title: 11970X6, IECs - WT


title: 3_H5_Norm_S353

status: Public on Sep 09 2021

type: SRA

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files of read counts for each sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Full length RNA-seq (Smartseq2)
Libraries were constructed using the smartseq2 protocol accoring to manufacturers instructions

tag: lane

tag: plate-position

tag: cell line

tag: condition

value: Norm

tag: sample-identity


title: 11970X9, IECs - dIEC

city: Salt Lake City

first: W. Zac

last: Stephens

state: UT

address: 15 N. Medical Drive, EEJMRB 4208, EEJMRB 4208

department: Pathology

country: USA

institute: University of Utah

data_processing:
Reads were aligned with novoalign
Counts matrices generated with Useq DefinedRegionDifferentialSeq
Genome_build: mm10
Supplementary_files_format_and_content: A tab-separated file with raw counts for each sample and genes as features is provided.

organism: Mus musculus

source_name: Ileum intestinal epithelial cells

extract_protocol:
400,000 Live, CD45-, EpCAM+ cells from the ileum were sorted and resuspended in Trizol then RNA was extracted with ZymoResearch Direct-zol RNA microprep kits.
Illumina TruSeq stranded RNA kit with RiboZero gold (human, mouse, rat) was used to construct libraries.

tag: tissue

value: Ileum

tag: genotype

value: H2-Ab1 fl/fl; Villin:Cre+

tag: cell type

value: Live, CD45-, EpCAM+ sorted intestinal epithelial cells

tag: Sex

value: female


title: 11970X2, IECs - WT

value: H2-Ab1 fl/fl; Villin:Cre-

value: male


title: 3_H1_Norm_S349


title: 4_A2_Norm_S20


title: 14393X11, DSS-treated ileum, dIEC

data_processing:
Reads were aligned with TopHat2
Gene level summary counts generaed with GenomicAlignments package
Gene's with less than 2 reads aligning were filtered.
Genome_build: mm10
Supplementary_files_format_and_content: A tab-separated file with raw counts for each sample and genes as features is provided.

source_name: Distal ileum

extract_protocol:
2 cm of distal ileum was collected in Trizol then RNA was extracted with ZymoResearch Direct-zol RNA microprep kits.
NEBnext Ultra directional library prep was used to create sequencing libraries

tag: treatment

value: Dextran Sodium Sulfate


title: 11970X10, IECs - WT


title: 3_H3_Norm_S351


title: 4_A10_Hypo_S46

value: hypoxia


title: 3_H4_Norm_S352


title: 3_G7_Hypo_S325


title: 3_H13_Hypo_S377


title: 3_H10_Hypo_S376


title: 11970X7, IECs - dIEC


title: 14393X7, DSS-treated ileum, WT


title: 3_G5_Norm_S305


title: 14393X8, DSS-treated ileum, WT


title: 3_G6_Norm_S306


title: Control_DHT_sgAr_rep.2

city: New York

first: Ivana

last: Grbesa

address: 413 E 69th St

department: Urology

institute: Weill Cornell Medicine

library_source: genomic

data_processing:
Reads were aligned to mouse genome  with Bowtie2 v.2.3.4.1.
Duplicates and mitochondrial reads were removed with Samtools v1.8. or as part of the ENCODE ATAC-seq pipeline
Peaks were called with Genrich (https://github.com/jsh58/Genrich) in ATAC-seq mode.
Genome_build: mm10 genome
Supplementary_files_format_and_content: peaks

molecule: genomic DNA

source_name: Control_DHT_sgAr_prostate organoids

growth_protocol: Murine organoids were grown in mouse organoid media as per standard protocol.

extract_protocol:
Samples were processed as previously described in Grbesa I, et al. J Vis Exp 2017. PMID 29155775
Libraries were made as described previously in Grbesa I, et al. J Vis Exp 2017. PMID 29155775

treatment_protocol: sgAr = sgRNA targeting AR exon 2 of NM_013476.4

tag: genotype/variation

value: :control with sgAr

tag: tissue/cell type

value: prostate

value: 1 nM DHT


title: 3_G3_Norm_S303


title: 3_G2_Norm_S302


title: 3_G9_Hypo_S327


title: 11970X3, IECs - dIEC


title: 14393X5, DSS-treated ileum, dIEC


title: 11970X5, IECs - dIEC


title: 14393X12, DSS-treated ileum, WT


title: 11970X1, IECs - dIEC


title: 3_G8_Hypo_S326


title: 14393X9, DSS-treated ileum, WT


title: 3_G1_Norm_S301


title: 3_G4_Norm_S304


title: 14393X3, DSS-treated ileum, dIEC


title: 3_G10_Hypo_S328


title: 3_F7_Hypo_S277


title: 14393X4, DSS-treated ileum, WT


title: 14393X1, DSS-treated ileum, dIEC


title: Endothelial cells, SPF1

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v12.0 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Genome_build: GRCm38
Supplementary_files_format_and_content: abundance measurments

source_name: Colon sorted endothelial cells

extract_protocol:
Colon endothelial cells were positive isolated using MACS-Beads (CD45-CD31+) and sorted for ICAM-1+ CD146+. Total RNA from 0,2x10^6 cells was extracted.
Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Pico chip on Agilent's bioanalyzer. Barcoded mRNA seq libraries were prepared from 20 ng total RNA using a NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® according to the manual. All quality controls were done using Invitrogen’s Qubit HS assay and fragment size was determined on Agilent’s 2100 Bioanalyzer HS DNA chip.

tag: strain

tag: mouse type

value: specific-pathogen-free

tag: group

value: conventional

value: colon

value: endothelial cell


title: 3_F9_Hypo_S279


title: Endothelial cells, SPF4


title: 3_F8_Hypo_S278


title: 14393X6, DSS-treated ileum, dIEC


title: Endothelial cells, GF4

value: germfree mice

value: germ-free


title: 3_H12_Hypo_S378


title: 3_G11_Hypo_S329


title: Endothelial cells, SPF3


title: 3_F5_Norm_S257

value: Norm


title: 3_F6_Norm_S258


title: Sle1b.miR-21KO Mouse 3

city: Hershey

first: Ziaur

last: Rahman

state: PA

address: 500 University Drive

department: Microbilogy and Immunology

institute: Pennsylvania State University College of Medicine

description: 7_miR21--Sle1b_3 - lib44690

data_processing:
The processing workflow was managed on the Galaxy platform. Reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
Sequence alignment was performed using STAR aligner (v2.4.2a) with the GRCm38 reference genome and gene annotations from Ensembl release 91.
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134), FASTQC (v0.11.3), and HTSeq-count
Genome_build: GRCm38
Supplementary_files_format_and_content: The file "P328-1_RawGeneCounts.csv" is a comma-separated matrix. The first four columns ("geneId", "geneName", "description", and "geneBiotype") describe one gene per row, with the "geneId" column containing Ensembl gene IDs. The remaining columns are named as "sampleId - libraryId" and contain raw read counts assigned to each library. Counts have not been filtered or normalized.

source_name: Sorted B cells

extract_protocol:
B cells were sorted from a single splenocyte suspension on a BD FACS Aria sorter.  RNA was extracted from B cells using a combination protocol.  Cells were lysed with Trizol reagent and processed until ethanol extraction, at which point samples were loaded onto Qiagen RNeasy columns and the remainder of the Qiagen isolation protocol was followed.
Libraries were prepared following the Nextera XT library preparation protocol

treatment_protocol: Mice were treated with IMQ cream on both ear surfaces.

value: IMQ

value: B cells


title: 3_G12_Hypo_S330


title: 14393X2, DSS-treated ileum, WT

value: Ileum


title: Endothelial cells, GF1


title: Endothelial cells, GF3


title: 3_F4_Norm_S256


title: Sle1b.miR-21KO Mouse 4

description: 8_miR21--Sle1b_4 - lib44691


title: 3_F12_Hypo_S282


title: Sle1b.miR-21KO Mouse 2

description: 6_miR21--Sle1b_2 - lib44689


title: 3_F11_Hypo_S281


title: Sle1b.miR-21KO Mouse 1

description: 5_miR21--Sle1b_1 - lib44688


title: 3_F10_Hypo_S280


title: Sle1b Mouse 4

description: 4_Sle1b_4 - lib44687


title: Sle1b Mouse 2

description: 2_Sle1b_2 - lib44685


title: 3_F1_Norm_S253


title: Sle1b Mouse 3

description: 3_Sle1b_3 - lib44686


title: Endothelial cells, SPF2


title: 3_E9_Hypo_S231


title: 3_E7_Hypo_S229


title: 3_F3_Norm_S255


title: 3_E8_Hypo_S230


title: Sle1b Mouse 1

description: 1_Sle1b_1 - lib44684


title: 3_E6_Norm_S210


title: 3_F2_Norm_S254


title: 3_E5_Norm_S209


title: colon, infected VAS, replicate 3

city: New York city

first: Zhi

last: Chai

state: NY

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description:
post-infection day 10
48b_S1
Colon_study_RawCounts.txt

data_processing:
Mapping were done in the Penn State Bioinformatics Consulting Center. Quality trimming and adapter removal was performed using trimmomatic.
The trimmed data were then mapped to the mouse genome (mm10, NCBI) using hisat2 alignment program. Hisat2 alignment was performed by specifying the 'rna-strandness' parameter. Default settings were used for all the other parameters.
Coverages were obtained using bedtools. Mapped data was visualized and checked with IGV. Reads mapped to each transcript were counted using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw Count values for each gene in each sample

source_name: colon-whole tissue

extract_protocol:
Tissue were collected at the end of each study, which were post-infection (p.i.) day 5 for the SI study and p.i. day 10 for the colon study. During tissue collection, the dissected colons were first cut open to remove fecal contents. Both lower SI and colon tissues were snap frozen in liquid nitrogen immediately upon tissue harvest. Total RNA were extracted from frozen intestine samples using the Qiagen RNeasy Midi Kit according to the manufacturer’s protocol.
Library preparation and sequencing were done in the Penn State Genomics Core Facility (University Park, PA). 200ng of RNA per sample were used as the input of TruSeq Stranded mRNA Library Prep kit to make barcoded libraries according to the manufacturer’s protocol (Illumina Inc. San Diego. CA. USA). The library concentration was determined by qPCR using the Library Quantification Kit Illumina Platforms (Kapa Biosystems. Boston. MA. USA). An equimolar pool of the barcoded libraries was made and the pool was sequencing on a HiSeq 2500 system (Illumina) in Rapid Run mode using single ended 150 (SI study) or 100 (colon study) base-pair reads.

treatment_protocol: Vitamin A deficient (VAD) and vitamin A sufficient (VAS) mice were generated. VAS or VAD diets were fed to pregnant mothers and the weanlings. VAS diet contained 25 μg of retinyl acetate per day whereas VAD diet did not contain any VA. At weaning, mice were maintained on their respective diets and assigned to one of the four treatment groups (non-infected VAD, infected VAD, non-infected VAS and infected VAS) until the end of the experiments. In terms of the oral inoculation of C. rodentium, bacteria were grown and cultured in Difco Luria-Bertani broth and agar (LB; Becton, Dickinson, & Co., Franklin Lakes, NJ) containing 50μg/mL nalidixic acid (Sigma Aldrich, St. Louis, MO, USA). Overnight cultures containing log phase bacteria were used to prepare oral inoculums. Individually housed mice (8-10 weeks of age) were fasted overnight and then gavaged with 5 × 10 9 CFU C. rodentium in 100 μl of sterile saline.

tag: age

value: 8-10 week

value: wild type


title: colon, infected VAS, replicate 1

description:
post-infection day 10
45b_S1
Colon_study_RawCounts.txt


title: colon, infected VAS, replicate 4

description:
post-infection day 10
49b_S1
Colon_study_RawCounts.txt


title: 3_E2_Norm_S206


title: colon, non-infected VAS, replicate 3

description:
not infected by C. rodentium
52b_S1
Colon_study_RawCounts.txt


title: 3_E3_Norm_S207


title: 3_E10_Hypo_S232


title: 3_E12_Hypo_S234


title: colon, non-infected VAS, replicate 1

description:
not infected by C. rodentium
43b_S1
Colon_study_RawCounts.txt


title: colon, non-infected VAS, replicate 2

description:
not infected by C. rodentium
51b_S1
Colon_study_RawCounts.txt


title: colon, infected VAD, replicate 5

description:
post-infection day 10
33b_S1
Colon_study_RawCounts.txt


title: colon, infected VAD, replicate 6

description:
post-infection day 10
34b_S1
Colon_study_RawCounts.txt


title: 3_E1_Norm_S205


title: 3_D9_Hypo_S183


title: 3_D8_Hypo_S182


title: colon, infected VAD, replicate 4

description:
post-infection day 10
31b_S1
Colon_study_RawCounts.txt


title: colon, infected VAS, replicate 2

description:
post-infection day 10
47b_S1
Colon_study_RawCounts.txt


title: colon, infected VAD, replicate 2

description:
post-infection day 10
26b_S1
Colon_study_RawCounts.txt


title: colon, infected VAD, replicate 3

description:
post-infection day 10
30b_S1
Colon_study_RawCounts.txt


title: colon, infected VAD, replicate 1

description:
post-infection day 10
25b_S1
Colon_study_RawCounts.txt


title: 3_D4_Norm_S160


title: colon, non-infected VAD, replicate 1

description:
not infected by C. rodentium
21b_S1
Colon_study_RawCounts.txt


title: 3_D7_Hypo_S181


title: 3_E4_Norm_S208


title: colon, non-infected VAD, replicate 3

description:
not infected by C. rodentium
23b_S1
Colon_study_RawCounts.txt


title: colon, non-infected VAD, replicate 2

description:
not infected by C. rodentium
22b_S1
Colon_study_RawCounts.txt


title: 3_D6_Norm_S162


title: 3_D2_Norm_S158


title: 3_D12_Hypo_S186


title: 3_D3_Norm_S159


title: 3_D5_Norm_S161


title: SI, infected VAS, replicate 1

description:
post-infection day 5
AT14_R1
SI_study_RawCounts.txt

source_name: SI-whole tissue

value: SI


title: SI, infected VAS, replicate 3

description:
post-infection day 5
AT16_R1
SI_study_RawCounts.txt


title: 3_E11_Hypo_S233

value: hypoxia


title: 3_D1_Norm_S157


title: 3_D11_Hypo_S185


title: SI, infected VAD, replicate 3

description:
post-infection day 5
AT9_R1
SI_study_RawCounts.txt


title: SI, infected VAD, replicate 2

description:
post-infection day 5
AT8_R1
SI_study_RawCounts.txt


title: 3_D10_Hypo_S184


title: SI, non-infected VAS, replicate 2

description:
not infected by C. rodentium
AT11_R1
SI_study_RawCounts.txt


title: 3_C8_Hypo_S134


title: 3_C5_Norm_S113


title: 3_C9_Hypo_S135


title: SI, non-infected VAS, replicate 1

description:
not infected by C. rodentium
AT10_R1
SI_study_RawCounts.txt


title: SI, infected VAD, replicate 1

description:
post-infection day 5
AT5_R1
SI_study_RawCounts.txt


title: 3_C3_Norm_S111


title: SI, non-infected VAD, replicate 1

description:
not infected by C. rodentium
AT1_R1
SI_study_RawCounts.txt


title: 3_C7_Hypo_S133


title: HF_Heavy-polysome_replicate-3

city: Rochester

first: Peng

last: Yao

address: 601 Elmwood Avenue

department: Medicine

institute: Aab Cardiovascular Research Institute

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - Trimmomatic-0.36 "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15"
MAPPING - STAR_2.5.2b "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - subread-1.5.0p3, featurecounts, "-s 2 -t exon -g gene_name"
Genome_build: GRCm38.p5 + Gencode-M12
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample

source_name: NIH/3T3 cells treated with 100 nM halofuginone at 37ºC for 24 hrs.

growth_protocol: NIH/3T3 cells were cultured in DMEM supplemented with 10% bovine calf serum (VWR) and 1% penicillin/streptomycin (ThermoFisher) at 37ºC.

extract_protocol:
The RNA extraction was performed using TRIzol reagent (ThermoFisher) following instructions in the manual. For the cell samples, total RNA was extracted using regular TRIzol reagent (1 ml for a plate of cells) and placed at room temperatur for 5 mins to lyse the cells. For the polysome profiling fraction samples, RNA extraction was performed using TRIzol LS reagent at a volume ratio of 1:3 following the manual.
Illumina TruSeq Stranded mRNA

treatment_protocol: NIH/3T3 cells were grown to ~60-70% confluency and treated with 100 nM halofuginone or the same volume of vehicle (PBS) at 37ºC for 24 hrs.

value: mouse fibroblasts


title: SI, non-infected VAD, replicate 2

description:
not infected by C. rodentium
AT2_R1
SI_study_RawCounts.txt


title: SI, non-infected VAS, replicate 3

description:
not infected by C. rodentium
AT12_R1
SI_study_RawCounts.txt


title: 3_C4_Norm_S112


title: 3_C2_Norm_S110


title: SI, infected VAS, replicate 2

description:
post-infection day 5
AT15_R1
SI_study_RawCounts.txt


title: 3_C11_Hypo_S137


title: HF_Heavy-polysome_replicate-2


title: 3_C6_Norm_S114


title: 3_C10_Hypo_S136


title: HF_Heavy-polysome_replicate-1


title: HF_Light-polysome_replicate-2


title: 3_B9_Hypo_S87


title: HF_Light-polysome_replicate-3


title: 3_C1_Norm_S109


title: HF_Light-polysome_replicate-1


title: HF_Ribosome-free_replicate-2


title: HF_Ribosome-free_replicate-3


title: HF_Ribosome-free_replicate-1


title: 3_B7_Hypo_S85


title: 3_B6_Norm_S66


title: 3_B8_Hypo_S86


title: SI, non-infected VAD, replicate 3

description:
not infected by C. rodentium
AT3_R1
SI_study_RawCounts.txt


title: HF_Total-RNA_replicate-2


title: Vehicle_Heavy-polysome_replicate-3

source_name: NIH/3T3 cells treated with 100 nM PBS at 37ºC for 24 hrs.


title: 3_B5_Norm_S65


title: 3_B4_Norm_S64


title: 3_B12_Hypo_S90


title: HF_Total-RNA_replicate-1


title: 3_B3_Norm_S63


title: 3_C12_Hypo_S138


title: Vehicle_Heavy-polysome_replicate-2


title: 3_B11_Hypo_S89


title: 3_B2_Norm_S62


title: Vehicle_Heavy-polysome_replicate-1


title: 3_B10_Hypo_S88


title: Vehicle_Light-polysome_replicate-2


title: 3_A9_Hypo_S39


title: Vehicle_Light-polysome_replicate-1


title: HF_Total-RNA_replicate-3


title: Vehicle_Ribosome-free_replicate-3


title: 3_A8_Hypo_S38


title: Vehicle_Ribosome-free_replicate-2


title: 3_A7_Hypo_S37


title: Vehicle_Total-RNA_replicate-3


title: Vehicle_Total-RNA_replicate-2


title: 3_A6_Norm_S18


title: Vehicle_Total-RNA_replicate-1


title: Vehicle_Ribosome-free_replicate-1


title: 3_A5_Norm_S17


title: MS-5_3; Sample_7A

city: Uppsala

first: Gustav

last: Arvidsson

state: Uppsala

address: Husargatan 3

department: Department of Medical Sciences

country: Sweden

institute: Uppsala Universitet

data_processing:
Short reads were indexed using the species-based short read separation software Xenome (v1.0.1) for human and mouse based on the ENSEMBL reference genomes specified below.
Species-specific PE short reads of human and murine origin were aligned to reference genomes GRCh38 and GRCm38 respectively using the splice aware short read aligner STAR (v2.5.1b) using PE read input with default options and –sjdbGTFfile pointing to the ENSEMBL .gtf annotation file corresponding to the reference genome file and –outFilterMultimapNmax set to 1.
Species specific read pairs were assigned to known features and counted using featurecounts from the Subread package (v1.5.2). Annotated genes were obtained from the Ensembl ftp repository (Homo_sapiens.GRCh38.87.gtf and Mus_musculus.GRCm38.87.gtf).
Data was later interrogated for differentially expressed genes using the Bioconductor package EdgeR (v3.22.5).
Genome_build: GRCh38.87 and GRCm38.87 were downloaded from the ENSEMBL ftp repository
Supplementary_files_format_and_content: GRCh38_featurecounts_count_table.csv: RAW read count table per feature for all samples with human content after species-based separation of reads of human origin and alignment to GRCh38. The count table contain count data for files from the current GEO accession number and for files originating from accession number GSE99501 processed using the present workflow.
Supplementary_files_format_and_content: GRCm38_featurecounts_count_table.csv: RAW read count table per feature for all samples with mouse content after species-based separation of reads of murine origin and alignment to GRCm38. The count table contain count data for files from the current GEO accession number and for files originating from accession number GSE99501 processed using the present workflow.

molecule: polyA RNA

growth_protocol: MS-5 cells and Rec-1 cells mono- or co-cultured in αMEM-glutamax (Gibco) supplemented with 10% H.I. FBS (Gibco), 2mM sodium pyruvate, 100U/mL penicillin and 100µg/mL streptomycin (Gibco). All cells were cultivated in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy (Qiagen) with QIAshredders following the protocol supplied by the manufacturer.
Libraries were constructed using Illumina Truseq 2.0 reagents according to manufacturers protocol, mRNA was purified by poly-T oligo-attached magnetic beads.

treatment_protocol: 5x10^5 MS-5 stromal cells were seeded 24h in advance to 10cm dishes and 5x10^6 Rec-1 cells were subsequently added. RNA was extracted following 24h of incubation at 37 degrees 5% CO2.

tag: cultivation

value: mono-cultured cell line

value: bone marrow derived stromal cell line


title: 3_A3_Norm_S15

tag: lane


title: MS-5_4; Sample_8A


title: 3_A12_Hypo_S42

tag: plate-position


title: MS-5_2; Sample_6A

tag: cell line


title: 3_A2_Norm_S14

tag: condition


title: 3_A11_Hypo_S41

tag: sample-identity


title: Vehicle_Light-polysome_replicate-3

tag: tissue


title: MS-5_1; Sample_5A

value: mouse bone marrow derived stromal cell line


title: 3_A10_Hypo_S40


title: 2_H9_Hypo_S369


title: BRG1_ChIP_CAL-120_Infigratinib_4hr_3

city: Boston

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

description: CAL-120 cells treated with infigratinib for 4h

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: breast cancer cells

growth_protocol: CAL-120 cells were cultured in DMEM plus 10% FBS

extract_protocol:
Cells were then lysed with 1% SDS lysis buffer (1% SDS, 10mM EDTA (pH=8), 50mM Tris-HCl (pH=8)) containing protease and deacetylase inhibitors, and sonicated for 5 min with settings of PIP 140, DF 5%, cpb 200 on a Covaris E220 (Covaris Inc., Woburn, MA) to obtain 200-600bp chromatin fragments.
libraries were constructed from 2 ng of DNA, using the ThruPLEX DNA-seq kit (#R400427, Rubicon Genomics), according to the manufacturer’s protocol; finished libraries were quantified by the Qubit dsDNA High-Sensitivity Assay Kit (#32854, Thermo Fisher Scientific), by an Agilent TapeStation 2200 system using D1000 ScreenTape (# 5067-5582, Agilent), and by RT-qPCR using the KAPA library quantification kit (# KK4835, Kapa Biosystems), according to the manufacturers’ protocols; ChIP-seq libraries were uniquely indexed in equimolar ratios, and sequenced to a target depth of 40M reads on an Illumina NextSeq500 run, with single-end 75bp reads.

treatment_protocol: CAL-120 cells were treated with DMSO or 300nM infigratinib.

tag: chip antibody

tag: chip antibody manufacturer

value: abcam

tag: chip antibody catalog number


title: 3_A1_Norm_S13


title: BRG1_ChIP_CAL-120_Infigratinib_12d_3

description: CAL-120 cells treated with infigratinib for 12d

tag: treatment


title: 2_H8_Hypo_S368


title: BRG1_ChIP_CAL-120_Infigratinib_4hr_2


title: BRG1_ChIP_CAL-120_Infigratinib_12d_2


title: BRG1_ChIP_CAL-120_Infigratinib_12d_1


title: 2_H7_Hypo_S367


title: 2_H6_Norm_S348


title: BRG1_ChIP_CAL-120_Infigratinib_4hr_1


title: 2_H4_Norm_S346


title: 2_H5_Norm_S347


title: 3_A4_Norm_S16


title: 2_H3_Norm_S345


title: 2_H2_Norm_S344


title: 3_B1_Norm_S61


title: 2_H12_Hypo_S372


title: 2_H11_Hypo_S371


title: 2_H10_Hypo_S370


title: 2_H1_Norm_S343


title: 2_G9_Hypo_S321


title: 2_G8_Hypo_S320


title: 2_G7_Hypo_S319


title: HUVEC_Control_sample_04

city: Melbourne

first: Tyrone

last: Chen

state: VIC

address: 305 Grattan St

department: Bioinformatics Core (RRID: SCR_025901); Organogenesis and Cancer Program

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Raw_counts.csv
Normalised_log2_CPM.csv

data_processing:
Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings
An aberrant sample DDX21_siRNA_01_sample_01 was removed. The file is included for reference only.
Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr, calcNormFactors and cpm
For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied
Genome_build: HS_GRCh38.97
Supplementary_files_format_and_content: Matrix table with normalised, batch corredted and log2 transformed CPM for every gene and every sample

extract_protocol: RNA-Seq libraries were prepared from purified total RNA using a modified Smart-Seq2 protocol developed by Picelli et al. (ref. 1, 2). 2 ng of purified total RNA (0.4 ng/µL) was combined with 1 µL of 10 µM oligo-dT primer (/5Biosg/AAGCAGTGGTATCAACGCAGAGTACT30VN; Integrated DNA Technologies) and 1 µL of dNTP mix (10 mM each; Invitrogen, y02256), then the protocol was continued as described (ref. 2). Briefly, the RNA was reverse transcribed with the Smart-Seq2 TSO (/5Biosg/AAGCAGTGGTATCAACGCAGAGTACATrGrGrG, Integrated DNA Technologies), followed by 12 cycles of PCR amplification to obtain enough cDNA to prepare a library. Volumes of reagents were scaled accordingly to maintain final concentration ratios as in the original protocol, except for the PCR preamplification where the Smart-Seq2 ISPCR primer (/5Biosg/AAGCAGTGGTATCAACGCAGAGT; Integrated DNA Technologies) was added to a final concentration of 0.25 µM. 0.5 ng of cDNA was prepped into a library using the Nextera XT DNA Library Prep Kit (Illumina, FC-131-1096), with 12 cycles of PCR used to amplify the final library. The final Nextera XT libraries were quantified on the Agilent Bioanalyzer with the High Sensitivity DNA kit (Agilent Technologies, 5067-4626). Libraries were pooled in equimolar ratios.

tag: cell type

value: HUVEC

tag: genotype

value: control

tag: abbreviatedname


title: HUVEC_DDX21_siRNA_01_sample_04

description:
Raw_counts.csv
Normalised_log2_CPM.csv

value: DDX21 knockdown (1)


title: HUVEC_DDX21_siRNA_02_sample_02

description:
Raw_counts.csv
Normalised_log2_CPM.csv

value: DDX21 knockdown (2)


title: HUVEC_Control_sample_03

description:
Raw_counts.csv
Normalised_log2_CPM.csv


title: HUVEC_DDX21_siRNA_01_sample_03

description:
Raw_counts.csv
Normalised_log2_CPM.csv


title: HUVEC_DDX21_siRNA_02_sample_01

description:
Raw_counts.csv
Normalised_log2_CPM.csv


title: HUVEC_DDX21_siRNA_01_sample_01

description:
Raw_counts.csv: NA
Normalised_log2_CPM.csv: NA
An aberrant sample DDX21_siRNA_01_sample_01 was removed. The file is included for reference only.


title: 2_G5_Norm_S299

value: Norm


title: HUVEC_Control_sample_02

description:
Raw_counts.csv
Normalised_log2_CPM.csv


title: HUVEC_DDX21_siRNA_01_sample_02

description:
Raw_counts.csv
Normalised_log2_CPM.csv


title: HUVEC_Control_sample_01

description:
Raw_counts.csv
Normalised_log2_CPM.csv


title: 2_G6_Norm_S300


title: 2_G3_Norm_S297


title: 2_G2_Norm_S296


title: 2_G11_Hypo_S323


title: 2_G10_Hypo_S322


title: BRG1_ChIP_CAL-120_DMSO_3

description: CAL-120 cells treated with infigratinib for 48h

treatment_protocol: CAL-120 cells were treated with DMSO or  300nM infigratinib, or gene knockout

value: DMSO


title: H3k27ac_ChIP_BRG_KO1_REP1

description: CAL-120 knocked out with BRG1

value: Diagenode


title: H3k27ac_ChIP_AAVS1_KO_REP1

description: CAL-120 knocked out with AAVS1


title: H3k27ac_ChIP_BRG_KO1_REP2

description: CAL-120 knocked out with BRG1


title: 2_G1_Norm_S295


title: BRG1_ChIP_CAL-120_Infigratinib_2d_3

description: CAL-120 cells treated with DMSO


title: BRG1_ChIP_CAL-120_Infigratinib_2d_2


title: 2_G4_Norm_S298


title: BRG1_ChIP_CAL-120_DMSO_2

description: CAL-120 cells treated with DMSO


title: HUVEC_DDX21_siRNA_02_sample_04

description:
Raw_counts.csv
Normalised_log2_CPM.csv


title: H3k27ac_ChIP_AAVS1_KO_REP2

description: CAL-120 knocked out with AAVS1


title: 2_F7_Hypo_S271


title: YAP_ChIP_CAL-120_Infigratinib_12d_2

value: YAP

value: Cell signaling Technology


title: BRG1_ChIP_CAL-120_DMSO_1

description: CAL-120 cells treated with DMSO


title: 2_F6_Norm_S252


title: YAP_ChIP_CAL-120_DMSO_2

description: CAL-120 cells treated with DMSO


title: 2_G12_Hypo_S324


title: 2_F8_Hypo_S272


title: 2_F9_Hypo_S273


title: 2_F4_Norm_S250


title: YAP_ChIP_CAL-120_Infigratinib_2d_2


title: YAP_ChIP_CAL-120_Infigratinib_4h_2


title: 2_F2_Norm_S248


title: K27ac_ChIP_CAL-120_Infigratinib_12d_2


title: 2_F3_Norm_S249


title: K27ac_ChIP_CAL-120_Infigratinib_2d_2


title: K27ac_ChIP_CAL-120_Infigratinib_4h_2


title: K27ac_ChIP_CAL-120_DMSO_2

description: CAL-120 cells treated with DMSO


title: HUVEC_DDX21_siRNA_02_sample_03

description:
Raw_counts.csv
Normalised_log2_CPM.csv


title: 2_F11_Hypo_S275


title: 2_F10_Hypo_S274


title: BRG1_ChIP_CAL-120_Infigratinib_2d_1


title: 2_F5_Norm_S251


title: YAP_ChIP_CAL-120_Infigratinib_2d_1


title: YAP_ChIP_CAL-120_Infigratinib_12d_1


title: 2_F1_Norm_S247


title: 2_E9_Hypo_S225


title: 2_E7_Hypo_S223


title: 2_E5_Norm_S203


title: 2_E4_Norm_S202


title: 2_E3_Norm_S201


title: YAP_ChIP_CAL-120_DMSO_1

description: CAL-120 cells treated with DMSO


title: CAL-120_Infigratinib_12D_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina Bcl2fastq v2.18
Reads were aligned to mm10 using STAR
For fpkm calculation cufflinks was used.
Genome_build: hg19
Supplementary_files_format_and_content: csv file of FPKM table

extract_protocol:
RNA was extracted from cells with the RNeasy Mini Kit (Qiagen).
The Dana-Farber Cancer Institute Molecular Biology Core Facilities prepared libraries from 500 ng of purified total RNA, using RNA sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit (NEB #E7760).  according to the manufacturer’s protocol; finished libraries were quantified by the Qubit dsDNA High-Sensitivity Assay Kit (#32854, Thermo Fisher Scientific), by an Agilent TapeStation 2200 system using D1000 ScreenTape (# 5067-5582, Agilent), and by RT-qPCR using the KAPA library quantification kit (# KK4835, Kapa Biosystems), according to the manufacturers’ protocols; pooled uniquely indexed RNA-seq libraries in equimolar ratios, and sequenced these to a target depth of 40M reads on an Illumina NextSeq500 run with single-end 75bp reads.

treatment_protocol: CAL-120 cells were treated with DMSO or  300nM infigratinib, gene knockouts

value: infigratinib for 12d


title: K27ac_ChIP_CAL-120_Infigratinib_12d_1


title: K27ac_ChIP_CAL-120_Infigratinib_2d_1


title: K27ac_ChIP_CAL-120_Infigratinib_4h_1


title: 2_E12_Hypo_S228


title: 2_F12_Hypo_S276


title: CAL-120_Infigratinib_12D_3


title: 2_E2_Norm_S200


title: CAL-120_Infigratinib_12D_1


title: 2_E11_Hypo_S227


title: 2_E1_Norm_S199


title: 2_E8_Hypo_S224


title: CAL-120_DMSO_3

description: CAL-120 cells treated with DMSO


title: 2_E10_Hypo_S226


title: YAP_ChIP_CAL-120_Infigratinib_4h_1


title: 2_D9_Hypo_S177


title: 2_D8_Hypo_S176


title: CAL-120_Infigratinib48H_2

value: infigratinib for 48h


title: CAL-120_DMSO_1

description: CAL-120 cells treated with DMSO


title: CAL-120_Infigratinib_4H_2

value: infigratinib for 4h


title: CAL-120_Infigratinib_48H_1


title: 2_D7_Hypo_S175

value: hypoxia


title: 2_E6_Norm_S204


title: 2_D6_Norm_S156


title: 2_D5_Norm_S155


title: MCF7_Day0

description:
Genome wide CRISPR KO screen
MCF7.counts.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
CRISPR library and data were analyzed by MAGeCK and MAGeCK-VISPR
Genome_build: hg19
Supplementary_files_format_and_content: csv file of sgRNA counts table

growth_protocol: The following cell lines were purchased from ATCC: CAL-120,  MCF7, MDA-MB-231, and MCF10A.  All cell lines were cultured in growth medium as specified by the manufacturer, and maintained at 37°C with 5% CO2. The cells were stored in liquid nitrogen at early passages and were cultured within 20 doublings.All cell lines have been authenticated by STR profiling at the Dana-Farber Cancer Institute.

extract_protocol:
Genomic DNA was extracted using the Blood & Cell Culture DNA Midi Kit (Qiagen),
3 rounds of PCR for library preparation. Each library was sequenced to generate 20~40 million reads, to achieve an average CRISPR library coverage of 200~300 ×.

treatment_protocol: CAL-120 cells were treated with DMSO or  300nM infigratinib for 35day


title: 2_D3_Norm_S153


title: CAL-120_infigratinib_4H_1


title: 2_D2_Norm_S152


title: MCF7_Day35


title: K27ac_ChIP_CAL-120_DMSO_1

description: CAL-120 cells treated with DMSO


title: 2_D4_Norm_S154


title: MCF10A_Day35

description:
Genome wide CRISPR KO screen
MCF10A.counts.txt


title: CAL-120_Iinfi_Day35

description:
Genome wide CRISPR KO screen
CAL-120.counts.txt


title: 2_D11_Hypo_S179


title: CAL-120_DMSO_2

description: CAL-120 cells treated with DMSO


title: CAL-120_DMSO_Day35


title: CAL-120_Day0


title: 2_D1_Norm_S151


title: 2_C9_Hypo_S129


title: 2_D12_Hypo_S180


title: HCT116 PUM2 knockdown replicate 3

city: Galveston

first: Nathan

middle: David

last: Elrod

state: TX

address: 1005 Strand Street

department: BMB

institute: University of Texas Medical Branch at Galveston

description: PAC-seq of Total RNA isolated from HCT116 cells treated with PUM2 siRNA

data_processing:
adapters were trimmed and reads with Q<30 were sicarded using fastp ver 0.14.1 using DPAC ver 1.14 wrapper script (Routh 2020)
alignments were made using Hisat2 version 2.1.0
bedgraphs were generated using bedtools (ver 2.26.0) genomecoverage -split -3
Genome_build: hg38
Supplementary_files_format_and_content: bed

source_name: Colon epithelial

growth_protocol: HCT116 cells were grown at 37°C with 5% CO2 in DMEM, supplemented with 10% (v/v) FBS and 1% (v/v) penicillin-streptomycin.

extract_protocol:
HCT116 cells were harvested after 48 hours RNAi treatment using SimplyRNA cells kit and Maxwell RSC instrument (Promega).
Using the purified RNA, PAC-seq libraries were prepared as previously described (Routh et al. 2017). One μg of total RNA was reverse transcribed with the partial P7 adapter (Illumina_4N_21T) and dNTPs with the addition of spiked-in azido-nucleotides (AzVTPs) at 5:1. The p5 adapter (IDT) was Click-ligated to the 5′end of the cDNA with CuAAC. The cDNA was then amplified for 16 cycles using the Universal primer and 3′ indexing primer, followed by purification on a 2% agarose gel with extraction of the 200-300 base pair amplicon. Barcoded libraries were then pooled and sequenced with single-end, 150 base-pair reads on a Nextseq 550 (Illumina)

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour PUM2 siRNAs (25 nM) using Dharmafect 4 knockdown replicate 3

tag: cell supplier

value: ATCC CCL-247

value: PUM2 knockdown


title: 2_C6_Norm_S108


title: HCT116 PUM2 knockdown replicate 1

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour PUM2 siRNAs (25 nM) using Dharmafect 4 knockdown replicate 1


title: HCT116 PUM1 knockdown replicate 3

description: PAC-seq of Total RNA isolated from HCT116 cells treated with PUM1 siRNA

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour PUM1 siRNAs (25 nM) using Dharmafect 4 knockdown replicate 3

value: PUM1 knockdown


title: 2_C5_Norm_S107


title: MCF10A_Day0


title: HCT116 PUM2 knockdown replicate 2

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour PUM2 siRNAs (25 nM) using Dharmafect 4 knockdown replicate 2


title: 2_C8_Hypo_S128


title: 2_C3_Norm_S105


title: 2_C7_Hypo_S127


title: HCT116 PUM1 PUM2 knockdown replicate 3

description: PAC-seq of Total RNA isolated from HCT116 cells treated with PUM1 and PUM2 siRNA

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour PUM1 PUM2 siRNAs (25 nM ea) using Dharmafect 4knockdown replicate 3

value: PUM1 PUM2 knockdown


title: HCT116 PUM1 PUM2 knockdown replicate 1

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour PUM1 PUM2 siRNAs (25 nM ea) using Dharmafect 4knockdown replicate 1


title: 2_C2_Norm_S104


title: HCT116 PUM1 knockdown replicate 2

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour PUM1 siRNAs (25 nM) using Dharmafect 4 knockdown replicate 2


title: HCT116 PUM1 PUM2 knockdown replicate 2

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour PUM1 PUM2 siRNAs (25 nM ea) using Dharmafect 4knockdown replicate 2


title: HCT116 CNOT7 CNOT8 knockdown replicate 2

description: PAC-seq of Total RNA isolated from HCT116 cells treated with CNOT7 and CNOT8 siRNA

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour CNOT7 CNOT8 siRNAs (25 nM ea) using Dharmafect 4 knockdown replicate 2

value: CNOT7 CNOT8 knockdown


title: 2_D10_Hypo_S178


title: 2_C11_Hypo_S131


title: HCT116 CNOT7 CNOT8 knockdown replicate 3

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour CNOT7 CNOT8 siRNAs (25 nM ea) using Dharmafect 4 knockdown replicate 3


title: HCT116 PUM1 knockdown replicate 1

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour PUM1 siRNAs (25 nM) using Dharmafect 4 knockdown replicate 1


title: 2_C10_Hypo_S130


title: 2_C1_Norm_S103


title: HCT116 CNOT7 CNOT8 knockdown replicate 1

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour CNOT7 CNOT8 siRNAs (25 nM ea) using Dharmafect 4 knockdown replicate 1


title: 2_B9_Hypo_S81


title: HCT116 CNOT1 knockdown replicate 3

description: PAC-seq of Total RNA isolated from HCT116 cells treated with CNOT1 siRNA

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour CNOT1 siRNAs (25 nM) using Dharmafect 4 knockdown replicate 3

value: CNOT1 knockdown


title: HCT116 CNOT1 knockdown replicate 2

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour CNOT1 siRNAs (25 nM) using Dharmafect 4 knockdown replicate 2


title: 2_B8_Hypo_S80


title: HCT116 CNOT1 knockdown replicate 1

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour CNOT1 siRNAs (25 nM) using Dharmafect 4 knockdown replicate 1


title: HCT116 Control replicate 3

description: PAC-seq of Total RNA isolated from HCT116 cells treated with control siRNA

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour Control siRNAs (25 nM) using Dharmafect 4 replicate 3

value: Control


title: 2_C4_Norm_S106


title: 2_B5_Norm_S59


title: 2_B6_Norm_S60


title: HCT116 Control replicate 2

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour Control siRNAs (25 nM) using Dharmafect 4 replicate 2


title: HCT116 Control replicate 1

treatment_protocol: HCT116 cells were plated 10^5 in 6-well plates for 24 hours folled by 48 hour Control siRNAs (25 nM) using Dharmafect 4 replicate 1


title: 2_B7_Hypo_S79


title: Control_3

city: Vari

first: Panagiota

last: Kafasla

address: 34 Fleming Str

department: IFBR

country: Greece

institute: B.S.R.C. "Al. Fleming"

data_processing:
Vertebrate Alternative Splicing and Transcription Tools (VAST-TOOLS) used for splicing quatification.
Sequenced reads were analised using VAST-TOOLS v2.2.2 mapped to hg38 whole genome
A minimum junction read coverage of 10 actual reads per sample was required, as described (Irimia et al., 2014). PSI values for single replicates were quantified for all types of alternative events, including single and complex cassette exons (S, C1, C2, C3, ANN), microexons (MIC) alternative 5’ss and 3’ss (Alt5, Alt3) and retained introns (IR-S, IR-C). A minimum ∆PSI of 15% was required to define differentially spliced events , as well as a minimum range of 5% between the PSI values of the two groups.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include PSI values for each Sample
Supplementary_files_format_and_content: alternative splicing quantification

extract_protocol:
RNA was harvested using Trizol reagent and treated with RQ1 DNase. IlluminaRNA Sample Prep Kit (TruSeq® Stranded mRNA Library Prep, Cat#20020594) was used with 1ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gastric cancer cell line


title: 2_C12_Hypo_S132


title: 2_B3_Norm_S57

value: Norm


title: 2_B4_Norm_S58


title: Control_2


title: 2_B2_Norm_S56


title: 2_B12_Hypo_S84


title: Control_1


title: 2_B11_Hypo_S83


title: IQGAP1 Knock-out 1


title: 2_B10_Hypo_S82


title: RZ-2994 treated Day 3 Rep 3

city: Cambridge

first: Gabriela

last: Alexe

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

description: KOPTK1 cells were grown in the presence of 2µM RZ-2994 vs DMSO, and cells collected at 24 and 72 hours of treatment. Three samples were collected per treatment condition per time point.  RNA was extracted from cells with an RNeasy Kit (Qiagen).

data_processing:
Illumina NextSeq 500 / Illumina Four-Channel SBS Sequencing  for base calling
Quality control tests for the mapped reads were performed using the FASTQC software (www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads were aligned to the GRCh37/hg19 human genes by using STAR v2.72b (Dobin et al., 2013) with standard parameters. Quality control tests for the aligned reads and for the replicate consistency were performed by using the qualimap v2.2 (Garcia-Alcalde et al., 2012) and the SARTools (Hugo Varet, 2015) pipelines.
Gene level reads(counts) were computed using the Feature Counts method implemented in the Bioconductor v3.10 RSubread package (Liao et al., 2014).
Differential gene expression was computed based on apeglm shrinkage fold change by using DESeq2 (Bioconductor v3.9)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include reads(counts) values for each sample.

source_name: KOPTK1 cell line

extract_protocol:
RNA was extracted from cells with an RNeasy Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2µM RZ-2994 vs DMSO, separately at 24 hours and 72 hours of treatment

tag: time

value: Day 3

tag: disease

value: T-ALL

tag: replicate

value: rep 3


title: RZ-2994 treated Day 3 Rep 2

growth_protocol: KOPTK1 cells were grown in the presence of 2µM RZ-2994 vs DMSO, and cells collected at 24 and 72 hours of treatment.

value: rep 2


title: 2_B1_Norm_S55

tag: lane


title: 2_A9_Hypo_S33

tag: plate-position


title: DMSO treated Day 3 Rep 3

tag: cell line

value: DMSO


title: DMSO treated Day 3 Rep 2


title: 2_A6_Norm_S12

tag: condition


title: IQGAP1 Knock-out 2


title: RZ-2994 treated Day 3 Rep 1

value: rep 1


title: DMSO treated Day 3 Rep 1


title: 2_A5_Norm_S11

tag: sample-identity


title: RZ-2994 treated Day 1 Rep 3

value: Day 1


title: 2_A3_Norm_S9


title: 2_A2_Norm_S8


title: RZ-2994 treated Day 1 Rep 2


title: RZ-2994 treated Day 1 Rep 1


title: DMSO treated Day 1 Rep 3


title: DMSO treated Day 1 Rep 2


title: DMSO treated Day 1 Rep 1


title: 2_A11_Hypo_S35

value: hypoxia


title: 2_A12_Hypo_S36


title: 2_A1_Norm_S7


title: 2_A8_Hypo_S32


title: 2_A7_Hypo_S31


title: 1_H9_Hypo_S363


title: 1_H8_Hypo_S362


title: 1_H7_Hypo_S361


title: 2_A4_Norm_S10


title: 1_H5_Norm_S341


title: 1_H6_Norm_S342


title: 1_H3_Norm_S339


title: 1_H4_Norm_S340


title: 2_A10_Hypo_S34


title: 1_H12_Hypo_S366


title: 1_H10_Hypo_S364


title: 1_H11_Hypo_S365


title: 1_H2_Norm_S338


title: 1_H1_Norm_S337


title: 26 thymus GFP- Tcon

city: Hannover

first: Christoph

last: Binz

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Institut für Immunologie

institute: Medizinische Hochschule Hannover

data_processing:
Fastq files were obtained after demultiplexing, basecalling and quality filtering during the sequencing run on a MiSeq machine.
Data were aligned to the IMGT database from 22.05.2018 using MiXCR (Bolotin, D. A., S. Poslavsky, I. Mitrophanov, M. Shugay, I. Z. Mamedov, E. V. Putintseva, and D. M. Chudakov. 2015. MiXCR: software for comprehensive adaptive immunity profiling. Nature methods 12: 380-381.)
Afterwards the samples were downsampled (Thymus samples to 20000 and spleen samples to 30000) using VDJTOOLS (Shugay, M., D. V. Bagaev, M. A. Turchaninova, D. A. Bolotin, O. V. Britanova, E. V. Putintseva, M. V. Pogorelyy, V. I. Nazarov, I. V. Zvyagin, V. I. Kirgizova, K. I. Kirgizov, E. V. Skorobogatova, and D. M. Chudakov. 2015. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLoS Comput. Biol. 11: e1004503.).
Supplementary_files_format_and_content: VDJTOOLS.txt files were generated using MiXCR.

source_name: thymus

extract_protocol:
The desired populations were sorted and the RNA was isolated employing the "RNeasy Plus Micro kit" from Qiagen (Hilden, Germany).
The cDNA was generated by employing ingredients from the TAKARA cDNA Synthesis Kit (TAKARA Bio Europe, France) according to an in-house modified protocol based on the manufacturer’s protocol. The DNA-amplicons for the Illumina sequencing were generated by using Advantage 2 PCR Kit (TAKARA Bio Europe, France). The DNA was then purified using Qiaquick Gel Extraction Kit (Qiagen Hilden, Germany). The purified product of each sample was indexed by an indexing-PCR with Nextera-Primers. Finally a pool of the samples was sequenced employing Illumina MiSeq v2 Reagent Kit (Illumina Inc, San Diego, CA, USA).

tag: strain

value: Foxp3hCD2 x RAG1GFP reporter mice (C57BL/6 background)

tag: population

value: CD4SP RAGGFP-CD25-Foxp3hCD2-

value: IAV, 10 dpi


title: Liver tissue  from YAP KO mice (AAV8-TBG-CRE treated) at Day 0 after TCPOBOP administration_rep2

type: RNA

city: Pittsburgh

first: George

middle: K.

last: Michalopoulos

state: Pennsylvania

address: 200 Lothrop Street

institute: University of Pittsburgh

description: Gene expression data at Day 0 post-TCPOBOP in YAP-KO mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: YAP KO mice liver tissue Day 0 post-TCPOBOP

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Following hepatocyte-specific deletion of YAP using AAV8-TBG-CRE, mice were treated with chemical mitogen TCPOBOP and liver tissues harvested at 0, 1, and 2 days after TCPOBOP treatment.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: 8-12 weeks old female YAPfl/fl mice were administered AAV8.TBG.PI.Cre.rBG (2.5 E11 viral particles per mouse, i.p.) to obtain hepatocyte specific YAP KO mice. AAV8.TBG.PI.eGFP.WPRE.bGH8 (2.5 E11 viral particles per mouse, i.p.) administered to YAPfl/fl mice served as wild-type (WT) control. Single dose of TCPOBOP (3 mg/kg; prepared in corn oil) was administered by oral gavage 10 days after AAV8 injection. Mice were sacrificed at various time points (0, 1 and 2 days) after TCPOBOP administration. Day 0 animals did not receive any treatment except AAV8 administration.

value: Day 0 post-TCPOBOP

value: YAP KO (hepatocyte-specific)

tag: mice

value: YAP fl/fl mice

tag: gender

value: female

tag: tissue

value: liver


title: Liver tissue  from YAP KO mice (AAV8-TBG-CRE treated) at Day 1 after TCPOBOP administration_pooled

description: Gene expression data at Day 1 post-TCPOBOP in YAP-KO mice

source_name: YAP KO mice liver tissue Day 1 post-TCPOBOP

tag: treatment

value: Day 1 post-TCPOBOP


title: 1_G9_Hypo_S315

data_processing:
Analysis of the data was performed using CGAT tools and pipelines (https://github.com/cgat-developers)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2 v2.1.0 with parameters --score-min L,0.0,-0.2
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files of read counts for each sample

extract_protocol:
Full length RNA-seq (Smartseq2)
Libraries were constructed using the smartseq2 protocol accoring to manufacturers instructions


title: Liver tissue  from YAP KO mice (AAV8-TBG-CRE treated) at Day 2 after TCPOBOP administration_rep3

description: Gene expression data at Day 2 post-TCPOBOP in YAP-KO mice

source_name: YAP KO mice liver tissue Day 2 post-TCPOBOP

value: Day 2 post-TCPOBOP

tag: genotype


title: Liver tissue  from YAP KO mice (AAV8-TBG-CRE treated) at Day 0 after TCPOBOP administration_rep1


title: Liver tissue  from WT mice (AAV8-TBG-GFP treated) at Day 2 after TCPOBOP administration_rep3

description: Gene expression data at Day 2 post-TCPOBOP in WT (control) mice

source_name: Control (WT) mice liver tissue Day 2 post-TCPOBOP

value: WT


title: Liver tissue  from YAP KO mice (AAV8-TBG-CRE treated) at Day 2 after TCPOBOP administration_rep2


title: 26 thymus GFP+ Tcon

value: CD4SP RAGGFP+CD25-Foxp3hCD2-


title: Liver tissue  from WT mice (AAV8-TBG-GFP treated) at Day 2 after TCPOBOP administration_rep2


title: 26 thymus GFP- Treg

value: CD4SP RAGGFP-CD25+Foxp3hCD2+


title: 26 thymus GFP+ Treg

value: CD4SP RAGGFP+CD25+Foxp3hCD2+


title: 1_G7_Hypo_S313


title: 25 thymus GFP- Tcon


title: 1_G6_Norm_S294

value: Norm


title: Liver tissue  from WT mice (AAV8-TBG-GFP treated) at Day 0 after TCPOBOP administration_rep1

description: Gene expression data at Day 0 post-TCPOBOP in WT (control) mice

source_name: Control (WT) mice liver tissue Day 0 post-TCPOBOP


title: Liver tissue  from WT mice (AAV8-TBG-GFP treated) at Day 0 after TCPOBOP administration_rep2


title: 1_G3_Norm_S291


title: 25 thymus GFP+ Tcon


title: 1_G2_Norm_S290


title: 1_G12_Hypo_S318


title: 25 thymus GFP+ Treg


title: 24 thymus GFP- Treg


title: Liver tissue  from WT mice (AAV8-TBG-GFP treated) at Day 1 after TCPOBOP administration_pooled

description: Gene expression data at Day 1 post-TCPOBOP in WT (control) mice

source_name: Control (WT) mice liver tissue Day 1 post-TCPOBOP


title: 1_G11_Hypo_S317


title: 24 thymus GFP+ Tcon


title: 1_G4_Norm_S292


title: 1_G8_Hypo_S314


title: 23 thymus GFP- Treg


title: 1_F9_Hypo_S267


title: 1_G5_Norm_S293


title: 1_G10_Hypo_S316


title: 23 thymus GFP- Tcon


title: 25 thymus GFP- Treg


title: 24 thymus GFP- Tcon


title: 1_F8_Hypo_S266


title: 23 thymus GFP+ Tcon


title: 22 thymus GFP- Tcon


title: 22 thymus GFP- Treg


title: 1_F7_Hypo_S265


title: 1_G1_Norm_S289


title: 1_F5_Norm_S245


title: 22 thymus GFP+ Tcon


title: 1_F3_Norm_S243


title: 22 thymus GFP+ Treg


title: 21 thymus GFP- Tcon


title: 21 thymus GFP+ Tcon


title: 21 thymus GFP- Treg


title: Liver tissue  from YAP KO mice (AAV8-TBG-CRE treated) at Day 2 after TCPOBOP administration_rep1


title: 21 thymus GFP+ Treg


title: 1_F2_Norm_S242


title: 1_F4_Norm_S244


title: 1_F12_Hypo_S270


title: 1_F1_Norm_S241


title: 1_E9_Hypo_S219


title: 1_F11_Hypo_S269


title: 1_F10_Hypo_S268


title: 1_E8_Hypo_S218


title: 20 thymus GFP- Tcon


title: Liver tissue  from WT mice (AAV8-TBG-GFP treated) at Day 2 after TCPOBOP administration_rep1


title: 20 thymus GFP+ Tcon


title: 1_F6_Norm_S246


title: 1_E7_Hypo_S217


title: 20 thymus GFP+ Treg


title: 19 thymus GFP- Tcon


title: wt_est_4

city: Umea

first: Johannes

last: Hanson

address: KBC

department: Plant Physiology, Umeå University

institute: Umeå Plant Science Centre

data_processing:
Raw sequencing reads were aligned to the Arabidopsis genome (TAIR10) using TopHat v2.0.13 (Trapnell et al. 2009) with the parameter settings: ‘bowtie1’, ‘no-novel-juncs’, ‘p 6’, ‘G’, ‘min-intron-length 40’, ‘max-intron-length 2000’
Aligned reads were summarized over annotated gene models using HTSeq-count v0.6.1 (40) with settings: ‘-stranded no’, ‘-i gene_id’. From the TAIR10 GTF file all ORFs (open reading frames) of which the annotation starts with ‘CPuORF’ were manually removed prior summarization to avoid misalignment of polycistronic mRNAs.
Normalized counts were imported to LIMMA (41) for statistical determination of differential gene expression. Genes for the normalized count that changed more than twofold with an associated P-value of less than 0.05 (Benjamini & Hochberg corrected) were considered to be differentially expressed.
Genome_build: TAIR10
Supplementary_files_format_and_content: normalized expereeion levels

organism: Arabidopsis

source_name: Arabidopsis seedlings

growth_protocol: Invitro grown Arabidopsis seedling (0.5 x MS media,0,8% agar, pH 5.8), 16h light cycle 120 μE m-1 s-1, 24°C

extract_protocol:
Qiagen Plant RNAna easy Kit
TruSeq RNA Sample Prep Kit v2

treatment_protocol: Treatent with 25µM Estardiol

tag: genotype/variation

value: wild type

value: 25 µM estradiol


title: wt_est_3


title: 1_E5_Norm_S197


title: 19 thymus GFP+ Tcon

value: Foxp3hCD2 x RAG1GFP reporter mice (C57BL/6 background)


title: wt_contr_3

value: Cotrol


title: 20 thymus GFP- Treg

value: IAV, 10 dpi


title: 19 thymus GFP+ Treg


title: 1_E2_Norm_S194


title: 19 thymus GFP- Treg


title: wt_contr_1


title: 1_E3_Norm_S195


title: amiS2_est_4


title: wt_contr_2


title: 18 thymus GFP- Treg

value: PBS


title: 1_E12_Hypo_S222

value: hypoxia


title: 18 thymus GFP+ Tcon


title: amiS2_est_1


title: amiS2_contr_4


title: wt_est_2


title: 18 thymus GFP+ Treg


title: amiS2_est_2


title: 1_E11_Hypo_S221


title: amiS2_est_3


title: 1_E4_Norm_S196


title: 18 thymus GFP- Tcon

value: CD4SP RAGGFP-CD25-Foxp3hCD2-


title: 1_E10_Hypo_S220


title: wt_est_1


title: 17 thymus GFP- Tcon


title: wt_contr_4


title: amiS2_contr_3


title: 1_E1_Norm_S193


title: amiS2_contr_2


title: 1_E6_Norm_S198


title: amiS2_contr_1


title: 17 thymus GFP- Treg


title: 1_D9_Hypo_S171


title: 17 thymus GFP+ Tcon


title: 1_D8_Hypo_S170


title: 17 thymus GFP+ Treg


title: 1_D6_Norm_S150


title: 1_D7_Hypo_S169


title: 16 thymus GFP- Tcon


title: 16 thymus GFP- Treg


title: 16 thymus GFP+ Tcon


title: 1_D5_Norm_S149


title: 1_D4_Norm_S148


title: 16 thymus GFP+ Treg


title: 15 thymus GFP- Tcon


title: dot-1.1 mutant, replicate 2

city: London

first: Ruben

last: Esse

address: Guy's Hospital, Great Maze Pond

department: Department of Medical and Molecular Genetics

institute: King’s College London

description: whole body RNA extracts, L3 stage, dot-1.1(gk1050594)

hyb_protocol: Samples were hybridized using standard Affymetrix hybridization kit materials.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Raw Affymetrix CEL files were normalized to produce gene-level expression values using the Robust Multiarray Average (RMA) in Affymetrix Expression Console (version 1.4.1.46).

organism: Caenorhabditis elegans

source_name: dot-1.1 mutant, whole body, L3

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Strains were maintained at 20°C under standard conditions. Hypochlorite-synchronized L1 stage animals were grown for 36 hours post-hatching at 20ºC on standard NGM plates with OP-50 E. coli. Third larval stage (L3) animals were collected in Trizol reagent and frozen at -80°C.

extract_protocol: Total RNA extraction was performed using the miRNeasy RNA isolation kit.

tag: larval stage

value: whole body


title: dot-1.1 mutant, replicate 3


title: mml-1 mutant, replicate 1

description: whole body RNA extracts, L3 stage, mml-1(gk402844)

source_name: mml-1, whole body, L3


title: mml-1 mutant, replicate 3


title: dot-1.1 mutant, replicate 1


title: mml-1 mutant, replicate 2


title: 15 thymus GFP- Treg


title: zfp-1 mutant, replicate 2

description: whole body RNA extracts, L3 stage, zfp-1(ok554)

source_name: zfp-1 mutant, whole body, L3

value: zfp-1(ok554) III


title: zfp-1 mutant, replicate 3


title: zfp-1 mutant, replicate 1


title: Wild-type, replicate 3

description: whole body RNA extracts, L3 stage, wild-type

source_name: wild-type, whole body, L3

value: wild-type


title: Wild-type, replicate 1


title: 1_D2_Norm_S146

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

institute: University of Oxford


title: 1_D12_Hypo_S174


title: 1_D3_Norm_S147


title: 15 thymus GFP+ Tcon


title: Wild-type, replicate 2


title: 1_D11_Hypo_S173


title: 23 thymus GFP+ Treg


title: ctrl_3weeks_1

city: Bologna

first: Federico

middle: Manuel

last: Giorgi

state: BO

address: Via Selmi 3

department: Department of Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

description: Dark treated adult shoots

hyb_protocol: Affymetrix standard hybridisation protocol

scan_protocol: Affymetrix standard scan protocol

data_processing:
Microarray data was pre-processed with RMA (Robust Microarray Normalization) and differential expression was calculated using limma with Benjamini-Hochberg p-value correction
Arabidopsis Gene 1.1 ST Array with Brainarray Custom CDF version 17 (GPL17133)
Arabidopsis Gene 1.1 ST Array with Brainarray Custom CDF version 17 (GPL17133)

organism: Arabidopsis thaliana

source_name: adult, control

label_protocol: Affymetrix standard labeling protocol

growth_protocol: Seeds were germinated on soil containing 2/3 peat and 1/3 perlite and transferred in single pots 1 week after germination. Plants were grown under 12 h photoperiod, with a light intensity of 100 ± 20 umol m-2

extract_protocol: Total RNA was extracted using the Spectrum RNA isolation Kit (Sigma-Aldrich)

treatment_protocol: At the end of the light phase (8.00 p.m.) 2-week (juvenile) and 3-week (adult) old plants were transferred to acquaria containing 35 l of deionized  water (depth of 25 cm) at room temperature. Control plants were placed in acquaria without water. The treatment lasted 24 h.

tag: age

value: 3-week old

value: control (darkness, 24h)


title: 1_D10_Hypo_S172


title: 15 thymus GFP+ Treg


title: ctrl_2weeks_1

description: Dark treated juvenile shoots

source_name: juvenile, control

value: 2-week old


title: ctrl_3weeks_2

description: Dark treated adult shoots


title: dark_2weeks_1

description: Submerged juvenile shoots

source_name: juvenile, submergence

value: dark submergence (24h)


title: ctrl_2weeks_2

description: Dark treated juvenile shoots


title: ocl4 maize anthers, 0.4 to 0.7 mm, fertile phenotype (score = 4); sample ZOO 21 #36 (small RNA-seq)

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: size selected small RNA

data_processing:
All reads from small RNA and RNA-seq libraries were trimmed to remove adapter sequences using a Perl script. After trimming off adapters, small RNA reads with the length between 18 and 34 were kept; PARE reads that are longer than 21-nt are discarded, and 21-nt PARE reads are chopped to 20-nt by removing the last nucleotide. Small RNA and PARE reads were mapped to the reference genome using bowtie, and RNA-seq reads were mapped using Tophat. We developed three websites and databases (for sRNA, PARE and RNA-seq, respectively) using the Maize AGPv2 genome, to store and analyze all libraries; we used these visualization tools extensively for this analysis. These Web sites are available at http://mpss.udel.edu/maize_sRNA2/ , http://mpss.udel.edu/maize_RNAseq2/ and http://mpss.udel.edu/maize_pare/
Genome_build: MAIZE_AGPv4_genome
Supplementary_files_format_and_content: tag counts

organism: Zea mays

source_name: dissected maize whole anthers

growth_protocol: The maize plants were grown in Stanford, CA under greenhouse conditions.

extract_protocol:
Total RNA was isolated using Tri reagent (Molecular Research Center, Cincinnati, OH) or Plant RNA Reagent (Invitrogen, Carlsbad, CA).
Small RNA and RNA-seq libraries were constructed using TruSeq™ Small RNA Sample Prep Kit and TruSeq™ RNA Sample Prep Kit (Illumina, San Diego, CA). All libraries were sequenced on an Illumina Hi-Seq 2000 instrument at the Delaware Biotechnology Institute, Newark, DE.

value: ocl4 mutant

tag: phenotype

value: fertile

value: anthers


title: ocl4 maize anthers, 0.4 to 0.7 mm, partial fertile phenotype (score = 1); sample ZOO 21 #35 (small RNA-seq)

description: size selected small RNA

value: partial fertile


title: 14 thymus GFP- Tcon

value: Foxp3hCD2 x RAG1GFP reporter mice (C57BL/6 background)


title: dark_3weeks_2

description: Submerged adult shoots

source_name: adult, submergence


title: dark_3weeks_1

description: Submerged adult shoots


title: ocl4 maize anthers, 0.4 to 0.7 mm, partial fertile phenotype (score = 2); sample ZOO 16#2 (small RNA-seq)

description: size selected small RNA


title: ocl4 maize anthers, 0.4 to 0.7 mm, partial fertile phenotype (score = 1); sample ZOO 19#24 (small RNA-seq)

description: size selected small RNA


title: 1_D1_Norm_S145

value: Norm


title: dark_2weeks_2

description: Submerged juvenile shoots


title: 24 thymus GFP+ Treg

source_name: thymus

value: CD4SP RAGGFP+CD25+Foxp3hCD2+

value: IAV, 10 dpi


title: 14 thymus GFP+ Treg

value: PBS


title: ocl4 maize anthers, 0.4 to 0.7 mm, sterile phenotype (score = 0); sample ZOO 19 #23 (small RNA-seq)

description: size selected small RNA

value: sterile


title: ocl4 maize anthers, 0.4 to 0.7 mm, partial fertile phenotype (score = 2); sample ZOO 16#2 (RNA-seq)


title: 1_C8_Hypo_S122

value: hypoxia


title: 14 thymus GFP+ Tcon

value: CD4SP RAGGFP+CD25-Foxp3hCD2-


title: ocl4 maize anthers, 0.4 to 0.7 mm, sterile phenotype (score = 0); sample ZOO 16 #6 (small RNA-seq)

description: size selected small RNA


title: ocl4 maize anthers, 0.4 to 0.7 mm, sterile phenotype (score = 0); sample ZOO 16#1 (small RNA-seq)

description: size selected small RNA


title: 13 spleen GFP- Tcon

source_name: spleen

value: CD4SP RAGGFP-CD25-Foxp3hCD2-


title: 1_C6_Norm_S102


title: ocl4 maize anthers, 0.4 to 0.7 mm, fertile phenotype (score = 4); sample ZOO 21 #36 (RNA-seq)


title: 1_C7_Hypo_S121


title: ocl4 maize anthers, 0.4 to 0.7 mm, partial fertile phenotype (score = 1); sample ZOO 21 #35 (RNA-seq)


title: 13 spleen GFP+ Tcon


title: ocl4 maize anthers, 0.4 to 0.7 mm, sterile phenotype (score = 0); sample ZOO 19 #28 (small RNA-seq)

description: size selected small RNA


title: ocl4 maize anthers, 0.4 to 0.7 mm, sterile phenotype (score = 0); sample ZOO 19 #28 (RNA-seq)


title: ocl4 maize anthers, 0.4 to 0.7 mm, sterile phenotype (score = 0); sample ZOO 16 #1 (RNA-seq)


title: 1_C4_Norm_S100


title: ocl4 maize anthers, 0.4 to 0.7 mm, sterile phenotype (score = 0); sample ZOO 16 #6 (RNA-seq)


title: 13 spleen GFP- Treg

value: CD4SP RAGGFP-CD25+Foxp3hCD2+


title: 1_C5_Norm_S101


title: ocl4 maize anthers, 0.4 to 0.7 mm, sterile phenotype (score = 0); sample ZOO 19 #23 (RNA-seq)


title: ocl4 maize anthers, 0.4 to 0.7 mm, partial fertile phenotype (score = 1); sample ZOO 19#24 (RNA-seq)


title: 158_screen_tcr_200306

city: Chapel Hill

first: Jonathan

middle: S

last: Serody

state: NC

address: 125 Mason Farm Rd.

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: 5' Rapid Amplification of cDNA Ends (5'RACE) for TCR.

data_processing:
[RNA-seq Quant]
Map paired end fastq reads to hg38 using STAR (https://github.com/alexdobin/STAR/archive/STAR_2.4.2a.tar.gz).
Quantify with Salmon (https://github.com/COMBINE-lab/salmon/releases/download/v0.6.0/SalmonBeta-0.6.0_DebianSqueeze.tar.gz).
Sort and index bam output from STAR using samtools (https://github.com/samtools/samtools/releases/download/1.7/samtools-1.7.tar.bz2).
QC using picard (/picard-tools-1.86/).
Calculate max read length (samtools).
Used biomaRt to interface with BioMart databases (biomaRt version 2.38.0); from ImPro Analysis Suite version 0.4-71. (biomaRt values used in query: unique ensembl_transcript_id from Salmon output (quant.sf) with version numbers removed (e.g. ENST00000456328.2 > ENST00000456328)).
[mixcr (TCR)]
Analyze TCR fastq data using mixcr (https://github.com/milaboratory/mixcr/releases/download/v2.1.9/mixcr-2.1.9.zip).
QC using fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip).
Quantify diversity metrics using vdjtools (https://github.com/mikessh/vdjtools/releases/download/1.1.7/vdjtools-1.1.7.zip).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: TCR diversity metrics (tab-delimited); RNA gene expression file (tab-delimited).

source_name: Peripheral Blood CD8 T cells_lymphocytes

extract_protocol:
CD8 T cell RNA from PBMC and Blast RNA from Bone Marrow were isolated by Qiagen RNeasy® Plus Micro Kit.
TCR profiling using the SMARTer Human TCR a/b Profiling Kit (Takara Bio USA, Inc., Cat. No 63516); Illumina TruSeq RNA Access.

tag: cell type

value: Pre-treatment with High dose Cytarabine and Pembrolizumab

tag: timepoint

value: Screening Timepoint


title: 153_screen_tcr_200306

value: Peripheral Blood CD8 T cells_lymphocytes


title: 1_C9_Hypo_S123

tag: lane

tag: plate-position


title: 152_screen_tcr_200305


title: 12 spleen GFP+ Tcon


title: 1_C2_Norm_S98

tag: cell line

tag: condition


title: 148_screen_tcr_190513


title: 1_C3_Norm_S99

tag: sample-identity


title: 13 spleen GFP+ Treg

tag: strain

tag: population


title: 12 spleen GFP- Tcon


title: 150_screen_tcr_200305


title: 14 thymus GFP- Treg


title: 144_screen_tcr_190212


title: 1_C11_Hypo_S125


title: 11 spleen GFP- Treg


title: 147_screen_tcr_190215


title: 1_C10_Hypo_S124


title: 123_screen_tcr_190212


title: 145_screen_tcr_190215


title: 1_C1_Norm_S97


title: 1_C12_Hypo_S126


title: 11 spleen GFP+ Tcon


title: 121_screen_tcr_180816


title: 125_screen_tcr_180925


title: 118_screen_tcr_180816


title: 142_screen_tcr_180925


title: 10 spleen GFP- Treg


title: 140_screen_tcr_190513


title: 11 spleen GFP- Tcon


title: 10 spleen GFP- Tcon


title: 113_screen_tcr_190212


title: 1_B8_Hypo_S74


title: 110_screen_tcr_180816


title: 10 spleen GFP+ Tcon


title: 11 spleen GFP+ Treg


title: 1_B7_Hypo_S73


title: 119_screen_tcr_190212


title: 1_B6_Norm_S54


title: 109_screen_tcr_170510


title: 157_screen_tcr_200306


title: 108_screen_tcr_170510


title: 10 spleen GFP+ Treg


title: 1_B9_Hypo_S75


title: 107_screen_tcr_170510


title: 104_screen_tcr_170510


title: 1_B5_Norm_S53


title: 9 spleen GFP- Tcon


title: 9 spleen GFP- Treg


title: 102_screen_tcr_170510


title: 1_B2_Norm_S50


title: ddx21_sibling_02

first: Benjamin

middle: M

last: Hogan

state: Victoria

address: 305 Grattan Street

department: Program in Organogenesis and Cancer

data_processing:
Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings
Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr, calcNormFactors and cpm
A batch effect was removed in edgeR using removeBatchEffect function
For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied
Genome_build: GRCz11 (GCA_000002035.4)
Supplementary_files_format_and_content: Matrix table with normalised, batch corredted and log2 transformed CPM for every gene and every sample

organism: Danio rerio

extract_protocol:
At 3 dpf double positve cells were sorted from Tg(fli1a:nEGFP);Tg(5.2lyve1b:DsRed) to isolate LECs and VECs
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: abbreviatedname

value: venous and lymphatic ECs (VECs, LECs)


title: ddx21_sibling_03


title: 9 spleen GFP+ Tcon


title: ddx21_sibling_04


title: 112_screen_tcr_180816


title: 9 spleen GFP+ Treg


title: ddx21_mutant_03


title: ddx21_mutant_02


title: 8 spleen GFP- Tcon


title: ddx21_sibling_01


title: 1_B12_Hypo_S78

department: NDORMS


title: 1_B10_Hypo_S76


title: 8 spleen GFP- Treg


title: 8 spleen GFP+ Tcon


title: adult_BAT_2_1

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

institute: University of Ulm

description: Adult BAT

data_processing:
assembled clean reads into Unigenes: using HISAT2: Version: v2.0.4 Parameters: -p 8 --phred64 --sensitive -I 1 -X 10000
map the clean reads to reference using Bowtie2: Version: v2.2.5 Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Supplementary_files_format_and_content: DeSeq2 output

source_name: BAT from adult mice

growth_protocol: specific patogen free animal facility, tissue are collected in day cycle, 9:30-10:30 am, n=3 in each group

extract_protocol: Tri Reagent (phenolic extarction) according to Sigma-Aldrich protocol

tag: developmental stage

value: 8 weeks

tag: tissue

value: brown adipose tissue (from interscapular region)

tag: Sex

value: male


title: 1_B1_Norm_S49


title: ddx21_mutant_01

tag: genotype/variation


title: 1_B4_Norm_S52


title: adult_BAT_1_1

description: Adult BAT


title: adult_BAT_3_1

description: Adult BAT


title: 8 spleen GFP+ Treg

value: Foxp3hCD2 x RAG1GFP reporter mice (C57BL/6 background)

tag: treatment


title: 1_A9_Hypo_S27


title: ddx21_mutant_04


title: 1_B11_Hypo_S77


title: infant_BAT_1_1

description: Infant BAT

source_name: BAT from infant mice (beige)

value: postnatal day 6

value: beige adipose tissue (from interscapular region)


title: mESCs, WT-WT, 475

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
1-WT-WT
475

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment and quatification with STAR version v2.7.3a using the default parameters
reads mapped to each transcript against the RefSeq mm38 annotation download on March 2018
Normalization using DeSeq2
Genome_build: mm38
Supplementary_files_format_and_content: comma separated file includes DeSeq2 rlog counts for each Sample

source_name: mESC

growth_protocol: [cell isolation protocol]  mES cells were cultivated in complete mES medium (FCS+LIF). Before analysis, harvested cells were subjected to SSEA-1 MACS sorting to correct for spontanious differentiation during culture. Two different mES cell clones were used in this study (with each WT and KO condition)

extract_protocol:
Cells lysed in TRIZOL (Invitrogen), and total RNA was extracted according to the manufacturer's protocol
Illumina TruSeq RNA Sample Preparation Kit v2
200 bp paired-end run was performed on a HiSeq1500

treatment_protocol: Trim71 conditional ("WT") cells were treated with 500 nM 4-OHT for 2 days to induce Trim71 mutation. Cells were further cultivated before cell harvest for at least 7 days to minimize indirect effects of the drug treatment.

tag: day

tag: clone

tag: genotype

value: Trimfl/fl - Lin28afl/fl

value: mESC


title: mESCs, KO-WT, 477

description:
1-KO-WT
477

value: Trim-/- - Lin28afl/fl

tag: cell type


title: mESCs, KO-KO, 478

description:
1-4-KO-KO
478


title: 7 spleen GFP- Treg

value: IAV, 10 dpi


title: infant_BAT_3_1

description: Infant BAT


title: 1_B3_Norm_S51

tag: lane

value: Norm


title: 1_A8_Hypo_S26

tag: plate-position

value: hypoxia


title: mESCs, KO-WT, 481

description:
1-KO-WT
481


title: 1_A7_Hypo_S25

tag: cell line


title: 7 spleen GFP+ Treg

value: CD4SP RAGGFP+CD25+Foxp3hCD2+


title: mESCs, KO-KO, 474

description:
C1-KO-KO
474


title: 1_A6_Norm_S6

tag: condition


title: 7 spleen GFP+ Tcon

value: CD4SP RAGGFP+CD25-Foxp3hCD2-


title: 1_A5_Norm_S5

tag: sample-identity


title: adult_WAT_3_1

description: Adult WAT

source_name: WAT from adult mice

value: inguinal white adipose tissue

tag: strain


title: mESCs, WT-KO, 472

description:
C1-WT-KO
472

value: Trimfl/fl - Lin28a-/-


title: mESCs, KO-WT, 473

description:
E3-KO-WT
473


title: adult_WAT_2_1

description: Adult WAT


title: 6 spleen GFP+ Tcon

tag: population


title: infant_WAT_2_1

description: Infant WAT

source_name: WAT from infant mice


title: 6 spleen GFP- Tcon

value: CD4SP RAGGFP-CD25-Foxp3hCD2-


title: 1_A4_Norm_S4


title: 7 spleen GFP- Tcon


title: mESCs, WT-WT, 471

description:
E3-WT-WT
471


title: mESCs, KO-KO, 470

description:
C1-KO-KO
470


title: infant_BAT_2_1

description: Infant BAT


title: 1_A10_Hypo_S28


title: 1_A11_Hypo_S29


title: 1_A3_Norm_S3


title: 6 spleen GFP- Treg

value: CD4SP RAGGFP-CD25+Foxp3hCD2+


title: 5 spleen GFP- Treg

value: PBS


title: 1_A12_Hypo_S30


title: adult_WAT_1_1

description: Adult WAT

value: 8 weeks

value: male


title: 6 spleen GFP+ Treg

value: Foxp3hCD2 x RAG1GFP reporter mice (C57BL/6 background)


title: infant_WAT_3_1

description: Infant WAT

value: postnatal day 6


title: 5 spleen GFP+ Tcon


title: 1_A2_Norm_S2


title: infant_WAT_1_1

description: Infant WAT


title: miR-722 +DOX rep3

city: West Lafayette

first: Qing

last: Deng

state: Indiana

address: 915 W. State Street

department: Department of Biological Sciences

institute: Purdue University

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq 4000.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg38 genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts, differential analysis from edgeR, and pathway analysis from DAVID

source_name: miR-722 HL-60 with DOX induction

growth_protocol: HL-60 cells were grown in 10% FBS RPMI with 1ug/ml puromycin selection and diffrentiated for 6 days in 1.3% RPMI.

extract_protocol:
total mRNA was extracted with qiagen rneasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: on day 4 of diffrentiation +/- DOX was added at 1ug/ml.

value: miR-722 +DOX

value: dHL-60 cells

value: myeloid progenitor cells


title: 5 spleen GFP- Tcon


title: pcnB-Rep2

city: Athens

first: Bijoy

last: Mohanty

state: GA

address: 120 E. Green Street

department: Genetics

institute: University of georgia

description: Transcriptome_all strains.csv

data_processing:
Analysis and visualization were performed by Cofactor Genomics.  Raw sequence data in FASTQ format were assessed for quality (FastQC, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and ribosomal RNA content (sortmeRNA, http://bioinfo.lifl.fr/RNA/sortmerna/).
NovoAlign (Novocraft, http://novocraft.com) was used to align the reads to a set of transcript sequences and parameters were set to allow multiple alignments of the transcriptome set to allow for isoforms.
Alignments to the MG1655 genome were performed using STAR (https://github.com/alexdobin/STAR).  Only unique alignments to the genome were allowed.The genome alignment loci from all samples were combined and clustered to generate genomic loci (“patches”) with contiguous read coverage. Patches overlapping reference genome annotation loci were labelled as such.
For each transcript or patch, the RPKM expression value was calculated for each sample. These RPKM values were the basis for expression comparison and statistics generation.  For each replicate group, the mean and coefficient of variation for each transcript or patch were calculated across the expression values for the samples in that group.  These means were considered to be the expression values for the replicate group.
P-values were calculated between the means of each pair of replicate groups using a Welch’s t-test corrected for false-discovery rate (FDR) by the method of Benjamini. Only the expression of transcripts with P-values of ≤ 0.05 were considered during the analysis.
Genome_build: MG1655
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample …

organism: Escherichia coli

source_name: Bacterial culture

growth_protocol: Bacterial strains were grown in a shaking water-bath shaker in Luria broth after dilutions from overnight standing cultures.  All the cultures were initially grown at 30°C until they reached 50 Klett units above background and then shifted to 44oC for one hour to inactivate the mutant RNase P (rnpA49). The cultures were maintained in exponential growth by dilutions with pre-warmed Luria broth.

extract_protocol:
The RNA samples were isolated using a modified RNAsnap™ protocol and treated with DNase I to remove any residual DNA. NanoDrop (NanoDrop 2000C) analysis was carried out to ensure that all RNA samples met the minimum requirement of UV absorption ratio of 260/280 >1.9 and 260/230 >2.0.  Furthermore, the integrity of the RNA samples was determined by separating 500 ng of total RNA from each isolate on a 1% agarose gel.
Cofactor Genomics, Inc (http://cofactorgenomics.com, Saint Louis, Missouri, USA) constructed the library and carried out the RNA-seq analysis.  In brief, species specific rRNA-probes were hybridized to the total RNA in order to remove ribosomal RNA from the samples. The resulting ribo-depleted RNA was then fragmented. First-strand cDNA synthesis was performed using reverse transcriptase and random primers in the presence of actinomycin D, followed by second-strand cDNA synthesis with DNA polymerase I and RNase H.  Double-stranded cDNAs were end-repaired and A-tailed for subsequent adaptor ligation.  Indexed adaptors were ligated to the A-tailed cDNAs. Enrichment by PCR was performed to generate the final cDNA sequencing library.
Libraries were sequenced as single-end 75 base-pair reads on an Illumina NextSeq500 Instrument following the manufacturer's protocols.

value: DpcnB

tag: temp

value: 1 hr growth at 44°C


title: pcnB-Rep1

description: Transcriptome_all strains.csv


title: 4 spleen GFP- Treg


title: mESCs, KO-WT, 465

description:
E3-KO-WT
465

value: Trim-/- - Lin28afl/fl

value: mESC


title: wildtype_27hpf_EC1

city: New Haven

first: Stefania

last: Nicoli

state: CT

address: 300 George street

department: Internal Medicine

institute: Yale University

data_processing:
The reads were demultiplexed using bcl2fastq provided by the 10X genomics.  The demultiplexed reads were aligned to the reference genome (Grz11, modified to add mCherry, GAL4, and eGFP) to obtain digital gene expression matrix data using cellranger program
The output of the cellranger was then processed using Seurat in R.
All the cells with less than 200 unique transcripts were eliminared.  All genes which are expressed in less than 3 cells were also eliminated.
The data was normalized using sctransform, and then clustered.  The clusters were projected for viualization in R using the PHATE algorithm.
Genome_build: GRCz11
Supplementary_files_format_and_content: Average Gene expression matrix for average gene expression per cluster, per condition.  This is a tab separated values file, where each row represents a gene, and each column represents the cluster, and the condition, and each cell represents normalized expression values across all the cells in that cluster for that condition.

source_name: endothelial cell

growth_protocol: Zebrafish were raised and maintained at 28.5˚C using standard methods and according to protocols approved by Yale University Institutional Animal Care and Use Committee (# 2017-11473).

extract_protocol:
Trunk tissue was dissected from 27 hpf zebrafish embryos under  0.1% tricaine anesthesia and then disassociated into a single cell suspension using 0.25 mg/ml liberase for 45 minutes. Tg(kdrl:hras-mCherry)s896 endothelial cells were isolated from the single cell suspension via FACS into 0.04% BSA in PBS and applied to the 10X genomics single cell RNA sequencing platform.
10 X genomics Chromium Next GEM Single Cell 3’ Library Construction Kit v2.1

value: trunk endothelium

value: endothelial cell

tag: developmental stage

value: 27 hours post fertilization

value: wildtype


title: mESCs, KO-WT, 469

description:
E3-KO-WT
469


title: miR-722 +DOX rep1


title: miR-722 -DOX rep3

source_name: miR-722 HL-60 without DOX induction

value: miR-722 -DOX


title: rnpA49 pcnB-Rep2

description: Transcriptome_all strains.csv

value: rnpA49 DpcnB


title: 4 spleen GFP+ Tcon

value: CD4SP RAGGFP+CD25-Foxp3hCD2-

value: PBS


title: mESCs, WT-KO, 476

description:
1-4-WT-KO
476

value: male

value: Trimfl/fl - Lin28a-/-


title: pcnB-Rep3

description: Transcriptome_all strains.csv


title: mESCs, WT-KO, 468

description:
C1-WT-KO
468


title: 4 spleen GFP+ Treg

value: Foxp3hCD2 x RAG1GFP reporter mice (C57BL/6 background)

value: CD4SP RAGGFP+CD25+Foxp3hCD2+


title: mESCs, WT-WT, 467

description:
E3-WT-WT
467

value: Trimfl/fl - Lin28afl/fl


title: 223mut_27hpf_EC1

tag: tissue

value: Tg(miR-223:KalTA4)ya363; Tg(5xUAS:eGFP)nkuasgfp1a; Tg(kdrl:hras-mCherry)s896; miR-223(ya303)


title: 5 spleen GFP+ Treg


title: 3 spleen GFP- Tcon

value: CD4SP RAGGFP-CD25-Foxp3hCD2-


title: vector +DOX rep3

source_name: vector HL-60 with DOX induction

value: vector +DOX

value: dHL-60 cells

value: myeloid progenitor cells


title: mESCs, WT-WT, 459

description:
1-WT-WT
459

tag: Sex

value: mESC


title: mESCs, KO-KO, 466

description:
C1-KO-KO
466


title: 3 spleen GFP+ Tcon


title: rnpA49-Rep2

description: Transcriptome_all strains.csv

value: 1 hr growth at 44°C


title: 4 spleen GFP- Tcon


title: mESCs, WT-KO, 464

description:
C1-WT-KO
464


title: rnpA49 pcnB-Rep3

description: Transcriptome_all strains.csv


title: rnpA49 pcnB-Rep1

description: Transcriptome_all strains.csv


title: 1_A1_Norm_S1

value: Norm


title: vector +DOX rep2


title: miR-722 +DOX rep2

value: miR-722 +DOX


title: miR-722 -DOX rep2

value: miR-722 -DOX


title: vector +DOX rep1


title: mESCs, KO-KO, 462

description:
1-4-KO-KO
462


title: mESCs, WT-KO, 460

description:
1-4-WT-KO
460


title: rnpA49-Rep3

description: Transcriptome_all strains.csv


title: vector -DOX rep3

source_name: vector HL-60 without DOX induction

value: vector -DOX


title: miR-722 -DOX rep1


title: GFP-HY5_Rep3

city: Paris

first: Clara

last: Bourbousse

address: 9 quai Saint Bernard

department: UMR 7622 LBD

country: France

institute: Sorbonne Université

description: RNA-seq

data_processing:
trimming using trim_galore with options “--paired --length 35”
mapping to the TAIR10 genome using STAR with options “--alignIntronMin 20 --alignIntronMax 100000 --outFilterMultimapNmax 20 --outMultimapperOrder Random --outFilterMismatchNmax 8 --outSAMtype BAM SortedByCoordinate --outSAMmultNmax 1 --alignMatesGapMax 10000”.
Browser tracks were generated using deeptools function bamCoverage with options “--binSize 10 --normalizeUsing RPKM”.
Read counts were retrieved using htseq-count with options "-s reverse --nonunique all -f bam -i ID -r pos -t locus -a 0"
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

source_name: 7-day-old Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were sterilized with a solution of 75% sodium hypochlorite and 0.1% Tween-20 and stratified at 4°C during 3 days in darkness.  Seedlings were grown in Murashige and Skoog (MS) medium.

extract_protocol:
RNA extraction was performed with FastPrep Plant Total RNA-purification kit, with DNAse treament
DNBseq

treatment_protocol: Light: white light (100 umol m-2 s-1) in a 16-h light/8-h dark period. Dark: continuous darkness.

tag: plant line

value: light

tag: sucrose


title: rnpA49-Rep1

description: Transcriptome_all strains.csv


title: Wild type-Rep1

description: Transcriptome_all strains.csv

value: Wild type


title: fusca_Rep3

description: RNA-seq

value: 2x35S::GFP-HY5/hy5 with fusca phenotype

tag: treatment


title: 2 spleen GFP- Tcon

value: Foxp3hCD2 x RAG1GFP reporter mice (C57BL/6 background)

value: PBS


title: 3 spleen GFP- Treg

value: CD4SP RAGGFP-CD25+Foxp3hCD2+


title: Wild type-Rep3

description: Transcriptome_all strains.csv


title: fusca_Rep1

description: RNA-seq


title: vector -DOX rep2


title: Wild type-Rep2

description: Transcriptome_all strains.csv


title: fusca_Rep2

description: RNA-seq


title: 1 spleen GFP- Tcon


title: WT_DL1

city: qingdao

first: RUIQI

last: SUN

state: China

address: No.72 Binhai Road,

country: China

institute: shandong university

description: WT terminal leaflet

data_processing:
The RNA was purified by electrophoresis through a TBE-urea polyacrylamide gel. The gel regions harboring 18-30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5' and 3' RNA adapter-ligated using T4 RNA ligase, and amplified for 18 PCR cycles
The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China).
Raw reads were trimmed by removing low-quality and adaptor sequences, then aligned to the A. thaliana genome using SOAP2 software.
Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the P value and the false discovery rate (FDR) (Audic and Claverie, 1997).
Genome_build: TAIR10.1
Supplementary_files_format_and_content: The_expression_of_gene_in_Arachis_hypogaea.xls (Gene IDs searchable at https://www.peanutbase.org)

organism: Arachis hypogaea

source_name: Arachis hypogaea wild type

growth_protocol: The plants grew in soil with a photoperiod of 16-h-day/8-h-night, temperature of 22°C and relative humidity of 70% in a growth chamber

extract_protocol:
Total RNA was isolated using TRIzol-RT reagent (Molecular Research Center)
First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

tag: age

value: terminal leaflet

value: wild type


title: GFP-HY5_Rep1

description: RNA-seq


title: 2 spleen GFP- Treg


title: 2 spleen GFP+ Tcon

value: CD4SP RAGGFP+CD25-Foxp3hCD2-


title: WT_Rep1

description: RNA-seq

value: WT


title: WT_SAM3

description: WT shoot apical

value: shoot apical

tag: genotype


title: WT_DL2

description: WT terminal leaflet


title: 2 spleen GFP+ Treg

value: CD4SP RAGGFP+CD25+Foxp3hCD2+


title: 1 spleen GFP+ Tcon


title: PDX_CB2

city: St Louis

first: Grant

middle: A

last: Challen

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

data_processing:
Single cell count: single cells were counted using Cellranger 3.1.0. Reads were further aligned to the Genome Reference Consortium Human genome, CRChg38. The aligned data were then annotated and UMI-collapsed using Cellranger (v3.1.0). Cells with more than 10% mitochondrial gene expression and with top 5% unique feature counts were excluded. Data reduction and cluster identification were performed using Seurat.
Alignment and UMI-collapse: Reference genome: the Genome Reference Consortium Human genome, CRChg38. Package: Cellranger 3.1.0
Cell exclusion: Cells with more than 10% mitochondrial gene expression and with top 5% unique feature counts were excluded
Principal component analysis: Data were reduced to 50 components.
Clustering identification: Reduction techniques: tSNE and UMAP
Genome_build: Reference genome: the Genome Reference Consortium Human genome, CRChg38
Supplementary_files_format_and_content: For each sample, three files are provided: barcodes.tsv.gz; features.tsv.gz; and matrix.mtx.gz

source_name: Cord blood mononuclear cells (sample 2)-derived human bone marrow cells in a xenograft model using humanized mice

extract_protocol:
17000 cells wereused for the construction of the scRNA library of each sample
Chromnium Single Cell 3’Reagent Kit v3 (10x Genomics) according to the manufacturer’s protocol

tag: source

value: Xenograft model

tag: antibody used for sorting

value: human CD45

value: Donor derived bone marrow cells


title: PDX_53

source_name: UPN#585953 PBMC-derived human bone marrow cells in a xenograft model using humanized mice


title: 3 spleen GFP+ Treg

first: Christoph

last: Binz

address: Carl-Neuberg-Straße 1

data_processing:
Fastq files were obtained after demultiplexing, basecalling and quality filtering during the sequencing run on a MiSeq machine.
Data were aligned to the IMGT database from 22.05.2018 using MiXCR (Bolotin, D. A., S. Poslavsky, I. Mitrophanov, M. Shugay, I. Z. Mamedov, E. V. Putintseva, and D. M. Chudakov. 2015. MiXCR: software for comprehensive adaptive immunity profiling. Nature methods 12: 380-381.)
Afterwards the samples were downsampled (Thymus samples to 20000 and spleen samples to 30000) using VDJTOOLS (Shugay, M., D. V. Bagaev, M. A. Turchaninova, D. A. Bolotin, O. V. Britanova, E. V. Putintseva, M. V. Pogorelyy, V. I. Nazarov, I. V. Zvyagin, V. I. Kirgizova, K. I. Kirgizov, E. V. Skorobogatova, and D. M. Chudakov. 2015. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLoS Comput. Biol. 11: e1004503.).
Supplementary_files_format_and_content: VDJTOOLS.txt files were generated using MiXCR.

source_name: spleen

extract_protocol:
The desired populations were sorted and the RNA was isolated employing the "RNeasy Plus Micro kit" from Qiagen (Hilden, Germany).
The cDNA was generated by employing ingredients from the TAKARA cDNA Synthesis Kit (TAKARA Bio Europe, France) according to an in-house modified protocol based on the manufacturer’s protocol. The DNA-amplicons for the Illumina sequencing were generated by using Advantage 2 PCR Kit (TAKARA Bio Europe, France). The DNA was then purified using Qiaquick Gel Extraction Kit (Qiagen Hilden, Germany). The purified product of each sample was indexed by an indexing-PCR with Nextera-Primers. Finally a pool of the samples was sequenced employing Illumina MiSeq v2 Reagent Kit (Illumina Inc, San Diego, CA, USA).


title: 1 spleen GFP+ Treg


title: SUSP_4; Sample_8D

city: Uppsala

first: Gustav

last: Arvidsson

address: Husargatan 3

department: Department of Medical Sciences

institute: Uppsala Universitet

data_processing:
Short reads were indexed using the species-based short read separation software Xenome (v1.0.1) for human and mouse based on the ENSEMBL reference genomes specified below.
Species-specific PE short reads of human and murine origin were aligned to reference genomes GRCh38 and GRCm38 respectively using the splice aware short read aligner STAR (v2.5.1b) using PE read input with default options and –sjdbGTFfile pointing to the ENSEMBL .gtf annotation file corresponding to the reference genome file and –outFilterMultimapNmax set to 1.
Species specific read pairs were assigned to known features and counted using featurecounts from the Subread package (v1.5.2). Annotated genes were obtained from the Ensembl ftp repository (Homo_sapiens.GRCh38.87.gtf and Mus_musculus.GRCm38.87.gtf).
Data was later interrogated for differentially expressed genes using the Bioconductor package EdgeR (v3.22.5).
Genome_build: GRCh38.87 and GRCm38.87 were downloaded from the ENSEMBL ftp repository
Supplementary_files_format_and_content: GRCh38_featurecounts_count_table.csv: RAW read count table per feature for all samples with human content after species-based separation of reads of human origin and alignment to GRCh38. The count table contain count data for files from the current GEO accession number and for files originating from accession number GSE99501 processed using the present workflow.
Supplementary_files_format_and_content: GRCm38_featurecounts_count_table.csv: RAW read count table per feature for all samples with mouse content after species-based separation of reads of murine origin and alignment to GRCm38. The count table contain count data for files from the current GEO accession number and for files originating from accession number GSE99501 processed using the present workflow.

organism:
Homo sapiens
Mus musculus

source_name: MS-5, Rec-1 (suspension fraction)

growth_protocol: MS-5 cells and Rec-1 cells mono- or co-cultured in αMEM-glutamax (Gibco) supplemented with 10% H.I. FBS (Gibco), 2mM sodium pyruvate, 100U/mL penicillin and 100µg/mL streptomycin (Gibco). All cells were cultivated in a humidified incubator at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using RNeasy (Qiagen) with QIAshredders following the protocol supplied by the manufacturer.
Libraries were constructed using Illumina Truseq 2.0 reagents according to manufacturers protocol, mRNA was purified by poly-T oligo-attached magnetic beads.

treatment_protocol: 5x10^5 MS-5 stromal cells were seeded 24h in advance to 10cm dishes and 5x10^6 Rec-1 cells were subsequently added. RNA was extracted following 24h of incubation at 37 degrees 5% CO2.

tag: cultivation

value: co-culture of two cell lines

tag: cell type

value: mouse bone marrow derived stromal and human mantle cell lymphoma cell line

value: MS-5, Rec-1 (suspension fraction)


title: PBMC_CB2

source_name: Mononuclear cells extracted from cord blood sample 2

value: Human

value: Cord blood mononuclear cells


title: WT_PE3

description: WT petiole

value: petiole


title: vector -DOX rep1

value: vector -DOX

tag: cell line

value: dHL-60 cells

value: myeloid progenitor cells


title: PBMC_CB1

source_name: Mononuclear cells extracted from cord blood sample 1


title: SUSP_3; Sample_7D


title: GFP-HY5_Rep2

description: RNA-seq

value: light


title: WT_Rep2

description: RNA-seq


title: PDX_CB1

source_name: Cord blood mononuclear cells (sample 1)-derived human bone marrow cells in a xenograft model using humanized mice


title: SK-N-AS, total

city: Parkville

first: Jack

middle: Aatto Laasonen

last: Cooper

address: 49 College Crescent

institute: University of Melbourne

data_processing:
fastq files were quality checked using FastQC (0.11.7)
fastq files were aligned to an ensembl GRCh38 genome using HISAT2 (2.1.0)
sam files were converted to bam files using samtools (1.4.1)
bam files were uploaded to Galaxy and converted to bigwig files using bamCoverage (3.1.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: "bigwig" files contain coverage data for the respective cell lines.

source_name: SK-N-AS

growth_protocol: KELLY cell lines were plated, suspended in 10% foteal bovine serum (FBS) and 100 U/mL penicillin streptomycin RPMI containing media, into 6-well plates for 48 hours. BE2C and SK-N-AS cell lines were plated, suspended in 10% foteal bovine serum (FBS) and 100 U/mL penicillin streptomycin DMEM containing media, into 6-well plates for 48 hours.

extract_protocol:
Each 6-well was treated with 500 µL of Nucleozol, and left at room temperature (RT) for 10 minutes. Samples were transferred to 1.5 mL tubes. Each sample was treated with 200 µL RNase-free water, then shaken by hand for 15 seconds. Samples were left to incubate at RT for  10 minutes, and then centrifuged at 14,000 x g for 15 minutes. Then, 500 µL supernatant of each sample was transferred to a new tube, and treated with isopropanol. After inverting 4-6 times, samples were left at RT for 10 minutes, then centrifuged (14,000 x g) for 10 minutes. A resulting RNA pellet was then washed twice with 70% ethanol (600 uL each time, 8,000 x g for 1.5 minutes) and re-suspended in 30 uL RNase-free water.
RNA samples were sent to the Australian Genome Research Facility (AGRF, Perth and Melbourne, Australia) for whole transcriptome library preparation using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, CA, USA) and ribosomal RNA depletion with the Ribo-Zero-Gold kit (Illumina, CA, USA).
Sequencing as performed using an Illumina HiSeq 2500 (Illumina, CA, USA) to generate 50 base pair single end reads, resulting in an average 20 million reads per sample. Raw sequencing files were quality checked using FastQC (0.11.7), with all files passing

treatment_protocol: After 48 hours of incubation at 37ºC and 5% carbon dioxide levels, cells were lysed using the Nucleozol reagent from Machery-Nagel ™.

value: Immortalized neuroblastoma cells

tag: phenotype

value: non-MYCN amplified/low-risk


title: PBMC_81

source_name: Peripheral blood mononuclear cells extracted from a myelofibrosis patient UPN#784981

value: Peripheral blood mononuclear cells


title: PDX_81

source_name: UPN#784981 PBMC-derived human bone marrow cells in a xenograft model using humanized mice


title: WT_PE1

description: WT petiole

value: wild type


title: KELLY, total

source_name: KELLY

value: MYCN amplified/high-risk


title: WT_SAM2

description: WT shoot apical

value: shoot apical


title: WT_SAM1

description: WT shoot apical


title: ADH_4; Sample_8C

source_name: MS-5, Rec-1 (adherent fraction)

value: MS-5, Rec-1 (adherent fraction)


title: WT_PE2

description: WT petiole