title: FT194_shRNF20_890 rep3

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

data_processing:
Base calling and demultiplexing were processed using CASAVA version 1.8
Reads were mapped using the GENCODE release 19 reference using STAR version 2.4.2a
Read counts were generated using the quantMode GeneCounts option in STAR.

source_name: ovarion cancer cell line

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit from Qiagen.
mRNA libraries were constructed using the Bioo Scientific NEXTflex Rapid Directional RNA-seq Library Prep Kit.

tag: cell line name


title: FT194_shRNF20_692 rep3

status: Public on Feb 25 2019

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: CK_PFC_biological rep 05

type: RNA

city: Toyoake

first: Hideo

last: Hagihara

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Institute for Comprehensive Medical Science

country: Japan

institute: Fujita Health University

description: Gene expression data from the PFC of Camk2a+/- mouse

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 (GCS3000)

data_processing: The data were analyzed with Affymetrix Expression Cosole (version 1.1). The normalization used in RMA is quantile normalization.

label: biotin

organism: Mus musculus

source_name: PFC of Camk2a+/- mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

extract_protocol: Trizol extraction of total RNA and cleanup byRNeasy Micro kit (QIAGEN) was performed according to the manufacturer's instructions.

tag: tissue

value: Medial prefrontal cortex

tag: genotype


title: Mix_ad3_rep2

city: Kiel

first: Hinrich

last: Schulenburg

address: Am Botanischen Garten 1-9

department: Evolutionary Ecology and Genetics, Zoological Institute

country: Germany

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to WS235 whole genome using STAR-2.5.3a
Read counts per gene is extracted via STAR-2.5.3a
Genome_build: WS235
Supplementary_files_format_and_content: tab-delimited text files include Raw reads counts for each Sample ...

organism: Caenorhabditis elegans

source_name: whole body

extract_protocol:
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 standard Illumina protocols

treatment_protocol: Worms were fed to OP50 and Ochrobactrum at the different stage (from L2 to adults)

tag: strain

value: N2/Wide type

tag: treatment

value: Mix

tag: time point

value: adults (3 days)

tag: medium

value: mNGM

tag: temperature


title: Mix_L3_rep2


title: CK_PFC_biological rep 03


title: FT194_shRNF20_692 rep2


title: OP_L3_rep3


title: Mix_ad7_rep2

value: adults (7 days)


title: CK_PFC_biological rep 01


title: OP_L2_rep3


title: FT194_shRNF20_692 rep1


title: MYb65_ad7_rep2


title: FT194_shRNF20_890 rep1


title: FT194_shRNF20_890 rep2


title: CK_PFC_biological rep 06


title: CK_PFC_biological rep 04


title: Mix_ad1_rep2

value: adults (72h)


title: MYb65_ad3_rep2


title: Veh_DG_biological rep 08

description: Gene expression data from the DG of vehicle-treated mouse.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 (GCS3000).

data_processing: The data were analyzed with Affymetrix Expression Console (version 1.1). The normalization used in RMA is quantile normalization.

source_name: DG of vehicle-treated mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA.

growth_protocol: No

extract_protocol: Trizol extraction of total RNA and cleanup by RNeasy Micro kit (QIAGEN) was performed according to the manufacturer's instructions.

treatment_protocol: No

tag: strain/background

tag: genotype/variation

value: Wild-type

value: Dentate gyrus

value: vehicle


title: MYb65_L4_rep2


title: MYb65_ad1_rep2


title: MYb65_L3_rep2


title: CK_PFC_biological rep 02


title: Mix_L2_rep2


title: FT194_shNTC rep2


title: MYb65_L2_rep2


title: Veh_DG_biological rep 07


title: MYb71_ad7_rep2


title: FT194_shNTC rep1


title: Veh_DG_biological rep 05


title: MYb71_L4_rep2


title: MYb71_ad1_rep2


title: MYb71_ad3_rep2


title: MYb71_L3_rep2


title: FT190_shRNF20_890 rep2


title: MYb71_L2_rep2


title: FT190_shRNF20_692 rep3


title: Mix_ad7_rep1


title: Mix_ad3_rep1


title: Veh_DG_biological rep 04


title: Veh_DG_biological rep 03


title: Mix_ad1_rep1


title: FT190_shRNF20_692 rep2


title: Mix_L4_rep1


title: Mix_L3_rep1


title: FT190_shRNF20_692 rep1


title: FT190_shRNF20_890 rep3


title: Veh_DG_biological rep 02


title: OP_ad3_rep2


title: FT190_shNTC rep3


title: Veh_DG_biological rep 01


title: OP_ad1_rep2


title: OP_L4_rep2


title: OP_ad7_rep2


title: FT190_shNTC rep2


title: OP_L2_rep2


title: FT190_shNTC rep1


title: OP_L3_rep2


title: Mix_L2_rep1


title: MYb65_ad3_rep1


title: FLX_DG_biological rep 07

description: Gene expression data from the DG of FLX-treated mouse.

source_name: DG of FLX-treated mouse

value: fluoxetine


title: MYb65_ad7_rep1


title: FT194_shRNF20_890

library_source: genomic

data_processing:
Base calling and demultiplexing were processed using CASAVA version 1.8
Reads were mapped using BWA-MEM to the 1000 Genomes (b37) build of the human genome reference.
Peaks were called using MACS2 with options BAMPE and -q=0.01.
Bigwig files were generated using bedGraphTobBgWig.
Genome_build: b37

molecule: genomic DNA

extract_protocol:
50,000 cells were washed in ice cold 1X PBS and re-suspended in 50 μl ice cold lysis buffer. Then nuclei were pelleted at 500 x g for 10 min at 40C. The pellet was then incubated with the transposition reaction mix for 30 min at 37°C and then purified using the MinElute PCR Purification kit (Qiagen, Hilden, Germany).
ATAC-seq libraries were constructed as described in Bustos, et al. 2017 Genome Data (PMID: 28239551).


title: MYb65_ad1_rep1


title: FT194_shRNF20_692


title: MYb65_L2_rep1


title: FLX_DG_biological rep 08


title: FT194_shNTC


title: MYb71_ad7_rep1


title: MYb71_ad3_rep1


title: MYb71_ad1_rep1


title: FLX_DG_biological rep 04


title: Veh_PFC_biological rep 08

description: Gene expression data from the PFC of vehicle-treated mouse.

source_name: PFC of vehicle-treated mouse


title: FLX_DG_biological rep 01


title: FLX_DG_biological rep 06


title: Veh_PFC_biological rep 07


title: MYb71_L3_rep1


title: FT190_shRNF20_692


title: FT190_shNTC


title: MYb71_L2_rep1


title: OP_ad7_rep1


title: OP_ad3_rep1


title: MYb71_L4_rep1


title: OP_ad1_rep1


title: FT190_shRNF20_890


title: MYb65_L4_rep1


title: WL23

city: Hershey

first: Wei

last: Li

state: PA

address: 500 University Drive, PO Box 850, MC H085

institute: Penn State Hershey College of Medicine

description: ln229 IR 7d-2

data_processing:
Sequencing data were analyzed using Strand NGS (Version 3.2). Briefly, reads were aligned to reference human genome and annotation file (GRCh38, build 38, RefSeq genes and transcripts, 2017_01_13). One-way ANOVA was performed using p-value threshold=0.05. For Hierarchical clustering analysis, genes showing changes above 2 folds were used. For ingenuity pathway analysis, 1.8-fold was used as the cut-off of downregulated genes, whereas 2-fold was used for upregulated genes. Direct relationships were chosen. For upstream analysis, the p-value cut-off is 0.01.
Genome_build: GRCh38, build 38, RefSeq genes and transcripts, 2017_01_13

source_name: LN229 GBM cell line

growth_protocol: LN229 cells were cultured in DMEM supplemented with 10% Fetal Bovine Serum and 1% Antibiotic-Antimycotic Solution at 37oC with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol (Thermo Fisher Scientific) by following the manufacture’s manual instruction.
The cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit (BioO Scientific) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 100 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled libraries were diluted to 2 nM in EB buffer (Qiagen) and then denatured using the Illumina protocol. The denatured libraries were diluted to 10 pM by pre-chilled hybridization buffer and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.

treatment_protocol: For radiation treatment, cells were seeded in complete medium on petri dish at a density of 5x10E4/cm2 24 hours before the treatment. The cells were then exposed to γ-ray once using a GammaCell 220 Cobalt 60 irradiator (Nordion International) with indicated doses. After irradiation, the medium was replaced with fresh complete medium.

tag: cell source

value: glioblastoma

tag: cell line

tag: cell type

value: stable cell line

value: ln229 IR 7d


title: WL22

description: ln229 IR 7d-1


title: OP_L4_rep1


title: Veh_PFC_biological rep 05


title: OP_L2_rep1


title: OP_L3_rep1


title: Veh_PFC_biological rep 06


title: WL21

description: ln229 NO-IR 7d-2

value: ln229 NO-IR 7d


title: CE1-4_PGE-2_treated

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
Trimmomatic was used to crop reads to length 50 and to remove the TruSeq3-PE-2 Illumina adapters
The reads were then aligned using tophat2 and bowtie1 with the no-novel-juncs argument set with mouse genome version mm10 and transcriptome defined by the mm10 genes.gtf table from http://genome.ucsc.edu
Reads that did not align or aligned to multiple locations were discarded.
Read counts were determined using htseq-count.
Genome_build: mm10
Supplementary_files_format_and_content: Rows correspond to the gene given in the first column. Columns correspond to specimens.

source_name: Mouse prostate cancer cell line CE1-4

extract_protocol:
Total RNA was isolated from the cell lines using RNeasy Mini Kit (Qiagen)
TruSeq Stranded Total RNA Library Prep Kit (Illumina) following low sample protocol

value: mouse prostate cancer

value: PGE-2 six hours


title: Veh_PFC_biological rep 04

value: Medial prefrontal cortex


title: Veh_PFC_biological rep 03


title: FLX_DG_biological rep 05


title: Veh_PFC_biological rep 02


title: WL18

description: ln229 IR 12h-1

value: ln229 IR 12h


title: CE1-4_untreated

value: untreated


title: FLX_DG_biological rep 03


title: WL17

description: ln229 NO-IR 12h-2

value: ln229 NO-IR 12h


title: FLX_DG_biological rep 02


title: WL16

description: ln229 NO-IR 12h-1


title: MYb65_L3_rep1

value: N2/Wide type

value: mNGM


title: FLX_PFC_biological rep 08

description: Gene expression data from the PFC of FLX-treated mouse.

source_name: PFC of FLX-treated mouse


title: FLX_PFC_biological rep 07


title: Veh_PFC_biological rep 01


title: MES1: LIB008660_TRA00016637

first: Alfred

last: Ramirez

address: One Joslin Place

institute: Joslin Diabetes Center

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences and mapped to the human genome hg19 using STAR (v2.3.0e) with relevant parameters --readFilesCommand bzcat --outFilterMismatchNmax 6 --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Count matrices were generated with HT-seq (v0.5.4) with the parameters htseq-count -i gene_id -q -m union -s reverse.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include raw counts for each sample

molecule: polyA RNA

source_name: Adipose

growth_protocol: Cells were growth on DMEM-H, 10%FBS, and 1% Penicillin-Streptomycin

extract_protocol:
RNA was isolated via Trizol Reagent
RNA libraries were prepared using NEBNext Sample Prep Master Mix kit

treatment_protocol: Cells were grown to 100% confluency and harvested for RNA

value: Preadipocytes

value: Mesenteric


title: WL20

description: ln229 NO-IR 7d-1


title: MES2: LIB008661_TRA00016640


title: FLX_PFC_biological rep 06

value: Wild-type


title: FT190_shRNF20_890 rep1


title: OM4: LIB009162_TRA00016647

value: Omental


title: WL19

description: ln229 IR 12h-2


title: OM3: LIB009162_TRA00016644


title: OM2: LIB009161_TRA00016639


title: FLX_PFC_biological rep 05

value: fluoxetine


title: FLX_PFC_biological rep 04


title: FLX_PFC_biological rep 02


title: FLX_PFC_biological rep 01


title: OM1: LIB008660_TRA00016638


title: MES3: LIB009162_TRA00016643


title: SC3: LIB009162_TRA00016642

value: Subcutaneous


title: SC4: LIB009162_TRA00016645


title: SC1: LIB008660_TRA00016636


title: SC2: LIB009161_TRA00016632


title: RT112 FM Replicate2

city: Belfast

first: Rebecca

middle: Elizabeth

last: Steele

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

data_processing:
RNA-Seq fastq reads were trimmed and aligned to Hg19 (GRCh37) using STAR.
Reads mapped to genes using HTSeq counts.
Differential expression analysis was performed on triplicate samples using DESeq2.
Genome_build: Hg19 (GRCh37)
Supplementary_files_format_and_content: counts

source_name: RT112 Cell line

extract_protocol:
Total RNA was extracted from cells using Ribozol™ RNA Extraction Reagent (Amresco) following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard protocol by Otogenetics Corporation (Atlanta, USA)

value: Prostate


title: RT112 APSCE Replicate3


title: RT112 FM Replicate1


title: RT112 APSCE Replicate1


title: CWR22Rv1 FM siCNTRL Replicate3

source_name: CWR22Rv1 Cell line


title: B6J_PFC_12W_biological rep 05

description: Gene expression data from the PFC of C57BL/6J mouse (12W).

source_name: PFC of C57BL/B6J mouse (12W)

tag: age


title: FLX_PFC_biological rep 03


title: B6J_PFC_12W_biological rep 01


title: B6J_PFC_2W_biological rep 06

description: Gene expression data from the PFC of C57BL/6J mouse (2W).

source_name: PFC of C57BL/B6J mouse (2W)


title: B6J_PFC_12W_biological rep 02


title: B6J_PFC_2W_biological rep 03


title: B6J_PFC_2W_biological rep 01


title: B6J_PFC_12W_biological rep 03


title: B6J_PFC_12W_biological rep 04


title: CWR22Rv1 FM siCNTRL Replicate2


title: B6J_PFC_12W_biological rep 06


title: B6J_PFC_2W_biological rep 04


title: B6J_PFC_2W_biological rep 05


title: RT112 FM Replicate3


title: CWR22Rv1 FM siCNTRL Replicate1


title: CWR22Rv1 FM siEX1 Replicate3


title: CWR22Rv1 FM siEX1 Replicate1


title: FT194_shNTC rep3


title: CWR22Rv1 APSCE siCNTRL Replicate2


title: CWR22Rv1 APSCE siCNTRL Replicate3


title: CWR22Rv1 APSCE siCNTRL Replicate1


title: CWR22Rv1 APSCE siEX1 Replicate3


title: CWR22Rv1 APSCE siEX1 Replicate2


title: CWR22Rv1 FM siEX1 Replicate2


title: SC3: Subcutaneous isolated preadipocytes 3

description: Isolated preads from SC adipose issue

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45C on GeneChip Murine Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 G7

data_processing: The data were imported into R, RMA normalized, log2 transformed, and differential gene expression performed with the R package Limma.

label: Biotin

source_name: Isolated preads from SC adipose issue

label_protocol: Double-stranded cDNA synthesis was reverse-transcribed from 15 µg of isolated mRNA by using the SuperScript Choice system (Invitrogen) with an oligo(dT) primer containing a T7 RNA polymerase promoter site. Double-stranded cDNA was purified with Phase Lock Gel (Eppendorf). Biotin-labeled cRNA was transcribed by using a BioArray RNA transcript labeling kit (Enzo).

growth_protocol: To obtain purified cell fractions, ten 7- to 9-week-old C57BL/6 males were sacrificed with CO2 inhalation, and epididymal and flank subcutaneous adipose tissue were removed under sterile conditions. Tissues from each depot were pooled, minced, and digested with 1 mg/ml collagenase for 30 min at 37°C in DMEM/Hams F-12 1:1 (DMEM/F12) containing 1% BSA and antibiotics (100 units/ml penicillin, 0.1 mg/ml streptomycin, 2.5 mg/ml fungizone, and 50 mg/ml gentamicin). Digested tissues were filtered through sterile 150-µm nylon mesh and centrifuged at 250 g for 5 min. The floating fraction consisting of pure isolated adipocytes was then removed. The pellet, representing the SVF containing preadipocytes and other cell types, was resuspended in erythrocyte lysis buffer consisting of 154 mM NH4Cl, 10 mM KHCO3, and 0.1 mM EDTA for 10 min.  For FACS analysis, erythrocyte-free SVF cells were incubated with a mix of antibodies against different surface markers in PBS-2%FBS and sorted using an Aria flow cytometer (BD Biosciences). Dead cells were removed using propidium iodide staining. Cells negative for Ter119, CD45 and CD31 and positive for both SCA1 and CD34 were considered as adipocyte precursor cells that were centrifuged and the cell pellet immediately frozen for posterior RNA extraction. Aproximately 1x10E6 (1 million) sorted cells per sample were used to isolate RNA for the microarray analysis (Each sample represents a pool of cells from 10 mice, so a total of 50 mice were used).

extract_protocol: RNeasy extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: No treatment

tag: gender

value: male

value: subcutaeous flank adipose tissue


title: LNCap APSCE Replicate 3

source_name: LNCaP Cell line


title: LNCap APSCE Replicate 2


title: PG5: Perigonadal isolated preadipocytes 5

description: Isolated preads from PG adipose tissue

source_name: Isolated preads from PG adipose tissue

value: epididymal adipose tissue


title: LNCap APSCE Replicate 1


title: SC4: Subcutaneous isolated preadipocytes 4

description: Isolated preads from SC adipose issue


title: SC2: Subcutaneous isolated preadipocytes 2

description: Isolated preads from SC adipose issue


title: PG4: Perigonadal isolated preadipocytes 4

description: Isolated preads from PG adipose tissue


title: LNCap FM Replicate 3


title: 2999275_Spleen_Necropsy

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

description:
Please note that the RNASeq data for this experiment was produced across four specimen types (venous whole blood (WB), capillary whole blood (WC), bone marrow (BM), and spleen tissue (SP)) using RNAprotect, RNAlater, and PAXgene sample collection and storage technologies.  Please carefully review the four README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E30M99FGMmKnDaZZ_11202018-Readme_MULTIPL-GEO.txt  E30M99YSMmKnDaSP_11202018-ReadmeRNALater_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmePaxgene_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmeRNAProtect_MULTIPL-GEO.txt
E30M99FGMmKnDaSP_Knowlesi-Genes-RawCounts-Results_MULTIPL-GEO.xlsx, E30M99FGMmKnDaSP_Mulatta-Genes-RawCounts-Results_MULTIPL-GEO.xlsx

data_processing:
Bases were called with Illumina RTA (Real-Time Analysis, v2.7.7) with default parameters. Illumina bcl2fastq v2.17.1.14 was used for demultiplexing. FASTQC (v0.10.1) was used to assess data quality, but the data were not filtered at this stage.
Reads were mapped to a composite reference assembly consisting of host, parasite, and ERCC control references with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Genome_build: RNA-Seq reads were mapped to both a host and parasite genome.  Host: An early version of a new  assembly (as of 5/2014) of the rhesus macaque (MacaM assembly, v4.0, created by Aleksey Zimin at the University of Maryland, Rob Norgren at the University of Nebraska Medical Center and their colleagues).  The MacaM assembly and annotation has been deposited in GenBank under BioProject accession  PRJNA214746. Parasite: Plasmodium knowlesi PK1 (A+) Malayan H strain  genome assembly and annotation was used. The assembly has been deposited in GenBank under the BioProject accession PRJNA377737.
Supplementary_files_format_and_content: Excel files contain raw counts at the gene level, for each individual. Raw counts are further classified by experimental Time Point and Specimen Type.    Note that in addition to raw counts, normalized data are available as supplementary files as described in the supplementary file E30M99FGMmKnDaZZ_11202018-Readme_MULTIPL-GEO.txt.  Normalized results contain data from from 2 experiments, this one (E30) and another known within MaHPIC as 'E06'.  See http://plasmodb.org/plasmo/mahpic.jsp for details on E06, which is also available in GEO and SRA. Corresponding fastq file information in the results files is only provided for E30.
Supplementary_files_format_and_content: Host and Parasite Raw Read Counts Column headers are defined as follows:    'Gene ID':  Identifiers of all Genes in the annotation.     'Gene Symbol': Symbols of all Genes in the annotation.    'Sample Identifier / Raw file list / Abundances': The raw file names and sample identifers both contain information regarding Specimen Type, NHP ID, and Time Point.  Abundances measures are from the raw files listed.     Notes:  There are 12 columns representing 2 animals for Time Points T01-T05 and Necropsy.    There is a read count entry per sample for every gene that appears in the annotation. For genes where there was no detection of expression by reads that mapped to their loci, the raw count is 0.

organism:
Plasmodium knowlesi
Macaca mulatta

source_name: Spleen

growth_protocol: Animals approved for use were moved into experimental housing 10 days prior to the start of the experiment.

extract_protocol:
RNASeq data for this experiment was produced across four specimen types: venous whole blood (WB), capillary whole blood (WC), bone marrow (BM), and spleen tissue (SP).  Samples were collected using RNAprotect (WC), RNAlater (SP), and PAXgene (WB, BM) sample collection and storage technologies.  Please carefully review the four README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E30M99FGMmKnDaZZ_11202018-Readme_MULTIPL-GEO.txt  E30M99YSMmKnDaSP_11202018-ReadmeRNALater_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmePaxgene_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmeRNAProtect_MULTIPL-GEO.txt    RNA was extracted using Tempus-Spin RNA isolation kits. The quality of all RNA samples was confirmed using a Bioanalyzer, with an RNA Integrity Number (RIN) greater than 8 recorded for all samples.
Approximately 1 μg of total RNA per sample was converted to double-stranded cDNA using poly-A beads to enrich for mRNA, and Illumina TruSeq Stranded mRNA Sample Prep kits to generate strand-specific libraries.   As a quality control, 92 spike-in RNAs of known concentration and GC proportions (ERCC Spike-In Control, Life Technologies) were added to constitute approximately 1% of the total RNA for each library.  Adapters were ligated to facilitate multiplexed sequencing on an Illumina HiSeq3000 at the Yerkes Genomics Core, aiming for 50 million paired-end 100 base pair (bp) reads per library.

treatment_protocol: Telemetry devices (DSI, model L11) with blood pressure sensors and ECG leads were surgically implanted in two malaria-naive male rhesus macaques (Macaca mulatta), approximately three years of age.  After a resting period of two weeks, physiological data that include activity, temperature, ECG, and blood pressure were continuously collected.  Two weeks after activation of the telemetry implant, the macaques were inoculated intravenously with cryopreserved salivary gland sporozoites. The cryopreserved batch of P. knowlesi sporozoites were produced, isolated and cryopreserved at the Centers for Disease Control and Prevention from Anopheles dirus.  After experimental infection, the macaques were profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, metabolomic, telemetric and histopathological measurements. The experiment was designed for terminal necropsies on days 11 (RKy15) or 19 (Red16).  The anti-malarial drug artemether was subcuratively administered selectively to one subject (REd16) during the primary parasitemia to suppress clinical complications. Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at five timepoints for functional genomic, proteomic, lipidomic, and immunological analyses. Physiological data were continuously captured via telemetry.  Within the MaHPIC, this project is known as ‘Experiment 30’.  This dataset was produced by Dr. Steven E. Bosinger, Nirav Patel, and Greg Tharp at the Emory University Yerkes Genomics Core. To access other publicly available results from E30 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp .  This page will be updated as datasets are released to the public.  The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC) and the MRMC Office of Research Protection Animal Care and Use Review Office (ACURO).    During the 20-day (plus 49 pre-inoculation days) period subjects experienced log phase infection.     Samples were collected either daily for select specimen types or on clinically determiend time point days. Time points were planned based on the expected progression of infection.  Sample collection at time points was planned to coincide with this expected clinical progression.  However, because of individual variations in the clinical progression of infection for each NHP the clinically defined stage of infection may differ between NHPs at the same time point.  For this reason it is imortant for anyone consuming these data to be aware of any differences between the 'Idealized' and 'Actual' disease progression for each NHP and the corresponding clinical stage of each NHP at each time point when samples were collected.  For this reason the supplementary file E30M99MEMmKnDaZZ_Supporting-Clinical-Information_MULTIPL.pdf is provided to clarify both the 'Idealized' or planned collection of time point samples and the clinically-defined 'Actual' disease progression for each NHP.  Anyone consuming these data should use this information to ensure they are aware of the clinical state of each NHP at each time point and be aware of differences between NHPs.  Time point 1 = Baseline 1 (Pre-implant) (inoculation day minus 49) - This baseline serves as a control 19 days prior to surgical implantation of telemetry devices. NHPs have not been implanted and are not infected.  Time point 2 = Baseline 2 (First post-implant) (inoculation day minus 15) - This baseline serves as a control 15 days after surgical implantation of the telemetry devices.  NHPs are not infected.   Time point 3 = Baseline 3 (Second post-implant) (inoculation day minus 7) - This baseline serves as a control 7 days after the first collection of daily blood sample and active collection of telemetry data.  NHPs are not infected.  Time point 4 = Log I (Progressive Increase of Parasitemia) - This time point examines responses prior to the peak of parasitemia, with an expected parasitemia at ~100-10,000/ul, after sporozoite inoculation.  We expect to see activation at cellular and immune level as well as differential physiological data captured via telemetry compared to baseline readings.  Time point 5 = Log II - This time point examines host immune, metabolic and physiological responses during the peak of infection when NHPs experience clinical signs of disease that should be severe in Rhesus infected with P. knowlesi. Anti-malaria treatment was administered for one NHP.  Necropsy = Terminal necropsies were scheduled based on the clinical evidence of progression to severe malaria to collect histopathological material.     Please carefully review the four README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E30M99FGMmKnDaZZ_11202018-Readme_MULTIPL-GEO.txt  E30M99YSMmKnDaSP_11202018-ReadmeRNALater_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmePaxgene_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmeRNAProtect_MULTIPL-GEO.txt

tag: collection time point (#),  non-time point experiment day relative to infection (daily, #), or necropsy

value: Necropsy

value: Male

tag: non human primate individual id

value: Spleen


title: 2999157_Bone-Marrow_Necropsy

description:
Please note that the RNASeq data for this experiment was produced across four specimen types (venous whole blood (WB), capillary whole blood (WC), bone marrow (BM), and spleen tissue (SP)) using RNAprotect, RNAlater, and PAXgene sample collection and storage technologies.  Please carefully review the four README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E30M99FGMmKnDaZZ_11202018-Readme_MULTIPL-GEO.txt  E30M99YSMmKnDaSP_11202018-ReadmeRNALater_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmePaxgene_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmeRNAProtect_MULTIPL-GEO.txt
E30M99FGMmKnDaBM_Knowlesi-Genes-RawCounts-Results_MULTIPL-GEO.xlsx, E30M99FGMmKnDaBM_Mulatta-Genes-RawCounts-Results_MULTIPL-GEO.xlsx

source_name: Bone Marrow

value: Bone Marrow


title: SC5: Subcutaneous isolated preadipocytes 5

description: Isolated preads from SC adipose issue


title: FACS sorted P2 lung alveolar type 2 cells biological replicate 4

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

description: Pup genotype: SPC-GFP

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Bioconductor

source_name: Differentiating alveolar type 2 cells from P2 mouse lungs

label_protocol: Standard Affymetrix protocol using Ovation RNA Amplification Kit V2 and FL-Ovation Biotin V2 (NuGEN)

growth_protocol: Timed matings of SPC-GFP mice with out-bred ICR strain. Day of birth = P0.

extract_protocol: Total RNA using Qaigen RNEasy Mini Kit as per manufacturer's instructions

treatment_protocol: P2 pups were dissected and GFP+ lungs selected under GFP-dissecting microscope. Lungs were dissociated to single cells using trypsin/EDTA and GFP+ cells isolated by flow cytometry.

value: Cells FACs-sorted from postnatal day 2 lung


title: SC1: Subcutaneous isolated preadipocytes 1

description: Isolated preads from SC adipose issue


title: PG1: Perigonadal isolated preadipocytes 1

description: Isolated preads from PG adipose tissue


title: 2999153_Whole-blood-Capillary_Necropsy

description:
Please note that the RNASeq data for this experiment was produced across four specimen types (venous whole blood (WB), capillary whole blood (WC), bone marrow (BM), and spleen tissue (SP)) using RNAprotect, RNAlater, and PAXgene sample collection and storage technologies.  Please carefully review the four README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E30M99FGMmKnDaZZ_11202018-Readme_MULTIPL-GEO.txt  E30M99YSMmKnDaSP_11202018-ReadmeRNALater_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmePaxgene_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmeRNAProtect_MULTIPL-GEO.txt
E30M99FGMmKnDaWC_Knowlesi-Genes-RawCounts-Results_MULTIPL.xlsx, E30M99FGMmKnDaWC_Mulatta-Genes-RawCounts-Results_MULTIPL.xlsx

source_name: Whole blood - Capillary

value: Whole blood - Capillary


title: FACS sorted P2 lung alveolar type 2 cells biological replicate 3

description: Pup genotype: SPC-GFP


title: FACS sorted P2 lung alveolar type 2 cells biological replicate 1

description: Pup genotype: SPC-GFP


title: FACS sorted P2 lung alveolar type 2 cells biological replicate 2

description: Pup genotype: SPC-GFP


title: CWR22Rv1 APSCE siEX1 Replicate1


title: PG2: Perigonadal isolated preadipocytes 2

description: Isolated preads from PG adipose tissue


title: PG3: Perigonadal isolated preadipocytes 3

description: Isolated preads from PG adipose tissue


title: 2998926_Spleen_Necropsy


title: LNCap FM Replicate 1


title: B6J_PFC_2W_biological rep 02

value: Medial prefrontal cortex


title: FACS sorted P2 lung alveolar type 2 cells biological replicate 5

description: Pup genotype: SPC-GFP


title: 36_2998804_Whole-blood-Capillary_Necropsy


title: SC_MEF_2UnitDevice2_U2

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

description: MID-RNA-Seq data. Name format: Cell Number(single cell SC)_Cell-Line_Device type and number_Unit Number

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1 and Cutadapt 1.12
Trimmed reads were aligned using Tophat 2.1.1
Aligned reads were analysed with Cufflinks 2.2.1 to obtain FPKM gene counts
Genome_build: hg19, mm9
Supplementary_files_format_and_content: The gene counts are reported in FPKM_tracking files

source_name: MEF cell line

growth_protocol: GM12878 cells(Coriell) were cultured in RPMI 1640 medium (11875-093, Gibco) plus 15% fetal bovine serum (26140-079, Gibco) and 100 U/ml penicillin-streptomycin (15140-122,Gibco).  MEF cells were obtained from ATCC(SCRC-1040) and cultured in DMEM (ATCC 30-2002) with 15% FBS and 1%PS . Both cell lines were cultured at 37 ℃ in a humidified incubator with 5% CO2. Cells were sub-cultured every 2-3 days to maintain them in exponential growth phase.

extract_protocol:
MEF cells were harvested at 80% confluence. They were detached by incubating with 0.25% trypsin with 0.1% EDTA (Thermo Fisher 25200056) for 1 min. Cells were centrifuged at 120 × g for 5 min. Then the supernatant was discarded and cells were resuspended in PBS and diluted to a concentration of 3.2 × 10^5 cells/ml.GM12878 cells were harvested in their exponential phase, centrifuged under the same set of conditions and resuspended in PBS and diluted to the same concentration.This solution was then promptly used for single cell capture on the MID-RNA-Seq device.
Library preparation was performed using the Nextera XT library preparation kit (Illumina FC-131-1024) using 5 μl of purified cDNA following manufacturer's instructions. Libraries were sequenced on Illumina HiSeq 4000 with single-end 50 nt read.
MID-RNA-Seq (Microfluidic Diffusion-based RNA-Seq), procedures are detailed in our paper

value: MEF


title: 2998789_Whole-blood-Venous_Necropsy

description:
Please note that the RNASeq data for this experiment was produced across four specimen types (venous whole blood (WB), capillary whole blood (WC), bone marrow (BM), and spleen tissue (SP)) using RNAprotect, RNAlater, and PAXgene sample collection and storage technologies.  Please carefully review the four README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E30M99FGMmKnDaZZ_11202018-Readme_MULTIPL-GEO.txt  E30M99YSMmKnDaSP_11202018-ReadmeRNALater_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmePaxgene_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmeRNAProtect_MULTIPL-GEO.txt
E30M99FGMmKnDaWB_Knowlesi-Genes-RawCounts-Results_MULTIPL-GEO.xlsx, E30M99FGMmKnDaWB_Mulatta-Genes-RawCounts-Results_MULTIPL-GEO.xlsx

source_name: Whole blood - Venous

value: Whole blood - Venous

tag: infected with

value: Plasmodium knowlesi


title: 2974505_Whole-blood-Capillary_Daily18

value: Daily, 18

tag: tissue


title: SC_MEF_2UnitDevice3_U2


title: LNCap FM Replicate 2


title: 2999138_Whole-blood-Venous_Necropsy


title: SC_MEF_2UnitDevice1_U2


title: Veh_DG_biological rep 06

source_name: DG of vehicle-treated mouse

value: Wild-type

value: Dentate gyrus

value: vehicle


title: 2967134_Whole-blood-Capillary_TimePoint5


title: 2968707_Whole-blood-Capillary_Daily12

value: Daily, 12


title: 37_2998804_Whole-blood-Venous_Necropsy


title: SC_MEF_2UnitDevice2_U1


title: 2971383_Whole-blood-Capillary_Daily14

value: Daily, 14


title: SC_MEF_2UnitDevice1_U1


title: 10pg_GM12878_4UnitDevice1_U3

source_name: GM12878 cell line


title: 10pg_GM12878_4UnitDevice1_U1


title: 10pg_GM12878_4UnitDevice1_U2


title: SC_MEF_2UnitDevice3_U1


title: 2967118_Whole-blood-Venous_TimePoint5


title: 2967045_Bone-Marrow_TimePoint5


title: SC_GM12878_2UnitDevice3_U2


title: 2967025_Whole-blood-Venous_TimePoint5


title: 2967138_Bone-Marrow_TimePoint5


title: SC_GM12878_2UnitDevice3_U1


title: 2966726_Bone-Marrow_TimePoint4


title: SC_GM12878_2UnitDevice2_U2


title: 2966722_Whole-blood-Capillary_TimePoint4


title: SC_GM12878_2UnitDevice2_U1


title: 2966633_Bone-Marrow_TimePoint4


title: 2966706_Whole-blood-Venous_TimePoint4


title: SC_GM12878_2UnitDevice1_U2


title: 2966629_Whole-blood-Capillary_TimePoint4


title: SC_GM12878_2UnitDevice1_U1


title: 10pg_GM12878_4UnitDevice1_U4


title: 2967041_Whole-blood-Capillary_TimePoint5


title: THP1 sgRosa rep2

city: New York

first: Omar

last: Abdel-Wahab

state: NY

address: 1275 York Ave

department: HOPP

institute: MSKCC

description:
CRISPER sgRosa
RBM39_THP1_annotated_combined.counts

data_processing:
The eCLIP data was processed similarly as described previously [pubmed ID 28766298] and is outlined shortly in the following. First, adapter sequences were trimmed from both reads of all read-pairs using cutadapt version 1.14 . Then, all remaining reads longer than 16 bases were aligned against the human reference genome sequence hg19/GRCh37 using STAR version 2.5.0c [REF ]. Only uniquely mapped reads were kept. Read-pair duplicates by position were removed using picard tools version 2.6.0. To identify binding sites, we first ran a custom script to identify clusters of overlapping reads that had a read-depth of at least 10 reads. Then, we calculated significant enrichments for all such identified clusters by comparing IP-samples versus input-samples using edgeR. More specifically, we ran bamutils count version 0.5.7  to counted stranded reads within all identified clusters for all samples. Using this output, we calculated differential coverage between IP-vs-input for each cluster with edgeR after normalizing for total sequencing depth per replicate (resulting in counts per million/CPM per cluster). Final binding sites were called by applying logFC > 2 and FDR < 0.05 thresholds between IP-vs-input.
RNA-seq analysis was done using in-house developed sub-pipeline (reference: Gong, Yixiao, et al. "lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets." BMC genomics 18.1 (2017): 434.). Specifically, sequencing reads of CD4 samples were aligned to reference genome hg38 using STAR-aligner (Dobin,A., Davis,C.A., Schlesinger,F., Drenkow,J., Zaleski,C., Jha,S., Batut,P., Chaisson,M. and Gingeras,T.R. (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29, 15–21) with parameters suggested by TCGA expression mRNA-seq pipeline(https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/), and the raw read counts were generated. Raw read counts of 151 TCGA LAML patients are downloaded from TCGA data portal. Then DESeq2 (Love,M.I., Huber,W. and Anders,S. (2014) Moderated estimation of fold change and dispersion for RNAseq data with DESeq2. Genome Biol, 15, 550) was used to perform differential expression analysis. Volcano plots were generated by R.
Genome_build: hg19
Supplementary_files_format_and_content: eCLIP BigWig read-depth normalized signal. RNA-seq coumt generated by HTSseq.

source_name: THP1 sgRosa

growth_protocol: All human leukemia cells were cultured in RPMI medium with 10% FBS and 1% penicillin streptomycin. The adherent cell lines were grown in DMEM medium with 10% FBS and 1% penicillin streptomycin. Cell lines transduced with lentivirus Cas9 puromycin (Addgene plasmid no. 65655) were selected with puromycin (Sigma Aldrich) 48 hours after transduction. All transfections were performed in HEK293T cells using Polyethylenimine (PEI) reagent at 4:2:3 ratios of sgRNA construct: pVSVG: pPax2 in OPTI-MEM solution. Viral supernatant was collected 48 hrs and 72 hrs post-transfection. Spin infections were performed at room temperature at 1,800 RPM for 30 mins with polybrene reagent (1:2000 dilution) (Fisher Scientific). CRISPR-mediated RBM39 knockout cells were harvested day 6 post-transduction and wash with 1x PBS. For analysis of sulfonamide vs. E7107 treated K562 cells, RNA sequencing was performed in biological duplicate for each cell line and drug treatment..

extract_protocol:
eCLIP studies were performed in duplicates by Eclipse Bioinnovations Inc (San Diego, www.eclipsebio.com) according to the published single-end seCLIP protocol [[can cite pubmed ID 28766298]] with the following modifications. 10 million Molm13 cells were UV crosslinked at 400 mJoules/cm2 with 254 nm radiation, and snap frozen. Cells were then lysed and treated with RNase I to fragment RNA as previously described. RBM39 antibody (A300-291A lot 001, Bethyl) was then pre-coupled to Protein G Dynabeads (Thermo Fisher), added to lysate, and incubated overnight at 4 deg C. Prior to immunoprecipitation, 2% of the sample was taken as the paired input sample, with the remainder magnetically separated and washed with lysis buffer only (as the standard high-salt eCLIP wash buffer gave poor immunoprecipitation yield). RNA adapter ligation, IP-western, reverse transcription, DNA adapter ligation, and PCR amplification were performed as previously described.
eCLIP library preparation  eCLIP studies were performed in duplicates by Eclipse Bioinnovations Inc (San Diego, www.eclipsebio.com) according to the published single-end seCLIP protocol [[can cite pubmed ID 28766298]] with the following modifications. 10 million Molm13 cells were UV crosslinked at 400 mJoules/cm2 with 254 nm radiation, and snap frozen. Cells were then lysed and treated with RNase I to fragment RNA as previously described. RBM39 antibody (A300-291A lot 001, Bethyl) was then pre-coupled to Protein G Dynabeads (Thermo Fisher), added to lysate, and incubated overnight at 4 deg C. Prior to immunoprecipitation, 2% of the sample was taken as the paired input sample, with the remainder magnetically separated and washed with lysis buffer only (as the standard high-salt eCLIP wash buffer gave poor immunoprecipitation yield). RNA adapter ligation, IP-western, reverse transcription, DNA adapter ligation, and PCR amplification were performed as previously described.
RNA-seq library preparation  CRISPR-mediated RBM39 knockout cells were harvested day 6 post-transduction and wash with 1x PBS. To extract total RNA, we used RNeasy Plus Mini Kit (Qiagen) and QIAshredder (Qiagen), which were performed according to manufacturer’s protocol. We isolated poly(A) mRNA using magnetic isolation method (NEB) using ~1 ug of total mRNA. To generate RNA-sequencing libraries, we used NEXTflex Rapid Directional (Bioo Scientific) protocol and NEXTflex RNA-seq barcodes (Bioo Scientific), which were carried out according to manufacturer’s protocol. RNA-seq barcoded libraries were then sequenced using Hi-Seq 4000 (150 cycles paired end).

value: CRISPER sgRosa


title: 2966613_Whole-blood-Venous_TimePoint4


title: THP1 sgRosa rep1

treatment_protocol: CRISPR-mediated RBM39 knockout cells were harvested day 6 post-transduction and wash with 1x PBS. To extract total RNA, we used RNeasy Plus Mini Kit (Qiagen) and QIAshredder (Qiagen), which were performed according to manufacturer’s protocol. We isolated poly(A) mRNA using magnetic isolation method (NEB) using ~1 ug of total mRNA. To generate RNA-sequencing libraries, we used NEXTflex Rapid Directional (Bioo Scientific) protocol and NEXTflex RNA-seq barcodes (Bioo Scientific), which were carried out according to manufacturer’s protocol. RNA-seq barcoded libraries were then sequenced using Hi-Seq 4000 (150 cycles paired end).


title: 3'mRNAseq_zPCF11deltaPAS1_hom_e5

city: Oxford

first: Kinga

last: Kamieniarz-Gdula

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

data_processing:
3’ mRNA-seq data were mapped according to the guidelines of QuantSeq library kit manufacturer (Lexogen). Unaligned bam files from HiSeq2500 were converted to FASTQ files with bam2fastx (TopHat 2 component (Kim et al., 2013)). After overview with FastQC reads were trimmed with BBtools (sourceforge.net/projects/bbmap/) script bbduk using following settings: k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20 .
After trimming control with FastQC curated reads were mapped with STAR2.5b (Dobin et al., 2013) aligner. STAR index was  generated with the GRCz10/danRer10 was used as the reference zebrafish genome together with the corresponding ENSEMBL annotation).
Aligned 3’ mRNA-seq reads were filtered to remove false positives due to internal priming of the QuantSeq assay on genome-encoded poly(A) stretches. To do this, first a crude genomic mask was generated that contained all loci harbouring 6 or more consecutive A bases as well as any 10 nucleotide windows containing more than 6 A bases. For genes expressed from the reverse strand, an analogous T-rich mask was generated. Those crude masks were then corrected to allow for detection of genuine PAS falling in A/T-rich regions by strand-specifically unmasking 20 nucleotide intervals centred at annotated 3’ gene ends. 3’ mRNA-seq reads falling into those refined strand-specific masks were then removed, and the filtered reads reduced to the most distal nucleotide (3’ end nucleotide).
Genome_build: GRCz10/danRer10
Supplementary_files_format_and_content: bigWig files: genome-coverage files, mean from replicates

organism: Danio rerio

source_name: single embryo head 32hpf

growth_protocol: Zebrafish (Danio rerio) were raised according to standard protocols (28°C water temperature, 14/10 hr light/dark cycle). TLAB fish, generated by crossing zebrafish AB and the natural variant TL (Tupfel Long-fin) stocks, served as wild-type zebrafish for all experiments. zPCF11 null and zPCF11 ∆PAS1 mutant zebrafish were generated by Cas9-mediated mutagenesis (Gagnon et al., 2014)

extract_protocol:
Dechorionated embryos of heterozygous Pcf11-mutant incrosses were cut in half with a razor blade at 19 hpf (zPCF11null) or 32 hpf (zPCF11deltaPAS1) and, and each head and tail was  collected individually in PCR tubes. The anterior halves (heads) were lysed in 10 µl of TCL buffer with 1% beta-mercaptoethanol and flash-frozen on dry ice for subsequent use for RNA isolation and sequencing. The posterior halves (tails) were used for genotyping of each individual sample. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads (A63987, Beckman Coulter).
Libraries were prepared according to the protocols of QuantSeq 3’mRNA-Seq library prep kit FW for Illumina (LEXOGEN Cat# SKU 015.96)
3-4 wild-type, 4-5 heterozygous, and six homozygous samples of both zPCF11 null and zPCF11 delta-PAS1 mutants were used for library preparation. RNA of selected samples was isolated and purified using Agencourt RNAClean XP magnetic beads (A63987, Beckman Coulter). Strand-specific libraries were generated using the QuantSeq 3' mRNA Library Prep Kit FW (Lexogen) and used for 100-bp single-end sequencing on the Illumina HiSeq 2500.

tag: molecule subtype

value: 3' end of mRNA

tag: genotype/treatment

value: zPCF11deltaPAS1 -/-


title: 2953379_Whole-blood-Capillary_Daily4

value: Daily, 4

value: Male


title: 2953387_Whole-blood-Capillary_Daily4


title: 2953395_Whole-blood-Capillary_Daily6

value: Daily, 6


title: 3'mRNAseq_zPCF11deltaPAS1_hom_e6


title: MOLM13-sgRosa rep1

description:
CRISPER sgRosa
RBM39_MOLM13_annotated_combined.counts

tag: treatment


title: THP1 sgRBM39 9-1 rep1

description:
CRISPER sgRBM39
RBM39_THP1_annotated_combined.counts

source_name: THP1 sgRBM39 9-1

value: CRISPER sgRBM39

tag: genotype

value: CRISPR-mediated RBM39 knockout


title: THP1 sgRBM39 15-1 rep3

source_name: THP1 sgRBM39 15-1


title: 2953363_Whole-blood-Capillary_Daily2

value: Daily, 2

value: Whole blood - Capillary


title: 2953371_Whole-blood-Capillary_Daily2


title: 3'mRNAseq_zPCF11deltaPAS1_hom_e3


title: 3'mRNAseq_zPCF11deltaPAS1_hom_e2


title: 2953355_Whole-blood-Capillary_Daily(-)2

value: Daily, -2


title: 2953347_Whole-blood-Capillary_Daily(-)2


title: MOLM13-sgRBM39-9-1 rep1

description:
CRISPER sgRBM39
RBM39_MOLM13_annotated_combined.counts


title: 3'mRNAseq_zPCF11deltaPAS1_hom_e1


title: THP1 sgRBM39 9-1 rep2


title: 3'mRNAseq_zPCF11deltaPAS1_het_e5

value: zPCF11deltaPAS1 +/-


title: 2953339_Whole-blood-Capillary_Daily(-)4

value: Daily, -4


title: 2953403_Whole-blood-Capillary_Daily6


title: 2953331_Whole-blood-Capillary_Daily(-)4


title: K562 par E7820 1uM rep2

description:
RNA-seq after E7820 1uM
annotated_combined.counts


title: K562 par E7820 1uM rep1


title: 3'mRNAseq_zPCF11deltaPAS1_hom_e4


title: 2953323_Whole-blood-Capillary_Daily(-)6

value: Daily, -6


title: 3'mRNAseq_zPCF11deltaPAS1_het_e3


title: K562 par E7820 100uM rep1

description:
RNA-seq after E7820 100uM
annotated_combined.counts


title: K562 par E7820 100uM rep2


title: K562 par E7107 rep2

description:
RNA-seq after E7107
annotated_combined.counts


title: 3'mRNAseq_zPCF11deltaPAS1_het_e2


title: MOLM13-sgRBM39-15-1 rep1


title: 3'mRNAseq_zPCF11deltaPAS1_het_e1


title: 2953238_Whole-blood-Capillary_TimePoint3


title: K562 par E7107 rep1


title: 2953315_Whole-blood-Capillary_Daily(-)6


title: 2953242_Bone-Marrow_TimePoint3

value: Bone Marrow


title: 3'mRNAseq_zPCF11deltaPAS1_wt_e2

value: zPCF11deltaPAS1 +/+


title: K562 par DMSO rep2

description:
RNA-seq after DMSO
annotated_combined.counts

source_name: K562 par DMSO

value: DMSO


title: 2953222_Whole-blood-Venous_TimePoint3

value: Whole blood - Venous

value: Plasmodium knowlesi


title: 3'mRNAseq_zPCF11deltaPAS1_wt_e1

value: 3' end of mRNA


title: 2953149_Bone-Marrow_TimePoint3


title: K562 par DMSO rep2b


title: 3'mRNAseq_zPCF11deltaPAS1_wt_e3


title: 3'mRNAseq_zPCF11deltaPAS1_het_e4


title: 3'mRNAseq_zPCF11null_hom_e6

source_name: single embryo head 19hpf

value: zPCF11null -/-


title: 3'mRNAseq_zPCF11null_hom_e5


title: K562 P95H E7820 1uM rep2


title: K562 par DMSO rep1


title: K562 P95H E7820 1uM rep1


title: 2953145_Whole-blood-Capillary_TimePoint3

value: Male


title: 2953129_Whole-blood-Venous_TimePoint3


title: 2951334_Whole-blood-Capillary_Daily(-)8

value: Daily, -8


title: 2951342_Whole-blood-Capillary_Daily(-)8


title: 3'mRNAseq_zPCF11null_hom_e4


title: 2951326_Whole-blood-Capillary_Daily(-)10

value: Daily, -10


title: K562 P95H E7820 100uM rep2


title: 3'mRNAseq_zPCF11null_hom_e2


title: K562 P95H E7107 rep2


title: 3'mRNAseq_zPCF11null_het_e4

value: zPCF11null +/-


title: K562 P95H E7107 rep1


title: 2951310_Whole-blood-Capillary_Daily(-)12

value: Daily, -12


title: 3'mRNAseq_zPCF11null_het_e3


title: 2951294_Whole-blood-Capillary_Daily(-)14

value: Daily, -14

value: Whole blood - Capillary


title: K562 P95H DMSO rep2

source_name: K562 P95H DMSO


title: 3'mRNAseq_zPCF11null_hom_e1


title: 2951302_Whole-blood-Capillary_Daily(-)12


title: K562 P95H DMSO rep2b


title: K562 P95H DMSO rep1


title: K562 K700E E7820 1uM rep2


title: 3'mRNAseq_zPCF11null_het_e2


title: 2944103_Bone-Marrow_TimePoint2


title: 2951286_Whole-blood-Capillary_Daily(-)14


title: 3'mRNAseq_zPCF11null_het_e1


title: 3'mRNAseq_zPCF11null_wt_e4

value: zPCF11null +/+


title: C6/36_Melpop_DV2 rep3

city: Philadelphia

first: Klaudia

last: Kuranda

address: 3737 Market St

department: Data Sciences

institute: Spark Therapeutics

description:
C6/36 cells infected with DENV2 virus and wMelpop symbiont
c636_dv2_mpop_3_vs_albo_w_annot_gene_count.txt

data_processing:
Raw reads were first screened using ssaha2 (Ning, Cox and Mullikin, 2001) and the UniVec database (accessed July 7th, 2013) to remove vector sequences, adapters, linkers, and primers commonly used in cloning cDNA or genomic DNA as well as Ae. albopictus rRNA sequences (GenBank accession L22060.1). After ssaha2 screening, cleaned reads were further filtered using SolexaQA V2.2 to retain contiguous reads longer than 50 bp with phred quality scores higher than 30.
Cleaned reads were mapped to the annotated scaffolds in the Ae. albopictus genome (Chen et al. 2015), using Hisat2 (Version 2.0.4).
Contigs were assembled from the sorted BAM files using Stringtie (Version 1.3.0). Transcripts were constructed and merged from all 11 libraries. Transcript counts at the gene level, not the isoform level, were obtained using Ballgown (Version 2.7). Reads counts were then processed in edgeR (Chen et al. 2015) in the R software environment (www.r-project.org).
Differentially expressed (DE) genes were identified as having an absolute value of log2 fold-change greater than 1 with a Benjamini-Hochberg (FDR)-corrected p-value less than 0.05.
Genome_build: AaloF1
Supplementary_files_format_and_content: tab-delimited text files include raw gene read numbers for each Sample ...

organism: Aedes albopictus

source_name: Cell culture

growth_protocol: The C6/36 cells were grown in minimum essential medium (MEM) containing 5% FBS, 2mM L-glutamine, 25 147 mM HEPES, pH 7.2, 1 mM sodium pyruvate, 1x non-essential amino acids, 100 U/ml 148 penicillin and 100 μg/ml streptomycin at 28 oC.

extract_protocol:
RNAs from monolayer of C6/36 cells were extracted with Trizol (Ambion Life Technologies) according to the manufacturer’s instructions. RNA quantity and integrity were determined on an Agilent 2100 Bioanalyzer. After three to five days post infection, culture supernatants were collected after centrifugation at 3,000 rpm for 5 minutes. Monolayer cells were used for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
The C6/36 cells, in which the endosymbiont wMelPop, stably replicates (referred here as wMelPop-C6/36 cells) were grown in the same medium and conditions as mentioned above.
Naïve C6/36 and wMelPop-C6/36 cells were infected with DENV2 in triplicate T-75 flasks. DENV2 stock was diluted in 2% FBS-supplemented with maintenance medium and added to 70% confluent monolayer cells at MOI of 1. Cells were incubated for an hour at room temperature. Then, the culture media were replaced with maintenance medium containing 5% FBS and the cells were incubated in a humidified 5% CO2 chamber at 37 oC.

tag: clone

value: DENV2 infected with wMelpop symbiont


title: 3'mRNAseq_zPCF11null_hom_e3


title: K562 K700E E7820 1uM rep1


title: K562 P95H E7820 100uM rep1


title: 3'mRNAseq_zPCF11null_wt_e3


title: 2944099_Whole-blood-Capillary_TimePoint2


title: K562 K700E E7820 100uM rep2


title: 2944083_Whole-blood-Venous_TimePoint2


title: 2951318_Whole-blood-Capillary_Daily(-)10


title: 3'mRNAseq_zPCF11null_wt_e2


title: K562 K700E E7820 100uM rep1


title: 2944010_Bone-Marrow_TimePoint2


title: C6/36_Melpop_DV2 rep1

description:
C6/36 cells infected with DENV2 virus and wMelpop symbiont
c636_dv2_mpop_1_vs_albo_w_annot_gene_count.txt


title: C6/36_Melpop rep3

description:
C6/36 cells with wMelpop symbiont
c636_mpop_3_vs_albo_w_annot_gene_count.txt

value: with wMelpop symbiont


title: 2944006_Whole-blood-Capillary_TimePoint2


title: K562 K700E E7107 rep1


title: WT_rna_rep2

city: Austin

first: Adam

middle: John

last: Hockenberry

state: TX

department: Department of Integrative Biology

institute: The University of Texas at Austin

description: Wild-type strain

data_processing:
The adapter sequence (located in adapters.fasta) was removed (when found) from the 3′ end of all reads using Cutadapt
Lanes were demultiplexed into constituent samples using Cutadapt, and concatenated together using 'cat' to form sample specific .fastq.gz files. (NOTE: These are the provided .fastq.gz files for each sample). Reads without barcodes were discarded from all further analysis.
For subsequent analysis, 5 nucleotides were removed from the 3' terminus of each read using Cutadapt
The 5' adapter sequence (found in adapters.fasta) was removed (when found) using Cutadapt
2 nucleotides were removed from the 5' terminus of each read using Cutadapt
RNA-seq reads only were aligned using Kallisto to a transcript index built from U00096.3 with "-k 17" and analyzed for differential expression using Sleuth resulting in the RNAseq_stat_summary.csv file
For ribosome profiling and translation efficiency analysis, both Ribo-seq and RNA-seq reads were mapped to U00096.3 using HISAT2 (--no-spliced-alignment flag) to create .sam and subsequently .bam files
Fully reproducible bioinformatic details with code can be found at: https://github.com/adamhockenberry/ribo-t-sequencing
Genome_build: genbank id: U00096.3
Supplementary_files_format_and_content: For both sample types (Ribo-seq and RNA-seq), the primary HISAT2 alignments were mapped to the 3' end position of the read to create initial .wig files for visualization and gene-level quantification. After visual inspection an offset of 16 nt was applied to align Ribo-seq data to ribosomal P-sites. The same offset/analysis was applied to RNA-seq for comparison/consistency. RPKM for each CDS was calculated for each sample's Ribo-seq and RNA-seq data from these .wig mappings. Statistical summaries/comparison of Ribo-seq and Translation Efficiency (TE) differences can be found in TE_stat_summary.csv

organism: Escherichia coli

source_name: wild-type strain

growth_protocol: The cultures of SQ171 (WT) and Ribo-T cells were grown overnight in LB medium supplemented with ampicillin (100 mg/ml) and spectinomycin (50 mg/ml). Cultures were diluted 100-fold into three conical baffled 1-litre flasks containing 100 mL of LB supplemented with the same antibiotics and with 0.2% glucose. Cultures were grown at 37 °C with vigorous shaking.

extract_protocol:
When the culture density reached A600 of ∼0.5 cells were harvested by rapid filtration, frozen in liquid nitrogen, and processed for ribosome profiling as described in [Becker, A.H., Oh, E., Weissman, J.S., Kramer, G. & Bukau, B. Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes. Nat Protoc 8, 2212-39 (2013)]. For the preparation of RNA-seq samples, total RNA was isolated from the cell lysates, short RNA and rRNA were subtracted using Ambion MEGAclear kit and MICROBexpress bacterial mRNA enrichment kit, respectively, and RNA was fragmented using the RNA Fragmentation Reagents kit from Ambion.
The library for next-generation sequencing was prepared using RNA fragments ranging in size from 20 to 45 nt. During data analysis, the first position of the P site codon was assigned at 15 nt away from the 3’ end of the read.

tag: strain/variation


title: K562 K700E E7107 rep2


title: 3'mRNAseq_zPCF11null_wt_e1


title: C6/36_Melpop rep2

description:
C6/36 cells with wMelpop symbiont
c636_mpop_2_vs_albo_w_annot_gene_count.txt


title: 2943990_Whole-blood-Venous_TimePoint2


title: K562 K700E DMSO rep2

source_name: K562 K700E DMSO


title: K562 K700E DMSO rep1


title: 2927676_Bone-Marrow_TimePoint1

source_name: Bone Marrow

value: Bone Marrow


title: WT_rna_rep1

description: Wild-type strain


title: WT_ribo_rep2

description: Wild-type strain

data_processing:
Library strategy: Ribo-seq
The adapter sequence (located in adapters.fasta) was removed (when found) from the 3′ end of all reads using Cutadapt
Lanes were demultiplexed into constituent samples using Cutadapt, and concatenated together using 'cat' to form sample specific .fastq.gz files. (NOTE: These are the provided .fastq.gz files for each sample). Reads without barcodes were discarded from all further analysis.
For subsequent analysis, 5 nucleotides were removed from the 3' terminus of each read using Cutadapt
The 5' adapter sequence (found in adapters.fasta) was removed (when found) using Cutadapt
2 nucleotides were removed from the 5' terminus of each read using Cutadapt
RNA-seq reads only were aligned using Kallisto to a transcript index built from U00096.3 with "-k 17" and analyzed for differential expression using Sleuth resulting in the RNAseq_stat_summary.csv file
For ribosome profiling and translation efficiency analysis, both Ribo-seq and RNA-seq reads were mapped to U00096.3 using HISAT2 (--no-spliced-alignment flag) to create .sam and subsequently .bam files
Fully reproducible bioinformatic details with code can be found at: https://github.com/adamhockenberry/ribo-t-sequencing
Genome_build: genbank id: U00096.3
Supplementary_files_format_and_content: For both sample types (Ribo-seq and RNA-seq), the primary HISAT2 alignments were mapped to the 3' end position of the read to create initial .wig files for visualization and gene-level quantification. After visual inspection an offset of 16 nt was applied to align Ribo-seq data to ribosomal P-sites. The same offset/analysis was applied to RNA-seq for comparison/consistency. RPKM for each CDS was calculated for each sample's Ribo-seq and RNA-seq data from these .wig mappings. Statistical summaries/comparison of Ribo-seq and Translation Efficiency (TE) differences can be found in TE_stat_summary.csv


title: C6/36_DV2 rep3

description:
C6/36 cells infected with DENV2 virus
c636_dv2_3_vs_albo_w_annot_gene_count.txt

value: DENV2 infected


title: C6/36_DV2 rep2

description:
C6/36 cells infected with DENV2 virus
c636_dv2_2_vs_albo_w_annot_gene_count.txt


title: C6/36_Melpop_DV2 rep2

description:
C6/36 cells infected with DENV2 virus and wMelpop symbiont
c636_dv2_mpop_2_vs_albo_w_annot_gene_count.txt


title: eCLIP RBM39 3

description: RBM39 eCLIP

source_name: eCLIP RBM39

tag: rip antibody

value: RBM39 antibody (A300-291A lot 001, Bethyl)


title: 2927658_Whole-blood-Venous_TimePoint1

value: Whole blood - Venous


title: 2927672_Whole-blood-Capillary_TimePoint1

description:
Please note that the RNASeq data for this experiment was produced across four specimen types (venous whole blood (WB), capillary whole blood (WC), bone marrow (BM), and spleen tissue (SP)) using RNAprotect, RNAlater, and PAXgene sample collection and storage technologies.  Please carefully review the four README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E30M99FGMmKnDaZZ_11202018-Readme_MULTIPL-GEO.txt  E30M99YSMmKnDaSP_11202018-ReadmeRNALater_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmePaxgene_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmeRNAProtect_MULTIPL-GEO.txt
E30M99FGMmKnDaWC_Knowlesi-Genes-RawCounts-Results_MULTIPL.xlsx, E30M99FGMmKnDaWC_Mulatta-Genes-RawCounts-Results_MULTIPL.xlsx

source_name: Whole blood - Capillary


title: C6/36_DV2 rep1

description:
C6/36 cells infected with DENV2 virus
c636_dv2_1_vs_albo_w_annot_gene_count.txt


title: WT_ribo_rep1

description: Wild-type strain


title: RIBOT_rna_rep2

description: Evolved fast growth strain

source_name: Wild-type strain with pRibo-T plasmid cured of plasmid carrying WT rRNA

value: SQ171 (+pRibo-T)


title: C6/36_naive rep3

description:
Naïve C6/36 cells
c636_3_vs_albo_w_annot_gene_count.txt

value: naïve cells


title: eCLIP RBM39 1

description: RBM39 eCLIP


title: 2927599_Bone-Marrow_TimePoint1

description:
Please note that the RNASeq data for this experiment was produced across four specimen types (venous whole blood (WB), capillary whole blood (WC), bone marrow (BM), and spleen tissue (SP)) using RNAprotect, RNAlater, and PAXgene sample collection and storage technologies.  Please carefully review the four README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E30M99FGMmKnDaZZ_11202018-Readme_MULTIPL-GEO.txt  E30M99YSMmKnDaSP_11202018-ReadmeRNALater_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmePaxgene_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmeRNAProtect_MULTIPL-GEO.txt
E30M99FGMmKnDaBM_Knowlesi-Genes-RawCounts-Results_MULTIPL-GEO.xlsx, E30M99FGMmKnDaBM_Mulatta-Genes-RawCounts-Results_MULTIPL-GEO.xlsx


title: RIBOT_rna_rep1

description: Evolved fast growth strain


title: C6/36_naive rep2

description:
Naïve C6/36 cells
c636_2_vs_albo_w_annot_gene_count.txt


title: 2974242_Whole-blood-Capillary_Daily16

value: Daily, 16


title: 2998808_Bone-Marrow_Necropsy

value: Necropsy

value: Male


title: eCLIP INPUT 3

description: INPUT

source_name: eCLIP INPUT


title: 2927595_Whole-blood-Capillary_TimePoint1


title: C6/36_naive rep1

description:
Naïve C6/36 cells
c636_1_vs_albo_w_annot_gene_count.txt


title: 2927581_Whole-blood-Venous_TimePoint1

description:
Please note that the RNASeq data for this experiment was produced across four specimen types (venous whole blood (WB), capillary whole blood (WC), bone marrow (BM), and spleen tissue (SP)) using RNAprotect, RNAlater, and PAXgene sample collection and storage technologies.  Please carefully review the four README files provided as supplementary files with this dataset for the details on the methods used for sequence generation and abundance measures.  README file names are as follows:  E30M99FGMmKnDaZZ_11202018-Readme_MULTIPL-GEO.txt  E30M99YSMmKnDaSP_11202018-ReadmeRNALater_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmePaxgene_MULTIPL-GEO.txt  E30M99YSMmKnDaZZ_11202018-ReadmeRNAProtect_MULTIPL-GEO.txt
E30M99FGMmKnDaWB_Knowlesi-Genes-RawCounts-Results_MULTIPL-GEO.xlsx, E30M99FGMmKnDaWB_Mulatta-Genes-RawCounts-Results_MULTIPL-GEO.xlsx

source_name: Whole blood - Venous

value: Plasmodium knowlesi


title: PAR-CLIP RBM39

description: RBM39 par-CLIP

source_name: PAR-CLIP RBM39


title: eCLIP INPUT 1

description: INPUT


title: RIBOT_ribo_rep2

description: Evolved fast growth strain


title: ΔrecA mutant strain, replicate3

status: Public on Feb 24 2019

city: Suita

first: Chiara

last: Furusawa

state: Osaka

address: Furuedai

institute: RIKEN Quantitative Biology Center

description: Gene expression of E. coli cells at mid-exponential growth phase

hyb_protocol: After confirmation of yields (> 825 ng) and specific activities (> 15 pmol/μg) of the Cy3-labbeled cRNAs using NanoDrop ND-2000, 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to custom designed the Agilent 8× 60K arrays for E. coli W3110, E.coli_K12_Expression_Ver.1, for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (AgilentG3_GX_1Color, Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: ExternalFullGEML_043017_D_F_20120907) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: ΔrecA mutant strain

label_protocol: 100 ng of purified total RNA samples were labelled using the Low Input Quick Amp WT Labeling Kit (Agilent Technologies) with Cyanine3 (Cy3) according to the manufacturer’s instructions.

growth_protocol: MDS42 and the ΔrecA mutant cells were inoculated from the frozen glycerol stock into 5 ml of modified M9 medium in test tubes and cultivated overnight at 34°C at 150 rpm. The overnight cultures were diluted to an OD600 of 0.1 into fresh modified M9 medium in test tubes and cultured.

extract_protocol: Two volumes of RNA Protect bacterial reagent (Qiagen) were added directly to one volume of the exponentially growing cultures to stabilize cellular RNA. The cells were harvested by centrifugation at 5,000×g for 10 min at 25°C, and total cellular RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Total RNA was treated with DNase I at room temperature for 15 min. The purified RNA samples were stores at – 80°C before microarray experiments. The quality of the purified RNA was evaluated using Agilent 2100 Bioanalyzer with an RNA 6000 Nano kit (Agilent Technologies). Only purified RNAs that had RIN (RNA integrity number) of 8.4 or more were utilized. The purified RNAs were stored at −80°C prior to transcriptome analysis.

treatment_protocol: Exponentially growing cultures (OD600 of ~1; mid-exponential growth phase) grown in the modified M9 medium were harvested for total RNA extraction.

value: {delta}recA mutant


title: ΔrecA mutant strain, replicate2


title: ΔrecA mutant strain, replicate1


title: Parental strain, replicate3

source_name: MDS42 strain

value: control


title: 2-month Dhh-Cre;Nf1 fl/fl nerve/DRG 10X Genomics single-cell RNA-Seq data set

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
Illumina HiSeq2500 used for basecalling
CellRanger software package used for alignment, filtering, barcode reading prior to post processing with ICGS in AltAnalyze.
Genome_build: mm10
-Read1 is the technical reads and it contains the barcode (first 16 nt) and umi (next 10 nt).
-Read2 is the biological read.
Supplementary_files_format_and_content: 10X Genomics Chromium Raw Gene BC Cellular Barcodes
Supplementary_files_format_and_content: 10X Genomics Chromium Raw Gene BC Cellular Genes
Supplementary_files_format_and_content: 10X Genomics Chromium Raw Gene BC Cellular Matrix

source_name: nerve/DRG

extract_protocol:
DRGs were cut into 1-2 mm3 pieces and dissociated in 20 mL L-15 medium (Mediatech) containing 0.5mg/mL collagenase type 1 (Worthington; Lakewood, NJ), and 2.5 mg/mL dispase protease type II (Cambrex; East Rutherford, NJ) at 37°C for 2 hours. Then, 30 mL DMEM medium containing 10% FBS was added to stop the reaction. Cells were centrifuged and supernatant was removed. Next, cells were resuspended in 5 mL DMED by trituration (30x) and filtered through 100um, 40um and 20um cell strainers sequentially. After straining, cells were centrifuged and resuspended in 1x PBS containing 0.1% BSA at 1000 cells/μL.
We utilized the 10X Genomics Chromium Instrument and cDNA synthesis kit (10x Genomics) to generate a barcoded cDNA library for single cell RNA-sequencing from approximately 10,000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library, we performed one full lane sequence on two paired-end 75bp Flow Cells using on an Illumina HiSeq2500.
10X Genomics Chromium v2 chemistry

tag: strain

value: nerve/DRG

value: 2 months


title: RIBOT_ribo_rep1

description: Evolved fast growth strain


title: siDNM2 24h replicate 3

city: Sevilla

first: Eloisa

last: Andujar

state: Sevilla

address: Avda Americo vespucio s/n

department: GENOMICS UNIT

country: Spain

institute: CABIMER-CSIC

hyb_protocol: Following fragmentation, 5.5 ug of single-stranded cDNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .CEL files were generated using Affymetrix GCOS software and further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis were performed using the limma package (oneChannelGUI interface) of R/Bioconductor project.

source_name: siDNM2 24h

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA Labeling Protocol (GeneChip® Whole Transcript Sense Target Labeling Assay Manual, Affymetrix, 2007).

growth_protocol: HeLa cells were cultivated in DMEM supplemented with 7% fetal bovine serum

extract_protocol: Rneasy mini Kit (Qiagen) of total RNA was performed according to the manufacturer's instruction.

treatment_protocol: siRNAs were transfected using oligofectamine as described by the manufacturer (Dharmacon Research) for 24 or 72h. SiRNA Universal Negative Control (siC001) were used as control.

value: HeLa cells


title: siControl 72h replicate 2

source_name: siControl 72h


title: wt replicate 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G and the images were acquired by Affymetrix default GeneChip® Operating System 1.4.0.036 (GCOS), and converted in .DAT files.

data_processing: The .DAT image files for each array were converted into .CEL files using Affymetrix GCOS software. These .CEL files were further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis were performed using the limma package (affylmGUI interface) of R/Bioconductor project.

organism: Saccharomyces cerevisiae

source_name: wild type

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA Labeling Protocol (GeneChip® 3' IVT Express Kit User Manual, Affymetrix, 2008-2010).

growth_protocol: The yeast cells were grown at 30ºC in suplemented minimal medium (SMM)

extract_protocol: Rneasy® mini kit (Qiagen) of total RNA was performed according to the manufacturer's instructions.


title: vps1Δ mutant replicate 2

source_name: vps1Δ mutant


title: vps1Δ mutant replicate 3


title: wt replicate 3


title: siControl 72h replicate 3


title: wt replicate 1


title: siControl 24h replicate 3

source_name: siControl 24h


title: Parental strain, replicate2


title: siDNM2 72h replicate 3

source_name: siDNM2 72h


title: vps1Δ mutant replicate 1


title: siDNM2 24h replicate 1


title: siDNM2 24h replicate 2


title: siDNM2 72h replicate 1


title: siDNM2 72h replicate 2


title: siControl 24h replicate 2


title: siControl 24h replicate 1


title: SHP-KO #2

status: Public on Feb 23 2019

city: Urbana

first: Young-Chae

last: Kim

state: IL

address: 394 Burrill Hall  407 S. Goodwin Ave

department: MIP

institute: University of Illinois at Urbana-Champaign

data_processing:
Using a HiSeq SBS sequencing kit version 4, Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).
Trimmomatic ver 0.38 was used to remove sequence adapters and low-quality bases and quality control was checked by FastQC ver 0.11.5
Sequencing alignment was performed by STAR ver 2.6.0c.
The differential expression profiles of RNA-seq were analyzed by the edgeR-based R (ver 3.5.0) pipeline
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include gene read counts, fold change, FDR between two conditions generated by edgeR

source_name: mouse intestine (Jejunum and Ileum)

extract_protocol:
RNA from the intestine (Jejunum and Ileum) was isolated with the RNeasy Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols. The cDNA library was sequenced using an Illumina HiSeq2000 (Illumina, San Diego, CA) to produce 100 bp reads.

treatment_protocol: Eight week-old wild-type (WT) and SHP-KO male mice were fasted overnight and refed for 6 h.

value: male

value: SHP-KO

value: intestine (Jejunum and Ileum)

value: fed 6 h after fasting O/N


title: siControl 72h replicate 1


title: SHP-KO #1


title: SHP-KO #3


title: T_gm_3

city: Fuzhou

first: Justice

last: Norvienyeku

state: N/A = Not Applicable

address: shangxia District RD.No#15, Fuzhou

country: China

institute: Fujian Agriculture and Forestry University

description:
Inoculated leaves
PolyA RNA
processed data: Gene_Expression_All_Samples.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house Perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data.
Rice (Oryza sativa Japonica group, IRGSP-1.0) reference genome and gene model annotation files were downloaded from Ensembl Plants genome website directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.4. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. Then, RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Oryza_sativa.IRGSP V1.0 (IRGSP-1.0 from Ensembl Plants genome database)
Supplementary_files_format_and_content: GeneExpression.AllSamples.txt: Tab-delimited text file includes RPKM values for each Sample.

organism: Oryza sativa Indica Group

source_name: Pi-gm rice cultivar

extract_protocol:
Total RNA was extracted using the RNAprep pure Plant Kit (Tiangen, Beijing) by following processes recommended by the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Susceptible (CO39 and NPB) and resistant (Pi_gm) rice cultivars were spray inoculated with P. oryzae spore and incubated for 12-hours.

tag: cultivar

value: Pi-gm

tag: seedlings age

value: 3 weeks

value: Leaves

value: Inoculated with Pyricularia oryzae

tag: sample group

value: Treatment


title: WT #3

value: wild-type


title: Parental strain, replicate1


title: WT #2


title: T_gm_2


title: T_Co39_3

source_name: CO39 rice cultivar


title: T_gm_1


title: 8199_SPF_KP_spl

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

institute: MIT

description: γδ T cells

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options. Estimated counts from rsem were upper-quartile normalized where the 75th percentile was set to 1000.
Genome_build: mm9
Supplementary_files_format_and_content: CJ_RNAseq_2018_rsem_est_counts_mm9.txt includes estimated read counts (from rsem) per gene for each sample.  CJ_RNAseq_2018_normalized_counts_mm9 includes normalized counts.

source_name: γδ T Cells from spleens of KP mice

extract_protocol:
Cells were directly sorted into TCL buffer. Whole transcriptome amplication was performed with Smartseq v2 protocol.
RNA libraries were prepared for sequencing with the Illumina Nextera kit according to the manufacturer's instructions.

value: spleen

tag: cell type

value: <gamma><delta> T cells


title: T_Co39_2


title: 8179_SPF_KP_spl

description: γδ T cells


title: T_Co39_1


title: 8171_SPF_KP_spl

description: γδ T cells


title: C_gm_2

description:
Non-inoculated leaves
PolyA RNA
processed data: Gene_Expression_All_Samples.txt

value: Non-inoculated

value: Control


title: 7943_SPF_KP_spl

description: γδ T cells


title: 7903_SPF_KP_spl

description: γδ T cells


title: 7889_SPF_KP_spl

description: γδ T cells


title: 5687_SPF_LucOS_spl

description: γδ T cells


title: 5682_SPF_LucOS_spl

description: γδ T cells


title: 8241_SPF_KP_lung

description: γδ T cells

source_name: γδ T Cells from tumor bearing lungs of KP mice

value: tumor bearing lungs


title: 5685_SPF_LucOS_spl

description: γδ T cells


title: 8197_SPF_KP_lung

description: γδ T cells


title: C_Co39_1


title: C_Co39_2


title: 8170_SPF_KP_lung

description: γδ T cells

value: C3HeB/Fe (C3H)


title: 7943_SPF_KP_lung

description: γδ T cells


title: C_Co39_3


title: 7903_SPF_KP_lung

description: γδ T cells


title: WT #1

tag: gender


title: 7889_SPF_KP_lung

description: γδ T cells


title: 8199_SPF_KP_lung

description: γδ T cells


title: 7137_SPF_Ad_lung

description: γδ T cells


title: C_gm_3


title: C_gm_1


title: TI_Dppa4_short_2D7_input

city: Chexbres

first: Alexandre

last: Coudray

state: Vaud

address: 11, Chemin de Baulet

department: Life Science

country: Switzerland

institute: EPFL

description: tissue culture

data_processing:
Alignement for ChIP-seqs were done with bowtie2
Peak calling for ChIP-seqs were done using MACS or ChIP-part module of the ChIP-seq analysis platform (http://ccg.vital-it.ch/chipseq/)
Genome_build: mm9
Supplementary_files_format_and_content: A bed file containing the output of the peak called by MACS or ChIP-Part is provided.

source_name: mouse embryonic stem cells

growth_protocol: mESCs were cultured in serum

extract_protocol:
ChIP and library preparation were done according to (De Iaco 2017)
Libraries were ligated with Illumina adaptors

treatment_protocol: Samples were transfected with the appropriate plasmid and RNA collected 2 days after transfection

value: mESC in serum, transfected with appropriate plasmid

tag: transfected with

tag: chip antibody

value: none (input)


title: TI_Dppa4_short_3A5_input

description: tissue culture


title: TI_Dppa4_FL_3A5_input

description: tissue culture


title: HBEC U2AF1 WT 4 ribosomes [WT_4]

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

description:
processed data file: Riboprofiles_counts.txt
wt_4_S4_L008

data_processing:
library strategy: ribosome profiling
RNA-Seq and Ribo-Seq  reads were aligned to the human genome h19 using TopHat. RNA-counter was used to quatify mapped reads.
For  PAR-CLIP, the analyis was performed as described previously using PARalyzer (Corcoran et al., 2011a) built into the PARpipe (Corcoran et al., 2011b) pipeline
Genome_build: h19

source_name: HBEC

growth_protocol: HEK 293 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) (Gibco, Catalog No. 11995065), respectively, supplemented with 10% fetal bovine serum (FBS, GE Healthcare, Catalog No. SH30071.03) and 100 units of penicillin and 0,1 mg/ ml of streptomycin (Sigma-Aldrich Co., Catalog No. P4333). Cells were cultivated at 37°C and 5% CO2, HBEC lines were cultured in Keratinocyte Serum Free Media supplemented with bovine pituitary extract and EGF as prescribed by the manufacturer (Invitrogen, Carlsbad, CA) at 37 oC and 5% CO2

extract_protocol:
Total RNA was extracted monosome and polysomes using TRIzol™ Reagent (Invitrogen, Catalog No. 15596026). PAR-CLIP was performed as previously  described (Benhalevy et al., 2016; Hafner et al., 2010)
RNA-seq  of the monosome and polysomes  was performed using the NEBNext Ultra II RNA Library Prep Kit for Illuminal.PAR-CLIP libraries were constructed as previously  described (Benhalevy et al., 2016; Hafner et al., 2010)

tag: cell line

value: HBEC


title: Ti_Dppa2_1A4_input

description: tissue culture

tag: tissue


title: HBEC U2AF1 WT 7 ribosomes [WT_7]

description:
processed data file: Riboprofiles_counts.txt
wt_7_S7_L008


title: HBEC U2AF1 WT 5 ribosomes [WT_5]

description:
processed data file: Riboprofiles_counts.txt
wt_5_S5_L008


title: HBEC U2AF1 WT 8-10 ribosomes [WT_8-10]

description:
processed data file: Riboprofiles_counts.txt
wt_8to10_S8_L008


title: 7131_SPF_Ad_lung

description: γδ T cells


title: 8171_SPF_KP_lung

description: γδ T cells


title: HA_Dppa4_short_3A5

description: tissue culture

value: anti-HA.11 (Covance)


title: TI_Dppa4_FL_2D7_input

description: tissue culture


title: TI_Dppa2_1B1_input

description: tissue culture


title: 5693_SPF_LucOS_lung

description: γδ T cells


title: HBEC U2AF1 WT 6 ribosomes [WT_6]

description:
processed data file: Riboprofiles_counts.txt
wt_6_S6_L008


title: HBEC U2AF1 WT 3 ribosomes [WT_3]

description:
processed data file: Riboprofiles_counts.txt
wt_3_S3_L008


title: 7133_SPF_Ad_lung

description: γδ T cells


title: HBEC U2AF1 WT 2 ribosomes [WT_2]

description:
processed data file: Riboprofiles_counts.txt
wt_2_S2_L008


title: HA_Dppa4_short_2D7

description: tissue culture


title: 5687_SPF_LucOS_lung

description: γδ T cells


title: HBEC U2AF1 WT monosomes [WT_1]

description:
processed data file: Riboprofiles_counts.txt
wt_1_S1_L008


title: HA_Dppa2_1B1

description: tissue culture


title: 5685_SPF_LucOS_lung

description: γδ T cells


title: HBEC U2AF1 S34F 8-10 ribosomes [S34F_8-10]

description:
processed data file: Riboprofiles_counts.txt
S34F_8to10_S16_L008


title: RNA-seq_WT_1C3

description: tissue culture

data_processing:
Reads were aligned to reads were mapped to the mouse genome (mm9) with Hisat2 (v2.1.0). Counts of mRNA reads on genes were computed using featureCounts (subread 1.6.2) with default parameters.
RNA-Seq differential expression analysis was performed Voom (limma)
Genome_build: mm9
Supplementary_files_format_and_content: *pileup files contain uniquely mapping raw reads while *mpileup files include multi-mapping reads.

extract_protocol:
Total RNA from cell lines was isolated using the High Pure RNA Isolation Kit (Roche).
TruSeq stranded RNA sample preparation kit (Illumina).

treatment_protocol: Some samples were transfected and RNA collected 2 days after transfection

value: mESC in serum

value: WT cells


title: RNA-seq_WT_3B1

description: tissue culture


title: HA_Dppa2_1A4

description: tissue culture


title: 5682_SPF_LucOS_lung

description: γδ T cells


title: HBEC U2AF1 S34F 7 ribosomes [S34F_7]

description:
processed data file: Riboprofiles_counts.txt
S34F_7_S15_L008


title: RNA-seq_Dppa4_KO_3A5_plus_DPPA4dSAP

description: tissue culture

value: Depleted of DPPA4 by CRISPR/Cas9 technology and transfected with truncated DPPA4


title: HBEC U2AF1 S34F 6 ribosomes [S34F_6]

description:
processed data file: Riboprofiles_counts.txt
S34F_6_S14_L008


title: RNA-seq_Dppa4_KO_3A5_plus_DPPA4

description: tissue culture

value: Depleted of DPPA4 by CRISPR/Cas9 technology and transfected with full-length DPPA4


title: RNA-seq_Dppa4_KO_2D7_plus_DPPA4dSAP

description: tissue culture


title: HA_Dppa4_FL_3A5

description: tissue culture


title: HBEC U2AF1 S34F 4 ribosomes [S34F_4]

description:
processed data file: Riboprofiles_counts.txt
S34F_4_S12_L008


title: HBEC U2AF1 S34F 5 ribosomes [S34F_5]

description:
processed data file: Riboprofiles_counts.txt
S34F_5_S13_L008


title: HA_Dppa4_FL_2D7

description: tissue culture


title: RNA-seq_WT_1B3

description: tissue culture


title: RNA-seq_Dppa4_KO_1D7_plus_DPPA4dSAP

description: tissue culture


title: RNA-seq_Dppa4_KO_3A5

description: tissue culture

value: Depleted of DPPA4 by CRISPR/Cas9 technology


title: RNA-seq_Dppa4_KO_2D7_plus_DPPA4

description: tissue culture


title: HBEC U2AF1 S34F 3 ribosomes [S34F_3]

description:
processed data file: Riboprofiles_counts.txt
S34F_3_S11_L008


title: HBEC U2AF1 S34F 2 ribosomes [S34F_2]

description:
processed data file: Riboprofiles_counts.txt
S34F_2_S10_L008


title: RNA-seq_Dppa4_KO_2D7

description: tissue culture


title: RNA-seq_Dppa4_KO_1D7_plus_DPPA4

description: tissue culture


title: HBEC U2AF1 S34F monosomes [S34F_1]

description:
processed data file: Riboprofiles_counts.txt
S34F_1_S9_L008


title: RNA-seq_Dppa2_KO_1A4

description: tissue culture

value: Depleted of DPPA2 by CRISPR/Cas9 technology


title: RNA-seq_Dppa2_KO_1B1

description: tissue culture


title: SS BAL CD14++CD16+ 3

city: Newcastle

first: Laura

last: Jardine

address: Framlington Place

department: Faculty of Medical Sciences

institute: Newcastle University

hyb_protocol: Transcripts were detected using a NanoString Immunology v2 panel according to the manufacturer's instructions. Experiments using blood and BAL DC2/3 included an additional 30-gene add-on to the Immunology v2 panel, designed to detect DC and monocyte/macrophage genes. Hybridisation occurred under 'High Sensitivity' settings.

scan_protocol: FOV 555

data_processing: Data normalization was performed in nSolver version 3.

source_name: Saline BAL, int. Monocyte

extract_protocol: Lysates from 1-2x10e4 cells per sorted population were prepared using 5μl buffer RLT (Qiagen) with 1% beta-mercaptoethanol (Sigma).

tag: sample type

value: Saline Control BAL

value: Saline

value: BAL, int. Monocyte


title: SS BAL DC2_3 2

source_name: Saline BAL, DC2/3

value: BAL, DC2/3


title: HEK_TIR1_ZNF143AID_Auxin_rep4

city: Farmington

first: Michael

middle: Joseph

last: Guertin

state: CT

address: 400 Farmington Ave

department: Center for Cell Analysis and Modeling

institute: University of Connecticut

description: nascent RNA

data_processing:
Library strategy: PRO-Seq
adapter trimming: cutadapt 1.14
FASTQ deduplication: fqdedup v0.1.0
FASTX trimming and reverse complementing: fastx_trimmer, fastx_reverse_complement 0.0.14. Note that the first 8 bases of the PE1 (or single) read are a UMI and need to be trimmed.
alignment: bowtie2 2.3.2
file manipulation: samtools 1.6
file manipulation: seqOutBias v1.1.3
all details and code: https://github.com/mjg54/znf143_pro_seq_analysis
Genome_build: hg38
Supplementary_files_format_and_content: stranded bigWig counts files

source_name: HEK-293T cells

growth_protocol: HEK293T cells were purchased from ATCC and were were grown in DMEM with 10% FBS, Penicillin/Streptomycin and 5% glutamine.

treatment_protocol: A final concentration of 500μM Auxin was added at indicated times

tag: genetic modification 1

value: TIR1 insertion into AAVS1 locus clonal expansion

tag: genetic modification 2

value: ZNF143 tagged C-terminally with AID and clonally expanded

tag: agent

value: Auxin

tag: time point

value: 90 minutes


title: SS BAL DC2_3 4

tag: treatment


title: SS BAL CD14++CD16+ 2


title: SS BAL DC2_3 3


title: SS BAL CD14++CD16+ 1


title: RNA-seq_Dppa4_KO_1D7

description: tissue culture

tag: genotype


title: RIP_SEQ_WT_IP

data_processing:
RNA-Seq and Ribo-Seq  reads were aligned to the human genome h19 using TopHat. RNA-counter was used to quatify mapped reads.
For  PAR-CLIP, the analyis was performed as described previously using PARalyzer (Corcoran et al., 2011a) built into the PARpipe (Corcoran et al., 2011b) pipeline
Genome_build: h19


title: HEK_TIR1_ZNF143AID_Auxin_rep3

description: nascent RNA


title: RIP_SEQ_WT_IgG


title: HEK_TIR1_ZNF143AID_ARF_Auxin_rep4

description: nascent RNA

tag: genetic modification 3

value: ARF16-PB1 domain expressed and cell sorted (not a clonal population)


title: HEK_TIR1_ZNF143AID_ARF_Auxin_rep3

description: nascent RNA


title: HEK_TIR1_ZNF143AID_Auxin_rep2

description: nascent RNA


title: SS BAL CD14++CD16- 2

source_name: Saline BAL, Classical Monocyte

value: BAL, Classical Monocyte


title: SS BAL CD14++CD16- 3


title: RIP_SEQ_WT_Cytosol

value: HBEC


title: RIP_SEQ_S34F_IP


title: HEK_TIR1_ZNF143AID_ARF_Auxin_rep2

description: nascent RNA


title: HEK_TIR1_ZNF143AID_ARF_rep4

description: nascent RNA


title: RNA-seq_Dppa2_KO_1B4

description: tissue culture

value: mESC in serum


title: HEK_TIR1_ZNF143AID_ARF_rep2

description: nascent RNA


title: HEK_TIR1_ZNF143AID_Auxin_rep1

description: nascent RNA


title: HEK_TIR1_ZNF143AID_ARF_rep1

description: nascent RNA


title: HEK_TIR1_ZNF143AID_ARF_rep3

description: nascent RNA


title: RIP_SEQ_S34F_IgG


title: PAR_CLIP_U2AF1_CHR_WT_RPI13_adapt_2947_B

data_processing:
library strategy: PAR CLIP-seq
RNA-Seq and Ribo-Seq  reads were aligned to the human genome h19 using TopHat. RNA-counter was used to quatify mapped reads.
For  PAR-CLIP, the analyis was performed as described previously using PARalyzer (Corcoran et al., 2011a) built into the PARpipe (Corcoran et al., 2011b) pipeline
Genome_build: h19


title: RIP_SEQ_S34F_Cytosol


title: RIP_SEQ_FS_IP


title: RIP_SEQ_FS_IgG


title: PAR_CLIP_U2AF1_CHR_WT_RPI13_adapt_2947_A


title: PAR_CLIP_U2AF_CYT_WT_RPI15_adapt_2949_B


title: HEK_TIR1_ZNF143AID_rep3

description: nascent RNA


title: HEK_TIR1_ZNF143AID_rep4

description: nascent RNA


title: HEK_TIR1_rep4

description: nascent RNA


title: HEK_TIR1_ZNF143AID_rep1

description: nascent RNA


title: SS BAL CD14++CD16- 1


title: HEK_TIR1_rep3

description: nascent RNA


title: HEK_TIR1_ZNF143AID_rep2

description: nascent RNA


title: RIP_SEQ_FS_Cytosol


title: LPS BAL DC3 2

source_name: LPS BAL, DC3

value: LPS BAL

value: LPS

value: BAL, DC3


title: HEK_TIR1_rep1

description: nascent RNA


title: LPS BAL PDC 2

source_name: LPS BAL, PDC

value: BAL, PDC


title: LPS BAL PDC 1


title: LPS BAL PDC 3


title: moDC 1

source_name: Healthy Control, Blood, monocyte-derived DC

value: Healthy Control

value: Healthy

value: Blood, monocyte-derived DC


title: SS BAL AM 4

source_name: Saline BAL, AM

value: Saline Control BAL

value: Saline

value: BAL, AM


title: SS BAL AM 2


title: moDC 2


title: SS BAL AM 1


title: SS BAL AM 3


title: HEK_TIR1_rep2

description: nascent RNA

value: TIR1 insertion into AAVS1 locus clonal expansion


title: PAR_CLIP_U2AF_CYT_WT_RPI15_adapt_2949_A


title: HEK293T_TIR1_Cl4_3hrAUXIN_rep2

description: nascent RNA

value: Auxin

value: 3 hours


title: PAR_CLIP_U2AF_CYT_S34F_RPI15_adapt_2950_B


title: HEK293T_TIR1_Cl4_3hrDMSO_rep2

description: nascent RNA

value: DMSO


title: PAR_CLIP_U2AF_CYT_S34F_RPI15_adapt_2950_A


title: HEK293T_TIR1_Cl4_3hrAUXIN_rep1

description: nascent RNA


title: HBEC U2AF1 Frame Shift 8-10 ribosomes [FS_8-10]

description:
processed data file: Riboprofiles_counts.txt
FS_8to10_S24_L008


title: LPS BAL DC3 1


title: HBEC U2AF1 Frame Shift 7 ribosomes [FS_7]

description:
processed data file: Riboprofiles_counts.txt
FS_7_S23_L008


title: LPS BAL DC2/3 7

source_name: LPS BAL, DC2/3

value: BAL, DC2/3


title: HEK293T_TIR1_Cl4_3hrDMSO_rep1

description: nascent RNA


title: HEK_TIR1_ZNF143AID_ARF_Auxin_rep1

description: nascent RNA

value: ZNF143 tagged C-terminally with AID and clonally expanded

value: ARF16-PB1 domain expressed and cell sorted (not a clonal population)

value: 90 minutes


title: HBEC U2AF1 Frame Shift 6 ribosomes [FS_6]

description:
processed data file: Riboprofiles_counts.txt
FS_6_S22_L008

value: HBEC


title: HBEC U2AF1 Frame Shift 5 ribosomes [FS_5]

description:
processed data file: Riboprofiles_counts.txt
FS_5_S21_L008


title: HBEC U2AF1 Frame Shift 4 ribosomes [FS_4]

description:
processed data file: Riboprofiles_counts.txt
FS_4_S20_L008


title: HBEC U2AF1 Frame Shift 2 ribosomes [FS_2]

description:
processed data file: Riboprofiles_counts.txt
FS_2_S18_L008


title: T_NPB_3

description:
Inoculated leaves
PolyA RNA
processed data: Gene_Expression_All_Samples.txt

organism: Oryza sativa Japonica Group

source_name: NPB rice cultivar

tag: cultivar

value: NPB

value: 3 weeks

value: Leaves

value: Inoculated with Pyricularia oryzae

value: Treatment


title: T_NPB_2

tag: seedlings age


title: LPS BAL DC2/3 6

value: LPS BAL

value: LPS


title: HBEC U2AF1 Frame Shift 3 ribosomes [FS_3]

description:
processed data file: Riboprofiles_counts.txt
FS_3_S19_L008


title: HBEC U2AF1 Frame Shift monosomes [FS_1]

description:
processed data file: Riboprofiles_counts.txt
FS_1_S17_L008


title: LPS BAL DC2/3 5


title: LPS BAL DC2/3 4


title: LPS BAL DC2/3 3


title: LPS BAL DC2/3 2