title: Ctrl_II620 [blood]

description:
SAKII620
Study subject II620, cell sample.


title: IEI_30 [blood]

status: Public on Oct 20 2021

type: RNA

city: Helsinki

first: Piia

last: Karisola

state: Southern Finland

address: Haartmaninkatu 3

department: Medical Faculty, Human Microbes Research Program Unit

country: Finland

institute: University of Helsinki

description:
SYM030
Study subject 30, cell sample.

hyb_protocol: Labeled cRNAs were hybridized to Agilent 2-color 60-mer oligo arrays according to the manufacturer's recommendations.

scan_protocol: Slides were washed and scanned with Agilent Microarray scanner G2505C, according to the manufacturer's recommendations.

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into eUtopia bioinformatics package and analyzed with BioConductor package Limma. Data was quantile normalized based on cutoff 0.75 and percentage of samples 75%. Replicate control probes were combined by their median values.

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

label_protocol: Samples were amplified using T7 RNA polymerase method and the cRNAs were further labeled with Cy3 and Cy5 dye, according to the manufacturer's recommendations.

growth_protocol: No cell culturing was involved.

extract_protocol: Total RNA was isolated from 2x10^6 PBMCs by AllPrep Plus (Qiagen). Quantity and quality of the samples were determined by NanoDrop spectrophotometer and Agilent Bioanalyzer 2100, respectively. Samples with RNA integrity number > 8 were selected and independent pools of two RNA samples were used for the analysis.

treatment_protocol: PBMCs were extracted from the blood by CPT tubes. Several control individuals underwent 2 different treatments, one set used inhaled corticosteroids (SAKII, N = 15) and the others did not (SAK, N = 21).

tag: diagnosis

value: IEI

tag: gender

value: Female

tag: age

tag: cell type

value: PBMC


title: T3_11

type: SRA

city: Colchester

first: Liudmila

last: Mikheeva

address: Wivenhoe Park

country: United Kingdom

institute: University of Essex

library_source: transcriptomic

data_processing:
Trimmed reads were aligned to Phaeodactylum tricornutum CCAP 1055/1 genome (GCF_000150955.2) using TopHat v2.1.2 with Bowtie2 v2.3.4.1. We used Picard tools (http://broadinstitute.github.io/picard/) to deduplicate reads and HTseq to count reads with parameters stranded=yes and type=exon.
Genome_build: Phaeodactylum tricornutum CCAP 1055/1
Supplementary_files_format_and_content: raw counts text files

organism: Phaeodactylum tricornutum

source_name: cell suspension

growth_protocol: Phaedactylum tricornutum was grown in K medium (Keller et al., 1987) with the addition of silicic acid (1.06 10-4 M) using an artificial seawater base and maintained under continuous illumination of 325±25 µmol photons m2 s-1.

extract_protocol:
Tri-Reagent as per manufacturers instructions including a DNAse treatment step
Preparation of dual-indexed, strand-specific RNASeq library from total RNA, using RiboZero rRNA depletion and the NEBNext Ultra Directional RNA library preparation kits according to manufacturet's instructions. Carried out by the centre for genomic research at the University of Liverpool.

treatment_protocol: See "overall design"

tag: control (c) or treatment (t)

value: T

tag: biological replicate

tag: time point

tag: strain

value: CCMP 2561


title: T3_09


title: T3_08


title: T3_06


title: T3_05


title: MOLM-13.WM1119.3

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

country: USA

institute: The Rockefeller University

data_processing:
Alignment-independent quantification using Salmon
Genome_build: mm10
Genome_build: hg38
Supplementary_files_format_and_content: TPM as txt file

growth_protocol: MOLM-13 cell line was cultured in RPMI (Corning, 10-041-CV) with 10% FBS (Life Technologies, 16000044) and 1% Penicillin Streptomycin (Gibco, 15-140-122). Mouse ER-Hoxa9 cells was cultured in RPMI (Corning, 10-041-CV) with 10% FBS (Life Technologies, 16000044), 1% Penicillin Streptomycin (Gibco, 15-140-122), 1% - 2% stem cell factor (SCF) conditioned media (generated from a Chinese hamster ovary (CHO) cell line that stably secretes SCF), and 0.5 µM β-estradiol (Fisher Scientific MP021016562).

extract_protocol:
RNA was extracted using Qiagen RNeasy  Kit.
RNA-seq libraries were build by a commercial company, Novogene, following standard protocols.

treatment_protocol: MOLM-13 cells were treated with 4uM WM-1119 for 4 days and ER-Hoxa9 cells were treated with 2uM WM-1119 for 4 days.

tag: cell line

tag: treatment


title: AAD_77 [blood]

description:
SYM077
Study subject 77, cell sample.

value: adult-onset asthma


title: Ctrl_615 [blood]

description:
SAK615
Study subject 615, cell sample.

value: healthy


title: T3_07


title: OII-A

city: Alicante

first: Luis

middle: M

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

data_processing:
Base calling using Illumina CASAVA software
Filtering of ribosomal and mitochondrial sequences and 5’end trimming of 2 bases (bowtie in TopHat Alignment  v1.0.1)
Assignment to genomic features (GenomicAlignment -R version 3.5.3)
Genome_build: Human GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text file with Ensembl ID and read counts for all the samples

source_name: Brain tumor

extract_protocol:
We deparaffined 3 slices of 10 µm-thickness from each FFPE-block according to the xylene protocol described in the RNeasy FFPE kit (Qiagen) handbook. Total RNA were obtained after purification and DNase digestion using the RNeasy FFPE kit (Qiagen) following manufacturer’s instructions.
The starting amount of total RNA was 100 ng following Illumina recommendations to prepare the sequencing library using the TruSeq RNA Exome library kit (Illumina).

treatment_protocol: No treatment

value: Oligodendroglioma grade II

value: Male


title: pCGY3402_recurrent

city: Calgary

first: Marco

last: Gallo

state: Alberta

address: 3330 Hospital Drive NW, Heritage Medical Research Building

department: Cumming School of Medicine

country: Canada

institute: University of Calgary

library_source: genomic

data_processing:
All raw base call (BCL) files generated by Illumina® sequencers were converted to FASTQ files using cellranger-atac mkfastq function, a wrapper around bcl2fastq from Illumina®, with additional 10x Genomics-specific features. Next, read filtering and alignment, barcode counting, and identification of transposase cut sites were detected using cellranger-atac count function using the cellranger-atac-specific GRCh38 reference package.
Genome_build: refdata-cellranger-atac-GRCh38-1.2.0 (GRCh38 with pre-generated indices and other data required to run CellRanger-ATAC)
Supplementary_files_format_and_content: Filtered peak-barcode matrix output from CellRanger-ATAC (containing only detected cellular barcodes)

molecule: genomic DNA

source_name: patient-derived pediatric glioblastoma

extract_protocol:
Flash frozen tissue samples were resuspended in cold ATAC resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin, 1% BSA in PBS) on ice and dissociated using a wide-bore P1000 pipette tip and vortexing, followed by 10 minutes of incubation on ice. Cells were spun down at 500x g for 5 minutes at 4 C, washed in the ATAC resuspension buffer, spun down again, and resuspended in ATAC-Tween wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA in PBS), then passed through a cell strainer top FACS tube (Falcon; #38030) to remove debris. Nuclei quality and quantity was evaluated using trypan blue on an Invitrogen Countess II device in duplicate, and a subset of nuclei was spun down in a fresh tube and resuspended in 10X sample dilution buffer.
Libraries were prepared according to 10X Genomics Chromium Single Cell ATAC Library & Gel Bead Kit Chemistry. Briefly, single nuclei were first treated in bulk with Tn5 transposase to preferentially insert sequencing adaptors into accessible DNA regions. Transposed nuclei are then partitioned into GEMs in the 10x Chromium Controller. All the DNA fragments from the same nucleus share a common 10x barcode. The barcoded, accessible DNA fragments are subsequently pooled for downstream processing and library preparation. Completed libraries were further quality checked for fragment size and distribution using an Agilent TapeStation prior to sequencing.Next generation sequencing was performed using Illumina NextSeq 500  per cell.

value: Recurrent glioblastoma

tag: tissue

value: glioblastoma


title: AND_84 [blood]

description:
SYM084
Study subject 84, cell sample.


title: IEI_23 [blood]

description:
SYM023
Study subject 23, cell sample.


title: OII-C


title: T3_03


title: pCGY2937_recurrent


title: MOLM-13.DMSO.1

value: DMSO


title: MOLM-13.DMSO.3


title: Ctrl_611 [blood]

description:
SAK611
Study subject 611, cell sample.


title: GS-A

value: Gliosarcoma of giant cells grade IV


title: pCGY4021_recurrent


title: T3_01


title: Ctrl_639 [blood]

description:
SAK639
Study subject 639, cell sample.


title: IEI_37 [blood]

description:
SYM037
Study subject 37, cell sample.


title: proliferative parental cell line_replicate 3 [THEP3]

first: Jose Javier

last: Bravo Cordero

state: NY

address: 1468 Madison Avenue, Annenberg 24-34

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Basecalls performed using CASAVA version 1.8
Mapped to hg19 using STAR v2.5 using the parameter mismatch =2
Quantification was done using HTSeq v 0.6.1, using the parameter -m union
For differential expression, samples with bio-replicate using DESeq2 v2_1.6.3 (padj<0.05)，samples without bio-replicate using EdgeR v3.16.5 (padj <0005 and log2FC >1).
Enrichment analysis ClusterProfiler v2.4.3 (padj < 0.05) or GO, DO, KEGG, Reactome enrichment analysis (DO only for Homo sapiens)
Protein-Protein Interaction Analysis NCBI BLAST v2.2.28 with e-value = 1e-10,
Alternative splicing using rMATS v3.2.1, default parameters
Fusion gene using Star-fusion v0.8.0 default parameters
SNP/InDel Analysis using GATK3 v3.4 (MQ < 40.0 and QD < 2.0) for SNP/InDel calling
SNP/InDel annotation using ANNOVAR v2.4 using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: readcount_genename.csv

source_name: proliferative parental cell line

growth_protocol: cell lines were injected orthotopically in nude Athymic mice. (500 000 cells per animal) Grown for 2 weeks and collected. Tumor were flash-freezed.

extract_protocol: Total RNA were extracted with the RNA kit Rneasy Mini kit from Qiagen,following the instruction provided by distributor. RNA purity and integrity  were verified by Nanodrop, agarose gel and Agilent 2100.

tag: origin

value: head and neck squamous cell carcinoma

tag: replicates


title: MOLM-13.DMSO.2


title: MOLM-13.WM1119.2


title: pCGY3749

source_name: primary patient-derived pediatric glioblastoma

value: primary glioblastoma


title: MOLM-13.WM1119.1


title: pCGY2932


title: Ctrl_II618 [blood]

description:
SAKII618
Study subject II618, cell sample.


title: AND_61 [blood]

description:
SYM061
Study subject 61, cell sample.


title: T3_02


title: C3_11

value: C


title: IEI_10 [blood]

description:
SYM010
Study subject 10, cell sample.


title: proliferative parental cell line_replicate 1 [THEP1]


title: dormant cell line with shRNA DDR1_replicate 3 [DHEPsD3]

source_name: dormant cell line with shRNA DDR1

value: shRNA DDR1


title: AND_56 [blood]

description:
SYM056
Study subject 56, cell sample.


title: AAD_29 [blood]

description:
SYM029
Study subject 29, cell sample.


title: C3_12


title: C3_08


title: T3_04


title: T3_00


title: APD_26 [blood]

description:
SYM026
Study subject 26, cell sample.


title: Ctrl_II627 [blood]

description:
SAKII627
Study subject II627, cell sample.


title: dormant cell line with shRNA DDR1_replicate 1 [DHEPsD1]


title: C3_10


title: dormant cell line with shRNA control_replicate 3 [DHEsC3]

source_name: dormant cell line with shRNA control

value: shRNA control


title: Snubar-96plex

city: Houston

first: Anil

middle: K

last: Sood

state: TX

address: 6767 Bertner Ave

department: genetics

institute: MDACC

description:
Snubar-96plex_ATAC and Snubar-96plex_BC
SnubarATAC-96plex: 96 samples mixture-scATAC and mixture-sample_barcode
For ATAC pair-end read: R1: READ1, R2: CELL BARCODE, R3: READ2. For BC pair-end read: R1: Sample barcode+ UMI, R2: CELL BARCODE
SnubarATAC single cell ATAC-seq and barcode library

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger atac V1.2.0 mkfastq
cellranger atac V1.2.0 count and cellranger-arc-1.0.0 count
Mixing experiment data was aligned to the combined reference genomes of human (hg19 reference) and mouse (mm10 reference). All other experimental data was aligned to human hg19 or mouse mm10 genome.
UMI counts and peak count are summarized
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI and Peak values for each Sample

growth_protocol: The A20 and K562 cell lines were purchased from the American Type Culture Collection and cultured based on ATCC guidelines. The MDA-MB-231 and MDA-MB-436  cell lines were obtained from the MD Anderson Characterized Cell Line Core Facility and were cultured in Dulbecco’s Modified Eagle’s Medium-high glucose medium supplemented with 10% FBS  and 1X penicillin-streptomycin. Mice were purchased from the Jackson Laboratory and housed in the Research Animal Support Facility at MD Anderson Cancer Center.

extract_protocol:
Cell nuclei for Snubar-ATAC were isolated according to Nuclei Isolation for Single Cell ATAC Sequencing Protocol (CG000169 Rev D, 10X Genomics) or Nuclei Isolation from Mouse Brain Tissue for Single Cell ATAC Sequencing Protocol (CG000212 Rev B, 10X Genomics). Nuclei used for SNubar-ARC were isolated according to Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing Protocol (10X Genomics, CG000365 Rev A).
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics protocols (CG000168 Rev A for Chromium Single Cell ATAC Reagent Kits,  CG000209 Rev D for Chromium Next GEM Single Cell ATAC Library Kit v1.1, or CG000338 Rev A for Chromium Next GEM Single Cell Multiome ATAC + Gene Expression)
single cell ATAC-seq, single cell RNA&ATAC co-assay, and barcode libraries

treatment_protocol: 28 mice were treated under 7 different conditions (4 mice in each group): 1) Control; 2) Chemotherapy + 2 Gy Radiotherapy; 3) 4 Gy Radiotherapy; 4) Chemotherapy + 2 Gy Radiotherapy + Talazoparib; 5) Chemotherapy + 2 Gy Radiotherapy + PD-L1 Blockade; 6) 4Gy Radiotherapy + PD-L1 Blockade; 7) 4Gy Radiotherapy + Talazoparib + PD-L1 Blockade.

tag: cell lines


title: C3_05


title: proliferative parental cell line_replicate 2 [THEP2]


title: dormant cell line with shRNA DDR1_replicate 2 [DHEPsD2]


title: AAD_62 [blood]

description:
SYM062
Study subject 62, cell sample.

value: Female


title: C3_07


title: dormant cell line with shRNA control_replicate 2 [DHEsC2]


title: Ctrl_622 [blood]

description:
SAK622
Study subject 622, cell sample.

value: PBMC


title: C3_04


title: AND_54 [blood]

description:
SYM054
Study subject 54, cell sample.


title: Ctrl_II623 [blood]

description:
SAKII623
Study subject II623, cell sample.


title: C3_06


title: dormant parental cell line_replicate 1 [DHEP1]

source_name: dormant parental cell line


title: AND_79 [blood]

description:
SYM079
Study subject 79, cell sample.


title: Snubar-HBCA1

description:
Snubar-HBCA1_ATAC and Snubar-HBCA1_BC
SnubarATAC-HumanNormalBreast-1-scATAC and sample_barcode
For ATAC pair-end read: R1: READ1, R2: CELL BARCODE, R3: READ2. For BC pair-end read: R1: Sample barcode+ UMI, R2: CELL BARCODE
SnubarATAC single cell ATAC-seq and barcode library

value: breast tissues, fresh normal, surgical sample


title: T2_11

value: CCMP 2561


title: Snubar-CoAssay_HBCA_BC

description: SnubarATAC&RNA-Coassay-fresh normal-sample_barcode

data_processing:
Basecalls performed using CASAVA version 1.8.1
cellranger atac V1.2.0 mkfastq
cellranger atac V1.2.0 count
reads are mapped to hg19
UMI counts are summarized are gene expression levels
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI and Peak values for each Sample

growth_protocol: Single cell suspensions are made from cell line and  fresh tumors

extract_protocol:
RNAs afe extracted from single cell suspensions
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics Single Cell Chromium 3’ protocol (PN-1000075)
single cell 3' RNAseq and ATAC-seq

treatment_protocol: samples are collected before treatment

value: fresh normal

tag: tag

value: surgical sample


title: C3_01


title: dormant parental cell line_replicate 3 [DHEP3]


title: C3_02


title: C3_00


title: dormant cell line with shRNA control_replicate 1 [DHEsC1]


title: IEI_55 [blood]

description:
SYM055
Study subject 55, cell sample.

value: IEI


title: APD_17 [blood]

description:
SYM017
Study subject 17, cell sample.

value: adult-onset asthma


title: Snubar-CoAssay_HBCA_ATAC

description: SnubarATAC&RNA-Coassay-fresh normal-scATAC


title: Ctrl_618 [blood]

description:
SAK618
Study subject 618, cell sample.

value: healthy


title: IEI_7 [blood]

description:
SYM007
Study subject 7, cell sample.


title: T2_12


title: dormant parental cell line_replicate 2 [DHEP2]


title: C3_03


title: T2_07

value: T


title: Ctrl_631 [blood]

description:
SAK631
Study subject 631, cell sample.


title: T2_10


title: Snubar-CoAssay_HBCA_RNA

description: SnubarATAC&RNA-Coassay-fresh normal-scRNA


title: T2_09


title: Control monocyte-derived small extracellular vesicles Replicate 3

city: Chengdu

first: Hongtao

last: Liu

state: Sichuan

address: No.82, qinglong street, qingyang district, chengdu

department: General surgery

country: China

institute: Chengdu third people's hospital

description: Gene expression in Monocyte-derived small extracellular vesicles

hyb_protocol: Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA)(typically of 1.5ug) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Images from scanning were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded

label_protocol: The cRNA labeled with Cyanine-3 (Cy3) was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations. The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion. Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Monocyte freshly drawn from healthy volunteers or CAD patients was irradiated, then diluted 1:1 with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2

tag: patient diagnosis

value: healthy control

value: male


title: AAD_43 [blood]

description:
SYM043
Study subject 43, cell sample.


title: T2_04


title: AND_81 [blood]

description:
SYM081
Study subject 81, cell sample.


title: Ctrl_II625 [blood]

description:
SAKII625
Study subject II625, cell sample.


title: Snubar-HBCA2

description:
Snubar-HBCA2_ATAC and Snubar-HBCA2_BC
SnubarATAC-HumanNormalBreast-2-scATAC and sample_ barcode
For ATAC pair-end read: R1: READ1, R2: CELL BARCODE, R3: READ2. For BC pair-end read: R1: Sample barcode+ UMI, R2: CELL BARCODE
SnubarATAC single cell ATAC-seq and barcode library


title: T2_05


title: Ctrl_620 [blood]

description:
SAK620
Study subject 620, cell sample.


title: Control monocyte-derived small extracellular vesicles Replicate 1

value: Monocyte-derived small extracellular vesicles


title: T2_06


title: AND_48 [blood]

description:
SYM048
Study subject 48, cell sample.


title: CD23_Docile_2

city: Melbourne

first: Andrea

last: Di Pietro

state: VIC

address: 305 Grattan Street

department: Cancer Immunology program

country: Australia

institute: Peter MacCallum Cancer Centre

description: BCR-Seq

data_processing:
Library strategy: BCR-seq
Raw sequence data (FASTQ files) were processed through pRESTO
Germline V and J genes were identified by aligning pre-processed data to the murine IgH germline repertoire using the IMGT/HighV-QUEST tool
Aligned reads were further processed with Change-O v0.4.6 (Gupta et al., 2015). The Change-O processing pipeline included filtering non-functional sequences and clustering sequences into clonal lineages
The frequency of mutation from germline, replacement to silent ratios (R/S ratio), and selection pressure (BASELINE, (Yaari et al., 2012)) were calculated using SHazaM v0.2.1 (Gupta et al., 2015).

organism: Mus musculus

source_name: Germinal Center B cells

extract_protocol:
Fresh cell pellets were lysed and genomic DNA was extracted using a genomic DNA purification kit.
DNA library was built using a KAPA HiFi HotStart ReadyMix PCR kit (KAPA, Roche, #KK2601), including VJ/JH primer mix which have sequences for Illumina platform indexes.
Library were amplified using the Nextera kit and purified libraries were sequenced at the MiSeq V2 platform

treatment_protocol: C57BL/6 CD23cre or Bmi1-floxed mice were either treated with LCMV WE or Docile for 14 days. Germinal Center B cells were sort-purified from total splenocytes.

value: LCMV Docile

tag: genotype/variation


title: Bmi1-floxed_Docile_1

description: BCR-Seq


title: CD23_Docile_1

description: BCR-Seq


title: Bmi1-floxed_WE_1

description: BCR-Seq

value: LCMV WE


title: Bmi1-floxed_WE_2

description: BCR-Seq


title: Bmi1-floxed_Docile_2

description: BCR-Seq


title: Control monocyte-derived small extracellular vesicles Replicate 2

value: female


title: T2_03


title: T2_01


title: CD23_WE_2

description: BCR-Seq


title: Monocyte-derived small extracellular vesicles in coronary atherosclerosis Replicate 1

value: coronary atherosclerosis


title: CD23_WE_1

description: BCR-Seq


title: IEI_47 [blood]

description:
SYM047
Study subject 47, cell sample.

tag: diagnosis

value: Female


title: Monocyte-derived small extracellular vesicles in coronary atherosclerosis Replicate 3

tag: gender


title: Monocyte-derived small extracellular vesicles in coronary atherosclerosis Replicate 2


title: Ctrl_II643 [blood]

description:
SAKII643
Study subject II643, cell sample.

tag: age

value: PBMC


title: IEI_4 [blood]

description:
SYM004
Study subject 4, cell sample.

tag: cell type


title: APD_15 [blood]

description:
SYM015
Study subject 15, cell sample.


title: T2_00

tag: control (c) or treatment (t)


title: HAS3_WT_LESION

city: Charlottesville

first: Gary

last: Owens

state: VA

address: 415 Lane Road MR5 Building Room 1322

institute: University of Virginia

data_processing:
Basecalls performed using CASAVA
Reads were aligned against mouse genome mm10 using the CellRanger software (10x Genomics).
Gene-barcode matrices were analyzed in R using Seurat v342. Cells were filtered for 200-5000 reads per UMI, 10% or less mitochondrial and less than 5% hemoglobin gene content.
Significant principal components of variation (PCs) were calculated using JackStraw test with 10000 repetitions, and clusters were calculated with 19 PCs
Differential expression analysis was done using MAST
Genome_build: mm10
Supplementary_files_format_and_content: Cell-gene-barcode matrices; gz file containing barcodes, genes and matrix.mtx (10x output filtered folder)

source_name: Atherosclerosis plaques

extract_protocol:
Individual atherosclerotic plaques from the brachiocephalic artery were removed from underlying media with forceps and deposited into FACS buffer (1% BSA in PBS) plus 1 ug/mL Actinomycin D,(Gibco, #11805017). Samples were then minced and digested with 1mL Liberase (Roche, #355374) plus 1ug/mL ActinomycinD for 1 hour at 37 degrees, then resuspended in PBS plus 0.04% UltraPure non-Acetylated BSA (ThermoFisher #AM2616) and filtered through 30um filters on ice. Samples were then either counted and submitted directly for scRNAseq or sorted by flow cytometry. Samples for flow were stained with Sytox Blue viability dye and sorted with a BD FACSAria Fusion cell sorter with gating on live, single cells that were eYFP+. Cells were collected into LoBind tubes containing 0.04% non-acetylated BSA.
2,000 cells in each group were targeted in Chromium 10X genomics libraries, which after barcoding, were pooled and sequenced on the Illumina NextSeqTM, 150 cycle high-output.

treatment_protocol: Animals were maintened in a Western Diet for 18 weeks

value: Mixture of cell types (SMC, Epithelial, Macrophage, others)

tag: diet

value: Western Diet

tag: molecule subtype

value: single-cell total RNA


title: C2_12

value: C

tag: biological replicate

tag: time point

tag: strain

value: CCMP 2561


title: AND_42 [blood]

description:
SYM042
Study subject 42, cell sample.

value: adult-onset asthma


title: BCD25_2

city: Cleveland

first: Chengfeng

last: Yang

state: OHIO

address: 2500 MetroHealth Drive

institute: Case Western Reserve University

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v4.0 (8 x 60K, Arraystar).

scan_protocol: After washing the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: BEAS-2B-Cadmium exposed cells

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis and Agilent 2100 Bioanalyzer.

tag: treatment

value: Cadmium exposed


title: BCD25_3


title: C2_11


title: HAS3_KO_LESION


title: SmallRNA.chicken.testis.WhiteLeghorn.adult.unox.rep3

city: Rochester

first: Xin

address: 601 Elmwood Ave

department: Biochemistry and Biophysics

institute: University of Rochester

description: Small RNAseq

data_processing:
Analyses were performed using piPipes v1.4. All data from the small RNA sequencing, ribosome profiling (Ribo-seq), RNA sequencing, and degradome sequencing were analyzed using the latest mouse genome release mm10 (GCA_000001635.7), and chicken genome release galGal6 (GCA_000002315.5). Generally, one mismatch is allowed for genome mapping.
For small RNA sequencing, libraries were normalized to the sum of total miRNA reads. Uniquely mapping reads >23 nt were selected for further piRNA analysis. To ensure precision of the mapping, a piRNA is counted only when the 5´-end of the piRNA maps to the transcript.
For RNA-seq reads, the tpm (transcripts per million) values were quantified using the Salmon software.
For Ribo-seq analysis, uniquely mapping reads between 26 nt and 32 nt were selected for further analysis.
Genome_build: Mouse: mm10 (GCA_000001635.7), Chicken: galGal6 (GCA_000002315.5)
Supplementary_files_format_and_content: For Small RNAseq, processed data files are unique genome alignment results in BED2 format (https://github.com/bowhan/piPipes/wiki/smallRNA-seq). For Ribo-seq, results are unique genome alignment bed13 files, with an additional sequence column after a regular bed12 format. For Degradome, unique mapping reads are in bed12 format. RNAseq quantification results are .sf files output by Salmon software.

organism: Gallus gallus

source_name: testis

growth_protocol: Mice were maintained and used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester. White Leghorn testes of the Cornell Special C strain from one-year old roosters were used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester.

extract_protocol:
Total RNAs were extracted using mirVana miRNA Isolation Kit (ThermoFisher, AM1560), and rRNAs were depleted from total RNAs with complementary DNA oligomers (IDT) and RNaseH (Invitrogen, Waltham, MA, USA)
1, Strand-specific RNA-seq: libraries were constructed following the TruSeq RNA sample preparation protocol. 2, Ribo-seq: Testes samples were lysed, RNase T1 & A treated and loaded on sucrose gradients, and 80S monosomes were recovered for library constrution. The 3'-adapter is TGGAATTCTCGGGTGCCAAGG. 3, Degradome: The RNAs were first oxidized at room temperature for 30 minutes with sodium periodate (Sigma, St. Louis, MO, USA) to block the 3´-ends from ligation, and were then size-selected to isolate RNA ≥ 200 nt (DNA Clean & Concentrator™-5, Zymo Research). 5´ adaptors were attached using T4 RNA ligase (Ambion) at 20°C for 3 hours. The ligated products were subjected to rRNA depletion with complementary DNA oligomers (IDT) and RNaseH (invitrogen). The rRNA depleted ligation products were reverse transcribed using a degenerate primer (5´-GCACCCGAGAATTCCANNNNNNNNC-3´). cDNA was amplified by PCR using KAPA HIFI Hotstart polymerase (Kapa Biosystems, Wilmington, MA, USA), and 250–350 nt dsDNA was isolated on 8% native PAGE gels. 4, Small RNAseq: Small RNA libraries were constructed and sequenced using oxidation to enrich for piRNAs by virtue of their 2´-O-methyl-modified 3´ termini. The oxidation procedure selects against in vitro-digested products with a 3´ phosphate. A 25-mer RNA with 2´-O-methyl-modified 3´ termini (5´-UUACAUAAGAUAUGAACGGAGCCCmG -3´) was used as a spike-in control. The 3'-adapter is TGGAATTCTCGGGTGCCAAGG.

treatment_protocol: The mice were anesthetized with Ketamine/Xylazine mixture (Ketamine 100 mg/kg; Xylazine 25 mg/kg) via intraperitoneal injection. After complete anesthesia, testes were exteriorized with a longitudinal incision around 1 cm at the center of abdomen. The tunica albuginea was penetrated using a sharp 26 G needle (BD, Franklin Lakes, NJ, USA, 30511) 1 mm from the vascular pedicle, and the needle was withdrawn to generate path for introducing a blunt end Hamilton needle (Hamilton, Reno, NV, USA, 7786-02). PBS containing 0.02% Fast Green FCF (Thermo Fisher Scientific, Waltham, MA, USA) with 4EGI was slowly injected using a Hamilton microsyringe (1705RN) into one testis, and vehicle control without drug was injected into the other testis. The needle was held in place for 30 seconds before removal to prevent back flow of the solution. Successful completion of injection was indicated by testis filled with green solution. The testes were returned to the abdominal cavity after injection. The incisions were sutured. At the end point, the mice were euthanized by cervical dislocation, and the testes were collected. For immunoprecipitations, anti-CBP80 rabbit antibody (Bethyl laboratories, A301-794A) or anti-eIF4E rabbit antibody (Bethyl laboratories, A301-153A) were used.

tag: tissue

value: whole testis

value: WhiteLeghorn

tag: genotype

value: adult

value: small RNA


title: C2_10


title: bottom bisected fragment T= 60 post surgery rep 3

city: San Francisco

first: Wallace

last: Marshall

state: CA

institute: UCSF

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Stentor genome (StentorDB), using tophat2 (-i 9 -I 101 --min-segment-intron 9 --min-coverage-intron 9 --max-segment-intron 101 --max-coverage-intron 101 -p 20). We used Trinity to build a transcriptome (--genome_guided_max_intron 1000). For quantification of transcript abundance, we aligned reads to the transcriptome using Kallisto (-t 15 -b 30). Transcriptome file is included here: SteCoe_Trinity_assembled_transcriptome_for_GEO.fasta
Genome_build: Stentor coeruleus (GCA_001970955.1)
Supplementary_files_format_and_content: For each Sample:
tsv file containing matrix of estimated counts, TPM, effective length for each gene.
HDF5 binary file containing run info, abundance estimates, bootstrap estimates, and transcript length information length.
json file containing information about the run
Trinity generated transcriptome (fasta)

organism: Stentor coeruleus

source_name: Stentor coeruleus cell

extract_protocol:
At each time point, a sample of cells was lysed into RNA-stabilizing buffers specified by the extraction kit, and then stored on ice until the end of the experiment when the RNA purification was performed in parallel on all samples. RNA was extracted at each time point using the Nucleospin RNA XS kit from Clontech (cat. num. 740902.250).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time

value: 60 minutes post surgery

value: bottom fragment

value: wild type


title: SmallRNA.chicken.testis.WhiteLeghorn.adult.unox.rep2

description: Small RNAseq


title: C2_09


title: C2_07


title: IEI_2 [blood]

description:
SYM002
Study subject 2, cell sample.

value: IEI


title: Ctrl_604 [blood]

description:
SAK604
Study subject 604, cell sample.

value: healthy

value: Female


title: C2_08


title: BCON_3

source_name: BEAS2-2B control cells

tag: tag

value: control


title: BCON_2


title: AAD_12 [blood]

description:
SYM012
Study subject 12, cell sample.

value: PBMC


title: BCD25_1


title: APD_36 [blood]

description:
SYM036
Study subject 36, cell sample.


title: BCON_1


title: Ctrl_602 [blood]

description:
SAK602
Study subject 602, cell sample.


title: untreated cells, baseline rep4

value: untreated cells

value: untreated


title: bottom bisected fragment T= 60 post surgery rep 1


title: SmallRNA.chicken.testis.WhiteLeghorn.adult.ox.rep3

description: Small RNAseq


title: C2_06

value: C

value: CCMP 2561


title: bottom bisected fragment T= 60 post surgery rep 2


title: SmallRNA.chicken.testis.WhiteLeghorn.adult.ox.rep2

description: Small RNAseq


title: C2_05


title: untreated cells, baseline rep2


title: SmallRNA.chicken.testis.WhiteLeghorn.adult.unox.rep1

description: Small RNAseq


title: untreated cells, baseline rep3


title: SmallRNA.chicken.testis.WhiteLeghorn.adult.ox.rep1

description: Small RNAseq


title: AAD_38 [blood]

description:
SYM038
Study subject 38, cell sample.

value: adult-onset asthma


title: Ctrl_II604 [blood]

description:
SAKII604
Study subject II604, cell sample.


title: C2_02


title: OA regeneration in cycloheximide, T=60, rep2

value: 60 minutes post sucrose shock

value: cycloheximide + sucrose shock


title: OA regeneration in DMSO, T=360, rep1

value: 360 minutes post sucrose shock

value: DMSO + sucrose shock


title: untreated cells, baseline rep1


title: C2_01


title: OA regeneration in cycloheximide, T=360, rep3


title: C2_00


title: T1_10

value: T


title: C2_03


title: AND_57 [blood]

description:
SYM057
Study subject 57, cell sample.


title: T2_02


title: OA regeneration in cycloheximide, T=360, rep2


title: APD_72 [blood]

description:
SYM072
Study subject 72, cell sample.


title: OA regeneration in cycloheximide, T=360, rep1


title: T1_09


title: T1_11


title: C2_04


title: IEI_14 [blood]

description:
SYM014
Study subject 14, cell sample.


title: Ctrl_II621 [blood]

description:
SAKII621
Study subject II621, cell sample.


title: 251485028910-2

city: Paris

first: Corneliu

last: Henegar

state: Ile de France

address: 15 Rue de l'Ecole de Medecine

country: France

institute: Institut national de la santé et de la recherche médicale

description: We studied three independent groups of subjects. Group 1 and 2 were composed of 30 subjects who underwent cardiac surgery for coronary artery disease (CAD) or for valve replacement, or myxoma resection (NCAD). Patients from the NCAD group had no clinical or angiographic sign of CAD, and had a left ventricular ejection fraction > 50%. Group 3 was composed of 15 non diabetic patients with CAD. EAT and SAT samples were obtained within 20 min after the start of surgery respectively near the proximal tract of the right coronary artery and the site of chest incision. Samples were frozen in liquid nitrogen and stored at -80 °C. In groups 1 and 2, total RNA obtained from SAT and EAT samples of 7 subjects (4 CAD and 3 NCAD) was prepared using the RNeasy total RNA Mini kit (Qiagen). RNA concentration and integrity were assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Massy, France). For microarray experiments, 1 µg of total RNA from each total RNA sample preparation was amplified by MessageAmp RNA Kit (Ambion, Austin, TX, USA) and 3 µg of amplified RNA was labeled with cyanin dyes (Cy) using the CyScribe First-Strand cDNA labeling kit (Amersham Biosciences, Orsay, France). (available at http://cmgm.stanford.edu/pbrown/protocols/index). Using pangenomic Agilent® cDNA microarrays, we compared the expression profiles of EAT and SAT from CAD and NCAD subjects. To this purpose we used a common reference pool that was generated by mixing equal amounts of total RNA extracted from adipose tissue samples of patients undergoing plastic surgery. Amplified RNA (aRNA) from the reference pool was labeled with Cy3, and aRNA from the 7 subjects (either EAT or SAT) was labeled with Cy5. A total of 13 pangenomic microarray hybridizations were performed for this differential comparison.

hyb_protocol: The labeled cDNA mixtures were hybridized according to the protocol described at http://cmgm.stanford.edu/pbrown/protocols/index

scan_protocol: The arrays were immediately scanned using a GenePix 4000A confocal Scanner (Axon Instruments). Images were analyzed using GenePix pro 3 software.

data_processing: After scanning the arrays, the images were analyzed and ratio intensities were filtered and normalized using Stanford Microarray Database Online resources (http://genome-www5.stanford.edu/).The VALUE field represents the log(base2) of the print-tip loess normalized R/G ratio (mean).

source_name: Pool

label_protocol: One microgram of total RNA from each sample preparation was amplified using the MessageAmp RNA kit (Ambion, Austin, TX), and 3 µg aRNA was Cy-dye labeled using the CyScribe first-strand cDNA labeling kit (Amersham Biosciences, Orsay, France) (available at http://cmgm.stanford.edu/pbrown/protocols/index).

extract_protocol: Total RNA from scWAT was prepared using the RNeasy RNA Mini Kit (Qiagen, Courtaboeuf, France).

tag: control

value: Pool of human subcutaneous adipose tissue

source_name: CAD patient

value: Subcutaneous adipose tissue (SC)


title: 251485029258-4


title: 251485034527-1

value: Epicardial adipose tissue (C)


title: AND_85 [blood]

description:
SYM085
Study subject 85, cell sample.

source_name: PBMC


title: APD_27 [blood]

description:
SYM027
Study subject 27, cell sample.


title: 251485028910-4


title: APD_73 [blood]

description:
SYM073
Study subject 73, cell sample.


title: Ctrl_627 [blood]

description:
SAK627
Study subject 627, cell sample.

value: healthy


title: 25148509257-4


title: 25148509258-1


title: T1_08

source_name: cell suspension


title: OA regeneration in cycloheximide, T=240, rep2

value: 240 minutes post sucrose shock

value: wild type


title: OA regeneration in DMSO, T=240, rep1


title: 251485028910-3


title: AAD_78 [blood]

description:
SYM078
Study subject 78, cell sample.

value: Female

value: PBMC


title: OA regeneration in cycloheximide, T=240, rep3


title: Ctrl_II615 [blood]

description:
SAKII615
Study subject II615, cell sample.


title: 251485028911-1

source_name: NCAD patient


title: AAD_31 [blood]

description:
SYM031
Study subject 31, cell sample.


title: OA regeneration in DMSO, T=180, rep1

value: 180 minutes post sucrose shock


title: T1_07


title: T1_05


title: OA regeneration in cycloheximide, T=240, rep1


title: 251485028911-4


title: T1_06


title: OA regeneration in cycloheximide, T=180, rep2


title: T1_02


title: T1_03


title: OA regeneration in cycloheximide, T=180, rep3


title: AND_64 [blood]

description:
SYM064
Study subject 64, cell sample.


title: T1_04


title: OA regeneration in cycloheximide, T=60, rep1


title: KO3_PGCLC_2

city: Muenster

first: Stefan

last: Schlatt

state: NRW

address: Albert-Schweitzer Campus 1, Building D11

department: Centre of Reproductive Medicine and Andrology

country: Germany

institute: Muenster University Hospital

description: DND1 Knock Out 3 - PGCLC - replicate 2

data_processing:
Samples were demultiplexed usign Illumina software bcl2fastq v2.19.0
Preudoalignment to the human genome and gene quantifications were performed with SALMON v1.4.0, based on the genomic annotation of GENCODE v36
Gene counts were read into the statistical software environment R v4.0.3 through the package tximeta v1.8.4
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Comma Separated Values (csv) matrix file of raw counts per gene for each sample

source_name: Primordial Germ Cell-Like Cell

growth_protocol: iPSCs were cultured in Matrigel-coated (Corning) plates with StemFlex medium (Thermo Fisher Scientific) and passaged every 3-4 days with TrypLE (Gibco) as single cells in the presence of 10 µM Y27632.

extract_protocol:
NucleoSpin® Mini RNA isolation kit (Macherey-Nagel)
NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: iPSCs were pre-differentiated to iMELCs in GMEM suplemented with 20% KSR (Gibco), 3µM CHIR99021 and 50 ng/ml ACTA on Matrigel coated plates for 2 days. PGCLCs were produced by spin-EB method in AggreWell 400 plates (StemmCell Technologies) in GMEM supplemented with 20% KSR, 200 ng/ml BMP4, 1000 U/ml LIF, 50 ng/ml EGF, 100 ng/ml SCF and 10 ng/ml Y27632 for 9-10 days.

value: Primordial Germ Cell-Like Cell (PGCLC)

value: DND1 Knockout

tag: cell line

value: KO 3


title: KO2_PGCLC_2

description: DND1 Knock Out 2 - PGCLC - replicate 2

value: KO 2


title: OA regeneration in cycloheximide, T=180, rep1

value: cycloheximide + sucrose shock


title: T1_01

value: CCMP 2561


title: KO1_PGCLC_2

description: DND1 Knock Out 1 - PGCLC - replicate 2

value: KO 1


title: OA regeneration in DMSO, T=120, rep1

value: 120 minutes post sucrose shock

value: DMSO + sucrose shock


title: IEI_25 [blood]

description:
SYM025
Study subject 25, cell sample.

tag: diagnosis

value: IEI


title: T1_00

value: T


title: 251485029164-4

value: Pool of human subcutaneous adipose tissue

value: Epicardial adipose tissue (C)


title: WT_PGCLC_2

description: Wild Type - PGCLC - replicate 2

value: Wildtype

value: WT


title: C1_12

value: C


title: 251485028911-3

value: Subcutaneous adipose tissue (SC)


title: KO1_PGCLC_1

description: DND1 Knock Out 1 - PGCLC - replicate 1

value: Primordial Germ Cell-Like Cell (PGCLC)


title: top bisected fragment T= 420 post surgery rep 3

value: 420 minutes post surgery

value: top fragment

value: wild type


title: Ctrl_II619 [blood]

description:
SAKII619
Study subject II619, cell sample.

value: healthy

tag: gender

value: Female

value: PBMC


title: C1_09

value: CCMP 2561


title: top bisected fragment T= 420 post surgery rep 2


title: WT_PGCLC_1

description: Wild Type - PGCLC - replicate 1


title: KO2_PGCLC_1

description: DND1 Knock Out 2 - PGCLC - replicate 1

value: DND1 Knockout

value: KO 2


title: 251485028910-1


title: AAD_68 [blood]

description:
SYM068
Study subject 68, cell sample.

value: adult-onset asthma

tag: age


title: AAD_76 [blood]

description:
SYM076
Study subject 76, cell sample.

tag: cell type


title: C1_10

tag: control (c) or treatment (t)


title: OA regeneration in cycloheximide, T=120, rep3

value: 120 minutes post sucrose shock

value: cycloheximide + sucrose shock


title: C1_11


title: IEI_32 [blood]

description:
SYM032
Study subject 32, cell sample.

value: IEI


title: Ctrl_638 [blood]

description:
SAK638
Study subject 638, cell sample.


title: KO3_iMeLCs_2

description: DND1 Knock Out 3 - iMeLCs - replicate 2

source_name: intercipient Mesoderm-Like Cell

value: intercipient Mesoderm-Like Cell (iMELC)

value: KO 3


title: C1_07

value: C


title: KO1_iMeLCs_2

description: DND1 Knock Out 1 - iMeLCs - replicate 2

value: KO 1


title: KO2_iMeLCs_2

description: DND1 Knock Out 2 - iMeLCs - replicate 2


title: bottom bisected fragment T= 420 post surgery rep 3

value: 420 minutes post surgery

value: bottom fragment


title: Ctrl_643 [blood]

description:
SAK643
Study subject 643, cell sample.


title: OA regeneration in cycloheximide, T=120, rep2

value: wild type


title: bottom bisected fragment T= 420 post surgery rep 2


title: C1_05


title: bottom bisected fragment T= 420 post surgery rep 1


title: C1_06


title: top bisected fragment T= 360 post surgery rep 3

value: 360 minutes post surgery

value: top fragment


title: C1_03


title: top bisected fragment T= 420 post surgery rep 1


title: top bisected fragment T= 360 post surgery rep 2


title: Ctrl_625 [blood]

description:
SAK625
Study subject 625, cell sample.

value: healthy

value: Female

value: PBMC


title: C1_02

value: CCMP 2561


title: KO2_iMeLCs_1

description: DND1 Knock Out 2 - iMeLCs - replicate 1

value: DND1 Knockout

value: KO 2


title: top bisected fragment T= 360 post surgery rep 1


title: WT_iMeLCs_2

description: Wild Type - iMeLCs - replicate 2

value: Wildtype

value: WT


title: 251485028911-2

value: Pool of human subcutaneous adipose tissue

value: Subcutaneous adipose tissue (SC)


title: C1_04

value: C


title: WT_iMeLCs_1

description: Wild Type -  iMeLCs - replicate 1

value: intercipient Mesoderm-Like Cell (iMELC)


title: AAD_65 [blood]

description:
SYM065
Study subject 65, cell sample.

value: adult-onset asthma


title: bottom bisected fragment T= 360 post surgery rep 3

value: bottom fragment


title: C1_01


title: KO1_iMeLCs_1

description: DND1 Knock Out 1 - iMeLCs - replicate 1

value: KO 1


title: KO3_iPSC_2

description: DND1 Knock Out 3 - iPSC - replicate 2

source_name: induced Pluripotent Stem Cell

value: induced Pluripotent Stem Cell (iPSC)

value: KO 3


title: Ctrl_623 [blood]

description:
SAK623
Study subject 623, cell sample.

value: healthy


title: bottom bisected fragment T= 360 post surgery rep 2

value: 360 minutes post surgery

value: wild type


title: KO2_iPSC_2

description: DND1 Knock Out 2 - iPSC - replicate 2


title: WT_iPSC_2

description: Wild Type - iPSC - replicate 2


title: APD_59 [blood]

description:
SYM059
Study subject 59, cell sample.

value: Female

value: PBMC


title: OA regeneration in cycloheximide, T=120, rep1

value: 120 minutes post sucrose shock

value: cycloheximide + sucrose shock


title: KO1_iPSC_2

description: DND1 Knock Out 1 - iPSC - replicate 2

value: DND1 Knockout


title: bottom bisected fragment T= 360 post surgery rep 1


title: C1_00

value: CCMP 2561


title: IEI_3 [blood]

description:
SYM003
Study subject 3, cell sample.

value: IEI


title: top bisected fragment T= 240 post surgery rep 3

value: 240 minutes post surgery

value: top fragment


title: Mouse 10x PTLp

city: Seattle

first: Hongkui

last: Zeng

state: WA

address: 615 Westlake Ave N

institute: Allen Institute for Brain Science

description:
processed data file:
metadata_10x.csv
expression_matrix_10x.hdf5
umap.2d.10x.csv

data_processing:
For Smart-seq v4 libraries, 50-base pair paired-end reads were aligned to GRCm38 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 01/18/2016 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/). Sequence alignment was performed using STAR v2.5.3 (Dobin et al., 2013) in twopassMode. PCR duplicates were masked and removed using STAR option “bamRemoveDuplicates”. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) sumarizeOverlaps function using “IntersectionNotEmpty”.
10xv2 libraries were sequenced on Illumina NovaSeq6000 and sequencing reads were aligned to the mouse pre-mRNA reference transcriptome (mm10) using the 10x Genomics CellRanger pipeline (version 3.0.0) with default parameters.
For Smart-seq v4, cells with fewer than 2,000 detected genes (count > 0) and less than 30% of reads mapped to the transcriptome were removed. Doublets were removed by first classifying cells into broad classes of excitatory, inhibitory, and non-neuronal based on known markers. For each class, we selected highly specific genes that are only present in this class against all other classes, and computed the eigengene (the first principle component based on the given gene set). Eigengenes for all classes were normalized in the range of 0 and 1, and we removed any cells that scored > 0.2 in more than one class
For 10xv2 libraries, cells that had < 1,500 detected genes (with UMI count > 0) were filtered out for downstream processing in each 10x run. Doublets were identified using a modified version of the DoubletFinder algorithm (McGinnis et al., 2019) and removed when doublet score > 0.3. Doublets were further removed by first classifying cells into broad cell classes (neuronal versus non-neuronal) based on the co-expression of any pair of broad class marker genes.
Genome_build: mm10
Supplementary_files_format_and_content: hdf5

molecule: polyA RNA

source_name: PTLp

growth_protocol: All procedures were carried out in accordance with Institutional Animal Care and Use Committee protocols at the Allen Institute for Brain Science. Animals were provided food and water ad libitum and were maintained on a regular 14/10-h day/night cycle at no more than five adult animals per cage. Animals were maintained on the C57BL/6J background, and newly received or generated transgenic lines were backcrossed to C57BL/6J. Experimental animals were heterozygous for the recombinase transgenes and the reporter transgenes. Standard tamoxifen treatment for CreER lines included a single dose of tamoxifen (40 μl of 50 mg ml−1) dissolved in corn oil and administered via oral gavage at postnatal day (P)10–14. Cux2-CreERT2;Ai140 mice received tamoxifen treatment at P35 ± 5 for five consecutive days. We excluded any animals with anophthalmia or microphthalmia.

extract_protocol:
We isolated single cells by adapting previously described procedures (Tasic et al., 2018). The brain was dissected, submerged in ACSF, embedded in 2% agarose, and sliced into 250-μm (SMART-Seq) or 350-μm (10x Genomics) coronal sections on a compresstome (Precisionary Instruments). Block-face images were captured during slicing. Regions of interest (ROIs) were then microdissected from the slices and dissociated into single cells with 1 mg/ml pronase (SMART-Seq before 28 June 2018, Sigma P6911-1G) and processed as previously described (Tasic et al., 2018). For all 10xv2 samples and for SSv4 samples after 28 June 2018, we improved our protocol with the following changes. Tissue pieces were digested with 30 U/ml papain (Worthington PAP2) in ACSF for 30 minutes at 30°C. Due to the short incubation period in a dry oven, we set the oven temperature to 35°C to compensate for the indirect heat exchange, with a target solution temperature of 30°C. Enzymatic digestion was quenched by exchanging the papain solution three times with quenching buffer (ACSF with 1% FBS and 0.2% BSA). Samples were incubated on ice for 5 minutes before trituration. The tissue pieces in the quenching buffer were triturated through a fire-polished pipette with 600-µm diameter opening approximately 20 times. The single cell suspension was passed through a 70-µm filter into a 15-ml conical tube with 500 ul of high BSA buffer (ACSF with 1% FBS and 1% BSA) at the bottom to help cushion the cells during centrifugation at 100 x g in a swinging bucket centrifuge for 10 minutes. The supernatant was discarded, and the cell pellet was resuspended in the quenching buffer. All cells were collected by fluorescence-activated cell sorting (FACS, BD Aria II) using a 130-μm nozzle. For SSv4, single cells were sorted into individual wells of 8-well PCR strips containing lysis buffer from the SMART-Seq v4 kit with RNase inhibitor (0.17 U/μl), immediately frozen on dry ice, and stored at −80°C. For 10x Genomics, 30,000 cells were sorted within 10 minutes into a tube containing 500 µl of quenching buffer. The resuspended cells were stored at 4°C until all samples were collected, usually within 30 minutes. Samples from the same ROI were pooled, cell concentration quantified, and immediately loaded onto the 10x Genomics Chromium controller.
For SSv4 processing, we used the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Cat# 634894) to reverse transcribe poly(A) RNA and amplify full-length cDNA. We performed reverse transcription and cDNA amplification for 18 PCR cycles (neurons) or 21 PCR cycles (non-neuronal cells) in 8-well strips, in sets of 12–24 strips at a time. All samples proceeded through Nextera XT DNA Library Preparation (Illumina Cat# FC-131-1096) using Nextera XT Index Kit V2 (Illumina Cat# FC-131-2001) and custom index sets (Integrated DNA Technologies). Custom index sets were validated to confirm the same performance as Nextera Index sets before being used on experimental samples. Nextera XT DNA Library prep was performed according to manufacturer’s instructions, with a modification to reduce the volumes of all reagents and cDNA input to 0.4x or 0.5x of the original protocol. Details are available in ‘Documentation’ on the Allen Institute data portal at: http://celltypes.brain-map.org.   For 10xv2 processing, we used Chromium Single Cell 3’ Reagent Kit v2 (10x Genomics Cat# 120237). We followed the manufacturer’s instructions for cell capture, barcoding, reverse transcription, cDNA amplification, and library construction. We targeted sequencing depth of 60,000 reads per cell.

tag: sample type

value: PTLp


title: IEI_9 [blood]

description:
SYM009
Study subject 9, cell sample.

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into eUtopia bioinformatics package and analyzed with BioConductor package Limma. Data was quantile normalized based on cutoff 0.75 and percentage of samples 75%. Replicate control probes were combined by their median values.

extract_protocol: Total RNA was isolated from 2x10^6 PBMCs by AllPrep Plus (Qiagen). Quantity and quality of the samples were determined by NanoDrop spectrophotometer and Agilent Bioanalyzer 2100, respectively. Samples with RNA integrity number > 8 were selected and independent pools of two RNA samples were used for the analysis.


title: AAD_13 [blood]

description:
SYM013
Study subject 13, cell sample.

value: adult-onset asthma


title: Mouse 10x MOs-FRP


title: KO3_iPSC_1

description: DND1 Knock Out 3 - iPSC - replicate 1


title: Mouse 10x SSp

source_name: SSp

value: SSp


title: AND_39 [blood]

description:
SYM039
Study subject 39, cell sample.


title: Mouse 10x SSs-GU-VISC-AIp

source_name: SSs-GU-VISC-AIp

value: SSs-GU-VISC-AIp


title: APD_53 [blood]

description:
SYM053
Study subject 53, cell sample.


title: AAD_18 [blood]

description:
SYM018
Study subject 18, cell sample.


title: KO1_iPSC_1

description: DND1 Knock Out 1 - iPSC - replicate 1

value: induced Pluripotent Stem Cell (iPSC)

value: KO 1


title: Ctrl_603 [blood]

description:
SAK603
Study subject 603, cell sample.

value: healthy


title: AAD_58 [blood]

description:
SYM058
Study subject 58, cell sample.


title: Mouse 10x AUD

source_name: AUD

value: AUD


title: Ctrl_621 [blood]

description:
SAK621
Study subject 621, cell sample.

value: Female


title: top bisected fragment T= 240 post surgery rep 2

value: wild type


title: KO2_iPSC_1

description: DND1 Knock Out 2 - iPSC - replicate 1

value: KO 2


title: WT_iPSC_1

description: Wild Type - iPSC - replicate 1

value: Wildtype

value: WT


title: AND_86 [blood]

description:
SYM086
Study subject 86, cell sample.

value: PBMC


title: IEI_5 [blood]

description:
SYM005
Study subject 5, cell sample.

value: IEI


title: sgKAT6A_input

data_processing:
Alignment using Bowtie2
Processing using Samtools
Generating bigwig files using deeptools
Genome_build: hg38
Supplementary_files_format_and_content: bw

source_name: AML cell

growth_protocol: AML cells were cultured in RPMI + 10%FBS

extract_protocol:
Genomic DNA was extracted following standard protocol
ChIP-seq library was prepared following standard methods

treatment_protocol: No special treatment other than lentivirus transduction of empty vector or sgRNA targeting KAT6A and Cas9

value: AML cell

value: KAT6A CRISPR targeting


title: bottom bisected fragment T= 240 post surgery rep 3

value: 240 minutes post surgery

value: bottom fragment


title: Ctrl_II611 [blood]

description:
SAKII611
Study subject II611, cell sample.


title: bottom bisected fragment T= 240 post surgery rep 2


title: Mouse 10x AId-AIv

source_name: AI

value: AI


title: empty vector_input

value: empty vector


title: Mouse 10x ENT

source_name: ENT

value: ENT


title: APD_71 [blood]

description:
SYM071
Study subject 71, cell sample.

value: adult-onset asthma


title: AAD_16 [blood]

description:
SYM016
Study subject 16, cell sample.


title: bottom bisected fragment T= 240 post surgery rep 1

source_name: Stentor coeruleus cell


title: Mouse 10x HIP

source_name: HIP

value: HIP


title: empty vector_ENL


title: Mouse 10x PAR-POST-PRE-SUB-ProS

source_name: PAR-POST-PRE-SUB-ProS

value: PAR-POST-PRE-SUB-ProS


title: top bisected fragment T= 180 post surgery rep 3

value: 180 minutes post surgery

value: top fragment


title: top bisected fragment T= 240 post surgery rep 1

value: wild type


title: Mouse 10x AId-AIv-AIp


title: Mouse TEa-PERI-ECT

source_name: TEa-PERI-ECT

value: TEa-PERI-ECT


title: sgKAT6A_ENL


title: top bisected fragment T= 180 post surgery rep 2


title: MOLM-13.WM1119_H3K9ac_no2

data_processing:
alignment using Bowtie2 to generate sam files
sam and bam files were processed with SAMtools
eak calling using MACS2
peaks were merged with BEDTools
read counts were calculated and normalized in the merged peaks for every sample
Genome_build: hg38
Supplementary_files_format_and_content: normalized count for each peaks across samples

growth_protocol: MOLM-13 cell line was cultured in RPMI (Corning, 10-041-CV) with 10% FBS (Life Technologies, 16000044) and 1% Penicillin Streptomycin (Gibco, 15-140-122).

extract_protocol:
ChIP-seq samples were prepared following standard protocol in this manuscript.
ChIP-seq libraries were prepared following the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) protocol, using NEBNext Multiplex Oligos Index Primers Sets

treatment_protocol: MOLM-13 cells were treated with 4uM WM-1119 for 4 days.

tag: antibody


title: MOLM-13.WM1119_H3K9ac_no3


title: MOLM-13.WM1119_H3K9ac_no1


title: bottom bisected fragment T= 180 post surgery rep 3


title: Ctrl_619 [blood]

description:
SAK619
Study subject 619, cell sample.

source_name: PBMC

value: healthy

value: Female


title: Mouse 10x TEa-PERI-ECT


title: Mouse 10x PL-ILA-ORB

source_name: PL-ILA-ORB

value: PL-ILA-ORB


title: Ctrl_605 [blood]

description:
SAK605
Study subject 605, cell sample.

value: PBMC


title: AND_80 [blood]

description:
SYM080
Study subject 80, cell sample.


title: Mouse 10x RSP

source_name: RSP

value: RSP


title: bottom bisected fragment T= 180 post surgery rep 2


title: Ctrl_II624 [blood]

description:
SAKII624
Study subject II624, cell sample.


title: top bisected fragment T= 180 post surgery rep 1


title: Mouse 10x ACA

source_name: ACA

value: ACA


title: MOLM-13.DMSO_H3K9ac_no1

value: DMSO


title: MOLM-13.DMSO_H3K9ac_no3


title: top bisected fragment T= 120 post surgery rep 3

value: 120 minutes post surgery


title: OA regeneration in DMSO, T=60, rep1

value: 60 minutes post sucrose shock

value: DMSO + sucrose shock


title: Mouse 10x VISl

source_name: VISl

value: VISl


title: MOLM-13.DMSO_H3K9ac_no2


title: MOLM-13.WM1119_input_no2


title: bottom bisected fragment T= 180 post surgery rep 1

value: bottom fragment


title: top bisected fragment T= 120 post surgery rep 2


title: MOLM-13.WM1119_input_no3


title: Mouse 10x VIS

source_name: VIS

value: VIS


title: Mouse 10x VISp

source_name: VISp

value: VISp


title: top bisected fragment T= 120 post surgery rep 1

value: top fragment


title: bottom bisected fragment T= 120 post surgery rep 3

value: wild type


title: Ctrl_II622 [blood]

description:
SAKII622
Study subject II622, cell sample.


title: AND_45 [blood]

description:
SYM045
Study subject 45, cell sample.

value: adult-onset asthma


title: MOLM-13.WM1119_input_no1


title: Mouse 10x VISm

source_name: VISm

value: VISm


title: APD_41 [blood]

description:
SYM041
Study subject 41, cell sample.

value: Female


title: APD_82 [blood]

description:
SYM082
Study subject 82, cell sample.


title: APD_44 [blood]

description:
SYM044
Study subject 44, cell sample.


title: AND_74 [blood]

description:
SYM074
Study subject 74, cell sample.


title: Ctrl_617 [blood]

description:
SAK617
Study subject 617, cell sample.

value: healthy


title: bottom bisected fragment T= 120 post surgery rep 2


title: BMDM_MHV_2

city: Beijing

first: Zeming

last: Zhang

address: 38 Xueyuan Rd , Haidian District,Beijing,China

institute: Institude of Systems Biomedicine

data_processing:
RNA sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), and sequenced on an Illumina Novaseq platform.
Illumina Casava 1.8 software used for basecalling and raw reads were gained.
After eliminating low-quality reads and reads with adaptors, clean reads were mapped to mouse genome reference sequence (GRCm38/mm10 Ensembl release 81) using HISAT2.
Gene expression was quantified as fragments per kilobase of coding sequence per million reads (FPKM) algorithm (for BMDM samples) or just read counts (for PM samples).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include ensemble gene ID and RPKM values for BMDM samples and raw counts for PM samples.

source_name: Bone marrow

growth_protocol: Isolated cells were seeded into 24-well plates at a density of 200 thousand cells per well. Cells were cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Culture supernatants were removed and total RNA of cultured cells was isolated via one-step RNA isolation method with Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 12 hours after seeding, cells were infected with MHV-A59 at 0.1 MOI for 12 hours.

value: Macrophage

value: 6 week old

tag: agent


title: Ctrl_II603 [blood]

first: Piia

institute: University of Helsinki

description:
SAKII603
Study subject II603, cell sample.

value: PBMC


title: bottom bisected fragment T= 120 post surgery rep 1


title: IEI_1 [blood]

description:
SYM001
Study subject 1, cell sample.

value: IEI


title: MOLM-13.DMSO_input_no1

value: DMSO


title: BMDM_MHV_1


title: AAD_11 [blood]

description:
SYM011
Study subject 11, cell sample.


title: HA_KAT6A_input

treatment_protocol: MOLM-13 cells were overexpressed with WT KAT6A with HA tag.


title: Oral apparatus post sucrose shock (T=420min) rep 4

value: sucrose shock


title: HA_KAT6A_HA

value: HA


title: BMDM_MOCK_2

value: mock


title: OA regeneration in cycloheximide, T=60, rep3

value: 60 minutes post sucrose shock

value: cycloheximide + sucrose shock


title: BMDM_MOCK_1


title: top bisected fragment T= 60 post surgery rep 2

value: 60 minutes post surgery


title: Oral apparatus post sucrose shock (T=360min) rep 4


title: Oral apparatus post sucrose shock (T=300min) rep 4


title: PM_MHV_2

source_name: Peritoneal cavity


title: APD_35 [blood]

description:
SYM035
Study subject 35, cell sample.


title: MDMs, C_3

city: Changchun

first: Yanhong

last: Bao

state: jilin

address: jilin changchun

institute: Jilin Agricultural University

data_processing:
A cDNA library constructed by technology from the pooled RNA was sequenced with Illumina Novaseq 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
And then we performed the paired-end sequencing on an illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Bos taurus

source_name: bovine peripheral blood mononuclear macrophages, untreated

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the mRNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bovine peripheral blood mononuclear macrophages

tag: infection

value: untreated


title: PM_MHV_1

tag: strain


title: MOLM-13.DMSO_input_no2

first: Jinyang

institute: The Rockefeller University

tag: treatment


title: top bisected fragment T= 60 post surgery rep 1

value: top fragment

value: wild type


title: Oral apparatus post sucrose shock (T=240min) rep 4


title: 20130009a_202822930173_R07C01

type: genomic

city: Ann Arbor

first: Siyu

state: MI

address: 100 Washtenaw avenue

department: Bioinformatics

institute: University of Michigan

hyb_protocol: Bisulfite conversion was performed using 350 ng input FFPE DNA with the Zymo EZ DNA Methylation Kit following manufacturer recommendations

scan_protocol: BeadChips were scanned and image data recorded by an iScan Reader with Methylation NXT settings

data_processing:
Methylation Profiles were generated using the GenomeStudio (v2011.1) Analysis Software with the Methylation Module and MethylationEPIC_v-1-0_B4 Manifest (Illumina). Raw data were pre-processed with R packages minfi and ChAMP.
the 'processed_beta_values_all.txt' contains average Beta

label: cy3, cy5

source_name: oral cavity_regimen 2_Baseline

label_protocol: Standard Illumina protocol

extract_protocol: The corresponding areas on unstained slides were microdissected for DNA isolation using the QIAamp DNA FFPE Tissue Kit (Qiagen, Hilden, Germany). All DNA samples were treated with RNAse using the QIAquick Nucleotide Removal Kit (Qiagen, Hilden, Germany). DNA quantity was assessed using the Qubit Broad Range Double Stranded DNA Assay (Thermo Fisher Scientific, Waltham, MA).

tag: patient id

tag: regimen

tag: tissue source

value: oral cavity

tag: time point

value: Baseline


title: Oral apparatus post sucrose shock (T=180min) rep 4

tag: time

tag: genotype


title: 20130009b_202822930173_R08C01

source_name: oral cavity_regimen 2_Month 1

value: Month 1


title: Ctrl_601 [blood]

city: Helsinki

last: Karisola

address: Haartmaninkatu 3

description:
SAK601
Study subject 601, cell sample.

tag: diagnosis

value: healthy

value: Female


title: 20250005b_202822930173_R06C01

source_name: oral cavity_regimen 1_Month 1


title: MDMs, C_2


title: Oral apparatus post sucrose shock (T=120min) rep 4

source_name: Stentor coeruleus cell


title: PM_MOCK_1

value: Macrophage

value: 6 week old


title: top bisected fragment T= 60 post surgery rep 3


title: Wild-type Vehicle

first: Yong

last: Huang

address: 1340 Jefferson Park Ave

institute: University of Viginia

data_processing:
Cellranger v3.1 coupled with STAR V2.7.2b for reads alignment and counts summary
Raw data and quality control were processed using R package 'Seurat'.
SCTransform' was used for normalization and variance stabilization
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: raw counts data and normalized data matrix in .gz

source_name: Lung mesenchymal cells

extract_protocol:
Mesenchymal cells were isolated from fresh lung by negative sorting of Cd45, Cd31, Cd326.
Cellular suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell Gel-Bead-in-Emulsions (GEMs) and perform single cell partitioning and barcoding.
10x Genomics Single Cell 3' RNA-seq kit v3 User Guide

value: Wild-type

tag: tissue

value: Lung

value: Vehicle


title: Oral apparatus post sucrose shock (T=90min) rep 4

value: sucrose shock


title: Oral apparatus post sucrose shock (T=60min) rep 4


title: PM_MOCK_2

tag: age

value: mock


title: MDMs, MAP_2

source_name: bovine peripheral blood mononuclear macrophages, infected with Mycobacterium avium subsp. paratuberculosis

tag: cell type

value: MAP


title: Pear1-/- Vehicle


title: MDMs, MAP_1

value: Bovine peripheral blood mononuclear macrophages


title: 20040007b_202822930173_R04C01


title: Wild-type Bleomycine

value: Bleomycin


title: Oral apparatus post sucrose shock (T=30min) rep 4


title: Tc1 Liver minION-seq, aligned mouse

city: Cambridge

first: Kevin

middle: Richard

last: Costello

state: Cambridgeshire

address: Genetics Building Downing St.

department: Department of Genetics

institute: Univerity of Cambridge

description:
Oxford nanoPore MinIon seq
Reads were aligned to both the hg19 chromosone 21 and mm10 genomes. reported bigwig is mapped to hg38 chromosone 22

data_processing:
For  Cut and run processing:  Basecalling was performed using CASAVA version 1.4 Reads were trimmed using trimgalore with the --trim1 option for paired end aligments. Reads were aligned using Bowtie version 1.2.3 using the following parameters -m 1 -X 1000 -m 1 --best. Files were sorted using Samtools sort and were filtered for PCR duplicates using picardTools Mark Duplicates with the REMOVE_DUPLICATES=true option ; reads were further filtere to remove all reads mapping to blacklisted sites as identified using RSEG deadzones.  Pileups of fragments were generated using genomeCoverageBed from bedtools version2.29.0. with the -pc option. bigWigs were generated using ucsctools wigToBigWig
For minION processing:  nanopolish index was run on individual files. minimap2 version 2.11 was run to align reads to both the mm10 genome and human chromosone 21. Files were then sorted and filtered with the -F 4 option using samtools. Methylation calling was preformed using nanopolish call-methylation with the -t 8 option
Genome_build: both mm10 and chromosone 21 of hg38; Tc1 Liver minION-seq, aligned t0 mm9 mouse
Supplementary_files_format_and_content: bigWig of human chromosone 21 with Cfp1 ChIP signal or CpG methylation percentage

source_name: Liver

extract_protocol:
Purified DNA from Tc1 mouse liver samples were prepared using the SQK-LSK109 ligation sequencing kit and run on R9 flow cells
1ug of DNA was end repaired with NEBNext FFPE DNA repair (NEB) and Ultra II End-prep (NEB). The repaired DNA was cleaned with KAPA Pure Beads (KAPA). Adapters were ligated using NEBNext quick T4 ligase (NEB)

value: Tc1 wildtype

value: B6129S-Tc(HSA21)1TybEmcf/J mice purchased from JAX Laboratory


title: Pear1-/- Bleomycine


title: 20040007a_202822930173_R03C01

source_name: oral cavity_regimen 1_Baseline

value: oral cavity


title: Oral apparatus pre sucrose shock rep 4

value: baseline

value: no treatment

value: wild type


title: MDMs, MAP_3


title: IDH1R132H+/ATRX-intact (snRNA-seq)

first: Aaron

last: Diaz

department: Neurological Surgery

institute: University of California, San Francisco

description: snRNA

data_processing:
We used CellRanger (version 3.0.2) to pre-process the sc/snRNA-seq data from the 10X Genomics platform.
The CellRanger ATAC software (version 1.1.0) was used for read alignment, deduplication, and identifying transposase cut sites.
The output matrix of CellRanger was further filtered for quality based on two criteria: 1) number of fragments > 1000; 2) fragments in promoter ratio > 0.2.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: Filtered peak matrix (.mtx)  files.  Bed files, peaks (TSV).

source_name: Brain

growth_protocol: All surgical procedures were conducted according to our Institutional Animal Care and Use Committee and NIH ethical guidelines. ATRX-KO and wildtype SB28 cells expressing IDH1R132H and a luciferase reporter were used to establish intracranial tumors in C57BL/6j mice, using 6 mice per cohort. Animals were anesthetized using isoflurane, each surgical procedure was performed after placing the animal in a stereotactic frame.  An aliquot of 5 × 104 SB28 cells was injected into the right parietal region of the brain. The injection site was 2 mm to the right of the central suture and 0.5 mm anterior to the lambda junction; depth of injection was 2-3 mm. The rate of injection was 1 ul/min.

extract_protocol:
Tissue processing, tagmentation, nuclei capture and library prep was performed by the 10X Genomics platform.
Single-cell/nucleus capture, reverse transcription, cell lysis, and library preparation were performed per manufacturer’s protocol.
Sequencing was performed according to 10X Genomics recommended protocols on an Illumina NovaSeq 6000.

treatment_protocol: Following euthanasia, mice were perfused with PBS, tumor tissue was harvested and snap frozen.

tag: Sex

value: Male


title: Oral apparatus post sucrose shock (T=420min) rep 3


title: 20040006b_202822930105_R08C01

value: Month 1


title: 20250005a_202822930173_R05C01

value: Baseline


title: 30010002a_202822930173_R01C01


title: Oral apparatus post sucrose shock (T=360min) rep 3


title: IDH1R132H+/ATRX-KO (snRNA-seq)

description: snRNA-seq

growth_protocol: All surgical procedures were conducted according to our Institutional Animal Care and Use Committee and NIH ethical guidelines. ATRX-KO and wildtype SB28 cells expressing IDH1R132H and a luciferase reporter were used to establish intracranial tumors in C57BL/6j mice, using 6 mice per cohort. Animals were anesthetized using isoflurane, each surgical procedure was performed after placing the animal in a stereotactic frame.  An aliquot of 5 × 104 SB28 cells was injected into the right parietal region of the brain. The injection site was 2 mm to the right of the central suture and 0.5 mm anterior to the lambda junction; depth of injection was 2-3 mm. The rate of injection was 1 l/min.


title: Oral apparatus post sucrose shock (T=300min) rep 3


title: IDH1R132H+/ATRX-intact (anti-CTCF snCUT&Tag)

data_processing:
Library strategy: snCUT&Tag
We used CellRanger (version 3.0.2) to pre-process the sc/snRNA-seq data from the 10X Genomics platform.
The CellRanger ATAC software (version 1.1.0) was used for read alignment, deduplication, and identifying transposase cut sites.
The output matrix of CellRanger was further filtered for quality based on two criteria: 1) number of fragments > 1000; 2) fragments in promoter ratio > 0.2.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: Filtered peak matrix (.mtx)  files.  Bed files, peaks (TSV).

growth_protocol: An ATRX CRISPR double-nickase plasmid (Santa Cruz Biotech sc-423734-NIC) was transfected into SB28 mouse glioma cells (a kind gift from Prof. Okada, UCSF) using FuGENE transfection reagent (Promega, Catalog number E2311). The CRISPR guide-RNAs used were CTAACTATGACTCAGAGTTAGAGAGAGAGATAAAAACCATGAGCAGAATT and CTAACTATGACTCAGAGTTAGAGAGAGAGATAAAAACCATGAGCAGAATT target exon 9 of ATRX. Non-targeting guide-RNAs were expressed in controls (Santa Cruz Biotech sc-437281). Following selection via puromycin, single cells were sorted into multi-well plates and expanded as clones. Homozygous knockout was validated by a cleavage assay (Thermofisher, Catalog number:  A24372), using primers F: CTACTTCCGGGTCAGATTTTGA and R: GCACCATCAGAGGAAACACC. Complete loss of ATRX protein was validated by Western blot (Abcam # ab97508). SB28ATRX-KO cells were transfected with plasmids expressing either IDH1R132H (ORIGENE, CAT#: RC400096) or wildtype IDH1 (Origene CAT#: RC210582) and selected via neomycin. Cells were cultured in RPMI media supplemented with 10% FBS and 100 U/mL penicillin and 0.1% streptomycin.

extract_protocol: Tagmentation for scATAC-seq, as well as nuclei capture and library prep for all single-cell assays, was performed via the 10X Genomics platform. Antibody incubation and tagmentation for scCUT&Tag was done as in Kaya-Okur Nature Communications 2019, with the following modifications. Cell lysis was performed via Nuclei EZ Prep (Sigma) according to manufacturer’s instructions. Nuclei purification was performed as above via sucrose gradient. Following centrifugation, nuclei were resuspended in 200 ul of Nuclei buffer (10X Genomics) with a 1:50 dilution of primary antibody (anti-CTCF Diagenode C15410210-50) and incubated overnight at 4 °C with slow rotation. Nuclei were spun down and resuspended in 200 ul of Nuclei buffer with a 1:50 dilution of secondary antibody (Antibodies-online ABIN3042027) and a 1:100 dilution of pA-Tn5 transposase loaded with Illumina barcodes (Diagenode C01070001), then incubated for 1 hr at room temperature with slow rotation. Nuclei were counted in a Countess II, then washed and resuspended with sufficient Nuclei buffer to achieve a concentration of 2000 nuclei/ul. To perform tagmentation, 5 ul of nuclei suspension was added to 7 ul of ATAC buffer (10X Genomics) and 2 ul of 1:100 loaded pA-Tn5 and incubated at 37 °C for 1 hr. Nuclei capture and library prep was then performed according to 10X Genomics scATAC-seq protocol. Sequencing was performed according to 10X Genomics recommended protocols on an Illumina NovaSeq 6000.

tag: genotype/variation


title: 20130011b_202822930105_R06C01


title: morning sleep deprivation MSD2

city: Evanston

first: Ravi

last: Allada

state: Illinois

address: Department fo neurobiology, Noerthwestern university,, 2205 Tech Drive

department: Department of neurobiology

institute: Northwestern university

data_processing:
Base calling and demultiplexing was performed with bcl2fastq.
Reads were pseudo aligned and quantified using Kallisto (v0.46.1) (Bray et al., 2016) against a prebuilt index file constructed from Ensembl reference transcriptomes (v96)
Kallisto was used to process paired end reads with 10 bootstraps.
Differential expression analysis of the resulting abundance estimate data was then performed with Sleuth (v0.30.0)
Gene-level abundance estimates were computed by summing transcripts per million (TPM) estimates for transcripts for each gene
It is abundance file which containe estimated count and TPM of the transcripts
Supplimentary data file containe Sleuth gene level differential expression results which are used for reaching the final conclusions in the manuscripts.

organism: Drosophila melanogaster

source_name: Brain (R5 Ellipsoid Body Neurons)

extract_protocol:
40-45 Brains from 7-10 day old flies expressing gfp in ~15 R5 ellipsoid body neurons in morning or evening +/- sleep deprivation conditions were dissected. Flourescent-activated cell sorting (FACS) was used to isolate individual cells. Total RNA was extracted using PicoPure kit and cDNA was created using a T7-oligo-dT primer and SuperScript III and served as a template to make and amplify new mRNA using T7 RNA polymerase and the Ambion MegaScript kit .
Libraries were generated using an Illumina TruSeq Stranded Kit

value: Brain (R5 Ellipsoid Body Neurons)

tag: group

value: morning sleep deprivation


title: 20040006a_202822930105_R07C01


title: Oral apparatus post sucrose shock (T=240min) rep 3


title: morning control, non-sleep deprived MC3

value: morning control, non-sleep deprived


title: 30010002b_202822930173_R02C01


title: Tc1 Liver minION-seq, aligned human

description:
Oxford nanoPore MinIon seq
Reads were aligned to both the hg19 chromosone 21 and mm10 genomes. reported bigwig is mapped to hg38 chromosone 21


title: Mttp-IKO2

city: St. Louis

first: Yan

last: Xie

state: MO

address: 660 South Euclid

department: Gastroenterology

institute: Washington University School of Medicine in St louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

extract_protocol:
Total liver RNA were extracted by TriZol reagent and RNA pools by genotype were used for NGS.
KAPA RiboErase

tag: strain background

value: MttpIKO

value: MCD diet for 3 weeks

value: liver


title: 20040005b_202822930105_R04C01


title: IDH1R132H+/ATRX-KO (anti-CTCF snCUT&Tag)


title: morning sleep deprivation MSD3


title: morning sleep deprivation MSD1


title: Oral apparatus post sucrose shock (T=120min) rep 3

value: sucrose shock


title: morning control, non-sleep deprived MC2


title: Mttp-IKO3


title: morning control, non-sleep deprived MC1


title: 20130011a_202822930105_R05C01


title: evening sleep deprivation ESD3

value: evening sleep deprivation


title: Mttp-IKO1


title: 20040005a_202822930105_R03C01


title: Oral apparatus post sucrose shock (T=180min) rep 3


title: WT3


title: evening sleep deprivation ESD2


title: Oral apparatus post sucrose shock (T=90min) rep 3


title: Oral apparatus post sucrose shock (T=60min) rep 3


title: 20310008b_202817030176_R06C01


title: 20130001b_202817030176_R08C01


title: WT1


title: evening sleep deprivation ESD1


title: evening control, non-sleep deprived EC1

value: evening control, non-sleep deprived


title: evening control, non-sleep deprived EC3


title: Oral apparatus post sucrose shock (T=420min) rep 2


title: Oral apparatus post sucrose shock (T=240min) rep 2


title: 20310008a_202817030176_R05C01


title: Primary Jak3 KO lung ECs 3

city: New York

first: José Gabriel

last: Barcia Durán

state: New York

address: 1300 York Avenue, Room A-809

institute: Weill Cornell Medicine

description: processed data file: genecounts_fig 2.txt

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Skewer (v0.2.2) for adapter trimming
Minion from Kraken tool (reaper-13-100) for adapter diagnosis
STAR (v2.7.6a) for alignment and gene count quantification using --quantMode GeneCounts
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene count matrix with ensembl IDs as tab separated file.

source_name: Primary Jak3 KO lung ECs

extract_protocol:
Cells were isolated by fluorescence-activated cell sorting and subjected to TRIzol treatment for RNA extraction and sequencing.
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

tag: strain/genotype

value: Lung endothelium

value: endothelial cells (ECs)


title: Primary Jak3 KO lung ECs 4


title: WT2


title: Primary Jak3 KO lung ECs 2


title: Oral apparatus post sucrose shock (T=180min) rep 2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Stentor genome (StentorDB), using tophat2 (-i 9 -I 101 --min-segment-intron 9 --min-coverage-intron 9 --max-segment-intron 101 --max-coverage-intron 101 -p 20). We used Trinity to build a transcriptome (--genome_guided_max_intron 1000). For quantification of transcript abundance, we aligned reads to the transcriptome using Kallisto (-t 15 -b 30). Transcriptome file is included here: SteCoe_Trinity_assembled_transcriptome_for_GEO.fasta
Genome_build: Stentor coeruleus (GCA_001970955.1)
Supplementary_files_format_and_content: For each Sample:
tsv file containing matrix of estimated counts, TPM, effective length for each gene.
HDF5 binary file containing run info, abundance estimates, bootstrap estimates, and transcript length information length.
json file containing information about the run
Trinity generated transcriptome (fasta)

extract_protocol:
At each time point, a sample of cells was lysed into RNA-stabilizing buffers specified by the extraction kit, and then stored on ice until the end of the experiment when the RNA purification was performed in parallel on all samples. RNA was extracted at each time point using the Nucleospin RNA XS kit from Clontech (cat. num. 740902.250).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Primary Jak3 WT lung ECs 4

source_name: Primary Jak3 WT lung ECs


title: Oral apparatus post sucrose shock (T=300min) rep 2


title: MOLM-13.DMSO_input_no3

last: Li

address: 1230 York Ave

value: DMSO

tag: cell line


title: Primary Jak3 KO lung ECs 1


title: evening control, non-sleep deprived EC2


title: 20020002a_202822930105_R01C01

last: Liu

value: oral cavity


title: Oral apparatus pre sucrose shock rep 3

value: baseline

tag: treatment

value: no treatment

value: wild type


title: 20230002a_202817030176_R01C01

tag: patient id

value: Baseline


title: 20310007b_202817030176_R04C01

tag: regimen

value: Month 1


title: LH2 cKO_no.2_2

city: Chiba City

first: Ryunosuke

last: Nozaki

state: Chiba Prefecture

address: 1-8-1 Inohana, Chuo-ku, Chiba, Japan

department: Depertment of Oral science

country: Japan

institute: Graduate School of Medecine, Chiba university

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: LH2F/F CAG-Cre, tamoxifen (-) medium  (after 24h tamoxifen treatment)

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Mouse tails were skinned and minced into 1-cm pieces, which were then placed on 30-mm tissue culture dishes coated with collagen I and containing Dulbecco's Modified Eagle's Medium (DMEM without sodium pyruvate; Nacalai Tesque, Kyoto, Japan), 10% fetal bovine serum (FBS; Sigma-Aldrich, St. Louis, MO, USA), and 50 units/ml penicillin. The plates were maintained at 37 °C with 5% CO2.

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Total RNA was extracted from cells with TRIzol Reagent (Invitrogen) and the SV Total RNA Isolation System (Promega), according to the manufacturer's instructions.

tag: strain

value: tail tissue fibroblast (TTF)

value: LH2 cKO


title: Oral apparatus post sucrose shock (T=30min) rep 3


title: Oral apparatus post sucrose shock (T=60min) rep 2


title: Primary Jak3 WT lung ECs 3


title: 20020002b_202822930105_R02C01

tag: tissue source

tag: time point


title: Oral apparatus post sucrose shock (T=360min) rep 2

tag: time

tag: genotype


title: Oral apparatus post sucrose shock (T=30min) rep 2


title: LH2 cKO_no.1_2

source_name: LH2F/F CAG-Cre, tamoxifen (+) medium (after 24h tamoxifen treatment)


title: control_2

source_name: LH2F/F CAG-Cre, tamoxifen (-) medium

value: tamoxifen (-) medium


title: 20020001a_202817030119_R07C01


title: LH2 cKO_no.2_1

value: tamoxifen (-) medium (after 24h tamoxifen treatment)


title: Primary Jak3 WT lung ECs 1

tag: tissue


title: Mouse 10x MOp

source_name: MOp

tag: sample type

value: MOp


title: Primary bone marrow ECs 2

description: processed data file: genecounts_fig 1.txt and genecounts_fig 2.txt

source_name: Primary bone marrow ECs

value: Bone marrow endothelium

tag: cell type


title: 20310007a_202817030176_R03C01

source_name: oral cavity_regimen 2_Baseline


title: Primary Jak3 WT lung ECs 2


title: 20310015a_202817030119_R05C01


title: 20230002b_202817030176_R02C01


title: E24_rep4: nsPEF, 24 h, TM3, replicate 4

city: Warsaw

first: Alicja

last: Trebinska-Stryjewska

address: gen. S. Kaliskiego 2

department: Institute of Optoelectronics

country: Poland

institute: Military University of Technology

description: Gene expression in nanosecond pulsed electric field (nsPEF)-exposed TM3 Leydig cells 24 h after treatment

hyb_protocol: 600 ng of Cy3-labeled cRNA was fragmented following the manufacturer's protocol at 60°C for 30 min; fragmentation reaction was stopped by adding 2 × Hi-RPM Hybridization buffer. Fragmented Cy3-labeled cRNA was hybridized to Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed following manufacturer's instructions with GE Wash Buffer 1 and 2 (Agilent).

scan_protocol: Microarray slides were scanned immediately after washing with the SureScan Microarray Scanner (Agilent) using the Agilent Microarray Scan Control program version 9.1 with the following settings: resolution, 3 µm; dye channel, green; green PMT sensitivity, 100%.

data_processing: Scanned images were analyzed with the Feature Extraction Software 12.0 using default parameters (protocol: GE1_1200_Jun14, grid: 074809_D_F_20190110) to obtain the background-subtracted and detrended Processed Signal intensities. Data were processed with GeneSpring version 14.9, and log2-transformed normalized signal intensities were obtained after normalization by a percentile shift (75th percentile). The baseline was set to the median of all samples. Normalized signal intensities were further used to create gene-level experiments (only genes detected in at least 2 out of 4 biological replicates in any condition were included). Differential gene expression was performed in GeneSpring using a two-way ANOVA with interaction (p <0.05) with Benjamini-Hochberg FDR multiple testing correction.

source_name: nsPEF, 24 h, TM3, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the Low Input Quick Amp Labeling Kit, One Color (Agilent) according to manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Addition of RNA Spike-In, One color (Agilent) served as an internal control. Cy3-labeled cRNA quality and quantity were assessed using 2100 Agilent Bioanalyzer (Agilent) and Agilent RNA 6000 Nano Reagent (Agilent).

growth_protocol: TM3 cell line (Leydig cells, Mus musculus, ATCC CRL-1714) was propagated in a medium composed of Ham's F12 and Dulbecco's modified Eagle’s medium (1:1) (DMEM/F12) supplemented with 5% horse serum, 2.5% fetal bovine serum, and antibiotic/antimycotic in 5% carbon dioxide at 37ºC until semi-confluent.

extract_protocol: After treatment, cells were washed twice with ice-cold PBS, centrifuged at 600xg for 5 min at 4ºC; cell pellets were frozen at -80ºC. Total RNA was isolated from the frozen pellets using the RNeasy Mini Kit (QIAGEN) according to manufacturer's instructions (including on-column DNaseI treatment). RNA was quantified using the QuantiFluor RNA System and Quantus Fluorometer (Promega). RNA quality was assessed with 2100 Agilent Bioanalyzer and Agilent RNA 6000 Nano Reagent. RIN ranged from 8.9 to 10.0.

treatment_protocol: Before the exposure, TM3 cells were washed two times in cold BD-PBS, resuspended at the density of 2.E+06 cells/ml in 1×binding buffer, passed through a 40-µm nylon cell strainer filter, and aliquoted into electroporation cuvettes (0.4 cm gap size width) in a volume of 200 µl per sample. Cells were either sham-exposed or exposed to nanosecond pulsed electric field (nsPEF): 80 pulses of quasi-rectangular shape, 60 ns pulse width, 5.5 kV amplitude at the repetition rate 26.4 pulses per minute. The electric field was 14 kV/cm, and the duration of treatment was 180 s.

value: Leydig cell, epithelial


title: 20130001a_202817030176_R07C01


title: Oral apparatus post sucrose shock (T=90min) rep 2

first: Wallace

last: Marshall

institute: UCSF

value: sucrose shock


title: 20310014b_202817030119_R04C01

source_name: oral cavity_regimen 1_Month 1


title: Oral apparatus post sucrose shock (T=120min) rep 2

source_name: Stentor coeruleus cell


title: Primary Jak3 KO bone marrow ECs 2

source_name: Primary Jak3 KO bone marrow ECs


title: Primary Jak3 KO bone marrow ECs 1


title: 20020001b_202817030119_R08C01


title: Primary bone marrow ECs 1


title: LH2 cKO_no.1_1

value: tamoxifen (+) medium (after 24h tamoxifen treatment)


title: S24_rep4: sham, 24 h, TM3, replicate 4

description: Gene expression in sham-exposed TM3 Leydig cells 24 h after treatment

source_name: sham, 24 h, TM3, replicate 4

value: sham-exposed


title: ER-Hoxa9.DMSO.2

data_processing:
Alignment-independent quantification using Salmon
Genome_build: mm10
Genome_build: hg38
Supplementary_files_format_and_content: TPM as txt file

extract_protocol:
RNA was extracted using Qiagen RNeasy  Kit.
RNA-seq libraries were build by a commercial company, Novogene, following standard protocols.

value: DMSO


title: ER-Hoxa9.DMSO.1


title: Oral apparatus post sucrose shock (T=360min) rep 1


title: MDMs, C_1

source_name: bovine peripheral blood mononuclear macrophages, untreated

value: Bovine peripheral blood mononuclear macrophages

tag: infection

value: untreated


title: Oral apparatus post sucrose shock (T=420min) rep 1


title: Oral apparatus post sucrose shock (T=60min) rep 1


title: Oral apparatus pre sucrose shock rep 2

value: baseline

value: no treatment


title: 20310015b_202817030119_R06C01

source_name: oral cavity_regimen 2_Month 1

value: oral cavity


title: ER-Hoxa9.WM1119.1


title: 20070004b_202817030109_R06C01

value: Month 1


title: 20070005b_202817030109_R08C01


title: Oral apparatus post sucrose shock (T=300min) rep 1

value: wild type


title: oe input

city: harbin

first: Qi

last: Jiang

state: heilongjiang

address: baojian road 157

department: Department of histology and embryology

institute: Harbin Medical University

data_processing:
After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8). Sequence quality was examined using the FastQC software. After passing Solexa CHASTITY quality filter, the clean reads were aligned to mouse reference genome UCSC MM10 using BOWTIE (V2.1.0). Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.2. Statistically significant ChIP-enriched regions (peaks) were identified by comparison of IP vs Input or comparison to a Poisson background model, using a p-value threshold of 10-4. Then the peaks were annotated by the nearest gene using the newest UCSC RefSeq database.
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: wig files were generated using MACS

growth_protocol: Mouse embryonic fibroblasts (MEFs) were obtained from 13.5-dpc embryos collected from  C57BL/6 females which had been mated with DBA/2 males. 293T and MEFs were cultured in Dulbecco's modified eagle medium (DMEM) containing 15%(vol/vol) fetal bovine serum (FBS), 1X MEM NEAA, 1X L-Glutamine and 1X Penicillin-Streptomycin. (FBS from BI and others from Invitrogen). For iPSC reprogramming, infected or drug treated 4F2A MEFs were cultured in KnockOut DMEM with 15% KnockOut Serum Replacement, 1X MEM NEAA, 1X L-Glutamine, 1X Penicillin-Streptomycin, 1X Sodium Pyruvate, 1000U/ml LIF, 1X 2-Mercaptoethanol and 2 μg/ml doxycycline (LIF from Millipore, doxycycline from Sigma-Aldrich and others from Invitrogen), the medium were changed every day.

extract_protocol:
48 hrs after infection,The DNA was extracted using H3K27me3 antibody.
10 ng DNA of each sample was converted to phosphorylated blunt-ended; An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments; Illumina's genomic adapters were ligated to the A tailed DNA fragments; PCR amplification was performed to enrich ligated fragments. The enriched product of ~200-1500 bp was size selected using AMPure XP beads.

value: Mouse embryonic fibroblasts (MEFs)

tag: genotype/variation

value: KDM6A overexpression

tag: chip antibody

value: Ig G 011000003 jackson