title: Tubes_DMSO_GFP_2

value: Differentiated myotubes

value: GFP


title: Tubes_Hyp_DMSO_None_1

status: Public on May 27 2020

type: SRA

city: Boston

first: Eran

last: Mick

state: MA

address: 185 Cambridge st

department: Molecular Biology

country: USA

institute: Massachusetts General Hospital

library_source: transcriptomic

data_processing:
Basecalling and demultiplexing was performed using bcl2fastq (v. 2.20.0.422)
Transcript quantification was performed using kallisto (v. 0.44) against Ensembl v. 93 transcript annotations.
Transcript-level abundance estimates were aggregated to the gene level and combined across 2 sequencing runs using tximport (v. 1.10.1) in R.
Genome_build: mm10
Supplementary_files_format_and_content: Gene level counts in each sample obtained as described above and not normalized. Mouse genes are listed by Ensembl gene ID and overexpressed transgenes are listed by name

molecule: polyA RNA

organism: Mus musculus

source_name: C2C12 cells

growth_protocol: C2C12 cells were cultured in T175 flasks in DMEM containing 10mM glucose, 4mM glutamine and no sodium pyruvate. Cells were seeded for experiments in 24-well plates. 1. Myoblast media was supplemented to 10% dialyzed fetal bovine serum when cells were not intended for differentiation. Expression of transgenes (Luciferase control, LbNOX, mitoLbNOX or NDI1) was induced by addition of 300ng/ml doxycycline 24 hours prior to the start of treatment. 2. Myoblast media was supplemented to 20% dialyzed fetal bovine serum when cells were intended for differentiation. Differentiation was induced after cells became confluent by switching to media supplemented to 2% dialyzed horse serum. Cells were considered largely post-mitotic 24 hours after the switch to low serum media. If protein expression was required, the cells were transduced with adenovirus expressing GFP, LbNOX or mitoLbNOX 48 hours after the switch to low serum media. Cells were considered differentiated myotubes 4 days after the switch to low serum media.

extract_protocol:
Cells were lysed in buffer RLT and RNA isolated with the Qiagen RNeasy kit
Smart-seq2; polyA selected

treatment_protocol: Treatments with mitochondrial inhibitors lasted for 10 hours, except chloramphenicol treatment which extended to 48 hours.

tag: cell line

value: C2C12 cells

tag: cell state

tag: protein expression

tag: treatment


title: Tubes_Oligo_GFP_1

value: Oligomycin


title: Tubes_Oligo_Pier_None_2


title: Tubes_Oligo_BAM15_None_1


title: T81_Pre

city: New York

first: Yongchao

last: Ge

state: NY

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Small RNA-seq reads were processed using the exceRpt pipeline (Rozowsky et al., 2019), as recommended by the ERC Consortium (https://exrna.org). The pipeline initially trims the reads using FASTX-Toolkit to remove remnants of the 3′-adapter sequence followed by removal of the reads of low-quality and homopolymer repeats, and subsequently aligns the trimmed reads to NCBI’s Univec database to filter out contaminants. The good reads were mapped to rRNA, and then to the human genome and transcriptome to obtain the counts of different gencode and RNA transcripts including miRNA and tRNA. The order of annotations is as follows: miRNAs (miRBase v21), tRNAs, piRNAs, gencode transcripts (hg38 Gencode v24; snRNAs, snoRNAs, miscRNAs, protein coding mRNAs, and lncRNAs), and circular RNAs. Mapping of the reads to the NCBI’s Univec database or rRNA or human genome/transcriptome was performed using STAR 2.4.2a (Dobin et al., 2013).
The pipeline does not include miRNA entries that have zero  reads.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited file including the counts of reads for all miRNA genes and for all samples

molecule: total RNA

organism: Homo sapiens

source_name: Plasma-derived exosomes

growth_protocol: Study participants performed an acute bout of aerobic exercise on a cycle ergometer as previously described (Distefano et al., 2018). Following a 6-min warm-up, participants cycled for 40 min at ~70% heart rate reserve, which was calculated during the maximum aerobic capacity test. Blood was drawn immediately after exercise (Post), and after 3 h of recovery (3h Post) via direct venipuncture using a 21-gauge butterfly needle, and blood samples were collected into K2-EDTA tubes PAXgene blood tubes (Becton-Dickson, Catalog #366643).

extract_protocol:
For exosomal RNA isolation, 700 µl of Qiazol (Qiagen, Germantown, MD, USA) were added to 50 µl of exosome preparation, and the mixture was incubated for 5 min at room temperature. After the addition of 140 µl of chloroform, the mixture was vortexed for 10 sec and incubated for 3 min at room temperature. After the upper aqueous phase was transferred to a fresh tube, a two-fold volume of absolute ethanol (Sigma-Aldrich, St. Louis, US) was added, and the mixture was vortexed briefly. Samples were then transferred to RNeasy mini spin columns (Qiagen) that were centrifuged at 10,000 x g for 30 sec at 4ºC, and flow-through was discarded. An 80-µl volume of DNase incubation mix was added directly onto the column membrane and samples were incubated for 15 min at room temperature. Following wash steps with RWT buffer, RPE buffer (Qiagen), and 85% ethanol, RNA pellets were dried by centrifugation at 10,000 x g for 1 min, and eluted in 15 µl of water.
Small RNA libraries were prepared from exosome-derived RNA using the NEB Next Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA, USA), according to the manufacturer’s instructions. Briefly, RNA-Seq libraries were constructed using 2 ng of exosomal RNA and 15 cycles of PCR amplification. Libraries were run on a 6% TBE gel for 60 min at 120 V, and bands between 140 to 160 bp were excised from the gel using a razor blade. Gel pieces were crushed into smaller pieces and incubated in water overnight on a rotator. Libraries were isolated using gel filtration columns. Following ethanol precipitation, the resulting pellets were each resuspended in 11 µl of ultrapure water. All libraries were analyzed on an Agilent 2100 Bioanalyzer using the Agilent High Sensitivity DNA kit.
Small RNA-Seq; for sequencing, libraries were pooled at equimolar concentrations, mixed with 5% PhiX (Illumina, San Diego, CA, USA), and single-end sequencing was performed on an Illumina MiSeq platform following the manufacturer’s recommendations.

treatment_protocol: Plasma was defrosted on ice and centrifuged at 3,200 x g for 15 min at 4ºC to remove particulate matter. Pre-cleared plasma (250 µl) was then mixed with an equal volume of thromboplastin D and incubated for 15 min at 37ºC. Supernatants were collected following centrifugation at 3,000 x g for 10 min at 4ºC, mixed with 100 µl of ExoQuick (System Biosciences Palo Alto, CA, USA) and 6.25 µl of RNAse (1 mg/ml), and incubated overnight at 4ºC. Exosomes were spun down at 1,500 x g for 25 min at 4ºC. Supernatants were then gently removed, and exosome pellets were resuspended in 50 µl of PBS with 1.25 µl of RNAse inhibitor (ThermoFisher Scientific, Waltham, MA, USA) and stored at -20ºC.

tag: tissue

value: Blood

tag: tissue component

value: Plasma

tag: source type

value: Nanosized extracellular vesicles

tag: subject group

value: Trained

tag: subject id

tag: time

value: Pre


title: T81_3hPost


title: Monosomy_10 16757

city: Manhattan

first: Tenzin

middle: C

last: Lhakhang

address: 550 First Avenue

institute: NYU School of Medicine

data_processing:
Alignment: Sequencing reads were aligned against the hg19 ensemble reference transcriptome using the STAR/2.5 aligner
Gene counting: Gene counting for each sample was performed using featureCounts/1.5.3.
Differential gene expression between euploid and aneuploid, euploid and mosaic, and aneuploid and mosaic embryos was calculated using DES-seq2/3.5 (R Bioconductor Package).
Pathway analysis: EnrichR was used to perform pathway enrichment analysis on the 60 most DEGs across all mosaic embryos compared to normal embryos.
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing normalized counts from DESeq2

source_name: Blastocyst Cells

growth_protocol: Cryopreserved human embryos which had undergone trophectoderm biopsy followed by PGT-A with NGS which had been donated for research were considered for the study.

extract_protocol:
Amplified complementary DNA from the samples was created using the SMATer v4 Ultra Low Kit with 12 polymerase chain reaction (PCR) cycles (Clontech, cat #634890).
RNA-seq library preparation was performed using the Low Input Library Prep (Clontech, cat #6348900) followed by amplification of the library with 5 PCR cycles.
RNA-seq: Sequencing on the Illumina HiSeq 2500 with 50 nucleotide length paired end reads was then performed.

treatment_protocol: Selected embryos were first thawed using standard protocols (Irving Scientific Vit Kit®-Thaw, Santa Anna, CA), washed three times in 50 uL of phosphate-buffered saline (PBS), and then placed into individual microcentrifuge tubes with 9.5 uL of PBS. Tubes were immediately frozen at -23 degrees Celsius and then transported on ice for processing with RNA-seq.

tag: sample type

value: Monosomy


title: T81_Post

value: Post


title: Sample_204P8

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

data_processing:
Tophat was used to align the sequence to the  mouse genome mm10
samtools was used to sort the bam files
samtools was used to convert bam files to sam files
HTSeq was used to count the read number of genes
Filtered out genes with reads count less than 10 in all the samples
DESeq was used to normalize the data and to the Variance Stabilizing Transformation
Genome_build: mm10
Supplementary_files_format_and_content: tex file were generated containing reads count

source_name: pancreatic cd8+ cells

extract_protocol: Rneasy Plus Micro kit following the protocol provided, https://www.qiagen.com/it/resources/resourcedetail?id=59b921cd-b65f-42d5-9a0b-1da673d7c01b&lang=en

tag: cell type

value: pancreatic cd8+ cells

tag: age

value: 20 weeks after birth

value: KC pancreas


title: T53_3hPost


title: T53_Post


title: Monosomy_1 16756


title: +FSL0260_con_rep3

type: RNA

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

description: with FSL0260

hyb_protocol: 600 ng of cRNAs was hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2539A ver. C and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: RMA normalization was performed for signals of microarray probes using limma package on R program.

organism: Arabidopsis thaliana

label_protocol: 200 ng of each RNA sample was used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: four-day-old wild-type plants (Arabidopsis thaliana ecotype Columbia) were grown on 1/2 MS, 0.1 % Agar medium.

extract_protocol: Total RNA was extracted from whole plants using RNeasy Plant Mini Kit  (QIAGEN).

treatment_protocol: The plants were treated 20 uM FSL0260 for 24 hours.

value: whole plant

tag: condition

value: unstress condition


title: Euploid 18

description: Euploid

value: Euploid


title: Monosomy_1 16782


title: Blasts_Oligo_Lb_2

value: Proliferating myoblasts

value: LbNOX


title: -FSL0260_con_rep2

description: without FSL0260


title: -FSL0260_con_rep1

description: without FSL0260


title: +FSL0260_con_rep2

description: with FSL0260


title: T34_3hPost


title: T34_Pre


title: -FSL0260_con_rep3

description: without FSL0260


title: T53_Pre


title: Blasts_CAP_Lb_1

value: C2C12 cells

value: Chloramphenicol


title: T13_3hPost

value: Blood


title: T34_Post

value: Plasma


title: T13_Post

value: Nanosized extracellular vesicles


title: Blasts_Pier_NDI1_2

value: Piericidin


title: Blasts_DMSO_mLb_3

value: mitoLbNOX

value: DMSO


title: Blasts_DMSO_mLb_1


title: T12_3hPost

value: Trained


title: T12_Pre

value: Pre


title: Euploid 17

description: Euploid


title: 24hr_HS_Oligo_None_1

value: 24hrs in differentiation media

value: Oligomycin


title: S76_3hPost

value: Sedentary


title: S80_Post

value: Post


title: Tubes_DMSO_Lb_1

value: Differentiated myotubes


title: Tubes_Oligo_Pier_None_3


title: Mutant DNAJC6 hMLO DIV 15

city: Seoul

first: wahyu

last: handoko

address: 222 Wangsimni-ro, Seongdong-gu, Seoul

department: Department of Biochemistry and Molecular Biology

country: South Korea

institute: Hanyang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: H9 hESC-derived Midbrain Organoid

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

value: H9 hESC-derived Midbrain Organoid

tag: timepoint

value: DIV 15

tag: genotype

value: Mutant DNAJC6


title: +FSL0260_con_rep1

description: with FSL0260

value: whole plant

value: unstress condition


title: T13_Pre

value: Blood

value: Plasma


title: Wildtype hMLO DIV 30

value: DIV 30

value: wild type


title: Wildtype hMLO DIV 15


title: T12_Post

value: Nanosized extracellular vesicles


title: S80_Pre


title: S60_Post


title: S73_Post


title: S73_Pre


title: S60_Pre


title: Mutant DNAJC6 hMLO DIV 4

value: DIV 4


title: S73_3hPost


title: S60_3hPost


title: S21_3hPost


title: S76_Post


title: Tubes_Oligo_BAM15_None_2

value: C2C12 cells


title: S21_Post


title: Tubes_Pier_Lb_3

value: LbNOX

value: Piericidin


title: S76_Pre

value: Sedentary

value: Pre


title: Wildtype hMLO DIV 4


title: Blasts_CAP_Luc_1

value: Proliferating myoblasts

value: Luciferase

value: Chloramphenicol


title: Mutant DNAJC6 hMLO DIV 0

value: H9 hESC

value: DIV 0

value: Mutant DNAJC6


title: Blasts_Oligo_Luc_2

value: Oligomycin


title: Wildtype hMLO DIV 0


title: S21_Pre

value: Blood

value: Plasma


title: Blasts_Anti_Luc_2

value: Antimycin


title: Blasts_CAP_Luc_2


title: Blasts_Pier_mLb_2

value: mitoLbNOX


title: KR-067_RN

city: Seongnam-si

first: Je-Gun

last: Joung

address: 335, Pangyo-ro, Bundang-gu

institute: CHA University

description: Replacement

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
The reads from the FASTQ files were mapped against the hg19 human reference genome using TopHat.
Raw read counts mapped onto genes were measured with the BAM format file by HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file include raw read count values for samples

source_name: RNA

extract_protocol:
Isolated total RNA (2 μg) was used in a reverse transcription reaction with poly (dT) primers using the SuperScriptTM II reverse transcriptase (Invitrogen/Life Technologies, Grand Island, NY, USA) according to the manufacturer’s protocols.
A RNA sequencing library was prepared through cDNA amplification, end-repair, adenylate 3’ends, adapter ligation, and amplification. The quality and quantity of the library were measured with a Bioanalyzer and Qubit.

tag: Sex

value: Male

value: Normal

tag: disease

value: Colorectal cancer liver metastases (CRCLM)

value: tissue

value: naive


title: NSTEMI_10

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

data_processing:
We used XSQTools (Applied Biosystems) with default parameters to remove reads with low quality base values and to generate .csfasta and .QV.qual files for each samples.
Using TopHat v2.0.11 with Bowtie 1 to handle colour space reads, we mapped all reads to the human genome version HG38/GRCh38.76 downloaded from the Ensembl database. We excluded 'haplotypes' and 'patches' sequences from the reference, in order to focus on primary assembly and to avoid under-estimation of gene expression.
We implemented the reference annotation based transcript (RABT) procedure, using Cufflinks suite v2.1.1 to create a new assembly for downstream analysis, integrating the information about known genes and transcripts position in the genome (Ensemble GTF release 76) with those reads mapped in intergenic or intronic regions.
We estimated genes and transcripts expression levels by Cuffquant (using default parameters, apart from -multi-read-correct -frag-bias-correct 'reference.fasta' and -mux-bundle-frags 100000000) and then Cuffnorm (with default parameters, apart from -total-hits-norm).
For each feature we computed both reads counts and fragments per kilobase of transcript per million fragments mapped (FPKM) values. Genes with a FPKM value ≥ 0.046 in at least 60% of samples were considered expressed. This threshold was obtained correlating RNA-Seq data with those from a qPCR gene expression array in preliminary experiments.
Genome_build: HG38/GRCh38.76
Supplementary_files_format_and_content: Tab-delimited text files include raw counts or FPKM values for each Sample. The header of the files reports gene name, Ensemble gene ID, chromosome location, gene length, biotype, biotype class and sample identifiers.
Supplementary_files_format_and_content: txt file containing raw expression measurements
Supplementary_files_format_and_content: txt file containing expression measurements expressed as fragments per kilobase of transcript per million fragments mapped (FPKM) values
Supplementary_files_format_and_content: txt file containing expression measurements as filtered and normalized counts

source_name: Peripheral blood

growth_protocol: Blood samples were collected and mantained into Tempus Blood RNA tubes until processing following manufacturer's instructions.

extract_protocol:
Total RNA was isolated using the Tempus Spin RNA Isolation Kit (Applied Biosystems) and was treated with RNase-free DNase-I to eliminate genomic contamination, following the manufacturer’s instructions.
Five µg of total RNA were precipitated, α- and β-globin mRNAs were depleted with GLOBINclear Whole Blood Globin Reduction kit (Applied Biosystems), and poly(A)+ RNA was enriched following MicroPoly(A) Purist kit protocol (Applied Biosystems). Libraries were prepared and pooled together using the multiplex SOLiD System Sequencing and Barcoding kits. Complementary DNA (cDNA) amplification reaction was conducted with 20 µL template in 100 µl end-volume reaction and with 16 PCR cycles. Clonally amplification of library templates was performed on SOLiD p1 DNA beads by emulsion PCR (ePCR) using 0.5 pM library template and E120 EZbeads scale.

value: Whole blood

tag: age (years)

tag: country of origin

value: Italy


title: NSTEMI_12

value: Female


title: Tubes_BAM15_None_1

tag: cell line

value: C2C12 cells

tag: cell state

value: Differentiated myotubes

tag: protein expression

tag: treatment


title: NSTEMI_11

tag: tissue


title: KR-066_RT

description: Replacement

value: Tumor


title: KR-065_DN

description: Desmoplastic


title: Blasts_DMSO_Lb_1

value: Proliferating myoblasts

value: LbNOX

value: DMSO


title: Blasts_DMSO_Lb_3


title: 24hr_HS_Pier_None_1

value: 24hrs in differentiation media

value: Piericidin


title: High.MLE [L93]

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

data_processing:
50 bp paired-end reads were aligned to the Drosophila melanogaster reference genome (release 6) using STAR aligner (version 2.5.3a) with providing GTF annotation (dmel-all-r6.17.gtf). Reads with multiple alignments were filtered by setting outFilterMultimapNmax parameter to 1.
BAM files were converted to normalized bedgraph coverages using genomeCoverageBed command (bedtools version 2.27.1) with -scale parameter set to divide by the total number of reads and multiplied by a million.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: Bedgraph: RNA-seq profiles normalized to the total number of reads.

organism: Drosophila melanogaster

extract_protocol:
vitRIP was performed with highly purified recombinant protein and 2 µg of total RNA, extracted from Drosophila cell lines or Drosophila heads. Two microgram of total RNA (10% was kept as RNA input) was incubated with purified recombinant protein for 30 minutes at 25°C in a total volume of 100 µl in vitRIP-100 buffer (25 mM HEPES-NaOH pH 7.6, 100 mM NaCl, 0.05% NP40, 3 mM MgCl2) supplemented with 10 µg BSA, 0.1 U/µl RNase-free recombinant DNase I and 0.8 U/µl RNasin recombinant RNase inhibitor with or without 1 mM ATP. Protein-RNA complexes were retrieved in 45 minutes at room temperature (22°C) on a rotating wheel using anti-FLAG, anti-MLE and anti-MSL1 antibodies, respectively. Following three washing steps, RNA was extracted using Proteinase K, phenol-chloroform extraction and ethanol precipitation in presence of 20 µg glycogen. Input material (10%) was treated equally. RNA-seq libraries were prepared with 30-40 ng of RNA material. Native RIP of endogenous MLE (eMLE) was essentially performed as described in (Ankush Jagtap et al., 2019) with modifications. For each replicate of specific (anti-MLE) and mock (bead control) RIP, 1 x 10e8 exponentially grown S2 cells were suspended in 1 ml of cold lysis buffer (20 mM HEPES-NaOH pH 7.6, 125 mM NaCl, 0.05 % SDS, 0.25 % sodium deoxycholate, 0.5 % NP40, 1.5 mM MgCl2, 0.25 mM DTT) supplemented with 0.05 U/µl RNase-free recombinant DNase I, 0.4 U/µl RNasin recombinant RNase inhibitor and 1x Complete EDTA-free protease inhibitor. Following incubation for 15 minutes on ice, the lysate was cleared by centrifugation and incubated with mock or specific anti-MLE antibody at 4°C for 2 hours on a rotating wheel. Following three washing steps, RNA was extracted using Proteinase K, phenol-chloroform extraction and ethanol precipitation in presence of 20 µg glycogen. Input material (2.5% of lysate) was treated equally. Of each sample, 40 ng RNA was used to prepare rRNA-depleted RNA-seq libraries.
Ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat; New England Biolabs) and samples were analyzed on a Bioanalyzer using the RNA 6000 Pico Kit (Agilent). Of the rRNA-depleted samples directional libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the recommended protocol. The quality of the libraries was assessed on a Bioanalyzer using the DNA 1000 or DNA High Sensitivity Kit (Agilent). Libraries were sequenced on an Illumina HiSeq1500 instrument in paired-end mode.

tag: purified protein

value: MLE:50 nM

tag: antibody

value: anti-MLE

value: IP


title: KR-032_RN

description: Replacement

value: Male

value: Normal

value: Colorectal cancer liver metastases (CRCLM)


title: NSTEMI_8

value: Whole blood


title: High.MLE_+DCCcore [L94]

value: MLE:50 nM; DCCcore (dimer):20 nM

tag: sample type


title: Low.MLE_+DCCcore [L92]

value: MLE:10 nM; DCCcore (dimer):20 nM


title: Tubes_DMSO_GFP_1

value: C2C12 cells

value: GFP


title: KR-031_RT

description: Replacement

value: Tumor

value: tissue

value: naive


title: Tubes_Pier_Lb_2

value: Differentiated myotubes

value: LbNOX


title: Input [L90]

value: Input


title: Tubes_Oligo_BAM15_None_3


title: KR-028_DN

description: Desmoplastic


title: High.MLE_+DCCcore [L85]


title: Tubes_BAM15_None_2


title: KR-026_DN

description: Desmoplastic


title: High.MLE [L84]

value: MLE:50 nM


title: KR-064_DT

description: Desmoplastic


title: KR-025_DT

description: Desmoplastic


title: Tubes_Oligo_None_1

value: Oligomycin


title: Blasts_DMSO48_Lb_2

value: Proliferating myoblasts


title: STEMI_15

value: Female

value: Italy


title: Low.MLE_MLE.IP [L91]

value: MLE:10 nM

value: anti-MLE

value: IP


title: Euploid 16

description: Euploid

value: Euploid


title: STEMI_14

value: Whole blood


title: Blasts_Oligo_Lb_1

value: C2C12 cells


title: Low.MLE_MLE.IP [L82]


title: Blasts_Pier_Lb_2

value: Piericidin


title: High.MLE.OrR.F [L73]

source_name: OrR

value: OrR

value: anti-FLAG


title: KR-019_RT

description: Replacement

value: Tumor

value: Colorectal cancer liver metastases (CRCLM)

value: tissue

value: naive


title: KR-020_RN

description: Replacement

value: Normal


title: Low.MLE_+DCCcore [L83]

value: MLE:10 nM; DCCcore (dimer):20 nM


title: Input [L81]

value: Input


title: KR-022_RN

description: Replacement

value: Female


title: KR-021_RT

description: Replacement


title: High.MLE.OrR.M [L75]

value: MLE:50 nM


title: KR-018_DN

description: Desmoplastic


title: Blasts_Anti_mLb_1

value: Proliferating myoblasts

value: mitoLbNOX

value: Antimycin


title: Blasts_Anti_Lb_2

value: LbNOX


title: OrR.F [L71]


title: KR-027_DT

description: Desmoplastic

value: Male


title: Blasts_DMSO_Luc_3

value: C2C12 cells

value: Luciferase

value: DMSO


title: KR-017_DT

description: Desmoplastic

value: Tumor


title: KR-016_DN

description: Desmoplastic

value: Colorectal cancer liver metastases (CRCLM)


title: KR-015_DT

description: Desmoplastic

value: tissue


title: Low.MLE_-ATP [L67]

value: MLE:5 nM

value: anti-FLAG

value: IP


title: Med.MLE_+ATP [L70]

value: MLE:20 nM


title: Low.MLE_-ATP [L68]


title: Low.MLE_+ATP [L69]


title: KR-014_RN

description: Replacement

value: Normal

value: naive


title: KR-013_RT

description: Replacement


title: Input [L66]

value: Input


title: KR-011_DT

description: Desmoplastic


title: cl8.High.MLE_+ATP [L65]

value: MLE:50 nM


title: KR-012_DN

description: Desmoplastic


title: OrR.M [L72]

value: OrR


title: cl8.High.MLE_-ATP [L64]


title: cl8.DCCcore+MLE_+ATP [L63]

value: DCCcore (dimer):40 nM; MLE:10 nM


title: KR-010_RN

description: Replacement

value: Female


title: KR-009_RT

description: Replacement


title: cl8.Input [L61]


title: KR-007_DT

description: Desmoplastic


title: KR-008_DN

description: Desmoplastic


title: KR-006_DN

description: Desmoplastic

value: Male


title: Subject:MO; Sample Day: Week 23 with respect to first challenge; Replicate 1

type: protein

city: Irvine

first: Arlo

middle: Zan

last: Randall

state: CA

address: 1 Technology Drive, Suite E309

institute: Antigen Discovery Inc

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MO-23

hyb_protocol: Serum samples were diluted 1:100 in a 3 mg mL-1 E. coli lysate solution in protein arraying buffer (Maine Manufacturing, Sanford, ME, USA) and incubated at room temperature for 30 min. Chips were rehydrated in blocking buffer for 30 min. Blocking buffer was removed, and chips were probed with pre-incubated serum samples using sealed, fitted slide chambers to ensure no cross-contamination of sample between pads. Chips were incubated overnight at 4°C with agitation. Chips were washed five times with TBS-0.05% Tween 20, followed by incubation with biotin-conjugated goat anti-human IgG (Jackson ImmunoResearch, West Grove, PA, USA) diluted 1:200 in blocking buffer at room temperature. Chips were washed three times with TBS-0.05% Tween 20, followed by incubation with streptavidin-conjugated SureLight P-3 (Columbia Biosciences, Frederick, MD, USA) at room temperature protected from light. Chips were washed three times with TBS-0.05% Tween 20, three times with TBS, and once with water. Chips were air dried by centrifugation at 1,000 x g for 4 min and dried overnight in dessicator before scanning.

scan_protocol: Probed microarrays (slides) were scanned using a GenePix 4300A High-Resolution Microarray Scanner (Molecular Devices, Sunnyvale, CA, USA) an image file (.tif) was saved for each array using GenePix Pro 7 software. The scanned image files were quantified using the Mapix software (Innopsys) auto gridding feature. For this process two input files are required: (1) a .gal file that defines the array and sub-array layout and (2) the tiff image file for an array. Once the auto-gridding is complete the overlay of the mapped array, subarray, and individual spot locations are shown in the graphical user interface (GUI). If the automatic gridding fails to map to the correct positions the mapping can be manually adjusted using the GUI. Once the gridding is confirmed to be correct the array spots are quantified and saved to an output .gpr file. For each spot on the slide the gpr file contains the foreground intensity (median of pixels inside of circle defining spot) and local background intensity (median of pixels just outside of circle defining spot).

data_processing: Foreground spot intensities were adjusted by local background by subtraction, and negative values were converted to 1. Data was normalized using the variance stabilization and calibration for microarray data (VSN) package implemented in R. The VSN model was built using only the 192 no-DNA control spot intensities for each sample.

label: biotin

molecule: protein

organism: Macaca mulatta

source_name: serum

label_protocol: Biotin-conjugated goat anti-human IgG (Jackson ImmunoResearch, West Grove, PA, USA)

growth_protocol: The human C. trachomatis serovar D (UW-3/Cx) was obtained from the American Type Culture Collection (ATCC; Manassas, VA) and was grown in HeLa-229 cells. Density gradient-purified elementary bodies (EB) were stored at -80 C in 0.2 M sucrose, 20 mM sodium phosphate (pH 7.4), and 5 mM glutamic acid (SPG).

treatment_protocol: To synchronize the menstrual cycle, one month before infection, all animals were treated intramuscularly with 1 mg of medroxyprogesterone acetate (MPA). Vaginal infection was performed by gently placing the inoculum on the os cervix through a speculum.  One group of six rhesus monkeys received 107 inclusion forming units (IFU) and a second group of six animals received 105 IFU of C. trachomatis serovar D. Three additional monkeys were administered SPG and served as mock-infection controls. Three monkeys from the group infected with 105 IFU and three monkeys from the group infected with 107 IFU underwent scheduled necropsies at 10 weeks post-infection. The remaining nine animals received a second injection of MPA (1 mg) and at 14 weeks from the initial infection 7 of 9 monkeys were inoculated vaginally with 105 IFU of C. trachomatis serovar D. Blood was collected the day before each inoculation and at regular intervals following post-inoculation until the study end-point.

tag: subject identifier

value: MO

tag: treatment group

value: 1st Ct dose:10^5 IFU; 2nd Ct does:10^5 IFU

tag: culture

value: anti-IgG antibody


title: cl8.DCCcore_+ATP [L62]

value: DCCcore (dimer):40 nM


title: Blasts_DMSO_Luc_1

value: C2C12 cells

value: Proliferating myoblasts

value: Luciferase

value: DMSO


title: Subject:MO; Sample Day: Week 18 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MO-18

extract_protocol: Serum samples were diluted 1:100 in a 3 mg mL-1 E. coli lysate solution in protein arraying buffer (Maine Manufacturing, Sanford, ME, USA) and incubated at room temperature for 30 min.


title: Subject:MO; Sample Day: Week 14 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MO-14


title: mock [L60]

value: n.a. (in vivo RIP)

value: anti-MLE

value: IP


title: eMLE [L59]


title: KR-005_DT

description: Desmoplastic

tag: age

value: Tumor

value: Colorectal cancer liver metastases (CRCLM)

value: tissue

value: naive


title: High.MLE_-ATP [L57]

value: MLE:50 nM

value: anti-FLAG


title: High.MLE_+ATP [L56]


title: eInput [L58]

value: Input


title: Med.MLE_+ATP [L55]

value: MLE:20 nM


title: Subject:MO; Sample Day: Week 4 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MO-4

value: MO

value: 1st Ct dose:10^5 IFU; 2nd Ct does:10^5 IFU

value: anti-IgG antibody


title: Subject:MO; Sample Day: Week 8 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MO-8


title: KR-004_DN

description: Desmoplastic

value: Female

value: Normal


title: KR-003_DT

description: Desmoplastic


title: Low.MLE_+ATP [L54]

value: MLE:5 nM


title: mock [L52]

value: n.a. (in vivo RIP)


title: eInput [L50]

value: anti-MLE


title: eMLE [L49]

value: IP


title: Subject:MN; Sample Day: Week 18 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MN-18

value: MN


title: Subject:MO; Sample Day: Week 0 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MO-0


title: Subject:MN; Sample Day: Week 14 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MN-14


title: eMLE [L51]


title: eInput [L48]


title: Subject:MN; Sample Day: Week 0 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MN-0


title: Subject:MN; Sample Day: Week 4 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MN-4


title: Input [L53]


title: Subject:MN; Sample Day: Week 8 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MN-8


title: Subject:MN; Sample Day: Week 23 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MN-23


title: Low.MLE_+ATP [L46]


title: Input [L43]


title: Subject:MM; Sample Day: Week 23 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MM-23

value: MM


title: High.MLE_-ATP [L45]


title: Subject:MM; Sample Day: Week 14 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MM-14


title: Subject:MM; Sample Day: Week 4 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MM-4


title: Subject:MM; Sample Day: Week 8 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MM-8


title: Subject:MM; Sample Day: Week 18 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MM-18


title: cl8.DCCcore+MLE_+ATP [L42]

value: DCCcore (dimer):40 nM; MLE:10 nM


title: Subject:MM; Sample Day: Week 0 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MM-0


title: cl8.DCCcore_+ATP [L41]

value: DCCcore (dimer):40 nM


title: DCCcore+MLE_+ATP [L40]


title: Subject:ML; Sample Day: Week 18 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
ML-18

value: ML

value: 1st Ct dose:10^7 IFU; 2nd Ct does:10^5 IFU


title: cl8.High.MLE_+ATP [L38]

value: MLE:50 nM

value: anti-FLAG


title: Subject:ML; Sample Day: Week 23 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
ML-23


title: cl8.High.MLE_-ATP [L37]


title: DCCcore_+ATP [L39]


title: Mutant DNAJC6 hMLO DIV 30

tag: cell type

value: H9 hESC-derived Midbrain Organoid

tag: timepoint

value: DIV 30

tag: genotype

value: Mutant DNAJC6


title: Subject:ML; Sample Day: Week 14 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
ML-14

value: anti-IgG antibody


title: cl8.Input [L36]

value: Input


title: Subject:ML; Sample Day: Week 4 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
ML-4


title: Subject:ML; Sample Day: Week 8 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
ML-8


title: HCT116_I_2_KO_eCLIP

city: DALLAS

first: David

middle: Reid

last: Corey

state: TX

address: 6001 Forest Park Road

department: Pharmacology

institute: UT-Southwestern Medical Center at Dallas

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, raw sequencing reads were adapter-trimmed and then mapped to hg38/Gencode v27 transcriptome using STAR-2.5.3a. Gene quantification and differential analysis were carried with Salmon (0.11.0) and DeSeq2. CLIPper and in-house scripts were used for eCLIP-seq peak calling and normalization.
Genome_build: hg38

growth_protocol: McCoy’s 5a Medium (GIBCO # 16600) + 10% FBS was used as the growth media for all the cell lines studies.

extract_protocol:
For RNA_seq samples, RNA was harvested using Trizol reagent. Illumina Whole Transcriptome RNA Sample Prep Kit (strand specific) was used with 50 ng-1 ug of total RNA for the construction of library. For the eCLIP-seq, cell cytoplasmic fraction was obtained wtih hypotonic buffer from 10 million cell and used for immunprecipitation or size-matched input samples.
RNA libraries were prepared for sequencing using standard Illumina protocols or eCLIP-seq protocol (Van Nostrand, et. al, Nature Methods, 2016, 13, 508-514)

value: human colon cancer cell line

tag: passages

tag: eclip antibody

tag: molecule subtype

value: eCLIP_size_matched input RNA


title: HCT116_I_1_KO_eCLIP

tag: cell line


title: healthy volunteer 3 - M-IL34

city: NANTES

first: Céline

last: Sérazin

address: 30 bd Jean monnet

country: France

institute: University of Nantes

data_processing:
counts
Genome_build: hg19
Supplementary_files_format_and_content: fastq files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
none provided by the submitter
3'RNA seq

value: macrophages


title: healthy volunteer 3 - M2


title: healthy volunteer 3 - M1


title: healthy volunteer 3 - M-MCSF

source_name: M-MCSF


title: High.MLE_+ATP [L35]

value: IP


title: HCT116_I_2_WT_eCLIP

value: wild type


title: Subject:MK; Sample Day: Week 23 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MK-23

value: MK


title: healthy volunteer 3 - M0

value: monocytes


title: HCT116_A2_1_KO_eCLIP

value: Aint_Ago2_3148 (gift from Jay A. Nelson lab, OHSU)

value: eCLIP_immunoprecipitated RNA


title: High.MLE_-ATP [L34]


title: Input [L33]


title: healthy volunteer 2 - M1


title: healthy volunteer 2 - M2


title: Subject:MK; Sample Day: Week 18 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MK-18

value: 1st Ct dose:10^7 IFU; 2nd Ct does:10^5 IFU


title: DCCcore+HKE_+ATP [L32]

value: DCCcore (dimer):40 nM; MLE-HKE:10 nM


title: Subject:MK; Sample Day: Week 14 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MK-14


title: Subject:ML; Sample Day: Week 0 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
ML-0

value: ML


title: Subject:MK; Sample Day: Week 8 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MK-8


title: HCT116_A2_2_KO_eCLIP


title: healthy volunteer 2 - M-MCSF


title: HCT116_A2_2_WT_eCLIP


title: healthy volunteer 2 - M-IL34


title: HCT116_I_1_WT_eCLIP


title: DCCcore+MLE_+ATP [L30]

value: DCCcore (dimer):40 nM; MLE:10 nM


title: healthy volunteer 2 - M0


title: DCCcore+GET_+ATP [L31]

value: DCCcore (dimer):40 nM; MLE-GET:10 nM


title: HCT116_A2_1_WT_eCLIP


title: DCCcore+MLE_-ATP [L29]


title: Embryos setd2-HO

city: Shanghai

first: Dianjia

last: Liu

address: Room 807, Building 11, 197 Ruijin Er Rd

department: Shanghai Institute of Hematology，State Key Laboratory of Medical Genomics

country: China

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCz11 whole genome using Hisat2 (v2.0.2).
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Mortazavi et al., Nature Methods, 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCz11
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include gene counts and FPKM values for each Sample.
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.

organism: Danio rerio

source_name: Zebrafish Embryos

extract_protocol:
Whole embryos of zebrafish RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using VAHTS mRNA-seq V2 Library Prep Kit for Illumina.

tag: strain

value: Tubingen

value: whole body


title: DCCcore_+ATP [L28]

value: DCCcore (dimer):40 nM


title: Embryos setd2-HE


title: Subject:MK; Sample Day: Week 0 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MK-0

value: anti-IgG antibody


title: healthy volunteer 1 - M1


title: healthy volunteer 1 - M2


title: DCCcore+HKE_+ATP [L27]


title: Embryos wildtype


title: DCCcore+GET_+ATP [L26]


title: Subject:MJ; Sample Day: Week 18 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MJ-18

value: MJ


title: Subject:MK; Sample Day: Week 4 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MK-4


title: Subject:MJ; Sample Day: Week 8 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MJ-8


title: Subject:MJ; Sample Day: Week 14 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MJ-14


title: healthy volunteer 1 - M-MCSF

value: macrophages


title: healthy volunteer 1 - M-IL34


title: Subject:MJ; Sample Day: Week 4 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MJ-4


title: Subject:MJ; Sample Day: Week 0 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MJ-0


title: DCCcore+MLE_+ATP [L25]

value: IP


title: DCCcore+MLE_-ATP [L24]


title: Subject:MJ; Sample Day: Week 23 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MJ-23


title: healthy volunteer 1 - M0


title: Subject:MI; Sample Day: Week 4 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MI-4

value: MI

value: 1st Ct dose:10^5 IFU; 2nd Ct does:none


title: Subject:MI; Sample Day: Week 8 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MI-8


title: Input [L22]

value: Input


title: High.MLE_+ATP [L20]

value: MLE:50 nM

value: anti-FLAG


title: Subject:MI; Sample Day: Week 0 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MI-0


title: DCCcore+MLE_+ATP [L18]


title: Subject:MH; Sample Day: Week 8 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MH-8

value: MH


title: Liver_IRR_9_3

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray hybridization intensity data were filtered to remove undetected and array control probes, before computing log z-score for each sample to identify and exclude possible outlying samples via clustering, scatter plots, and principal components analysis. After removal of the outlying samples, a sample-specific quantile normalization of the filtered raw average signal was employed to yield quantile normalized log scale z-scores. These quantile z-scores were used to ensure a standard normal distribution in further statistical analysis, including ANOVA, t- and z-testing. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a combination of thresholds, including p<value 0.05, 30% false discovery rate (FDR), and average signal intensity of comparison >0. The gene expression change z-ratio values were then used as input to perform Parametric Analysis of Gene Set Enrichment (PAGE) testing. For each gene set change, an aggregate z-score, and p-value with false discovery change was calculated and reported for statistical significance.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: mt-Keima mice were imported from Toren Finkel’s lab  via Jurrien Dean’s lab at National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). Mice were maintained at the National Institute on Aging (NIA), Baltimore on a standard NIH diet in a 12h light/dark cycle. All animal experiments were performed using protocols approved by the appropriate institutional animal care and use committee of the NIA. Both male and female adult mice were included in the experiments.

extract_protocol: RNA was purified with PureLink™RNA isolation kit following manufacturer's protocol (Thermo).

treatment_protocol: Mice were subjected to whole body IR in a Nordion Gamma cell 40 Exactor Irradiator by placing them in a stereotaxic cube box where they were exposed to IR or not (sham). IR (6Gy) was delivered at a rate of 0.74 Gy/min. After exposure, mice were returned to home cages and sacrificed by cervical dislocation 48h after irradiation.

tag: included in analysis

value: Yes

value: Liver

value: mt-keima

tag: treatment

value: IRR

tag: Sex

value: M

value: 9 months

tag: post-treatment survival

value: 48 hrs


title: Liver_IRR_10_3

tag: tissue

value: F


title: Subject:MH; Sample Day: Week 4 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MH-4

tag: subject identifier

tag: sample type

value: anti-IgG antibody


title: Liver_IRR_8_3

value: 8 months


title: Subject:MG; Sample Day: Week 8 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MG-8

value: MG

tag: treatment group

tag: culture


title: Liver_IRR_6_3

tag: age


title: Liver_IRR_7_3


title: DCCcore_+ATP [L16]

tag: purified protein

value: DCCcore (dimer):40 nM

tag: antibody

value: IP


title: OrR.M [L11]

value: OrR

value: Input


title: Input [L15]


title: Liver_CTR_1_3

tag: genotype

value: CTR


title: High.MLE.OrR.F [L14]

value: MLE:50 nM

value: anti-FLAG


title: DCCcore_+ATP [L23]


title: Subject:MG; Sample Day: Week 0 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MG-0

value: 1st Ct dose:10^5 IFU; 2nd Ct does:none


title: High.MLE.OrR.M [L13]


title: Liver_CTR_5_3

value: Yes

value: Liver

value: mt-keima


title: Subject:MH; Sample Day: Week 0 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MH-0

value: MH


title: Subject:MG; Sample Day: Week 4 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MG-4


title: OrR.F [L12]


title: Subject:MF; Sample Day: Week 4 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MF-4

value: MF

value: 1st Ct dose:10^7 IFU; 2nd Ct does:none


title: High.MLE_+ATP [IP1]


title: Liver_CTR_4_3

value: M

value: 48 hrs


title: Liver_CTR_3_1

value: F

value: 9 months


title: Heart_IRR_9_2

value: Heart

value: IRR


title: Liver_CTR_2_1

value: 8 months


title: HCT116_WT_2_RNAseq

value: human colon cancer cell line

tag: passages

value: wild type


title: Subject:MF; Sample Day: Week 0 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MF-0

value: anti-IgG antibody


title: HCT116_WT_1_RNAseq


title: HCT116_A1A2A3_KO_3_RNAseq


title: HCT116_WT-3_RNAseq


title: HCT116_A1A2A3_KO_2_RNAseq


title: Subject:ME; Sample Day: Week 4 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
ME-4

value: ME


title: Heart_IRR_10_2

value: Yes


title: HCT116_A1A2A3_KO_1_RNAseq


title: Ctrl ab + tumor-focused radiation

city: Helsinki

first: Pauliina

last: Kallio

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description: Melanoma tumor treated with control ab + tumor-focused radiation

data_processing:
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
We used the Seurat R package 3.1.1 for quality control, filtering, and analysis of the data
Cells were filtered based on unique feature counts and the percentage of mitochondrial genes
Cells with more than 10-15% of mitochondrial genes were filtered out
The expression matrix was further filtered by removing genes with expression in less than three cells and cells with less than 200 expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered data was combined for CCA and further analysis, and saved as A_combined.Robj

source_name: Mouse melanoma tumor

extract_protocol:
In order to obtain single cell solution, incubated in Hanks' balanced salt solution (HBSS, 14175-053, Gibco) supplemented with 1 mg/mL collagenase type I (LS004196, Worthington), 1 mg/mL collagenase H (11074032001, Roche), 4 mg/mL dispase II (04942078001, Sigma) and 1000 U/mL benzonase (sc-202391, ChemCruz) for 30 min at +37°C with gentle shaking, followed by 15 min incubation with Trypsin-EDTA (25200056, Thermo Fisher Scientific) and red blood cell lysis buffer (ACK Lysing Buffer, A1049201, Gibco) for 10 minutes in RT. Cells were transferred into 0.04% BSA-HBSS for analysis.
Single cells were analyzed using the 10x Chromium Single-Cell 3′RNA-sequencing system (10x Genomics, Pleasanton, CA, USA) with the Reagent Kit v3 as instructed by the manufacturer. Briefly, the cells were first loaded into Chromium Single-Cell Chip v3 (10x Genomics, Pleasanton, CA, USA), followed by generation of Gel beads in EMulsion (GEM) aiming at 10 000 cell captures per sample. This was followed by cDNA purification, amplification (12 cycles), and library construction (sample index PCR 14 cycles) as instructed by the manufacturer.
The sample libraries were sequenced on an Illumina NovaSeq 6000 sequencer using read lengths of 26bp (Read 1), 8bp (i7 Index), 0 bp (i5 Index) and 91bp (Read 2). Chromium single-cell 3’ RNA-sequencing barcodes and read data were demultiplexed and converted to FASTQ files, and aligned reads and gene-cell matrices were generated using Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA, USA). Reads were aligned to mouse reference genome mm10.

treatment_protocol: Mice were treated with indicated treatments.

value: Mouse melanoma tumor

value: 20 weeks


title: Heart_IRR_8_2

value: mt-keima


title: Subject:ME; Sample Day: Week 0 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
ME-0


title: Heart_IRR_7_2


title: Heart_IRR_6_1

value: No


title: Ctrl ab + whole-body radiation

description: Melanoma tumor treated with control ab + whole-body radiation


title: Input [IN1]

value: Input


title: HCT116_A1A2_KO_3_RNAseq


title: Heart_CTR_5_2

value: CTR


title: Subject:MD; Sample Day: Week 8 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MD-8

value: MD

value: 1st Ct dose:10^7 IFU; 2nd Ct does:none


title: Subject:ME; Sample Day: Week 8 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
ME-8


title: Heart_CTR_3_2

value: F

value: 9 months

value: 48 hrs


title: HCT116_A1A2_KO_2_RNAseq


title: Anti-Ang2 no IR

description: Melanoma tumor treated with Ang2 blocking antibodies

value: treated with Ang2 blocking antibodies


title: Subject:MD; Sample Day: Week 4 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MD-4


title: Heart_CTR_4_2

value: Heart

value: M

value: 8 months


title: Subject:MD; Sample Day: Week 0 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MD-0

value: anti-IgG antibody


title: Heart_CTR_2_2

value: Yes


title: Anti-Ang2 + whole-body radiation

description: Melanoma tumor treated with Ang2 blocking antibodies + whole-body radiation

value: Mouse melanoma tumor


title: Control immunoprecipitation, biological rep 3

type: genomic

city: Lexington

first: Sharyn

middle: E

last: Perry

state: KY

address: 1405 Veterans Dr.

department: Plant and Soil Sciences

institute: University of Kentucky

description: nonspecific DNA

hyb_protocol: The UK Microarray core facility performed the hybridization and scan using the Affymetrix hybridization kit

scan_protocol: Affymetrix Scanner 3000 7G

data_processing: Normalization was using quantile in CisGenome

molecule: genomic DNA

label_protocol: Samples (7.5 microgram of DNA) were processed following the Affymetrix protocol to fragment and biotin label

growth_protocol: An embryonic culture was derived from zygotic Arabidopsis embryos that constitutively express AGL15. The test culture also has proABI3:ABI3-c-myc in the abi3-5 mutant background. The culture was grown on MS media supplemented with 10 g L-1 sucrose, 0.5 g L-1 MES and 7 g L-1 agar (pH 5.6-5.7) with kanamycin and/or hygromycin and maintained at 23°C to 24°C with a 23-h-light/1-h-dark regime.

extract_protocol: ChIP was performed as in Wang and Perry, 2013, Plant Physiology 161:1251-1264  using c-myc antibody

treatment_protocol: Tissue was fixed in MC buffer (10 mM potassium phosphate pH 7, 50 mM NaCl, 0.1 M sucrose) with 1% formaldehyde for one hour on ice under vacuum. The reaction was quenched with addition of cold glycine to 0.125 M and incubation on ice continued 10-30 min, after which the tissue was washed with cold MC buffer and flash frozen.

value: IP without antibody

value: embryonic culture tissue

tag: genotype/variation

value: expressing ABI3-10x-cmyc


title: HCT116_A2_KO_3_RNAseq

tag: cell line

value: human colon cancer cell line


title: Subject:MC; Sample Day: Week 23 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MC-23

value: MC

value: 1st Ct dose:0; 2nd Ct does:0


title: Control immunoprecipitation, biological rep 2

description: nonspecific DNA


title: HCT116_A2_KO_2_RNAseq


title: ABI3-myc IP with anti-myc antibody, biological rep 3

description: DNA recovered by co-IP with ABI3-myc

value: IP with c-myc antibody


title: HCT116_A2_KO_1_RNAseq


title: Subject:MC; Sample Day: Week 18 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MC-18


title: Subject:MC; Sample Day: Week 14 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MC-14


title: Heart_CTR_1_2

value: mt-keima

value: CTR


title: Cerebrum_IRR_10

value: IRR

value: F

value: 9 months

value: 48 hrs


title: Cerebrum_IRR_9

value: M


title: Ctrl ab no IR

description: Melanoma tumor without treatment

tag: strain

value: 20 weeks

value: without treatment


title: ABI3-myc IP with anti-myc antibody, biological rep 2

description: DNA recovered by co-IP with ABI3-myc


title: Subject:MC; Sample Day: Week 4 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MC-4

value: anti-IgG antibody


title: Subject:MC; Sample Day: Week 8 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MC-8


title: HCT116_A1_KO_3_RNAseq


title: ABI3-myc IP with anti-myc antibody, biological rep 1

description: DNA recovered by co-IP with ABI3-myc


title: HCT116_A1_KO_2_RNAseq


title: Subject:MC; Sample Day: Week 0 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MC-0


title: Subject:MB; Sample Day: Week 23 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MB-23

value: MB

value: 1st Ct dose:0; 2nd Ct does:10^5 IFU


title: HCT116_A1_KO_1_RNAseq


title: HCT116_A1A2_KO_1_RNAseq


title: DhtrA 10 minutes after treatment with 3mM H2O2 3rd triplicate

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

description:
reverse transcribed from total bacterial RNA
B.anthracis_htrA_vs_WT_Oxidative_Stress_RNA_Seq_CountsTable

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were mapped to the B. anthracis Ames Ancestor reference genome (NC_007530) using Novoalign
The HTSeq software served for quantifying the number of reads mapped to each gene
Analysis of differentially expressed genes under various conditions was performed using the R package DESeq
Genome_build: B. anthracis Ames Ancestor, accession number NC_007530
Supplementary_files_format_and_content: txt files

organism: Bacillus anthracis str. Vollum

source_name: Mutated bacteria

growth_protocol: Overnight starter cultures was used to inoculate a fresh BHI culture. Bacteria were grown from 0.05 OD to 1 OD (3 hours), washed once and resuspended in fresh media with or without 3 mM H2O2.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen), residual DNA was digested using RNase-free DNase (Qiagen).
Libraries were generated using TruSeq RNA Library Prep Kit v2 (Illumina), assessed for correct sizing using a high sensitivity Bioanalyzer DNA chip (Agilent), quantified by qPCR and normalized to 2 nM. Pooling and clustering of libraries were  performed using the Illumina cBot system; 150-bp paired-end sequencing was performed on the Illumina Genome Analyzer IIx system with TruSeq SBS kit v2 reagents.

treatment_protocol: One ml of all cultures was collected 10 minutes after treatment with H2O2 and used to prepare RNA.

value: pXO1-; pXO2-

value: DhtrA

value: after H2O2 treatment


title: Cerebrum_CTR_5

tag: included in analysis

value: Yes


title: Cerebrum_IRR_8

tag: treatment

value: 8 months


title: Cerebrum_IRR_7

value: mt-keima

tag: Sex


title: Subject:MB; Sample Day: Week 18 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MB-18


title: Cerebrum_IRR_6

tag: post-treatment survival


title: DhtrA 10 minutes after treatment with 3mM H2O2 2nd triplicate


title: Cerebrum_CTR_4

tag: tissue

value: CTR


title: DhtrA 10 minutes after treatment with 3mM H2O2 1st triplicate


title: DhtrA mutant in the absence of H2O2 2nd duplicate

value: no H2O2 treatment


title: Subject:MB; Sample Day: Week 8 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MB-8

tag: subject identifier


title: Subject:MB; Sample Day: Week 4 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MB-4

tag: sample type


title: DhtrA mutant in the absence of H2O2 1st duplicate


title: Subject:MB; Sample Day: Week 14 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MB-14

tag: treatment group


city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

description:
Legionella pneumophila ∆lpr10 + plpr10 grown to post-exponential phase, biological replicate 3
comp_3

hyb_protocol: Hybridization protocol was performed as previously described (Hovel-Miner, G. 2009. JB, 191: 2461)

scan_protocol: Scanning and image acquisition was performed on a InnoScan 710 using the mapix software. Spot intensity an local background was measured.

data_processing:
Data were processed with the mapix software. Values from each channel were background subtracted and the % contribution of each spots to the total fluorscence in each channel was calculated.
The slides were scanned using both channel, as the scanner can acquire    both signal at the same time; however, only one channel (AlexaFluor    647) was used, the other channel was not used.

label: Alexa Fluor 647

organism: Legionella pneumophila subsp. pneumophila

source_name: ∆lpr10 + plpr10

label_protocol: RNA: 15 ug of Total RNA was labeled with amino-allyl dUTP during reverse transcriptase and subsequently coupled with the succinimidyl ester fluorescent dye AlexaFluor 647 as previously described (Hovel-Miner, G 2009. JB, 191:2461).

growth_protocol: Each strain was grown at 37oC for 3 days from a -80oC frozen stock by streaking on CYE agar.

extract_protocol: RNA: TRIzol reagent (Invitrogen).

treatment_protocol: Each strain was inoculated into AYE broth at an OD600 of 0.1 and grown at 37°C with shaking until post-exponential phase.

value: {delta}lpr10 + plpr10

tag: condition

value: AYE broth, post-exponential phase


title: WT 10 minutes after treatment with 3mM H2O2 3rd triplicate

source_name: WT Bacteria

value: WT


description:
Legionella pneumophila ∆lpr10 + plpr10 grown to post-exponential phase, biological replicate 1
comp_1


description:
Legionella pneumophila ∆lpr10, grown to post-exponential phase, biological replicate 3
lpr10_3


description:
Legionella pneumophila ∆lpr10 + plpr10 grown to post-exponential phase, biological replicate 2
comp_2


title: Subject:MA; Sample Day: Week 23 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MA-23

value: MA

value: 1st Ct dose:0; 2nd Ct does:0

tag: culture


description:
Legionella pneumophila ∆lpr10, grown to post-exponential phase, biological replicate 2
lpr10_2


description:
Legionella pneumophila ∆lpr10, grown to post-exponential phase, biological replicate 1
lpr10_1


title: Cerebrum_CTR_2

value: F

tag: age

value: 48 hrs


title: Cerebrum_CTR_3

value: 9 months


title: WT 10 minutes after treatment with 3mM H2O2 1st triplicate


title: Cerebellum_IRR_10

value: IRR


title: Cerebellum_IRR_9

value: M


title: Subject:MA; Sample Day: Week 18 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MA-18

value: anti-IgG antibody


title: Subject:MA; Sample Day: Week 14 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MA-14


title: WT in the absence of H2O2 2nd duplicate

value: pXO1-; pXO2-


description:
Legionella pneumophila KS79 grown to post-exponential phase, biological replicate 3
WT_3

source_name: WT

value: KS79 (WT)


title: Subject:MB; Sample Day: Week 0 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MB-0

value: MB

value: 1st Ct dose:0; 2nd Ct does:10^5 IFU


title: Cerebrum_CTR_1

value: Yes

value: mt-keima

value: CTR

value: 8 months


title: WT in the absence of H2O2 1st duplicate

value: WT

value: no H2O2 treatment


title: Subject:MA; Sample Day: Week 8 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MA-8

value: MA

value: 1st Ct dose:0; 2nd Ct does:0


title: WT 10 minutes after treatment with 3mM H2O2 2nd triplicate

description:
reverse transcribed from total bacterial RNA
B.anthracis_htrA_vs_WT_Oxidative_Stress_RNA_Seq_CountsTable

value: after H2O2 treatment


title: Cerebellum_IRR_7

value: F

value: 9 months

value: 48 hrs


title: Cerebellum_IRR_8

value: IRR

value: M


title: DhtrA mutant before treatment with H2O2  2nd duplicate

value: pXO1-; pXO2-

value: DhtrA

value: before H2O2 treatment


title: Subject:MA; Sample Day: Week 4 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MA-4

value: anti-IgG antibody


title: Subject:MF; Sample Day: Week 8 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MF-8

value: MF

value: 1st Ct dose:10^7 IFU; 2nd Ct does:none


title: DhtrA mutant before treatment with H2O2 1st duplicate


title: WT before treatment with H2O2 2nd duplicate


title: Cerebellum_IRR_6

value: Yes

value: mt-keima

value: 8 months


title: MOLM-13 A5-KD

city: Zhengzhou

first: Jiazhen

last: Wang

address: 156 Jinshui East Road

institute: Henan University of Chinese Medicine

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using bowtie2 with default parameters
Peaks were called by MACS2
Normalized ATAC signal was generated by deeptools
Genome_build: hg38
Supplementary_files_format_and_content: .narrowPeak files were calculated by MACS2; .bw files were generated by deeptools

growth_protocol: The human acute leukemia cell lines MOLM-13 were maintained in Roswell Park Memorial Institute 1640 medium (RPMI-1640) with 10% FBS, 100 IU ml−1 penicillin and 100μg ml−1 streptomycin.

extract_protocol:
DNA
MOLM-13 cells were pelleted by centrifugation at 500g for 5 min at 4 °C. All supernatant was removed carefully. Fifty microliters of transposase mixture (25μl of 2× TD buffer, 1μl of Tn5, 0.5μl of 1% digitonin, and 23.5μl of nuclease-free water) were added to the cells, and the pellet was disrupted by pipetting. Transposition reactions were incubated at 37 °C for 30 min with agitation at 300 rpm. Transposed DNA was purified using a QIAGEN MinElute Reaction Cleanup kit (28204), and purified DNA was eluted in 10 μl of elution buffer (10 mM Tris-HCl, pH 8).

value: KDM4C knock-down


title: Subject:MA; Sample Day: Week 0 with respect to first challenge; Replicate 1

description:
Serum samples were exposed to Chlamydia trachomatis protein microarrays and bound antibody to individual protein spots was measured by fluorescence.
MA-0

value: MA

value: 1st Ct dose:0; 2nd Ct does:0


description:
Legionella pneumophila KS79 grown to post-exponential phase, biological replicate 1
WT_1

value: KS79 (WT)

value: AYE broth, post-exponential phase


title: WT before treatment with H2O2 1st duplicate

value: WT


title: Cerebellum_CTR_4

value: CTR

value: 48 hrs


title: Cerebellum_CTR_3

value: F

value: 9 months


title: salivary gland of wild type mouse at week 20, M30

first: Junho

last: Lee

state: Seoul

address: 88, Olympic-ro 43-gil, Songpa-gu, Seoul

department: Pathology

institute: Asan

description: Gene expression data from salivary glands at 20-week-old wild type mouse, M30

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

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

data_processing:
Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC).
data2.xlsx = data processing: Filtered by main or consensus probes
- Preprocessed data (22206 probes).
data3.xlsx = Statistical Test: significant cut-off by Fold change, independent t-test
- cut-off: probes with | fc | >= 1.5 & raw.p <0.05.
- Significant data (212 probes).

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

growth_protocol: All mice were maintained under specific pathogen-free conditions in the Laboratory Animal Facility at the School of Dentistry, Seoul National University.

extract_protocol: The salivary glands, including parotid, sublingual, and submandibular glands, were subjected to RNA extraction using the easy-BLUETM Total RNA Extraction Kit (iNtRON Biotechnology, Seongnam, Gyeonggi, Korea).

treatment_protocol: Mice were anesthetized with isoflurane before extracting salivary glands.

value: wild type

value: salivary gland (parotid, submandibular, and sublingual)


title: salivary gland of Nfkbiz-deficient mouse at week 20, M49

description: Gene expression data from salivary glands at 20-week-old Nfkbiz-deficient mouse, M49

value: Nfkbiz-deficient


title: salivary gland of wild type mouse at week 20, M55

description: Gene expression data from salivary glands at 20-week-old wild type mouse, M55


title: Cerebellum_CTR_2


title: Cerebellum_CTR_5


title: salivary gland of Nfkbiz-deficient mouse at week 20, M47

description: Gene expression data from salivary glands at 20-week-old Nfkbiz-deficient mouse, M47

value: female

value: ICR


title: Human thymus, CD34+, OP9JAG2 cultured, 10d, replicate 2

status: Public on May 26 2020

city: Ghent

first: Tom

last: Taghon

address: Corneel Heymanslaan 10

department: Diagnostic Sciences

country: Belgium

institute: Ghent University

description: Gene expression data from human CD34+ thymocytes cultured on OP9JAG2 (10d)

hyb_protocol: Affymetrix Generic Hybridization

scan_protocol: Affymetrix Genechip Scanner 3000 7G

label_protocol: 3' IVT Express Kit

growth_protocol: CD34+ thymocytes were cultured on OP9 stromal cells in the presence of SCF, IL7 and FLT3L for 5 days or 10 days.

extract_protocol: Total RNA was harvested using the miRNeasy Mini Kit (Qiagen) with Dnase treatment on-column.

treatment_protocol: CD34+ thymocytes were used immediately for gene expression profiling or cultured on OP9 stromal cells for 5 - 10 days and sorted for CD45+.

value: thymus

tag: cell type

tag: agent

tag: time point


title: Human thymus, CD34+, OP9JAG1 cultured, 10d, replicate 2

description: Gene expression data from human CD34+ thymocytes cultured on OP9JAG1 (10d)


title: Control immunoprecipitation, biological rep 1

description: nonspecific DNA

value: IP without antibody

value: embryonic culture tissue

tag: genotype/variation

value: expressing ABI3-10x-cmyc


title: MOLM-13 control

tag: cell line

value: wild-type


title: Human thymus, CD34+, OP9DLL4 cultured, 10d, replicate 2

description: Gene expression data from human CD34+ thymocytes cultured on OP9DLL4 (10d)


title: Human thymus, CD34+, OP9DLL1 cultured, 10d, replicate 2

description: Gene expression data from human CD34+ thymocytes cultured on OP9DLL1 (10d)


title: Human thymus, CD34+, OP9DLL4 cultured, 5d, replicate 2

description: Gene expression data from human CD34+ thymocytes cultured on OP9DLL4 (5d)


title: Human thymus, CD34+, OP9DLL1 cultured, 5d, replicate 2

description: Gene expression data from human CD34+ thymocytes cultured on OP9DLL1 (5d)


title: Human thymus, CD34+, control ex vivo isolated, replicate 2

description: Gene expression data from ex vivo isolated human CD34+ thymocytes

value: control ex vivo isolated

tag: origin

value: ex vivo isolated


title: Cerebellum_CTR_1

tag: included in analysis

value: Yes

tag: genotype

value: mt-keima

value: M

value: 8 months


title: Human thymus, CD34+, OP9JAG2 cultured, 5d, replicate 2

description: Gene expression data from human CD34+ thymocytes cultured on OP9JAG2 (5d)


title: Human thymus, CD34+, OP9DLL4 cultured, 10d, replicate 1


title: Human thymus, CD34+, OP9JAG2 cultured, 10d, replicate 1


title: Human thymus, CD34+, OP9DLL1 cultured, 5d, replicate 1


title: Human thymus, CD34+, OP9JAG1 cultured, 5d, replicate 1

description: Gene expression data from human CD34+ thymocytes cultured on OP9JAG1 (5d)


title: Human thymus, CD34+, OP9JAG1 cultured, 5d, replicate 2


title: GES1_WT_RNAseq

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

data_processing:
Basecalls performed with
Low quality reads were removed by using fastq_quality_fileter (fastx_toolkit v0.0.14) with parameters -q 20 -p 80
Reads were aligned to hg19 genome assembly with Hisat v2.2.1.0 for RNA-Seq and Bowtie2 (version 2.2.3) for ChIP-Seq.
Reads with more than two mismatches were removed form aligned reads for RNA-Seq and ChIP-Seq. Then, multiply mapped reads were removed for ChIP-Seq followed by PCR duplicates by using picard-tools-1.1119.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1for RNA-seq. Reads on black list regions (wgEncodeDacMapabilityConsensusExcludable.bed) were removed and remaing reads were converted to BedGraph format with HOMER v4.9.1 for ChIP-seq.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: GES1_WT, GES1_EB, MKN7_WT, MKN7_EB, NCC24 and SNU719 cells were cultured in RPMI1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
ChIP samples were purified by QIAquick PCR purification kit (Qiagen, Hilden, Germany) and total RNAs were collected using RNeasy (Invitrogen, Carlsbad, CA)
Libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) for ChIP-seq. TruSeq Stranded mRNA Sample Prep Kit (Illumina) were used for RNA-seq following the manufacturer’s protocol.

tag: infection


title: Human thymus, CD34+, OP9JAG1 cultured, 10d, replicate 1


title: Human thymus, CD34+, OP9JAG2 cultured, 5d, replicate 1


title: Human thymus, CD34+, OP9DLL4 cultured, 5d, replicate 1


title: LDB1_0Dox

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Single-end reads were processed to remove low-quality bases and sequencing adaptors using Trimmomatic v0.32.
Reads were then aligned to the human genome (version hg38) using Bowtie2 v2.2.6 with the parameter --very-sensitive-local.
Peaks were identified using MACS2 v2.1.1 with default settings.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph files produced by MACS2

source_name: hESC H9 cell line

growth_protocol: Culture and enzymatic passaging of hESC lines was conducted as previously reported by Ng et al. (2008) Nat. Protoc. 3, 768–776.

extract_protocol:
ChIP was performed on CD34+ magnetic sorted samples after single crosslink. Antibodies were used against the following antigens (manufacturer, cat #): LMO2 (R&D Systems, AF2726-SP), LDB1 (Abcam, 96799)
ChIP libraries for Illumina sequencing were prepared using the KAPA Hyper Prep Kit (Roche, KR0961), as detailed by the manufacturer. Quality control of the libraries was performed using a High Sensitivity DNA chip on an Agilent Technologies 2100 Bioanalyser instrument and libraries were quantified using the RT-qPCR-based method KAPA Library Quantification Kit for Illumina Sequencing Platforms, following the manufacturer’s protocol.

treatment_protocol: Hematopoietic differentiation of human ESCs was performed following the spin Embryo Body (EB) method in STAPEL medium with supplements used as reported  by Ng et al (2016) Blood 120, 4038–4048. with some modifications, detailed below. Albumin was substituted for a 1:1 mixture of albumin from rice endosperm (ScienCell Research Labs cat# OsSA) and Bovostar acid stripped Bovine Serum Albumin (BSA, Bovogen cat# BSAS 0.1). For the first 4 days, 7.5 ng/ml ACTIVIN A (ACT, R&D Systems cat# 338-AC) and 0.5 μM CHIR99021 (Tocris Biosciences cat# 4423) were used and 3.5 µM SB431542 (Sapphire Bioscience cat# 13031) and 3 µM CHIR99021 were added 4-6 hours before the day 2 time point and until day 4. After day 4, 5 ng/ml BMP4 and 10 ng/ml Insulin-like growth factor 2 (IGF2, PeproTech cat# 100-12) were used instead of the original concentrations. Adherent cultures after d8 were supplemented with 20 ng/ml BMP4, 100 ng/ml stem cell factor (SCF, PeproTech cat# 300-07), 100 ng/ml FMS-like tyrosine kinase 3 receptor (FLT3) ligand (PeproTech cat# 300-19), 50 ng/ml Thrombopoietin (TPO, PeproTech cat# 300-18), 50 ng/ml vascular endothelial growth factor (VEGF, PeproTech cat# 100-20), 25 ng/ml Interleukin (IL) 3 (PeproTech cat# 200-03), 25 ng/ml IL6 (PeproTech cat# 200-06), 20 ng/ml IGF2, 10 ng/ml basic Fibroblast Growth Factor (FGF2, PeproTech cat# 100-18B) and 1x Penicillin/Streptomycin (Pen/Strep, 5000 U/ml and 5000 U/ml respectively, Thermo Fisher Scientific cat# 15140122). Plates were toped up with media every 3 days and half-media changes were performed when the media capacity of the plate was reached. Upon Dox treatment, adherent cultures were supplemented with a ‘5-factor’ cytokine mix including 100 ng/ml SCF, 100 ng/ml FLT3 ligand, 50 ng/ml TPO, 25 ng/ml IL3 and 25 ng/ml IL-6. For analysis, EBs were harvested at different time points and dissociated into single-cell suspensions using TryPLE select (Invitrogen) for non-adherent EBs and Collagenase Type 1 or Type 4 (Worthington, CLS-1 or CLS-4) for adherent EB cultures and passed through 23- and 25-gauge needles and a 40µm filter.

tag: target

tag: antibody


title: LDB1_5Dox


title: Human thymus, CD34+, OP9DLL1 cultured, 10d, replicate 1

tag: tissue


title: LMO2_0Dox

value: R&D Systems, AF2726-SP


title: Human thymus, CD34+, OP9LIE cultured, 5d, replicate 2

description: Gene expression data from human CD34+ thymocytes cultured on OP9LIE (5d)


title: GES1_EB_RNAseq

value: Epstein-barr virus


title: LMO2_5Dox


title: Human thymus, TCR_GDhiCD1lo, replicate 2

description: Gene expression data from ex vivo isolated human GDhiCD1lo thymocytes

treatment_protocol: Cell suspension from child thymus was stained for specific cell surface markers in order to sort out dinsinct T cell subsets. Cord blood CD34+Lin+ HPCs were sorted following Lymphoprep and CD34+ enrichment.


title: MKN7_EB_shATF3_RNAseq

data_processing:
Low quality reads were removed by using fastq_quality_fileter (fastx_toolkit v0.0.14) with parameters -q 20 -p 80
Reads were aligned to hg19 genome assembly with Hisat v2.2.1.0 for RNA-Seq and Bowtie2 (version 2.2.3) for ChIP-Seq.
Reads with more than two mismatches were removed form aligned reads for RNA-Seq and ChIP-Seq. Then, multiply mapped reads were removed for ChIP-Seq followed by PCR duplicates by using picard-tools-1.1119.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1for RNA-seq and Aligned reads were converted to BedGraph format with bedtools v2.20.1 for ChIP-seq.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. Bedgraph files are generated from bedtools and converted to bigwig file.

growth_protocol: MKN7_WT, MKN7_EB, NCC24 and SNU719 cells were cultured in RPMI1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

value: gastric cancer cell line

value: Epstein-barr virus infected with ATF3-targeted shRNA


title: Human thymus, CD34+, control ex vivo isolated, replicate 1


title: Human thymus, CD4hiCD8hiCD3lo, replicate 2

description: Gene expression data from ex vivo isolated human CD4hiCD8hiCD3lo thymocytes


title: Human thymus, CD34+, OP9LIE cultured, 5d, replicate 1


title: Human thymus, TCR_GDhiCD1hi, replicate 2

description: Gene expression data from ex vivo isolated human TCR_GDhiCD1hi thymocytes


title: Human thymus, CD34hiCD1loCD4lo, replicate 2

description: Gene expression data from ex vivo isolated human CD34hiCD1loCD4lo thymocytes


title: Human thymus, CD8hiCD3hi, replicate 1

description: Gene expression data from ex vivo isolated human CD8hiCD3hi thymocytes

source_name: Human thymus, CD8hiCD3hi, replicate 1


title: Human thymus, TCR_GDhiCD1lo, replicate 1


title: Human cord blood, CD34+Lin-, replicate 2

description: Gene expression data from ex vivo isolated human cord blood CD34+Lin- HPCs

value: cord blood


title: Human thymus, CD4hiCD3hi, replicate 1

description: Gene expression data from ex vivo isolated human CD4hiCD3hi thymocytes

source_name: Human thymus, CD4hiCD3hi, replicate 1


title: Human thymus, CD4hiCD3loCD28hi, replicate 2

description: Gene expression data from ex vivo isolated human CD4hiCD3loCD28hi thymocytes


title: Human thymus, CD34hiCD1hiCD4lo, replicate 2

description: Gene expression data from ex vivo isolated human CD34hiCD1hiCD4lo thymocytes


title: MKN7_EB_shNON_RNAseq

value: Epstein-barr virus infected with non-targeted shRNA


title: Human thymus, CD8hiCD3hi, replicate 2

source_name: Human thymus, CD8hiCD3hi, replicate 2

value: thymus


title: Human thymus, CD4hiCD3loCD28lo, replicate 2

description: Gene expression data from ex vivo isolated human CD4hiCD3loCD28lo thymocytes


title: Human thymus, CD4hiCD3hi, replicate 2

source_name: Human thymus, CD4hiCD3hi, replicate 2


title: Human thymus, TCR_GDhiCD1hi, replicate 1


title: Human thymus, CD4hiCD8hiCD3hi, replicate 1

description: Gene expression data from ex vivo isolated human CD4hiCD8hiCD3h thymocytes


title: MKN7_EB_RNAseq

value: Epstein-barr virus infected


title: MKN7_WT_RNAseq

value: WT


title: Human thymus, CD34hiCD1hiCD4hi, replicate 2

description: Gene expression data from ex vivo isolated human CD34hiCD1hiCD4hi thymocytes


title: Human thymus, CD4hiCD8hiCD3hi, replicate 2


title: MKN7_WT_shNON_RNAseq

value: non-targeted shRNA


title: Human thymus, CD4hiCD3loCD28hi, replicate 1


title: HIV_Neg_2_1043_PBMCS_CD8

city: Durban

first: Daniel

last: Muema

address: 719 Umbilo Road

country: South Africa

institute: Africa Health Research Institute

data_processing:
The raw data were demultiplexed and processed using Trimmomatic version 0.36 to remove adaptors and leading/trailing low-quality bases.
The sequences were aligned on the human reference genome GRCh37 (hg19) using the TopHat module (version 2.1.1) and bowtie (version 2.2.4).
The mapped reads were then sorted using the Picard SortSam module. Duplicate reads were identified using the Picard MarkDuplicates module and removed.
The Cufflinks module (Version 2.2.1) was used for subsequent analyses. The transcripts for each sample were assembled and the numbers of reads quantified for each transcript. The expression levels were expressed as Fragments Per Kilobase of transcript per Million fragments mapped (FPKM). The assembled transcripts for all samples were merged to obtain a master transcriptome assembly (Cuffmerge) followed by assessment of differential expression (Cuffdiff).
Genome_build: hg19

source_name: Peripheral blood mononuclear cells

extract_protocol:
For work on unsorted cells, total RNA was extracted from RNAlater-stored cellular pellets using Qiagen RNeasy Micro kit (Qiagen, Hilden, Germany). For work on purified CD8+ T cells, cells were sorted into 70% TRIzol LS Reagent (Thermo Fisher Scientific, Waltham, MA, USA)  followed by isolation of both RNA and DNA using the TRIzol/chloroform method. Total RNA was then extracted using Qiagen RNeasy Micro kit. Enrichment for messenger RNA was done using the NEBNext Poly(A) mRNA Magnetic Isolation kit (New England Biolabs, Ipswich, MA, USA).
RNA libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) in accordance to the manufacturer's instructions.

value: Peripheral blood mononuclear cells

value: Sorted CD8 T cells

tag: disease state

value: HIV negative


title: HIV_Neg_1_1027_PBMCS_CD8


title: HIV_Neg_4_1058_PBMCS_CD8


title: shsix2.2-11

city: St. Louis

first: Jeffrey

middle: R

last: Millman

state: MO

address: 700 Rosedale Avenue

institute: Washington University in St. Louis

description: RNeasy Mini Kit (Qiagen, 74016)

data_processing:
All sequencing data were generated by the Washington University Genome Technology Access Center (GTAC)
Bulk RNA sequencing files were generated by Illumina sequencer and processed by GTAC
Genome_build: h_sapien reference build Ensembl_R76
Supplementary_files_format_and_content: Bulk RNA sequencing data presented in counts as tab-delimited txt file.

source_name: SC-Beta Cell

growth_protocol: Cells were differentiatied as described in Velazco-Cruz et. al. Stem Cell Reports. 2019.

extract_protocol:
RNA was extracted on Stage 6 Day 12 with the Rneasy Mini Kit (Qiagen, 74016), including a Dnase treatement (Qiagen, 79254) during extraction.
Library construction for bulk RNA sequencing was prepared using standard Illumina protocols

treatment_protocol: Stage 6 Day 1 cells were transduced with lentiviral delivered shRNA's targeting GFP (control) or SIX2.

value: ES-Derived Endocrine Cells

tag: Stage

value: Stage 6


title: shsix2.2-12

description: RNeasy Mini Kit (Qiagen, 74016)


title: Human thymus, CD4hiCD8hiCD3lo, replicate 1

value: ex vivo isolated


title: HIV_Pos_2_1040_PBMCS_CD8

value: HIV positive


title: HIV_Neg_3_1049_PBMCS_CD8


title: HIV_Pos_3_1009_PBMCS_CD8


title: shsix2.2-9

description: RNeasy Mini Kit (Qiagen, 74016)


title: shsix2.2-10

description: RNeasy Mini Kit (Qiagen, 74016)


title: Human thymus, CD34hiCD1hiCD4hi, replicate 1


title: HIV_Pos_1_106_PBMCS_CD8


title: shsix2.2-8

description: RNeasy Mini Kit (Qiagen, 74016)


title: shgfp-6

description: RNeasy Mini Kit (Qiagen, 74016)


title: HIV_Neg_1_1027_BAL_CD8

source_name: Bronchoalveolar lavage cells

value: Bronchoalveolar lavage cells


title: Human thymus, CD34hiCD1hiCD4lo, replicate 1


title: HIV_Neg_2_1043_BAL_CD8


title: Human thymus, CD34hiCD1loCD4lo, replicate 1


title: HIV_Neg_4_1058_BAL_CD8


title: shgfp-5

description: RNeasy Mini Kit (Qiagen, 74016)


title: HIV_Neg_3_1049_BAL_CD8


title: shgfp-4

description: RNeasy Mini Kit (Qiagen, 74016)


title: shgfp-3

description: RNeasy Mini Kit (Qiagen, 74016)


title: HIV_Pos_3_1009_BAL_CD8


title: shgfp-2

description: RNeasy Mini Kit (Qiagen, 74016)


title: HIV_Pos_2_1040_BAL_CD8


title: shgfp-1

description: RNeasy Mini Kit (Qiagen, 74016)


title: HIV_Neg_4_1058_PBMCS

value: Bulk (unsorted cells)


title: HIV_Neg_3_1049_PBMCS


title: HIV_Neg_1_1027_PBMCS


title: HIV_Neg_2_1043_PBMCS


title: MOLM13 shALKBH5-#1 Rep1

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

description: MOLM13 shALKBH5-#1 Rep1

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to the  human GRCh38 using the STAR aligner. The aligned reads were then assigned to genes using RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: table delimited text file containing the expression of genes

source_name: AML cell line MOLM13

growth_protocol: NOMO-1 cells were  routinely  kept in RPMI1640 mediun with 10% FBS at 0.5*10^6 cells/ml and were passeged every other day.

extract_protocol:
The total RNA were extracted with QIAzol lysis reagent.
FastTrack MAG Maxi mRNA isolation kit

treatment_protocol: About 1*10^6 cells were infected with lentivirus targeting FTO collected from 6 cm dish with existence of 1ug/ml polybrene for spinoculation (1,200 rpm, 32℃，1 hour). 48 hours later, the positive cells were selected with 1ug/ml puromucin for 1 week. As durg treatment, NOMO-1 cells were seed in 10 cm dishes at 0.5*10^6 cells/ml and treated with 100nM CS1, 500nM CS2 or DMSO for 72 hours.

value: Acute myeloid leukemia

tag: lentivirus


title: HIV_Pos_3_1009_PBMCS


description:
Legionella pneumophila KS79 grown to post-exponential phase, biological replicate 2
WT_2

tag: strain

value: KS79 (WT)

tag: condition

value: AYE broth, post-exponential phase


title: HIV_Pos_2_1040_PBMCS

tag: cell type


title: Human thymus, CD4hiCD3loCD28lo, replicate 1


title: NOMO1 shNS Rep3

description: NOMO1 shNS Rep3

source_name: AML cell line NOMO-1

value: shNS


title: HIV_Neg_4_1058_BAL


title: NOMO1 shALKBH5-#1 Rep3

description: NOMO1 shALKBH5-#1 Rep3


title: NOMO1 shALKBH5-#1 Rep2

description: NOMO1 shALKBH5-#1 Rep2


title: MOLM13 shNS Rep 1

description: MOLM13 shNS Rep 1


title: shsix2.2-7

description: RNeasy Mini Kit (Qiagen, 74016)


title: Human cord blood, CD34+Lin-, replicate 1

value: cord blood


title: HIV_Neg_3_1049_BAL


title: MOLM13 shNS Rep 3

description: MOLM13 shNS Rep 3


title: HIV_Pos_1_106_PBMCS


title: HIV_Neg_2_1043_BAL


title: HIV_Pos_1_106_BAL_CD8


title: ALKBH5 OE Flag-IP 3

extract_protocol:
Total RNA was extracted from both input and immunoprecipitated RNA using TRIzol followed by Direct-zol RNA Miniprep (Zymo).
RNA fragmentation, RIP-Seq and library preparation were performed according to previous protocals (Huang et al., 2018)

tag: tumor

value: ALKBH5 OE

value: anti-Flag antibody (Sigma-Aldrich)


title: HIV_Neg_1_1027_BAL


title: ALKBH5 OE Flag-IP 1


title: ALKBH5 OE input 3


title: HIV_Pos_3_1009_BAL


title: ALKBH5 OE input 1


title: MOLM13 shALKBH5-#1 Rep3

description: MOLM13 shALKBH5-#1 Rep3


title: HIV_Pos_2_1040_BAL


title: shALKBH5-#1 ActD 12h

description: shALKBH5-#1 ActD 12h

tag: treatment

value: ActD

tag: time point