title: CSF cells, HD4

description: Library name: LIB_03630


title: CSF cells, RR-MS3

status: Public on Feb 01 2025

type: SRA

city: Bethesda

first: Shinji

last: Ashdia

state: MD

address: 10 Center Drive

department: NIAID

country: USA

institute: NIH

description: Library name: LIB_02383

library_source: transcriptomic single cell

data_processing:
In single cell RNA-seq data analysis, each raw data was counted, and QC was checked by Cellranger ver.7.0 (10X Genomics). Doublet cells were excluded by using DoubletFinder ver.2.0 and protein library from CITE-seq was denoised by using dsb package.
Assembly: human reference genome (hg38)
Supplementary files format and content: Tab-separated values (TSV) file, Indicate that the file contains processed data, such as gene expression matrices, cell metadata,generated by the 10x Cell Ranger pipeline.

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: CSF cells

extract_protocol:
CSF was collected on ice and processed according to a written standard operating procedure by investigators blinded to diagnoses, clinical, and imaging outcomes. Aliquots were assigned alphanumeric identifiers and centrifuged for 10 minutes at 300g at 4°C within 30 minutes of collection.
The pelleted CSF cells were processed by flow cytometry or processed for single cell RNA sequencing. Fresh CSF cells were collected as described in sample processing. Cells were labelled with 79 Totalseq B antibodies (Biolegend, USA) and washed with PBS with 1% Bovine Serum Albumin (Thermo Fisher Scientific, USA). Labeled cells were fixed by using fixed RNA feature barcode kit (10x Genomics, USA) and stored at -80 degree.  Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) method was used to analyze transcriptome and surface protein information based on  single-cell readout. After probe hybridization, gene expression library and surface protein library were constructed by using Chromium Next GEM Single cell 3` LT Reagent kits v3.1 (Dual index) (10X Genomics, USA) following the protocol (CG000400). Single-cell fixed RNA libraries and single-cell feature barcode libraries were sequenced  on a NextSeq 2000 P3 28 cycle + 90 cycle asymmetrical run.  Demultiplexing yielded over 27 million reads per sample when allowing for 1 mismatch per index adapter.

tag: sample id

tag: tissue

value: CSF cells

tag: disease state

value: Multiple sclerosis


title: CSF cells, PP-MS5

description: Library name: LIB_03405


title: Human MN shCtrl Soma Rep2

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

description: Library name: HumanMN_ShSCRsoma5

library_source: transcriptomic

data_processing:
Adapters were trimmed using Cutadapt
Transcript abundances were calculated using salmon
Gene-level abundances were calculated using tximport
Assembly: mm10, hg38
Supplementary files format and content: Salmon-calculated transcript abundances

molecule: polyA RNA

organism: Mus musculus

source_name: Human iPS motor neuron

growth_protocol: CAD cells were grown in DMEM/F12. N2A cells were grown in DMEM. Both were supplemented with 10% FBS. To differentiate cells, FBS was removed.

extract_protocol:
RNA was extracted with Zymo Quick RNA microprep kits
Libraries were constructed using Kapa RNA Hyperprep kits

treatment_protocol: To induce TDP-43 loss, 2 ug / mL doxycycline was added for 48 hrs

tag: cell type

value: Human iPS motor neuron

tag: treatment

value: scramble shRNA

tag: compartment

value: soma


title: 17-AAG/SPDL1-sgRNA2 #1

city: London

first: Chi

last: Zhang

address: 15 Cotswold Road

department: Division of Cancer Therapeutics

country: United Kingdom

institute: The Institute of Cancer Research

description: 17-AAG/SPDL1-sgRNA2-treated replicate#1

data_processing:
Raw reads were aligned to GRCh38 genome assembly and GENCODE GRCh38.p13 annotation using STAR programme, followed by processing of the resultant file using SAMtools.
Read counting on genomic features was carried out using Rsubread, and the R package DESeq2 was used to perform statistic-based quantifications.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel table with quantification results, generated by DESeq2

source_name: H2228 Cell line

growth_protocol: NCI-H2228 [H2228] (ATCC, CRL-5935) cells were cultured in RPMI medium (Sigma-Aldrich) supplemented with 10% FBS (PAN Biotech).

extract_protocol:
Total RNA from T-47D cells were extracted using MagNA pure 96 instrument (Roche), and RNA integrity number was measured by BioAnalyzer 2100 (Agilent).
RNA libraries were constructed and sequenced by BGI using poly-dT enrichment in conjunction with DNB technology on BGISEQ-500 instrument.
RNA-seq, non-strand-specific and pair-ended.

treatment_protocol: Cas9-expressing H2228 cells were constructed with pLEX_311-Cas9v2 vector and lentiviral helper plasmids and selected using puromycin. Non-targeting and SPDL1-targeting sgRNA  were purchased with Sigma Aldrich (TRCN0000135058, TRCN0000135059, TRCN0000160944, TRCN0000164576). CRISPR KO cells were treated with DMSO or 6 nM tanespimycin (Selleckchem) for 10 d prior to mRNA extractions.

tag: crispr sgrna

value: SPDL1-targeting, sgRNA2

tag: drug treatments

value: tanespimycin

tag: strain


title: Human MN shCtrl Soma Rep1

description: Library name: HumanMN_ShSCRsoma4


title: 6 tpo AKPS dmso

city: Utrecht

first: Saskia

middle: van

last: Mil

address: Universiteitsweg 100

department: Center for Molecular Medicine

country: Netherlands

institute: UMC Utrecht

data_processing:
Quality control was doen with FastQC (v0.11.8)
TrimGalore (v0.6.5) was used to trim reads based on quality and adapter presence after which FastQC was used to check the resulting quality.
rRNA reads were filtered out using SortMeRNA (v 4.3.3)
Reads were aligned to the reference genome using the STAR (v. 2.73a) aligner
QC on the mapped files was done using Sambamba (v0.7.0), RSeQC (v3.0.1) and PreSeq (v2.0.3)
Assembly: Readcounts were generated using the Subread Featurecounts module (v2.0.0) and normalization using edgeR (v 3.28).
Supplementary files format and content: Hs_GRCh38_gatk_sorted.fasta
Supplementary files format and content: tab-delimited text file containing the raw data counts

source_name: colon

extract_protocol:
RNA was isolated using the Macherey-Nagel Nucleospin RNA isolation kit.
Libraries were prepared using the TruSeq stranded mRNA polyA kit

treatment_protocol: Organoids were lentivirally transduced with either FXRa3, FXRa4 or GFP and treated with either DMSO or obeticholic acid (OCA) for 3 days.

value: colon

tag: cell line

value: TPO AKPS

value: dmso


title: CSF cells, HD2

description: Library name: LIB_02382


title: CSF cells, NIND1

description: Library name: LIB_02381


title: 4 wt oca

value: WT

value: oca


title: 11 tpo AKPS gfp dmso


title: Human MN shCtrl Neurite Rep3

description: Library name: HumanMN_ShSCRneurite6

value: neurite


title: 17-AAG/SPDL1-sgRNA1 #4

description: 17-AAG/SPDL1-sgRNA1-treated replicate#4

value: SPDL1-targeting, sgRNA1


title: Human MN shCtrl Neurite Rep2

description: Library name: HumanMN_ShSCRneurite5


title: 17-AAG/SPDL1-sgRNA1 #3

description: 17-AAG/SPDL1-sgRNA1-treated replicate#3


title: CSF cells, RR-MS2

description: Library name: LIB_02379


title: 3 wt oca


title: CSF cells, PP-MS2

description: Library name: LIB_02380


title: 7 tpo AKPS dmso


title: 17-AAG/SPDL1-sgRNA1 #2

description: 17-AAG/SPDL1-sgRNA1-treated replicate#2


title: Human MN shCtrl Neurite Rep1

description: Library name: HumanMN_ShSCRneurite4


title: 2 wt dmso


title: WT Soma Rep3

description: Library name: WT.soma.rep3

source_name: CAD

value: CAD

tag: genotype

value: WT TDP-43 overexpression


title: LoVo R4sh3

city: Guangzhou

first: Long

last: Yu

state: --- Select One ---

address: dongfengdonglu

country: China

institute: Sun Yat-sen University Cancer Center

data_processing:
Raw fastq sequences were treated with Trimmomatictools (v 0.36) using the following options: :TRAILING:20, SLIDINGWINDOW:4:15 MINLEN:52, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 52).
Paired-end reads were aligned to the human reference genome hg38 with HISAT2. HTSeq v0.12.4 was used to count the reads numbers mapped to each gene.
Quantification of gene expression level.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes counts and TPM values.

molecule: total RNA

source_name: LoVo

extract_protocol:
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China) according to the manufacturer's protocol.
The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit (Thermo Fisher Scientific, USA). The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).

treatment_protocol: Compare the mRNA changes in LoVo cells after 72 hours of RIPK4 gene interference.

value: LoVo

value: RIPK4 gene interference


title: CSF cells, RR-MS1

description: Library name: LIB_02378

value: CSF cells

value: Multiple sclerosis


title: WT Soma Rep2

description: Library name: WT.soma.rep2


title: 1 wt dmso


title: CSF cells, PP-MS1

description: Library name: LIB_02360


title: 17-AAG/SPDL1-sgRNA2 #2

description: 17-AAG/SPDL1-sgRNA2-treated replicate#2


title: CSF cells, HD1

description: Library name: LIB_02359


title: 17-AAG/SPDL1-sgRNA1 #1

description: 17-AAG/SPDL1-sgRNA1-treated replicate#1


title: 5 tpo AKPS dmso


title: 17-AAG/NTC-sgRNA #4

description: 17-AAG/NTC-sgRNA-treated replicate#4

value: Non-targeting control


title: LoVo R4sh2


title: WT Soma Rep1

description: Library name: WT.soma.rep1

value: soma


title: LoVo R4sh1


title: 17-AAG/NTC-sgRNA #3

description: 17-AAG/NTC-sgRNA-treated replicate#3


title: CSF cells, SP-MS1

description: Library name: LIB_02358


title: WT Neurite Rep3

description: Library name: WT.neurite.rep3


title: LoVo nc3

value: Control


title: 17-AAG/NTC-sgRNA #2

description: 17-AAG/NTC-sgRNA-treated replicate#2

value: tanespimycin


title: 17-AAG/NTC-sgRNA #1

description: 17-AAG/NTC-sgRNA-treated replicate#1


title: WT Neurite Rep1

description: Library name: WT.neurite.rep1


title: DMSO/SPDL1-sgRNA2 #4

description: DMSO/SPDL1-sgRNA2-treated replicate#4

value: SPDL1-targeting, sgRNA2

value: DMSO


title: LoVo nc2


title: DMSO/SPDL1-sgRNA2 #3

description: DMSO/SPDL1-sgRNA2-treated replicate#3


title: LoVo nc1


title: Q331K Soma Rep2

description: Library name: Q331K.soma.rep2

value: Q331K TDP-43 overexpression


title: DMSO/SPDL1-sgRNA2 #2

description: DMSO/SPDL1-sgRNA2-treated replicate#2


title: Q331K Soma Rep1

description: Library name: Q331K.soma.rep1


title: DMSO/SPDL1-sgRNA2 #1

description: DMSO/SPDL1-sgRNA2-treated replicate#1


title: LoVo det3

treatment_protocol: Compare the mRNA changes in SW620 and LoVo cells under adherent and suspension conditions for 72 hours.

value: detach


title: Q331K Soma Rep3

description: Library name: Q331K.soma.rep3


title: LoVo det2


title: LoVo det1


title: Q331K Neurite Rep3

description: Library name: Q331K.neurite.rep3


title: Q331K Neurite Rep2

description: Library name: Q331K.neurite.rep2


title: DMSO/SPDL1-sgRNA1 #3

description: DMSO/SPDL1-sgRNA1-treated replicate#3


title: LoVo att3

value: attach


title: DMSO/SPDL1-sgRNA1 #2

description: DMSO/SPDL1-sgRNA1-treated replicate#2


title: WT Neurite Rep2

description: Library name: WT.neurite.rep2

value: neurite


title: LoVo att1


title: LoVo att2


title: SLAM -dox t12 Rep3

description: Library name: SLAMseq_WT_t12_Rep3

value: TetOff TDP-43

value: minus dox


title: DMSO/SPDL1-sgRNA1 #1

description: DMSO/SPDL1-sgRNA1-treated replicate#1

value: SPDL1-targeting, sgRNA1


title: Q331K Neurite Rep1

description: Library name: Q331K.neurite.rep1

value: CAD


title: DMSO/NTC-sgRNA #4

description: DMSO/NTC-sgRNA-treated replicate#4


title: 620 det3


title: 620 det2


title: DMSO/NTC-sgRNA #3

description: DMSO/NTC-sgRNA-treated replicate#3


title: DMSO/SPDL1-sgRNA1 #4

description: DMSO/SPDL1-sgRNA1-treated replicate#4


title: SLAM -dox t12 Rep2

description: Library name: SLAMseq_WT_t12_Rep2


title: intestine_wildtype_control_rep3

type: RNA

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description: small intestine wild-type mice, control diet (chow).

hyb_protocol: According to standard Affymetrix protocols.

data_processing: GCRMA version 2.20, empirical Bayes

label: biotin

extract_protocol: TRIzol reagent (Invitrogen), according to manufacturer's instructions

tag: Strain

value: 129S1/SvJae (wild-type)

tag: Gender

value: male

tag: Age

value: 14 weeks

tag: Tissue

value: small intestine


title: intestine_wildtype_5d_WY14643_rep4

description: small intestine wild-type mice, treated with WY14,643 for 5 days. The WY14.643 was present in the diet at 0.1% w/w.

scan_protocol: According to standard Affymetrix protocols.


title: intestine_PPARa-knockout_5d_WY14643_rep4

description: Small intestine PPARalpha knockout mice, treated with WY14,643 for 5 days. The WY14.643 was present in the diet at 0.1% w/w.

data_processing: GCRMA version 2.20, emperical Bayes

label_protocol: According to standard Affymetrix protocols.

value: 129S4/SvJae (PPARalpha knockout)


title: SLAM -dox t0 Rep2

description: Library name: SLAMseq_WT_t0_Rep2


title: intestine_PPARa-knockout_5d_WY14643_rep2


title: intestine_wildtype_control_rep4

description: Small intestine wild-type mice, control diet (chow).


title: intestine_PPARa-knockout_5d_WY14643_rep1


title: SLAM -dox t12 Rep1

description: Library name: SLAMseq_WT_t12_Rep1


title: intestine_wildtype_5d_WY14643_rep2


title: intestine_wildtype_control_rep2

value: 129S1/SvJae wild-type


title: 620 att3


title: intestine_PPARa-knockout_5d_WY14643_rep3


title: intestine_wildtype_5d_WY14643_rep3


title: intestine_wildtype_5d_WY14643_rep1


title: DMSO/NTC-sgRNA #1

description: DMSO/NTC-sgRNA-treated replicate#1

value: Non-targeting control


title: intestine_PPARa-knockout_control_rep4

description: Small intestine of PPARalpha knockout mice, control diet (chow).


title: SLAM -dox t0 Rep1

description: Library name: SLAMseq_WT_t0_Rep1


title: 620 att2


title: heart, dKO 3

city: La Jolla

first: Stephan

last: Lange

state: CA

address: 9500 Gilman Dr

department: Medicine

institute: UC San Diego

description: Library name: dKO.3

data_processing:
fastq files were aligned to mouse reference genome GRCm38
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. More information: https://github.com/nf-core/rnaseq
Assembly: mouse reference genome GRCm38
Supplementary files format and content: tab-delimited text files include FPKM and TPM values for each Sample

source_name: heart

extract_protocol:
Total RNA was isolated using Trizol as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA Kit, according to the manufacturer’s instructions.

value: heart


title: intestine_PPARa-knockout_control_rep3


title: 620 det1


title: heart, dKO 2

description: Library name: dKO.2


title: 620 att1


title: SLAM no4su Rep2

description: Library name: SLAMseq_no4SU2


title: siControl_DMSO_control_2

city: Munich

last: Hamperl

state: Bayern

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz-Zentrum Munich

description:
23L013312
tissue culture

data_processing:
bowtie2 (version 2.3.0) with default parameters was used to discard reads mapping to rRNA (GenBank identifier U13369.1) and to verify the absence of mycoplasma contamination.
STAR version 2.5.3a was used to map all remaining reads with length at least 18 nt against the human genome (Ensembl 90) (parameters: --outFilterMismatchNmax 40 --outFilterScoreMinOverLread 0.2 --outFilterMatchNminOverLread 0.2 --alignEndsType Extend5pOfReads12 --outSAMattributes nM MD NH). Then, the GRAND-SLAM program (version 2.0.7) was run (parameters –trim 15 -modelall) to count reads and to estimate the new-to-total RNA ratio (NTR) for each sample and each mRNA.
Assembly: GRCh38 (Ensembl 90)
Supplementary files format and content: Tab-delimited text file includes read counts and new-to-total RNA ratios (MAP columns).
Library strategy: SLAM-seq

source_name: U-2OS Tet-ON

growth_protocol: Human osteosarcoma-derived cells (U2OS) that express the tetracycline regulated transactivator Tet-ON were used for all experiments. U2OS Tet-ON cells were cultured in DMEM (GIBCO) supplemented with 10% Tet-ON approved FBS, 4.5 g/L D-Glucose and L-Glutamine, 110 mg/L sodium pyruvate and penicillin/streptomycin in 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated using Trizol and resulting RNA samples mixed with in vitro transcribed 4sU incorporated spike-in RNA from selected RNAs of the ERCC RNA Spike-in Mix.
Library preparation was carried out using the Lexogen QuantSeq 3’ V2 kit using the manufacturer's protocol.
4sU-RNA was used for library preparation. The concentration and size distribution of the libraries were determined on a Bioanalyzer (Agilent Technologies).
Alkylation of RNA was carried out using 10 mM iodoacetamide, and the reaction quenched with 1M DTT.

treatment_protocol: siControl (Dharmacon, D-001810-10-20) or siCGGBP1 (Dharmacon, L-015703-00-0020) were transfected at a ratio of 50 nM siRNA per 2 µL transfection reagent into U-2OS Tet-ON cells and collected after 72h of transcription. 60min prior to harvesting, medium was changed to 4sU containing medium with the indicated final concentrations.

value: U-2OS Tet-ON

value: osteosarcoma cancer cell line

value: Control knockdown

value: 60min 200uM 4sU


title: SLAM no4su Rep1

description: Library name: SLAMseq_no4SU1


title: heart, dKO 1

description: Library name: dKO.1


title: DMSO/NTC-sgRNA #2

description: DMSO/NTC-sgRNA-treated replicate#2

value: DMSO


title: intestine_PPARa-knockout_control_rep1

value: (129S4/SvJae (PPARalpha knockout)


title: SLAM +dox t12 Rep3

description: Library name: SLAMseq_KO_t12_Rep3

value: TetOff TDP-43

value: plus dox


title: siControl_DMSO_control_1

description:
23L013311
tissue culture

value: 60min 0uM 4sU


title: heart, obsl1 knockout 3

description: Library name: OL1.3


title: Sample GbExp87_1B_ctrl

city: San Giuliano Terme

first: Paolo

last: Aretini

state: Pisa

address: Via Ferruccio Giovannini 13

country: Italy

institute: Fondazione Pisana per la Scienza

description:
Library name: GbExp87_1B_ctrl
Column name in TPM_Data.txt: GbExp87_1B_ctrl

data_processing:
Sequence reads were mapped to GRCh38  using STAR-2.7.9a
TPM (Transcripts Per Kilobase Million) were calculate with RSEM using the command rsem-calculate-expression
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text includes TPM (Transcripts Per Kilobase Million) for each samples

source_name: Glioblastoma Fresh Tissue

extract_protocol:
RNA was extracted using the Maxwell® 16 Tissue LEV Total RNA Purification Kit. 500ng of total RNA was used to construct the sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA, following the manufacturer's recommendations

value: Glioblastoma Fresh Tissue

tag: batch


title: Sample GbExp83_ctrl

description:
Library name: GbExp83_ctrl
Column name in TPM_Data.txt: GbExp83_ctrl


title: intestine_wildtype_control_rep1

description: no additionals

hyb_protocol: Perfomed with standard affymetrix protocol

source_name: small intestine

extract_protocol: TRIZOL, Promega

value: 129S1/SvJae (wild-type)

value: male


title: SLAM +dox t12 Rep2

description: Library name: SLAMseq_KO_t12_Rep2

value: CAD


title: siCGGBP1_DMSO_3

description:
CGGBP1.DMSO C
23L013308
tissue culture

value: CGGBP1 knockdown

value: 60min 75uM 4sU


title: siControl_DMSO_3

description:
ctrl.DMSO C
23L013307
tissue culture


title: Sample GbExp81_ctrl

description:
Library name: GbExp81_ctrl
Column name in TPM_Data.txt: GbExp81_ctrl


title: siCGGBP1_DMSO_2

description:
CGGBP1.DMSO B
23L013304
tissue culture


title: SLAM +dox t12 Rep1

description: Library name: SLAMseq_KO_t12_Rep1


title: SLAM no4su Rep3

description: Library name: SLAMseq_no4SU3

value: minus dox


title: SLAM +dox t0 Rep2

description: Library name: SLAMseq_KO_t0_Rep2


title: Sample GbExp64_ctrl

description:
Library name: GbExp64_ctrl
Column name in TPM_Data.txt: GbExp64_ctrl


title: SLAM +dox t0 Rep1

description: Library name: SLAMseq_KO_t0_Rep1


title: SLAM +dox t0 Rep3

description: Library name: SLAMseq_KO_t0_Rep3


title: heart, control 3

description: Library name: CTL.3

value: heart

value: wildtype


title: 231 CELLS-si-NC

city: Jiaxing

first: Huadong

last: Ni

address: zhonghuan nan road 1882

institute: Department of Anesthesiology and Pain Research Center, The Affiliated Hospital of Jiaxing University

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Sequence quality was examined using the FastQCsoftware(v0.11.7)
The trimmed reads (trimmed 5'   , 3'   -adaptor bases using cutadapt(v1.17)) were aligned to reference genome(GRCh37) using Hisat2 software(v2.1.0);
The transcript abundance for each sample was estimated with StringTie(v1.3.3), and the FPKM value for gene and transcript level was calculated with R package Ballgown(v2.10.0).
Assembly: GRCh37
Supplementary files format and content: the FPKM value of detected mRNA for each sample

source_name: breast

growth_protocol: Cells were cultured L15 culture medium with 10% FBS

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

treatment_protocol: YBX1 was knocked down by transfection with YBX1 SIRNA in 231 cells

value: breast

value: 231 cell

value: siNC


title: heart, control 2

description: Library name: CTL.2


title: Sample GbExp80-1_ctrl

description:
Library name: GbExp80-1_ctrl
Column name in TPM_Data.txt: GbExp80-1_ctrl


title: RBNS 5nM Rep1

description: RNA Bind-N-Seq is an in vitro binding assay using purified protein and thousands of defined RNA sequences. The concentrations refer to the concentration of protein in that experiment. Multiple concentrations are used to approximate binding curves (Kd, etc.).


title: RBNS 50nM Rep2


title: heart, obsl1 knockout 1

description: Library name: OL1.1


title: Sample GbExp47_ctrl

description:
Library name: GbExp47_ctrl
Column name in TPM_Data.txt: GbExp47_ctrl


title: RBNS 50nM Rep1


title: PCC 7806  Replicate C time 7

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using an in-house program (https://github.com/baj12/clean_ngs).Only sequences at least 25 nt in length were considered for further analysis.
Bowtie version 1.2.2, with default parameters, was used for alignment on the reference genome (PCC 7806 from NCBI)
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t gene -g ID -s 1)
Count data were analyzed using R version 3.3.1 and the Bioconductor package DESeq2 version 1.12.3. The normalization and dispersion estimation were performed with DESeq2 using the default parameters but statistical tests for differential expression were performed with applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between the biological conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially  expressed.
Assembly: PCC 7806 from NCBI
Supplementary files format and content: Count matrix from featureCounts

organism: Microcystis aeruginosa

source_name: Microscystis aeruginosa PCC 7806

growth_protocol: The culture, sampling, nucleic acid extraction, and RNA sequencing were carried out at the Pasteur Cultures of Cyanobacteria (PCC) collection at the Institut Pasteur in 2017. A preculture of M. aeruginosa strain PCC 7806 was grown at 22 °C in 40 mL of the BG11 growth medium (Rippka et al., 1979) amended with 10 mM NaHCO3 under a 13/11 h light/dark cycle. Then, the culture was transferred into three separate flasks (named A, B and C). The triplicate cultures of 40 mL were progressively transferred to a final set of three cultures with a volume of 1250 mL each in fresh BG11 medium supplemented with 20 mM NaHCO3 and synchronized in an INFORS incubator with 1% CO2 and agitation under the same light/dark cycle and temperature conditions. Synchronization involved three consecutive transfers, aiming for an initial optical density at 750 nm (OD) of 0.05 and growing for a month. Sampling was performed during the mid-exponential phase (OD of 0.6-0.7) for each biological replicate, over a period of 24 h at eight time points: (i) at 7 am, 60 min before the transition from dark to light (t1_N); (ii) 9 am, 60 min after the transition from dark to light (t2_D); (iii) 12 am (t3-D); (iv) 4 pm (t4_D); (v) 8 pm, 1 h before the transition from light to dark (t5_D); (vi) 10 pm, 60 min after the transition from light to dark (t6_N); (vii) 2 am, i.e. the middle of the night (t7_N), and (viii) in the end of the night period (t8_N, 24-h after the first sampling point). The sampling procedure involved the removal of 150 mL of culture, which were centrifuged, rinsed with sterile water, and centrifuged again. The resulting pellets were flash-frozen in liquid nitrogen and stored at -80 °C until further processing. To minimize batch effects, the samples were randomized before subsequent processing.

extract_protocol:
RNA extraction was carried out using a Trizol reagent (Life Technologies) and the NucleoSpin miRNA kit (Macherey-Nagel). Firstly, 1 mL of Trizol preheated at 65 °C was added to the frozen pellets and incubated at 65 °C for 12 min with vortexing three times. After centrifugation (10 min at 4 °C and 12,000 rcf), the upper phase was transferred to a new tube and mixed with 500 µL of Trizol preheated at 65 °C. RNA extraction was achieved by adding 400 µL of chloroform, and incubating samples for 3 min at room temperature before centrifugation (10 min, 4°C, 12000 rcf). The upper phase was again transferred to a new tube for extraction with 400 µL of Trizol and 400 µL of chloroform with similar incubation and centrifugation conditions. The upper phase obtained from this step was then further processed using the NucleoSpin miRNA kit according to the manufacturer's instructions. The final purified RNA was eluted in 20 µL of RNase/DNase-free sterile water. The absence of genomic DNA contamination was confirmed by PCR targeting the 16S rRNA gene using specific primers. The quality and quantity of RNA were assessed using a Nanodrop spectrophotometer (ThermoFisher Scientific) and a Bioanalyzer (Agilent) with RNA Nano chips.
Library preparation was conducted using the TruSeq Stranded mRNA sample preparation kit (Illumina, San Diego, California) following the manufacturer's instructions. Ribosomal RNA (rRNA) depletion was performed using the Ribo-Zero rRNA removal kit (bacteria, #MRZB12424, Illumina) with 5 µg of total RNA. The rRNA-depleted RNA was then fragmented using divalent ions at 94°C for 8 min. The resulting fragmented RNA samples were reverse-transcribed using random primers, followed by complementary-strand synthesis to generate double-stranded cDNA fragments. There was no need for an end repair step in this process. A 3'-end adenine was added, and specific Illumina adapters were ligated to the cDNA fragments. The ligated products were amplified by PCR. The quality of the resulting oriented libraries was assessed using Bioanalyzer DNA1000 Chips (Agilent, # 5067-1504) and quantified using spectrofluorimetry (Quant-iT™ High-Sensitivity DNA Assay Kit, #Q33120, Invitrogen). Sequencing was performed on the Illumina HiSeq2500 platform of the Institut Pasteur, generating single-end 65 bp reads with strand specificity. Each lane of sequencing accommodated a mixture of 18 multiplexed samples.

tag: cell density

value: Microscystis aeruginosa PCC 7806


title: Sample GbExp36_ctrl

description:
Library name: GbExp36_ctrl
Column name in TPM_Data.txt: GbExp36_ctrl


title: RBNS 500nM Rep2


title: Sample GbExp48_ctrl

description:
Library name: GbExp48_ctrl
Column name in TPM_Data.txt: GbExp48_ctrl


title: AAH-14: Dac51-SK-UT-1 RNA

city: Chicago

first: Qiwei

last: Yang

state: IL

address: 5821 S Drexel Ave

department: Obstetrics and Gynecology

institute: The University of Chicago

data_processing:
Base calling was performed using the Illumina NovaSeq 6000 platform
Adapters were trimmed using Trim Galore! (0.6.7)
Trimmed sequences were aligned to the reference genome and projected to the transcriptome using STAR (4.0.2)
Raw gene counts were quantified using Salmon (1.5.2)
Assembly: GRCh38, transcriptome mapped to Gencode V34 gene annotations
Supplementary files format and content: matrix of raw counts with genes in rows and samples in columns

source_name: uterine leiomyosarcoma cell line

growth_protocol: The uterine leiomyosarcoma cell line (SK-UT-1) was cultured and maintained in ATCC-formulated Eagle’s Minimum Essential Medium with 10% of fetal bovine serum

extract_protocol:
Cell pellets were  flash-frozen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The SK-UT-1 cell line was treated with  Dac51 (5 uM) for 48 hours or vehicle control.

value: uterus

value: leiomyosarcoma

value: FTO inhibitor


title: heart, obscurin knockout 3

description: Library name: Obsc.3

value: Obsc-/-


title: PCC 7806  Replicate C time 5


title: AAH-12: VEH-SK-UT-1 RNA

value: DMSO (VEH)


title: Sample GbExp74_ctrl

description:
Library name: GbExp74_ctrl
Column name in TPM_Data.txt: GbExp74_ctrl

value: Glioblastoma Fresh Tissue


title: siControl_DMSO_2

description:
ctrl.DMSO B
23L013303
tissue culture

value: U-2OS Tet-ON

value: osteosarcoma cancer cell line

value: Control knockdown


title: PCC 7806  Replicate C time 6


title: RBNS 0nM Rep1

value: CAD


title: intestine_PPARa-knockout_control_rep2

value: 129S4/SvJae (PPARalpha knockout)

value: male

value: 14 weeks

value: small intestine


title: heart, obscurin knockout 2

description: Library name: Obsc.2

value: heart


title: siCGGBP1_DMSO_1

description:
CGGBP1.DMSO A
23L013300
tissue culture

value: CGGBP1 knockdown

value: 60min 75uM 4sU


title: AAH-11: VEH-SK-UT-1 RNA

value: uterus


title: siControl_DMSO_1

description:
ctrl.DMSO A
23L013299
tissue culture


title: Sample GbExp60_ctrl

description:
Library name: GbExp60_ctrl
Column name in TPM_Data.txt: GbExp60_ctrl


title: heart, obsl1 knockout 2

description: Library name: OL1.2


title: RBNS Input Rep1

description: Library name: RBNS_Input_Rep1


title: RBNS 500nM Rep1


title: Sample GbExp54_ctrl

description:
Library name: GbExp54_ctrl
Column name in TPM_Data.txt: GbExp54_ctrl


title: Sample GbExp55_ctrl

description:
Library name: GbExp55_ctrl
Column name in TPM_Data.txt: GbExp55_ctrl


title: RBNS 5nM Rep2


title: Sample GB36

description:
Library name: GB36
Column name in TPM_Data.txt: GB36


title: 231 CELLS-si-YBX1

value: breast

value: 231 cell


title: heart, control 1

description: Library name: CTL.1

value: wildtype


title: AAH-09: VEH-SK-UT-1 RNA

value: leiomyosarcoma

value: DMSO (VEH)


title: MPRA Soma +dox Rep2

description: Library name: MPRA_Soma_PlusDox_Rep2

value: TetOff TDP-43

value: plus dox

value: soma


title: PCC 7806  Replicate C time 1

value: Microscystis aeruginosa PCC 7806


title: PCC 7806  Replicate C time 2


title: AAH-16: Dac51-SK-UT-1 RNA

value: FTO inhibitor


title: PCC 7806  Replicate C time 8


title: AAH-15: Dac51-SK-UT-1 RNA


title: Sample GbExp34_2_ctrl

description:
Library name: GbExp34_2_ctrl
Column name in TPM_Data.txt: GbExp34_2_ctrl

value: Glioblastoma Fresh Tissue


title: MPRA Soma +dox Rep1

description: Library name: MPRA_Soma_PlusDox_Rep1

value: CAD


title: heart, obscurin knockout 1

description: Library name: Obsc.1

value: Obsc-/-


title: Sample GB31

description:
Library name: GB31
Column name in TPM_Data.txt: GB31


title: AAH-13: Dac51-SK-UT-1 RNA


title: PCC 7806  Replicate C time 3


title: Sample GbExp33_ctrl

description:
Library name: GbExp33_ctrl
Column name in TPM_Data.txt: GbExp33_ctrl


title: MPRA Soma +dox Rep3

description: Library name: MPRA_Soma_PlusDox_Rep3


title: Sample GB30-1

description:
Library name: GB30-1
Column name in TPM_Data.txt: GB30-1


title: Sample GB42

description:
Library name: GB42
Column name in TPM_Data.txt: GB42


title: PCC 7806  Replicate C time 4


title: Sample GB33

description:
Library name: GB33
Column name in TPM_Data.txt: GB33


title: Sample GB29-2

description:
Library name: GB29-2
Column name in TPM_Data.txt: GB29-2


title: PCC 7806  Replicate B time 5


title: HTZ-1 hermaphrodite germline knockout rep 3

city: San Francsisco

first: Diana

last: Chu

address: 1600 Holloway Ave

department: Biology

institute: San Francisco State University

description: Count data columns: Wormbase gene ID, raw read count

data_processing:
FastQC v0.11.9 on default settings
Cutadapt v2.10 with -m 1 option
STAR v2.7.3a with a maximum of 10 alignments per read allowed
HTSeq v0.12.4 on default settings
DESeq2 v1.30.0 on default settings
Assembly: WBcel235/ce11; GCF_000002985.6
Supplementary files format and content: HTSeq raw count files with Wormbase gene IDs in column
Supplementary files format and content: Processed files are in tab delimited from HTSeq where column 1 represents the Wormbase gene ID and the second column represents the raw RNA-seq read count

organism: Caenorhabditis elegans

source_name: hermaphrodite gonads

growth_protocol: C. elegans strains were maintained using standard conditions on NGM (Nematode Growth Medium) agar plates. Maintained at 19C with OP50 E. coli (cultured in lysogeny broth) spotted on plates.

extract_protocol:
Trizol extraction; Perfomed by Azenta Life Sciences.
NEBNext Ultra II RNA Library Prep. Perfomed by Azenta Life Sciences.

treatment_protocol: Wildtype and deletion mutant samples (mixed-stage embryos or young adults) were isolated onto a NGM agar plate with M9 solution to wash away OP50 coating the samples until the M9 solution fully evaporates. For germline extraction, dissection buffer (levamisol) was added to plate to inhibit C. elegans movement. C. elegans were dissected with syringe needles at the pharynx to allow germline release from body. Germlines were isolated and collected into Trizole for tissue preservation.

value: hermaphrodite gonads


title: AAH-10: VEH-SK-UT-1 RNA


title: Sample GB28

description:
Library name: GB28
Column name in TPM_Data.txt: GB28


title: Sample GB32

description:
Library name: GB32
Column name in TPM_Data.txt: GB32


title: Hermaphrodite wildtype rep 3

value: wild-type


title: Hermaphrodite wildtype rep 2


title: MPRA Soma -dox Rep4

description: Library name: MPRA_Soma_MinusDox_Rep4

value: minus dox


title: PCC 7806  Replicate B time 8


title: PCC 7806  Replicate B time 7


title: Sample GB24-2

description:
Library name: GB24-2
Column name in TPM_Data.txt: GB24-2


title: MPRA Soma -dox Rep3

description: Library name: MPRA_Soma_MinusDox_Rep3


title: HTZ-1 hermaphrodite germline knockout rep 1


title: Hermaphrodite wildtype rep 1


title: MPRA Neurite +dox Rep3

description: Library name: MPRA_Neur_PlusDox_Rep3

value: neurite


title: HTAS-1 mixed embryo knockout rep 6

source_name: whole embryo

value: whole embryo


title: PCC 7806  Replicate B time 2


title: PCC 7806  Replicate B time 6


title: MPRA Soma -dox Rep2

description: Library name: MPRA_Soma_MinusDox_Rep2


title: HTZ-1 hermaphrodite germline knockout rep 2


title: PCC 7806  Replicate B time 4


title: Sample GB25-6

description:
Library name: GB25-6
Column name in TPM_Data.txt: GB25-6


title: HTAS-1 mixed embryo knockout rep 4


title: PCC 7806  Replicate B time 3


title: MPRA Neurite +dox Rep4

description: Library name: MPRA_Neur_PlusDox_Rep4


title: MPRA Neurite +dox Rep1

description: Library name: MPRA_Neur_PlusDox_Rep1


title: HTAS-1 mixed embryo knockout rep 5


title: Sample GB24-1

description:
Library name: GB24-1
Column name in TPM_Data.txt: GB24-1


title: Sample GB23-2

description:
Library name: GB23-2
Column name in TPM_Data.txt: GB23-2


title: PCC 7806  Replicate B time 1


title: MPRA Soma -dox Rep1

description: Library name: MPRA_Soma_MinusDox_Rep1


title: PCC 7806  Replicate A time 7


title: PCC 7806  Replicate A time 8


title: Sample GB23-1

description:
Library name: GB23-1
Column name in TPM_Data.txt: GB23-1


title: HTAS-1 mixed embryo knockout rep 2


title: MPRA Neurite -dox Rep4

description: Library name: MPRA_Neur_MinusDox_Rep4


title: HTAS-1 mixed embryo knockout rep 3


title: MPRA Neurite -dox Rep2

description: Library name: MPRA_Neur_MinusDox_Rep2


title: MPRA Neurite +dox Rep2

description: Library name: MPRA_Neur_PlusDox_Rep2


title: PCC 7806  Replicate A time 5


title: Sample GB21-1

description:
Library name: GB21-1
Column name in TPM_Data.txt: GB21-1


title: MPRA Neurite -dox Rep3

description: Library name: MPRA_Neur_MinusDox_Rep3


title: MPRA Soma +dox Rep4

description: Library name: MPRA_Soma_PlusDox_Rep4


title: Sample GB19-2

description:
Library name: GB19-2
Column name in TPM_Data.txt: GB19-2


title: HTAS-1 mixed embryo knockout rep 1


title: Sample GB21-2

description:
Library name: GB21-2
Column name in TPM_Data.txt: GB21-2


title: Mixed embryo wildtype control rep 6


title: PCC 7806  Replicate A time 4


title: Mixed embryo wildtype control rep 5


title: N2A Soma +dox Rep3

description: Library name: N2A.Soma.PlusDox.Rep3


title: PCC 7806  Replicate A time 3


title: Sample GB18

description:
Library name: GB18
Column name in TPM_Data.txt: GB18


title: Mixed embryo wildtype control rep 4


title: N2A Soma +dox Rep2

description: Library name: N2A.Soma.PlusDox.Rep2


title: PCC 7806  Replicate A time 2


title: PCC 7806  Replicate A time 1


title: Mixed embryo wildtype control rep 3


title: PCC 7806  Replicate A time 6


title: N2A Soma +dox Rep1

description: Library name: N2A.Soma.PlusDox.Rep1


title: MDA-MB-231

city: Jinju

first: Hye Jung

last: Kim

address: 816 Bungil 15

department: College of Medicine, Department of Pharmacology

country: South Korea

institute: Gyeongsang National University

description: Library name: MDA-MB-231

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: cell lines

growth_protocol: MDA-MB-231 and RT-R-MDA-MB-231 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin.

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

treatment_protocol: RT-R-MDA-MB-231 was generated by repeatedly applying 2 Gy dose of X-rays irradiation until a final dose of 50 Gy was achieved.

value: cell lines

value: triple negative breast cancer


title: RT-R-MDA-MB-231

description: Library name: RT-R-MDA-MB-231


title: MM2

city: Boston

first: Johannes

last: Waldschmidt

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Library name: BB212100013

data_processing:
Processing and quality filtering of scRNA-seq data was carried out using trimmomatic, START, HTSeq and RSEM. Four different parameters were used to filter out low quality cells: i) library size, ii) number of genes detected, and iv) percentage of reads mapping to house-keeping genes. Cells that fell below three median absolute deviations were excluded from downstream analyses. As an additional approach to remove bad-quality cells without any predefined cut-offs we used the R package mvoutlier.
Assembly: hg19
Supplementary files format and content: .rds
Supplementary files format and content: Combined_htseq_count_matrix

source_name: T cells

extract_protocol:
Full-length single-cell RNA-seq libraries were preprared using Smart-seq2. Pooled sequencing of Nextera libraries was carried out using a NextSeq 500 (Illumina, C>A). All sequenced reads were paired-end and 36-base pair (bp) read length. A sequencing depth of 1x10e6 war aimed for in each cell.
cDNA

treatment_protocol: CD3+ T-cells were isolated from the peripheral blood at the time of relapse to ide-cel anti-BCMA CAR-T cells in two MM patients either i)before or ii)during salvage therapy with nivolumab plus IMiD-dexamethasone

value: T cells

value: see Table 1

value: nivolumab-Pd


title: N2A Soma -dox Rep3

description: Library name: N2A.Soma.MinusDox.Rep3

value: TetOff TDP-43


title: RNA_seq_sa-/-_mutant_rep2

city: Stanford

first: Kazuteru

last: Hasegawa

address: Lorry Lokey Stem Cell Research Building (SIM1), G2165 265 Campus Drive

institute: Stanford University

description:
total RNA with rRNA depletion
RNA-seq for sa-/- replicate2

data_processing:
trim adaptors and low quality bases. trim_galore/0.4.1
map with STAR/2.5.1b
count reads for each gene or promoter STAR
Genome_build: dm6
Supplementary_files_format_and_content: raw_counts.txt are raw read counts by STAR

organism: Drosophila melanogaster

source_name: testis

growth_protocol: in molasses medium, 22C for 12 days

extract_protocol:
100 pairs of testes from < 2 day old male flies were used per replicate. The testis were dissected in PBS on ice. Total RNA was extracted using RNeasy Mini Kit (Qiagen 74104).
Ribosomal RNA was depleted using Ribo-Zero rRNA Removal Kit (Illumina MRZH116). Library preparation was then carried out using SMARTer Stranded RNA-Seq Kit (Clonetech 634839).

tag: developmental stage enriched

value: mature spermaocyte


title: Mixed embryo wildtype control rep 1

tag: tissue


title: N2A Soma -dox Rep2

description: Library name: N2A.Soma.MinusDox.Rep2

value: soma


title: MPRA Neurite -dox Rep1

description: Library name: MPRA_Neur_MinusDox_Rep1


title: RNA_seq_sa-/-_mutant_rep1

description:
total RNA with rRNA depletion
RNA-seq for sa-/- replicate1


title: MM1

description: Library name: BB21210001

value: nivolumab-Rd


title: HTZ-1 male germline knockout rep 3

source_name: male gonads

value: male gonads


title: N2A Soma -dox Rep1

description: Library name: N2A.Soma.MinusDox.Rep1


title: Sample GB19-1

description:
Library name: GB19-1
Column name in TPM_Data.txt: GB19-1

value: Glioblastoma Fresh Tissue


title: HTZ-1 male germline knockout rep 2


title: N2A Neurite +dox Rep3

description: Library name: N2A.Neurite.PlusDox.Rep3

value: plus dox


title: RNA_seq_Klp59D_KD_rep2

description:
total RNA with rRNA depletion
RNA-seq for Klp59D Knock Down replicate 2

growth_protocol: in molasses medium, 22C for 3 days

treatment_protocol: 30C for 8 days

value: w;Klp59DRNAi;bam-Gal4, UAS-dicer2


title: RNA_seq_Klp59D_KD_rep1

description:
total RNA with rRNA depletion
RNA-seq for Klp59D Knock Down replicate 1


title: N2A Neurite +dox Rep2

description: Library name: N2A.Neurite.PlusDox.Rep2


title: Pateint 6, timepoint 1, scBCR-seq

city: Suwon

first: Seung-Jun

last: Paek

address: Worldcup-ro

department: Department of Physiology

institute: Ajou University School of Medicine

description:
P6_1_scBCR
10x Genomics

data_processing:
10x Genomics Cell Ranger (version 6.0.0) was used for sequencing reads mapping against the GRCh38 human reference genome, UMI counting and cell filtering. A reference genome was applied from 10X Genomics.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values and matrix files (scRNA gene expression)
Supplementary files format and content: Commna--separated values and matrix files (TCR, BCR clonotypes)

source_name: Peripheral blood mononuclear cell

extract_protocol:
Frozen cells were resuspended using 1xPBS solution and then filtered through a 40 µm filter. A small portion of the cell solution was mixed with AOPI and placed on a cell counting slide to check the viability (LUNA-FL™ Automated Fluorescence Cell Counter). Cells with viability over 70% were used for sequencing.
scRNA-seq: Chromium Next GEM Single Cell 5’ Kit v2 and Chromium Next GEM Chip K Single Cell Kit were used to generate barcoded 5’ single cell library (10X Genomics Chromium Instrument). Each cDNA library that passed the quality control (Agilent Bioanalyzer) was sequenced on an Illumina NovaSeq6000 and NextSeq500.
scV(D)J-seq: TCR and BCR sequencing was performed using cDNA synthesized by the nested-PCR enrichment method. TCR and BCR libraries were generated using the Chromium Single Cell Human TCR and BCR Amplification Kit (10X Genomics), and each library was checked for quality control (Agilent Bioanalyzer) before sequencing.

value: Peripheral blood mononuclear cell

tag: Sex

value: Female

tag: disease state

value: Remission


title: Pateint 5, timepoint 1, scBCR-seq

description:
P5_1_scBCR
10x Genomics


title: N2A Neurite +dox Rep1

description: Library name: N2A.Neurite.PlusDox.Rep1

data_processing:
Adapters were trimmed using Cutadapt
Transcript abundances were calculated using salmon
Gene-level abundances were calculated using tximport
Assembly: mm10, hg38
Supplementary files format and content: Salmon-calculated transcript abundances

extract_protocol:
RNA was extracted with Zymo Quick RNA microprep kits
Libraries were constructed using Kapa RNA Hyperprep kits

tag: treatment

value: neurite


title: RNA_seq_Tektin-C_KD_rep2

description:
total RNA with rRNA depletion
RNA-seq for Tektin-C Knock Down replicate 2

value: w;Tekin-CRNAiRNAi;bam-Gal4, UAS-dicer2


title: Wildtype control male germline for for rep 2

description: Count data columns: Wormbase gene ID, raw read count

value: wild-type


title: Mixed embryo wildtype control rep 2

value: whole embryo


title: N2A Neurite -dox Rep3

description: Library name: N2A.Neurite.MinusDox.Rep3

value: minus dox

tag: compartment


title: Wildtype control male germline for for rep 3


title: RNA_seq_B9d1_KD_rep2

description:
total RNA with rRNA depletion
RNA-seq for B9d1 Knock Down replicate 2

value: young spermatocyte

value: w;B9d1RNAi;bam-Gal4, UAS-dicer2


title: Pateint 6, timepoint 1, scRNA-seq

description:
P6_1_scRNA
10x Genomics


title: RNA_seq_Tektin-C_KD_rep1

description:
total RNA with rRNA depletion
RNA-seq for Tektin-C Knock Down replicate 1

value: mature spermaocyte

value: w;Tekin-CRNAi;bam-Gal4, UAS-dicer2


title: Wildtype control male germline for rep 1


title: RNA_seq_B9d1_KD_rep1

description:
total RNA with rRNA depletion
RNA-seq for B9d1 Knock Down replicate 1


title: N2A Neurite -dox Rep2

description: Library name: N2A.Neurite.MinusDox.Rep2

value: TetOff TDP-43


title: HTAS-1 male germline knockout rep 3

value: male gonads


title: Pateint 5, timepoint 1, scRNA-seq

description:
P5_1_scRNA
10x Genomics


title: HTAS-1 male germline knockout rep 2


title: m6A-IP_DF2 siRNA #2

city: Houston

first: Ann-Bin

last: Shyu

state: Texas

address: 6431 Fannin Street, Rm 6.200

institute: The University of Texas Health Science Center at Houston

data_processing:
Reads are aligned to hg38 genome by HISAT2 and only uniquely mapped reads are kept.
reads are sorted and marked for duplication using PicardTools.
MoAIMS was used to perform the m6A peak calling.
Note - the RNA-seq fastq files from two technical repeats (one found in this submission and the other in previous submission, GSE181079) for each sample were merged first prior to data processing to generate peak calling files.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files contains m6A peaks sites for control and DF2 knockdown treatments.

source_name: human bone osteosarcoma

growth_protocol: Human U2OS cell line was purchased from ATCC and cultured following the manufacturer's protocol.

extract_protocol:
RNA samples were extracted using RNeasy Mini Kit (QIAGEN) following manufacture's protocol.
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells with or without YTHDF2 knock-down were collected for total cytoplasmic RNA extraction. Following RNA fragmentation step, fragmented RNA samples were subject to m6A-RNA IP.

value: human bone osteosarcoma

tag: cell type

value: epithelia cells

value: WT

value: DF2 siRNA #2

value: anti-m6A antibody (SYSY #202003)


title: RNA_seq_WT_rep1

description:
total RNA with rRNA depletion
RNA-seq for Wild-type replicate1

growth_protocol: in molasses medium, 22C for 10 days

value: all stages of male germ cells


title: m6A-IP_DF2 siRNA #1

value: DF2 siRNA #1


title: HTAS-1 male germline knockout rep 1


title: HTZ-1 male germline knockout rep 1


title: CAD Soma +dox Rep3

city: Aurora

last: Taliaferro

institute: University of Colorado Anschutz Medical Campus

description: Library name: CAD.Soma.PlusDox.Rep3

source_name: CAD

value: CAD

value: plus dox

value: soma


title: Pateint 6, timepoint 1, scTCR-seq

description:
P6_1_scTCR
10x Genomics

value: Peripheral blood mononuclear cell

value: Female

value: Remission


title: Lamb3

city: Nanjing

first: Zhen

last: Zhang

institute: Nanjing Agricultural University

data_processing:
ACGT101-miR (LC Sciences, Houston, Texas, USA)
Length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs
Hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi)
Differential expression of miRNAs based on normalized deep-sequencing counts was analyzed by selectively using Fisher exact test, Chi-squared 2X2 test, Chi-squared nXn test, Student t test, or ANOVA based on the experiments design.
To predict the genes targeted by most aboundant miRNAs, two computational target prediction algorithms (TargetScan 50 and Miranda 3.3a) were used to identify miRNA binding sites.
Genome_build: mm9

organism: Capra hircus

source_name: Longissimus dorsi muscle

extract_protocol:
A total amount of 2.5 ng RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were prepared with TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, USA). Briefly, the 3’ adenylated adaptor and reverse transcription synthetic first chain were ligated, then PCR amplification and the size were selected. PAGE gel was used for electrophoresis fragment screening purposes, rubber cutting recycling as the pieces get small RNA libraries. At last, PCR products were purified and the library quality was sequenced with Illumina hiseq2000 / 2500.

tag: development stage

value: 1 day of age

tag: breed

value: Haimen goat

value: Longissimus dorsi muscle


title: Input_DF2 siRNA #2

tag: cell line

value: no


title: Wildtype control male germline rep 3

value: male gonads

tag: genotype

value: wild-type


title: CAD Soma +dox Rep1

first: Matthew

description: Library name: CAD.Soma.PlusDox.Rep1

value: TetOff TDP-43


title: Pateint 5, timepoint 1, scTCR-seq

description:
P5_1_scTCR
10x Genomics


title: Input_DF2 siRNA #1

value: human bone osteosarcoma

value: epithelia cells

value: WT


title: Lamb2


title: Wildtype control male germline rep 2


title: Lamb1


title: CAD Soma -dox Rep3

description: Library name: CAD.Soma.MinusDox.Rep3

value: minus dox


title: Wildtype control male germline rep 1


title: N2A Neurite -dox Rep1

description: Library name: N2A.Neurite.MinusDox.Rep1

value: neurite


title: RNA_seq_WT_rep2

description:
total RNA with rRNA depletion
RNA-seq for Wild-type replicate2

value: all stages of male germ cells


title: CAD Soma -dox Rep2

description: Library name: CAD.Soma.MinusDox.Rep2

value: CAD

value: soma


title: Fetus3

value: 75 day of pregnancy


title: Input_control 1

value: control siRNA


title: S41, input

library_source: genomic

data_processing:
FastQC v0.11.9 on default settings
The technical replicates of both datasets were merged, and the sequences were then mapped to the C. elegans genome (WBcel235/ce11; GCF_000002985.6) with Bowtie v1.1.2 on default settings.
MACS2 was used to call peaks and to create Bedgraph files with the following settings: -g ce --bdg --keep-dup = auto --broad --broad-cutoff = 0.01 --nomodel --extsize = 250.
The Bedgraph files were scaled to 10 million total autosomal reads. The X chromosome reads were not included for scaling due to the different X:A ratios between sperm and converted to bigwig by using the bedGraphToBigWig UCSC Genome Browser tool.
Peak annotations were conducted with the R-Bioconductor package ChIPseeker v1.33.1.
Assembly: WBcel235/ce11; GCF_000002985.6
Supplementary files format and content: bigWig files from MACS2; peaks files from ChIPseeker

molecule: genomic DNA

source_name: sperm

growth_protocol: CB1489 was grown in liquid culture (S-medium with HB101 Escherichia coli) at 20C. Adult males were filtered away from hermaphrodite using a 20-micron Nytex mesh.

extract_protocol:
Sperm extracts were prepared using protocols from PMC6193031. Briefly, fixed sperm chromatin was digested with micrococcal nuclease, and treated with a Covaris and lysis buffer to facilitate chromatin solubilization. For ChIP, 1ug of polyclonal antibodies to HTAS-1 (N-terminal and C-terminal) and HTZ-1 proteins were used with the extract from ~2.6 million sperm cells  and with 80uL of Dynabeads (sheep anti-mouse IgG)
MicroPlex Library Kit v2 (Diagenode) was used to construct the libraries from 10uL of isolated DNA (2ng total DNA for input, and unknown amount for ChIP DNA). A real-time qPCR machine was used to monitor library amplification to avoid overamplification.

treatment_protocol: C. elegans spermatids were isolated using protocols from PMC6193031.

value: sperm

tag: chip antibody


title: Normal-407

city: shijiazhuang

first: qingxian

last: wang

address: No.139 Ziqiang Road, Qiaoxi District

department: Department of Orthopedic Trauma

institute: Orthopedic Research Institution of Hebei Province

data_processing:
seqenced reads were inmmed for adptor sequnce and masked for low-complexily sequence
mapped to human reference genome
Obtain mapped data(reads, etc., for subsequent transcription assembly and expression count
The distribution of reads compared to the genome in different regions of the reference genome was statistically analyzed, and the target regions were divided into CDS(coding region) Intron(Intron) Intergenic region and UTR(5' and 3 untranslated region).
The FPKM value of each gene/transcript in the sample was calculated, and the value was taken as the expression amount of gene/transcript in the sample
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Gene/transcript COUNT expression matrix

source_name: controls

extract_protocol: RNA libraries were prepared for sequencing using standard illumina protacal

tag: gender

value: female

value: blood serum

tag: condition

value: control (fracture)

tag: age


title: CAD Soma +dox Rep2

description: Library name: CAD.Soma.PlusDox.Rep2

value: plus dox


title: CAD Neurite +dox Rep3

description: Library name: CAD.Neurite.PlusDox.Rep3


title: CAD Soma -dox Rep1

description: Library name: CAD.Soma.MinusDox.Rep1


title: S39, input


title: Fetus1

value: Haimen goat

value: Longissimus dorsi muscle


title: Fetus2


title: S39, HTZ-1, ChIP

value: Rabbit and rat α-HTZ-1 antibodies were raised against the C-terminal 19 amino acids (NKKGAPVPGKPGAPGQGPQ) and affinity purified


title: S41, HTZ-1, ChIP


title: CAD Neurite +dox Rep2

description: Library name: CAD.Neurite.PlusDox.Rep2

value: TetOff TDP-43


title: Vitamin D-treated intestine

city: Durham

first: Hiroki

last: Kitai

state: NC

address: 2 Genome Ct. Rm 2017

department: Medicine, Division of Nephrology

institute: Duke University

data_processing:
Libraries were sequenced using HiSeq X ten
FASTQ files were processed using Cell Ranger v6.0.1 or v7.0.0 to get UMI expression matrix files.
Assembly: mm10
Supplementary files format and content: h5

source_name: small intesitine

extract_protocol:
Duodenum fragments were incubated in 10 mM EDTA-PBS for 20 min at 4 oC, and then washed with PBS with gentle shaking. Cell suspensions were then filtered through a 70-um cell strainer to separate villous and cryptic fractions (Crypts: <70 um, Villi, >70 um). Crypts were digested with TrypLE Express and villi with collagenase type 1 at 37°C for 1 min 15 sec. S-MEM was added to stop the reaction. The single-cell suspension was resuspended and filtered through a 40-um cell strainer, and mechanical dissociation was performed using a 1 mL syringe/23 gauge needle. Dead cells were removed from the crypt cell suspension using a dead-cell removal kit. The crypt and villous cells were mixed at a 1:1 ratio, and the final cell suspension was used for library generation.
Followed standard procedure of Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1

treatment_protocol: Mice (C57BL6/J) received bodyweight-adjusted doses of calcitriol (0.5 µg/ml) via intraperitoneal injection. Kidneys and intestines were harvested at 12 hours after a single calcitriol injection.

value: small intesitine

tag: strain

value: WT

value: calcitriol


title: Normal-80


title: CAD Neurite +dox Rep1

description: Library name: CAD.Neurite.PlusDox.Rep1

value: neurite


title: control intestine

value: vehicle


title: Vitamin D-treated kidney

source_name: kidney

extract_protocol:
Kidneys were dissociated with liberase TM, hyaluronidase, DNaseI at 37 oC for 20 min, followed by incubation with 0.25% trypsin EDTA at 37 oC for 10 min. Trypsin was inactivated using 10% fetal bovine serum in PBS. Cells were then resuspended in PBS supplemented with 0.04% bovine serum albumin then filtered through 40 µm strainer and used for GEM generation.
Followed standard procedure of Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1

value: kidney


title: Normal-2


title: Case-392

source_name: vein thrombosis

value: vein thrombosis


title: m6A-IP_control 1

value: human bone osteosarcoma

value: epithelia cells

value: control siRNA

value: anti-m6A antibody (SYSY #202003)


title: S41-N, HTAS-1, ChIP

value: sperm

value: Anti-HTAS-1 (ZK1251.1) rabbit antibodies (animals 2390 and 2391) were raised and affinity purified against the N-terminal peptide MARLKQRPNRILNTSTKTSSA with a C-terminal cysteine linker.  Peptides were coupled to Imject mcKLH (Pierce) for injection and coupled to divinylsulfone (Sigma) for affinity purification.


title: CAD Neurite -dox Rep2

description: Library name: CAD.Neurite.MinusDox.Rep2

value: CAD

value: minus dox


title: S41-C, HTAS-1, ChIP

value: Anti-HTAS-1 (at 1∶1000, polyclonal rabbit antibodies 3656 and 3657 generated against the last 15 amino acids of the C-terminal, LPKKKAKEDDKENNS)


title: S39, HTAS-1, ChIP


title: Case-153

value: female

value: blood serum


title: Control kidney

value: WT

value: no treatment


title: CAD Neurite -dox Rep1

description: Library name: CAD.Neurite.MinusDox.Rep1

value: TetOff TDP-43

value: neurite


title: HNP RNA CrossDisorder MPRA Rep 21

status: Public on Jan 29 2025

city: Chapel Hill

first: Hyejung

last: Won

address: 116 Manning Drive, CB# 7250

institute: University of North Carolina at Chapel Hill

description: RNA Replicate 21

data_processing:
Extracted RNA was processed to cDNA using SuperScript IV Reverse Transcriptase (Invitrogen, cat#18090050) using a primer that targets the downstream of the barcodes (Lib_Hand_RT). The cDNA was amplified with primers Lib_Hand and Lib_seq_Luc_R using NEBNext 2X Q5 Hifi HS Mastermix. The PCR product was cleaned up with Zymo DNA Clean and Concentrator kit-25 (Zymo, cat#D4033). We also amplified 4uL of DNA from each well with 4 reactions of PCR using primers, Lib_Hand_RT and Lib_Seq_Luc_R, and NEBNext 2X Q5 Hifi HS Mastermix. The PCR product was cleaned up with Zymo Clean and Concentrator kit-25. We then added P5/P7 adapter sequences and demultiplexing indices to the resulting cDNA and DNA libraries by PCR using primers, P5_seq_Luc_F and P7_Ind_#_Han, and NEBNext 2X Q5 Hifi HS Mastermix. The PCR product was cleaned up and size selected using AMPure XP Beads (Beckman Coulter, cat#A63881) using 0.7X and 0.9X ratios to select for a DNA fragment at 273bps. The libraries were subsequently sequenced via NovaSeq SP using Custom cycles of 35 x 8 x 0 with 20% Phix and custom sequencing primers.
Barcode-variant relationships were decoded from the barcode mapping step. From mapped barcodes, we generated barcode reference files and aligned our variant-barcode pairs using BWA. From the alignment we created RNA and DNA count matrices using featureCounts84 (version 2.0.6) using the following parameters: --minOverlap = 20, --fracOverlap = 1, --fracOverlapFeature = 1. We excluded barcodes which were mapped to more than one variant. RNA and DNA barcode counts were then aggregated for each variant. When applying quality control (QC) metrics, we first identified and filtered out outlier barcodes, defined as individual barcodes that had a median(log2(RNA/DNA)) > 2 + median(log2(RNA/DNA)) for that variant. We also filtered out (1) variants with <5 barcodes per allele, (2) variants where each individual barcode did not appear in at least one replicate, and (3) variants which did not have measured risk and protective allelic pairs. At this stage, each variant was mapped to an average of 7.63 barcodes. Finally, variants were removed if, for either allele, the proportion of total read counts (DNA + RNA) from individual barcodes that could be spuriously mapped by allowing mismatches was greater than 30%.
Supplementary files format and content: unique_bcdat.tsv.gz file represents a variant-barcode mapping file used for the MPRA study.

source_name: Human neural progenitors

growth_protocol: Donor #88 (genetically male, HNPs obtained at gestation week 14) was used for all experiments. Briefly, 800,000 cells were plated per 6-well which was previously coated with Poly-L-Ornithine (10 μg/ml; Sigma-Aldrich, cat#P3655-100MG) and fibronectin (5 μg/ml; Sigma-Aldrich, cat#F1141-5MG) and fed using Neurobasal A media (Thermo Fisher, cat#10888022) with primocin (100 μg/ml; Invitrogen, cat#ant-pm-2), BIT 9500 (10%; STEMCELL, cat#09500), Glutamax 100X (1%; Fisher Scientific, cat#5112367), Heparin (1 μg/ml; Sigma-Aldrich, cat#H3393-100KU), and growth factors: FGF (20 μg/ml; PeproTech, cat#AF-100-15), LIF (2 ng/ml; PeproTech, cat# 300-05), EGF (20 μg/ml; PeproTech, cat#AF-100-15), and PDGF (20 ng/ml; PeproTech, cat#100-00AB). 48 hours after plating, the cells were half-fed using the same media with two times the amount of growth factors and nucleic acid transfection enhancer (NATE) at 1:50 final dilution (InvivoGen, cat#lyec-nate).

extract_protocol:
72 hours after transfection, DNA and RNA were extracted from the cells by Quick-DNA/RNA Miniprep Plus Kit (Zymo, cat#D7003) using 600uL of shield buffer and 600uL lysis buffer per well.
The synthesized 200bp library oligo library was diluted to 1:20 and amplified usingMPRA-chip-primer-F and MPRA-chip-primer-R and NEBNext 2X Q5 Hifi HS Mastermix (NEB, cat#M0453S). The resulting PCR reaction was cleaned up with Zymo DNA Clean and Concentrator kit-5 (Zymo, cat#D4033). Random barcodes were added via PCR using MPRA-bc-primer-F and MPRA-bc-primer-R using NEBNext 2X Q5 Hifi HS Mastermix. The resulting PCR product was cleaned up with Zymo DNA Clean and Concentrator kit-5. The MPRA vector, Donor_eGP2AP_RC (addgene: ID#133784), and oligo library were digested with SpeI-HF (NEB, cat#R3133S) and MluI-HF (NEB, cat#R3198S). The digested oligo library and Donor_eGP2AP_RC plasmid were ligated together using T7 DNA ligase (NEB, cat#M0318S). The ligation mix was transformed into 6 reactions of Endura Electrocompetent cells (Lucigen, cat#60242-1) via electroporation. The bacteria was grown for 1 hour at 37ºC, then plated and incubated overnight on a 10 cm LB plate with kanamycin at 37ºC. The bacteria was collected by scraping and subsequently cultured in 4L of LB with kanamycin at 30ºC overnight. The LB culture was subjected to maxiprep using ZymoPURE II Plasmid Maxiprep Kit. The minimal promoter (minP) and luciferase (Luc) sequence was digested from the pMPRAdonor2 plasmid (addgene: ID#49353) using KpnI-HF (NEB, cat#R3142S) and XbaI (NEB, cat#R0145S). The band was extracted from a 1% agarose gel using Zymo Gel DNA recovery kit (Zymo, cat#D4008). The Donor_eGP2AP_RC plasmid containing the library and barcode was digested with KpnI-HF and XbaI and cleaned up with the Zymo DNA Clean and Concentrator kit-5. The digested plasmid and the minP-Luc fragment were ligated together using T7 DNA ligase. The ligase reaction was transformed into Endura Electrocompetent cells, which were plated on a 10 cm LB plate with kanamycin and grown at 37ºC overnight. The plate was scraped and grown in 4L of LB with kanamycin at 30ºC overnight. The LB culture was subjected to maxiprep using ZymoPURE II Plasmid Maxiprep Kit. (Zymo, cat#D4203). The library and barcode region was amplified off the plasmid with BC_Map_P5_R and BC_Map_P7_F_Ind_# using NEBNext 2X Q5 Hifi HS Mastermix, which added sequencing adapters and indices for demultiplexing. This PCR product was size selected and cleaned up using SparQ beads (VWR, cat#76302-834), and sequenced for barcode mapping via 2x150bp Novaseq SP with 20% Phix and custom sequencing primers: BC_Map_R1seq, BC_Map_R2seq, and BC_Map_Index. Barcodes were assigned to each oligo sequence as previously described using the custom code: https://github.com/kiminsigne-ucla/bc_map.

treatment_protocol: We transfected each well with 2.5ug of MPRA plasmid library and 1ug of pUC19 (ThermoScientific, cat#SD0061) using Lipofectamine STEM (Invitrogen, cat#STEM00015) according to the instructions. 48 hours after transfection, cells were half-fed

value: Human neural progenitors


title: HNP RNA CrossDisorder MPRA Rep 20

description: RNA Replicate 20


title: HNP RNA CrossDisorder MPRA Rep 22

description: RNA Replicate 22


title: HNP RNA CrossDisorder MPRA Rep 14

description: RNA Replicate 14


title: HNP RNA CrossDisorder MPRA Rep 18

description: RNA Replicate 18


title: HNP RNA CrossDisorder MPRA Rep 17

description: RNA Replicate 17


title: HNP RNA CrossDisorder MPRA Rep 15

description: RNA Replicate 15


title: Case-73

value: vein thrombosis


title: HNP RNA CrossDisorder MPRA Rep 19

description: RNA Replicate 19


title: HNP RNA CrossDisorder MPRA Rep 10

description: RNA Replicate 10


title: HNP RNA CrossDisorder MPRA Rep 8

description: RNA Replicate 8


title: CAD Neurite -dox Rep3

description: Library name: CAD.Neurite.MinusDox.Rep3


title: HNP RNA CrossDisorder MPRA Rep 12

description: RNA Replicate 12


title: HNP RNA CrossDisorder MPRA Rep 9

description: RNA Replicate 9


title: HNP RNA CrossDisorder MPRA Rep 13

description: RNA Replicate 13


title: HNP RNA CrossDisorder MPRA Rep 7

description: RNA Replicate 7


title: HNP RNA CrossDisorder MPRA Rep 5

description: RNA Replicate 5


title: HNP RNA CrossDisorder MPRA Rep 16

description: RNA Replicate 16


title: HNP RNA CrossDisorder MPRA Rep 2

description: RNA Replicate 2


title: HNP RNA CrossDisorder MPRA Rep 4

description: RNA Replicate 4


title: HNP RNA CrossDisorder MPRA Rep 3

description: RNA Replicate 3


title: HNP RNA CrossDisorder MPRA Rep 1

description: RNA Replicate 1


title: HNP DNA CrossDisorder MPRA Rep 21

description: DNA Replicate 21


title: HNP DNA CrossDisorder MPRA Rep 20

description: DNA Replicate 20


title: HNP DNA CrossDisorder MPRA Rep 17

description: DNA Replicate 17


title: HNP DNA CrossDisorder MPRA Rep 19

description: DNA Replicate 19


title: HNP DNA CrossDisorder MPRA Rep 16

description: DNA Replicate 16


title: HNP DNA CrossDisorder MPRA Rep 14

description: DNA Replicate 14


title: HNP RNA CrossDisorder MPRA Rep 11

description: RNA Replicate 11


title: HNP DNA CrossDisorder MPRA Rep 15

description: DNA Replicate 15


title: HNP DNA CrossDisorder MPRA Rep 13

description: DNA Replicate 13


title: HNP DNA CrossDisorder MPRA Rep 11

description: DNA Replicate 11


title: HNP DNA CrossDisorder MPRA Rep 12

description: DNA Replicate 12


title: HNP DNA CrossDisorder MPRA Rep 9

description: DNA Replicate 9


title: HNP DNA CrossDisorder MPRA Rep 6

description: DNA Replicate 6


title: HNP DNA CrossDisorder MPRA Rep 7

description: DNA Replicate 7


title: HNP RNA CrossDisorder MPRA Rep 6

description: RNA Replicate 6


title: HNP DNA CrossDisorder MPRA Rep 4

description: DNA Replicate 4


title: HNP DNA CrossDisorder MPRA Rep 8

description: DNA Replicate 8


title: HNP DNA CrossDisorder MPRA Rep 2

description: DNA Replicate 2


title: HNP DNA CrossDisorder MPRA Rep 22

description: DNA Replicate 22


title: HNP DNA CrossDisorder MPRA Rep 18

description: DNA Replicate 18


title: HNP DNA CrossDisorder MPRA Rep 10

description: DNA Replicate 10


title: Male Duodenum replicate 3, snRNAseq

status: Public on Jan 04 2025

city: Cleveland

first: Marissa

last: Scavuzzo

state: OH

address: 2109 Adelbert Rd

department: Genetics

institute: Case Western Reserve University

description:
Library name: Sample 7
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Filtered datasets in h5 format are from CellBender (https://github.com/broadinstitute/CellBender).
Assembly: mm10
Supplementary files format and content: h5 files

source_name: Duodenum

growth_protocol: Mouse duodenal tissue was dissected from the junction of the stomach to approximately 3cm distal at the turn of the intestine, flushed with PBS to remove luminal contents, and snap frozen in liquid nitrogen. Snap frozen tissues were stored at -80oC until nuclei isolation.

extract_protocol:
We used CitraPrep to isolate nucle from high degradative tissues. Frozen tissue was placed into a petri dish on ice and cut into 0.2cm cubed pieces or smaller using clean scissors and forceps in 1mL of CitraHB (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH pH 7.8, 10mM citric acid, 0.5U/uL RNasin, 0.5U/uL SUPERase RNase inhibitor, 1mM DTT, 0.15mM spermine tetrahydrochloride, 0.5mM spermidine trihydrochloride, and cOmplete, EDTA-free protease inhibitor). Chopped tissue (totaling less than 1.5cm cubed) was transferred to the glass dounce homogenizer on ice and 4mL of CitraHB was added. Tissue was incubated on ice for 7 minutes. Tissue was homogenized 20x with loose pestle before adding 320uL of NP-40 and homogenizing 40x with tight pestle. If tissue does not homogenize, an electric homogenizer with short bursts may be used. Nuclei were observed under the microscope for quality control before proceeding. Tissue lysate was filtered through a 40um strainer into a 50mL conical tube. Next, 5mL of 50% iodixanol solution (5 volumes OptiPrep and 1 volume of Diluent composed of 150mM KCl, 30mM MgCl2, 120mM Tricine-KOH pH 7.8 mixed, plus 10mM citric acid, 0.5U/uL RNasin, 0.5U/uL SUPERase RNase inhibitor, 1mM DTT, 0.15mM spermine, and 0.5mM spermidine) was added to the filtered tissue lysate to make a 25% iodixanol solution and vortexed to mix. The tissue lysate was slowly underlaid with 30% iodixanol solution (30% OptiPrep in CitraHB with 0.5U/uL RNasin, 0.5U/uL SUPERase RNase inhibitor, 1mM DTT, 0.15mM spermine, and 0.5mM spermidine), then slowly underlaid with 40% iodixanol solution (40% OptiPrep in CitraHB with 0.5U/uL RNasin, 0.5U/uL SUPERase RNase inhibitor, 1mM DTT, 0.15mM spermine, and 0.5mM spermidine). Without disturbing the layers, the 50mL tube was weighed and balanced before centrifugation at 10,000g for 18 minutes at 4oC with no brake. Nuclei were collected from the interface layer with a 1000mL pipette and placed into a new tube with 10mL nuclei wash buffer (1x PBS, 1% BSA, 0.5U/uL RNasin, and 0.5U/uL SUPERase RNase inhibitor) and vortexed before filtering through a 20um filter. Nuclei were pelleted by centrifugation at 500g for 5 minutes at 4oC. Supernatant was removed and tissue was washed a second time. The pellet was resuspended in 250uL of nuclei wash buffer and nuclei were counted using a hemocytometer.
Library was performed according to the manufacter’s instructions (single cell 3’ GEM v3.1 protocol, 10x Genomics). Briefly, GCs 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 retrotranscripted to cDNA, which contains an Ilumina 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 apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Duodenum

value: male


title: Male Duodenum replicate 1, snRNAseq

status: Public on Dec 23 2024

description:
Library name: Sample 3
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Filtered datasets in h5 format are from CellBender (https://github.com/broadinstitute/CellBender).
Assembly: mm10
Supplementary files format and content: h5 files
Supplementary files format and content: Supplementary files provided as .rds


title: Male Duodenum replicate 2, snRNAseq

description:
Library name: Sample 4
10x Genomics

value: wildtype


title: Female Duodenum replicate 3, snRNAseq

description:
Library name: Sample 5
10x Genomics


title: Female Duodenum replicate 2, snRNAseq

description:
Library name: Sample 2
10x Genomics


title: Female Duodenum replicate 1, snRNAseq

description:
Library name: Sample 1
10x Genomics


title: HNP DNA CrossDisorder MPRA Rep 3

description: DNA Replicate 3


title: HNP DNA CrossDisorder MPRA Rep 1

description: DNA Replicate 1


title: PBMC (cartridge 4)

status: Public on Jan 06 2025

city: Newcastle upon tyne

first: Tegan

last: McTaggart

address: Framlington Place

institute: Newcastle University

description: BD Rhapsody

data_processing:
For human scRNAseq, fastq files were transferred to seven brdiges platform and files were checked for quality control and DBEC files (.csv, .mtx, .tsv) were obtained through the BD Rhapsody Targeted Analysis Pipeline run. The DBEC files were imported to R using ReadMtx() function.
Assembly: hs1 (human data)
Supplementary files format and content: C1_Sample_Tag_Metrics.csv, C2_Sample_Tag_Metrics.csv, C3_Sample_Tag_Metrics.csv: assigned sample tag for each putative cell
Supplementary files format and content: C1_Sample_Tag_ReadsPerCell.csv, C2_Sample_Tag_ReadsPerCell.csv, C3_Sample_Tag_ReadsPerCell.csv: Reads per bioproduct per cell
Supplementary files format and content: C1 barcodes.tsv, C2 barcodes.tsv, C3 barcodes.tsv: cell barcode
Supplementary files format and content: C1 matrix.mtx, C2 matrix.mtx, C3 matrix.mtx: cell matrix
Supplementary files format and content: C1 features.tsv, C2 features.tsv, C3 features.tsv: gene expression
Supplementary files format and content: C1 sample tag.csv, C2 sample tag.csv, C3 sample tag.csv: sample tag

source_name: PBMC

extract_protocol:
PBMCs isolated from healthy control and patient blood, as per manufacturers instruction
As per manufacturer's instruction

value: PBMC

value: Immune cells


title: HNP DNA CrossDisorder MPRA Rep 5

description: DNA Replicate 5


title: RCC20, EOT

status: Public on Nov 26 2024

first: Pavlos

last: Msaouel

address: 1155 Pressler Street, Unit 1374

department: Genitourinary Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

description: 10x Genomics

data_processing:
The fastq files from single-cell sequencing were preprocessed using Cell Ranger software (version 7.1.0)32 with default parameters. Reads were aligned to the human reference genome hg38 (version 2020-A, 10x Genomics) to calculate the expression matrix, which contained the number of unique molecular identifiers (UMIs) for every cell and gene. To ensure high-quality data for downstream analysis, careful selection of samples and cells was performed. Cells with gene expression of fewer than 500 genes were removed to eliminate cell debris, empty drops, and low-quality cells. Cells with a mitochondrial versus endogenous genes expression ratio exceeding 25% were also discarded. Additionally, genes expressed in fewer than 3 cells were excluded from the expression matrix. Subsequently, the Seurat package33 was used for data preprocessing. The raw expression matrix was log2 transformed with the NormalizeData function, scaled with the ScaleData function using default parameters, and the top 2000 genes with the highest standardized variance were identified using the FindVariableFeatures function. Principal component analysis (PCA) was performed using the RunPCA function with default parameters.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Subcutaneous tissue

extract_protocol:
Tumor biopsy samples were thoroughly minced to size < 1mm and transferred to 2.0ml Eppendorf tube containing 0.1 mg/ml Liberase TM and 0.2 mg/ml DNase I (MillieporeSigma) in RPMI1640/0.1% BSA. Tubes were then incubated at 37 degrees Celsius for 15 minutes with gentle rotation. Samples were filtered through 70 µm filters, spun down, and red blood cell lysis was performed with ACK lysis buffer (ThermoFisher, catalog #A1049201). Cell viability will be determined with Trypan blue exclusion assay. Only the samples with >60% viability were further processed on Chromium iX (10x Genomics) to generate 5' v2 gel beads-in-emulsions (GEMs).
The barcoded cDNA was purified and amplified for the final generation of 10x single cell RNA sequencing (scRNAseq) libraries. After quantification with a high sensitivity DNA chip run on a Bioanalyzer 2100 system (Agilent), the libraries were sequenced as recommended by the manufacturer (approximately 50,000 reads per cell) on a NovaSeq 6000 system.

value: Subcutaneous tissue

value: clear cell renal cell carcinoma


title: RCC16, EOT

description: 10x Genomics

source_name: Liver

value: Liver


title: RCC26, Baseline

description: 10x Genomics

source_name: Lymph node

value: Lymph node


title: RCC21, Baseline

description: 10x Genomics


title: RCC16, Baseline

description: 10x Genomics


title: RCC16, C2

description: 10x Genomics


title: RCC29, Baseline

description: 10x Genomics

source_name: Kidney

value: Kidney


title: Male Duodenum replicate 4, snRNAseq

description:
Library name: Sample 8
10x Genomics


title: RCC27, Baseline

description: 10x Genomics

source_name: Lung

value: Lung


title: Female Duodenum replicate 4, snRNAseq

description:
Library name: Sample 6
10x Genomics

value: female


title: RCC24, C2

description: 10x Genomics


title: RCC19, Baseline

description: 10x Genomics

source_name: Peritoneum

value: Peritoneum


title: RCC20, Baseline

description: 10x Genomics


title: RCC12, Baseline

description: 10x Genomics


title: RCC13, Baseline

description: 10x Genomics


title: P05_R1 scRNAseq

status: Public on Nov 15 2024

city: Shanghai

first: Ya

last: Han

address: Siping road

institute: Tongji University

data_processing:
The CeleScope pipeline from Singleron was employed to process the fastq file. The data process encompassed filtering out low-quality reads, aligning reads to the GRCh38 reference genome, assigning cell barcodes, and extracting the unique molecular identifier (UMI) barcode.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bladder

extract_protocol:
The fresh tissues were stored in the sCelLiveTM Tissue Preservation Solution (Singleron Bio Com, Nanjing, China) on ice after the surgery within 30 mins. The specimens were washed with Hanks Balanced Salt Solution (HBSS) for 3 times and then digested with 2 ml sCelLiveTM Tissue Dissociation Solution (Singleron) by Singleron PythoN TM Automated Tissue Dissociation System (Singleron) at 37 °C for 15 mins. Afterwards, the GEXSCOPE red blood cell lysis buffer (Singleron, 2ml) was added, and cells were incubated at 25°C for another 10 mins to remove red blood cells.The solution was then centrifuged at 500 × g for 5 mins and suspended softly with PBS. Finally, the samples were stained with trypan blue (Sigma, United States) and the cellular viability was evaluated microscopically.
Single-cell suspensions (1×105 cells/ml) with PBS (HyClone) were loaded into microfluidic devices using the Singleron Matrix Single Cell Processing System (Singleron). Subsequently, the scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE Single Cell RNA Library Kits (Singleron). Individual libraries were diluted to 4 nM and pooled for sequencing. At last, pools were sequenced on Illumina HiSeq X with 150 bp paired end reads.

value: Bladder

value: All cell

tag: tumor stage

value: Recurrence

value: TURBT


title: P05_R2 scRNAseq


title: P04_R2 scRNAseq


title: RCC27, C2

description: 10x Genomics


title: BM_TICAM2_CTRL_rep6

status: Public on Jan 21 2025

type: genomic

city: Blacksburg

first: Blake

middle: Alexander

last: Caldwell

state: VA

address: 149 Life Sciences I Building, 970 Washington Street SW

department: Biological Sciences

institute: Virginia Tech

description: Total monocytes, LS column purified

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: SeSAMe software v1.14.2

label: Cy5 and Cy3

source_name: Bone marrow monocytes, Ticam2-/- CTRL mice

label_protocol: Standard Illumina Protocol

extract_protocol: Bone marrow monocytes from in vivo experiments were isolated using LS columns (Miltenyi). Genomic DNA was prepared for all samples using a DNeasy Blood and Tissue Kit (Qiagen).

treatment_protocol: Sepsis was induced by intraperitoneal injection of cecal slurry in 6- to 8-week-old C57BL/6 WT male mice. Briefly, whole ceca were dissected from 12-week-old C57BL/6 mice euthanized by cervical dislocation. Cecal contents were extracted and mixed with sterile water (250 µg/µL), sequentially filtered through 860 µm and 190 µm mesh strainers, mixed with an equal volume of 30% glycerol in PBS (final concentration 125 µg/µL), and placed in -80˚C storage. For cecal slurry injections, frozen cecal slurry (CS) stock was rapidly thawed in 37˚C water bath and injected (0.9 mg/g mouse weight) into the peritoneal cavity of recipient mice. After 5 days, mice were injected with a second 0.9 mg/g dose of CS, and then euthanized by cervical dislocation 2 or 7 days later. Bone marrow cells were collected as previously described and subjected to LS column purification (Miltenyi) of bone marrow monocytes following the manufacturer’s protocol.

value: Male

value: CTRL

tag: cs experimental day

value: Bone marrow monocytes


title: BM_TICAM2_CTRL_rep5

description: Total monocytes, LS column purified

tag: tissue


title: RCC18, Baseline

description: 10x Genomics


title: RCC18, EOT

description: 10x Genomics


title: RCC14, Baseline

description: 10x Genomics


title: BM_TICAM2_CSd7_rep5

description: Total monocytes, LS column purified

source_name: Bone marrow monocytes, TICAM2-/- CS mice, day 7

tag: Sex

value: CS

value: Day 7


title: BM_TICAM2_CSd7_rep1

description: Total monocytes, LS column purified


title: P04_R1 scRNAseq


title: P03_R2 scRNAseq

value: Primary

value: Sigmoidectomy


title: P03_R1 scRNAseq

source_name: Ureter

value: Ureter


title: BM_TICAM2_CTRL_rep3

description: Total monocytes, LS column purified


title: BM_TICAM2_CTRL_rep2

description: Total monocytes, LS column purified


title: BM_TICAM2_CSd7_rep2

description: Total monocytes, LS column purified


title: P02_R2 scRNAseq


title: P01_R2 scRNAseq


title: P02_R1 scRNAseq


title: BM_TICAM2_CTRL_rep4

description: Total monocytes, LS column purified


title: P01_R1 scRNAseq


title: Hippocampus_Control_rep1

status: Public on Nov 14 2024

city: Beijing

first: Zizheng

last: Suo

address: No. 17, Panjiayuan Nanli, Chaoyang District

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description: 10x Genomics

data_processing:
The demultiplexing,barcoded processing,gene counting and aggregation were made using the Cell Ranger software v3.0.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hippocampus

extract_protocol:
Hippocampal cells were isolated using the Adult Brain Dissociation Kit (Miltenyi Biotec), with freshly dissected brain tissues enzymatically digested and suspended in 0.5% BSA-PSA. Tissues were washed in cold D-PBS, dissected, and treated with enzyme mixes in a gentleMACS C Tube. Post gentleMACS processing, samples were filtered through a 70 µm MACS SmartStrainer, washed, and centrifuged. The supernatant was removed, cells were treated with Debris Removal Solution, and the final cell suspension was prepared for analysis.
scRNA-seq libraries were prepared according to the Single Cell 3’ Reagent Kits v2 manual. Cells were encapsulated with reagents and beads containing Illumina linkers, 10X cell barcodes, UMIs, and poly dT on a microfluidic chip to form GEMs. After cell lysis within each GEM, mRNA was reverse transcribed to cDNA, tagged with a unique barcode. The pooled cDNA was then amplified and prepared for sequencing.

value: Hippocampus


title: Hippocampus_Surgery_rep1

description: 10x Genomics


title: Hippocampus_Surgery_rep2

description: 10x Genomics


title: Hippocampus_Control_rep2

description: 10x Genomics


title: Liver-34

status: Public on Oct 31 2024

first: Alan

middle: C.

last: Mullen

state: MA

address: 55 Fruit St.

department: Department of Medicine

institute: Massachusetts General Hospital

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Assembly: GRCh38 (human)
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Frozen samples were dissociated on a GentleMACS in 1mL of TST buffer (https://www.nature.com/articles/s41591-020-0844-1). Nuclei were counted and resuspended in PBS+BSA+RNAse inhibitor before loading on a 10x 3' v3.1 channel.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, after nuclei loading and gel bead-in-emulsion (GEM) formation, the poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina 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 apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Samples were placed in cryo-tubes after removal of liquid by gently wiping it samples on the side of the container. Tubes were then covered in dry ice and transferred to −80 °C for long-term storage.

value: M

tag: disease state

value: F3 fibrosis

value: Liver


title: Liver-33

value: F

value: F2 fibrosis


title: Liver-32

value: F4 fibrosis


title: ESCs Transcriptome

status: Public on Oct 16 2024

city: Wuhan

first: Wei

last: Jiang

address: Donghu Road 116, District Wuchang

department: Medical Research Institute

institute: Wuhan University

data_processing:
Base-calling was performed using Illumina’s standard software (e.g., bcl2fastq) with default parameters to convert raw sequencing data to FASTQ files.
Reads from FASTQ files were aligned to the human reference genome (Gh38) using HISAT2 (2.2.1).
SAM files were converted to BAM format using SAMtools (1.6) with the sort command to generate sorted BAM files.
FeatureCounts from the Subread package (2.0.6) was used to count reads aligned to genes.
Assembly: Gh38, T2T
Supplementary files format and content: Tab-delimited text files include raw counts for each sample, generated based on the GRCh38 reference genome with a general GTF annotation file
Supplementary files format and content: Tab-delimited text files include raw counts for each sample, generated based on the T2T (CHM13) reference genome with a repeat sequence-specific GTF annotation file

source_name: H9 cell

extract_protocol:
Total RNA was extracted from the biological material using the RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
Libraries were constructed using the Smart-seq2 protocol, which involves reverse transcription of polyA RNA, followed by amplification and sequencing.

value: H9 cell

value: embryonic stem cells


title: BM_TICAM2_CTRL_rep1

description: Total monocytes, LS column purified

value: Male

tag: treatment


title: BM_TICAM2_CSd7_rep3

description: Total monocytes, LS column purified


title: Hippocampus_Control_rep3

description: 10x Genomics


title: ffEPSCs Transcriptome

value: feeder-free extended pluripotent stem cells


title: Yki111,168,250 + Dp male accessory gland 10days rep2

status: Public on Oct 01 2024

city: Ann Arbor

first: Laura

last: Buttitta

state: Michigan

address: 5218 BSB, University of Michigan

department: MCDB

institute: University Of Michigan

description:
Bulk_TPM_genes.csv
Bulk_TPM_transcripts.csv

data_processing:
Used module Bioinformatics , Cutadapt v 1.18,  and Kallisto
Sequence reads were trimmed from adapter/low-quality sequences using Cutadapt v 1.18. Trim low-quality bases with quality score less than 20. Discard reads shorter than 25 bases after trimming. Discards a pair of reads if either read is too short.
Assembly: Trimmed sequance reads were mapped to Drosophila Melanogaster BDGP6.32 using Kallisto (parameter setting using 100 bootstrap sampling)
Read count extracted and normalized using Sleuth
Supplementary files format and content: comma-separated values files include TPM counts for each sample Bulk_TPM_genes.csv
Supplementary files format and content: comma-separated values files include TPM counts for each sample Bulk_TPM_transcripts.csv

source_name: male accessory gland

growth_protocol: Flies were reared at 25ºC for 10 days

extract_protocol:
Their accessory glands were extracted and immediately placed in TRIzol (Invitrogen 15596026) for RNA preservation. Following the manufacturer's instructions, we isolated RNA from these samples
RNA  libraries for RNA-Seq were prapaired using TruSeq Stranded mRNA library prep kit from Illumina, with poly-A selection to enrich for mRNA.

value: male accessory gland

value: y,w,hs-flp12; UAS E2F1, UAS-Dp/Uas-P35; UAS-Yki 111,168,250/Act>CD2>gal4, Uas-GFP(nls)

tag: time

value: 10 days


title: Yki111,168,250, Dp male accessory gland 10days rep3


title: Yki111,168,250 + Dp male accessory gland 10days rep1


title: p454_K4me3_R2_(230817_DJ_Hs_p454_K4me3_R2_230801)

status: Public on Sep 27 2024

city: Grand Rapids

first: Derek

middle: H

last: Janssens

state: MI

address: 333 Bostwick Ave. NE

department: Epigenetics

institute: Van Andel Institute

description: AutoCUTnTag for H3K4me3 Replicate 2 in p454. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads. 2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the repeat-masked hg19 Homo sapiens reference sequence obtained from UCSC. 3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments. 4. We used bedtools 2.30.0 "genomecov" to make a normalized count hg19 track which is the fraction of counts at each base pair scaled by the size of the hg19 reference sequence (3095693983) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .hg19.bw)
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: infant BALL sample p454

extract_protocol:
AutoCUTnTag DOI: dx.doi.org/10.17504/protocols.io.bgztjx6n
Specified separately for each sample, see above.
PMID 31036827

tag: cell type

value: infant BALL sample p454

tag: group

tag: antibody

value: Rabbit H3K4me3 Active Motif 39159


title: Hippocampus_Surgery_rep3

description: 10x Genomics


title: RCC24, Baseline

description: 10x Genomics

value: Lung

value: clear cell renal cell carcinoma


title: p454_ENL_R1_(230817_DJ_Hs_p454_ENL_R1_230801)

description: AutoCUTnTag for ENL Replicate 1 in p454. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital

value: Rabbit ENL Cell Signaling Technologies D9M4B


title: p454_ENL_R2_(230817_DJ_Hs_p454_ENL_R2_230801)

description: AutoCUTnTag for ENL Replicate 2 in p454. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital


title: p454_Dot1L_R2_(230817_DJ_Hs_p454_Dot1L_R2_230801)

description: AutoCUTnTag for Dot1L Replicate 2 in p454. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital

value: Rabbit Dot1L Cell Signaling Technologies D4O2T


title: p454_Dot1L_R1_(230817_DJ_Hs_p454_Dot1L_R1_230801)

description: AutoCUTnTag for Dot1L Replicate 1 in p454. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital


title: p454_AFF1_2_(240410_DJ_Hs_p454_AFF1_2_05T_040324)

description: AutoCUTnRUN for AFF1-2 in p454. This sample contains the KMT2A-AFF1 translocation and is an infant BALL from Texas Children's Hospital

extract_protocol:
AutoCUTnRUN DOI: dx.doi.org/10.17504/protocols.io.ufeetje
Specified separately for each sample, see above.
PMID 31036827

value: Rabbit AFF1-2 Thermo Fisher Scientific PA5-77068


title: p318_K4me3_R2_(230817_DJ_Hs_p318_K4me3_R2_230801)

description: AutoCUTnTag for H3K4me3 Replicate 2 in p318. This sample contains the KMT2A-AFF1 translocation and is an infant AML lineage-switching sample (paired with p279) from Texas Children's Hospital

source_name: infant AML lineage-switching sample p318


title: p318_K4me3_R1_(230817_DJ_Hs_p318_K4me3_R1_230801)

description: AutoCUTnTag for H3K4me3 Replicate 1 in p318. This sample contains the KMT2A-AFF1 translocation and is an infant AML lineage-switching sample (paired with p279) from Texas Children's Hospital

value: infant AML lineage-switching sample p318


title: p318_ENL_R2_(230817_DJ_Hs_p318_ENL_R2_230801)

description: AutoCUTnTag for ENL Replicate 2 in p318. This sample contains the KMT2A-AFF1 translocation and is an infant AML lineage-switching sample (paired with p279) from Texas Children's Hospital


title: p318_ENL_R1_(230817_DJ_Hs_p318_ENL_R1_230801)

description: AutoCUTnTag for ENL Replicate 1 in p318. This sample contains the KMT2A-AFF1 translocation and is an infant AML lineage-switching sample (paired with p279) from Texas Children's Hospital


title: p318_AFF1_1_(240410_DJ_Hs_p318_AFF1_1_05T_040324)

description: AutoCUTnRUN for AFF1-1 in p318. This sample contains the KMT2A-AFF1 translocation and is an infant AML lineage-switching sample (paired with p279) from Texas Children's Hospital

value: Mouse AFF1-1 MyBioSource MBS190886


title: BM_TICAM2_CSd7_rep4

description: Total monocytes, LS column purified

value: CS

value: Day 7

value: Bone marrow monocytes


title: p318_AFF1_2_(240410_DJ_Hs_p318_AFF1_2_05T_040324)

description: AutoCUTnRUN for AFF1-2 in p318. This sample contains the KMT2A-AFF1 translocation and is an infant AML lineage-switching sample (paired with p279) from Texas Children's Hospital


title: p318_Dot1L_R1_(230817_DJ_Hs_p318_Dot1L_R1_230801)

description: AutoCUTnTag for Dot1L Replicate 1 in p318. This sample contains the KMT2A-AFF1 translocation and is an infant AML lineage-switching sample (paired with p279) from Texas Children's Hospital


title: p279_K4me3_R2_(230817_DJ_Hs_p279_K4me3_R2_230801)

description: AutoCUTnTag for H3K4me3  Replicate 2 in p279. This sample contains the KMT2A-AFF1 translocation and is an infant BALL lineage-switching sample (paired with p318) from Texas Children's Hospital

source_name: infant B-ALL lineage-switching sample p279


title: p279_K4me3_R1_(230817_DJ_Hs_p279_K4me3_R1_230801)

description: AutoCUTnTag for H3K4me3 Replicate 1 in p279. This sample contains the KMT2A-AFF1 translocation and is an infant BALL lineage-switching sample (paired with p318) from Texas Children's Hospital

value: infant B-ALL lineage-switching sample p279


title: p279_AFF1_2_(240410_DJ_Hs_p279_AFF1_2_05T_040324)

description: AutoCUTnRUN for AFF1-2 in p279. This sample contains the KMT2A-AFF1 translocation and is an infant BALL lineage-switching sample (paired with p318) from Texas Children's Hospital


title: p279_Dot1L_R2_(230817_DJ_Hs_p279_Dot1L_R2_230801)

description: AutoCUTnTag for Dot1L Replicate 2 in p279. This sample contains the KMT2A-AFF1 translocation and is an infant BALL lineage-switching sample (paired with p318) from Texas Children's Hospital