title: MDA-MB-231 non-resistant PARP1 ChIP-Seq

city: Lodz

first: Magdalena

last: Strachowska

address: Pomorska 141/143

institute: University of Lodz

description: Library name: P1MW

data_processing:
In silico stage of the study, which aimed to identify the transcription factor playing a crucial role in PARP1-dependent expression of ABC transporters, was initiated by analyzing the results obtained by the ChIP-Seq method using the UseGalaxy platform (RRID:SCR_006281). First, after removing the adapters, the quality of the obtained reads was checked. Then the reads were mapped to the human hg19 genome using the Bowtie 2 tool. In the next step, PARP1-rich regions were selected via the MACS2 peak calling tool at p-value = 0.001. Next, the bedtools intersect intervals tool found common regions for PARP1-enriched narrow peak sequences and regions occurring within ± 170,000 from the transcription initiation site (TSS) of PARP1-dependent genes encoding ABCC3, ABCC4 and ABCC5 transporters. The XSTREME tool from the MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) allowed the generation of a list of transcription factors for the identified motifs
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
The chromatin immunoprecipitation (ChIP) method was performed according to the published protocol included in the publication by Wisnik et al.. MDA-MB-231 wild-type and doxorubicin-resistant cell lines were seeded at a density of 10 million cells per 150 mm diameter dish. After 24 hours, the cells were fixed with 1% formaldehyde, and after a 10-minute incubation, the process was arrested with 125 mM glycine and cell were rinsed 3-times with cold PBS. After incubation with appropriate buffers containing PIC and PMSF inhibitors, cells were resuspended in lysis buffers. Isolated chromatin was sonicated using a Diagenode Bioruptor sonicator, followed by centrifugation for 10 min at 10,000 rpm at 4°C. Conjugated antibodies with magnetic beads were added to the prepared samples. After a 24-hour incubation at 4°C, the immunoprecipitated chromatin was rinsed in purification buffers, which was followed by an overnight desquamation process at 65°C. DNA was isolated by phenol:chloroform:isoamyl (PCI) alcohol extraction.
For ChIP-Seq involving PARP1 the library for sequencing was constructed using the NEBNext® Ultra™ DNA Library Prep Kit with Sample Purification Beads for Illumina® according to the protocol provided by the manufacturer, and sequenced using the NextSeq 500/550 High Output Kit v2.5 (75 Cycles) at the Department of Clinical Genetics, University of Medical Sciences, Lodz, Poland.

value: doxorubicin-resistant MDA-MB-231


title: Sample-2 Day-4 LNP-RNA

status: Public on Dec 04 2025

type: SRA

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

description: Library name: p22167-s032_RKr19-D4

library_source: transcriptomic

data_processing:
Sequencing data was aligned to Mmul10 Ensembl release 100 using STAR 2.7.3a. Transcript abundance estimates were calculated using the STAR '--quantMode GeneCounts'.
Assembly: Mmul10 Ensembl release 100
Supplementary files format and content: Tab separated reads-per-gene table from STAR --quantMode, with Gene Symbols in first column and counts for Unstranded, Sense stranded and Anti-sense stranded interpretations of the alignments. Library prep was Unstranded

molecule: total RNA

organism: Macaca mulatta

source_name: Bood

extract_protocol:
Blood was collected into PAXgene Blood RNA tubes (BD Biosciences) and the RNA was extracted using the MagMAX for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes (ThermoFisher Scientific).
RNA quality was assessed using a TapeStation 4200 (Agilent) and then one microgram of total RNA was subjected to globin transcript depletion using the GLOBINclear Kit, human (ThermoFisher Scientific). Ten nanograms of the globin-depleted RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer's instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Nextera XT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on a TapeStation 4200 (Agilent), pooled at equimolar concentrations, and sequenced with PE100 reads on an Illumina NovaSeq 6000

tag: tissue

value: Bood

tag: Sex

value: Male

tag: treatment

value: LNP-RNA

tag: timepoint

value: Day 4


title: Δkmt6a, ChIP-seq H3K27me3, biol rep 2

city: Jena

first: Tongta

last: Sae-Ong

address: Adolf-Reichwein-Straße 23

department: Microbiome Dynamics

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (Leibniz-HKI)

library_source: genomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore v.0.6.7 (parameters -- quality: 20, phread33, stringency: 1)
Trimmed sequence reads were mapped to Fusarium oxysporum f. sp. lycopersici (Fol) using Novoalign V3.09.00 (parameters -k -c 20)
For RNA-seq: Reads were counted per feature using Rsubread’s featureCounts v.1.6.0
For RNA-seq: Read counts were normalized by the “Median by-Ratio Normalization (MRN)” method from EBSeq
For ChIP-seq: Reads were normalized using bamCoverage deeptools v.3.5.1 (parameters --normalizeUsing RPGC --effectiveGenomeSize 56213053 --binSize 10 --extendReads 150 --smoothLength 150 –centerReads)
For ChIP-seq: Means of all replicates were calculated and combined to one output file by using WiggleTools 1.2.11
For ChIP-seq: Peaks from each mean file were called by using Homer v.4.11 (parameters -style histone -region -size 500 -minDist 1000 -C 0)
Assembly: UvA_Fol4287 (GCA_001703175.2)
Supplementary files format and content: An excel file includes a matrix of raw read count values for every sample (RNAseq_raw_counts.xls)
Supplementary files format and content: Peak file format from Homer contains all identified peaks for every genotype

molecule: genomic DNA

organism: Fusarium oxysporum f. sp. lycopersici

source_name: Δkmt6a, ChIP-seq H3K27me3

extract_protocol:
RNA-seq: isolation of total RNA using Trizol reagent according to the manufacturer's instructions. ChIP-seq: cross-linking, antibody hybridization, de-crosslinking and purification of gDNA as previously described (Janevska et al., 2018, Genetics 208: 153-171)
PolyA enrichment for RNA-seq (library preparation and sequencing at the University of Amsterdam, Netherlands), ChIP-seq library preparation and sequencing by CRG Barcelona (Spain)

tag: cell line

tag: cell type

value: Vegetative mycelium

tag: genotype


title: MDA-MB-231 resistant to doxorubicin PARP1 ChIP-Seq

middle: Alicja

country: Poland

description: Library name: P1MD

organism: Homo sapiens

growth_protocol: For the first five passages, the MDA-MB-231 triple-negative breast cancer line was cultured in L15 medium with supplementation of 15% FBS, penicillin-streptomycin antibiotics (sequentially 50 U/mL and 50 µg/mL) without CO2 (as recommended by the manufacturer Sigma-Aldrich). Then, over the next two weeks, the cells were adapted to DMEM medium with 10% bovine serum FBS, including the antibiotics penicillin-streptomycin (successively 50 U/mL and 50 µg/mL) and cultured in an atmosphere of 5% CO2.

treatment_protocol: Doxorubicin at a concentration of 1 µM was added to proliferating MDA-MB-231 cells. Cells were treated with selected anthracycline for 48 h every 4 weeks for a total number of 6 cycles in single doses, bearing in mind recovery of the cells to a normal proliferative process. Then, after 48 hours, the drug was removed from the culture, and the cells were cultured in DMEM medium without the addition of doxorubicin until the next treatment cycle.


title: 688M PDA cells, H3K36me2, shKdm8-1, hypoxia, replicate 1

city: New Brunswick

first: Shin-Heng

last: Chiou

state: NJ

address: 195 Little Albany St, Room 3001

department: Medicine

institute: Rutgers Cancer Institute of New Jersey

description: Library name: Sample 21

data_processing:
ChIP-Seq reads that passed the QC process were aligned to a mm39 genome build using bowtie2 (v2.4.1). Bam files were filtered for reads mapped to blacklisted regions and duplicated reads. Peaks were called using MACS3 (v3.0.0a6) with mapped bam files (--nomodel --broad --nolambda --keep-dup all -p 0.01 -B --SPMR) and only reads with low false discovery rate (qValue > 5) were included in the analysis.
Assembly: mm39
Supplementary files format and content: BigWig

organism: Mus musculus

source_name: Pancreatic

growth_protocol: PDA 688M cells expressing the control or Kdm8-targeting shRNAs (shKdm8_1 and shKdm8_2) were maintained in DMEM media with 10% FBS and antibiotics in humidified 5% CO2 at 37C

extract_protocol:
Briefly, 2.5x10^7-1x10^8 688M cells were cultured for each ChIP. To crosslink, formaldehyde solution was directly added to cell culture media to a final concentration of 1% for 10 min, followed by quenching with 125 mM glycine solution. Fixed cells were rinsed twice in ice-cold PBS and lysed in ice-cold lysis buffer (50mM HEPES-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, with protease inhibitor cocktail). Lysates were transferred to a 1.5 ml TPX tube (Diagenode) and sonicated using Bioruptor (Diagenode) three times of 10 min (output level: high, interval: 0.5). An aliquot (50 μl) of the lysates was reserved for QC and input library. For immunoprecipitation, 4mg of ChIP-grade antibodies against H3K36me2 (ab9049, abcam) or H3K27me3 (ab192985, abcam) were added to the lysate (containing ~50μg of sheared gDNA) and rotated overnight at 4°C, followed by an incubation with 25 μl of Protein A Dynabeads (Life Technology) for 2 hours at 4°C. The beads were washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate) prior to elution and reverse crosslink through an incubation with 400 μl of digestion buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65°C for 2 hours with agitation every 30 min. Eluted DNA samples were purified by organic extraction and ethanol precipitation.
DNA libraries were prepared using KAPA Hyperprep Kit (Roche) and sequenced on the Illumina Nova-seq X platform.

treatment_protocol: PDA 688M cells were either cultured in normoxia (atmospheric O2) or hypoxia (<0.5% O2) for 48 hours prior to chromatin extraction.

value: Pancreatic

value: pancreatic ductal adenocarcinoma cells

value: hypoxia

tag: batch


title: Δkmt6a, ChIP-seq H3K27me3, biol rep 1


title: 688M PDA cells, H3K36me2, shKdm8-2, hypoxia, replicate 2

description: Library name: Sample 24


title: RevSiUnR2

city: Springfield

first: Yahaira

last: Bermudez

state: MA

address: 15 Oakhurst street

department: Microbiology

institute: University of Massachusetts, Amherst

description:
Library name: Revertant vIL-6 and SiIL-6 UnReactivated Replicate 2
The vIL-6 revertant (vIL-6-REV) restores vIL-6 protein expression by reverting the vIL-6-STOP mutations back to the wild-type sequence using BAC recombination. Not reactivated

data_processing:
Using the Galaxy Server (Galaxy Version 25.0) all processing was done using default parameters, reads wre aligned to human genome (hg38) using HISAT2
After alignment transcripts were assembled and differential expression analysis were performed using FeatureCounts and DeSeq2. Data normalization was acquired using Galaxy DeSeq2 default parameters.
Analysis was performed between latent and lytic Revertant vIL-6 (WT) and Delta vIL-6 null iSLK cells with either knockdown of IL-6 or scramble control
Assembly: UCSC Human Genome Hg38
Supplementary files format and content: Excel Sheets, tabular data with gene ID, log2(fold_change), p_value, and q_value, additional calulcations for the -log10(p_value)

source_name: renal

growth_protocol: Human iSLK epithelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol Reagent and RNA was harvested following manufacturer's protocol
RNA libraries were prepared using NextSeq500 Mid-150 cycle kit by genomic resources lab at University of Massachusetts Amherst

treatment_protocol: Samples were treated either with scramble siRNA (control) or siRNA targeting IL-6 for knockdown, then viral lytic reactivation was induced with 1ul/ml doxycycline and Sodium Butyrate or left in a Latent state.  Samples were collected 48hrs after lytic reactivation (Latent samples were collected at same time as first group of lytic replicates)

value: renal

value: epithelial

value: vIL-6 WT and Knockdown IL-10

value: si-RNA targeting IL-6 Unreactivated (Latent)


title: Sample-10 Day-2 sam-RNA

description: Library name: p22167-s030_RZm19-D2

value: sam-RNA

value: Day 2


title: Δash1, ChIP-seq H3K27me3, biol rep 2

source_name: Δash1, ChIP-seq H3K27me3


title: Δash1, ChIP-seq H3K27me3, biol rep 1


title: RevSiUnR3

description:
Library name: Revertant vIL-6 and SiIL-6 UnReactivated Replicate 3
The vIL-6 revertant (vIL-6-REV) restores vIL-6 protein expression by reverting the vIL-6-STOP mutations back to the wild-type sequence using BAC recombination. Not reactivated

value: vIL-6 WT and Knockdown IL-11


title: Sample-9 Day-2 sam-RNA

description: Library name: p22167-s029_RPm19-D2


title: 688M PDA cells, H3K36me2, shGFP, hypoxia, replicate 2

description: Library name: Sample 20


title: 688M PDA cells, H3K36me2, shGFP, hypoxia, replicate 1

description: Library name: Sample 19


title: RevSiUnR1

description:
Library name: Revertant vIL-6 and SiIL-6 UnReactivated Replicate 1
The vIL-6 revertant (vIL-6-REV) restores vIL-6 protein expression by reverting the vIL-6-STOP mutations back to the wild-type sequence using BAC recombination. Not reactivated

value: vIL-6 WT and Knockdown IL-9


title: WT, ChIP-seq H3K27me3, biol rep 2

source_name: WT, ChIP-seq H3K27me3

value: WT


title: RevSiReact3

description:
Library name: Revertant vIL-6 and SIL-6 Reactivated Replicate 3
The vIL-6 revertant (vIL-6-REV) restores vIL-6 protein expression by reverting the vIL-6-STOP mutations back to the wild-type sequence using BAC recombination. Viral expression is induced with addition of doxycycline and sodium butyrate for lytic reactivation.

value: vIL-6 WT and Knockdown IL-8

value: si-RNA targeting IL-6 lytic reactivated


title: Sample-8 Day-2 sam-RNA

description: Library name: p22167-s028_RKf19-D2

value: Bood

value: Male


title: RevSiReact2

description:
Library name: Revertant vIL-6 and SIL-6 Reactivated Replicate 2
The vIL-6 revertant (vIL-6-REV) restores vIL-6 protein expression by reverting the vIL-6-STOP mutations back to the wild-type sequence using BAC recombination. Viral expression is induced with addition of doxycycline and sodium butyrate for lytic reactivation.

value: vIL-6 WT and Knockdown IL-7


title: Sample-7 Day-2 sam-RNA

description: Library name: p22167-s027_RFg19-D2


title: Δkmt6a, ChIP-seq H3K36me3, biol rep 2

source_name: Δkmt6a, ChIP-seq H3K36me3

value: Vegetative mycelium


title: RevSiReact1

description:
Library name: Revertant vIL-6 and SIL-6 Reactivated Replicate 1
The vIL-6 revertant (vIL-6-REV) restores vIL-6 protein expression by reverting the vIL-6-STOP mutations back to the wild-type sequence using BAC recombination. Viral expression is induced with addition of doxycycline and sodium butyrate for lytic reactivation.

value: vIL-6 WT and Knockdown IL-6


title: Sample-6 Day-2 sam-RNA

description: Library name: p22167-s026_RAt19-D2


title: 688M PDA cells, H3K36me2, shKdm8-1, normoxia, replicate 2

description: Library name: Sample 16

value: Pancreatic

value: pancreatic ductal adenocarcinoma cells

value: normoxia


title: 688M PDA cells, H3K36me2, shKdm8-2, normoxia, replicate 1

description: Library name: Sample 17


title: Sample-4 Day-2 LNP-RNA

description: Library name: p22167-s024_RKn19-D2

value: LNP-RNA


title: Δash1, ChIP-seq H3K36me3, biol rep 2

source_name: Δash1, ChIP-seq H3K36me3


title: Δkmt6a, ChIP-seq H3K36me3, biol rep 1


title: RevScramUnR3

description:
Library name: Revertant vIL-6 Scramble Unreactivated Replicate 3
The vIL-6 revertant (vIL-6-REV) restores vIL-6 protein expression by reverting the vIL-6-STOP mutations back to the wild-type sequence using BAC recombination. Not reactivated

value: renal

value: epithelial

value: vIL-6 WT

value: si-RNA scramble control  Unreactivated (Latent)


title: Δash1, ChIP-seq H3K36me3, biol rep 1


title: 688M PDA cells, H3K36me2, shKdm8-1, normoxia, replicate 1

description: Library name: Sample 15


title: Sample-5 Day-2 LNP-RNA

description: Library name: p22167-s025_ROj19-D2

value: Day 2


title: 688M PDA cells, H3K36me2, shGFP, normoxia, replicate 2

description: Library name: Sample 14


title: Sample-3 Day-2 LNP-RNA

description: Library name: p22167-s023_RKd19-D2


title: 688M PDA cells, H3K36me2, shGFP, normoxia, replicate 1

description: Library name: Sample 13


title: RevScramUnR1

description:
Library name: Revertant vIL-6 Scramble Unreactivated Replicate 1
The vIL-6 revertant (vIL-6-REV) restores vIL-6 protein expression by reverting the vIL-6-STOP mutations back to the wild-type sequence using BAC recombination. Not reactivated


title: WT, ChIP-seq H3K36me3, biol rep 2

source_name: WT, ChIP-seq H3K36me3

value: WT


title: 688M PDA cells, H3K36me2, shKdm8-2, normoxia, replicate 2

description: Library name: Sample 18


title: WT, ChIP-seq H3K36me3, biol rep 1


title: Sample-2 Day-2 LNP-RNA

description: Library name: p22167-s022_RKr19-D2


title: RevScramReact3

description:
Library name: Revertant vIL-6 Scramble Reactivated Replicate 3
The vIL-6 revertant (vIL-6-REV) restores vIL-6 protein expression by reverting the vIL-6-STOP mutations back to the wild-type sequence using BAC recombination. Viral expression is induced with addition of doxycycline and sodium butyrate for lytic reactivation.

value: si-RNA scramble control lytic reactivated


title: WT, ChIP-seq H3K27me3, biol rep 1


title: RevScramReact2

description:
Library name: Revertant vIL-6 Scramble Reactivated Replicate 2
The vIL-6 revertant (vIL-6-REV) restores vIL-6 protein expression by reverting the vIL-6-STOP mutations back to the wild-type sequence using BAC recombination. Viral expression is induced with addition of doxycycline and sodium butyrate for lytic reactivation.


title: 688M PDA cells, H3K27me3, shKdm8-2, hypoxia, replicate 1

description: Library name: Sample 11

value: hypoxia


title: Sample-1 Day-2 LNP-RNA

description: Library name: p22167-s021_RCl19-D2

value: Bood


title: RevScramUnR2

description:
Library name: Revertant vIL-6 Scramble Unreactivated Replicate 2
The vIL-6 revertant (vIL-6-REV) restores vIL-6 protein expression by reverting the vIL-6-STOP mutations back to the wild-type sequence using BAC recombination. Not reactivated


title: RevScramReact1

description:
Library name: Revertant vIL-6 Scramble Reactivated Replicate 1
The vIL-6 revertant (vIL-6-REV) restores vIL-6 protein expression by reverting the vIL-6-STOP mutations back to the wild-type sequence using BAC recombination. Viral expression is induced with addition of doxycycline and sodium butyrate for lytic reactivation.


title: Δkmt6a, RNA-seq, biol rep 4 [S12]

description: Sample S12

source_name: Δkmt6a, RNA-seq


title: Δkmt6a, RNA-seq, biol rep 3 [S11]

description: Sample S11


title: Sample-10 Day-1 sam-RNA

description: Library name: p22167-s020_RZm19-D1

value: Male

value: sam-RNA

value: Day 1


title: DeltaSiUnR3

description:
Library name: Delta vIL-6 and SiIL-6 Unreactivated Replicate 3
The vIL-6-STOP virus lacks vIL-6 protein expression due to the addition of stop codons and mutated start codons in the vIL-6 open reading frame within the iSLK BAC16 genome. Not reactivated

value: vIL-6 null and Knockdown IL-11

value: si-RNA targeting IL-6 unreactivated (Latent)


title: Δkmt6a, RNA-seq, biol rep 2 [S10]

description: Sample S10

value: Vegetative mycelium


title: Δkmt6a, RNA-seq, biol rep 1 [S09]

description: Sample S09


title: Sample-9 Day-1 sam-RNA

description: Library name: p22167-s019_RPm19-D1


title: DeltaSiUnR1

description:
Library name: Delta vIL-6 and SiIL-6 Unreactivated Replicate 1
The vIL-6-STOP virus lacks vIL-6 protein expression due to the addition of stop codons and mutated start codons in the vIL-6 open reading frame within the iSLK BAC16 genome. Not reactivated

value: vIL-6 null and Knockdown IL-9


title: 688M PDA cells, H3K27me3, shGFP, hypoxia, replicate 2

description: Library name: Sample 8

value: Pancreatic

value: pancreatic ductal adenocarcinoma cells


title: DeltaSiUnR2

description:
Library name: Delta vIL-6 and SiIL-6 Unreactivated Replicate 2
The vIL-6-STOP virus lacks vIL-6 protein expression due to the addition of stop codons and mutated start codons in the vIL-6 open reading frame within the iSLK BAC16 genome. Not reactivated

value: renal

value: epithelial

value: vIL-6 null and Knockdown IL-10


title: Sample-8 Day-1 sam-RNA

description: Library name: p22167-s018_RKf19-D1


title: Sample-7 Day-1 sam-RNA

description: Library name: p22167-s017_RFg19-D1


title: 688M PDA cells, H3K27me3, shKdm8-2, hypoxia, replicate 2

description: Library name: Sample 12


title: Δash1, RNA-seq, biol rep 4 [S08]

description: Sample S08

source_name: Δash1, RNA-seq


title: 688M PDA cells, H3K27me3, shGFP, hypoxia, replicate 1

description: Library name: Sample 7


title: DeltaSiReact3

description:
Library name: Delta vIL-6 and SiIL-6 Reactivated Replicate3
The vIL-6-STOP virus lacks vIL-6 protein expression due to the addition of stop codons and mutated start codons in the vIL-6 open reading frame within the iSLK BAC16 genome. Viral expression is induced with addition of doxyxycline and sodium butyrate for lytic reactivation.

value: vIL-6 null and Knockdown IL-8

value: si-RNA targeting IL-6 lytic reactivated


title: Δash1, RNA-seq, biol rep 3 [S07]

description: Sample S07


title: Sample-6 Day-1 sam-RNA

description: Library name: p22167-s016_RAt19-D1


title: Sample-5 Day-1 LNP-RNA

description: Library name: p22167-s015_ROj19-D1

value: LNP-RNA


title: 688M PDA cells, H3K27me3, shKdm8-2, normoxia, replicate 1

description: Library name: Sample 5

value: normoxia


title: 688M PDA cells, H3K27me3, shKdm8-2, normoxia, replicate 2

description: Library name: Sample 6


title: Δash1, RNA-seq, biol rep 2 [S06]

description: Sample S06


title: 688M PDA cells, H3K27me3, shKdm8-1, hypoxia, replicate 2

description: Library name: Sample 10

value: hypoxia


title: Sample-4 Day-1 LNP-RNA

description: Library name: p22167-s014_RKn19-D1

value: Bood

value: Male


title: 688M PDA cells, H3K27me3, shKdm8-1, hypoxia, replicate 1

description: Library name: Sample 9


title: Sample-4 Day-4 LNP-RNA

description: Library name: p22167-s034_RKn19-D4

value: Day 4


title: DeltaSiReact1

description:
Library name: Delta vIL-6 and SiIL-6 Reactivated Replicate1
The vIL-6-STOP virus lacks vIL-6 protein expression due to the addition of stop codons and mutated start codons in the vIL-6 open reading frame within the iSLK BAC16 genome. Viral expression is induced with addition of doxyxycline and sodium butyrate for lytic reactivation.

value: vIL-6 null and Knockdown IL-6


title: 688M PDA cells, H3K27me3, shKdm8-1, normoxia, replicate 2

description: Library name: Sample 4


title: S4_KMS28_PE_D1_A

type: RNA

city: Salamanca

first: Ignacio

middle: J

last: Cardona-Benavides

address: Campus Miguel Unamuno

department: Hematology

country: Spain

institute: Centro de Investigación del Cáncer

description: Gene expression data from KMS28-PE (pleural exudade) cell line

hyb_protocol: Hybridization  was performed on Thermo Fisher's Clariom S Human Array as per the manufacturers protocol.

scan_protocol: Washing and scanning were performed using GeneChip System of Thermo Fisher (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: Raw data were quantile normalized, background corrected and log2 transformed with the Robust Multi-array Average (RMA) algorithm using the oligo package (v.1.60) in R (v4.3.2).  BrainArray custom CDF files (version 25 Ensembl) at  gene level were used as reference.

label: biotin

source_name: KMS28-PE, CCND1 overexpression, replicate A

label_protocol: As per manufacturer's instructions (Thermo Fisher)

growth_protocol: KMS28-BM and KMS28-PE multiple myeloma cell lines were cultured in RPMI 1640 medium supplemented with 10-20% fetal bovine serum (FBS), while HEK293T cells were grown in 10% FBS-DMEM medium. Both media were supplemented with Penicillin/Streptomycin (Gibco Life Technologies).

extract_protocol: RNA extraction was performed using the AllPrep DNA/RNA Mini Kit (Qiagen).

treatment_protocol: Gene overexpression of cyclin D1 and cyclin D2 was achieved using plasmids designed by VectorBuilder™: pLV-EGFP-MSCV>hCCND1 [NM_053056.3] and pLV-EGFP-MSCV>hCCND2 [NM_001759.4], respectively.

value: CCND1 overexpression


title: DeltaScramUnR3

description:
Library name: Delta vIL-6 Scramble Unreactivated Replicate 3
The vIL-6-STOP virus lacks vIL-6 protein expression due to the addition of stop codons and mutated start codons in the vIL-6 open reading frame within the iSLK BAC16 genome. Not reactivated

value: vIL-6 null

value: si-RNA scramble control  Unreactivated (Latent)


title: Sample-3 Day-1 LNP-RNA

description: Library name: p22167-s013_RKd19-D1

value: Day 1


title: DeltaScramUnR2

description:
Library name: Delta vIL-6 Scramble Unreactivated Replicate 2
The vIL-6-STOP virus lacks vIL-6 protein expression due to the addition of stop codons and mutated start codons in the vIL-6 open reading frame within the iSLK BAC16 genome. Not reactivated


title: 688M PDA cells, H3K27me3, shKdm8-1, normoxia, replicate 1

description: Library name: Sample 3

value: Pancreatic

value: pancreatic ductal adenocarcinoma cells


title: WT, RNA-seq, biol rep 3 [S03]

description: Sample S03

source_name: WT, RNA-seq

value: Vegetative mycelium

value: WT


title: Sample-1 Day-1 LNP-RNA

description: Library name: p22167-s011_RCl19-D1


title: WT, RNA-seq, biol rep 4 [S04]

description: Sample S04


title: DeltaScramUnR1

description:
Library name: Delta vIL-6 Scramble Unreactivated Replicate 1
The vIL-6-STOP virus lacks vIL-6 protein expression due to the addition of stop codons and mutated start codons in the vIL-6 open reading frame within the iSLK BAC16 genome. Not reactivated

value: renal

value: epithelial


title: WT, RNA-seq, biol rep 2 [S02]

description: Sample S02


title: DeltaSiReact2

description:
Library name: Delta vIL-6 and SiIL-6 Reactivated Replicate2
The vIL-6-STOP virus lacks vIL-6 protein expression due to the addition of stop codons and mutated start codons in the vIL-6 open reading frame within the iSLK BAC16 genome. Viral expression is induced with addition of doxyxycline and sodium butyrate for lytic reactivation.

value: vIL-6 null and Knockdown IL-7

value: si-RNA targeting IL-6 lytic reactivated


title: DeltaScramReact3

description:
Library name: Delta vIL-6  Scramble Reacivated  Replicate 3
The vIL-6-STOP virus lacks vIL-6 protein expression due to the addition of stop codons and mutated start codons in the vIL-6 open reading frame within the iSLK BAC16 genome. Viral expression is induced with addition of doxycycline and sodium butyrate for lytic reactivation.

value: si-RNA scramble control unreactivated


title: 688M PDA cells, H3K27ac, shKdm8-2, hypoxia, replicate 2

description: Library name: Sample 12

extract_protocol:
Briefly, 2.5x10^7-1x10^8 688M cells were cultured for each ChIP. To crosslink, formaldehyde solution was directly added to cell culture media to a final concentration of 1% for 10 min, followed by quenching with 125 mM glycine solution. Fixed cells were rinsed twice in ice-cold PBS and lysed in ice-cold lysis buffer (50mM HEPES-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, with protease inhibitor cocktail). Lysates were transferred to a 1.5 ml TPX tube (Diagenode) and sonicated using Bioruptor (Diagenode) three times of 10 min (output level: high, interval: 0.5). An aliquot (50 μl) of the lysates was reserved for QC and input library. For immunoprecipitation, 4mg of ChIP-grade antibody against H3K27ac (ab4729, abcam) were added to the lysate (containing ~50μg of sheared gDNA) and rotated overnight at 4°C, followed by an incubation with 25 μl of Protein A Dynabeads (Life Technology) for 2 hours at 4°C. The beads were washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate) prior to elution and reverse crosslink through an incubation with 400 μl of digestion buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65°C for 2 hours with agitation every 30 min. Eluted DNA samples were purified by organic extraction and ethanol precipitation.
DNA libraries were prepared using KAPA Hyperprep Kit (Roche) and sequenced on the Illumina Nova-seq X platform.

value: hypoxia


title: WT, RNA-seq, biol rep 1 [S01]

description: Sample S01


title: Sample-2 Day-1 LNP-RNA

description: Library name: p22167-s012_RKr19-D1

value: Bood

value: Male

value: LNP-RNA


title: Sample-9 Day-0 sam-RNA

description: Library name: p22167-s009_RPm19-D0

value: sam-RNA

value: Day 0


title: Sample-10 Day-0 sam-RNA

description: Library name: p22167-s010_RZm19-D0


title: DeltaScramReact2

description:
Library name: Delta vIL-6  Scramble Reacivated  Replicate 2
The vIL-6-STOP virus lacks vIL-6 protein expression due to the addition of stop codons and mutated start codons in the vIL-6 open reading frame within the iSLK BAC16 genome. Viral expression is induced with addition of doxycycline and sodium butyrate for lytic reactivation.

value: vIL-6 null

value: si-RNA scramble control lytic reactivated


title: 688M PDA cells, H3K27ac, shKdm8-1, hypoxia, replicate 2

description: Library name: Sample 11

value: Pancreatic


title: S20

city: Zhuhai

first: Hongzhen

last: Tang

state: Guangdong

address: Cuijing Road, Qianshan, Xiangzhou District

country: China

institute: BioMega Spatiotemporal Pathology Research Center

hyb_protocol: Overnight (37 °C) hybridisation with 980-plex CosMx ISH probe mix

scan_protocol: Cyclic RNA imaging & Z-stack acquisition on NanoString CosMx SMI (0.34 µm pixel, 100 × objective)

data_processing: AtoMx SIP v3.0 for segmentation & molecule assignment ; downstream analysis in Python 3.8 (squidpy + scanpy 1.9.6 : PCA 50 PC, KNN, UMAP, Louvain r = 1)

molecule: polyA RNA

source_name: gastric cancer

label_protocol: not applicable — in-situ FISH, no separate molecular label

growth_protocol: primary tumour tissue

extract_protocol: Sections baked 60 °C o/n; HIER; PK; fiducials; formalin re-fix; NHS-acetate block

value: gastric cancer

tag: fov

tag: age

tag: grade

tag: stage#

tag: Stage

value: IV

tag: ln

tag: t

tag: n

tag: m


title: 688M PDA cells, H3K27me3, shGFP, normoxia, replicate 1

description: Library name: Sample 1

tag: tissue

value: pancreatic ductal adenocarcinoma cells

value: normoxia


title: 688M PDA cells, H3K27me3, shGFP, normoxia, replicate 2

description: Library name: Sample 2


title: Sample-8 Day-0 sam-RNA

description: Library name: p22167-s008_RKf19-D0

tag: Sex


title: Δash1, RNA-seq, biol rep 1 [S05]

description: Sample S05

value: Vegetative mycelium

tag: treatment


title: 688M PDA cells, H3K27ac, shGFP, hypoxia, replicate 2

description: Library name: Sample 10


title: DeltaScramReact1

description:
Library name: Delta vIL-6  Scramble Reacivated  Replicate 1
The vIL-6-STOP virus lacks vIL-6 protein expression due to the addition of stop codons and mutated start codons in the vIL-6 open reading frame within the iSLK BAC16 genome. Viral expression is induced with addition of doxycycline and sodium butyrate for lytic reactivation.

value: renal

value: epithelial


title: S4

value: IIIa


title: mRNA_60min_rep2

city: Ithaca

first: Saori

last: Uematsu

state: New York

address: 526 Campus Road, Cornell University

institute: Cornell University

description: Library name: Sample_11

data_processing:
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Assembly: GRCh39.p13
Supplementary files format and content: comma-delimited text files including read counts mapped to each transcript.

extract_protocol:
From polysome profiling samples, an aliquot of ribosome fractions representing monosome and polysome were collected followed by digestion with E. coli RNase I (Ambion, 750 U per 100 A260 units) by incubation at 4 ºC for 1 h. RNA was extracted using Trizol LS reagent (Invitrogen) followed by ethanol precipitation. The ribosome-protected mRNA fragments (RPFs) were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 25-35 nt were excised and dissolved by soaking in 400 µL RNA elution buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.1 U/µL SUPERase·In) at 4 ºC for overnight. The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. To enrich capped small RNAs, 50 μg of total cellular RNA was fractionated using the RNA Clean & Concentrator kit (Zymo research). Briefly, adjusted RNA Binding Buffer was prepared by mixing an equal volume of buffer and 100% ethanol. Total RNA sample were mixed with 2 volumes of the adjusted buffer and transferred to the column. The mix was then centrifuged at 16,000 g for 30 s, and the flow-through was collected. 1 volume of ethanol were mixed with flow-through and transferred to a new column. The mix were centrifuged at 16,000 g for 30 s, and the flow-through was discarded. The column was washed by RNA Prep Buffer and Wash buffer, and the bound RNA was eluted with 50 μl DNase/RNase-Free water.  The eluted RNAs were dephosphorylated with 50 U of CIP (NEB) in a 100 μl reaction containing 1 × rCutSmart Buffer and 0.5 U/μl SUPERase·In at 37 °C for 1 h, followed by phenol-chloroform extraction and ethanol precipitation. Three-fourths of resulting RNAs were decapped with 0.75 μl of 5 U/μl Cap-Clip Acid Pyrophosphatase (Cellscript) in 1 × Cap-Clip Acid Pyrophosphatase Buffer at 37 °C for 1 h, followed by phenol-chloroform extraction and ethanol precipitation. The remaining one-fourth RNAs were phosphorylated with 20 U of T4 PNK in a 20 μl reaction containing 0.5 U/μl SUPERase·In, 2 mM ATP and 1 × T4 PNK Buffer at 37 °C for 1 h, followed by ethanol precipitation.
10~200 ng RNAs were mixed with 10 U T4 PNK (NEB), 1 µL homemade Ezra enzyme, 5 U Poly(A) Polymerase (NEB), and 20 U SUPERase·In in Ezra buffer and incubated at 37 ºC for 30 min followed by 70 ºC for 10 min. Ligation was performed for 60 min at 25 ºC by adding a 10 µL reaction mixture (0.5 μM biotinylated 5’ end adaptor, 1 × T4 Rnl2 reaction buffer, 20 U SUPERase·In, 15% PEG8000 and 10 U T4 RNA ligase 2 truncated KQ (NEB)). The ligated RNA sample was mixed with 10 µL of pre-washed streptavidin beads (NEB) and incubated at room temperature for 10 min. After washing once with 2 × SSC, beads were re-suspended in 12 µL nuclease-free water and mixed with 8 µL cDNA synthesis mixture (5 μM reverse transcription primer, 5 × first strand buffer, 0.1 M DTT, 10 mM dNTP, SuperScript III) followed by incubation at 50 ºC for 30 min. After washing once with 2 × SSC, the cDNA was amplified by PCR using barcoded sequencing primers. PCR was performed by mixing 1 × HF buffer, 0.5 mM dNTP, 0.25 μM PCR primers and 0.025 U Phusion polymerase. PCR was carried out under the following conditions: 98 ºC, 30 s; (98 ºC, 5 s; 68 ºC, 15 s; 72 ºC, 20 s) for 14 cycles; 72 ºC, 2 min. PCR products were separated on a 8% polyacrylamide TBE gel (Invitrogen). DNA products with the expected size around 180 bp were excised and recovered from DNA elution buffer (300 mM NaCl, 1 mM EDTA). After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled and sequenced using NextSeq 500 (Illumina).

value: WT


title: mRNA_360min_rep2

description: Library name: Sample_12


title: Sample-6 Day-0 sam-RNA

description: Library name: p22167-s006_RAt19-D0

value: Bood

tag: timepoint


title: S101


title: Sample-7 Day-0 sam-RNA

description: Library name: p22167-s007_RFg19-D0

value: Male


title: S78

value: Ia


title: 688M PDA cells, H3K27ac, shKdm8-1, normoxia, replicate 2

description: Library name: Sample 8

tag: cell line


title: mRNA_0min_rep2

description: Library name: Sample_10


title: Sample-5 Day-0 LNP-RNA

description: Library name: p22167-s005_ROj19-D0

value: LNP-RNA


title: S84


title: 688M PDA cells, H3K27ac, shGFP, normoxia, replicate 2

description: Library name: Sample 7

tag: cell type


title: S103


title: Sample-3 Day-0 LNP-RNA

description: Library name: p22167-s003_RKd19-D0

value: Day 0


title: RPF_360min_rep2

description: Library name: Sample_9

library_source: other

data_processing:
The 5’ and 3’ adapters of the reads were trimmed by Cutadapt (version 2.8) using the following parameters:  -a “A{10}” -m 15 –max-n=0.1. The trimmed reads with length shorter than 15 nucleotides were excluded from the analysis.
The trimmed reads were first aligned to rRNAs using Bowtie (version 1.2.3) with the following parameters: -v 0 –norc.
The reads unaligned to rRNAs were then mapped to the custom mouse transcriptome using STAR (version 2.7.10a) with default parameters. To avoid ambiguity, reads mapped to multiple positions or with >2 mismatches were disregarded for further analysis.
Assembly: GRCh39.p13
Supplementary files format and content: comma-delimited text files including read counts mapped to each transcript.
Library strategy: Ribo-Seq

molecule: other

tag: genotype


title: RPF_0min_rep2

description: Library name: Sample_7


title: Sample-2 Day-0 LNP-RNA

description: Library name: p22167-s002_RKr19-D0


title: 688M PDA cells, H3K27ac, shKdm8-2, hypoxia, replicate 1

description: Library name: Sample 6

value: hypoxia

tag: batch


title: mRNA_60min_rep1

description: Library name: Sample_5


title: Light drinker 3, post-induction

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

department: Internal Medicine

institute: Wake Forest School of Medicine

description: Library name: LD_P3

data_processing:
Demultiplexed raw sequence reads were analyzed using a Partek Flow (Illumina) pipeline. Four random bases at the 5’ end and the poly(A) tract plus downstream sequence at the 3’ end of reads were trimmed. Reads with less than 15 bases were excluded for alignment.
Trimmed reads were first aligned using Bowtie against the Macaca mulatta mature miRNA (miRBase v22) reference based on Mmul_8.0.1 genome assembly. Aligned reads with at least one read across all samples per feature were quantified in Flow using an expectation/maximization (E/M) algorithm in Partek Flow.
Unaligned reads from the first round of alignment were iteratively aligned against the Macaca mulatta precursor miRNA (miRbase v22) reference. Afterward, unaligned reads from the second round of alignment were aligned using BWA against the Macaca mulatta transciptome  (Mmul_8.0.1, Ensembl release 97). Aligned reads with at least 10 read counts across all samples per feature were quantified by the Partek E/M method.
Read counts for mature miRNAs and gene transcripts were normalized by the trimmed-mean of means method.
Assembly: Macaca mulatta (Mmul_8.0.1)
Supplementary files format and content: Text file with raw counts for miRNAs.
Supplementary files format and content: Text file with raw counts for transcripts.
Supplementary files format and content: Text file with normalized counts for miRNAs.
Supplementary files format and content: Text file with normalized counts for transcripts.

source_name: liver

extract_protocol:
Total RNA was extracted from rhesus monkey livers using the Direct-zol RNA Miniprep Plus kit (Zymo Research). RNA samples were quantified by Qubit assays (Thermo Fisher) and RNA integrity was determined using an RNA ScreenTape kit on the TapeStation 4200 system (Agilent).
Both mRNA and miRNA libraries were generated using 500 ng RNA from each sample (RIN > 8.5) and a NEXTFLEX Combo-Seq kit (PerkinElmer) by following the manufacturer’s instructions. The mRNA and miRNA libraries from each sample were combined into one library for sequencing. Libraries were quantified using a KAPA Library Quantification kit (Roche Sequencing and Life Science).
Pooled ibraries were sequenced (1 x 76 bp) using the NovaSeq 6000 system (Illumina).

treatment_protocol: Liver biopsies were performed to obtain samples before the induction phase. During the induction phase of 90 days, monkeys drank 0.5 g ethanol/kg/day, 1 g ethanol/kg/day, and 1.5 g ethanol/kg/day for 30 days at each dose. Liver biopsies were performed to obtain samples at the end of the induction phase.

value: liver

value: male

value: post-induction


title: S7

value: gastric cancer

tag: fov

value: IIIb


title: Sample-1 Day-0 LNP-RNA

description: Library name: p22167-s001_RCl19-D0


title: 688M PDA cells, H3K27ac, shKdm8-1, hypoxia, replicate 1

description: Library name: Sample 5

value: Pancreatic

value: pancreatic ductal adenocarcinoma cells


title: Sample-4 Day-0 LNP-RNA

description: Library name: p22167-s004_RKn19-D0


title: RPF_60min_rep2

description: Library name: Sample_8


title: 688M PDA cells, H3K27ac, shGFP, normoxia, replicate 1

description: Library name: Sample 1

value: normoxia


title: Very heavy drinker 3, post-induction

description: Library name: VHD_P3


title: 688M PDA cells, H3K27ac, shKdm8-2, normoxia, replicate 2

description: Library name: Sample 9


title: mRNA_360min_rep1

description: Library name: Sample_6


title: 688M PDA cells, H3K27ac, shKdm8-2, normoxia, replicate 1

description: Library name: Sample 3


title: mRNA_0min_rep1

description: Library name: Sample_4


title: S75

tag: age

value: IV


title: RPF_360min_rep1

description: Library name: Sample_3


title: 688M PDA cells, H3K27ac, shKdm8-1, normoxia, replicate 1

description: Library name: Sample 2


title: Light drinker 3, baseline

description: Library name: LD_B3

value: baseline


title: S107

tag: grade

value: IIIa


title: S70

tag: stage#

value: Ib


title: 688M PDA cells, ATAC-Seq, shKdm8, hypoxia, replicate 2

description: Library name: Sample 8

data_processing:
ATAC-Seq reads that passed the QC process were aligned to a mm39 genome build using bowtie2 (v2.4.1). Bam files were filtered for reads mapped to blacklisted regions and duplicated reads. Insertion bed files were made with bedtools (v2.25.0) accounting for the +4/-5 bp offsets by Tn5. Peaks were called using MACS3 (v3.0.0a6) with mapped bam files (--nomodel --broad --nolambda --keep-dup all -p 0.01 -B --SPMR) and only reads with low false discovery rate (qValue > 5) were included in the analysis.
Assembly: mm39
Supplementary files format and content: BigWig

extract_protocol:
Briefly, viable 688M PDA cells were first treated with DNase in HBSS for 30 min at 37C prior to nuclei release in pre-chilled ATAC resuspension buffer (Tris-HCL pH 7.4, digitonin, Tween-20, NP40). Transposition was carried out in transposition mixture (1xTD buffer, 100nM Tn5 transposase, digitonin, Tween-20) for 30 min at 37C in a thermomixer with 1000 rpm. Transposed fragments were cleaned up with a Zymo DNA Clean and Concentrator-5 Kit. Partially amplified libraries were first quantified by qPCR to determine additional cycles needed and fully amplified using the NEBNext 2x MasterMix.
Libraries were sequenced on an Illumina NextSeq 2000 sequencer.

treatment_protocol: PDA 688M cells were either cultured in normoxia (atmospheric O2) or hypoxia (<0.5% O2) for 48 hours prior to performing the ATAC-Seq protocol.


title: S17

tag: Stage


title: 688M PDA cells, H3K27ac, shGFP, hypoxia, replicate 1

description: Library name: Sample 4


title: S76

tag: ln


title: Very heavy drinker 2, post-induction

description: Library name: VHD_P2


title: S51

tag: t


title: RPF_0min_rep1

description: Library name: Sample_1

value: WT


title: Very heavy drinker 1, post-induction

description: Library name: VHD_P1


title: S58

tag: n


title: S18

tag: m


title: 688M PDA cells, ATAC-Seq, shGFP, normoxia, replicate 2

description: Library name: Sample 5

tag: tissue


title: Light drinker 2, post-induction

description: Library name: LD_P2


title: Very heavy drinker 3, baseline

description: Library name: VHD_B3


title: Light drinker 1, post-induction

description: Library name: LD_P1


title: S111

tag: Sex


title: SKBR3 GSK126 + Lapatinib REP 3

city: Boston

first: Naiara

last: Perurena

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital

description: Library name: SKBR3-EL3

data_processing:
Gene counts were quantified with STAR and DESeq2 normalized.
Assembly: hg19
Supplementary files format and content: DESeq2 normalized counts are provided in txt format.

extract_protocol:
Qiagen RNeasy Plus Mini Kit
Roche Kapa mRNA HyperPrep

value: HER2+ breast cancer

tag: treatment

value: GSK126 + Lapatinib


title: S47


title: SKBR3 GSK126 + Lapatinib REP 1

description: Library name: SKBR3-EL1


title: 688M PDA cells, ATAC-Seq, shGFP, hypoxia, replicate 1

description: Library name: Sample 3


title: 688M PDA cells, ATAC-Seq, shKdm8, hypoxia, replicate 1

description: Library name: Sample 4


title: S104


title: SKBR3 GSK126 REP 3

description: Library name: SKBR3-E3


title: 688M PDA cells, ATAC-Seq, shGFP, hypoxia, replicate 2

description: Library name: Sample 7


title: SKBR3 GSK126 + Lapatinib REP 2

description: Library name: SKBR3-EL2


title: 688M PDA cells, ATAC-Seq, shGFP, normoxia, replicate 1

description: Library name: Sample 1


title: Very heavy drinker 2, baseline

description: Library name: VHD_B2


title: S92


title: RPF_60min_rep1

description: Library name: Sample_2


title: 688M PDA cells, ATAC-Seq, shKdm8, normoxia, replicate 2

description: Library name: Sample 6


title: Very heavy drinker 1, baseline

description: Library name: VHD_B1


title: 688M PDA cells, ATAC-Seq, shKdm8, normoxia, replicate 1

description: Library name: Sample 2


title: Light drinker 2, baseline

description: Library name: LD_B2


title: S28


title: SKBR3 Lapatinib REP 3

description: Library name: SKBR3-DL3

value: Lapatinib


title: S40


title: Light drinker 1, baseline

description: Library name: LD_B1


title: Cortex, Single cell, Injured, Ancrod - biol rep 4

city: Miami

first: Jae

last: Lee

state: FL

address: 1095 NW 14th Terrace #48

institute: University of Miami

description: Library name: 1-jLee12152023

library_source: transcriptomic single cell

data_processing:
The resulting sequences were then  aligned and filtered using Cell Ranger’s v7.1.0 count pipeline to generate gene–barcode count  matrices. In brief, base call files for each sample were demultiplexed into FASTQ reads and  then aligned to the mouse mm39 reference genome using the STAR splice–aware aligner.  Confidently mapped exonic and intronic reads were further aligned to annotated transcripts.  After barcode and UMI quality filtering and sequence correction, reads were grouped by  barcode, UMI, and gene annotation and used for UMI counting. The output was a count matrix  containing all UMI counts for every droplet. Sequence alignment and transcript counts were  performed using Cell Ranger version 7.1.0 with the 10X Genomics pre–built Cell Ranger  mouse reference package, from GRCm39.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values in a matrix file of genes by cells

molecule: cytoplasmic RNA

source_name: Right Sensorimotor Cortex Injury Site

extract_protocol:
Cortical lesion microdissection Injury sites were isolated 6 days after injury. Mice were anesthetized with Avertin and  transcardially perfused with ice–cold, oxygenated artificial cerebrospinal fluid. The meninges  were removed, and the injury site and surrounding spared tissue were excised in an approximate  5 mm by 5 mm square, to a depth of up to but not including the corpus callosum. Tissue dissociation All steps were  performed with pre–chilled solutions on ice or at 4°C unless otherwise noted. The tissue was  roughly chopped with a razor blade, resuspended in Cutting Solution, then centrifuged at 300g  for 2 min at room temperature (RT). After aspirating the supernatant, the sample was processed  using the Miltenyi Neural Tissue Dissociation Kit–P (cat #130–092–628), according to  manufacturer’s guidelines. During the second enzyme digestion step, cells were triturated 10  times each in 1,000, 750, and 500 uM fire–polished Pasteur pipettes. After the final  centrifugation, supernatant was aspirated, and cells were resuspended in 1 mL Red Blood Cell  Lysis buffer and incubated at RT for 1 min. This was stopped with 5 mL MACS Buffer and  centrifuged at 300g for 5 min. The resulting single–cell pellet was then incubated with Miltenyi  Myelin Removal Beads II, according to manufacturer’s guidelines. Cell–bead suspensions were  passed through an equilibrated LS column that was then washed with 2 mL of MACS buffer.  After centrifugation at 300g for 5 min and supernatant aspiration, cells were resuspended in 50 uL of FACS buffer and kept on ice until sequencing.
Single–cell suspensions were checked for viability, density, and purity using AOPI Stain  imaged on an Nexcelom K2 Cellometer. Samples were diluted to ~1,000 cells/uL and had a  minimum viability of 80%. ~6,000 cells per sample were sequenced with ~100,000 mean reads  and ~13,000 median UMI counts per cell. Sample libraries were prepared with the 10X  Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (Dual Index) and multiplexed on the  sequencer with Dual Index Kit TT (Set A), according to manufacturer’s protocols. These  libraries were then sequenced using paired–end sequencing on eight channels of an Illumina  Novaseq X 10–billion–read flow cell with a 300–cycle kit.

treatment_protocol:
Treated mice were depleted of fibrinogen with ancrod (NIBSC, 74/581). Briefly, mice received 2.4 U ancrod, 2.0 mg per kg body weight, or saline solution (control), per day via osmotic minipumps  (Alzet, Model: 2002, 0.5 μL/h) implanted subcutaneously in their back 2 d before stroke  induction. Ancrod was secreted for the duration of the experiment until the mice were perfused.
injury protocol: Photothrombosis was used to induce stroke in the cortex of adult mice as described. Briefly, 20 min after  injection of the photosensitive dye Rose Bengal (Sigma–Aldrich, 330000; 10 μL/g body weight,  intraperitoneal), a cold light illuminator was positioned stereotaxically to deliver light (150 W)  to the cortex (AP, 0 mm; ML, −2.4mm, according to Paxinos and Watson). The region of  interest (4–mm diameter) was illuminated for 6 min, and after the light exposure ended, the  wound was sutured.

value: Right Sensorimotor Cortex Injury Site

value: Unenriched

value: Female

value: Ancrod

tag: animal id

tag: pump id

tag: batch (injury_and_sequencing)

tag: biologoical replicate

value: biol rep 4


title: Cortex, Single cell, Injured, Saline - biol rep 4

description: Library name: 9-jLee12152023

tag: cell type

tag: genotype

value: Saline


title: SKBR3 GSK126 REP 2

description: Library name: SKBR3-E2

tag: cell line


title: SKBR3 Lapatinib REP 2

description: Library name: SKBR3-DL2


title: V312 CM9+ CD8+ T cells

city: Minneapolis

first: David

last: Masopust

address: 2101 6th St. SE

institute: University of Minnesota

data_processing:
RNA sequencing (50-bp single-end) with the HiSeq 2500 Illumina was done at the University of Minnesota Genomics Center (UMGC). The sequences were processed with the Collection of Hierarchical UMII-RIS Pipelines (CHURP, v 0.2.2) developed by the Research Informatics Solutions (RIS) group at the Minnesota Supercomputing Institute. The reference implementation of the CHURP package is at: https://github.com/msi-ris/CHURP.git 64. For whole tissue cell lysates, 2x 50bp FastQ paired-end reads were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30. For CM9-specific CD8 T cells, 2 x 50bp FastQ paired-end reads were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30 and headcrop 3. Quality control on raw sequence data for all samples was performed with FastQC.
Read mapping was performed via Hisat2 (v2.1.0) using the Macaca mulata genome (Mmul_10) as reference.
Assembly: Mmul_10
Supplementary files format and content: csv files contain raw read counts for each sample

source_name: vagina and cervix

extract_protocol:
For bulk RNA sequencing experiments, reproductive tract tissue was isolated directly into RNAlater (Qiagen). Tissue was homogenized in Trizol (Sigma-Aldrich) using a Tissuemiser homogenizer (Fisher Scientific), and RNA was extracted using a RNeasy mini kit as per the manufacturer’s instructions (QIAGEN). RNA integrity was assessed using capillary electrophoresis with the Agilent 2100 BioAnalyzer system (Agilent Technologies).
Sequencing libraries for CM9-specific CD8 T cells were prepared using the Clontech SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit. Libraries for whole tissue cell extracts were prepared using the TruSeq stranded mRNA library prep kit (Illumina).

value: vagina and cervix

value: CM9-specific CD8 T cells from vagina and cervix

value: female

tag: haplotype

tag: vaccination

value: heterologous virus vectors VSVnj, rVV, rAd5 encoding SIV-gag

value: 20mg CM9 peptide intravaginal challenge

tag: timepoint


title: S49

value: gastric cancer

tag: fov

tag: age

tag: grade

tag: stage#

tag: Stage

value: IIIa

tag: ln


title: V238 CM9+ CD8+ T cells

tag: tissue

tag: Sex

tag: treatment


title: S110

tag: t

tag: n

tag: m


title: Cortex, Single cell, Injured, Ancrod - biol rep 1

description: Library name: 4-jLee12142023

tag: cell type

tag: genotype

tag: animal id

tag: pump id

tag: batch (injury_and_sequencing)

tag: biologoical replicate

value: biol rep 1


title: SKBR3 DMSO REP 1

description: Library name: SKBR3-D1

tag: cell line

value: HER2+ breast cancer

value: WT

value: DMSO


title: S48

tag: fov

tag: age

tag: grade

value: IIIb


title: Cortex, Single cell, Injured, Saline - biol rep 2

description: Library name: 7-jLee12142023

value: Right Sensorimotor Cortex Injury Site

value: Unenriched

value: biol rep 2


title: SKBR3 DMSO REP 2

description: Library name: SKBR3-D2


title: RPm15 CM9+ CD8+ T cells

tag: haplotype

tag: vaccination

tag: timepoint


title: RRw14 CM9+ CD8+ T cells

tag: tissue

tag: Sex

tag: treatment

value: no intravaginal challenge


title: S57

tag: stage#

tag: Stage

value: IV

tag: ln

tag: t

tag: n

tag: m


title: SKBR3 DMSO REP 3

description: Library name: SKBR3-D3

tag: cell type

tag: genotype


title: Cortex, Single cell, Injured, Ancrod - biol rep 2

description: Library name: 5-jLee12142023

value: Female

value: Ancrod

tag: animal id

tag: pump id

tag: batch (injury_and_sequencing)

tag: biologoical replicate


title: RPp10 CM9+ CD8+ T cells

value: vagina and cervix

value: CM9-specific CD8 T cells from vagina and cervix

value: female

tag: haplotype

tag: vaccination


title: Cortex, Single cell, Injured, Ancrod - biol rep 3

description: Library name: 6-jLee12142023

tag: tissue

value: biol rep 3


title: Patient LH 41 Targeted Baseline DNA Sequencing, Male, Stable Disease

city: Buffalo

first: Spencer

last: Rosario

address: Elm & Carlton Sts

institute: Roswell Park Comprehensive Cancer Center

description: Library name: Patient LH 41

data_processing:
Raw reads that passed thequality filter were demultiplexed and pre-processed using FastQC for sequencing base quality control. For the initial routine analysis, we implemented the standard Archer Analysis 6.2.7 default “somatic” filter, applying a minimum AF of 2.7%. No filter was used for variants reported in the initial routine analysis with AF below 2.7%. Variant annotation was performed using the Archer Analysis 6.2.7 as well as the IGV (Integrative Genomics Viewer, Broad Institute, Boston, MA, United States).
Assembly: GRCh38
Supplementary files format and content: Cleaned_Archer .txt file includes mutations for each sample

source_name: colorectal tumor

extract_protocol:
The purification genomic DNA from formalin-fixed paraffine-embedded (FFPE) tumor samples was prepared using the Truxtrac FFPE total NA Plus Kit (Covaris). Samples were provided as either FFPE slides, cores or curls. The FFPE samples were emulsified in Tissue Lysis Buffer in the presence of Proteinase K on the Covaris E220 sonicator. This was followed by an incubation at 56 °C for a short duration. The RNA-containing supernatant was separated from the DNA-containing tissue by a centrifugation step. RNA was then de-crosslinked, DNAse digested, and purified over an RNA-specific spin column. Sequentially, DNA was released from the DNA-containing tissue by the Covaris E220 sonicator. The resuspension was then put through an additional Proteinase K digestion, following a de-crosslinking step at 80 °C. DNA was then purified over a DNA-specific spin column.
Final libraries were validated for appropriate size on a 4200 TapeStation D1000 Screentape (Agilent Technologies, Inc.). The sequencing libraries were quantitated using KAPA Biosystems qPCR kit (Roche), and were pooled together in an equimolar fashion, following experimental design criteria. They were then pooled, denatured, and diluted to 1.6pM with 20% PhiX control library added.

treatment_protocol: Targeted sequencing was performed using the Archer VariantPlex panel which targets 290 regions of interest across 31 genes, following manufacturer’s recommended protocol (research DNA sequencing). Briefly, two rounds of Anchored Multiplex PCR (AMP) using gene specific primers (GSP) from the desired panel generate target amplicons with complete adapter sequences were used for Illumina sequencing.

value: colorectal tumor

tag: subject id

value: Patient LH 41

tag: Sex

value: Male

tag: disease status

value: Stable Disease

value: RAS wt


title: S60

value: gastric cancer

tag: fov

tag: age

tag: grade

tag: stage#

tag: Stage


title: S22

tag: ln

tag: t

tag: n

tag: m


title: D4_uterus

source_name: uterus

value: uterus

tag: cell type

value: all

value: heterologous virus vectors VSVnj, rVV, VSVindiana, and rAd5 encoding SIV-gag

tag: treatment

tag: timepoint


title: Patient LH 33 Targeted Baseline DNA Sequencing Male, Stable Disease

description: Library name: Patient LH 33

value: Patient LH 33

tag: genotype


title: Whole kidneys of proximal tubules-specific conditional knockout mice(CKO) mice

city: Tokushima

first: Kazuhiro

last: Hasegawa

address: 3-18-15 Kuramoto-cho

department: Department of Nephrology

country: Japan

institute: Tokushima University Graduate School of Biomedical Sciences

description: Library name: CKO

data_processing:
Sequencing was conducted on a NovaSeq sequencer (Illumina), resulting in an average read length of 100 bp.
The STAR aligner (version 2.7.3a) was used for sequence alignment; HTSeq for raw read counting; DESeq2 for normalization; Cufflinks (version 2.2.1) for estimating gene expression levels, which were reported as fragments per kilobase of transcript per million mapped reads (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/); and FastQC for data quality assessment, excluding low-quality reads from further analysis.
Filtering criteria exclude genes with at least one zero count.
In order to reduce systematic bias, size factors were estimated from the read count data (calcNormFactors method). Using them, the read count data was normalized with Trimmed mean of M-values (TMM) method in edgeR library. Then, statistical test was performed with the normalized data.
Assembly: mm10
Supplementary files format and content: A tab-delimited text file containing raw counts for 45,777 genes.
Supplementary files format and content: A tab-delimited text file containing TMM-normalized counts for the 19,550 filtered genes.

source_name: Kidneys

growth_protocol: Mice were fed ad libitum with the standard chow diet with constant access to water under a 12:12 h light/dark cycle as previously described.

extract_protocol:
RNA was extracted from RNAeasy Kit
Library preparation was performed using the TruSeq Stranded mRNA kit (Illumina, San Diego, CA, USA).

treatment_protocol: No treatment

tag: tissue

value: Kidneys


title: RBc15 CM9+ CD8+ T cells

tag: haplotype

tag: vaccination

value: heterologous virus vectors VSVnj, rVV, rAd5 encoding SIV-gag

value: no intravaginal challenge


title: Cortex, Single cell, Injured, Saline - biol rep 1

description: Library name: 3-jLee12142023

value: Right Sensorimotor Cortex Injury Site

value: Unenriched

tag: Sex

value: Female

value: Saline

tag: animal id

tag: pump id

tag: batch (injury_and_sequencing)

tag: biologoical replicate

value: biol rep 1


title: SKBR3 GSK126 REP 1

description: Library name: SKBR3-E1

tag: cell line

value: HER2+ breast cancer

value: WT


title: S108

tag: fov

tag: age

tag: grade

tag: stage#

tag: Stage

value: IIIa

tag: ln


title: Cortex, Single cell, Injured, Saline - biol rep 3

description: Library name: 8-jLee12142023

tag: cell type

tag: treatment

value: biol rep 3


title: D4_vagina

source_name: vagina

tag: tissue

value: vagina

value: female

tag: timepoint


title: Patient LH 26 Targeted Baseline DNA Sequencing, Male, Stable Disease

description: Library name: Patient LH 26

value: colorectal tumor

tag: subject id

value: Patient LH 26

value: Male

tag: disease status

value: Stable Disease

tag: genotype

value: RAS wt


title: Whole kidneys of control mice

description: Library name: Control

value: Kidneys


title: SKBR3 Lapatinib REP 1

description: Library name: SKBR3-DL1

value: Lapatinib


title: S116

value: gastric cancer

tag: Sex

tag: t

tag: n

tag: m


title: Patient 38 Targeted Baseline DNA Sequencing, Male, Progressive Disease

description: Library name: Patient 38

value: Patient 38

value: Progressive Disease


title: Patient 37 Targeted Baseline DNA Sequencing, Female, Progressive Disease

description: Library name: Patient 37

value: Patient 37

value: Female


title: S97

tag: fov

value: Ib


title: Patient 39 Targeted Baseline DNA Sequencing, Male, Stable Disease

description: Library name: Patient 39

value: Patient 39


title: BMDC, M. elsdenii-treated, biol rep 1

city: Shanghai

first: Xinxin

last: Hou

address: 1200 Cailun Road

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference- based approach.
Assembly: GRCm39
Supplementary files format and content: Comma-Separated Values file includes raw counts for each sample

source_name: bone marrow

growth_protocol: BM was flushed with RPMI medium and passed through a 70 mm cell strainer to yield a single cell suspension. Then cells were treated with RBC lysis buffer to remove red blood cells. Cells were cultured in RPMI complete medium supplemented with 20ng/ml recombinant murine GM-CSF (Peprotech) and 10ng/ml IL4 (Peprotech), and the medium were half-exchanged every second day. BM-derived cells were collected on day 6 and stimulated with the indicated ratio (MOI 100:1) of M. elsdenii or PBS for another 24 hours and afterwards harvested for RNA-seq.

extract_protocol:
Total RNA was isolated by QIAzolLysisReagent (Qiagen) and qualified by agarose gel electrophoresis.
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA.

value: bone marrow

value: dendritic cells

value: WT

tag: pre-treatment

value: Cells were stimulated to BMDC cell differentiation

value: M. elsdenii


title: S96

tag: age

tag: grade

value: IIIa


title: S66

tag: stage#

tag: Stage

value: IV


title: D4_ectocx

source_name: ectocervix

value: ectocervix

tag: cell type

value: all

value: female

tag: haplotype

tag: vaccination

value: heterologous virus vectors VSVnj, rVV, VSVindiana, and rAd5 encoding SIV-gag

value: no intravaginal challenge


title: D3_vagina

tag: tissue

value: vagina

tag: treatment

tag: timepoint


title: BMDC, M. elsdenii-treated, biol rep 3

tag: genotype


title: D4_endocx

source_name: endocervix

value: endocervix

tag: Sex


title: BMDC, M. elsdenii-treated, biol rep 2


title: Patient 35 Targeted Baseline DNA Sequencing, Male, Stable Disease

description: Library name: Patient 35

value: colorectal tumor

tag: subject id

value: Patient 35

value: Male

tag: disease status

value: Stable Disease

value: RAS wt


title: Patient 22 Targeted Baseline DNA Sequencing, Male, Progressive Disease

description: Library name: Patient 22

value: Patient 22

value: Progressive Disease


title: D3_endocx


title: S45

value: gastric cancer

value: Ib

tag: ln

tag: t

tag: n

tag: m


title: BMDC, PBS-treated, biol rep 1

value: bone marrow

value: dendritic cells

value: WT

tag: pre-treatment

value: Cells were stimulated to BMDC cell differentiation

value: PBS


title: Patient 32 Targeted Baseline DNA Sequencing, Male, Partial Regression

description: Library name: Patient 32

value: Patient 32

value: Partial Regression


title: D3_uterus

value: uterus

value: all

value: female

value: heterologous virus vectors VSVnj, rVV, VSVindiana, and rAd5 encoding SIV-gag

value: no intravaginal challenge


title: BMDC, PBS-treated, biol rep 3


title: Patient 21 Targeted Baseline DNA Sequencing, Male, Stable Disease

description: Library name: Patient 21

value: colorectal tumor

value: Patient 21

value: Male

value: Stable Disease

value: RAS wt


title: D3_ectocx

value: ectocervix


title: D16_vagina

value: vagina

value: 20mg CM9 peptide intravaginal challenge


title: S100

value: gastric cancer

tag: fov

tag: age

tag: grade

tag: stage#

value: IV


title: BMDC, PBS-treated, biol rep 2

value: bone marrow

tag: cell type

value: dendritic cells

value: WT

value: Cells were stimulated to BMDC cell differentiation

value: PBS


title: Lung from a 24 month old INKBRITE mouse (TOP) and from a 3 month old Dermo1-cre;Tnfaip3f/f mouse (BOTTOM)

city: San Francisco

first: Nancy

last: Allen

state: CA

address: 513 Parnassus Ave.

institute: UCSF

hyb_protocol: Samples were prepared for the Xenium analysis according to standard 10x protocol

data_processing: The experiment.xenium output from 10x was directly utilized for visualization in the Xenium Explorer application. Clustering and gene expression analysis was performed in R using Seurat.

label: Xenium Mouse Probe Set

source_name: Lung

label_protocol: Xenium Mouse Probe Set

extract_protocol: After euthanasia the lung was perfused with PBS via injection through the right ventricle. The lung was then gently insufflated via the trachea with 4% PFA. After overnight fixation the lung was washed four times with PBS and gradually dehydrated with increasing concentrations of ethanol. Once in 100% ethanol lungs were incubated in xylene for 1 hour and subsequently embedded in paraffin. Using a microtome 5um sections were cut and mounted onto the Xenium slide.

value: Female

tag: tissue

value: Lung


title: Patient 19 Targeted Baseline DNA Sequencing, Male, Stable Disease

description: Library name: Patient 19

value: colorectal tumor

value: Patient 19


title: S13

tag: Stage

value: IIIb


title: S41

value: Ia


title: D16_uterus

value: uterus

value: all

value: female

tag: haplotype

tag: vaccination

value: heterologous virus vectors VSVnj, rVV, VSVindiana, and rAd5 encoding SIV-gag

tag: treatment

tag: timepoint


title: D16_endocx

value: endocervix

tag: Sex

value: 20mg CM9 peptide intravaginal challenge


title: Patient 18 Targeted Baseline DNA Sequencing, Male, Progressive Disease

description: Library name: Patient 18

tag: subject id

value: Patient 18

value: Male

tag: disease status

value: Progressive Disease

tag: genotype

value: RAS wt


title: S93

value: gastric cancer

value: Ib

tag: ln

tag: t

tag: n

tag: m


title: Patient 17 Targeted Baseline DNA Sequencing, Male, Stable Disease

description: Library name: Patient 17

value: Patient 17

value: Stable Disease


title: D16_ectocx

value: ectocervix


title: S68

tag: fov

tag: age

tag: grade

value: IIIb


title: TERMS_103023

city: Philadelphia

first: D Kacy

last: Cullen

state: PA

address: 3320 Smith Walk, 105E Hayden Hall

department: Neurosurgery/Bioengineering

institute: University of Pennsylvania

description: Library name: TERMS_103023

data_processing:
fastq files trimmed with fastp
trimmed fastq mapped to mRatBN7.2 transcripts with salmon
counts summarized to gene level with tximeta
Assembly: mRatBN7.2 / Ensembl v113
Supplementary files format and content: tab-delimted text, raw counts per gene (ensembl ID)

organism: Rattus norvegicus

source_name: brain cortex

growth_protocol: Cortical astrocytes isolated from postnatal day 0-1 Sprague-Dawley pups. At Passage 4, astrocytes were used for TE-RMS fabrication or planar astrocytes plating

extract_protocol:
Rneasy Plus Universal Mini Kit (Qiagen, cat. No. 73404)
SMART-Seq mRNA LP (Takara Bio, cat. No. 634768) for library prep following manufacturer instructions

treatment_protocol: 2D astrocytes plated on collagen. TE-RMS astrocytes pipetted into microchannel molds filled with collagen

tag: tissue

value: brain cortex

tag: cell line

value: Passage 4

tag: cell type

value: astrocytes

tag: condition

value: TERMS

tag: run


title: 2Dastro_090123

description: Library name: 2Dastro_090123


title: Patient 14 Targeted Baseline DNA Sequencing, Male, Stable Disease

description: Library name: Patient 14

value: colorectal tumor

value: Patient 14


title: D13_vagina

value: vagina

value: all

value: female

tag: haplotype

tag: vaccination

value: heterologous virus vectors VSVnj, rVV, VSVindiana, and rAd5 encoding SIV-gag

tag: treatment

value: 20mg CM9 peptide intravaginal challenge

tag: timepoint


title: D13_uterus

value: uterus

tag: Sex


title: Patient 16 Targeted Baseline DNA Sequencing, Female, Stable Disease

description: Library name: Patient 16

tag: subject id

value: Patient 16

value: Female

tag: disease status

tag: genotype

value: RAS wt


title: D13_endocx

value: endocervix


title: S109

value: gastric cancer

tag: stage#

tag: Stage

value: Ib

tag: ln

tag: t

tag: n

tag: m


title: S38

tag: tissue

tag: fov

tag: age

tag: grade

value: IIIa


title: S88

value: II


title: 2Dastro_072823

description: Library name: 2Dastro_072823

value: brain cortex

tag: cell line

value: Passage 4

tag: cell type

value: astrocytes

tag: condition

tag: run


title: S89

tag: Sex

value: IIIb


title: TERMS_090123

description: Library name: TERMS_090123

value: TERMS


title: Patient 1 Targeted Baseline DNA Sequencing, Male, Stable Disease

description: Library name: Patient 1

value: colorectal tumor

tag: subject id

value: Patient 1

value: Male

tag: disease status

value: Stable Disease


title: D13_ectocx

value: ectocervix

value: all

value: female

tag: haplotype

tag: vaccination

value: heterologous virus vectors VSVnj, rVV, VSVindiana, and rAd5 encoding SIV-gag

tag: treatment

value: 20mg CM9 peptide intravaginal challenge

tag: timepoint


title: TERMS_072823

description: Library name: TERMS_072823


title: Visium WT 20mo Sample

city: New Orleans

first: Surjyadipta

last: Bhattacharjee

state: Louisiana

address: 2020 Gravier Street, Suite D, 8th floor

department: Neuroscience Center of Excellence

institute: LSU Health, New Orleans

description: Library name: Spatial_WT_20mo

data_processing:
Cell Ranger ARC (cellranger-arc) from 10x Genomics was used to pricess Chromium Single Cell Multiome ATAC + Gene Expression (GEX) sequencing data. BCL files from from the Illumina NovaSeq were demultiplexed into paired-end, gzip-compressed FASTQ files using the default parameters of cellranger-arc mkfastq. Following this, the cellranger-arc count function was employed for read alignment, filtering, barcode counting, peak calling, and the quantification of both ATAC and GEX molecules. The rat genome mRatBN7 and its annotated transcriptome was used as a reference for alignment. Only confidently mapped reads with valid barcoes, unique molecular identities (UMIs) and non-PCR duplicates were retained. Spatial sequencing data was processed using Space Ranger from 10x Genomics.
Assembly: mRatBN7
Supplementary files format and content: Cell Ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for each sample from filtered_feature_bc_matrix folder for RNA-seq component.
Supplementary files format and content: Cell Ranger output files: fragments.tsv.gz for each sample for ATAC-seq component
Supplementary files format and content: Space Ranger output files: aligned_fiducials.jpg.gz, detected_tissue_image.jpg.gz, scalefactors_json.json.gz, tissue_hires_image.png.gz, tissue_lowres_image.png.gz, tissue_positiones_list.csv.gz for spatial information for each sample and barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz for sequencing information for each sample
Library strategy: Spatial Transcriptomics

source_name: Total RNA from coronal brain section from 10x Genomics Visium Spatial Transcriptomics platform for a WT rat at 20 months of age

extract_protocol:
Hippocampus from 10-month and 20-month-old female McGill-R955-hTau transgenic rat and age-matching WT controls were dissected and snap-frozen at -80°C until further use. The tissues were minced and homogenized, and single-nuclei were isolated following 10x Genomics protocol (Pleasanton, CA, CG000505). Briefly, frozen tissues were minced, lysed, and dissociated in lysis buffer and then filtered on Nuclei Isolation Column by centrifugation. Nuclei pellets were washed with debris removal buffer, and nuclei were resuspended with 50 µL resuspension buffer. Nuclei concentration was determined with Luna-FL cell counter (Logos Biosystems, Annandale, VA). For tissues used for Spatial sequencing: 10-month and 20-month-old females McGill-R955-hTau transgenic rat and age-matching WT controls were perfused with 10% formalin, and the fixed brains were embedded in OCT compound, coronally sectioned at 10 µm using CryoStar NX50 cryotome (Epredia Kalamazoo, MI) and mounted onto microscope slides. Tissue sections were transferred onto the fiducial frames of a Visium Spatial Gene Expression slide (PN-2000233, 10x Genomics, Pleasanton, CA) using the Visium CytAssist.
Using the 10x Genomics Chromium Controller and following downstream protocols, RNA and ATAC libraries were generated on a cell-by-cell basis using microfluidic partitioning to capture single cells and prepare barcoded, next-generation sequencing (NGS) libraries. The mRNA and ATAC libraries were sequenced using a NovaSeq 6000 system (Illumina, San Diego, CA) targeting at minimum 80,000 and 50,000 reads per cell for mRNA and ATAC, respectively.  For spatial sequencing: The tissues underwent spatial barcoding, and cDNA library was generated from the tissue mRNA as outlined in the Visium Spatial Gene Expression User Guide (CG000239, 10x Genomics). The mRNA transcriptome was mapped to a 55 µm spatial resolution, corresponding to 1-10 cells per spot. The mRNA library was sequenced using a Nextseq 2000 platform.

value: Brain


title: HtH7 MADD knockout, replicate 3

city: Chicago

first: Jason

middle: M

last: Wood

state: IL

address: 900 S Ashland Ave rm 1057

department: Research Informatics Core

institute: University of Illinois at Chicago

description: Library name: PRA030323_018

data_processing:
FastQC  version 0.11.9 was used to assess the sequence quality of the raw RNA-seq data.
Cutadapt  version 1.18 was used to trim low-quality bases and adapters from all sequences.
BWA MEM version 0.7.17 was used to assess ribosomal RNA content by comparison with human rRNA sequences.
All reads were then mapped to the human reference genome (hg38) in a splice-aware manner using STAR version 2.7.6a.
Levels of duplicate PCR products were assessed using Picard MarkDuplicate (Picard toolkit. 2019).
Gene expression quantification was performed using featureCounts against the Ensembl gene IDs.
Alternative splicing features (isoforms, exons, or splice junctions) were annotated by comparison with Ensembl transcript sequences using Kalisto.
Exon-level expression was quantified against flattened gene exon annotations using featureCounts and splice junctions were quantified using STAR.
Assembly: hg38
Supplementary files format and content: Gzipped tab-delimited text file containing a list of genes (Ensembl ID) and their counts in each of the samples

growth_protocol: The human ATC cell lines 8505C, C643 and HTH7 were procured from the University of Colorado Cancer Center, Aurora, CO, USA. All the cell lines were tested for mycoplasma and other pathogens before initiating experiments (MycoFluor™, Thermo Fisher Scientific, Inc) and were used at a low passage number (5-15). The cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 media supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic (penicillin and streptomycin)-antimycotic (Amphotericin B) (Gibco). The cells were incubated at 37 °C in a humidified CO2 incubator.

extract_protocol:
Genomic total mRNA was extracted using the RNeasy mini kit, Qiagen (catalog no. 74104).
Libraries were equipped with the 3′ QuantSeq mRNA-Seq Library Prep Kit REV for Illumina (Lexogen) according to the manufacturer's instructions.

treatment_protocol: The CRISPR/Cas9 MADD single-guide RNA (sgRNA) targeting exon 3 of the human MADD gene was designed via the IDT online service: Predesigned Alt-R ® CRISPR/Cas9 guide RNA  (https://sg.idtdna.com/site/order/designtool/index/CRISPR_PREDESIGN). The sgRNA sequences used were sgRNA1 3’ AGTATACAAACACTCTCGGA 5’ and sgRNA2 5’ 6  AAGAAACTGGGCATCCCTCG 3’ in chromosome 11 at site 748-767 and 810-829, respectively. SgRNA1 has on target and off target scores of 89 and 70, respectively. The sgRNA2 on-target and off target scores are 61 and 74, respectively. The negative control consisted of a nontargeting control sgRNA. The double-stranded guide sequence oligonucleotides were ligated into the Lenti-iCas plasmid (#84232, Adgene), which was linearized via the Sac 1 restriction enzyme. The Cas9 plasmid was constructed for editing activity with ERT (1 µM, 4HT). The cells were seeded into 6-well plates at a density of 2×10^5 cells/well and cultured in 2 ml of RPMI medium supplemented with containing 10% FBS without antibiotics for 24 hours in a CO2 incubator. Lipofectamine 3000 (3.75 μl) (Invitrogen, Carlsbad, CA, USA) and sgRNA 1&2 and Cas9 plasmid DNA were separately diluted in 250 μl of portions of Opti-MEM reduced serum medium (Invitrogen). After 5 minutes of incubation at room temperature, the diluted Lipofectamine 3000 and plasmid DNA were mixed. The DNA-liposome complex was incubated for 20-30 minutes at room temperature and then directly added dropwise to the cultured cells in 2 ml of RPMI medium. The culture medium was replaced with RPMI medium containing 10% FBS with antibiotics after transfection for 24 hours in a CO2 incubator. The efficiency of transfected cells was detected by fluorescence microscopy using the OFP channel after 48 hours of incubation. The transfected cells were then sorted using a cell sorter (MoFlo Astrios EQ, Beckman) at 570 nm to isolate the successfully transfected population. The sorted cells were subsequently treated with 1 μM 4HT for 24 hours to induce MADD gene knockout.

tag: genotype

value: MADD knockout


title: V312_vag

value: vagina

value: heterologous virus vectors VSVnj, rVV, rAd5 encoding SIV-gag


title: S52

value: gastric cancer

tag: stage#

tag: Stage

value: II

tag: ln

tag: t

tag: n

tag: m


title: 2Dastro_103023

description: Library name: 2Dastro_103023

tag: tissue

value: brain cortex

tag: cell line

value: Passage 4

tag: cell type

value: astrocytes


title: HtH7 MADD knockout, replicate 2

description: Library name: PRA030323_017


title: S105

tag: fov

tag: Sex

tag: age

tag: grade

value: IIIb


title: V312_UTER

value: uterus

tag: haplotype

tag: vaccination


title: Patient 12 Targeted Baseline DNA Sequencing, Male, Stable Disease

description: Library name: Patient 12

value: colorectal tumor

tag: subject id

value: Patient 12

value: Male

tag: disease status

value: Stable Disease

value: RAS wt


title: Visium Tau 20mo Sample

description: Library name: Spatial_Tau_20mo

source_name: Total RNA from coronal brain section from 10x Genomics Visium Spatial Transcriptomics platform for a Tau rat at 20 months of age


title: Visium WT 10mo Sample

description: Library name: Spatial_WT_10mo

source_name: Total RNA from coronal brain section from 10x Genomics Visium Spatial Transcriptomics platform for a WT rat at 10 months of age


title: S115

tag: stage#

value: IV


title: HtH7 MADD knockout, replicate 1

description: Library name: PRA030323_016

tag: genotype


title: S65

tag: Stage

tag: ln


title: S36

value: IIIa

tag: t

tag: n


title: HtH7 Control, replicate 3

description: Library name: PRA030323_015

value: Control


title: Liver tumor, STS2, day27

city: Hu Bei

first: Kun

last: Cheng

state: --- Select One ---

address: No. 1037 Luoyu Road, Hongshan District, Wuhan

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.

description:
Library name: fpkm_STS2
Column_name in raw counts_All_Samples.txt: fpkm_STS2

data_processing:
The processed data files (FPKM expression matrix) were generated as follows: 1. Raw sequencing reads (FASTQ files) were quality-checked using FastQC, and adapters and low-quality bases were trimmed using Trimmomatic with the following parameters: minimum length = 50 bp, quality score threshold = 20. 2. The cleaned reads were aligned to the GRCh38 reference genome using HISAT2 with default parameters. 3. Gene expression levels were quantified using StringTie to calculate FPKM values. The reference annotation file used was GENCODE v34. 4. The FPKM values for all samples were merged into a single expression matrix using a custom R script. Rows represent genes, and columns represent samples. 5. FPKM values were log2-transformed for downstream analysis. 6. Genes with low expression (FPKM < 1 in all samples) were filtered out.
Assembly: GRCm39 (mm39)
Supplementary files format and content: File Format: The processed data is provided in an Excel file (.xlsx format).  Content Description:  The file contains gene expression data with the following columns:  st_gene_id: Unique identifier for each gene.  gene_id: Gene identifier.  gene_symbol: Symbol or name of the gene.  fpkm_STS1, fpkm_STS2, fpkm_STS3: Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values for three different samples (STS1, STS2, STS3).  fpkm_control1, fpkm_control2, fpkm_control3: FPKM values for three control samples (control1, control2, control3).  Each row represents a unique gene and its corresponding expression values across the samples and controls.  The data is organized in a tabular format, with genes listed in rows and expression values in columns.

source_name: Hepa 1-6

extract_protocol:
Total RNA was extracted from cells using the TRIzol Reagent Kit (Invitrogen, USA) or FastPure Cell/Tissue Total RNA Isolation Kit V2 (RC112-01, Vazyme Biotech Co.,Ltd), and the RNA concentration was measured using the NanoDrop 2000 (Thermo Fisher Scientific).
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification.We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

value: Hepa 1-6

value: tumor cell

value: WT


title: V312_endo

tag: tissue

value: endocervix

value: all

value: female

value: heterologous virus vectors VSVnj, rVV, rAd5 encoding SIV-gag

tag: treatment

value: 20mg CM9 peptide intravaginal challenge

tag: timepoint


title: V238_vag

value: vagina

tag: cell type


title: Liver tumor, STS3, day27

description:
Library name: fpkm_STS3
Column_name in raw counts_All_Samples.txt: fpkm_STS3

tag: cell line


title: V312_ecto

value: ectocervix

tag: Sex


title: Liver tumor, STS1, day27

description:
Library name: fpkm_STS1
Column_name in raw counts_All_Samples.txt: fpkm_STS1


title: S95

source_name: gastric cancer

value: gastric cancer

tag: fov

tag: age

tag: grade

value: Ia

tag: m


title: V238_UTER

value: uterus

tag: haplotype

tag: vaccination


title: HtH7 Control, replicate 1

description: Library name: PRA030323_013

tag: genotype


title: Visium Tau 10mo Sample

description: Library name: Spatial_Tau_10mo

source_name: Total RNA from coronal brain section from 10x Genomics Visium Spatial Transcriptomics platform for a Tau rat at 10 months of age

value: Brain


title: HtH7 Control, replicate 2

description: Library name: PRA030323_014


title: V238_endo


title: S14

tag: stage#

tag: Stage

value: II


title: S46

value: IV

tag: ln

tag: t


title: Liver tumor, control2, day27

description:
Library name: fpkm_control2
Column_name in raw counts_All_Samples.txt: fpkm_control2


title: C643 MADD knockout, replicate 2

description: Library name: PRA030323_011

value: MADD knockout


title: V238_ecto

tag: tissue


title: C643 MADD knockout, replicate 3

description: Library name: PRA030323_012


title: Liver tumor, control3, day27

description:
Library name: fpkm_control3
Column_name in raw counts_All_Samples.txt: fpkm_control3

value: Hepa 1-6


title: S54

tag: n


title: C643 MADD knockout, replicate 1

description: Library name: PRA030323_010


title: Liver tumor, control1, day27

description:
Library name: fpkm_control1
Column_name in raw counts_All_Samples.txt: fpkm_control1

value: tumor cell


title: RTl14_vag

tag: treatment

tag: timepoint


title: C643 Control, replicate 3

description: Library name: PRA030323_009

tag: cell line

value: Control


title: RTl14_uter

tag: cell type

tag: Sex


title: B2A, CD8 T cells, isotype

city: Changsha

first: Liwen

last: Wang

state: Hunan

address: 138 Tongzipo road

department: Department of Hematology

institute: Third Xiangya Hospital, Central South University

description: Library name: sample4

data_processing:
Raw FASTQ files were trimmed and filtered by Fastp (version 0.19.5), and then aligned to the reference genome using Bowtie2 (version 2.4.1).
The reads were counted by FeatureCounts (version 2.0.6).
Assembly: GRCm39/mm39
Supplementary files format and content: Tab-delimited text file includes raw counts for total sample

source_name: Bone marrow

extract_protocol:
Total RNA was extracted using the RNA rapid extraction kit (RNAfast200, Cat#220011) for RNA sequencing
Transcriptome sequencing was performed on the DNBSEQ platform with paired-end (PE150) cycles

value: Bone marrow

value: CD8 T cells

tag: strain

value: isotype


title: C643 Control, replicate 2

description: Library name: PRA030323_008


title: S74

data_processing: AtoMx SIP v3.0 for segmentation & molecule assignment ; downstream analysis in Python 3.8 (squidpy + scanpy 1.9.6 : PCA 50 PC, KNN, UMAP, Louvain r = 1)

tag: fov

tag: age

tag: grade


title: S114

value: IIIb

tag: m


title: B1A, CD8 T cells, isotype

description: Library name: sample3

value: female


title: RTl14_ecto

value: all

tag: haplotype

tag: vaccination

value: heterologous virus vectors VSVnj, rVV, rAd5 encoding SIV-gag

value: 20mg CM9 peptide intravaginal challenge


title: RTl14_endo

value: endocervix


title: C643 Control, replicate 1

description: Library name: PRA030323_007

tag: genotype


title: S35

value: gastric cancer

tag: stage#

tag: Stage

value: IIIa

tag: ln


title: 8505C MADD knockout, replicate 3

description: Library name: PRA030323_006


title: S27

tag: tissue

tag: t

tag: n


title: 8505C MADD knockout, replicate 2

description: Library name: PRA030323_005

tag: cell line


title: A1A, CD8 T cells, NK1.1 blockade

description: Library name: sample1

tag: cell type

tag: treatment

value: NK1.1 blockade


title: RRw14_vag

value: vagina

tag: Sex

value: no intravaginal challenge

tag: timepoint


title: RRw14_uter

value: uterus


title: 8505C MADD knockout, replicate 1

description: Library name: PRA030323_004

value: MADD knockout


title: RRw14_endo


title: 8505C Control, replicate 3

description: Library name: PRA030323_003

value: Control


title: siHK2-2

city: Wuhan

first: Tianhao

last: Zou

address: 1277 Jiefang Avenue

institute: Huazhong University of Science and Technology

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adapter sequence/low quality sequence using CLC Genomics Workbench (parameter-Quality limit: 0.05).
Trimmed sequence reads were mapped to GRCm39/mm39 using CLC Genomics Workbench (parameters-mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic workbench.
Assembly: mm39
Supplementary files format and content: xlsx file includes TPM for each sample.

source_name: MEFs

extract_protocol:
RNA was extracted by Trizol method.
1) By utilizing the structural characteristic that most eukaryotic mRNAs carry a polyA tail, mRNAs with polyA tails were enriched by Oligo(dT) magnetic beads; 2) The purified mRNAs were cleaved into small fragments with fragmentation buffer at a suitable temperature; 3) First-strand cDNAs were produced by reverse transcription using a random hexamer primer; 4) Second-strand cDNAs are synthesized (strand-specific library: dUTPs were used instead of dTTPs in the second-strand synthesis to incorporate dUTPs in the second-strand cDNAs, while the high-fidelity DNA polymerase used in this method could not amplify uracil-containing DNA templates, thus realizing the strand specificity), while simultaneously performing end repair and dA-Tailing; 5) Sequencing adapter ligation was performed, followed by DNA magnetic bead purification and fragment selection after ligation was completed to yield a library with 250-350 bp insert fragments; 6) The ligated products were amplified by PCR and purified again using DNA magnetic beads, where the products were solubilized with nuclear-free water; 7) After the initial library was constructed, a Qubit fluorescence quantifier was used for concentration detection, followed by a Qsep400 high-throughput biofragment analyzer for fragment size detection; 8) The double-stranded DNA library obtained by PCR was subjected to single-stranded cyclization to obtain a single-stranded circular DNA library; 9) The final library was amplified with phi29 before uploading to make DNA nanoballs (DNB) with more than 300 copies of a molecule, and the DNBs were loaded into the sequencing chip and sequenced on the BGI sequencing platform.

value: MEFs


title: RRw14_ecto

value: ectocervix


title: S59

extract_protocol: Sections baked 60 °C o/n; HIER; PK; fiducials; formalin re-fix; NHS-acetate block

tag: fov

tag: age


title: siHK2-1


title: S106

tag: grade

value: IV

tag: m


title: S69


title: 8505C Control, replicate 2

description: Library name: PRA030323_002


title: A2A, CD8 T cells, NK1.1 blockade

description: Library name: sample2

value: Bone marrow

value: CD8 T cells

tag: strain


title: RPp10_vag

value: all

value: female

tag: haplotype

tag: vaccination


title: S56

tag: stage#

tag: Stage

value: Ib


title: RPp10_UTER

tag: tissue

value: heterologous virus vectors VSVnj, rVV, rAd5 encoding SIV-gag

value: 20mg CM9 peptide intravaginal challenge


title: 8505C Control, replicate 1

description: Library name: PRA030323_001

tag: genotype


title: S91

value: gastric cancer

tag: ln

tag: t

tag: n


title: siControl-2

tag: cell line

tag: treatment

value: siControl


title: RPp10_endo

value: endocervix

tag: cell type

tag: Sex

tag: timepoint


title: S83

tag: fov

tag: age

tag: grade


title: siHK2-3


title: siControl-1


title: siControl-3


title: S15

value: II

tag: m


title: UM-UC-3 cells, shCDH11#2, 1

city: Toon

first: Osuke

last: Arai

state: Japan

address: Ehime

department: Urology

institute: Ehime Univercity

data_processing:
Fastq files were trimmed using CLC Genomics Workbench (Filgen)
Assembly: hg38
Supplementary files format and content: Comma-separated values file includes raw counts for each Sample

extract_protocol:
Ctrl and CDH11 KD cell lines were precultured in 12-well plate (2 × 105 cells/well) for 24 hours. Total RNA samples were extracted using RNeasy spin column kits and DNase I.
RNA integrity number was verified using an Agilent 2100 Bioanalyzer.RNA-seq was performed on an Illumina NextSeq 500 with a read configuration of 75 bp for single reads; 3 million reads were generated per sample.

value: CDH11 knockdown


title: UM-UC-3 cells, shCDH11#2, 3


title: HI3

first: Jinyang

last: Gu

address: 1277 Jiefang avenue

institute: Union hospital, Tongji medical college, Huazhong university of science and technology

source_name: Liver

value: Liver

value: WT

value: HFD-IRI


title: RPp10_ecto

value: ectocervix

tag: haplotype

tag: vaccination


title: HI2


title: S102

city: Zhuhai

first: Hongzhen

last: Tang

address: Cuijing Road, Qianshan, Xiangzhou District

institute: BioMega Spatiotemporal Pathology Research Center

tag: stage#

tag: Stage

value: IV


title: RPm15_vag

tag: tissue

value: vagina


title: UM-UC-3 cells, shCDH11#1, 3


title: S85

value: IIIb

tag: ln


title: RPm15_UTER

source_name: uterus

value: uterus

value: all


title: HI1

tag: genotype


title: UM-UC-3 cells, shCDH11#1, 2


title: RPm15_endo

value: female


title: S99

value: Ib

tag: t

tag: n


title: UM-UC-3 cells, shCDH11#2, 2

tag: cell line

tag: treatment


title: HS3

value: HFD-Sham


title: UM-UC-3 cells, shCDH11#1, 1


title: HS2


title: UM-UC-3 cells, shCtrl, 3


title: S44

value: gastric cancer

tag: Sex


title: RPm15_ecto

tag: cell type

value: heterologous virus vectors VSVnj, rVV, rAd5 encoding SIV-gag

value: 20mg CM9 peptide intravaginal challenge

tag: timepoint


title: RNf15_vag


title: RNf15_ecto


title: S23

tag: fov

tag: age

value: Ia


title: S55

tag: grade

tag: m


title: RMs16_vag

tag: haplotype

tag: vaccination

value: no intravaginal challenge


title: NI2

value: Liver

value: ND-IRI


title: NI3

value: WT


title: HEK293T cells, Parental, rep 3

city: Albany

first: Cara

middle: T

last: Pager

state: NY

address: 1400 Washington Avenue

institute: University at Albany, State University of New York

data_processing:
After sequencing the quality of the fastq files were checked using the program FastQC (version 0.11.9).
STAR (version 2.7.10a) was used to align the fastq files to the hg38 genome with the --quantModeGeneCounts option added to count the reads per gene.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files contain the raw read count abundances for each sample.

growth_protocol: HEK293Tcells (parental) were stably transfected using the piggyBAC transposon system tointegrate both ATG-(CAG)60-Myc-NLuc and ATG-(CAG)0-Myc-FLucconstructs into the HEK293T cell genome. Cells were single cellsorted and clonesthat express both integrands at high (clone 37) and low (clone 15) levels were selectedfor detailedcharacterisation by RNA sequencing. Parental, clone 15 and clone 37cell lines were cultured in DMEM supplementedwith 10% fetal bovine serum (FBS)and 1x penicillin/streptomycin in a humidified atmosphere at 37 degrees C at 5%CO2.

extract_protocol:
RNA for CAG containingreporter cell lines was extracted using Aurum total RNA mini kit (BioRad) withon-column DNase treatment, following themanufacturer’s protocol. The Qubit RNA high sensitivity assay wasused to obtain RNA concentrations(Thermo Fisher Scientific). RNA quality waschecked via capillary electrophoresis on a 5300 fragment analyzer (AgilentBioanalyzer) using the RNA AnalysisDNF-471 RNA kit (Agilent).
The NEBNext Ultra IIDirectional RNA Library Prep Kit (Illumina) with NEBNext rRNA Depletion Kit(New EnglandBiolabs) was used to prepare RNA-seq libraries, with a total of500 ng input RNA from each sample. The manufacturer’sprotocols were followed,with the following exceptions: 40× adaptor dilutions were used, and 13 cyclesof libraryamplification were performed. The resulting libraries were pooled inequimolar amounts, quantified using the NEBNextLibrary Quant Kit for Illumina(New England Biolabs), quality checked via capillary electrophoresis on the5300fragment analyzer (Agilent Bioanalzyer) using the DNF-474 HS NGS kit(Agilent). Libraries with sufficient quantitywere sequenced using paired-end, 75 base pairsequencing (parental and clone 37), or 100 base pair sequencing (clone 15) onthe Illumina NextSeq 500 sequencer at the University at AlbanyCenter for functional genomics. All datasets had total read depths greaterthan 40 million reads.

value: Human embryonic kidney

value: Parental


title: UM-UC-3 cells, shCtrl, 2


title: UM-UC-3 cells, shCtrl, 1


title: S62

tag: stage#

tag: Stage


title: HEK293T cells, Parental, rep 2


title: NI1

tag: tissue


title: RMs16_uter


title: NS3

tag: genotype

value: ND-Sham


title: RMs16_endo

value: endocervix


title: S63

value: IV

tag: ln

tag: t


title: RMs16_ecto

value: ectocervix

value: all


title: NS2