title: A2

description:
Library name: A2
Control (0 g/kg), Replicate 2


title: Akkermansia muciniphila KCTC 15667 (ATCC BAA-835), co-culture with PBS

status: Public on Jul 17 2025

type: SRA

city: Seoul

first: Daye

last: Mun

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

library_source: transcriptomic

data_processing:
Preprocessed trimmed reads were mapped to known reference genomes using the Bowtie software.
After read mapping, the HTSeq program was used to extract gene-specific read counts for each sample based on the gene annotation of the species.
edgeR was used to perform differentially expressed genes (DEGs) analysis to select DEGs between the two groups.
Assembly: ASM2022v1
Supplementary files format and content: text file includes FPKM values for all samples

molecule: total RNA

organism: Akkermansia muciniphila

source_name: A. muciniphila KCTC 15667

extract_protocol:
RNA was isolated using TRIzol reagent (Invitrogen, USA) and an RNeasy Mini kit (Qiagen, Germany).
Libraries were prepared using the NEBNext rRNA Depletion (Bacteria) and TruSeq Stranded Total RNA Library Prep Gold Kit.

tag: cell line

value: A. muciniphila KCTC 15667

tag: genotype


title: WT Neutrophils, lung, sorted from infected WT mice, 72h pi. Input

city: New York

first: YAHUI

last: GUO

state: NY

address: 407 East 68th street, ZRC1641

department: HOPP

country: USA

institute: Memorial Sloan-Kettering Cancer Center (MSKCC)

description: 400k cells were used

library_source: genomic

data_processing:
CUT&RUN datasets were processed by trimming paired reads for adaptors and low-quality sequences using Trimmomatic (v0.39) and aligning to the mm10 reference genome with Bowtie 2 (v2.4.1).
Peaks were identified using MACS2 (v2.2.7.1) with input samples as control, employing narrow peak parameters and cutoff - analysis - ple-5 - keep - dup all -B - SPMR. Irreproducible discovery rate (IDR) calculations were performed using ENCODE project scripts (IDR v2.0.4.2).
Reproducible peaks with an IDR value of 0.05 or less in each condition were retained, aggregated, and merged to create the final atlas, which was annotated with the UCSC Known Gene model.
Reads were mapped to this atlas and counted using the summarize Overlaps function from the Genomic Alignment package (v1.34.1).
Assembly: GRCm38.p6
Supplementary files format and content: Bigwig
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Mus musculus

source_name: lung

growth_protocol: To prepare single cell lung suspensions for flow cytometry. After perfusing murine lungs, they were placed in a gentle MACS™ C tube and mechanically homogenized in 5 ml RPMI-1640, 10% FBS, and 0.1 mg/ml DNAse using a gentle MACS™ Octo Dissociator (Miltenyi Biotech) without the use of collagenase. The lung cell suspensions were then lysed of RBCs, enumerated, and stained with fluorophore-conjugated antibodies prior to flow cytometric analysis. We used BD Aria for flow cytometric sorting, cell always stays on ice or sorted at 4℃. Neutrophils were identified as CD45+ CD11b+ Ly6Clo Ly6G+ cells

extract_protocol:
For CUT&RUN, 400,000 sorted neutrophils were used for H3K4me3 and STAT1 analysis. Anti-H3K4me3 (Epicypher, cat. no. 13-0028) or polyclonal anti-STAT1 antibodies (Proteintech, cat. no. 10144-2-AP) were employed for each target. Sorted cells were washed with PBS and resuspended in Antibody Buffer (1 ´ eBioscience Perm/Wash Buffer, 1´ Roche cOmplete EDTA-free Protease Inhibitor, 0.5 µM Spermidine, and 2 µM EDTA in H2O). They were incubated overnight at 4°C with control IgG, H3K4me3, or STAT1 antibodies diluted 1:100 in Antibody Buffer in a 96-well V-bottom plate. Following antibody incubation, cells were washed twice with Buffer 1 (1´ eBioscience Perm/Wash Buffer, 1´ Roche cOmplete EDTA-free Protease Inhibitor, 0.5 µM Spermidine in H2O) and resuspended in 50 µL of Buffer 1 plus 1´ pA/G-MNase (Cell Signaling, cat. no. 57813). This mixture was incubated on ice for 1 hour, then washed twice with Buffer 2 (0.05% w/v Saponin, 1´ Roche cOmplete EDTA-free Protease Inhibitor, 0.5 µM Spermidine in 1X PBS) three times. Cells were resuspended in Calcium Buffer (Buffer 2 plus 2 µM CaCl2) and incubated on ice for 30 minutes to activate the pA/G-MNase reaction. An equal volume of 2´ STOP Buffer (Buffer 2 plus 20 µM EDTA plus 4 µM EGTA) and 1 pg of Saccharomyces cerevisiae spike-in DNA (Cell Signaling, cat. no. 29987) were added. Samples were incubated at 37 °C for 15 minutes, followed by DNA isolation and purification using the Qiagen MinElute Kit per the manufacturer’s instructions.
Immunoprecipitated DNA was quantified by PicoGreen, and the size was evaluated using an Agilent BioAnalyzer: fragments between 100 and 600 bp were size selected using aMPure XP beads (Beckman Coulter, cat. no. A63882).  KAPA HTP Library Preparation Kit (Kapa Biosystems, cat. no. KK8234) was used to prepare Illumina sequencing libraries according to the manufacturer’s instructions with 0.001–0.5 ng input DNA and 14 cycles of PCR. Barcoded libraries were run on the NovaSeq 6000 in a PE100 run using S4 kit version 1.5 with XP mode to generate approximately 23 million paired reads per sample.

treatment_protocol: cells sorted from naïve mice have no treatment; cells sorted from infected mice, mice were infected with ECA10 A. fumigatus for 72h

tag: tissue

value: lung

tag: cell type

value: neutrophils

value: wildtype

tag: treatment

value: 72h pi with 3*10^7 CEA10


title: Akkermansia muciniphila KCTC 15667 (ATCC BAA-835), co-culture with BCEVs


title: Ovary, aged_1

city: Shenzhen

first: Liming

last: Gui

address: 1120 Lianhua Street

department: Obstetrics and Gynaecology

country: China

institute: Peking University Shenzhen Hospital

data_processing:
Clean reads were then mapped to the reference genome using the HISAT2 (v2.0.5) software
The featureCounts (v1.5.0-p3) tool was utilized to count the number of reads mapped to each gene.
The Fragments Per Kilobase of transcript sequence per Million mapped reads (FPKM) value for each gene was calculated based on its length and the number of mapped reads
Differential expression analysis was conducted between two groups, with two biological replicates per group, using the DESeq2 R package (1.20.0).
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: ovary

extract_protocol:
Total RNA was then extracted from the ovarian tissue using TRIzol reagentaccording to the manufacturer's instructions (Invitrogen)
These libraries were sequenced on the Illumina NovaSeq 6000 platform (Novogene) to generate high-quality sequencing data

treatment_protocol: young (7~8 weeks), adult (27~28 weeks), aged mice (73~74 weeks) treated with vehicle, and aged mice (73~74 weeks) treated with HEP14 (aged+HEP14 mice).

value: ovary

value: WT

value: 73~74 weeks


title: FFPE_DNA_1558

type: genomic

city: Munich

first: Guokun

last: Zhang

address: Marchioninistr. 15

country: Germany

institute: IBE LMU

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner setting

data_processing:
Sesame R package, normalization method = "db", background subtraction = "noobsb"
The Matrix_processed.txt contains Average Beta
The Matrix_signal_intensities.txt contains unmethylated and methylated signal intensities.
Average Beta

label: Cy5 and Cy3

organism: Homo sapiens

source_name: breast cancer

label_protocol: Standard Illumina Protocol

extract_protocol: standard genomic DNA extraction from FFPE tissue

tag: age (years)

tag: gender

value: Female

tag: cohort

value: validation

value: 3 weeks endocrine therapy treated

tag: response

value: non-responder


title: Ovary, adult_HEP14_3

value: 27~28 weeks


title: FFPE_DNA_798


title: FFPE_DNA_788


title: Ovary, adult_HEP14_1


title: A7

city: Haidian

first: Awais

last: Ali

state: Beijing

address: Room No. 106, International Student Dormitory, Chinese Academy of Agricultural Sciences

institute: Majorbio

description:
Library name: A7
Control (0 g/kg), Replicate 7

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances.
Assembly: Gallus_gallus  genome  GCF_016699485.2
Supplementary files format and content: tab-delimited text files include TPM values for each Sample ...

organism: Gallus gallus

source_name: Liver

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions. The RNA-seq transcriptome librariy was prepared following Illumina Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq X Plus platform(PE150) using NovaSeq Reagent Kit.

value: Liver


title: FFPE_DNA_820

value: responder


title: Ovary, adult_3


title: Ovary, adult_2


title: FFPE_DNA_503


title: FFPE_DNA_530


title: FFPE_DNA_795


title: FFPE_DNA_720


title: Ovary, adult_1


title: Ovary, young_4

value: 7~8 weeks


title: Ovary, aged_2


title: FFPE_DNA_1556


title: Ovary, young_1


title: Ovary, young_2


title: FFPE_DNA_658


title: Ovary, young_3


title: Heart, KO-TAC, 12 weeks, rep3

city: Tokyo

first: Jin

last: Komuro

address: 35 Shinanomachi Shinjuku-ku

department: Cardiology

country: Japan

institute: Keio University School of Medcine

data_processing:
Reads with phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore version 0.6.10. Quality-filtered reads were then aligned to the mouse reference genome GRCm38 (mm10) using the HiSAT2 (v 2.2.1) aligner using default settings and sorted the data using samtools version 1.15 (Pertea et al., 2016). Aligned reads were quantified using StringTie version 2.2.1 (Pertea et al., 2016) per gene ID against Gencode version 25 (Mudge and Harrow, 2015). Differential gene expression analysis was done using the R package DEseq2 (v 1.42.0). Read counts were normalized by taking the median of each gene count across samples and dividing each sample gene count by the relative ratio of library sizes between the calculated median and sample size. The averaged normalized expressions values of the samples were used to calculate fold change and p-values.
Assembly: GRCm38 (mm10)
Supplementary files format and content: csv file includes raw counts for each Sample

source_name: Heart

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™II Directional RNA Library Prep Kit following manufacturer's protocols.

value: Heart

value: c-Myc Knockout

value: TAC


title: FFPE_DNA_652


title: Ovary, adult_HEP14_4


title: FFPE_DNA_760


title: FFPE_DNA_624


title: FFPE_DNA_603


title: Heart, KO-TAC, 12 weeks, rep2


title: FFPE_DNA_593


title: Heart, KO-TAC, 12 weeks, rep1


title: Ovary, adult_HEP14_2


title: Heart, TAC, 12 weeks, rep3


title: Ovary, adult_4


title: Heart, TAC, 12 weeks, rep2


title: Heart, TAC, 12 weeks, rep1


title: P3-2 (Patient 3, Region 2)

city: Stockholm

first: Nidhi

last: Sharma

state: Stockholm

address: Tomtebodavägen 23, Solna

department: Oncology-Pathology

country: Sweden

institute: Science for life laboratory, Karolinska Institute

data_processing:
The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.  Softwares used: bedtools (2.29.2), bioconductor-summarizedexperiment (1.20.0), bioconductor-tximeta (1.8.0), deseq2 (1.28.0), dupradar (1.18.0), fastqc (0.11.9), nextflow (20.11.0-edge), nf-core/rnaseq (3.0), picard (2.23.9), preseq (2.0.3), qualimap (2.2.2-dev), rseqc (3.0.1), salmon (1.4.0), samtools (1.10), star (2.6.1d), stringtie (2.1.4), subread (2.0.1), trimgalore (0.6.6), ucsc (377)
Assembly: Homo sapiens, GRCh38)
Supplementary files format and content: tab-delimited file contains raw gene counts for each sample.

source_name: Brain

extract_protocol:
The sections collected in tubes were first washed in PBS to remove the blood, centrifuged, and the tissue pellets were used for subsequent DNA, RNA, and protein extraction with the AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Hilden, Germany) as per the manufacturer’s protocol. The quality control and concentration of the RNA samples were measured using the Agilent 2100 Bioanalyzer system.
Illumina RiboZero GOLD was used for ribosomal depletion from samples and Illumina TruSeq Stranded total RNA was used for RNA library construction. Multiplex sequencing in 0.25 lane on NovaSeq6000 (NovaSeq Control Software 1.7.5/RTA v3.4.4) with more than 50M reads/sample and a sequencing depth of 2 x 150 pairs, using 'NovaSeqXp' workflow in 'S4' mode flowcell. Out of 16 samples, 4 samples (P1-R2, P4-R2, P2-R3, P2-R4) failed the reception control library quality control step and were not sequenced.
RNA-seq, Illumina TruSeq Stranded total RNA, Illumina RiboZero GOLD, -, 1301

value: Brain

tag: patient

tag: region

tag: disease state

value: MBM


title: FFPE_DNA_579


title: FFPE_DNA_585


title: FFPE_DNA_519


title: Heart, control, rep2

value: control


title: Heart, control, rep1


title: FFPE_DNA_476


title: Tg-JW-65_3 [TJW97]

city: MEMPHIS

first: Zhengjun

last: Wang

state: TN

address: 71 S Manassas Street

institute: University of Tennessee Health Science Center

data_processing:
Transcript abundance from RNA-seq reads were quantified using Salmon
gene-level counts were obtained using tximport against the C57BL/6 J mouse genome annotation Genome Reference Consortium Mouse Build 39 (GRCm39),
RAW counts were processed with DESeq2.
Assembly: GRCm39
Supplementary files format and content: normalized counts

source_name: hippocampus

extract_protocol:
Total RNA was extracted from micro punched samples using the RNeasy Mini kit. 800ng of total RNA was used for the construction of sequencing libraries.
After the QC procedures, mRNA from eukaryotic organisms is enriched from total RNA using oligo(dT) beads. For prokaryotic samples, rRNA is removed using a specialized kit that leaves the mRNA. The mRNA from either eukaryotic or prokaryotic sources then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added, with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation and AMPure XP beads is used to purify the cDNA. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/ul before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM).

value: hippocampus

value: 5xFAD Tg


title: Heart, control, rep3

value: WT


title: FFPE_DNA_452

value: Female


title: FFPE_DNA_504

value: validation


title: FFPE_DNA_451

value: 3 weeks endocrine therapy treated


title: Tg_2 [T79]

value: vehicle


title: FFPE_DNA_1555


title: FFPE_DNA_446

value: non-responder


title: Tg_1 [T1]


title: FFPE_DNA_1553


title: FFPE_DNA_400


title: FFPE_DNA_1552


title: nTg_2 [N77]

value: nTg


title: nTg_3 [N82]


title: FFPE_DNA_474


title: FFPE_DNA_1554


title: nTg_1 [N14]


title: Tg_3 [T817]


title: Tg-JW-65_2 [TJW95]


title: FFPE_DNA_1551


title: FFPE_DNA_1550

value: responder


title: Control vehicle replicate B

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, and gene counting was performed using CellRanger v2.1.0
Assembly: mm10
Supplementary files format and content: filtered gene barcode matrices from CellRanger output: genes.tsv, barcodes.tsv and matrix.mtx
Supplementary files format and content: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/2.1/output/overview

molecule: polyA RNA

source_name: Pancreatic islet

extract_protocol:
Islets were isolated using standard protocols with the inclusion of 10% FBS in place of BSA into HBSS solutions post-digestion. Islets were pooled from 2-3 mice per group, dissociated with 0.05% trypsin, and stained using propidium iodide for subsequent FACS sorting for live (PI-negative) cells. 3500 cells per sample were loaded in duplicate for each group and processed according to the manufacturer's instructions using 10x Single Cell 3' v2.
According to the manufacturer's instructions using 10x Genomics Single Cell 3' v2.
According to the manufacturer's instructions 10x Genomics Single Cell Library Contruction Kit

treatment_protocol: 12- to 15-week-old Sirt2flox/flox; Pdx1-CreER mice or controls (combination of Sirt2flox/+; Pdx1-CreER Sirt2+/+; Pdx1-CreER mice) were treated every other day with 6 mg tamoxifen for 4 total doses. Mice were then treated with either PBS or the insulin receptor antagonist S961 (Celtek Peptides) at 20 nmol/week by osmotic minipumps (Alzet 1007D) for 1 week.

value: Pancreatic islet

value: Sirt2+/+; Pdx1-CreER or Sirt2flox/+; Pdx1-CreER

value: PBS


title: Control vehicle replicate A

description: 10x Genomics


title: Sirt2 KO vehicle replicate B

description: 10x Genomics

value: Sirt2flox/flox; Pdx1-CreER


title: Sirt2 KO vehicle replicate A

description: 10x Genomics


title: FFPE_DNA_1547


title: FFPE_DNA_1549


title: Tg-JW-65_1 [TJW91]


title: FFPE_DNA_1545


title: Sirt2 KO S961 replicate B

description: 10x Genomics


title: FFPE_DNA_1546


title: Control S961 replicate B

description: 10x Genomics


title: FFPE_DNA_1540


title: Control S961 replicate A

description: 10x Genomics


title: FFPE_DNA_1542


title: FFPE_DNA_1543


title: FFPE_DNA_1541


title: FFPE_DNA_1537


title: FFPE_DNA_1536


title: FFPE_DNA_1533


title: FFPE_DNA_1534


title: NanoString_RNA_1112

type: RNA

data_processing: Raw data was normalized using NanoString BC360 standard normalization protocol. The normalized data is log2 transformed, with constants added for consistency across different assays.

extract_protocol: Used standard RNA purification kit to isolate RNA from FFPE tissue

value: breast cancer

tag: age


title: FFPE_DNA_1531


title: Sirt2 KO S961 replicate A

description: 10x Genomics


title: FFPE_DNA_1529


title: NanoString_RNA_830


title: NanoString_RNA_819


title: NanoString_RNA_831


title: NanoString_RNA_824


title: FFPE_DNA_1528


title: NanoString_RNA_818


title: FFPE_DNA_1527


title: FFPE_DNA_1526


title: FFPE_DNA_1525


title: NanoString_RNA_815


title: NanoString_RNA_809


title: FFPE_DNA_1522


title: FFPE_DNA_1524


title: NanoString_RNA_827


title: NanoString_RNA_806


title: FFPE_DNA_1521


title: FFPE_DNA_1532


title: NanoString_RNA_802


title: NanoString_RNA_805


title: NanoString_RNA_801


title: NanoString_RNA_800


title: FFPE_DNA_1520


title: NanoString_RNA_799


title: NanoString_RNA_817


title: FFPE_DNA_1519


title: NanoString_RNA_790


title: FFPE_DNA_1518


title: FFPE_DNA_1516


title: FFPE_DNA_1517


title: NanoString_RNA_786


title: FFPE_DNA_1515


title: NanoString_RNA_811


title: NanoString_RNA_781


title: FFPE_DNA_1514


title: NanoString_RNA_779


title: FFPE_DNA_1513


title: NanoString_RNA_778


title: FFPE_DNA_1512


title: NanoString_RNA_773


title: FFPE_DNA_1510


title: D3

description:
Library name: D3
10X Arg (18g/kg), Replicate 3

value: Liver


title: NanoString_RNA_770


title: NanoString_RNA_768


title: FFPE_DNA_1509


title: FFPE_DNA_1505


title: FFPE_DNA_1507


title: FFPE_DNA_1502


title: NanoString_RNA_763


title: NanoString_RNA_758


title: FFPE_DNA_1501


title: FFPE_DNA_1500


title: NanoString_RNA_783


title: NanoString_RNA_764


title: NanoString_RNA_756


title: NanoString_RNA_762


title: NanoString_RNA_752


title: FFPE_DNA_1495


title: FFPE_DNA_1498


title: NanoString_RNA_754


title: NanoString_RNA_747


title: NanoString_RNA_745


title: NanoString_RNA_744


title: FFPE_DNA_1494


title: FFPE_DNA_1492


title: FFPE_DNA_1490


title: NanoString_RNA_743


title: FFPE_DNA_1489


title: NanoString_RNA_740


title: NanoString_RNA_739


title: NanoString_RNA_741


title: FFPE_DNA_1488


title: NanoString_RNA_736


title: FFPE_DNA_1487


title: FFPE_DNA_1499


title: FFPE_DNA_1486


title: FFPE_DNA_1485


title: NanoString_RNA_735


title: FFPE_DNA_1483


title: FFPE_DNA_1482


title: NanoString_RNA_734


title: NanoString_RNA_731


title: FFPE_DNA_1484


title: FFPE_DNA_1493


title: FFPE_DNA_1481


title: NanoString_RNA_729


title: NanoString_RNA_726


title: NanoString_RNA_728


title: FFPE_DNA_1480


title: FFPE_DNA_1479


title: FFPE_DNA_1478


title: FFPE_DNA_1477


title: FFPE_DNA_1476


title: NanoString_RNA_711


title: NanoString_RNA_710


title: NanoString_RNA_708


title: NanoString_RNA_714


title: FFPE_DNA_1472


title: NanoString_RNA_707


title: NanoString_RNA_697


title: FFPE_DNA_1471


title: FFPE_DNA_1470


title: FFPE_DNA_1469


title: NanoString_RNA_715


title: FFPE_DNA_1468


title: FFPE_DNA_1467


title: FFPE_DNA_1466


title: NanoString_RNA_693


title: NanoString_RNA_692


title: NanoString_RNA_689


title: NanoString_RNA_688


title: FFPE_DNA_1465


title: NanoString_RNA_687


title: FFPE_DNA_1464


title: NanoString_RNA_681


title: FFPE_DNA_1474


title: FFPE_DNA_1461


title: FFPE_DNA_1460


title: NanoString_RNA_703


title: NanoString_RNA_678


title: NanoString_RNA_676


title: NanoString_RNA_674


title: NanoString_RNA_696


title: FFPE_DNA_1458


title: FFPE_DNA_1455


title: NanoString_RNA_673


title: NanoString_RNA_671


title: FFPE_DNA_1453


title: NanoString_RNA_672


title: FFPE_DNA_1451


title: NanoString_RNA_670


title: FFPE_DNA_1450


title: NanoString_RNA_669


title: FFPE_DNA_1448


title: FFPE_DNA_1447


title: FFPE_DNA_1445


title: FFPE_DNA_1443


title: NanoString_RNA_661


title: NanoString_RNA_662


title: NanoString_RNA_665


title: FFPE_DNA_1459


title: NanoString_RNA_660


title: FFPE_DNA_1442


title: NanoString_RNA_655


title: NanoString_RNA_654


title: FFPE_DNA_1441


title: FFPE_DNA_1440


title: NanoString_RNA_649


title: FFPE_DNA_1439


title: FFPE_DNA_1437


title: NanoString_RNA_643


title: NanoString_RNA_647


title: FFPE_DNA_1435


title: FFPE_DNA_1436


title: FFPE_DNA_1434


title: FFPE_DNA_1548


title: NanoString_RNA_641


title: NanoString_RNA_634


title: NanoString_RNA_640


title: NanoString_RNA_637


title: FFPE_DNA_1430


title: NanoString_RNA_632


title: FFPE_DNA_1426


title: FFPE_DNA_1424


title: FFPE_DNA_1429


title: FFPE_DNA_1422


title: FFPE_DNA_1431


title: NanoString_RNA_627


title: NanoString_RNA_619


title: NanoString_RNA_623


title: FFPE_DNA_1420


title: FFPE_DNA_1418


title: FFPE_DNA_1419


title: NanoString_RNA_642


title: NanoString_RNA_618


title: NanoString_RNA_612


title: FFPE_DNA_1415


title: FFPE_DNA_1414


title: FFPE_DNA_1416


title: NanoString_RNA_611


title: NanoString_RNA_613


title: FFPE_DNA_1413


title: FFPE_DNA_1411


title: NanoString_RNA_719


title: NanoString_RNA_610


title: NanoString_RNA_609


title: NanoString_RNA_600


title: NanoString_RNA_598


title: FFPE_DNA_1410


title: FFPE_DNA_1409


title: FFPE_DNA_1407


title: NanoString_RNA_596


title: NanoString_RNA_595


title: FFPE_DNA_1406


title: NanoString_RNA_615


title: FFPE_DNA_1402


title: NanoString_RNA_589


title: FFPE_DNA_1403


title: FFPE_DNA_1401


title: NanoString_RNA_586


title: FFPE_DNA_1400


title: NanoString_RNA_583


title: FFPE_DNA_1396


title: FFPE_DNA_1395


title: FFPE_DNA_1399


title: FFPE_DNA_1398


title: NanoString_RNA_581


title: NanoString_RNA_597


title: FFPE_DNA_1392


title: NanoString_RNA_577


title: NanoString_RNA_580


title: FFPE_DNA_1393


title: NanoString_RNA_575


title: NanoString_RNA_574


title: NanoString_RNA_576


title: FFPE_DNA_1405


title: FFPE_DNA_1391


title: NanoString_RNA_594


title: FFPE_DNA_1389


title: NanoString_RNA_587


title: NanoString_RNA_572


title: FFPE_DNA_1388


title: FFPE_DNA_1387


title: FFPE_DNA_1386


title: NanoString_RNA_569


title: NanoString_RNA_570


title: NanoString_RNA_564


title: FFPE_DNA_1385


title: FFPE_DNA_1382


title: NanoString_RNA_562


title: NanoString_RNA_563


title: FFPE_DNA_1380


title: FFPE_DNA_1511


title: NanoString_RNA_559


title: NanoString_RNA_558


title: NanoString_RNA_571


title: NanoString_RNA_561


title: FFPE_DNA_1376


title: FFPE_DNA_1374


title: NanoString_RNA_557


title: FFPE_DNA_1375


title: FFPE_DNA_1373


title: NanoString_RNA_554


title: NanoString_RNA_556


title: FFPE_DNA_1372


title: NanoString_RNA_552


title: NanoString_RNA_550


title: NanoString_RNA_549


title: FFPE_DNA_1371


title: FFPE_DNA_1384


title: FFPE_DNA_1370


title: FFPE_DNA_1369


title: FFPE_DNA_1368


title: FFPE_DNA_1379


title: NanoString_RNA_545


title: FFPE_DNA_1366


title: NanoString_RNA_546


title: FFPE_DNA_1365


title: FFPE_DNA_1378


title: FFPE_DNA_1364


title: NanoString_RNA_541


title: NanoString_RNA_553


title: NanoString_RNA_538


title: NanoString_RNA_536


title: NanoString_RNA_537


title: FFPE_DNA_1360


title: NanoString_RNA_527


title: NanoString_RNA_529


title: FFPE_DNA_1359


title: FFPE_DNA_1358


title: FFPE_DNA_1357


title: NanoString_RNA_548


title: FFPE_DNA_1356


title: NanoString_RNA_521


title: FFPE_DNA_1355


title: NanoString_RNA_517


title: NanoString_RNA_516


title: FFPE_DNA_1354


title: FFPE_DNA_1353


title: FFPE_DNA_1363


title: NanoString_RNA_514


title: FFPE_DNA_1352


title: FFPE_DNA_1351


title: FFPE_DNA_1361


title: FFPE_DNA_1348


title: FFPE_DNA_1350


title: FFPE_DNA_1345


title: FFPE_DNA_1342


title: FFPE_DNA_1341


title: NanoString_RNA_505


title: NanoString_RNA_506


title: NanoString_RNA_515


title: NanoString_RNA_502


title: NanoString_RNA_507


title: NanoString_RNA_497


title: NanoString_RNA_498


title: NanoString_RNA_501


title: FFPE_DNA_1344


title: FFPE_DNA_1340


title: NanoString_RNA_486


title: FFPE_DNA_1339


title: FFPE_DNA_1338


title: FFPE_DNA_1337


title: FFPE_DNA_1335


title: FFPE_DNA_1334


title: NanoString_RNA_471


title: NanoString_RNA_468


title: FFPE_DNA_1333


title: NanoString_RNA_487


title: NanoString_RNA_493


title: NanoString_RNA_466


title: NanoString_RNA_463


title: FFPE_DNA_1328


title: FFPE_DNA_1330


title: FFPE_DNA_1327


title: FFPE_DNA_1326


title: NanoString_RNA_460


title: NanoString_RNA_478


title: FFPE_DNA_1325


title: NanoString_RNA_499


title: FFPE_DNA_1324


title: NanoString_RNA_477


title: NanoString_RNA_455


title: NanoString_RNA_458


title: NanoString_RNA_450


title: NanoString_RNA_448


title: NanoString_RNA_447


title: NanoString_RNA_453


title: FFPE_DNA_1323


title: FFPE_DNA_1322


title: NanoString_RNA_444


title: NanoString_RNA_443


title: FFPE_DNA_1321


title: FFPE_DNA_1320


title: FFPE_DNA_1332


title: NanoString_RNA_442


title: FFPE_DNA_1319


title: NanoString_RNA_440


title: FFPE_DNA_1317


title: FFPE_DNA_1315


title: NanoString_RNA_439


title: FFPE_DNA_1314


title: FFPE_DNA_1313


title: FFPE_DNA_1310


title: FFPE_DNA_1311


title: NanoString_RNA_438


title: NanoString_RNA_437


title: FFPE_DNA_1307


title: FFPE_DNA_1309


title: NanoString_RNA_435


title: FFPE_DNA_1308


title: NanoString_RNA_431


title: NanoString_RNA_430


title: NanoString_RNA_425


title: NanoString_RNA_422


title: FFPE_DNA_1306


title: NanoString_RNA_540


title: NanoString_RNA_421


title: NanoString_RNA_441


title: FFPE_DNA_768

value: discovery


title: FFPE_DNA_767


title: FFPE_DNA_1318


title: NanoString_RNA_420


title: NanoString_RNA_436


title: NanoString_RNA_418


title: FFPE_DNA_423


title: NanoString_RNA_414


title: FFPE_DNA_422


title: FFPE_DNA_357


title: FFPE_DNA_356


title: FFPE_DNA_806


title: NanoString_RNA_423


title: FFPE_DNA_367


title: FFPE_DNA_681


title: NanoString_RNA_407


title: NanoString_RNA_408


title: NanoString_RNA_413


title: FFPE_DNA_680


title: NanoString_RNA_405


title: NanoString_RNA_398


title: NanoString_RNA_397


title: FFPE_DNA_639


title: NanoString_RNA_396


title: FFPE_DNA_748


title: FFPE_DNA_747


title: FFPE_DNA_389


title: NanoString_RNA_393


title: NanoString_RNA_394


title: FFPE_DNA_388


title: NanoString_RNA_391


title: NanoString_RNA_385


title: FFPE_DNA_831


title: NanoString_RNA_382


title: FFPE_DNA_678


title: NanoString_RNA_381


title: FFPE_DNA_679


title: NanoString_RNA_403


title: FFPE_DNA_734


title: NanoString_RNA_380


title: FFPE_DNA_735


title: NanoString_RNA_384


title: NanoString_RNA_399


title: FFPE_DNA_817


title: NanoString_RNA_371


title: FFPE_DNA_590


title: FFPE_DNA_560


title: FFPE_DNA_479


title: FFPE_DNA_561


title: NanoString_RNA_368


title: NanoString_RNA_370


title: NanoString_RNA_367


title: FFPE_DNA_793


title: FFPE_DNA_480


title: NanoString_RNA_365


title: FFPE_DNA_574


title: FFPE_DNA_575


title: NanoString_RNA_363


title: NanoString_RNA_362


title: FFPE_DNA_456


title: NanoString_RNA_361


title: FFPE_DNA_455


title: FFPE_DNA_615


title: NanoString_RNA_360


title: FFPE_DNA_614


title: NanoString_RNA_377


title: NanoString_RNA_355


title: NanoString_RNA_354


title: FFPE_DNA_528


title: FFPE_DNA_529


title: NanoString_RNA_352


title: FFPE_DNA_394


title: FFPE_DNA_395


title: intestine sample from shrimp reared in low dissolved oxygen, biological rep8

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

data_processing:
Data was processed within OmicsBox v3.3.2
Quality control was performed on raw reads using Trimmomatic v0.39
Quality reads were aligned to the Pacific white shrimp Kehai No.1 genome using the STAR aligner v2.7.8a (parameters – 2-pass mapping=true; overhang=149; feature=exon)
Read counts were extracted from BAM files using HTseq v2.0.5 ‘count’ feature (parameters – Quantification Level=exon; Group by=parent; Overlap Mode=union; stranded=strand specific reverse)
Assembly: Kehai No.1 (GCF_003789085.1)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Penaeus vannamei

source_name: intestine

extract_protocol:
Total RNA was extracted from tissues using the Rneasy Plus Mini Kit (Qiagen) per the manufacturer’s protocol. 250 ng of total RNA from each sample was used for library construction.
RNA libraries for RNA-seq were prepared using the Illumina Stranded mRNA Ligation Kit per the manufacturer’s protocol.

value: intestine

tag: aeration level_(cubic_feet_per_second)

tag: aeration treatment_group

value: low


title: intestine sample from shrimp reared in medium dissolved oxygen, biological rep8

value: medium


title: intestine sample from shrimp reared in low dissolved oxygen, biological rep7


title: intestine sample from shrimp reared in medium dissolved oxygen, biological rep6


title: FFPE_DNA_676

value: Female


title: FFPE_DNA_819


title: NanoString_RNA_351


title: intestine sample from shrimp reared in medium dissolved oxygen, biological rep7


title: intestine sample from shrimp reared in medium dissolved oxygen, biological rep5


title: FFPE_DNA_675


title: FFPE_DNA_677


title: FFPE_DNA_674


title: intestine sample from shrimp reared in high dissolved oxygen, biological rep7

value: high


title: intestine sample from shrimp reared in high dissolved oxygen, biological rep8


title: intestine sample from shrimp reared in low dissolved oxygen, biological rep6


title: intestine sample from shrimp reared in low dissolved oxygen, biological rep5


title: FFPE_DNA_707

value: 3 weeks endocrine therapy treated


title: FFPE_DNA_704


title: intestine sample from shrimp reared in high dissolved oxygen, biological rep6


title: FFPE_DNA_359


title: intestine sample from shrimp reared in high dissolved oxygen, biological rep5


title: intestine sample from shrimp reared in medium dissolved oxygen, biological rep4


title: NanoString_RNA_353


title: FFPE_DNA_600


title: FFPE_DNA_623


title: FFPE_DNA_358


title: intestine sample from shrimp reared in medium dissolved oxygen, biological rep3


title: intestine sample from shrimp reared in low dissolved oxygen, biological rep4


title: FFPE_DNA_502


title: FFPE_DNA_622


title: intestine sample from shrimp reared in high dissolved oxygen, biological rep3


title: intestine sample from shrimp reared in low dissolved oxygen, biological rep3


title: FFPE_DNA_636


title: FFPE_DNA_637


title: intestine sample from shrimp reared in low dissolved oxygen, biological rep1


title: intestine sample from shrimp reared in low dissolved oxygen, biological rep2


title: intestine sample from shrimp reared in high dissolved oxygen, biological rep2


title: FFPE_DNA_498


title: intestine sample from shrimp reared in high dissolved oxygen, biological rep1


title: FFPE_DNA_523


title: FFPE_DNA_497


title: intestine sample from shrimp reared in medium dissolved oxygen, biological rep2


title: intestine sample from shrimp reared in medium dissolved oxygen, biological rep1


title: FFPE_DNA_522


title: gill sample from shrimp reared in low dissolved oxygen, biological rep8

source_name: gill

value: gill


title: FFPE_DNA_370


title: FFPE_DNA_410


title: FFPE_DNA_371

value: non-responder


title: FFPE_DNA_406


title: gill sample from shrimp reared in low dissolved oxygen, biological rep7


title: FFPE_DNA_407


title: gill sample from shrimp reared in medium dissolved oxygen, biological rep8


title: gill sample from shrimp reared in medium dissolved oxygen, biological rep7


title: intestine sample from shrimp reared in high dissolved oxygen, biological rep4


title: gill sample from shrimp reared in medium dissolved oxygen, biological rep6


title: FFPE_DNA_696


title: FFPE_DNA_697


title: FFPE_DNA_411


title: gill sample from shrimp reared in medium dissolved oxygen, biological rep5


title: FFPE_DNA_752


title: gill sample from shrimp reared in high dissolved oxygen, biological rep7


title: gill sample from shrimp reared in low dissolved oxygen, biological rep6


title: gill sample from shrimp reared in high dissolved oxygen, biological rep8


title: FFPE_DNA_633


title: gill sample from shrimp reared in low dissolved oxygen, biological rep5


title: FFPE_DNA_429


title: gill sample from shrimp reared in high dissolved oxygen, biological rep5


title: gill sample from shrimp reared in high dissolved oxygen, biological rep6


title: FFPE_DNA_430


title: gill sample from shrimp reared in medium dissolved oxygen, biological rep4


title: FFPE_DNA_711


title: gill sample from shrimp reared in medium dissolved oxygen, biological rep3


title: gill sample from shrimp reared in low dissolved oxygen, biological rep4


title: gill sample from shrimp reared in low dissolved oxygen, biological rep3


title: FFPE_DNA_377


title: FFPE_DNA_717


title: FFPE_DNA_807


title: gill sample from shrimp reared in high dissolved oxygen, biological rep4


title: FFPE_DNA_751


title: gill sample from shrimp reared in high dissolved oxygen, biological rep3


title: FFPE_DNA_716


title: gill sample from shrimp reared in low dissolved oxygen, biological rep2


title: FFPE_DNA_442


title: gill sample from shrimp reared in low dissolved oxygen, biological rep1


title: FFPE_DNA_727


title: gill sample from shrimp reared in high dissolved oxygen, biological rep2


title: FFPE_DNA_441


title: FFPE_DNA_632


title: FFPE_DNA_726


title: gill sample from shrimp reared in medium dissolved oxygen, biological rep2


title: FFPE_DNA_710


title: gill sample from shrimp reared in medium dissolved oxygen, biological rep1


title: FFPE_DNA_559


title: Ras17-T2-2H , TRIP-cDNA library,0.5mM CuSO4, 2 hours, rep2

city: Umeå

first: Anastasiya

last: Yushkova

address: Försörjningsvägen 2A, Byggnad 6L, NUS

department: Molecular biology

institute: Umeå University

description: Library name: R17-T2-2H-A35

library_source: other

data_processing:
The initial fastq.gz file with reads obtained after sequencing the TRIP library pool was parsed according to the sequencing index using sabre (https://anaconda.org/bioconda/sabre), yielding raw file 1 and raw file 2 data.
Raw file 1 for TRIP normalization libraries was further parsed  by the promoter index using awk-based bash script, resulting in raw data files 3-6
The parsed fastq files with "normalization", "expression", and "mapping" reads were grouped by individual TRIP experiment and processed with TRIP Analysis Software Kit (TASK) software (Akhtar et al., 2014)
Barcode lists were filtered to remove PCR-induced variants by identifying and excluding low-frequency "mutant" barcodes at the same genomic position. Only barcodes with mapping quality >10 and present in both biological replicates were retained as genuine insertions. Each insertion was assigned a TRIP signal calculated as the ratio of barcode counts (RPM) in the expression vs. normalization samples.
Assembly: dm6
Supplementary files format and content: CSV dataset containing all validated TRIP insertions, including barcode sequence, genomic position, TRIP signal, and associated cluster information (processed data file)

molecule: other

organism: Drosophila melanogaster

source_name: cultured cells

growth_protocol: Cells were grown to confluence in Schneider's medium (Lonza) supplemented with 10% FBS, 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate

extract_protocol:
TRIP-mapping libraries: Genomic DNA was MboI-digested, circularized, and used for three rounds of inverse PCR to amplify TRIP barcodes and insertion sites. Libraries were cleaned, quantified, and pooled at 10 nM. TRIP-normalization and TRIP-cDNA libraries: Genomic DNA or 10% of cDNA was PCR-amplified in two rounds to introduce sequencing adaptors. Libraries were cleaned, quantified, and pooled.
Fractions of TRIP-mapping, TRIP-normalization and TRIP-cDNA libraries were combined into a single 10nM pool at ratios 1:2:2. The pool was sequenced on 1 lane of 10B flow cell using the NovaSeq X Plus system and XLEAP-SBS sequencing chemistry.

treatment_protocol: To induce transcription of the transgenic GFP, 3x106 cells plated in triplicate two days earlier were treated with 0.5mM CuSO4 for 2 hours at 250C. The control cell cultures were grown in the same way, but without the addition of supplementary CuSO4.

value: cultured cells

value: Ras17 (control)

value: embryonic cells

value: Ras[V12] transformed otherwise wild type cells

value: 0.5mM CuSO4, 2 hours


title: FFPE_DNA_609


title: Sist-KO-T2-2H , TRIP-cDNA library,0.5mM CuSO4, 2 hours, rep2

description: Library name: L10-T2-2H-A34

value: Siesta-KO

value: Ras[V12] transformed cells with the deletion of Siesta gene


title: FFPE_DNA_608

value: responder


title: Psc-Su(z)2-KO-T2-2H , TRIP-cDNA library,0.5mM CuSO4, 2 hours, rep2

description: Library name: Psc-T2-2H-A33

value: Ras[V12] transformed cells with the deletion of Psc/Su(z)2 gene locus


title: FFPE_DNA_527

value: discovery


title: Sce-KO-T2-2H , TRIP-cDNA library,0.5mM CuSO4, 2 hours, rep2

description: Library name: Sce-T2-2H-A32

value: Ras[V12] transformed cells with the deletion of Sce gene


title: Ras17-T2 , TRIP-cDNA library, rep2

description: Library name: R17-T2-A31

value: no treatment


title: FFPE_DNA_562

value: Female


title: gill sample from shrimp reared in high dissolved oxygen, biological rep1

value: high


title: Psc-Su(z)2-KO-T2 , TRIP-cDNA library ,rep2

description: Library name: Psc-T2-A29


title: Sist-KO-T2 , TRIP-cDNA library, rep2

description: Library name: L10-T2-A30


title: Sce-KO-T2 , TRIP-cDNA library, rep2

description: Library name: Sce-T2-A28


title: FFPE_DNA_809

value: 3 weeks endocrine therapy treated


title: FFPE_DNA_564


title: FFPE_DNA_558


title: FFPE_DNA_466


title: Sist-KO-T1-2H , TRIP-cDNA library,0.5mM CuSO4, 2 hours, rep1

description: Library name: L10-T1-2H-A26


title: Psc-Su(z)2-KO-T1-2H , TRIP-cDNA library,0.5mM CuSO4, 2 hours, rep1

description: Library name: Psc-T1-2H-A25


title: FFPE_DNA_582


title: FFPE_DNA_583


title: FFPE_DNA_499


title: FFPE_DNA_563


title: Sce-KO-T1-2H , TRIP-cDNA library,0.5mM CuSO4, 2 hours, rep1

description: Library name: Sce-T1-2H-A24


title: Ras17-T1 , TRIP-cDNA library, rep1

description: Library name: R17-T1-A23


title: NanoString_RNA_375

value: breast cancer


title: Sist-KO-T1 , TRIP-cDNA library, rep1

description: Library name: L10-T1-A22


title: FFPE_DNA_500

value: non-responder


title: Ras17-N2 , TRIP-normalization library, rep2

description: Library name: Ras17-N-A19

value: cultured cells


title: FFPE_DNA_783


title: Psc-Su(z)2-KO-T1 , TRIP-cDNA library, rep1

description: Library name: Psc-T1-A21


title: FFPE_DNA_784


title: FFPE_DNA_506


title: FFPE_DNA_526


title: FFPE_DNA_565


title: Ras17-T1-2H , TRIP-cDNA library,0.5mM CuSO4, 2 hours, rep1

description: Library name: R17-T1-2H-A27

value: Ras17 (control)


title: FFPE_DNA_641


title: FFPE_DNA_638


title: Psc-Su(z)2-KO-N2 , TRIP-normalization library, rep2

description: Library name: Psc-N-A17

value: embryonic cells


title: Ras17-N1 , TRIP-normalization library, rep1

description: Library name: Ras17-N-A15

value: Ras[V12] transformed otherwise wild type cells


title: Sist-KO-N2 , TRIP-normalization library, rep2

description: Library name: L10-N-A18


title: FFPE_DNA_505


title: FFPE_DNA_829


title: FFPE_DNA_762


title: Psc-Su(z)2-KO-N1 , TRIP-normalization library, rep1

description: Library name: Psc-N-A13


title: FFPE_DNA_462


title: Sce-KO-T1 , TRIP-cDNA library, rep1

description: Library name: Sce-T1-A20


title: FFPE_DNA_469


title: Sce-KO-N1 , TRIP-normalization library, rep1

description: Library name: Sce-N-A12


title: FFPE_DNA_512


title: Sist-KO-N1 , TRIP-normalization library, rep1

description: Library name: L10-N-A14


title: FFPE_DNA_581


title: Ras17-M1 , TRIP-mapping library, rep1

description: Library name: Ras17-T1-A5


title: FFPE_DNA_1112


title: Psc-Su(z)2-KO-M1 , TRIP-mapping library, rep1

description: Library name: Psc-A2


title: Sist-KO-M2 , TRIP-mapping library, rep2

description: Library name: L10-A8


title: Sist-KO-M1 , TRIP-mapping library, rep1

description: Library name: L10-A3


title: Ras17-M2 , TRIP-mapping library, rep2

description: Library name: Ras17-T2-A10


title: FFPE_DNA_515


title: FFPE_DNA_640


title: Psc-Su(z)2-KO-M2 , TRIP-mapping library, rep2

description: Library name: Psc-A7


title: Sce-KO-N2 , TRIP-normalization library, rep 2

description: Library name: Sce-N-A16


title: Sce-KO-M2 , TRIP-mapping library, rep2

description: Library name: Sce-A6


title: FFPE_DNA_439


title: FFPE_DNA_440


title: FFPE_DNA_514


title: FFPE_DNA_580


title: FFPE_DNA_421


title: Sce-KO-M1 , TRIP-mapping library, rep1

description: Library name: Sce-A1


title: Sample_WJ-3830-Ras17-7-H3K27me3, rep 2

description: Library name: Ras17-7-H3K27me3

data_processing:
Reads were aligned to the dm6 genome assembly using bowtie2 (v2.4.4)  and the following parameters –phred33 --no-discordant --very-sensitive-local -p 32
The alignment output was further filtered using samtools (v1.3.1) to remove reads with a mapping quality score less than 30 (-h -b -@ 32 -q 30)
The resulting filtered BAM files were used as input to generate .bedGraph profiles using the MACS3 (Zhang et al., 2008) pileup command with the BAMPE output option (*.bedGraph)
Futher, the genome was segmented into 50bp bins using the bedtools makewindows -w 50 command. Then, the number of sequence tags for each bin i was calculated using the bedtools map -o mean command.
Normalized ChIP yield at genomic position i was calculated as: Y(i) = R′₍ᵢ₎ / (R′ × F_proc × F_lib × 10⁻⁶), where R′₍ᵢ₎ is the number of reads overlapping bin i, R′ is the total number of reads in the ChIP library, F_proc is the fraction of ChIP DNA used for library prep, and F_lib is the fraction of the library used for sequencing
Bins with input signals exceeding the mean + 3 SD were excluded to remove artifacts from repetitive regions
The genome was divided into 1kb bins using bedtools makewindows -w 1000 and each bin was assigned mean normalized ChIP-seq values computed for H2AK118ub signals from ChIP-seq assays with chromatins from the control, Psc/Su(z)2-KO and Siesta-KO cells.
For all H2AK118ub ChIP-seq datasets, 1kb bins with normalized ChIP-seq signals exceeding three standard deviations from the mean normalized signal of ChIP-seq assays with chromatin from RING1-KO cells were considered significantly enriched.
The mean normalized H2AK118ub ChIP-seq values for each genetic background were utilized to segregate the 1kb bins into 3 groups by unsupervised k-means clustering using stats package (4.4.3) https://www.R-project.org/ and the following parameters: centers = 3 and nstart = 25.
Assembly: dm6
Supplementary files format and content: Normalized read count profiles in .bedgraph format with ChiP signal calculated per 50bp genomic bin and removed artifacts from repetitive regions (processed data column N)
Supplementary files format and content: CSV dataset containing H2AK118ub and H3K27me3 ChIP-seq signals, calculated per 1000 bp genomic bin, along with corresponding cluster annotations for each bin (processed data column O)

extract_protocol:
Cells were crosslinked by adding the formaldehyde solution directly to the cell culture to a final concentration of 1.8% and incubating for 10 minutes at 25C. The reaction was stopped by adding glycine pH 7.0 to a final concentration of 0.125 M. Cells were extensively washed and 0.5 ml of pelleted crosslinked cells were resuspended in 5 ml cold TE buffer.
Cell suspension was supplemented with 0.1u/ml MNase and 2mM CaCl2 and incubated at 37C for 25 min. The treated cells were lysed by ultrasound and resulting lysates adjusted to RIPA (140mM NaCl, 10mM Tris-HCl pH8.0, 1mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% DOC)
ChIP was done essentially as described in (Schwartz et al., 2006) with the following modifications. Crosslinked cell lysates containing 100µg of DNA was used for immunoprecipitations in a total volume of 500µl of RIPA. The resulting immunoprecipitated DNA was dissolved in 40µl of water for ChIP-seq library preparation.
2ng of immunoprecipitated DNA were processed using NEBNext Ultra II DNA Library preparation Kit for Illumina (cat# E76455) and index oligonucleotides from NEBNext Multiplex Oligos for Illumina (cat# E7335).

tag: antibody

value: anti-H3K27me3, Abcam, #ab6002


title: FFPE_DNA_420


title: FFPE_DNA_618


title: FFPE_DNA_694


title: Sample_WJ-3830-Ras17-6-Psc, rep 1

description: Library name: Ras17-6-Psc

value: anti-Psc, custom-made, available through Agrisera, #AS174129


title: FFPE_DNA_763


title: Sample_WJ-3830-Ras17-6-H3K27me3, rep 1

description: Library name: Ras17-6-H3K27me3


title: Sample_WJ-3830-SceA7-3-RING, rep 1

description: Library name: SceA7-3-RING

value: anti-RING1, custom-made, available through Agrisera, #AS163829


title: Sample_WJ-3830-Ras17-7-Psc, rep 2

description: Library name: Ras17-7-Psc


title: Sample_WJ-3830-SceA7-4-RING, rep 2

description: Library name: SceA7-4-RING


title: Sample_WJ-3830-Ras17-7-RING, rep 2

description: Library name: Ras17-7-RING


title: FFPE_DNA_695


title: Sample_WJ-3830-Psc4-15-H2Aub, rep 1

description: Library name: Psc4-15-H2Aub

value: anti-H2AK118ub, Cell Signalling Technology, #8240


title: Sample_WJ-3830-Ras17-6-H2Aub, rep 1

description: Library name: Ras17-6-H2Aub


title: Sample_WJ-3830-Psc4-16-H2Aub, rep 2

description: Library name: Psc4-16-H2Aub

value: Ras[V12] transformed cells with the deletion of Psc/Su(z)2 gene locus


title: FFPE_DNA_744

value: discovery


title: FFPE_DNA_665


title: FFPE_DNA_764


title: FFPE_DNA_619


title: FFPE_DNA_627


title: Sample_WJ-3830-Ras17-7-H2Aub, rep 2

description: Library name: Ras17-7-H2Aub


title: FFPE_DNA_743

value: responder


title: Sample_WJ-3830-L10-8-H2Aub, rep 1

description: Library name: L10-8-H2Aub

value: Siesta-KO

value: Ras[V12] transformed cells with the deletion of Siesta gene


title: FFPE_DNA_664

value: Female


title: Sample_WJ-3830-L10-9-H2Aub, rep 2

description: Library name: L10-9-H2Aub


title: Sample_WJ-3830-SceA7-4-H2Aub, rep 2

description: Library name: SceA7-4-H2Aub

value: Ras[V12] transformed cells with the deletion of Sce gene


title: Sample_WJ-3830-SceA7-3-H2Aub, rep 1

description: Library name: SceA7-3-H2Aub


title: FFPE_DNA_662

value: 3 weeks endocrine therapy treated


title: FFPE_DNA_669

value: non-responder


title: Sample_WJ-3830-Ras17-6-RING, rep 1

description: Library name: Ras17-6-RING

value: cultured cells


title: FFPE_DNA_478


title: FFPE_DNA_822


title: Sample_WJ-3830-Ras17-7-Input, rep 2

description: Library name: Ras17-7-Input

value: Ras17 (control)

value: Input


title: FFPE_DNA_477


title: Sample_WJ-3830-Ras17-6-Input, rep 1

description: Library name: Ras17-6-Input

value: embryonic cells

value: Ras[V12] transformed otherwise wild type cells


title: Sample_WJ-3830-Psc4-16-Input, rep 2

description: Library name: Psc4-16-Input


title: Sample_WJ-3830-Psc4-15-Input, rep 1

description: Library name: Psc4-15-Input


title: FFPE_DNA_463


title: Sample_WJ-3830-L10-8-Input, rep 1

description: Library name: L10-8-Input


title: FFPE_DNA_392


title: Sample_WJ-3830-L10-9-Input, rep 2

description: Library name: L10-9-Input


title: FFPE_DNA_393


title: FFPE_DNA_402


title: FFPE_DNA_594


title: FFPE_DNA_1211

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPICv2 (EPICv2) BeadChips using standard Illumina protocol

data_processing:
RnBeads package, normalization method = "scaling.internal",   normalization background method = "sesame.noobsb"
The Matrix_processed.txt contains Average Beta. Context-specific probes (n=3197), including "CC", "CAG", "CAH", "CTG", "CTH" and "Other", were removed.
The Matrix_signal_intensities.txt contains unmethylated and methylated signal intensities.

value: breast cancer


title: FFPE_DNA_403


title: FFPE_DNA_1209


title: Sample_WJ-3830-SceA7-4-Input, rep 2

description: Library name: SceA7-4-Input


title: FFPE_DNA_464


title: FFPE_DNA_1200


title: FFPE_DNA_595


title: FFPE_DNA_501


title: FFPE_DNA_415


title: FFPE_DNA_414


title: FFPE_DNA_1203


title: FFPE_DNA_1198


title: FFPE_DNA_460


title: FFPE_DNA_1195


title: FFPE_DNA_427


title: FFPE_DNA_1194


title: FFPE_DNA_1193


title: FFPE_DNA_737


title: FFPE_DNA_736


title: FFPE_DNA_1189


title: Sample_WJ-3830-SceA7-3-Input, rep 1

description: Library name: SceA7-3-Input


title: FFPE_DNA_369


title: FFPE_DNA_1170


title: FFPE_DNA_1167


title: FFPE_DNA_1166


title: FFPE_DNA_682


title: FFPE_DNA_1162


title: FFPE_DNA_589


title: FFPE_DNA_538


title: FFPE_DNA_588


title: FFPE_DNA_1157


title: FFPE_DNA_1159


title: FFPE_DNA_683


title: FFPE_DNA_598


title: FFPE_DNA_1148


title: FFPE_DNA_818


title: FFPE_DNA_1146


title: FFPE_DNA_1161


title: FFPE_DNA_645


title: FFPE_DNA_1150


title: FFPE_DNA_1151


title: FFPE_DNA_779


title: FFPE_DNA_786


title: FFPE_DNA_1141


title: FFPE_DNA_368


title: FFPE_DNA_1176


title: FFPE_DNA_612


title: FFPE_DNA_1135


title: FFPE_DNA_539


title: FFPE_DNA_1111


title: FFPE_DNA_613


title: FFPE_DNA_481


title: FFPE_DNA_482


title: FFPE_DNA_1105


title: FFPE_DNA_605


title: FFPE_DNA_1101


title: FFPE_DNA_604


title: FFPE_DNA_1097


title: FFPE_DNA_1096


title: FFPE_DNA_1094


title: FFPE_DNA_435


title: FFPE_DNA_1093


title: FFPE_DNA_390


title: FFPE_DNA_436


title: FFPE_DNA_1092


title: FFPE_DNA_644


title: FFPE_DNA_537


title: FFPE_DNA_1140


title: FFPE_DNA_1091


title: FFPE_DNA_536


title: FFPE_DNA_1089


title: FFPE_DNA_433


title: FFPE_DNA_1088


title: FFPE_DNA_571


title: FFPE_DNA_1084


title: FFPE_DNA_570


title: FFPE_DNA_1110


title: FFPE_DNA_1079


title: FFPE_DNA_352


title: FFPE_DNA_391


title: FFPE_DNA_353


title: FFPE_DNA_1077


title: FFPE_DNA_1078


title: FFPE_DNA_576


title: FFPE_DNA_1074


title: FFPE_DNA_577


title: FFPE_DNA_1072


title: FFPE_DNA_1069


title: FFPE_DNA_655


title: FFPE_DNA_1066


title: FFPE_DNA_654


title: FFPE_DNA_484


title: FFPE_DNA_1065


title: FFPE_DNA_483


title: FFPE_DNA_1064


title: FFPE_DNA_1063


title: FFPE_DNA_450


title: FFPE_DNA_434


title: FFPE_DNA_449


title: FFPE_DNA_1061


title: FFPE_DNA_1087


title: FFPE_DNA_1060


title: FFPE_DNA_729


title: FFPE_DNA_1053


title: FFPE_DNA_453


title: FFPE_DNA_1055


title: FFPE_DNA_728


title: FFPE_DNA_1051


title: FFPE_DNA_1049


title: FFPE_DNA_746


title: FFPE_DNA_745


title: FFPE_DNA_1048


title: FFPE_DNA_1046


title: FFPE_DNA_363


title: FFPE_DNA_1044


title: FFPE_DNA_362


title: FFPE_DNA_650


title: FFPE_DNA_1039


title: FFPE_DNA_651


title: FFPE_DNA_1034


title: FFPE_DNA_355


title: FFPE_DNA_1029


title: FFPE_DNA_1030


title: FFPE_DNA_1027


title: FFPE_DNA_660


title: FFPE_DNA_661


title: FFPE_DNA_1028


title: FFPE_DNA_535


title: FFPE_DNA_454


title: FFPE_DNA_1019


title: FFPE_DNA_534


title: FFPE_DNA_739


title: FFPE_DNA_1017


title: FFPE_DNA_740


title: FFPE_DNA_1023


title: FFPE_DNA_552


title: FFPE_DNA_1015


title: FFPE_DNA_1014


title: FFPE_DNA_544


title: FFPE_DNA_553


title: FFPE_DNA_1013


title: FFPE_DNA_354


title: FFPE_DNA_776


title: FFPE_DNA_1002


title: FFPE_DNA_771


title: FFPE_DNA_1000


title: FFPE_DNA_811


title: FFPE_DNA_997


title: FFPE_DNA_493


title: FFPE_DNA_702


title: FFPE_DNA_982


title: FFPE_DNA_996


title: FFPE_DNA_703


title: FFPE_DNA_980


title: FFPE_DNA_568


title: FFPE_DNA_978


title: FFPE_DNA_569


title: FFPE_DNA_974


title: FFPE_DNA_467


title: FFPE_DNA_973


title: FFPE_DNA_468


title: FFPE_DNA_634


title: FFPE_DNA_969


title: FFPE_DNA_970


title: FFPE_DNA_629


title: FFPE_DNA_1010


title: FFPE_DNA_968


title: FFPE_DNA_964


title: FFPE_DNA_545


title: FFPE_DNA_551


title: FFPE_DNA_1006


title: FFPE_DNA_550


title: FFPE_DNA_714


title: FFPE_DNA_448


title: FFPE_DNA_952


title: FFPE_DNA_949


title: FFPE_DNA_715


title: FFPE_DNA_945


title: FFPE_DNA_946


title: FFPE_DNA_815


title: FFPE_DNA_447


title: FFPE_DNA_941


title: FFPE_DNA_755


title: FFPE_DNA_756


title: FFPE_DNA_554


title: FFPE_DNA_936


title: FFPE_DNA_935


title: FFPE_DNA_630


title: FFPE_DNA_934


title: FFPE_DNA_631


title: FFPE_DNA_437


title: FFPE_DNA_932


title: FFPE_DNA_438


title: FFPE_DNA_925


title: FFPE_DNA_769


title: FFPE_DNA_924


title: FFPE_DNA_770


title: FFPE_DNA_963


title: FFPE_DNA_646


title: FFPE_DNA_647


title: FFPE_DNA_918


title: FFPE_DNA_915


title: FFPE_DNA_548


title: FFPE_DNA_960


title: FFPE_DNA_938


title: FFPE_DNA_405


title: FFPE_DNA_911


title: FFPE_DNA_549


title: FFPE_DNA_808


title: FFPE_DNA_910


title: FFPE_DNA_471


title: FFPE_DNA_909


title: FFPE_DNA_472


title: FFPE_DNA_907


title: FFPE_DNA_902


title: FFPE_DNA_905


title: FFPE_DNA_621


title: FFPE_DNA_926


title: FFPE_DNA_643


title: FFPE_DNA_896


title: FFPE_DNA_901


title: FFPE_DNA_921


title: FFPE_DNA_741


title: FFPE_DNA_742


title: FFPE_DNA_895


title: FFPE_DNA_913


title: FFPE_DNA_826


title: FFPE_DNA_687


title: FFPE_DNA_620


title: FFPE_DNA_894


title: FFPE_DNA_649


title: FFPE_DNA_891


title: FFPE_DNA_408


title: FFPE_DNA_810


title: FFPE_DNA_885


title: FFPE_DNA_868


title: FFPE_DNA_824


title: FFPE_DNA_642


title: FFPE_DNA_875


title: FFPE_DNA_871


title: FFPE_DNA_486


title: FFPE_DNA_610


title: FFPE_DNA_611


title: FFPE_DNA_409


title: FFPE_DNA_850


title: FFPE_DNA_867


title: FFPE_DNA_858


title: FFPE_DNA_816


title: FFPE_DNA_847


title: FFPE_DNA_656


title: FFPE_DNA_890


title: FFPE_DNA_849


title: FFPE_DNA_657


title: FFPE_DNA_884


title: FFPE_DNA_841


title: FFPE_DNA_708


title: FFPE_DNA_328


title: FFPE_DNA_709


title: FFPE_DNA_689


title: FFPE_DNA_323


title: FFPE_DNA_688


title: FFPE_DNA_516


title: FFPE_DNA_307


title: FFPE_DNA_517


title: FFPE_DNA_312


title: FFPE_DNA_864


title: FFPE_DNA_723


title: FFPE_DNA_300


title: FFPE_DNA_566


title: FFPE_DNA_724


title: FFPE_DNA_305


title: ATACseq_LSEC_Maf_KO4

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

data_processing:
The trimmed reads were mapped to the mouse mm10 genome using botwie2 (v. 2.4.4) (-t -X2000 --no-mixed –no-discordant).
samtools view -F 1804 -f 2 -u and MarkDuplicates.jar was used to remove PCR duplicated from bam files.
Accesible areas were called with macs2 callpeak -t bam -f BAMPE -n name_ouput  --broad --nomodel -g hs -q 0.01 --bdg --shift -75 --extsize 150 --keep-dup all
Detected peaks were annotated with annotatePeaks.pl from homer (v4.11)
Quantification of bam files on merged peaks was performed using bedtools (v2.30.0) multicov (defaults settings). Differential binding was performed using DESEQ2 (v1.42.1). The annotation of the peaks to genome areas was done using the R script  from the repository (01peaks_Annot_fromHomer.Rmd)
Bam files were merged with bamtools merge (v. 2.5.1) (default settings) and converted to BigWig files with the help of bamCoverage (v. 3.5.1) settings (-bs 20 --smoothLength 40 -p max  --normalizeUsing RPKM -e 150)
Assembly: mm10 from UCSC genome
Supplementary files format and content: bigWig files and DESEQ2 differential peak matrix

source_name: Liver sinusoidal endothelial cell (LSEC)

growth_protocol: LSEC were isolated from three 12 weeks old control and MafLSEC-KO mice using a modified protocol from (https://doi.org/10.1038/nmeth.4396)

extract_protocol:
50.000 LSEC cells were Tagmented: Illumina Nextera Tagmentation kit; Adapters: Dual Index adapters from the IDT for Illumina-Nextera  DNA Indexes (Plate C); Size Selection: size selection was performed using Ampure XP beads to select for fragments between200-800 bp; Quality and quantity was assessed using the Agilent Bioanalyzer.
Libraries were mixed in equimolar ratios and sequenced on NextSeq550 platform using v2.5 chemistry (15058251, 15057931, 15057941, 20022408, Illumina Nextseq 500/550).

value: Isolated LESC

value: MafLSEC-KO

value: 12 weeks old


title: FFPE_DNA_296


title: FFPE_DNA_556

value: discovery


title: FFPE_DNA_557


title: ATACseq_LSEC_Maf_KO3

value: Liver sinusoidal endothelial cell (LSEC)


title: FFPE_DNA_844

value: responder


title: ATACseq_LSEC_Maf_KO2


title: FFPE_DNA_289


title: FFPE_DNA_286


title: FFPE_DNA_546


title: ATACseq_LSEC_Maf_KO1


title: ATACseq_LSEC_Maf_CTR3

value: Ctr


title: FFPE_DNA_282

value: Female


title: ATACseq_LSEC_Maf_CTR4


title: ATACseq_LSEC_Maf_CTR2


title: FFPE_DNA_340


title: FFPE_DNA_443


title: FFPE_DNA_256


title: FFPE_DNA_269


title: FFPE_DNA_547


title: FFPE_DNA_444


title: ALL12 BASELINE

city: Irvine

first: ABEL

last: PLAZA FLORIDO

state: California

address: 101 Academy, Suite 150 Irvine

department: Department of Pediatrics, UC Irvine School of Medicine

institute: Pediatric Exercise and Genomics Research Center (PERC)

description: ALL12 BASELINE

data_processing:
Library preparations, RNA sequencing, and data processing were performed at the UC Irvine High Throughput Facility, with whole transcriptome sequencing conducted on an Illumina HiSeq platform (~200M X2 paired-end 100 bp reads).
The reads for whole transcriptome sequencing were downloaded and analyzed using FASTQC (v. 0.11.2), then trimmed using Trimmomatic(v.0.32) with Illumina TruSeq adapter sequences, PHRED quality score 15 and minimum length 20 bases.
The trimmed reads were aligned to the Human hg19 reference genome with transcriptome annotation and post-processed using Tophat2(v.2.0.12), Bowtie2(v.2.2.3), and Samtools(v.0.1.19).
Expression levels were quantified both with fragment per kilobase per million mapped reads using Cufflinks (v. 2.1.1) and with raw counts using HTSeq(v.0.6.1p1.)
Assembly: grch37 (Human hg19 reference)
Supplementary files format and content: all_merged.txt: tab delimited file, raw counts of all samples

source_name: Blood (NK cells)

extract_protocol:
The isolated NK cells were washed with PBS and resuspended in Trizol, and RNA was extracted using the Trizol method. The RNA was then treated with DNase and purified using Zymo RNA cleanup columns. RNA concentration was measured with a Nanovue spectrophotometer, and RNA integrity was assessed using an Agilent Bioanalyzer, with RIN scores averaging above 8.0.
Library preparations, RNA sequencing, and data processing were performed at the UC Irvine High Throughput Facility, with whole transcriptome sequencing conducted on an Illumina HiSeq platform (~200M X2 paired-end 100 bp reads).

tag: health status

value: acute lymphoblastic leukemia (ALL)

value: Blood (NK cells)

tag: time

value: time 1

tag: Sex

value: male


title: ALL11 BASELINE

description: ALL11 BASELINE

tag: tissue


title: ALL10  PEAK

description: ALL10  PEAK

value: time 2


title: FFPE_DNA_375

value: 3 weeks endocrine therapy treated

value: non-responder


title: ALL12 PEAK

description: ALL12 PEAK


title: ALL10 BASELINE

description: ALL10 BASELINE


title: FFPE_DNA_374


title: ALL09  PEAK

description: ALL09  PEAK


title: ALL09 BASELINE

description: ALL09 BASELINE


title: FFPE_DNA_244


title: FFPE_DNA_228


title: FFPE_DNA_607


title: FFPE_DNA_255


title: FFPE_DNA_606


title: ATACseq_LSEC_Maf_CTR1

tag: cell type

tag: genotype


title: ALL08  PEAK

description: ALL08  PEAK

value: female


title: FFPE_DNA_224

value: breast cancer

tag: treatment


title: ALL07 BASELINE

description: ALL07 BASELINE


title: ALL08 BASELINE

description: ALL08 BASELINE


title: FFPE_DNA_616

tag: age (years)

tag: gender


title: FFPE_DNA_221

tag: cohort

tag: response


title: FFPE_DNA_617


title: ALL05  PEAK

description: ALL05  PEAK


title: ALL11 PEAK

description: ALL11 PEAK


title: ALL05 BASELINE

description: ALL05 BASELINE


title: FFPE_DNA_217


title: FFPE_DNA_214


title: ALL02 PEAK

description: ALL02 PEAK


title: ALL03  PEAK

description: ALL03  PEAK


title: ALL03 BASELINE

description: ALL03 BASELINE


title: ALL02 BASELINE

description: ALL02 BASELINE


title: FFPE_DNA_396


title: CONT 59 PEAK

description: CONT 59 PEAK

value: healthy control (CON)


title: FFPE_DNA_397


title: FFPE_DNA_210


title: CONT 59 BASELINE

description: CONT 59 BASELINE


title: CONT 58 PEAK

description: CONT 58 PEAK


title: FFPE_DNA_205


title: FFPE_DNA_416


title: CONT 58 BASELINE

description: CONT 58 BASELINE


title: FFPE_DNA_417


title: ALL07  PEAK

description: ALL07  PEAK


title: FFPE_DNA_200


title: CONT 56 PEAK

description: CONT 56 PEAK


title: CONT 57 BASELINE

description: CONT 57 BASELINE


title: FFPE_DNA_198


title: FFPE_DNA_385


title: FFPE_DNA_384


title: CONT 56 BASELINE

description: CONT 56 BASELINE


title: CONT 55 PEAK

description: CONT 55 PEAK


title: FFPE_DNA_180


title: FFPE_DNA_509


title: CONT 54 PEAK

description: CONT 54 PEAK


title: CONT 55 BASELINE

description: CONT 55 BASELINE


title: FFPE_DNA_176


title: FFPE_DNA_166


title: CONT 54 BASELINE

description: CONT 54 BASELINE


title: FFPE_DNA_381


title: CONT 53 PEAK

description: CONT 53 PEAK


title: FFPE_DNA_165


title: CONT 53 BASELINE

description: CONT 53 BASELINE


title: CONT 57 PEAK

description: CONT 57 PEAK


title: CONT 52 BASELINE

description: CONT 52 BASELINE


title: FFPE_DNA_380


title: CONT 51 PEAK

description: CONT 51 PEAK


title: CONT 51 BASELINE

description: CONT 51 BASELINE


title: FFPE_DNA_378


title: Drosophila melanogaster egg, 1h30m-2h AEL, Rep2, Batch2

first: Yeon

last: Choi

address: 1470 Madison Ave

institute: Iicahn school of medicine at mount sinai

description: DME_unfertilized_egg_1h30m-2h_Rep2_Batch2

data_processing:
Sequence reads underwent pre-processing using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/, version 0.0.13), including 3′ adaptor sequence removal, followed by filtering out of the sequence reads with artifacts (e.g. long homopolymer) or those of low quality (Phred quality <30 in >5% of nucleotides). In addition, sequence reads shorter than 18 nt were removed after 3′ adaptor removal. To obtain the read count for each gene, we created a reference genome using RSEM (v1.3.1, Li, 2011 https://doi.org/10.1186/1471-2105-12-323) and STAR (v2.5.3a, Dobin, 2013 10.1093/bioinformatics/bts635), with the UCSC Genome Browser dm6 genome sequence and RefGene annotation. Individual gene read counts and normalized counts (TPM) were obtained using the ‘rsem-calculate-expression’ command with ‘--star’ and ‘--forward-prob 0.0’ parameters.
Assembly: dm6
Supplementary files format and content: genes.results contains gene expression level estimated by RSEM

source_name: unfertilized egg

growth_protocol: The fly lines w1118, smg1, and Df(Scf) were obtained from the Bloomington Drosophila Stock Center (Bloomington, IN, USA), whereas tud1 was obtained from the Kyoto Stock Center (Kyoto, Japan). w1118 was used as the wild-type control. smg1/Df(Scf) has been previously described as a null allele of smg (27). Unfertilized activated eggs were produced from w1118 virgin females mated with sterile males (sons of tud1 mothers) (28). Fly eggs and embryos were collected on grape juice plates for the designated time frame at 25 °C. The first collection at 0.5 h or 1 h each day was discarded to exclude embryos that had been retained within the female oviduct for a prolonged time.

extract_protocol:
To prepare RNA and protein samples, fly embryos and unfertilized eggs were dechorionated with bleach and homogenized in lysis buffer [8 M urea, 50 mM ammonium bicarbonate, 1× protease inhibitor cocktail (Calbiochem, San Diego, CA, USA), and RNasin RNase inhibitor (Promega, Madison, WI, USA)] on ice. To isolate the total RNA, TRIzol reagent was immediately added to an aliquot of the fresh lysate. The remaining lysates were frozen for mass spectrometric (MS) analysis.
Total RNA isolated from fly embryos or unfertilized eggs using TRIzol was analyzed with an Agilent 2100 Bioanalyzer for quality checks. RNA-seq libraries were generated by Macrogen, Inc. (Seoul, South Korea) using the TruSeq Stranded RNA LT kit.

value: unfertilized egg

tag: time point

value: 1h30m-2h AEL


title: FFPE_DNA_154


title: Drosophila melanogaster egg, 1h-1h30m AEL, Rep2, Batch2

description: DME_unfertilized_egg_1h-1h30m_Rep2_Batch2

value: 1h-1h30m AEL


title: FFPE_DNA_379

value: discovery


title: FFPE_DNA_133

value: responder


title: Drosophila melanogaster egg, 30m-1h AEL, Rep2, Batch2

value: 30m-1h AEL


title: Drosophila melanogaster egg, 0-30m AEL, Rep2, Batch2

value: 0-30m AEL


title: FFPE_DNA_805

value: Female


title: Drosophila melanogaster egg, 1h30m-2h AEL, Rep2, Batch1

description: DME_unfertilized_egg_1h30m-2h_Rep2_Batch1


title: Drosophila melanogaster egg, 1h-1h30m AEL, Rep2, Batch1

description: DME_unfertilized_egg_1h-1h30m_Rep2_Batch1


title: Drosophila melanogaster egg, 30m-1h AEL, Rep2, Batch1


title: FFPE_DNA_107


title: FFPE_DNA_510


title: FFPE_DNA_351


title: CONT 52 PEAK

description: CONT 52 PEAK

value: Blood (NK cells)


title: FFPE_DNA_802


title: FFPE_DNA_106


title: FFPE_DNA_801


title: FFPE_DNA_104


title: Drosophila melanogaster embryo, 3h-4h30m AEL, Rep2

source_name: embryo

value: embryo

value: 3h-4h30m AEL


title: Drosophila melanogaster embryo, 2h-3h AEL, Rep2

value: 2h-3h AEL


title: FFPE_DNA_158

value: 3 weeks endocrine therapy treated


title: FFPE_DNA_692


title: Drosophila melanogaster embryo, 1h30m-2h AEL, Rep2


title: Drosophila melanogaster embryo, 1h-1h30m AEL, Rep2


title: Drosophila melanogaster embryo, 30m-1h AEL, Rep2


title: FFPE_DNA_693

value: non-responder


title: FFPE_DNA_99


title: FFPE_DNA_94


title: FFPE_DNA_130


title: FFPE_DNA_457


title: Drosophila melanogaster egg, 1h30m-2h AEL, Rep1


title: FFPE_DNA_93


title: shGFP

city: Pamplona

first: Alfonso

last: Calvo

state: Navarra

address: Avenida Pío XII 55

country: Spain

institute: CIMA Universidad de Navarra

description: Library name: ShGFP

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCh38 human assembly using STAR v2.6.1c with default parameters.
featureCounts v1.6.0 software and Gencode v32 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: H209 variants

growth_protocol: In this experiment, we silenced YES1 in the SCLC human cell line H209, using  shRNAs shRNAs targeting YES1 (sh-YES1) were cloned into the lentiviral Tet-pLKO-puro plasmid (Addgene #21915). shRNA against GFP (shGFP) was used as control and lentiviral particles for both shRNAs were produced. Cell lines were infected by adding lentiviral particles containing the plasmid. Depletion of YES1 was induced by treating the cells with 1 µg/mL of doxycycline every two days.

extract_protocol:
RNA was processed using Trizol and cleaned using Qiagen columns. RNA quality was analysed using Experion™ (Bio-Rad) and only RNAs with RQI>7 were included in the experiment.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

value: H209 variants


title: Drosophila melanogaster egg, 30m-1h AEL, Rep1


title: Drosophila melanogaster egg, 1h-1h30m AEL, Rep1


title: FFPE_DNA_92

value: breast cancer

tag: age


title: sh490

description: Library name: sh490


title: FFPE_DNA_773


title: FFPE_DNA_458


title: Drosophila melanogaster egg, 0-30m AEL, Rep1


title: sh1362

description: Library name: sh1362


title: FFPE_DNA_88


title: Drosophila melanogaster egg, 0-30m AEL, Rep2, Batch1


title: Drosophila melanogaster embryo, 0-30m AEL, Rep2


title: FFPE_DNA_778


title: FFPE_DNA_87


title: OVSAHO cells, 10 nM 11KDHT Biol. Repl. 3

city: Ljubljana

first: Marija

last: Gjorgoska

state: Outside North America

address: Vrazov trg 2

country: Slovenia

institute: Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana

description:
Library name: Sample 15
Column name in FPKM_All_Samples.txt: 11KDHT_10nM_C

data_processing:
Raw reads were processed with fastp software to remove adapter sequences, poly-N reads, and low-quality reads. Clean reads were aligned to the reference genome (Homo Sapiens [GRCh38/hg38]) using HISAT2 v2.0.5.
Gene-level counts were generated using featureCounts v1.5.0-p3, and gene expression was quantified as FPKM.
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample
Assembly: GRCh38

source_name: Cell line

growth_protocol: OVSAHO cells were maintained in RPMI (R5886; Sigma-Aldrich, USA), supplemented with 10% FBS (F9665; Sigma-Aldrich, USA) and 2 mM L-glutamine. Cells were maintained in humidified athmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Macherey Nagel RNA extraction kit ((#740933.5, Macherey-Nagel GmbH&Co, Germany).
mRNA sequencing was performed at Novogene Inc. mRNA was enriched using poly-T oligo-attached magnetic beads and fragmented. First-strand cDNA synthesis was performed using random hexamer primers, followed by second-strand synthesis using dUTP for directional libraries. Libraries were prepared by end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. Library quality was assessed by Qubit, real-time PCR, and Bioanalyzer to determine concentration and fragment size distribution. Libraries were pooled and sequenced on an Illumina platform using paired-end 150 bp (PE150) reads, generating approximately 12 Gb of raw data per sample.

treatment_protocol: OVSAHO cells were seeded at cell density 2 millions/well in 6-well plates in complete culture media. After 24h, the culture media was replaced with phenol-red free, steroid-free culture media with L-glutamine as a supplement. 5 uL of steroid in ethanol/well was added. Cells were incubated for 72h in humidified athmosphere with 5% CO2 at 37C.

value: OVSAHO

value: High-grade serous ovarian cancer cell line

value: Wild type

value: 10 nM 11-keto-dihydrotestosterone (11KDHT)

tag: batch


title: FFPE_DNA_670

value: discovery


title: OVSAHO cells, 10 nM 11KDHT Biol. Repl. 2

description:
Library name: Sample 14
Column name in FPKM_All_Samples.txt: 11KDHT_10nM_B


title: Drosophila melanogaster embryo, 3h-4h30m AEL, Rep1


title: Drosophila melanogaster embryo, 2h-3h AEL, Rep1


title: OVSAHO cells, 10 nM 11KDHT Biol. Repl. 1

description:
Library name: Sample 13
Column name in FPKM_All_Samples.txt: 11KDHT_10nM_A


title: Drosophila melanogaster embryo, 1h30m-2h AEL, Rep1

value: 1h30m-2h AEL


title: FFPE_DNA_81

value: responder


title: FFPE_DNA_79


title: Drosophila melanogaster embryo, 1h-1h30m AEL, Rep1

value: 1h-1h30m AEL


title: FFPE_DNA_432

value: Female


title: OVSAHO cells, 10 nM 11KT Biol. Repl. 2

description:
Library name: Sample 11
Column name in FPKM_All_Samples.txt: 11KT_10nM_B

value: 10 nM 11-keto-testosterone (11KT)


title: FFPE_DNA_84


title: FFPE_DNA_431


title: OVSAHO cells, 10 nM 11KT Biol. Repl. 1

description:
Library name: Sample 10
Column name in FPKM_All_Samples.txt: 11KT_10nM_A


title: FFPE_DNA_487


title: Drosophila melanogaster embryo, 30m-1h AEL, Rep1

value: embryo

value: 30m-1h AEL


title: FFPE_DNA_78


title: FFPE_DNA_77


title: Drosophila melanogaster embryo, 0-30m AEL, Rep1

value: 0-30m AEL


title: FFPE_DNA_671

value: 3 weeks endocrine therapy treated


title: OVSAHO cells, 10 nM DHT Biol. Repl. 3

description:
Library name: Sample 9
Column name in FPKM_All_Samples.txt: DHT_10nM_C

value: 10 nM dihydrotestosterone (DHT)


title: WT Neutrophils, lung, sorted from infected mixed chimeric mice, 72h pi. Rep.6

description:
WT-9
celled were sorted from a mixed chimeric mice

data_processing:
The quality of the sequenced reads was assessed with FastQC v0.11.7 and QoRTs v1.3.6.
Sequence adapters were trimmed using Trim Galore v0.6.7.
Reads were aligned with default parameters to the mouse reference genome (GRCm38.p6) using STAR v2.6.0c.
Gene expression estimates were obtained with featureCounts v1.6.2 using composite gene models from Gencode (version M17).
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

source_name: lung

extract_protocol:
To prepare single cell lung suspensions for flow cytometry. After perfusing murine lungs, they were placed in a gentle MACS™ C tube and mechanically homogenized in 5 ml RPMI-1640, 10% FBS, and 0.1 mg/ml DNAse using a gentle MACS™ Octo Dissociator (Miltenyi Biotech) without the use of collagenase. The lung cell suspensions were then lysed of RBCs, enumerated, and stained with fluorophore-conjugated antibodies prior to flow cytometric analysis. We used BD Aria for flow cytometric sorting, cell always stays on ice or sorted at 4℃. Neutrophils were identified as CD45+ CD11b+ Ly6Clo Ly6G+ cells, pDCs as CD45+ CD11cint SiglecF- CD19- NK1.1- CD11b- B220+ SiglecH+ cells
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 1.9-2.0 ng total RNA with RNA integrity numbers ranging from 7.8 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech cat. no.  63488), with 12 cycles of amplification. Subsequently, 7.4-10 ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems cat. no. KK8504) using 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 or NovaSeq 6000 in a PE50 (HiSeq) or PE100 (NovaSeq) run, using the HiSeq 3000/4000 SBS Kit or NovaSeq 6000 S4 Reagent Kit (200 Cycles) (Illumina).  An average of 40 million paired reads were generated per sample and the percent of mRNA bases per sample averaged 84%.

value: lung

value: neutrophil

value: 72h pi with 3*10^7 CEA10

value: wildtype


title: OVSAHO cells, 10 nM DHT Biol. Repl. 2

description:
Library name: Sample 8
Column name in FPKM_All_Samples.txt: DHT_10nM_B

value: OVSAHO

value: High-grade serous ovarian cancer cell line

value: Wild type


title: FFPE_DNA_488

data_processing:
Sesame R package, normalization method = "db", background subtraction = "noobsb"
The Matrix_processed.txt contains Average Beta
The Matrix_signal_intensities.txt contains unmethylated and methylated signal intensities.
Average Beta

value: discovery

value: non-responder


title: FFPE_DNA_76

value: breast cancer

value: responder


title: OVSAHO cells, 10 nM 11KT Biol. Repl. 3

description:
Library name: Sample 12
Column name in FPKM_All_Samples.txt: 11KT_10nM_C

value: 10 nM 11-keto-testosterone (11KT)


title: FFPE_DNA_718

value: Female


title: FFPE_DNA_719


title: WT Neutrophils, lung, sorted from infected mixed chimeric mice, 72h pi. Rep.5

description:
WT-8
celled were sorted from a mixed chimeric mice

growth_protocol: To prepare single cell lung suspensions for flow cytometry. After perfusing murine lungs, they were placed in a gentle MACS™ C tube and mechanically homogenized in 5 ml RPMI-1640, 10% FBS, and 0.1 mg/ml DNAse using a gentle MACS™ Octo Dissociator (Miltenyi Biotech) without the use of collagenase. The lung cell suspensions were then lysed of RBCs, enumerated, and stained with fluorophore-conjugated antibodies prior to flow cytometric analysis. We used BD Aria for flow cytometric sorting, cell always stays on ice or sorted at 4℃. Neutrophils were identified as CD45+ CD11b+ Ly6Clo Ly6G+ cells, pDCs as CD45+ CD11cint SiglecF- CD19- NK1.1- CD11b- B220+ SiglecH+ cells


title: FFPE_DNA_72


title: FFPE_DNA_597


title: OVSAHO cells, 10 nM DHT Biol. Repl. 1

description:
Library name: Sample 7
Column name in FPKM_All_Samples.txt: DHT_10nM_A


title: Neuro2a cells treated with VP64, no sgRNA control_Rep3

city: San Francisco

first: Nadav

last: Ahituv

address: 1550 4th Street

institute: UCSF

description: Library name: Sample_7_10

data_processing:
sequences were mapped to mm39 with STAR 2.7.8a
counts were computed using featureCounts with gtf provided from Ensembl: Mus_musculus.GRCm39.113
gene counts were normalized to counts per million (CPM)
Differential expression was characterized using DESeq2 version 1.44 and R version 4.4
Assembly: mm39
Supplementary files format and content: Neuro2a_CPM.tsv.gz, tab seperated counts per million for Neuro2a
Supplementary files format and content: Mice_CPM.tsv.gz,  tab seperated counts per million for Mice sorted neurons
Supplementary files format and content: CRISPRa_vs_VP64_deseq2_Neuro2a.tsv.gz
Supplementary files format and content: WT_vs_HET_deseq2_Mice_sorted_neurons.tsv.gz
Supplementary files format and content: CRISPRa_vs_HET_deseq2_Mice_sorted_neurons.tsv.gz
Supplementary files format and content: CRISPRa_vs_WT_deseq2_Mice_sorted_neurons.tsv.gz

growth_protocol: Mice were maintained on a C57BL/6J background on a 12:12 light-dark cycle (light on at 6 AM) with ad libitum food and water, with daily health monitoring. Neuro2a Cells were grown and maintained in DMEM with 10% FBS and 1% Pen/Strep

extract_protocol:
For Mice: Nuclei were isolated from 200 mg of cortex using the Singulator™ 100 System (S2 Genomics), Nuclei were sorted for NueN positivity using BD FACSAria™ Fusion (BD Biosciences), and total RNA was extracted using the miRNeasy kit (Qiagen). For Neuro2a RNA was isolated using the RNeasy Mini Kit (Qiagen)
Novogene mRNA library preparation (polyA enrichment)

treatment_protocol: Mice: 500 nL of rAAV at a 1:1 ratio of sgRNA and sadCas9-VP64 was injected into the mPFC and mice were used in experiments 4 weeks post injection. Cells were treated with either 750 ng of sgRNA and 750 ng of sadCas9-VP64 plasmid, or only sadCas9-VP64

value: Neuroblastoma


title: FFPE_DNA_825

extract_protocol: standard genomic DNA extraction from FFPE tissue


title: Neuro2a cells treated with VP64, no sgRNA control_Rep6

description: Library name: Sample_8_9


title: OVSAHO cells, Control Biol. Repl. 3

description:
Library name: Sample 3
Column name in FPKM_All_Samples.txt: Control_C

value: Control (ethanol)


title: OVSAHO cells, 10 nM T Biol. Repl. 3

description:
Library name: Sample 6
Column name in FPKM_All_Samples.txt: T_10nM_C

value: 10 nM testosterone (T)


title: OVSAHO cells, Control Biol. Repl. 2

description:
Library name: Sample 2
Column name in FPKM_All_Samples.txt: Control_B


title: FFPE_DNA_799

value: 3 weeks endocrine therapy treated


title: Neuro2a cells treated with VP64, no sgRNA control_Rep1

description: Library name: Sample_7_7


title: WT Neutrophils, lung, sorted from infected mixed chimeric mice, 72h pi. Rep.3

description:
WT-2
celled were sorted from a mixed chimeric mice

value: lung


title: Neuro2a cells treated with VP64, no sgRNA control_Rep5

description: Library name: Sample_8_7


title: OVSAHO cells, Control  Biol. Repl. 1

description:
Library name: Sample 1
Column name in FPKM_All_Samples.txt: Control_A


title: OVSAHO cells, 10 nM T Biol. Repl. 2

description:
Library name: Sample 5
Column name in FPKM_All_Samples.txt: T_10nM_B


title: FFPE_DNA_800


title: WT Neutrophils, lung, sorted from infected mixed chimeric mice, 72h pi. Rep.2

description:
WT-1
celled were sorted from a mixed chimeric mice

value: neutrophil


title: HEK293T_FAM98BKO_FL_-DOX

city: Boston

first: Raghu

last: Chivukula

state: MA

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description: Library name: JY6_14_12_L

data_processing:
Adapters were trimmed from the ends of reads using Cutadapt v4.6. Trimmed read pairs were merged using BBMerge v39.06. UMIs were trimmed and reads under 15 bp were filtered using fastp v0.23.4. Trimmed reads were mapped to the reference human genome hg38 augmented with mature tRNA sequences built with tRAX using Bowtie2 v2.3.4.1 with parameters -k 100 --very-sensitive --ignore-quals --np 5. Read mappings were filtered using tRAX choosemappings.py with parameter --minnontrnasize=15. Reads aligned to non-tRNA small RNA genes were counted using htseq-count from HTSeq v2.0.1. Reads aligned to tRNA genes and mature tRNA sequences were counted using a custom script. Reads with 5’ end mapping within 5 nt of the 5’ end of a tRNA feature were counted as 5’ tRNA fragments while reads with 3’ end mapping within 5 nt of the 3’ end of a tRNA feature were counted as 3’ tRNA fragments. tRNA fragments were further classified as previously described based on the position of the 3’ end of 5’ fragments and 5’ end of 3’ fragments. Reads containing at least 3 nt of leader or trailer were counted as derived from pre-tRNAs. Analysis of differential tRNA fragment abundance was performed using DESeq2, using miRNA counts to calculate library size factors.
Assembly: hg38
Supplementary files format and content: Tab-delimited files delineating counts for tRNA and non-tRNA species identified in cerebellum and HEK293T cell samples.

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was extracted from human cerebellum samples using TRIzol reagent (ThermoFisher).
2.5 μg of total RNA was dephosphorylated with 10 units of T4 polynucleotide kinase (NEB) in dephosphorylation buffer (700 mM bis-tris, 100 mM MgCl2, 50 mM DTT, pH 6) at 37°C for 30 minutes, then fractionated using an RNA Clean & Concentrator-5 kit (Zymo) according to the manufacturer’s instructions. cDNA was synthesized from 20 ng of the small RNA fraction using an ordered two-template relay kit (Karnateq) according to the manufacturer’s instructions. Following cDNA synthesis, reactions were combined with 1 μL RNase A (ThermoScientific) and 1 μL thermostable RNase H (NEB), incubated at 50°C for 10 minutes, further combined with 1 μL proteinase K (NEB) and 30 μL cDNA stop solution (50 mM tris-HCl, 20 mM EDTA, 0.1% SDS, pH 7.4), incubated at 50°C for 10 minutes, and denatured at 95°C for 5 minutes. cDNA was purified using an Oligo Clean & Concentrator kit (Zymo), mixed 1:1 with 2X Gel Loading Buffer II (Ambion) and subjected to denaturing 8% polyacrylamide gel electrophoresis. The gel was stained with SYBR Gold (Invitrogen) and the region between approximately 97 nt and 135 nt was extracted according to ssDNA size standards. cDNA was eluted from gel fragments, precipitated with ethanol, and quantitated by qPCR using PowerUp SYBR Green (Applied Biosystems). Sequences of qPCR primers used are provided in table S6. cDNA was amplified and indexed using Q5 (NEB) and xGen unique dual index primers (IDT). For HEK293T libraries, reactions with 3.1 pM input cDNA were amplified for 15 cycles; for human brain libraries, reactions with 25 pM input cDNA were amplified for 12 cycles. Amplified libraries were purified using a Monarch PCR & DNA cleanup kit (NEB) and subjected to native 8% polyacrylamide gel electrophoresis. The gel was stained with SYBR Gold (Invitrogen) and the region between approximately 150 bp and 210 bp was extracted. Libraries were eluted from gel fragments, precipitated with ethanol, and sequenced on a NovaSeq X Plus 25B flow cell.

treatment_protocol: As indicated, doxycycline (DOX) was added to the culture medium at a concentration of 10ng/mL.

value: no doxycycline


title: Neuro2a cells treated with VP64, no sgRNA control_Rep4

description: Library name: Sample_8_6


title: OVSAHO cells, 10 nM T Biol. Repl. 1

description:
Library name: Sample 4
Column name in FPKM_All_Samples.txt: T_10nM_A


title: STAT1 KO Neutrophils, lung, sorted from infected mixed chimeric mice, 72h pi. Rep.5

first: YAHUI

last: GUO

address: 407 East 68th street, ZRC1641

institute: Memorial Sloan-Kettering Cancer Center (MSKCC)

description:
KO-8
celled were sorted from a mixed chimeric mice

value: 72h pi with 3*10^7 CEA10

value: STAT1 KO


title: WT Neutrophils, lung, sorted from infected mixed chimeric mice, 72h pi. Rep.1

description:
WT-10
cells were pooled from 10 mice

value: wildtype


title: FFPE_DNA_596


title: Neuro2a cells treated with VP64, no sgRNA control_Rep2

description: Library name: Sample_7_8


title: pDC, lung, sorted from infected mice lung, 72h pi. rep.3

description:
lung1-10
celled were sorted from a mixed chimeric mice

value: pDC


title: pDC, lung, sorted from infected mice lung, 72h pi. rep.4

description:
lung11-20
cells were pooled from 10 mice


title: FFPE_DNA_586

value: discovery


title: Neuro2a cells treated with CRISPRa_Rep4

description: Library name: Sample_8_1


title: cerebellum_FXTAS_2388

description: Library name: JY6_14_8_L

source_name: cerebellum

value: cerebellum


title: STAT1 KO Neutrophils, lung, sorted from infected mixed chimeric mice, 72h pi. Rep.4

description:
KO-7
celled were sorted from a mixed chimeric mice


title: WT Neutrophils, lung, sorted from infected mixed chimeric mice, 72h pi. Rep.4

description:
WT-7
celled were sorted from a mixed chimeric mice


title: FFPE_DNA_685

source_name: breast cancer

value: non-responder


title: FFPE_DNA_413


title: STAT1 KO Neutrophils, lung, sorted from infected mixed chimeric mice, 72h pi. Rep.6

description:
KO-9
celled were sorted from a mixed chimeric mice


title: Neuro2a cells treated with CRISPRa_Rep6

description: Library name: Sample_8_5


title: FFPE_DNA_361


title: FFPE_DNA_587


title: Neuro2a cells treated with CRISPRa_Rep5

description: Library name: Sample_8_4


title: FFPE_DNA_412

value: responder


title: Neuro2a cells treated with CRISPRa_Rep1

description: Library name: Sample_7_1


title: HEK293T_FAM98BKO_FL_+DOX

description: Library name: JY6_14_10_L

value: doxycycline


title: cerebellum_FXTAS_4555

description: Library name: JY6_14_5_L


title: pDC, bone marrow, sorted from naïve mice BM, rep.2

description:
BM-2
cells were pooled from 3 mice

source_name: bone marrow

value: bone marrow

value: naive

value: naïve


title: CRISPRa_rep3

description: Library name: Mice_15

source_name: Cortex

value: Cortex

value: Neurons

value: AAV-sadCas9-VP64 + rAAV-Scn2a-sgRNA injection


title: STAT1 KO Neutrophils, lung, sorted from infected mixed chimeric mice, 72h pi. Rep.3

description:
KO-2
celled were sorted from a mixed chimeric mice

value: lung

value: neutrophil


title: cerebellum_control_5671

description: Library name: JY6_14_4_L


title: cerebellum_FXTAS_5006

description: Library name: JY6_14_7_L


title: FFPE_DNA_373

value: Female

value: 3 weeks endocrine therapy treated


title: Neuro2a cells treated with CRISPRa_Rep3

description: Library name: Sample_7_4

value: Neuroblastoma


title: Neuro2a cells treated with CRISPRa_Rep2

description: Library name: Sample_7_2


title: cerebellum_FXTAS_5746

description: Library name: JY6_14_6_L


title: STAT1 KO Neutrophils, lung, sorted from infected mixed chimeric mice, 72h pi. Rep.1

description:
KO-10
celled were sorted from a mixed chimeric mice

value: 72h pi with 3*10^7 CEA10

value: STAT1 KO


title: pDC, bone marrow, sorted from naïve mice BM, rep.1

description:
BM-1
cells were pooled from 3 mice

value: pDC

value: wildtype


title: STAT1 KO Neutrophils, lung, sorted from infected mixed chimeric mice, 72h pi. Rep.2

description:
KO-1
celled were sorted from a mixed chimeric mice


title: pDC, bone marrow, sorted from naïve mice BM, rep.4

description:
BM24-26
cells were pooled from 3 mice


title: Het_rep3

description: Library name: Mice_17


title: CRISPRa_rep2

description: Library name: Mice_12


title: cerebellum_control_77549

description: Library name: JY6_14_3_L

value: cerebellum


title: FFPE_DNA_398

value: discovery

value: responder


title: cerebellum_control_46694

description: Library name: JY6_14_2_L


title: cerebellum_control_24508

description: Library name: JY6_14_1_L


title: pDC, bone marrow, sorted from naïve mice BM, rep.3

description:
BM21-23
cells were pooled from 3 mice

value: bone marrow

value: naive


title: pDC, bone marrow, sorted from infected mice BM, 72h pi. rep.3

description:
BM1-10
cells were pooled from 10 mice


title: Het_rep1

description: Library name: Mice_7

value: Cortex


title: FFPE_DNA_399

value: non-responder


title: pDC, bone marrow, sorted from infected mice BM, 72h pi. rep.4

description:
BM11-20
cells were pooled from 10 mice


title: J85_Sas_HFD [SAMPLE 43]

city: Lille

first: Alexandre

last: Berthier

address: U1011, Bâtiment J&K, Bd du Pr Leclerc

country: France

institute: Inserm

hyb_protocol: Following fragmentation, 3.5 microgrammes of ssDNA were hybridized for 16 hr at 45C on MoGene 2.0 Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing:
data were processed using our in-house Galaxy instance with “GIANT” (Galaxy-based interactive tools for Analysis of Transcriptomic data).  It consists of modules allowing to perform quality control (QC), Robust Multi-Average method normalization, LIMMA differential analysis using apt-probeset-summarize tool (v.2.10.0). Normalization done on probeset level with NetAffx Annotation Release 36. Matrix values are Log2 RMA.
probe group file:MoGene-2_0-st.pgf and MoGene-2_0-st.clf
meta-probeset file:MoGene-2_0-st-v1.na36.mm10.probeset.csv

label: biotin

source_name: Liver

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

extract_protocol: rna extraction with trizol followed by 2 volume of 100% EtOH and rneasy column (macherey nagel) with Dnase treatment

tag: strain

value: male

value: Liver

value: PBS

tag: diet

value: High Fat Diet

tag: sacrifice day


title: WT_rep2

description: Library name: Mice_11

value: Neurons

value: WT


title: FFPE_DNA_360

first: Guokun

last: Zhang

address: Marchioninistr. 15

institute: IBE LMU

value: Female

value: 3 weeks endocrine therapy treated


title: FFPE_DNA_372


title: FFPE_DNA_700


title: J85_Sas_CD [SAMPLE 44]

value: Chow Diet


title: FFPE_DNA_521


title: FFPE_DNA_691


title: pDC, lung, sorted from infected mice lung, 72h pi. rep.2

city: New York

description:
11-20L
cells were pooled from 10 mice

value: lung

value: pDC

value: 72h pi with 3*10^7 CEA10

value: wildtype


title: FFPE_DNA_520

value: discovery

value: responder


title: J85_S961_HFD [SAMPLE 41]


title: J7_S961_CD [SAMPLE 45]


title: Het_rep2

description: Library name: Mice_8

value: Cortex


title: pDC, bone marrow, sorted from infected mice BM, 72h pi. rep.1

description:
1-10b
cells were pooled from 10 mice

value: bone marrow


title: cdse16rep1,cdse16rep2

city: Shanghai

first: Qian

last: Wen

address: 320 Yueyang Road, Xuhui District

institute: Shanghai Institute of Nutrition and Health

description: Library name: Sample16

data_processing:
fastp
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
The clear reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample

source_name: liver

extract_protocol:
Collect the livers of mice from each treatment group and extract RNA using Trizol.
Total RNA was extracted and assessed for quality and quantity. mRNA was enriched using poly(A) selection with Oligo(dT) beads. The mRNA was then fragmented and reverse transcribed into cDNA using random primers. After second-strand synthesis, end repair and adapter ligation were performed. The resulting libraries were purified and amplified by PCR. Sequencing was carried out on the Illumina NovaSeq  platform.

value: liver

value: Combined treatment of selenium and cadmium


title: CRISPRa_rep1

description: Library name: Mice_10

value: AAV-sadCas9-VP64 + rAAV-Scn2a-sgRNA injection


title: J85_S961_HFD [SAMPLE 40]

value: male

value: Liver

value: High Fat Diet


title: J85_Sas_CD [SAMPLE 42]

value: PBS


title: pDC, bone marrow, sorted from infected mice BM, 72h pi. rep.2

description:
11-20b
cells were pooled from 10 mice


title: cdse15rep1,cdse15rep2

description: Library name: Sample15

value: WT


title: FFPE_DNA_830

city: Munich

value: Female

value: 3 weeks endocrine therapy treated


title: WT_rep1

description: Library name: Mice_9

value: Neurons


title: J7_S961_CD [SAMPLE 39]

value: Chow Diet


title: FFPE_DNA_790

value: non-responder


title: 542_S

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
adapter sequences as well as 17 first bases were removed using Cutadapt tool (V.1.16.6). Sequences were mapped on mm10 genome using bowtie2 tool (v.2.3.4.3), then low mapping quality (phred scale < 30) and mitochondrial chromosome reads were removed using filter tool (2.4.1) as well as duplicate reads (Picard Markduplicate tool v.2.18.2.2). Replicates were then merged with SAM merge 2 (v.1.1.2) and Bigwig files were generated
Assembly: mm10
Supplementary files format and content: Bigwig

extract_protocol: ATAC-Seq on mouse Liver under high fat diet after transient insulin resistance event (IR) or not (Ctrl). Each condition has been conduced in triplicate.

value: IR + HFD


title: pDC, lung, sorted from infected mice lung, 72h pi. rep.1

description:
1-10L
cells were pooled from 10 mice

value: lung

value: pDC

value: 72h pi with 3*10^7 CEA10

value: wildtype


title: cdse13rep1,cdse13rep2

description: Library name: Sample13

value: liver

value: Combined treatment of selenium and cadmium


title: FFPE_DNA_781

value: discovery

value: responder


title: 539_S

value: Liver


title: WT_rep3

description: Library name: Mice_16

value: Cortex


title: J20_S961_CD [SAMPLE 34]

value: male


title: J20_S961_CD [SAMPLE 37]


title: J85_Sas_CD [SAMPLE 36]

value: PBS


title: FFPE_DNA_424

value: Female

value: 3 weeks endocrine therapy treated


title: FFPE_DNA_782


title: 521_S

value: WT


title: FFPE_DNA_525

value: non-responder


title: J7_S961_CD [SAMPLE 33]

value: Chow Diet


title: cdse14rep1,cdse14rep2

description: Library name: Sample14


title: 534_Ctrl

value: HFD


title: se44rep1,se44rep2

description: Library name: Sample12

value: Single selenium treatment


title: J20_S961_CD [SAMPLE 35]


title: 529_Ctrl


title: se41rep1,se41rep2

description: Library name: Sample11


title: J85_S961_HFD [SAMPLE 30]

value: High Fat Diet


title: cd6rep1,cd6rep2

description: Library name: Sample8

value: Single cadmium treatment


title: J7_Sas_CD [SAMPLE 32]


title: se40rep1,se40rep2

description: Library name: Sample10

value: liver


title: 527_Ctrl