title: F_P7_normal_mesench_1_DC20_E13

value: Proliferating myofibroblast


title: F_P7_normal_mesench_1_DC20_B14

status: Public on May 27 2021

type: SRA

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

library_source: transcriptomic

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

molecule: total RNA

organism: Mus musculus

source_name: distal lung

extract_protocol:
no extraction
plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

tag: sequencing run

tag: gender

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: normal

tag: cell type

value: mesenchymal

tag: cell subtype

value: Early alveolar fibroblast

tag: mousename

tag: coverage

tag: number of genes


title: JCYL008D

city: Tianjin

first: Yuping

last: Lin

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

country: China

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

data_processing:
Illumina Casava_v1.8.0 software used for basecalling. Sequenced reads were trimmed for adaptor sequence.
Sequence reads were assembled and analyzed in CLC Genomics Workbench 7.0 (CLC Bio, Aarhus, Denmark). The Saccharomyces cerevisiae S288C genome was downloaded from RefSeq at the NCBI (sequence assembly version R64-1-1, http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2/) including 16 chromosomes and the mitochondrial genome. The genes for XYL1 (xylose reductase gene), XYL2 (xylitol dehydrogenase gene), and XKS1 (xylulose kinase gene) from Scheffersomyces stipitis, as well as cdt-2 (coding for cellodextrin transporter 2), gh43-2 (coding for β-xylosidase) and gh43-7 (coding for a xylosyl-xylitol-specific β-xylosidase) from N. crassa were manually annotated and combined with the S. cerevisiae S288C genome as the reference. Expression values were normalized by calculating the reads per kilobase of mRNA exon per million mapped reads (RPKM), and further normalized using the option of “By totals”.
Genome_build: R64; Saccharomyces cerevisiae S288C
Supplementary_files_format_and_content: Excel file includes RPKM values for all the samples.

organism: Saccharomyces cerevisiae

extract_protocol:
Total RNA was extracted using the RiboPure Yeast kit (Ambion, Austin, TX, USA), according to manufacturer's instructions, except cells were disrupted by bead-beating 3 times for 30 sec, with a 30 sec pause between runs.
4 µg of total RNA were used to prepare the multiplexing libraries with barcodes following the standard instructions of the Illumina TruSeq RNA Sample Prep Kit.

tag: strain

value: Engineered SR8U containing xylose-utilizing and xylodextrin-degrading pathway

tag: growth condition

value: Anaerobically

tag: carbon source

value: Xylodextrins

tag: xylose feeding condition

value: 2 h with xylose feeding


title: JCYL007D


title: F_P7_normal_mesench_1_DC20_C8

value: Myofibroblast


title: F_P7_normal_mesench_1_DC20_E19

value: Early adventitial fibroblast


title: F_P7_normal_mesench_1_DC20_L7

value: Early airway smooth muscle


title: F_P7_normal_mesench_2_DC20_G2


title: JCYL007C

value: 1 h with xylose feeding


title: F_P7_normal_mesench_2_DC20_L16


title: F_P7_normal_mesench_1_DC20_I13


title: JCYL008B

value: 0.5 h with xylose feeding


title: JCYL008C


title: JCYL007B


title: F_P7_normal_mesench_1_DC20_A16


title: F_P7_normal_mesench_1_DC20_C22


title: F_P7_normal_mesench_1_DC20_L14

value: Proliferating fibroblast


title: F_P7_normal_mesench_2_DC20_C5


title: JCYL007A

value: No xylose feeding


title: F_P7_normal_mesench_2_DC20_K3


title: JCYL005H

data_processing:
Illumina Casava_v1.8.0 software used for basecalling. Sequenced reads were trimmed for adaptor sequence.
Sequence reads were assembled and analyzed in CLC Genomics Workbench 7.0 (CLC Bio, Aarhus, Denmark). The Saccharomyces cerevisiae S288C genome was downloaded from RefSeq at the NCBI (sequence assembly version R64-1-1, http://www.ncbi.nlm.nih.gov/assembly/GCF_000146045.2/) including 16 chromosomes and the mitochondrial genome. The genes for a cellodextrin transporter gene (cdt-1) and an intracellular β-glucosidase gene (codon-optimized gh1-1) from Neurospora crassa; XYL1 (xylose reductase gene), XYL2 (xylitol dehydrogenase gene), and XKS1 (xylulose kinase gene) from Scheffersomyces stipitis, as well as cdt-2 (coding for cellodextrin transporter 2), gh43-2 (coding for β-xylosidase) and gh43-7 (coding for a xylosyl-xylitol-specific β-xylosidase) from N. crassa were manually annotated and combined with the S. cerevisiae S288C genome as the reference. Expression values were normalized by calculating the reads per kilobase of mRNA exon per million mapped reads (RPKM), and further normalized using the option of “By totals”.
Genome_build: GCF_000146045.2
Supplementary_files_format_and_content: Excel file includes RPKM values for all the samples.

source_name: Anaerobically xylosextrins-grown cells

value: Engineered SR8U containing cellobiose-utilizing, xylose-utilizing and xylodextrin-degrading pathways


title: F_P7_normal_mesench_2_DC20_A16


title: JCYL003E

source_name: Anaerobically glucose-depleted cells

value: Engineered BY4742 containing cellobiose-utilizing pathway

value: Glucose


title: JCYL001E


title: F_P7_normal_mesench_1_DC20_A19

value: F

value: normal


title: JCYL004H


title: F_P7_normal_mesench_2_DC20_I7

value: mesenchymal


title: F_P7_normal_mesench_2_DC20_K11

value: Early alveolar fibroblast


title: JCYL006G

source_name: Anaerobically xylose-grown cells

value: Anaerobically

value: Xylose


title: F_P7_normal_mesench_1_DC20_L5

value: Vascular smooth muscle


title: JCYL005G


title: JCYL004G


title: F_P7_normal_mesench_2_DC20_B9


title: JCYL008A

value: Engineered SR8U containing xylose-utilizing and xylodextrin-degrading pathway

value: Xylodextrins


title: F_P7_normal_mesench_1_DC20_H16

value: Early airway smooth muscle


title: JCYL006F

source_name: Anaerobically cellobiose-grown cells

value: Cellobiose


title: F_P7_normal_mesench_2_DC20_D12

value: Myofibroblast


title: JCYL004F


title: JCYL005F


title: F_P7_normal_mesench_2_DC20_H23


title: F_P7_normal_mesench_1_DC20_D20


title: JCYL004E

source_name: Anaerobically glucose-grown cells


title: JCYL002E


title: JCYL006E


title: JCYL006D

source_name: Aerobically xylosextrins-grown cells

value: Aerobically


title: JCYL005D


title: F_P7_normal_mesench_1_DC20_B19

value: Proliferating pericyte


title: F_P7_normal_mesench_1_DC20_I14


title: F_P7_normal_mesench_2_DC20_E21


title: F_P7_normal_mesench_2_DC20_D17


title: F_P7_normal_mesench_2_DC20_J12


title: JCYL006C

source_name: Aerobically xylose-grown cells

value: Engineered SR8U containing cellobiose-utilizing, xylose-utilizing and xylodextrin-degrading pathways


title: F_P7_normal_mesench_2_DC20_F18

value: Early adventitial fibroblast


title: F_P7_normal_mesench_2_DC20_J5


title: JCYL005C


title: F_P7_normal_mesench_1_DC20_N17


title: JCYL004C


title: F_P7_normal_mesench_1_DC20_K21

value: Pericyte


title: F_P7_normal_mesench_2_DC20_P20

value: F


title: JCYL006B

source_name: Aerobically cellobiose-grown cells


title: JCYL005E

value: Glucose


title: F_P7_normal_mesench_1_DC20_O20

value: normal

value: mesenchymal


title: JCYL005B


title: JCYL004B


title: F_P7_normal_mesench_2_DC20_H16

value: Early alveolar fibroblast


title: F_P7_normal_mesench_2_DC20_J8


title: F_P7_normal_mesench_1_DC20_G14


title: JCYL005A

source_name: Aerobically glucose-grown cells


title: F_P7_normal_mesench_2_DC20_D6


title: JCYL004A


title: JCYL004D


title: F_P7_normal_mesench_1_DC20_O12


title: F_P7_normal_mesench_1_DC20_P14

value: Proliferating myofibroblast


title: HFD_4W_rep5

city: Los Angeles

first: Zhengyi

last: Zhang

address: Westwood

country: USA

institute: UCLA

library_source: genomic

data_processing:
Reads were mapped to the mouse genome (NCBI37/mm9) using Bowtie2 and were removed from the subsequent analysis if they were duplicated, mapped to mitochondrial genome, or aligned to unmapped contiguous sequences. Peak calling was performed using MACS2. The reads were converted to reads per thousand base pairs peak per million mapped reads (RPKM) by dividing by the total number of reads per sample. The average RPKM from four replicates was used to quantify the accessibility across all called peaks.
genome build: mm9
Supplementary_files_format_and_content: bedGraph

molecule: genomic DNA

source_name: Liver

extract_protocol:
DNA was running on 0.7% agarose gel and purified by Qiagen gel extraction kit (REF: 28706).
ATAC-Seq libraries were prepared using the Nextera Tn5 Transposase and DNA library preparation kit (Illumina) as described from original Buenstero protocol (Buenrostro, 2015).

tag: tissue

value: Liver

tag: age

value: 10 weeks

tag: genotype

value: WT

value: High fat diet feeding


title: HFD_4W_rep3


title: HFD_4W_rep1


title: F_P7_normal_mesench_1_DC20_K18

tag: sequencing run

tag: gender


title: HFD_4W_rep4


title: F_P7_normal_mesench_1_DC20_N2

tag: plate

tag: well

value: Early airway smooth muscle


title: HFD_4W_rep2

tag: treatment


title: F_P7_normal_mesench_1_DC20_N20

tag: timepoint

tag: cell type


title: F_P7_normal_mesench_1_DC20_P21

tag: cell subtype

tag: mousename


title: Western_4W_rep5

value: Western diet feeding


title: F_P7_normal_mesench_2_DC20_N23

tag: coverage

tag: number of genes


title: Western_4W_rep4

tag: strain


title: F_P7_normal_mesench_2_DC20_N16

value: Myofibroblast


title: Western_4W_rep3


title: Western_4W_rep2


title: F_P7_normal_mesench_1_DC20_E7


title: JCYL006A

tag: growth condition

value: Aerobically

tag: carbon source


title: F_P7_normal_mesench_1_DC20_O14


title: F_P7_normal_mesench_1_DC20_I15


title: Western_4W_rep1

tag: tissue


title: Chow_4W_rep5

tag: age

value: Chow diet feeding


title: F_P7_normal_mesench_2_DC20_I2


title: Chow_4W_rep4

tag: genotype


title: F_P7_normal_mesench_2_DC20_H20

tag: sequencing run


title: F_P7_normal_mesench_2_DC20_P11

tag: gender


title: GM12878 siMETTL3, Nucleus RNA, rep3

city: Guangzhou

first: Liqiang

last: Tan

address: Zhongshan road 2,74

institute: Sun Yat-sen 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 hg19 whole genome using hisat2 -p 32 -X 1000 --dta --fr --no-unal --add-chrname --no-mixed --no-discordant.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Homo sapiens hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Homo sapiens

growth_protocol: GM12878 cells were cultured in Roswell Park Memorial Institute Medium 1640 (Corning), supplemented with 15% FBS (Biological Industries) at 37 ℃ with 5% CO2

extract_protocol:
RNA-seq libraries of the input, cytoplasmic, and nuclear RNAs of GM12878 with and without METTL3 knockdown were prepared using the VAHTS® mRNA-seq V2 Library Prep Kit for Illumina from Vazyme and sequenced on Illumina HiSeq 2500 platform to generate 150 bp paired-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control and siMETTL3(siNC and specific siRNA using LipoFiter reagent (HANBIO))

value: Blood

tag: cell line

value: METTL3 knockdown

tag: fraction

value: Nucleus RNA


title: GM12878 siMETTL3, Total RNA, rep3

value: Total RNA


title: GM12878 siMETTL3, Total RNA, rep2


title: F_P7_normal_mesench_2_DC20_A6

value: F

tag: plate

tag: well

tag: treatment

value: normal


title: F_P7_normal_mesench_1_DC20_H21

tag: timepoint

tag: cell type

value: mesenchymal

tag: cell subtype


title: Chow_4W_rep3


title: GM12878 siMETTL3, Nucleus RNA, rep2


title: Chow_4W_rep2


title: F_P7_normal_mesench_2_DC20_E4

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_normal_mesench_2_DC20_G15

value: Early alveolar fibroblast


title: GM12878 siMETTL3, Cytosol RNA, rep1

value: Cytosol RNA


title: e6-bcf-33-wtcr-mu-14809

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

data_processing:
Rna-seq reads were aligned with STAR-aligner using the genome build GRCM38.
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited .txt files include 2 columns: ensemble feature identifier and count number.

extract_protocol:
Mice tissue sections were frozen until RNA extraction was performed. RNA was extracted using Trizol reagent (Thermo Fisher) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Skeletal muscle

value: 15 months

tag: Sex

value: Female


title: GM12878 Control, Total RNA, rep3

tag: tissue

value: Control


title: GM12878 siMETTL3, Nucleus RNA, rep1

tag: genotype


title: Chow_4W_rep1

value: Liver

tag: age

value: 10 weeks

value: WT


title: F_P7_normal_mesench_1_DC20_D9

tag: sequencing run

tag: gender

value: Early adventitial fibroblast


title: GM12878 Control, Nucleus RNA, rep3

value: Blood

tag: cell line

tag: fraction


title: e6-bcf-32-mut-mu-14809


title: F_P7_normal_mesench_2_DC20_M4

tag: plate

tag: well


title: GM12878 Control, Total RNA, rep2


title: GM12878 Control, Cytosol RNA, rep3


title: e6-bcf-29-mut-mu-14809


title: GM12878 siMETTL3, Cytosol RNA, rep3

value: METTL3 knockdown


title: F_P7_normal_mesench_1_DC20_P1

tag: timepoint

tag: treatment


title: GM12878 Control, Nucleus RNA, rep2

value: Nucleus RNA


title: GM12878 siMETTL3, Cytosol RNA, rep2


title: GM12878 Control, Cytosol RNA, rep2


title: F_P7_normal_mesench_1_DC20_B15

tag: cell type

tag: cell subtype


title: e6-bcf-24-wtcr-mu-14809


title: GM12878 Control, Cytosol RNA, rep1


title: GM12878 Control, Total RNA, rep1

value: Total RNA


title: e6-bcf-28-wtcr-mu-14809


title: GM12878 siMETTL3, Total RNA, rep1


title: e6-bcf-23-mut-mu-14809


title: HEYA8i-ECM1b (A8i-B)

city: Shanghai

first: Gong

last: Yang

address: Dong'an Rd

institute: Fudan Univesity Shanghai Cancer Center

data_processing:
Cufflinks (v2.2.1) was used to estimate the gene expression levels in the alignment file
Trim Galore software was used to dynamically remove adapter sequence fragments and low-quality fragments at the 3' ends
FastQC software was used to conduct quality control of the preprocessed data
Differentially expressed genes (DEGs) between different time points (12 hpt vs. 0 hpt, 36 hpt vs. 0 hpt, and 72 hpt vs. 0 hpt) were determined using the MA-plot-based method with random sampling (MARS) model in the DEGseq package
DEGs were chosen for functional and signaling pathway enrichment analysis using the GO and KEGG databases
Genome_build: GRCm38
Supplementary_files_format_and_content: gene sample event count with symbol.txt

source_name: human ovary

growth_protocol: Cells were cultured with RPMI1640 supplemented with 10% FBS, 50 U/ml penicillin, and 50 μg/ml streptomycin at 5% of carbon dioxide

extract_protocol:
Total RNA was extracted by Trizol reagent with the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HEYA8i-ECM1b (A8i-B)

value: ovarian cancer

tag: genotype/variation

value: HEYA8i-derived cells with stable expression of ECM1b


title: HEYA8i-ECM1a (A8i-A)

value: HEYA8i-ECM1a (A8i-A)

value: HEYA8i-derived cells with stable expression of ECM1a


title: F_P7_normal_mesench_2_DC20_A1

value: F

value: normal

value: mesenchymal

value: Early airway smooth muscle

tag: mousename

tag: coverage

tag: number of genes


title: HEYA8i (A8i)

value: HEYA8i (A8i)

value: HEYA8-derived cells with stable silencing of ECM1


title: e6-bcf-22-mut-mu-14809

tag: strain

tag: tissue

value: Skeletal muscle

value: 15 months

tag: Sex

value: Female


title: F_P7_normal_mesench_1_DC20_F12

tag: sequencing run

value: Proliferating myofibroblast


title: F_P7_normal_mesench_1_DC20_D12

tag: gender


title: HEYA8 (A8)

tag: cell line

value: HEYA8 (A8)

value: HEY-derived cells


title: e6-bcf-21-wtcr-mu-14809

tag: genotype

value: WT

tag: age


title: Treg_non_GVHD_PB5

city: TianJin

first: Changlu

last: Xu

state: TianJin

address: 288 Nanjing Rd, Heping

department: State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description:
P5_PB
Treg_non_GVHD_PB_gene_counts.csv.gz
Non_GVHD_PB_Treg_barcodes_samples_info.csv

data_processing:
10X Genomics CellRanger version 3.0.2 were used to the basecalling.
Cell Ranger (version 3.0.2) software from 10X Genomics (http://www.10xgenomics.com) was used to aligned and quantified sequencing raw data with default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma separated values files include UMI values for each cell

molecule: polyA RNA

source_name: human regulatory T cells

extract_protocol: The libraries were constructed and  sequenced on Illumina Hiseq X Ten platform in 150 bp pair-ended manner (sequenced by Novogene).

value: human regulatory T cells

tag: tissue/cell type

value: Peripheral Blood

tag: development stage

value: Adult

value: Male

tag: disease

value: AA


title: F_P7_normal_mesench_1_DC20_I6

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: normal

tag: cell type

value: Myofibroblast


title: e6-bcf-18-mut-mu-14809


title: Treg_non_GVHD_PB3

description:
P3_PB
Treg_non_GVHD_PB_gene_counts.csv.gz
Non_GVHD_PB_Treg_barcodes_samples_info.csv

value: AML


title: Treg_non_GVHD_PB2

description:
P2_PB
Treg_non_GVHD_PB_gene_counts.csv.gz
Non_GVHD_PB_Treg_barcodes_samples_info.csv


title: 95 Severe Covid-19

city: Créteil

first: cecile

last: lefebvre

address: 51 Avenue du Marechal De Lattre de Tassigny

country: France

institute: INSERM U955_VRI

description:
Data_RNAseq_norm_counts_geo.csv
Data_RNAseq_raw_counts_geo.csv

data_processing:
Base calls were performed using Illumina CASAVA 1.8.2
Transcript reads were aligned to the hg18 human reference genome using Salmon v0.8.2 (Patro et al., 2017) and quantified relative to annotation model "hsapiens_gene_ensembl" recovered from the R package biomaRt v2.42.1 (Durinck et al., 2009). Quality control of the alignment was performed via MultiQC v1.4 (Patro et al., 2017). Finally, counts were normalized as counts per million
Genome_build: hg18
Supplementary_files_format_and_content: Counts were normalized as counts per million

source_name: Blood

extract_protocol:
Total RNA was purified from whole blood with the Tempus™ Spin RNA Isolation Kit (Invitrogen) and globine mRNA depletion carried out with GLOBINclear™ Kit
mRNA libraries were prepared with the Illumina TruSeq® Stranded mRNA kit. Single read of 101 bp sequencing was performed on the Illumina HiSeq 2500 at Vaccine Research Institute genomic Platform

tag: status

value: Severe Covid-19


title: e6-bcf-15-mut-mu-14809

tag: strain

value: Skeletal muscle


title: GM12878 Control, Nucleus RNA, rep1

tag: tissue

value: Blood

value: Control

tag: fraction

value: Nucleus RNA


title: F_P7_normal_mesench_2_DC20_C22

tag: sequencing run

value: mesenchymal

tag: cell subtype

value: Early airway smooth muscle

tag: mousename

tag: coverage

tag: number of genes


title: F_P7_normal_mesench_2_DC20_C18

tag: gender


title: F_P7_normal_mesench_2_DC20_M13

value: Early adventitial fibroblast


title: e6-bcf-14-wtcr-mu-14809

tag: genotype

value: WT

tag: age

value: 15 months

tag: Sex

value: Female


title: 92 Severe Covid-19


title: Treg_non_GVHD_PB1

description:
P1_PB
Treg_non_GVHD_PB_gene_counts.csv.gz
Non_GVHD_PB_Treg_barcodes_samples_info.csv

value: human regulatory T cells

tag: tissue/cell type

value: Peripheral Blood

tag: development stage

value: Adult

value: Male

tag: disease

value: RCC


title: Treg_non_GVHD_BM4

description:
P6_BM
Treg_non_GVHD_BM_gene_counts.csv.gz
Non_GVHD_BM_Treg_barcodes_samples_info.csv

tag: cell type

value: Bone Marrow

value: ALL


title: Treg_non_GVHD_BM3

description:
P3_BM
Treg_non_GVHD_BM_gene_counts.csv.gz
Non_GVHD_BM_Treg_barcodes_samples_info.csv

value: AML


title: 91 Severe Covid-19

tag: status

value: Severe Covid-19


title: F_P7_normal_mesench_1_DC20_H12

value: F

tag: plate

tag: well

tag: timepoint

tag: treatment

value: normal

value: Early alveolar fibroblast


title: e6-bcf-13-wtcr-mu-14809

tag: strain

tag: tissue

value: Skeletal muscle


title: F_P7_normal_mesench_2_DC20_I18

tag: sequencing run

value: mesenchymal

tag: cell subtype

tag: mousename

tag: coverage


title: 87 Severe Covid-19


title: e6-bcf-11-mut-mu-14809

tag: genotype

tag: age


title: Treg_non_GVHD_PB4

description:
P4_PB
Treg_non_GVHD_PB_gene_counts.csv.gz
Non_GVHD_PB_Treg_barcodes_samples_info.csv

tag: tissue/cell type

tag: gender

value: MDS


title: 101 Severe Covid-19


title: e6-bcf-07-mut-mu-14809

value: 15 months

tag: Sex


title: 85 Severe Covid-19


title: Treg_non_GVHD_BM1

description:
P1_BM
Treg_non_GVHD_BM_gene_counts.csv.gz
Non_GVHD_BM_Treg_barcodes_samples_info.csv

tag: cell type

tag: development stage

tag: disease


title: F_P7_normal_mesench_2_DC20_N2

tag: plate

tag: well

tag: number of genes


title: F_P7_normal_mesench_2_DC20_J7

tag: timepoint

tag: treatment

value: Proliferating myofibroblast


title: 83 Severe Covid-19

tag: status


title: 84 Severe Covid-19


title: Treg_GVHD_PB5

description:
P11_PB
Treg_GVHD_PB_gene_counts.csv.gz
GVHD_PB_Treg_barcodes_samples_info.csv

value: human regulatory T cells


title: e6-bcf-05-mut-mu-14809

tag: strain

tag: tissue

value: Female


title: F_P7_normal_mesench_1_DC20_H5

tag: sequencing run

tag: cell subtype

value: Myofibroblast

tag: mousename

tag: coverage


title: F_P7_normal_mesench_2_DC20_N11

tag: gender

value: Vascular smooth muscle


title: 82 Severe Covid-19


title: Treg_GVHD_PB4

description:
P10_PB
Treg_GVHD_PB_gene_counts.csv.gz
GVHD_PB_Treg_barcodes_samples_info.csv

tag: tissue/cell type

value: Peripheral Blood

value: Adult

value: Male

tag: age


title: e6-bcf-03-mut-mu-14809

tag: genotype

tag: Sex


title: 77 Severe Covid-19


title: F_P7_normal_mesench_1_DC20_M7

tag: plate

tag: cell type


title: Treg_GVHD_PB3

description:
P9_PB
Treg_GVHD_PB_gene_counts.csv.gz
GVHD_PB_Treg_barcodes_samples_info.csv

tag: development stage

tag: disease


title: 81 Severe Covid-19


title: F_P7_normal_mesench_1_DC20_L22

tag: well

tag: timepoint

tag: treatment

tag: number of genes


title: e6-bcf-04-wtcr-mu-14809

tag: strain

tag: tissue

value: WT


title: Treg_GVHD_PB2

description:
P8_PB
Treg_GVHD_PB_gene_counts.csv.gz
GVHD_PB_Treg_barcodes_samples_info.csv


title: e6-a2f-51-wtcr-mu-14810

value: 9 months


title: F_P7_normal_mesench_2_DC20_M23

tag: sequencing run

value: F

tag: cell subtype

tag: mousename


title: e6-bcf-06-wtcr-mu-14809


title: Treg_non_GVHD_BM2

description:
P2_BM
Treg_non_GVHD_BM_gene_counts.csv.gz
Non_GVHD_BM_Treg_barcodes_samples_info.csv

tag: tissue/cell type

value: Bone Marrow

tag: gender

value: AA


title: F_P7_normal_mesench_2_DC20_J17

value: normal

value: Early adventitial fibroblast

tag: coverage


title: e6-a2f-48-wtcr-mu-14810

value: Skeletal muscle

tag: genotype

tag: age

tag: Sex


title: 74 Severe Covid-19

tag: status

value: Severe Covid-19


title: Treg_GVHD_PB6

description:
P12_PB
Treg_GVHD_PB_gene_counts.csv.gz
GVHD_PB_Treg_barcodes_samples_info.csv

tag: cell type

tag: development stage

tag: disease

value: AML


title: Treg_GVHD_BM3

description:
P10_BM
Treg_GVHD_BM_gene_counts.csv.gz
GVHD_BM_Treg_barcodes_samples_info.csv

value: human regulatory T cells


title: 73 Severe Covid-19


title: e6-a2f-47-mut-mu-14810

value: Female


title: Treg_GVHD_PB1

description:
P7_PB
Treg_GVHD_PB_gene_counts.csv.gz
GVHD_PB_Treg_barcodes_samples_info.csv

value: MDS


title: 72 Severe Covid-19


title: e6-a2f-42-wtcr-mu-14810


title: F_P7_normal_mesench_2_DC20_J1

tag: plate

tag: well

tag: timepoint

tag: treatment

value: mesenchymal

value: Early alveolar fibroblast


title: F_P7_normal_mesench_1_DC20_C3

tag: sequencing run

tag: number of genes


title: Treg_GVHD_BM2

description:
P8_BM
Treg_GVHD_BM_gene_counts.csv.gz
GVHD_BM_Treg_barcodes_samples_info.csv

value: Adult


title: e6-a2f-52-mut-mu-14810

tag: strain

tag: tissue


title: 71 Severe Covid-19


title: Treg_GVHD_BM1

description:
P7_BM
Treg_GVHD_BM_gene_counts.csv.gz
GVHD_BM_Treg_barcodes_samples_info.csv

tag: tissue/cell type

tag: gender

value: Male


title: F_P7_normal_mesench_2_DC20_M9

tag: cell subtype

value: Myofibroblast

tag: mousename

tag: coverage


title: HD9_BM.TCR

description: TCR

data_processing:
10X Genomics CellRanger version 3.0.2 were used to the basecalling.
Cell Ranger (version 3.0.2) software from 10X Genomics (http://www.10xgenomics.com) was used to aligned and quantified sequencing raw data with default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma separated values files include UMI values for each cell and barcode information

source_name: Bone Marrow

value: M

tag: age

value: healthy donor


title: 70 Severe Covid-19

tag: status


title: e6-a2f-40-wtcr-mu-14810

tag: genotype

value: WT

value: 9 months

tag: Sex


title: e6-a2f-39-mut-mu-14810


title: 69 Severe Covid-19


title: 67 Severe Covid-19


title: HD8_PB.TCR

description: TCR

source_name: Peripheral Blood

tag: cell type

value: Peripheral Blood

tag: development stage

value: F

tag: disease


title: e6-a2f-36-wtcr-mu-14810

value: Skeletal muscle


title: e6-a2f-37-mut-mu-14810


title: F_P7_normal_mesench_1_DC20_D17

tag: plate

tag: well

tag: timepoint

tag: treatment

value: normal


title: 66 Severe Covid-19

value: Severe Covid-19


title: HD7_PB.TCR

description: TCR

value: human regulatory T cells

tag: tissue


title: F_P7_normal_mesench_2_DC20_E23

tag: sequencing run

tag: number of genes


title: 65 Severe Covid-19


title: HD6_PB_tcon

description: TCR

tag: gender


title: F_P7_normal_mesench_1_DC20_M1

tag: cell subtype

tag: mousename


title: 62 Severe Covid-19


title: F_P7_normal_mesench_2_DC20_N17

tag: coverage


title: 58 Severe Covid-19

tag: status


title: F_P7_normal_mesench_2_DC20_G22


title: HD6_PB.TCR

description: TCR

tag: age


title: F_P7_normal_mesench_1_DC20_P7


title: 56 Severe Covid-19


title: F_P7_normal_mesench_1_DC20_A10


title: HD5_PB.TCR

description: TCR


title: HD4_PB.TCR

description: TCR


title: F_P7_normal_mesench_2_DC20_N14

value: Proliferating fibroblast


title: HD4_BM.TCR

description: TCR

value: Bone Marrow


title: WT1 E16.5

city: Rochester

first: Eric

last: Small

state: NY

address: 601 Elmwood Avenue, Box CVRI

institute: University of Rochester

data_processing:
Demultiplexing from basecalls using cellranger-2.1.1 mkfastq
Cell counting against mm10 using cellranger-2.1.1 count
Genome_build: mm10
Supplementary_files_format_and_content: filtered gene matrices containing a mapping between the barcodes, genes, and counts for each sample

source_name: Epicardium-Derived Cells

growth_protocol: Hearts were removed from mouse embryos at embryonic age (E)12.5 or E16.5 for the collection of epicardial cells. Following heart removal, the extraction protocol was immediately performed. For the collection of endothelial cells, hearts were removed from mouse embryos at E14.5. Ex vivo hearts were cultured for 2 hours in M199/DMEM High Glucose media containing 1% FBS and 1% Pen-Strep at conditions of 5% CO2 and 37℃. Following the 2 hour incubation the extraction protocol was performed.

extract_protocol:
Cell isolation of epicardial cells at E12.5 and E16.5 for scRNA-seq: EPDCs were collected from Wt1CreERT2/+ ; R26mTmG/+ embryos that were administered 4-OHT at E9.5 and E10.5 via pregnant dams. A total of 7 E12.5 staged hearts were pooled from 2 dams; and a total of 17 E16.5 staged hearts were pooled from 4 dams based on visual confirmation of green fluorescent protein (GFP) expression in the epicardium using a Zoe Fluorescent Cell Imager (Bio-rad). Hearts negative for the expression of the Wt1CreERT2 allele, exhibited tdTomato fluorescence alone and were either discarded or used as tdTomato positive fluorescent controls for flow cytometry. Developmentally timed C57BL/6J embryos were utilized for flow cytometry as non-fluorescence controls. Additionally, genomic DNA was isolated from all embryos and all visually screened Wt1CreERT2 ; R26mTmG/+ positive embryos were confirmed using transgene specific primers followed by PCR (genotyping). Following the digestion protocol describe above, EPDCs were gated as single cells (based on FSC x SSC dimensions), DAPI negative, tdTomato negative and GFP positive. TdTomato positive cells were sorted for downstream gene expression analysis. EPDCs collected via FACS were immediately processed for single cell capture and sequencing. Cell isolation of endothelial cells at E14.5 for scRNA-seq: Endothelial cells (ECs) were collected from Wt1CreERT2/+ mice (Control) and Wt1CreERT2/+ ; Mrtf-a-/- ; Mrtf-bflox/flox (MRTFepiDKO) after administration of 4-OHT at E9.5 and E10.5 via pregnant dams. A total of 10 Control hearts were pooled from 2 dams; and a total of 7 MRTFepiDKO hearts were pooled from 2 dams. Prior to digestion, hearts were placed in HBSS at 37°C and 5% CO2 and genomic DNA from all embryos was subjected to genotyping to detect the Wt1CreERT2 allele within two hours. Following confirmation of positive embryos, hearts were subjected to the digestion protocol described above. After filtering and centrifuging cells, ECs were incubated with fluorescently conjugated bodies to select for vascular cells (CD31-APC; BD Biosciences 551262) and exclude hematopoietic cells (CD45-FITC; BD Biosciences 553079) for 30 minutes in 0.5% BSA in DPBS and on ice. After antibody labeling, cells were washed and centrifuged at 200g for 5 minutes and then in 10%FBS/DMEM buffer. ECs were gated as single cells, DAPI negative, CD45-FITC negative and CD31 positive. ECs collected were immediately processed for single cell capture and sequencing.
Cellular suspensions were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-in-Emulsions (GEMs). Single-cell RNA-Seq libraries were prepared using Chromium Single-Cell 3′ Library & Gel Bead Kit (10x Genomics). The beads were dissolved and cells were lysed per manufacturer’s recommendations. GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken and the pooled post-GEM-RT reaction mixtures were recovered and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, PN37002D, ThermoFisher Scientific). The entire purified post GEM-RT product was amplified by PCR. This amplification reaction generated sufficient material to construct a 3’ cDNA library.  Enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification. Sequence data was generated using Illumina’s HiSeq2500v4.

tag: background strain

tag: genotype

value: Wt1CreERT2/+ ; R26 mTmG/+

tag: developmental stage

value: heart

value: Epicardium-Derived Cells

value: 4-Hydroxytamoxifen 75mg/kg administered at E9.5 and E10.5

tag: 10x library


title: HD8_BM.TCR

description: TCR

tag: cell type

tag: development stage

value: Adult

tag: disease


title: 43-C Severe Covid-19


title: 42-C Severe Covid-19


title: e6-a2f-34-wtcr-mu-14810

tag: strain

tag: Sex

value: Female


title: F_P7_normal_mesench_2_DC20_B15

source_name: distal lung

tag: sequencing run

tag: plate

tag: well

tag: timepoint

tag: treatment

value: mesenchymal

value: Early alveolar fibroblast


title: Treg_HD_PB_tcon

description: TCR

value: human conventional T cells

tag: tissue

tag: gender

value: M

value: healthy donor


title: 41-C Severe Covid-19

tag: status


title: e6-a2f-32-mut-mu-14810

value: Skeletal muscle

tag: age

value: 9 months


title: KO E14.5 CD31Pos

source_name: Endothelial Cells

tag: background strain

tag: genotype

value: Wt1CreERT2/+; MRTF-A -/- ; MRTF-B fl/fl

value: Endothelial Cells


title: WT E14.5 CD31Pos

tag: developmental stage

tag: 10x library


title: F_P7_normal_mesench_2_DC20_I13

value: F

value: normal

tag: cell type

tag: cell subtype

tag: mousename

tag: coverage

tag: number of genes


title: Treg_HD_PB8

description:
Treg_HD_PB_gene_counts.csv.gz
HD_PB_Treg_barcodes_samples_info.csv

value: human regulatory T cells

value: Peripheral Blood

tag: development stage

tag: disease


title: Human pleural mesothelioma cell line Meso241 CNV

type: genomic

city: Nantes

first: Jean-Francois

last: Fonteneau

address: 8 quai Moncousu BP70721

institute: INSERM

description: Hybridized to CytoscanHD

hyb_protocol: DNA (500 ng) was processed and hybridized to Affymetrix CytoScanHD Array according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the GeneChip Scanner 3000 7G

data_processing:
The detection, determination and visualization of gains, losses were performed using Affymetrix Chromosome Analysis Suite software (ChAS v3.1.1.27).
Copy number variant using CN and SNP probe

label: Biotin

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Human pleural mesothelioma were established from pleural effusions cells cultured in RPMI containing 10% heat-inactivated fetal calf serum, 100U/mL penicillin, 100μg/mL streptomycin and 2mM L-glutamine (all reagents from Gibco-Invitrogen) and cultured at 37°C in a 5% CO2 atmosphere.

extract_protocol: Genomic DNA was extracted with Nucleospin® Blood kit (Macherey-Nagel) according to the manufacturer's instructions.

value: Mesothelioma


title: 38-C Severe Covid-19

description:
Data_RNAseq_norm_counts_geo.csv
Data_RNAseq_raw_counts_geo.csv

value: Severe Covid-19


title: Human pleural mesothelioma cell line Meso182 CNV

description: Hybridized to CytoscanHD


title: Treg_HD_PB7

value: Adult


title: e6-a2f-29-mut-mu-14810

tag: strain

tag: Sex

value: Female


title: WT1 E12.5

value: Wt1CreERT2/+ ; R26 mTmG/+

tag: tissue

value: heart

value: Epicardium-Derived Cells

tag: treatment

value: 4-Hydroxytamoxifen 75mg/kg administered at E9.5 and E10.5


title: F_P7_normal_mesench_2_DC20_I21

tag: sequencing run

tag: gender

tag: plate

tag: well

tag: timepoint

value: mesenchymal

value: Early airway smooth muscle


title: Treg_HD_PB6

value: M

tag: age

value: healthy donor


title: 36-C Severe Covid-19

tag: status


title: 37-C Severe Covid-19


title: F_P7_normal_mesench_2_DC20_J11

tag: cell type

tag: cell subtype


title: Human pleural mesothelioma cell line Meso156 CNV

description: Hybridized to CytoscanHD


title: Treg_HD_PB5


title: Human pleural mesothelioma cell line Meso152 CNV

description: Hybridized to CytoscanHD


title: Treg_HD_PB4


title: 34-C Severe Covid-19


title: F_P7_normal_mesench_2_DC20_D10

value: Early alveolar fibroblast

tag: mousename

tag: coverage


title: Human pleural mesothelioma cell line Meso150 CNV

description: Hybridized to CytoscanHD


title: 33-C Severe Covid-19


title: Human pleural mesothelioma cell line Meso148 CNV

description: Hybridized to CytoscanHD


title: Treg_HD_PB3

tag: development stage


title: F_P7_normal_mesench_1_DC20_N16

value: F

value: Myofibroblast

tag: number of genes


title: Human pleural mesothelioma cell line Meso144 CNV

description: Hybridized to CytoscanHD


title: 32-C Severe Covid-19


title: Treg_HD_PB2

value: human regulatory T cells

tag: disease


title: 30-C Severe Covid-19


title: F_P7_normal_mesench_2_DC20_P12

value: normal

value: Pericyte


title: Human pleural mesothelioma cell line Meso122 CNV

description: Hybridized to CytoscanHD

value: Mesothelioma


title: 29-C Severe Covid-19

value: Severe Covid-19


title: F_P7_normal_mesench_1_DC20_K14


title: F_P7_normal_mesench_1_DC20_K6


title: Human pleural mesothelioma cell line Meso95 CNV

description: Hybridized to CytoscanHD


title: Treg_HD_BM6

description:
Treg_HD_BM_gene_counts.csv.gz
HD_BM_Treg_barcodes_samples_info.csv

value: Bone Marrow

value: Adult


title: F_P7_normal_mesench_1_DC20_H11


title: Human pleural mesothelioma cell line Meso75 CNV

description: Hybridized to CytoscanHD


title: 28-C Severe Covid-19


title: F_P7_normal_mesench_2_DC20_M19


title: F_P7_normal_mesench_1_DC20_E10


title: Treg_HD_BM5


title: 25-C Severe Covid-19


title: F_P7_normal_mesench_2_DC20_C20


title: Treg_HD_BM4


title: Human pleural mesothelioma cell line Meso70 CNV

description: Hybridized to CytoscanHD


title: Human pleural mesothelioma cell line Meso62 CNV

description: Hybridized to CytoscanHD


title: F_P7_normal_mesench_1_DC20_J13


title: 24-C Severe Covid-19


title: Treg_HD_BM3


title: Treg_HD_BM2


title: 21-C Severe Covid-19


title: Treg_HD_BM1


title: Human pleural mesothelioma cell line Meso55 CNV

description: Hybridized to CytoscanHD


title: Human pleural mesothelioma cell line Meso56 CNV

description: Hybridized to CytoscanHD


title: Treg_HD_PB1

value: Peripheral Blood


title: 19-C Severe Covid-19


title: F_P7_normal_mesench_2_DC20_D21


title: 26-C Severe Covid-19


title: Human pleural mesothelioma cell line Meso52 CNV

description: Hybridized to CytoscanHD


title: YOH

first: lihua

last: Yuan

address: cailun road num 1200

institute: Shanghai university of traditional Chinese medicine

data_processing:
For RNA-Seq comparison, Sequencing reads were mapped to rat with STAR by default parameter. The read counts for each genes were calculated by featurecounts. The count files were used as input to DESeq2 for differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: DESeq was used for calling differential expression.tab-delimited text files include normalized read counts,foldChange,pvalue

source_name: MII Oocytes

growth_protocol: All included patients received standard antagonist protocol for ovarian stimulation. In brief, patients were injected with recombinant FSH (Gonal-F, Merck, Italy) on the 2nd day of the menstrual cycle with a starting dose of 150IU/d, transvaginal ultrasound scanning and hormone of blood sampling were applied to monitor follicle growth. When more than two follicles were larger than 18mm in diameter, 0.1mg of Gonadotrophin releasing hormone agonist (Triptorelin, Ferring GmbH, Germany) was injected subcutaneously and 4000IU of human chorionic gonadotropin was injected intramuscularly to trigger final maturation. After 36 hours of triggering, transvaginal oocyte retrieval was performed under the guidance of ultrasound scanning under anesthesia.

extract_protocol:
Oocytes were exposed to solution with 80IU hyaluronidase (Sigma, USA) and manipulated with pipettes to remove cumulus cells. Then oocyte were rinsed in Ca2+/Mg2+ free PBS solution and individually placed in 0.2 ml PCR tubes containing 10μl Invitrogen TRIzol. The samples was stored at -80℃ pending further processing until RNA was isolated with the E.Z.N.A. ®Total RNA kit ‖ ( (OMEGA, USA).
RNA from single oocyte was amplified by Smart-seq2

value: Oocyte

value: less than 30 years


title: 18-C Severe Covid-19


title: F_P7_normal_mesench_1_DC20_G4

value: mesenchymal

value: Proliferating myofibroblast


title: YOG


title: F_P7_normal_mesench_2_DC20_L2


title: 12-C Severe Covid-19


title: Human pleural mesothelioma cell line Meso43 CNV

description: Hybridized to CytoscanHD


title: F_P7_normal_mesench_2_DC20_I15


title: YOF


title: Human pleural mesothelioma cell line Meso37 CNV

description: Hybridized to CytoscanHD


title: YOD


title: 1-C Severe Covid-19


title: F_P7_normal_mesench_2_DC20_L23


title: YOC


title: F_P7_normal_mesench_2_DC20_G19

value: Proliferating fibroblast


title: 3538-V Healthy

value: Healthy


title: YOB


title: 3136-V Healthy


title: OOH

value: greater than 40 years


title: Human pleural mesothelioma cell line Meso36 CNV

description: Hybridized to CytoscanHD


title: Human pleural mesothelioma cell line Meso34 CNV

description: Hybridized to CytoscanHD


title: F_P7_normal_mesench_1_DC20_O5

value: F


title: Human pleural mesothelioma cell line Meso35 CNV

description: Hybridized to CytoscanHD


title: F_P7_normal_mesench_1_DC20_O19

value: Myofibroblast


title: Human pleural mesothelioma cell line Meso30 CNV

description: Hybridized to CytoscanHD


title: 3054-V Healthy


title: F_P7_normal_mesench_2_DC20_M5

value: Early airway smooth muscle


title: F_P7_normal_mesench_1_DC20_B6

value: normal


title: 9-C Severe Covid-19


title: 2064-V Healthy


title: OOG


title: OOF


title: 1995-V Healthy


title: Ps4

city: Poznań

first: Aleksandra

last: Obrepalska-Steplowska

address: 20 Władysława Węgorka

country: Poland

institute: Institute of Plant Protection - National Research Institute

description:
sRNA
Small RNA-Seq
processed data file: top_expressed_RPM_txt.txt

data_processing:
Adapter-free sRNA reads were subjected to quality filtering with fastq_quality_filter from FASTX-Toolkit package (http://hannonlab.cshl.edu/fastx_toolkit/) using –p 95 and –q 20 parameters. Sequence redundancy and counting read occurrences (i.e. raw expression values) were done with fastx_collapser from the same package.
Short reads were compared against noncoding RNAs from RFAM (Kalvari et al., 2017) and miRNA precursors from miRBase (Kozomara and Griffiths-Jones, 2014). The comparison was performed with Bowtie (Langmead et al., 2009) allowing for no mismatches.
Supplementary_files_format_and_content: top_expressed_RPM_txt.txt: Tab-delimited text file includes reads per million (RPM) values for each Sample.

organism: Nicotiana benthamiana

source_name: virus treated plant leaf

growth_protocol: N. benthamiana plants were grown in controlled conditions in separate greenhouse chambers with 14 h light/10 h dark in 21 °C day/16 °C night cycles.

extract_protocol:
Total RNA was extracted according to (Wieczorek et al., 2013) followed by DNA digestion using DNase I, RNase-free (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions.
Small RNA libraries were prepared for sequencing according to "Normal Small RNA Library Construction Protocol" (BGI, Denmark).

treatment_protocol: Four four-leaf-stage seedlings per condition were carborundum-dusted and rub-inoculated with 10 µg of PSV-P infectious clones, alone or in combination with 1 µg of satRNA-P infectious clone (obtained as previously described), in 0.05 M phosphate buffer, pH 7.5. Mock-inoculated (0.05 M phosphate buffer, pH 7.5) plants were used as controls. Plant material (all leaves including the inoculated ones) was harvested at five days post inoculation.

value: PSV-P+satRNA

value: Treated plant leaf


title: F_P7_normal_mesench_2_DC20_N9

value: Pericyte


title: OOE


title: 1951-V Healthy


title: Ps2


title: Ps3


title: Ps1


title: 1918-V Healthy


title: OOD


title: P4

value: PSV-P


title: OOA


title: 1406-V Healthy


title: F_P7_normal_mesench_1_DC20_L11


title: F_P7_normal_mesench_1_DC20_F21

value: Vascular smooth muscle


title: 507-V Healthy


title: 1189-V Healthy


title: P2


title: F_P7_normal_mesench_2_DC20_C12

value: Adventitial fibroblast


title: P3


title: F_P7_normal_mesench_1_DC20_C17


title: P1


title: F_P7_normal_mesench_2_DC20_L11

value: Early alveolar fibroblast


title: pSBtet_GP_MLLex1_9_AF6ex2_30pSBtet_RP_AF6ex1_MLLex10_37_3

city: Frankfurt am Main

first: Lukas

last: Jost

address: Altenhöferallee 3

country: Germany

institute: GenXPro GmbH

data_processing:
Library strategy: MACE-seq
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and bad quality as well as MACE specific polyA stretches; PCR artifacts were deduplicated based on Unique Molecular Identifier sequences
Cleaned reads were mapped onto GRCh38 genome using bowtie2 and raw counts were obtained using HTSeq
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count values for each group
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: stably transfected HEK293T cells were expanded in DMEM/FCS

extract_protocol:
Qiagen RNA Purification with DNAse I treatment
Massive Analysis of cDNA ends (MACE-Seq)

treatment_protocol: transgene induction was carried out with 1µg/ml doxyxcycline

value: HEK293T kidney cells

tag: transduction

value: empty vector (pSBTet-GP)

value: transgene was induced for 48h by 1µg/ml Doxycycline


title: pSBtet_GP_MLLex1_9_AF6ex2_30pSBtet_RP_AF6ex1_MLLex10_37_1


title: pSBtet_GP_MLLex1_21_AF6ex2_30_pSBtet_RB_AF6ex1_MLLex22_37_3


title: pSBtet_GP_MLLex1_9_AF6ex2_30pSBtet_RP_AF6ex1_MLLex10_37_2


title: F_P7_normal_mesench_2_DC20_C1

value: mesenchymal


title: Cerebellum 2Month WT rep4

city: Greenville

first: Jessica

middle: M

last: Ellis

state: NC

address: 115 Heart Drive

institute: Department of Physiology at the Bro

data_processing:
eva;uate sequence quality
trim reads
map reads to genome
generate hit counts for genes/exons
Genome_build: Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Supplementary_files_format_and_content: excel file with gene counts per sample by column and ensemble IDs

source_name: Cerebellum

extract_protocol:
Brains were removed and cerebellum dissected out, flash frozen in liquid nitrogen and RNA was harvested using Trizol then sent to Genewiz.
RNA libraries were prepared for with poly-A RNA by Genewiz

tag: strain

tag: tissue

value: cerebellum

value: 2 months

tag: genotype

value: control


title: F_P7_normal_mesench_2_DC20_O6

tag: sequencing run

tag: gender

value: F

tag: treatment

value: Myofibroblast


title: Cerebellum 2Month WT rep3


title: M3

value: Mock


title: M4


title: pSBtet_GP_MLLex1_21_AF6ex2_30_pSBtet_RB_AF6ex1_MLLex22_37_1


title: M2


title: pSBtet_GP_MLLex1_21_AF6ex2_30_pSBtet_RB_AF6ex1_MLLex22_37_2


title: F_P7_normal_mesench_2_DC20_J19

tag: plate

tag: well

tag: timepoint

value: normal


title: Cerebellum 2Month WT rep2

tag: age


title: Cerebellum 2Month WT rep1


title: F_P7_normal_mesench_1_DC20_H3

tag: cell type

tag: cell subtype


title: F_P7_normal_mesench_1_DC20_A14

tag: mousename

tag: coverage


title: Cerebellum 2Month KO rep3


title: F_P7_normal_mesench_2_DC20_E8

value: Proliferating myofibroblast

tag: number of genes


title: Cerebellum 2Month KO rep2


title: Cerebellum 2Month KO rep4


title: F_P7_normal_mesench_1_DC20_B13


title: RIG_Case_43

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

hyb_protocol: At least 300 ng of DNA was used per sample for the subsequent bisulfite conversion using the Zymo EZ-96 DNA Methylation kit. Next, the Infinium HD FFPE Restoration kit was used to restore degraded FFPE DNA to a state that is amplifiable by the Infinium HD FFPE methylation whole-genome amplification kit. Restored DNA was then plate-purified (with the Zymo ZR-96 DNA Clean & Concentrator-5), amplified, fragmented, precipitated, re-suspended, and hybridized to an Illumina Infinium Methylation EPIC 850K BeadChip array for 22 h and 30 min (by using the Illumina Infinium Methylation EPIC assay kit).

scan_protocol: After hybridization, arrays were manually disassembled and washed. Subsequent X-Staining of array features was processed on a Tecan Freedom Evo robotics system. Arrays were then manually coated and imaged using an Illumina iScan system with autoloader.

data_processing: DNA methylation data analysis was performed using the open source statistical programming language R (R Core Team, 2016). Raw data files generated by the iScan array scanner were read and pre-processed using the minfi Bioconductor package50. With the minfi package, the same preprocessing steps as in Illumina’s Genomestudio software were performed. In addition, the following filtering criteria were applied: removal of probes targeting the X and Y chromosomes, removal of probes containing nucleotide polymorphism (dbSNP132 Common) within five base pairs of and including the targeted CpG-site, and removal of probes not mapping uniquely to the human reference genome (hg19), allowing for one mismatch. In total, 394,848 common probes of Illumina 450K and EPIC arrays were kept for clustering analysis.

label: Cy5 and Cy3

source_name: RIG tumor

label_protocol: Not provided

extract_protocol: Tumor DNA was extracted from FFPE material by using the Maxwell16 FFPE Plus LEV purification kit and the Maxwell 16 instrument (Promega, Madison, WI) according to the manufacturer’s instructions.

value: Radiation-induced high-grade glioma (RIG)


title: RIG_Case_30


title: Cerebellum 2Month KO rep1


title: pSBtet_GP_MLLex1_21_AF6ex2_30_3


title: MockControl_wDOX2

value: exMLL-AF6 & AF6-shMLL


title: pSBtet_GP_MLLex1_21_AF6ex2_30_2


title: Cerebellum 18Month WT rep4

value: 18 months

value: natural aging


title: F_P7_normal_mesench_1_DC20_E21

data_processing:
Mapping against human genome with VEEV-TC83-GFP added as an additional chromosome (using STAR 2.5.2b)
Counting gene expression using htseq-count 0.10
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts table: raw read counts, not notmalized, rows are gene names, columns are cell names. Metadata file: rows are cell names, columns are metadata.

value: Early alveolar fibroblast


title: MockControl_wDOX1

value: HEK293T kidney cells


title: Cerebellum 18Month WT rep2


title: RIG_Case_31


title: MockControl_wDOX3


title: F_P7_normal_mesench_1_DC20_E5

value: Vascular smooth muscle


title: RIG_Case_29


title: pSBtet_GP_MLLex1_21_AF6ex2_30_1

value: transgene was induced for 48h by 1µg/ml Doxycycline


title: RIG_Case_42


title: F_P7_normal_mesench_1_DC20_J22

value: mesenchymal

value: Early adventitial fibroblast


title: MLLex1_9_AF6ex2_30_wDOX3

value: MLL-AF6 & AF6-MLL


title: M1

value: Treated plant leaf


title: RIG_Case_34


title: RIG_Case_28


title: F_P7_normal_mesench_2_DC20_E14

value: F


title: Cerebellum 18Month WT rep1

value: cerebellum

value: control


title: Cerebellum 18Month KO rep4


title: MLLex1_9_AF6ex2_30_wDOX1


title: Cerebellum 18Month WT rep3


title: F_P7_normal_mesench_1_DC20_P10

value: normal


title: AF6ex1_MLLex22_37_wDOX3


title: RIG_Case_26


title: F_P7_normal_mesench_1_DC20_P3

value: Early airway smooth muscle


title: RIG_Case_25

value: Radiation-induced high-grade glioma (RIG)


title: F_P7_normal_mesench_1_DC20_I7

value: Proliferating fibroblast


title: Cerebellum 18Month KO rep3

value: 18 months


title: F_P7_normal_mesench_1_DC20_G7


title: Cerebellum 18Month KO rep2

value: natural aging


title: F_P7_normal_mesench_1_DC20_F13

value: Myofibroblast


title: AF6ex1_MLLex10_37_wDOX3

value: HEK293T kidney cells


title: MLLex1_9_AF6ex2_30_wDOX2


title: RIG_Case_23


title: Cerebellum 18Month KO rep1


title: RIG_Case_22


title: AF6ex1_MLLex22_37_wDOX2


title: F_P7_normal_mesench_1_DC20_F15


title: AF6ex1_MLLex10_37_wDOX2


title: 3-week-wild-type replicate5 [Shank2-3W-WT5]

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.2) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.26.0).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: 3 week

tag: Sex

value: male

value: Wild-type

value: brain; medial prefrontal cortex


title: 3-week-wild-type replicate4 [Shank2-3W-WT4]


title: RIG_Case_27


title: F_P7_normal_mesench_1_DC20_P18

value: mesenchymal

value: Early adventitial fibroblast


title: RIG_Case_21


title: 3-week-wild-type replicate3 [Shank2-3W-WT3]


title: F_P7_normal_mesench_2_DC20_D8

value: F

value: Vascular smooth muscle


title: 3-week-wild-type replicate2 [Shank2-3W-WT2]


title: RIG_Case_20


title: RIG_Case_24


title: F_P7_normal_mesench_1_DC20_D21


title: RIG_Case_19


title: 3-week-wild-type replicate1 [Shank2-3W-WT1]


title: RIG_Case_18


title: F_P7_normal_mesench_1_DC20_F9


title: RWPE1+mAKT ATAC

city: Bloomington

first: Brady

middle: Guy

last: Strittmatter

state: IN

address: 1001 E Jordan Street

department: Molecular and Cellular Biochemistry

institute: Indiana University Bloomington

data_processing:
ChIP-Seq: Reads were aligned using Bowtie2.3.2 to hg19
ChIP-Seq: hg19 Blacklist Regions were removed using bedtools2.26.0
ChIP-Seq: Duplicate reads were removed using Picard2.14.0
ChIP-Seq: Peaks were called with MACS2.2.7.1 using p-value .01 for  and .001 for
ATAC-Seq: Reads were aligned using Bowtie2.3.2 to hg19
ATAC-Seq: Duplicate reads were removed using Picard2.14.0
ATAC-Seq: Peaks were called with MACS2.2.7.1 using p-value .001 and broad setting
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 peakfile

source_name: RWPE1 normal prostate epithelial cell line

growth_protocol: Cell line was obtained from ATCC and cultured in KSFM supplemented with EGF, bovine pituitary extract, and Penn/Strep. Cells were passged every 5 days and cultured in puromycin (10ug/mL) and hygromycin (200ug/mL).

extract_protocol:
Nuclear lysates were incubated with 5uL of indicated antibody and 50uL of Dynabeads for 4 hours in dilution buffer(20mM Tris, 2mM EDTA,150mM NaCl, 1% Triton X-100,  2 mg/mL BSA) followed by 4 washes with wash buffer(20mM Tris, .25% NP-40, .05% SDS,  2mM EDTA, 250mM NaCl). ChIPs were then incubated with RNAse A (5Prime) and Proteinase K (Sigma) followed by DNA extraction with Qiagen PCR purification kit. Total Cellular RNA was extracted using Qiagen RNeasy kit followed DNAse treatment (Turbo) and  poly-A selection using oligo dT beadsd (Ambion). Poly-A selected RNA was then reverse transcribed using random hexamer primers and SuperScript III. Double stranded DNA was then produced from cDNA fragments using DNA ligase and DNA polymerase.
Isolated DNA was sonicated for 30 minutes (30sec on / 30 sec off) followed by End Repair with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. End repaired DNA was 3' Adenylated with Klenow exo (3' to 5') followed by ligation of Illumina TruSeq adaptors with T4 DNA ligase. Ligated DNA fragments were subject to 15 cycles of PCR with Q5 polymerase followed by size selection with AMPure XP beads.
ATAC-Seq libraries were generated using ActiveMotif ATAC-Seq kit. 50,000 cells were spun down, washed with PBS, and lysed with ATAC-Lysis buffer followed by tagmentation. Tagmented DNA was purified and PCR amplified for 10 cycles followed by SPRI bead cleanup.

treatment_protocol: Retroviruses were produced in HEK-293T cells with pN8E gagpol delta5, pN8E VSV-G,  ERG in pLHCX, and mAKT in pBabe-puro. Plasmids were transfected into HEK cells using Transit-LT1 and viruses were collected over 3 days followed by filtration of the media. RWPE1 cells were transduced for 4 hours with 8 ug/mL polybrene followed by addition of KSFM and either hygro/puromycin for 72 hours.

value: RWPE1+mAKT ATAC

value: Retrovirally transduced and selected to express PQCXIH and pBabe-Puro-Myr-AKT


title: RWPE1-ERG ATAC

value: RWPE1-ERG ATAC

value: Retrovirally transduced and selected to express pQCXIH-ERG uniprot isoform 1 and pBabe-Puro


title: 3-week-knock-out replicate5 [Shank2-3W-KO5]

value: Knock-out


title: F_P7_normal_mesench_2_DC20_A7

first: Fabio

last: Zanini

address: High and Botany St

institute: University of New South Wales

extract_protocol:
no extraction
plate-based illumina-compatible Tn5 transposase single cell RNA-Seq

value: normal

value: Proliferating myofibroblast


title: RIG_Case_16

value: Radiation-induced high-grade glioma (RIG)


title: AF6ex1_MLLex22_37_wDOX1

value: HEK293T kidney cells

tag: transduction

value: transgene was induced for 48h by 1µg/ml Doxycycline


title: F_P7_normal_mesench_2_DC20_G14

value: Pericyte


title: 3-week-knock-out replicate4 [Shank2-3W-KO4]

value: 3 week

value: male

tag: tissue


title: RIG_Case_15


title: RWPE1-ERG+mAKT ATAC

value: RWPE1-ERG+mAKT ATAC

value: Retrovirally transduced and selected to express pQCXIH-ERG and pBabe-Puro-Myr-AKT


title: VCaP+LY294002 Input

source_name: VCaP Prostate Cancer cell line

value: VCaP Prostate Cancer cell line

value: Treated with 1uM LY294002 on day 1, day 3, and day 6.


title: 3-week-knock-out replicate3 [Shank2-3W-KO3]

tag: genotype

value: brain; medial prefrontal cortex


title: AF6ex1_MLLex10_37_wDOX1


title: RWPE1-Vector ATAC

value: RWPE1-Vector ATAC

value: Retrovirally transduced and selected to express pQCXIH and pBabe-puro


title: F_P7_normal_mesench_2_DC20_D18

tag: sequencing run

value: F

value: mesenchymal

value: Early alveolar fibroblast


title: RIG_Case_14B


title: 3-week-knock-out replicate2 [Shank2-3W-KO2]

value: Knock-out


title: F_P7_normal_mesench_1_DC20_F10

tag: gender

value: normal


title: VCaP+LY294002 ERG ChIP

tag: treatment

tag: chip antibody

value: ERG (CM421 Biocare)


title: VCaP Input

value: Treated with DMSO on day 1, day 3, and day 6.


title: 3-week-knock-out replicate1 [Shank2-3W-KO1]


title: RIG_Case_13

value: Radiation-induced high-grade glioma (RIG)


title: VCaP ERG ChIP


title: 3-week-hetero replicate5 [Shank2-3W-HT5]

value: 3 week

value: hetero


title: RIG_Case_12B


title: RWPE1-ERG+mAKT RNA-Seq Replicate 3

data_processing:
ChIP-Seq: Reads were aligned using Bowtie2.3.2 to hg19
ChIP-Seq: hg19 Blacklist Regions were removed using bedtools2.26.0
ChIP-Seq: Duplicate reads were removed using Picard2.14.0
ChIP-Seq: Peaks were called with MACS2.2.7.1 using p-value .01 for  and .001 for
RNA-Seq: reads were aligned with Tophat2.1.1 and Bowtie2.3.2
RNA-Seq: Differential Gene expression was determined using CuffDIff
Genome_build: hg19

extract_protocol:
Nuclear lysates were incubated with 5uL of indicated antibody and 50uL of Dynabeads for 4 hours in dilution buffer(20mM Tris, 2mM EDTA,150mM NaCl, 1% Triton X-100,  2 mg/mL BSA) followed by 4 washes with wash buffer(20mM Tris, .25% NP-40, .05% SDS,  2mM EDTA, 250mM NaCl). ChIPs were then incubated with RNAse A (5Prime) and Proteinase K (Sigma) followed by DNA extraction with Qiagen PCR purification kit. Total Cellular RNA was extracted using Qiagen RNeasy kit followed DNAse treatment (Turbo) and  poly-A selection using oligo dT beadsd (Ambion). Poly-A selected RNA was then reverse transcribed using random hexamer primers and SuperScript III. Double stranded DNA was then produced from cDNA fragments using DNA ligase and DNA polymerase.
Isolated DNA was sonicated for 30 minutes (30sec on / 30 sec off) followed by End Repair with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. End repaired DNA was 3' Adenylated with Klenow exo (3' to 5') followed by ligation of Illumina TruSeq adaptors with T4 DNA ligase. Ligated DNA fragments were subject to 15 cycles of PCR with Q5 polymerase followed by size selection with AMPure XP beads.

value: normal prostate epithelial cell line

tag: cell line

tag: retrovirus


title: F_P7_normal_mesench_1_DC20_J8

tag: plate

tag: well

tag: timepoint

value: Early adventitial fibroblast


title: 3-week-hetero replicate4 [Shank2-3W-HT4]

tag: age

value: male


title: 3-week-hetero replicate3 [Shank2-3W-HT3]


title: RIG_Case_12


title: RWPE1-ERG+mAKT RNA-Seq Replicate 2

tag: cell type

value: Retrovirally transduced and selected to express pQCXIH-ERG and pBabe-Puro-Myr-AKT


title: RIG_Case_11


title: F_P7_normal_mesench_2_DC20_G3

tag: cell subtype

value: Proliferating fibroblast

tag: mousename

tag: coverage

tag: number of genes


title: 3-week-hetero replicate1 [Shank2-3W-HT1]

tag: strain background

tag: Sex

tag: tissue

value: brain; medial prefrontal cortex


title: RWPE1-mAKT RNA-Seq Replicate 3

value: Retrovirally transduced and selected to express PQCXIH and pBabe-Puro-Myr-AKT


title: RIG_Case_09


title: RWPE1-ERG+mAKT RNA-Seq Replicate 1


title: F_P7_normal_mesench_2_DC20_M8

tag: sequencing run

tag: gender

value: F


title: RWPE1-mAKT RNA-Seq Replicate 2


title: 3-week-hetero replicate2 [Shank2-3W-HT2]

tag: genotype


title: F_P7_normal_mesench_2_DC20_N6

tag: treatment

value: mesenchymal


title: RWPE1-mAKT RNA-Seq Replicate 1

tag: cell line

tag: retrovirus


title: 12-week-wild-type replicate4 [Shank2-12W-WT4]

value: 12 week

value: Wild-type


title: 12-week-wild-type replicate3 [Shank2-12W-WT3]


title: RIG_Case_08


title: RIG_Case_05


title: F_P7_normal_mesench_1_DC20_J18

tag: plate

tag: well

value: normal

value: Pericyte


title: RWPE1-ERG RNA-Seq Replicate 3

value: Retrovirally transduced and selected to express pQCXIH-ERG uniprot isoform 1 and pBabe-Puro


title: F_P7_normal_mesench_2_DC20_K19

tag: timepoint

value: Myofibroblast


title: F_P7_normal_mesench_1_DC20_K11

tag: cell type

value: Early alveolar fibroblast


title: RIG_Case_02B

value: Radiation-induced high-grade glioma (RIG)


title: RWPE1-ERG RNA-Seq Replicate 2

value: normal prostate epithelial cell line


title: RIG_Case_14


title: 12-week-wild-type replicate2 [Shank2-12W-WT2]

tag: age


title: 12-week-wild-type replicate1 [Shank2-12W-WT1]


title: F_P7_normal_mesench_2_DC20_E15

tag: cell subtype

value: Vascular smooth muscle

tag: mousename


title: RWPE1-ERG RNA-Seq Replicate 1


title: 12-week-knock-out replicate4 [Shank2-12W-KO4]

value: male

value: Knock-out


title: F_P7_normal_mesench_1_DC20_N5

tag: coverage

tag: number of genes


title: RIG_Case_06


title: F_P7_normal_mesench_2_DC20_D13


title: RWPE1-Vector RNA-Seq Replicate 3

value: Retrovirally transduced and selected to express pQCXIH and pBabe-puro


title: RIG_Case_01


title: 12-week-knock-out replicate3 [Shank2-12W-KO3]

tag: strain background

tag: Sex

value: brain; medial prefrontal cortex


title: F_P7_normal_mesench_1_DC20_J2

tag: sequencing run


title: 12-week-knock-out replicate1 [Shank2-12W-KO1]

tag: tissue


title: F_P7_normal_mesench_2_DC20_H21

tag: gender


title: RWPE1-Vector RNA-Seq Replicate 2


title: HeLa-tet-NSM rep 2

city: St. Louis

first: Alex

last: Rosenberg

state: MO

address: 660 S. Euclid Ave.

department: Molecular Microbiology

institute: Washington University in St. Louis

data_processing:
Demultiplexed fastq files were imported into Partek Flow (Partek, Inc.) Reads were then mapped to the Homo sapiens hg38 genome build (NCBI GenBank assembly ID GCA_000001405.15) using the STAR aligner with default parameters , and the number of reads per gene was quantified based on the human Ensembl Transcripts release 100. For differential expression analyses, we first normalized gene expression values by dividing the number of reads per gene by the total number of reads per sample to obtain counts per million (CPM) values. Pair-wise comparisons of sample types (3 biological replicates each) were performed using the Partek gene-specific analysis (GSA) algorithm, which is a multimodel approach that determines the best response distribution (e.g. lognormal, Poisson, or negative binomial) for each gene based on Akaike information criteria (AICc) model selection rather than fitting all data to one distribution. Genes were not included in the analysis if their mean CPM value over all samples was less than 1. Genes were considered significantly differentially expressed between WT and the deletion strains ( Dnsm, Dist , Dnsm/Dist) if the P value was less than 0.05 and the absolute fold change was greater than 1.5
Quantification and statistical analysis were done with Partek Flow package.
Genome_build: Homo sapiens hg38
Supplementary_files_format_and_content: .txt files containing gene expression changes between HeLa-tet andHeLa-tet-NSM±IFNγ and HeLa-tet+IFNγ.  Within these files the abundance measurements are represented as LSMean values.

source_name: HeLa-tet-NSM

extract_protocol:
HeLa cells, HeLa-tet and HeLa-tet-TgNSM-TY cell lines were seed at a density of 0.06x10e6 /ml in T25 flasks in presence of DOX 1µg/ml. After 48 hr culture media was replaced for fresh DOX media ±IFNγ 100U/ml. Cells were collected 6 hr post ±IFNγ media swap and their RNA was extracted and purified from using the RNeasy kit (QIAGEN).
Total RNA from three independent biological replicates was submitted to the Genome Access Technology Center (Washington University School of Medicine) for library prep and sequencing. Total RNA integrity was determined using Agilent Bioanalyzer. Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. For bradyzoite and HeLa cells experimnts fragments were sequenced on an Illumina illumina NovaSeq 6000 using paired-end reads extending 150 bases.

treatment_protocol: IFN-γ 100U/ml treatment for 6hr of HeLa-tet/Hela-tet-NSM 48 hr after DOX treatment 1µg/ml.

value: HeLa-tet-NSM

tag: treatment

value: control


title: F_P7_normal_mesench_1_DC20_E12

city: Kensington

value: F

value: mesenchymal


title: RWPE1-Vector RNA-Seq Replicate 1

tag: cell line


title: HeLa-tet-NSM rep 3


title: 12-week-knock-out replicate2 [Shank2-12W-KO2]

value: 12 week

tag: genotype


title: RWPE1-ERG+mAKT Input

tag: retrovirus

value: Retrovirally transduced and selected to express pQCXIH-ERG and pBabe-Puro-Myr-AKT

tag: chip ab


title: 12-week-hetero replicate4 [Shank2-12W-HT4]

value: hetero


title: F_P7_normal_mesench_1_DC20_O2

tag: plate

tag: well

tag: timepoint

value: normal


title: HeLa-tet-NSM rep 1


title: RWPE1-ERG+mAKT ERG ChIP

tag: cell type

value: ERG (CM421 Biocare)


title: RIG_Case_02


title: 12-week-hetero replicate3 [Shank2-12W-HT3]

tag: age


title: HeLa-tet-NSM IFN 100U 6hrs rep 3

source_name: HeLa-tet-NSM IFN 100U 6hrs

value: IFN


title: 12-week-hetero replicate2 [Shank2-12W-HT2]


title: RWPE1-ERG ERK2 ChIP

value: Retrovirally transduced and selected to express pQCXIH-ERG uniprot isoform 1

value: ERK2 (D-2 SCBT)


title: HeLa-tet-NSM IFN 100U 6hrs rep 2


title: RWPE1-Vector ERK2 ChIP

value: normal prostate epithelial cell line

value: Retrovirally transduced and selected to express pQCXIH


title: HeLa-tet-NSM IFN 100U 6hrs rep 1


title: F_P7_normal_mesench_1_DC20_H10

tag: cell subtype

value: Early alveolar fibroblast

tag: mousename

tag: coverage


title: 12-week-hetero replicate1 [Shank2-12W-HT1]

tag: strain background

tag: Sex

value: male


title: RWPE1-ERG S96E Input

value: Retrovirally transduced and selected to express pQCXIH-ERG S96E


title: RWPE1-ERG S96E H3K27me3 ChIP

value: Retrovirally transduced and selected to express pQCXIH-ERG S96E uniprot isoform 1


title: HeLa-tet rep 3

source_name: HeLa-tet

value: HeLa-tet

value: control


title: F_P7_normal_mesench_2_DC20_M15

tag: sequencing run

value: F

value: mesenchymal

value: Myofibroblast

tag: number of genes


title: F_P7_normal_mesench_2_DC20_A14

tag: gender

tag: treatment


title: F_P7_normal_mesench_2_DC20_O3

value: Proliferating myofibroblast


title: RWPE1-ERG Input

tag: cell line

value: Retrovirally transduced and selected to express pQCXIH-ERG


title: F_P7_normal_mesench_1_DC20_N1

value: normal


title: F_P7_normal_mesench_1_DC20_J23


title: RWPE1-Vector Input

tag: retrovirus


title: RWPE1-ERG H3K27me3 ChIP

tag: chip ab


title: HeLa-tet IFN 100U 6hrs rep 3

source_name: HeLa-tet IFN 100U 6hrs

value: IFN


title: F_P7_normal_mesench_1_DC20_B3

tag: plate

value: Early airway smooth muscle


title: RWPE1-Vector H3K27me3 ChIP


title: F_P7_normal_mesench_2_DC20_L3

tag: well


title: F_P7_normal_mesench_2_DC20_D23

tag: timepoint

value: Vascular smooth muscle


title: HeLa-tet IFN 100U 6hrs rep 2


title: F_P7_normal_mesench_1_DC20_K8

tag: cell type


title: Scramble_CSC_3

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

data_processing:
STAR 2.6.1 aligned to HG38
Quantified to Ensembl human genome 92
Normalized via Log2 Counts per million with offset of 1
Lognormal shrinkage was used to remove batch effect between runs and one of the outlier, Cx43 shRNA_CSC_3, was removed from further analysis.
Counts with a maximum of less than 1 were filtered out for a normal distribution
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files, includes RPKM values for each sample

source_name: Breast Cancer Cell line

growth_protocol: The CSCs from MDA-MB-231 with CDH2, Cx43 and Scramble knockdown cultured in DMEM supplemented with 10% FBS, L-glutamine and penicillin and streptomycin

extract_protocol:
Total RNA extraction was performed according to manufacturer’s protocols with the RNeasy Mini Kit (Qiagen). Ribosomal RNA was depleted with Ribo-Zero gold from Illumina (San Diego, CA)
Libraries were prepared using the NEB Ultra II Library Preparation Kit and NEBNext® Multiplex Oligos for Illumina (Dual Index Primers Set 1) (New England BioLabs) following the manufacturer’s protocol.

treatment_protocol: The CSCs from MDA-MB-231 with CDH2, Cx43 and Scramble knockdown were sorted using Flow cytometry. Cells were then incubated overnight at 37C / 5% CO2

tag: knocked down

value: scramble negative control


title: ME1_LYL1ChIPseq

city: Randwick

first: Julie

last: Thoms

address: Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St

department: Adult Cancer Program

institute: UNSW Sydney

data_processing:
Adapter removal with cutadapt
Genome alignment with bwa mem
Removal of PCR duplicates with MarkDuplicates using options REMOVE_DUPLICATES=TRUE
Create bigwig files with bamCoverage using options --binSize 10 --exactScaling (additional paramter for single end data only --extendReads 200 )
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files

source_name: ME-1 cell line (DSMZ ACC 537)

growth_protocol: Cells grown in RPMI supplemented with FBS

extract_protocol:
Cells were fixed in 1% formaldehyde, nuclei extracted, chromatin sonicated, and protein-bound DNA fragment immunoprecipited overnight, and DNA purified.
Antibodies used for immunoprecipitation were: LYL1 (Santa Cruz #sc374164X), TAL1 (Abcam #ab155195), LMO2 (R&D # AF2726), FLI1 (Abcam # ab15289), ERG (Santa Cruz #sc345X), GATA2 (Santa Cruz #sc9008), RUNX1 (Abcam #ab23980), H3K27Ac (Abcam #ab4729).
Standard ChIP seq libraries (BGI and Novogene)

value: ME-1 (DSMZ ACC 537)

value: acute myeloid leukemia cell line

value: unperturbed cells

tag: chip anitbody

value: LYL1 (Santa Cruz #sc374164X)


title: F_P7_normal_mesench_1_DC20_A1

tag: cell subtype

tag: mousename


title: CD34 shLUC control Rep 2

data_processing:
Alignment to hg19 genome with TopHat2 (standard paramters)
Differential expression analysis using DeSeq2 with standard parameters and paired sample information included as a regression variable. Calculation was performed with shLUC as the treated and shERG as the untreated sample.
Genome_build: hg19
Supplementary_files_format_and_content: text files containing normalized read counts and DeSeq2 output

source_name: human cord blood CD34+ cells_control

growth_protocol: Human cord blood CD34+ cells pooled from multiple donors and lentivirally transduced as previously described (Unnikrishnan et al NAR 44:10644 2016)

extract_protocol: Total RNA extracted using miRNeasy kit (Qiagen)

treatment_protocol: Control shRNA targetting luciferase or treatment shRNA targetting ERG

value: CD34+ haematopoietic stem and progenitor cells (HSPCs)


title: F_P7_normal_mesench_2_DC20_O17

value: Early alveolar fibroblast

tag: coverage


title: HeLa-tet rep 2

value: HeLa-tet

value: control


title: Scramble_CSC_2


title: HeLa-tet rep 1


title: ME1_IgG_ChIPseq

value: IgG


title: CD34 shERG Rep 1

source_name: human cord blood CD34+ cells_ERG knockdown

value: ERG knockdown


title: Scramble_CSC_1


title: ME1_H3K27Ac_ChIPseq

value: H3K27Ac (Abcam #ab4729)


title: CD34 shLUC control Rep 1


title: Cx43 shRNA_CSC_2


title: ME1_FLI1ChIPseq

value: FLI1 (Abcam # ab15289)


title: Sirt1KO-3

city: RTP

first: Xiaojiang

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

data_processing:
RNA-SEQ reads (223-283M per sample) were aligned to the UCSC mm10 reference genome using STAR
The quantification results from FeatureCounts were then analyzed with the Bioconductor package DESeq2, which fits a negative binomial distribution to estimate technical and biological variability.
Genome_build: mm10
Supplementary_files_format_and_content: excel table; log2 transformed and normalized abundance measurements by DESeq2

source_name: Embryonic stem cells

extract_protocol:
total RNA isolated using Qiagen RNeasy mini kit.
The integrity of the total RNA was determined using a bioanalyzer (Agilent) and concentration were assessed by Qubit (ThermoFisher Scientific).  A TruSeq RNA kit (Illumina, San Diego, CA) was utilized to prepare the poly(A)-enriched RNA-seq libraries that were sequenced on the Illumina NovaSeq 6000 in a 75-base paired-end mode according to the manufacturer’s protocol.

tag: background strain

value: Male

value: embryonic stem cells

tag: genotype

value: Sirt1 KO


title: ME1_LMO2ChIPseq


title: Sirt1KO-2


title: KG1_TAL1_ChIPseq

source_name: KG-1 cell lines (DSMZ ACC 14)

value: KG-1 (DSMZ ACC 14)

value: TAL1 (Abcam #ab155195)


title: ME-1 scRNAseq

data_processing:
Conversion of raw .bcl files to fastq format using CellRanger software version 2.0.1 (10X Genomics).
Unique molecular identifier (UMI) count matrices were generated using CellRanger software version 2.0.1 (10X Genomics).
Code used for analysis is available at https://github.com/iosonofabio/heptad_paper
Genome_build: hg38
Supplementary_files_format_and_content: TSV files containing expression tables, expression tables in loom format, RNA velocity in loom format

growth_protocol: Cells were grown in RPMI supplemented with 20% FBS.

extract_protocol:
extrtaction and library construction ovcured in the 10X workflow as described below
Single cell RNA-seq libraries were prepared with approximately 2000 cells using the Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics) as per manufacturer’s protocol. cDNA amplification was undertaken for 11 cycles and the subsequent sample index (SI) PCR for 12 cycles. Libraries were sequenced using the Illumina NextSeq500 platform with 150bp PE reads (Illumina) at a depth of approximately 100K reads/cell.

value: ME-1 (DSMZ ACC 537)

value: acute myeloid leukemia


title: KG1_H3K27Ac_ChIPseq

value: acute myeloid leukemia cell line

value: unperturbed cells


title: KG1_RUNX1_ChIPseq

value: RUNX1 (Abcam #ab23980)


title: CDH2 shRNA_CSC_3


title: CD34 shERG Rep 2

value: CD34+ haematopoietic stem and progenitor cells (HSPCs)


title: [delta]nsm/[delta]ist rep 3

description: TgIST TgNSM KO vs WT.txt

data_processing:
Demultiplexed fastq files were imported into Partek Flow (Partek, Inc.) Reads were then mapped to the Homo sapiens hg38 genome build (NCBI GenBank assembly ID GCA_000001405.15) using the STAR aligner with default parameters , and the number of reads per gene was quantified based on the human Ensembl Transcripts release 100. For differential expression analyses, we first normalized gene expression values by dividing the number of reads per gene by the total number of reads per sample to obtain counts per million (CPM) values. Pair-wise comparisons of sample types (3 biological replicates each) were performed using the Partek gene-specific analysis (GSA) algorithm, which is a multimodel approach that determines the best response distribution (e.g. lognormal, Poisson, or negative binomial) for each gene based on Akaike information criteria (AICc) model selection rather than fitting all data to one distribution. Genes were not included in the analysis if their mean CPM value over all samples was less than 1. Genes were considered significantly differentially expressed between WT and the deletion strains ( Dnsm, Dist , Dnsm/Dist) if the P value was less than 0.05 and the absolute fold change was greater than 1.5
Quantification and statistical analysis were done with Partek Flow package.
Genome_build: Homo sapiens hg38
Supplementary_files_format_and_content: txt files containing gene expression changes between wt and ∆nsm or ∆ist or ∆nsm/∆ist

source_name: HFF

extract_protocol:
Bradyzoites were differentiated in HFF cells cultured in T25 flasks. The monolayers were infected with 0.2x106 parasites expressing mNeon under the control of BAG1 promoter and mCardinal under TUB promoter per T25 flask in D10 medium for 2 hr at 37°C to allow for invasion. For high pH bradyzoite induction, the media was changed to RPMI-HEPES (Thermo Fisher) lacking sodium bicarbonate pH 8.2. then grown for an additional 5 days at 37°C at ambient CO2 levels (~0.03% CO2). The media was changed every 2 days (to prevent acidification). Bradyzoites were stimulated with human IFN-γ (R&D systems) at final experimental concentration of 100 U/ml for 6 hr after 5 days in differentiation media prior to being washed with PBS and dislodged with trypsin. A minimum of 3×103 mNeon/mCard positive HFF cells were collected into RT lysis buffer + 10 μl/ml 2-mercaptoethanol using a Sony SY3200 “Synergy cell sorter (Sony). RNA was extracted and purified from all samples using the RNeasy Mini kit (QIAGEN)
Library preparation was performed with 1-10ng of total RNA. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: IFN-γ 100U/ml treatment for 6hr of 5 day old bradyzoite infected HFFs prior to FACS sorting and RNA extraction

tag: strain

value: ME49 [delta]nsm/[delta]ist

tag: tissue

value: Foreskin

tag: age

value: 5 day old bradyzoite infected HFFs


title: KG1_LYL1_ChIPseq

tag: cell line

tag: treatment

value: LYL1 (Santa Cruz #sc374164X)


title: Sirt1WT-3

tag: gender

value: wild-type


title: Sirt1WT-2


title: HeLa-tet IFN 100U 6hrs rep 1

value: HeLa-tet

value: IFN


title: KG1_LMO2_ChIPseq


title: Sirt1WT-1

value: Male

value: embryonic stem cells


title: CDH2 shRNA_CSC_1


title: [delta]ist rep 3

description: TgIST KO vs WT.txt

value: ME49 [delta]ist


title: [delta]nsm rep 3

description: TgNSM KO vs WT.txt

value: ME49 [delta]nsm


title: KG1_IgGChIPseq

value: KG-1 (DSMZ ACC 14)

value: IgG


title: AD_GKO

city: New York

first: Peng

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Sample demultiplexing, barcode processing and single-cell counting was performed using the Cell Ranger Single-Cell Software Suite (10x Genomics, version 3.0.2).
Cellranger count was used to align samples to the reference genome (mm10). The counting matrix were imported into Seurat package (version 3.0) in R (version 3.6.2) for subsequent analysis.
Genome_build: mm10

source_name: hippocampus

extract_protocol:
Single nuclei were isolated based on the published protocol with modifications of Krishnaswami et al., 2016. After dissection, hippocampi were homogenized in a cold Dounce homogenizer after dissection. The homogenate was centrifuged at 1,000g for 8 min at 4 °C to pellet nuclei. Nuclei were resuspended in 1 ml 29% iodixanol buffer and centrifuged at 13,500 g for 20 min at 4°C. Supernatant and floating myelin were removed after centrifugation. Nuclei were resuspended in 100 µl nuclei storage buffer and filtered using a 40 µm cell strainer. Nuclei were stained with trypan blue to and counted using a hemocytometer.
RNA libraries were prepared for sequencing using standard 10X Genomics protocols

value: hippocampus

value: 6 month


title: Cx43 shRNA_CSC_1


title: NIPBL_Input_Patient3

city: Hospitalet de Llobregat

first: Ethel

last: Queralt

state: Barcelona

address: Avenida Gran Via de L'Hospitalet 199

country: Spain

institute: Instituto de Investigación Biomédica de Bellvitge (IDIBELL)

data_processing:
ChipSeq fastq files were trimmed with Trim Galore
ChIP-seq reads were aligned to the hg19 reference genome with Bwa mem. Reads with mapping quality <3 werre removed.
MANorm software was used to identify differential enrichment regions between Patient and Control samples. A significance threshold of -log10 adjusted value of p > 2 was used to identify regions differentially enriched between samples.
Mouse spike in chromatin was used to normalize across Nipbl samples. Reads were first aligned to a combined reference genome consisting of the human hg19 and the mouse mm10 genome assemblies. Then, for each sample, those reads mapping uniquely to mm10 were quantified. Since the proportion of mouse spike-in DNA was the same across samples, the differences in mm10 read coverage between samples were used to normalize the Nipbl sample signal. Specifically, the bam files with the greatest number of uniquely mapped reads to mm10 were downsampled so that all samples would yield the same amount of unique mm10 reads. The R package NCIS was used to calculate a scaling factor between IP and INPUT samples that was used by the peak calling software Macs2 to sensitively call peaks across all bam files.
All peaks were annotated using Homer software and custom R scripts. Specifically, the distance to TSS and gene names were annotated using Homer, and the distance to CpG and Enhancers were annotated using R’s GRanges methods. CpG island information was obtained from UCSC queries using rtracklayer and Enhancer information was obtained from the Enhancer Atlas database (http://www.enhanceratlas.org/).
Genome_build: hg19

growth_protocol: Primary dermal fibroblast were grown in Dulbecco’s modified Eagle’s medium (DMEM+GlutaMAX) supplemented with 10% FBS

extract_protocol: ChIP-Seq for SMC1A or NIPBL was performed in primary human dermal fibroblast cells from a healthy donor and CdLS patients.

tag: subject status

value: Cornelia de Lange syndrome (CdLS) patient

value: primary dermal fibroblasts

tag: chip antibody

value: none (input)


title: NIPBL_Patient3

value: Nipbl 3B9, Novus Biological


title: ME49 WT rep 3

description: TgNSM KO vs WT.txt

value: ME49 WT

value: Foreskin

value: 5 day old bradyzoite infected HFFs


title: KG1_GATA2_ChIPseq

value: acute myeloid leukemia cell line

value: unperturbed cells

value: GATA2 (Santa Cruz #sc9008)


title: [delta]ist rep 2

description: TgIST KO vs WT.txt


title: AD_WT

value: J20;wild type


title: GKO_3

value: 7 month

value: GSAP -/-


title: KG1_FLI1_ChIPseq

value: KG-1 (DSMZ ACC 14)

value: FLI1 (Abcam # ab15289)


title: KG1_ERG_ChIPseq

value: ERG (Santa Cruz #sc345X)


title: NIPBL_Input_Control

value: control


title: GKO_2

value: hippocampus


title: NIPBL_Control

value: primary dermal fibroblasts


title: CDH2 shRNA_CSC_2


title: PDGF-DD rep3

city: shanghai

first: zebei

last: zhang

address: 197 ruijin No.2 road

institute: shanghai institute of hypertension

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) .  After that, Ericscript (v0.5.5)  and rMATS(V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5)  was applied to align the clean reads to thegene set, a database for this organism built by BGI(Beijing  Genomic  Institute  in  ShenZhen),  which  known  and  novel,  coding transcripts  were  included, then expression level of gene was calculated by RSEM (v1.2.12).
Differential  expression  analysis  was performed  using  the  DESeq2(v1.4.5) with Q  value ≤ 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: MS excel files include FPKM values for each Sample ...

source_name: primary cardiac fibroblasts

growth_protocol: Primary cardiac fibroblasts(CFs) were isolated from 1-2week-old global PDGF-D KO mice. Briefly, the heart was enzymatically digested and mechanically dissociated according to manufacturer instruction. After dissociation, the sample was applied to a 70μm filter to remove any remaining larger particles from the CF suspension. CFs were cultured in DMEM supplemented with 15% FBS and 1% penicillin and streptomycin.

extract_protocol:
RNA of cardiac fibroblast was harvested using Trizol reagent. The mix of cell and Trizol was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3mL chloroform/isoamyl alcohol (24:1). The mix was shackedvigorously for 15s, and then centrifugedat 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phasewhere RNA remained was transferredinto a new tube withequal volume of supernatant of isopropyl alcohol,then centrifugedat 13,600rpm for 20 minutes at 4°C.After deserting the supernatant,the RNA pellet was washed twice with 1 mL75% ethanol,then the mix was centrifuged at 13,600rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China)

treatment_protocol: cells were treated by saline or PDGF-DD (20μM) for 12 hours.

value: heart

value: PDGF-D -/-

value: 1-2 weeks


title: [delta]nsm rep 2

description: TgNSM KO vs WT.txt

value: ME49 [delta]nsm

value: Foreskin


title: GKO_1

last: Xu


title: ME49 WT rep 2

description: TgNSM KO vs WT.txt

value: ME49 WT

value: 5 day old bradyzoite infected HFFs


title: Sirt1KO-1

value: Male

value: embryonic stem cells

value: Sirt1 KO


title: [delta]nsm/[delta]ist rep 1

description: TgIST TgNSM KO vs WT.txt

value: ME49 [delta]nsm/[delta]ist


title: PDGF-DD rep2


title: SMC1A_Patient4

value: Cornelia de Lange syndrome (CdLS) patient


title: WT_3

value: 7 month

value: wild type


title: [delta]nsm/[delta]ist rep 2

description: TgIST TgNSM KO vs WT.txt


title: WT_2


title: PDGF-DD rep1


title: control rep3

value: control


title: WT_1

value: hippocampus


title: [delta]nsm rep 1

description: TgNSM KO vs WT.txt


title: SMC1A_Patient3

value: primary dermal fibroblasts


title: control rep2

value: heart


title: [delta]ist rep 1

description: TgIST KO vs WT.txt

value: ME49 [delta]ist


title: SMC1A_Input_Patient3

value: none (input)


title: ME49 WT rep 1

description: TgNSM KO vs WT.txt


title: control rep1

value: 1-2 weeks


title: SMC1A_Input_Control


title: Mix-2/4cell-Blasto

city: Fukuoka

first: Yu-ichi

last: Tsukada

address: 744 Motooka, Fukuoka Nishi-ku

department: INAMORI Frontier Research Center Advanced Biological Information Research Division

country: Japan

institute: Kyushu University

data_processing:
The reads were aligned to the reference genome GRCm38 with the software HISAT2 (ver. 2.2.6).
Per gene unique molecular identifier (UMI) counts were produced by HTSeq (ver.0.6.1) where a consensus read was counted for each group of duplicate reads sharing the same UMI tag.
The UMI counts were normalized as described and were input to DESeq2 (ver. 1.10.1) to determine differentially expressed genes.
Genome_build: GRCm38

source_name: embryo

extract_protocol:
Cell capture were performed according to the manufacturer’s instructions of Fluidigm C1. RNA from each sample was uniquely barcoded and libraries were constructed using the CELSeq2 protocol as described in Hashimshony et al (Genome Biology 2016).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: mixed blastomere stage

value: 2 and 4 cell


title: SMC1A_Input_Patient4

tag: cell type


title: SMCA1_Control


title: AS11

status: Public on May 26 2021

city: Durham

first: Steve

last: Taylor

address: 303 Research Dr

department: Division of Infectious Diseases

institute: Duke University School of Medicine

description: In vivo blood sample

data_processing:
Real Time Analysis (RTA3) was used for base calling on the NovaSeq6000
Sequenced reads were trimmed for adaptor sequence and low quality bases, then mapped to ASM276v2 transcriptome using Salmon with parameters -p 8 -g $GTF-file --validateMappings
Transcripts per kilobase of exon Per Megabase of library size (TPM) were extracted from each quantification file output by Salmon using tximport.
Genome_build: ASM276v2
Supplementary_files_format_and_content: comma-delimited text files include TPM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Plasmodium falciparum

source_name: HbAS patient 11

extract_protocol:
RNA was extracted from in vitro samples using Trizol reagent, and extracted from in vivo samples using Trizol LS. Kapa Stranded mRNA-seq library prep kit was used with at least 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Plasmodium falciparum:asexual blood stage

value: P. falciparum natural infection

tag: hemoglobin genotype

value: HbAS

tag: parasite stage

value: Ring

tag: hours post-invasion

tag: patient age

tag: patient sex

tag: abo

value: B

tag: parasite density (parasites/ul)

tag: date


title: AS13

description: In vivo blood sample

source_name: HbAS patient 13

tag: tissue

tag: strain

value: Trophozoite

value: Male

value: A


title: AS16

description: In vivo blood sample

source_name: HbAS patient 16


title: AS15

description: In vivo blood sample

source_name: HbAS patient 15

value: O


title: AS12

description: In vivo blood sample

source_name: HbAS patient 12

value: Female

value: AB


title: AS10

description: In vivo blood sample

source_name: HbAS patient 10


title: AS08

description: In vivo blood sample

source_name: HbAS patient 8


title: AS05

description: In vivo blood sample

source_name: HbAS patient 5


title: AS04

description: In vivo blood sample

source_name: HbAS patient 4


title: AS06

description: In vivo blood sample

source_name: HbAS patient 6


title: AS09

description: In vivo blood sample

source_name: HbAS patient 9


title: AS03

description: In vivo blood sample

source_name: HbAS patient 3


title: AA15

description: In vivo blood sample

source_name: HbAA patient 15

value: HbAA


title: AS01

description: In vivo blood sample

source_name: HbAS patient 1


title: AA16

description: In vivo blood sample

source_name: HbAA patient 16


title: Mix-1/8cell-Blasto

value: 1 and 8 cell


title: AS07

description: In vivo blood sample

source_name: HbAS patient 7


title: AA14

description: In vivo blood sample

source_name: HbAA patient 14


title: AA13

description: In vivo blood sample

source_name: HbAA patient 13


title: 16 Minute BMH-21-Treated NETseq Replicate 1

city: Birmingham

first: Abigail

last: Huffines

address: 720 20th St S

institute: University of Alabama at Birmingham

description:
BMH-21 16 Minutes 1
VEH_vs_BMH_sumnorm_16Minutes.csv

data_processing:
Library strategy: NET-seq
Base-calling was done by using bcl2fastq software (version 2.20.00).
Reads were deduplicated based on the UMI sequence with fqtrim (version 0.9.7) with the "-C" option.
Reads containing the sequence 5'-AGNNNNNNNNTG-3' at the 5' end were isolated, and cutadapt (version 1.12) was used to remove this sequence. The cutadapt parameters "-g -no-indels" were used.
Cutadapt (version 1.12) was used to remove the 3' sequence 5'-CTGTAGGCACCAT-3' from reads, with the parameters "-a -no-indels".
Alignment was performed using STAR (version 2.7.1a), and reads were aligned to the Saccharomyces cerevisiae genome assembly R64-1-1. The STAR alignIntronMax parameter was set to 1.
SAMtools (version 1.6) was used to sort and index output BAM files from alignment.
Sorted BAM files were converted to BED files using BEDTools (version 2.26.0).
BEDTools (version 2.26.0) was used to generate genome coverage files, with the genomecov function and parameters "-strand" and "+strand"
Data processing and visualization was performed using R (version 4.0.2).
Genome_build: S. cerevisiae R64-1-1
Supplementary_files_format_and_content: Processed data files are in .csv file format.

source_name: yeast

growth_protocol: Yeast was grown at 30ºC with nutation until the OD600 reached 0.3.

extract_protocol:
RNA extraction protocol was based on Clarke et. al., NETSeq reveals heterogeneous nucleotide incorporation by RNA polymerase I, PNAS, 2018. 115 (50), E11633-E11641. In brief, cells were treated (as described in "treatment protocol" section) and then harvested via filtration and flash frozen. Cells were lysed under cryogenic conditions for 10-one minute cycles with a mikro dismembranator II. Immunoprecipitation was done as described in previously published methods, by incubating samples with anti-HA magnetic beads at 4ºC for 3 hours. Finally, RNA was extracted from the samples by using an acidic phenol-chloroform extraction,  and was precipitated at -80ºC at least overnight with an ammonium acetate ethanol solution.
The library construction protocol was based on methods from  Huffines et. al., Spt4 Promotes Pol I Processivity and Transcription Elongation, Genes, 2021. In brief, following RNA extraction, a UMI-containing DNA linker (5’-/5rApp/CANNNNNNNNCTCCACGAGTCATCCGC /3ddC/-3’) was ligated to the 3' end of the isolated RNAs. The residual linker was enzymatically digested, and samples were precipitated. Reverse transcription was performed, and samples were gel extracted to remove any remaining reverse transcription primer. Samples were then circularized, amplified, and PCRCleanDX magnetic beads were used to remove contaminating oligos and purify libraries for sequencing.

treatment_protocol: At OD600 = 0.3, each culture was treated with either vehicle phosphate buffer or BMH-21 for the allotted treatment time. Cultures were returned to 30ºC immediately after treatment was added, and remained at 30ºC until the treatment time elapsed. At that point, cultures were quickly harvested.

tag: treatment time

value: 16 minutes


title: 16 Minute BMH-21-Treated NETseq Replicate 3

description:
BMH-21 16 Minutes 3
VEH_vs_BMH_sumnorm_16Minutes.csv

tag: treatment


title: AS14

description: In vivo blood sample

source_name: HbAS patient 14


title: 16 Minute Vehicle-Treated NETseq Replicate 2

description:
Vehicle 16 Minutes 2
VEH_vs_BMH_sumnorm_16Minutes.csv

value: vehicle


title: 16 Minute BMH-21-Treated NETseq Replicate 2

description:
BMH-21 16 Minutes 2
VEH_vs_BMH_sumnorm_16Minutes.csv


title: 16 Minute Vehicle-Treated NETseq Replicate 3

description:
Vehicle 16 Minutes 3
VEH_vs_BMH_sumnorm_16Minutes.csv


title: AA11

description: In vivo blood sample

source_name: HbAA patient 11