title: WMD8

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Sequenced reads were quality-tested using FASTQC.
Reads were aligned to the D. melanogaster genome dm6 (from The FlyBase Consortium/Berkeley Drosophila Genome Project/Celera Genomics) using the alignment algorithm STAR84 (version 2.5.3a). Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations) and --outFilterIntronMotifs RemoveNoncanonical.
Raw gene expression was quantified using the software HOMER across exons, and the top isoform value was used to represent gene expression.
In brief, cells containing the bottom 10% of cell counts were filtered, TMM normalization and size-factor correction was applied using the edgeR package, and cells falling in the bottom 5% of normalized counts were removed. Then, the bottom 10% of genes with normalized counts > 32 in a cell were removed as non-expressed genes.
Expression values were log2 transformed, and tSNE was performed to generate the plots.
The scrattch.hicat R package was used to perform hierarchical iterative clustering on the normalized expression table.
For differential expression analysis between the wild-type and ∆nvy mutant, genes with expression values of 0 in 75% or more of the cells were filtered out. Genes that met the following criteria were considered as DEGs: (1) p-values by Mann-Whitney U-test lower than 0.05, (2) adjusted p-values by Benjamini-Hochberg FDR test lower than 0.2, and (3) the fold-change greater than 10 (|log2FC| > 3.321928095).
For DEGs that showed behavioral phenotypes in the RNAi experiments, predicted biological processes and human orthologs were taken from the “Gene Ontology” and “Human Orthologs (via DIOPT v7.1)” sections in FlyBase (http://flybase.org/), respectively.
Genome_build: dm6
Supplementary_files_format_and_content: raw count table in tab-delimited text format

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: Fruit flies were used. Animals were reared in groups of 15 individuals, from eclosion to day 6 in vials with standard fly medium.

extract_protocol:
Single cells were sorted via fluorescent-activated cell sorting. Each cell was sorted in a separate well of a 96 well plate  filled with freshly made lysis buffer, prepared according to Takara standard protocol. The contact with the lysis buffer lysed the cells, freeing their content, mRNA included. As soon as collection was completed (15-20 minute/genotype), samples were frozen in dry ice and stored until used at -80°C.
Sequencing libraries were prepared using the Nextera XT kit (Illumina #FC-131-1096) and mixed into 24 pools (12 samples per pool).After purification using the Agencourt AMPure XT beads (Beckman Coulter #A63881), the sample quality was checked with both the Qubit 3 Fluorometer and the High Sensitivity D1000 ScreenTape assay (Agilent Technologies #5067-5584). The libraries were equimolarly pooled, and the final concentration was estimated by qPCR. Sequencing of 75 bp paired-end reads was performed with the Illumina Nextseq 500 sequencer.
Nextera XT

treatment_protocol: Wild-type and nervy-mutant frui flies were reared in groups for 6 days, anestethized on ice and dissected in Schneider's Drosophila medium

value: single octopaminergic/tyraminergic neuron, expressing a membrane-bound GFP reporter.

value: Wildtype

tag: collection strategy

value: Fluorescent-Activated Cell Sorting


title: WMD7

status: Public on Jun 22 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: Sex

value: Male

tag: cell type

tag: genotype


title: 11_R

city: Fort Collins

first: Thomas

middle: J

last: LaRocca

state: CO

address: 1582 Campus Delivery

institute: Colorado State University

data_processing:
Adapters trimmed & file QC by Fastp
Reads aligned with STAR (hg38) and counting with LiBiNorm
Differential expression analyzed with DESeq2
Supplementary files format and content: count matrix

molecule: polyA RNA

organism: Homo sapiens

source_name: healthy adult woman

extract_protocol:
RNA for polyA RNA-seq extracted using Trizol and Zymo spin columns.
PolyA libraries were prepared according to manufacturer's instructions using the Illumina TruSeq kit

tag: pre or post

value: pre

tag: r or nr

value: R

value: PBMC

value: female


title: WMD5


title: NM32-3

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

data_processing:
Image analysis and base calling performed by RTA 2.0
Reads were aligned to the mm10 version of the mouse genome as reference using STAR v2.7.3a after removal of contaminants  (rDNA, tRNA, mtrDNA) were removed using Bowtie2 (version 2.2.5)
Reads aligned to STAR were quantified to the mm10-RefSeq Transcripts v99 (released 2021-08-02)and normalized by TMM and transformed by log2 (TMM + 1 + log2)
Normalized counts were used to determine differential gene expression between the groupus by DESEQ2
All analyses were corrected for multiple comparisons at false discovery rate (FDR) 0.05 (at least)
Genome_build: mm10
Supplementary_files_format_and_content: txt files contain raw and normalized counts

organism: Mus musculus

source_name: Bone marrow from femur

extract_protocol:
Bone marrow was released from femurs by centrifugation at 5700 g for 30 seconds into RNAlater followed by TRI Reagent lysis and RNA isolation by the TRI Reagent protocol
Illumina Stranded mRNA Prep protocol, mRNA from total RNA via oligo-dt magnetic beads then converted to cDNA, fragmented and end repaired, then 3’ ends adenylated and ligated with pre-index anchors, ligated fragments amplified and indexed then multiplexed and sequenced on the Illumina NextSeq 500.

tag: age

value: 32 weeks old


title: WMD6


title: PM1

value: 3 weeks old

value: PrxCre +/ Nox4 fl/fl


title: NM32-2


title: 9_R


title: NM32-1


title: 10_R

value: post


title: 7_R


title: 8_R


title: NM3


title: WMD3


title: limbDistBlack

city: Dunedin

first: Caroline

last: Beck

state: Otago

address: 340 Great King Street, North Dunedin

department: Zoology

country: New Zealand

institute: University of Otago

description: distal limb bud sample 1

data_processing:
Basecall completed by sequencing facility using bcl2fastq
Raw data was trimmed and filtered with trimmomatic (version 0.39) using the following parameters: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 MINLEN:36
An index of the latest Xenopus laevis genome (XENLA_9.2) was built using HISAT2 (version 2.2.1), this was used to align sequenced transcripts
BAM files were converted to SAM files and sorted using samtools (version 1.10)
Alignments in sorted SAM files were counted with featureCounts (version 2.0.1)
Differential expression was calculated using the R package DESeq2 (version 1.30.1)
Genome_build: XENLA_9.2
Supplementary_files_format_and_content: tab-delimited text file including counts of each alignment for each sample
Supplementary_files_format_and_content: tab-delimited text file summary of counting process
Supplementary_files_format_and_content: comma seperated file including all differentially expressed genes that meet a significance threshold of 0.05
Supplementary_files_format_and_content: featureCounts RNA-Seq count table
Supplementary_files_format_and_content: featureCounts summary file
Supplementary_files_format_and_content: Genes with significant differential expression, calculated by DESeq2

organism: Xenopus laevis

source_name: tadpole limb bud

growth_protocol: wild type

extract_protocol:
Qiagen RNeasy mini kit, following manufacturers protocol, on column DNase treatment
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries using standard Illumina protocols

tag: strain

value: wildtype

tag: developmental stage

value: Stage 51 tadpole

tag: tissue

value: hind limb


title: WMD22


title: limbDistRed

description: distal limb bud sample 2


title: 6_R


title: 14_NR

value: NR


title: WMD1


title: NM1


title: 4_R


title: limbMidRed

description: medial limb bud sample 2


title: NF32-3

value: Female


title: 5_R


title: limbProxRed

description: proximal limb bud sample 2


title: limbMidBlack

description: medial limb bud sample 1


title: WMD2

value: single octopaminergic/tyraminergic neuron, expressing a membrane-bound GFP reporter.


title: NF32-2


title: NF32-1


title: limbProxBlack

description: proximal limb bud sample 1


title: WMD17

value: Wildtype


title: 3_R


title: NM2


title: 2_R


title: WMD15

value: Fluorescent-Activated Cell Sorting


title: 1_R


title: NF3


title: WMD14

value: Male


title: NF2


title: NF1


title: VERO E6_T16B_SARS-CoV-2, IC90

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

country: Canada

institute: University of Toronto

library_source: genomic

data_processing:
Library strategy: CRISPRseq
FASTQ files were pre-processed to extract Cas9 guide sequence using a bespoke Perl script.
The Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'.
Trimmed FASTQ files were then aligned to the TKOv3 FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.
Supplementary_files_format_and_content: tab-delimited read count matrix

molecule: genomic DNA

organism: Chlorocebus sabaeus

source_name: kidney epithelium cell line

growth_protocol: Cells were cultured in DMEM or EMEM media (as indicated) supplemented with 10% FBS and 1% Penicillin/Streptomycin and serially passaged for up to 15 doublings each, in triplicates.

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA Purification kit (Promega) or QIAamp DNA mini kit according to manufacturer’s instructions
For each sample, the gRNA cassette was amplified directly from genomic DNA using primers harboring Illumina TruSeq adaptors with i5 and i7 barcodes. The resulting sequencing libraries were pooled and gel-purified.

treatment_protocol: Cells that exhibited cytopathic effects (CPE) were infected at low MOI (Calu-3: 0.0005; Vero E6: 0.001, HEK293+A+T: 1) in serum free media for 1hr, virus inoculum was removed and replaced with regular culture media, after >80% CPE was achieved, surviving cells were maintained in standard media until confluence was reached.  Cells that did not exhibit CPE were infected at MOI 1 Huh7 or MOI  10 (Caco-2) and were repeatedly exposed to fresh virus at every passage for 3 rounds.

tag: cell line

value: VERO E6

tag: crispr library

tag: treatment

value: Infected w/ SARS-CoV-2 at IC90

tag: growth medium

value: DMEM + 10% FBS +1% PenStrep


title: WMD21


title: VERO E6_T16A_SARS-CoV-2, IC90


title: WMD18


title: WMD12


title: VERO E6_T7C_Control

value: Control


title: WMD11


title: human right ventricle rep 1

city: Akita

first: Yosuke

last: Okamoto

address: 1-1-1 Hondo

department: Cell Physiology

country: Japan

institute: Akita University Graduate School of Medicine

data_processing:
NovaSeq Control software v1.4.0 was used for basecalling.
fastp software (version 0.12.4) was used for read quality control and adapter removal.
Reads were aligned using STAR software (version 2.7.0a).
The fasta and gtf files of GRCh38/release105 obtained from the Ensemble database were used as reference genome and gene annotation information. The count values of each gene were quantified from the alignment results by featureCounts software. We calculated the Transcripts Per Kilobase Million (TPM) values based on the calculated gene lengths and gene counts
Assembly: GRCh38
Supplementary files format and content: Comma separted values (CSV) file indludes Transcripts Per Kilobase Million (TPM) values.

source_name: donated heart

extract_protocol:
RNAs were extracted in our laboratory using QIAGRNAs were extracted in our laboratory using QIAGEN RNeasy mini columns (Cat. No. 74004).
First, extracted RNAs were purified by poly(A) capture. Resultant mRNAs were then fragmented and reverse-transcribed into single-stranded complementary DNAs (cDNAs). Subsequently, cDNAs were double-stranded by a DNA polymerase. During the polymerase reactions, deoxy UTP (dUTP) were mixed in nucleotide materials. Both ends of double-stranded DNA (ds DNA) were ligated to a 13 bp adapter sequence. Next, the ds DNAs were subjected to PCR amplification for the multi-sized DNA library preparation.

value: human right ventricle

value: male


title: VERO E6_T7B_Control


title: human right ventricle rep 2


title: human sinoatrial node rep 3

value: human sinoatrial node

value: female


title: VERO E6_T16C_SARS-CoV-2, IC90


title: WT_HSC_3

city: Kumamoto

first: Tomomasa

last: Yokomizo

address: 2-2-1 Honjo, Chuo-ku

institute: Kumamoto University

data_processing:
mRNA profile generated by deep sequencing using Illumina Next-Seq 500.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2.
Transcripts per kilobase million (TPM)  were calculated by StringTie.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: WT HSCs

growth_protocol: Mice were housed in a specific-pathogen free animal facility.

extract_protocol:
Lysis buffer containing 100 cells was directly used for cDNA synthesis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Single-cell suspensions were prepared by mechanical dissociation. Hematopoietic fractions were isolated by cell sorter.

value: fetal liver

tag: Stage

value: Embryonic day 14.5

tag: markers


title: WT_KL_3

source_name: WT KLs


title: VERO E6_T7A_Control


title: WT_KL_2


title: human right ventricle rep 3


title: VERO E6_T0


title: WT_HSC_2


title: human sinoatrial node rep 1


title: WMB7


title: WT_KL_1


title: WMB6


title: human pulmonary vein rep 2

value: human pulmonary vein


title: human pulmonary vein rep 3


title: WT_HSC_1


title: WMB4


title: WMB3


title: human left ventricle rep 3

value: human left ventricle


title: YS_3

source_name: nascent hematopoietic cells

treatment_protocol: Single-cell suspensions were prepared by treating tissues with collagenase [0.125% in PBS/10% fetal calf serum (FCS)/1% penicillin/streptomycin] for 1 h at 37°C. Hematopoietic fractions were isolated by cell sorter.

value: yolk sac

value: nascent hematopoietic cells

value: Embryonic day 10.5

value: Hlf-tdTomato knock-in


title: Evi1_HSC_3

source_name: Evi1-induced HSCs


title: Evi1_HSC_1


title: WMB5

value: Male

value: single octopaminergic/tyraminergic neuron, expressing a membrane-bound GFP reporter.

value: Wildtype

value: Fluorescent-Activated Cell Sorting


title: WMB8


title: WMB35


title: WMD10


title: Evi1_HSC_2


title: WMB33


title: human pulmonary vein rep 1


title: WMB9


title: human sinoatrial node rep 2


title: human left ventricle rep 2


title: EP_2

value: caudal half


title: WMB36


title: EP_1


title: human left ventricle rep 1


title: YS_2


title: human left appendage rep 3

value: human left appendage


title: human right atrium rep 1

value: human right atrium

value: male


title: WMB29


title: human left appendage rep 2

value: female


title: YS_1


title: EP_3


title: WMB28


title: WMB34


title: human left appendage rep 1


title: WMB32


title: WMB31


title: WMB26


title: human right atrium rep 3


title: WMB27


title: WMB30


title: human right atrium rep 2


title: human left atrium rep 2

value: human left atrium


title: Aif1-/- rep3

city: Bronx

first: Prameladevi

last: Chinnasamy

state: New York

address: Golding 105

department: Medcine-Cardiology

institute: Albert Einstein College of Medicine

data_processing:
Base calls from Illumina HiSeq 500 Sequencing System
Adapters were removed from reads with trim_galore (v0.5) under default parameters
Reads were mapped to GRCm38  reference with tophat (v2.0.13) with parameters: --no-coverage-search -p 1 -g 1
gene counts were generated with htseq (v0.6.1p1) using parameters: --strand=no and using release 84 of the GRCm38 ensembl geneset:    ftp://ftp.ensembl.org/pub/release-84/gtf/mus_musculus/Mus_musculus.GRCm38.84.gtf.gz
Genome_build: GRCm38
Supplementary_files_format_and_content: count files are tab delimited txt containing the number of reads mapped to each gene.

source_name: Bone Marrow  derived Macrophages

growth_protocol: Bone marrow derived monocytes isolated from the femur and tibia of 8 week old WT and Aif1-/- mice were differentiated into macrophages and immortalized with SV40 large T antigen.  These immortalized macrophage cell lines were maintained in α-MEM containing 10% FBS, 120 ng/ml CSF-1 (Chiron Corp), 1% penicillin, 1% streptomycin, and 1% L-glutamine.

extract_protocol:
Cell monolayers were harvested by trizol (Invitrogen/Life Technologies) and total RNA was extracted according to the manufacturer's protocol.
Total RNA (200 ng) was used to prepare libraries using KAPA Stranded RNA-seq kit with RiboErase as described (Kapabiosystems, KR1151-v3.15). Briefly, total RNA was subjected to rRNA depletion, and double stranded cDNA (dscDNA) was synthesized followed by fragmentation. A- tailing was done at the 3’end of the dscDNA library fragments and then subjected to library amplification followed by adapter ligation for Illumina sequencing. Control RNA was spiked in (ERCC RNA Spike-In control mixes, Life Technologies) as an internal control for the library preparation and sequencing. PCR-amplified cDNA libraries were quantified on the Agilent 2100 Bioanalyzer and diluted to 10 pM for cluster generation and sequencing.

value: Cultured Bone Marrow Macrophages

tag: passages

value: 3 to 5


title: Aif1-/- rep1


title: WT rep3

value: WT


title: WMB2

tag: collection strategy


title: Aif1-/- rep2


title: human left atrium rep 3

tag: Sex


title: WT rep1

tag: cell type


title: human left atrium rep 1


title: WT rep2

tag: genotype


title: WMB24


title: VDD HF female 3

city: Marseille

first: Jean-Francois

last: Landrier

address: 27 Boulevard Jean Moulin

country: France

description:
vdd_lf_f_vs_vdd_hf_f.txt
ctrl_hf_f_vs_vdd_hf_f.txt

data_processing:
Sickle was used to eliminate reads having a phred score of less than 20 and a length of less than 25 bp (v1,33).
MultiQC was used to assess the quality of the trim reads (v1.0)
Trim readings were aligned with the STAR aligner (v2.7.0d) with the "outFilterMis-  matchNoverLmax" and "outFilter- MultimapNmax" options set to 0.08 and 1, respectively.
Cufflinks (v2.2.1) was used to find transcripts, with the "library-type" option set to fr- firstrand and a GTF file obtained from GENCODE ("Comprehensive gene annotation,"  vM1) serving as the genomic annotation.
Cuffmerge was used to integrate the GTF files  created by Cufflinks for each sampl
Unknown transcripts (class code“u”) were identified using the “class code” supplied  by Cuffmerge to each transcript
For further analysis, only de novo transcripts with counts  greater than 0 in at least one RNA-seq sample were preserved
These newly created tran-  scripts were joined with the GENCODE GTF file to create the final genomic annotation,  which was then quantified using FeatureCounts (v1.6.1).
DESEQ2 was used to compare  gene expression patterns between conditions.
Reads from Watson and Crick strands were  picked using SAMtools (v1.9) and sent into the RseQC program suite's bam2wig.py script  to build bigwig files (v2.6.4).
The IGV genome browser was used to visualize RNA-seq  profile
Assembly: mm10
Supplementary files format and content: txt
Supplementary files format and content: txt

source_name: white adipose tissue

growth_protocol: Males and females offspring, at 6 weeks old were randomly assigned to receive a low fat diet (AIN-93M Maintenance Purified Diet) or a high fat diet (DIO Rodent Purified Diet with   45% Energy from Fat) for 8 weeks.

extract_protocol:
TRIzol reagent (Thermo Fischer Scientific, Les Ulis, France) was used to extract total 89 RNA from retroperitoneal adipose tissue
Illumina TruSeq  Stranded mRNA kit

treatment_protocol: Female mice (15 per group) were randomly assigned to one of two experimental groups: control (CTRL, AIN-93G with vitamin D3, 1.0 IU/g) or vitamin D deficient (VDD, AIN-93G without vitamin D3, 0.0 IU/g) for 8 weeks, and then were mated with the males.  After birth, the females were all fed the control diet (AIN-93G) until weaning of the offsprings.    diet (AIN-93M Maintenance Purified Diet) or a high fat diet (DIO Rodent Purified Diet with   45% Energy from Fat) for 8 weeks.  offspring.

value: white adipose tissue

value: adipose tissue

value: vitamin D deficient mothers (VDD, AIN-93G without vitamin D3, 0.0 IU/g) + High fat diet (DIO Rodent Purified Diet with 45% Energy from Fat)


title: VDD LF female 3

description:
ctrl_lf_f_vs_vdd_lf_f.txt
vdd_lf_f_vs_vdd_hf_f.txt

value: vitamin D deficient mothers (VDD, AIN-93G without vitamin D3, 0.0 IU/g) + Low fat diet (AIN-93M Maintenance Purified Diet)


title: VDD HF female 2


title: WMB23

value: Male


title: VDD HF female 1


title: WMB20

value: single octopaminergic/tyraminergic neuron, expressing a membrane-bound GFP reporter.


title: WMB22

value: Wildtype


title: CTRL HF female 2

description:
ctrl_lf_f_vs_ctrl_hf_f.txt
ctrl_hf_f_vs_vdd_hf_f.txt

value: CTRL mothers (CTRL, AIN-93G with vitamin D3, 1.0 IU/g) + High fat diet (DIO Rodent Purified Diet with 45% Energy from Fat)


title: CTRL HF female 1


title: CTRL LF female 3

description:
ctrl_lf_f_vs_ctrl_hf_f.txt
ctrl_lf_f_vs_vdd_lf_f.txt

value: CTRL mothers (CTRL,  AIN-93G with vitamin D3, 1.0 IU/g) + Low fat diet (AIN-93M Maintenance Purified Diet)


title: WMB17

value: Fluorescent-Activated Cell Sorting


title: WMB15


title: VDD LF female 2


title: VDD LF female 1


title: WMB21


title: WMB12


title: CTRL LF female 1


title: CTRL HF female 3


title: WMB19


title: WMB11


title: WMB1


title: WMB25


title: WMB13


title: VDD HF male 3

description:
vdd_lf_m_vs_vdd_hf_m.txt
ctrl_hf_m_vs_vdd_hf_m.txt


title: WMB14


title: WMB10


title: CTRL LF female 2


title: VDD HF male 1


title: VDD LF male 1

description:
ctrl_lf_m_vs_vdd_lf_m.txt
vdd_lf_m_vs_vdd_hf_m.txt


title: WFD4

value: Female


title: VDD LF male 2


title: WFD3


title: CTRL HF male 3

description:
ctrl_lf_m_vs_ctrl_hf_m.txt
ctrl_hf_m_vs_vdd_hf_m.txt


title: WFB9


title: WFD2


title: VDD HF male 2


title: CTRL HF male 1


title: WFD1


title: WMB16


title: WFB7


title: CTRL HF male 2


title: WFD5


title: VDD LF male 3


title: siSF3B1_Input_rep1

city: Zurich

first: Patrik

last: Simmler

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

data_processing:
SnakePipes “ChIP-seq” pipeline34 was used for the analysis of the sequencing data according to the developer’s guidelines.
In brief, reads were trimmed, deduplicated and aligned simultaneously to the masked genomes of homo sapiens (GRCh38.p13) and drosophila melanogaster (BDGP6.32) published by Ensembl. Three replicates for each condition were used.
On average, 86 million (SD: 18 million) reads per sample were uniquely mapped to the hybrid genome.
Peaks were identified by MACS235, using merged reads of two chromatin inputs per condition for background normalization.
Assembly: GRCh38.p13
Supplementary files format and content: bigwig files

source_name: PDAC cell line (ATCC)

growth_protocol: Panc1 cells were treated either with control siRNA (siCtrl) or siRNA targeting SF3B1 (siSF3B1) and exposed 1% O2 for 8 hours.

extract_protocol:
Cells were fixed in paraformaldehyde (3.7%) for 5 minutes under hypoxia, then glycine was added for 7 minutes to quench the reaction. Cells were collected by scraping and spun down at 500g for 5 minutes. The pellet was frozen for subsequent ChIP reaction.
The NEBNext® Ultra™ II DNA Library Prep Kit from NEB ( New England Biolabs, Ipswich, MA) in the succeeding steps. ChIP samples (1 ng) were end-repaired and adenylated.  Adapters containing the index for multiplexing were ligated to the fragmented DNA samples. Fragments containing adapters on both ends were enriched by PCR.  The quality and quantity of the enriched libraries were measured using Qubit® (1.0) Fluorometer and the Tapestation (Agilent, Waldbronn, Germany).  The product is a smear with an average fragment size of approximately 300 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The libraries were sequenced single read 100 bp using the Illumina Novaseq 6000 (Illumina, Inc, California, USA). Reads were quality-checked with fastqc which computes various quality metrics for the raw reads.

treatment_protocol: HIF1a ChIP was performed after 8 hours of incubation in hypoxia according to standard protocol (see manuscript for more details)

tag: protocol

value: Hypoxia

tag: sirna

tag: fraction

value: Input-DNA

tag: antibody


title: siCtrl_Input_rep3

value: siCtrl


title: CTRL LF male 3

description:
ctrl_lf_m_vs_ctrl_hf_m.txt
ctrl_lf_m_vs_vdd_lf_m.txt


title: siSF3B1_Input_rep3


title: CTRL LF male 2


title: CTRL LF male 1


title: siCtrl_Input_rep1


title: WFB6


title: siSF3B1_ChIP_rep4

value: ChIP-DNA

value: Antibody HIF-1α (D2U3T) Rabbit mAb #14179 (CellSignaling-Technologies) was used for ChIP


title: siSF3B1_ChIP_rep3


title: WFB5


title: siSF3B1_ChIP_rep5


title: WFB46


title: treat_Merip_rep3

city: hangzhou

first: wenzheng

last: qu

address: Kaixuan Road

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.
Fragments Per Kilobase of transcript sequence per  Millions (FPKM) were calculated based on the length of the gene and reads count mapped  to this gene.FPKM considers the effect of sequencing depth and gene length for  the reads count at the same time, and is currently the most commonly used method for  estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include count and FPKM values for each Sample and genes.

source_name: hippocampus

extract_protocol:
Total RNA was harvested using Trizol reagent from brain samples.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: New born pups were randomly grouped, and housed in standard cage and different environment.

value: hippocampus

tag: strain

value: untreated

tag: molecule subtype

value: IP RNA

tag: rip antibody


title: WFB8


title: WFB4


title: treat_Merip_rep2

tag: tissue


title: siCtrl_ChIP_rep4

tag: cell line


title: siCtrl_ChIP_rep5


title: WFB45


title: ctrl_Merip_rep2

tag: treatment


title: siCtrl_ChIP_rep3


title: ctrl_Merip_rep1


title: treat_rep3

value: total RNA


title: rHAPLN1_1.R3

city: Shenzheng

first: Yong

last: Chen

state: China

address: No. 1017, Dongmen North Road, Luohu District, Shenzhen, Shenzhen P. R. China.

institute: Shenzhen People's Hospital

data_processing:
Raw sequencing data was first filtered by Trimmomatic (v. 0.36), and low-quality reads were discarded. The reads contaminated with adaptor sequences were trimmed.
Clean data were mapped to the human reference genome from UCSC (https://genome.ucsc.edu/) using STRA software (v. 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by feature Counts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Assembly: hg19,human reference genome from UCSC (https://genome.ucsc.edu/).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

source_name: Knee joint synovium

extract_protocol: Total RNA (2 g) was used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Seqhealth Co., Ltd. China). PCR products corresponding to 200-500 bps were enriched, quantified and sequenced with Novaseq 6000 sequencer (Illumina), PE150 model.

treatment_protocol: Fibroblast-like synoviocytes (FLSs) treated with rHAPLN1 (50 ng/ml) for 48 h.

value: Fibroblast-like synoviocytes


title: rHAPLN1_1.R2

value: treated with rHAPLN1 (50 ng/ml) for 48 h


title: WFB42

value: single octopaminergic/tyraminergic neuron, expressing a membrane-bound GFP reporter.


title: treat_rep1


title: treat_rep2


title: rHAPLN1_1.R1


title: WFB40

value: Wildtype


title: ctrl_rep3


title: treat_Merip_rep1


title: WFB41


title: ctrl_rep1


title: WFB44


title: FABP/LPS-treated donor 3

city: Leiden

first: Bruno

last: Guigas

address: Albinusdreef 2

department: Parasitology

country: Netherlands

institute: Leiden University Medical Center

description: Replicate 3

data_processing:
Trimming of low-quality sequences and adapter content has been performed with cutadapt v. 2.4, with the following parameters: --error-rate 0.1 --quality-cutoff 20 --minimum-length 10.
The alignment of reads to the GRCh38 human reference genome has been performed using STAR v. 2.7.7a with the following options: -outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000.
The duplicate alignments have been flagged by the MarkDuplicates program from the Picard v.2.24.0 software suite.
The alignment filtering was performed with the samtools v. 1.10 software, with the following parameters: -q 1 -f3 -F1280.
The read quantification has been performed per exon on gene level using htseq-count script from the HTSeq v. 0.13.5 python package, using Ensembl GRCh38 version 102 genome annotation.
Differential expression analysis has been performed in R programming language v. 4.0.3 with DESeq2 v. 1.30.0 R package.
Genome_build: GRCh38
Supplementary_files_format_and_content: HTSeq counts.tsv files were generated with htseq-count script, they contain counts for each gene for each sample in tab-delimited format; pbmcs_deseq2_results.annotated.counts.wide.csv file contains DESeq2 differential expression results statistics together with library-size normalized expression counts for each sample, annotated with gene name and description in comma-delimited format.

source_name: PBMC

growth_protocol: Human monocytes were isolated with CD14 beads positive selection and differentiated for 5-6 days to dendritic cells with GM-CSF and IL-4. Dendritic cells were harvested on the 6th, counted and re-plated in concentration 0,5x10^6/ml,

extract_protocol:
Total RNA was isolated with an RNA purification kit (Marcherey-Nagel) and was subjected to poly(A) enrichment using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
Strand-specific cDNA libraries were constructed with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs). Sequencing was performed using NovaSeq6000 (Illumina) sequencer in PE150 mode.

treatment_protocol: The next day (day 7th) cells were stimulated with LPS alone or LPS and fhFABP1 for 5h. After 5h cells were harvested, washed 2x with PBS and frozen in liquid nitrogen. They were stored in -80 for 2-3 weeks.

value: monocyte derived DCs

value: FABP and LPS treated


title: WFB3

value: Fluorescent-Activated Cell Sorting


title: WFB38

value: Female


title: WFB37


title: GBMXB CAR neutrophil Nanodrug_2

city: West Lafayette

first: Yun

last: Chang

state: IN

address: 480 Stadium Drive

department: Chemical Engineering

institute: Purdue University

data_processing:
Casava1.8 software used for basecalling
RNA-seq reads were aligned to the hg19 genome assembly using HISAT2
the RefSeq transcript levels (RPKMs) were quantified using the python script rpkmforgenes.py
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

growth_protocol: U87MG cells were cultured in MEM medium contained with 10% FBS

extract_protocol:
RNA of U87MG cells was harvested using Trizol reagent. Clontech SMARTer Stranded Total RNA-Seq Kit was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using Clontech SMARTer Stranded Total RNA-Seq Kit

treatment_protocol: The U87MG cells were treated with CAR Neutrophils, Nanodrug, or CAR Neutrophil loaded with nanodrug for 24 hours

value: Brain

value: U87MG cells

value: Tumor cells

value: Glioblastoma

value: U87MG cells treated with CAR Neutrophils loaded with nanodrug for 24 hours


title: LPS control donor 3

description: Replicate 3

value: LPS control


title: WFB43


title: ctrl_Merip_rep3

value: hippocampus

value: untreated


title: WFB39


title: ctrl_rep2

value: total RNA


title: FABP/LPS-treated donor 2

description: Replicate 2


title: LPS control donor 2

description: Replicate 2


title: FABP/LPS-treated donor 1

description: Replicate 1


title: GBM Nanodrug_1

value: U87MG cells treated with Nanodrug for 24 hours


title: WFB35


title: WFB36


title: GBMXB CAR neutrophil Nanodrug_1


title: GBM Nanodrug_2


title: WFB31


title: GBM CAR neuttrophil_1

value: U87MG cells treated with CAR Neutrophils for 24 hours


title: WFB33

value: single octopaminergic/tyraminergic neuron, expressing a membrane-bound GFP reporter.


title: WFB32

value: Wildtype


title: WFB30


title: LPS control donor 1

description: Replicate 1

value: monocyte derived DCs


title: GBM CAR neuttrophil_2


title: WFB2


title: WFB29


title: U87MG Control2

value: Normal culture


title: WFB27

value: Fluorescent-Activated Cell Sorting


title: U87MG Control1


title: WFB25

value: Female


title: WFB24


title: WFB23


title: WFB28


title: WFB34


title: WFB26


title: WFB18


title: WFB1


title: WFB21


title: WFB22


title: WFB20


title: Chronic Antibody Mediated Rejection - 014

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

description:
isolated single nuclei - RNA
KUT-014

data_processing:
Count matrices were generated using cellranger
Seurat objects were created using count matrices and the counts were normalized for library size
Seurat objects of normalized counts for all samples were integrated into one combined object
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files of raw counts for each sample generated using cellranger

source_name: Kidney allograft

extract_protocol:
single nuclei were isolated from human kidney core needle biopsies under low lysis buffer and rotated using a stirrod for a total of 20 min. Nuclei were then washed by centrifugation and buffer replacement and subjected to 70um and 40um filtering.
Libraries prepared under standard 10x and illumina guidelines. Libraries were generated using the 10x 5' Gene Expression kit
single nuclei RNA-seq through 10x genomics platform

tag: group

value: Chronic Antibody Mediated Rejection

tag: mean reads per cells

tag: fraction of reads mapped to genome (%)


title: WFB19

source_name: Brain

tag: collection strategy


title: WFB17

tag: Sex


title: WFB15

tag: cell type


title: Acute Tubular Necrosis - 538

description:
isolated single nuclei - RNA
ATN-538

value: Acute Tubular Necrosis


title: Chronic Antibody Mediated Rejection - 442

description:
isolated single nuclei - RNA
CAMR-442


title: WFB16

tag: genotype


title: WFB14


title: Acute Tubular Necrosis  - 505

description:
isolated single nuclei - RNA
ATN-505


title: Normal Kidney - 363

description:
isolated single nuclei - RNA
Normal-363

value: Normal Kidney


title: AvLO1

city: Hong Kong

first: Jie

last: Zhou

address: 102 Pokfulam Road, Pokfulam, Hong Kong

department: Microbiology

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Sequencing reads were mapped to the human reference genome GRCh38 with RNA-Seq aligner STAR.
Clean reads were quantified based on the number of reads spanning the back-splicing junction, and their fragments per kb for a million reads (FPKM) were calculated using HTSeq 0.13.5.
Aligned BAM files were sorted by SAMtools.
GenomicAlignments and DESeq2 R packages (version 1.18.1) were used for read counting and differential expression analysis.
Genes with an absolute value of log2 fold change greater than 1 and adjusted P-value (Benjamini-Hochberg) less than 0.05 were considered as differentially expressed.
Genome_build: GRCh38
Supplementary_files_format_and_content: allSample.FPKM.tsv: Tab-delimited text file includes FPKM values for each Sample.
Supplementary_files_format_and_content: all.log2FC.txt: Tab-delimited text file of log2 fold change.

source_name: 3D alveolar organoids

extract_protocol:
Samples were harvested for RNA extraction using RNeasy Mini Kit (Qiagen, Cas.74106).
After a quality check with Bioanalyzer, RNA specimens were applied to library preparation by KAPA mRNA HyperPrep Kit. In brief, Poly-A containing mRNA was collected by using poly-T oligo-attached magnetic beads. The purified mRNA was fragmented to 200 ~ 300 bp by incubating at 94°C for 6 min in the presence of magnesium ions. The fragmented mRNA was then applied as a template to synthesize the first-strand cDNA by using random hexamer-primer and reverse transcriptase. In the second strand cDNA synthesis, the mRNA template was removed and a replacement strand was generated to form the blunt-end double-stranded (ds) cDNA. The ds cDNA underwent 3’ adenylation and indexed adaptor ligation. The adaptor-ligated libraries were enriched by 15 cycles of polymerase chain reaction (PCR). The libraries were denatured and diluted to optimal concentration.

value: 3D alveolar organoids

tag: differentiation state

value: distal differentiated


title: WFB12


title: AvLO3


title: WFB10


title: 3DAO3

source_name: 3D airway organoids

value: 3D airway organoids

value: proximal differentiated


title: AvLO2


title: MMD5

value: Male

value: Mutant


title: MMD4


title: 2DAO3

source_name: 2D airway organoids

value: 2D airway organoids


title: WFB13


title: 3DAO2


title: MMD7


title: 3DAO1


title: MMD6


title: MMD3


title: MMD2


title: LO3

source_name: Lung organoids

value: Lung organoids

value: undifferentiated


title: MMD1

value: single octopaminergic/tyraminergic neuron, expressing a membrane-bound GFP reporter.


title: 2DAO1


title: 2DAO2


title: LO2


title: WFB11

value: Wildtype


title: LO1


title: MMD16


title: MMD13


title: Healthy control_H9 [miRNA-seq]

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: PBMCs derived from healthy control_H9

data_processing:
Before analysis of the small RNA-Seq data, reads were trimmed the adapter sequences and mapped to human hg19 reference genome.
miRNA-seq analysis was conducted using a StrandNGS version 3.0 software (Strand life science)  according to the small RNA alignment and small RNA analysis pipeline using default parameters.
Relative small RNA expression levels were calculated using DESeq algorithm.
Genome_build: hg19
Supplementary_files_format_and_content: Read count

source_name: Healthy control

extract_protocol:
Total RNA isolation of leukocytes from 31 COVID-19 patients on day1 and 16 healthy controls in the mRNA/miRNA sequence cohort was performed using the PAXgene™ Blood RNA System (BD Bioscience, San Jose, CA, USA).
Small RNA libraries were constructed following manufacturer instructions using the NEBNext Small RNA Library Prep Set for Illumina (NEB).
Libraries were sequenced on the HiSeq 2500 platform (Illumina) in 50-base pair single-end reads.

tag: subject status

value: Healthy control

value: peripheral blood mononuclear cells


title: Healthy control_H8 [miRNA-seq]

description: PBMCs derived from healthy control_H8


title: MMD10

city: San Diego

first: April

last: Williams

address: 10010 N Torrey Pines Rd

data_processing:
Sequenced reads were quality-tested using FASTQC.
Reads were aligned to the D. melanogaster genome dm6 (from The FlyBase Consortium/Berkeley Drosophila Genome Project/Celera Genomics) using the alignment algorithm STAR84 (version 2.5.3a). Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations) and --outFilterIntronMotifs RemoveNoncanonical.
Raw gene expression was quantified using the software HOMER across exons, and the top isoform value was used to represent gene expression.
In brief, cells containing the bottom 10% of cell counts were filtered, TMM normalization and size-factor correction was applied using the edgeR package, and cells falling in the bottom 5% of normalized counts were removed. Then, the bottom 10% of genes with normalized counts > 32 in a cell were removed as non-expressed genes.
Expression values were log2 transformed, and tSNE was performed to generate the plots.
The scrattch.hicat R package was used to perform hierarchical iterative clustering on the normalized expression table.
For differential expression analysis between the wild-type and ∆nvy mutant, genes with expression values of 0 in 75% or more of the cells were filtered out. Genes that met the following criteria were considered as DEGs: (1) p-values by Mann-Whitney U-test lower than 0.05, (2) adjusted p-values by Benjamini-Hochberg FDR test lower than 0.2, and (3) the fold-change greater than 10 (|log2FC| > 3.321928095).
For DEGs that showed behavioral phenotypes in the RNAi experiments, predicted biological processes and human orthologs were taken from the “Gene Ontology” and “Human Orthologs (via DIOPT v7.1)” sections in FlyBase (http://flybase.org/), respectively.
Genome_build: dm6
Supplementary_files_format_and_content: raw count table in tab-delimited text format

extract_protocol:
Single cells were sorted via fluorescent-activated cell sorting. Each cell was sorted in a separate well of a 96 well plate  filled with freshly made lysis buffer, prepared according to Takara standard protocol. The contact with the lysis buffer lysed the cells, freeing their content, mRNA included. As soon as collection was completed (15-20 minute/genotype), samples were frozen in dry ice and stored until used at -80°C.
Sequencing libraries were prepared using the Nextera XT kit (Illumina #FC-131-1096) and mixed into 24 pools (12 samples per pool).After purification using the Agencourt AMPure XT beads (Beckman Coulter #A63881), the sample quality was checked with both the Qubit 3 Fluorometer and the High Sensitivity D1000 ScreenTape assay (Agilent Technologies #5067-5584). The libraries were equimolarly pooled, and the final concentration was estimated by qPCR. Sequencing of 75 bp paired-end reads was performed with the Illumina Nextseq 500 sequencer.
Nextera XT

value: Fluorescent-Activated Cell Sorting


title: Healthy control_H2 [miRNA-seq]

description: PBMCs derived from healthy control_H2


title: Healthy control_H7 [miRNA-seq]

description: PBMCs derived from healthy control_H7


title: MMB9


title: MMB8


title: Healthy control_H25 [miRNA-seq]

description: PBMCs derived from healthy control_H25


title: MMB5


title: MMB7


title: Healthy control_H21 [miRNA-seq]

description: PBMCs derived from healthy control_H21


title: Healthy control_H24 [miRNA-seq]

description: PBMCs derived from healthy control_H24


title: Healthy control_H1 [miRNA-seq]

description: PBMCs derived from healthy control_H1


title: MMB46


title: MMB6


title: Healthy control_H19 [miRNA-seq]

description: PBMCs derived from healthy control_H19


title: Healthy control_H22 [miRNA-seq]

description: PBMCs derived from healthy control_H22


title: Healthy control_H23 [miRNA-seq]

description: PBMCs derived from healthy control_H23


title: MMB42


title: MMB4


title: MMD11


title: Healthy control_H15 [miRNA-seq]

description: PBMCs derived from healthy control_H15


title: MMB45


title: Sample_HEC1B_Sh_FOXA2_3

city: Dallas

first: Subhransu

middle: S

last: Sahoo

state: Texas

address: 5323 Harry Hines Blvd

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
Single-end 76 bp read length Fastq files were checked for quality using fastqc (v0.11.5) and fastq_screen (v0.11.4)
Fastq files were mapped to human genome using STAR(v2.5.3a)
Read counts were generated using featureCounts (subread, v1.4.6)
Differential expression was performed using edgeR
Normalized read counts generated using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited files that includes normalized read counts for each sample per gene

source_name: HEC1B cells trasfected with 29-mer FOXA2 specific shRNA in pGFP-C-shLenti vector (FOXA2KD HEC1B)

growth_protocol: HEC1B cells with or without FOXA2 knockdown were cultured in MEM medium supplemented with 10% FBS and antibiotics (50 U/mL penicillin and 50 mg/L streptomycin) in a humidified atmosphere at 370C containing 5% CO₂.

extract_protocol: Total RNA from HEC1B cells with or without FOXA2 knockdown was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: HEC1B cells with or without FOXA2 knockdown were treated with puromycin to select positively transfected cells.

value: HEC1B cells

tag: genotype/variation


title: Healthy control_H20 [miRNA-seq]

description: PBMCs derived from healthy control_H20


title: Healthy control_H14 [miRNA-seq]

description: PBMCs derived from healthy control_H14


title: MMB43

institute: Salk Institute for Biological Studies


title: MMB40


title: Healthy control_H16 [miRNA-seq]

description: PBMCs derived from healthy control_H16


title: MMB41


title: Sample_HEC1B_Sh_FOXA2_1

value: trasfected with 29-mer FOXA2 specific shRNA in pGFP-C-shLenti vector (FOXA2KD HEC1B)


title: Sample_HEC1B_Sh_EV_3

source_name: HEC1B cells trasfected with 29-mer scrambled shRNA in pGFP-C-shLenti vector (HEC1B)


title: Sample_HEC1B_Sh_FOXA2_2


title: Healthy control_H11 [miRNA-seq]

description: PBMCs derived from healthy control_H11


title: MMB39


title: COVID-19 patient_COV99 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV99

source_name: COVID-19 patient

value: COVID-19 patient


title: COVID-19 patient_COV97 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV97


title: Sample_HEC1B_Sh_EV_2

value: trasfected with 29-mer scrambled shRNA in pGFP-C-shLenti vector (HEC1B)


title: MMB38


title: MMB44


title: MMB37


title: MMB36


title: COVID-19 patient_COV90 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV90


title: Sample_HEC1B_Sh_EV_1


title: Sample_F3

source_name: Ishikawa cells transduced with FOXA2 lentiviral particles (ISK-FOXA2)

growth_protocol: Ishikawa cells with or without FOXA2 were cultured in MEM medium supplemented with 5% FBS and antibiotics (50 U/mL penicillin and 50 mg/L streptomycin) in a humidified atmosphere at 370C containing 5% CO₂.

extract_protocol: Total RNA from Ishikawa cells with or without FOXA2 was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: Ishikawa cells with or without FOXA2 were treated with puromycin to select positively transduced cells.

value: Ishikawa cells


title: MMB3


title: COVID-19 patient_COV86 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV86


title: MMB34


title: COVID-19 patient_COV81 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV81


title: MMB33


title: COVID-19 patient_COV87 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV87


title: MMB35


title: Sample_F1

value: transduced with FOXA2 lentiviral particles (ISK-FOXA2)


title: Sample_F2


title: Sample_E3

source_name: Ishikawa cells transduced with pLenti empty vector (ISK)


title: COVID-19 patient_COV75 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV75


title: MMB32


title: COVID-19 patient_COV73 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV73


title: COVID-19 patient_COV72 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV72


title: MMB31


title: Sample_E1

value: transduced with pLenti empty vector (ISK)


title: COVID-19 patient_COV78 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV78


title: MMB30

value: Male


title: COVID-19 patient_COV70 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV70


title: MMB2

value: Mutant


title: Sample_E2


title: P28

city: Boston

first: Sarah

last: Morton

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

description:
t cell receptor
iRepetoire sequencing

data_processing:
iRepetoire provided .fq.gz files
Genome_build: hg38
Supplementary_files_format_and_content: Clonotype data generated by MiXCR analysis of multiplex amplicon PCR data from iRepetoir. Settings: T-cell receptor B analysis, 5- end v-primers, 3'end j-primers, species homo sapiens, adapters present

source_name: peripheral blood

extract_protocol: none provided by the submitter

tag: gestational age at birth

tag: gestational age at sample


title: MMB29


title: COVID-19 patient_COV6 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV6


title: P27

description:
t cell receptor
iRepetoire sequencing


title: P26

description:
t cell receptor
iRepetoire sequencing


title: MMB28


title: MMB27


title: P25_1

description:
t cell receptor
iRepetoire sequencing


title: COVID-19 patient_COV62 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV62


title: P24_3

description:
t cell receptor
iRepetoire sequencing


title: MMB25


title: COVID-19 patient_COV59 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV59


title: MMB23


title: COVID-19 patient_COV57 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV57


title: COVID-19 patient_8 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_8

data_processing:
Before analysis of the small RNA-Seq data, reads were trimmed the adapter sequences and mapped to human hg19 reference genome.
miRNA-seq analysis was conducted using a StrandNGS version 3.0 software (Strand life science) according to the small RNA alignment and small RNA analysis pipeline using default parameters.
Relative small RNA expression levels were calculated using DESeq algorithm.
Genome_build: hg19
Supplementary_files_format_and_content: Read count

extract_protocol:
Total RNA isolation of leukocytes from 10 COVID-19 patients on day1 and five healthy controls in the mRNA/miRNA sequence cohort was performed using the PAXgene™ Blood RNA System (BD Bioscience, San Jose, CA, USA).
Small RNA libraries were constructed following manufacturer instructions using the NEBNext Small RNA Library Prep Set for Illumina (NEB).
Libraries were sequenced on the HiSeq 2500 platform (Illumina) in 50-base pair single-end reads.

tag: subject id

tag: time point

value: day1;  at the time of admission


title: MMB24


title: P24_2

description:
t cell receptor
iRepetoire sequencing


title: P29

description:
t cell receptor
iRepetoire sequencing


title: COVID-19 patient_10 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_10


title: COVID-19 patient_7 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_7


title: P24_1

description:
t cell receptor
iRepetoire sequencing


title: P23

description:
t cell receptor
iRepetoire sequencing


title: COVID-19 patient_COV50 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV50


title: MMB21


title: MMB22


title: COVID-19 patient_6 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_6


title: COVID-19 patient_COV68 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV68


title: P22

description:
t cell receptor
iRepetoire sequencing


title: COVID-19 patient_COV53 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV53


title: COVID-19 patient_5 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_5


title: COVID-19 patient_COV65 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV65


title: COVID-19 patient_COV45 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV45


title: MMB20


title: MMB1


title: COVID-19 patient_9 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_9


title: COVID-19 patient_4 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_4


title: COVID-19 patient_COV43 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV43


title: COVID-19 patient_COV41 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV41


title: P21_1

description:
t cell receptor
iRepetoire sequencing


title: COVID-19 patient_COV38 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV38


title: COVID-19 patient_COV35 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV35


title: COVID-19 patient_3 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_3


title: MMB18


title: P20_2

description:
t cell receptor
iRepetoire sequencing


title: P17

description:
t cell receptor
iRepetoire sequencing


title: COVID-19 patient_COV27 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV27


title: P21_2

description:
t cell receptor
iRepetoire sequencing


title: MMB15


title: COVID-19 patient_1 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_1


title: Healthy control_3 [miRNA-seq]

description: PBMCs derived from healthy control_3

tag: age

tag: gender

value: female


title: COVID-19 patient_COV33 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV33


title: MMB13


title: Healthy control_5 [miRNA-seq]

description: PBMCs derived from healthy control_5

value: male


title: P16_2

description:
t cell receptor
iRepetoire sequencing


title: COVID-19 patient_COV1 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV1


title: MMB16

value: single octopaminergic/tyraminergic neuron, expressing a membrane-bound GFP reporter.


title: Healthy control_4 [miRNA-seq]

description: PBMCs derived from healthy control_4


title: COVID-19 patient_COV112 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV112


title: P16_1

description:
t cell receptor
iRepetoire sequencing


title: MMB19


title: Healthy control_2 [miRNA-seq]

description: PBMCs derived from healthy control_2


title: HEK293+ACE2+TMPRSS2_T12C_MOI 1, MOI 2

data_processing:
Library strategy: CRISPRseq
FASTQ files were pre-processed to extract Cas9 guide sequence using a bespoke Perl script.
The Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'.
Trimmed FASTQ files were then aligned to the TKOv3 FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.
Supplementary_files_format_and_content: tab-delimited read count matrix

source_name: immortalized embryonic kidney cell line

extract_protocol:
Genomic DNA was extracted using the Wizard Genomic DNA Purification kit (Promega) or QIAamp DNA mini kit according to manufacturer’s instructions
For each sample, the gRNA cassette was amplified directly from genomic DNA using primers harboring Illumina TruSeq adaptors with i5 and i7 barcodes. The resulting sequencing libraries were pooled and gel-purified.

tag: cell line

tag: crispr library

tag: treatment

value: Infected w/ SARS-CoV-2 at MOI 1 then MOI 2

tag: growth medium

value: DMEM + 10% FBS +1% PenStrep


title: P16_3

description:
t cell receptor
iRepetoire sequencing


title: P18

description:
t cell receptor
iRepetoire sequencing


title: MMB17

tag: collection strategy


title: P20

description:
t cell receptor
iRepetoire sequencing


title: MMB12

tag: Sex


title: HEK293+ACE2+TMPRSS2_T12B_MOI 1, MOI 2


title: MMB14

tag: cell type


title: MMB10

tag: genotype


title: COVID-19 patient_2 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_2

value: peripheral blood mononuclear cells


title: P16_4

description:
t cell receptor
iRepetoire sequencing


title: P15B

description:
t cell receptor
iRepetoire sequencing


title: COVID-19 patient_COV108 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV108


title: COVID-19 patient_COV102 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV102


title: MMB11

value: Fluorescent-Activated Cell Sorting


title: Placenta_GDM_No_Sample60 [HF2_909]

type: genomic

first: Zhong-Cheng

last: Luo

state: Ontario

address: 60 Murray, L5-240, LTRI

department: Lunenfeld-Tanenbaum Research Institute

institute: Mount Sinai Hospital, University of Toronto

description: There are a total of 96 samples in 12 slides in the experiments (36 samples are not a part of the present study)

hyb_protocol: Not Provided

scan_protocol: Not Provided

data_processing: Illumina

label: Cy5 and Cy3

source_name: Placenta tissue from the fetal side

label_protocol: Not Provided

extract_protocol: DNA was extracted from fetal-side placental samples using Dneasy Blood & Tissue Kit (Qiagen, Cat No. 69504)

tag: tissue

value: Placenta tissue from the fetal side

value: Female

tag: gestational diabetes

value: No

tag: maternal age

tag: pre-pregnancy body mass index

tag: primiparity

value: Yes

tag: mode of delivery

value: vaginal delivery

tag: slide


title: P14

description:
t cell receptor
iRepetoire sequencing

tag: gestational age at birth

tag: gestational age at sample


title: Placenta_GDM_No_Sample59 [HF2_414]


title: P15A

description:
t cell receptor
iRepetoire sequencing


title: Healthy control_1 [miRNA-seq]

description: PBMCs derived from healthy control_1

tag: subject status

value: Healthy control

tag: age

tag: gender


title: MFD4


title: COVID-19 patient_COV105 [miRNA-seq]

description: PBMCs derived from COVID-19 patient_COV105

value: COVID-19 patient


title: MFD3


title: HEK293+ACE2+TMPRSS2_T12C_Control

first: Jason

last: Moffat

address: 686 Bay Street, Room 13.9705

tag: cell line

tag: crispr library

tag: treatment

value: Control

tag: growth medium


title: Placenta_GDM_No_Sample58 [HF2_317]

tag: Sex

value: Male


title: P13_3

description:
t cell receptor
iRepetoire sequencing


title: Placenta_GDM_No_Sample57 [HF2_671]

tag: tissue


title: HEK293+ACE2+TMPRSS2_T12B_Control


title: P13_2

description:
t cell receptor
iRepetoire sequencing


title: Placenta_GDM_No_Sample56 [GF4_756]

tag: gestational diabetes


title: Placenta_GDM_No_Sample55 [GF4_842]

tag: maternal age

value: c-section


title: HEK293+ACE2+TMPRSS2_T12A_Control


title: P13_1

description:
t cell receptor
iRepetoire sequencing


title: MFD2

tag: cell type

tag: genotype

value: Mutant

tag: collection strategy


title: MFD1


title: P12

description:
t cell receptor
iRepetoire sequencing


title: Placenta_GDM_No_Sample54 [XH2_389]

tag: pre-pregnancy body mass index

tag: primiparity

tag: mode of delivery

tag: slide


title: MFB9


title: HEK293+ACE2+TMPRSS2_T0


title: MFB8


title: CACO-2_T39C_Control

source_name: colon adenocarcinoma cell line


title: HEK293+ACE2+TMPRSS2_T12A_MOI 1, MOI 2


title: MFB7


title: CACO-2_T39B_Control


title: P10

description:
t cell receptor
iRepetoire sequencing

tag: gestational age at birth

tag: gestational age at sample


title: Placenta_GDM_No_Sample53 [HF2_675]


title: T20

description:
t cell receptor
iRepetoire sequencing


title: CACO-2_T39A_Control

tag: cell line


title: T19_2

description:
t cell receptor
iRepetoire sequencing


title: Placenta_GDM_No_Sample52 [XH2_363]


title: MFB6


title: MFB5


title: CACO-2_T37C_SARS-CoV-2, MOI 10, infection #3

tag: crispr library

value: Infected w/ SARS-CoV-2 at MOI 10


title: Placenta_GDM_No_Sample51 [GF4_912]


title: CACO-2_T37B_SARS-CoV-2, MOI 10, infection #3

tag: treatment


title: Placenta_GDM_No_Sample50 [HF2_573]


title: CACO-2_T37A_SARS-CoV-2, MOI 10, infection #3

tag: growth medium


title: T17

description:
t cell receptor
iRepetoire sequencing


title: Placenta_GDM_No_Sample49 [HF2_637]

tag: Sex


title: CACO-2_T0


title: T16

description:
t cell receptor
iRepetoire sequencing


title: T14

description:
t cell receptor
iRepetoire sequencing


title: T18

description:
t cell receptor
iRepetoire sequencing


title: MFB49

value: single octopaminergic/tyraminergic neuron, expressing a membrane-bound GFP reporter.


title: MFB4


title: MFB46


title: Placenta_GDM_No_Sample47 [HF2_354]

tag: tissue


title: CALU-3_T43A_SARS-CoV-2, MOI 0.0005, 90% CPE

source_name: lung adenocarcinoma cell line

value: Infected w/ SARS-CoV-2 at MOI 0.0005 (90% CPE)

value: EMEM + 10% FBS + 1% PenStrep


title: T13_2

description:
t cell receptor
iRepetoire sequencing


title: CALU-3_T43C_SARS-CoV-2, MOI 0.0005, 90% CPE


title: CALU-3_T43B_SARS-CoV-2, MOI 0.0005, 90% CPE


title: Placenta_GDM_No_Sample45 [XH2_173]

tag: gestational diabetes


title: MFB48


title: T19_1

description:
t cell receptor
iRepetoire sequencing


title: CALU-3_T25C_Control


title: T12

description:
t cell receptor
iRepetoire sequencing


title: MFB44


title: MFB50


title: MFB45


title: Placenta_GDM_No_Sample44 [HF2_1029]

tag: maternal age


title: Placenta_GDM_No_Sample46 [HF2_709]


title: Placenta_GDM_No_Sample48 [HF2_33]


title: CALU-3_T25A_Control


title: MFB47

tag: cell type


title: T13_1

description:
t cell receptor
iRepetoire sequencing


title: Placenta_GDM_No_Sample42 [HF2_455]


title: T11

description:
t cell receptor
iRepetoire sequencing


title: CALU-3_T0


title: Placenta_GDM_No_Sample40 [HF2_636]


title: HUH-7_T15C_SARS-CoV-2 (infection 2)

source_name: hepatocellular carcinoma cell line

value: Infected w/ SARS-CoV-2 at MOI 1

value: DMEM + 10% FBS +1% PenStrep


title: Placenta_GDM_No_Sample43 [HF2_774]

value: Placenta tissue from the fetal side


title: MFB43

source_name: Brain

value: Female

tag: genotype

value: Fluorescent-Activated Cell Sorting


title: Placenta_GDM_No_Sample38 [HF2_1048]

value: No

value: Yes


title: MFB3

tag: collection strategy


title: HUH-7_T14C_Control


title: MFB39


title: HUH-7_T15B_SARS-CoV-2 (infection 2)


title: MFB41


title: Placenta_GDM_No_Sample36 [HF2_385]

tag: pre-pregnancy body mass index

value: vaginal delivery


title: HUH-7_T14B_Control


title: MFB40


title: T09

description:
t cell receptor
iRepetoire sequencing


title: Placenta_GDM_No_Sample41 [XH2_97]

tag: primiparity


title: CALU-3_T25B_Control


title: MFB42


title: HUH-7_T0


title: Placenta_GDM_No_Sample39 [HF2_969]

tag: mode of delivery


title: PolyA_plus_Don002_d13_rep1

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

country: United Kingdom

institute: The University of Oxford

data_processing:
Mapping: STAR --runThreadN 4 --outFilterMultimapNmax 1
Duplicate removal: samtools rmdup
Genome_build: hg19
Supplementary_files_format_and_content: bigwig: forward reads (deeptools) - bamCoverage -p4 --binSize 1 --normalizeUsingRPKM --filterRNAstrand forward
Supplementary_files_format_and_content: bigwig: reverse reads (deeptools) - bamCoverage -p4 --binSize 1 --normalizeUsingRPKM --filterRNAstrand reverse

source_name: CD34 Culture

growth_protocol: Fresh blood was sourced either as 100 ml whole blood collected from three healthy donors (two males, one female) using EDTA Vacuettes (Becton Dickson) or 5 ml leukocyte cones (NHS Blood & Transport). Whole cell counts were performed on a Pentra ES60 (Horiba) for donor blood to ensure clinically healthy red blood cell counts. Blood was diluted with PBS and overlaid onto Histopaque-1077 (Sigma) and centrifuged for 30 min at 630 rcf (no brake). Peripheral Blood Mononuclear Cells (PBMCs) were washed in PBS and MACS buffer (PBS, 2 µM EDTA, 0.5% BSA) and stained with Human CD34 Microbead kit (Miltenyi Biotec) following the manufacturer’s instruction for 30 minutes (4 ºC) before being passed successively through two LS Columns (Miltenyi Biotec) with three MACs buffer washes. Counting of cells was performed on a Luna FL (Logos) after staining with acridine orange (AO) and propidium iodide (PI). CD34+ cells were either stored in freezing buffer (90% FBS, 10% DMSO) or resuspended in Phase I mediumfor a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 0.5-2.5x105 cells were resuspended on day 0 in Phase I media at 105 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase II media at 3x105 cells ml-1. Cells were counted on day 9 and diluted to 3x105 cells ml-1 Phase II media. On day 11, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase III media at 106 cells ml-1. Cells were counted on days 13 and 15 and diluted to 106 cells ml-1 in Phase III media. Reproducibility between differentiations was confirmed morphologically with cytospins and immunologically with six FACS cell surface markers (CD34, CD36/Fatty acid translocase, CD71/Transferrin receptor, CD235a/Glycophorin A, CD49d/α-Integrin, CD233/Band).

extract_protocol:
isolation protocol: 1-5x10^6 cells were fixed in 1 ml TRI-reagent (Sigma), snap frozen and stored at -80ºC for less than one year.
RNA was extracted by addition of 0.1 ml 1-bromo-3-chloropropane, pipette mixing and separation in a Phase Lock gel Heavy tube (5Prime) and then precipitation with 1 µl of GlycoBlue and an equal volume (~500 µl) isopropanol and centrifugation (10 min, 12,000 rcf, 4 ºC). The RNA pellet was washed with 75 % ethanol, resuspended in DEPC-treated water, and stored at -80 ºC for less than one year.
For RNA-seq total RNA was treated with Turbo DNAse (Invitrogen) at 25 ºC for 60 min, then RNA was separated using phenol-chloroform isoamylalcohol and a PhaseLock Light-gel tube (5Prime).  Treated RNA was precipitated at -80 ºC overnight with sodium acetate, glycoblue, and 75 % ethanol, before centrifugation (12,000 rcf, 4 ºC), 75 % ethanol wash and resuspension in DEPC-treated water. Globin and rRNA sequences were depleted from up to 5 µg of treated RNA using Globin-Zero Gold (Illumina), before PolyA selection with NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs), and indexing with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturers’ instructions.

value: Erythroid

tag: day of differentiation

value: Day 13

tag: donor id


title: PolyA_plus_Don003_d10_rep1

value: Day 10


title: HUH-7_T15A_SARS-CoV-2 (infection 2)

city: Toronto

institute: University of Toronto


title: PolyA_plus_Don003_d7_rep1

value: Day 7


title: PolyA_plus_Don003_d13_rep1


title: PolyA_plus_Don003_d10_rep2


title: Placenta_GDM_No_Sample37 [XH2_2]

value: Male

tag: gestational age at birth

tag: slide


title: MFB36

value: Mutant


title: PolyA_plus_Don002_d13_rep2


title: KC3-PM2_5

city: Goyang-si

first: Young Rok

last: Seo

address: Dongguk-ro 32

department: Life science

country: South Korea

institute: Dongguk University

data_processing:
FASTQC v0.11.7 for quality check
Trimmomatic 0.38 for trimming
HISAT2 ver 2.1.0 and Bowtie2 2.3.4.1 for reference mapping
StringTie ver 1.3.4d for transcript assembling
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Excel file include fold change, p-value, FPKM values of each groups

source_name: KC3-PM2_5 (NHEK)

growth_protocol: Normal human epidermal keratinocytes (NHEKs) from the neonatal foreskin donors were purchased from Lonza (Basel, Switzerland) and were cultured in KBM-GOLD medium supplemented with  insulin, human epidermal growth factor, bovine pituitary extract, hydrocortisone, epinephrine, transferrin, and gentamicin/amphotericin B (all supplements from Lonza).

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. The RNA concentration was spectrophotometrically determined, and RNA integrity was analyzed using a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA)
TruSeq Stranded mRNA Sample Preparation Guide, Part #  15031047 Rev. E

treatment_protocol: NHEKs grown to confluence were cultured with PM 2.5 (100 μg/mL) in KBM-Gold medium without supplements for 24 hr.

value: Normal Human Epidermal Keratinocytes


title: MFB37

value: single octopaminergic/tyraminergic neuron, expressing a membrane-bound GFP reporter.


title: PolyA_plus_Don003_d13_rep2


title: HUH-7_T14A_Control

tag: cell line

tag: crispr library

value: Control


title: KC2-PM2_5

source_name: KC2-PM2_5 (NHEK)


title: MFB34


title: Placenta_GDM_No_Sample35 [XH2_74]


title: PolyA_plus_Don002_d10_rep1


title: Placenta_GDM_No_Sample34 [HF2_980]


title: PolyA_plus_Don002_d10_rep2


title: MFB38


title: Placenta_GDM_No_Sample31 [HF2_693]


title: Placenta_GDM_No_Sample32 [HF2_504]


title: KC2-control

source_name: KC2-control (NHEK)


title: Placenta_GDM_No_Sample33 [XH2_7]

value: c-section


title: MFB35


title: Placenta_GDM_Yes_Sample29 [YF4_679]


title: Placenta_GDM_Yes_Sample30 [YF4_838]


title: PolyA_plus_Don001_d13_rep1


title: PolyA_plus_Don001_d10_rep2


title: MFB33


title: PolyA_plus_Don001_d7_rep1


title: PolyA_plus_Don001_d13_rep2


title: MFB31


title: KC3-control

source_name: KC3-control (NHEK)


title: KC-control

source_name: KC-control (NHEK)


title: MFB30


title: Placenta_GDM_Yes_Sample28 [YF4_282]


title: KC-PM2_5

source_name: KC-PM2_5 (NHEK)


title: PolyA_plus_Don001_d10_rep1


title: Placenta_GDM_Yes_Sample26 [XH2_4562]


title: Placenta_GDM_Yes_Sample27 [XH2_4576]


title: MFB29


title: Patient3-library

city: Shenzhen

first: Chao

state: Outside the US or Canada

address: Shenzhen,china

institute: Peking University Shenzhen Hospital

description: LDQ

data_processing:
Quality control
Converted to a Cell Ranger-specific FASTQ file using an in-house Perl script
Aligned reads with the GRCH38 human reference using STAR software (v2.5.3)
The mapped reads were then filtered out for valid cell barcodes and UMIs
Generate a gene-cell matrix for downstream analysis
Assembly: GRCH38(hg38)
Supplementary files format and content: count_mtx.tsv.gz, the UMI counts of each cell in the sample.

source_name: Colorectum

extract_protocol:
The concentration of single-cell suspension was adjusted to 1000 cells/uL by using cell resuspension buffer. Single cell suspension was then loaded onto a microfluidic chip and single cell RNA-seq libraries were constructed according to the manufacturer's instructions (MGI DNBelab C4 system).
An scRNA-seq library was prepared using the DNBelab C4 system as previously described. Briefly, the single-cell suspension was transformed into the scRNA-seq library of barcodes through the steps of droplet encapsulation, emulsification and fragmentation, mRNA capture bead collection, reverse transcription, cDNA amplification and purification. An indexed sequencing library was constructed according to the manufacturer's instructions. The sequencing library was quantified using the Qubit SSDNA Assay Kit (Thermo Fisher Scientific).

value: female

tag: age

value: MSI-H


title: Patient4-library

description: LKX

tag: Sex


title: MFB32

value: Female


title: MFB28

value: Fluorescent-Activated Cell Sorting


title: Placenta_GDM_Yes_Sample24 [XH2_2223]

tag: tissue

value: Placenta tissue from the fetal side


title: MFB2


title: MFB27


title: Placenta_GDM_Yes_Sample23 [XH2_2067]

tag: gestational diabetes

value: Yes


title: MFB26


title: MFB25


title: Control DRG at P60, biological rep3

type: RNA

city: Beijing

first: Zijing

last: Liu

address: Fengtai District, #20 East St.

institute: Beijing Institute of Biotechnology

description: Gene expression data from control DRG.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000.

data_processing: The Affymetrix GeneChip command console (version 4.0, Affymetrix) was used to analyze array images and obtain raw data. Next, Genespring software (version 12.5, Agilent Technologies) was employed to complete the basic analysis of the raw data.

label: biotin

source_name: Control DRG

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mouse DRGs dissected from P60 mice

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: not applicable

value: DRG


title: Patient2-library

description: CWJ

value: male


title: Placenta_GDM_Yes_Sample25 [XH2_2960]

tag: maternal age


title: MFB24

tag: cell type


title: Placenta_GDM_Yes_Sample22 [XH2_2046]

value: No


title: Placenta_GDM_Yes_Sample20 [XH2_615]


title: MFB23

tag: genotype


title: MFB22

tag: collection strategy


title: Placenta_GDM_Yes_Sample21 [XH2_1953]

tag: pre-pregnancy body mass index


title: MFB21


title: Placenta_GDM_Yes_Sample17 [XH2_408]

tag: primiparity


title: Plants at day 5 not treated and inoculated with Z. tritici _ repetition 3

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

institute: University of Lille

description:
Gene expression after 5 days of treatment
C3-D5-i

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Wheat Gene Expression Microarrays GE 4x44 (Agilent, Santa Clara, CA, USA) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Scanner GenePix 4200B (Molecular Device) using one color scan setting

data_processing: The scanned images were analyzed with GenePix Pro Software 6.0 (Molecular Device) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Triticum aestivum

source_name: Wheat plants at day 5 not treated and inoculated (i) with Z. tritici

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seeds of the cultivar (cv.) Alixan (Limagrain, France), susceptible to STB, were pregerminated in square Petri dishes (12 × 12 cm) on moist filter paper as described by Siah et al. (2010), and germinated grains were delicately transferred into three-liter pots filled with universal loam (Gamm Vert, France). The prepared pots were then placed in the greenhouse at 21 ± 2°C with a 16/8 h day-night cycle. For each condition and each sampling modality, three pots harboring 12 wheat plants each (n=36), were used.

extract_protocol: Total RNA was extracted from wheat leaves using RNeasy Plant Mini Kit (Qiagen, Courtaboeuf, France). RNA quality was determined with Nanodrop by analyzing their absorbance ratios A260/280 and A260/230, which were found to range between 2.0 and 2.2. Moreover, RNA quality was also examined with Bioanalyzer 2100 (Agilent, France) and a minimal RNA integrity number (RIN) of 0.8 was required for all samples

treatment_protocol: At day 0 (DO), corresponding to three weeks after sowing, plants were hand-sprayed with 30 mL of either a solution of 100 mg.L-1 rhamnolipid from Bacillus subtilis mock (control) treatment. At two days after treatment (D2), half of the plants treated with rhamnolipid, as well as control plants, were inoculated by hand-spraying 30 mL of Z. tritici spore suspension (106 spores.mL-1), mixed with 0.05 % of Tween 20, on the plants of each pot. Leaf samples were harvested at two (D2), five (D5) and fifteen (D15) days after treatment for transcriptomic analyses.  For each condition, i.e. plants treated with rhamnolipid (M) or not (control, C), and inoculated with Z. tritici (i) or not (Ni), nine third leaves sampled from three different pots (three leaves per pot), were randomly harvested, bulked per pot, immediately frozen in liquid nitrogen and stored at -80°C for further analyses. Thereafter, 100 mg of frozen pooled leaves were ground in a mortar with liquid nitrogen for RNA extraction.

tag: cultivar

value: Alixan

value: leaves

value: three weeks after sowing at D0

tag: treatment

value: at day 5 not treated

tag: inoculation

value: inoculated (i) with Z. tritici


title: Control DRG at P60, biological rep2

description: Gene expression data from control DRG.


title: Placenta_GDM_Yes_Sample19 [XH2_508]

tag: gestational age at birth

tag: mode of delivery


title: podocytes, OASIS2

first: Masanori

last: Obana

address: Yamadaoka 1-6

institute: Osaka University

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μμl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μμl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method.  A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

organism: Mus

source_name: podocyte cell line, OASIS overexpression

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μμg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: The immortalized murine podocyte cell line was differentiated under nonpermissive conditions (10-14 days at 37°C, no interferon-γ)

extract_protocol: Total RNA was prepared from murine pococyte cells, using QIAzol® Lysis Reagent (Qiagen).

treatment_protocol: To induce overexpression of OASIS in podocytes, the cells were incubated in RPMI-1640 medium containing lentivirus vector, at a multiplicity of infection of 200–500, with 8 μg/mL polybrene (Nacalai Tesque, Kyoto, Japan) and 10% FBS, for 24 h. A lentivirus expressing venus was used as control. Post the lentiviral infection, the medium was changed to RPMI-1640 with 10% FBS. Forty-eight hours after treatment with the lentiviral vectors, total RNA was extracted from the OASIS-overexpressing podocytes.

value: murine podocyte cell line

value: OASIS overexpression by lentivirus


title: MFB20

value: single octopaminergic/tyraminergic neuron, expressing a membrane-bound GFP reporter.

value: Mutant


title: Placenta_GDM_Yes_Sample18 [XH2_412]

value: c-section

tag: slide


title: Plants at day 5 not treated and inoculated with Z. tritici _ repetition 2

description:
Gene expression after 5 days of treatment
C2-D5-i


title: Meis1 mutant DRG at P60, biological rep3

description: Gene expression data from Meis1 mutant DRG.

source_name: Meis1 mutant DRG

value: Meis1 mutant


title: Meis1 mutant DRG at P60, biological rep1


title: Plants treated 5 days with rhamnolipid and inoculated with Z. tritici _ repetition 3

description:
Gene expression after 5 days of treatment
R3-D5-i

source_name: Wheat plants treated 5 days (D5) with rhamnolipid (M) and inoculated (i) with Z. tritici


title: Plants at day 5 not treated and inoculated with Z. tritici _ repetition 1

description:
Gene expression after 5 days of treatment
C1-D5-i


title: Control DRG at P60, biological rep1

description: Gene expression data from control DRG.

value: Control


title: Placenta_GDM_Yes_Sample16 [XH2_327]

source_name: Placenta tissue from the fetal side

value: Placenta tissue from the fetal side

value: Male


title: podocytes, Venus1

source_name: podocyte cell line, venus expression (control)

value: Venus expression by lentivirus


title: Meis1 mutant DRG at P60, biological rep2

value: DRG


title: podocytes, OASIS1


title: podocytes, Venus2


title: MFB19

value: Female

value: Fluorescent-Activated Cell Sorting


title: MFB1


title: Plants treated 5 days with rhamnolipid and inoculated with Z. tritici _ repetition 2

description:
Gene expression after 5 days of treatment
R2-D5-i

value: Alixan

value: leaves

value: treated 5 days (D5) with rhamnolipid (M)


title: Placenta_GDM_Yes_Sample15 [XH2_203]

value: Yes

value: vaginal delivery


title: MFB18


title: Micorwell-seq datasets of Xenopus_NF66_COL125

city: Hangzhou

first: Haide

address: 866 Yuhangtang road

institute: Zhejiang University

data_processing:
Base call files were performed with Illumina bcl2fastq.
Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. We took a dark reaction for R1, where R1 measured 24bp and R2 measured 150bp. The cell barcode is at position 1-18 of R1, and the UMI barcode is at position 19-24 of R1.
scRNA-seq reads were aligned to the Xenopus laevis J-strain 9.2 genome assembly using STAR (version 2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix (DGE) based on UMI counts. The cell barcode is tagged with XC, the UMI is tagged with XM, and the gene is tagged with GE.
Assembly: Xenopus laevis J-strain 9.2
Supplementary files format and content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMI counts, with genes as rows and cells as columns.

extract_protocol:
Tissues or whole-body single-cell dissociation and lysate
Library preparations were performed with the Microwell-seq protocol

tag: strain

value: wild-type

value: one year elder

value: whole organism


title: Micorwell-seq datasets of Xenopus_NF66_COL123

tag: age


title: Micorwell-seq datasets of Xenopus_NF66_COL124


title: Placenta_GDM_Yes_Sample14 [XH2_99]

tag: Sex

value: c-section


title: Plants treated 5 days with rhamnolipid and inoculated with Z. tritici _ repetition 1

description:
Gene expression after 5 days of treatment
R1-D5-i

tag: tissue

value: three weeks after sowing at D0

value: inoculated (i) with Z. tritici


title: Plants at day 5 not treated and not inoculated _ repetition 3

description:
Gene expression after 5 days of treatment
C3-D5-Ni

source_name: Wheat plants at day 5 not treated and not inoculated (Ni) with Z. tritici

value: at day 5 not treated

value: not inoculated (Ni) with Z. tritici


title: Micorwell-seq datasets of Xenopus_NF66_COL121


title: Micorwell-seq datasets of Xenopus_NF66_COL122


title: Placenta_GDM_Yes_Sample13 [HF2_921]

value: Placenta tissue from the fetal side

value: Male

tag: gestational diabetes


title: Plants at day 5 not treated and not inoculated _ repetition 2

description:
Gene expression after 5 days of treatment
C2-D5-Ni


title: MFB16

source_name: Brain

value: Female

value: single octopaminergic/tyraminergic neuron, expressing a membrane-bound GFP reporter.

value: Mutant


title: Placenta_GDM_Yes_Sample11 [HF2_492]

tag: maternal age

value: No


title: Placenta_GDM_Yes_Sample12 [HF2_657]


title: Micorwell-seq datasets of Xenopus_NF59_COL98


title: MFB14

tag: cell type

value: Fluorescent-Activated Cell Sorting


title: MFB13

tag: genotype


title: MFB15

tag: collection strategy


title: Micorwell-seq datasets of Xenopus_NF59_COL96


title: Plants at day 5 not treated and not inoculated _ repetition 1

description:
Gene expression after 5 days of treatment
C1-D5-Ni

value: Alixan

value: leaves


title: Micorwell-seq datasets of Xenopus_NF59_COL97

value: wild-type


title: Micorwell-seq datasets of Xenopus_NF59_COL95

value: one year elder


title: Placenta_GDM_Yes_Sample9 [GF4_711]

value: Yes

tag: pre-pregnancy body mass index


title: Placenta_GDM_Yes_Sample8 [GF4_613]

tag: primiparity

value: c-section


title: MFB11


title: MFB17


title: MFB12


title: Plants treated 5 days with rhamnolipid and not inoculated with Z. tritici _ repetition 3

description:
Gene expression after 5 days of treatment
R3-D5-Ni

source_name: Wheat plants treated 5 days (D5) with rhamnolipid (M) and not inoculated (Ni) with Z. tritici

tag: cultivar

value: three weeks after sowing at D0


title: Plants treated 5 days with rhamnolipid and not inoculated with Z. tritici _ repetition 1

description:
Gene expression after 5 days of treatment
R1-D5-Ni

tag: treatment

value: treated 5 days (D5) with rhamnolipid (M)


title: Placenta_GDM_Yes_Sample7 [XH2_2187]


title: Micorwell-seq datasets of Xenopus_NF54_COL117

value: whole organism


title: Plants treated 5 days with rhamnolipid and not inoculated with Z. tritici _ repetition 2

description:
Gene expression after 5 days of treatment
R2-D5-Ni

tag: inoculation

value: not inoculated (Ni) with Z. tritici


title: Plants at day 2 not treated and not inoculated _ repetition 3

description:
Gene expression after 2 days of treatment
C3-D2-Ni

source_name: Wheat plants at day 2 not treated and not inoculated (Ni) with Z. tritici

value: at day 2 not treated


title: Micorwell-seq datasets of Xenopus_NF54_COL116


title: MFB10


title: Placenta_GDM_Yes_Sample6 [GF4_156]

value: Placenta tissue from the fetal side

tag: gestational age at birth

value: vaginal delivery


title: Placenta_GDM_Yes_Sample10 [HF2_45]

value: Female

tag: mode of delivery


title: Plants at day 2 not treated and not inoculated _ repetition 2

description:
Gene expression after 2 days of treatment
C2-D2-Ni


title: Plants at day 2 not treated and not inoculated _ repetition 1

description:
Gene expression after 2 days of treatment
C1-D2-Ni


title: Placenta_GDM_Yes_Sample5 [GF4_119]

description: There are a total of 96 samples in 12 slides in the experiments (36 samples are not a part of the present study)

value: Male

tag: slide


title: Micorwell-seq datasets of Xenopus_NF54_COL115

tag: strain


title: Placenta_GDM_Yes_Sample4 [CM5_493]


title: Placenta_GDM_Yes_Sample3 [CM5_185]


title: Micorwell-seq datasets of Xenopus_NF54_COL100

tag: age


title: mouse splenic T cells, anti-CD3/CD28 stimulated+DMGV, 24h, biol rep 3

city: Guangzhou

first: Jongdae

last: Lee

state: Guangdong

address: No.195, Dongfengxi Road,

department: School of Basic Medicines

institute: Guangzhou Medical University

description: Column SL3

data_processing:
HISAT2 (v2.0.4)
Sequencing quality was assessed using Agilent 4200 Bioanalyzer. The sequencing data was filtered with SOAPnuke (v1.5.2) to remove the reads containing the sequencing adapter; Reads whose low-quality base ratio (base quality less than or equal to 5) was more than 20% were removed; After removing reads whose unknown base ('N' base) ratio is more than 5%, the clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4), and then expression level of gene was calculated by STRING TIE (v1.2.3).
To get an insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by P value with a rigorous threshold (P value ≤ 0.05) by Bonferroni.
Assembly: mm9
Supplementary files format and content: csv file of read counts for all genes for each sample
Supplementary files format and content: csv file of read counts for all transcripts for each sample
Supplementary files format and content: csv file include FPKM values of all genes for each sample
Supplementary files format and content: csv file include FPKM values of all transcripts for each sample

source_name: spleen

growth_protocol: mouse splenic T cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotices in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using TRIzol (ThermoFisher Scientific).
RNAseq libraries were prepared using the VAHTS TM mRNAseq V2 Library Prep Kit for Illumina® (Vazyme #NR601), and libraries were sequenced on an Illumina Xten to a read depth of 25–35 million reads per sample.

treatment_protocol: mouse splenic T cells were stimulated with anti-CD3/CD28 activators for 24h with or without small molecule DMGV.

value: spleen

tag: cell line

value: primary T cells

value: splenic CD3+ T cells

value: WT

value: anti-CD3/CD28 activator+DMGV (100ng/ml)


title: Plants treated 2 days with rhamnolipid and not inoculated with Z. tritici _ repetition 1

description:
Gene expression after 2 days of treatment
R1-D2-Ni

source_name: Wheat plants treated 2 days (D2) with rhamnolipid (M) and not inoculated (Ni) with Z. tritici

value: Alixan

tag: tissue

value: leaves


title: Plants treated 2 days with rhamnolipid and not inoculated with Z. tritici _ repetition 2

description:
Gene expression after 2 days of treatment
R2-D2-Ni

value: treated 2 days (D2) with rhamnolipid (M)


title: Micorwell-seq datasets of Xenopus_NF48_COL94

last: Chen

value: wild-type

value: one year elder


title: Plants treated 2 days with rhamnolipid and not inoculated with Z. tritici _ repetition 3

description:
Gene expression after 2 days of treatment
R3-D2-Ni

value: three weeks after sowing at D0


title: Placenta_GDM_Yes_Sample1 [CM5_167]

tag: Sex

tag: gestational diabetes

value: Yes

value: c-section


title: Placenta_GDM_Yes_Sample2 [CM5_181]

value: Placenta tissue from the fetal side

tag: maternal age


title: Sample_R19039495-NOVA20190905YMKD-2-MRNA192806HZ-sg2

first: Xiaoli

last: Jin

state: Zhejiang

address: Yuhangtang road 866

data_processing:
The clean reads were mapped to the reference genome of Nipponbare (MSU7.v7.0) using the Bowtie 2 (Cock et al. 2010; Langmead et al. 2009) in HISAT2 version 2.1.0 (Kim et al. 2015)
The isoforms of the same gene were decided using the RSEM software (Li and Dewey 2011). The transcript abundance was measured in terms of Transcripts Per Million (TPM) in the StringTie software.
Gene co-expression analysis was carried out using WGCNA.
Deseq2 (version 1.12.4) was used for differentially expressed gene (DEG) analysis with q-value < 0.001 and |Fold Change| > 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa

source_name: Grain cells

extract_protocol: RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Grains

value: Grain cells

tag: genotype

value: Mutant

tag: time

value: Mature period


title: Sample_R19039495-NOVA20190905YMKD-2-MRNA192806HZ-sg3


title: Micorwell-seq datasets of Xenopus_skin_COL64

value: skin


title: Micorwell-seq datasets of Xenopus_NF48_COL92

value: whole organism


title: Sample_R19039495-NOVA20190905YMKD-2-MRNA192806HZ-NBR3

value: Wild type

value: Control


title: Micorwell-seq datasets of Xenopus_spleen_COL122

value: spleen


title: Micorwell-seq datasets of Xenopus_NF48_COL91


title: Progeria‐HGADFN168‐P27‐R1

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: Tennessee

address: 1311 Cumberland Avenue

department: Department of Biochemistry & Cellular and Molecular Biology

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 https://github.com/dekkerlab/cMapping
Iterative correction was performed using method described by Imakaev et al.
Assembly: hg19
Supplementary files format and content: Each .tar.gz file contains the iteratively corrected and raw matrix.gz files for 40 kb, 100 kb, 250 kb, and 2.5 Mb in their respective directories.  Bin size indicated as “C-40000” for example.  All matrices are for individual chromosomes except for the 2.5 Mb bin size

source_name: Skin fibroblast (HGADFN168, Progeria Research Foundation)

growth_protocol: Fibroblast lines were grown to confluency prior to crosslinking.

extract_protocol:
Briefly, 5-20 million cells were fixed with 1% formaldehyde, suspended in cell lysis buffer for permeabilization, and homogenized by douncing.  Samples were then digested overnight with HindIII or DpnII (as indicated per sample).  Ends were filled in with biotin and ligated.  Then, crosslinking was reversed.
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.

tag: enzyme

value: HindIII

tag: condition

value: WT

tag: media

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

tag: passage

value: Passage 27

tag: hi-c protocol

value: Belton et al., 2012


title: Sample_R19039495-NOVA20190905YMKD-2-MRNA192806HZ-NBR1

tag: treatment


title: mouse splenic T cells, anti-CD3/CD28 stimulated+DMGV, 24h, biol rep 2

description: Column SL2

value: primary T cells

tag: cell type

value: splenic CD3+ T cells

value: anti-CD3/CD28 activator+DMGV (100ng/ml)


title: mouse splenic T cells, anti-CD3/CD28 stimulated+DMGV, 24h, biol rep 1

description: Column SL1


title: Sample_R19039495-NOVA20190905YMKD-2-MRNA192806HZ-NBR2

value: Grains


title: Progeria‐HGADFN168‐P12‐R1

value: Passage 12


title: Micorwell-seq datasets of Xenopus_skin_COL63

value: wild-type

value: one year elder


title: mouse splenic T cells, anti-CD3/CD28 stimulated, 24h, biol rep 3

description: Column Stm3

value: anti-CD3/CD28 activator


title: mouse splenic T cells, anti-CD3/CD28 stimulated, 24h, biol rep 2

description: Column Stm2


title: Micorwell-seq datasets of Xenopus_NF48_COL93

value: whole organism


title: Micorwell-seq datasets of Xenopus_pancreas_COL123

value: pancreas


title: Micorwell-seq datasets of Xenopus_oviduct_COL67

value: oviduct


title: Progeria‐HGADFN167‐P12‐R1

source_name: Skin fibroblast (HGADFN167, Progeria Research Foundation)

value: HGPS (2036C>T, GLY608GLY)


title: Progeria‐HGADFN167‐P19‐R1

value: HindIII

value: Passage 19


title: Micorwell-seq datasets of Xenopus_ovary_COL69

value: ovary


title: Micorwell-seq datasets of Xenopus_ovary_COL70


title: Progeria‐AG11513‐P7‐R2

source_name: Skin fibroblast (Coriell: https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=AG11513&Product=CC)

value: DpnII

value: Passage 7

value: Golloshi et al., 2018


title: mouse splenic T cells, anti-CD3/CD28 stimulated, 24h, biol rep 1

description: Column Stm1

value: spleen

value: primary T cells

value: splenic CD3+ T cells

value: WT


title: Micorwell-seq datasets of Xenopus_muscle_COL126

value: wild-type

value: muscle


title: foxm1 mutant heart 3dpa expt. 3

city: Pittsburgh

first: Michael

last: Tsang

state: PA

address: 3501 Fifth Ave. BST3-5062

department: Cell Biology

institute: University of Pittsburgh

data_processing:
fastq files were analyzed using CLC genomics workbench 20.0
sequence reads were mapped onto Danio rerio GRC.z11
EDGE test was performed using CLC genomics workbench
Assembly: Danio rerio GRC.z11
Supplementary files format and content: Zuppo_3dpa_vs._uninj.xlsx
Supplementary files format and content: Zuppo_WT_vs_foxm1mut_3dpa.xlsx

organism: Danio rerio

source_name: Heart

growth_protocol: Zebrafish adult at 6-1year of age

extract_protocol:
Adutls hearts were injured through ventricular resection and allowed to recover until 3 days post amputation.
Ventricles were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent and Quiagen RNeasy micro kit (Cat# 74004).

value: Heart


title: foxm1 mutant heart 3dpa expt. 2


title: foxm1 mutant heart 3dpa expt. 4


title: Progeria‐AG11513‐P7‐R1


title: WT heart 3dpa expt. 3

value: AB*


title: Micorwell-seq datasets of Xenopus_muscle_COL125

value: one year elder