title: SEM_LIN28B_3

city: Oxford

first: Rebecca

last: Ling

state: Select

address: MRC WIMM

department: Paediatrics

country: United Kingdom

institute: University of Oxford

description:
Library name: Sample 27
KD3

data_processing:
SeqNado pipeline (https://github.com/alsmith151/SeqNado)
Assess read quality with the fastQC package
Perform trimming using Trim Galore
Map trimmed reads to the human genome assembly(hg38) using STAR
Assembly: hg38
Supplementary files format and content: fastq

source_name: SEM

extract_protocol:
RNA extraction was performed using a RNeasy Micro Kit (Qiagen).
RNA extraction (SEM cell and fetal liver) Library preparation and sequencing were performed using using the Ultra II Directional RNA Library Prep Kit (NEB, E7765). RNA libraries were sequenced by paired-end sequencing using a 150-cycle high output kit on a Nextseq 500 (Illumina). Adult bone marrow library preparation using small cell number modified SMARTseq 2 protocol.

treatment_protocol: SEM and Fetal liver cells had lentiviral transduction with control or LIN28B KD.

value: SEM

value: LIN28B KD

value: Lentiviral transduction


title: SEM_LIN28B_2

status: Public on Jun 16 2026

type: SRA

description:
Library name: Sample 26
KD2

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: genotype

tag: treatment

tag: batch


title: PE3_VEGFA3_48h_293_500k_PEI_mock_rep1

city: Shanghai

first: Zhu

last: Ming

address: No. 500, Dongchuan Road

country: China

institute: East China Normal University

description: Library name: PE3_VEGFA3_48h_293_500k_PEI_mock_rep1

library_source: genomic

data_processing:
Tracking-seq/2: Data were analyzed using Offtracker (https://github.com/Lan-lab/offtracker)
GUIDE-seq-2: Data were analyzed using guideseq (https://github.com/tsailabSJ/guideseq)
Assembly: hg38
Supplementary files format and content: BigWig of genome-editing signals

molecule: genomic DNA

extract_protocol:
Tracking-seq/2: Cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2 antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA. GUIDE-seq-2 were performed according to doi: 10.1101/2025.02.10.637517
Tracking-seq/2: The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit.GUIDE-seq-2 libraries were constructed according to doi: 10.1101/2025.02.10.637517


title: Muscle, ID ELMIH030, After_exercise, Group 2

city: Amsterdam

first: Georges

last: Janssens

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

description: Library name: Sample_62

data_processing:
Analysis for read mapping was performed in R v4.1.0 and Bioconductor v3.13. Reads were subjected to quality control FastQC v0.11.15 and trimmed using Trimmomatic v0.36 and aligned using HISAT2 v2.1.0 to the GRCh38 (v94) human genome reference assembly. Counts were obtained using HTSeq (v0.11.0, default parameters) using the corresponding GTF taking into account the directions of the reads. Statistical analyses were performed using the edgeR v3.34.1 and limma/voom v 3.48.344 R packages. All genes with more than 2 counts in at least 4 of the samples were kept. Count data were transformed to log2-counts per million (logCPM), normalized by applying the trimmed mean of M-values method and precision weighted using voom. Genes were reannotated using the Ensembl genome database (v104) and the biomaRt package.
Assembly: GRCh38 (v94)
Supplementary files format and content: Count data, 93 human muscle samples with annotation of 58735 Ensembl Gene IDs

source_name: Muscle

extract_protocol:
Human muscle tissues were homogenized with a 5 mm steel bead using a TissueLyser II (QIAGEN) for 5 min at frequency of 30 times/second. RNA was extracted according to the instructions of the RNaesy Mini Kit (QIAGEN). Contaminating genomic DNA was removed using RNase-Free DNase (QIAGEN). RNA was quantified with a NanoDrop 2000 spectrophotometer (Thermo Scientific; Breda, The Netherlands) and stored at -80°C until use.
RNA libraries were prepared and sequenced with the Illumina platform by Genome Scan (Leiden, The Netherlands). The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp). Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used. NovaSeq control software NCS v1.6 was used.

tag: tissue

value: Muscle


title: SEM_LIN28B_1

description:
Library name: Sample 25
KD1


title: PE3_VEGFA2_48h_293_500k_PEI_T7_rep3

description: Library name: PE3_VEGFA2_48h_293_500k_PEI_T7_rep3


title: Muscle, ID ELMIH039, Before_exercise, Group 2

description: Library name: Sample_61


title: SEM_Ctrl_3

description:
Library name: Sample 24
EV3

value: Ctrl


title: PE3_VEGFA2_48h_293_500k_PEI_T5_rep3

description: Library name: PE3_VEGFA2_48h_293_500k_PEI_T5_rep3


title: SEM_Ctrl_1

description:
Library name: Sample 22
EV1


title: Xeno_4_LIN28Blow

description:
Library name: Sample 21
Xeno4_LIN28Blow

source_name: Xenograft

value: Xenograft

value: CRISPRedited fetal CD34+


title: Muscle, ID ELMIH138, Before_exercise, Group 1

description: Library name: Sample_59


title: PE3_VEGFA2_48h_293_500k_PEI_mock_rep3

description: Library name: PE3_VEGFA2_48h_293_500k_PEI_mock_rep3


title: Xeno_2_LIN28Bhi

description:
Library name: Sample 19
Xeno2_LIN28Bhi


title: PE3_HEK4_48h_293_500k_PEI_T7_rep3

description: Library name: PE3_HEK4_48h_293_500k_PEI_T7_rep3


title: Xeno_1_LIN28Bhi

description:
Library name: Sample 18
Xeno1_LIN28Bhi


title: Muscle, ID ELMIH100, Before_exercise, Group 1

description: Library name: Sample_58


title: FL_CD34_L28BKD_3

description:
Library name: Sample 17
18039-KD

source_name: Human fetal liver

value: Human fetal liver

tag: cell type


title: FL_CD34_L28BKD_2

description:
Library name: Sample 16
17818-KD


title: PE3_HEK4_48h_293_500k_PEI_T7_rep2

description: Library name: PE3_HEK4_48h_293_500k_PEI_T7_rep2


title: Muscle, ID ELMIH133, After_exercise, Group 4

description: Library name: Sample_57


title: FL_CD34_L28BKD_1

description:
Library name: Sample 15
14707-KD


title: FL_CD34_Ctrl_3

description:
Library name: Sample 14
18039-EV


title: Muscle, ID ELMIH014, After_exercise, Group 4

description: Library name: Sample_56


title: FL_CD34_Ctrl_2

description:
Library name: Sample 13
17818-EV


title: FL_CD34_Ctrl_1

description:
Library name: Sample 12
14707-EV


title: PE3_HEK4_48h_293_500k_PEI_T5_rep2

description: Library name: PE3_HEK4_48h_293_500k_PEI_T5_rep2


title: Muscle, ID ELMIH107, Before_exercise, Group 4

description: Library name: Sample_55


title: ABM_LMPP_5

description:
Library name: Sample 11
692ABM_LMPP4

source_name: Adult bone marrow

value: Adult bone marrow

value: LMPP

value: wt


title: PE3_HEK4_48h_293_500k_PEI_mock_rep3

description: Library name: PE3_HEK4_48h_293_500k_PEI_mock_rep3


title: Muscle, ID ELMIH010, Before_exercise, Group 4

description: Library name: Sample_54


title: ABM_LMPP_3

description:
Library name: Sample 9
016ABM_LMPP3


title: PE3_HEK4_48h_293_500k_PEI_mock_rep2

description: Library name: PE3_HEK4_48h_293_500k_PEI_mock_rep2


title: ABM_LMPP_4

description:
Library name: Sample 10
016ABM_LMPP5


title: ABM_LMPP_2

description:
Library name: Sample 8
014ABM_LMPP2


title: Hippocampus, 3h, NMEC, rep2

city: Tianjin

first: zhiyue

last: Wu

address: No. 288 Nanjing Road, Heping District, Tianjin, China

institute: Institute of Hematology & Blood Diseases Hospital

description:
Library name: Sample 8
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v7.0.1. (https://www.10xgenomics.com/support/software/cell-ranger/)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
scRNA-seq was performed with cortex and hippocampus cells from18-day-old C57BL/6N mice. Single-cell dissociation was performed following published protocols with modifications. 1× 107 CFU of NMEC WT strain in 100 μL sterile PBS were injected intravenously in which doses bacteria develop a high level of bacteremia followed by bacterial traversal of the BBB mimicking the pathogenesis of human meningitis. Three or six hours later, mice were transcardially perfused using ice cold Hank’s balanced salt solution (HBSS) and the brains were quickly dissected and placed on ice. Single cell suspensions were performed as previously described. Briefly, brains in ice cold HBSS were minced using a scalpel and then Dounce homogenized 15-20 times each with the loose and tight pestles while simultaneously rotating the pestle. Cell suspension was then passed through pre-wet 70 mm filter, and spun down at 300 g for 5 min in a centrifuge set to 4℃.
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, single cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Escherichia coli (NMEC) infection in mice

value: Hippocampus

value: WT

value: infected, NMEC, 3h


title: ABM_LMPP_1

description:
Library name: Sample 7
014ABM_LMPP1


description: Library name: HiFicas9_VEGFA2_48h_293_500k_PEI_T5-KU-60648_rep3


title: ABM_MPP_3

description:
Library name: Sample 6
692ABMMPP

value: MPP


title: Muscle, ID ELMIH080, Before_exercise, Group 3

description: Library name: Sample_52


title: ABM_MPP_2

description:
Library name: Sample 5
016ABMMPP


description: Library name: HiFicas9_VEGFA2_48h_293_500k_PEI_T5-KU-60648_rep2


title: Muscle, ID ELMIH041, After_exercise, Group 2

description: Library name: Sample_51


title: ABM_HSC_3

description:
Library name: Sample 3
692ABMHSC

value: HSC


title: ABM_HSC_2

description:
Library name: Sample 2
016ABMHSC


description: Library name: HiFicas9_VEGFA2_48h_293_500k_PEI_T5-KU-60648_rep1


title: Muscle, ID ELMIH049, Before_exercise, Group 2

description: Library name: Sample_50


title: ABM_HSC_1

description:
Library name: Sample 1
014ABMHSC


description: Library name: HiFicas9_VEGFA2_48h_293_500k_PEI_mock_rep3


title: SEM_LIN28B_RIP_3

description:
Library name: LIN28BRIP3_bio_rep_3
LIN28BRIP3

data_processing:
SeqNado pipeline (https://github.com/alsmith151/SeqNado)
Assess read quality with the fastQC package
Perform trimming using Trim Galore
Map trimmed reads to the human genome assembly(hg38) using STAR
Assembly: hg38
Supplementary files format and content: feature_counts_RIPseq_LIN28B.tsv

source_name: B-ALL cell line

extract_protocol:
RIPseq performed using RNA cleanup
RNA extraction (SEM cell and fetal liver) Library preparation and sequencing were performed using using the Ultra II Directional RNA Library Prep Kit (NEB, E7765). RNA libraries were sequenced by paired-end sequencing using a 150-cycle high output kit on a Nextseq 500 (Illumina). Adult bone marrow library preparation using small cell number modified SMARTseq 2 protocol.

treatment_protocol: SEM cells with RIPseq with immunoprecipitation with either LIN28B or IgG

value: B-ALL cell line

value: B-ALL

value: LIN28B immunoprecipitation


title: Muscle, ID ELMIH106, After_exercise, Group 1

description: Library name: Sample_49


title: SEM_LIN28B_RIP_2

description:
Library name: LIN28BRIP2_biol_rep_2
LIN28BRIP2

value: SEM


title: Muscle, ID ELMIH062, Before_exercise, Group 1

description: Library name: Sample_48

value: Muscle


description: Library name: HiFicas9_VEGFA2_48h_293_500k_PEI_mock_rep2


title: SEM_LIN28B_RIP_1

description:
Library name: LIN28BRIP1_biol_rep_1
LIN28BRIP1


title: SEM_IGG_RIP_2

description:
Library name: IGGRIP3_bio_rep_2
IGGRIP3

value: IgG immunoprecipitation


title: SEM_IGG_RIP_1

description:
Library name: IGGRIP_biol_rep_1
IGGRIP2


title: Muscle, ID ELMIH130, After_exercise, Group 4

description: Library name: Sample_47


title: 30711-015

city: Madrid

first: Eva

last: P. Cuevas

state: Madrid

address: Ramiro de Maeztu 9

department: Biomedicine

country: Spain

institute: CIB-CSIC

description:
Library name: 15
NextSeq (Illumina Inc.) sequencing instrument

data_processing:
All primary analysis is carried out using CLC Genomics Server 21.0.4.
The workflow “QIAseq miRNA Quantification” of CLC Genomics Server with standard parameters is used to map the reads to miRBase version 22. length < 15 nt or length > 55 nt. They are then deduplicated using their UMI. Reads are grouped into UMI groups when they (1) start at the same position based on the end of the read to which the UMI is ligated (i.e., Read2 for paired data), (2) are from the same strand, and (3) have identical UMIs.
Groups that contain only one read (singletons) are merged into non-singleton groups if the singleton’s UMI can be converted to a UMI of a non-singleton group by introducing an SNP (the biggest group is chosen).
Assembly: All reads that don’t map to miRBase, neither with perfect matches nor as isomiRs (maximum 2 mismatches and/or alternative start/end position of 2 nt), are mapped to the human genome GRCh38 with ENSEMBL GRCh38 version 97 annotation. This is carried out using the “RNA-Seq Analysis” workflow of CLC Genomics Server with standard parameters.
Supplementary files format and content: Raw Expression Values of miRNAs and piRNAs

source_name: cell line

growth_protocol: The cells were cultured in suspension in RPMI 1640 medium (1x106 cells/mL) supplemented with 1% penicillin/ streptomycin and 10% (v/v) fetal bovine serum (FBS) in T flasks held upright at 37 °C in a humidified 5 % CO2 atmosphere.

extract_protocol:
RNA was isolated from approximately 2 million cells using the miRNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions with an elution volume of 40 μl.
The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN). A total of 100 ng total RNA was converted into miRNA NGS libraries. After adapter ligation, UMIs were introduced in the reverse transcription step. The cDNA was amplified using PCR (16 cycles) and during the PCR indices were added. After PCR the samples were purified. Library preparation was quality controlled using capillary electrophoresis (Tape D1000). Based on quality of the inserts and the concentration measurements, the libraries were pooled in equimolar ratios. The library pool(s) were quantified using qPCR. The library pool(s) were then sequenced on a NextSeq (Illumina Inc.) sequencing instrument according to the manufacturer instructions (1x75, 1x6). Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq2 software (Illumina inc.).
The library pool(s) were quantified using qPCR. The library pool(s) were then sequenced on a NextSeq (Illumina Inc.) sequencing instrument according to the manufacturer instructions (1x75, 1x6). Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq2 software (Illumina inc.).

value: cell line

value: Immortalized lymphocytes

value: SOD1 ALS


description: Library name: HiFicas9_HEK4_48h_293_500k_PEI_T5-KU-60648_rep3


title: 30711-014

description:
Library name: 14
NextSeq (Illumina Inc.) sequencing instrument


title: Muscle, ID ELMIH018, After_exercise, Group 4

description: Library name: Sample_46


title: 30711-013

description:
Library name: 13
NextSeq (Illumina Inc.) sequencing instrument


description: Library name: HiFicas9_HEK4_48h_293_500k_PEI_T5-KU-60648_rep2


title: 30711-012

description:
Library name: 12
NextSeq (Illumina Inc.) sequencing instrument


title: Muscle, ID ELMIH133, Before_exercise, Group 4

description: Library name: Sample_45


title: 30711-011

description:
Library name: 11
NextSeq (Illumina Inc.) sequencing instrument


title: 30711-010

description:
Library name: 10
NextSeq (Illumina Inc.) sequencing instrument

value: Sporadic ALS


title: Muscle, ID ELMIH014, Before_exercise, Group 4

description: Library name: Sample_44


description: Library name: HiFicas9_HEK4_48h_293_500k_PEI_mock_rep3


title: 30711-008

description:
Library name: 8
NextSeq (Illumina Inc.) sequencing instrument


title: Muscle, ID ELMIH076, After_exercise, Group 3

description: Library name: Sample_43


title: ABM_MPP_1

description:
Library name: Sample 4
014ABMMPP

value: Adult bone marrow


title: 30711-007

description:
Library name: 7
NextSeq (Illumina Inc.) sequencing instrument


description: Library name: HiFicas9_HEK4_48h_293_500k_PEI_mock_rep2


title: 30711-006

description:
Library name: 6
NextSeq (Illumina Inc.) sequencing instrument


title: Muscle, ID ELMIH039, After_exercise, Group 2

description: Library name: Sample_42


title: 30711-005

description:
Library name: 5
NextSeq (Illumina Inc.) sequencing instrument

value: Control


title: 30711-004

description:
Library name: 4
NextSeq (Illumina Inc.) sequencing instrument


description: Library name: HiFicas9_HEK4_48h_293_500k_PEI_mock_rep1


title: Muscle, ID ELMIH131, Before_exercise, Group 2

description: Library name: Sample_41


title: 30711-003

description:
Library name: 3
NextSeq (Illumina Inc.) sequencing instrument


title: CBE_VEGFA2_24h_293_500k_PEI_T7_rep3

description: Library name: CBE_VEGFA2_24h_293_500k_PEI_T7_rep3


title: 30711-002

description:
Library name: 2
NextSeq (Illumina Inc.) sequencing instrument


title: 30711-001

description:
Library name: 1
NextSeq (Illumina Inc.) sequencing instrument


title: Muscle, ID ELMIH138, After_exercise, Group 1

description: Library name: Sample_40


description: Library name: HiFicas9_VEGFA2_48h_293_500k_PEI_mock_rep1


title: CBE_VEGFA2_24h_293_500k_PEI_T5_rep3

description: Library name: CBE_VEGFA2_24h_293_500k_PEI_T5_rep3


title: NB-1_L3KO_DOX+_H2AK119ub

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

data_processing:
Short reads were trimmed by trimmomatic (v0.39) .
Reads were mapped by bowtie2 (v2.2.5)
Duplicated reads were removed by MarkDuplicates of Picard tools (v2.18.29).
Peak call were performed by hiddenDomains (v3.1) for with default parameters.
Bigwig files were generated using deepTools (v3.5.1) bamCompare command with the following arguments (--binsize 200 --scaleFactors).
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: Human neuroblastoma cell line NGP and NB-1 were cultured in RPMI1640 (Wako) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 μg/ml penicillin/streptomycin (Sigma–Aldrich) in an incubator with humidified air at 37 °C with 5% CO2.

extract_protocol:
ChIP assays were performed as previous papers (Orlando V et al., 1997, Methods, Fujimura Y et al., 2006, Development). Cross-linked chromatin prepared from the indicated cells was precipitated by each antibodies.
NEBNext Ultra II DNA Library Kit for Illumina (NEB) was used to generate libraries from samples. All procedures were performed according to the protocols suggested by the manufacturers. The concentration of libraries was measured by Qubit 2.0 Fluorometer with Qubit dsDNA HS Assay Kit (Invitrogen).

treatment_protocol: Doxycycline (DOX) was added to cells in culture and collected after 8 days. The efficiency of DOX-inducible knockout was evaluated by western blot.

value: neuroblastoma cell line

value: DOX


title: Muscle, ID ELMIH053, After_exercise, Group 1

description: Library name: Sample_39


title: NB-1_L3KO_DOX-_H2AK119ub

value: control


title: CBE_VEGFA2_24h_293_500k_PEI_mock_rep3

description: Library name: CBE_VEGFA2_24h_293_500k_PEI_mock_rep3


title: Muscle, ID ELMIH054, Before_exercise, Group 1

description: Library name: Sample_38


title: NB-1_L3KO_DOX-_MYCN


title: CBE_HEK4_24h_293_500k_PEI_T7_rep3

description: Library name: CBE_HEK4_24h_293_500k_PEI_T7_rep3


title: NB-1_L3KO_DOX+_MYCN


title: Muscle, ID ELMIH032, Before_exercise, Group 2

description: Library name: Sample_70


title: Muscle, ID ELMIH120, After_exercise, Group 4

description: Library name: Sample_37


description: Library name: HiFicas9_HEK4_48h_293_500k_PEI_T5-KU-60648_rep1


title: NB-1_L3KO_DOX-_PCGF6


title: CBE_HEK4_24h_293_500k_PEI_T7_rep2

description: Library name: CBE_HEK4_24h_293_500k_PEI_T7_rep2


title: Muscle, ID ELMIH026, After_exercise, Group 2

description: Library name: Sample_67


title: NGP_L3KO_DOX+_H2AK119ub

source_name: NGP

value: NGP


title: PE3_VEGFA3_48h_293_500k_PEI_T5_rep3

description: Library name: PE3_VEGFA3_48h_293_500k_PEI_T5_rep3


title: 30711-009

description:
Library name: 9
NextSeq (Illumina Inc.) sequencing instrument


title: Muscle, ID ELMIH107, After_exercise, Group 4

description: Library name: Sample_36


title: Hippocampus, 3h, NMEC, rep1

description:
Library name: Sample 7
10x Genomics

value: Hippocampus

value: WT

value: infected, NMEC, 3h


title: Isocortex, 3h, NMEC, rep2

description:
Library name: Sample 6
10x Genomics

source_name: Isocortex

value: Isocortex


title: NGP_L3KO_DOX-_H2AK119ub


title: CBE_HEK4_24h_293_500k_PEI_T5_rep3

description: Library name: CBE_HEK4_24h_293_500k_PEI_T5_rep3


title: Muscle, ID ELMIH071, Before_exercise, Group 4

description: Library name: Sample_35


title: NGP_L3KO_DOX+_MYCN


title: CBE_HEK4_24h_293_500k_PEI_T5_rep2

description: Library name: CBE_HEK4_24h_293_500k_PEI_T5_rep2


title: Isocortex, 6h, PBS, rep2

description:
Library name: Sample 2
10x Genomics

value: infected, PBS, 6h


title: NGP_L3KO_DOX-_MYCN


title: NGP_L3KO_DOX+_PCGF6


title: NGP_L3KO_DOX-_PCGF6


title: Muscle, ID ELMIH027, Before_exercise, Group 4

description: Library name: Sample_34

value: Muscle


title: CBE_HEK4_24h_293_500k_PEI_mock_rep3

description: Library name: CBE_HEK4_24h_293_500k_PEI_mock_rep3


title: Muscle, ID ELMIH076, Before_exercise, Group 3

description: Library name: Sample_33


title: NGP_H2AK119ub

growth_protocol: Human neuroblastoma cell line NGP was cultured in RPMI1640 (Wako) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 μg/ml penicillin/streptomycin (Sigma–Aldrich) in an incubator with humidified air at 37 °C with 5% CO2.

treatment_protocol: Without treatment

value: Without


title: NGP_input (for H2AK119ub)


title: CBE_HEK4_24h_293_500k_PEI_mock_rep2

description: Library name: CBE_HEK4_24h_293_500k_PEI_mock_rep2


title: Muscle, ID ELMIH007, After_exercise, Group 2

description: Library name: Sample_32


title: NGP_RING1B


title: NGP_L3MBTL2


title: SEM_Ctrl_2

description:
Library name: Sample 23
EV2

value: SEM

value: Ctrl

value: Lentiviral transduction


title: CBE_EMX1_24h_293_500k_PEI_T5_rep3

description: Library name: CBE_EMX1_24h_293_500k_PEI_T5_rep3


title: NGP_input


title: Muscle, ID ELMIH099, After_exercise, Group 1

description: Library name: Sample_30


title: CBE_EMX1_24h_293_500k_PEI_T5_rep2

description: Library name: CBE_EMX1_24h_293_500k_PEI_T5_rep2


title: T. gondii cMUT, actinomycin D, biological replicate 3

city: Cambridge

first: Sebastian

last: Lourido

state: Massachusetts

address: 455 Main Street Room 661G

department: Biology

country: USA

institute: Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology

description:
Library name: cMUT_ActD_REP3
Column cMUT_ActD_REP3 in Processed_Data.csv

data_processing:
Reads were trimmed using Cutadapt (v4.8) with standard Illumina TruSeq adapter sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC for R1; AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT for R2) and a minimum read length of 43 bp.
Trimmed reads were aligned to the Toxoplasma gondii GT1 genome (ToxoDB release 68) using STAR (v2.7.1a) with --quantMode GeneCounts, --outSAMtype BAM SortedByCoordinate, and --limitOutSJcollapsed 5000000.
Differential expression analysis was performed in R using DESeq2. Log2 fold change estimates were computed using the apeglm shrinkage method and adjusted p-values were calculated using the Wald test.
Genes were considered differentially expressed at |log2 fold change| ≥ 0.5, adjusted p-value ≤ 0.05.
Assembly: ToxoDB-68_TgondiiGT1 (Toxoplasma gondii GT1, ToxoDB release 68)
Supplementary files format and content: Processed_Data.csv: csv-delimited file containing raw read counts for each sample (one column per sample, one row per gene). Gene IDs follow ToxoDB GT1 annotation.

organism: Toxoplasma gondii

source_name: tachyzoite

growth_protocol: cWT and cMUT parasites were infected onto confluent HFF monolayers in T12.5 flasks and grown for 18 h at ambient oxygen conditions.

extract_protocol:
RNA was harvested by adding 400 uL TRIzol directly to each flask. Total RNA was extracted by two sequential rounds of TRIzol/chloroform:isoamyl alcohol (24:1) phase separation, collecting the aqueous phase each time. RNA was precipitated with isopropanol, washed twice with 70% ethanol, and resuspended in RNase-free water. RNA concentration was measured using a NanoDrop spectrophotometer.
Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit with poly(A) mRNA Magnetic Isolation (NEB). Paired-end sequencing (75 x 75 bp) was performed on an Element Biosciences AVITI platform.

treatment_protocol: Parasites were treated with actinomycin D (5 ug/mL in DMSO) or vehicle (DMSO) for 4 h. Intracellular parasites were washed once with PBS.

value: tachyzoite

value: cMUT (delta-TgPRO)

value: actinomycin D (5 ug/mL, 4 h)


title: NB-1_L3KO_DOX+_PCGF6

value: neuroblastoma cell line


title: NGP_PCGF6


title: Muscle, ID ELMIH026, Before_exercise, Group 2

description: Library name: Sample_31


title: Muscle, ID ELMIH012, Before_exercise, Group 2

description: Library name: Sample_60


title: CBE_EMX1_24h_293_500k_PEI_T5_rep1

description: Library name: CBE_EMX1_24h_293_500k_PEI_T5_rep1


title: T. gondii cWT, actinomycin D, biological replicate 3

description:
Library name: cWT_ActD_REP3
Column cWT_ActD_REP3 in Processed_Data.csv

value: cWT


title: T. gondii cMUT, DMSO vehicle, biological replicate 3

description:
Library name: cMUT_vehicle_REP3
Column cMUT_vehicle_REP3 in Processed_Data.csv

value: DMSO (vehicle)


title: Xeno_3_LIN28Blow

description:
Library name: Sample 20
Xeno3_LIN28Blow

value: Xenograft

value: CRISPRedited fetal CD34+


title: Muscle, ID ELMIH116, Before_exercise, Group 1

description: Library name: Sample_29


title: T. gondii cWT, DMSO vehicle, biological replicate 3

description:
Library name: cWT_vehicle_REP3
Column cWT_vehicle_REP3 in Processed_Data.csv


title: Muscle, ID ELMIH004, After_exercise, Group 4

description: Library name: Sample_28


title: CBE_EMX1_24h_293_500k_PEI_mock_rep3

description: Library name: CBE_EMX1_24h_293_500k_PEI_mock_rep3


title: T. gondii cMUT, actinomycin D, biological replicate 2

description:
Library name: cMUT_ActD_REP2
Column cMUT_ActD_REP2 in Processed_Data.csv


title: T. gondii cWT, actinomycin D, biological replicate 2

description:
Library name: cWT_ActD_REP2
Column cWT_ActD_REP2 in Processed_Data.csv


title: Muscle, ID ELMIH010, After_exercise, Group 4

description: Library name: Sample_27


title: CBE_EMX1_24h_293_500k_PEI_mock_rep2

description: Library name: CBE_EMX1_24h_293_500k_PEI_mock_rep2


title: T. gondii cMUT, DMSO vehicle, biological replicate 2

description:
Library name: cMUT_vehicle_REP2
Column cMUT_vehicle_REP2 in Processed_Data.csv


title: CBE_EMX1_24h_293_500k_PEI_mock_rep1

description: Library name: CBE_EMX1_24h_293_500k_PEI_mock_rep1


title: T. gondii cWT, DMSO vehicle, biological replicate 2

description:
Library name: cWT_vehicle_REP2
Column cWT_vehicle_REP2 in Processed_Data.csv


title: T. gondii cMUT, actinomycin D, biological replicate 1

description:
Library name: cMUT_ActD_REP1
Column cMUT_ActD_REP1 in Processed_Data.csv


title: Muscle, ID ELMIH001, Before_exercise, Group 4

description: Library name: Sample_26


title: T. gondii cWT, actinomycin D, biological replicate 1

description:
Library name: cWT_ActD_REP1
Column cWT_ActD_REP1 in Processed_Data.csv


title: T. gondii cMUT, DMSO vehicle, biological replicate 1

description:
Library name: cMUT_vehicle_REP1
Column cMUT_vehicle_REP1 in Processed_Data.csv


description: Library name: Cas9_VEGFA3_48h_293_500k_PEI_T5-KU-60648_rep3


title: PE3_HEK4_48h_293_500k_PEI_T5_rep3

description: Library name: PE3_HEK4_48h_293_500k_PEI_T5_rep3


title: T. gondii cWT, DMSO vehicle, biological replicate 1

description:
Library name: cWT_vehicle_REP1
Column cWT_vehicle_REP1 in Processed_Data.csv


title: Muscle, ID ELMIH021, After_exercise, Group 3

description: Library name: Sample_25


description: Library name: Cas9_VEGFA3_48h_293_500k_PEI_T5-KU-60648_rep2


title: Muscle, ID ELMIH033, After_exercise, Group 2

description: Library name: Sample_24


title: Skin_K14creVsirfl/fl_UV3hrs_rep4

city: LEBANON

first: SLADJANA

last: SKOPELJA-GARDNER

address: ONE MEDICAL CENTER DR

institute: DARTMOUTH COLLEGE

description:
Library name: 188364_16_S31
Column name in featurecounts.readcounts.ann_1.tsv: 647_Kcre_UV3H
featurecounts.readcounts.ann_1.tsv

data_processing:
Reads were trimmed using Cutadapt v4.6  (Bulk RNA)
Reads were aligned GRCm38 using hisat2 version 2.1.0 (Bulk RNA)
Reads were quantified using featurecounts (subread) version 2.0.1 (Bulk RNA)
Assembly: GRCm38.97 (Bulk RNA)
Supplementary files format and content: TSV file containing counts matrix (raw counts for bulk RNA)

source_name: Skin

growth_protocol: 12-week old female mice were used.

extract_protocol:
Total RNA from skin was isolated using the RNeasy Fibrous Tissue kit (Qiagen). cDNA was reverse transcribed using the iScript cDNA synthesis kit (Bio-rad) and quantitative PCR performed with iTaq Universal SYBR Green Supermix (Bio-rad). For single cell RNA: Formalin fixed paraffin embedded (FFPE) skin tissues blocks were prepared for the 10x Genomics Flex assay following demonstrated manufacturer’s protocol CG000606. For each block, 4 x 25um sections were placed into C tubes, deparaffinized with xylene, rehydrated with progressive dilutions of ethanol and dissociated in Liberase TM solution on a gentleMACS instrument (Miltenyi). The resulting cell/nuclei suspension was filtered through a 70um strainer and quantified using AO/PI staining on a Luna FX7 automated fluorescent cell counter.
RNA quantity and integrity were assessed using a Qubit fluorometer (Thermo Fisher Scientific) and an Agilent Bioanalyzer 2100 (Agilent Technologies), respectively. Only samples with RNA integrity number (RIN) ≥ 8 were used for library preparation. rRNA depletion was performed using the Ribo-Zero Gold rRNA Removal Kit (Illumina) to enrich for coding and noncoding RNAs. cDNA libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. Sequencing was performed on an Illumina HiSeq 2000 platform to generate 100 bp paired-end reads, aiming for a depth of approximately [e.g., 30–50 million reads] per sample.

treatment_protocol: Mice were shaved and naired 5 days prior to acute UVB exposure (500mj/cm2) or no exposure. Mice were euthanized 1 day after UV exposure and skin was isolated and placed in RNAlater.

value: Skin


description: Library name: Cas9_VEGFA3_48h_293_500k_PEI_T5-KU-60648_rep1


title: Skin_K14creVsirfl/fl_NoUV, skin_Vsirfl/fl_NoUV, Skin_K14creVsir/fl_UVD1, Skin_Vsirfl/fl_UVD1

description: Library name: 211642_Pool_GEX

data_processing:
Raw fastq files were processed using the cellranger v9.0.0 pipeline prior to downstream analysis.
Assembly: mm10
Supplementary files format and content: h5 matrix files per sample

growth_protocol: 12-week old femail mice were used.

extract_protocol:
Formalin fixed paraffin embedded (FFPE) skin tissues blocks were prepared for the 10x Genomics Flex assay following demonstrated manufacturer’s protocol CG000606. For each block, 4 x 25um sections were placed into C tubes, deparaffinized with xylene, rehydrated with progressive dilutions of ethanol and dissociated in Liberase TM solution on a gentleMACS instrument (Miltenyi). The resulting cell/nuclei suspension was filtered through a 70um strainer and quantified using AO/PI staining on a Luna FX7 automated fluorescent cell counter.
The 10x Genomics Flex assay was performed according to the manufacturers protocol (CG000527). Briefly, cells were thawed from -80C, counted, and up to 1x106 cells were used as input into the hybridization reaction using the Mouse Transcriptome Probe Kit containing sample specific barcodes. Samples were pooled and loaded onto a 10x Genomics Chromium X instrument to capture 10,000 cells per sample. The concentration and size of sequencing libraries from the two pools were measured by Qubit (Thermo Fisher) and Tape Station (Agilent), respectively, and pooled for sequencing on a NextSeq2000 instrument (Illumina) to targeting 25,000 reads/cell.

treatment_protocol: Mice were shaved and naired 5 days prior to acute UVB exposure (250mj/cm2) or no exposure. Mice were euthanized 1 day after UV exposure and skin was isolated and placed in RNAlater.

value: Vsirfl/fl and K14creVsirfl/fl

value: NoUV and UV3hr


title: Skin_K14creVsirfl/fl_UV3hrs_rep3

description:
Library name: 188364_15_S30
Column name in featurecounts.readcounts.ann_1.tsv: 575_Kcre_UV3H
featurecounts.readcounts.ann_1.tsv


title: Muscle, ID ELMIH008, After_exercise, Group 2

description: Library name: Sample_23


title: Skin_K14creVsirfl/fl_UV3hrs_rep2

description:
Library name: 188364_14_S29
Column name in featurecounts.readcounts.ann_1.tsv: 574_Kcre_UV3H
featurecounts.readcounts.ann_1.tsv


title: Human histone-mark CUT&RUN multi-time-point sample DMSO_H3K9me3_2

city: Boston

first: Nilay

last: Sethi

address: 450 Brookline Avenue, D742

department: MCO

institute: Dana-Farber cancer institute

description:
Library name: histone_mark_cutrun_DMSO_H3K9me3_2
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K9me3; DMSO control; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/DMSO_H3K9me3_2_1.fq.gz and histone_mark_cutrun/DMSO_H3K9me3_2_2.fq.gz.

data_processing:
Sequencing reads were demultiplexed and delivered as compressed FASTQ files.
Read quality was assessed and adapter/low-quality sequence was removed as needed.
Human ATAC-seq, CUT&RUN, and RNA-seq reads were aligned to the hg38 reference genome.
Assay-specific downstream analyses were performed to generate accessibility, occupancy, peak, and expression outputs.
Assembly: hg38
Supplementary files format and content: Tar.gz archive containing processed data files for this study, including per-sample processed outputs generated from ATAC-seq, CUT&RUN, and RNA-seq datasets.

source_name: colon

growth_protocol: HT29-dTAG and LS180 human colon cancer cells were maintained under standard cell-culture conditions at 37 C in a humidified incubator with 5% CO2.

extract_protocol:
For ATAC-seq, nuclei were prepared and transposed using standard assay workflows. For CUT&RUN, chromatin-protein complexes were captured and digested using standard CUT&RUN procedures. For RNA-seq, total RNA was isolated using standard RNA extraction methods.
Sequencing libraries were prepared using standard Illumina-compatible ATAC-seq, CUT&RUN, and RNA-seq library construction workflows.

treatment_protocol: For the main time-course datasets, cells were treated with DMSO or SOX9-degradation/recovery conditions and harvested at the indicated time points (DMSO, D2, D4, D5, D7, D10, and D13). Additional samples include ARID1A/ARID1B perturbation and SOX9-variant conditions as noted in the sample descriptions.

value: colon

value: epithelial cell

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; DMSO control; CUT&RUN target H3K9me3


title: GEX counts of multiplex sSL0236 containing tissue & timepoint(s) CTX (L); P4

city: Klosterneuburg

first: Gaia

last: Novarino

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (ISTA)

description:
Library name: sSL0236_GEX
sSL0236_GEX_filtered_feature_bc_matrix.h5
sSL0236_GEX_QC_categories.csv
cx_p4_diet_seurat_RNA_assay.rds

data_processing:
Pre-processing was done per 10X lane (i.e., per multiplexing group of 4-6 samples). Peaks for the snATAC-seq modality were called for each run separately using MACS2 (v2.2.7.1) within Signac. A set of consensus peaks for the snATAC-seq analysis was created according to Signac. CMO demultiplexing information was taken from Cellranger output and added as metadata. Doublets were identified using scDblFinder6 (v1.14.0), separately for snRNA-seq and snATAC-seq modality. snRNA-seq parameters for the scDblFinder function were dims = 50, cluster = TRUE, knownUse = “discard”. snATAC-seq features were first aggregated (aggregateFeatures function, k = 500) and parameters for scDblFinder were dims = 50, aggegateFeatures = TRUE. Cells identified as doublets based on CMO data were included as known doublets (knownDoublets parameter). Quality control metrics such as the percentage of mitochondrial reads, nucleosome signal, and transcription start site (TSS) enrichment were calculated per run. After removing known and estimated doublets outlier thresholds for snRNA-seq read counts (nCount_RNA) or snATAC-seq read counts (nCount_ATAC) were derived using the isOutlier function from the scuttle package7 (v1.10.2) with parameters nmads = 3, type = “both”, log = TRUE. Nuclei falling outside these thresholds or with more than 5% of mitochondrial reads were removed. Complete datasets for each time point/tissue were created by integrating individual Seurat objects representing separate 10X lanes (i.e., multiplexing groups). snRNA-seq data were normalized using SCTransform8,9 from Seurat with parameter vst.flavor = “v2”. Integration of normalized snRNA-seq data was performed according to Seurat using the reciprocal PCA method with the following non-default parameters: SelectIntegrationFeatures(nfeatures = 2500), FindIntegrationAnchors(reduction = “rpca”), IntegrateData(dims = 1:50). Integration of snATAC-seq data was performed at the level of the LSI embedding using IntegrateEmbeddings(dims.to.integrate = 1:50) function with the integration anchors derived from snRNA-seq data. Identification of cell types was performed using the combination of both modalities, snRNA-seq and snATAC-seq. A PCA embedding was derived for the integrated snRNA-seq data, weighted nearest neighbor (WNN) graph was calculated using the FindMultimodalNeighbors function with the integrated LSI and integrated PCA reductions as input and dims_atac = 2:50, dims_rna = 1:50. The resulting WNN graph was used for UMAP visualization of the dataset and identification of clusters
Samples used for multi-omics analyses were de-multiplexed, and the raw sequencing data was converted to FASTQ format using bcl2fastq (v2.20.0.422). Joint processing of the gene expression and ATAC modalities was performed using the cellranger-arc software (v2.0.0). The mm10 reference genome was used for the alignment (refdata-cellranger-arc-mm10-2020-A-2.0.0, obtained from https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-mm10-2020-A-2.0.0.tar.gz). To capture CMO reads, the gene expression modality was separately processed using the cellranger count pipeline (v7.0.0 and v7.1.0), aligning it against the mm10 reference genome (refdata-gex-mm10-2020-A, obtained from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz). Each nucleus was assigned to the sample of origin as part of further demultiplexing, for which a Gaussian mixture model was fitted to the CMO count distributions. The probability that a given CMO read count was derived from background or positive signal was then inferred (as described in2).
Assembly: mm10
Supplementary files format and content: Cellranger output files (GEX): filtered feature matrix (h5 format); QC categories (csv)
Supplementary files format and content: Cellranger output files (ATAC): filtered feature matrix (h5 format); atac fragments (tsv & index); atac peak annotation (tsv & bed)
Supplementary files format and content: Downstream pipeline: integrated seurat object (RDS); pipeline input sample table (xlsx)

molecule: nuclear RNA

source_name: Cortex

extract_protocol:
Single nuclei were extracted using the 10X Genomics nuclei isolation kit (Chromium Nuclei Isolation Kit CG000505, Rev A). Samples were pooled after barcoding with cholesterol-modified oligos (CMOs) and a CMO Co-Anchor. Afterwards, single nuclei of pooled samples were encapsulated in Gel-Beads-in  emulsions (GEMs) on a 10X Chromium Controller using Chromium Next GEM Chip J Single Cell kit (PN-1000230), Chromium Next GEM Single Cell Multiome GEM Kit A (PN-1000232), Chromium Next GEM Single Cell Multiome Gel Bead Kit A (PN-1000231) as instructed by the manufacturer.
The library was prepared according to the 10X protocol using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, CG000338 Rev F. The hasthag oligo (HTO) libraries were prepared alongside cDNA amplification. Here, an ADT additive primer was added to the reaction. During cDNA cleanup, supernatant was saved to purify Hash-DNA. HTO libraries were generated using unique combinations of i5 and i7 indices.

value: Cortex

value: mixed

value: mixed samples (multiplex)


title: Cas9_VEGFA3_48h_293_500k_PEI_mock_rep3

description: Library name: Cas9_VEGFA3_48h_293_500k_PEI_mock_rep3


title: Skin_K14creVsirfl/fl_UV3hrs_rep1

description:
Library name: 188364_13_S28
Column name in featurecounts.readcounts.ann_1.tsv: 281_Kcre_UV3H
featurecounts.readcounts.ann_1.tsv


title: Muscle, ID ELMIH029, Before_exercise, Group 2

description: Library name: Sample_22

value: Muscle


title: Skin_Vsirfl/fl_UV3hrs_rep4

description:
Library name: 188364_12_S27
Column name in featurecounts.readcounts.ann_1.tsv: 646_FL_UV3H
featurecounts.readcounts.ann_1.tsv

value: Vsirfl


title: Cas9_VEGFA3_48h_293_500k_PEI_mock_rep2

description: Library name: Cas9_VEGFA3_48h_293_500k_PEI_mock_rep2


title: Skin_Vsirfl/fl_UV3hrs_rep3

description:
Library name: 188364_11_S26
Column name in featurecounts.readcounts.ann_1.tsv: 573_FL_UV3H
featurecounts.readcounts.ann_1.tsv


title: Muscle, ID ELMIH128, After_exercise, Group 1

description: Library name: Sample_21


title: Cas9_VEGFA3_48h_293_500k_PEI_mock_rep1

description: Library name: Cas9_VEGFA3_48h_293_500k_PEI_mock_rep1


title: Skin_Vsirfl/fl_UV3hrs_rep2

description:
Library name: 188364_10_S25
Column name in featurecounts.readcounts.ann_1.tsv: 572_FL_UV3H
featurecounts.readcounts.ann_1.tsv


title: Skin_Vsirfl/fl_UV3hrs_rep1

description:
Library name: 188364_09_S24
Column name in featurecounts.readcounts.ann_1.tsv: 279_FL_UV3H
featurecounts.readcounts.ann_1.tsv


title: Muscle, ID ELMIH042, After_exercise, Group 1

description: Library name: Sample_20


title: Skin_K14creVsirfl/fl_NoUV_rep4

description:
Library name: 188364_08_S23
Column name in featurecounts.readcounts.ann_1.tsv: 641_Kcre_NOUV
featurecounts.readcounts.ann_1.tsv

value: NoUV


title: Muscle, ID ELMIH106, Before_exercise, Group 1

description: Library name: Sample_19


description: Library name: Cas9_VEGFA2_48h_293_50k_PEI_T5-KU-60648_rep1


title: Skin_K14creVsirfl/fl_NoUV_rep2

description:
Library name: 188364_06_S21
Column name in featurecounts.readcounts.ann_1.tsv: 566_Kcre_NOUV
featurecounts.readcounts.ann_1.tsv


title: Skin_K14creVsirfl/fl_NoUV_rep3

description:
Library name: 188364_07_S22
Column name in featurecounts.readcounts.ann_1.tsv: 567_Kcre_NOUV
featurecounts.readcounts.ann_1.tsv


title: Muscle, ID ELMIH114, After_exercise, Group 3

description: Library name: Sample_53


title: Skin_Vsirfl/fl_NoUV_rep3

description:
Library name: 188364_03_S18
Column name in featurecounts.readcounts.ann_1.tsv: 565_FL_NOUV
featurecounts.readcounts.ann_1.tsv


title: Skin_K14creVsirfl/fl_NoUV_rep1

description:
Library name: 188364_05_S20
Column name in featurecounts.readcounts.ann_1.tsv: 265_Kcre_NOUV
featurecounts.readcounts.ann_1.tsv


title: Muscle, ID ELMIH089, After_exercise, Group 4

description: Library name: Sample_18


title: Skin_Vsirfl/fl_NoUV_rep4

description:
Library name: 188364_04_S19
Column name in featurecounts.readcounts.ann_1.tsv: 640_FL_NOUV
featurecounts.readcounts.ann_1.tsv


title: Cas9_VEGFA2_48h_293_500k_PEI_T7_rep2

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_T7_rep2


title: Muscle, ID ELMIH130, Before_exercise, Group 4

description: Library name: Sample_17


title: Cas9_VEGFA2_48h_293_500k_PEI_T5_rep3

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_T5_rep3


title: Skin_Vsirfl/fl_NoUV_rep1

description:
Library name: 188364_01_S16
Column name in featurecounts.readcounts.ann_1.tsv: 263_FL_NOUV
featurecounts.readcounts.ann_1.tsv


title: Muscle, ID ELMIH114, Before_exercise, Group 3

description: Library name: Sample_16


title: Skin_Vsirfl/fl_NoUV_rep2

description:
Library name: 188364_02_S17
Column name in featurecounts.readcounts.ann_1.tsv: 564_FL_NOUV
featurecounts.readcounts.ann_1.tsv


title: Skin_VISTAKO_NoUV_rep3

description:
Library name: SSG_034_S23
Column name in featurecounts.readcounts.ann.tsv: SSG_034
featurecounts.readcounts.ann.tsv

value: Vsir-/-


title: Skin_VISTAKO_UV3hrs_rep3

description:
Library name: SSG_035_S24
Column name in featurecounts.readcounts.ann.tsv: SSG_035
featurecounts.readcounts.ann.tsv


description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_STL127705_rep3


title: Muscle, ID ELMIH022, After_exercise, Group 2

description: Library name: Sample_15


title: Skin_VISTAKO_UV3hrs_rep2

description:
Library name: SSG_033_S22
Column name in featurecounts.readcounts.ann.tsv: SSG_033
featurecounts.readcounts.ann.tsv


title: Skin_VISTAKO_NoUV_rep2

description:
Library name: SSG_032_S21
Column name in featurecounts.readcounts.ann.tsv: SSG_032
featurecounts.readcounts.ann.tsv


title: Skin_VISTAKO_UV3hrs_rep1

description:
Library name: SSG_031_S20
Column name in featurecounts.readcounts.ann.tsv: SSG_031
featurecounts.readcounts.ann.tsv


title: Skin_WT_UV3hrs_rep3

description:
Library name: SSG_029_S18
Column name in featurecounts.readcounts.ann.tsv: SSG_029
featurecounts.readcounts.ann.tsv

value: WT


title: Muscle, ID ELMIH007, Before_exercise, Group 2

description: Library name: Sample_13


title: Skin_WT_NoUV_rep3

description:
Library name: SSG_028_S17
Column name in featurecounts.readcounts.ann.tsv: SSG_028
featurecounts.readcounts.ann.tsv


title: Skin_VISTAKO_NoUV_rep1

description:
Library name: SSG_030_S19
Column name in featurecounts.readcounts.ann.tsv: SSG_030
featurecounts.readcounts.ann.tsv


title: Skin_WT_NoUV_rep2

description:
Library name: SSG_026_S15
Column name in featurecounts.readcounts.ann.tsv: SSG_026
featurecounts.readcounts.ann.tsv


title: Muscle, ID ELMIH050, Before_exercise, Group 1

description: Library name: Sample_11


title: Skin_WT_UV3hrs_rep1

description:
Library name: SSG_025_S14
Column name in featurecounts.readcounts.ann.tsv: SSG_025
featurecounts.readcounts.ann.tsv


title: Human histone-mark CUT&RUN multi-time-point sample DMSO_H3K27me3_1

description:
Library name: histone_mark_cutrun_DMSO_H3K27me3_1
CUT&RUN sample from a multi-time-point histone-mark profiling dataset; time points include DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; target H3K27me3; DMSO control; source directory histone_mark_cutrun; paired FASTQ files histone_mark_cutrun/DMSO_H3K27me3_1_1.fq.gz and histone_mark_cutrun/DMSO_H3K27me3_1_2.fq.gz.

value: multi-time-point histone-mark CUT&RUN dataset covering DMSO, D2, D4, D5, D7, D10, and D13; histone marks include H3K27Ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3; DMSO control; CUT&RUN target H3K27me3


title: GEX counts of multiplex sSL0240 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0240_GEX
sSL0240_GEX_filtered_feature_bc_matrix.h5
sSL0240_GEX_QC_categories.csv
cx_p4_diet_seurat_RNA_assay.rds


title: Muscle, ID ELMIH112, After_exercise, Group 4

description: Library name: Sample_10


title: Skin_WT_NoUV_rep1

description:
Library name: SSG_024_S13
Column name in featurecounts.readcounts.ann.tsv: SSG_024
featurecounts.readcounts.ann.tsv


title: GEX counts of multiplex sSL0237 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0237_GEX
sSL0237_GEX_filtered_feature_bc_matrix.h5
sSL0237_GEX_QC_categories.csv
cx_p4_diet_seurat_RNA_assay.rds


title: ATAC counts of multiplex sSL0240 containing tissue & timepoint(s) CTX (L); P4

description:
Library name: sSL0240_ATAC
sSL0240_ATAC_filtered_feature_bc_matrix.h5
sSL0240_ATAC_fragments.tsv.gz
sSL0240_ATAC_fragments.tsv.gz.tbi
sSL0240_ATAC_peak_annotation.tsv
sSL0240_ATAC_peaks.bed
cx_p4_diet_seurat_RNA_assay.rds

library_source: genomic single cell


title: Early flowering, well-watered

city: Nugegoda

first: Dona Vihara

middle: Sugandhika

last: Kaluthanthri

state: Western province

address: Gangodawila

department: Botany

country: Sri Lanka

institute: University of Sri Jayewardenepura

data_processing:
Total RNA was sequenced using a HiSeq 2500 sequencer following HCS 2.2.70 sequencing control software.
Filtering Criteria - To exclude gene with at least one zero Counts.
Normalization : TMM Normalization - In order to reduce systematic bias, size factors were estimated from the read count data (calcNormFactors method). Using them, the read count data was normalized with Trimmed mean of M-values (TMM) method in edgeR library. Then, statistical test was performed with the normalized data.
Signal+1 and Logarithm for Visualization - log2(Counts per Million reads (CPM)+1) and log2(TMM normalized count+1) values were used for data visualization. Raw read counts are scattered around wide range and most of them lean to the low level. Therefore, logarithm transformation facilitates to reduce the range of the read counts and flatten a data distribution. To prevent a negative value resulting from logarithm transformation, 1 was added to PM(Counts per Million reads) or normalized read count. These logarithm figures were used only for visualization. To proceed a statistical test, TMM normalized count was adopted for exact test (exactTest) in edgeR.
Assembly: GCF_000003195.3
Supplementary files format and content: Microsoft excel worksheet, include gene counts for each sample
Supplementary files format and content: Microsoft excel worksheet, include transcript count for each sample

organism: Sorghum bicolor

source_name: Flag leaf

growth_protocol: A total of fifty biological replicates of each germplasm accession was maintained in a net house under controlled environment at the Department of Botany, Faculty of Applied Seeds of each germplasm accession were sown in small plastic pots filled with normal soil at a depth of 1/2 inch keeping uniform space between the seeds. Pots were irrigated soon after sowing. Approximately 25-day old seedlings were later transplanted separately in large plastic pots filled with approximately 5 kg mixture of soil and compost (1:1). The pots were arranged in five blocks with 10 replicates from each accession following the Completely Randomized Design (CRD).

extract_protocol:
All leaves were frozen in liquid nitrogen immediately after collecting and were then stored at minus 80 °C. Total RNA was separately isolated from frozen flag leaves samples (those collected from three different plants of each group when pollen shed began) using NucleoSpin® RNA Plant kit (MACHEREY-NAGEL). RNA quality and integrity were assessed using Quantus™ Fluorometer (Promega) prior to RNA-sequencing (at Macrogen Inc., Seoul, South Korea).
The cDNA library preparation was done using a TrueSeq Stranded mRNA LT Sample prep kit.

treatment_protocol: The plants from each germplasm accession were divided into two groups: the well-watered (WW) and drought-stressed (DS) groups. Drought stress was administered to 25 days old seedlings from the DS group by withdrawing water whilst the remaining (control) plants were well-watered. The WW pots were maintained at potentials >−0.2 MPa (15–20 % soil water content) with irrigation, while DS pots were maintained at <−1.5 MPa (5–8 % soil water content). When pollen shed began, flag leaf tissues were harvested from three different plants in each replicate group and condition.

value: Flag leaf

value: Early flowering

value: Well-Watered


title: Intermediate flowering, drought-stressed

value: Intermediate flowering

value: Drought-Stressed


title: Intermediate flowering, well-watered


title: Muscle, ID ELMIH080, After_exercise, Group 3

description: Library name: Sample_08


title: Late flowering, drought-stressed

value: Late flowering


title: Muscle, ID ELMIH102, After_exercise, Group 2

description: Library name: Sample_07


title: Healthy human donor (3), CAR T cells, JUN+BATF, RNA

status: Public on Jun 17 2026

city: Stanford

first: Oliver

last: Takacsi-Nagy

state: CA

address: 234 Pasteur Dr. (BMI 4600)

department: Pathology

institute: Stanford University School of Medicine

description:
Library name: Chronic_HA_3H-JUN+BATF_RNA
Column name in both processed data files: Donor3_JUN+BATF

data_processing:
Basecalls were performed using bcl-convert Version 4.3.6 from Illumina and samples demultiplexed using Fulcrum Genomics fqtk v0.3.1.
Reads were pre-processed and pseudoaligned for transcript quantification using Salmon (v1.5.2) and the nf-core/rnaseq pipeline (v3.5) with default parameters.
DESeq2 (v1.50.2) was used to variance-stabilize (normalized) Salmon quantifications (raw).
Assembly: hg38
Supplementary files format and content: Two csv files, one for raw counts and one for normalized (DESeq VST) counts; column names correspond to Samples in both.

source_name: Primary Human T Cell

growth_protocol: Primary human T cells were negatively selected from PBMCs isolated from leukoreduction chambers from three healthy blood donors and activated by CD3/28 agonism in X-VIVO 15 supplemented with 5% FBS and 50 IU/mL recombinant human IL-2. 48 hours post-activation, T cells were electroporated with Cas9 ribonucleoprotein and a plasmid homology-directed repair template to enable integration of a multicistronic cassette encoding tNGFR, CD19-28z and variable natural and engineered FLAG-tagged AP-1 transcription factors within the continuous reading frame of the TRAC locus. Pre- and post-editing cells were maintained at 0.5-1e6/ml. Six days post-editing, CAR T cells were challenged with GD2-expressing Nalm6 targets for two days and then challenged a second time for three days (engineered leukemia cell line, 1:4 Effector:Target ratio).

extract_protocol:
2e5-5e5 live CAR T cells (tNGFR+) were enriched magnetically and preserved in Zymo DNA/RNA shield. RNA extraction was performed by Plasmidsaurus.
Performed by Plasmidsaurus. The general workflow consisted of: reverse transcription, second strand synthesis, tagmentation, indexing and amplification.

treatment_protocol: All T cells in this sample were treated the same, the only difference between the T cells is which healthy human donor they were isolated from and which transcription factor they were edited to express.

value: Primary Human T Cell

tag: individual

value: Healthy Donor 3

tag: tf expressed

value: JUN+BATF


title: 3Pseq_EXOSC3_dTAG_noPAP_rep3

city: Aarhus

first: Jerome

middle: O

last: Rouviere

address: Universitetsbyen 81

country: Denmark

institute: Aarhus University

description: Library name: 3Pseq_EXOSC3_dTAG_noPAP_rep3

data_processing:
The raw sequence reads received from service providers were first quality checked using FastQC (Babraham Bioinformatics group). For RNAseq libraires, reads were then trimmed for adaptors and filtered using Trim Galore (Babraham Bioinformatics group). Trimmed reads were mapped to hg38, using Hisat2 in paired-end mode. Mapped files were sorted and checked for pairing using SAMtools. Reads were then deduplicated using MarkDuplicates (Picard – Broad Institute) and further filtered to keep only unique mappers by using SAMtools. Relative samples size was then estimated by generating coverage counts using htseq-count (HTSeq-counts) over the Genecode annotation and analyzing then with DEseq2 to define size factors. In the case of fractionated pA+ RNAseq, size factors were measured separately for the nuclear and cytoplasmic fractions to avoid any compensation of compartment specific phenotypes. Finally, reads were converted to bigwig (bw) files normalized to size factors, with a binning of 5, using bamCoverage (Deeptools). For iCLIP libraires,using only "R1" reads, adaptors were trimmed using Trim Galore, UMI deduplication was performed using seqkit. The first 15nt were trimmed with Trim Galore, and reads were filtered to be bellow 100bp length using seqkit. Reads were mapped to hg38 using STAR allowing only unique mappers. To get single positions, using a combination of Bedtools and bash script, mapped bam files were converted to bed, shifted one base, filtered to contain only primary assemby chromosomes (except chrM) and separated by strand. The resulting bedgraph files where then converted to bw (without binning) using bedGraphToBigWig.  For 3'end sequencing, adapters and A18 stretches were trimmed using Trim Galore. Mapping to hg38 was performed using STAR. A combinations of samtools and bash code was used to keep only unique mappers, reduce the reads to their 5'end (due to Quant-seq REV sequencing) and filter them to only correspond to the primary assembly chromosomes (except chrM). Htseq-count, was used on the resulting mapped files, over the last exon of protein coding genes and the output was used to define size factor with DEseq2 which was used in bamCoverage to convert the files to bw (without binning)
Assembly: hg38
Supplementary files format and content: bigwig (bw) - normalized coverage with a binning of 5 for RNAseq and no binning for iCLIP and 3'end seq

source_name: cervix

growth_protocol: HeLa and HCT116 cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
Total RNA was extracted using TRIZOL reagent according to manufacturer’s instructions
For iCLIP libraries were constructed in-house and seqenced by Lexogen. For all other libraries construction and sequencing were paid services from Lexogen

treatment_protocol: When specified, cells were treated with dTAGV-1 at a concentration of 500nM for 4H

value: cervix

value: HeLa Kyoto

value: 4H dTAGV-1 500nM


title: 3Pseq_EXOSC3_dTAG_noPAP_rep2

description: Library name: 3Pseq_EXOSC3_dTAG_noPAP_rep2


title: Late flowering, well-watered


title: Muscle, ID ELMIH032, After_exercise, Group 2

description: Library name: Sample_06

value: Muscle


description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_Olaparib_rep3


title: Cas9_VEGFA2_48h_293_500k_PEI_mock_rep3

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_mock_rep3


title: Cas9_VEGFA2_48h_293_500k_PEI_RocE_rep3

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_RocE_rep3


title: Cas9_VEGFA2_48h_293_500k_PEI_RE1B_rep3

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_RE1B_rep3


title: Cas9_VEGFA2_48h_293_500k_PEI_RE1B_rep2

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_RE1B_rep2


title: Cas9_VEGFA2_48h_293_500k_PEI_RI-1_rep3

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_RI-1_rep3


title: 3Pseq_EXOSC3_dTAG_noPAP_rep1

description: Library name: 3Pseq_EXOSC3_dTAG_noPAP_rep1


description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_NU7441_rep3


title: Cas9_VEGFA2_48h_293_500k_PEI_KP32_rep3

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_KP32_rep3


title: Muscle, ID ELMIH054, After_exercise, Group 1

description: Library name: Sample_05


title: 3Pseq_EXOSC3_dTAG_EPAP_rep2

description: Library name: 3Pseq_EXOSC3_dTAG_EPAP_rep2

value: 4H dTAGV-1 500nM - EPAP


title: Cas9_VEGFA2_48h_293_500k_PEI_KP32_rep2

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_KP32_rep2


title: Muscle, ID ELMIH088, Before_exercise, Group 4

description: Library name: Sample_04


title: 3Pseq_EXOSC3_DMSO_noPAP_rep3

description: Library name: 3Pseq_EXOSC3_DMSO_noPAP_rep3

value: 4H DMSO


title: 3Pseq_EXOSC3_DMSO_noPAP_rep2

description: Library name: 3Pseq_EXOSC3_DMSO_noPAP_rep2


title: Muscle, ID ELMIH033, Before_exercise, Group 2

description: Library name: Sample_03


title: 3Pseq_EXOSC3_DMSO_EPAP_rep3

description: Library name: 3Pseq_EXOSC3_DMSO_EPAP_rep3

value: 4H DMSO - EPAP


title: Cas9_VEGFA2_48h_293_500k_PEI_EXO_rep3

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_EXO_rep3


title: Muscle, ID ELMIH022, Before_exercise, Group 2

description: Library name: Sample_02


title: Cas9_VEGFA2_48h_293_500k_PEI_EXO_rep2

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_EXO_rep2


title: 3Pseq_EXOSC3_DMSO_EPAP_rep1

description: Library name: 3Pseq_EXOSC3_DMSO_EPAP_rep1


title: 3Pseq_EXOSC3_DMSO_noPAP_rep1

description: Library name: 3Pseq_EXOSC3_DMSO_noPAP_rep1


title: Muscle, ID ELMIH128, Before_exercise, Group 1

description: Library name: Sample_01


title: 3Pseq_EXOSC3_dTAG_EPAP_rep1

description: Library name: 3Pseq_EXOSC3_dTAG_EPAP_rep1


title: Frac_HCT116_LENG8_4HdTAG_Nuc_rep3b

description: Library name: Frac_HCT116_LENG8_4HdTAG_Nuc_rep3b

value: colon


title: Cas9_VEGFA2_48h_293_500k_PEI_EXO1_rep3

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_EXO1_rep3


title: 3Pseq_EXOSC3_DMSO_EPAP_rep2

description: Library name: 3Pseq_EXOSC3_DMSO_EPAP_rep2


title: Frac_HCT116_LENG8_4HdTAG_Nuc_rep2b

description: Library name: Frac_HCT116_LENG8_4HdTAG_Nuc_rep2b


title: Subject 6 - human cells transfected with miR-339 mimic

city: Stockholm

first: Nicolas

last: Pillon

address: Solnavägen 9

country: Sweden

institute: Karolinska Institutet

description: Library name: P29458_1012

data_processing:
Quality and adapter trimming of reads was performed using Cutadapt (v3.5). Sample quality was assessed using FastQC (v0.11.8) and MultiQC (v1.14). Reads were aligned to the Ensembl GRCh38/GRCm38 reference genome using STAR (v2.7.9d). Counts for each gene were obtained using featureCounts (v1.5.1).
Assembly: GRCh38/GRCm38
Supplementary files format and content: CSV file, raw counts following featureCounts
Supplementary files format and content: CSV file, raw counts following featureCounts

source_name: skeletal muscle

growth_protocol: Mouse C2C12 muscle cells were obtained from the American Type Culture Collection (ATCC® CRL-1772™). Primary cells were isolated from vastus lateralis skeletal muscle biopsies derived from six healthy individuals (two females, four males, 35±17 years old, BMI 22.6±1.9 kg/m2). The ethical committee at Karolinska Institutet approved the protocols. Mouse and human cells were cultured and differentiated as described (Abdelmoez et al, 2020). Differentiation was monitored under the microscope and the absence of mycoplasma contamination was routinely confirmed by PCR.

extract_protocol:
On the fifth day of differentiation, cells were harvested for gene expression analysis using QIAzol Lysis Reagent.
Libraries were generated using TruSeq Stranded Total RNA (Illumina) following manufacturer's instructions.

treatment_protocol: Muscle cells were transfected on the first and third day of differentiation, with either miR-339-5p mirVana® miRNA mimic (Thermo Fisher Scientific, MC12347) or negative Control #1 mirVana™ miRNA mimic (Thermo Fisher Scientific, 4464059). Transfections were performed using Lipofectamine RNAiMAX as transfection reagent. In primary human skeletal muscle cells, transfection was performed with 25 nM miRNA mimics for 5 hours. For C2C12, miRNA mimics were used at a final concentration of 200 nM for 24h.

value: skeletal muscle

value: primary

value: skeletal myotube

value: miR-339-5p overexpression


title: Frac_HCT116_LENG8_4HdTAG_Nuc_rep1b

description: Library name: Frac_HCT116_LENG8_4HdTAG_Nuc_rep1b


title: Cas9_VEGFA2_48h_293_500k_PEI_EXO1_rep2

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_EXO1_rep2


title: Subject 6 - human cells transfected with negative control miRNA mimic

description: Library name: P29458_1011

value: control


title: Frac_HCT116_LENG8_4HdTAG_Cyto_rep3b

description: Library name: Frac_HCT116_LENG8_4HdTAG_Cyto_rep3b


title: Frac_HCT116_LENG8_4HdTAG_Cyto_rep1b

description: Library name: Frac_HCT116_LENG8_4HdTAG_Cyto_rep1b


title: Cas9_VEGFA2_48h_293_500k_PEI_DIDS_rep3

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_DIDS_rep3


title: Frac_HCT116_0HdTAG_Nuc_rep3b

description: Library name: Frac_HCT116_0HdTAG_Nuc_rep3b

value: WT


title: Frac_HCT116_0HdTAG_Nuc_rep2b

description: Library name: Frac_HCT116_0HdTAG_Nuc_rep2b


title: Subject 5 - human cells transfected with negative control miRNA mimic

description: Library name: P29458_1009


description: Library name: Cas9_VEGFA2_48h_293_100k_PEI_T5-KU-60648_rep1


title: Frac_HCT116_0HdTAG_Nuc_rep1b

description: Library name: Frac_HCT116_0HdTAG_Nuc_rep1b


title: Frac_HCT116_0HdTAG_Cyto_rep3b

description: Library name: Frac_HCT116_0HdTAG_Cyto_rep3b


description: Library name: Cas9_IDS_48h_293_500k_PEI_T5-KU-60648_rep3


title: Frac_HCT116_0HdTAG_Cyto_rep2b

description: Library name: Frac_HCT116_0HdTAG_Cyto_rep2b


title: Frac_HCT116_0HdTAG_Cyto_rep1b

description: Library name: Frac_HCT116_0HdTAG_Cyto_rep1b


title: Subject 5 - human cells transfected with miR-339 mimic

description: Library name: P29458_1010


description: Library name: Cas9_IDS_48h_293_500k_PEI_T5-KU-60648_rep2


title: Frac_HCT116_4HdTAG_Nuc_rep1b

description: Library name: Frac_HCT116_4HdTAG_Nuc_rep1b


description: Library name: Cas9_IDS_48h_293_500k_PEI_T5-KU-60648_rep1


title: Frac_HCT116_4HdTAG_Nuc_rep2b

description: Library name: Frac_HCT116_4HdTAG_Nuc_rep2b


title: Frac_HCT116_4HdTAG_Cyto_rep3b

description: Library name: Frac_HCT116_4HdTAG_Cyto_rep3b


title: Subject 3 - human cells transfected with negative control miRNA mimic

description: Library name: P29458_1005


title: Frac_HCT116_4HdTAG_Cyto_rep2b

description: Library name: Frac_HCT116_4HdTAG_Cyto_rep2b


title: Cas9_IDS_48h_293_500k_PEI_mock_rep3

description: Library name: Cas9_IDS_48h_293_500k_PEI_mock_rep3


title: Frac_HCT116_4HdTAG_Cyto_rep1b

description: Library name: Frac_HCT116_4HdTAG_Cyto_rep1b


title: Subject 2 - human cells transfected with miR-339 mimic

description: Library name: P29458_1004


title: Subject 4 - human cells transfected with miR-339 mimic

description: Library name: P29458_1008


title: Frac_HCT116_ZFC3H1_4HdTAG_Nuc_rep3

description: Library name: Frac_HCT116_ZFC3H1_4HdTAG_Nuc_rep3


title: Frac_HCT116_ZFC3H1_4HdTAG_Nuc_rep1

description: Library name: Frac_HCT116_ZFC3H1_4HdTAG_Nuc_rep1


title: Cas9_IDS_48h_293_500k_PEI_mock_rep2

description: Library name: Cas9_IDS_48h_293_500k_PEI_mock_rep2


title: Frac_HCT116_ZFC3H1_4HdTAG_Nuc_rep2

description: Library name: Frac_HCT116_ZFC3H1_4HdTAG_Nuc_rep2


title: Subject 1 - human cells transfected with miR-339 mimic

description: Library name: P29458_1002


title: Frac_HCT116_4HdTAG_Nuc_rep2

description: Library name: Frac_HCT116_4HdTAG_Nuc_rep2


title: Frac_HCT116_4HdTAG_Nuc_rep1

description: Library name: Frac_HCT116_4HdTAG_Nuc_rep1


title: Frac_HCT116_0HdTAG_Nuc_rep3

description: Library name: Frac_HCT116_0HdTAG_Nuc_rep3


title: s918_AOMS_Hardship-1

city: Leuven

first: Bernard

middle: Klaas

last: van der Veer

state: Vlaams-Brabant

address: Herestraat 49 - box 651

department: Deparment of Human Genetics

country: Belgium

institute: KU Leuven

description: Library name: 918

data_processing:
TrimGalore (v0.6.4_dev)
Bismark (v0.22.3)
methyldackel (v0.5.0)
Assembly: hg38
Supplementary files format and content: bedGraph file - file containing methylation calls generated with methyldackel

source_name: PBMC

extract_protocol: Zymo-Seq RRBS Library Kit

value: PBMC

tag: disease onset

value: Adult

tag: hardship


title: Frac_HCT116_0HdTAG_Nuc_rep2

description: Library name: Frac_HCT116_0HdTAG_Nuc_rep2


title: Frac_HCT116_0HdTAG_Nuc_rep1

description: Library name: Frac_HCT116_0HdTAG_Nuc_rep1


description: Library name: Cas9_HEK4_48h_293_500k_PEI_T5-KU-60648_rep3


title: Frac_HCT116_GANP_4HdTAG_Nuc_rep3

description: Library name: Frac_HCT116_GANP_4HdTAG_Nuc_rep3


title: s917 (P-00226167)_AOMS_Hardship-1

description: Library name: 917 (P-00226167)


title: Frac_HCT116_GANP_4HdTAG_Nuc_rep2

description: Library name: Frac_HCT116_GANP_4HdTAG_Nuc_rep2


description: Library name: Cas9_HEK4_48h_293_500k_PEI_STL127705_rep3


title: s916 (P-00225925)_AOMS_Hardship-1

description: Library name: 916 (P-00225925)


title: Frac_HCT116_ZFC3H1_4HdTAG_Cyto_rep3

description: Library name: Frac_HCT116_ZFC3H1_4HdTAG_Cyto_rep3


title: s915_AOMS_Hardship-0

description: Library name: 915


title: Frac_HCT116_ZFC3H1_4HdTAG_Cyto_rep1

description: Library name: Frac_HCT116_ZFC3H1_4HdTAG_Cyto_rep1


title: Cas9_HEK4_48h_293_500k_PEI_RI-1_rep3

description: Library name: Cas9_HEK4_48h_293_500k_PEI_RI-1_rep3


title: Subject 4 - human cells transfected with negative control miRNA mimic

description: Library name: P29458_1007


title: Frac_HCT116_4HdTAG_Nuc_rep3b

description: Library name: Frac_HCT116_4HdTAG_Nuc_rep3b


title: Subject 3 - human cells transfected with miR-339 mimic

description: Library name: P29458_1006


title: s914_AOMS_Hardship-1

description: Library name: 914


title: Frac_HCT116_4HdTAG_Cyto_rep2

description: Library name: Frac_HCT116_4HdTAG_Cyto_rep2


title: Subject 2 - human cells transfected with negative control miRNA mimic

description: Library name: P29458_1003


title: s911_AOMS_Hardship-1

description: Library name: 911


title: Frac_HCT116_4HdTAG_Nuc_rep3

description: Library name: Frac_HCT116_4HdTAG_Nuc_rep3


title: Cas9_HEK4_48h_293_500k_PEI_T7_rep3

description: Library name: Cas9_HEK4_48h_293_500k_PEI_T7_rep3


description: Library name: Cas9_HEK4_48h_293_500k_PEI_Olaparib_rep3


title: Frac_HCT116_0HdTAG_Cyto_rep3

description: Library name: Frac_HCT116_0HdTAG_Cyto_rep3


title: Frac_HCT116_0HdTAG_Cyto_rep2

description: Library name: Frac_HCT116_0HdTAG_Cyto_rep2


title: s909_AOMS_Hardship-0

description: Library name: 909


title: Frac_HCT116_0HdTAG_Cyto_rep1

description: Library name: Frac_HCT116_0HdTAG_Cyto_rep1


title: Cas9_HEK4_48h_293_500k_PEI_NU7441_rep3

description: Library name: Cas9_HEK4_48h_293_500k_PEI_NU7441_rep3


title: Frac_HCT116_GANP_4HdTAG_Cyto_rep3

description: Library name: Frac_HCT116_GANP_4HdTAG_Cyto_rep3


title: s908_AOMS_Hardship-1

description: Library name: 908


title: Frac_HCT116_GANP_4HdTAG_Cyto_rep2

description: Library name: Frac_HCT116_GANP_4HdTAG_Cyto_rep2


title: Cas9_HEK4_48h_293_500k_PEI_mock_rep3

description: Library name: Cas9_HEK4_48h_293_500k_PEI_mock_rep3


title: Frac_HCT116_GANP_4HdTAG_Cyto_rep1

description: Library name: Frac_HCT116_GANP_4HdTAG_Cyto_rep1


description: Library name: Cas9_HEK4_48h_293_500k_PEI_KU-60648_rep3


title: LENG8_iCLIP_rep2

description: Library name: LENG8_iCLIP_rep2

data_processing:
The raw sequence reads received from service providers were first quality checked using FastQC (Babraham Bioinformatics group). For RNAseq libraires, reads were then trimmed for adaptors and filtered using Trim Galore (Babraham Bioinformatics group). Trimmed reads were mapped to hg38, using Hisat2 in paired-end mode. Mapped files were sorted and checked for pairing using SAMtools. Reads were then deduplicated using MarkDuplicates (Picard – Broad Institute) and further filtered to keep only unique mappers by using SAMtools. Relative samples size was then estimated by generating coverage counts using htseq-count (HTSeq-counts) over the Genecode annotation and analyzing then with DEseq2 to define size factors. In the case of fractionated pA+ RNAseq, size factors were measured separately for the nuclear and cytoplasmic fractions to avoid any compensation of compartment specific phenotypes. Finally, reads were converted to bigwig (bw) files normalized to size factors, with a binning of 5, using bamCoverage (Deeptools). For iCLIP libraires,using only "R1" reads, adaptors were trimmed using Trim Galore, UMI deduplication was performed using seqkit. The first 15nt were trimmed with Trim Galore, and reads were filtered to be bellow 100bp length using seqkit. Reads were mapped to hg38 using STAR allowing only unique mappers. To get single positions, using a combination of Bedtools and bash script, mapped bam files were converted to bed, shifted one base, filtered to contain only primary assemby chromosomes (except chrM) and separated by strand. The resulting bedgraph files where then converted to bw (without binning) using bedGraphToBigWig.  For 3'end sequencing, adapters and A18 stretches were trimmed using Trim Galore. Mapping to hg38 was performed using STAR. A combinations of samtools and bash code was used to keep only unique mappers, reduce the reads to their 5'end (due to Quant-seq REV sequencing) and filter them to only correspond to the primary assembly chromosomes (except chrM). Htseq-count, was used on the resulting mapped files, over the last exon of protein coding genes and the output was used to define size factor with DEseq2 which was used in bamCoverage to convert the files to bw (without binning)
Assembly: hg38
Supplementary files format and content: bigwig (bw) - normalized coverage with a binning of 5 for RNAseq and no binning for iCLIP and 3'end seq
Library strategy: iCLIP


title: Cas9_HEK4_48h_293_500k_PEI_RocE_rep3

description: Library name: Cas9_HEK4_48h_293_500k_PEI_RocE_rep3

data_processing:
Tracking-seq/2: Data were analyzed using Offtracker (https://github.com/Lan-lab/offtracker)
GUIDE-seq-2: Data were analyzed using guideseq (https://github.com/tsailabSJ/guideseq)
Assembly: hg38
Supplementary files format and content: BigWig of genome-editing signals


title: LENG8_iCLIP_rep1

description: Library name: LENG8_iCLIP_rep1


description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_T5-KU-60648_rep3


title: Frac_HCT116_ZFC3H1_4HdTAG_Cyto_rep2

description: Library name: Frac_HCT116_ZFC3H1_4HdTAG_Cyto_rep2


title: noUV_iCLIP_control

description: Library name: noUV_iCLIP_control

value: no UV crosslink


title: s60_POMS_Hardship-1

description: Library name: 60

value: Pediatric


title: UAP56_iCLIP_rep1

description: Library name: UAP56_iCLIP_rep1

value: cervix

value: HeLa Kyoto


title: Cas9_HEK4_48h_293_500k_PEI_IBR2_rep3

description: Library name: Cas9_HEK4_48h_293_500k_PEI_IBR2_rep3


title: Frac_ZFC3H1_4HdTAG_Nuc_rep5

description: Library name: Frac_ZFC3H1_4HdTAG_Nuc_rep5

data_processing:
The raw sequence reads received from service providers were first quality checked using FastQC (Babraham Bioinformatics group). Reads were then trimmed for adaptors and filtered using Trim Galore (Babraham Bioinformatics group). Trimmed reads were mapped to hg38, using Hisat2 in paired-end mode. Mapped files were sorted and checked for pairing using SAMtools. Reads were then deduplicated using MarkDuplicates (Picard – Broad Institute) and further filtered to keep only unique mappers by using SAMtools. Relative samples size was then estimated by generating coverage counts using htseq-count (HTSeq-counts) over the Genecode annotation and analyzing then with DEseq2 to define size factors. In the case of fractionated pA+ RNAseq, size factors were measured separately for the nuclear and cytoplasmic fractions to avoid any compensation of compartment specific phenotypes. Finally, reads were converted to bigwig (bw) files normalized to size factors, with a binning of 5, using bamCoverage (Deeptools).
Assembly: hg38
Supplementary files format and content: bigwig (bw) - normalized coverage with a binning of 5

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
Total RNA was extracted using TRIZOL reagent according to manufacturer’s instructions
Library construction and sequencing were paid services from the Beijing Genome Institute (BGI) in case of total pA+ RNAseq and from Lexogen for the fractionated and exogenously expressing ZFC3H1 pA+ RNAseq.

treatment_protocol: When specified, cels were treated with dTAGV-1 at a concentration of 500nM for 4H

value: 4H dTAGV-1 500nM


title: s59_AOMS_Hardship-0

description: Library name: 59


title: Frac_ZFC3H1_4HdTAG_Nuc_rep4

description: Library name: Frac_ZFC3H1_4HdTAG_Nuc_rep4


title: Frac_ZFC3H1_4HdTAG_Nuc_rep3

description: Library name: Frac_ZFC3H1_4HdTAG_Nuc_rep3


title: Cas9_HEK4_48h_293_500k_PEI_EXO_rep3

description: Library name: Cas9_HEK4_48h_293_500k_PEI_EXO_rep3

extract_protocol:
Tracking-seq/2: Cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2 antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA. GUIDE-seq-2 were performed according to doi: 10.1101/2025.02.10.637517
Tracking-seq/2: The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit.GUIDE-seq-2 libraries were constructed according to doi: 10.1101/2025.02.10.637517


title: s58_POMS_Hardship-1

description: Library name: 58


title: Frac_ZFC3H1_4HdTAG_Cyto_rep5

description: Library name: Frac_ZFC3H1_4HdTAG_Cyto_rep5


title: Cas9_HEK4_48h_293_500k_PEI_EXO1_rep3

description: Library name: Cas9_HEK4_48h_293_500k_PEI_EXO1_rep3


title: Frac_ZFC3H1_4HdTAG_Cyto_rep4

description: Library name: Frac_ZFC3H1_4HdTAG_Cyto_rep4


title: Frac_ZFC3H1_4HdTAG_Cyto_rep3

description: Library name: Frac_ZFC3H1_4HdTAG_Cyto_rep3


title: s57_POMS_Hardship-1

description: Library name: 57


title: Cas9_HEK4_48h_293_500k_PEI_DIDS_rep3

description: Library name: Cas9_HEK4_48h_293_500k_PEI_DIDS_rep3


title: Frac_LENG8_4HdTAG_Nuc_rep5

description: Library name: Frac_LENG8_4HdTAG_Nuc_rep5


title: s56_POMS_Hardship-1

description: Library name: 56


title: Frac_LENG8_4HdTAG_Nuc_rep4

description: Library name: Frac_LENG8_4HdTAG_Nuc_rep4


title: Cas12a_DNMT1-3_48h_293_500k_PEI_T5_rep3

description: Library name: Cas12a_DNMT1-3_48h_293_500k_PEI_T5_rep3


title: s55_AOMS_Hardship-1

description: Library name: 55


title: Frac_LENG8_4HdTAG_Cyto_rep5

description: Library name: Frac_LENG8_4HdTAG_Cyto_rep5


title: Cas12a_DNMT1-3_48h_293_500k_PEI_T5_rep2

description: Library name: Cas12a_DNMT1-3_48h_293_500k_PEI_T5_rep2


title: Frac_LENG8_4HdTAG_Cyto_rep4

description: Library name: Frac_LENG8_4HdTAG_Cyto_rep4


title: s54_POMS_Hardship-1

description: Library name: 54


title: Frac_LENG8_4HdTAG_Cyto_rep3

description: Library name: Frac_LENG8_4HdTAG_Cyto_rep3


description: Library name: Cas12a_DNMT1-3_48h_293_500k_PEI_T5-KU-60648_rep3


title: C2C12 n=1, mouse cells transfected with negative control miRNA mimic

description: Library name: P29458_1013


title: Frac_Hela_4HdTAG_Nuc_rep5

description: Library name: Frac_Hela_4HdTAG_Nuc_rep5


title: Human CUT&RUN BAF-subunit reduced-time-point batch sample dT29_BRD9_R1

description:
Library name: cutrun2_dT29_BRD9_R1
CUT&RUN sample from the second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set: DM, R, and T; target BRD9; R condition/time point; source directory cutrun2; paired FASTQ files cutrun2/dT29_BRD9_R1_1.fq.gz and cutrun2/dT29_BRD9_R1_2.fq.gz.

value: epithelial cell

value: BRD9 perturbation

value: second CUT&RUN batch covering additional BAF subunits with a reduced condition/time-point set:DM, R, and T; R condition/time point; CUT&RUN target BRD9


description:
Library name: Frac_Hela_4HdTAG_Nuc_rep4_technical_issue
Warning: rRNA contamined - excluded from all analyses


title: s52_AOMS_Hardship-0

description: Library name: 52


title: Frac_Hela_4HdTAG_Cyto_rep5

description: Library name: Frac_Hela_4HdTAG_Cyto_rep5


description: Library name: Cas12a_DNMT1-3_48h_293_500k_PEI_T5-KU-60648_rep2


title: Frac_Hela_4HdTAG_Nuc_rep3

description: Library name: Frac_Hela_4HdTAG_Nuc_rep3


title: Frac_Hela_4HdTAG_Cyto_rep4

description: Library name: Frac_Hela_4HdTAG_Cyto_rep4


description: Library name: Cas12a_DNMT1-3_48h_293_500k_PEI_mock_rep3


description: Library name: Cas12a_DNMT1-3_48h_293_500k_PEI_mock_rep2


title: Frac_Hela_4HdTAG_Cyto_rep3

description: Library name: Frac_Hela_4HdTAG_Cyto_rep3


title: s51_POMS_Hardship-0

description: Library name: 51


title: Frac_Hela_0HdTAG_Nuc_rep4

description: Library name: Frac_Hela_0HdTAG_Nuc_rep4


title: Frac_Hela_0HdTAG_Nuc_rep5

description: Library name: Frac_Hela_0HdTAG_Nuc_rep5


title: s50_AOMS_Hardship-0

description: Library name: 50


description: Library name: Cas12a_DNMT1-3_48h_293_500k_PEI_KU60648_rep3


title: Frac_Hela_0HdTAG_Nuc_rep3

description: Library name: Frac_Hela_0HdTAG_Nuc_rep3


title: Frac_Hela_0HdTAG_Cyto_rep5

description: Library name: Frac_Hela_0HdTAG_Cyto_rep5


title: s49_POMS_Hardship-0

description: Library name: 49


title: Frac_Hela_0HdTAG_Cyto_rep4

description: Library name: Frac_Hela_0HdTAG_Cyto_rep4


description: Library name: Cas12a_DNMT1-3_48h_293_500k_PEI_KU60648_rep2


title: s48_AOMS_Hardship-1

description: Library name: 48


title: Frac_Hela_0HdTAG_Cyto_rep3

description: Library name: Frac_Hela_0HdTAG_Cyto_rep3


description: Library name: Cas12a_CCR5-1_48h_293_500k_PEI_T5-KU-60648_rep3


title: Frac_GANP_4HdTAG_Nuc_rep5

description: Library name: Frac_GANP_4HdTAG_Nuc_rep5


title: s47_AOMS_Hardship-1

description: Library name: 47


title: Frac_GANP_4HdTAG_Nuc_rep4

description: Library name: Frac_GANP_4HdTAG_Nuc_rep4


title: Frac_HCT116_4HdTAG_Cyto_rep3

description: Library name: Frac_HCT116_4HdTAG_Cyto_rep3

value: colon


title: Cas9_HEK4_48h_293_500k_PEI_RE1B_rep3

description: Library name: Cas9_HEK4_48h_293_500k_PEI_RE1B_rep3


title: Frac_HCT116_4HdTAG_Cyto_rep1

description: Library name: Frac_HCT116_4HdTAG_Cyto_rep1


title: s53_AOMS_Hardship-1

description: Library name: 53


title: s46_POMS_Hardship-1

description: Library name: 46


description: Library name: Cas12a_CCR5-1_48h_293_500k_PEI_T5-KU-60648_rep2


title: Frac_GANP_4HdTAG_Cyto_rep5

description: Library name: Frac_GANP_4HdTAG_Cyto_rep5


description: Library name: Cas12a_CCR5-1_48h_293_500k_PEI_mock_rep3


title: Frac_GANP_4HdTAG_Cyto_rep4

description: Library name: Frac_GANP_4HdTAG_Cyto_rep4


title: Frac_GANP_4HdTAG_Nuc_rep3

description: Library name: Frac_GANP_4HdTAG_Nuc_rep3


title: s45_AOMS_Hardship-1

description: Library name: 45


title: Frac_GANP_4HdTAG_Cyto_rep3

description: Library name: Frac_GANP_4HdTAG_Cyto_rep3


description: Library name: Cas12a_CCR5-1_48h_293_500k_PEI_mock_rep2


title: Rescue_ZFC3H1_4HdTAG_rep3

description: Library name: Rescue_ZFC3H1_4HdTAG_rep3


title: s44_POMS_Hardship-0

description: Library name: 44


title: ABE_VEGFA3_24h_293_500k_PEI_T5_rep3

description: Library name: ABE_VEGFA3_24h_293_500k_PEI_T5_rep3


title: Rescue_ZFC3H1_4HdTAG_rep2

description: Library name: Rescue_ZFC3H1_4HdTAG_rep2


title: Rescue_ZFC3H1_4HdTAG_rep1

description: Library name: Rescue_ZFC3H1_4HdTAG_rep1


title: s43_AOMS_Hardship-0

description: Library name: 43


description: Library name: Rescue_ZFC3H1_4HdTAG_expre_ZFC3H1wt_rep3

value: 4H dTAGV-1 500nM - ectopic expression of WT ZFC3H1


title: ABE_VEGFA3_24h_293_500k_PEI_T5_rep2

description: Library name: ABE_VEGFA3_24h_293_500k_PEI_T5_rep2


description: Library name: Rescue_ZFC3H1_4HdTAG_expre_ZFC3H1wt_rep2


title: s42_AOMS_Hardship-1

description: Library name: 42


description: Library name: Rescue_ZFC3H1_4HdTAG_expre_ZFC3H1wt_rep1


description: Library name: Rescue_ZFC3H1_4HdTAG_expre_ZFC3H1d730747_rep3

value: 4H dTAGV-1 500nM - ectopic expression of ZFC3H1Δ730-747


title: ABE_VEGFA3_24h_293_500k_PEI_T5_rep1

description: Library name: ABE_VEGFA3_24h_293_500k_PEI_T5_rep1


title: s41_AOMS_Hardship-0

description: Library name: 41


title: s907_AOMS_Hardship-0

description: Library name: 907


description: Library name: Rescue_ZFC3H1_4HdTAG_expre_ZFC3H1d730747_rep2


title: ABE_VEGFA3_24h_293_500k_PEI_mock_rep3

description: Library name: ABE_VEGFA3_24h_293_500k_PEI_mock_rep3


title: s906_AOMS_Hardship-0

description: Library name: 906


description: Library name: Rescue_ZFC3H1_4HdTAG_expre_ZFC3H1d730747_rep1


title: s40_POMS_Hardship-1

description: Library name: 40


title: ABE_VEGFA3_24h_293_500k_PEI_mock_rep2

description: Library name: ABE_VEGFA3_24h_293_500k_PEI_mock_rep2


title: Rescue_ZFC3H1_0HdTAG_rep3

description: Library name: Rescue_ZFC3H1_0HdTAG_rep3


title: s39_POMS_Hardship-0

description: Library name: 39


title: Rescue_ZFC3H1_0HdTAG_rep2

description: Library name: Rescue_ZFC3H1_0HdTAG_rep2


title: Rescue_ZFC3H1_0HdTAG_rep1

description: Library name: Rescue_ZFC3H1_0HdTAG_rep1


title: ABE_VEGFA3_24h_293_500k_PEI_mock_rep1

description: Library name: ABE_VEGFA3_24h_293_500k_PEI_mock_rep1


title: HO127

city: Rochester

first: Martin

last: Fernandez-Zapico

state: MN

address: 200 1st St SW

institute: Mayo Clinic

description: Library name: Sample 15

data_processing:
Fastq files of paired-end RNA-Seq reads were aligned with STAR 2.7.8a  to the reference genome GRCh38.
Gene level counts were obtained using htseq v0.9.1
Assembly: GRCh38
Supplementary files format and content: tab-deliminted text file contains raw counts for each sample

source_name: Tumor

growth_protocol: PDOs were grown in PaTOM media

extract_protocol:
mRNA extracted using the Qiagen Rneasy Micro Kit. 400 ng of total RNA according to manufacturers instructions for Illumina TruSeq Stranded mRNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: Tumor

value: liver metastais

value: Colorectal cancer


title: s38_POMS_Hardship-0

description: Library name: 38


title: UAP56_iCLIP_rep2

description: Library name: UAP56_iCLIP_rep2

value: WT


title: HO123

description: Library name: Sample 14


title: Cas9_HEK4_48h_293_500k_PEI_KP32_rep3

description: Library name: Cas9_HEK4_48h_293_500k_PEI_KP32_rep3


title: ABE_VEGFA2_24h_293_500k_PEI_T7_rep3

description: Library name: ABE_VEGFA2_24h_293_500k_PEI_T7_rep3


title: HO98

description: Library name: Sample 13


title: s37_POMS_Hardship-0

description: Library name: 37

value: PBMC


title: HO90

description: Library name: Sample 12


title: ABE_VEGFA2_24h_293_500k_PEI_T5_rep3

description: Library name: ABE_VEGFA2_24h_293_500k_PEI_T5_rep3


title: HO46

description: Library name: Sample 11


title: s36_AOMS_Hardship-1

description: Library name: 36

value: Adult


title: HO12

description: Library name: Sample 10


title: ABE_VEGFA2_24h_293_500k_PEI_mock_rep3

description: Library name: ABE_VEGFA2_24h_293_500k_PEI_mock_rep3


title: HO211

description: Library name: Sample 9

value: peritoneal metastsis


title: s35_AOMS_Hardship-1

description: Library name: 35


title: HO199

description: Library name: Sample 8


title: HO198

description: Library name: Sample 7


title: ABE_HEK4_24h_293_500k_PEI_T7_rep3

description: Library name: ABE_HEK4_24h_293_500k_PEI_T7_rep3


title: s34_POMS_Hardship-1

description: Library name: 34

value: Pediatric


title: HO197

description: Library name: Sample 6


title: ABE_HEK4_24h_293_500k_PEI_T7_rep2

description: Library name: ABE_HEK4_24h_293_500k_PEI_T7_rep2


title: HO196

description: Library name: Sample 5


title: s32_AOMS_Hardship-1

description: Library name: 32


title: HO195

description: Library name: Sample 4


title: ABE_HEK4_24h_293_500k_PEI_T5_rep3

description: Library name: ABE_HEK4_24h_293_500k_PEI_T5_rep3


title: HO179

description: Library name: Sample 3


title: s31_AOMS_Hardship-1

description: Library name: 31


title: HO178

description: Library name: Sample 2


title: s30_AOMS_Hardship-0

description: Library name: 30


title: HO176

description: Library name: Sample 1


title: ABE_HEK4_24h_293_500k_PEI_T5_rep2

description: Library name: ABE_HEK4_24h_293_500k_PEI_T5_rep2


title: V5

city: Wuhan

first: Longpeng

last: Li

address: No. 461 Luoyu Rd. Hongshan District, Wuhan

institute: Wuhan Sports University

description:
Library name: V5
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software.
Assembly: mRatBN 7.2
Supplementary files format and content: Cell Ranger output files: barcode.tsv.gz,features.tsv.gz,matrix.mtx.gz

organism: Rattus norvegicus

source_name: blood

extract_protocol:
At the experimental endpoint, animals were euthanized under isoflurane anesthesia in accordance with institutional animal welfare guidelines. A midline laparotomy was performed to expose the abdominal aorta and inferior vena cava. Arterial blood was collected from the abdominal aorta, and venous blood was obtained from the inferior vena cava. Blood samples were immediately transferred into anticoagulant-containing tubes and gently mixed for subsequent PBMC isolation and analysis.
Single-cell RNA sequencing libraries were generated using the 10x Genomics Chromium Controller and Chromium Single Cell 3’ v3 reagent kits (10X Genomics, USA), following the manufacturer’s instructions. Briefly, cells were adjusted to approximately 1,000 cells/μL and loaded to generate single-cell gel bead-in-emulsions (GEMs). After reverse transcription, GEMs were disrupted, and barcoded cDNA was purified and amplified. The amplified cDNA was subsequently fragmented, A-tailed, adaptor-ligated, and indexed by PCR. Final libraries were quantified using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific, USA) and assessed for size distribution on the Bioanalyzer 2200 (Agilent, USA), followed by paired-end sequencing (150 bp) on the DNBSEQ-T7 platform (MGI, China).

value: blood

value: venous peripheral blood mononuclear cells


title: s29_AOMS_Hardship-1

description: Library name: 29


title: ABE_HEK4_24h_293_500k_PEI_mock_rep3

description: Library name: ABE_HEK4_24h_293_500k_PEI_mock_rep3


title: V4

description:
Library name: V4
10x Genomics


title: V3

description:
Library name: V3
10x Genomics


title: ABE_HEK4_24h_293_500k_PEI_mock_rep2

description: Library name: ABE_HEK4_24h_293_500k_PEI_mock_rep2


title: V2

description:
Library name: V2
10x Genomics


title: s28_POMS_Hardship-1

description: Library name: 28


title: V1

description:
Library name: V1
10x Genomics


title: PE3_VEGFA2_48h_HEK293T_500k_PEI_T7_rep2

description: Library name: PE3_VEGFA2_48h_HEK293T_500k_PEI_T7_rep2

data_processing:
Data were mapped to hg38 (human) using chromap.
Reads overlaped the ENCODE blacklist are removed
Bedtools was used to generate bedGraph files, which were then normalized and converted to BigWig files by bedGraphToBigWig
Assembly: hg38
Supplementary files format and content: BigWig of genome-editing signals

extract_protocol:
Cells were fixed with Concanavalin A bead, washed, and resuspended with buffer containing RPA2/MRE11/IgG antibodies. pA-MNase was added to cleavage the DNA. Cleavaged fragments were collected and then digested with DNase. For Tracking-seq, DNA was purified with DNA Clean Beads and then HL-dsDNase was added to remove dsDNA.
The strand-specific ssDNA libraries were constructed using VAHTS ssDNA Library Prep Kit. CUT&RUN-MRE11 library was constructed using NEBNext® Ultra™ II DNA Library Prep Kit.


title: s27_POMS_Hardship-0

description: Library name: 27


title: A5

description:
Library name: A5
10x Genomics

value: arterial peripheral blood mononuclear cells


title: A4

description:
Library name: A4
10x Genomics


title: PE3_VEGFA2_48h_HEK293T_500k_PEI_T7_rep1

description: Library name: PE3_VEGFA2_48h_HEK293T_500k_PEI_T7_rep1


title: Frac_LENG8_4HdTAG_Nuc_rep3

description: Library name: Frac_LENG8_4HdTAG_Nuc_rep3

value: cervix

value: HeLa Kyoto

value: 4H dTAGV-1 500nM


title: PE3_VEGFA2_48h_HEK293T_500k_PEI_T5_rep2

description: Library name: PE3_VEGFA2_48h_HEK293T_500k_PEI_T5_rep2


title: A3

description:
Library name: A3
10x Genomics


title: A2

description:
Library name: A2
10x Genomics


title: s26_POMS_Hardship-1

description: Library name: 26


title: A1

description:
Library name: A1
10x Genomics


title: s25_AOMS_Hardship-0

description: Library name: 25


title: PE3_VEGFA2_48h_HEK293T_500k_PEI_T5_rep1

description: Library name: PE3_VEGFA2_48h_HEK293T_500k_PEI_T5_rep1


title: Cauda sperm, High-fat diet, rep4

city: Santa Cruz

first: Andrew

middle: David

last: Holmes

state: California

address: 1156 High Street

department: Molecular, Cell, and Developmental Biology

institute: UC Santa Cruz

description: Library name: HF_CASP_4

data_processing:
Sequences were trimmed with  "cutadapt --no-indels -O 15 -m 2 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC" ,"cutadapt -u 7" , and then "cutadapt -u -1" to remove the adapter, the UMI, and the TPRT base (the UMI was not used for removing duplicates)  Only reads >65 bases were used for most analyses
Data was mapped and counted using TRAX, which uses an all-best mapping approach and uses Deseq2 for normalization and detection of differential expression
Assembly: mm10
Supplementary files format and content: tab-delimited raw counts for calculated by tRAX, with mitochondrial tRNA counts appended

source_name: Sperm

growth_protocol: Mice were group-housed (maximum of 5 per cage) with a 12-hour light-dark cycle (lights off at 6 pm) and free access to food and water ad libitum.

extract_protocol:
Samples were vortexed for 5 minutes to ensure complete breakdown of the sperm, followed by centrifugation at 12,000 RCF for 4 minutes. The aqueous phase was then removed and transferred to a low-binding RNase/DNase-free microcentrifuge tube, followed by the addition of 20 µg of glycoblue (Invitrogen) and 1 volume of Isopropanol. The RNA was then precipitated for 30 minutes or greater at -20°C, followed by centrifugation at 18,000 RCF for 30 minutes at 4°C, and one wash with 70% cold ethanol followed by centrifugation at 12,000 RCF for 10 minutes at 4°C. Finally, the RNA was reconstituted in nuclease-free water.
Library was constructed using Ottr-seq protocol.  Input RNA was PNK treated and labelled at the 3’ end by incubation in buffer containing ddATP for 90 minutes in 30˚C, followed by an addition of ddGTP and another incubation at 30˚C for 30 minutes. The reaction was stopped by incubating at 65°C for 5 minutes, followed by the addition of 5 mM MgCl2 and 0.5 units of shrimp alkaline phosphatase (NEB, cat# M0371S) at 37°C for 15 minutes, then stopped by the addition of 5 mM EGTA, and incubated at 65°C for 5 minutes. Samples were then incubated in templated cDNA synthesis buffer, adaptors, and dNTPs at 37˚C for 20 minutes, followed by heat inactivation at 65˚C for 5 minutes and RNase A/H treatment. cDNA was size selected on a 10% PAGE urea gel to minimize adaptor dimers. Size selected cDNA was PCR amplified for 12 cycles with Q5 high fidelity polymerase (NEB, cat# M0491S). The final PCR product was cleaned up with AMPure XP beads (Beckman, cat # A63881) and finally separated by 6% TBE gel to remove adaptor dimers. The desired product was excised from the gel and eluted in 400ul elution buffer (300 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA) overnight at -20, followed by isopropanol precipitation and resuspension in 9µl nuclease-free H2O.

treatment_protocol: Animals were raised on one of four diets – a low protein diet (LP; 10% of protein rather than 18%, remaining mass made up with sucrose, BioServ, cat# S3156), control for low protein diet (C; BioServ AIN-93g, cat# F3156), a high fat diet (HF; 60% of fat calories rather than 16%, BioServ, cat# S3282) , or control for high-fat diet  (C_HF; 7.2% fat calories, BioServ, cat# S4031)

value: Sperm

value: High-fat diet


title: Cauda sperm, High-fat diet, rep3

description: Library name: HF_CASP_3


title: s23_AOMS_Hardship-1

description: Library name: 23


title: Cauda sperm, High-fat diet, rep2

description: Library name: HF_CASP_2


city: Shanghai

first: Zhu

last: Ming

address: No. 500, Dongchuan Road

institute: East China Normal University

description: Library name: PE3_VEGFA2_48h_HEK293T_500k_PEI_mock_rep2


title: Cauda sperm, High-fat diet, rep1

description: Library name: HF_CASP_1


title: Cas9_VEGFA2_48h_293_500k_PEI_RocE_rep2

description: Library name: Cas9_VEGFA2_48h_293_500k_PEI_RocE_rep2


title: s21_POMS_Hardship-0

description: Library name: 21


title: Cauda sperm, High-fat control diet, rep4

description: Library name: C_HF_CASP_4

value: High-fat control diet


description: Library name: PE3_VEGFA2_48h_HEK293T_500k_PEI_mock_rep1


title: Cauda sperm, High-fat control diet, rep5

description: Library name: C_HF_CASP_5


title: s20_POMS_Hardship-1

description: Library name: 20


title: PE3_HEK4_48h_HEK293T_500k_PEI_T7_rep1

description: Library name: PE3_HEK4_48h_HEK293T_500k_PEI_T7_rep1


title: Cauda sperm, High-fat control diet, rep2

description: Library name: C_HF_CASP_2


title: s19_AOMS_Hardship-1

description: Library name: 19


title: Cauda sperm, High-fat control diet, rep3

description: Library name: C_HF_CASP_3


title: Cauda sperm, High-fat control diet, rep1

description: Library name: C_HF_CASP_1


title: PE3_HEK4_48h_HEK293T_500k_PEI_T5_rep1

description: Library name: PE3_HEK4_48h_HEK293T_500k_PEI_T5_rep1


title: Cauda sperm, Low-protein diet, rep5

description: Library name: LP_CASP_5

value: Low-protein diet


title: s18_POMS_Hardship-0

description: Library name: 18


title: Cauda sperm, Low-protein diet, rep4

description: Library name: LP_CASP_4


title: PE3_HEK4_48h_HEK293T_500k_PEI_mock_rep1

description: Library name: PE3_HEK4_48h_HEK293T_500k_PEI_mock_rep1


title: Cauda sperm, Low-protein diet, rep3

description: Library name: LP_CASP_3


title: Cauda sperm, Low-protein diet, rep2

description: Library name: LP_CASP_2


title: s17_POMS_Hardship-0

description: Library name: 17