

value: Left

value: death


title: MEL1_Control_1_d125

description: 10x Genomics


title: 8G_AZA_060320, RNA

value: azacytidine


title: Tumor-36

source_name: colorectal cancer patient #36

value: FFPE

value: tumor

value: Male

value: no death


title: 8E_AZA_060320, RNA


title: Tumor-37

source_name: colorectal cancer patient #37

value: Stage IIIC

value: Grade II


title: MEL1_Control2_d60

description: 10x Genomics

value: Organoid

value: progenitors and neurons


title: 22q11_del_2_d60

description: 10x Genomics

value: 22q11.2 deletion


title: Tumor-35

source_name: colorectal cancer patient #35

value: Grade III


title: 8C_DAC_060320, RNA

source_name: Peripheral blood

value: Peripheral blood

value: promyeloblast

value: Acute promyelocytic leukemia

value: Female


title: 8B_DAC_060320, RNA

value: decitabine


title: 22q11_del_1_d60

description: 10x Genomics


title: Tumor-33

source_name: colorectal cancer patient #33

value: Stage IIA

value: Left


title: 7H_AZA_060320, RNA

value: azacytidine


title: 7G_AZA_060320, RNA


title: Tumor-34

source_name: colorectal cancer patient #34

value: FFPE

value: tumor

value: Stage IIC


title: MEL1_Control1_d60

description: 10x Genomics

value: WT


title: Tumor-39

source_name: colorectal cancer patient #39

value: Male

value: Stage IIIB

value: Grade II

value: no death


title: 7F_AZA_060320, RNA


title: MEL1_dFB_d75

description: 10x Genomics

value: Organoid

value: progenitors and neurons


title: 7D_DAC_060320, RNA

value: Peripheral blood

value: promyeloblast


title: MEL1_vFB_d75

description: 10x Genomics


title: Tumor-31

source_name: colorectal cancer patient #31

value: Female

value: death


title: 8F_AZA_060320, RNA

value: Acute promyelocytic leukemia


title: 7E_AZA_060320, RNA


title: 7C_DAC_060320, RNA

value: decitabine


title: 7B_DAC_060320, RNA


title: A549-miR-NC3

city: Tokyo

first: Yu

last: Fujita

address: Nishi-shimbashi

country: Japan

institute: The Jikei University Scho of Med

data_processing:
Raw sequence data generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's Bcl2fastq (v2.17.1.14). One mismatch was allowed for index sequence identification.
Supplementary files format and content: FPKMs

growth_protocol: The cells are maintained in RPMI 1640 medium with 10% fetal bovine serum (FBS, Gibco Life Technologies) and 1% antibiotic-antimycotic (Invitrogen) at 37 °C in 5% CO2. LFs were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 10% FBS and 1% antibiotic-antimycotic solution at 37 °C in 5% CO2.

extract_protocol:
Total RNA was extracted from NSCLC cells or EVs using QIAzol and the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
RNA quantity and quality were determined using Agilent Bioanalyzer (Agilent Technologies). RNA library preparation with polyA selection and Illumina HiSeq 2 × 150 bp sequencing was performed by GeneWiz Inc. Image analysis and base calling were conducted by the HiSeq Control Software (HCS).

treatment_protocol: MiRNA transfection at 25 nM was conducted with Lipofectamine 3000 reagent (Thermo Fisher Scientific) according to the manufacturer’s protocol.

value: Human lung adenocarcinoma cells

value: control


title: Tumor-30

source_name: colorectal cancer patient #30

value: FFPE

value: tumor

value: Stage IIA

value: Left


title: 8D_DAC_060320, RNA


title: Purified immune cells, anti-PD-1, aspartame

city: Indianapolis

first: Yuan

last: Liu

state: IN

address: 410 W. 10th Street

institute: Indiana University

description: Library name: Aspartame diet + anti-PD-1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were madeusing the Cell Ranger software v2.1.1 (https://support.10xgenomics.comsingle-cellgene-expression/software/pipelinesatestwhat-is-cell-ranger)
The barcode, gene identifier and UMI count matrix files were integrated using Seurat V2 (https://satijalab.org/seurat/) to generate the gene expression profile.
Assembly: Mouse mm10
Supplementary files format and content: processed data file with .rds format, content of expression profile of all samples (UMI count)

organism: Mus musculus

source_name: Tumor

growth_protocol: Mice were housed in specific pathogen–free conditions under standard 12-hour light/dark cycles. Animals received either regular chow or aspartame diet ad libitum for 2 weeks prior to tumor inoculation and during the course of tumor progression and treatment.

extract_protocol:
Tumors were enzymatically dissociated using a cocktail of collagenase IV, DNase I, and hyaluronidase. Immune cells were enriched by density gradient centrifugation and sorted as CD45⁺ cells by fluorescence-activated cell sorting (FACS). Total RNA was extracted from individual cells as part of the 10x Genomics single-cell protocol.
The single cell capture and library construction were performed by following the Chromium Single Cell 3ʹ Reagent Kits v3 protocol (CG000184). Briefly, cells were resuspended in PBS with 0.04% BSA at a concentration of 700-1200 cells/µl and more than 85% viability. The single cells were loaded onto Chromium Next GEM Chip B (PN-1000073) with partitioning oil and barcoded singe cell gel beads. The barcoded and full-length cDNA is produced after incubation of the gel beads-in-emulsion (GEMs) and amplified via PCR for library construction. The library preparation is performed by following the protocol of Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (PN-1000092). The quality of the final libraries was examined using Agilent High Sensitive DNA Kit (#5067-4626) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA) , and the library concentrations were determined by qPCR using Kapa Library Quantification kit (#KK4824, Roche Diagnostics) on a QuantStudio3 (ThermoFisher Scientific). The libraries were pooled evenly and went for the paired-end sequencing on an Illumina NextSeq 550 System (Illumina, Inc., USA) using High Output Kit v2.5 (#20024907, Illumina, Inc., USA).

treatment_protocol: Tumor-bearing mice were treated with anti–PD-1 antibody (10 mg/kg, intraperitoneally, twice per week for 3 doses). Tumors and tumor-infiltrating immune cells were harvested 17–18 days after inoculation for downstream scRNA-seq analysis.

value: Tumor

value: CD45 tumor-infiltrating immune cells

tag: strain

value: anti-PD-1, aspartame


title: 7A_DAC_060320, RNA


title: Purified immune cells, anti-PD-1, chow

description: Library name: Chow diet + anti-PD-1

value: anti-PD-1, chow


title: A549-miR-NC2


title: Tumor-29

source_name: colorectal cancer patient #29

tag: tissue type

value: Stage IIIB

value: Grade III


title: 8A_DAC_060320, RNA

value: Peripheral blood

value: promyeloblast


title: 6H_AZA_060320, RNA

value: Female

value: azacytidine


title: A549-miR-NC1


title: Tumor-28

source_name: colorectal cancer patient #28

tag: gender

value: Male

value: Grade II

value: no death


title: Control_mannital_C

city: Durham

first: Ari

last: Sadanandom

address: Stockton Rd

department: Biosciences

country: United Kingdom

institute: Durham University

data_processing:
The fastq files were quality control checked by FastQCand the adaptors and low quality reads were removed by Trimmomatic. High quality reads were then mapped to Araport11, the duplicated reads were discarded by Picard  and the read abundant were quantified by HTSeq.
Assembly: Araprot11
Supplementary files format and content: raw_counts.csv

organism: Arabidopsis thaliana

source_name: Whole seedling

extract_protocol:
RNeasy Plant Mini Kit (Qiagen)
cDNA was synthesized using Invitrogen SuperScript II Reverse Transcriptase

value: Whole seedling

tag: ecotype


title: 6G_AZA_060320, RNA

value: Acute promyelocytic leukemia


title: Tumor-27

source_name: colorectal cancer patient #27

value: FFPE

value: tumor

tag: tumor stage

value: Stage IIB

tag: grade


title: A549-miR-19a2

value: Human lung adenocarcinoma cells


title: Control_mannital_B


title: Tumor-26

source_name: colorectal cancer patient #26

tag: localization

value: Left

tag: overall survival time


title: Control_mannital_A

tag: tissue


title: Tumor-32

source_name: colorectal cancer patient #32

value: Stage IVA

value: death


title: A549-miR-19a3

tag: treatment


title: 6F_AZA_060320, RNA

tag: cell type


title: 6E_AZA_060320, RNA

tag: cell line


title: Tumor-25

source_name: colorectal cancer patient #25

value: Stage IIA


title: 300mM_Manital_C

value: 300mM Manital


title: A549-miR-19a1


title: 6D_DAC_060320, RNA

value: Peripheral blood

value: promyeloblast

tag: disease/cancer type

value: decitabine


title: Tumor-24

source_name: colorectal cancer patient #24

value: Female

value: Stage IIIB

value: Grade I

tag: overall_event (death from any cause)


title: error rates from Taq pol V2 IL processing SAR-CoV-2 RNA

city: Konstanz

first: Luisa

middle: Barbara

last: Huber

state: Baden-Württemberg

address: Universitätsstraße 10

department: Department of Chemistry

country: Germany

institute: Universität Konstanz

description: (2*75 bp)

library_source: other

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 (SARS-CoV-2 RNA 100 bp)
High quality data were filtered and aligned to the RNA reference
A frameshift correction was performed e.g. caused by phasing or pre-phasing during sequencing. Those reads with a misalignment higher than 24% were removed from the data set
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 3 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.
To normalize the error rates of each Taq pol variant according to its amplification activity, the individual amplification and doubling numbers of each enzyme were included in the calculation.
Each error rate for each position in the template was divided by the individual doubling number and plotted using Microsoft excel software
Assembly: SARS-CoV-2 RNA reverse transcript in DNA for reference: ACTGCTGCAATATTGTTAACGTATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAGTAACCAGA
Supplementary files format and content: excel-files include position, reference RNA sequence and error rates
Library strategy: DNA Amplicon-Seq

molecule: other

organism: Severe acute respiratory syndrome coronavirus 2

source_name: in vitro synthesized (purchased from European Commission Joint Research Centre (EURM-019))

extract_protocol:
in vitro SARS-CoV-2 RNA was purchased from European Commission Joint Research Centre (EURM-019)
RT-PCR with Taq pol variants was conducted similarly to the RT-PCR screening approach using purified enzymes. 10 µL reaction mix contained 250 μM dNTPs (each), 670 nM forward and reverse primer (each, giving the 100 bp transcript from the nCov_N1 gene, Supplementary Table S1), 0.5 M betaine, 100 nM Taq pol aptamer, 30 nM respective Taq pol variant, 10.000 copies of SARS-CoV-2 RNA template in 1x Taq reaction buffer (50 mM Tris-HCl (pH 9.2), 16 mM (NH4)2SO4, 2.5 mM MgCl2, 0.1% (v/v) Tween 20). After preincubation at 61°C for 150 s, 10 cycles with 95°C for 5 s and 61°C for 150 s were carried out. Then, 35 cycles with 95°C for 10 s and 57°C for 35 s followed.
To determine the DNA product concentration, each reaction mix was analysed by using the 4150 TapeStation System (Agilent), High Sensitivity D1000 ScreenTapes (Agilent) and High Sensitivity D1000 Reagents (Agilent). Sample preparation and measurement was carried out according to the guidelines of the company. Each reaction was loaded twice and 1 ng of a 100 bp reference DNA with the same sequence was applied as a control. Afterwards, remaining reaction mix was purified by agarose gel electrophoresis (2.5% agarose gel in 1x TAE buffer), excision of the respective band and applying the NucleoSpin Gel and PCR clean-up kit XS (Macherey-Nagel). Elution was achieved by adding 7 µL elution buffer to the column (for better recovery, elution was loaded again). DNA concentration was determined by using the 4150 TapeStation System (Agilent) as described above. In the next step, DNA was repaired by using 0.35 nM purified DNA, 0.1 µL PreCR Repair mix (NEB) with 100 µM of dNTP (each), 1x NAD+ (provided by the manufacturer) and 1x ThermoPol reaction buffer (NEB) to reach 20 µL reaction volume. Repair was performed at 37°C for 20 min. Unique molecular identifier (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 (each) 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 purified by agarose gel electrophoresis as described above. This time, buffer NTI was diluted with Milli-Q water in a ratio of 2:1 and then used for dissolving gel pieces at 50°C. DNA concentration was determined with a qPCR approach, where an DNA oligonucleotide with a similar length was applied as reference in different template concentrations. 1x NEBNext Ultra II Q5 Mastermix (NEB) was used for PCR with 1.6 µL DNA, 400 nM forward and reverse primer (each), 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 for 10 s, 60°C for 30 s and 72°C for 30 s and a final elongation step with 72°C for 2 min was conducted. Fluorescent intensity was measured after each of the 35 cycles and melting curves were determined at the end of the reaction. For analysis, Cq values of reactions with reference DNA were plotted against the decadic logarithm of the template concentrations and linear regression was employed. DNA concentrations of samples to be analysed were calculated using the linear predictor function. Results were multiplied by two. DNA was repaired once again by using 0.05 µL PreCR mix (NEB), 1x NAD+, 100 µM of dNTP (each), 48.9 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 22 fM) and 1x NEBNext Ultra II Q5 Mastermix (NEB) was used for reaction in 25 µL end volume. After an initial denaturation step at 98°C for 5 min, a three-step cycling protocol with 35 PCR cycles followed with 98°C for 10 s, 70°C for 30 s and 72°C for 30 s and a final elongation step at 72°C for 2 min was conducted. Reaction was analysed 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, the mixture was diluted 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 (load twice). After performing the repair reaction on the whole eluate as described above (25 µL reaction volume), DNA was purified by using the QIAEX II System (Qiagen). Here, 2 µL particle slurry was used for each sample and elution of DNA was achieved by adding 18 µL Milli-Q water 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 ranged between 19–64 nM. After quality control with Bioanalyzer 2100 (Agilent), DNA libraries were pooled and sequenced in paired-end mode (2*75 bp) on an IIlumina NextSeq 2000 instrument.


title: error rates from Taq pol V3 processing SAR-CoV-2 RNA

description: (2*75 bp)

value: in vitro synthesized (purchased from European Commission Joint Research Centre (EURM-019))


title: Tumor-23

source_name: colorectal cancer patient #23

value: Male

value: Stage IIIC

value: Grade III

value: Right


title: 300mM_Manital_A

value: Whole seedling


title: 6B_DAC_060320, RNA

source_name: Peripheral blood

value: Acute promyelocytic leukemia

tag: Sex


title: Tumor-22

source_name: colorectal cancer patient #22

value: FFPE

value: tumor

value: Left


title: 150mM_salt_C

value: 150mM salt


title: 150mM_salt_B


title: error rates from Mut_RT processing SAR-CoV-2 RNA

description: (2*75 bp)


title: 6A_DAC_060320, RNA

value: Peripheral blood

tag: age


title: 150mM_salt_A


title: Tumor-20

source_name: colorectal cancer patient #20

value: Stage IIA

value: no death


title: 250nM_Flg22_C

value: 250nM Flg22


title: 5G_AZA_060320, RNA

value: promyeloblast

value: Female

tag: batch

value: azacytidine


title: error rates from RT-Taq processing SAR-CoV-2 RNA

description: (2*75 bp)

value: in vitro synthesized (purchased from European Commission Joint Research Centre (EURM-019))


title: 5F_AZA_060320, RNA


title: ARC tissue from subject KM212

city: New Brunswick

first: Kevin

last: Moran

state: NJ

address: 84 Lipman Drive, Bartlett Hall Room 305B

institute: Rutgers University

description:
Library name: ARC212
library name reflects column name in rnaseq_counts_ham.csv

data_processing:
remove reads with a homo-polymer run of “A” ≥ 8 bases and retain reads with minimum 20 bases and remove PCR duplicates.
Processed reads were then mapped to the annotated BCM_Maur_2.0 Mesocricetus auratus genome using Bowtie2 and STAR (Dobin et al., 2013; Harris et al., 2022).
Assembly: BCM_Maur_2.0 Mesocricetus auratus genome
Supplementary files format and content: processed reads csv file provide raw counts of all transcripts

organism: Mesocricetus auratus

source_name: arcuate nucleus of the hypothalamus (ARC)

extract_protocol:
Samples were homogenized in 100 μl lysis buffer (Thermo Fisher Scientific, Waltham, MA; MagMax Total RNA isolation kit, Cat. No. A27828) with 0.7% beta-mercaptoethanol by vortexing at 3000 rpm speed for 15–20 s. Lysates were incubated at room temperature for 5 min and stored at − 80°C until RNA extraction. Once dissection of all individuals was completed, we proceed to RNA extraction using the KingFisher Flex (Thermo Fisher Scientific, Cat. No. 5400630l) with an additional DNase step to remove DNA contamination added according to the manufacturer's protocol. Samples from each brain region of all animals were extracted in the same batch. RNA quality was determined using RNA 6000 Nano Assay with BioAnalyzer (Agilent Technologies, Santa Clara, CA) and RNA concentration was determined with Quant-it RNA High Sensitivity assay kit (Thermo Fisher Scientific, Cat. No. Q33140). RNA samples were normalized to 100 ng/μl and stored at − 80°C before sequencing.
All samples were processed in the same batch throughout the process. Libraries were constructed with a protocol modified from (Meyer et al., 2011) and (Lohman et al., 2016). Reads were sequenced on the NovaSeq 6000 SR100 with minimum reads of 4 million and the target reads per sample of 5 million.

tag: genotype

value: WT

value: control


title: Tumor-19

source_name: colorectal cancer patient #19

tag: tissue type

value: Stage IIIC

value: Grade III

value: death


title: 300mM_Manital_B

value: Whole seedling

value: 300mM Manital


title: 250nM_Flg22_B


title: Tumor-18

source_name: colorectal cancer patient #18

value: FFPE

value: tumor

tag: gender

value: Male

value: Grade II

value: Right


title: 6C_DAC_060320, RNA

value: Peripheral blood

value: Acute promyelocytic leukemia

value: decitabine


title: 250nM_Flg22_A

tag: ecotype

value: 250nM Flg22


title: 5D_DAC_060320, RNA

value: promyeloblast

value: Female


title: 5E_AZA_060320, RNA

value: azacytidine


title: DMH tissue from subject KM212

description:
Library name: DMH212
library name reflects column name in rnaseq_counts_ham.csv

source_name: dorsomedial hypothalamus (DMH)

value: dorsomedial hypothalamus (DMH)

value: WT

value: control


title: error rates from Taq pol V2 processing SAR-CoV-2 RNA

description: (2*75 bp)

value: in vitro synthesized (purchased from European Commission Joint Research Centre (EURM-019))


title: Mock_C

value: Whole seedling

value: Mock


title: Tumor-21

source_name: colorectal cancer patient #21

value: FFPE

value: tumor

tag: tumor stage

value: Stage IIA

value: Left

value: death


title: DMH tissue from subject KM211

description:
Library name: DMH211
library name reflects column name in rnaseq_counts_ham.csv

value: stress


title: Tumor-16

source_name: colorectal cancer patient #16

value: Male

tag: grade

value: Grade II

value: no death


title: 5H_AZA_060320, RNA

value: Peripheral blood

value: promyeloblast

value: Acute promyelocytic leukemia

value: Female


title: Tumor-15

source_name: colorectal cancer patient #15

value: Stage IIIB

value: Grade I

tag: localization


title: Mock_B

source_name: Whole seedling

value: Whole seedling


title: LH tissue from subject KM211

description:
Library name: LH211
library name reflects column name in rnaseq_counts_ham.csv

source_name: lateral hypothalamus (LH)

value: lateral hypothalamus (LH)

value: WT


title: Mock_A

value: Mock


title: Tumor-14

source_name: colorectal cancer patient #14

value: FFPE

value: tumor

value: Stage I

value: Grade III

tag: overall survival time


title: ARC tissue from subject KM210

description:
Library name: ARC210
library name reflects column name in rnaseq_counts_ham.csv

tag: tissue

value: arcuate nucleus of the hypothalamus (ARC)

value: stress


title: Tumor-13

source_name: colorectal cancer patient #13

value: Male

value: Grade II

value: Left

value: no death


title: 5A_DAC_060320, RNA

value: Peripheral blood

value: promyeloblast

value: Acute promyelocytic leukemia

value: Female

tag: treatment

value: decitabine


title: 4H_AZA_060320, RNA

tag: cell type

value: azacytidine


title: LH tissue from subject KM212

description:
Library name: LH212
library name reflects column name in rnaseq_counts_ham.csv

value: lateral hypothalamus (LH)

value: WT

value: control


title: hnRNPA1_KO_rep2

city: Sendai city

first: Yasuaki

last: Watanabe

state: Miyagi

address: 2-1, Seiryo-machi

department: Neurology

institute: Tohoku University

description: Library name: hnRNPA1KO_2

data_processing:
Reads trimmed with Trim_Galore to remove adapters and low-quality bases
Trimmed reads aligned to GRCh38 genome using STAR aligner.
Differential gene expression analyzed using DESeq2.
Gene Ontology and pathway analysis performed using iDEP software.
Assembly: GRCh38
Supplementary files format and content: Format: Tab-separated values (TSV) Content: Gene-level raw read counts obtained using featureCounts from RNA-seq data. Each row represents a gene (GENCODE gene ID), and each column corresponds to a sample. Read counts were derived from BAM files aligned to the GRCh38 reference genome.

growth_protocol: SH-SY5Y WT and RNA-binding protein (RBP)-knockout (KO) cells cultured in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 1% MEM–nonessential amino acids, and 1% sodium pyruvate, at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA extracted using Promega SV Total RNA Isolation System.
Illumina TruSeq Standard mRNA LT Sample Prep Kit used for RNA-seq library preparation following manufacturer's instructions.

tag: cell line

value: Neuroblastoma

value: hnRNPA1 KO


title: Tumor-17

source_name: colorectal cancer patient #17

value: FFPE

value: tumor

value: Stage IIA


title: Tumor-12

source_name: colorectal cancer patient #12

value: Stage I

value: Grade II


title: hnRNPA1_KO_rep1

description: Library name: hnRNPA1KO_1


title: DMH tissue from subject KM210

description:
Library name: DMH210
library name reflects column name in rnaseq_counts_ham.csv

value: dorsomedial hypothalamus (DMH)

value: stress


title: LH tissue from subject KM210

description:
Library name: LH210
library name reflects column name in rnaseq_counts_ham.csv


title: ARC tissue from subject KM211

description:
Library name: ARC211
library name reflects column name in rnaseq_counts_ham.csv

value: arcuate nucleus of the hypothalamus (ARC)


title: FUS_KO_rep2

description: Library name: FUSKO_2

value: FUS KO


title: Tumor-11

source_name: colorectal cancer patient #11

value: Female

value: Left

value: no death


title: 4G_AZA_060320, RNA

source_name: Peripheral blood

value: Peripheral blood

value: promyeloblast

tag: disease/cancer type

value: Acute promyelocytic leukemia

value: azacytidine


title: 4F_AZA_060320, RNA


title: ARC tissue from subject KM209

description:
Library name: ARC209
library name reflects column name in rnaseq_counts_ham.csv

value: WT

value: control


title: FUS_KO_rep1

description: Library name: FUSKO_1

value: Neuroblastoma


title: 4E_AZA_060320, RNA


title: 5C_DAC_060320, RNA

value: decitabine


title: 5B_DAC_060320, RNA


title: Tumor-9

source_name: colorectal cancer patient #9

value: FFPE

value: tumor

value: Stage IIIA

tag: overall_event (death from any cause)


title: MATR3_KO_rep2

description: Library name: MATR3KO_2

value: MATR3 KO


title: 4D_DAC_060320, RNA

tag: Sex


title: MATR3_KO_rep1

description: Library name: MATR3KO_1


title: LH tissue from subject KM209

description:
Library name: LH209
library name reflects column name in rnaseq_counts_ham.csv

value: lateral hypothalamus (LH)


title: Tumor-8

source_name: colorectal cancer patient #8

value: Stage IIIB

value: Grade II


title: 4C_DAC_060320, RNA

value: Female

tag: age


title: ARC tissue from subject KM208

description:
Library name: ARC208
library name reflects column name in rnaseq_counts_ham.csv

source_name: arcuate nucleus of the hypothalamus (ARC)


title: Tumor-7

source_name: colorectal cancer patient #7

value: Stage I

value: Left


title: Tumor-6

source_name: colorectal cancer patient #6

value: Male

value: Stage IIA

value: no death


title: DMH tissue from subject KM208

description:
Library name: DMH208
library name reflects column name in rnaseq_counts_ham.csv

source_name: dorsomedial hypothalamus (DMH)

value: dorsomedial hypothalamus (DMH)

value: WT


title: 4B_DAC_060320, RNA

value: Peripheral blood

value: promyeloblast

value: Acute promyelocytic leukemia

tag: batch


title: TDP43_KO_rep1

description: Library name: TARDBPKO_1

value: Neuroblastoma

tag: genotype

value: TDP-43 KO


title: 4A_DAC_060320, RNA

value: decitabine


title: WT_rep2

description: Library name: WT_2


title: LH tissue from subject KM208

description:
Library name: LH208
library name reflects column name in rnaseq_counts_ham.csv

value: lateral hypothalamus (LH)

value: control


title: ARC tissue from subject KM207

description:
Library name: ARC207
library name reflects column name in rnaseq_counts_ham.csv

value: arcuate nucleus of the hypothalamus (ARC)


title: WT_rep1

description: Library name: WT_1


title: Tumor-4

description: Gene expression data from 49 colorectal cancer patients and paired normal FFPE tissues

source_name: colorectal cancer patient #4

value: FFPE

tag: tissue type

value: tumor

value: Stage IIIB

value: Grade III

value: Right

value: death


title: Tumor-5

source_name: colorectal cancer patient #5

tag: gender

value: Female

value: Stage IIIC

value: Grade II

value: Left


title: Tumor-10

source_name: colorectal cancer patient #10

value: Stage I


title: 3G_AZA_060320, RNA

value: Peripheral blood

value: promyeloblast

value: Acute promyelocytic leukemia

value: azacytidine


title: DMH tissue from subject KM209

description:
Library name: DMH209
library name reflects column name in rnaseq_counts_ham.csv

value: dorsomedial hypothalamus (DMH)

value: WT

value: control


title: 3H_AZA_060320, RNA


title: RNAseq UL3 dH1 cloneB Rep2

city: Research Triangle Park

first: Nolan

middle: Garrity

last: Gokey

state: North Carolina

address: 111 TW Alexander Dr, Building 101 Room C432

department: DIR

institute: NIEHS

description:
Library name: Sample 6
RNAseq

data_processing:
Adapter sequences were trimmed from reads using Cutadapt (Martin 2011) and low quality reads were removed.
RNA-seq reads were mapped to the human reference genome (T2Tv2) using STAR (Dobin et al., 2013) with default parameters.
Gene counts and differential expression analysis
were performed using Salmon (Patro, Duggal et al. 2017))
Replicates were depth normalized based on Salmon size-factors and merged with Bedtools Quinlan, A. R. and I. M. Hall (2010).
Assembly: T2Tv2
Supplementary files format and content: bigwig files

source_name: human osteosarcoma cell line

growth_protocol: All cell lines were cultured in DMEM medium (Gibco, Grand Island, NY, USA), supplemented with 10% fetal bovine serum (Atlanta Biologicals, Atlanta, GA, USA), and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
RNA isolated using using TRIzol (Invitrogen) and ethanol precipiated.
Libraries were generated using the Ribo-Zero Gold and the TruSeq Stranded Total RNA library kit according to manufacturer's instructions (Illumina) at Expression Analysis (Durham, NC).

treatment_protocol: Live cells were pulsed with 4-thio-uracil for 10min

value: human osteosarcoma cell line

value: UL3 cells

value: osteosarcoma

value: vehicle


title: LH tissue from subject KM207

description:
Library name: LH207
library name reflects column name in rnaseq_counts_ham.csv

source_name: lateral hypothalamus (LH)

value: lateral hypothalamus (LH)


title: Tumor-3

source_name: colorectal cancer patient #3

value: FFPE

value: tumor

value: Male

value: Stage IIA

value: Grade III

value: Right

value: no death


title: 3F_AZA_060320, RNA

value: Peripheral blood

value: promyeloblast

value: Acute promyelocytic leukemia

value: Female


title: Tumor-2

source_name: colorectal cancer patient #2

value: Stage IIC

value: Grade I

value: Left


title: RNAseq UL3 dH1 cloneB Rep1

description:
Library name: Sample 5
RNAseq

value: human osteosarcoma cell line

value: UL3 cells

value: osteosarcoma


title: ARC tissue from subject KM206

description:
Library name: ARC206
library name reflects column name in rnaseq_counts_ham.csv

value: arcuate nucleus of the hypothalamus (ARC)

value: WT

value: stress


title: RNAseq UL3 dH1 cloneA Rep2

description:
Library name: Sample 4
RNAseq

value: vehicle


title: Tumor-1

source_name: colorectal cancer patient #1

value: FFPE

value: tumor

value: Stage IIIB

value: Grade III


title: TDP43_KO_rep2

description: Library name: TARDBPKO_2

value: Neuroblastoma

value: TDP-43 KO


title: 3D_DAC_060320, RNA

value: Peripheral blood

value: promyeloblast

value: Acute promyelocytic leukemia

value: Female

value: decitabine


title: RNAseq UL3 dH1 cloneA Rep1

description:
Library name: Sample 3
RNAseq

value: human osteosarcoma cell line

value: UL3 cells


title: DMH tissue from subject KM206

description:
Library name: DMH206
library name reflects column name in rnaseq_counts_ham.csv

value: dorsomedial hypothalamus (DMH)


title: Paired normal-49

source_name: Paired normal tissue of colorectal cancer patient #49

value: normal


title: 3C_DAC_060320, RNA


title: LH tissue from subject KM206

description:
Library name: LH206
library name reflects column name in rnaseq_counts_ham.csv

value: lateral hypothalamus (LH)

value: WT

value: stress


title: Paired normal-48

source_name: Paired normal tissue of colorectal cancer patient #48

value: FFPE


title: 3B_DAC_060320, RNA

source_name: Peripheral blood


title: ARC tissue from subject KM205

description:
Library name: ARC205
library name reflects column name in rnaseq_counts_ham.csv

value: arcuate nucleus of the hypothalamus (ARC)


title: Paired normal-47

source_name: Paired normal tissue of colorectal cancer patient #47


title: RNAseq UL3 Rep1

description:
Library name: Sample 1
RNAseq

value: osteosarcoma

value: wild-type

value: vehicle


title: 3A_DAC_060320, RNA

value: Peripheral blood


title: DMH tissue from subject KM207

description:
Library name: DMH207
library name reflects column name in rnaseq_counts_ham.csv

value: control


title: DMH tissue from subject KM205

description:
Library name: DMH205
library name reflects column name in rnaseq_counts_ham.csv


title: 2H_AZA_060320, RNA

value: promyeloblast

value: Acute promyelocytic leukemia

value: azacytidine


title: Paired normal-46

source_name: Paired normal tissue of colorectal cancer patient #46

value: Male


title: 4sUseq UL3 dH1 cloneB Rep2

description:
Library name: Sample 6
4sU-nascent-RNAseq

extract_protocol:
then RNA isolated using using TRIzol (Invitrogen), Dnase digested (NEB), the nascent RNAs biotinylated (Biotonium)and nascent RNA's captured on streptavidin magnetic beads (Promega).
Libraries were generated using the Ribo-Zero Gold and the TruSeq Stranded Total RNA library kit according to manufacturer's instructions (Illumina) at Expression Analysis (Durham, NC).

value: human osteosarcoma cell line

value: UL3 cells


title: 3E_AZA_060320, RNA

value: Female


title: 4sUseq UL3 dH1 cloneB Rep1

description:
Library name: Sample 5
4sU-nascent-RNAseq


title: 2G_AZA_060320, RNA


title: LH tissue from subject KM205

description:
Library name: LH205
library name reflects column name in rnaseq_counts_ham.csv

value: lateral hypothalamus (LH)


title: Paired normal-44

source_name: Paired normal tissue of colorectal cancer patient #44

value: normal


title: 4sUseq UL3 dH1 cloneA Rep2

description:
Library name: Sample 4
4sU-nascent-RNAseq


title: Paired normal-45

source_name: Paired normal tissue of colorectal cancer patient #45


title: ARC tissue from subject KM204

description:
Library name: ARC204
library name reflects column name in rnaseq_counts_ham.csv

source_name: arcuate nucleus of the hypothalamus (ARC)

value: WT


title: 2F_AZA_060320, RNA


title: DMH tissue from subject KM204

description:
Library name: DMH204
library name reflects column name in rnaseq_counts_ham.csv

source_name: dorsomedial hypothalamus (DMH)

value: dorsomedial hypothalamus (DMH)


title: Paired normal-43

source_name: Paired normal tissue of colorectal cancer patient #43

value: FFPE


title: Paired normal-42

source_name: Paired normal tissue of colorectal cancer patient #42


title: LH tissue from subject KM204

description:
Library name: LH204
library name reflects column name in rnaseq_counts_ham.csv


title: 2E_AZA_060320, RNA


title: RNAseq UL3 Rep2

description:
Library name: Sample 2
RNAseq

value: osteosarcoma


title: 2D_DAC_060320, RNA

value: decitabine


title: ARC tissue from subject KM203

description:
Library name: ARC203
library name reflects column name in rnaseq_counts_ham.csv

value: arcuate nucleus of the hypothalamus (ARC)

value: stress


title: 4sUseq UL3 Rep1

description:
Library name: Sample 1
4sU-nascent-RNAseq

value: wild-type

value: vehicle


title: Paired normal-41

description: Gene expression data from 49 colorectal cancer patients and paired normal FFPE tissues

source_name: Paired normal tissue of colorectal cancer patient #41


title: 2C_DAC_060320, RNA

value: Peripheral blood

value: promyeloblast

value: Acute promyelocytic leukemia


title: Paired normal-40

source_name: Paired normal tissue of colorectal cancer patient #40

value: Male


title: DMH tissue from subject KM203

description:
Library name: DMH203
library name reflects column name in rnaseq_counts_ham.csv


title: 2B_DAC_060320, RNA


title: LH tissue from subject KM203

description:
Library name: LH203
library name reflects column name in rnaseq_counts_ham.csv

source_name: lateral hypothalamus (LH)


title: Paired normal-38

source_name: Paired normal tissue of colorectal cancer patient #38


title: ES114, WT, rep3, input

city: Bloomington

first: Center for Genomics and Bioinformatics

last: IU

address: 1001 E Third St

department: Biology

institute: Center for Genomics and Bioinformatics

description: Library name: WGS_WT_rep3

library_source: genomic

data_processing:
Adapters and low quality bases were trimmed using fastp version 0.21.0 with following specific parameters "-l 25 --detect_adapter_for_pe -g -p "
Reads were mapped to GCF_000011805.1 - Aliivibrio fischeri ES114 genome sequence using bowtie2 version 2.3.5.1.
The over replication of DNA around the origin was addressed and the background from the controls was removed using custom scripts indicated in the manuscript.
The peak calls were made using the callpeak command of MACS2 version v2.2.9.1. The peak comparison was made across the following contrasts: WT vs litR, qrr1 vs litR and qrr1 vs WT.
Assembly: GCF_000011805.1 - Aliivibrio fischeri ES114
Supplementary files format and content: Tab delimited text files reporting peakcalls by MACS version 2.2.9.1

molecule: genomic DNA

organism: Aliivibrio fischeri

source_name: Bacteria

growth_protocol: 50 ml cultures of cells were grown shaking at 24°C in LBS + 10 mM CaCl2 until they reached an OD600 of 1.0

extract_protocol:
For the whole genome sequencing (WGS; input) samples, a 3 ml aliquot was pelleted before crosslinking and gDNA was extracted using the ThermoFisher GeneJet DNA Purification Kit. The DNA was diluted to 10 ng/µl in 100 µl of elution buffer and sonicated at 4°C twice with a Qsonica Q800R2 Water Bath Sonicator at 20% amplitude with continuous pulses. WGS samples were stored at -20°C until library preparation. The remaining cultures (47 ml) (immunoprecipitation (IP) samples) were crosslinked by adding 1% formaldehyde (Fisher Scientific) and rocked for 30 min at room temperature. The reactions were quenched with 0.5 M glycine and rocked for 5 min at room temperature. Cultures were pelleted at 4°C, washed 2 times with 1 ml cold 1x TBS, frozen with liquid nitrogen, and stored at -80°C until needed. During lysis, pellets were resuspended in ChIP Solution A (12.5 mM Tris pH 8, 12.5 mM EDTA, 62.5 mM NaCl, 25% sucrose, 1 mM PMSF) with 1 mg/ml lysozyme for 45 min at 37°C. An equal volume of 2x IP Buffer was added to the solution followed by 1 mM PMSF and 1x Protease Inhibitor Cocktail. Samples were sonicated twice for 20 min at 70% amplitude with 10 sec on/off pulses and then centrifuged to clear cell debris. Sonicated lysates were pre-cleared by rotating for 1 h at 4°C using 50 µl washed Protein A Magnetic Sepharose beads (Cytiva #28967062). Pre-cleared lysates were incubated with 4 µl anti-LuxR (V. campbellii) and rotated overnight at 4°C. The next day, 50 µl Protein A magnetic beads were added to the lysate-antibody mixtures and rotated for 1 h at 4°C. The resin was washed 3 times with 1x IP Buffer, 3 times with Wash Buffer, once with 1x TE, and eluted with TES at 65°C for 20 min. Crosslinks were reversed at 65°C overnight and then treated with 0.2 mg/ml RNaseA (NEB #T3018L) and 0.2 mg/ml Proteinase K (NEB #P8107S). DNA was extracted using a phenol:chloroform:isoamyl alcohol (25:24:1) mixture with ethanol precipitation, then purified using AmpureXP beads (Beckman Coulter, Inc.).
WGS and IP libraries were prepared for Illumina NextSeq550 high-throughput paired-end sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645)

value: Bacteria

tag: strain


title: Paired normal-39

source_name: Paired normal tissue of colorectal cancer patient #39

tag: tumor stage


title: ARC tissue from subject KM202

description:
Library name: ARC202
library name reflects column name in rnaseq_counts_ham.csv


title: DMH tissue from subject KM202

description:
Library name: DMH202
library name reflects column name in rnaseq_counts_ham.csv


title: 2A_DAC_060320, RNA

value: Female


title: 1H_Unt_060320, RNA

value: untreated


title: 4sUseq UL3 dH1 cloneA Rep1

description:
Library name: Sample 3
4sU-nascent-RNAseq

source_name: human osteosarcoma cell line

value: human osteosarcoma cell line

value: UL3 cells


title: Paired normal-37

source_name: Paired normal tissue of colorectal cancer patient #37

value: normal

tag: grade


title: 1G_Unt_060320, RNA

source_name: Peripheral blood


title: ES114, WT, rep3, ChIP

description: Library name: antiLuxR_WT_rep3

value: WT

tag: chip antibody

value: anti-LuxR (Vibrio campbellii strain ATCC BAA-1116)


title: 4sUseq UL3 Rep2

description:
Library name: Sample 2
4sU-nascent-RNAseq

value: osteosarcoma


title: Paired normal-36

source_name: Paired normal tissue of colorectal cancer patient #36

value: FFPE

tag: localization

tag: overall survival time


title: Paired normal-35

source_name: Paired normal tissue of colorectal cancer patient #35

tag: tissue


title: ES114, WT, rep2, ChIP

description: Library name: antiLuxR_WT_rep2

tag: cell type


title: LH tissue from subject KM202

description:
Library name: LH202
library name reflects column name in rnaseq_counts_ham.csv

value: lateral hypothalamus (LH)

tag: treatment

value: stress


title: 1F_Unt_060320, RNA

tag: cell line

tag: disease/cancer type


title: Paired normal-34

source_name: Paired normal tissue of colorectal cancer patient #34

tag: overall_event (death from any cause)


title: ARC tissue from subject KM201

description:
Library name: ARC201
library name reflects column name in rnaseq_counts_ham.csv

value: arcuate nucleus of the hypothalamus (ARC)

value: control


title: ES114, WT, rep1, input

description: Library name: WGS_WT_rep1


title: 1E_Unt_060320, RNA

value: Peripheral blood

value: promyeloblast

tag: Sex

tag: age


title: DMH tissue from subject KM201

description:
Library name: DMH201
library name reflects column name in rnaseq_counts_ham.csv

value: dorsomedial hypothalamus (DMH)

tag: genotype


title: 1D_Unt_060320, RNA

value: Acute promyelocytic leukemia

tag: batch


title: Paired normal-33

source_name: Paired normal tissue of colorectal cancer patient #33

tag: tissue type

tag: gender

value: Female


title: LH tissue from subject KM201

description:
Library name: LH201
library name reflects column name in rnaseq_counts_ham.csv


title: ES114, WT, rep1, ChIP

description: Library name: antiLuxR_WT_rep1

value: Bacteria

tag: strain


title: 1C_Unt_060320, RNA

value: untreated


title: Paired normal-32

source_name: Paired normal tissue of colorectal cancer patient #32

value: Male

tag: tumor stage

tag: grade


title: ES114, Dqrr1, rep3, input

description: Library name: WGS_dqrr1_rep3


title: ARC tissue from subject KM200

description:
Library name: ARC200
library name reflects column name in rnaseq_counts_ham.csv

source_name: arcuate nucleus of the hypothalamus (ARC)


title: ES114, WT, rep2, input

description: Library name: WGS_WT_rep2


title: 1B_Unt_060320, RNA


title: DMH tissue from subject KM200

description:
Library name: DMH200
library name reflects column name in rnaseq_counts_ham.csv

source_name: dorsomedial hypothalamus (DMH)


title: Paired normal-31

source_name: Paired normal tissue of colorectal cancer patient #31

value: normal

tag: localization


title: 1A_Neg_060320, RNA


title: ES114, Dqrr1, rep2, input

description: Library name: WGS_dqrr1_rep2


title: LH tissue from subject KM200

description:
Library name: LH200
library name reflects column name in rnaseq_counts_ham.csv

value: WT


title: 12H_Neg_060320, RNA


title: ES114, Dqrr1, rep3, ChIP

description: Library name: antiLuxR_dqrr1_rep3

tag: chip antibody

value: anti-LuxR (Vibrio campbellii strain ATCC BAA-1116)


title: ARC tissue from subject KM199

description:
Library name: ARC199
library name reflects column name in rnaseq_counts_ham.csv

tag: tissue


title: The change of mRNA levels upoon puromycin treatment, replicate 2

first: Yoon Ki

last: Kim

address: Anam-ro 145, Seongbuk-gu

institute: Korea University

description:
Puro_2
Biological replicate 2 of 2

hyb_protocol: The synthesis of target cRNA probes and hybridization were performed using Agilent's Low RNA Input Linear Amplification kit (Agilent Technology, USA) according to manufacturer's instructions.

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner

data_processing: Quantification was performed by Feature Extraction Software (Agilent Technology, Palo Alto, CA), and analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

growth_protocol: HeLa cells were grown with Dulbecco’s Modified Eagles Medium (HyClone) supplemented with 10% (vol/vol) fetal bovine serum (HyClone) and 1% (vol/vol) penicillin/streptomycin (HyClone)

extract_protocol: Total RNAs were extracted using Trizol as manufacturer's instructions

treatment_protocol: HeLa cells were treated or untreated with 400 ug/ml puromycin for 12 h before harvesting

value: HeLa

tag: treated with

value: none (untreated)

source_name: HeLa_Puromycin treated

value: 400 ug/ml puromycin for 12 h


title: Paired normal-30

source_name: Paired normal tissue of colorectal cancer patient #30

value: FFPE

tag: overall survival time


title: Paired normal-29

source_name: Paired normal tissue of colorectal cancer patient #29


title: The change of mRNA levels upoon puromycin treatment, replicate 1

description:
Puro_1
Biological replicate 1 of 2

label_protocol: The synthesis of target cRNA probes and hybridization were performed using Agilent's Low RNA Input Linear Amplification kit (Agilent Technology, USA) according to manufacturer's instructions.

tag: cell line


title: ES114, Dqrr1, rep2, ChIP

description: Library name: antiLuxR_dqrr1_rep2

tag: cell type


title: 12G_Unt_060320, RNA

tag: disease/cancer type

tag: treatment


title: Paired normal-28

source_name: Paired normal tissue of colorectal cancer patient #28

tag: overall_event (death from any cause)


title: ES114, Dqrr1, rep1, input

description: Library name: WGS_dqrr1_rep1

source_name: Bacteria

tag: genotype


title: DMH tissue from subject KM199

description:
Library name: DMH199
library name reflects column name in rnaseq_counts_ham.csv

value: stress


title: ES114, Dqrr1, rep1, ChIP

description: Library name: antiLuxR_dqrr1_rep1


title: LH tissue from subject KM199

description:
Library name: LH199
library name reflects column name in rnaseq_counts_ham.csv

source_name: lateral hypothalamus (LH)

value: lateral hypothalamus (LH)


title: Paired normal-27

description: Gene expression data from 49 colorectal cancer patients and paired normal FFPE tissues

source_name: Paired normal tissue of colorectal cancer patient #27


title: 12E_Unt_060320, RNA

value: Peripheral blood

tag: Sex

tag: age

tag: batch


title: Paired normal-25

source_name: Paired normal tissue of colorectal cancer patient #25

tag: tissue type

tag: gender


title: 12B_Unt_060320, RNA

source_name: Peripheral blood

value: promyeloblast


title: Paired normal-26

source_name: Paired normal tissue of colorectal cancer patient #26

tag: tumor stage

tag: grade


title: Paired normal-24

source_name: Paired normal tissue of colorectal cancer patient #24

tag: localization


title: ARC tissue from subject KM197

description:
Library name: ARC197
library name reflects column name in rnaseq_counts_ham.csv

tag: tissue

value: arcuate nucleus of the hypothalamus (ARC)


title: ES114, DlitR, rep2, input

description: Library name: WGS_dlitR_rep2

tag: strain

value: DlitR


title: ARC tissue from subject KM198

description:
Library name: ARC198
library name reflects column name in rnaseq_counts_ham.csv

value: control


title: ES114, DlitR, rep3, ChIP

description: Library name: antiLuxR_dlitR_rep3

value: Bacteria

tag: chip antibody


title: 12D_Unt_060320, RNA

tag: cell line

value: Acute promyelocytic leukemia

value: Female

value: untreated


title: LH tissue from subject KM198

description:
Library name: LH198
library name reflects column name in rnaseq_counts_ham.csv

value: WT


title: DMH tissue from subject KM198

description:
Library name: DMH198
library name reflects column name in rnaseq_counts_ham.csv

value: dorsomedial hypothalamus (DMH)


title: 12C_Unt_060320, RNA

tag: cell type


title: ES114, DlitR, rep2, ChIP

description: Library name: antiLuxR_dlitR_rep2

value: anti-LuxR (Vibrio campbellii strain ATCC BAA-1116)


title: DMH tissue from subject KM197

description:
Library name: DMH197
library name reflects column name in rnaseq_counts_ham.csv


title: ES114, DlitR, rep3, input

description: Library name: WGS_dlitR_rep3


title: 11G_AZA_060320, RNA

tag: disease/cancer type

value: azacytidine


title: Paired normal-23

source_name: Paired normal tissue of colorectal cancer patient #23

value: normal

value: Male

tag: overall survival time


title: 11H_AZA_060320, RNA

tag: treatment


title: LH tissue from subject KM197

description:
Library name: LH197
library name reflects column name in rnaseq_counts_ham.csv

tag: genotype

value: stress


title: ES114, DlitR, rep1, input

description: Library name: WGS_dlitR_rep1


title: 12A_Unt_060320, RNA

tag: Sex


title: ES114, DlitR, rep1, ChIP

description: Library name: antiLuxR_dlitR_rep1


title: Paired normal-20

source_name: Paired normal tissue of colorectal cancer patient #20

value: FFPE

tag: overall_event (death from any cause)


title: 12F_Unt_060320, RNA

value: Peripheral blood

tag: age

tag: batch


title: DMH tissue from subject KM196

description:
Library name: DMH196
library name reflects column name in rnaseq_counts_ham.csv


title: 11F_AZA_060320, RNA

value: promyeloblast


title: Paired normal-21

source_name: Paired normal tissue of colorectal cancer patient #21

tag: tissue type

tag: gender


title: ARC tissue from subject KM196

description:
Library name: ARC196
library name reflects column name in rnaseq_counts_ham.csv

source_name: arcuate nucleus of the hypothalamus (ARC)


title: Paired normal-22

source_name: Paired normal tissue of colorectal cancer patient #22

tag: tumor stage

tag: grade


title: Paired normal-19

source_name: Paired normal tissue of colorectal cancer patient #19

tag: tissue

tag: localization


title: Pregnant smoke exposure 12

city: Utrecht

first: Ali

last: dehghani

state: - None -

address: Jonkvrouw Sanderijndreef 1113

country: Netherlands

institute: utrecht university

description: Library name: SP_12

data_processing:
Differential expression analysis was conducted through DESeq2 (v1.4.5), evaluating fold changes (FC), and correcting p values for multiple testing using false discovery rate (FDR) to generate adjusted p values. Genes were considered differentially expressed if FC > 1 and FDR < 0.05.
The expression threshold for downstream analysis was set at a minimum of 0.5 count per million (CPM) in at least two samples to remove low abundance genes, and counts data were transformed using EdgeR:28 log2(CPM + c), where constant “c” = 4.
Assembly: NCBI GCF_000001635.27_GRCm39
Supplementary files format and content: csv file including read count for all samples
Supplementary files format and content: csv file including FPKM for all samples

source_name: lung

extract_protocol:
RNA sequencing (RNA-seq) was conducted on lung tissue samples. RNA extraction from snap-frozen lung tissues was carried out using TRIzol® Reagent.
Libraries were constructed from samples of acceptable quality for strand-specific mRNA sequencing on the DNA nanoball (DNB) SEQ platform G400 (BGI, Shenzhen, China) using paired-end sequencing (PE150).

treatment_protocol: the pregnant and non-pregnant female mice were exposed to CS from the reference cigarettes 1R6F during preganncy and lactation for 6 weeks.

value: lung

tag: strain

value: BALB/cByJ

value: 16.5 weeks


title: 11E_AZA_060320, RNA

tag: cell line


title: Pregnant smoke exposure 11

description: Library name: SP_11


title: LH tissue from subject KM196

description:
Library name: LH196
library name reflects column name in rnaseq_counts_ham.csv

value: lateral hypothalamus (LH)


title: Paired normal-18

source_name: Paired normal tissue of colorectal cancer patient #18

extract_protocol: RNA was extracted using the Qiagen FFPE RNeasy kit.


title: Pregnant smoke exposure 17

description: Library name: SP_17


title: ARC tissue from subject KM195

description:
Library name: ARC195
library name reflects column name in rnaseq_counts_ham.csv

value: arcuate nucleus of the hypothalamus (ARC)

value: control


title: Non-pregnant smoke exposure 14

description: Library name: SNP_14

value: Female


title: 11C_DAC_060320, RNA

tag: cell type

value: Acute promyelocytic leukemia

value: decitabine


title: Non-pregnant smoke exposure 12

description: Library name: SNP_12


title: DMH tissue from subject KM195

description:
Library name: DMH195
library name reflects column name in rnaseq_counts_ham.csv

source_name: dorsomedial hypothalamus (DMH)

value: dorsomedial hypothalamus (DMH)

value: WT


title: 11B_DAC_060320, RNA

tag: disease/cancer type


title: Paired normal-15

source_name: Paired normal tissue of colorectal cancer patient #15

value: normal

tag: overall survival time


title: ARC tissue from subject KM194

description:
Library name: ARC194
library name reflects column name in rnaseq_counts_ham.csv

tag: treatment


title: LH tissue from subject KM195

description:
Library name: LH195
library name reflects column name in rnaseq_counts_ham.csv

tag: genotype


title: Pregnant air exposure 11

description: Library name: AP_11

tag: Sex


title: Paired normal-14

source_name: Paired normal tissue of colorectal cancer patient #14

tag: overall_event (death from any cause)


title: 11A_DAC_060320, RNA

tag: age


title: 10H_AZA_060320, RNA

tag: batch

value: azacytidine


title: Paired normal-13

source_name: Paired normal tissue of colorectal cancer patient #13

tag: tissue type

value: Male


title: Non-pregnant smoke exposure 13

description: Library name: SNP_13


title: Paired normal-17

source_name: Paired normal tissue of colorectal cancer patient #17

value: FFPE

tag: gender


title: 10G_AZA_060320, RNA

value: Peripheral blood


title: LH tissue from subject KM194

description:
Library name: LH194
library name reflects column name in rnaseq_counts_ham.csv

source_name: lateral hypothalamus (LH)

value: stress


title: DMH tissue from subject KM194

description:
Library name: DMH194
library name reflects column name in rnaseq_counts_ham.csv


title: Paired normal-16

source_name: Paired normal tissue of colorectal cancer patient #16

tag: tumor stage


title: Pregnant air exposure 10

description: Library name: AP_10

value: lung


title: Paired normal-12

source_name: Paired normal tissue of colorectal cancer patient #12

tag: grade


title: 10F_AZA_060320, RNA

source_name: Peripheral blood

tag: tissue

value: promyeloblast


title: Pregnant air exposure 7

description: Library name: AP_7

value: BALB/cByJ

value: 16.5 weeks


title: 11D_DAC_060320, RNA


title: Non-pregnant smoke exposure 17

description: Library name: SNP_17


title: Paired normal-11

source_name: Paired normal tissue of colorectal cancer patient #11

tag: localization


title: ARC tissue from subject KM193

description:
Library name: ARC193
library name reflects column name in rnaseq_counts_ham.csv

value: arcuate nucleus of the hypothalamus (ARC)


title: DMH tissue from subject KM193

description:
Library name: DMH193
library name reflects column name in rnaseq_counts_ham.csv

value: control


title: Paired normal-10

description: Gene expression data from 49 colorectal cancer patients and paired normal FFPE tissues

source_name: Paired normal tissue of colorectal cancer patient #10

value: Female


title: Non-pregnant air exposure 9

description: Library name: ANP_9

tag: strain


title: 10D_DAC_060320, RNA

tag: cell line

value: Acute promyelocytic leukemia


title: Non-pregnant air exposure 10

description: Library name: ANP_10


title: 10E_AZA_060320, RNA

tag: cell type


title: 10C_DAC_060320, RNA

tag: disease/cancer type

value: decitabine


title: Paired normal-8

source_name: Paired normal tissue of colorectal cancer patient #8

tag: overall survival time


title: LH tissue from subject KM193

description:
Library name: LH193
library name reflects column name in rnaseq_counts_ham.csv

value: lateral hypothalamus (LH)

tag: treatment


title: 10B_DAC_060320, RNA


title: Non-pregnant air exposure 8

description: Library name: ANP_8


title: Paired normal-6

source_name: Paired normal tissue of colorectal cancer patient #6


title: 10A_DAC_060320, RNA


title: Non-pregnant air exposure 7

description: Library name: ANP_7


title: Paired normal-7

source_name: Paired normal tissue of colorectal cancer patient #7


title: iNSCs3

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

country: China

institute: Shanghai Jiao Tong University

data_processing:
RNA-seq data were trimmed and aligned to mouse genome (mm9), then Hisat2 was used to mapping the reads with default parameters.
DEseq2 was used to calculate the significant different genes under the parameters: adjust of p value < 0.05 and log2 fold change > 1.
Assembly: mm9
Supplementary files format and content: count, fpkm

source_name: neural stem cell-like cells

growth_protocol: SSCs were cultured on mitotically inactivated STO (SIM mouse embryo-derived thioguanine- and ouabain-resistant) cell feeders in minimum essential medium alpha (MEMa; Invitrogen) supplemented with 10% fetal bovine serum (FBS) (Life Technologies), 10 ng/mL mouse leukemia inhibitory factor (LIF) (Santa Cruz Biotechnology), 20 ng/mL mouse epidermal growth factor (EGF) (PeproTech), 10 ng/mL basic fibroblast growth factor (bFGF) (PeproTech), 20 ng/mL mouse glial cell line-derived neurotrophic factor (GDNF) (PeproTech), 1mM non-essential amino acids (NEAA) (Gibco), 2 mM L-glutamine (Sigma), 1 mM sodium pyruvate (Amresco), 25 μg/mL insulin (Sigma), 100 μg/mL human transferrin (Sigma), 1x vitamin (Sigma), 60 μM putrescine (Sigma), 60 ng/mL progesterone (Sigma), 100 IU/mL penicillin (Gibco), 100 μg/mL streptomycin (Gibco),  and 0.1 mM β-mercaptoethanol (Sigma).

extract_protocol:
Total RNA was extracted from cells using Trizol Reagent (Invitrogen, Carlsbard, CA, USA). RNA quantity and quality were determined with 2100 Bioanalyzer (Agilent Technologies).
RNA-Seq libraries was prepared using the KAPA Stranded mRNA-Seq kit (KAPA Biosystems, Wilmington, MA, USA), following the manufacturer's protocol

treatment_protocol: Two days before transdifferentiation, SSCs were digested with 0.05% trypsin. After 2 h of differential plating, the supernatant was collected and about 10,000 SSCs were inoculated into 24-well plates coated with laminin. After 24 h of culture, the medium was changed to transdifferentiation medium A (SSCs medium + 1 μM retinoic acid) for 24 h, followed by transdifferentiation medium B (MEM/F12 medium and neurobasal medium 1:1 mixture, 0.5% N2, 1% B27, 25 μg/mL bovine serum albumin (BSA), 25 μg/mL insulin, 2 mM L-glutamine, 0.1 mM β-mercaptoethanol, 10 μM SB431542, 1% FBS + 20 ng/mL bFGF), and the medium was changed every 2 days.

value: spermatogonial stem cells (SSCs)

tag: developmental stage

value: transdifferentiation for 6 days

value: male


title: yolksac, infected live4

city: HONGKONG

first: JINGYAO

last: WANG

address: Hong Kong Kowloon Tat Chee Avenue

institute: CITYU

description: Library name: PL2_YS1

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

organism: Gallus

source_name: yolksac

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

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

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

value: yolksac

tag: group

value: APEC infection


title: yolksac, infected live3

description: Library name: PL22_YS2


title: Abortive tissue 1

type: genomic

city: Shenzhen

first: Tong

last: Zhang

address: Longgang District Maternity & Child Healthcare Hospital of Shenzhen City

description: Hybridized to Cytoscan Optima

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CHAS 4.3.0) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CHAS 4.3.0. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: Abortive tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA is extracted from prenatal specimens or aborted tissue using the Qiagen DNA Blood mini kit. The quality and quantity of DNA were evaluated by spectrophotometer and agarose gel electrophoresis.

tag: Sex


title: Paired normal-5

city: ankara

first: nevin

last: belder

address: gumusdere

institute: ankara university

data_processing:
The data were analyzed with Partek Genomics Suite Version 6.6
The Affymetrix CEL files were pre-processed with Genomics Suite v6.6 (Partek) using the robust multi-array analysis (RMA) algorithm.

source_name: Paired normal tissue of colorectal cancer patient #5

value: FFPE

value: normal

tag: overall_event (death from any cause)


title: RNA from lysis A8

city: Loma Linda

first: Charles

last: Wang

address: 11021 Campus Street

department: Department of Basic Sciences

institute: Loma Linda University

data_processing:
Fastq files were generated using bcl2fastq v2.19.0.316
Cellular barcodes and the linker sequences are read by Read 2. The first bases of barcode (BC) no. 1, BC no. 2 and BC no. 3 should locatebe located within the 84th-87th, 47th-50th and 10th-13th bases of Read 2.
A bowtie reference index was generated with all possible cellular barcode combinations (96×96×12) and barcode sequences were mapped to the cellular barcode reference using bowtie with the parameters: -v 1 -m 1 --norc (reads with more than 1 barcode mismatch and can be assigned to more than 1 cell were discarded).
Nextera adaptor sequences were trimmed from 3' of DNA and RNA libraries, Poly-dT sequences were further trimmed from 3' of RNA libraries and low-quality reads (minimal length: L=30, minimal base calling quality: Q=30) were excluded from further analysis.
Cleaned reads were first mapped to Rnor 7.0 reference genome with STAR (v.2.6.0a) for RNA or bowtie2  for DNA.
RNA alignment files were converted to a matrix with cells as columns and genes as rows. DNA alignment files were converted to a matrix with cells as columns and 5-kb bins (instead of peaks) as rows.
Three antibodies (against H3K4me1, H3K4me3, and H3K27me3) were used in the original experiment and all data lised here includes the H3K4me3 capture. However, H3K4me3 data was excluded in the analysis due to poor recovery on both DNA and RNA.
Assembly: Rnor7.0
Supplementary files format and content: Processed data was in h5ad format which contends cell IDs and gene (RNA) or peak (DNA) counting matrix.

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: P7 cortex

growth_protocol: Pregnant Sprague-Dawley rats were purchased from Charles River Laboratories (Portage, MI) and were housed under controlled temperature (22 ºC) and photoperiod (12-h light and 12-h dark cycle) with food and water ad libitum.

extract_protocol:
10x Genomics protocol CG000124 (Isolation of nuclei for singel cell RNA sequencing).
The experiment was  performed with help provided by Epigenome Technologies, INC. following the detailed protocol published by Zhu et al (Nature Methods, 2021. 18(3): p. 283-292).
Combinatory indexing of single nuclei and DNA tagmentation with antibody guided, protein A-fused Tn5 transposase.

treatment_protocol: E-cigarette aerosol was delivered with a puff duration of 4 sec, 3 puffs in an inter-puff interval of 30 sec per vaping episode, and one episode per 1 hour in the dark phase of 12 hrs each day, which generates similar nicotine blood pharmacokinetics in the pregnant rats to those observed in human e-cigarette users. The dams were exposed to e-cigarettes for a total of 17 days from gestational day 4 (E4) to E20.

value: P7 cortex

value: Sprague-Dawley

tag: genotype

value: brain tissue


title: iNSCs2


title: RNA from lysis A7


title: yolksac, infected live1

description: Library name: PL10_YS1


title: yolksac, infected live2

description: Library name: PL17_YS2


title: Abortive tissue 2

institute: Longgang District Maternity & Child Healthcare Hospital of Shenzhen City

description: Hybridized to Cytoscan Optima


title: SSCs3

source_name: spermatogonial stem cells

value: testis

value: neural stem cell-like cells (iNSCs)


title: yolksac,  infected dead3

description: Library name: PL23_YS1


title: Paired normal-4

source_name: Paired normal tissue of colorectal cancer patient #4

tag: tissue type

value: Male


title: DNA from lysis A14

library_source: genomic single cell


title: Paired normal-3

source_name: Paired normal tissue of colorectal cancer patient #3

tag: gender


title: iNSCs1


title: Paired normal-9

source_name: Paired normal tissue of colorectal cancer patient #9

value: Female

tag: tumor stage


title: DNA from lysis A8


title: RNA from lysis A14


title: DNA from lysis A7


title: SSCs2


title: Paired normal-2

source_name: Paired normal tissue of colorectal cancer patient #2

tag: grade


title: yolksac,  infected dead2

description: Library name: PL18_YS3

tag: tissue


title: yolksac,  infected dead1

description: Library name: PL13_YS1


title: spr-5; met-2_mep-1 RNAi rep2

city: kennesaw

first: Brandon

middle: Scott

last: Carpenter

state: GA

address: 370 Paulding Avenue, Room 119

department: Molecular and Cellular Biology

institute: Kennesaw State University

description: Library name: Sample 11

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

organism: Caenorhabditis elegans

source_name: whole animal L1 Larvae

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

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

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

value: whole animal L1 Larvae


title: yolksac,  negative control3

description: Library name: N10_YS1

value: Negative control

value: PBS


title: spr-5; met-2_mep-1 RNAi rep3

description: Library name: Sample 12


title: iNSCs2_CCND1_IP

data_processing:
For ChIP pair-end raw data, we first trimmed the adaptor sequences and low-quality reads with BBmap (version 38.16), then aligned to the mm9 reference genome using bowtie2 (version 2.3.4.1)(Langmead and Salzberg, 2012) with default parameters.
PCR duplicates were removed using Samtools (version 2.0.1) (Li et al., 2009) and generated normalized genome coverage tracks from uniquely mapping reads (MAPQ>10) using deepTools2 (version 3.1).
Assembly: mm9
Supplementary files format and content: bigwig file

source_name: iNSCs

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 5 min at room temperature and quenched with 125mM glycine. Cells were then put on ice, resuspended in cold cell lysis buffer (140mM NaCl, 1mM EDTA pH 8.0, 1% TritonX-100 and 0.1% SDS and Protease Inhibitors (Roche)). Nuclei were sonicated into 200-1000 bp. The chromatin fragments were pre-cleared and then immunoprecipitated with Protein A+G Magnetic beads coupled with anti-CCND1 (ab134175, Abcam).After reverse crosslinking, immunoprecipitated DNAs and input DNAs were end-repaired and ligated adapters to the DNA fragments using NEBNext Ultra End-Repair/dA-Tailing Module (E7442, NEB) and NEBNext Ultra Ligation Module (E7445, NEB). High-throughput sequencing of the ChIP fragments was performed using Illumina NextSeq 500 following the manufacturer's protocols.
Library was prepared with NEBNext Ultra End-Repair/dA-Tailing Module (E7442, NEB) and NEBNext Ultra Ligation Module (E7445, NEB). High-throughput sequencing of the ChIP fragments was performed using Illumina NextSeq 500 following the manufacturer's protocols.

value: spermatogonial stem cells (SSCs)

tag: antibody

value: anti-CCND1 (ab134175, Abcam)


title: iNSCs2_CCND1_Input


title: Paired normal-1

source_name: Paired normal tissue of colorectal cancer patient #1

tag: localization


title: spr-5; met-2_mep-1 RNAi rep1

description: Library name: Sample 10


title: yolksac,  negative control2

description: Library name: N9_YS1


title: SSCs1

value: male


title: iNSCs1_CCND1_IP


title: spr-5; met-2_control RNAi rep3

description: Library name: Sample 9


title: yolksac,  negative control1

description: Library name: N8_YS1

value: yolksac


title: KO_DRA_11

city: Manchester

first: James

middle: Edward

last: Parkinson

state: Greater Manchester

address: Oxford Road

department: DIIIRM

institute: University of Manchester

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

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

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

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

source_name: Allergic mouse lung

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

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

value: Whole Lung


title: KO_DRA_12


title: liver, infected live4

description: Library name: PL2_L2

source_name: liver

value: liver

value: APEC infection


title: SSCs2_CCND1_IP

source_name: SSCs


title: KO_DRA_10


title: liver, infected live3

description: Library name: PL22_L1


title: spr-5; met-2_control RNAi rep2

description: Library name: Sample 8


title: spr-5; met-2_control RNAi rep1

description: Library name: Sample 7


title: liver, infected live2

description: Library name: PL17_L1


title: iNSCs1_CCND1_Input


title: WT_mep-1 RNAi rep3

description: Library name: Sample 6

value: N2; (mep-1 RNAi)


title: SSCs2_CCND1_Input


title: SSCs1_CCND1_Input


title: liver, infected live1

description: Library name: PL10_L1


title: SSCs1_CCND1_IP


title: B6_DRA_07


title: KO_DRA_08


title: WT_mep-1 RNAi rep2

description: Library name: Sample 5


title: B6_DRA_05


title: B6_DRA_06


title: WT_mep-1 RNAi rep1

description: Library name: Sample 4


title: liver, infected dead1

description: Library name: PL13_L1


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

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

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

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

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

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

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

tag: genetic background

value: hybrid 129-C57BL/6

tag: cell line

value: embryonic stem cells (ESC)


title: WT_control RNAi rep3

description: Library name: Sample 3


title: guidedNOMe-seq in ADNP N-terminal mutant mESC, replicate 1

description:
Library name: ADNPdN_gNOMe-seq_r1
MiSeq v3 600bp paired-end

tag: cell type


title: B6_DRA_04


title: B6_DRA_03


title: KO_DRA_09


title: liver, negative control2

description: Library name: N9_L1


title: guidedNOMe-seq in ADNP PxVxL mutant mESC, replicate 1

description:
Library name: ADNPpxvxl_gNOMe-seq_r1
MiSeq v3 600bp paired-end


title: liver, negative control1

description: Library name: N8_L1


title: WT_control RNAi rep1

description: Library name: Sample 1