title: Sample12ATAC

first: Jo

middle: Anne

last: Stratton

address: 3801 University street

department: Neurology and Neurosurgery

description:
Library name: Sample12ATAC
ATAC_matrix.csv.gz

library_source: genomic single cell

data_processing:
Demultiplexing, genome alignment, gene quantification, and peak accessibility in single nuclei were performed with the Cell Ranger ARC 50. Specifically, processed using the cellranger-arc count v.2.0.2 and the aligned against human genome GRCh38 to generate the count matrices for the RNA and ATAC modalities pipeline (v.7.0.1). Considering the multiplexed content of the fastq files in which we have merged two patients within one bead, the BAM files generated from cellranger-arc count were demultiplexed through SNP information of the sample using 1000 Genomes based common variants (genome1K.phase3.SNP_AF5e2.chr1toX.hg38.vcf). The subsequent data processing, normalization, and batch integration on both assays were done using Seurat (v.5.0.1) and Signac (v.1.12.0) in the R environment v.4.1.2.
Assembly: GRCh38
Supplementary files format and content: csv files containg gene barcode matrix for the GEX component and ATAC component

source_name: Ependymal cells from MS patient

extract_protocol:
Nuclei extraction followed a modified protocol from Nagy et al., 2021, with all steps performed on ice or at 4°C using pre-chilled buffers. Samples were added to a pre-filled douncer (Wheaton 357542) with 750µL lysis buffer, followed by an additional 750µL to dislodge tissue. Tissue was dounced 10 times with a loose pestle and 5 times with a tight pestle, avoiding air bubbles. Homogenized solutions (1.5mL) were mixed with 3.5mL lysis buffer, incubated on ice for 5 minutes, and lysis was stopped by adding 5mL wash buffer. The solution was filtered through a 30µM strainer (Miltenyi Biotech 130-098-458) and centrifuged at 500g for 5 minutes at 4°C. The pellet was resuspended in 5mL wash buffer and subjected to two additional rounds of filtration and centrifugation. After the third round, nuclei were resuspended in 3.1mL wash buffer and 900µL chilled debris removal solution (Miltenyi Biotech 130-109-398), overlaid with 4mL wash buffer, and centrifuged at 3000g for 10 minutes. The top two phases were discarded, and the nuclei-containing bottom phase was diluted to 15mL with wash buffer, inverted, and centrifuged at 1000g for 10 minutes. The pellet was resuspended in buffer for single-nucleus RNA sequencing. Two aliquots per sample were stained with DRAQ5 (ThermoFisher 65-0880-92) for quality control using a 40x objective and manual counting with a hemocytometer.
Single nucleus RNA sequencing was completed as per the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (CG000338, Rev E to Rev F). In brief, this included transposition, GEM generation and barcoding, post-GEM cleanup, pre-amplification PCR, ATAC library construction, cDNA amplification, and gene expression library construction. The quality of both ATAC and RNA libraries was evaluated at Genome Quebec using a LabChip® GX Touch™ nucleic acid analyzer system. Multiome libraries were sequenced using an Illumina NovaSeq 6000 instrument at a sequencing depth and read length recommended by the Multiome protocol (CG000338).

value: Brain

value: Ependymal cells

tag: subject status

value: MS patient

value: Primary cells


title: Sample11ATAC

status: Public on Jul 10 2026

type: SRA

city: Montreal

state: Quebec

country: Canada

institute: McGill University

description:
Library name: Sample11ATAC
ATAC_matrix.csv.gz

molecule: genomic DNA

organism: Homo sapiens

source_name: Ependymal cells from control patient

tag: tissue

tag: cell type

value: control patient


title: PIB_only_SC_2

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

description: Library name: PIB_only_SC_2

library_source: transcriptomic

data_processing:
FASTQ files were preprocessed using the nf-core smRNA-seq pipeline (v2.4.0) with default parameters, except for UMI extraction, which was done using the following options: --umitools_extract_method regex --umitools_bc_pattern '.+(?P<discard_1>AACTGTAGGCACCATCAAT){s<=2}(?P<umi_1>.{12})(?P<discard_2>.*)
Assembly: Reference list of human mature miRNA sequences from miRbase
Supplementary files format and content: smRNA.counts.csv.gz

molecule: total RNA

source_name: skin

growth_protocol: HDFs were cultured on gelatin-coated plates in complete DMEM (high glucose) supplemented with 10% FBS, 2 mM GlutaMAX, 1 mM sodium pyruvate, penicillin/streptomycin. Dendritic cell controls were sorted directly after enrichment and sorting from peripheral blood.

extract_protocol:
5000-10000 cells were sorted in RLT lysis buffer. RNA was exracted with the miRNeasy Tissue/Cells Advanced Kit according to manufacturer's protocol.
Libraries were prepared using the QIAseq miRNA UDI Library Kit by Qiagen.

treatment_protocol: HDFs were trasduced on day -1 of reprogramming and sorted on day 9 by FACS.

value: skin

value: human dermal fibroblast

tag: genotype

value: WT

tag: treatment

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) on day -1 of reprogramming.

tag: time

value: Cells were collected on day 9 of reprogramming.

tag: sorted cells

value: alive (DAPI-) and CD45+


title: PIB_only_SC_1

description: Library name: PIB_only_SC_1


title: Whole blood DNA methylation, HISPANIC CONTROL, 77yo M, 207097320046_R08C01

type: genomic

city: San Francisco

first: Sebastián

last: Cruz-González

state: California

country: USA

institute: UCSF

hyb_protocol: DNA methylation was quantified using the Illumina Infinium MethylationEPIC BeadChip (EPIC v1.0, ~850K CpG sites) according to the manufacturer's standard Infinium HD Assay protocol.

scan_protocol: BeadChips were scanned on an Illumina iScan system to generate raw IDAT files.

data_processing:
All quality control and data normalization were performed using the openSeSAMe pipeline from the SeSAMe R package (Zhou et al., 2018). Probes of poor design were removed, as well as probes with detection P-value > 0.05 in more than 5% of samples. Non-CG probes and probes on X, Y, and mitochondrial chromosomes were also removed. Samples with incomplete bisulfite conversion (GCT score > 1.5) and principal component analysis outliers were excluded. Noob normalization was performed with SeSAMe using a nonlinear dye-bias correction.
processed value definition: Beta values representing the ratio of methylated probe intensity to overall intensity (methylated + unmethylated + offset). Values range from 0 (unmethylated) to 1 (fully methylated).

label: Cy3 and Cy5

source_name: whole blood

label_protocol: Bisulfite conversion of genomic DNA was performed prior to hybridization following standard protocols for the Illumina Infinium MethylationEPIC BeadChip array. Samples were randomized across plates and chips to ensure that ancestry, age, and sex were not confounded with each batch.

extract_protocol: Genomic DNA was extracted from whole blood samples at external processing sites associated with each cohort. Standard column-based DNA extraction methods were used according to each site's established protocols.

tag: Sex

value: Male

tag: disease state

value: Healthy control

value: whole blood

tag: ethnicity

value: HISPANIC

tag: cohort

value: PRADI

tag: age


title: PIB_only_L_2

description: Library name: PIB_only_L_2


title: Rw0N5d-2

city: Qingdao

first: Junyi

last: Mu

address: No. 72, Binhai Road, Jimo District, Qingdao City

country: China

institute: Shandong Unoversity

description: Library name: Mu11

data_processing:
The construction and sequencing of the mRNA library were performed on the DNBSEQ platform at the high-throughput laboratory of Wuhan Huada Gene Technology Service Co., LTD, with a sequencing length of PE150. Sequencing data was filtered using the software SOAPnuke. The quality-controlled clean reads were then aligned to the reference genome (IWGSC RefSeq v1.1) using HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) and Bowtie2.
\
Assembly: IWGSC RefSeq v1.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Triticum aestivum

source_name: leaf

growth_protocol: These materials were grown in a greenhouse with white light at 400 μmol·m-2·s-1, with a relative humidity of 50%, and a photoperiod of 16 hours of daylight (22°C) and 8 hours of nighttime (16°C). After germinating for 3 days under normal growth conditions, the endosperm was removed, and the seedlings were transferred to wheat nutrient culture medium containing 1.5 mM KCl, 1 mM MgSO4, 0.2 mM KH2PO4, 0.1 mM Fe(III)-EDTA, 1 µM H3BO3, 1µM ZnSO4, 1 µM MnSO4, 0.5 µM CuSO4, 0.05 µM Na2MoO4, 2.5 mM Ca(NO3)2 or CaCl2, pH = 6.0.

extract_protocol:
The leaves of wheat were collected and subjected to total RNA extraction using the TriZol RNA extraction kit (TransGen Biotech).
mRNA enrichment from total RNA was performed using Oligo(dT) magnetic beads to isolate polyA-tailed mRNA. The RNA was fragmented, reverse-transcribed with random N6 primers, and converted into double-stranded cDNA. The DNA ends were blunt-ended, 5'-phosphorylated, and A-tailed, followed by ligation to a bubble-shaped adapter with a 3'-T overhang. The ligated products were PCR-amplified, heat-denatured into single strands, and circularized using a bridge primer to generate single-stranded circular DNA libraries. After quality control, qualified libraries were sequenced.

treatment_protocol: For drought tolerance analysis, wheat seedlings were germinated under normal conditions and transplanted into soil tanks once the first leaf emerged from the coleoptile (each tank contained 12 identical small black pots, with nine seedlings per pot, in a mixture of vermiculite and Pindstrup substrate peat soil at a 3:1 ratio, 2 L wheat growth medium per tank with 5 mM nitrate;  no additional water was supplied, allowing natural evapotranspiration).  Soil moisture content and above-ground fresh weight were measured every three days from one random pot. For survival rate analysis, seedlings were considered to be under drought stress when soil moisture content fell below 5%, and after one day of drought, they were re-watered with 2 L of wheat growth medium containing either 0- or 5- mM nitrate per tank.  For RW (re-watering) or RWN (re-watering with nitrate) analysis, wheat seedlings subjected to one day of drought were re-watered with wheat growth medium containing 0- or 5- mM nitrate.

value: leaf


title: Whole blood DNA methylation, HISPANIC AD, 77yo M, 207097420079_R08C01

value: Alzheimer's disease

value: CuADI


title: PIB_only_L_1

description: Library name: PIB_only_L_1


title: Sample8ATAC

description:
Library name: Sample8ATAC
ATAC_matrix.csv.gz

value: Brain

value: Ependymal cells

value: MS patient


title: Sample9ATAC

description:
Library name: Sample9ATAC
ATAC_matrix.csv.gz

value: Primary cells


title: Whole blood DNA methylation, HISPANIC CONTROL, 89yo M, 207097420152_R07C01


title: PIB_only_G_1

description: Library name: PIB_only_G_1

value: skin

value: human dermal fibroblast


title: Whole blood DNA methylation, HISPANIC AD, 84yo F, 207080920090_R02C01

value: Female


title: PIB_only_G_2

description: Library name: PIB_only_G_2

value: WT

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) on day -1 of reprogramming.

value: Cells were collected on day 9 of reprogramming.


title: HDF_MCS_SC_2

description: Library name: HDF_MCS_SC_2

value: Cells were transduced an empty (MCS) control lentiviral vector on day -1 of reprogramming.

value: alive (DAPI-) and Azami Green+


title: Rw0N3h-2

description: Library name: Mu8


title: Sample7ATAC

description:
Library name: Sample7ATAC
ATAC_matrix.csv.gz

value: control patient


title: HDF_MCS_SC_1

description: Library name: HDF_MCS_SC_1


title: Sample4ATAC

description:
Library name: Sample4ATAC
ATAC_matrix.csv.gz


title: Whole blood DNA methylation, HISPANIC CONTROL, 91yo M, 207097420112_R02C01

value: Male

value: Healthy control

value: whole blood

value: HISPANIC

value: PERUVIAN


title: HDF_MCS_L_2

description: Library name: HDF_MCS_L_2


title: Whole blood DNA methylation, HISPANIC CONTROL, 79yo M, 207080910061_R07C01

value: PRADI


title: Sample3ATAC

description:
Library name: Sample3ATAC
ATAC_matrix.csv.gz

value: Brain

value: Ependymal cells


title: HDF_MCS_L_1

description: Library name: HDF_MCS_L_1

value: skin


title: HDF_MCS_G_2

description: Library name: HDF_MCS_G_2

value: human dermal fibroblast


title: HDF_MCS_G_1

description: Library name: HDF_MCS_G_1


title: Sample2ATAC

description:
Library name: Sample2ATAC
ATAC_matrix.csv.gz

value: MS patient

value: Primary cells


title: pDC_C_2

description: Library name: pDC_C_2

source_name: blood

value: blood

value: plasmacytoid dendritic cells

value: WT

value: alive (7-AAD-) and HLA-DR+ CD11c- CD123+


title: Sample1ATAC

description:
Library name: Sample1ATAC
ATAC_matrix.csv.gz

value: control patient


title: HUVEC, mechanical stretch, rep 6

city: Jyväskylä

first: Riikka

last: Kivelä

address: Rautpohjankatu 8

country: Finland

institute: University of Jyväskylä

description:
Library name: HUVEC_12
Column name in counts_all.tsv: HUVEC_12

data_processing:
Sequence reads were trimmed at Novogene by removing adapter reads, removing reads containing >10% of unsolvable bases and removing reads containing >50% of low quality bases (Qphred ≤ 5)
Read alignment was done with Bowtie2 software with human GRCh38.95 genome build as reference
Aligned reads were quantified with featureCounts in Rsubread
Quantified reads normalized with CPM with edgeR and lowly expressed genes were filtered
Differential gene expression analysis was done with R/Bioconductor limma-voom pipeline
Assembly: GRCh38.95
Supplementary files format and content: Tab-delimited text file contains raw counts for all cell lines (12 samples per cell line). File named "counts_all.tsv"

source_name: HUVEC

extract_protocol:
RNA was collected with a column-based RNA isolation kit (NucleoSpin RNA, Macherey-Nagel).
Library construction, quality control and sequencing was carried out at Novogene (Cambridge, United Kingdom)

treatment_protocol: 5h cyclic uniaxial mechanical loading (1Hz, 12% elongation) with C-stretch device (IonOptix).

tag: cell line

value: HUVEC

value: mechanical loading


title: Whole blood DNA methylation, HISPANIC AD, 78yo F, 207097420049_R04C01

value: Female

value: Alzheimer's disease

value: whole blood


title: pDC_B_2

description: Library name: pDC_B_2


title: Sample12GEX

description:
Library name: Sample12GEX
GEX_matrix.csv.gz

library_source: transcriptomic single cell

molecule: polyA RNA


title: Sample11GEX

description:
Library name: Sample11GEX
GEX_matrix.csv.gz


title: pDC_A_1

description: Library name: pDC_A_1


title: pDC_A_2

description: Library name: pDC_A_2


title: Whole blood DNA methylation, HISPANIC AD, 82yo F, 207097320053_R03C01

value: HISPANIC

value: PRADI


title: Whole blood DNA methylation, HISPANIC AD, 88yo F, 207097420112_R04C01


title: DC2_B_2

description: Library name: DC2_B_2

value: type 2 dendritic cell

value: alive (7-AAD-) and HLA-DR+ CD11c+ CD1c+ CD141-


title: DC2_C_1

description: Library name: DC2_C_1


title: Sample9GEX

description:
Library name: Sample9GEX
GEX_matrix.csv.gz

value: Brain

value: Ependymal cells


title: Whole blood DNA methylation, HISPANIC CONTROL, 73yo F, 207097320053_R04C01

value: Healthy control


title: DC2_B_1

description: Library name: DC2_B_1

value: blood


title: Sample8GEX

description:
Library name: Sample8GEX
GEX_matrix.csv.gz

value: MS patient

value: Primary cells


title: DC2_A_2

description: Library name: DC2_A_2

value: WT


title: Sample7GEX

description:
Library name: Sample7GEX
GEX_matrix.csv.gz

value: control patient


title: DC1_C_2

description: Library name: DC1_C_2

value: type 1 dendritic cell

value: alive (7-AAD-) and HLA-DR+ CD11c+ CD141+


title: Whole blood DNA methylation, HISPANIC AD, 77yo M, 207097420010_R07C01

value: Male


title: DC1_B_2

description: Library name: DC1_B_2


title: Sample4GEX

description:
Library name: Sample4GEX
GEX_matrix.csv.gz


title: Sample3GEX

description:
Library name: Sample3GEX
GEX_matrix.csv.gz


title: DC1_A_1

description: Library name: DC1_A_1


title: Whole blood DNA methylation, HISPANIC AD, 92yo F, 207097420080_R01C01

value: Female

value: Alzheimer's disease


title: Whole blood DNA methylation, HISPANIC CONTROL, 78yo F, 207097420015_R07C01

value: whole blood

value: HISPANIC


title: PIB_124_3

description: Library name: PIB_124_3

library_source: genomic

data_processing:
CUT&Tag sequencing were preprocessed using the nf-core CUT&Tag pipeline. Reads were aligned to the hg38 reference genome using Bowtie2 with default settings. Peak calling was performed individually for each sample individually using MACS2, and a consensus peak set across all samples was generated using BEDTools72Read counts for the consensus peak regions were quantified using featureCounts.
Assembly: hg38
Supplementary files format and content: count table (.txt)
Library strategy: CUT&Tag

growth_protocol: HDFs were cultured on gelatin-coated plates in complete DMEM (high glucose) supplemented with 10% FBS, 2 mM GlutaMAX, 1 mM sodium pyruvate, and penicillin/streptomycin.

extract_protocol:
500,000 HDFs from donor 1, co-transduced with PIB and miRNA-124, miRNA-142, or the scrambled control, were FACS-sorted on day 3 (CD45+). Empty vector-transduced cells were sorted as controls (DAPI-).  Cells were frozen in FBS with 10 % DMSO and delivered to Active Motif, where quantitative Cut&Tag with a spike-in control was performed to quantify distribution and prevalence of the H3K27me3 mark.
After thawing, counting and viability analysis, cells were incubated overnight with concanavalin A beads and 1 µL of the primary anti-H3K27me3 antibody per reaction. After incubation with a secondary antibody (1:100), cells were washed and tagmentation was performed at 37 °C using protein-A-Tn5. Tagmentation was halted by the addition of EDTA, SDS and proteinase K at 55 °C, after which DNA extraction and ethanol purification was performed, followed by PCR amplification and barcoding. Indexes and reaction conditions were set according to manufacturer’s recommendations for the CUT&Tag-IT assay kit protocol. Following magnetic bead cleanup , the resulting DNA libraries were quantified and sequenced on an Illumina NextSeq 2000 sequencer.

treatment_protocol: HDFs were trasduced on day -1. Cells were sorted on day 3 by FACS.

value: skin

value: HDF

value: human dermal fibroblast

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and for a miR-124 hairpin on day -1 of reprogramming.

value: Cells were collected on day 3 of reprogramming.

value: alive (DAPI-) and CD45+


title: PIB_SCR_3

description: Library name: PIB_SCR_3

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and for a scrambled miRNA hairpin on day -1 of reprogramming.


title: PIB_124_1

description: Library name: PIB_124_1


title: PIB_SCR_2

description: Library name: PIB_SCR_2


title: Whole blood DNA methylation, HISPANIC CONTROL, 88yo F, 207080910133_R04C01

value: Healthy control

value: PRADI


title: PIB_SCR_1

description: Library name: PIB_SCR_1

value: WT


title: HDF_MCS_3

description: Library name: HDF_MCS_3

value: Cells were transduced an empty (MCS) control lentiviral vector on day -1 of reprogramming.

value: alive (DAPI-)


title: GEX, healthy donor BC5087

city: Stanford

first: Laura

last: Amaya

state: CA

address: 269 Campus Drive

institute: Stanford University

data_processing:
Demultiplexed scRNA- and scATAC-seq fastq files were processed using the Cell Ranger ARC pipeline (version 2.0.0) from 10x Genomics, generating barcoded count matrices for gene expression and ATAC data.
Assembly: hg38
Supplementary files format and content: Fragments and filtered features matrix

source_name: Blood

extract_protocol:
CD4+ T cells were purified by FACS as for the bulk ATAC-seq. Nuclei were isolated from 40,000 cells according to the Demonstrated Protocol: Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing (10x Genomics CG000365). In summary, cells were washed twice by centrifugation with PBS with 0.04% bovine serum albumin (BSA; Miltenyi Biotec), then lysed with 45 µl chilled Lysis Buffer. After 3.5 min incubation on ice, the lysate was washed with 50 µl chilled Wash Buffer, supernatants removed, and pellets washed again without disruption by adding 45 µl of chilled Diluted Nuclei Buffer to each tube. Nuclei were then resuspended in 7 µl of Diluted Nuclei Buffer, and an 2 µl aliquot used for manual counting with hemocytometer and 0.4% Trypan Blue solution. After counting, nuclei concentration was adjusted to achieve maximum targeted nuclei recovery and promptly processed for single-cell library generation using the manufacturer’s protocol.
Libraries were prepared according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338 Rev F). Paired-end 150-bp sequencing was done either on NexSeq 500 using the v2.5high-output kit (sample from healthy donor 10242) or using Illumina NovaSeq 6000, targeting a depth of 250 million read pairs per sample.

value: Blood

value: T cell

value: CD4+ T cell

tag: individual

value: healthy donor


title: HDF_MCS_2

description: Library name: HDF_MCS_2


title: ATAC, healthy donor BC0202


title: HDF_MCS_1

description: Library name: HDF_MCS_1


title: GEX, healthy donor BC0202


title: A673_Brunello_DMSO

city: Dallas

first: Jiwoong

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Library name: A673_Brunello_DMSO

library_source: other

data_processing:
Trim Galore was used for quality and adapter trimming. STAR was employed to align the reads onto the human genome, SAMtools was employed to sort the alignments, and HTSeq Python package was employed to count reads per gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include sgRNA gene read counts for each sample
Library strategy: CRISPR Screen

molecule: other

growth_protocol: Ewing sarcoma cell lines were cultured in RPMI (sigma R7256) + 5-10% FBS + 2mM L-glutamine with pen/strep antibiotics.

extract_protocol:
Samples were prepared according to the Illumina Nextera protocol
Libraries were constructed according to the Illumina Nextera protocol.

treatment_protocol: Ewing’s sarcoma cell lines engineered with the auxin inducible degron in the EWSR1-FLI1 fusion were treated with 5-Ph-IAA for 24 hours at a final concentration of 300nM.

value: Ewing sarcoma cell line

value: DMSO


title: Whole blood DNA methylation, HISPANIC AD, 79yo M, 207080910061_R05C01

value: Male

value: Alzheimer's disease

value: whole blood

value: HISPANIC


title: A673_Brunello_D0

description: Library name: A673_Brunello_D0


title: Whole blood DNA methylation, HISPANIC AD, 92yo F, 207097420191_R01C01

value: Female


title: pDC_C_1

description: Library name: pDC_C_1

value: blood

value: plasmacytoid dendritic cells

value: alive (7-AAD-) and HLA-DR+ CD11c- CD123+


title: Whole blood DNA methylation, HISPANIC AD, 75yo F, 207080920090_R04C01

value: PRADI


title: pDC_B_1

description: Library name: pDC_B_1

value: WT


title: d3_PIB_AG_SCR_SC_1

description: Library name: d3_PIB_AG_SCR_SC_1

data_processing:
FASTQ files were preprocessed using the nf-core RNA-seq pipeline (v3.14.0) with default parameters, except for UMI extraction, which was done using the following options: --with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*".
Briefly, paired-end reads were aligned to the human genome (Ensembl release 110) using STAR, and transcript quantification was performed with Salmon.
Assembly: hg38
Supplementary files format and content: count tables (.txt)

growth_protocol: HDFs were cultured on gelatin-coated plates in complete DMEM (high glucose) supplemented with 10% FBS, 2 mM GlutaMAX, 1 mM sodium pyruvate, and penicillin/streptomycin supplemented with the JAK inhibitor ruxolitinib (10 μM).

extract_protocol:
5000-10000 cells were sorted into RLT lysis buffer. RNA was exracted with the miRNeasy Tissue/Cells Advanced Kit according to manufacturer's protocol.
Libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian kit by Takara.

treatment_protocol: HDFs were trasduced on day -1 and/or transfected with PIB-encoding mRNAs and miRNA mimics on day 0 of reprogramming. Cells were sorted on day 3 or 6 by FACS.

value: skin

value: human dermal fibroblast

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) on day -1 of reprogramming and transfected with a scrambled miRNA mimic on day 0.

value: Cells were collected on day 3 of reprogramming.

value: live (DAPI-) and CD45+


title: ATAC, Patient month 9

value: Blood

value: T cell

value: CD4+ T cell

value: Patient month 9


description: Library name: A673_EWSFLI_SMASh_3-11_Danoprevir_24h_rep2

data_processing:
Trim Galore was used for quality and adapter trimming. STAR was employed to align the reads onto the human genome, SAMtools was employed to sort the alignments, and HTSeq Python package was employed to count reads per gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene read counts for each sample

treatment_protocol: Ewing’s sarcoma cell lines were treated with CCT251921 or SW393109 for 24 hours at a final concentration of 100nM.  A673 EWS-FLI AID cells were trated with DMSO or 300nM 5-Ph-IAA.  A673 EWS-FLI1 SMASh cells were treated with DMSO or 316nM danoprevir.

value: Ewing sarcoma cell line

value: EWS-FLI-SMASh

value: Danoprevir


title: Whole blood DNA methylation, HISPANIC AD, 77yo M, 207097420032_R02C01

value: Male

value: Alzheimer's disease

value: whole blood

value: HISPANIC


title: DC2_C_2

description: Library name: DC2_C_2

value: blood

value: type 2 dendritic cell

value: WT

value: alive (7-AAD-) and HLA-DR+ CD11c+ CD1c+ CD141-


title: Whole blood DNA methylation, HISPANIC AD, 82yo F, 207097420011_R04C01

value: Female

value: PRADI


description: Library name: A673_EWSFLI_SMASh_3-11_Danoprevir_24h_rep1


title: Whole blood DNA methylation, HISPANIC CONTROL, 84yo M, 207097420152_R01C01

value: Healthy control


title: GEX, Patient month 9

value: Blood

value: T cell


description: Library name: A673_EWSFLI_SMASh_2-4_Danoprevir_24h_rep2


title: DC2_A_1

description: Library name: DC2_A_1


title: DC1_C_1

description: Library name: DC1_C_1

value: type 1 dendritic cell

value: alive (7-AAD-) and HLA-DR+ CD11c+ CD141+


description: Library name: A673_EWSFLI_SMASh_2-4_Danoprevir_24h_rep1

value: Ewing sarcoma cell line

value: EWS-FLI-SMASh


title: Whole blood DNA methylation, HISPANIC CONTROL, 70yo M, 207097420080_R08C01

value: Male


description: Library name: A673_EWSFLI_SMASh_3-11_Danoprevir_12h_rep2

value: Danoprevir


title: Nymphaea colorata floral bud stage 4-2

city: Shanghai

first: Chang

last: Liu

address: Xinjiangwancheng street, Yangpu District, Shanghai

institute: Fudan University

description:
Library name: Sample S4-2
Fresh frozen Spatial transcriptome sequencing

data_processing:
Sequences were aligned to corresponding genome to gene expression count using BSTMatrix's default settings
Raw sequencing data were processed using BSTMatrix to generate matrix files
Assembly: Phytozome, Nymphaea colorata v1.2, https://phytozome-next.jgi.doe.gov/info/Ncolorata_v1_2
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: barcodes_pos.tsv.gz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: he_lowres_image.png: low-res image of tissue
Supplementary files format and content: he_hires_image.png: hi-res image of tissue
Library strategy: Spatial Transcriptomics

organism: Nymphaea colorata

source_name: floral bud

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10μm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with BMK S1000 Gene Expression Slides

value: floral bud


title: Whole blood DNA methylation, HISPANIC AD, 84yo F, 207097320052_R07C01

value: Alzheimer's disease

value: whole blood

value: HISPANIC


title: DC1_B_1

description: Library name: DC1_B_1

value: blood

value: WT


description: Library name: A673_EWSFLI_SMASh_3-11_Danoprevir_12h_rep1


title: Nymphaea colorata floral bud stage 4-1

description:
Library name: Sample S4-1
Fresh frozen Spatial transcriptome sequencing


title: DC1_A_2

description: Library name: DC1_A_2


title: Sample2GEX

description:
Library name: Sample2GEX
GEX_matrix.csv.gz

value: Brain

value: Ependymal cells

value: MS patient

value: Primary cells


title: Whole blood DNA methylation, HISPANIC CONTROL, 68yo F, 207080910104_R01C01

value: Female

value: Healthy control

value: PRADI


description: Library name: A673_EWSFLI_SMASh_2-4_Danoprevir_12h_rep1

value: Ewing sarcoma cell line


description: Library name: A673_EWSFLI_SMASh_3-11_Danoprevir_6h_rep2

value: EWS-FLI-SMASh


title: Nymphaea colorata floral bud stage 3

description:
Library name: Sample S3
Fresh frozen Spatial transcriptome sequencing


description: Library name: A673_EWSFLI_SMASh_2-4_Danoprevir_12h_rep2


title: Sample1GEX

description:
Library name: Sample1GEX
GEX_matrix.csv.gz

value: control patient


title: PIB_124_2

description: Library name: PIB_124_2

value: skin

value: HDF

value: human dermal fibroblast

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and for a miR-124 hairpin on day -1 of reprogramming.

value: Cells were collected on day 3 of reprogramming.

value: alive (DAPI-) and CD45+


description: Library name: A673_EWSFLI_SMASh_3-11_Danoprevir_6h_rep1

value: Danoprevir


title: Whole blood DNA methylation, HISPANIC CONTROL, 75yo F, 207097420082_R01C01

value: whole blood

value: HISPANIC


title: Nymphaea colorata floral bud stage 2

description:
Library name: Sample S2
Fresh frozen Spatial transcriptome sequencing

value: floral bud


description: Library name: A673_EWSFLI_SMASh_2-4_Danoprevir_6h_rep2


title: Whole blood DNA methylation, HISPANIC CONTROL, 76yo F, 207080910085_R01C01


title: Whole blood DNA methylation, HISPANIC CONTROL, 77yo F, 207097420102_R05C01


description: Library name: A673_EWSFLI_SMASh_2-4_Danoprevir_6h_rep1


title: A673_EWSFLI_SMASh_3-11_DMSO_24h_rep2

description: Library name: A673_EWSFLI_SMASh_3-11_DMSO_24h_rep2

value: DMSO


title: ATAC,  healthy donorBC5087

value: Blood

value: T cell

value: CD4+ T cell

value: healthy donor


title: Whole blood DNA methylation, HISPANIC AD, 83yo M, 207097420032_R03C01

value: Male

value: Alzheimer's disease

value: PRADI


title: Nymphaea colorata floral bud stage 1

description:
Library name: Sample S1
Fresh frozen Spatial transcriptome sequencing


title: A673_EWSFLI_SMASh_3-11_DMSO_24h_rep1

description: Library name: A673_EWSFLI_SMASh_3-11_DMSO_24h_rep1

value: Ewing sarcoma cell line

value: EWS-FLI-SMASh


title: L.serriola, YJ6 infected, dro, bio rep 3

city: Gwangju

first: Jeong

last: Seorin

address: 123, Cheomdangwagi-ro, Buk-gu

country: South Korea

institute: Gwangju Institute of Science and Technology

data_processing:
The adaptors were removed and reads of poor quality were trimmed using Trimmomatic.
Bases with a quality score of less than three from the ends of the reads were removed, and bases not meeting the mean quality threshold of 15 with a window size of four were removed using the sliding window trimming approach.
Reads shorter than 36 bp were eliminated from the library.
New Tuxedo method' with HISAT2 and StringTie was utilized for the reference genome annotation and alignment assembly.
After the initial assembly based on the reference gene model annotation file, a merged sturucture consisting of a complete set of assemblies from all samples was produced using the StringTie --merge module. The assembly was then conducted again based on the resulting merged list of transcript.
Assembly: NC_056623.2
Supplementary files format and content: csv file includes raw counts of genes for each sample

organism: Lactuca serriola

source_name: root

growth_protocol: Plants were placed in a walk-in chamber at 22 oC under a 12/12 h light/dark photoperiod for 34 days.

extract_protocol:
The root tissues of L. serriola were pulverized using TissueLyser II and then RNA was extracted with the RNeasy Mini Kit (QIAGEN) following the manufacture's instruction.
rRNA was removed using the RiboMunus Plant Kit for RNA-Seq (Invitrogen) then the library was contructed using the TruSeq Stranded Total RNA preparation kit with Ribo-Zero Plant (Illumina) following the manufacture's instruction.

treatment_protocol: Drought treatment was applied as water discontinuation for six days.

value: root

value: YJ6-infected plants under drought condition


title: Whole blood DNA methylation, HISPANIC AD, 77yo M, 207097420049_R06C01


title: A673_EWSFLI_SMASh_2-4_DMSO_24h_rep2

description: Library name: A673_EWSFLI_SMASh_2-4_DMSO_24h_rep2


title: L.serriola, YJ6 infected, dro, bio rep 2


title: Whole blood DNA methylation, HISPANIC AD, 90yo F, 207080910104_R03C01

value: Female


title: A673_EWSFLI_SMASh_2-4_DMSO_24h_rep1

description: Library name: A673_EWSFLI_SMASh_2-4_DMSO_24h_rep1


title: A673_EWSFLI_SMASh_3-11_DMSO_12h_rep1

description: Library name: A673_EWSFLI_SMASh_3-11_DMSO_12h_rep1


title: L.serriola, YJ6 infected, dro, bio rep 1


title: A673_EWSFLI_SMASh_3-11_DMSO_12h_rep2

description: Library name: A673_EWSFLI_SMASh_3-11_DMSO_12h_rep2


title: A673_EWSFLI_SMASh_2-4_DMSO_12h_rep2

description: Library name: A673_EWSFLI_SMASh_2-4_DMSO_12h_rep2


title: Whole blood DNA methylation, HISPANIC AD, 72yo F, 207097420065_R01C01


title: L.serriola, YJ6 infected, con, bio rep 3

value: YJ6-infected plants under benign water condition


title: A673_EWSFLI_SMASh_3-11_DMSO_6h_rep2

description: Library name: A673_EWSFLI_SMASh_3-11_DMSO_6h_rep2


title: Whole blood DNA methylation, HISPANIC AD, 70yo F, 207097420191_R04C01

value: whole blood


title: A673_EWSFLI_SMASh_2-4_DMSO_12h_rep1

description: Library name: A673_EWSFLI_SMASh_2-4_DMSO_12h_rep1


title: Whole blood DNA methylation, HISPANIC CONTROL, 69yo F, 207080910117_R08C01

value: Healthy control

value: HISPANIC


title: L.serriola, YJ6 infected, con, bio rep 2


title: A673_EWSFLI_SMASh_3-11_DMSO_6h_rep1

description: Library name: A673_EWSFLI_SMASh_3-11_DMSO_6h_rep1

value: DMSO


title: Whole blood DNA methylation, HISPANIC AD, 85yo F, 207097320052_R06C01


title: A673_EWSFLI_SMASh_2-4_DMSO_6h_rep2

description: Library name: A673_EWSFLI_SMASh_2-4_DMSO_6h_rep2


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo F, 207097420061_R02C01


title: L.serriola, YJ6 infected, con, bio rep 1


title: Whole blood DNA methylation, HISPANIC AD, 75yo F, 207080920090_R06C01


title: L.serriola, uninfected, dro, bio rep 3

value: uninfected plants under drought condition


title: A673_EWSFLI_AID_IAA_rep1

description: Library name: A673_EWSFLI_AID_IAA_rep1

value: EWS-FLI-AID

value: IAA


title: A673_EWSFLI_SMASh_2-4_DMSO_6h_rep1

description: Library name: A673_EWSFLI_SMASh_2-4_DMSO_6h_rep1


title: A673_EWSFLI_AID_DMSO_rep2

description: Library name: A673_EWSFLI_AID_DMSO_rep2


title: A673_EWSFLI_AID_IAA_rep2

description: Library name: A673_EWSFLI_AID_IAA_rep2


title: A673_Brunello_SW393109

description: Library name: A673_Brunello_SW393109


title: Whole blood DNA methylation, HISPANIC AD, 82yo M, 207097420065_R04C01


title: L.serriola, uninfected, dro, bio rep 2


title: Whole blood DNA methylation, HISPANIC AD, 85yo F, 207097420048_R06C01


title: A673_EWSFLI_AID_DMSO_rep1

description: Library name: A673_EWSFLI_AID_DMSO_rep1


title: TC32_RNAseq_CCT251921_rep4

description: Library name: TC32_RNAseq_CCT251921_rep4

value: WT


title: TC32_RNAseq_CCT251921_rep2

description: Library name: TC32_RNAseq_CCT251921_rep2


title: TC32_RNAseq_CCT251921_rep1

description: Library name: TC32_RNAseq_CCT251921_rep1


title: L.serriola, uninfected, dro, bio rep 1


title: Whole blood DNA methylation, HISPANIC CONTROL, 72yo F, 207097420011_R03C01


title: L.serriola, uninfected, con, bio rep 3

value: uninfected plants under benign water condition


title: TC32_RNAseq_CCT251921_rep3

description: Library name: TC32_RNAseq_CCT251921_rep3


title: Whole blood DNA methylation, HISPANIC AD, 86yo F, 207097420040_R05C01

value: Alzheimer's disease


title: TC32_RNAseq_SW393109_rep3

description: Library name: TC32_RNAseq_SW393109_rep3


title: TC32_RNAseq_SW393109_rep4

description: Library name: TC32_RNAseq_SW393109_rep4


title: Whole blood DNA methylation, HISPANIC AD, 88yo F, 207097320046_R07C01

value: PRADI


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo F, 207097420192_R07C01


title: TC32_RNAseq_DMSO_rep4

description: Library name: TC32_RNAseq_DMSO_rep4

value: Ewing sarcoma cell line


title: TC32_RNAseq_DMSO_rep3

description: Library name: TC32_RNAseq_DMSO_rep3


title: DUP217_Poly_Rep4

city: BAR HARBOR

first: CGDS

last: Data

state: ME

address: 159 OLD BAR HARBOR RD

institute: MDI Biological Laboratory

description: Library name: DUP217_Poly_Rep4

data_processing:
fastq files were run through the nextflow nf-core/rnaseq version 3.14.0 with default parameters and "remove_ribo_rna = true"
Raw counts were run through the CombatSeq R package to remove replicate batch effect
Batch-corrected counts file was uploaded into NIH SEQUIN app and analyzed using DEseq2
Assembly: Ensembl Release 111
Supplementary files format and content: Tab-separated file containing Salmon gene counts
Supplementary files format and content: Comma-separated file containing batch-corrected, non-normalized counts for NIH SEQUIN app
Supplementary files format and content: Comma-separated file containing metadata for NIH SEQUIN app
Library strategy: Polysome-seq

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans strains were maintained according to standard procedures on OP50-seeded NGM plates at 20 C. Synchronized populations were generated by bleaching 500-1,000 gravid adults in a solution of 8 mL M9 buffer, 1 mL 6.25 M NaOH, and 1 mL 5% NaOCl for 5-10 minutes. Embryos were pelleted at 1,200 x g for 1 minute, washed three times in 10 mL M9 buffer, and approximately 3,000-3,500 eggs per plate were cultured at 20 C to day 1 of adulthood.

extract_protocol:
Trizol RNA extraction
Roche Kapa stranded mRNASeq kit

treatment_protocol: No treatment was applied. Synchronized worms were grown to day 1 of adulthood, harvested (100-150 uL packed volume), and washed three times in M9 buffer to remove residual bacteria prior to lysis and fractionation.

tag: fraction

value: Polysome

tag: developmental stage

value: synchronized young adults

tag: strain

value: lotr-1(sam113[3xFLAG::gfp::lotr-1]) I

value: whole animal


title: TC32_RNAseq_DMSO_rep2

description: Library name: TC32_RNAseq_DMSO_rep2


title: DUP217_Poly_Rep3

description: Library name: DUP217_Poly_Rep3


title: A673_RNAseq_CCT251921_rep4

description: Library name: A673_RNAseq_CCT251921_rep4


title: L.serriola, uninfected, con, bio rep 1

value: root


title: Whole blood DNA methylation, HISPANIC CONTROL, 71yo M, 207080910133_R01C01

value: Male

value: whole blood


title: TC32_RNAseq_SW393109_rep1

description: Library name: TC32_RNAseq_SW393109_rep1


title: TC32_RNAseq_DMSO_rep1

description: Library name: TC32_RNAseq_DMSO_rep1


title: Whole blood DNA methylation, HISPANIC AD, 85yo F, 207097420112_R03C01

value: Female

value: HISPANIC


title: A673_RNAseq_CCT251921_rep3

description: Library name: A673_RNAseq_CCT251921_rep3


title: DUP217_Poly_Rep2

description: Library name: DUP217_Poly_Rep2


title: A673_RNAseq_CCT251921_rep2

description: Library name: A673_RNAseq_CCT251921_rep2


title: A673_RNAseq_CCT251921_rep1

description: Library name: A673_RNAseq_CCT251921_rep1


title: A673_RNAseq_SW393109_rep4

description: Library name: A673_RNAseq_SW393109_rep4


title: A673_RNAseq_SW393109_rep3

description: Library name: A673_RNAseq_SW393109_rep3


title: A673_RNAseq_SW393109_rep2

description: Library name: A673_RNAseq_SW393109_rep2


title: A673_RNAseq_SW393109_rep1

description: Library name: A673_RNAseq_SW393109_rep1


title: DUP217_Lysate_Rep2

description: Library name: DUP217_Lysate_Rep2

data_processing:
fastq files were run through the nextflow nf-core/rnaseq version 3.14.0 with default parameters and "remove_ribo_rna = true"
Raw counts were run through the CombatSeq R package to remove replicate batch effect
Batch-corrected counts file was uploaded into NIH SEQUIN app and analyzed using DEseq2
Assembly: Ensembl Release 111
Supplementary files format and content: Tab-separated file containing Salmon gene counts
Supplementary files format and content: Comma-separated file containing batch-corrected, non-normalized counts for NIH SEQUIN app
Supplementary files format and content: Comma-separated file containing metadata for NIH SEQUIN app

value: Lysate


title: Whole blood DNA methylation, HISPANIC AD, 86yo F, 207080910004_R01C01


title: DUP207_Poly_Rep4

description: Library name: DUP207_Poly_Rep4

value: lotr-1(sam117[3xFLAG::gfp::lotr-1]) I


title: BT869_Control_Day3_Rep3

city: Oxford

first: Alan

last: Jiao

state: MA

address: Old Road Campus Research Building

country: United Kingdom

institute: Ludwig Institute for Cancer Research, Oxford University

data_processing:
Reads were aligned to hg38 using STAR v2.7.9a
Gene counts were generated using featureCounts from the Rsubread v2.6.1 package, using the inbuilt hg38 genome annotation and default parameters
Assembly: hg38
Supplementary files format and content: tab-delimited text file with raw counts for each sample
Supplementary files format and content: tab-delimited text file with TPMs (transcripts per million) for each sample

growth_protocol: DIPG-XIII cells were maintained in tumor stem medium as gliomaspheres in low attachment culture flasks in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Direct-zol RNA Miniprep Plus columns (Zymo Research)
0.2-0.5ug of total RNA was used for library construction. cDNA libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina according to the manufacturer's protocol.

treatment_protocol: Differentiation was induced by treatment with DMEM/F-12 medium containing 10% FBS

value: Glioma

value: Serum differentiation


title: MUT_CT

type: RNA

city: Nagoya

first: YINGYI

last: KONG

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Graduate School of Medicine

country: Japan

institute: NAGOYA UNIVERSITY

hyb_protocol: A custom 50-gene probe panel (ID: TCMFHM) was used. Probe hybridization was performed at 50°C for approximately 18 h. Following stringent washes, adjacently hybridized probe pairs were ligated for 2 h at 37°C and amplified by rolling circle amplification (RCA) for 2 h at 30°C. Tissue autofluorescence was reduced by chemical quenching, and nuclei were counterstained with DAPI. Slides were mounted in Xenium imaging buffer and sealed in Xenium cassettes.

scan_protocol: Imaging and transcript decoding were performed on the 10x Genomics Xenium Analyzer (software v2.0.1.0) through iterative cycles of fluorescent probe binding, imaging, and signal removal, using four fluorescent channels per cycle. Images were acquired at 200 nm/pixel resolution with a 20× objective; Z-stack images were collected at 0.75 μm intervals. Adjacent fields of view were tiled and computationally stitched using DAPI nuclear signals as fiducial landmarks.

data_processing: Transcripts were decoded by matching fluorescent puncta to the predefined barcode codebook; only transcripts with Q-score ≥20 were retained. Cell segmentation was performed using the Xenium onboard segmentation pipeline: DAPI images were used to identify nuclear boundaries, expanded isotropically up to 15 μm or until reaching neighboring cell boundaries, generating non-overlapping cell polygons. Decoded transcripts within each polygon were assigned to the corresponding cell to produce a cell-by-gene expression matrix.

label: Xenium probe set

organism: Rattus norvegicus

source_name: kidney

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Kidney specimens were fixed in phosphate-buffered 10% formalin for 48 h and paraffin-embedded. FFPE tissue sections (5 μm) were processed using the Xenium FFPE in situ transcriptomics protocol (10x Genomics, v1.0; Demonstrated Protocol CG000580). Sections were deparaffinized, rehydrated, and subjected to antigen retrieval and RNA exposure, followed by enzymatic digestion under RNase-free conditions.

treatment_protocol: Ferric nitrilotriacetate (Fe-NTA) was administered intraperitoneally under the carcinogenesis protocol. Kidney specimens were obtained at 1 and 3 weeks. Untreated wild-type and Brca1(L63X/+) rats served as controls.

value: kidney

tag: tissue preservation method

value: FFPE

value: untreated control


title: DUP207_Poly_Rep3

description: Library name: DUP207_Poly_Rep3

tag: tissue


title: BT869_Control_Day3_Rep2

tag: cell type

value: WT


title: Whole blood DNA methylation, AA CONTROL, 74yo F, 207097320021_R02C01

value: Healthy control

value: AA

value: REAAADI


title: DUP207_Poly_Rep2

description: Library name: DUP207_Poly_Rep2

value: Polysome

value: synchronized young adults

tag: genotype

value: whole animal


title: BT869_Control_Day0_Rep3

tag: treatment


title: Whole blood DNA methylation, NHW AD, 75yo M, 207097420102_R03C01

value: Male

value: Alzheimer's disease

value: whole blood

value: NHW


title: L.serriola, uninfected, con, bio rep 2

value: root

value: uninfected plants under benign water condition


title: TC32_RNAseq_SW393109_rep2

description: Library name: TC32_RNAseq_SW393109_rep2

value: Ewing sarcoma cell line


title: DUP217_Poly_Rep1

description: Library name: DUP217_Poly_Rep1

value: lotr-1(sam113[3xFLAG::gfp::lotr-1]) I


title: WT_CT

value: kidney

value: FFPE

value: wild-type


title: Whole blood DNA methylation, HISPANIC AD, 86yo M, 207097420048_R07C01

value: HISPANIC

value: PRADI


title: Whole blood DNA methylation, HISPANIC AD, 75yo F, 207097420061_R06C01

value: Female


title: DUP207_Lysate_Rep4

description: Library name: DUP207_Lysate_Rep4

value: Lysate

value: lotr-1(sam117[3xFLAG::gfp::lotr-1]) I


title: BT869_Control_Day0_Rep2

value: Glioma

value: WT

value: Serum differentiation

tag: time


title: Whole blood DNA methylation, HISPANIC AD, 93yo F, 207097420114_R05C01

value: Alzheimer's disease

value: whole blood


title: DUP217_Lysate_Rep3

description: Library name: DUP217_Lysate_Rep3

value: synchronized young adults

value: whole animal


title: DUP217_Lysate_Rep4

description: Library name: DUP217_Lysate_Rep4


title: Whole blood DNA methylation, HISPANIC AD, 93yo F, 207097320021_R08C01


title: DUP217_Lysate_Rep1

description: Library name: DUP217_Lysate_Rep1


title: A673_RNAseq_DMSO_rep4

description: Library name: A673_RNAseq_DMSO_rep4

value: Ewing sarcoma cell line

value: DMSO


title: A673_RNAseq_DMSO_rep1

description: Library name: A673_RNAseq_DMSO_rep1


title: Whole blood DNA methylation, HISPANIC AD, 74yo M, 207097420082_R03C01

value: Male


title: A673_RNAseq_DMSO_rep3

description: Library name: A673_RNAseq_DMSO_rep3


title: MUT_Fe1w

value: kidney

value: FFPE

value: Fe-NTA i.p. for 1 week


title: DNFB, ear skin, mouse No. 3

city: Kaifeng

first: ruizhen

last: wang

address: Jinming Avenue, Kaifeng City, Henan Province

institute: Henan University

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format. SOAPnuke(Version v1.5.2)  Official Websitehttps://github.com/BGI-flexlab/SOAPnuke
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads.HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these
Species: Mus_musculus；Source: NCBI；Reference Genome Version: GCF_000001635.27_GRCm39

organism: Mus musculus

source_name: ear skin

growth_protocol: Healthy C57BL/6 mice (6-8 weeks) were selected and bred in Specific pathogen-free (SPF) animal chambers in separate cages. The room temperature was maintained at 20-27℃ and the normal day and night alternated, during which the normal diet was guaranteed.

extract_protocol:
After the completion of the experiment, the ear tissue samples of mice were collected for RNA extraction and sent to Wuhan Huada BGI Sequencing Company for sequencing.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSeq platform (BGI-Wuhan, China).

treatment_protocol: All mice were intraperitoneally smeared with 25 μL of 0.5 % DNFB on the first day. On the sixth day, 10 μL 0.25 % DNFB was applied to the left ear of mice, and 10 μL DNFB solvent ( 80 % acetone + 20 % olive oil ) was applied to the right ear.After 6 days of continuous operation, the ears were collected for RNA-Seq.

value: ear skin

value: DNFB


title: Whole blood DNA methylation, AA AD, 91yo F, 207097320053_R07C01

value: Female

value: AA

value: REAAADI


title: A673_RNAseq_DMSO_rep2

description: Library name: A673_RNAseq_DMSO_rep2

value: WT


title: DUP207_Lysate_Rep3

description: Library name: DUP207_Lysate_Rep3

value: Lysate

value: lotr-1(sam117[3xFLAG::gfp::lotr-1]) I


title: MUT_Fe3w

value: Fe-NTA i.p. for 3 weeks


title: Whole blood DNA methylation, AA CONTROL, 79yo F, 207097420065_R08C01

value: Healthy control

value: whole blood


title: DNFB, ear skin, mouse No. 2


title: BT869_Control_Day0_Rep1

value: Glioma

value: Serum differentiation


title: Whole blood DNA methylation, AA AD, 84yo F, 207080920105_R03C01

value: Alzheimer's disease


title: DUP207_Lysate_Rep2

description: Library name: DUP207_Lysate_Rep2

value: synchronized young adults

value: whole animal


title: BT869_ASCL1KO_Day3_Rep2


title: DNFB, ear skin, mouse No. 1


title: DUP207_Lysate_Rep1

description: Library name: DUP207_Lysate_Rep1


title: Whole blood DNA methylation, AA CONTROL, 74yo M, 207097420040_R02C01

value: Male


title: Vehicle, ear skin, mouse No. 3

value: ear skin

value: vehicle


title: Whole blood DNA methylation, AA CONTROL, 68yo M, 207080920105_R01C01


title: BT869_ASCL1KO_Day3_Rep3


title: WT_Fe3w

value: kidney

value: FFPE

value: wild-type


title: DUP185_Poly_Rep4

description: Library name: DUP185_Poly_Rep4

value: Polysome


title: BT869_ASCL1KO_Day3_Rep1


title: Vehicle, ear skin, mouse No. 2


title: Whole blood DNA methylation, AA AD, 82yo F, 207097420061_R07C01

value: Female

value: AA

value: REAAADI


title: BT869_ASCL1KO_Day0_Rep3


title: Whole blood DNA methylation, AA AD, 82yo F, 207097420079_R06C01


title: Vehicle, ear skin, mouse No. 1


title: DUP185_Poly_Rep3

description: Library name: DUP185_Poly_Rep3


title: DUP185_Poly_Rep2

description: Library name: DUP185_Poly_Rep2


title: BT869_ASCL1KO_Day0_Rep2


title: Whole blood DNA methylation, AA CONTROL, 67yo F, 207080910004_R03C01

value: Healthy control


title: β-thal patient 5

city: Fuzhou

first: hailong

last: Huang

address: 18 Daoshan Road, Gulou District

department: Medical Genetic Diagnosis and Therapy Center

institute: Fujian Maternity and Child Health Hospital

description: Biological replicate 5 of 5

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystar Human circRNA Epitranscriptomic Arrays (8x15K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C

data_processing:
Array images were analyzed using Agilent Feature Extraction software (v11.0.1.1). Raw IP (Cy5) and Sup (Cy3) intensities were normalized by the average of log2-scaled Spike-in RNA intensities. After normalization, probes with Present or Marginal QC flags in at least 5 of 10 samples were retained. Hierarchical clustering was performed using R software. CircRNA–miRNA interactions were predicted via Arraystar's software integrating TargetScan and miRanda.
"m6A quantity" was defined as the methylation amount calculated from IP (Cy5) normalized intensities. Differentially m6A-methylated circRNAs between groups were identified by filtering based on fold change and statistical significance (p-value) thresholds.

source_name: β-thal patient 5_IP

label_protocol: "IP" and "Sup" RNAs were treated with RNase R, and then amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

extract_protocol: Total RNA was extracted from peripheral blood samples using TRIzol reagent followed by chloroform phase separation and isopropanol precipitation. RNA pellets were washed with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and purity were assessed via NanoDrop spectrophotometry, and integrity was verified by agarose gel electrophoresis. For m⁶A-circRNA epitranscriptomic microarray, enriched m⁶A-containing RNA was immunoprecipitated using an anti-m⁶A antibody, followed by RNase R digestion to remove linear RNAs, leaving circular RNAs for subsequent microarray analysis.

value: peripheral blood

value: 8 mo

tag: gender

value: male

source_name: β-thal patient 5_Input


title: Whole blood DNA methylation, AA CONTROL, 73yo F, 207080910061_R08C01

tag: Sex

value: whole blood


title: BT869_Control_Day3_Rep1

value: Glioma

value: WT

value: Serum differentiation


title: WT_Fe1w

value: Fe-NTA i.p. for 1 week


title: Whole blood DNA methylation, AA AD, 78yo F, 207080910133_R03C01

tag: disease state

value: Alzheimer's disease


title: β-thal patient 4

description: Biological replicate 4 of 5

source_name: β-thal patient 4_IP

value: 6 mo

value: female

source_name: β-thal patient 4_Input


title: DUP185_Poly_Rep1

description: Library name: DUP185_Poly_Rep1

value: synchronized young adults

value: whole animal


title: K27MKO_TSM_rep3

description:
raw_counts_DIPGXIII.txt
TPM_DIPGXIII.txt

source_name: DIPG-XIII

value: DIPG-XIII


title: Whole blood DNA methylation, NHW CONTROL, 80yo F, 207080920090_R05C01

value: Female

tag: ethnicity

value: NHW


title: DUP185_Lysate_Rep3

description: Library name: DUP185_Lysate_Rep3

value: Lysate


title: K27MKO_TSM_rep2


title: Whole blood DNA methylation, NHW CONTROL, 83yo M, 207097420049_R03C01

value: Male

value: Healthy control

tag: cohort


title: β-thal patient 2

description: Biological replicate 2 of 5

source_name: β-thal patient 2_IP

value: peripheral blood

tag: age

value: 8 mo

value: male

source_name: β-thal patient 2_Input


title: DUP185_Lysate_Rep2

description: Library name: DUP185_Lysate_Rep2


title: K27MKO_TSM_rep1

tag: cell line

value: Glioma


title: β-thal patient 1

description: Biological replicate 1 of 5

source_name: β-thal patient 1_IP

value: 11 mo

source_name: β-thal patient 1_Input


title: DUP185_Lysate_Rep1

description: Library name: DUP185_Lysate_Rep1


title: K27MKO_DM_Week10_rep2

value: Serum differentiation


title: DUP167_Poly_Rep4

description: Library name: DUP167_Poly_Rep4

value: Polysome


title: Whole blood DNA methylation, AA CONTROL, 77yo M, 207097420010_R04C01

source_name: whole blood

value: whole blood

value: AA

value: REAAADI


title: K27MKO_DM_Week10_rep1


title: Healthy control 4

description: Biological replicate 4 of 5

source_name: Healthy control 4_IP

value: female

source_name: Healthy control 4_Input


title: K27MKO_DM_Day3_rep2

value: DIPG-XIII


title: DUP167_Poly_Rep3

description: Library name: DUP167_Poly_Rep3

value: synchronized young adults

value: whole animal


title: Whole blood DNA methylation, NHW CONTROL, 90yo M, 207097420061_R03C01

value: NHW


title: K27MKO_DM_Day3_rep1


title: Whole blood DNA methylation, NHW AD, 77yo F, 207097650112_R08C01

value: Female

value: Alzheimer's disease


title: Healthy control 2

description: Biological replicate 2 of 5

source_name: Healthy control 2_IP

value: peripheral blood

source_name: Healthy control 2_Input


title: Whole blood DNA methylation, NHW AD, 86yo F, 207097650070_R06C01


title: DUP167_Lysate_Rep4

description: Library name: DUP167_Lysate_Rep4

source_name: whole animal

value: Lysate


title: DKO_TSM_rep2

value: ASCL1-KO; K27M-KO


title: IL-4 C1q_EV

city: Hangzhou

first: Mengying

last: An

state: Zhejiang

address: 西湖区浙大路38号

institute: Zhejiang University

description:
Library name: SAMPLES3
Total RNA enriched for small RNAs was extracted from extracellular vesicles derived from IL-4/C1q treated primary rat astrocytes and subjected to miRNA sequencing.

data_processing:
Raw sequencing reads were processed using ACGT101-miR (v4.2) to remove adapter dimers, low-complexity sequences, and reads corresponding to common non-coding RNA families including rRNA, tRNA, snRNA, and snoRNA.
Unique reads ranging from 18–26 nt were mapped to species-specific precursor sequences in miRBase v22.1 for identification of known and novel miRNAs, allowing terminal variation and one mismatch.
Reads that could not be assigned were aligned against precursor sequences and genomes from other species, and candidate precursor structures were predicted using RNAfold.
Differential expression analysis was performed using Fisher exact test. Differentially expressed miRNAs were visualized using volcano plots based on log2 fold change and P values.
Functional enrichment analyses including Gene Ontology (GO) and KEGG pathway analyses were performed using overlapping candidate miRNAs.
Assembly: Rattus norvegicus; miRBase release 22.1
Supplementary files format and content: Processed data files contain filtered miRNA expression matrices, miRNA annotations, normalized abundance values, differential expression results, and functional enrichment analysis outputs.

source_name: extracellular vesicles

extract_protocol:
Primary astrocytes were harvested after treatment and total RNA was extracted using a commercial RNA extraction kit according to the manufacturer’s instructions. RNA concentration and purity were evaluated prior to library preparation, and only qualified RNA samples were used for sequencing.
Small RNA libraries were generated from extracellular vesicle-derived RNA according to standard protocols for miRNA sequencing, including adapter ligation, reverse transcription, amplification, and library purification. Final libraries were sequenced on an Illumina sequencing platform.

value: extracellular vesicles

value: leave blank

value: Wild type

value: IL-4/C1q treated

tag: batch


title: DUP167_Lysate_Rep3

description: Library name: DUP167_Lysate_Rep3

tag: fraction


title: IL-1a TNFa C1q_EV

description:
Library name: SAMPLES2
Total RNA enriched for small RNAs was extracted from extracellular vesicles derived from IL-1a/TNFa/C1q treated primary rat astrocytes and subjected to miRNA sequencing.

value: IL-1a/TNFa/C1q treated


title: DUP167_Lysate_Rep2

description: Library name: DUP167_Lysate_Rep2

tag: developmental stage


title: UT_EV

description:
Library name: SAMPLES1
Total RNA enriched for small RNAs was extracted from extracellular vesicles derived from primary rat astrocytes and subjected to miRNA sequencing.

value: Untreated


title: Whole blood DNA methylation, NHW AD, 83yo M, 207215820034_R05C01

data_processing:
All quality control and data normalization were performed using the openSeSAMe pipeline from the SeSAMe R package (Zhou et al., 2018). Probes of poor design were removed, as well as probes with detection P-value > 0.05 in more than 5% of samples. Non-CG probes and probes on X, Y, and mitochondrial chromosomes were also removed. Samples with incomplete bisulfite conversion (GCT score > 1.5) and principal component analysis outliers were excluded. Noob normalization was performed with SeSAMe using a nonlinear dye-bias correction.
processed value definition: Beta values representing the ratio of methylated probe intensity to overall intensity (methylated + unmethylated + offset). Values range from 0 (unmethylated) to 1 (fully methylated).

value: Male

value: whole blood


title: DRG_rat_FishOilDiet_Injury_LeftSide4

city: Loma Linda

first: Hoang

middle: Viet

last: Dinh

address: 11085 CAMPUS STREET, MTH-105

department: Center for Health Disparities

institute: Loma Linda university

description: Library name: G6_55L

data_processing:
Raw FASTQ reads underwent fastp QC (adapter/poly-N/low-quality removal; Q20/Q30/GC calculated). Clean reads were Hisat2-aligned (v2.0.5) to the reference genome (with splice junction database). Gene expression was quantified via featureCounts (v1.5.0-p3) as FPKM
Assembly: ncbi_rattus_norvegicus_gcf_000002265_2_rn_celera
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: cvs file for FPKM values of each sample

source_name: Dorsal Root Ganglia

growth_protocol: Female Sprague-Dawley rats were housed in ventilated cages with ad libitum access to food and water, under a 12-hour light/dark cycle

extract_protocol:
total mRNA of DRG was isolated using the Qiagen AllPrep kit (cat. no. 80004) for simultaneous mRNA/DNA/protein. RNA integrity was assessed via Bioanalyzer 2100 (Agilent Technologies, CA, USA).
Messenger RNA is purified from total RNA using poly-T magnetic beads, fragmented, and converted to cDNA using random hexamer primers, with second-strand synthesis using dTTP for non-strand-specific libraries or dUTP for strand-specific libraries. Both library types undergo end repair, A-tailing, adapter ligation, size selection, amplification, and purification, followed by quality control using Qubit, real-time PCR, and a bioanalyzer. Libraries are then pooled and sequenced on an Illumina platform to analyze gene expression.

treatment_protocol: After 1 week of acclimatization, rats were divided randomly into two dietary groups (n=20 each): a control diet (AIN-93G-based) and a fish oil-enriched diet with modified n-3 fatty acid sources. Following 4 weeks of dietary intervention, each group was subdivided by surgical procedure: control/sham, control/chronic constriction injury (CCI), fish oil/sham, and fish oil/CCI. A 3–4 mm incision exposed the left sciatic nerve below the femur, and four loose chromic gut 4.0 ligatures (Ethicon, USA) were tied 1 mm apart proximal to the trifurcation, ensuring minimal nerve compression. Sham rats underwent identical exposure without ligatures. Muscle was sutured, skin closed with stainless steel staples, and rats recovered for 1 week with daily monitoring

value: Dorsal Root Ganglia

value: WT_Fish Oil Diet_CCI

value: chronic constriction injury of Sciatic Nerve


title: DKO_DM_Day3_rep2

value: DIPG-XIII

value: Glioma

value: Serum differentiation


title: Whole blood DNA methylation, NHW AD, 76yo M, 207215830119_R05C01

value: Alzheimer's disease

value: NHW


title: DRG_rat_FishOilDiet_Injury_LeftSide3

description: Library name: G6_51L


title: RNA-seq of C. elegans with mutation in nlg-1 (tm474) young adult_biol rep 2

city: Ondo

first: Omamuyovwi

middle: Meashack

last: Ijomone

state: Ondo

address: Medical Village, Laje Road

department: Anatomy

country: Nigeria

institute: University of Medical Sciences

description:
Library name: Sample-62
Column name in raw_counts.csv: nlg-1 (tm474): Sample.62

data_processing:
The enriched RNAs were fragmented for 8 minutes at 94 °C. First-strand and second-strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and an indexed adapter was ligated to the cDNA fragments. Limited-cycle PCR was used for library enrichment.
The incorporated dUTP in the second-strand cDNA quenched the amplification of the second strand, which helped to preserve the strand specificity.
The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA) and quantified by using Qubit 4.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The libraries were clustered on a flowcell and sequenced on an Illumina NovaSeq platform in a 2x150 bp paired-end configuration. Raw sequence data were converted to fastq files and de-multiplexed using Illumina's bcl2fastq 2.20 software.
Assembly: WBcel235 (Ensembl)
Supplementary files format and content: csv file contains raw counts for each sample

source_name: whole-organism

growth_protocol: All C. elegans strains were handled and maintained at 20 °C on Nematode Growth Medium (NGM) agar plates seeded with Escherichia coli OP50 as a food source. Worms were transferred periodically onto fresh NGM plates using a sterile worm pick or agar chunking technique to ensure healthy propagation

extract_protocol:
Approximately 20,000 worms were transferred into 15 mL tubes using 85 mM NaCl supplemented with 0.1% Tween 20. Following subsequent washes, the worms were transferred to 2.0 mL tubes, snap-frozen in liquid nitrogen, and stored at −80 °C for subsequent analysis. Total RNA was extracted from the resulting lysates using the RNeasy Plus Universal Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration was quantified using a Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA), and RNA integrity was assessed using an Agilent 4200 TapeStation system (Agilent Technologies, Palo Alto, CA, USA).
rRNA depletion was performed using the QIAGEN FastSelect rRNA HMR Kit (Qiagen, Germantown, MD, USA). Strand-specific libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, Ipswich, MA, USA) following the manufacturer’s instructions.

value: whole-organism


title: DKO_DM_Day3_rep1

value: ASCL1-KO; K27M-KO


title: Whole blood DNA methylation, NHW AD, 68yo M, 207215820075_R07C01

extract_protocol: Genomic DNA was extracted from whole blood samples at external processing sites associated with each cohort. Standard column-based DNA extraction methods were used according to each site's established protocols.


title: DKO_DM_Week10_rep1


title: RNA-seq of C. elegans with mutation in nlg-1 (tm474) young adult_biol rep 1

description:
Library name: Sample-61
Column name in raw_counts.csv: nlg-1 (tm474): Sample.61


title: Control_TSM_rep3

value: WT


title: Whole blood DNA methylation, NHW AD, 87yo M, 207221680059_R06C01


title: DRG_rat_FishOilDiet_Injury_LeftSide1

description: Library name: G6_43L


title: Control_TSM_rep2


title: DRG_rat_FishOilDiet_Injury_RightSide3

description: Library name: G5_51R


title: Whole blood DNA methylation, NHW AD, 81yo M, 207221680026_R06C01


title: DKO_DM_Week10_rep2


title: RNA-seq of C. elegans with mutation in nlg-1 (ok259) young adult_biol rep 2

description:
Library name: Sample-47
Column name in raw_counts.csv: nlg-1 (ok259): Sample.47


title: Control_TSM_rep1


title: DUP167_Lysate_Rep1

description: Library name: DUP167_Lysate_Rep1

value: Lysate

value: synchronized young adults

tag: strain

value: whole animal


title: Whole blood DNA methylation, NHW AD, 89yo F, 207215820065_R01C01

value: Female


title: DRG_rat_FishOilDiet_Injury_RightSide2

description: Library name: G5_47R


title: Control_Sph_DM_Week10_rep2


title: RNA-seq of C. elegans with mutation in nlg-1 (ok259) young adult_biol rep 1

description:
Library name: Sample-46
Column name in raw_counts.csv: nlg-1 (ok259): Sample.46


title: Whole blood DNA methylation, NHW AD, 92yo M, 207219630122_R03C01

value: Male


title: RNA-seq of C. elegans with mutation in nrx-1 (tm1961) young adult_biol rep 3

description:
Library name: Sample-33
Column name in raw_counts.csv: nrx-1 (tm1961): Sample.33


title: Control_Sph_DM_Week10_rep1


title: DRG_rat_FishOilDiet_Control_LeftSide3

description: Library name: G4_52L

value: WT_Fish Oil Diet_Control

value: Control


title: Control_Sph_DM_BackInTSM_rep2


title: Whole blood DNA methylation, NHW AD, 75yo F, 207219740068_R02C01

value: whole blood


title: Whole blood DNA methylation, NHW AD, 89yo M, 207096540017_R04C01


title: DRG_rat_FishOilDiet_Control_LeftSide2

description: Library name: G4_48L

value: Dorsal Root Ganglia


title: RNA-seq of C. elegans with mutation in nrx-1 (tm1961) young adult_biol rep 1

description:
Library name: Sample-31
Column name in raw_counts.csv: nrx-1 (tm1961): Sample.31


title: Control_Sph_DM_BackInTSM_rep1

value: DIPG-XIII


title: Whole blood DNA methylation, NHW AD, 84yo F, 207215820061_R07C01


title: DRG_rat_FishOilDiet_Control_LeftSide1

description: Library name: G4_44L


title: RNA-seq of C. elegans with mutation in nrx-1 (ok1649) young adult_biol rep 3

description:
Library name: Sample-18
Column name in raw_counts.csv: nrx-1 (ok1649): Sample.18


title: Whole blood DNA methylation, NHW AD, 81yo F, 207215820121_R03C01


title: Control_DM_Day3_rep2

value: Glioma


title: DRG_rat_FishOilDiet_Injury_RightSide1

description: Library name: G5_43R

value: WT_Fish Oil Diet_CCI

value: chronic constriction injury of Sciatic Nerve


title: RNA-seq of C. elegans with mutation in nrx-1 (ok1649) young adult_biol rep 2

description:
Library name: Sample-17
Column name in raw_counts.csv: nrx-1 (ok1649): Sample.17


title: DRG_rat_SoyOilDiet_Injury_LeftSide3

description: Library name: G3_53L

value: WT_Soy Oil Diet_Injury


title: Whole blood DNA methylation, NHW AD, 83yo F, 207215830065_R07C01

value: Alzheimer's disease

value: NHW


title: Control_DM_Day3_rep1

value: WT

value: Serum differentiation


title: BT869_ASCL1KO_Day0_Rep1


title: DUP185_Lysate_Rep4

description: Library name: DUP185_Lysate_Rep4

value: Lysate

value: synchronized young adults


title: Whole blood DNA methylation, NHW AD, 74yo M, 207219630122_R05C01


title: β-thal patient 3

description: Biological replicate 3 of 5

source_name: β-thal patient 3_IP

value: peripheral blood

value: female

source_name: β-thal patient 3_Input


title: Whole blood DNA methylation, AA AD, 83yo M, 207097420040_R06C01

value: Male

value: AA

value: REAAADI


title: RNA-seq of C. elegans with mutation in nrx-1 (tm1961) young adult_biol rep 2

description:
Library name: Sample-32
Column name in raw_counts.csv: nrx-1 (tm1961): Sample.32

value: whole-organism


title: Whole blood DNA methylation, NHW CONTROL, 90yo F, 207080910085_R07C01

value: Female

value: Healthy control

value: whole blood


title: Control_Adh_DM_Week10_rep2

value: DIPG-XIII

value: Glioma


title: RNA-seq of C. elegans with mutation in nrx-1 (ok1649) young adult_biol rep 1

description:
Library name: Sample-16
Column name in raw_counts.csv: nrx-1 (ok1649): Sample.16


title: DRG_rat_SoyOilDiet_Injury_LeftSide2

description: Library name: G3_49L

value: Dorsal Root Ganglia

value: WT_Soy Oil Diet_Injury

value: chronic constriction injury of Sciatic Nerve


title: Healthy control 5

description: Biological replicate 5 of 5

source_name: Healthy control 5_IP

value: male

source_name: Healthy control 5_Input


title: Whole blood DNA methylation, NHW AD, 81yo F, 207215820045_R01C01

value: Alzheimer's disease

value: NHW


title: Healthy control 3

description: Biological replicate 3 of 5

source_name: Healthy control 3_IP

value: peripheral blood

source_name: Healthy control 3_Input


title: RNA-seq of C. elegans N2 wild-type young adult_biol rep 3

description:
Library name: Sample-03
Column name in raw_counts.csv: Control: Sample.03

value: WT


title: Control_Adh_DM_Week10_rep1

source_name: DIPG-XIII

value: Serum differentiation


title: DRG_rat_SoyOilDiet_Injury_LeftSide1

description: Library name: G3_45L


title: Whole blood DNA methylation, NHW AD, 69yo F, 207096540063_R07C01


title: DUP167_Poly_Rep1

description: Library name: DUP167_Poly_Rep1

value: Polysome

value: synchronized young adults

value: whole animal


title: Healthy control 1

description: Biological replicate 1 of 5

source_name: Healthy control 1_IP

value: female

source_name: Healthy control 1_Input


title: DKO_TSM_rep3

value: ASCL1-KO; K27M-KO


title: DUP167_Poly_Rep2

description: Library name: DUP167_Poly_Rep2


title: RNA-seq of C. elegans N2 wild-type young adult_biol rep 2

description:
Library name: Sample-02
Column name in raw_counts.csv: Control: Sample.02

value: whole-organism


title: DRG_rat_SoyOilDiet_Injury_RightSide3

description: Library name: G2_53R


title: ASCL1KO_TSM_rep3

value: DIPG-XIII


title: DRG_rat_SoyOilDiet_Injury_RightSide2

description: Library name: G2_49R


title: RNA-seq of C. elegans N2 wild-type young adult_biol rep 1

description:
Library name: Sample-01
Column name in raw_counts.csv: Control: Sample.01


title: Whole blood DNA methylation, NHW AD, 84yo F, 207215830104_R02C01

source_name: whole blood

value: Female

value: whole blood


title: ASCL1KO_TSM_rep2

description:
raw_counts_DIPGXIII.txt
TPM_DIPGXIII.txt

value: Glioma


title: Whole blood DNA methylation, NHW AD, 74yo F, 207215830018_R03C01


title: Whole blood DNA methylation, NHW AD, 81yo M, 207215820046_R07C01

value: Male


title: DKO_TSM_rep1


title: DRG_rat_SoyOilDiet_Injury_RightSide1

description: Library name: G2_45R

value: Dorsal Root Ganglia

value: WT_Soy Oil Diet_Injury

value: chronic constriction injury of Sciatic Nerve


title: CRISPIRi guide library from single cell mRNA sequenicing of A549 perturbed cells, channel 2

first: Hani

last: Goodarzi

address: 600 16th street

description:
Library name: A549_ch2_sgRNA
CRISPRi guide rna from single cell perturb seq of A549 cells

data_processing:
STAR version 2.7.11b
Assembly: hg38
Supplementary files format and content: .H5AD files contain raw single cell mRNA counts, with cell filtering and guide calling
Supplementary files format and content: .MTX files countain cellXfeature (gene or guide depending on library) for each channel

source_name: Lung

extract_protocol:
10x 5'
Chromium Next GEM Single Cell 5' HT Kit v2

value: Lung

value: Basal

value: Single-cell perturb seq


title: ASCL1KO_TSM_rep1

value: Serum differentiation


title: Whole blood DNA methylation, NHW AD, 79yo F, 207215830126_R06C01

value: Alzheimer's disease

value: NHW


title: DRG_rat_SoyOilDiet_Control_LeftSide4

description: Library name: G1_54L

value: WT_Soy Oil Diet_Control

value: Control


title: ASCL1KO_DM_Week10_rep2


title: Single cell mRNA sequenicing of A549 perturbed cells, channel 2

description:
Library name: A549_ch2_WTS
mRNA library of single cell perturb seq experiment


title: Whole blood DNA methylation, NHW AD, 79yo M, 207219770143_R07C01


title: CRISPIRi guide library from single cell mRNA sequenicing of A549 perturbed cells, channel 1

description:
Library name: A549_ch1_sgRNA
CRISPRi guide rna from single cell perturb seq of A549 cells


title: DRG_rat_SoyOilDiet_Control_LeftSide3

description: Library name: G1_50L


title: ASCL1KO_DM_Week10_rep1


title: ASCL1KO_DM_Day3_rep2


title: Whole blood DNA methylation, NHW AD, 75yo M, 207215820044_R08C01


title: DRG_rat_SoyOilDiet_Control_LeftSide1

description: Library name: G1_42L


title: HEK293T_siMTA3_sRNA_3

city: Urbana

first: Ruiying

last: Cheng

state: IL

address: B520 Chemical & Life Sciences Laboratory

department: School of Molecular & Cellular Biology

institute: The University of Illinois Urbana-Champaign

description: Library name: siMTA3_sRNA_3

data_processing:
Small RNA sequencing (sRNA-seq) reads were processed using a standardized pipeline. Raw single-end reads were trimmed with Trim_Galore to remove adapter sequences and low-quality bases, and read quality was assessed using FastQC. Trimmed reads were aligned to the custom THP1_active_PolIIIgenes_100exp index using Bowtie2/2.3.5.1, and resulting SAM files were converted, sorted, and indexed as BAM files using SAMtools/1.9-IGB-gcc-4.9.4. Genome-normalized coverage tracks were generated using deepTools/3.2.1.  Reads counts at RNA central noncoding genes (gene body +- 50bp) were obtained with BEDTools/2.28.0 (coverage function, -counts mode).
Assembly: GRCh38.109
Supplementary files format and content: Bigwig

extract_protocol:
small RNA seq: Total steady-state small RNA was purified from equal numbers (~2 million cells per small RNA-seq experiment) of HEK293T cells treated with siRNA using the mirVana™ PARIS™ RNA and Native Protein Purification Kit (Catalog# AM1556, Invitrogen) according to manufacturer's protocol for sRNA enrichment . The small RNA were treated with Antartic Phosphatase and PNK and libraries were constructed with the NEBNext Small RNA Sample Prep kit (NEB).
Samples are quantified using Bioanalyzer and sequenced with Nova X 25B paired-reads 300-cycle on the NovaSeq X Plus platform


title: ASCL1KO_DM_Day3_rep1


title: Whole blood DNA methylation, NHW AD, 88yo F, 207221680026_R05C01

first: Sebastián

last: Cruz-González


title: WI38-ONT

city: Singapore

first: XIAORAN

last: CHAI

address: 8 College Rd, Singapore 169857

country: Singapore

institute: Duke-NUS Medical School

description: Library name: Sample 19

data_processing:
For PacBio sequencing, consensus HiFi reads were generated on-instrument using the default CCS function.
For Nanopore sequencing, base calling was performed using dorado-0.9.5 with “super accurate” mode.
Assembly: CHM13-v2.0
Supplementary files format and content: Tab-delimited text file includes telomere/subtelomere length and number of TRF1/TRF2 binding sites on each read.

extract_protocol:
Genomic DNA from cultured cells was extracted using the Gentra Puregene Genomic DNA Purification Kit (Qiagen)
For PacBio sequencing, SMRTBELL EXPRESS TEMPLATE PREP KIT 2.0 was used. For Nanopore sequencing, Ligation Sequencing Kit V14 was used.

value: fibroblast


title: HEK293T_siMTA3_sRNA_2

description: Library name: siMTA3_sRNA_2


title: Whole blood DNA methylation, NHW AD, 79yo F, 207215820046_R04C01

city: San Francisco

institute: UCSF


title: SJSA1-ONT

description: Library name: Sample 17


title: RKO-SmiI

description: Library name: Sample 15

source_name: RKO

value: RKO

value: colon carcinoma cell


title: Whole blood DNA methylation, NHW AD, 75yo F, 207215830113_R08C01

value: Female

value: whole blood


title: CnT_H3K27me3_K27MKO_Wk10_Rep1

data_processing:
*library strategy: CUT&TAG-Direct
Reads were aligned to the human hg38 (target genome) and E. coli K-12 MG1655 (spike-in genome) using Bowtie2 v2.3.5.1, with settings --no-unal --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700
Spike-in-normalized bigwig track files were created using bamCoverage from deepTools v3.3.1, with settings --binSize=20 --smoothLength=60 --normalizeUsing BPM --scaleFactor $scale_factor.
Scale factors were calculated as the ratio of total reads / spike-in reads
Assembly: hg38, E. coli K-12 (MG1655)
Supplementary files format and content: bigWig

extract_protocol:
CUT&TAG-Direct was performed with anti-H3K27me3 (CST 9733). Tagmented genomic DNA was extracted using 1%SDS/Proteinase K
Released, tagmented DNA from ~50,000 starting cells was amplified using non-hot-start polymerase (NEB M0541S) using the following program: 58oC, 5 mins; 72oC, 5mins; 98oC 30s; (98oC 10s, 63oC 30s) x 12 cycles total, 72oC, 1min.

value: DIPG-XIII

value: Glioma

tag: cut&tag antibody


title: HEK293T_siHDAC2_sRNA_3

description: Library name: siHDAC2_sRNA_3


title: Whole blood DNA methylation, NHW AD, 85yo F, 207215820075_R06C01

tag: tissue


title: CnT_H3K27me3_K27MKO_TSM_Rep2

tag: cell type


title: HEK293T_siHDAC2_sRNA_2

description: Library name: siHDAC2_sRNA_2


title: Raji-ONT

description: Library name: Sample 14

source_name: Raji

value: Raji

value: B lymphocyte


title: Whole blood DNA methylation, NHW AD, 76yo F, 207097650067_R06C01


title: CnT_H3K27me3_K27MKO_TSM_Rep1

tag: genotype


title: IMR90SV40-RsaI

description: Library name: Sample 12


title: HEK293T_siHDAC2_sRNA_1

description: Library name: siHDAC2_sRNA_1

tag: treatment


title: CnT_H3K27me3_K27MKO_Day3_Rep2

tag: time


title: Whole blood DNA methylation, NHW AD, 81yo M, 207221680011_R03C01

value: Male


title: HEK293T_siHDAC1_sRNA_3

description: Library name: siHDAC1_sRNA_3


title: IMR90-ONT

description: Library name: Sample 11


title: CnT_H3K27me3_K27MKO_Day3_Rep1


title: Whole blood DNA methylation, NHW AD, 78yo F, 207215820048_R03C01


title: HEK293T_siHDAC1_sRNA_2

description: Library name: siHDAC1_sRNA_2


title: IGROV1-SmiI

description: Library name: Sample 9

value: human ovarian carcinoma cells


title: Whole blood DNA methylation, NHW AD, 76yo F, 207215830027_R01C01


title: CnT_H3K27me3_DKO_Wk10_Rep2

value: DKO


title: HeLa-ONT

description: Library name: Sample 8

source_name: HeLa

value: HeLa

value: human epithelial cell


title: CnT_H3K27me3_DKO_Wk10_Rep1

value: Serum differentiation


title: Whole blood DNA methylation, NHW AD, 85yo M, 207215820046_R06C01

value: Alzheimer's disease

value: NHW


title: 293T-ONT

description: Library name: Sample 6

value: human embryonic kidney


title: CnT_H3K27me3_Control_TSM_Rep2

value: WT


title: Whole blood DNA methylation, NHW AD, 88yo F, 207219630128_R05C01


title: HEK293T_siCon_sRNA_2

description: Library name: siCon_sRNA_2

value: control siRNA


title: ht1080.ONT-inHouse-WGSHT1080

description: Library name: ht1080.ONT-inHouse-WGSHT1080

data_processing:
For HiFi sequenicng and Revio sequencing, consensus HiFi reads were generated on-instrument using the default CCS function.
For Nanopore sequencing, base calling was performed using dorado-0.9.5 with “super accurate” mode.
Assembly: CHM13-v2.0
Supplementary files format and content: tab-delimited text file includes telomere/subtelomere length and number of TRF1/TRF2 binding sites on each read.

extract_protocol:
Genomic DNA from cultured cells was extracted using the Gentra Puregene Genomic DNA Purification Kit (Qiagen)
For HiFi and Revio sequencing, SMRTBELL EXPRESS TEMPLATE PREP KIT 2.0 was used. For Nanopore sequencing, Ligation Sequencing Kit V14 was used.

value: human fibrosarcoma cell line


title: Whole blood DNA methylation, NHW CONTROL, 82yo F, 207215820121_R06C01

value: Female

value: Healthy control

value: whole blood


title: CnT_H3K27me3_Control_TSM_Rep1

value: DIPG-XIII

value: Glioma


title: HEK293T_siCon_sRNA_1

description: Library name: siCon_sRNA_1


title: hct116.AITULWGS100k

description: Library name: hct116.AITULWGS100k

value: human colorectal carcinoma cell line


title: Whole blood DNA methylation, NHW CONTROL, 75yo M, 207215830114_R07C01

value: Male


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I2376

city: Tel Aviv

first: Lubna

last: Khair

address: Weizmann 6

country: Israel

institute: Sourasky medical center

description:
Library name: I2376_S41
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: RDEB; Gene: COL7A1; Mutation: c.567delG, p.Gln189Hisfs*16; Age: 7; Sex: male; Sample ID: I2376; Mutation group: 11; Family: w; Used in differential analysis: no; Exclusion reason: group_not_tested(missing_severity). Instrument model: Illumina NextSeq 2000

data_processing:
Raw sequencing reads were quality-checked, adapter-trimmed, and aligned to the human reference genome (GRCh38) using Bismark in non-directional mode. CpG methylation calls were extracted using the Bismark methylation extractor. Methylation percentages were calculated as the number of methylated reads divided by the total reads covering each CpG site. Differentially methylated regions (DMRs) and differentially methylated CpGs (DMCs) were identified using the methylKit package in R after standard coverage filtering, removal of extreme coverage outliers, and false discovery rate (FDR) correction (FDR < 0.05).
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data include CpG methylation calls, methylation percentages, differentially methylated CpGs (DMCs), differentially methylated regions (DMRs), and methylKit output files generated from RRBS analysis.

source_name: peripheral blood

extract_protocol:
Genomic DNA was extracted from peripheral blood leukocytes using the Gentra Puregene Blood Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. For samples collected as saliva, genomic DNA was isolated using standard laboratory procedures. DNA concentration and purity were assessed prior to library preparation.
Reduced Representation Bisulfite Sequencing (RRBS) libraries were prepared using the Zymo-Seq RRBS Library Prep Kit (Zymo Research, Irvine, CA, USA). Genomic DNA was quantified using a Qubit 4 fluorometer, digested with MspI, end-repaired, A-tailed, ligated to methylated adapters, and subjected to bisulfite conversion followed by PCR amplification. Library quality and fragment size distribution were assessed using an Agilent TapeStation 4200. Libraries were pooled equimolarly and sequenced on an Illumina NextSeq 2000 platform using paired-end 2 × 51 bp reads.

value: peripheral blood

value: leukocytes

value: COL7A1 c.567delG, p.Gln189Hisfs*16


title: hct116.Inhouse-ONT-run1

description: Library name: hct116.Inhouse-ONT-run1


title: Whole blood DNA methylation, NHW CONTROL, 80yo F, 207215830126_R04C01


title: hPIB-142_d9_S_CD45_1

city: Lund

first: Ilia

last: Kurochkin

address: BMC A12, Sölvegatan 17

institute: Lund University

description: Library name: hPIB-142_d9_S_CD45_1

data_processing:
FASTQ files were preprocessed using the nf-core RNA-seq pipeline (v3.14.0) with default parameters, except for UMI extraction, which was done using the following options: --with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*". Technical replicates were merged together.
Briefly, paired-end reads were aligned to the human genome (Ensembl release 110) using STAR, and transcript quantification was performed with Salmon.
Assembly: hg38
Supplementary files format and content: count tables (.txt)

source_name: skin

extract_protocol:
1000-2000 cells were sorted intro PBS with 2 % FBS, pelleted and frozen at -80 °C. RNA was exracted using TRIzol according to manufacturer's protocol.
Libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian kit by Takara.

treatment_protocol: HDFs were transduced on day -1 with lentiviral vectors encoding for PIB and with lentiviral vectors encoding for miRNA hairpins. Cells were sorted on day 3, 6 or 9. Human dendritic cells were enriched from peripheral blood and sorted for subtype-specific markers.

value: skin

value: human dermal fibroblast

value: Cells were transduced with lentivirus coding for Pu.1, Irf8, Batf3 (PIB) and with a lentivirus coding for human miR-142 on day -1 of reprogramming.

value: Cells were collected on day 9 of reprogramming.

tag: sorted cells

value: live (DAPI-) and CD45+ HLA-DR-

tag: technical replicates


title: 15_MX9_Gpm3_gid11

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

country: Germany

institute: Institute of Molecular Biology (IMB)

description:
Library name: Sample 15
MX9-Gpm3-tFT library in gid11∆ background (saturation mutagenesis of residues 2-10)

data_processing:
Demultiplexed fastq files were checked for raw data quality and potential DNA contamination using FastQC (v0.11.9) and FastQScreen (v0.13) software.
Cutadapt (v4.0) was used to trim adapter sequences and for NextSeq-specific 3’ end quality trimming applying a threshold of 20.
Reads were filtered for a minimum length of 15 nucleotides and a maximum expected number of errors equal to 1 computed from quality values using Cutadapt (v4.0).
Read pairs were assembled using the paired-end read merger PEAR (v0.9.11) to reconstruct amplicon sequences based on a minimum of 10 bases overlap of the paired reads. Unassembled read pairs were discarded.
The variable region and the bin barcode were subsequently extracted from the assembled sequences by applying a design-specific regular expression with the extract command in UMI-Tools (v1.1.2) using flanking common sequences.
Reads were counted for each observed combination of variable region and bin barcode, and were exported as a count matrix in text format. Bin barcodes in order 1 (low stability) to 8 (high stability): TCGTTAAGC, GTCATCGAA, TGGCAACGT, GTGAGGTCT, ACTACCAGG, TGACCACCT, CAGTCACAA, GGACTGTAT
Protein stability indices (PSIs) per sequence variant were calculated from count data either per nucleotide sequence or per translated amino acid sequence as described (PMID 29727619) using the analysis pipeline available at: https://gitlab.rlp.net/imbforge/NGSpipe2go/-/tree/MPSprofiling
Assembly: Not applicable, because no alignment applied
Supplementary files format and content: tab delimited text files (tsv) containing counts of each observed combination of variable region (column ‘sequence’) and bin barcode (column ‘id’).

organism: Saccharomyces cerevisiae

source_name: yeast strain yKEK092 transformed with the desired plasmid variants

growth_protocol: Yeast cells were grown at 30°C in synthetic complete (SC) glucose medium lacking histidine to log-phase and shifted to SC ethanol medium lacking histidine for 24h before sorting.

extract_protocol:
Yeast cells were lysed by mechanical shearing and then the plasmids therein were isolated by column-purification.
The variable regions were PCR-amplified with the incorporation of unique barcode IDs for each stability bin. The PCR products were pooled proportionally according to the number of cells sorted into each bin, and then used as the template for another PCR for adding the sample barcodes and illumina sequencing adaptors.

treatment_protocol: Yeast cells were sorted into 8 stability bins according to the tFT readout. The cells sorted into each bin were separately grown to saturation.

value: MATalpha can1delta::STE2pr-SpHIS5 lyp1delta::STE3pr-LEU2 his3delta1 leu2delta0 ura3delta0 leu2delta0::GAL1pr-I-SCEI-natNT2 gid11delta::kanMX6


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I171

description:
Library name: I171_S39
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: RDEB; Gene: COL7A1; Mutation: c.567delG, p.Gln189Hisfs*16; Age: 21; Sex: female; Sample ID: I171; Mutation group: 11; Family: v; Used in differential analysis: no; Exclusion reason: group_not_tested(missing_severity). Instrument model: Illumina NextSeq 2000


title: CnT_H3K27me3_Control_Day3_Rep1

value: WT

value: Serum differentiation


title: Whole blood DNA methylation, NHW CONTROL, 70yo F, 207097650075_R04C01

tag: Sex

value: Female

tag: disease state

value: Healthy control

value: NHW


title: 14_MX9_Gpm3_gid9

description:
Library name: Sample 14
MX9-Gpm3-tFT library in gid9∆ background (saturation mutagenesis of residues 2-10)

source_name: yeast strain yKEK114 transformed with the desired plasmid variants

value: MATalpha can1delta::STE2pr-SpHIS5 lyp1delta::STE3pr-LEU2 his3delta1 leu2delta0 ura3delta0 leu2delta0::GAL1pr-I-SCEI-natNT2 gid9delta::kanMX6


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient EB5601003

description:
Library name: EB5601003_S38
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: RDEB; Gene: COL7A1; Mutation: c.2767G>A, p.Gly923Arg /c.7371insA; Clinical severity: Mild; Sample ID: EB5601003; Mutation group: 10; Family: u; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000

value: COL7A1 c.2767G>A, p.Gly923Arg /c.7371insA


title: CnT_H3K27me3_Control_Adh_Wk10_Rep2

value: DIPG-XIII

value: Glioma


title: 13_MX9_Gpm3_WT

description:
Library name: Sample 13
MX9-Gpm3-tFT library in wild type background (saturation mutagenesis of residues 2-10)

source_name: yeast strain yMaM330 transformed with the desired plasmid variants

value: MATalpha can1delta::STE2pr-SpHIS5 lyp1delta::STE3pr-LEU2 his3delta1 leu2delta0 ura3delta0 leu2delta0::GAL1pr-I-SCEI-natNT2


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient EB5601002

description:
Library name: EB5601002_S37
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: RDEB; Gene: COL7A1; Mutation: c.2767G>A, p.Gly923Arg /c.7371insA; Clinical severity: Mild; Sample ID: EB5601002; Mutation group: 10; Family: u; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000

value: peripheral blood

value: leukocytes


title: CnT_H3K27me3_Control_Adh_Wk10_Rep1


title: 12_MX9_Phm8_gid11

description:
Library name: Sample 12
MX9-Phm8-tFT library in gid11∆ background (saturation mutagenesis of residues 2-10)

value: yeast strain yKEK092 transformed with the desired plasmid variants


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient EB5601001

description:
Library name: EB5601001_S36
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: RDEB; Gene: COL7A1; Mutation: c.2767G>A, p.Gly923Arg /c.7371insA; Clinical severity: Moderate; Age: 20; Sex: male; Sample ID: EB5601001; Mutation group: 10; Family: u; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000


title: CnT_H3K27me3_ASCL1KO_Wk10_Rep2


title: Whole blood DNA methylation, NHW CONTROL, 82yo M, 207221680059_R02C01

value: Male

value: whole blood

tag: ethnicity

tag: cohort


title: 11_MX9_Phm8_gid9

description:
Library name: Sample 11
MX9-Phm8-tFT library in gid9∆ background (saturation mutagenesis of residues 2-10)

value: yeast strain yKEK114 transformed with the desired plasmid variants


title: Whole blood DNA methylation, NHW CONTROL, 73yo M, 207215820131_R06C01

tag: age


title: 10_MX9_Phm8_WT

description:
Library name: Sample 10
MX9-Phm8-tFT library in wild type background (saturation mutagenesis of residues 2-10)

value: yeast strain yMaM330 transformed with the desired plasmid variants

tag: batch


title: Whole blood DNA methylation, NHW CONTROL, 65yo F, 207228480079_R02C01


title: 09_MXZ_Gpm3_gid11

description:
Library name: Sample 9
MXZ-Gpm3-tFT library in gid11∆ background (combinatorial mutagenesis of residues 2 and 3)

value: MATalpha can1delta::STE2pr-SpHIS5 lyp1delta::STE3pr-LEU2 his3delta1 leu2delta0 ura3delta0 leu2delta0::GAL1pr-I-SCEI-natNT2 gid11delta::kanMX6


title: RRBS of genomic DNA from peripheral blood leukocytes of epidermolysis bullosa patient I463

description:
Library name: I463_S33
Reduced Representation Bisulfite Sequencing (RRBS) of genomic DNA extracted from peripheral blood leukocytes.; Disease: epidermolysis bullosa; EB subtype: JEB; Gene: LAMB3; Mutation: c.1977-1G>A /  c.1977-1G>A; Clinical severity: Mild; Age: 54; Sex: female; Sample ID: I463; Mutation group: 8; Family: r; Used in differential analysis: yes. Instrument model: Illumina NextSeq 2000


title: CnR_H3K27me3_K27MKO_Wk10_Rep1

data_processing:
Reads were aligned to the human hg38 (target genome) and Saccharomyces cerevisiae sacCer3 (spike-in genome) using Bowtie2 v2.3.5.1, with settings --no-unal --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700
Spike-in-normalized bigwig track files were created using bamCoverage from deepTools v3.3.1, with settings --binSize=20 --smoothLength=60 --normalizeUsing BPM --scaleFactor $scale_factor.
Scale factors were calculated as the ratio of total reads / spike-in reads
Assembly: hg38, sacCer3
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN (Cleavage under targets and release using nuclease). Enriched genomic DNA fragments were extracted using Monarch PCR & DNA Cleanup columns (NEB T1030S).
3-15ng of genomic DNA was used for library construction. Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's protocol.

tag: cell line

value: Serum differentiation

tag: cut&run antibody