title: single-cell RNA-seq library consisting of human fetal hepatocyte organoids and primary human hepatocyte organoids

city: Utrecht

first: Delilah

last: Hendriks

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
FH_organoids+PHH_organoids
10x Genomics

library_source: transcriptomic single cell

data_processing:
Illumina output demultiplexed (bcl files) converted to fastq files using mkfastq (CellRanger v7.1.0)
Alignment, filtering, barcode and UMI counting done using CellRanger count (CellRanger v7.1.0)
Donor genotype demultiplexing to distinguish human fetal hepatocyte organoids from primary human hepatocyte organoids using souporcell (v2.0)
Assembly: Genome Reference Consortium Human Build 38
Supplementary files format and content: filtered_feature_bc_matrix.h5 file and a clusters TSV file containing the genotype demultiplexing information to distinguish fetal from adult cells

molecule: polyA RNA

source_name: human fetal hepatocyte organoids (FH donor 4) and primary human hepatocyte organoids (PHH donor 3)

extract_protocol:
Both human fetal hepatocyte organoids and primary human hepatoctye organoids were dissociated into single cells using Accutase and cell suspensions were washed . To enhance viability, the Dead Cell Removal kit (Miltenyi) was used with MS columns after dissociation. Live cells were manually counted using Trypan blue and both cell suspensions (fetal and adult cells) were mixed together and resuspended in 1X PBS containing 0.04% BSA at an optimal concentration of 700-1200 cells/ul.
Libraries were prepared using the 10x Genomics Chromium 3’ Gene Expression solution v3.0/v3.1

value: wild type


title: mouse_B6129SF2J_HFPO_DA_24_50_uM_116

status: Public on Apr 30 2024

type: SRA

city: Asheville

first: Melissa

middle: Marie

last: Heintz

state: NC

address: 31 College Place, Suite B118

country: USA

institute: ToxStrategies

library_source: transcriptomic

data_processing:
Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing
fastqs were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches
Assembly: probe-based targeted sequencing
Supplementary files format and content: comma-separated text files include raw count values for each gene_probe

molecule: total RNA

organism: Mus musculus

source_name: primary hepatocytes

growth_protocol: Hepatocytes were isolated from the livers of 8 – 12 week-old male CD-1 mice (CD-1 IGS, strain code: 022) purchased from Charles River (Raleigh, NC) and 11 week-old male B6129SF2/J mice (stock #101045) and 11 week-old male PPARa-null mice (B6;129S4-Pparatm1Gonz/J, stock #008154) purchased from The Jackson Laboratory (Bar Harbor, ME). Rat hepatocytes were isolated from the livers of 8 – 12 week-old male Sprague Dawley (SD, strain code: 001) rats purchased from Charles River. Human hepatocytes were isolated from a pool of 10 donor livers (5 male and 5 female). Hepatocytes from all species/strains were isolated using a two-step enzymatic digestion of liver tissue as described in Mudra and Parkinson (2001).   Primary hepatocytes were plated in a collagen-sandwich configuration on 48-well plates. Hepatocytes were maintained in Modified Eagle's medium, Dr. Chee’s modification (MCM; Gibco, Grand Island, NY) supplemented with 11.5% NaHCO3 (Sigma Aldrich), 0.88% L-arginine (Sigma Aldrich), 3% L-glutamine (Sigma Aldrich), 0.05% thymidine (Sigma Aldrich), 1% (v/v) ITS+ (BD Biosciences, Bedford, MA), 1% (v/v)  penicillin/streptomycin (5,000 U/mL penicillin, 5,000 μg/mL streptomycin (Sigma Aldrich), and  0.001% 10 mM dexamethasone (Sigma Aldrich). Cell cultures were incubated in a humidified culture chamber (37 ± 2 °C at 95% relative humidity, 95/5% air/CO2).

extract_protocol:
Following treatment with HFPO-DA or positive controls (i.e., GW7647, rosiglitazone, acetaminophen or d-galactosamine) for 12, 24 or 72 h, hepatocytes were lysed using TempO-Seq® Enhanced Lysis Buffer and processed according to the TempO-Seq® protocol by BioSypder Technologies.
TempO-Seq® protocol by BioSypder Technologies

treatment_protocol: Using 48-well plates, CD-1, B6129SF2/J and PPARa-KO mouse hepatocytes were seeded at a density of 0.6 x 10^6 cells/mL, and rat and human hepatocytes were seeded at a density of 1.3 x 10^6 cells/mL. After a 24 h adaptation period, hepatocytes from each species/strain were treated for 12, 24 or 72 h with supplemented MCM media containing solvent control in the presence or absence of HFPO-DA (0.1, 5, 50 or 500 μM) or one of the following positive controls: GW7647 (0.01, 0.1, 1 or 10 μM), rosiglitazone (0.01, 0.1, 1 or 10 μM), acetaminophen (0.3, 1, 3 or 10 mM) or d-galactosamine (0.3, 1, 3 or 10 mM). Deionized water (1%) served as the solvent control for HFPO-DA and dimethylsulfoxide (DMSO, 0.1%; cell culture grade; Sigma Aldrich) served as the solvent control for the remaining test chemicals. Treatment solutions were replaced every 24 h. For each species/strain, treatment groups were performed in triplicate wells for 12 and 72 h treatment durations, and quadruplicate wells for the 24 h treatment duration.

tag: strain

tag: cell type

value: primary hepatocytes

tag: chemical

tag: concentration

tag: concentration units

value: uM

tag: exposure duration_(hours)


title: H3K36me3_heart_E16_EC_cell_131

city: Beijing

first: Yaxi

last: Liu

address: 5 Yiheyuan Road

country: China

institute: Peking University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were de-multiplexed to generate single cell profiles by custom scripts. For spliting single cell, we cut the first 21 bp of the read1 and the first 27 bp of the read2.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Cells with less than 1,000 non-duplicated were excluded.
Bed files were generated from bam files using bedtools (v2.25.0) bamToBed.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bed files. Each single cell bed file contain non-duplicated alignments as is in the bam file.  These files contain single cell genome-wide coverage files after  sorting and uniqing and removing duplicates. Since one cell only contains two copies of each genomic locus for assay, we usually use non-duplicated reads information to reflect peak information in one single cell (PMID: 31471188).

molecule: genomic DNA

source_name: E16.5 heart

extract_protocol:
Following CoBATCH protocol.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

treatment_protocol: Organs were digested with 0.06 Collagenase II at 37 °C. "Aged" animals are 17-19 months old.

tag: developmental stage

tag: tissue

value: heart

tag: tissue preparation

value: Fixed by methanol

tag: chip antibody

value: H3K36me3, Active motif, Cat. 61101


title: 4-1BB- CD8+ TIL, patient 1

city: Daejeon

first: Seung Hyuck

last: Jeon

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
FASTQ files were mapped to the human genomic DNA reference (GRCh38/hg38) using Hisat2
StringTie was used to quantify gene expression based on the aligned reads.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM expression for each Sample

organism: Homo sapiens

source_name: CD8+ tumor-infiltrating T cells

extract_protocol:
Total RNA was extracted from the sorted cells using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara).
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara).

value: CD8+ tumor-infiltrating T cells

tag: cell line

value: primary

value: CD8+ T cell


title: H3K36me3_heart_E16_EC_cell_132


title: H3K36me3_heart_E16_EC_cell_130


title: H3K36me3_heart_E16_EC_cell_129


title: mouse_B6129SF2J_Rosiglitzone_24_10_uM_114

value: Rosiglitzone


title: mouse_B6129SF2J_HFPO_DA_24_50_uM_115


title: H3K36me3_heart_E16_EC_cell_128


title: mouse_B6129SF2J_Rosiglitzone_24_10_uM_113


title: sgPARP1_3

city: Qingyuan

first: Qingtian

last: Huang

address: 35 Yinquan North Road, Qingcheng District

institute: Guangzhou Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

source_name: cell line

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: cell line

value: Human hepatocellular carcinomas cell

tag: genotype

value: PARP1 KO


title: sgPARP1_2


title: WT_3

value: WT


title: WT_2


title: H3K36me3_heart_E16_EC_cell_126


title: mouse_B6129SF2J_Rosiglitzone_24_10_uM_112


title: mouse_B6129SF2J_Rosiglitzone_24_10_uM_111


title: WT_1


title: H3K36me3_heart_E16_EC_cell_125


title: mouse_B6129SF2J_GW7647_24_10_uM_109


title: mouse_B6129SF2J_GW7647_24_10_uM_108


title: H3K36me3_heart_E16_EC_cell_124


title: H3K36me3_heart_E16_EC_cell_123


title: 8L1, adjacent

city: York

first: Paul

middle: M

last: Kaye

state: North Yorkshire

address: University of York, Heslington

country: United Kingdom

institute: Hull York Medical School, University of York

description: 10x Visium for FFPE spatial transcriptomics

data_processing:
Raw sequencing data was used to generate FASTQ files using default settings
Spatial 3' v1 chemistry using spaceranger-1.3.0 was used to align reads to GrCh38-2020-A genome using the Visium Human Transcriptome Probe Set to obtain gene expression matrices
Assembly: GRCh38-2020-A
Supplementary files format and content: .h5: Feature barcode matrices file in the HDF5 format
Supplementary files format and content: _detected_tissue_image.jpg: Image showing spots over tissue section
Supplementary files format and content: _scalefactors_json.json: Json file for scalefactors
Supplementary files format and content: _tissue_hires_image.png: tissue section image in high resolution
Supplementary files format and content: _tissue_lowres_image.png: tissue section image in low resolution
Supplementary files format and content: _tissue_positions_list.csv: spatial barcodes and their xy co-ordinates on tissue
Library strategy: Spatial Transcriptomics

source_name: Skin

extract_protocol:
Biopsies were formalin-fixed and embedded in paraffin. 5μm sections were cut with cryostat and placed on 10x Visium spatial transcriptomics slide
Manufacturer's instructions (10x Visium for FFPE) were followed to prepare sequencing libraries

treatment_protocol: Five Phlebotomus duboscqi sand flies infected with L. major MHOM/IL/2019/MRC-02 were allowed access for 30 min to the volar aspect of the proximal forearm, approximately 2-3 centimetres distal to the antecubital fossa, using a bespoke biting chamber with a variable aperture. Participants were considered for therapeutic biopsy when a clinically apparent lesion of >3mm diameter was observed.

value: Skin

tag: participant

tag: treatment

value: Leishmania major infected lesional skin


title: 9R1, adjacent


title: CAAHR-23-F

city: Gainesville

first: Terence

last: Ryan

address: 1864 Stadium Rd

institute: University of Florida

data_processing:
The reads were first mapped to the latest UCSC genome set using Bowtie2 version 2.1.0
The mitochondria reads, duplicate reads and non-unique reads were removed before peak calling
MACS2 was used for peak calling using BAMPE mode
Differentially peaks were identified using the edgeR program
Assembly: mm10
Supplementary files format and content: Data are provided in fastq format. The reads were first mapped to the latest UCSC genome set using Bowtie2 version 2.1.0 [1] The mitochondria reads, duplicate reads and non-unique reads were removed bdfore peak calling.

source_name: Skeletal muscle (gastrocnemius)

extract_protocol:
Nuclei were isolated from snap frozen gastrocnemius muscle using gentle homogenization, filtering, and centrifugation. Quality was assessed with AOPI staining.
Library construction was perform by Quick Biology Inc. using Illumina-based materials.

treatment_protocol: Mice were treated eith either AAV-GFP or AAV-CAAHR using intramuscular injection.

value: Skeletal muscle (gastrocnemius)


title: 8C2, lesion


title: 8C1, lesion


title: sgPARP1_1


title: H3K36me3_heart_E16_EC_cell_122


title: H3K36me3_heart_E16_EC_cell_121


title: H3K36me3_heart_E16_EC_cell_120


title: H3K36me3_heart_E16_EC_cell_127


title: CAAHR-15-F


title: 1L2, adjacent


title: CAAHR-10-F


title: mouse_B6129SF2J_GW7647_24_10_uM_110


title: mouse_B6129SF2J_HFPO_DA_24_5_uM_104


title: H3K36me3_heart_E16_EC_cell_119


title: 1C2, lesion


title: H3K36me3_heart_E16_EC_cell_118


title: mouse_B6129SF2J_GW7647_24_10_uM_107


title: GFP-2-F


title: 1C1, lesion


title: H3K36me3_heart_E16_EC_cell_116


title: GFP-1-F


title: mouse_B6129SF2J_Rosiglitzone_24_1_uM_102


title: H3K36me3_heart_E16_EC_cell_117


title: mouse_B6129SF2J_Rosiglitzone_24_1_uM_101


title: 3L1, adjacent


title: mouse_B6129SF2J_Rosiglitzone_24_1_uM_100


title: mouse_B6129SF2J_HFPO_DA_24_5_uM_106


title: H3K36me3_heart_E16_EC_cell_115


title: mouse_B6129SF2J_HFPO_DA_24_5_uM_105


title: 3C2, lesion


title: mouse_B6129SF2J_Rosiglitzone_24_1_uM_99


title: H3K36me3_heart_E16_EC_cell_114


title: ABT263 treated mouse ovary 9 months old 2

city: Columbia

first: Lei

last: Lei

state: MO

address: 920 East Campus Dr

department: of Obstetrics, Gynecology and Women's Health

institute: University of Missouri School of Medicine

description: B023AB2 ABT9month

data_processing:
Spliced Transcripts Alignment to a Reference (STAR) software
Assembly: mm10
Supplementary files format and content: excel file includes raw counts for each sample

source_name: ovary

extract_protocol:
TRIzolTM Plus RNA purification kit (Invitrogen, 12183555)
NEBNext® UltraTM RNA, Library Prep Kit for Illumina® (NEB, USA)

value: ovary

tag: condition

value: ABT263 treated mouse

tag: age

value: 9 months


title: 3C1, lesion


title: 1L1, adjacent


title: GFP-3-F


title: H3K36me3_heart_E16_EC_cell_113

value: heart


title: ABT263 treated mouse ovary 9 months old 1

description: B022AB2 ABT9month


title: ABT263 treated mouse ovary 6 months old 3

description: B021AB1 ABT6month

value: 6 months


title: rat_GW7647_12_0.1_uM_7

organism: Rattus norvegicus

value: Sprague Dawley

value: primary hepatocytes

value: uM


title: mouse_B6129SF2J_GW7647_24_1_uM_98


title: mouse_B6129SF2J_HFPO_DA_24_5_uM_103


title: 3R1, adjacent


title: mouse_B6129SF2J_GW7647_24_1_uM_97


title: ABT263 treated mouse ovary 6 months old 2

description: B020AB1 ABT6month


title: mouse_B6129SF2J_GW7647_24_1_uM_96


title: ABT263 treated mouse ovary 6 months old 1

description: B019AB1 ABT6month


title: mouse_B6129SF2J_GW7647_24_1_uM_95


title: ABT263 treated mouse ovary 9 months old 3

description: B024AB2 ABT9month


title: natural aging mouse ovary 25 months old 3

description: B018NA6 25 month

value: natural aging mouse

value: 25 months


title: mouse_B6129SF2J_Acetominophen_24_1_mM_94

value: Acetominophen

value: mM


title: mouse_B6129SF2J_Acetominophen_24_1_mM_93


title: H3K36me3_heart_E16_EC_cell_110

value: Fixed by methanol

value: H3K36me3, Active motif, Cat. 61101


title: H3K36me3_heart_E16_EC_cell_108


title: natural aging mouse ovary 25 months old 2

description: B017NA6 25 month


title: H3K36me3_heart_E16_EC_cell_107


title: mouse_B6129SF2J_Acetominophen_24_1_mM_92


title: natural aging mouse ovary 25 months old 1

description: B016NA6 25month


title: natural aging mouse ovary 18 months old 3

description: B015NA5 18 month

value: 18 months


title: natural aging mouse ovary 18 months old 2

description: B014NA5 18 month


title: H3K36me3_heart_E16_EC_cell_112


title: H3K36me3_heart_E16_EC_cell_105


title: mouse_B6129SF2J_Acetominophen_24_0.3_mM_90


title: mouse_B6129SF2J_Acetominophen_24_1_mM_91


title: natural aging mouse ovary 18 months old 1

description: B013NA5 18 month


title: H3K36me3_heart_E16_EC_cell_111


title: H3K36me3_heart_E16_EC_cell_104


title: natural aging mouse ovary 12 months old 3

description: B012NA4 12 month

value: 12 months


title: mouse_B6129SF2J_Acetominophen_24_0.3_mM_89


title: H3K36me3_heart_E16_EC_cell_103


title: mouse_B6129SF2J_Acetominophen_24_0.3_mM_88


title: natural aging mouse ovary 12 months old 2

description: B011NA4 12 month


title: H3K36me3_heart_E16_EC_cell_102


title: H3K36me3_heart_E16_EC_cell_109


title: mouse_B6129SF2J_Rosiglitzone_24_0.1_uM_86

value: Rosiglitzone


title: mouse_B6129SF2J_Acetominophen_24_0.3_mM_87


title: H3K36me3_heart_E16_EC_cell_101


title: natural aging mouse ovary 12 months old 1

description: B010NA4 12 month

value: ovary


title: natural aging mouse ovary 9 months old 3

description: B09NA3 9 month


title: H3K36me3_heart_E16_EC_cell_100


title: mouse_B6129SF2J_Rosiglitzone_24_0.1_uM_85


title: natural aging mouse ovary 9 months old 2

description: B08NA3 9 month


title: H3K36me3_heart_E16_EC_cell_99


title: mouse_B6129SF2J_Rosiglitzone_24_0.1_uM_84


title: H3K36me3_heart_E16_EC_cell_98


title: natural aging mouse ovary 6 months old 3

description: B06NA2 6 month


title: mouse_B6129SF2J_Rosiglitzone_24_0.1_uM_83


title: mouse_B6129SF2J_Rosiglitzone_24_0.01_uM_82


title: H3K36me3_heart_E16_EC_cell_97


title: H3K36me3_heart_E16_EC_cell_96


title: natural aging mouse ovary 6 months old 2

description: B05NA2 6 month


title: natural aging mouse ovary 6 months old 1

description: B04NA2 6 month


title: H3K36me3_heart_E16_EC_cell_95


title: mouse_B6129SF2J_Rosiglitzone_24_0.01_uM_80


title: H3K36me3_heart_E16_EC_cell_94


title: H3K36me3_heart_E16_EC_cell_106


title: mouse_B6129SF2J_Rosiglitzone_24_0.01_uM_79


title: H69M cells, sheIF6, polysomal RNA, replicate 2

city: Chengdu

first: Haoning

last: Peng

state: Sichuan

address: No.37 Guoxue Alley, Wuhou District

department: Department of Thoracic Surgery

institute: West China Hospital, Sichuan University

library_source: other

data_processing:
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR
Count data were generated using HTSeq
Assembly: hg38
Supplementary files format and content: tab delimited text file includes read counts for each sample

molecule: other

growth_protocol: H69_shNTC cells, H69_sheIF6 cells, H69M_shNTC cells and H69M_sheIF6 cells were maintained in RPMI 1640 supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Polysome-bound RNA were extracted from sucrose based fraction after polysome profiling using TRIzol LS (ThermoFisher) according to manufacturer’s protocol and were quantified by Nanodrop microvolume spectrophotometers (Thermo Fisher Scientific). Cytoplasmic RNA were extracted from cell lysate in hypotonic buffer (5 mM Tris-HCl pH 7.5, 2.5 mM MgCl2, 1.5 mM KCl, 100 μg.ml-1 cycloheximide, 2 mM DTT, 100 U/ml RNase inhibitor (Promega), 0.5% sodium deoxycholate, 0.5% Triton X-100) using TRIzol LS and were quantified by Nanodrop as well.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations

value: SCLC cells

value: eIF6 knockdown

value: normal

tag: fraction

value: polysomal RNA


title: natural aging mouse ovary 3 months old 3

description: B03NA1 3 month

value: 3 months


title: natural aging mouse ovary 3 months old 2

description: B02NA1 3 month


title: H69M cells, sheIF6, polysomal RNA, replicate 1


title: H3K36me3_heart_E16_EC_cell_93

value: heart

tag: strain


title: H69M cells, shNTC, polysomal RNA, replicate 2

tag: cell type

value: WT


title: mouse_B6129SF2J_GW7647_24_0.1_uM_78

value: primary hepatocytes

tag: chemical

value: uM


title: H3K36me3_heart_E16_EC_cell_92


title: mouse_B6129SF2J_GW7647_24_0.1_uM_77

tag: concentration


title: H69M cells, shNTC, polysomal RNA, replicate 1


title: natural aging mouse ovary 3 months old 1

description: B01NA1 3 month

value: natural aging mouse


title: natural aging mouse ovary 9 months old 1

description: B07NA3 9 month

value: 9 months


title: mouse_B6129SF2J_GW7647_24_0.1_uM_76

tag: concentration units


title: H3K36me3_heart_E16_EC_cell_91

value: Fixed by methanol


title: H69M cells, sheIF6, cytoplasmic RNA, replicate 2

molecule: cytoplasmic RNA

value: cytoplasmic RNA


title: mouse_B6129SF2J_Rosiglitzone_24_0.01_uM_81

tag: exposure duration_(hours)


title: mouse_B6129SF2J_GW7647_24_0.1_uM_75


title: H3K36me3_heart_E16_EC_cell_90

tag: developmental stage

value: H3K36me3, Active motif, Cat. 61101


title: H69M cells, sheIF6, cytoplasmic RNA, replicate 1


city: Boston

last: DCIC

state: MA

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

description: lab: Danwei Huangfu, MSKCC  award: 1U01DK128852-01  4DN accession: 4DNEXUDU96VW  description: in situ Hi-C on PDX1-eGFP dCAS9-KRAB H1 differentiated to endoderm of foregut with Arima - A1, A2 - 4DNEXUDU96VW  replicate_information: Biological replicate 2 ,Technical replicate 1 digestion_enzyme: Arima - A1, A2 digestion_time: 30.0 digestion_temperature: 37.0 crosslinking_method: 1% Formaldehyde crosslinking_time: 10.0 crosslinking_temperature: 23.0 ligation_time: 15.0 ligation_temperature: 23.0 ligation_volume: 0.082 biotin_removed: No biosample_quantity: 2000000.0 biosample_quantity_units: cells fragment_size_selection_method: SPRI beads fragment_size_range: 200-600 fragmentation_method: sonication donor sex: male  donor life_stage: embryonic  donor 4DN accession: 4DNIN3RG3ZKE description: Huang Lab hESC to PP differentiation download:https://data.4dnucleome.org/protocols/017e237c-116e-49f0-8bae-8fd4c3deeaf2@@download/attachment/Huang_lab_PP_diff_protocol.pdf

data_processing:
Hi-C Post-alignment Processing 0.2.6: https://data.4dnucleome.org/workflows/4DNWFT69RBY4/ This is a subworkflow of the Hi-C data processing pipeline. It takes a bam file as input and performs parsing, sorting, filtering and deduping. It produces two output files, a lossless, filter-annotated bam file and a filtered pairs (contact list) file. Detailed Steps are as follows: 1. Parsing and sorting bam file using pairsamtools  software 2. Merging pairsam files using pairsamtools  software 3. Marking duplicates to pairsam file using pairsamtools  software 4. Filtering duplicate and invalid reads using pairsamtools  software
Assembly: GRCh38
Supplementary files format and content: File type: contact list-replicate (pairs). Description: Pairs files are generated during analysis of genomic contact data and consist of a list of pairs of genomic loci, represented by chromosomal position.
Supplementary files format and content: PFG-stage .bed file containing called TADs

source_name: stem cell

growth_protocol: All differentiation experiments were performed on hESCs grown on vitronectin. hESCs were maintained in E8 medium for 2 days to reach ~80% confluence. hESCs were rinsed with 1X DPBS (without Mg2+ and Ca2+) and first differentiated into DE using S1/2 media, supplemented with 100 ng/ml Activin A (Bon Opus Biosciences) for three days and CHIR99021 (Stemgent, 04-0004-10) for two days (1st day, 5 µM; 2nd day, 0.5 µM).  DE cells were rinsed with 1X DPBS (without Mg2+ and Ca2+) and then exposed to S1/2 media supplemented with 50 ng/ml of KGF (FGF7) (PeproTech, 100-19) and 0.25mM vitamin C (Sigma-Aldrich, A4544) for 2 days to reach GT stage. Cells were switched to S3/4 media supplemented with 50 ng/ml of FGF7, 0.25 mM vitamin C, and 1µM retinoic acid (RA) (Sigma-Aldrich, R2625) for 2 days to reach PFG stage.  description: Huang Lab hESC to PP differentiation protocol download:https://data.4dnucleome.org/protocols/017e237c-116e-49f0-8bae-8fd4c3deeaf2/@@download/attachment/Huang_lab_PP_diff_protocol.pdf

extract_protocol:
description: Arima Hi-C Protocol v01  download: https://data.4dnucleome.org/protocols/1686012d-09fd-44e5-b01b-14789205a091/@@download/attachment/Arima_HiC_Kit_V01.pdf
KAPA HyperPrep kit (KAPA, KK8502)

tag: tissue

value: stem cell

value: stem cell derived cell line

value: pancreatic precursor cells - H1

value: Early pancreatic differentiation


title: H3K36me3_heart_E16_EC_cell_89

tag: tissue preparation


title: mouse_B6129SF2J_GW7647_24_0.01_uM_74


title: H1-hESC,  NF2 KO2, Day 14, Replicate 3

city: Singapore

first: Roger

last: Foo

address: 14 Medical Drive, MD6

country: Singapore

institute: National University of Singapore

description:
KO2_D14_3
fpkm.txt

data_processing:
Fastq files were processed and adaptors were trimmed using trim-galore to sequence length of 50. Paired end reads were mapped against the human reference genome hg38 using STAR aligner.
Mapped gene counts were computed using Htseq-count and normalized to Counts per Million (CPM) and Fragments Per Kilobase of exon per million mapped fragments (FPKM).
Differential gene expression analysis were performed using the edgeR package for individual timepoint comparison.
Contrasts were set comparing the average expression of both NF2 knockout lines versus the average expression of wiltype lines for every differentiation time point, and fitting a negative binomial generalized log-linear model to read counts for each gene using the glmFIT function.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: tab-delimited text file include fpkm value for each sample

growth_protocol: hESCs were maintained in mTesR1 media, and hESC-CMs were maintained RPMI with Insulin in humidified incubator with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using Trizol Reagent and Direct-Zol RNA Miniprep kit across cardiomyocyte differentiation time points, and 1ug of Total RNA was used for library preparations.
RNA-seq libraries were prepared using illumina TruSeq Stranded Total RNA Library Prep HMR kit using manufacturer's instructions

treatment_protocol: hESCs were maintained in mTesR1 media at Day 0, hESCs were then induced to Mesendoderm with 7um CHIR99021 (Day 1) before changing to RPMI without insulin until Day 3. At Day 3, cells were treated with 5uM IWP2 (Day 3) until Day 5, before changing back to RPMI without insulin. RPMI with insulin is added from Day 7 onwards thereafter.

value: human embryonic stem cells

tag: time

value: Day 14

value: NF2 KO

value: Cardiomyocyte Differentiation


title: H69M cells, shNTC, cytoplasmic RNA, replicate 2

tag: cell line

value: SCLC cells

value: normal


title: H69M cells, shNTC, cytoplasmic RNA, replicate 1

tag: genotype

value: WT


title: mouse_B6129SF2J_GW7647_24_0.01_uM_73

value: primary hepatocytes

value: uM


title: H3K36me3_heart_E16_EC_cell_88

value: heart

tag: chip antibody


title: H1-hESC,  NF2 KO2, Day 14, Replicate 1

description:
KO2_D14_1
fpkm.txt

tag: treatment


title: H1-hESC,  NF2 KO2, Day 14, Replicate 2

description:
KO2_D14_2
fpkm.txt


title: mouse_B6129SF2J_GW7647_24_0.01_uM_72


title: H3K36me3_heart_E16_EC_cell_87

value: Fixed by methanol


title: H1-hESC,  NF2 KO2, Day 5, Replicate 3

description:
KO2_D5_3
fpkm.txt

value: Day 5


title: H3K36me3_heart_E16_EC_cell_86

value: H3K36me3, Active motif, Cat. 61101


title: H69 cells, sheIF6, polysomal RNA, replicate 1

value: eIF6 knockdown

value: polysomal RNA


title: H69 cells, sheIF6, polysomal RNA, replicate 2


title: mouse_B6129SF2J_GW7647_24_0.01_uM_71


title: H3K36me3_heart_E16_EC_cell_85


title: mouse_B6129SF2J_HFPO_DA_24_0.1_uM_70


title: H1-hESC,  NF2 KO2, Day 5, Replicate 2

description:
KO2_D5_2
fpkm.txt


title: H69 cells, shNTC, polysomal RNA, replicate 2


title: H1-hESC,  NF2 KO2, Day 5, Replicate 1

description:
KO2_D5_1
fpkm.txt


description: lab: Danwei Huangfu, MSKCC  award: 1U01DK128852-01  4DN accession: 4DNEXMHLGGWC  description: in situ Hi-C on PDX1-eGFP dCAS9-KRAB H1 differentiated to endoderm of foregut with Arima - A1, A2 - 4DNEXMHLGGWC  replicate_information: Biological replicate 1 ,Technical replicate 1 digestion_enzyme: Arima - A1, A2 digestion_time: 30.0 digestion_temperature: 37.0 crosslinking_method: 1% Formaldehyde crosslinking_time: 10.0 crosslinking_temperature: 23.0 ligation_time: 15.0 ligation_temperature: 23.0 ligation_volume: 0.082 biotin_removed: No biosample_quantity: 2000000.0 biosample_quantity_units: cells fragment_size_selection_method: SPRI beads fragment_size_range: 200-600 fragmentation_method: sonication donor sex: male  donor life_stage: embryonic  donor 4DN accession: 4DNIN3RG3ZKE description: Huang Lab hESC to PP differentiation download:https://data.4dnucleome.org/protocols/017e237c-116e-49f0-8bae-8fd4c3deeaf2@@download/attachment/Huang_lab_PP_diff_protocol.pdf

value: stem cell

value: stem cell derived cell line

value: pancreatic precursor cells - H1


title: mouse_B6129SF2J_HFPO_DA_24_0.1_uM_69


title: H69 cells, shNTC, polysomal RNA, replicate 1


title: H3K36me3_heart_E16_EC_cell_84


title: H1-hESC,  NF2 KO2, Day 1, Replicate 3

description:
KO2_D1_3
fpkm.txt

value: human embryonic stem cells

value: Day 1


title: mouse_B6129SF2J_HFPO_DA_24_0.1_uM_68


title: H3K36me3_heart_E16_EC_cell_83


title: H69 cells, sheIF6, cytoplasmic RNA, replicate 2

value: cytoplasmic RNA


title: H1-hESC,  NF2 KO2, Day 1, Replicate 2

description:
KO2_D1_2
fpkm.txt

value: NF2 KO

value: Cardiomyocyte Differentiation


title: H3K36me3_heart_E16_EC_cell_82


title: mouse_B6129SF2J_HFPO_DA_24_0.1_uM_67


title: H1-hESC,  NF2 KO2, Day 1, Replicate 1

description:
KO2_D1_1
fpkm.txt


title: H69 cells, sheIF6, cytoplasmic RNA, replicate 1

value: SCLC cells

value: normal


title: H3K36me3_heart_E16_EC_cell_81


title: H1-hESC,  NF2 KO2, Day 0, Replicate 3

description:
KO2_D0_3
fpkm.txt

value: Day 0


title: mouse_B6129SF2J_DMSO_12_0_na_66

value: primary hepatocytes

value: DMSO

value: solvent control


title: H3K36me3_heart_E16_EC_cell_80

value: heart

value: Fixed by methanol

value: H3K36me3, Active motif, Cat. 61101


title: H69 cells, shNTC, cytoplasmic RNA, replicate 1

value: WT


title: mouse_B6129SF2J_DMSO_12_0_na_65


title: H1-hESC,  NF2 KO2, Day 0, Replicate 1

description:
KO2_D0_1
fpkm.txt


title: mouse_B6129SF2J_DMSO_12_0_na_64


title: H1-hESC,  NF2 KO1, Day 14, Replicate 3

description:
KO1_D14_3
fpkm.txt

value: Day 14


title: H3K36me3_heart_E16_EC_cell_79


title: H69M cells, polysome RNA, replicate 3

description:
H69M_poly_4
H69_H69M_poly_count.txt

growth_protocol: H69, H196 and H69M cells were maintained in RPMI 1640 supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37°C

value: polysomal RNA


title: H1-hESC,  NF2 KO1, Day 14, Replicate 2

description:
KO1_D14_2
fpkm.txt

value: human embryonic stem cells


title: H3K36me3_heart_E16_EC_cell_78


title: mouse_B6129SF2J_Deionized_water_12_0_na_62


title: H3K36me3_heart_E16_EC_cell_77


title: H69M cells, polysome RNA, replicate 2

description:
H69M_poly_3
H69_H69M_poly_count.txt


title: H1-hESC,  NF2 KO1, Day 14, Replicate 1

description:
KO1_D14_1
fpkm.txt


title: H3K36me3_heart_E16_EC_cell_76


title: mouse_B6129SF2J_Deionized_water_12_0_na_61


title: H69M cells, cytoplasmic RNA, replicate 3

description:
H69M_input_4
H69_H69M_cyto_count.txt


title: H69 cells, shNTC, cytoplasmic RNA, replicate 2


title: mouse_B6129SF2J_HFPO_DA_12_500_uM_60

value: uM


title: H3K36me3_heart_E16_EC_cell_75


title: H69M cells, cytoplasmic RNA, replicate 2

description:
H69M_input_3
H69_H69M_cyto_count.txt

value: cytoplasmic RNA


title: H1-hESC,  NF2 KO1, Day 5, Replicate 3

description:
KO1_D5_3
fpkm.txt

value: Day 5

value: NF2 KO


title: H1-hESC,  NF2 KO1, Day 5, Replicate 2

description:
KO1_D5_2
fpkm.txt

value: Cardiomyocyte Differentiation


title: mouse_B6129SF2J_HFPO_DA_12_500_uM_59


title: H69M cells, cytoplasmic RNA, replicate 1

description:
H69M_input_2
H69_H69M_cyto_count.txt

value: SCLC cells

value: normal


title: mouse_B6129SF2J_Deionized_water_12_0_na_63

value: primary hepatocytes


title: H3K36me3_heart_E16_EC_cell_73


title: mouse_B6129SF2J_HFPO_DA_12_500_uM_58


title: H1-hESC,  NF2 KO1, Day 5, Replicate 1

description:
KO1_D5_1
fpkm.txt


title: H69 cells, polysomal RNA, replicate 6

description:
H69_poly_4
H69_H69M_poly_count.txt


title: H1-hESC,  NF2 KO1, Day 1, Replicate 3

description:
KO1_D1_3
fpkm.txt

value: Day 1


title: mouse_B6129SF2J_HFPO_DA_12_50_uM_57


title: H69 cells, polysomal RNA, replicate 5

description:
H69_poly_3
H69_H69M_poly_count.txt


title: H69M cells, polysome RNA, replicate 1

description:
H69M_poly_2
H69_H69M_poly_count.txt


title: H3K36me3_heart_E16_EC_cell_72


title: H3K36me3_heart_E16_EC_cell_71


title: H69 cells, polysomal RNA, replicate 4

description:
H69_poly_2
H69_H69M_poly_count.txt


title: mouse_B6129SF2J_HFPO_DA_12_50_uM_56


title: H1-hESC,  NF2 KO1, Day 1, Replicate 2

description:
KO1_D1_2
fpkm.txt


title: mouse_B6129SF2J_HFPO_DA_12_50_uM_55


title: H1-hESC,  NF2 KO1, Day 1, Replicate 1

description:
KO1_D1_1
fpkm.txt


title: mouse_B6129SF2J_Rosiglitzone_12_10_uM_54

value: Rosiglitzone


title: H3K36me3_heart_E16_EC_cell_70

value: heart


title: H1-hESC,  NF2 KO1, Day 0, Replicate 3

description:
KO1_D0_3
fpkm.txt

value: Day 0


title: H3K36me3_heart_E16_EC_cell_69

value: Fixed by methanol

value: H3K36me3, Active motif, Cat. 61101


title: H3K36me3_heart_E16_EC_cell_74


title: H3K36me3_heart_E16_EC_cell_68


title: H1-hESC,  NF2 KO1, Day 0, Replicate 1

description:
KO1_D0_1
fpkm.txt


title: H69 cells, cytoplasmic RNA, replicate 5

description:
H69_input_3
H69_H69M_cyto_count.txt

value: WT


title: mouse_B6129SF2J_Rosiglitzone_12_10_uM_53


title: H69 cells, cytoplasmic RNA, replicate 4

description:
H69_input_2
H69_H69M_cyto_count.txt


title: H3K36me3_heart_E16_EC_cell_67


title: mouse_B6129SF2J_Rosiglitzone_12_10_uM_52


title: H196 cells, polysomal RNA, replicate 3

description:
H196_3
H69_H196_poly_count.txt

value: polysomal RNA


title: H3K36me3_heart_E16_EC_cell_66


title: H196 cells, polysomal RNA, replicate 2

description:
H196_2
H69_H196_poly_count.txt


title: mouse_B6129SF2J_D_Galactosamine_12_10_mM_51

value: mM


title: H1-hESC,  NF2 WT2, Day 14, Replicate 2

description:
WT2_D14_2
fpkm.txt

value: human embryonic stem cells

value: Day 14


title: mouse_B6129SF2J_D_Galactosamine_12_10_mM_50


title: H3K36me3_heart_E16_EC_cell_65


title: H196 cells, polysomal RNA, replicate 1

description:
H196_1
H69_H196_poly_count.txt


title: mouse_B6129SF2J_D_Galactosamine_12_10_mM_49


title: H69 cells, cytoplasmic RNA, replicate 6

description:
H69_input_4
H69_H69M_cyto_count.txt

value: cytoplasmic RNA


title: H196 cells, cytoplasmic RNA, replicate 3

description:
H196_3
H69_H196_cyto_count.txt


title: H1-hESC,  NF2 WT2, Day 14, Replicate 3

description:
WT2_D14_3
fpkm.txt


title: H1-hESC,  NF2 WT2, Day 5, Replicate 2

description:
WT2_D5_2
fpkm.txt

value: Day 5


title: H3K36me3_heart_E16_EC_cell_64


title: H3K36me3_heart_E16_EC_cell_63


title: mouse_B6129SF2J_Acetominophen_12_10_mM_47

value: Acetominophen


title: H196 cells, cytoplasmic RNA, replicate 2

description:
H196_2
H69_H196_cyto_count.txt

value: SCLC cells


title: H3K36me3_heart_E16_EC_cell_62


title: H1-hESC,  NF2 WT2, Day 5, Replicate 1

description:
WT2_D5_1
fpkm.txt

value: Cardiomyocyte Differentiation


title: H196 cells, cytoplasmic RNA, replicate 1

description:
H196_1
H69_H196_cyto_count.txt

value: normal


title: mouse_B6129SF2J_Acetominophen_12_10_mM_46

value: primary hepatocytes


title: H1-hESC,  NF2 WT2, Day 1, Replicate 3

description:
WT2_D1_3
fpkm.txt

value: Day 1


title: mouse_B6129SF2J_Acetominophen_12_10_mM_48


title: H1-hESC,  NF2 WT2, Day 14, Replicate 1

description:
WT2_D14_1
fpkm.txt


title: H69 cells, polysomal RNA, replicate 3

description:
H69_3
H69_H196_poly_count.txt


title: H1-hESC,  NF2 WT2, Day 1, Replicate 2

description:
WT2_D1_2
fpkm.txt


title: H3K36me3_heart_E16_EC_cell_61

value: heart


title: H3K36me3_heart_E16_EC_cell_60


title: H69 cells, polysomal RNA, replicate 1

description:
H69_1
H69_H196_poly_count.txt


title: H1-hESC,  NF2 WT2, Day 5, Replicate 3

description:
WT2_D5_3
fpkm.txt


title: H1-hESC,  NF2 WT2, Day 0, Replicate 3

description:
WT2_D0_3
fpkm.txt

value: Day 0


title: mouse_B6129SF2J_HFPO_DA_12_5_uM_44

value: uM


title: H1-hESC,  NF2 WT2, Day 1, Replicate 1

description:
WT2_D1_1
fpkm.txt


title: mouse_B6129SF2J_HFPO_DA_12_5_uM_43


title: H69 cells, polysomal RNA, replicate 2

description:
H69_2
H69_H196_poly_count.txt


title: mouse_B6129SF2J_D_Galactosamine_12_3_mM_42


title: H3K36me3_heart_E16_EC_cell_58

value: Fixed by methanol

value: H3K36me3, Active motif, Cat. 61101


title: H3K36me3_heart_E16_EC_cell_57


title: H1-hESC,  NF2 WT2, Day 0, Replicate 1

description:
WT2_D0_1
fpkm.txt

value: WT


title: H3K36me3_heart_E16_EC_cell_59


title: H1-hESC,  NF2 WT1, Day 14, Replicate 2

description:
WT1_D14_2
fpkm.txt


title: H69 cells, cytoplasmic RNA, replicate 2

description:
H69_2
H69_H196_cyto_count.txt


title: H69 cells, cytoplasmic RNA, replicate 1

description:
H69_1
H69_H196_cyto_count.txt


title: H1-hESC,  NF2 WT1, Day 14, Replicate 1

description:
WT1_D14_1
fpkm.txt


title: mouse_B6129SF2J_D_Galactosamine_12_3_mM_41

value: mM


title: mouse_B6129SF2J_D_Galactosamine_12_3_mM_40


title: DBTRG cells, soft gel 3D cultured, replicate 3

city: Wuhan

first: Bincan

last: He

address: 1 Shizishan Rd

institute: Huazhong Agricultural University

data_processing:
The application in reads alignment procedure was Hisat2, whose reference genome was hg38 with the default parameters in our paired reads. HTSeq package was used to construct count matrix with mapping results.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: brain

extract_protocol:
Total RNA was extracted from the cells by TRIzol® Reagent according the manufacturer’s instructions (Invitrogen).
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.

value: brain

value: DBTRG

value: Glioblastoma cells

value: soft gel 3D cultured


title: H1-hESC,  NF2 WT1, Day 5, Replicate 2

description:
WT1_D5_2
fpkm.txt

value: human embryonic stem cells

value: Day 5


title: H3K36me3_heart_E16_EC_cell_55


title: H3K36me3_heart_E16_EC_cell_54


title: DBTRG cells, soft gel 3D cultured, replicate 2


title: H1-hESC,  NF2 WT1, Day 5, Replicate 1

description:
WT1_D5_1
fpkm.txt

value: Cardiomyocyte Differentiation


title: mouse_B6129SF2J_HFPO_DA_12_5_uM_45


title: mouse_B6129SF2J_Acetominophen_12_3_mM_39

value: Acetominophen


title: H3K36me3_heart_E16_EC_cell_53


title: mouse_B6129SF2J_Acetominophen_12_3_mM_38

value: primary hepatocytes


title: H1-hESC,  NF2 WT1, Day 1, Replicate 2

description:
WT1_D1_2
fpkm.txt

value: Day 1


title: DBTRG cells, soft gel 3D cultured, replicate 1


title: mouse_B6129SF2J_Acetominophen_12_3_mM_37


title: DBTRG cells, rigid dish 2D cultured, replicate 3

value: rigid dish 2D cultured


title: H69 cells, cytoplasmic RNA, replicate 3

description:
H69_3
H69_H196_cyto_count.txt

value: SCLC cells

value: normal

value: cytoplasmic RNA


title: H3K36me3_heart_E16_EC_cell_51

value: heart

value: Fixed by methanol

value: H3K36me3, Active motif, Cat. 61101


title: H1-hESC,  NF2 WT1, Day 1, Replicate 1

description:
WT1_D1_1
fpkm.txt

value: WT


title: DBTRG cells, rigid dish 2D cultured, replicate 2

value: brain

value: DBTRG


title: DBTRG cells, rigid dish 2D cultured, replicate 1

value: Glioblastoma cells


title: H1-hESC,  NF2 WT1, Day 0, Replicate 1

description:
WT1_D0_1
fpkm.txt

value: human embryonic stem cells

value: Day 0


title: H3K36me3_heart_E16_EC_cell_50


title: H3K36me3_heart_E16_EC_cell_56


title: mouse_B6129SF2J_Rosiglitzone_12_1_uM_34

value: Rosiglitzone

value: uM


title: H3K36me3_heart_E16_EC_cell_49


title: 4 control subjects and 8 patients with chronic spontaneous urticaria

city: Dublin

first: Conor

last: Finlay

address: Trinity Translational Medicine Institute, Trinity College Dublin, St. James' Hospital Campus, Trinity College Dublin, Dublin 8

department: School of Medicine

country: Ireland

institute: Trinity College Dublin

description:
Combined WTA (RNA), AbSeq (CITE-seq) and Sample Tag libraries
scRNA-seq of FACS-sorted PBMC with enriched progenitors from 4 control subjects and 8 paitents with chronic spontaneous urticaria

data_processing:
bcl2fastq
Assembly: Release 29 (GRCh38.p12)
Supplementary files format and content: BD Rhapsody WTA Analysis pipeline (Revision 11) outputs

source_name: Blood

extract_protocol:
Our study sample comprised patients with a clinical diagnosis of CSU under hospital care and healthy controls with no diagnosis of atopic disease or self-reported atopic dermatitis, allergic rhinitis, asthma, food allergy, CSU or spontaneous angioedema. Ethical approval was granted by the Joint Research Ethics Committee in Tallaght University Hospital and St. James’s Hospital, Dublin. Using flow cytometry, we assessed the number of Lineage-CD34+CD117+ cells per ml of peripheral blood enumerating cells which were FcεRI negative, FcεRI positive and FcεRIhi. A subset of individuals (n=12) underwent scRNA-seq. Patients completed the Urticaria Control Test (UCT), a measure of disease control assessing hives and swellings over the past 4 weeks (20). For patients who were omalizumab naïve at the time of sampling and went on to receive omalizumab, we sought to compare individuals who responded to omalizumab within 90 days of treatment versus those who did not. We defined 'responders’ as individuals with a UCT score ≥ 9, 90 days after their first dose of omalizumab and ‘non-responders’ as individuals with a UCT score ≤ 8, 90 days after their first dose. 90 days corresponds to 3 doses of 300mg omalizumab received every 30 days. scRNA-seq was performed using the BD Rhapsody Single Cell Analysis System (BD Biosciences). Briefly, sorted cells populations (2 cryopreserved, 10 fresh) were incubated with Human FcX (BioLegend), before labelling cells with antibodies from the Human Single Cell Sample Multiplexing Kit (BD Biosciences). Single cell capture was performed using the BD Rhapsody Express instrument, BD Rhapsody cartridges and the BD Cartridge Reagent Kit. After cell lysis, an on-bead cDNA reaction was performed using the BD Rhapsody cDNA kit. cDNA libraries were prepared using the BD Rhapsody Whole Transcriptome Analysis library preparation kit. Sequencing was performed using an S1 100 cycle Kit on a Novaseq 6000 (with a final sequencing concentration of 300 pM with 20% PhiX (Illumina). Paired-end sequencing was performed with the following cycle allotment: RI 64, R2 58, i7 8, resulting in 1.2 billion quality reads aligning to cells. Bioinformatics was performed using the BD Rhapsody WTA Analysis pipeline (Revision 11). Data was aligned to human genomic sequence and annotation (GRCh38, Release 29). Of a total of 14,964 cells were identified, 244 had an undetermined sample tag call and 2,606 cells were identified as doublets.
cDNA libraries were prepared using the BD Rhapsody Whole Transcriptome Analysis library preparation kit.

value: Blood

value: Sorted PBMC

value: Mixed


title: mouse_B6129SF2J_GW7647_12_1_uM_33

value: primary hepatocytes


title: H.sapiens iPSC heavy polysomal fraction biol rep 2

city: Santa Cruz

first: Jeremy

last: Sanford

state: CA

address: 1156 High St

institute: University of California, Santa Cruz

description:
hips_polh_jd963
human_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

data_processing:
mapping to hg38/panTro6/ponAbe3 with STAR (v 2.7)
repeatmasking with bowtie2
identification of unannotated transcripts with Stringtie
identification and quantification of pairwise alternative splicing events with in house python scripts (junctionCounts)
Assembly: hg38, panTro6, ponAbe3
Supplementary files format and content: *_splice_lib_events.gtf - tab delimited file in GTF format containing all identified splice events for each cell line
Supplementary files format and content: all_species_junctioncounts_restricted.tsv - tab delimited file containing pairwise splicing events (between all combinations of cell lines), the number of reads supporting the isoforms and the percent spliced in (PSI) value
Supplementary files format and content: all_distances.tsv - tab delimited file containing multiple distance metrics computed between pair wise splicing events
Supplementary files format and content: all_dpsi.tsv - tab delimited file containing delta PSI values for all events contained in all_species_junctioncounts_restricted.tsv
Supplementary files format and content: all_ddpsi.tsv - tab delimited file containing delta delta PSI values for all events contained in all_species_junctioncounts_restricted.tsv

growth_protocol: C305 cells were cultured on matrigel in mTeSR, Eip-8919-1A and Jos-C31 were cultured on vitronectin in Essential 8 media

extract_protocol:
Frac-seq experiments were performed as previously published (Sterne-Weiler et al. 2013) using human, chimpanzee, and orangutan iPSC lines, with modification to the number of fractions collected. Cytosolic extracts from cell lines/tissues are fractionated by sucrose gradient centrifugation. We collected the total cytosolic lysate, the monoribosomal fraction (80s), as well as light (P2-4), medium (P5-8), and heavy (P9+) polyribosomal fractions.
polyA+ selected RNA from each fraction and individually barcoded libraries using the Bioo NEXTflex Directional RNASeq kit.

treatment_protocol: not applicable

value: iPSC

value: heavy polysomal fraction


title: OCIAML2_ARM_4

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

data_processing:
Sequencing reads were pseudo aligned to genome and genes quantified using Kallisto
Assembly: GRCh38v96
Supplementary files format and content: Tab delimited table containing gene symbol and sample normalized counts

source_name: hematopoietic

extract_protocol:
Total RNA was extracted using QIAGEN RNAeasy plus mini kit following manufacturer's instructions
Libraries were prepared using TruSeq Stranded mRNA LT Sample Prep Kit
First stranded libraries

value: hematopoietic

value: AML


title: H3K36me3_heart_E16_EC_cell_48

value: heart

value: Fixed by methanol

value: H3K36me3, Active motif, Cat. 61101


title: mouse_B6129SF2J_GW7647_12_1_uM_32


title: OCIAML2_ARM_3


title: H.sapiens iPSC heavy polysomal fraction biol rep 1

description:
hips_polh_jd957
human_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv


title: H3K36me3_heart_E16_EC_cell_47


title: H3K36me3_heart_E16_EC_cell_52


title: H.sapiens iPSC medium polysomal fraction biol rep 2

description:
hips_polm_jd962
human_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

value: medium polysomal fraction


title: mouse_B6129SF2J_GW7647_12_1_uM_31


title: OCIAML2_ARM_2


title: H3K36me3_heart_E16_EC_cell_46


title: H1-hESC,  NF2 WT1, Day 0, Replicate 3

description:
WT1_D0_3
fpkm.txt

value: WT

value: Cardiomyocyte Differentiation


title: mouse_B6129SF2J_Rosiglitzone_12_1_uM_35


title: mouse_B6129SF2J_D_Galactosamine_12_1_mM_30

value: mM


title: H.sapiens iPSC medium polysomal fraction biol rep 1

description:
hips_polm_jd956
human_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv


title: OCIAML2_ARM_1


title: H.sapiens iPSC light polysomal fraction biol rep 2

description:
hips_poll_jd961
human_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

value: light polysomal fraction


title: mouse_B6129SF2J_D_Galactosamine_12_1_mM_29


title: OCIAML2_AZ2_4


title: H3K36me3_heart_E16_EC_cell_45


title: H3K36me3_heart_E16_EC_cell_44


title: H.sapiens iPSC light polysomal fraction biol rep 1

description:
hips_poll_jd955
human_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv


title: H3K36me3_heart_E16_EC_cell_43


title: mouse_B6129SF2J_D_Galactosamine_12_1_mM_28


title: OCIAML2_AZ2_3


title: H3K36me3_heart_E16_EC_cell_42


title: mouse_B6129SF2J_Acetominophen_12_1_mM_27

value: Acetominophen


title: OCIAML2_AZ2_2


title: H.sapiens iPSC mono-ribosomal fraction biol rep 1

description:
hips_mono_jd954
human_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

value: mono-ribosomal fraction


title: mouse_B6129SF2J_Acetominophen_12_1_mM_26


title: H3K36me3_heart_E16_EC_cell_41


title: OCIAML2_AZ2_1


title: H.sapiens iPSC total cytosolic lysate biol rep 2

description:
hips_cyto_jd958
human_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

value: total cytosolic lysate


title: mouse_B6129SF2J_Acetominophen_12_1_mM_25


title: H3K36me3_heart_E16_EC_cell_39


title: OCIAML2_DMSO_4

value: DMSO-treated


title: H.sapiens iPSC total cytosolic lysate biol rep 1

description:
hips_cyto_jd952
human_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv


title: OCIAML2_DMSO_3


title: WT3

city: Cologne

first: Muhammad Sajid

last: Hussain

address: Weyertal 115b

department: Cologne Center for Genomics

country: Germany

institute: University of Cologne

data_processing:
For data analysis, we used the QuickNGS pipeline of Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne
Reads were mapped to the Homo sapiens reference genome version GRCh38 using TopHat2 (version 2.0.10) and abundance estimation with Cufflinks (version 2.1.1)
DESeq2 is used for differential gene expression analysis
The results were uploaded into the QuickNGS database for further analyses
Assembly: GRCh38

source_name: Skin biopsy from control individual

growth_protocol: We generated primary fibroblasts from skin biopsies from the patients and control individual. Cells were grown with DMEM Medium supplemented with fetal bovine serum, L-glutamine and antibiotics (Penicillin/Streptomycin)

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

value: Primary fibroblasts

value: Wild type

tag: disease state

value: Control


title: H3K36me3_heart_E16_EC_cell_38


title: WT2


title: mouse_B6129SF2J_D_Galactosamine_12_0.3_mM_23

value: primary hepatocytes


title: OCIAML2_DMSO_2

value: hematopoietic

value: AML


title: OCIAML2_DMSO_1


title: H3K36me3_heart_E16_EC_cell_37

value: heart

value: Fixed by methanol


title: WT1


title: mouse_B6129SF2J_Rosiglitzone_12_1_uM_36

value: Rosiglitzone

value: uM


title: mouse_B6129SF2J_Acetominophen_12_0.3_mM_21


title: H3K36me3_heart_E16_EC_cell_36

value: H3K36me3, Active motif, Cat. 61101


title: H.sapiens iPSC mono-ribosomal fraction biol rep 2

description:
hips_mono_jd960
human_splice_lib_events_restricted.gtf
all_species_junctioncounts_restricted.tsv
all_distances.tsv
all_dpsi.tsv
all_ddpsi.tsv

value: iPSC


title: MOLM14_ARM_4


title: H3K36me3_heart_E16_EC_cell_40


title: H3K36me3_heart_E16_EC_cell_35


title: MOLM14_ARM_3


title: CYHR1_SPN2

source_name: Skin biopsy from patient

value: syndromic microcephaly


title: mouse_B6129SF2J_Acetominophen_12_0.3_mM_20

value: Acetominophen

value: mM


title: MOLM14_ARM_2


title: CYHR1_SPN1


title: mouse_B6129SF2J_D_Galactosamine_12_0.3_mM_24


title: mouse_B6129SF2J_Acetominophen_12_0.3_mM_19


title: mouse_B6129SF2J_Rosiglitzone_12_0.1_uM_18


title: H3K36me3_heart_E16_EC_cell_33


title: MOLM14_ARM_1


title: MOLM14_AZ2_4


title: mouse_B6129SF2J_Rosiglitzone_12_0.1_uM_17


title: mouse_B6129SF2J_D_Galactosamine_12_0.3_mM_22


title: CYHR1_GMN2


title: H3K36me3_heart_E16_EC_cell_32


title: mouse_B6129SF2J_Rosiglitzone_12_0.1_uM_16


title: mouse_B6129SF2J_Rosiglitzone_12_0.01_uM_15


title: H3K36me3_heart_E16_EC_cell_30


title: MOLM14_AZ2_2


title: H3K36me3_heart_E16_EC_cell_29


title: CYHR1_SPN3


title: U2OS_3.3_Rep3

city: Bologna

first: Giovanni

last: Capranico

state: BO

address: Via Selmi 3

department: FABIT

country: Italy

institute: University of Bologna

data_processing:
reads were trimmed using Trimmomatic
Alignment was performed using Hisat2
Transcript quantification was performed with stringtie
All tools were ran with default parameters
Genome_build: hg38
Supplementary_files_format_and_content: Data files contain transcript abundance for each gene

source_name: U-2 OS cells

growth_protocol: cells were cultured in DMEM  before collection

extract_protocol:
total RNA was extracted with TRIzol reagent (Ambion)
NEBNext Ultra Directional RNA library prep protocol

value: Bone

tag: disease

value: Osteosarcoma

value: TDP1 H493R


title: H3K36me3_heart_E16_EC_cell_34


title: U2OS_3.3_Rep2


title: MOLM14_AZ2_1


title: mouse_B6129SF2J_Rosiglitzone_12_0.01_uM_14


title: CYHR1_GMN3

value: Primary fibroblasts


title: U2OS_3.3_Rep1


title: mouse_B6129SF2J_Rosiglitzone_12_0.01_uM_13


title: H3K36me3_heart_E16_EC_cell_28


title: H3K36me3_heart_E16_EC_cell_27


title: mouse_B6129SF2J_GW7647_12_0.1_uM_12


title: MOLM14_DMSO_3

value: DMSO-treated


title: mouse_B6129SF2J_GW7647_12_0.1_uM_11

value: primary hepatocytes


title: H3K36me3_heart_E16_EC_cell_31


title: H3K36me3_heart_E16_EC_cell_26


title: U2OS_1P_Rep2


title: U2OS_1P_Rep3


title: CYHR1_GMN1


title: MOLM14_AZ2_3

value: hematopoietic


title: H3K36me3_heart_E16_EC_cell_25


title: U2OS_1P_Rep1


title: mouse_B6129SF2J_GW7647_12_0.1_uM_10


title: H3K36me3_heart_E16_EC_cell_24


title: MOLM14_DMSO_1

value: AML


title: mouse_B6129SF2J_GW7647_12_0.01_uM_9


title: U2OS_WT_rep3

value: Wild Type


title: Sample_14_EVA71_Mock_6h

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description:
Sample 14, 6 hours post mock infection
10X Genomics

data_processing:
10x Genomics Cell Ranger 7.0.0 was used to demultiplex, generate FastQ files, and aggregate samples
Assembly: GRCh38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: RD (ATCC, CCL-136)

extract_protocol:
RD cells were plated on the day before the experiment (~2x106 cells in T-25 flasks). One extra flask was used to count the cells before to ensure the cells count for MOI calculation. Inoculums of 0.3 MOI were prepared fresh using Free FBS media of the three viruses (EV-A71, EV-D68 and CV-B3 P1). After removing the media, and washing with warm PBS, the cells were incubated for 1 hour with the inoculums (rocked each 10 minutes) at 37°C, for EV-A71 and CV- B3), and 33°C for EV-D68. After 1 hour, the inoculum was removed and 5% FBS media was added. The cells were incubated into their respective temperatures (37°C and 33°C) until the time point of collection (6 hpi). Mock-infected cells were also collected at 6 hpi. After 6 hpi, the cells were submitted to the standard protocol of sample preparation proposed by 10X Genomics (Chromium Single Cell 5' Reagent Kits User Guide (v2 Chemistry Dual Index), Document Number - CG00331 - Rev E, Aug, 2022). Briefly, the media is removed, and the cells are washed with warm PBS. TrypLE is added (2mL) to dissociating the cells and 2 mL of media is added to homogenize the cells. The cells are counted and also checked about their viability, after counting them, they are centrifuged at 500 x g for 5 minutes. Then, the supernatant is removed and the cells are washed with 1x PBS with 0.04% Bovine Serum Albumin (BSA), and centrifuged again at 500 x g for 5 minutes. After that, supernatant is removed and the appropriate volume of PBS/BSA is added to achieve the concentration of cells desired (~1000 cells/uL). Count the cells again and also check about cell viability. Once the cell's concentration is achieved the cells are moved to ice.
For the preparation of the cDNA and sequencing library generation, we followed the instructions from the user guide Chromium Next GEM Single Cell 5’ Reagent Kit v2 (Dual index) with one modification. The modification consists of a primer spike-in approach during the RT master mix preparation step.

value: RD (ATCC, CCL-136)


title: H3K36me3_heart_E16_EC_cell_23

value: heart

value: Fixed by methanol


title: MOLM14_DMSO_4


title: Sample_13_EVA71_6h_P5

description:
Sample 13, 6 hours post infection with Enterovirus A71
10X Genomics


title: H3K36me3_heart_E16_EC_cell_22

value: H3K36me3, Active motif, Cat. 61101


title: U2OS_WT_rep2


title: mouse_B6129SF2J_HFPO_DA_12_0.1_uM_6

city: Asheville

last: Heintz

address: 31 College Place, Suite B118

institute: ToxStrategies

data_processing:
Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing
fastqs were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches
Assembly: probe-based targeted sequencing
Supplementary files format and content: comma-separated text files include raw count values for each gene_probe

extract_protocol:
Following treatment with HFPO-DA or positive controls (i.e., GW7647, rosiglitazone, acetaminophen or d-galactosamine) for 12, 24 or 72 h, hepatocytes were lysed using TempO-Seq® Enhanced Lysis Buffer and processed according to the TempO-Seq® protocol by BioSypder Technologies.
TempO-Seq® protocol by BioSypder Technologies

value: uM


title: Sample_12_EVA71_6h_P3

description:
Sample 12, 6 hours post infection with Enterovirus A71
10X Genomics


title: H3K36me3_heart_E16_EC_cell_20

city: Beijing

last: Liu

address: 5 Yiheyuan Road

institute: Peking University

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were de-multiplexed to generate single cell profiles by custom scripts. For spliting single cell, we cut the first 21 bp of the read1 and the first 27 bp of the read2.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Cells with less than 1,000 non-duplicated were excluded.
Bed files were generated from bam files using bedtools (v2.25.0) bamToBed.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bed files. Each single cell bed file contain non-duplicated alignments as is in the bam file.  These files contain single cell genome-wide coverage files after  sorting and uniqing and removing duplicates. Since one cell only contains two copies of each genomic locus for assay, we usually use non-duplicated reads information to reflect peak information in one single cell (PMID: 31471188).

extract_protocol:
Following CoBATCH protocol.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.


title: H3K36me3_heart_E16_EC_cell_21


title: Sample_11_EVA71_6h_P1

description:
Sample 11, 6 hours post infection with Enterovirus A71
10X Genomics


title: mouse_B6129SF2J_GW7647_12_0.01_uM_7


title: U2OS_WT_rep1


title: SEP3Δtet-AGΔtet

city: Grenoble

first: Romain

last: BLANC-MATHIEU

address: 17 Avenue des martyrs

institute: CEA

data_processing:
Alignment to genome is done by Bowtie2
poor quality and multimapped reads are filtered out using samtools
peak-calling is done by MACS2 with parameters (-q 0.001 --call-summits)
Peaks called where Control read coverage is too high are removed from analysis
replicates are treated by MSPC to create consensus peaks
Assembly: Consensus peaks are reworked around maximum of peaks.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: 2-weeks old seedlings of Arabidopsis thaliana

extract_protocol:
Genomic DNA was extracted by chloroform isoamyl alcohol dna extraction protocol
Libraries were contructed using Truseq Illumina kits
Illumina TruSeq adaptors with single end index

value: seedlings

value: bulk

value: no treatment


title: MOLM14_DMSO_2


title: mouse_B6129SF2J_HFPO_DA_12_0.1_uM_5

first: Melissa


title: mouse_B6129SF2J_HFPO_DA_12_0.1_uM_4


title: SYO1 cells, C10 (SW43) 10µM, 2h, biol rep 3

city: St Louis

first: Rony

last: Takchi

address: 660 South Euclid Avenue

department: Surgery

institute: Washington University St Louis

description: SW43 10uM 3

data_processing:
Base calls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
mRNA expression was analyzed using Partek Flow software.
Adapters were removed, and reads were aligned to the hg38 assembly with STAR and quantified to hg38-Ensembl transcripts release 105.
Reads were normalized to total counts per million. Features containing fewer than 10 reads were not included in the analysis.
Assembly: Homo sapiens (human) - hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: SYO1 synovial sarcoma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Bulk RNA sequencing (RNAseq) was performed by the Genome Technology Access Center at the Washington University School of Medicine in St. Louis. Total RNA was isolated using TRIzol.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: After plating in SYO1 cells overnight (24h) in a 6-well plate, cells were treated for 2 hours in triplicates with either DMSO as negative control, C0 (SV95) 10µM, C6 (SV119) 10µM, or C10 (SW43) 10µM.

value: biphasic synovial sarcoma

value: WT

value: C10 (SW43) 10microM

value: 2 hours


title: SYO1 cells, C10 (SW43) 10µM, 2h, biol rep 2

description: SW43 10uM 2


title: SEP3Δtet3M-AG


title: H3K36me3_heart_E16_EC_cell_19

first: Yaxi


title: H3K36me3_heart_E16_EC_cell_18


title: mouse_B6129SF2J_GW7647_12_0.01_uM_8


title: SYO1 cells, C10 (SW43) 10µM, 2h, biol rep 1

description: SW43 10uM 1


title: SYO1 cells, C6 (SV119) 10µM, 2h, biol rep 3

description: SV119 10uM 3

value: C6 (SV119) 10microM


title: H3K36me3_heart_E16_EC_cell_16


title: ΔvanS, TY+ramoplanin, replicate 2

first: Boris

middle: R

last: Belitsky

address: 136 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University School of Medicine

data_processing:
Burrows-Wheeler short-read aligner
Custom scripts
DESeq2
Assembly: GCF_000009205.2_ASM920v2
Supplementary files format and content: tab-delimited text file includes FPKM values for all samples

organism: Clostridioides difficile 630

source_name: Clostridioides difficile 630∆erm

growth_protocol: Complex TY medium, exponential growth

extract_protocol:
Cell quenching with 1:1 (vol/vol) solution of ethanol/acetone. RNA isolation using the Direct-zol RNA MiniPrep Plus kit.
Shishkin, A. A., G. Giannoukos, A. Kucukural, D. Ciulla, M. Busby, C. Surka, J. Chen, R. P. Bhattacharyya, R. F. Rudy, M. M. Patel, N. Novod, D. T. Hung, A. Gnirke, M. Garber, M. Guttman and J. Livny (2015). "Simultaneous generation of many RNA-seq libraries in a single reaction." Nat. Methods 12: 323-325.

value: bacterial cell

value: deleted vanS

value: ramoplanin, 0.0625 ug/ml


title: mouse_B6129SF2J_GW7647_12_10_uM_3

source_name: primary hepatocytes

value: primary hepatocytes


title: mouse_B6129SF2J_GW7647_12_10_uM_2


title: mouse_B6129SF2J_GW7647_12_10_uM_1


title: ΔvanS, TY+vancomycin, replicate 2

value: vancomycin, 1.8 ug/ml


title: SYO1 cells, C6 (SV119) 10µM, 2h, biol rep 2

description: SV119 10uM 2


title: ΔvanS, TY+vancomycin, replicate 1


title: H3K36me3_heart_E16_EC_cell_17

source_name: E16.5 heart

value: heart


title: ATAC_UN_6

city: Geneve

first: Alan Yue Yang

last: Teo

address: Chem. des Mines 9, Campus Biotech

department: SV

country: Switzerland

institute: EPFL

description: 10x v3

data_processing:
Reads were aligned using Cellranger arc v.1.0.1. For snRNA-seq, the final data matrix is generated as per Cellranger arc pipeline. For snATAC-seq, both gene-level and peak matrices are generated following Snapatac pipeline. The gene-level features are generated based on GENCODE vM10 and the peak features are derived using MACS2.
Data were analyzed using Seurat v3
Assembly: mm10-1.2.0 (GRCm38.101)
Supplementary files format and content: tab-delimited text files include UMI values for each cell with tab delimeters

source_name: Mid thoracic spinal cord

extract_protocol:
Single-nucleus dissociation of the mouse lumbar spinal cord was performed according to our established procedures. Following euthanasia by isoflurane inhalation and cervical dislocation, the spinal cord injury site was immediately dissected and frozen on dry ice. Spinal cords were doused in 500 µL sucrose buffer (0.32 M sucrose, 10 mM HEPES [pH 8.0], 5 mM CaCl2, 3 mM Mg acetate, 0.1 mM EDTA, 1 mM DTT) and 0.1% Triton X-100 with the Kontes Dounce Tissue Grinder. 2 mL of sucrose buffer was then added and filtered through a 40 µm cell strainer. The lysate was centrifuged at 3200 g for 10 min at 4°C. The supernatant was then decanted, and 3 mL of sucrose buffer was added to the pellet for 1 min. We homogenized the pellet using an Ultra-Turrax and 12.5 mL of density buffer (1 M sucrose, 10 mM HEPES [pH 8.0], 3 mM Mg acetate, 1 mM DTT) was added below the nuclei layer. The tube was centrifuged at 3200 g at 4°C and supernatant poured off. Nuclei on the bottom half of the tube wall were collected with 100 µL PBS with 0.04% BSA and 0.2 U/µL RNase inhibitor. Finally, nuclei were resuspended through a 30 µm strainer, and adjusted to 1000 nuclei/µL. snRNA-seq library preparation was carried out using the 10x Genomics Chromium Multiome ATAC + Gene Expression Kit Version 3. The nuclei suspension was added to the Chromium RT mix to achieve loading numbers of 10,000 nuclei. For downstream cDNA synthesis (13 PCR cycles), library preparation and sequencing, the manufacturer’s instructions were followed.
We used 10x Chromium Single Cell Multiome ATAC + Gene Expression kit to profile the mid thoracic spinal cord of mice.

value: spinal cord

tag: condition

value: uninjured

value: wild type


title: SYO1 cells, C6 (SV119) 10µM, 2h, biol rep 1

description: SV119 10uM 1


title: ΔvanS, TY, replicate 2

value: untreated


title: SYO1 cells, C0 (SV95) 10µM, 2h, biol rep 3

description: SV95 10uM 3

value: C0 (SV95) 10microM


title: ΔvanS, TY, replicate 1


title: ATAC_UN_20

description: 10x v3

tag: strain


title: H3K36me3_heart_E16_EC_cell_13

value: Fixed by methanol

value: H3K36me3, Active motif, Cat. 61101


title: ΔvanS, TY+ramoplanin, replicate 1

tag: cell type


title: SYO1 cells, C0 (SV95) 10µM, 2h, biol rep 2

description: SV95 10uM 2

value: biphasic synovial sarcoma

value: WT


title: ATAC_UN_1

description: 10x v3


title: wt, TY+ramoplanin, replicate 1

value: wild-type


title: H3K36me3_heart_E16_EC_cell_11


title: H3K36me3_heart_E16_EC_cell_12


title: SYO1 cells, C0 (SV95) 10µM, 2h, biol rep 1

description: SV95 10uM 1

value: 2 hours


title: wt, TY+ramoplanin, replicate 2

value: bacterial cell


title: ATAC_D7_1

description: 10x v3

value: 7 days post SCI


title: H3K36me3_heart_E16_EC_cell_15


title: SYO1 cells, control, 2h, biol rep 3

description: Control 3

value: DMSO


title: ATAC_D7_17

description: 10x v3


title: wt, TY+vancomycin, replicate 2


title: H3K36me3_heart_E16_EC_cell_9


title: ATAC_2M_2

description: 10x v3

value: 2 months post SCI


title: wt, TY+vancomycin, replicate 3

value: vancomycin, 1.8 ug/ml


title: ATAC_2M_7

description: 10x v3


title: SYO1 cells, control, 2h, biol rep 2

description: Control 2


title: H3K36me3_heart_E16_EC_cell_10

value: heart


title: SYO1 cells, control, 2h, biol rep 1

description: Control 1


title: wt, TY+vancomycin, replicate 1


title: H3K36me3_heart_E16_EC_cell_14


title: H3K36me3_heart_E16_EC_cell_8


title: ATAC_2M_18

description: 10x v3

value: spinal cord


title: wt, TY, replicate 3

description: reanalysis of GSM6513440


title: wt, TY, replicate 2

description: reanalysis of GSM6513439


title: osteoarthritis (OA8),mRNAseq

city: Busan

first: Jaewan

last: Jeon

address: 875, Haeun-daero, Haeundae-gu, Busan, Republic of Korea

institute: Jaewan Jeon

data_processing:
raw reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39.
Trimmed sequence reads were mapped to GRCh38 using Star aligner v2.7.9a.
The transcript assembly was reconstructed with StringTie v2.2.1 and then FPKM values were calculated based on the read counts.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read count values, FPKM, and TPM for each Sample

source_name: synovial tissue

extract_protocol:
RNA was extracted using QIAzol® Lysis Reagent (Cat. No. 79306), RNeasy® Mini Kit (Cat. No. 74106), Tungsten Carbide Beads  (Cat. No. 69997). Only high-quality RNA preparations, with RIN greater than 7.0, were used for RNA library construction.
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101).

value: synovial tissue

tag: subject status

value: osteoarthritis patient

value: osteoarthritis


title: H3K36me3_heart_E16_EC_cell_7


title: RNA_UN_6

description: 10x v3

value: uninjured

value: wild type


title: H3K36me3_heart_E16_EC_cell_6

value: Fixed by methanol

value: H3K36me3, Active motif, Cat. 61101


title: RNA_UN_20

description: 10x v3


title: osteoarthritis (OA6),mRNAseq


title: wt, TY, replicate 1

description: reanalysis of GSM6513438

value: untreated


title: KO T1D - A3676

city: Saint Louis

first: Erica

middle: L

last: Scheller

address: 660 S Euclid Ave

institute: Washington University

data_processing:
The DNBSEQ platform was used to perform paired-end 100 bp sequence reads, generating an average of 4.56G Gb per sample.
Sequencing data was filtered using SOAPnuke, a filtering algorithm that removes reads containing the adaptor, reads with N content >5%, and reads with base quality score <15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads.
After filtering, HISAT and Bowtie2 were used to align clean reads to the Mus musculus reference genome version GCF_000001635.26_GRCm38.p6 with an average mapping ratio of 97.7% and 80.2%, respectively --> read counts.
Read counts were normalized per sample to generate TPM values
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes normalized TPM counts for each Sample

source_name: Bone

extract_protocol:
For extraction of bone RNA samples, tibia and femur from one hind limb were cleaned with gauze to remove soft tissue, epiphyses were removed to expose the marrow cavity, and bones were placed into a 0.5 mL tube with an 18-gauge needle hole in the bottom nested in a 1.5 mL tube. Marrow was separated by centrifugation at 1000*g for 1 min. The marrow-depleted bone was placed into a RINO 1.5 mL Screw Cap tube (MidSci) with stainless steel beads and 1 mL TRIzol. Bones were snipped with dissection scissors into fragments before bullet homogenization for 5 min. Samples in TRIzol were further incubated at RT for 5 min for complete digestion before extraction with chloroform and PureLink RNA Mini Kit (Invitrogen 12183025) according to manufacturer instructions. RNA was eluted in 30 µL RNase free water and stored at -80 ˚C until use.
Approximately 1 µg of RNA was submitted for RNAseq by BGI Tech Global where polyA mRNA was enriched by oligo dT, fragmented, and reverse transcribed using random N6-primed RT followed by second-strand cDNA synthesis with dUTP. The synthesized cDNA underwent end-repair and 3’ adenylation, prior to adaptor ligation to the ends of the fragments. The dUTP-marked strand was selectively degraded by Uracil-DNA-Glycolase and the remaining strand was PCR-amplified to generate a cDNA library suitable for sequencing on a DNBSEQ platform.

treatment_protocol: To induce type 1 diabetes (T1D), WT and Sarm1-KO mice were fasted overnight prior to i.p. injection with 100 mg/kg streptozotocin (STZ, Sigma S0130) made fresh in saline and used within 5-minutes of reconstitution. Food was returned to the cage one hour after STZ injection. Control mice received saline only. Fasting, injection, and re-feeding was repeated on Day 2. Blood glucose was measured on Day 3 with a standard glucometer by using a lancet to obtain a drop of blood from the vein at the tip of the tail (Bayer Contour). STZ was administered again on Day 4 following the same procedure if fed blood glucose levels did not reach 300 mg/dL.

value: Bone

tag: Sex

value: Female

tag: age

tag: duration of_disease


title: RNA_UN_1

description: 10x v3


title: H3K36me3_heart_E16_EC_cell_5

tag: developmental stage


title: H3K36me3_heart_E16_EC_cell_4

tag: tissue


title: osteoarthritis (OA5),mRNAseq


title: osteoarthritis (OA4),mRNAseq


title: RNA_D7_17

description: 10x v3


title: KO T1D - A3674


title: RNA_D7_1

description: 10x v3


title: RNA_2M_7

description: 10x v3


title: H3K36me3_heart_E16_EC_cell_3

tag: tissue preparation


title: KO T1D - A3683


title: KO T1D - A3675


title: osteoarthritis (OA2),mRNAseq


title: H3K36me3_heart_E16_EC_cell_2


title: RNA_2M_2

description: 10x v3


title: osteoarthritis (OA3),mRNAseq


title: H3K36me3_heart_E16_EC_cell_1


title: osteoarthritis (OA7),mRNAseq


title: KO T1D - A3682


title: Ctrl7 ,mRNAseq

value: patients requiring surgery due to sports damage

value: control


title: ChIP-seq Input rep2

city: Neuherberg

first: Boyan

last: Bonev

state: Deutschland

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

description:
Ngn2_chip_D2.bw
Ngn2_ChIP_peaks.bed.gz

data_processing:
Alignment of the raw reads to the mouse genome (mm10), post-alignment filtering and peak calling was performed by the ENCODE ChIP-seq pipeline. A high confidence reproducible peak set was generated by implementing a statistical procedure called irreproducible discovery rate (IDR) within the ENCODE ChIP-seq pipeline. Bigwig files were generated using Deeptools2 (version 3.1.3) with the following paramters: CPM normalization, bin size 10, MAPQ >=30
Processed data files represent Bigwig files for merged replicate Bigwig file and bed file with coordinates of high confidence peak set
Assembly: mm10

source_name: ChIP-seq primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus input rep4

extract_protocol:
The cortex of post-natal mice aged P5/6 was isolated, mechanically dissociated to obtain a single cell suspension and cultured in medium containing 10% FBS, glucose, pen/strep, B27 supplement, epidermal growth factor and fibroblast growth factor. After culturing for 7 days, the astrocyte enriched culture was reseded on to T-25 flasks and infected with a doxycycline-inducible lentiviral construct. The lentiviral constructs were induced by addition of doxycycline (2ug/ml) for 2 consecutive days in medium containing glucose, pen/strep, glutamine and B27 supplement. Approximately 4 million cells are harvested and cross-linked for 10 minutes at room temperature using 1% formaldehyde. The cross-linking reaction is quenched by the addition of 125mM glycine and the cells are incubated during the quencing reaction at room temperature for 5 minutes. The cross-linked cells are lysed and sonicated using a Bioruptor pico sonication device (settings: 20 cycles, 30 seconds ON/30 seconds OFF) to achieve a fragment size distribution ranging from 150-200bp. The fragment size distribution of the sonicated chromatin is quality controlled using an Agilent 2100 bioanalyser. The chromatin immunoprecipitation was performed by incubating the soniicated chromatin with anti-FLAG antibody (Sigma, F1804) over-night at 4 degree celcius. Thereafter, the antibody-protein-DNA complex was incubated with Dynabeads Protein G for 3 hours at 4 degrees. Following 5 wash steps with LiCL buffer and 1 wash step with TE buffer, the DNA-protein complexes were eluted. The eluate was de-crosslinked by incubation over-night at 65 degree celcius. The de-crossliked DNA was treated with RNase (37 degree celcius for 90 minutes) and Proteinase K (55 degree celcius for 120 minutes). The DNA was purified by UltraPure Phenol:Choloroform:Isoamylalcohol (25:24:1, v/v) (ThermoFisher Scientific) following manufacturer's instructions, followed by ethanol precipitation. The resulting DNA pellet was resuspended in low TE and quantified using Qubit dsDNA HS kit (Thermo Fisher Scientific) following manufacturer;s instructions)
The ChIP-seq library was prepared using the MicroPlex Library preparation kit v2 from Diagenode following manufacturer's instructions

value: Brain

value: primary mouse cortical astrocytes

value: R26-M2rtTA (homozygous)

value: Doxycycline (2 microg/ml) was freshly added to the differentiation medium every 24 hours


title: osteoarthritis (OA1),mRNAseq


title: lineage negative HI d7-1 to 4

city: Pittsburgh

first: Partha

last: Dutta

state: PA

address: 200 Lothrop Street

department: Medicine

institute: University of Pittsburgh

description: Bone marrow HSPC were sorted

data_processing:
Partek Flow (version 10.0.22.1204) software was used to analyze the single cell RNA seq data using the count matrix generated after the sequencing of the libraries.
The cells were filtered using these criteria: 12,000 read counts, 2,500 detected features, 8% mitochondrial reads, and 50% ribosomal counts.
The total UMI counts were normalized using Partek-recommended normalization method with CPM (counts per million) with Log2 transformation.
After the normalization, we filtered the data further by excluding the features where the gene expression values were <=1 in at least 99% of cells.
The graph based clustering analysis was performed by employing Louvain algorithm. To visualize the single cell data, we performed a t-distributed statistical neighbor embedding (tSNE) dimensional reduction and generated the plots.
Assembly: mm10
Supplementary files format and content: The files include the count matrices.

source_name: Bone marrow

extract_protocol:
We used pico pure RNA extraction kit (Applied Biosystems) to extract RNA from sorted cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: HSPC

value: HI


title: Ctrl6 ,mRNAseq

value: synovial tissue


title: KO Control - A3766

value: Control


title: KO T1D - A3681


title: KO Control - A3673


title: RNA_2M_18

description: 10x v3

value: spinal cord

value: 2 months post SCI

value: wild type


title: lineage negative HI d2-1 to 4

description: Bone marrow HSPC were sorted


title: Ctrl5 ,mRNAseq


title: ChIP-seq Ngn2 rep3

description:
Ngn2_chip_D2.bw
Ngn2_ChIP_peaks.bed.gz

source_name: ChIP-seq primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus rep3


title: lineage negative Sham-1 to 3

description: Bone marrow HSPC were sorted

value: Sham


title: KO Control - A3672

value: Bone


title: ChIP-seq Input rep1

description:
Ngn2_chip_D2.bw
Ngn2_ChIP_peaks.bed.gz

source_name: ChIP-seq primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus input rep3


title: KO Control - A3680

value: Female


title: Ctrl3 ,mRNAseq

value: patients requiring surgery due to sports damage


title: lineage positive HI d7-1 to 4

description: Bone marrow leukocytes were sorted

value: leukocytes


title: ChIP-seq Ngn2 rep1

description:
Ngn2_chip_D2.bw
Ngn2_ChIP_peaks.bed.gz

source_name: ChIP-seq primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus rep1

value: Brain


title: lineage positive HI d2-1 to 4

description: Bone marrow leukocytes were sorted


title: ChIP-seq Ngn2 rep2

description:
Ngn2_chip_D2.bw
Ngn2_ChIP_peaks.bed.gz

source_name: ChIP-seq primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus rep2

value: primary mouse cortical astrocytes


title: Ctrl2 ,mRNAseq

value: control


title: ChIP-seq Input rep3

description:
Ngn2_chip_D2.bw
Ngn2_ChIP_peaks.bed.gz

source_name: ChIP-seq primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus input rep5

value: R26-M2rtTA (homozygous)

value: Doxycycline (2 microg/ml) was freshly added to the differentiation medium every 24 hours


title: Ctrl1 ,mRNAseq


title: KO Control - A3679


title: Bulk ATAC-seq PmutNgn2 rep3

description:
PmutNgn2_D2.bw
PmutNgn2_ATAC_peaks.bed.gz

data_processing:
Alignment of the raw reads to the mouse genome (mm10), post-alignment filtering and peak calling was performed by the ENCODE ATAC-seq pipeline. A high confidence reproducible peak set was generated by implementing a statistical procedure called irreproducible discovery rate (IDR) within the ENCODE ATAC-seq pipeline. Bigwig files were generated using Deeptools2 (version 3.1.3) with the following paramters: CPM normalization, bin size 10, MAPQ >=30
Processed data files represent Bigwig files for each replicate, merged replicate Bigwig file and bed file with coordinates of high confidence peak set
Assembly: mm10
Library strategy: OMNI ATAC-seq

source_name: Bulk ATAC-seq primary mouse astrocytes transduced with PmutNgn2 expressing doxycycline-inducible lentivirus rep3

extract_protocol:
The cortex of post-natal mice aged P5/6 was isolated, mechanically dissociated to obtain a single cell suspension and cultured in medium containing 10% FBS, glucose, pen/strep, B27 supplement, epidermal growth factor and fibroblast growth factor. After culturing for 7 days, the astrocyte enriched culture was reseded on to poly-D-lysine coated 6 well plates and infected with a doxycycline-inducible lentiviral construct. The lentiviral constructs were induced by addition of doxycycline (2ug/ml) for 2 consecutive days in medium containing glucose, pen/strep, glutamine and B27 supplement.  At 48 hours post-doxycycline induction, the transduced astrocytes were isolated with FACS  based on GFP expression
Directly after FACS isolation, the nuclei of 50,000 cells were transposed with a modified Tn5 transposase (Illumina Tagment DNA TDE1 Enzyme and Buffer kit, 20034198) according to the OMNI-ATAC-seq protocol (Corces et al., 2017), the trasposed DNA was isolated using the DNA clean and concentrator kit from Zymo Research (D4014) and the ATAC-seql ibraries were prepared using NEBNext Ultra II  Q5 Master mix  from NEB (M0544S) according to manufacturer's instructions. The size distribution of the ATAC-seq libraries was analysed using an Agilent 2100 Bioanalyser


title: lineage positive Sham-1 to 4

description: Bone marrow leukocytes were sorted

value: Bone marrow


title: ps+1d_PHHdonor2

city: Utrecht

first: Delilah

last: Hendriks

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
Quality control on the sequence reads from the raw FASTQ files was done with FastQC.
TrimGalore was used to trim reads based on quality and adapter presence after which FastQC was again used to check the resulting quality.
rRNA reads were filtered out using SortMeRNA after which the resulting reads were aligned to the reference genome fasta (genome.fa) using the STAR aligner.
Followup QC on the mapped (bam) files was done using Sambamba, RSeQC and PreSeq.
Read counts were then generated using the Subread FeatureCounts module with the Homo_sapiens.GRCh37.74.gtf file as annotation
Assembly: Genome Reference Consortium Human Build 37
Supplementary files format and content: CSV files containing DESeq2 normalized transcript counts

source_name: primary human hepatocytes

extract_protocol:
total RNA was isolated using TRIzol Reagent (Thermo Fisher)
RNA libraries were prepared using TruSeq Stranded mRNA polyA kit (Illumina)

value: primary human hepatocytes


title: WT T1D - A3909

value: WT


title: 7d_PHHdonor2


title: Bulk ATAC-seq PmutNgn2 rep1

source_name: Bulk ATAC-seq primary mouse astrocytes transduced with PmutNgn2 expressing doxycycline-inducible lentivirus rep1


title: SC912 - 4

city: Montreal

first: Jian Hui

last: Wu

state: Quebec

address: 3755 Cote-Saint-Catherine

country: Canada

institute: Jewish General Hospital, McGill University

description: treated with 2 μM SC912 for 24 hours

data_processing:
The data quality was assessed using FastQC v.0.11.5, before and after trimming.
The raw trimmed reads are aligned to the GRCh38.13 genome using the STAR sligner, v.2.6.0c.
Exploratory analysis was performed using R v.3.6.1.
The filtered STAR alignments are processed to extract raw read counts for genes using htseq-count v.0.6.1p2
Differential gene expression analysis was performed with DESeq2, and gene expression was quantified as FPKM
Assembly: GRCh38.13
Supplementary files format and content: HTseq text file contains raw counts for each sample

source_name: prosate

growth_protocol: LNCaP-95 cells were cultured in phenol red-free RMPI-1640 media supplemented with 10% charcoal-stripped serum, 2 mM L-glutamine, and antibiotics.

extract_protocol:
RNA extraction was perfomed using RNA queous TM total RNA Isolation Kit (Applied Biosystems).
RNA-seq libraries were prepared from total RNA using stranded poly (A) mRNA library preparation (NEBNext).

treatment_protocol: LNCaP-95 cells were treated with DMSO or 2 μM SC912 for 24 hours.

value: prosate

value: prostate carcinoma cell


title: SC912 - 3

description: treated with 2 μM SC912 for 24 hours


title: WT T1D - A3906


title: Ctrl4 ,mRNAseq

value: synovial tissue


title: KO Control - A3670

value: Control


title: 48h_PHHdonor2

value: wild type


title: 24h_PHHdonor2


title: Bulk ATAC-seq Ngn2 rep2

description:
Ngn2_D2.bw
Ngn2_ATAC_peaks.bed.gz

source_name: Bulk ATAC-seq primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus rep2


title: SC912 - 2

description: treated with 2 μM SC912 for 24 hours


title: WT T1D - A3905

value: Bone


title: Bulk ATAC-seq Ngn2 rep3

description:
Ngn2_D2.bw
Ngn2_ATAC_peaks.bed.gz

source_name: Bulk ATAC-seq primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus rep3


title: WT T1D - A1787

value: Female


title: SC912 - 1

description: treated with 2 μM SC912 for 24 hours


title: WT T1D - A1758


title: 14h_PHHdonor2


title: cells_PHHdonor2


title: Bulk ATAC-seq PmutNgn2 rep2

source_name: Bulk ATAC-seq primary mouse astrocytes transduced with PmutNgn2 expressing doxycycline-inducible lentivirus rep2


title: Bulk ATAC-seq GFP rep3

description:
GFP_D2.bw
GFP_ATAC_peaks.bed.gz

source_name: Bulk ATAC-seq primary mouse astrocytes transduced with GFP expressing doxycycline-inducible lentivirus rep3


title: DMSO - 4

description: treated with DMSO for 24 hours

value: DMSO


title: WT T1D - A1764


title: Bulk ATAC-seq GFP rep2

description:
GFP_D2.bw
GFP_ATAC_peaks.bed.gz

source_name: Bulk ATAC-seq primary mouse astrocytes transduced with GFP expressing doxycycline-inducible lentivirus rep2


title: DMSO - 2

description: treated with DMSO for 24 hours


title: Bulk ATAC-seq Ngn2 rep1

description:
Ngn2_D2.bw
Ngn2_ATAC_peaks.bed.gz

source_name: Bulk ATAC-seq primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus rep1


title: ps+1d_PHHdonor1


title: 7d_PHHdonor1


title: DMSO - 3

description: treated with DMSO for 24 hours


title: WT Control - A3904

source_name: Bone


title: 48h_PHHdonor1


title: Bulk RNA-seq PmutNgn2 rep3

data_processing:
Raw reads were aligned to the mouse genome (mm10) using STAR (version 2.7.1a) and number of counts per gene was performed using the following parameter: --quantMode GeneCounts
Processed data file represents a tab-delimited text file with read counts per gene performed using STAR (version2.7.1a) in --quantMode GeneCounts
Assembly: mm10

source_name: Bulk RNA-seq primary mouse astrocytes transduced with PmutNgn2 expressing doxycycline-inducible lentivirus rep3

extract_protocol:
The cortex of post-natal mice aged P5/6 was isolated, mechanically dissociated to obtain a single cell suspension and cultured in medium containing 10% FBS, glucose, pen/strep, B27 supplement, epidermal growth factor and fibroblast growth factor. After culturing for 7 days, the astrocyte enriched culture was reseded on to poly-D-lysine coated 6 well plates and infected with a doxycycline-inducible lentiviral construct. The lentiviral constructs were induced by addition of doxycycline (2ug/ml) for 2 consecutive days in medium containing glucose, pen/strep, glutamine and B27 supplement.  At 48 hours post-doxycycline induction, the transduced astrocytes were isolated with FACS  based on GFP expression
Directly after FACS isolation, cell were resuspended in TRIzol, the RNA was extracted using RNA Clean and Concemtrator kit from Zymo Research (cat No. R1013) and the RNA-seq libraries were prepared using NEBNext Ultra II FS DNA library Prep kit from Illumina (#E7805S) according to manufacturer's instructions


title: WT Control - A3903


title: Bulk RNA-seq PmutNgn2 rep2

source_name: Bulk RNA-seq primary mouse astrocytes transduced with PmutNgn2 expressing doxycycline-inducible lentivirus rep2


title: 24h_PHHdonor1


title: WT Control - A3767


title: 14h_PHHdonor1


title: Bulk RNA-seq PmutNgn2 rep1

source_name: Bulk RNA-seq primary mouse astrocytes transduced with PmutNgn2 expressing doxycycline-inducible lentivirus rep1


title: WT Control - A3907


title: Bulk RNA-seq Ngn2 rep3

source_name: Bulk RNA-seq primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus rep3


title: cells_PHHdonor1


title: sc_72h_FHdonor3


title: sc_48h_FHdonor3


title: Bulk RNA-seq Ngn2 rep1

source_name: Bulk RNA-seq primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus rep1


title: Bulk RNA-seq GFP rep3

source_name: Bulk RNA-seq primary mouse astrocytes transduced with GFP expressing doxycycline-inducible lentivirus rep3


title: sc_24h_FHdonor3


title: Bulk RNA-seq Ngn2 rep2

source_name: Bulk RNA-seq primary mouse astrocytes transduced with Ngn2 expressing doxycycline-inducible lentivirus rep2


title: Bulk ATAC-seq GFP rep1

description:
GFP_D2.bw
GFP_ATAC_peaks.bed.gz

source_name: Bulk ATAC-seq primary mouse astrocytes transduced with GFP expressing doxycycline-inducible lentivirus rep1


title: sc_14h_FHdonor3


title: Bulk RNA-seq GFP rep2

source_name: Bulk RNA-seq primary mouse astrocytes transduced with GFP expressing doxycycline-inducible lentivirus rep2


title: DMSO - 1

description: treated with DMSO for 24 hours

source_name: prosate


title: sc_0h_FHdonor3


title: Bulk RNA-seq GFP rep1

source_name: Bulk RNA-seq primary mouse astrocytes transduced with GFP expressing doxycycline-inducible lentivirus rep1


title: J2 Eluate3

city: Göttingen

first: Heike

last: Krebber

address: Grisebachstraße 8

department: Molecular Genetics

institute: Georg-August Universität Göttingen

data_processing:
Sequences were aligned to the genome reference sequence of Saccharomyces cerevisiae (sacCer3, obtained from UCSC, https://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/bigZips/) using the STAR software (48; version 2.5) allowing for 2 mismatches.
Subsequently, abundance measurement of reads overlapping with exons or introns was conducted with featureCounts (subread version 1.5.0-p1, Ensembl (EF4.68) supplemented with the coordinates of UTRs, CUTs and SUTs and Xrn1-sensitive unstable transcripts.
Data was processed in the R/Bioconductor environment (www.bioconductor.org, R version 3.6.1) using the DESeq2 package (version 1.24.0).
Assembly: Ensembl (EF4.68)
Supplementary files format and content: Tab delimated text file
Supplementary files format and content: List of transcripts with their log2foldchange and normalized counts for each sample

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Growth at 25°C until 1*10^7 cells/ml

extract_protocol:
RNA was extracted using Trizol
"TruSeq RNA Sample Prep Kit v2" according to the manufacturer's protocol

treatment_protocol: no further treatment

value: yeast

value: Wild type S288C


title: J2 Eluate2


title: sc_48h_FHdonor1


title: Tax-CTL,  long PR2909_07_a

city: Saitama

first: Hideki

last: Nakasone

address: 1-847, Amanuma-cho, Omiya-ku

department: Hematology

country: Japan

institute: Jichi Medical University Saitama Medical Center

description:
Tax-CTL,  long
250cells

data_processing:
NovaSeq Control Software 1.7.5
Real Time Analysis (RTA) 3.4.4
bcl2fastq2 2.20
DRAGEN Bio-IT Platform 3.7.5
Assembly: GRCh38.primary_assembly.genome.fa.gz
Assembly: gencode.v39.primary_assembly.annotation.gtf.gz
Assembly: GENCODE
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: peripheral blood

extract_protocol:
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio, Inc.)  with modified direct lysis protocol
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio, Inc.)  with modified thermal cylces, and standarad Illumina kit

value: peripheral blood

value: sorted CTL

tag: disease type

value: HTLV-1 carrier

tag: clinical outcomes

value: long-term survivor


title: WT Control - A1757

tag: genotype


title: J2 Elaute1


title: HAOEC M(Hb) 4

type: RNA

city: Gaithersburg

first: Atsushi

last: Sakamoto

address: 19 Firstfield Road

institute: CVPath Institute

hyb_protocol: All reactions and hybridizations were carried out according to the manufacturer's protocol (Affymetrix; Thermo Fisher Scientific). Affymetrix GeneChip Human Clariom S array (Thermo Fisher Scientific) were washed using the GeneChipTM Fluidics Station 450 (Thermo Fischer Scientific).

scan_protocol: Affymetrix GeneChip Human Clariom S arrays were scanned with the GeneChip Scanner 7000 (Thermo Fisher Scientific).

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) 4.0 software (Thermo Fischer Scientific) using default analysis setting. GO enrichment analysis of unbiased differentially expressed genes (DEGs) were conducted by Metascape online bioinformatics resources.

label: biotin

source_name: HAOEC, M(Hb), 6h.

label_protocol: GeneChipTM WT Plus Reagent Kit were used for generating biotinylated ss-cDNA for hybridization.

growth_protocol: HAOEC (Cell applications) were cultured using MesoEndo Cell Growth medium (Cell applications) in humidified air (5% of CO2) at 37 °C.

extract_protocol: Total RNA was extracted using Rneasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Human Peripheral blood mononuclear cells (PBMC) collected from healthy volunteers (Astarte Biologics) were seeded into culture plates (3-4 x 106 cell/well). After 6 hours incubation, non-attached cells were removed, and culture media was replaced. Remaining monocyte/macrophage fraction were differentiated over 6 days into macrophages with RPMI 1640 medium supplemented with 10% human serum and penicillin-streptomycin in humidified air (5% of CO2) at 37 °C. Prior to use, human hemoglobin and haptoglobin were reconstituted in RPMI 1640 medium, which were added to cultured monocytes at 6 hours after plating (hemoglobin:haptoglobin complexes [HH], final concentration of 0.1 mg/ml,). After differentiation of human monocytes over 6-days with or without HH, supernatant from control macrophages [M(con)] and HH-differentiated [M(Hb)] macrophages were used in further experiments. HAOECs were cultivated for 6 hours in M(con) or M(Hb) macrophage supernatant.

tag: agent

value: M(Hb) supernatant

tag: time pont

value: 6 hours

value: HAOEC


title: sc_24h_FHdonor1

tag: treatment


title: Tax-CTL,  long PR2909_06_a

description:
Tax-CTL,  long
401cells

value: chronic ATL


title: J2 Unbound3


title: sc_14h_FHdonor1


title: HAOEC M(Hb) 3


title: HAOEC M(con) 3

source_name: HAOEC, M(con), 6h.

value: M(con) supernatant


title: HAOEC M(Hb) 2


title: HAOEC M(con) 2


title: Tax-CTL,  early death PR2909_05_a

description:
Tax-CTL,  early death
250cells

value: smoldering ATL

value: early death


title: J2 Unbound2


title: sc_0h_FHdonor1

value: wild type


title: HAOEC M(Hb) 1


title: Tax-CTL,  early death PR2909_04_a

description:
Tax-CTL,  early death
500cells

value: acute ATL


title: J2 Unbound1


title: sc_72h_FHdonor1


title: ps+1d_FHdonor2

source_name: human fetal liver tissue

value: human fetal liver tissue


title: HAOEC M(con) 1


title: Tax-CTL,  early death PR2909_03_a

description:
Tax-CTL,  early death
500cells