title: PAO1161 EV_1_control_for_PA3458_RNA-seq

status: Public on Apr 12 2021

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

description:
gene expression data from empty vector control
PAO1161 EV_1

data_processing:
Sequencing data were quality-checked and filtered using FASTP version 0.20.0.
Reads were mapped to P. aeruginosa PAO11161 genome (CP032126) using Bowtie2 version 2.3.4.3 using default settings.
The number of reads mapping to individual genes was counted using FeatureCounts v 2.0.1 (with the -s2 option).
Differential expression analysis was conducted using edgeR ver 3.28.0.
Genome_build: CP032126
Supplementary_files_format_and_content: Raw counts of sequencing (FeatureCounts output summarized for all samples).
A table with DE data for all genes and normalized abundance measurements (EdgeR output).

organism: Pseudomonas aeruginosa

source_name: empty vector control (EV)

growth_protocol: The competent P. aeruginosa PAO1161 cells were prepared as described previously (Irani and Rowe, 1997) and transformed using pKKB2.11 carrying araC araBADp-PA3458 or empty vector (araC araBADp) to obtain PAO1161/ pKKB2.11 (araC araBADp-PA3458 ) and PAO1161/ pKGB8 (araC araBADp), respectively. Transformants were selected on L agar plates supplemented with 150 μg/ml chloramphenicol and were verified by isolation of plasmid DNA and its digestion. Bacteria from single colonies were used to inoculate L broth (DifcoTM L Broth, Lennox, BD) liquid cultures with supplementation (75 µg/ml chloramphenicol) and grown overnight with shaking at 37oC. Three independent overnight cultures for each strain were diluted 1:100 into fresh L broth with chloramphenicol (75 mg/ml) and 0.02% arabinose and grown with shaking at 37oC. Samples from the cultures were taken at regular intervals to measure the optical density at 600 nm (OD600). Aliquots of 2 ml from logarithmic phase cultures (OD600 = 0.5) were subjected to RNA extraction.

extract_protocol:
Total RNA was isolated from three independent replicates of each strain. 2 ml of cultures which reached optical density 0.4-0.6 at 600 nm were mixed with 4 ml of RNAprotect Bacteria Reagent (Qiagen). RNA was isolated with an RNeasy mini-kit (Qiagen) according to the manufacturer’s protocol. Total RNA was digested with DNase (TURBO DNA-free Kit, Ambion) to eliminate genomic DNA.
rRNA was depleted using Ribo-Zero rRNA Removal Kit (Bacteria) (MRZMB126,Illumina) according to manufacturer instructions. Libraries were prepared according to instructions accompanying the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, E7370S).

treatment_protocol: All cultures were incubated at 37oC in L broth (DifcoTM L Broth, Lennox, BD) supplemented with 75 μg/mL chloramphenicol and 0.02% arabinose with shaking until reaching exponential phase of growth (OD600 = 0.5).

value: PAO1161/pKGB8 (araC araBADp)

value: empty vector control (EV)

tag: growth phase

value: logarithmic phase of liquid culture


title: Smart-seq2: Macrophages3

status: Public on May 04 2021

type: SRA

city: Chicago

first: Hoang Van

last: Phan

state: Illinois

address: 5640 S Ellis Ave

department: Priztker School of Molecular Engineering

country: USA

institute: The University of Chicago

description: Prox-seq using Smart-seq2 pipeline

library_source: genomic

data_processing:
Sequencing data was aligned using a custom Java program to identify the Prox-seq probe barcodes.
Count data was analyzed in Python and RStudio. Cells with fewer total UMI count lower than 10 were discarded.
Protein data caclulated from PLA count data was used to cluster the cells in Seurat v3.
Supplementary_files_format_and_content: The file Smart-seq2_rawfiles_and_SRR_IDs.txt.gz is available on the series record and contains the raw file name and associated SRR for each single cell.

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral macrophages

growth_protocol: PBMCs and macrophages are kept in RPMI media with 10% FBS

extract_protocol:
PLA products were extracted from single cells following plate-based Smart-Seq2 pipeline
Sequencing library was prepared from PLA products using PCR

treatment_protocol: Macrophages are treated with LPS or PAM2CSK4 or both for 5 minutes, 2 hours or 12 hours

tag: cell type

value: Primary human macrophages

tag: donor type

value: Healthy donor

tag: treatment

value: LPS 2 hours


title: PAO1161 EV_3_control_for_PA3458_RNA-seq

description:
gene expression data from empty vector control
PAO1161 EV_3

library_source: transcriptomic

molecule: total RNA

tag: strain

tag: genotype


title: Smart-seq2: Macrophages9

description: Prox-seq using Smart-seq2 pipeline

value: LPS/PAM 2 hours


title: Smart-seq2: Macrophages6

description: Prox-seq using Smart-seq2 pipeline

value: PAM 2 hours


title: RATCB11diat

status: Public on Apr 09 2021

city: Montferrier-sur-Lez

first: Maxime

last: Galan

address: 755 avenue du campus Agropolis

country: France

institute: INRA

data_processing:
genome build: rn4
Demultiplexing was performed using bcl2fastq 2.17 (Illumina).
Alignment was performed with TopHat 2.0.13 (with Bowtie 2.2.3) to the rn4 version of the Rattus norvegicus genome. The transcript annotation was retrieved from UCSC on July 17, 2015.
Counting of reads aligned to a gene was performed with HTSeq-count 0.6.1p1.
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component.
Supplementary_files_format_and_content: Tab-separated text file. First column is the gene identifier (gene symbol), the following columns are the raw counts (non-normalized) for each sample.

organism: Rattus rattus

source_name: Spleen (pool of RNA)

extract_protocol:
All Prep 96 DNA/RNA (Qiagen)
RNA-Seq libraries were prepared with the 'TruSeq Stranded RNA sample preparation Kit' (Illumina) according to the manufacturer's instructions.

tag: nb. of males and females in the pool

value: males:5 - females:5

tag: locality

value: Diattacounda


title: Smart-seq2: Macrophages5

description: Prox-seq using Smart-seq2 pipeline

value: PAM 5 minutes


title: Smart-seq2: Macrophages1

description: Prox-seq using Smart-seq2 pipeline


title: Smart-seq2: PBMC

description: Prox-seq using Smart-seq2 pipeline

source_name: Peripheral blood mononuclear cells

value: Primary human white blood cells


title: Smart-seq2: Macrophages2

description: Prox-seq using Smart-seq2 pipeline

value: LPS 5 minutes


title: RATCB16tob

value: males:4 - females:4

value: Tobor


title: PAO1161 EV_2_control_for_PA3458_RNA-seq

description:
gene expression data from empty vector control
PAO1161 EV_2


title: RATCB15tob

value: males:3 - females:3


title: RATCB7sou

value: Soutouta


title: Lo1

data_processing:
genome build: mm10
Demultiplexing was performed using CASAVA 1.8.2 (Illumina).
Alignment was performed with TopHat 2.0.9 (with Bowtie 2.1.0) to the mm10 version of the Mus muculus genome. The transcript annotation was retrieved from UCSC on March 6, 2013.
Counting of reads aligned to a gene was performed with HTSeq-count 0.5.4p5.
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component.
Supplementary_files_format_and_content: Tab-separated text file. First column is the gene identifier (gene symbol), the following columns are the raw counts (non-normalized) for each sample.

organism: Mus musculus

value: Lougué


title: Ischemia Reperfusion Injury Model

status: Public on Jun 01 2021

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

data_processing:
Expression counts determined by spaceranger 1.0.0 and reference genomes GRCh38-3.0.0 and mm10-3.0.0
The remaining processing and normalization steps described on the paper were not performed on the provided processed data
Genome_build: Hg38 and mm10
Supplementary_files_format_and_content: position and counts on csv files, images on tiff files.
Supplementary_files_format_and_content: Human_Nephrectomy.tar.gz - Spots position, filtered counts matrix, and images for the Human Nephrectomy, as outputted from SpaceRanger.
Supplementary_files_format_and_content: Sham_Model.tar.gz - Spots position, filtered counts matrix, and images for the Sham murine model, as outputted from SpaceRanger.
Supplementary_files_format_and_content: IRI_Model.tar.gz - Spots position, filtered counts matrix, and images for the Ischemia Reperfusion Injury murine model, as outputted from SpaceRanger.
Supplementary_files_format_and_content: CLP_Model.tar.gz - Spots position, filtered counts matrix, and images for the Cecal Ligation Puncture murine model, as outputted from SpaceRanger.

source_name: Kidney

extract_protocol:
Human Kidney tissue was obtained from a deceased donor nephrectomy intended for transplant. It was frozen on OCT within 24 h. 10 um of tissue was cut on a cryotome and placed on a 10x Visium capture slide. RNA was extracted according to protocol.
Murine Kidney tissue was obtained from a mice upon sacrifice and immediately frozen on OCT. 10 um of cross-sectional tissue was cut on a cryotome and placed on a 10x Visium capture slide. RNA was extracted according to protocol.
CG000239_VisiumSpatialGeneExpression_UserGuide_RevD, 10X Genomics

tag: disease

value: Ischemia Reperfuion Injury

tag: tissue source

value: Nephrectomy

tag: storage

value: OCT at -80C

tag: gender

value: Male


title: RATCB13mar

value: Marsassoum


title: RATCB12diat


title: RATCB10diak

value: DiakeneWolof


title: Do2

value: Dodel


title: Lo2


title: RATCB9diak


title: RATCB8sou

value: males:5 - females:5


title: RATCB5ked

value: Kedougou


title: RATCB6ked


title: Ae2

value: Aere Lao


title: RATCB14mar


title: Ae1


title: Th1

value: Thilene


title: Do1


title: RATCB1bad

value: BadiNieriko


title: Da2

value: males:4 - females:4

value: Dagathie


title: Mb2

value: Mbakhana


title: Mb1


title: Th2


title: TEA-seq of leukapheresis-purified, 0.01% digitonin permeabilized, FACS neutrophil-depleted PBMCs, well 1

status: Public on Apr 02 2021

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
X061-AP0C1W1_leukopak_perm-cells_tea_fulldepth_adt_counts.csv.gz
X061-AP0C1W1_leukopak_perm-cells_tea_fulldepth_atac_filtered_fragments.tsv.gz
X061-AP0C1W1_leukopak_perm-cells_tea_fulldepth_atac_filtered_metadata.csv.gz
X061-AP0C1W1_leukopak_perm-cells_tea_fulldepth_atac_window_20k.h5
X061-AP0C1W1_leukopak_perm-cells_tea_fulldepth_cellranger-arc_filtered_feature_bc_matrix.h5
X061-AP0C1W1_leukopak_perm-cells_tea_fulldepth_cellranger-arc_per_barcode_metrics.csv.gz
X061-AP0C1W1_leukopak_perm-cells_tea_fulldepth_rna_counts.h5
X061-AP0C1W1
The FASTQs are from human subjects and will be provided via dbGAP
OTHER: TEA-seq

data_processing:
Demultiplexing of raw base call files into FASTQ files was performed using bcl2fastq2 (Illumina v2.20.0.422, parameters: --create-fastq-for-index-reads, --minimum-trimmed-read-length=8, --mask-short-adapter-reads=8, --ignore-missing-positions, -ignore-missing-filter, --ignore-missing-bcls, -r 24 -w 24 -p 80). The --use-bases-mask option was used to adjust the read lengths for each library type as follows: Y28n*,I10,I10n*,Y90n* for Gene Expression, Y50n*,I8n*,Y16,Y50n* for ATAC, and Y28n*,I8n*,n*,Y90n* for ADT.
For analysis of TEA-seq data alone, the full available sequencing depth from each library for each well was used for alignment. To perform comparisons between methodologies, all scRNA-seq and scATAC-seq libraries were downsampled to 200 million FASTQ entries (200M of each sequenced read; ~20,000 reads per expected cell recovered at ~10,000 cell expected recovery), and all ADT libraries were downsampled to 48M reads. RNA and ATAC libraries were aligned using cellranger-arc software (v1.0.0, 10x Genomics) against 10x genomics reference refdata-cellranger-arc-GRCh38-2020-A using default parameters. ADT barcode counting was performed using BarCounter.
genome_build: Ensembl GRCh38-3.0.0
processed_data_files_format_and_content: Fragment TSVs (Tab separated), Single cell CSVs (Commas separated), and HDF5 file (Hierarchical Data Format).

source_name: peripheral blood mononuclear cells

extract_protocol:
Biological specimens were purchased from BioIVT as cryopreserved PBMCs. All sample collections were conducted by BioIVT under IRB-approved protocols, and all donors sign informed consent forms. PBMCs sourced from BioIVT were isolated using leukapheresis. Following isolation, PBMCs were subjected to RBC lysis, washing, and counting. PBMC aliquots were cryopreserved in Cryostor CS10 (StemCell Technologies, 07930) and stored in vapor phase liquid nitrogen.
Cryopreserved PBMCs were thawed, stained for FACS, depleted of neutrophils, dead cells, and debris through FACS, stained with TotalSeq-A antibodies, and permeabilized using 0.01% digitonin. ATAC and Gene Expression libraries were prepared according to the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide (CG000338 Rev A) with several modifications. To generate a high-quality reference dataset, we generated four 10x Genomics wells of TEA-seq. For each well, transposition was performed by diluting 15,400 permeabilized cells to a final volume of 5 µl in isotonic Tagmentation Buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 3 mM MgCl2, RNase Inhibitor 1U/µl (Lucigen NxGen, F83923-1)). Cells were mixed with 10 µl of a transposition master mix consisting of 7 µl ATAC Buffer B (10x Genomics, 2000193) and 3 µl ATAC Enzyme B (Tn5 transposase; 10x Genomics, 2000265) per reaction. Transposition was performed by incubating the prepared reactions on a C1000 Touch thermal cycler with 96–Deep Well Reaction Module (Bio-Rad, 1851197) at 37°C for 60 minutes, followed by a brief hold at 4°C. A Chromium NextGEM Chip J (10x Genomics, 2000264) was placed in a Chromium Next GEM Secondary Holder (10x Genomics, 3000332) and 50% Glycerol (Teknova, G1798) was dispensed into all unused wells. A master mix composed of Barcoding Reagent Mix (10x Genomics, 2000267), Reducing Agent B (10x Genomics, 2000087), Template Switch Oligo (10x Genomics, 3000228), and Barcoding Enzyme Mix (10x Genomics, 2000266) was then added to each sample well, pipette-mixed, and loaded into row 1 of the chip. Chromium Single Cell Multiome Gel Beads v1.1 (10x Genomics, 2000261) were vortexed for 30 seconds and loaded into row 2 of the chip, along with Partitioning Oil (10x Genomics, 2000190) in row 3. A 10x Gasket (10x Genomics, 3000072) was placed over the chip and attached to the Secondary Holder. The chip was loaded into a Chromium Single Cell Controller instrument (10x Genomics, 120270) for GEM generation. At the completion of the run, GEMs were collected, and reverse transcription and barcoding were performed by incubating GEMs on a C1000 Touch thermal cycler with 96–Deep Well Reaction Module at 37°C for 45 min, 25°C for 30 min, followed by a brief hold at 4°C. Upon completion of the GEM incubation 5 µl of Quenching Agent (10x Genomics, 2000269) was immediately added and mixed with the reaction solution.   GEMs were separated into a biphasic mixture through addition of Recovery Agent (10x Genomics, 220016), the aqueous phase was retained and cleared of barcoding reagents using Dynabead MyOne SILANE (10x Genomics, 2000048) and 2.0x bead:sample ratio SPRIselect reagent (Beckman Coulter, B23318) cleanups, incubating for 10 minutes after each bead addition step.  Barcoded ATAC and cDNA fragments were amplified using a PCR reaction consisting of 45 µl of template, 50 µl of Pre-Amp Mix (10x Genomics, 2000270), 5 µl of Pre-Amp Primers (10x Genomics, 2000271), and 1 µl of ADT-Rev-AMP (0.2 µM Supplementary File 5). Amplification was performed in a C1000 Touch thermal cycler with 96–Deep Well Reaction Module: 72°C for 5 min, 98°C for 3 min, for 7 cycles of: 98°C for 20 sec, 63°C for 30 sec, 72°C for 1 min, with a final extension of 72°C for 1 min. Amplified fragments were purified using a 2.0x bead:sample ratio SPRIselect reagent (Beckman Coulter, B23318) bead clean-up, incubating for 10 minutes after bead addition.  Sequencing ready ATAC libraries were constructed by amplifying barcoded ATAC fragments in a sample indexing PCR consisting of SI-PCR Primer B (10x Genomics, 2000128), Amp Mix (10x Genomics, 2000047) and Sample Index Plate N, Set A (10x Genomics, 3000427) as described in the 10x Multiome User Guide. Amplification was performed in a C1000 Touch thermal cycler with 96–Deep Well Reaction Module: 98°C for 45 sec, then 9 cycles of: 98°C for 20 sec, 67°C for 30 sec, 72°C for 20 sec, with a final extension of 72°C for 1 min. Final ATAC libraries were prepared using a dual-sided 0.6x/1.6x bead:sample SPRIselect reagent (Beckman Coulter, B23318) size-selection clean-up.  cDNA fragments were amplified using a PCR reaction consisting of 35 µl of template, 50 µl of Amp Mix (10x Genomics, 2000047), 15 µl of cDNA Primers (10x Genomics, 2000089), and 1 µl of ADT-Rev-AMP (2 µM Supplementary File 5). Amplification was performed in a C1000 Touch thermal cycler with 96–Deep Well Reaction Module: 98°C for 3 min, then 8 cycles of: 98°C for 15 sec, 63°C for 20 sec, 72°C for 1 min, with a final extension of 72°C for 1 min. cDNA and ADT fragments were separated using a dual-sided SPRIselect reagent (Beckman Coulter, B23318) size-selection clean-up. Large cDNA fragments were retained in an initial 0.6x bead:sample SPRIselect incubation, reactions were incubated on a magnet, and small unbound fragments containing ADTs were transferred to new wells where they were subjected to an additional 2.0x bead:sample SPRIselect cleanup.  ADT fragments were amplified in a 15 cycle indexing PCR, substituting SI-PCR-Oligo primer (10 µM Supplementary File 5) for SI-P5-22. Final ADT libraries were prepared using a dual-sided 1.6x bead:sample SPRIselect reagent (Beckman Coulter, B23318) clean-up.  cDNA Fragmentation, End-Repair, and A-tailing were performed in a joint reaction containing 25% of cDNA sample as described in the 10x Multiome User Guide. Briefly, cDNA was diluted in Buffer EB (Qiagen, 1014609), and combined with master mix of Fragmentation Buffer (10x Genomics, 2000091) and Fragmentation Enzyme (10x Genomics, 2000090). The reaction was incubated in a C1000 Touch thermal cycler with 96–Deep Well Reaction Module: 4°C start, 32°C for 5 min, 65°C for 30 min, followed by a brief hold at 4°C. Reactions were purified using a dual-sided 0.6x/0.8x bead:sample SPRIselect reagent (Beckman Coulter, B23318) size-selection clean-up. Ligation was performed by mixing each sample with a master mix consisting of Ligation Buffer (10x Genomics, 2000092), DNA Ligase (10x Genomics, 220110), and Adapter Oligos (10x Genomics, 2000094), and incubating in a C1000 Touch thermal cycler with 96–Deep Well Reaction Module for 15 minutes at 20°C, followed by a brief hold at 4°C. Ligation reactions were purified using a 0.8x bead:sample SPRIselect reagent (Beckman Coulter, B23318) clean-up.  Sequencing ready Gene Expression libraries were constructed by amplifying cDNA fragments in a sample indexing PCR consisting of Amp Mix (10x Genomics, 2000047) and Dual Index TT Set A (10x Genomics, 3000431) as described in the 10x Multiome User Guide. Amplification was performed in a C1000 Touch thermal cycler with 96–Deep Well Reaction Module: 98°C for 45 sec, for 14 cycles of: 98°C for 20 sec, 54°C for 30 sec, 72°C for 20 sec, with a final extension of 72°C for 1 min. Final Gene Expression libraries were prepared using a dual-sided 0.6x/0.8x bead:sample SPRIselect reagent (Beckman Coulter, B23318) size-selection clean-up.

value: BioIVT

value: leukapheresis

value: permeabilized cells

value: 0.01% digitonin

value: FACS

value: Dead Cell/Debris/Neutrophil Depletion

value: TEA-seq


title: Kolf2-C1_Day25_Rep4

status: Public on Mar 07 2021

city: Cambridge

first: Davide

last: Chiarugi

address: Box 289, Addenbrooke’s Hospital

department: Metabolic Research Laboratories

country: United Kingdom

institute: WT-MRC Institute of Metabolic Science

description:
Raw_counts_K2.csv
K2_D25_4

data_processing:
Raw fastq files were trimmed using Cutadapt 2.10 and aligned to the reference features using STAR v. 2.7
The amount of reads per feature was quantified using Feature Counts 1.6.2 of the Subread package
Genome_build: genome-build GRCh38.p12, NCBI_Assembly:GCF_000001405.38, NCBI Homo sapiens Annotation Release 109
Supplementary_files_format_and_content: Processed data files contains the reads counts for each feature as comma separated values

source_name: human induced pluripotent stem cell -brown adipocytes precursors

growth_protocol: undifferentiated human pluripotent stem cells were maintained in Essential 8™ (E8) medium

extract_protocol:
RNA was extracted using the  RNeasy Qiagen Kit following the manufacturer's instructions
Library construction (poly(A) pulldown, fragmentation, 1st, and 2nd strand synthesis, end prep, and ligation) was carried out using 'NEB Ultra II RNA custom kit' on a Agilent Bravo WS automation system.

treatment_protocol: For differentiation, pluripotent cells were plated into Matrigel-coated 12-well plates and induced when 70% confluent. At days 0-4, chemically defined medium (CDM; BSA and insulin-free) was used. From days 6-30, complete medium (DMEM-F12 Ham) ) was used.

value: cell line

tag: cell line

tag: days of differentiation

value: male


title: Kolf2-C1_Day25_Rep1

description:
Raw_counts_K2.csv
K2_D25_1


title: RATCB4bou

value: Boutougoufara


title: Cr2

value: males:5 - females:5

value: Croisement Boube


title: RATCB3bou


title: Healthy5_snRNAseq

status: Public on Feb 21 2021

city: St. Louis

first: Yoshiharu

last: Muto

state: MO

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

institute: Washington University in St. Louis

description: snRNA-seq

data_processing:
Fastq files was processed with Cellranger 3.1.0 by "count" function with pre mRNA reference generated from refdata-cellranger-GRCh38-3.0.0 by manufacture's instruction.
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered barcode-feaure matrix

molecule: nuclear RNA

source_name: Human Kidney

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche) and RNase inhibitors (Promega, N2615 and Life Technologies, AM2696). Samples were cut into < 2 mm pieces, homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and centrifuged at 500g for 5 minutes at 4°C. The pellet was resuspended, washed with 4 ml of buffer, and incubated on ice for 5 minutes. Following centrifugation, the pellet was resuspended in nuclei suspension buffer (1x PBS, 1% BSA, 0.1% RNase inhibitor), filtered through a 5-μm cell strainer (43–50020–50; pluriSelect)
10xGenomics snRNA-seq library(5' kit)

tag: age

value: Female

tag: race

value: NHW

tag: egfr

tag: global glomerulosclerosis

tag: ifta

tag: tissue

value: kidney


title: Healthy4_snRNAseq

description: snRNA-seq

value: Male


title: Nd2

value: Ndombo


title: Cr1


title: Healthy3_snRNAseq

description: snRNA-seq


title: RATCB2bad

value: males:4 - females:4

value: BadiNieriko


title: Nd1


title: Kolf2-C1_Day25_Rep2

description:
Raw_counts_K2.csv
K2_D25_2

tag: cell type


title: Kolf2-C1_Day25_Rep5

description:
Raw_counts_K2.csv
K2_D25_5


title: Kolf2-C1_Day25_Rep3

description:
Raw_counts_K2.csv
K2_D25_3


title: Da1

value: Dagathie


title: Healthy4_snATACseq

description: snATAC-seq

data_processing:
Fastq files was processed with CellrangerATAC 1.2.0 by "count" function with refdata-cellranger-atac-GRCh38-1.2.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered barcode-peak matrix and fragment file

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche). Samples were cut into < 2 mm pieces, homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and centrifuged at 500g for 5 minutes at 4°C. The pellet was resuspended, washed with 4 ml of buffer, and incubated on ice for 5 minutes. Following centrifugation, the pellet was resuspended in Nuclei Buffer (10× Genomics, PN-2000153), filtered through a 5-μm cell strainer (43–50020–50; pluriSelect)
10xGenomics snATAC-seq library(v1 chemistry)


title: Healthy1_snATACseq

description: snATAC-seq


title: AP2_1_TraesCS6A02G243500_IWGSC1.1_DAP-seq_Rep1

status: Public on Feb 04 2021

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

country: China

institute: Fudan University

data_processing:
Library strategy: DAP-seq
Sequencing reads were cleaned with Trim Galore v0.4.4, Trimmomatic v0.36 and sickle, including removing bases with low quality score (<25) and irregular GC content, and cutting sequencing adaptors followed by filtering short reads.
The cleaned reads were mapped to International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0 using BWA 0.7.5a-r405  for ChIP-seq,  HISAT2 2.1.020 for RNA-seq data, all with default settings.
For ChIP-seq, MACS1.3.7 was used to identify read-enriched regions (peaks) with combined criteria: P value < 1e–5 and fold-change >32.  ChIP-seq data Target genes were defined as genes with a peak within or nearby the gene body (±2 kb).
For DAP-seq, MACS2.2.6 was used to identify protein binding sites (peaks). TF peaks which overlap with Halo peaks were removed. The top 6,000 peaks, ranked first by -log10(qvalue), then by fold enrichment, were used to discover novel DNA-binding motifs by MEME-ChIP in MEME software toolkit.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: In ChIP-seq, peak files were provided; In lncRNA-seq, read counts for genes (IWGSC RefSeq v1.0) were provided. In DAP-seq, peak files were provided.

organism: Triticum aestivum

source_name: Triticum aestivum leaves

growth_protocol: 16h light, 8h dark, 22°C

extract_protocol:
Chromatin or RNA was extracted from 14-days-old seedlingss, using standard protocols. 2μg total RNA (rRNA depleted) were used to prepare lncRNA-seq，2.2 μg DNA extracted from the harvested seedlings were used to prepare ChIP-seq. For DAP-seq, genomic DNA was extracted from leaves (14-days-old). 5μg gDNA was used to prepare DAP-seq library.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 2000/2500 system (Illumina) to produce 150-bp paired-end reads.
For DAP-seq, genomic DNA was extracted from wheat leaves using Plant DNAzol Reagent (invitrogen) and fragmented. DNA was then end repaired using the End-It kit (Lucigen) and A-tailed using Klenow (3′–5′ exo-; NEB). Truncated Illumina Y-adapter was ligated to DNA using T4 DNA Ligase (Promega).

treatment_protocol: For hormone and NaCl treatments, germinated seeds were grown in Hoagland solution at 22 °C under long-days conditions for 7 days. The 7-day-old seedlings in Hoagland were treated with 100μm ABA, 100μm MeJA, 500μm SA and 150mM NaCl, respectively, followed by incubation for 7 days.

value: leaves

tag: cultivar

value: Chinese Spring

tag: chip antibody

value: Halo

tag: chip antibody manufacturer

value: Promega

tag: chip antibody catalog #


title: AP2_1_TraesCS6A02G243500_IWGSC1.1_DAP-seq_Rep2


title: Healthy2_snATACseq

description: snATAC-seq

value: HIS


title: Healthy3_snATACseq

description: snATAC-seq


title: Healthy2_snRNAseq

description: snRNA-seq


title: Healthy1_snRNAseq

description: snRNA-seq


title: Input_PF

status: Public on Feb 01 2021

city: Granada

first: Carlos

last: Cordon-Obras

address: Av del Conocimiento

country: Spain

institute: Instituto Parasitologia Lopez Neyra

data_processing:
The 37-bp tags were aligned to the reference genome of T. brucei TREU 927 strain (version 36) using bowtie2 software with default options for paired-end reads and end-to-end alignment. MACS2 software (version 2.1.1) was employed to perform the peak calling. Default parameters were set with a false discovery rate of 5% and an additional fold enrichment cutoff of 1.5 for peak consideration.
Genome_build: TriTrypDB-36_TbruceiTREU927_Genome
Supplementary_files_format_and_content: bigWig graph file showing RNA pol II enrichment over input.

organism: Trypanosoma brucei brucei

source_name: Culture

growth_protocol: Maintained at 37 ºC with 5% CO2 atmosphere in HMI-9 medium supplemented with 20% of calf fetal serum.

extract_protocol:
T. brucei BS cultures (TREU927 strain) were harvested at 1 x 10E6 parasites per ml and fixed with 1% formaldehyde (5 x 10E7 total parasites per IP). Pellets were resuspended 0.5 ml of lysis buffer, sonicated to shear the chromatin (~300pb in length), diluted 1:5 in ChIP dilution buffer and pre-cleared with Sepharose® 4B beads (Sigma©). Pre-cleared chromatin was incubated overnight at 4 ºC with 10 μg of affinity purified anti-RPB1 antiserum. Next, protein G Sepharose® (Sigma©) was added and incubated for 2h at 4 ºC. Beads were then washed and immunoprecipitated DNA fragments recovered in 200 ul elution buffer. After crosslink reversal, DNA was extracted with phenol:chloroform, ethanol precipitated and resuspended in 50 μl of miliQ water. Four different immunoprecipitates were pulled, concentrated to a final volume of 10 μl using the MinElute® PCR Purification Kit (Qiagen©) and quantified with Qubit® 3.0 fluorometer (ThermoFisher Scientific©) using the QubitTM dsDNA HS Assay Kit.
Libraries for NGS were generated with NEBNext® UltraTM II DNA Library preparation kit and indexed with NEBNext® Multiplex Oligos (Illumina®). Paired-end sequencing was run in NextSeqTM 500 device using NextSeqTM 500/550 High Output Kit v2.5 (75 cycles).

tag: strain

tag: Stage

value: Bloodstream form


title: RPB1_prebleed_ChIP


title: Healthy5_snATACseq

description: snATAC-seq


title: RPB1_PF_ChIP


title: RPB1_BF_ChIP


title: secondary differentiation at day 15 (KCTiP) rep 3

status: Public on Jan 15 2021

city: Milan

first: Fabio

last: Marchiano

address: Via Alessandro Manzoni 56

country: Italy

institute: Humanitas

data_processing:
STAR (v2.5.1b) for reads mapping
featureCounts (1.6.2) for reads count
DESeq2 (v 1.22.2) for gene expression analysis
Genome_build: ENSEMBL GRCh38 release 77
Supplementary_files_format_and_content: raw count matrix and excel tables containing the results of the differential expression analysis + normalized counts

molecule: polyA RNA

source_name: iPSC cell culture

growth_protocol: For wildtype samples, NCRM1 cell line was differentiated into myogenic cultures as described in (Chal et al., 2016) and cells were harvested on day 0, day 8, day 16, day 24 and day 32 of differentiation. For secondary differentiation, 3-week old primary myogenic cultures were enzymatically dissociated and myogenic progenitors were replated at a density of 35-40,000/cm2 onto Matrigel (Corning, 354277) coated dishes in skeletal muscle growth media (SKGM-2, Lonza CC-3245) with 10 μM ROCK inhibitor (R&D Systems, 1254). Samples were collected after two days in SKGM culture. The cultures were further differentiated in three different conditions - KC (DMEM/F12 supplemented with 2% knockout serum replacement (Invitrogen, 10828028), 0.2% Pen/Strep (Life Technologies, 15140122), 1x ITS (Life Technologies, 41400045) and 1 μM CHIR (Tocris, 4423), KCTi (KC supplemented with 10 μM TGFβ inhibitor SB431542 (Tocris,1614)) and KCTiP (KCTi supplemented with 10 μM Prednisolone (Sigma Aldrich, P6004)). For each condition, cells were harvested after 7 and 15 days of differentiation. For each time point samples were collected from three independent experiments.For DMD samples, two isogenic DMD cell lines and parental wildtype line were differentiated into myogenic cultures as described in (Chal et al., 2016). Cells were replated for secondary differentiation in SKGM and were cultured in KC medium for one week. Samples were collected from three independent experiments.

extract_protocol:
RNA was isolated using NucleoSpin RNA kit (Macherey and Nagel, 740955) with on-column DNA digestion following the manufacturer’s protocol.
Libraries were prepared using Roche Kapa mRNA HyperPrep sample preparation kits from 100ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on two Illumina NextSeq500 runs with single-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

value: iPSC

tag: age + media

value: day 15 (KCTiP)


title: secondary differentiation at day 15 (KCTiP) rep 2


title: Input_for_prebleed


title: Input_BF


title: Banna Minipig Inbred Line (BMI)

status: Public on Dec 31 2020

city: Kunming

first: Jinlong

last: Huo

state: Yunnan

address: Jin-hei

department: Faculty of Animal Science and Technology

institute: Yunnan Agricultural University

data_processing:
Library strategy: DNA-Seq
Low quality reads were removed using the NGS QC Toolkit.
Genome mapping was performed using bowtie2 by mapping reads to the Sus Scrofa genome assembly Sscrofa11.1.
Short variant calling was performed using BCFtools and the results were further filtered using samtools.
PLINK v1.90b6.20 was used to identify ROHs with '--homozyg --homozyg-window-snp 20 --homozyg-snp 50 --homozyg-kb 100 --homozyg-density 50 --homozygwindow-het 5' parameters
GO analysis was performed using ENRICHR (https://maayanlab.cloud/Enrichr/) and semantic analysis was performed using REVIGO (http://revigo.irb.hr/) to reduce the redundancy and better visualize the differences between GO terms.
Genome_build: Sus scrofa genome (assembly Sscrofa11.1, Breed: Duroc, https://www.ncbi.nlm.nih.gov/assembly/GCF_000003025.6/)
Supplementary_files_format_and_content: BMI.susScr11.vcf: Variant Call Format (vcf).

organism: Sus scrofa

source_name: BMI

extract_protocol:
DNA was extracted using classic method of phenol-chloroform
library was constructed with insert size at 500 bps on blood samples and sequenced on the Illumina HiSeqTM 2000 platform

value: blood

tag: breed

value: Banna Minipig Inbred Line (BMI)


title: secondary differentiation at day 15 (KCTiP) rep 1

tag: cell line


title: blood_222

status: Public on Dec 07 2020

type: genomic

city: Davis

first: Anita

last: Oberbauer

state: CA

address: One Shields Ave.

department: Animal Science Department

institute: University of California, Davis

description: Bovine genomic DNA extracted from the tail coccygeal vein was genotyped using the BovineHD Beadchip array (Illumina)

hyb_protocol: Hybridization was performed according to the Infinium HD Super Assay documentation using the automated protocol.

scan_protocol: Scanning was performed according to the Infinium HD Super Assay documentation using the automated protocol.

data_processing:
The Illumina GenomeStudio Genotyping Module was used to determine genotypes from the intensity data files (IDAT files) outputted from scanning the BeadChip.
The Illumina GenomeStudio Genotyping Module called genotypes and generated SNP statistics.

label: C-Bio, G-Bio, A-DNP, T-DNP

organism: Bos taurus

source_name: blood from coccygeal vein in the tail

label_protocol: According to the Infinium HD Super Assay documentation (https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/infinium_assays/infinium-hd-super-assay/infinium-hd-super-assay-reference-guide-11322427-03.pdf), labels were added during allele-specific base extension.

extract_protocol: Whole blood sampled from the coccygueal vein of the tail were centrifuged, and the resulting buffy coat layer was stored at 4C until DNA extraction. Genomic DNA was extracted from buffy coat using the QIAGEN QIAamp DNA Blood Mini Kit according to the manufacturer's instructions.

tag: digital dermatitis binary phenotype

value: case

tag: digital dermatitis quantitative phenotype

tag: farm

value: A

tag: Sex

value: female

value: whole blood

tag: noninfectious claw lesion phenotype


title: blood_221

value: control


title: blood_220

value: B


title: blood_219


title: blood_217

value: D


title: blood_218


title: blood_216


title: blood_215


title: blood_211


title: blood_214


title: blood_213


title: blood_212


title: blood_209


title: blood_210


title: blood_205


title: blood_208


title: blood_207


title: blood_204


title: blood_201


title: blood_206


title: blood_203


title: blood_198


title: blood_199


title: blood_194


title: blood_196


title: blood_200


title: blood_195


title: blood_197


title: blood_202


title: blood_189


title: blood_190


title: blood_188


title: blood_187


title: blood_192


title: blood_186


title: blood_183

value: C


title: blood_185


title: blood_184


title: blood_181


title: blood_182


title: blood_193


title: blood_178


title: blood_171


title: blood_173


title: blood_174


title: blood_170


title: blood_191


title: blood_179


title: blood_177


title: blood_168


title: blood_172


title: blood_169


title: blood_164


title: blood_166


title: blood_163


title: blood_165


title: blood_180


title: blood_162


title: blood_160


title: blood_158


title: blood_161


title: blood_155


title: blood_157


title: blood_175


title: blood_156


title: blood_154


title: blood_159


title: blood_167


title: blood_153


title: blood_176


title: blood_152


title: blood_151


title: blood_149


title: blood_148


title: blood_146


title: blood_147


title: blood_150


title: blood_144


title: blood_145


title: blood_142


title: blood_140


title: blood_136


title: blood_139


title: blood_134


title: blood_135


title: blood_137


title: blood_133


title: blood_131


title: blood_127


title: blood_124


title: blood_130


title: blood_126


title: blood_128


title: blood_141


title: blood_121


title: blood_123


title: blood_120


title: blood_138


title: blood_125


title: blood_143


title: blood_129


title: blood_118


title: blood_115


title: blood_122


title: blood_112


title: blood_117


title: blood_116


title: blood_113


title: blood_111


title: blood_110


title: blood_109


title: blood_108


title: blood_107


title: blood_106


title: blood_105


title: blood_104


title: blood_103


title: blood_119


title: blood_100


title: blood_101


title: blood_99


title: blood_96


title: blood_97


title: blood_114


title: blood_95


title: blood_93


title: blood_94


title: blood_91


title: blood_90


title: blood_89


title: blood_92


title: blood_88


title: blood_87


title: blood_84


title: blood_80


title: blood_81


title: blood_132


title: blood_102


title: blood_79


title: blood_78


title: blood_77


title: blood_76


title: blood_75


title: blood_98


title: blood_73


title: blood_69


title: blood_65


title: blood_72


title: blood_67


title: blood_68


title: blood_85


title: blood_66


title: blood_71


title: blood_86


title: blood_70


title: blood_82


title: blood_62


title: blood_64


title: blood_83


title: blood_61


title: blood_60


title: blood_54


title: blood_57


title: blood_55


title: blood_56


title: blood_53


title: blood_51


title: blood_63


title: blood_50


title: blood_52


title: blood_48


title: blood_49


title: blood_47


title: blood_45


title: blood_43


title: blood_44


title: blood_46


title: blood_59


title: blood_40


title: blood_38


title: blood_41


title: blood_35


title: blood_34


title: blood_42


title: blood_36


title: blood_37


title: blood_32


title: blood_74


title: blood_31


title: blood_29


title: blood_28


title: blood_30


title: blood_27


title: blood_26


title: blood_24


title: blood_25


title: blood_23


title: blood_21


title: blood_58


title: blood_39


title: blood_18


title: blood_20


title: blood_15


title: blood_16


title: blood_10


title: blood_14


title: blood_33


title: blood_17


title: blood_19


title: blood_6


title: blood_8


title: blood_9


title: blood_12


title: blood_13


title: blood_7


title: blood_5


title: blood_11


title: blood_4


title: blood_3


title: blood_2


title: blood_1


title: blood_22


title: D175: Female 29 yrs Lung

status: Public on Nov 23 2020

city: Cincinnati

first: LungMAPP

last: DCC

state: OH

address: 3333 Burnet Ave

institute: LungMAP DCC

data_processing:
Library strategy: snATAC-seq
For each sequenced snATAC-Seq libraries, we obtained four FASTQ files paired-end DNA reads as well as the combinatorial indexes for i5 (768 different PCR indices) and T7 (96 different tagmentation indices). We selected all reads with <= 2 mistakes per individual index (Hamming distance between each pair of indices is 4) and subsequently integrated the full barcode at the beginning of the read name in the FASTQ files (https://gitlab.com/Grouumf/ATACdemultiplex/). Next, we used trim galore (v.0.4.4) to remove adapter sequences from reads prior to read alignment. We aligned reads to the hg19 reference genome using bwa mem (v.0.7.17) (Li and Durbin, 2009) and subsequently used samtools (Li et al., 2009) to remove unmapped, low map quality (MAPQ<30), secondary, and mitochondrial reads. We then removed duplicate reads on a per-cell basis using MarkDuplicates (BARCODE_TAG) from the picard toolkit. As an initial quality cutoff, we set a minimum of 1,000 reads (unique, non-mitochondrial) and observed 120,090 cells passing this threshold.    We used a previously described pipeline to identify snATAC-seq clusters (Chiou et al., 2019). Briefly, we used scanpy (Wolf et al., 2018) to uniform read depth-normalize and log-transform read counts within 5 kb windows. We then identified highly variable (hv) windows (min_mean=0.01, min_disp=0.25) and regressed out the total read depth across hv windows (usable counts) within each experiment. We then merged cells across experiments and extracted the top 50 PCs, using Harmony (Korsunsky et al., 2019) to correct for potential confounding factors including donor-of-origin and biological sex. We used Harmony-corrected components to build a nearest neighbor graph (n_neighbors=30) using the cosine metric, which was used for UMAP visualization (min_dist=0.3) and Leiden clustering (resolution=1.5) (Traag et al., 2019).    Prior to the final clustering results, we performed iterative clustering to identify and remove cells mapping to clusters with aberrant quality metrics. First, we removed 3,183 cells mapping in clusters with low read depth. Next, we removed 20,718 cells mapping in clusters with low fraction of reads in peaks. Finally, we re-clustered the cells at high resolution and removed 5,209 cells mapping in potential doublet sub-clusters. On average, these sub-clusters had higher usable counts, promoter usage, and accessibility at more than one marker gene promoter. After removing all of these cells, our final clusters consisted of 90,980 cells. To identify marker genes for each cluster, we used linear regression models with gene accessibility as a function of cluster assignment and usable counts across single cells.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file and .mtx

source_name: Biopsy from small airway

extract_protocol:
Lung tissue was homogenized using mortar and pestle on liquid nitrogen. 1 ml nuclei permeabilization buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 0.1% IGEPAL-CA630 (Sigma) and 0.01% Digitonin (Promega) in water (Corces et al., 2017)) was added to 30 mg of ground lung tissue and tissue was resuspended by pipetting for 8-15 times. Nuclei suspension was incubated for 10 min at 4°C and filtered with 30 μm filter (CellTrics).
Combinatorial barcoding single nucleus ATAC-seq was performed as described previously with modifications (Cusanovich et al., 2015; Fang et al., 2019; Preissl et al., 2018) and using new sets of oligos for tagmentation and PCR. Nuclei suspension was pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf) and resuspended in 500 μL high salt tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% DMF) and counted using a hemocytometer. Concentration was adjusted to 2,000 nuclei/9 μl, and 2,000 nuclei were dispensed into each well of one 96-well plate. For tagmentation, 1 μL barcoded Tn5 transposomes (Fang et al., 2019) was added using a BenchSmart™ 96 (Mettler Toledo), mixed five times and incubated for 60 min at 37 °C with shaking (500 rpm). To inhibit the Tn5 reaction, 10 μL of 40 mM EDTA were added to each well with a BenchSmart™ 96 (Mettler Toledo) and the plate was incubated at 37 °C for 15 min with shaking (500 rpm). Next, 20 μL 2 x sort buffer (2 % BSA, 2 mM EDTA in PBS) was added using a BenchSmart™ 96 (Mettler Toledo). All wells were combined into a FACS tube and stained with 3 μM Draq7 (Cell Signaling). Using a SH800 (Sony), 20 2n nuclei were sorted per well into eight 96-well plates (total of 768 wells) containing 10.5 μL EB (25 pmol primer i7, 25 pmol primer i5, 200 ng BSA (Sigma). Preparation of sort plates and all downstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). After addition of 1 μL 0.2% SDS, samples were incubated at 55 °C for 7 min with shaking (500 rpm). 1 μL 12.5% Triton-X was added to each well to quench the SDS. Next, 12.5 μL NEBNext High-Fidelity 2× PCR Master Mix (NEB) were added and samples were PCR-amplified (72 °C 5 min, 98 °C 30 s, (98 °C 10 s, 63 °C 30 s, 72°C 60 s) × 12 cycles, held at 12 °C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRI Beads (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRI Beads (Beckmann Coulter, 1.5x). Libraries were quantified using a Qubit fluorimeter (Life technologies) and the nucleosomal pattern was verified using a Tapestation (High Sensitivity D1000, Agilent).
Single-nucleus ATAC-Seq libraries were sequenced on a HiSeq4000 or NextSeq500 sequencer (Illumina) using custom sequencing primers with following read lengths: 50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2).

tag: age

value: 29 yrs

value: F

tag: race

value: White

tag: clinpathdx

value: Normal growth and structure

tag: assessement of tissue quality

value: Very Good

tag: type of death

value: DCD

tag: Cause of death

value: Head trauma


title: D122: Male 31 yrs Lung

value: 31 yrs

value: M

value: Unkn

value: Normal growth and development, mild chronic bronchiolitis, anthracotic pigment

value: Excellent

value: DBD


title: D231: Female 33 yrs Lung

data_processing:
Library strategy: snRNA-seq
Sequencing reads were demultiplexed (cellranger mkfastq) and processed (cellranger count) using the Cell Ranger software package v3.0.2 (10x Genomics). Reads were aligned to the human reference hg38 (Cell Ranger software package v3.0.2). Reads mapping to intronic and exon sequences were retained. Resulting UMI feature-barcode count matrices were loaded into Seurat (Stuart et al., 2019). All genes represented in >=3 nuclei and cells with 500-4000 detected genes were included for downstream processing. UMI counts were log-normalized and scaled by a factor of 10,000 using the NormalizeData function. Top 3000 variable features were identified using the FindVariableFeatures function and finally scaled using the ScaleData function. Barcode collisions were removed for individual datasets using DoubletFinder (McGinnis et al., 2019) with following parameters: pN =0.15 and pK = 0.005, anticipated collision rate = 10%. Clusters were assigned a doublet score (pANN) and classification as “doublet” or “singlet”; called doublets and cells with a pANN score > 0 were removed. UMI matrices for datasets were merged and corrected for batch effects due to experiment date, donor, and sex using the Harmony package (Korsunsky et al., 2019). UMAP coordinates and clustering were performed using the RunUMAP, FindNeighbors, and FindClusters functions in Seurat with principal components 1-23. 25-26, and 28. Clusters were annotated, and putative doublets as defined by expression of canonically mutually exclusive markers were excluded from analysis; remaining cells were re-clustered using the previously described parameters. Final cluster annotation was done using canonical markers. For genes of interest such as (e.g. ACE2, TMPRSS2), nuclei with at least one UMI for the gene were considered “expressing”. To analyze changes in percentage of nuclei expressing we performed One-way ANOVA (ANalysis Of VAriance) with post-hoc Tukey HSD (Honestly Significant Difference) using GraphPad Prism version 8.0.0 for Windows, GraphPad Software, San Diego, California USA, www.graphpad.com. Due to one potential outlier in the 30wkGA group (D062) we performed in addition a simple t-test comparing 3 yr to 30 yr groups. Differential gene expression analysis between ACE2+ and ACE2- AT2 cells we used FindAllMarkers with parameters logfc = 0, min.pct = 0, test.use = “wilcox”, verbose = TRUE. Cells were filtered using the following commonly used criteria: >500 expressed genes and <10% UMIs mapped to mitochondrial DNAs. In addition, cells with greater than or equal to 40,000 UMIs were excluded from the downstream analysis; this filtration criterion was selected based on the distribution of UMIs in single cells in individual donors. Seurat (version 3) (Stuart et al., 2019) was used to identify AT2 cells from individual aged donors. Nuclei from the 9 libraries generated in this study and cells from libraries for the 4 aged donors were integrated using the Seurat 3 standard integration pipeline (Stuart et al., 2019).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited separated value (tsv) file and .mtx

extract_protocol:
30 mg pulverized lung tissue was resuspended in 500 μl of nuclei permeabilization buffer (0.1% Triton X-100 (Sigma-Aldrich, T8787), 1X protease inhibitor, 1 mM DTT, and 0.2 U/μl RNase inhibitor (Promega, N211B), 2% BSA (Sigma-Aldrich, SRE0036) in PBS). Sample was incubated on a rotator for 5 minutes at 4°C and then centrifuged at 500 rcf for 5 minutes (4°C, run speed 3/3). Supernatant was removed and pellet was resuspended in 400 μl of sort buffer (1 mM EDTA 0.2 U/μl RNase inhibitor (Promega, N211B), 2% BSA (Sigma-Aldrich, SRE0036) in PBS) and stained with DRAQ7 (1:100; Cell Signaling, 7406). 75,000 nuclei were sorted using a SH800 sorter (Sony) into 50 μl of collection buffer consisting of 1 U/μl RNase inhibitor in 5% BSA; the FACS gating strategy sorted based on particle size and DRAQ7 fluorescence. Sorted nuclei were then centrifuged at 1000 rcf for 15 minutes (4°C, run speed 3/3) and supernatant was removed. Nuclei were resuspended in 35 μl of reaction buffer (0.2 U/μl RNase inhibitor (Promega, N211B), 2% BSA (Sigma-Aldrich, SRE0036) in PBS) and counted on a hemocytometer. 12,000 nuclei were loaded onto a Chromium controller (10x Genomics).
Droplet-based Chromium Single Cell 3’ solution (10x Genomics, v3 chemistry)(Zheng et al., 2017) was used to generate snRNA-seq libraries.   Libraries were generated using the Chromium Single Cell 3’ Library Construction Kit v3 (10x Genomics, 1000078) according to manufacturer specifications. CDNA was amplified for 12 PCR cycles. SPRISelect reagent (Beckman Coulter) was sued for size selection and clean-up steps. Final library concentration was assessed by Qubit dsDNA HS Assay Kit (Thermo-Fischer Scientific) and fragment size was checked using Tapestation High Sensitivity D1000 (Agilent) to ensure that fragment sizes were distributed normally about 500 bp.
Single-nucleus RNA-Seq libraries were sequenced using the NextSeq500 and a HiSeq4000 (Illumina) with these read lengths: 28 + 8 + 91 (Read1 + Index1 + Read2).

value: 33 yrs

value: Black/AA

value: Normal growth and development, patchy mild mixed inflammation

value: Anoxic/hypoxic brain injury


title: D046: Male 3 yr Lung

value: 3 yr

value: Normal growth and development

value: Brain / C-spine trauma


title: D139: Female 3 yr Lung

value: F

value: White

value: Brain injury


title: D150: Male 29 wkGA Lung

value: 29 wkGA

value: Normal lung growth; late canalicular/early saccular

value: Very Good

value: DCD

value: Anencephaly


title: D032: Male 3 yr Lung

value: M

value: Head Trauma


title: D175: Female 29 yrs Lung

value: 29 yrs

value: Normal growth and structure

value: Head trauma


title: Pancreatic tumors, KRAS KO (scRNAseq)

status: Public on Nov 11 2020

city: Stony Brook

first: Jinyu

last: Li

state: NY

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

data_processing:
*I1_001.fastq.gz: contains the 8 nt sample index.
*R1_001.fastq.gz: contains the cell barcode (first 16 nt) and UMI (next 10 nt)
*R2_001.fastq.gz: contains the 150  nt RNA sequence.
Single Cell sequencing data were pre-processed by cellranger 3.0.1 from 10X Genomics using default settings.
Downstreaming analysis was performed by Seurat 3.0
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

source_name: mouse pancreas

growth_protocol: CRISPR/Cas9 was used to generate a KRAS-null derivative of a tumorigenic KRASG12D p53R172H cell line. The KRAS-null cells were cultured on gelatinized plates in DMEM with 5% FBS supplemented with antibiotics and antimycotics. Syngeneic mice were injected with these cells and tumors were harvested when they were 1 cm in size.

extract_protocol:
Pancreatic tumors for each sample set was pooled in from two mice. These tumors were digested both mechanically and enzymaticaly (collagenase Type II, DNaseI, Accutase) and a single cell suspension of viable cells was prepared. mRNA from each individual cell was captured and tagged with barcodes using 10X Genomics microfluidic platform.
Barcoded cDNA library was prepared using the manufacturer's instructions, 10X Genomics.

tag: tissue of origin for tumor

value: pancreas

tag: genetic alteration

value: KRAS-/-


title: D046: Male 3 yr Lung

value: 3 yr

value: Normal growth and development


title: D139: Female 3 yr Lung

value: F

value: Excellent

value: DBD


title: Pancreatic tumors, KRAS KO BRAF/MYC (scRNAseq)

growth_protocol: Sequential transformation with MYC and activated BRAF expression plasmids were used to generate a MYC/BRAF derivative of the KRAS-null cell line.   The MYC/BRAF cells were cultured on gelatinized plates in DMEM with 5% FBS supplemented with antibiotics and antimycotics. Syngeneic mice were injected with these cells and tumors were harvested when they were 1 cm in size.

tag: strain

value: KRAS-/- BRAFV600E MYCT58A


title: D088: Female 31 wkGA Lung

value: 31 wkGA

value: Unkn

value: Normal lung growth; late saccular

value: Good


title: D122: Male 31 yrs Lung

value: 31 yrs

value: M

value: Normal growth and development, mild chronic bronchiolitis, anthracotic pigment


title: BJ5ta_30min_R1_HiC

status: Public on Sep 04 2020

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee,Knoxville

data_processing:
Sequenced reads were mapped to the hg19 genome using bowtie2
Filtering was carried out using the dekkerlab-cMapping pipeline available on github
Iterative correction was performed using method described by Imakaev et al.
All processed Hi-C contact maps were scaled to a sum of 1 million
Genome_build: hg19
Supplementary_files_format_and_content: each .tar file contains the iteratively corrected and raw matrix.gz files for 40 kb, 250 kb, and 2.5 Mb in their respective directories

growth_protocol: Fibroblast lines were grown to confluency prior to X-ray exposure. For the GM12878 suspension cell line, cells were passaged at a density around 500,000 cells per 1 mL of medium. For irradiation experiments, GM12878 cells were grown to a density of 1 million cells per 1 mL of medium prior to X-ray exposure.

extract_protocol:
Briefly, 5-20 million cells were fixed with 1% formaldehyde, suspended in cell lysis buffer for permeabilization, and homogenized by douncing. Crosslinked chromatin was digested overnight with HindIII. Sticky ends were filled in with biotin-dCTP, and the blunt ends of interacting fragments were ligated together. DNA was purified by two phenol-chloroform extractions and ethanol precipitation. Biotin-dCTP at unligated ends was removed, and the DNA was sheared to a target size of 200-400 bp by a Covaris sonicator
Biotinylated DNA was pulled down using streptavidin coated magnetic beads and prepared for multiplex sequencing on an Illumina platform using the NEBNext Ultra II kit (NEB). All end preparation, adaptor ligation, and PCR amplification steps were carried out on bead bound DNA libraries.

treatment_protocol: Treated cells were X-rayed using 5 Gy X-rays and fixed for Hi-C after 30 mins, 24 hours, or split after 24 hours and allowed to recover for 5 days. The treated cells and their control counterparts were then fixed for Hi-C. ATM inhibitor treated cells were subjected to 10um KU-55933 for 1 hour before experiment began. ATMiC was subjected to KU-55933, but not IR.

tag: cell type

value: Foreskin fibroblast

tag: condition

tag: media

value: 4:1DMEM:Medium199,10%FBS, 0.01mgHygroB


title: BJ5ta_24hr_R1_HiC

tag: cell line


title: D032: Male 3 yr Lung

value: White

value: Very Good

value: Head Trauma


title: D110: Male 4 mon Lung

value: 4 mon

value: Normal lung growth and structure, Mildly increased alveolar macrophages,


title: H-MAT 2

status: Public on Aug 28 2020

city: West Hollywood

first: AGCT

last: Core

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

data_processing:
Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20.
Then reads were aligned to the transcriptome using STAR (version 2.6.1)/ RSEM (version 1.2.28) with default parameters, using a custom human GRCh38 transcriptome reference downloaded from http://www.gencodegenes.org, containing all protein coding and long non-coding RNA genes based on human GENCODE version 33 annotation.
Expression counts for each gene in all samples were normalized by a modified trimmed mean of the M-values normalization method and the unsupervised PC analysis (PCA) was performed with DESeq2 Bioconductor package version 1.26.0 in R version 3.6.3. Each gene was fitted into a negative binomial generalized linear model, and the Wald test was applied to assess the differential expressions between two sample groups by DESeq2. Benjamini and Hochberg procedure was applied to adjust for multiple hypothesis testing, and differential expression gene candidates were selected with a false discovery rate less than 0.05. For visualization of coordinated gene expression in samples, a two-way hierarchical clustering with Pearson correlation distance matrix was performed with samples and DEG candidates using the Bioconductor g-plots package (version 3.0.3) in R.
Genome_build: GRCh38
Supplementary_files_format_and_content: Expression matrix in CSV format

source_name: Mesenteric adipose tissue

extract_protocol:
Mesenteric adipose tissue was excised from surgical specimens and flash frozen in liquid nitrogen until use. RNA was harvested using E.Z.N.A.® Total RNA Kit II and E.Z.N.A.® MicroElute RNA Clean Up Kit
Library construction was performed using the Illumina TruSeq Stranded Total RNA library preparation kit.

tag: tissue

value: Healthy mesenteric fat

tag: cohort

value: Healthy ileal controls


title: D062: Male 29 wkGA Lung

value: 29 wkGA

tag: Sex

value: RDS; early saccular lung

value: Excellent

value: DCD

value: DandyWalker brain anomaly


title: H-MAT 1


title: D062: Male 29 wkGA Lung

value: Unkn


title: CrF 3

value: Creeping fat

value: Crohn's disease


title: D231: Female 33 yrs Lung

value: 33 yrs

value: F

value: Black/AA

value: Normal growth and development, patchy mild mixed inflammation

value: Anoxic/hypoxic brain injury


title: D088: Female 31 wkGA Lung

value: 31 wkGA

value: Normal lung growth; late saccular

value: Good

value: Anencephaly


title: CrF 1


title: CrF 2


title: H-MAT 4

value: Healthy mesenteric fat

value: Healthy ileal controls


title: HUVEC_H_T3d_HiC

status: Public on Aug 17 2020

city: La Jolla

first: Sheng

last: Zhong

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California San Diego

description: in situ ligation of proximal genomic DNA

data_processing:
Library strategy: HiC-Seq
Illumina Casava1.8 software used for base calling
Pre-truncation of reads that contain a potential ligation junction performed using HiCtool (v2.1)
Paired-end read pairs were independently aligned to the hg38 genome assembly using Bowtie 2 (2.2.9) to avoid any proximity constraint
Unmapped reads and reads mapped with MAPQ < 30 were removed using SAMTools (1.6)
Deduplication of reads and generation of observed contact matrices using HiFive package (1.4)
Data normalization using the matrix balancing approach of Hi-Corrector (1.2) incorporated into HiCtool (v2.1)
Genome_build: hg38
Supplementary_files_format_and_content: The processed BEDPE file shows the valid chromatin interaction read pairs. BEDPE format (https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format), the 1,2,3 and 9 colums show the genomic coordinate of the first read, while the 4, 5, 6, and 10 columns of the second read.

source_name: Human umbilical Vein Endothelial Cells treatment combining high glucose (HG, to mimic hyperglycemia) and TNFalpha (to mimic inflammation) for 3 days

growth_protocol: HUVECs were grown following the manufacturer's protocol

extract_protocol:
The HiC libraries generation followed instruction of Arima HiC kit. Briefly, ~5-10 million cells were crosslinked with 1% formaldehyde at room temperature (RT) for 10 min. Approximately 1 million crosslinked cells (2-5 ug of DNA) were lysed with Arima's Lysis Buffer and digested with Arima restriction enzyme cocktail. The 5'-overhangs were then filled in and labeled with biotinylated nucleotides. Then, spatially proximal digested ends of DNA were ligated.
The ligated DNA was purified and sheared by Covaris ultra-sonicator to obtain average DNA size of 400 bp. Then, the biotinylated fragments were enriched with Arima Enrichment Beads. Afterwards, KAPA Hyper Prep reagents were used in a custom end-repair, dA-tailing and adaptor ligation protocol. The bead-bound Arima HiC libraries were PCR amplified, producing the sequence-ready Arima HiC libraries.

treatment_protocol: HUVECs were treated with 25mM Mannitol in the control group; Cells in the H_T groups were treated with 25mM D-Glucose and 5ng/mL TNF for 3 days (3d) or 7 days (7d)

value: HUVEC

tag: assay

value: Hi-C


title: HUVEC_H_T7d_iMARGI

description: in situ ligation of nuclear RNA and genomic DNA

data_processing:
Library strategy: iMARGI-Seq
Illumina Casava1.8 software used for base calling
Paired-end read pairs were aligned to the hg38 genome assembly using bwa mem (0.7.17) with parameter '-SP5M'
pairtools (v0.2.0) and in-house scripts were used to parse, deduplicate and filter the mapped read pairs.
Genome_build: hg38
Supplementary_files_format_and_content: The processed BEDPE file shows the valid RNA-DNA interaction read pairs. BEDPE format (https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format), the 1,2,3 and 9 colums show the genomic coordinate of RNA end (Read 1), and the 4, 5, 6, and 10 columns show that of DNA end (Read 2).

source_name: Human umbilical Vein Endothelial Cells treatment combining high glucose (HG, to mimic hyperglycemia) and TNFalpha (to mimic inflammation) for 7 days

extract_protocol:
Approximately 5 million cells were used for construction of an iMARGI sequencing library. Cells were crosslinked in 1% formaldehyde at room temperature (RT) for 10 minutes with rotation. Crosslinking reaction was quenched with glycine at 0.2 M concentration and incubated at RT for 10 minutes. Cells were pelleted, washed using 1 × PBS and aliquoted into ~ 5 million in each tube. To prepare nuclei, crosslinked cells was incubated in 1 mL of cell lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% Nonidet P-40, 1× protease inhibitor) on ice for 15 minutes and homogenized with dounce homogenizer pestle A for 20 strokes on ice. Nuclei were pelleted and weighed to estimate the pellet volume (10 mg of nuclei pellet was estimated to be about 10 µL). Nuclei pellet were incubated with SDS buffer (0.5× Cutsmart buffer, 0.5% SDS) with 1:3 volume ratio at 62 °C for 10 minutes with mixing and immediately quenched with a final of 1% Triton X-100. To digest chromatin, washed nuclei pellet was re-suspended in AluI chromatin digestion mix (2.3 U/µL AluI (NEB), 0.3 U/µL RNasinPlus, 1× Cutsmart buffer) and incubated at 37 °C overnight with mixing. After chromatin digestion, 1 µL of RNase I (1:10 diluted in 1× PBS) was directly added to the reaction mixture and incubated at 37 °C for 3 minutes to fragment RNA. Nuclei were pelleted and washed twice using PNK wash buffer (20 mM Tris-HCl pH 7.5, 10 mM MgCl2). To prepare the RNA and DNA ends for linker ligation, nuclei were incubated in 200 µL RNA 3´ end dephosphorylation reaction mix (0.5 U/µL T4 PNK (NEB), 0.4 U/µL RNasinPlus, 1× PNK phosphatase buffer pH 6.5) at 37°C for 30 minutes with mixing. Nuclei were washed twice with PNK buffer, resuspended in 200 µL DNA A-tailing mix (0.3 U/µL Klenow fragment 3´-5´ exo- (NEB), 0.1 mM dATP, 0.1% Triton X-100, 1× NEB buffer 2) and incubated at 37°C for 30 minutes with mixing. The same linker sequence as described in the previous MARGI paper was used. For in situ RNA-linker ligation, nuclei were resuspended in 200 µL ligation mix (38 µL adenylated and annealed linker, 10 U/ µL T4 RNA ligase 2-truncated KQ (NEB), 1× T4 RNA ligase reaction buffer, 20% PEG 8000, 0.1% Triton X-100, 0.4 U/µL RNasinPlus) and incubated at 22°C for 6 hour and then 16°C overnight with mixing. After ligation, the nuclei were washed five times with PNK buffer to remove excess free linker. For in situ RNA-DNA proximity ligation, nuclei were resuspended in 2 mL of proximity ligation mixture (4 U/µL T4 DNA ligase (NEB), 1× DNA ligase reaction buffer, 0.1% Triton X-100, 1 mg/mL BSA (NEB), 0.5 U/µL RNasinPlus) and incubated at 16 °C overnight.
To reverse crosslinking, nuclei were washed twice with 1× PBS, resuspended in 250 µL of extraction buffer (1 mg/mL Proteinase K [NEB], 50 mM Tris-HCl pH 7.5, 1% SDS, 1 mM EDTA, 100 mM NaCl) and incubated at 65 °C for 3 hours. DNA and RNA were extracted by adding an equal volume of Phenol:Chloroform:Isoamyl Alcohol (pH 7.9, Ambion) followed by ethanol precipitation. The subsequent steps including removal of biotin from non-proximity ligated linkers, pulldown of RNA-DNA chimera, reverse transcription of RNA, DNA denaturation, circularization, oligo annealing and BamHI (NEB) digestion and sequencing library generation were performed as previously described. iMARGI libraries were subsequently subject to pair-end 100-cycle sequencing on Illumina HiSeq 4000. The circularization and library construction strategy can phase RNA and DNA ends into Read 1 and Read 2. Since AluI restriction enzyme recognizes "AGCT" sequence and leaves "CT" at the 5´ end of the cut, we expect the first two bases of DNA end (Read 2) to be enriched with "CT".

value: iMARGI


title: HUVEC_H_T7d_HiC


title: HUVEC_control_iMARGI

source_name: Human umbilical Vein Endothelial Cells cultured under osmotic control (25 mM mannitol)


title: HUVEC_H_T3d_iMARGI


title: H-MAT 3


title: HUVEC_control_HiC


title: HUVEC_control_scRNA_2

description: Single-cell RNA sequencing assay

data_processing:
10X Genomics cellranger (v3.0) was used to process sequencing data produced from Chromium Single Cell Gene Expression
Genome_build: hg38
Supplementary_files_format_and_content: Three processed data files per each sample: a matrix file (.mtx format) with UMI counts per each gene (rows) and single cell (columns); genes list (.tsv format) with the list of genes (features) detected; cell barcodes list (.tsv format) with the list of barcodes of the single cells in the sample.

source_name: Human umbilical Vein Endothelial Cells cultured under osmotic control (25 mM mannitol), replicate 2

extract_protocol:
HUVECs in culture were washed with 1XPBS after removing the growth medium, trypsinized and washed once in 1XPBS/0.04%BSA, then subjected to cell counting and single cell isolation using the 10X Genomics Chromium Controller
10X Genomics Single Cell 3' v2. gene expression

value: scRNA-seq


title: HUVEC_H_T7d_scRNA_1

description: Single-cell RNA sequencing assay

source_name: Human umbilical Vein Endothelial Cells treatment combining high glucose (HG, to mimic hyperglycemia) and TNFalpha (to mimic inflammation) for 7 days, replicate 1


title: HUVEC_control_scRNA_1

description: Single-cell RNA sequencing assay

source_name: Human umbilical Vein Endothelial Cells cultured under osmotic control (25 mM mannitol), replicate 1


title: HUVEC_H_T7d_scRNA_2

description: Single-cell RNA sequencing assay

source_name: Human umbilical Vein Endothelial Cells treatment combining high glucose (HG, to mimic hyperglycemia) and TNFalpha (to mimic inflammation) for 7 days replicate 2


title: HUVEC_H_T3d_scRNA_1

description: Single-cell RNA sequencing assay

source_name: Human umbilical Vein Endothelial Cells treatment combining high glucose (HG, to mimic hyperglycemia) and TNFalpha (to mimic inflammation) for 3 days, replicate 1


title: Retina Slc6a4 KO 3

status: Public on Jul 11 2020

city: Pittsburgh

first: Takaaki

last: Kuwajima

state: PA

address: 1622 Locus Street, 7.396

department: Ophthalmology

institute: University of Pittsburgh School of Medicine

data_processing:
Sequencing platform: NextSeq500 (Illumina)
Sequenced reads were trimmed for adaptor sequence
Genome_build: GRCm38.99
Supplementary_files_format_and_content: tab-delimited text files include p- values below 0.05 including FDR p-value, fold change, and raw gene counts for each sample

source_name: Retina

extract_protocol:
RNA quality was verified by the University of Pittsburgh Health Genomics Core using Agilent   Tapestation RNA and Qubit Fluorometric Quantification. RNA samples with a   RNA integrity number of (RIN) >7 were utilized. Briefly, cDNA was synthesized with   SuperScript IV and strands underwent Adenylation of 3’ ends followed by adapter   ligation and library amplification with indexing. Library preparation was conducted with  TruSeq Total RNA library kit (Illumina) using at least 1 µg of total RNA following the manufacture’s  instruction. Modifications during the library preparation include rRNA reduced RNA cleaned up   was done with AMPureXP beads and library amplified with 13 cycles of PCR and cleaned up with   37µl AMPureXP beads. Sequencing was performed using 1 High Output 150 flowcell.
Library was prepared following manufacturer’s instructions with the following modifications.
RNA Seq, Library kit:TruSEq Total RNA, Library type: Stranded Total RNA

treatment_protocol: 8-week-old animals were anesthetized with ketamine/xylazine. The optic nerve in the left eye   was crushed using #5 Dumont forceps, applying pressure for 5s ~1 mm behind the optic disc.   After 24 hours after injury, injured retina was dissected and total RNA was extracted.

value: Retina

tag: age

value: Postnatal day 56

tag: genotype

tag: treatment

value: optic nerve crush


title: CrF 4

value: Creeping fat

value: Crohn's disease


title: Retina Slc6a4 KO 1


title: Retina WT 3

value: wildtype


title: Retina Slc6a4 KO 2


title: H9ESC_BA_Day50CTR_Rep1

status: Public on Aug 01 2020

city: Athens

first: Liang

last: Zhang

state: GA

address: 325 Riverbend Road

department: Biochemistry and Molecular Biology, Center for Molecular Medicine

institute: University of Georgia

data_processing:
Constructed libraries were sequenced in illumina NextSeq 500 platform and basecalling was perfomed in Real-Time Analysis (RTA) System V2 (illumina).
Sequence data (fastq) were mapped to hg19 using STAR (V2.6.1.C) on default setting with "-quantMode GeneCounts" to obtain read count of each sample.
Raw readcount of each samples were collected and analyzed in R Studio (Version 1.0.143) with RNA-Seq analysis package "limma_3.32.10 ","edgeR_3.18.1" and "DESeq2_1.16.1" following published analytic pipelines (Law, Charity W et al. 2016; Love, Michael et al. 2014) .
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include raw read counts of each sample.

source_name: Derived from human embryonic stem cells (WA09 WiCell, WAe009-A)

growth_protocol: The human embryonic stem cell (hESCs) WA09 (Sex: female, WiCell, WAe009-A) and induced pluripotent stem cell (hiPSCs) line K3 (Sex: male, Si-Tayeb et al., 2010) were cultured at polystyrene culture plates coated with Geltrex LDEV-free hESC qualified reduced growth factor basement membrane.  Media for PSC maintenance, sphere formation, paraxial mesoderm and brown adipocyte differentiations were accomplished using a defined base medium (DM) supplemented with specific factors. DM was composed of DMEM/F-12 w/o glutamine supplemented with 2% Probumin,1x Antibiotic-Antimyotic, 1x MEM non-essential amino acids,1x Trace Elements A,1x Trace Elements B,1x Trace Elements C,50 mg/mL Ascorbic Acid, 10 mg/mL Transferrin, 0.1 mM 2-mercaptoethanol and 1x glutagro. The hPSC complete maintenance medium (CMM) was composed of DM supplemented with 8 ng/mL human basic-FGF 200 ng/mL LONG® R3 human IGF-I,10 ng/mL Activin A and 10 ng/mL human Heregulin-β 1. hESCs and hiPSCs were cultured in CMM with media changes every 24 hrs and passaged at 90% confluency using Accutase.

extract_protocol:
Total RNA were extracted using E.Z.N.A. Total RNA kit I (Omega, R6834), according to manufacture's protocol.
RNA samples with RNA Integrity number above 8.0 were seleced for library preparation in Geogia Genomic and Bioinformatic Core (https://dna.uga.edu/). KAPA Stranded mRNA-Seq Kit  for Illumina® Platforms (KR0960-v5.17) were used for library constructions of all RNA-Seq samples included in this study.
Pair-end stranded libraries were construced and then sequenced in NextSeq platform with read length 75 bp. Each sample has more than 30 millions read per end.

treatment_protocol: Paraxial mesoderm (PM) cells were generated in a three-step process using rotational suspension culture. First a single-cell suspension containing one million cells/mL was seeded in 6-well suspension plates at a volume of 5.5 mL in hPSC MM plus 10 mM Y-27632 dihydrochloride. The plate was then placed on an Innova 2000 platform shaker at 97 RPM in a 5% CO2, 37°C incubator for 24 hrs. The following day, medium was replaced with hPSC CMM for an additional 24 hrs and maintained in suspension culture. After 24 hrs in CMM, the medium was exchanged for mesoderm induction medium (MesoIM) and cultured for further 48 hrs with medium changes every day. Mesoderm induction medium was composed of DM supplemented with 10 ng/mL BMP4, 20 ng/mL bFGF, 200 ng/mL LONG® R3 human IGF-I and 250 nM rapamycin. After MIM, cells were washed once with DM and then switched to paraxial mesoderm medium (PM) for an additional 96 hrs in suspension with daily medium changes. PMP was composed of DM supplemented with the following factors: 20 ng/mL bFGF, 200 ng/mL LONG® R3 human IGF-I, 250 nM Rapamycin, 25 ng/mL WNT3a, 50 ng/mL Noggin, 2 mM (2'Z,3'E)-6-Bromoindirubin-3'-oxime (BIO) and 5 mM forskolin. Brown adipocyte (BA) differentiation from a PM precursor was performed in two steps using sequential media formulations designated as brown adipocyte 'priming' medium (BA1) and brown adipocyte 'maturation' medium (BA2). PM spheres were disassociated into single cells suspension using Accumax and seeded on Geltrex coated plate with BA1 medium. BA1 was composed of DM supplemented with the 8 ng/mL bFGF, 100 ng/mL BMP7, 200 ng/mL LONG® R3 human IGF-I, 10 mM Y-27632 dihydrochloride, 2uM Rosiglitazone,1 mM Dexamethasone, 1 nM T3 thyroid hormone, 500 mM IBMX (3-Isobutyl-1-methylxanthine) and 10 mM SB. Cells were cultured in BA1 for 8 days with media changes every 48 hrs. After initial priming stage, medium was switched to BA2. BA2 is formulated the same as BA1 excluding SB 431542 and supplemented with 1:500 Chemically Defined Lipid. Cells are maintained in BA2 with daily medium change for additional 35-40 days.

value: Brown adipocytes differentiated from H9ESC derived paraxial mesoderm

tag: time

value: differentiation time point day 50

tag: differentiation method

value: Brown adipocytes differentition using defined differentiation medium as described in the protocols section.

tag: forskolin treatment

value: NO


title: Retina WT 1


title: Mock hiPSC-CMs (rep 3)

status: Public on Jun 19 2020

data_processing:
Raw sequencing data was demultiplexed by bcl2fastq v.2.20
Raw reads obtained from RNA-Seq were aligned to the transcriptome using STAR (version 2.5.0) (Dobin A et al., 2013) / RSEM (version 1.2.25) (Li B and Dewey CN, 2011) with default parameters, using a custom human GRCh38 transcriptome reference downloaded from http://www.gencodegenes.org, containing all protein coding and long non-coding RNA genes based on human GENCODE version 33 annotation.
Expression counts for each gene in all samples were normalized by a modified trimmed mean of the M-values normalization method and the unsupervised PC analysis (PCA) was performed with DESeq2 Bioconductor package version 1.10.1in R version 3.6.3.
Each gene was fitted into a negative binomial generalized linear model, and the Wald test was applied to assess the differential expressions between two sample groups by DESeq2.
Benjamini and Hochberg procedure was applied to adjust for multiple hypothesis testing, and differential expression gene candidates were selected with a false discovery rate less than 0.05. For visualization of coordinated gene expression in samples, a two-way hierarchical clustering with Pearson correlation distance matrix was performed with samples and DEG candidates using the Bioconductor g-plots package (version 3.0.3) in R
Genome_build: GRCh38
Supplementary_files_format_and_content: expression matrix of raw counts in csv format

source_name: hiPSC-CMs

growth_protocol:
HiPSC Derivation:     The appropriate institutional review board (IRB) and stem cell research oversight committee (SCRO) were consulted at UCLA and Cedars-Sinai Medical Center. The 02iCTR hiPSC line was derived from human peripheral blood mononuclear cells and has been published previously (Laperle et al., 2020). This cell line was obtained from the Cedars-Sinai Medical Center iPSC core facility and was derived under their IRB-SCRO protocol “Pro00032834: iPSC Core Repository and Stem Cell Program”.
HiPSC-CM Differentiation:    The iPSC differentiation work in the Svendsen Lab is carried out under “Pro00021505: Svendsen Stem Cell Program”, authorized by the Cedars-Sinai Medical Center IRB. The hiPSC-CMs were generated from hiPSCs using a small-molecule mediated differentiation approach that modulates Wnt signaling (Sharma et al., 2015). Briefly, this approach uses the CHIR99021 GSK3β inhibitor to initiate mesoderm specification, followed by Wnt-C59 Wnt inhibitor to initiate cardiac specification. Cells began beating at approximately day 7 post-differentiation. Cardiomyocytes were metabolically selected from other differentiated cells by using glucose deprivation as previously described (Sharma et al., 2015). After selection, hiPSC-CMs were replated as a monolayer into 96-well plate format at 100,000 cells per well in hiPSC-CM culture medium, RPMI 1640 + B27 supplement with insulin.

extract_protocol:
Samples were harvested in TRIZOL and total RNA was extracted using a Qiagen RNAEasy Mini Kit, as per manufacturer's instructions.
The SMART-Seq V4 Ultra Low RNA Input Kit for Sequencing (Takara Bio USA, Inc., Mountain View, CA) was used for reverse transcription and generation of double stranded cDNA for library preparation using the Nextera XT Library Preparation kit (Illumina, San Diego, CA).  Total RNA quality was analyzed via the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and RNA quantified using QubitTM (ThermoFisher Scientific, Waltham, MA) fluorometric quantitation.  An input of 10 ng total RNA was used for oligo(dT)-primed reverse transcription, cDNA amplification, and cDNA cleanup.  The cDNA was analyzed on the 4200 TapeStation (Agilent Technologies).  Quantification of cDNA was performed using Qubit.  cDNA normalized to 30 pg/ml was fragmented and sequencing primers added simultaneously.  A limiting-cycle PCR added Index 1 (i7) adapters, Index 2 (i5) adapters, and sequences required for cluster formation on the sequencing flow cell.  Indexed libraries were cleaned up, library size verification performed on the 4200 TapeStation, and library quantified via Qubit.  Libraries were sequenced on a NextSeq 500 using with a 1x75 bp read length and coverage of ~60M reads/cell.

treatment_protocol: SARS-CoV-2 infection of hiPSC-CMs:     SARS-CoV-2, isolate USA-WA1/2020, was obtained from the Biodefense and Emerging Infections (BEI) Resources of the National Institute of Allergy and Infectious Diseases (NIAID). Importantly, all studies involving SARS-CoV-2 infection of hiPSC-CMs were conducted within a Biosafety Level 3 facility at UCLA. SARS-CoV-2 was passaged once in Vero-E6 cells and viral stocks were aliquoted and stored at -80oC. Virus titer was measured in Vero-E6 cells by TCID50 assay. Vero-E6 cells were cultured in DMEM growth media containing 10% fetal bovine serum, 2 mM L-glutamine, penicillin (100 units/ml), streptomycin (100 units/ml), and 10 mM HEPES. Cells were incubated at 37°C with 5% CO2.  For hiPSC-CM infection, viral inoculum (MOI of 0.01) was prepared using serum-free media. Culture media from each well containing hiPSC-CMs was removed and replaced with 250 µL of prepared inoculum. For mock infection, serum-free media (250 µL/well) alone was added. The inoculated plates were incubated for 1 hour at 37°C with 5% CO2. The inoculum was spread by gently tilting the plate sideways at every 15 minutes. At the end of incubation, the inoculum was replaced with fresh hiPSC-CM culture medium. Cells remained at 37°C with 5% CO2 for 72 hours before analysis.

value: Human iPSC-cardiomyocytes (hiPSC-CMs)

tag: infection

value: mock

tag: time (duration)

value: 72 hour infection (mock)


title: Retina WT 2

tag: strain


title: Mock hiPSC-CMs (rep 2)

tag: cell type


title: Mock hiPSC-CMs (rep 1)


title: SARS-CoV-2 Infected hiPSC-CMs (rep 3)

value: 72 hour infection (MOI 0.1)


title: SARS-CoV-2 Infected hiPSC-CMs (rep 2)


title: HUVEC_H_T3d_scRNA_2

description: Single-cell RNA sequencing assay

source_name: Human umbilical Vein Endothelial Cells treatment combining high glucose (HG, to mimic hyperglycemia) and TNFalpha (to mimic inflammation) for 3 days, replicate 2

value: HUVEC


title: H9ESC_BA_Day50CTR Rep2


title: SARS-CoV-2 Infected hiPSC-CMs (rep 1)


title: Drop-seq: RNA

status: Public on May 16 2020

city: Chicago

first: Hoang Van

last: Phan

address: 5640 S Ellis Ave

institute: The University of Chicago

description:
N701-SEEneg-cDNA_S1
Prox-seq using Drop-seq pipeline (Figure 2)

data_processing:
The first 19 bases of read 2 of Drop-seq cDNA fastq files were trimmed using FASTX-toolkit.
Drop-seq RNA data was processed with Drop-seq tools v2.3.0 from McCarroll lab, using the human reference genome GRCh38
Both Drop-seq and Smart-seq2 PLA probe barcodes were extracted from the raw reads using a custom Java program
Drop-seq data was analyzed with Seurat v3.0.2. Drop-seq RNA data: cells with fewer than 200 detected genes were removed, genes detected in fewer than 5 cells were removed, and only cells detected in both RNA and PLA data sets were kept. RNA data was log-normalized and scaled, PLA was CLR transformed and scaled. Cells were clustered and visualized with t-SNE
Smart-seq2 PLA data were processed using Python and RStudio. Cells with fewer than 500 detected UMIs were removed. The UMI count data was used for further analysis.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files containing UMI counts of genes and PLA products of each single cell

source_name: Jurkat and Raji cells

extract_protocol:
Single cells were lysed and captured by ceramics according to Drop-seq
Libraries were prepared according to a modified Drop-seq protocol
RNA and/or PLA products were extracted from single cells following Drop-seq and Smart-seq2 method.
sequencing library was prepared  from RNA and PLA products using tagmentation and PCR

value: Human-derived T and B cells

tag: passages


title: 2114127_6

status: Public on Jun 10 2020

city: Philadelphia

first: Tomoya

last: Sakamoto

address: Smilow Center for Translational Research 11th FL (Room 11-172) 3400 Civic Center Blvd Bldg 421

department: Cardiovascular Institute

institute: University of Pennsylvania

data_processing:
Sequenced reads were assessed with FastQC v0.11, then mapped to mm10 whole genome using STAR with the following parameter “--outSAMstrandField intronMotif” to indicate for RNA-seq read alignment.
Partek Genomics Suite v6.6 was applied for quantification based on RefSeq transcript model.
For differential gene expression analysis, we used edgeR to perform exact test. Genes were excluded in differential analysis if their expressions levels measured in RPKM were <=1 in all of the samples.
Genome_build: mm10

source_name: AAV-Luc-injected  ERRa/g floxed P35 ventricles

growth_protocol: ERRa and g floxed mice, kindly provided by Dr. Anastasia Kralli (Johns Hopkins), were injected with AAV-cTnT-Cre (Addgene #69916) or Luc (Addgene #69915) at postnatal day 0 to 1 to generate cardiac-specific ERRa and ERRg postnatal KD mouse. The bi-ventricles of the mice were harvest at P35.

extract_protocol:
Bi-ventricles were harvested from the P35 mice and RNA was harvested using Qiazol (QIAGEN). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA).
The sequencing libraries were clustered on a single lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

value: Postnatal age 35 days

value: Luc (Addgene #69915)


title: 2114127_4


title: Drop-seq: PLA Jurkat and Raji

description:
Jurkat_Raji_Dropseq_PLA_count.txt.gz
Prox-seq using Drop-seq pipeline (Figure 2)

extract_protocol:
Single cells were lysed and captured by ceramics according to Drop-seq
Libraries were prepared by PCR to attach custom sequencing adapters
RNA and/or PLA products were extracted from single cells following Drop-seq and Smart-seq2 method.
sequencing library was prepared  from RNA and PLA products using tagmentation and PCR


title: Smart-seq2: PLA  Jurkat and Raji

description:
Jurkat_Raji_plate_PLA_count.txt.gz
Prox-seq using Smart-seq2 pipeline (Figures 2 and 3)

data_processing:
The first 19 bases of read 2 of Drop-seq cDNA fastq files were trimmed using FASTX-toolkit.
Drop-seq RNA data was processed with Drop-seq tools v2.3.0 from McCarroll lab, using the human reference genome GRCh38
Both Drop-seq and Smart-seq2 PLA probe barcodes were extracted from the raw reads using a custom Java program
Drop-seq data was analyzed with Seurat v3.0.2. Drop-seq RNA data: cells with fewer than 200 detected genes were removed, genes detected in fewer than 5 cells were removed, and only cells detected in both RNA and PLA data sets were kept. RNA data was log-normalized and scaled, PLA was CLR transformed and scaled. Cells were clustered and visualized with t-SNE
Smart-seq2 PLA data were processed using Python and RStudio. Cells with fewer than 500 detected UMIs were removed. The UMI count data was used for further analysis.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files containing UMI counts of genes and PLA products of each single cell
Supplementary_files_format_and_content: tab-delimited text files containing UMI counts of genes and PLA products of each single cell

extract_protocol:
Single cells were sorted into 96-well plates and lysed according to Smart-seq2
Libraries were prepared by PCR to attach custom sequencing adapters
RNA and/or PLA products were extracted from single cells following Drop-seq and Smart-seq2 method.
sequencing library was prepared  from RNA and PLA products using tagmentation and PCR


title: 2114127_3

source_name: AAV-Cre-injected  ERRa/g floxed P35 ventricles

value: AAV-cTnT-Cre (Addgene #69916)


title: No_Cholesterol_C

status: Public on Apr 21 2020

city: Houston

first: Benson

last: Otarigho

state: Texas

address: 6767 Bertner Avenue

department: Department of Genetics

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Fq file dataset were uploaded into Galaxy Tool Version 2.11.40.2 that was used for the analyses
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Caenorhabditis elegans genome WS220
The  htseq-count were further analyesd for the  differentially expressed features from count tables using DESeq2
Genome_build: Caenorhabditis elegans genome WS220
Supplementary_files_format_and_content: tabular files include htseq-count/values for each Sample ...

organism: Caenorhabditis elegans

source_name: Whole organism

growth_protocol: Approximately 40 gravid animals were placed for 3 hours on 10-cm NGM plates (seeded with E. coli OP50) in order to have a synchronized population, which developed and grew to L4 larval stage at 20oC

extract_protocol:
Total RNA was extracted using the RNeasy Plus Universal Kit (Qiagen, Netherlands). Purification of Total RNA was done using the TURBO DNase.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

treatment_protocol: Animals were washed off the plates with M9 and frozen in QIAzol by ethanol/dry ice and stored at -80 prior to RNA extraction.

value: Wild type

value: Whole organism

value: L4 stage

value: 0µg/ml cholesterol


title: No_Cholesterol_A


title: 2117354_1


title: 2114134_2


title: 2114134_1


title: donor_23_mac_CD31_pos

status: Public on Apr 23 2020

city: Iowa City

first: Andrew

last: Voigt

state: Iowa

address: 375 Newton Road

institute: University of Iowa

data_processing:
FASTQ files were generated from the raw BCL files using Illumina’s bcl2fastq conversion program.
Sequenced reads were mapped to the CellRanger human genome build hg19 (v3.0.0) with CellRanger (v3.0.1) using the CellRanger default human GTF and the following parameter: --expect-cells=8000.
The sixteen samples (paired samples from eight single-cell donors, including 4 previously described donors in GSE135922) were collectively aggregated with the cellranger aggr function with the following parameter: --normalized=mapped.
Cells were filtered with the Seurat (v3.0.2) subset function. Cells with nUMIs less than 1100 (to remove cells with poor read quality) or greater than 10000 (to remove cells likely to be doublets) were removed. Cells with greater than 30% of reads originating from mitochondrial genes were also removed. Mitochondrial genes were identified with the following command: seurat_obj[["mito.genes"]] <- PercentageFeatureSet(seurat_obj, pattern = "^MT-")
For each of the sixteen libraries, reads were normalized with the Seurat (v3.0.2) NormalizeData function, and variable features were found with the following commands: my_choroid_object <- NormalizeData(my_choroid_object, normalization.method = "LogNormalize", scale.factor = 10000), my_choroid_object <- FindVariableFeatures(my_choroid_object, selection.method = “vst”, nfeatures = 2000)
Integration anchors from the first 25 dimensions of the canonical correlation analysis were used to integrate data with the following commands: choroid.anchors <- FindIntegrationAnchors(object.list = my_choroid_object_list, dims=1:25), choroid.combined <- IntegrateData(anchorset = choroid.anchors, dims = 1:25)
Data scaling, principal component analysis, and clustering were performed with the following commands: CD31.combined <- ScaleData(CD31.combined, verbose = FALSE), CD31.combined <- RunPCA(CD31.combined, npcs = 30, verbose = FALSE), CD31.combined <- RunUMAP(CD31.combined, reduction = "pca", dims = 1:23), CD31.combined <- FindNeighbors(CD31.combined, reduction = "pca", dims = 1:23), CD31.combined <- FindClusters(CD31.combined, resolution = 0.35)
Genome_build: hg 19
Supplementary_files_format_and_content: Processed expression data matrix files are provided in tab-delimited format for count(*_count.tsv) and processed/normalized (*_processed) expression values. For processed/normalized files, log-normalized expression values (from GetAssayData(object = seurat_object)) were appended to relevant metadata (barcode, cluster label, and donor number from the manuscript). Each row represents a unique cell, and columns correspond to metadata and log normalized gene expression values. For count files, raw counts were obtained (from GetAssayData(object = seurat_object, slot = “counts”)) for each cell type in each cluster and appended to relevant metadata (barcode, cluster label, and donor number from the manuscript).

source_name: RPE/choroid

extract_protocol:
A 12-mm macular centered punch of RPE/choroid was acquired from four human donors (Donors 8-11). After dissection away from the retina and sclera, the RPE/choroid was finely diced into small squares (approximately 1 mm x 1 mm) with a razor blade. The resulting suspension was dissociated in 450 units/mL of collagenase II (Gibco, Grand Island NY) reconstituted in Hank’s Balanced Salt Solution containing calcium chloride and magnesium chloride (Life technologies, Grand Island NY). Dissociated cells were resuspended in DMSO-based Recovery Cell Culture Freezing Media (Life Technologies Corporation, Grand Island NY). Suspensions were placed in a Cryo-Safe cooler (CryoSafe, Summerville SC) to cool at 1°C/minute in a -80°C freezer for 3-8 hours before storage in liquid nitrogen.
Cryopreserved cells from single-cell donors 22-25 were rapidly thawed before pre-enrichment for endothelial cells. Cells were incubated for 15 minutes with anti-CD31 microbeads (Miltenyi Biotech, Bergisch Gladbach Germany) according to the manufacturer’s instructions before automated autoMACs magnetic separation (Miltenyi Biotech, Bergisch Gladbach Germany) into CD31+ and CD31-cell fractions. Sequencing of both CD31-positive and CD31-negative fractions was performed on pooled libraries using the Illumina NovaSeq platform (San Diego, CA).
Single-cell RNA-Seq

tag: region

value: macula

value: positive

value: adult


title: Cholesterol_1_C

value: 5µg/ml cholesterol (control)


title: Ch_4_C

data_processing:
Fq file dataset were uploaded into Galaxy Tool Version 2.11.40.2 that was used for the analyses
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Caenorhabditis elegans genome WS220
The htseq-count were further analyesd for the differentially expressed features from count tables using DESeq2
Genome_build: Caenorhabditis elegans genome WS220
Supplementary_files_format_and_content: tabular files include htseq-count/values for each Sample

value: Wild type (N2)

value: 20µg/ml cholesterol


title: Cholesterol_1_B


title: No_Cholesterol_B


title: Cholesterol_1_A


title: Ch_1_C


title: Ch_1_A


title: Ch_4_A


title: 2117354_2


title: Ch_1_B


title: 2114127_5


title: Brain, Re-Cappable-seq enrich library, replicate 2

status: Public on Apr 10 2020

city: Ipswich

first: Bo

last: Yan

state: MA

address: County Road

institute: New England Biolabs

description:
Re-Cappable-seq enrich library, replicate 2
5'end sequencing

data_processing:
adapter sequence was trimmed using trim_galore
The trimmed reads were mapped to the human genome using STAR
The number of reads starting at any position were counted using a customized script
Genome_build: gencode GRCh38.p5 Release 24
Supplementary_files_format_and_content: tab-delimited gtf file
Supplementary_files_format_and_content: number of reads starting at TSS

source_name: illumina

extract_protocol:
Total RNA was purified using Trizol
NEB Small RNA library prep

value: Brain


title: donor_22_mac_CD31_pos


title: Brain, Re-Cappable-seq enrich library, replicate 1

description:
Re-Cappable-seq enrich library, replicate 1
5'end sequencing


title: A549 total RNA-seq

description: total RNA RNA-seq

growth_protocol: Human lung carcinoma A549 cells (ATCC) were cultured in F12 media supplemented with L-glutamine.

extract_protocol:
Total RNA was purified using the RNeasy RNA purification kit (Qiagen)
NEB Ultra II

value: A549 cancer cell


title: A549 rRNA depletion RNA-seq

description: rRNA del RNA-seq

extract_protocol:
Total RNA was purified using the RNeasy RNA purification kit (Qiagen)
NEB rRNA depletion and NEB Ultra II