title: C_H3K4me3.ctrl.st5.rep2

description:
processed data file:
h3k4me3.subtract_input.ctrl.mean.bw

value: H3K4me3 (Diagenode, Cat. No. C15410003-50)


title: G7dP3-3

status: Public on Oct 13 2021

type: SRA

city: wuhan

first: wu

middle: xiao

last: man

address: Donghu South Road

country: China

institute: Institute of Hydrobiology, Chinese Academy of Sciences

library_source: transcriptomic

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GCGD:Grass Carp Genome Database http://bioinfo.ihb.ac.cn/gcgd/php/index.php?page=download
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Ctenopharyngodon idella

source_name: grass carp

extract_protocol:
Gills were removed, flash-frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）.First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: tissue

value: gill

tag: age

value: three mouths

value: grass carp were cultured at saline-alkali water with the concentration of 3percent

value: 7 days post infected with Flavobacterium cloumnare


title: Tail3

city: Vienna

first: Luis Enrique

last: Cabrera Quio

address: Campus Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

data_processing:
Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode
BAM files containing sequencing reads were converted to fastq files using samtools (v1.9)
Barcoded libraries were demultiplexed using fastx-toolkit (v0.0.14)
Sequencing adapters were trimmed with cutadapt (v1.18) and only reads longer than 25 bases were kept
Reads were aligned to GRCz11 with Hisat2 v2.1.0, using the Ensembl transcriptome release 102. The following parameters were used: hisat2 -q --dta --rna-strandness R -k 12 --no-unal
Quantification at the gene level (to obtain transcript per million (TPM)) was perfomed using Kallisto (v0.43.0)
Genome_build: GRCz11
Supplementary_files_format_and_content: Tab delimited files containing TPM

molecule: polyA RNA

organism: Danio rerio

source_name: zebrafish tail

growth_protocol: Zebrafish (Danio rerio) were raised according to standard protocols (28°C water temperature; 14/10 hour light/dark cycle)

extract_protocol:
Total RNA was extracted using the standard TRIzol (Invitrogen) protocol. To obtain polyA+ RNA, the poly(A) selection kit from LEXOGEN was used.
Strand-specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina

tag: genotype

value: wild-type

value: tail

tag: strain

value: TLAB


title: AEC-1-AEC-1-3_FKDL202561884-1a-3

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Peking Union Medical College

description: E10.0 AEC (single-cell)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were firstly trimmed for adaptor sequences and low quality bases using trimmomatic (version 0.36) with parameters ‘LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 HEADCROP:20 CROP:101 MINLEN:101’, then mapped to GENCODE (vM22) mouse genome (mm10) with STAR (version 2.7.3a) using parameters ‘--outSAMattributes All --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic’.
Isofrorm-level expression was quantified as transcripts per million reads (TPM) with Salmon (version 1.1.0) using aligned transcriptome bam files from STAR output. R package ‘tximport’ was used to map transcripts to gene-level expression.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM at gene and isoform level.

organism: Mus musculus

source_name: mouse embryonic cells

growth_protocol: Wildtype AECs and HECs were sorted from the E10 embryonic AGM region of C57 mice. Wildtype (WT) and mutant (KO) HECs were sorted from the E10 embryonic AGM region of Srsf2 conditional knockout mice.

extract_protocol:
Morphologically deformed cells were discarded. Living single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette; 0.05 μl of 1:200,000 dilution of External RNA Controls Consortium (ERCC) RNA spike-in Mix1 (Ambion) was added to lysis buffer per reaction.
The cDNA libraries from single cells were generated as described previously. "Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nature  Methods, 6, 377–382 (2009)."

treatment_protocol: FACS-sorted cells were kept on ice until lysed and reverse transcribed.

value: AGM

tag: developmental stage

value: wild type


title: Naive2_Naïve CD4 T-cells (sorted for live cells)

city: Rehovot

first: Roni

last: Rak

address: Herzl 229

department: Animal Science

country: Israel

institute: Agriculture Research Organization

description: Mars-seq sequencing of naïve T-cells

data_processing:
library strategy: MARS-seq
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) and mapped to genome /shareDB/iGenomes/Mus_musculus/UCSC/mm10/Sequence/STAR_index using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (default parameters).
The pipeline quantifies the genes annotated in RefSeq (that have expanded with 1000 bases toward 5’ edge and 100 bases toward 3’ bases): /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.3utr.gtf.
Counting was done using htseq-count (DOI: 10.1093/bioinformatics/btu638) (union mode).
Further analysis is done for genes having minimum 5 read in at least one sample.
Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI: 10.1186/s13059-014-0550-8) with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Genome_build: Pipeline was constructed using Snakemake (DOI: 10.1093/bioinformatics/bts480).
Supplementary_files_format_and_content: read counts , RPKM, and DE was calculated using DESeq2.

growth_protocol: Naïve cells were extracted from six spleens of B6 mice using the StemCell CD62L+CD44+ kit (female, 7 weeks, 6-9% naive). Each two spleens were pooled to a total of 3 samples extracted separately. A portion from the naïve state was taken to FASC sorted for live cells followed by RNA extraction. The remaining naive cells were activated by addition of anti-CD3/anti-CD28 activation bead (1:1 bead:cell ratio, thermoFisher Scientific Cat#11131D)    Cells were grown at 0.25 cell/ml in 24 wells, and were collected at 20h, 48h, and 72h after activation. At 20h only live cells were sorted. At 48 and 72 h cells were sorted into CD62L+CD44+ (memory T-cells) and CD62L-CD44+(effector T-cells). The cells were stained as followed, and analyzed using ARIAIII FACS:

extract_protocol:
RNA was extracted using TRI-reagent (Sigma-Aldirch), according to standard protocol.
mRNA sequencing for the first biological repeat was preform using MARS-Seq protocol as described  (Jaitin, D. A. et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 343, 776–9 (2014))

treatment_protocol: cells were centrifuged at 12,000 rpm for 1 min, frozen in liquid nitrogen and stored at -80 ̊C until RNA extraction.

tag: activation stage

value: naïve

tag: cell type

value: CD4 T-cells


title: G7dP6-3

value: grass carp were cultured at saline-alkali water with the concentration of 6percent


title: BT48

city: Baltimore

first: JP

last: Courneya

state: United States of America

address: 685 W Baltimore St., HSF2 Room 480

country: USA

institute: University of Maryland, Baltimore

data_processing:
gene alignment: STAR
transcript abundance: HTSeq 0.6.1p2
differential gene expression: DESeq2
Genome_build: hg19 / GRCh37
Supplementary_files_format_and_content: counts

organism: Homo sapiens

source_name: Normal Human Lung Fibroblasts

extract_protocol:
Following treatments cells were flash-frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Library preparation for RNA-Seq was performed using the TruSeq Stranded Total Library Preparation workflow with Ribo-Zero Gold rRNA removal mix (Illumina, Catalog# 20020598), which depletes samples of both cytoplasmic and mitochondrial rRNA.

tag: plasmid

tag: activation

value: TGF-B

tag: activation time


title: C_H3K4me3.ctrl.st5.rep1

city: Freiburg

first: Michael

last: Rauer

address: Breisacherstr. 153

department: Medical Faculty

country: Germany

institute: University of Freiburg

library_source: genomic

data_processing:
Raw short read sequencing was processed uniformly using default parameters of snakepipes-v2.0.2 (Bhardwaj et al., 2019)). ChIP-seq samples were processed with the DNA-mapping workflow (–trim, --dedup, –properPairs), followed by assay-specific workflow, i.e. ChIP-seq.
Differential Pol II occupancy was determined using the method described in Blythe and Wieschaus, 2015. In brief, reads were countered per transcript using featureCounts (-t transcript -g transcript_id -f -O -Q 3 --primary -s 0). Reads were counted multiple times if they overlap several isoforms. Then, per transcript read counts were processed with edgeR (Robinson et al., 2010) to compute differential Pol2 occupancy. Like in the published method, transcripts spanning less than 125 nucleotides were discarded and only transcripts with read counts across replicates sum more that 10 reads were considered.
Genome_build: dm6, ensembl 96
Supplementary_files_format_and_content: Supplementary files are bigwigs contains library size and input corrected bigwig tracks and the promoter quantification of the Rpb3 (pol2) ChIP-seq.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: embryos

extract_protocol:
ChIP-seq experiments were performed as in Zenk et al., 2017. Briefly, nuclei were extracted in lysis buffer (140 mM NaCl, 15 mM HEPES [pH 7.6], 1 mM EDTA, 0.5 mM EGTA, 1 % TritonX100, 0.5 mM DTT, 0.1 % Sodium Deoxycholate, 10 mM Sodium Butyrate, 1X Protease Inhibitors) and subsequent ultrasound treatment (Covaris E220, 45 sec, peak power 75, duty factor 10, cycles burst 200). Fixed chromatin was then sheared using Covaris E220 (900 sec, peak power 140, duty factor 5, cycle burst 200) and precleared overnight. Each sample was incubated with the relevant antibody and concentration for at least 4 hrs at 4°C. Samples were then washed, eluted and decrosslinked overnight by incubation at 65°C. Next, samples were treated with RNaseA(50mg/mL final concentration) for 30min at 37°C and ProteinaseK (200mg/mL, final) for 3 hrs at 56°C.
Libraries were prepared according to manufacturer’s instructions using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Libraries were quality controlled by capillary electrophoresis on the Fragment Analyzer system (Advanced Analytical).

tag: timepoint

tag: assay

value: ChIP-seq

tag: chip antibody


title: RNAseq.dom-kd.st5.rep3

data_processing:
Raw short read sequencing was processed uniformly using default parameters of snakepipes-v2.0.2 (Bhardwaj et al., 2019)). RNA-seq was processed using the mRNA-seq workflow(–trim option).
Genome_build: dm6, ensembl 96
Supplementary_files_format_and_content: Supplementary file is a featureCounts table of number of reads per genes (stranded)

extract_protocol:
RNA extraction was performed as in Zenk et al., 2017. Briefly, chloroform extraction was performed followed RNA precipitation with Isopropanol. Samples were then washed twice with 80% EtOH and resuspended in TURBO DNase (Ambion AM2238) reaction mix. Finally, DNase was inactivated.
RNA libraries were prepared using the Illumina TruSeq Stranded Total RNA protocol

value: RNA-seq


title: Testis1

source_name: zebrafish testis

value: testis


title: 48hi1_activated CD4 T-cells, 48 hours after activation, high CD62L

description: Mars-seq sequencing of  T-cells 48h after in-vitro activation, sorted for high CD62L

value: 48 hours


title: CD8SP short-read [CD8SP_L004]

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent's Institute of Medical Research

data_processing:
PacBio circular consensus sequencing data were processed using Iso-Seq SMRT Link (version 5.0.1.9585) to identify high-quality full-length sequences.
High-quality full-length sequences were mapped to mouse genome by GMAP (version2016-11-07). Cupcake ToFU (v9.0.2) was used to collapse redundant sequences and unify the CD4SP and CD8SP libraries.
SQANTI2 (version3.6) was used to perfom isoform quality assessment and annotation.
Filtered high-quality full-length PacBio transcripts were served as a reference.
FastQC was used to check Illumina short reads quality and Trimmomatic was used to trim and remove low quality reads.
RSEM (version 1.3.1) was used to align processed Illumina short reads to previously contructed full-length transcript reference.
SUPPA2 (version2.3) was used to identify alternative splicing patterns in full-length transcript reference and percentage of spliced-in (PSI) values were quantified using processed Illumina short reads.
Identifying splicing isoforms based on only Illumina data: Illumina short reads quaility was checked by FastQC and filtered and trimmed by Trimmomatic. Processed short reads were aligned to mouse reference by TopHat  (v2.0.14) and then assembled by Cufflinks (v2.1.1). Two assemblies of CD4SP and CD8SP were compared by Cuffcompare.
Genome_build: GRCm38.97
Supplementary_files_format_and_content: PacBio long-read annotation information and normalised read counts. GTF files from Illumina short reads assemblies (including FPKM values)

source_name: CD8SP thymocytes

growth_protocol: C57BL/6 mice at 6-8-week of age were euthanised by asphyxiation with CO2 and the thymi were excised and placed in RPMI 1640 medium. Thymi were passed through a 100µm stainless steel mesh to produce single cell suspensions of thymocytes.

extract_protocol:
Total RNA was then extracted from the sorted cells with on GenElute Total RNA Purification columns (Sigma).
PacBio libraries were constructed following the IsoSeq Express Template Preparation for Sequel Systems protocol (www.pacb.com). For this procedure, first strand cDNA synthesis was performed using SMARTer PCR cDNA Synthesis Kit (Clontech), which also add necessary adaptor sequences for subsequent PCR amplification. PCR amplification of the cDNA was then performed using PrimerSTAR GXL DNA Polymerase (Clontech) and purified using AMPure PB magnetic beads (PacBio). The purified cDNAs were then end-repaired and ligated using the Template Prep Kit (PacBio) to generate the circular SMRTbell libraries. Each library was then sequenced on individual PacBio SMRT cells. For Illumina libraries, the RNA concentration and integrity of samples were first determined with a LabChip GX (Perkin Elmer). Paired-end RNA-seq libraries were then constructed with the TruSeq total RNA sample preparation kit with rRNA-depletion (Illumina) and sequenced on an Illumina NextSeq at the Ramaciotti Centre for Genomics, University of New South Wales.

treatment_protocol: Two or three thymi were pooled for each sample and then depleted of CD4 expression cells (DP and CD4SP) or CD8 expressing cells (DP and CD8SP) using anti-CD4 or CD8 MACS magnetic beads (Miltenyi). The depleted samples were then sorted for mature CD4SP (CD4+CD8-TCRß+CD24-) or CD8SP (CD8+CD4-TCRß+CD24-) thymocytes on a FACS Aria Fusion (BD).

value: thymus

value: Sorted for mature CD8SP (CD8+CD4-TCRbeta+CD24-) from CD4 depleted samples


title: 3324


title: Tail1


title: BT24


title: B24


title: Tail2


title: Spleen2

source_name: zebrafish spleen

value: spleen


title: G7dcon2

value: gill

value: three mouths

value: untreated

value: 7 days post infected with Flavobacterium cloumnare


title: 20h2_activated CD4 T-cells, 20 hours after activation (sorted for live cells)

description: Mars-seq sequencing of  T-cells 20h after in-vitro activation

value: 20 hours


title: CD8SP short-read [CD8SP_L003]


title: G7dP3-2

value: grass carp were cultured at saline-alkali water with the concentration of 3percent


title: CD8SP short-read [CD8SP_L001]


title: G7dP3-1


title: Naive1_Naïve CD4 T-cells (sorted for live cells)

description: Mars-seq sequencing of naïve T-cells

value: naïve


title: Input-RELACS.dom-kd.st5_rep2

data_processing:
Library strategy: RELACS ChIP-seq
Raw short read sequencing was processed uniformly using default parameters of snakepipes-v2.0.2 (Bhardwaj et al., 2019)). ChIP-seq samples were processed with the DNA-mapping workflow (–trim, --dedup, –properPairs), followed by assay-specific workflow, i.e. ChIP-seq.
Differential Pol II occupancy was determined using the method described in Blythe and Wieschaus, 2015. In brief, reads were countered per transcript using featureCounts (-t transcript -g transcript_id -f -O -Q 3 --primary -s 0). Reads were counted multiple times if they overlap several isoforms. Then, per transcript read counts were processed with edgeR (Robinson et al., 2010) to compute differential Pol2 occupancy. Like in the published method, transcripts spanning less than 125 nucleotides were discarded and only transcripts with read counts across replicates sum more that 10 reads were considered.
Genome_build: dm6, ensembl 96
Supplementary_files_format_and_content: Supplementary files are bigwigs contains library size and input corrected bigwig tracks.

extract_protocol:
RELACS protocol was performed as described previously by Arrigoni, et al. 2018. Briefly, embryos were thawed in RELACS lysis buffer (10 mM Tris-HCl [pH 8], 10 mM NaCl, 0.2% Igepal, 1x Protease inhibitor cocktail) and the nuclei were isolated by sonication using the NEXSON procedure(Arrigoni et al., 2016). To digest the chromatin, 25 µl of 10x CutSmart buffer (NEB), 2.5 µl 100x Protease inhibitor cocktail and 1 µl of CviKI-1 (50 U/µl, NEB R0710S) were added. The digestion reaction was incubated overnight at 20 °C. End repair and A-tailing was performed and customized adapters (Arrigoni et al., 2018) were ligated to the fragments. Once barcoded, the samples were pooled together. Chromatin was then sheared by sonication (Covaris E220, MicroTubes, 5min, peak power 105, duty factor 2, cycles burst 200). This chromatin was used for automated ChIP with the IP-Star Diagenode system. IPs and Inputs were decrosslinked and DNA was purified.
Libraries were prepared using the NEB Ultra II DNA Library Prep Kit for Illumina (E7645S and E6440) following the manufacturer’s instructions

value: RELACS

value: none (input)


title: H2Av-RELACS.dom-kd.st5_rep2

value: Histone H2Av antibody (Active Motif, Cat. No. 39715, lot No.8614002)


title: G7dcon3


title: Input-RELACS.dom-kd.st5_rep1


title: Spleen1

value: wild-type

value: TLAB


title: Skin3

source_name: zebrafish skin

value: skin


title: RNAseq.dom-kd.st5.rep2

value: RNA-seq


title: RNAseq.dom-kd.st5.rep4


title: RNAseq.dom-kd.st5.rep1


title: G7dcon1


title: H2Av-RELACS.dom-kd.st5_rep1


title: G7dP6-1

value: grass carp were cultured at saline-alkali water with the concentration of 6percent


title: CD8SP short-read [CD8SP_L002]

value: thymus

value: Sorted for mature CD8SP (CD8+CD4-TCRbeta+CD24-) from CD4 depleted samples


title: G48P6-1

value: gill

value: 3 days post infected with Flavobacterium cloumnare


title: RNAseq.ctrl.st5.rep2


title: Input-RELACS.ctrl.st5_rep2


title: Skin1


title: Spleen3

value: spleen


title: CD4SP short-read [CD4SP_L001]

source_name: CD4SP thymocytes

value: Sorted for mature CD4SP (CD4+CD8-TCRbeta+CD24-) from CD8 depleted samples


title: G48P3-3

value: three mouths


title: CD4SP short-read [CD4SP_L002]


title: H2Av-RELACS.ctrl.st5_rep2


title: 8ECKO

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description:
8ECKO
UCP2f/f;Tie2-cre

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Brain endothelial cell

extract_protocol:
Total RNA was harvested by Trizol reagent.2 ug of total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

value: Brain endothelial cell


title: G48P6-3


title: G48P3-1

value: grass carp were cultured at saline-alkali water with the concentration of 3percent


title: CD4SP short-read [CD4SP_L003]


title: G48con3

value: untreated


title: 1ECKOE15

description:
1ECKOE15
UCP2f/f;Tie2-cre


title: Liver3

source_name: zebrafish liver

value: liver


title: CD4SP short-read [CD4SP_L004]


title: G48con1


title: Muscle3

source_name: zebrafish muscle

value: muscle


title: TECs 3xAireKI batch1

city: Tsurumi-ku, Yokohama

first: Hideyuki

last: Yoshida

state: Kanagawa

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN IMS

data_processing:
Illumina bcl2fastq software was used for generating FASTQ files
FASTQ files were processed using Fastp, and reads were demultiplexed and mapped to the mm10 reference genome via Cell Ranger (v3.0.0). Processing data by the Cell Ranger pipeline was performed using the HOKUSAI supercomputer at RIKEN and the NIG supercomputer at ROIS National Institute of Genetics. Expression count matrices were prepared by counting unique molecule identifiers.
Supplementary files format and content are described at http://software.10xgenomics.com/single-cell/overview/welcome
Genome_build: mm10
Supplementary_files_format_and_content: Unfiltered feature-barcode matrices containing all barcodes in MEX format

source_name: thymic epithelial cells

extract_protocol:
Mouse thymus was enzymatically  digested and then CD45-EpCAM+ cells were FACS-sorted. single‑cell emulsions were generated using a Chromium instrument from 10× Genomics.
RNA libraries were prepared for sequencing using Chromium Single Cell 3′ Reagent Kits v2 Chemistry
In brief, cell suspensions were loaded onto a Chromium instrument (10× Genomics) to generate a single?cell emulsion. scRNA-seq libraries were prepared using Chromium Single Cell 3' Reagent Kits v2 Chemistry and sequenced in multiplex on the Illumina HiSeq platform (rapid mode).

value: 8 weeks old

value: thymic epithelial cells


title: Liver1

value: wild-type

value: TLAB


title: H2Av-RELACS.ctrl.st5_rep1

value: RELACS

value: Histone H2Av antibody (Active Motif, Cat. No. 39715, lot No.8614002)


title: Muscle1


title: Skin2

value: skin


title: G24P6-2

value: gill

value: grass carp were cultured at saline-alkali water with the concentration of 6percent

value: 24 hours post infected with Flavobacterium cloumnare


title: Muscle2


title: G48P3-2

value: 3 days post infected with Flavobacterium cloumnare


title: TECs WT batch1

value: thymus

value: Aire+/+


title: Input-RELACS.ctrl.st5_rep1

value: none (input)


title: 3WT

description:
3WT
WT

value: Brain endothelial cell


title: G24P6-3

value: three mouths


title: Brain NC rep3

city: Wuhan

first: Lin

last: Shao

address: Donghu Rd185#, Wuhan, Hubei

institute: Wuhan University

data_processing:
reads were aligned to the mm10 genome assembly(Gencode vM20) using STAR_2.5.3a
featureCounts was used to perform reads counting
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: Brain

extract_protocol:
RNaseR was used to digest linear RNA before library construction
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain

tag: treatment

value: untreated


title: G48con2


title: TECs WT batch2

value: 8 weeks old

value: thymic epithelial cells


title: Heart3

source_name: zebrafish heart

value: wild-type

value: heart

value: TLAB


title: ATAC.ctrl.st5.rep2

data_processing:
Raw short read sequencing was processed uniformly using default parameters of snakepipes-v2.0.2 (Bhardwaj et al., 2019)). ATAC-seq were processed with the DNA-mapping workflow (–trim, --dedup, –properPairs), followed by assay-specific workflow, i.e. ATAC-seq by the ATAC-seq workflow.
Genome_build: dm6, ensembl 96
Supplementary_files_format_and_content: Supplementary files are bigwigs contains library size corrected bigwig tracks of ATAC fragments

extract_protocol:
ATAC-Seq protocol was performed as described previously by Buenrostro et. al, 2015 with the following modifications in sample preparation: Embryos were dechorionated in 50% bleach for 2 min, and crosslinked with 5mL of fixative. The fixative consisted of bufferA (60 mM KCl, 15 mM NaCl, 15 mM HEPES [pH 7.6], 4 mM MgCl2) supplemented with 1%PFA. Embryos were fixed for 15 min in an orbital shaker at maximum speed. The crosslinking was stopped by adding a final concentration of 225 mM glycine followed by incubation for 5 min in a rotating wheel. After washing with bufferA + 0.1% Triton X100, the embryos were hand-staged on a cooling station under a microscope with transmitted light. 25 embryos were used per replicate. Fixed embryos were then resuspendend in 1ml bufferA (60 mM KCl, 15 mM NaCl, 15 mM HEPES [pH 7.6], 4 mM MgCl2) and crushed with ultrasound (Covaris E220, 45 sec, peak power 75, duty factor 10, cycles burst 200). Nuclei were pelleted by centrifugation (3200g, 10min at 4°C). We proceeded using the protocol of Buenrostro et. al, 2015. Briefly, nuclei were resuspended in transposition reaction. Samples were then incubated at 37°C for 30 min and immediately purified using the Qiagen MinElute PCR Purification Kit, according to manufacturer’s instructions. Transposed DNA was eluted in 10μl of elution buffer (buffer EB, Qiagen MinElute PCR Purification Kit) and amplified as stated in Buenrostro et al., 2015
For library amplification, all the sequences of custom primers were taken from Buenrostro et al., 2013. The number of PCR cycles for each sample was determined using qPCR as recommended by Buenrostro, et al., 2015, and the remaining 45 μl PCR reaction was further amplified. DNA from these libraries was then purified using AMPure beads (Beckman Coulter, A63881) following the manufacturer’s instructions.

value: ATAC-seq


title: Intestine2

source_name: zebrafish intestine

value: intestine


title: G24P3-1

source_name: grass carp

value: gill

value: grass carp were cultured at saline-alkali water with the concentration of 3percent


title: Liver2

value: liver


title: Brain NC rep1


title: TECs 3xAireKI batch2

value: thymus


title: 3WTE15

description:
3WTE15
WT


title: G48P6-2

value: grass carp were cultured at saline-alkali water with the concentration of 6percent

value: 3 days post infected with Flavobacterium cloumnare


title: Heart1


title: G24P3-3

value: 24 hours post infected with Flavobacterium cloumnare


title: mouse CD47 PDL1 Combo D20

type: RNA

city: San Diego

first: Wenjing

last: Yanf

state: CA

address: 10770 Science Center Drive

department: Oncology

institute: Pfizer

description: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

hyb_protocol: nCounter RNA count data were normalized using the geometric mean of the positive controls and HKGs. Extensive quality control analysis was applied to raw and normalized data to identify batch effects and issues with control probes and the samples.

scan_protocol: A LLOD threshold was set for the counts on the basis of the maximum count of the background controls (negative).

data_processing: Genes with normalized counts less than LLOD were flagged as low-expressing genes. The curated data were subjected to statistical analysis using ANOVA tests followed by pathway analysis using IPA and GSEA

label: florousence

source_name: MC38 Tumor

label_protocol: Samples were prepared using an nCounter Prep Station, and code set/RNA complexes were immobilized on nCounter cartridges for data collection

growth_protocol: C57BL/6 mice were 6-10 weeks of age at time of MC38 tumor inoculation. MC38 murine cancer cells in serum-free PBS were inoculated in the right flank at 5 x 10^5 cells per implant and allowed to grow for 10 days.

extract_protocol: Total RNA (50–100 ng) was used in the nCounter assay (NanoString Technologies) using mouse-specific nCounter PanCancer Immune Profiling and PanCancer Pathways Panels supplemented with custom-made 30-plex code set or human-specific nCounter PanCancer Immune Profiling Panel following the manufacturer’s recommendations.

treatment_protocol: At day 10 post-tumor implant, vehicle control (PBS), CD47/PD-L1 mBisAb, amCD47, amPDL1, or the combination were administrated by I.P every 3 to 4 days. Tumors were then harvested at day 20 and day 24 post-tumor implant.

value: MC38 tumor bearing mice

tag: treatments

value: CD47 PDL1 Combo

value: Day 20


title: mouse CD47 PDL1 Bispecific D24

value: CD47 PDL1 Bispecific

value: Day 24


title: mouse PDL1 D20


title: ATAC.dom-kd.st5.rep2


title: Brain3

source_name: zebrafish brain

value: wild-type

value: brain


title: mouse CD47 PDL1 Bispecific D20


title: G24con2

value: three mouths

value: untreated


title: mouse CD47 PDL1 Combo D24


title: mouse Control D24

value: Control


title: Brain 4AP rep2

value: Brain

value: Intraperitoneal injection of 4-aminopyridine


title: G24P6-1

value: gill


title: G24P3-2

value: grass carp were cultured at saline-alkali water with the concentration of 3percent


title: Intestine3

value: intestine

value: TLAB


title: Intestine1


title: mouse Control D20


title: Heart2

value: heart


title: mouse PDL1 D24

value: MC38 tumor bearing mice


title: Brain NC rep2


title: G24con3

value: 24 hours post infected with Flavobacterium cloumnare


title: Mouse CD47 D20

value: Day 20


title: EVs-Con

status: Public on Oct 12 2021

city: Changchun

first: Dongxu

last: Wang

state: Jilin

address: Xi'an Road #5333

department: Laboratory Animal Center, College of Animal Science

institute: Jilin University

description: miRNAs

data_processing:
The samples were detected by dnbseq platform, and the differences of miRNA expression were compared.
The raw data of sequencing contains low-quality and contaminated reads. These reads need to be removed before data analysis to ensure the reliability of the results.
After obtaining the clean reads, we used bowtie2 to align the clean reads to the reference genome sequence.
miRNA detection
Genome_build: Homo_sapiens
Supplementary_files_format_and_content: Statistics of Sequencing Quality
Supplementary_files_format_and_content: Statistics of Filtered Reads
Supplementary_files_format_and_content: *tag_info.txt: Tag count of sequences and mapped miRNA ID

source_name: Human tongue squamous carcinoma cells(SCC9)

growth_protocol: Human TSCC cell line SCC9 is cultured in Dulbecco’s Modified Eagle Medium F12

extract_protocol:
Lyse extracellular vesicles,extract miRNAs and  inspected by Dnbseq platform
RNA libraries were prepared for sequencing using standard DNBSEQ protocols

treatment_protocol: SCC9 cells were treated with 40 μM of chrysin for 48 h

tag: disease state

value: Tumor stage

tag: cell line

tag: molecule subtype

value: extracellular miRNA


title: Brain 4AP rep3

tag: tissue


title: Brain 4AP rep1


title: Brain1

tag: genotype

value: wild-type


title: Brain2

value: brain

tag: strain


title: DRG59: 201926380-01_S_2_1

city: Coral Gables

first: Sandra

last: Rieger

state: FL

address: 5151 San Amaro Drive

department: Biology

institute: University of Miami

description: sRieger_RiegerHarrisonTaxol11202019_201926380-01_S_2_1

data_processing:
Remaining adapters and poor quality sequences were trimmed with Trimmomatic (version 0.38)116 with the following parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:15. Sequence quality was then verified using FastQC and summarised with MultiQC (version 1.9)
Using STAR17 (version 2.7.5a_2020-06-19), sequences were aligned to mouse genome assembly m38 with Ensembl version 100 annotations using the --quantMode GeneCounts parameter. Mapping quality was verified using MultiQC
Gene counts from STAR alignment were imported into the R environment using Rstudio (R Version 4.0.3; R studio version 1.3.1093) and the package base version 4.0.3. The package dplyr version 1.0.5 was used to construct individual raw gene count matrices per tissue type, skin and dorsal root ganglion neurons (DRGs), each consisting of 32 samples from both treatment groups
Count matrices were normalized using the variance stabilized transformation function from the DESeq2 package

source_name: DRGs

extract_protocol: Oligo-dT

treatment_protocol: Paclitaxel or Vehicle treatment was injected at days 0,2,4, & 6, and samples were collected at timepoints 4,7,11, and 23 days

tag: Sex

value: male

value: DRGs


title: DRG58: 201926381-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926381-01_S_2_1


title: DRG57: 201926393-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926393-01_S_2_1


title: DRG58: 201926381-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926381-01_S_1_1


title: DRG57: 201926393-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926393-01_S_1_1


title: G24con1

tag: age

value: three mouths

value: untreated


title: DRG60: 201926365-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926365-01_S_2_1


title: DRG44: 201926386-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926386-01_S_1_1


title: DRG60: 201926365-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926365-01_S_1_1


title: DRG42: 201926375-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926375-01_S_2_1


title: DRG41: 201926382-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926382-01_S_2_1


title: DRG59: 201926380-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926380-01_S_1_1


title: EVs-Chrysin

description: miRNAs

value: Chrysin


title: DRG42: 201926375-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926375-01_S_1_1


title: DRG41: 201926382-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926382-01_S_1_1


title: DRG43: 201926369-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926369-01_S_2_1


title: DRG25: 201926417-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926417-01_S_2_1


title: DRG43: 201926369-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926369-01_S_1_1


title: DRG25: 201926417-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926417-01_S_1_1


title: mouse CD47 D24

description: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

value: Day 24


title: DRG27: 201926367-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926367-01_S_2_1


title: DRG28: 201926360-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926360-01_S_1_1


title: DRG11: 201926410-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926410-01_S_1_1


title: DRG28: 201926360-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926360-01_S_2_1


title: DRG10: 201926402-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926402-01_S_2_1


title: DRG10: 201926402-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926402-01_S_1_1


title: DRG26: 201926415-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926415-01_S_2_1


title: DRG26: 201926415-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926415-01_S_1_1


title: DRG11: 201926410-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926410-01_S_2_1


title: DRG27: 201926367-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926367-01_S_1_1


title: DRG51: 201926405-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926405-01_S_2_1


title: DRG09: 201926356-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926356-01_S_1_1


title: DRG12: 201926399-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926399-01_S_2_1


title: DRG09: 201926356-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926356-01_S_2_1


title: DRG51: 201926405-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926405-01_S_1_1


title: DRG12: 201926399-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926399-01_S_1_1


title: DRG49: 201926401-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926401-01_S_1_1


title: DRG50: 201926370-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926370-01_S_1_1


title: DRG33: 201926411-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926411-01_S_2_1


title: DRG50: 201926370-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926370-01_S_2_1


title: DRG52: 201926403-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926403-01_S_2_1


title: DRG49: 201926401-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926401-01_S_2_1


title: DRG52: 201926403-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926403-01_S_1_1


title: DRG36: 201926408-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926408-01_S_2_1


title: DRG35: 201926364-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926364-01_S_2_1


title: DRG20: 201926396-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926396-01_S_2_1


title: DRG34: 201926358-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926358-01_S_2_1


title: DRG18: 201926414-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926414-01_S_2_1


title: DRG18: 201926414-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926414-01_S_1_1


title: DRG34: 201926358-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926358-01_S_1_1


title: DRG17: 201926361-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926361-01_S_1_1


title: DRG20: 201926396-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926396-01_S_1_1


title: DRG35: 201926364-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926364-01_S_1_1


title: DRG17: 201926361-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926361-01_S_2_1


title: DRG33: 201926411-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926411-01_S_1_1


title: DRG36: 201926408-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926408-01_S_1_1


title: DRG19: 201926400-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926400-01_S_1_1


title: DRG05: 201926413-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926413-01_S_2_1


title: DRG06: 201926387-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926387-01_S_2_1


title: DRG07: 201926366-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926366-01_S_2_1


title: DRG07: 201926366-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926366-01_S_1_1


title: DRG08: 201926362-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926362-01_S_2_1


title: DRG05: 201926413-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926413-01_S_1_1


title: DRG06: 201926387-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926387-01_S_1_1


title: DRG08: 201926362-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926362-01_S_1_1


title: SKIN57: 201926313-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926313-01_S_2_1

source_name: Skin

value: Skin


title: SKIN57: 201926313-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926313-01_S_1_1


title: SKIN58: 201926319-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926319-01_S_2_1


title: SKIN60: 201926299-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926299-01_S_1_1


title: SKIN43: 201926298-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926298-01_S_2_1


title: SKIN41: 201926332-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926332-01_S_1_1


title: SKIN60: 201926299-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926299-01_S_2_1


title: SKIN59: 201926343-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926343-01_S_1_1


title: SKIN28: 201926338-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926338-01_S_1_1


title: SKIN42: 201926310-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926310-01_S_1_1


title: SKIN26: 201926334-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926334-01_S_1_1


title: SKIN42: 201926310-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926310-01_S_2_1


title: SKIN44: 201926331-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926331-01_S_2_1


title: SKIN44: 201926331-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926331-01_S_1_1


title: SKIN28: 201926338-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926338-01_S_2_1


title: SKIN26: 201926334-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926334-01_S_2_1


title: SKIN43: 201926298-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926298-01_S_1_1


title: SKIN27: 201926336-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926336-01_S_2_1


title: SKIN27: 201926336-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926336-01_S_1_1


title: SKIN59: 201926343-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926343-01_S_2_1


title: SKIN25: 201926294-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926294-01_S_2_1


title: SKIN11: 201926339-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926339-01_S_1_1


title: SKIN10: 201926306-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926306-01_S_1_1


title: SKIN11: 201926339-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926339-01_S_2_1


title: SKIN09: 201926296-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926296-01_S_2_1


title: SKIN09: 201926296-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926296-01_S_1_1


title: SKIN12: 201926326-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926326-01_S_1_1


title: SKIN10: 201926306-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926306-01_S_2_1


title: SKIN50: 201926328-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926328-01_S_2_1


title: SKIN51: 201926354-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926354-01_S_1_1


title: SKIN25: 201926294-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926294-01_S_1_1


title: SKIN51: 201926354-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926354-01_S_2_1


title: SKIN52: 201926295-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926295-01_S_2_1


title: SKIN49: 201926304-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926304-01_S_1_1


title: SKIN50: 201926328-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926328-01_S_1_1


title: SKIN36: 201926346-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926346-01_S_1_1


title: SKIN33: 201926329-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926329-01_S_1_1


title: SKIN52: 201926295-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926295-01_S_1_1


title: SKIN34: 201926337-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926337-01_S_2_1


title: SKIN49: 201926304-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926304-01_S_2_1


title: SKIN18: 201926335-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926335-01_S_2_1


title: SKIN06: 201926344-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926344-01_S_1_1


title: SKIN08: 201926350-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926350-01_S_1_1


title: SKIN17: 201926355-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926355-01_S_2_1


title: SKIN17: 201926355-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926355-01_S_1_1


title: SKIN08: 201926350-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926350-01_S_2_1


title: SKIN34: 201926337-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926337-01_S_1_1


title: SKIN06: 201926344-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926344-01_S_2_1


title: SKIN20: 201926349-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926349-01_S_1_1


title: SKIN07: 201926301-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926301-01_S_2_1


title: SKIN19: 201926321-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926321-01_S_2_1


title: SKIN18: 201926335-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926335-01_S_1_1


title: SKIN05: 201926297-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926297-01_S_1_1


title: SKIN36: 201926346-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926346-01_S_2_1


title: SKIN35: 201926324-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926324-01_S_1_1


title: SKIN33: 201926329-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926329-01_S_2_1


title: CAL_Colon_6

city: Shanghai

first: Ruifeng

last: Ding

address: No. 415 Fengyang Road, Huangpu District

department: Department of Anesthesiology

institute: Changzheng Hospital, Second Affiliated Hospital of Naval Medical University

data_processing:
NEXTSEQ 500 (Illumina) and single-end 75-bp read flow cells were used in this study
The quality of sequencing data was evaluated using FastQC (v0.11.9). Adapters and low-quality reads were trimmed by Trimmomatic (v0.39).
All the remaining qualiﬁed reads were mapped to the Rattus norvegicus genome (Rnor_6.0) using HiSat2 (v2.1.0). Then, FeatureCounts (v1.6.5) was employed for gene quantiﬁcation to build an expression matrix.
Genome_build: Rattus norvegicus genome (Rnor_6.0)
Supplementary_files_format_and_content: csv file include raw count values for each tissue

organism: Rattus norvegicus

source_name: CAL

extract_protocol:
Total RNA of kidney cortex and colon was extracted using TRIzol reagent according to the manufacturer’s instructions. cDNA libraries were prepared by TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme, Nanjing, China). Index-labeled libraries sized at 250–1000 bp fragment length were recovered by using VANTS® DNA Clean Beads (Vazyme, Nanjing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colon

value: CAL


title: CAL_Colon_3


title: SKIN07: 201926301-01_S_1_1

description: sRieger_RiegerHarrisonTaxol11202019_201926301-01_S_1_1


title: CAL_Colon_4


title: SKIN05: 201926297-01_S_2_1

description: sRieger_RiegerHarrisonTaxol11202019_201926297-01_S_2_1


title: CAL_Colon_2


title: CAL_Colon_5


title: HS_Colon_4

source_name: HS

value: HS


title: HS_Colon_5


title: 24hr_RNA-seq_rep3

city: SEVENOAKS

first: Anna

middle: Rita

last: Lamstaes

state: Kent

address: 99 Solefields Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description: 3'-end RNA-seq

data_processing:
Fastq files were quality checked, trimmed using trimmomatic and aligned using Hisat2. SAMtools were used to filter low quality and duplicate reads. Samples were spike-in normalised.
Genome_build: hg38
Supplementary_files_format_and_content:
Spike-in normalized Bigwig

source_name: Hepatocellular Carcinoma

growth_protocol: Hep3B cells grown in DMEM with 10% FBS and 1xP/S, 37oC, 5% CO2

extract_protocol:
Cells were washed with cold PBS and lysed in Qiazol. 2% of drosophila sg4 cells were added. RNA was extracted with chloroform, vortexing and centrifuging for 15min, 4oc, 13000g. RNA was precipitated with isopropanol and the pellet resuspended in 1x DNase buffer and 7.5U DNase (Qiagen). The pellet was DNase treated for 30min at 37oc. Again this was precipitated with isopropanol, washing three times in 75% ethanol, drying at RT and resuspending in RNase-free h2o.
QuantSeq 3' mRNA-seq library prep kit for ion torrent (Lexogen)

treatment_protocol: 24hr 10ng/ml IFNγ

value: 24hr IFNγ

tag: spike-in

value: Drosophila spike in


title: 24hr_RNA-seq_rep1

description: 3'-end RNA-seq


title: 2hr_RNA-seq_rep2

description: 3'-end RNA-seq

treatment_protocol: 2hr 10ng/ml IFNγ

value: 2hr IFNγ


title: 24hr_RNA-seq_rep2

description: 3'-end RNA-seq


title: 2hr_RNA-seq_rep3

description: 3'-end RNA-seq


title: CAL_Colon_1


title: 0.5hr_RNA-seq_rep3

description: 3'-end RNA-seq

treatment_protocol: 0.5hr 10ng/ml IFNγ

value: 0.5hr IFNγ


title: NC_Colon_5

source_name: NC

value: NC


title: 0.5hr_RNA-seq_rep1

description: 3'-end RNA-seq


title: 0.5hr_RNA-seq_rep2

description: 3'-end RNA-seq


title: HS_Colon_2


title: NC_Colon_3


title: NC_Colon_4


title: 2hr_RNA-seq_rep1

description: 3'-end RNA-seq


title: NC_Colon_2


title: NC_Colon_1


title: CAL_Cortex_4

value: Cortex


title: CAL_Cortex_3


title: HS_Colon_3


title: CAL_Cortex_5


title: CAL_Cortex_6


title: HS_Cortex_3


title: HS_Colon_1


title: CAL_Cortex_1


title: Unt_RNA-seq_rep3

description: 3'-end RNA-seq

treatment_protocol: Untreated

value: Untreated


title: CAL_Cortex_2


title: 2hr_SNU-seq_rep2

data_processing:
Library strategy: SNU-seq
Fastq files were quality checked, trimmed using trimmomatic to remove the artificial poly(A) tail and aligned using Hisat2. SAMtools were used to filter low quality and duplicate reads. Samples were spike-in normalised. BEDtools was used to create a 3'-end bedgraph file.
Genome_build: hg38
Supplementary_files_format_and_content:
Forward strand single-nucleotide resolution bedgraph
Reverse strand single-nucleotide resolution bedgraph

extract_protocol:
Cells were washed with cold PBS before lysing in Qiazol on ice. Samples were spiked with Saccharomyces cerevisiae RNA (0.01%). RNA was purified by addition of chloroform, vortexing and centrifuging for 15min, 4oc, 13000g. RNA was precipitated with isopropanol, washing three times in 75% ethanol, drying at RT and resuspending in RNase-free h2o. RNA was biotinylated and captured with streptavidin. A poly(A) tail was artificially added.
QuantSeq 3' mRNA-seq library prep kit for ion torrent (Lexogen)

value: Saccharomyces cerevisiae spike in

tag: rna subtype

value: Nascent RNA


title: NC_Cortex_5


title: Unt_SNU-seq_rep3


title: 2hr_SNU-seq_rep1


title: 24hr_SNU-seq_rep2


title: NC_Cortex_4


title: 0.5hr_SNU-seq_rep1


title: HS_Cortex_1


title: 24hr_SNU-seq_rep3


title: AA: 3057__80_S32

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

description:
AA_vs_EA_ALL_Lo_to_Hi_SerVitD
Lo_to_Hi_SerVitD_AA

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

source_name: Prostate Core Biopsy

extract_protocol:
100–200 ng of total RNA was used to prepare RNA-Seq libraries using the TruSeq RNA Sample Prep Kit (Illumina, CA, USA), following the protocol described by the manufacturer. High-throughput sequencing (HTS) was performed using an Illumina HiSeq2500 with each sample sequenced to a minimum depth of ∼ 50 million reads.
To prepare RNA-Seq libraries using the SMART-Seq® v4 RNA-seq kit (Clontech Laboratories, Mountain View, CA), 10 pg–10 ng of total RNA was used following the protocol described by the manufacturer.

treatment_protocol: Patients underwent a medically indicated prostate biopsy procedure because of rising serum levels of the prostate-specific antigen (PSA), or to monitor a low-risk prostate cancer, as part of the standard of care for “active surveillance.” Deidentified subjects donated a biopsy core (per the IRB-approved informed consent document) which was processed in the MUSC Genomic Center for RNA sequencing (RNA-seq).

tag: race

value: AA

tag: vitamin d serum level

value: HI

value: prostate

tag: patient diagnosis

value: early stage prostate cancer


title: Unt_RNA-seq_rep1

description: 3'-end RNA-seq


title: Acc1_KO_2nd_RNA

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

institute: KAZUSA DNA Research Institute

description: Memory Th2 cells were cultured with IL-2 (15 ng/mL), IL-33 (10 ng/mL) and 4-OHT (100 nM) for 5 days in vitro, and 4 hrs stimulation with PMA plus ionomycin after the cultivation.

data_processing:
Read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using Bowtie (version 0.12.8) and TopHat (version 1.3.2).
Fragments per kilobase of exon per million mapped reads (FPKM) for each gene were calculated using Cufflinks (version 2.0.2).
Genome_build: mm10
Supplementary_files_format_and_content: Text files include FPKM values for each Sample

source_name: Five-day cultured memory Th2 cells with 4-OHT derived from Acaca fl/fl ERT2-Cre+ mice

growth_protocol: See "Material and Methods".

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
For cDNA library construction, we used TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s protocol.

treatment_protocol: Pharmacolgical drug was not treated in this assay


title: NC_Cortex_2


title: Unt_SNU-seq_rep2


title: Acc1_KO_1st_RNA


title: NC_Cortex_1


title: 0.5hr_SNU-seq_rep2


title: NC_Cortex_3


title: HS_Cortex_2


title: 24hr_SNU-seq_rep1


title: AA: 3054__76_S29


title: HS_Cortex_4


title: Unt_SNU-seq_rep1


title: AA: 3051__73_S26

value: LO


title: EA: 3056__78_S31

description:
AA_vs_EA_ALL_Lo_to_Hi_SerVitD
Lo_to_Hi_SerVitD_EA

value: EA


title: NCsA1

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

description:
Sample 15
MmuPV_Hypo3.xlsx

data_processing:
DNA from the RRBS libraries were sequenced in Illumina HiSeq Machines, Base-calling was perfromed using RTA software and demultiplexed to obtain individual Fastq files.
DNA methylation analysis was perfromed using a fragment based approach with our own in house developed pipeline called DMAP (Stockwell et al Bioinformatics, 2014).
Genome_build: mus_GRCh38
Supplementary_files_format_and_content: Excel file contains methylation information of MspI fragments where enough information ( at least 2 CpG covered by 10 reads) was obtained. An ANOVA test was applied to the fragments of the experimental and control groups and regions showing the largest methylation difference (fold change of  1.5) with significant P-values were identified.

source_name: Tail epidermis

extract_protocol:
DNA from placental tissue was extracted using QIAamp DNA mini kit (Qiagen) following the manufacturer’s protocol.
Genomic DNA was digested with MspI (New England Biolabs, Ipswich, MA) followed by end repair and addition of 30 A overhangs. Methylated adaptors (Illumina, San Diego, CA) with a 30 T overhang were then ligated with the generated fragments. Following adaptor ligation, DNA fragments ranging from 40 to 220 bp (preligation size) were cut from a 3% (w/v) NuSieve GTG agarose gel (Lonza, Basel, Switzerland) and subsequently bisulphite modified using the EZ DNA methylation kit (Zymo Research, Irvine, CA). The final library was amplified by PCR. The resulting library was sequenced on an Illumina platform with a single-ended, 100bp run.

treatment_protocol: Sample 1-6 received CsA treatment for 109 days and samples were harvested 31 days after last CsA treatment. Samples 7-12 received CsA treatment for 129 days and samples were harvested 0 days after last CsA treatment. Samples 13-14 received CsA treatment for 137 days and samples were harvested 3 days after last CsA treatment. Samples 15-16 never received CsA treatment.

value: Balb/c

tag: infection

value: PBS mock-infected

value: Tail epidermis

value: no CsA


title: EA: 3053__75_S28


title: BT 2041

city: Salamanca

first: Juan Carlos

last: Montero

state: Salamanca

address: Campus Miguel de Unamuno s/n

country: Spain

institute: Institute of Biomedical Research of Salamanca (IBSAL)

description: Gene expression data from samples of patients with triple negative breast cancer.

hyb_protocol: hybridizations were performed according to protocols from Affymetrix. Briefly, 100 ng of total RNA were amplified and labeled and then hybridized to Human Gene 1.0 ST oligonucleotide arrays (Affymetrix, CA, USA).

scan_protocol: Scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 645, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: The array data was analyzed using the dChip software.

label: Biotin

source_name: Triple negative breast cancer

label_protocol: 100 ng of total RNA were amplified and labeled using the WT Plus reagent kit (Affymetrix).

growth_protocol: Samples obtained from patients with triple negative breast cancer.

extract_protocol: 10-20 mg of each sample was used to isolate total RNA using PureLink RNA Mini Kit (Ambion, Life Technologies, Carlsbad, CA, USA).

treatment_protocol: The samples corresponding to the TNBC subtype were determined in the pathological anatomy service. For the extraction of total RNA, areas of the tumor were selected to avoid necrotic or non-tumor areas.

value: Triple negative breast cancer

value: Tumor


title: AA: 3055__77_S30


title: EA: 3049__71_S25


title: CsA2

description:
Sample 14
MmuPV_Hypo3.xlsx
MmuPV_Hypo4.xlsx

value: CsA


title: Control_1st_RNA

description: Memory Th2 cells were cultured with IL-2 (15 ng/mL) and IL-33 (10 ng/mL) for 5 days in vitro, and 4 hrs stimulation with PMA plus ionomycin after the cultivation.

source_name: Five-day cultured memory Th2 cells derived from Acaca fl/fl ERT2-Cre+ mice


title: AA: 3050__72_S25


title: BT 2428


title: CsA1

description:
Sample 13
MmuPV_Hypo3.xlsx
MmuPV_Hypo4.xlsx


title: BT 845


title: Control_2nd_RNA


title: BT 1569


title: BT 2939


title: EA: 3052__74_S27


title: BT 278


title: BT 1603


title: AC3

description:
Sample 12
MmuPV_Hypo2.xlsx
MmuPV_Hypo4.xlsx

tag: group

value: Active


title: AC2

description:
Sample 11
MmuPV_Hypo2.xlsx
MmuPV_Hypo4.xlsx

tag: treatment


title: NCsA2

description:
Sample 16
MmuPV_Hypo3.xlsx


title: BT 1790


title: BT 3035


title: BT 503


title: AA: 3048__70_S23


title: BT 37


title: EA: 3047__69_S22


title: BT 2561T


title: EA: 3045__67_S20


title: AC1

description:
Sample 10
MmuPV_Hypo2.xlsx
MmuPV_Hypo4.xlsx


title: BT 1041


title: BT 730


title: BT 795


title: AA: 3042__64_S17


title: A2

description:
Sample 8
MmuPV_Hypo2.xlsx
MmuPV_Hypo5.xlsx

value: MmuPV1 infected


title: AA: 3043__65_S18


title: Vector ctrl_48h_diff_Rep2

city: Luxembourg

first: Ann-Christin

last: Hau

address: 1, Rue Louis Rech

department: National Center of Pathology

country: Luxembourg

institute: Laboratoire National de sante

hyb_protocol: Labelled cDNA products were randomly fragmented and hybridized with 5.5µg onto each Mouse Gene 1.0 ST arrays (Affymetrix) using the GeneChip® Hybridization Oven 645 (Affymetrix).

scan_protocol: After hybridization, arrays were washed and stained using the Affymetrix GeneChip® WT Terminal Labeling and Hybridization Kit together with the GeneChip® Fluidics Station 450 (Affymetrix), before being scanned using a GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: After scanning, CEL files were imported into Partek Genomics Suite version 7.19.1125 (Partek Inc.) and collectively normalized using the Robust Multi-Array (RMA) method

label: biotin

source_name: SVZ-neurospheres

label_protocol: 40ng of total RNAs were reverse transcribed into cDNA, then transcribed into cRNAs that were labelled with Biotin using the GeneChip® WT PLUS Reagent Kit (Affymetrix) according to the manufacturer’s standard protocol (P/N 703174 Rev. 2)

extract_protocol: RNA was isolated with the RNeasy Mini Kit (QIAGEN) including on-column DNaseI digestion, followed by EtOH precipitation to ensure sufficient RNA quality

value: infection with pCLIG


title: AA: 3044__66_S19


title: BT 2561N

description: Gene expression data from samples of normal breast tissue.

source_name: Normal breast

value: control

value: Normal tissue


title: A1

description:
Sample 7
MmuPV_Hypo2.xlsx
MmuPV_Hypo5.xlsx


title: EA: 3040__59_S15

value: HI


title: A3

description:
Sample 9
MmuPV_Hypo2.xlsx
MmuPV_Hypo5.xlsx


title: Pbx1 Knockdown_48h_diff_Rep1

value: transfection with siRNAs targeting Pbx1 followed by infection with pCLIG expressing Pax6


title: Pbx1 Overexpression_48h_diff_Rep1

value: infection with pCLIG expressing Pbx1


title: Neurogenic Ctrl_48h_diff_Rep1

value: transfection with non-targeting siRNAs followed by infection with pCLIG expressing Pax6


title: EA: 3038__57_S13

value: EA

value: prostate

value: early stage prostate cancer


title: R3

description:
Sample 3
MmuPV_Hypo1.xlsx
MmuPV_Hypo5.xlsx

value: Balb/c

value: Tail epidermis

value: Regressed


title: RC3

description:
Sample 6
MmuPV_Hypo1.xlsx

value: PBS mock-infected


title: AA: 3039__58_S14

value: LO


title: Pbx1 Knockdown_48h_diff_Rep2


title: Pbx1 Overexpression_48h_diff_Rep2


title: HBL1_MEN1703_rep1

city: Warszawa

first: Michal

last: Pawlak

address: Indiry Gandhi 14

department: Department of Experimental Hematology

country: Poland

institute: Institute of Hematology

description: replicate 1

hyb_protocol: Standard Illumina protocol

scan_protocol: Arrays were scanned on a BeadArray reader

data_processing: idat files were processed to either non-normalized or cubic spline normalized counts by using GenomeStudio V2011.1 (Illumina). For downstream analysis data were converted to gct file (expression_gene_pattern.gct) using Genepattern's IlluminaExpressionFileCreator.

label_protocol: biotin

growth_protocol: DHL-4 and U-2932  cell lines were maintained in RPMI 1640 medium supplemented with 10% FBS, and HBL-1 cells were grown in IMDM medium supplemented with 10% FBS.

extract_protocol: Following treatment, RNA were isolated using GeneMATRIX Universal RNA purification kit (EURx), measured and quality controlled on Bioanalyzer (Agilent), and subsequently profiled on an Illumina Human HT_12 V3 Expression BeadChip.

treatment_protocol: DHL-4, HBL-1 and U-2932 cells were treated in biological duplicates with DMSO (control) or 1.5 µM MEN1703 for 24 hours.

tag: cell type

value: Human diffuse large B-cell lymphoma cell line


title: U2932_MEN1703_rep1

description: replicate 1


title: U2932_dmso_rep2

description: replicate 2

value: DMSO, 24 h


title: RC1

description:
Sample 4
MmuPV_Hypo1.xlsx

value: CsA


title: U2932_dmso_rep1

description: replicate 1


title: lump_robo_gh18

city: Santa Cruz

first: Lindsay

last: Hinck

address: 831 California St

institute: University of California, Santa Cruz

data_processing:
all reads trimmed at 3' end to 75x75bp
paired-end map to mouse RepeatMasker elements with bowtie. Use remaining (not mapped to repeat elements) reads in next steps
paired-end map (repeat-filtered reads) mapped to mm9 with tophat
duplicate mappings removed with samtools rmdup
differential expression analysis with DESeq on per-gene, per-sample read counts, 3 replicates per condition
use DESeq sizeFactors to report per-sample normalized read counts for significant genes
Genome_build: mm9
Supplementary_files_format_and_content: for each gene, the read counts, normalized by DESeq sizeFactors, are shown for all replicates.

source_name: Luminal Progenitors

growth_protocol: Robo1+/- were bred with Robo1+/-; Robo1+/+ and Robo1-/- were adult nulliparus; luminal progenitors were FACS purified and collected.

extract_protocol:
Luminal progenitor cells LPs were purified by fluorescence-activated cell sorting (FACS) (Lin-CD24loCD29+CD61+). Isolate total RNAs from the FACS purified luminal progenitor cells.
Illumina TruSeq RNA sample preparation protocol.

treatment_protocol: Mammary glands were harvested from Robo1+/+ and Robo1-/- littermate mice. Total RNAs were then extracted from FACS purified luminal progenitor cells, harvested from Robo1+/+ or Robo1-/- mice (n=3 per genotype, two animals per n) using TRIreagent LS (Sigma, T3934). Poly(A)+ RNA sequencing libraries were made from each sample using the TruSeq RNA library preparation kit v.1 (Illumina). Libraries were then pooled in equimolar amounts and sequenced on a HiSeq 2000 Sequencing system.

value: Nulliparus

value: Mammary gland


title: EA: 3037__56_S12


title: U2932_MEN1703_rep2

description: replicate 2


title: RC2

description:
Sample 5
MmuPV_Hypo1.xlsx


title: AA: 3041__63_S16

value: AA


title: lump_robo_gh12


title: lump_wild_gh15


title: AA: 3033__49_S8


title: lump_robo_gh06


title: EA: 3035__53_S10

value: HI


title: Vector ctrl_48h_diff_Rep1

value: infection with pCLIG


title: PECs Zc3h12a-S513A LPS0h rep2

city: Kyoto

first: Kotaro

last: Akaki

address: Sakyo-ku, Yoshidakonoecho

department: Department of Medical Chemistry

institute: Kyoto University

data_processing:
Base-calling was performed using RTA 2.4.11
Acquired data was analyzed using Galaxy (Afgan et al., 2018). Briefly, identified reads were mapped on the murine genome (mm10) using HISAT2 (paired end, unstranded) (Galaxy Version 2.1.0), and the mapped reads were counted using featureCounts (Galaxy Version 1.6.3).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: thioglycollate-elicited peritoneal exudate cells (PECs)

growth_protocol: Mice were intraperitoneally injected with 2 ml of 4% (w/v) Brewer’s thioglycollate medium. 3.5 days after the injection, peritoneal macrophages were collected and cultured in RPMI-1640 with 10 % FBS, 1 % Penicillin/Streptomycin, and 100 μM 2-mercaptoethanol.

extract_protocol:
After the LPS stimulation, RNA was collected and isolated using TRIzol Reagent.
cDNA library was prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) and sequenced on NextSeq 500 System (Illumina) according to the manufacturer’s instructions.

treatment_protocol: PECs were stimulated with LPS (100 ng/ml) for 0, 4, or8 hours

value: LPS 0 hour

value: peritoneal exudate cells (PECs)


title: R2

description:
Sample 2
MmuPV_Hypo1.xlsx
MmuPV_Hypo5.xlsx

value: MmuPV1 infected


title: PECs Zc3h12a-S513A LPS4h rep2

value: LPS 4 hours


title: R1

description:
Sample 1
MmuPV_Hypo1.xlsx
MmuPV_Hypo5.xlsx

value: Balb/c


title: PECs Zc3h12a-S513A LPS8h rep2

value: LPS 8 hours


title: AA: 3036__55_S11

description:
AA_vs_EA_ALL_Lo_to_Hi_SerVitD
Lo_to_Hi_SerVitD_AA

value: prostate

value: early stage prostate cancer


title: m-mTERT-G1-Hippocampus-3

city: Houston

first: Chang-Jiun

last: Wu

state: TX

address: 1515 Holcombe Blvd

department: Genomic Medicine

institute: University of Texas, MD Anderson Cancer Center

description: m-mTERT-G1-Hippocampus replicate 3

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 using STAR software.
The HTSeq-count program was used to generate raw read counts for each gene
Normalized counts were generated by DESeq2 package in R
Genome_build: GRCm38
Supplementary_files_format_and_content: normalized counts

extract_protocol:
RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mouse hippocampus

value: mTert KO (G1)


title: lump_wild_gh09


title: EA: 3031__45_S6

value: EA

value: LO


title: lump_wild_gh03

value: Nulliparus


title: Neurogenic Ctrl_48h_diff_Rep2

value: transfection with non-targeting siRNAs followed by infection with pCLIG expressing Pax6


title: DHL4_MEN1703_rep1

description: replicate 1

value: Human diffuse large B-cell lymphoma cell line


title: m-mTERT-G1-Hippocampus-2

description: m-mTERT-G1-Hippocampus replicate 2


title: HBL1_dmso_rep1

description: replicate 1

source_name: HBL-1, DMSO

value: DMSO, 24 h


title: AA: 3034__52_S9

value: AA


title: DHL4_MEN1703_rep2

description: replicate 2


title: DHL4_dmso_rep1

description: replicate 1


title: HBL1_MEN1703_rep2

description: replicate 2


title: HBL1_dmso_rep2

description: replicate 2


title: DHL4_dmso_rep2

description: replicate 2


title: m-mTERT-WT-Hippocampus-3

description: m-mTERT-WT-Hippocampus replicate 3

value: mTert WT


title: m-mTERT-WT-Hippocampus-1

description: m-mTERT-WT-Hippocampus replicate 1


title: AA: 3028__42_S3

value: HI


title: m-mTERT-G1-Cortex-3

description: m-mTERT-G1-Cortex replicate 3

value: Mouse cerebral cortex


title: AA: 3027__41_S2


title: m-mTERT-G1-Cortex-1

description: m-mTERT-G1-Cortex replicate 1


title: m-mTERT-WT-Hippocampus-2

description: m-mTERT-WT-Hippocampus replicate 2


title: m-mTERT-G1-Hippocampus-1

description: m-mTERT-G1-Hippocampus replicate 1


title: PECs Zc3h12a-S513A LPS4h rep1

value: LPS 4 hours

value: peritoneal exudate cells (PECs)


title: AA: 3026__40_S1


title: PECs Zc3h12a-S513A LPS0h rep1

value: LPS 0 hour


title: PECs Zc3h12a-S513A LPS8h rep1

value: LPS 8 hours


title: AA: 3030__44_S5

value: prostate

value: early stage prostate cancer


title: Input_wildtype_1

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

data_processing:
Single-end reads (50 bp) were mapped to the reference genome (Schizosaccharomyces pombe ASM294v2) using bowtie2 (version 2.2.9).
Reads were counted in either 250 bp or 10 kb windows (bins) using the windowCounts() function from the csaw R/Bioconductor package (version 1.18.0). Normalization factors were calculated by the normFactors() function using the “TMM” method on count matrices with 10 kb bins and applied on count matrices with 250 bp bins. Normalized, log2-transformed count matrices were obtained by the cpm() function (edgeR package, version 3.26.8). ChIP samples were normalized by their corresponding inputs (i.e. subtraction in log2-scale). Input-normalized count matrices were converted to coverage vectors using the coverage() function (GenomicRanges package, version 1.38.0) and exported as bigwig files (rtracklayer package, version 1.44.4).
genome build: Schizosaccharomyces pombe ASM294v2
processed data files format and content: Bigwig format. Normalized coverage.

organism: Schizosaccharomyces pombe

source_name: whole cell

extract_protocol:
100 mL yeast cultures were grown to mid-log phase to OD600 = 0.6. The cultures were cooled down at RT for 10 min and fixed with 1% FA for 20 min at RT on the shaker. Cross-linking was stopped with 150 mM Glycine for 10 min at RT. Cells were washed 2x with 30 mL ice-cold dH2O, the pellet was frozen in liquid nitrogen and kept at -80°C until further processing. Pellets were resuspended in 1 mL FA(1) buffer (50 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100 (v/v), 0,1% NaDeoxycholate (w/v), 0,1% SDS (w/v), supplemented with Roche protease inhibitors. Cells were broken in a bead beater (Precellys): 9x30s. After centrifugation, the supernatant and the pellet were sonicated for 15 min at 4°C. Chromatin extracts were spun down for 10 min at 14000 rpm at 4°C. 500 µl chromatin was used and 1 µl of H3K9me2 antibodies (Abcam, Ab1220). Samples were incubated with antibodies O/N at 4°C. 25 µl of FA(1)-washed Dynabeads were added to each sample and they were incubated for 2 hours at 4°C. Samples were then washed 3x for 5 min at RT with FA(1) buffer, FA(2) buffer (FA(1) buffer with 500 mM NaCl), once with LiCl buffer (10 mM TrisHCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0,5% NP-40 (v/v), 0,5% NaDeoxycholate (w/v)) and once with TE buffer. DNA was eluted from the antibodies with ChIP Elution buffer (50 mM Tris HCl, pH 7.5, 10 mM EDTA, 1% SDS) for 15 min at 65°C. DNA was treated with RNAseA, Proteinase K and de-crosslinked O/N at 65°C. DNA was purified with Zymo Research ChIP DNA Clean and Concentrator kit according to the manual instructions. To obtain enough material for the library preparation three technical IP replicates were pulled.
ChIP-seq libraries were prepared with 2 ng of DNA with NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manual instructions. The libraries were sequenced at LAFUGA at the Gene Center (LMU).

value: WT

tag: chip antibody

value: none (Input)


title: Input_wildtype_2


title: PECs WT LPS8h rep2


title: PECs WT LPS8h rep1


title: AA: 3029__43_S4

value: LO


title: PECs WT LPS4h rep1


title: PECs WT LPS0h rep2


title: m-mTERT-WT-Cortex-3

description: m-mTERT-WT-Cortex replicate 3


title: AA: 3001__38


title: PECs WT LPS4h rep2


title: m-mTERT-G1-Cortex-2

description: m-mTERT-G1-Cortex replicate 2

value: mTert KO (G1)


title: PECs WT LPS0h rep1


title: EA: 3166__39

value: EA


title: m-mTERT-WT-Cortex-1

description: m-mTERT-WT-Cortex replicate 1


title: 24hr_CapC_rep1

description: Two sequencing runs were performed to obtain the desired sequencing depth

data_processing:
Library strategy: CaptureC
Reads were mapped using the Capture-C published scripts found at https://github.com/telenius/captureC/releases (Davies2015,Telenius2020). Following mapping, reads were normalized and comparisons between conditions were made using the published scripts found at https://github.com/djdownes/CaptureCompare/ (Telenius2020).
If paired-end sequencing reads overlap they are flash combined, otherwise the separate non-flashed paired reads are taken forward. The flashed and unflashed reads undergo in silico NlaIII digestion. Any flashed reads not containing an NlaIII restriction enzyme site are discarded. Digested fragments are aligned to the hg38 genome using Bowtie and sorted into capture and reporter fragments. Aligned fragments are filtered; reads must contain a capture site plus a reporter site, PCR duplicates are removed, as are reads with low-quality alignment scores. The script also checks for regions of the genome that may be non-specifically captured by the probes and removes all reads containing these regions.
Genome_build: hg38
Supplementary_files_format_and_content:
CD274 capture, BigWig normalized to reads in cis
IRF1 capture, BigWig normalized to reads in cis
STAT1 capture, BigWig normalized to reads in cis
Myc capture, BigWig normalized to reads in cis

extract_protocol:
Cells were harvested in cold PBS and fixed in 1\%~formaldehyde for 10min. Fixed cells were resuspended in lysis buffer, resuspended in PBS and snap-frozen in liquid nitrogen. Thawed cells were pelleted and resuspended in digested overnight with NlaIII. Digested DNA within nuclei were  ligated with T4 DNA ligase overnight. Nuclei were treated with Proteinase K and RNaseA followed by phenol:choloform purification of DNA. The DNA was sonicated to predominantly 200bp fragments. The sonicated material underwent end-repair, dA-tailing, adapter ligation and PCR addition of indices using the NEBNext DNA library Prep Reagent Set and NEBNext Multiplex Oligos for Illumina as per manufacturers instructions, purifying with AxyPrep beads after each step. Indexed libraries were pooled and mixed with human COT DNA, TS-HE universal oligo,  TS-HE Index oligo. This DNA was dried in a heated vacuum centrifuge and resuspended in 1x~hybridisation buffer and hybridisation component A). This DNA-hybridisation mix was denatured and captured by biotinylated probes. Hybridised DNA was washed, amplified and purified. 2 rounds of hybridization were performed.
NEBNext DNA library Prep Reagent Set and NEBNext Multiplex Oligos for Illumina

tag: cell line

value: 24hr IFNγ


title: 2hr_CapC_rep2

value: 2hr IFNγ


title: H3K9me2_pob3_delta_1

value: pob3 delta

value: H3K9me2 - Abcam (ab1220)


title: H3K9me2_wildtype_2


title: #63 SPF f18 incident

city: Yokohama

first: Kosuke

last: Miyauchi

address: 1-7-22 Suehiro-sho

institute: RIKEN Center for Integrative Medical Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Skin were removed, treated with RNALater, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skin

value: 20 weeks

value: Stat3f/f K5cre


title: Input_pob3_delta_2


title: AA: 2993__29

value: AA

value: HI


title: EA: 2997__34

description:
AA_vs_EA_ALL_Lo_to_Hi_SerVitD
Lo_to_Hi_SerVitD_EA


title: Input_pob3_delta_1


title: 0.5hr_CapC_rep2

value: 0.5hr IFNγ


title: EA: 2998__35

value: prostate


title: H3K9me2_pob3_delta_2


title: 0.5hr_CapC_rep1


title: m-mTERT-WT-Cortex-2

description: m-mTERT-WT-Cortex replicate 2

value: Mouse cerebral cortex

value: mTert WT


title: #58 SPF m42 noincident


title: H3K9me2_wildtype_1

value: WT


title: 24hr_CapC_rep2


title: #57 SPF m41 noincident


title: EA: 2990__25

value: early stage prostate cancer


title: AA: 2999__36


title: EA: 3000__37


title: 2hr_CapC_rep1


title: #61 SPF m46 incident


title: 24_input_rep3

data_processing:
Library strategy: ChIPmentation
Genome_build: hg38

extract_protocol:
Cells were washed and collected in PBS. The cell pellet was resuspended in RT PBS and fixed for 5min with 1% formaldehyde before quenching with 0.125M Glycine. 5000 fixed drosophila sg4 cells (0.05%) were added as a spike-in control. The cell pellet was obtained, washed in cold PBS and incubated in swelling buffer. The subsequent nuclear pellet was resuspended in lysis buffer and sonicated to fragments of ~200bp. One tenth of the sample was taken as input control. Samples were incubated overnight with the required antibody, 5ul of H2AV drosophila Ab and blocked ProteinA dynabeads. IPs were stingically washed. IPs were tagmented (Nextera DNA Library Prep Kit) and tagmented DNA eluted off the beads. The eluted IPs, and Input controls were decrosslinked, RNase and proteinase K treated. The input controls were tagmented.
Nextera DNA library prep kit and Nextera index kit (Illumina)

value: Input control


title: Unt_CapC_rep2

value: Untreated


title: 24_input_rep2

value: 24hr IFNγ


title: EA: 2996__33

value: EA


title: EA: 2991__27


title: #59 SPF m44 noincident


title: EA: 2992__28


title: 2_input_rep3

value: 2hr IFNγ


title: AA: 2983__17

value: LO


title: AA: 2985__19


title: AA: 2995__32


title: Unt_CapC_rep1


title: #55 SPF m31 noincident

value: Skin


title: #52 SPF m28 noincident

value: 20 weeks


title: #53 SPF m29 noincident

value: Stat3f/f K5cre


title: EA: 2994__31


title: Rabbit 1

first: Bridget

middle: Diane

last: De Lay

address: 6431 Fannin St., MSB 2.121

department: Pathology and Laboratory Medicine

institute: University of Texas McGovern Medical School

data_processing:
Cutadapt v2.3 was used to remove standard Illumina sequencing adapters and enforce a minimum read length of 18 nt.
Bowtie2 v2.3.4.1 was used to align reads to NCBI RefSeq NC_021490 using default parameters and seed substring lengths set to 18 nt.
SAM files were converted to BAM files and the BAM files were name-sorted using samtools.
HTSeq with filtering set to 0 was used to create count tables from the name-sorted BAM files.
Differential expression analysis was performed with DESeq2 and R.
Genome_build: NC_021490
Supplementary_files_format_and_content: DESeq2_NO_FILTER-results-with-normalized.csv: Comma-separated values file with output from DESeq2 giving normalized counts for each gene. Log2-fold change values and adjusted p-values are given for the comparison between the in vitro and rabbit samples.

organism: Treponema pallidum

source_name: New Zealand white rabbit testes

growth_protocol: Treponema pallidum 'Nichols' were cultivated in vitro in TpCM-2 medium with Sf1Ep cottontail rabbit epithelial cells or in New Zealand white rabbits inocuated intratesticularly with 2-5 x 107 organisms per testis.

extract_protocol:
Ten days after infection, rabbits were euthanized and the testes were aseptically removed and rinsed in phosphate buffered saline (PBS). Testes extracts were prepared by finely mincing the testes and stirring in extraction buffer (PBS with 20% heat-inactivated rabbit serum and 1 mM DTT, pre-equilibrated with 95% N2:5% CO2) for 10 min at room temperature, followed by centrifugation at 1000 x g for 2 x 5 min to remove rabbit tissue. The resulting supernatant containing T. pallidum was treated with RNAprotect Bacteria reagent (Qiagen) to stabilize the RNA and incubated at room temperature for 5 minutes. Bacteria were pelleted by centrifugation for 10 minutes at 10K x g and used immediately used for RNA extraction. In vitro-cultivated organisms were harvested from T75 flasks after 7 days of growth. TpCM-2 was removed, placed in a 50 mL tube, and the flask was rinsed with 2.5 mL trypsin-EDTA. The trypsin-EDTA wash was put into the tube with reserved TpCM-2. 2.5 mL of trypsin-EDTA was added to the flask and incubated at 37°C for five min. The reserved TpCM-2 was then added back to the flask, pipetted to resuspend the Sf1Ep-T. pallidum mixture, and returned to the tube. The tube was centrifuged at 100 x g for 7 min and the supernatant was treated with RNAprotect Bacteria reagent (Qiagen) for 5 minutes at room temperature. Bacteria were pelleted by centrifugation for 10 minutes at 10K x g.
T. pallidum RNA was extracted using a Qiagen RNeasy kit as per manufacturer’s instructions. DNase digestion was performed using Qiagen RNase-free DNase set. cDNA libraries were prepared with an Ovation Complete Prokaryotic RNAseq Library Preparation kit and sequenced on an Illumina NovaSeq6000 S4 system (150bp paired end reads) by Psomagen Inc. (Seoul, South Korea).

value: Nichols

value: From infected New Zealand white rabbit testes


title: AA: 2987__22

value: AA


title: AA: 2988__23

value: HI

value: prostate


title: #50 SPF m26 noincident

source_name: Skin


title: 24_input_rep4


title: 2_input_rep1


title: in vitro set 2C

source_name: in vitro culture

value: Cultivated in TpCM2 medium with Sf1Ep cottontail rabbit epithelial cells


title: #42 SPF m35 noincident


title: #43 SPF m36 incident


title: EA: 2981__15


title: 24_input_rep1


title: 2_input_rep2


title: #45 SPF m38 noincident


title: #38 SPF f45 incident


title: AA: 2980__14


title: 2_input_rep4


title: EA: 2982__16


title: Rabbit 2


title: EA: 2986__21


title: 0.5_input_rep2

value: 0.5hr IFNγ


title: #34 GF f12 noincident


title: #46 SPF m30 incident


title: 0.5_input_rep4


title: in vitro set 2B


title: 0_input_rep4


title: AA: 2976__10

value: early stage prostate cancer


title: 0.5_input_rep3

value: Input control


title: 0_input_rep3

value: Untreated


title: in vitro set 2A


title: in vitro set 1A


title: AA: 2977__11


title: in vitro set 1C


title: #39 SPF f46 incident


title: #30 GF f9 noincident


title: 0_Input_rep2


title: #32 GF f11 incident


title: AA: 2975__9


title: EA: 2978__12


title: JGHL66

city: Los Angeles

first: Mehdi

last: Bouhaddou

address: 611 Charles E Young Drive, Boyer Hall 530

institute: UCLA

data_processing:
Unaligned reads were mapped to human reference for expression counting; all mouse reads were discarded. Reads were classified as "human", "mouse", "both", "neither", and "ambiguous" using Xenome (v1.0.0).
Adapters were trimmed and reads failing QC were removed using fastp (v0.20.0).
Remaining reads were mapped against an Ensembl GRCh38.90 reference.
Expression counts were estimated using RSEM (v1.3.1).
mRNA sequencing data (in units of FPKM) was median centered across patients by dividing by the median expression value for each gene. The log2 of these values were then calculated to generate the final RNA expression values used for subsequent analyses.
Genome_build: Ensembl GRCh38.90 reference
Supplementary_files_format_and_content: Processed data file contains transcripts per million (TPM) counts per gene isoform for all samples.

source_name: Patient-derived xenograph sample

growth_protocol: PDX samples were grown in NOD-SCID gamm mice as previously described (Li H et al 2014)

extract_protocol:
Total RNA was extracted using the RNAeasy kit from Qiagen.
Standard library preps were created by QB3-Berkeley Genomics core.

treatment_protocol: PDX tumors were treated as described in the manuscript.

tag: disease state

value: Head and neck cancer patient

tag: cetuximab response

value: not tested

tag: predicted cetuximab response

value: Resistant


title: 0.5_input_rep1

source_name: Hepatocellular Carcinoma


title: #27 GF f6 noincident

tag: strain

tag: tissue

tag: genotype


title: #25 GF f4 incident

tag: age


title: EA: 2979__13

value: EA


title: 0_Input_rep1


title: in vitro set 1B


title: EA: 2974__8


title: JGHL65

value: Sensitive


title: EA: 2972__6

value: LO


title: JGHL64


title: #19 GF m18 noincident

value: Skin

value: 20 weeks

value: Stat3f/f K5cre


title: JGHL62


title: #24 GF f3 noincident


title: JGHL63


title: 24hr_CTCF_rep2

data_processing:
Library strategy: ChIPmentation
Fastq files were quality checked, paired and trimmed using trimmomatic and aligned using Bowtie2. SAMtools were used to filter low quality and duplicate reads. Samples were spike-in normalized, or normalized based on sequencing depth. MACS2 was used to call peaks using input reads as a control.
Genome_build: hg38
Supplementary_files_format_and_content:
Bigwig

value: 24hr IFNγ

value: CTCF


title: #18 GF m17 noincident


title: 24hr_CTCF_rep1


title: AA: 2971__5

value: AA

value: prostate


title: 2hr_CTCF_rep2

value: 2hr IFNγ


title: #14 GF m14 incident


title: 2hr_CTCF_rep1


title: AA: 2973__7

value: HI

value: early stage prostate cancer


title: 0.5hr_CTCF_rep2

value: 0.5hr IFNγ


title: #12 GF m13 incident


title: JGHL60

value: Head and neck cancer patient


title: F_GMP_CB14

city: Vancouver

first: Elizabeth

last: Bulaeva

state: BC

address: 675 West 10th Avenue

department: Terry Fox Laboratory

country: Canada

institute: British Columbia Cancer Agency

description:
pooled donors
ribo-depleted RNA

data_processing:
Adaptor sequences were stripped from the resulting 125-nucleotide sequence reads and the sequences uniformly trimmed to 75 nucleotides.
Trimmed reads were aligned using BWA mem v0.7.6a (-M -P parameters) to a transcriptome reference consisting of genomic sequence (GRCh37-lite July 2010) supplemented by read-length-specific exon–exon junction sequences (Ensembl v69)
Reads were sorted using Sambamba v0.5.5
The sorted bam files were repositioned to GRCh37-lite using JAGuaR v2.2.2 to assign sequences that aligned across exon–exon junctions to their correct ‘split’ genomic coordinates.
An in-house RNA quality control and analysis pipeline was used to generate a report and calculate a normalization constant for computing RPKM values (reads per kilobase per million mapped reads)
Genome_build: hg19 Ensembl v69
Supplementary_files_format_and_content: Tab delimited files containing 6 columns:
1. Ensembl ID (protein coding genes only)
2. N - reads (total in all exons)
3. RPKM - total
5. RPKM - min of all exons
6. RPKM - max of all exons

source_name: Human AML generated in NRG-3GS mice

growth_protocol: Cells were injected intravenously into the tail vein of NRG-3GS mice, and harvested at sacrifice, when the mice were moribund.

extract_protocol:
RNA was extracted from snap-frozen cells using the All prep DNA/RNA Mini Kit (Qiagen, 80204 - lysis steps) and  mirVana miRNA Isolation Kit (Life Technologies, AM1560 - extraction steps) followed by ethanol precipitation. RNA was quantified using an Agilent Bioanalyzer (Life Technologies) and 500 ng of total RNA was ribosomal RNA (rRNA) depleted using a NEBNext rRNA Depletion Kit (New England BioLabs, E6310L).
First strand cDNA was generated using a Maxima H minus First Strand cDNA Synthesis Kit (Thermo Scientific, K1652) with added Actinomycin D (1 μg, Sigma, A9415). The product was puri- fied using in-house-prepared 20% PEG in 1 M NaCl Sera-Mag bead solution at a 1.8× ratio and then eluted in 35 μl of Qiagen EB buffer. Second-strand cDNA was synthesized in a 50 μl volume using SuperScript Choice System for cDNA Synthesis (Life Technologies, 18090-019) with 12.5 mM GeneAmp dNTP Blend with dUTP. Double-stranded cDNA was purified with 20% PEG in 1 M NaCl Sera-Mag bead solution at a 1.8× ratio and eluted in 40 μl of Qiagen EB buffer, and fragmented using Covaris E220 (55 s, 20% duty factor, 200 cycles per burst). Sheared cDNA was end repaired/phosphorylated, single A-tailed, and adaptor ligated using custom reagent formulations (New England BioLabs, E6000B-10) and in-house-prepared Illumina forked adaptor. PEG (20%) in 1 M NaCl Sera-Mag bead solution was used to purify the template between each of the enzymatic steps. To complete the pro- cess of generating strand directionality, adaptor-ligated template was digested with 5 U of AmpErase Uracil N-Glycosylase (Life Technologies, N8080096). Libraries were then indexed and PCR amplified using Phusion Hot Start II High Fidelity Polymerase (Thermo Scientific, F 549-L).

tag: coord blood pool

tag: initiating cell population

value: GMPs

tag: cell type analyzed

value: hCD33+ GFP+ cells from mouse bone marrow


title: #10 GF m11 noincident


title: D_GMP_CB16a

description:
pooled donors
ribo-depleted RNA

value: hCD33+ GFP+ cells from mouse spleen


title: #2 GF m2 noincident

value: Stat3f/+ K5cre


title: E_GMP_C9835np

description:
pooled donors
ribo-depleted RNA


title: 0.5hr_CTCF_rep1


title: JGHL59

value: not tested

value: Sensitive


title: JGHL56


title: Unt_CTCF_rep2

value: Untreated


title: JGHL58


title: C_CD34+38-_C9183p

description:
pooled donors
ribo-depleted RNA

value: CD34+CD38- cells


title: B_CD34+38-_C9835np

description:
pooled donors
ribo-depleted RNA


title: Unt_CTCF_rep1


title: KStat3f/f5cre 14 day #3

source_name: Cultured keratinocytes

value: Skin

value: neonatal

value: Stat3f/f K5cre


title: Stat3f/fK5cre 7 day #3


title: A_CD34+38-_CB16a

description:
pooled donors
ribo-depleted RNA


title: 24hr_K4me3_rep2

data_processing:
Library strategy: ChIPmentation
Fastq files were quality checked, paired and trimmed using trimmomatic and aligned using Bowtie2. SAMtools were used to filter low quality and duplicate reads. Samples were spike-in normalized, or normalized based on sequencing depth. MACS2 was used to call peaks using input reads as a control.
Genome_build: hg38
Supplementary_files_format_and_content:
Spike-in normalized Bigwig

value: 24hr IFNγ

tag: spike-in

value: Drosophila spike in


title: Stat3f/fK5cre 0 day #3


title: JGHL54

value: Resistant


title: JGHL55


title: JGHL57


title: JGHL53


title: Stat3f/fK5cre 14 day #2


title: 2hr_K4me3_rep2

value: 2hr IFNγ


title: JGHL52


title: Stat3f/fK5cre 7 day #2


title: JGHL51


title: 2hr_K4me3_rep1


title: JGHL50


title: 0.5hr_K4me3_rep1

value: 0.5hr IFNγ


title: 0.5hr_K4me3_rep2


title: Stat3f/fK5cre 0 day #2


title: iPSC-RPE-3_CC-HS_ACA_RS21 [HM7FMBBXX_16496342_S38_L005]

city: Bethesda

first: David

last: McGaughey

state: MD

address: 10 Center Dr

department: NEI

institute: NIH

data_processing:
salmon 0.9.1
gencode.v27.basic.annotation.gtf.gz
tximport with tx2gene collapse
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv, tximport collapsed to genes

growth_protocol: mature iPSC-RPE were cultured in MEM based media supplemented with FBS and other growth factors

extract_protocol:
Total RNA
Total RNAs (5 μg) from two biological replicates were pooled for cDNA library construction. cDNA library preparation and sequencing were carried out on an Illumina HiSeq 4000 platform

treatment_protocol: RPE cells were treated with CI-HS, CC-HS and two drugs.

value: iPSC derived RPE


title: iPSC-RPE-2_CC-HS_ACA_RS20 [HMLLWBBXX_16496343_S52_L008]


title: iPSC-RPE-3_CC-HS_ACA_RS21 [HMLLWBBXX_16496342_S51_L006]


title: iPSC-RPE-3_CC-HS_ACA_RS21 [HMLLWBBXX_16496342_S51_L007]


title: JGHL49

value: Head and neck cancer patient


title: iPSC-RPE-3_CC-HS_ACA_RS21 [HMLLWBBXX_16496342_S51_L008]


title: iPSC-RPE-2_CC-HS_ACA_RS20 [HMLLWBBXX_16496343_S52_L006]


title: Unt_K4me3_rep2


title: iPSC-RPE-2_CC-HS_ACA_RS20 [HM7FMBBXX_16496343_S39_L005]


title: Stat3f/fK5cre 7 day #1


title: K5cre 14 day #2


title: iPSC-RPE-2_CC-HS_ACA_RS20 [HMLLWBBXX_16496343_S52_L007]


title: 24hr_K4me3_rep1


title: Unt_K4me3_rep1


title: JGHL48


title: K5cre 7 day #2


title: 24hr_k27ac_rep2


title: Stat3f/fK5cre 14 day #1


title: K5cre 0 day #2


title: JGHL47


title: JGHL46


title: 24hr_k27ac_rep1


title: iPSC-RPE-1_CC-HS_ACA_RS7 [HM7FMBBXX_16496350_S46_L005]


title: JGHL44


title: 2hr_k27ac_rep2


title: iPSC-RPE-1_CC-HS_ACA_RS7 [HMLLWBBXX_16496350_S59_L007]


title: K5cre 0 day #1


title: 0.5hr_k27ac_rep2


title: iPSC-RPE-3_CC-HS_L-475_RS14 [HMLLWBBXX_16496349_S58_L007]


title: 0.5hr_k27ac_rep1


title: JGHL41


title: JGHL42


title: K5cre 7 day #1


title: iPSC-RPE-3_CC-HS_L-475_RS14 [HMLLWBBXX_16496349_S58_L006]


title: iPSC-RPE-3_CC-HS_L-475_RS14 [HMLLWBBXX_16496349_S58_L008]


title: iPSC-RPE-1_CC-HS_ACA_RS7 [HMLLWBBXX_16496350_S59_L008]


title: K5cre 14 day #1


title: Unt_k27ac_rep2


title: JGHL43


title: JGHL39