title: PANC1 HOXC6 B2 (shRNA#2) replicate 1

description:
Sample_PDAC7_007
HOXC6 B2 (shRNA#2)


title: OFT_d5.5_R2 [176130]

status: Public on Oct 30 2023

type: SRA

city: Vienna

first: Clara

last: Schmidt

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology GmbH

library_source: transcriptomic

data_processing:
Reads were preprocessed using umi2index (Lexogen) to add the UMI sequence to the read identifier, and trimmed using BBDuk v38.06 (ref = polyA.fa.gz,truseq.fa.gz k = 13 ktrim = r useshortkmers = t mink = 5 qtrim = r trimq = 10 min length = 20). Reads mapping to abundant sequences included in the iGenomes NCBI GRCh38 references were removed using bowtie2 v2.3.4.1 alignment. The remaining reads were analyzed using genome and gene annotation for the GRCh38 assembly obtained from Homo sapiens Ensembl release 94. Reads were aligned to the genome using star v2.6.0c, and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting (-s 1). Differential gene expression analysis on raw counts, and principal component analysis on variance stabilized, transformed count data were performed using DESeq2 v1.18.1.
Assembly: GRCh38
Supplementary files format and content: featurecounts.count.gene.tsv: Tab-delimited text files with per gene read counts.

molecule: total RNA

organism: Homo sapiens

source_name: cardiac

growth_protocol:
hPSCs (WTC line) are seeded in a 24-well plate (TPP, #92024) at 30-40k cells per well in E8 + ROCKi (5μM Y-27632, Tocris #1254). All differentiation media are based on CDM. 24 hours after seeding in the 24-well plate, the cells are induced with mesoderm induction media. Mesoderm induction media is made up of CDM containing FGF2 (30 ng/ml, Cambridge University), LY294002 (5 μM, Tocris, #1130), Activin A (specific concentrations for different cardioid subtype, Cambridge University), BMP4 (10 ng/ml, R&D Systems RD-314-BP-050), and CHIR99021 (specific concentrations for different cardioid subtypes, see below, R&D Systems RD-4423/50). After 36-40 hours, cells are dissociated with TrypleE (Gibco, #12605010) and seeded in a Corning ultra-low attachment 96 well plate (Corning, #7007) at 15-20k cells/well in Cardiac Mesoderm Patterning Media One made up of CDM containing ROCKi and for all protocols besides the LV cardioids 1 μg/ml of insulin (Roche, #11376497001) plus specific factors depending on cardioid subtype (see below). After seeding, the cells are spun down in a centrifuge for 4 mins at 200g. At day 2.5, the cells are fed with Cardiac Mesoderm Patterning Media One. For the next two days, the medium is changed to Cardiac Mesoderm Patterning Media Two, made up of CDM containing specific factors depending on the cardioid subtype (see below) and exchanged daily. For the subsequent two days, media is exchanged every day with Cardiomyocyte Differentiation Media CDM medium  containing BMP4 (10ng/ml), FGF2 (8 ng/ml), and insulin (10 μg/ml)). This medium was termed Cardiomyocyte Specification Media (Hofbauer et al., 2021b). For the subsequent days of culture, media is exchanged every other day with CDM containing insulin (10 μg/ml).
*******************************************************
Specific media composition of cardioid subtypes:
*******************************************************
(1) Mesoderm Induction Media for WTC lines (day 0 – 1.5)
For LV (FHF-derived) cardioid differentiations, Activin is used at 5 ng/mL and CHIR99021 at 3 μM.
For RV (aSHF-derived), atria (pSHF-derived), and OFT differentiations Activin is used at 50 ng/mL and CHIR99021 at 4 μM. For AVC differentiation, Activin is used at 10 ng/mL and CHIR99021 at 2 μM.
---
(2) Cardiac Mesoderm Patterning Media 1 (day 1.5 – 3.5)
LV (FHF-derived): BMP4 (10ng/ml), FGF2 (8 ng/ml), insulin (10 μg/ml), C59 (2 μM, Tocris, #5148/10) and retinoic acid (50 nM, Sigma Aldrich, #R2625) (Hofbauer et al., 2021b).
RV (aSHF-derived): The TGF-beta inhibitor SB 431542 (10 μM, Tocris, #1614/10) and either C59 (2 μM) or XAV-939 (5 μM, SelleckChem, # S1180) (Figures 1-4).
OFT (aSHF-derived): SB 431542 (10 μM) and XAV-939 (5μM).
Atria (pSHF-derived): SB 431542 (10 μM), XAV-939 (5μM) and retinoic acid (500 nM).
AVC (pSHF-derived): SB 431542 (10 μM), XAV-939 (5μM), retinoic acid (500nM) and BMP4 (10ng/ml).
---
(3) Cardiac Mesoderm Patterning Media 2 (day 3.5 – 5.5)
LV: BMP4 (10ng/ml), FGF2 (8 ng/ml), insulin (10 μg/ml), C59 (2 μM) and retinoic acid (50 nM)) (Hofbauer etal., 2021b).
RV: either C59 (2 μM)(Figures 5-7) or XAV-939 (Figures 1-4) (5μM), BMP4 (10ng/ml), FGF2 (8 ng/ml), insulin (10 μg/ml), and retinoic acid (500nM).
OFT: XAV-939 (5μM), BMP4 (10ng/ml), FGF2 (8 ng/ml) and insulin (10 μg/ml).
Atria and AVC: XAV-939 (5μM), BMP4 (10ng/ml), FGF2 (8 ng/ml), insulin (10 μg/ml), and retinoic acid (500 nM).

extract_protocol:
RNA was isolated using an in-house RNA bead isolation kit semi-automated using KingFisher devices (KingFisher Duo Prime).
Using the QuantSeq 30 mRNA-Seq Library Prep Kit FWD (Lexogen GmbH, #015), the bulk RNA-seq library was generated according to the manufacturer’s instructions. After the preparation of the library, samples were checked for an adequate size distribution with a fragment analyzer.Then the RNA-seq library was submitted to the Vienna Biocenter Core Facilities (VBCF) Next-Generation-Sequencing (NGS) facility for sequencing.

tag: tissue

value: cardiac

tag: cell line

value: WTC

tag: cell type

value: cardiac progenitors


title: B3

city: Guangzhou

first: Zhenxing

last: Liang

state: Guangdong

address: 26 Yuancun Erheng Rd

country: China

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

description: All.counts.exp.txt

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15, b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome.
Count counting.
Genome_build: GRCh38
Supplementary_files_format_and_content: All.counts.exp.txt: Tab-delimited text file contains counts for each sample.

source_name: macrophage treated with rGAS6 rep3

growth_protocol: Human peripheral blood monocytes (PBMs) were isolated from healthy volunteer donors by density-gradient centrifugation with Ficoll-Hypaque (Pharmacia, Peapack, NJ) as previously described (6-7). PBMs were seeded at 2 × 10e6/ml in 24-well plates in DMEM medium (GIBCO) with 10% heat-inactivated human AB serum (Gemini Bio- Products, West Sacramento, CA), 50 U of penicillin per ml, 50 μg of streptomycin per mL, 2 mM L-glutamine and 100ng/ml human M-CSF. By repeated gentle washing with a warm medium and replacement of supernatants, nonadherent cells were removed after 5 days of culture.

extract_protocol:
Prefrontal cortex were harvested, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Macrophages were treated with 200 ng/ml rGAS6.

tag: diagnosis

value: healthy

value: macrophage

tag: passages

value: primary cell

tag: treatment


title: B1

description: All.counts.exp.txt

source_name: macrophage treated with rGAS6 rep1


title: A3

description: All.counts.exp.txt

source_name: macrophage rep3


title: A2

description: All.counts.exp.txt

source_name: macrophage rep2


title: A1

description: All.counts.exp.txt

source_name: macrophage rep1


title: B2

description: All.counts.exp.txt

source_name: macrophage treated with rGAS6 rep2


title: 4OFT_d5.5_R1 [176129]


title: control1A

first: HUI

last: CHEN

address: Guangzhou Huangpu Road

department: medicine

institute: Jinan University School of Medicine

data_processing:
The clean reads were mapped to the reference genome using HISAT2 . After that, Ericscript (v0.5.5)  and rMATS (V3.2.5)  were used to detect fusion genes and differential splicing genes (DSGs), respectively
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: COV434 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells)
The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).

treatment_protocol: Use 4HC at a concentration of 15 μM to act on COV434 cells for 24 hours

value: granulosa cells

tag: genotype

value: WT


title: Atria_d5.5_R3 [176125]


title: AVC_d5.5_R3 [176128]


title: AVC_d5.5_R1 [176323]


title: Atria_d5.5_R2 [176322]


title: AVC_d5.5_R2 [176127]


title: Atria_d5.5_R1 [176321]


title: LV_d4.5_R1 [176120]


title: LV_d4.5_R3 [176320]


title: LV_d4.5_R2 [176319]


title: RV_d4.5_R3 [176119]


title: RV_d4.5_R2 [176118]


title: HAP1 cells, wild type (WT6), replication experiment, rep 6

city: Providence

first: Eric

last: Morrow

address: 70 Ship Street

country: USA

institute: Brown University

description:
Paired with MUT6
6WT-6

data_processing:
Sequence reads quality control (FastQC/0.11.5)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimgalore/0.4.0
Trimmed sequence reads were mapped to UCSC/hg38 using HISAT2 (2.1.0) and STAR (star/2.5.3a) seperately
Read count extraction and normalization were performed using StringTie(1.3.3b) and HTSeq (0.9.1) seperately
differential expressed genes were identified using DESeq2 (1.20.0)
Assembly: UCSC/hg38
Supplementary files format and content: CSV file  include read count generated from StringTie for each sample

growth_protocol: HAP1 cells were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). >=2ug of total RNA was used for the construction of sequencing libraries.
poly-A-tailed mRNA selection RNA-seq

value: chronic myelogenous leukemia (CML) cell

value: CRIPSR/Cas9-mediated genome editing


title: HAP1 cells, wild type (WT6), replication experiment, rep 5

description:
Paired with MUT6
6WT-5


title: HAP1 cells, wild type (WT6), replication experiment, rep 3

description:
Paired with MUT6
6WT-3


title: HAP1 cells, SLC9A6 mutant (MUT6), replication experiment, rep 1

description:
c.351_352insG, p.Tyr118Val fs*8
61

value: SLC9A6 knockout


title: HAP1 cells, wild type (WT6), replication experiment, rep 4

description:
Paired with MUT6
6WT-4


title: HAP1 cells, SLC9A6 mutant (MUT6), replication experiment, rep 5

description:
c.351_352insG, p.Tyr118Val fs*8
65


title: HAP1 cells, SLC9A6 mutant (MUT6), replication experiment, rep 2

description:
c.351_352insG, p.Tyr118Val fs*8
62


title: HAP1 cells, SLC9A6 mutant (MUT6), replication experiment, rep 3

description:
c.351_352insG, p.Tyr118Val fs*8
63


title: HAP1 cells, SLC9A6 mutant (MUT6), replication experiment, rep 6

description:
c.351_352insG, p.Tyr118Val fs*8
66


title: HAP1 cells, SLC9A6 mutant (MUT4), replication experiment, rep 6

description:
c.351_354delGTAT, p.Tyr118 Ala fs*8
46


title: HAP1 cells, wild type (WT6), replication experiment, rep 1

description:
Paired with MUT6
6WT-1


title: HAP1 cells, wild type (WT6), replication experiment, rep 2

description:
Paired with MUT6
6WT-2


title: HAP1 cells, SLC9A6 mutant (MUT6), replication experiment, rep 4

description:
c.351_352insG, p.Tyr118Val fs*8
64


title: HAP1 cells, SLC9A6 mutant (MUT4), replication experiment, rep 3

description:
c.351_354delGTAT, p.Tyr118 Ala fs*8
43


title: HAP1 cells, SLC9A6 mutant (MUT4), replication experiment, rep 5

description:
c.351_354delGTAT, p.Tyr118 Ala fs*8
45


title: HAP1 cells, SLC9A6 mutant (MUT4), replication experiment, rep 4

description:
c.351_354delGTAT, p.Tyr118 Ala fs*8
44


title: HAP1 cells, SLC9A6 mutant (MUT4), replication experiment, rep 1

description:
c.351_354delGTAT, p.Tyr118 Ala fs*8
41


title: HAP1 cells, wild type (WT4), replication experiment, rep 6

description:
Paired with MUT1 and MUT4
4WT-6


title: HAP1 cells, wild type (WT4), replication experiment, rep 3

description:
Paired with MUT1 and MUT4
4WT-3


title: HAP1 cells, wild type (WT4), replication experiment, rep 5

description:
Paired with MUT1 and MUT4
4WT-5


title: HAP1 cells, wild type (WT4), replication experiment, rep 2

description:
Paired with MUT1 and MUT4
4WT-2


title: HAP1 cells, wild type (WT4), replication experiment, rep 4

description:
Paired with MUT1 and MUT4
4WT-4


title: HAP1 cells, wild type (WT4), replication experiment, rep 1

description:
Paired with MUT1 and MUT4
4WT-1


title: AVC_d4.5_R3 [176113]


title: RV_d4.5_R1 [176117]


title: OFT_d4.5_R3 [176116]


title: AVC_d4.5_R2 [176112]


title: Atria_d4.5_R3 [176110]


title: Atria_d4.5_R1 [176108]


title: OFT_d4.5_R2 [176115]


title: AVC_d4.5_R1 [176111]


title: OFT_d4.5_R1 [176318]


title: HAP1 cells, SLC9A6 mutant (MUT4), replication experiment, rep 2

description:
c.351_354delGTAT, p.Tyr118 Ala fs*8
42


title: Atria_d4.5_R2 [176317]


title: HAP1 cells, SLC9A6 mutant (MUT6), experiment 1, rep 6

description:
c.351_352insG, p.Tyr118Val fs*8
66_S50


title: 24 hours post-injury bio replicate 1 scATAC-seq

city: Bethesda

first: Whitney

middle: E

last: Heavner

state: MD

address: Building 35 Rm 2B-203

department: NINDS

institute: National Institutes of Health

description: 10x Genomics

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Detailed additional processing steps are available at https://github.com/koenvandenberge/hbcRegenOE
Assembly: mm10
Supplementary files format and content: tab separated values files and matrix files
Supplementary files format and content: processed count matrix for gene scores (geneMatArchrHbc.rds)
Supplementary files format and content: processed count matrix for peak data (peakMatArchrHbc_v2.rds)

molecule: genomic DNA

organism: Mus musculus

source_name: olfactory epithelium

growth_protocol: Olfactory epithelium was dissected from adult mouse

extract_protocol:
The dorsal olfactory epithelium (OE) was surgically removed and dissociated: OE from each animal was individually processed in approximately 1 mL of pre-warmed (37°C) dissociation medium (150 units papain dissolved in 5 mL Neurobasal medium with 2.5 mM Cysteine and 2.5 mM ethylenediaminetetraacetic acid) with 100 units DNAse I and incubated at 37°C for 25 mins. Samples were then washed three times with 10% fetal bovine serum in phosphate buffered saline (PBS-FBS) and strained through a 35 μm nylon mesh filter cap into a 5 mL polypropylene tube to remove debris. Propidium iodide (PI) was added to cells at a final concentration of 2 ug/mL just before loading them onto a BD FACSAria cell sorter. After running negative controls (no YFP, no PI and no YFP, PI only), YFP-positive/PI-negative cells were collected in a low-binding 1.5 mL tube containing 10% FBS in PBS on ice. Cells were centrifuged at 500g for 5 min at 4°C. After supernatant removal, cells were resuspended in 200 μl 0.04% BSA in PBS and centrifuged again at 500g for 5 min at 4°C. 195 μl supernatant was removed, and 45 μl cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40, 0.01% Digitonin, 1% BSA) was added and mixed with the pellet by gently pipetting up and down 3 times. Samples were incubated on ice for 3 min, and 50 μl cold wash buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, 1% BSA) was added to each without mixing. Samples were centrifuged at 500g for 5 min at 4°C. 95 ul supernatant was carefully removed, 45ul cold 1X Nuclei Buffer was added to each sample without mixing, and samples were centrifuged again at 500g for 5 min at 4°C. 48 μl supernatant was removed without disturbing the pellet, which was then resuspended in the remaining (~5 μl ) buffer for use in single cell ATACseq.
A Chromium Single Cell ATAC Library & Gel Bead Kit (PN-1000111) was used according to the manufacturer’s instructions (10X Chromium Single Cell ATAC Reagents Kits User Guide Rev B). Briefly, 5 μl of each sample resuspended in 1X Nuclei Buffer was added to 10 μl Transposition Mix, mixed by pipetting 6 times, and incubated in a thermal cycler at 37°C for 1 hour. After addition of barcoding master mix, the Chromium Chip E Single Cell Kit (PN-1000086) and Chromium i7 Multiplex Kit N, Set A (PN-1000084) were used for GEM generation. Libraries were constructed using 13 rounds of PCR.

value: olfactory epithelium

tag: age

value: 8 weeks

value: horizontal basal cell

value: Krt5Cre^ER; Rosa26^LSL-YFP/LSL-YFP

value: methimazole


title: 24 hours post-injury bio replicate 2 scATAC-seq

description: 10x Genomics

value: 6 weeks


title: 24 hours post-injury bio replicate 3 scATAC-seq

description: 10x Genomics

value: 6-7 weeks


title: Uninjured bio replicate 3 scATAC-seq

description: 10x Genomics

value: control


title: Uninjured bio replicate 1 scATAC-seq

description: 10x Genomics


title: Uninjured bio replicate 2 scATAC-seq

description: 10x Genomics


title: HAP1 cells, SLC9A6 mutant (MUT6), experiment 1, rep 3

description:
c.351_352insG, p.Tyr118Val fs*8
63_S47


title: HAP1 cells, SLC9A6 mutant (MUT6), experiment 1, rep 5

description:
c.351_352insG, p.Tyr118Val fs*8
65_S49


title: HAP1 cells, SLC9A6 mutant (MUT6), experiment 1, rep 2

description:
c.351_352insG, p.Tyr118Val fs*8
62_S46


title: LV_d3.5_R2 [176316]

value: cardiac

value: WTC

value: cardiac progenitors


title: aSHF_d3.5_R3 [176104]


title: LV_d3.5_R3 [176107]


title: aSHF_d3.5_R2 [176103]


title: aSHF_d3.5_R1 [176102]


title: HAP1 cells, SLC9A6 mutant (MUT6), experiment 1, rep 4

description:
c.351_352insG, p.Tyr118Val fs*8
64_S48


title: LV_d3.5_R1 [176105]


title: HAP1 cells, SLC9A6 mutant (MUT6), experiment 1, rep 1

description:
c.351_352insG, p.Tyr118Val fs*8
61_S45


title: HAP1 cells, wild type (WT6), experiment 1, rep 6

description:
Paired with MUT6
6WT-6_S44


title: AVC_d3.5_R3 [176101]


title: AVC_d3.5_R2 [176315]


title: HAP1 cells, wild type (WT6), experiment 1, rep 5

description:
Paired with MUT6
6WT-5_S43


title: HAP1 cells, wild type (WT6), experiment 1, rep 4

description:
Paired with MUT6
6WT-4_S42


title: 2nd_allmixed,biol rep4,scRNAseq,ADT_HTO

first: Byunghyun

last: Kang

state: Maryland

address: 9000 Rockville Pike

institute: NIAID

description: ADT&HTO: processed data include mRNA, ADT and HTO

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and quantifying ADTs and HTOs were performed using CellRanger 3.1.0 in NIH biowulf.
Assembly: mm10
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz - mRNA,ADT,HTO all included
Library strategy: CITE-seq

molecule: protein

source_name: ear

extract_protocol:
CD45+ hematopoietic and CD45- nonhematopoietic cells were FACs-sorted from the ears of either naïve or infected WT and eoCre : Il4/13f/f mice and mixed at 9:1 ratio (CD45+:CD45-),  and then processed through the Chromium Single cell 3’ v3.1 Library kit (10x Genomics) per the manufacturer’s protocol.
Library preparation was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x genomics). Briefly, 8,300 sorted cells were loaded for GEM formation, targeting 5,000 single cells for analysis from each ear. The RNAs from lysed single cells in gel beads were reversed transcribed into cDNA with Barcodes. Library fragment-size distribution was assessed using the Bioanalyzer 2100 and the DNA high-sensitivity chip (Agilent Technologies), followed by amplification, fragmentation, adapter ligation, and size selection to generate both 3’ gene expression libraries and cell surface protein libraries.

treatment_protocol: uninfected / L.major infected

tag: strain

value: ear

value: mixed CD45+ and CD45-

value: 6-8 weeks

value: uninfected+L.major infected

tag: exprmt

tag: library type

value: ADT,HTO

tag: adt

value: TotalSeq-B0157 anti-mouse CD45.2, TotalSeq-B0115 anti-mouse FceR1a, TotalSeq-B0002 anti-mouse CD8a, TotalSeq-B0431 anti-mouse SiglecF, TotalSeq-B0810 anti-mouse CD138, TotalSeq-B0120 anti-mouse TCRb, TotalSeq-B0211 anti-mouse TCRgd2

tag: hto

value: TotalSeq-B0301 to 0304 anti-mouse Hashtag 1 to 4


title: HAP1 cells, wild type (WT6), experiment 1, rep 3

description:
Paired with MUT6
6WT-3_S41

value: chronic myelogenous leukemia (CML) cell

value: WT

value: CRIPSR/Cas9-mediated genome editing


title: 2nd_allmixed,biol rep4,scRNAseq,GEX

description: GEX: processed data include mRNA, ADT and HTO

molecule: polyA RNA

value: mRNA


title: Atria_d3.5_R3 [176314]


title: glomerular tissues control-1

type: RNA

city: Hefei

first: Xianjin

last: Xu

address: Changning Street

institute: Hefei Ion Medical Center, the First Affiliated Hospital of USTC

description: Gene expresison without any treatment

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven

scan_protocol: The Agilent Scanner G2505C was used to scan the slides

data_processing: Agilent Feature Extraction software was applied to asses the array images. Quantile normalization and subsequent data processing were performed with the GeneSpring GX v11.5.1 software package (Agilent Technologies).

organism: Rattus norvegicus

source_name: glomerular tissues control-1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA was prepared using Trizol Reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: SD

value: glomerular tissues

tag: gender

value: Male


title: control -3 heart ventricles from E12.5

city: Xi'an

first: Luo

last: Yuru

state: Shannxi

address: 28 Xianning West Road

department: Health Science Center

institute: Xi'an Jiaotong University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Assembly: mm10
Supplementary files format and content: txt files of FPKM value for each sample

source_name: heart ventricles

extract_protocol:
Total RNA was extracted from heart ventricles using TRIzol reagent (Sigma)
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L)

value: heart ventricles

value: CTL


title: LSD1CKO-3 heart ventricles from E12.5


title: control -2 heart ventricles from E12.5


title: LSD1CKO-2 heart ventricles from E12.5


title: LSD1CKO-1 heart ventricles from E12.5


title: control-1 heart ventricles from E12.5


title: glomerular tissues TCM-4

description: Gene expresison without any treatment

source_name: glomerular tissues TCM-4


title: glomerular tissues control-3

description: Gene expresison without any treatment

source_name: glomerular tissues control-3


title: glomerular tissues TCM-2

description: Gene expresison without any treatment

source_name: glomerular tissues TCM-2


title: glomerular tissues model-4

description: Gene expresison without any treatment

source_name: glomerular tissues model-4


title: glomerular tissues control-2

description: Gene expresison without any treatment

source_name: glomerular tissues control-2


title: 2nd_allmixed,biol rep3,scRNAseq,ADT_HTO


title: HAP1 cells, wild type (WT6), experiment 1, rep 2

description:
Paired with MUT6
6WT-2_S40


title: con periodontal ligament cell exosomes

city: Shanghai

first: Fang

last: Qu

state: Shanghai

address: No.639 Zhizaoju Road

department: Department of Prosthodontics

institute: Shanghai Ninth People’s Hospital

data_processing:
Briefly, raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.2). Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged human pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch. The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach. Differentially expressed miRNAs between two samples were filtered through Fold change. Ddifferentially expressed miRNA between two groups were filtered by Fold Change and P-value. miRNA targets were performed by popular miRNA target prediction softwares, miRNA-targets networks were plotted by cytoscape software (v2.8.0), and the GO and KEGG pathway analysis were performed based on the top 100 differentially expressed miRNA target genes.
Assembly: Raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Firstly, Q30 was used to perform quality control. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.2). Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs.
Supplementary files format and content: miRNA expression for all samples (raw).xlsx

source_name: periodontal ligament cell

growth_protocol: Premolars extracted for orthodontic reasons were collected sterilely with the consent of the patients or their parents. This study was designed in accordance with the Declaration of Helsinki, and the experimental protocol was approved by the ethics committee of Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine. The approval number is SH9H-2020-TK17-1.The periodontal ligament tissue was scraped from the middle 2/3 of the root. Primary culture of human periodontal ligament cells (PDLCs) was performed using the tissue in high-glucose DMEM (HyClone, Thermo Fisher Scientific, MA, USA) supplemented with 10% fetal bovine serum (FBS, Gibco, Thermo Fisher Scientific, MA, USA) and 1% penicillin/streptomycin (Gibco, Thermo Fisher Scientific, MA, USA).

extract_protocol:
RNA extraction protocol
Briefly, total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: 1) 3'-adaptor ligation; 2) 5'-adaptor ligation; 3) cDNA synthesis; 4) PCR amplification; 5) Size selection of ~150 bp PCR amplicons (corresponding to ~22nt miRNAs) The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina HiSeq sequencer following the manufacturer's instructions.

treatment_protocol: The PDLCs were seeded into 6-well flexible basal cell culture plates. A dynamic cyclic stretch strain of 20% was applied by using the Flexcell Tension Plus system (FX-500T, Flexcell International, Hillsborough, NC, USA) after replacing the culture medium with exosome-free serum. The loading cycle was 10 seconds (5 seconds of stretch and 5 seconds of relaxation) at a frequency of 0.1 Hz (6 times/minute) for 6 hours. Cells cultured on the same kind of plates (BioFlex, Flexcell International) but without stretch served as time-matched non-stretched controls.After stretch loading, the cell culture supernatant was collected, and the exosomes were extracted by using Qiagen exoEasy Maxi Kit (QIAGEN GmbH, Hilden, Germany). Total RNA from exosomes was extracted. The miRNAs were subjected to second-generation Illumina HiSeq high-throughput sequencing.

value: periodontal ligament cell

value: non cyclic stretch


title: HAP1 cells, wild type (WT6), experiment 1, rep 1

description:
Paired with MUT6
6WT-1_S39


title: control empty vector rep3.RNA

city: Worcester

first: Junhui

last: Li

state: MA

address: 364 Plantation St

institute: University of Massachusetts Medical School

data_processing:
The first 14 bases in each of raw reads were removed with FASTX-Toolkit(version 0.0.14).
The RNA-seq analysis was performed using OneStopRNAseq (version 1.0.0)
FastQC (version 0.11.5) and MultiQC (version 1.6) were used for raw reads quality control and QoRTs (version 1.3.6) for post-alignment quality control.
Reads were aligned to the reference genome assembly hg38 with star (version 2.7.5a) and annotated with gencode.v34.primary_assembly. Aligned exon reads were counted toward gene expression with featureCounts (version 2.0.0) with default settings except the following parameters ‘-Q 20 --minOverlap 1 --fracOverlap 0’ for single-end strict-mode analysis.
Differential expression (DE) analysis was performed with DESeq2 (version 1.28.1). Within DE analysis, 'ashr' was used to create log2 Fold Change (LFC) shrinkage for each comparison. Significantly differentially expressed genes (DEGs) were filtered with the criteria FDR < 0.05 and absolute log2 fold change (|LFC|) > 0.585.
Assembly: hg38
Supplementary files format and content: Gene expression matrix: This is a tabular file that represents the gene expression levels for each sample in the dataset. It typically includes rows representing genes or transcripts and columns representing individual samples. The values in the matrix can be raw read counts, normalized expression values (e.g., TPM or FPKM), or log-transformed expression values.
Supplementary files format and content: Differential expression analysis results: These files contain the results of differential gene expression analysis, identifying genes that show significant expression differences between different conditions or groups. The files may include statistics such as fold change, p-values, adjusted p-values, and gene annotations.

source_name: breast

growth_protocol: MCF10A cells  were maintained in DMEM/F12 supplemented with 5% donor horse serum, 20 ng/ml epidermal growth factor, 10 mg/ml insulin, 1 ng/ml cholera toxin, 100 mg/ml hydrocortisone, 50 U/ml penicillin , and 50 mg/ml streptomycin in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
MCF10A cells stably expressing pMSCVpuro-pre-miR-203a or pMSCVpuro were lysed for 30 minutes on ice in cell lysis buffer then centrifuged for 30 minutes at 14,000 rpm at 4°C. The supernatant was used as cell lysate for the IP. Mouse anti-AGO2 (Abcam) was coupled to Protein G Dynabeads (Thermo Fisher Scientific) and added to lysates. Antibody-lysate mixtures were rotated for 4 hours at 4°C [to bind RISC in each sample]. The beads were washed in IP wash buffer supplemented with a protease inhibitor cocktail and eluted in Trizol (Invitrogen).
mRNA purification, cDNA synthesis, and amplification were carried out according to the TrueSeq RNA sample preparation guide (Illumina).

treatment_protocol: MCF10A cells were transduced with a retrovirus expressing a expressing pMSCVpuro-pre-miR-203a or pMSCVpuro control and then cultured under puromycin selection

value: breast

value: immortalized mammary epithelial cells


title: HAP1 cells, SLC9A6 mutant (MUT4), experiment 1, rep 6

description:
c.351_354delGTAT, p.Tyr118 Ala fs*8
46_S38

value: SLC9A6 knockout


title: treated with pre-miR203a vector rep2.RNA


title: treated with pre-miR203a vector rep1.RNA


title: HAP1 cells, SLC9A6 mutant (MUT4), experiment 1, rep 4

description:
c.351_354delGTAT, p.Tyr118 Ala fs*8
44_S36


title: control empty vector rep2.RNA


title: HAP1 cells, SLC9A6 mutant (MUT4), experiment 1, rep 3

description:
c.351_354delGTAT, p.Tyr118 Ala fs*8
43_S35


title: Atria_d3.5_R2 [176097]

source_name: cardiac

value: cardiac

value: WTC

value: cardiac progenitors


title: Atria_d3.5_R1 [176096]


title: LV_d1.5_R3 [176313]


title: HAP1 cells, SLC9A6 mutant (MUT4), experiment 1, rep 5

description:
c.351_354delGTAT, p.Tyr118 Ala fs*8
45_S37

value: chronic myelogenous leukemia (CML) cell


title: LV_d1.5_R1 [176093]


title: AVC_d1.5_R3 [176092]


title: LV_d1.5_R2 [176094]


title: glomerular tissues control-4

description: Gene expresison without any treatment

source_name: glomerular tissues control-4


title: glomerular tissues TCM-3

description: Gene expresison without any treatment

source_name: glomerular tissues TCM-3


title: glomerular tissues TCM-1

description: Gene expresison without any treatment

source_name: glomerular tissues TCM-1


title: HAP1 cells, SLC9A6 mutant (MUT4), experiment 1, rep 2

description:
c.351_354delGTAT, p.Tyr118 Ala fs*8
42_S34


title: control empty vector rep1.RNA


title: 2nd_allmixed,biol rep1,scRNAseq,ADT_HTO

value: ear

value: mixed CD45+ and CD45-

value: 6-8 weeks

value: uninfected+L.major infected

value: ADT,HTO

value: TotalSeq-B0157 anti-mouse CD45.2, TotalSeq-B0115 anti-mouse FceR1a, TotalSeq-B0002 anti-mouse CD8a, TotalSeq-B0431 anti-mouse SiglecF, TotalSeq-B0810 anti-mouse CD138, TotalSeq-B0120 anti-mouse TCRb, TotalSeq-B0211 anti-mouse TCRgd2

value: TotalSeq-B0301 to 0304 anti-mouse Hashtag 1 to 4


title: 2nd_allmixed,biol rep2,scRNAseq,GEX

value: mRNA


title: 2nd_allmixed,biol rep3,scRNAseq,GEX


title: 1st_koinf, scRNAseq, ADT

description: ADT: processed data include mRNA and ADT

value: L.major infected

value: ADT

value: TotalSeq-B0182 anti-mouse CD3, TotalSeq-B0001 anti-mouse CD4, TotalSeq-B0014 anti-mouse CD11b, TotalSeq-B0106 anti-mouse CD11c, TotalSeq-B0093 anti-mouse CD19, TotalSeq-B0118 anti-mouse NK1.1, TotalSeq-B0015 anti-mouse Ly6G, TotalSeq-B0012 anti-mouse c-Kit, TotalSeq-B0847 anti-mouse ICOS, TotalSeq-B0114 anti-mouse F4/80


title: 2nd_allmixed,biol rep2,scRNAseq,ADT_HTO


title: 2nd_allmixed,biol rep1,scRNAseq,GEX


title: 1st_koinf, scRNAseq, GEX

description: GEX: processed data include mRNA and ADT


title: HAP1 cells, SLC9A6 mutant (MUT4), experiment 1, rep 1

description:
c.351_354delGTAT, p.Tyr118 Ala fs*8
41_S33

value: CRIPSR/Cas9-mediated genome editing


title: glomerular tissues model-3

description: Gene expresison without any treatment

source_name: glomerular tissues model-3

value: SD

value: glomerular tissues

value: Male


title: AVC_d1.5_R1 [176090]

value: cardiac

value: WTC

value: cardiac progenitors


title: AVC_d1.5_R2 [176091]


title: AVC_d3.5_R1 [176099]


title: 1st_wtinf, scRNAseq, ADT

value: ear

value: mixed CD45+ and CD45-

value: wt


title: glomerular tissues model-2

description: Gene expresison without any treatment

source_name: glomerular tissues model-2


title: HAP1 cells, SLC9A6 mutant (MUT1), experiment 1, rep 5

description:
c.351delG, p.Tyr118Met fs*9
15_S31

value: chronic myelogenous leukemia (CML) cell

value: SLC9A6 knockout


title: 1st_wtinf, scRNAseq, GEX

value: 6-8 weeks


title: HAP1 cells, SLC9A6 mutant (MUT1), experiment 1, rep 6

description:
c.351delG, p.Tyr118Met fs*9
16_S32


title: HAP1 cells, SLC9A6 mutant (MUT1), experiment 1, rep 4

description:
c.351delG, p.Tyr118Met fs*9
14_S30


title: SHF_d1.5_R2 [176088]


title: SHF_d1.5_R3 [176089]


title: control empty vector rep2.RIP

description:
AB9
FPKM.xlsx

data_processing:
The first 14 bases in each of raw reads were removed with FASTX-Toolkit(version 0.0.14).
The RNA-seq analysis was performed using OneStopRNAseq (version 1.0.0)
FastQC (version 0.11.5) and MultiQC (version 1.6) were used for raw reads quality control and QoRTs (version 1.3.6) for post-alignment quality control.
Reads were aligned to the reference genome assembly hg38 with star (version 2.7.5a) and annotated with gencode.v34.primary_assembly. Aligned exon reads were counted toward gene expression with featureCounts (version 2.0.0) with default settings except the following parameters ‘-Q 20 --minOverlap 1 --fracOverlap 0’ for single-end strict-mode analysis.
Differential expression (DE) analysis was performed with DESeq2 (version 1.28.1). Within DE analysis, 'ashr' was used to create log2 Fold Change (LFC) shrinkage for each comparison. Significantly differentially expressed genes (DEGs) were filtered with the criteria Pvalue < 0.05 and absolute log2 fold change (|LFC|) > 0.375.
Assembly: hg38
Supplementary files format and content: Gene expression matrix: This is a tabular file that represents the gene expression levels for each sample in the dataset. It typically includes rows representing genes or transcripts and columns representing individual samples. The values in the matrix can be raw read counts, normalized expression values (e.g., TPM or FPKM), or log-transformed expression values.
Supplementary files format and content: Differential expression analysis results: These files contain the results of differential gene expression analysis, identifying genes that show significant expression differences between different conditions or groups. The files may include statistics such as fold change, p-values, adjusted p-values, and gene annotations.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen).
mRNA purification, cDNA synthesis, and amplification were carried out according to the TrueSeq RNA sample preparation guide (Illumina).

value: breast

value: immortalized mammary epithelial cells


title: treated with pre-miR203a vector rep1.RIP

description:
AB8
FPKM.xlsx


title: WI-38_N_G3

city: Beijing

first: yongpan

last: an

address: xueyuanlu

institute: Peking University

data_processing:
Illumina Casava software used for basecalling.
Read quality was checked for each sample using fastx_toolkit_0.0.14.
High-quality reads were then imported into HISAT2 to get mapped reads.
Mapped Reads are spliced using StringTie software, based on the selected reference genome sequence.
The functional annotations of gene/transcript in NR, Swiss-PROt, Pfam, EggNOG, GO and KEGG were summarized.
RSEM software conducts quantitative analysis of gene and transcript expression levels respectively. The quantitative index is TPM, which refers to the number of transcripts as the unit of calculation.
After obtaining the Read Counts of genes/transcripts, DESeq2, DEGseq or edgeR can be used to conduct sample or intergroup gene/transcript differential expression analysis for multiple (≥2) items to identify the differentially expressed genes/transcripts.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: cell

growth_protocol: WI-38 cells were provided by the National Institutes for Food and Drug Control. The cells were counted and inoculated for each passage at the same density, and incubated in MEM (Gibco) supplemented with 10% FBS (Gibco) in an incubator at 37°C and 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Knockdown of the SRC gene or administration of GW8510 intervention in senescent WI-38 cells.

tag: time point

value: PD45 (45 generation cells)


title: control empty vector rep1.RIP


title: 1st_koun, scRNAseq, GEX

source_name: ear

value: uninfected

value: mRNA


title: 1st_wtun, scRNAseq, ADT

value: ADT

value: TotalSeq-B0182 anti-mouse CD3, TotalSeq-B0001 anti-mouse CD4, TotalSeq-B0014 anti-mouse CD11b, TotalSeq-B0106 anti-mouse CD11c, TotalSeq-B0093 anti-mouse CD19, TotalSeq-B0118 anti-mouse NK1.1, TotalSeq-B0015 anti-mouse Ly6G, TotalSeq-B0012 anti-mouse c-Kit, TotalSeq-B0847 anti-mouse ICOS, TotalSeq-B0114 anti-mouse F4/80


title: WI-38_N_G2


title: HAP1 cells, SLC9A6 mutant (MUT1), experiment 1, rep 2

description:
c.351delG, p.Tyr118Met fs*9
12_S28

value: CRIPSR/Cas9-mediated genome editing


title: WI-38_N_G1


title: 1st_wtun, scRNAseq, GEX


title: treated with pre-miR203a vector rep2.RIP

description:
AB10
FPKM.xlsx


title: 6h-stretched periodontal ligament cell exosomes

value: periodontal ligament cell

value: cyclic stretch for 6h


title: HAP1 cells, SLC9A6 mutant (MUT1), experiment 1, rep 3

description:
c.351delG, p.Tyr118Met fs*9
13_S29


title: HAP1 cells, SLC9A6 mutant (MUT1), experiment 1, rep 1

description:
c.351delG, p.Tyr118Met fs*9
11_S27


title: human T47D control + PKAi (replicate 1)

city: Nottingham

first: Sarah

middle: Joanne

last: Storr

state: Nottinghamshire

address: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

data_processing:
Quality control using Trim Galore
Pseudoalignment using Kallisto
Assembly: human
Supplementary files format and content: Kallisto h5 abundance files

extract_protocol:
mRNA was purified from total RNA via poly-T oligo attached magnetic beads prior to fragmentation which was followed by first strand cDNA synthesis using random hexamer primers then second strand cDNA synthesis.
The library was complete following end-repair, A-tailing, adapter ligation, size selection, amplification and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyser for size detection before being sequenced on Illumina NovaSeq

value: human T47D control + PKAi (replicate 1)


title: 1st_koun, scRNAseq, ADT

value: ear


title: SHF_d1.5_R1 [176087]

value: cardiac

value: WTC

value: cardiac progenitors


title: WI-38_siSRC4_3

value: DMSO


title: human T47D DARPP-32 siRNA knockdown + PKAi (replicate 3)


title: HAP1 cells, wild type (WT4), experiment 1, rep 6

description:
Paired with MUT1 and MUT4
14WT-6_S26

value: chronic myelogenous leukemia (CML) cell

value: WT


title: human T47D DARPP-32 siRNA knockdown + PKAi (replicate 2)

value: breast


title: WI-38_siSRC4_2

value: PD45 (45 generation cells)


title: HAP1 cells, wild type (WT4), experiment 1, rep 5

description:
Paired with MUT1 and MUT4
14WT-5_S25


title: human T47D DARPP-32 siRNA knockdown +PKAi (replicate 1)


title: HAP1 cells, wild type (WT4), experiment 1, rep 4

description:
Paired with MUT1 and MUT4
14WT-4_S24


title: WI-38_siSRC4_1


title: WI-38_siSRC2_3


title: human T47D control + E2 (replicate 3)

value: human T47D control + E2 (replicate 3)


title: human T47D control + E2 (replicate 2)

value: human T47D control + E2 (replicate 2)


title: WI-38_siSRC2_2


title: HAP1 cells, wild type (WT4), experiment 1, rep 3

description:
Paired with MUT1 and MUT4
14WT-3_S23


title: human T47D control + E2 (replicate 1)

value: human T47D control + E2 (replicate 1)


title: HAP1 cells, wild type (WT4), experiment 1, rep 2

description:
Paired with MUT1 and MUT4
14WT-2_S22


title: WI-38_siSRC2_1


title: WI-38_NC3


title: human T47D DARPP-32 siRNA knockdown + E2 (replicate 3)


title: MCF7 ATAC As rep2

city: Grand Forks

first: Sergei

last: Nechaev

state: North Dakota

address: Columbia Hall Room 1733c, 501 North Columbia Road Stop 9061

department: Biomedical Sciences

institute: University of North Dakota

library_source: genomic

data_processing:
Adapter-trimmed raw reads were aligned to hg19 genome using hisat2, followed by converting to BigWig format using bamCoverage with the default bin size of 50 bp, signal was normalized using counts per million (CPM) and duplicate reads were removed using MarkDuplicates. Peaks were called in each replicate using MACS2 with a q-value or FDR cut-off of 0.01.
Assembly: hg19
Supplementary files format and content: bw - bigwig files.
Supplementary files format and content: narrowPeak - peaks called for each replicate

growth_protocol: All cells were purchased from the American Type Culture Collection and used within the first 15 passages. Cells were grown in 15 cm dishes as before {Samarakkody et al., 2015, #72840} and growth media was replaced with fresh media 24 hours before treatments {Mahat and Lis, 2017, #290391; Vihervaara et al., 2017, #282616}.

extract_protocol:
Fresh cells were subjected to ATAC library construction protocol
ATAC-seq was done using the original protocol and buffer {Buenrostro et al., 2013, #304248}. Incubation with Tn5 transposase was done in a shaking heating block at 37°C and 500 RPM for 30 minutes followed by real-time PCR amplification with Nextera dual index primers and NEBNext High-Fidelity 2x PCR mix with added Evagreen dye to avoid overamplification.

treatment_protocol: Heat-Shock treatment was started by placing a dish onto a heated water surface for 1 minute to raise the temperature quickly and continued in a 42°C 5% CO2 incubator for the remaining time. Arsenic treatment was performed by the addition of 500 mM Sodium meta-arsenite (Sigma) at the ambient 37°C with 5% CO2 {Khalil et al., 2006, #243125}.

value: mammary gland, adenocarcinoma

value: Arsenic


title: human T47D DARPP-32 siRNA knockdown + E2 (replicate 2)


title: human T47D control + PKAi (replicate 2)

value: human T47D control + PKAi (replicate 2)


title: human T47D control + PKAi (replicate 3)

value: human T47D control + PKAi (replicate 3)


title: HG+CD200, rep3

city: Saint Louis

first: Charles

middle: W.

last: Pfeifer

state: Missouri

address: 660 S. Euclid Ave., Campus Box 8096

department: Ophthalmology and Visual Sciences

institute: Washington University School of Medicine in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04.
All gene counts were then imported into the R/Bioconductor package EdgeR and normalization size factors were calculated to adjust for samples of differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples ≥1 count-per-million were excluded from further analysis. Size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights function and were fitted using a Limma generalized linear model. The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with an absolute fold change (FC) > 1.50 with a Benjamini-Hochberg false-discovery rate adjusted p-value < 0.05.
Assembly: Mouse Ensembl GRCm38.101
Supplementary files format and content: all.gene_counts.tsv: Raw gene counts for all samples
Supplementary files format and content: Merged_Differential_Expression.tsv: Contains results from differential gene expression analysis performed comparing HG v. NG, HG+CD200 v. HG, NG+CD200 v. NG, and HG+CD200 v. NG

extract_protocol:
RNA was harvested using the RNeasy Plus Mini Kit (Qiagen). Total RNA integrity was determined using 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). All samples contained RNA of high quality (RIN > 9.0).
mRNA was fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol: Transcardiac perfusion of anesthetized (ketamine/xylazine) mice was performed with ice-cold PBS with heparin (3U/mL) prior to surgical dissection of eyes into ice-cold PBS (10% FBS) to isolate the retina from the RPE-choroid complex. Retinas of both eyes were pooled for each animal before undergoing papain-based enzymatic digestion (Worthington Biochemical) for 40 minutes in a water bath at 28⁰C. Samples were then moved to a separate water bath at 8⁰C for 8 minutes. Digested material was then homogenized by gentle trituration with a pipette before being spun down by centrifugation at 300g for 5 minutes at 4⁰C. Supernatant was then discarded and the sample resuspended with FACS buffer (HBSS, 1% BSA, 1mM EDTA) containing ovomucoid inhibitor. FACS was carried out with a Beckman Coulter MoFlo cytometer provided by the Siteman Cancer Center Flow Cytometry core equipped with a 120µm nozzle and 350nm (UV)/530nm (green) excitation lasers to isolate GFP-positive, DAPI-negative (viable) cells. Cells were sorted directly into RLT lysis buffer (Qiagen) and snap-frozen.

value: Microglia

value: High glucose + CD200Fc (50ng/mL)


title: NG, rep1

value: Normal glucose


title: NG+CD200, rep2

value: Normal glucose + CD200Fc (50ng/mL)


title: HG+CD200, rep2


title: NG, rep3


title: NG+CD200, rep1


title: NG+CD200, rep3


title: NG, rep2


title: MCF7 ATAC HS rep2

value: Heat shock


title: HG+CD200, rep1


title: HG, rep3

value: High glucose


title: human T47D control (replicate 2)

value: human T47D control (replicate 2)


title: HG, rep2


title: WI-38_Y3

value: DMSO

value: PD30 (30 generation cells)


title: WI-38_Y2


title: WI-38_NC1

value: PD45 (45 generation cells)


title: WI-38_NC2


title: human T47D control (replicate 3)

value: breast

value: human T47D control (replicate 3)


title: human T47D DARPP-32 siRNA knockdown + E2 (replicate 1)


title: MCF7 ATAC As rep1


title: HAP1 cells, wild type (WT4), experiment 1, rep 1

description:
Paired with MUT1 and MUT4
14WT-1_S21

value: chronic myelogenous leukemia (CML) cell

value: WT

value: CRIPSR/Cas9-mediated genome editing


title: MCF7 ATAC HS rep1

value: mammary gland, adenocarcinoma


title: WI-38_Y1


title: human T47D control (replicate 1)

value: human T47D control (replicate 1)


title: MCF7 ATAC NHS rep2

value: Untreated


title: human T47D DARPP-32 siRNA knockdown (replicate 1)


title: MCF7 As RNA Pol II rep 2

data_processing:
Raw files were adapter-trimmed with trimmomatic and aligned to hg19 genome using hisat2. For HSF1 ChIP-seq, raw fastq files were randomly subset to 40M read pairs prior to alignment. After removing PCR duplicates with MarkDuplicates (Picard),   peaks were called using MACS2 with FDR cutoff 0.01 and then merged between replicates . Read coverage was calculated using bamCoverage and read counts were normalized to sequencing depth. Signal was calculated using multibigwigsummary.
Assembly: hg19
Supplementary files format and content: bw - bigwig files.
Supplementary files format and content: narrowPeak - peaks called for each replicate

extract_protocol:
Approximately 2x107 cells were crosslinked with 1% ethanol-free formaldehyde (Thermo) in serum-free DMEM/F12 media at 25C for 10min, quenched with 125mM Glycine, and lysed in buffer (1% Sodium-Dodecyl Sulfate (SDS), 50mM Tris (pH=8), 10mM EDTA, 1X PMSF and protease inhibitor cocktail) followed by disruption in the Covaris S2 sonicator for 6 minutes (with peak power = 140, Duty factor = 5, Cycles/burst = 200). Protein A and Protein G Dynabeads (Invitrogen) premixed at 1:1 ratio were used for pre-clearing for 1 hour at 4C. One percent of each precleared sample was taken as input, with at least two inputs taken for each sample and averaged for ChIP percent input calculation. Samples were incubated with 5g of primary antibodies in 2 ml of dilution buffer (1% Triton-X, 2mM EDTA, 20mM Tris pH=8.0, 150mM NaCl, 1X Phenylmethylsulfonyl fluoride (PMSF) and cOmplete protease inhibitor cocktail (Sigma)) with slow rotation overnight at 4C followed by washing
DNA library was prepared from validated ChIP material using NEBNext Ultra II DNA library kit (New England Biolabs) protocol without size selection. Final PCR amplification of cDNA templates was done using TruSeq Illumina Small RNA PCR primers, 250 M dNTP mix, 1x HF buffer, 1M Betaine, 1xEvagreen dye (Biotium) and Phusion DNA polymerase.

tag: chip antibody

value: Rpb1 NTD (D8L4Y), Cell Signaling

value: Arsenic


title: 8wk STZ, rep3

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04.
All gene counts were then imported into the R/Bioconductor package EdgeR and normalization size factors were calculated to adjust for samples of differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples ≥1 count-per-million were excluded from further analysis. Size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights function and were fitted using a Limma generalized linear model. The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with an absolute fold change (FC) > 1.50 with a Benjamini-Hochberg false-discovery rate adjusted p-value < 0.05.
Assembly: Mouse Ensembl GRCm38.101
Supplementary files format and content: all.gene_counts.tsv: Raw gene counts for all samples
Supplementary files format and content: STZ_Control_Differential_Expression.tsv: Contains results from differential gene expression analysis performed comparing 8wk STZ vs. Control and 4wk STZ vs. Control

source_name: retina

extract_protocol:
RNA was harvested using the RNeasy Plus Micro Kit (Qiagen). RNA quantity and quality was determined using a 2100 Bioanalyzer and RNA Pico kit (Agilent Technologies). 1.0-2.0ng of total RNA was used for the construction of libraries for each sample. All samples contained RNA of high quality (RIN>8.0).
ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases

value: retina

value: Microglia

value: 8wk STZ


title: MCF7 HS RNA Pol II rep 2

value: Heat shock


title: human T47D DARPP-32 siRNA knockdown (replicate 2)


title: ADSC

data_processing:
Basecalls performed using CASAVA version 1.8.
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter.
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:
* MT% < 20%;
* Cell Gene Number < Median Gene Number * 2;
* Cell Gene Number > 200.
PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples. Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: MTX file and TSV files contain counts for each barcodes and genes.

source_name: Adipose-derived stem cells

growth_protocol: Adipose tissues were washed with phosphate-buffer saline (PBS) to remove debris and red blood cells. Adipose tissues were cut into pieces and treated with 0.25% collagenase type I for 30 min at 37°C. Then equal volume Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Thermo Fisher Scientific, USA) with 10% fetal bovine serum (FBS; Gibco) was added to neutralize the collagenase activity. Finally, cells were plated on dishes in DMEM with 1 g/L glucose and 10% FBS. After the third passage, we identified the cells by flow cytometric analysis with 3 stem cell positive markers, CD105, CD90, CD73, and 7 negative markers CD45, CD79a, CD19, CD34, CD14, CD11b and HLA-DR.

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v3 (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10x Genomics Single Cell 3’ Library Gel Bead Kit V2 and prepared for sequencing using standard Illumina protocols.

value: Adipose-derived stem cells


title: 8wk STZ, rep1


title: MCF7 ATAC NHS rep1


title: 8wk STZ, rep4


title: 4wk STZ, rep3

value: 4wk STZ


title: MCF7 NHS RNA Pol II rep 2


title: 8wk STZ, rep2


title: MCF7 As RNA Pol II rep 1


title: MCF7 HS RNA Pol II rep 1


title: EC5/Ectopic endometrial tissue of E

city: Nanjing

first: Hengmei

last: SHI

state: Jiangsu

address: No. 123 Tianfei Road, Qinhuai District, Nanjing City, Jiangsu Province

institute: Women’s Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital)

data_processing:
Raw sequencing data QC
Mapping Summary: Alignment information of sequence mapping to reference genome
Identification of tRF&tiRNA
Differential expression analysis of tRF&tiRNA
The scatter plots of differentially expression tRF&tiRNA. Supervised analysis: For each group comparison, we generate a hierarchical clustering heatmap and a volcano plot to display significantly differentially expressed tRFs & tiRNAs.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for each Sample
Supplementary files format and content: tab-delimited text file includes CPM values for each Sample

source_name: Ectopic endometrial tissue

extract_protocol:
Total RNA was extracted from frozen tissues using Trizol LS (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions. 1-2 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries are size-selected for the RNAbiotypes to be sequenced using an automated gel cutter. The libraries are qualified and absolutely quantified using Agilent BioAnalyzer 2100. For standard small RNA sequencing on Illumina NextSeq instrument, the sequencing type is 50bp single- read.
tRF&tiRNA-seq

value: Ectopic endometrial tissue


title: EU2/Eutopic endometrial tissue of B

source_name: Eutopic endometrial tissue

value: Eutopic endometrial tissue


title: EU4/Eutopic endometrial tissue of D


title: HO53_24h_3

city: Reykjavik

first: Iwona

middle: Teresa

last: Myszor

address: Vatnsmyrarvegur 16

country: Iceland

institute: University of Iceland

data_processing:
Illumina NovaSeq 6000
Kallisto version 0.45.0
sleuth R package version 0.30
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: Kallisto h5 and tsv abundance measurements

source_name: bronchus

growth_protocol: BCi-NS1.1 cell line (BCi) was cultured in Bronchial/Tracheal Epithelial cell growth medium (BEGM) supplemented with retinoic acid and Penicillin-Streptomycin (20 U/ml, 20 µg/ml, respectively) at 37°C and 5% CO2. The ALI (air-liquid interphase) culture of BCi cells was established by seeding 4.5-5×105 of BCi cells (up to passage 21) on the 12-well trans-well inserts with 0.4 μm porous membrane coated with collagen IV from human placenta for 1 h, mimicking basal membrane. BCi cells were seeded in Dulbecco´s Modified Eagle Medium F-12 Nutrient Mixture (DMEM/F-12) supplemented with 10% FBS in the presence of antibiotics penicillin (50 U/ml) and streptomycin (50 μg/ml). The next day medium in BCi culture was replaced with medium supplemented with 2% UltorserG (UG) and after 2-3 days post-seeding ALI culture was established by aspiration of the medium from the upper chamber and exposition of the cell layer to air. Medium in the lower chamber was replaced every 2-3 days. ALI culture of BCi cells was maintained until trans-epithelial electrical resistance (TEER) reached 800-1000 Ω×cm2, that usually took place between 3-4 weeks of ALI culture.

extract_protocol:
Total RNA was extracted using NucleoSpin RNA kit (Machinery-Nagel).
The quality (RIN score) and quantity of isolated total RNA samples was assessed using the DNA 5K/RNA chip for the LabChip GX (Perkin-Elmer). cDNA libraries derived from Poly-A mRNA were generated using Illumina´s TruSeq RNA v2 Sample Prep Kit. Briefly, Poly-A mRNA was isolated from total RNA samples (0.2–1 μg input) using hybridization to Poly-T beads. The Poly-A mRNA was fragmented at 94°C, and first-strand cDNA was prepared using random hexamers and the SuperScript II reverse transcriptase. Following second-strand cDNA synthesis, end repair, addition of a single A base, indexed adaptor ligation, AMPure bead purification, and PCR amplification, the resulting cDNA sequencing libraries were measured on the LabChip GX, diluted to 3 nM and stored at -20 °C.

treatment_protocol: The treatment compound HO53 was added to the lower chamber of the trans-well insert to obtain 75 µM final concentration. Samples in triplicates for each treatment group (HO53 treatment vs control/untreated cells) were collected after 4 h, 8 h and 24 h.

tag: culture

value: air-liquid interphase day 26


title: EC2/Ectopic endometrial tissue of B

tag: tissue


title: EC3/Ectopic endometrial tissue of C


title: 4wk STZ, rep2


title: HG, rep1

tag: cell line

value: High glucose


title: EU3/Eutopic endometrial tissue of C


title: HO53_24h_1


title: MCF7 NHS RNA Pol II rep 1

tag: cell type


title: EC4/Ectopic endometrial tissue of D


title: Control, rep3

value: Control


title: 4wk STZ, rep1


title: EU1/Eutopic endometrial tissue of A


title: ctrl_24h_3

value: untreated - 24h


title: Control, rep2


title: HO53_24h_2


title: ctrl_24h_2


title: Control, rep1


title: EU5/Eutopic endometrial tissue of E


title: ctrl_24h_1


title: HO53_8h_2


title: EC1/Ectopic endometrial tissue of A


title: treated with pre-miR203a vector rep3.RNA

value: breast

value: immortalized mammary epithelial cells


title: human T47D DARPP-32 siRNA knockdown (replicate 3)


title: HCC cells, day 7 (+dox), rep 3

city: Stanford

first: Dean

last: Felsher

state: CA

address: 269 Campus Drive

department: Medicine

institute: Stanford University

data_processing:
STAR (version 2.7.9a) was used to align reads with the option --sjdbOverhang '149'. featureCounts (version 2.0.3) was used to quantify read counts.
Assembly: mm10
Supplementary files format and content: Raw counts

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit.
RNA-Seq libraries were constructed by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: hepatocellular carcinoma

value: LAP-tTA/tetO-MYC

value: day 7, doxycycline (MYC off)


title: HCC cells, day 7 (+dox), rep 2


title: Retinosphere Supplement  Reprogramming Control scRNA

city: Seattle

first: Thomas

last: Reh

state: Washington

address: 1959 NE Pacific Street, UW School of Medicine, Seattle, WA 98195

department: Department of Neurobiology and Biophysics

institute: University of Washington

description:
repro_supplement_retinosphere_control
10x Genomics

library_source: transcriptomic single cell

data_processing:
Read demutliplexing and intensity to fastq conversion done using cellranger mkfastq or cellranger-atac mkfastq
(RNA samples only): Gene by cell matricies were created using cellranger count
(Multiome samples only): Reads were alligned, peaks were called, and fragment files and peak x cell matricies were created using cellranger-atac count
(Multiome samples only): Peaks were re-called using Macs2 (through Signac) and new peak x cell matricies were created using Signac::FeatureMatrix()
Downstream processing was preformed in R using Seurat, Signac, ChromVar, and Monocle3
Assembly: GRCh38-2020-A
Supplementary files format and content: (Multiome samples only): CellRanger outputs: filtered feature bc matrices h5, fragment files, and barcode metrics
Supplementary files format and content: (RNA samples only): CellRanger outputs: filter feature bc matrices h5

extract_protocol:
Tissue was dissociated with papaine and DNase (Worthington),. Cultured cells were dissociated with Accutase (Sigma). All dissociated cells spun at 300 g (4 C), then resuspended in culture medium to reach 1000 cells/uL.
10x Chromium Single Cell 3' V3.1 (scRNA-seq) and 10x Chromonium Next Gem Single Cell Multiome ATAC + Gene Expression (Multiome)

value: retina

value: MG culture

tag: cellranger version


title: Retinosphere Supplement Reprogramming ASCL1 scRNA

description:
repro_supplement_retinosphere_ascl1
10x Genomics


title: BFCN, 2N, Control, 17-21

city: Orangeburg

first: Stephen

middle: D.

last: Ginsberg

state: New York

address: 140 Old Orangeburg Road

department: Centre for Dementia Research

institute: Research Foundation for Mental Hygiene

data_processing:
The reads with adapter contamination/ low quality were trimmed using Trimmomatic 0.39.
Trimmed sequence reads were aligned to the reference  genome (GRCm39-mm10) using STAR Aligner. Gene counts were extracted using RSEM.
Downstream Analysis was performed using R with the gene counts obtained from the RSEM. Genes with over 0.1 counts per million were retained followed by TMM normalization.
Assembly: mm10
Supplementary files format and content: tab delimited text files with gene counts of all samples per column
Supplementary files format and content: tab delimited text files with gene counts of one sample per one file

source_name: basal forebrain cholinergic neurons from MS/VDB area

growth_protocol: Breeder pairs (female Ts65Dn and male C57Bl/6J Eicher × C3H/HeSnJ F1 mice) were purchased from Jackson Laboratories (Bar Harbor, ME, USA) and mated at the Nathan Kline Institute.

extract_protocol:
Brain tissues were immediately flash frozen and 20 μm-thick tissue sections were cryostat cut (−25°C) in the coronal plane and mounted on polyethylene naphthalate (PEN) membrane slides. Sections were stained with rapid antibody detection method for ChAT positive neurons.  ChAT-IR neurons were isolated by laser capture microdissection (LMD7000) and stored in Qiazol at -80*C until ~500 neurons per sample were collected.  RNase-free precautions were employed throughout, and solutions were made with 18.2 mega Ohm RNase-free water.   RNA from ~500 BFCNs was purified using miRNeasy Micro kit (Qiagen) following the manufacturer's specifications, with a the optional DNase digestion step done twice sequentially.
RNA libraries were prepared by using SMARTer Stranded Total RNA-Seq kit-Pico input Mammalian with minor modifications to utilize full volume of RNA.
RNA-seqSamples were quantified (Agilent 2100 HS DNA kit), and samples below 2 nM of library were excluded. Samples were pooled in equimolar concentrations and assayed on an Illumina HiSeq-4000 using a single read 50 cycle protocol at the NYUGSOM Genome Technology Center.

treatment_protocol: Breeder pairs were assigned to receive one of two choline-controlled experimental diets: (i) control rodent diet containing 1.1 g/kg choline chloride or (ii) choline-supplemented diet containing 5.0g/kg choline chloride. Pups received choline normal or choline supplemented diet as per their respective dam's diet from E0-P21 and starting at weaning all offspring had ad libitum access to water and the control diet

value: ChN


title: BFCN, Ts65Dn, Control, 17-173

value: basal forebrain cholinergic neurons from MS/VDB area


title: BFCN, 2N, Control, 17-172


title: BFCN, 2N, Control, 17-56


title: BFCN, Ts65Dn, Control, 17-157


title: Retinosphere Reprogramming Control GFP scRNA

description:
repro_retinosphere_gfp
10x Genomics


title: HCC cells, day 1 (+dox), rep 3

value: day 1, doxycycline (MYC off)


title: HCC cells, day 7 (+dox), rep 1


title: Retinosphere Supplement Reprogramming ASCL1 Notch Inhibitor scRNA

description:
repro_supplement_retinosphere_ascl1_notch
10x Genomics


title: BFCN, 2N, Control, 17-154


title: HCC cells, day 1 (+dox), rep 2


title: BFCN, Ts65Dn, Control, 17-192


title: Retinosphere Reprogramming ASCL1 scRNA

description:
repro_retinosphere_ascl1
10x Genomics


title: Retinal Reprogramming control GFP paired snRNA snATAC [snRNA-seq]

description:
repro_organoids_gfp_gex
10x Genomics

molecule: nuclear RNA


title: HCC cells, day 1 (+dox), rep 1


title: HCC cells, day 0 (no dox), rep 3

value: day 0


title: Retinal Reprogramming ASCL1 paired snRNA snATAC [snRNA-seq]

description:
repro_organoids_ascl1_gex
10x Genomics


title: ctrl_8h_3

value: untreated - 8h


title: HO53_8h_1


title: HO53_8h_3


title: ctrl_8h_2


title: HCC cells, day 0 (no dox), rep 2


title: Retinal Reprogramming ASCL1 paired snRNA snATAC [snATAC-seq]

description:
repro_organoids_ascl1_atac
10x Genomics


title: BFCN, Ts65Dn, Control, 17-153R


title: BFCN, Ts65Dn, Treatment, 17-03

value: ChP


title: BFCN, Ts65Dn, Control, 16-490


title: BFCN, 2N, Treatment, 16-90


title: Day 76 Human Fetal Retina Center paired snRNA snATAC [snRNA-seq]

description:
d76p_fetal_gex
10x Genomics


title: HCC cells, day 0 (no dox), rep 1


title: mCD19-CAR.SP.rep3

city: Cambridge

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
Illumina NovaSeq 6000 using v3 chemistry. Software: NovaSeq Control v1.7.0, RTA 3.4.4. BCL files were converted to fastq cellranger mkfastq (see characteristics for version)
Sequencing data was aligned to the mm10 reference genome and converted to fastq files using bcl2fastq (v2.20.0.422). Cell count matrices were generated using cellranger (v.5.0).
Genome_build: mm10 with GENCODE M23
Supplementary_files_format_and_content: *.tar.gz is a tar archive of filtered_feature_bc_matrix

source_name: Spleen

growth_protocol: Mice were transplanted with 3x10^6 B-ALL cells and challenged with 10^7 CAR-T cells targeting either mouse CD19 or a control epitope (human EGFRvIII). Upon becoming moribund, mice were sacrificed and B-ALL cells were sorted from the bone marrow and spleen. For each sample, approximately 10,000 live B-ALL cells were sorted for single cell transcriptional profiling.

extract_protocol:
Single-cell expression libraries were prepared using the 10x Genomics Chromium v3 reagents.
scRNA-Seq

value: B-ALL cells

value: Spleen

value: CAR-T cells targeting CD19


title: Retinal Reprogramming control GFP paired snRNA snATAC [snATAC-seq]

description:
repro_organoids_gfp_atac
10x Genomics


title: Day 76 Human Fetal Retina Center paired snRNA snATAC [snATAC-seq]

description:
d76p_fetal_atac
10x Genomics


title: mCD19-CAR.SP.rep2


title: Day 76 Human Fetal Retina Periphery paired snRNA snATAC [snATAC-seq]

description:
d76c_fetal_atac
10x Genomics


title: Day 76 Human Fetal Retina Periphery paired snRNA snATAC [snRNA-seq]

description:
d76c_fetal_gex
10x Genomics


title: ctrl_8h_1

value: air-liquid interphase day 26


title: mCD19-CAR.SP.rep1


title: HO53_4h_2


title: HO53_4h_1


title: BFCN, Ts65Dn, Treatment, 16-272


title: BFCN, Ts65Dn, Treatment, 15-36


title: HO53_4h_3


title: ctrl_4h_1

value: untreated - 4h


title: mCD19-CAR.BM.rep3

source_name: Bone marrow

value: Bone marrow


title: BFCN, Ts65Dn, Control, 16-357


title: BFCN, 2N, Treatment, 16-273


title: BFCN, 2N, Treatment, 15-334


title: Day 59 Human Fetal Retina Paired snRNA snATAC [snRNA-seq]

description:
d59_fetal_gex
10x Genomics


title: ctrl_4h_3


title: mCD19-CAR.BM.rep2


title: BFCN, Ts65Dn, Treatment, 15-245


title: Day 59 Human Fetal Retina Paired snRNA snATAC [snATAC-seq]

description:
d59_fetal_atac
10x Genomics


title: mCD19-CAR.BM.rep1


title: BFCN, Ts65Dn, Treatment, 15-199


title: ctrl_4h_2


title: BFCN, Ts65Dn, Treatment, 16-206


title: CTR-CAR.SP.rep3

value: CAR-T cells targeting EGFRvIII


title: CTR-CAR.SP.rep2


title: BFCN, 2N, Control, 15-145


title: BFCN, 2N, Control, 15-147


title: CTR-CAR.SP.rep1


title: CTR-CAR.BM.rep3


title: BFCN, Ts65Dn, Treatment, 15-140


title: BFCN , Ts65Dn, Treatment, 14-90


title: 839T_siB7H3_2

city: New York

first: Tiphaine

middle: Christiane

last: Martin

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

description: B7H3 specific siRNA treatment to human melanoma cell line 839T, Replicate 2

data_processing:
Reads were mapped to the human genome using STAR vSTAR_2.5.2a
Counts of reads mapping to each gene were quantified using featureCounts utility from the Subread package v1.4.6-p5
Expression as log(counts per million) was computed using edgeR v.3.30 package for R v.4.0.2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include raw counts and expression for each sample

source_name: Skin

growth_protocol: Human melanoma cell lines were cultured using standard methods.

extract_protocol:
Total RNA was extracted from samples using the RNeasy Protect Mini Kit (Qiagen). The RNA Integrity Number of each sample was determined using the 2100 Bioanalyzer instrument (Agilent Technologies). Samples were selected with stringent criteria based on RNA Integrity Number of 7.0 or greater, and a minimum of 500 ng of total RNA. Total RNA was subjected to ribosomal RNA depletion and further used as input for library construction by the Illumina TruSeq Standard Total RNA library Pre Gold kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were transfected with ON-TARGETplus Non-targeting Control Pool or ON-TARGETplus B7H3 siRNA (Dharmacon) for 72 hours.

value: Skin

value: siRNA B7H3


title: 839T_siB7H3_3

description: B7H3 specific siRNA treatment to human melanoma cell line 839T, Replicate 3


title: CTR-CAR.BM.rep2


title: CTR-CAR.BM.rep1


title: Peritoneal cell, no histamine, rep1

city: Seoul

first: Kwang

middle: H

last: Kim

address: 50 Yonsei-ro

country: South Korea

institute: Yonsei University College of Medicine

description: 10x Genomics

data_processing:
The scRNA-seq data were processed using Cellranger (release 3).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Peritoneal cavity

extract_protocol:
The total peritoneal cells from mice were isolated using 10-ml syringe with ice cold PBS.
Libraries were prepared using the chromium controller according to the 10× Single Cell 3′ v3 protocol (10x Genomics, Pleasanton, CA, USA).

value: Peritoneal cavity

value: Immune cells

value: Hdc-/-

tag: Sex

value: Male


title: 839T_siControl_1

description: siRNA Control treatment to human melanoma cell line 839T, Replicate 1

tag: treatment

value: siRNA Control


title: 688(A)T_siB7H3_3

description: B7H3 specific siRNA treatment to human melanoma cell line 688(A)T, Replicate 3


title: 839T_siControl_3

description: siRNA Control treatment to human melanoma cell line 839T, Replicate 3


title: 839T_siB7H3_1

description: B7H3 specific siRNA treatment to human melanoma cell line 839T, Replicate 1


title: 839T_siControl_2

description: siRNA Control treatment to human melanoma cell line 839T, Replicate 2


title: HTO_Multiplexed_sample2 (anti-B7-H3 and anti-B7-H3 + anti-CD47) 3 reps

description: CD45+ sorted cells from the tumor  with anti-B7-H3 antibody treatment or anti-B7-H3 + anti-CD47 treatment, replicates 1,2,3

data_processing:
BCL files were first base-called and demultiplexed using cellranger mkfastq v5.0.1
Alignment to mouse reference mm10 and feature counting were performed using cellranger count v5.0.1
we mapped HTO barcodes to samples of origin
read and analyzed data using Bioconductor libraries including DropletUtils (v1.12.3) and scater (v.1.20.1)
We filtered out the cells with high percent of mitochondrial and then performed library size normalization.
We merged all data using R BiocSingular library (v1.8.1), renormalized to adjust for differences in depth using R batchelor library (v1.8.1), reduced dimensionality using UMAP method, and proceeded to Louvain clusterin
Using R SingleR (v.1.6.1) and celldex (v1.2.0) libraries, we annotated the clusters and each cell individually using the Wilcoxon method with the fine pruned labels from the Immunological Genome Project  reference, which consists of microarray profiles of pure mouse immune cells
To identify differentially expressed genes between treatments, we used FindMarker of R Seurat library (v4.0.2)
Genome_build: mouse reference mm10
Supplementary_files_format_and_content: CellRanger files information about features, barcodes and read count matrices

source_name: Skin tumor

extract_protocol:
The sorted CD45+ cells were stained with diluted hashtag antibodies according to New York Genome Center hashing protocol. The RNA samples were prepared for sequencing using standard 10x Genomics protocol.
Gene expression libraries were made following the 10x Genomics demonstrated protocol. hashtag oligonucleotides (HTO) libraries were prepared according to the New York Genome Center hashing protocol.

treatment_protocol: We injected immunocompetent C57BL/6J mice with YUMM2.1 cells subcutaneously to generate allografts, followed by treatment with IgG control, anti-B7-H3, anti-CD47, or anti-B7-H3 + anti-CD47 once the tumors reached 20-50 mm3.

value: YUMM 2.1

value: anti-B7-H3 and anti-B7-H3 + anti-CD47

tag: molecule subtype

value: hashtag-labelled single cell RNA


title: 688(A)T_siB7H3_2

description: B7H3 specific siRNA treatment to human melanoma cell line 688(A)T, Replicate 2


title: 688(A)T_siB7H3_1

description: B7H3 specific siRNA treatment to human melanoma cell line 688(A)T, Replicate 1


title: AR2153, SP

data_processing:
Illumina NextSeq 500 using v3 chemistry. NextSeq Software: Control v4.0.0.19, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Paired-end RNA-seq data was used to quantify transcripts from the mm10 mouse assembly with the Ensembl version 101 annotation using Salmon version 1.3.0 Gene level summaries were prepared using tximport version 1.18.0 running under R version 4.0.3
Genome_build: mm10 with ensembl version 101 annotation
Supplementary_files_format_and_content: tab delimited text of integer count data
Supplementary_files_format_and_content: tab delimited text of l2tpm data

growth_protocol: Mice were transplanted with 3x10^6 B-ALL cells and challenged with 10^7 CAR-T cells targeting either mouse CD19 or a control epitope (human EGFRvIII). Upon becoming moribund, mice were sacrificed and B-ALL cells were sorted from the bone marrow and spleen.  Approximately 10^6 live B-ALL cells were sorted for bulk transcriptional profiling.

extract_protocol:
Macherey-Nagel Nucleospin RNA Plus kit
RNAseq libraries were created from 250ng of total RNA using the NEBNext UltraII Directional RNA Library Prep kit (New England Biolabs) using half volume reagents and 14 cycles 518  of PCR. Illumina library quality was confirmed using the Fragment Analyzer and qPCR

value: B-ALL cells


title: AR2153, BM

source_name: Bone Marrow

value: Bone Marrow


title: 688(A)T_siControl_3

description: siRNA Control treatment to human melanoma cell line 688(A)T, Replicate 3


title: Donor 190806B_D7_SUV39H1 KO

city: Paris

first: Sebastian

last: Amigorena

address: 26 rue d'Ulm

country: France

institute: Institut Curie

hyb_protocol: following manufacturer’s instructions

scan_protocol: following manufacturer’s instructions

data_processing: After passing internal quality control process, the calculated background was subtracted from raw gene expression data, then the data was normalized to the housekeeping genes with nSolver 4.0 software

label: not provided

source_name: CAR T cells

label_protocol: RNA was quantified using Nanodrop and quality controlled using an Agilent Bioanalyzer following manufacturer’s instructions. 300 ng of total RNA from all the samples were used as input for the NanoString nCounter® CAR-T Characterization

growth_protocol: CAR T cell production: To produce CAR T cells total CD8+ T cells (heterologous populations of naïve, memory, and effector cells) purified from peripheral blood mononuclear cells (PBMCs) were isolated from anonymous healthy donor leukapheresis ring (provided by EFS-Etablissement Francais du Sang) by density gradient centrifugation using Lymphoprep. T cells were plated at a concentration 106 cells /ml (5 x 10^5 cells in 24 well plate) using X-VIVO 15 media supplemented with 5% human serum (Sigma Aldrich) and 0.5 µM β–mercaptoethanol (referred to as complete X-VIVO), and stimulated with Dynabeads human T-Activator CD3/CD28 in a ratio of 1 bead per cell.   CAR transduction was achieved by lentiviral particles obtained from Flash Therapeutics and CARs were under the control of EF1a promoter. T cells were transduced approximately 24 hours after activation at a multiplicity of infection of 5. Viral vectors were added in 500 µl of complete X-VIVO with a final concentration of 4 µg/mL of Polybrene. After 16-18 hours the supernatant was almost completely discarded, and cell suspension was completed to a final volume of 2 mL with complete X-VIVO containing 100 IU/ml of rhIL-2. The following day, cells were subjected to CRISPR-Cas9 nucleofection (to invalidate SUV39H1): cells were harvested and activation beads were removed with magnets. crRNA targeting SUV39H1 and tracrRNA were first annealed at equimolar concentration to form the duplex at 95°C for 5 min. RNPs were then formed by combining precomplexed duplex (crRNA:tracrRNA) with Hifi Cas9 Nuclease V3 at a molar ratio of 3:1 and incubating them 10 min at room temperature. Nucleofection was done with P3 Primary Cell 4D-Nuleofector® X kit S adding between 1 to 2 x 10^6 cells with 10 µg of Cas9 in 5 µl of RNP and 20 µl of nucleofection solution. After electroporation using the EO-115 program (4D-Nucleofector Core Unit, Lonza), 200 µl of complete X-VIVO 15 with 500 IU/ml rhIL-2 was added to each reaction and cells were cultured at 32°C. After 16 h, cells were diluted in complete X-VIVO 15 with 500 IU/ml rhIL-2 at a concentration of 10^6 cells/ml. Cells were collected after 72 h (D0) and were also re-plated again in complete X-VIVO supplemented with 100 IU/ml of recombinant human rhIL-2 in a concentration 106 cells and re-activated with Dynabeads human T-Activator CD3/CD28 in a ratio of 1 bead per cell. Cells were diluted every 3-4 days to maintain the cell concentration and were re-plated and re-activated every 7 days.

extract_protocol: Total RNA was purified from CAR T cells at day 0 using RNeasy Mini Kit according to manufacturer’s instructions, and reverse transcription (RT) was done for cDNA synthesis from 200 ng of RNA using reverse transcriptase according to the manufacturer’s instructions.

tag: donor id

value: Donor 190806B

tag: timepoint

tag: genotype

value: SUV39H1 KO


title: Donor 190806B_D7_Mock

value: Mock


title: Donor 190806B_D0_SUV39H1 KO


title: Donor 190806B_D0_Mock


title: Donor 190723B_D21_SUV39H1 KO

value: Donor 190723B


title: Donor 190806B_D21_SUV39H1 KO


title: Donor 190723B_D21_Mock


title: Donor 190806B_D21_Mock


title: 688(A)T_siControl_2

description: siRNA Control treatment to human melanoma cell line 688(A)T, Replicate 2


title: AR2152, SP

tag: strain

value: Spleen

value: CAR-T cells targeting CD19


title: BFCN, 2N, Treatment, 14-125

value: basal forebrain cholinergic neurons from MS/VDB area

value: ChP


title: GEX_Multiplexed_sample1 (IgGControl and anti-CD47) 3 reps

description: CD45+ sorted cells from the tumor  with IgG control treatment or anti-CD47 treatment, replicates 1,2,3

value: Isotype control and anti-CD47


title: AR2152, BM


title: Donor 190723B_D7_Mock


title: NoV△B2: Ago2 IP 3 dpi

first: Yang

address: 2005 Songhu Road

institute: Fudan University

description: zebrafish infection with NoV△B2 by microinjection

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to virus genome using bowtie 1.1.2 with perfect match.
Genome_build: AF174533.1,AF174534.1;J02363.1;NC_001560.1
Supplementary_files_format_and_content: mapping results files generated by bowtie1.1.2

organism: Danio rerio

source_name: zebrafish whole body

extract_protocol:
Total RNA was extracted from zebrafish using TRIzol reagent.
Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.

tag: zebrafish background

value: AB

tag: infection

tag: injection way

value: microinjection

value: zebrafish whole body


title: HTO_Multiplexed_sample1 (IgG_Control and anti-CD47) 3 reps

value: YUMM 2.1


title: Donor 190723B_D0_Mock


title: Donor 190723B_D0_SUV39H1 KO


title: Donor 190514C_D21_SUV39H1 KO

value: Donor 190514C


title: Peritoneal cell, WT, rep1

description: 10x Genomics

value: Peritoneal cavity

value: Immune cells

value: Wild type

value: Male


title: Donor 190514C_D21_Mock


title: glomerular tissues model-1

city: Hefei

first: Xianjin

last: Xu

address: Changning Street

institute: Hefei Ion Medical Center, the First Affiliated Hospital of USTC

description: Gene expresison without any treatment

data_processing: Agilent Feature Extraction software was applied to asses the array images. Quantile normalization and subsequent data processing were performed with the GeneSpring GX v11.5.1 software package (Agilent Technologies).

source_name: glomerular tissues model-1

extract_protocol: RNA was prepared using Trizol Reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: SD

value: glomerular tissues

tag: gender


title: GEX_Multiplexed_sample2 (anti-B7-H3 and anti-B7-H3 + anti-CD47) 3 reps

value: anti-B7-H3 and anti-B7-H3 + anti-CD47

value: hashtag-labelled single cell RNA


title: 688(A)T_siControl_1

description: siRNA Control treatment to human melanoma cell line 688(A)T, Replicate 1

value: Skin

value: siRNA Control


title: AR2151, SP

value: B-ALL cells

value: Spleen

value: CAR-T cells targeting CD19


title: MYC-Low HCC cells

data_processing:
sgRNA raw counts were produced using the MAGeCK count command
Assembly: Mouse GeCKO v2 library
Supplementary files format and content: sgRNA raw counts
Library strategy: CRISPR screen

extract_protocol:
Genomic DNA was isolated and purified using QIAGEN Genomic-tips
HiSeq libraries were constructed by PCR amplification following published methods (Shalem et al., Science, 2014)

value: hepatocellular carcinoma

value: LAP-tTA/tetO-MYC

value: day 7, doxycycline (MYC-low)

tag: condition

value: CONTROL


title: Donor 190514C_D7_SUV39H1 KO

value: Donor 190514C

value: SUV39H1 KO


title: NoV: zebrafish 24 hpi

description: zebrafish infection with NoV by microinjection

value: whole body

value: NoV

value: microinjection

value: AB


title: Baseline (day 0) HCC cells

value: day 0

value: BASELINE


title: NoV△B2: zebrafish 24 hpi


title: Donor 190723B_D7_SUV39H1 KO

value: Donor 190723B


title: AR2151, BM

value: Bone Marrow


title: AR2150, BM

value: B-ALL cells

value: CAR-T cells targeting EGFRvIII


title: AR2150, SP

value: Spleen


title: AR2148, SP


title: AR2148, BM


title: VSV: zebrafish 24 hpi

description: zebrafish infection with VSV by microinjection

value: VSV


title: AR2147, SP


title: NSUN2 KO ovary ribo

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

data_processing:
For ribo-seq samples, adapters were trimmed with cutadapt (--max-n 1 -m 18 -e 0.25 --trim-n -q 20 --trimmed-only -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGTCGGACTGTAGAACTCTGAAC); for mRNA sample, adapters were trimmed with cutadapt (--max-n 1 -m 18 -e 0.25 --trim-n -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAG). Then reads were trimmed to 30 bp. Only read 1 was used in the subsequence analysis. Clean reads were mapped to reference genome with Tophat2. Aligned reads were sorted; and gene read counts were called via HTSeq-count. Translation efficiency was calculated with custom scripts.
Genome_build: dm3
Supplementary_files_format_and_content: TXT files generated by custom scripts

organism: Drosophila melanogaster

source_name: RPF

extract_protocol: The ovaries were collected and lysed with the lysis buffer. RNA was digested with micrococcal nuclease in the lysis buffer. Digestion was quenched and placing the reaction on ice. Lysates were loaded on the gradients. Gradients were centrifuged and then fractionated using the Gradient Master. The fraction that contained only the entire monosome peak was collected and then digested with Proteinase K supplied with 1 % SDS. The RNA was extracted. Ribosome-protected fragments (RPFs) between 28-30 nt were isolated and rRNA was depleted. The library was generated using VAHTS Small RNA Library Prep Kit for Illumina.

value: NSUN2 KO

value: ovary


title: WT ovary ribo

value: wild-type


title: Donor 190514C_D0_Mock

value: Donor 190514C

value: Mock


title: Donor 190514C_D0_SUV39H1 KO

value: SUV39H1 KO


title: Donor 190514C_D7_Mock


title: Hoxc4-au_ChIRP-seq_evenProbes_rep2

first: Mengxi

last: Jiang

address: 455 Main Street

institute: Whitehead Institute

data_processing:
High-throughput sequencing libraries were sequenced with Illumina HISEQ. The single 40bp reads with adapter sequences, suggested by FastQC ((http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), were removed with cutadapt (http://cutadapt.readthedocs.io/en/stable/guide.html) with -m 20 and --quality-base=64 parameters.  Then, reads were mapped to mouse genome mm9 with bowtie (PMID:19261174). Only uniquely mapped reads were used for estimating fragment size by strand cross correlation analysis (PMID: 24244136). Peaks of each biological replicate were called by MACS2 (PMID:18798982) against its corresponding input control with extension size 95 and p-value cutoff 1x10-5
Genome_build: mm9
Supplementary_files_format_and_content: tab delimitated file from MACS2

source_name: epidydimal derived preadipocytes

extract_protocol:
Crosslinked and sonicated cell lysates were incubated with both even and odd biotin-labeled probes against Hoxc4-au and followed by DNA isolation and sequencing.
Libraries were prepared for ChIRP-Seq using Swift Science’s Accel-NGS Library Preparation Kit for Illumina Platforms according to manufacturer’s directions. The swift kit makes library from 10pg-100ng of double-stranded input material. Briefly, the sample undergoes a series of incubations and purifications. The sample, through multiple incubations, repairs both 5’ and 3’ termini and sequentially attaches Illumina adapter sequences to the ends of fragmented dsDNA. The multiple bead-based clean-ups are used to remove oligonucleotides and small fragments, and to change enzymatic buffer composition between steps

Library strategy: ChIRP-Seq

value: epidydimal derived preadipocytes


title: WT ovary mRNA

source_name: RNA

extract_protocol: The ovaries were collected and poly(A)+ RNA was separated from total RNA. The library was constructed with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.


title: Input_ChIRP-seq_rep2


title: NSUN2 KO ovary mRNA


title: Hoxc4-au_ChIRP-seq_oddProbes-rep1


title: AR2147, BM


title: MYC-High HCC cells

value: hepatocellular carcinoma

value: LAP-tTA/tetO-MYC

value: day 7

value: SL


title: Hoxc4-au_ChIRP-seq_oddProbes-rep2


title: Hoxc4-au_ChIRP-seq_evenProbes_rep1


title: Input_ChIRP-seq_rep1


title: RCC4, IFNg + TNF treated, biol rep 3, Illumina

city: York

first: Joshua

last: Lee

address: University Road

department: Hull York Medical School

institute: University of York

data_processing:
Reads were first processed with FASTQC, with sequence adaptors trimmed using cutadapt (version 1.18). Processed reads were aligned to reference genome (hg38) using HISAT2 (2.1.0), with gene expression quantified by featurecounts (2.0.0).
Assembly: hg38
Supplementary files format and content: Tab-delimited count matrix files containing raw read counts mapped to the reference genome

growth_protocol: Cells were maintained at 37C in a humidified atmosphere of 5% CO2 and grown in complete Dulbecco’s Modified Eagle’s Medium (DMEM). Complete DMEM media was prepared by using DMEM, supplemented with 10% foetal bovine serum (FCS), 1% 200 mM L-Glutamine and 1% penicillin/streptomycin.

extract_protocol:
Cells were first washed with ice-cold PBS (Gibco), followed by lysis with Qiazol (Qiagen). Total RNA was extracted using RNeasy RNA extraction kit (Qiagen) with an additional Dnase I digestion (QIAGEN) according to manufacturer's instruction. Poly(A)+ RNA molecules were enriched from total RNA with the Dynabeads mRNA purification kit (Thermo Fisher).
Sequencing libraries were generated using Ultra III directional RNA library prep kit (NEB) according to manufacturer's instructions.

treatment_protocol: Cells were treated with pro-inflammatory cytokines IFN-γ (1000U/mL)  and TNF (25 ng/mL) for 24 hours before harvested for RNA extraction. 3 flasks of T75s were used for each biological replicate

value: Renal cell carcinoma epithelial cell

value: IFNg + TNF treated


title: RCC4, IFNg + TNF treated, biol rep 2, Illumina


title: RCC4, IFNg + TNF treated, biol rep 1, Illumina


title: Patient 52

status: Public on Oct 29 2023

city: Bialystok

first: Magdalena

last: Niemira

address: Kilinskiego 1

country: Poland

institute: Medical University of Bialystok

description: miRNA isolated from patients serum  was analyzed by the human v3 miRNA expression assay kit code set (Nanostring Tech.)

hyb_protocol: Standard nanostring nCounter miRNA Hybridization Protocol; The final hybridization reaction contained the following components: 10 μL Reporter CodeSet, 10 μL hybridization buffer, a 5 μL aliquot from the miRNA Sample Preparation Protocol, and 5 μL Capture ProbeSet.

scan_protocol: Raw count data were collected and captured by the nCounter Digital Analyzer for image capture (555 fields of view).

data_processing: The miRNA data analysis was performed using nSolver Analysis (version 4·0) software. Each miRNA count data was subtracted from the geometric mean of the negative controls. Profiling data were then normalized by the geometric mean of the positive controls and the geometric mean of the top 100 most highly-expressed microRNAs.

source_name: ovary

label_protocol: Standard nanostring miRNA protocols (nCounter Human v3 miRNA Expression Assays (NanoString Technologies,Seattle, USA))

extract_protocol: Total RNA was extracted from 400 mL of serum sample using miRNeasy Serum/Plasma Kit (Qiagen, Gaithersburg, MD, USA) according to the manufacturer’s protocol.

tag: age


title: Patient 60

tag: tissue


title: Patient 63


title: Patient 57


title: Patient 56


title: Patient 68


title: Patient 65


title: Patient 59


title: Patient 58


title: Patient 62


title: Patient 64


title: Patient 55


title: Patient 66


title: Patient 67


title: Patient 69


title: Patient 61


title: Patient 70


title: Donor 190514B_D0_Mock

value: Donor 190514B


title: Donor 190514B_D0_SUV39H1 KO


title: Donor 190514B_D7_SUV39H1 KO


title: Donor 190514B_D7_Mock