title: PV neurons, PV-Cre lsl-eGFP-GluA2, biol rep 7

city: Baltimore

first: Ingie

last: Hong

address: Neuroscience, 725 North Wolfe Street, Hunterian 1001

department: The Solomon H. Snyder Department of Neuroscience

institute: Johns Hopkins Medical Institute

data_processing:
We processed RNA-seq reads with bcbio-nextgen v1.2.3, aligning to GRCm38 with the STAR aligner and quantifying counts per gene with Sailfish using the Ensembl annotation.
We used DESeq2 to analyze differential expression.
Assembly: GRCm38, GENCODE vM16
Supplementary files format and content: "combined_counts.csv" contains raw counts for genes, "tximport-tpm.csv" contains TPM values for genes, "all.csv" contains differential expression analysis for the two genotypes.

source_name: brain, cortex

extract_protocol:
We cut brain slices from adult PV-Cre;lsl-eGFP and PV-Cre;lsl-eGFP-GluA2 mice (113.1 ± 11.6 days old) in NMDG cutting solution + Trehalose and diced them into small pieces <1 mm3. Extracellular proteins were digested with pronase (2 mg/ml; 8 U/µl) at 34-37°C, after which the slice pieces were fixed in 4% PFA in PBS (with 0.1 U/ml RNase inhibitor, Promega) for 15 mins and dissociated into single cells through careful trituration. We filtered the single cells through a 40 μm filter, labeled them with the cell-permeable nuclear dye DRAQ5 (1:1,000 dilution) to identify nuclei-containing cells, and then subjected them to FACS. DRAQ5+/GFP+ or DRAQ5+/GFP-GluA2+ cells were sorted, and over 20K cells were collected per mouse cortex to provide extensive coverage of low-expressing PV interneuron transcripts. We treated the fixed cells with Proteinase K before RNA extraction (RecoverAll Total Nucleic Acid Isolation Kit for FFPE, Thermo Fisher Scientific) to liberate RNA from protein-protein and protein-nucleic acid crosslinks generated by fixation.
We prepared cDNA libraries from PV-Cre;lsl-eGFP and PV-Cre;lsl-eGFP-GluA2 mouse brains (NEBNext Ultra RNA Library Prep Kit for Illumina, NEB) from RNA enriched with mRNA through bead-based polyA selection.
cDNA libraries were barcoded and sequenced together on an Illumina Hiseq 2500 sequencer, generating 150-bp paired-end reads.

treatment_protocol: Transgenic mice conditionally expressing eGFP or eGFP-GluA2 in PV intereneurons were used to test the effect of calcium-permeable AMPA receptor removal.

value: brain, cortex

value: cortical PV interneuron


title: P14_male_mct8_fl_ctrl_retina_sup_B3

status: Public on Jul 05 2024

type: SRA

city: Bethesda

first: Hong

last: Liu

state: MD

address: 9000 Rockville Pike

department: NIDDK

country: USA

institute: NIH

library_source: transcriptomic single cell

data_processing:
Libraries were multiplex sequenced. Some samples were sequenced on Illumina HiSeq2500 and 3000 Sequencers (NIDDK Genomics Facility), and some with an Illumina NovaSeq6000  (NHLBI Genomics Facility).
Single-end, 50 base reads were collected and converted by bcl2fastq (version 2) into fastq files and aligned on (GRCm38/mm10) using STAR (version 2.7.10b)
Reads were counted by FeatureCounts (subread v2.0.6) and normalized as counts per million mapped reads (cpm). To compare transcript abundance, data were quantified using Kallisto (v0.46.0) as transcripts per million reads (TPM).
Assembly: GRCm38/mm10
Supplementary files format and content: comma-separated text file includes transcripts per kilobase million for RPE and counts-per-million for retina and single-cone sample

molecule: total RNA

organism: Mus musculus

source_name: retina

extract_protocol:
For single cell analyses, cones labeled with a Thrb2Cre driver were dissociated from superior and inferior pieces of retina of Mct8-KO and control male mice at 2 months of age. Cones were isolated individually by micromanipulator to minimize contamination by rods, then examined visually for cone morphology and integrity before library construction. For dissected retina and isolated RPE cells, all samples were taken from superior and inferior areas around the vertical mid-line of the eye, then incubated in RNAprotect Cell reagent before RNA extraction with Qiagen RNeasy kit.
Single cell RNA-seq library library construction with SMART-Seq v4 Ultra Low Input RNA kit and ThruPLEX DNA-Seq Kit, purified RNA from different retina and RPE samples were constructed into RNA-seq libraries with SMARTer stranded total RNA sample prep kit and ThruPLEX DNA-Seq Kit.

tag: strain

tag: tissue

value: retina

tag: cell type

tag: genotype

value: Mct8 fl/y

tag: age


title: P14_male_mct8_fl_cre_cko_sup_A1

value: Mct8 fl/y;Best1cre


title: PV neurons, PV-Cre lsl-eGFP, biol rep 8

library_source: transcriptomic

molecule: polyA RNA

tag: treatment

value: eGFP (control)


title: Sample38

city: Aurora

first: Sunita

last: Sharma

state: CO

address: 13001 East 17th Place

department: Anschutz Campus - Sch of Med - Pulmonary Sciences

institute: University of Colorado - Anschutz Medical Campus

data_processing:
examined the quality of the sequencing reads (FastQC) and removed adaptors and low quality base calls (Cutadapt).
Sequences were aligned to the human genome (GENCODE GRCh37)
Read counts overlapping each gene were reported using STAR
Removed genes detected with 0 reads in greater than or equal to 75% of samples or with a range of reads less than or equal to 100.
Corrected for unwanted technical effects using two normalization factors estimated using Removal of Unwanted Variance using Residuals (RUVr) using RUVSeq (ver.
Assembly: GENCODE GRCh37
Supplementary files format and content: Filename: seq_express_filter.csv; Format: Raw gene counts aligned to the genome and filtered to remove those with 0 reads in greater than or equal to 75% of samples or with a range of reads less than or equal to 100.
Supplementary files format and content: Filename: seq_express_norm.csv; Format: Normalized gene counts from DESeq2 Model adjusting for vape status, age, sex, recruitment center, and two normalization (RUVr) factors.

organism: Homo sapiens

source_name: Nasal-epithelial

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit (Qiagen, Valencia, CA) and sequenced using Illumina chemistry (Nugen Universal Plus mRNASEQ kit [Redwood City, CA]; NovaSeq6000 [Illumina: San Diego, CA]) through the Genomics and Microarray Core at the University of Colorado Anschutz Medical Campus.
Sequencing libraries will be prepared using the standard TruSeq RNA Sample Prep Kit v2 Protocol (Illumina, San Diego, CA).

value: Nasal-epithelial

tag: vape 6mo_lab

tag: Sex

value: Female

tag: age (yrs)

tag: ruv k1

tag: ruv k2


title: PV neurons, PV-Cre lsl-eGFP, biol rep 9


title: PV neurons, PV-Cre lsl-eGFP-GluA2, biol rep 6


title: Sample41


title: PV neurons, PV-Cre lsl-eGFP-GluA2, biol rep 2


title: P14_male_mct8_fl_ctrl_retina_sup_A1


title: Sample39


title: PV neurons, PV-Cre lsl-eGFP, biol rep 6


title: PV neurons, PV-Cre lsl-eGFP-GluA2, biol rep 1


title: PV neurons, PV-Cre lsl-eGFP, biol rep 7


title: PV neurons, PV-Cre lsl-eGFP-GluA2, biol rep 5


title: Sample37


title: PV neurons, PV-Cre lsl-eGFP-GluA2, biol rep 4


title: P14_female_mct8_het_cre_cko_retina_inf_D8

value: Mct8 fl/null;Best1cre


title: PV neurons, PV-Cre lsl-eGFP, biol rep 5


title: PV neurons, PV-Cre lsl-eGFP, biol rep 4


title: P14_female_mct8_het_cre_cko_retina_inf_D7


title: PV neurons, PV-Cre lsl-eGFP, biol rep 3


title: PV neurons, PV-Cre lsl-eGFP, biol rep 2


title: Sample36


title: Sample34


title: 2m_cone_KO_inf_43

value: inferior-cone

value: 2 month


title: P14_male_mct8_fl_ctrl_retina_sup_A2


title: P14_female_mct8_het_cre_cko_retina_inf_D6


title: PV neurons, PV-Cre lsl-eGFP, biol rep 1


title: 2m_cone_KO_inf_42


title: 2m_cone_KO_inf_41


title: PV neurons, PV-Cre lsl-eGFP-GluA2, biol rep 3


title: Sample33


title: Sample32

value: Male


title: P14_female_mct8_het_cre_cko_retina_inf_D4


title: 2m_cone_KO_inf_39


title: P14_female_mct8_het_cre_cko_retina_inf_D5


title: 2m_cone_KO_inf_38


title: Sample31


title: 2m_cone_KO_inf_37


title: Sample30


title: 2m_cone_KO_inf_40


title: 2m_cone_KO_inf_35


title: Sample29


title: 2m_cone_KO_inf_34


title: Sample28


title: P14_female_mct8_het_cre_cko_retina_inf_A1


title: 2m_cone_KO_inf_33


title: 2m_cone_KO_inf_32


title: P14_female_mct8_het_cre_cko_retina_inf_A2


title: 2m_cone_KO_inf_36


title: 2m_cone_KO_inf_31


title: 2m_cone_KO_inf_30


title: P14_female_mct8_het_ctrl_retina_inf_D5

value: Mct8 fl/null


title: 2m_cone_KO_inf_29


title: Sample26


title: Sample27


title: 2m_cone_KO_inf_26


title: Sample25


title: P14_female_mct8_het_ctrl_retina_inf_D4


title: 2m_cone_KO_inf_25


title: P14_female_mct8_het_cre_cko_retina_inf_B3


title: 2m_cone_KO_inf_24


title: 2m_cone_KO_inf_27


title: 2m_cone_KO_inf_23


title: Sample24


title: P14_female_mct8_het_ctrl_retina_inf_A2


title: P14_female_mct8_het_ctrl_retina_inf_D3


title: P14_female_mct8_het_ctrl_retina_inf_A1


title: 2m_cone_KO_sup_42

value: superior-cone


title: 2m_cone_KO_inf_20


title: P14_female_mct8_het_cre_cko_retina_sup_D8


title: P14_female_mct8_het_cre_cko_retina_sup_D7


title: 2m_cone_KO_sup_41


title: P14_female_mct8_het_ctrl_retina_inf_D6


title: 2m_cone_KO_inf_21


title: 2m_cone_KO_inf_28


title: Sample22


title: Sample21


title: 2m_cone_KO_sup_40


title: Sample19


title: 2m_cone_KO_sup_39


title: Sample18


title: Sample20


title: 2m_cone_KO_sup_34


title: P14_female_mct8_het_cre_cko_retina_sup_D6


title: 2m_cone_KO_sup_36


title: Sample17


title: 2m_cone_KO_sup_33


title: 2m_cone_KO_sup_37


title: 2m_cone_KO_sup_35


title: Sample23

description: This sample was removed from the study due to inability to determine vape status within the previous 6 months


title: 2m_cone_KO_sup_38


title: P14_female_mct8_het_cre_cko_retina_sup_C3


title: 2m_cone_KO_inf_22


title: 2m_cone_KO_sup_32


title: 2m_cone_KO_sup_31


title: P14_female_mct8_het_cre_cko_retina_sup_D4


title: Sample15


title: 2m_cone_KO_sup_29


title: P14_female_mct8_het_cre_cko_retina_sup_D5


title: Sample14


title: 2m_cone_KO_sup_27


title: P14_female_mct8_het_ctrl_retina_sup_D6


title: P14_female_mct8_het_cre_cko_retina_sup_A2


title: P14_female_mct8_het_cre_cko_retina_sup_A1


title: 2m_cone_KO_sup_30


title: P14_female_mct8_het_ctrl_retina_sup_D5


title: Sample16


title: 2m_cone_KO_sup_24


title: Sample12


title: 2m_cone_KO_sup_23


title: Sample11


title: 2m_cone_KO_sup_28


title: P14_female_mct8_het_ctrl_retina_sup_D4


title: P14_female_mct8_het_ctrl_retina_sup_A3


title: 2m_cone_ctrl_inf_44


title: 2m_cone_KO_sup_26


title: 2m_cone_ctrl_inf_43


title: Sample13


title: 2m_cone_KO_sup_25


title: P14_female_mct8_het_ctrl_retina_sup_A2


title: 2m_cone_ctrl_inf_40


title: Sample10


title: 2m_cone_ctrl_inf_42


title: 2m_cone_ctrl_inf_38


title: 2m_cone_ctrl_inf_39


title: 2m_cone_KO_sup_21


title: Sample09


title: 2m_cone_ctrl_inf_37


title: RPE_sup_4

source_name: RPE

value: RPE

value: Superior-RPE

value: wt

value: 8 month


title: Sample05


title: 2m_cone_ctrl_inf_34


title: 2m_cone_KO_sup_22


title: RPE_sup_2

value: 6 month


title: 2m_cone_ctrl_inf_41

value: retina


title: 2m_cone_ctrl_inf_33


title: 2m_cone_ctrl_inf_32


title: Sample08


title: RPE_sup_5

value: 9 month


title: 2m_cone_ctrl_inf_30


title: Sample02


title: Sample07


title: 2m_cone_ctrl_inf_27


title: 2m_cone_ctrl_inf_36


title: RPE_sup_3

value: 7 month


title: Sample06


title: 2m_cone_ctrl_sup_42


title: 2m_cone_ctrl_inf_35


title: 2m_cone_ctrl_sup_41


title: 2m_cone_ctrl_inf_31


title: Sample04


title: Sample03


title: RPE_inf_5

value: inferior-RPE

value: 4 month


title: 2m_cone_ctrl_sup_39


title: 2m_cone_ctrl_sup_38


title: YT22

city: Xuzhou

first: Yang

last: Su

address: No. 209, Tongshan Road

department: Cancer Institute

country: China

institute: Xuzhou Medical University

data_processing:
CLC Genomics Workbench v11.0.1
FPKM data

source_name: tumor tissue

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: tumor tissue

tag: disease state

value: Gastric cancer

tag: tnm

value: IIIA

tag: os(day)

tag: death

value: No

tag: gender

value: male


title: 2m_cone_KO_inf_18

value: inferior-cone

value: 2 month


title: 2m_cone_ctrl_inf_29


title: 2m_cone_ctrl_inf_28


title: YT21

value: IIB


title: RPE_inf_4

value: RPE

value: 3 month


title: Sample01

value: Nasal-epithelial

value: Female


title: 2m_cone_KO_inf_17

value: retina


title: RPE_inf_2

value: wt


title: 2m_cone_ctrl_sup_37

value: superior-cone


title: 2m_cone_ctrl_sup_35


title: RPE_inf_3

value: inferior-RPE


title: YT23

value: IIIC

value: Yes


title: 2m_cone_ctrl_sup_34


title: 2m_cone_KO_inf_19


title: 2m_cone_ctrl_sup_40


title: YT19

value: tumor tissue

value: Gastric cancer

value: IIIB


title: 2m_cone_KO_inf_16


title: 2m_cone_ctrl_sup_31


title: 2m_cone_ctrl_sup_43


title: 2m_cone_ctrl_sup_36


title: YT20

value: IB

value: No

value: male


title: 2m_cone_KO_inf_15

value: inferior-cone

value: 2 month


title: 2m_cone_ctrl_sup_33


title: YT18

value: IIB


title: 2m_cone_KO_inf_14


title: YT17


title: YT15

value: IIA

value: female


title: 2m_cone_ctrl_sup_32

value: retina


title: 2m_cone_ctrl_sup_28


title: 2m_cone_KO_inf_13


title: 2m_cone_ctrl_sup_26


title: YT14


title: CAL27_Control screen

city: Hubei

first: Yang-Ying-Fan

last: Feng

address: Luonan stress

institute: wuhan university

description: sgControl

library_source: genomic

data_processing:
The guide DNA region was PCR-amplified and sequenced using Illumina HiSeq 2500 single-read sequencing for 50 cycles. Quality analysis were perfromed using FastQC (v0.12). Adapter trimming and data cleaning were performed with Fastp (v0.23.4). MAGeCK (v0.5.9.5) was applied to identify hits from the clean data with default parameters, while the RRA algorithm (v0.5.9) compared differences between PD-L1 KO and its control screen hits.
Assembly: None
Supplementary files format and content: CP_all.count_normalized.txt: txt file contains normalized counts of library targets.
Supplementary files format and content: sgCD274_vs_sgControl.gene_summary.txt: tab-delimited file contains differential gene essentiality calculated by Mageck RRA.

molecule: genomic DNA

source_name: epithelial cell

growth_protocol: Human HNSCC cell lines CAL27 were cultured in DMEM supplemented with 10% fetal bovine serum and 100 U/mL penicillin, and 100 mg/mL streptomycin. Cells were cultured under standard conditions at 37 °C with 5% CO2.

extract_protocol:
genomic DNA was extracted using the QIAamp Blood Maxi kit (Qiagen #51194)
libraries were constructed following the previously described method in Shalem O et al Science 2014

treatment_protocol: The Human CRISPR Knockout Pooled Library (Brunello) (#73178, Addgene), comprising 76,441 sgRNAs targeting 19,114 genes, was incorporated into lentiviral particles, and introduced into CAL27 cells at a low multiplicity of infection (MOI < 0.3). 20 million cells of each cell line (Control and PD-L1 KO) were utilized and subjected to 2 days of selection with 10 mg/ml puromycin. Post-puromycin selection, the cell lines underwent ten subcultures, followed by the collection of cells and extraction of genomic DNA.

value: epithelial cell

tag: cell line

value: cell line

value: WT


title: 2m_cone_KO_inf_11

tag: strain


title: 2m_cone_ctrl_sup_25

tag: tissue

value: superior-cone


title: 2m_cone_KO_inf_10

tag: cell type


title: P14_female_mct8_het_ctrl_retina_sup_A1

tag: genotype

value: Mct8 fl/null


title: 2m_cone_ctrl_sup_30

tag: age


title: YT13

value: tumor tissue

value: IIIA


title: CAL27_PD-L1 KO screen

value: PD-L1 knockout


title: 2m_cone_ctrl_sup_23


title: YT12

value: Gastric cancer

value: Yes


title: 11-2D-iEC-rep2

city: Boston

first: Allen Chilun

last: Luo

state: Massachusetts

address: 300 Longwood Ave

department: Cardiac Surgery

institute: Boston Children's Hospital

data_processing:
Sequencing data were processed using Illumina's bcl2fastq 2.17 software for file conversion and de-multiplexing. Quality control, adapter trimming, and read alignment to the hg38 genome were conducted using Trimmomatic v.0.36 and STAR aligner. Gene expression quantification was performed with feature Counts (Subread package v.1.5.2). Differential expression analysis utilized DESeq2, identifying differentially expressed genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1. Gene ontology and principal component analysis were carried out to explore biological processes and sample variance, respectively.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text files include count values for all samples (bulk RNA-seq)

source_name: Cell line

extract_protocol:
For bulk RNA-seq, the total RNA was extracted using the Qiasymphony RNA kit (Qiagen, cat. no. 931636).
For bulk RNA-seq, sequencing libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, cat. no. E7770S), including mRNA enrichment, cDNA synthesis, and PCR enrichment. Library quality and quantification were assessed using Agilent TapeStation and Qubit 2.0 Fluorometer, respectively. Sequencing was performed on an Illumina HiSeq 2500 platform in a 2 × 150 paired-end mode.

value: Cell line

value: Doxycycline-inducible ETV2 endothelial cells

tag: treatment

value: Doxycycline-inducible ETV2


title: 2m_cone_KO_inf_08

value: inferior-cone

value: 2 month


title: 2m_cone_ctrl_sup_24


title: YT11

value: No

value: male


title: 2m_cone_KO_inf_09

value: retina


title: 2m_cone_ctrl_sup_21


title: YT10

value: IIIB


title: 2m_cone_ctrl_sup_22


title: 2m_cone_KO_inf_07


title: 2m_cone_ctrl_sup_27


title: 2m_cone_KO_inf_12


title: 9-S1ETV2

value: modRNA-inducible ETV2 endothelial cells

value: modRNA-inducible ETV2


title: 2m_cone_KO_inf_06


title: MDA-MB-231GlnIND cells, replicate 3

city: COLD SPRING HARBOR

first: Yijian

last: Qiu

state: NY

address: 1 BUNGTOWN RD

department: Cancer center

institute: COLD SPRING HARBOR LABS

data_processing:
After the final libraries passed quality control through Qubit and Bioanalyzer, the samples were pooled and subjected to sequencing as paired-end 76 cycles using a high output NextSeq500 run.
RNA-seq raw data was analyzed using the Galaxy server (https://usegalaxy.org/).
FASTQ files were uploaded to the Galaxy server and quality-checked by FastQC. Paired-ended reads were mapped to a reference genome (human hg19) and assigned to genes using the STAR and FeatureCounts functions, with the maximum number of mismatches and maximum number of alignments allowed both set to 2.
For differential gene expression analysis, combined raw read counts were used as input for DESeq under Differential expression analysis (with replicates) in the RNA-Seq section with Fit Type set to Parametric.
Assembly: hg19
Supplementary files format and content: Tab-delimited tabular files contains Feature_counts for each sample
Supplementary files format and content: Tab-delimited csv files contains a Feature_counts matrix that contains all the samples

growth_protocol: MDA-MB-231 cells were in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS). MDA-MB-231GlnIND cells were grown in glutamine-free RPMI 1640 supplemented with 10% dialyzed fetal bovine serum (dFBS).  All cells were maintained at 37°C under a 5% CO2 atmosphere.

extract_protocol:
Total RNA isolation was carried out using the RNeasy Mini Kit (QIAGEN) and QIAshredder (QIAGEN) from cells that were snap-frozen on plates.
Libraries were constructed using the Kapa mRNA HyperPrep kit (Roche Molecular Systems). The total RNA fraction was enriched for mRNA via oligo-dT beads, and the first cDNA strand was synthesized using random priming, following by the combined second strand synthesis and A-tailing. Illumina adaptor ligation was then performed, followed by library amplification utilizing high-fidelity, low bias PCR.

value: Human triple negatvie breast cancer cells

value: Glutamine-free medium (> 6 weeks)


title: 8-S1ETV2


title: 2m_cone_KO_inf_05


title: MDA-MB-231GlnIND cells, replicate 2


title: 12-2D-iEC-rep3


title: 2m_cone_ctrl_sup_29

value: superior-cone


title: MDA-MB-231GlnIND cells, replicate 1


title: 7-S1ETV2


title: 2m_cone_KO_inf_04


title: MDA-MB-231 cells, replicate 3

value: Glutamine-replete medium


title: YT5

value: tumor tissue

value: Gastric cancer

value: IIA


title: 5-ECFC

value: Cell line

value: ECFC

value: Primary endothelial cells


title: YT6

value: Yes


title: YT9

value: IA

value: No


title: 10-2D-iEC-rep1

value: Doxycycline-inducible ETV2 endothelial cells

value: Doxycycline-inducible ETV2


title: 4-ECFC


title: 2m_cone_KO_inf_02

value: retina

value: inferior-cone

value: 2 month


title: 2m_cone_KO_inf_01


title: YT3

value: IB

value: male


title: 3-hiPS-BJ273-rep3

value: Human induced pluripotent stem cell


title: 2m_cone_KO_sup_20

value: superior-cone


title: MDA-MB-231 cells, replicate 1

value: Human triple negatvie breast cancer cells

value: Glutamine-replete medium


title: 2m_cone_ctrl_sup_20


title: Hs3st3a1;3b1 DKO male_KDY-2994

first: Vaishali

middle: N

last: Patel

state: Maryland

department: NIDCR

institute: National Institutes of Health

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCh38.v25human genome using STAR v2.5.2a in single-pass mode with the following parameters: --outFilterMultimapNmax 20 –outFilterType BySJout --alignSJoverhangMin 1 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: mm10
Supplementary files format and content: Raw counts expression matrix.
Supplementary files format and content: Filtered counts expression matrix. Genes with less than 5 counts in at least one sample were removed.
Supplementary files format and content: TMM-normalized Counts Per Million expression matrix.

source_name: Kidney

extract_protocol:
Tissue lysed by sonication and RNA extracted using RNAqueous-4PCR Total RNA isolation kit
Library preparation was performed according to the manufacturer’s instructions for the Illumina Nextera XT unstranded library kit. The libraries were then pooled and sequenced on a HiSeq2500 sequencer (Illumina).

value: Kidney

value: Hs3st3a1;3b1 double knockout


title: MDA-MB-231 cells, replicate 2


title: 6-ECFC

value: Cell line

value: ECFC

value: Primary endothelial cells


title: 2m_cone_KO_sup_19


title: 2-hiPS-BJ273-rep2


title: YT2

value: tumor tissue

value: Gastric cancer

value: IIB

value: No


title: YT8

value: IIA


title: YT7

value: IA


title: 2m_cone_KO_inf_03

value: retina

value: inferior-cone

value: 2 month


title: YT1

value: IIIA

value: male


title: 1-hiPS-BJ273-rep1

value: Human induced pluripotent stem cell


title: 2m_cone_KO_sup_18

value: superior-cone


title: 2m_cone_KO_sup_17


title: ET10

value: IIIB

value: female


title: Hs3st3a1;3b1 DKO male_KDY-2749

value: Kidney

value: Hs3st3a1;3b1 double knockout


title: Hs3st3a1;3b1 DKO male_KDY-2764


title: ET11

value: tumor tissue


title: ET9

value: Gastric cancer

value: IB


title: WT-3

city: Helsinki

first: Liang

last: Wang

address: Viikinkaari 5

country: Finland

institute: University of Helsinki

data_processing:
Data filtering
Reads containing ploy-N and low-quality reads
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Brain tissue

growth_protocol: All mice were housed in a controlled environment with a 12-hour light/12-hour dark cycle (lights on at 7:00 a.m. and off at 19:00 p.m.) and a constant ambient temperature (23 ± 3°C).

extract_protocol:
Total RNA was extracted using TRIzol RNA isolation reagent (ThermoFisher) following the protocol provided by the manufacturer.
The library preparation and RNA sequencing were carried out in the Shanghai Meiji Biomedical Technology Co., Ltd. (Shanghai, China).

treatment_protocol: CRISPR/Cas9-mediated gene editing was used to delete the ORF of mouse Fam92a1. Two target sequences of sgRNA (upstream sgRNA, 5'-GGTTATCATCTACCAATGTC-3'; downstream sgRNA, 5'-TAGACTTCCAGCCGCAGTGG-3') and Cas9 mRNA were transcribed in vitro and injected into the cytoplasm of fertilized eggs of C57BL/6 genetic background.  All mice of three different FAM92A1 genotype were the offspring from the mating of FAM92A1 heterozygous.

value: Hippocampus

value: Wild type


title: HE-3

value: Heterozygous


title: YT4

value: No


title: HO-3

value: Homozygous


title: 2m_cone_KO_sup_15

value: retina

value: 2 month


title: WT_male KDY-3729

value: Wildtype

value: male


title: 2m_cone_KO_sup_16

value: superior-cone


title: 2m_cone_KO_sup_14


title: HO-2


title: ET8

value: IIA


title: Hs3st3a1;3b1 DKO male_KDY-3701


title: HE-2


title: ET7

value: IA


title: WT_male KDY-2758

value: Kidney


title: WT_male KDY-2761


title: ET6

value: IIIB


title: WT-2


title: 2m_cone_KO_sup_12


title: HO-1


title: ET5

value: tumor tissue


title: DKOTAM2

city: New York

first: Jorge

last: Moscat

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

description: Prkci/Prkz-DKO

data_processing:
Sequenced reads were trimmed to remove low-quality bases at ends and were then mapped to the reference genome (GRCm39) using STAR.
Assembly: mm39
Supplementary files format and content: normalized gene expression values for all mouse genes (mm39) for all samples from DESEQ2

source_name: colon organoids

growth_protocol: Isolated crypts were cultured in Advanced DMEM/F12 with B27, WNT3A, EGF, Noggin and R-spndin 1

extract_protocol:
RNA was harvested using Trizol reagent and purified using Quick-RNA MiniPrep kit (Zymo Research).
Library preparations and sequencing were conducted at GENEWIZ, LLC

treatment_protocol: Organoids were treated with 4-OH tamoxifen or vehicle upon passage and cultured for 3 days before RNA extraction

value: 8 weeks old


title: ET4

value: Gastric cancer

value: IV


title: DKOveh3

description: WT (wild type)

value: Vehicle (Ethanol)


title: HE-1

value: Hippocampus

value: Heterozygous


title: 2m_cone_KO_sup_10


title: DKOTAM1

description: Prkci/Prkz-DKO


title: 2m_cone_KO_sup_11


title: WT-1

value: Wild type


title: 2m_cone_KO_sup_09

value: retina


title: 2m_cone_KO_sup_08

value: 2 month


title: DKOveh1

description: WT (wild type)


title: 2m_cone_KO_sup_13


title: 2m_cone_KO_sup_07


title: ELS - SbD_72 [AATB72]

first: Molly

middle: S

last: Estill

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

data_processing:
library strategy: CUT&RUN-seq
Adaptor trimming was achieved using Trim-Galore (v0.6.5) followed by a secondary trimming step using Cutadapt (v2.10).
Raw reads of each sample were aligned to mm10 using Bowtie2 (v2.4.1). Duplicate read pairs were removed using ‘rmdup’ module of SAMtools (v1.10).
Peaks were called using macs2 (v2.2.6). Region analysis software (https://github.com/shenlab-sinai/NGS-Data-Charmer/blob/master/Snakefile) was utilized to annotate peaks obtained using MACS software.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing the output of diffReps (version 1.55.4)

source_name: Nucleus accumbens

extract_protocol:
Isolated nuclei was incubated with respective antibodies followed by DNA fragmentation with Micrococcal nuclease incubation. DNA was isolated using the NucleoSpin Gel and PCR Clean-Up kit
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit complemented with NEBNext® Multiplex Oligos for Illumina. 15nM of DNA was used as starting material for IgG and IP samples. Libraries for H3K27me1 were amplified using 13 cycles on the thermocycler. Libraries for H3K27me2 were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected at 250-350bp in length using AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Male mice exposed to chronic social defeat stress (CSDS) or early life stress (ELS)

value: Nucleus accumbens

value: Male

tag: antibody

value: Wildtype

value: Early life stress - Subthreshold defeat


title: DKOTAM3

description: Prkci/Prkz-DKO


title: Normal PBMC5

city: Xi'an

first: Xi

last: Zhang

state: Shanxi

address: Northwest University, 229 North Taibai Road, Xi'an

department: 1 School of Life Science, Northwest University, Xi'an, Shaanxi 710069, China 2 Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Medicine, Northwest University, Xi'an, Shaanxi 710069, China

institute: Northwest University

data_processing:
All raw RNA-seq reads were filtered by R package trim_fastq to remove adapters, rRNA and low-quality reads.
The QC criteria included: removing bases below Phred quality 20, containing over two “N”, or shorter than 75.
The output reads were then indexed by aligner STAR and mapped to reference genome by BAM.
Normalized read counts were generated and compared between groups to generate DEGs using R package DESeq2.
Assembly: hg19
Supplementary files format and content: The number of mapped reads on each sample transcript is counted with featurecount software

source_name: Blood

extract_protocol:
Buffycoat or PBMCs were isolated from whole blood. Total RNA was isolated using Trizol (Invitrogen, Waltham, MA, USA) and the purity and concentration were verified using a NanoDrop ND-1000 instrument (ThermoFisher Scientific, Waltham, MA, USA). The integrity of the RNA was assessed by a 2100 Bioanalyzer gel image analysis system (Agilent, Santa Clara, CA, USA). Only RNA samples with an integrity number of 7 or higher were processed for RNA-seq. At least 100 ng mRNA per sample was submitted for library preparation.
Qualified RNA samples were enriched and synthesized into cDNA for library preparation. RNA-seq libraries were constructed using the TruSeq RNA Sample Prep Kit. The libraries from qualified RNA samples were sequenced in the 150 nt paired-end mode on an Illumina NovaSeq 6000 platform. After quality filtering, over 30 billion clean reads were obtained in each library and then used for down-stream analysis.

value: Blood

tag: timepoint

value: Normal

tag: Sex

value: male

value: Healthy


title: Std - SbD_71 [AATB71]

value: Standard - Subthreshold defeat


title: Std - Control_69 [AATB69]

value: Standard - Control


title: ELS - Control_70 [AATB70]

value: Early life stress - Control


title: Normal PBMC4


title: Normal PBMC3

value: female


title: 2m_cone_KO_sup_06

value: superior-cone


title: ET1

value: tumor tissue

value: Gastric cancer

value: IIIA

value: No


title: ELS - SbD_68 [AATB68]

value: Nucleus accumbens


title: 2m_cone_KO_sup_04

value: retina

value: 2 month


title: Normal PBMC2


title: 2m_cone_KO_sup_03


title: Normal PBMC1


title: ET3

value: IIB


title: post-treatment blood21

value: Blood

value: post-treament

value: NSCLC


title: ELS - Control_66 [AATB66]

value: Male

value: Wildtype


title: Std - SbD_67 [AATB67]

value: Standard - Subthreshold defeat


title: Std - Control_65 [AATB65]

value: Standard - Control


title: ET2

value: IIIB

value: Yes

value: male


title: 2m_cone_KO_sup_02

value: superior-cone


title: pre-treatment blood17

value: pre-treament


title: Std - SbD_63 [AATB63]


title: 2m_cone_KO_sup_05


title: 2m_cone_ctrl_inf_26

value: inferior-cone


title: ELS - SbD_64 [AATB64]

value: Nucleus accumbens

value: Early life stress - Subthreshold defeat


title: 2m_cone_KO_sup_01

value: retina

value: 2 month


title: 2m_cone_ctrl_inf_25


title: ELS - Control_62 [AATB62]

value: Early life stress - Control


title: post-treatment blood19

value: Blood

value: post-treament


title: pre-treatment blood16

value: female

value: NSCLC


title: Std - Control_61 [AATB61]

value: Male

value: Wildtype


title: post-treatment blood20


title: 2m_cone_ctrl_inf_22


title: Resilient_60 [AATB60]

value: Resilient


title: 2m_cone_ctrl_inf_23


title: pre-treatment blood15


title: post-treatment blood18


title: 2m_cone_ctrl_inf_21


title: DKOveh2

description: WT (wild type)

value: Vehicle (Ethanol)

value: 8 weeks old


title: Susceptible_59 [AATB59]

value: Susceptible


title: Control_58 [AATB58]

description:
RESvsCON_me2_diff.nb.txt
SUSvsCON_me2_diff.nb.txt

value: Control


title: 2m_cone_ctrl_inf_20

value: inferior-cone


title: Resilient_57 [AATB57]

value: Nucleus accumbens


title: 2m_cone_ctrl_inf_19


title: Susceptible_56 [AATB56]


title: pre-treatment blood13

value: pre-treament

value: male


title: 2m_cone_ctrl_inf_18

value: retina

value: 2 month


title: post-treatment blood16

value: Blood


title: post-treatment blood17

value: post-treament


title: Control_55 [AATB55]


title: pre-treatment blood12


title: 2m_cone_ctrl_inf_17


title: 2m_cone_ctrl_inf_16


title: post-treatment blood15


title: Susceptible_53 [AATB53]


title: 2m_cone_ctrl_inf_24


title: 2m_cone_ctrl_inf_15


title: pre-treatment blood11


title: Control_52 [AATB52]


title: 2m_cone_ctrl_inf_14


title: post-treatment blood14


title: Resilient_51 [AATB51]


title: pre-treatment blood10


title: Control_49 [AATB49]


title: Susceptible_50 [AATB50]


title: pre-treatment blood9


title: pre-treatment blood14

value: female


title: post-treatment blood13

value: NSCLC


title: ELS - SbD_48 [AATB48]

value: Male

value: Early life stress - Subthreshold defeat


title: 2m_cone_ctrl_inf_12


title: Std - SbD_47 [AATB47]

value: Wildtype

value: Standard - Subthreshold defeat


title: 2m_cone_ctrl_inf_11


title: 2m_cone_ctrl_inf_13


title: 2m_cone_ctrl_inf_09


title: pre-treatment blood8


title: 2m_cone_ctrl_inf_10


title: ELS - Control_46 [AATB46]

value: Early life stress - Control


title: post-treatment blood12


title: Std - Control_45 [AATB45]

value: Standard - Control


title: Resilient_54 [AATB54]

value: Resilient


title: 2m_cone_ctrl_inf_08

value: inferior-cone


title: ELS - SbD_44 [AATB44]

value: Nucleus accumbens


title: 2m_cone_ctrl_inf_07


title: pre-treatment blood7

value: pre-treament


title: 2m_cone_ctrl_inf_06


title: post-treatment blood10

value: male


title: Std - SbD_43 [AATB43]


title: pre-treatment blood6


title: post-treatment blood11


title: 2m_cone_ctrl_inf_04

value: retina


title: ELS - Control_42 [AATB42]


title: 2m_cone_ctrl_inf_05

value: 2 month


title: post-treatment blood9

value: Blood


title: 2m_cone_ctrl_inf_03


title: post-treatment blood8

value: post-treament


title: ELS - SbD_40 [AATB40]


title: Std - SbD_39 [AATB39]


title: ELS - Control_38 [AATB38]


title: 2m_cone_ctrl_inf_02


title: 2m_cone_ctrl_inf_01


title: post-treatment blood7


title: Std - Control_37 [AATB37]


title: Resilient_36 [AATB36]


title: 2m_cone_ctrl_sup_19

value: superior-cone


title: post-treatment blood6

value: NSCLC


title: Control_34 [AATB34]

description:
RESvsCON_me1_diff.nb.txt
SUSvsCON_me1_diff.nb.txt

value: Male

value: Control


title: 2m_cone_ctrl_sup_16


title: 2m_cone_ctrl_sup_17


title: pre-treatment blood4


title: 2m_cone_ctrl_sup_18


title: Std - Control_41 [AATB41]

value: Wildtype


title: 2m_cone_ctrl_sup_14


title: Susceptible_35 [AATB35]

value: Susceptible


title: pre-treatment blood3

value: female


title: Resilient_33 [AATB33]


title: 2m_cone_ctrl_sup_15


title: pre-treatment blood2


title: Susceptible_32 [AATB32]


title: post-treatment blood3


title: 2m_cone_ctrl_sup_13


title: Control_31 [AATB31]


title: pre-treatment blood5


title: post-treatment blood2


title: Resilient_30 [AATB30]


title: 2m_cone_ctrl_sup_12


title: post-treatment blood5


title: 2m_cone_ctrl_sup_10


title: post-treatment blood1


title: Susceptible_29 [AATB29]


title: pre-treatment blood1


title: Control_28 [AATB28]


title: 2m_cone_ctrl_sup_08


title: P34_M1-1

city: Wuhan

first: Qinglei

last: Gao

state: Hubei

address: Jiefang Avenue

department: Department of Gynecological Oncology

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology

data_processing:
FASTQ files were processed using kallisto-bustools (Melsted et al., 2021) to obtain gene-level UMI counts for each droplet, with GENCODE v37 human genome as the reference. The kallisto-bustools workflow was set to be “standard” so that only exonic reads would be counted towards the final UMI count.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: High-grade serous ovarian carcinoma

extract_protocol:
Fresh tumor samples were shipped in Mylteni Biotec® Tissue Storage Solution and maintained at 4°C until processing. A volume of 8 cm3 (2 x 2 x 2 cm) tumor tissue derived from one patient would be cut into three pieces, one of which was dissociated as single-cell suspensions for scRNA-seq.
For the generation of single-cell suspension, tumor tissues were dissociated using the gentleMACS™ Dissociator with Heaters and the Tumor Dissociation Kit, human, as per the manufacturer’s instructions, right after they were received by the laboratory. Immediately following dissociation, all single-cell suspensions were filtered using MACS Smart Strainers (70µm and 40µm). They were then treated with Red Blood Cell Lysis Solution and one or two rounds of dead cell removal using the Dead Cell Removal Kit, depending on the number of dead cells in each sample. All samples were processed as per the manufacturer’s instructions. Finally, the cell pellets were re-suspended with 1 x PBS for scRNA-seq.
The scRNA-seq library was prepared with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 from 10X Genomics according to the manufacturer’s instructions. In brief, the single-cell suspensions dissociated from tumors (derived from P01-P34) were centrifugated and washed twice with 1 x PBS, and then the signal cell pellets were re-suspended within 1 x PBS supplemented with 0.04% BSA at a final concentration of 1 x 106 cell/ml. About 10 μl of cell suspensions (≈10000 cells) were mixed with barcoded Single Cell 3ʹ v3.1 Gel Beads and Partitioning Oil to generate nanoliter-scale Gel beads in EMulsion (GEMs). Next, the GEMs were performed a reverse transcription PCR using a T100 Thermal Cycler (Bio-Rad) at a volume of 125 μl according to a program of 530C for 45 min, 850C for 5 min, and held at 40C to obtain full-length cDNA with barcoding. After that, incubating with Dynabeads Cleanup Mix to purify first-strand cDNA from the PCR mix, and then amplifying the cDNA in Amplification Reaction Mix using T100 Thermal Cycler (Bio-Rad) programmed at 980C for 3 min, 980C for 15 seconds, 630C for 20 seconds, 720C for 1 min (step 2 to step 4 for total 12 of cycles), and held at 40C. Subsequently, the amplified cDNA was used to generate a signal cell 3ʹ gene expression dual index library using Chromium Next GEM Single Cell 3' Library Kit v3.1. Finally, the well-prepared single cell 3ʹ gene expression libraries were sequenced by Illumina NovaSeq 6000 sequencer.

value: High-grade serous ovarian carcinoma

value: all cells (unsorted)


title: 2m_cone_ctrl_sup_09


title: 2m_cone_ctrl_sup_07


title: P34_M2-1


title: Control_25 [AATB25]


title: P33_M2-1


title: 2m_cone_ctrl_sup_06


title: Resilient_27 [AATB27]

value: Resilient


title: P33_M1-1


title: Susceptible_26 [AATB26]

value: Nucleus accumbens


title: post-treatment blood4


title: 2m_cone_ctrl_sup_05


title: 2m_cone_ctrl_sup_04


title: Std - SbD_23 [AATB23]

value: IgG

value: Standard - Subthreshold defeat


title: ELS - SbD_24 [AATB24]

value: Early life stress - Subthreshold defeat


title: P32_M1-1


title: P32_M2-1


title: 2m_cone_ctrl_sup_03

value: retina

value: 2 month


title: ELS - Control_22 [AATB22]

value: Early life stress - Control


title: 2m_cone_ctrl_sup_11

value: superior-cone


title: P31_P2-1


title: 2m_cone_ctrl_sup_02


title: P31_P1-1


title: Std - Control_21 [AATB21]

value: Standard - Control


title: ELS - SbD_20 [AATB20]

value: Male


title: P30_M2-1


title: Std - SbD_19 [AATB19]


title: Hippocampus, post-onset 3, snRNAseq

city: Ann Arbor

first: Sophie

last: Hill

state: MI

address: 1241 E. Catherine St

department: Human Genetics

institute: University of Michigan

data_processing:
Data preprocessing was performed by the University of Michigan Advanced Genomics Core using the 10X Genomics Cell Ranger pipelines (cellranger mkfastq, cellranger count, and cellranger multi).
Assembly: Mm10
Supplementary files format and content: Tab-separated values and matrix files

molecule: nuclear RNA

source_name: Hippocampus

extract_protocol:
snRNA-seq sample collection was performed on fresh tissue over two batches: batch 1 (pre-onset 1 and control 1) and batch 2 (pre-onset 2&3 and control 2&3)At postnatal day 50 (n = 3 each), mice were euthanized and their brains were removed (Fig 1A-B). Bilateral hippocampi were immediately dissected and placed in a Dounce homogenizer with 1 mL lysis buffer: EZ Prep Lysis Buffer from Nuclei EZ Prep (Sigma #NUC101), 1mM DTT, 27U/mL Protector RNase inhibitor (Sigma #3335399001). Hippocampi were homogenized as follows: 25X with pestle A, 25X with pestle B, wait 2.5 minutes, 15X with pestle B, wait 2.5 minutes, 15X with pestle B. Samples were filtered through 30 um MACS strainers (Myltenyi, 130-098-458) and an additional 1 mL lysis buffer was added. Samples were centrifuged (500 rcf, 5 minutes, 4°C) and supernatant was discarded. Samples were resuspended in 750 uL wash buffer: 5mM MgCl2, 10mM Tris buffer pH 8.0, 25 mM KCl, 1mM DTT, 27U/mL Protector RNase inhibitor, 1% bovine serum albumin. Samples were filtered through 30 um MACS strainers and centrifuged (500 rcf, 5 minutes, 4°C). Supernatant was discarded and pellets were resuspended in 1 mL wash buffer. Nuclei were stained with propidium iodide at a final concentration of 0.4ug/mL. Sorting was performed at the University of Michigan Flow Cytometry Core on a MoFlo Astrios Cell Sorter (Beckman Coulter). Sorted nuclei were collected in pre-washed tubes containing 100 uL wash buffer.
Library preparation and sequencing were performed by the University of Michigan Advanced Genomics Core using the 10X Genomics single-nucleus 3’ gene expression platform targeting 10,000 nuclei per sample and 60,000 reads per nucleus. Paired-end sequencing was performed on the NovaSeq6000.

value: Hippocampus

value: Adult

value: F

tag: batch


title: P29_P1-1


title: P30_M1-1


title: Std - Control_17 [AATB17]

value: Wildtype


title: ELS - SbD_16 [AATB16]


title: ELS - Control_18 [AATB18]


title: Hippocampus, post-onset 1, snRNAseq


title: Std - SbD_15 [AATB15]


title: Mtb infected Zeb2 fl/fl rep5

city: Chicago

first: Shabaana

last: Khader

state: Illinois

address: 920 East 58th Street

institute: The University of Chicago

data_processing:
RNA-seq reads were then aligned and quantitated to the Ensembl release primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
The read count data of each gene were generated using featureCounts from Rsubread package
Assembly: mm10
Supplementary files format and content: tab-delimited text file contain raw read counts

source_name: Lung tissue

extract_protocol:
Qiagen RNeasy micro kit
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara- Clontech). Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: Lung tissue

value: CD11c cells sorted from Lung tissue

value: wild type

tag: agent

value: Mtb HN878

value: 50 days post infection


title: P28_M2-1

value: High-grade serous ovarian carcinoma

value: all cells (unsorted)


title: P28_P1-1


title: Hippocampus, post-onset 2, snRNAseq


title: Mtb infected Zeb2 fl/fl rep3


title: P27_P1-1


title: Mtb infected Zeb2 fl/fl rep2


title: ELS - Control_14 [AATB14]

value: Nucleus accumbens

value: IgG


title: Mtb infected Zeb2 fl/fl rep4


title: CSDS_Resilient_12 [AATB12]

description:
RESvsCON_me1_diff.nb.txt
RESvsCON_me2_diff.nb.txt

value: Resilient


title: Mtb infected Zeb2 fl/fl rep1


title: P26_M1-1


title: 2m_cone_ctrl_sup_01

value: retina

value: superior-cone

value: 2 month


title: P26_M2-1


title: Uninfected Zeb2 fl/fl rep5

value: Uninfected


title: CSDS_Susceptible_11 [AATB11]

description:
SUSvsCON_me1_diff.nb.txt
SUSvsCON_me2_diff.nb.txt

value: Male

value: Susceptible


title: P25_M2-1


title: CSDS_Control_10 [AATB10]

description:
RESvsCON_me1_diff.nb.txt
RESvsCON_me2_diff.nb.txt
SUSvsCON_me1_diff.nb.txt
SUSvsCON_me2_diff.nb.txt

value: Wildtype

value: Control


title: P29_P2-1


title: P25_M1-1


title: CSDS_Resilient_9 [AATB9]


title: CSDS_Susceptible_8 [AATB8]


title: Uninfected Zeb2 fl/fl rep2

value: Lung tissue

value: CD11c cells sorted from Lung tissue


title: Uninfected Zeb2 fl/fl rep1

value: wild type


title: P23_P1-1


title: Std - Control_13 [AATB13]

value: Standard - Control


title: Uninfected Zeb2 fl/fl rep3


title: Hippocampus, pre-onset 3, snRNAseq

value: Hippocampus

value: F


title: CSDS_Susceptible_5 [AATB5]

value: Nucleus accumbens


title: CSDS_Resilient_6 [AATB6]

value: IgG


title: P21_P1-1

value: High-grade serous ovarian carcinoma

value: all cells (unsorted)


title: P22_M2-1


title: CSDS_Control_4 [AATB4]


title: Hippocampus, pre-onset 2, snRNAseq


title: P20_M1-1


title: Hippocampus, pre-onset 1, snRNAseq


title: CSDS_Control_7 [AATB7]


title: P22_M1-1


title: CSDS_Resilient_3 [AATB3]

value: Resilient


title: Uninfected Zeb2 fl/fl rep4


title: Hippocampus, control 3, snRNAseq


title: CSDS_Susceptible_2 [AATB2]


title: P19_M1-1


title: P18_M1-1


title: Hippocampus, control 2, snRNAseq


title: CSDS_Control_1 [AATB1]


title: P17_P1-1


title: P24_M1-1


title: Ath RPFs, ligation-free Ribo-seq

city: Potsdam

first: Reimo

last: Zoschke

address: Am Mühlenberg 1

country: Germany

institute: Max Planck Institute of Molecular Plant Physiology

description:
ligation_free
counts_over_CDS-Arabidopsis_ligation.xlsx

data_processing:
The Arabidopsis GTF gene annotations (v45) and TAIR10 genome were downloaded from ensembl (https://plants.ensembl.org/index.html). Cutadapt (Martin, 2011) was used to remove adapters and UMIs. Ribo-seq contaminants are generally defined as rRNA, tRNA and snoRNA. These sequences were extracted from the gene annotation file, and converted to fasta format using bedtools (Quinlan and Hall, 2010). Importantly, the nuclear 25S and 5S are missing from the Arabidopsis gene annotations. Thus, these sequences were obtained from the following sources: 25S rRNA (https://www.ncbi.nlm.nih.gov/nuccore/X52320.1) and the 5S rRNA database (http://combio.pl/rrna/). Contaminants were filtered out using STAR aligner (Dobin et al., 2013) with the following parameters: --outFilterMismatchNoverLmax 0.1 --outReadsUnmapped Fastx –outSAMmultNmax 1. After contaminant filtering, the remaining reads were mapped to the genome using STAR aligner using the following parameters: --outFilterMismatchNoverLmax 0.1 --alignIntronMax 8000 --outSAMmultNmax 1. Mapped reads were counted over annotated CDS using FeatureCounts (Liao et al., 2014) using the parameters: -M -s 1 -t CDS -g gene_id.
Assembly: Arabidopsis: TAIR10 genome  (https://plants.ensembl.org/index.html) using the Arabidopsis GTF gene annotations (v45)
Supplementary files format and content: "counts_over_CDS-Arabidopsis_ligation.xlsx" contains the number of reads mapping to annotated Arabidopsis coding sequences (CDS)
Library strategy: Ribosome Profiling (Ribo-seq)

organism: Arabidopsis thaliana

source_name: 14-day old seedlings

growth_protocol: The tissue were derived from 14-day old Arabidopsis seedlings (Col-0), grown on ½ Murashige and Skoog media with 1% agar, grown at 100 µmol m-2s-1 for 12h/12h light/dark cycles at 20 °C.

extract_protocol:
RPF isolation: RPFs were isolated as previously described (Trösch et al., 2018) with modifications described below. The units (U) of ribonuclease used in this study are normalized to one mL of plant lysate, derived from 100 mg of plant fresh weight. 300 mg frozen plant tissue was homogenized in liquid nitrogen with a mortar and pestle followed by the addition of 3 mL ribosome extraction buffer (0.2 M sucrose, 0.2 M KCl, 40 mM Tris-OAc pH 8.0, 10 mM MgCl2, 10 mM 2-Mercaptoethanol, 2% (v/v) polyoxyethylene (10) tridecyl ether, 1% (v/v) Triton X-100, 100 μg/mL chloramphenicol, 100 μg/mL cycloheximide). After brief mixing, a 0.5 mL aliquot of the lysate was flash frozen and stored at -80 °C for later total RNA extraction using TRIzol reagent (ThermoFisher cat# 15596026). This total RNA can be used for standard RNA-seq experiments. This step is especially important if the calculation of translation efficiencies is desired (i.e., the normalization of Ribo-seq data to RNA-seq data). The remaining lysate was filtered through glass wool, followed by centrifugation for 10 min at 15,000 x g at 4 °C to remove cell debris. 2.5 mL of the clarified lysate were incubated at specified concentrations of RNase1 or MNase for 1 h at room temperature with gentle rotation to degrade mRNA regions that are not covered and protected by translating ribosomes. Since Ca2+ is a known cofactor of MNase, samples digested with MNase include 5 mM CaCl2. The ribonuclease-treated lysate contains mainly monosomes which were loaded onto a 2 mL sucrose cushion (30% (w/v) sucrose, 40 mM Tris-Acetate pH 8.0, 100 mM KCl, 15 mM MgCl2, 0.1 mg/mL chloramphenicol, 0.1 mg/mL cycloheximide, 0.2% β-MeEtOH) and centrifuged (OptimaTM L-80 XP Ultracentrifuge - Beckman Coulter) for 1.5 h at 303,800 x g at 4 °C. The supernatant was then carefully aspirated and the pelleted monosomes resuspended in 0.5 mL footprint isolation buffer (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0, 100 mM NaCl, 1% (w/v) SDS, 0.1 M EGTA pH 8.0). The RNA was immediately extracted from this pellet using 0.5 mL TRIzol reagent. Next RPFs were size-selected through electrophoresis on a 12% denaturing polyacrylamide gel (19:1, acrylamide:bisacrylamide) prepared in 1x TBE buffer (89 mM Tris, 89 mM Boric Acid, 2mM EDTA pH 8.0) containing 8 M urea. To this end, 25 μg RNA were resuspended in 40 μL of ribosome footprint loading buffer (90% (v/v) deionized formamide, 20 mM Tris-HCl pH 7.5, 20 mM EDTA pH 8.0, 0.04% (w/v) bromophenol blue, and 0.04% (w/v) xylene cyanol) and denatured for 10 min at 70 °C. The gel was run in 1x TBE buffer with a constant power of 30 W at constant temperature of 12 °C (achieved by a cooling unit). Co-migrating pre-stained RNA ladder (Biodynamics Laboratory cat# DM253) was used to visualize the regions of the gel to excise RPFs. All RPFs that were not rRNA-depleted were size-selected between 20-50 nt. All rRNA-depleted RPFs were size-selected between 20-35 nt. RNA was eluted from the excised gel piece in 4 mL TESS (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0, 0.1 M NaCl, 0.2% (w/v) SDS) by overnight incubation at 4 °C with gentle rotation. Eluted RNA was isolated with 4 mL of phenol:chloroform:isoamyl alcohol (25:24:1), followed by overnight ethanol precipitation at -20 °C. To increase purity and further narrow the volume, the RNA pellet was resuspended in 0.1 M NaCl (500 μL) and subjected to a second round of phenol:chloroform:isoamyl alcohol (25:24:1) extraction, followed by two washes with chloroform:isoamylalcohol (24:1) and overnight ethanol precipitation at -20 °C. The received RPF pellet was washed twice with 75% ethanol and resuspended in 20 μL RNase-free water.
For the ligation-free strategy, RPFs were directly used as input for the D-plex small RNA-seq kit (Diagenode cat#C05030001), according to manufacturer’s instructions. For the RNA-ligase strategy, the terminal ends of the RPFs were first repaired using T4 polynucleotide kinase, and used as input into the NEXTflex small RNA-seq kit V4 (Perkin Elmer, cat#NOVA-5132-31), according to the manufacturer’s instructions.

value: 14-day old seedlings

tag: nuclease treatment

value: 600 Units RNaseI

tag: rrna depletion

value: yes

value: Wild type

tag: molecule type

value: ribosome protected fragment


title: P16_M2-1


title: Ath RPFs, ligation-based Ribo-seq

description:
ligation_based
counts_over_CDS-Arabidopsis_ligation.xlsx


title: 4850_E14.5 BRN1/2 cKO

first: Soraia

last: Barao

address: 725 N Wolfe St PCTB 1015

institute: JHU

description: 10x Genomics

data_processing:
Demultiplexing and FASTQ generation was completed using Illumina’s BaseSpace software. Data were aligned to the mouse reference genome (refdata-gex-mm10-2020-A) publicly available at the 10X genomics’ website using the Cell Ranger pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cortex

extract_protocol:
Cortex of E12.5 and E14.5 embryos was dissected and dissociated into single cells using the Papain Dissociation System (#LK0031500, Worthington Biochemical). Individual collected cells were processed for scRNAseq using.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, The NextGEM protocol was run on the 10X Chromium Controller to create GEMs, composed of a single cell, gel bead with unique barcode and UMI primer, and RT reagents. 100 µl of emulsion is retrieved from the chip and incubated (45 min at 53°C, 5 min at 85°C, cool to 4°C), generating barcoded cDNA from each cell. The GEMs were broken using Recovery Agent and cDNA cleaned, following manufacturer’s instructions using MyOne SILANE beads. cDNA was amplified for 11 cycles (3 min at 98°C, 11 cycle: 15 sec at 98°C, 20 sec at 63°C, 1 min at 72°C; 1 min at 72°C, cool to 4°C).  Samples were cleaned using 0.6X SPRIselect beads. Quality control (QC) was completed using Qubit and Bioanalyzer to determine size and concentrations. 10 µl of amplified cDNA was carried into library prep. Fragmentation, end repair and A-tailing were completed (5 min at 32°C, 30 min at 65°C, cool to 4°C), and samples were cleaned up using double sided size selection (0.6X, 0.8X) with SPRIselect beads. Adaptor ligation (15 min at 20°C, cool to 4°C), 0.8X cleanup and amplification were performed by PCR using unique i7 index sequences. Libraries underwent a final cleanup using double sided size selection (0.6X, 0.8X) with SPRIselect beads. Library QC was performed using Qubit, Bioanalyzer and KAPA library quantification qPCR kit.

value: Cortex

value: BRN1/2 cKO

value: female

tag: developmental stage

tag: collection date


title: P16_M1-1


title: 4220_E14.5 BRN1/2 cKO

description: 10x Genomics

value: male


title: TM1 with A603 phenazine and T6SS mutant replicate B

first: William

middle: P

last: Robins

state: MA

address: 77 Avenue Louis Pasteur NRB 1039

department: Microbiology

institute: Harvard Medical School

data_processing:
CLC Genomics Workbench v8
Reads were trimmed for quaility (quality score 0.05 cutoff) and made reverse complement for mapping due to strand specific sequencing
Mapped reads were analyzed using the CLC DGE tool
Assembly: Asembled and annnotated TaMai1 and A603 genomes provided in manuscript
Supplementary files format and content: Excel sheet with subsheets for comparisons
Supplementary files format and content: Mapping depth and RPKM provided in processed files

organism:
Vibrio parahaemolyticus
Aeromonas dhakensis

source_name: bacterial

growth_protocol: Mono or mixed culture spotted on agar

extract_protocol:
Zymo Direct-zol RNA extraction kit
NEB Ultra RNA directional library kit and Epicentre Ribozero bacterial rRNA depletion

value: bacterial

tag: molecule subtype

value: rRNA depleted mRNA


title: E6_E12.5 BRN1/2 cKO

description: 10x Genomics


title: TM1 with A603 phenazine and T6SS mutant replicate A


title: P15_M2-1


title: P15_M1-1


title: D5_E12.5 BRN1/2 cKO

description: 10x Genomics


title: TM1 with A603 T6SS mutant replicate B


title: TM1 with A603 T6SS mutant replicate A


title: P14_P2-1


title: D3_E12.5 Control

description: 10x Genomics

value: Control


title: Hippocampus, control 1, snRNAseq

value: Hippocampus

value: F

tag: strain


title: P14_P1-1

tag: tissue

value: High-grade serous ovarian carcinoma


title: TM1 with A603 phenazine mutant replicate A

tag: cell type


title: C6_E14.5 Control

description: 10x Genomics

tag: genotype


title: TM1 with A603 replicate B


title: C5_E14.5 Control

description: 10x Genomics


title: P13_M2-1

value: all cells (unsorted)


title: C1_E14.5 BRN1/2 cKO

description: 10x Genomics


title: TM1 with A603 replicate A


title: 14-5-5_E14.5 BRN1/2 cKO

description: 10x Genomics


title: P12_P2-1


title: P15_P1-1


title: 14-5-2_E14.5 Control

description: 10x Genomics


title: P12_P1-1


title: 12-5-3_E12.5 BRN1/2 cKO

description: 10x Genomics


title: PSS,scRNAseq

city: HeFei

first: zhang

middle: xiao

last: jing

state: AnHui

address: 81 Meishan Road

department: dermatology

institute: Anhui Medical University

description: 10x genomics

data_processing:
FACS-sorted live cells were submitted to BGI for 10x genomics library  preparation
We used the official software cell ranger v2.1.1 (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is-cell-ranger) provided by 10X Genomics to generate expression matrix, feature, barcode files
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

organism: Homo

extract_protocol:
A total of 30ml peripheral blood was collected from each sample, and peripheral blood mononuclear cells (PBMCs) were isolated using density gradient centrifugation with Ficoll-Paque plus (17144003, Cytiva). After washing twice in PBS, PBMCs were preserved in serum-free cell lyophilization solution (abs9417, absin) and were stored in liquid nitrogen at −196°C until thawing.
After PBMC resuscitation, add APC-CD19 (555415, BDBiosciences) and FITC-CD45 (555482, BDBiosciences) and incubate for 30 min. After incubation, centrifuge, wash, and resuspend with an appropriate volume of resuspended buffer and filter through 40 µm cell sieve. Centrifuge at 4°C, discard the supernatant and resuspend the appropriate volume of resuspended buffer. Cells were FACS-sorted by SH800S Cell Sorter (SH800S, SONY) and collected in 15mL tubes with 5mL of media. Data were analyzed using FlowJo v.10 software.

value: Blood


title: E2_E12.5 Control

description: 10x Genomics


title: SLE,scRNAseq

description: 10x genomics


title: P12_M2-1


title: TM1 with A603 phenazine mutant replicate B


title: P11_M2-1


title: P11_M1-1


title: SW1783 Water extract of Aconitum carmichaeli Debeaux (Low dose)_rep3

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

description: sample 2-3-3

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.5). The trimmed reads were then aligned to the human reference genome hg38 using the STAR (v2.7.3a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCh38.84.
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

growth_protocol: Human astrocytoma cell line, SW1783 (HTB-13) was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). SW1783 cells were maintained in Leibovitz’s L-15 medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, without CO2 incubator. The cells were subcultured every 3 or 4 days, depending on the cell density.

extract_protocol:
Total RNA was isolated according to the manufacturer’s protocol. The concentration of the isolated RNA was determined using an Agilent RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany), and RNA quality was evaluated by assessing the RNA integrity number (RIN > 7).
A total RNA (1 microgr) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: Dulbecco's Modified Eagle Medium (DMEM), phosphate-buffered saline (PBS), TrypLE Express, penicillin-streptomycin, and fetal bovine serum (FBS) were purchased from Gibco (Grand Island, NY, USA). Leibovitz's L-15 medium was purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). Cell culture flasks and multiwell culture plates were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Dimethyl sulfoxide (DMSO), wortmannin, LY294002, Thioridazine were purchased from Sigma-Aldrich (St. Louis, MO, USA) and QIAzol lysis reagents was purchased from Qiagen (Germantown, MD, USA). The Ez-Cytox cell viability assay kit was purchased from Dogen Bio (Seoul, Korea). The dried Poria cocos Wolf (Polyporaceae) were supplied from Kwangmyung-dang Medicinal Herbs Co. (Ulsan, Republic of Korea), and their morphology was carefully validated by Dr. Goya Choi, Herbal Medicine Resources Research Center Korea Institute of Oriental Medicine (KIOM), Republic of Korea. A voucher specimen (2-22-0221) was deposited in the Korean Herbarium of Standard Herbal Resources of KIOM (Naju, Republic of Korea). The crushed material was extracted at 100 ± 3℃ for 3 hours by water refluxed system (MS-DM609, Misung Scientific, Yangu, Republic of Korea) and filtered through 5 um cartridge filter (KOC Biotech, Daejeon, Republic of Korea). The filtrates were concentrated under 40℃ using a rotary evaporator (Ev-1020t, SciLab, Seoul, Republic of Korea), and then freeze dried (LP20, IlShin Biobase, Dongduchen, Republic of Korea). The yield of PC was 24.2 % and final extracts were homogenized and stored at air-tight container in 4℃ cold room. For the in vitro investigation, homogenous PC was vigorously vortexed for 30 min at room temperature in phosphate-buffered saline (PBS; Thermo Fisher Scientific, Rockford, IL, USA) containing 2% DMSO and then sterilized by filtering through a 0.22 um membrane. The stock solution of PC (10mg/mL) was aliquoted in 1.5mL tube and stored at -80°C until use.

tag: cell line

value: ACDW 20 μg/mL

tag: time


title: P10_P2-1


title: P10_P1-1


title: P13_M1-1


title: SW1783 Water extract of Aconitum carmichaeli Debeaux (Medium dose)_rep2

description: sample 2-2-2

tag: treatment

value: ACDW 100 μg/mL


title: SW1783 Water extract of Aconitum carmichaeli Debeaux (Medium dose)_rep3

description: sample 2-3-2


title: SW1783 Water extract of Aconitum carmichaeli Debeaux (Low dose)_rep1

description: sample 2-1-3


title: Alveolar macrophages from Cpt1a-KO mouse (sample #6), LPS

city: Taipei

first: Kuei-Pin

last: Chung

address: No 7, Chung-Shan South Rd

department: Laboratory Medicine

country: Taiwan

institute: National Taiwan University Hospital

description:
N11020-17
read_count_Macrophage.txt

data_processing:
Trimming adaptor sequences and removing reads of low quality were performed by cutadapt (v2.4).
Quantified reads were aligned to the mouse genome (GRCm38) by STAR (v2.7.2a) and then gene-level read counts were generated based on the annotations of Gencode (vM25)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: Lung

extract_protocol:
Cell as input and lysis accroding to manufacturer's instructions of SMART-Seq Stranded Kit (Takara)
Libraries were prepared using the SMART-Seq Stranded Kit (Takara)

treatment_protocol: LPS (2 mg/kg; Sigma L2637) was given through intra-tracheal route to the murine lungs to induce acute lung injury.

value: Lung

value: Primary alveolar macrophages

value: Cpt1a-KO (AT2 cell-specific)

value: Intra-tracheal LPS


title: P09_P2-1


title: Alveolar macrophages from Cpt1a-KO mouse (sample #5), LPS

description:
N11020-16
read_count_Macrophage.txt


title: Alveolar macrophages from Cpt1a-KO mouse (sample #4), LPS

description:
N11020-15
read_count_Macrophage.txt


title: P09_M1-1


title: HC,scRNAseq

description: 10x genomics


title: SW1783 Water extract of Aconitum carmichaeli Debeaux (Medium dose)_rep1

description: sample 2-1-2


title: P08_P2-1


title: 12-5-1_E12.5 Control

city: Baltimore

description: 10x Genomics

value: Cortex


title: Alveolar macrophages from Cpt1a-KO mouse (sample #8), LPS

description:
N11020-24
read_count_Macrophage.txt


title: Alveolar macrophages from Cpt1a-KO mouse (sample #2), LPS

description:
N11020-11
read_count_Macrophage.txt


title: SW1783 Water extract of Aconitum carmichaeli Debeaux (High dose)_rep2

description: sample 2-2-1

value: ACDW 500 μg/mL


title: P08_P1-1


title: Alveolar macrophages from Cpt1a-KO mouse (sample #7), LPS

description:
N11020-18
read_count_Macrophage.txt


title: Alveolar macrophages from Cpt1a-KO mouse (sample #1), LPS

description:
N11020-10
read_count_Macrophage.txt


title: Alveolar macrophages from control mouse (sample #8), LPS

description:
N11020-23
read_count_Macrophage.txt


title: SW1783 Water extract of Aconitum carmichaeli Debeaux (Low dose)_rep2

description: sample 2-2-3


title: P08_M2-1


title: SW1783 Vehicle(DMSO)_rep3

description: sample 1-3-1

value: 2% DMSO


title: SW1783 Water extract of Aconitum carmichaeli Debeaux (High dose)_rep1

description: sample 2-1-1


title: P06_P2-1


title: Alveolar macrophages from control mouse (sample #4), LPS

description:
N11020-19
read_count_Macrophage.txt


title: P06_P1-1


title: Alveolar macrophages from control mouse (sample #6), LPS

description:
N11020-21
read_count_Macrophage.txt


title: P08_M1-1


title: P07_M1-1


title: P06_M1-1


title: SW1783 Vehicle(DMSO)_rep2

description: sample 1-2-1


title: Alveolar macrophages from control mouse (sample #3), LPS

description:
N11020-14
read_count_Macrophage.txt


title: P05_M2-1


title: Alveolar macrophages from control mouse (sample #5), LPS

description:
N11020-20
read_count_Macrophage.txt


title: Water extract of Aconitum carmichaeli Debeaux (Low dose)_rep2

description: sample 2-2-3

growth_protocol: Human colorectal adenocarcinoma cell line, HT29 (HTB-38) were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). HT29 cells were maintained in DMEM medium supplemented with 10% (v/v) heat-inactivated FBS, 100 IU/mL penicillin, and 100 mg/mL streptomycin at 37 °C, 5% CO2 incubator. The cell was subcultured every 3 or 4 days, depending on the cell density.


title: Water extract of Aconitum carmichaeli Debeaux (Low dose)_rep3

description: sample 2-3-3


title: Alveolar macrophages from Cpt1a-KO mouse (sample #3), LPS

description:
N11020-12
read_count_Macrophage.txt


title: P05_M1-1


title: Alveolar macrophages from control mouse (sample #2), LPS

description:
N11020-13
read_count_Macrophage.txt


title: Alveolar macrophages from control mouse (sample #1), LPS

description:
N11020-09
read_count_Macrophage.txt


title: SW1783 Vehicle(DMSO)_rep1

description: sample 1-1-1


title: SW1783 Water extract of Aconitum carmichaeli Debeaux (High dose)_rep3

description: sample 2-3-1


title: Alveolar macrophages from control mouse (sample #3), baseline

description:
N11020-08
read_count_Macrophage.txt

value: Baseline


title: Water extract of Aconitum carmichaeli Debeaux (Medium dose)_rep2

description: sample 2-2-2


title: Water extract of Aconitum carmichaeli Debeaux (Low dose)_rep1

description: sample 2-1-3


title: Alveolar macrophages from control mouse (sample #2), baseline

description:
N11020-07
read_count_Macrophage.txt


title: P04_P1-1


title: Alveolar macrophages from control mouse (sample #1), baseline

description:
N11020-06
read_count_Macrophage.txt


title: Water extract of Aconitum carmichaeli Debeaux (Medium dose)_rep1

description: sample 2-1-2


title: P04_P1-2


title: P04_M2-1


title: Water extract of Aconitum carmichaeli Debeaux (High dose)_rep3

description: sample 2-3-1


title: AT2 cells from Cpt1a-KO mouse (#624), LPS

description:
N10909-43
read_count_AT2.txt

extract_protocol:
For AT2 cells, Trizol was used for RNA extraction. For alveolar macrophages,
Libraries were prepared using the SureSelect RNA Library Preparation Kit (Agilent)

value: Primary AT2 cells


title: Water extract of Aconitum carmichaeli Debeaux (High dose)_rep2

description: sample 2-2-1


title: P04_M1-1


title: Water extract of Aconitum carmichaeli Debeaux (High dose)_rep1

description: sample 2-1-1


title: P03_M1-1


title: AT2 cells from Cpt1a-KO mouse (#622), LPS

description:
N10909-41
read_count_AT2.txt


title: AT2 cells from Cpt1a-KO mouse (#621), LPS

description:
N10909-40
read_count_AT2.txt


title: P02_P2-1


title: Vehicle(DMSO)_rep2

description: sample 1-2-1


title: Water extract of Aconitum carmichaeli Debeaux (Medium dose)_rep3

description: sample 2-3-2


title: AT2 cells from Cpt1a-KO mouse (#620), baseline

description:
N10909-35
read_count_AT2.txt


title: AT2 cells from Cpt1a-KO mouse (#619), baseline

description:
N10909-34
read_count_AT2.txt


title: Vehicle(DMSO)_rep1

description: sample 1-1-1


title: P02_M2-1


title: P02_M1-1


title: PSS,scATACseq

description: 10x genomics

data_processing:
FACS-sorted live cells were submitted to BGI for 10x genomics library  preparation
We used the official software cell ranger v2.1.1 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-iscell-ranger-atac) provided by 10X Genomics to generate expression matrix, feature, barcode files
Assembly: hg38
Supplementary files format and content: 1000 fragments
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
CD45+CD19+ B cells were sorted using SH800S Cell Sorter (SH800S, SONY). Samples were lysed in cold lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40(Roche)) for 3 min on ice to prepare the nuclei. Immediately after cell lysis, nuclei were centrifuged at 500 g for 5 min, and the supernatant was discarded carefully. Nuclei extracts were then incubated with Tn5 transposase (cat no. TD501, Vazyme Biotech) at 37℃ for 30 min. After DNA purification with the MinElute Kit (Qiagen), PCR was performed to amplify the library for 12–15 cycles based on the quantitative data regarding the optimum number of PCR cycles. The PCR conditions were as follows: 98℃ for 30 sec and cycling at 98℃ for 10 sec, 63℃ for 30 sec, and 72℃ for 1 min.
After PCR amplification, the sample libraries were purified and sequenced on the MGISEQ-2000 platform with the 150-bp paired-end configuration.


title: AT2 cells from Cpt1a-KO mouse (#617), baseline

description:
N10909-32
read_count_AT2.txt


title: SLE,scATACseq

description: 10x genomics


title: scTCR-seq_02008

data_processing:
For scRNA-seq data, FASTQ files were processed using the CeleScope (https://github.com/singleron-RD/CeleScope) “rna” workflow, designed for transcriptome sequencing data generated through the Singleron platform, to obtain gene-level UMI counts for each droplet, with GENCODE v37 human genome as the reference. Briefly, after using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and cutadapt (Martin, 2011) to quality control and filter the data, reads were compared with the reference genome using STAR (Dobin et al., 2013). Finally, featureCounts (Liao et al., 2014) was used to output the gene count matrices.
For paired same-cell scTCR-seq data, FASTQ files were processed using CeleScope “flv_CR” workflow, designed for full-length VDJ enrichment sequencing data generated through the Singleron platform, to obtain TCR alpha and beta-chain CDR3 nucleotide sequences.
Assembly: hg38
Supplementary files format and content: Comma-separated values files
Library strategy: scTCR-seq

extract_protocol:
Fresh tumor samples were shipped in Mylteni Biotec® Tissue Storage Solution and maintained at 4°C until processing. A volume of 8 cm3 (2 x 2 x 2 cm) tumor tissue derived from one patient would be cut into three pieces, one of which was dissociated as single-cell suspensions for scTCR-seq.
For the generation of single-cell suspension, tumor tissues were dissociated using the gentleMACS™ Dissociator with Heaters and the Tumor Dissociation Kit, human, as per the manufacturer’s instructions, right after they were received by the laboratory. Immediately following dissociation, all single-cell suspensions were filtered using MACS Smart Strainers (70µm and 40µm). They were then treated with Red Blood Cell Lysis Solution and one or two rounds of dead cell removal using the Dead Cell Removal Kit, depending on the number of dead cells in each sample. All samples were processed as per the manufacturer’s instructions. Finally, the cell pellets were re-suspended with 1 x PBS for scTCR-seq.
For sorting of CD3+ T cells from tumors, these single-cell suspensions dissociated from tumor tissues (derived from P35-P44) were preincubated with Fixable Viability Dye (Biolegend, 423105) to mark alive cells within 1 x PBS for about 30 min, and then labeled with surface antibodies including CD45-PE (Biolegend, 3685110), CD3-APC (Biolegend, 300312), and CD19-FITC (Biolegend, 302206). Sorting for scTCR-seq was performed using a FACSAria (BD Biosciences).
The scTCR-seq library was generated using the sCircle® Single Cell Full-Length Immunoreceptor Library Kit according to the manufacturer’s instructions. In brief, the sorted CD3+ T cells from P35-P44 were suspended in cold PBS at a concentration of about 3 x 105 cells/ml. About 100 μl of homogenous cell suspension was injected into a well-prepared microchip via the inlet port slowly and stood for 5 min (room temperature) allowing the signal cell to fully fall into microwells. Following cell loading, 60 μl of the Barcode Beads resuspension was loaded into the microchip and incubated for 1 min. After washing with PBS three times, about 100 μl of prepared Lysis Mix was injected into the microchip to lyse cells, leading to the released mRNA binding to Barcode Beads. Immediately following mRNA capture, barcode beads retrieval was performed with a Singleton Magnetic Rack and pre-chilled Wash Buffer A (supplied by the Library Kit) to obtain the Barcode Beads with bound mRNA. Then the mRNA was reversely transcribed in a thermal mixer preheated to 42°C at 1300 rpm for 90 minutes, followed by cDNA amplification using a T100 Thermal Cycler (Bio-Rad). Next, the amplified cDNA should be purified before library preparation, and then programmed at cDNA circularization, digestion, and purification. After three rounds of TCR enrichment were performed, the immune receptor enriched library was prepared through a process of fragmentation, adapter ligation, purification of the Adapter-Ligated cDNA, enriched library amplification, and purification and size selection of the amplified enriched libraries. Lastly, Illumina NovaSeq 6000 Sequencer was employed to sequence the well-prepared libraries.

value: T cells


title: HC,scATAC-seq

description: 10x genomics


title: P01_P2-1


title: scTCR-seq_01060


title: P01_P1-1


title: AT2 cells from control mouse (#755), LPS

description:
N10909-39
read_count_AT2.txt


title: AT2 cells from Cpt1a-KO mouse (#618), baseline

description:
N10909-33
read_count_AT2.txt


title: P03_M2-1


title: scTCR-seq_01056


title: AT2 cells from control mouse (#747), LPS

description:
N10909-37
read_count_AT2.txt


title: AT2 cells from control mouse (#746), LPS

description:
N10909-36
read_count_AT2.txt


title: AT2 cells from Cpt1a-KO mouse (#623), LPS

description:
N10909-42
read_count_AT2.txt


title: scTCR-seq_01055


title: Vehicle(DMSO)_rep3

description: sample 1-3-1


title: scTCR-seq_01054


title: AT2 cells from control mouse (#744), baseline

description:
N10909-31
read_count_AT2.txt


title: AT2 cells from control mouse (#741), baseline

description:
N10909-29
read_count_AT2.txt


title: scTCR-seq_01052


title: scTCR-seq_01050


title: AT2 cells from control mouse (#742), baseline

description:
N10909-30
read_count_AT2.txt


title: scTCR-seq_01051


title: AT2 cells from control mouse (#748), LPS

description:
N10909-38
read_count_AT2.txt


title: scTCR-seq_01053


title: scTCR-seq_01049


title: YL701, 1mM Auxin, 3 h, rep3

city: New Haven

first: Valerie

last: Reinke

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University School of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Assembly: ce11
Supplementary files format and content: tab-delimited text files include featurecount values of piRNA precursor for each Sample, bam files of merged small RNA-seq data

organism: Caenorhabditis elegans

source_name: Isolated germ nuclei

growth_protocol: Gravid adults were bleached and synchronized by L1 starvation. Starved L1s were plated on peptone-enriched NGM plates seeded with OP50. For auxin-mediated knockdown, L1 worms were grown on peptone enriched plates at 22C for 45 hours, then moved to peptone enriched plates with 1 mM auxin or ETOH plates for 3hours. Worms were harvested, washed with M9 and floated on sucrose to remove remaining bacteria.

extract_protocol:
Samples were subjected to three freeze/thaw cycles (thawed for 2 min at 37 °C/flash frozen for 1 min). Samples were centrifuged for 5 min at 14800 g, and supernatants transferred to a new tube and mixed 1:1 with cold 100% ethanol. RNA isolation was performed with Direct-zol RNA microprep kit(Zymo Research #R2062). RNA was eluted with 15 μL of nuclease-free water (Zymo Research) and treated with 2 μLQuick CIP (NEB M0525S) in rCutSmart Buffer (NEB B6004S) ina total reaction volume of 20 μL at 37 °C for 90 min. CIP-treated RNA samples were heat-inactivated for 2 min at 80 °C, suspended in 100 μL Trizol (Invitrogen) and purified with Direct-zol RNA microprep kit (Zymo Research #R2062). The RNA was then treated with 1.5 μL RppH (NEB M0356S) in a total reaction volume of 20 μL for 1 h at 37 °C, resuspended in 100 μL Trizol(Invitrogen) and purified with Direct-zol RNA microprep kit (Zymo Research #R2062). The Yale Center for Genome Analysis (YCGA) prepared the small RNA library with the QiaSeq miRNA library prep kit (Qiagen) and performed sequencing on an Illumina NovaSeq using 75 bp paired-end sequencing. The RNA quality and fragment size distribution were confirmed with a Bioanalyzer.
RNA libraries for small RNA-seq were prepared using Qiagen micro mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Worms were grown on peptone enriched plates supplemented with ETOH or 1mM Auxin plates final concentration.

value: Isolated germ nuclei

value: wrdSi51 [mex-5p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II:0.77); ISW-1::eGFP::AID III.

value: 3 H Auxin

value: 3 hours

value: small RNA


title: YL701, 1mM Auxin, 3 h, rep2


title: YL701, ETOH Control, 3 h, rep2

value: 3 H ETOH


title: YL701, ETOH Control, 3 h, rep3


title: YL701, 1mM Auxin, 3 h, rep1


title: YL701, ETOH Control, 3 h, rep1


title: Isolated germ nuclei high salt YL701 3h KD input for H3  rep 1

description:
A fraction of the input total chromatin that was used for H3 Native ChIP on strain YL701 isolated germ nuclei treated with 3 h 1mM Auxin
High_salt_H3_IP_ISW1_AUXIN_DANPOS.bw
High_salt_H3_IP_ISW1_AUXIN_merged-High_salt_H3_IP_3hr_ETOH_merged.positions.integrative.txt

data_processing:
Reads were aligned to ce11 with bowtie2.
Low-quality (q<30), duplicate reads and modENCODE-blacklisted reads were discarded.
For Histone modification data, reads were normalized to RPM then custom R scripts were used for z-score values. For Native ChIP-seq, the merged bam files were GC corrected and then mononucleosome sized fragments were selected (140-200 bp). For H3 NChIP data, the filtered bam files were converted to bigwig tracks and nucleosomes were identified by DANPOS3, using input as control with parameters using input as control with parameters  -m 1 –extend 70 -c 93260000 -u 0 -z 1 -a 1 -e 1 -b.
Replicates were used as input for peak calling with MACS2.
Assembly: ce11
Supplementary files format and content: bigWig, narrowPeak (except for Input sample), tab-delimited text filess DANPOS nucleosome output for each Sample

growth_protocol: Gravid adults were bleached and synchronized by L1 starvation. Starved L1s were plated on peptone-enriched NGM plates seeded with OP50. For wild-type and prde-1(mj207)V strains, L1s were grown until young adult at 20˚C. For auxin-mediated knockdown, L1 worms were grown on peptone enriched plates for 45 hours, then moved to peptone enriched plates with 1 mM auxin or ETOH plates for 3hours. Worms were harvested, washed with M9 and floated on sucrose to remove remaining bacteria.

extract_protocol:
For histone modification ChIP-seq, isolated germ cell nuclei were sonicated in a Misonix S-4000 water bath sonicator, and immunoprecipated overnight using 5 µg of anti-H3K27me3, anti-H3K36me3, or anti-H3K9me3 antibody. For each For histone modification ChIP-seq, isolated germ cell nuclei were sonicated in a Misonix S-4000 water bath sonicator, and immunoprecipated overnight using 5 µg of anti-H3K27me3, anti-H3K36me3, or anti-H3K9me3 antibody. For each IP, 90ng of Drosophila spike-in chromatin and 0.5 μg of Drosophila-specific H2Av antibody was added. The wash steps were performed as in previously described (Han et al 2019). For Native ChIP-seq, 12 million nuclei were incubated with Lysis Buffer 1 (1 mM Tris–HCl pH7.5, 1 mM PMSF, 1 mM DTT, 0.1% Tween 20, 0.2% NP-40, 0.01% digitonin) for 10min. Then 10U of Mnase was added and digested at 37°C for 4 min and 30 sec. The reaction was stopped with 4 μL of 0.5M EDTA and spun for 17000g for 10 min at 4°C. Supernatant was collected and nuclei pellet was incubated with lysis buffer 2 (1 mM Tris–HCl pH7.5,1 mM PMSF, 1 mM DTT, 0.1% Tween 20, 1% Triton X-100 + 1x Complete Protease Inhibitor Cocktail) for 2 hours. Supernatants were combined and chromatin was pre-cleared with blocked beads. Chromatin was immunoprecipated overnight with 5 µg of anti-H3 antibody. For each IP, 10ng of Drosophila spike-in chromatin and 0.5 μg of Drosophila-specific H2Av antibody was added. After overnight incubation, , 40μL of pre-blocked beads were added and incubated 4°C for 2 hours. For the high salt wash, the ChIP samples with beads were washed 2 times with FA-150mM NaCl (50mM HEPES pH 7.5, 1mM EDTA pH 8.0, 1% Triton X-100, 0.1% Na deoxycholate, 150mM NaCl and 1x cOmplete proteinase inhibitor cocktail EDTA-free (Roche)) and 2 times with FA-500mM NaCl (50mM HEPES pH 7.5, 1mM EDTA pH 8.0, 1% Triton X-100, 0.1% Na deoxycholate, 500mM NaCl and 1x cOmplete proteinase inhibitor cocktail EDTA-free (Roche)). For the low salt wash, the ChIP samples were washed 2 times with FA-75mM NaCl (50mM HEPES pH 7.5, 1mM EDTA pH 8.0, 1% Triton X-100, 0.1% Na deoxycholate, 75mM NaCl and 1x cOmplete proteinase inhibitor cocktail EDTA-free (Roche)) and 2 times with FA-150mM NaCl (50mM HEPES pH 7.5, 1mM EDTA pH 8.0, 1% Triton X-100, 0.1% Na deoxycholate, 150mM NaCl and 1x cOmplete proteinase inhibitor cocktail EDTA-free (Roche)). DNA was eluted twice with elution buffer (100mM NaHCO3, 0.2% SDS, 5 mM DTT, 1x TE) at 65°C for 15 min. Samples were treated with RNAse, and incubated with proteinase K overnight at 55°C.
DNA was purified on Zymo ChIP DNA Clean & Concentrator kit (Zymo Research #D5205) and used for ChIP library preparation. Samples were sequenced on an Illumina NovaSeq using 100bp paired-end sequencing.

treatment_protocol: For Histone modification ChIP-seq samples, worms were crosslinked in 2% formaldehyde in M9 buffer for 28 minutes rotating at room temperature. Crosslinking was quenched with 1 M Tris pH 7.5, followed by two washes with M9. Wormed were washed For Histone modification ChIP-seq samples, worms were crosslinked in 2% formaldehyde in M9 buffer for 28 minutes rotating at room temperature. Crosslinking was quenched with 1 M Tris pH 7.5, followed by two washes with M9. Wormed were washed with NPB (50 mM HEPES pH 7.5, 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA, 0.1% Tween 20, 0.2 mM DTT, 0.5 mM PMSF, 0.5 mM spermidine, 0.25 mM spermine, and 1x Complete Protease Inhibitor Cocktail) and resuspended in 6mL of NPB. Worms were dounced with fifteen loose strokes and 23 tight strokes. The sample was vortexed twice on medium-high speed for 30 s, followed by 5 min on ice. Worm debris was filtered with four 30μm strainers (MACS) and seven 20 μm strainers (Pluriselect). Dapi-stained nuclei were counted using a hemocytometer. The nuclei were transferred to a 1.5 ml tube and flash frozen in liquid nitrogen. For Native ChIP-seq, worms were washed with NPB and resuspended in 6mL NPB. Worms were dounced with fifteen loose strokes and 23 tight strokes. The sample was vortexed twice on medium-high speed for 30 s, followed by 5 min on ice. Worm debris was filtered with four 30μm strainers (MACS) and seven 20 μm strainers (Pluriselect). Dapi-stained nuclei were counted using a hemocytometer. The nuclei were transferred to a 1.5 ml tube.

value: Young adult

tag: antibody

value: Auxin, high salt


title: Isolated germ nuclei high salt YL701 3h KD input for H3  rep 2


title: Isolated germ nuclei low salt YL701 3h KD input for H3  rep 1

description:
A fraction of the input total chromatin that was used for H3 Native ChIP on strain YL701 isolated germ nuclei treated with 3 h 1mM Auxin
Low_salt_H3_IP_ISW1_AUXIN_DANPOS.bw
Low_salt_H3_IP_ISW1_AUXIN_merged-Low_salt_H3_IP_3hr_ETOH_merged.positions.integrative.txt


title: Isolated germ nuclei high salt YL701 3h KD H3  rep 1

description:
Native-ChIP was performed with anti-H3 with high salt was conditions on strain YL701 isolated germ nuclei treated with 3 h 1mM Auxin
High_salt_H3_IP_ISW1_AUXIN_DANPOS.bw
High_salt_H3_IP_ISW1_AUXIN_merged-High_salt_H3_IP_3hr_ETOH_merged.positions.integrative.txt


title: Isolated germ nuclei high salt YL701 3h KD H3  rep 2


title: Differentiated PC12 cells expressing AR111Q K387/519R, DHT treatment, rep3

city: Philadelphia

first: Diane

middle: E

last: Merry

state: PA

address: 1020 Locust St.

department: Biochemistry and Molecular Biology

institute: Thomas Jefferson University

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus_norvegicus.Rnor_6.0_ERCC reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
Assembly: Rattus_norvegicus.Rnor_6.0_ERCC
Supplementary files format and content: csv file includes raw counts for all samples
Supplementary files format and content: txt files include raw counts for each sample

organism: Rattus norvegicus

source_name: PC12 cells

growth_protocol: PC12 cells were maintained in DMEM supplemented with 5% fetal bovine serum, 10% horse serum, 4mM glutamine, 100 U/ml Penicillin-Streptomycin, 100 ug G418 sulfate, and 200 µg/mL hygromycin at 37°C, 10% CO2.

extract_protocol:
RNA was extracted using TRIzol Reagent (Invitrogen) and purified using Direct-zol RNA Miniprep Kit
mRNA enrichment, mRNA fragmentation, and random priming; first and second strand cDNA synthesis; end repair, 5' Phosphorylation, and da-Tailing; adaptor ligation, PCR enrichment, and sequencing via polyA selection

treatment_protocol: PC12 cells were induced to differentiate through treatment with 50 ng/mL nerve growth factor. Cells were treated with Doxycycline to induce expression of the androgen receptor and the androgen DHT

value: PC12 cells

value: ratpheochromocytoma

value: NGF-mediated differentiation


title: Differentiated PC12 cells expressing AR111Q K387/519R, DHT treatment, rep2


title: Isolated germ nuclei low salt YL701 3h KD H3  rep 2

description:
Native-ChIP was performed with anti-H3 with low salt was conditions on strain YL701 isolated germ nuclei treated with 3 h 1mM Auxin
Low_salt_H3_IP_ISW1_AUXIN_DANPOS.bw
Low_salt_H3_IP_ISW1_AUXIN_merged-Low_salt_H3_IP_3hr_ETOH_merged.positions.integrative.txt


title: AT2 cells from control mouse (#740), baseline

description:
N10909-28
read_count_AT2.txt

value: Lung


title: Differentiated PC12 cells expressing AR111Q K387/519R, DHT treatment, rep1


title: Differentiated PC12 cells with low expression of AR111Q V582F (matched to AR111Q K387/519R), DHT treatment, rep3


title: Isolated germ nuclei high salt YL701 ETOH control input for H3  rep 2

description:
A fraction of the input total chromatin that was used for H3 Native ChIP strain YL701 isolated germ nuclei treated with 3 h ETOH
High_salt_H3_IP_3hr_ETOH_DANPOS.bw
High_salt_H3_IP_ISW1_AUXIN_merged-High_salt_H3_IP_3hr_ETOH_merged.positions.integrative.txt

value: ETOH, low salt


title: Isolated germ nuclei low salt YL701 3h KD H3  rep 1


title: Isolated germ nuclei high salt YL701 ETOH control input for H3  rep 1


title: Isolated germ nuclei low salt YL701 ETOH control input for H3  rep 2

description:
A fraction of the input total chromatin that was used for H3 Native ChIP strain YL701 isolated germ nuclei treated with 3 h ETOH
Low_salt_H3_IP_3hr_ETOH_DANPOS.bw
Low_salt_H3_IP_ISW1_AUXIN_merged-Low_salt_H3_IP_3hr_ETOH_merged.positions.integrative.txt


title: Differentiated PC12 cells with low expression of AR111Q V582F (matched to AR111Q K387/519R), DHT treatment, rep1


title: Differentiated PC12 cells with high expression of AR111Q V582F (matched to AR112Q), DHT treatment, rep3


title: Isolated germ nuclei low salt YL701 ETOH control input for H3  rep 1


title: Isolated germ nuclei high salt YL701 ETOH control H3  rep 2

description:
Native-ChIP was performed with anti-H3 with high salt was conditions on strain YL701 isolated germ nuclei treated with 3 h ETOH
High_salt_H3_IP_3hr_ETOH_DANPOS.bw
High_salt_H3_IP_ISW1_AUXIN_merged-High_salt_H3_IP_3hr_ETOH_merged.positions.integrative.txt


title: Differentiated PC12 cells with high expression of AR111Q V582F (matched to AR112Q), DHT treatment, rep2


title: Isolated germ nuclei low salt YL701 3h KD input for H3  rep 2


title: Differentiated PC12 cells expressing AR112Q, DHT treatment, rep3


title: Isolated germ nuclei low salt YL701 ETOH control H3  rep 2

description:
Native-ChIP was performed with anti-H3 with low salt was conditions on strain YL701 isolated germ nuclei treated with 3 h ETOH
Low_salt_H3_IP_3hr_ETOH_DANPOS.bw
Low_salt_H3_IP_ISW1_AUXIN_merged-Low_salt_H3_IP_3hr_ETOH_merged.positions.integrative.txt


title: Isolated germ nuclei high salt YL701 ETOH control H3  rep 1


title: Differentiated PC12 cells with high expression of AR111Q V582F (matched to AR112Q), DHT treatment, rep1


title: Isolated germ nuclei low salt YL701 ETOH control H3  rep 1


title: Medulla_p8_SCA7_2

status: Public on Jul 04 2024

city: Durham

first: Debolina

middle: D

last: Biswas

state: North Carolina

address: 203, Research Drive, Room 141

institute: Duke Univeristy

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R
Assembly: mm10
Supplementary files format and content: text file contains raw count of samples

source_name: Medulla

extract_protocol:
RNA was extracted using Qiagen QIA RNeasy mini kit
Library was contructed by Standard Illumina hybridization and scannig protocol

value: Medulla

tag: age


title: Medulla_p8_SCA7_1


title: Cervical_p8_SCA7_1

source_name: Cervical spinal cord

value: Cervical spinal cord


title: Differentiated PC12 cells expressing AR112Q, DHT treatment, rep2


title: Medulla_p8_WT_2

value: Wildtype


title: Cervical_p8_WT_1


title: Medulla_p8_WT_1


title: Medulla_5wk_WT_2

value: 5 weeks


title: Differentiated PC12 cells expressing AR112Q, DHT treatment, rep1


title: Differentiated PC12 cells with low expression of AR111Q V582F (matched to AR111Q K387/519R), DHT treatment, rep2


title: Medulla_5wk_WT_1


title: Cervical_5wk_WT_1


title: Medulla_5wk_SCA7_2


title: Cervical_5wk_SCA7_2


title: Medulla_5wk_SCA7_1


title: Cervical_5wk_WT_2


title: Medulla_9wk_WT_5

value: 9 weeks


title: Medulla_9wk_WT_4


title: Cervical_9wk_WT_5


title: Cervical_p8_SCA7_2


title: Cervical_5wk_SCA7_1


title: Medulla_9wk_SCA7_5


title: Cervical_9wk_WT_4


title: Medulla_9wk_WT_3


title: Medulla_9wk_SCA7_4


title: Cervical_9wk_WT_3


title: Cervical_9wk_SCA7_4


title: Cervical_9wk_SCA7_3


title: Medulla_9wk_SCA7_2


title: Cervical_9wk_SCA7_2


title: Medulla_9wk_SCA7_3


title: Cervical_9wk_WT_2


title: Medulla_9wk_WT_1


title: Cervical_9wk_WT_1


title: Medulla_9wk_WT_2


title: Medulla_9wk_SCA7_1


title: ADVTa1 2

city: Nanjing

first: kua

last: liu

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

data_processing:
Raw paired-end fastq reads were filtered by TrimGaloreto discard the adapters and low quality bases via calling the Cutadapt tool
The clean reads obtained were then aligned to the mm10/hg19 mouse/human genome using HISAT2, followed by reference genome-guided transcriptome assembly and gene expression quantification using StringTie
Differentially expressed genes (DEGs) were identified by DEseq2(for sample with replications)or edgeR (for sample with no replication) with a cut-off value of log2|fold-change|>1 and p-value <0.05.
Assembly: mm10
Supplementary files format and content: processes data files includes FPKM for each sample

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424), which yielded > 2 μg of total RNA per sample.
Whole mRNAseq libraries were generated by ApexBio Technology LLC. (Shanghai China) using Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit ® (12310ES, China) following manufacturer’s recommendations. Amplify cDNA for the synthesis of the second chain of cDNA. Purify cDNA products by AMPure XP system (Beckman Coulter, Beverly, USA).

value: ADV combined with Ta1


title: ADVTa1 1


title: Ta1 3


title: Ta1 2


title: Ta1 1


title: ADVTa1 3


title: ADV 2

value: ADV


title: ADV 3


title: ADV 1


title: Ctrl 3

value: PBS


title: Ctrl 1


title: RAW264.7, SB+LPS2

city: Guangdong Guangzhou, China

first: chen

last: xi

address: 1 Xinzao Road, Xinzao Town, Panyu District, Guangzhou City, Guangdong Province,

institute: Guangzhou medical university

data_processing:
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: ensembl_94_mus_musculus_grcm38_primary
Supplementary files format and content: tab-delimited text files include FPKM values  for each Sample

source_name: connective tissue

extract_protocol:
Total RNA was extracted with AG RNAex Pro Reagent (AG21102, Accurate Biology, Hunan, China) as the manufacture’s instruction.  RNA purity and concentration were measured using Nanophotometer Pearl (IMPLEN, CA, USA).
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Beijing, China).

value: connective tissue

value: macrophage

value: SB+LPS

value: macrophage M1 polarization


title: RAW264.7, SB+LPS3


title: Ctrl 2


title: RAW264.7, SP+LPS3

value: SP+LPS


title: RAW264.7, SP+LPS2


title: RAW264.7, SP+LPS1


title: Cervical_9wk_SCA7_5


title: RAW264.7, control2

value: control


title: RAW264.7, LPS2

value: LPS


title: RAW264.7, LPS3


title: P4_Opn4WT_sample4

city: Cincinnati

first: Shane

middle: Peter

last: D'Souza

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital

data_processing:
Adapters and low-quality reads were trimmed/filtered using Trimmomatic v0.39
Reads were pseudoaligned to the mouse reference genome (GRCm38) and counts were quantified using Kallisto v0.46.1
Differential gene expression analysis was performed using Sleuth v0.30.8
Assembly: mm10
Supplementary files format and content: comma-delimited text file includes raw counts for each sample
Supplementary files format and content: comma-delimited text file includes DEGs from Sleuth
Supplementary files format and content: comma-delimited text file includes TPMs from Kallisto

source_name: Neural retina

extract_protocol: Library preparation was performed at Azenta (Formerly Genewiz).

value: Neural retina

value: standard lighting


title: Cervical_9wk_SCA7_1


title: RAW264.7, control3


title: RAW264.7, LPS1


title: P4_Opn4WT_sample1


title: P4_Opn4KO_sample4


title: RAW264.7, control1


title: P4_Opn4WT_sample3


title: P4_Opn4KO_sample5


title: P4_Opn4WT_sample2