title: mESC CGR8 cells, CHX 0 h, replicate A

tag: cell type

value: ROSA26 SLT knock-in

value: 0.1 µg/mL CHX


title: Male/KO/CL1

status: Public on Oct 07 2025

type: SRA

city: Nice

first: Jean-Francois

last: Louet

address: C3M 151 route Saint Antoine de Ginestière 151 route Saint Antoine de Ginestière

country: France

institute: INSERM

description: Library name: SAMPLES 26/M31

library_source: transcriptomic

data_processing:
Raw reads were quality controlled, and the raw data were filtered using the filtering software SOAPnuke (v1.5.2). The filtered clean reads were aligned to the reference genome sequence (mouse genome GRCm38 (mm10)) using HISAT2 software (v2.0.4).
Assembly: (mouse genome GRCm38 (mm10))
Supplementary files format and content: FPKM_Samples_group1.xls
Supplementary files format and content: FPKM_Samples_group2.xls

molecule: total RNA

organism: Mus musculus

source_name: White adipose tissue

extract_protocol:
Frozen mouse subcutaneous adipose tissue was homogenized in RLT buffer (Qiagen), and RNA extracted using the RNeasy Mini Kit (Qiagen)
The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and single end 50 (pair end 100/150) bases reads were generated in the way of combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: CL316,243 (0.5 mg/kg body weight) or Nacl during seven days by IP

tag: tissue

value: White adipose tissue

tag: genotype

value: KO

tag: treatment

tag: Sex

value: Male


title: Male/KO/Ctrl1

description: Library name: SAMPLES 22/M21

value: Nacl


title: Male/WT/CL4

description: Library name: SAMPLES 21/M14

value: WT


title: Male/WT/CL2

description: Library name: SAMPLES 19/M12


title: Male/WT/CL1

description: Library name: SAMPLES 18/M11


title: Male/WT/Ctrl4

description: Library name: SAMPLES 17/M4


title: Female/KO/CL3

description: Library name: SAMPLES 13/F33

value: Female


title: Female/WT/CL4

description: Library name: SAMPLES 7/F14


title: Male/WT/Ctrl1

description: Library name: SAMPLES 14/M1


title: Female/WT/CL3

description: Library name: SAMPLES 6/F13


title: Female/KO/Ctrl2

description: Library name: SAMPLES 9/F22


title: Female/WT/Ctrl1

description: Library name: SAMPLES 1/F2


title: Female/WT/Ctrl3

description: Library name: SAMPLES 3/F4


title: Female/KO/Ctrl3

description: Library name: SAMPLES 10/F24


title: Female/KO/CL2

description: Library name: SAMPLES 12/F32


title: Female/WT/CL1

description: Library name: SAMPLES 4/F11


title: Female/KO/Ctrl1

description: Library name: SAMPLES 8/F21


title: Female/KO/CL1

description: Library name: SAMPLES 11/F31


title: Female/WT/CL2

description: Library name: SAMPLES 5/F12


title: Female/WT/Ctrl2

description: Library name: SAMPLES 2/F3


title: Male-WT2

description:
Library name: M2
M2_023HInserm_ATAC_genes.csv

library_source: genomic

data_processing:
The resulting material was quantified using Qubit (Invitrogen) and TapeStation (Agilent) and sequenced using PE42 sequencing on the NovaSeq 6000 (Illumina).
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed and only reads corresponding to matched pairs and unique reads (mapping quality ≥ 1) were used for further analysis.
Alignments were extended in silico at their 3' ends to a length of 200 bp and assigned to 32 nt bins along the genome.
The resulting histograms (genomic "signal maps") were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm with a p-value cut-off of 1e-7, without a control file and with the -nomodel option
Assembly: mouse (mm10)
Supplementary files format and content: 023HInserm_ATAC_genes.xlsx

molecule: genomic DNA

source_name: WAT

extract_protocol:
Frozen mouse SATs were sent to Active Motif for the ATAC-seq assay. They were initially ground to a fine powder using liquid nitrogen and resuspended in appropriate lysis buffer (Active Motif).
Isolated nuclei were quantified using the Countess II FL automated cell counter (Thermo Fisher) and 100,000 nuclei were labelled as previously described (Buenrostro et al., 2013), with some modifications based on (Corces et al., 2017), using the enzyme and buffer provided in the ATAC-Seq kit (Active Motif). The labelled DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR and purified using Agencourt AMPure SPRI beads (Beckman Coulter).

value: WAT


title: Male-WT1

description:
Library name: M1
M1_023HInserm_ATAC_genes.csv


title: Male/KO/Ctrl3

description: Library name: SAMPLES 24/M23


title: Fem-WT2

description:
Library name: F2
F2_023HInserm_ATAC_genes.csv


title: Fem-WT1

description:
Library name: F1
F1_023HInserm_ATAC_genes.csv


title: Male/KO/Ctrl2

description: Library name: SAMPLES 23/M22


title: Male/WT/CL3

description: Library name: SAMPLES 20/M13


title: Control, 20 weeks ON dox - pancreas 2

city: Ann Arbor

first: Emily

middle: L

last: Lasse-Opsahl

state: Michigan

address: 1500 E Medical Center Dr Rm 6110

department: Cancer Biology

country: USA

institute: University of Michigan

description: Library name: Control_20wk_panc2

library_source: transcriptomic single cell

data_processing:
Raw data were processed and aligned by the University of Michigan Advanced Genomics Core. Cell Ranger count version 8.0.0-9.0.1 (10× Genomics, Pleasanton, CA) was used with default settings, with an initial expected cell count of 10,000.
Assembly: GRCm39-2024-A
Supplementary files format and content: Raw and filtered Cell Ranger outputs

source_name: 2 female control mice given doxycycline chow for 20 weeks. Mice were pooled.

extract_protocol:
The pancreas was harvested from the mouse. Lungs were first perfused with PBS before being harvested from the mouse. Pancreas and lung tissue was then mechanically minced and incubated with Collagenase P (Sigma-Aldrich, #11249002001) for 30 minutes at 37°C under constant shaking. All tissue was then subject to serial filtration through 500-, 100-, and 40-um mesh. To remove red blood cells, single cells were then subject to ACK Lysis buffer (Gibco, A1049201) until most red blood cells were lysed. We enriched for live cells using the MACS Dead Cell Removal Kit (Miltenyi Biotec, #130-090-101).
Samples were run using 50-cycle, paired-end reads on the Illumina NovaSeq 6000 (Illumina, San Diego, CA) to a depth of 100,000 reads.

value: Pancreas

tag: number of_mice_pooled

tag: cell ranger_version

tag: transcriptome

tag: run date


title: KPC, 8 months old - lung 1

description:
Library name: PMN_KPC_lung1
1 female KPC mouse aged to 8 months old.

source_name: Lung

value: Lung


title: Control, 20 weeks ON dox - pancreas 1

description: Library name: Control_20wk_panc1


title: KPC, 4 months old - lung 2

description:
Library name: PMN_KPC_lung2
1 male KPC mouse aged to 4 months old.


title: Male/WT/Ctrl3

description: Library name: SAMPLES 16/M3


title: Male/WT/Ctrl2

description: Library name: SAMPLES 15/M2


title: iKRAS, 16 weeks ON - pancreas 3

description:
Library name: iKRAS_16wk_panc3
1 female iKras mouse had induction of KrasG12D expression by giving doxycycline chow for 16 weeks.

source_name: Pancreas


title: iKRAS, 16 weeks ON - pancreas 2

description:
Library name: iKRAS_16wk_panc2
1 male iKras mouse and 1 female iKras mouse had induction of KrasG12D expression by giving doxycycline chow for 16 weeks. Mice were pooled.


title: iKRAS, 16 weeks ON - pancreas 1

description:
Library name: iKRAS_16wk_panc1
1 female iKras mouse had induction of KrasG12D expression by giving doxycycline chow for 16 weeks.


title: iKRAS, 16 weeks ON + 1 week OFF - pancreas 2

description:
Library name: iKRAS_16wk_1wkOFF_panc2
1 male iKras mouse had induction of KrasG12D expression by giving doxycycline chow for 16 weeks then taken off for 1 week.


title: Control for KPC, 14 months old - lung 1

description:
Library name: Control_Aged_lung1
1 male control mouse aged to 14 months old.


title: iKRAS, 16 weeks ON + 1 week OFF - lung 1

description:
Library name: iKRAS_16wk_1wkOFF_lung1
1 female iKras mouse had induction of KrasG12D expression by giving doxycycline chow for 16 weeks then taken off for 1 week.


title: P5combMEIS_1

city: Baltimore

first: Patrick

last: Leavey

state: Maryland

address: 733 N Broadway, 332

department: Neuroscience

institute: Johns Hopkins School of Medicine

description:
Library name: P5 MEIS1 + MEIS2 1
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Seurat V5 was used to perform downstream analysis following the standard pipeline.
Assembly: MM10_GFP
Supplementary files format and content: Cell-by-gene count matrix for all the samples as csv
Supplementary files format and content: Metadata for the cell-by-gene count matrix as csv

molecule: polyA RNA

source_name: Retinal Explant

extract_protocol:
Worthington Papain Dissociation System was used to generate single cell suspension
scRNA-Seq following 10x 3’ Reagents v3.1 Kit guideline

value: Retinal Explant

tag: mouse line

value: CD1 wildtype

tag: age

value: Postnatal Day 5

value: Electroporated with 50:50 MEIS1/MEIS2 construct

tag: library type

value: mRNA


title: iKRAS, 16 weeks ON + 1 week OFF - pancreas 1

description:
Library name: iKRAS_16wk_1wkOFF_panc1
1 female iKras mouse had induction of KrasG12D expression by giving doxycycline chow for 16 weeks then taken off for 1 week.


title: P5MEIS2_1

description:
Library name: P5 MEIS2 1
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

value: Electroporated with MEIS2 construct


title: P5combMEIS_2

description:
Library name: P5 MEIS1 + MEIS2 2
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: Control, 16 weeks ON dox - pancreas 2

description:
Library name: Control_16wk_panc2
1 male control mouse and 1 female control mouse given doxycycline chow for 16 weeks. Mice were pooled.


title: Control, 16 weeks ON dox - pancreas 3

description:
Library name: Control_16wk_panc3
1 female control mouse given doxycycline chow for 16 weeks.


title: Control, 16 weeks ON dox - pancreas 1

description:
Library name: Control_16wk_panc1
1 male control mouse given doxycycline chow for 16 weeks.


title: P5MEIS1_2

description:
Library name: P5 MEIS1 2
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: P2combMEIS_2

description:
Library name: P2 MEIS1 + MEIS2 2
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

value: Postnatal Day 2


title: P5MEIS2_2

description:
Library name: P5 MEIS2 2
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: P2combMEIS_1

description:
Library name: P2 MEIS1 + MEIS2 1
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: P5MEIS1_1

description:
Library name: P5 MEIS1 1
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: P2MEIS2_2

description:
Library name: P2 MEIS2 2
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

value: Electroporated with MEIS1 construct


title: P2MEIS2_1

description:
Library name: P2 MEIS2 1
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: P5ctrl3

description:
Library name: P5ctrl3
3' mRNA: BAM file which can be converted to fastq files using bamtofastq

value: Electroporated with GFP control construct


title: P2MEIS1_1

description:
Library name: P2 MEIS1 1
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: P2MEIS1_2

description:
Library name: P2 MEIS1 2
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: KC, 17.5 months old - lung 1

description:
Library name: PMN_KC_lung1
KC, 17.5 months old - lung 1


title: P5ctrl4

description:
Library name: P5ctrl4
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: P5ctrl2

description:
Library name: P5ctrl2
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: P2ctrl3

description:
Library name: P2ctrl3
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: iKRAS, 16 weeks ON + 1 week OFF - lung 2

description:
Library name: iKRAS_16wk_1wkOFF_lung2
1 male iKras mouse had induction of KrasG12D expression by giving doxycycline chow for 16 weeks then taken off for 1 week.


title: P2ctrl4

description:
Library name: P2ctrl4
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: P2ctrl2

description:
Library name: P2ctrl2
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: Control for KPC, 4 months old - lung 2

description:
Library name: Control_Aged_lung2
1 female control mouse aged to 4 months old.


title: iKRAS;P53, 20 weeks ON dox - metastatic lung - lung2

description:
Library name: iKRASP53_20wk_Mets_lung2
1 female iKras;p53 mouse had induction of KrasG12D expression by giving doxycycline chow for 20 weeks.

data_processing:
Raw data were processed and aligned by the University of Michigan Advanced Genomics Core. Cell Ranger count  (10× Genomics, Pleasanton, CA) was used with default settings, with an initial expected cell count of 10,000.
Assembly: GRCm39-2024-A
Supplementary files format and content: Raw and filtered Cell Ranger outputs

extract_protocol:
Lungs were first perfused with PBS before being harvested from the mouse. Lung tissue was then mechanically minced and incubated with Collagenase P (Sigma-Aldrich, #11249002001) for 30 minutes at 37°C under constant shaking. All tissue was then subject to serial filtration through 500-, 100-, and 40-um mesh. To remove red blood cells, single cells were then subject to ACK Lysis buffer (Gibco, A1049201) until most red blood cells were lysed. We enriched for live cells using the MACS Dead Cell Removal Kit (Miltenyi Biotec, #130-090-101). Bone marrow was taken from both femurs by flushing with PBS. The resulting bone marrow suspension was subject to ACK lysis buffer (Gibco, A1049201) to remove red blood cells and then run through a 70-um mesh.
Samples were run using 50-cycle, paired-end reads on the Illumina NovaSeq 6000 (Illumina, San Diego, CA) to a depth of 100,000 reads.

value: November 2024


title: P5ctrl1

description:
Library name: P5ctrl1
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: Control, 20 weeks ON dox - lung1

description:
Library name: Control_20wk_lung1
2 female control mice given doxycycline chow for 20 weeks. Mice were pooled.

value: June 2024


title: Control, 20 weeks ON dox - lung2

description:
Library name: Control_20wk_lung2
2 female control mice given doxycycline chow for 20 weeks. Mice were pooled.


title: stp2Δ SC III

city: Jena

first: Enrico

last: Garbe

address: Albert-Einstein-Straße 10

department: (Epi-)Genetics of Fungal Infections

country: Germany

institute: HKI Jena

description: Genewiz

data_processing:
Fastq files were assessed for sequence quality using FastQC (version 0.11.9) and a genome index from file C_albicans_SC5314_A22_current_chromosomes.fasta from http://www.candidagenome.org/ was created with bowtie2 (version 2.4.2). Mapping of reads to the index was performed with bowtie2. Reads were counted and assigned to the corresponding genome using featureCounts (version 2.0.6). Contrasts were calculated using R package DESeq2 (version 1.28.1). R version 4.0.4 was used.
Assembly: C_albicans_SC5314_A22_current_chromosomes.fasta
Supplementary files format and content: NG-14036_WT_1h_Glucose_3_1_lib230916_5687_5, NG-14036_WT_1h_Glucose_2_1_lib228678_5715_7, NG-14036_WT_1h_Glucose_2_1_lib228678_5697_3, NG-14036_WT_1h_Glucose_1_1_lib230902_5687_5, NG-14036_stp2_1h_Glucose_3_1_lib230917_5687_5, NG-14036_stp2_1h_Glucose_2_1_lib228679_5715_7, NG-14036_stp2_1h_Glucose_2_1_lib228679_5697_3, NG-14036_stp2_1h_Glucose_1_1_lib230903_5687_5, WT-1h-SC-3, WT-1h-SC-2, WT-1h-SC-1, stp2d-1h-SC-3, stp2d-1h-SC-2, stp2d-1h-SC-1, tab seperated text files containing counts of samples

organism: Candida albicans

source_name: liquid culture

growth_protocol: C. albicans were generally maintained on YPD agar plates and ON cultures prepared in liquid YPD (30°C) for experimental use on the subsequent day.

extract_protocol:
Total RNA was isolated from C. albicans cells using phenol-chlororform extraction as previously reported (https://doi.org/10.1128/mbio.03142-21): "For total RNA isolation, cells were resuspended in 440 μL acetate EDTA buffer (50 mM sodium acetate, 10 mM EDTA) with 10% SDS, and 440 μL of acid-phenol-chloroform with isoamyl alcohol (Ambion, Germany) was added. The suspension was thoroughly mixed, incubated for 5 min at 65°C, frozen at −20°C for 30 min, and subsequently thawed at 65°C for 5 min. The phases were separated via 4 min of centrifugation at 16,000 × g, the upper aqueous phase was transferred, and a 1/10 volume of sodium acetate (pH 5.3) and 1 volume of 2-propanol were added to precipitate the RNA for at least 30 min at −20°C. The supernatant was discarded after 10 min of centrifugation at 12,000 × g, and the RNA pellet was washed twice with 80% ethanol and finally solved in 300 μL nuclease-free H2O. The quality and quantity of the RNA were assessed using 2100 bioanalyzer (Agilent Technologies, CA, USA) and Nanodrop (Thermo Fisher Scientific, MA, USA) measurements."
Strand-specific cDNA library wer used for sequencing. Libraries were created via poly-A enrichment, mRNA fragmentation, random primed cDNA synthesis, adapter ligation and adapter-specific PCR amplification.

treatment_protocol: Cells from ON-cultures were harvested and transferred to fresh YPD medium (Starting OD 0.3) and incubated (37°C) until early log-phase (OD 1) was reached. Cells were then harvested, washed and transferred to indicated test medium (OD 0.3) and incubated for 1 h at 37°C. cells were then collected and snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: liquid culture


title: stp2Δ SC I

description: Genewiz


title: iKRAS;P53, 20 weeks ON dox - only primary tumor - lung1

description:
Library name: iKRASP53_20wk_PDA_lung1
1 female iKras;p53 mouse had induction of KrasG12D expression by giving doxycycline chow for 20 weeks.


title: WT SC III

description: Genewiz

value: wild type


title: stp2Δ SC II

description: Genewiz


title: WT SC II

description: Genewiz


title: stp2Δ SD I_1

description: GATC


title: stp2Δ SD I

description: GATC


title: stp2Δ SD II

description: GATC


title: Control, 16 weeks ON dox - lung3

description:
Library name: Control_16wk_lung3
1 female control mouse given doxycycline chow for 16 weeks.

value: March 2024


title: stp2Δ SD III

description: GATC


title: WT SC I

description: Genewiz


title: Control, 16 weeks ON dox - lung2

description:
Library name: Control_16wk_lung2
1 male control mouse and 1 female control mouse given doxycycline chow for 16 weeks. Mice were pooled.

value: November 2022


title: WT SD III

description: GATC


title: WT SD II

description: GATC


title: WT SD II_1

description: GATC


title: iKRAS, 16 weeks ON dox - lung2

description:
Library name: iKRAS_16wk_lung2
1 male iKras mouse and 1 female iKras mouse had induction of KrasG12D expression by giving doxycycline chow for 16 weeks. Mice were pooled.


title: P2ctrl1

description:
Library name: P2ctrl1
3' mRNA: BAM file which can be converted to fastq files using bamtofastq


title: Control, 16 weeks ON dox - lung1

description:
Library name: Control_16wk_lung1
1 male control mouse given doxycycline chow for 16 weeks.

value: December 2021


title: KO

city: Suzhou

first: Mintao

last: Ji

address: Renai road

country: China

institute: Soochow University

description: Library name: Sample2

data_processing:
Raw Reads were filtered to remove adapters and low quality reads (including Reads with N ratio greater than 10% were removed, and Reads with bases quality value Q<=10 accounting for more than 50% of the entire Read were removed), and then high-quality Clean Reads provided in FASTQ format were obtained for subsequent information analysis.The Bowtie2 software was used to compare the high-quality Reads obtained from the sequencing of each sample with the reference genome to obtain the alignment efficiency of the sample Reads and the position information of the Reads on the genome. DeepTools v2.07 was used to map the density distribution of sequencing Read in the 3 kb of interval upstream and downstream of the TSS of each gene, and the results were presented as heat maps.MACS2 v2.1.1 software was used to perform peak extraction.The ChIPseeker package was used for functional annotation of genome-wide Peak. The average Peak number of the TSS region was counted. The Peak region was annotated according to the distance relationship between the Peak region and the functional elements of each gene on the genome.Meme-chip 4.11.2 was used to identify and annotate Motif.Using Tomtom to align the detected Motif sequence with a known Motif. DiffBind package was used for Difference Peak analysis.According to the distance relationship between the differential Peak regions and the functional elements of each gene on the genome, the differential Peak region was annotated.The R package clusterProfiler was used to perform enrichment analysis of Biological process (BP), Molecular function (MF), and Cellular component (CC) of genes associated with different Peak regions. The enrichment analysis used a hypergeometric test to find GO items that were significantly enriched compared to the whole genomic background.The R package clusterProfiler was performed to analyze KEGG pathway enrichment of genes associated with different Peak regions. The enrichment analysis used a hypergeometric test to find KEGG pathway that were significantly enriched compared to the whole genomic background.Motif analysis was performed on the difference Peak obtained from the difference Peak analysis results, and the MEME-ChIP software was also used to identify and annotate the Motif. Using Tomtom to align the detected Motif sequence with a known Motif.
Assembly: GRCm38
Supplementary files format and content: bigWig

source_name: intestine

extract_protocol:
Cell nuclei were extracted using gradient centrifugation, and DNA was purified using Qiagen PCR (28006) purification kit.
ATAC was performed according to ATAC-seq protocol by Biomarker Technologies Biotechnology Ltd. In brief, native nuclei were purified from cell as previously described (Buenrostro et al.,2015). The Nextera DNA Library Preparation Kit (Illumina) was used to perform the transposition according to the manufacturer’s manual. 40 000 nuclei were pelleted and resuspended with transposase, for 30 minutes at 37 ℃. The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen). After Samples were PCR-amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA). Subsequent libraries were purified with the MinElute PCR Purification Kit (Qiagen) and subjected to sequencing on Illumina Novaseq 6000 using PE150.

value: intestine

tag: cell line

value: intestinal immune cells

value: DPF2 KO mice


title: STP1206

city: Bedford Park

first: Claire

middle: Trelford

last: Roberts

state: South Australia

address: HMRB Building, Loading Bay via Sports Road

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description: Library name: STP1206

data_processing:
Trimming of low-quality bases and adapters was performed using fastp (v0.23.2) with the parameters --cut_right, --cut_window_size 4, --cut_mean_quality 20, and --length_required 75.
Trimmed paired-end reads were aligned to the human genome (GRCh38) using STAR (v2.7.10a) with a sex-informed genome annotation from the XYalign package. Using the pre-built genome index, alignment was performed with the following parameters: --outFilterType BySJout, --outFilterMismatchNmax 999, --outSAMtype BAM SortedByCoordinate and --outSAMmapqUnique 60. Read group information was specified with --outSAMattrRGline.
Read alignments were processed to remove PCR duplicates using Picard MarkDuplicates (v2.26.0, with -REMOVE_DUPLICATES=TRUE).
Gene-level quantification was performed using featureCounts (v2.0.3) with the following parameters: -a gencode.v29.annotation.gtf, -s 2, -p, --countReadPairs, and -T 16.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Homo sapiens

source_name: chorionic villus

extract_protocol:
Tissue samples obtained after delivery of neonate and placenta. Tissue biopsies from placentae were washed in phosphate-buffered saline (PBS) before being submerged in RNAlater Stabilisation Solution (Thermo Fisher Scientific, Massachusetts, USA) and stored at -80oC. Tissue was disrupted by homogenizing for 3.5 mins at 30 Hz (TissueLyser, QIAGEN) in 600 μl Buffer RLT Plus (RNeasy Plus Mini Kit; QIAGEN, Victoria, Australia). Total RNA was extracted from the supernatant using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pregnancies were classified based on clinical diagnosis of late-onset preeclampsia (diagnosed ≥34 weeks’ gestation according to ISSHP criteria) or uncomplicated.

value: chorionic villus

value: male

value: Control


title: STP1087

description: Library name: STP1087

value: female


title: STP1082

description: Library name: STP1082


title: iKRAS, 16 weeks ON dox - lung1

description:
Library name: iKRAS_16wk_lung1
1 female iKras mouse had induction of KrasG12D expression by giving doxycycline chow for 16 weeks.

value: Lung


title: STP0944

description: Library name: STP0944

value: Preeclampsia


title: STP1002

description: Library name: STP1002


title: STP0932

description: Library name: STP0932


title: STP0903

description: Library name: STP0903


title: STP0912

description: Library name: STP0912


title: STP0888

description: Library name: STP0888


title: WT

description: Library name: Sample1

value: WT mice


title: iKRAS, 16 weeks ON dox - lung3

description:
Library name: iKRAS_16wk_lung3
1 female iKras mouse had induction of KrasG12D expression by giving doxycycline chow for 16 weeks.


title: STP0761

description: Library name: STP0761


title: intestine KOIR, scRNA-seq

description: Library name: Sample2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation weremade using the Cell Ranger 7.0.0
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The isolated intestinal cells were resuspended in digestion buffer and incubated at 37 'C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer. Alive immune cells were sorted using a FACS according to the presence or absence of GFP or Tdtomato signal. Immune cells were washed and resuspended in PBS supplemented with 0.05% BSA.
Library was performed according to the manufacter's instructions. Briefly, immune cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gelbead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in everysingle GEM was retrotranscripted to cDNA, which contains an llumina R1 primel sequence, Unique Molecular ldentifier (UMl) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRlselect reagent for subsequent library construction.

value: immune cells

value: 10 Gy X-ray irradiation


title: STP0852

description: Library name: STP0852


title: STP0788

description: Library name: STP0788


title: STP0692

description: Library name: STP0692


title: WT SD I

description: GATC

value: liquid culture


title: KOIR

description: Library name: Sample2

data_processing:
Raw sequencing data were processed using BSTMatrix (v1.0). Sequences were aligned to GRCm38 genome.
Assembly: GRCm38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features tsv.gz: list of gene lDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: barcodes_pos.tsv.gz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: he_roi_small.png: low-res image of tissue
Library strategy: Spatial Transcriptomics

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10um frozen sections were cut with cryostat
Reverse transcription (RT), second-strand cDNA synthesis, adaptor ligation and a second RT was generated and libraries were constructed according to the performer’s protocol. Sequencing handles and indexes were added in an indexing PCR and the finished libraries were purified and quantified. Sequencing was performed on the Illumina NovaSeq 6000 with a sequencing depth of at least 50,000 reads per sopt(100μm) and 150bp (PE150) paired-end reads (performed by Biomarker Technologies Corporation, Beijing, China).Primer spots were stained by hybridization of fluorescently labeled probes and imaged on the Metafer Slide Scanning platform. The resulting spot image was loaded into the BSTMatrix and BSTViewer along with the previously obtained BF tissue image of the same area. The two images were aligned and the built-in tissue recognition tool was used to extract spots covered by tissue.

value: intestinal cells


title: WTIR

description: Library name: Sample1


title: STP0795

description: Library name: STP0795


title: STP0636

description: Library name: STP0636


title: STP0677

description: Library name: STP0677


title: STP0593

description: Library name: STP0593


title: 197_SG_SC: 18 months, synaptosomes sucrose cushion

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq v2.20.0.422.
Per sample, the reads were mapped to the Mus musculus genome GRCm38 and respective annotation Release 85 [PMID: 29155950] using tophat2 v2.1 [PMID: 23618408] (parameters: --no-coverage-search --no-convert-bam --no-novel-juncs --no-novel-indels -T).
Read counts were introduced into the statistical environment R in order to calculate RPMs (reads per million mappable reads) and RPKMs (reads per kilobase and million mappable reads). For calculation of RPKMs lengths of transcripts were taken from featureCounts output.
Assembly: GRCm38.85
Supplementary files format and content: csv file contains read counts per gene and sample

source_name: brain - cortex

growth_protocol: Tissue from wild-type C57BL/6 mice was obtained from Janvier facility. Mice were housed in standard cages and fed standard lab chow and water ad libitum. Euthanasia was carried out by cervical dislocation in accordance with the European Council Directive of 22 September 2010 (2010/63/EU). The scientific purposes of the experiments were approved by the local authorities and supervised by the local veterinary (Anzeige N. O_AC_04, O_AC_08, O_AC_10 and O_AC_23-27).

extract_protocol:
Synaptosome samples were processed for RNA extraction according to (Smalheiser et al., 2014), and RNA was then extracted from the appositely prepared synaptosome samples and from TH samples through acidic phenol-chloroform extraction according to (Chomczynski, 1993). The synaptosomes were diluted in synaptosomal RNA buffer (50 mM Hepes, pH 7.5, 125 mM NaCl, 100 mM sucrose, 2 mM K acetate, 10 mM EDTA) containing protease inhibitors (1 tablet/10 mL, Roche, Cat. N. 11836170001), 160 U/mL Superase-In (Invitrogen, Cat.N. AM2694), 160 U/mL Rnase-OUT (Invitrogen, Cat. N. 10777019), quickly pelleted at 20.000 g for 20 min and rinsed twice in 4 × volume of synaptosomal RNA buffer and spundown again 20.000 g for 20 minutes. They were then resuspended in 100 μL of synaptosomal RNA buffer and RNA was extracted with standard Trizol protocol (Chomczynski & Sacchi, 1987) using Qiazol lysis reagent (Qiagen Cat. N. 79306).
Libraries were prepared from 30-150 ng of input material (total RNA) using NEBNext Ultra II Directional RNA Library Preparation Kit in combination with NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) and NEBNext Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors RNA) following the manufacturer's instructions (New England Biolabs).

treatment_protocol: Synaptosomes were extracted from cerebral cortices of 3 weeks-, 5 months- and 18/19 months-old mice as previously described (Gray & Whittaker, 1962; Moczulska et al., 2014). Briefly, the cortex was dissected and transferred to ice-cold synaptosomal buffer (10 mM HEPES, 1 mM EDTA, 2 mM EGTA, 0.5 mM DTT, 0.32 M sucrose, pH 7) containing protein inhibitors (1 tablet/10 mL, Roche). Samples were homogenized using a pestle (Sigma-Aldrich) with 12 strokes on ice. The homogenate was then centrifuged for 10min at 1.000g at 4°C and the supernatant was centrifuged again for 40min at 10.000g at 4°C. The obtained pellet, that contains the synaptosomes, was then resuspended in ice-cold synaptosomal buffer and layered over a discontinuous sucrose gradient (0.8M/1M/1.18M sucrose). The samples were then centrifuged for 2h at 50.512g at 4°C (Beckman Coulter Optima XPN-80 ultracentrifuge). The interface between 1M and 1.18M was withdrawn (synaptosome sample) and stored at -80°C. Ribosome associated RNAs were purified using a sucrose cushion as previously described (Fusco et al., 2021). Briefly, pelleted synaptosomes or 50µL of TH were lysed with 1mL ribosome lysis buffer (20 mM Tris pH 7.4, 150 mM NaCl, 5 mM MgCl2, 24 U/mL TurboDNase, 100 µg/mL cycloheximide, 1% Triton-X-100, 1 mM DTT, RNasin(R) Plus RNase inhibitor 200 U/mL and 1x cOmplete EDTA-free protease inhibitor). TH samples were then homogenized with a syringe and a 0.4x20mm needle on ice and centrifuged for 10min at 10.000g at 4°C. TH and SYN were then loaded on 3mL sucrose solution (34% sucrose, 20 mM Tris pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/mL cycloheximide) in a thickwall ultraclear tube (Beckman, 344062) and centrifuged for 40 min at 4 °C at 55.000 rpm (367,600 × g) with a SW60 rotor. Ribosome-containing pellet was directly collected in Qiazol (Qiagen Cat. N. 79306) and processed for RNA extraction.

value: brain - cortex

tag: strain

value: 18 months

tag: fraction

value: synaptosomes sucrose cushion


title: intestine, WTIR, scRNA-seq

description: Library name: Sample1

value: intestine


title: 196_SG_SC: 18 months, synaptosomes sucrose cushion


title: STP0378

description: Library name: STP0378


title: STP0793

description: Library name: STP0793


title: 198_SG_SC: 18 months, synaptosomes sucrose cushion


title: 195_SG_SC: 18 months, synaptosomes sucrose cushion


title: STP0582

description: Library name: STP0582


title: STP0230

description: Library name: STP0230


title: STP0596

description: Library name: STP0596


title: STP0583

description: Library name: STP0583


title: 193_SG_SC: 6 months, synaptosomes sucrose cushion

value: 6 months


title: STP0867

description: Library name: STP0867


title: 194_SG_SC: 6 months, synaptosomes sucrose cushion


title: STP0275

description: Library name: STP0275


title: 191_SG_SC: 6 months, synaptosomes sucrose cushion


title: STP0023

description: Library name: STP0023


title: STP0016

description: Library name: STP0016


title: SCP4913

description: Library name: SCP4913


title: 192_SG_SC: 6 months, synaptosomes sucrose cushion


title: 190_SG_SC: 3 weeks, synaptosomes sucrose cushion

value: 3 weeks


title: STP0105

description: Library name: STP0105

value: chorionic villus


title: SCP4748

description: Library name: SCP4748


title: 189_SG_SC: 3 weeks, synaptosomes sucrose cushion

value: male


title: SCP4733

description: Library name: SCP4733

value: Control


title: STP0148

description: Library name: STP0148


title: SCP4726

description: Library name: SCP4726

value: female


title: SCP4706

description: Library name: SCP4706


title: 188_SG_SC: 3 weeks, synaptosomes sucrose cushion


title: 187_SG_SC: 3 weeks, synaptosomes sucrose cushion


title: SCP4809

description: Library name: SCP4809


title: STP0282

description: Library name: STP0282


title: SCP4538

description: Library name: SCP4538


title: SCP4536

description: Library name: SCP4536


title: SCP4578

description: Library name: SCP4578


title: SCP4319

description: Library name: SCP4319


title: 198_SG_input: 18 months, synaptosomes cortex

value: synaptosomes cortex


title: 197_SG_input: 18 months, synaptosomes cortex


title: SCP4196

description: Library name: SCP4196


title: SCP4164

description: Library name: SCP4164

value: Preeclampsia


title: SCP4157

description: Library name: SCP4157


title: 196_SG_input: 18 months, synaptosomes cortex


title: SCP4378

description: Library name: SCP4378


title: SCP4154

description: Library name: SCP4154


title: 194_SG_input: 6 months, synaptosomes cortex


title: SCP4073

description: Library name: SCP4073


title: SCP4059

description: Library name: SCP4059


title: SCP4139

description: Library name: SCP4139


title: SCP3992

description: Library name: SCP3992


title: SCP3962

description: Library name: SCP3962


title: 193_SG_input: 6 months, synaptosomes cortex


title: SCP3929

description: Library name: SCP3929


title: 191_SG_input: 6 months, synaptosomes cortex


title: SCP3954

description: Library name: SCP3954


title: SCP3780

description: Library name: SCP3780


title: 192_SG_input: 6 months, synaptosomes cortex


title: SCP3843

description: Library name: SCP3843


title: 189_SG_input: 3 weeks, synaptosomes cortex


title: SCP3877

description: Library name: SCP3877


title: 190_SG_input: 3 weeks, synaptosomes cortex


title: SCP3412

description: Library name: SCP3412


title: T42B_PTC-596

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

description: Library name: PACE_163

library_source: other

data_processing:
FASTQ files were pre-processed to extract Cas9 guide sequence using a bespoke Perl script.
The Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'.
Trimmed FASTQ files were then aligned to the TKOv3 FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.
Assembly: hg19
Supplementary files format and content: tab-delimited read count matrix
Library strategy: CRISPR Screen

molecule: other

growth_protocol: Cells were cultured in Neurocult Complete media for 42 days.

extract_protocol:
Genomic DNA was extracted using Puregene Cell and Tisssue kit (Qiagen), as per manufacturer's instructions, and quantified using spectrophotometry. For each sample, the gRNA cassette was amplified directly from genomic DNA using primers harbouring Illumina TruSeq adaptors with i5 and i7 barcodes. The resulting sequencing libraries were pooled and gel purified.
For each sample, the gRNA cassette was amplified directly from genomic DNA using primers harboring Illumina TruSeq adaptors with i5 and i7 barcodes. The resulting sequencing libraries were pooled and gel-purified.

treatment_protocol: Cells were transduced with the TKOv3 library at an MOI ~ 0.3, followed by selection with puromycin.

value: medulloblastoma


title: T42C_PTC-596

description: Library name: PACE_164


title: 187_SG_input: 3 weeks, synaptosomes cortex


title: T42A_PTC-596

description: Library name: PACE_162


title: 188_SG_input: 3 weeks, synaptosomes cortex


title: T42B_Control

description: Library name: PACE_120

value: DMSO


title: T42C_Control

description: Library name: PACE_121


title: LU65_AMGR_Biol_rep3

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

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:
KRASG12C cell lines (H358 and LU65) were chronically treated with Sotorasib starting from their IC50s.
The treatment dose was doubled in every next passage for 4-6 passages and then maintained at constant dose of Sotorasib (0.4 µM for H358 and 1 µM for LU65)

value: epithelial cells

value: KRAS G12C

value: Maintained in drug


title: 195_SG_input: 18 months, synaptosomes cortex

value: brain - cortex


title: LU65_AMGR_Biol_rep1


title: LU65_Biol_rep3

value: No treatment


title: 196_TH_SC: 18 months, total homogenate sucrose cushion

value: 18 months

value: total homogenate sucrose cushion


title: LU65_AMGR_Biol_rep2


title: 195_TH_SC: 18 months, total homogenate sucrose cushion


title: LU65_Biol_rep1


title: SCP3660

description: Library name: SCP3660


title: H358_AMGR_Biol_rep3


title: H358_Biol_rep3


title: H358_AMGR_Biol_rep1


title: SCP3628

description: Library name: SCP3628


title: 192_TH_SC: 6 months, total homogenate sucrose cushion

value: 6 months


title: H358_Biol_rep2


title: 198_TH_SC: 18 months, total homogenate sucrose cushion


title: H358_Biol_rep1


title: 191_TH_SC: 6 months, total homogenate sucrose cushion


title: RNA-seq in Hofbauer cells (placental villous macrophages of fetal origin) (patient 3, rep1)

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

description: RNA-seq

data_processing:
alignment to hg19 reference genome with HISAT2 (v2.1.0) using default parameters
transcript assembly with StringTie (v1.3.4d)
generation of coverage (bigWig) files with bamCoverage2 (v3.1.3) of deepTools using -binsize 1 --normalizeUsing RPKM parameters
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: The isolation of Hofbauer cells were performed as described earlier by Tang et al., 2011. The freshly isolated cells were further purified by fluorescence activated cell sorting based on cell viability and the cell surface expression of CD163.

extract_protocol:
Total RNA was isolated from cells using Tri Reagent (MRC) according to the manufacturer’s protocol.
Indexed cDNA libraries were prepared from 1 µg of total RNA following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol. Briefly, the mRNA Poly-A was selected on oligo (dT) magnetic beads and fragmented by divalent cations at 94°C for 5 min. Reverse transcription was performed using SuperScript II reverse transcriptase (Life Technologies, Inc.) and random primers. After second strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. cDNA libraries were purified and size selected after PCR with AMPure XP beads (Beckman Coulter, Inc, Fullerton, C.A USA).

value: Hofbauer cells

tag: gestational age_(weeks_+_days)

tag: c-section indication

value: myopia

tag: sex of_newborn_assigned_at_birth

value: Male


title: RNA-seq in Hofbauer cells (placental villous macrophages of fetal origin) (patient 3, rep2)

description: RNA-seq

tag: tissue

tag: cell type


title: 190_TH_SC: 3 weeks, total homogenate sucrose cushion

value: 3 weeks

value: male


title: RNA-seq in Hofbauer cells (placental villous macrophages of fetal origin) (patient 2, rep1)

description: RNA-seq

value: placenta previa


title: RNA-seq in Hofbauer cells (placental villous macrophages of fetal origin) (patient 2, rep2)

description: RNA-seq


title: LU65_Biol_rep2

tag: genotype

tag: treatment


title: 188_TH_SC: 3 weeks, total homogenate sucrose cushion

tag: Sex


title: RNA-seq in Hofbauer cells (placental villous macrophages of fetal origin) (patient 1, rep1)

description: RNA-seq

value: previus C-section


title: 197_TH_SC: 18 months, total homogenate sucrose cushion


title: ATAC-seq in Hofbauer cells (placental villous macrophages of fetal origin) (patient 3, rep1)

description: ATAC-seq

data_processing:
alignment to hg19 reference genome with BWA v0.7.10 using default parameters
bam generation with SAMtools v1.7 using default parameters
tag directory generation with HOMER's makeTagDirectory using -checkGC parameter
generation of coverage (bedgraph) files with HOMER's makeUCSCfile using -fsize 1e50 -norm parameters
Assembly: hg19
Supplementary files format and content: bedgraph

growth_protocol: Isolation were completed according to the protocol (Tang et al., 2011), modified by Laszlo Nagy.

extract_protocol:
Cells were lysed with the following lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL). After lysis, nuclei were subjected to tagmentation.
Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol.

treatment_protocol: No treatment.


title: 193_TH_SC: 6 months, total homogenate sucrose cushion


title: 187_TH_SC: 3 weeks, total homogenate sucrose cushion


title: H358_AMGR_Biol_rep2


title: 194_TH_SC: 6 months, total homogenate sucrose cushion


title: T42A_Control

description: Library name: PACE_119

value: medulloblastoma


title: ATAC-seq in Hofbauer cells (placental villous macrophages of fetal origin) (patient 1, rep2)

description: ATAC-seq


title: 198_TH_input: 18 months, total homogenate cortex

value: total homogenate cortex


title: ATAC-seq in Hofbauer cells (placental villous macrophages of fetal origin) (patient 1, rep1)

description: ATAC-seq


title: RNA-seq in Hofbauer cells (placental villous macrophages of fetal origin) (patient 4, rep1)

description: RNA-seq

value: Female


title: sample5

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: No. 3, Qingchun East Rd

department: Sir Run Run Shaw Hospital

institute: Zhejiang University

data_processing:
Raw RNA-seq data were trimmed by fastp (v0.20.1) to remove adapter sequence and reads with low sequencing quality, paired-end sequencing was carried out with the Illumina HiSeq 2500 with paired-end 150-bp read length.
Clean reads were aligned to the human genome (hg38) using HISAT2 software (v2.1.0) with the default parameter settings.
Transcript assembly was performed by stringtie software (v2.0) and expression of transcripts sharing each gene_id was quantified as Fragments Per Kilobase of exon model per Million mapped fragments(FPKM).
Assembly: hg38
Supplementary files format and content: Excel files include FPKM values for each sample

source_name: HLECs

growth_protocol: HLECs cultured in endothelial cell medium (ECM) (ScienCell Research Laboratories) supplemented with 5% FBS and cultured in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
Cells were havested and total RNA was isolated using trizol (Invitrogen, USA).
3 μg RNA per sample were used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina®

treatment_protocol: We added recombinant S100A6 and the control double distilled water to each HLEC culture medium

value: HLECs


title: 197_TH_input: 18 months, total homogenate cortex


title: sample4


title: sample6


title: sample3

value: recombinant S100A6


title: sample2


title: 196_TH_input: 18 months, total homogenate cortex

value: brain - cortex


title: 195_TH_input: 18 months, total homogenate cortex


title: 189_TH_SC: 3 weeks, total homogenate sucrose cushion


title: 194_TH_input: 6 months, total homogenate cortex


title: sample1


title: Ly1_Jib04_500nM_3

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14  to the reference genome UCSC mm10 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts in tab-delimited text file

source_name: OCI-Ly1 Cells

growth_protocol: OCI-Ly1 cells were cultured in IMDM+10%FBS with Penn-strep

extract_protocol:
RNAeasy mini-kit from Qiagen was used to prepare RNA from cells
Ribo-zero

treatment_protocol: Indicated concentration of JIB-04 were added to the cells for 48 hours and cells were processed for RNA-seq

value: OCI-Ly1 Cells

value: DLBCL cell line

value: Jib04 500nM


title: ATAC-seq in Hofbauer cells (placental villous macrophages of fetal origin) (patient 3, rep2)

description: ATAC-seq


title: Ly1_Jib04_500nM_1


title: Ly1_Jib04_500nM_2


title: Ly1_DMSO_3

value: DMSO


title: 192_TH_input: 6 months, total homogenate cortex

value: 6 months


title: Ly1_Jib04_150nM_2

value: Jib04 150nM


title: Ly1_Jib04_150nM_3


title: Ly1_Jib04_150nM_1


title: 193_TH_input: 6 months, total homogenate cortex


title: 191_TH_input: 6 months, total homogenate cortex


title: Ly1_DMSO_2


title: neutrophil, DSP-1001660011515-H-H08

city: Chicago

first: weijie

last: guo

state: IL

address: 929 East 57th Street, GCIS W423N

institute: university of Chicago

data_processing:
FASTQ files were first processed by the NanoString GeoMx NGS Pipeline v2.0.
Briefly, raw reads were pre-processed by trimming low-quality bases and adapter sequences. Filtered reads were then stitched and aligned, followed by extraction of barcode and UMI sequences. Barcodes were matched to a reference set of known probe barcodes, allowing for a maximum of one mismatch. To remove duplicates, reads sharing the same barcode were collapsed based on unique molecular identifiers (UMIs).
Raw data from NanoString GeoMx NGS Pipeline were then imported to R using GeomxTools package to generate GeoMxSet object. The raw count data was first normalized with "q_norm" method. To facilitate data processing, GeoMxSet object was further coerced into Seurat object and standard Seurat pipe lines were applied for analysis.
Assembly: mm10
Supplementary files format and content: tsv files and mtx file
Library strategy: Spatial Transcriptomics

source_name: TME

extract_protocol:
Fresh frozen tissues were OCT embedded, and 5um frozen sections were cut with cryostat
Fresh frozen tumor sections were mounted onto slides, followed by immunofluorescent staining with specific antibodies targeting protein markers of interest to delineate distinct tissue regions. After staining, high-resolution digital images were acquired to visualize and identify regions of interest (ROIs). ROIs were selected based on morphological and biological relevance. These regions were then subjected to UV light-based spatially resolved photocleavage to release oligonucleotide tags bound to the target mRNA transcripts. The released tags were collected were collected into 96-well plates. Library preparation was performed according to the NanoString GeoMx-NGS Readout Library Prep manual. Briefly, the released tags were dried and reconstituted in 10 µL nuclease free water, and 4 µL was used in a PCR reaction. NanoString barcoded primers were used to amplify the tags and add Illumina adaptor sequences and sample demultiplexing barcodes. PCR products were pooled in equal volumes and purified with two rounds of AMPure XP beads (Beckman Coulter).

value: TME

value: neutrophil


title: neutrophil, DSP-1001660011515-H-H09


title: 190_TH_input: 3 weeks, total homogenate cortex

value: 3 weeks

value: male


title: Ly1_DMSO_1


title: neutrophil, DSP-1001660011515-H-H07


title: neutrophil, DSP-1001660011515-H-H06


title: 187_TH_input: 3 weeks, total homogenate cortex


title: 188_TH_input: 3 weeks, total homogenate cortex


title: neutrophil, DSP-1001660011515-H-G10


title: neutrophil, DSP-1001660011515-H-H05


title: neutrophil, DSP-1001660011515-H-H01


title: 189_TH_input: 3 weeks, total homogenate cortex


title: neutrophil, DSP-1001660011515-H-G06


title: neutrophil, DSP-1001660011515-H-G02


title: neutrophil, DSP-1001660011515-H-G01


title: neutrophil, DSP-1001660011515-H-G04


title: VP mouse, high-fat diet, 5 weeks

city: Seattle

first: David

middle: J

last: Ottenheimer

state: WA

address: 1959 NE Pacific St

institute: University of Washington

data_processing:
We aligned the sequencing results to reference genomes using the 10x Genomics Cloud Analysis tool, using their provided mouse reference genome, Mouse (mm10) 2020-A, and creating our own rat reference genome with 10x Genomics Cell Ranger software. FASTA and GTF files for Rattus norvegicus (mRatBN7.2) were downloaded from Ensembl. The filtered matrices uploaded here only include cell-associated barcodes according to the 10x Cell Ranger cell calling algorithm.
Assembly: Mouse: mm10 2020-A, Rat: mRatBN7.2
Supplementary files format and content: Feature-Barcode matrix for cell-associated barcodes

molecule: nuclear RNA

source_name: Ventral pallidum

extract_protocol:
For experiments utilizing mice, all mice were anesthetized with isoflurane and transcardially perfused with ice-cold NMDG buffer. Brains were extracted and sliced on a fresh-tissue vibratome. Typically, 4 tissue slices of 300µM thickness were collected for bilateral VP mi-crodissection with a scalpel, resulting in 8 VP tissue samples. Samples were flash-frozen on dry ice and transferred to -80 C for storage. For experiments utilizing rats, rats were injected with 0.7 mL Euthasol for terminal anesthesia, and then perfused with ice-cold NMDG buffer. VP tissue samples were collected using the same procedure employed for mice excepting for with 400µM slices. We also collected 8 NAc tissue samples from the same rats. VP tissue samples from each experimental group (mice) and from all rats were pooled together for a total of 5 nuclear isolation batches by combining samples in a glass Dounce homogenizer containing lysis buffer. We did the same for NAc tissue samples from rats for an additional nuclear isolation batch. After homogenization and a five-minute incubation, samples were diluted using wash buffer, passed through a 40 uM cell strainer, and centrifuged at 500 x g for 10 minutes at 4 C to remove debris and pellet nuclei. This pellet was resuspended in a homogenate solution and combined 1:1 with a 50% iodixanol solution. To further clean up the nuclei pellet using density gradient centrifugation, we underlaid the resulting 25% iodixanol layer with a 30% layer and centrifuged at 3000 x g for 15 minutes at 4 C.
We used the 10X Genomics Chromium 3’ Next GEM kit v3.1 (Dual Index) to generate cDNA libraries from each nuclear isolation batch. Isolated nuclei preparations were diluted to a concentration of 1,000/uL and loaded onto the 10X chip, targeting capture of 10,000 single barcoded nuclei. We loaded rat nuclei preparations into two lanes on the chip, resulting in two VP and two NAc reactions. We then prepared libraries for sequencing following the Next GEM protocol.

treatment_protocol: Mice were placed on high-fat diet (Bio-Serv F3282, 2 weeks), control diet (facility chow, 2 weeks), high-fat diet (Bio-Serv F3282, 5 weeks), or a diet with normal fat levels but otherwise matched to the high-fat chow (Bio-Serv F4031, 5 weeks).

value: Ventral pallidum

tag: mixed gender

tag: developmental stage

value: Adult

value: High-fat diet, 5 weeks


title: neutrophil, DSP-1001660011515-H-F10


title: neutrophil, DSP-1001660011515-H-F08


title: VP mouse, matched diet, 5 weeks

value: Matched diet, 5 weeks


title: Lats1/2CKO right atrium with Csf1r inhibitor injection (snMultiomics-ATAC)

city: Houston

first: Yi

last: Zhao

state: Texas

address: 6770 Bertner Avenue

institute: The Texas Heart Institute at Baylor College of Medicine

description: Lats1/2CKO + Inhibitor Multiome-ATAC

data_processing:
Raw sequencing reads were aligned to the genome (build mm10) using the 10X Genomics toolkit cellranger-arc-2.0.2 with default parameters.
Assembly: mm10
Supplementary files format and content: TSV files: Tab-separated tables. MTX files: long-format matrix files

source_name: Heart right atrium

extract_protocol:
Single-nuclei were extracted following 10X nucleus extraction kits following manufacturer's protocols
Joint snRNA and snATAC sequencing was performed by using the scMultiomics platform from 10X Genomics. Isolated nuclei were loaded into the 10X Genomics Chromium Controller to obtain the gel beads in emulsion. The sequencing libraries were then prepared according to the manufacturer’s protocols for the Single-cell multiomics kit. Sequencing was performed by using the NovaSeq 6000 system.
snMultiomics (snRNA and snATAC)

treatment_protocol: GW2580 (80 ug/g, LC laboratories, G-5903) was administrated by gavage twice daily starting on the first day of tamoxifen injection until the day of collecting the hearts

value: Heart right atrium

value: Tcf21iCre; Lats1/2FF; Rosa26_Sun1GFP

value: Csf1r inhibitor injection


title: VP mouse, control diet, 2 weeks

value: Control diet, 2 weeks


title: neutrophil, DSP-1001660011515-H-F05


title: VP mouse, high-fat diet, 2 weeks

value: High-fat diet, 2 weeks


title: neutrophil, DSP-1001660011515-H-F03


title: neutrophil, DSP-1001660011515-H-F01


title: Lats1/2CKO right atrium with vehicle injection (snMultiomics-ATAC)

description: Lats1/2CKO + Vehicle Multiome-ATAC

value: Vehicle injection


title: neutrophil, DSP-1001660011515-H-E07


title: Control right atrium with Csf1r inhibitor injection (snMultiomics-ATAC)

description: Control + Inhibitor Multiome-ATAC

value: Lats1/2FF; Rosa26_Sun1GFP


title: neutrophil, DSP-1001660011515-H-E08


title: neutrophil, DSP-1001660011515-H-G08


title: neutrophil, DSP-1001660011515-H-E11


title: neutrophil, DSP-1001660011515-H-E06


title: Control right atrium with vehicle injection (snMultiomics-ATAC)

description: Control + Vehicle Multiome-ATAC


title: neutrophil, DSP-1001660011515-H-E04


title: neutrophil, DSP-1001660011515-H-E03


title: neutrophil, DSP-1001660011515-H-D11


title: neutrophil, DSP-1001660011515-H-D05


title: neutrophil, DSP-1001660011515-H-D04


title: Lats1/2CKO right atrium with vehicle injection (snMultiomics-RNA)

description: Lats1/2CKO + Vehicle Multiome-RNA


title: neutrophil, DSP-1001660011515-H-D02


title: neutrophil, DSP-1001660011515-H-D03


title: Lats1/2CKO right atrium with Csf1r inhibitor injection (snRNA only)

description: Lats1/2CKO + Inhibitor snRNA


title: neutrophil, DSP-1001660011515-H-C12


title: Control right atrium with vehicle injection (snMultiomics-RNA)

description: Control + Vehicle Multiome-RNA


title: neutrophil, DSP-1001660011515-H-C06


title: neutrophil, DSP-1001660011515-H-C09


title: neutrophil, DSP-1001660011515-H-D01


title: Control right atrium with Csf1r inhibitor injection (snRNA only)

description: Control + Inhibitor snRNA


title: NAC rat, batch 2

organism: Rattus norvegicus

source_name: Nucleus accumbens

value: Nucleus accumbens

value: Sprague Dawley


title: NAC rat, batch 1


title: neutrophil, DSP-1001660011515-H-C02

value: TME


title: neutrophil, DSP-1001660011515-H-C05

value: neutrophil


title: neutrophil, DSP-1001660011515-H-C01


title: Lats1/2CKO female left atrium

description: Lats1/2CKO LA Female

data_processing:
Raw sequencing reads were aligned to the genome (build mm10) using the 10X Genomics toolkit CellRanger version 7.1.0 (cellranger count) with default parameters.
Assembly: mm10
Supplementary files format and content: TSV files: Tab-separated tables. MTX files: long-format matrix files

source_name: Heart left atrium

extract_protocol:
Single-nuclei were extracted following 10X nucleus extraction kits following manufacturer's protocols
SnRNA-seq was performed by using the 10X Genomics platform. Isolated nuclei were loaded into the 10X Genomics Chromium Controller to obtain the gel beads in emulsion. The sequencing libraries were then prepared according to the manufacturer’s protocols for the Single-cell 3’ Reagents Kits v3. Sequencing was performed by using the NovaSeq 6000 system.

value: Heart left atrium


title: VP rat, batch 2


title: neutrophil, DSP-1001660011515-H-B11


title: neutrophil, DSP-1001660011515-H-B06


title: VP rat, batch 1


title: Control female left atrium

description: Control LA Female

value: Tcf21iCre; Rosa26_Sun1GFP


title: Lats1/2CKO male left atrium

description: Lats1/2CKO LA Male


title: Control male left atrium

description: Control LA Male


title: neutrophil, DSP-1001660011515-H-B05


title: XP945c9_33

city: Dallas

first: Bingqing

last: Xie

address: 6001 Forest Park Rd

department: Internal medicine

institute: University of Texas Southwestern medical center

description: Library name: XP945c9_33

data_processing:
Fastq files for sample with multi-run sequencing were concatenated.
Fastq files were aligned to the combined genome of mm10 and hg38 using Star v2.7.3a.
Mouse reads were removed from the resulting bam files using XenofilteR.
Raw counts were summarized by featureCount (subread v2.0.6) on the filtered bam file.
Assembly: hg38
Supplementary files format and content: tab-delimited text files with raw counts for each sample

source_name: Kidney tumor

growth_protocol: For drug trials, ~60 mm3 fragments from stably growing tumorgrafts were implanted subcutaneously into 4 to 6-week-old female non-obese diabetic (NOD)/severe combined immunodeficiency (SCID) mice. The study was carried out only in female mice, as mice could be housed in same cages. When tumor volumes reached ~300–600 mm3 or when mice showed signs of hypercalcemia (weakness, weight loss, reduced locomotor activity, etc) blood was drawn to measure calcium level. Calcium levels were measured from ~150 µl blood drawn through a cheek bleed.

extract_protocol:
The RNA was isolated based on the established protocol (PMID: 24136348)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. The libary preparationa nd RNAseq was carried out by Novogene

treatment_protocol: Briefly, treatments were administered via oral gavage every 12-hours and every 24-hours during weekend. The vehicle solution consisted of 10% ethanol, 30% PEG400, 60% MCT (0.5% methyl cellulose, and 0.5% Tween 80). PT2399 (MedChemExpress) was administered at 100 mg/kg in 10% ethanol, 30% PEG400, and 60% MCT (0.5% methyl cellulose, 0.5% Tween 80 (aq)). Treatment doses were adjusted weekly based on mouse weight.

value: Kidney tumor

value: Treatment not applicable

tag: batch


title: Control right atrium with Csf1r inhibitor injection (snMultiomics-RNA)

description: Control + Inhibitor Multiome-RNA


title: XP945c13_V2

description: Library name: XP945c13_V2

value: Vehicle


title: XP945c13_V1

description: Library name: XP945c13_V1


title: neutrophil, DSP-1001660011515-H-A07


title: Lats1/2CKO female right atrium

description: Lats1/2CKO RA Female


title: neutrophil, DSP-1001660011515-H-A05


title: neutrophil, DSP-1001660011515-H-A06


title: Lats1/2CKO male right atrium

description: Lats1/2CKO RA Male


title: Lats1/2CKO right atrium with Csf1r inhibitor injection (snMultiomics-RNA)

description: Lats1/2CKO + Inhibitor Multiome-RNA


title: Control female right atrium

description: Control RA Female


title: XP945c13_P1

description: Library name: XP945c13_P1


title: neutrophil, DSP-1001660011515-H-A03


title: XP899c9_V1

description: Library name: XP899c9_V1


title: Control + Csf1r Inhibitor

description: Control + Low TAM + Csf1r Inhibitor

data_processing:
Raw sequencing reads were aligned to the genome (build mm10) using the 10X Genomics toolkit spaceranger-2.0.1 with default parameters.
Assembly: mm10
Supplementary files format and content: TSV files: Tab-separated tables. MTX files: long-format matrix files; Tif: high resolution H&E image

source_name: Whole heart

extract_protocol:
Visium Spatial RNA-seq: Frozen (10-μm) or formalin-fix-paraffin-embedded (FFPE, 7-μm) tissue sections from mouse hearts were mounted on 10X Visium slide capture areas, each with 5000 barcoded RNA capture spots. Hematoxylin and eosin (H&E)-stained images of whole tissue sections were obtained by using the BioTek Cytation 5 with image stitching. For forzen sections, optimal permeabilization time for the release of mRNA from 10-μm thick tissue sections for both genotypes was 12 minutes, determined by using the Visium Tissue Optimization Kit.
For frozen sections, spatially barcoded cDNA libraries were generated from mRNA released from each tissue section by using the Visium Spatial Gene Expression Reagent Kit, before being sequenced on an Illumina NovaSeq 6000 with 150 cycle paired-end setting (read 1 = 28 cycles, read 2 = 90 cycles, index 1 = 10 cycles, index 2 = 10 cycles). For FFPE sections, mouse whole transcriptome probe (Visium Spatial Gene Expression for FFPE reagent kits, mouse transcriptome) panels were added to the permeabilized tissue. Probes were bonded to spatial barcodes before adding sample indexes and generating libraries. Libraries were then sequenced on an Illumina NovaSeq 6000 with 150 cycle paired-end setting (read 1 = 28 cycles, read 2 = 50 cycles, index 1 = 10 cycles, index 2 = 10 cycles).

value: Whole heart

value: Low dose TAM + Csf1r Inhibitor


title: neutrophil, DSP-1001660011515-H-A02


title: Control + Vehicle

description: Control + Low TAM + Vehicle

value: Low dose TAM + Vehicle


title: XP899c9_P2

description: Library name: XP899c9_P2


title: Lats1/2CKO + Vehicle

description: Lats1/2CKO + Low TAM + Vehicle

value: Tcf21iCre; Lats1/2FF; Rosa26_Sun1GFP


title: Lats1/2CKO + Csf1r Inhibitor

description: Lats1/2CKO + Low TAM + Csf1r Inhibitor


title: XP771bc27_V2

description: Library name: XP771bc27_V2


title: Lats1/2CKO

description: Lats1/2CKO + High TAM

value: Tcf21iCre; Lats1/2FF

value: High dose TAM


title: neutrophil, DSP-1001660011514-G-G10


title: neutrophil, DSP-1001660011514-G-G08


title: neutrophil, DSP-1001660011514-G-G06


title: Control

description: Control + High TAM


title: XP945c13_P2

description: Library name: XP945c13_P2


title: Control male right atrium

description: Control RA Male

value: Heart right atrium


title: neutrophil, DSP-1001660011514-G-G02


title: Cardiac myofibroblasts_siBcat1

city: Fukuoka

first: Miciho

last: Nakaya

state: Fukuoka

address: Maidashi 3-1-1, Higashiku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Kyushu University

data_processing:
Sequence reads were treated with FastQC and the adapter sequence, low quality bases and reads with length shorter than 36bp were removed by using Trimmomatic program.
Trimmed sequenced reads were mapped to the mouse reference gene (mm10) using HISAT2.
Known genes and transcripts were assembled with StringTie and calculated in the read count and normalized value as FPKM and TPM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM or Read_Count for each Sample

source_name: Cardiac myofibroblasts

growth_protocol: Isolated cardiac myofibroblasts were grown in DMEM with 10% FBS and 1% penicillin–streptomycin and cultured in a 5 % CO2 incubator at 37°C.

extract_protocol:
Total RNA from cardiac myofibroblasts treated with siRNA was extracted using the QIAGEN RNeasy plus Mini Kit (Qiagen) according to manufacturer’s protocol. Library construction was performed by Macrogen Japan, using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) and the libraries read on the Illumina NovaSeq 6000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cardiac myofibroblasts were transfected with 12.5 nM of siRNA [siControl (ambion #4390844) or siBcat1 (ambion #s629889)] using Lipofectamine RNAiMAX (Invitrogen) and cultured for 72 hours.

value: Cardiac myofibroblasts isolated 3-days after myocardial infarction


title: XP899c9_V2

description: Library name: XP899c9_V2


title: XP771bc27_P1

description: Library name: XP771bc27_P1


title: neutrophil, DSP-1001660011514-G-F11


title: XP374c8_V2

description: Library name: XP374c8_V2


title: neutrophil, DSP-1001660011514-G-G01


title: neutrophil, DSP-1001660011514-G-G12


title: XP374c8_V1

description: Library name: XP374c8_V1


title: XP899c9_P1

description: Library name: XP899c9_P1


title: neutrophil, DSP-1001660011514-G-F08


title: neutrophil, DSP-1001660011514-G-F06


title: neutrophil, DSP-1001660011514-G-F04


title: XP374c8_P1

description: Library name: XP374c8_P1


title: neutrophil, DSP-1001660011514-G-F03


title: neutrophil, DSP-1001660011514-G-F02


title: XP289c20_42

description: Library name: XP289c20_42


title: neutrophil, DSP-1001660011514-G-G11


title: XP1676c4_88

description: Library name: XP1676c4_88


title: neutrophil, DSP-1001660011514-G-F01


title: XP289c19_43

description: Library name: XP289c19_43


title: XP771bc27_P2

description: Library name: XP771bc27_P2


title: XP1676c3_51

description: Library name: XP1676c3_51


title: neutrophil, DSP-1001660011514-G-E11


title: neutrophil, DSP-1001660011514-G-E12


title: XP1657dc3_48

description: Library name: XP1657dc3_48


title: XP165c13_95

description: Library name: XP165c13_95


title: Cardiac myofibroblasts_siCtrl

value: siControl


title: neutrophil, DSP-1001660011514-G-E08


title: XP771bc27_V1

description: Library name: XP771bc27_V1


title: XP374c8_P2

description: Library name: XP374c8_P2


title: XP1631c10_P1

description: Library name: XP1631c10_P1


title: XP1631c10_V2

description: Library name: XP1631c10_V2


title: neutrophil, DSP-1001660011514-G-E07


title: neutrophil, DSP-1001660011514-G-E10


title: neutrophil, DSP-1001660011514-G-E09


title: neutrophil, DSP-1001660011514-G-E04


title: RNA-seq in Hofbauer cells (placental villous macrophages of fetal origin) (patient 1, rep2)

description: RNA-seq

value: Hofbauer cells

value: previus C-section

value: Male


title: XP1631c10_P2

description: Library name: XP1631c10_P2


title: XP1487c20_V1

description: Library name: XP1487c20_V1


title: neutrophil, DSP-1001660011514-G-E06

value: TME

value: neutrophil


title: XP1487c20_V2

description: Library name: XP1487c20_V2

value: Kidney tumor


title: ATAC-seq in Hofbauer cells (placental villous macrophages of fetal origin) (patient 2, rep1)

description: ATAC-seq

value: placenta previa


title: neutrophil, DSP-1001660011514-G-E03


title: XP1487c20_P2

description: Library name: XP1487c20_P2


title: neutrophil, DSP-1001660011514-G-E01


title: neutrophil, DSP-1001660011514-G-D10


title: neutrophil, DSP-1001660011514-G-D09


title: XP1169c13_V2

description: Library name: XP1169c13_V2

value: Vehicle


title: XP143c13_66

description: Library name: XP143c13_66

value: Treatment not applicable


title: neutrophil, DSP-1001660011514-G-D07


title: XP1631c10_V1

description: Library name: XP1631c10_V1


title: neutrophil, DSP-1001660011514-G-D06


title: neutrophil, DSP-1001660011514-G-C04


title: XP1169c13_P2

description: Library name: XP1169c13_V4


title: XP1169c13_P1

description: Library name: XP1169c13_V3


title: XP1152c8_V1

description: Library name: XP1152c8_V01


title: neutrophil, DSP-1001660011514-G-B10


title: neutrophil, DSP-1001660011514-G-B11


title: XP1152c8_P1

description: Library name: XP1152c8_P1


title: XP1152c8_P2

description: Library name: XP1152c8_P2


title: XP1139c8_V2

description: Library name: XP1139c8_V2


title: XP1139c9_60

description: Library name: XP1139c9_60


title: neutrophil, DSP-1001660011514-G-B06


title: neutrophil, DSP-1001660011514-G-B07


title: neutrophil, DSP-1001660011514-G-C01


title: neutrophil, DSP-1001660011514-G-B08


title: XP1487c20_P1

description: Library name: XP1487c20_P1


title: XP1139c8_V1

description: Library name: XP1139c8_V1


title: neutrophil, DSP-1001660011514-G-B01


title: neutrophil, DSP-1001660011514-G-B03


title: neutrophil, DSP-1001660011514-G-B04


title: XP1087c7_V2

description: Library name: XP1087c7_V2a


title: XP1087c7_V1

description: Library name: XP1087c7_V1a


title: neutrophil, DSP-1001660011514-G-A12


title: XP1087c7_P2

description: Library name: XP1087c7_P2


title: neutrophil, DSP-1001660011514-G-A08


title: XP1087c7_P1

description: Library name: XP1087c7_P1


title: neutrophil, DSP-1001660011514-G-C03


title: neutrophil, DSP-1001660011514-G-A09


title: neutrophil, DSP-1001660011514-G-A07


title: XP1059c7_V2

description: Library name: XP1059c7_V2


title: XP1059c7_V1

description: Library name: XP1059c7_V1


title: XP1152c8_V2

description: Library name: XP1152c8_V14


title: neutrophil, DSP-1001660011514-G-A06


title: XP1059c7_P2

description: Library name: XP1059c7_P2


title: XP1059c7_P1

description: Library name: XP1059c7_P1


title: neutrophil, DSP-1001660011514-G-A02


title: brain-APOE4-M-2

type: RNA

city: Atlanta

first: Karen

middle: N

last: McFarland

state: GA

address: 100 Woodruff Circle

department: Pharmacology

institute: Emory University

hyb_protocol: RNA/codesets were hybridized at 65 degrees Celsius for 18 hours.

scan_protocol: Hybridization cartridges were prepared on the NanoString Prep Station following manufacturer's instructions. Cartridges were scanned on the NanoString Digital Analyzer at a "high" resolution (280 FOV).

data_processing:
RCC files were loaded into nSolver 4.0 to extract raw and normalized count data. Data was extracted using the background thresholding function with a threshold count value set to 20. The geometric mean was used to compute normalization factors for positive control and probes as well as codesets.
Probe Name: gene name; Accession #: NCBI sequence accession ID; Class Name: codeset type, endogenous, housekeeping, positive control or negative control; Analyte Type: mRNA or SYSTEM (control probe)

source_name: forebrain

label_protocol: Hybridization reactions between RNA and codesets was set up following manufacturer's protocol.

extract_protocol: Frozen pulverized forebrain tissue was incubated in TRIzol reagent (Invitrogen) followed by phase separation and RNA isolation with ethanol precipitation. RNA was further purified with PureLink RNA Mini kit with on-column DNase treatment (Invitrogen). RNA quality and quantity were measured with the NanoDrop Microvolume spectrophotometers (Thermo) and on the Agilent Bioanalyzer 2100 with the Eurkaryote Total RNA Nano chip.

treatment_protocol: Mice were housed in conventional air-filtered cages and maintained on standard diet and water.

value: M

tag: age (months)


title: brain-APOE4-F-2

value: F


title: scRNA_sublibrary_7

city: San Antonio

first: Pei

last: Wang

state: TX

address: 7703 Floyd Curl Dr

institute: UT Health San Antonio

description:
Library name: scRNA_sublibrary_7
Each sub-library contain a subset of cells from 5 different samples including WT_organoid, KPT_organoid, KPTN_organoid, KPT_tumor and KPTN_tumor samples

data_processing:
Processing of the raw sequencing reads including alignment, demultiplexing and separation of human and mice transcripts were performed using a ParseBiosciences-Pipeline software v1.1.2 which was designed to be compatible with the sample preparation protocol.
Assembly: GRCh38 and GRCm38
Supplementary files format and content: 3 processed files are uploaded. 1) a csv file includes all gene ID and gene name for both human and mouse genome. 2) a csv file for cell metadata including barcoding information for 3 rounds of split and pool in 96 well plate format. Samples were separated started from the first round barcode (bc1_wind). 3) a count matrix file includes gene counts of each cell.

source_name: pancreas

growth_protocol: Engineered human primary pancreatic acinar cells were cultred as 3D organoid in serum free advanced DMEM/F-12 media supplemented with Wnt3a conditioned medium (50%), recombinant human R-Spondin 1 (500 ng/ml), Noggin (200 ng/ml), FGF10 (100 ng/ml), EGF (50 ng/ml), PGE II (1 nM), A83-01 (0.5 µM), Nicotinamide (10 mM), Penicillin/Streptomycin (1 mM), HEPES (10 mM), GlutaMax (1X).

extract_protocol:
Cell pellets of cultured organoids were collected and stored in Trizol for total RNA extraction using Zymo Direct-zol RNA Miniprep Kit (Zymo Research, Irvine, CA, R2063) following manufacturer’s instructions. Tumor tissues were flash frozen in liquid nitrogen and ground into fine powder with the addition of Trizol, followed by RNA extraction using Zymo Direct-zol RNA Miniprep Kit.
Single cell RNA seq samples were prepared using an EvercodeTM Fixation V2 kit and EvercodeTM WT V2 Kit (Parse Biosciences, Seattle, WA) following manufacturer’s instructions. Briefly, organoid culture or tumor tissues were dissociated into single cells by enzyme digestion and flow sorting. The single cells were subject to a fixation procedure followed by a split-pool combinatorial barcoding protocol in 96 well format using the Evercode Kits. The barcoded cDNAs were equally dispersed into 8 indexed sub-libraries and were submitted for high throughput sequencing analysis.

value: pancreas

value: primary acinar


title: scRNA_sublibrary_6

description:
Library name: scRNA_sublibrary_6
Each sub-library contain a subset of cells from 5 different samples including WT_organoid, KPT_organoid, KPTN_organoid, KPT_tumor and KPTN_tumor samples


title: brain-APOE4-F-1


title: XP1139c8_73

description: Library name: XP1139c8_73


title: scRNA_sublibrary_8

description:
Library name: scRNA_sublibrary_8
Each sub-library contain a subset of cells from 5 different samples including WT_organoid, KPT_organoid, KPTN_organoid, KPT_tumor and KPTN_tumor samples


title: brain-APOE4-M-1


title: scRNA_sublibrary_5

description:
Library name: scRNA_sublibrary_5
Each sub-library contain a subset of cells from 5 different samples including WT_organoid, KPT_organoid, KPTN_organoid, KPT_tumor and KPTN_tumor samples


title: XP1169c13_V1

description: Library name: XP1169c13_V1


title: brain-APOE3-F-2


title: scRNA_sublibrary_3

description:
Library name: scRNA_sublibrary_3
Each sub-library contain a subset of cells from 5 different samples including WT_organoid, KPT_organoid, KPTN_organoid, KPT_tumor and KPTN_tumor samples


title: scRNA_sublibrary_4

description:
Library name: scRNA_sublibrary_4
Each sub-library contain a subset of cells from 5 different samples including WT_organoid, KPT_organoid, KPTN_organoid, KPT_tumor and KPTN_tumor samples


title: brain-APOE3-M-1


title: scRNA_sublibrary_1

description:
Library name: scRNA_sublibrary_1
Each sub-library contain a subset of cells from 5 different samples including WT_organoid, KPT_organoid, KPTN_organoid, KPT_tumor and KPTN_tumor samples


title: brain-APOE3-F-3


title: brain-APOE3-M-2


title: XP945c13_V1 [ATAC-seq]

description: Library name: XP945c13_V1

data_processing:
Fastq files were aligned to the human genome hg38 and mm10 using BWA(0.7.17-r1188), for both single eng and pair end sequencing runs.
Reads aligned to mm10 were filtered using XenofilteR.
Narrow peaks were called by MASC2 (v2.2.7.1)
Assembly: hg38
Supplementary files format and content: bw and peak file for each sample.

extract_protocol:
For ATAC-seq, the tumors were finely chopped, washed, and were lysed using ice-cold lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin). Nuclei were washed again in cold lysis buffer without NP40 and Digitonin and then incubated with Tn5 transposase mixture (2.5µl of Tn5, 1% Digitonin, 10% Tween-20 in 1x TD buffer) at 370C for 30 min in a Thermomixer (Eppendorf). DNA was purified using the DNA Clean and Concentrator-5 kit (Zymo Research) and used in a PCR with Nextera adapters.
ATAC-seq libraries were constructed using purified DNA and Nextera DNA Indexes by PCR.


title: brain-APOE3-F-1


title: brain-APOE3-M-3


title: XP945c13_P2 [ATAC-seq]

description: Library name: XP945c13_P2


title: brain-APOE2-M-3


title: neutrophil, DSP-1001660011514-G-A04


title: brain-APOE2-M-2


title: XP899VB2 [ATAC-seq]

description: Library name: XP899VB2


title: brain-APOE2-M-1


title: XP899c9_P2 [ATAC-seq]

description: Library name: XP899c9_P2


title: XP771bc27_V1 [ATAC-seq]

description: Library name: XP771bc27_V1


title: XP490c2_P1 [ATAC-seq]

description: Library name: XP490c2_P1


title: scRNA_sublibrary_2

description:
Library name: scRNA_sublibrary_2
Each sub-library contain a subset of cells from 5 different samples including WT_organoid, KPT_organoid, KPTN_organoid, KPT_tumor and KPTN_tumor samples


title: XP374V [ATAC-seq]

description: Library name: XP374V


title: XP771bc27_P2 [ATAC-seq]

description: Library name: XP771bc27_P2


title: XP490c2_V1 [ATAC-seq]

description: Library name: XP490c2_V1


title: brain-APOE2-F-1


title: brain-APOE2-F-2


title: brain-mApoe-M-4

value: mApoe


title: brain-APOE2-F-3


title: brain-mApoe-M-3


title: brain-mApoe-M-2


title: XP296c4_V1 [ATAC-seq]

description: Library name: XP296c4_V1


title: brain-mApoe-M-1


title: brain-mApoe-F-2


title: brain-mApoe-F-3


title: XP296c4_P1 [ATAC-seq]

description: Library name: XP296c4_P1


title: XP1631c10_P2 [ATAC-seq]

description: Library name: XP1631c10_P2


title: brain-mApoe-F-1


title: XP1631c10_V1 [ATAC-seq]

description: Library name: XP1631c10_V1


title: XP1487V [ATAC-seq]

description: Library name: XP1487V


title: XP1487P [ATAC-seq]

description: Library name: XP1487P


title: SCC cell, Itga6 high CD80 positive, replicate 1

description: Library name: a6Hi_CD80Pos_1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutdapt (v3.2)
Genes were counted by using kallisto (v0.44.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: skin SCC

extract_protocol:
RNA was harvested using zymo Quick-RNA Microprep Kit
RNA libraries for RNA-seq were prepared using NEBNext® Single Cell/Low Input RNA Library Prep Kit following manufacturer's protocols.

value: skin SCC


title: XP1087c7_P1 [ATAC-seq]

description: Library name: XP1087c7_P1


title: XP1152c8_P2 [ATAC-seq]

description: Library name: XP1152c8_P2


title: SCC cell, Itga6 low CD80 negative, replicate 2

description: Library name: a6Low_CD80neg_2


title: SCC cell, Itga6 high CD80 positive, replicate 2

description: Library name: a6Hi_CD80Pos_2


title: SCC cell, Itga6 low CD80 negative, replicate 1

description: Library name: a6Low_CD80neg_1


title: XP1087c7_V2a [ATAC-seq]

description: Library name: XP1087c7_V2a


title: XP1152c8_V2 [ATAC-seq]

description: Library name: XP1152c8_V2


title: XP374P [ATAC-seq]

description: Library name: XP374P


title: immune cells, DMBA/TPA induced tumor, sub library 8

data_processing:
The raw FASTQ ﬁles were processed by spipe.v1.1.1(Parse Biosciences) using mm10 as a reference.
Assembly: mm10
Supplementary files format and content: tsv files and mtx file

source_name: CD45+ immune cell

extract_protocol:
Tumors were collected 2 days after last dose of immunotherapy and total CD45 positive immune cells were sorted. Immediately after sorting, the sorted immune cells were fixed with Evercode Cell Fixation v2 (Parse Biosciences).
the fixed cells were prepared using Evercode WT v2 kit (Parse Biosciences) according to manufacturer’s instructions. Input cell numbers and volumes were calculated using WT_100K_Sample_Loading_Table_V1.3.0 (Parse Biosciences). All the samples were processed together with Evercode WT v2 kit (Parse Biosciences) and 8 sub-libraries were generated. The quality of sub-libraries was checked by the Agilent Tape Station system (Agilent) and sequenced by Illumina NovaSeqX.

value: CD45+ immune cell


title: immune cells, DMBA/TPA induced tumor, sub library 7


title: immune cells, DMBA/TPA induced tumor, sub library 6


title: XP1059c7_P1 [ATAC-seq]

description: Library name: XP1059c7_P1


title: XP1059c7_V1 [ATAC-seq]

description: Library name: XP1059c7_V1


title: immune cells, DMBA/TPA induced tumor, sub library 3


title: HCCV47 [ATAC-seq]

description: Library name: HCCV47

source_name: Liver tumor

value: Liver tumor


title: immune cells, DMBA/TPA induced tumor, sub library 4


title: HCCV50 [ATAC-seq]

description: Library name: HCCV50


title: XP289c20_42 [ATAC-seq]

description: Library name: XP289c20_42


title: HCCP46 [ATAC-seq]

description: Library name: HCCP46


title: XP945c9_33 [ATAC-seq]

description: Library name: XP945c9_33


title: immune cells, DMBA/TPA induced tumor, sub library 2


title: Sox2Hi SCC tumor neutrophil, treated, replicate 2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutdapt (v3.2)
Genes were counted by using kallisto (v0.44.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene count values for each Sample

source_name: neutrophil

tag: graft

value: Sox2Hi SCC tumor neutrophil

value: treated


title: Sox2Hi SCC tumor neutrophil, treated, replicate 1


title: XP1676c4_88 [ATAC-seq]

description: Library name: XP1676c4_88


title: XP1676c3_51 [ATAC-seq]

description: Library name: XP1676c3_51


title: XP289c19_43 [ATAC-seq]

description: Library name: XP289c19_43


title: Sox2low control  tumor neutrophil, treated, replicate 2

value: Sox2low control  tumor neutrophil


title: XP165c13_95 [ATAC-seq]

description: Library name: XP165c13_95


title: Sox2Hi SCC tumor neutrophil, naïve, replicate 1

value: naïve


title: XP1657dc3_48 [ATAC-seq]

description: Library name: XP1657dc3_48


title: Sox2low control  tumor neutrophil, treated, replicate 1

value: neutrophil


title: Sox2Hi SCC tumor neutrophil, naïve, replicate 2


title: XP1139c8_73 [ATAC-seq]

description: Library name: XP1139c8_73

value: Kidney tumor


title: XP143c13_66 [ATAC-seq]

description: Library name: XP143c13_66


title: Sox2low control  tumor neutrophil, naïve, replicate 3


title: Sox2low control  tumor neutrophil, naïve, replicate 2


title: immune cells, DMBA/TPA induced tumor, sub library 5


title: Sox2low control  tumor neutrophil, naïve, replicate 1


title: PDVC57 cell, Sox2 overexpression, replicate 2

value: Sox2 overexpression


title: PDVC57 cell, Sox2 overexpression, replicate 1


title: immune cells, DMBA/TPA induced tumor, sub library 1


title: PDVC57 cell, Sox2 KO, replicate 2

value: Sox2 KO


title: Sox2Hi SCC tumor neutrophil, naïve, replicate 3


title: PDV cell, IgG, replicate 1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutdapt (v3.2)
The raw sequencing reads were aligned using Bowtie2 (v2.3.4.3) to the mm10 reference genome (UCSC). The aligned reads were de-duplicated with Picard (v.2.8.1)
bigWig files were generated using the deepTools. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: Cut&Run

source_name: PDV cell

extract_protocol:
Cells were fixed with 1% formaldehyde for 1min. After quenching, cells were permeabilized and immobilized onto Concanavalin-A beads and incubated overnight with IgG or Sox2 antibody.
Cut & Run libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to the manufacture’s protocol. Libraries were validated using the Fragment Analyzer.

value: PDV cell

tag: antibody

value: IgG


title: PDV cell, Sox2 antibody, replicate 1

tag: cell line

value: Sox2 antibody


title: PDV cell, IgG, replicate 2


title: PDV cell, Sox2 antibody, replicate 2


title: XP1139c9_60 [ATAC-seq]

description: Library name: XP1139c9_60

value: Treatment not applicable


title: H358_AMGR_T1R2

data_processing:
Preprocessing of raw sgRNA reads is done by adapter removal and alignment to the plasmid library (CRISPR.v2).
Raw reads are processed using Cutadapt to remove sequencing adapters and trim the reads to 20 bp.
Trimmed reads are then mapped to the plasmid library and sgRNAs counts generated using MAGeCK.
For downstream analysis, we used edgeR package to normalize the libraries across samples.
Specifically, using the control probes as reference, we calculated the normalization factors and quantified log-scaled counts-per-million (CPM) values.
Similarly, differential expression analysis is done using the quasi-likelihood framework in edgeR package.
Furthermore, in order to aggregate sgRNA level statistics to gene level, we used the ‘camera’ to account for inter-sgRNA correlations.
Assembly: Raw reads were processed using Cutadapt to remove sequencing adapters and trim the reads to  20 bp. Trimmed reads were then mapped to the plasmid library, and sgRNAs counts were generated using MAGeCK .
Supplementary files format and content: For downstream analysis, we used the edgeR package to normalize the libraries across samples. Specifically, using the control probes as references, we calculated the normalization factors and quantified log-scaled counts-per-million values.
Supplementary files format and content: Similarly, differential expression analysis was done using the quasi-likelihood framework in the edgeR package. Furthermore, to aggregate sgRNA level statistics to gene level, we used the camera to account for inter-sgRNA correlations.The gene-aggregation test returned a list of genes with their corresponding estimated false discovery rates (FDRs) in the case of either a loss of function or gain of function. A stringent cutoff of FDR <0.15 was considered to define negatively or positively enriched genes in the screen.
Library strategy: CRISPR

source_name: Lung

growth_protocol: H358 cells were chronically treated with sotorasib starting from their IC50s.

extract_protocol:
A pooled kinome-wide CRISPR-Cas9 knockout screen was carried out using a lentiviral single guide RNA (sgRNA) library that contained 3,052 unique sgRNAs targeting 763 human kinases.The sgRNAs incorporated in the cells were amplified from genomic DNA and subjected to sequencing.
After transduction at a low multiplicity of infection (MOI = 0.3) followed by selection with puromycin, one-third of the infected cells were harvested as the baseline (T0) for sequencing, and the rest of the cells were continuously cultured for additional 2 weeks to allow gene editing (T1)

treatment_protocol: The treatment dose was doubled in every next passage for 4-6 passages and then maintained at constant dose of 400 nM. The resistant line was then designated as Sotorasib-R H358.

value: Lung

value: Sotorasib-R H358 Addgene pooled libraries (#75314)_Replicate 2


title: PDVC57 cell, Sox2 overexpression, replicate 3


title: H358_Parental_T1R2

value: H358-P Addgene pooled libraries (#75314)_Replicate 2


title: H358_AMGR_T1R1

value: Sotorasib-R H358 Addgene pooled libraries (#75314)_Replicate 1


title: PDVC57 cell, Sox2 KO, replicate 3


title: H358_Parental_T1R1

value: H358-P Addgene pooled libraries (#75314)_Replicate 1


title: PDVC57 cell, Sox2 KO, replicate 1


title: Sotorasib-R H358 (H358-AMGR) T0 Reference

value: Sotorasib-R H358


title: lung, ECV18W, 3 months, SAMPLE 56

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

hyb_protocol: Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarrays were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: lung

label_protocol: manufacturer's instructions

extract_protocol: Total RNA extracted using manufacturer's instructions

value: lung

tag: time

value: 3 months


title: lung, CS, 3 months, SAMPLE 59

value: CS


title: lung, CS, 3 months, SAMPLE 48


title: lung, ECV18W, 3 months, SAMPLE 54


title: lung, Control, 3 months, SAMPLE 49

value: Control


title: lung, CS, 3 months, SAMPLE 46


title: H3K4me3_DMSO_1

data_processing:
Fastq files of pair-end reads were mapped with Bowtie 1.1.2  using parameters -k 1 -m 1 -e 70 -l 51 --best to the human reference genome hg19.
HOMER 4.8.2 was used to identify peaks for each sample against the background using default parameters.
Occupancy profiles were generated by HOMER in bedGraph format and converted to bigWig format using bedGraphToBigWig provided by UCSC.
Genome_build: hg19
Supplementary_files_format_and_content: peak calls in bed format;  bigwig files for occupancy profile.

source_name: OCI-Ly1 Cells

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature before termination with 0.125 M glycine. Cells were then lysed in ChIP buffer (0.6% SDS, 10 mM EDTA, and 50 mM Tris-HCl, pH 8.1) and cross-linked chromatin was sonicated to obtain DNA fragments of 300–800 bp. Chromatin was then centrifuged (10 min, 4°C, 13,000 rpm) and the supernatant was diluted 6-fold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8, and 167 mM NaCl) with protease inhibitors (Roche Diagnostics). Diluted chromatin was incubated with 5 μg of primary antibody overnight at 4C under agitation. Antibodies were pelleted using 50 μL of dynabeads (ThermoFisher Scientific). Beads were sequentially washed once with the ChIP wash buffer 1 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 150 mM NaCl), the ChIP wash buffer 2 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8, and 500 mM NaCl), the ChIP wash buffer 3 (0.25 M LiCl, 1% IGEPAL-CA630, 1% deoxycholic acid, 1 mM EDTA, 10 mM Tris pH 8), and finally the ChIP wash buffer 4 (10 mM Tris-HCl, 1 mM EDTA). Chromatin was eluted using ChIP Elution Buffer (1% SDS, 100mM NaHCO3). The cross-link between protein and DNA was reversed by heat incubation (65°C, overnight), and proteins were then digested with proteinase K. DNA was recovered by phenol-chloroform extraction and ethanol precipitation in presence of 20 µg of glycogen (Sigma Aldrich).
ChIP-seq libraries were prepared using NEBNext DNA library preparation reagents (E6040); the protocol and reagents concentrations described in the Illumina Multiplex ChIP-seq DNA sample Prep Kit. Libraries were indexed using a single indexed PCR primer. Libraries were quantified by Qubit (Invitrogen), and sequenced using a HiSeq 2000 (Illumina) to generate 50 bp single end reads.

treatment_protocol: Indicated concentration of JIB-04 were added to the cells for 48 hours and cells were processed for chip-seq

value: DLBCL cell line

tag: chip-antibody

value: EpiGentek A-4033-050

value: DMSO


title: lung, ECV30W, 3 months, SAMPLE 53


title: lung, ECV30W, 3 months, SAMPLE 50


title: lung, ECV18W, 3 months, SAMPLE 45


title: H358-Parental T0 Reference


title: lung, Control, 3 months, SAMPLE 58


title: lung, ECV30W, 3 months, SAMPLE 55


title: lung, CS, 6 Months, SAMPLE 44

value: 6 Months


title: lung, ECV18W, 3 months, SAMPLE 51


title: H3K4me3_DMSO_2


title: lung, CS, 3 months, SAMPLE 57


title: lung, Control, 6 Months, SAMPLE 43


title: lung, ECV18W, 6 Months, SAMPLE 42


title: lung, Control, 3 months, SAMPLE 47


title: H3K4me3_500_2


title: H3K4me3_150_1


title: lung, CS, 6 Months, SAMPLE 38


title: H3K27Ac_DMSO_2

value: Active Motif, 39135


title: H3K27Ac_500_2


title: H3K27Ac_150_2


title: lung, Control, 6 Months, SAMPLE 39


title: lung, ECV18W, 6 Months, SAMPLE 41


title: lung, Control, 3 months, SAMPLE 52


title: H3K27Ac_150_1


title: H3K27Ac_DMSO_1


title: H3K27Ac_500_1


title: Input_DMSO_3

value: none (input)


title: Input_DMSO_1


title: H3K4me3_500_1


title: H3K4me3_150_2


title: Input_500_2


title: Input_DMSO_2


title: lung, Control, 6 Months, SAMPLE 37


title: Input_500_1


title: lung, ECV18W, 6 Months, SAMPLE 33


title: lung, ECV30W, 3 months, SAMPLE 31


title: lung, Control, 3 months, SAMPLE 28


title: Input_150_1


title: lung, ECV30W, 6 Months, SAMPLE 40


title: H3K9me3_DMSO_2

value: Abcam, Ab8898


title: NT2 cells, HYDIN2 knockdown, rep2

city: Pune

first: Yash

middle: Lahu

last: Kuber

state: Maharashtra

address: Nccs, inside pune university, ganeshkhind

department: Biotechnology

country: India

institute: National center for cell science

description: Library name: Sample 3

data_processing:
The raw reads were filtered using Trimmomatic for quality scores and adapters. Filtered reads were aligned to the Human genome (hg38) using STAR aligner to quantify reads mapped to each transcript. Total number of uniquely mapped reads were counted using feature counts. The uniquely mapped reads were then subjected to differential gene expression using DeSeq2.
Assembly: GRCh38
Supplementary files format and content: Delimited text file with read counts of all samples.

growth_protocol: NT2 cells were grown in Dulbecco's Modified Essential medium supplemented with 10% FBS, maintained in humidified incubator at 37C with 5% CO2.

extract_protocol:
RNA was harvested using Rneasy Mini Kit (cat #74104).
A modified NEBNext RNA ultra II directional protocol is used to prepare the libraries for total RNA sequencing.

value: human embryonal carcinoma

value: HYDIN2 knockdown


title: NT2 cells, HYDIN2 knockdown, rep3

description: Library name: Sample 4


title: lung, CS, 6 Months, SAMPLE 34


title: lung, CS, 3 months, SAMPLE 29


title: lung, CS, 3 months, SAMPLE 27


title: lung, ECV18W, 6 Months, SAMPLE 35


title: lung, Control, 3 months, SAMPLE 26


title: H3K9me3_DMSO_1


title: lung, Control, 6 Months, SAMPLE 32


title: lung, ECV18W, 3 months, SAMPLE 30


title: lung, ECV30W, 6 Months, SAMPLE 36


title: NT2 cells, empty vector

description: Library name: Sample 1

value: Wild type