title: BP_submerged_slow_pool3

description: HSS pool 3


title: AP_submerged_fast_pool3

status: Public on Oct 10 2018

type: RNA

city: Leioa

first: Daniel

last: Prieto

address: Barrio Sarriena s/n

country: Spain

institute: University of the Basque Country

description: LSF pool 3

hyb_protocol: Samples were manually hybridized with SureHyb hybridization chambers (Agilent technologies). Hybridization was done in the oven of Agilent technologies following the Agilent protocol. Characteristics: 600 ng of marked cRNA; 40 µl volume; 65 ºC temperature; 20 hours duration at 10 rpm in the hybridization

scan_protocol: The scanning was carried out on the DNA microarrays G2565CA scanner with ozone –barrier slide covers with the Scan control Software version 8.5.1., using the default protocol AgilentG3_GX_1Color. The Scanning resolution was 3 µm and green channel

data_processing: We used Agilent Feature Extraction Software (ver. 10.7.3.1) (Agilent Technologies) to process the microarray images and to quantify the fluorescence of the probes

molecule: total RNA

organism: Mytilus galloprovincialis

source_name: F mussels reared in AP diet. Experiment I

label_protocol: We used “One-Color Microarray-Based Exon Analysis” marking protocol from Agilent. Samples were marked using “Low Input Quick Amp WT Labeling kit, One-Color” (p/n 5190-2943) kit.

growth_protocol: Mussels were reared in laboratory under different nutritional conditions

extract_protocol: The RNA was extracted with Ribopure system (Ambion kit). The analysis of the quality and integrity of RNA was checked with Fragment AnalyzerTM Automated CE System equipment from advanced analytical with DNF-471 Standard Sensitivity RNA Analysis kit, (15 nt) and Fragment AnalyzerTM 1.1.0.11 software version. RNA quality was checked using PROSize 2.0.

treatment_protocol: Fast and slow growing individuals were obtained in each rearing condition. Mussels were dissected and gills were obtained to extract the RNA. Samples were stored immersed in RNA later at -80 ºC until the RNA was extracted

tag: growth

value: F

tag: diet

value: AP

tag: emersion

value: submerged

tag: tissue

value: Gill sample


title: Adult3_circRNA

type: SRA

city: Yangling

first: Hui

last: Li

state: Shaanxi

address: College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China

country: China

institute: Northwest A&F University

description: circRNA

library_source: transcriptomic

data_processing:
From the raw FASTQ files, adapter was removed using Trim Galore and filtered data were aligned to the Bos taurus reference genome (bosTau7) from UCSC (http://genome.ucsc.edu/) with TopHat2 (version 2.0.14)
Linear transcripts assembly and abundance estimation were first performed using CuffLinks, and then the reads of fusion transcripts, obtained from TopHat2, which did not align to the linear RNA were identified.
Then the program TopHat-Funsion was done with the fusion transcripts and the transcripts obtained from the assembled linear RNA to obtain back-spliced junctions reads. Only circRNAs within 100 kb, with two or more supporting reads, and with no more than two mismatches were kept.
CircRNAs were normalized as the number of uniquely mapped fragments per kilobase of exon per million fragments mapped (FPKM).
Genome_build: Btau_4.6.1
Supplementary_files_format_and_content: [Additional file 1] All circRNAs candidates
Supplementary_files_format_and_content: [Additional file 2] 1,287 circRNAs candidates contained at least one unique back-spliced read were videntified in bovine muscle tissues.
Supplementary_files_format_and_content: [Additional file 3] 589 circRNAs were found in mixed sample using  rRNA−&RNase R+ method.
Supplementary_files_format_and_content: [Additional file 4] List of differentially expressed circRNAs identified in skeletal muscle.
Supplementary_files_format_and_content: [Additional file 5] 537 terms enriched in molecular function of Gene Ontology enrichment (circRNA-hosting gene of all samples).
Supplementary_files_format_and_content: [Additional file 6] 330 terms enriched in cellular component of Gene Ontology enrichment (circRNA-hosting gene of all samples).
Supplementary_files_format_and_content: [Additional file 7] 1482 terms enriched in biological processes of Gene Ontology enrichment (circRNA-hosting gene of all samples).
Supplementary_files_format_and_content: [Additional file 8] 152 KEGG pathways were enriched in bovine muscle tissues (circRNA-hosting gene of all samples).

organism: Bos taurus

source_name: adult longissimus muscle

growth_protocol: Six longissimus muscle samples from Qinchuan cattles of two developmental states (embryonic, 90 d; and adult, 24 M old) were collected from Yiming abattoir, a local slaughterhouse of Xi’An, P.R. China. Tissue samples were snap-frozen in liquid nitrogen and stored at –80°C freezer until use.

extract_protocol:
Total RNA was assessed by electrophoresis on a denaturing agarose gel and quantified by NanoDrop spectrophotometer (NanoDrop, USA) and Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). The total RNA samples (3 mg) were treated with the epicentre Ribo-ZeroTM Kit to remove rRNA before constructing the RNA-seq libraries. For RNase R treatment, ribosome-depleted RNA was incubated for 15 min at 37°C with 5 units μg−1 of RNase R (Epicentre Technologies, Madison, WI).
Then the rRNA depleted RNA samples or circRNAs samples were fragmented and used to synthesize first- and second-strand complementary DNA (cDNA) with random hexamer primers, dNTPs and DNA Polymerase I. The cDNA fragments were cleaned and concentrated using AMPure XP beads, then the ends were repaired and modified with T4 DNA polymerase Klenow DNA polymerase to add A and adapter at the 3’ end of the DNA fragments. The ligated cDNA products were purified with AMPure XP beads and treated with uracil DNA glycosylase to remove the second-strand cDNA.
Purified first-strand cDNA was subjected to PCR amplification, and the libraries were quality controlled with an Agilent 2100 Bioanalyzer and sequenced by HiSeq 2500 (Illumina, San Diego, CA) on a 150 bp paired-end (PE) run.

tag: breed

value: Qinchuan

value: skeletal muscle

tag: developmental stage

value: adult

tag: age


title: Adult2_circRNA

department: College of Animal Science and Technology

description: circRNA


title: BP_submerged_fast_pool2

description: HSF pool 2

source_name: F mussels reared in BP diet. Experiment I

value: BP


title: BP_submerged_fast_pool1

description: HSF pool 1


title: Mix sample_circRNA

description: circRNA

value: embryo+adult

value: 90 d and 24 M


title: mLEC_EPZ5676_Input

city: Seoul

first: Chanhyeok

last: Park

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

country: South Korea

institute: KIST (Korea Institute of Science and Technology)

library_source: genomic

data_processing:
ChIP-seq raw reads were aligned to mouse mm9 genome using Bowtie2 (v2.2.9).
SAMtools (v1.2) was used for the data arrangement.
ChIP-seq peaks were called using the following MACS2 (v2.1.0) parameters: -B --nomodel -f BAM -g mm --broad -p 1e-5.
Genome_build: mm9
Supplementary_files_format_and_content: The bigwig files were generated using bedGraphToBigWig

molecule: genomic DNA

organism: Mus musculus

source_name: Lymphatic endothelial cell

growth_protocol: Primary mouse dermal LECs derived from C57BL/6 were were grown in CellBiologics culture medium (cat# M1168) supplemented with VEGF, ECGS, Heparin, EGF, Hydrocortisone, L-glutamine, Antbiotic-Antimycotic solution, FBS). Cells were maintained in a humidified incubator equilibrated with 5% CO2 at 37°C.

extract_protocol:
The primary mouse dermal LECs derived from C57BL/6 were were maintained in CellBiologics culture medium supplemented with VEGF, ECGS, Heparin, EGF, Hydrocortisone, L-glutamine, Antbiotic-Antimycotic solution, FBS). Approximately 1-3 x 10^7 cells were used for each ChIP-Seq assay. The chromatin was precipitated by H3K79me2 antibody (ab3594, Abcam) and immunoprecipitated DNAs were purified with treatment of proteinase K, phenol/chloroform and ethanol precipitation.
ChIP-Seq libraries were produced using Truseq ChIP Sample kit (Illumina) according to manufacturer’s instruction.

treatment_protocol: The primary mouse dermal LECs were treated with either DMSO or 2M of EPZ5676.

tag: strain

value: Skin

tag: cell type

value: Mouse primary dermal lymphatic endothelial cell

tag: passages

tag: treatment

tag: chip antibody

value: input


title: BP_submerged_fast_pool3

description: HSF pool 3


title: antagomiR-122+CL4

city: Jerusalem 9112001

first: chofit

last: chai

address: Ein Karem

department: gene therapy

country: Israel

institute: hadassah

description: every sample represent one mouse

data_processing:
base-calling with bcl2fastq (v2.15.0.4), default parameters
quality-trimming at both ends, using in-house Perl scripts, with a quality threshold of 32.
adapter removal with cutadapt (version 1.7.1), using parameters -O 1, --match-read-wildcards and -m 15.
filtering by quality with fastq_quality_filter of the FASTX package (version 0.0.14), using parameters -q20 and -p 90.
Alignment with TopHat (v2.0.13), using parameters -G Ensembl_78_genes.gtf, -N 5, --read-gap-length 5, --read-edit-dist 10, --segment-length 20, --read-realign-edit-dist 2, --coverage-search and –microexon-search.
Quantification, normalization and differential expression were done with the Cufflinks package (v2.2.1). cuffquant using parameters -b, -u and -M; cuffdiff using default parameters.
Genome_build: GRCm38
Supplementary_files_format_and_content: An Excel file, where the first 14 columns are gene details (according to column headers), next are FPKM values per each sample (as computed with Cufflinks), next are cuffdiff results for comparing antagomiR-122 to antagomiR-cont samples.

source_name: Liver

growth_protocol: Male C57BL/6 mice, 7-8 weeks old, were purchased from Harlan Laboratories (Jerusalem, Israel). All mice were kept in a pathogen-free facility, under a 12 h light/dark cycle

extract_protocol:
Livers were removed,  frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL/6 mice were tail vain injected with 5 µg/mice antagomiR-122 or antagomiR-control, 48 hours later they were injected s.c with 1mg/kg CL316243, 2 hours later they were sacrificed.

value: antagomiR-122 and CL316243

value: liver


title: antagomiR-122+CL2

description: every sample represent one mouse


title: antagomiR-122+CL1

description: every sample represent one mouse


title: antagomiR-cont+CL4

description: every sample represent one mouse

value: antagomiR-control and CL316243


title: antagomiR-122+CL3

description: every sample represent one mouse


title: BP_submerged_slow_pool4

description: HSS pool 4

source_name: S mussels reared in BP diet. Experiment I

value: S


title: antagomiR-cont+CL2

description: every sample represent one mouse


title: AP_submerged_slow_pool1

description: LSS pool 1

source_name: S mussels reared in AP diet. Experiment I


title: AP_submerged_fast_pool4

description: LSF pool 4

value: F


title: AP_submerged_fast_pool1

description: LSF pool 1

value: AP


title: BP_submerged_slow_pool1

description: HSS pool 1

value: submerged


title: antagomiR-cont+CL1

description: every sample represent one mouse


title: RNAseq.KO.1-1

status: Public on Oct 09 2018

city: Atlanta

first: Ying

last: Cheng

state: GA

address: 615 Michael Street

department: Human Genetics

country: USA

institute: Emory University

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to mm9 using tophat v2.0.13 and differential RPKM expression values were extracted using cuffdiff v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited file; including gene name, sample name, RPKM value, log2 folder change value

source_name: Mice cortex

growth_protocol: All the mice were housed in the animal facilities of the Institute of Zoology, Chinese Academy of Sciences.Institutional Animal Care and Use Committee.

extract_protocol:
Mouse cortex were dissected from the brain. RNA was then reverse transcribed using a SuperScript® III First-Strand Synthesis System (Invitrogen).
RNA-seq libraries were generated from duplicated samples per condition using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer’s protocol. The RNA-seq libraries were sequenced as 50-cycle pair-end runs using Illumina HiSeq 2000.

value: brain

tag: tissue compartment

value: cortex

tag: genotype

value: miR-137 KO


title: RNAseq.Het.1-2


title: RNAseq.KO.2-1


title: RNAseq.KO.1-2


title: RNAseq.Het.1-1


title: RNAseq.Het.2-1


title: RNAseq.WT.2-2

value: wildtype


title: RNAseq.Het.2-2


title: RNAseq.WT.2-1


title: RNAseq.WT.1-1


title: antagomiR-cont+CL3

description: every sample represent one mouse


title: RNAseq.WT.1-2


title: Naïve 3

city: Toronto

first: David

middle: G

last: Brooks

state: Ontario

address: 610 University Avenue

department: Research

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
Base calling was performed using RTA 2.4.11
bcl2fastq2 2.19.1 was used to convert from bcl to fastq
reads were aligned to the GRCm38 genome using hisat2 2.1.0
samtools 1.3.1 was used to sort the alignment sam file from hisat2
genes counts were quantified using htseq-count 0.9.1
Genome_build: GRCm38 build 88
Supplementary_files_format_and_content: Tab delimited text file showing raw counts for each gene (by ensembl ID) for each sample

source_name: GP33-specific CD8 TCR transgenic cells

extract_protocol:
LCMV-Gp33-specific CD8 T cell transgenic (P14) cells were transferred into mice that had been infected 21 days earlier with LCMV-Cl13 (late prime) or into naïve mice immediately infected with LCMV Cl-13 (early prime). Sixty hours post-infection mice were sacrificed and splenocytes from 4-5 mice were pooled and single cell suspensions were stained for virus-specific P14 cells and FACSorted directly into RLT buffer. Naive P14 T cells were directly islated from P14 mice. RNA was isolated using a single cell RNA purification kit (Norgen Biotech Corp.) according to manufacturer’s instructions. SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) was used per manufacturer’s instructions for amplification of RNA and subsequent cDNA synthesis.
All samples proceeded through NexteraXT DNA Library Preparation (Illumina) using NexteraXT Index Kit V1 or V2 Set A (Illumina) following manufacturer’s instructions.

value: CD8 T cell

tag: cell subtype

value: Naive


title: Late Prime 3

value: Late Prime


title: Naïve 2


title: Naïve 1


title: Late Prime 1


title: control mouse brain, RiboLace RIBOseq, P5, rep 2

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

description: active ribosome profiling with RiboLace from a control mouse brain at P5

data_processing:
Raw reads were processed by removing 5’ adapters, discarding reads shorter than 20 nucleotides and trimming the first nucleotide (using Trimmomatic v0.36). Reads mapping on rRNAs and tRNAs (downloaded from the SILVA rRNA and the Genomic tRNA databases respectively) were removed. The remaining reads were aligned to the mouse transcriptome (Ensembl v81, corresponding to GENCODE mouse M6) with Bowtie2 (v2.2.6) employing the default settings. All reads aligning to the very same region were collapsed to avoid potential PCR duplicates, and only strand-specific reads were kept.  The number of ribosome protected fragments was determined with samtools idxstats.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text files including a brief annotation and transcript-specific counts of ribosome protected fragments

molecule: cytoplasmic RNA

source_name: control mouse brain, active ribosome profiling with RiboLace, biological replicate 2

growth_protocol: Heterozygos Taiwanese mice (Smn+/-; SMN2tg/0) were used in this study (Hsieh-Li et al., 2000; Riessland et al., 2010; Somers et al., 2015). All mice were on a congenic FVB background, with colonies at the University of Edinburgh established from breeding pairs purchased from Jackson Labs. Litters were retrospectively genotyped using standard PCR protocols. All mice were housed within the animal care facilities in Edinburgh under standard SPF conditions. All animal procedures and breeding were performed in accordance with University of Edinburgh institutional guidelines and under appropriate project and personal licenses granted by the UK Home Office.

extract_protocol:
Cytoplasmic lysates were prepared pulverizing frozen mouse brains in a pestle and mortar cooled by liquid nitrogen and dissolving the powder in lysis buffer. Lysates were clarified by two following centrifugations.
For RiboLace Ribo-Seq, the RNA absorbance of the lysate (at 260 nm) was measured by Nanodrop ND-1000 UV-VIS Spectrophotometer and the lysate diluted to 1.7 a.u. A260/µL. ARTseq nuclease was used to footprint ribosomes for 45 min at 20°C. The reaction was added directly to the RiboLace beads and the suspension incubated on a wheel for at least 1 hour in orbital rotation, 3 rpm at 4°C. After incubation, the tubes were kept on ice on a magnetic stand for 5 min to capture the beads–bounded-ribosomes. The supernatant was discarded (unbound fraction) and beads washed two times with 500 µL of a buffer. Ribosome Protected Fragments (RPFs) were extracted with acid-phenol:chloroform:isoamylalcohol and isopropanol precipitation and size selected (25-35 nt) by UREA Page. RPFs were treated to remove 3’ phosphate, ligated to the 3’ adaptor and purified by UREA page. Ligated RPFs were retrotranscribed and the cDNA circularized. Libraries were finally amplified by PCR using Illumina PCR Primer Index. Libraries were sequenced on an Illumina HiSeq2500.

treatment_protocol: Neonatal mice were euthanized at P5 by overdose of anaesthetic, before decapitation to allow the brain to be removed. Following isolation, all tissues were immediately snap-frozen on dry ice and then transferred to -80 °C for storage.

value: Smn+/-; SMN2tg/0

tag: rna fraction

value: RiboLace-RIBOseq

tag: Stage

tag: replicate


title: Early Prime 3

value: Early Prime


title: RNAseq.KO.2-2


title: Early Prime 2


title: IFNβ

city: Rockville

first: Yukun

last: Guan

state: MD

address: 5625 Fishers Lane, Room 2S-30

institute: NIAAA

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 transcription reference using bwa.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

organism: Homo sapiens

source_name: THP1 cells

extract_protocol:
Total RNA was isolated using TRIzol reagent, according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: agent

value: IFNB


title: VACV

value: VACV


title: Control

value: media


title: Mn


title: control mouse brain, RiboLace RIBOseq, P5, rep 1

source_name: control mouse brain, active ribosome profiling with RiboLace, biological replicate 1


title: PD-15

status: Public on Oct 08 2018

city: La Jolla

first: Jenhan

last: Tao

state: CA

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: UC San Diego

data_processing:
Reads from each RNA-Seq sample were aligned to the hg38 genome using STAR.
Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to calculate RPKM from the gene bodies of RefSeq genes and other analyses in the study. Statistical tests in this study were performed using custom Python scripts.
Genome_build: hg38
Supplementary_files_format_and_content: Processed files include a expression text file that contains expression values for each sample (RNA-Seq expression data, using default HOMER parameters).  All genomic coordinates are relative to hg38 human assembly.

molecule: polyA RNA

source_name: Monocyte cells

extract_protocol:
Isolation of untouched monocytes from PBMCs by using the Pan Monocyte Isolation Kit (Order No. 130-096-537)
According to Gosselin et al., Cell, 2014

tag: group

value: Parkinson's disease

tag: age [y]

tag: Sex

value: male

tag: disease stage [hoehn & yahr]


title: PD-21


title: PD-14


title: PD-23


title: Late Prime 2


title: PD-12


title: Control-49

value: Control


title: PD-11


title: Control-48


title: PD-09


title: Control-44


title: PD-08


title: Early Prime 1


title: Control-20


title: Control-27


title: Control-17


title: Control-22


title: RNA-seq [RNA-Oct4-GFP-H-ESC]

city: Shanghai City

first: Naihe

last: Jing

address: Yueyang Road 320

institute: shanghai institute of biochemistry and cell biology

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For the RNA-seq data, the annotation of the transcriptome were defined by combining the UCSC mm10 refSeq genes. Then the cleaned reads were aligned to the mm10 reference genome using TopHat (version 2.0.9) with the default parameters. HTSeq were used to count the number of reads mapped in each annotated genes based on the mapping results. This results were further used for the calculating of differential expressed genes using DESeq2
Unique reads were mapped to mm10 using bowtie (version 0.12.8), and then peaks were called using MACS (macs 14 1.4.2) with default parameter. Chromatin states were identified and characterized using ChromHMM (v1.11).
Genome_build: mm10
Supplementary_files_format_and_content: the bedgraph files for ChIPseq; the 'Genes.FPKM.DR-ESC.Oct4-GFP-ESC.Norm.xls fils include the expression (FPKM) of all the RefSeq genes for each sample.

source_name: mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells Oct4-GFP-ESC were cultured in standard medium supplemented with serum plus LIF (10 ng/ml), Oct4-GFP ESCs were supported with extra mitomycin C-treated fibroblast feeder cells;

extract_protocol:
RNA from cells were extracted by Trizol (invitrogen, 15596018), then precipitated by isopropanol; genomic DNA were extrated by phenol chloroform extraction and precipitated by ethanol.
Libraries of genomic DNA were construted by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L);  Libraries of polyA RNA were constructed by using NEBNext poly(A) RNAseq library preparation kits (EE6100L).

treatment_protocol: The neural differentation protocol were adapted from previous report (Nat Biotechnol, 2003. 21(2): p. 183-6) in N2B27 medium (50% DMEM/F12 and 50% Neurobasal medium (both from GIBCO) supplemented with 1 × N2, 1 × B27 (GIBCO), 0.1% bovine serum albumin fraction V (Roche), 1 mM Glutamine (GIBCO) and 0.1 mM β-mercaptoethanol (GIBCO)); Oct4-GFP-H ESC were enriched by sorting for high GFP signal Oct4-GFP cells; DR-ESC were enriched by sorting GFP positive cells in day8 neural differentiation system and further cultured in embryonic stem cell medium; NPC(GFP-) cells were enriched by sorting GFP negative cells in day8 neural differentiation system.

value: mouse embryonic stem cells


title: RNA-seq [RNA-NPC(GFP-)]

source_name: mouse neural progenitor cells

value: mouse neural progenitor cells


title: RNA-seq [RNA-Oct4-GFP-ESC]


title: tmk2glucose3

city: Campinas

first: Gabriela

middle: F

last: Persinoti

state: São Paulo

address: Rua Giuseppe Máximo Scalfaro, 10.000

department: Brazilian Biorenewables National Laboratory LNBR

country: Brazil

institute: Brazilian Center for Research in Energy and Materials CNPEM

data_processing:
Base calls and demultiplexing was performed with Illumina bcl2fastq version 1.8.4
The Illumina HiSeq 2500 system was used to sequence the transcriptome of Trichoderma reesei, yielding approximately 10 - 15 million 100-bp paired-end reads per sample. These sequences were firstly quality checked and filtered using FASTQC and Trimommatic v.0.32 (Bolger, et al, 2014).
Trimmed reads were mapped to the Trichoderma reesei 2.0 reference genome available the JGI Genome Portal (http://genome.jgi-psf.org/Trire2/Trire2.home.html) using Tohat2 v2.0.4 (Kim et al, 2013), allowing two mismatches and only unique alignments.
Samtools version 0.1.18 (Li et al., 2009) was used to process the alignments files which were visualized using the Integrative Genomics Viewer (Thorvaldsdottir et al., 2012).
Aligned reads were quantified using htseq-count v0.6.0 (Anders et al 2105) with Trichoderma reesei gene modes, that includes 9129 genes models.
Bioconductor DESeq2 package version v 1.6.3 (Love et al, 2014) was employed to perform the differential expression analysis, using two-fold change, i.e., log2 fold change ≥ 1 or ≤ -1 and adjusted p-value ≤ 0.05 as thresholds.
Genome_build: http://genome.jgi-psf.org/Trire2/Trire2.home.html
Supplementary_files_format_and_content: Processed data files are presented as tab delimited txt format. Raw count and TPM data are provided, being expressed as “Protein ID” “Sample ID”
Supplementary_files_format_and_content: Gene expression results are expressed as Log 2 Fold Change between indicated samples and the respective adjusted p-value calculated by DESeq2.

organism: Trichoderma reesei

source_name: mycelia

growth_protocol: The parental and mutant strains were grown in MEX medium at 30°C for 7-10 days for complete sporulation.

extract_protocol:
Total RNA was extracted using the TRIzol kit (Invitrogen) according to manufacture's instructions.
RNA-seq libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: For gene expression assays, a spore suspension containing approximately 107 cells mL-1 was inoculated into 200 mL of Mandels-Andreotti medium (Schmollet al. 2009) containing 2% of glucose as the carbon source, and 1% of sugarcane bagasse or 1% of glycerol. Cultures on glucose were incubated at 30º C for 48h. For sugarcane bagasse cultures, strains were first growth on MEX medium 1% glycerol for 24 h, then transferred to sugarcane bagasse media for 48h.

tag: strain/genotype

value: mutant tmk2

value: glucose


title: RNA-seq [RNA-DR-ESC]


title: K27ac ChIP [Oct4-GFP-ESC-K27ac]

tag: antibody


title: tmk2glycerol3

value: glycerol


title: tmk2glycerol1


title: tmk2glucose2


title: tmk2cane3

value: sugarcane


title: 10APM_G4_input_n3

first: Yu-Jia

last: Shiah

address: MaRS Centre 661 University Avenue Suite 510

department: Informatics and Bio-computing

institute: Ontario Institute for Cancer Research

data_processing:
ChIP-seq reads were aligned using STAR aligner (v2.5.2a) mapped against GRCh37 with Gencode Annotations v24 lifted to GRCh37
Reads with low mapping  quality (MAPQ < 20) were filtered out after alignment
All filtered BAM files were then sorted using SAMtools (v1.3). Duplicated reads that match to the same genomic locations and strands were removed using picard tool (v2.7.1, MarkDuplicates)
Quality control and  fragment size estimation were conducted using ENCODE phantompeakqualtools
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Narrow peaks were identified using MACS2 (v2.1.0) with default settings. For samples with very few peaks (< 1000), MACS2 was re-run without building the shifting model but with the use of a fragment size that was calculated using phantomepeakqualtools settings

source_name: MCF10A cell line

growth_protocol: MCF10A cells were cultured in DMEM/F12 (1:1) media with 5% horse serum (HS) (Gibco), 0.1 μg/mL cholera toxin (Sigma), 0.02 μg/mL epidermal growth factor (EGF) (R&D Systems), 0.5 μg/mL hydrocortisone (Sigma), and 10 μg/mL insulin (Sigma).

extract_protocol:
ChIP was performed with 10×10^6 cells per reaction. Cells were crosslinked in 1% formaldehyde, quenched in 0.125 M glycine, and lysed in Cell Lysis Buffer (50 mM Tris pH 8.1, 10 mM EDTA, 1% SDS). Lysates were sonicated with Bioruptor Pico (Diagenode) and diluted in Dilution Buffer (20 mM Tris pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) with pre-incubated mixture of antibody and Dynabeads Protein A and Protein G (Invitrogen). After overnight incubation, samples were washed three times with Washing Buffer (50 mM HEPES pH 7.6, 0.5 M LiCl, 1 mM EDTA, 0.7% sodium deoxycholate, 1% NP-40) then two times with TE Buffer. DNA was eluted overnight in Decrosslinking Buffer (0.1 M NaHCO3, 1% SDS) and purified with QIAquick PCR Purification Kit (Qiagen).
Samples were quantified using Qubit fluorometric quantitation (Thermo Fisher). Sample libraries were prepared using ThruPLEX DNA-seq kit as per the manufacturer’s protocol (Rubicon Genomics) and sequenced using Illumina HiSeq2500 with Single Read 50bp protocol multiplexed to achieve an average of 25M reads per sample at the Princess Margaret Genomics Centre (Toronto, Canada).

treatment_protocol: Asynchronously growing cells were seeded and treated with 2 μg/mL doxycycline (Sigma) for 72 hours to induce shRNA.

tag: cell type

value: immortalized breast epithelial cells

tag: plasmid 1

value: pBABE-hygro-MYC

tag: plasmid 2

tag: plasmid 3

value: pLKO-tetON-puro-shG9a 4

value: Input


title: K27ac ChIP [DR-ESC-K27ac  ]


title: Control-30


title: tmk2cane2

tag: treatment


title: 10APM_G4_input_n2

tag: chip antibody


title: tmk2glycerol2


title: K27me3 ChIP [Oct4-GFP-ESC-K27M3]


title: K27me3 ChIP [DR-ESC-K27M3]


title: tmk1glycerol3

value: mutant tmk1


title: K4me1 ChIP [Oct4-GFP-ESC-K4M1 ]


title: 10APM_G4_input_n1


title: 10APM_G1_input_n3

value: pLKO-tetON-puro-shG9a 1


title: tmk1glycerol2


title: 10APM_G1_input_n2


title: tmk2glucose1


title: tmk1glucose3


title: 10APM_S_input_n3

value: pLKO-tetON-puro-shSCR


title: tmk1glycerol1


title: tmk1glucose2


title: K4me3 ChIP [Oct4-GFP-ESC-K4M3]


title: 10APM_G1_input_n1


title: tmk1glucose1


title: genomic input sequencing [DR-ESC-IN]


title: 10APM_S_input_n2


title: 10APM_G4_MYC_n3

value: MYC (N262, homemade)


title: 10APM_S_input_n1


title: K4me1 ChIP [DR-ESC-K4M1]


title: genomic input sequencing [Oct4-GFP-ESC-IN]


title: KO-LSK (Utx/p53 DKO-LSK)

city: Shanghai

first: Liting

last: Zheng

address: 320 Yueyang Road

institute: Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences

data_processing:
Basecalls performed using bcl2fastq version 1.8.4
Deleted adaptor, reads with N>3%,and low-quality sequence from sequenced reads, then mapped the reads to mm9 whole genome using tophat v2.1.0 with parameters --no-mixed --no-discordant
Reads Per Kilobase of exon per Megabase of library size (RPKM) for each refseq genes and differentially expressed transcripts annotated with refseq were obtained using gfold v1.1.4.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files generated by gfold including gfold reliable fold change and RPKM values for each refseq genes

source_name: hematopoietic stem cell

extract_protocol:
LSK cells were sorted directly into TRIzol (Invitrogen),then column-purified with Direct-zol RNA MiniPrep Kit (Zymo research) to obtain total RNA.The RNA samples were tested with Agilent 2100/agarose electrophoresis.
RNA libraries were prepared using standard Illumina protocols. 1.RNA was purified with Ampli-oligT,then reversely transcripted with SMART cDNA Library Construction Kit to get the first strand of cDNA; 2.The DNA was amplified and purified with Ampure xp beads agencourt; 3.Fragmentation, purification, and amplification of DNA with Thermal cyclerS1000 (Bio-Rad); 4.Test the DNA with agarose electrophoresis to obtain a 250bp-350bp main band, then purified with Ampure xp beads agencourt; 5.Test the quanlity of libraries with StepOne Plus qPCR (ABI).

treatment_protocol: LSK (Lin-Ckit+Sca1+) cells were sorted from 8-week-old p53 KO and Utx/p53 DKO mice

tag: strain background

tag: genotype/background

value: Utx/p53 DKO

tag: age

value: 8 weeks old

value: hematopoietic stem cell

tag: sorted fraction

value: LSK (Lin-Ckit+Sca1+) cells


title: tmk1cane2


title: tmk2cane1


title: K4me3 ChIP [DR-ESC-K4M3]

value: mouse embryonic stem cells


title: 10APM_G4_MYC_n2


title: WT-LSK (p53 KO-LSK)

value: p53 KO


title: PD-10

value: Parkinson's disease

value: male


title: tmk1cane1

value: sugarcane


title: QM6Aglycerol3

value: parental QM6a

value: glycerol


title: 10APM_G4_MYC_n1

value: immortalized breast epithelial cells

value: pBABE-hygro-MYC

value: pLKO-tetON-puro-shG9a 4


title: QM6Aglycerol2


title: tmk1cane3

value: mutant tmk1


title: QM6Aglycerol1


title: QM6Aglucose3

value: glucose


title: 10APM_S_MYC_n3

value: pLKO-tetON-puro-shSCR

value: MYC (N262, homemade)


title: QM6Aglucose2


title: QM6Acane3


title: 10APM_S_MYC_n1


title: QM6Aglucose1


title: QM6Acane1


title: QM6Acane2


title: 10APM_G1_MYC_n2

value: pLKO-tetON-puro-shG9a 1


title: 10APM_G1_MYC_n1


title: 10APM_S_MYC_n2


title: pro-B cells 1

status: Public on Oct 07 2018

city: Parkville

first: Rhys

last: Allan

state: Victoria

address: 1G Royal Parade

department: Molecular Immunology

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Reads pairs from each sample were aligned to the mouse genome and counted into 50 kB bin pairs using the R package diffHic v1.6.0.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files give the number of reads supporting each interaction, where an interaction corresponds to a pair of 50 kB bins. The .mtx files are space-delimited text files in Matrix Market Exchange format with integer entries. The first two columns give the indices of the two interacting genomic bins and the third column gives the read count. Bin pairs with no reads are omitted. The indices correspond to rows of the BED format file GenomicRegions.bed.gz. The processed data files can be read into R using the readMTX2IntSet function of the diffHic package or the readMM function of the Matrix package.

source_name: Pro-B cells

extract_protocol:
As outlined in Rao et al, Cell, 2014
In situ HiC was performed as previously published (Rao et al, Cell, 2014). Primary immune cell libraries were generated in biological duplicate, while wild type and Pax5-/- libraries were in biological triplicate.

value: Pro-B cells

tag: strain

tag: gender

tag: tissue

value: Bone marrow


title: Plasmablasts 2

source_name: LPS-stimulated plasmablasts

value: Plasmablasts

value: Spleen

value: 4 day in vitro LPS stimulation


title: pro-B cells 3

value: male


title: Pax5-/- Pax5:ER pro-B cells, untreated 1

tag: genotype/variation

value: Pax5-/- Pax5:ER


title: pro-B cells 2


title: Pax5-/- Pax5:ER pro-B cells, untreated 2


title: Plasmablasts 1


title: MEFs 2

source_name: MEFs

value: MEFs

value: Embryo


title: Pax5-/- pro-B cells 3


title: LSKs 2

source_name: Bone marrow LSKs

value: LSKs


title: Pax5-/- pro-B cells 2


title: MEFs 1


title: LSKs 1


title: Tr/MZ B cells 2

source_name: Splenic Tr/MZ B cells

value: Tr/MZ B cells

value: spleen


title: 10APM_G1_MYC_n3

value: immortalized breast epithelial cells

value: pBABE-hygro-MYC


title: Granulocytes 1

source_name: Bone marrow granulocytes

value: Granulocytes


title: CD4+ T cell 1

source_name: Splenic CD4+ T cells

value: CD4+ T cells


title: Pax5-/- Pax5:ER pro-B cells, 24hr b-estradiol treated 2

value: 24 hour b-estradiol treated Pax5:ER pro-B cells


title: Pax5-/- Pax5:ER pro-B cells, 24hr b-estradiol treated 1

extract_protocol:
In situ Hi-C was performed as described by Rao et al (Cell, 2014, PMID 25497547).
Libraries were prepared for sequencing on an Illumina NextSeq 500 using standard Illumina protocols.

value: Pro-B cells

value: bone marrow

value: 24 hour b-estradiol


title: Tr/MZ B cells 1


title: Follicular B cells 2

source_name: Splenic follicular B cells

value: follicular B cells


title: Wildtype pro-B cell RNA 1

data_processing:
Reads were mapped to the mouse genome using Rsubread v1.16.1 with unique alignment. Read pairs were counted by gene using the featureCounts function and Rsubread's built-in RefSeq annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of read pairs mapped to that gene.

growth_protocol: B220+ cells from wild type and Pax5-/- bone marrow were expanded on an OP9 cell layer in MEM+Glutamax (Gibco) supplemented with 10mM HEPES, 1mM Sodium Pyruvate, 1x non essential amino acids (Sigma) and 50μM beta mercaptoethanol (Sigma).

extract_protocol: RNA was isolated from cells using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.

value: wildtype

value: female

value: Bone marrow


title: Activated B cells 1

source_name: LPS-stimulated B cells

value: Activated B cells

value: male

value: Spleen

value: 4 day in vitro LPS stimulation


title: Pax5-/- pro-B cell RNA 2

source_name: Pax5 -/- pro-B cells

growth_protocol: B220+ cells from wild type and Pax5-/- bone marrow were expanded on an OP9 cell layer in MEM+Glutamax (Gibco) supplemented with 10mM HEPES, 1mM Sodium Pyruvate, 1x non essential amino acids (Sigma) and 50μM beta mercaptoethanol (Sigma). At day 7, the IgM- fraction was isolated using immunomagnetic depletion, following manufacturer’s instructions.


title: Pax5-/- pro-B cell RNA 1


title: Pax5-/- pro-B cells 1


title: mLEC_DMSO_Input

source_name: Lymphatic endothelial cell

value: Skin

value: Mouse primary dermal lymphatic endothelial cell

tag: passages

value: DMSO

value: input


title: Granulocytes 2

value: Granulocytes


title: CD4+ T cell 2

value: CD4+ T cells


title: Activated B cells 2


title: gld-2 (ccr-4  RNAi) rep1

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

institute: Monash University

description:
Run 2, Illumina index 10
Protocol: PAT-Seq

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stripped of trailing poly(A) and adaptor sequence (allowing for up to 1 in 5 sequencing errors).
Reads are aligned using Bowtie2 (v2.2.4, http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Multi-mapping reads are assigned a location at random from the best alignments.
Alignments are extended where the stripped poly(A) sequence matches the reference genome. The remaining, untemplated, poly(A) length is taken as the poly(A) tail length for that read. A read is called as having a poly(A) tail if this length is at least 4 As.
Reads aligning to genes are counted. Transcript locations were downloaded from the Refseq track of the UCSC genome browser. Overlapping transcripts (mostly isoforms) were merged. As 3'UTR annotations are not always accurate, reads up to 1000 bases down-strand of a gene are counted towards that gene. Where a read might be assigned to multiple genes, it is assigned to the gene with annotated 3' end nearest to the alignment's 3' end. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Genome_build: ce10
Supplementary_files_format_and_content: count.csv contains counts of reads aligning to each gene in each sample.  tail_count.csv contains counts of reads with a poly(A) tail aligning to each gene in each sample. This is used when detecting differential tail length as the more reads there are, the higher the accuracy of the average in tail.csv.  tail.csv contains the average poly(A) tail length observed in reads with a poly(A) tail for each gene in each sample.  These files are sufficient for differential expression and differential tail length analysis with the statistics package "Fitnoise".    gene.csv lists the genomic locations of the genes that were used. Locations are 1-based.

organism: Caenorhabditis elegans

source_name: gld-2 (ccr-4  RNAi) rep1

growth_protocol: C. elegans N2 (wildtype) worms were grown on 15 cm plates with Nematode Growth Medium spotted with concetrated E. coli OP50.

extract_protocol:
Total RNA was extracted from snap frozen cell pellets Trizol extraction. 1 microgram of this was input into the library preperation.
Library construction was by the PAT-seq approach. Breifly this involves a modified the ePAT approach to tagging adenylated RNA to generate libraries suitable for deep sequencing.  Briefly, adenylated RNA is sequence specifically extended by dNTPs using Klenow polymerase and an annealed DNA anchor oligonucleotide. This takes advantage of the native function of DNA polymerase to extend an RNA primer from a DNA template in second strand synthesis. Importantly, any unwanted priming to internal poly(A)-tracts in RNA is avoided by a requirement for 3’ extension in subsequent fragment selection and reverse transcription. No ribosome depletion is necessary. Here, the anchor sequence was compatible with the Illumina index primers and included a 5’ biotin moiety to facilitate handling. In a second step, the 3’ tagged RNA was subject to limited fragmentation by RNase T1. This cleaves RNA after G-residues and ensures that cleavage is only possible within the body of the RNA, not the poly(A)-tract or the DNA sequence of the extended tag. The fragmented RNA was 5’ phosphorylated to allow RNA Ligase 2 mediated ligation of an Illumina compatible splinted-linker to the RNA fragments. Reverse transcription was primed from the anchor sequence. Note: All manipulations after limited fragmentation were performed in association with streptavidin magnetic beads. The cDNA PAT-seq libraries was eluted from beads, size-selected by Urea PAGE and amplified with primers that introduce the features for directional Illumina sequencing and indexing. In samples analysed here, the window of selection was between 120-300 bases. This size range was selected to allow for ≥ 25 bases of 3’UTR sequence to map reads to the genome, the an average yeast poly(A)-tail of ~25 bases (maximum ~90 bases), the majority of reads would contain heterogeneous 5’ sequence of sufficient length to map uniquely to the yeast genome. Note: all reads run in 5’ to 3’ direction from unique sequence into a variable length of poly(A) homopolymers. This means that color balance is preserved and that any low fidelity within the homopolymers is limited to the end of the read.
9pM of libraries per lane using Illumina c-bot. Illumina protocol 15006165 Rev J, July 2012
1 x 150bp sequencing using Illumina protocol 15035788 Rev A, Oct 2012

treatment_protocol: To induce RNAi, C. elegans N2 (wildtype) worms were grown on 15 cm plates with Nematode Growth Medium spotted with concentrated E. coli HT115(DE3) expressing dsRNA of interest.

tag: developmental stage

value: young adult

value: whole worm


title: 1+2 cell egg rep2

description:
Run 2, Illumina index 19
Protocol: PAT-Seq

source_name: 1+2 cell egg rep2

value: One and two cell embryos

value: embryo


title: gld-2 (ccf-1  RNAi) rep1

description:
Run 2, Illumina index 9
Protocol: PAT-Seq

source_name: gld-2 (ccf-1  RNAi) rep1


title: gld-2 (caf-1  RNAi) rep2

description:
Run 2, Illumina index 13
Protocol: PAT-Seq

source_name: gld-2 (caf-1  RNAi) rep2


title: Follicular B cells 1

value: follicular B cells

value: spleen


title: gld-2 (caf-1  RNAi) rep1

description:
Run 2, Illumina index 7
Protocol: PAT-Seq

source_name: gld-2 caf-1  RNAi) rep1


title: gld-2 (ccf-1  RNAi) rep2

description:
Run 2, Illumina index 15
Protocol: PAT-Seq

source_name: gld-2 (ccf-1  RNAi) rep2


title: gld-2  (pcb19 non targetting control RNAi) rep2

description:
Run 2, Illumina index 11
Protocol: PAT-Seq


title: gld-2 (panl-2  RNAi) rep2

description:
Run 2, Illumina index 14
Protocol: PAT-Seq

source_name: gld-2 (panl-2  RNAi) rep2


title: gld-2 (parn-1  RNAi) rep1

description:
Run 2, Illumina index 6
Protocol: PAT-Seq

source_name: gld-2 (parn-1  RNAi) rep1


title: 1+2 cell egg rep1

description:
Run 2, Illumina index 17
Protocol: PAT-Seq

source_name: 1+2 cell egg rep1


title: gld-2 (ccr-4  RNAi) rep2

description:
Run 2, Illumina index 16
Protocol: PAT-Seq

source_name: gld-2 (ccr-4  RNAi) rep2


title: gld-2  (pcb19 non targetting control RNAi) rep1

description:
Run 2, Illumina index 5
Protocol: PAT-Seq


title: gld-2 (panl-2  RNAi) rep1

description:
Run 2, Illumina index 8
Protocol: PAT-Seq

source_name: gld-2 (panl-2  RNAi) rep1


title: Sample_Plate2_A4_AMCA

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

institute: Weizmann Institute of Science

description: cell lysate

data_processing:
cutadapt used to trim poly A and poly T,  low quality and adapter (fastq raw files submitted are after trimming)
Reads were mapped with TopHat (v2.0.13)
iGenomes Danio_rerio UCSC danRer10 gene counts were calculated with HTSeq-count (parameters: -s no -t exon -m intersection-strict -i gene_id)
DESeq2 was used to normalize and detect differentially expressed genes (AMCA+ versus AMCA-)
Genome_build: danRer10
Supplementary_files_format_and_content: Output of HTSeq and DESeq2

organism: Danio rerio

source_name: hypophysis

growth_protocol: Adult zebrafish were raised and bred according to standard protocols.

extract_protocol:
Dissected pituitaries (5 groups; n= 7 per group) were immediately transferred into ice cold HBS buffer in a 1.5 ml tube until dissociation. The buffer were replaced with 250µL ice cold PBS +/+ and pituitary were then dissociated using prewarmed Liberase TM (Roche) for 12minutes and trypsination along with DNASe for 5 minutes at 30 degree C with occasional pipetting.  Dissociation was stopped by adding 50µl of FBS and dissociated cells were pelleted by centrifuging at 500g at 4°C for 5 minutes. Cells were resuspended in 2mL of resuspension buffer (Leibovitz L-15 with 0.3mM Glutamine (GIBCO), 0.8mM CaCl2, Pen 50 U/mL + Strep 0.05/mL, FBS 1%) and filtered with a 40 μm cell strainer (BD Transduction Laboratories, San Jose, CA). Propidium iodide was added to label dead cells.  High-speed FACS was performed using an SORP-FACSAria machine (BD, Bioscience, San Jose, CA) with 70µm nozzle. A two-gate FACS technique was used to select only AMCA+ cells from non-fluorescent and auto-fluorescent cells. As a control, non AMCA (AMCA-) cells were sorted. The cells were collected into a 384-well sterile plate filled with the 1X lysis buffer and RNAsin (SMARTer Ultra Low Input RNA Kit for Sequencing - v3 (Takara Bio USA, Inc. CA)). The samples were incubated at room temperature for 5 minutes and snap frozen in liquid nitrogen before storage at -80°C. Two independent FACS experiments were performed, yielding six samples (3 AMCA+ and 3 AMCA-) from 3 groups and four samples (2 AMCA+ and 2 AMCA -) from 2 groups. Samples were thawed, reverse transcribed and amplified to create full length transcriptome using the SMARTer® Ultra™ Low Input RNA for Sequencing - v3 kit. Amplification was performed with 15 cycles. Following the amplification, clean-up was done using Ampure XP beads (Beckman Coulter).
The amplified cDNA products were sheared by ultrasonicator (Covaris E220X).  About 3ng of sheared, amplified cDNA from each sample were processed as previously described (Blecher-Gonen R. et al. Nat. Prot. (2013)). Different barcode was ligated to each sample to allow multiplexing of 10 samples on 1 sequencing lane. Between 18-22 million single end 61bp reads were sequenced per sample on Illumina HiSeq 2500 v4 instrument.

treatment_protocol: Adult TL male zebrafish were injected with 10ul of PBS with 4.6 mM β-Ala-Lys-Ne AMCA (Biotrend # BP0352). 3 hours after injection pituitaries were dissected as described in Toro et al., Gene Expr Patterns (2009).

value: TL

value: hypophysis

value: 12 months

tag: Sex

tag: b-ala-lys-ne amca labelling

value: Neg

value: non-pituicytes


title: Sample_Plate2_A5_AMCA

description: cell lysate

value: male

value: Pos

tag: cell type

value: pituicytes


title: cbp-3 rep3

description:
Run 1, Illumina index 20
Protocol: PAT-Seq

source_name: cbp-3 rep3


title: Sample_Plate2_A6_AMCA

description: cell lysate


title: gld-2 (parn-1  RNAi) rep2

description:
Run 2, Illumina index 12
Protocol: PAT-Seq

source_name: gld-2 (parn-1  RNAi) rep2


title: Sample_Plate2_A2_AMCA

description: cell lysate


title: gld-2 rep2

description:
Run 1, Illumina index 15
Protocol: PAT-Seq

source_name: gld-2 rep2


title: cbp-3 rep2

description:
Run 1, Illumina index 19
Protocol: PAT-Seq

source_name: cbp-3 rep2


title: cbp-3 rep1

description:
Run 1, Illumina index 17
Protocol: PAT-Seq

source_name: cbp-3 rep1


title: Sample_Plate2_A1_AMCA

description: cell lysate


title: gld-2 rep1

description:
Run 1, Illumina index 14
Protocol: PAT-Seq

source_name: gld-2 rep1


title: gld-2 rep3

description:
RUn 1, Illumina index 16
Protocol: PAT-Seq

source_name: gld-2 rep3


title: Sample_Plate1_A8_AMCA

description: cell lysate


title: Sample_Plate2_A3_AMCA

description: cell lysate


title: N2 rep3

description:
Run 1, Illumina index 13
Protocol: PAT-Seq

source_name: N2 rep3


title: N2 rep1

description:
Run 1, Illumina index 11
Protocol: PAT-Seq

source_name: N2 rep1


title: Sample_Plate1_A7_AMCA

description: cell lysate


title: Sample_Plate1_A5_AMCA

description: cell lysate


title: highARA_f1_17

status: Public on Oct 06 2018

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

data_processing:
Sequence quality was assessed using FastQC v0.11.5, finding high quality (Phred scores almost universally above 30) and close to zero adapter contamination on the raw reads
Libraries were mapped to the GRCz10 (Genome Reference Consortium Zebrafish Build 10) assembly based on both RefSeq (GCF 000002035.5 GRCz10) and Ensembl using the default parameters of HISAT2 (Kim D et al., Nat Methods. 2015 Apr;12(4):357-60) resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts (Liao Y et al. Bioinformatics. 2014 Apr 01;30(7):923-30) and pre-filtered to exclude combined mean read counts smaller than 10.
Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis.
Genome_build: GCF 000002035.5 GRCz10
Supplementary_files_format_and_content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies, either against the zebrafish genome available in refseq database (counts_ensembl.txt) or the refseq database (counts_refseq.txt)

source_name: Liver

growth_protocol: F0 embryos were collected randomly and larvae were fed with Gemma micro® (Skretting) as a start feed from 5 days post fertilization (DPF) and Artemia nauplii (Silver Star Artemia) from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks (containing 60 fish each until 44 DPF and thereafter reduced to 20 fish each) per diet group. All fish were kept under steadily monitored standard conditions with 28 ± 1°C, 14 h light - 10 h dark period, conductivity of 500 µS and pH 7.5 in tanks in a reverse osmosis water treatment system (Aquatic Habitats recirculation system). F0 generation was mated at 97 DPF.

extract_protocol:
Livers were briefly rinsed in 1x PBS, snap frozen with liquid nitrogen and stored at -80°C for transcriptome analysis (RNA-sequencing). Total RNA was extracted using QIAzol Lysis Reagent (Qiagen) and RNA samples were DNase treated with the DNA-freeTM DNA Removal Kit (Ambion) in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop® ND-1000 Spectrophotometer (NanoDrop Technologies, USA). RNA integrity (RIN) was determined using an Agilent 2100 Bioanalyser (RNA 6000 Nano LabChip kit, Agilent Technologies, USA). RIN values from the 12 extracted RNA samples were on average 9.06 ± 0.39
The Norwegian Sequencing Centre (CEES) performed RNA-sequencing (RNA-seq) and library preparation using TruSeqTM Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: For the parental fish (F0) the experimental diets (high or low arachinoic acid) were given twice a day from 27 DPF until sampling at 154-156 DPF . F1 generation, both progeny of High ARA group and Low ARA group was fed the control feed (low arachidonic acid) and sampled at 140-142 DPF

value: High arachidonic acid group

tag: generation

value: F1 generation

value: liver


title: N2 rep2

description:
Run 1, Illumina index 12
Protocol: PAT-Seq

source_name: N2 rep2

value: young adult


title: Human_CD4Tcells_Activated_NFATc1_24h_4032

city: Cincinnati

first: Harinder

last: Singh

state: OH

address: 3333 Burnet Ave

institute: CCHMC

description: BioWardrobe ID: 4032

data_processing:
Data analysis was performed using BioWardrobe (PMID: 26248465).
RNA-seq reads were aligned to the genome by STAR (v2.4.2a PMCID: PMC3530905) with ”--outFilterMultimapNmax 1 –outFilterMismatchNmax. 2”
RPKM values were calculated using the EM algorithm (http://biorxiv.org/highwire/filestream/3259/field_highwire_adjunct_files/0/012799-1.docx).
ChIP-Seq reads were uniquely mapped using BowTie (v1.1.1 PMID: 19261174) with maximum of one mismatch.
Peaks were called using MACS2 (v2.1.0.20140616 PMID: 18798982).
Genome_build: mm10,hg19
Supplementary_files_format_and_content: RNA-Seq: csv file includes RPKM values for each sample.
Supplementary_files_format_and_content: ChIP-Seq: csv files include MACS2 peaks for each sample

source_name: Blood

growth_protocol: Resting B cells, FO B cells or naïve CD4 T cells were isolated from 6- to 8-week-old mice with the Naive B cell Isolation Kit, FO & MZ B cell Isolation Kit or naïve CD4 T cell Isolation Kit, respectively,  according to the manufacturer’s protocols (Miltenyi Biotec). 0.5 X 10^6 cells/ml B cells were  stimulated with F(ab’) 2 fragment goat anti–mouse IgM (10 μg ml -1 , Jackson ImmunoResearch  Laboratories), a-CD40 (10 μg ml -1 , FGK4.5; BioXCell), recombinant human IL-2 (100 U ml -1 ,  Roche), recombinant mouse IL-4 (5 ng ml -1 , Peprotech,) and recombinant mouse IL-5  (Peprotech, 1.5 ng ml -1 ). For naïve B1-8i B Cells, NP (50)-Ficoll (0.1 μg ml -1 , Biosearch  Technologies), a-CD40, recombinant human IL-2, recombinant murine IL-4 and recombinant  mouse IL-5 were used for activation. Naïve CD4 T cells were stimulated at cell density of 1 X  10^6 cells/ml with plate coated a-CD3 (5 μg ml -1 , 145-2C11, BioLegend) and a-CD28 (1 μg ml -1 ,  37.51, BioLegend). The NFAT inhibitor 11R-VIVIT (EMD) dissolved in DMSO was added at the initiation of cultures at a final concentration of 5 μM. For retroviral transduction, HA-IRF4,  HA-IRF8 or HA-NFATc2 were cloned into MSCV-IRES-GFP retroviral plasmids (Addgene).  Plat-E packaging cells were used to produce retroviral particles. 10^5 activated B cells were  centrifuged at 1,500 g for 2 h at 32 °C with viral particles in the presence of polybrene (8 μg ml -  1, Sigma). Transduced cells were cultured for an additional 2 days before ChIP-seq analysis (see  below). Human Naive CD4 T cells were purified from filters obtained at Hoxworth Blood Center using Ficoll centrifugation followed by negative selection using Stem Cell Naive T cell Magnetic Purification kit.

extract_protocol:
ChIP assays were performed with activated B cells by  fixing for 10 min at 25 °C with 11% formaldehyde followed by chromatin isolation and shearing  by sonication for 7 min (10% duty cycle, 175 pulses and 200 bursts; Covaris). 5 or 10 μg  chromatin was subjected to immunoprecipitation with a-H3K27Ac (1 μg; Diagenode), a-  NFATc1 (1 μg, 7A6; Santa Cruz Biotechnology), a-NFATc2 (1 μg, 4G6-G5; Santa Cruz  Biotechnology), a-IRF4 (1 μg, M-17; Santa Cruz Biotechnology) or a-IRF8 (2 μg, C-19; Santa  Cruz Biotechnology).   After washing, elution, and reversal of cross-links, DNA was isolated by  phenol/chloroform extraction and used in PCR reactions that were performed with the primers  provided in the Extended Data For ChIP-seq analyses, activated B cells (24 h) were  transduced with retroviral vectors as described above. Cells (48 h after transduction) were  crosslinked with formaldehyde as described above and chromatin was subjected to  immunoprecipitation with a-HA (1 μg, 12CA5; Roche). For ChIP-seq analysis with hCD4 T  cells a-CD3 and a-CD28 beads were used for activation. Cross-linked chromatin was  immunoprecipitated with a-NFATc1, a-NFATc2 (1 μg, 25A10.D6.D2, ThermoFIscher  Scientific) or a-IRF4 using IP-STAR robot (Diagenode). DNA libraries were prepared with a ThruPLEX-FD Prep Kit (Rubicon  Genomics) or using chipmentation aproach. The amplified products were purified with AMPure XP beads (Beckman Coulter)  and subjected to single or paired end-sequencing on an Illumina HiSeq2500 machine. Each sample was  used to generate ~1 X 10^7 reads. RNA-seq libraries were generated from 300 ng total RNA with an  RNA Sample Prep Kit (Illumina) according to the manufacturer’s protocol. The libraries were  subjected to paired-end sequencingat CCHMC DNA sequencing core using . Each sample was used to generate ~2 X 10^7 reads.
RNA  libraries for single read sequencing were prepared by using standard Illumina protocols. ChIP libraries were prepared by using ThruPLEX DNA kit (Rubicon) or by chipmentation.

treatment_protocol: For ChIP-Seq, B  cells were stimulated with F(ab’) 2 fragment goat anti–mouse IgM, a-CD40, IL-2,IL-4 and IL-5. Naïve CD4 T cells were stimulated with plate coated a-CD3 and a-CD28. For RNA-seq, B cells were stimulated in the absence or presence of 11R-VIVT. Human T cells were stimulated with anti-CD3/28 beads.

value: CD4 T cells

tag: chip antibodies

value: NFATc1 (Santa Cruz Biotechnology; sc-7294X; 7A6; monoclonal)


title: Human_CD4Tcells_Activated_NFATc2_24h_4410

description: BioWardrobe ID: 4410

value: NFATc2 (Thermo Fischer scientific; MA1-025; 2510.D6.D2; monoclonal)


title: highARA_f1_18

tag: treatment


title: Human_CD4Tcells_Activated_IRF4_48h_3879

description: BioWardrobe ID: 3879

value: IRF4 (Santa Cruz Biotechnology; sc-6059X; M-17; polyclonal)


title: highARA_f1_15


title: highARA_f1_13


title: high_ARA_f0_18

value: F0 generation


title: highARA_f1_14


title: high_ARA_f0_16


title: high_ARA_f0_13


title: high_ARA_f0_14


title: highARA_f1_16


title: Sample_Plate1_A6_AMCA

description: cell lysate

value: TL


title: cont_f1_11

value: Low arachidonic acid group


title: cont_f0_9


title: cont_f0_8


title: high_ARA_f0_17


title: cont_f0_7


title: cont_f0_12


title: high_ARA_f0_15


title: cont_f0_11


title: cont_f0_10


title: cont_f1_8


title: cont_f1_9


title: cont_f1_7


title: NucleopRNA HeLa

city: Lisboa

first: Kenny

last: Rebelo

address: Av. Professor Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

description: RNA from HeLa nucleoplasm fraction

data_processing:
For mNET-seq data, adaptor trimming was preformed using Cutadapt (v1.8.3), only keeping the reads with more than 10 bases.
mNET-seq data was then aligned to the human/mouse genome (build hg19/mm10) using TopHat (v2.0.13), with a minimum anchor length of 5 bases and allowing only for unique alignments.
For ChrRNA-seq data, alignment was preformed using TopHat (v2.0.13) with a minimum anchor length of 5 bases, allowing only for unique alignments and allowing read pairs to be separated by up to 3kb.
To aquire the last nucleotide incorporated by the polymerase in the aligned mNET-seq reads, a combination of SAMtools and inhouse python scripts was used
Then, both Nucleoplasm RNA-seq and mNET-seq singe-nucleotide aligned reads were separated by strand using SAMtools, selecting the strands according to the read flag.
To make bedgraphs of the reads aligning in different strands, genomeCoverageBed (v2.17.0) was used.
After that, the values in the bedgraphs were normalized to reads per 108 sequences using an inhouse python script.
Finally, to convert the bedgraphs to bigWig, the program bedGraphToBigWig from UCSC was used.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: processed data files are in bigWig format; the scores in the files represent the number of reads per 108 sequences

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in DMEM with 10% fetal bovine serum and TAP cells were maintained in RPMI with 10% fetal bovine serum

extract_protocol:
Nascent RNAs were purified from Pol II IP products of solubilized chromatin.
Libraries were prepared acooding to the protocols of Trueseq small RNA library preparation kit (Illumina) and NEBNext small RNA library preparation kit for mNET-seq; NEBNext Ultra II directional RNA library preparation kit (NEB) for Chromatin-bound RNA-seq and Nucleoplasm RNA-seq

treatment_protocol: 1% Empigen was added IP buffer and IP washing buffer

tag: cell line

value: HeLa

tag: modification


title: mNET Long S5P NEBkit rep1

description: nascent RNA from S5P phosphorylated Pol II prepared with NEB library preparation kit

data_processing:
Library strategy: mNET-seq
For mNET-seq data, adaptor trimming was preformed using Cutadapt (v1.8.3), only keeping the reads with more than 10 bases.
mNET-seq data was then aligned to the human/mouse genome (build hg19/mm10) using TopHat (v2.0.13), with a minimum anchor length of 5 bases and allowing only for unique alignments.
For ChrRNA-seq data, alignment was preformed using TopHat (v2.0.13) with a minimum anchor length of 5 bases, allowing only for unique alignments and allowing read pairs to be separated by up to 3kb.
To aquire the last nucleotide incorporated by the polymerase in the aligned mNET-seq reads, a combination of SAMtools and inhouse python scripts was used
Then, both Nucleoplasm RNA-seq and mNET-seq singe-nucleotide aligned reads were separated by strand using SAMtools, selecting the strands according to the read flag.
To make bedgraphs of the reads aligning in different strands, genomeCoverageBed (v2.17.0) was used.
After that, the values in the bedgraphs were normalized to reads per 108 sequences using an inhouse python script.
Finally, to convert the bedgraphs to bigWig, the program bedGraphToBigWig from UCSC was used.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: processed data files are in bigWig format; the scores in the files represent the number of reads per 108 sequences

value: S5P (MBL international, MABI0603/CMA303, phospho-Ser5)


title: mNET Long S2P empigen rep2

description: nascent RNA from S2P phosphorylated Pol II

value: S2P (MBL international, MABI0602/CMA302, phospho-Ser2)

value: Empigen


title: mNET Long S2P control rep2


title: mNET Long S2P control rep1


title: mNET Long S2P empigen rep1


title: mNET Long S5P empigen rep2

description: nascent RNA from S5P phosphorylated Pol II


title: mNET Long S5P NEBkit rep2


title: mNET Long S5P control rep2


title: cont_f1_12


title: mNET Long S5P empigen rep1


title: mNET Short S2P control rep2


title: mNET Short S2P empigen rep1


title: mNET Short S5P empigen rep2


title: mNET Short S2P control rep1


title: mNET Short S5P empigen rep1


title: mNET Short S5P control rep2


title: mNET Short S5P control rep1


title: mNET Short S5P rep1


title: mNET S5P Middle-F

value: S5P  (Abcam,ab5131, phospho-Ser5)


title: mNET S5P Heavy-F


title: mNET S5P Emp

description: nascent RNA from S5P phosphorylated Pol II, treated with Empigen

value: S5P (MBL international, MABI0603/CMA603, phospho-Ser5)


title: mNET S5P abcam


title: mNET Long S5P control rep1


title: mNET Long S5P rep1


title: mNET Thr4 rep1

description: nascent RNA from T4P phosphorylated Pol II

value: T4P (Active motif, 6D7, phospho-Thr4)


title: cont_f1_10

value: F1 generation


title: mNET S5P control

description: nascent RNA from S5P phosphorylated Pol II, control for Empigen treatment


title: mNET Ser7 rep1

description: nascent RNA from S7P phosphorylated Pol II

value: S7P (Active motif, 4E12, phospho-Ser7)


title: mNET Tyr1 rep1

description: nascent RNA from Tyr1 phosphorylated Pol II

value: Y1P (Abcam, 3D12, phospho-Tyr1)


title: Murine_Bcells_Activated_DMSO_48h_2440

description: BioWardrobe ID: 2440

source_name: Splenic

value: B cells


title: Murine_Bcells_Activated_DMSO_24h_2449

description: BioWardrobe ID: 2449


title: Murine_Bcells_Activated_NFATinhibitor_48h_2441

description: BioWardrobe ID: 2441


title: Murine_Bcells_Activated_24h_2433

description: BioWardrobe ID: 2433


title: Murine_Bcells_Activated_48h_2439

description: BioWardrobe ID: 2439


title: Murine_Bcells_Activated_4h_2430

description: BioWardrobe ID: 2430


title: Murine_Tcells_Activated_H3K27Ac_48h_3106

description: BioWardrobe ID: 3106

value: CD4 T cells

value: H3K27Ac (Diagenode; C1541096; A1723-041D; polyclonal)


title: Murine_Tcells_Unstimulated_H3K27Ac_0h_3103

description: BioWardrobe ID: 3103


title: Murine_Bcells_Unstimulated_0h_2429

description: BioWardrobe ID: 2429


title: Murine_Tcells_Activated_H3K27Ac_24h_3105

description: BioWardrobe ID: 3105


title: Murine_Bcells_Activated_DMSO_4h_2431

description: BioWardrobe ID: 2431


title: Murine_Bcells_Activated_HAIRF4_72h_3813

description: BioWardrobe ID: 3813

value: HA ( Roche; 11583816001; 12CA5; Monoclonal)


title: Murine_Bcells_Activated_HANFATc2_72h_3815

description: BioWardrobe ID: 3815


title: Murine_Bcells_Activated_H3K27Ac_48h_2627

description: BioWardrobe ID: 2627


title: Murine_Bcells_Activated_H3K27Ac_4h_2625

description: BioWardrobe ID: 2625


title: Murine_Bcells_Activated_H3K27Ac_24h_2626

description: BioWardrobe ID: 2626


title: Murine_Bcells_Unstimulated_H3K27Ac_0h_2624

description: BioWardrobe ID: 2624


title: Murine_Bcells_Activated_NFATinhibitor_4h_2432

description: BioWardrobe ID: 2432


title: Murine_Tcells_Activated_H3K27Ac_4h_3104

description: BioWardrobe ID: 3104


title: Murine_Bcells_Activated_NFATinhibitor_24h_2436

description: BioWardrobe ID: 2436


title: NucleopRNA TAP

description: RNA from TAP nucleoplasm fraction

source_name: TAP cells

value: Mouse lymphoid cell


title: TAP mNET Long S5P empigen rep2


title: Murine_Bcells_Activated_H3K27Ac_72h_3823

description: BioWardrobe ID: 3823


title: TAP mNET Long S5P control rep2


title: TAP mNET Long S5P control rep1


title: Murine_Bcells_Activated_HAIRF8_72h_3814

description: BioWardrobe ID: 3814


title: TAP mNET Short S5P empigen rep2


title: TAP mNET Long S5P empigen rep1


title: TAP mNET Short S5P empigen rep1


title: TAP mNET Short S5P control rep2


title: TAP mNET Short S5P control rep1


title: M35.AM.AcuteIT.Metformin.PM.3

status: Public on Oct 05 2018

city: Chicago

first: Alexander

middle: V

last: Misharin

state: IL

address: 240 E Huron

department: Pulmonary and Critical Care

institute: Northwestern University

data_processing:
Basecalls performed using Illumina RTA2 software (Part of the NextSeq System Suite v2.1.2).
FASTQ files were generated using bcl2fastq2 software v2.19 and processed using Ceto pipeline (https://github.com/ebartom/NGSbartom on 2016/10/30).
Demultiplexed reads (FASTQ files) were trimmed and mapped to mm10 version of the mouse genome using TopHat2 aligner and mapped to the genomic features using HTSeq script (ref http://dx.doi.org/10.1093/bioinformatics/btu638) and processed using edgeR package (ref https://bioconductor.org/packages/release/bioc/html/edgeR.html) to estimate differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include raw counts values for each sample generated using htseq algorithm.

source_name: Alveolar macrophages

growth_protocol: Male C57Bl/6j mice were purchased from Jackson laboratory (stock 00664) and at age 10 weeks administered with metformin in the drinking water (100 mg/kg/day) for 24 hours prior to exposure to intratracheally instilled with standardized PM from the US National Institute of Standards and Technology (NIST) 10 μg/animal and harvested 24 hours afterwards.

extract_protocol:
Mice were euthanized, alveolar macrophages (~100K cells) were isolated via FACS as described before (Misharin et al., AJRCMB, 2013; Misharin et al., JEM, 2017). Cells were immediately lysed in 350 ul of RLTplus buffer supplemented with BME. RNA was extracted using Qiagen RNeasy Plus protocol with genomic DNA removal step. All samples had RIN over 7 according to Agilent TapeStation 4200.
RNA-seq libraries were prepared from 100 ng of total RNA, starting with poly(A) enrichment and followed by NEB Next RNA Ultra I chemistry. Libraries were quantified and assessed on Qubit fluorimeter (Invitrogen) and TapeStation 4200, correspondingly, multiplexed and sequenced on NextSeq 500 instrument (Illumina), using V2 high output reagent kit, 75 bp, single end reads, to the average sequencing depth of 6x10^6 reads per sample. Over 94% of reads had Q score over 30.

tag: pm exposure

value: PM

tag: metformin treatment

value: Metformin

value: lung

value: Alveolar macrophages

value: male

value: 10 weeks


title: M36.AM.AcuteIT.Metformin.PM.4

tag: age


title: M33.AM.AcuteIT.Metformin.PM.1

tag: strain


title: M31.AM.AcuteIT.Vehicle.PM.3

value: Vehicle


title: M30.AM.AcuteIT.Vehicle.PM.2


title: M28.AM.AcuteIT.Metformin.PBS.4

value: PBS


title: M24.AM.AcuteIT.Vehicle.PBS.4


title: M29.AM.AcuteIT.Vehicle.PM.1


title: M27.AM.AcuteIT.Metformin.PBS.3


title: C.alb. Yeast +Cyt-D 2

city: Los Angeles

first: vineela

last: gangalapudi

state: CALIFORNIA

address: 8723 Alden drive

department: Biomedical sciences

institute: Cedars- sinai Medical center

data_processing:
We used the STAR aligner to map the samples, and Qced them using Rseqc then used DEseq2 for DE to get the significantly differentially expressed genes between different treatment groups.
Genome_build: Gencode_vM8
Supplementary_files_format_and_content: Excel table includes the count values for each sample calculated by STAR.

source_name: Bone marrow derived dendritic cells

growth_protocol: the mice were 8-10 weeks old

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Quiagen)
Total RNA was quantified using both the NanoDrop to assess sample contamination by proteins or carryover reagents from RNA isolation, and the Qubit fluorometer (Invitrogen). Samples were then qualified using the Bioanalyzer that analyzes the integrity of the total RNA by measuring the ratio between the 18S and 28S ribosomal peaks. Libraries were constructed using SMARTer Ultra Low Input RNA v3 kit (Clontech), indexed using Nextera indices (Illumina). Final libraries were again quantitated with the Qubit fluorometer and checked for size via the Fragment Analyzer. Libraries were diluted to 4nM and pooled in equal volumes for denaturation, hybridization, and sequencing on an Illumina NextSeq 500 (Illumina) with single end 75bp sequencing chemistry.

tag: phenotype

value: C.alb. Yeast +Cyt-D


title: C.alb. Yeast +Cyt-D 1


title: C.alb. Hyphae 2

value: C.alb. Hyphae


title: C.alb. Yeast 1

value: C.alb. Yeast


title: C.alb. Hyphae 1


title: C.alb. Yeast 2


title: M25.AM.AcuteIT.Metformin.PBS.1

tag: tissue


title: M22.AM.AcuteIT.Vehicle.PBS.2


title: M21.AM.AcuteIT.Vehicle.PBS.1


title: No stimulation 1

value: No stimulation


title: E10.5_YS_HE_rep2

city: Philadelphia

first: Long

last: Gao

state: PA

address: 4002 Colket Translational Research Building (CTRB) 3501 Civic Center Boulevard

institute: The Children’s Hospital of Philadelphia

data_processing:
Paired-end reads were mapped to the reference mouse genome
Uniquely mapped reads with fewer than 2 mismatches were used
Cufflinks was used to assemble transcripts and estimate expression level
Gene level read count was estimated using FeatureCounts
Differential gene expression ananlysis was conducted using EBSeq
Genome_build: mm9
Supplementary_files_format_and_content: Gene level FPKM values across all samples(excel file)

source_name: hemogenic endothelial cell from E10.5 yolk sac

growth_protocol: B6C3F1/J 3-week old female mice were purchased from Jackson Laboratories (Stock no: 100010). Females were injected with 5 IU pregnant mares serum gonadotrophin (Sigma) and 48 hours later with 5 IU human chorionic gonadotrophin (Sigma). Females were immediately paired overnight with Runx1GFP(Runx1tm4Dow, 15784726, 14630789) homozygous males. The morning post mating is considered embryonic day (E) 0.5. Embryos at the time of harvest (E9.5, E10.5) were staged by counting somites. Embryos that showed abnormal development were discarded.

extract_protocol:
Yolk sacs (YS) were removed from embryos and vitalline vessels were kept with the embryonic portion. The head, cardiac and pulmonary regions, liver, digestive tube, tail and limb buds were removed from E9.5 and E10.5 embryos. The remaining portion containing the aorta-gonad-mesonephros region, portions of somite, umbilical and vitalline vessels were collected as embryonic region (EM). Embryos were digested for 1hr in 0.125% collagenase (Sigma) in PBS/10% FBS (Gibco)/1% Pen/Strept and washed then resuspended in PBS/10%FBS/PS.
Embryonic tissues were labeled with the following antibodies from eBiosciences (clone, Antibody Registry ID): CD41-PE (MWReg30, AB_2538354), CD31-PEcy7 (390, AB_469616), CD45-APC (30-F11, AB_469392), and kit-APC-efluor780 (2B8, AB_1272177). DAPI (Invitrogen) was used for viability. Samples were sorted on a BD Influx into Trizol-LS (Thermo) or PBS/20%FBS/PS/25mM HEPES. RNA was isolated using Qiagen RNeasy Microkit with DNAse step performed on column or using Turbo DNA-freeTM Kit (Thermo).

value: Runx1tm4Dow x B6C3F1

value: hemogenic endothelial cell

tag: facs

value: Runx1-GFP+, CD31+, kit lo/-, CD41-, CD45-


title: E10.5_YS_HE_rep1


title: E10.5_YS_EC_rep2

source_name: endothelial cell isolated from E10.5 yolk sac

value: Endothelial cell

value: Runx1-GFPneg, CD31+, kit-, CD41-, CD45-


title: E10.5_YS_EC_rep1


title: E10.5_EMB_HE_rep2

source_name: hemogenic endothelial cell from E10.5 AGM + vitalline and umbillical vessels


title: No stimulation 2


title: E10.5_EMB_HE_rep1


title: M23.AM.AcuteIT.Vehicle.PBS.3


title: E10.5_EMB_EC_rep2

source_name: endothelial cell isolated from E10.5 AGM+ vitalline and umbillical vessels


title: E10.5_EMB_EC_rep1


title: E9.5_YS_HE_rep2

source_name: hemogenic endothelial cell from E9.5 yolk sac


title: E9.5_YS_HE_rep1


title: E9.5_YS_EC_rep2

source_name: endothelial cell from E9.5 yolk sac


title: E9.5_YS_EC_rep1


title: E9.5_EMB_HE_rep2

source_name: hemogenic endothelial cell from E9.5 AGM + vitalline and umbillical vessels


title: E9.5_EMB_EC_rep1

source_name: endothelial cell isolated from E9.5 AGM+ vitalline and umbillical vessels


title: E9.5_EMB_HE_rep1


title: E9.5_EMB_EC_rep2


title: Control_tissue [SVA601]

city: Minneapolis

first: Chris

middle: H

last: Wendt

state: MN

address: 420 Delaware St SE

department: Medicine

institute: University of Minnesota

data_processing:
50bp FastQ paired-end reads (n=XXX Million per sample) were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30
Quality control checks on raw sequence data for each sample were performed with FastQC
Read mapping was performed via Bowtie (v2.2.4.0)
Gene quantification was done via Cuffquant for FPKM values and Feature Counts for raw read counts
Genome_build: hg19
Supplementary_files_format_and_content: FPKM, raw read counts

source_name: Emphysematous lung from non-cancer lungs_232532

extract_protocol:
Frozen lung tissue samples ranging in weight from 25-60 mg were individually ground to a fine powder using a liquid nitrogen cooled ceramic mortar and pestle. For RNA quality control (QC), approximately 20% of each sample was processed with TRI Reagent (Sigma Aldrich, St Louis, MO). Once the initial RNA QC was completed, polyribosome preparations were performed in random sample pairs. For this purpose, the remainder of each frozen powdered sample was solubilized in 100 µL of lysis buffer (10 mM Tris-HCl at pH 8.0, 150 mM NaCl, 5 mM MgCl2, 1% Nonidet-P40, 1% sodium deoxycholate, 40 mM dithiothreitol, 500 U/mL RNAsin (Promega, Madison, WI), 40 mM VRC (vanadyl ribonucleoside complex), and 150 µg/ml cycloheximide) and mixed by pipetting. Nuclei and insoluble material were removed by centrifugation (12,000 x g, 10 seconds, at 4°C). Extraction buffer (50 µL; 0.2 M Tris-HCl at pH 7.5, 0.3 M NaCl, 10 mM PMSF) was added to the supernatant and the sample was mixed by pipetting. The sample was centrifuged (12,000 x g, 5 min, at 4° C) and 25% of the supernatant was processed with TRI Reagent to generate a cytosolic total RNA sample. The remaining supernatant was layered onto a 5 mL, linear sucrose gradient (0.5–1.5 M), 10 mM Tris-HCl pH 7.5, 140 mM NaCl, 3 mM MgCl2, 10 mM DTT. Gradients were centrifuged (200,000 x g in a Beckman SW55Ti rotor for 80 minutes at 4o C) and the gradients were fractionated into ten, 0.5 mL fractions utilizing an ISCO density gradient fractionator with absorbance monitored at 254 nm. Each fraction was collected into a tube containing 50 µL 1%SDS and 20 µL 0.5 M EDTA. The polyribosomal mRNA from fractions 7, 8, 9 and 10 were individually processed with 1 mL of TRI Reagent and 200 µL chloroform and the resultant RNA pellets from these four fractions were combined to create the polyribosomal mRNA sample corresponding to each tissue sample. Polyribosomal mRNA and cytosolic RNA were sent to the University of Minnesota Genomics Core for quality assessment by Caliper High Sensitivity Lab Chip. Those samples passing the Caliper QC were processed into indexed library samples for analysis by RNA sequencing. This was accomplished using the SMART-Seq protocol.
Libraries were quantified using a fluorimetric PicoGreen assay. Library size was assessed using capillary electrophoresis on an Agilent BioAnalyzer 2100 and only libraries quantifying higher than 10 nM were analyzed. Libraries were pooled and assessed using Kapa qPCR to ensure adapters were ligated to DNA fragments and functional. Nextera libraries were hybridized to a single read flow cell and individual fragments were clonally amplified by bridge amplification on the Illumina cBot. Once clustering was complete, the flow cell was loaded on a HiSeq 2000 and sequenced using Illumina SBS chemistry. Upon completion of read 1, an 8-base pair index read for Index 1 was performed. The Index 1 product was removed and the template was reannealed to the flow cell surface. The run proceeded with 8 chemistry-only cycles, followed by an 8-base pair index read to read Index 2.

value: Lung tissue

tag: fraction

value: Heavy, Polyribosomal-bound RNA

tag: group

value: Control


title: Control_tissue [SVA600]

value: Total RNA


title: Lung_tumor_adjacent [SVA599]

source_name: Tissue adjacent to lung tumor_LU1689B


title: Control_tissue [SVA593]

source_name: Emphysematous lung from non-cancer lungs_243699


title: Lung_tumor_adjacent [SVA598]


title: Control_tissue [SVA594]

source_name: Emphysematous lung from non-cancer lungs_266688


title: Lung_tumor [SVA597]

source_name: Lung tumor tissue_LU1689A


title: Control_tissue [SVA592]


title: Lung_tumor_adjacent [SVA591]

source_name: Tissue adjacent to lung tumor_LU1517B


title: mNET Short S2P empigen rep2

source_name: HeLa cells

value: HeLa

value: S2P (MBL international, MABI0602/CMA302, phospho-Ser2)

value: Empigen


title: Lung_tumor [SVA588]

source_name: Lung tumor tissue_LU1517A


title: Lung_tumor_adjacent [SVA587]

source_name: Tissue adjacent to lung tumor_LU1228B


title: Lung_tumor [SVA589]


title: Lung_tumor [SVA585]

source_name: Lung tumor tissue_LU1228A


title: Lung_tumor [SVA584]


title: Lung_tumor_adjacent [SVA586]


title: Lung_tumor_adjacent [SVA590]


title: Control_tissue [SVA539]

source_name: Emphysematous lung from non-cancer lungs_201128


title: Control_tissue [SVA538]


title: Control_tissue [SVA536]

source_name: Emphysematous lung from non-cancer lungs_192270


title: Control_tissue [SVA595]


title: Lung_tumor [SVA596]


title: Control_tissue [SVA537]


title: Lung_tumor [SVA533]

source_name: Lung tumor tissue_LU1675A


title: Lung_tumor_adjacent [SVA534]

source_name: Tissue adjacent to lung tumor_LU1675B


title: Lung_tumor [SVA532]


title: Lung_tumor_adjacent [SVA535]


title: Lung_tumor_adjacent [SVA530]

source_name: Tissue adjacent to lung tumor_LU1654B


title: Lung_tumor_adjacent [SVA531]


title: Lung_tumor [SVA528]

source_name: Lung tumor tissue_LU1654A


title: Lung_tumor [SVA529]


title: Lung_tumor_adjacent [SVA526]

source_name: Tissue adjacent to lung tumor_LU2531B


title: Lung_tumor_adjacent [SVA527]


title: Lung_tumor [SVA525]

source_name: Lung tumor tissue_LU2531A


title: Myd88-/- CONVD 3

city: Leiden

first: Bjorn

middle: Erik Vind

last: Koch

address: Einsteinweg 55

department: Institute of Biology

country: Netherlands

institute: Leiden University

description: myd88-/-, conventionalized at 3 days post fertilization, RNA isolated at 5 days post fertilization. Biological replicate 3

data_processing:
Basecalling: Illumina HCS version 1.15.1
GeneTiles was used for quantification and visualization of the RNAseq data
Bowtie2 is used to align the reads in the fastq file to the genome (obtained from Ensemble). Bowtie2 generates SAM files that contain the reads together with the location on the genome.
Samtools is used to convert and compress the SAM files into a binary BAM file. Samtools is furthermore used to sort the reads in the BAM files based on the aligned read location in the genome, resulting in a sorted BAM file.
The BAM files are indexed to be able to quickly find the aligned reads based on a location in the genome, i.e. to be able to quickly search the BAM file. The index is a saved as a BAI file.
Using the available annotation from Ensemble we can search the BAM file for reads within a gene (using exon starting positions and lengths). This is done with a python script. The output of this script is a tab separated file (tsv) containing the read counts per gene.
We used DESeq, an R-script to perform statistical analysis. The DESeq script is used to normalise the reads per gene, based on (divided by) the total number of reads obtained per sample. Then variance and average of the measurement compared to the control can be expressed as a P-value, by calculating the dispersion per gene using DESeq. The size factors as well as the P-values are stored in ‘tsv’ files.
Using a script, all tsv files are combined into xlsx files , e.g. per experiment, chromosome, per filtered results of most significant reads or highest ratio between measurement and control.
Genome_build: GRz10
Supplementary_files_format_and_content: xlsx file containing read counts per gene

source_name: Whole larvae

growth_protocol: Zebrafish were handled in compliance with animal welfare regulations and maintained according to standard protocols (http://zfin.org). The breeding of myd88-/- mutant fish was approved by the local animal welfare committee (DEC) of Leiden University (license number 10612, protocol 12232).

extract_protocol:
15 larvae were pooled together, snap frozen in liquid nitrogen and stored at -80º C until extraction. Total RNA was extracted by trizol method (Invitrogen), according to the manufacturer’s protocol. Each sample was further cleaned up on RNeasy mini spin column (Quiagen) according to the supplier’s protocol. RNA integrity was assessed by bioanalyzer (Aglient); all samples were found to have a RIN ≥ 9.
A total of 3 μg of RNA was used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, USA). Two minor modifications were made to the protocol provided by the manufacturer. In the step describing the adapter ligation, 1 μl instead of 2.5 μl adaptor was used. In the library size selection step, the library fragments were isolated with a double Ampure XP purification with a 0.7× beads to library ratio. The resulting mRNAseq library was sequenced using an Illumina HiSeq2500 instrument in accordance with the descriptions provided by the manufacturer, with a read length of 1×50 nucleotides. Image analysis and base calling were done by the Illumina HCS version 1.15.1.

treatment_protocol: Germ-free and conventionalized zebrafish embryonic groups were generated by the "natural breeding method" as previously described (Nat Protoc 3:1862–1875). For monoassociated treatment groups specific bacteria (Exiguobacterium ZWU0009 and Chryseobacterium ZOR0023) were grown fresh over night at 28°C on tryptic soy agar plates. Colonies were suspended in sterilized egg water and adjusted to a final A600 optical density of 0,05. Larvae were kept in this water from 3 to 5 DPF.

tag: Stage

value: 5 Days Post Fertilization

value: Conventionalized

tag: genotype


title: Myd88-/- Germ-free 3

description: myd88-/-, germ-free, RNA isolated at 5 days post fertilization. Biological replicate 3

value: Germ-free


title: Myd88-/- CONVD 1

description: myd88-/-, conventionalized at 3 days post fertilization, RNA isolated at 5 days post fertilization. Biological replicate 1


title: Myd88-/- CONVD 2

description: myd88-/-, conventionalized at 3 days post fertilization, RNA isolated at 5 days post fertilization. Biological replicate 2


title: Lung_tumor_adjacent [SVA523]

source_name: Tissue adjacent to lung tumor_LU1551B


title: Myd88-/- Germ-free 2

description: myd88-/-, germ-free, RNA isolated at 5 days post fertilization. Biological replicate 2


title: Myd88-/- Germ-free 1

description: myd88-/-, germ-free, RNA isolated at 5 days post fertilization. Biological replicate 1


title: Lung_tumor [SVA520]

source_name: Lung tumor tissue_LU1551A


title: Lung_tumor [SVA521]


title: Lung_tumor_adjacent [SVA522]


title: WT Chrys 3

description: Wildtype, monoassociated with Chryseobacterium at 3 days post fertilization, RNA isolated at 5 days post fertilization. Biological replicate 3

value: Monoassociated (Chryseobacterium)

value: WT


title: WT Chrys 2

description: Wildtype, monoassociated with Chryseobacterium at 3 days post fertilization, RNA isolated at 5 days post fertilization. Biological replicate 2


title: WT Chrys 1

description: Wildtype, monoassociated with Chryseobacterium at 3 days post fertilization, RNA isolated at 5 days post fertilization. Biological replicate 1


title: WT Exi 3

description: Wildtype, monoassociated with Exiguobacterium  at 3 days post fertilization, RNA isolated at 5 days post fertilization. Biological replicate 3

value: Monoassociated (Exiguobacterium)


title: WT Exi 2

description: Wildtype, monoassociated with Exiguobacterium  at 3 days post fertilization, RNA isolated at 5 days post fertilization. Biological replicate 2


title: Lung_tumor [SVA516]

source_name: Lung tumor tissue_LU1577A


title: WT CONVD 3

description: Wildtype, conventionalized at 3 days post fertilization, RNA isolated at 5 days post fertilization. Biological replicate 3


title: Lung_tumor_adjacent [SVA518]

source_name: Tissue adjacent to lung tumor_LU1577B


title: WT Exi 1

description: Wildtype, monoassociated with Exiguobacterium at 3 days post fertilization, RNA isolated at 5 days post fertilization. Biological replicate 1


title: Lung_tumor [SVA524]


title: WT CONVD 2

description: Wildtype, conventionalized at 3 days post fertilization, RNA isolated at 5 days post fertilization. Biological replicate 2


title: Control_tissue [SVA514]

source_name: Emphysematous lung from non-cancer lungs_223106


title: Control_tissue [SVA515]


title: WT Germ-free 3

description: Wildtype, germ-free, RNA isolated at 5 days post fertilization. Biological replicate 3


title: Control_tissue [SVA512]

source_name: Emphysematous lung from non-cancer lungs_182894


title: WT Germ-free 2

description: Wildtype, germ-free, RNA isolated at 5 days post fertilization. Biological replicate 2


title: Control_tissue [SVA513]


title: WT CONVD 1

description: Wildtype, conventionalized at 3 days post fertilization, RNA isolated at 5 days post fertilization. Biological replicate 1


title: Lung_tumor_adjacent [SVA511]

source_name: Tissue adjacent to lung tumor_LU1795B


title: Lung_tumor_adjacent [SVA510]


title: WT Germ-free 1

description: Wildtype, germ-free, RNA isolated at 5 days post fertilization. Biological replicate 1


title: Lung_tumor [SVA509]

source_name: Lung tumor tissue_LU1795A


title: Lung_tumor [SVA508]


title: Lung_tumor_adjacent [SVA519]


title: Control_tissue [SVA507]

source_name: Emphysematous lung from non-cancer lungs_235584


title: Lung_tumor [SVA517]


title: Control_tissue [SVA506]


title: Lung_tumor_adjacent [SVA502]

source_name: Tissue adjacent to lung tumor_LU2465B


title: Control_tissue [SVA505]

source_name: Emphysematous lung from non-cancer lungs_291578


title: Lung_tumor [SVA500]

source_name: Lung tumor tissue_LU2465A


title: Lung_tumor [SVA501]


title: Lung_tumor_adjacent [SVA503]


title: Control_tissue [SVA499]

source_name: Emphysematous lung from non-cancer lungs_295167


title: Control_tissue [SVA504]


title: Control_tissue [SVA498]


title: Control_tissue [SVA496]

source_name: Emphysematous lung from non-cancer lungs_276977


title: Lung_tumor_adjacent [SVA494]

source_name: Tissue adjacent to lung tumor_LU2756B


title: T3M4 C1GALT1 knockout

city: Omaha

first: Surinder Kumar

last: Batra

state: Nebraska

address: 42nd and Emile

department: Biochemistry and Molecular Biology

institute: University of Nebraska Medical Center

data_processing:
FASTQ quality inspection was done using FastQC
RNA-seq data was mapped to the human genome hg19 (GRCh37 genome build) using Tophat2 (v.2.0.9).
Cufflinks 2.2.1 was used to compute transcript abundance and the differential expression. The FPKM values were used to normalize and quantify each transcripts.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values, fold-change

source_name: Pancreas

extract_protocol:
RNAeasy kit (Qiagen) was used to isolate RNA. RNA quality was checked with an Agilent Bioanalyzer (Agilent Technologies, Inc.) and all of the RINs (RNA integrity numbers) were 10.
Library preparation was achieved using the Illumina TruSeq RNA Sample Preparation Kit

treatment_protocol: CRISPR/Cas9 C1GALT1 knockout was carried out in human T3M4 PDAC cells.

value: Cancer

tag: cell type

value: T3M4 PDAC cells

tag: genotype/variation

value: C1GALT1 knockout


title: T3M4 Control

value: control


title: Lung_tumor_adjacent [SVA495]

value: Lung tissue


title: Lung_tumor [SVA493]

source_name: Lung tumor tissue_LU2756A

value: Heavy, Polyribosomal-bound RNA


title: 4s(TPD039p1_posi)

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: PD-1 positive in T cells from blood

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: hg19

source_name: Nivolumab bound peripheral blood CD8 T cells

growth_protocol: Mononuclear cells in freshly collected peripheral blood were enriched by Ficoll-Paque.

extract_protocol:
RNA was prepared from sorted CD8 T cells (2-5x104 cells/each population) by the miRNeasy Isolation kit.
cDNA was generated using a Clontech SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech, Mountain View, CA, USA). Each cDNA sample was sheared (200 - 500 bp) using the Covaris S220 (Covaris, Woburn, MA, USA) and prepared using KAPA Library Preparation Kits (Kapa Biosystems, Wilmington, MA) for 75 bp single-end reads, according to the manufacturer’s instructions.

treatment_protocol: Nivolumab bound and unbound peripheral blood CD8 T cells (CD45+CD56-CD19-TCRab+CD8a+) was sorted by a BD FACSAria II.

value: peripheral blood T cells


title: 5s(TPD040p1_nega)

description: PD-1 negative in T cells from blood

source_name: Nivolumab unbound peripheral blood CD8 T cells


title: 5s(TPD040p1_posi)

description: PD-1 positive in T cells from blood


title: 3s(OPD047p1_posi)

description: PD-1 positive in T cells from blood


title: 2s(OPD046p1_nega)

description: PD-1 negative in T cells from blood


title: C-6.1

city: Menlo Park

first: Christina

last: Fan

address: 4040, Campbell Ave

institute: BD Biosciences

data_processing:
BD Rhapsody pipeline for whole transcriptome analysis was used to identify the molecular index sequences (position 49-56) and align reads to predfined cell label sequences (position 1-8,22-30,43-51) on Read1, and to align reads (Read2) to the human transcriptome (hg19, gencode annotation) using STAR with default parameters. A unique cell label is a combination of the cell label sequences in the 3 indicated positions on Read1.
cell label sequence for position 1-8: TTAACGCG,TGTGCTGA,TCGAGTTG,TTGGCGAT,GCATCCAA,TATACGCG,GAGTTCTG,ATGCTTGG,TCCTCAAC,CCTAATCC,CGAACGTT,TTGCCGTT,AGCTCAAC,ATCCGGTA,AAGCAAGC,CACTCAGA,CAAGGTTC,AGGATGGT,TAGGATGG,ACACACAC,CACATCTC,TCCACTTG,TCCATGCT,GCAAGGAT,GGATATGG,TTGCATCC,CAGACACT,GGATAACG,CTAGTGGT,TGTGACTG,TATAGCCG,TCTGGTCT,ATGGATGG,GCAAGGTA,TGGATGCT,CAACTCGA,GCATGCAT,TCCTTGGT,AAGCAACG,AACGCGAA,TCTCTGTG,AATACGCC,AACGATGG,TCGACAAC,TAGCCGAT,TGCACTTC,GATCCATG,TGGTTGGT,CAACGTAC,ATTAGCCG,TCCAACCT,CTTGGATG,ACGAACCT,CCATTAGG,GCAAGCTT,ACAGCACT,AGTCTCTC,AGTGAGTG,TTCCATGC,CCATAACG,TGGACTTG,TTAAGCCG,TCGACTTC,GCATGGTT,CTTCCAAC,CAACCATG,TCCTAGCT,GTGACACT,GCAATAGG,TGACACAC,TTGCCGAA,TTCCAAGG,AACCTAGC,AAGCCGTT,AACGCCTA,TTAACGGC,ATCCTTGC,GGTACGAA,AACGGCTT,CACTGAGT,GGTTCCTT,CTTCTCCT,CTAGGTTG,AAGGATGC,TCAGACTG,TGTGGACT,TTCCTTGG,TAGGTTCG,AGCTTGGT,ATTACGCG,AACCATGC,TGCAACGT,AGGTGAAC,TGTCTGTC,GATCTGGT,CTGACTGA,
cell label sequence for position 22-30: TGGTCTTC,CAACAGCT,GGTACGTT,TGGAGTTC,TTGCAAGC,TTATGGCG,CAACACGT,CCAACCAA,TCTCTGAC,CTTGTGCT,AGCTTCCT,AGTCCTCT,GAACCATC,CTTGACGA,CATCCTTG,CCTATTGC,TGGTTCCT,TGCATGGT,CCTAGCTT,GCATAAGG,CACATGAC,CCAATTCC,AAGCCGAA,ACTCAGAC,GCAATTCG,GATCTCCT,GACTCTGA,AGCAACGA,ACTGACTG,GCCGTTAA,CAACCAAC,AAGCTTGC,CAAGTGCT,GATGACCT,ACCTGATG,GTCTGTGA,CAACCTTC,AGGTACGA,ATCCAAGC,AGCTCATG,GTTCTGCT,TGCTTGCT,ACTGCTCT,ATGCCGTA,CCATATCC,AGTGGTCT,TGAGTCTG,CGATATGC,CGATTAGC,GATGACGA,TTCGATGG,GTTGCTTC,CTGAACTG,TAGCCGTA,ACCACAAC,GAACGATG,TGCTGTTC,AATTGCCG,TGTGCTCT,GGATGGAT,GATGGATG,GATGGTTC,ACGATGCT,CAAGGATG,GCAACGTT,TGCTCTTG,ATTACGGC,TGCTGATG,CTCAACTC,TGCACATG,CTTGGTTC,ACTGGACT,CTCTTCTC,TGGTTCGA,GTTCCATC,GGTTGCAT,TGGTACGT,GCGGTATT,GTTGTCCT,TTGCTTCG,ACACGACT,CATGGTAC,TCCTCATG,GGATGCAA,TTGCATGG,GATCCAAC,GATCAGCT,TGACCTGA,TGCATCCT,CGAATAGG,ATCCATCC,CTTCCTTC,AGGTCTTG,TGACTGAC,GGTTCGAT,GTTGCATG,
cell label sequence for position 43-51: CTGACTCT,GACTGACT,TAGCTTGG,CATGGTTG,CCATAAGC,TTCGAACG,CTCTCTGA,ACACTGTG,ATATGCCG,AACGGCAA,GCGGTTAT,ACTGTCTC,TGTCCACT,GAACTGCT,TCAGACAC,ACACACTG,ATAACGCC,GGTATTGC,CCAATACG,TCTCTCTC,TCTGACTC,AAGGTACG,GATGTGCT,GCCGTATA,TCTGTCTG,GTCTTCTG,TCGACATG,TCCTTCCT,CGATAAGG,TTGCAACG,GGTTCCAA,TGAGGAGT,GCATCCTT,CATCTGCT,CACACTCT,GATGAGGT,CGAACCAT,ACTGACAC,ACTCCACT,GCCGTAAT,TGAGGTCT,GTCTTGTC,AAGCATCC,CTGTTCTG,TCGAGTAC,CCTAATGG,CATGTCCT,GATGCTTG,GTGAGTCT,GCCGATAT,TCAGCTCT,GACTCTCT,CGAACGAA,TGCAAGCT,CAGAACTC,TCTGAGTG,ATGCATGC,AGTGGAGT,TGACCTCT,AGGAGTAC,TAGCTTCC,CTAGCAAC,GGTATTCG,CCTTCGAT,CTTCAGCT,TTCCGGTT,TCCAAGGT,GACATCTG,GGTTAAGG,GGATGGTA,TCCTGTTG,ACCTGAAC,ACTGAGTC,GTCTAGTG,ATGCGGTT,AACCAAGG,AGGACATG,AAGGTTGG,GCATTACG,TTGGTTGG,CGAATTGC,ACGACATC,CCAATAGC,ATGGTTGC,CTAGTCCT,TGACTCTC,GCAACCAT,AGGAGTTG,TCTGGTGA,AGCTGTTG,CTTGCTTG,CTCAAGTG,ATGCAAGG,CTAGGTAC,CCATGGTA,TATTGGCG,
Reads with the identical cell label, molecular index, and gene identity, are collapsed and counted as 1 molecule
Counts of molecule per gene per cell label are organized in a cell by gene matrix format, which is the final processed data file
Genome_build: hg19
Supplementary_files_format_and_content: Data tables containing number of molecules per gene per cell

source_name: C-6.1: hiPSC-derived 3D culture (pallium)

growth_protocol: Differentiation of human iPSC into hCS

extract_protocol:
Dissociated single cells from were loaded onto the BD Rhapsody single cell gene expression analysis system
mRNA from individual cells were captured by barcoded oligo probes on a BD Rhapsody bead. Capture probes contain cell labels (total of 27 bases) and molecule index (8 randomers) such that when cDNAs were extended by reverse transcriptase, each cDNA molecule was tagged with a cell specific sequence and a molecular index sequence. cDNA were then universally amplified following by adaptor ligation. 3' end of transcripts were enriched using random priming and sequenced on Illumina HiSeq2500.

treatment_protocol: Patterning for pallium; single cell trituration (no reporter used)


title: 2s(OPD046p1_posi)

description: PD-1 positive in T cells from blood


title: C-6.2

source_name: C-6.2: hiPSC-derived 3D culture (pallium)


title: 1s (OPD026p1_posi)

description: PD-1 positive in T cells from blood


title: 1s(OPD026p1_nega)

description: PD-1 negative in T cells from blood


title: TPD039_P2-nega

description: PD-1 negative in T cells from blood

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

extract_protocol:
RNA was prepared from sorted CD8 T cells (2-5x104 cells/each population) by the miRNeasy Isolation kit.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.


title: TPD039_P2+posi

description: PD-1 positive in T cells from blood