title: Mantella_pooled skin_R1

city: Storrs

first: John

middle: Henri

last: Malone

state: CT

address: 181 Auditorum Road, Unit 3197

department: Institute of Systems Genomics and Department of Molecular and Cell Biology

institute: University of Connecticut

data_processing:
We assembled the skin transcriptome de novo using Trinity v.2.4.0 (Grabherr et al. 2011; Haas et al. 2013) with a minimum contig length of 300. We mapped the reads to the assembly using Bowtie2 version 2.3.1 (default parameters, no unaligned reads output) and used RSEM v.1.3.0 to identify gene expression levels. We searched for matches for each transcript against the amino acid Swissprot database (The UniProt Consortium 2017) and Database of Anuran Defense Peptides (http://split4.pmfst.hr/dadp/) using Blastx v.2.2.29+.
Genome_build: None available
Supplementary_files_format_and_content: Trinity assemblies as a FASTA file. RSEM as tab-delimited file.

organism: Mantella betsileo

source_name: Dorsal and ventral skin

growth_protocol: Five adult frogs that were raised from captive bred adults were obtained from a pet dealer. The frogs were processed immediately upon arrival.

extract_protocol:
Total RNA was extracted using a Qiagen RNA extraction kit.
The cDNA library, DNA sequencing, and bioinformatic processing was conducted under contract by BGI-America, and follows their published procedures. Briefly, mRNA from the Mantella skin samples was enriched by purification on oligo-dT and fragmented into about 200 nt fragments. cDNA copies were generated via random hexamer priming, and sequenced on an Illumina HiSeq 2000 sequencer.

treatment_protocol: Frogs were anesthetized using carbon dioxide. Skins were dissected and placed in All-Protect reagent (QIAGEN) prior to RNA extraction.

value: captive bred

tag: gender

value: unknown

value: Dorsal and ventral skin

tag: develompental stage

value: Adult


title: RNA-seq for WT mouse liver 1

status: Public on Jan 07 2019

type: SRA

city: Stanford

first: Zhen

last: Shi

state: California

address: 279 Campus Drive

country: USA

institute: Stanford

description: polyA RNA

library_source: transcriptomic

data_processing:
For Ribo-seq, a layered alignment was performed to first discard reads mapping to mouse ribosomal RNA (rRNA) sequences using Burrows-Wheeler Aligner (BWA). Non-rRNA reads were then aligned against the mouse transcriptome (GRCm38 build 76) using RSEM and bowtie2. Reads were aligned strand-specifically to exclude anti-sense or other non-transcript reads. For each gene, total number of Ribosome Protected Fragments (RPFs) and RNA reads were counted and fed into the downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Text files include normalized read values for protein-coding genes

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Mouse liver tumours were micro-dissected immediately after animal euthanization. Liver perfusion (with ice cold PBS containing 10 mg/ml cycloheximide (CHX)) and placed in ice cold PBS containing 10 mg/ml CHX for 5 min. Tumours were minced into small pieces with a scalpel and incubated for 20 min in 0.5% collagenase supplemented with 10 mg/ml CHX. After spun down, tumour was resuspended in 4 ml trypsin containing 5 mg/ml CHX for 10 to 15 min at 37 °C, followed by filtering through a 40 m cell strainer and resuspension in the lysis buffer (20 mM Tris pH 7.5, 150 mM NaCl, 15 mM MgCl2, 100 μg/ml cycloheximide, 1 mM DTT, 0.5% Triton X-100, 0.1 mg/ml heparin, 8% glycerol, 20 U/ml TURBO™ DNase, 1x Combined Protease and Phosphatase Inhibitor)
All Ribo-Seq libraries were prepared as described in Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. After removing the nuclei and mitochondria, lysate was treated with RNase A/T1 mix (0.5 mg RNase A (Ambion, AM2272) and 1,000 U RNase T1 (Life Technologies, 2280)) to digest mRNAs that are not protected by the ribosome. The digestion was stopped by adding SUPERase-In™ RNase Inhibitor (20 U/μl, Ambion, AM2696), followed by centrifuging to pellet ribosomes. Ribosome-protected fragments were purified by TRIzol®, and two biological replicates were performed for each type of Ribo-Seq and all Ribo-Seq libraries (three biological replicates for WT liver).

tag: genotype

value: Wild type

tag: strain

tag: sample type

value: polyA RNA


title: RNA-seq for WT mouse liver 2

description: polyA RNA


title: Ribo-seq for KRAS(G12D) mouse liver tumor 1

description: ribosome protected RNA

data_processing:
Library strategy: Ribo-seq
For Ribo-seq, a layered alignment was performed to first discard reads mapping to mouse ribosomal RNA (rRNA) sequences using Burrows-Wheeler Aligner (BWA). Non-rRNA reads were then aligned against the mouse transcriptome (GRCm38 build 76) using RSEM and bowtie2. Reads were aligned strand-specifically to exclude anti-sense or other non-transcript reads. For each gene, total number of Ribosome Protected Fragments (RPFs) and RNA reads were counted and fed into the downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Text files include normalized read values for protein-coding genes

value: Alb Cre specific expression of LSL-KRAS(G12D)

value: ribosome protected RNA


title: CMV-Cre_NOVA2_cTag-CLIP_Cortex_3

status: Public on Jan 09 2019

city: New York

first: Yuhki

last: Saito

state: NY

address: 1230 York avenue

institute: The Rockefeller University

description:
processed data file:
mm10.e18.5.Cortex.NOVA2-cTagCLIP.CMV-Cre.bedgraph.gz

data_processing:
collapsing of exact sequences
stripping of degenerate linker (5nt; ends with a G)
removal of 3'adaptor (GTGTCAGTCACTTCCAGCGG)
alignment with novoalign (unambiguous mapping on mm10)
collapsing of PCR duplicates (unique CLIP tags)
clustering of unique reads
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files generated from NOVA2 cTag-CLIP unique tags for genome browser

source_name: Cortex

extract_protocol:
Tissues were UV-irradiated and subjected to NOVA2 cTag-CLIP with mouse anti-GFP (Heiman et al., 2014), clones 19F7 and 19C8 (detailed desription in accompanying paper).
partial RNAse digestion, RNA linker ligation and PCR amplificiation. NOVA2-AcGFP bound fragments were ligated to a degenerate 5'linker and a 3'linker.

tag: tissue

value: brain

tag: age

value: embryonic day 18.5


title: s64root_total

status: Public on Jan 06 2019

city: Houghton

first: Yinan

last: Yuan

state: MICHIGAN

address: UJ Noblet 100B, 1400 townsend drive

department: School of Forest Resources and Environmental Science

institute: Michigan Technological University

data_processing:
RTA version 1.18.64 and 1.18.66.3 used for basecalling
Sequence reads are mapped to Populus genome (v3 assembly) through TopHat v2.1.0 with default setting and stranded library parameter --library-type fr-firststrand
Read counts per gene was carried out with htseq-count version 0.6.0. The parameters set for read count of sense transcripts is: htseq-count -s reverse and for read count of antisense transcripts: htseq-count -s yes . The count files generated were fed into DESeq2 for expreesion analysis.  For gene expression analysis of intronic reads, an intron gff file of Populus genome is first created with a custom R script, then fed into DEXSeq to count reads mapped to each intron genomic feature in a strand-specific manner, and finally intron counts derived from each gene are merged to produce the count files which are fed into DESeq2 for differential intronic expression analysis.
Genome_build: Populus genome v3 assembly at:
https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa
Supplementary_files_format_and_content: text files with read count for each annotated gene loci; the identifiers (e.g. Potri.001G000100, Potri.001G000200 etc.) are searchable at:
https://phytozome.jgi.doe.gov/pz/portal.html#!search?show=BLAST&method=Org_Ptrichocarpa

organism: Populus trichocarpa

source_name: drought treated_long-term_root

growth_protocol: Vegetative propagation from stem cuttings of Populus trichocarpa are used to generate poplar plants for drought treatments. The rooted cuttings are grown in the greenhouse with temperature range of 20-35C.

extract_protocol:
Total RNAs were extracted from root and leaf tissues of control and treated plants using a CTAB method and treated with DNase I.
Stranded RNA libraries were constructed though TruSeq stranded RNA library preparation (Illumina). For mRNA libraries, library preparations were followed exactly with the instruction of TruseSeq mRNA stranded kit, and for total RNA libraries, total RNAs were first treated with two rounds of Ribo-Zero rRNA removal kit to deplete rRNA, then proceeded with total RNA as library source and  followed the same procedure as stranded mRNA library construction.

treatment_protocol: All plantss were watered to field capacity (FC) for two months, and then proceeded for drought treatment. Stressed plants were subjected to water stress by withholding water, and control plants were continually watered to FC. For short-term treatment, plants were kept at 40% of FC for 24 hours before apex leaf tissues were harvested; and for long-term treatments, plants were stressed at 40% of FC for 25 days until leaf and root tissues were collected.

tag: type

value: drought treated

tag: drought treatment

value: long-term

value: root

tag: molecule subtype

value: total RNA


title: s68root_total


title: RNA-seq for MYC(Tg); KRAS(G12D) mouse liver tumor 2

description: polyA RNA

value: Alb Cre specific expression of HA-epitope tagged c-MYC (human) and LSL-KRAS(G12D)


title: c70root_total

value: control


title: s68ml_mRNA

source_name: drought treated_long-term_mature leaves

value: mature leaves

value: mRNA


title: RNA-seq for MYC(Tg); KRAS(G12D) mouse liver tumor 1

description: polyA RNA


title: s64root_mRNA


title: c70root_mRNA


title: c63root_mRNA


title: s68root_mRNA


title: NOVA2_CLIP_Cerebellum_2

description:
processed data file:
mm10.P28.Cerebellum.NOVA2-CLIP.bedgraph.gz

source_name: Cerebellum

value: Postnatal day 28


title: c63root_total


title: s64ml_mRNA


title: c70ml_mRNA

source_name: control_long-term_mature leaves


title: s68yl_mRNA

source_name: drought treated_long-term_young leaves

value: young leaves


title: s68apex_mRNA

source_name: drought treated_long-term_apex

value: apex


title: c63apex_mRNA


title: s35apex

source_name: drought treated_short-term_apex

value: short-term


title: c49ml

source_name: control_short-term_mature leaves


title: c70apex_mRNA


title: s69ml


title: c19apex


title: c70yl_mRNA

source_name: control_long-term_young leaves


title: c19ml


title: s64apex_mRNA


title: c49apex


title: c63ml_mRNA


title: Lso-neg_week4_rep2

status: Public on Jan 04 2019

city: College Station

first: Ordom

middle: Brian

last: Huot

state: Texas

address: 2475 Texas A&M University

department: Entomology

institute: Texas A&M University

description:
Transcriptome of plant exposed to Lso-negative psyllids at week 4
P6
Barcode: ATTCCT

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's HCS 2.2.38 and RTA 1.18.61 software with default parameter settings.
Sequencer basecall (.bcl) files were formatted into fastq files using bcl2fastq 1.8.4 script configureBclToFastq.pl. The sequence raw reads were cleaned using cutadapt 1.0 to remove barcode tags and adaptors. Individual samples were processed with FastQC, and the QC reports were checked as final confirmation of sequence quality.
The processed sequences were uploaded to Discovery Environment (DE) web interface and platform at CyVerse (www.iplantcollaborative.org) (Goff et al., 2011). Tuxedo RNA-Seq apps (TopHat2, Cufflinks2, Cuffmerge2, Cuffdiff2) within DE interface were used to map sequences against the S. lycopersicum genome, Ensembl 14 (Sato et al., 2012), to assemble transcripts, to create full transcriptome, and to identify differentially expressed genes (DEGs) according to the published protocol (Trapnell et al., 2012). The analyses were done with the default false discovery rate (FDR = 0.05) and adjusted with Benjamini-Hochberg correction for multiple comparisons.
Transcriptomes of plants from control and Lso-negative psyllids treatments were compared to evaluate plant response to herbivory. Transcriptomes of plants from control and Lso-positive psyllids treatments were compared to evaluate plant response to herbivory and infection. Transcriptomes of plants from Lso-negative psyllid and Lso-positive psyllid treatments were compared to evaluate the difference in plant responses to Lso-negative and Lso-positive Bactericera cockerelli. Each comparison was done with respect to each time point (week1, week2, week4). In total, nine comparisons were performed.
Genome_build: SL2.40 (source: Ensemblplants)
Supplementary_files_format_and_content: Differentially expressed genes (DEGs) found in each comparative trancriptoms including relative gene expression based on fold change, total FPKMs, q-values (adjusted for multiple comparison), and gene identification

organism: Solanum lycopersicum

source_name: Lso-neg, week4, Tomato leaf

growth_protocol: Tomato plants, Solanum lycopersicum cv. Moneymaker were grown from seed in Sun Gro® Metro-Mix 900 soil and transplanted into 4-inch square pots four weeks later. Plants were watered and fertilized weekly according to the label rate of the Miracle-Gro® Water Soluble Tomato Plant Food (18-18-21 NPK). At six-week-old each plant was assigned to the insect treatment

extract_protocol:
Leaf tissues collected and flash frozen by liquid nitrogen. Plant RNA samples were extracted from plant tissues using Qiagen Plant Rneasy Mini Kit. TURBO DNA-free Kits from Life Technologies were to romove potential DNA contaminant.
Illumina TruSeq RNA Sample Prep Kit was used with 2 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tomato plants were exposed to no insect (control), 5 male and 5 female Lso-negative psyllids (Lso-neg, P), or 5 male and 5 female Lso-positive psyllids (Lso-pos, L). The treatment lasted for 1, 2 or 4 weeks. There were 27 plants belong to 3 treatment groups and 3 exposure times

value: Leaf

tag: insect treatment

value: Lso-negative psyllids

tag: time


title: Lso-neg_week4_rep1

description:
Transcriptome of plant exposed to Lso-negative psyllids at week 4
P3
Barcode: CGTACG


title: Lso-neg_week2_rep3

description:
Transcriptome of plant exposed to Lso-negative psyllids at week 2
P8
Barcode: CGATGT

source_name: Lso-neg, week2, Tomato leaf


title: Lso-neg_week2_rep2

description:
Transcriptome of plant exposed to Lso-negative psyllids at week 2
P5
Barcode: ACTGAT


title: Lso-neg_week1_rep1

description:
Transcriptome of plant exposed to Lso-negative psyllids at week 1
P1
Barcode: GTGGCC

source_name: Lso-neg, week1, Tomato leaf


title: Lso-neg_week1_rep2

description:
Transcriptome of plant exposed to Lso-negative psyllids at week 1
P4
Barcode: GAGTGG


title: Lso-neg_week2_rep1

description:
Transcriptome of plant exposed to Lso-negative psyllids at week 2
P2
Barcode: GTTTCG


title: c63yl_mRNA


title: Lso-pos_week2_rep3

description:
Transcriptome of plant exposed to Lso-positive psyllids at week 2
L8
Barcode: GTCCGC

source_name: Lso-pos, week2, Tomato leaf

value: Lso-positive psyllids


title: Lso-neg_week4_rep3

description:
Transcriptome of plant exposed to Lso-negative psyllids at week 4
P9
Barcode: TTAGGC


title: s35ml


title: Lso-neg_week1_rep3

description:
Transcriptome of plant exposed to Lso-negative psyllids at week 1
P7
Barcode: ATCACG


title: s69apex


title: Lso-pos_week4_rep3

description:
Transcriptome of plant exposed to Lso-positive psyllids at week 4
L9
Barcode: GTGAAA

source_name: Lso-pos, week4, Tomato leaf


title: s64yl_mRNA


title: Lso-pos_week4_rep2

description:
Transcriptome of plant exposed to Lso-positive psyllids at week 4
L6
Barcode: ATGTCA


title: Lso-pos_week4_rep1

description:
Transcriptome of plant exposed to Lso-positive psyllids at week 4
L3
Barcode: CTTGTA


title: Lso-pos_week2_rep1

description:
Transcriptome of plant exposed to Lso-positive psyllids at week 2
L2
Barcode: GGCTAC


title: Lso-pos_week2_rep2

description:
Transcriptome of plant exposed to Lso-positive psyllids at week 2
L5
Barcode: AGTTCC


title: control_week2_rep3

description:
Transcriptome of plant exposed to no insect (control) at week 2
C8
Barcode: ACTTGA

source_name: control, week2, Tomato leaf

value: Control (no insect)


title: Lso-pso_week1_rep2

description:
Transcriptome of plant exposed to Lso-positive psyllids at week 1
L4
Barcode: AGTCAA

source_name: Lso-pso, week1, Tomato leaf


title: control_week4_rep2

description:
Transcriptome of plant exposed to no insect (control) at week 4
C6
Barcode: GCCAAT

source_name: control, week4, Tomato leaf


title: control_week2_rep1

description:
Transcriptome of plant exposed to no insect (control) at week 2
C2
Barcode: CGATGT


title: control_week1_rep3

description:
Transcriptome of plant exposed to no insect (control) at week 1
C7
Barcode: CAGATC

source_name: control, week1, Tomato leaf


title: control_week2_rep2

description:
Transcriptome of plant exposed to no insect (control) at week 2
C5
Barcode: GCCAAT


title: control_week1_rep1

description:
Transcriptome of plant exposed to no insect (control) at week 1
C1
Barcode: ATCACG


title: Lso-pos_week1_rep1

description:
Transcriptome of plant exposed to Lso-positive psyllids at week 1
L1
Barcode: TAGCTT

source_name: Lso-pos, week1, Tomato leaf


title: Input r2

city: Chicago

first: Maria

middle: Paula

last: Zappia

state: IL

address: 900 S Ashland Ave

department: Biochemistry and Molecular Genetics

institute: University of Illinos at Chicago

library_source: genomic

data_processing:
Illumina bcl2fastq-1.8.3 software used for basecalling
ChIPseq data analysis: Illumina pipeline analyzed short reads were uniquely aligned using the program BOWTIE (version 2)  (Langmead 2009) allowing at most two mismatches against the Drosophila reference genome BDGP5.77. Replicates are concatenated to have more coverage.
Peak caller algorithm MACS (version 1.4.2) (Zhang 2009) was used to determine enriched peak region with parameters: --nomodel, --tsize=50, --shiftsize=160. Shift size were determined using Pyicos (Althammer S et al, 2011) strand correlation method. Other parameters were kept default.
Genome_build: BDGP5.77
Supplementary_files_format_and_content: Called Peak BED

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: flight muscles

growth_protocol: Flies were kept at 25 °C in vials containing standard cornmeal- agar medium. About 96h after pupa formation (APF), flight muscles were dissected from pharate animals

extract_protocol:
Chromatin from flight muscles was extracted using homogenizer and fixed in 1.8% formaldehyde. Then lysates were sheared using a Sonifier, and chromatin was immunoprecipitated with antibodies as in Zappia, M. P. and Frolov, M. V. Nat. Commun. 7:10509 (2016)
ChIPSeq libraries were generated using an Illumina ChIP-SEQ kit

treatment_protocol: no treatment

tag: chip antibody

tag: developmental stage

value: Pharate stage (96h APF at 25 degrees C)


title: Input r1


title: Rbf r2

value: anti-Rbf (mouse, DX3/DX5, ratio 1:1, Du W. et al, Genes Dev. 1996;10(10):1206-18)


title: Rbf-KD mature flight muscle replicate 2

data_processing:
Illumina bcl2fastq2-v2.17.1.14 software was used for basecalling
RNAseq data analysis: Quality analysis of RAW reads was done using the tool FASTQC
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Drosophila genome BDGP 5.77 (Ensembl database) using TopHat v2.1.1; Bowtie 2 v2.3.2 with option -m 2 -g 1
Counting was done using SubRead package, featureCount tool. Absolute count was normalized to library size using DEseq2 (v 1.14.1), and differential expression was calculated
Genome_build: BDGP5.77
Supplementary_files_format_and_content: tab-delimited text files; abundance measurement absolute transcript count data

source_name: Flight muscles

growth_protocol: Flies were kept at 25 °C in vials containing standard cornmeal- agar medium. Wandering third instar larvae were harvested, wing discs were dissected, and notum was cut off and collected. About 96h after pupa formation (APF), flight muscles were dissected from pharate animals

extract_protocol:
Total RNA from dissected tissue was extracted using Trizol reagent and following manufacturer procedures. Samples were treated with DNAse, RNA quality was assessed using 2100 bioanalyzer
Total RNA libraries (Ribo-Zero depletion) were prepared using Illumina TruSEQ Stranded kits

value: Pharate (96h APF at 25 degrees C)

value: Flight muscle

value: P{UAS-Dicer2.D}1; +; P{GAL4-Mef2.R}3/ P{UAS-Rbf-RNAi[GD:10696]}


title: Rbf r1


title: Rbf-KD myoblasts replicate 3

source_name: Adult muscle precursors

value: Third instar larva (wandering L3 at 25 degrees C)

value: Notum (wing disc was cut)


title: WT mature flight muscle replicate 2

value: P{UAS-Dicer2.D}1; P{UAS-mCherry-RNAi}attP2 ; P{GAL4-Mef2.R}3


title: Rbf-KD mature flight muscle replicate 1


title: PCOS 4 Forskolin

city: Hershey

first: Jan

middle: M

last: McAllister

state: Pennsylvania

address: 500 University Dr

department: Pathology

institute: Penn State College of Medicine

data_processing:
basecall using illumina bcl2fastq v1.8.4
The 3' adaptor is removed from raw reads and reads with the length between 18 to 25 nt constitute the mappable reads.
The mappable reads were aligned against dog genome and miRbase using Bowtie.
Genome_build: Homo sapiens, NCBI build 37.1; miRbase v20;
Supplementary_files_format_and_content: Report_4642-comparison.xls: read counts and values after normalization of miRNAs identified in Home sapiens

organism: Homo sapiens

source_name: PCOS theca cells Patient 4

extract_protocol: Illumina Truseq Small RNA Preparation

value: polycystic ovary syndrome (PCOS) theca cells


title: PCOS 4 Control


title: PCOS 3 Control

source_name: PCOS theca cells Patient 3


title: PCOS 2 Control

source_name: PCOS theca cells Patient 2


title: PCOS 2 Forskolin


title: WT mature flight muscle replicate 1


title: PCOS 3 Forskolin


title: control_week4_rep1

description:
Transcriptome of plant exposed to no insect (control) at week 4
C3
Barcode: TTAGGC


title: PCOS 1 Forskolin

source_name: PCOS theca cells Patient 1


title: PCOS 1 Control


title: Rbf-KD myoblasts replicate 1


title: Normal 4 Forskolin

source_name: normal theca cells Patient 4

value: normal theca cells


title: Normal 4 Control


title: WT myoblasts replicate 3


title: Rbf-KD myoblasts replicate 2


title: Normal 3 Forskolin

source_name: normal theca cells Patient 3


title: WT myoblasts replicate 2


title: Normal 3 Control


title: Normal 2 Forskolin

source_name: normal theca cells Patient 2


title: Normal 2 Control


title: Normal 1 Forskolin

source_name: normal theca cells Patient 1


title: Normal 1 Control


title: ox.aba.rep2

status: Public on Jan 03 2019

city: Yokohama

first: Masanori

last: Okamoto

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

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

data_processing:
Low quality and artificial sequence trimming were achieved by trim_galore (version 0.2.8) with parameters "-f fastq -e 0.1 -q 30 -O 1 -a GCCGTCTTCTGCTTG --paired"
The qualified reads were mapped to the cDNAs of the wheat reference genome with an additional sequence of the transgenic TaPYL4 transcript, by utilizing the kallisto-sleuth pipeline (v0.44.0; Harold et al., 2017 [PMID: 28581496]).
The reference genome information was retrieved from WheatMine (https://urgi.versailles.inra.fr/WheatMine/)
Genome_build: IWGSC RefSeq v1.1 (IWGSC, 2018 [PMID: 30115783])
Supplementary_files_format_and_content: Standard kallisto output; a tab-delimited text file includes the estimated read count and TPM (transcripts per million) values for every transcript.

organism: Triticum aestivum

growth_protocol: All wheat plants were cultivated in greenhouse under natural lighting condition. Average day and night-time temperatures recorded 23oC and 21oC, respectively. Measured average daytime and night-time RHs were 56% and 67%, respectively.

extract_protocol:
Each total RNA was isolated using an RNeasy Plant mini kit (Qiagen) and evaluated for quality and quantity with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and an Agilent RNA 6000 Nano Kit (Agilent Technologies).
Library preparation was performed according to the TruSeq RNA Sample Preparation v2 guide (Illumina, Woburn, MA, USA). Oligo-(dT) magnetic beads were used to isolate poly-(A) mRNA from total RNA, with fragmentation buffer then added to cut mRNA into short fragments. Using these short fragments as templates, first-strand cDNAs were synthesized using random hexamer primers and SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA, USA). After second-strand cDNA synthesis, end-repaired and dA-tailed fragments were connected with sequencing adaptors. The adapter-ligated cDNA fragments were amplified by 15 cycles of PCR, and the products were cleaned using AMPure XP magnetic beads (Beckman Coulter, Brea, CA, USA). Library quality and concentration were assessed using an Agilent Bioanalyzer 2100 and Agilent DNA 1000 kit (Agilent Technologies). More precise quantification of the libraries was achieved by quantitative real-time PCR using a KAPA Library Quantification kit (Kapa Biosystems, Wilmington, MA, USA).

treatment_protocol: Null and TaPYLox lines were treated by spray with 0.05% Tween20 as control. These lines were also treated by spray with 0.05% Tween20 containing 25 uM ABA as ABA treatment. And, drought stress was subjected to these lines by decreasing <8% water content. After 24h treatment, all leaves of these treated lines were detached and frozen by liquid nitrogen.

value: 32 day-after sowing

value: whole leaves

tag: genotype/variation

value: TaPYLox

tag: stress

value: ABA


title: ox.wwc.rep3

value: control


title: ox.aba.rep1


title: ox.dc.rep2

value: drought


title: ox.dc.rep3


title: ox.dc.rep1


title: ox.aba.rep3


title: null.aba.rep2

value: wild type


title: WT myoblasts replicate 1


title: null.dc.rep1


title: ox.wwc.rep2


title: ox.wwc.rep1


title: null.wwc.rep3


title: null.aba.rep1


title: null.wwc.rep1


title: null.dc.rep2


title: null.aba.rep3


title: null.dc.rep3


title: null.wwc.rep2


title: control_week4_rep3

description:
Transcriptome of plant exposed to no insect (control) at week 4
C9
Barcode: GATCAG

value: Leaf

value: Control (no insect)


title: glc+.12h_repA_breakdown

city: Berkeley

first: Sean

middle: D.

last: Gallaher

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

description: total RNA - rRNA

data_processing:
alignment with RNA-Star 2.4.0j
FPKM calculation with cuffdiff v2.2.1 with --multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand
Genome_build: not published at time of GEO submission. The fasta file with genome sequence and gff with gene annotation is available on GSE92513.
Supplementary_files_format_and_content: cuffdiff output

organism: Chromochloris zofingiensis

source_name: algae cultures

growth_protocol:
Chromochloris zofingiensis cells were grown at 25°C in liquid cultures (Proteose medium supplemented with Chu’s micronutrient solution) with shaking at 100–150 rpm under a diurnal light cycle (16 h light, 8 h dark) in 100 μmol photons m^−2 s^−1 medium light.
Experiments were conducted when cultures were at density ~4.5e6 cells/mL.

extract_protocol:
Total RNA was isolated by TRIzol extraction followed by purification by QIAgen miRNeasy mini kit.
Total RNA was depleted of rRNA by Ribo-Zero rRNA Removal Kit for Plant Leaf. Libraries were prepared with the Illumina-compatible KAPA Stranded RNA-Seq kit from Kapa Biosystems.

treatment_protocol: Transition from glucose-free media to media with 10 mM glcose.

tag: glucose

value: glc+ (10 mM)


title: glc+.6h_repB_breakdown

description: total RNA - rRNA


title: glc+.12h_repD_breakdown

description: total RNA - rRNA


title: glc+.6h_repC_breakdown

description: total RNA - rRNA


title: glc+.12h_repC_breakdown

description: total RNA - rRNA


title: glc+.6h_repD_breakdown

description: total RNA - rRNA


title: glc+.6h_repA_breakdown

description: total RNA - rRNA


title: glc+.3h_repD_breakdown

description: total RNA - rRNA


title: glc+.3h_repB_breakdown

description: total RNA - rRNA


title: glc+.1h_repD_breakdown

description: total RNA - rRNA


title: glc+.0.5h_repC_breakdown

description: total RNA - rRNA


title: glc+.12h_repB_breakdown

description: total RNA - rRNA


title: glc+.1h_repA_breakdown

description: total RNA - rRNA


title: glc+.1h_repC_breakdown

description: total RNA - rRNA


title: glc+.1h_repB_breakdown

description: total RNA - rRNA


title: glc+.3h_repC_breakdown

description: total RNA - rRNA


title: glc-.12h_repC_breakdown

description: total RNA - rRNA

value: glc-


title: glc+.0.5h_repA_breakdown

description: total RNA - rRNA


title: glc+.0.5h_repB_breakdown

description: total RNA - rRNA


title: glc-.6h_repC_breakdown

description: total RNA - rRNA


title: glc-.12h_repA_breakdown

description: total RNA - rRNA


title: glc-.6h_repA_breakdown

description: total RNA - rRNA


title: glc-.6h_repD_breakdown

description: total RNA - rRNA


title: glc-.3h_repD_breakdown

description: total RNA - rRNA


title: glc-.3h_repC_breakdown

description: total RNA - rRNA


title: glc-.3h_repB_breakdown

description: total RNA - rRNA


title: glc-.3h_repA_breakdown

description: total RNA - rRNA


title: glc-.1h_repB_breakdown

description: total RNA - rRNA


title: glc-.1h_repD_breakdown

description: total RNA - rRNA


title: glc-.6h_repB_breakdown

description: total RNA - rRNA


title: glc-.1h_repA_breakdown

description: total RNA - rRNA


title: glc+.3h_repA_breakdown

description: total RNA - rRNA


title: glc-0.5h_repD_breakdown

description: total RNA - rRNA


title: glc+.0.5h_repD_breakdown

description: total RNA - rRNA


title: glc-0.5h_repC_breakdown

description: total RNA - rRNA


title: glc-.12h_repB_breakdown

description: total RNA - rRNA


title: glc-0.5h_repB_breakdown

description: total RNA - rRNA


title: glc-.0h_repB_breakdown

description: total RNA - rRNA


title: glc-.0h_repC_breakdown

description: total RNA - rRNA


title: glc-0.5h_repA_breakdown

description: total RNA - rRNA


title: glc-.0h_repD_breakdown

description: total RNA - rRNA


title: glc-.0h_repA_breakdown

description: total RNA - rRNA


title: glc-.12h_repD_biogenesis

description: total RNA - rRNA

growth_protocol:
Chromochloris zofingiensis cells were grown at 25°C in liquid cultures (Proteose medium supplemented with Chu’s micronutrient solution plus 20 mM glc)
with shaking at 100–150 rpm under a diurnal light cycle (16 h light, 8 h dark) in 100 μmol photons m^−2 s^−1 medium light.
Experiments were conducted after 72 h of growth with glucose when cultures were at density ~7.5e6 cells/mL.

treatment_protocol: Transition from media with 20 mM glcose to glucose-free media.


title: glc-.12h_repC_biogenesis

description: total RNA - rRNA


title: glc-.6h_repD_biogenesis

description: total RNA - rRNA


title: glc-.6h_repC_biogenesis

description: total RNA - rRNA


title: glc-.6h_repA_biogenesis

description: total RNA - rRNA


title: glc-.1h_repC_breakdown

description: total RNA - rRNA


title: glc-.12h_repA_biogenesis

description: total RNA - rRNA


title: glc-.6h_repB_biogenesis

description: total RNA - rRNA


title: glc-.12h_repB_biogenesis

description: total RNA - rRNA


title: glc-.3h_repB_biogenesis

description: total RNA - rRNA


title: glc-.3h_repD_biogenesis

description: total RNA - rRNA


title: glc-.3h_repC_biogenesis

description: total RNA - rRNA


title: glc-.1h_repD_biogenesis

description: total RNA - rRNA


title: glc-.3h_repA_biogenesis

description: total RNA - rRNA


title: glc-.1h_repC_biogenesis

description: total RNA - rRNA


title: glc-.1h_repB_biogenesis

description: total RNA - rRNA


title: glc-.1h_repA_biogenesis

description: total RNA - rRNA


title: glc-.0.5h_repD_biogenesis

description: total RNA - rRNA


title: glc+.12h_repD_biogenesis

description: total RNA - rRNA

value: glc+ (20 mM)


title: glc-.0.5h_repB_biogenesis

description: total RNA - rRNA


title: glc+.12h_repC_biogenesis

description: total RNA - rRNA


title: glc-.0.5h_repC_biogenesis

description: total RNA - rRNA


title: glc+.12h_repB_biogenesis

description: total RNA - rRNA


title: glc+.6h_repC_biogenesis

description: total RNA - rRNA


title: glc+.6h_repB_biogenesis

description: total RNA - rRNA


title: glc+.6h_repA_biogenesis

description: total RNA - rRNA


title: glc+.12h_repA_biogenesis

description: total RNA - rRNA


title: glc+.3h_repD_biogenesis

description: total RNA - rRNA


title: glc+.6h_repD_biogenesis

description: total RNA - rRNA


title: glc+.3h_repA_biogenesis

description: total RNA - rRNA


title: glc+.3h_repC_biogenesis

description: total RNA - rRNA


title: glc-.12h_repD_breakdown

description: total RNA - rRNA


title: glc+.1h_repA_biogenesis

description: total RNA - rRNA


title: glc+.1h_repC_biogenesis

description: total RNA - rRNA


title: glc+.1h_repD_biogenesis

description: total RNA - rRNA


title: glc+0.5h_repD_biogenesis

description: total RNA - rRNA


title: glc+.3h_repB_biogenesis

description: total RNA - rRNA


title: glc+0.5h_repC_biogenesis

description: total RNA - rRNA


title: glc+.1h_repB_biogenesis

description: total RNA - rRNA


title: glc+0.5h_repA_biogenesis

description: total RNA - rRNA


title: glc+0.5h_repB_biogenesis

description: total RNA - rRNA


title: glc+.0h_repD_biogenesis

description: total RNA - rRNA


title: glc+.0h_repB_biogenesis

description: total RNA - rRNA


title: glc+.0h_repA_biogenesis

description: total RNA - rRNA


title: HP1alpha_gamma_KO (M1283)

status: Public on Jan 02 2019

city: montpellier

first: florence

last: cammas

address: 208 rue des apothicaires

country: France

institute: ircm

data_processing:
Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2.
Reads not mapping to rRNA sequences were mapped onto the mm10 assembly of mouse genome using Tophat v2.0.10 and bowtie2 v2.1.0 aligner.
Gene expression was quantified using HTSeq v0.5.4p3 and annotations from Ensembl release 75.
Data normalization was performed with DESeq2 v1.0.19 Bioconductor package
Genome_build: mm10
Supplementary_files_format_and_content: The processed data file is a tabulated text file with the following columns : Ensembl gene id, Gene name and one column for each sample containing the normalized read counts.

source_name: HP1a-/-, HP1gliver-/-_liver

extract_protocol:
livers were dissected washed in saline buffer, cut in small pieces (about 5mm3) and flash frozen in liquid nitrogen. Total RNA was extracted using Trizol reagents
Libraries of template molecules suitable for strand specific high throughput DNA sequencing were created using “TruSeq Stranded Total RNA with Ribo-Zero Gold Prep Kit” (catalog # RS-122-2301, Illumina Inc.). Briefly, starting with 300 ng of total RNA, the first step involved the removal of cytoplasmic and mitochondrial ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C). Then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). Final cDNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent).

tag: strain background

value: C57BL/6, 129svPas

value: HP1a-/-, HP1gliver-/-

value: 5 weeks

value: liver


title: HP1alpha_gamma_KO (M1308)


title: HP1alpha_gamma_KO (M1696)


title: HP1alpha_KO (M1096)


title: HP1alpha_KO (M1097)


title: control (M63)

value: WT


title: control (M1284)


title: control (M1697)


title: olfactory bulb RNA-seq rep1

city: Beijing

first: Qin

last: Ma

address: NO.1 Beichen West Road, Chaoyang District

department: Chinese Academy of Sciences

country: China

institute: Beijing Institute of Genomics

description: RNA-seq

data_processing:
First, the raw FASTQ data files generated by the Illumina HiSeq 2000 platform were mapped to the mouse reference sequence (mm10) for mRNA analysis with the default parameters. Then the normalized FPKM levels of each sample with default parameters using the cufﬂinks program (cufﬂinks v2.2.1) were calculated.
genome build: mm10
processed data files format and content: bigwig or text files with 5hmC or 5mC level or gene FPKM. 5hmC or 5mC level calculation is as follows: we counted the number of 'C' bases from sequencing reads as hydroxymethylated or methylated (denoted as NC) and the number of 'T' bases as unmodified (denoted as NT). The hydroxymethylation level or methylation level was estimated as NC/(NC + NT) in 1Mb windows.  Bigwig files are available on the series record.

source_name: olfactory bulb

extract_protocol:
The tissues for the technical replicates are from independent mouse, and at least two replicates are included in different assay as indicated. RNA (Life Tech, at#: 15596-018) were extracted according to the manufacturers’ instructions.
Libraries were prepared using the NEB Ultra™ Directional RNA Library Prep Kit according to the manufacturer’s protocol and sequenced using an Illumina Hiseq 2000.

value: 8 week

value: olfactory bulb


title: MDA MB 231 d4 FBXO32 R1

city: Mainz

first: Abhijeet

last: Pataskar

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

data_processing:
The FASTQ files were aligned human genome (hg19) using TopHat v2.0.8
Samtools v0.1.19 was used for File format conversions (bam to sam)
Reads at transcripts were counted using HTSeq (v0.5.4p1)
Normalization (for library size) was done using DESeq
Differential expression analysis was done using DESeq
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing normalized read counts

source_name: MDA MB 231

growth_protocol: HMEC cells were obtained from Lonza and cultured according to manufacturer’s guidelines. MDA-MB-231 cells were obtained from ATCC and cultured in  DMEM, 10% FBS. All cells were cultured at 37°C with 7% CO2 in a humid incubator. For TGF-β time course experiments, HMEC cells were treated with 5 ng/ml TGF-β (rhTGF-β1 240-B, R&D systems) for indicated time points with TGF-β replenishment and medium change every 2 days.

extract_protocol:
RNA was isolated using Trizol according to manufacture instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For all siRNA mediated knockdown experiments, cells were seeded at same starting density and transfected with ON-TARGET plus SMART pool siRNAs (i.e. a mixture of 4 siRNA provided as a single reagent) (Dharmacon) every second day. For siRNA transfections, Lipofectamine RNAiMax (Invitrogen, 13778-150) was used according to the manufacturer's instructions. For experiments during TGF-β-induced EMT, TGF-β-induction performed at the same time when siRNA was added

tag: cell line

value: MDA MB 231

tag: cell type

value: Mesenchymal cancer cells

tag: transfection

value: d4 FBXO32


title: cerebellum RNA-seq rep1

description: RNA-seq

source_name: cerebellum

tag: strain

value: cerebellum


title: cerebellum RNA-seq rep2

description: RNA-seq

tag: tissue


title: cortex RNA-seq rep1

description: RNA-seq

source_name: cortex

tag: age

value: cortex


title: cortex RNA-seq rep2

description: RNA-seq


title: MDA MB 231 d4 NTC R1

value: d4 NTC


title: HMEC d4 siCTBP1 R2

source_name: HMEC

value: Human Primary Breast Epithelial Cell

value: Primary cell

value: d4 siCTBP1


title: HMEC d4 siCTBP1 R1


title: glc+.0h_repC_biogenesis

description: total RNA - rRNA

value: glc+ (20 mM)


title: olfactory bulb RNA-seq rep2

description: RNA-seq


title: MDA MB 231 d4 NTC R2


title: HMEC d4 NTC R1


title: HP1alpha_beta_KO (MR4)

source_name: HP1a-/-, HP1bliver-/-_liver

value: C57BL/6, 129svPas

value: HP1a-/-, HP1bliver-/-


title: HMEC d4 NTC R2


title: HMEC d4 FBXO32 R2


title: HMEC Untreated R2


title: HMEC Untreated R1


title: cerebellum TAB-seq rep3

description: TAB-seq

data_processing:
Paired reads were mapped uniquely to the reference genome (mm10, UCSC) by Bismark.The 5hmC level of the biological replicates were calculated in 1Mb regions throughout the genome
After PCR duplication remove, we calculated the 5hmC or 5mC level of each CpG sites. The processed bigwig files indicate the 5hmC and 5mC level in CpG sites coverd by more than 5 reads.
genome build: mm10
processed data files format and content: bigwig or text files with 5hmC or 5mC level or gene FPKM. 5hmC or 5mC level calculation is as follows: we counted the number of 'C' bases from sequencing reads as hydroxymethylated or methylated (denoted as NC) and the number of 'T' bases as unmodified (denoted as NT). The hydroxymethylation level or methylation level was estimated as NC/(NC + NT) in 1Mb windows.  Bigwig files are available on the series record.

extract_protocol:
The tissues for the technical replicates are from independent mouse, and at least two replicates are included in different assay as indicated. Genomic DNA (Qiagen, Cat#: 51306) were extracted according to the manufacturers’ instructions.
The sequencing libraries were constructed as described with minor modification. Briefly, genomic DNA with spike-in controls was glycosylated and oxidized using the kit from Wisegene (Cat#: K001). Then, the DNA was further directed to bisulfite conversion using the EZ DNA methylation Gold kit (Zymo Research) according to the instruction manual. The library was sequenced using Illumina HiSeq X Ten. Paired reads were mapped uniquely to the reference genome (mm10, UCSC) by Bismark. Efficient conversion of unmodified cytosine to uracil and efficient conversion of 5mC to 5caU/U were calculated by spiked M.SssI-treated lambda DNA.


title: cerebellum TAB-seq rep1

description: TAB-seq


title: control_week1_rep2

description:
Transcriptome of plant exposed to no insect (control) at week 1
C4
Barcode: TGACCA

source_name: control, week1, Tomato leaf

value: Leaf

value: Control (no insect)


title: cerebellum oxBS-seq rep2

description: oxBS-seq

data_processing:
Paired reads were mapped uniquely to the reference genome (mm10, UCSC) by Bismark.The 5mC level of the biological replicates were calculated in 1Mb regions throughout the genome
After PCR duplication remove, we calculated the 5hmC or 5mC level of each CpG sites. The processed bigwig files indicate the 5hmC and 5mC level in CpG sites coverd by more than 5 reads.
genome build: mm10
processed data files format and content: bigwig or text files with 5hmC or 5mC level or gene FPKM. 5hmC or 5mC level calculation is as follows: we counted the number of 'C' bases from sequencing reads as hydroxymethylated or methylated (denoted as NC) and the number of 'T' bases as unmodified (denoted as NT). The hydroxymethylation level or methylation level was estimated as NC/(NC + NT) in 1Mb windows.  Bigwig files are available on the series record.

extract_protocol:
The tissues for the technical replicates are from independent mouse, and at least two replicates are included in different assay as indicated. Genomic DNA (Qiagen, Cat#: 51306) were extracted according to the manufacturers’ instructions.
The sequencing libraries were constructed as described with little modifications. Briefly, genomic DNA (0.5 to 1 μg) was end-repaired, A-tailed, and ligated to methylated adaptors following the manufacturer’s instructions. The ligated fragments were then purified using Bio-Rad Micro Bio-Spin P-6 SSC column (SSC buffer). After the purification, the samples were denaturized using 1M NaOH and oxidized using oxidant solution (15mM KRuO4 in 0.05M NaOH). After the purification, the DNA was further directed to bisulfite conversion using the EZ DNA methylation Gold kit (Zymo Research) according to the instruction manual. The library was sequenced using Illumina HiSeq X Ten. Paired reads were mapped uniquely to the reference genome (mm10, UCSC) by Bismark. Efficient conversion of 5hmC to uracil were calculated by spiked 5hmC control from Zymo Research (Cat#: D5405)


title: cerebellum oxBS-seq rep1

description: oxBS-seq


title: olfactory bulb TAB-seq rep3

description: TAB-seq


title: MDA MB  231 d4 siFBXO32 R2


title: olfactory bulb TAB-seq rep1

description: TAB-seq


title: olfactory bulb oxBS-seq rep2

description: oxBS-seq


title: olfactory bulb TAB-seq rep2

description: TAB-seq


title: cortex TAB-seq rep1

description: TAB-seq


title: cortex TAB-seq rep3

description: TAB-seq


title: cortex TAB-seq rep2

description: TAB-seq


title: cortex oxBS-seq rep3

description: oxBS-seq


title: cortex oxBS-seq rep2

description: oxBS-seq


title: CCR4-1KO-3

city: University Park

first: Scott

middle: E.

last: Lindner

address: W224 Millennium Science Complex

department: Biochemistry and Molecular Biology

institute: Penn State University

description:
Plasmodium yoelii 17XNL
CCR4-1-KO-3
Processed data file: SuppTable3_Complete_RNAseq_DEseq2_output.xlsx

data_processing:
Tophat2: each batch of reads was aligned to the reference genome (PY17X v32).
htseq-count: These reads were then aligned to the annotated transcriptome of P. yoelii (v32 from PlasmoDB) using htseq-count. We utilized the Union method for reads overlapping annotated transcripts.
DESeq2: The count files from htseq-count were merged and compared across conditions using DESeq2. All 6 WT replicates were combined, as well as all 4 of the CCR4-1KO replicates. These were compared by the mean fit type with outlier replacement turned on to normalize variance between the count files.
All data sets were aligned to the PY17X Genome v32 obtained from PlasmoDB. The same version of the annotated transcriptome was used for the ht-seq count step of the analysis.
Genome_build: PY17X Genome v32
Supplementary_files_format_and_content: SuppTable3_Complete_RNAseq_DEseq2_outout.xlsx: Excel workbook; The processed data file contains the output from the DESeq2 program using our WT and CCR4-1KO data sets. These have been combined with the normalized read outputs for each run, as well as supplemented with the means and standard error of the mean for each batch. Additionally, each gene is annotated with functional GO terms from PlasmoDB.org.

organism: Plasmodium yoelii yoelii 17XNL

source_name: Schizonts, CCR4-1KO

extract_protocol:
Gametocyte samples were collected as described above. Following purification by an Accudenz gradient, mouse RBCs were subjected to lysis with 0.1% w/v saponin in 1xPBS, then washed with 1xPBS. Released parasites were then lysed immediately. RNA from the samples was isolated by the QIAgen RNeasy Kit (QIAgen, Cat No. 74104) using the manufacturer’s protocol with the additional on-column DNaseI digestion. RNA yields were quantified spectrophotometrically (NanoDrop 2000c, Thermo Scientific), and RNA samples were submitted to the Penn State Genomics Core Facility. The quality of all samples was confirmed by measuring RNA Integrity Number (RIN) using the Agilent Bioanalzyer.
A barcoded library was made from each sample by using the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, Cat# RS-122-2101) according to the manufacturer's protocol. qPCR was performed to determine the concentration of each library and an equimolar pool was made of all libraries. The library pool was sequenced on an Illumina HiSeq 2500 in Rapid Run mode according to the manufacturer's protocol.
100 nt single read RNA-sequencing.

value: ccr4-1 knockout

value: Schizont

value: Whole body


title: HMEC d4 FBXO32 R1


title: CCR4-1KO-1

description:
Plasmodium yoelii 17XNL
CCR4-1-KO-1
Processed data file: SuppTable3_Complete_RNAseq_DEseq2_output.xlsx


title: WildType-5

description:
Plasmodium yoelii 17XNL
489-5
Processed data file: SuppTable3_Complete_RNAseq_DEseq2_output.xlsx

source_name: Schizonts, WT

value: Wild type


title: WildType-4

description:
Plasmodium yoelii 17XNL
489-4
Processed data file: SuppTable3_Complete_RNAseq_DEseq2_output.xlsx


title: WildType-3

description:
Plasmodium yoelii 17XNL
489-3
Processed data file: SuppTable3_Complete_RNAseq_DEseq2_output.xlsx


title: CCR4-1KO-2

description:
Plasmodium yoelii 17XNL
CCR4-1-KO-2
Processed data file: SuppTable3_Complete_RNAseq_DEseq2_output.xlsx


title: WildType-1

description:
Plasmodium yoelii 17XNL
489-1
Processed data file: SuppTable3_Complete_RNAseq_DEseq2_output.xlsx


title: WildType-2

description:
Plasmodium yoelii 17XNL
489-2
Processed data file: SuppTable3_Complete_RNAseq_DEseq2_output.xlsx


title: olfactory bulb oxBS-seq rep1

description: oxBS-seq

value: 8 week

value: olfactory bulb


title: glc-.0.5h_repA_biogenesis

description: total RNA - rRNA

value: glc-


title: MDA_msLung_12h IP_Rep2

status: Public on Jan 01 2019

first: Danilo

middle: G

last: Macalinao

address: 1275 York Avenue

institute: MSKCC

description:
processed data file:
Flura-seq in vivo RawCounts.csv

data_processing:
Samples were barcoded
run on a Hiseq 2000 platform in a 50bp/50bp paired-end run, using the TruSeq SBS Kit v3 (Illumina).
An average of 25 million paired reads were generated per sample.
The data were analyzed using the STAR-HTSeq-DESeq2 pipeline as previously described.
Flura-seq in vivo experiments were aligned to hybrid genome containing combined human and mouse genome. Mouse gene is indicated by "m" in front of the gene name whereas human gene is indicated by "h" in front of the gene name. For the other reamining experiments, the reads were aligned to human genome.
Genome_build: hg19, mm10, Hybrid genome containing hg19 and mm10
Supplementary_files_format_and_content: Three separate count files in csv format are provided for three different experiments (5-FC Time course, Flura-seq in vivo, and TGFB treatment)

organism:
Homo sapiens
Mus musculus

source_name: MDA_msLung_12h IP

growth_protocol: MDA231-BrM2 cells  were cultured in DMEM with 10% fetal bovine serum (FBS) and 2 mM L-Glutamine.

extract_protocol:
mRNAs were isolated by Oligo dT magnetic beads. Either the mRNAs were sequenced directly or immunoprecipitated with anti-BrdU antibody, and bound mRNAs were eluted using BrdU solution, and the eluted mRNAs were sequenced.
TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions. For the immunopurified RNAs, the RNAs were amplified by SMARTer amplification and library was prepared by Nextera Kit followinf manufacturer's protocol.

treatment_protocol: For TGFB experiments, cells were treated with TGFB or SB-505124 for 150 minutes. 5-FC treatment was done for 3 hours for TGFB experiments, and 4 hours or 12 hours for other experiments as indicated.

value: MDA231 Lung Xenograft

value: breast cancer cell line

tag: metastatic derivative

value: Parental

tag: sample group

value: Dox 2d, 250 mg/Kg 5-FC, 12h


title: MDA_msLung_4h IP_Rep1

source_name: MDA_msLung_4h IP

value: Dox 2d, 250 mg/Kg 5-FC, 4h


title: MDA_msLung_12h IP_Rep1


title: MDA_msLung_4h Input_Rep1

source_name: MDA_msLung_4h Input


title: MDA_msLung_4h Input_Rep2


title: cortex oxBS-seq rep1

description: oxBS-seq

value: cortex


title: CCR4-1KO-4

description:
Plasmodium yoelii 17XNL
CCR4-1-KO-4
Processed data file: SuppTable3_Complete_RNAseq_DEseq2_output.xlsx


title: WildType-6

description:
Plasmodium yoelii 17XNL
489-6
Processed data file: SuppTable3_Complete_RNAseq_DEseq2_output.xlsx


title: PAS-seq_hlp1_prmt10_double_mutant_rep2

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

description: high-throughput profiling of polyadenylation in hlp1 prmt10 double (mutant)

data_processing:
library strategy: PAS-seq
Tags less than 20 nt after removal of the 3’ linker and 4 nt random barcodes were discarded. All tags were reverse-complemented because the tags were sequenced from 3'-end of transcripts (Fu et al., 2011). Trimmed tags were then mapped to the Arabidopsis genome (TAIR10) using Bowtie (0.12.7) (Langmead et al., 2009), allowing 2 mismatches. Only uniquely mapped tags were kept for downstream analyses. Uniquely located tags with six or more continuous adenines downstream from the poly(A) junction in a 10-nt window were identified as internal priming tags and discarded (Shepard et al., 2011).
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files were generated using MACS program

organism: Arabidopsis thaliana

growth_protocol: All of the Arabidopsis thaliana lines used in this study were in the Col background. Plant growth, flowering time analysis, and plant transformation were performed as reported previously (Pei et al., 2007). The atprmt10-1 (Niu et al., 2007) and flc-3 (Michaels and Amasino, 1999) mutants were described previously. The hlp1-1 mutant was isolated from the SALK collection (SALK_021452). Seedlings were grown on Murashige and Skoog (MS) plates containing 3% sucrose.

extract_protocol:
The seedlings were ground into fine power in liquid nitrogen and RNA was extracted by TRNzol reagent (Tiangen).
Poly(A) site sequencing was performed as described with modifications at the HITS-3’ adaptor and sequencing primer (Fu et al., 2011; Shepard et al., 2011). Briefly, poly(A) RNAs were purified using a mRNA purification kit (Invitrogen), and heat fragmented at 95°C for 30 min. Reverse transcription (Superscript, Invitrogen) was carried out using our modified HITS-3’ adaptor at 42°C for 30 min, then the HITS-5’ adaptor (a SMART oligo) was added and incubated for an additional 30 min. The cDNAs were purified using a Qiagen PCR Cleanup kit and second strand cDNAs were synthesized by 3 cycles of PCR using Phusion DNA polymerase (NEB) and the PE1.0 and PE2.0 primers. The PCR products were separated on a 2% agarose gel and the 200-300 bp bands were excised and purified. Gel-extracted DNAs were further amplified by a 13-cycle PCR. The PCR products were purified using a Qiagen PCR Cleanup kit.

tag: background

value: col

value: hlp1 prmt10 double mutant

value: seedlings


title: PAS-seq_VLD_to_AAA_mutant_rep2

description: high-throughput profiling of polyadenylation in VLD->AAA (mutant)

value: VLD->AAA mutant


title: PAS-seq_prmt10_mutant_rep2

description: high-throughput profiling of polyadenylation in prmt10 (mutant)

value: prmt10 mutant


title: PAS-seq_hlp1_prmt10_double_mutant_rep1


title: MDA_msLung_12h Input_Rep2

source_name: MDA_msLung_12h Input


title: PAS-seq_HLP1_del_RRM_mutant_rep1

description: high-throughput profiling of polyadenylation in HLP1_del_RRM (mutant)

value: HLP1_del_RRM mutant


title: PAS-seq_VLD_to_AAA_mutant_rep1


title: PAS-seq_HLP1_del_RRM_mutant_rep2


title: TX-24hr-4

city: Salt Lake City

first: Sumati

last: Gupta

state: Utah

address: 2000 Circle of Hope

department: Medicine

institute: Huntsman Cancer Institute

data_processing:
Reference files were generated by combining the chromosome sequences from hg19 with splice junction sequences.  The splice junction sequences were generated using the USeq (v8.6.8) application MakeTranscriptome using a radius of 46.  Ensembl transcript annotations (build 66) were downloaded from the UCSC table browser.
Reads were aligned to the transcriptome reference index described above using Novoalign (v2.08.01), allowing up to 50 alignments for each read.  USeq’s SamTranscriptomeParser application was used to select the best alignment for each read and convert the coordinates of reads aligning to splices back to genomic space.
Differential gene expression was measured using USeq’s (v8.6.8) DefinedRegionDifferentialSeq application.  Briefly, the numbers of reads aligned to each gene were calculated.  The counts were then used in DESeq2, which normalizes the signal and determines differential expression.
Genome_build: hg19
Supplementary_files_format_and_content: Deseq2 output files containing Ensembl Gene ID, common name, log2 fold change, FDR and raw counts.

source_name: NGP neuroblastoma

growth_protocol: NGP neuroblastoma cell lines (donated by Rod Stewart lab) were cultured in DMEM supplemented with 10% FBS, 100 units/ml of penicillin, and 100ug/ml streptomycin

extract_protocol:
RNA was extracted using RNAeasy kit (Qiagen). Intact poly (A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads
sequencing libraries were prepared as described using the Illumina TruSeq RNA Library Preparation Kit v2 (RS-122-2001, RS-122-2002).  Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 10 nM and equal volumes were pooled in preparation for Illumina sequence analysis.
Sequencing libraries (18 pM) were denatured chemically and applied to an Illumina TruSeq v3 single read flowcell using an Illumina cBot.  Using an Illumina TruSeq SR Cluster Kit v3-cBot-HS (GD-401-3001) hybridized molecules were clonally amplified and annealed to sequencing primers.   Following transfer of the flowcell to an Illumina HiSeq instrument (HCS v2.0.12 and RTA v1.17.21.3), a 50 cycle single read sequence run was performed using TruSeq SBS v3 sequencing reagents (FC-401-3002).

treatment_protocol: One million NGP cells per well were plated in 6 well plates and treated with vehicle (DMSO) or 3 µM HCI-2509 for 4 and 24 hours in quadruplicate.

tag: treatment

value: 3 µM HCI-2509 for 24 hrs

value: NGP


title: MDA_msLung_12h Input_Rep1


title: MDA_msLung_4h IP_Rep2


title: PAS-seq_E152Q_mutant_rep1

description: high-throughput profiling of polyadenylation in E152Q (mutant)

value: E152Q mutant


title: PAS-seq_E152Q_mutant_rep2


title: TX-24hr-3


title: VEH-4hr-3

value: vehicle (DMSO) for 4 hrs


title: VEH-4hr-4


title: TX-4hr-4

value: 3 µM HCI-2509 for 4 hrs


title: VEH-24hr-3

value: vehicle (DMSO) for 24 hrs


title: TX-4hr-3


title: VEH-4hr-1


title: TX-4hr-2


title: VEH-24hr-2


title: PAS-seq_prmt10_mutant_rep1


title: TX-24hr-1


title: VEH-24hr-1


title: TX-4hr-1


title: VEH-24hr-4


title: TX-24hr-2


title: VEH-4hr-2


title: normal.ct-962

city: La Jolla

first: Kang

last: Zhang

address: 9500 Gilman Dr

institute: UCSD

description: cell-free DNA

data_processing:
unique molecular identifiers were extracted from each read using custom script
reads were adaptor and quality trimmed using Trim-galore and Cutadapt 1.4.1 with parameters -e 0.1 -q 20 -O 1
BisReadMapper1.3 (D.Diep, K.Zhang) using Bowtie2 was used to align reads to in-silico bisulfite-converted genome sequence
C and Ts were extracted from reads at the targeted positions using only reads with unique identifiers and methylation frequencies were calculated using custom scripts (BamExtractor, D.Diep, K.Zhang)
Genome_build: hg19
Supplementary_files_format_and_content: text file containing beta values and numbers of C and T for all samples at all analyzed CpG markers

source_name: blood serum

extract_protocol:
cfDNA extraction from 1.5 ml of serum samples was performed using QIAamp cfDNA Kit (Qiagen) according to manufacturer’s recommendations
10 ng of cfDNA was bisulfite-converted using EZ DNA Methylation-Lightning™ Kit (Zymo). Bis-DNA specific "padlock" probes (molecular inversion probes, MIPS) were used to capture genomic regions and provide adaptors for NGS library construction. Nextera-XT compatible barcoding primers were used to amplify DNA for sequencing. Library (~300bp) was purified using AMPure beads.
custom-made libraries were sequenced on HiSeq2500 using 150PE reads

value: blood serum

tag: group

value: healthy control


title: normal.ct-964

description: cell-free DNA


title: normal.ct-965

description: cell-free DNA


title: normal.ct-953

description: cell-free DNA


title: normal.ct-970

description: cell-free DNA


title: normal.ct-967

description: cell-free DNA


title: normal.ct-959

description: cell-free DNA


title: normal.ct-956

description: cell-free DNA


title: normal.ct-961

description: cell-free DNA


title: normal.ct-955

description: cell-free DNA


title: normal.ct-960

description: cell-free DNA


title: normal.ct-968

description: cell-free DNA


title: normal.ct-958

description: cell-free DNA


title: normal.ct-969

description: cell-free DNA


title: normal.ct-966

description: cell-free DNA


title: normal.ct-950

description: cell-free DNA


title: normal.ct-951

description: cell-free DNA


title: normal.ct-948

description: cell-free DNA


title: normal.ct-947

description: cell-free DNA


title: normal.ct-949

description: cell-free DNA


title: normal.ct-946

description: cell-free DNA


title: normal.ct-945

description: cell-free DNA


title: normal.ct-963

description: cell-free DNA


title: normal.ct-944

description: cell-free DNA


title: normal.ct-957

description: cell-free DNA


title: normal.ct-954

description: cell-free DNA


title: normal.ct-943

description: cell-free DNA


title: normal.ct-952

description: cell-free DNA


title: normal.ct-932

description: cell-free DNA


title: normal.ct-933

description: cell-free DNA


title: normal.ct-941

description: cell-free DNA


title: normal.ct-939

description: cell-free DNA


title: normal.ct-938

description: cell-free DNA


title: normal.ct-940

description: cell-free DNA


title: normal.ct-924

description: cell-free DNA


title: normal.ct-928

description: cell-free DNA


title: normal.ct-922

description: cell-free DNA


title: normal.ct-927

description: cell-free DNA


title: normal.ct-926

description: cell-free DNA


title: normal.ct-937

description: cell-free DNA


title: normal.ct-929

description: cell-free DNA


title: normal.ct-935

description: cell-free DNA


title: normal.ct-942

description: cell-free DNA


title: normal.ct-931

description: cell-free DNA


title: normal.ct-925

description: cell-free DNA


title: normal.ct-923

description: cell-free DNA


title: normal.ct-930

description: cell-free DNA


title: normal.ct-920

description: cell-free DNA


title: normal.ct-936

description: cell-free DNA


title: normal.ct-934

description: cell-free DNA


title: normal.ct-919

description: cell-free DNA


title: normal.ct-921

description: cell-free DNA


title: normal.ct-918

description: cell-free DNA


title: normal.ct-916

description: cell-free DNA


title: normal.ct-917

description: cell-free DNA


title: cerebellum TAB-seq rep2

description: TAB-seq

value: 8 week

value: cerebellum


title: normal.ct-911

description: cell-free DNA


title: normal.ct-914

description: cell-free DNA


title: normal.ct-910

description: cell-free DNA


title: normal.ct-912

description: cell-free DNA


title: normal.ct-908

description: cell-free DNA


title: normal.ct-907

description: cell-free DNA


title: normal.ct-909

description: cell-free DNA


title: normal.ct-897

description: cell-free DNA


title: normal.ct-903

description: cell-free DNA


title: normal.ct-899

description: cell-free DNA


title: normal.ct-905

description: cell-free DNA


title: normal.ct-900

description: cell-free DNA


title: normal.ct-915

description: cell-free DNA


title: normal.ct-893

description: cell-free DNA


title: normal.ct-898

description: cell-free DNA


title: normal.ct-896

description: cell-free DNA


title: normal.ct-892

description: cell-free DNA


title: normal.ct-889

description: cell-free DNA


title: normal.ct-894

description: cell-free DNA


title: normal.ct-904

description: cell-free DNA


title: normal.ct-888

description: cell-free DNA


title: normal.ct-890

description: cell-free DNA


title: normal.ct-891

description: cell-free DNA


title: normal.ct-887

description: cell-free DNA


title: normal.ct-913

description: cell-free DNA


title: normal.ct-886

description: cell-free DNA


title: normal.ct-885

description: cell-free DNA


title: normal.ct-906

description: cell-free DNA


title: normal.ct-883

description: cell-free DNA


title: normal.ct-901

description: cell-free DNA


title: normal.ct-895

description: cell-free DNA


title: normal.ct-884

description: cell-free DNA


title: normal.ct-902

description: cell-free DNA


title: normal.ct-882

description: cell-free DNA


title: normal.ct-881

description: cell-free DNA


title: normal.ct-880

description: cell-free DNA


title: normal.ct-876

description: cell-free DNA


title: normal.ct-875

description: cell-free DNA


title: normal.ct-878

description: cell-free DNA


title: normal.ct-873

description: cell-free DNA


title: normal.ct-874

description: cell-free DNA


title: normal.ct-877

description: cell-free DNA


title: normal.ct-870

description: cell-free DNA


title: normal.ct-869

description: cell-free DNA


title: normal.ct-868

description: cell-free DNA


title: normal.ct-866

description: cell-free DNA


title: normal.ct-865

description: cell-free DNA


title: normal.ct-864

description: cell-free DNA


title: normal.ct-879

description: cell-free DNA


title: normal.ct-867

description: cell-free DNA


title: normal.ct-871

description: cell-free DNA


title: normal.ct-862

description: cell-free DNA


title: normal.ct-863

description: cell-free DNA


title: normal.ct-861

description: cell-free DNA


title: normal.ct-860

description: cell-free DNA


title: normal.ct-859

description: cell-free DNA


title: normal.ct-857

description: cell-free DNA


title: normal.ct-855

description: cell-free DNA


title: normal.ct-854

description: cell-free DNA


title: normal.ct-858

description: cell-free DNA


title: normal.ct-856

description: cell-free DNA


title: normal.ct-853

description: cell-free DNA


title: normal.ct-850

description: cell-free DNA


title: normal.ct-849

description: cell-free DNA


title: normal.ct-852

description: cell-free DNA


title: normal.ct-847

description: cell-free DNA


title: normal.ct-872

description: cell-free DNA


title: normal.ct-846

description: cell-free DNA


title: normal.ct-844

description: cell-free DNA


title: normal.ct-845

description: cell-free DNA


title: normal.ct-842

description: cell-free DNA


title: normal.ct-843

description: cell-free DNA


title: normal.ct-851

description: cell-free DNA


title: normal.ct-848

description: cell-free DNA


title: normal.ct-839

description: cell-free DNA


title: normal.ct-836

description: cell-free DNA


title: normal.ct-838

description: cell-free DNA


title: normal.ct-841

description: cell-free DNA


title: normal.ct-840

description: cell-free DNA


title: normal.ct-834

description: cell-free DNA


title: normal.ct-833

description: cell-free DNA


title: normal.ct-828

description: cell-free DNA


title: normal.ct-832

description: cell-free DNA


title: normal.ct-827

description: cell-free DNA


title: normal.ct-831

description: cell-free DNA


title: normal.ct-824

description: cell-free DNA


title: normal.ct-829

description: cell-free DNA


title: normal.ct-822

description: cell-free DNA


title: normal.ct-837

description: cell-free DNA


title: normal.ct-823

description: cell-free DNA


title: normal.ct-826

description: cell-free DNA


title: normal.ct-835

description: cell-free DNA


title: normal.ct-825

description: cell-free DNA


title: normal.ct-821

description: cell-free DNA


title: normal.ct-815

description: cell-free DNA


title: normal.ct-830

description: cell-free DNA


title: normal.ct-814

description: cell-free DNA


title: normal.ct-811

description: cell-free DNA


title: normal.ct-818

description: cell-free DNA


title: normal.ct-809

description: cell-free DNA


title: normal.ct-807

description: cell-free DNA


title: normal.ct-816

description: cell-free DNA


title: normal.ct-812

description: cell-free DNA


title: normal.ct-810

description: cell-free DNA


title: normal.ct-808

description: cell-free DNA


title: normal.ct-806

description: cell-free DNA


title: normal.ct-805

description: cell-free DNA


title: normal.ct-804

description: cell-free DNA


title: normal.ct-803

description: cell-free DNA


title: normal.ct-802

description: cell-free DNA


title: normal.ct-800

description: cell-free DNA


title: normal.ct-799

description: cell-free DNA


title: normal.ct-817

description: cell-free DNA


title: normal.ct-820

description: cell-free DNA


title: normal.ct-801

description: cell-free DNA


title: normal.ct-813

description: cell-free DNA


title: normal.ct-793

description: cell-free DNA


title: normal.ct-798

description: cell-free DNA


title: normal.ct-795

description: cell-free DNA


title: normal.ct-791

description: cell-free DNA


title: normal.ct-792

description: cell-free DNA


title: normal.ct-796

description: cell-free DNA


title: normal.ct-797

description: cell-free DNA


title: normal.ct-794

description: cell-free DNA


title: normal.ct-789

description: cell-free DNA


title: normal.ct-790

description: cell-free DNA


title: normal.ct-788

description: cell-free DNA


title: normal.ct-787

description: cell-free DNA


title: normal.ct-783

description: cell-free DNA


title: normal.ct-786

description: cell-free DNA


title: normal.ct-785

description: cell-free DNA


title: normal.ct-782

description: cell-free DNA


title: normal.ct-779

description: cell-free DNA


title: normal.ct-778

description: cell-free DNA


title: normal.ct-781

description: cell-free DNA


title: normal.ct-777

description: cell-free DNA


title: normal.ct-780

description: cell-free DNA


title: normal.ct-776

description: cell-free DNA


title: normal.ct-769

description: cell-free DNA


title: normal.ct-765

description: cell-free DNA


title: normal.ct-770

description: cell-free DNA


title: normal.ct-774

description: cell-free DNA


title: normal.ct-775

description: cell-free DNA


title: normal.ct-766

description: cell-free DNA


title: normal.ct-773

description: cell-free DNA


title: normal.ct-759

description: cell-free DNA


title: normal.ct-771

description: cell-free DNA


title: normal.ct-772

description: cell-free DNA


title: normal.ct-768

description: cell-free DNA


title: normal.ct-763

description: cell-free DNA


title: normal.ct-764

description: cell-free DNA


title: normal.ct-762

description: cell-free DNA


title: normal.ct-767

description: cell-free DNA


title: normal.ct-755

description: cell-free DNA


title: normal.ct-760

description: cell-free DNA


title: normal.ct-784

description: cell-free DNA


title: normal.ct-761

description: cell-free DNA


title: normal.ct-819

description: cell-free DNA


title: normal.ct-752

description: cell-free DNA


title: normal.ct-758

description: cell-free DNA


title: normal.ct-756

description: cell-free DNA


title: normal.ct-750

description: cell-free DNA


title: normal.ct-749

description: cell-free DNA


title: normal.ct-757

description: cell-free DNA


title: normal.ct-746

description: cell-free DNA


title: normal.ct-745

description: cell-free DNA


title: normal.ct-751

description: cell-free DNA


title: normal.ct-754

description: cell-free DNA


title: normal.ct-741

description: cell-free DNA


title: normal.ct-743

description: cell-free DNA


title: normal.ct-748

description: cell-free DNA


title: normal.ct-753

description: cell-free DNA


title: normal.ct-740

description: cell-free DNA


title: normal.ct-736

description: cell-free DNA


title: normal.ct-747

description: cell-free DNA


title: normal.ct-738

description: cell-free DNA


title: normal.ct-734

description: cell-free DNA


title: normal.ct-730

description: cell-free DNA


title: normal.ct-739

description: cell-free DNA


title: normal.ct-732

description: cell-free DNA


title: normal.ct-733

description: cell-free DNA


title: normal.ct-742

description: cell-free DNA


title: normal.ct-737

description: cell-free DNA


title: normal.ct-735

description: cell-free DNA


title: normal.ct-729

description: cell-free DNA


title: normal.ct-728

description: cell-free DNA


title: normal.ct-727

description: cell-free DNA


title: normal.ct-725

description: cell-free DNA


title: normal.ct-744

description: cell-free DNA


title: normal.ct-721

description: cell-free DNA


title: normal.ct-723

description: cell-free DNA


title: normal.ct-726

description: cell-free DNA


title: normal.ct-724

description: cell-free DNA


title: normal.ct-720

description: cell-free DNA


title: normal.ct-718

description: cell-free DNA


title: normal.ct-719

description: cell-free DNA


title: normal.ct-716

description: cell-free DNA


title: normal.ct-715

description: cell-free DNA


title: normal.ct-717

description: cell-free DNA


title: normal.ct-713

description: cell-free DNA


title: normal.ct-714

description: cell-free DNA


title: normal.ct-712

description: cell-free DNA


title: normal.ct-711

description: cell-free DNA


title: normal.ct-731

description: cell-free DNA


title: normal.ct-709

description: cell-free DNA


title: normal.ct-708

description: cell-free DNA


title: normal.ct-707

description: cell-free DNA


title: normal.ct-710

description: cell-free DNA


title: normal.ct-706

description: cell-free DNA


title: normal.ct-705

description: cell-free DNA


title: normal.ct-722

description: cell-free DNA


title: normal.ct-703

description: cell-free DNA


title: normal.ct-699

description: cell-free DNA


title: normal.ct-702

description: cell-free DNA


title: normal.ct-697

description: cell-free DNA


title: normal.ct-700

description: cell-free DNA


title: normal.ct-694

description: cell-free DNA


title: normal.ct-692

description: cell-free DNA


title: normal.ct-695

description: cell-free DNA


title: normal.ct-693

description: cell-free DNA


title: normal.ct-689

description: cell-free DNA


title: normal.ct-690

description: cell-free DNA


title: normal.ct-685

description: cell-free DNA


title: normal.ct-687

description: cell-free DNA


title: normal.ct-686

description: cell-free DNA


title: normal.ct-688

description: cell-free DNA


title: normal.ct-682

description: cell-free DNA


title: normal.ct-680

description: cell-free DNA


title: normal.ct-704

description: cell-free DNA


title: normal.ct-683

description: cell-free DNA


title: normal.ct-701

description: cell-free DNA


title: normal.ct-678

description: cell-free DNA


title: normal.ct-684

description: cell-free DNA


title: normal.ct-696

description: cell-free DNA


title: normal.ct-674

description: cell-free DNA


title: normal.ct-681

description: cell-free DNA


title: normal.ct-698

description: cell-free DNA


title: normal.ct-676

description: cell-free DNA


title: normal.ct-675

description: cell-free DNA


title: normal.ct-673

description: cell-free DNA


title: normal.ct-671

description: cell-free DNA


title: normal.ct-691

description: cell-free DNA


title: normal.ct-670

description: cell-free DNA


title: normal.ct-669

description: cell-free DNA


title: normal.ct-668

description: cell-free DNA


title: normal.ct-666

description: cell-free DNA


title: normal.ct-667

description: cell-free DNA


title: normal.ct-663

description: cell-free DNA


title: normal.ct-662

description: cell-free DNA


title: normal.ct-679

description: cell-free DNA


title: normal.ct-660

description: cell-free DNA


title: normal.ct-658

description: cell-free DNA


title: normal.ct-677

description: cell-free DNA


title: normal.ct-659

description: cell-free DNA


title: normal.ct-665

description: cell-free DNA


title: normal.ct-655

description: cell-free DNA


title: normal.ct-656

description: cell-free DNA


title: normal.ct-657

description: cell-free DNA


title: normal.ct-653

description: cell-free DNA


title: normal.ct-652

description: cell-free DNA


title: normal.ct-654

description: cell-free DNA


title: normal.ct-649

description: cell-free DNA


title: normal.ct-646

description: cell-free DNA


title: normal.ct-647

description: cell-free DNA


title: normal.ct-672

description: cell-free DNA


title: normal.ct-645

description: cell-free DNA


title: normal.ct-644

description: cell-free DNA


title: normal.ct-648

description: cell-free DNA


title: normal.ct-643

description: cell-free DNA


title: normal.ct-640

description: cell-free DNA


title: normal.ct-664

description: cell-free DNA


title: normal.ct-637

description: cell-free DNA


title: normal.ct-661

description: cell-free DNA


title: normal.ct-636

description: cell-free DNA


title: normal.ct-641

description: cell-free DNA


title: normal.ct-642

description: cell-free DNA


title: normal.ct-633

description: cell-free DNA


title: normal.ct-631

description: cell-free DNA


title: normal.ct-634

description: cell-free DNA


title: normal.ct-630

description: cell-free DNA


title: normal.ct-650

description: cell-free DNA


title: normal.ct-625

description: cell-free DNA


title: normal.ct-627

description: cell-free DNA


title: normal.ct-626

description: cell-free DNA


title: normal.ct-629

description: cell-free DNA


title: normal.ct-632

description: cell-free DNA


title: normal.ct-651

description: cell-free DNA


title: normal.ct-624

description: cell-free DNA


title: normal.ct-628

description: cell-free DNA


title: normal.ct-621

description: cell-free DNA


title: normal.ct-620

description: cell-free DNA


title: normal.ct-622

description: cell-free DNA


title: normal.ct-619

description: cell-free DNA


title: normal.ct-623

description: cell-free DNA


title: normal.ct-639

description: cell-free DNA


title: normal.ct-618

description: cell-free DNA


title: normal.ct-617

description: cell-free DNA


title: normal.ct-616

description: cell-free DNA


title: normal.ct-638

description: cell-free DNA


title: normal.ct-615

description: cell-free DNA


title: normal.ct-635

description: cell-free DNA


title: normal.ct-613

description: cell-free DNA


title: normal.ct-610

description: cell-free DNA


title: normal.ct-611

description: cell-free DNA


title: normal.ct-609

description: cell-free DNA


title: normal.ct-614

description: cell-free DNA


title: normal.ct-608

description: cell-free DNA


title: normal.ct-612

description: cell-free DNA


title: normal.ct-607

description: cell-free DNA


title: normal.ct-606

description: cell-free DNA


title: normal.ct-603

description: cell-free DNA


title: normal.ct-601

description: cell-free DNA


title: normal.ct-599

description: cell-free DNA


title: normal.ct-604

description: cell-free DNA


title: normal.ct-602

description: cell-free DNA


title: normal.ct-605

description: cell-free DNA


title: normal.ct-600

description: cell-free DNA


title: normal.ct-597

description: cell-free DNA


title: normal.ct-598

description: cell-free DNA


title: normal.ct-586

description: cell-free DNA


title: normal.ct-596

description: cell-free DNA


title: normal.ct-590

description: cell-free DNA


title: normal.ct-591

description: cell-free DNA


title: normal.ct-595

description: cell-free DNA


title: normal.ct-587

description: cell-free DNA


title: normal.ct-589

description: cell-free DNA


title: normal.ct-594

description: cell-free DNA


title: normal.ct-593

description: cell-free DNA


title: normal.ct-584

description: cell-free DNA


title: normal.ct-585

description: cell-free DNA


title: normal.ct-578

description: cell-free DNA


title: normal.ct-582

description: cell-free DNA


title: normal.ct-581

description: cell-free DNA


title: normal.ct-577

description: cell-free DNA


title: normal.ct-575

description: cell-free DNA


title: normal.ct-580

description: cell-free DNA


title: normal.ct-573

description: cell-free DNA


title: normal.ct-571

description: cell-free DNA


title: normal.ct-576

description: cell-free DNA


title: normal.ct-572

description: cell-free DNA


title: normal.ct-592

description: cell-free DNA


title: normal.ct-568

description: cell-free DNA


title: normal.ct-569

description: cell-free DNA


title: normal.ct-570

description: cell-free DNA


title: normal.ct-567

description: cell-free DNA


title: normal.ct-588

description: cell-free DNA


title: normal.ct-583

description: cell-free DNA


title: normal.ct-561

description: cell-free DNA


title: normal.ct-562

description: cell-free DNA


title: normal.ct-560

description: cell-free DNA


title: normal.ct-579

description: cell-free DNA


title: normal.ct-557

description: cell-free DNA


title: normal.ct-563

description: cell-free DNA


title: normal.ct-565

description: cell-free DNA


title: normal.ct-559

description: cell-free DNA


title: normal.ct-558

description: cell-free DNA


title: normal.ct-574

description: cell-free DNA


title: normal.ct-552

description: cell-free DNA


title: normal.ct-555

description: cell-free DNA


title: normal.ct-566

description: cell-free DNA


title: normal.ct-556

description: cell-free DNA


title: normal.ct-551

description: cell-free DNA


title: normal.ct-549

description: cell-free DNA


title: normal.ct-545

description: cell-free DNA


title: normal.ct-554

description: cell-free DNA


title: normal.ct-547

description: cell-free DNA


title: normal.ct-548

description: cell-free DNA


title: normal.ct-553

description: cell-free DNA


title: normal.ct-543

description: cell-free DNA


title: normal.ct-542

description: cell-free DNA


title: normal.ct-541

description: cell-free DNA


title: normal.ct-540

description: cell-free DNA


title: normal.ct-546

description: cell-free DNA


title: normal.ct-544

description: cell-free DNA


title: normal.ct-564

description: cell-free DNA


title: normal.ct-536

description: cell-free DNA


title: normal.ct-539

description: cell-free DNA


title: normal.ct-538

description: cell-free DNA


title: normal.ct-537

description: cell-free DNA


title: normal.ct-535

description: cell-free DNA


title: normal.ct-534

description: cell-free DNA


title: normal.ct-533

description: cell-free DNA


title: normal.ct-532

description: cell-free DNA


title: normal.ct-531

description: cell-free DNA


title: normal.ct-529

description: cell-free DNA


title: normal.ct-530

description: cell-free DNA


title: normal.ct-526

description: cell-free DNA


title: normal.ct-528

description: cell-free DNA


title: normal.ct-525

description: cell-free DNA


title: normal.ct-527

description: cell-free DNA


title: normal.ct-523

description: cell-free DNA


title: normal.ct-520

description: cell-free DNA


title: normal.ct-522

description: cell-free DNA


title: normal.ct-521

description: cell-free DNA


title: normal.ct-517

description: cell-free DNA


title: normal.ct-519

description: cell-free DNA


title: normal.ct-515

description: cell-free DNA


title: normal.ct-518

description: cell-free DNA


title: normal.ct-513

description: cell-free DNA


title: normal.ct-512

description: cell-free DNA


title: normal.ct-514

description: cell-free DNA


title: normal.ct-516

description: cell-free DNA


title: normal.ct-511

description: cell-free DNA


title: normal.ct-509

description: cell-free DNA


title: normal.ct-507

description: cell-free DNA


title: normal.ct-510

description: cell-free DNA


title: normal.ct-506

description: cell-free DNA


title: normal.ct-508

description: cell-free DNA


title: normal.ct-505

description: cell-free DNA


title: normal.ct-503

description: cell-free DNA


title: normal.ct-504

description: cell-free DNA


title: normal.ct-501

description: cell-free DNA


title: normal.ct-500

description: cell-free DNA


title: normal.ct-502

description: cell-free DNA


title: normal.ct-499

description: cell-free DNA


title: normal.ct-524

description: cell-free DNA


title: normal.ct-498

description: cell-free DNA


title: normal.ct-496

description: cell-free DNA


title: normal.ct-493

description: cell-free DNA


title: normal.ct-495

description: cell-free DNA


title: normal.ct-488

description: cell-free DNA


title: normal.ct-489

description: cell-free DNA


title: normal.ct-490

description: cell-free DNA


title: normal.ct-494

description: cell-free DNA


title: normal.ct-491

description: cell-free DNA


title: normal.ct-486

description: cell-free DNA


title: normal.ct-485

description: cell-free DNA


title: normal.ct-484

description: cell-free DNA


title: normal.ct-482

description: cell-free DNA


title: normal.ct-481

description: cell-free DNA


title: normal.ct-479

description: cell-free DNA


title: normal.ct-476

description: cell-free DNA


title: normal.ct-477

description: cell-free DNA


title: normal.ct-475

description: cell-free DNA


title: normal.ct-474

description: cell-free DNA


title: normal.ct-478

description: cell-free DNA


title: normal.ct-472

description: cell-free DNA


title: normal.ct-497

description: cell-free DNA


title: normal.ct-483

description: cell-free DNA


title: normal.ct-471

description: cell-free DNA


title: mock_control3

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

description: expressed RNA after mock-control transfection

data_processing:
Basecalling based on Illumina Casava1.7 software
The raw RNA sequencing data were  mapped to the human genome (hg19) using STAR by requiring minimal mapped nucleotides no less than 90nt.
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons.
edgeR was used to estimate gene expression changes in log2 fold-change between miR-941 mimics transfection and mock-control transfection.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene ID and expression level in reads count for each sample

source_name: 293T cells - mock-control transfection

growth_protocol: 293T was cultured in DMEM/HIGH GLUCOSE (HyClone,SH30243.018), supplemented with 10％ heat-inactivated fetal calf serum (hyclone，SH30070),100U/ml penicillin, 100ug/ml streptomycin.

extract_protocol:
Total RNA were extracted with Trizol reagent (Invitrogen).
A cDNA library was generated from rRNA-depleted RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq2000 by a 1X100 bp run.

treatment_protocol: The miR-941 duplex (mimics) transfection experiments were conducted in a highly transfectable derivative of human embryonic kidney 293 cells (293T cells) in triplicates. Briefly, miR-941 duplex Lipofectamine 2000 (Invitrogen) complexes were prepared before transfection freshly according to the manufacturer's protocol. The 293T cells were firstly plated 24h before transfection in 0.5ml of growth medium without antibiotics, and then transfected in six-well plates using miR-941 duplex Lipofectamine 2000 with a final oligonucleotide concentration of 10 nmol/L. In parallel, negative control transfections with mock oligonucleotide (a scrambled oligo) were conducted according to the manufacturer's instructions. The transfection experiments with miR-941 duplex Lipofectamine 2000 and negative control oligonucleotides were carried out in three independent replicates.


title: normal.ct-473

description: cell-free DNA


title: mock_control1

value: highly transfectable derivative of human embryonic kidney 293 cells (293T cells)


title: normal.ct-470

description: cell-free DNA


title: normal.ct-487

description: cell-free DNA


title: normal.ct-469

description: cell-free DNA


title: normal.ct-492

description: cell-free DNA


title: miR941_mimics3

description: expressed RNA after miR-941 mimics transfection

source_name: 293T cells - miR-941 mimics transfection


title: miR941_mimics2


title: normal.ct-468

description: cell-free DNA


title: control_empty_vector3

description: expressed RNA after empty vector transfection

source_name: 293T cells - empty vector transfection


title: miR941_mimics1


title: normal.ct-467

description: cell-free DNA


title: normal.ct-480

description: cell-free DNA


title: normal.ct-465

description: cell-free DNA


title: normal.ct-466

description: cell-free DNA


title: control_empty_vector2


title: normal.ct-464

description: cell-free DNA


title: normal.ct-463

description: cell-free DNA


title: control_empty_vector1


title: sponge_miR941_3

description: expressed RNA after TP73-AS1 sponge and miR-941 transfection

source_name: 293T cells - TP73-AS1 sponge and miR-941 transfection


title: normal.ct-462

description: cell-free DNA


title: sponge_miR941_2


title: normal.ct-461

description: cell-free DNA


title: sponge_miR941_1


title: normal.ct-460

description: cell-free DNA


title: normal.ct-459

description: cell-free DNA


title: PFC4

description: expressed RNA, rRNA depleted

data_processing:
Basecalling based on Illumina Casava1.7 software
The raw RNA sequencing data were mapped to human genome (hg19) using BWA-MEM with default parameters except “-T 19” (filters out alignments with score <19), as recommended by CIRI.
To obtain more comprehensive circular RNAs, we predicted circular RNAs using CIRI with low stringency requirement with parameter (-low).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include identified circular RNA ID and loci information (chromosome, start and end) for each sample

source_name: Prefrontal cortex

extract_protocol:
Total RNA was isolated using Trizol as recommended by manufacturer. Ribosomal RNA was depleted from total RNA using the Ribominus Kit (Invitrogen)
A cDNA library was generated from rRNA-depleted RNA according to the standard Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq2000 by a 1X100 bp run.

treatment_protocol: Human PFC samples were frozen in -80C

value: Prefrontal cortex

value: postnatal 53 years


title: mock_control2


title: PFC3

description: expressed RNA, rRNA depleted

value: postnatal 443 years


title: normal.ct-458

description: cell-free DNA


title: normal.ct-457

description: cell-free DNA


title: normal.ct-456

description: cell-free DNA


title: PFC1

description: expressed RNA, rRNA depleted

value: postnatal 66 years


title: normal.ct-455

description: cell-free DNA


title: PFC2

description: expressed RNA, rRNA depleted

value: postnatal 204 days


title: normal.ct-454

description: cell-free DNA


title: MDA_TGFB_IP_Rep3

description:
processed data file:
TGFB treatment RawCounts.csv

value: breast cancer cell line

value: Parental

value: TGFB


title: MDA_TGFB_IP_Rep1


title: MDA_SB_IP_Rep3


title: normal.ct-453

description: cell-free DNA


title: normal.ct-452

description: cell-free DNA


title: MDA_TGFB_IP_Rep2


title: normal.ct-451

description: cell-free DNA


title: MDA_SB_IP_Rep1


title: MDA_SB_IP_Rep2


title: normal.ct-449

description: cell-free DNA


title: MDA_TGFBCon_Rep3


title: MDA_TGFBCon_Rep2


title: normal.ct-448

description: cell-free DNA


title: normal.ct-446

description: cell-free DNA


title: MDA_SBCon_Rep3


title: MDA_SBCon_Rep2


title: MDA_TGFBCon_Rep1


title: normal.ct-445

description: cell-free DNA


title: MDA_SBCon_Rep1


title: normal.ct-447

description: cell-free DNA


title: normal.ct-443

description: cell-free DNA


title: normal.ct-444

description: cell-free DNA


title: normal.ct-442

description: cell-free DNA


title: MDA_FC250uM12hr_Rep2

description:
processed data file:
5-FC Time course RawCounts.csv


title: MDA_FC250uM4hr_Rep2


title: MDA_FC250uM12hr_Rep1


title: normal.ct-441

description: cell-free DNA


title: MDA_FC50uM12hr_Rep2


title: normal.ct-440

description: cell-free DNA


title: MDA_FC250uM4hr_Rep1


title: MDA_FC50uM4hr_Rep2

value: Dox+, 50uM 5-FC, 4h


title: normal.ct-438

description: cell-free DNA


title: normal.ct-450

description: cell-free DNA


title: normal.ct-439

description: cell-free DNA


title: MDA_FC50uM4hr_Rep1


title: normal.ct-436

description: cell-free DNA


title: normal.ct-435

description: cell-free DNA


title: MDA_Con-Dox_Rep1

value: Dox-


title: normal.ct-437

description: cell-free DNA


title: normal.ct-434

description: cell-free DNA


title: MDA_Con-Dox_Rep2


title: normal.ct-433

description: cell-free DNA


title: normal.ct-429

description: cell-free DNA


title: normal.ct-431

description: cell-free DNA


title: normal.ct-428

description: cell-free DNA


title: normal.ct-427

description: cell-free DNA


title: normal.ct-430

description: cell-free DNA


title: normal.ct-425

description: cell-free DNA


title: normal.ct-426

description: cell-free DNA


title: normal.ct-424

description: cell-free DNA


title: MDA_FC50uM12hr_Rep1


title: normal.ct-423

description: cell-free DNA


title: normal.ct-422

description: cell-free DNA


title: normal.ct-420

description: cell-free DNA


title: normal.ct-421

description: cell-free DNA


title: normal.ct-418

description: cell-free DNA


title: normal.ct-419

description: cell-free DNA


title: normal.ct-415

description: cell-free DNA


title: normal.ct-414

description: cell-free DNA


title: normal.ct-411

description: cell-free DNA


title: normal.ct-412

description: cell-free DNA


title: normal.ct-407

description: cell-free DNA


title: normal.ct-410

description: cell-free DNA


title: normal.ct-409

description: cell-free DNA


title: normal.ct-432

description: cell-free DNA


title: normal.ct-405

description: cell-free DNA


title: normal.ct-404

description: cell-free DNA


title: normal.ct-406

description: cell-free DNA


title: normal.ct-403

description: cell-free DNA


title: normal.ct-401

description: cell-free DNA


title: normal.ct-400

description: cell-free DNA


title: normal.ct-402

description: cell-free DNA


title: normal.ct-399

description: cell-free DNA


title: normal.ct-397

description: cell-free DNA


title: normal.ct-417

description: cell-free DNA


title: normal.ct-550

description: cell-free DNA


title: normal.ct-416

description: cell-free DNA


title: normal.ct-396

description: cell-free DNA


title: normal.ct-391

description: cell-free DNA


title: normal.ct-392

description: cell-free DNA


title: normal.ct-390

description: cell-free DNA


title: normal.ct-393

description: cell-free DNA


title: normal.ct-388

description: cell-free DNA


title: normal.ct-389

description: cell-free DNA


title: normal.ct-413

description: cell-free DNA


title: normal.ct-387

description: cell-free DNA


title: normal.ct-408

description: cell-free DNA


title: normal.ct-385

description: cell-free DNA


title: normal.ct-386

description: cell-free DNA


title: normal.ct-382

description: cell-free DNA


title: normal.ct-381

description: cell-free DNA


title: normal.ct-379

description: cell-free DNA


title: normal.ct-376

description: cell-free DNA


title: normal.ct-375

description: cell-free DNA


title: normal.ct-380

description: cell-free DNA


title: normal.ct-377

description: cell-free DNA


title: normal.ct-378

description: cell-free DNA


title: normal.ct-398

description: cell-free DNA


title: normal.ct-394

description: cell-free DNA


title: normal.ct-395

description: cell-free DNA


title: normal.ct-373

description: cell-free DNA


title: normal.ct-372

description: cell-free DNA


title: normal.ct-369

description: cell-free DNA


title: normal.ct-370

description: cell-free DNA


title: normal.ct-371

description: cell-free DNA


title: normal.ct-368

description: cell-free DNA


title: normal.ct-383

description: cell-free DNA


title: normal.ct-384

description: cell-free DNA


title: normal.ct-365

description: cell-free DNA


title: normal.ct-363

description: cell-free DNA


title: normal.ct-362

description: cell-free DNA


title: normal.ct-364

description: cell-free DNA


title: normal.ct-366

description: cell-free DNA


title: normal.ct-360

description: cell-free DNA


title: normal.ct-358

description: cell-free DNA


title: normal.ct-357

description: cell-free DNA


title: normal.ct-374

description: cell-free DNA


title: normal.ct-356

description: cell-free DNA


title: normal.ct-355

description: cell-free DNA


title: normal.ct-353

description: cell-free DNA


title: normal.ct-350

description: cell-free DNA


title: normal.ct-354

description: cell-free DNA


title: normal.ct-352

description: cell-free DNA


title: normal.ct-347

description: cell-free DNA


title: normal.ct-349

description: cell-free DNA


title: normal.ct-348

description: cell-free DNA


title: normal.ct-344

description: cell-free DNA


title: normal.ct-343

description: cell-free DNA


title: normal.ct-345

description: cell-free DNA


title: normal.ct-346

description: cell-free DNA


title: normal.ct-367

description: cell-free DNA


title: normal.ct-341

description: cell-free DNA


title: normal.ct-361

description: cell-free DNA


title: normal.ct-359

description: cell-free DNA


title: normal.ct-339

description: cell-free DNA


title: normal.ct-336

description: cell-free DNA


title: normal.ct-340

description: cell-free DNA


title: normal.ct-335

description: cell-free DNA


title: normal.ct-337

description: cell-free DNA


title: normal.ct-338

description: cell-free DNA


title: normal.ct-334

description: cell-free DNA


title: normal.ct-331

description: cell-free DNA


title: normal.ct-333

description: cell-free DNA


title: normal.ct-332

description: cell-free DNA


title: normal.ct-351

description: cell-free DNA


title: normal.ct-330

description: cell-free DNA


title: normal.ct-329

description: cell-free DNA


title: normal.ct-326

description: cell-free DNA


title: normal.ct-328

description: cell-free DNA


title: normal.ct-325

description: cell-free DNA


title: normal.ct-324

description: cell-free DNA


title: normal.ct-321

description: cell-free DNA


title: normal.ct-327

description: cell-free DNA


title: normal.ct-342

description: cell-free DNA


title: normal.ct-323

description: cell-free DNA


title: normal.ct-319

description: cell-free DNA


title: normal.ct-320

description: cell-free DNA


title: normal.ct-322

description: cell-free DNA


title: normal.ct-318

description: cell-free DNA


title: normal.ct-315

description: cell-free DNA


title: normal.ct-314

description: cell-free DNA


title: normal.ct-313

description: cell-free DNA