title: Notch 1 ICD Stage 28 Sample 1


title: 7822-JF-30

status: Public on Dec 14 2024

type: SRA

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

country: USA

institute: Michigan Medicine

library_source: transcriptomic

data_processing:
For bulk RNA-seq, tissue was processed, RNA was isolated as previously described by our group (38), and 150bp paired-end reads were generated. The reads were adapter trimmed and aligned to the human genome hg38, with only the uniquely mapped reads used for expression level quantification. DESeq2 was used to perform read normalization and differential expression analyses.
Assembly: hg38
Supplementary files format and content: gene by sample count matrix

molecule: total RNA

organism: Homo sapiens

source_name: skin

extract_protocol:
Fresh frozen tissue via 3 mm punch biopsies were collected from LP lesional skin and normal appearing skin for bulk RNA-sequencing.
RNA sequencing was performed by the U-M Advanced Genomics Core on the Novaseq 6000 platform

tag: tissue

value: skin


title: keratin + trace-elements; T. rubrum STRB012; rep III [12_A_III]

city: Nanchang

first: Oliver

last: Blechert

address: Fusheng Road 666

country: China

institute: Affiliated Hospital of Jiangxi University of Chinese Medicine

data_processing:
mRNA fragments mapped with hisat2
assigned to gene IDs and counted with htseq-count
normalized to counts per million (CPM)
Assembly: Trichophyton  rubrum assembly ASM15142v1
Supplementary files format and content: xls file with data normalized to counts per million (CPM)

organism: Trichophyton rubrum

source_name: hyphae

growth_protocol: The fungus has been pre-cultured in liquid keratin medium (2 g keratin, 1.8g KH2PO4 and 0.1g MgSO4 per liter; pH 5.8) for two weeks at 28°C with 140rpm.

extract_protocol:
RNA extraction kit for plants from Tiangen, Beijing
NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: After pre-culture, the fungus has been aliquot to keratin medium (1 g keratin, 1.8g KH2PO4 and 0.1g MgSO4), keratin medium with trace-elements (1.0 mM CaCl2, 1.0 mM MnCl2, 1.0 mM ZnSO4, 0.2 mM CoCl2, 0.2 mM NiCl2, 0.1 mM H3BO3, 0.1 mM CuSO4, 0.1 mM FeCl3, 0.1 mM KI, 0.1 mM Na2MoO4) and keratin medium with glucose (20g/l).

tag: strain

tag: cell type

value: hyphae

tag: genotype

value: WT

tag: treatment

value: trace-elements


title: Notch 1 ICD Stage 18 Sample 3

city: Williamsburg

first: Margaret

middle: S

last: Saha

state: Virginia

address: 540 Landrum Drive

department: Biology

institute: College of Wiliam & Mary

description:
Illumina Hi-Seq High-Ouput v3 - PE 50 Cycle
Column 1: gene symbol, Column 2: Counts

data_processing:
Quality checks were performed on the raw data using FASTQC . If adapters were present, the sequences were trimmed with Trim Galore
Sequences were aligned to the reference Xenopus laevis genome using HISAT2 and sorted by name
Ran HTSeq counts program on terminal to obtain counts for genes
Assembly: Xenopus laevis 10.1 genome (NCBI)
Supplementary files format and content: tab delimited text file that includes the HTSeq counts for each sample along with gene symbols

molecule: polyA RNA

organism: Xenopus laevis

source_name: Xenopus laevis embryos (neurula, tailbud, swimming tadpole stages)

extract_protocol:
RNA was extracted with 4-bromoanisole and purified using the RNeasy Mini Kit (Qiagen)
RNA libraries for RNA-seq were prepared using Illumina Truseq Stranded mRNA Prep Kit following manufacturer's protocols.

tag: time

value: Stage 18 (neurula stage)

value: ICD treatment


title: Notch 1 ICD Stage 38 Sample 3

value: Xenopus laevis embryos (neurula, tailbud, swimming tadpole stages)

value: Stage 38 (swimming tadpole stage)


title: ATACseq of D17 hiPSC-CMs Rep3

city: Boston

first: Seong Won

last: Kim

state: MA

address: 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
Library name: hiPSC D17 rep3
PGP1_D17_ATAC_hg38_nolocal_bb.bb
PGP1_D17_ATAC_hg38.bigWig

library_source: genomic

data_processing:
Sequencing reads were aligned to the hg38 reference genome using BWA-MEM. Biological replicates were merged, and peaks were called using HOMER .
Assembly: hg38
Supplementary files format and content: Biological replicates were merged, and HOMER was used to generate bigwig and bigbed files, which are linked to the corresponding rep1 sample records.

molecule: genomic DNA

extract_protocol:
50,000 cells were harvested and lysed to isolate nuclei, which were treated with Tn5 transpose (Nextera DNA Sample Prep Kit, Illumina).
Fragmented DNA was amplified using barcoded PCR primers, and pooled libraries were sequenced to a depth of 10 million reads per sample (Illumina Next-Seq).

tag: cell line

value: hiPSC-CM


title: 7822-JF-2


title: keratin + trace-elements; T. rubrum STRB012; rep II [12_A_II]


title: Notch 1 ICD Stage 18 Sample 2


title: ATACseq of D17 hiPSC-CMs Rep2

description:
Library name: hiPSC D17 rep2
PGP1_D17_ATAC_hg38_nolocal_bb.bb
PGP1_D17_ATAC_hg38.bigWig


title: 7822-JF-29


title: Notch 1 ICD Stage 18 Sample 1


title: 7822-JF-28


title: keratin; T. rubrum STRB012; rep VI [12_K_VI]

value: keratin


title: ATACseq of D17 hiPSC-CMs Rep1

description:
Library name: hiPSC D17 rep1
PGP1_D17_ATAC_hg38_nolocal_bb.bb
PGP1_D17_ATAC_hg38.bigWig


title: Notch 1 GFP Stage 38 Sample 3

value: GFP treatment


title: keratin + trace-elements; T. rubrum STRB012; rep I [12_A_I]


title: 7822-JF-27


title: keratin; T. rubrum STRB012; rep V [12_K_V]


title: 7822-JF-26


title: Notch 1 GFP Stage 38 Sample 2


title: ATACseq of D8 hiPSC-CMs Rep2

description:
Library name: hiPSC D8 rep2
PGP1_D08_ATAC_hg38_nolocal_bb.bb
PGP1_D08_ATAC_hg38.bigWig


title: keratin + trace-elements; T. rubrum STRB012; rep IV [12_A_IV]


title: ATACseq of D8 hiPSC-CMs Rep1

description:
Library name: hiPSC D8 rep1
PGP1_D08_ATAC_hg38_nolocal_bb.bb
PGP1_D08_ATAC_hg38.bigWig


title: Notch 1 GFP Stage 38 Sample 1


title: 7822-JF-25


title: 7822-JF-24


title: ATACseq of D4 hiPSC-CMs Rep2

description:
Library name: hiPSC D4 rep2
PGP1_D04_ATAC_hg38_nolocal_bb.bb
PGP1_D04_ATAC_hg38.bigWig


title: Notch 1 GFP Stage 28 Sample 3

value: Stage 28 (tailbud stage)


title: ATACseq of D4 hiPSC-CMs Rep1

description:
Library name: hiPSC D4 rep1
PGP1_D04_ATAC_hg38_nolocal_bb.bb
PGP1_D04_ATAC_hg38.bigWig


title: keratin; T. rubrum STRB012; rep II [12_K_II]


title: Notch 1 GFP Stage 28 Sample 2


title: 7822-JF-23


title: keratin; T. rubrum STRB012; rep I [12_K_I]


title: ATACseq of D0 hiPSCs Rep2

description:
Library name: hiPSC D0 rep2
PGP1_D00_ATAC_hg38_nolocal_bb.bb
PGP1_iPSC_ATAC_hg38.bigWig

value: hiPSC


title: Notch 1 GFP Stage 28 Sample 1


title: keratin + glucose; T. rubrum STRB012; rep VI [12_G_VI]

value: glucose


title: keratin; T. rubrum STRB012; rep III [12_K_III]


title: Notch 1 GFP Stage 18 Sample 3


title: hiPS-EC_149_2

city: Porvoo

first: Sabina

middle: Henrika

last: Selenius

address: Mika Waltarin katu 49

department: Stem Cells and Metabolism Research Program (STEMM), New Children's Hospital Pediatric Research Center

country: Finland

institute: Univeristy of Helsinki, Helsinki University Hospital

data_processing:
Chipster software 47
Differential expression was calculated using DEseq2.
Assembly: Homo_sapiens.GRCh38.95
Supplementary files format and content: Raw counts for each sample and repeat

source_name: hiPS

extract_protocol:
RNA was harvested using the Nucleospin RNA Plus Extraction kit (740984, Macherey-Nagel)
llumina Stranded Total RNA Prep with Ribo-Zero Plus.

value: hiPS

value: ErBB2 mutation

value: Endothelial cell differentiation


title: Notch 1 GFP Stage 18 Sample 2


title: 7822-JF-20

value: skin


title: keratin; T. rubrum STRB012; rep IV [12_K_IV]

value: hyphae


title: 7822-JF-21


title: keratin + glucose; T. rubrum STRB012; rep IV [12_G_IV]

value: WT


title: 7822-JF-1


title: keratin + glucose; T. rubrum STRB012; rep III [12_G_III]


title: 7822-JF-19


title: hiPS-EC_47_2


title: hiPS-EC_K1_2


title: hiPS-EC_149_1


title: 7822-JF-18


title: hiPS-EC_24.3_2


title: keratin + glucose; T. rubrum STRB012; rep I [12_G_I]


title: hiPS-EC_K1_1


title: 7822-JF-22


title: 7822-JF-17


title: 7822-JF-16


title: ATACseq of D0 hiPSCs Rep1

description:
Library name: hiPSC D0 rep1
PGP1_D00_ATAC_hg38_nolocal_bb.bb
PGP1_iPSC_ATAC_hg38.bigWig


title: hiPS-EC_24.3_1


title: keratin + trace-elements; T. rubrum STRB008; rep VI [8_A_VI]

value: trace-elements


title: hiPS-EC_47_1


title: 7822-JF-15


title: keratin + trace-elements; T. rubrum STRB008; rep V [8_A_V]


title: keratin + glucose; T. rubrum STRB012; rep V [12_G_V]


title: keratin + trace-elements; T. rubrum STRB008; rep IV [8_A_IV]


title: 7822-JF-13


title: keratin + trace-elements; T. rubrum STRB008; rep III [8_A_III]


title: 7822-JF-14


title: G(-)OM-2

city: Goyang-si

first: Seo-Young

last: Park

address: 32, Dongguk-ro, Ilsandong-gu

country: South Korea

institute: Dongguk university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: bone marrow stromal/stem cells

growth_protocol: The hBMSCs were seeded onto 100 mm dishes at density of 1 × 107 cells per dish in αMEM supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin 100X.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Osteogenic differentiation was induced with osteogenic medium (OM: DMEM with 10% FBS, 10 mM glycerolphosphate, 1% penicillin–streptomycin, 100 nM dexamethasone, 50 nM L-ascorbic acid-2-phosphate). DMEM with low glucose was used to make 5.5 mM glucose-supplemented osteogenic medium and DMEM without glucose was used to make glucose-free osteogenic medium (OM)

tag: passages

value: 4 to 6

value: bone marrow


title: Notch 1 GFP Stage 18 Sample 1

value: Xenopus laevis embryos (neurula, tailbud, swimming tadpole stages)

value: Stage 18 (neurula stage)


title: 7822-JF-12


title: keratin + trace-elements; T. rubrum STRB008; rep II [8_A_II]


title: keratin + trace-elements; T. rubrum STRB008; rep I [8_A_I]


title: 7822-JF-11


title: keratin + glucose; T. rubrum STRB012; rep II [12_G_II]


title: G(+)OM-3


title: keratin; T. rubrum STRB008; rep VI [8_K_VI]


title: ICD Stage 38 Sample 3

description:
Illumina HiSeq 3000/4000 - PE 150 Cycle
Column 1: gene symbol, Column 2: Counts

organism: Xenopus borealis

source_name: Xenopus Borealis embryos (neurula, tailbud, swimming tadpole stages)

extract_protocol:
RNA was extracted with 4-bromoanisole and purified using the RNeasy Mini Kit (Qiagen)
Illumina Truseq Stranded mRNA Library prep kit

value: Stage 38 (swimming tadpole stage)

value: ICD Treatment


title: 7822-JF-10


title: G(+)OM-2


title: keratin; T. rubrum STRB008; rep V [8_K_V]

value: keratin


title: keratin; T. rubrum STRB008; rep IV [8_K_IV]


title: ICD Stage 38 Sample 2

value: Xenopus Borealis embryos (neurula, tailbud, swimming tadpole stages)


title: ICD Stage 38 Sample 1


title: G(+)CM-3


title: THP1, shIRF2BP2, H3K27ac, ChIP

city: New York

first: Zhengxi

last: Sun

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Medical Center

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software
Sequences were then aligned to the Homo sapiens genome (hg19/GRCh37) using the Bowtie2 aligner (67) (v2.3.4.1)
Duplicate reads were removed using sambamba markdup. Peaks were determined algorithmically using Model-based Analysis of ChIP-Seq 2 algorithm (v1.4.2) with q < 0.05
Heatmaps for regions of interest were plotted with deeptools (v3.5.1)
Assembly: hg19
Supplementary files format and content: bigwig for each samples

growth_protocol: THP-1 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-Glutamine, 1X Penicillin/Streptomycin, 1 mM Sodium Pyruvate, and 20 mM HEPES. All cells were maintained at 37°C and in a 5% CO2 atmosphere.

extract_protocol:
THP-1 cells transduced with shRNAs were selected with puromycin for 1 week and induced for 4 days with doxycycline before sorting by flow cytometry. 10 million cells per condition were crosslinked with 1% formaldehyde at the density of 1 ml 1% formaldehyde per 1 million cells and incubated at room temperature (RT) for exactly 10 minutes rotating before quenched by 2.5M glycine (20x, final concentration 125 nM) at RT for 5 minutes rotating. Cells were lysed in Nuclei Isolation Buffer (final concentration 15 mM Tris pH 7.5, 60 mM KCl, 15 mM NaCl, 15 mM MgCl2, 1 mM CaCl2, 250 mM Sucrose, 1 mM DTT and protease inhibitor) on ice for 5 minutes. Additional NP-40 with a final concentration 0.3% was added into the reaction for 5 minutes at RT to facilitate the lysis. Nuclei pellets were then spun down, resuspended in 130 ul Nuclei Lysis Buffer (final concentration 50 mM Tris pH 8.0, 10 mM EDTA pH 8.0, 1% SDS, protease inhibitor) and sheared for ~15 cycles using a Diagenode Bioruptor instrument. 0.5% of the sheared chromatin was saved at -80 degrees for input and the rest were incubated in 1 ml IP dilution buffer (final concentration 0.01% SDS, 1% Triton X-100, 1.2 mM EDTA pH 8.0, 16.7 mM Tris pH 8.0, 167 mM NaCl and protease inhibitor) with 5 ug H3K27ac antibody (active motif #39133) at 4 degrees rotating overnight. 25 ul protein G Dynabeads (invitrogen, #10003D) per reaction were added the next day into the sample and incubated at 4 degrees rotating for 4 hours. Samples were then washed twice sequentially with low salt (0.1% SDS, 1% Triton X-100, 2 mM EDTA pH 8.0, 20 mM Tris pH 8.0, 150 mM NaCl), high salt (0.1% SDS, 1% Triton X-100, 2 mM EDTA pH 8.0, 20 mM Tris pH 8.0, 500 mM NaCl), LiCl (10 mM Tris pH 8.0, 250 mM LiCl, 1% NP40, 1% sodium deoxycholate, 2 mM EDTA pH 8.0) and TE buffers (1 mM Tris pH 8.0, 0.5M EDTA pH 8.0) with each incubate for 5 minutes rotating at 4 degree. Samples were then eluted in a 50 ul elution buffer (100 mM sodium bicarbonate, 1% SDS) twice (total 100 ul). RNAse A, proteinase K and 0.3 M NaCl were added to the samples to reverse cross-linking overnight at 65 degrees. DNA was then purified using phenol/chloroform.
ChIP-seq libraries were prepared using ThruPLEX® DNA-Seq Kit (Takara Bio #R400674). Library were pooled and indexed using DNA Single Index Kit (Takara Bio #R400697) before being sequenced on a NovaSeq instrument

value: human AML

value: IRF2BP2 knockdown

tag: chip antibody

value: H3K27ac (Active Motif, # 39034)


title: G(+)CM-2


title: G(-)OM-3


title: THP1, scramble, H3K27ac, ChIP


title: keratin; T. rubrum STRB008; rep II [8_K_II]


title: ICD Stage 28 Sample 3

value: Stage 28 (tailbud stage)


title: pNET, scRNA-seq

city: Moscow

first: Alesya

last: Maluchenko

address: Kulakova str. 20

country: Russia

institute: Moscow Center for Advanced Studies

description: SurfSeq 5000

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0. Quality control included removal of cells with inappropriate gene-umi relationship using gene.vs.molecule.cell.filter (pagoda2 package), high mitochondrial (> 20 %) or ribosomal (> 20 %) RNA content. Droplets, containing multiplets were removed using Scrublet package. Expression profile was corrected for ambient RNA using DecontX from celda package. Next, cells containing > 500 UMIs and > 250 unique genes were remained.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix file

source_name: pancreatic neuroendocrine tumor

extract_protocol:
Fresh tumor tissues were mechanically chopped with scalpels on a plate and enzymatically digested with collagenase type IV (Servicebio) and DNAse I (Magen). Following digestion, the cell suspension was subjected to erythrocyte removal using the red blood cell lysis buffer (QuantoBio). Cell suspension was filtered through a 70 μm strainer (MACS), and dissociated cells were pelleted and re-suspended in phosphate buffer saline (PBS) with 0.04% BSA (bovine serum albumin).
The Chromium Next GEM Single Cell 5' v2 Kit (10× Genomics, USA) and the Chromium Single Cell Controller Instrument were used to generate a 10× single-cell library according to the manufacturer’s instructions.

value: pancreatic neuroendocrine tumor

tag: age

tag: Sex

value: female


title: G(-)OM-1

description: NG-before


title: ICD Stage 28 Sample 2


title: THP1, Input


title: G(+)CM-1

description: UN-before


title: ICD Stage 28 Sample 1


title: keratin; T. rubrum STRB008; rep I [8_K_I]

value: hyphae


title: THP1, sgNT, rep 2

data_processing:
Sequence alignment was performed with STAR (version 2.7.3a) using GRCh37.p13 human assembly
Differential analysis was done using DESeq2 (version 1.32.0)
KEGG and GO pathway analyses were done with the R package clusterProfiler (version 4.0.0)
Assembly: hg19
Supplementary files format and content: excel files includes tpm counts for each sample

growth_protocol: THP-1 and MOLM-13 cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-Glutamine, 1X Penicillin/Streptomycin, 1 mM Sodium Pyruvate, and 20 mM HEPES. All cells were maintained at 37°C and in a 5% CO2 atmosphere.

extract_protocol:
THP-1 or MOLM-13 cells were transduced with the indicated sgRNAs for 4 days before sorting for GFP+ cells. Experiments were performed in duplicates with two sgRNAs targeting IRF2BP2. RNA was extracted using the RNeasy Kit (QIAGEN #74004). PolyA mRNA was enriched using NEXTFLEX PolyA Beads(#NOVA-512991)
Libraries were constructed using NEXTFLEX Rapid Directional RNA-seq kit (#NOVA-5198-01)

value: WT


title: adult_thy_untreated

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

data_processing:
The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline (version 7.0.0). The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix.
Assembly: Zebrafish Ensembl GRCz11 reference
Supplementary files format and content: count matrices from the NovaSeq platforms

organism: Danio rerio

source_name: 13 weeks post-fertilization

growth_protocol: Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital (ARCH) guidelines.

extract_protocol:
Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi into 0.5% BSA in HBSS without calcium or magnesium at room temperature. Live cells were sorted (85 um nozzle) on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Sorted cells were assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended in 0.5% BSA in DPBS.
Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits (10x Genomics, Inc.). A targeted recovery of between 4,000 and 6,000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide (Rev D). The final transcriptome libraries were pooled and sequenced at the Harvard University Bauer Core (https://bauercore.fas.harvard.edu/) on an Illumina NovaSeq 6000 (Read 1: 28 cycles, i7 index: 8 cycles, i5 index: 0 cycles, Read 2: 91 cycles).

value: 13 weeks post-fertilization


title: keratin + glucose; T. rubrum STRB008; rep VI [8_G_VI]

value: glucose


title: THP1, sgNT, rep 1


title: adult_thy_liberase_2


title: adult_thy_liberase_1


title: THP1, sgIRF2BP2#2, rep 2

value: IRF2BP2 knockout


title: ICD Stage 18 Sample 2


title: keratin + glucose; T. rubrum STRB008; rep V [8_G_V]


title: G(+)OM-1

description: HG-before

value: 4 to 6

value: bone marrow


title: keratin + glucose; T. rubrum STRB008; rep IV [8_G_IV]


title: keratin; T. rubrum STRB008; rep III [8_K_III]


title: ICD Stage 18 Sample 1

value: Stage 18 (neurula stage)


title: keratin + glucose; T. rubrum STRB008; rep III [8_G_III]


title: TTg, Heart failure, replicate3, RNA-seq

city: Tsukuba

first: Yu

last: Yamada

state: Ibaraki

address: 1-1-1 Tennoudai

department: Cardiovascular

country: Japan

institute: University of Tsukuba

data_processing:
FASTQ files were imported to CLC Genomics Workbench (Ver 10.1.1, Qiagen).
Reads were mapped to mouse reference genome (mm10).
CLC Main Workbench(Ver 21.0.4, Qiagen) was used for the downstream analysis.
Total counts were normalized by scaling method. Transformed values (log2-converted after adding 1 to the normalized expression value) were used for Heatmap creation.
Low-expression genes (normalized expression value did not exceed 10 in any sample) were excluded before DGE analysis.
Differentially expressed genes were identified using Empirical Analysis of DGE tool.
Assembly: mm10
Supplementary files format and content: Microsoft Excel file  with raw counts, normalized expression values and transformed values for every gene

organism: Mus musculus

source_name: Whole ventricle

extract_protocol:
Mice were sacrificed by CO2 inhalation, and hearts were immediately cannulated and perfused with cold PBS. After the heart was harvested, the atria and valves were removed, and  RNA was extracted using Trizol reagent.
500 ng total RNA is used for rRNA-depletion (NEB, E6310), followed by directional library synthesis (NEB, E7420)

treatment_protocol: The HFpEF (Heart failure with preserved ejection fraction) model was induced by administering a high-fat diet (HFD, 60% kilocalories from fat) and Nω-Nitro-L-arginine methyl ester hydrochloride (L-NAME, Sigma, Cat# N5751-25G) for 15 weeks. L-NAME was dissolved in drinking water (1.0 g/L）. Tamoxifen (2 mg/day; Sigma, T5648) was administered intraperitoneally for 5 consecutive days at week 5.

value: Whole ventricle

value: hybrid of C57BL/6 and ICR

value: Tcf21iCre/R26 tdTomato/MGTH2A

value: male

value: LNAME+High fat diet, tamoxifen i.p. at week 5

tag: group


title: THP1, sgIRF2BP2#1, rep 2

value: human AML


title: keratin + glucose; T. rubrum STRB008; rep II [8_G_II]


title: TTg, Heart failure, replicate2, RNA-seq


title: GFP Stage 38 Sample 2

value: Xenopus Borealis embryos (neurula, tailbud, swimming tadpole stages)

value: Stage 38 (swimming tadpole stage)

value: GFP Treatment


title: keratin + glucose; T. rubrum STRB008; rep I [8_G_I]

value: hyphae


title: GFP Stage 38 Sample 1


title: Ctrl, Heart failure, replicate3, RNA-seq

value: Tcf21iCre/R26 tdTomato


title: MOLM13, sgNT, rep 2

value: WT


title: TTg, Heart failure, replicate1, RNA-seq


title: ICD Stage 18 Sample 3

value: ICD Treatment


title: PALMD+/-3

city: Beijing

first: Jichao

last: Zhang

address: 2 Anzhen Ave

institute: Beijing Anzhen Hospital, Capital Medical University

data_processing:
Perl script was used to filter the original data (Raw Data). The steps are: 1) Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed ); 2) Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads); 3) Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads); 4) Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads).
The reference genomes and the annotation file were downloaded from ENSEMBL database(http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index,and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes
Genome_build: Mus_musculus.GRCm38.90.chr
Supplementary_files_format_and_content: FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes

source_name: aorta

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manual instructions. For tissue samples, grind about 60mg with liquid nitrogen into powder and transfer the powder samples into the 2ml tube contains 1.5ml Trizol reagent. The mix was centrifuge at 12000×g for 5min at 4°C. The supernatant was transferred to a new 2.0ml tube which was added 0.3ml of Chloroform/isoamyl alcohol (24:1) per 1.5ml of Trizol reagent. After the mix was centrifuged at 12000×g for 10min at 4°C, the aqueous phase was transferred to a new 1.5mL tube which was add equal volume of supernatant of isopropyl alcohol. The mix was centrifuged at 12000×g for 20min at 4°C and then removed the supernatant. After washed with 1ml 75% ethanol, the RNA pellet was air-dried in the biosafety cabinet and then dissolved by add 25µL~100µL of DEPC-treated water. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
 A total amount of 2μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® （NR604-01/02）following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Then we added fragmentation buffer to break the mRNA into short fragments. First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. And then, the double stranded cDNA was purified byAMPure P beads or QiaQuick PCR kit. The purified double stranded cDNA was repaired at the end, added a tail and connected to the sequencing connector, then the fragment size was selected, and finally the final cDNA library was obtained by PCR enrichment.

treatment_protocol: Mice (8 weeks old) were feed with normal diet  7 weeks.

value: aorta

value: PALMD+/-


title: GFP Stage 28 Sample 3

value: Stage 28 (tailbud stage)


title: Ctrl, Heart failure, replicate2, RNA-seq


title: PALMD+/-2


title: MOLM13, sgIRF2BP2#2, rep 2

value: IRF2BP2 knockout


title: PALMD+/-1


title: GFP Stage 38 Sample 3


title: Ctrl, Heart failure, replicate1, RNA-seq

value: Whole ventricle


title: GFP Stage 28 Sample 1


title: THP1, sgIRF2BP2#2, rep 1


title: MOLM13, sgIRF2BP2#2, rep 1


title: Ctrl3

value: wild type


title: GFP Stage 18 Sample 3

value: Stage 18 (neurula stage)


title: MOLM13, sgIRF2BP2#1, rep 2


title: Ctrl, normal chow, replicate2, RNA-seq

value: hybrid of C57BL/6 and ICR

value: male

value: normal chow, tamoxifen i.p. at week 5

value: Ctrl


title: Ctrl2


title: MOLM13, sgIRF2BP2#1, rep 1

value: human AML


title: GFP Stage 18 Sample 2

value: Xenopus Borealis embryos (neurula, tailbud, swimming tadpole stages)

value: GFP Treatment


title: Ctrl, normal chow, replicate1, RNA-seq

value: Tcf21iCre/R26 tdTomato


title: Ctrl1


title: GFP Stage 18 Sample 1


title: Mouse Lung ILC Pool 2

status: Public on Dec 13 2024

city: OKLAHOMA CITY

first: Susan

middle: E

last: Kovats

state: OK

address: 825 NE 13TH ST.

institute: OKLAHOMA MEDICAL RESEARCH FOUNDATION

description: Pooled male & female cells. Read 1 contains the 16bp Cell Barcode followed by a 12bp UMI. Read 2 contains a potential hashtag followed by the 3' mRNA sequence.

data_processing:
Single-cell multiplexing and sequencing. Cell capture was performed using the 10x Genomics Chromium system followed by sequencing on an Illumina HiSeq 3000, each according to the manufacturer’s protocol. Following qPCR quantification of the final library, each library was loaded onto a single lane of a HiSeq 3000 using read lengths of 28 bp for the first read, 98 bp for the second read, and an 8 base index read. Upon completion of sequencing the raw bcl files were processed using the 10x Genomics Cell Ranger (v3.0.2) informatics pipeline, using the mm10 murine reference genome. The protocol was repeated to produce two total cell pools, yielding transcriptome profiles for 4976 and 5516 cells for pool 1 and pool 2, respectively.
Single-cell RNA-seq quality control and cell sex determination. We performed quality control on each pool separately by removing cells under any of the following conditions: 1) The number of expressed genes fell outside the 1st or 99th quantile across all cells in the pool; 2) The proportion of mitochondrial reads was above the 99th quantile across all cells; 3) The sex of the donor mouse was not determined, or 4) the probability of being a cell doublet was estimated to be greater than 33% as estimated by the Scrublet method 31. This probability threshold was chosen based on the 99th percentile of Scrublet estimates across all cells. 7388 total cells remained after quality control. Cell hashing antibody tags labeling male and female mouse cell pools were recovered from reads via native cellranger count functionality as well as the CITE-seq-count tool (https://cite-seq.com/). We also used the following scheme to determine cell donor sex: If the sum expression of Y-chromosome-specific genes Uty, Ddx3y and Eif2s3y was positive and zero Xist counts were observed, then the cell is male. Otherwise, if Xist expression is positive and the sum of the above Y-chromosome genes is zero, then the cell is female.
Assembly of pooled datasets and clustering. To control for technical variation across pools, we performed data integration using R package Seurat v3.0. Pools were individually normalized using the SCTransform function with default options. Next, 5000 anchor features were selected across both pools and datasets were merged with the IntegrateData function. Linear dimensionality reduction was performed using PCA and retaining the first 90 principal components. Clustering was performed using the Louvain method via the FindNeighbors and FindClusters functions with the following options: dims=1:50, resolution=0.3.
Genome_build: mm10
Supplementary_files_format_and_content: matrix_counts.mtx contains normalized gene expression counts from Seurat's SCTransform function post-integration across both pools of sequencing data. The data is presented in MatrixMarket format.
Supplementary_files_format_and_content: matrix_rowData.txt provides the gene symbols corresponding to the rows in matrix_counts.mtx.
Supplementary_files_format_and_content: matrix_ccolData.txt provides the metadata corresponding to the columns in matrix_counts.mtx. The columns of this file are Barcode (The cellular barcode, followed by an underscore, and a number indicating Pool 1 or 2), tech (indicates pool of sequencing, either Round 1 or Round 2 for pool 1 or pool 2, respectively), sex (The predicted sex of the cell based on sex-determining genes or hashtags when available), seurat_clusters (The numerical indicator of clusters identified during the analysis),  UMAP_1 and UMAP_2 (coordinates of the UMAP projection used to plot the data in two dimensions)

source_name: Lung ILC

extract_protocol: Single cell RNA sequencing (scRNA-seq) preprocessing and analysis: Female and male mice were infected with PR8 virus intranasally, and lungs were harvested at day 7 p.i.  Lung ILCs were pooled from 4-5 female or male mice and sorted as lineage-negative (CD3, CD5, TCRβ, B220, CD11b, CD11c, TER119, Gr-1, CD19) CD90+IL-7Rα+ cells using a BD FACS Aria II instrument. Female and male ILCs were tagged with distinct Totalseq anti-mouse Hashtag (1 and 2) mAbs (anti-CD45 and MHCI) (Biolegend) to facilitate separation of the ILCs by sex in the sequencing analysis.

treatment_protocol: Mice were infected intranasally with PR8 virus and administered BrdU (0.8 mg per mouse) by intraperitoneal injection at day 4, 5 and 6 p.i.  Incorporation of BrdU was detected in lung cells of infected mice at day 7 p.i. by flow cytometry using the manufacturer’s protocol (BD Biosciences).

value: 12-16 weeks

tag: hashtag

tag: chemistry

value: 10x Chromium Single Cell 3' v3


title: Mouse Lung ILC Pool 1

description: Pooled male & female cells. Read 1 contains a 16bp barcode and 10bp UMI. Hashtags were lost for this round of sequencing and will not be present on Read 2. Sex is determined by expression of sex chromosome-specific gene expression.

value: 10x Chromium Single Cell 3' v2


title: Fetal sample of baby from mother 80

type: genomic

city: Ciudad Autónoma de Buenos Aires

first: Bruno

middle: Gabriel

last: Berardino

state: Buenos Aires

address: Intendente Güiraldes 2160, Ciudad Universitaria

department: Biological Chemistry Department

country: Argentina

institute: University of Buenos Aires

description: Umbilical cord blood genomic DNA from newborn

hyb_protocol: Starting with 500 ng of genomic DNA, bisulfite conversion and DNAm profiling were performed according to the manufacturer's instructions for Illumina Human Methylation EPIC BeadChip Array. Assays were performed at Diagenode Inc.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommenden Illumina scanner setting.

data_processing: ewastools and DMRcate on R environment (v4.2.1)

label: Cy3 and Cy5

source_name: Umbilical cord blood

label_protocol: Standard Illumina protocol.

extract_protocol: The umbilical cord blood and maternal peripheral blood were collected in EDTA blood collection tubes at delivery and immediately frozen to -80°C until use. Samples were thawed on ice and genomic DNA was extracted using the DNA PuriPrep-S kit (INBIO Highway, Argentina). This protocol includes incubation with an isotonic erythrocyte lysis solution which enriches the sample in leucocytes. DNA integrity was assessed by agarose gel electrophoresis with ethidium bromide staining and samples were quantified using QubitTM dsDNA BR Assay Kit (ThermoFisher, Argentina).

tag: array

value: Array 6

tag: plate position

tag: aitid

value: Male

tag: adverse childhood experiences

tag: maltreatment

value: Umbilical cord blood

tag: concentration ng/ul

tag: total amount (ng)

tag: volume (ul)


title: Fetal sample of baby from mother 92

value: Female

tag: tissue


title: Maternal sample 57

description: Whole blood genomic DNA from pregnant woman in her third trimester

source_name: Whole blood

value: Whole blood


title: Maternal sample 97

value: Array 5


title: Fetal sample of baby from mother 52


title: Maternal sample 63


title: Fetal sample of baby from mother 34


title: Fetal sample of baby from mother 44


title: Maternal sample 5


title: Fetal sample of baby from mother 21


title: Fetal sample of baby from mother 42


title: Maternal sample 7


title: Fetal sample of baby from mother 63


title: Maternal sample 86

value: Array 4


title: Maternal sample 92


title: Maternal sample 85


title: Maternal sample 65


title: Fetal sample of baby from mother 38


title: Fetal sample of baby from mother 65


title: Fetal sample of baby from mother 85


title: Fetal sample of baby from mother 24


title: Fetal sample of baby from mother 86

value: Array 3


title: Maternal sample 21


title: Maternal sample 80


title: Maternal sample 8


title: Fetal sample of baby from mother 57


title: Maternal sample 49


title: Maternal sample 27

value: Array 2


title: Fetal sample of baby from mother 27


title: Fetal sample of baby from mother 53


title: Fetal sample of baby from mother 8


title: Fetal sample of baby from mother 97


title: Fetal sample of baby from mother 25


title: Maternal sample 24


title: Maternal sample 52


title: Fetal sample of baby from mother 5


title: Maternal sample 25


title: Fetal sample of baby from mother 7


title: Maternal sample 62

value: Array 1


title: Fetal sample of baby from mother 49


title: Maternal sample 59


title: Maternal sample 34


title: Maternal sample 44


title: Fetal sample of baby from mother 59


title: Monocytes From HD number 33_b

city: Badalona

first: eva

last: martinez caceres

address: Cami des escoles s/n

country: Spain

institute: Institut Germans Trias i Pujol

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
iDATs were analyzed using a standard pipeline, with the shinyepico package (1.0.0) of the Bioconductor project
Normalized (minfi preprocessNoob + preprocessQuantile) Beta values
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: Monocytes were isolated from MS patients and Healthy donors using CD14 positive enrichment by negative selection followed by CD14 positive selection

extract_protocol: Total DNA was isolated using the Dneasy DNA kit (Qiagen) according to manufacturer’s instruction

tag: gender


title: Monocytes From HD number 32_b


title: Monocytes From HD number 31_b


title: Monocytes From HD number 30_b


title: Maternal sample 53


title: Fetal sample of baby from mother 62


title: Monocytes From HD number 28_b


title: Monocytes from MS patient number 24_b


title: Monocytes from MS patient number 23_b


title: Monocytes From HD number 27_b


title: Monocytes from MS patient number 21_b


title: Monocytes from MS patient number 20_b


title: Monocytes from MS patient number 19


title: Monocytes from MS patient number 17


title: Monocytes From HD number 29_b


title: Monocytes from MS patient number 22_b


title: Maternal sample 38


title: Monocytes From HD number 17


title: Maternal sample 42


title: Monocytes from MS patient number 16


title: Monocytes From HD number 14_b


title: Monocytes from MS patient number 15_b


title: Monocytes From HD number 13_b


title: Monocytes From HD number 12


title: Monocytes from MS patient number 10


title: Monocytes from MS patient number 9


title: Monocytes From HD number 8


title: Monocytes from MS patient number 6


title: Monocytes from MS patient number 4


title: Monocytes From HD number 2


title: Monocytes from MS patient number 26_c


title: Monocytes from MS patient number 25_b


title: THP1, sgIRF2BP2#1, rep 1

tag: cell line

tag: cell type

value: human AML

tag: genotype

value: IRF2BP2 knockout


title: Monocytes From HD number 1_b


title: Monocytes from MS patient number 25


title: Monocytes From HD number 33


title: Monocytes From HD number 29


title: Monocytes from MS patient number 41_b


title: Monocytes from MS patient number 23


title: mDCs From MS patient number 41


title: Monocytes from MS patient number 36


title: Monocytes from MS patient number 41


title: Monocytes From HD number 28


title: tolDCs from HD healthy donor 42


title: mDCs from HD healthy donor 38


title: Monocytes From HD number 14


title: Monocytes from MS patient number 26_b


title: mDCs From MS patient number 10


title: mDCs From MS patient number 21


title: tolDCs From MS patient number 34


title: tolDCs From MS patient number 26


title: tolDCs From MS patient number 21


title: mDCs From MS patient number 24


title: tolDCs From MS patient number 43


title: Monocytes from MS patient number 34


title: Monocytes From HD number 13


title: Monocytes From HD number 42


title: tolDCs from HD healthy donor 31


title: Monocytes from MS patient number 24


title: tolDCs from HD healthy donor 35


title: mDCs from HD healthy donor 31


title: Monocytes From HD number 39


title: Monocytes From HD number 31


title: Monocytes from MS patient number 21


title: Monocytes from MS patient number 26


title: Monocytes from MS patient number 18


title: Monocytes From HD number 37


title: mDCs From MS patient number 36


title: tolDCs From MS patient number 24


title: mDCs From MS patient number 25


title: Monocytes From HD number 32


title: mDCs From MS patient number 26


title: PP2A-CKO

city: Hangzhou

first: Kaixiang

last: Zhu

address: 866  Yuhangtang Road

department: school of medicine

institute: Zhejiang university

description:
Library name: Sample 2
cKO CD8+ T cells

data_processing:
Raw data (fastq format) of single-cell transcriptomic were pre-analyzed by MobiVision V3.1 (MobiDrop), and reads were aligned to Mus musculus reference GRCm39. Filtered cell–gene matrix was obtained with MobiVision v3.2.
Assembly: mm10
Supplementary files format and content: Compressed tab-separated value files and matrix files

source_name: CD8+ T cells

extract_protocol:
Single cell RNA-seq analysis was  implemented on CD8+ TILs isolated from tumor bearing mice
Isolated CD8+ TILs were loaded into microfluidic chip of Chip A Single Cell Kit v2.1 [MobiDrop (Zhejiang) Co. Ltd., catalog no. S050100301] to generate droplets with MobiNova-100 [MobiDrop (Zhejiang) Co. Ltd., catalog no. A1A40001]. After encapsulation, droplets suffer light cut by MobiNovaSP-100 [MobiDrop (Zhejiang) Co. Ltd., catalog no. A2A40001], while oligos diffuse into reaction mix. The mRNAs were captured by cell barcodes with cDNA amplification in droplets. Following reverse transcription, cDNAs with barcodes were amplified, and a library was constructed using the High Throughput Single-Cell 3’ Transcriptome Kit v2.1 [MobiDrop (Zhejiang) Co. Ltd., catalog no. S050200301] and the 3’ Dual Index Kit [MobiDrop (Zhejiang) Co. Ltd., catalog no. S050300301].

value: CD8+ T cells

value: cKO

tag: treatment

value: no treatment


title: PP2A-WT

description:
Library name: Sample 1
WT CD8+ T cells

value: WT


title: Monocytes from MS patient number 43


title: mDCs from HD healthy donor 39


title: Monocytes From HD number 30


title: CKO2

description:
Library name: Sample 5
column name in featureCounts_pp2a.txt: CKO2

data_processing:
STAR
featureCounts
Assembly: mm10
Supplementary files format and content: txt file includes raw counts for each sample

extract_protocol:
Bulk RNA-seq analysis was then implemented on anti-CD3 (0.1 ng/μl) plus anti-CD28 (3 ng/μl)-treated naïve CD8+ T cells
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol

value: stimulated with anti-CD3+CD28


title: tolDCs From MS patient number 41


title: Monocytes From HD number 27


title: CKO1

description:
Library name: Sample 4
column name in featureCounts_pp2a.txt: CKO1


title: WT3

description:
Library name: Sample 3
column name in featureCounts_pp2a.txt: WT3


title: Monocytes from MS patient number 20


title: WT2

description:
Library name: Sample 2
column name in featureCounts_pp2a.txt: WT2


title: Monocytes From HD number 1


title: 207675480016_R16C01

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings using the deIdentifiy() function.

source_name: Human primary cell DNA

extract_protocol: Genomic DNA was extracted from 30-70 mg of tissue or 5.0 x 10^6 cells for cell lines using commercially available QIAGEN QIAamp Mini Kit (QIAGEN, 51304), following the manufacturer’s protocol. DNA was quantified using a Qubit 4 Fluorometer (Invitrogen).

value: Blood R315178

tag: modification


title: WT1

description:
Library name: Sample 1
column name in featureCounts_pp2a.txt: WT1


title: tolDCs from HD healthy donor 38

value: Male


title: Monocytes From HD number 38


title: 207675480016_R15C01

value: Blood R315185


title: tolDCs From MS patient number 36

value: Female


title: Monocytes from healthy donor 45


title: tolDCs from HD healthy donor 39


title: Monocytes From MS patient number 15


title: Ctrl, normal chow, replicate3, RNA-seq

value: Whole ventricle

tag: time

tag: strain

value: hybrid of C57BL/6 and ICR

value: Tcf21iCre/R26 tdTomato

tag: Sex

value: male

value: normal chow, tamoxifen i.p. at week 5

tag: group

value: Ctrl


title: CKO3

description:
Library name: Sample 6
column name in featureCounts_pp2a.txt: CKO3


title: 207675480016_R13C01


title: 207675480016_R12C01

value: Blood R315218


title: Monocytes from healthy donor 17


title: 207675480016_R11C01

value: Blood R315141


title: mDCs from HD healthy donor 37


title: Monocytes From MS patient number 25


title: 207675480016_R10C01


title: 207675480016_R09C01


title: tolDCs From MS patient number 25


title: mDCs From MS patient number 43


title: 207675480016_R08C01

value: Blood R311882


title: 207675480016_R07C01

value: Blood R315134


title: tolDCs From MS patient number 10


title: 207675480016_R06C01


title: MOLM13, sgNT, rep 1

value: human AML


title: 207675480016_R14C01


title: 207675480016_R05C01


title: Monocytes From MS patient number 40


title: Monocytes From MS patient number 22


title: mDCs From MS patient number 34


title: GFP Stage 28 Sample 2

value: Xenopus Borealis embryos (neurula, tailbud, swimming tadpole stages)

value: Stage 28 (tailbud stage)

value: GFP Treatment


title: mDCs from HD healthy donor 35


title: 207675480016_R03C01

value: Blood R315165


title: 207675480016_R02C01

value: Blood R315166


title: 207675480016_R04C01


title: tolDCs from HD healthy donor 37

value: Male


title: 207675480015_R16C03

value: Blood R315182


title: 207675480015_R16C02

value: Blood R315151


title: 207675480016_R01C01


title: Monocytes from healthy donor 35

value: Female


title: 207675480015_R16C01

value: Blood R315156


title: 207675480015_R15C03

value: Blood R315184


title: Monocytes From MS patient number 24


title: 207675480015_R15C02

value: Blood R315174


title: 207675480015_R14C03


title: 207675480015_R14C02


title: 207675480015_R15C01

value: Blood R311874


title: mDCs from HD healthy donor 42


title: 207675480015_R14C01


title: 207675480015_R13C03


title: 207675480015_R13C01


title: 207675480015_R12C03

value: Blood R315215


title: 207675480015_R13C02


title: 207675480015_R11C03

value: Blood R315212


title: 207675480015_R11C02

value: Blood R315220


title: 207675480015_R12C02

value: Blood R315203


title: 207675480015_R12C01

value: Blood R315145


title: 207675480015_R11C01

value: Blood R315194


title: 207675480015_R10C02


title: 207675480015_R10C01


title: 207675480015_R09C03


title: 207675480015_R09C01


title: 207675480015_R10C03


title: 207675480015_R08C03

value: Blood R315158


title: 207675480015_R09C02


title: 207675480015_R08C02

value: Blood R315172


title: 207675480015_R08C01

value: Blood R315222


title: 207675480015_R07C02

value: Blood R315181


title: 207675480015_R07C03

value: Blood R315159


title: 207675480015_R07C01

value: Blood R311895


title: dAluSz, SHAPE-JuMP experiment, untreated, primer RT3

city: Chapel Hill

first: Justin

last: Waldern

state: NC

address: 250 Bell Tower Dr

institute: The University of North Carolina at Chapel Hill

description:
Library name: dAluSz_rep1_JuMP_RT3_untreated
JuMP_data.tar.gz

library_source: other

data_processing:
Shapemapper2 v2.1.5
ShapeJumper  v1.0
JuMP filtering: SHAPE-JuMP frequencies were calculated with using the data from normalizeDeletionRates.py in the ShapeJumper package, with low count (<20) JuMP events omitted. Low count JuMP events were omitted because they can be artificially high in this system due to both a low JuMP count and a low read depth (i.e., 1 event in 1 read is a 100% frequency), where the low read depth occurs on JuMPs deep into the read from the poor processivity of the reverse transcriptase. Differences are taken as the AMT-treated minus the untreated values.
Assembly: GRCh38/hg38
Supplementary files format and content: MaP_profiles.tar.gz contains files of the format _profile.txt from ShapeMapper v2.1.5. Each row in these tables describes per-nucleotide mutation rates and normalized reactivity profiles
Supplementary files format and content: JuMP_data.tar.gz contain csv files of processed -JuMP data. These files contain position information for each deletion recorded (nucleotide_position_i, and nucleotide_position_j), as well as information on the counts and read-depth normalized frequencies of deletions in AMT-treated and untreated conditions

molecule: other

source_name: in vitro

growth_protocol: For in-cell probing (library names include "DMSic") HeLa cells (ATCC number CCL 2) were cultured in high glucose DMEM (Gibco) supplemented with10% fetal bovine serum (Sigma) and 0.5 % pen/strep (Gibco). Cells were maintained at 37° C and 5% CO2. Plasmid constructs were transfected into cells, and cells were later DMS probed

extract_protocol:
For in-cell probing, RNA was isolated with Trizol reagent. For in vitro probing, RNA was generated by in vitro transcription with NEB HiScribe T7 High Yield RNA Synthesis kit
For MaP RT, superscript II was used to generate cDNA. For JuMP, C8 enzyme was used to perform RT. In-cell and SHAPE-JuMP libraries were constructed with two rounds of PCR to add Illumina adaptor sequences and barcodes. In vitro MaP libraries were prepared using the NEBNext Ultra II FS DNA Library Prep kit for Illumina

value: in vitro

value: dAluSz

value: untreated


title: 207675480015_R06C03


title: dAluSz, SHAPE-JuMP experiment, AMT-treated, primer RT3

description:
Library name: dAluSz_rep1_JuMP_RT3_AMT
JuMP_data.tar.gz

value: AMT


title: 207675480015_R06C02


title: 207675480015_R06C01


title: neonatal blood spot, B549300

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

country: United Kingdom

institute: Newcastle University

hyb_protocol: DNA was bisulfite modified using the EZ-96 DNA Methylation kit (Zymo Research) with 4µl of each sample hybridized to Infinium MethylationEPIC BeadChip microarrays for genome-wide DNA methylation assessment.

data_processing: Minfi version 1.36.0 and IlluminaHumanMethylationEPICmanifest version 0.3.0

source_name: neonatal blood spot

extract_protocol: DNA was extracted using the Qiagen QIAamp DNA investigator kit, 500ng of which was bisulfite modified using the EZ-96 DNA Methylation kit (Zymo Research) with 4µl of each sample hybridized to Infinium MethylationEPIC BeadChip microarrays for genome-wide DNA methylation assessment.

tag: year sample taken

value: Male

value: blood

tag: developmental stage

value: neonate


title: dAluSz, SHAPE-JuMP experiment, untreated, primer RT1

description:
Library name: dAluSz_rep1_JuMP_RT1_untreated
JuMP_data.tar.gz


title: neonatal blood spot, B529300


title: neonatal blood spot, B409100


title: neonatal blood spot, B288900

value: Female


title: neonatal blood spot, B489300


title: dAluSz, SHAPE-JuMP experiment, AMT-treated, primer RT1

description:
Library name: dAluSz_rep1_JuMP_RT1_AMT
JuMP_data.tar.gz


title: 207675480015_R05C02


title: 207675480015_R05C03


title: neonatal blood spot, B389100


title: neonatal blood spot, B369100


title: neonatal blood spot, B329100


title: 207675480015_R05C01


title: dAluSq2, SHAPE-JuMP experiment, untreated, primer RT3

description:
Library name: dAluSq2_rep1_JuMP_RT3_untreated
JuMP_data.tar.gz


title: neonatal blood spot, B569400


title: neonatal blood spot, B208600


title: dAluSq2, SHAPE-JuMP experiment, AMT-treated, primer RT3

description:
Library name: dAluSq2_rep1_JuMP_RT3_AMT
JuMP_data.tar.gz


title: neonatal blood spot, B228600


title: neonatal blood spot, B188600


title: neonatal blood spot, B128500


title: neonatal blood spot, B429200


title: neonatal blood spot, B108400


title: neonatal blood spot, B148500


title: dAluSq2, SHAPE-JuMP experiment, AMT-treated, primer RT1

description:
Library name: dAluSq2_rep1_JuMP_RT1_AMT
JuMP_data.tar.gz


title: neonatal blood spot, B048400


title: neonatal blood spot, B469300


title: 207675480015_R04C03

value: Blood R315139


title: neonatal blood spot, B168600


title: neonatal blood spot, B449200


title: neonatal blood spot, B088400


title: d189AluSq2, SHAPE-JuMP experiment, AMT-treated, primer RT1, replicate 2

description:
Library name: d189AluSq2_rep2_JuMP_RT1_AMT
JuMP_data.tar.gz


title: 207675480015_R03C01

value: Blood R311861


title: 207675480015_R04C01

value: Blood R311886


title: 207675480015_R04C02

value: Blood R315140


title: 207675480015_R03C02

value: Blood R315146


title: neonatal blood spot, B248600


title: 207675480015_R03C03

value: Blood R315213


title: 207675480015_R02C01


title: d189AluSq2, SHAPE-JuMP experiment, AMT-treated, primer RT3, replicate 2

description:
Library name: d189AluSq2_rep2_JuMP_RT3_AMT
JuMP_data.tar.gz


title: neonatal blood spot, B068400


title: 207675480015_R01C03


title: 207675480015_R02C02


title: d189AluSq2, SHAPE-JuMP experiment, untreated, primer RT1, replicate 2

description:
Library name: d189AluSq2_rep2_JuMP_RT1_untreated
JuMP_data.tar.gz


title: neonatal blood spot, B309000


title: d189AluSq2, SHAPE-JuMP experiment, untreated, primer RT3, replicate 1

description:
Library name: d189AluSq2_rep1_JuMP_RT3_untreated
JuMP_data.tar.gz


title: 207675480015_R02C03


title: d189AluSq2, SHAPE-JuMP experiment, AMT-treated, primer RT3, replicate 1

description:
Library name: d189AluSq2_rep1_JuMP_RT3_AMT
JuMP_data.tar.gz


title: d189AluSq2, SHAPE-JuMP experiment, untreated, primer RT1, replicate 1

description:
Library name: d189AluSq2_rep1_JuMP_RT1_untreated
JuMP_data.tar.gz


title: d189AluSq2, SHAPE-JuMP experiment, AMT-treated, primer RT1, replicate 1

description:
Library name: d189AluSq2_rep1_JuMP_RT1_AMT
JuMP_data.tar.gz


title: d157AluSq2, SHAPE-JuMP experiment, untreated, primer RT3, replicate 2

description:
Library name: d157AluSq2_rep2_JuMP_RT3_untreated
JuMP_data.tar.gz


title: 207675480015_R01C02


title: d157AluSq2, SHAPE-JuMP experiment, AMT-treated, primer RT3, replicate 1

description:
Library name: d157AluSq2_rep1_JuMP_RT3_AMT
JuMP_data.tar.gz


title: d157AluSq2, SHAPE-JuMP experiment, AMT-treated, primer RT3, replicate 2

description:
Library name: d157AluSq2_rep2_JuMP_RT3_AMT
JuMP_data.tar.gz


title: 207675480015_R01C01


title: 207854510108_R15C03

value: Liver

tag: age

value: F


title: neonatal blood spot, B028400


title: neonatal blood spot, B268700


title: 207854510108_R15C01

value: Heart

value: M


title: d157AluSq2, SHAPE-JuMP experiment, untreated, primer RT1, replicate 2

description:
Library name: d157AluSq2_rep2_JuMP_RT1_untreated
JuMP_data.tar.gz

value: in vitro


title: Wild type, SHAPE-JuMP experiment, untreated, primer RT3, replicate 2

description:
Library name: WT_rep2_JuMP_RT3_untreated
JuMP_data.tar.gz

value: wild type

value: untreated


title: 207854510108_R16C03

value: Lung


title: dAluSq2, SHAPE-JuMP experiment, untreated, primer RT1

description:
Library name: dAluSq2_rep1_JuMP_RT1_untreated
JuMP_data.tar.gz


title: neonatal blood spot, B509300

value: Male

value: blood


title: neonatal blood spot, B349100

value: Female

value: neonate


title: 207854510108_R16C02

value: Thymus


title: d157AluSq2, SHAPE-JuMP experiment, AMT-treated, primer RT1, replicate 2

description:
Library name: d157AluSq2_rep2_JuMP_RT1_AMT
JuMP_data.tar.gz

value: AMT


title: d157AluSq2, SHAPE-JuMP experiment, untreated, primer RT3, replicate 1

description:
Library name: d157AluSq2_rep1_JuMP_RT3_untreated
JuMP_data.tar.gz


title: 207854510108_R16C01

value: Testis


title: Wild type, SHAPE-JuMP experiment, AMT-treated, primer RT3, replicate 2

description:
Library name: WT_rep2_JuMP_RT3_AMT
JuMP_data.tar.gz


title: d157AluSq2, SHAPE-JuMP experiment, untreated, primer RT1, replicate 1

description:
Library name: d157AluSq2_rep1_JuMP_RT1_untreated
JuMP_data.tar.gz


title: d157AluSq2, SHAPE-JuMP experiment, AMT-treated, primer RT1, replicate 1

description:
Library name: d157AluSq2_rep1_JuMP_RT1_AMT
JuMP_data.tar.gz


title: 207854510108_R15C02

value: Ovary


title: 207854510108_R14C02


title: 207854510108_R14C01


title: Wild type, SHAPE-JuMP experiment, untreated, primer RT1, replicate 2

description:
Library name: WT_rep2_JuMP_RT1_untreated
JuMP_data.tar.gz


title: Wild type, SHAPE-JuMP experiment, AMT-treated, primer RT1, replicate 2

description:
Library name: WT_rep2_JuMP_RT1_AMT
JuMP_data.tar.gz


title: 207854510108_R14C03

value: Bladder


title: 207854510108_R13C03

value: Liver


title: 207854510108_R13C02

value: F


title: Wild type, SHAPE-JuMP experiment, untreated, primer RT3, replicate 1

description:
Library name: WT_rep1_JuMP_RT3_untreated
JuMP_data.tar.gz


title: 207854510108_R12C02

value: Spleen


title: Wild type, SHAPE-JuMP experiment, AMT-treated, primer RT1, replicate 1

description:
Library name: WT_rep1_JuMP_RT1_AMT
JuMP_data.tar.gz


title: 207854510108_R12C01

value: M


title: 207854510108_R13C01

value: Heart


title: Wild type, SHAPE-JuMP experiment, AMT-treated, primer RT3, replicate 1

description:
Library name: WT_rep1_JuMP_RT3_AMT
JuMP_data.tar.gz

value: in vitro

value: wild type


title: ddAlu, in vitro SHAPE experiment, untreated, replicate 2

description:
Library name: ddAlu_SHAPE_untreated_rep2
MaP_profiles.tar.gz

value: ddAlu

value: untreated


title: 207854510108_R11C03

value: Placenta


title: ddAlu, in vitro SHAPE experiment, 5NIA-treated, replicate 2

description:
Library name: ddAlu_SHAPE_5NIA_rep2
MaP_profiles.tar.gz

value: SHAPE (5NIA)


title: 207854510108_R10C03

value: Eye


title: 207854510108_R11C01


title: ddAlu, in vitro SHAPE experiment, 5NIA-treated, replicate 1

description:
Library name: ddAlu_SHAPE_5NIA_rep1
MaP_profiles.tar.gz


title: 207854510108_R11C02


title: dAluSz, in vitro SHAPE experiment, untreated, replicate 2

description:
Library name: dAluSz_SHAPE_untreated_rep2
MaP_profiles.tar.gz

value: dAluSz


title: ddAlu, in vitro SHAPE experiment, untreated, replicate 1

description:
Library name: ddAlu_SHAPE_untreated_rep1
MaP_profiles.tar.gz


title: dAluSz, in vitro SHAPE experiment, untreated, replicate 1

description:
Library name: dAluSz_SHAPE_untreated_rep1
MaP_profiles.tar.gz


title: d189AluSq2, SHAPE-JuMP experiment, untreated, primer RT3, replicate 2

description:
Library name: d189AluSq2_rep2_JuMP_RT3_untreated
JuMP_data.tar.gz


title: 207854510108_R12C03


title: Wild type, SHAPE-JuMP experiment, untreated, primer RT1, replicate 1

description:
Library name: WT_rep1_JuMP_RT1_untreated
JuMP_data.tar.gz


title: 207854510108_R09C03


title: 207854510108_R10C01


title: dAluSz, in vitro DMS experiment, untreated

description:
Library name: dAluSz_DMSiv_untreated
MaP_profiles.tar.gz


title: dAluSz, in vitro DMS experiment, DMS-treated

description:
Library name: dAluSz_DMSiv_DMS
MaP_profiles.tar.gz

value: DMS


title: 207854510108_R09C01


title: dAluSq2, in vitro SHAPE experiment, untreated, replicate 2

description:
Library name: dAluSq2_SHAPE_untreated_rep2
MaP_profiles.tar.gz


title: 207854510108_R08C03

value: Colon


title: 207854510108_R08C02

value: Stomach


title: dAluSq2, in vitro SHAPE experiment, untreated, replicate 1

description:
Library name: dAluSq2_SHAPE_untreated_rep1
MaP_profiles.tar.gz


title: 207854510108_R08C01

value: Testis


title: dAluSq2, in vitro SHAPE experiment, 5NIA-treated, replicate 2

description:
Library name: dAluSq2_SHAPE_5NIA_rep2
MaP_profiles.tar.gz


title: dAluSq2, in vitro SHAPE experiment, 5NIA-treated, replicate 1

description:
Library name: dAluSq2_SHAPE_5NIA_rep1
MaP_profiles.tar.gz


title: 207854510108_R07C03


title: 207854510108_R07C02

value: Bladder


title: 207854510108_R10C02

value: F


title: dAluSq2, in vitro DMS experiment, untreated

description:
Library name: dAluSq2_DMSiv_untreated
MaP_profiles.tar.gz


title: dAluSq2, in vitro DMS experiment, DMS-treated

description:
Library name: dAluSq2_DMSiv_DMS
MaP_profiles.tar.gz


title: 207854510108_R07C01

value: Thyroid


title: d189AluSq2, in vitro SHAPE experiment, untreated, replicate 2

description:
Library name: d189AluSq2_SHAPE_untreated_rep2
MaP_profiles.tar.gz


title: 207854510108_R06C02

value: Trachea

value: M


title: dAluSz, in vitro SHAPE experiment, 5NIA-treated, replicate 2

description:
Library name: dAluSz_SHAPE_5NIA_rep2
MaP_profiles.tar.gz

value: in vitro


title: dAluSz, in vitro SHAPE experiment, 5NIA-treated, replicate 1

description:
Library name: dAluSz_SHAPE_5NIA_rep1
MaP_profiles.tar.gz


title: d189AluSq2, in vitro SHAPE experiment, untreated, replicate 1

description:
Library name: d189AluSq2_SHAPE_untreated_rep1
MaP_profiles.tar.gz


title: 207854510108_R06C03


title: 207854510108_R09C02


title: 207854510108_R06C01


title: d189AluSq2, in vitro SHAPE experiment, 5NIA-treated, replicate 1

description:
Library name: d189AluSq2_SHAPE_5NIA_rep1
MaP_profiles.tar.gz


title: 207854510108_R05C03


title: d189AluSq2, in vitro SHAPE experiment, 5NIA-treated, replicate 2

description:
Library name: d189AluSq2_SHAPE_5NIA_rep2
MaP_profiles.tar.gz


title: d157AluSq2, in vitro SHAPE experiment, untreated, replicate 2

description:
Library name: d157AluSq2_SHAPE_untreated_rep2
MaP_profiles.tar.gz


title: d157AluSq2, in vitro SHAPE experiment, untreated, replicate 3

description:
Library name: d157AluSq2_SHAPE_untreated_rep3
MaP_profiles.tar.gz


title: 207854510108_R05C01


title: 207854510108_R05C02


title: d157AluSq2, in vitro SHAPE experiment, untreated, replicate 1

description:
Library name: d157AluSq2_SHAPE_untreated_rep1
MaP_profiles.tar.gz


title: 207854510108_R04C03

value: Liver


title: d157AluSq2, in vitro SHAPE experiment, 5NIA-treated, replicate 3

description:
Library name: d157AluSq2_SHAPE_5NIA_rep3
MaP_profiles.tar.gz


title: 207854510108_R04C02


title: 207854510108_R04C01

value: Spinal Cord


title: 207854510108_R03C03


title: d157AluSq2, in vitro SHAPE experiment, 5NIA-treated, replicate 2

description:
Library name: d157AluSq2_SHAPE_5NIA_rep2
MaP_profiles.tar.gz


title: 207854510108_R03C02


title: Wild type, in vitro SHAPE experiment, untreated

description:
Library name: WT_SHAPE_untreated
MaP_profiles.tar.gz

value: wild type

value: untreated


title: 207854510108_R03C01


title: 207854510108_R02C03


title: Wild type, in vitro SHAPE experiment, 5NIA-treated, replicate 2

description:
Library name: WT_SHAPE_5NIA_rep2
MaP_profiles.tar.gz

value: SHAPE (5NIA)


title: Wild type, in vitro DMS experiment, untreated, replicate 1

description:
Library name: WT_DMSiv_untreated_rep1
MaP_profiles.tar.gz


title: 207854510108_R02C01

value: Heart


title: Wild type, in vitro DMS experiment, untreated, replicate 2

description:
Library name: WT_DMSiv_untreated_rep2
MaP_profiles.tar.gz


title: Wild type, in vitro SHAPE experiment, 5NIA-treated, replicate 1

description:
Library name: WT_SHAPE_5NIA_rep1
MaP_profiles.tar.gz


title: 207854510108_R02C02


title: Wild type, in vitro DMS experiment, DMS-treated, replicate 1

description:
Library name: WT_DMSiv_DMS_rep1
MaP_profiles.tar.gz


title: Wild type, in vitro DMS experiment, DMS-treated, replicate 2

description:
Library name: WT_DMSiv_DMS_rep2
MaP_profiles.tar.gz


title: 207854510108_R01C02


title: 207854510108_R01C03


title: 207854510108_R01C01


title: PC9-GR cells, rep 3

city: Kaohsiung City

first: Yu-Peng

last: Liu

state: Not Applicable

address: No.100, Shin-Chuan 1st Road, Sanmin Dist.

country: Taiwan

institute: Kaohsiung Medical University

data_processing:
Initially, the sequences generated went through a filtering process to obtain qualified reads.
Trimmomatics was implemented to trim or remove the reads according to the quality score.
Qualified reads after filtering low-quality data were analyzed using TopHat/Cufflinks for gene expression estimation.
The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
For differential expression analysis, CummeRbund was employed to perform statistical analyses of gene expression profiles.
Assembly: The reference genome and gene annotations were retrieved from Ensembl database.
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample
Supplementary files format and content: tab-delimited txt file includes FPKM and fold change for each sample

source_name: Lung adenocarcinoma

growth_protocol: PC9 and PC9-GR cell lines were cultured in RPMI-1640 medium supplemented with 10% fetal bovine albumin (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted by Trizol® Reagent according to the instruction manual. RNA purified was quantified at OD260 nm by using a ND-1000 spectrophotometer and qualitated by using a Bioanalyzer 2100.
Library construction of all samples were used by Agilent's SureSelect Strand Specific RNA Library Preparation Kit.

treatment_protocol: The PC9-GR cells were routinely maintained in the complete medium containing 10 μM gefitinib. Prior to the total RNA extraction, PC9-GR cells were cultured in a complete medium without gefitinib for a duration of 7 days.

value: Lung adenocarcinoma

value: epithelial cells

value: EGFR exon19 del

value: gefitinib resistant cell line


title: PC9-GR cells, rep 2


title: PC9-GR cells, rep 1


title: PC9 cells, rep 3

value: parental cell line


title: d157AluSq2, in vitro SHAPE experiment, 5NIA-treated, replicate 1

description:
Library name: d157AluSq2_SHAPE_5NIA_rep1
MaP_profiles.tar.gz


title: 207854510026_R16C03

value: Adrenal


title: 207854510026_R16C02

value: Esophagus

value: F


title: 207854510026_R15C03

value: Thymus


title: PC9 cells, rep 1


title: 207854510026_R15C01

value: Spleen

value: M


title: Endpoint_LNenzaRbioRep2

city: Vancouver

first: Nathan

middle: A

last: Lack

state: BC

address: 2660 Oak S

country: Canada

institute: Vancouver Prostate Centre

description:
Library name: Endpoint_LNenzaRbioRep2
Endpoint- biological replicate 2

data_processing:
MAGeCK algorithm39 (version 0.5.9.2) was used through all steps of the analysis such as sgRNA quantification and identification of significantly depleted genes. For each sample, R1 fastq files were processed by MAGeCK's count function to provide sgRNA level counts shown below. Biological replicates were presented as individual input files during sgRNA counting. All samples were combined and median normalized by `–norm-method “median”` argument of MAGeCK’s count. Identification of essential genes was calculated by MAGeCK’s test function. For each comparison, replicates were pooled as “-t Arep1,Arep2,Arep3” and “-c Brep1,Brep2,Brep3” for conditionA and conditionB respectively. In addition, negative control sgRNA were supplied with “--control-sgrna” function. Median normalized combined tables were used for visualization. R (version 2021.09.0) and ggplot2 package (version 3.3.5) were used for boxplot and density plots. For area under the curve (AUC) analysis, publicly available python code “AUC Calculation (https://github.com/mhegde)’ downloaded from the source 80. AUC calculation was run following the instructions on GitHub (https://github.com/mhegde/auc-calculation). All calculated AUC data were plotted using R (version 2022.07.2).
Supplementary files format and content: data.count_normalized_publication.txt: files contain normalized counts from every sample from that batch.
Supplementary files format and content: RepMerged-gene_summary.txt: files contain analysis related to merged samples.
Library strategy: CRISPR Screen

source_name: Prostate

growth_protocol: LNCaP, RWPE-1 and HEK293T cell lines were purchased from ATCC. LNCaP-abl (Abl) cell line was a kind gift from Dr.Helmut Klocker and MR49F cell line was a kind gift from Dr. Amina Zoubeidi and Dr. Martin Gleave from Vancouver Prostate Center. ENZA-R cell line was generated by chronically treating LNCaP cells with increasing doses of enzalutamide in Koc University. LNCaP cells were cultured in RPMI 1640 (Gibco, USA) supplemented with 10% fetal bovine serum (Gibco, USA) and 1 % penicillin/streptomycin (Gibco, USA). LNCaP-abl cells were cultured in RPMI 1640 (Gibco, USA) supplemented with 5% charcoal-stripped fetal bovine serum (Gibco, USA) and 1 % penicillin/streptomycin (Gibco, USA). MR49F and ENZA-R cells were cultured in RPMI 1640 (Gibco, USA) supplemented with 10% fetal bovine serum (Gibco, USA), 1 % penicillin/streptomycin (Gibco, USA) and 10 μM enzalutamide. RWPE-1 cells were cultured in Keratinocyte SFM media (Gibco, USA) supplemented with 0.05 mg mL-1 bovine pituitary extract and 5 ng mL-1 human recombinant epidermal growth factor (Gibco, USA). HEK293T cells were cultured in DMEM (Gibco, USA), supplemented with 10% FBS and 1% penicillin/streptomycin. All cell lines were maintained in a humidified incubator at 37°C with 5% CO2. Cells were regularly tested for mycoplasma.

extract_protocol:
From the collected cells, genomic DNA was isolated by PureLink Genomic DNA mini kit (Invitrogen, K1820) according to the manufacturer’s instructions.
Integrated sgRNA sequences were amplified by PCR reaction. For this, 4 μg genomic DNA was amplified for 25 cycles by using Kapa HiFi HotStart ReadyMix (Roche, KK2602) mixed with 10 μM external forward and reverse primers. To introduce sequencing adapters, external PCR products were pooled and amplified for 15 cycles using internal primers. PCR product was gel-isolated. After quality check, PCR products were sequenced by Genewiz, USA. Each screen was repeated three times.

value: Prostate

value: ENZA-R

value: Prostate carcinoma

value: Enzalutamide

tag: batch


title: PC9 cells, rep 2


title: Baseline_LNenzaR_bioRep2

description:
Library name: Baseline_LNenzaR_bioRep2
Baseline - biological replicate 2


title: 207854510026_R14C02


title: Baseline_LNenzaR_bioRep1

description:
Library name: Baseline_LNenzaR_bioRep1
Baseline - biological replicate 1


title: 207854510026_R14C03


title: 207854510026_R14C01

value: Stomach


title: Endpoint_LNenzaR_bioRep1

description:
Library name: Endpoint_LNenzaR_bioRep1
Endpoint- biological replicate 1


title: 207854510026_R13C03


title: MR49F_INPUT

data_processing:
Reads are aligned to hg38 genome with BWA (v0.7.10).
Reads with less quality alignmet (MAPQ < 30), PCR duplicates (samtools fixmate - markdup as recommended), and chrMT alignments are removed.
MACS2 (v2.1.0) is used to call peaks, FDR threshold 0.01.
Bigwig files were generated using bedGraphToBigWig.
Assembly: hg38
Supplementary files format and content: narrowPeak
Supplementary files format and content: BigWig

growth_protocol: LNCaP cells were cultured in RPMI 1640 (Gibco, USA) supplemented with 10% fetal bovine serum (Gibco, USA) and 1 % penicillin/streptomycin (Gibco, USA). MR49F cells were cultured in RPMI 1640 (Gibco, USA) supplemented with 10% fetal bovine serum (Gibco, USA), 1 % penicillin/streptomycin (Gibco, USA) and 10 uM enzalutamide.

extract_protocol:
The cells were first fixed at room temperature with 2mM DSG (Thermo Scientific, Cat.No. 20593) for 45 min prior to 1% formaldehyde fixation for 10 min. The cells sequentially lysed with LB1 (50 mM HEPES-KOH (pH 7.6), 140 mM NaCl, 1 mM EDTA, 10% (vol/vol) glycerol, 0.5% (vol/vol) NP-40/Igepal CA-630 and 0.25% (vol/vol) Triton X-100), LB2 (10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) to enrich for nucleus. The nucleus was further lysed in LB3 and sonicated for 10 mins (30 sec ‘On’ and 30 sec ‘Off’ cycles) using Bioruptor (Diagenode). The IP was performed overnight at 4°C with 4 µg of BRG1 (Abcam, ab110641) or SMARCC2 (Bethyl Lab A301-039A) conjugated protein G magnetic beads (Thermo Scientific). The DNA was then purified using the Monarch DNA cleanup kit (NEB) after overnight de-crosslinking at 65°C.
The library for high throughput sequencing was prepared using the Ultra II DNA library kit (NEB) according to the manufacturer's instructions.


title: MR49F_SMARCC2

tag: chip antibody

value: Bethyl Lab A301-039A


title: MR49F_BRG1

value: Abcam, ab110641


title: LNCaP_INPUT

source_name: LNCaP

value: LNCaP


title: 207854510026_R13C01

value: Larynx


title: 207854510026_R12C02


title: LNCaP_SMARCC2


title: LNCaP_BRG1


title: 207854510026_R11C03


title: 207854510026_R12C01


title: 207854510026_R16C01

value: Lung


title: 207854510026_R11C02

value: Kidney


title: 207854510026_R11C01


title: 207854510026_R10C03

value: Adrenal


title: 207854510026_R15C02

value: Lymph Node


title: 207854510026_R13C02


title: 207854510026_R10C02

value: Esophagus


title: 207854510026_R10C01

value: F


title: 207854510026_R09C02


title: 207854510026_R09C01


title: 207854510026_R12C03


title: 207854510026_R08C02


title: 207854510026_R08C03


title: 207854510026_R08C01


title: 207854510026_R06C03


title: 207854510026_R07C02


title: 207854510026_R07C01


title: 207854510026_R07C03


title: 207854510026_R06C02


title: 207854510026_R09C03


title: SRC439-T2

city: Stanford

first: Ajay

last: Subramanian

state: CA

address: 450 Serra Mall

department: Radiation Oncology

institute: Stanford University School of Medicine

description: Bulk RNAseq

data_processing:
FASTQ files were quasi-aligned to Gencode version 27 transcript models, and expression levels were summarized using Salmon.
After restricting to protein coding genes, expression levels per gene were summarized as TPM.
Assembly: GRCh38.
Supplementary files format and content: Tab-delimited text file, including TPM for each sample.

source_name: Soft tissue sarcoma

extract_protocol:
Bulk RNA was isolated from one to two 10 micron FFPE scrolls per sample using RNAstorm FFPE RNA Extraction Kits (Cell Data Sciences).
Sequencing libraries were prepared using SMARTer Stranded Total RNA-Seq v2-Pico Input Mammalian Kits (Takara Bio USA, Inc.).

value: Soft tissue sarcoma

value: Tumor

value: Chemoradiation Post-treatment


title: SRC437-T3

description: Bulk RNAseq


title: SRC436-T2

description: Bulk RNAseq


title: SRC436-T1

description: Bulk RNAseq

value: Chemoradiation Pre-treatment


title: SRC439-T1

description: Bulk RNAseq


title: SRC438-T1

description: Bulk RNAseq


title: SRC435-T2

description: Bulk RNAseq


title: SRC437-T1

description: Bulk RNAseq


title: SRC439-T3

description: Bulk RNAseq


title: SRC434-T2

description: Bulk RNAseq


title: SRC438-T3

description: Bulk RNAseq


title: 207854510026_R05C03

value: Prostate

value: M


title: SRC437-T2

description: Bulk RNAseq


title: SRC436-T4

description: Bulk RNAseq


title: 207854510026_R06C01

value: Stomach


title: SRC435-T3

description: Bulk RNAseq


title: SRC438-T2

description: Bulk RNAseq


title: SRC434-T1

description: Bulk RNAseq


title: SRC436-T3

description: Bulk RNAseq


title: 207854510026_R05C02


title: SRC432-T2

description: Bulk RNAseq


title: SRC435-T1

description: Bulk RNAseq


title: 207854510026_R05C01


title: 207854510026_R04C03

value: Thymus


title: SRC431-T4

description: Bulk RNAseq


title: SRC431-T3

description: Bulk RNAseq


title: 207854510026_R02C03


title: 207854510026_R03C02


title: SRC430-T4

description: Bulk RNAseq


title: 207854510026_R02C01

value: Spleen


title: 207854510026_R01C01

value: Heart


title: SRC431-T2

description: Bulk RNAseq


title: 207854510026_R04C02


title: SRC430-T3

description: Bulk RNAseq


title: SRC430-T2

description: Bulk RNAseq


title: SRC428-T2

description: Bulk RNAseq


title: 207854510026_R02C02


title: SRC429-T2

description: Bulk RNAseq


title: 207854510026_R03C01


title: 207854510026_R01C02


title: 207854510026_R03C03

value: Trachea


title: SRC429-T1

description: Bulk RNAseq


title: 207854510026_R04C01


title: 207854510120_R16C03


title: SRC429-T3

description: Bulk RNAseq


title: SRC432-T1

description: Bulk RNAseq


title: SRC428-T1

description: Bulk RNAseq


title: SRC430-T1

description: Bulk RNAseq


title: 207854510120_R16C02


title: 207854510120_R16C01

value: Lung


title: SRC427-T2

description: Bulk RNAseq


title: 207854510026_R01C03


title: SRC428-T3

description: Bulk RNAseq


title: 207854510120_R15C03


title: SRC431-T1

description: Bulk RNAseq


title: 207854510120_R15C01


title: SRC427-T1

description: Bulk RNAseq


title: Ctrl 11-A50

city: Brussels

first: Alia

last: Hadefi

address: 808 route de lennik

department: Gastroenterology

country: Belgium

institute: CUB Hopital Erasme

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BC11

data_processing:
Sequenced reads were trimmed for adaptor sequence (Trimmomatic-0.36)
Paired-end reads were mapped against the human reference genome (GRCm38.p4/mm10) using the STAR_2.5.3a software to generate read alignments.
Following transcript assembly, gene level counts were obtained using HTSeq-0.9.1
Assembly: human reference genome (GRCm38.p4/mm10)
Supplementary files format and content: tab-delimited txt file includes CPM values for each sample.
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample.

source_name: Duodenum

growth_protocol: Sato's protocol (Nature, 2009) was followed for Crypt isolation of human  small intestine epithelium. Expansion of small intestine organoids was performed over the course of time of 20 days and then replate twice before being frozen (for the majority at passage 2) in order to constitute a biobank.

extract_protocol:
Total RNA was extracted with the MIRVANA MIRNA ISO KIT (Thermo Fisher scientific, Life technologies Europe, Bleiswijk, NL) following the manufacturer’s instructions.
Indexed cDNA libraries were obtained using the NEBNext Ultra II directional RNA Library Prep Kit for Illumina® E7760L (NEW ENGLAND BioLabs Inc) following manufacturer recommendations

value: Duodenum

tag: disease state

value: Controls

value: tissue (biopsy)


title: 207854510120_R13C02

tag: tissue

value: Kidney


title: 207854510120_R14C01


title: 207854510120_R14C02

value: Esophagus

value: F


title: 207854510120_R13C03


title: 207854510120_R13C01

value: Larynx


title: Ctrl 7-A46

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BC7


title: Ctrl 5-A44

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BC5


title: Ctrl 4-A43

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BC4


title: 207854510120_R12C03

value: Adrenal


title: Ctrl 10-A49

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BC10


title: Ctrl 12-A51

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BC12


title: 207854510120_R12C02


title: SRC427-T3

description: Bulk RNAseq

value: Soft tissue sarcoma

value: Tumor

value: Chemoradiation Post-treatment


title: 207854510120_R12C01

value: Stomach


title: Ctrl 9-A48

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BC9


title: Ctrl 3-A41

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BC3


title: 207854510120_R11C02

value: M


title: 207854510120_R11C03

value: Prostate


title: Ctrl 1-A40

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BC1


title: 207854510120_R14C03


title: Ctrl 13-A52

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BC13


title: MASH 13-A39

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BN13

value: MASH


title: 207854510120_R11C01


title: Ctrl 8-A47

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BC8


title: 207854510120_R10C03


title: MASH 11-A37

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BN11


title: 207854510120_R10C01


title: MASH 8-A34

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BN8


title: MASH 10-A36

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BN10


title: 207854510120_R09C03


title: 207854510120_R09C02


title: 207854510120_R09C01


title: 207854510120_R08C03


title: MASH 9-A35

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BN9


title: MASH 7-A33

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BN7


title: 207854510120_R08C02


title: MASH 4-A30

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BN4


title: MASH 5-A31

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BN5


title: 207854510120_R08C01


title: 207854510120_R15C02

value: Lymph Node


title: MASH 3-A29

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BN3


title: 207854510120_R07C02


title: 207854510120_R07C03


title: MASH 1-A27

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BN1


title: 207854510120_R06C03


title: MASH 12-A38

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BN12


title: MASH 13-A63

description:
Adult stem cells duodenum derived organoids
CP20M_organoids_MASH vs Controls excel file complete gene expression_14052024.txt
MDEO13

source_name: Duodenum (epithelium)

value: Duodenum (epithelium)

value: organoids


title: Ctrl 6-A45

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BC6

value: Duodenum

value: Controls


title: 207854510120_R10C02


title: MASH 12-A62

description:
Adult stem cells duodenum derived organoids
CP20M_organoids_MASH vs Controls excel file complete gene expression_14052024.txt
MDEO12


title: 207854510120_R06C02


title: 207854510120_R05C03


title: MASH 9-A60

description:
Adult stem cells duodenum derived organoids
CP20M_organoids_MASH vs Controls excel file complete gene expression_14052024.txt
MDEO9


title: MASH 5-A57

description:
Adult stem cells duodenum derived organoids
CP20M_organoids_MASH vs Controls excel file complete gene expression_14052024.txt
MDEO5


title: MASH 8-A59

description:
Adult stem cells duodenum derived organoids
CP20M_organoids_MASH vs Controls excel file complete gene expression_14052024.txt
MDEO8


title: MASH 2-A55

description:
Adult stem cells duodenum derived organoids
CP20M_organoids_MASH vs Controls excel file complete gene expression_14052024.txt
MDEO2


title: 207854510120_R05C01


title: 207854510120_R05C02

value: Kidney


title: 207854510120_R07C01


title: MASH 1-A54

description:
Adult stem cells duodenum derived organoids
CP20M_organoids_MASH vs Controls excel file complete gene expression_14052024.txt
MDEO1


title: 207854510120_R04C02


title: MASH 2-A28

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BN2

value: tissue (biopsy)


title: 207854510120_R04C01

value: Spleen

value: F


title: Ctrl 9-A24

description:
Adult stem cells duodenum derived organoids
CP20M_organoids_MASH vs Controls excel file complete gene expression_14052024.txt
CDEO9


title: 207854510120_R04C03

value: Thymus


title: Ctrl 7-A23

description:
Adult stem cells duodenum derived organoids
CP20M_organoids_MASH vs Controls excel file complete gene expression_14052024.txt
CDEO7


title: Ctrl 11-A25

description:
Adult stem cells duodenum derived organoids
CP20M_organoids_MASH vs Controls excel file complete gene expression_14052024.txt
CDEO11


title: 207854510120_R03C02

value: Lung


title: 207854510120_R03C03

value: Trachea


title: Ctrl 4-A20

description:
Adult stem cells duodenum derived organoids
CP20M_organoids_MASH vs Controls excel file complete gene expression_14052024.txt
CDEO4


title: 207854510120_R06C01


title: 207854510120_R03C01

source_name: Human cell line DNA


title: Ctrl 6-A22

description:
Adult stem cells duodenum derived organoids
CP20M_organoids_MASH vs Controls excel file complete gene expression_14052024.txt
CDEO6


title: Ctrl 3-A18

description:
Adult stem cells duodenum derived organoids
CP20M_organoids_MASH vs Controls excel file complete gene expression_14052024.txt
CDEO3


title: 207854510120_R02C02


title: Proliferating cells, sample C, 2-4 deletion

city: Boston

first: Frank

last: Naya

address: 24 Cummington Mall

institute: Boston University

description: Library name: 2-4CP

data_processing:
Reads were aligned to mm10 (bowtie2)
PR duplicates were identified and removed (Picard)
Reads aligning to blacklist regions specified by ENCODE were remoed (bedtools)
Peaks were called using MACS2 with default parameters for paird-end analysis with q-value cutoff of 0.05
Assembly: mm10
Supplementary files format and content: narrowPeaks

source_name: Inmortalized

growth_protocol: Growth: Proliferation: DMEM, 10% fetal bovine serum, 1 X penicillin/streptomycin/glutamine; Differentiation: DMEM, 2% horse serum, 1 X penicillin/streptomycin/glutamine

extract_protocol:
Cells were collected and processed according to Active motive ATAC-Seq kit protocol
Library prep was performed using ATAC-Seq Kit Active Motif Kit 53150

value: Inmortalized

value: 2-4 deletion


title: Proliferating cells, sample C, No deletion

description: Library name: pXCP

value: No deletion


title: mDCs from MS patient 44

data_processing:
kallisto alignment
Assembly: NCBI build 36
Supplementary files format and content: tsv

source_name: Blood

extract_protocol:
Monocytes were isolated from MS patients and Healthy donors using CD14 positive enrichment by negative selection followed by CD14 positive selection
poly A enrichment

tag: sample group

value: Blood

tag: cohort

value: MS

value: dendritic cell

tag: gender

value: Female


title: 207854510120_R01C03


title: tolDCs from MS patient 44

tag: cell type


title: tolDCs from MS patient 43


title: Proliferating cells, sample B, No deletion

description: Library name: pXBP

tag: genotype


title: Proliferating cells, sample B, 2-7 deletion

description: Library name: 2-7BP

value: 2-7 deletion


title: Proliferating cells, sample A, No deletion

description: Library name: pXAP


title: mDCs from MS patient 43


title: Proliferating cells, sample A, 2-4 deletion

description: Library name: 2-4AP


title: tolDCs from healthy donor 39

value: HD

value: Male


title: 207854510094_R16C03

tag: modification

value: M


title: Proliferating cells, sample B, 2-4 deletion

description: Library name: 2-4BP


title: Differentiating cells (Day 3), sample C, No deletion

description: Library name: pXC3


title: Ctrl 1-A17

description:
Adult stem cells duodenum derived organoids
CP20M_organoids_MASH vs Controls excel file complete gene expression_14052024.txt
CDEO1

value: Duodenum (epithelium)

value: Controls

value: organoids


title: 207854510120_R02C03

value: Thymus

value: F


title: Differentiating cells (Day 3), sample B, No deletion

description: Library name: pXB3


title: 207854510094_R16C02


title: Differentiating cells (Day 3), sample B, 2-7 deletion

description: Library name: 2-7B3


title: mDCs from healthy donor 39


title: tolDCs from healthy donor 38


title: 207854510120_R02C01

value: Spleen


title: Differentiating cells (Day 3), sample C, 2-4 deletion

description: Library name: 2-4C3

value: Inmortalized


title: mDCs from healthy donor 38


title: Differentiating cells (Day 3), sample B, 2-4 deletion

description: Library name: 2-4B3

value: 2-4 deletion


title: Differentiating cells (Day 3), sample A, No deletion

description: Library name: pXA3

value: No deletion


title: Differentiating cells (Day 3), sample A, 2-7 deletion

description: Library name: 2-7A3


title: 207854510120_R01C02

value: Lung


title: SRC434-T3

description: Bulk RNAseq

value: Soft tissue sarcoma

value: Tumor

tag: treatment

value: Chemoradiation Post-treatment


title: 207854510094_R15C03

value: Liver


title: 207854510120_R01C01


title: Differentiating cells (Day 3), sample A, 2-4 deletion

description: Library name: 2-4A3


title: Proliferating cells, sample A, 2-7 deletion

description: Library name: 2-7AP

value: 2-7 deletion


title: tolDCs from healthy donor 37

value: Blood

value: HD

value: dendritic cell

value: Male


title: VCaP, SQK-DCS109, default

city: Chicago

first: Rendong

last: Yang

state: IL

address: 420 E Superior St

department: Urology

institute: Northwestern University

description: direct cDNA long read sequencing,  dorado's default parameter

data_processing:
For Nanopore direct RNA sequencing using kits SQK-RNA002 and SQK-RNA004, raw FASTQ files were generated with Dorado v0.5.2 utilizing models "rna002_70bps_hac@v3" and "rna004_130bps_hac@v3.0.1," respectively.
Adapter trimming was disabled, generating untrimmed FASTQ files (–no-trim); otherwise, default FASTQ files were produced.
For Nanopore direct cDNA sequencing using the SQK-DCS109 kit, raw FASTQ files were generated with Dorado v0.5.2 using the "dna_r9.4.1_e8_hac@v3.3" model.
Raw fastq reads were align to reference genome hg38 using minmap2 v2.26 with “-ax splice -uf -k14” options.
Assembly: hg38
Supplementary files format and content: The processing of oriented and trimmed Nanopore direct cDNA reads was performed using Pychopper (https://github.com/epi2me-labs/pychopper, version 2.7.9) and Cutadapt (version 4.2), following the protocol outlined by Grünberger et al. (2022).
Supplementary files format and content: Gene counts were calculated by IsoQuant (v3.1.2)

source_name: VCaP

extract_protocol:
Total RNA was extracted  using the RNeasy Mini Kit (Qiagen, Cat# 74104) according to the protocol of the manufacturer. The quality and concentration of RNA were assessed using an Agilent 2100 Bioanalyzer.
Poly(A)+ RNA was then enriched from the total RNA using the Dynabeadstm mRNA Purification Kit (Invitrogen, Cat# 65001), which utilizes oligo (dT) beads for selective mRNA binding.

tag: cell line

value: VCaP

value: epithelial cell

value: WT


title: 207854510094_R15C02

value: Ovary

tag: Sex

value: F


title: VCaP, SQK-RNA002, untrimmed

description: direct RNA long read sequencing, dorado's adapter trimming disabled


title: mDCs from healthy donor 37


title: 207854510094_R14C03

value: Bladder

value: M


title: 207854510094_R15C01

value: Heart


title: tolDCs from MS patient 36

value: MS

value: Female


title: mDCs from MS patient 36


title: 207854510094_R14C02

value: Thymus


title: 207854510094_R16C01

value: Testis


title: U2OS-switchover cells, No Dox, 24 hours ⍺-amanitin, replicate 2

city: Worcester

first: Michael

last: Lee

address: 368 Plantation Street

institute: UMASS Chan Medical School

description:
Library name: NODox_24h_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

data_processing:
Basecalling and demultiplexing was performed using BCL Convert v4.3.6
Transcript abundance was estimated using Kallisto (0.46.1) with parameters --bootstrap-samples 30 --single-overhang --rf-stranded. The ensembl GRCh38 cdna transcriptome build was used, appended with ERCC control transcript sequences.
Gene-level counts were generated in R using the tximport package. Counts were normalized to ERCC spike-ins using DESeq2, implemented with the function "estimateSizeFactors" with the option "controlGenes" set to the identities of the 92 ERCC transcripts. Counts were filtered for protein coding genes.
Assembly: GRCh38
Supplementary files format and content: CSV file of ERCC spike-in normalized counts for each sample

growth_protocol: Cells were maintained in high glucose DMEM supplemented with 10% fetal bovine serum, penicillin/streptomycin, and glutamine in a humidified incubator with 5% CO2 at 37C

extract_protocol:
At assay endpoint cells were trypsinized, counted using a hemacytometer, pelleted, washed with PBS, and moved immediately to RNA extraction. Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, 74134) according to manufacturer protocol. To facilitate absolute RNA quantification, polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were diluted 1:100 in nuclease-free water, and added to each sample at 1 µL/100,000 cells. ERCC spike-ins were added immediately following lysis of cells in RLT-plus buffer, and prior to all subsequent total RNA extraction steps using the RNeasy Plus kit. mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490).
RNAseq libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit using the NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7765 and E7600).

treatment_protocol: Cells were seeded onto six-well plates (100,000 cells per well) and left to adhere overnight. The following day, the media was removed and replaced with fresh media with or without 2 µg/mL doxycycline. 48 hours later, 10 µM ⍺-amanitin was gently added to the existing media.

value: osteosarcoma

value: Switchover

value: 10 µM ⍺-amanitin

tag: time

value: 24 hours


title: U2OS-switchover cells, No Dox, 24 hours ⍺-amanitin, replicate 1

description:
Library name: NODox_24h_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS-switchover cells, No Dox, 0 hours ⍺-amanitin, replicate 2

description:
Library name: NODox_0h_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: 0 hours


title: U2OS-switchover cells, No Dox, 12 hours ⍺-amanitin, replicate 1

description:
Library name: NODox_12h_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: 12 hours


title: U2OS-switchover cells, No Dox, 12 hours ⍺-amanitin, replicate 2

description:
Library name: NODox_12h_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: tolDCs from healthy donor 35

value: Blood

value: HD

value: dendritic cell


title: 207854510094_R14C01


title: U2OS-switchover cells, No Dox, 0 hours ⍺-amanitin, replicate 1

description:
Library name: NODox_0h_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: 207854510094_R13C03

value: Liver


title: U2OS-switchover cells, Dox treated, 24 hours ⍺-amanitin, replicate 1

description:
Library name: Dox_24h_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: Dox + 10 µM ⍺-amanitin


title: mDCs from healthy donor 35


title: MASH 6-A32

description:
Adult duodenum
CP20M_Biopsies CTRL and MASH excel file complete expression profile_14052024.txt
BN6

value: Duodenum

value: MASH

value: tissue (biopsy)


title: U2OS-switchover cells, Dox treated, 12 hours ⍺-amanitin, replicate 2

description:
Library name: Dox_12h_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS-switchover cells, Dox treated, 24 hours ⍺-amanitin, replicate 2

description:
Library name: Dox_24h_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: tolDCs from MS patient 34

value: MS

value: Male


title: U2OS-switchover cells, Dox treated, 12 hours ⍺-amanitin, replicate 1

description:
Library name: Dox_12h_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: 207854510094_R13C02

value: Ovary

value: F


title: U2OS-switchover cells, Dox treated, 0 hours ⍺-amanitin, replicate 2

description:
Library name: Dox_0h_r2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: osteosarcoma

value: Switchover


title: 207854510094_R13C01

value: Heart

value: M


title: U2OS-switchover cells, Dox treated, 0 hours ⍺-amanitin, replicate 1

description:
Library name: Dox_0h_r1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: 0 hours


title: VCaP, SQK-RNA002, default

description: direct RNA long read sequencing, dorado's default parameter

value: VCaP

value: epithelial cell

value: WT


title: 207854510094_R12C03

value: Eye