title: T2H6_0601

description:
P.falciparum parasite isolate
H6_sample166


title: Wouter29

status: Public on Feb 07 2022

type: SRA

city: Groningen

first: Emma

last: Gerrits

email: e.gerrits@rug.nl, e.gerrits@umcg.nl

state: Groningen

address: Antonius Deusinglaan 1

department: BSCS

country: Netherlands

institute: UMCG

library_source: transcriptomic

data_processing:
Data processing was performed with the Lexogen Quantseq 2.3.1 FWD UMI pipeline on the BlueBee Genomics Platform (1.10.18)
Supplementary_files_format_and_content: Countfile where each column is a sample and each row is a gene.

molecule: total RNA

organism: Homo sapiens

source_name: Cell line

growth_protocol: DMEM + 10% FCS +1% pen/strep

extract_protocol:
Qiagen ALL-PREP
Lexogen QuantSeq 3'mRNA-seq Libray prep kit (FWD with UMI) from Illumina.

treatment_protocol: For U2OS cells: no treatment, 72 hours of growth under normal conditions. For HEK293T cells: 24 hour treatment with camptothecin or vehicle (DMSO), 48 hour recovery, harvest

tag: cell line

tag: treatment/group

value: Camptothecin-treated


title: T2H6_0562

city: Singapore

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description:
P.falciparum parasite isolate
H6_sample163

data_processing:
Standard Illumina pipeline was used for base calling and demultiplexing
Sequenced reads were trimmed for adapter, primer and low quality bases from 3'-ends using Trimgalore (version 0.4.4)
Trimmed reads then mapped to Plasmodium falciparum 3D7 genome (genedb version 3) using HiSAT2 (version 2.1.0) with parameters --min-intronlen 60 --max-intronlen 2500 --fr
Uniquely mapped and properly oridented reads were extracted using samtools (version: 1.8) and raw count generated by bedtools (v2.27.1)
Normalized count - Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated, except gene length in the formula is replaced with mapped length
Genome_build: Genome_build: Plasmodium falciparum 3D7 geneDB version 3
Supplementary_files_format_and_content: Tab-delimited text file includes Log2 FPKM values for each sample

organism: Plasmodium falciparum

source_name: P.falciparum field isolate from patient

growth_protocol: All samples used in this study (Except ring 3D7 batch controls) were collected from patients involved in Tracking Resistance to Artemisinin Collaboration 2 (TRAC2), a multi-site study that took place between Aug 7, 2015, and Feb 8, 2018. Following collection, blood was subsequently depleted of plasma and buffy coat. Hour 0 samples were additionally purified from white blood cells (WBC) using CF11 columns following the Worldwide Antimalarial Resistance Network (WWARN) protocols. 0.2 to 0.5 mL of packed red blood cells (pRBC) from each sample was homogenized by mixing with 10 volumes of TRIzol (Invitrogen), frozen at -80oC.

extract_protocol:
Total RNA was extracted using Trizol and ZYMO DirectZol96 extraction kit following protocol described in Kucharski, M., Tripathi, J., Nayak, S. et al. A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples. Malar J 19, 363 (2020).
Reverse transcription and cDNA synthesis was done following modifed Smart-Seq2 protocol using only oligo(d)T primers to enrich for mRNA transcripts (Kucharski, M., Tripathi, J., Nayak, S. et al. A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples. Malar J 19, 363 (2020)). Purified amplicon (cDNA) was used to generate sequencing libraries using Illumina Nextera XT kit as described in manufacturer’s protocol. Libraries were analyzed on the Bioanalyser High-Sensitivity DNA chips (Agilent, Cat. No.: 5067-4626), subsequently pooled (24 samples per lane) and sequenced on Illumina HiSeq4000 platform generating 150 bp paired end reads with 110 Gb data output generated per lane.

treatment_protocol: In brief, samples were collected from the venous blood of malaria-infected patients at admission to the clinic (Hour 0, 0hr) and 6 hours after their respective treatment (Hour 6, 6hr). Depending on their location, patients were randomly assigned different double or triple Artemisinin Combination Therapy (ACT) as follows: Thailand, Cambodia, Vietnam, and Myanmar - dihydroartemisinin-piperaquine or dihydroartemisinin-piperaquine plus mefloquine; Cambodia - artesunate-mefloquine or dihydroartemisinin-piperaquine plus mefloquine; Laos, Myanmar, Bangladesh - artemether-lumefantrine or artemether-lumefantrine plus amodiaquine.

tag: isolate

value: In vivo, Blood stage

tag: treatment

value: After ACT treatment, 6h


title: Control_8hr_371874

status: Public on Feb 08 2022

city: Seattle

first: Shreeram

last: Akilesh

state: Washington

address: 1959 NE Pacific St, Box 356100

country: USA

institute: University of Washington

data_processing:
Base calls generated in real-time on the NovaSeq 6000 instrument (RTA 3.1.5);demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4).
Reads aligned to  reference genome (GENCODE human release 30 GRCh38) using STAR (v2.6.1d)
Aligned data were read into R and summarized as counts per gene using the Bioconductor GenomicAlignments package
Differential analysis was performed by voom method in the Bioconductor limma package.
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed data file is a tab-delimited matrix of gene counts, with Ensembl IDs in the first column, and the sample names in the header

source_name: 3D human kidney proximal tubule MPS

growth_protocol: Nortis Triplex™ devices were filled with 6 mg/mL of rat tail collagen I, and left overnight at room temperature to allow the collagen I matrix to solidify.  The mandrels of the MPS platforms were removed, leaving behind hollow channels through the collagen I matrix.  Cell chambers were coated with a 5 µg/mL mouse collagen IV to facilitate human PTECs adhesion.  T-flask cultures of PTECs were trypsinized to obtain single cell suspensions.  The cells were resuspended with PTEC maintenance media at a concentration of ~20 ×10^6 cells/mL and 2-2.5 µL were injected into the collagen IV-coated channels of the MPS.  The cells were allowed to attach for 3 hours before starting perfusion at a rate of 1.0 µL/min.  PTECs were cultured under flow for at least 7 days to form the tubule cell structures.  Only kidney MPS that exhibited tubules with >90% channel coverage and continuous media flow characteristics were selected for use in functional experiments.

extract_protocol:
Cells cultured in the kidney MPS were isolated by injecting 100 uL buffer RLT (Qiagen, 79216) and the lysate was collected at the outflow port into an additional 900 uL of buffer RLT then frozen at -80°C until extraction. Total RNA was isolated using the Qiagen RNeasy Micro Kit.
Total RNA was normalized to 2ng in a total volume of 9ul and then transcribed to cDNA in a dedicated PCR clean workstation using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio, Mountain View, CA).  Sequencing libraries were constructed from cDNA using the SMARTer ThruPLEX DNA-Seq kit (Takara Bio).  Final libraries were quantified and library insert size distribution was checked using the Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Base calls generated in real-time on the NovaSeq 6000 instrument (RTA 3.1.5);demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4).

treatment_protocol: Kidney MPS were exposed to maintenance media or maintenance media spiked with 2% normal human serum or 720 ug/mL albumin for either 8 hours or 7 days.

tag: tissue

value: 3D human kidney proximal tubule MPS

value: Control

tag: donor

tag: exposure time


title: HMEC_siSTAG2_2_3

city: Boston

first: Stephen

middle: J

last: Elledge

state: MA

address: 77 Avenue Louis Pasteur NRB160

institute: Brigham and Women's Hospital | HHMI

data_processing:
For U937 cells, RNA-seq reads were mapped using STAR version 2.4.2a. The STAR genome index was generated from human reference sequence hg19 (FASTA downloaded from UCSC genome browser) and coding transcripts from GENCODE Release 19 (GTF downloaded from http://www.gencodegenes.org/). Reads mapping to genes were quantified with featureCounts from the R package Subread (v2.0.1). Transcripts per million (TPM) were quantified from the count data.
For HMECs, each RNA-seq sample was aligned to the hg19 genome using STAR version 2.7.0a.
For HMECs, reads mapping to genes were quantified with featureCounts.
For HMECs, differential expression was quantified using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts matrix, TPM normalized counts matrix, differential expression output

molecule: polyA RNA

source_name: HMEC

growth_protocol: U937 cells were grown in RPMI+10%FBS+1%P/S/G, HMEC cells were grown in HuMEC media supplemented with HuMEC supplement kit

extract_protocol:
HMECs Total RNA was purified from 1 million cells using Rneasy plus isolation kit (QIAGEN) following the manufacturer instructions
HMEC RNA-seq libraries were prepared with the NEBnext Ultra II Directional RNA Library kit according to the standard protocol.

treatment_protocol: HMECs were treated with no-targeting siRNAs or STAG2 targeting siRNAs. HMECs were transfected with 5uL per 6-well plate of Lipofectamine RNAiMAX transfection reagent and 40nM siRNA duplex (Dharmacon).

value: HMEC

tag: cell type

value: Mammary Epithelial Cells

tag: genotype/variation

value: STAG2-siRNA 1


title: T2H6_0584

description:
P.falciparum parasite isolate
H6_sample164


title: T2H6_0559

description:
P.falciparum parasite isolate
H6_sample162


title: T2H6_0558

description:
P.falciparum parasite isolate
H6_sample161


title: C1_ASH2L_CUT&RUN

city: Cambridge

first: Yun

last: Zhang

email: zhangyunbio@gmail.com, barc@wi.mit.edu

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

library_source: genomic

data_processing:
Library strategy: CUT&RUN
CUT&RUN paired-end reads were aligned using bowtie2 to the human genome (GRCh38), with the parameters: --very-sensitive --no-discordant -X 1000 --phred64
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files in counts per million (cpm) were generated using bamCoverage from deepTools

molecule: genomic DNA

source_name: HMLER

growth_protocol: Cells were cultured in 2:1:1 MEGM (Lonza Bullet kit), DMEM and F12 media, supplemented with insulin (10 μg/ml), EGF (10 ng/ml), hydrocortisone (1 μg/ml), and 1x Pen/Strep (50 I.U./mL penicillin and 50 μg/mL streptomycin, Sigma-Aldrich #P4333).

extract_protocol: Libraries were prepared using Swift Science’s Accel-NGS Library Preparation Kit for Illumina Platforms according to manufacturer’s directions.

tag: genotype

value: wild type

value: HMLER

tag: cut&run antibody


title: T2H6_0533

description:
P.falciparum parasite isolate
H6_sample159


title: C1-sgKMT2D-Epi_EZH2_CUT&RUN


title: T2H6_0540

description:
P.falciparum parasite isolate
H6_sample160


title: C1-sgEED-Epi_EZH2_CUT&RUN

value: EED-KO


title: T2H6_0529

description:
P.falciparum parasite isolate
H6_sample156


title: HMEC_siSTAG2_2_2


title: T2H6_0532

description:
P.falciparum parasite isolate
H6_sample158


title: Control_12, classical monocyte

city: Birmingham

first: Peter

middle: Christopher

last: Allen

state: Alabama

address: 1720 University Blvd

department: Graduate Biomedical School

institute: University of Alabama at Birmingham

data_processing:
Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA).
Reads were trimmed using cutadapt.
Quality scores were assessed using FastQC.
Reads were aligned to the Homo sapiens genome build hg19 using STAR.
Individual sample reads were quantified using HTseq.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: Control, classical monocyte

extract_protocol:
Total RNA was extracted from classical monocytes isolated from 16 female African American patients and 18 female African American controls using the RNeasy Kits (Qiagen) according to the manufacturers guideline.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: Female

tag: race

value: AA

tag: age

tag: disease status

tag: disease subset

value: classical monocyte


title: HMEC_siCtrl_2_2

value: Non Targeting siRNA 2


title: C1-sgControl_ASH2L_CUT&RUN


title: T2H6_0520

description:
P.falciparum parasite isolate
H6_sample155


title: C2-Epi_EZH2_CUT&RUN


title: C1-sgControl_EZH2_CUT&RUN


title: T2H6_0518

description:
P.falciparum parasite isolate
H6_sample154


title: T2H6_0515

description:
P.falciparum parasite isolate
H6_sample152


title: HMEC_siCtrl_1_2

value: Non Targeting siRNA 1


title: T2H6_0516

description:
P.falciparum parasite isolate
H6_sample153


title: C1_EZH2_CUT&RUN


title: HMEC_siCtrl_1_1


title: T2H6_0512

description:
P.falciparum parasite isolate
H6_sample150


title: T2H6_0511

description:
P.falciparum parasite isolate
H6_sample149


title: C1-sgKMT2D-Mes_2_RNA-seq

data_processing:
RNASeq paired-end reads were aligned using STAR (v2.7.1a) to the human genome (GRCh38) with Ensembl annotation (v93) in gtf format: default parameters were used, and an overhang of 100.
featureCounts was used to obtain counts with -s 2 (reversely stranded) and using Ensembl gtf annotation (v93).
Genome_build: GRCh38

extract_protocol:
total RNA was isolated directly from cultured cells or sorted cells using Trizol (Invitrogen) and Direct-zol RNA miniprep kits (Zymo Research).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: HMEC_NT_2

value: No siRNA


title: HMEC_siSTAG2_2_1


title: T2H6_0530

description:
P.falciparum parasite isolate
H6_sample157


title: T2H6_0510

description:
P.falciparum parasite isolate
H6_sample148


title: T2H6_0501

description:
P.falciparum parasite isolate
H6_sample147


title: T2H6_0500

description:
P.falciparum parasite isolate
H6_sample146


title: HMEC_siCtrl_2_1


title: HMEC_NT_1


title: C1-sgKMT2D-Epi_2_RNA-seq


title: C1-sgKMT2D-Mes_1_RNA-seq


title: T2H6_0497

description:
P.falciparum parasite isolate
H6_sample144


title: C1-sgKMT2D-Epi_1_RNA-seq


title: T2H6_0496

description:
P.falciparum parasite isolate
H6_sample143


title: Wouter15

value: WT


title: C1-sgEED-Mes_2_RNA-seq


title: T2H6_0495

description:
P.falciparum parasite isolate
H6_sample142

value: In vivo, Blood stage


title: T2H6_0493

description:
P.falciparum parasite isolate
H6_sample141

value: After ACT treatment, 6h


title: Wouter16

value: ATM KO


title: T2H6_0514

description:
P.falciparum parasite isolate
H6_sample151


title: C1-sgEED-Mes_1_RNA-seq


title: Wouter13


title: T2H6_0488

description:
P.falciparum parasite isolate
H6_sample138


title: T2H6_0481

description:
P.falciparum parasite isolate
H6_sample136


title: T2H6_0489

description:
P.falciparum parasite isolate
H6_sample139


title: Wouter12


title: C1-sgEED-Epi_1_RNA-seq


title: T2H6_0483

description:
P.falciparum parasite isolate
H6_sample137


title: T2H6_0479

description:
P.falciparum parasite isolate
H6_sample135


title: Wouter11


title: T2H6_0498

description:
P.falciparum parasite isolate
H6_sample145


title: T2H6_0470

description:
P.falciparum parasite isolate
H6_sample133


title: T2H6_0469

description:
P.falciparum parasite isolate
H6_sample132


title: C1-sgControl_2_RNA-seq


title: Wouter10


title: T2H6_0478

description:
P.falciparum parasite isolate
H6_sample134


title: C1-sgControl_1_RNA-seq


title: T2H6_0468

description:
P.falciparum parasite isolate
H6_sample131


title: T2H6_0465

description:
P.falciparum parasite isolate
H6_sample129


title: Wouter1


title: Wouter8

value: Camptothecin-treated


title: Wouter14


title: T2H6_0466

description:
P.falciparum parasite isolate
H6_sample130


title: T2H6_0492

description:
P.falciparum parasite isolate
H6_sample140


title: C1-sgEED-Epi_2_RNA-seq


title: C2-Mes_2_RNA-seq


title: C2-Mes_1_RNA-seq


title: Wouter7

value: DMSO-treated


title: Wouter6


title: C2-Epi_2_RNA-seq


title: SSc_42, classical monocyte

source_name: SSc, classical monocyte

value: Systemic sclerosis (SSc)

value: dcSSc


title: C2-Epi_1_RNA-seq

value: wild type


title: C1_2_RNA-seq

value: HMLER


title: Wouter5


title: C1_1_RNA-seq


title: Wouter4


title: T2H6_0431

description:
P.falciparum parasite isolate
H6_sample125


title: T2H6_0441

description:
P.falciparum parasite isolate
H6_sample127


title: T2H6_0436

description:
P.falciparum parasite isolate
H6_sample126


title: T2H6_0430

description:
P.falciparum parasite isolate
H6_sample124


title: T2H6_0419

description:
P.falciparum parasite isolate
H6_sample118


title: T2H6_0428

description:
P.falciparum parasite isolate
H6_sample122


title: T2H6_0427

description:
P.falciparum parasite isolate
H6_sample121


title: Wouter17


title: T2H6_0400

description:
P.falciparum parasite isolate
H6_sample116


title: HCT116_FUSO_2 _IP

city: Hangzhou

first: Wei

last: Zhuo

state: Zhejiang

address: 866 Yuhangtang Road

department: School of Medicine

country: China

institute: Zhejiang University

data_processing:
Clean reads were obtained by removing reads containing adapter and low quality reads from raw data by trim_galore version 0.3.3.
RNA-seq and m6A-seq reads were aligned to human genome hg19 by HISAT2 version 2.1.0
Peaks were called using exomePeak version 1.4.2.
mRNA expression levels were analyzed based on Input sample sequencing data. And FPKM of each gene was quantified using stringTie analysis.
Genome_build: hg19
Supplementary_files_format_and_content: The m6A enriched peaks of four samples  were separately list in txt files named HCT116_Control_1-peak.txt, HCT116_Control_2-peak.txt, HCT116_FUSO_1-peak.txt and HCT116_FUSO_1-peak.txt. Format: chr; chromStart; chromEnd; name score; strand; thickStart; thickEnd; itemRgb; blockCount; blockSizes; blockStarts.
Supplementary_files_format_and_content: FPKM of each gene was quantified in four input samples, which were listed in the txt file named mRNA_Expression_SUMMARY_FPKM.txt. Format: gene_id; Control_1_FPKM; Control_2_FPKM; FUSO_1_FPKM; FUSO_2_FPKM.

source_name: HCT116 cells were treated with Fusobacterium nucleatum

growth_protocol: HCT116 CRC cell line was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA), and cultured in Maccoy 5A (Genom, China) with 10 % fetal bovine serum.

extract_protocol:
Total polyadenylated RNA was isolated from HCT116 cells treated with or without Fusobacterium nucleatum using TRIZOL reagent followed by isolation through NEBNext Poly(A) mRNA Magnetic Isolation Kit (New England Biolabs, UK).
Libraries were prepared according to Illumina's instructions.

treatment_protocol: HCT116 cells were treated with or without Fusobacterium nucleatum.

value: colorectal cancer

tag: treated microbiota

value: Fusobacterium nucleatum

tag: chip antibody

value: m6A Antibody (Synapic Systems, Cat. No. 202003)


title: T2H6_0398

description:
P.falciparum parasite isolate
H6_sample114


title: HCT116_FUSO_2_input

tag: cell line


title: T2H6_0399

description:
P.falciparum parasite isolate
H6_sample115

tag: isolate


title: HCT116_FUSO_1_IP


title: T2H6_0429

description:
P.falciparum parasite isolate
H6_sample123

tag: treatment


title: T2H6_0379

description:
P.falciparum parasite isolate
H6_sample112


title: HCT116_FUSO_1_input

tag: tissue


title: T2H6_0378

description:
P.falciparum parasite isolate
H6_sample111


title: T2H6_0420

description:
P.falciparum parasite isolate
H6_sample119


title: Wouter3

tag: treatment/group


title: SMS-CTR SIX1 KD5 MYOD1

city: Aurora

first: Heide

middle: L

last: Ford

state: CO

address: 12800 East 19th Ave Rm 6401I

department: Pharmacology

institute: University of Colorado Anschutz Medical Campus

data_processing:
ChIPseq reads were quality assessed by FastQC, MultiQC and filtered with BBDuk.
ChIPseq reads were aligned to the hg38 human and to the dm6 fly (Drosophila melanogaster) genome assembly using Bowtie2 (v2.3.4.3).
Samtools (v.1.11) was used to select the mapped reads (samtools view -b - q 30) and sort the bam files.
PCR duplicates were removed using Picard MarkDuplicates tool.
The normalization ratio of each sample was calculated by dividing the total number of mapped reads mapping to the fly genome of each sample by the the total number of mapped reads mapping to the fly genome of the sample with the lowest number of reads mapping to the Drosophila genome. Using the normalization ratio, random sub-sampling of the reads was performed using samtools view -hs.
Bedtools genomecov was used to create bedgraph files from the bam files.
Igvtools toTDF was used to create tdf files.
Peaks were called using MACS2 (v2.1.2) with default parameters (-gsize hs --qvalue 0.01)
Genome_build: hg38
Supplementary_files_format_and_content: tdf files

source_name: Fusion Negative Rhabdomyosarcoma

growth_protocol: Cells were cultured along with spike-in Drosophila S2 cells at a 1:10 ratio with RMS cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIPseq libraries were assembled using the KAPA HyperPrep ChIP library kit following manufacturer’s settings and were sequenced on an Illumina Nextseq500 machine.

value: Fusion Negative Rhabdomyosarcoma

value: SIX1 KD

value: MYOD1 (Abcam, ab133627)

value: SMS-CTR


title: T2H6_0447

description:
P.falciparum parasite isolate
H6_sample128


title: HCT116_Control_2_IP

source_name: HCT116 cells were treated with PBS


title: T2H6_0405

description:
P.falciparum parasite isolate
H6_sample117


title: T2H6_0367

description:
P.falciparum parasite isolate
H6_sample109


title: Wouter2


title: T2H6_0365

description:
P.falciparum parasite isolate
H6_sample108


title: T2H6_0377

description:
P.falciparum parasite isolate
H6_sample110


title: HCT116_Control_1 _IP


title: SMS-CTR SIX1 KD6 SIX1

value: SIX1 (Atlas, HPA0011893)


title: SMS-CTR SIX1 KD5 SIX1


title: T2H6_0387

description:
P.falciparum parasite isolate
H6_sample113

value: In vivo, Blood stage


title: T2H6_0356

description:
P.falciparum parasite isolate
H6_sample105

value: After ACT treatment, 6h


title: SMS-CTR SIX1 KD6 MYOD1


title: T2H6_0355

description:
P.falciparum parasite isolate
H6_sample104


title: HCT116_Control_2_input


title: T2H6_0362

description:
P.falciparum parasite isolate
H6_sample106


title: SMS-CTR SCRAMBLE SIX1

value: control


title: HCT116_Control_1_input


title: T2H6_0354

description:
P.falciparum parasite isolate
H6_sample103


title: T2H6_0349

description:
P.falciparum parasite isolate
H6_sample102


title: T2H6_0423

description:
P.falciparum parasite isolate
H6_sample120


title: mutant

city: Portland

first: Yu

last: Sang

address: 3181 SW Sam Jackson Park Rd

institute: OHSU

data_processing:
The RNA sequence data were analyzed using a workflow constructed for Galaxy (https://usegalaxy.org)
The RNA reads were aligned to the C. elegans genome (WS230) using the aligner STAR. Counts were normalized for sequencing depth and RNA composition across all samples. Differential gene expression analysis was then performed using normalized samples. Genes exhibiting at least a twofold change were considered differentially expressed. The differentially expressed genes were subjected to SimpleMine tools from WormBase (https://www.wormbase.org/tools/mine/simplemine.cgi) to obtain information such as the WormBase ID and gene names, which were employed for further analyses
Genome_build: WS230
Supplementary_files_format_and_content: Differential expressed genes

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Approximately 100 gravid animals were placed on 10-cm NGM plates (seeded with E. coli OP50) for 3 h to obtain a synchronized population, which developed and grew to the L4 larval stage at 20 ˚C.

extract_protocol:
Animals were washed off the plates with M9, frozen in QIAzol using ethanol/dry ice, and stored at -80˚C prior to RNA extraction. Total RNA was extracted using the RNeasy Plus Universal Kit (Qiagen, Netherlands). Residual genomic DNA was removed using TURBO DNase (Life Technologies, Carlsbad, CA).
A total of 6 µg of total RNA was reverse-transcribed with random primers using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, CA).  Library construction and RNA sequencing on the BGISEQ-500 platform was performed and paired-end reads of 100 bp were obtained for subsequent data analysis.

treatment_protocol: Synchronized L4 worms were washed three times in M9 buffer and transferred to E. faecium lawns grown on 2% agar BHI plates for colonization for 8 h at 25˚C

tag: agent

value: E. faecium


title: T2H6_0339

description:
P.falciparum parasite isolate
H6_sample100


title: T2H6_0340

description:
P.falciparum parasite isolate
H6_sample101


title: SMS-CTR SIX1 KD6 H3K27ac

tag: cell type

value: H3K27ac (Abcam, ab4729)


title: WT


title: T2H6_0334

description:
P.falciparum parasite isolate
H6_sample99


title: SMS-CTR SCRAMBLE MYOD1


title: T2H6_0333

description:
P.falciparum parasite isolate
H6_sample98


title: SMS-CTR SCRAMBLE H3K27ac


title: SMS-CTR SIX1 KD6 INPUT

value: Input


title: SMS-CTR SIX1 KD5 H3K27ac


title: Skeletal Muscle_Rat4

city: New York

first: Venugopalan

last: Nair

state: NY

address: 1468 Madison Avenue

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The ATAC-seq data were processed (trimmed, aligned, filtered, and quality controlled) using the Encode ATAC-seq pipeline v1.7.0 (https://www.encodeproject.org/atac-seq/).
For all samples, read quality was assessed using FastQC (Andrews, 2021).
Trimmomatic (Bolger et al., 2014) was used to remove adapters and low-quality base pairs and reads identified by FastQC.
Reads for each sample were aligned to the rat genome (rn6.0) using Bowtie2 (Li and Durbin, 2010).
After alignment, we removed reads mapping to the mitochondrial genome. As a general measure of sensitivity to Tn5 transposase fragmentation, ATAC-seq signal was defined as a number of transposase cuts mapping to each bp (or a total count of cuts mapping to a selected genomic interval). The cuts were defined as 5’ ends of ATAC-seq reads, with additional shifting by +4 bp and -5bp for reads mapping to the plus and minus strands, respectively (Buenrostro et al., 2013).
Duplications were removed by Picard (https://broadinstitute.github.io/picard/). MACS2 (Zhang et al., 2008) was applied on each merged bam file to call peaks (with option --nomodel --extsize 200 --shift 100).
Genome_build: rn6
Supplementary_files_format_and_content: Peak files

organism: Rattus norvegicus

source_name: Gastrocnemius muscle

growth_protocol: All animal procedures in this study were conducted in accordance with the guidelines of University of Florida for the care and use of laboratory animals (IACUC # 201709757). Rats were obtained from the National Institute on Aging colony at 8 months of age. They were allowed 2 weeks to acclimate to a reverse light cycle (lights off at 8am: lights on at 8pm).

extract_protocol:
Tissue samples were transferred to 1.1 ml micronic tubes (Micronic, USA) and resuspended in 600 µl of homogenization buffer (320 mM Sucrose, 10 mM Tris-HCl pH 7.8, 100 nM EDTA, 5 mM CaCl2, 3 mM Mg(AC)2, 167 µM β-mercaptoethanol, 1X protease inhibitor). Three, 2.8 mm ceramic beads (Omni International, Kennesaw, GA, USA) were added to each micronic tube. Tubes were vortexed briefly and kept on ice. The tissue samples were homogenized in a Bead Ruptor Elite bead mill homogenizer with Omni BR Cryo cooling unit (Omni International) using 2 cycles of the following settings: speed: 1.0, time: 20 sec and speed: 2.1, time: 20 sec, dwell time: 20 sec at both speeds, while cooled by liquid nitrogen to 10°C. Following homogenization, each tissue homogenate was filtered through a mini 20 µm pluriStrainer (pluriSelect, Leipzig, Germany). The number of nuclei in the filtrate was counted using an Automated Cell Counter (Cellometer K2 Image cytometer, Nexcelom) following staining with the Propidium Iodide (PI) dye.
Approximately 75,000 nuclei were transferred into a fresh tube and diluted in 1 ml of ATAC-seq resuspension buffer [ATAC-seq RSB (Corces et al., 2017) + 0.1% Tween 20 (Sigma, St. Louis, MO, USA)]. Nuclei were centrifuged using Centrifuge 5418 R (Eppendorf) at 725 RCF for 10 minutes, and the supernatant was carefully aspirated. Nuclei were incubated in 50 µl transposition reaction mixture containing 25 µl of 2X TD buffer (Illumina, Inc., San Diego, CA, United States), 16.6 µl of PBS, 0.5 µl of 1% digitonin (Sigma), 0.5 µl of 10% Tween-20, 1.5 µl of Tn5 transposase (Illumina, 0.8 U/μl), and 6 µl of nuclease-free water using a thermomixer (USA Scientific, Ocala, FL, USA) set at 37 °C for 30 min with a speed of 1000 rpm. Transposed DNA was purified using a DNA clean and concentrator kit (Zymo Research, Irvine, CA, USA), according to the manufacturer’s protocol. Following PCR amplification, libraries were purified using Agencourt Ampure XP beads (Beckman Coulter, Indianapolis, IN, USA) double-size selection (0.5x:1.3x). Library quality was assessed using the Agilent Bioanalyzer High-Sensitivity DNA kit and the Qubit dsDNA high sensitivity assay kit (Thermo Fisher). All libraries were pooled and sequenced with 100-bp paired-end reads on the Illumina Novaseq 6000 at the New York Genome Center.

treatment_protocol: For tissue collection, rats were anesthetized via isoflurane, secondary euthanasia was performed via decapitation, and gastrocnemius muscle (skeletal muscle) and abdominal white adipose tissue (adipose tissue) were dissected out and quickly frozen in liquid nitrogen and stored at -80C until nuclei extraction.

tag: strain

value: Fischer 344

value: 8 months

tag: Sex

value: male

value: Gastrocnemius muscle


title: T2H6_0327

description:
P.falciparum parasite isolate
H6_sample97


title: Skeletal Muscle_Rat5


title: T2H6_0320

description:
P.falciparum parasite isolate
H6_sample95


title: T2H6_0364

description:
P.falciparum parasite isolate
H6_sample107


title: T2H6_0310

description:
P.falciparum parasite isolate
H6_sample93


title: T2H6_0326

description:
P.falciparum parasite isolate
H6_sample96


title: T2H6_0293

description:
P.falciparum parasite isolate
H6_sample89


title: T2H6_0314

description:
P.falciparum parasite isolate
H6_sample94


title: SMS-CTR SIX1 KD5 INPUT

tag: genotype


title: Skeletal Muscle_Rat3


title: T2H6_0304

description:
P.falciparum parasite isolate
H6_sample91


title: T2H6_0297

description:
P.falciparum parasite isolate
H6_sample90


title: T2H6_0305

description:
P.falciparum parasite isolate
H6_sample92


title: T2H6_0290

description:
P.falciparum parasite isolate
H6_sample88


title: T2H6_0281

description:
P.falciparum parasite isolate
H6_sample86


title: Skeletal Muscle_Rat1


title: Adipose Tissue_Rat5

source_name: White adipose tissue

value: White adipose tissue


title: Adipose Tissue_Rat4


title: T2H6_0274

description:
P.falciparum parasite isolate
H6_sample85


title: T2H6_0289

description:
P.falciparum parasite isolate
H6_sample87


title: 6 mM VPA for 5 days, sample 1

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description:
counts.matrix.norm_anno
VPA-6mM_1

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q20 in a window of nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (GRCh38) using STAR 2.5.3a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10 %.
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.62. Only genes with a minimum fold change of ± 1.5 (log2 ± 0.59), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensemble gene identifiers.
Genome_build: hg38
Supplementary_files_format_and_content: library size normalized counts

source_name: pancreatic ductal epithelioid carcinoma cells

growth_protocol: The cell line Panc-1 was purchased from American Type Culture Collection (ATCC, distributor LGC Standards). Cells were maintained as a monolayer in 25 mmol/L glucose Dulbecco’s modified Eagles medium (DMEM, Sigma) with 10 % fetal bovine serum supplemented with 100 units/ml penicillin, 100 mg/ml streptomycin, and 2 mmol/L-glutamine. Cells were cultured at 37°C with 5 % CO2 and 95 % humidity. Cells were passaged by trypsinization. They were washed once with PBS (without Ca2+ and Mg2+) and treated with pre-warmed 0.05%trypsin / EDTA (1x) solution. After a short incubation period of 3-5 min at 37°C, cells were detached and diluted with warm DMEM culture medium and centrifuged for 4 min at 1000 rpm before the medium was removed. Cells were resuspended with culture medium and seeded into new flasks. For the experiments, cells with a confluence of 50 - 60 % were employed.

extract_protocol:
Panc-1-cell RNA was isolated using a RNeasy Mini kit (Qiagen). Total RNA concentration and purity was determined using a NanoDrop 1000 Spectrophotometer (NanoDrop) at a sample absorbance of 260/280 nm. To avoid genomic DNA contaminaton, samples were treated by DNase I (Qiagen). Total RNA and library integrity were verified with LabChip Gx Touch 24 (Perkin Elmer).
1 μg of total RNA was used as input 81 for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech) following standard 82 instructions.

treatment_protocol: For VPA treatment, VPA was dissolved in aqua dest. and sterile filtered. Cells were plated in culture dishes and incubated overnight with VPA (Sigma) at final concentrations of 0.5, 1, 2, 4, or 6 mM for three to eight days. Every 24 h, culture media were replaced by fresh medium enriched with VPA. Aqua dest. was used for control treatments.

tag: passages


title: 0 mM VPA for 5 days, sample 2

description:
counts.matrix.norm_anno
WT_2


title: 0 mM VPA for 5 days, sample 1

description:
counts.matrix.norm_anno
WT_1


title: 6 mM VPA for 5 days, sample 2

description:
counts.matrix.norm_anno
VPA-6mM_2


title: T2H6_0267

description:
P.falciparum parasite isolate
H6_sample83


title: T2H6_0266

description:
P.falciparum parasite isolate
H6_sample82


title: T2H6_0262

description:
P.falciparum parasite isolate
H6_sample79


title: Adipose Tissue_Rat2


title: T2H6_0265

description:
P.falciparum parasite isolate
H6_sample81


title: Skeletal Muscle_Rat2


title: 1 mM VPA for 5 days, sample 2

description:
counts.matrix.norm_anno
VPA-1mM_2


title: SMS-CTR SCRAMBLE INPUT


title: Adipose Tissue_Rat1


title: T2H6_0261

description:
P.falciparum parasite isolate
H6_sample78


title: Adipose Tissue_Rat3


title: T2H6_0263

description:
P.falciparum parasite isolate
H6_sample80


title: Adipose Tissue_Rat10

first: Yongchao

last: Ge

address: One Gustave L Levy Place #1137

data_processing:
Raw data were processed using bcl2fastq Conversion Software (Illumina) to obtain FASTQ files, and the FASTQ files were aligned to the rn6 genome using STAR (Dobin et al., 2013).
Gene expression was quantified with featureCounts (Liao et al., 2014).
Genome_build: rn6
Supplementary_files_format_and_content: tab delimited file including the counts of reads for all genes and for all samples

extract_protocol:
Skeletal muscle (10mg) and white adipose (30mg) samples were homogenized in a Bead Ruptor Elite bead mill homogenizer with Omni BR Cryo cooling unit (Omni International) twice for 20 sec at a speed of 4.2 m/s, while cooled by liquid nitrogen to 10°C . Tissue homogenates were processed for total RNA extraction using the Agencourt RNAdvance Tissue Kit (Beckman Coulter) on a BioMek FXP Laboratory Automation Workstation (Beckman Coulter). Concentration and integrity (RIN) of isolated RNA were determined using Quant-iT™ RiboGreen™ RNA Assay Kit (Thermo Fisher) and an RNA Standard Sensitivity Kit (DNF-471, Agilent Technologies, Santa Clara, CA, USA) on a Fragment Analyzer Automated CE system (Agilent Technologies), respectively.
cDNA libraries were constructed from 300 ng of total RNA using the Universal Plus mRNA-Seq kit (Tecan Genomics, San Carlos, CA, United States) in a Biomek i7 Automated Workstation (Beckman Coulter).  Library concentration was assessed fluorometrically using the Qubit dsDNA HS Kit (Thermo Fisher), and quality was assessed with the Genomic DNA 50Kb Analysis Kit (DNF-467, Agilent Technologies).

treatment_protocol: For tissue collection, rats were anesthetized via isoflurane, secondary euthanasia was performed via decapitation, and gastrocnemius muscle (skeletal muscle) and abdominal white adipose tissue (adipose tissue) were dissected out and quickly frozen in liquid nitrogen.

value: Fischer 344 x Brown Norway


title: T2H6_0258

description:
P.falciparum parasite isolate
H6_sample77


title: T2H6_0257

description:
P.falciparum parasite isolate
H6_sample76


title: Adipose Tissue_Rat9


title: T2H6_0250

description:
P.falciparum parasite isolate
H6_sample75


title: T2H6_0273

description:
P.falciparum parasite isolate
H6_sample84


title: T2H6_0240

description:
P.falciparum parasite isolate
H6_sample74


title: T2H6_0226

description:
P.falciparum parasite isolate
H6_sample73


title: T2H6_0224

description:
P.falciparum parasite isolate
H6_sample72


title: Adipose Tissue_Rat8


title: T2H6_0219

description:
P.falciparum parasite isolate
H6_sample71


title: Adipose Tissue_Rat7


title: 1 mM VPA for 5 days, sample 1

description:
counts.matrix.norm_anno
VPA-1mM_1


title: Adipose Tissue_Rat6


title: T2H6_0216

description:
P.falciparum parasite isolate
H6_sample69


title: T2H6_0209

description:
P.falciparum parasite isolate
H6_sample67


title: T2H6_0218

description:
P.falciparum parasite isolate
H6_sample70


title: Adipose Tissue_Rat4


title: T2H6_0215

description:
P.falciparum parasite isolate
H6_sample68


title: T2H6_0197

description:
P.falciparum parasite isolate
H6_sample63


title: Adipose Tissue_Rat5


title: T2H6_0196

description:
P.falciparum parasite isolate
H6_sample62


title: T2H6_0203

description:
P.falciparum parasite isolate
H6_sample66


title: T2H6_0199

description:
P.falciparum parasite isolate
H6_sample64


title: XG2 8 hours DMSO

city: Bethesda

first: David

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

description:
CTRL
XG2_H8_DMSO

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 human genome using STAR2
Raw read counts per gene were called with Htseq-Count
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files of raw count of each gene and each sample

source_name: XG2 human multiple myeloma cell line

growth_protocol: XG2 and SKMM1 cells were grown in advanced RPMI supplemented with 4% FBS with pen/strep and glutamine.

extract_protocol:
RNA wass extracted using the Qiagen AllPrep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The myeloma cell lines XG2 and SKMM1 were grown at 1 x 10^6 cells/ml and either treated with DMSO or 100 nM everolimus for 3 or 8 hours.  5 x 10^6 cells were collected for each sample.

value: DMSO

tag: time

value: 8 hr

value: multiple myelom cell


title: XG2 3 hours 100 nM everolimus

description:
TREATMENT
XG2_H3_EVER

value: 100 nM everolimus

value: 3 hr


title: XG2 8 hours 100 nM everolimus

description:
TREATMENT
XG2_H8_EVER


title: XG2 3 hours DMSO

description:
CTRL
XG2_H3_DMSO


title: Adipose Tissue_Rat3

tag: age


title: Adipose Tissue_Rat1


title: Adipose Tissue_Rat2


title: T2H6_0193

description:
P.falciparum parasite isolate
H6_sample60

value: In vivo, Blood stage


title: 201222_31_AAS

type: RNA

city: Seoul

first: Jieun

last: Kim

state: Yongsan-gu

department: Department of Laboratory Medicine

country: South Korea

institute: Soonchunhyang University Seoul Hospital

description: Gene expression data from normal bonemarrow

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16 hours.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin

source_name: Bonemarrow

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: The sample was clinical bone marrow samples used in diagnosis, which does not require specific growth condition

extract_protocol: RNA was extracted from proband’s BM samples at initial diagnosis using an RNeasy Micro kit (Qiagen) and then evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) for RNA integrity. cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer.

treatment_protocol: Mononuclear cells (MNCs) were isolated by density gradient separation from the BM of the patients

value: Female

value: normal bonemarrow


title: 201222_29_KOY

description: Gene expression data from B-ALL at initial diagnosis

value: B-ALL bonemarrow


title: T2H6_0189

description:
P.falciparum parasite isolate
H6_sample59

value: After ACT treatment, 6h


title: SKMM1 8 hours 100 nM everolimus

description:
TREATMENT
SKMM1_H8_EVER

source_name: SKMM1 human multiple myeloma cell line


title: Skeletal Muscle_Rat10


title: 201222_27_LSY

description: Gene expression data from AML at initial diagnosis

value: Male

value: AML bonemarrow


title: 201222_26_LYO


title: T2H6_0172

description:
P.falciparum parasite isolate
H6_sample58


title: T2H6_0200

description:
P.falciparum parasite isolate
H6_sample65


title: T2H6_0156

description:
P.falciparum parasite isolate
H6_sample56


title: SKMM1 8 hours DMSO

description:
CTRL
SKMM1_H8_DMSO


title: SKMM1 3 hours 100 nM everolimus

description:
TREATMENT
SKMM1_H3_EVER


title: T2H6_0154

description:
P.falciparum parasite isolate
H6_sample55


title: T2H6_0195

description:
P.falciparum parasite isolate
H6_sample61


title: Skeletal Muscle_Rat9

value: 8 months


title: T2H6_0150

description:
P.falciparum parasite isolate
H6_sample54


title: SKMM1 3 hours DMSO

description:
CTRL
SKMM1_H3_DMSO


title: T2H6_0171

description:
P.falciparum parasite isolate
H6_sample57


title: T2H6_0146

description:
P.falciparum parasite isolate
H6_sample53


title: T2H6_0143

description:
P.falciparum parasite isolate
H6_sample52


title: T2H6_0138

description:
P.falciparum parasite isolate
H6_sample50


title: Skeletal Muscle_Rat7

value: male


title: T2H6_0141

description:
P.falciparum parasite isolate
H6_sample51


title: T2H6_0136

description:
P.falciparum parasite isolate
H6_sample49


title: Skeletal Muscle_Rat6

value: Gastrocnemius muscle


title: T2H6_0131

description:
P.falciparum parasite isolate
H6_sample48


title: T2H6_0123

description:
P.falciparum parasite isolate
H6_sample46


title: Skeletal Muscle_Rat4


title: DP25836_10

city: Houston

first: Cintia

last: de Paiva

state: TX

address: 6565 Fannin Street, Room NC 505G

department: Ophthalmology

institute: Baylor College of Medicine

hyb_protocol: One hundred nanograms of total RNA were hybridized with the NanoString Technologies nCounter Gene Expression GE- Mouse -Inflammation v2 Panel Codeset. Overnight hybridization occurred for 20 hours at 65°C. Removal of excess probes with magnetic bead purification was performed on the nCounter Prep Station (software v4.0.11.2) on the High Sensitivity assay. Briefly, the probe-mRNA structure was affinity purified by its 3’ end to remove excess reporter probes, then by its 5’ end to remove excess capture probes. Once unbound probes were washed away, the tripartite structure was bound to the streptavidin-coated cartridge by the biotin capture probe, aligned by an electric current (negative to positive), and immobilized. Photobleaching and fluorophore degradation was prevented with the addition of SlowFade.

scan_protocol: The cartridge containing immobilized samples was transferred to the nCounter Digital Analyzer (software v3.0.1.4) and scanned at 555 field of view (FOV). An epi-fluorescent microscope and CCD camera identified sets of fluorescent spots, which were tabulated for data output. Quality control metrics were recorded using the nSolver Analysis Software v4.0.6.2.

data_processing: Data processing was analyzed with nCounter and ROSALIND software. Data in Matrix is after normalization by ROSALIND.

organism: Mus musculus

source_name: conjunctiva, Desiccating stress, Tributyrin

extract_protocol: Conjunctival tissue collected from female C57BL/6J mice was placed in Qiagen RLT buffer with beta-mercaptoethanol, sonicated and flash-frozen in liquid nitrogen. For RNA isolation, tissue was chopped with surgical scissors then sonicated, and RNA was extracted using Qiagen RNeasy Plus. RNA quantity and quality was measured with NanoDrop and Bioanalyzer.

treatment_protocol: Mice were exposed to desiccating stress (DS) conditions which included a drafty low humidity (<30% relative humidity) environment and QID pharmacological inhibition of tear secretion by subcutaneous injection of scopolamine hydrobromide. During DS, mice received daily gavage of tributyrin or vehicle control.

value: female

value: conjunctiva

tag: group

value: DS5 TB CJ

tag: age (weeks)


title: DP25838_11


title: Skeletal Muscle_Rat3

value: Fischer 344 x Brown Norway


title: Skeletal Muscle_Rat8


title: DP25839_12


title: T2H6_0130

description:
P.falciparum parasite isolate
H6_sample47

source_name: P.falciparum field isolate from patient


title: T2H6_0122

description:
P.falciparum parasite isolate
H6_sample45


title: T2H6_0109

description:
P.falciparum parasite isolate
H6_sample42


title: DP25835_09


title: T2H6_0115

description:
P.falciparum parasite isolate
H6_sample44


title: T2H6_0114

description:
P.falciparum parasite isolate
H6_sample43


title: T2H6_0104

description:
P.falciparum parasite isolate
H6_sample40


title: T2H6_0106

description:
P.falciparum parasite isolate
H6_sample41


title: T2H6_0103

description:
P.falciparum parasite isolate
H6_sample39


title: Skeletal Muscle_Rat2


title: DP25833_07

source_name: conjunctiva, Desiccating stress, Vehicle control

value: DS5 Veh CJ


title: Skeletal Muscle_Rat5


title: T2H6_0102

description:
P.falciparum parasite isolate
H6_sample38


title: 201222_28_HIS

description: Gene expression data from B-ALL at initial diagnosis


title: Skeletal Muscle_Rat1


title: DP25832_06


title: CRC_89

city: Tokyo

first: Fuyuki

last: Miya

state: Tokyo

address: 35 Shinanomachi, Shinjuku-ku

country: Japan

institute: Keio University

data_processing:
The sequencing reads (100bp paired-end, ~45 millions reads) were aligned to the reference human genome (hg38) with STAR-2.7.1a with parameters -twopassMode.
The mapped reads were assigned to genes (Ensembl database annotation version GRCh38.98) using FeatureCount from the Bioconductor package Rsubread.
The resulting FeatureCounts were then normalized as either transcripts per million (TPM) by R package neuMatIdx.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include Ensembl_ENSG_ID and raw counts/normalized data for each sample.

source_name: Sigmoid colon

extract_protocol:
Total RNA was extracted from 10μm sections of formalin-fixed paraffin embedded (FFPE) blocks using RecoverAll Total Nucleic Acid Isolation Kit for FFPE kit (ThermoFisher).
Illumina TruSeq RNA Exome Kit

tag: overall survival (os) (month)

tag: outcome

value: Dead

tag: t stage

tag: n stage

tag: ajcc/uicc-tnm stage

value: IIIC


title: T2H6_0098

description:
P.falciparum parasite isolate
H6_sample36

tag: isolate

value: In vivo, Blood stage

tag: treatment


title: CRC_88

source_name: Rectum

value: Female

value: IIB


title: T2H6_0095

description:
P.falciparum parasite isolate
H6_sample35


title: DP25831_05

tag: tissue


title: DP25834_08


title: IHMA87_EX_2

city: Zurich

first: Julian

last: Trouillon

address: Otto-Stern-Weg 3

department: Institute of Molecular Systems Biology

country: Switzerland

institute: ETH Zurich

data_processing:
Library strategy: rGRIL-seq
reads were first aligned on vfr mRNA sequence using CLC Genomic Workbench 7.0.
Reads aligning to vfr mRNA were then aligned against the corresponding entire genome deleted of vfr gene, to identify chimeric reads using CLC Genomic Workbench 7.0.
Genome_build: PAO1, PA14, IHMA87
Supplementary_files_format_and_content: excel table, feature counts of enriched chimeric reads

organism: Pseudomonas aeruginosa

source_name: purified RNA from vfr rGRIL-seq in IHMA87

growth_protocol: aerobic growth in LB at 37°C

extract_protocol:
After in vivo RNA ligation by overexpression of T4 RNA ligase and cell lysis, total RNA were extracted and enriched for vfr-containing chimeric transcripts using sDNA probes specific to vfr mRNA.
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA library kit


title: IHMA87_ST_2


title: IHMA87_ST_1


title: CRC_87

source_name: Ascending colon

value: Alive


title: CRC_86

source_name: Transverse colon

value: IV


title: T2H6_0079

description:
P.falciparum parasite isolate
H6_sample28

data_processing:
Standard Illumina pipeline was used for base calling and demultiplexing
Sequenced reads were trimmed for adapter, primer and low quality bases from 3'-ends using Trimgalore (version 0.4.4)
Trimmed reads then mapped to Plasmodium falciparum 3D7 genome (genedb version 3) using HiSAT2 (version 2.1.0) with parameters --min-intronlen 60 --max-intronlen 2500 --fr
Uniquely mapped and properly oridented reads were extracted using samtools (version: 1.8) and raw count generated by bedtools (v2.27.1)
Normalized count - Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated, except gene length in the formula is replaced with mapped length
Genome_build: Genome_build: Plasmodium falciparum 3D7 geneDB version 3
Supplementary_files_format_and_content: Tab-delimited text file includes Log2 FPKM values for each sample

extract_protocol:
Total RNA was extracted using Trizol and ZYMO DirectZol96 extraction kit following protocol described in Kucharski, M., Tripathi, J., Nayak, S. et al. A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples. Malar J 19, 363 (2020).
Reverse transcription and cDNA synthesis was done following modifed Smart-Seq2 protocol using only oligo(d)T primers to enrich for mRNA transcripts (Kucharski, M., Tripathi, J., Nayak, S. et al. A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples. Malar J 19, 363 (2020)). Purified amplicon (cDNA) was used to generate sequencing libraries using Illumina Nextera XT kit as described in manufacturer’s protocol. Libraries were analyzed on the Bioanalyser High-Sensitivity DNA chips (Agilent, Cat. No.: 5067-4626), subsequently pooled (24 samples per lane) and sequenced on Illumina HiSeq4000 platform generating 150 bp paired end reads with 110 Gb data output generated per lane.

value: After ACT treatment, 6h


title: T2H6_0086

description:
P.falciparum parasite isolate
H6_sample30


title: T2H6_0090

description:
P.falciparum parasite isolate
H6_sample31


title: T2H6_0093

description:
P.falciparum parasite isolate
H6_sample33


title: CRC_85

value: Male


title: T2H6_0084

description:
P.falciparum parasite isolate
H6_sample29


title: T2H6_0091

description:
P.falciparum parasite isolate
H6_sample32


title: IHMA87_EX_1


title: T2H6_0094

description:
P.falciparum parasite isolate
H6_sample34


title: PA14_ST_2

source_name: purified RNA from vfr rGRIL-seq in PA14


title: CRC_83


title: T2H6_0077

description:
P.falciparum parasite isolate
H6_sample26


title: T2H6_0101

description:
P.falciparum parasite isolate
H6_sample37


title: T2H6_0072

description:
P.falciparum parasite isolate
H6_sample25


title: PA14_EX_2


title: PA14_ST_1


title: CRC_81

source_name: Cecum


title: T2H6_0068

description:
P.falciparum parasite isolate
H6_sample23


title: CRC_82


title: T2H6_0070

description:
P.falciparum parasite isolate
H6_sample24


title: T2H6_0067

description:
P.falciparum parasite isolate
H6_sample22


title: T2H6_0061

description:
P.falciparum parasite isolate
H6_sample19


title: T2H6_0078

description:
P.falciparum parasite isolate
H6_sample27


title: T2H6_0060

description:
P.falciparum parasite isolate
H6_sample18


title: CRC_84


title: PA14_EX_1


title: T2H6_0064

description:
P.falciparum parasite isolate
H6_sample21


title: CRC_77


title: PAO1_ST_2

source_name: purified RNA from vfr rGRIL-seq in PAO1


title: CRC_78


title: PAO1_ST_1


title: PAO1_EX_1


title: T2H6_0057

description:
P.falciparum parasite isolate
H6_sample17


title: CRC_79

value: IIIA


title: T2H6_0053

description:
P.falciparum parasite isolate
H6_sample16


title: CRC_76


title: T2H6_0031

description:
P.falciparum parasite isolate
H6_sample12


title: T2H6_0045

description:
P.falciparum parasite isolate
H6_sample13


title: T2H6_0046

description:
P.falciparum parasite isolate
H6_sample14


title: PAO1_EX_2


title: T2H6_0049

description:
P.falciparum parasite isolate
H6_sample15


title: T2H6_0030

description:
P.falciparum parasite isolate
H6_sample11


title: T2H6_0063

description:
P.falciparum parasite isolate
H6_sample20


title: CRC_80

value: IIA


title: BisRNA-seq_Pf_S_rep2

city: shanghai

first: meng

last: liu

address: 1239,SiPing Road

institute: TongJi University

description:
Pf_S_2
mRNA
m5C.Pf.txt

data_processing:
Library strategy: RNA-BisSeq
Raw sequencing data were filtered to remove low-quality reads and adapter contaminations with cutadapt. Reads with average quality score >= 20 and length >=50bp were kept. Clean reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) or to the Plasmodium yoelii 17X genome (Py17x v45, obtained from PlasmoDB) using software meRanGs suit meRanGh align. Only unambiguously aligned reads were used to call m5C sites using meRanCall suit from meRanGh(40) (FDR < 0.01). Analysis of the Dhfr spike-in revealed C-T conversion around 98% (Dataset S1). Candidate cytosine positions were covered by at least 20 reads, methylated cytosine depth greater than 5 and m5C methylation level greater than 0.1. m5C sites detected in both two replicates were considered as valid m5C sites and used for further analysis.
Genome_build: Pf 3D7 v32 and Py17x v45
Supplementary_files_format_and_content: *.txt: Tab-delimited text files containing m5c level of genes at different stages in Plasmodium.

growth_protocol: P. falciparum parasite-infected red blood cells were cultured in T75 flask at 2% hematocrit in the presence of 5% O2 and 5% CO2 (rest N2) in RPMI 1640 supplemented with 25mM Hepes, 50mg/l Hypoxanthine, 0.21% NaHCO3, 0.5% Albumax I and 20mg/l Gentamicin; P. yoelii parasite-infected ICR mice (female, 5 to 6 weeks old) were housed in the Animal Care Center of Xiamen University and kept at room temperature under a 12 h light/dark cycle at a constant relative humidity of 45%.

extract_protocol:
The parasite pellets were washed twice with precooling 1 X PBS and then resuspended in 1 mL TRIzol (Invitrogen). Total RNA was extracted using the Direct-zol RNA Kit (Zymo Research) according to the manufacturer’s instructions. mRNA enrichment from the total RNA was performed using the Dynabeads™ mRNA Purification Kit (invitrogen) as per the manufacturer’s instructions.
RNA bisulfite treatment and purification of converted RNA was performed using the Methylamp™ RNA Bisulfite Conversion Kit (Epigentek Group Inc.) according to the manufacturer’s instructions. One ug mRNAs along with 5 ng Dhfr RNA (1:2000) as methylation conversion control were used and as input RNA. The converted RNA was subsequently used for fragmentation and library construction using the KAPA Stranded mRNA-Seq Kit (KAPA) according to the instructions provided by the manufacturer.

treatment_protocol: Phenylhydrazine (80 μg/g mouse body weight) was used to treat with the ICR mouse through intraperitoneal injection; For P. falciparum, 50 mM N-acetyl-D-glucosamine was added to the cultures for three consecutive days to kill the asexual-stage parasites after sexual commitment. P. falciparum schizont-stage parasite cultures were synchronized by repeated sorbitol and percoll-sorbitol treatments ((Lambros and Vanderberg, 1979).

value: Pf NF54

value: Wild type

tag: host

value: Human

tag: developmental stage

value: Schizont

value: Whole body


title: CRC_75

tag: Sex


title: T2H6_0024

first: Zbynek

last: Bozdech

description:
P.falciparum parasite isolate
H6_sample9


title: CRC_74

value: I


title: T2H6_0026

description:
P.falciparum parasite isolate
H6_sample10


title: PAO1_WT_600_1

description: adaptor-ligated cDNA

data_processing:
Read trimming using Trimmomatic
Alignment using Bowtie2
Differencial analysis using DESeq2
Peak calling using PEAKachu
Genome_build: PAO1, PA14, IHMA87
Supplementary_files_format_and_content: excel table, DESeq2 analysis results

source_name: purified RNA from co-immunoprecipitation with Hfq

extract_protocol:
After cell lysis by bead bashing, anti-FLAG magnetic beads were used to immunoprecipitate Hfq and its bound RNAs, RNA was then isolated by phenol-chloroform extraction.
RNA libraries were prepared for sequencing using NEBNext Ultra II Directional RNA library kit

tag: strain

tag: variables

value: WT; 600 minutes


title: CRC_73


title: PAO1_WT_400_2

description: adaptor-ligated cDNA

value: WT; 400 minutes


title: BisRNA-seq_Pf_G3_rep1

description:
Pf_G3_1
mRNA
m5C.Pf.txt

tag: genotype

value: Gametocyte


title: BisRNA-seq_Pf_G3_rep2

description:
Pf_G3_2
mRNA
m5C.Pf.txt


title: T2H6_0022

description:
P.falciparum parasite isolate
H6_sample8

value: In vivo, Blood stage


title: PAO1_WT_400_1

description: adaptor-ligated cDNA


title: BisRNA-seq_Pf_G2_rep1

description:
Pf_G2_1
mRNA
m5C.Pf.txt


title: CRC_71

tag: age

value: Female

value: Dead


title: T2H6_0021

description:
P.falciparum parasite isolate
H6_sample7


title: T2H6_0020

description:
P.falciparum parasite isolate
H6_sample6


title: CRC_70

value: IV


title: PAO1_WT_600_2

description: adaptor-ligated cDNA


title: T2H6_0019

description:
P.falciparum parasite isolate
H6_sample5

value: After ACT treatment, 6h


title: PAO1_Hfq_600_2

description: adaptor-ligated cDNA

value: Hfq; 600 minutes


title: CRC_69

value: Male


title: BisRNA-seq_Pf_G1_rep1

description:
Pf_G1_1
mRNA
m5C.Pf.txt


title: PAO1_Hfq_600_1

description: adaptor-ligated cDNA


title: CRC_72

value: IIIC


title: BisRNA-seq_Pf_S_rep1

description:
Pf_S_1
mRNA
m5C.Pf.txt

value: Pf NF54


title: T2H6_0014

description:
P.falciparum parasite isolate
H6_sample4


title: CRC_68


title: BisRNA-seq_Pf_G2_rep2

description:
Pf_G2_2
mRNA
m5C.Pf.txt

value: Wild type


title: CRC_67


title: T2H6_0005

description:
P.falciparum parasite isolate
H6_sample2


title: RNA_seq_Pf_S_rep1

description:
Pf_S_1
mRNA
Fpkm.Pf.txt

data_processing:
Low-quality and adaptor sequences were trimmed using cutadapt (v1.18)(42) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20. RNA sequencing reads were aligned using hisat2 (v2.1.0)(43) with strand specific mode (--rna-strandness RF) to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) or to the Plasmodium yoelii 17X genome (Py17x v45, obtained from PlasmoDB). Mapped reads were subsequently assembled into transcripts guided by the PlasmoDB gff annotation files (Pf3D7 v32/ Py17x v45) using featureCounts (v1.6.1)(44) with parameters: -M -p -B -C -s 2. Read counts were obtained using featureCounts (v1.6.1).
Genome_build: Pf 3D7 v32 and Py17x v45
Supplementary_files_format_and_content: *.txt: Tab-delimited text files for gene expression.

extract_protocol:
Parasites were harvested and total RNA was isolated using TRIzol (Life) according to the manufacturer’s manual and further purified using the Direct-zol RNA Kit (ZYMO RESEARCH) for removal of gDNA. Residual gDNA was digested with TURBO DNA-freeTM DNaseI (Ambion) and the RNA was quantified by NanoDrop.
The poly(A) RNA isolation, mRNA enrichment and library construction were performed as described using 15 cycles of library amplification. The mRNA was enriched by poly(A) selection with the KAPA mRNA Capture Beads (KAPA), and fragmented to about 300–400 nucleotides (nt) in length, then all subsequent steps were performed in accordance with an KAPA Stranded mRNA-Seq Kit Illumina platform (KAPABIOSYSTEMS KK8421-96 libraries).

treatment_protocol: Phenylhydrazine (80 μg/g mouse body weight) was used to treat with the ICR mouse through intraperitoneal injection; For P. falciparum, 50 mM N-acetyl-D-glucosamine was added to the cultures for three consecutive days to kill the asexual-stage parasites after sexual commitment. P. falciparum schizont-stage parasite cultures were synchronized by repeated sorbitol and percoll-sorbitol treatments (Lambros and Vanderberg, 1979).

value: Human


title: PAO1_Hfq_400_1

description: adaptor-ligated cDNA

value: Hfq; 400 minutes


title: PAO1_WT_200_2

description: adaptor-ligated cDNA

value: WT; 200 minutes


title: T2H6_0009

description:
P.falciparum parasite isolate
H6_sample3


title: RNA_seq_Pf_G3_rep2

description:
Pf_G3_2
mRNA
Fpkm.Pf.txt

value: Whole body


title: CRC_66


title: RNA_seq_Pf_S_rep2

description:
Pf_S_2
mRNA
Fpkm.Pf.txt

value: Schizont


title: PAO1_Hfq_200_2

description: adaptor-ligated cDNA

value: Hfq; 200 minutes


title: T2H6_0004

description:
P.falciparum parasite isolate
H6_sample1


title: PAO1_WT_200_1

description: adaptor-ligated cDNA


title: RNA_seq_Pf_G3_rep1

description:
Pf_G3_1
mRNA
Fpkm.Pf.txt

value: Gametocyte


title: PAO1_Hfq_200_1

description: adaptor-ligated cDNA


title: PA14_WT_600_2

description: adaptor-ligated cDNA

value: WT; 600 minutes


title: T20702

description:
P.falciparum parasite isolate
H0_sample195

value: In vivo, Blood stage

value: Prior to ACT treatment, 0h


title: RNA_seq_Pf_G2_rep2

description:
Pf_G2_2
mRNA
Fpkm.Pf.txt


title: CRC_64

value: Female

value: Dead

value: IV


title: T20707

description:
P.falciparum parasite isolate
H0_sample196


title: RNA_seq_Pf_G2_rep1

description:
Pf_G2_1
mRNA
Fpkm.Pf.txt


title: T20692

description:
P.falciparum parasite isolate
H0_sample194


title: RNA_seq_Pf_G1_rep2

description:
Pf_G1_2
mRNA
Fpkm.Pf.txt


title: PA14_WT_400_2

description: adaptor-ligated cDNA

value: WT; 400 minutes


title: PAO1_Hfq_400_2

description: adaptor-ligated cDNA


title: PA14_WT_600_1

description: adaptor-ligated cDNA


title: CRC_62


title: PA14_WT_400_1

description: adaptor-ligated cDNA


title: T20688

description:
P.falciparum parasite isolate
H0_sample193


title: CRC_60


title: CRC_65

value: Male


title: RNA_seq_Pf_G1_rep1

description:
Pf_G1_1
mRNA
Fpkm.Pf.txt

value: Pf NF54


title: CRC_59

value: Alive

value: IIA


title: T20687

description:
P.falciparum parasite isolate
H0_sample192


title: PA14_WT_200_2

description: adaptor-ligated cDNA


title: T20686

description:
P.falciparum parasite isolate
H0_sample191


title: T20674

description:
P.falciparum parasite isolate
H0_sample190


title: CRC_58


title: CRC_63

value: IIIC


title: PA14_Hfq_600_2

description: adaptor-ligated cDNA

value: Hfq; 600 minutes


title: T20659

description:
P.falciparum parasite isolate
H0_sample189


title: CRC_57


title: PA14_Hfq_600_1

description: adaptor-ligated cDNA


title: T20656

description:
P.falciparum parasite isolate
H0_sample188


title: CRC_56


title: PA14_Hfq_400_2

description: adaptor-ligated cDNA

value: Hfq; 400 minutes


title: T20654

description:
P.falciparum parasite isolate
H0_sample187


title: CRC_55

value: IIIB


title: TKO;NfibR388K_ATAC_rep2

city: Smithville

first: Bin

last: Liu

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

data_processing:
Reads mapped to mouse genome reference GRCm38, ATAC peak calling by Genrich
read count by ht-seq count for RNA-seq and featureCounts for ATAC
DESeq was used for the analysis of differentially expressed genes and differential peaks
Genome_build: GRCm38
Supplementary_files_format_and_content: text

source_name: small cell lung cancer cells

extract_protocol: none provided by the submitter

treatment_protocol: SCLC was induced in 8-week-old mice by Adenovirus-Cre delivered to the lungs by intratracheal installation. Animals were aged for 28 weeks after tumor induction and cancer cells isolated from the lungs and analyzed by RNA-seq and ATAC-seq. Tumors from three indpendent animals for each genotype were analized.

tag: cell type

value: SCLC cells from GEMM

value: Rb1L/L; Rbl1L/L; p53L/L:NfibR388K


title: TKO;NfibR388K_ATAC_rep3


title: TKO;Carm1_ATAC_rep2

value: Rb1L/L; Rbl1L/L; p53L/L;Carm1L/L


title: TKO;Carm1_ATAC_rep3


title: PA14_Hfq_400_1

description: adaptor-ligated cDNA


title: T20652

city: Singapore

address: 60 Nanyang Drive

institute: Nanyang Technological University

description:
P.falciparum parasite isolate
H0_sample186

value: In vivo, Blood stage


title: CRC_54


title: TKO;Carm1_ATAC_rep1


title: TKO_ATAC_rep3

value: Rb1L/L; Rbl1L/L; p53L/L


title: TKO;NfibR388K_ATAC_rep1


title: CRC_53

value: Female


title: PA14_Hfq_200_2

description: adaptor-ligated cDNA

value: Hfq; 200 minutes


title: PA14_WT_200_1

description: adaptor-ligated cDNA

value: WT; 200 minutes


title: PA14_Hfq_200_1

description: adaptor-ligated cDNA


title: TKO_ATAC_rep2


title: T20649

description:
P.falciparum parasite isolate
H0_sample184

value: Prior to ACT treatment, 0h


title: TKO_ATAC_rep1


title: CRC_61

value: Dead


title: CRC_51

value: Male


title: IHMA87_WT_600_2

description: adaptor-ligated cDNA

value: WT; 600 minutes


title: T20613

description:
P.falciparum parasite isolate
H0_sample183


title: IHMA87_WT_600_1

description: adaptor-ligated cDNA


title: TKO;Carm1_RNA_rep3


title: TKO;Carm1_RNA_rep2


title: T20603

description:
P.falciparum parasite isolate
H0_sample181


title: TKO;Carm1_RNA_rep1


title: T20651

description:
P.falciparum parasite isolate
H0_sample185


title: IHMA87_WT_400_2

description: adaptor-ligated cDNA

value: WT; 400 minutes


title: IHMA87_WT_400_1

description: adaptor-ligated cDNA


title: CRC_49

value: IV


title: CRC_47

value: IIA


title: TKO;NfibR388K_RNA_rep2


title: CRC_48

value: IIIA


title: T20597

description:
P.falciparum parasite isolate
H0_sample178


title: IHMA87_WT_200_2

description: adaptor-ligated cDNA


title: TKO;NfibR388K_RNA_rep1


title: IHMA87_WT_200_1

description: adaptor-ligated cDNA


title: TKO;NfibR388K_RNA_rep3


title: CRC_50

value: Alive


title: T20601

description:
P.falciparum parasite isolate
H0_sample179


title: CRC_46


title: T20584

description:
P.falciparum parasite isolate
H0_sample177


title: CRC_52


title: CRC_45


title: IHMA87_Hfq_600_2

description: adaptor-ligated cDNA

value: Hfq; 600 minutes


title: TKO_RNA_rep3

value: SCLC cells from GEMM


title: IHMA87_Hfq_600_1

description: adaptor-ligated cDNA


title: T20605

description:
P.falciparum parasite isolate
H0_sample182


title: T20575

description:
P.falciparum parasite isolate
H0_sample176


title: CRC_44


title: IHMA87_Hfq_400_2

description: adaptor-ligated cDNA

value: Hfq; 400 minutes


title: CRC_43


title: IHMA87_Hfq_400_1

description: adaptor-ligated cDNA


title: T20602

description:
P.falciparum parasite isolate
H0_sample180

value: In vivo, Blood stage


title: TKO_RNA_rep2

value: Rb1L/L; Rbl1L/L; p53L/L


title: TKO_RNA_rep1


title: T20567

description:
P.falciparum parasite isolate
H0_sample175


title: T20562

description:
P.falciparum parasite isolate
H0_sample174


title: IHMA87_Hfq_200_2

description: adaptor-ligated cDNA


title: T20542

description:
P.falciparum parasite isolate
H0_sample172


title: IHMA87_Hfq_200_1

description: adaptor-ligated cDNA


title: CRC_40


title: CRC_41

value: IIIC


title: CRC_38

value: Female


title: T20533

description:
P.falciparum parasite isolate
H0_sample170


title: T20540

description:
P.falciparum parasite isolate
H0_sample171


title: CRC_39

source_name: Descending colon


title: T20532

description:
P.falciparum parasite isolate
H0_sample169


title: CRC_37


title: H3 ATRX KO rep2

city: Colchester

first: Vladimir

middle: B

last: Teif

address: Wivenhoe Park

department: School of Life Sciences

country: United Kingdom

institute: University of Essex

description: H3 ChIP-seq

data_processing:
ChIP-seq H3 reads were mapped to the mouse genome mm9 using Bowtie2 allowing up to two mismatches and only unique alignments.
For SUV39H-dependent heterochromatin, H3K9me3 peaks were called using MACS2, comparing the WT and the DKO datasets against the common Input. Peaks present in WT but not in the DKO were retained as SUV39H-dependent peaks (n = 36,764). For ATRX-dependent heterochromatin, H3K9me3 peaks were called using MACS2 on both replicates of the WT and both replicates of the ATRX-DKO against the ChIP-Seq input. Peaks present in the intersection of the WT replicates, which were not in the union of the KO replicates, were used (n = 13,113). Manipulations with BED files were performed using bedTools.
Genome_build: mm9
Supplementary_files_format_and_content: BED file format, containing ATRX-dependent H3K9me3 peaks

source_name: mouse embryonic stem cells

extract_protocol:
Cells were fixed in 1% formaldehyde (Thermo Scientific 28906) in PBS for 10 minutes and stopped by addition of glycine to a final concentration of 125 mM. Cells were washed twice with PBS/0.5 mM PMSF, dissolved in swelling buffer (25 mM Hepes pH7.8, 1 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT, 0.5 mM PMSF, protease inhibitor COMPLETE from Roche) and incubated on ice for 10 minutes. After pelleting they were digested with MNase at 37°C for 15 minutes in a buffer containing 25 mM KCl, 4 mM MgCl2, 1 mM CaCl2, 50 mM Tris/HCl pH7.4 and 1x protease inhibitor from Cell Signalling. Chromatin was fragmented with a Covaris S2 sonicator (parameters: 900 s, burst 200, cycle 20%, intensity 8) in sonication buffer (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5% N-lauroylsarcosine, 0.1% Na-deoxycholate) and centrifuged at 13000 rpm and 4°C for 15 minutes. The supernatant was mixed with 4 µg normal rabbit IgG (R&D Systems, AB-105-C, lot: ER1212071) and incubated with ChIP-grade protein G magnetic beads (Cell Signalling 9006S, 25 µl/sample) at 4°C for 1:45 h (pre-clearance). 1/20 of the supernatant was used as input sample and the remaining material was used for the IP reaction by adding 4 µg of anti-H3K9me3 antibody (Abcam, ab8898, lot: GR148830-2). The sample was incubated for 2 h at 4°C, protein G magnetic beads were added and incubated at 4°C overnight. On the next day, the IP samples were washed with sonication buffer, high-salt buffer (50 mM Hepes pH 7.9, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), Li buffer (20 mM Tris pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate) and finally twice with TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). Subsequently, the DNA-antibody complexes were eluted by incubation with a buffer containing 50 mM Tris pH 8.0, 1 mM EDTA, 1% SDS, 50 mM NaHCO3 at 37°C for 15 minutes. IP samples and input control were treated with RNase A added to a final concentration of 10 µg/ml for one hour at 37°C. Then Proteinase K (Genaxxon Bioscience M3037) and NaCl were added to final concentrations of 80 µg/ml and 200 mM, respectively and samples were incubated over night at 65°C for protein digestion and reversal of crosslinks. DNA was precipitated and the input samples were used to assess the fragment size by gel electrophoresis on a 2% agarose E-Gel and on a DNA1000 bioanalyzer ChIP. Experiments were conducted for two replicates of each cell line.
The libraries were prepared with the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, NEB #E7370) according to the manufacturer’s instructions. In the size selection step, insert fragments of 150 bp corresponding to 270 bp total library size (including insert and adaptors) were selected. 13 PCR amplification cycles were carried out and the library size and quality were checked for by gel electrophoresis. All samples were sequenced on an Illumina HiSeq 2000 platform at the DKFZ Sequencing Core Facility.
Illumina NEBNext Ultra

treatment_protocol: Wild type murine embryonic stem cell (ESC) wt26 and two ATRX knock out cell lines (KO1-40 and KO1-45) were constructed as described previously (Sadic et al., EMBO Rep, 2015). Cells were cultured on 0.2% v/v gelatine (in PBS) in high glucose DMEM (gibco 31053-028) supplemented with 1 mM sodium pyruvate and 4 mM L-Glutamine (PAA M11-006), 15% v/v FCS (Sigma F7524, lot: 091M3398), 1% v/v Penicillin-Streptomycin (PAN Biotech P06-07100), 100 µM β-mercaptoethanol (Sigma 63689), 1% v/v non-essential amino acids and 0.41% v/v LIF (self-made; supernatant from LIF-producing cells; batch: 7/26/14). Chromatin immunoprecipitation. Cells were fixed in 1% formaldehyde (Thermo Scientific 28906) in PBS for 10 minutes and stopped by addition of glycine to a final concentration of 125 mM. Cells were washed twice with PBS/0.5 mM PMSF, dissolved in swelling buffer (25 mM Hepes pH7.8, 1 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT, 0.5 mM PMSF, protease inhibitor COMPLETE from Roche) and incubated on ice for 10 minutes. After pelleting they were digested with MNase at 37°C for 15 minutes in a buffer containing 25 mM KCl, 4 mM MgCl2, 1 mM CaCl2, 50 mM Tris/HCl pH7.4 and 1x protease inhibitor from Cell Signalling. Chromatin was fragmented with a Covaris S2 sonicator (parameters: 900 s, burst 200, cycle 20%, intensity 8) in sonication buffer (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5% N-lauroylsarcosine, 0.1% Na-deoxycholate) and centrifuged at 13000 rpm and 4°C for 15 minutes. The supernatant was mixed with 4 µg normal rabbit IgG (R&D Systems, AB-105-C, lot: ER1212071) and incubated with ChIP-grade protein G magnetic beads (Cell Signalling 9006S, 25 µl/sample) at 4°C for 1:45 h (pre-clearance). 1/20 of the supernatant was used as input sample and the remaining material was used for the IP reaction by adding 4 µg of anti-H3K9me3 antibody (Abcam, ab8898, lot: GR148830-2). The sample was incubated for 2 h at 4°C, protein G magnetic beads were added and incubated at 4°C overnight. On the next day, the IP samples were washed with sonication buffer, high-salt buffer (50 mM Hepes pH 7.9, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), Li buffer (20 mM Tris pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate) and finally twice with TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). Subsequently, the DNA-antibody complexes were eluted by incubation with a buffer containing 50 mM Tris pH 8.0, 1 mM EDTA, 1% SDS, 50 mM NaHCO3 at 37°C for 15 minutes. IP samples and input control were treated with RNase A added to a final concentration of 10 µg/ml for one hour at 37°C. Then Proteinase K (Genaxxon Bioscience M3037) and NaCl were added to final concentrations of 80 µg/ml and 200 mM, respectively and samples were incubated over night at 65°C for protein digestion and reversal of crosslinks. DNA was precipitated and the input samples were used to assess the fragment size by gel electrophoresis on a 2% agarose E-Gel and on a DNA1000 bioanalyzer ChIP. Experiments were conducted for two replicates of each cell line.

tag: antibody

value: ATRX knock out


title: H3 ATRX KO rep1

description: H3 ChIP-seq

growth_protocol: Cells were cultured on 0.2% v/v gelatine (in PBS) in high glucose DMEM (gibco 31053-028) supplemented with 1 mM sodium pyruvate and 4 mM L-Glutamine (PAA M11-006), 15% v/v FCS (Sigma F7524, lot: 091M3398), 1% v/v Penicillin-Streptomycin (PAN Biotech P06-07100), 100 µM β-mercaptoethanol (Sigma 63689), 1% v/v non-essential amino acids and 0.41% v/v LIF (self-made; supernatant from LIF-producing cells; batch: 7/26/14).


title: H3 WT rep1

description: H3 ChIP-seq

value: wild type


title: IgG ATRX KO rep2

description: IgG ChIP-seq

value: IgG


title: IgG ATRX KO rep1

description: IgG ChIP-seq


title: T20529

description:
P.falciparum parasite isolate
H0_sample167

value: Prior to ACT treatment, 0h


title: CRC_35

value: Male

tag: overall survival (os) (month)

value: Dead


title: IgG WT rep2

description: IgG ChIP-seq


title: T20559

description:
P.falciparum parasite isolate
H0_sample173


title: CRC_34

tag: outcome

value: IV


title: T20520

description:
P.falciparum parasite isolate
H0_sample166


title: CRC_42

tag: t stage


title: IgG WT rep1

description: IgG ChIP-seq


title: T20518

description:
P.falciparum parasite isolate
H0_sample165


title: H3 WT rep2

description: H3 ChIP-seq


title: AT2aKO 04

first: Bernice

last: Wong

address: 8 College Road

department: Cardiovascular and Metabolic Disorders

institute: Duke-NUS Medical School

description: harvested 2 weeks post tamoxifen induction

data_processing:
Analysis was performed using Partek Flow (version 10)
Paired-end reads were aligned to mm10 genome using STAR alignment 2.7.3a and annotated using RefSeq
Features were filtered using standard parameters and median ratio normalized
Gene expression analysis was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheets containing median ratio normalized counts

source_name: Lung

extract_protocol:
AT2 cells were harvested from deeply anesthetized AT2aKO and 2afl/fl control mice as described by Sinha et. al Bio Protoc 6 (2016) with modifications. Lungs were digested in 30U/ml Dispase II in calcium and magnesium-free Hank’s balanced salt solution. CD45 –ve cells were first enriched from whole lung cell suspension using magnetic separation on LS Columns using CD45 MicroBeads. AT2 cells were purified using Biotinylated anti-mouse CD326/EpCAM antibody and anti-biotin MicroBeads.
1ug RNA per sample was used for library prepration using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) according to manufacturer’s instructions

tag: cell line

value: Inducible KO

value: 9 weeks

value: Lung


title: AT2aKO 03


title: CRC_33

tag: n stage

tag: ajcc/uicc-tnm stage


title: T20516

description:
P.falciparum parasite isolate
H0_sample164

tag: isolate

tag: treatment


title: AT2aKO 02

tag: tissue


title: T20515

description:
P.falciparum parasite isolate
H0_sample163


title: CRC_32

value: Alive


title: T20514

description:
P.falciparum parasite isolate
H0_sample162


title: CRC_31


title: T20512

description:
P.falciparum parasite isolate
H0_sample161


title: LL 04

value: Floxed control


title: T20530

description:
P.falciparum parasite isolate
H0_sample168


title: AT2aKO 01


title: CRC_28

value: IIIB


title: CRC_29


title: CRC_30


title: T20511

description:
P.falciparum parasite isolate
H0_sample160

value: In vivo, Blood stage


title: LL 03


title: CRC_36


title: LL 01


title: T20500

description:
P.falciparum parasite isolate
H0_sample157


title: T20510

description:
P.falciparum parasite isolate
H0_sample159


title: T20501

description:
P.falciparum parasite isolate
H0_sample158


title: CRC_27


title: CRC_25


title: CRC_26


title: BisRNA-seq_Pf_G1_rep2

description:
Pf_G1_2
mRNA
m5C.Pf.txt

value: Pf NF54

value: Wild type

tag: host

value: Human

tag: developmental stage

value: Gametocyte

value: Whole body


title: Input ATRX KO rep2

description: Input

extract_protocol:
Cells were fixed in 1% formaldehyde (Thermo Scientific 28906) in PBS for 10 minutes and stopped by addition of glycine to a final concentration of 125 mM. Cells were washed twice with PBS/0.5 mM PMSF, dissolved in swelling buffer (25 mM Hepes pH7.8, 1 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT, 0.5 mM PMSF, protease inhibitor COMPLETE from Roche) and incubated on ice for 10 minutes. After pelleting they were digested with MNase at 37°C for 15 minutes in a buffer containing 25 mM KCl, 4 mM MgCl2, 1 mM CaCl2, 50 mM Tris/HCl pH7.4 and 1x protease inhibitor from Cell Signalling. Chromatin was fragmented with a Covaris S2 sonicator (parameters: 900 s, burst 200, cycle 20%, intensity 8) in sonication buffer (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5% N-lauroylsarcosine, 0.1% Na-deoxycholate) and centrifuged at 13000 rpm and 4°C for 15 minutes. The supernatant was mixed with 4 µg normal rabbit IgG (R&D Systems, AB-105-C, lot: ER1212071) and incubated with ChIP-grade protein G magnetic beads (Cell Signalling 9006S, 25 µl/sample) at 4°C for 1:45 h (pre-clearance). 1/20 of the supernatant was used as input sample and the remaining material was used for the IP reaction by adding 4 µg of anti-H3K9me3 antibody (Abcam, ab8898, lot: GR148830-2). The sample was incubated for 2 h at 4°C, protein G magnetic beads were added and incubated at 4°C overnight. On the next day, the IP samples were washed with sonication buffer, high-salt buffer (50 mM Hepes pH 7.9, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), Li buffer (20 mM Tris pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate) and finally twice with TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). Subsequently, the DNA-antibody complexes were eluted by incubation with a buffer containing 50 mM Tris pH 8.0, 1 mM EDTA, 1% SDS, 50 mM NaHCO3 at 37°C for 15 minutes. IP samples and input control were treated with RNase A added to a final concentration of 10 µg/ml for one hour at 37°C. Then Proteinase K (Genaxxon Bioscience M3037) and NaCl were added to final concentrations of 80 µg/ml and 200 mM, respectively and samples were incubated over night at 65°C for protein digestion and reversal of crosslinks. DNA was precipitated and the input samples were used to assess the fragment size by gel electrophoresis on a 2% agarose E-Gel and on a DNA1000 bioanalyzer ChIP. Experiments were conducted for two replicates of each cell line.
The libraries were prepared with the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, NEB #E7370) according to the manufacturer’s instructions. In the size selection step, insert fragments of 150 bp corresponding to 270 bp total library size (including insert and adaptors) were selected. 13 PCR amplification cycles were carried out and the library size and quality were checked for by gel electrophoresis. All samples were sequenced on an Illumina HiSeq 2000 platform at the DKFZ Sequencing Core Facility.

tag: chip antibody

value: no antibody

value: ATRX knock out

value: embryonic stem cells


title: T20498

description:
P.falciparum parasite isolate
H0_sample156

value: Prior to ACT treatment, 0h


title: CRC_24

tag: Sex

value: Male

value: Dead

value: IV


title: Input ATRX KO rep1

description: Input

tag: genotype


title: CRC_23

tag: age


title: Input WT rep2

description: Input

value: wild type

tag: cell type


title: T20496

description:
P.falciparum parasite isolate
H0_sample154


title: CRC_22

value: Alive


title: LL 02

value: Floxed control

value: 9 weeks

value: Lung


title: H3K9me3 ChIP-seq ATRX KO rep2

description: H3K9me3 ChIP-seq


title: CRC_21

value: Female

value: IIIB


title: T20493

description:
P.falciparum parasite isolate
H0_sample152

value: In vivo, Blood stage


title: T20495

description:
P.falciparum parasite isolate
H0_sample153


title: CRC_20


title: H3K9me3 ChIP-seq ATRX KO rep1

description: H3K9me3 ChIP-seq


title: T20492

description:
P.falciparum parasite isolate
H0_sample151


title: H3K9me3 ChIP-seq WT rep2

description: H3K9me3 ChIP-seq


title: CRC_19


title: T20489

description:
P.falciparum parasite isolate
H0_sample150


title: H3K9me3 ChIP-seq WT rep1

description: H3K9me3 ChIP-seq


title: CRC_18

value: IIB


title: CRC_17


title: T20497

description:
P.falciparum parasite isolate
H0_sample155


title: T20488

description:
P.falciparum parasite isolate
H0_sample149


title: CRC_16


title: Control, classical monocyte, 3794-PSR-0081

type: genomic

first: Peter

last: Allen

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation EPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
GenomeStudio software + R v3.5.1
Illumina GenomeStudio software used for generating DNA methylation data for 850,000 CpGs in form of Beta Values.
CpG probes with detection p-values over 0.01 were filtered out.
Batch effects were corrected for using an empirical Bayes approach, ComBat.
Infinium chemistry corrections were performed to correct for differences in beta scores between probe types.
hg19
tab-delimited .txt files include imputed and non-imputed autosomal chromosome and chr X betas.  See Supplementary files linked to the Series record.

label: Cy3, Cy5

source_name: Control, classical monocyte

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: disease status

value: Control

tag: disease subtype

value: female

tag: race

value: AA

tag: age at blood collection

value: classical monocyte


title: Control, classical monocyte, 3794-PSR-0082


title: Input WT rep1

description: Input

value: no antibody

value: embryonic stem cells


title: Control, classical monocyte, 3794-PSR-0080


title: T20481

description:
P.falciparum parasite isolate
H0_sample147

value: Prior to ACT treatment, 0h


title: Control, classical monocyte, 3794-PSR-0079


title: CRC_15

tag: overall survival (os) (month)

tag: outcome

tag: t stage

value: IV


title: T20479

description:
P.falciparum parasite isolate
H0_sample146

tag: isolate


title: CRC_13

value: Male

value: Dead

tag: n stage

tag: ajcc/uicc-tnm stage


title: CRC_14

value: Alive


title: T20478

description:
P.falciparum parasite isolate
H0_sample145

tag: treatment


title: Control, classical monocyte, 3794-PSR-0075


title: T20470

description:
P.falciparum parasite isolate
H0_sample144


title: Control, classical monocyte, 3794-PSR-0076


title: Control, classical monocyte, 3794-PSR-0074


title: T20469

description:
P.falciparum parasite isolate
H0_sample143


title: T20468

description:
P.falciparum parasite isolate
H0_sample142


title: Control, classical monocyte, 3794-PSR-0072


title: Control, classical monocyte, 3794-PSR-0078


title: CRC_10

value: IIIC


title: T20466

description:
P.falciparum parasite isolate
H0_sample141


title: CRC_11


title: CRC_9

value: I


title: Control, classical monocyte, 3794-PSR-0070


title: Control, classical monocyte, 3794-PSR-0071


title: CRC_8


title: T20462

description:
P.falciparum parasite isolate
H0_sample139


title: CRC_6


title: T20465

description:
P.falciparum parasite isolate
H0_sample140


title: SSc, classical monocyte, 3794-PSR-0062

source_name: SSc, classical monocyte

value: Systemic sclerosis (SSc)

value: dcSSc


title: T20441

description:
P.falciparum parasite isolate
H0_sample137

source_name: P.falciparum field isolate from patient

value: In vivo, Blood stage


title: CRC_5

value: Female


title: Control, classical monocyte, 3794-PSR-0068

value: Control


title: T20447

description:
P.falciparum parasite isolate
H0_sample138


title: CRC_7


title: CRC_4


title: SSc, classical monocyte, 3794-PSR-0058

value: female


title: T20431

description:
P.falciparum parasite isolate
H0_sample135


title: SSc, classical monocyte, 3794-PSR-0060

value: AA


title: CRC_3


title: CRC_12


title: SSc, classical monocyte, 3794-PSR-0056

value: lcSSc

value: classical monocyte


title: CRC_2


title: T20483

description:
P.falciparum parasite isolate
H0_sample148


title: SSc, classical monocyte, 3794-PSR-0055


title: CRC_1


title: T20430

description:
P.falciparum parasite isolate
H0_sample134


title: T20429

description:
P.falciparum parasite isolate
H0_sample133


title: T20428

description:
P.falciparum parasite isolate
H0_sample132


title: U937_STAG2-A2-H4

city: Boston

first: Stephen

last: Elledge

address: 77 Avenue Louis Pasteur NRB160

institute: Brigham and Women's Hospital | HHMI

data_processing:
For U937 cells, RNA-seq reads were mapped using STAR version 2.4.2a. The STAR genome index was generated from human reference sequence hg19 (FASTA downloaded from UCSC genome browser) and coding transcripts from GENCODE Release 19 (GTF downloaded from http://www.gencodegenes.org/). Reads mapping to genes were quantified with featureCounts from the R package Subread (v2.0.1). Transcripts per million (TPM) were quantified from the count data.
For HMECs, each RNA-seq sample was aligned to the hg19 genome using STAR version 2.7.0a.
For HMECs, reads mapping to genes were quantified with featureCounts.
For HMECs, differential expression was quantified using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts matrix, TPM normalized counts matrix, differential expression output

extract_protocol:
U937 cells Total RNA was purified from 1 million cells using Rneasy plus isolation kit (QIAGEN) following the manufacturer instructions and 1uL of a 1:10 diltion of ERCC Spike-in mix (Thermo Fisher) was added to each sample.
U937 RNA-Seq libraries were prepared with the TruSeq mRNA kit from Illunima according to the standard protocol.

tag: cell line

value: Acute Myeloid Leukemia

tag: genotype/variation


title: SSc, classical monocyte, 3794-PSR-0054

address: 1720 University Blvd

institute: University of Alabama at Birmingham

tag: Sex


title: T20427

description:
P.falciparum parasite isolate
H0_sample131

value: Prior to ACT treatment, 0h


title: U937_STAG2-A2-G4


title: SSc, classical monocyte, 3794-PSR-0053


title: SSc, classical monocyte, 3794-PSR-0052


title: SSc, classical monocyte, 3794-PSR-0050


title: T20423

description:
P.falciparum parasite isolate
H0_sample129


title: T20420

description:
P.falciparum parasite isolate
H0_sample128


title: T20436

description:
P.falciparum parasite isolate
H0_sample136


title: U937_GC3_E1

value: Wild-Type


title: SSc, classical monocyte, 3794-PSR-0049

value: ssSSc


title: T20419

description:
P.falciparum parasite isolate
H0_sample127


title: SSc, classical monocyte, 3794-PSR-0046


title: T20405

description:
P.falciparum parasite isolate
H0_sample126


title: U937_GC1_A2


title: Single Cell GEM well 2 (NA19160, NA18855)

city: Chicago

first: Anthony

last: Hung

state: IL

address: 920 E 58th St

institute: University of Chicago

description:
Single Cell sample 2
ANT2

data_processing:
Reads from bulk RNA sequencing were mapped to the hg38 genome using STAR (version 2.6.1b). Gene expression levels were quantified using the featureCounts function in Subread (version 1.6.5) using standard parameters to generate the counts.txt file.
Reads from 10X cell barcodes and UMIs from raw scRNA-seq reads were extracted and remaining reads were mapped to genes in the hg38 genome using STARsolo from the STAR software with default parameters (version 2.6.1b) to generate barcodes.tsv, genes.tsv, and matrix.mtx files. Demuxlet was used to deconvolute sample identity of individual cell droplets and detect multiplets in multiplexed samples with default parameters. Previously collected and imputed genotype data for the three Yoruba individuals from the HapMap and 1000 Genomes Project were used as input for demuxlet to generate the demuxlet.best files.
Genome_build: hg38
Supplementary_files_format_and_content: bulk RNAseq - counts.txt file
Supplementary_files_format_and_content: scRNAseq -  barcodes.tsv, genes.tsv, and matrix.mtx files, demuxlet.best files

source_name: iPSC-derived chondrogenic cells

growth_protocol: Undifferentiated iPSCs were cultured on Matrigel-coated plates in Essential 8 (E8) medium at 37°C, 5% CO2, and atmospheric O2 until iPSCs reached 30% confluency. E8 medium was subsequently changed to mesenchymal stem cell (MSC) culture medium, which consisted of low glucose Dulbecco’s Modified Eagle Medium (DMEM) with 20% stem cell-qualified fetal bovine serum (FBS), and 100 mg/mL Penicillin/Streptomycin. The MSC medium was changed every day for 3 days, at which point cells were 80-100% confluent. On day 3, cells were detached from the Matrigel-coated petri dishes using a 0.05% Trypsin/EDTA solution and cultured on uncoated polystyrene flasks in MSC medium. The medium was changed every 2-3 days until the cells reached 90% confluency. The cells were then sub-cultured at a ratio of 1:3 until passage 4, at which point cells were classified as iPSC-derived MSCs. iPSC-derived MSCs were detached from culture flasks using 0.05% Trypsin/EDTA and seeded at a density of 250,000 cells/well onto the center of wells of BioFlex Type I Collagen coated 6-well Culture Plates (FlexCell International BF-3001C) using BioFlex cell seeders (FlexCell International). Cells were seeded using a regimen of 15% elongation for 2 hours followed by overnight culture in MSC culture medium. After seeding, cells were cultured in serum-free chondrogenic differentiation medium, consisting of high glucose DMEM, 100 mg/mL Penicillin/Streptomycin, 50mg/mL L-Proline, 200mM GlutaMax, 50mg/mL L-Ascorbic acid-2-Phosphate, 11g/L Sodium pyruvate, 5mM Dexamethasone, 1x ITS Premix, and supplemented with 10 ng/mL TGF-β3. The chondrogenic medium was changed every 2-3 days for 14 days.

extract_protocol: One GEM well of a Chromium single cell chip was used targeting a collection of 5000 cells contained NA19160 strain-treatment and NA18855 control cells in equal proportions. Single cell cDNA libraries were established following the 10x Genomics Chromium Single Cell protocol. In brief, the RNA of the captured cells was released by lysis, barcoded via a reverse transcription process, and amplified to produce a gene expression library. The library was sequenced to 100 base pairs, paired-end on one lane using the Illumina HiSeq4000 at the University of Chicago Genomics Core Facility according to manufacturer instructions.

treatment_protocol: Plates for strained samples were loaded onto the Flexercell baseplate (located in an incubator at 37°C, 5% CO2 , and atmospheric O2), and a vacuum was used to deform the cell culture plate membrane and create uniform biaxial cyclic tensile strain. Specifically, 2.5% elongation (15kPa) of CTS was applied to the cells at a rate of 0.5 Hz for 24 hours. Control samples were cultured in the same incubator without cyclic tensile strain.

value: Control, Cyclic Tensile Strain

tag: technical replicate

value: pooled male and female


title: T20400

description:
P.falciparum parasite isolate
H0_sample125


title: SSc, classical monocyte, 3794-PSR-0061

city: Birmingham


title: Single Cell GEM well 1 (NA19160, NA18855, NA18856)

description:
Single Cell sample 1
ANT1

extract_protocol: One GEM well of a Chromium single cell chip was used targeting a collection of 5000 cells contained NA19160 control, NA18856 control, and NA18855 strain-treatment cells combined in equal proportions. Single cell cDNA libraries were established following the 10x Genomics Chromium Single Cell protocol. In brief, the RNA of the captured cells was released by lysis, barcoded via a reverse transcription process, and amplified to produce a gene expression library. The library was sequenced to 100 base pairs, paired-end on one lane using the Illumina HiSeq4000 at the University of Chicago Genomics Core Facility according to manufacturer instructions.


title: T20399

description:
P.falciparum parasite isolate
H0_sample124


title: T20398

description:
P.falciparum parasite isolate
H0_sample123


title: NA19160 Strain Replicate 2

description:
Bulk sample 17
counts.txt.gz
YG-AH-07_S7_L002_R1_001

extract_protocol:
RNA was extracted from cells following CTS or control treatments using the ZR-Duet™ DNA/RNA MiniPrep kit (Zymo D7001).
Illumina TruSeq RNA Sample Preparation Kit v2 (RS-122-2001 & -2002, Illumina)

value: Cyclic Tensile Strain

value: M


title: T20426

description:
P.falciparum parasite isolate
H0_sample130


title: T20392

description:
P.falciparum parasite isolate
H0_sample122


title: U937_STAG2-A2-F11


title: T20387

description:
P.falciparum parasite isolate
H0_sample121


title: U937_GC3_E3


title: NA19160 Control Replicate 3

description:
Bulk sample 15
counts.txt.gz
YG-AH-14_S14_L002_R1_001


title: NA19160 Control Replicate 2

description:
Bulk sample 14
counts.txt.gz
YG-AH-08_S8_L002_R1_001


title: T20379

description:
P.falciparum parasite isolate
H0_sample120


title: NA19160 Control Replicate 1

description:
Bulk sample 13
counts.txt.gz
YG-AH-02_S2_L002_R1_001


title: T20378

description:
P.falciparum parasite isolate
H0_sample119


title: T20377

description:
P.falciparum parasite isolate
H0_sample118


title: NA18856 Strain Replicate 3

description:
Bulk sample 12
counts.txt.gz
YG-AH-17_S17_L002_R1_001


title: T20369

description:
P.falciparum parasite isolate
H0_sample117


title: NA19160 Strain Replicate 3

description:
Bulk sample 18
counts.txt.gz
YG-AH-13_S13_L002_R1_001


title: T20365

description:
P.falciparum parasite isolate
H0_sample116


title: NA19160 Strain Replicate 1

description:
Bulk sample 16
counts.txt.gz
YG-AH-01_S1_L002_R1_001


title: T20364

description:
P.falciparum parasite isolate
H0_sample115


title: T20362

description:
P.falciparum parasite isolate
H0_sample114


title: NA18856 Control Replicate 2

description:
Bulk sample 8
counts.txt.gz
YG-AH-12_S12_L002_R1_001


title: NA18856 Strain Replicate 1

description:
Bulk sample 10
counts.txt.gz
YG-AH-05_S5_L002_R1_001


title: NA18856 Control Replicate 1

description:
Bulk sample 7
counts.txt.gz
YG-AH-06_S6_L002_R1_001