title: WT, Expansion (18 mm) heart ventricles

description:
Library name: WT-Expansion_18 mm
10x Genomics

value: 2.5 months old


title: A549 cells, circulating tumor cells, replicate 3

status: Public on Dec 17 2025

type: SRA

city: Pamplona

first: Karmele

last: Valencia

state: Navarra

address: Avenida Pío XII, 55

department: Innovación Terapéutica en Cáncer de Pulmón

country: Spain

institute: Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra

description:
Library name: Sample 6
Column name in human_countmatrix_030325.csv: ACTC3

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
Trimmed sequence reads were mapped to GRCh38.113 using STAR.
Extraction of read counts and construction of the count matrix were performed using featureCounts.
Assembly: GRCh38
Supplementary files format and content: comma-delimited file cointaing raw counts for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: A549 cells were mantained in RPMI medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
RNA extraction was performed using Macherey-Nagel RNA NucleoSpin kit.
Library preparation was performed using the Illumina Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s protocol. All sequencing libraries were constructed from 100 ng of total RNA according to the manufacturer's instruction.

tag: cell line

tag: cell type

value: immortalized human cell line isolated from pulmonary adenocarcinoma

tag: genotype

value: WT


title: WT, Establishment (14 mm) heart ventricles

city: Montreal

first: Rubén

last: Marín-Juez

address: 3175 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: CHU Sainte-Justine

description:
Library name: WT-Establishment_14 mm
10x Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed individually in 10x Genomics Cloud Analysis using the Cell Ranger Count v6.1.2 pipeline and reads were aligned to GRCz11 v4.3.2 reference genome. Filtered gene expression matrices were imported and further processed in Seurat v4. Samples were integrated to create a single aggregated Seurat object, and low-quality cells containing less than 200 unique features were removed. Batch effect correction was performed using the data integration and ScTransform functions in Seurat.
Assembly: GRCz11 v4.3.2 reference genome
Supplementary files format and content: Tab separated values files and matrix files

organism: Danio rerio

source_name: Heart ventricle

extract_protocol:
One pool of ventricles per developmental stage, initiation (10 mm) 25 ventricles, establishment (14 mm) 18 ventricles, expansion (18 mm) 12 ventricles and maturation (28 mm) 5 ventricles) was prepared using WT zebrafish. Euthanatized fish were dissected, and ventricles were extracted in calcium- , magnesium-free HBSS (Sigma, Cat. no. H9394) supplemented with 20 U/ml of heparin (Sigma, Cat no. H3393). Ventricles were washed in fresh HBSS and transferred into 1 ml of 1 mg/ml of collagenase (Gibco, Cat. no. 17101015) dissolved in HBSS for around 30 min digestion on a thermal mixer at 32 ⁰C and 700 rpm. Ventricles were mechanically disrupted by pipetting every 10 min. Samples were centrifuged at 2000 rpm for 5 min at RT and supernatants discarded. Cells were digested with 1 ml of 1x TrypLE Express Enzyme (Gibco, Cat. no. 12605010) for 15 min on a thermal mixer at 32 ⁰C and 700 rpm and pipetted every 5 min. Enzymatic digestion was stopped by adding 1 ml of 20% fetal bovine serum (Thermo, Cat no. A3160701) in HBSS to extracts. Tissue extracts were strained through a 70 μm cell strainer and centrifuged at 2000 rpm for 5 min at RT. The supernatants were discarded, and pellets were washed with 1 ml of 20% fetal bovine serum in HBSS. After centrifuge at 2000 rpm for 5 min at RT, cells were resuspended in 80 μl of 20% fetal bovine serum in HBSS and strained through a 40 μm cell strainer. Cells were counted and viability (>85%) was assessed using 0.4% Trypan Blue (Sigma, T8154). Cells were kept on ice and immediately processed for scRNA-seq.
For scRNA-seq experiment, 14000 cells were used for each sample and the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics, Cat. no. PN-1000269) was used following manufacturer’s protocol. Each sample was indexed individually using the Dual Index Kit TT Set A (10x Genomics, Cat. no. PN-1000215).

tag: tissue

value: Heart ventricle

tag: age

value: 2 months old

tag: strain

value: AB

tag: batch


title: A549 cells, circulating tumor cells, replicate 2

description:
Library name: Sample 5
Column name in human_countmatrix_030325.csv: ACTC2


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-B11

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Regions of mouse brain were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: 9 months

tag: brain region

value: CP

tag: gender

value: M


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-B12


title: WT, Initiation (10 mm) heart ventricles

description:
Library name: WT-Initiation_10mm
10x Genomics

value: 1.5 months old


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-A24


title: A549 cells, circulating tumor cells, replicate 1

description:
Library name: Sample 4
Column name in human_countmatrix_030325.csv: ACTC1


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-D23


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-A23


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-A12


title: A549 cells, parental, replicate 3

description:
Library name: Sample 3
Column name in human_countmatrix_030325.csv: AP3


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-P22


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-P9


title: 30% calorie-restricted diet  throughout gestation-4

city: Dalian

first: Li

last: Zhang

address: 222 Zhongshan Road, Xigang District

country: China

institute: The First Affiliated Hospital of Dalian Medical University

description: Library name: SGA-4

data_processing:
Real-Time Analysis and bcl2fastq were performed.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp.
Trimmed sequence reads were mapped to rn7.
Read count extraction were performed using htseq-count,and normalized counts using FPKM.
Assembly: rn7
Supplementary files format and content: processed data.xlsx

organism: Rattus norvegicus

source_name: hepatocyte cell line

extract_protocol:
RNA was extracted by using TRlpure reagent (BioTeke, Beijing, China). Approximately 200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina®  following manufacturer's protocols.

value: Liver

value: hepatocyte


title: 30% calorie-restricted diet  throughout gestation-5

description: Library name: SGA-5


title: A549 cells, parental, replicate 2

description:
Library name: Sample 2
Column name in human_countmatrix_030325.csv: AP2


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-C23


title: 30% calorie-restricted diet  throughout gestation-3

description: Library name: SGA-3


title: A549 cells, parental, replicate 1

description:
Library name: Sample 1
Column name in human_countmatrix_030325.csv: AP1


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-C11


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-P21


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-P10


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-B23


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-O9


title: 30% calorie-restricted diet  throughout gestation-2

description: Library name: SGA-2


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-O22


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-O10


title: MOLM-13, IFNGR1 knockout, TNF-alpha and IFN-gamma stimulated, clone B9, rep6

city: Munich

first: Monika

last: Sponheimer

address: Feodor-Lynen-Strasse 25

department: Gene Center

country: Germany

institute: LMU Munich

description: Library name: MOLM-13 IFNGR1 knockout TNF-alpha and IFN-gamma stimulated, 6

data_processing:
Quality assesment of the fastq data files was conducted using fastqc (v0.11.5), followed by poly A trimming using cutadapt (v4.1). Subsequent read filtering, mapping, and conducting were performed using the zUMIs pipeline (v.2.9.7), with reads mapped to the human genome (hg38). Bulk-fastq data was sample-demultiplexed using deML.
Assembly: hg38
Supplementary files format and content: raw counts for each sample
Supplementary files format and content: csv files

growth_protocol: MOLM-13 cells were maintained in RPMI1640 supplemented with 10% fetal-bovine-serum and 0.5 mg/ml penecillin-streptomycin-glutamine in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA isolation and library preparation were performed according to the Prime-seq protocol. RNA was isolated from cell lysates and cDNA synthesized using Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific, EP0753) with barcoded oligo-dT primers (E3V7NEXT) and a custom template-switching oligo. Libaries were prepared from 30 ng of pooled cDNA.
Libraries were prepared using the NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs, E7805S) using a prime-seq specific custom ligation-adapter and dual-indexing with TruSeq i5 and Nextera i7 primers via PCR.

treatment_protocol: 2 x 105 MOLM-13 cells were exposed to 2.5 ng/ml IFN-gamma and/or 5 ng/ml TNF-a for 72 hours

value: acute myeloid leukemia

value: IFNGR1 knock out

tag: treatment

value: TNF-alpha and IFN-gamma stimulated


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-N9


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-O21


title: MOLM-13, IFNGR1 knockout, TNF-alpha and IFN-gamma stimulated, clone A4, rep4

description: Library name: MOLM-13 IFNGR1 knockout TNF-alpha and IFN-gamma stimulated, 4


title: normal diet-5

description: Library name: AGA-5


title: MOLM-13, IFNGR1 knockout, TNF-alpha and IFN-gamma stimulated, clone C4, rep5

description: Library name: MOLM-13 IFNGR1 knockout TNF-alpha and IFN-gamma stimulated, 5


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-A11


title: normal diet-4

description: Library name: AGA-4


title: normal diet-3

description: Library name: AGA-3


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-N10


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-N21


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-M9


title: MOLM-13, IFNGR1 knockout, TNF-alpha and IFN-gamma stimulated, clone C4, rep2

description: Library name: MOLM-13 IFNGR1 knockout TNF-alpha and IFN-gamma stimulated, 2


title: MOLM-13, IFNGR1 knockout, TNF-alpha and IFN-gamma stimulated, clone A5, rep3

description: Library name: MOLM-13 IFNGR1 knockout TNF-alpha and IFN-gamma stimulated, 3


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-M21


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-M22


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-M10


title: MOLM-13, IFNGR1 knockout, TNF-alpha and IFN-gamma stimulated, clone B9, rep1

description: Library name: MOLM-13 IFNGR1 knockout TNF-alpha and IFN-gamma stimulated, 1


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-L9


title: normal diet-1

description: Library name: AGA-1


title: normal diet-2

description: Library name: AGA-2


title: MOLM-13, IFNGR1 knockout, IFN-gamma stimulated, clone B9, rep6

description: Library name: MOLM-13 IFNGR1 knockout IFN-gamma stimulated, 6

value: IFN-gamma stimulated


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-L21


title: 30% calorie-restricted diet  throughout gestation-1

description: Library name: SGA-1


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-L10


title: MOLM-13, IFNGR1 knockout, IFN-gamma stimulated, clone C4, rep5

description: Library name: MOLM-13 IFNGR1 knockout IFN-gamma stimulated, 5


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-N22


title: MOLM-13, IFNGR1 knockout, IFN-gamma stimulated, clone A4, rep4

description: Library name: MOLM-13 IFNGR1 knockout IFN-gamma stimulated, 4


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-K22


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-K9


title: 514_TNYGKUV

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description: Library name: lib33371

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads.
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: Raw counts are provided in .csv format. Each row is a gene, each column is a sample.

source_name: whole blood

extract_protocol:
Whole blood was collected in Tempus Blood RNA Tubes (Thermo Fisher Scientific), RNA was extracted using MagMax for Stabilized Blood Tubes RNA Isolation Kit (Thermo Fisher Scientific), followed by globin reduction using GlobinClear Human (Thermo Fisher Scientific).
To generate sequencing libraries, total RNA (0.5 ng) was added to reaction buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), and reverse transcription was performed followed by PCR amplification to generate full-length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit Fluorometer (Life Technologies). Dual-index, single-read sequencing of pooled libraries was carried out on a HiSeq 2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 5 million reads per sample.

value: whole blood

tag: donor id

value: male

tag: visit

tag: group

value: Placebo


title: 513_TNYCAXJ

description: Library name: lib33370

value: ATG-GCSF


title: 515_TNYGWV7

description: Library name: lib33372


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-K10


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-K21


title: 512_TNYGW8Y

description: Library name: lib33369

value: female

value: ATG


title: MOLM-13, IFNGR1 knockout, IFN-gamma stimulated, clone C4, rep2

description: Library name: MOLM-13 IFNGR1 knockout IFN-gamma stimulated, 2


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-J22


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-J9


title: 510_TNYA3X7

description: Library name: lib33367


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-J21


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-J10


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-L22


title: MOLM-13, IFNGR1 knockout, TNF-alpha stimulated, clone B9, rep6

description: Library name: MOLM-13 IFNGR1 knockout TNF-alpha stimulated, 6

value: TNF-alpha stimulated


title: 509_TNYA2T2

description: Library name: lib33366


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-I22

value: 9 months


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-I9

value: CP


title: 508_TNY9TJW

description: Library name: lib33365


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-I10

value: M


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-I21


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-H9


title: MOLM-13, IFNGR1 knockout, TNF-alpha stimulated, clone A4, rep4

description: Library name: MOLM-13 IFNGR1 knockout TNF-alpha stimulated, 4


title: MOLM-13, IFNGR1 knockout, IFN-gamma stimulated, clone A5, rep3

description: Library name: MOLM-13 IFNGR1 knockout IFN-gamma stimulated, 3


title: 507_TNY70PH

description: Library name: lib33364


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-H22


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-H21


title: MOLM-13, IFNGR1 knockout, TNF-alpha stimulated, clone A5, rep3

description: Library name: MOLM-13 IFNGR1 knockout TNF-alpha stimulated, 3


title: 506_TNY6UP9

description: Library name: lib33363


title: 505_TNY88GM

description: Library name: lib33362


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-H10


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-G22


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-G9


title: MOLM-13, IFNGR1 knockout, TNF-alpha stimulated, clone C4, rep2

description: Library name: MOLM-13 IFNGR1 knockout TNF-alpha stimulated, 2


title: MOLM-13, IFNGR1 knockout, IFN-gamma stimulated, clone B9, rep1

description: Library name: MOLM-13 IFNGR1 knockout IFN-gamma stimulated, 1


title: 511_TNYGW83

description: Library name: lib33368


title: MOLM-13, IFNGR1 knockout, TNF-alpha stimulated, clone B9, rep1

description: Library name: MOLM-13 IFNGR1 knockout TNF-alpha stimulated, 1


title: 504_TNYA5HX

description: Library name: lib33361


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-G10


title: MOLM-13, IFNGR1 knockout, TNF-alpha stimulated, clone C4, rep5

description: Library name: MOLM-13 IFNGR1 knockout TNF-alpha stimulated, 5


title: MOLM-13, IFNGR1 knock out, unstimulated, clone B9, rep6

description: Library name: MOLM-13 IFNGR1 knockout unstimulated, 6

value: unstimulated


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-F21


title: MOLM-13, IFNGR1 knock out, unstimulated, clone C4, rep5

description: Library name: MOLM-13 IFNGR1 knockout unstimulated, 5


title: 503_TNYAHXN

description: Library name: lib33360


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-F22


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-E9


title: 502_TNY9R23

description: Library name: lib33359


title: MOLM-13, IFNGR1 knock out, unstimulated, clone A4, rep4

description: Library name: MOLM-13 IFNGR1 knockout unstimulated, 4


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-E22


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-E21


title: 501_TNYA3JC

description: Library name: lib33358


title: MOLM-13, IFNGR1 knock out, unstimulated, clone A5, rep3

description: Library name: MOLM-13 IFNGR1 knockout unstimulated, 3


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-E10


title: MOLM-13, IFNGR1 knock out, unstimulated, clone C4, rep2

description: Library name: MOLM-13 IFNGR1 knockout unstimulated, 2


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-F9


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-D10


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-C9


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-D22


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-D21


title: 498_TNY9CCJ

description: Library name: lib33355


title: 499_TNYA3HH

description: Library name: lib33356


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-C22


title: MOLM-13, IFNGR1 knock out, unstimulated, clone B9, rep1

description: Library name: MOLM-13 IFNGR1 knockout unstimulated, 1


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-G21


title: MOLM-13, wildtype, TNF-alpha and IFN-gamma stimulated, clone B4, rep5

description: Library name: MOLM-13 wildtype TNF-alpha and IFN-gamma stimulated, 5

value: wildtype


title: MOLM-13, wildtype,TNF-alpha and IFN-gamma stimulated, clone B10, rep6

description: Library name: MOLM-13 wildtype TNF-alpha and IFN-gamma stimulated, 6


title: 496_TNY906V

description: Library name: lib33353


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-C10


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-B22


title: 497_TNY6XM7

description: Library name: lib33354


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-C21


title: MOLM-13, wildtype,TNF-alpha and IFN-gamma stimulated, clone C9, rep4

description: Library name: MOLM-13 wildtype TNF-alpha and IFN-gamma stimulated, 4


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-B9


title: 495_TNY8TMA

description: Library name: lib33352


title: MOLM-13, wildtype, TNF-alpha and IFN-gamma stimulated, clone B5, rep3

description: Library name: MOLM-13 wildtype TNF-alpha and IFN-gamma stimulated, 3


title: 500_TNY7PR6

description: Library name: lib33357


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-D9


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-B21


title: MOLM-13, wildtype,TNF-alpha and IFN-gamma stimulated, clone B4, rep2

description: Library name: MOLM-13 wildtype TNF-alpha and IFN-gamma stimulated, 2


title: 494_TNY6XN0

description: Library name: lib33351


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-B10


title: 493_TNY7JCL

description: Library name: lib33350


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-A21


title: MOLM-13, wildtype, TNF-alpha and IFN-gamma stimulated, clone B10, rep1

description: Library name: MOLM-13 wildtype TNF-alpha and IFN-gamma stimulated, 1


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-P8


title: 492_TNY6M3W

description: Library name: lib33349


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-P20


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-P7


title: 490_TNY8NW5

description: Library name: lib33347


title: MOLM-13, wildtype, IFN-gamma stimulated, clone B10, rep6

description: Library name: MOLM-13 wildtype IFN-gamma stimulated, 6


title: 489_TNY7PTL

description: Library name: lib33346


title: MOLM-13, wildtype, IFN-gamma stimulated, clone C9, rep4

description: Library name: MOLM-13 wildtype IFN-gamma stimulated, 4


title: 488_TNY8H7U

description: Library name: lib33345


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-P19


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-O7


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-O8


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-A9


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-O19


title: MOLM-13, wildtype, IFN-gamma stimulated, clone B5, rep3

description: Library name: MOLM-13 wildtype IFN-gamma stimulated, 3


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-N7


title: MOLM-13, wildtype, IFN-gamma stimulated, clone B4, rep2

description: Library name: MOLM-13 wildtype IFN-gamma stimulated, 2


title: 487_TNY6M7H

description: Library name: lib33344


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-N20


title: MOLM-13, wildtype, IFN-gamma stimulated, clone B10, rep1

description: Library name: MOLM-13 wildtype IFN-gamma stimulated, 1


title: 486_TNY878W

description: Library name: lib33343


title: MOLM-13, wildtype, IFN-gamma stimulated, clone B4, rep5

description: Library name: MOLM-13 wildtype IFN-gamma stimulated, 5


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-O20


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-A22


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-F10


title: AMB_201117_9mo_5E_6E_4_P2-5-L10-A10


title: 485_TNY7WHG

description: Library name: lib33342


title: MOLM-13, wildtype, TNF-alpha stimulated, clone B10, rep6

description: Library name: MOLM-13 wildtype TNF-alpha stimulated, 6


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-M8


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-M7


title: 484_TNY5UHX

description: Library name: lib33341


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-N19


title: MOLM-13, wildtype, TNF-alpha stimulated, clone B4, rep5

description: Library name: MOLM-13 wildtype TNF-alpha stimulated, 5


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-M20


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-N8


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-L20


title: MOLM-13, wildtype, TNF-alpha stimulated, clone C9, rep4

description: Library name: MOLM-13 wildtype TNF-alpha stimulated, 4


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-L8


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-L7


title: 481_TNY7WJ7

description: Library name: lib33338


title: MOLM-13, wildtype, TNF-alpha stimulated, clone B5, rep3

description: Library name: MOLM-13 wildtype TNF-alpha stimulated, 3


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-L19


title: 482_TNY5UJX

description: Library name: lib33339


title: 480_TNY6V8P

description: Library name: lib33337


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-K8


title: MOLM-13, wildtype, TNF-alpha stimulated, clone B4, rep2

description: Library name: MOLM-13 wildtype TNF-alpha stimulated, 2


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-K20


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-K19


title: MOLM-13, wildtype, TNF-alpha stimulated, clone B10, rep1

description: Library name: MOLM-13 wildtype TNF-alpha stimulated, 1


title: 478_TNY7WR3

description: Library name: lib33335


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-J8


title: MOLM-13, wildtype, unstimulated, clone B10, rep6

description: Library name: MOLM-13 wildtype unstimulated, 6


title: 479_TNXV7K

description: Library name: lib33336


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-J7


title: 477_TNY054Y

description: Library name: lib33334


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-J20


title: MOLM-13, wildtype, unstimulated, clone B4, rep5

description: Library name: MOLM-13 wildtype unstimulated, 5


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-M19


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-I8


title: 476_TNY5UCH

description: Library name: lib33333


title: 475_TNY44X4

description: Library name: lib33332


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-I7


title: MOLM-13, wildtype, unstimulated, clone C9, rep4

description: Library name: MOLM-13 wildtype unstimulated, 4


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-I20


title: 474_TNYGKP7

description: Library name: lib33331


title: MOLM-13, wildtype, unstimulated, clone B5, rep3

description: Library name: MOLM-13 wildtype unstimulated, 3


title: MOLM-13, wildtype, unstimulated, clone B4, rep2

description: Library name: MOLM-13 wildtype unstimulated, 2


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-H7


title: 473_TNY6963

description: Library name: lib33330


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-K7


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-H20


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-H19


title: HVG-90-IL

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: ct.A_P_9

data_processing:
Fatsq files were aligned to Hg19 using Star aligner via RSEM to obtain estimated raw counts. Those counts were used to get the differential expression using DESeq2 in R.
Assembly: Hg19
Supplementary files format and content: Text file with Raw RSEM estimated counts

molecule: polyA RNA

source_name: Ileum

extract_protocol:
Total RNA was extracted using Rneasy plus  Mini Kit (Qiagen)
Lexogen Quantseq

value: Ileum

value: Organoids


title: 472_TNYHNH8

description: Library name: lib33329


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-G7


title: HVG-89-IL

description: Library name: ct.A_P_8


title: 471_TNYHCY4

description: Library name: lib33328


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-J19


title: 470_TNYCAY1

description: Library name: lib33327


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-F8


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-G19


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-G20


title: HVG-88-IL

description: Library name: ct.A_P_7


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-F7


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-F20


title: HVG-87-IL

description: Library name: ct.A_P_6


title: 469_TNYCC0M

description: Library name: lib33326


title: 468_TNYA3VM

description: Library name: lib33325


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-H8


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-F19


title: HVG-83-IL

description: Library name: ct.A_P_5


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-I19


title: 467_TNYA3TA

description: Library name: lib33324


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-E7


title: MOLM-13, wildtype, unstimulated, clone B10, rep1

description: Library name: MOLM-13 wildtype unstimulated, 1

value: acute myeloid leukemia


title: HVG-75-IL

description: Library name: ct.A_P_4


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-E19


title: 466_TNYC5KX

description: Library name: lib33323


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-E20


title: HVG-73-IL

description: Library name: ct.A_P_3


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-D8


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-G8


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-D7


title: HVG-70-IL

description: Library name: ct.A_P_2


title: 465_TNYC61C

description: Library name: lib33322


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-D19


title: 464_TNY6RU0

description: Library name: lib33321


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-C8


title: HVG-93-IL

description: Library name: ct.A_P_10


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-C20


title: 463_TNY70TK

description: Library name: lib33320


title: HVG-69-IL

description: Library name: ct.A_P_1


title: 462_TNY6UNU

description: Library name: lib33319


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-C19


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-B8


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-C7


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-E8


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-B20


title: 461_TNY88H8

description: Library name: lib33318


title: HVG-91-IL

description: Library name: ct.A_N_5


title: HVG-92-IL

description: Library name: ct.A_N_6


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-B19


title: 460_TNY88CG

description: Library name: lib33317


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-A8


title: HVG-86-IL

description: Library name: ct.A_N_4


title: 459_TNY9A60

description: Library name: lib33316


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-D20


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-A7


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-A20


title: 458_TNY8NLL

description: Library name: lib33315


title: HVG-85-IL

description: Library name: ct.A_N_3


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-A19


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-P6


title: HVG-82-IL

description: Library name: ct.A_N_2


title: 457_TNY8K88

description: Library name: lib33314


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-P5


title: HVG-71-IL

description: Library name: ct.A_N_1


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-P17


title: 456_TNY9NV8

description: Library name: lib33313


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-O5


title: 455_TNY9R05

description: Library name: lib33312


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-O6


title: HVG-81-IL

description: Library name: H.A_P_6


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-P18


title: AMB_201117_9mo_5E_6E_4_P2-4-M9-B7


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-O17


title: HVG-79-IL

description: Library name: H.A_P_5


title: 454_TNY9V0M

description: Library name: lib33311


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-N6


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-O18


title: 453_TNY8TGH

description: Library name: lib33310


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-N5


title: HVG-66-IL

description: Library name: H.A_P_3


title: HVG-77-IL

description: Library name: H.A_P_4


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-M6


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-N18


title: 452_TNY7W75

description: Library name: lib33309


title: HVG-63-IL

description: Library name: H.A_P_2


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-N17


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-M5


title: HVG-50-IL

description: Library name: H.A_P_1


title: 451_TNY6W0L

description: Library name: lib33308


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-M18


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-M17


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-L6


title: HVG-76-IL

description: Library name: H.A_N_7


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-L5


title: 449_TNY6025

description: Library name: lib33306


title: 450_TNY7J81

description: Library name: lib33307


title: 448_TNY07YU

description: Library name: lib33305


title: HVG-74-IL

description: Library name: H.A_N_6


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-L18


title: HVG-72-IL

description: Library name: H.A_N_5


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-L17


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-K5


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-K6


title: 446_TNY5XTY

description: Library name: lib33303


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-J6


title: 447_TNY6066

description: Library name: lib33304


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-J5


title: HVG-61-IL

description: Library name: H.A_N_4


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-I6


title: HVG-60-IL

description: Library name: H.A_N_3


title: HVG-58-IL

description: Library name: H.A_N_1


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-J17


title: HVG-59-IL

description: Library name: H.A_N_2


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-I18


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-I5


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-I17


title: HVG-89-CL

description: Library name: ct.A_P_9

source_name: Colon

value: Colon


title: 444_TNYPP2

description: Library name: lib33301


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-H6


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-K18


title: HVG-87-CL

description: Library name: ct.A_P_7


title: 443_TNY8TTN

description: Library name: lib33300


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-H17


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-G6


title: 442_TNY8TW0

description: Library name: lib33299


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-H5


title: HVG-84-CL

description: Library name: ct.A_P_6


title: 445_TNY89P0

description: Library name: lib33302


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-J18


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-H18


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-K17


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-G18


title: 437_TNY715V

description: Library name: lib33294


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-F18


title: HVG-88-CL

description: Library name: ct.A_P_8


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-F17


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-E5


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-E18


title: HVG-93-CL

description: Library name: ct.A_P_11


title: HVG-75-CL

description: Library name: ct.A_P_4


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-E17


title: HVG-90-CL

description: Library name: ct.A_P_10


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-D6


title: 440_TNY877V

description: Library name: lib33297


title: HVG-69-CL

description: Library name: ct.A_P_1


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-C6


title: HVG-92-CL

description: Library name: ct.A_N_7


title: 432_TNY6ULK

description: Library name: lib33289


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-C5


title: HVG-91-CL

description: Library name: ct.A_N_6


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-C17


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-G5


title: HVG-86-CL

description: Library name: ct.A_N_5


title: 439_TNY695R

description: Library name: lib33296


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-D17


title: 429_TNY5UA5

description: Library name: lib33286


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-C18


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-B18


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-B17


title: HVG-83-CL

description: Library name: ct.A_P_5


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-G17


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-F6


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-A18


title: 438_TNY8GVV

description: Library name: lib33295


title: HVG-71-CL

description: Library name: ct.A_N_2


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-A17


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-P4


title: HVG-67-CL

description: Library name: ct.A_N_1


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-F5


title: HVG-73-CL

description: Library name: ct.A_P_3


title: 441_TNY876T

description: Library name: lib33298


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-E6


title: HVG-70-CL

description: Library name: ct.A_P_2


title: 425_TNYHPAH

description: Library name: lib33282


title: 435_TNZLAG

description: Library name: lib33292


title: 434_TNY0Y19

description: Library name: lib33291


title: 436_TNY5UN4

description: Library name: lib33293


title: 424_TNY7L0T

description: Library name: lib33281


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-D5


title: HVG-77-CL

description: Library name: H.A_P_4


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-O3


title: 433_TNY75V7

description: Library name: lib33290


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-O16


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-D18


title: 431_TNY03NL

description: Library name: lib33288


title: 430_TNY44WJ

description: Library name: lib33287


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-B6


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-B5


title: 422_TNYHG2R

description: Library name: lib33279


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-N4


title: HVG-85-CL

description: Library name: ct.A_N_4


title: 428_TNY6MAM

description: Library name: lib33285


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-N3


title: HVG-82-CL

description: Library name: ct.A_N_3


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-A6


title: AMB_201117_9mo_5E_6E_4_P2-3-L14-A5


title: 427_TNY5UU7

description: Library name: lib33284


title: 420_TNYCY2X

description: Library name: lib33277


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-N15


title: 426_TNYGKN5

description: Library name: lib33283


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-P15


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-P16


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-O4


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-P3


title: HVG-74-CL

description: Library name: H.A_N_6


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-O15


title: HVG-81-CL

description: Library name: H.A_P_5


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-M16


title: 423_TNYGKCW

description: Library name: lib33280


title: HVG-63-CL

description: Library name: H.A_P_2


title: HVG-72-CL

description: Library name: H.A_N_5


title: 421_TNYCU69

description: Library name: lib33278


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-L16


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-N16


title: HVG-61-CL

description: Library name: H.A_N_4


title: HVG-50-CL

description: Library name: H.A_P_1


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-L15


title: HVG-60-CL

description: Library name: H.A_N_3


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-M4


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-K3


title: HVG-66-CL

description: Library name: H.A_P_3


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-K16


title: 415_TNY6RRJ

description: Library name: lib33272


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-L4


title: HVG-58-CL

description: Library name: H.A_N_1


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-K15


title: HVG-76-CL

description: Library name: H.A_N_7


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-J15


title: 412_TNY9TMJ

description: Library name: lib33269


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-I4


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-I3


title: 411_TNY8GHH

description: Library name: lib33268


title: 419_TNYA3R0

description: Library name: lib33276


title: 410_TNYCGHC

description: Library name: lib33267


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-H4


title: F70B-Bn_S15

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

data_processing:
Genome alignment, quality control, and differential gene expression were analyzed using Partek Flow (Partek, St. Louis, MO, USA).
The trimming of raw reads (both ends) was based on a minimum quality score of 20 and a minimum read length of 25.
Contaminants were removed using Bowtie 2 v2.2.5, and the reads were aligned to the human genome (hg38) using STAR 2.7.3 a.
Aligned reads were quantified using RefSeq Transcripts 96. Features (genes) were filtered to retain only those with at least five reads in ≥ 80% of the samples.
Assembly: hg38
Supplementary files format and content: .txt

source_name: Breast

extract_protocol:
Qiagen All Prep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) and MagMAX®FFPE RNA Ultra Kit  (Applied Biosystems®, Foster City, CA, USA)
Illumina TruSeq RNA Exome Library prep kit was used to prepare genomic libraries according to the manufacturer’s protocol, with minor modifications, including increasing RNA input to 300ng, selecting samples with DV200 >30%, reducing the PCR to between 9 cycles, and extending the hybridization time to 16 h.

value: Breast

tag: molecular subtype

tag: biopsy time

value: Baseline

tag: treatment response

value: No Response


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-H3


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-H16


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-M15


title: 418_TNY7WWR

description: Library name: lib33275

value: whole blood

value: male


title: 408_TNY9PCR

description: Library name: lib33265

value: female

value: ATG-GCSF


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-G4


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-L3


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-G3


title: F34-B_S9


title: 416_TNY7LXV

description: Library name: lib33273

value: Placebo


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-K4

value: 9 months


title: F31B-Bn_S10


title: 405_TNY7U24

description: Library name: lib33262


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-F16

value: CP


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-M3

value: M


title: HVG-49-CL

description: Library name: H.A_N_2


title: 417_TNYAKNW

description: Library name: lib33274


title: 414_TNY79C0

description: Library name: lib33271


title: F81-B_S3

value: TNBC


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-J4


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-J3


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-J16


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-F4


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-I16


title: F08B-Bn_S8


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-E3


title: F71B-Tn-C_S2

value: Complete


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-I15


title: 413_TNY79GA

description: Library name: lib33270


title: 409_TNY99CG

description: Library name: lib33266


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-H15


title: 407_TNY9U8M

description: Library name: lib33264


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-G16


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-G15


title: F80-B_S2


title: 406_TNY8V2G

description: Library name: lib33263

value: ATG


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-E16


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-E15


title: F58B-Tn_S2


title: 402_TNY9R5W

description: Library name: lib33259


title: F51B-Bn_S7


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-F3


title: F20B-Bn-C_S13


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-E4


title: 403_TNY8P08

description: Library name: lib33260


title: 404_TNY9Y0R

description: Library name: lib33261


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-F15


title: 400_TNY47C5

description: Library name: lib33257


title: F07B-Tn-C_S3


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-D15


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-C4


title: 315B-Tn-C_S4


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-D3


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-D4


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-C16


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-C15


title: 401_TNY8WX6

description: Library name: lib33258


title: 300B_S6

value: LumA


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-D16


title: 314B-Bn_S9


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-B16


title: 295-B_S8


title: 309B_S5


title: 399_TNY8P07

description: Library name: lib33256


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-C3


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-B4


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-B3


title: 397_TNY8N0A

description: Library name: lib33254


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-B15


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-A4


title: 293BA-C_S15


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-A15


title: 395_TNY8WW8

description: Library name: lib33252


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-A3


title: 394_TNY8RV2

description: Library name: lib33251


title: 275B-A_S6


title: AMB_201117_9mo_5E_6E_4_P2-2-O21-A16


title: 393_TNY8CKP

description: Library name: lib33250


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-P13


title: 307-B_S7


title: 398_TNY7W67

description: Library name: lib33255


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-P2


title: 261B-Bp-C_S15


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-P1


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-O2


title: 392_TNY8R8T

description: Library name: lib33249


title: 260B-Bp-C_S5


title: 391_TNY7WUT

description: Library name: lib33248


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-O14


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-O13


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-O1


title: 390_TNY8RXY

description: Library name: lib33247


title: 396_TNY8606

description: Library name: lib33253


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-N13


title: 388_TNYPMC

description: Library name: lib33245


title: 389_TNY5CGA

description: Library name: lib33246


title: 277B-Bp_S13


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-P14


title: 247B-A_S1


title: 239B-Bn_S1


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-N14


title: 226B-Tn_S12


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-N1


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-N2


title: 387_TNY6K45

description: Library name: lib33244


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-M13


title: 255B-H2_S9


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-M14


title: 219B-Bn_S16


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-L2


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-L14


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-M1


title: 385_TNY4A1L

description: Library name: lib33242


title: 386_TNY5WWP

description: Library name: lib33243


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-L13


title: 213B-H2-C_S5


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-L1


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-K2


title: 208B-Bp_S8


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-M2


title: 384_TNYGYA3

description: Library name: lib33241


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-K14


title: B205_S12


title: 383_TNYCVXH

description: Library name: lib33240


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-K13


title: 200B-Tn-C_S4


title: 382_TNYCY40

description: Library name: lib33239


title: 189B_S12


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-J14


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-J2


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-K1


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-J13


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-I14


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-I2


title: 380_TNY9T2P

description: Library name: lib33237


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-J1


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-I13


title: 188B-Bn-C_S16


title: 187B-Bn_S14


title: 379_TNYAP3R

description: Library name: lib33236


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-I1


title: 175B-Bp-C_S11


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-H2


title: 163B_S11


title: 378_TNYC6WR

description: Library name: lib33235


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-H14


title: 377_TNZLHY

description: Library name: lib33234


title: 160B-A_S11


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-H13


title: 381_TNY9G77

description: Library name: lib33238


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-G2


title: 375_TNY79KK

description: Library name: lib33232


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-H1


title: 376_TNY6U8H

description: Library name: lib33233


title: 146BBp-C_S7


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-G1


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-G13


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-F14


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-F13


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-F2


title: 374_TNY79HM

description: Library name: lib33231


title: 373_TNY6U4J

description: Library name: lib33230


title: 145B-Bp-C_S1


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-E2


title: 372_TNY7M17

description: Library name: lib33229


title: 142B-Bp-C_S2


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-G14


title: 125B-Bn_S10


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-F1


title: B138_S11


title: 371_TNY8GJ6

description: Library name: lib33228


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-E13


title: 155B-Bn-C_S1


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-D2


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-D14


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-E14


title: 369_TNY2HGG

description: Library name: lib33226


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-D13


title: 117B-Bp_S3


title: 368_TNY940Y

description: Library name: lib33225


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-D1


title: 115-B_S7


title: 367_TNY9T54

description: Library name: lib33224


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-C2


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-C13


title: 116BBp-C_S11


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-C14


title: 370_TNY9G9N

description: Library name: lib33227


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-C1


title: 366_TNY9A0K

description: Library name: lib33223


title: 090B-Bn_S6


title: 108-B_S4


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-B13


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-B2


title: 084B-Bn_S10


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-B14


title: 365_TNY8YVX

description: Library name: lib33222


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-E1


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-B1


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-A14


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-A2


title: 363_TNY7TAX

description: Library name: lib33220


title: 066-B_S3


title: 069B_S4


title: 362_TNY4657

description: Library name: lib33219


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-A1


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-P24


title: 058-B_S1


title: 065BBn-C_S9


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-P23


title: 051B-Bn-C_S4


title: AMB_201117_9mo_5E_6E_4_P2-1-J12-A13


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-P12


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-O12


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-O23


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-O24


title: 359_TNY467M

description: Library name: lib33216


title: 361_TNY8RW4

description: Library name: lib33218


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-O11


title: 047B-Bn-C_S3


title: 050B-A_S9


title: 357_TNY7WP6

description: Library name: lib33214


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-N12


title: 364_TNY4JMR

description: Library name: lib33221


title: 358_TNY8KA8

description: Library name: lib33215


title: 018B-Bp-C_S12


title: 356_TNY525V

description: Library name: lib33213


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-N11


title: 014B-Tn_S14


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-P11


title: 360_TNY75LG

description: Library name: lib33217


title: 355_TNY465P

description: Library name: lib33212


title: 354_TNY7TJG

description: Library name: lib33211


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-M23


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-M12


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-M11


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-N24


title: M. abscessus PBS starvation stress, biological replicate 3

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

description: Library name: P_3

data_processing:
Sequenced reads were aligned to M. abscessus genome using bowtie2 v2.3.4.3
Reads counting was performed using FeatureCounts (Annotation of the genome was retrieved from Mycobrowser). For every annotated gene, the number of reads overlapping the gene at least by one nucleotide was calculated. Only unambiguously mapped reads were used. The processed data files represent these counts for each sample.
Assembly: CU458896.1
Supplementary files format and content: csv table, processed files contain raw counts - the numbers of overlapping reads for every annotated gene in each sample

organism: Mycobacteroides abscessus

source_name: Bacterial cell culture

growth_protocol: Starter cultures were initially grown from frozen stocks in Sauton medium, containing: KH2PO4 , 0.5 g; MgS4 ·7H2O, 1.4 g; L-asparagine, 4 g; glycerol, 60 mL; ferric ammonium citrate, 0.05 g; sodium citrate, 2 g; 1% ZnSO4  · 7H2O, 0.1 mL; H2O, to 1 L; pH 7.0 (adjusted with 1 M NaOH) with 10% ADS (0.5% BSA, 0.2% dextrose, 0.085% sodium chloride) and 0.05% Tween-80 (Neofroxx GmbH, Germany) at 37 °C with shaking at 200 rpm for 3-4 days.

extract_protocol:
Bacterial cultures were rapidly cooled on ice, centrifuged, and subjected to disruption with 0.1 mm zirconia beads in a Bead Beater homogenizer (BioSpec Products, Bartlesville, OK, USA) as previously described (Rustad et al., 2009). Total RNA was isolated through phenol-chloroform extraction, treated with Turbo DNase (Life Technologies, Gaithersburg, MD, USA) to remove traces of genomic DNA, purified with the RNeasy Mini Kit (Qiagen, Venlo, The Netherlands).
RNA samples were depleted of 16S and 23S rRNA using NEBNext® rRNA Depletion Kit (Bacteria) (NEB). Sequencing libraries were generated using the resulting ribosomal transcript-depleted RNA and NEBNext Ultra II Directional RNA Library Prep Kit (NEB) according to the manufacturers’ protocol.

treatment_protocol: For induction of dormant non-culturable state in potassium deficient conditions a starter culture was inoculated (0.25%) into potassium-free Sauton media in which K+ ions were equimolarly substituted for Na+ ions (Salina et al., 2014) with addition of 10% ADS and 0.05% Tween-80 and incubated in loose-capped flasks at 37 °C with shaking at 200 rpm for 6-7 weeks. For nutrient deprivation a log-phase culture with OD600=1.5 was washed twice with 10 mM PBS (8.1 mM Na2HPO4, 1.5 mM KH2PO4, 137 mM NaCl and 2.7 mM KCl) containing 0.025% of tyloxapol, diluted to OD600=0.25 in the same buffer with 0.025% of tyloxapol and incubated standing at 37 °C for 6 weeks.

value: Bacterial cell culture

value: PBS


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-L23


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-N23


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-L24


title: 353_TNY6VC7

description: Library name: lib33210


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-L12


title: M. abscessus PBS starvation stress, biological replicate 1

description: Library name: P_1


title: M. abscessus K⁺-induced dormancy, biological replicate 3

description: Library name: D_3

value: potassium (K⁺) deficiency


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-L11


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-K23


title: 352_TNY6V6X

description: Library name: lib33209


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-K12


title: 351_TNY4XH7

description: Library name: lib33208


title: M. abscessus K⁺-induced dormancy, biological replicate 2

description: Library name: D_2


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-M24


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-K11


title: 350_TNY7J3G

description: Library name: lib33207


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-J24


title: M. abscessus K⁺-induced dormancy, biological replicate 1

description: Library name: D_1


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-J11


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-I24


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-I12


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-H12


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-H24


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-I11


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-J23


title: pRS315-FUS(1-163)12E-  GAL4(G4)-distr. - 4h M.SssI - replicate 1

city: Garching

first: Frauke

last: Huth

address: James-Franck Str. 1

department: Department of Biosciences

institute: Technical University Munich

description:
Library name: ASKFG1_240
Rapamycin induced Abf1- Anchor Away with pRS315-FUS(1-163)12E-  GAL4(G4)-distr.., formaldehyde crosslinked and methylated  4h M.SssI - replicate 1

data_processing:
The S.cerevisiae reference genome SacCer3 build R64-1-1 was used for alignment with additional entries representing pUC19-ftz and pFMP233.
Both natural and modified bases were called for Oxford Nanopore sequencing reads, and reads were filtered and demultiplexed with Dorado (version 1.0.0+4a76f8aa, Oxford Nanopore Technologies (ONT) Basecalling Software, (C) Oxford Nanopore Technologies plc.). The resulting reads were mapped to the S. cerevisiae genome (SacCer3 build R64-2-1) with minimap2 (version 2.17), sorted using samtools sort (samtools version 1.9) and indexed with samtools index (samtools version 1.15). Methylation information was added to the bam files using modkit repair (ONT, version 0.1.13). For computational analysis in R (R version 4.2.0. and 4.3.1; tidyverse version 2.0.0.), the methylation probabilities were extracted from bam files using modkit pileup (ONT, version 0.1.13). The modkit pileup output corresponds to the averaged methylation probabilities over all reads per genomic coordinate per sample. The genome average methylation was calculated for each sample by averaging the modkit pileup output for 5mC modifications over all coordinates. As slight batch effects were visible on this level of genome average methylation, we introduced a correction factor which adjusts the average methylation per genomic coordinate such that the overall genomic average methylation is equal to that of the WT.
Assembly: SacCer3 R64-1-1
Supplementary files format and content: The files are tab separated values files containing the information about the fraction of bases modified (avg) or occipied (occ = 1-avg) per genomic coordinate (chr, pos and strand). Additionally, information on the modified base (modbase), the x-fold coverage (cov) as well as the factor used for batch effect correction (factor) is stored.

organism: Saccharomyces cerevisiae

growth_protocol: The Abf1 anchor away strain ABF1-aa-V5 clone A9 was obtained from Wim de Jonge and Frank Holstege (de Jonge et al., Mol Syst Biol. 2020). The strain was transformed with pRS315-based plasmids encoding wildtype Abf1, select Abf1 constructs, or the empty pRS315 plasmid as a control. At least three independent clones were isolated and stored as glycerol cultures after transformation and used for biologically independent replicate experiments. Anchor away strains were grown to log phase, ca. OD600 of 0.4, in YNB –leucine media.

extract_protocol:
Chromatin was prepared from formaldehyde-crosslinked yeast cultures as described by Oberbeckmann et al. (Genome Res., 2019). Chromatin corresponding to 0.1 g wet cell pellet was washed in cold Kladde Buffer (20 mM HEPES-NaOH pH 7.5, 70 mM NaCl, 0.25 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0, 0.5% (v/v) glycerol), resuspended in 870 µl of Kladde Buffer and incubated with 4000 units M.SssI methyltransferase at 25 °C. After 90 min, 4000 units M.SssI were added, together with plasmid pUC19-ftz, which was included as spike-in control. After 180 min, one 430 µl aliquot was removed, and plasmid pFMP233 (Lieleg et al., Mol. Cell. Biol., 2015) was added to the remaining aliquot as a second spike-in control. The reaction was further incubated for 60 min (240 min total) at 25 °C. A similar degree of CpG methylation after 180 vs. 240 min in combination with ongoing CpG methylation as probed by methylation of the spike-in plasmids indicated saturated CpG methylation. After DNA methylation, the reaction was stopped by the addition of 1/10 volume 10x Stop Buffer. The resulting DNA was purified by proteinase K digestion, phenolization, ethanol precipitation, and then resuspended in TE Buffer.
Nanopore sequencing libraries were prepared and sequenced on a PromethION by the Laboratory for Functional Genomics (LaFuGa), Gene Center, LMU Munich.

treatment_protocol: The strains were incubated for 75 min with 8 µg/mL rapamycin.

value: ABF1-aa-V5 clone A9


title: 349_TNY4YV4

description: Library name: lib33206


title: M. abscessus PBS starvation stress, biological replicate 2

description: Library name: P_2


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-G23


title: 348_TNY4YWT

description: Library name: lib33205


title: pRS315-Gal4(768-881) shuffle 1 - 4h M.SssI - replicate 2

description:
Library name: ASKGS2_240
Rapamycin induced Abf1- Anchor Away with pRS315-Gal4(768-881) shuffle 1, formaldehyde crosslinked and methylated  4h M.SssI - replicate 2


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-J12


title: M. abscessus active growth, biological replicate 3

description: Library name: A_3


title: M. abscessus active growth, biological replicate 2

description: Library name: A_2


title: 346_TNY03MR

description: Library name: lib33203


title: 343_TNYH4AM

description: Library name: lib33200


title: 347_TNY4JKJ

description: Library name: lib33204


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-K24


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-I23


title: M. abscessus active growth, biological replicate 1

description: Library name: A_1


title: pRS315-FUS(1-163)12E-  GAL4(G4)-distr. - 4h M.SssI - replicate 2

description:
Library name: ASKFG2_240
Rapamycin induced Abf1- Anchor Away with pRS315-FUS(1-163)12E-  GAL4(G4)-distr.., formaldehyde crosslinked and methylated  4h M.SssI - replicate 2


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-H23


title: 345_TNY677P

description: Library name: lib33202


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-G11


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-H11


title: 344_TNYJ106

description: Library name: lib33201


title: pRS315-FUS(1-163)12E-  GAL4(G4)-distr. - 3h M.SssI - replicate 2

description:
Library name: ASKFG2_180
Rapamycin induced Abf1- Anchor Away with pRS315-FUS(1-163)12E-  GAL4(G4)-distr.., formaldehyde crosslinked and methylated  3h M.SssI - replicate 2


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-F23


title: 342_TNYGW8L

description: Library name: lib33199


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-G24


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-F11


title: pRS315-Gal4(768-881) shuffle 1 - 3h M.SssI - replicate 2

description:
Library name: ASKGS2_180
Rapamycin induced Abf1- Anchor Away with pRS315-Gal4(768-881) shuffle 1, formaldehyde crosslinked and methylated 3h M.SssI - replicate 2


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-E24


title: 339_TNY8K57

description: Library name: lib33196


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-F24


title: 341_TNYC5M8

description: Library name: lib33198


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-F12


title: pRS315-Gal4(768-881) shuffle 1 - 3h M.SssI - replicate 1

description:
Library name: ASKGS1_180
Rapamycin induced Abf1- Anchor Away with pRS315-Gal4(768-881) shuffle 1, formaldehyde crosslinked and methylated 3h M.SssI - replicate 1


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-E23


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-G12


title: pRS315-FUS(1-163)12E aromatic clusters -  3h M.SssI - replicate 2

description:
Library name: ASK471_180
Rapamycin induced Abf1- Anchor Away with pRS315-FUS(1-163)12E aromatic clusters, formaldehyde crosslinked and methylated  3h M.SssI - replicate 2


title: 340_TNY9GJJ

description: Library name: lib33197


title: pRS315-FUS(1-163)12E-  GAL4(G4)-distr. - 3h M.SssI - replicate 1

description:
Library name: ASKFG1_180
Rapamycin induced Abf1- Anchor Away with pRS315-FUS(1-163)12E-  GAL4(G4)-distr.., formaldehyde crosslinked and methylated  3h M.SssI - replicate 1


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-E12


title: pRS315-Gal4(768-881) shuffle 1 - 4h M.SssI - replicate 1

description:
Library name: ASKGS1_240
Rapamycin induced Abf1- Anchor Away with pRS315-Gal4(768-881) shuffle 1, formaldehyde crosslinked and methylated  4h M.SssI - replicate 1


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-D23


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-E11


title: 337_TNVBJT

description: Library name: lib33194


title: 338_TNYG5LH

description: Library name: lib33195


title: pRS315-FUS(1-163)12E aromatic clusters clusters - 4h M.SssI - replicate 2

description:
Library name: ASK471_240
Rapamycin induced Abf1- Anchor Away with pRS315-FUS(1-163)12E aromatic clusters clusters, formaldehyde crosslinked and methylated  4h M.SssI - replicate 2


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-D12


title: pRS315-FUS(1-163)12E aromatic clusters - 4h M.SssI - replicate 1

description:
Library name: ASK470_240
Rapamycin induced Abf1- Anchor Away with pRS315-FUS(1-163)12E aromatic clusters, formaldehyde crosslinked and methylated  4h M.SssI - replicate 1


title: pRS315-FUS(1-163)12E aromatic clusters - 3h M.SssI - replicate 1

description:
Library name: ASK470_180
Rapamycin induced Abf1- Anchor Away with pRS315-FUS(1-163)12E aromatic clusters, formaldehyde crosslinked and methylated 3h M.SssI - replicate 1


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-D11


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-C24


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-C23


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-C12


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-C11


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-B23


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-B24


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-D24


title: 334_TNY87J6

description: Library name: lib33191


title: 333_TNY93YA

description: Library name: lib33190


title: pRS315-EM Shuffle - 3h M.SssI - replicate 1

description:
Library name: ASK468_180
Rapamycin induced Abf1- Anchor Away with pRS315-EM Shuffle, formaldehyde crosslinked and methylated  3h M.SssI - replicate 1


title: pRS315-EM Shuffle - 3h M.SssI - replicate 2

description:
Library name: ASK469_180
Rapamycin induced Abf1- Anchor Away with pRS315-EM Shuffle, formaldehyde crosslinked and methylated  3h M.SssI - replicate 2


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-B12


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-A24


title: pRS315-EM Shuffle - 4h M.SssI - replicate 2

description:
Library name: ASK469_240
Rapamycin induced Abf1- Anchor Away with pRS315-EM Shuffle, formaldehyde crosslinked and methylated  4h M.SssI - replicate 2


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-A12


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-A23


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-B11


title: 330_TNY0Y1Y

description: Library name: lib33187


title: AMB_201117_9mo_5E_6E_4_P1-6-M6-A11


title: 332_TNY6PR6

description: Library name: lib33189


title: pRS315-EM Shuffle - 4h M.SssI - replicate 1

description:
Library name: ASK468_240
Rapamycin induced Abf1- Anchor Away with pRS315-EM Shuffle, formaldehyde crosslinked and methylated  4h M.SssI - replicate 1


title: 331_TNY0414

description: Library name: lib33188


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-P9


title: 335_TNYA96C

description: Library name: lib33192


title: 336_TNY9GG6

description: Library name: lib33193


title: pRS315 - no Abf1 - 4h M.SssI - replicate 2

description:
Library name: ASK461_240
Rapamycin induced Abf1- Anchor Away with pRS315 - no Abf1, formaldehyde crosslinked and methylated  4h M.SssI - replicate 2


title: 329_TNY829K

description: Library name: lib33186


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-P22


title: 328_TNYA3LP

description: Library name: lib33185


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-O9


title: pRS315 - no Abf1 - 3h M.SssI -replicate 2

description:
Library name: ASK461_180
Rapamycin induced Abf1- Anchor Away with pRS315 - no Abf1, formaldehyde crosslinked and methylated  3h M.SssI -replicate 2


title: pRS315 - no Abf1 - 4h M.SssI - replicate 1

description:
Library name: ASK460_240
Rapamycin induced Abf1- Anchor Away with pRS315 - no Abf1, formaldehyde crosslinked and methylated  4h M.SssI - replicate 1


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-O22


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-O21


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-N9


title: 326_TNY8TAY

description: Library name: lib33183


title: pRS315-WT Abf1 - 4h M.SssI - replicate 1

description:
Library name: ASK459_240
Rapamycin induced Abf1- Anchor Away with pRS315-Abf1, formaldehyde crosslinked and methylated 4h M.SssI - replicate 1


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-N22


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-N21


title: 325_TNY9AVV

description: Library name: lib33182


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-N10


title: 324_TNY8NNJ

description: Library name: lib33181


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-M22


title: 323_TNY9957

description: Library name: lib33180


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-M9


title: pRS315-FUS(1-163)12E - 3h M.SssI - replicate 2

description:
Library name: ASK458_180
Rapamycin induced Abf1- Anchor Away with pRS315-FUS(1-163)12E, formaldehyde crosslinked and methylated  3h M.SssI - replicate 2


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-M21


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-M10


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-P21


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-L21


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-L9


title: 322_TNY8TG8

description: Library name: lib33179


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-L22


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-P10


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-O10


title: pRS315-WT Abf1 - 3h M.SssI - replicate 2

description:
Library name: ASK455_180
Rapamycin induced Abf1- Anchor Away with pRS315-Abf1, formaldehyde crosslinked and methylated  3h M.SssI - replicate 2


title: 327_TNY9NV4

description: Library name: lib33184


title: pRS315 - no Abf1 - 3h M.SssI - replicate 1

description:
Library name: ASK460_180
Rapamycin induced Abf1- Anchor Away with pRS315 - no Abf1, formaldehyde crosslinked and methylated 3h M.SssI - replicate 1


title: 321_TNY9WJC

description: Library name: lib33178


title: pRS315-WT Abf1 - 4h M.SssI - replicate 2

description:
Library name: ASK455_240
Rapamycin induced Abf1- Anchor Away with pRS315-Abf1, formaldehyde crosslinked and methylated 4h M.SssI - replicate 2


title: 320_TNY6MHJ

description: Library name: lib33177


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-K9


title: pRS315-FUS(1-163)12E - 4h M.SssI - replicate 1

description:
Library name: ASK454_240
Rapamycin induced Abf1- Anchor Away with pRS315-FUS(1-163)12E , formaldehyde crosslinked and methylated  4h M.SssI - replicate 1


title: 319_TNY080L

description: Library name: lib33176


title: pRS315-FUS(1-163)12E - 4h M.SssI - replicate 2

description:
Library name: ASK458_240
Rapamycin induced Abf1- Anchor Away with pRS315-FUS(1-163)12E, formaldehyde crosslinked and methylated  4h M.SssI - replicate 2


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-K22


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-K21


title: pRS315-FUS(1-163)12E - 3h M.SssI - replicate 1

description:
Library name: ASK454_180
Rapamycin induced Abf1- Anchor Away with pRS315-FUS(1-163)12E, formaldehyde crosslinked and methylated 3h M.SssI - replicate 1


title: pRS315-WT Abf1 - 3h M.SssI - replicate 1

description:
Library name: ASK459_180
Rapamycin induced Abf1- Anchor Away with pRS315-Abf1, formaldehyde crosslinked and methylated  3h M.SssI replicate 1


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-K10


title: 318_TNY59KL

description: Library name: lib33175


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-J22


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-J9


title: 317_TNY876R

description: Library name: lib33174


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-J21


title: M. Myotis VSV-infected nasal epithelial cells smallRNA-seq replicate 2

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

country: France

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

description: Library name: MM_VSV2_1

data_processing:
Raw reads were pre-cleanned by the sequencing platform, including adapter, contaminant and low-quality removal (Phred+33). Before alignment, redundant sequences were collapsed to one copy using fastq_collapser from FASTX-Toolkit 0.0.14 and a read-size filter was applied (18-35 bp). HEK293T and M. myotis short reads were then respectively aligned to human genome assembly GRCh38 and M. myotis genome mMyoMyo1.p. Mapping was performed using Bowtie 1.3.1 with parameters ‘-v 1 -a --best --strata’. Unmapped reads were next separately aligned against virus genomes SINV-GFP and VSV-GFP using the following parameters ‘-v 2 -y -m 30 -a --best --strata’. siRNA signature was finally research on 22nt mapped reads by the python tool signature (Antonieski, 2014) with 22 22 1 22 options.
Assembly: GRCh38/hg38 ; mMyoMyo1.p ; FJ478454.1
Supplementary files format and content: Read counts after mapping on different genomes.

organism: Myotis myotis

source_name: Nasal epithelial cell

growth_protocol: All cells were maintened in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from cell lysates using Trizol Reagent (15586018, InVitrogen) to which 200 µl of chloroform was added before centrifugation for 15 minutes at 12,000 xg at 4°C. For small RNA extraction, supernatants were collected and nucleic acids were precipitated in 3 volumes of 100% ethanol + 10% 1M sodium acetate for 30 minutes at -80°C. RNA was pelleted for 10 min at 12,000 xg at 4°C then washed with 70% ethanol and reconstituted in RNase free water.
Samples were shipped to BGI for library preparation. Sequencing was realized on DNBSEQ technology, for 50bp single-end reads and standard output of 20 million reads per sample.

value: Nasal epithelial cell

tag: infection

value: VSV-GFP


title: M. Myotis VSV-infected nasal epithelial cells smallRNA-seq replicate 1

description: Library name: MM_VSV1_1


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-J10


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-L10


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-I9


title: M. Myotis SINV-infected nasal epithelial cells smallRNA-seq replicate 2

description: Library name: MM_SINV2_1

value: SINV-GFP


title: 316_TNY8789

description: Library name: lib33173

value: whole blood

value: male


title: 315_TNY69JR

description: Library name: lib33172

value: Placebo


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-I21

value: 9 months


title: M. Myotis SINV-infected nasal epithelial cells smallRNA-seq replicate 1

description: Library name: MM_SINV1_1


title: 314_TNY698H

description: Library name: lib33171


title: M. Myotis mock nasal epithelial cells smallRNA-seq replicate 2

description: Library name: MM_m2_1

value: mock


title: M. Myotis mock nasal epithelial cells smallRNA-seq replicate 1

description: Library name: MM_m1_1


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-H10

value: CP

value: M


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-I10


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-H9


title: 312_TNY0Y34

description: Library name: lib33169

value: female


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-H22


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-G21


title: 313_TNY7WMU

description: Library name: lib33170


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-G22


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-F9


title: Methylation, skeletalmuscle-control5

type: genomic

city: Budapest

first: Zsolt

last: Radák

address: Budapest, Alkotás u. 42-48, 1123

department: Research Center for Molecular Exercise Science

country: Hungary

institute: University of sports science, Hungary

description: Column name in M_matrix.csv: 208706080071_R05C02

hyb_protocol: Illumina

scan_protocol: 200 ng DNA bisulfite-converted (EZ DNA Methylation Kit, Zymo); processed on Illumina Mouse Methylation BeadChip (MM285) per Infinium workflow; scanned on Illumina iScan System.

data_processing:
Raw IDAT imported to R (≥4.3) with minfi; detection p computed; keep probes with >80% samples p<0.01.
Background/dye-bias normalization: preprocessNoob; export β (0–1) and M (logit(β)) values.
Probe annotation: IlluminaMouseMethylation Manifest 12.v1 (mm10); CpG-island context and UCSC feature assigned.
array annotation IlluminaMouseMethylationanno.12.v1.mm10
M_matrix.csv;rows: CpG probe IDs; columns: samples; values: M
beta_matrix.csv;rows: CpG probe IDs; columns: samples; values: β

label: cy3, cy5

source_name: gastrocnemius muscle

label_protocol: Illumina

growth_protocol: Male BALB/c mice (~2 months) were housed in a temperature- and humidity-controlled room on a 12:12 h light–dark cycle with ad libitum access to chow and water. After 1-week acclimation, animals were randomized to intervention groups.

extract_protocol: ~20–30 mg gastrocnemius; DNA extracted with Genomic DNA Mini Kit (Tissue),Geneaid.

treatment_protocol: Mice were randomized into five groups for 6 weeks: Control (PBS i.p.), Lactate (sodium L-lactate 500 mg/kg i.p), HIIT (treadmill intervals with individualized intensity), MCT1/2 inhibitor (AR-C155858 i.p. before sessions), and HIIT + inhibitor. Gastrocnemius muscle was harvested 48 h after the final session.

value: gastrocnemius muscle

tag: Sex

value: skeletal muscle tissue

value: BALB/c

value: PBS injection


title: 311_TNY0428

description: Library name: lib33168

value: ATG-GCSF


title: Methylation, skeletalmuscle-control4

description: Column name in M_matrix.csv: 208706080071_R04C02

tag: cell type


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-F22


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-G10


title: 310_TNY6W0X

description: Library name: lib33167

value: ATG


title: Methylation, skeletalmuscle-control3

description: Column name in M_matrix.csv: 208706080071_R03C02


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-F21


title: Methylation, skeletalmuscle-control2

description: Column name in M_matrix.csv: 208706080071_R02C02


title: 309_TNY3JLU

description: Library name: lib33166


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-I22


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-F10


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-H21


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-E9


title: Methylation, skeletalmuscle-control1

description: Column name in M_matrix.csv: 208706080071_R01C02


title: Methylation, skeletalmuscle-hiitmct5

description: Column name in M_matrix.csv: 208706080071_R05C01

value: HIIT+MCT1/2 inhibitor


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-E22


title: 307_TNY7WPM

description: Library name: lib33164


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-G9


title: 305_TNY7J4R

description: Library name: lib33162


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-E10


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-D21


title: 304_TNY4YUM

description: Library name: lib33161


title: Methylation, skeletalmuscle-hiitmct4

description: Column name in M_matrix.csv: 208706080071_R04C01


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-D22


title: 306_TNY526K

description: Library name: lib33163


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-C22


title: Methylation, skeletalmuscle-hiitmct3

description: Column name in M_matrix.csv: 208706080071_R03C01


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-C9


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-D10


title: Methylation, skeletalmuscle-hiitmct2

description: Column name in M_matrix.csv: 208706080071_R02C01


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-C21


title: Methylation, skeletalmuscle-hiit6

description: Column name in M_matrix.csv: 209204190023_R06C02

value: HIIT


title: 308_TNY6V9V

description: Library name: lib33165


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-C10


title: 303_TNY7UYP

description: Library name: lib33160


title: Methylation, skeletalmuscle-hiitmct1

description: Column name in M_matrix.csv: 208706080071_R01C01


title: 302_TNYGKGM

description: Library name: lib33159


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-B9


title: Methylation, skeletalmuscle-hiit5

description: Column name in M_matrix.csv: 209204190023_R05C02


title: 301_TNYCUG5

description: Library name: lib33158


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-E21


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-B21


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-B22


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-B10


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-A9


title: 300_TNYA3X8

description: Library name: lib33157


title: Methylation, skeletalmuscle-hiit4

description: Column name in M_matrix.csv: 209204190023_R04C02


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-D9


title: 299_TNY8K7L

description: Library name: lib33156


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-A21


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-A22


title: Methylation, skeletalmuscle-hiit3

description: Column name in M_matrix.csv: 209204190023_R03C02


title: AMB_201117_9mo_5E_6E_4_P1-5-D5-A10


title: Methylation, skeletalmuscle-hiit2

description: Column name in M_matrix.csv: 209204190023_R02C02


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-P7


title: 297_TNY8K27

description: Library name: lib33154


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-P8


title: Methylation, skeletalmuscle-hiit1

description: Column name in M_matrix.csv: 209204190023_R01C02


title: 298_TNYCJN9

description: Library name: lib33155


title: 296_TNYAKPU

description: Library name: lib33153


title: Methylation, skeletalmuscle-lactate5

description: Column name in M_matrix.csv: 209204190023_R05C01

value: Lactate administration


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-O8


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-O7


title: Methylation, skeletalmuscle-lactate6

description: Column name in M_matrix.csv: 209204190023_R06C01


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-O20


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-P19


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-O19


title: Methylation, skeletalmuscle-lactate4

description: Column name in M_matrix.csv: 209204190023_R04C01


title: 294_TNY6MXM

description: Library name: lib33151

value: whole blood


title: 293_TNY9VYJ

description: Library name: lib33150


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-N20


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-N19


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-N8


title: Methylation, skeletalmuscle-lactate3

description: Column name in M_matrix.csv: 209204190023_R03C01

value: male


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-N7


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-M8


title: 291_TNY9R4C

description: Library name: lib33148


title: 292_TNY8MLJ

description: Library name: lib33149


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-P20


title: Methylation, skeletalmuscle-lactate2

description: Column name in M_matrix.csv: 209204190023_R02C01


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-M7


title: Methylation, skeletalmuscle-mct6

description: Column name in M_matrix.csv: 208706080078_R06C02

value: MCT1/2 inhibitor


title: Methylation, skeletalmuscle-lactate1

description: Column name in M_matrix.csv: 209204190023_R01C01


title: 290_TNY82WP

description: Library name: lib33147


title: 289_TNY6MJA

description: Library name: lib33146


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-L8

value: 9 months


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-M19


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-M20


title: 295_TNYAKL3

description: Library name: lib33152


title: Methylation, skeletalmuscle-mct5

description: Column name in M_matrix.csv: 208706080078_R05C02


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-L7


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-L20


title: Methylation, skeletalmuscle-mct4

description: Column name in M_matrix.csv: 208706080078_R04C02


title: 286_TNY0TJK

description: Library name: lib33143


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-K7


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-K20


title: 287_TNY7JAM

description: Library name: lib33144


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-K19


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-J8


title: Methylation, skeletalmuscle-mct1

description: Column name in M_matrix.csv: 208706080078_R01C02


title: 288_TNY3560

description: Library name: lib33145


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-J20


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-L19


title: Methylation, skeletalmuscle-mct3

description: Column name in M_matrix.csv: 208706080078_R03C02


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-K8


title: Methylation, skeletalmuscle-mct2

description: Column name in M_matrix.csv: 208706080078_R02C02


title: 285_TNY6W33

description: Library name: lib33142

value: Placebo


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-J19

value: CP


title: 284_TNY6W36

description: Library name: lib33141


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-I20

value: M


title: 283_TNY55JL

description: Library name: lib33140

value: female


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-I8


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-I7


title: MDC_P4_H1, hS32, time point D25

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

description: Library name: P3361_RNA_21

data_processing:
Reads were aligned to human genome GRCh38 p7 using the STAR aligner (Dobin et al., 2013), v. 2.7.3a using the GENCODE annotation v. 25. Gene counts were obtained from featureCounts (Liao et al., 2014) from the Subread package, v. 2.0.3. Differential gene expression analysis was performed with the R package DESeq2 (Love et al., 2014), v. 1.38 using the custom seasnap pipeline (https://github.com/bihealth/seasnap-pipeline). All p-values obtained in differential gene expression analysis and gene set enrichment analysis were corrected for false discovery rate (FDR) using the Benjamini-Hochberg procedure (Benjamini and Hochberg, 2018). For the purpose of visualization and principal component analysis, reads were normalized using the regularized logarithm transformation as implemented in the DESeq2 rlog function.
Assembly: GRCh38 p7
Supplementary files format and content: Tab separated values (TSV) file containing raw counts as calculated with featureCounts

growth_protocol: Neural progenitor cells (NPCs) were derived from the BIHi005-A hiPSC line and the H1 hESC line. For primary expansion, 6-well plates were coated with Geltrex (Thermo Fisher, A1413302). Geltrex was initially diluted 1:10 in ice- cold KnockOut DMEM/F-12 (Thermo Fisher, 12660012) to create a stock solution, which was then further diluted 1:11 in ice-cold KnockOut DMEM/F-12. Plates were coated with 1 ml per well and incubated at room temperature for 1 hour. NPCs were thawed and washed in KnockOut DMEM/F-12 supplemented with 10 µM ROCK inhibitor Y-27632 (STEMCELL Technologies, 72304). Cells were then resuspended in Neural Expansion Medium (NEM), consisting of a 50:50 mixture of Advanced DMEM/F-12 (Thermo Fisher, 12634-010) and Neurobasal Medium (Thermo Fisher, 21103-049), with 1:50 Neural Induction Supplement (Thermo Fisher, A1647701) and 1:100 Penicillin- Streptomycin (Thermo Fisher, 15140-122), containing 10 µM ROCK inhibitor. Cells were seeded at a density of 5 × 10⁵ cells per well in 6-well plates. Cell counting was performed using a Neubauer counting chamber, counting 4 × 16 squares. Medium was changed daily without ROCK inhibitor until the NPCs reached confluence. NPCs were expanded and passaged twice before initiating differentiation. For differentiation, 7.5 × 10⁵ NPCs were seeded into Geltrex-coated wells of a 6-well plate. The differentiation medium consisted of a 50:50 mixture of Neurobasal Medium and DMEM/F-12 with Glutamax supplement (Thermo Fisher, 31331-028), with 1:200 N2 Supplement, 1:100 B27 Supplement, 1% Penicillin-Streptomycin, 250 µM dibutyryl cyclic AMP (db-cAMP), 150 µM ascorbic acid, 20 ng/ml brain-derived neurotrophic factor (BDNF), 20 ng/ml glial cell line- derived neurotrophic factor (GDNF), and 2 mM Glutamax. Medium was changed every two days. On day 15, cells were replated onto Geltrex-coated 6 well plates at same density. On day 25, cells were replated on 8-well chamber slides (Nunc Lab-Tek II Chamber Slide System, ThermoScientific, 177402PK). The slides were first coated with poly-DL-ornithine hydrobromide (POR) (Merck, P8638-25mg) diluted in 0.15 mM borate buffer to a final concentration of 0.05 µg/µl, followed by a second coating with laminin (Merck, L2020) diluted in H₂O to a final concentration of 2 µg/cm². Cells were seeded at a density of 0.5 × 10⁵ cells per well. All OGD and immunofluorescence experiments were performed using neuronal cultures grown on 8-well chamber slides. Cultures were maintained in an incubator under a controlled atmosphere at 37°C, 100% humidity, and 5% CO₂ until the day of the experiment.

extract_protocol:
Total RNA was isolated from  on differentiation days 15, 25, and 40 using TRIzol™ Reagent (Thermo Fisher Scientific). Following DNase digestion with Promega RQ1 RNase-Free DNase (M6101), RNA was purified using a phenol-chloroform extraction protocol, and RNA concentration was measured with a NanoDrop spectrophotometer.
Sequencing libraries were prepared according to the NEBNext Ultra II RNA Poly(A) Workflow which included the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490), NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L), NEBNext Sample Purification Beads, and NEBNext Multiplex Oligos for Illumina (Set 4, E6443). Each library was generated with an input of 400 ng total RNA per sample. Paired-end RNA libraries were sequenced on the NovaSeq X Plus platform (Illumina) in PE100 mode with a loading concentration of 200 pM. Sequencing was conducted by the Core Facility Genomics at the Berlin Institute of Health (BIH).

treatment_protocol: untreated, 10 ng/ml hS3 continuously treated, and 20 ng/ml hS3 continuously treated hiPSC- and hESC-derived neuronal cultures

tag: cell line

tag: time point


title: MDC_P4_H1, hS32, time point D40

description: Library name: P3361_RNA_22


title: MDC_P4_H1, hS32, time point D15

description: Library name: P3361_RNA_20


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-H8

tag: age


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-I19

tag: strain


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-H7


title: 282_TNY8MXG

description: Library name: lib33139

tag: tissue


title: 281_TNY8MX5

description: Library name: lib33138


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-J7

tag: brain region


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-H20

tag: gender


title: MDC_P4_H1, hS31, time point D40

description: Library name: P3361_RNA_19

tag: treatment


title: MDC_P4_H1, hS31, time point D25

description: Library name: P3361_RNA_18


title: 279_TNY8RWX

description: Library name: lib33136

tag: donor id


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-G19


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-G20


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-G7


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-H19


title: 280_TNY8ULA

description: Library name: lib33137

tag: visit


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-G8


title: 277_TNY715G

description: Library name: lib33134

tag: group


title: MDC_P4_H1, hS31, time point D15

description: Library name: P3361_RNA_17


title: 278_TNY8RVJ

description: Library name: lib33135


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-F7


title: MDC_P4_H1, untreated, time point D25

description: Library name: P3361_RNA_15

value: untreated


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-E7


title: 275_TNY6M66

description: Library name: lib33132


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-E8


title: 274_TNY040C

description: Library name: lib33131


title: MDC_P4_H1, untreated, time point D15

description: Library name: P3361_RNA_14


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-E20


title: BIH005_A, hS32, time point D40

description: Library name: P3361_RNA_13


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-E19


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-D8


title: BIH005_A, hS32, time point D25

description: Library name: P3361_RNA_12


title: MDC_P4_H1, untreated, time point D40

description: Library name: P3361_RNA_16


title: 273_TNY0Y0W

description: Library name: lib33130


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-D7


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-F8


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-F20


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-D20


title: 276_TNY6Y72

description: Library name: lib33133


title: BIH005_A, hS31, time point D40

description: Library name: P3361_RNA_10


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-C20


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-C8


title: 270_TNY7UHT

description: Library name: lib33127


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-C7


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-B8


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-F19


title: BIH005_A, hS32, time point D15

description: Library name: P3361_RNA_11


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-B7


title: 269_TNY5UH0

description: Library name: lib33126


title: BIH005_A, untreated, time point D40

description: Library name: P3361_RNA_07


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-B19


title: 268_TNY7L8J

description: Library name: lib33125


title: 271_TNY7WJ5

description: Library name: lib33128


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-A8


title: BIH005_A, untreated, time point D25

description: Library name: P3361_RNA_06


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-A7


title: 272_TNY3JMX

description: Library name: lib33129


title: 267_TNY79A0

description: Library name: lib33124


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-D19


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-A20


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-A19


title: 266_TNY7763

description: Library name: lib33123


title: BIH005_A, hS31, time point D25

description: Library name: P3361_RNA_09


title: BIH005_A, untreated, time point D15

description: Library name: P3361_RNA_05


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-C19


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-P6


title: MDC_P4_H1, untreated, time point NPC

description: Library name: P3361_RNA_03

value: NPC


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-P18


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-P5


title: BIH005_A, hS31, time point D15

description: Library name: P3361_RNA_08


title: 264_TNY65X0

description: Library name: lib33121


title: 263_TNY663T

description: Library name: lib33120


title: Superb-seq, 293FT K562 U2OS, benchmarking, 10k cells, rep2

first: Graham

last: McVicker

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

description:
Library name: SCRNA_04
Three sets of paired-end FASTQ files, one per sequencing run. Two on Illumina NovaSeq X Plus, one on Element AVITI.

data_processing:
Split-pipe was used to pre-process, align, and annotate reads using default settings. Input FASTQ files, output BAM file.
Sheriff was used to process aligned reads into edit and gene counts. Input BAM file, output count matrices and summary tables.
Assembly: hg38
Supplementary files format and content: Tab-separated text files of edit counts, gene counts, and metadata

growth_protocol: Suspension cells (K562) were grown in RPMI-1640. Adherent cells (293FT, U2OS) were grown in DMEM, dissociated with TrypLE. All cell cultures were supplemented with 10% heat-inactivated FBS and penicillin/streptomycin, and incubated at 37°C, 5% CO2.

extract_protocol:
After in situ transcription, cells were immediately washed and processed into scRNA-seq cDNA by Evercode WT Mini v2 or v3 kit (Parse Biosciences). Barcoded cDNA was extracted from fixed cells by SPRI beads according to kit instructions.
Superb-seq libraries were prepared by Evercode WT Mini v2 or v3 kit (Parse Biosciences).

treatment_protocol: Cells were edited by electroporation with Cas9-guide ribonucleoprotein (RNP) and Superb-seq T7 promoter. Pools of unedited (electroporation only) or edited cells were fixed by Evercode Cell Fixation kit (Parse Biosciences) and subjected to overnight in situ transcription.

value: Pooled + IST


title: BIH005_A, untreated, time point NPC

description: Library name: P3361_RNA_01


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-P17


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-O5


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-O18


title: 265_TNY03LG

description: Library name: lib33122


title: AMB_201117_9mo_5E_6E_4_P1-4-C17-B20


title: 262_TNY65Y3

description: Library name: lib33119


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-O6


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-N6


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-O17


title: 261_TNYH6HU

description: Library name: lib33118


title: Superb-seq, 293FT K562 U2OS, benchmarking, 10k cells, rep1

description:
Library name: SCRNA_03
Three sets of paired-end FASTQ files, one per sequencing run. Two on Illumina NovaSeq X Plus, one on Element AVITI.


title: WSU-FSCCL IgG1 W375* replicate 3

city: London

first: Pavel

last: Tolar

address: Institute of Immunity and Transplantation, Rowland Hill St

country: United Kingdom

institute: University College London

description: Library name: WSUFSCCL_IgG1_W375*_3

data_processing:
Data were processed by Novogene Novomagic. Raw reads were filtered to remove reads containing adapters or reads of low quality (containing undetermined nucleotides or Qphred <= 5 bases accounting for more than 50% of the entire read length). Reads were mapped to the reference genome using the HISAT2. Gene counts were extracted and gene expression levels were estimated by calculating the number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM).
Assembly: GRCh38
Supplementary files format and content: Excel spreadsheet containing raw read counts and FPKM values of the individual samples

source_name: B Lymphoma

growth_protocol: Cells were cultured in RPMI (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1X MEM non-essential amino acids (Gibco), 1X GlutaMAX (Gibco), 50µM 2-mercaptoethanol (Sigma Aldrich), 100U/ml penicillin and 100µg/ml streptomycin and maintained at 37°C in humidified incubators with 5% CO2. The cell lines were authenticated by STR and tested mycoplasma-free.

extract_protocol:
RNA was isolated from 5x106 cells by Novogene using QIAGEN Rneasy
Library was constructed by Novogene using mRNA library preparation (poly A enrichment)

treatment_protocol: Stable WSU-FSCCL cells expressing Cas9 were established. The WSU-FSCCL Cas9 cells were lentivirally transduced with a dual-targeting sgRNA lentiGuide-mCherry construct  targeting IgM and IgG1 switch regions. mCherry+ IgM+ or mCherry+ IgG+ cells were sorted by flow cytometry. IGHG1 mutation W375* was introduced into IgG1+ cells by prime editing and cells were cultured for 15 weeks during which W375* cells overgrew WT cells (>77%). NU-DHL1 cells were nucleofected with Cas9/sgRNA complexes targeting the IgM and IgG1 switch regions. IgM+ or  IgG+ cells were sorted by flow cytometry. IGHG1 mutation W375* was introduced into IgG1+ cells by prime editing and cells were cultured for 15 weeks during which W375* cells overgrew WT cells (>95%).

value: B Lymphoma

value: WSU-FSCCL

value: Class-switching induced by CRISPR/Cas9 targeting of IgM and IgG1 immunoglobulin switch regions

value: Flow sorting for cells expressing surface IgG1


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-N5


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-N18


title: WSU-FSCCL IgG1 W375* replicate 2

description: Library name: WSUFSCCL_IgG1_W375*_2


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-N17


title: 260_TNYA3XL

description: Library name: lib33117

value: ATG


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-M5


title: WSU-FSCCL IgG1 W375* replicate 1

description: Library name: WSUFSCCL_IgG1_W375*_1


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-M6


title: WSU-FSCCL IgG1 WT replicate 2

description: Library name: WSUFSCCL_IgG1_WT_2


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-M18


title: 259_TNY9T1K

description: Library name: lib33116

value: ATG-GCSF


title: 258_TNYCUJ7

description: Library name: lib33115

value: whole blood


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-L6


title: 257_TNY5CAR

description: Library name: lib33114


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-M17


title: 256_TNY8K24

description: Library name: lib33113


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-K6


title: WSU-FSCCL IgG1 WT replicate 1

description: Library name: WSUFSCCL_IgG1_WT_1


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-L18


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-L17


title: NU-DHL1 IgG1 W375* replicate 2

description: Library name: NUDHL1_IgG1_W375*_2


title: NU-DHL1 IgG1 W375* replicate 3

description: Library name: NUDHL1_IgG1_W375*_3


title: NU-DHL1 IgG1 W375* replicate 1

description: Library name: NUDHL1_IgG1_W375*_1


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-K17


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-K5


title: 255_TNY88VH

description: Library name: lib33112


title: 254_TNYA3K8

description: Library name: lib33111

value: male


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-J6


title: NU-DHL1 IgG1 WT replicate 3

description: Library name: NUDHL1_IgG1_WT_3


title: 253_TNY6PT0

description: Library name: lib33110


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-J5


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-I6


title: AMB_201117_9mo_5E_6E_4_P1-3-B21-J18