title: KOPTK1, shELK3, rep3

description: RNAseq_shELK3_shControl_KOPTK1_CUTLL1_reads_counts.txt

value: ELK3 knockdown


title: Organoids_ISC_3d_2081_1

status: Public on Apr 02 2025

type: SRA

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: Library name: ISC_3d_2081_1

library_source: transcriptomic

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.6.1a), and quantified transcript counts using featureCounts (2.0.6).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

molecule: total RNA

organism: Mus musculus

source_name: Organoids

growth_protocol: All animal experiments in this study were performed in accordance with protocols approved by the Memorial Sloan Kettering Institutional Animal Care and Use Committee (approval number: 11-06-012). The mice were housed with a 12 h light/dark cycle between 8:00 and 20:00 in a temperature-controlled room (22 ± 1°C) with free access to water and food. Both male and female mice were used in equal proportions for all experiments. .

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

treatment_protocol: Crypts were isolated from mice with the described phenotype and cultured in ENR-CV media for six days before adding DM-αKG or doxycycline. Organoids were then maintained under the indicated treatment for three days.

tag: mouse strain

value: Mix

tag: cell type

value: Organoids

tag: time

tag: genotype

value: TetO. shOgdh; Cag-rtTA

tag: treatment

value: doxycycline


title: KO_veh_GATA2_Rep2

city: Madison

first: Emery

middle: H

last: Bresnick

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

library_source: genomic

data_processing:
CUT&Tag FASTQ files were first processed by removing the adapter ‘CTGTCTCTTATACACATCT’ using the Cutadapt software (version 4.5) and then aligned to the mouse genome (version mm10) by Bowtie2 (version 2.5.1). Duplicated fragments were marked and removed by Picard (version 3.1.1). Signals were generated by deepTools's bamCoverage function (version 3.5.4) to convert BAM files into bigWig files using RPGC normalization excluding Chromosome M.
Assembly: mm10
Supplementary files format and content: bigWig files of CUT&Tag signals
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Fetal Liver

extract_protocol:
DNA was purified by spin columns (Cell Signaling 14209S) for GATA2 and PU.1 samples and by phenol-chloroform extraction and ethanol precipitation for H3K4me3 samples.
1.31 ul of DNA was used in a 25-ul PCR reaction to determine the number of cycles for library prepration.

tag: tissue

value: Fetal Liver

tag: cell line

value: myelo-erythoid progenitor

value: vehicle

tag: antibody

value: GATA2 (in house)


title: KOPTK1, shELK3, rep2

city: wuhan

first: dan

middle: hu

last: liu

state: hubei

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province, P.R. China

country: China

institute: wuhan university

data_processing:
Raw sequencing files were filtered using Fastp, and then aligned against the human reference genome (GRCh38/hg38) using STAR.
Filtered reads were processed using samtools, and differential analysis was performed using DESeq2
Assembly: hg38
Supplementary files format and content: bigwig files for shFTO and its corresponding shControl
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quality and quantity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >8.0. The poly (A) mRNA was purified from the total RNA using the Dynabeads mRNA purification kit (Invitrogen).
RNA libraries were then constructed using the NEB Next Ultra Directional RNA Library Prep Kit (NEB)

value: T-cell acute lymphoblastic leukemia


title: KO_veh_GATA2_Rep3


title: IntestCrypts_aKG_Day10_R1_Mouse_1

description: Library name: IntestCrypts_aKG_Day10_R1_Mouse_1

source_name: Murine crypts

treatment_protocol: DM-aKG supplementation, mice were injected (intraperitoneally) once daily with 600 mg/kg of DM-aKG (349631-5G, Sigma-Aldrich) dissolved in PBS. For the vehicle control, mice were injected with PBS.

value: Murine crypts

value: 600 mg/ Kg DM-aKG


title: KOPTK1, shControl for shELK3, rep3

value: WT


title: KO_veh_GATA2_Rep1


title: 90_Tg_8p

city: Strasbourg

first: Salim

last: Megat

state: Alsace

address: 1 rue Eugène Boeckel

country: France

institute: Center for Research in Biomedicine of Strasbourg (CRBS)

description: Library name: CNRX153

data_processing:
Raw counts were imported into R.4.3.1 and batch effects were removed on raw counts using the Combat-Seq method 62. Combat-seq uses a negative binomial regression method that retain the integer nature or raw counts. Batch-corrected counts were then processed following the the ARMOR workflow 63. The ARMOR workflow uses the edgeR-QL framework which provides more accurate type I error rate control, as it accounts for the uncertainty of the dispersion estimates. After visual inspection of sample clustering using PCA and definition of DEG contrast, differential expression was performed between presymptomatic and symptomatic Sod1G86R mice compared to controls for both cell types. Significance was fixed at FDR<0.05
Assembly: mm10
Supplementary files format and content: normalized_counts

source_name: Brain

extract_protocol:
RNA was extracted with Trizol (Invotrogen)
Full length cDNA was obtained using the SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Clontech, CA) according to the manufacturer’s instructions

value: Brain

value: corticospinal neuron


title: KOPTK1, shELK3, rep1


title: KO_combo_GATA2_Rep4

value: IFNg and Pam3CSK4


title: 105_WT_11m

description: Library name: CNRX102

value: wild type genotype


title: 90_Tg_6p

description: Library name: CNRX139


title: IntestCrypts_Control_R1_Mouse_3

description: Library name: IntestCrypts_Control_R1_Mouse_3

value: PBS


title: KO_combo_GATA2_Rep3


title: 90_Tg_5p

description: Library name: CNRX119


title: IntestCrypts_Control_R1_Mouse_2

description: Library name: IntestCrypts_Control_R1_Mouse_2


title: KOPTK1, shControl for shELK3, rep1


title: KO_combo_GATA2_Rep2


title: 90_Tg_3p

description: Library name: CNRX65


title: CUTLL1, shELK3, rep2

value: ELK3 knockdown


title: IntestCrypts_Control_R1_Mouse_1

description: Library name: IntestCrypts_Control_R1_Mouse_1


title: 60_Tg_7p

description: Library name: CNRX131


title: CUTLL1, shELK3, rep3


title: 60_Tg_5p

description: Library name: CNRX95


title: DKO_veh_GATA2_Rep4


title: ROCK1cKOF_aIGM_plus_acD40_TLR9_plus_Hemin_rep3

city: Brooklyn

first: Juan

last: Rivera-Correa

state: NY

address: 285 Jay st, Room A-302-E

department: Biological Sciences

institute: NYC College of Technology

description:
CD23Cre Rock 1 f/f, IgM + CD40+ TLR9 + hemin , day 3
In-vitro

data_processing:
Read quality was assessed and adaptors trimmed using FASTP
Reads were  mapped to the mouse genome (mm10)
Reads in exons were counted against Gencode v27 with STAR2.6 Aligner
Read count extraction and normalization were performed using CLC genomic benchwork
Differential gene expression analysis was performed in R using edgeR 3.24.3
Genes with low expression levels (<2 counts per million in at least 1 group) were filtered from all downstream analyses
Supplementary files format and content: Tab-delimited text files include logCPM values for each Sample

source_name: CD23+ B cells

growth_protocol: CD23+ B cells were puriﬁed from single cell suspensions of splenocytes with biotinylated anti-CD23 (BD Bioscience; #553137) and streptavidin microbeads (Miltenyi Biotec; #130-048-101) as described 71. Cells were cultured for 3 d in RPMI 1640 medium (Corning) supplemented with 10% FBS, 100 U/mL Penicillin, 100mg/mL Streptomycin, non-essential amino acids (Corning), 2 mM L-Glutamine (Corning), 25 mM HEPES (pH 7.2–7.6), and 50 μM β-Mercaptoethanol

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Stimulated with 5 μg/mL F(ab’)2 anti-mouse IgM (Jackson ImmunoResearch), 5 μg/mL puriﬁed anti-mouse CD40 (BioXcell), a TLR9 ligand (TLR9-L, CpG ODN 1668, 1mg/ml) (Invivogen, Cat# tlrl-1668-1) and hemin (heme, 60mM) in various combinations.

value: CD23+ B cells

value: ROCK1 KO

value: IgM + CD40 +TLR9 + hemin

value: 3 days


title: ROCK1cKOF_aIGM_plus_acD40_TLR9_plus_Hemin_rep2


title: 60_Tg_3p

description: Library name: CNRX91


title: ROCK1cKOF_aIGM_plus_acD40_TLR9_plus_Hemin_rep1


title: IntestCrypts_Control_R1_Mouse_4

description: Library name: IntestCrypts_Control_R1_Mouse_4


title: 60_Tg_1p

description: Library name: CNRX71


title: CUTLL1, shControl, rep2


title: CUTLL1, shELK3, rep1


title: ROCK1cKOF_aIGM_plus_aCD40_TLR9_rep3

description:
CD23Cre Rock 1 f/f, IgM + CD40+ TLR9 , day 3
In-vitro

value: IgM + CD40 +TLR9


title: 30_Tg_6p

description: Library name: CNRX105


title: DKO_veh_GATA2_Rep1

value: Fetal Liver

value: myelo-erythoid progenitor

value: vehicle


title: ROCK1cKOF_aIGM_plus_aCD40_TLR9_rep2


title: DKO_combo_GATA2_Rep4

value: GATA2 (in house)


title: ROCK1cKOF_aIGM_plus_aCD40_TLR9_rep1


title: 30_Tg_4p

description: Library name: CNRX81


title: DKO_combo_GATA2_Rep3


title: DKO_veh_GATA2_Rep3


title: 30_Tg_3p

description: Library name: CNRX79


title: 105_Tg_9p

description: Library name: CNRX109


title: ROCK1cKOF_aIGM_plus_acD40_plus_Hemin_rep2

description:
CD23Cre Rock 1 f/f, IgM + CD40 + hemin , day 3
In-vitro

value: IgM + CD40 + hemin


title: CUTLL1, shControl, rep3

value: T-cell acute lymphoblastic leukemia

value: WT


title: DKO_combo_GATA2_Rep1


title: DKO_combo_GATA2_Rep2


title: KOPTK1, shControl for shELK3, rep2


title: KOPTK1, ELK3 ChIP, rep2

data_processing:
Raw sequencing files were filtered using Fastp, and then aligned against the human reference genome  (GRCh38/hg38) using bowtie2.
MACS2 identified the ELK3-enriched regions in each ELK3-immunoprecipitation sample with the corresponding input library as control.
Tracks of signal were computed using MACS2 bdgcmp module with parameter ‘-m FE’, and then visualized using the Integrative Genomics Viewer  (IGV) visualization tool.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak  (except for Input sample)

extract_protocol:
DNA was purified using the phenol-chloroform extraction and ethanol precipitation.
Library preparation was done using the VAHTS Universal DNA Library Prep Kit for Illumina V4  (Vazyme).

tag: chip antibody

value: ELK3 (Novus, NBP1-8396)


title: 105_Tg_13p

description: Library name: CNRX157

value: Brain

value: corticospinal neuron


title: ROCK1cKOF_aIGM_plus_acD40_plus_Hemin_rep1


title: KOPTK1, input, rep3


title: KO_combo_GATA2_Rep1

value: IFNg and Pam3CSK4


title: WT_veh_PU1_Rep4

value: wild type


title: 90_Tg_8m

description: Library name: CNRX154


title: KOPTK1, input, rep2


title: WT_veh_PU1_Rep3


title: ROCK1cKOF_aIGM_plus_acD40_rep3

description:
CD23Cre Rock1 f/f, IgM + CD40 , day 3
In-vitro

value: CD23+ B cells

value: IgM + CD40


title: 90_Tg_6m

description: Library name: CNRX140


title: KOPTK1, input, rep1


title: CUTLL1, shControl, rep1


title: KOPTK1, ELK3 ChIP, rep1


title: A549,MYC+M2,CUT&Tag

city: Nanjing

first: Feng

last: Jiang

state: Jiangsu

address: Baiziting 42

institute: Jiangsu Institute of Cancer Research

data_processing:
Sequencing data were quality controlled using "fastqc" software.
Aligning to Genome with Bowtie2 and removal of repetitive fragments.
Subsequent analyses were performed using deeptools software.
Assembly: hg38
Supplementary files format and content: bw files were uploaded.

source_name: LUAD cell line

growth_protocol: Cancer cells were maintained in DMEM (KeyGEN BioTech) supplemented with 10% Fetal Bovine Serum (Corning) and 1% penicillin-streptomycin at 37°C and 5% CO2.

extract_protocol:
CUT&Tag for capturing histone binding DNA fragments were using Hyperactive Universal CUT&Tag Assay Kit (Vazyme, #TD903-01) via manufacturer protocol. H3K27ac antibody(CST, #8173)
DNA libraries preparing were using TruePrep Index Kit (Vazyme, #TD202) via manufacturer protocol.

treatment_protocol: c-Myc-expression vector (pcDNA3-cmyc, Addgene, #16011, RR_ID:Addgene_16011) and pcDNA3 empty vector (Keris Biotechnology Co.) were transfected by Lipo3000, which was performed using the manufacturer's standard plasmid transfection method. Noncontact cocultures of A549 cells and M2-like macrophages were performed for 72 hours with the use of 3μm Insert Systems (Corning).

value: LUAD cell line

value: LUAD


title: ROCK1cKOF_aIGM_plus_acD40_rep1

value: ROCK1 KO

value: 3 days


title: ROCK1cKOF_aIGM_plus_acD40_plus_Hemin_rep3


title: WT_veh_PU1_Rep1

value: Fetal Liver

value: myelo-erythoid progenitor


title: 90_Tg_3m

description: Library name: CNRX66


title: 90_Tg_5m

description: Library name: CNRX120


title: DKO_veh_GATA2_Rep2

value: vehicle

value: GATA2 (in house)


title: A549,EV+M2,CUT&Tag


title: WT_combo_PU1_Rep4


title: A549,MYC+Veh,CUT&Tag

value: MYC+Veh


title: WT_aIGM_plus_acD40_TLR9_plus_Hemin_rep2

description:
Rock1 f/f, IgM + CD40+ TLR9 + hemin , day 3
In-vitro

value: WT

value: IgM + CD40 +TLR9 + hemin


title: WT_combo_PU1_Rep3


title: A549,EV+Veh,CUT&Tag

value: EV+Veh


title: WT_aIGM_plus_acD40_TLR9_plus_Hemin_rep3


title: WT_combo_PU1_Rep2


title: WT_aIGM_plus_acD40_TLR9_plus_Hemin_rep1


title: 60_Tg_3m

description: Library name: CNRX92

value: Brain


title: KOPTK1, ELK3 ChIP, rep3

value: T-cell acute lymphoblastic leukemia

value: ELK3 (Novus, NBP1-8396)


title: Patient 1,Acinar-tissue,CUT&Tag

source_name: LUAD Tissue

value: LUAD Tissue

value: Tissue

value: Acinar-subtype


title: WT_combo_PU1_Rep1

value: wild type

value: IFNg and Pam3CSK4


title: 60_Tg_7m

description: Library name: CNRX132


title: ROCK1cKOF_aIGM_plus_acD40_rep2

value: CD23+ B cells

value: ROCK1 KO

value: IgM + CD40

value: 3 days


title: WT_aIGM_plus_aCD40_TLR9_rep2

description:
Rock1 f/f, IgM + CD40+ TLR9 , day 3
In-vitro

value: IgM + CD40 +TLR9


title: WT_aIGM_plus_aCD40_TLR9_rep3


title: WT_veh_PU1_Rep2

value: Fetal Liver

value: myelo-erythoid progenitor

value: vehicle


title: 30_Tg_3m

description: Library name: CNRX80


title: KO_veh_PU1_Rep4


title: Healthy control 3

city: Paris

first: Chloé

last: Grolleau

address: 1 avenue Claude Vellefaux

department: Hopital saint Louis

institute: INSERM U1342, eq 16

library_source: transcriptomic single cell

data_processing:
All provided R1 and R2 FASTQ files are already demultiplexed by sample index.
Data pre-processing (read quality control, extraction, alignment, deduplication and assignment) was performed from raw FASTQ files to count matrices using Cytonaut v1.4 (https://cytonaut-scipio.bio) with Cytonaut's pre-processing module v6.12.6.
Detection of cell-associated barcodes was done for each sample by applying the distance-based knee method of UMI-tools double-checked by manual inspection.
The provided processed data is composed of one count matrix per sample at full sequencing depth.
Data post-processing (filtering, normalization, HVG, batch correction, PCA, 2D embedding, clustering, DGE) was performed using Seurat v4.3.0.1 and cell annotation was performed manually based on markers found in the literature for cell types typically present in the human skin. Pseudo-time analysis was performed using Monocle v3.0.
Assembly: The reference genome sequences and annotations are based on Ensembl release v99 for human species (GRCh38). Unique Genome Name in Cytonaut v6.7.0: Human_Scipio_2022_A; Species: Homo_sapiens; Genome Source: ensembl; Genome Version: GRCh38; Genome Link: ftp.ensembl.org//pub/release-99/fasta/homo_sapiens/dna/; Annotation Source: ensembl; Annotation Version: 99; Annotation Link: ftp.ensembl.org//pub/release-99/gtf/homo_sapiens/
Supplementary files format and content: Tab Separated Values (TSV format) including all count matrix information (genes in first column, then one column per cell-associated barcode)

source_name: skin

extract_protocol:
5 patients with active cutaneous lichen planus were recruited for this study and contributed for 4mm skin biopsies. 3 healthy controls were recruited for skin biopsy from plastic breast surgery waste. The study was approved by the by our institutional ethic committee (Comité de Protection des Personnes Ile de France IV), and all patients were consented. Skin biopsies were transferred in NaCl 9‰ and immediately digested for 4h30 at 37°C using whole skin dissociation kit (Miltenyi) according to the manufacturer protocol. Single cell suspension obtained was then processed with Asteria kit (Scipio Bioscience) with 30,000 cells input in 2 kits for each sample to generate 3' enriched cDNA with corresponding cell barcode.
The cell barcoded cDNA was fragmented, end-repaired then adapter was ligated to the extremities using NEBNext Ultra II FS DNA libary kit for illumina. Selective amplification of cDNA fragment containing the cell barcode was done with custum P5-R1 library primer from Asteria kit and indexed P7-R2 primier from NEBNext Mulitplex Oligos kit. Libraries were sequenced on the illumina NovaSeq 6000 sequencer to generate paired-end read. 25 bases for read1 and 70 bases for read2. read1 contains cell barcode and read2 contains 3' sequence of cDNA.

value: skin

tag: disease

value: Healthy control


title: 30_Tg_2m

description: Library name: CNRX62

value: Brain


title: WT_aIGM_plus_aCD40_TLR9_rep1

value: WT


title: KO_veh_PU1_Rep2


title: WT_aIGM_plus_aCD40_plus_Hemin_rep3

description:
Rock1 f/f, IgM + CD40 + hemin , day 3
In-vitro

value: IgM + CD40 + hemin


title: KO_veh_PU1_Rep3


title: Healthy control 1.2

description:
HC1 was sequenced in two stages
processed data count_matrix_HC1.csv was generated from both Healthy control 1.1 and Healthy control 1.2 samples, and is linked to the Healthy control 1.1 sample records.


title: Healthy control 2


title: 105_Tg_13m

description: Library name: CNRX158


title: KO_veh_PU1_Rep1


title: WT_aIGM_plus_aCD40_plus_Hemin_rep1


title: Healthy control 1.1

description: HC1 was sequenced in two stages


title: KO_combo_PU1_Rep4


title: WT_aIGM_plus_aCD40_plus_Hemin_rep2


title: 105_Tg_12m

description: Library name: CNRX152


title: Patient 1,MP-tissue,CUT&Tag

value: LUAD Tissue

value: Tissue

value: LUAD

value: MP-subtype


title: Lichen planus 3

value: Lichen planus


title: KO_combo_PU1_Rep3

value: IFNg and Pam3CSK4


title: KO3-F

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

description: Library name: 12

data_processing:
The reads were mapped to the mouse genome mm10, and raw gene read counts were generated using the Mayo Clinic RNA-sequencing analytic pipeline, MAP-RSeq
Conditional quantile normalization (CQN) on the raw gene counts was used to correct for GC bias and gene length differences and obtain similar quantile-by-quantile distributions of gene expression levels across samples.
Assembly: mm10
Supplementary files format and content: .tsv file with raw gene counts

source_name: Cortex

growth_protocol: The Abca7-floxed mice (Abca7floxp/floxp) were crossed with 5×FAD+/− mice [29] or Camk2a-Cre+/− mice to generate the founders: 5×FAD+/−; Abca7floxp/floxp mice and Abca7floxp/floxp; Camk2a-Cre+/− mice (nAbca7−/−). By breeding the mice, 5×FAD+/-; Abca7floxp/floxp; Camk2a-Cre+/- mice (5×FAD; nAbca7-/-) were generated. The 5×FAD+/−; Abca7floxp/floxp; Camk2a-Cre-/- littermates were used as controls (5×FAD; control).

extract_protocol:
Total RNAs were extracted from the samples using TRIzol RNA Isolation Reagents (Thermo Fisher Scientific) and RNeasy Mini Kit with DNase (QIAGEN)
RNA libraries were prepared and sequenced with Illumina HiSeq 4000 at the Mayo Clinic Center for Individualized Medicine’s Medical Genome Facility.

value: Cortex

value: KO

tag: age


title: WT_aIGM_plus_acD40_rep2

description:
Rock1 f/f, IgM + CD40 , day 3
In-vitro

value: CD23+ B cells

value: IgM + CD40

value: 3 days


title: 60_Tg_5m

description: Library name: CNRX96


title: Lichen planus 2


title: KO_combo_PU1_Rep2

value: Fetal Liver

value: myelo-erythoid progenitor


title: KO_combo_PU1_Rep1


title: KO2-F

description: Library name: 11


title: WT_aIGM_plus_acD40_rep3

description:
Rock1 f/f, IgM + CD40 , day 3
In-vitro


title: WT_aIGM_plus_acD40_rep1

description:
Rock1 f/f, IgM + CD40 , day 3
In-vitro


title: Lichen planus 1

value: skin


title: PB_PCs_ROCK1_KO_rep3

description:
P. yoelii-infected CD23Cre Rock1 f/f D.10
Ex-vivo

source_name: PB/ PCs

value: PB/ PCs

value: ROCK1 KO

value: P. yoelii infection

value: 10 days


title: PB_PCs_ROCK1_KO_rep2


title: KO1-F

description: Library name: 10


title: 105_Tg_9m

description: Library name: CNRX110

value: Brain


title: PC3 cells, TBX2 Neo (EV)3

city: Lubbock

first: Srinivas

last: Nandana

state: TX

address: CBB Lbk Genl 3601 4th St Stop 6540

department: Cell Biology Biochemistry

institute: Texas Tech University Health Science Center

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the homo sapiens reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by Deseq2 software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: Prostate cancer epithelial cells

growth_protocol: PC3Neo (EV) and PC3TBX2DN cells were maintained in DMEM medium supplemented with 10%FBS and 1% penstrep  in humidified condition in 5%Co2 incubator.

extract_protocol:
RNA was extracted using Rneasy mini kit
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

treatment_protocol: The cells were maintained in selection marker puromycin at 5µg/ml concentration.

value: Prostate cancer epithelial cells

value: Epithalia


title: DKO_veh_PU1_Rep4

value: vehicle


title: DKO_veh_PU1_Rep3


title: PB_PCs_ROCK1_KO_rep1


title: DKO_veh_PU1_Rep2


title: KO2-M

description: Library name: 8


title: KO3-M

description: Library name: 9


title: PC3 cells, TBX2 Neo (EV)2


title: PC3 cells, TBX2 Neo (EV)1


title: KO1-M

description: Library name: 7


title: DKO_veh_PU1_Rep1


title: PC3 cells, TBX2 dominants negative DN3


title: PC3 cells, TBX2 dominants negative DN2


title: PB_PCs_ROCK1_WT_rep1

description:
P. yoelii-infected Rock1 f/f D.10
Ex-vivo

value: WT


title: WT3-F

description: Library name: 6

value: Cortex


title: 105_Tg_10m

description: Library name: CNRX128


title: DKO_combo_PU1_Rep4

value: IFNg and Pam3CSK4


title: DKO_combo_PU1_Rep3


title: PC3 cells, TBX2 dominants negative DN1


title: WT2-F

description: Library name: 5


title: Naive_Bs_ROCK1_KO_rep3

source_name: Naive Bs

value: Naive Bs


title: gDNA_VH1855B

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

data_processing:
FastQ files resulting from library sequencing were aligned to the reference genome (hg38) using BWA version 0.7.17-r1188 following best practices [https://pubmed.ncbi.nlm.nih.gov/19451168/]
The resulting aligned BAM files were sorted and processed for PCR duplicates removal, base quality score recalibration and indel realignment using samtools 1.9 [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002/], the Genome Analysis Tool Kit (GATK) version 4.1.4.1 and picard version 2.17.0 [https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1110s43].
Somatic and germline single nucleotide variants and small indels, as well as copy num-ber variations were called using GATK’s Haplotype Caller version 4.1.4.1 following best practices [https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1110s43]
Assembly: hg38.p11
Supplementary files format and content: vcf (4.2 standard)
Supplementary files format and content: bed file standard

source_name: Whole blood

extract_protocol:
MagMAXTM Cell-Free DNA Isolation Kit
Sequencing libraries were prepared following TruSight Oncology 500 ctDNA Reference Guide (Document # 1000000092559 v00) with the corresponding kit [Illumina Inc. TruSight Oncology 500 ctDNA Kit (48 samples) Cat.# 20039252].
Using End Repair A-Tailing Master Mix, input DNA (30ng for ctDNAs and 40ng for sonicated-gDNAs) was blunt-ended and the 3' ends were A-tailed. Then, UMI1 adapters that contain unique molecular indexes (UMIs) were ligated to DNA fragments. After ligation product clean-up, library fragments were amplified using primers that add index sequences for sample multiplexing. Following this step, a pool of oligos specific to the 523 genes targeted by TruSight Oncology 500 ctDNA panel were hybridized to DNA libraries. In the next step, targeted regions of the enriched DNA libraries were bound with capture probes a second time. The second hybridization ensures high specificity of the captured regions. Then, Streptavidin Magnetic Beads were used to capture the probes hybridized to the targeted regions of interest. Resuspension buffer was used to rinse the captured libraries and remove nonspecific binding from the beads. Finally, enriched libraries were amplified, and a final clean-up step was performed.

value: Whole blood

tag: disease state

value: hepatocellular carcinoma

value: immunotherapy


title: PB_PCs_ROCK1_WT_rep3


title: Naive_Bs_ROCK1_KO_rep2


title: HUDEP-2 cells, 4-17, Pol-II

city: Guangzhou

first: Xiuqin

last: Bao

address: No. 1838, Guangzhou avenue north, baiyun district, Guangzhou

institute: Southern Medical University

data_processing:
All clean reads passed quality control with FASTQC and were mapped onto hg19 with bowtie2.
After removal of duplicates with picard, the bam data were ranked, and an index was created with samtools.
We used MACS2 to generate peak calls with input as the control and set a 200-bp bandwidth in the shiftingmodel to denote the peak with p < 0.01.
Assembly: hg19
Supplementary files format and content: tdf files were generated using the MACS

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

value: Human umbilical cord blood-derived erythroid progenitor

value: POI-II


title: WT1-F

description: Library name: 4


title: Lichen planus 4

value: skin

value: Lichen planus


title: DKO_combo_PU1_Rep1

value: Fetal Liver

value: myelo-erythoid progenitor


title: WT3-M

description: Library name: 3


title: Naive_Bs_ROCK1_KO_rep1

value: ROCK1 KO

value: P. yoelii infection

value: 10 days


title: WT2-M

description: Library name: 2


title: gDNA_NV_8


title: gDNA_NV_7


title: m77WtSpi1Wt_veh_Rep4

data_processing:
RNA-seq reads were aligned by STAR (version 2.5.2b) to the mouse genome (version mm10) with GENCODE basic gene annotations (version M22).
Gene expression levels were quantified by RSEM (version 1.3.0)
Assembly: mm10
Supplementary files format and content: TSV: RSEM quantification results at the gene level

extract_protocol:
RNA was extracted using Trizol and was cleaned up using Qiagen columns.
TruSeq Stranded Total RNA Gold (Human/Mouse/Rat mitochondrial + cytoplasmic rRNA reduction)

value: wild type

value: Vehicle


title: Naive_Bs_ROCK1_WT_rep3

value: WT


title: WT1-M

description: Library name: 1

value: Cortex


title: Naive_Bs_ROCK1_WT_rep2

value: Naive Bs


title: gDNA_NV_6

value: Whole blood


title: m77WtSpi1Wt_veh_Rep2


title: X24-M

description: Library name: 24

value: KO


title: X23-M

description: Library name: 23


title: Activated_Bs_ABs_ROCK1_KO_rep3

source_name: Activated B s

value: Activated B s


title: Naive_Bs_ROCK1_WT_rep1


title: gDNA_NV_3

value: hepatocellular carcinoma

value: immunotherapy


title: m77WtSpi1Wt_veh_Rep1


title: DKO_combo_PU1_Rep2

value: IFNg and Pam3CSK4


title: X22-M

description: Library name: 22


title: m77WtSpi1Wt_combo_Rep4


title: X21-M

description: Library name: 21


title: gDNA_NV_22


title: gDNA_NV_20


title: m77WtSpi1Wt_combo_Rep3


title: Activated_Bs_ABs_ROCK1_KO_rep2


title: m77WtSpi1Wt_combo_Rep2


title: Activated_Bs_ABs_ROCK1_KO_rep1


title: X20-M

description: Library name: 20


title: gDNA_NV_2


title: m77WtSpi1Wt_veh_Rep3


title: X18-M

description: Library name: 18


title: m77KoSpi1Wt_veh_Rep4


title: Activated_Bs_ABs_ROCK1_WT_rep3


title: m77KoSpi1Wt_veh_Rep3


title: gDNA_NV_16


title: m77WtSpi1Wt_combo_Rep1


title: gDNA_NV_18


title: gDNA_NV_17


title: ROCK1_KO_rep1

description:
NP-CGG-immunized CD23Cre Rock1 f/f D.7
Ex-vivo

source_name: GCBs

value: GCBs

value: NP-CGG-immunized

value: 7 days


title: 30_Tg_4m

description: Library name: CNRX82

value: Brain


title: gDNA_NV_1


title: m77KoSpi1Wt_pam3_Rep4

value: Fetal Liver

value: myelo-erythoid progenitor


title: Activated_Bs_ABs_ROCK1_WT_rep2

value: P. yoelii infection

value: 10 days


title: Activated_Bs_ABs_ROCK1_WT_rep1

description:
P. yoelii-infected Rock1 f/f  D.10
Ex-vivo

value: WT


title: gDNA_NV_4


title: ROCK1_WT_rep3

description:
NP-CGG-immunized Rock 1 f/f D.7
Ex-vivo


title: PB_PCs_ROCK1_WT_rep2

value: PB/ PCs


title: gDNA_AB_8


title: X17-M

description: Library name: 17

value: Cortex


title: ROCK1_KO_rep3

value: ROCK1 KO


title: m77KoSpi1Wt_veh_Rep2

value: Vehicle


title: X19-M

description: Library name: 19

value: KO


title: gDNA_NV_14

value: Whole blood

value: hepatocellular carcinoma


title: X16-M

description: Library name: 16


title: ROCK1_KO_rep2


title: ROCK1_WT_rep1

description:
NP-CGG-immunized Rock 1 f/f D.7
Ex-vivo


title: X15-M

description: Library name: 15


title: X10-F

description: Library name: 10


title: X14-M

description: Library name: 14


title: X11-F

description: Library name: 11


title: m77KoSpi1Wt_ifng_Rep4

value: IFNg


title: gDNA_AB_9

value: immunotherapy


title: X13-M

description: Library name: 13


title: X9-F

description: Library name: 9


title: ROCK1_WT_rep2

description:
NP-CGG-immunized Rock 1 f/f D.7
Ex-vivo

value: GCBs

value: NP-CGG-immunized


title: m77KoSpi1Wt_pam3_Rep2


title: gDNA_AB_3


title: gDNA_AB_5


title: X12-F

description: Library name: 12


title: m77KoSpi1Wt_ifng_Rep3


title: gDNA_AB_6


title: m77KoSpi1Wt_veh_Rep1


title: gDNA_AB_1


title: m77KoSpi1Wt_pam3_Rep1


title: gDNA_AB_2


title: m77KoSpi1Wt_ifng_Rep2


title: m77KoSpi1Wt_ifng_Rep1


title: X8-F

description: Library name: 8


title: gDNA_AB_4


title: CTRL_YL05007D

type: RNA

city: Milano

first: Alessandra

last: Trojani

address: Piazza dell'Ospedale Maggiore, 3

country: Italy

institute: ASST Grande Ospedale Metropolitano Niguarda

description:
Gene expression data from BM CD34+/lin- cells
RNA extraction protocol: ONEDIRECT_2

hyb_protocol: cDNA wad hybridized to Affymetrix HTA 2.0 using the GeneChip platform (Affymetrix).

scan_protocol: Affymetrix GeneChip Scanner 3000 was used according to the manufacturer’s instructions to scan the signals.

data_processing: The data were normalized using the RMA method from the oligo package (version 1.42.0) from the Bioconductor repository (version 3.4). In this step, the measured signal intensities of the 6 million probes were summarized into probe sets specific for a given gene locus, realizing a one-to-one assignment of probe sets and genes. Data were first pre-processed using ComBat to adjust for batch effects and quantile normalization.

label: biotin

label_protocol: cDNA was prepared starting from the previously extracted RNA (50 ng) using Ovation Pico WTA System V2 kit (NuGEN) and Encore Biotin Module Kit (NuGEN) following the manufacturer’s instructions. cDNA was prepared starting from 3 µl of the BM CD34+/lin- cells resuspended in Prelude direct Lysis module (NuGEN), using Ovation One Direct System kit followed by Encore Biotin Module Kit (NuGEN) adhering to the manufacturer’s instructions.

growth_protocol: The cells were resuspend in 50 µl of RNAlater (Thermo Fisher Scientific, Milano, Italy) and store at -20°C. Preserve the BM CD34+/lin- cells in 50 µl of RNAlater when the number of the cell count was equal to 10,000 or more and the cells were stored at -20°C. If the number of BM CD34+/lin- cells was less than 10,000, resuspend the cells in 10 µl of Prelude direct Lysis module (NuGEN, AC Leek, The Netherlands) and immediately after, store the cells at -80°C.

extract_protocol: RNA extraction was performed using MagMAX 96 Total RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Quality and yield of the extracted RNA were measured using Nanodrop (Thermo Fisher Scientific). We did not perform RNA extraction of the BM CD34+/lin- cells stored in Prelude direct Lysis module (NuGEN) because of the too low number of cells and perform the RNA processing starting from the cells.

treatment_protocol: The cells were not treated prior to the extraction of total RNA.

value: control

value: CD34+/lin- cells

tag: timepoint


title: X6-F

description: Library name: 6


title: CTRL_TA05002D


title: m77KoSpi1Wt_combo_Rep4

value: Fetal Liver

value: myelo-erythoid progenitor

value: IFNg and Pam3CSK4


title: m77KoSpi1Wt_combo_Rep3


title: X7-F

description: Library name: 7


title: cfDNA_NV_8

library_source: other

molecule: other

source_name: plasma

value: plasma


title: X5-F

description: Library name: 5


title: cfDNA_VH1855B


title: m77KoSpi1Wt_combo_Rep2


title: cfDNA_NV_7


title: CTRL_OT05004D


title: m77KoSpi1Wt_combo_Rep1


title: cfDNA_NV_6


title: X3-F

description: Library name: 3


title: X2-F

description: Library name: 2


title: m77KoSpi1Ko_veh_Rep4


title: cfDNA_NV_4


title: CTRL_MZ05009D


title: CTRL_MP05003D


title: X1-F

description: Library name: 1


title: cfDNA_NV_3


title: CTRL_FC05006D


title: CTRL_DG05008D


title: X4-F

description: Library name: 4


title: CTRL_DD05001D


title: DIV14 pyramidal neuron CLIP library

city: San Diego

first: Norjin

last: Zolboot

state: CA

address: 10550 North Torrey Pines Rd, DNC-222

department: Neuroscience

institute: The Scripps Research Institute

description: Library name: DIV14-PN-CLIP

data_processing:
UMIs were pruned from read sequences using UMI-tools (v1.1.1). UMI sequences were saved by incorporating them into the read names in the FASTQ files to be utilized in subsequent analysis steps.
3' adapters were trimmed from reads using cutadapt (v3.2) and reads shorter than 18 bp in length were removed.
Reads were then mapped to a database of mouse repetitive elements and rRNA sequences compiled from Dfam and Genbank. All non-repeat mapped reads were mapped to the mouse genome (mm10) using STAR (v2.7.7a).
PCR duplicates were removed using UMI-tools (v1.1.1) by utilizing UMI sequences from the read names and mapping positions.
Peaks were identified within eCLIP samples using the peak caller CLIPper.
Assembly: mm10
Supplementary files format and content: bigWig for CLIP and input

source_name: embryonic cortices

growth_protocol: Primary cultured neurons were maintained in Neurobasal medium supplemented with B27 Plus and GlutaMAX in a humidified incubator at 37 °C, 5% CO2. Half media changes were performed every 3 days

extract_protocol:
Cells were washed once with DPBS, covered in DPBS and UV crosslinked on leveled ice at 400 mJoules/cm2 with 254 nm radiation. While on ice, cells were collected with a scraper into a tube, washed once with DPBS, pelleted, flash frozen in liquid nitrogen and stored until use at -80 °C. Cell pellet was aliquoted and lysed using 1mL of eCLIP lysis mix. Anti-AGO2 antibody (Eclipse Bioinnovations Inc.) pre-coupled to anti-mouse Dynabeads were washed with eCLIP Lysis Buffer, added to cell lysate or sonicated tissue lysate, and then incubated overnight at 4 °C. After immunoprecipitation, 2% of the sample was taken as the paired input sample, with the remainder magnetically separated and washed with eCLIP high stringency wash buffers. IP and input samples were cut from the membrane at the relative band size to 75 kDa above.
RNA adapter ligation, IP-western, reverse transcription, DNA adapter ligation, and PCR amplification were performed as previously described in Van Nostrand et al. (2017)

value: embryonic cortices

value: pyramidal neurons

value: WT


title: m77KoSpi1Ko_veh_Rep2

value: Vehicle


title: DIV14 pyramidal neuron input library

description: Library name: DIV14-PN-input


title: CTRL_BS05005D


title: CTRL_AG01001D


title: m77KoSpi1Ko_veh_Rep1


title: cfDNA_NV_22


title: m77KoSpi1Ko_pam3_Rep4


title: m77KoSpi1Wt_pam3_Rep3


title: m77KoSpi1Ko_veh_Rep3


title: cfDNA_NV_2


title: Bu-KAI-24

city: Rochester

first: Shuwen

last: Zhang

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

description:
Library name: Bu-KAI-24
10X Genomics

data_processing:
The single cell sequence preprocessing was performed using the standard 10x Genomics Cell Ranger Single Cell Software Suite v.3.1.0.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files (cellranger output)

source_name: brain cortex

extract_protocol:
Mice were transcardially perfused with PBS and the cortical tissues were quickly dissected and enzymatically digested using the Neural Tissue Dissociation kit (P; Cat# 130-092-628; Miltenyi Biotec) at 37°C in the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec). The myelin was then removed using magnetic bead separation (Myelin Removal Beads II, Cat# 130-096-733; Miltenyi Biotec) followed by the red blood cell lysis (Cat# 130-094-183; Miltenyi Biotec) and dead cell removal (Cat# 130-090-101; Miltenyi Biotec) according to the manufacturer’s instructions. The final cell pellet was suspended in Ca/Mg-free PBS supplemented with 0.5% FBS for downstream analysis. In all samples, more than 90% of the cells were viable based on trypan blue examination.
scRNA-seq was performed on isolated cortical samples using the chromium platform (10x Genomics) with the 3′ gene expression V3 kit, using a targeted input of ∼6,000–9,000 cells per sample. In brief, gel-beads in emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs using Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly-A-tailing, adaptor ligation, and 10x-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using the TapeStation (Agilent) analysis and then sequenced on a HiSeq 4000 instrument (Illumina) targeting a depth of 25,000–50,000 reads per cell.

value: brain cortex

value: Ctrl

tag: Sex

value: Male


title: Bu-KAI-23

description:
Library name: Bu-KAI-23
10X Genomics

value: TAM


title: Bu-KAI-22

description:
Library name: Bu-KAI-22
10X Genomics


title: cfDNA_NV_18

value: hepatocellular carcinoma

value: immunotherapy


title: cfDNA_NV_20


title: m77KoSpi1Ko_pam3_Rep2

source_name: Fetal Liver


title: m77KoSpi1Ko_pam3_Rep1


title: m77KoSpi1Ko_ifng_Rep4

value: IFNg


title: cfDNA_NV_16


title: m77KoSpi1Ko_pam3_Rep3


title: XX07012_0

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)

value: diagnosis

value: nilotinib


title: Bu-KAI-20

description:
Library name: Bu-KAI-20
10X Genomics

value: Female


title: cfDNA_NV_14


title: ZG18002_12

description:
Gene expression data from BM CD34+/lin- cells
RNA extraction protocol: ONEDIRECT_1

value: CD34+/lin- cells


title: Bu-KAI-19

description:
Library name: Bu-KAI-19
10X Genomics


title: ZG18002_0

description:
Gene expression data from BM CD34+/lin- cells
RNA extraction protocol: PICO


title: XX07011_12


title: XX07012_12


title: XX07010_12


title: XX07011_0


title: m77KoSpi1Ko_ifng_Rep3

value: Fetal Liver

value: myelo-erythoid progenitor


title: m77KoSpi1Ko_ifng_Rep2


title: Bu-KAI-17

description:
Library name: Bu-KAI-17
10X Genomics


title: cfDNA_AB_8

value: plasma


title: cfDNA_NV_1


title: m77KoSpi1Ko_combo_Rep3

value: IFNg and Pam3CSK4


title: m77KoSpi1Ko_combo_Rep4


title: Bu-KAI-16

description:
Library name: Bu-KAI-16
10X Genomics


title: cfDNA_AB_6


title: Bu-KAI-18

description:
Library name: Bu-KAI-18
10X Genomics

value: WT


title: cfDNA_NV_17


title: Bu-KAI-15

description:
Library name: Bu-KAI-15
10X Genomics

value: brain cortex


title: m77KoSpi1Ko_combo_Rep2


title: cfDNA_AB_5


title: m77KoSpi1Ko_combo_Rep1


title: XX07010_0


title: XX01010_0


title: XX07009_12


title: XX01010_12


title: cfDNA_AB_3


title: Bu-KAI-13

description:
Library name: Bu-KAI-13
10X Genomics


title: m77KoSpi1Ko_ifng_Rep1


title: D_L. animalisWU + EGF (litter 2)

city: St. Louis

first: Rodney

middle: D

last: Newberry

address: 660 S. Euclid Ave

department: Medicine

institute: Washington University School of Medicine

description: d

data_processing:
Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software
Assembly: mm10
Supplementary files format and content: tab delimited text file contain raw counts for each sample

source_name: mesenteric lymph node

extract_protocol:
MLNs were pooled from multiple pups from DOL17 mice litters CD45+ MHCII+ CD11c+ cells were isolated by FACS and RNA was extracted using TriZol (Invitrogen Life Technologies)
RNA sequencing library preparation used NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA)

value: mesenteric lymph node

value: lymphocytes

value: Lactobacillus animalis and EGF


title: XX07009_0


title: cfDNA_AB_1

value: hepatocellular carcinoma


title: B_L. animalisWU (litter 2)

description: b

value: Lactobacillus animalis


title: Bu-KAI-12

description:
Library name: Bu-KAI-12
10X Genomics

value: Ctrl


title: cfDNA_AB_2

value: immunotherapy


title: C_L. animalisWU + EGF (litter 1)

description: c


title: VL07005_12

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)


title: Bu-KAI-14

description:
Library name: Bu-KAI-14
10X Genomics

value: Male


title: VL07005_0

value: diagnosis

value: nilotinib


title: VE13001_12

value: CD34+/lin- cells


title: cfDNA_AB_4


title: Bu-KAI-10

description:
Library name: Bu-KAI-10
10X Genomics

value: Female


title: IL4,In Labor 4

first: Sun

last: Yue

address: jiangdong

institute: Nanjing Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

source_name: uterine muscle

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Uterine smooth muscle (2.0 × 0.5 × 0.5 cm3) was cut from the site of incision at the lower edges of the uterus during cesarean section. Samples were then washed three times with ice-cold sterile phosphate-buffered saline(PBS), and then stored in liquid nitrogen.

value: uterine muscle

value: In labor


title: IL5,In Labor 5


title: Bu-KAI-21

description:
Library name: Bu-KAI-21
10X Genomics

value: WT

value: TAM


title: Bu-KAI-9

description:
Library name: Bu-KAI-9
10X Genomics

value: brain cortex


title: A1 delta infected with vUNG-repair_4

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
100-bp single-end sequencing was performed using an Illumina NovaSeq 6000 sequencer (Illumina) according to the manufacturer's instructions.
Illumina RTA v3.4.4 software was used for base calling.
The sequencing data were aligned to mouse genome (mm10) by using TopHat (version 2.1.1).
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Mouse brain

extract_protocol:
Total RNA was then isolated with miRNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.
Sequencing libraries were constructed with the TruSeq stranded mRNA Library Prep kit (Illumina).

treatment_protocol: C57BL/6 WT or mAPOBEC1-KO mice were infected intracranially with1×10³ of the indicated viruses. At 5 days post-infection, the mice were killed, and their brains were homogenized in M-tubes (Miltenyi Biotec) using QIAzol Lysis Reagent (QIAGEN) on program RNA01 of the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec).

value: Mouse brain

tag: infection

value: Human herpesvirus 1


title: IL3,In Labor 3


title: Bu-KAI-11

description:
Library name: Bu-KAI-11
10X Genomics


title: VE13001_0


title: A1 delta infected with vUNG-repair_3


title: UF10002_0


title: UF10002_12


title: IL2,In Labor 2


title: A1 delta infected with vUNG-repair_2


title: Bu-KAI-8

description:
Library name: Bu-KAI-8
10X Genomics


title: Bu-KAI-7

description:
Library name: Bu-KAI-7
10X Genomics


title: IL1,In Labor 1


title: cfDNA_AB_9

value: plasma

value: hepatocellular carcinoma


title: NIL4,Not in Labor 4

value: Not in labor


title: Bu-KAI-4

description:
Library name: Bu-KAI-4
10X Genomics

value: Ctrl


title: A1 delta infected with vUNG-S302A_2


title: NIL5,Not in Labor 5


title: TF07016_12

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)


title: TF07016_0


title: NIL3,Not in Labor 3


title: Bu-KAI-3

description:
Library name: Bu-KAI-3
10X Genomics


title: SS01020_0


title: A_L. animalisWU (litter 1)

description: a

value: mesenteric lymph node

value: lymphocytes

value: Lactobacillus animalis


title: B6 Wt infected with vUNG-repair_4


title: Bu-KAI-6

description:
Library name: Bu-KAI-6
10X Genomics

value: Male


title: A1 delta infected with vUNG-repair_1


title: Bu-KAI-2

description:
Library name: Bu-KAI-2
10X Genomics

value: Female


title: SS01020_12

value: CD34+/lin- cells

value: nilotinib


title: NIL2,Not in Labor 2

value: uterine muscle


title: Bu-KAI-5

description:
Library name: Bu-KAI-5
10X Genomics

value: WT

value: TAM


title: B6 Wt infected with vUNG-repair_2

value: Mouse brain


title: B6 Wt infected with vUNG-repair_3

value: Human herpesvirus 1


title: A1 delta infected with vUNG-S302A_1


title: mouse_cortex_10x_v2_beads_inhouse_1

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

description:
Library name: HYA__e9082f__20240430_Mouse_Cortex-d-ATAC
re-sequenced on Illumina NovaSeqX and Nextseq 2000

library_source: genomic single cell

data_processing:
In house generated data (prefix HYA and FDM):  Barcode reads (read 2) were trimmed to exclude the intersub-barcode PCR adapters MAWK
In house generated data (prefix HYA and FDM):  Barcode reads (read 2) were trimmed using trimgalore, corrected to a whitelist allowing 1 mismatch (in PUMATAC pipeline, nextflow version: nextflow-21.04.3), and appended to the fastq sequence identifier of the paired-end ATAC-seq reads (read 1 and read 3)
For all samples (mouse (in house generated and commercial), fly and barnyard cell lines): Reads were mapped to reference genomes using bwa-mem2 and fragemnet files were created with create_fragments_file by the (in PUMATAC pipeline, nextflow version: nextflow-21.04.3)
For mouse samples a data matrix (cistopic_obj) was generated using  pycistopic version 2.0a0. Cells passing the Otsu threshold in PUMATAC (nextflow version: nextflow-21.04.3) were included.
For Drosophila samples a data matrix (cistopic_obj) was generated using  pycistopic version 2.0a0. Cells passing  the trhshold of TSS_enrichment >2 and number of unique fragments > 800 in PUMATAC (nextflow version: nextflow-21.04.3) were included.
Assembly: For mouse samples: mm10, for hybrid samples in the barnyard: GRCh38_GRCm10 hybrid genome, for fly samples: dm6
Supplementary files format and content: For mouse and Drosophila samples: standard tab-separated fragments files, count matrix and metadata inforamtion for cell data (barcode) and region data in tsv format
Supplementary files format and content: For barnyard: standard tab separated fragment file

growth_protocol:
Barnyard cell culture: cultured in RPMI1640 (ThermoFisher 11875093) medium supplemented with 10% FBS (ThermoFisher 10270–106), 1% penicillin/streptomycin (Life Technologies 15140122), and 10 ug/mL insulin (Sigma Aldrich I9278) and passaged twice per week. Melanoma cell lines were derived by physical resection of primary cutaneous lesions. Mouse melanoma cells were cultured in DMEM (ThermoFisher 13345364) supplemented with 10% FBS and 1% penicillin/streptomycin and passaged once per week. All cell lines tested negative for mycoplasma prior to use.
Mouse: The mice were housed under standard housing conditions in a pathogen-free facility with a 14 hr light, 10 hr dark light cycle from 7 to 21 hr. Mice used in the study were 60 days old.
Drosophila: All flies were raised on a yeast-based medium and kept at 25 °C on a 12h/12h day/night light cycle. For embryo collection, flies were transferred to cages fixed to a plate with a normal yeast-based medium 24 hours before embryo collection. On the day of embryo collection, the plate was exchanged for a juice plate. The juice was prepped by adding 20 g agar and 22 g sucrose to 300 ml distilled water, boiling, and then mixing in 100 ml apple juice, 10 ml 95% ethanol, and 5 ml 100% glacial acetic acid. The flies laid eggs for four hours. Sixteen hours later, the embryos aged between 16 to 20 hours were collected from the juice plate with a small brush and transferred to a 70 µm nylon mesh filter.

extract_protocol:
Mouse: The nuclei were extracted from mouse cortex samples that were snap-frozen in liquid nitrogen and stored at -80 °C. We transferred ~1 cm3 of frozen mouse cortex to 500 μL of ice-cold homogenization buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 320 mM sucrose, 0.1 mM EDTA, 0.5% BSA, 0.1% IGEPAL CA-630, 1× complete protease inhibitor, and 1 mM DTT) in a Dounce Homogenizer. The tissue was left to thaw for 2 min before the tissue was homogenized with 10 strokes of the loose pestle and 5 strokes of the tight pestle. Before the end of a 5-minute incubation, the homogenate was filtered through a 70 μm cell strainer (Corning), and the homogenizer and strainer were washed with homogenization buffer to obtain a final volume of 1 mL. The filtrate was transferred to a 1.5 mL DNA LoBind tube (Eppendorf) and centrifuged at 500 xg for 5 minutes. The supernatant was discarded, and the pellet was topped up to 520 μL with wash buffer 1 (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 320 mM sucrose, 0.1 mM EDTA, 0.5% BSA, 1× complete protease inhibitor, and 1 mM DTT) and resuspended. Next, we added 520 μL gradient medium (50% Optiprep, 10 mM Tris-HCl pH 7.5, 1 mM CaCl2, 5 mM MgCl2, 75 mM sucrose, 1× complete protease inhibitor, and 1 mM DTT) and mixed the entire volume by gentle pipetting. In a 2 mL DNA LoBind tube we layered 790 μL Optiprep cushion (29% Optiprep, 31 mM Tris-HCl pH 8, 77.5 mM KCl, 15.5 mM MgCl2, 129.2 mM sucrose) at the bottom and 1040 μL of the sample on top, gently without disrupting the cushion. The tube was then centrifuged at 9000 xg for 20 minutes at 4 °C. After the centrifugation the debris on top was carefully removed with a 1 mL tip and the rest of the supernatant was also carefully removed until 50 μL was left in the tube. The pellet was gently resuspended before we mixed it with 50 μL 0.2× permeabilization buffer (20 mM Tris-HCl pH 7.5, 20 mM NaCl, 6 mM MgCl2, 0.2% Tween-20, 0.02% IGEPAL CA-630, 0.02% Digitonin, 2% BSA, and 2 mM DTT) and left the nuclei suspension for 2 minutes on ice before we stopped the permeabilization by mixing it with 1 mL of wash buffer 2 (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA). The nuclei were pelleted by centrifugation at 500 xg for 5 minutes at 4 °C. The nuclei were resuspended in PBS with 0.04% BSA. For Drosophila, the nuclei were isolated by using an adapted protocol based on the nuclei isolation protocol for single-cell ATAC sequencing (10x Chromium CG000169-RevE).  Similar to mouse, for the barnyard, the cell lines were mixed to equal parts and a pellet of one million dissociated cells or fewer was incubated on ice in 200 μL of ATAC lysis buffer (1% BSA, 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.1% Tween-20, 0.1% NP-40, 3 mM MgCl2, 70 μM Pitstop in DMSO, 0.01% digitonin) for 5 minutes. 1 mL of ATAC nuclei wash buffer (1% BSA, 10 mM Tris-HCl pH 7.5, 0.1% Tween-20, 10 mM NaCl, 3 mM MgCl2) was added and the nuclei were pelleted at 500 xg, 4 °C for 5 minutes. The resulting pellet was resuspended in 100 μL of ice-cold PBS and filtered with a 40 μm strainer (Flowmi).
Nuclei, resuspended in PBS (supplemented with 0.04% BSA), were tagmented for one hour at 37 °C in 15 μL ATAC reaction mix (10% DMF, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 5 ng/µL Tn5, 70 µM Pitstop in DMSO, 0.1% Tween-20, 0,01% Digitonin). Tagmented nuclei were placed on ice and 95 µL of PCR mix (1.25× Phusion HF buffer, 15% Optiprep, 1.25 mM dNTPs, 75 mM DTT, 0.0625 U/µL Phusion HF polymerase, 0.0625 U/μL Deep Vent polymerase, 0.0125 U/μL ET SSB) was added. Next, 110 μL of nuclei mixed in PCR mix was co-encapsulated with 45 μL of HyDrop-ATACv2 beads in HFE-7500 Novac oil with EA-008 surfactant (RAN Biotech) using the Onyx microfluidics platform (Droplet Genomics). The resulting emulsion was split over two PCR tubes and was placed in a thermocycler with the following program: 72 °C – 15 mins, 98 °C – 3 mins, 12 cycles of 98 °C – 10 s; 55 °C – 30 s; 72 °C – 1 min; 72 °C – 5 mins, and finally the amplification products were cooled to 4 °C. To break the emulsion and remove excess oil, 125 μL of recovery agent (20% PFO in HFE) was added and the PCR tubes were inverted 10 times to mix before the oily phase was removed. Next, we added 180 μL GITC mix (5M GITC, 25 mM EDTA, 50 mM Tris-HCl pH 7.4), 10 μL Dynabeads, and 10 μL 2.4 M DTT to each of the aliquots, and mixed everything by pipetting up and down 10 times and incubating for 10 minutes. Dynabeads were pelleted on a magnet and washed twice with 80% ethanol. Elution was done in 50 μL of EB-DTT-Tween (24 mM DTT, 0.1% Tween-20 in EB (10 mM Tris-HCl pH 8.5)). Next, a 1.2× Ampure bead purification was performed according to manufacturer’s recommendations. Elution was done with 40 μL of EB-DTT (10 mM DTT in EB). The library was completed by amplifying the eluate in a total volume of 100 μL PCR mix (1× KAPA HiFi, 1 μM index i7 primer, 1 μM Universal P5 primer) with the following program: 95 °C – 3 mins, 12 cycles of 98 °C – 10 s; 63°C – 30 s; 72 °C – 1 min; 72 °C – 1 min, and finally a hold stage at 4 °C. The final libraries were subjected to 0.4×–1.2× doublesided Ampure purification and eluted in 20 μL elution buffer.

value: brain cortex

value: divers cells of brain cortex

tag: strain

value: C57B/6J background

value: female

value: 60 days

tag: batch


title: SMR18001_12

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)


title: NIL1,Not in Labor 1

value: Not in labor


title: mouse_cortex_HyDrop_v2_F_beads_8

description:
Library name: HYA__2eb25d__20240430_Mouse_Cortex-b-ATAC
re-sequenced on Illumina NovaSeqX and Nextseq 2000


title: SF01015_12


title: B6 Wt infected with vUNG-repair_1


title: COV434 pIND20 BRG1-2.1 +DOX rep1

first: Jessica

middle: Diane

last: Lang

state: Wisconsin

address: 1111 HIGHLAND AVE WIMR 2766

department: Pathology and Laboratory Medicine

data_processing:
TopHat 1.2 was used to align fastq to genome assembly GRCh37.62. Parameters: th_paired_end="yes"; th_mate_inner_dist=35; th_mate_std_dev=40; convertBAM2SAM="no"
Cufflinks 1.3 was used to assemble alignments and estimate relative abundances (FPKM). Default parameters used
Assembly: GRCh37.62
Supplementary files format and content: Gene list and FPKM in FPKM Tracking format

source_name: SCCOHT cell line COV434 with inducible SMARCA4

extract_protocol:
RNA extracted with Qiagen RNeasy Mini Kit. Experiment was repeated as three independent experiments.
0.25-1ug of total RNA was prepared using the Illumina TruSeq mRNA v2 kit to produce unstranded RNA libraries following the manufacturer’s protocol. Final RNA libraries were quantified using the Qubit BR Reagent kit and Agilent Tapestation D1000 tapes. Libraries were equimolar pooled and paired end sequenced across two lanes of a NovaSeq6000 (151x9x151).

tag: doxycycline

value: yes


title: COV434 pIND20 BRG1-2.1 -DOX rep3

value: no


title: B6 Wt infected with vUNG-S302A_3


title: B6 Wt infected with vUNG-S302A_4


title: mouse_cortex_HyDrop_v2_I_beads_1

description:
Library name: HYA__76b206__20240430_Mouse_Cortex-a-ATAC
re-sequenced on Illumina NovaSeqX and Nextseq 2000

tag: cell type


title: Bu-KAI-1

description:
Library name: Bu-KAI-1
10X Genomics

value: Female


title: COV434 pIND20 BRG1-2.1 -DOX rep2


title: B6 Wt infected with vUNG-S302A_2


title: COV434 pIND20 BRG1-2.1 +DOX rep3


title: LIMYB-32 L4 rep2 (Seedling)_2

city: Vicosa

first: Elizabeth

middle: Pacheco

last: Fontes

state: Minas Gerais

address: Av. PH Rolfs, S/N

department: Biochemistry

country: Brazil

institute: Universidade Federal de Vicosa

description: Sonicated DNA

data_processing:
ChIP-seq peaks were calculated with the software ChIPpeakAnno and MACS2
Putative target genes and peak distribution of the ChIP-seq data were figured out using the ChIPpeakAnno software
The binding intensity was measured from log2 (normalized counts of reads/peaks) and evaluated at E-value cut-off of 1e-05 for sequence identification.
Supplementary_files_format_and_content: peaks file

organism: Arabidopsis thaliana

source_name: LIMYB-32 L4 rep2 (Seedling)

growth_protocol: seedlings were germinated for up to 12 days on half-strength Murashige and Skoog (MS 1 / 2 ) plates containing 1% (w/v) sucrose and 0.8% (w/v) agar, grown under the same conditions.

extract_protocol:
Nuclei isolation (Yamaguchi et al., 2014); Seedlings (600 mg) harboring a YFP-LIMYB transgene were crosslinked using 1% formaldehyde in PBS solution
Truseq ChIP lib prep (IP-202-1012, IP-202-1014)

value: seedling

value: cell plant

value: anti-GFP - IgG antibody (Thermo Fisher Scientific, MA, USA, cat.# A11122

value: LIMYB overexpression line

tag: line


title: COV434 pIND20 BRG1-2.1 +DOX rep2

city: Madison

institute: University of Wisconsin-Madison


title: SF01015_0

value: CD34+/lin- cells

value: diagnosis

value: nilotinib


title: RW14003_12


title: RW14003_0


title: SMR18001_0


title: COV434 pIND20 BRG1-2.1 -DOX rep1


title: RS06004_0


title: RS06004_12


title: COV434 parental +DOX rep2

source_name: SCCOHT cell line COV434


title: B6 Wt infected with vUNG-S302A_1

value: Mouse brain

value: Human herpesvirus 1


title: COV434 parental +DOX rep3


title: LIMYB-32 L4 rep2 (Seedling)_1

description: Sonicated DNA

treatment_protocol: Seedlings (600 mg) harboring a YFP-LIMYB transgene were crosslinked using 1% formaldehyde in PBS solution

tag: genotype


title: RS01001_12

tag: treatment


title: LIMYB-32 L4 rep1 (Seedling)_2

description: Sonicated DNA

source_name: LIMYB-32 L4 rep1 (Seedling)

tag: tissue


title: RR02001_12


title: WAT-HFD-3

city: HeFei

first: Zhihua

last: Wang

state: Anhui

address: No. 443, Mount Huangshan Road, Shushan District

institute: University of Science and Technology of China

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality  clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value＝＜20) bases.
Short reads alignment tool Bowtie2　(version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1
For each transcription region, a FPKM (fragment per kilobase of  transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: mm39
Supplementary files format and content: files include Count and FPKM values for each Sample

source_name: mouse white adipose tissue

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.

value: mouse white adipose tissue

value: WAT-HFD


title: LIMYB-32 L3 rep1 (Seedling)_2

description: Sonicated DNA

source_name: LIMYB-32 L3 rep1 (Seedling)


title: WAT-HFD-1


title: LIMYB-32 L3 rep2 (Seedling)_2

description: Sonicated DNA

source_name: LIMYB-32 L3 rep2 (Seedling)


title: COV434 parental +DOX rep1


title: LIMYB-32 L3 rep1 (Seedling)_1

description: Sonicated DNA


title: WAT-H100-1


title: WAT-HFD-2


title: RS01001_0


title: RR02001_0


title: WAT-H100-2


title: LIMYB-32 L4 rep1 (Seedling)_1

description: Sonicated DNA


title: COV434 parental -DOX rep2


title: RA07018_0


title: RP01021_0


title: Liver-H100-3

source_name: mouse liver

value: mouse liver


title: RG06007_12

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)


title: LIMYB-32 L1 rep1- (Seedling)

description: Sonicated DNA

source_name: LIMYB-32 L1 rep1- (Seedling)


title: RA07018_12


title: COV434 parental -DOX rep1


title: LIMYB-32 L3 rep2 (Seedling)_1

description: Sonicated DNA


title: RP01021_12


title: RG06007_0


title: COV434 parental -DOX rep3


title: Liver-H100-5


title: ESCC290N

city: Shanghai

first: Zihan

last: Yu

address: 130 Dongan road, Xuhui district, shanghai

institute: Fudan University

data_processing:
Illumina bcf2fastq v2.20 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: mRNA_Expression_FPKM_Summary.txt

source_name: Esophageal Squamous Cell Cancer

extract_protocol:
RNAstormTM Kit (Cell Data cat. CD501) was used to extract FFPE RNA according the manufacturer's instructions.
Libraries were constructed by ribosomal RNA depletion methods. Ribosomal RNA were depleted using Ribo-off® rRNA Depletion Kit (H/M/R) (Vazyme #N406), and RNA libraries were constructed using VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme #NR605).

tag: idividual

value: ESCC

value: N


title: ESCC291T

value: T


title: Erastin MDA-MB-231 (sh-IGFBP6) rep2

city: Moscow

first: Sergey

last: Nikulin

address: 7, Vavilova st.

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

description: Library name: IGFBP6_Erastin_2

data_processing:
The adapters were trimmed with Cutadapt v4.4 (Martin, 2011).
Reads were mapped with STAR 2.7.7a (Dobin et al., 2013).
Count matrix was generated with featureCount tool from ssubread-2.0.1 aligner (Liao et al., 2013, 2014).
Assembly: GENCODE release 37 GRCh38.primary assembly.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

growth_protocol: Human MDA-MB-231 BC cells were cultured in a complete cell culture medium comprising Dulbecco’s modified Eagle’s medium (DMEM) with high glucose (Gibco, USA), supplemented with 10% (v/v) fetal bovine serum (Gibco, USA), 2 mM L-glutamine (PanEco, Russia), and 1% (v/v) antibiotic-antimycotic solution (Gibco, USA). Cells were seeded in 6-well plates at a density of 800 000 cells per well and cultured at 37⁰C with 5% CO2 in complete DMEM for 24 hours.

extract_protocol:
Cells were lysed with the QIAzol Lysis Reagent (Qiagen, Germany). RNA isolation was performed using miRNeasy Micro Kit (Qiagen, Germany) according to the manufacturer's protocol. Nanodrop ND-1000 (Thermo Fisher Scientific, USA) was used to assess quantity and purity of the extracted RNA. Total RNA samples were also QC-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
Libraries for mRNA sequencing were prepared from total RNA samples using MGIEasy RNA Library Prep Set (MGI Tech Co., China). Ribosomal RNA was depleted using the MGIEasy rRNA Depletion Kit V1.2 (MGI Tech Co., China), following the manufacturer’s instructions.

treatment_protocol: After 24 hours, the medium was replaced with treatment media containing 200 μM DHA, 2.5 μM erastin, and a control medium with 0.5% (v/v) DMSO and 0.5% (v/v) ethanol. The cells were then incubated for an additional 24 hours. Following this incubation, the medium was removed, the cells were washed twice with DPBS (PanEco, Russia) and lysed.

tag: cell line

value: IGFBP6 knockdown

value: 2.5 μM Erastin in DMSO and 0.5% (v/v) Ethanol


title: LIMYB-32 L1 rep2 (Seedling)

description: Sonicated DNA

source_name: LIMYB-32 L1 rep2 (Seedling)

value: seedling

value: cell plant

tag: chip antibody


title: ESCC290T


title: Liver-H100-2


title: Erastin MDA-MB-231 (sh-IGFBP6) rep3

description: Library name: IGFBP6_Erastin_3


title: QL18005_0


title: Liver-H100-4


title: Liver-HFD-5

value: Liver-HFD


title: ESCC289T


title: ESCC291N


title: Blood cells, diluted artificial seawater buffer

city: Boston

first: Tal

middle: Deborah

last: Scully

state: MA

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

description:
Library name: Cr_blood_asw
10x Genomics, Chromium Next GEM Single Cell 3′ v3.1

data_processing:
Single cell analysis (alignment, cell identification, gene counts) done by 10X Genomics Cell Ranger 6.1.2. No additional cell filtering or preprocessing was done on the processed data files.
Assembly: Ciona robusta genome HT 2019 assembly with KY21 gene models (Ghost Database http://ghost.zool.kyoto-u.ac.jp/download_ht.html ), plus mitochondrial genes from Ensembl KH (GCA_000224145.1) Ciona intestinalis genome. Fasta and gtf files for the combined genome are available on https://github.com/AllonKleinLab/paper-data/tree/master/Scully_mannitol_2025/C_robusta_genome_HT2019_KY21_with_Ensembl_mito
Supplementary files format and content: H5 Hierarchical Data Format

organism: Ciona robusta

source_name: blood

growth_protocol: Animals were collected from the wild (Carlsbad, California, USA) and kept in a saltwater aquarium system the lab for 1-2 days prior to sample collection.

extract_protocol:
Animals were relaxed by incubating for 3 hours at 4 °C in about 400 mL artificial seawater with approximately 5 g of 99% L-menthol crystals (3 adults per 400 mL volume). Relaxed adults were dissected to expose the endostyle and large blood vessel on the ventral side of the animal. Blood was drawn from this vessel using a zero dead space tuberculin syringe with a 25G needle, then transferred to a microcentrifuge tube on ice which had previously been coated with bovine serum albumin (BSA) by washing with 0.5 mL of 10% (v./v.) BSA in Dulbecco’s phosphate-buffered saline (DPBS). Pooled blood was split into two tubes coated with 10% (v./v.) BSA in DPBS. Cells were pelleted by spinning at 800 g for 10 min at 4 °C in a swinging bucket centrifuge. The supernatant was gently removed, and cells were resuspended to a concentration of 1000-2000 cells/uL in the appropriate buffer: Ca2+- and Mg2+-free artificial seawater (CMF-ASW; 0.5 M NaCl, 9 mM KCl, 5 mM HEPES, pH 7.4) for Cr_blood_asw, or 0.7 M D-mannitol in PBS for Cr_blood_mannitol.
Library preparation was performed following the manufacturer's instructions for Chromium Next GEM Single Cell 3′ v3.1 Kits (10X Genomics 1000123, 1000127, and 1000190), with the following exception: When preparing the RT mix prior to cell encapsulation, the manufacturer protocol instructs to add nuclease-free water, then to add the cell suspension. The Cr_blood_asw sample was diluted with nuclease-free water as directed. The Cr_blood_mannitol sample was instead diluted with 0.7 M D-mannitol in PBS.

value: blood

value: wild-caught animals from Carlsbad, CA, USA

value: prepared in high-salt buffer (Ca- and Mg-free buffered artificial seawater)


title: QL18005_12

value: CD34+/lin- cells

value: nilotinib


title: Liver-HFD-4


title: WAT-H100-3

value: mouse white adipose tissue


title: ESCC286T


title: Erastin MDA-MB-231 (sh-LUC) rep3

description: Library name: LUC_Erastin_3

value: WT


title: ESCC286N


title: Erastin MDA-MB-231 (sh-LUC) rep2

description: Library name: LUC_Erastin_2


title: Liver-H100-1

value: mouse liver


title: Erastin MDA-MB-231 (sh-IGFBP6) rep1

description: Library name: IGFBP6_Erastin_1


title: Liver-HFD-2


title: ESCC285T


title: ESCC285N


title: Erastin MDA-MB-231 (sh-LUC) rep1

description: Library name: LUC_Erastin_1


title: Liver-HFD-3


title: DHA MDA-MB-231 (sh-IGFBP6) rep3

description: Library name: IGFBP6_DHA200_3

value: 200 μM DHA in Ethanol and 0.5% (v/v) DMSO


title: PM07002_12

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)


title: ESCC273T

value: ESCC


title: DHA MDA-MB-231 (sh-IGFBP6) rep2

description: Library name: IGFBP6_DHA200_2


title: ESCC273N

value: N


title: PP10001_12


title: mESCs pre-culture condition 6, bulk ChIC-seq for H3K27me3

city: Utrecht

first: Peter

last: Zeller

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: ChICseq

data_processing:
ChIC-seq data was mapped using the ChIC Snakemake pipeline (Koster et al., 2012) of the SingleCellMultiOmics package (version 0.1.30). The CPM-normalised coverage was computed in 100 bp bins using deepTools (Ramirez et al., 2016) (v3.0) bamCoverage with options -normalizeUsing CPM -skipNAs -ignore X MT. We used the mm10 gencode (Frankish, 2019) (v23) annotation to define promoter (TSS +- 10 kb), gene body (signal >10 kb downstream of TSS, only on genes longer than 10 kb), intergenic regions and repbase database (2022) to define repeat regions.
Assembly: GRCm38 genome (Ensembl 97)
Supplementary files format and content: bigwig files
Library strategy: ChIC-seq

source_name: 129S1/SvImJ / C57BL/6 mESCs

growth_protocol: 129S1/SvImJ / C57BL/6 mESCs were cultured in a humidified incubator (5 % CO2, 37 °C) on 0.1 % gelatin-coated cell culture dishes in ESLIF medium (GMEM (Gibco) containing 10 % fetal bovine serum (FBS), 1 % Sodium Pyruvate, 1 % non- essential amino acids, 1 % GlutaMAX, 1 % penicillin-streptomycin, 0.2 % b-mercaptoethanol, and 1000 units/mL mouse leukaemia inhibitory factor (mLIF, ESGRO)). Cells were split every second day by washing with PBS0, dissociating with TrypLE for ~5 mins, centrifuging at 300 g for 3 mins, and replating the pellet 1:5 on gelatinised plates. Pre-culture conditions consisted of different pulse timings and lengths with 2i medium (48.1 % DMEM/F12 (Gibco) and 48.1 % Neurobasal (Gibco) containing 0.5 % N-2 supplement (Gibco, # 17502048), 1 % B-27 supplement (Gibco, # 17504044), 1 % GlutaMAX, 1.1 % penicillin-streptomycin, 0.2 % b-mercaptoethanol, 1000 units/mL mouse leukaemia inhibitory factor (mLIF, ESGRO), 0.03 % chiron (CHIR99021, Tocris # 4423) and 0.01 % PD032509 (Sigma, # PZ0162). During pre-culture conditions, cells were split at day 2 and 3; medium was refreshed at day 2 and 4.

extract_protocol:
mESCs were dissociated by washing with PBS0, dissociating with TrypLE for ~5 mins, centrifuging at 300 g for 3 mins, re-suspended in PBS0 supplemented with 5 % FBS, and filtered through a 35 μm filter (Falcon, 352235). Prior to fluorescence-activated cell sorting (FACS), DAPI was added to the cell suspension to assess cell viability.
Plate-based ChIC-seq was performed according to Zeller et al., 2023

value: 129S1/SvImJ / C57BL/6 mESCs

value: mESCs

tag: antibody


title: Liver-HFD-1


title: DHA MDA-MB-231 (sh-IGFBP6) rep1

description: Library name: IGFBP6_DHA200_1

value: IGFBP6 knockdown


title: ESCC271T

value: T


title: mESCs pre-culture condition 5, bulk ChIC-seq for H3K27me3

description: ChICseq


title: mESCs pre-culture condition 4, bulk ChIC-seq for H3K27me3

description: ChICseq


title: PG10005_12


title: mESCs pre-culture condition 2, bulk ChIC-seq for H3K27me3

description: ChICseq


title: PG10005_0

value: diagnosis


title: DHA MDA-MB-231 (sh-LUC) rep3

description: Library name: LUC_DHA200_3


title: PF07015_12


title: ESCC271N


title: PP10001_0


title: ESCC270N


title: PF07015_0


title: DHA MDA-MB-231 (sh-LUC) rep2

description: Library name: LUC_DHA200_2


title: DHA MDA-MB-231 (sh-LUC) rep1

description: Library name: LUC_DHA200_1


title: PM07002_0


title: ESCC268T


title: ESCC270T


title: mESCs pre-culture condition 6, bulk bisulfite sequencing

description: bisulfite sequencing

data_processing:
WGBS-seq data was mapped using the snakePipes (Bhardwaj et al., 2019) WGBS mapping workflow (v 1.3.1) to GRCm38 (mm10) genome with default parameters. WGBS workflow applies paired-end trimming using fastp (Chen et al., 2018) (v0.20) with options -q 5 -l 30 -M 5, mapping using bwa mem (Li, 2013) with options -T 40 -B 2 -L 10 -CM -U 100 -p and bwa-meth (Pedersen et al., 2014) (v0.2.2) for methylation encoding, followed by CpG methylation calling using methyldackyl (https://github.com/dpryan79/MethylDackel, v0.5.0) with options -mergeContext -maxVariantFrac 0.25 -minDepth 4.
Assembly: GRCm38 genome (Ensembl 97)
Supplementary files format and content: bedgraph files

extract_protocol:
mESCs were dissociated by washing with PBS0, dissociating with TrypLE for ~5 mins, centrifuging at 300 g for 3 mins, re-suspended in PBS0 supplemented with 5 % FBS, and filtered through a 35 μm filter (Falcon, 352235). Prior to fluorescence-activated cell sorting (FACS), DAPI was added to the cell suspension to assess cell viability.
For bisulfite sequencing, cells were pelleted after dissociation by centrifuging at 300 g for 3 mins, followed by DNA extraction using the Qiagen DNeasy Blood & Tissue Kit (69504) according to the manufacturer's guidelines. 100 ng DNA was used as input for the Zymo Research Pico Methyl-Seq Library Prep Kit (D5456).


title: mESCs pre-culture condition 1, bulk ChIC-seq for H3K27me3

description: ChICseq


title: Control MDA-MB-231 (sh-IGFBP6) rep3

description: Library name: IGFBP6_Ctrl_3

value: 0.5% (v/v) DMSO and 0.5% (v/v) Ethanol


title: PC18003_0


title: Control MDA-MB-231 (sh-LUC) rep3

description: Library name: LUC_Ctrl_3


title: mESCs pre-culture condition 5, bulk bisulfite sequencing

description: bisulfite sequencing


title: ESCC265N


title: Control MDA-MB-231 (sh-IGFBP6) rep2

description: Library name: IGFBP6_Ctrl_2


title: mESCs pre-culture condition 3, bulk bisulfite sequencing

description: bisulfite sequencing


title: Control MDA-MB-231 (sh-LUC) rep2

description: Library name: LUC_Ctrl_2


title: ESCC268N


title: ESCC265T


title: Control MDA-MB-231 (sh-IGFBP6) rep1

description: Library name: IGFBP6_Ctrl_1


title: PAP11001_0


title: mESCs pre-culture condition 2, bulk bisulfite sequencing

description: bisulfite sequencing


title: mESCs pre-culture condition 3, bulk ChIC-seq for H3K27me3

description: ChICseq


title: ESCC262N


title: PA05007_12


title: mESCs pre-culture condition 4, bulk bisulfite sequencing

description: bisulfite sequencing


title: PC18003_12


title: PA05007_0


title: ESCC262T


title: METH SS-GrpXI-R10

city: Baltimore

first: Michael

middle: T

last: McCoy

state: Maryland

address: Molecular Neuropsychiatry Branch, 251 Bayview Blvd. Suite 200, 251 Bayview Blvd. Suite 200, 251 Bayview Blvd. Suite 200

institute: NIDA

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus norvegicus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts were added to the table
Assembly: Rattus norvegicus Rnor6.0
Supplementary files format and content: counts

organism: Rattus norvegicus

source_name: Dorsal striatum

extract_protocol:
RNA was extracted using the protocol from RNeasy Mini Handbook (Qiagen)
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).  RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).  The sequencing libraries were clustered on two flowcell lanes. After clustering, the flowcells were loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

treatment_protocol:
Training: Rats were randomly segregated into two groups of saline (n = 6) or METH (0.1 mg/kg /infusion) (n = 18). On each training day, rats were trained to lever press on a fixed-ratio-1 (FR1) schedule for three 3-h daily sessions (total 9 h/d) with 30 min off intervals in between each session to intravenously self-administer (SA) METH for 20 days.
Footshock phase: Subsequently, all METH SA rats were given the opportunity to earn METH accompanied by a concurrent delivery of a 0.5-s footshock through the grid floor at 50% of the reinforced lever-presses. We set the initial footshock at 0.18 mA and increased the shock intensity by 0.06 mA up to a final current of 0.42 mA (with a total of 11 punishment days).
DA D1 antagonist (SCH23390) treatment phase: Next, we assessed the METH-seeking behavior by intraperitoneal (i.p.) administrations of different doses of a DA D1R antagonist. METH SA rats received i.p. injections of DA D1 receptor antagonist, SCH 23390 (0.1, 0.25 and 0.5 mg/kg) following a Latin-square design at training days 32 – 37 (a total of six days) and the control rats (CT) were the saline SA group that received only sterile saline injection. All injections were administered 30 min before each behavioral session. During the SCH23390 treatment phase (total of 6 days), the footshock continued with a current of 0.42 mA for all the METH self-administered rats.
Resurgence phase: Resurgence was characterized by the continuation of lever pressing on the previously set footshock condition (0.42 mA) but without the D1 antagonist treatment (training days 38-42). Responding on levers was recorded for a total of 5 days during this phase.
Withdrawal: The animals were euthanized 30 days later, the brain region was dissected, snap frozen on dry ice and then stored in the -70C freezer.

value: Sprague Dawley

value: Dorsal striatum

tag: age

value: adult

value: wild type

value: METH Shock Sensitive


title: Control MDA-MB-231 (sh-LUC) rep1

description: Library name: LUC_Ctrl_1

value: WT


title: PAP11001_12

tag: disease state

value: CD34+/lin- cells

value: nilotinib


title: ESCC259N


title: AAV_sh3

city: Changsha

first: Zicong

state: Hunan

address: No.139，Renmin Road Central Changsha-Hunan-China

institute: The Second Xiangya Hospital of Central South University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
TPM were calculated using a protocol. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text file include TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every Sample

source_name: 17-day old oxygen-induced retinopathy (OIR) C57BL/6J mice

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
The sequencing library was performed on NovaSeq X Plus platform(PE150) using NovaSeq Reagent Kit.

value: retina

value: AAV KO


title: ESCC259T

value: ESCC


title: AAV_sh4


title: ESCC250T


title: METH SS-GrpXI-R04


title: AAV_sh2


title: METH SS-GrpXI-L07


title: mESCs pre-culture condition 1, bulk bisulfite sequencing

description: bisulfite sequencing

value: 129S1/SvImJ / C57BL/6 mESCs


title: METH SS-GrpXI-L05


title: AAV_sh1


title: ESCC242T


title: ESCC250N

value: N


title: METH SS-GrpXI-L04


title: ESCC242N


title: METH SS-GrpXI-L01


title: MS01003_12

data_processing: The data were normalized using the RMA method from the oligo package (version 1.42.0) from the Bioconductor repository (version 3.4). In this step, the measured signal intensities of the 6 million probes were summarized into probe sets specific for a given gene locus, realizing a one-to-one assignment of probe sets and genes. Data were first pre-processed using ComBat to adjust for batch effects and quantile normalization.

extract_protocol: RNA extraction was performed using MagMAX 96 Total RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Quality and yield of the extracted RNA were measured using Nanodrop (Thermo Fisher Scientific). We did not perform RNA extraction of the BM CD34+/lin- cells stored in Prelude direct Lysis module (NuGEN) because of the too low number of cells and perform the RNA processing starting from the cells.

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)

tag: timepoint


title: AAV_NC4

value: control


title: NFV01006_0

value: diagnosis


title: MP06008_0


title: MP06008_12


title: MS01003_0


title: METH SR-GrpXI-R07

value: METH Shock Resistant


title: ESCC237T

value: T


title: AAV_NC1


title: ESCC237N


title: METH SR-GrpXI-R03

value: Sprague Dawley

value: Dorsal striatum


title: AAV_NC3


title: Tumor infiltrating CD8+ T cells from PepS452A mice5

city: Los Angeles

first: Richard

last: Ainsworth

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

description: mRNA CD8 A5

data_processing:
Reads aligned to mouse genome GRCm38.p6 using STAR version=2.7.9a
Transcript abundance was quantified using RSEM version 1.3.0
Assembly: GRCm38.p6 genome assembly
Supplementary files format and content: matrix_tpm: Matrix of Transcripts per Million (TPM) for all 10 samples

source_name: MC38 Tumor

growth_protocol: MC38 Tumor were injected into 8-week old mice and collected after 18 days

extract_protocol:
RNA samples were extracted by using RNeasy Micro kit (Qiagen)
library was prepared with NEBNext Ultra II Directional RNA library prep kit for Illumina, with 40ng input

treatment_protocol: Tumor infiltrating CD8+ T cells were sorted from the single cell suspension after collagenase digestion

value: MC38 Tumor

value: CD8+ T cells

value: MC38 cell injection


title: ESCC229N


title: METH SR-GrpXI-L06

value: adult

value: wild type


title: NFV01006_12

first: Alessandra

address: Piazza dell'Ospedale Maggiore, 3

value: CD34+/lin- cells

value: nilotinib


title: ESCC229T

value: ESCC


title: MD01014_12


title: METH SR-GrpXI-R02


title: MS01022_12


title: LR07019_0


title: ESCC228N


title: METH SR-GrpXI-L02


title: ESCC227T


title: AAV_NC2

value: retina


title: ESCC227N

value: N


title: Tumor infiltrating CD8+ T cells from PepS452A mice4

description: mRNA CD8 A4


title: LR07014_12

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)


title: Saline CT-GrpXI-R12

value: Control


title: Tumor infiltrating CD8+ T cells from PepS452A mice1

description: mRNA CD8 A1


title: Saline CT-GrpXI-R06


title: METH SR-GrpXI-L03


title: MD01014_0

value: diagnosis


title: LR07014_0


title: LR07019_12


title: ESCC226N


title: ESCC226T


title: Saline CT-GrpXI-R05


title: Tumor infiltrating CD8+ T cells from PepWT mice5

description: mRNA CD8 WT5

value: WT


title: ESCC215T

value: T


title: Tumor infiltrating CD8+ T cells from PepS452A mice3

description: mRNA CD8 A3


title: Tumor infiltrating CD8+ T cells from PepWT mice3

description: mRNA CD8 WT3


title: Saline CT-GrpXI-L9

value: Sprague Dawley


title: ESCC215N


title: Saline CT-GrpXI-L12

value: Dorsal striatum


title: LP10006_12


title: Tumor infiltrating CD8+ T cells from PepWT mice4

description: mRNA CD8 WT4

value: MC38 Tumor


title: Tumor infiltrating CD8+ T cells from PepS452A mice2

description: mRNA CD8 A2

value: CD8+ T cells


title: MS01022_0


title: Tumor infiltrating CD8+ T cells from PepWT mice2

description: mRNA CD8 WT2

value: MC38 cell injection


title: Saline CT-GrpXI-L10

value: adult


title: LP10006_0


title: Tumor infiltrating CD8+ T cells from PepWT mice1

description: mRNA CD8 WT1


title: ESCC213N


title: ESCC211T


title: ESCC211N


title: WE_2

city: Daejeon

first: Keun Bon

last: Ku

address: 291 Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Paired-end sequencing reads were generated on the Illumina sequencing NovaSeq platform.
Before starting analysis, Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality.
The cleaned reads were aligned to the Mus musculus (mm10) using HISAT v2.1.0 (KIM et al, 2015), based on the HISAT and Bowtie2 implementations.
The reference genome sequence and gene annotation data were downloaded from NCBI Genome assembly and NCBI RefSeq database respectively.
Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b.
Assembly: Gene-level and Transcript-level quantification were calculated as raw read count, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million).
Supplementary files format and content: mm10
Supplementary files format and content: Read_Count, FPKM, TPM

source_name: Lung

extract_protocol:
RNA was extracted using Rnaeasy mini plus kit(Qiagen)
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Reference Guide

treatment_protocol: Distilled water, water electrospray or sodium hypochlorite (0.01%) treated 5 times through the intra-nasal route

value: Lung

value: Water electrospray


title: ESCC213T


title: Muscle harvested from bat immediately after 1h heat shock followed by 4h recovery, replicate 2

city: Singapore

first: Leon Jia Wei

last: Tang

address: 21 Lower Kent Ridge Rd

country: Singapore

institute: National University of Singapore

description:
Es_Mc_R_2
es_counttable.csv

data_processing:
STAR (version 2.7)
featureCounts
Assembly: GRCm39 for mice. Custom-in-house genome for bat (Chan et al, Unpublished)
Supplementary files format and content: comma separated

organism: Eonycteris spelaea

source_name: Muscle

extract_protocol:
TRIzol total RNA extraction
NEBNext Ultra Directional RNA Library Prep Kit for Illumina

value: Muscle


title: JHCA05002_12

city: Milano

last: Trojani

institute: ASST Grande Ospedale Metropolitano Niguarda

value: CD34+/lin- cells

value: nilotinib


title: Muscle harvested from bat immediately after 1h heat shock followed by 4h recovery, replicate 3

description:
Es_Mc_R_3
es_counttable.csv


title: WE_1


title: SH_3

value: Sodium hypochilorite


title: ESCC210N

value: ESCC

value: N


title: LM15001_12

value: Chronic Phase- Chronic Myeloid Leukemia (CP-CML)


title: ESCC210T


title: LM15001_0

value: diagnosis


title: LD07006_12


title: Muscle harvested from bat immediately after 1h heat shock followed by 4h recovery, replicate 1

description:
Es_Mc_R_1
es_counttable.csv


title: SH_2

value: WT


title: Muscle harvested from bat immediately after 1h heat shock, replicate 3

description:
Es_Mc_Hs_3
es_counttable.csv


title: ESCC209T

value: T


title: LD07006_0


title: GT01017_12


title: WE_3


title: JHCA05002_0


title: SH_1


title: GVD01008_0


title: GVD01008_12


title: Muscle harvested from bat immediately after 1h heat shock, replicate 2

description:
Es_Mc_Hs_2
es_counttable.csv


title: ESCC209N


title: DW_3

value: Distilled water


title: ESCC199T


title: DW_2


title: ESCC199N


title: Muscle harvested from Ctl bat, replicate 2

description:
Es_Mc_Ctl_2
es_counttable.csv


title: Muscle harvested from Ctl bat, replicate 3

description:
Es_Mc_Ctl_3
es_counttable.csv


title: ESCC196T


title: ESCC196N


title: anti-CD40L treated LNSCs after HTx_2

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

description: 10x Genomics

data_processing:
Reads were demultiplexed, aligned to the GRCm38 mm10 assembly reference genome, and filtered; and cell barcodes and UMIs were quantified using the Cell Ranger 6.1 with default parameters (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). 6.7 x 103 cells per sample were captured on the 10X Chromium chip.
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.2.
the samples are integrated together using Harmony (v1.2.0)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lymph node

extract_protocol:
LNs were harvested from C57BL/6 mice (8-12 weeks) and digested enzymatically. CD45- cells were purified with the CD45 negative selection beads and were stained with anti-mouse CD45 before sorting for viable CD45- cells.
About 1.0 x  10^4 LNSCs were run on the  the 10X Chromium Controller (10X Genomics) to partition single cells into nanoliter-scale droplets containing uniquely barcoded beads and processed for sequencing library preparation using the Chromium Single Cell 3’ Reagent Kit (v3 chemistry).
Generated cDNA libraries were sequenced on a NovaSeq 6000 sequencing system at the Institute for Genome Sciences in the University of Maryland, Baltimore.

value: Lymph node

value: CD45 negative stromal cells

value: C57BL/6 mice

value: 8-12 weeks old

tag: procedure and_treatment

value: day8 after heart transplantation with anti-CD40L


title: anti-CD40L treated LNSCs after HTx_1

description: 10x Genomics


title: Muscle harvested from bat immediately after 1h heat shock, replicate 1

description:
Es_Mc_Hs_1
es_counttable.csv


title: ESCC194N


title: Muscle harvested from Ctl bat, replicate 1

description:
Es_Mc_Ctl_1
es_counttable.csv


title: LNSCs after HTx_2

description: 10x Genomics

value: day8 after heart transplantation without anti-CD40L


title: DW_1

value: Lung