title: B6-3

city: Cleveland

first: Shanshan

last: Zhang

state: OH

address: 10900 Euclid Avenue

department: Department of Genome and Genetics

institute: Case Western Reserve University

data_processing: The paired-end Hi-C reads were mapped to human genome mm10 using BOWTIE. Only first 36 bases were used for mapping. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed. For every loop anchor, we first count Hi-C reads from the anchor to every fragment within 2Mb range and then map the contact fragments to ~5kb anchor resolution. We used HiCorr to correct bias in raw contacts between every two anchors, and apply DeepLoop on the bias-corrected contact ratio from HiCorr. The file column names are "anchor_loc1", "anchor_loc2", "raw_reads","HiCorr_bias_corrected.ratio","DeepLoop_enhanced"

source_name: mouse strain B6 beta cells

growth_protocol: To obtain beta cells, islets from 10-week-old mice were first digested into single cells as follows. Firstly, the islets were washed with Hanks’ Balanced Salt Solution (Sigma, H6648) at room temperature for 5 minutes, followed by centrifuging at 180g for 2 minutes to pellet the islets. The pellets were then resuspended and digested with room temperature Accutase Cell Dissociation reagent (Gibco, A1110501) by incubating at 37ºC for about 5 minutes in non-treated 6-well plates (USA scientific, CC7672-7506). Dissociation was monitored by checking occasionally under a microscope. The obtained cells were then transferred and filtered through a sterile cell strainer (Fisher, 22-363-547) to remove clumps, and further broken down by pipetting up and down several times with a 1ml tip till all observed were single cells. The cells were collected and washed with 1xPBS before fixed for staining. The fixation and permeabilization of cells were done following the recommended assay procedures with BD Cytofix/ Cyto perm solution (BD biosciences). After that, the permeabilized cells were stained with anti-insulin antibody from BD biosciences (#565689) and sorted on a flowcytometer (BD FACSAria II) to collect mouse beta cells.

extract_protocol:
The nuclei were first extracted by lysing the cells with cell lysis buffer as before. The extracted nuclei were then subjected to HindIII digestion followed by proximity ligation with T4 DNA ligase to create spatial ligates. After proximity ligation, the DNA was extracted and prepared for the secondary restriction enzyme (DpnII) digestion. All DNA obtained was subjected to DpnII cutting before being self-ligated to form self- circes. The unligated DNA was then removed using Lambda exonuclease.
The self-circles were re-linearized by digesting again with HindIII. All DNA recovered was applied to generate the sequenceable libraries using the Illumina Truseq platform. Briefly, fragment ends were first repaired with the DNA end-repair enzyme cocktail. Then, a base “A” was added to each end by Klenow fragment (NEB, M0212) before ligated to a modified Truseq adapter using Quick ligase (NEB, M0202). We used the regular i7 indexes as sample index and i5 as fragment index by changing it to random indexes (i5: NNNNNN).

value: beta cells


title: B6-4

status: Public on Jan 31 2024

type: SRA

country: USA

library_source: genomic

data_processing: The paired-end Hi-C reads were mapped to human genome mm10 using BOWTIE. Only first 36 bases were used for mapping. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological li

molecule: genomic DNA

organism: Mus musculus

tag: cell type


title: CDS1_siCTRL_H3K27ac

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

data_processing:
Single-end reads were trimmed using TrimGalore version (v) 0.6.4 (https://github.com/FelixKrueger/TrimGalore) and aligned to the human genome assembly GRCh37 (hg19) using STAR v 2.5.0a.
Multiple matches, as well as regions present in the ENCODE project DAC Exclusion List Regions (data set ENCSR636HFF), were removed and maximum three redundant reads kept for subsequent analyses.
Significantly enriched genomic regions for TF and histone mark ChIP-seq were detected using MACS2 v 2.2.6. FDR cutoff was set to 5.00e-02
False-positive rate was reduced by intersecting MACS peaks with enriched genomic bins defined as described in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9046276/
Assembly: Hg19
Supplementary files format and content: CPM-normalized BigWig files were generated using bamCoverage

organism: Homo sapiens

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Branson sonifier SFX250 sonicator followed by chromatin immunoprecipitation using desired antibodies.
ChIp-seq libraries were prepared using the Illumina Truseq ChIP Library Preparation Kit. 5 ng of DNA was used as a starting material for input and samples. Libraries were amplified using 16 cycles on the thermocycler. Post amplification libraries were size selected at 200-500bp in lenght using SPRI beads from Beckman Coulter.

tag: cell line

value: human CIC-DUX4 sarcoma cell line

tag: chip antibody

value: H3K27ac (Active Motif, #39134)


title: NSTEMI_AVSc_6

city: Milano

first: Gualtiero

middle: Ivanoe

last: Colombo

address: Via Carlo Parea, 4

country: Italy

institute: Centro Cardiologico Monzino IRCCS

library_source: transcriptomic

data_processing:
We used XSQTools (Applied Biosystems) with default parameters to remove reads with low quality base values and to generate .csfasta and .QV.qual files for each samples. Fiannly, cs.fasta and .QV.qual files were converted into .fastq format.
Sequential aligning of raw reads was performed against the GRCh38 Human Genome reference (release 99) with the “Spliced Transcripts Alignment to a Reference” (STAR v. 2.7.5c) software, and with “Bowtie2” (v. 2.4.1) to align locally any reads not mapped by STAR. We excluded 'haplotypes' and 'patches' sequences from the reference, in order to focus on primary assembly and to avoid under-estimation of gene expression.
We implemented the reference annotation based transcript (RABT) procedure, using StringTie suite v2.1.4 to create a new assembly for downstream analysis, integrating the information about known genes and transcripts position in the genome (Ensemble GTF release 99) with those reads mapped in intergenic or intronic regions.
Gene expression quantification were computed by “featureCounts” (v.2.0.1) grouping meta-features by 'gene name'.
Assembly: HG38/GRCh38.99
Supplementary files format and content: Tab-delimited text files include raw counts values for each Sample. The header of the files reports gene name, Ensemble gene ID, chromosome location, gene length, biotype, biotype class and sample identifiers.

molecule: total RNA

source_name: Whole blood

growth_protocol: Blood samples were collected and mantained into Tempus Blood RNA tubes at -80 °C until processing, following manufacturer's instructions.

extract_protocol:
Total RNA was isolated using the Tempus Spin RNA Isolation Kit (Applied Biosystems) and was treated with RNase-free DNase-I to eliminate genomic contamination, following the manufacturer’s instructions.
Five µg of total RNA were precipitated, α- and β-globin mRNAs were depleted with GLOBINclear Whole Blood Globin Reduction kit (Applied Biosystems), and poly(A)+ RNA was enriched following MicroPoly(A) Purist kit protocol (Applied Biosystems). Libraries were prepared and pooled together using the multiplex SOLiD System Sequencing and Barcoding kits. Complementary DNA (cDNA) amplification reaction was conducted with 20 µL template in 100 µl end-volume reaction and with 16 PCR cycles. Clonally amplification of library templates was performed on SOLiD p1 DNA beads by emulsion PCR (ePCR) using 0.5 pM library template and E120 EZbeads scale.

tag: tissue

value: Whole blood

tag: Sex

value: Male

tag: age

tag: acs

value: NSTEMI

tag: avsc

value: Yes


title: STEMI_AVSc_4

value: STEMI


title: STEMI_noAVSc_22

value: No


title: STEMI_noAVSc_17


title: CIC4_H3K4me3

source_name: CIC4 Primary tumor

value: CIC4 Primary tumor

value: soft tissue sarcoma

value: H3K4me3 (Merck/Millipore, #04-745)


title: CIC4_Input


title: STEMI_noAVSc_15


title: CDS1_siQ_H3K27ac


title: STEMI_noAVSc_16


title: STEMI_noAVSc_12


title: CDS1_siQ_Input


title: STEMI_AVSc_3

value: Female


title: STEMI_noAVSc_14


title: B6-2


title: Cast-4

source_name: mouse strain Cast beta cells


title: B6-1


title: CIC4_H3K27Ac


title: STEMI_noAVSc_13


title: CIC4_H3K4me1

value: H3K4me1 (Abcam, #ab8895)


title: Cast-2


title: NSTEMI_AVSc_5


title: CIC3_Input

source_name: CIC3 Primary tumor

value: CIC3 Primary tumor


title: Cast-3


title: NSTEMI_AVSc_4


title: STEMI_AVSc_2


title: NSTEMI_noAVSc_11


title: STEMI_noAVSc_10


title: CIC3_H3K4me3


title: CIC3_H3K4me1


title: STEMI_noAVSc_11


title: NSTEMI_AVSc_3


title: CDS1_H3K27ac_2


title: STEMI_noAVSc_9


title: STEMI_noAVSc_8


title: CIC2_Input

source_name: CIC2 Primary tumor

value: CIC2 Primary tumor


title: NSTEMI_AVSc_2


title: NSTEMI_noAVSc_10


title: CIC2_H3K4me3


title: STEMI_noAVSc_7


title: SKV3_MCI_E2f4VP16_Rep3

city: Iowa City

first: Amy

middle: Leanne

last: Ryan

state: IA

address: 51 Newton Road

department: Anatomy and Cell Biology

institute: The University of Iowa

data_processing:
FASTQ reads were trimmed to remove bases 1-12 due to lack of sequence complexity
Reads were filtered to remove those with quality scores of less than 30 for 90% of the read
Reads were aligned to mm10 GRCm38 transcriptome for differential analysis.
Table of counts were assembled for all transcripts for all samples and are expressed as RSEM as in (https://doi.org/10.1186/1471-2105-12-323).
Assembly: mm10
Supplementary files format and content: Counts per transcript normalized by RSEM.

source_name: MEF

growth_protocol: Primary mouse embryonic fibroblasts were grown in DMEM supplemented with 10% fetal bovine serum (FBS) 0.1 mM non-essential amino acid (#11140-050; invitrogen) in a 37 °C humidified incubator with 5% CO2. Only MEFs with less than 4 passages were used in all experiments.

extract_protocol:
Treated MEFs were washed with PBS, and RNA was harvested using Quick-RNA prep kit (ZYMO research).
RNAseq libraries were constructed with Illumina Truseq RNA Sample Preparation kit v2 according to the manufacturer’s instructions and sequenced on a HiSeq 2500 at 1x50 base pairs to a depth of 20-40 million reads.
Each RNAseq condition was performed in triplicate, using treated MEF cells with 3 different experiments.

treatment_protocol: Primary MEFs were plated with 10% FBS-DMEM for overnight then treated with 2% FBS-DMEM. Six hours after serum-reduced treatment, siRNAs were transfected into MEFs using Lipofectamine RNAiMAX (Invitrogen) according to manufacturer’s instructions. Eighteen hours later, the cells were washed with 2% FBS-DMEM then infected with pAd/CMV/V5 vector expressing pAd/CMV/V5 vector encoding 3xFLAG-Multicilin, NLS-6xmyc-E2f4ΔTA-VP16-T2A-3xFLAG-Multicilin, and NLS-6xmyc-E2f4WT-T2A-3x-FLAG-Multicilin. Adenovirus infection was performed by adding the adenovirus crude lysates to the MEF cells for four hours, washing with pre-warmed PBS once, then growing infected cells with 2% FBS-DMEM. The cells were subjected to RNA extraction 2 days after infection.

value: MEF

value: Mouse Embryonic Fibroblasts

value: Control

tag: genotype

value: MCIDAS_E2f4VP16 Overexpression

tag: treatment

value: Day 4


title: SKR3_siRbl2_MCI_Rep3

value: MCIDAS Overexpression


title: Cast-1

value: beta cells


title: SKV1_MCI_E2f4VP16_Rep1


title: CIC2_H3K4me1


title: SKR2_siRbl2_MCI_Rep2


title: CIC2_H3K27Ac

value: H3K27ac (Active Motif, #39134)


title: NSTEMI_noAVSc_8

value: Whole blood

value: Male

value: NSTEMI


title: STEMI_noAVSc_5

value: STEMI

value: No


title: NSTEMI_noAVSc_7

value: Female


title: TCP_rep2

city: Durham

first: Charles

middle: A

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

data_processing:
Resulting reads were subjected to adapter trimming using Trimmomatic v0.32, aligned to GRCh38 with the STAR v2.4 aligner, and counts were retrieved using featureCounts from subread version 1.4.6p4 with Gencode v22 gene annotations used as reference.
Differential expression analysis was performed using edgeR quasi-likelihood methodology and data was visualized using Degust and Rstudio.
Genes with significant differential expression were determined using a threshold of FDR < 0.05 and absolute value of Log2(FC) > 1.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files with gene count measurements calculated with RSEM.
Supplementary files format and content: Comma-separated values file containing differential expression results.

source_name: HFF

growth_protocol: Primary human neonatal fibroblasts (HFF cells) were acquired from ATCC (CRL-2097) and cultured in DMEM with 10% FBS, 1% AntiAnti, and 1% NEAA (Sigma) on tissue culture plastic. All work was performed within 30 doublings from the initial passage of the vial.

extract_protocol:
RNA was isolated from the cells using the Norgen Total RNA Purification Kit (#17250) according to the manufacturer's protocol, and samples were run on a RNA TapeStation (Agilent) to verify all samples had a RIN score > 8.
cDNA Libraries were built from our RNA inputs using the TruSeq Stranded Library Prep Kit (Illumina #RS-122-2101) according to manufacturer’s instructions. Quality control was performed by running the amplified libraries out on a High Sensitivity D1000 Tapestation (Agilent) to confirm expected size, and Qubit dsDNA HS assays were performed to determine a final concentration. Libraries were diluted to 10nM and pooled together in equal volumes, followed by sequencing performed on an Illumina HiSeq 2500 using a 50bp PE RapidRun kit.

treatment_protocol: 40k HFF cells were seeded on 50 kPa dishes and TCP dishes, while 70k HFF cells were seeded on 1 kPa dishes to achieve the same effective plating density due to slightly reduced HFF attachment rates (and spreading) on 1kPa hydrogels. 20 hours after seeding, cells were trypsinized spun down at 300g for 5 minutes.

value: HFF

value: Human foreskin fibroblasts

value: wild-type

value: Tissue culture plastic


title: CIC3_H3K27Ac

value: CIC3 Primary tumor

value: soft tissue sarcoma


title: NSTEMI_noAVSc_6


title: SKR1_siRbl2_MCI_Rep1

value: MEF

value: Mouse Embryonic Fibroblasts


title: SKN3_Non_infected_Rep3

value: Control

value: Day 4


title: NSTEMI_noAVSc_5


title: SKV2_MCI_E2f4VP16_Rep2

value: MCIDAS_E2f4VP16 Overexpression


title: TCP_rep1


title: STEMI_noAVSc_3

value: Whole blood


title: SKN2_Non_infected_Rep2


title: NSTEMI_noAVSc_9

value: Male


title: STEMI_noAVSc_2


title: SKN1_Non_infected_Rep1


title: 50kPa_rep2

value: 50kPa surface


title: NSTEMI_noAVSc_4

value: NSTEMI


title: NSTEMI_noAVSc_3

value: No


title: 50kPa_rep1


title: NSTEMI_noAVSc_2


title: SKC3_siCTL_MCI_Rep3

value: siRNA Control

value: MCIDAS Overexpression


title: NSTEMI_noAVSc_1


title: STEMI_AVSc_1

value: Female

value: STEMI

value: Yes


title: STEMI_noAVSc_4


title: SKC2_siCTL_MCI_Rep2


title: NSTEMI_AVSc_1


title: 1kPa_rep1

value: HFF

value: Human foreskin fibroblasts

value: wild-type

value: 1kPa surface


title: BDC4_1kPa_3

data_processing:
FastQC was used to identify read quality, and adapter reads were trimmed using Trimmomatic v0.32 19 followed by Bowtie 26 alignment (v1.0) of the reads to the reference genome using the settings: -v 2 –best –strata -m 1 with duplicate reads removed using Picard MarkDuplicates (v1.13) and ENCODE hg38 blacklist reads removed using bedtools2 v2.25.
Peak calling was performed using MACS2 with narrowPeak settings and a threshold of FDR < 0.001 28, and a master peak set was generated as the union set of all called peaks across every sample analyzed (224,906 unique regions total).
Count matrices were made using featureCounts and DEseq2 v1.36 was used for differential accessibility analysis.
Annotation of genomic regions was performed using ChIPSeeker, interactive visualization of processed data was done using Degust and Rstudio along with ggplot2 and tidyverse plugins were used to generate data visualizations.
Sequencing-depth normalized ATAC bigWig files were generated using deeptools bamCoverage v3.0.1 31.
Assembly: hg38
Supplementary files format and content: narrowPeak files containing signal profiles for each sample.
Supplementary files format and content: Supplementary files with comma-separated values files containing differential accessibility results comparing substrate stiffness conditions.

extract_protocol:
Omni-ATAC-seq protocol was used to minimize mitochondrial reads from the preps, however no trypsinization was used and instead on-plate disruption/removal of nuclei (using the digitonin present in the lysis buffer) was used to better preserve nuclear mechanical context and connectivity prior to transposition by the Tn5.
The Omni-ATAC-seq protocol was used to minimize mitochondrial reads from the preps, however no trypsinization was used and instead on-plate disruption/removal of nuclei (using the digitonin present in the lysis buffer) was used to better preserve nuclear mechanical context and connectivity prior to transposition by the Tn5.  Following the final PCR, libraries were cleaned with a 0.5x/1.8x double-sided SPRI clean. Libraries were subjected to quality control by determining the number of cycles required to reach 25% of the peak threshold in the diagnostic PCR, as well as running the amplified libraries out on a High Sensitivity D1000 Tapestation (Agilent) to confirm expected size, and Qubit dsDNA HS assays were performed to determine a final concentration. Libraries were individually diluted to 6nM and then pooled at equal volumes prior to sequencing on an Illumina HiSeq 4000 using a single lane of 50bp single end reads.

treatment_protocol: Cells were seeded on Matrigen dishes of varying stiffness (1, 12, 50 kPa elastic modulus) at slightly variable densities to account for reduced HFF attachment on softer substrates (70k, 45k, 40k HFF cells seeded per group respectively) and allowed to culture for 20 hours overnight. For Y-27632 ROCKi experiments, the cells were seeded as normal, but 1 hour prior to harvest 10uM Y-27632 ROCKi (StemCell Tech) in growth media was added to the cells.


title: STEMI_noAVSc_6


title: knockdown_control-2_R1.fq.gz

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

country: China

institute: PICB

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking, RNA-seq data were mapped to the mouse genome (mm10) using Hisat2 using default parameters。
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons using Featurecounts
Assembly: mm10 (mouse)
Supplementary files format and content: tab-delimited text files include gene ID and expression level in reads count for each sample

extract_protocol:
Total RNA were extracted with Trizol reagent (Invitrogen) and prepared into cDNA library according to the standard Illumina RNA-seq instruction.
The cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq2500 by a 2X150 bp run.

value: MEF

value: knockdown control


title: STEMI_noAVSc_1


title: SKC1_siCTL_MCI_Rep1

value: Mouse Embryonic Fibroblasts

value: Day 4


title: K9TCC_Mx, Input

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

data_processing:
Basecalling was performed with RTA 2.4.11
Reads were aligned with BWA-MEM and converted to BAM files using samtools 1.10
Peaks were called with MACS2 2.2.1
Spatial clustering using SICER2
Assembly: canFam3.1
Supplementary files format and content: peak text files
Supplementary files format and content: bed files

organism: Canis lupus familiaris

growth_protocol: Cell lines were grown to 70%-80% confluency in DMEM/F12 media.

extract_protocol:
Cells were harvested using a Cell Lifter in PBS, pelleted and lysed in three stages with a protease inhibitor cocktail (Roche #11873580001) at each step. DNA in pelleted nuclei was sheared on ice using a GEX130 Ultrasonic processor in 3 mL volumes at 30% output, 25s ON, then 60s OFF; repeated 8X. MagBead previously bound with antibody with histone modification washed with PBS, resuspended and added to fragmented DNA and incubated at 4C o/n. Beads with bound DNA strands were washed 5X, rinsed with PBS. Final rinse was aspirated and 115 uL of elution buffer was added and incubated at 65C for 15 minutes vortexing every 2 min followed by an o/n incubation on a Thermomixer R.
Libraries were constructed using paired-end libraries with inserts averaging 320 bps and run on an Illumina HiSeq 2000 with 100 bp reads.

treatment_protocol: Cells were cross-linked using 1/10th volumes of 11% formaldehyde quenced with 1/20 volume of 1M glycine after 10 minutes. 2X wash with 1X PBS.

value: Canine urothelial


title: K9TCC_Mx, H3K4me1

value: H3K4me1 (AbCam, #ab8895)


title: K9TCC_Mx, H3K4me3

value: H3K4me3 (AbCam, #ab8580)


title: K9TCC_Mx, H3K27ac

value: H3K27ac (AbCam #ab4729)


title: knockdown_control-1_R1.fq.gz


title: BDC4_1kPa_2


title: BDC4_1kPa_1


title: CK1a_siRNA-2_R1.fq.gz

value: CK1a knockdown


title: 1kPa_rep2


title: K9TCC_Ab, Input


title: BDC4_50kPa_B2_Y27_2

value: 50kPa + 10uM Y-27632 ROCKi


title: BDC4_50kPa_B2_Y27_1


title: K9TCC_Ab, H3K4me3


title: OV_control-2_R1.fq.gz

value: overexpression control


title: BDC4_50kPa_B2_1


title: CK1a_siRNA-1_R1.fq.gz


title: PCM6 cells, empty vector, replicate 2

city: Indianapolis

first: Brian

last: Walker

state: IN

address: 980 W Walnut St

department: Medicine

institute: Indiana University

data_processing:
Reads were aligned to the GRCh38 primary assembly with GENCODE comprehensive gene annotation for reference chromosomes (release 45) using STAR (v2.7.11a).
The aligned reads were then quantified to their respective genes using featureCounts (v2.0.6).
Assembly: GRCh38
Supplementary files format and content: raw count matrices - txt file with genes as rows and samples as columns (first column is gene lengths)

source_name: cell line

extract_protocol:
RNA was extracted in duplicate using the RNeasy Mini kit (Qiagen).
100 nanograms of total RNA was used for library preparation utilizing the Illumina Stranded mRNA Prep kit.

value: cell line

value: myeloma cell line

value: WT

value: 2 day growth


title: PCM6 cells, PBX1 overexpression vector, replicate 2

value: PBX1 overexpression


title: PCM6 cells, PBX1 overexpression vector, replicate 1

value: 1 day growth


title: OV_control-1_R1.fq.gz

value: MEF


title: PCM6 cells, empty vector, replicate 1


title: CK1a_OV-2_R1.fq.gz

value: CK1a overexpression


title: K9TCC_Ab, H3K27ac


title: MM1-S cells, PBX1 overexpression vector, replicate 1


title: BDC4_12kPa_2

value: HFF

value: Human foreskin fibroblasts

value: wild-type


title: MM1-S cells, PBX1 overexpression vector, replicate 2


title: BDC4_12kPa_3


title: MM1-S cells, empty vector, replicate 2


title: MM1-S cells, empty vector, replicate 1


title: CK1a_OV-1_R1.fq.gz


title: SSTC3_Control-2_R1.fq.gz

source_name: TREX4-KO BMDM

value: TREX4-KO BMDM

value: DMSO treatment


title: K9TCC_Ab, H3K4me1

value: Canine urothelial

value: H3K4me1 (AbCam, #ab8895)


title: BDC4_50kPa_Y27

value: 50kPa + 10uM Y-27632 ROCKi


title: BDC4_50kPa_2


title: IS6A [IS1A in processed data]

city: Beijing

first: Zhen

last: Wang

address: No.1 Shuaifuyuan

institute: Peking uinon medical college

data_processing:
Raw data of FASTQ format were firstly processed through in-house perl scripts.In this step, clean data were obtained by removing following reads: (1) reads with adapter; (2) reads with more than 3 N; (3) reads with more than 20% nucleotides with Qphred<=5; At the same time, Q20, Q30 and GC content of the clean data were calculated.
Then, map the clean reads to the silva database to remove the rRNA. All the downstream analyses were based on the clean data without rRNA.
Paired-end clean reads were aligned to the reference genome using Hisat2.
Featurecount was used to count the reads numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: xls files include readcount for each sample
Supplementary files format and content: xls files include fpkm for each sample

source_name: Bilateral paraspinal muscle

extract_protocol:
Total RNA was extracted using the TRIzol method. 1 μg of Total RNA was used for library construction.
RNA library for RNA-seq was prepared as fllows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

value: Bilateral paraspinal muscle

tag: subject status

value: idiopathic scoliosis patient


title: SSTC3_Control-1_R1.fq.gz

source_name: TREX3-KO BMDM

value: TREX3-KO BMDM


title: IS37A [IS5A in processed data]


title: IS37T [IS5T in processed data]


title: ART1

city: Wuhan

first: Guo

last: Chen

address: No. 169, East Lake Road, Wuchang District

institute: Zhongnan Hospital of Wuhan University

library_source: transcriptomic single cell

data_processing:
After quality control, the UMI count matrix was log normalized. Then top 2000 variable genes were used to create potential Anchors with FindIntegrationAnchors function of Seurat. Subsequently, IntegrateData function was used to integrate data. To reduce the dimensionality of the scRNA-Seq dataset, principal component analysis (PCA) was performed on an integrated data matrix. With Elbowplot function of Seurat, top 50 PCs were used to perform the downstream analysis. The main cell clusters were identified with the FindClusters function offered by Seurat, with resolution set as default (res = 0.4). Finally, cells were clustered into 17 major cell types. And then they were visualized with tSNE or UMAP plots. To identify the cell type for each cluster, we detected gene markers for each cell clusters using the “FindMarkers” function in Seurat package (v4.0.4), then we annotated cell types using previously published marker genes
Assembly: hg38
Supplementary files format and content: Cellranger count outputs were upload in h5 format

source_name: PBMC

extract_protocol:
PBMCs was subjected to scRNA seq library construction on the 10X Genomics platform using Chromium™ Single Cell 3' V3 Reagent Kits and a Chromium instrument according to the manufacturer’s protocol
Single-cell RNA-seq libraries were prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits V3.1 (Dual Index) (10×Genomics) using successfully dissociated single-cell suspensions. Chromium Controller (10×Genomics) was first used to generate Gel Beads-in-emulsion (GEMs), post GEM-RT cleanup, cDNA amplification and cleanup（SPRIselect Reagent Kit）. Following fragmented cDNA, end repair and A tailing, the DNAs were ligated to dual Adaptor (Dual Index Kit TT Set A)，the ligated products were amplified and purified, quantified (Qubit 4.0) and stored at -80℃ before sequencing. After purification of ligation product and size fractioning to 300-600bps. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.

value: PBMC

tag: disease state

value: HIV-1 infected patients


title: ART2


title: IS15T [IS3T in processed data]


title: IS33A [IS4A in processed data]


title: IS33T [IS4T in processed data]


title: IS6T [IS1T in processed data]


title: NEO (exposed to an inaccessible nonedible object), rep 5

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

institute: Centre Médical Universitaire de Genève

description:
1106-NEO-5
exposed to an inaccessible nonedible object (NEO; wooden dowel pins in a wire mesh)

data_processing:
Data quality was checked by FastQC software.
Reads were mapped to murine genome sequence (GRCm38 from Genome Reference Consortium) by HiSAT2
Gene counts were acquired by applying featureCounts. Expression reads matrix  cutoff was setup at 10 reads
Read counts were normalized to CPMs (count per million) using the R package, EdgeR
Assembly: Mouse reference genome mm10
Supplementary files format and content: txt file containing all the gene expressions (CPM) for all the samples. Each column is a sample. Each row is a gene.

source_name: Hypothalamus

growth_protocol: Mice were maintained on a 12h-light/12h-dark cycle with free access to water and food

extract_protocol:
Nucleus arcuate (ARC)-enriched microdissections were ice-cold homogenized in 0.25 ml homogenization buffer (50 mM Tris, 100 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT, 200 U/mL Promega RNasin, 1 mg/mL heparin, 100 mg/mL cycloheximide, Sigma protease inhibitor mixture at pH 7.5). To pull down, 2 ml of mouse monoclonal anti-HA antibody (HA.11, ascites fluid; Covance) was added to the homogenate and allowed to rotate for 2 h at 4°C. Then, 200 ml of Dynabead protein G magnetic beads (Invitrogen) were added and further incubated for 2 h at 4°C with rotation. Immunoprecipitates (IPs) were washed 3 times for 10 min with gentle rotation at 4°C in high-salt buffer (50 mM Tris, 300 mM KCl, 12 mM MgCl2, 1% Nonidet P-40, 1 mM DTT, 100 mg/mL cycloheximide at pH 7.5). After the final wash, RNA was stripped from the beads with Quiagen RLT buffer and total RNA was prepared according to manufacturer’s instructions using the RNeasy-plus Mini kit (Qiagen). Yield and concentration were measured with the Quant-iT™ RiboGreen™ RNA assay kit (Invitrogen). RNA integrity was assessed on a 2100 Bioanalyzer device (Agilent Technologies) using the RNA 6000 Pico kit (Agilent Technologies). Only samples with RIN > 8 were used for RNA-Seq analysis.
cDNA libraries were synthetized from 0.5 ng RNA with the SMARTer Ultra Low Input RNA kit v4 (Clontech). Sequencing libraries were prepared with the NexteraXT kit (Illumina)

treatment_protocol: Mice were fasted overnight (16 h) with free access to water and allowed to habituate to experimental room for 1 h before food presentation. Then, either  caged food pellet (SENS) or caged nonedible object (NEO) were introduced in the home cage. food pellets and nonedible object (consisting of wood sticks of the same size and color as food pellets) were caged using a metal mesh. Mice were housed in pairs or triplets. To minimize circadian clock interference, food perception paradigm was performed on the same time of day (around ZT6±1 h).

value: Hypothalamus

value: POMC neurons

value: POMCRiboTag mice

value: NEO

tag: antibody

tag: fraction

value: Translating RNA from ribosomes


title: BDC4_12kPa_1

value: HFF

value: Human foreskin fibroblasts


title: IS12T [IS2T in processed data]


title: SSTC3-2_R1.fq.gz_

source_name: TREX2-KO BMDM

value: TREX2-KO BMDM

value: SSTC3 treatment


title: IS15A [IS3A in processed data]


title: BDC3_50kPa_1

value: wild-type


title: CS7T [CS1T in processed data]

value: congenital scoliosis patient


title: MDA-MB-231, shAHR#3, Replicate 3

city: Buffalo

first: Spencer

last: Rosario

address: Elm & Carlton Sts

institute: Roswell Park Comprehensive Cancer Center

description: Sample 9

data_processing:
Raw reads that passed the Illumina RTA quality filter were demultiplexed and pre-processed using FastQC for sequencing base quality control.
Genome alignment of raw reads to the human reference genome (GRCh38.p13) using STAR
Mapped reads were quantified at the gene level as a raw counts matrix using featureCounts from Subread
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited .txt file includes raw counts for each sample

source_name: Mammary

growth_protocol: MDA-MB-231 were cultured in DMEM media (Invitrogen).Media was supplemented with 10% fetal bovine serum (Invitrogen) and 1% antibiotic-antimycotic (Invitrogen), in a humidified atmosphere with 5% CO2 at 37oC.

extract_protocol:
Total cellular RNA was isolated using the PureLink RNA Mini kit with on-column DNase treatment (Thermo Fisher Sceintific)
sequencing libraries were prepared with the TruSeq Stranded mRNA kit (Illumina) from 500 ng total RNA following manufacturer’s instructions

value: Mammary

value: Mammary Epithelial Cells

value: proliferation


title: MDA-MB-231, shAHR#3, Replicate 2

description: Sample 8


title: BDC4_50kPa_1


title: BDC3_50kPa_2


title: IS12A [IS2A in processed data]

value: Bilateral paraspinal muscle

value: idiopathic scoliosis patient


title: MDA-MB-231, shAHR#2, Replicate 3

description: Sample 6


title: CS7A [CS1A in processed data]


title: CS6T [CS4T in processed data]


title: BDC3_1kPa_2


title: CS6A [CS4A in processed data]


title: CS5A [CS3A in processed data]


title: MDA-MB-231, shAHR#2, Replicate 2

description: Sample 5


title: BDC3_50kPa_3


title: BDC3_1kPa_1


title: CS5T [CS3T in processed data]


title: ET_24hr_3: Electronic and tobacco-exposure 24 hours-replicate 3

city: Hsinchu City

first: Sing-Hang

last: Huang

address: Rm. 304, No.75, Bo’ai St., East Dist.

department: Institute of Bioinformatics and Systems Biology

country: Taiwan

institute: National Chiao Tung University

description: Electronic and tobacco, exposure 24 hours, replicate 3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.1.0 with parameters -p 8 --mm --dta
Fragments Per Kilobase of transcript per Million (FPKM) were calculated using stringtie v1.3.4d with parameter -e -B -p 8
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample

source_name: BEAS-2B bronchial epithelial cell line

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

value: bronchial epithelial

value: Electronic and tobacco

tag: time

value: 24 hours


title: CS2A [CS2A in processed data]


title: MDA-MB-231, shAHR#2, Replicate 1

description: Sample 4


title: CS10A [CS5A in processed data]


title: MDA-MB-231, PLKO-GFP, Replicate 3

description: Sample 3

value: GFP-PLKO


title: MDA-MB-231, shAHR#3, Replicate 1

description: Sample 7


title: CS10T [CS5T in processed data]


title: MDA-MB-231, PLKO-GFP, Replicate 1

description: Sample 1


title: CS2T [CS2T in processed data]


title: ET_24hr_1: Electronic and tobacco-exposure 24 hours-replicate 1

description: Electronic and tobacco, exposure 24 hours, replicate 1


title: MDA-MB-231, PLKO-GFP,Replicate 2

description: Sample 2


title: CT_24hr_3: Charcoal and tobacco-exposure 24 hours-replicate 3

description: Charcoal and tobacco, exposure 24 hours, replicate 3

value: Charcoal and tobacco


title: CT_24hr_2: Charcoal and tobacco-exposure 24 hours-replicate 2

description: Charcoal and tobacco, exposure 24 hours, replicate 2


title: hDIV4-media-3

city: Richardson

first: Theodore

middle: J

last: Price

state: TX

address: 800 W Campbell Rd.

institute: University of Texas at Dallas

data_processing:
Sequence reads were mapped to gencode vM16 (mouse) and v27 (human) using STAR 2.6.1c
Assembly: GRCm38.p5(mouse)/GRCh38.p10(human)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Neuronal cultures, 24 hours in control media

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen) following manufacturer's instructions.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA (Illumina) following manufacturer's instructions

value: Dorsal Root Ganglia

value: Neuron (Primary Cell)

value: 24 hours in control media


title: CT_24hr_1: Charcoal and tobacco-exposure 24 hours-replicate 1

description: Charcoal and tobacco, exposure 24 hours, replicate 1


title: hDIV4-media-2


title: EC109 cell,  siMETTL3 1

city: changzhi

first: Pu

last: wang

state: shanxi

address: jiefang road 163

institute: changzhi medical college

data_processing:
CLC Genomics vvorkbench v 11.0.1
Sequence readswere trmeofor aoaptorsequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit. 0.05)
RNA was harvested using Rneasy mini plus kit (Qiagen).1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA librariesSMARTER MRNfollowina manufacturer's protocols.
Assembly: hg38

growth_protocol: The cells are cultured in DMEM high glucose medium at 37°C with 5% carbon dioxide.

extract_protocol:
Pellet cells by centrifugation, resuspend cell pellet in Trizol reagent.
The RNA library for RNA-seq was prepared using the SMARTer mRNA-seq Library Prep Kit according to the manufacturer’s protocol.

treatment_protocol: Adipogenic differentiation was inducedow ireatmenf of 2-day post confluent cells (desianated day 0. D0) with 10ug/ml insulin (Sigma),

value: Esophageal squamous cell carcinoma


title: EC109 cell,  siMETTL14 1


title: EC109 cell, heat shock and siMETTL3 2


title: EC109 cell,  siMETTL14 2


title: EC109 cell, heat shock 2


title: EC109 cell,  siMETTL3 2


title: EC109 cell, heat shock 1


title: EC109 cell, heat shock and siMETTL3 1


title: EC109 cell, si control 2


title: CNT_24hr_3: Charcoal and non-tobacco-exposure 24 hours-replicate 3

description: Charcoal and non, tobacco, exposure 24 hours, replicate 3

value: Charcoal and non-tobacco


title: hDIV4-media-1


title: ET_24hr_2: Electronic and tobacco-exposure 24 hours-replicate 2

description: Electronic and tobacco, exposure 24 hours, replicate 2


title: EC109 cell, si control 1


title: CNT_24hr_2: Charcoal and non-tobacco-exposure 24 hours-replicate 2

description: Charcoal and non, tobacco, exposure 24 hours, replicate 2


title: hDIV4-24hrec-3

source_name: Neuronal cultures, 30mM KCl treated for 24 hours + 24 hours recovery in control media

value: KCl for 24 hours + 24 hours recovery in control media


title: hDIV4-24hrec-2


title: hDIV4-24hrec-1


title: C_24hr_3: Charcoal-exposure 24 hours-replicate 3

description: Charcoal, exposure 24 hours, replicate 3

value: Charcoal


title: CNT_24hr_1: Charcoal and non-tobacco-exposure 24 hours-replicate 1

description: Charcoal and non, tobacco, exposure 24 hours, replicate 1


title: hDIV4-24hKCl-3

source_name: Neuronal cultures, 30mM KCl treated for 24 hours

value: KCl for 24 hours


title: C_24hr_2: Charcoal-exposure 24 hours-replicate 2

description: Charcoal, exposure 24 hours, replicate 2


title: hDIV4-24hKCl-2


title: WT.EZ.3.NucleosomeFree.bam

city: WEST HOLLYWOOD

first: Moray

last: Campbell

state: CA

address: 8687 Melrose Avenue, Office B227.5G

institute: Cedars-Sinai Medical Center

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQC and Trimmomatic
Trimmed sequence reads were mapped to hg38 using RSubread
Differential chromatin accessability was analyzed with Rsubread/csaw along with TF motif analyses (MotifDb) all in R
Assembly: hg38
Supplementary files format and content: Significant regions are presented with genomic coordinates and signficance

source_name: prostate

growth_protocol: 22Rv1 cells in triplicate were treated with either vehicle, OSU-ERb-12 alone (100 nM) or E2 alone (100nM), Enza (1 microMolar) or the combinations for 6h and ATAC-Seq was undertaken. Cell lines were authenticated by STR profiling and confirmed mycoplasma free.

extract_protocol: Mixing, cleanup and library preparation, quantification and sequencing was performed using NovaSeq6000 S1 PE150bp Sequencing as per protocol51 (28846090). (ATAC-Seq data were separated into nucleosome free (NF), mono-, di- and tri-nucleosome compartments (ATACSeqQC)

treatment_protocol: Cells were grown to 70% confluence and treated as indicated in biological triplicate samples and analyzed by ATAC-Seq.

value: prostate

value: prostate cancer

value: WT

value: OSU-ERb-12 plus Enzalutamide  (6h)

value: genomic DNA


title: WT.EZ.2.NucleosomeFree.bam


title: WT.EZ.1.NucleosomeFree.bam


title: C_24hr_1: Charcoal-exposure 24 hours-replicate 1

description: Charcoal, exposure 24 hours, replicate 1

value: bronchial epithelial


title: WT.2.NucleosomeFree.bam


title: WT.1.NucleosomeFree.bam


title: hDIV4-24hKCl-1


title: EZ.3.NucleosomeFree.bam

value: Enzalutamide, 1microMolar, 6h


title: IC_24hr_2: Control-exposure 24 hours-replicate 2

description: Control, exposure 24 hours, replicate 2

value: Control

value: 24 hours


title: IC_24hr_3: Control-exposure 24 hours-replicate 3

description: Control, exposure 24 hours, replicate 3


title: EZ.1.NucleosomeFree.bam


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM486]

city: Berlin

first: Anna

last: Dolnik

address: Augustenburger Platz 1

department: Campus Virchow-Klinikum (CVK)

country: Germany

institute: Charité Universitätsmedizin Berlin

data_processing:
base-calling was performed according Illumina recommendations bcl2fastq-1.8.4.
50 bp single-end reads (Illumina) were aligned to reference genome hg38 (ENSEMBL) and Homo_sapiens.GRCh38.98.gtf.-transcriptome annotation release (ENSEMBL) using STAR two-pass mode ( star 2.7).
GRCh38.98.gtf.-transcriptome annotation release (ENSEMBL, release 98) was used for quantification, performed by RSEM 1.3.0, followed by TPM normalisation in RSEM-1.3.0.
Assembly: hg38
Supplementary files format and content: output of rsem package: txt table with normalized counts

source_name: CD138+  cells or bone marrow with CD138+ over 75%

extract_protocol:
RNA extraction was performed using AllPrep Kit (Qiagen) according manufacturer instructions.
Library was generated using TruSeq RNA Exome Kit (Illumina) followed by sequencing on NextSeq (Illumina).

value: multiple myeloma relapse


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM376]

value: CD138+  cells or bone marrow with CD138+ over 75%


title: C.2.NucleosomeFree.bam

value: Vehicle


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM331]


title: C.3.NucleosomeFree.bam


title: ET_2hr_3: Electronic and tobacco-exposure 2 hours-replicate 3

description: Electronic and tobacco, exposure 2 hours, replicate 3

value: Electronic and tobacco

value: 2 hours


title: IC_24hr_1: Control-exposure 24 hours-replicate 1

description: Control, exposure 24 hours, replicate 1


title: C.1.NucleosomeFree.bam


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM318]

value: multiple myeloma


title: shPRKAA1, replicate 3

city: chengdu

first: Xiangqi

state: China

address: No.17, Section 3, Renmin South Road

institute: Sichuan University Huaxi Second Hospital

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
paired-end clean reads were aligned to the reference genome usinghisat2 (v2.0.5)
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: raw counts for each sample

source_name: human umbilical vein endothelial cells (HUVECs)

extract_protocol:
RNA was harvested using TRIzol reagent
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775L)

value: PRKAA1 knockdown

value: TGFβ-treated


title: ET_2hr_2: Electronic and tobacco-exposure 2 hours-replicate 2

description: Electronic and tobacco, exposure 2 hours, replicate 2


title: shPRKAA1, replicate 2

value: human umbilical vein endothelial cells (HUVECs)


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2105]


title: shPRKAA1, replicate 1


title: ET_2hr_1: Electronic and tobacco-exposure 2 hours-replicate 1

description: Electronic and tobacco, exposure 2 hours, replicate 1


title: shCtrl, replicate 3

value: control


title: shCtrl, replicate 2


title: EZ.2.NucleosomeFree.bam

value: prostate

value: prostate cancer

value: WT


title: shCtrl, replicate 1


title: CT_2hr_3: Charcoal and tobacco-exposure 2 hours-replicate 3

description: Charcoal and tobacco, exposure 2 hours, replicate 3

value: bronchial epithelial

value: Charcoal and tobacco


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1431]

value: MGUS


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM190]


title: WT.3.NucleosomeFree.bam

value: genomic DNA


title: NR_basal_3

city: Madrid

first: Alicia

last: Sanchez

address: Joaquín Rodrigo, 2 Majadahonda

country: Spain

institute: Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana

description:
DESeq2_results_12m_vs_0_NR_W_LFC
DESeq2_results_12m_vs_0_RNR_W_LFC
DESeq2_results_R_vs_NR_t0_W_LFC

data_processing:
Reads were mapped to Homo Sapiens genome GRCh38_v109 with HISAT2 v2.1.
RNAseq counts were obtained using HTseq V0.11.1 and processed with DESeq2 v1.40.2 under R version 4.3.1.
Gene set enrichment analysis were performed with GSEA v4.3.2
Assembly: GRCh38_v109
Supplementary files format and content: DESeq2 results in TSV format
Supplementary files format and content: The following comparisons were analyzed: 12 months vs baseline in Responders + Non-responders (DESeq2_results_12m_vs_0_RNR_W_LFC); 12 months vs baseline in Non-responders (DESeq2_results_12m_vs_0_NR_W_LFC), 12 months vs baseline in Responders (DESeq2_results_12m_vs_0_R_W_LFC); Responders vs Non-responders at baseline (DESeq2_results_R_vs_NR_t0_W_LFC); Responders vs Non-responders at 12 months (DESeq2_results_R_vs_NR_t12m_W_LFC

source_name: Cells

growth_protocol: PBMCs were isolated from peripheral blood samples by Ficoll-Paque density gradient centrifugation and cryopreserved in liquid nitrogen until use.

extract_protocol:
Total RNA from PBMCs was extracted using the Maxwell 16 LEV simply RNA Cells kit (Promega Biotech Ibérica) on the Maxwell 16 instrument, according to the manufacturer’s instructions.
Poly(A)+ mRNA fraction was isolated from total RNA and cDNA libraries were obtained following Illumina’s recommendations. Briefly, poly(A)+ RNA was isolated on poly-T oligo-attached magnetic beads and chemically fragmented prior to reverse transcription and cDNA generation. The cDNA went through an end repair process, addition of a single “A” base to the 3’ end and ligation to the adapters. Finally, the products were purified and enriched with PCR to create the indexed final double stranded DNA library. The quality and quantity of the libraries were analysed in tapeStation 4200, using the High Sensitivity assay (Agilent Technologies)

value: Cells

value: Primary

value: Peripheral blood mononuclear cells

value: Non-responder

value: Basal


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM380]

value: CD138+  cells or bone marrow with CD138+ over 75%

value: multiple myeloma


title: CT_2hr_1: Charcoal and tobacco-exposure 2 hours-replicate 1

description: Charcoal and tobacco, exposure 2 hours, replicate 1

value: 2 hours


title: R_treat_3

description:
DESeq2_results_12m_vs_0_R_W_LFC
DESeq2_results_12m_vs_0_RNR_W_LFC
DESeq2_results_R_vs_NR_t12m_W_LFC

value: Responder

value: Treated


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM248]


title: NR_treat_2

description:
DESeq2_results_12m_vs_0_NR_W_LFC
DESeq2_results_12m_vs_0_RNR_W_LFC
DESeq2_results_R_vs_NR_t12m_W_LFC


title: R_treat_4


title: R_treat_5


title: NR_treat_5


title: CNT_2hr_2: Charcoal and non-tobacco-exposure 2 hours-replicate 2

description: Charcoal and non, tobacco, exposure 2 hours, replicate 2

value: Charcoal and non-tobacco


title: CNT_2hr_3: Charcoal and non-tobacco-exposure 2 hours-replicate 3

description: Charcoal and non, tobacco, exposure 2 hours, replicate 3


title: R_basal_5

description:
DESeq2_results_12m_vs_0_R_W_LFC
DESeq2_results_12m_vs_0_RNR_W_LFC
DESeq2_results_R_vs_NR_t0_W_LFC


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM191]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM185]


title: NR_treat_4


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1187]


title: CNT_2hr_1: Charcoal and non-tobacco-exposure 2 hours-replicate 1

description: Charcoal and non, tobacco, exposure 2 hours, replicate 1


title: C_2hr_3: Charcoal-exposure 2 hours-replicate 3

description: Charcoal, exposure 2 hours, replicate 3

value: Charcoal


title: R_basal_3


title: NR_basal_4


title: R_basal_4


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM278]


title: CT_2hr_2: Charcoal and tobacco-exposure 2 hours-replicate 2

description: Charcoal and tobacco, exposure 2 hours, replicate 2


title: C_2hr_2: Charcoal-exposure 2 hours-replicate 2

description: Charcoal, exposure 2 hours, replicate 2


title: R_treat_1


title: NR_basal_2


title: C_2hr_1: Charcoal-exposure 2 hours-replicate 1

description: Charcoal, exposure 2 hours, replicate 1


title: R_basal_1


title: R_treat_2


title: NR_basal_5


title: NR_treat_1


title: R_basal_2


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1432]


title: NR_basal_1


title: IC_2hr_3: Control-exposure 2 hours-replicate 3

description: Control, exposure 2 hours, replicate 3

value: Control


title: IC_2hr_2: Control-exposure 2 hours-replicate 2

description: Control, exposure 2 hours, replicate 2

value: bronchial epithelial


title: IC_2hr_1: Control-exposure 2 hours-replicate 1

description: Control, exposure 2 hours, replicate 1


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1984]


title: PFA ependymoma, high cell density area, case 54,  sample 3

city: Hamburg

first: Swenja

last: Gödicke

address: Martinistrasse 52

institute: Research Institute Children‘s Cancer Center Hamburg

data_processing:
NanoString’s GeoMx NGS Pipeline v.2.3.4 was used to convert the fastsq files to Digital Count Conversion files. Quality control (QC) was performed using Nanostring GeoMx analysis suite. For #28 low, #41 high, #54 high and #59 high each, one out of the three samples had to be excluded after running QC due to a too low percentage of stitched and aligned reads and/or a too low negative probe count. Signals were scaled to nuclei count using the geometric mean method for each ROI and normalized for each probe against the 75th percentile of the cumulative signal of the respective ROI. Background correction was performed by geometric mean method against the average background calculated by signal to noise ratio using the negative probe counts.
Assembly: GRCh38.p13
Supplementary files format and content: ROI.dcc: Spatial Transcriptomics data as Digital Count Conversion files
Supplementary files format and content: RawCountMatrixafterQC_SpatialTranscriptomics_PFEPNA.xlsx: gene expression count data after QC in Excel table format, segment and target properties, dataset summary with processing parameters and annotations
Supplementary files format and content: ProcessedCountMatrix_SpatialTranscriptomics_PFEPNA.xlsx: gene expression count data after QC, scaling, normalization and background correction in Excel Table format, segment and target properties, dataset summary with processing parameters and annotations
Library strategy: Spatial Transcriptomics

source_name: PFA ependymoma

extract_protocol:
Posterior fossa type A (PF-EPN-A) tumor areas with both high and low cell density areas were selected on H&E-stained slides from FFPE tissues. Tissue sections (5 µm) of the corresponding areas were processed according to published protocols [Merritt et al. 2020, PMID: 32393914]. RNA-preserving antigen retrieval was performed, followed by RNA target exposure with proteinase K. In situ hybridization of all targets (n=18,677) on the tissue sections was performed overnight at 37°C, followed by stringent washes to remove off-target probes. Subsequently, antibodies against GFAP (Novus, NBP2-33184DL594, 5 µg/ml), Ki-67 (CST, 9027S, 6 µg/ml), and OLIG2 (Millipore, AB9610, 1:200) were used to visualize target areas as well as DAPI for nuclei counterstains. Three areas of low and high cell density each were selected with the custom polygon region of interest (ROI) tool for each case.
These selected areas were illuminated individually via UV light on a GeoMx DSP, resulting in photocleavage of oligonucleotides present within each ROI. Each aspirate contained photocleaved DNA oligos comprising an analyte identifier, a unique molecular identifier (UMI) barcode, and a primer binding site. Illumina adapter sequences and unique dual-sample indices were added when PCR was performed on the aspirates. Sequencing was performed using Illumina's NovaSeq 6000 with the S4 Reagent Kit v1.5 35 cycles flowcell, and paired end reads.

value: PFA ependymoma

tag: cell density_of_sample_region

value: high


title: PFA ependymoma, low cell density area, case 54,  sample 3

value: low


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1931]


title: PFA ependymoma, low cell density area, case 54,  sample 1


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1900]


title: PFA ependymoma, high cell density area, case 54,  sample 2


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM536]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM198]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2146]


title: NR_treat_3

value: Cells


title: PFA ependymoma, low cell density area, case 28,  sample 3


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1433]


title: PFA ependymoma, low cell density area, case 28,  sample 1


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2144]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2134]


title: PFA ependymoma, low cell density area, case 59,  sample 3


title: PFA ependymoma, high cell density area, case 28,  sample 2


title: PFA ependymoma, low cell density area, case 54,  sample 2


title: PFA ependymoma, high cell density area, case 28,  sample 1


title: KMS-11 panobinostat

type: RNA

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

country: Japan

institute: Akita univ.

hyb_protocol: As materials and methods for miRNA microarray protocol version 2.4 (Agilent).

scan_protocol: Agilent G2600D SureScan Microarray Scanner System.

data_processing: GeneSpring (Agilent), computed normalized signal intencity with 75%tile normalization.

source_name: KMS-11 panobinostat

growth_protocol: 48 h culture

extract_protocol: Total RNA was extracted with Trizol.

treatment_protocol: RPMI1640 plus 10% FCS.

tag: cellline

tag: drug

value: panobinostat


title: MM.1S vorinostat

source_name: MM.1S vorinostat

label_protocol: As materials and methods for miRNA microarray protocol version 2.4 (Agilent).

value: vorinostat


title: KMS-11 DMSO

source_name: KMS-11 DMSO

value: DMSO


title: KMS-11 vorinostat

source_name: KMS-11 vorinostat


title: PFA ependymoma, low cell density area, case 59,  sample 2


title: Saccharomyces cerevisiae, main screen, repression library, low fluorescence fraction, round2, rep2

city: Heidelberg

first: Staffan Andreas

last: Johansson

address: Meyerhofstraße 1

institute: EMBL Heidelberg

description:
PCR amplicons
MF_ReadCounts.txt
sample24

library_source: other

data_processing:
Reads were demultiplexed using jemultiplexer using barcodes with S=TRUE MM=3 BRED=FALSE
Reads were trimmed (fastx_trimmer -Q33) and aligned (bwa aln -t 20  -n 6 -k 2 -O 3) against indexed guides
Read count extraction and enumeration into count tables were performed using R and the Rsamtools package
Assembly: sacCer3
Supplementary files format and content: Tab-delimited text files include count values for each experimental sample and guide
Library strategy: Amplicon sequencing

molecule: other

organism: Saccharomyces cerevisiae

source_name: Ethanol red

growth_protocol: Growth in YPAD or SCAA medium with geneticin (400 μg/mL) and shaking at 30 °C

extract_protocol:
Cells were disrupted using a FastPrep vortexing machine with added acid-washed glass beads, followed by plasmid extraction using the QIAprep Spin Miniprep Kit (Qiagen)
The 20-bp variable guide-RNA region on the extracted plasmids was PCR amplified using Q5 High-Fidelity DNA Polymerase (NEB) and primers specific to the flanking regions, with added overhanging sequences resulting in the introduction of 4 to 6-bp barcodes followed by Illumina sequencing adapters on the amplified product.

treatment_protocol: Addition of 500 ng/μl anhydrotetracycline (aTc) during droplet formation

tag: cell line

value: Ethanol red

tag: screen

value: main

tag: library

value: repression

tag: fluorescence fraction

tag: round

tag: replicate


title: PFA ependymoma, low cell density area, case 59,  sample 1

tag: tissue


title: PFA ependymoma, high cell density area, case 54,  sample 1


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2129]

tag: cell type

value: CD138+  cells or bone marrow with CD138+ over 75%

value: multiple myeloma


title: PFA ependymoma, high cell density area, case 59,  sample 2


title: PFA ependymoma, high cell density area, case 59,  sample 3


title: PFA ependymoma, low cell density area, case 28,  sample 2


title: PFA ependymoma, high cell density area, case 59,  sample 1


title: Saccharomyces cerevisiae, main screen, repression library, high fluorescence fraction, round2, rep2

description:
PCR amplicons
MF_ReadCounts.txt
sample23


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2116]


title: PFA ependymoma, low cell density area, case 41,  sample 3


title: Saccharomyces cerevisiae, main screen, repression library, low fluorescence fraction, round2, rep1

description:
PCR amplicons
MF_ReadCounts.txt
sample22


title: PFA ependymoma, low cell density area, case 41,  sample 2


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2115]


title: PFA ependymoma, high cell density area, case 28,  sample 3


title: PFA ependymoma, low cell density area, case 41,  sample 1


title: Saccharomyces cerevisiae, main screen, repression library, high fluorescence fraction, round2, rep1

description:
PCR amplicons
MF_ReadCounts.txt
sample21


title: MM.1S panobinostat

source_name: MM.1S panobinostat


title: PFA ependymoma, high cell density area, case 41,  sample 2


title: Saccharomyces cerevisiae, main screen, activation library, low fluorescence fraction, round5, rep2

description:
PCR amplicons
MF_ReadCounts.txt
sample20

value: activation


title: MM.1S DMSO

source_name: MM.1S DMSO


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2108]

value: multiple myeloma relapse


title: PFA ependymoma, high cell density area, case 41,  sample 3


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2121]


title: Saccharomyces cerevisiae, main screen, activation library, high fluorescence fraction, round5, rep2

description:
PCR amplicons
MF_ReadCounts.txt
sample19


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1973]


title: PFA ependymoma, high cell density area, case 41,  sample 1


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1968]


title: PFA ependymoma, high cell density area, case 55,  sample 3


title: PFA ependymoma, low cell density area, case 55,  sample 2


title: PFA ependymoma, high cell density area, case 55,  sample 2


title: PFA ependymoma, low cell density area, case 55,  sample 3


title: PFA ependymoma, low cell density area, case 55,  sample 1


title: Saccharomyces cerevisiae, main screen, activation library, low fluorescence fraction, round5, rep1

description:
PCR amplicons
MF_ReadCounts.txt
sample18


title: Saccharomyces cerevisiae, main screen, activation library, high fluorescence fraction, round5, rep1

description:
PCR amplicons
MF_ReadCounts.txt
sample17


title: PFA ependymoma, high cell density area, case 55,  sample 1


title: Saccharomyces cerevisiae, main screen, activation library, low fluorescence fraction, round4, rep2

description:
PCR amplicons
MF_ReadCounts.txt
sample16


title: PFA ependymoma, low cell density area, case 38,  sample 2


title: PFA ependymoma, low cell density area, case 38,  sample 3


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1902]

value: MGUS


title: PFA ependymoma, low cell density area, case 38,  sample 1


title: Saccharomyces cerevisiae, main screen, activation library, high fluorescence fraction, round4, rep2

description:
PCR amplicons
MF_ReadCounts.txt
sample15


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1897]


title: PFA ependymoma, high cell density area, case 38,  sample 3


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1857]


title: Saccharomyces cerevisiae, main screen, activation library, low fluorescence fraction, round4, rep1

description:
PCR amplicons
MF_ReadCounts.txt
sample14


title: PFA ependymoma, high cell density area, case 38,  sample 2


title: Saccharomyces cerevisiae, main screen, activation library, high fluorescence fraction, round4, rep1

description:
PCR amplicons
MF_ReadCounts.txt
sample13


title: PFA ependymoma, high cell density area, case 38,  sample 1


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1926]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1404]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1394]


title: Saccharomyces cerevisiae, main screen, activation library, high fluorescence fraction, round3, rep2

description:
PCR amplicons
MF_ReadCounts.txt
sample11


title: PL_M_72420

city: Los Angeles

first: Margareta

middle: D

last: Pisarska

address: 8635 West Third Street Suite 160

department: Obstetrics and Gynecology

description:
RawCounts_124CVS-43Placenta.csv.gz
TPM_124CVS-43Placenta.csv.gz
FPKM_124CVS-43Placenta.csv.gz
DESeq2_First-versus-Third-Trimester_sexAdjusted_124CVS-43PL.csv.gz

data_processing:
Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20 (Illumina, San Diego, California).
Sequencing reads were aligned to the human genome using STAR v2.6.1 and RSEM v1.2.28 with default parameters, using a custom human GRCh38 transcriptome reference downloaded from GENCODEgenes.org which contained all protein coding and long non-coding RNA genes based on human GENCODE version 23 annotation.
Each gene was fitted into a negative binomial generalized linear model to compare first versus third trimester (adjusted for fetal sex). The Wald test was applied to get pvalues and the Benjamini-Hochberg false discovery rate procedure was applied to get adjusted pvalues (padj) or FDR values. Differential expression analysis was performed for the full cohort (124 first trimeter samples and 43 third trimester samples) as well as a sub-cohort of 23 subjects (46 samples) with matched data. Fetal sex differences were also analyzed at each trimester.
Assembly: GENCODE release 23
Supplementary files format and content: "RawCounts_124CVS-43Placenta.csv.gz" is a matrix of GENCODE/Ensembl Gene IDs with gene symbols (rows) and sample titles (columns). Values are raw sequencing counts which were used as input for DESeq2 differential expression analysis. Gene ID information is from the GENCODE human genome annotations.
Supplementary files format and content: "TPM_124CVS-43Placenta.csv.gz" is a matrix of GENCODE/Ensembl Gene IDs with gene symbols (rows) and sample names (columns). Values are transcripts per million which are useful to rank gene expression.
Supplementary files format and content: "FPKM_124CVS-43Placenta.csv.gz" is a matrix of GENCODE/Ensembl Gene IDs with gene symbols (rows) and sample names (columns). Values are fragments per million (FPKMs) which are useful to rank gene expression.
Supplementary files format and content: "DESeq2_First-versus-Third-Trimester_sexAdjusted_124CVS-43PL.csv.gz" is the differential expression analysis results spreadsheet comparing human placenta at first versus third trimester, adjusted for fetal sex. Individual sample columns at the end of the file are counts normalized by sequencing depth but not by gene length, which DESeq2 refers to as "baseMeans" or "normalized counts". Column descriptions are above the header row, describing the data source ("biomaRt" refers to Ensembl.org's BioMart server accessed through bioconductor package biomaRt, "DESeq2" means it is output from the DESeq2 analysis, etc).

molecule: polyA RNA

source_name: Placenta: fetal surface at delivery

growth_protocol: Singleton human pregnancies conceived without fertility treatment ("spontaneous" or "unassisted" pregnancy). Chorionic villus sampling confirmed normal karyotype for all subjects, including those without tissue collected at first trimester. All pregnancies resulted in live births, including those without tissue collected at delivery.

extract_protocol:
Placenta tissue was submerged in RNAlater RNA stabilization reagent (QIAGEN) and stored at -80C until further processing. Tissue was thawed on ice and homogenized using sonication and/or by passing tissue through needles, then total RNA was isolated using the AllPrep DNA/RNA/miRNA Universal kit (QIAGEN). Polyadenylated RNA was selected during the library preparation process.
For library preparation, 1 ug of the total RNA elution was used with the Illumina TruSeq Stranded mRNA library preparation kit (Illumina), with polyA mRNA selection then cDNA synthesis using SuperScript II reverse transcriptase (Invitrogen) and random primers. The cDNA was converted into double stranded DNA and PCR-amplified, then purified with Agencourt AMPure XP beads (Beckman Coulter). Sample libraries were multiplexed and sequenced on a NovaSeq 6000 platform (Illumina) using 75bp single-end mRNA-sequencing, with average 30 million reads per sample.

treatment_protocol: Fresh placenta tissue collected after chorionic villus sampling or delivery, submerged in RNAlater RNA stabilizing reagent (QIAGEN), and stored at -80C to preserve RNA quality until further processing.

tag: subject id

value: Placenta:fetal surface at delivery

tag: sample collection_method

value: Biopsy after delivery

tag: sample trimester

value: Third trimester

tag: sample gestational_age_in_days

tag: fetal sex

value: Male

tag: fetal race

value: CaucasianAsian

tag: fetal ethnicity

value: NonHispanic

tag: mode of_conception

value: Spontaneous/unassisted

tag: rna integrity_number

tag: sequencing plate_name

tag: matched sample


title: PL_F_72439

value: Female

value: Caucasian

value: Hispanic


title: PL_F_72426


title: PL_F_72475


title: Saccharomyces cerevisiae, main screen, activation library, low fluorescence fraction, round3, rep1

description:
PCR amplicons
MF_ReadCounts.txt
sample10

tag: cell line

value: Ethanol red

tag: screen

value: main

tag: library

value: low


title: PL_M_72416


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1908]

value: CD138+  cells or bone marrow with CD138+ over 75%

tag: subject status

value: multiple myeloma


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2113]


title: PL_F_72424

tag: tissue


title: PL_M_72408


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1887]

tag: cell type


title: Saccharomyces cerevisiae, main screen, repression library, low fluorescence fraction, round1, rep2

description:
PCR amplicons
MF_ReadCounts.txt
sample8

value: repression

tag: fluorescence fraction

tag: round

tag: replicate


title: Saccharomyces cerevisiae, main screen, activation library, high fluorescence fraction, round3, rep1

description:
PCR amplicons
MF_ReadCounts.txt
sample9

value: activation

value: high


title: PL_M_72388

tag: subject id

value: Placenta:fetal surface at delivery

tag: sample collection_method

value: Biopsy after delivery

tag: sample trimester

tag: sample gestational_age_in_days


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1907]

value: MGUS


title: PL_F_72402

value: Third trimester

tag: fetal sex

tag: fetal race

value: Multiracial

tag: fetal ethnicity

tag: mode of_conception


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2147]


title: PL_F_72387

value: NonHispanic

value: Spontaneous/unassisted

tag: rna integrity_number

tag: sequencing plate_name

tag: matched sample


title: No template control

tag: cell density_of_sample_region


title: Saccharomyces cerevisiae, main screen, repression library, high fluorescence fraction, round1, rep2

description:
PCR amplicons
MF_ReadCounts.txt
sample7

tag: cell line

tag: screen

tag: library


title: PL_M_72373

tag: tissue

value: Male


title: Saccharomyces cerevisiae, main screen, activation library, low fluorescence fraction, round3, rep2

description:
PCR amplicons
MF_ReadCounts.txt
sample12

tag: fluorescence fraction

tag: round

tag: replicate


title: PL_F_72375

tag: subject id

tag: sample collection_method

tag: sample trimester

value: Female

value: Caucasian


title: Saccharomyces cerevisiae, main screen, repression library, low fluorescence fraction, round1, rep1

description:
PCR amplicons
MF_ReadCounts.txt
sample6

value: Ethanol red

value: main


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2143]

tag: cell type

value: CD138+  cells or bone marrow with CD138+ over 75%

tag: subject status


title: PL_F_72367

tag: sample gestational_age_in_days

tag: fetal sex

tag: fetal race

tag: fetal ethnicity

tag: mode of_conception


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2142]

value: multiple myeloma


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2136]


title: PL_F_72391

value: Hispanic

tag: rna integrity_number

tag: sequencing plate_name

tag: matched sample


title: PL_M_72358

tag: tissue


title: PL_F_72359

value: CaucasianAsian


title: PL_M_72361


title: PL_M_72351


title: PL_M_72350


title: PL_M_72344

value: AfricanAmerican


title: Saccharomyces cerevisiae, main screen, activation library, low fluorescence fraction, round2, rep1

description:
PCR amplicons
MF_ReadCounts.txt
sample2

tag: cell line

tag: screen

tag: library

value: activation

tag: fluorescence fraction

value: low


title: PL_M_72343

tag: subject id

value: Placenta:fetal surface at delivery

tag: sample collection_method

value: Biopsy after delivery


title: PL_F_72340

tag: sample trimester

value: Third trimester


title: PL_M_72355

value: NonHispanic


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2117]

tag: cell type

tag: subject status


title: PL_M_72334

tag: sample gestational_age_in_days

tag: fetal sex

value: BiracialOther

value: Spontaneous/unassisted


title: Saccharomyces cerevisiae, main screen, activation library, high fluorescence fraction, round2, rep1

description:
PCR amplicons
MF_ReadCounts.txt
sample1

value: high

tag: round

tag: replicate


title: PL_M_72319

value: Male

tag: fetal race

value: Caucasian

tag: fetal ethnicity

tag: mode of_conception

tag: rna integrity_number


title: PL_M_72330

tag: tissue

value: Multiracial

tag: sequencing plate_name

tag: matched sample


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2114]

value: CD138+  cells or bone marrow with CD138+ over 75%


title: Saccharomyces cerevisiae, early screen, activation library, high fluorescence fraction, round1, rep2

description:
PCR amplicons
LC_MF_ReadCounts.txt
LC_sample4

tag: cell line

value: Ethanol red

tag: screen

value: early

tag: library

tag: fluorescence fraction


title: PL_M_72316

tag: subject id

tag: sample collection_method

tag: sample trimester


title: Saccharomyces cerevisiae, main screen, repression library, high fluorescence fraction, round1, rep1

description:
PCR amplicons
MF_ReadCounts.txt
sample5

value: main

value: repression


title: PL_F_72314

tag: sample gestational_age_in_days

tag: fetal sex

value: Female

value: CaucasianAsian


title: Saccharomyces cerevisiae, early screen, activation library, low fluorescence fraction, round1, rep2

description:
PCR amplicons
LC_MF_ReadCounts.txt
LC_sample3

value: activation

value: low

tag: round

tag: replicate


title: PL_M_72311

value: Placenta:fetal surface at delivery

value: Biopsy after delivery

value: Third trimester

tag: fetal race

tag: fetal ethnicity


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2128]

tag: cell type

tag: subject status

value: multiple myeloma


title: Saccharomyces cerevisiae, main screen, activation library, low fluorescence fraction, round2, rep2

description:
PCR amplicons
MF_ReadCounts.txt
sample4


title: Saccharomyces cerevisiae, early screen, activation library, high fluorescence fraction, round1, rep1

description:
PCR amplicons
LC_MF_ReadCounts.txt
LC_sample2

value: high


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1983]


title: PL_M_72306

tag: tissue

value: Male

value: Hispanic

tag: mode of_conception

value: Spontaneous/unassisted

tag: rna integrity_number

tag: sequencing plate_name


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2127]

value: CD138+  cells or bone marrow with CD138+ over 75%


title: Saccharomyces cerevisiae, early screen, activation library, low fluorescence fraction, round1, rep1

description:
PCR amplicons
LC_MF_ReadCounts.txt
LC_sample1

tag: cell line

value: Ethanol red

tag: screen

tag: library


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1979]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1981]


title: Toxicity, day 9 bio rep 4

city: Copenhagen

first: Kristoffer

address: Ole Maaløes Vej 5

department: Biology

country: Denmark

institute: University of Copenhagen

data_processing:
Barcodes of 18 bases were mapped to variants using exact match.
Normalized populations per FACS gate were used to calculate a protein stability index (PSI) and that was finally normalized to an abundance score where 1 is wildtype and 0 the median PSI of nonsence variants
Toxicity scores were calculated as the slope estimated by a linear regression of the variant frequency at each time point normalized to wildtype
A variant-barcode map was made from long-read sequencing of the plasmid before transfection. Reads were aligned to the synthetic barcode-gfp-ASPA construct using BWA software
Assembly: NA
Supplementary files format and content: abundance_aspa.csv and toxicity_aspa.csv: Colon separated file format contaning abundance and toxicity scores
Supplementary files format and content: barcode_map.csv.gz: Colon separated file format containing the map between barcodes and protein variants
Library strategy: VAMP-seq

organism: synthetic construct

extract_protocol:
Genomic DNA extraction was performed using Qiagen DNeasy blood & tissue kit (Cat. No. 69506)
A site-saturation library of codon optimized human ASPA were custom synthesized and barcoded. Constructs of ASPA variants fused to GFP and an IRES-mCherry expression control were integrated into a HEK293T landing pad cell line


title: Toxicity, day 7 bio rep 4


title: PL_M_72273

tag: subject id

tag: sample collection_method

value: Caucasian

tag: matched sample


title: PL_F_72290

tag: sample trimester

tag: sample gestational_age_in_days

tag: fetal sex


title: PL_M_72275

tag: fetal race

value: NonHispanic


title: PL_F_72298

tag: fetal ethnicity


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1976]

tag: cell type


title: PL_F_72155


title: PL_M_72268


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1971]

tag: subject status


title: PL_M_72145

tag: tissue


title: PL_F_72115

value: AfricanAmerican

tag: mode of_conception


title: Toxicity, day 5 bio rep 4


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1964]


title: Toxicity, day 0 bio rep 4


title: PL_M_71997

tag: rna integrity_number


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1963]


title: Toxicity, day 9 bio rep 3


title: Toxicity, day 7 bio rep 3


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1959]


title: PL_F_71987

value: Female

tag: sequencing plate_name


title: CVS_F_72466

source_name: Placenta: chorionic villi

value: Placenta:chorionic villi

value: Chorionic villus sampling (CVS)

value: First trimester


title: CVS_M_72416

value: CaucasianAsian


title: Toxicity, day 5 bio rep 3

tag: cell line


title: CVS_F_72402

value: Multiracial


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1899]


title: CVS_F_72387


title: Toxicity, day 0 bio rep 3


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1895]


title: PL_M_72039

value: Placenta:fetal surface at delivery

value: Biopsy after delivery

value: Third trimester


title: CVS_M_72380

value: Male


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1985]

value: multiple myeloma


title: CVS_F_72391

value: Hispanic

value: Spontaneous/unassisted


title: CVS_M_72388


title: Toxicity, day 7 bio rep 2


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1861]

value: CD138+  cells or bone marrow with CD138+ over 75%


title: CVS_M_72373


title: PL_F_72114

value: Caucasian


title: CVS_M_72361


title: CVS_M_72351

value: NonHispanic


title: Saccharomyces cerevisiae, main screen, activation library, high fluorescence fraction, round2, rep2

description:
PCR amplicons
MF_ReadCounts.txt
sample3

value: Ethanol red

tag: screen

value: main

value: activation

tag: fluorescence fraction

value: high

tag: round

tag: replicate


title: CVS_M_72350

tag: subject id

value: Placenta:chorionic villi

tag: sample collection_method

value: Chorionic villus sampling (CVS)

value: First trimester

tag: matched sample


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1938]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1823]


title: CVS_M_72341

tag: sample trimester

tag: sample gestational_age_in_days

tag: fetal sex


title: CVS_F_72340

value: Female

tag: fetal race

tag: fetal ethnicity


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1392]

tag: cell type

tag: subject status


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1898]


title: Toxicity, day 7 bio rep 1


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2148]


title: CVS_M_72308

tag: tissue

tag: mode of_conception

tag: rna integrity_number


title: Toxicity, day 5 bio rep 1

tag: cell line


title: CVS_M_72334

value: BiracialOther

tag: sequencing plate_name


title: Toxicity, day 9 bio rep 1


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2145]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2141]


title: Toxicity, day 5 bio rep 2


title: Toxicity, day 0 bio rep 1


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2140]


title: CVS_F_72290


title: CVS_M_72287


title: CVS_M_72324


title: CVS_M_72268


title: CVS_F_72298


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2132]


title: Abundance, FACS gate A rep 3 bio rep 4


title: CVS_M_72306


title: PL_M_72287

value: Placenta:fetal surface at delivery

value: Biopsy after delivery

value: Third trimester


title: CVS_M_72054

value: Male


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2135]

value: multiple myeloma


title: Abundance, FACS gate B rep 3 bio rep 4


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2133]

value: CD138+  cells or bone marrow with CD138+ over 75%


title: CVS_M_72111

value: Caucasian

value: Hispanic

value: Spontaneous/unassisted


title: Abundance, FACS gate D rep 3 bio rep 4


title: CVS_F_72098

value: NonHispanic


title: CVS_F_72069


title: CVS_F_72155

value: CaucasianAsian


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2131]


title: CVS_F_72091


title: Abundance, FACS gate D rep 2 bio rep 4


title: CVS_M_72003


title: CVS_M_72039


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2125]


title: CVS_M_71997


title: Abundance, FACS gate C rep 3 bio rep 4


title: CVS_F_72011

value: AfricanAmerican


title: Abundance, FACS gate C rep 2 bio rep 4


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2123]


title: CVS_F_72034

value: Placenta:chorionic villi


title: Abundance, FACS gate A rep 2 bio rep 4


title: CVS_M_71905

value: Chorionic villus sampling (CVS)


title: CVS_M_71895

value: First trimester


title: CVS_M_71955


title: CVS_F_71869

value: Female


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2112]


title: CVS_F_71949


title: Abundance, FACS gate D rep 1 bio rep 4


title: CVS_F_71849


title: CVS_M_71861


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2119]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2109]


title: CVS_F_71822


title: Abundance, FACS gate B rep 1 bio rep 4


title: Abundance, FACS gate A rep 1 bio rep 4


title: Abundance, FACS gate C rep 1 bio rep 4


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1988]


title: Abundance, FACS gate D rep 3 bio rep 3


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2122]


title: CVS_M_72275


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1987]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2110]


title: CVS_M_71758


title: CVS_F_71757


title: CVS_M_71756


title: CVS_F_71743


title: Abundance, FACS gate B rep 3 bio rep 3


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1986]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1982]


title: Abundance, FACS gate C rep 3 bio rep 3


title: CVS_M_71731


title: CVS_F_71707


title: CVS_F_71793


title: CVS_M_71806


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1980]


title: Abundance, FACS gate A rep 3 bio rep 3


title: CVS_M_71673


title: CVS_F_71702


title: Abundance, FACS gate D rep 2 bio rep 3


title: CVS_F_71652


title: CVS_M_71637


title: Abundance, FACS gate B rep 2 bio rep 4


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1978]


title: Abundance, FACS gate C rep 2 bio rep 3


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1977]


title: CVS_M_71624


title: CVS_F_71620


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1975]


title: CVS_M_71503


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1972]


title: CVS_M_71491


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1965]


title: CVS_F_71485


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1960]


title: CVS_F_72375


title: CVS_M_71451


title: CVS_F_71527


title: CVS_F_71579

value: Asian


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1957]


title: CVS_F_71607


title: CVS_F_72439


title: Toxicity, day 0 bio rep 2


title: CVS_F_71419


title: CVS_F_71440


title: CVS_F_71424


title: Toxicity, day 9 bio rep 2


title: CVS_M_71412


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1927]


title: CVS_F_71418


title: CVS_M_71445


title: CVS_M_71394


title: CVS_F_71369


title: CVS_F_71335


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1914]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1949]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1906]


title: CVS_M_71314


title: Abundance, FACS gate D rep 1 bio rep 3


title: Abundance, FACS gate A rep 2 bio rep 3


title: Abundance, FACS gate A rep 1 bio rep 3


title: Abundance, FACS gate B rep 1 bio rep 3


title: Abundance, FACS gate B rep 2 bio rep 3


title: Abundance, FACS gate C rep 1 bio rep 3


title: Abundance, FACS gate D rep 3 bio rep 2


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1904]

value: plasmacell leukemia


title: CVS_F_71218


title: CVS_F_71250


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1903]


title: CVS_F_71318


title: CVS_F_71203


title: CVS_M_71186


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1901]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1896]


title: CVS_F_71179


title: CVS_M_71171


title: CVS_M_71286


title: CVS_F_71146


title: Abundance, FACS gate B rep 3 bio rep 2


title: Abundance, FACS gate A rep 3 bio rep 2


title: Abundance, FACS gate C rep 3 bio rep 2


title: CVS_F_71759


title: Abundance, FACS gate C rep 2 bio rep 2


title: Abundance, FACS gate B rep 2 bio rep 2


title: Abundance, FACS gate A rep 2 bio rep 2


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1894]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1890]


title: CVS_M_72273


title: Abundance, FACS gate D rep 1 bio rep 2


title: CVS_F_71099


title: Abundance, FACS gate D rep 2 bio rep 2


title: CVS_M_71282


title: CVS_F_71104


title: CVS_M_71127


title: Abundance, FACS gate C rep 1 bio rep 2


title: Abundance, FACS gate B rep 1 bio rep 2


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1889]


title: CVS_M_71086


title: CVS_M_71038


title: Abundance, FACS gate A rep 1 bio rep 2


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1825]


title: CVS_F_71016


title: Abundance, FACS gate D rep 2 bio rep 1


title: CVS_M_71128


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1822]


title: Abundance, FACS gate C rep 2 bio rep 1


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1824]


title: Abundance, FACS gate B rep 2 bio rep 1


title: CVS_M_70956


title: CVS_F_70964


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1821]


title: Abundance, FACS gate A rep 2 bio rep 1


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1816]


title: CVS_M_70973


title: CVS_F_70965


title: CVS_F_70922


title: CVS_M_70913


title: CVS_M_70932


title: Abundance, FACS gate D rep 1 bio rep 1


title: CVS_M_70949


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1828]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1814]


title: CVS_F_71035


title: Abundance, FACS gate C rep 1 bio rep 1


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1813]


title: CVS_M_70911


title: CVS_F_71095


title: CVS_M_70906


title: CVS_M_70903

value: BiracialOther


title: CVS_M_70910


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1406]


title: CVS_M_70893


title: CVS_F_70879


title: CVS_F_70866


title: Abundance, FACS gate A rep 1 bio rep 1


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1400]


title: CVS_F_70847


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1399]


title: CVS_M_70838


title: FACS gate D rep 3 bio rep 4

data_processing:
Barcodes of 18 bases were mapped to variants using exact match. Normalized populations per FACS gate were used to calculate a protein stability index (PSI) and that was finally normalized to an abundance score where 1 is wildtype and 0 the median PSI of nonsence variants
A variant-barcode map was made from long-read sequencing of the plasmid before transfection. Reads were aligned to the synthetic barcode-gfp-parkin construct using BWA software
Assembly: NA
Supplementary files format and content: vamp_parkin.csv: Colon separated file format contaning abundance scores
Supplementary files format and content: barcode_map.csv.gz: Colon separated file format containing the map between barcodes and protein variants
Library strategy: VAMP-seq

extract_protocol:
Genomic DNA was extracted from cells using the DNeasy blood & tissue Kit (Qiagen) following the manufacturer’s protocol titled “Protocol: Purification of Total DNA from Animal Blood or Cells (Spin-Column Protocol)”
A site-saturation library of codon optimized human parkin were custom synthesized and barcoded. Constructs of PRKN variants fused to GFP and an IRES-mCherry expression control were integrated into a HEK293T landing pad cell line


title: FACS gate C rep 3 bio rep 4


title: CVS_M_70830


title: CVS_F_70807


title: FACS gate B rep 3 bio rep 4


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1397]


title: CVS_F_70805


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1395]


title: FACS gate A rep 3 bio rep 4


title: CVS_M_70801


title: CVS_M_70784


title: CVS_M_70774


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1387]


title: CVS_M_70747


title: CVS_F_70738


title: FACS gate D rep 2 bio rep 4


title: FACS gate C rep 2 bio rep 4


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1386]


title: Abundance, FACS gate B rep 1 bio rep 1


title: CVS_F_70710


title: CVS_M_70707


title: CVS_F_70696


title: CVS_M_70705


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1377]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1383]


title: FACS gate A rep 2 bio rep 4


title: FACS gate B rep 2 bio rep 4


title: FACS gate D rep 1 bio rep 4


title: FACS gate C rep 1 bio rep 4


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1306]


title: FACS gate B rep 1 bio rep 4


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM2130]


title: mRNA single end RNAseq of primary CD138+ multiple myelom cells or bone marrow with CD138+ content over 75% [MM1317]


title: IMR90 cells, ER-RAS 3 days 4OHT, Replicate C

city: Montréal

first: Gerardo

last: Ferbeyre

state: Québec

address: 900 rue Saint-Denis

country: Canada

institute: Centre de recherche du CHUM (CRCHUM)

data_processing:
Trimmomatic version 0.35 - STAR version 2.5.1b - DESeq2 version 1.18.1
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35.
Trimmed sequences reads were mapped to GRCh38 using STAR version 2.5.1b.
Gene expressions were obtained as readcount directly from STAR and normalization of gene readcounts was performed using DESeq2 version 1.18.1.
Assembly: GRCh38/hg38
Supplementary files format and content: Excel file include normalize gene readcounts for all samples.

growth_protocol: IMR90 cells were maintained in DMEM supplemented with 10% premium fetal bovine serum (FBS), 1% penicillin/streptomycin sulfate and 2 mM L-glutamine in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were harvested in TRIzol at the end of treatment and RNA was harvested according to the manufacturer’s instructions. Once at the precipitation step, RNA samples were loaded on a RNeasy column (Qiagen Mini Kit #74106). 1000 ng of total RNA was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using the KAPA mRNAseq Hyperprep kit (KAPA, Cat no. KK8581) following manufacturer's protocols.

treatment_protocol: Uncommitted control cells were treated with for 30h and committed cells were treated for 72h with 100nM of 4OHT.

value: Normal Human Diploid Fibroblasts

tag: genotype

value: ER-RAS

tag: treatment

tag: time

value: Day 3


title: FACS gate D rep 3 bio rep 3


title: IMR90 cells, ER-RAS 3 days 4OHT, Replicate B


title: FACS gate C rep 3 bio rep 3


title: FACS gate A rep 1 bio rep 4


title: IMR90 cells, ER-RAS 1.5 days 4OHT, Replicate C

value: Day 1.5


title: FACS gate B rep 3 bio rep 3


title: IMR90 cells, ER-RAS 1.5 days 4OHT, Replicate A


title: IMR90 cells, ER-RAS 1.5 days 4OHT, Replicate B


title: FACS gate B rep 2 bio rep 3


title: FACS gate A rep 3 bio rep 3


title: FACS gate D rep 2 bio rep 3


title: FACS gate C rep 2 bio rep 3