title: whole blood, subject 11244d58, sample time point T2, library prep Plate_16


title: PN120 Cell 678

status: Public on Dec 06 2022

type: SRA

city: Stanford

first: Christin

middle: S

last: Kuo

state: CA

address: 240 Pasteur Dr.

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Raw sequence reads were demultiplexed using bcl2fastq (v1.8.4, Illumina)
sequences aligned to the mouse reference genome (GRCm38-mm10, UCSC, supplemented with Zsgreen1 sequence) with STAR
number of reads that mapped to each annotated gene (gene counts) determined with HTSEQ (v0.6.1p1, default parameters except Stranded set to false and Mode set to intersection-nonempty)
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: lung

tag: age

value: postnatal 21 days

tag: genotype

value: wild type

tag: group


title: PN120 Cell 676


title: whole blood, subject 0f8becc0, sample time point T4, library prep Plate_14

city: New York

first: Ryan

middle: Conrad

last: Thompson

state: NY

address: 1 Gustave L. Levy Place

department: Charles Bronfman Institute for Personalized Medicine

institute: Icahn School of Medicine at Mount Sinai

description: See https://www.synapse.org/#!Synapse:syn35874390/ for full clinical data, RNA-seq QC data, and other data and metadata.

data_processing:
Quality-filtered raw data was converted into FASTQ files using bcl2fastq (Illumina).
RNA-seq reads were aligned to the GRCh38 primary assembly with Gencode gene annotation v30 by STAR (v2.7.3a) using per-sample 2-pass mapping (--twopassMode Basic) and chimeric alignment options (--chimOutType Junctions SeparateSAMold -chimSegmentMin 15 -chimJunctionOverhangMin 15).
RNA-seq QC metrics were calculated by fastqc (v0.11.8) and Picard Tools (v2.22.3).
Quantification was done at the gene-level with antisense specificity using featureCounts (Subread R package v1.6.3 and strandness option -s 2) with gene-level grouping / primary alignments only / count all overlapped features (-t exon -g gene_id -primary -O).
MultiQC was used to compile and summarize per-sample statistics from STAR, Picard Tools and featureCounts (e.g. gene-level counts, mtRNA counts, globinRNA counts, etc.) into an interactive HTML report.
We excluded samples with DV200 below 80% as well as samples with fewer than 10 million mapped reads counted by featureCounts.
To remove the unwanted signal due to globin gene expression in whole blood, counts for all annotated globin genes (gene symbols CYGB, HBA1, HBA2, HBB, HBD, HBE1, HBG1, HBG2, HBM, HBQ1, HBZ, and MB) were discarded, and the remaining count matrix was transformed to counts per million (CPM).
Genes with CPM ≥1 in ≥36 samples (half the number of subjects with no positive PCR or antibody test for SARS-CoV-2 during the study period) were included in our analyses (21,194).
Gene expression was normalized for composition bias using the trimmed mean of M-values method, implemented by calcNormFactors in the edgeR package and transformed to normalized log2 CPM with observation weights computed by voomWithDreamWeights from the variancePartition package.
Batch effects were residualized from the data by fitting a linear mixed model to the normalized log2 CPM and weights for each gene with random effects for library prep plate (the batch effect to be residualized out) and blood sample ID (the biological signal to be retained) using dream, and then subtracting the best linear unbiased predictors for library prep plate while retaining the differences between blood samples and the residuals.
The technical replicates for each batch control sample were summarized to a single residualized expression value equal to the weighted mean of the technical replicates with a weight equal to the sum of the individual weights of the technical replicates.
Assembly: GRCh38 primary genome assembly with Gencode v30 gene annotation (corresponds to Ensembl version 96)
Supplementary files format and content: rnaseq_raw_count_matrix.csv: comma-delimited raw RNA-seq read counts
Supplementary files format and content: rnaseq_logCPM_matrix.csv: comma-delimited filtered, normalized, batch-corrected log2 counts per million computed by voomWithDreamWeights with values for technical replicates summarized to a single weighted mean value per blood sample
Supplementary files format and content: rnaseq_voom_weight_matrix.csv: comma-delimited voom weight matrix corresponding to normalized batch-corrected log2 CPM values

organism: Homo sapiens

source_name: whole blood

extract_protocol:
Frozen blood samples were thawed and total RNA was extracted from the samples using a modification of the MagMax protocol for Stabilized Blood Tubes RNA Isolation Kit (Thermo Fisher, #4451893).
Samples that yielded sufficient RNA (>50 ng) were barcoded and prepared for pooled whole transcriptome sequencing using the TruSeq Stranded Total RNA Library Prep Gold (Illumina, #20020599), which is designed to remove ribosomal, globin, and mitochondrial RNA. Libraries were amplified with 15 cycles of PCR, pooled, and sequenced on a NovaSeq 6000 (Illumina) using Sprime flow cells with 100 base pair paired-end reads, targeting a mean of 50 million read pairs per sample. For a minority of samples in which the first extraction failed (N=24), RNA was re-extracted from the supernatant saved from the first centrifugation pellet. The extraction protocol was repeated starting with the second wash step after re-pelleting the RNA.

value: whole blood

tag: subject id

tag: blood sample_id

tag: library prep_plate

tag: Sex

value: Male

tag: sampling time_point_label

tag: days since_first_sample

tag: patient classification_at_first_sample

tag: covid-19 positive

value: Positive


title: whole blood, subject 0f8becc0, sample time point T4, library prep Plate_18


title: whole blood, subject 0f8becc0, sample time point T4, library prep Plate_16


title: whole blood, subject 112d83e0, sample time point T1, library prep Plate_14

value: Negative


title: PN120 Cell 675


title: whole blood, subject 0f8becc0, sample time point T4, library prep Plate_12


title: whole blood, subject 0f8becc0, sample time point T4, library prep Plate_10


title: PN120 Cell 674


title: PN120 Cell 673


title: PN120 Cell 672


title: PN120 Cell 683


title: whole blood, subject 0f8becc0, sample time point T4, library prep Plate_8


title: PN120 Cell 671


title: whole blood, subject 11244d58, sample time point T12, library prep Plate_14


title: whole blood, subject 0f8becc0, sample time point T4, library prep Plate_4


title: whole blood, subject 0f8becc0, sample time point T4, library prep Plate_6


title: PN120 Cell 670


title: whole blood, subject 11244d58, sample time point T1, library prep Plate_11


title: whole blood, subject 0f8becc0, sample time point T4, library prep Plate_3


title: PN120 Cell 669


title: whole blood, subject 0f8becc0, sample time point T2, library prep Plate_12


title: PN120 Cell 668


title: PN120 Cell 667


title: PN120 Cell 677


title: whole blood, subject 0f06b495, sample time point T12, library prep Plate_14


title: PN120 Cell 665


title: PN120 Cell 666


title: whole blood, subject 0f06b495, sample time point T8, library prep Plate_14


title: whole blood, subject 0f06b495, sample time point T4, library prep Plate_10


title: PN120 Cell 664


title: whole blood, subject 0f06b495, sample time point T1, library prep Plate_9


title: PN120 Cell 663


title: whole blood, subject 0f06b495, sample time point T2, library prep Plate_17


title: PN120 Cell 662


title: whole blood, subject 0e81d28b, sample time point T1, library prep Plate_5

value: Female


title: PN120 Cell 661


title: whole blood, subject 0e17de76, sample time point T2, library prep Plate_15


title: PN120 Cell 660


title: PN120 Cell 659


title: whole blood, subject 0d273be0, sample time point T13, library prep Plate_17


title: PN120 Cell 658


title: whole blood, subject 0f8becc0, sample time point T1, library prep Plate_5


title: PN120 Cell 657


title: whole blood, subject 0d273be0, sample time point T12, library prep Plate_11


title: whole blood, subject 0d273be0, sample time point T2A, library prep Plate_11


title: whole blood, subject 0c02dbf2, sample time point T4, library prep Plate_8


title: PN120 Cell 656


title: PN120 Cell 654


title: whole blood, subject 0d273be0, sample time point T1, library prep Plate_14


title: whole blood, subject 0c02dbf2, sample time point T1, library prep Plate_3


title: PN120 Cell 655


title: whole blood, subject 0b4c8b59, sample time point T4, library prep Plate_16


title: PN120 Cell 653


title: whole blood, subject 0b4c8b59, sample time point T2, library prep Plate_3


title: PN120 Cell 651


title: PN120 Cell 652


title: PN120 Cell 648


title: whole blood, subject 0b4c8b59, sample time point T1, library prep Plate_7


title: PN120 Cell 649


title: whole blood, subject 0a2680d2, sample time point T12, library prep Plate_9


title: PN120 Cell 650


title: PN120 Cell 647


title: whole blood, subject 0a2680d2, sample time point T8, library prep Plate_4


title: whole blood, subject 0e17de76, sample time point T1, library prep Plate_18


title: whole blood, subject 0a2680d2, sample time point T2, library prep Plate_15


title: whole blood, subject 0a2680d2, sample time point T1, library prep Plate_18


title: PN120 Cell 645


title: PN120 Cell 644


title: whole blood, subject 089e98ea, sample time point T1, library prep Plate_16


title: whole blood, subject 089e98ea, sample time point T1, library prep Plate_14


title: PN120 Cell 642


title: PN120 Cell 643


title: whole blood, subject 089e98ea, sample time point T1, library prep Plate_12


title: PN120 Cell 641


title: PN120 Cell 640


title: whole blood, subject 089e98ea, sample time point T1, library prep Plate_10


title: whole blood, subject 089e98ea, sample time point T1, library prep Plate_4


title: whole blood, subject 0a7ea79e, sample time point T1, library prep Plate_19


title: whole blood, subject 089e98ea, sample time point T1, library prep Plate_2


title: PN120 Cell 637


title: PN120 Cell 639


title: whole blood, subject 06f24a67, sample time point T13, library prep Plate_15


title: PN120 Cell 646


title: PN120 Cell 635


title: PN120 Cell 634


title: PN120 Cell 636


title: whole blood, subject 06f24a67, sample time point T8, library prep Plate_13


title: whole blood, subject 06f24a67, sample time point T12, library prep Plate_18


title: whole blood, subject 06f24a67, sample time point T4, library prep Plate_3


title: PN120 Cell 633


title: PN120 Cell 632


title: whole blood, subject 06cabf6c, sample time point T8, library prep Plate_7


title: whole blood, subject 06f24a67, sample time point T1, library prep Plate_9


title: whole blood, subject 089e98ea, sample time point T1, library prep Plate_8


title: PN120 Cell 629


title: whole blood, subject 06cabf6c, sample time point T4, library prep Plate_7


title: whole blood, subject 089e98ea, sample time point T1, library prep Plate_6


title: PN120 Cell 628


title: PN120 Cell 631


title: whole blood, subject 06cabf6c, sample time point T2, library prep Plate_11


title: whole blood, subject 0631e306, sample time point T1, library prep Plate_6


title: PN120 Cell 627


title: PN120 Cell 626


title: whole blood, subject 0631e306, sample time point T2, library prep Plate_11


title: PN120 Cell 638


title: PN120 Cell 625


title: whole blood, subject 05fd9717, sample time point T1, library prep Plate_13


title: PN120 Cell 624


title: PN120 Cell 623


title: PN120 Cell 622


title: whole blood, subject 056d5843, sample time point T4, library prep Plate_17


title: whole blood, subject 056d5843, sample time point T1, library prep Plate_6


title: whole blood, subject 04a0e89f, sample time point T8, library prep Plate_13


title: PN120 Cell 620


title: whole blood, subject 04a0e89f, sample time point T4, library prep Plate_6


title: PN120 Cell 619


title: PN120 Cell 630


title: whole blood, subject 06cabf6c, sample time point T1, library prep Plate_11


title: whole blood, subject 04a0e89f, sample time point T2B, library prep Plate_18


title: PN120 Cell 618


title: whole blood, subject 04a0e89f, sample time point T2, library prep Plate_6


title: PN120 Cell 617


title: whole blood, subject 044e2a83, sample time point T2, library prep Plate_8


title: whole blood, subject 0424041d, sample time point T4, library prep Plate_6


title: PN120 Cell 616


title: PN120 Cell 614


title: PN120 Cell 615


title: PN120 Cell 612


title: whole blood, subject 041fe111, sample time point T2, library prep Plate_6


title: whole blood, subject 0424041d, sample time point T1, library prep Plate_9


title: PN120 Cell 613


title: PN120 Cell 611


title: whole blood, subject 056d5843, sample time point T8, library prep Plate_17


title: whole blood, subject 05f57419, sample time point T1, library prep Plate_7


title: whole blood, subject 041fe111, sample time point T1, library prep Plate_5


title: PN120 Cell 621


title: whole blood, subject 03ca6bb0, sample time point T4, library prep Plate_10


title: whole blood, subject 03ca6bb0, sample time point T2, library prep Plate_3


title: PN120 Cell 609


title: PN120 Cell 610


title: whole blood, subject 03564ed9, sample time point T0, library prep Plate_13


title: PN120 Cell 608


title: PN120 Cell 605


title: PN120 Cell 607


title: whole blood, subject 030a3354, sample time point T12, library prep Plate_14


title: whole blood, subject 030a3354, sample time point T8, library prep Plate_10


title: PN120 Cell 606


title: whole blood, subject 030a3354, sample time point T2, library prep Plate_11


title: PN120 Cell 604


title: PN120 Cell 602


title: whole blood, subject 02da55fa, sample time point T8, library prep Plate_19


title: PN120 Cell 600


title: PN120 Cell 601


title: whole blood, subject 030a3354, sample time point T1, library prep Plate_15


title: whole blood, subject 044e2a83, sample time point T1, library prep Plate_9


title: whole blood, subject 02da55fa, sample time point T4, library prep Plate_10


title: whole blood, subject 02da55fa, sample time point T2, library prep Plate_8


title: whole blood, subject 03ca6bb0, sample time point T1, library prep Plate_13


title: whole blood, subject 028f3d47, sample time point T1, library prep Plate_10


title: whole blood, subject 0223e0e5, sample time point T1, library prep Plate_14


title: PN120 Cell 595


title: PN120 Cell 599


title: PN120 Cell 597


title: PN120 Cell 596


title: whole blood, subject 0223e0e5, sample time point T4, library prep Plate_18


title: whole blood, subject 0184426f, sample time point T4, library prep Plate_18


title: whole blood, subject 009619bd, sample time point T4, library prep Plate_11


title: PN120 Cell 598


title: whole blood, subject 02da55fa, sample time point T1, library prep Plate_4


title: PN120 Cell 593


title: PN120 Cell 592


title: whole blood, subject 03564ed9, sample time point T4, library prep Plate_13


title: whole blood, subject 009619bd, sample time point T1, library prep Plate_9


title: PN120 Cell 603


title: PN120 Cell 591


title: PN120 Cell 590


title: whole blood, subject 005cd7b9, sample time point T13, library prep Plate_18


title: PN120 Cell 589


title: whole blood, subject 005cd7b9, sample time point T12, library prep Plate_15


title: PN120 Cell 587


title: PN120 Cell 588


title: whole blood, subject 005cd7b9, sample time point T1, library prep Plate_11


title: whole blood, subject 005cd7b9, sample time point T8, library prep Plate_16


title: PN120 Cell 586


title: PN120 Cell 584


title: PN120 Cell 594


title: whole blood, subject 0028c054, sample time point T1, library prep Plate_13


title: whole blood, subject 0028c054, sample time point T1, library prep Plate_19


title: whole blood, subject 0028c054, sample time point T1, library prep Plate_15


title: whole blood, subject 0028c054, sample time point T1, library prep Plate_17


title: whole blood, subject 009619bd, sample time point T2, library prep Plate_13


title: PN120 Cell 585


title: PN120 Cell 580


title: PN120 Cell 581


title: whole blood, subject 0028c054, sample time point T1, library prep Plate_7


title: PN120 Cell 579


title: whole blood, subject 0028c054, sample time point T1, library prep Plate_9


title: PN120 Cell 582


title: PN120 Cell 578


title: whole blood, subject 0028c054, sample time point T1, library prep Plate_2


title: whole blood, subject 0028c054, sample time point T1, library prep Plate_11


title: whole blood, subject 009619bd, sample time point T0, library prep Plate_9


title: PN120 Cell 577


title: whole blood, subject 0028c054, sample time point T1, library prep Plate_5


title: Bio4-72h-sgSOD-1000k

city: Cambridge

first: Maria

middle: I.

last: Zavodszky

state: MA

address: 225 Binney Street

institute: Biogen

description: processed data from all samples

data_processing:
In-house RNAseq anbalysis workflow version 3.0.3
The fastq files were generated from the bcl files using bcl2fastq v2.20 (Illumina).
The RNA-seq analysis pipeline consisted of alignment with STAR version 2.5.2a, followed by quantification of gene expression with RSEM v1.2.26.
Data quality metrics and plots for visualization were generated with Quickomics.
Differential expression analysis was performed with DESeq2 version 1.30.0. The function apeglm was used for LFC shrinkage to reduce noise and preserve large differences[6]. Cutoff values used for significant differential expression were fold change > 2 and adjusted p-value < 0.05.
Assembly: Human.GRCh38.v34.l1_5.ERCC
Supplementary files format and content: tab-delimited text file with raw read counts for each sample
Supplementary files format and content: tab-delimited text file with normalized TPM values for each sample

molecule: polyA RNA

extract_protocol:
The cells were harvested in QIAzol (Qiagen 79306) for RNA extraction using miRNeasy mini kit (Qiagen 217004). 250ng of RNA input with 6 minutes at 94C fragmentation and 12 library amplification pcr cycles was used for library preparation.
RNA libraries for RNA-seq were prepared using Kapa mRNA hyperprep library kit following manufacturer's protocol

tag: time

tag: cell line

tag: cell type

value: epithelial

tag: treatment


title: Bio3-72h-sgSOD-1000k

description: processed data from all samples


title: PN120 Cell 576

tag: strain


title: Bio2-72h-sgSOD-1000k

description: processed data from all samples


title: PN120 Cell 574

tag: tissue


title: PN120 Cell 573

tag: age


title: Bio1-72h-sgSOD-1000k

description: processed data from all samples

tag: genotype


title: PN120 Cell 583

tag: group


title: Bio4-72h-sgLacZ-1000k-2

description: processed data from all samples


title: PN120 Cell 572


title: Bio4-72h-sgLacZ-1000k-1

description: processed data from all samples


title: Bio3-72h-sgLacZ-1000k-2

description: processed data from all samples


title: PN120 Cell 570


title: Bio3-72h-sgLacZ-1000k-1

description: processed data from all samples


title: PN120 Cell 571


title: Bio2-72h-sgLacZ-1000k-2

description: processed data from all samples


title: PN120 Cell 569


title: PN120 Cell 568


title: PN120 Cell 567


title: PN120 Cell 566


title: Bio4-72h-untransduced-2

description: processed data from all samples

value: untransduced


title: PN120 Cell 565


title: Bio1-72h-sgLacZ-1000k-1

description: processed data from all samples


title: Bio1-72h-sgLacZ-1000k-2

description: processed data from all samples


title: Bio2-72h-sgLacZ-1000k-1

description: processed data from all samples


title: PN120 Cell 564


title: PN120 Cell 563


title: PN120 Cell 562


title: PN120 Cell 561


title: PN120 Cell 560


title: PN120 Cell 575


title: Bio2-72h-untransduced-2

description: processed data from all samples


title: Bio3-72h-untransduced-2

description: processed data from all samples


title: Bio1-72h-untransduced-2

description: processed data from all samples


title: Bio4-72h-untransduced-1

description: processed data from all samples


title: PN120 Cell 559


title: Bio2-72h-untransduced-1

description: processed data from all samples


title: PN120 Cell 558


title: Bio1-72h-untransduced-1

description: processed data from all samples


title: PN120 Cell 556


title: PN120 Cell 557


title: Bio4-48h-sgSOD-1000k

description: processed data from all samples


title: Bio3-48h-sgSOD-1000k

description: processed data from all samples


title: PN120 Cell 554


title: PN120 Cell 555


title: Bio1-48h-sgSOD-1000k

description: processed data from all samples


title: Bio4-48h-sgLacZ-1000k-2

description: processed data from all samples


title: Bio2-48h-sgSOD-1000k

description: processed data from all samples


title: PN120 Cell 552


title: Bio4-48h-sgLacZ-1000k-1

description: processed data from all samples


title: PN120 Cell 551


title: PN120 Cell 550


title: Bio3-48h-sgLacZ-1000k-1

description: processed data from all samples


title: Bio3-48h-sgLacZ-1000k-2

description: processed data from all samples


title: Bio3-72h-untransduced-1

description: processed data from all samples


title: PN120 Cell 549


title: PN120 Cell 548


title: Bio2-48h-sgLacZ-1000k-1

description: processed data from all samples


title: Bio2-48h-sgLacZ-1000k-2

description: processed data from all samples


title: PN120 Cell 547


title: PN120 Cell 545


title: Bio1-48h-sgLacZ-1000k-2

description: processed data from all samples


title: Bio4-48h-untransduced-1

description: processed data from all samples


title: Bio4-48h-untransduced-2

description: processed data from all samples


title: PN120 Cell 546


title: Bio1-48h-sgLacZ-1000k-1

description: processed data from all samples


title: PN120 Cell 544


title: PN120 Cell 543


title: Bio3-48h-untransduced-2

description: processed data from all samples


title: PN120 Cell 553


title: Bio3-48h-untransduced-1

description: processed data from all samples


title: Bio2-48h-untransduced-2

description: processed data from all samples


title: PN120 Cell 542


title: Bio2-48h-untransduced-1

description: processed data from all samples


title: PN120 Cell 539


title: PN120 Cell 538


title: Bio1-48h-untransduced-2

description: processed data from all samples


title: PN120 Cell 540


title: Bio1-48h-untransduced-1

description: processed data from all samples


title: PN120 Cell 537


title: PN120 Cell 536


title: Patient260

city: San Francisco

first: Charles

last: Langelier

address: HSE 401, 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

description: Definite

data_processing:
Pseudoalignment with kallisto version 0.46.1 (with bias correction) to all transcripts associated with human protein-coding and long non-coding RNA genes in ENSEMBL v. 99.
Gene-level counts generated from transcript-level abundance estimates using the R package tximport with the scaledTPM method.
Assembly: ENSEMBL v. 99
Supplementary files format and content: Gene counts (rows) for each sample (columns)
Supplementary files format and content: Annotation of adjudicated LRTI status for each sample.

source_name: Tracheal aspirate

extract_protocol:
Tracheal aspirate (TA) was collected within 24 hours of intubation, mixed 1:1 with DNA/RNA Shield (Zymo) and frozen at -80°C. RNA was extracted from 300µl of patient TA using bead-based lysis and the Allprep DNA/RNA kit (Qiagen), which included a DNase treatment step.
RNA was reverse transcribed to generate cDNA and sequencing library preparation was performed using the NEBNext Ultra II Library Prep Kit.

value: Tracheal aspirate


title: Patient258

description: Suspected


title: Patient259

description: Definite


title: PN120 Cell 534


title: Patient257

description: Definite


title: Patient255

description: Definite


title: PN120 Cell 532


title: PN120 Cell 535


title: PN120 Cell 541


title: Patient254

description: Indeterminate


title: PN120 Cell 533


title: PN120 Cell 529


title: Patient256

description: Definite


title: PN120 Cell 531


title: PN120 Cell 528


title: Patient252

description: Definite


title: PN120 Cell 527


title: Patient261

description: Definite


title: Patient251

description: Definite


title: Patient250

description: No Evidence


title: Patient249

description: Definite


title: PN120 Cell 525


title: PN120 Cell 524


title: Patient247

description: No Evidence


title: PN120 Cell 530


title: PN120 Cell 523


title: Patient246

description: Definite


title: PN120 Cell 522


title: Patient245

description: Definite


title: PN120 Cell 519


title: PN120 Cell 520


title: Patient253

description: Definite


title: Patient244

description: Definite


title: Patient243

description: No Evidence


title: Patient242

description: Definite


title: PN120 Cell 517


title: PN120 Cell 518


title: Patient240

description: Definite


title: PN120 Cell 526


title: Patient241

description: Definite


title: PN120 Cell 516


title: Patient238

description: Indeterminate


title: PN120 Cell 513


title: Patient237

description: No Evidence


title: PN120 Cell 514


title: Patient248

description: Suspected


title: PN120 Cell 512


title: PN120 Cell 511


title: Patient236

description: No Evidence


title: PN120 Cell 510


title: Patient234

description: No Evidence


title: Patient235

description: Definite


title: Patient233

description: Definite


title: PN120 Cell 509


title: PN120 Cell 521


title: PN120 Cell 508


title: Patient232

description: Indeterminate


title: Patient231

description: Definite


title: Patient230

description: Definite


title: PN120 Cell 506


title: PN120 Cell 505


title: Patient229

description: Suspected


title: PN120 Cell 507


title: Patient228

description: Suspected


title: Patient239

description: Suspected


title: PN120 Cell 504


title: PN120 Cell 515


title: Patient227

description: Definite


title: Patient225

description: Definite


title: Patient223

description: Definite


title: Patient224

description: Suspected


title: Patient222

description: No Evidence


title: PN120 Cell 502


title: PN120 Cell 501


title: PN120 Cell 499


title: PN120 Cell 498


title: PN120 Cell 500


title: PN120 Cell 497


title: Patient220

description: Definite


title: Patient221

description: Suspected


title: PN120 Cell 494


title: Patient218

description: Definite


title: Patient219

description: Suspected


title: PN120 Cell 496


title: PN120 Cell 493


title: Patient217

description: Indeterminate


title: PN120 Cell 492


title: Patient216

description: Definite


title: Patient226

description: No Evidence


title: Patient215

description: Suspected


title: Patient214

description: Definite


title: PN120 Cell 491


title: PN120 Cell 503


title: PN120 Cell 490


title: Patient213

description: Suspected


title: PN120 Cell 489


title: PN120 Cell 488


title: Patient212

description: Indeterminate


title: Patient210

description: Definite


title: Patient211

description: Suspected


title: Patient209

description: Definite


title: PN120 Cell 495


title: PN120 Cell 485


title: PN120 Cell 484


title: PN120 Cell 486


title: Patient208

description: No Evidence


title: PN120 Cell 482


title: PN120 Cell 483


title: PGF2a3

city: Shanghai

first: Yan

last: Zhao

address: 320 Yueyang Road

country: China

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

description: 500nM Prostaglandin F2α (Cayman, 16010) for 6 hours

data_processing:
We use internal software SOAPnuke (v1.5.2) to filter reads
We use HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts)(v2.0.4) to do the mapping step.
We mapped clean reads to reference using Bowtie2 (v2.2.5), and then calculate gene expression level with RSEM (v1.2.12).
Genome_build: NCBI GRCh38
Supplementary_files_format_and_content: tab-delimited .xls files include FPKM values for each sample

source_name: human retinal microvascular endothelial cells

growth_protocol: Human retinal microvascular endothelial cells cultured at 37°C with 5% CO2 in a humid atmosphere using ECM (Sciencell, SC-1001).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen，15596018).
RNA libraries were prepared for sequencing using standard BGI protocols

tag: source

value: Cell Biologics, H-6065

tag: culture medium

value: ECM (Sciencell, SC-1001)

value: 500nM Prostaglandin F2alpha (Cayman, 16010) for 6 hours


title: Patient207

description: Suspected


title: PN120 Cell 481


title: PN120 Cell 480


title: Patient206

description: Definite


title: PN120 Cell 479


title: DMSO3

description: 0.1%DMSO for 6 hours

value: 0.1percent DMSO for 6 hours


title: PN120 Cell 476


title: Patient205

description: Definite


title: DMSO2

description: 0.1%DMSO for 6 hours


title: PN120 Cell 478


title: Patient204

description: Definite


title: PN120 Cell 474


title: PN120 Cell 475


title: DMSO1

description: 0.1%DMSO for 6 hours


title: PN120 Cell 487


title: PN120 Cell 473


title: PN120 Cell 472


title: PN120 Cell 471


title: PN120 Cell 470


title: Patient201

description: Definite


title: Patient202

description: No Evidence


title: PGF2a2


title: PN120 Cell 468


title: PGF2a1


title: PN120 Cell 477


title: PN120 Cell 466


title: PN120 Cell 467


title: PN120 Cell 465


title: Patient199

description: Definite


title: Blood mononuclear cells, OGD, 18hrs, rep3

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: 18 h under the OGD condition

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: The cultures containing a high-glucose medium without serum were placed in a mixture of 95% N2 and 5% CO2  for 18 h.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

treatment_protocol: The cultures containing a low-glucose medium without serum were placed in a hypoxia chamber, which was first flushed with 100% N2  for 1 h and then closed for 18 h.

value: male

tag: ethnicity

value: Asian

value: blood

value: peripheral blood mononuclear cells (PBMCs)

tag: stress

value: oxygen-glucose deprivation

tag: sample type

value: Exosome


title: Blood mononuclear cells, OGD, 18hrs, rep2

tag: Sex


title: PN120 Cell 464

value: lung

value: postnatal 21 days

value: wild type


title: Patient198

description: Suspected


title: PN120 Cell 462


title: PN120 Cell 461


title: PN120 Cell 463


title: Patient203

description: Suspected


title: Blood mononuclear cells, normoxia, 18hrs, rep3

source_name: 18 h under the normoxic condition

value: normoxia


title: Blood mononuclear cells, OGD, 18hrs, rep1


title: PN120 Cell 460


title: Patient197

description: Indeterminate


title: PN120 Cell 469


title: PN120 Cell 459


title: Patient196

description: No Evidence


title: Blood mononuclear cells, normoxia, 18hrs, rep1


title: Blood mononuclear cells, normoxia, 18hrs, rep2


title: ABA-100(9.7℃)rep3

city: wenzhou

first: Xing

last: Liu

address: xueshan street

institute: Zhejiang Institute of Subtropical Crops

data_processing:
The raw paired-end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean data from K. obovata samples was used to do denovo assembly with Trinity (http://trinityrnaseq.sourceforge.net/)
All the assembled transcripts were searched against the (National Center for Biotechnology Information) NCBI protein non-redundant (NR), Clusters of Orthologous Genes (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases using BLASTX to identify the proteins that had the highest sequence similarity with the given transcripts to retrieve their function annotations and a typical cut-off E-values less than 1.0×10−5 was set. Blast2GO software
Assembly: genome assembly
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Kandelia obovata

source_name: leaf

extract_protocol:
Total RNA from each sample was extracted using TRIzol® Reagent according to the manufacturer’s instructions (Invitrogen, Carlsbard, CA, USA) and genomic DNA was removed using DNase I (TaKara, Shiga, Japan)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: leaf

value: tissue

value: experiment type

value: ABA, 9.7℃


title: PN120 Cell 457


title: ABA-100(9.7℃)rep2


title: Patient200

description: Suspected

value: Tracheal aspirate


title: Patient195

description: Definite


title: ABA-100(9.7℃)rep1


title: PN120 Cell 455


title: Patient193

description: Suspected


title: ABA-100(-5.3℃)rep3


title: PN120 Cell 454


title: PN120 Cell 452


title: PN120 Cell 451


title: PN120 Cell 453


title: ABA-100(-5.3℃)rep2


title: ABA-100(-5.3℃)rep1


title: Patient191

description: Suspected


title: Patient192

description: No Evidence


title: PN90 Cell 448


title: PN120 Cell 449


title: ABA-100(-4.1℃)rep3


title: PN120 Cell 458


title: PN90 Cell 447


title: PN120 Cell 450


title: ABA-100(-4.1℃)rep2


title: PN90 Cell 446


title: PN90 Cell 445


title: PN90 Cell 444


title: Patient190

description: Suspected


title: Patient189

description: Definite


title: PN90 Cell 442


title: Patient194

description: Suspected


title: PN90 Cell 443


title: PN120 Cell 456


title: Patient188

description: No Evidence


title: ABA-100(10.2℃)rep3


title: PN90 Cell 441


title: ABA-100(10.2℃)rep2


title: PN90 Cell 438


title: PN90 Cell 440


title: ABA-100(10.2℃)rep1


title: Patient186

description: No Evidence


title: PN90 Cell 437


title: Patient185

description: Definite


title: Patient187

description: Indeterminate


title: PN90 Cell 436


title: CK(9.7℃) rep3


title: PN90 Cell 435


title: Patient184

description: Indeterminate


title: ABA-100(-4.1℃)rep1


title: PN90 Cell 434


title: CK(9.7℃) rep2


title: Patient183

description: Suspected


title: PN90 Cell 432


title: Patient182

description: No Evidence


title: CK(9.7℃) rep1


title: PN90 Cell 430


title: PN90 Cell 433


title: PN90 Cell 431


title: PN90 Cell 428


title: CK(-5.3℃) rep3


title: PN90 Cell 439


title: PN90 Cell 429


title: PN90 Cell 427


title: Patient180

description: Definite


title: PN90 Cell 426


title: CK(-5.3℃) rep2


title: CK(-5.3℃) rep1


title: Patient179

description: Indeterminate


title: PN90 Cell 425


title: CK(-4.1℃) rep3


title: Patient178

description: No Evidence


title: PN90 Cell 423


title: PN90 Cell 422


title: CK(-4.1℃) rep1


title: PN90 Cell 420


title: Patient176

description: Indeterminate


title: Patient175

description: No Evidence


title: Patient177

description: No Evidence


title: Patient181

description: Suspected


title: PN90 Cell 418


title: CK(10.2℃) rep3


title: PN90 Cell 421


title: CK(10.2℃) rep2


title: Patient174

description: Suspected


title: CK(10.2℃) rep1


title: Patient173

description: No Evidence


title: PN90 Cell 414


title: PN90 Cell 413


title: PN90 Cell 415


title: PN90 Cell 416


title: PN90 Cell 412


title: PN90 Cell 424


title: PN90 Cell 411


title: Patient172

description: No Evidence


title: IME4_SPO_T4_EXP1_R3

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters "--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC -A AGATCGGAAGAGC".
BWA (version 0.5.9-r16) (Li & Durbin, 2009) using default parameters was used to perform the read mapping independently to  the S. cerevisiae (SK1)
Genomic alignments were filtered to only include those that were primary, properly paired, uniquely mapped, not soft-clipped, maximum insert size of 2kb and fewer than 3 mismatches using BamTools (version 2.4.0; (Barnett et al, 2011)).
Read counts relative to protein coding genes were obtained using the featureCounts tool from the Subread package (version 1.5.1) (Liao et al, 2014). The parameters used were “-O --minOverlap 1 --nonSplitOnly --primary -s 2 -p -B -P -d 0 -D 1000 -C --donotsort”.
Genome_build: Genome_build: SK1 assembly from Keeney lab (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts generated by featureCounts where gene names are rows and columns represent all samples generated in the study.

organism: Saccharomyces cerevisiae

source_name: yeast strains in small batch culture

growth_protocol: Cells were grown in yeast extract-peptone-dextrose (YPD) medium in conical flasks at 30 °C, shaking at 300 RPM in incubators, then switched to pre-sporulation medium for 17 h and further to sporulation medium..

extract_protocol:
Cell pellets were washed once with sterile water and snap-frozen in liquid nitrogen. Total RNA was extracted using the hot acid phenol protocol (acid phenol:chloroform:isoamyl alcohol 125:24:1) and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in DEPC-treated sterile water.
Total RNA from yeast was incubated with rDNase (Machery-Nagel rDNase Set) and column purified (Machery-Nagel NucleoSpin RNA) prior to sequencing library preparation. Total RNA was used to generate strand-specific libraries for polyadenylated RNA sequencing using the TruSeq Stranded mRNA Library Prep Kit (Illumina RS-122-2101) according to the manufacturer’s instructions. Library quality control was performed using the Agilent 2200 TapeStation with D1000 screentape (Agilent Technologies). Each library was sequenced on the HiSeq 2500 platform using V4 chemistry (Illumina) and typically generated ~55 million 101 bp strand-specific paired-end reads per sample.

treatment_protocol: Cells were collected immediately after shifting to sporulation medium (0h) or after 4 hours (4h).

tag: strain background

value: FW725  (MATa/alpha, ho::LYS2, ura3, leu2::hisG, his3::hisG, trp1::hisG, ime4::HIS3)

value: 4h SPO


title: PN90 Cell 409


title: CK(-4.1℃) rep2


title: IME4_SPO_T4_EXP1_R2


title: Patient171

description: No Evidence


title: PN90 Cell 419


title: PN90 Cell 408


title: Patient170

description: Indeterminate


title: PN90 Cell 407


title: PN90 Cell 417


title: PN90 Cell 406


title: IME4_SPO_T4_EXP1_R1


title: PN90 Cell 405


title: Patient169

description: Indeterminate


title: IME4_SPO_T0_EXP1_R2

value: 0h SPO


title: PN90 Cell 404


title: IME4_SPO_T0_EXP1_R3


title: Patient168

description: Suspected


title: PN90 Cell 410


title: Patient167

description: Indeterminate


title: PN90 Cell 400


title: IME4_SPO_T0_EXP1_R1


title: PN90 Cell 399


title: PN90 Cell 401


title: PHO92_SPO_T4_EXP1_R3

value: FW3528 (MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, pho92::HYG)


title: PN90 Cell 398


title: PHO92_SPO_T4_EXP1_R2


title: PN90 Cell 403


title: PN90 Cell 402


title: Patient165

description: Suspected


title: PN90 Cell 396


title: Patient164

description: Definite


title: PN90 Cell 395


title: PHO92_SPO_T4_EXP1_R1


title: Patient166

description: No Evidence


title: PN90 Cell 397


title: PN90 Cell 394


title: Patient163

description: No Evidence


title: PN90 Cell 393


title: PHO92_SPO_T0_EXP1_R3


title: PN90 Cell 392


title: PN90 Cell 391


title: PN90 Cell 390


title: PHO92_SPO_T0_EXP1_R2


title: PHO92_SPO_T0_EXP1_R1


title: Patient161

description: Indeterminate


title: PN90 Cell 389


title: PN90 Cell 388


title: Patient159

description: Indeterminate


title: WT_SPO_T4_EXP1_R3

value: FW1511 (MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG)


title: PN90 Cell 387


title: Patient160

description: Suspected


title: PN90 Cell 386


title: WT_SPO_T4_EXP1_R1


title: WT_SPO_T4_EXP1_R2


title: PN90 Cell 383


title: Patient157

description: Definite


title: Patient158

description: Definite


title: PN90 Cell 381


title: PN90 Cell 382


title: PN90 Cell 380


title: WT_SPO_T0_EXP1_R2


title: WT_SPO_T0_EXP1_R3


title: PN90 Cell 379


title: Patient162

description: Suspected


title: Patient156

description: Definite


title: PN90 Cell 378


title: Patient155

description: Indeterminate


title: WT_SPO_T0_EXP1_R1


title: NDT80_SPO_T4_EXP2_R3

value: FW4911 (MATa/alpha, ho::LYS2, lys2, leu2::hisG, ura3, his3::hisG, trp1::hisG, ndt80∆::LEU2)


title: PN90 Cell 377


title: Patient154

description: Indeterminate


title: PN90 Cell 376


title: PN90 Cell 375


title: PN90 Cell 374


title: PN90 Cell 385


title: PN90 Cell 384


title: NDT80_SPO_T4_EXP2_R2


title: PN90 Cell 373


title: Patient153

description: Suspected


title: PN90 Cell 371


title: PN90 Cell 372


title: NDT80_SPO_T4_EXP2_R1


title: PN90 Cell 370


title: PN90 Cell 369


title: NDT80_SPO_T0_EXP2_R3


title: Patient150

description: Suspected


title: PN90 Cell 367


title: PN90 Cell 365


title: NDT80_SPO_T0_EXP2_R2


title: Patient151

description: Definite


title: Patient149

description: Suspected


title: PN90 Cell 366


title: NDT80_SPO_T0_EXP2_R1


title: Patient148

description: Definite


title: PN90 Cell 364


title: PN90 Cell 362


title: IME1_SPO_T4_EXP2_R3

value: FW81 (MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, ime1::HISMx6)


title: PN90 Cell 363


title: PN90 Cell 361


title: IME1_SPO_T4_EXP2_R2


title: PN90 Cell 360


title: Patient152

description: No Evidence


title: Patient147

description: Suspected


title: IME1_SPO_T4_EXP2_R1


title: Patient146

description: Suspected


title: PN90 Cell 358


title: PN90 Cell 359


title: Patient145

description: Suspected


title: IME1_SPO_T0_EXP2_R3


title: PN90 Cell 368


title: PN90 Cell 356


title: Patient144

description: Indeterminate


title: IME1_SPO_T0_EXP2_R2


title: PN90 Cell 354


title: PN90 Cell 353


title: IME1_SPO_T0_EXP2_R1


title: PN90 Cell 351


title: WT_SPO_T4_EXP2_R3


title: WT_SPO_T4_EXP2_R2


title: PN90 Cell 350


title: Patient143

description: Definite


title: Patient141

description: No Evidence


title: PN90 Cell 355


title: PN90 Cell 348


title: WT_SPO_T4_EXP2_R1


title: PN90 Cell 347


title: WT_SPO_T0_EXP2_R3


title: PN90 Cell 346


title: PN90 Cell 345


title: Patient140

description: Definite


title: Patient139

description: Definite


title: PN90 Cell 343


title: WT_SPO_T0_EXP2_R2


title: PN90 Cell 357


title: Patient138

description: Indeterminate


title: PN90 Cell 342


title: PN90 Cell 341


title: Patient137

description: Definite


title: PN90 Cell 340


title: PN90 Cell 352


title: Patient142

description: Suspected


title: WT_SPO_T0_EXP2_R1


title: WT_4TUiCLIP_SPO_R1

description:
4TU-iCLIP
NO BED FILE for this sample

data_processing:
Reads were demultiplexed using iCount demultiplex, and subsequently trimmed for adapter sequences and also for PHRED score > 30 using Trim Galore! (Krueger, 2017).
Due to the high ncRNA content in miCLIP libraries a sequential mapping strategy was used for all libraries, which is available as a Snakemake (Koster and Rahmann, 2012) pipeline from www.github.com/ulelab/ncawareclip. Mapping was first to representative Saccharomyces cerevisiae snRNA and rRNA sequences downloaded from NCBI (Pruitt et al., 2005), followed by mature tRNA sequences (3′ CCA and 5’ G added) and the SacCer3 mitochondrial chromosome before being mapped to the SK1 MvO genome (available from http://cbio.mskcc.org/public/SK1_MvO/).
PCR duplicates were removed using the unique molecular identifiers (UMIs). The start positions of uniquely mapping reads were taken as crosslinks.
Peaks were called on iCLIP and miCLIP data with Clippy v1.2.0 (https://github.com/ulelab/clippy/releases/tag/v1.2.0) specifically with settings -n 20 -up 50 -down 100 -x 2.75 -hc 0.8 -mg 10 -mb 10 --no_exon_info. Reproducible, high quality replicate samples, as determined by principal component analysis (PCA), replicate correlations, library size and regional crosslink locations, were combined for peak calling.
Note: UMIs are present in raw fastq headers following the "rbc:" delimiter.
Genome_build: SK1 MvO genome (available from http://cbio.mskcc.org/public/SK1_MvO/).
Supplementary_files_format_and_content: Peak bed files represent peaks called on merged replicate data.
Supplementary_files_format_and_content: Normalised strand-specific bigWig files represent crosslinks across the genome / total genomic crosslinks * 10^6.

extract_protocol:
For miCLIP, Total RNA was extracted using the hot acid phenol protocol (acid phenol:chloroform:isoamyl alcohol 125:24:1) and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in DEPC-treated sterile water. For polyA selection was done with oligodT dynabeads and up to 10 µg polyA RNA was fragmented to around 150-200 n . 4 ug mRNA was incubated with 5 µg anti-m6A for 2h at 4 °C with rotation. polyA RNA was cross-linked twice to the antibody with 2x0.15 J/cm2 UV light (254 nm) in a Stratalinker and then incubated with 30 µl protein G beads for 1.5 h at 4 °C with rotation. For iCLIP and 4-TU-iCLIP, Crosslinked cells were collected and resuspended in lysis buffer and pebbles prepared in liquid nitrogen. Cells were subjected to cryogenic lysis by freezer mill grinding under liquid nitrogen. The resultant yeast “grindate” powder was resuspended in lysis buffer, clarified  and subjected to DNase and RNase treatment before setting up the lysates for immunoprecipitation with V5 antibody.  The immunoprecipitation was carried out overnight at 4 degrees.
Immunoprecipitation was followed by 3'end RNA dephosphorylation and adaptor ligation followed by adapter removal. 10% of the sample was labelled with [gamma-P32]ATP  in order to visualize mRNA-antibody complexes by SDS-PAGE and western blotting of both labelled and non-labelled fractions. RNA was extracted from the membrane and subjected to RT reaction and purificatio followed by circularization, PCR and purification of cDNA library before sequencing. For mock miCLIP, the entire protocol was also performed with 1 μg input mRNA omitting IP, P32 labelling, SDS-PAGE/western blotting steps.

treatment_protocol: For miCLIP, Cells were collected 4 hours after shifting to sporulation medium. For iCLIP, cells were crosslinked at UV 254 nm after 4 hours in sporulation medium whereas for 4-TU-iCLIP, cells were grown for 4 hours in sporulation medium in the presence of 4-TU and then cross linked at UV 365 nm.

value: FW4256(MATa/alpha his3delta::CG-HIS3::pARO10-FUR4-R294A ura3- CAN1)

tag: meiosis conditions

tag: antibody


title: Patient135

description: Definite


title: Patient134

description: Suspected


title: Patient136

description: Definite


title: PN90 Cell 337

value: lung


title: PN90 Cell 349

value: postnatal 21 days


title: PN90 Cell 336

value: wild type


title: PN90 Cell 339


title: GIS2_iCLIP_IME4del_SPO_R3

description:
iCLIP
Gis2_all.bed

value: FW3380(MATa/alpha, ho::LYS2, ura3, leu2::hisG, his3::hisG, trp1::hisG, ime4::HIS3, GIS2-3V5::KAN-MX)


title: PN90 Cell 338


title: Patient133

description: Suspected


title: PN90 Cell 332


title: PN90 Cell 333


title: PN90 Cell 331


title: Patient132

description: Definite


title: PN90 Cell 334


title: PN90 Cell 330


title: GIS2_iCLIP_WT_SPO_R3

description:
iCLIP
Gis2_all.bed

value: FW3312(MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, GIS2-3V5::KAN-MX)


title: GIS2_iCLIP_WT_SPO_R4

description:
iCLIP
Gis2_all.bed


title: Patient131

description: Suspected


title: PN90 Cell 328


title: PN90 Cell 329


title: GIS2_iCLIP_IME4del_SPO_R1

description:
iCLIP
Gis2_all.bed


title: Patient130

description: Definite


title: PN90 Cell 326


title: GIS2_iCLIP_WT_SPO_R2

description:
iCLIP
Gis2_all.bed


title: PN90 Cell 344


title: GIS2_iCLIP_WT_SPO_R1

description:
iCLIP
Gis2_all.bed


title: PN90 Cell 327


title: GIS2_iCLIP_IME4del_SPO_R2

description:
iCLIP
Gis2_all.bed


title: PN90 Cell 335


title: Patient129

description: Definite


title: PN90 Cell 325


title: PN90 Cell 324


title: PHO92_4TUiCLIP_IME4del_SPO_R3

description:
4TU-iCLIP
Pho92_all.bed

value: FW4505(MATa/alpha his3delta::CG-HIS3::pARO10-FUR4-R294A ura3- CAN1, Pho92-3V5::KAN-MX, ime4::NAT)


title: Patient128

description: Definite


title: PN90 Cell 323


title: PN90 Cell 322


title: PN90 Cell 321


title: PHO92_4TUiCLIP_IME4del_SPO_R2

description:
4TU-iCLIP
Pho92_all.bed


title: Patient127

description: Suspected


title: PHO92_4TUiCLIP_IME4del_SPO_R1

description:
4TU-iCLIP
Pho92_all.bed


title: Patient126

description: Suspected


title: PN90 Cell 319


title: Patient125

description: No Evidence


title: PHO92_4TUiCLIP_WT_SPO_R3

description:
4TU-iCLIP
Pho92_all.bed

value: FW4472(MATa/alpha his3delta::CG-HIS3::pARO10-FUR4-R294A ura3- CAN1, Pho92-3V5::KAN-MX)


title: Patient124

description: Definite


title: PN90 Cell 315


title: PN90 Cell 314


title: PN90 Cell 316


title: PN90 Cell 313


title: PHO92_4TUiCLIP_WT_SPO_R2

description:
4TU-iCLIP
Pho92_all.bed


title: PN90 Cell 312


title: Patient123

description: Suspected


title: Patient122

description: No Evidence


title: PN90 Cell 311


title: miCLIP_IME4del_SPO_R3

description:
miCLIP
m6A_allIme4Dependent.bed


title: Patient121

description: Definite


title: PN90 Cell 309


title: PN90 Cell 320


title: PN90 Cell 318


title: miCLIP_IME4del_SPO_R2

description:
miCLIP
m6A_allIme4Dependent.bed


title: miCLIP_IME4del_SPO_R1

description:
miCLIP
m6A_allIme4Dependent.bed


title: PN90 Cell 307


title: PN90 Cell 308


title: PN90 Cell 317


title: Patient120

description: Suspected


title: PN90 Cell 306


title: Patient119

description: No Evidence


title: miCLIP_WT_SPO_R4

description:
miCLIP
m6A_allIme4Dependent.bed


title: PN90 Cell 304


title: PHO92_4TUiCLIP_WT_SPO_R1

description:
4TU-iCLIP
Pho92_all.bed


title: PN90 Cell 305


title: miCLIP_WT_SPO_R2

description:
miCLIP
m6A_allIme4Dependent.bed


title: miCLIP_WT_SPO_R3

description:
miCLIP
m6A_allIme4Dependent.bed


title: PN90 Cell 303


title: PN90 Cell 302


title: PN90 Cell 300


title: miCLIP_WT_SPO_R1

description:
miCLIP
m6A_allIme4Dependent.bed


title: PN90 Cell 299


title: PN90 Cell 301


title: Patient116

description: No Evidence


title: PN90 Cell 310


title: PN90 Cell 298


title: Patient115

description: Definite


title: PN90 Cell 296


title: mock_miCLIP_IME4del_SPO_R3

description:
mock miCLIP
m6A_allIme4Dependent.bed


title: mock_miCLIP_IME4del_SPO_R2

description:
mock miCLIP
m6A_allIme4Dependent.bed


title: Patient118

description: Indeterminate


title: PN90 Cell 293


title: PN90 Cell 294


title: Patient113

description: Indeterminate


title: PN90 Cell 295


title: Patient114

description: Suspected


title: PN90 Cell 292


title: mock_miCLIP_WT_SPO_R2

description:
mock miCLIP
m6A_allIme4Dependent.bed


title: PN90 Cell 290


title: PN90 Cell 289


title: mock_miCLIP_IME4del_SPO_R1

description:
mock miCLIP
m6A_allIme4Dependent.bed


title: Patient117

description: Definite


title: mock_miCLIP_WT_SPO_R3

description:
mock miCLIP
m6A_allIme4Dependent.bed


title: Patient111

description: Definite


title: PN90 Cell 288


title: mock_miCLIP_WT_SPO_R1

description:
mock miCLIP
m6A_allIme4Dependent.bed


title: Patient110

description: Indeterminate


title: PN90 Cell 286


title: PN90 Cell 291


title: Patient109

description: Definite


title: PN90 Cell 287


title: PN90 Cell 297


title: PN90 Cell 285


title: PN90 Cell 284


title: Patient108

description: No Evidence


title: Nr5a2_mit_2

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

data_processing:
RNA-seq alignments were done using STAR and gene expression estimates were obtained using RSEM. Differentially expressed genes were assessed with DESeq2
ChIP-seq alignments weredone with Bowtie2 ; only those with a single discovered alignment were kept. Peaks were called against relevant inputs for all mitotic samples using MACS2 and filtered to have (1) MACS2 FDR < 0.05 in all three replicates, (2) mean enrichment over the input > 2, (3) FDR of the enrichment over the input < 0.05
Assembly: mm10
Supplementary files format and content: .txt file with TPM for all considered genes across samples
Supplementary files format and content: .txt file with Nr5a2 peak coordinates with mitotic status indicated

source_name: ES cells

extract_protocol:
Trizol extraction and DNaseI digestion
RNA-seq libraries, ribo-depleted, stranded and paired-end were prepared by Novogene Co Ltd; ChIP-seq libraries

value: ES cells

tag: cell line

value: wild-type cells

value: ctl


title: PN90 Cell 283


title: PN90 Cell 282


title: Patient112

description: Indeterminate

value: Tracheal aspirate


title: Nr5a2_mit_1

tag: cell type


title: PN90 Cell 281


title: Patient107

description: Definite


title: PN90 Cell 280


title: PN90 Cell 279


title: PN90 Cell 278


title: Patient105

description: Definite


title: PN90 Cell 277


title: Nr5a2_int_3

tag: treatment


title: Nr5a2_mit_3


title: Patient104

description: No Evidence


title: Nr5a2_int_2


title: PN90 Cell 276

tag: strain


title: PN90 Cell 273

tag: tissue


title: PN90 Cell 274

tag: age


title: PN90 Cell 275

tag: genotype


title: input_mit_3


title: Nr5a2_int_1


title: Patient103

description: Definite


title: PN90 Cell 271

tag: group


title: Patient102

description: Suspected


title: PN90 Cell 272


title: PN90 Cell 270


title: PN90 Cell 269


title: PN90 Cell 268


title: input_mit_1


title: Patient101

description: Suspected


title: input_int_3


title: PN90 Cell 267


title: Patient100

description: Definite


title: Patient106

description: Definite


title: input_int_2


title: Patient99

description: Definite


title: PN90 Cell 266


title: PN90 Cell 265


title: input_int_1


title: PN90 Cell 261


title: input_mit_2


title: PN90 Cell 259


title: Patient98

description: No Evidence


title: Patient97

description: Definite


title: auxinRNAseq_plus_t120_3

description: reactivation.txt

value: E14Tg2a derivative

value: Auxin-induced degradation of Esrrb and Nr5a2


title: PN90 Cell 263


title: PN90 Cell 262


title: PN90 Cell 257


title: Patient96

description: Suspected


title: Patient95

description: Suspected


title: PN90 Cell 260


title: auxinRNAseq_plus_t120_1

description: reactivation.txt


title: Patient94

description: Definite


title: auxinRNAseq_plus_t120_2

description: reactivation.txt


title: auxinRNAseq_plus_t90_2

description: reactivation.txt


title: PN90 Cell 258


title: PN90 Cell 253


title: PN90 Cell 264


title: PN90 Cell 254


title: PN90 Cell 252


title: PN90 Cell 255


title: Patient93

description: Definite


title: PN90 Cell 251


title: PN90 Cell 250


title: auxinRNAseq_plus_t60_3

description: reactivation.txt


title: Patient91

description: Definite


title: PN90 Cell 249


title: Patient90

description: Suspected


title: PN90 Cell 248


title: auxinRNAseq_plus_t60_2

description: reactivation.txt


title: PN90 Cell 247


title: auxinRNAseq_plus_t60_1

description: reactivation.txt


title: Patient89

description: Indeterminate


title: PN90 Cell 245


title: auxinRNAseq_plus_t90_3

description: reactivation.txt


title: Patient88

description: No Evidence


title: PN90 Cell 256


title: auxinRNAseq_plus_t50_3

description: reactivation.txt


title: auxinRNAseq_plus_t50_2

description: reactivation.txt


title: PN90 Cell 244


title: auxinRNAseq_plus_t90_1

description: reactivation.txt


title: PN90 Cell 243


title: PN90 Cell 241


title: Patient92

description: No Evidence


title: auxinRNAseq_plus_t50_1

description: reactivation.txt


title: Patient86

description: Definite


title: PN90 Cell 239


title: Patient87

description: Definite


title: PN90 Cell 240


title: Patient85

description: No Evidence


title: PN90 Cell 238


title: PN21 Cell 237


title: PN21 Cell 236


title: auxinRNAseq_plus_t40_3

description: reactivation.txt


title: PN90 Cell 246


title: auxinRNAseq_plus_t40_2

description: reactivation.txt


title: PN21 Cell 235


title: Patient83

description: Suspected


title: auxinRNAseq_plus_t40_1

description: reactivation.txt


title: PN21 Cell 233


title: PN21 Cell 232


title: PN90 Cell 242


title: auxinRNAseq_plus_t30_3

description: reactivation.txt


title: PN21 Cell 234


title: PN21 Cell 231


title: auxinRNAseq_plus_t30_2

description: reactivation.txt


title: Patient81

description: Definite


title: Patient82

description: Indeterminate


title: auxinRNAseq_plus_t30_1

description: reactivation.txt


title: PN21 Cell 227


title: PN21 Cell 230


title: PN21 Cell 229


title: PN21 Cell 228


title: Patient80

description: Definite


title: PN21 Cell 226


title: auxinRNAseq_plus_t20_3

description: reactivation.txt


title: PN21 Cell 224


title: PN21 Cell 225


title: Patient79

description: Definite


title: PN21 Cell 223


title: auxinRNAseq_plus_t20_2

description: reactivation.txt


title: Patient78

description: Definite


title: PN21 Cell 222


title: Patient84

description: No Evidence


title: PN21 Cell 221


title: auxinRNAseq_plus_t20_1

description: reactivation.txt


title: Patient77

description: Definite


title: auxinRNAseq_plus_mit_3

description: reactivation.txt


title: Patient76

description: No Evidence


title: PN21 Cell 219


title: PN21 Cell 218


title: auxinRNAseq_plus_mit_2

description: reactivation.txt


title: PN21 Cell 217


title: Patient75

description: No Evidence


title: auxinRNAseq_plus_mit_1

description: reactivation.txt


title: auxinRNAseq_plus_asy_3

description: reactivation.txt


title: Patient73

description: Suspected


title: auxinRNAseq_plus_asy_2

description: reactivation.txt


title: PN21 Cell 214


title: PN21 Cell 212


title: Patient72

description: Definite


title: PN21 Cell 216


title: PN21 Cell 215


title: PN21 Cell 211


title: PN21 Cell 213


title: auxinRNAseq_plus_asy_1

description: reactivation.txt


title: Patient71

description: Definite


title: PN21 Cell 210


title: PN21 Cell 208


title: PN21 Cell 209


title: PN21 Cell 207


title: Patient70

description: Definite


title: PN21 Cell 220


title: auxinRNAseq_minus_t120_2

description: reactivation.txt


title: PN21 Cell 206


title: PN21 Cell 205


title: Patient69

description: Definite


title: auxinRNAseq_minus_t120_1

description: reactivation.txt


title: Patient74

description: Suspected


title: PN21 Cell 202


title: auxinRNAseq_minus_t90_3

description: reactivation.txt


title: Patient68

description: Suspected


title: PN21 Cell 204


title: PN21 Cell 203


title: Patient67

description: Indeterminate


title: PN21 Cell 200


title: PN21 Cell 198


title: Patient65

description: Definite


title: auxinRNAseq_minus_t120_3

description: reactivation.txt


title: auxinRNAseq_minus_t90_2

description: reactivation.txt


title: auxinRNAseq_minus_t90_1

description: reactivation.txt


title: PN21 Cell 199


title: Patient64

description: Definite


title: PN21 Cell 196


title: Patient63

description: Definite


title: PN21 Cell 195


title: auxinRNAseq_minus_t60_3

description: reactivation.txt


title: PN21 Cell 193


title: PN21 Cell 197


title: PN21 Cell 194


title: auxinRNAseq_minus_t60_2

description: reactivation.txt


title: auxinRNAseq_minus_t60_1

description: reactivation.txt


title: Patient62

description: Indeterminate


title: PN21 Cell 192


title: PN21 Cell 190


title: PN21 Cell 191


title: auxinRNAseq_minus_t50_3

description: reactivation.txt


title: PN21 Cell 201


title: Patient61

description: Suspected


title: Patient66

description: Suspected


title: PN21 Cell 188


title: Patient60

description: Definite


title: PN21 Cell 187


title: PN21 Cell 185


title: PN21 Cell 186


title: Patient59

description: No Evidence


title: Patient58

description: Suspected


title: auxinRNAseq_minus_t40_3

description: reactivation.txt


title: Patient57

description: Definite


title: auxinRNAseq_minus_t50_1

description: reactivation.txt


title: PN21 Cell 184


title: PN21 Cell 181


title: PN21 Cell 183


title: auxinRNAseq_minus_t40_2

description: reactivation.txt


title: PN21 Cell 182


title: PN21 Cell 180


title: auxinRNAseq_minus_t40_1

description: reactivation.txt


title: Patient55

description: Definite


title: Patient56

description: Definite


title: PN21 Cell 189


title: auxinRNAseq_minus_t50_2

description: reactivation.txt


title: PN21 Cell 178


title: PN21 Cell 177


title: Patient54

description: Definite


title: auxinRNAseq_minus_t30_1

description: reactivation.txt


title: PN21 Cell 175


title: auxinRNAseq_minus_t30_3

description: reactivation.txt


title: PN21 Cell 179


title: Patient53

description: Definite


title: PN21 Cell 173


title: PN21 Cell 174


title: PN21 Cell 172


title: PN21 Cell 171


title: PN21 Cell 170


title: PN21 Cell 176


title: Patient51

description: No Evidence


title: Patient52

description: Definite


title: PN21 Cell 168


title: auxinRNAseq_minus_t20_2

description: reactivation.txt


title: auxinRNAseq_minus_t20_3

description: reactivation.txt


title: auxinRNAseq_minus_t20_1

description: reactivation.txt


title: PN21 Cell 167


title: PN21 Cell 169


title: Patient50

description: Definite


title: auxinRNAseq_minus_t30_2

description: reactivation.txt


title: Patient49

description: Definite


title: auxinRNAseq_minus_mit_3

description: reactivation.txt


title: PN21 Cell 165


title: PN21 Cell 166


title: PN21 Cell 164


title: auxinRNAseq_minus_mit_2

description: reactivation.txt


title: Patient48

description: Definite


title: PN21 Cell 163


title: PN21 Cell 162


title: auxinRNAseq_minus_mit_1

description: reactivation.txt


title: Patient47

description: Definite


title: Patient46

description: Indeterminate


title: PN21 Cell 160


title: PN21 Cell 159


title: auxinRNAseq_minus_asy_3

description: reactivation.txt


title: PN21 Cell 161


title: Patient45

description: Definite


title: PN21 Cell 158


title: auxinRNAseq_minus_asy_2

description: reactivation.txt


title: auxinRNAseq_minus_asy_1

description: reactivation.txt


title: PN21 Cell 153


title: Patient43

description: No Evidence


title: PN21 Cell 155


title: PN21 Cell 156


title: RGC, EU labeled, Immunopanning, P14 [SEP63]

city: Seoul

first: Jane

last: Jung

state: Yonsei-ro, Seodaemun-gu

department: Department of Anatomy

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
The sequence reads were processed in Salmon on mm10 (GENCODE M24).
Read counts were merged at the gene-level by tximport.
Assembly: mm10
Supplementary files format and content: comna-separated text files include TPM and count values for each Sample

source_name: Eye

extract_protocol:
Following vitreal EU injections, we dissected out superior colliculi from three animals and isolated total RNA using TRIzol reagent (Invitrogen 15596029). Twenty µg of total RNA was reacted with biotin-azide using Click-iT™ Nascent mRNA capture kit (Invitrogen C10365) to label EU-containing RNAs with a biotin tag. The tagged RNAs were affinity-purified using MyOne™ streptavidin T1-dynabeads resuspended in 50 µl nuclease-free water.
Purified RNAs were converted to double-stranded (ds) DNA using the previously described method (Shigeoka et al., 2016) with slight modification.
Amplified cDNAs were converted to sequencing libraries using Nextera XT DNA library preparation kit (Illumina FC-131-1024) and sequenced in Novaseq 6000.

value: Eye

tag: axotomy

value: naïve

tag: technique

value: EU labeled, immunopanning


title: Patient42

description: No Evidence


title: PN21 Cell 150


title: PN21 Cell 152


title: PN21 Cell 151


title: PN21 Cell 149


title: RGC, EU labeled, Immunopanning, P14 [SEP11]


title: Patient41

description: Definite


title: Eye, fmr1ko, FACS, P14 [SX33]

value: FACS


title: PN21 Cell 147

value: lung


title: Patient40

description: No Evidence


title: Patient44

description: Indeterminate


title: PN21 Cell 157

value: postnatal 21 days


title: PN21 Cell 146

value: wild type


title: Eye, fmr1ko, FACS, P14 [SX32]


title: Patient39

description: Suspected


title: PN21 Cell 145


title: RGC, EU labeled, Immunopanning, P14 [SEP82]


title: Eye, fmr1ko, FACS, P14 [SX31]


title: PN21 Cell 143


title: PN21 Cell 142


title: PN21 Cell 154


title: Patient37

description: Definite


title: PN21 Cell 141


title: Eye, FACS, P14 [SX12]


title: Patient36

description: Suspected


title: PN21 Cell 138


title: Eye, FACS, P14 [SX13]


title: Patient35

description: Indeterminate


title: PN21 Cell 137


title: PN21 Cell 148


title: PN21 Cell 139


title: PN21 Cell 144


title: SC, fmr1ko, EU labeled, P14 [AX63]

source_name: SC (superior colliculus)

value: SC (superior colliculus)

value: EU labeled


title: Patient34

description: No Evidence


title: Eye, FACS, P14 [SX11]


title: PN21 Cell 135


title: Patient33

description: Definite


title: SC, fmr1ko, EU labeled, P14 [AX62]


title: PN21 Cell 134


title: PN21 Cell 133


title: PN21 Cell 132


title: Patient38

description: Definite


title: PN21 Cell 131


title: PN21 Cell 140


title: Patient32

description: Indeterminate


title: SC, fmr1ko, axon-TRAP, P14 [AR53]

value: axon-TRAP


title: PN21 Cell 129


title: Patient31

description: Definite


title: PN21 Cell 130


title: PN21 Cell 126


title: PN21 Cell 136


title: SC, fmr1ko, axon-TRAP, P14 [AR51]


title: PN21 Cell 125


title: PN21 Cell 127


title: PN21 Cell 124


title: SC, fmr1ko, axon-TRAP, P14 [AR52]


title: Patient28

description: Indeterminate


title: PN21 Cell 123


title: SC, sarm1ko, EU labeled, P14 + 7d chase [AX73]

value: axotomized

value: P14 + 7d chase


title: PN21 Cell 122


title: SC, sarm1ko, EU labeled, P14 + 7d chase [AX72]


title: SC, fmr1ko, EU labeled, P14 [AX61]


title: PN21 Cell 121


title: Patient27

description: No Evidence


title: PN21 Cell 119


title: Patient26

description: Indeterminate


title: PN21 Cell 120


title: PN21 Cell 128


title: PN21 Cell 118


title: PN21 Cell 117


title: SC, EU labeled, P14 [AX33]


title: PN21 Cell 115


title: SC, EU labeled, P14 [AX32]


title: Patient25

description: No Evidence


title: Patient24

description: Indeterminate


title: PN21 Cell 116


title: PN21 Cell 114


title: PN21 Cell 112


title: SC, EU labeled, P14 [AX31]


title: PN21 Cell 111


title: Patient22

description: Definite


title: Patient23

description: Indeterminate


title: SC, sarm1ko, EU labeled, P14 + 7d chase [AX71]


title: SC, axon-TRAP, P14 [AR12]


title: Patient21

description: Suspected


title: PN21 Cell 108


title: SC, axon-TRAP, P14 [AR11]


title: SC, axon-TRAP, P14 [AR13]


title: PN21 Cell 106


title: PN21 Cell 107


title: Patient19

description: No Evidence


title: PN21 Cell 105


title: SC, EU labeled, P10+4d chase [AX23]

value: P10 + 4d chase


title: SC, EU labeled, P10+4d chase [AX22]


title: PN21 Cell 110


title: PN21 Cell 109


title: PN21 Cell 103


title: PN21 Cell 104


title: PN21 Cell 102


title: PN21 Cell 101


title: Patient18

description: Indeterminate


title: SC, EU labeled, P10+4d chase [AX21]


title: PN21 Cell 113


title: PN21 Cell 100


title: Patient16

description: Definite


title: SC, EU labeled, P10 [AX43]


title: Patient17

description: Definite


title: PN21 Cell 98


title: Patient29

description: Suspected


title: SC, EU labeled, P10 [AX42]


title: PN21 Cell 99


title: PN21 Cell 96


title: PN21 Cell 97


title: SC, EU labeled, P10 [AX41]


title: SC, axon-TRAP, P10 [AR23]


title: Patient13

description: Definite


title: Drosophila-adult head-Nlg3 KO-rep3

city: Nanjing

first: Hao

last: Xie

state: Jiangsu

address: 2#, Sipailou street

institute: Southeast University

data_processing:
The clean reads were subjected to further analysis based on the RNA-seq pipeline, by Bowtie, TopHat, CuffLinks, and CummeRbund software suite
The Cuffdiff program within Cufflinks was used to test for statistically significant differences between w1118 and dnlg3KO88/dnlg3KO127. The downstream statistical analyses and plots were performed in R (v3.1.1; http://www.r-project.org/).
Volcano plots, MA plots and bubble plots were generated in R with the function pheatmap of the gplots package. GO analysis was conducted using DAVID and Cytoscape (v3.4.0) with the BiNGO plugin (v3.0.3)
Assembly: BDGP5.25
Supplementary files format and content: csv file include FPKM values for all 6 Samples

organism: Drosophila melanogaster

source_name: adult head

extract_protocol:
Total RNA was extracted from 100 adult flies’ heads for each group by using Trizol total RNA isolation reagent (Invitrogen). RNA-seq data were obtained by the service provided by BGI (Shenzhen, China).
Standard RNA-Seq
Enrich mRNA by oligo dT

value: adult head

value: no


title: PN21 Cell 95


title: SC, axon-TRAP, P10 [AR22]


title: Patient12

description: Definite

value: Tracheal aspirate


title: PN21 Cell 94


title: Drosophila-adult head-Nlg3 KO-rep2


title: SC, axon-TRAP, P10 [AR21]


title: Drosophila-adult head-WT-rep3


title: PN21 Cell 93


title: Patient11

description: Definite


title: SC, EU labeled, 8 week [AX53]


title: PN21 Cell 92


title: Patient10

description: Definite


title: Patient15

description: Indeterminate


title: PN21 Cell 91


title: Patient9

description: Definite


title: PN21 Cell 90


title: Drosophila-adult head-WT-rep1


title: SC, EU labeled, 8 week [AX51]


title: Patient8

description: Definite


title: NBC_3-D7

city: Nantes

first: David

last: Chiron

address: 8 quai Moncousu

institute: CRCI2NA, INSERM_U1307, CNRS_6075, Nantes_Université

data_processing:
Paired-end sequencing (2x100 cycles) was carried out with 4 samples by lane on HiSeq® 2500 system (Illumina) in TruSeq v3 chemistry according to the instructions of HiSeq® 2500 System Guide, part#15035786 v01 (Illumina)
After demultiplexing and quality control with fastQC_0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), illumina adapter were trimmed with cutadapt-1.2.11 and reads with Phred quality score below 30 were filtered with prinseq-lite-0.20.3
Reads were aligned against human hg19 reference genome with tophat2.0.103, reads count and differential analysis was realized with Gfold
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: CD19+ sorted MCL or normal B cells were cocultured for 7 days with L-40L cells and growth factors as described in doi: 10.1182/blood-2016-06-720490

extract_protocol:
Total RNA was extracted with RNeasy Mini kit (Qiagen) and quantified using a Nanodrop®ND-1000 spectrophotometer (Thermo Scientific). Quality and integrity of RNA samples were assessed using the 2100 Bioanalyzer and RNA 6000 Nano LabChip kit series II (Agilent Technologies).
Library construction was performed from 500ng of total RNA with SureSelect Strand-Specific RNA Library Prep for Illumina Multiplexed kit (Ref 5190-6410 , Agilent Technologies) according to Agilent_PrepLib_G9691-90010_juillet2015_vD protocol. Fragments size of libraries was controlled on D1000 ScreenTape with 2200 TapeStation system (Agilent Technologies). Libraries with P5-P7 adaptors were specifically quantified on LightCylcer ® 480 Instrument II (Roche Life Science) and normalized with DNA Standards (1-6) (Ref KK4903, KAPABIOSYSTEMS - CliniSciences). Each library was pooled and prepared according to Denaturing and diluting libraries protocol for the Hiseq and GAIIx, part#15050107 v02 (Illumina) for cluster generation on cBotTM system.

value: normal naive CD5+ B cells isolated from cord blood B cells (NBC) were cultured with growth factors (interleukin-10 [IL10]:50 ng/mL, B-cell activating factor [BAFF]:50 ng/mL, insulin-like growth factor-1 [IGF1]:10 ng/mL, interleukin-6 [IL6]:1 ng/mL) on adherent CD40L-expressing cells  for 7 days

tag: patient's number


title: RGC, immunopanning, P14 [SP25]

value: Eye

value: immunopanning


title: Drosophila-adult head-Nlg3 KO-rep1


title: NBC_3-D0

source_name: normal naive CD5+ B cells isolated from cord blood B cells (NBC)


title: Patient7

description: Definite


title: PN21 Cell 88


title: Patient6

description: Definite


title: PN21 Cell 87


title: NBC_2-D0

value: normal naive CD5+ B cells isolated from cord blood B cells (NBC)


title: Patient5

description: Definite


title: RGC, immunopanning, P14 [SP12]

value: naïve


title: NBC_2-D7


title: SC, EU labeled, 8 week [AX52]


title: PN21 Cell 86

value: lung


title: Drosophila-adult head-WT-rep2


title: Patient4

description: Definite


title: PN21 Cell 85

value: postnatal 21 days


title: sample3_GEX

city: Warsaw

first: Pawel

last: Segit

address: Pasteur 3

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

description: sample3 (hashed 6 samples: female control, male control, female tumor D14, male tumor D14, female tumor D21, male tumor D21); 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Raw sequencing data (BCL files) were demultiplexed and coverted to fastq files using the CellRanger v3.0.1 (10x Genomics) and bcl2fastq v2.20.0.422 (Illumina)
Cell Ranger v4.0.0 count was used to align the demultiplexed reads to the reference genome (mm10), perform filtering, barcode counting, UMI (unique molecule identifier) counting and estimate the number of cells.
Data analysis was performed in R using Seurat v3 package.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: brain CD11b+, mRNA-derived cDNA

extract_protocol:
Animals were perfused transcardially with ice-cold phosphate-buffered saline (PBS), in order to remove blood cells from the brain. Next, brains were dissected and tumor-bearing hemispheres or whole brains (controls) were dissociated enzymatically.
Cell encapsulation and library preparation was performed with Chromium Controller (10x Genomics) and Chromium Next GEM Single Cell 3’ Reagent Kit v3 with Feature Barcoding technology for Cell Surface Protein (10x Genomics) according to the producer’s user guide (CG000185 Rev D).

value: Brain

value: 12 weeks

tag: library type

value: mRNA

tag: antibodies/tags


title: NBC_1-D7


title: sample3_ADT

description: sample3 (hashed 6 samples: female control, male control, female tumor D14, male tumor D14, female tumor D21, male tumor D21); Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

library_source: other

molecule: protein

source_name: brain CD11b+, ADT-derived cDNA

value: ADT

value: (CITE-seq, conjugated in-house) Recombinant Anti-TMEM119 antibody [106-6] - BSA and Azide free; (CITE-seq, conjugated in-house) Purified anti-mouse CD74 (CLIP) Antibody; (CITE-seq, conjugated in-house) Anti-CD52 (CAMPATH-1) (Mouse) mAb; (CITE-seq) TotalSeq™-B0014 Anti-CD11b; (CITE-seq) TotalSeq™-B0096 Anti-CD45; (CITE-seq) TotalSeq™-B0013 Anti-Ly-6C; (CITE-seq) TotalSeq™-B0116 Anti-Gr-1; (CITE-seq) TotalSeq™-B0190 Anti-CD274 (PD-L1); (CITE-seq) TotalSeq™-B0078 Anti- CD49d; (CITE-seq) TotalSeq™-B0117 Anti-I-A/I-E (MHCII); TotalSeq™-B0301 anti-mouse Hashtag 1 Antibody; TotalSeq™-B0302 anti-mouse Hashtag 2 Antibody; TotalSeq™-B0303 anti-mouse Hashtag 3 Antibody; TotalSeq™-B0304 anti-mouse Hashtag 4 Antibody; TotalSeq™-B0305 anti-mouse Hashtag 5 Antibody; TotalSeq™-B0306 anti-mouse Hashtag 6 Antibody


title: Patient3

description: Definite


title: PN21 Cell 84

value: wild type


title: sample2_GEX

description: sample2 (hashed 6 samples: female control, male control, female tumor D14, male tumor D14, female tumor D21, male tumor D21); 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: NBC_1-D0


title: MCL_4-D0

source_name: CD19+ MCL cells

value: CD19+ MCL cells


title: Patient1

description: No Evidence


title: Patient2

description: Definite


title: MCL_4-D7

value: CD19+ MCL cells cultured with growth factors (interleukin-10 [IL10]:50 ng/mL, B-cell activating factor [BAFF]:50 ng/mL, insulin-like growth factor-1 [IGF1]:10 ng/mL, interleukin-6 [IL6]:1 ng/mL) on adherent CD40L-expressing cells  for 7 days


title: PN21 Cell 89


title: PN21 Cell 83


title: RGC, immunopanning, P14 [SP24]


title: Wnt5a+anti-Ptk7 rep 6

city: South San Francisco

last: Garfield

address: 1 DNA Way

department: OMNI Bx

institute: Genentech

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie v4.2.2
GSNAP v2013-11-01 was used for alignment, through the HTSeqGenie wrapper, against the mouse reference genome (NCBI Build 38).
Read counts were scaled by library size, quantile normalized and precision weights were calculated using the voom R package
Differential expression analysis was performed using the limma package
Assembly: mm10
Supplementary files format and content: TSV count matrices

source_name: Small intestine, Jejunum

growth_protocol: Mouse intestinal organoids were cultured in Intesticult, which is referred as complete culture media (STEMCELL technologies).

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit (Qiagen).
cDNA library was generated from 2 ng of total RNA using Smart-Seq V4 Ultra Low Input RNA Kit (Takara). 150 pg of cDNA was used to make sequencing libraries by Nextera XT DNA Sample Preparation Kit (Illumina)

treatment_protocol: Organoids were either cultured in quiescent or senescent conditioned media or Wnt5a containing media with IgG or anti-Ptk7 antibodies.

value: Small intestine, Jejunum

value: Intestinal organoids


title: MCL_3-D7


title: sample2_ADT

description: sample2 (hashed 6 samples: female control, male control, female tumor D14, male tumor D14, female tumor D21, male tumor D21); Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads


title: PN21 Cell 82

source_name: Lung


title: PN21 Cell 81


title: MCL_3-D0


title: Wnt5a+anti-Ptk7 rep 5


title: OCI-AML3 cell line

city: Chapel Hill

first: Kelly

middle: Shea

last: Olsen

state: NC

address: 5230E Marsico Hall, 125 Mason Farm Road

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
fastq files were aligned via STAR-SALMON
DESeq2 in R was utilized for alignment and read count extraction
DESeq2 values calculated with respect to average value for each gene as "reference" as there was no normal control sample for this experiment
DESeq2 output comparing all cell lines to average values of all is included, as well as STAR-SALMON outputs
Assembly: aligned using GRCh37

growth_protocol: cells were cultured in RPMI 1640 + 10% FBS with 1% L-Glutamine and 1% Penicillin/Streptomycin

extract_protocol:
RNA was isolated from 5 million cells per cell line with the Qiagen AllPrep DNA/RNA extraction kits
Illumina Stranded mRNA prep

value: cancer cell line


title: PN21 Cell 80


title: MCL_2-D7


title: U937A2 cell line


title: Wnt5a+anti-Ptk7 rep 4


title: PN21 Cell 79


title: MCL_2-D0


title: NB4 cell line


title: Monomac1 cell line


title: PN21 Cell 78


title: Nomo1 cell line


title: MCL_1-D7


title: PN21 Cell 77


title: MCL_1-D0


title: siEIF4A3-METTL3_eCLIP-rep2

city: Boston

first: Xin

last: Yang

address: Karp Building, 6th floor, 06007E, 1 Blackfan Circle

institute: Boston childrens' hospital

description: clip-RNA

data_processing:
For meRIP-seq: m6A peaks were called using Exomepeaks2; The differential m6A regions were identified using RADAR software.
For eCLIP-seq: extract unique molecular identifiers with umi_tools; Trims adapters & adapter-dimers with cutadapt; Maps to repeat elements with STAR and filter; Maps filtered reads to genome with STAR; Removes PCR-duplicates with umi_tools; Calls enriched peak regions (peak clusters) with CLIPPER; Uses size-matched input sample to normalize and calculate fold-change enrichment within enriched peak regions with custom perl scripts; IDR analysis is run as a second processing pipeline (merge_peaks) available with additional documentation on github
Assembly: hg38
Supplementary files format and content: tab-delimited text files include m6A peaks, differential m6A regions, and METTL3 binding clusters

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was harvested using Trizol. polyA RNA was purified using magnetic-oligo(dT) beads. Chromatin fraction was used to extract caRNA.
For meRIP-seq, m6A modified polyA or caRNA fragments were immunoprecipitated using anti-m6A antibody and then subjected to libraries construction SMARTER smRNA-Seq Library Prep Kit following manufacturer's protocols. For eCLIP-seq, experiments were performed following the ECODE eCLIP-seq protocol.
meRIP-seq
eCLIP-seq

value: HeLa

value: epithelial cell

value: EIF4A3 knockdown


title: Wnt5a+IgG rep 6


title: PN21 Cell 76

data_processing:
Raw sequence reads were demultiplexed using bcl2fastq (v1.8.4, Illumina)
sequences aligned to the mouse reference genome (GRCm38-mm10, UCSC, supplemented with Zsgreen1 sequence) with STAR
number of reads that mapped to each annotated gene (gene counts) determined with HTSEQ (v0.6.1p1, default parameters except Stranded set to false and Mode set to intersection-nonempty)
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols


title: siEIF4A3-METTL3_eCLIP-rep1

description: clip-RNA


title: Wnt5a+IgG rep 5


title: siCtrl-METTL3_eCLIP-rep2

description: clip-RNA

value: WT


title: PN21 Cell 74

value: lung


title: Wnt5a+anti-Ptk7 rep 1


title: Wnt5a+IgG rep 4


title: siCtrl-METTL3_eCLIP-rep1

description: clip-RNA


title: PN21 Cell 73

value: postnatal 21 days


title: RNA-Seq Rat NPCs 5 [H2]

city: Chongqing

first: Yuyao

last: Zhang

address: No.83, Xinqiao Zhengjie, Shapingba District

institute: Xiqiao hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: counts, FPKM values for each Sample

organism: Rattus norvegicus

source_name: nucleus pulposus cells (NPCs)

growth_protocol: NPCs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: H group NPCs were treated with lactate (10 mM) for 8 h

value: nucleus pulposus cells (NPCs)

value: wt

value: Sprague Dawley

tag: Sex

value: male

value: lactate(10 mM)


title: RNA-Seq Rat NPCs 6 [H3]

tag: strain background


title: PN21 Cell 75

city: Stanford

last: Kuo

institute: Stanford University

value: wild type


title: RNA-Seq Rat NPCs 3 [CON3]


title: siEIF4A3SMInput

description: clip-RNA


title: Wnt5a+anti-Ptk7 rep 2


title: PN21 Cell 72


title: Wnt5a+IgG rep 3


title: Wnt5a+IgG rep 2


title: RNA-Seq Rat NPCs 2 [CON2]


title: Patient14

description: No Evidence

source_name: Tracheal aspirate

value: Tracheal aspirate


title: siCtrl-SMInput

description: clip-RNA


title: Wnt5a+IgG rep 1


title: siEIF4A3-caRNA_meRIP_rep2

description: chromatin associated RNA


title: PN21 Cell 70


title: PGM-134: SB1003_totalRNA-seq

city: St John's

first: Marc

middle: Patrick

last: Grüll

state: Newfoundland

address: 230 Elizabeth Ave

department: Biology

country: Canada

institute: Memorial University of Newfoundand

data_processing:
In house software used for data processing
TSSAR software used for detection of transcription start sites and transcription termination sites
In house pipeline used for operon detection
Supplementary_files_format_and_content: allData_transcripts: combined file for each strain containing dRNA-seq 5' and 3' data
Supplementary_files_format_and_content: dRNA_seq_TSSs: correspond to the dRNA-seq 5' data
Supplementary_files_format_and_content: dRNASeq_TTSs: correspond to the dRNA-seq 3' data

organism: Rhodobacter capsulatus SB 1003

source_name: SB1003 total RNA

growth_protocol: R. capsulatus cells were grown aerobically in RCV minimal medium for one day. Cells were then transferred to an anaerobic photosynthetic tube containing YPS medium. The anaerobic cultures were prepared to have an initial optical density of 20 Klett Units (KU). Cultures were grown for 15-16 hours.

extract_protocol:
500μ of culture were transferred into 100μl 95% Ethanol and 5% Phenol. Samples were spun down for 2 minutes and the pellets were stored at -80°C. Small RNA was extracted following the Macherey-Nagel protocol for DNA, RNA, and protein purification kit for small RNA fraction.
Libraries for 5' and 3' targeted sequencing were prepared following a newly developed protocol based on dRNA-seq. Libraries for total RNA seq were prepared following the Ion Torrent Ion Total RNA-Seq Kit V2 for whole RNA Libraries protocol.

tag: growth phase

value: Early Stationary

value: whole organism


title: RNA-Seq Rat NPCs 4 [H1]


title: siEIF4A3-caRNA_meRIP_rep1

description: chromatin associated RNA


title: Complete culture media+IgG rep 6

value: Small intestine, Jejunum

value: Intestinal organoids

value: Complete culture media+IgG


title: PN21 Cell 69

first: Christin

address: 240 Pasteur Dr.


title: Complete culture media+IgG rep 5


title: Complete culture media+IgG rep 4


title: PGM-109: SB1003_TEXminus_3prime_dRNA-seq


title: siCtrl-caRNA_meRIP_rep2

description: chromatin associated RNA

value: HeLa

value: epithelial cell


title: PN21 Cell 67


title: siCtrl-caRNA_meRIP_rep1

description: chromatin associated RNA

value: WT


title: PGM-108: SB1003_TEXplus_3prime_dRNA-seq


title: Complete culture media+IgG rep 3


title: PGM-107: SB1003_TEXminus_3prime_dRNA-seq


title: PN21 Cell 65

value: lung


title: PN21 Cell 71

value: postnatal 21 days


title: PGM-106: SB1003_TEXplus_3prime_dRNA-seq


title: PN21 Cell 66


title: PGM-104: SB1003_TEXplus_5prime_dRNA-seq


title: Complete culture media+IgG rep 1


title: RNA-Seq Rat NPCs 1 [CON1]

value: nucleus pulposus cells (NPCs)


title: Complete culture media+IgG rep 2


title: siEIF4A3-caRNA_input_rep2

description: chromatin associated RNA

value: EIF4A3 knockdown


title: siCtrl-caRNA_input_rep2

description: chromatin associated RNA


title: PN21 Cell 64


title: Senescent CM+anti-Ptk7 rep 6

value: Senescent CM+anti-Ptk7


title: PGM-105: SB1003_TEXminus_5prime_dRNA-seq


title: PN21 Cell 63


title: PN21 Cell 68


title: PGM-96: SB1003_TEXplus_5prime_dRNA-seq


title: Senescent CM+anti-Ptk7 rep 5


title: PGM-95: SB1003_TEXminus_5prime_dRNA-seq


title: Senescent CM+anti-Ptk7 rep 4


title: siEIF4A3-caRNA_input_rep1

description: chromatin associated RNA


title: PN21 Cell 62


title: Senescent CM+anti-Ptk7 rep 3


title: PN21 Cell 61


title: WT_TOTAL_R3

growth_protocol: Cells were grown in yeast extract-peptone-dextrose (YPD) medium in conical flasks at 30 °C, shaking at 300 RPM in incubators, then switched to pre-sporulation medium for 17 h and further to sporulation medium for 4 h.

extract_protocol:
Cell pellets were  snap-frozen in liquid nitrogen. Total RNA was extracted using the hot acid phenol protocol (acid phenol:chloroform:isoamyl alcohol 125:24:1) and TE-SDS buffer, then precipitated in ethanol with 0.3 M sodium acetate before re-suspension in DEPC-treated sterile water. Further RNA was treated with DNase and for the case of polysomal RNA it was isolated after polysome frationation with acid phenol and ethanol purification.
Total RNA was treated with rDNase and for the case of polysomal RNA it was isolated after polysome fractionation and purification with isopropanol precipitation, acid phenol extraction and and ethanol precipitation.

treatment_protocol: No treatment

tag: strain backgorund

value: FW1511 (MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG)

tag: gene deletion

tag: condition

value: Sporulation medium 4h


title: Patient20

description: Definite

data_processing:
Pseudoalignment with kallisto version 0.46.1 (with bias correction) to all transcripts associated with human protein-coding and long non-coding RNA genes in ENSEMBL v. 99.
Gene-level counts generated from transcript-level abundance estimates using the R package tximport with the scaledTPM method.
Assembly: ENSEMBL v. 99
Supplementary files format and content: Gene counts (rows) for each sample (columns)
Supplementary files format and content: Annotation of adjudicated LRTI status for each sample.

extract_protocol:
Tracheal aspirate (TA) was collected within 24 hours of intubation, mixed 1:1 with DNA/RNA Shield (Zymo) and frozen at -80°C. RNA was extracted from 300µl of patient TA using bead-based lysis and the Allprep DNA/RNA kit (Qiagen), which included a DNase treatment step.
RNA was reverse transcribed to generate cDNA and sequencing library preparation was performed using the NEBNext Ultra II Library Prep Kit.


title: PN21 Cell 60

value: wild type


title: Senescent CM+anti-Ptk7 rep 2

tag: cell type

tag: treatment


title: siALKBH5-polyA_RNA_meRIP_rep2

tag: tissue

tag: cell line

value: ALKBH5 knockdown


title: WT_TOTAL_R2


title: PN21 Cell 59

tag: strain

tag: age

tag: genotype


title: siALKBH5-polyA_RNA_meRIP_rep1


title: Senescent CM+anti-Ptk7 rep 1


title: WT_TOTAL_R1


title: PN21 Cell 58

tag: group


title: Senescent CM+IgG rep 6

value: Senescent CM+IgG


title: siCtrl-polyA_RNA_meRIP_rep2


title: siCtrl-caRNA_input_rep1

description: chromatin associated RNA


title: PHO92_TOTAL_R3

value: FW3528 (MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG, pho92::HYG)

value: PHO92 deletion


title: siCtrl-polyA_RNA_meRIP_rep1


title: PN21 Cell 57


title: siEIF4A3-polyA_RNA_meRIP_rep1


title: Senescent CM+IgG rep 5

value: Small intestine, Jejunum

value: Intestinal organoids


title: PHO92_TOTAL_R2


title: siEIF4A3-polyA_RNA_meRIP_rep2

value: HeLa


title: siEIF4A3-polyA_RNA_input_rep2

value: epithelial cell


title: PN21 Cell 56


title: PHO92_TOTAL_R1


title: siEIF4A3-polyA_RNA_input_rep1


title: PN21 Cell 55


title: Senescent CM+IgG rep 4


title: Senescent CM+IgG rep 3


title: Patient30

description: No Evidence

value: Tracheal aspirate


title: WT_POLYSOME_R2

tag: molecule subtype

value: polysome RNA


title: siALKBH5-polyA_RNA_input_rep2


title: PN21 Cell 54

value: lung

value: postnatal 21 days


title: WT_POLYSOME_R1


title: Senescent CM+IgG rep 2


title: PHO92_POLYSOME_R2


title: siALKBH5-polyA_RNA_input_rep1


title: Senescent CM+IgG rep 1


title: siCtrl-polyA_RNA_input_rep2

value: WT


title: PN21 Cell 52


title: siCtrl-polyA_RNA_input_rep1


title: Quiescent CM+ IgG rep 6

value: Quiescent CM+ IgG


title: PHO92_POLYSOME_R1


title: PN21 Cell 51


title: Quiescent CM+ IgG rep 5


title: PA2x-treated root, 14 days after transplantation, rep 3

city: Ghent

first: Willem

last: Desmedt

address: Valentin Vaerwyckweg 1

department: Plants and Crops

country: Belgium

institute: Ghent University

data_processing:
Quality assesment using FastQC v0.11.8
Trimming with Trimmomatic v0.38 (Phred > 20, length > 40)
Mapping to rice reference genome (MSU 7.0) using STAR v2.6.1d
Counting reads using R GenomicAlignments package (summarizeOverlaps function)
Normalization and differential expression analysis using the R DeSeq2 package
Genome_build: MSU 70.
Supplementary_files_format_and_content: DeSeq2-output in a csv file
Supplementary_files_format_and_content: count table (normalized using DeSeq2)

organism: Oryza sativa Japonica Group

source_name: Rice root

growth_protocol: Rice seedlings (cv. Kitaake) were  germinated on wet tissue paper (28°C, dark), transplanted to individual PVC tubes 5 days after germination and placed in a growth chamber (28°C, 12 hours of light)

extract_protocol:
Plants were washed, pooled (4 plants per sample) and root and shoot tissues were ground seperately in liquid nitrogen. RNA was extracted using a Qiagen RNEasy Plant Mini Kit per manufacturer's instructions.
QuantSeq 3′mRNA-Seq Library Prep Kit (Lexogen) as per manufacturer's instruction, starting from 2 µg RNA.

treatment_protocol: Plants were foliarly sprayed with a solution containing 0.1 v/v% Tween 20 and the active compound 13 days post transplantation.

value: root

tag: cultivar

value: Kitaake

value: 14 days post transplantation

tag: treatment time

value: 7&13 days post transplantation

value: Piperonylic acid (300 microM)


title: iPSC 106 undifferentiated

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

description: iPSC 106 undifferentiated

data_processing:
Quality Control: FastQC
Trimming adaptor and low quality seqs: Trimmomatic
Alignment: Star-aligner
Read counting: FeatureCount
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

source_name: iPSC

growth_protocol: The iPSC lines were cultured on tissue culture plastic coated with vitronectin (0.5 µg/cm2) in StemMACS iPS-Brew XF (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany).

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA Plus Kit (Macherey-Nagel, Düren, Germany).
Library preparation was carried out using QuantSeq 3´-mRNA (Lexgon) according to the manufacturer's instructions. Sequencing was done using NovaSeq 6000 sequencer (Ilumina). Library preparation and sequencing was carried out by Life&Brain (Bonn, Germany).

tag: gender

value: male

tag: time (days)

tag: sample group

value: undifferentiated


title: PN21 Cell 50

value: wild type


title: PA2x-treated root, 14 days after transplantation, rep 2


title: PN21 Cell 49


title: Wnt5a+anti-Ptk7 rep 3

value: Small intestine, Jejunum

value: Intestinal organoids


title: iPSC 106 ENDO

description: iPSC 106 ENDO

value: endoderm


title: Quiescent CM+ IgG rep 2


title: PN21 Cell 48


title: PA2x-treated root, 14 days after transplantation, rep 1


title: iPSC 106 ECTO

description: iPSC 106 ECTO

value: ectoderm


title: Quiescent CM+ IgG rep 3


title: PN21 Cell 47


title: Quiescent CM+ IgG rep 1


title: iPSC 104 undifferentiated

description: iPSC 104 undifferentiated

value: female


title: PN21 Cell 53

value: lung


title: PN21 Cell 46

value: postnatal 21 days


title: iPSC 104 MESO

description: iPSC 104 MESO

value: mesoderm


title: PN21 Cell 45


title: PN21 Cell 44