title: Total small RNAs;E16.5;Tex15-/- [RR557]

description:
RR557
Small RNA
Processed data file: GEO_tex15_mappers.csv.gz

value: total small RNAs


title: E14 Dnmt3a/b dKO.B 2i RRBS Rep2

status: Public on Nov 27 2020

type: SRA

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

country: Italy

institute: University of Padua

library_source: genomic

data_processing:
Sequencing reads were mapped to mouse genome reference (mm10/GRC.m38.p6) with BSMAP (v2.89) using RRBS mode (parameters: -s 12 -D C-CGG -v 0.01 –n 1).
CpG methylation levels were extracted from aligned reads as the ratio of the number of Cs over the total number of Cs and Ts using the methratio.py script. CpG methylation ratios from both strands were combined (parameters: –g)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited text files include single-base resolution DNA methylation measurements for each sample.

molecule: genomic DNA

organism: Mus musculus

source_name: E14 Dnmt3a/b dKO.B 2i RRBS

growth_protocol: Mouse ES cells were cultured without feeders on gelatine-coated plates (0.2% gelatine) in serum-free KSR-based medium (Life Technologies) supplemented with: 1 μM PD0325901, 3 mM CHIR99021 (2i); and 100 units/m LIF (2iLIF).

extract_protocol: 500ng of DNA was digested at 37°C with 200U of MspI restriction endonuclease (NEB). Digested DNA was than end repaired, dA-tailed, and ligated to methylated adapters, using the Illumina TruSeq DNA Sample Prep Kit, following manufacturer’s instructions.

tag: strain background

tag: cell type

value: mouse embryonic stem cell E14

tag: genotype

value: Dnmt3a/b knock-out

tag: growth condition


title: E14 Dnmt3a/b dKO.A 2iLIF RRBS rep2

source_name: mouse embryo

tag: strain


title: E14 Dnmt3a/b dKO.B 2iLIF RRBS rep1


title: S3-/- -48h R1

library_source: transcriptomic

data_processing:
Reads were aligned to mouse transcriptome (Mus musculus transcriptome generated by rsem-prepare-reference with ENSEMBL93 GTF) and mouse genome (GRCm38.p6) using HISAT2 v. 2.1.0. Gene expression levels were quantified with RSEM v. 1.3.1 using transcriptome alignments.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text RSEM output files including for each sample: gene_id, transcript_id(s), length, effective_lenght, expected_count, TPM, FPKM.

molecule: total RNA

extract_protocol:
Total RNA was isolated using Total RNA Purification kit (Norgen Biotek), according to manufactorer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mouse ES cells stabilized in 2iLIF were cultured in absence of 2iLIF for 48 hours to mimic differentiation process.

value: mouse embryonic stem cell

tag: genotype/variation

value: Stat3 knock-out

tag: phenotype

value: adherent

value: without 2iLIF for 48 hours


title: LungTTH1

city: Rochester

first: Yougnmin

last: Son

address: 200 1st Stabile 8-21

country: USA

institute: Mayo Clinic

data_processing:
Illumina’s RTA software used for basecalling.
Paired-end RNA-seq reads were aligned to the mouse reference genome (GRCm38/mm10) using RNA-seq spliced read mapper Tophat2 (v2.1.1).
Pre- and post-alignment quality controls, gene level raw read count and normalized read count (i.e. FPKM) were performed using RSeQC package (v2.3.6) with NCBI mouse RefSeq gene model.
For functional analysis, GSEA was used to identify enriched gene sets, from the hallmark collection of MSigDB, having up-regulated and down-regulated genes, using a weighted enrichment statistic and a log2 ratio metric for ranking genes.
Genome_build: mm10

source_name: Lung CD4+ T cells

extract_protocol:
Single cells from lung or spleen were isolated, and RNA was extracted using RNeasy Plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Lung

tag: cell markers

tag: infection

value: Influenza A/PR8/34 (28 d.p.i.)


title: E14 Dnmt3a/b dKO.A 2iLIF RRBS rep1


title: Total small RNAs;E16.5;Tex15+/- [RR553]

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description:
RR553
Small RNA
Processed data file: GEO_tex15_mappers.csv.gz

data_processing:
Reads were sorted into individual libraries based on the barcodes, the 3' adapter sequences were removed and mapped to the mouse genome (mm10). The software used for processing the data (genomic coordinates, etc.) from the raw data files were in-house tools developed by the Sachidanandam lab (Olson et al., 2008). Only reads perfectly matching the genome were kept for further analysis using R (R Core Team, 2017) and Bioconductor (Huber et al., 2015).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: GEO_tex15_mappers.csv.gz: The file contains mapping of the reads corresponding to individual small RNAs to mouse genome (mm10).

source_name: testes

growth_protocol: To analyze the function of Tex15 throughout the spermatogenesis, the knock-out mouse of the Tex15 was prepared.

extract_protocol:
Total small RNAs were isolated from E16.5 embryos. Briefly, total RNA from E16.5 testes was separated on 15% UREA polyacrylamide gel. The gel was cut between 16-40 nts to isolate total small RNAs. RNAs present in endogenous MILI, and MIWI2, complexes were isolated. Briefly, immunoprecipitations were treated with Proteinase K in 300 μl reaction at 42 °C for 15 min (10 mM Tris-HCl pH 7.5, 5 mM EDTA, 0.5% SDS). RNAs present in the sample were purified by phenol-chloroform extraction and precipitated with ethanol. Approximately 10-20% of the sample was labelled at the 5′ end with polynucleotide kinase (PNK, ThermoFisher Scientific) and [γ 32P] ATP (3000 Ci/mmol, Perkin Elmer), and resolved by 15% urea-PAGE for quality check.
Libraries were prepared (barcoded at 3′ end) using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB Catalogue No. E7300) following manufacturer instructions. The synthesized cDNA libraries were resolved on 3% high-resolution MethaPhor agarose (Lonza, cat. No. 50180) gels in TAE buffer. Fragments in the size-range of ~160 bp were gel-extracted with the use of MinElute Gel Extraction Kit (Qiagen, cat No. 28604). Multiple libraries with different barcodes (at 3′ end) were mixed in equimolar ratios and sequenced with the Illumina HiSeq 2000 platform (EMBL GeneCore facility, Heidelberg).

value: testes

tag: gender

value: male

tag: age

tag: purification

tag: ip antibody


title: Total small RNAs;E16.5;Tex15-/- [RR555]

description:
RR555
Small RNA
Processed data file: GEO_tex15_mappers.csv.gz


title: E14 Dnmt3a/b dKO.A 2i RRBS Rep1

source_name: E14 Dnmt3a/b dKO.A 2i RRBS


title: Total small RNAs;E16.5;Tex15-/- [RR556]

description:
RR556
Small RNA
Processed data file: GEO_tex15_mappers.csv.gz


title: CeA, Control Diet/Non-Dep #16

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: Control Diet/Non-Dep #16 CeA abundance

data_processing:
Adapters were trimmed and filtered using tagseq_clipper.pl and tagseq_trim_launch.pl https://github.com/z0on/tag-based_RNAseq
Raw 3'UTR biased-sequencing files were evaluated for quality control using FastQC (0.11.8).
Reads were mapped to the mouse reference genome (UCSC, mm10) using the alignment tool Bowtie2 (v2.3.4.3).
HTSeq (v.0.11.0), was used for counting mapped sequencing reads.
Quantified read counts were normalized and analyzed for differential expression using DESeq2 (v 1.10.1), between microglia intact and microglia depleted animals, within the R statistical computing environment (v3.5.1)
Genome_build: GRCm38.p6.genome.fa.gz from ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M17/GRCm38.primary_assembly.genome.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample

source_name: central nucleus of the amygdala

extract_protocol:
medial prefrontal cortex was fresh dissected, flash frozen on dry ice.The remainder of the brain was flash frozen in OCT and sliced at 300um. The CeA was then punched and the RNA from each region was isolated using Trizol reagent and MagMAX-96 Total RNA Isolation Kit . DNA contamination removed using DNA-free kit.  (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA was fragmented then first strand synthesis occurred using majority deoxycytidine nucleotides which served as an anchor for the switch oligos. swOligo used: /5Me-isodC/iisodG/iMeisodC/CCATGCGGCTACACGACGC TCTTCCGATCTNNMWrGrGrG. cDNA strand with portions of adapter were added then amplified, followed by second PCR to add index portion of the adapter.
Samples were then pooled, size selected with Pippin then sequenced on a Single End Run using the HiSeq 2500 for mPFC and NovaSeq 6000 for CeA for a read depth of ~4 million reads per sample

treatment_protocol: Treated with PLX5622 (1200mg/kg) for 28 days prior to beginning chronic intermittent ethanol exposure paired with two-bottle choice drinking (15%) for four weeks, sacrified 24 hours after last ethanol exposure.

value: central nucleus of the amygdala

value: post-natal day 119

tag: chow

value: Control Diet

tag: ethanol exposure

value: Non-Dependent (Non-Dep)


title: Total small RNAs;E16.5;Tex15+/- [RR552]

description:
RR552
Small RNA
Processed data file: GEO_tex15_mappers.csv.gz


title: E14 Dnmt3a/b dKO.B 2i RRBS Rep1


title: Total small RNAs;E16.5;Tex15+/- [RR554]

description:
RR554
Small RNA
Processed data file: GEO_tex15_mappers.csv.gz


title: MitoS3.B 2iLIF R2

source_name: MitoS3.B 2iLIF_mESCs

value: Stat3 knock-out expressing MLS-NES-Stat3 construct (clone B)


title: E14 Dnmt3a/b dKO.B 2iLIF RRBS rep2


title: S3+/+ -48h R2

value: Stat3 wild-type


title: CeA, Control Diet/Non-Dep #15

description: Control Diet/Non-Dep #15 CeA abundance


title: MitoS3.B 2iLIF R1


title: CeA, Control Diet/Non-Dep #14

description: Control Diet/Non-Dep #14 CeA abundance


title: E14 Dnmt3a/b dKO.A 2i RRBS Rep2


title: E14 2i RRBS Rep2

source_name: E14 2i RRBS

value: Dnmt3a/b wild type


title: S3+/+ -48h R1


title: Ovary, gcCbfb;Runx2KO Rep4

city: Lexington

first: Misung

last: Jo

state: Kentucky

address: 800 Rose street

department: Ob/Gyn

institute: University of Kentucky

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).
Adaptors have been trimmed from the 3'-end of the reads. Sequence of adaptors used to make the libraries (used portion in bold font for adaptor trimming); AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG (NNNNNNNN= 8 nt index)
Salmon2 version 0.11.3 was used to quasi-map reads to the transcriptome and quantify the abundance of each transcript.
Gene-level counts were then estimated based on transcript-level counts using the “bias corrected counts without an offset” method from the tximport package.
TMM normalization was performed and normalized log2-based count per million values (logCPM) were calculated using edgeR’s cpm() function with prior.count = 3 to help stabilize fold-changes of extremely low expression genes
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: An excel file incluldes normalized logCPM values for all samples

source_name: ovary

extract_protocol:
Ovaries were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Libraries were prepared using a Illumina TruSeq RNA Sample Prep Kit.
RNA libraries were prepared using a Illumina TruSeq RNA Sample Prep Kit according to the manufacturer' instruction.

treatment_protocol: PMSG and hCG

value: ovary

value: post natal day 27


title: Ovary, gcCbfb;Runx2KO Rep3


title: MitoS3.A 2iLIF R1

source_name: MitoS3.A 2iLIF_mESCs

value: mouse embryonic stem cell

value: Stat3 knock-out expressing MLS-NES-Stat3 construct (clone A)


title: Ovary, Wild-type Rep4

value: Wild-type


title: Ovary, gcCbfb;Runx2KO Rep1


title: E14 2iLIF RRBS Rep2

source_name: E14 2iLIF RRBS

value: mouse embryonic stem cell E14


title: MitoS3.A 2iLIF R2

value: adherent


title: E14 2i RRBS Rep1


title: Ovary, Wild-type Rep3


title: Ovary, gcCbfb;Runx2KO Rep2


title: S3+/+ 2i RRBS Rep2

source_name: S3+/+ 2i RRBS


title: E14 2iLIF RRBS Rep1


title: S3-/- 2iLIF R2

source_name: S3-/- 2iLIF_mESCs

value: Stat3 knock-out


title: Glucose Pulse_5min

city: Geneva

first: Sevil

last: Zencir

address: 30, quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

data_processing:
For ChIP-Seq raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800"
For ChIP-Seq, data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For ChIP-seq the reads were shifted by 100 bp and extended by 50 bp
For ChIP-Seq, reads mapped uniquely to the sacCer3 genome were first normalized to total number of mapped reads in sacCer3 and then to total number of uniquely mapped reads in 972-h pombe in the same sample as described in (Hu et al. 2015)
For ChEC-seq experiments the mapped reads were extended by 1 bp only to indicate cut sites and then, the signal for each protein tested was normalized to the signal of free MNase using a Bayesian approach
Genome_build: sacCer3, 972-h pombe
Supplementary_files_format_and_content: BigWig files were obtained using GALAXY

organism: Saccharomyces cerevisiae

source_name: whole organism

growth_protocol: Cells were grown at 30 degrees in YPD to mid-log phase before treatment

extract_protocol:
RNAPII and Hmo1 ChIP-seq was performed as described previously (Ribaud et al., 2012) (PMID: 21952045) with the following modification. A defined amount (5% of total chromatin) of previously cross-linked chromatin from S.pombe was added to S.cerevisiae chromatin prior to immunoprecipitation step)
ChIP-seq libraries were prepared by using TruSeq ChIP library preparation kit (Illumina)

value: W303 background; Mat a leu2-3,112 his3-11,15 ura3-1 ade2-1 trp1-1 can1-100

tag: treatment

value: 5 minutes glucose pulse

tag: antibody

value: Anti-RNA polymerase II CTD repeat YSPTSPS (Abcam ab5131)


title: Sfp1_ChEC

extract_protocol: Libraries were constructed as described (PMID 27797823).

treatment_protocol: 150 sec of Ca+2 treatment

value: YDS2 background; MATa SFP1-3xFLAG-MNase-HphMX


title: Ovary, Wild-type Rep2


title: S3+/+ 2i RRBS Rep1

tag: cell type


title: S3+/+ 2iLIF R2

source_name: S3+/+ 2iLIF_mESCs

tag: strain background


title: Ovary, Wild-type Rep1

tag: genotype


title: S3+/+ 2iLIF R1

tag: growth condition


title: iWAT_fKO_S10

city: Houston

first: Sean

last: Hartig

address: One Baylor Plaza, BCM130

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
Reads were mapped to the UCSC mouse reference genome mm10 using HISAT2.
Stringtie was used to caluclate expression level as reads per kilobase million (RPKM).
Gene set enrichment analysis was performed with Molecular Signatures Database and normalized enrichment scores were calculated for the Hallmark gene sets
Hierarchial cluster analysis was performed by Euclidean distance using Log2 fold change over STAT1 fl/fl controls of any significantly altered (p<0.05) genes
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: inguinal White Adipose Tissue (iWAT)

growth_protocol: Mice were given ad lib access to food and water

extract_protocol:
Total RNA was extracted using the Zymo Direct-zol RNA kit according to manufacturer's protocol. Two tissue extractions (~40 mg each) were extracted per sample and combined by Zymo RNA Clean & Concentrator kit according to manufacturer's protocol
RNA libraries were prepared with Ovation RNA-seq System V2 (NuGen) and Ovation Ultralow Library System V2 (NuGen) using input RNA
Size selection for libraries was performed using SPRIselect beads (Beckman Coulter) and purities of the libraries were analyzed using the High Sensitivity DNA chip on Bioanalyzer 2100 (Agilent). Prepped libraries were pooled and sequenced using Illumina NextSeq 500 generating ~20 million 76bp paired-end reads per sample

treatment_protocol: Mice were placed on HFD for 18 weeks, beginning at 6 weeks of age

tag: strain

value: White Adipose Tissue

tag: location

value: inguinal

value: 6.5 months

value: ADIPOQ-Cre;STAT1 fl/fl

value: HFD 18 weeks


title: Ifh1_ChEC

extract_protocol:
Cells were pelleted at 3,000 x g and washed three times with 1 mL Buffer A (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine, Roche cOmplete EDTA-free mini protease inhibitors, 1 mM PMSF), centrifuging as above between washes. Cells were resuspended in 600 µL Buffer A containing 0.1% digitonin and permeabilized at 30C for 5 min. CaCl2 was added to 2 mM and ChEC digests were performed at 30C. 5 min after CaCl2 addition, a 100 µL aliquot of the digest was transferred to a tube containing 100 µL 2X stop buffer (400 mM NaCl, 20 mM EDTA, 4 mM EGTA) and 1% SDS. Protein was then was digested with 80 µg proteinase K at 55C for 30 m. Nucleic acids were extracted with an equal volume of phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated with 2.5 volumes 100% ethanol and 30 µg Glycogen (Roche). Pellets were washed once with 1 mL 100% ethanol, dried, and resuspended in 30 µL 0.1X TE buffer, pH 8.0. RNA was digested with 10 µg RNase A at 37C for 20 m. Prior to generating sequencing libraries, ChEC DNA was subjected to size-selection using Ampure XP beads (ThermoFischer). A beads:sample ratio of 2.5:1 was used and the unbound fraction, containing small DNA fragments, was extracted to remove RNase and precipitated as above, and used for library preparation.
Libraries were constructed as described (PMID 27797823).

value: YDS2 background; MATa IFH1-3xFLAG-MNase-HphMX


title: S3+/+ 2i R2

source_name: S3+/+ 2i_mESCs

tag: genotype/variation

value: Stat3 wild-type

tag: phenotype


title: iWAT_Ctrl_S9

tag: tissue

value: STAT1 fl/fl


title: S3-/- 2iLIF R1

value: mouse embryonic stem cell


title: iWAT_Ctrl_S8


title: H3_siME1

city: beijing

first: wei

last: li

address: No.5 Dongdansantiao street, Dongcheng district

country: China

institute: Peking Union Medical College

data_processing:
Raw ChIP-seq data were aligned to the mm8 build of the mouse genome using BWA software
Then, all mapped reads were sorted by SAMtools(2) with the options “-f 2 -q 10 -b -@ 20”.Peak calling for ChIP-seq data was carried out by MACS2 under parameter “-g mm -p 0.005 --nomodel --extsize 189 --call-summits”. The overlapping and unique peaks for two sets of DNA binding sites were calculated by intersect command in BEDTools with default options.
Genome_build: mm8
Supplementary_files_format_and_content: In order to normalize sequencing depth for each sample, we utilized bamCompare from deepTools to generate bigWig file based on two BAM files that are compared to each other. Finally, peaks were ordered by binding strength, and heatmaps were plotted by deepTools

source_name: 3T3-L1 preadipocytes cells

extract_protocol:
For ChIP-seq analysis, briefly, 3T3-L1 cells were treated with siRNA for 2 days and confluent cells were induced to differentiate into adipocytes. Cell were cross-linked, and the cell lysates were sonicated to generate DNA fragments and subjected to immunoprecipitation using Ac-H2B, Ac-H3 or HDAC3 antibodies as described above. Bound DNA fragments were eluted for ChIP-seq library construction and sequencing.
Libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: Briefly, 3T3-L1 preadipocytes cells were transfected with control, ME1, or ME2 siRNAs as indicated and two days later induced to differentiate into adipocytes. After another 7 days, cells were washed in PBS buffer and subsequently cross-linked with 1% formaldehyde solution at room temperature (RT) for 15 min.After washing in cold PBS, cross-linking reaction was stopped by the addition of 0.125M glycine with gently shaking for 5min. Cells were then centrifuged and lysed in 300 μL SDS lysis buffer (50mM Tris-HCl pH 8.0, 10mM EDTA pH 8.0 , 1% SDS,protease inhibitors) for 15 minutes on ice. Cell lysates were sonicated to generate DNA fragments approximately 200-1000 bp and subjected to immunoprecipitation with indicated antibodies against Ac-H2B and Ac-H3. Immunoprecipitations were carried out overnight, samples were then washed with low salt buffer, high salt buffer, LiCl salt buffer and TE buffer sequentially. Histone-DNA complexes were eluted using elution buffer (1%SDS, 100 mM NaHCO3), incubated at 65ºC for overnight in the presence of 0.54 M NaCl. The next day, DNase-free RNase(10 mg/ml)was added into samples and incubated for 1 hour at 37℃.Samples were then incubated with Proteinase K for another 1 hour at 55ºC.Finally, DNA were purified using Qiaex II beads (Qiagen) and analyzed by quantitative PCR (qPCR).

tag: cell line

value: preadipocytes cells

tag: sirna transfection

tag: chip antibody

value: Acetyl-histone H3 Millipore, cat. #07-373, lot.3089577


title: H3_siME2


title: Double_depletion_Ifh1_Sfp1_Rapamycin60

treatment_protocol: 60 minutes rapamycin

value: W303 background; Mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 SFP1-FRB::KANMX IFH1-FRB::HIS


title: H3_siC

value: Negative control


title: S3+/+ 2i R1

value: adherent


title: Double_Ifh1_Sfp1_Control

treatment_protocol: No rapamycin


title: iWAT_Ctrl_S7

tag: age


title: MIWI2 IP;P0;Tex15-/- [RR565]

description:
RR565
Small RNA
Processed data file: GEO_tex15_mappers.csv.gz

value: testes

tag: gender

value: male

tag: purification

value: MIWI2 IP

tag: ip antibody

value: MIWI2 (rabbit polyclonal) (Pandey et al., 2013; PMID:24067652)


title: MIWI2 IP;P0;Tex15-/- [RR564]

description:
RR564
Small RNA
Processed data file: GEO_tex15_mappers.csv.gz


title: iWAT_fKO_S5

value: White Adipose Tissue

value: inguinal

tag: treatment


title: Tunicamycin_Control

treatment_protocol: No tunicamycin

value: W303 background; Mat a leu2-3,112 his3-11,15 ura3-1 ade2-1 trp1-1 can1-100

tag: antibody

value: Anti-RNA polymerase II CTD repeat YSPTSPS (Abcam ab5131)


title: H2B_siC

tag: cell type

value: acetyl-histone H2B Millipore, cat. #06-599, lot.3092508


title: iWAT_Ctrl_S4

value: 6.5 months

tag: genotype

value: HFD 18 weeks


title: Tunicamycin_30min

treatment_protocol: 30 minutes tunicamycin


title: MIWI2 IP;P0;Tex15+/- [RR563]

description:
RR563
Small RNA
Processed data file: GEO_tex15_mappers.csv.gz


title: H2B_siME2


title: Glucose_Control

treatment_protocol: No glucose


title: WT_t42_Hmo1

treatment_protocol: 5 minutes heat shock at 42°C

value: anti-Hmo1 (Pocono Farm )


title: MILI IP;P0;Tex15-/- [RR560]

description:
RR560
Small RNA
Processed data file: GEO_tex15_mappers.csv.gz

value: MILI IP

value: MILI (mouse monoclonal) (Reuter et al., 2009; PMID:19465913)


title: iWAT_fKO_S1

value: ADIPOQ-Cre;STAT1 fl/fl


title: MILI IP;P0;Tex15-/- [RR561]

description:
RR561
Small RNA
Processed data file: GEO_tex15_mappers.csv.gz


title: MIWI2 IP;P0;Tex15+/- [RR562]

description:
RR562
Small RNA
Processed data file: GEO_tex15_mappers.csv.gz


title: WT_t30_Hmo1

treatment_protocol: No heat shock


title: H2B_siME1

value: preadipocytes cells


title: iWAT_fKO_S6


title: WT_Rapamycin20_RNAPII

treatment_protocol: 20 minutes rapamycin


title: O61_EN1

first: Barry

middle: A.

last: Ball

address: 108 Gluck Equine Research Center,

department: Veterinary Scinece

description: raw files stranded

data_processing:
The Fastq files were evaluated for read quality using FastQC 0.11.4
Trim Galore 0.4.1 was used for adapter and read quality trimming (Phred score threshold of 30).
Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using STAR 2.5.3a (Dobin, Davis et al. 2013)
Reads were annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1
Fragments per kilobase per million (FPKM) were used to determine the expression level of genes
Cuffdiff 2.2.1 was used to calculate differentially expressed genes (DEGs) between samples from the control and urea groups
Significance level was set at FDR-adjusted p-value of the test statistic < 0.05 using a Benjamini-Hochberg correction
Genome_build: EquCab 3.0
Supplementary_files_format_and_content: Normalized abundance measurements- Cufflink Gene.FPKM.Tracking

organism: Equus caballus

source_name: Uterus

extract_protocol:
Total RNA was isolated from all samples using RNeasy Mini Kit (#74104; Qiagen), and DNA digestion was performed on-column using RNase-free DNase I (#79254: Qiagen), followed by cleanup procedures. All procedures were performed according to the manufacturer’s instructions. After extraction, RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). All samples had a 260/280 ratio >2.0 and RNA integrity number (RIN) > 8.0.
A total of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). The first-strand cDNA was synthesized using random hexamer primer and M- MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After the adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with a hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min, followed by 5 min at 95 °C before PCR. PCR was subsequently performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. PCR products were purified (AMPure XP system), and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on NovaSeq 6000, and 125 bp/150 bp paired-end reads were generated.

treatment_protocol: Placentitis was induced in six mares at approximately 290d of gestation (placentitis group), and six mares with gestationally age-matched (290 d) pregnancies did not receive any treatment (control group). . For induction of placentitis in the former group, Streptococcus equi subsp. zooepidemicus was introduced intracervically.

value: Endometrium

tag: group

value: Placentitis


title: WT_Rapamycin5_RNAPII

treatment_protocol: 5 minutes rapamycin

tag: strain


title: WT_Vehicle20_RNAPII


title: eWAT_fKO_S10

source_name: epididymal White Adipose Tissue (eWAT)

tag: location

value: epididymal


title: iWAT_Ctrl_S3

value: STAT1 fl/fl


title: O78_EN1

description: raw files stranded


title: eWAT_Ctrl_S9


title: O79_EN1

description: raw files stranded


title: eWAT_Ctrl_S8


title: iWAT_fKO_S2


title: eWAT_Ctrl_S7


title: O77_EN1

description: raw files stranded


title: O76_EN1

description: raw files stranded


title: SI1_H3_1

value: HDAC3 Santa Cruz, cat. Sc376957, lot.J2717


title: Top1_Top2_Vehicle_Hmo1

treatment_protocol: No auxin

value: RP10 background; TOP2-AID*-MYC-HPH TOP1-AID-KanMX6 MATalpha


title: O73_EN1

description: raw files stranded


title: eWAT_fKO_S6

value: White Adipose Tissue


title: O62_EN1

description: raw files stranded

value: Control


title: Rpa135_depletion_Rapamycin60_RNAPII

value: W303 background; Mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 RPA135-FRB::KANMX

value: Anti-RNA polymerase II CTD repeat YSPTSPS (Abcam ab5131)


title: eWAT_Ctrl_S4

value: 6.5 months


title: O80_EN1

description: raw files stranded


title: eWAT_fKO_S5

value: HFD 18 weeks


title: eWAT_Ctrl_S3


title: Rpa135_Vehicle_RNAPII


title: L60_EN1

description: raw files stranded


title: CARA_Rapamycin20_RNAPII

value: W303 background; Mat a rpa43::hyg rrn3::hyg +pGEN with Rpa43-rrn3 fusion


title: CARA_Vehicle_RNAPII


title: eWAT_fKO_S2


title: L56_EN1

description: raw files stranded


title: eWAT_fKO_S1


title: Abf1_depletion_Rapamycin20_RNAPII

value: W303 background; Mat alpha tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 ABF1-FRB::KanMX


title: TH-MYCN NB mouse model, 5d comb. treatment, repeat 4

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
RNAseq reads were aligned with Tophat v2.1.1 to mm10
reads were counted using the “summarizeOverlaps” function from the R package “GenomicAlignments"
differentially expressed genes were called with edgeR
differential exon usage was determined with DEXseq after mapping with hisat2
gene set enrichment analysis was carried out with GSEA and the MSigDB gene sets Hallmarks, C2, C5
Genome_build: mm10
Supplementary_files_format_and_content: count files were generated with edgeR

molecule: polyA RNA

source_name: tumor

extract_protocol:
tumors were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard NEB protocols

value: TH-MYCN

value: tumor

tag: time after treatment

value: 5 days


title: ZFP57_SAL

type: genomic

city: L'Hospitalet de Llobregat, Barcelona

first: Jose Ramon

last: Hernandez

address: Av. Gran Via de l'Hospitalet 199-203

department: Cancer Epigenetics and Biology Program (PEBC)

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)

description: bisulphite converted DNA from ZFP57 patient saliva sample 1

hyb_protocol: bisulphite converted DNAs were amplified, fragmented and hybridised to Illumina HumanMethylationEPIC and HumanMethylation450 Beadchips using standard Illumina protocol

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

data_processing: Minfi package for the R statistical software and in-house R scripts

label: Cy5 and Cy3

organism: Homo sapiens

source_name: patient saliva sample 1

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was extracted from samples using standard phenol/chloroform extraction protocol

value: saliva

tag: individual

value: patient

value: male


title: NC_H3_1

value: preadipocytes cells

value: Negative control


title: TH-MYCN NB mouse model, 5d comb. treatment, repeat 3

tag: tissue


title: L53_EN1

description: raw files stranded

value: Endometrium


title: Abf1_Vehicle_RNAPII


title: ZFP57_BL2

description: bisulphite converted DNA from ZFP57 patient blood sample 2

source_name: patient blood sample 2

value: blood


title: O61_CA1

description: raw files stranded

value: Chorioallantois

value: Placentitis


title: K56_EN1

description: raw files stranded

value: Control


title: ZFP57_BRO

description: bisulphite converted DNA from ZFP57 brother blood sample 1

source_name: brother blood sample 1

value: brother


title: Nalm6-CX-d1-input

city: Hershey

first: chunhua

last: song

state: PA

address: 500 University Drive

department: Pediatrics

institute: Pennsyvania  State University College of Medicine

description:
YD-22
input_ChIP-seq

data_processing:
Alignment of the filtered reads to the human reference genome (GRCh38) was done using bowtie2 (version 2.3.4.3)  Only sequences aligning uniquely to the human genome were used to identify peaks. Peaks were called using MACS2 (version 2.1.1) and annotated using homer (version 4.10) by supplying GRCh38.78.gtf as the annotation file.
Genome_build: GRCh38
Supplementary_files_format_and_content: The final processed peak calling results from MACS2 are provided as text files.

source_name: Nalm6 leukemia cells

growth_protocol: 10% FBS RPMI1640 + A/P + b-ME in 5% CO2, 37°C, change media every 2-3 days, cell density in  2x10^5 to 1x10^6

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-SEQ libraries were created using ChIP-SEQ DNA sample prep kit (Illumina). The unique dual index sequences (NEXTFLEX® Unique Dual Index Barcodes, BioO Scientific) were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl, pH 8.5 and then denatured using the Illumina protocol.
The denatured libraries were loaded onto an S1 flow cell on an Illumina NovaSeq 6000 (Illumina) and run for 2X50 cycles according to the manufacturer's instructions. De-multiplexed and adapter-trimmed sequencing reads were generated using Illumina bcl2fastq (released version 2.20.0.422). BBDuk (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/) was used to trim/filter low quality sequences using “qtrim=lr trimq=10 maq=10” option.

treatment_protocol: JM-1 and Nalm6 cells were treated with CX4945 (20uM) for one day.

tag: cell line

value: pre-B ALL leukemia cells

tag: culture condition

value: CK2 inhibitor CX-4945


title: TH-MYCN NB mouse model, 5d comb. treatment, repeat 2


title: CB_82

description: bisulphite converted DNA from control cord blood 82

hyb_protocol: bisulphite converted DNAs were amplified, fragmented and hybridised to HumanMethylation450 Beadchip using standard Illumina protocol

source_name: cord blood 82

extract_protocol: genomic DNA was extracted from placenta samples using standard phenol/chloroform extraction protocol

value: cord blood

value: female


title: Nalm6-CX-d1-IK-2

description:
YD-19
Ikaros_ChIP-seq

tag: chip antibody

value: Affinity-purified anti-Ikaros antibody


title: CB_40

description: bisulphite converted DNA from control cord blood 40

source_name: cord blood 40


title: WT_Vehicle5_RNAPII

value: W303 background; Mat a leu2-3,112 his3-11,15 ura3-1 ade2-1 trp1-1 can1-100

value: Anti-RNA polymerase II CTD repeat YSPTSPS (Abcam ab5131)


title: ZFP57_BL1

description: bisulphite converted DNA from ZFP57 patient blood sample 1

source_name: patient blood sample 1

value: patient


title: SI2_H3_1

tag: sirna transfection

value: HDAC3 Santa Cruz, cat. Sc376957, lot.J2717


title: O79_CA1

description: raw files stranded


title: TH-MYCN NB mouse model, 5d comb. treatment, repeat 1

value: TH-MYCN

value: tumor

value: 5 days


title: Nalm6-CX-d1-IK-1

description:
YD-16
Ikaros_ChIP-seq


title: TH-MYCN NB mouse model, 24h comb. treatment, repeat 4


title: O78_CA1

description: raw files stranded


title: CB_37

description: bisulphite converted DNA from control cord blood 37

source_name: cord blood 37

tag: gender

value: male


title: HD6

city: Edinburgh

first: Nizar

middle: N.

last: Batada

address: Crew Road

country: United Kingdom

institute: Institute for Genetics and Molecular Medicine, University of Edinburgh

data_processing:
Illumina Novaseq S1 software used for basecalling for HD4_HD5 and HD6 and Illumina HiSeq2500 software used for BC1 and BC2
Initial processing was done using Cell Ranger (v2.1.1) mkfastq and count
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimeted text files include raw counts for each sample

source_name: γδ-T cells from PBMCs

extract_protocol: as per manufacturer's guidelines (10X-Chromium)

tag: gating strategy

value: double positive for CD3 and pan-γδ

tag: dissociation protocol

value: Ficol gradient followed by cryopreservation in 10% DMSO


title: ZFP57_LYM

description: bisulphite converted DNA from ZFP57 patient lymphobalsts sample 1

source_name: patient lymphoblasts sample 1

value: lymphoblasts


title: O77_CA1

description: raw files stranded

value: Chorioallantois

value: Placentitis


title: TH-MYCN NB mouse model, 24h comb. treatment, repeat 3


title: HD4_HD5


title: O76_CA1

description: raw files stranded


title: TH-MYCN NB mouse model, 24h comb. treatment, repeat 2


title: O80_CA1

description: raw files stranded

value: Control


title: O73_CA1

description: raw files stranded


title: 697-WT-input

source_name: 697 ALL leukemia cells

value: pre-B ALL leukemia cells


title: CB_36

description: bisulphite converted DNA from control cord blood 36

source_name: cord blood 36

value: cord blood


title: REH-WT-input-2

source_name: REH ALL leukemia cells

value: REH


title: TH-MYCN NB mouse model, untreated, repeat 3

value: untreated


title: TH-MYCN NB mouse model, untreated, repeat 2


title: O62_CA1

description: raw files stranded


title: JM1-CX-d1-input-1

source_name: CX4945-treated JM-1 ALL leukemia cells

tag: treatment

value: CK2 inhibitor CX-4945


title: CB_23

description: bisulphite converted DNA from control cord blood 23

source_name: cord blood 23


title: CB_76

description: bisulphite converted DNA from control cord blood 76

source_name: cord blood 76

value: female


title: CB_17

description: bisulphite converted DNA from control cord blood 17

source_name: cord blood 17


title: CB_20

description: bisulphite converted DNA from control cord blood 20

source_name: cord blood 20


title: Top1_Top2_depletion_Auxin20_Hmo1

source_name: whole organism

treatment_protocol: 20 minutes auxin

value: RP10 background; TOP2-AID*-MYC-HPH TOP1-AID-KanMX6 MATalpha

tag: antibody

value: Anti-RNA polymerase II CTD repeat YSPTSPS (Abcam ab5131)


title: TH-MYCN NB mouse model, untreated, repeat 1

source_name: tumor

value: TH-MYCN

value: tumor


title: L56_CA1

description: raw files stranded

source_name: Uterus


title: S3-/- 2iLIF R1 RRBS

source_name: mouse embryo

extract_protocol: 500ng of DNA was digested at 37°C with 200U of MspI restriction endonuclease (NEB). Digested DNA was than end repaired, dA-tailed, and ligated to methylated adapters, using the Illumina TruSeq DNA Sample Prep Kit, following manufacturer’s instructions.

tag: cell type

value: mouse embryonic stem cell

value: Stat3 knock-out

tag: phenotype

value: adherent

tag: growth condition


title: JM1-WT-input-1

source_name: JM-1 ALL leukemia cells


title: L53_CA1

description: raw files stranded

tag: group


title: REH-WT-IK-2

value: Ikaros antibody, A303-516A, Bethyl


title: CB_18

description: bisulphite converted DNA from control cord blood 18

source_name: cord blood 18


title: 697-WT-IK

value: Affinity-purified anti-Ikaros antibody


title: S3+/+ 2iLIF R2 RRBS

tag: strain

tag: genotype

value: Stat3 wild-type


title: L60_CA1

description: raw files stranded

value: Chorioallantois

value: Control


title: K56_CA1

description: raw files stranded


title: JM1-CX-d1-IK-1

source_name: CX4945-treated JM1 ALL leukemia cells

value: pre-B ALL leukemia cells


title: CB_70

description: bisulphite converted DNA from control cord blood 70

source_name: cord blood 70

value: cord blood


title: S3+/+ 2iLIF R1 RRBS


title: Sample_Lung_Total

status: Public on Nov 26 2020

city: St Louis

first: Farshid

last: Guilak

state: Missouri

address: Couch Building, 3rd Floor, #3213

department: Orthopaedics

institute: Washington University in St Louis

data_processing:
Cell Ranger to align reads to the mouse genome
Genome_build: GRCm38

source_name: Total population

extract_protocol:
Cell suspensions were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell Gel Bead-in-Emulsions (GEMs). Libraries were prepared using Chromium Single-Cell 3′ Library & Gel Bead Kit (10x Genomics). The beads were dissolved and cells were lysed per manufacturer’s recommendations.  GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA.  After incubation, GEMs were broken and the pooled post-GEM-RT reaction mixtures were recovered and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, PN37002D, ThermoFisher Scientific).  The entire purified post GEM-RT product was amplified by PCR. This amplification reaction generated sufficient material to construct a 3’ gene expression library.
For 3’ gene expression library, enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by End Repair, A-tailing, Adaptor Ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification. Paired-end reads were generated for each sample using Illumina’s NextSeq550v2.

treatment_protocol: Whole lungs were removed and put into complete DMEM with 1 mg/mL of collagenase type II (Fisher Scientific; Catalog #NC9693955). Complete DMEM consisted of 10% FBS (Invitrogen), Penicillin/streptomycin (Invitrogen; Cat #15-140-122), vitamins (Invitrogen; Cat #11120052), Glutamax (Invitrogen; Cat #10566016), non-essential amino acids (Invitrogen; Cat #11140050), and sodium pyruvate (Invitrogen; Cat #11-360-070).  Lungs were incubated at 37˚C for 30 minutes and then mashed through a 100 µm cell strainer (Thermo Fisher Scientific; Cat #08-771-19).  ACK Lysing Buffer (Thermo Fisher Scientific; Cat #A1049201) was added to the single cell suspension and this mixture was spun down at 1,200 RPM for 5 minutes. The ACK was washed out with 50 mL of isolation buffer. Isolation buffer consisted of 1 mM EDTA and 2.5% FBS in PBS.   For Mk isolation, a negative selection protocol was used that included biotinylated anti- CD11b (BioLegend; Cat #NC0200884), B220 (BioLegend; Cat #NC0200885), CD3epsilon (BioLegend; Cat #100304), and CD146 (BioLegend; Cat #134716) antibodies and incubating in a 5 mL polystyrene tube (Laboratory Product Sales; Cat #L285601) with 50 µL/mL of rat serum. All antibodies were 5 µg/mL final concentration and streptavidin beads (STEMCELL Technologies; Cat #19860) at 75 µL/mL of sample (under 1 x 109 cells) concentration added. Each sample was then added to a magnet and incubated for 3-5 minutes and non-bound cells transferred to a 15 mL tube with pre-warmed complete DMEM.   Cells from tibias and femurs were isolated by flushing the bone marrow with isolation buffer using a 20-gauge needle (BD Biosciences, Cat# 14-826D).  If Mks were used for experimentation, the same procedure as the lungs were used for the BM.  For bone marrow derived dendritic cells we followed the protocol provided by Abcam (https://www.abcam.com/protocols/bmdc-isolation-protocol).

value: Lung total population


title: CB_15

description: bisulphite converted DNA from control cord blood 15

source_name: cord blood 15


title: CB_13

description: bisulphite converted DNA from control cord blood 13

source_name: cord blood 13


title: JM1-WT-IK-1


title: Sample_Lung_MK

source_name: Megakaryocyte enriched population from the lung

value: Lung Mk enriched population


title: uninfected_memory_7

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

data_processing:
Raw sequence data were assessed for quality and content using FastQC
Paired end sequences were aligned to the Ensembl release 96 murine transcripts set, using bowtie2 v2.2.7, applying parameters --very-sensitive -p 30 --no-mixed --no-discordant --no-unal.
The bowtie2 alignment outputs were stored as sorted, indexed bam files, and counts for each transcript obtained from the bam files using samtools idxstats.
Raw counts were imported into the R/Bioconductor environment using the DESeq2 package.
Genome_build: Murine transcript sequences (coding and non-coding) were obtained from Ensembl release 96 in fasta format and made into a bowtie2-searchable database using bowtie2-build; annotation information was obtained for the transcripts using Ensembl BioMart.
Supplementary_files_format_and_content: Processed files contain the outputs from samtools idxstats, namely three tab-separated columns comprising transcript name, transcript length, and read counts for the given sample.  A combined file, with the data from all the samples, is also available as NWRmatrix.xls.gz

source_name: flow sorted spleen inflammatory monocytes

growth_protocol:
C57Bl/6J mice were bred and housed in individually ventilated cages under specific pathogen free conditions (22°C, 50% humidity) at the University of Edinburgh, UK. Since we have previously shown that mosquito transmission resets expression of the large sub-telomeric multi-gene families that control malaria parasite virulence, and in turn shapes the host immune response during the pathogenic blood-stage of infection (Spence, P.J., et al., Vector transmission regulates immune control of Plasmodium virulence. Nature, 2013. 498(7453): p. 228-31), we transmitted Plasmodium chabaudi chabaudi AJ (96AJ15) and AS (28AS11, both obtained from the European Malaria Reagent Repository (malariaresearch.eu)) through Anopheles stephensi mosquitoes (strain SD500, reared in house at the University of Edinburgh). For more information about mosquito transmission please see our published protocol: Spence, P.J., et al., Mosquito transmission of the rodent malaria parasite Plasmodium chabaudi. Malar J, 2012. 11: p. 407. Mice were injected intravenously with 200 sporozoites, which establish a blood-stage infection 52 hours later. To capture the acute response, we isolated inflammatory monocytes from the spleen for RNAseq on day 7 of blood-stage infection (n= 5 AJ, & AS). infection with P. chabaudi AJ causes severe symptoms (acute hyperparasitaemia, severe anaemia, hypothermia and prostration) while acute AS infection is mild (no hyperparasitaemia, no measurable clinical manifestations of disease other than low-grade anaemia). More than 50% of mice remain chronically infected with P. chabaudi AJ for 40 days (verified by quantitative PCR before sequencing, n = 5). the response to acute and chronic malaria infection was evaluated relative to uninfected age-matched control mice (n = 7).
To evaluate if the tolerant state of spleen inflammatory monocytes from chronically malaria-infected mice is reversible, we stimulated them in vitro with LPS (n = 5) and compared their transcriptional response to LPS stimulated spleen monocytes isolated from uninfected age-matched control mice (n = 4).
Chronic P. chabaudi AJ infection was drug treated using 100 mg/kg chloroquine diphosphate salt (Sigma, dissolved in water) administered by oral gavage daily for 10 days. Memory responses of once-malaria infected mice were assessed 30 days after the start of chloroquine treatment (n = 6) and compared to uninfected age-matched control mice that received an identical chloroquine regimen (n = 6).
To answer if memory of first malaria infection alters the spleen inflammatory monocyte response to second malaria exposure we developed a novel reinfection model: mice were first infected with the avirulent P. chabaudi clone AS to induce chronic recrudescing parasitaemia and then chloroquine treated after 40 days of blood-stage infection to clear circulating and sequestered parasites. 30 days later, mice were infected for a second time - but now with the virulent parasite clone AJ. Critically, parasite density and the dynamics of red cell loss between first infection with P. chabaudi AS and second infection are identical. We therefore completely remove pathogen load as confounding factor when analysing the host response to reinfection. The transcriptional response  of inflammatory spleen monocytes to second infection was assessed at day 7 of blood-stage infection (n = 5) relative to uninfected age-matched control mice, which were also chloroquine treated (n = 5).

extract_protocol:
Total RNA was extracted using 1 - Bromo 3 - chloropropane (Sigma, #B9673) and Isopropanol (VWR, #437423R). total RNA was quantified and assessed for quality and integrity by Bioanalyser (RNA Pico 6000 Chips, Agilent). cDNA was generated from > 2 ng of RNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories) and amplified using 11 cycles of PCR. Amplified cDNA was purified using Agencourt AMPure XP beads (Beckman Coulter), quantified by Qubit (Qubit 2.0 Fluorometer - dsDNA HS assay, ThermoFisher) and quality assessed by Bioanalyser (DNA HS Kit, Agilent).
Sequencing libraries were constructed from 150 pg of cDNA using the Nextera XT DNA Library Preparation Kit (Illumina) according to manufacturers instruction. Library DNA was purified and short fragments were removed with AMPure XP beads. libraries were quantified by Qubit (dsDNA HS assay) and library fragment quality and size distribution assessed by Bioanalyser (DNA HS Kit). Equimolar library pools were sequenced at the Wellcome Trust Clinical Research Facility, Western General Hospital (Edinburgh, UK) using the NextSeq 550 platform (Illumina) generating 75 bp paired end reads.

treatment_protocol:
We assessed the ex vivo transcriptome of 10,000 spleen inflammatory monocytes (Lineage- Ly6G- CD11b+ CD11c- Ly6C+) by flow sorting directly into 1.5 ml eppendorf tubes containing 1 ml Trizol Reagent (ThermoFisher, #15596026). Tubes were inverted ten times and incubated for 5 minutes at room temperature before snap freezing and storage at - 80°C.
To evaluate the transcriptional response of spleen inflammatory monocytes to LPS stimulation in vitro we flow-sorted 30,000 monocytes into a polypropylene tube with IMDM supplemented with 5 % FBS and 8 mM L-Glutamine. Following a gently spin (450 xg for 10 minutes, slow brake), monocytes were resuspended in 90 ul pre-warmed IMDM with 10 % FBS and 8 mM L-Glutamine and transferred to a ultra low attachment flat bottom 96 well cell culture plate (Corning). To stimulate cells 0.3 ng*µl-1 LPS (Lipopolysaccharides from Escherichia coli 0111:B4, Sigma) was added. Cell culture plates were incubated for 4 hours at 37 ̊C and 7 % CO2. RNA from both adherent and non-adherent cells was preserved in 1 ml Trizol Reagent and stored at - 80°C.

tag: malaria infection

value: uninfected age-matched to second infection drug treated


title: second_infection_4

value: flow sorted spleen inflammatory monocytes

value: acute blood-stage (day 7) of second infection


title: uninfected_memory_11


title: second_infection_3


title: uninfected_memory_10


title: uninfected_memory_9


title: CB_10

description: bisulphite converted DNA from control cord blood 10

source_name: cord blood 10

tag: tissue

value: female


title: second_infection_2


title: second_infection_5


title: CB_12

description: bisulphite converted DNA from control cord blood 12

source_name: cord blood 12

value: male


title: uninfected_memory_6

value: uninfected age-matched to memory drug treated


title: uninfected_memory_5


title: second_infection_1


title: Sample_BM_MK

source_name: Megakaryocyte enriched population from the bone marrow

value: Bone Marrow MK enriched population


title: CB_35

description: bisulphite converted DNA from control cord blood 35

source_name: cord blood 35


title: uninfected_memory_3


title: uninfected_memory_2


title: uninfected_memory_1


title: AJ_memory_6

value: 30 days after drug cure of chronic mosquito transmitted P. chabaudi AJ


title: AJ_memory_5


title: AJ_memory_3


title: CB_08

description: bisulphite converted DNA from control cord blood 8

source_name: cord blood 8


title: CB_09

description: bisulphite converted DNA from control cord blood 9

source_name: cord blood 9


title: S3-/- 2iLIF R2 RRBS

value: mouse embryonic stem cell

value: Stat3 knock-out

value: adherent


title: AJ_memory_1


title: CB_05

description: bisulphite converted DNA from control cord blood 5

source_name: cord blood 5


title: Blood_3

description: bisulphite converted DNA from control blood 3

source_name: blood 3

value: blood


title: uninfected_LPS_3

value: uninfected age-matched to chronic

tag: in vitro lps stimulation

value: LPS 0.3 ng*µl-1 for 4 hours


title: uninfected_LPS_2


title: uninfected_LPS_4


title: AJ_chronic_LPS_5

value: chronic blood-stage infection (day 40) with mosquito transmitted P. chabaudi AJ


title: AJ_chronic_LPS_4


title: CB_04

description: bisulphite converted DNA from control cord blood 4

source_name: cord blood 4

value: cord blood


title: AJ_chronic_LPS_3


title: Blood_1

description: bisulphite converted DNA from control blood 1


title: Blood_2

description: bisulphite converted DNA from control blood 2

source_name: blood 2


title: uninfected_6


title: AJ_chronic_LPS_2


title: uninfected_4


title: uninfected_5


title: uninfected_3

value: uninfected age-matched to acute


title: uninfected_7


title: ZFP57_MOM

description: bisulphite converted DNA from ZFP57 mother blood sample 1

source_name: mother blood sample 1

tag: individual

value: mother


title: uninfected_1

value: flow sorted spleen inflammatory monocytes


title: AJ_chronic_LPS_1


title: uninfected_LPS_1


title: AJ_chronic_5


title: AJ_memory_2


title: CB_07

description: bisulphite converted DNA from control cord blood 7

source_name: cord blood 7


title: uninfected_2


title: AJ_chronic_3


title: AJ_chronic_4


title: AJ_chronic_2


title: AJ_chronic_1


title: AS_acute_4

value: acute blood-stage infection (day 7) with mosquito transmitted P. chabaudi AS


title: AS_acute_5


title: AS_acute_3


title: AS_acute_2


title: AS_acute_1


title: AJ_acute_4

value: acute blood-stage infection (day 7) with mosquito transmitted P. chabaudi AJ


title: AJ_acute_5


title: AJ_acute_2


title: AJ_acute_3


title: single-nuclei data from whole kidney (middle slice) control mouse_rep2

city: Hannover

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

institute: Hannover Medical School

description:
10x v3.1 chemistry
chX012_1

data_processing:
In the fastq files, R1 contains the barcodes. BP 1-12 is the cell barcode, 13-20 the UMI.
Digital expression matrices were generated using the Cellranger software version 3.0.2.
All datasets were imported as Seurat objects into R using Seurat version 2.3.1. Cells were filtered using a lower gene number (nGene) cutoff of 500  and an upper cutoff of 5000. Data were then log-normalized and scaled according to the number of unique molecular identifiers (UMIs). All all single-nuclei data samples were merged into one Seurat object. Clustering was performed using highly variable genes (Seurat parameters: x.low.cutoff = 0.0125, x.high.cutoff=Inf, y.cutoff=0.5) on all cells using Seurat’s default settings. TSNE plots were generated using 30 principal components from PCA with highly variable genes, a perplexity of 30 and a resolution of 0.6. All other parameters were at default levels.
Supplementary_files_format_and_content: barcode, genes and expression matrix form Cellranger software.

molecule: nuclear RNA

source_name: mouse whole kidney

extract_protocol:
After mice were sacrificed, kidneys were immediately put in ice-cold PBS. A middle slice (1-2mm) containing cortex, outer and inner medulla was then obtained. All samples were then put in 4°C-cold RNAlater for 24 hours and then to -80°C. For the generation of the single-nuclei suspensions (all reactions at 4°C), specimens were thoroughly minced in nuclear lysis buffer 1 (nuclear lysis buffer (Sigma) + Ribolock (1U/µl) + VRC (10mM)) and homogenated using a dounce homogenizer with pastel A (Sigma D8938-1SET), filtered (100µm), homogenized again (douncer with pastel B), filtered through a 35µm strainer and centrifuged (5min, 500g). The pellet was then resuspended in nuclear lysis buffer 2 (nuclear lysis buffer + Ribolock (1U/µl)). To remove debris from the suspension, we underlayed the suspension with lysis buffer containing 10% sucrose and 1U/µl of Ribolock. After centrifugation (5min, 500g), the supernatant and debris were carefully removed. Pelleted nuclei were resuspended in PBS/0.04%BSA + Ribolock (1U/µl), filtered through a 20µm strainer and stained with DAPI. The nuclei suspension was then FACS-sorted (BD FACS Aria II), counted after FACS-sorting and subjected to single-cell sequencing.
Library construction followed the exact protocol from 10xgenomics v2 chemistry for 3° scRNA-seq.

tag: strain background

tag: genotype/variation

value: control

value: mouse whole kidney


title: AJ_acute_1


title: uninfected_H3K4me1_2

description:
H3K4me1_MEMORY_ChIP_AMC
H3K4me1_MEMORY_ChIP_AMC.tagdir.tar.gz
H3K4me1_MEMORY_ChIP_AMC.bedgraph
H3K4me1_MEMORY_ChIP_AMC.tdf.gz

data_processing:
Raw sequence data were assessed for quality and content using FastQC
Sequences were aligned to the Mus musculus genome (mm10) using bowtie2 with parameters --very-sensitive -p 30 --no-discordant --no-unal . The bowtie2 alignment outputs were stored as sorted, indexed bam files generated using samtools.
Samples were pooled as detailed and converted into tag directories using Homer software (http://homer.ucsd.edu/homer/; v4.10)
Alignments were converted to bedgraph format using Homer script makeUCSCfile.
Wig format outputs were converted to TDF format for viewing in IGV  using igvtools v2.3.93 (parameters: toTDF -z 7 -f p98)
Genome_build: mm10
Supplementary_files_format_and_content: Three types of processed file are provided for each sample pool.  Firstly, a tarred gzip archive of the Homer derived tag counts. Secondly, the tags were converted into bedgraph format, prior to conversion to wiggle format. Thirdly, the wiggle format files were coverted to a comcpressed TDF format more suitable for IGV viewing.

source_name: flow sorted bone marrow inflammatory monocytes

growth_protocol: C57Bl/6J mice were bred and housed in individually ventilated cages under specific pathogen free conditions (22°C, 50% humidity) at the University of Edinburgh, UK. Since we have previously shown that mosquito transmission resets expression of the large sub-telomeric multi-gene families that control malaria parasite virulence, and in turn shapes the host immune response during the pathogenic blood-stage of infection (Spence, P.J., et al., Vector transmission regulates immune control of Plasmodium virulence. Nature, 2013. 498(7453): p. 228-31), we transmitted Plasmodium chabaudi chabaudi AJ 96AJ15 (obtained from the European Malaria Reagent Repository (malariaresearch.eu)) through Anopheles stephensi mosquitoes (strain SD500, reared in house at the University of Edinburgh) according to our published protocol: Spence, P.J., et al., Mosquito transmission of the rodent malaria parasite Plasmodium chabaudi. Malar J, 2012. 11: p. 407. Mice were injected intravenously with 200 P. chabaudi AJ sporozoites, which, following 52 hours development in the liver, establish a severe acute blood-stage infection (hyperparasitaemia, severe anaemia, hypothermia and prostration) lasting approximately 2 weeks. Thereafter > 50 % of mice remain chronically infected (verified after 40 days by quantitative PCR). Chronic P. chabaudi AJ infection was then drug treated using 100 mg/kg chloroquine diphosphate salt (Sigma, dissolved in water) administered by oral gavage daily for 10 days. Memory responses of once-malaria infected mice were assessed 30 days after the start of chloroquine treatment and compared to uninfected age-matched control mice that received an identical chloroquine regimen.

extract_protocol:
Chromatin was immunoprecipitated using the True MicroChIP kit (Diagenode) with a modified protocol: cells were lysed before chromatin shearing using a Bioruptor Pico Sonicator (Diagenode; 5 cycles: 30 seconds ON - 30 seconds OFF; fragments 100 - 300 bp). 10 % of sheared chromatin was kept as input control and 90 % was immunoprecipitated using antibodies against either H3K27ac, H3K4me1 or H3K9me (all Diagenode) over night at 4 ̊C. The next morning Protein A coated beads (Diagenode) were added and, following a 6 hour incubation at 4 ̊C, unbound chromatin fragments were removed by thorough washing. ChIP and input DNA was then decrosslinked from proteins and purified using MicroChip DiaPure columns (Diagenode).
Sequencing libraries were prepared using the MicroPlex v2 Library preparation kit (Diagenode) according to manufacturers instructions. Library amplification was monitored in real time using a Lightcycler 480 (Roche) to determine optimal cycle number. Amplified libraries were quantified using Qubit (dsDNA HS assay) and fragment quality and size distribution assessed by Bioanalyser (DNA HS Kit). Following equimolar pooling, libraries were purified using AMPure XP beads and quantity and quality of the library pool confirmed. Pooled libraries were sequenced by Edinburg Genomics, University of Edinburgh (UK) on HiSeq 4000 (75 bp paired end reads) or NovaSeq S1 (100 bp paired end reads, both Illumina).

treatment_protocol: 30 days after chloroquine treatment of once-P. chabaudi AJ malaria infected mice and uninfected age-matched controls, bone marrow cells from both femurs and tibias (pooled from two mice) were stained with antibodies and gently fixed in PBS with 1 % paraformaldehyde (Alpha Aesar) and 10 % FBS for exactly 10 minutes at room temperature. Fixation was quenched with 125 mM Glycine (Sigma). 50,000 bone marrow inflammatory monocytes (Lineage- Ly6G- cKit- CD135- CD11b+ Ly6C+) were then flow-sorted into polypropylene tubes with IMDM supplemented with 5 % FBS and 8 mM L-Glutamine. We flow-sorted multiple replicates from one biological sample, which were then chromatin-immunoprecipitated using three different antibodies. Sorted monocytes were pelleted by centrifugation and washed in HBSS (Gibco) with protease inhibitors (complete ULTRA Tablets Protease Inhibitor Cocktail, Roche) and 5 mM sodium butyrate (Alpha Aesar). Cell pellets were stored at - 80 ̊C.

tag: infection

value: uninfected age-matched

tag: chip antibody

tag: tag


title: uninfected_H3K27ac_2

description:
H3K27ac_MEMORY_ChIP_AMC
H3K27ac_MEMORY_ChIP_AMC.tagdir.tar.gz
H3K27ac_MEMORY_ChIP_AMC.bedgraph
H3K27ac_MEMORY_ChIP_AMC.tdf.gz


title: input_uninfected_H3K27ac_and_H3K4me1_2

description:
H3K27ac_MEMORY_INPUT_AMC
H3K27ac_MEMORY_INPUT_AMC.tagdir.tar.gz
H3K27ac_MEMORY_INPUT_AMC.bedgraph
H3K27ac_MEMORY_INPUT_AMC.tdf.gz

value: not immunoprecipitated:input


title: memory_H3K27ac_2

description:
H3K27ac_MEMORY_ChIP_AJ
H3K27ac_MEMORY_ChIP_AJ.tagdir.tar.gz
H3K27ac_MEMORY_ChIP_AJ.bedgraph
H3K27ac_MEMORY_ChIP_AJ.tdf.gz

value: 30 days after drug cure of chronic mosquito transmitted P. chabaudi AJ


title: memory_H3K4me1_2

description:
H3K4me1_MEMORY_ChIP_AJ
H3K4me1_MEMORY_ChIP_AJ.tagdir.tar.gz
H3K4me1_MEMORY_ChIP_AJ.bedgraph
H3K4me1_MEMORY_ChIP_AJ.tdf.gz


title: uninfected_H3K4me1_1


title: DC-antiPD1&D18 rep3

city: Beijing

first: Liangliang

last: Wang

address: #30 Shuangqing Road

institute: Tsinghua University

data_processing:
Illumina Casava1.7 software used for basecalling.
The short sequence reads were aligned to mouse mm10 reference genome using STAR (2.4.0)
The data assembled and quantified by HTSeq (0.6.1) with Gencode M8 as annotation.
DESeq2 was used for differential gene expression analysis among subgroups.
Hierarchical clustering and principal component analysis were plotted applying FactoMineR and gplots libraries in R. log2 [FPKM]
Genome_build: mm10
Supplementary_files_format_and_content: Normalized_log2-gene-counts for each sample, the format is Tab-delimited text.

source_name: MC38 tumors

growth_protocol: Six-week old C57BL/6 female mice were subcutaneously injected in the right flank with 1×106 MC38 cells. Mice were pooled and randomly divided into different groups with comparable average tumor size 100 mm3, 7-10 days after tumor cells injection.

extract_protocol:
The different subtypes cells, including CD8+ T cells , T helper cells, and dendritic cells in MC38 tumors were analyzed by flow cytometry and then sorted into lysis buffer. The RNA extraction, and reverse transcription were then performed following the Smart-Seq2 protocol (S Picelli et al. Nat Methods. 2013).
cDNA library construction were performed also following the Smart-Seq2 protocol (S Picelli et al. Nat Methods. 2013).

treatment_protocol: D18 (25 μg per mouse) was administered once each week and anit-PD-1 antibody (200 μg per mouse) were injected intraperitoneally twice each week. One is anti-PD-1 antibody treatment group and another is anti-PD-1 antibody plus D18 treatment group. The mice were treated for two weeks.

tag: background strain

value: MC38 tumors

value: DC

tag: treatments

value: anti-PD-1 antibody plus D18


title: DC-antiPD1&D18 rep2

tag: cell type


title: uninfected_H3K27ac_1


title: memory_H3K27ac_1


title: input_memory_H3K27ac_and_H3K4me1_1

description:
H3K27ac_MEMORY_INPUT_AJ
H3K27ac_MEMORY_INPUT_AJ.tagdir.tar.gz
H3K27ac_MEMORY_INPUT_AJ.bedgraph
H3K27ac_MEMORY_INPUT_AJ.tdf.gz


title: single-nuclei data from whole kidney (middle slice) Hoxb7Cre;Grhl2 fl/fl mouse_rep2

description:
10x v3.1 chemistry
chX012_2

value: Hoxb7Cre;Grhl2 fl/fl


title: memory_H3K4me1_1


title: DC-antiPD1 rep1

value: anti-PD-1 antibody


title: DC-antiPD1 rep2


title: DC-antiPD1 rep3


title: CD4T-antiPD1&D18 rep3

value: CD4 T


title: DC-antiPD1&D18 rep1


title: CD4T-antiPD1&D18 rep2


title: CD4T-antiPD1&D18 rep1


title: CD4T-antiPD1 rep3


title: input_memory_H3K27ac_and_H3K4me1_2


title: input_uninfected_H3K27ac_and_H3K4me1_1


title: CD4T-antiPD1 rep1


title: CD4T-antiPD1 rep2


title: CD8T-antiPD1&D18 rep3

value: CD8 T


title: CD8T-antiPD1&D18 rep2


title: CD8T-antiPD1 rep3


title: CD8T-antiPD1&D18 rep1


title: CD8T-antiPD1 rep1


title: CD8T-antiPD1 rep2


title: B0968_KO_Control_S24

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

data_processing:
STAR v2.5.3
RSEM v1.3.0
limma v3.38.3
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Clic4 KO at Day 0

extract_protocol:
Qiagen Rneasy
Illumina TruSeq v4

value: lung

tag: age

value: 6 weeks

value: Clic4 KO

tag: time

value: Day 0


title: single-nuclei data from whole kidney (middle slice) Hoxb7Cre;Grhl2 fl/fl mouse

description: 10x v2 chemistry

data_processing:
Digital expression matrices were generated using the Cellranger software version 3.0.2.
All datasets were imported as Seurat objects into R using Seurat version 2.3.1. Cells were filtered using a lower gene number (nGene) cutoff of 500  and an upper cutoff of 5000. Data were then log-normalized and scaled according to the number of unique molecular identifiers (UMIs). All all single-nuclei data samples were merged into one Seurat object. Clustering was performed using highly variable genes (Seurat parameters: x.low.cutoff = 0.0125, x.high.cutoff=Inf, y.cutoff=0.5) on all cells using Seurat’s default settings. TSNE plots were generated using 30 principal components from PCA with highly variable genes, a perplexity of 30 and a resolution of 0.6. All other parameters were at default levels.

value: kidney

tag: rna fraction

value: nuclear RNA


title: B0843_WT_14_Days_S9

source_name: WT at Day 14

tag: strain

value: 8 weeks

value: WT

value: Day 14


title: uninfected_memory_8

source_name: flow sorted spleen inflammatory monocytes

value: uninfected age-matched to second infection drug treated


title: B0834_WT_14_Days_S8

tag: genotype


title: B0830_KO_14_Days_S30

source_name: Clic4 KO after 14 days


title: B0851_WT_14_Days_S10


title: B0813_KO_14_Days_S28


title: single-nuclei data from whole kidney (middle slice) control mouse

description: 10x v2 chemistry

value: control


title: B0770_KO_Control_S21


title: B0776_KO_14_Days_S26


title: B0769_WT_14_Days_S6


title: B0777_KO_14_Days_S27


title: B0745_WT_Control_S4

source_name: WT at Day 0


title: B0743_WT_Control_S2


title: B0742_WT_Control_S1


title: B0738_KO_14_Days_S25


title: B0744_WT_Control_S3


title: B0831_WT_14_Days_S7


title: B0768_WT_14_Days_S5


title: Input DNA (replicate)

city: Bangalore

first: Manchanahalli

middle: Rangaswamy

last: Satyanarayana Rao

state: Karnataka

address: Jakkur, Bengaluru, Karnataka

department: Molecular Biology and Genetics Unit (MBGU)

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

data_processing:
Quality Control Analysis and modification were performed in a three step procedure. Firstly, FASTQC was used to extract the sequence  quality measures from the raw files. Secondly, Adaptor clipping was done with a stringent overlap condition of 1bp using trim_galore.The pairs in which this step resulted in reduction of sequence length to below 20bp were removed. Finally, pairs where read quality was found to be less than 20 were removed.
Bowtie2 was used to align the paired end reads for each sample. For this purpose UCSC Rattus  norvegicus genome (rn6) was used as a reference. SAM files were converted to  respective BAM files using SAMtools, which were subsequently sorted and filtered off duplicates. Resulting processed  BAM files were the passed through another quality check using BAMQC. BED files were prepared with bedtools for visualisation and  peak identification corresponding to each BAM file. For both the conditions (treated and control/input) replicates were merged using SAMtools merge
Peak identification was done using macs2 for the mergerd treated BAM  against the merged input/control sample as control.  p-value 1e-05  was used as cutoff.
Peak reigions were annotated to find basic annotations related to the overlaps using Homer
Selected regions with high enriched peaks were validated using ChIP-PCR
Genome_build: rn6
Supplementary_files_format_and_content: H1T2_peaks

organism: Rattus norvegicus

source_name: testicular cells

extract_protocol:
Nuclei were prepared from 35-50days old rat testis, decondensed and chromatin immunoprecipitation was done using anti-H1T2 antibodies. Immunocomplexes were captured on 50 μl protein A Dynabeads. Beads with bound immunocomplexes were washed, eluted and reverse cross-linked at 65°C overnight and DNA was recovered using Qiagen PCR purification kit. Input was prepared with 5% of the sonicated chromatin.
Library DNA was purified using Qiagen DNA purification kit. Sequencing was performed with Illumina HiSeq X Ten system, and raw sequence reads containing adaptor sequences were trimmed and filtered with Phred quality threshold as 20. Read pairs falling below 20 bp after clipping were removed

value: testis

value: round/Elongating spermatids


title: H1T2_ChIPSeq


title: H1T2_ChIPSeq (replicate)


title: Input DNA


title: AJ_memory_4

value: flow sorted spleen inflammatory monocytes

tag: malaria infection

value: 30 days after drug cure of chronic mosquito transmitted P. chabaudi AJ


title: Empty vector FLAG IP 2

city: Seattle

first: Robert

middle: K.

last: Bradley

state: Washington

address: 1100 Fairview Ave N

department: Public Health Sciences/Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: IP for FLAG tag using empty vector (biological replicate 2)

data_processing:
Reads aligned to GRCh38/hg38 and GENCODE Release 32.
PCR duplicates and reads aligning to repetitive sequences were removed.
Genome_build: UCSC GRCh38/hg38
Supplementary_files_format_and_content: bigWig files show read coverage.

source_name: K562 cells

extract_protocol:
Cells were lysed with RNase I to fragment RNA as previously described (Van Nostrand, E.L. et al. (2017) Methods Mol Biol). FLAG antibody (F-1084, Sigma-Aldrich) was then pre-coupled to Protein G Dynabeads (Thermo Fisher), added to lysate, and incubated overnight at 4 degrees Celcius. Prior to immunoprecipitation, 2% of the sample was taken as the paired input sample, with the remainder magnetically separated and washed with lysis buffer only.
Library construction was performed by excising the area from ∼65 kDa to ∼140 kDa. RNA adapter ligation, IP-western, reverse transcription, DNA adapter ligation, and PCR amplification were performed as previously described (Van Nostrand, E.L. et al. (2017) Methods Mol Biol).
Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP) by Eclipse Bioinnovations Inc (San Diego, www.eclipsebio.com) according to the published protocol (Van Nostrand, E.L. et al. (2017) Methods Mol Biol).

treatment_protocol: 10 million K562 cells expressing either a FLAG-tagged empty vector or N-terminal FLAG-tagged ZRSR2 were UV crosslinked at 400 mJoules/cm2 with 254 nm radiation and snap frozen.

tag: genetic tag

value: FLAG

tag: transgene

value: Empty vector FLAG

tag: index 1 sequence

value: GAGATTCC

tag: index 2 sequence

value: TAATCTTA


title: ZRSR2 FLAG input 1

description: Input for ZRSR2 with N-terminal FLAG tag (biological replicate 1)

value: ZRSR2 with N-terminal tag FLAG

value: ATTCAGAA


title: ZRSR2 FLAG IP 1

description: IP for ZRSR2 with N-terminal FLAG tag (biological replicate 1)

value: CTGAAGCT

value: AGGCGAAG


title: ZRSR2 FLAG input 2

description: Input for ZRSR2 with N-terminal FLAG tag (biological replicate 2)

value: TCCGGAGA

value: CAGGACGT


title: Empty vector FLAG input 1

description: Input for FLAG tag alone using empty vector (biological replicate 1)


title: Empty vector FLAG input 2

description: Input for FLAG tag alone using empty vector (biological replicate 2)

value: GTACTGAC


title: Empty vector FLAG IP 1

description: IP for FLAG tag using empty vector (biological replicate 1)

value: CGCTCATT


title: ZRSR2 FLAG IP 2

description: IP for ZRSR2 with N-terminal FLAG tag (biological replicate 2)

value: TAATGCGC


title: rpm_uninfected_3

type: RNA

hyb_protocol: According to manufacturers instruction GeneChiP Whole Transcript Pico Reagents Kit.

scan_protocol: According to manufacturers instruction Affymetrix mouse exon 1.0 ST array

data_processing: Data were processed in R/Bioconductor using the oligo, pd.mta.1.0 and mta10sttranscriptcluster packages.  Transcript level analyses were performed using limma and eBayes on rma() normalised data.

label: biotin

source_name: flow sorted splenic red pulp macrophages

label_protocol: RNA was processed according to manufacturers instruction using the GeneChiP Whole Transcript Pico Reagents Kit and run on the mouse exon 1.0 ST array (both Affymetrix) by Hologic (Manchester, UK).

growth_protocol: C57Bl/6J mice were bred and housed in individually ventilated cages under specific pathogen free conditions (22°C, 50% humidity) at the University of Edinburgh, UK. Malaria infections were initiated when mice were approximately 9 weeks of age by intravenous injection of 200 sporozoites (according to our published protocol: Spence, P.J., et al., Mosquito transmission of the rodent malaria parasite Plasmodium chabaudi. Malar J, 2012. 11: p. 407). We mosquito transmitted two distinct Plasmodium chabaudi chabaudi clones, which we obtained from the European Malaria Reagent Repository (malariaresearch.eu) at the University of Edinburgh: P. chabaudi AS (28AS11) and P. chabaudi AJ (96AJ15). Anopheles stephensi mosquitoes (strain SD500) were reared in house at the University of Edinburgh. we initiated all experimental infections with sporozoites, since we have previously shown that mosquito transmission resets expression of the large sub-telomeric multi-gene families that control parasite virulence, and in turn shapes the host immune response during the pathogenic blood-stage of malaria infection (Spence, P.J., et al., Vector transmission regulates immune control of Plasmodium virulence. Nature, 2013. 498(7453): p. 228-31). 100 days after infection parasitaemia resolves without intervention.

extract_protocol: Total RNA was extracted using 1 - Bromo 3 - chloropropane (Sigma, #B9673) and Isopropanol (VWR, #437423R).

treatment_protocol: 10,000 red pulp macrophages (lineage-, autofluorescent, F4/80+, B220-, CD11bint, CD11cint) were flow-sorted directly into 1.5 ml eppendorf tubes containing 1 ml Trizol Reagent (ThermoFisher, #15596026). Tubes were inverted ten times and incubated for 5 minutes at room temperature before snap freezing and storage at - 80°C.

value: uninfected age-matched


title: uninfected_memory_4

value: uninfected age-matched to memory drug treated


title: rpm_AS_3

value: 100 days after infection with mosquito transmitted P. chabaudi AS


title: rpm_uninfected_4


title: rpm_uninfected_2


title: rpm_AS_1


title: rpm_AJ_3

value: 100 days after infection with mosquito transmitted P. chabaudi AJ


title: Ak18

city: Singapore

first: Wharton

middle: O Yinn

last: Chan

address: 8 College Road

department: Emerging Infectious Disease

country: Singapore

institute: Duke NUS Medical School

data_processing:
Alignment by STAR 2.7.5a
Count Table Generation by FeatureCounts (Rsubread v2.0.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab separated count values

source_name: Nasal Epithelial Cells

growth_protocol: Fully differentiated Human Nasal Epithelial Cells

extract_protocol:
RNA extracted from cell lysates using EZNA RNA extraction kit  (Omega Biotech) according to manufacturer's instructions
TruSeq Stranded Total Human RNA Prep kit (Illumina) according to manufacturer’s instructions

treatment_protocol: Uninfected, or infected with SARS-CoV-2 wild-type or ∆382 strain at MOI of 0.1 for indicated period

tag: hpi

tag: virus

tag: donor


title: Ak21


title: Ak20


title: rpm_AS_2


title: rpm_AJ_2


title: rpm_uninfected_5


title: rpm_AS_4


title: Ak16


title: Ak17


title: Ak15

value: SARS-CoV-2 wild-type


title: rpm_uninfected_1


title: rpm_AJ_1


title: Ak14


title: Ak11


title: Ak12


title: Ak8


title: Ak7


title: Ak4


title: Ak13


title: Ak3


title: Ak5


title: Ak2


title: Ak6


title: 2D_EpCAM+ scRNA-seq_81

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

data_processing:
Illumina bcl2fastq-1.8.4 software was used to demultiplex data and convert BCL files from HiSeq2500 systems running RTA versions 1.18.64 to standard FASTQ file formats for downstream analysis.
Sequenced reads were mapped to GRCh38 whole genome using STAR 2.6.1a aligner following ENCODE standard option in STAR manual.
Reads aligned to each gene were counted using featureCount.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample .

source_name: 2D_EpCAM+ scRNA-seq

growth_protocol:
FD-AO EpCAM+ cells were induced from isolated CPM-high progenitor cells on day 21 and cocultured with human fetal fibroblasts for 14 days under the treatment of dexamethasone, 8-Br-cAMP, 3-Isobutyl-1-methylxanthine, KGF (no and twice passages (P0 and P2).
P2 FD-AO EpCAM+ cells were cultured in two-demensional condition for 7day under the treatment of dexamethasone, 8-Br-cAMP, 3-Isobutyl-1-methylxanthine, KGF and Y27632.

extract_protocol:
Single cells were captured and separated on the each chamber of medium-sized (17-25 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) .
The first-strand cDNA was synthesized and amplified on the independent chamber using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

tag: source cell type

value: human induced pluripotent stem cell (hiPSC)-derived alveolar type2 (AT2)

value: hiPSC-derived 2D alveoalr type 1 (2D-iAT1)

tag: culture condition

value: two-demensional culturer

value: hiPSC-derived EpCAM+ cells


title: 2D_EpCAM+ scRNA-seq_79


title: 2D_EpCAM+ scRNA-seq_82


title: 2D_EpCAM+ scRNA-seq_83


title: 2D_EpCAM+ scRNA-seq_80


title: Ak9


title: 2D_EpCAM+ scRNA-seq_77


title: 2D_EpCAM+ scRNA-seq_74


title: 2D_EpCAM+ scRNA-seq_75


title: 2D_EpCAM+ scRNA-seq_71


title: 2D_EpCAM+ scRNA-seq_72


title: 2D_EpCAM+ scRNA-seq_73


title: 2D_EpCAM+ scRNA-seq_70


title: 2D_EpCAM+ scRNA-seq_68


title: 2D_EpCAM+ scRNA-seq_76


title: 2D_EpCAM+ scRNA-seq_66


title: 2D_EpCAM+ scRNA-seq_65


title: 2D_EpCAM+ scRNA-seq_64


title: Ak1


title: 2D_EpCAM+ scRNA-seq_78


title: 2D_EpCAM+ scRNA-seq_61


title: 2D_EpCAM+ scRNA-seq_58


title: 2D_EpCAM+ scRNA-seq_63


title: 2D_EpCAM+ scRNA-seq_59


title: 2D_EpCAM+ scRNA-seq_57


title: 2D_EpCAM+ scRNA-seq_62


title: 2D_EpCAM+ scRNA-seq_55


title: 2D_EpCAM+ scRNA-seq_53


title: 2D_EpCAM+ scRNA-seq_54


title: 2D_EpCAM+ scRNA-seq_60


title: 2D_EpCAM+ scRNA-seq_56


title: 2D_EpCAM+ scRNA-seq_69


title: 2D_EpCAM+ scRNA-seq_52


title: 2D_EpCAM+ scRNA-seq_46


title: 2D_EpCAM+ scRNA-seq_67


title: 2D_EpCAM+ scRNA-seq_47


title: 2D_EpCAM+ scRNA-seq_48


title: 2D_EpCAM+ scRNA-seq_50


title: 2D_EpCAM+ scRNA-seq_51


title: 2D_EpCAM+ scRNA-seq_49


title: 2D_EpCAM+ scRNA-seq_43


title: 2D_EpCAM+ scRNA-seq_41


title: 2D_EpCAM+ scRNA-seq_45


title: 2D_EpCAM+ scRNA-seq_44


title: 2D_EpCAM+ scRNA-seq_40


title: 2D_EpCAM+ scRNA-seq_39


title: 2D_EpCAM+ scRNA-seq_38


title: Ak10


title: 2D_EpCAM+ scRNA-seq_35


title: 2D_EpCAM+ scRNA-seq_36


title: 2D_EpCAM+ scRNA-seq_37


title: 2D_EpCAM+ scRNA-seq_34


title: 2D_EpCAM+ scRNA-seq_42


title: 2D_EpCAM+ scRNA-seq_26


title: 2D_EpCAM+ scRNA-seq_14


title: 2D_EpCAM+ scRNA-seq_30


title: 2D_EpCAM+ scRNA-seq_12


title: 2D_EpCAM+ scRNA-seq_27


title: 2D_EpCAM+ scRNA-seq_22


title: 2D_EpCAM+ scRNA-seq_24


title: 2D_EpCAM+ scRNA-seq_21


title: 2D_EpCAM+ scRNA-seq_20


title: 2D_EpCAM+ scRNA-seq_15


title: 2D_EpCAM+ scRNA-seq_23


title: 2D_EpCAM+ scRNA-seq_25


title: 2D_EpCAM+ scRNA-seq_17


title: 2D_EpCAM+ scRNA-seq_11


title: 2D_EpCAM+ scRNA-seq_18


title: 2D_EpCAM+ scRNA-seq_10


title: 2D_EpCAM+ scRNA-seq_29


title: 2D_EpCAM+ scRNA-seq_8


title: 2D_EpCAM+ scRNA-seq_9


title: 2D_EpCAM+ scRNA-seq_32


title: 2D_EpCAM+ scRNA-seq_6


title: 2D_EpCAM+ scRNA-seq_33


title: 2D_EpCAM+ scRNA-seq_28


title: 2D_EpCAM+ scRNA-seq_16


title: 2D_EpCAM+ scRNA-seq_19


title: 2D_EpCAM+ scRNA-seq_4


title: 2D_EpCAM+ scRNA-seq_2


title: 2D_EpCAM+ scRNA-seq_3


title: 2D_EpCAM+ scRNA-seq_1


title: P0_FF-AO_EpCAM+ scRNA-seq_90

description: Single  " P0_FF-AO_EpCAM+" cells were captured and separated on the each chamber of medium-sized (10-17 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) Then, first-strand cDNA was synthesized and amplified on the independent chamber using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

source_name: EpCAM+ cells

growth_protocol:
FD-AO EpCAM+ cells were induced from isolated CPM-high progenitor cells on day 21 and cocultured with human fetal fibroblasts for 14 days under the treatment of dexamethasone, 8-Br-cAMP, 3-Isobutyl-1-methylxanthine, KGF with and without passages (P0 and P2).
FF SFTPC+ cells were induced from isolated CPM-high progenitor cells on day 21. Briefly, CPM-high progenitor cell aggregates were formed on non-adherent cell culture plates for 2 days, followed by Matrigel-embedded three-dimensional culture for 5 days under the treatment of dexamethasone, 8-Br-cAMP, 3-Isobutyl-1-methylxanthine, KGF, Y27632, CHIR99021, and SB431542 WITHOUT co-culturing human fetal lung fibroblasts.

extract_protocol:
Single cells were captured and separated on the each chamber of medium-sized (10-17 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) .
The first-strand cDNA was synthesized and amplified on the independent chambera using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

treatment_protocol: P2 FD-AO EpCAM+ cells were treated with DMSO or 10 μM XAV-939 from day 2 to 14.

value: FF-AO

tag: cell types

tag: passage

tag: compound


title: P0_FF-AO_EpCAM+ scRNA-seq_83


title: P0_FF-AO_EpCAM+ scRNA-seq_87


title: P0_FF-AO_EpCAM+ scRNA-seq_85


title: P0_FF-AO_EpCAM+ scRNA-seq_92


title: P0_FF-AO_EpCAM+ scRNA-seq_86


title: P0_FF-AO_EpCAM+ scRNA-seq_88


title: 2D_EpCAM+ scRNA-seq_7

tag: cell type


title: P0_FF-AO_EpCAM+ scRNA-seq_91


title: P0_FF-AO_EpCAM+ scRNA-seq_82


title: P0_FF-AO_EpCAM+ scRNA-seq_80


title: P0_FF-AO_EpCAM+ scRNA-seq_84


title: P0_FF-AO_EpCAM+ scRNA-seq_79


title: P0_FF-AO_EpCAM+ scRNA-seq_74


title: P0_FF-AO_EpCAM+ scRNA-seq_77


title: P0_FF-AO_EpCAM+ scRNA-seq_75


title: 2D_EpCAM+ scRNA-seq_5


title: P0_FF-AO_EpCAM+ scRNA-seq_73


title: P0_FF-AO_EpCAM+ scRNA-seq_72


title: Ak19


title: P0_FF-AO_EpCAM+ scRNA-seq_89


title: P0_FF-AO_EpCAM+ scRNA-seq_81


title: P0_FF-AO_EpCAM+ scRNA-seq_70


title: P0_FF-AO_EpCAM+ scRNA-seq_68


title: P0_FF-AO_EpCAM+ scRNA-seq_71


title: P0_FF-AO_EpCAM+ scRNA-seq_66


title: P0_FF-AO_EpCAM+ scRNA-seq_63


title: P0_FF-AO_EpCAM+ scRNA-seq_65


title: P0_FF-AO_EpCAM+ scRNA-seq_76


title: P0_FF-AO_EpCAM+ scRNA-seq_62


title: P0_FF-AO_EpCAM+ scRNA-seq_60


title: P0_FF-AO_EpCAM+ scRNA-seq_59


title: P0_FF-AO_EpCAM+ scRNA-seq_58


title: P0_FF-AO_EpCAM+ scRNA-seq_64


title: P0_FF-AO_EpCAM+ scRNA-seq_61


title: P0_FF-AO_EpCAM+ scRNA-seq_55


title: P0_FF-AO_EpCAM+ scRNA-seq_57


title: P0_FF-AO_EpCAM+ scRNA-seq_54


title: P0_FF-AO_EpCAM+ scRNA-seq_53


title: P0_FF-AO_EpCAM+ scRNA-seq_52


title: P0_FF-AO_EpCAM+ scRNA-seq_50


title: P0_FF-AO_EpCAM+ scRNA-seq_49


title: P0_FF-AO_EpCAM+ scRNA-seq_51


title: P0_FF-AO_EpCAM+ scRNA-seq_67


title: P0_FF-AO_EpCAM+ scRNA-seq_46


title: P0_FF-AO_EpCAM+ scRNA-seq_45


title: P0_FF-AO_EpCAM+ scRNA-seq_44


title: P0_FF-AO_EpCAM+ scRNA-seq_43


title: P0_FF-AO_EpCAM+ scRNA-seq_48


title: P0_FF-AO_EpCAM+ scRNA-seq_47


title: P0_FF-AO_EpCAM+ scRNA-seq_56


title: P0_FF-AO_EpCAM+ scRNA-seq_41


title: P0_FF-AO_EpCAM+ scRNA-seq_39


title: P0_FF-AO_EpCAM+ scRNA-seq_38


title: P0_FF-AO_EpCAM+ scRNA-seq_37


title: P0_FF-AO_EpCAM+ scRNA-seq_34


title: P0_FF-AO_EpCAM+ scRNA-seq_42


title: P0_FF-AO_EpCAM+ scRNA-seq_31


title: P0_FF-AO_EpCAM+ scRNA-seq_32


title: P0_FF-AO_EpCAM+ scRNA-seq_29


title: P0_FF-AO_EpCAM+ scRNA-seq_28


title: P0_FF-AO_EpCAM+ scRNA-seq_30


title: P0_FF-AO_EpCAM+ scRNA-seq_25


title: P0_FF-AO_EpCAM+ scRNA-seq_27


title: P0_FF-AO_EpCAM+ scRNA-seq_26


title: P0_FF-AO_EpCAM+ scRNA-seq_36


title: P0_FF-AO_EpCAM+ scRNA-seq_20


title: P0_FF-AO_EpCAM+ scRNA-seq_21


title: P0_FF-AO_EpCAM+ scRNA-seq_40


title: P0_FF-AO_EpCAM+ scRNA-seq_24


title: P0_FF-AO_EpCAM+ scRNA-seq_22


title: P0_FF-AO_EpCAM+ scRNA-seq_23


title: P0_FF-AO_EpCAM+ scRNA-seq_35


title: P0_FF-AO_EpCAM+ scRNA-seq_19


title: P0_FF-AO_EpCAM+ scRNA-seq_15


title: P0_FF-AO_EpCAM+ scRNA-seq_16


title: P0_FF-AO_EpCAM+ scRNA-seq_14


title: P0_FF-AO_EpCAM+ scRNA-seq_33


title: P0_FF-AO_EpCAM+ scRNA-seq_12


title: P0_FF-AO_EpCAM+ scRNA-seq_13


title: P0_FF-AO_EpCAM+ scRNA-seq_69


title: P0_FF-AO_EpCAM+ scRNA-seq_17


title: P0_FF-AO_EpCAM+ scRNA-seq_11


title: P0_FF-AO_EpCAM+ scRNA-seq_7


title: P0_FF-AO_EpCAM+ scRNA-seq_8


title: P0_FF-AO_EpCAM+ scRNA-seq_6


title: P0_FF-AO_EpCAM+ scRNA-seq_3


title: P0_FF-AO_EpCAM+ scRNA-seq_4


title: P0_FF-AO_EpCAM+ scRNA-seq_9


title: P0_FF-AO_EpCAM+ scRNA-seq_5


title: P0_FF-AO_EpCAM+ scRNA-seq_2


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_90

description: Single  " P2_FD-AO_XAV-939_EpCAM+" cells were captured and separated on the each chamber of medium-sized (10-17 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) Then, first-strand cDNA was synthesized and amplified on the independent chamber using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

value: FD-AO


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_85


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_88


title: P0_FF-AO_EpCAM+ scRNA-seq_1


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_89


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_84


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_86


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_87


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_83


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_81


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_82


title: P0_FF-AO_EpCAM+ scRNA-seq_10


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_78


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_79


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_76


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_73


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_72


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_75


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_77


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_80


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_70


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_71


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_74


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_68


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_67


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_66


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_64


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_62


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_65


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_61


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_63


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_59


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_60


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_58


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_57


title: 2D_EpCAM+ scRNA-seq_31


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_55


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_54


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_51


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_53


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_52


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_50


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_49


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_69


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_48


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_45


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_46


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_44


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_43


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_47


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_41


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_42


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_39


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_40


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_37


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_38


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_36


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_34


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_56


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_32


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_33


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_30


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_29


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_27


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_28


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_24


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_25


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_26


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_23


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_17


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_21


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_22


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_19


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_18


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_35


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_20


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_16


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_12


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_14


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_11


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_13


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_15


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_10


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_9


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_8


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_31


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_7


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_6


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_4


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_5


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_1


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_2


title: P2_FD-AO_XAV-939_EpCAM+ scRNA-seq_3


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_90

description: Single " P2_FD-AO_DMSO_EpCAM+" cells were captured and separated on the each chamber of medium-sized (10-17 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) Then, first-strand cDNA was synthesized and amplified on the independent chamber using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.

value: DMSO


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_89


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_91


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_88


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_87


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_86


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_85


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_84


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_82


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_83


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_76


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_79


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_75


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_80


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_78


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_77


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_74


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_72


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_71


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_73


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_70


title: 2D_EpCAM+ scRNA-seq_13


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_68


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_69


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_64


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_62


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_61


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_63


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_81


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_60


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_58


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_57


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_56


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_55


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_53


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_49


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_50


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_54


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_51


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_48


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_45


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_47


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_44


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_42


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_66


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_41


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_43


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_67


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_65


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_39


title: P0_FF-AO_EpCAM+ scRNA-seq_18


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_38


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_40


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_37


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_59


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_36


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_35


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_34


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_33


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_52


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_32


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_31


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_28


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_30


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_29


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_27


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_26


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_25


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_22


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_23


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_24


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_21


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_19


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_18


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_17


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_20


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_16


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_13


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_12


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_14


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_11


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_10


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_9


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_5


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_3


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_1


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_2


title: P2_FD-AO_EpCAM+ scRNA-seq_91

description: Single " P2_FD-AO EpCAM+" cells were captured and separated on the each chamber of medium-sized (10-17 µm) C1 integrated fluidic circuit (IFC) with the C1 system (Fluidgm) Then, first-strand cDNA was synthesized and amplified on the independent chamber using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing.


title: P2_FD-AO_EpCAM+ scRNA-seq_92


title: P2_FD-AO_EpCAM+ scRNA-seq_89


title: P2_FD-AO_EpCAM+ scRNA-seq_88


title: P2_FD-AO_EpCAM+ scRNA-seq_87


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_46


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_15


title: P2_FD-AO_EpCAM+ scRNA-seq_86


title: P2_FD-AO_EpCAM+ scRNA-seq_84


title: P2_FD-AO_EpCAM+ scRNA-seq_83


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_8


title: P2_FD-AO_EpCAM+ scRNA-seq_82


title: P2_FD-AO_EpCAM+ scRNA-seq_81


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_7


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_4


title: P2_FD-AO_DMSO_EpCAM+ scRNA-seq_6


title: Pt2_2

type: protein

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

institute: Fondo Edo Tempia

hyb_protocol: Hybridization was performed at Somalogic

scan_protocol: Agilent scanner for microarrays

data_processing: Sample data is  rst normalized to remove hybridization variation within a run followed by median normalization across all samples to remove other assay biases within the run and finally calibrated to remove assay differences between runs.

molecule: protein

source_name: Fibroblast

label_protocol: Labeling was performed at Somalogic

growth_protocol: Cells were grown at 37 °C with 5% CO2 in Dulbecco’s modified Eagle’s medium, containing 10% FBS, 4.5 g/L glucose and 1% antibiotics/antimycotics; primary cells from humans were grown at 37 °C with 5% CO2 in Dulbecco’s modified Eagle’s medium, containing 10% FBS, 4.5 g/L glucose and 1% antibiotics/antimycotics.

extract_protocol: All samples (fibroblasts and cell models) were washed twice with PBS 1X and then homogenized in M-PER™ Mammalian Protein Extraction Reagent (Thermo Scientific, Rodano (MI), Italy) containing inhibitors of proteases (Roche Diagnostics, Monza (MB), Italy), following the manufacturer’s standard protocol.

treatment_protocol: Cell lines were treated with CRISPR/Cas9 gene editing to produce clones harboring a loss-of function mutation in SACS; both cell lines and primary fibroblasts were treated with 20 μM carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone (FCCP) for 2 hours to induce mitochondrial damage and fragmentation.

tag: individual

value: primary fibroblasts

tag: treatment

tag: mutation in sacs


title: Ctrl2_1

value: WT


title: SH-SY5Y WT+FCCP_2

source_name: SH-SY5Y WT

tag: cell line

value: FCCP


title: Ctrl1_2


title: P2_FD-AO_EpCAM+ scRNA-seq_90


title: P2_FD-AO_EpCAM+ scRNA-seq_80


title: SH-SY5Y SACS KO+FCCP_1

source_name: SH-SY5Y SACS KO

value: KO


title: SH-SY5Y SACS KO_2


title: Ctrl3_2


title: P2_FD-AO_EpCAM+ scRNA-seq_78


title: P2_FD-AO_EpCAM+ scRNA-seq_79


title: P2_FD-AO_EpCAM+ scRNA-seq_76


title: SH-SY5Y WT_2


title: P2_FD-AO_EpCAM+ scRNA-seq_85


title: P2_FD-AO_EpCAM+ scRNA-seq_75


title: SH-SY5Y SACS KO+FCCP_3


title: P0_FF-AO_EpCAM+ scRNA-seq_78


title: P2_FD-AO_EpCAM+ scRNA-seq_74