title: 4C-seq-SHH-viewpoint-WT-rep2

city: San Francisco

first: Nadav

last: Ahituv

state: CA

address: 1550 4th Street

institute: UCSF

data_processing:
library strategy: 4C-seq
ChIP-seq:
All chipseq samples (CTCF-WT, CTCF-Mut, RAD21-WT, RAD21-Mut) were processed according to ENCODE guidelines for transcription factor ChIP-seq analysis.
Raw reads were aligned against GRCh37(hg19) using bowtie2. Duplicate reads were marked using Picard’s MarkDuplicates and multimapping, low quality, duplicated and non-properly paired reads were removed. Library complexity measures and flagstats were generated for each BAM file.
BAM files were converted to tagAlign format and two subsampled pseudoreplicates were generated for each sample with half the total reads. Peak calling, fold change and p-value signal tracks were generated using MACS2.
Irreproducible Discovery Rate (IDR) analysis was performed using self-pseudoreplicates and the main samples to obtain self-consistent sets of peaks. Final peak calls were filtered by ENCODE blacklist (Amemiya et al., 2019) and an IDR of 2% and a signal value > 30.
4C-seq:
Raw reads were trimmed to 50 bp with cutadapt 2.4.
Valid 4Cseq reads containing 4C reading primer were extracted from fastq file and parsed into raw .txt file aligned against the restriction-enzyme digested genome GRCh37(hg19) using 4Cseqpipe version 0.7 (van de Werken et al. 2012).
Raw files were translated into final graphical depictions of contact profiles around viewpoints, using 4Cseqpipe version 0.7 (van de Werken et al. 2012).
Genome_build: hg19
Supplementary_files_format_and_content: png; bigwig

growth_protocol: Lymphoblastoid cells were maintained in RPMI1640 medium (Life Technologies, catalog no. 11875093) containing 15% fetal bovine serum (FBS) and penicillin-streptomycin.

extract_protocol:
ChIP-seq: Lymphoblastoid cells (1x10^7 cells) were ﬁxed in phosphate-buffered saline (PBS) with 0.96% formaldehyde for 8 minutes at room temperature. Crosslinking was quenched with 125 mM Glycine. The cells were washed with PBS and precipitated via centrifugation. The cell pellet was stored in -80°C until use.
ChIP-seq: Libraries were prepared using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences, catalog no. 21024) according to manufacturer’s protocol.
4C-seq: 4C-seq was performed and ibraries were prepared according to standard procedures (Krijger et al. Methods 170, 17–32 (2020))

tag: condition

value: Acheiropodia patient

value: Lymphoblast cells

tag: viewpoint

value: SHH promoter viewpoint


title: 4C-seq-SHH-viewpoint-WT-rep1

status: Public on Jul 30 2020

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type


title: RNAseq_Ad_lib_WT_ZT1_rep1

city: Houston

first: Dongyin

last: Guan

state: TX

address: 1 Baylor Plaza, ABBR

institute: Baylor College of Medicine

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the University of California, Santa Cruz (UCSC) mm9 genome browser using STAR. The tag directories were established and normalized read counts were measured with RefSeq genes using Homer.
Genome_build: mm9

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was extracted from liver tissue or isolated endothelial cells and kupffer cells using Trizol reagent followed by RNeasy Mini Kit (#74104).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: strain

tag: gender

value: male

tag: diet

value: normal chow

tag: genotype/variation

value: WT

tag: tissue

value: Liver


title: 5-1_mtN02-YB04-1

city: Ithaca

first: Andrew

last: Clark

state: NY

address: 215 Tower Road

institute: Cornell University

data_processing:
All Scripts Used For Processing + Analysis Can Be Found on github.com/mam737/mitoY_RNASEQ
FastQC v0.11.5 - evaluate quality of raw reads
Trimmomatic v0.36 - remove low qualtiy reads, crop first 10 bp, remove adapters, and drop reads shorter than 20 bp long
Star v2.6- align reads to reference genome
HTSeq-Count v0.11.0 - count reads
DESeq2 - Differential Expression Analsis
Genome_build: Drosophila melanogaster Genome Reference 6.18
Genome_build: ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.18_FB2017_05/
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: 10 pooled 3-5 day old whole fly males

growth_protocol: All flies during the crossing process were maintained in vials on standard sucrose-yeast medium in climate controlled growth chambers with a 12:12 hours light:dark cycle at 25℃

extract_protocol:
For each sample, 10 3-5 day old adult males were collected, pooled, and flash frozen on dry ice. RNA was harvested using a Trizol reagent. Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used.
RNA libraries were prepared for sequencing using standard Illumina protocols accompannying the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD

treatment_protocol: N/A - this experiment was only to look at differences between otherwise isogenic lines w/ unique mitochondrial-Y combinations

value: whole fly

tag: Sex

tag: mitochondrial haplogroup

value: Global Diversity Line N02

tag: y haplotype

value: Global Diversity Line B04

tag: bio replicate

value: A

tag: batch


title: RAD21-ChIP-seq-INPUT-WT-rep2

data_processing:
ChIP-seq:
All chipseq samples (CTCF-WT, CTCF-Mut, RAD21-WT, RAD21-Mut) were processed according to ENCODE guidelines for transcription factor ChIP-seq analysis.
Raw reads were aligned against GRCh37(hg19) using bowtie2. Duplicate reads were marked using Picard’s MarkDuplicates and multimapping, low quality, duplicated and non-properly paired reads were removed. Library complexity measures and flagstats were generated for each BAM file.
BAM files were converted to tagAlign format and two subsampled pseudoreplicates were generated for each sample with half the total reads. Peak calling, fold change and p-value signal tracks were generated using MACS2.
Irreproducible Discovery Rate (IDR) analysis was performed using self-pseudoreplicates and the main samples to obtain self-consistent sets of peaks. Final peak calls were filtered by ENCODE blacklist (Amemiya et al., 2019) and an IDR of 2% and a signal value > 30.
4C-seq:
Raw reads were trimmed to 50 bp with cutadapt 2.4.
Valid 4Cseq reads containing 4C reading primer were extracted from fastq file and parsed into raw .txt file aligned against the restriction-enzyme digested genome GRCh37(hg19) using 4Cseqpipe version 0.7 (van de Werken et al. 2012).
Raw files were translated into final graphical depictions of contact profiles around viewpoints, using 4Cseqpipe version 0.7 (van de Werken et al. 2012).
Genome_build: hg19
Supplementary_files_format_and_content: png; bigwig

value: Normal

tag: antibody

value: none (input)


title: RAD21-ChIP-seq-WT-rep2

value: RAD-21 (Abcam, catalog no. ab992)


title: WT_prog_6.5_HB_rep3

city: Stockholm

first: Johan

last: Ericson

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Instituet

description:
P1201_518
WT_Prog_6.5_Control-P1201_518

data_processing:
Clustered using cBot and sequenced on HiSeq2500 (HiSeq Control Software 2.2.38/RTA 1.18.61) with a 1x51 setup in RapidHighOutput mode. Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite
Reads were mapped with Tophat/2.0.4 to the Mouse genome assembly, build GRCm38 using default parameters settings.
Gene counts were generated using htseq/0.6.1 on bam files with duplicates included.
FPKMs for genes and transcripts were generated using cufflinks/2.1.1 on bamfiles with duplicates included.
Voom normalized logCPM values were obtained using voom function from R limma package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM, Counts and Voom normalized values for each sample

source_name: Prominin-1 sorted neural progenitors (6 days)

growth_protocol: Cells were grown in monolayer conditions.

extract_protocol:
ZymoPureTM kit
Illumina TruSeq; polyA-selection

treatment_protocol: RA and SAG applied 0-3 DDC (days in differentiation conditions)

value: wild type

tag: cell status

value: d6.5 ESC differentiation


title: WT_prog_6.5_HB_rep2

description:
P1201_517
WT_Prog_6.5_Control-P1201_517

value: Prominin-1 sorted neural progenitors (6 days)


title: 4-6_mtN01-YZW139-2

value: Global Diversity Line N01

value: Global Diversity Line ZW139

value: B


title: RAD21-ChIP-seq-INPUT-WT-rep1

value: Lymphoblast cells


title: 4C-seq-SHH-viewpoint-Mut-rep1

value: SHH promoter viewpoint


title: 4-6_mtN01-YZW139-1

value: male


title: 5-3_mtN02-YN03-2

value: Global Diversity Line N03


title: 4C-seq-SHH-viewpoint-Mut-rep2


title: 5-1_mtN02-YB04-2

value: whole fly


title: WT_prog_6.5_HB_rep1

description:
P1201_516
WT_Prog_6.5_Control-P1201_516


title: 4-5_mtN01-YZH23-1

value: Global Diversity Line ZH23


title: RAD21-ChIP-seq-WT-rep1


title: WT_prog_5.5_HB_rep3

description:
P1201_515
WT_Prog_5.5_Control-P1201_515

source_name: Prominin-1 sorted neural progenitors (5 days)

value: d5.5 ESC differentiation


title: 4-5_mtN01-YZH23-2


title: 4-4_mtN01-YN07-2

value: Global Diversity Line N07


title: spinal cord at E14_Nfix+/+_biological rep 3

type: RNA

city: Brisbane

first: Michael

last: Piper

state: QLD

address: Building 81, University of Queensland, St Lucia

department: School of Biomedical Science

country: Australia

institute: University of Queensland

description: Gene expression data from wild-type embryonic mouse spinal cords at E14.5

hyb_protocol: A GeneChip® Mouse Transcriptome Array (Affymetrix) was used according to the standard Affymetrix protocol.

scan_protocol: GeneTitan (Life Technologies) was used to scan the GeneChip®.

data_processing: Microarray data in the form of .CEL files were processed by running an SST-RMA (gene level) analysis on all samples using the Affymetrix Expression Console software (build 1.4.1.46) using default settings for background correction, normalization and summarization. The resulting .CHP files were then imported into the Affymetrix Transcription Analysis Console (TAC) software and sample files were compared in differential gene expression analyses between Nfix-/- and wild-type samples. Algorithm parameters selected included: genome version mm10, one-way between-subject ANOVA (unpaired) and ANOVA p-value (condition pair) <0.05.

label: biotin

source_name: Nfix+/+ mus musculus E14.5 spinal cord

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Heterozygous male and female mice were placed together overnight to produce time-mated litters. The presence of a vaginal plug the following day indicated a successful mating was likely, and this was designated E0.5. Polymerase chain reactions (PCR) confirmed the genotypes of each mouse.

extract_protocol: Total RNA was extracted using an Rneasy Micro kit (QIAGEN) according to manufacturer's instructions.

treatment_protocol: Embryos were extracted from the anaesthetised mother at E14.5 and whole spinal cords were dissected, then snap frozen using dry ice.

tag: genotype

value: Nfix+/+

value: spinal cord

tag: developmental stage


title: RAD21-ChIP-seq-INPUT-Mut-rep2

tag: condition

value: Acheiropodia patient

value: none (input)


title: spinal cord at E14_Nfix+/+_biological rep 4


title: spinal cord at E14_Nfix+/+_biological rep 2


title: spinal cord at E14_Nfix+/+_biological rep 1


title: WT_prog_5.5_HB_rep2

description:
P1201_514
WT_Prog_5.5_Control-P1201_514

value: wild type

value: Prominin-1 sorted neural progenitors (5 days)


title: spinal cord at E14_Nfix-/-_biological rep 4

description: Gene expression data from Nfix-/- embryonic mouse spinal cords at E14.5

source_name: Nfix-/- mus musculus E14.5 spinal cord

value: Nfix-/-


title: RAD21-ChIP-seq-Mut-rep1

value: RAD-21 (Abcam, catalog no. ab992)


title: WT_prog_4.5_HB_rep3

description:
P1201_509
WT_Prog_4.5_Control-P1201_509

source_name: Prominin-1 sorted neural progenitors (4 days)

value: d4.5 ESC differentiation


title: RAD21-ChIP-seq-INPUT-Mut-rep1

value: Lymphoblast cells


title: 4-3_mtN01-YN03-1

value: Global Diversity Line N01

value: A


title: 4-3_mtN01-YN03-2

value: male

value: Global Diversity Line N03

value: B


title: P1Pro- (replicate 3)

city: Mutilva Baja

first: Junkal

last: Garmendia

address: Pamplona, 123

country: Spain

institute: Instituto de Agrobiotecnologia, Consejop Superior de Investigaciones Científicas

description: Nicotiana benthamiana, nahG-expressing plants

data_processing:
Raw RNA-seq reads were filtered to remove poor quality reads and adapter contaminations with Trimmomatic.
The remaining reads were mapped to the N. benthamiana transcriptome (Transcriptome assembly v5, primary transcripts (Nakasugi et al., 2014)) using Bowtie2 with very-sensitive option activated.
Transcript read counts were obtained by RSEM software (Li and Dewey, 2011), and rRNA counts were discarded.
Genome_build: N. benthamiana transcriptome (Transcriptome assembly v5, primary transcripts (Nakasugi et al., 2014) http://benthgenome.qut.edu.au/,  http://sefapps02.qut.edu.au/downloads/Nbv5_transcriptome_primary.fa.gz)

organism: Nicotiana benthamiana

source_name: Virus-infected Nicotiana benthamiana leaves

growth_protocol: Plants of the wild-type Nicotiana benthamiana and N. benthamiana nahG transgenic line expressing a SA hydroxylase gene (Ying X.-B., et al. (2010); Plant Cell 22:1358–1372.) were grown in a greenhouse with a 16 h light/8 h dark photoperiod, in a 19 23°C temperature range.

extract_protocol:
For each experimental condition, three biological replicates (each sample was a pool of ≥ 2 infected plants) were used for transcriptomic analysis (RNA-seq). Plant tissue was ground in a mortar in liquid nitrogen and total RNA was extracted with the FavorPrep plant total RNA mini kit (Favorgen), including on-column DNAse I treatment. Following a second DNAse I digestion, samples were purified by organic extraction and sodium acetate precipitation. Ribosomal RNA molecules were depleted by the RiboMinus plant kit (Invitrogen). Recovered RNA was quantified using a fluorescent RNA-binding dye (QuantiFluor RNA system, Promega), and analyzed in a Bioanalyzer with the RNA 6000 pico kit (Agilent).
Libraries were prepared using the TruSeq stranded mRNA kit (Illumina), omitting the mRNA enrichment step, and were sequenced (2 x 100-nt paired-end reads) in an Illumina HiSeq 2000 at the Centro Nacional de Análisis Genómico (CNAG-CRG, Spain).

treatment_protocol: Plants were inoculated with plum pox virus (PPV) or the P1Pro clone, a PPV deletion mutant that lacks the self-cleavage inhibitory domain of the P1 leader protease (Pasin F., et al. (2014); PLOS Pathog. 10:e1003985). Viral clones were delivered by Agrobacterium-mediated infection, and upper uninoculated leaves were collected after 14 days.

tag: virus

value: P1Pro - Plants inoculated with pSN-PPV P1Pro[V164], a pSN-PPV-based clone with the truncated P1 lacking residues 2-163

value: Upper uninoculated leaves

value: 14 days post-agroinoculation


title: WT_prog_4.5_HB_rep1

description:
P1201_507
WT_Prog_4.5_Control-P1201_507

tag: cell type

value: Prominin-1 sorted neural progenitors (4 days)


title: WT_prog_4.5_HB_rep2

description:
P1201_508
WT_Prog_4.5_Control-P1201_508

tag: strain


title: P1Pro- (replicate 2)


title: P1Pro- (replicate 1)


title: CTCF-ChIP-seq-INPUT-WT-rep2

source_name: CTCF-ChIP-seq-INPUT-WT

value: Normal


title: P1Pro+ (replicate 3)

description: Nicotiana benthamiana, wild-type plants


title: CTCF-ChIP-seq-WT-rep2

source_name: CTCF-ChIP-seq-WT

value: CTCF (Active Motif, catalog no. 61311)


title: WT_prog_5.5_HB_rep1

description:
P1201_513
WT_Prog_5.5_Control-P1201_513

value: wild type

value: d5.5 ESC differentiation


title: 4-4_mtN01-YN07-1

value: whole fly

value: Global Diversity Line N07


title: 4-2_mtN01-YB11-1

value: Global Diversity Line B11


title: 4-2_mtN01-YB11-2


title: spinal cord at E14_Nfix-/-_biological rep 3

value: Nfix-/-

value: spinal cord


title: CTCF-ChIP-seq-INPUT-WT-rep1

value: Lymphoblast cells

value: none (input)


title: spinal cord at E14_Nfix-/-_biological rep 2


title: P1Pro+ (replicate 2)

description: Nicotiana benthamiana, wild-type plants


title: CTCF-ChIP-seq-WT-rep1


title: spinal cord at E14_Nfix-/-_biological rep 1


title: 10698X16: TLT

city: Salt Lake City

first: Philip

middle: J

last: Moos

state: UT

department: Pharmacology & Toxicology

institute: University of Utah

data_processing:
RNA sequencing reads for the treated and control samples were aligned using MapSplice v12_07, quantified using RSEM, and gene counts were normalized using upper quantile normalization. This was the same methodology used to normalize the PANCAN12 TCGA dataset, which we obtained from TCGA fully processed for use in this analysis. To generate a TLT sensitivity signature, we used the DESeq2 package (version 1.4.5) in the Bioconductor framework (version 2.14.0, version 3.1.0 of R) to identify genes that were significantly deregulated (adjusted p < 0.05) between the treated and control samples. One hundred forty-six genes were found to be significantly deregulated, out of which only 131 were found in the TCGA dataset. To use DEseq2, the reads had to be re-mapped using the Rsubread Bioconductor package. We used this package to map the reads to version hg19 of the human genome and to summarize the data to gene-level values. We predicted TLT sensitivity for the PANCAN12 TCGA dataset using the Bayesian binary regression algorithm version 2.0 (BinReg2.0) used as a MATLAB plug-in.
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands) with on-column digestion of the genomic DNA, as described in the manufacturer’s protocol. RNA sequencing was performed at the Huntsman Cancer Institute High Throughput Genomics Core Facility using 50-cycle, single-read sequencing (version 3) on an Illumina HiSeq instrument. To construct mRNA focused libraries from total RNA, the Illumina TruSeq RNA Sample Prep Kit (version 2) with oligo dT selection was used.
Genome_build: hg19
Supplementary_files_format_and_content: excel with tabs for the normalized data

source_name: topsentinol L trisulfate

growth_protocol: Cells were cultured at 37 °C in 5% CO2 in DMEM or RPMI with 10% fetal bovine serum (FBS) in T75 flasks up to 90% confluency.

extract_protocol:
Total RNA was extracted and purified following 6 h of incubation with TLT or DMSO using the Qiagen RNeasy minikit protocol. The samples were kept at −80 °C until further use. RNA was quantified by Nanodrop spectrophotometer ND-1000 and the RNA samples were assessed for quality using an Agilent 2200 TapeStation prior to expression analysis. All RNA samples had RNA Integrity Numbers (RIN) ranging from 8 to 10.
Libraries were prepared using Illumina TruSeq RNA Library Prep Kits.  HiSeq2000 50 Cycle Single Read Sequencing was performed with a maximum of 8 multiplexed samples per lane to ensure sufficient depth of sequencing.

treatment_protocol: For the treatment, cells were seeded onto 6-well plates and allowed to grow overnight. Cells were treated with the EC75 dose of TLT or DMSO as the vehicle control in the presence of 5% fetal bovine serum. The cells were then incubated for 6 h, after which the media was aspirated and the cells were lysed with RLT buffer to begin the RNA extraction protocol.

tag: cell line

tag: passages

tag: treatment

value: TLT


title: 10698X15: TLT


title: 10698X14: TLT


title: 4-1_mtN01-YB04-1

tag: tissue

value: male

value: Global Diversity Line N01

value: Global Diversity Line B04

value: A


title: CTCF-ChIP-seq-Mut-rep2

source_name: CTCF-ChIP-seq-Mut

value: Acheiropodia patient


title: CTCF-ChIP-seq-INPUT-Mut-rep2

source_name: CTCF-ChIP-seq-INPUT-Mut


title: 10698X13: TLT


title: 3-6_mtI02-YZW139-2

tag: Sex

value: Global Diversity Line I02

value: Global Diversity Line ZW139

value: B


title: PPV+ (replicate 3)

description: Nicotiana benthamiana, wild-type plants

value: PPV - Plants inoculated with pSN-PPV, an infectious clone of a GFP-tagged plum pox virus (PPV) isolate adapted to Nicotiana spp.

value: Upper uninoculated leaves

value: 14 days post-agroinoculation


title: PPV+ (replicate 2)

description: Nicotiana benthamiana, wild-type plants


title: CTCF-ChIP-seq-INPUT-Mut-rep1


title: 3-6_mtI02-YZW139-1

value: whole fly

tag: mitochondrial haplogroup


title: 10698X11: DMSO

source_name: Vehicle control

value: DMSO


title: PPV+ (replicate 1)

description: Nicotiana benthamiana, wild-type plants


title: 10698X12: DMSO


title: 3-5_mtI02-YZH23-2

tag: y haplotype

value: Global Diversity Line ZH23


title: CTCF-ChIP-seq-Mut-rep1

value: Lymphoblast cells

value: CTCF (Active Motif, catalog no. 61311)


title: 4-1_mtN01-YB04-2

tag: bio replicate


title: 10698X10: DMSO


title: 3-5_mtI02-YZH23-1

tag: batch


title: P1Pro+ (replicate 1)

description: Nicotiana benthamiana, wild-type plants

value: P1Pro - Plants inoculated with pSN-PPV P1Pro[V164], a pSN-PPV-based clone with the truncated P1 lacking residues 2-163


title: CR96_2

city: Charlottesville

first: Jeffrey

last: Smith

state: Virginia

address: 1340 JPA  PO Box 800733 Charlottesville, VA 22908 Telephone:

department: Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
Barcoded cDNA was sequenced on an Illumina Nextseq 500. Individual lanes were pooled together for unique samples.
Reads were then mapped to the sacCer3 genome using bowtie2 with default options.
Bam files were then converted into transcript (gene) counts using bedtools.
The counts matrix was annotated with sample names and further analyzed in edgeR (DESeq2, ggplot) and metaboanalyst online program to produce the figures in the paper.
To generate Volcano plots, ggplot was used and only genes <.05 FDR utilized.
Genome_build: sacCer3
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

organism: Saccharomyces cerevisiae

growth_protocol: All cells were grown in Synthetic Complete (SC) medium with 2% glucose (NR) added at the time of inoculation

extract_protocol:
Cell pellets were obtained, frozen in -80 and RNA was harvested using Trizol reagent. 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using standard NEBNext Ultra library RNA library kit for Illumina protocols.

treatment_protocol: CR conditioned medium or NR conditioned medium (filtered and concentrated x10) or water was supplemented to NR (2%) cultures

tag: collection time point

value: 96 hours

value: added CRCM 2% at inoculation


title: 10698X9: DMSO


title: H115 TLS

city: TROMSØ

first: Kristin

middle: Andreassen

last: Fenton

state: Troms

address: MH Building

department: Medical Biology

country: Norway

institute: UiT Norges arktiske universitet

description:
Proteinuric
deseq_out_counts.tab

data_processing:
Illumina: Alignments and assignment of reads to genes. Eurofins Genomics performed alignments and assignment of reads to genes. The alignment of reads to a reference sequence was performed using the BWA-backtrack v0.6.2-r126, http:// bio-bwa.sourceforge.net/(Date of last excess 18.06.2019) . Raw read counts were created using HTSeq with python. Reads with unique mapping positions were considered for read counting. Paired-end reads that were mapped to the same reference with about the expected insert size were counted as one read. Paired-end reads that were mapped to different references or with an unexpected insert size were counted as two reads. If only one read of a pair was mapped, it was counted as one read. Only reads overlapping exon-features were counted. All reads mapping to features with the same identifier were summed. The gene-attribute was used as feature identifier. Reads mapping to multiple features with different identifier was ignored for read counting. The mean read length was 100.0 (Eurofins genomics).
Illumina: Filtering and normalization for composition bias. The CPM function from the edgeR library was used to generate the counts per million (cpm) values, the CPM values were further filtered. The ratio of RNA production was estimated by using a weighted trimmed mean of log expression ratios, trimmed mean of M values (TMM). The calcNormFactors function from edgeR package calculated the normalization factors between libraries. These normalization factors are re- scaled by the mean of the normalized library sizes. Normalized read counts were obtained by dividing raw read counts by these re-scaled normalization factors. This was performed to eliminate composition biases between libraries 27. Multidimensional scaling plot (MDS) was generated with the plotMDS function from limma package. Distances between samples was calculated with leading fold change defined as the root-mean-square of the largest 500 log2-fold changes between samples.
Illumina: Differential expression analysis. Differential expression analysis was performed using the edgeR package 28. Differential expression data was filtered to contain FDR<0.05. An empirical Bayes procedure was used to shrink the dispersions towards a consensus value, borrowing information between genes. The results were tested for DE using the GLM likelihood ratio test. The likelihood ratio test was performed by estimating two groups and by comparing the fit of one group to the fit of the other. To deal with multiple tests, individual tests with separate computations were made to test for different contrasts.  Three different contrasts were made to test the hypothesis that the different coefficients in each contrast, i.e the three different groups, were equal. The glmLRT function from edgeR was used to conduct likelihood ratio tests for the coefficients in the linear model, like Fishers exact test, and adapted for over dispersed data
Ion Torrent: All sequences were imported and analyzed in CLC Genomics Workbench 8 (CLCbio, Aarhus Denmark). Adaptor sequences were trimmed and we conducted RNA-Seq tool using Mus_musculus GRCm 38.80 as a reference genome by default
Ion Torrent: Filtering and normalization for composition bias. The CPM function from the edgeR library was used to generate the counts per million (cpm) values, the CPM values were further filtered. The ratio of RNA production was estimated by using a weighted trimmed mean of log expression ratios, trimmed mean of M values (TMM). The calcNormFactors function from edgeR package calculated the normalization factors between libraries. These normalization factors are re- scaled by the mean of the normalized library sizes. Normalized read counts were obtained by dividing raw read counts by these re-scaled normalization factors. This was performed to eliminate composition biases between libraries 27. Multidimensional scaling plot (MDS) was generated with the plotMDS function from limma package. Distances between samples was calculated with leading fold change defined as the root-mean-square of the largest 500 log2-fold changes between samples.
Ion Torrent: Differential expression analysis. Differential expression analysis was performed using the edgeR package 28. Differential expression data was filtered to contain FDR<0.05. An empirical Bayes procedure was used to shrink the dispersions towards a consensus value, borrowing information between genes. The results were tested for DE using the GLM likelihood ratio test. The likelihood ratio test was performed by estimating two groups and by comparing the fit of one group to the fit of the other. To deal with multiple tests, individual tests with separate computations were made to test for different contrasts.  Three different contrasts were made to test the hypothesis that the different coefficients in each contrast, i.e the three different groups, were equal. The glmLRT function from edgeR was used to conduct likelihood ratio tests for the coefficients in the linear model, like Fishers exact test, and adapted for over dispersed data
Genome_build: mm9
Supplementary_files_format_and_content: GEN141016_F Profiling table.xlsx
Supplementary_files_format_and_content: Differential expressed TLS_kidney_LN genes.xlsx

source_name: TLS

extract_protocol:
Illumina: Total RNA samples were prepared for sequencing using the Qiagen Allprep total RNA kit (Qiagen). Briefly, tissue sections (20-30µg) taken from the middle of the kidneys were lyzed and homogenized in 600 µl Buffer RLT in 2 mL Magna Lyser green beads tubes (Roche Life sciences, Norway) at 600 rpm for 30 sec using the Precellys 24 tissue homogenizer (Bertin Thechnologies, France). The lysates were centrifuged at full speed for 3 min, the supernatant was carefully transferred to the AllPrep spin column, and RNA isolation was performed according to the manufacturer’s protocol. The Isolated RNA were analyzed by Agilent. Only RNA samples of high quality (RNA Integrity number (RIN) ≥8.0) were used.
Ion Torrent: Total RNA of lymph nodes of four and eight weeks, proteinuric mice, immune aggregates, dissected manually under the loupe (magnification:1:10) of protein uric kidney and kidney tissue from the same kidney purified by TRIzol regent (Ambion, Thermo Fisher, Oslo, Norway) according to manufacturer’s instructions. Total RNA of lymph nodes from anti-dsDNA antibody positive mice were isolated using miRNeasy mini kit (Qiagen, Oslo, Norway). The concentration and quality of extracted total RNA were assessed using the AgilentR RNA 6000 nano kit with the AgilentR 2100 BioanalyzerR instrument (Agilent, Matriks AS, Norway). All RNA used in this study had RNA integrity value (RIN value) ≥ 7.
Illumina: RNA libraries were prepared for sequencing using standard Illumina protocols
Ion Torrent: Polyadenylated (poly(A)) mRNA was isolated from total RNA using Dynabeads mRNA Direct Micro Kit (Ambion, Thermo Fisher) followed by its fragmentation using RNase III with an average sizes of 100-200 nt. The fragmented mRNA was cleaned up and determined the yield and size distribution using the AgilentR RNA 6000 Pico kit with the AgilentR 2100 BioanalyzerR instrument. After adapter ligation at both ends of fragmented mRNA, performed reverse transcription, followed by PCR amplification.  After purification of amplified cDNA analyzed to assess the yield and size distribution using AgilentR High Sensitivity DNS kit with AgilentR 2100 BioanalyzerR instrument.

value: TLS

tag: age

value: 25 weeks old


title: CR24_2

value: 24 hours


title: RNASeq_siFem1b/Keap1 #3 technical replicate

city: Berkeley

last: Rape

address: 1951 Oxford St Li Ka Shing Center, 330A

institute: University of California, Berkeley

description: Libraries were sequenced twice to yield a technical replicate. These files are denoted with a "b"

data_processing:
For RNAseq samples, reads were aligned to transcripts with kallisto (0.44.0) under the following parameters (kallisto quant -i mm10.idx -o filename R1.fastq.gz R2.fastq.gz -b 200). Processed RNAseq data include tab-delimited text files of TPM values and normalized est_count values.
Genome_build: mm10
Supplementary_files_format_and_content: TSV (tab separate values) are presetend. Values contained contain transcript names (Ensembl identifiers), transcirpt lengths, estimated transcript counts, and TPMs

growth_protocol: C2C12s were grown subconfluenly in DMEM+10%FBS

extract_protocol:
Total RNA was extracted from sub-confluent C2C12s treated with siFem1b, siKeap1, siFem1bsiKeap1,  or siCNTRL siRNAs (in triplicate) using a NucleoSpin Plus RNA extraction kit (Machery-  Nagel)
Total RNA was polyA selected, end-repaired, adaptor ligated, and PCR amplified with desired indeces

treatment_protocol: C2C12s were treated with indicated siRNAs for 48 hrs before harvesting and RNA extraction

value: undifferentiated myoblast

tag: sirna


title: 3-4_mtI02-YN07-2

value: male

value: Global Diversity Line I02

value: Global Diversity Line N07


title: H6 TLS

description:
Proteinuric
deseq_out_counts.tab

value: 39 weeks old


title: H20 TLS

description:
Proteinuric
deseq_out_counts.tab

value: 36 weeks old


title: RNASeq_siFem1b/Keap1 #2 technical replicate


title: RNAseq_Ad_lib_WT_ZT22_rep1

tag: gender

tag: diet

value: normal chow

tag: genotype/variation

value: WT

value: Liver


title: 10698X7: TLT

value: TLT


title: 10698X8: TLT


title: RNASeq_siFem1b #3 technical replicate

tag: cell type


title: H20 K

description:
Proteinuric
deseq_out_counts.tab

source_name: Kidney

tag: strain

value: Kidney


title: 10698X6: TLT

tag: cell line


title: RNASeq_siFem1b #2 technical replicate


title: H117 K

description:
Proteinuric
deseq_out_counts.tab

value: 32 weeks old


title: 3-4_mtI02-YN07-1

value: whole fly

value: A


title: 3-3_mtI02-YN03-1

value: Global Diversity Line N03


title: 3-3_mtI02-YN03-2

value: B


title: H115 K

description:
Proteinuric
deseq_out_counts.tab

value: 25 weeks old


title: 10698X5: TLT

tag: passages


title: 3-2_mtI02-YB11-2

value: Global Diversity Line B11


title: RNASeq_siFem1b #1 technical replicate

value: undifferentiated myoblast


title: 10698X4: DMSO

tag: treatment

value: DMSO


title: H6 K

description:
Proteinuric
deseq_out_counts.tab

tag: tissue


title: 3-2_mtI02-YB11-1

tag: Sex

value: male

value: Global Diversity Line I02


title: H20 LN

description:
Proteinuric
deseq_out_counts.tab

source_name: Lymph node

value: Lymph node

value: 36 weeks old


title: RNASeq_siKeap1 #3 technical replicate


title: 10698X3: DMSO


title: RNASeq_siKeap1 #2 technical replicate


title: 10698X2: DMSO


title: H117 LN

description:
Proteinuric
deseq_out_counts.tab


title: 3-1_mtI02-YB04-2

tag: mitochondrial haplogroup

value: Global Diversity Line B04


title: H6 LN

description:
Proteinuric
deseq_out_counts.tab

value: 39 weeks old


title: RNASeq_siFem1b/Keap1 #1 technical replicate


title: RNASeq_siKeap1 #1 technical replicate


title: L25

description:
Ab positive <5 weeks
deseq_out_counts.tab

value: 18 weeks old


title: 10698X1: DMSO


title: RNASeq_siCont #3 technical replicate

value: siCont


title: 2-6_mtB39-YZW139-2

value: Global Diversity Line B39

tag: y haplotype

value: Global Diversity Line ZW139


title: RNASeq_siCont #2 technical replicate


title: RNASeq_siCont #1 technical replicate


title: 2-6_mtB39-YZW139-1

value: whole fly

tag: bio replicate

value: A


title: 2-5_mtB39-YZH23-2

value: Global Diversity Line ZH23

value: B

tag: batch


title: D10

value: 28 weeks old


title: RNASeq_siFem1b/Keap1 #3

value: undifferentiated myoblast


title: 2-5_mtB39-YZH23-1


title: C45

description:
Young
deseq_out_counts.tab

value: 4 weeks old


title: 2-4_mtB39-YN07-2

value: male

value: Global Diversity Line N07


title: RNASeq_siFem1b/Keap1 #2


title: 3-1_mtI02-YB04-1

value: Global Diversity Line I02


title: 2-4_mtB39-YN07-1


title: D11

value: Lymph node

value: 29 weeks old


title: 2-3_mtB39-YN03-2

value: Global Diversity Line N03


title: RNASeq_siFem1b #3


title: RNASeq_siFem1b #2


title: 2-3_mtB39-YN03-1


title: RNASeq_siFem1b/Keap1 #1


title: 2-2_mtB39-YB11-2

value: Global Diversity Line B11


title: RNASeq_siFem1b #1


title: 2-2_mtB39-YB11-1


title: RNASeq_siKeap1 #3


title: 2-1_mtB39-YB04-2

value: Global Diversity Line B04


title: Healthy control monocytes-1

city: Seoul

first: Hee Young

last: Kim

address: 103 Daehak-ro, Jongno-gu,

department: Department of Microbiology and Immunology

country: South Korea

institute: Seoul National University College of Medicine

description: Gene expression data from monocytes of healthy donor

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16 hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

source_name: human monocyte derived from healthy control

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Periperal blood mononuclear cells were isolated by density gradient centrifugation using Bicoll separating solution. monocytes were separated using CD14 magnetic beads.

extract_protocol: Total RNA of all samples was prepared using RNA purification kit (Qiagen) and checked for integrity and purity by OD 260/280 ratio, and on the Agilent 2100 Bioanalyzer

treatment_protocol: The monocytes of three ESRD patients and three HCs were separated using CD14 magnetic beads.

tag: disease state

value: Healthy control

value: human monocytes


title: RNASeq_siKeap1 #2


title: Healthy control monocytes-2


title: Healthy control monocytes-3


title: ESRD patient monocytes-2

description: Gene expression data from monocytes of ESRD patient

source_name: human monocyte derived from ESRD patient

value: End-stage renal disease (ESRD)


title: RNASeq_siKeap1 #1


title: RNASeq_siCont #3

value: siCont


title: ESRD patient monocytes-3


title: ESRD patient monocytes-1


title: 1-6_mtB38-YZW139-1

source_name: 10 pooled 3-5 day old whole fly males

value: whole fly

value: Global Diversity Line B38

value: Global Diversity Line ZW139

value: A


title: SPMS-OPC_differentiated from SPMS- iPSC-03-c1_biological rep3.1

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

institute: GENyO

description:
SPMS-OPC_expr_3.1
Passage 2-4 of early OPC

hyb_protocol: Illumina samples hybridization was performed following Whole-Genome Gene Expression Direct Hybridization Assay Guide, Illumina (BD-901-1002 Part # 11322355 Rev. A) protocol.

scan_protocol: Illumina BeadChips were scanned with an Illumina iScan software.

data_processing: For Illumina samples, raw data was obtained with Illumina GenomeStudio software. To generate the processed expression matrix, limma package (Ritchie et al., 2015) was used to correct the background with the NormExp method (McGee and Chen, 2016) and to apply quantile normalization.

source_name: SPMS-iPS-03 differentiated to early OPC-cell line 1

label_protocol: Illumina samples were labeled following Illumina Total PrepTMRNA Amplification Kit protocol, Ambion by Life Technologies protocol.

growth_protocol: All cultures were maintained at 37°C in a humidified atmosphere containing 5% CO2 with appropriate cell culture media.

extract_protocol: RNA was isolated using RNeasy kit (Qiagen) according to manufacturer´s protocol.

treatment_protocol: 100 ng of total RNA was hybridized to 2.5 ug of labelled ss-DNA.

tag: diagnosis

value: SPMS

value: female

value: early OPC-like cells differentiated from iPS cell lines


title: RNASeq_siCont #2

value: undifferentiated myoblast

tag: sirna


title: SPMS-OPC_differentiated from SPMS- iPSC-04_biological rep4

description:
SPMS-OPC_expr_4
Passage 2-4 of early OPC

source_name: SPMS-iPS-04 differentiated to early OPC

tag: gender


title: 1-5_mtB38-YZH23-2

value: male

value: Global Diversity Line ZH23

value: B


title: PCS-treated human monocytes-3

description: Gene expression data from PCS-treated group of human monocytes

growth_protocol: Mononuclear cells were isolated from peripheral blood by density gradient centrifugation using Bicoll separating solution. And then monocytes were separated through a negative selection using pan-monocyte microbeads,

treatment_protocol: The separated monocytes were treated with IS 1000 μM and PCS 500 μM for 24 hours.

value: healthy control

value: p-cresyl sulfate (PCS)


title: SPMS-OPC_differentiated from SPMS- iPSC-03-c2_biological rep3.3

description:
SPMS-OPC_expr_3.2
Passage 2-4 of early OPC

source_name: SPMS-iPS-03 differentiated to early OPC-cell line 2


title: IS-treated human monocytes-3

description: Gene expression data from IS-treated group of human monocytes

value: indoxyl sulfate (IS)


title: SPMS-OPC_differentiated from SPMS- iPSC-02_biological rep2

description:
SPMS-OPC_expr_2
Passage 2-4 of early OPC

source_name: SPMS-iPS-02 differentiated to early OPC


title: 1-5_mtB38-YZH23-1


title: CT-OPC_differentiated from CT-iPSC-03_biological rep3

description:
CT-OPC_expr_3
Passage 2-4 of early OPC

source_name: CT-iPS-03 differentiated to early OPC

value: healthy


title: PCS-treated human monocytes-2

value: human monocytes


title: SPMS-OPC_differentiated from SPMS- iPSC-01-c1_biological rep1.1

description:
SPMS-OPC_expr_1.1
Passage 2-4 of early OPC

source_name: SPMS-iPS-01 differentiated to early OPC-cell line 1


title: PCS-treated human monocytes-1


title: sup_plus_3

city: Ann Arbor

first: Yingjie

last: Bian

state: MI

address: 109 Zina Pitcher Pl

department: Surgery

institute: University of Michigan

description:
Sample_119008
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt

data_processing:
Sequencing was performed by the UM DNA Sequencing Core, using the Illumina Hi-Seq 4000 platform, single end, 50 cycles, stranded mRNA prep.
We checked the quality of the raw reads data for each sample using FastQC (version 0.11.3) to identify features of the data that may indicate quality problems (e.g. low quality scores, over-represented sequences, inappropriate GC content).
We used the Tuxedo Suite software package for alignment, differential expression analysis, and post-analysis diagnostics. Briefly, we aligned reads to the reference mRNA transcriptome (mm10) using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.). We used default parameter settings for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments.
We used FastQC for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
We used Cufflinks/CuffDiff (version 2.2.1) for expression quantitation, normalization, and differential expression analysis, using mm10.fa as the reference genome sequence. For this analysis, we used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile–norm” for normalization of expression values. We generated diagnostic plots using the CummeRbund R package.
Genome_build: mRNA transcriptome (mm10/GRCm38)
Supplementary_files_format_and_content: depth_normalized_counts.txt
Supplementary_files_format_and_content: phenotype_repFpkms.txt

source_name: CD8+ T cells

growth_protocol: CD8+ T cells were first activated with anti-CD3/CD28 for 2 days, and then cultured with media for 36h.

extract_protocol: RNA was isolated from these cells using Direct-zolTM RNA miniprep Plus kit (ZOMO research, Irvine, CA, USA).

treatment_protocol: CD8+ T cells were cultured with fresh medium without methionine (fresh-), fresh medium with methionine (fresh+), B16F10 supernatants (Sup-), and B16F10 supernatants with methionine supplementation (Sup+) for 36h.

value: CD8+ T cells

tag: medium

value: B16F10 supernatants + methionine


title: IS-treated human monocytes-2


title: IS-treated human monocytes-1


title: CT-OPC_differentiated from CT- iPSC-01-c2_biological rep1.2

description:
CT-OPC_expr_1.2
Passage 2-4 of early OPC

source_name: CT-iPS-01 differentiated to early OPC-cell line 2


title: CT-OPC_differentiated from CT-iPSC-02_biological rep2

description:
CT-OPC_expr_2
Passage 2-4 of early OPC

source_name: CT-iPS-02 differentiated to early OPC


title: 1-6_mtB38-YZW139-2

value: whole fly

value: Global Diversity Line B38


title: SPMS-OPC_differentiated from SPMS- iPSC-01-c2_biological rep1.2

description:
SPMS-OPC_expr_1.2
Passage 2-4 of early OPC

source_name: SPMS-iPS-01 differentiated to early OPC-cell line 2


title: control group of human monocytes-1

description: Gene expression data from control group of human monocytes

value: control


title: sup_plus_2

description:
Sample_119007
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt


title: 1-4_mtB38-YN07-2

value: Global Diversity Line N07


title: RNASeq_siCont #1

value: siCont


title: M13

description:
Proteinuric
GEN141016_F Profiling table.xlsx

value: Kidney

tag: age

value: 36 weeks old


title: sup_plus_1

description:
Sample_119006
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt

tag: cell type


title: M14

tag: strain

value: 28 weeks old


title: M15

value: 37 weeks old


title: GVK7.BC6

city: Frederick

first: Scott

last: Durum

state: MD

address: Building 560, Room 31-71

department: CCR

institute: National Cancer Institute

data_processing:
library strategy: Linear Amplification-Mediated High-throughput genome-wide translocation sequencing (LAM-HTGTS)
Align with HiSAT (hihsat2, Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 2015) giving suggested breakpoints of individual samples.
Select the breakpoints with a deletion around 90,000 bp (which indicates the switch recombination process).
The breakpoints were further evaluated using UCSC BLAT program (Genome Research 12(4):656-64 · May 2002).
Genome_build: mm10
Supplementary_files_format_and_content: text containing potential breakpoints

source_name: KO7 B Cells with LPS+IL4

growth_protocol: CTRL (Hells+/-) and KO (Hells-/-) B cells derived from spleen were grown in RPIM1640 (GIBCO) supplemented with 10% Fetal Bovine Serum (FBS, Omega Scientific), 1x GlutaMAXTM (Gibco), 1x Non Essential Amino Acids and 50 U/ml Pen/Strep (Gibco). Each sample represents purified B cells derived from an individual mouse, except sample GVK2.Oct that represents.  pooled lymphocytes from seven KO animals.  "Hells" is official genome symbol for "Lsh" (Lymphoid-specific helicase).

extract_protocol:
genomic DNA were extracted according to Frederick Alt's lab protocol (Panchakshari RA, et al., Proc Natl Acad Sci U S A. ( 2018)23;115(4):762-767)
Linear amplification-mediated high-throughput genome-wide sequencing (LAM-HTGTS) libraries were generated as described by Frederick Alt's lab protocol (Panchakshari RA, et al., Proc Natl Acad Sci U S A. ( 2018)23;115(4):762-767). Sequencing runs were performed on an Illumina Miseq with 300-base-pair (bp) paired mode using miseq-500V2 kit
Linear Amplification-Mediated High-throughput genome-wide translocation sequencing (LAM-HTGTS)

treatment_protocol: B cells were stimulated with LPS(25µg/ml)+IL4(10ng/ml) for 72 hrs.

value: Lsh-/-

value: spleen

value: murine B lymphocyte

tag: marker


title: GVK2.Oct

source_name: KO pooled B Cell with LPS+IL4


title: GVC5.BC5

source_name: Ctrl5 B Cells with LPS+IL4

value: Lsh+/-


title: sup_plus_0

description:
Sample_119005
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt


title: M12

source_name: Kidney


title: 1-3_mtB38-YN03-2

value: male

value: Global Diversity Line N03

value: B


title: control group of human monocytes-2

source_name: human monocyte derived from healthy control

value: healthy control

value: human monocytes


title: 1-3_mtB38-YN03-1

value: whole fly

value: Global Diversity Line B38

value: A


title: M10

description:
Ab positive <5 weeks
GEN141016_F Profiling table.xlsx

value: 26 weeks old


title: control group of human monocytes-3

value: control


title: M11

value: Kidney

value: 39 weeks old


title: M9

value: 29 weeks old


title: CT-OPC_differentiated from CT- iPSC-01-c1_biological rep1.1

description:
CT-OPC_expr_1.1
Passage 2-4 of early OPC

source_name: CT-iPS-01 differentiated to early OPC-cell line 1

value: healthy

value: female

value: early OPC-like cells differentiated from iPS cell lines


title: sup_minus_3

description:
Sample_119004
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt

value: CD8+ T cells

value: B16F10 supernatants


title: 1-2_mtB38-YB11-1

source_name: 10 pooled 3-5 day old whole fly males

value: male

value: Global Diversity Line B11


title: GVC3.BC16

source_name: Ctrl3 B Cells with LPS+IL4

value: Lsh+/-

value: spleen

value: murine B lymphocyte


title: GVC4.BC17

source_name: Ctrl4 B Cells with LPS+IL4


title: 1-4_mtB38-YN07-1

value: whole fly

value: Global Diversity Line B38

value: Global Diversity Line N07


title: sup_minus_1

description:
Sample_119002
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt


title: GVK5.BC15

source_name: KO5 B Cells with LPS+IL4

value: Lsh-/-


title: 1-1_mtB38-YB04-2

value: Global Diversity Line B04

value: B


title: sup_minus_0

description:
Sample_119001
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt


title: sup_minus_2

description:
Sample_119003
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt


title: M8

value: Kidney

value: 28 weeks old


title: GVK4.BC12

source_name: KO4 B Cells with LPS+IL4


title: 1-1_mtB38-YB04-1

value: A


title: GVK3.BC11

source_name: KO3 B Cells with LPS+IL4


title: M7


title: M6

value: 29 weeks old


title: 1-2_mtB38-YB11-2


title: GVK6.BC18

source_name: KO6 B Cells with LPS+IL4


title: fresh_plus_3

description:
Sample_119000
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt

source_name: CD8+ T cells

value: CD8+ T cells

value: fresh + methionine


title: M5

description:
Young
GEN141016_F Profiling table.xlsx

value: 5 weeks old


title: g_BLTus_Cb_pBAD_plt_rep1

city: Moscow

first: Anton

last: Kuzmenko

email: dr.ant.kuz@gmail.com, antonk@img.ras.ru

address: Akademika Kurchatova square 2

country: Russia

institute: Institute of Molecular Genetics, Russian Academy of Sciences

description: Reference genome: NC_012971.2

data_processing:
All libraries were quality checked before further processing using FastQC (v. 0.11.8).
The adaptor sequence (5’-AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3’) was trimmed using cutadapt (v. 2.7). Example usage: cutadapt -j 4 -a 'TGGAATTCTCGGGTGCCAAGGC' path_to_fastq
Reads were aligned onto the reference genome allowing zero mismatches via bowtie (v. 1.2.3). Example usage: bowtie -p 4 -v 0 -m 1 -S --un path_to_the_file_with_unalligned_reads --max path_to_the_file_with_multimappers path_to_the_reference_fasta path_to_the_file_trimmed_fastq > file_name.bam
Alligned .sam files were converted to binary .bam, sorted and indexed using samtools (v. 1.9).
Genome coverage in the 1 Kb windows (RPKM) for uniquely mapped reads (total or strand-specific) were calculated using bedtools (v. 2.28.0). Example usage: bedtools coverage -counts -a path_to_the_bed -b path_to_the_sorted_bam > file_name.bedGraph
Supplementary_files_format_and_content: bedGraph files including count data for the 1kb genomic windows
Genome_build: NC_012971.2

organism: Escherichia coli

source_name: Bacterial Cell Lysates

growth_protocol: Cells were grown in LB media supplemented with 0.2% glucose, ampicillin and 0.01% L-arabinose, and aerated at 30˚C until OD 600 = 6.0.

extract_protocol:
Genomic DNA was extracted from exponentially grown E. coli cells harvested at OD 600 =1.0 according to the published protocol (He, F. E. coli Genomic DNA Extraction Bio-101, e97, doi:10.21769/BioProtoc.97  (2011))
Preparation of genomic DNA libraries was carried out using the NEBNext Ultra II FS DNA Library Prep Kit (NEB) according to the manufacturer’s instructions. The approximate insert size was selected to be in the range of 150-250 bp. Barcodes were introduced to both ends during library amplification step with NEBNext multiplex oligos for Illumina (NEB). Genomic DNA libraries were sequenced using HiSeq2500 platform (Illumina) in the rapid run mode (50 nt single end reads).

value: BL21(DE3) Tus-

tag: genotype


title: g_BLTus_Cb_pBAD_exp_rep1

description: Reference genome: NC_012971.2

growth_protocol: Cells were grown in LB media supplemented with 0.2% glucose, ampicillin and 0.01% L-arabinose, and aerated at 30˚C until OD 600 = 0.5.


title: fresh_plus_1

description:
Sample_118998
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt


title: GVK2.BC10

source_name: KO2 B Cells with LPS+IL4


title: GVK1.BC9

source_name: KO1 B Cells with LPS+IL4


title: fresh_plus_0

description:
Sample_118997
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt


title: GVC2.BC8

source_name: Ctrl2 B Cells with LPS+IL4

value: Lsh+/-


title: g_BLTus_noAgo_pBAD_plt_rep1

description: Reference genome: NC_012971.2


title: M4

description:
Young
GEN141016_F Profiling table.xlsx


title: g_BLTus_noAgo_pBAD_exp_rep1

description: Reference genome: NC_012971.2


title: M3

description:
Young
GEN141016_F Profiling table.xlsx


title: M2

description:
Young
GEN141016_F Profiling table.xlsx


title: g_BL_Cb_pBAD_exp_rep1

description: Reference genome: NC_012971.2

value: E. coli B F- ompT gal dcm Ion hsdAB(rB-mB-) [gamma](DE3 [lacI lacUV5- T7po7 ind1 sam7 nin5]) [malB+]K-12([gamma]S) pBAD_HisB_CbAgo [malB+]K-12([gamma]S) pBAD_HisB_CbAgo


title: fresh_plus_2

description:
Sample_118999
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt


title: g_BL_Cb_pBAD_plt_rep1

description: Reference genome: NC_012971.2


title: Sample9_chd-overexpressing_repeat3

city: Tübingen

first: Katherine

middle: Wallace

last: Rogers

address: Max-Planck-Ring 9

country: Germany

institute: Friedrich Miescher Laboratory of the Max Planck Society

data_processing:
Demultiplexing of all libraries for each sequencing lane using the Illumina bcl2fastq 2.17.1.14 software. 1 or 2 mismatches or Ns were allowed in the barcode read when the barcode distances between all libraries on the lane allowed for it.
Clipping of sequencing adapter remnants from all raw reads: reads with final length < 20 bases were discarded.
Filtering of rRNA sequences using RiboPicker 0.4.3 (http://ribopicker.sourceforge.net/).
Alignment against reference with STAR 2.4.1b (https://github.com/alexdobin/STAR/releases). Post-alignment filtering of reads aligning to rRNA or tRNA regions; Counting of aligned reads with htseq-count (http://www-huber.embl.de/users/anders/HTSeq/).
Differential expression analysis with edgeR 3.2.3 (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html), DESeq 1.12.0 (http://bioconductor.org/packages/release/bioc/html/DESeq.html) and cuffdiff 2.1.1 (http://cufflinks.cbcb.umd.edu). The raw p-values from the statistical tests were adjusted for multiple testing by the Benjamini-Hochberg false discovery rate (FDR) method. Genes for which the tests had an FDR below 5 % (i.e. 0.05) were considered to be differentially expressed.
Genome_build: Danio rerio GRCz10.
Supplementary_files_format_and_content: Files including read counts for each sample and differential gene expression analyses comparing uninjected vs. bmp-overexpressing, uninjected vs. chd-overexpressing, and bmp-overexpressing vs. chd-overexpressing samples using edgeR 3.2.3, DESeq 1.12.0, and cuffdiff 2.1.1.

organism: Danio rerio

source_name: Whole embryo

growth_protocol: Embryos were reared at 28°C in embryo medium (250 mg/L Instant Ocean salt, 1 mg/L methylene blue in reverse osmosis water adjusted to pH 7 with NaHCO3).

extract_protocol:
To prepare total RNA, the TRIzol reagent (Invitrogen) manufacturer’s protocol was followed until aqueous phase recovery, then 6.25 μl Co-Precipitant Pink (Bioline) was added to 250 μl aqueous phase, followed by 375 μl 100% EtOH. After vortexing briefly, samples were transferred to RNeasy Mini kit (Qiagen) spin columns and centrifuged at 13600 rpm at 4°C for 1 min. Flow-through was discarded and columns were washed twice with RPE buffer (Qiagen). RNA was eluted in 50 μl H2O. Total RNA concentration was measured using a NanoDrop spectrophotometer (ThermoScientific).
Libraries were prepared by LGC Genomics GmbH (Berlin, Germany) for Illumina NextSeq 500 V2 sequencing. For mRNA isolation and cDNA synthesis, the following kits were used: NEBNext Poly(A) mRNA Magnetic Isolation Module, NEBNext RNA First Strand Synthesis Module, and the NEBNext UltraII Non-Directional RNA Second Strand Synthesis Module. Resulting cDNAs were purified on MinElute Columns (Qiagen) and used to prepare sequecing libraries with the "Encore Rapid DR Multiplex System" (NuGen). Libraries were amplified (12 cycles) using standard Illumina primers.

treatment_protocol: Wild type TE zebrafish embryos were dechorionated with Pronase (Roche, 11459643001) and injected at the one-cell stage with 10 pg mRNA encoding zebrafish BMP2b, 100 pg mRNA encoding zebrafish Chordin (Chd, BMP inhibitor), or left uninjected. When uninjected siblings reached shield stage (~6.75 hpf), embryos were snap-frozen in liquid nitrogen.

value: TE

tag: Stage

value: Shield (early gastrulation)

value: Whole embryo

tag: number of embryos


title: fresh_minus_2

description:
Sample_118995
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt

value: fresh


title: fresh_minus_1

description:
Sample_118994
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt


title: g_BL_noAgo_pBAD_plt_rep1

description: Reference genome: NC_012971.2


title: P4

city: Atlanta

first: Lisa

last: Mills

state: GA

address: 1600 Clifton Road

institute: CDC

data_processing:
The Rsubread package align function was used to align single end reads to the Mus musculus genome (GRCm38.93), BAM file created after alignment
Duplicate BAM files were merged together
Genes were counted using the featureCounts function of Rsubread
Genome_build: GRCm38.93
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample in cvs file

source_name: Splenic plasmablast

extract_protocol:
10,000 plasmablasts (CD138+B220int 229 ) were sorted from the spleens of pregnant and Pregnancy Confounds Influenza-Specific Humoral Responses Pregnancy Confounds Influenza-Specific Humoral Responses
Single-end RNA sequencing was performed on samples in duplicate to increase sequencing depth (101 base pair reads).

value: Balb/c

tag: day post infection (dpi)

tag: preganancy status

value: Pregnant


title: P3


title: Sample7_chd-overexpressing_repeat1

tag: tissue


title: g_BL_noAgo_pBAD_exp_rep1

description: Reference genome: NC_012971.2


title: 2-1_mtB39-YB04-1

value: whole fly

tag: Sex

value: male

tag: mitochondrial haplogroup

value: Global Diversity Line B39

tag: y haplotype

value: Global Diversity Line B04

tag: bio replicate


title: Sample6_bmp-overexpressing_repeat3


title: Sample8_chd-overexpressing_repeat2


title: P1


title: fresh_minus_3

description:
Sample_118996
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt


title: Sample5_bmp-overexpressing_repeat2


title: GVC1.BC7

source_name: Ctrl1 B Cells with LPS+IL4

value: spleen

value: murine B lymphocyte


title: hFUS overexpression Hemizygous, mouse ID 28 [RMH1556]

city: Singapore

first: Shuo-Chien

last: Ling

state: Singapore

address: 12 Science Drive 2, MD1, 16-03-H

department: Physiology

country: Singapore

institute: National University of Singapore

data_processing:
RNA-seq read quantification was performed using Kallisto 0.44.0 (-b 50 –single -l 200 -s 20)
DEG calling was performed using Sleuth 0.28.1 using FDR < 0.1 cutoff
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv file with gene abundance for all samples. Gene abundance given in raw Counts calculated by importing the Kallisto alignment output into the tximport R package

source_name: wt-FUS transgene hemizygote_hippocampus

extract_protocol:
Hippocampi were removed, flash frozen under liquid nitrogen, and RNA was harvested using Trizol reagent.
Libraries were prepared using Illumina TruSeq RNA Sample Prep Kit as per manufacturer directions

tag: strain background

tag: genotype/variation

value: wt-FUS transgene hemizygote

tag: age category

tag: age (days)

value: Female

value: Hippocampus


title: Sample4_bmp-overexpressing_repeat1


title: hFUS overexpression Hemizygous, mouse ID 27 [RMH1555]

tag: gender


title: Sample3_uninjected_repeat3

tag: strain


title: M1

description:
Young
GEN141016_F Profiling table.xlsx

source_name: Kidney

value: Kidney

tag: age

value: 5 weeks old


title: NP3

value: Non-pregnant


title: Nontransgenic mouse ID 147 [RMH1554]

source_name: non-transgenic control_hippocampus

value: non-transgenic control


title: NP2


title: Nontransgenic mouse ID 442 [RMH1553]

value: Male


title: Sample2_uninjected_repeat2

value: TE

value: Shield (early gastrulation)

value: Whole embryo


title: fresh_minus_0

description:
Sample_118993
processed data file: depth_normalized_counts.txt
processed data file: phenotype_repFpkms.txt

tag: cell type

value: CD8+ T cells

tag: medium

value: fresh


title: NP1

value: Balb/c


title: hFUS overexpression Hemizygous, mouse ID 85 [RMH1557]


title: Sample1_uninjected_repeat1

tag: Stage

tag: number of embryos


title: P2

tag: day post infection (dpi)

tag: preganancy status

value: Pregnant


title: 100 ng/ml HHQ replicate 4, 72 hours after treatment

city: Haverford

first: Jamie

middle: William

last: Becker

state: PA

address: 370 Lancaster Ave

department: Biology

institute: Haverford College

data_processing:
Sequenced reads were conservatively trimmed to remove adaptors, low-complexity and low-quality sequence, and rRNA reads (including chloroplast and mitochondria rRNA) using Trimmomatic (V0.38) and the following settings: ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 MAXINFO:40:0.5 MINLEN:50.
Transcript abundances were determined using Salmon (V0.12.0) and the Ensembl gene predictions for Emiliania huxleyi CCMP1516 (the non-axenic form of CCMP2090;ftp://ftp.ensemblgenomes.org/pub/protists/release-41/fasta/emiliania_huxleyi/cdna/) as a transcript target index (k-mer size = 23).  Salmon was run in the quasi-mapping mode with default settings and the following flags: --validateMappings and –gcBias.
Gene-level summarized fragment counts were obtained using the tximport R package with default settings (V1.10.0).  Transcript and gene IDs were linked using the general feature format file for Emiliania huxleyi CCMP1516 available from Ensembl Genomes (ftp://ftp.ensemblgenomes.org/pub/protists/release-41/gff3/emiliania_huxleyi).
Genome_build: GCA_000372725.1
Supplementary_files_format_and_content: tab-delimited text file with gene-level summarized estimated transcript counts, along with associated annotation data

organism: Emiliania huxleyi CCMP1516

source_name: Eukaryotic phytoplankton culture

growth_protocol: Batch 2 L cultures of axenic Emiliania huxleyi strain CCMP2090 were grown in natural seawater-based f/2-Si medium in sterile acid-washed polycarbonate bottles.  Cultures were maintained on a 14:10 light (80 +/- 5 µmol photons m^-2 s^-1):dark cycle at 17.5 - 17.8 degrees Celsius.

extract_protocol:
Cell biomass was collected via centrifugation of 400 ml of culture and total RNA extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s recommendations using 350 µl RLT plus buffer per sample and the optional centrifugation (14,000 RPM for 1 min) step to ensure membranes were dry prior to elution with 30 µl RNase free water.  Eluent was reapplied to the membrane, and incubated for 8 min at room temperature before eluting again to increase yield.
Strand-specific RNAseq library construction performed using the KAPA Stranded mRNA-Seq library preparation kit with KAPA mRNA capture beads (Kapa Biosystems).

tag: treatment

value: 100 ng/ml 2-heptyl-4-quinolone (HHQ) prepared in dimethyl sulfoxide (DMSO; final concentration 0.002%)

tag: timepoint

value: 72 hours after treatment


title: LN_P_10

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

country: China

institute: The Second Hospital of Shandong University

description: Small RNA

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel,expression profiles

source_name: serum exosome

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

tag: tissue

value: serum exosome

tag: ln metastasis

value: Yes

tag: disease state

value: esophageal squamous cell carcinoma (ESCC) patient


title: 100 ng/ml HHQ replicate 3, 72 hours after treatment


title: LN_P_9

description: Small RNA


title: 100 ng/ml HHQ replicate 2, 72 hours after treatment


title: LN_P_8

description: Small RNA


title: 100 ng/ml HHQ replicate 1, 72 hours after treatment


title: NP4


title: LN_P_6

description: Small RNA


title: LN_P_5

description: Small RNA


title: 10 ng/ml HHQ replicate 4, 72 hours after treatment

value: 10 ng/ml 2-heptyl-4-quinolone (HHQ) prepared in dimethyl sulfoxide (DMSO; final concentration 0.002%)


title: LN_P_3

description: Small RNA


title: 10 ng/ml HHQ replicate 3, 72 hours after treatment


title: 10 ng/ml HHQ replicate 1, 72 hours after treatment


title: Nontransgenic mouse ID 441 [RMH1552]

tag: strain background

tag: genotype/variation

value: Hippocampus


title: LN_P_2

description: Small RNA


title: 1 ng/ml HHQ replicate 4, 72 hours after treatment

value: 1 ng/ml 2-heptyl-4-quinolone (HHQ) prepared in dimethyl sulfoxide (DMSO; final concentration 0.002%)


title: 10 ng/ml HHQ replicate 2, 72 hours after treatment


title: LN_No_10

description: Small RNA

value: No


title: LN_P_1

description: Small RNA


title: 1 ng/ml HHQ replicate 3, 72 hours after treatment


title: 1 ng/ml HHQ replicate 2, 72 hours after treatment


title: Sox2 ChIP-Seq in Mouse E16 Forestomach

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

country: Canada

institute: UNIV HEALTH NETWORK

data_processing:
For ChIP-Seq, the filtered single-end reads were aligned to mouse reference genome (GRCm38) using Bowtie2 with default parameters. ChIP-Seq peaks were then called by MACS2 -callpeak with parameters “--keep-dup=1” and “--SPMR”. ENCODE mm10 blacklist regions (https://www.encodeproject.org/annotations/ENCSR636HFF/) were excluded from the called peaks for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Tab separated txt files containing ChIP-Seq peak regions.

source_name: Mouse E16 embryonic tissue

growth_protocol: All animal husbandry was conducted in adherence to the standards proposed by the Canadian Council on Animal care and approved by the institutional animal care committees, The Centre for Phenogenomics, Toronto.

extract_protocol:
After isolation of embryonic epithelium using dispase for forestomach and EDTA for the hindstomach, intestine and colon, epithelial pellets were fixed in 1% PFA for 10 minutes at room temperature, quenched with 1/20th volume of 2.5M glycine for 5 minutes, washed twice with cold 1x PBS and flash frozen. When enough sample was acquired (approximately 0.1g of tissue per region), fixed pellets were pooled, dounced in cold PBS with protease inhibitor, and filtered through a 70µm mesh. Samples were then incubated in cold cell membrane and nuclear lysis buffers containing non-denaturating detergents for 30 mins each on a shaker at 4˚C. Washed samples were then pelleted and resuspend in 300µl of sonication buffer containing 0.1% SDS. Sonication was conducted using the Diagenode bioruptor (Diagenode, B01020001) at high power for 40 cycles, 30s ON/OFF. Sonicated samples were cleared with 1:10 dilution of 30% Triton-X and added to antibody bound beads. The next day, beads were washed with high and low salt buffers and treated with Proteinase K overnight at 65˚C. DNA was isolated using phenol/chloroform extraction and 10ng of immunoprecipitated DNA was used for cDNA library construction using the Rubicon DNA-seq Thruplex 48S kit. Libraries were size selected and submitted to be sequenced at 50 base pair read length, single end reads with 15-20 million reads per library.
ThruPLEX DNA-Seq kit

treatment_protocol: No treatment

value: forestomach

tag: chip antibody


title: 1 ng/ml HHQ replicate 1, 72 hours after treatment


title: LN_No_9

description: Small RNA


title: Vehicle control replicate 4, 72 hours after treatment

value: 0.002% dimethyl sulfoxide (DMSO)


title: LN_P_7

description: Small RNA


title: LN_No_7

description: Small RNA


title: LN_No_8

description: Small RNA


title: Vehicle control replicate 3, 72 hours after treatment


title: LN_No_6

description: Small RNA


title: Vehicle control replicate 2, 72 hours after treatment


title: Vehicle control replicate 1, 72 hours after treatment


title: LN_No_4

description: Small RNA


title: 100 ng/ml HHQ replicate 4, 24 hours after treatment

value: 24 hours after treatment


title: LN_No_5

description: Small RNA


title: LN_P_4

description: Small RNA


title: LN_No_3

description: Small RNA


title: 100 ng/ml HHQ replicate 3, 24 hours after treatment


title: LN_No_2

description: Small RNA


title: LN_No_1

description: Small RNA


title: 100 ng/ml HHQ replicate 2, 24 hours after treatment


title: 100 ng/ml HHQ replicate 1, 24 hours after treatment


title: 10 ng/ml HHQ replicate 4, 24 hours after treatment


title: K562 cells, FAM122A KO#1

city: Shanghai

first: Jing

last: Chen

address: 280 South Chongqing Road

institute: Shanghai Jiao-Tong University School of Medicine

data_processing:
RNA quality was determined with the Bioanalyzer (Agilent2100)，
cDNA Libraries were prepared using the standard illuminaTruSeq kit and then sequenced using the Illumina 2500 platform.
FastQC software was used to check the quality of sequence data and Trimmomatics v0.36 was used to remove adapters and reads with poor quality.
The reads were then aligned to the human hg19 reference genome by STAR v2.4.2a.
Differential gene expression was determined using EdgeR，a bioconductor package in R and gene annotation enrichment analysis of Gene ontology terms was performed using GOstats, a bioconductor package in R or DAVID Bioinformatics Resources 6.8
Genome_build: hg19
Supplementary_files_format_and_content: text file include all genes expression

growth_protocol: K562 cells were cultured in RPMI 1640 medium (Invitrogen supplemented with 10% FBS (Invitrogen) and 1% penicillin/streptomycin

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: genotype

value: FAM122A knockout


title: K562 cells, NC#1

value: control


title: 10 ng/ml HHQ replicate 1, 24 hours after treatment

tag: strain


title: 1 ng/ml HHQ replicate 4, 24 hours after treatment


title: 10 ng/ml HHQ replicate 2, 24 hours after treatment


title: K562 cells, FAM122A KO#2


title: 1 ng/ml HHQ replicate 1, 24 hours after treatment


title: 1 ng/ml HHQ replicate 3, 24 hours after treatment


title: Vehicle control replicate 3, 24 hours after treatment


title: Vehicle control replicate 2, 24 hours after treatment


title: P 2h C6

city: Pozuelo de Alarcón

first: joaquín

last: Giner Lamia

state: Madrid

address: Campus de Montegancedo

department: Biotecnologia

institute: CBGP-Universidad Politecnica de Madrid

description:
P 2h
Synechocystis sp PCC PETP cells grown in BG11C-Cu after copper addition

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence,  then mapped to Synechocystis sp. PCC 6803  (NC_000911.1) whole genome using bowtie v2.2.4 with default parameters for paired-end reads.
SAM files were filtered by average insert size (< 1000) and  transformed to BAM files using Samtools v1.2
Raw counts were calculated using htseq-count from Htseq framework v0.11.0 with default mode (union)
Genome_build: Synechocystis sp. PCC 6803 (NC_000911.1)
Supplementary_files_format_and_content: raw counts of sequencing reads

organism: Synechocystis sp. PCC 6803

growth_protocol: cells were grown to the  exponential phase (0.8-1.2 OD 750nm and 4-6 µg chlorophyl/ml) in BG11C-Cu

extract_protocol:
cells were collected by centrifugation and total RNA was extracted by phenol-chloroform method. RNA samples were further purified by RNeasy MinElute Cleanup Kit (Cat No./ID: 74204)
library construction of cDNA molecules was carried out using Illumina Kapa Stranded Total RNA with Ribo-Zero Library Preparation Kit

treatment_protocol: Cells were collected before and after being  treated with Cu 0.5 µM for 2h

tag: growth phase

value: exponential

value: petP-

tag: copper

value: 0.5 micromolar


title: Vehicle control replicate 1, 24 hours after treatment


title: P 0h C5

description:
P 0h
Synechocystis sp PCC PETP cells grown in BG11C-Cu


title: R 2h C4

description:
R 2h
Synechocystis sp PCC PETR cells grown in BG11C-Cu after copper addition

value: petR-


title: Parent culture replicate 3, used for inoculation

value: time zero


title: R 0h C3

description:
R 0h
Synechocystis sp PCC PETR cells grown in BG11C-Cu


title: Parent culture replicate 4, used for inoculation


title: Vehicle control replicate 4, 24 hours after treatment


title: K562 cells, NC#2


title: 10 ng/ml HHQ replicate 3, 24 hours after treatment


title: Parent culture replicate 2, used for inoculation


title: WT 2h C2

description:
WT 2h
Synechocystis sp PCC WT cells grown in BG11C-Cu after copper addition

value: WT


title: WT 0h C1

description:
WT 0h
Synechocystis sp PCC WT cells grown in BG11C-Cu


title: SPMS-iPS cell line (OSK reprogramming) from somatic samples SPMS-MnSC-04

description:
SPMS-iPS_expr_4
Passage 10-20 of iPSC

hyb_protocol: For Affymetrix samples, 100 ng of total RNA was hybridized with 2.5 ug of labeled ss-DNA following the Affymetrix protocol.

scan_protocol: Affymetrix arrays were scanned with Affymetrix 3000 7G Scanner.

data_processing: For Affymetrix expression samples, CEL files were generated with Affymetrix® GeneChip® Command Console® 2.0 software. Normalized CHP files were obtained applying SST (Signal Space Transformation)-RMA (Robust Microarray Analysis; Irizarry et al. 2003) method with Thermofisher TAC 4.0 (Transcriptome Analysis Console) software.

source_name: MnSC-donor SPMS-04 reprogrammed to iPSC with OSK

label_protocol: Affymetrix samples were biotin-labeled following the manufacturer protocol (Affymetrix, WT PLUS).

tag: diagnosis

value: SPMS

tag: gender

value: female

tag: cell type

value: iPSC reprogrammed from primary MnSC cell lines


title: 1 ng/ml HHQ replicate 2, 24 hours after treatment


title: P 2h B6

source_name: Synechocystis sp PCC PETP cells grown in BG11C-Cu after copper addition


title: P 0h B5

source_name: Synechocystis sp PCC PETP cells grown in BG11C-Cu


title: Parent culture replicate 1, used for inoculation


title: SPMS-iPS cell line (OSK reprogramming) from somatic samples SPMS-MnSC-03

description:
SPMS-iPS_expr_3
Passage 10-20 of iPSC

source_name: MnSC-donor SPMS-03 reprogrammed to iPSC with OSK


title: R 2h B4

source_name: Synechocystis sp PCC PETR cells grown in BG11C-Cu after copper addition


title: R 0h B3

source_name: Synechocystis sp PCC PETR cells grown in BG11C-Cu


title: WT 2h B2

source_name: Synechocystis sp PCC WT cells grown in BG11C-Cu after copper addition


title: SPMS-iPS cell line (OSK reprogramming) from somatic samples SPMS-MnSC-01

description:
SPMS-iPS_expr_1
Passage 10-20 of iPSC

source_name: MnSC-donor SPMS-01 reprogrammed to iPSC with OSK


title: WT 0h B1

source_name: Synechocystis sp PCC WT cells grown in BG11C-Cu


title: SPMS-iPS cell line (OSK reprogramming) from somatic samples SPMS-MnSC-02

description:
SPMS-iPS_expr_2
Passage 10-20 of iPSC

source_name: MnSC-donor SPMS-02 reprogrammed to iPSC with OSK


title: P 2h A6


title: CT-iPS cell line (OSK reprogramming) from somatic samples CT-MnSC-02

description:
CT-iPS_expr_2
Passage 10-20 of iPSC

source_name: MnSC-donor CT-02 reprogrammed to iPSC with OSK

value: healthy


title: CT-iPS cell line (OSK reprogramming) from somatic samples CT-MnSC-03

description:
CT-iPS_expr_3
Passage 10-20 of iPSC

source_name: MnSC-donor CT-03 reprogrammed to iPSC with OSK


title: P 0h A5


title: TM5_2_23_3_ampB_10_µg _ml-1

city: Dresden

first: Thorsten

last: Mascher

address: Zellescherweg 20b

institute: TU Dresden

data_processing:
reverse complement of fastq files with fastx_reverse_complement (version: FASTX Toolkit 0.0.14)
mapping with bowtie2 (cmd: bowtie2 --mm --very-sensitive; version: 2.3.4.1)
filter for mapped reads and convert to sorted bam (cmd: samtools view -F 4 -Shb {input} | samtools sort -o {output.bam}; Version: 1.8)
counting features with FeatureCounts (cmd: featureCounts -s 1 -t 'gene' -g 'ID' -a annotation.gff; version: subread=1.6.1)
DESeq2 normalized counts and differential gene expression (version: bioconductor-deseq2=1.18.1, R version 3.4)
Genome_build: Assembly ASM904v1 (RefSeq: GCF_000009045.1); Annotation based on Nicolas P et al., 2012 (https://www.ncbi.nlm.nih.gov/pubmed/22383849) supplementary table S5
Supplementary_files_format_and_content: tab-delimited text files with counts, log-fold changes, and adjusted p-values

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: whole cells

growth_protocol: Overnight cultures of B. subtilis W168 (Nicolas et al., 2012) were prepared in LB (Sigma L3522) and incubated at 37°C, 220rpm. On the next day, 10 ml day culture of LB (Sigma L3522) was inoculated 1:100 and grown till OD600 = 0.4. Subsequently, a second day culture of 200 ml LB (Sigma L3522) was started to an OD600 = 0.1. Once this second day culture reached OD600 = 0.5, cells were split into 25 ml aliquots and either exposed to amphotericin B (10 µg ml-1, final concertation) or remained untreated for 10 min. After that, cells were directly placed onto ice and centrifuged at 4° C and 8000 rpm for 3 min. The falcons containing the cell pellets were then frozen in liquid nitrogen and kept at -80 °C.

extract_protocol:
B. subtilis cells were disrupted using a micro-dismembrator. Total RNA isolation was performed with a phenol-chloroform isoamyl-alcohol (25:24:1, pH 5.5) extraction method.
rRNA was subtracted from the samples with the Illumina Ribo-Zero rRNA removal Kit (Bacteria) according to manufacturer instructions. The cDNA library was prepared using the NEB Ultra directional RNA library prep kit for Illumina according to instructions and sequencing was performed on an Illumina HiSeq3000 system.

treatment_protocol: Triplicates of non-induced (TM5_2_05_1 - TM5_2_05_3) and triplicates of amphotericin B (10 µg ml-1) induced (TM5_2_23_1 - TM5_2_23_3) samples

value: trp+

value: logaritmic phase

value: whole cells


title: TM5_2_23_2_ampB_10_µg _ml-1


title: TM5_2_23_1_ampB_10_µg _ml-1


title: R 2h A4


title: primary MnSCs from SPMS donor-_biological rep2

description:
SPMS-MnSC-02
All experiments were performed in passage 2-4.

source_name: human female primary MnSC-from SPMS donor_02

value: primary MnS


title: primary MnSCs from SPMS donor-_biological rep3

description:
SPMS-MnSC-03
All experiments were performed in passage 2-4.

source_name: human female primary MnSC-from SPMS donor_03


title: R 0h A3


title: primary MnSCs from healthy donor-_biological rep1

description:
CT-MnSC-01
All experiments were performed in passage 2-4.

source_name: human female primary MnSC-from healthy donor_01


title: AngIV-1: myocardial tissues from mice, diabetes mellitus+high-dose angiotensin IV, rep1

city: jinan

first: meng

last: zhang

address: Jinan 250012, Shandong, China

institute: Shandong University

description: Gene expression data from

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: myocardial tissues from mice, FBG≥16.7mM, 6 months + high-dose AngIV treatment for 4 months

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

growth_protocol: Diabetes was induced in mice via intraperitoneal injection of streptozotocin  for 5 days consecutively. Two weeks after STZ injection, mice with fasting blood glucose (FBG) ≥16.7mM were chosen for subsequent experiments.In the NC group, mice were intraperitoneally injected with vehicle daily for 5 days.

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

treatment_protocol: High-dose AngIV (2.88 mg/kg/day) was infused in the treatment group of mice from the end of 8 weeks to the end of 24 weeks.

value: negative control

value: myocardium


title: DM-1: myocardial tissues from mice, diabetes mellitus, rep1

description: Gene expression data from

source_name: myocardial tissues from mice, FBG≥16.7mM, 6 months

value: diabetes mellitus


title: primary MnSCs from SPMS donor-_biological rep1

description:
SPMS-MnSC-01
All experiments were performed in passage 2-4.

source_name: human female primary MnSC-from SPMS donor_01


title: CT-iPS cell line (OSK reprogramming) from somatic samples CT-MnSC-01

description:
CT-iPS_expr_1
Passage 10-20 of iPSC

source_name: MnSC-donor CT-01 reprogrammed to iPSC with OSK


title: AngIV-3: myocardial tissues from mice, diabetes mellitus+high-dose angiotensin IV, rep3

description: Gene expression data from


title: AngIV-4: myocardial tissues from mice, diabetes mellitus+high-dose angiotensin IV, rep4

description: Gene expression data from


title: AngIV-2: myocardial tissues from mice, diabetes mellitus+high-dose angiotensin IV, rep2

description: Gene expression data from


title: primary MnSCs from healthy donor-_biological rep3

description:
CT-MnSC-03
All experiments were performed in passage 2-4.

source_name: human female primary MnSC-from healthy donor_03


title: NC-4: myocardial tissues from mice, negative control, rep4

description: Gene expression data from

source_name: myocardial tissues from mice, negative control, 6 months


title: DM-4: myocardial tissues from mice, diabetes mellitus, rep4

description: Gene expression data from


title: TM5_2_05_3_no_treatment


title: WT 2h A2

value: exponential


title: TM5_2_05_2_no_treatment


title: TM5_2_05_1_no_treatment


title: NC-3: myocardial tissues from mice, negative control, rep3

description: Gene expression data from


title: DM-2: myocardial tissues from mice, diabetes mellitus, rep2

description: Gene expression data from


title: DM-3: myocardial tissues from mice, diabetes mellitus, rep3

description: Gene expression data from


title: WT 0h A1


title: primary MnSCs from healthy donor-_biological rep2

description:
CT-MnSC-02
All experiments were performed in passage 2-4.

source_name: human female primary MnSC-from healthy donor_02


title: NC-2: myocardial tissues from mice, negative control, rep2

description: Gene expression data from


title: WHIM11-BLU9931 treated [SG188-WHIM11-GFP-Luc BLU1]

status: Public on Jul 29 2020

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

hyb_protocol: Labeled tumor and reference RNA were mixed and co-hybridized overnight on Agilent custom 44K whole genome microarrays

scan_protocol: Microarrays were scanned on an Agilent G2565CA Microarray Scanner System, read it with the scan Control Software 8.5.1 and data was extracted with Feature Extraction Software 11.5.1

data_processing: Microarray raw data were uploaded into the UNC Microarray Database and Lowess normalization was performed on the Cy3 and Cy5 channels

source_name: Human universal, Stratagene, Human Reference B

label_protocol: 1 ug of Total RNA was amplified and labeled using Agilent’s Low RNA Input Linear Amplification Kit. RNA labeling tumor (Cy5 CTP) and reference (Cy3 CTP) were measured by NanoDrop

growth_protocol: PDX WHIM11 tumors were engrafted in the mammary fat pad of NSG mice by subcutaneous injection of 1.0 × 10^6 cells in RPMI:Matrigel (1:1) in a total volume of 200 μl

extract_protocol: Tumor tissue was disrupted using roto-stator homogenization. RNA was isolated using the RNeasy Mini Kit (QUIAGEN) according to manufacturer protocol. Isolated RNA was quantified using a NanoDrop® Spectrophotometer.

treatment_protocol: Tumors treated with BLU9931 (0.6g/Kg/day) or Lapatinib (0.22g/kg/day) for 18 days

tag: reference

value: High-quality total RNA. Comprised of 10 different cell lines for broad gene coverage on human microarrays

source_name: Patient derived breast tumor tissue

value: WHIM11 tumor

tag: agent

value: BLU9931 treated for 18 days


title: WHIM11-BLU9931 treated [SG192-WHIM11-GFP-Luc-BLU5]


title: WHIM11-Lapatinib treated [SG202-WHIM11-GFP-Luc-Lap5]

value: Lapatinib treated for 18 days


title: WHI11-Untreated [SG184-WHIM11-GFP-Luc-Ctrl2]

value: Untreated


title: WHIM11-Lapatinib treated [SG198-WHIM11-GFP-Luc-Lap1]


title: NC-1: myocardial tissues from mice, negative control, rep1

description: Gene expression data from


title: WHI11-Untreated [SG187-WHIM11-GFP-Luc-Ctrl5]


title: MDA.MB.453_Control [MDA-MB-453-P11-48h BLU9931-2]

growth_protocol: MDA-MB-453, CAMA-1 and T47D are derived from metastatic carcinoma pericardial effusion and MCF7 derived from adenocarcinoma pleural effusion. Cell cultures were incubated at 37ºC in a humidified 5% CO2 atmosphere. All cell lines were maintained in complete growth media (corresponding media supplemented with a mix of penicillin/streptomycin plus fungizone (ratio 9:1) at 1% (GIBCO), 1% of L-GlutaMAX™ 200 mM and 10% of fetal bovine serum (FBS) (Sigma-Aldrich)).

extract_protocol: Cell line lysate was prepared using QIAshredder tubes (QIAGEN). RNA was isolated using the RNeasy Mini Kit (QUIAGEN) according to manufacturer protocol. Isolated RNA was quantified using a NanoDrop® Spectrophotometer.

treatment_protocol: Cell were infected with a FGFR4 expressing lentiviral vector or treated with BLU9931 at IC50 doses

source_name: Breast cancer cell line

value: MDA-MB-453 cell line

value: Treated with BLU9931 for 48h at the IC50 doses


title: WHIM11-Lapatinib treated [SG199-WHIM11-GFP-Luc-Lap2]


title: WHI11-Untreated [SG183-WHIM11-GFP-Luc-Ctrl1]


title: WHIM11-BLU9931 treated [SG189-WHIM11-GFP-Luc BLU2]


title: MDA.MB.453_Control [MDA-MB-453-P11-48h BLU9931-1]


title: WHI11-Untreated [SG185-WHIM11-GFP-Luc-Ctrl3]


title: MDA.MB.453_Control [MDA-MB-453-P12-48h BLU9931-1]


title: MDA.MB.453_FGFR4 ACTIVE [MDA-MB-453-P12-Ctrl Tt-1]

value: Untreated (DMSO only at IC50 concentrations)


title: MDA.MB.453_FGFR4 ACTIVE [MDA-MB-453-P11-Ctrl Tt-2]


title: WHIM11-Lapatinib treated [SG200-WHIM11-GFP-Luc-Lap3]


title: WHIM11-BLU9931 treated [SG190-WHIM11-GFP-Luc-BLU3]


title: CAMA.1_Control [CAMA-1-P6-48h BLU9931-2]

value: CAMA-1 cell line


title: MDA.MB.453_FGFR4 ACTIVE [MDA-MB-453-P11-Ctrl Tt-1]


title: CAMA.1_Control [CAMA-1-P6-48h BLU9931-1]


title: CAMA.1_FGFR4 ACTIVE [CAMA-1-P9-Ctrl Tt-2_SG]


title: CAMA.1_FGFR4 ACTIVE [CAMA-1-P9-Ctrl Tt-1_SG]


title: CAMA.1_Control [CAMA-1-P5-48h BLU9931-1]


title: CAMA.1_Control [CAMA-1-P9-48h BLU9931-1_SG]


title: T47D_FGFR4 ACTIVE [T47D-FGFR4-GFP-P28-1]

value: T47D cell line

value: Transduced with FGFR4 expressing lentiviral vector


title: MDA.MB.453_Control [MDA-MB-453-P12-48h BLU9931-2]


title: WHI11-Untreated [SG186-WHIM11-GFP-Luc-Ctrl4]


title: T47D_Control [T47D-RFP-GFP-P28-1]

value: Transduced with empty/control expressing lentiviral vector


title: MDA.MB.453_FGFR4 ACTIVE [MDA-MB-453-P12-Ctrl Tt-2]


title: CAMA.1_Control [CAMA-1-P9-48h BLU9931-2_SG]


title: T47D_FGFR4 ACTIVE [T47D-FGFR4-GFP-P27-1]


title: CAMA.1_Control [CAMA-1-P5-48h BLU9931-2]


title: MCF7_FGFR4 ACTIVE [MCF7-FGFR4-GFP-P29-2]

value: MCF7 cell line


title: CAMA.1_FGFR4 ACTIVE [CAMA-1-P6-Ctrl Tt-2]


title: T47D_Control [T47D-RFP-GFP-P28-2]


title: CAMA.1_FGFR4 ACTIVE [CAMA-1-P6-Ctrl Tt-1]


title: T47D_FGFR4 ACTIVE [T47D-FGFR4-GFP-P28-2]


title: TRACE_seq_mRNA_oligodT_primer_replicate_2

city: Beijing

first: Chengqi

last: Yi

address: No.5 YiHeYuan Road

institute: Peking University

data_processing:
Raw reads from sequencing were firstly subjected to Trim_galore (v0.6.4_dev) for quality control and adaptor trimming with parameters -q 20 --stringency 3 --length 20
Then trimmed reads were mapped to human (hg19) genome and transcriptome(downloaded from the table browser of UCSC database) using STAR (v2.7.1a) with parameters --runThreadN 20 --outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outFilterIntronMotifs RemoveNoncanonicalUnannotated
rRNA contamination were determined through directly mapping to the dataset of human rRNA sequence downloaded from NCBI by bowtie2 (v2.2.9) with parameters -N 1 -p 20 -q
Performances related to the processing of sam/bam file were done with the help of Samtools (v1.9)
The FPKM value for annotated genes was calculated by cuffnorm (v2.2.1). Gene body coverage and nucleotide composition for each position of the first 30 bases of each sequence read per library were calculated by QoRTs (v1.1.6). Reads distribution and GC content distribution of mapped reads were calculated by RseQC (v2.6.4), and median coefficient of variation of gene coverage over the 1000 most highly expressed transcripts per library and insert size of library were calculated by Picard Tools (v2.20.6). Library complexity was calculated by Preseq (v2.0.0).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample using 293T RNA as input and Tab-delimited text files include counts for each genes in each sample using mESC RNA as input.

source_name: human embryonic kindey cells

growth_protocol: HEK293T cells used in this study were daily maintained in DMEM medium (GIBCO) supplemented with 10% FBS (GIBCO) and 1% penicillin/streptomycin (GIBCO) at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cells with TRIzol (Invitrogen), according to the manufacturer’s instructions. The resulting total RNA was treated with DNase I (NEB) to avoid genomic DNA contamination. Phenol/chloroform extraction and ethanol precipitation were then performed to purify and concentrate total RNA. For mRNA isolation, two successive rounds of poly(A)+ selection were performed using oligo(dT)25 dynabeads (Invitrogen).
Reverse transcription was carried out using Superscript IV reverse transcriptase (Invitrogen) and then tagmentation reaction was performed with Tn5 transposase (Vazyme). Strand extension reaction was performed by directly adding Bst 3.0 DNA Polymerase and 1X NEBNext Q5 Hot Start HiFi PCR Master Mix (NEB) to tagmentation products and incubating at 72°C for 15 min, followed by Bst 3.0 DNA Polymerase inactivation at 95°C for 5 min. Next, 0.2 μM indexed primers were added to perform enrichment PCR.The library was purified twice using 1X Agencourt AMPure XP beads (Beckman Coulter) and sequenced on the Illumina Hiseq X10 platform which generated 2 x 150 bp of paired-end raw reads.

value: HEK293T cells

tag: transposase

value: TruePrep Tagment Enzyme (Vazyme, S601-01)


title: Smart_seq2_20ng_replicate_2

value: TruePrep Tagment Enzyme (Vazyme, TD503-01)


title: Smart_seq2_2ng_replicate_1


title: TRACE_seq_mRNA_random_primer_replicate_2


title: Smart_seq2_20ng_replicate_1


title: TRACE_seq_mRNA_oligodT_primer_replicate_1


title: Smart_seq2_2ng_replicate_2


title: TRACE_seq_mRNA_random_primer_replicate_1


title: NEBNext_Ultra_II_mRNA_replicate_1


title: NEBNext_Ultra_II_mRNA_replicate_2


title: MCF7_FGFR4 ACTIVE [MCF7-FGFR4-GFP Ctrl -1]


title: TRACE_seq_2ng_replicate_2


title: MCF7_Control [MCF7-RFP-GFP-P32-Ctrl-1]


title: TRACE_seq_2ng_replicate_1


title: MCF7_FGFR4 ACTIVE [MCF7-FGFR4-GFP-Control-2]


title: MCF7_FGFR4 ACTIVE [MCF7-FGFR4-GFP-P29-2 Array 18]


title: T47D_Control [T47D-RFP-GFP-P27-1]


title: CAMA.1_FGFR4 ACTIVE [CAMA-1-P5-Ctrl Tt-1]


title: TRACE_seq_20ng_replicate_2


title: MCF7_FGFR4 ACTIVE [MCF7-FGFR4-GFP-P29-1]


title: MCF7_FGFR4 ACTIVE [MCF7-FGFR4-GFP-Control-1]


title: MCF7_FGFR4 ACTIVE [MCF7-FGFR4-GFP Ctrl -2]


title: CAMA.1_FGFR4 ACTIVE [CAMA-1-P5-Ctrl Tt-2]


title: T47D_Control [T47D-RFP-GFP-P27-2]


title: T47D_FGFR4 ACTIVE [T47D-FGFR4-GFP-P27-2]


title: MCF7_Control [MCF7-RFP-GFP-P29-1]


title: MCF7_Control [MCF7-RFP-GFP-P29-2]


title: MCF7_FGFR4 ACTIVE [MCF7-FGFR4-GFP-P31-Ctrl-1]


title: MCF7_Control [MCF7-RFP-GFP-P31-Ctrl-1]


title: MCF7_FGFR4 ACTIVE [MCF7-FGFR4-GFP-P29-1 Array 18]