title: CBO-MOK20008W-B02, KO

description:
Library name: PAX6-B2-KO-DAY7_GT23-02007_TCGTAGTG-CCAAGTCT_S201_L004_R1_001
KOLF2.2J derived knockout cell line,PAX6 KO, differentiated to cortical brain organoid


title: Naive_IgG_rep1 [CT96-1_Naïve_IgG_rep1]

status: Public on Feb 03 2025

type: SRA

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

department: Urology

country: USA

institute: UCSF

library_source: genomic

data_processing:
library strategy: CUT&Tag
Nextflow/cutandrun
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: mESCs

growth_protocol: Mouse ESCs were seeded and next day differentiated to formative state by removal of Lif+2i and growth for ~63h. Naive controls were grown in parallel in the presence of Lif+2i.

extract_protocol: Libraries were constructed using custom adaptors.

tag: culture conditions

value: Naive

tag: cell line

tag: cell type

value: mESC cell line

tag: treatment time


title: APPPS1_NLRP3_4m__7_2_13, time 4m

city: Luxembourg

first: Michael T.

last: Heneka

address: 6, Avenue du Swing,  4367 Esch-Belval

country: Luxembourg

institute: University of Luxembourg

library_source: transcriptomic

data_processing:
Adapters (NexteraPE) were removed using trimmomatic. Trimmed reads were mapped using TopHat and mm10 reference genome. Finally, count matrix was calculated using HTSeq.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

molecule: total RNA

source_name: CD11b+ cells

extract_protocol:
miRNA easy kit (Qiagen) was used for RNA isolation, and Qubit and Bioanalyzer for quality control.
Following manufacturer’s protocol, 10 ng input and SMART-Seq® v4 Ultra® Low Input RNA Kit (Takra Bio) was used for library construction.  Libraries were prepared in 2 batches. Samples were pooled 7-8 per pool, sequenced on Hiseq 2500, paired end sequencing with 125 bp read.

tag: genotype

value: CD11b+ cells

tag: age


title: Torin 6h, adipocytes

city: Singapore

first: Jia

last: Li

address: 8 College Road

country: Singapore

institute: Duke-NUS

data_processing:
For the RNA-seq data, we first removed Illumina adapter sequences using Cutadapt and filtered out trimmed reads with a length less than 30 base pairs. Reads were then mapped to the mm10 genome and GENCODE gene annotation version M10 using STAR alignment.
Quantification of gene expression was performed using fragment counting mode with FeatureCounts. Gene expression was normalized to Transcripts Per Million (TPM).
Assembly: mm10
Supplementary files format and content: Tab-based text file include normalized log2 (TPM) values for each sample

source_name: adipocytes

extract_protocol:
Fresh adipose tissues from the mice and adipocyte cultures specified in the text were immediately immersed in TriZol reagent (Thermo Fisher) and homogenized. RNA was extracted from the clear layer following chloroform phase separation using the miRNeasy Mini Kit (Qiagen), following the manufacturer's instructions
Strand-specific RNA-seq libraries were prepared and sequenced by Novogene

value: adipocytes

value: WT

tag: treatment

value: treatment with Torin 6h


title: CBO-MOK20002-WT1-Day9, WT

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: RFX4_WT_GT24-00980_CATAGAGT-TGGTGGCA_S205_L007_R1_001
KOLF2.2J differentiated to cortical brain organoid

data_processing:
Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: csv files including raw and normalised counts

organism: Homo sapiens

extract_protocol:
mRNA was captured using magnetic oligo-dT beads according to KAPA mRNA HyperPrep Kit
KAPA mRNA HyperPrep Kit Illumina NovaSeq X

value: iPSC

tag: editing strategy

value: Not applicable

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 9

tag: model system

value: Cortical brain (dorsal forebrain patterning)

tag: parental cell_line


title: APPPS1_NLRP3_12m__7_1_46, time 12m


title: CBO-MOK20002P-E09-Day9, KO

description:
Library name: RFX4_PTC_E09_GT24-00979_TGCGAGAC-CAACAATG_S202_L007_R1_001
KOLF2.2J derived knockout cell line,RFX4 PTC, differentiated to cortical brain organoid

value: Termination codon


title: Form_H2A_rep1

value: Formative


title: Naive_H4K8ac_rep2


title: APPPS1_12m_Mxo4_7_1_59, time 12m


title: Torin 12h, adipocytes

value: treatment with Torin 12h


title: Glu 6h, adipocytes

value: Glucose deprivation 6h


title: CBO-MOK20002P-B12-Day9, KO

description:
Library name: RFX4_PTC_B12_GT24-00978_GACGTCTT-GGTGAACC_S207_L007_R1_001
KOLF2.2J derived knockout cell line,RFX4 PTC, differentiated to cortical brain organoid


title: Naive_H4K8ac_rep1


title: Naive_H4K20m1_rep2


title: CBO-MOK20002P-A09-Day9, KO

description:
Library name: RFX4_PTC_A09_GT24-00977_AGTACTCC-AACAGGTT_S201_L007_R1_001
KOLF2.2J derived knockout cell line,RFX4 PTC, differentiated to cortical brain organoid


title: Glu 3h, adipocytes

value: Glucose deprivation 3h


title: Naive_H3K9m3_rep2


title: WT_4m__7_1_5, time 4m


title: CBO-MOK20002C-C08-Day9, KO

description:
Library name: RFX4_CE_C08_GT24-00976_TGGCCGGT-GCGCTCTA_S206_L007_R1_001
KOLF2.2J derived knockout cell line,RFX4 CE, differentiated to cortical brain organoid

value: Critical exon


title: Naive_H4K20m1_rep1


title: Torin 3h, adipocytes

value: treatment with Torin 3h


title: Glu 12h, adipocytes

value: Glucose deprivation 12h


title: APPPS1_12m__7_1_36, time 12m


title: WT_12m__6_2_39, time 12m


title: Aicar 3h, adipocytes

value: treatment with Aircar 3h


title: Aicar 6h, adipocytes

value: treatment with Aircar 6h


title: CBO-MOK20002C-B08-Day9, KO

description:
Library name: RFX4_CE_B08_GT24-00974_GTCTACAC-ACCTTGGC_S203_L007_R1_001
KOLF2.2J derived knockout cell line,RFX4 CE, differentiated to cortical brain organoid


title: CBO-MOK20002C-C06-Day9, KO

description:
Library name: RFX4_CE_C06_GT24-00975_CAATTAAC-ATATCTCG_S200_L007_R1_001
KOLF2.2J derived knockout cell line,RFX4 CE, differentiated to cortical brain organoid


title: Naive_H3K9ac_rep2

value: Naive

value: mESC cell line


title: CBO-MOK20002W-A02-Day9, KO

description:
Library name: RFX4_KO_B04_GT24-00973_ACTCGTGT-GTTCCAAT_S208_L007_R1_001
KOLF2.2J derived knockout cell line,RFX4 KO, differentiated to cortical brain organoid

value: Full coding region


title: APPPS1_NLRP3_12m_Mxo4_6_2_53, time 12m

value: CD11b+ cells


title: Aicar 12h, adipocytes

value: adipocytes

value: WT

value: treatment with Aircar 12h


title: WT_6m__6_2_18, time 6m


title: NLRP3_4m__6_2_10, time 4m


title: Naive_H3K9ac_rep1


title: AA 6h, adipocytes

value: Amino acid deprivation 6h


title: CBO-MOK20002-WT-Day8, WT

description:
Library name: RFX_WT_Day8_GT23-05645_TTACAGGA-GCTTGTCA_S90_L002_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: iPSC

value: Not applicable

value: day 8

value: Cortical brain (dorsal forebrain patterning)


title: APPPS1_6m__6_1_21, time 6m


title: Naive_H3K4m3_rep1


title: Steap4AKO iWAT, KO 3

city: Cleveland

first: Lizi

last: Zhang

state: Ohio

address: 2109 Adelbert Rd

department: Biochemistry

institute: Case Western Reserve University

data_processing:
RNA-Seq reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR (version 2.7.0e).
The mapped reads were assigned to gene using RSEM (version 1.3.3), with default union-counting mode.
Differential gene expression analysis were performed by DESeq2 R package (R 4.2.0, DEseq2 version 1.12.4)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized counts for each Sample

source_name: iWAT

extract_protocol:
Total RNA was extracted from iWAT of HFD-fed Steap4f/f and Steap4AKO mice with the RNeasy Lipid Tissue Mini Kit (Qiagen, Cat#74804) following the manufacturer’s instructions.
Sequencing library preparation and RNA-seq were conducted by Novogene.

tag: tissue

value: iWAT


title: Steap4AKO iWAT, KO 2


title: Naive_H3K4m2_rep1


title: Naive_H3K4m3_rep2


title: NLRP3_6m__7_1_32, time 6m


title: APPPS1_NLRP3_6m__6_1_30, time 6m


title: AA 3h, adipocytes

value: Amino acid deprivation 3h


title: AA 12h, adipocytes

value: Amino acid deprivation 12h


title: CBO-MOK20002C-F05-Day8, KO

description:
Library name: RFX_CE_F5_Day8_GT23-05641_GTCGGAGC-TTATAACC_S73_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 CE, differentiated to cortical brain organoid

value: Critical exon


title: WT_6m__5_2_17, time 6m


title: CBO-MOK20002W-A04-Day9, KO

description:
Library name: RFX4_KO_A02_GT24-00971_GCCACAGG-ATGGCATG_S204_L007_R1_001
KOLF2.2J derived knockout cell line,RFX4 KO, differentiated to cortical brain organoid

value: day 9


title: Naive_H3K9m3_rep1

value: Naive


title: APPPS1_4m__6_1_2, time 4m


title: NLRP3_12m__6_1_48, time 12m


title: Naive_H3K36m1_rep2

value: mESC cell line


title: CBO-MOK20002P-F11-Day8, KO

description:
Library name: RFX_PTC_F11_Day8_GT23-05644_CCGTGAAG-ATCCACTG_S93_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 PTC, differentiated to cortical brain organoid

value: Termination codon


title: CBO-MOK20002P-B12-Day8, KO

description:
Library name: RFX_PTC_B12_Day8_GT23-05643_TCCAACGC-AAGTCCAA_S95_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 PTC, differentiated to cortical brain organoid


title: CBO-MOK20002P-A09-Day8, KO

description:
Library name: RFX_PTC_A9_Day8_GT23-05642_CTTGGTAT-GGACTTGG_S105_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 PTC, differentiated to cortical brain organoid


title: Naive_H3K36m2_rep2


title: CBO-MOK20002W-B04-Day9, KO

description:
Library name: RFX4_KO_A04_GT24-00972_ATTGTGAA-GCAATGCA_S199_L007_R1_001
KOLF2.2J derived knockout cell line,RFX4 KO, differentiated to cortical brain organoid

value: Full coding region


title: NLRP3_4m__5_2_12, time 4m

value: CD11b+ cells


title: WT_12m_Mxo4_5_1_62, time 12m

value: WT


title: Steap4f/f iWAT, WT 6


title: Steap4f/f iWAT, WT 1


title: Naive_H3K27m3_rep2


title: CBO-MOK20002W-C04-Day8, KO

description:
Library name: RFX_KO_C4_Day8_GT23-05638_GCAGAATT-TGGCCGGT_S87_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 KO, differentiated to cortical brain organoid


title: APPPS1_12m_Mxo4_5_2_56, time 12m


title: CXD101_P1, RNAseq

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Tumor

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro Kit (Qiagen) following the manufacturer’s instruction.
Library preparation was performed using the TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

value: Tumor

value: PMN-MDSCs

value: myeloid cells

tag: isolation

value: FACS isolation from tumor


title: Steap4f/f iWAT, WT 5


title: Naive_H3K36m2_rep1


title: MS275_P2, RNAseq


title: Steap4f/f iWAT, WT 2


title: APPPS1_NLRP3_4m__5_1_14, time 4m


title: MS275_P1, RNAseq


title: CBO-MOK20002C-C06-Day8, KO

description:
Library name: RFX_CE_C6_Day8_GT23-05640_ACTAAGAT-CCGCGGTT_S89_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 CE, differentiated to cortical brain organoid

value: iPSC

value: day 8


title: Naive_H3K36m1_rep1


title: CBO-MOK20002P-F11-Day7, KO

description:
Library name: RFX_PTC_F11_Day7_GT23-05634_ATGTAAGT-CATAGAGT_S84_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 PTC, differentiated to cortical brain organoid

value: day 7

value: Cortical brain (dorsal forebrain patterning)


title: Vehicle_P1, RNAseq

value: Vehicle


title: CBO-MOK20002C-B08-Day8, KO

description:
Library name: RFX_CE_B8_Day8_GT23-05639_ATGAGGCC-CAATTAAC_S78_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 CE, differentiated to cortical brain organoid

value: Critical exon


title: Naive_H2BK5ac_rep2


title: Naive_H3K27m3_rep1


title: WT_6m__5_1_19, time 6m


title: CBO-MOK20002W-B04-Day8, KO

description:
Library name: RFX_KO_B4_Day8_GT23-05637_AACGTTCC-AGTACTCC_S69_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 KO, differentiated to cortical brain organoid


title: CBO-MOK20002P-B12-Day7, KO

description:
Library name: RFX_PTC_B12_Day7_GT23-05633_CGGCGTGA-ACAGGCGC_S76_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 PTC, differentiated to cortical brain organoid


title: Naive_H3K4m2_rep2


title: Form_RNApolS2-5p_rep2

value: Formative


title: Naive_H3K27ac_rep2

value: Naive


title: CBO-MOK20002W-A04-Day8, KO

description:
Library name: RFX_KO_A4_Day8_GT23-05636_GGTACCTT-GACGTCTT_S103_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 KO, differentiated to cortical brain organoid


title: CBO-MOK20002-WT-Day7, WT

description:
Library name: RFX_WT_Day7_GT23-05635_GCACGGAC-TGCGAGAC_S55_L002_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: Not applicable


title: APPPS1_NLRP3_12m__4_2_44, time 12m


title: CXD101_M1, RNAseq

value: M-MDSCs


title: WT_12m__5_1_40, time 12m


title: APPPS1_NLRP3_12m_Mxo4_4_2_52, time 12m


title: CBO-MOK20002C-F05-Day7, KO

description:
Library name: RFX_CE_F5_Day7_GT23-05631_TGACGAAT-GCCTACTG_S59_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 CE, differentiated to cortical brain organoid


title: APPPS1_6m__4_2_24, time 6m


title: CBO-MOK20002P-A09-Day7, KO

description:
Library name: RFX_PTC_A9_Day7_GT23-05632_TAATACAG-GTGAATAT_S58_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 PTC, differentiated to cortical brain organoid

value: Termination codon


title: CBO-MOK20002C-C06-Day7, KO

description:
Library name: RFX_CE_C6_Day7_GT23-05630_CAGTAGGC-ATTCGTCA_S64_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 CE, differentiated to cortical brain organoid


title: CXD101_P2, RNAseq


title: CXD101_M2, RNAseq


title: Form_Rad21_rep2

value: mESC cell line


title: Naive_H3K27ac_rep1


title: APPPS1_12m_Mxo4_4_1_58, time 12m

value: CD11b+ cells


title: Form_RNApolS2-5p_rep1


title: CBO-MOK20002C-B08-Day7, KO

description:
Library name: RFX_CE_B8_Day7_GT23-05629_TTGGACTC-CTGCTTCC_S94_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 CE, differentiated to cortical brain organoid


title: Vehicle_P2, RNAseq

value: Tumor

value: WT


title: APPPS1_6m__4_2_23, time 6m


title: MS275_M2, RNAseq

value: myeloid cells


title: WT_4m__4_2_7, time 4m


title: Naive_H2BK5ac_rep1


title: Vehicle_M1, RNAseq

value: FACS isolation from tumor


title: CBO-MOK20002W-C04-Day7, KO

description:
Library name: RFX_KO_C4_Day7_GT23-05628_CCAAGTCT-TCATCCTT_S100_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 KO, differentiated to cortical brain organoid

value: iPSC

value: Full coding region


title: Form_Rad21_rep1


title: APPPS1_12m__4_1_37, time 12m


title: Vehicle_M2, RNAseq


title: APPPS1_4m__4_1_3, time 4m


title: WT_12m__3_2_34, time 12m


title: CBO-MOK20002W-A04-Day7, KO

description:
Library name: RFX_KO_A4_Day7_GT23-05626_TCTCTACT-GAACCGCG_S71_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 KO, differentiated to cortical brain organoid

value: day 7


title: Form_H4K20m1_rep2


title: MS275_M1, RNAseq


title: Form_H4K20m1_rep1


title: NLRP3_12m_Mxo4_3_2_55, time 12m


title: CXD101_M1, ATACseq

description:
CXD101_M1_CXD101_M2_vs_MS275_M1_MS275_M2_peaks.narrowPeak
CXD101_M1_CXD101_M2_vs_Vehicle_M1_Vehicle_M2_peaks.narrowPeak

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 151+151-base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
ATAC-seq reads were aligned to mm10 genome using Bowtie2 version v2.3.5.1.
Narrow peak coordinate data was generated by MACS2 version 2.2.7.1 software.
Assembly: mm10
Supplementary files format and content: narrow peak coordinate data (output of MACS2)

extract_protocol:
Cells were lysed with ATAC lysis buffer of ATAC-seq Kit (Active Motif, USA) and nuclei were isolated by centrifugation.
ATAC-seq libraries were prepared using the ATAC-seq Kit according to the manufacturer’s protocol.


title: CXD101_M2, ATACseq


title: Form_H4K8ac_rep1


title: APPPS1_NLRP3_6m__3_2_31, time 6m


title: CBO-MOK20002P-F11-Day6, KO

description:
Library name: RFX_PTC_F11_Day6_GT23-05624_AGTTCAGG-TCTGTTGG_S77_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 PTC, differentiated to cortical brain organoid

value: day 6

value: Cortical brain (dorsal forebrain patterning)


title: MS275_M2, ATACseq

description:
MS275_M1_MS275_M2_vs_CXD101_M1_CXD101_M2_peaks.narrowPeak
MS275_M1_MS275_M2_vs_Vehicle_M1_Vehicle_M2_peaks.narrowPeak


title: CBO-MOK20002P-B12-Day6, KO

description:
Library name: RFX_PTC_B12_Day6_GT23-05623_TGGATCGA-TATCGCAC_S56_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 PTC, differentiated to cortical brain organoid


title: Form_H3K9m3_rep2


title: Form_H4K8ac_rep2


title: CBO-MOK20002W-B04-Day7, KO

description:
Library name: RFX_KO_B4_Day7_GT23-05627_CTCTCGTC-AGGTTATA_S72_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 KO, differentiated to cortical brain organoid


title: CBO-MOK20002P-A09-Day6, KO

description:
Library name: RFX_PTC_A9_Day6_GT23-05622_CAAGCTAG-CGCTATGT_S91_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 PTC, differentiated to cortical brain organoid


title: WT_6m__3_1_20, time 6m


title: Form_H3K9m3_rep1


title: WT_12m_Mxo4_3_1_61, time 12m


title: Form_H3K9ac_rep2


title: Form_H3K4m3_rep2


title: Form_H3K9ac_rep1


title: CBO-MOK20002C-C06-Day6, KO

description:
Library name: RFX_CE_C6_Day6_GT23-05620_ATCCACTG-ACGCACCT_S101_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 CE, differentiated to cortical brain organoid

value: Critical exon


title: CBO-MOK20002C-F05-Day6, KO

description:
Library name: RFX_CE_F5_Day6_GT23-05621_GCTTGTCA-GTATGTTC_S92_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 CE, differentiated to cortical brain organoid


title: APPPS1_NLRP3_4m__3_1_9, time 4m


title: APPPS1_4m__3_2_6, time 4m


title: Sample1-EAE-Neg_S8

city: Boston

first: Zhaorong

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description: Library name: Sample1-EAE-Neg_S8

data_processing:
The raw fastq files was aligned to GRCm38 mouse reference genome and quantified using Kallisto
Assembly: GRCm38
Supplementary files format and content: Tar-zipped folder of kallisto output

source_name: Brain

extract_protocol:
Sorted cells were lysed and RNA isolated using the Qiagen RNeasyMicro kit (Qiagen, 74004) with on-column DNase I digestion (Qia-gen, 79254). For the transcriptome of Acly+Ep300+ astrocyte subsets was isolated and sequenced using the FIND-seq/Smart-seq3 protocol.
The DNA library was prepared using the Nextera XT Library Prep Kit (Illumina, FC-131-1024), following the manufacturer’s protocol.

value: Brain

value: Astrocytes


title: MS275_M1, ATACseq


title: CBO-MOK20002C-B08-Day6, KO

description:
Library name: RFX_CE_B8_Day6_GT23-05619_AAGTCCAA-TACTCATA_S53_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 CE, differentiated to cortical brain organoid


title: Sample1-EAE-p300_S2

description: Library name: Sample1-EAE-p300_S2


title: APPPS1_12m__2_2_35, time 12m


title: Form_H3K4m2_rep1

value: Formative


title: Vehicle_M2, ATACseq

description:
Vehicle_M1_Vehicle_M2_vs_CXD101_M1_CXD101_M2_peaks.narrowPeak
Vehicle_M1_Vehicle_M2_vs_MS275_M1_MS275_M2_peaks.narrowPeak

value: M-MDSCs

value: Vehicle


title: APPPS1_NLRP3_12m_Mxo4_2_2_54, time 12m


title: Sample1-EAE-double_S1

description: Library name: Sample1-EAE-double_S1


title: CBO-MOK20002W-C04-Day6, KO

description:
Library name: RFX_KO_C4_Day6_GT23-05618_GGACTTGG-CGTCTGCG_S81_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 KO, differentiated to cortical brain organoid


title: CBO-MOK20002W-B04-Day6, KO

description:
Library name: RFX_KO_B4_Day6_GT23-05617_TTATAACC-TCGATATC_S79_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 KO, differentiated to cortical brain organoid


title: NLRP3_6m__2_2_26, time 6m


title: Sample1-EAE-ACLY_S7

description: Library name: Sample1-EAE-ACLY_S7


title: EAE_5ADB.AclyKD_Astrocytes_4

description: Library name: EAE_5ADB.AclyKD_Astrocytes_4


title: Form_H3K36m2_rep2

value: mESC cell line


title: WT_4m__2_2_4, time 4m

value: CD11b+ cells


title: NLRP3_12m__3_1_47, time 12m


title: CBO-MOK20002W-A04-Day6, KO

description:
Library name: RFX_KO_A4_Day6_GT23-05616_CCGCGGTT-CTAGCGCT_S54_L002_R1_001
KOLF2.2J derived knockout cell line,RFX4 KO, differentiated to cortical brain organoid


title: EAE_5ADB.AclyKD_Astrocytes_3

description: Library name: EAE_5ADB.AclyKD_Astrocytes_3


title: Form_H3K36m2_rep1


title: Form_H3K4m3_rep1


title: CBO-MOK20002-WT-Day6, WT

description:
Library name: RFX_WT_Day6_GT23-05625_GACCTGAA-CTCACCAA_S97_L002_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: Not applicable


title: CBO-MOK20006-WT, WT

description:
Library name: LHX9_WT_Day14_GT23-09937_GCAATGCA-AACGTTCC_S25_L002_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: day 14


title: Form_H3K4m2_rep2


title: NLRP3_12m_Mxo4_2_1_51, time 12m


title: CBO-MOK20006P-A12, KO

description:
Library name: LHX9_PTC_A12_Day14_GT23-09936_ATGGCATG-GGTACCTT_S19_L002_R1_001
KOLF2.2J derived knockout cell line, LHX9 PTC, differentiated to cortical brain organoid

value: Termination codon


title: CBO-MOK20006P-A10, KO

description:
Library name: LHX9_PTC_A10_Day14_GT23-09935_GGAGCGTC-GCACGGAC_S18_L002_R1_001
KOLF2.2J derived knockout cell line, LHX9 PTC, differentiated to cortical brain organoid


title: APPPS1_12m__2_1_38, time 12m


title: Form_H3K36m1_rep1


title: Form_H3K36m1_rep2


title: APPPS1_NLRP3_6m__2_1_25, time 6m


title: EAE_5ADB.AclyKD_Astrocytes_1

description: Library name: EAE_5ADB.AclyKD_Astrocytes_1


title: Form_H3K27m3_rep2


title: EAE_5ADB.Scramble_Astrocytes_4

description: Library name: EAE_5ADB.Scramble_Astrocytes_4


title: CBO-MOK20006P-A09, KO

description:
Library name: LHX9_PTC_A9_Day14_GT23-09934_AAGATACT-ATGTAAGT_S17_L002_R1_001
KOLF2.2J derived knockout cell line, LHX9 PTC, differentiated to cortical brain organoid


title: EAE_5ADB.Scramble_Astrocytes_3

description: Library name: EAE_5ADB.Scramble_Astrocytes_3


title: NLRP3_4m__2_1_8, time 4m


title: Form_H3K27m3_rep1


title: CBO-MOK20006C-D03, KO

description:
Library name: LHX9_CE_D3_Day14_GT23-09933_GCGCAAGC-CGGCGTGA_S20_L002_R1_001
KOLF2.2J derived knockout cell line, LHX9 CE, differentiated to cortical brain organoid


title: NLRP3_12m__1_2_42, time 12m


title: EAE_5ADB.Scramble_Astrocytes_2

description: Library name: EAE_5ADB.Scramble_Astrocytes_2


title: Form_H3K27ac_rep2


title: CBO-MOK20006C-B06, KO

description:
Library name: LHX9_CE_B6_Day14_GT23-09932_ATATGGAT-TAATACAG_S16_L002_R1_001
KOLF2.2J derived knockout cell line, LHX9 CE, differentiated to cortical brain organoid


title: Form_H3K27ac_rep1


title: EAE_5ADB.Scramble_Astrocytes_1

description: Library name: EAE_5ADB.Scramble_Astrocytes_1


title: EAE_5ADB.AclyKD_Astrocytes_2

description: Library name: EAE_5ADB.AclyKD_Astrocytes_2


title: CBO-MOK20006C-A05, KO

description:
Library name: LHX9_CE_A5_Day14_GT23-09931_CGGACAAC-AATCCGGA_S13_L002_R1_001
KOLF2.2J derived knockout cell line, LHX9 CE, differentiated to cortical brain organoid


title: Form_H2BK5ac_rep2


title: EAE_4OTR.Ep300KD_Astrocytes_3

description: Library name: EAE_4OTR.Ep300KD_Astrocytes_3


title: Vehicle_M1, ATACseq

description:
Vehicle_M1_Vehicle_M2_vs_CXD101_M1_CXD101_M2_peaks.narrowPeak
Vehicle_M1_Vehicle_M2_vs_MS275_M1_MS275_M2_peaks.narrowPeak

value: Tumor

value: myeloid cells

value: WT

value: FACS isolation from tumor


title: CBO-MOK20006W-B02, KO

description:
Library name: LHX9_KO_B2_Day14_GT23-09930_TAAGTGGT-GGCTTAAG_S12_L002_R1_001
KOLF2.2J derived knockout cell line, LHX9 KO, differentiated to cortical brain organoid

value: iPSC

value: Full coding length


title: APPPS1_NLRP3_4m__1_2_11, time 4m


title: CBO-MOK20006W-A04, KO

description:
Library name: LHX9_KO_A4_Day14_GT23-09929_CTACGACA-TTGGACTC_S22_L002_R1_001
KOLF2.2J derived knockout cell line, LHX9 KO, differentiated to cortical brain organoid

value: Cortical brain (dorsal forebrain patterning)


title: Form_H2BK5ac_rep1


title: NLRP3_6m__1_1_27, time 6m


title: sWAT full-length

data_processing:
Quality control (QC) of raw Pac-Bio reads was carried out using SMRT Link Portal, and subsequent analysis was conducted utilizing the Iso-Seq3 pipeline (v3.8.2). Specifically, Circular Consensus Sequences (HiFi reads) were generated using CCS (v6.4.0). Following this, primer and SMRT adapters were removed using Lima (v2.7.1).
Artificial concatemer reads were removed and polyA tails were trimmed in Iso-Seq3 Refine. Full-length, non-chimeric (FLNC) reads were then generated and mapped to the monkey genome (fas5, Ensembl v92) using minimap2 (v2.24). Reads that mapped to multiple locations were excluded from downstream analysis.
Based on the Pac-Bio mapping results, full transcript information was generated. These full-length transcripts with multiple exons were used to generate isoform annotation. Transcripts are grouped to genes by its annotated  splice sites.
Assembly: fas5
Supplementary files format and content: Tab-based text file include raw gene counts for each tissue

organism: Macaca fascicularis

source_name: sWAT

extract_protocol:
The RNAs of the same tissue from 5 different monkeys are pooled together as one sample.
The full-length RNA-seq libraries were prepared and sequenced by Novogene in their Pac-Bio Sequel II platoform.

value: sWAT


title: EAE_4OTR.Ep300KD_Astrocytes_1

description: Library name: EAE_4OTR.Ep300KD_Astrocytes_1

value: Brain

value: Astrocytes


title: CBO-MOK20006W-A01, KO

description:
Library name: LHX9_KO_A1_Day14_GT23-09928_TCGTAGTG-CCAAGTCT_S27_L002_R1_001
KOLF2.2J derived knockout cell line, LHX9 KO, differentiated to cortical brain organoid


title: EAE_4OTR.Ep300KD_Astrocytes_2

description: Library name: EAE_4OTR.Ep300KD_Astrocytes_2


title: APPPS1_12m_Mxo4_1_1_57, time 12m


title: oWAT full-length

source_name: oWAT

value: oWAT


title: MCF-7, incubated 4OHEE2 (exp)

city: Tainan

first: Trang

middle: Quynh

last: Do

state: Taiwan

address: No. 1, Daxue Rd, East District, Tainan City, 701

department: Chemistry

country: Taiwan

institute: National Cheng Kung University

data_processing:
Raw FASTQ reads were quality and adaptor trimmed by fastp 0.20.0. Trimmed reads were mapped to the human reference genome GRCh38 by bowtie2 2.3.4.3
The control reads provided background information for deducing the folds of peak enrichment by MACS 2.2.4 with minimum FDR (q-value) cutoff value set to 0.05
The genecoverage plot was created with Rstudio
Assembly: hg38
Supplementary files format and content: bedgraph and narrowpeak

growth_protocol: MCF-7 cells were cultured in 15-cm dishes supplemented with DMEM and 10% FBS. The cells were maintained in a humidified incubator at 37°C and 5% CO2

extract_protocol:
When cells reached 80% confluence (1 × 107 cells), cells were harvested and crosslinked with 1% formaldehyde. The reaction was quenched in 125 mM glycine. Cells were then re-suspended in 800 μL cytosol extraction buffer (10 mM HEPES, 10 mM KCl, 1.5 mM DTT, 1% Triton X-100, 1x protease inhibitor, 5% glycerol) and incubated on ice for 15 minutes to permeabilize the cells. The pellets were subsequently digested with 4000 gel units of MNase for 1 hour at 37 °C in 100 μL of digestion buffer (50 mM Tris-HCl [pH 7.9], 5 mM CaCl2, 100 μl/mL bovine serum albumin) and arrested with 5 mM EDTA. The chromatin was harvested from the resulting supernatant by centrifugation at 16,000xg for 10 minutes and was determined to contain 500 μg total protein (determined by BCA assay) and 100 μg total DNA (measured by Thermo Scientific µdrop plate). The chromatin samples were  incubated with either solvent/ 4OHEE2 prior to DNA purification. The DNA adduct were then enriched by performing click probe-seq experiment. A total 10 ng DNA from three biological replicates were pooled together and sequencing.
The NGS library was constructed with an SSEL XT Low Input Reagent Kit with IDT for Illumina – TruSeq DNA UD Indexes following the manufacturer’s protocol by Welgene Co. core facility

value: 4OHEE2 (Exp)


title: APPPS1_NLRP3_12m__1_1_49, time 12m


title: EAE_4OTR.Scramble_Astrocytes_3

description: Library name: EAE_4OTR.Scramble_Astrocytes_3


title: WT_4m__1_1_1, time 4m


title: WT_12m_Mxo4_1_2_60, time 12m


title: MCF-7, incubated solvent (control/mock)

value: ACN (control)


title: muscle full-length

source_name: muscle

value: muscle


title: EAE_4OTR.Scramble_Astrocytes_1

description: Library name: EAE_4OTR.Scramble_Astrocytes_1


title: liver full-length

source_name: liver

value: liver


title: APPPS1_NLRP3_6m__1_2_28, time 6m

value: CD11b+ cells


title: immunoprecipitate, HHO1-2L-3FLAG, quiescent state, strain yTT6336

status: Public on Feb 02 2025

city: Seattle

first: Toshio

last: Tsukiyama

address: 1100 Fairview Ave N

institute: Fred Hutch Cancer Center

description: Library name: IP_WT_Q_Hho1_6336

data_processing:
Raw sequencing data were processed using Real-Time Analysis (RTA) software (version 3.10.30), followed by basecalling and sample demultiplexing with bcl2fastq (version 2.20) to generate FASTQ files.
ChIP-seq reads in FASTQ format were trimmed for adapter sequences and low-quality bases using Atria (version 4.0.3). For more details, see github.com/kalavattam/protocol_chipseq_signal_norm.
Paired-end ChIP-seq reads were aligned to a concatenated S. cerevisiae S288C (version R64-5-1) and S. pombe 972h- (version 2024-11-01) reference genome using Bowtie2 (version 2.5.4). For more details, see github.com/kalavattam/protocol_chipseq_signal_norm.
Alignments were filtered with Samtools (version 1.2.1) to retain those marked as properly paired (flag 0x2) with MAPQ scores greater than or equal to 1, allowing multi-mapping alignments with up to five mismatches. BAM files were then separated by species, with S. cerevisiae (main model organism) and S. pombe (spike-in organism) alignments written to organism-specific directories. For more details, see github.com/kalavattam/protocol_chipseq_signal_norm.
Filtered ChIP-seq alignments were used to generate 30 bp-binned signal tracks in bedGraph format. Fragment-bin overlaps were computed as "normalized coverage" (PMID: 37160995), a probability distribution of fragment density across the genome. Log-ratio tracks were generated by applying a log2 transformation to the IP-to-input normalized coverage ratio. IP efficiency tracks were computed as the product of the siQ-ChIP global normalizer (α; PMID: 32994221, 37160995) and the ratio of IP to input normalized coverage. Spike-in-scaled signal tracks were computed as the product of a separate scaling factor, derived from the proportion of S. pombe alignments in IP and input samples (PMID: 25437568), and the ratio of IP to input normalized coverage. For more details, see github.com/kalavattam/protocol_chipseq_signal_norm.
Assembly: S. cerevisiae S288C (version R64-5-1, sacCer3); S. pombe 972h- (version 2024-11-01)
Supplementary files format and content: Gzip-compressed bedGraph files containing binned signal values: normalized coverage, log2-transformed IP-to-input normalized coverage ratios, IP efficiency (siQ-ChIP), and spike-in-scaled signal.
Supplementary files format and content: Gzip-compressed tab-separated value (TSV) file containing sample metadata required for computing siQ-ChIP α proportionality constants.
Supplementary files format and content: Gzip-compressed FASTA file containing processed, concatenated S. cerevisiae and S. pombe reference genome sequences.
Supplementary files format and content: Gzip-compressed GFF3 file containing processed, concatenated S. cerevisiae and S. pombe genome feature annotations.

organism: Saccharomyces cerevisiae

growth_protocol: To obtain G1-arrested cells, cultures were grown to an OD600 of 0.2, treated with 5 μg/mL alpha factor for 80 minutes, and then collected. G2/M-arrested cells were obtained by growing cultures to an OD600 of 0.7, treating with 15 μg/mL nocodazole for over 120 minutes, and then collected. Quiescent cells were generated by culturing for 7 days, followed by purification using a Percoll density gradient.

extract_protocol:
Cells were disrupted using silica beads, followed by sonication with a Bioruptor UCD-200 (Diagenode) to fragment chromatin. Sonication was performed at high power for 15 minutes, with 30-second on/off cycles. For immunoprecipitation, S. cerevisiae chromatin was mixed with S. pombe spike-in chromatin prior to antibody incubation, with 1 µg of S. cerevisiae chromatin combined with 2.65 ng of S. pombe chromatin in 300 µL of buffer. Input samples consisted of 20 µL of chromatin, while 280 µL was used for immunoprecipitation. Immunoprecipitation was performed using 20 µL of Dynabeads Protein G (Invitrogen) pre-incubated with 2 µL of anti-FLAG M2 antibody (Sigma). Immunoprecipitation reactions were incubated with the antibody-conjugated beads for 90 minutes at room temperature with rotation. Beads were then washed under increasingly stringent conditions, and chromatin was eluted at 75°C. Crosslinks were reversed overnight at 65–75°C, followed by sequential RNase A and Proteinase K treatments. DNA was purified using a MinElute PCR Purification Kit (Qiagen), and concentrations were measured using PicoGreen quantification. The entire immunoprecipitation procedure was performed in three separate batches, with equivalent chromatin and bead amounts used across replicates.
ChIP-seq libraries were prepared using the Ovation Ultralow System V2 (Tecan). Input libraries were generated from 66.7 ng of starting material, while IP libraries were generated from 1 µg of DNA. Libraries underwent 11 cycles of PCR amplification on a thermocycler and were purified with AMPure XP (Agencourt) beads to retain fragments greater than 100 bp. Final library quality was assessed using a TapeStation system. Libraries were sequenced on a NextSeq 2000 (Illumina) using a 50-bp paired-end configuration with single 8-bp indexes.

treatment_protocol: Cells were fixed with 1% formaldehyde for 20 minutes. Crosslinking was quenched by adding glycine to a final concentration of 125 mM and incubating for 5 minutes at room temperature. Cells were then washed twice with cold PBS (phosphate buffered saline, used to remove residual fixative and quenching solution) before proceeding to lysis.

tag: strain

tag: cell cycle

value: Quiescence

value: MATa prototroph HHO1-2L-3FLAG

value: control

tag: chip antibody

value: FLAG M2 (Sigma, F1804)


title: immunoprecipitate, HMO1-2L-3FLAG, quiescent state, strain yTT7750

description: Library name: IP_WT_Q_Hmo1_7750

value: MATa prototroph HMO1-2L-3FLAG


title: immunoprecipitate, HHO1-2L-3FLAG, G2/M state, strain yTT6337

description: Library name: IP_WT_G2M_Hho1_6337

value: nocodazole


title: immunoprecipitate, HMO1-2L-3FLAG, G2/M state, strain yTT7751

description: Library name: IP_WT_G2M_Hmo1_7751


title: immunoprecipitate, HHO1-2L-3FLAG, G2/M state, strain yTT6336

description: Library name: IP_WT_G2M_Hho1_6336


title: EAE_4OTR.Scramble_Astrocytes_2

description: Library name: EAE_4OTR.Scramble_Astrocytes_2


title: immunoprecipitate, HMO1-2L-3FLAG, G1 state, strain yTT7750

description: Library name: IP_WT_G1_Hmo1_7750

value: alpha factor


title: input, HMO1-2L-3FLAG, quiescent state, strain yTT7750

description: Library name: in_WT_Q_Hmo1_7750


title: input, HMO1-2L-3FLAG, quiescent state, strain yTT7751

description: Library name: in_WT_Q_Hmo1_7751


title: immunoprecipitate, HHO1-2L-3FLAG, G1 state, strain yTT6336

description: Library name: IP_WT_G1_Hho1_6336


title: immunoprecipitate, HHO1-2L-3FLAG, G1 state, strain yTT6337

description: Library name: IP_WT_G1_Hho1_6337


title: immunoprecipitate, HMO1-2L-3FLAG, quiescent state, strain yTT7751

description: Library name: IP_WT_Q_Hmo1_7751


title: input, HHO1-2L-3FLAG, quiescent state, strain yTT6336

description: Library name: in_WT_Q_Hho1_6336


title: input, HMO1-2L-3FLAG, G2/M state, strain yTT7751

description: Library name: in_WT_G2M_Hmo1_7751


title: input, HHO1-2L-3FLAG, G2/M state, strain yTT6337

description: Library name: in_WT_G2M_Hho1_6337


title: input, HHO1-2L-3FLAG, quiescent state, strain yTT6337

description: Library name: in_WT_Q_Hho1_6337


title: input, HMO1-2L-3FLAG, G1 state, strain yTT7751

description: Library name: in_WT_G1_Hmo1_7751


title: input, HMO1-2L-3FLAG, G2/M state, strain yTT7750

description: Library name: in_WT_G2M_Hmo1_7750


title: input, HHO1-2L-3FLAG, G1 state, strain yTT6337

description: Library name: in_WT_G1_Hho1_6337


title: input, HHO1-2L-3FLAG, G2/M state, strain yTT6336

description: Library name: in_WT_G2M_Hho1_6336


title: input, HMO1-2L-3FLAG, G1 state, strain yTT7750

description: Library name: in_WT_G1_Hmo1_7750


title: Dmel_OSS_siTj_2_lnRNA

city: BOSTON

first: NELSON

middle: C

last: LAU

state: MA

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

description: Library name: Dmel_OSS_siTj_2_lnRNA

data_processing:
Small RNA samples were run through the Mosquito Small RNA Genomics (MSRG) pipeline. Outputs from MSRG include the alignment to genes and TEs. Total RNA libraries were sequenced as 50PE reads but were processed to look like small RNA reads so that they could also be run using the MSRG pipeline. All reads were trimmed to 35nt, R1 was reverse complemented to be in the same orientation as R2, and then the reverse complemented R1 was merged with R2. The resulting FASTQ file was then run through MSRG and processed just like the small RNA libraries. Differential expression for OSS knockdowns were done in R using DESeq2 on gene counts from the MSRG pipeline. The “cooksCutoff ” and “independentFiltering ” arguments in the results() function were set to FALSE. The piRNA cluster counting was performed from the SAM file from MSRG was filtered based on region of interest. CUT&RUN data underwent the same quality control and alignment procedures as ChIP-seq data, using FastQC and Bowtie2. However, duplicate reads were retained due to the nature of CUT&RUN, which is reasonable to generate duplicate reads. Peaks were called against IgG controls, keeping all duplicates with MACS2. H3K4me3 peaks were called using narrow peak mode, while H3K9me3 peaks were called using broad peak mode. Unlike ChIP-seq, blacklist regions were not filtered because CUT&RUN data has different characteristics, and no specific blacklist file is available. Additionally, CUT&RUN data was mapped to the E. coli genome to verify spike-in proportions. The calculated scale factors from this mapping were used to normalize the BigWig files.
Assembly: Dm6
Supplementary files format and content: BigWig files and gene counts text files

organism: Drosophila melanogaster

source_name: OSS

extract_protocol:
Total RNA was extracted using the protocol from the NEB Total RNA Miniprep kit. OSS cell nuclei lysate was prepared according to the Epicypher Cut&Run kit.  The chromatin lysate extract for TJ ChIPseq was prepared by this following protocol: OSS cells were grown in T75 flasks at 25o C and fixed with 2% p-formaldehyde in 1X PBS for 10 minutes at room temperature. Cells were then quenched with final concentration 0.125M glycine and harvested using a cell scrapper. Cells were pelleted and washed two times with cold 1X PBS +1% BSA. Next the cell pellet was resuspended in 500µL of MNase Lysis Buffer supplemented with 1mM DTT and 0.2% SDS. Cell lysate was then transferred to Micro Tube TPX Plastic tubes (Diagenode) and sonicated with medium wavelength for 10 cycles of 15 seconds on/ 30 seconds off using the Bioruptor UCD-200 (Diagenode). Samples were moved back to normal tubes and cell debris was pelleted. Supernatant was moved into a new tube and brought up to 2mL with ChIP-Dilution Buffer.
Small RNA libraries were generated following the protocol of the commercial NEBNext Small RNA library preparation kit for Illumina sequencing.  RNAseq libraries were generated following the protocol of the commercial ZymoSeq RiboFree Total RNA Library preparation kit.  The CUT&Run libraries were generated following the protocol of the commercial Epicypher Cut&Run library prep kit.  The ChIP-seq libraries were generated following the NEBNext Ultra II DNA Library Prep Kit for Illumina.

tag: cell line

value: OSS


title: Dmel_OSS_siPiwi_3_lnRNA

description: Library name: Dmel_OSS_siPiwi_3_lnRNA


title: immunoprecipitate, HHO1-2L-3FLAG, quiescent state, strain yTT6337

description: Library name: IP_WT_Q_Hho1_6337


title: Dmel_OSS_siTj_3_lnRNA

description: Library name: Dmel_OSS_siTj_3_lnRNA


title: input, HHO1-2L-3FLAG, G1 state, strain yTT6336

description: Library name: in_WT_G1_Hho1_6336


title: Dmel_OSS_siPiwi_2_lnRNA

description: Library name: Dmel_OSS_siPiwi_2_lnRNA


title: immunoprecipitate, HMO1-2L-3FLAG, G2/M state, strain yTT7750

description: Library name: IP_WT_G2M_Hmo1_7750


title: Dmel_OSS_siPiwi_1_lnRNA

description: Library name: Dmel_OSS_siPiwi_1_lnRNA


title: Dmel_OSS_siGFP_3_lnRNA

description: Library name: Dmel_OSS_siGFP_3_lnRNA


title: Dmel_OSS_siCi_2_lnRNA

description: Library name: Dmel_OSS_siCi_2_lnRNA


title: immunoprecipitate, HMO1-2L-3FLAG, G1 state, strain yTT7751

description: Library name: IP_WT_G1_Hmo1_7751


title: Dmel_OSS_siGFP_2_lnRNA

description: Library name: Dmel_OSS_siGFP_2_lnRNA


title: Dmel_OSS_siCi_3_lnRNA

description: Library name: Dmel_OSS_siCi_3_lnRNA


title: Dmel_OSS_siGFP_1_lnRNA

description: Library name: Dmel_OSS_siGFP_1_lnRNA


title: Dmel_OSS_siCi_1_lnRNA

description: Library name: Dmel_OSS_siCi_1_lnRNA


title: Dmel_FPSE2B_WT_lnRNA

description: Library name: Dmel_FPSE2B_WT_lnRNA

source_name: ovary

value: ovary


title: Dmel_FPSE2B_Mut_lnRNA

description: Library name: Dmel_FPSE2B_Mut_lnRNA


title: Dmel_FPSE2A_WT_lnRNA

description: Library name: Dmel_FPSE2A_WT_lnRNA


title: Dmel_OSS_siTj_1_lnRNA

description: Library name: Dmel_OSS_siTj_1_lnRNA


title: PIEZO2GOF mouse 11, Cre-, HFD

city: La Jolla

first: Yu

last: Wang

address: 10550 N. Torrey Pines Rd.

institute: Scripps Research

description:
Library name: gof_21
gof.tar

data_processing:
Salmon and DESeq2
Assembly: GRCm39 reference genome (Ensembl version 109)
Supplementary files format and content: salmon quant output

molecule: polyA RNA

source_name: inguinal adipose tissue

extract_protocol:
Total RNA extracted by Trizol and Qiagen RNAeasy kit. 100 ngs total RNA was polyA selected, fragmented and then converted to double stranded cDNA followed by ligation of sequencing adapters.
Total RNA samples were prepared into RNAseq libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs E7760L) following manufacturer’s recommended protocol. Briefly, for each sample 100 ngs total RNA was polyA selected, fragmented and then converted to double stranded cDNA followed by ligation of sequencing adapters.

value: inguinal adipose tissue

value: PIEZO2 GOF f/f

value: Cre- ,HFD


title: PIEZO2GOF mouse 11, Cre+, HFD

description:
Library name: gof_22
gof.tar

value: Cre+ ,HFD


title: PIEZO2GOF mouse 10, Cre-, HFD

description:
Library name: gof_20
gof.tar


title: PIEZO2GOF mouse 10, Cre+, HFD

description:
Library name: gof_19
gof.tar


title: Dmel_FPSE1_WT_lnRNA

description: Library name: Dmel_FPSE1_WT_lnRNA


title: PIEZO2GOF mouse 9, Cre+, Chow

description:
Library name: gof_18
gof.tar

value: Cre+ ,Chow


title: PIEZO2GOF mouse 9, Cre-, Chow

description:
Library name: gof_17
gof.tar

value: Cre- ,Chow


title: PIEZO2GOF mouse 8, Cre-, Chow

description:
Library name: gof_16
gof.tar


title: Dmel_FlamKG_Mut_lnRNA

description: Library name: Dmel_FlamKG_Mut_lnRNA


title: Dmel_FPSE1_Mut_lnRNA

description: Library name: Dmel_FPSE1_Mut_lnRNA


title: Dmel_FlamKG_WT_lnRNA

description: Library name: Dmel_FlamKG_WT_lnRNA


title: PIEZO2GOF mouse 8, Cre+, Chow

description:
Library name: gof_15
gof.tar


title: Dmel_FlamBG_Mut_lnRNA

description: Library name: Dmel_FlamBG_Mut_lnRNA


title: Dmel_FlamBG_WT_lnRNA

description: Library name: Dmel_FlamBG_WT_lnRNA


title: PIEZO2GOF mouse 7, Cre-, HFD

description:
Library name: gof_13
gof.tar


title: Dmel_FITS_WT_lnRNA

description: Library name: Dmel_FITS_WT_lnRNA


title: PIEZO2GOF mouse 6, Cre+, HFD

description:
Library name: gof_12
gof.tar


title: PIEZO2GOF mouse 6, Cre-, HFD

description:
Library name: gof_11
gof.tar


title: Dmel_FITS_Mut_lnRNA

description: Library name: Dmel_FITS_Mut_lnRNA


title: Dmel_OSS_siTj_3_smRNA

description: Library name: Dmel_OSS_siTj_3_smRNA

library_source: other

molecule: other


title: PIEZO2GOF mouse 7, Cre+, HFD

description:
Library name: gof_14
gof.tar


title: PIEZO2GOF mouse 5, Cre+, HFD

description:
Library name: gof_10
gof.tar


title: PIEZO2GOF mouse 5, Cre-, HFD

description:
Library name: gof_09
gof.tar


title: Dmel_OSS_siTj_1_smRNA

description: Library name: Dmel_OSS_siTj_1_smRNA


title: Dmel_OSS_siPiwi_3_smRNA

description: Library name: Dmel_OSS_siPiwi_3_smRNA


title: Dmel_FPSE2A_Mut_lnRNA

description: Library name: Dmel_FPSE2A_Mut_lnRNA


title: PIEZO2GOF mouse 4, Cre+, Chow

description:
Library name: gof_07
gof.tar


title: PIEZO2GOF mouse 3, Cre+, Chow

description:
Library name: gof_06
gof.tar


title: Dmel_OSS_siTj_2_smRNA

description: Library name: Dmel_OSS_siTj_2_smRNA


title: PIEZO2GOF mouse 3, Cre-, Chow

description:
Library name: gof_05
gof.tar


title: Dmel_OSS_siPiwi_1_smRNA

description: Library name: Dmel_OSS_siPiwi_1_smRNA


title: Dmel_OSS_siGFP_3_smRNA

description: Library name: Dmel_OSS_siGFP_3_smRNA


title: Dmel_OSS_siGFP_2_smRNA

description: Library name: Dmel_OSS_siGFP_2_smRNA


title: PIEZO2GOF mouse 2, Cre-, HFD

description:
Library name: gof_03
gof.tar


title: PIEZO2GOF mouse 2, Cre+, HFD

description:
Library name: gof_04
gof.tar


title: Dmel_OSS_siGFP_1_smRNA

description: Library name: Dmel_OSS_siGFP_1_smRNA


title: PIEZO2GOF mouse 1, Cre-, Chow

description:
Library name: gof_02
gof.tar


title: Dmel_OSS_siCi_3_smRNA

description: Library name: Dmel_OSS_siCi_3_smRNA


title: PIEZO2FF mouse 12, Cre-, chow

description:
Library name: lof_24
lof.tar

value: PIEZO2 f/f

value: Cre-, chow


title: Dmel_OSS_siCi_1_smRNA

description: Library name: Dmel_OSS_siCi_1_smRNA


title: PIEZO2FF mouse 12, Cre+, chow

description:
Library name: lof_23
lof.tar

value: Cre+, chow


title: Dmel_FPSE2B_WT_smRNA

description: Library name: Dmel_FPSE2B_WT_smRNA


title: Dmel_OSS_siCi_2_smRNA

description: Library name: Dmel_OSS_siCi_2_smRNA


title: PIEZO2FF mouse 11, Cre-, chow

description:
Library name: lof_22
lof.tar


title: PIEZO2FF mouse 11, Cre+, chow

description:
Library name: lof_21
lof.tar


title: PIEZO2GOF mouse 4, Cre-, Chow

description:
Library name: gof_08
gof.tar


title: Dmel_FPSE2B_Mut_smRNA

description: Library name: Dmel_FPSE2B_Mut_smRNA


title: Dmel_FPSE2A_Mut_smRNA

description: Library name: Dmel_FPSE2A_Mut_smRNA


title: Dmel_OSS_siPiwi_2_smRNA

description: Library name: Dmel_OSS_siPiwi_2_smRNA


title: Dmel_FPSE2A_WT_smRNA

description: Library name: Dmel_FPSE2A_WT_smRNA


title: Dmel_FPSE1_WT_smRNA

description: Library name: Dmel_FPSE1_WT_smRNA


title: PIEZO2FF mouse 9, Cre+, HFD

description:
Library name: lof_18
lof.tar

value: Cre+, HFD


title: Dmel_FPSE1_Mut_smRNA

description: Library name: Dmel_FPSE1_Mut_smRNA


title: PIEZO2FF mouse 8, Cre-, chow

description:
Library name: lof_15
lof.tar


title: PIEZO2FF mouse 7, Cre-, HFD

description:
Library name: lof_14
lof.tar

value: Cre-, HFD


title: PIEZO2FF mouse 8, Cre+, chow

description:
Library name: lof_16
lof.tar


title: PIEZO2FF mouse 9, Cre-, HFD

description:
Library name: lof_17
lof.tar


title: PIEZO2FF mouse 7, Cre+, HFD

description:
Library name: lof_13
lof.tar


title: Dmel_FITS_WT_smRNA

description: Library name: Dmel_FITS_WT_smRNA


title: Dmel_FlamBG_WT_smRNA

description: Library name: Dmel_FlamBG_WT_smRNA


title: Dmel_FlamBG_Mut_smRNA

description: Library name: Dmel_FlamBG_Mut_smRNA


title: PIEZO2FF mouse 6, Cre-, chow

description:
Library name: lof_11
lof.tar


title: Dmel_FlamKG_Mut_smRNA

description: Library name: Dmel_FlamKG_Mut_smRNA


title: Dmel_FITS_Mut_smRNA

description: Library name: Dmel_FITS_Mut_smRNA


title: PIEZO2FF mouse 5, Cre+, chow

description:
Library name: lof_10
lof.tar


title: PIEZO2FF mouse 5, Cre-, chow

description:
Library name: lof_09
lof.tar


title: Dmel_OSS_Tj39_3_ChIP

description: Library name: Dmel_OSS_Tj39_3_ChIP


title: PIEZO2FF mouse 10, Cre+, chow

description:
Library name: lof_20
lof.tar


title: Dmel_OSS_Input_3_ChIP

description: Library name: Dmel_OSS_Input_3_ChIP


title: PIEZO2FF mouse 10, Cre-, chow

description:
Library name: lof_19
lof.tar


title: PIEZO2FF mouse 4, Cre-, HFD

description:
Library name: lof_07
lof.tar


title: Dmel_OSS_IgG_2_ChIP

description: Library name: Dmel_OSS_IgG_2_ChIP


title: Dmel_OSS_Tj39_1_ChIP

description: Library name: Dmel_OSS_Tj39_1_ChIP


title: Dmel_OSS_Input_2_ChIP

description: Library name: Dmel_OSS_Input_2_ChIP


title: Dmel_OSS_IgG_3_ChIP

description: Library name: Dmel_OSS_IgG_3_ChIP


title: PIEZO2FF mouse 4, Cre+, HFD

description:
Library name: lof_08
lof.tar


title: PIEZO2FF mouse 2, Cre-, HFD

description:
Library name: lof_04
lof.tar


title: PIEZO2FF mouse 3, Cre+, HFD

description:
Library name: lof_05
lof.tar


title: PIEZO2GOF mouse 1, Cre+, Chow

description:
Library name: gof_01
gof.tar


title: Dmel_FlamKG_WT_smRNA

description: Library name: Dmel_FlamKG_WT_smRNA


title: Dmel_OSS_Tj39_2_ChIP

description: Library name: Dmel_OSS_Tj39_2_ChIP


title: PIEZO2FF mouse 3, Cre-, HFD

description:
Library name: lof_06
lof.tar


title: PIEZO2FF mouse 6, Cre+, chow

description:
Library name: lof_12
lof.tar


title: PIEZO2FF mouse 1, Cre-, HFD

description:
Library name: lof_02
lof.tar


title: Dmel_OSS_H3K9me3_siTj_CutRun

description: Library name: Dmel_OSS_H3K9me3_siTj_CutRun

data_processing:
Small RNA samples were run through the Mosquito Small RNA Genomics (MSRG) pipeline. Outputs from MSRG include the alignment to genes and TEs. Total RNA libraries were sequenced as 50PE reads but were processed to look like small RNA reads so that they could also be run using the MSRG pipeline. All reads were trimmed to 35nt, R1 was reverse complemented to be in the same orientation as R2, and then the reverse complemented R1 was merged with R2. The resulting FASTQ file was then run through MSRG and processed just like the small RNA libraries. Differential expression for OSS knockdowns were done in R using DESeq2 on gene counts from the MSRG pipeline. The “cooksCutoff ” and “independentFiltering ” arguments in the results() function were set to FALSE. The piRNA cluster counting was performed from the SAM file from MSRG was filtered based on region of interest. CUT&RUN data underwent the same quality control and alignment procedures as ChIP-seq data, using FastQC and Bowtie2. However, duplicate reads were retained due to the nature of CUT&RUN, which is reasonable to generate duplicate reads. Peaks were called against IgG controls, keeping all duplicates with MACS2. H3K4me3 peaks were called using narrow peak mode, while H3K9me3 peaks were called using broad peak mode. Unlike ChIP-seq, blacklist regions were not filtered because CUT&RUN data has different characteristics, and no specific blacklist file is available. Additionally, CUT&RUN data was mapped to the E. coli genome to verify spike-in proportions. The calculated scale factors from this mapping were used to normalize the BigWig files.
Assembly: Dm6
Supplementary files format and content: BigWig files and gene counts text files
Library strategy: CUT&Run


title: C2C12 myoblasts, LMNA-R482L, rep2

city: Saint Petersburg

first: Oksana

last: Ivanova

address: 2 Akkuratova street

department: Institute of Molecular Biology and Genetics

country: Russia

institute: Almazov National Medical Research Centre

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing was made by inbuilt Nextseq 2000 software, barcoded processing and gene counting were made using Cell Ranges software v6.1.2 with the 10X pre-built mouse reference (refdata-gex-mm10-2020-A) (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Matrices in the Hierarchical Data Format (HDF5 or H5) produced by Cell Ranger

source_name: C2C12 myoblasts

extract_protocol:
After C2C12 cells culturing in 6-well plates in proliferation medium (DMEM supplemented with 4.5 g/L D-glucose, L-glutamine, penicillin-streptomycin, and 20% FCS), C2C12 cells were harvested using Trypsin, washed with PBS and resuspended in PBS.
Library was performed according to the manufacturer's instructions (Single Cell 3' v3.1 protocol, 10X Genomics). Briefly, C2C12 cells suspensions with the targeted cell recovery rate 5000 cells per sample were loaded onto 10x Genomics Single Cell fluidics chips to generate GEMs (Gel Beads-in-emulsion) which include gel beads coated with specific oligonucleotide barcodes to index each cell’s transcriptome and Unique Molecular Identifiers (UMI) to define individual transcripts. Uniquely barcoded RNAs were reverse transcribed, and individual cDNAs were amplified using a bench top Veriti™ 96-well thermal cycler (Applied Biosystems). Each library was barcoded with different indexes from a Chromium i7 Multiplex Kit. Barcoded libraries were then pooled and sequenced on the Illumina NextSeq 2000 system.

value: C2C12 myoblasts

tag: cell type

value: myoblasts

value: bearing mutation R482L


title: Dmel_OSS_H3K9me3_siGFP_CutRun

description: Library name: Dmel_OSS_H3K9me3_siGFP_CutRun


title: PIEZO2FF mouse 1, Cre+, HFD

description:
Library name: lof_01
lof.tar


title: C2C12 myoblasts, LMNA-R482L, rep1

description: 10X Genomics


title: Dmel_OSS_H3K4me3_siGFP_CutRun

description: Library name: Dmel_OSS_H3K4me3_siGFP_CutRun


title: C2C12 myoblasts, LMNA-WT

description: 10X Genomics

value: wild-type


title: Dmel_OSS_H3K9me3_Plain_1_CutRun

description: Library name: Dmel_OSS_H3K9me3_Plain_1_CutRun

value: OSS


title: Exp 2 non-targeting sg1 (540)

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

data_processing:
The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 run with paired-end 75bp reads at the Dana-Farber Cancer Institute Molecular Biology Core Facilities. Sequenced reads were mapped to reference genome and transcript.
Reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned to the hg19 assembly using the gene, transcript, and exon features of Ensembl (release 67) gene model. Expression was estimated using RSEM (version 1.2.30).
Assembly: hg19
Supplementary files format and content: comma-delimited text files include RSEM expected read count values for each sample

source_name: Hematopoietic

growth_protocol: SET-2 cells were grown in RPMI supplemented with 1% P/S and 20% FCS at a density of 500,000-1,500,000 cells/ml.

extract_protocol:
Total RNA was extracted from on day 20 (biological replicate 1) and 25 (biological replicate 2) post sgRNA transduction using the RNeasy Mini Kit (Qiagen) with on-column DNAse I digestion as per manufacturer’s protocol.
RNA-Seq libraries were prepared using Roche Kapa mRNA HyperPrep sample preparation kits from 200ng of purified total RNA according to the manufacturer’s protocol.

value: Hematopoietic

value: Essential thrombocythemia at megakaryoblastic leukemic transformation

value: ZRSR2 wildtype


title: Dmel_OSS_H3K4me3_Plain_2_CutRun

description: Library name: Dmel_OSS_H3K4me3_Plain_2_CutRun


title: Dmel_OSS_H3K9me3_Plain_2_CutRun

description: Library name: Dmel_OSS_H3K9me3_Plain_2_CutRun


title: Exp 2 non-targeting sg2 (541)


title: Exp 2 ZRSR2 KO sg2 (538)

value: ZRSR2 KO


title: Exp 2 ZRSR2 KO sg1 (537)


title: Dmel_OSS_H3K4me3_Plain_1_CutRun

description: Library name: Dmel_OSS_H3K4me3_Plain_1_CutRun


title: Exp 1 ZRSR2 KO sg2 (138)


title: Exp 1 non-targeting sg2 (141)


title: Exp 1 non-targeting sg1 (140)


title: X25Kpa_R2.FPKM

city: Changsha

first: kangtao

last: wang

state: Hunan

address: No. 87 Xiangya Road

department: Department of General and Vascular Surgery

country: China

institute: Xiangya Hospital, Central South University

description: FASTQ files undergo quality assessment and potential coding prediction. Afterward, the reads are normalized to FPKM, and a matrix file is created.

data_processing:
Clean reads were aligned to the reference genome using HISAT. Transcript assembly was then performed with StringTie to identify novel transcript structures.
The coding potential of newly identified transcripts was predicted using a combination of three software tools—CPC, txCdsPredict, and CNCI—as well as the Pfam database. Transcripts were classified as mRNA or lncRNA only if at least three of these evaluation methods agreed on the classification.
Clean reads were aligned to the reference sequence using Bowtie2. Gene and transcript expression levels were calculated with RSEM, and FPKM normalization was applied to facilitate comparison across samples.
Assembly: hg18
Supplementary files format and content: tab-delimited text file includes FPKM for each Sample

source_name: Human Colorectal Cancer Cell Line

growth_protocol: W480 cells were maintained in Leibovitz's L-15 medium (Gibco) with 10% fetal bovine serum (FBS), 2mM L-glutamine, 0.1mg/mL streptomycin, and 100U/mL penicillin at 37°C in a standard humidity incubator.

extract_protocol:
Cells were harvested by scraping, and the reaction was stopped with a complete medium. The cell suspension was centrifuged, washed with PBS, and treated with TRIzol reagent (Life Technologies) for RNA extraction.
The library construction was carried out following the Illumina HiSeq platform guidelines and in accordance with the requirements set by BGI (formerly known as Berry Genomics and now referred to as BGI Genomics).

treatment_protocol: SW480 cells were cultured on 6-well plates coated with 2 kPa or 25 kPa hydrogels (MATRIGEN, USA). Plates were washed with PBS, and 2 ml of cell suspension at 1×10^6 cells/ml was added to each well. Each stiffness condition was tested in triplicate, and cells were incubated at 37°C in a CO2-free incubator for 72 hours.

value: Human Colorectal Cancer Cell Line

value: Human Colorectal Cancer Cell

value: WT

value: 25kpa hardness medium culture


title: OVCAR3 cells, 45μM Atovaquone treated, 48 hours, batch C, replicate 3

city: Madison

first: Alexander

middle: J

last: Fagan

state: WI

address: 1300 University Ave Room 1220

department: Department of Statistics

institute: UW-Madison

description: Library name: IC75_48_C_3

data_processing:
Gene expression counts were obtained using RSEM (RRID:SCR_000262) with the STAR aligner (RRID:SCR_004463).
Assembly: GRCh38 release 112
Supplementary files format and content: Tab-delimited text file containing estimated counts for each sample

growth_protocol: OVCAR3 (RRID:CVCL_0465) and OVCAR5 ((RRID:CVCL_1628) cell lines of female biological sex were utilized. Cells were maintained in the recommended culture media and incubated at 37°C in a humidified atmosphere with 5% CO2. Cell lines were used within six months of purchase or validated by Single Tandem Repeat (STR) analysis performed by the Translational Research Initiatives in Pathology (TRIP) laboratory at the University of Wisconsin, Madison. Cell lines were tested for mycoplasma regularly using the MycoscopeTM PCR Mycoplasma Detection

extract_protocol:
RNA extraction was performed using the RNeasy Mini kit from Qiagen.
Library preparation and RNA sequencing were performed by Novogene.

treatment_protocol: OVCAR3 cells were treated with atovaquone and vehicle (DMSO) at the stated concentrations and collected at different time points post-treatment using TRIzol. Three biological replicates were used for each experimental condition.

value: High-grade serous ovarian adenocarcinoma

value: 45μM Atovaquone

value: Hour 48

tag: replicate

tag: batch

value: C


title: OVCAR3 cells, 45μM Atovaquone treated, 48 hours, batch C, replicate 1

description: Library name: IC75_48_C_1

tag: genotype


title: OVCAR3 cells, untreated, 24 hours, batch A, replicate 1

description: Library name: NT_24_A_1

tag: treatment

value: untreated

value: Hour 24

value: A


title: Exp 1 ZRSR2 KO sg1 (137)


title: OVCAR3 cells, untreated, 24 hours, batch C, replicate 1

description: Library name: NT_24_C_1

value: B


title: X25Kpa_R3.FPKM


title: OVCAR3 cells, 45μM Atovaquone treated, 48 hours, batch C, replicate 2

description: Library name: IC75_48_C_2


title: X25Kpa_R1.FPKM


title: OVCAR3 cells, 30μM Atovaquone treated, 48 hours, batch C, replicate 3

description: Library name: IC50_48_C_3

value: 30μM Atovaquone


title: OVCAR3 cells, 30μM Atovaquone treated, 48 hours, batch C, replicate 1

description: Library name: IC50_48_C_1


title: Dmel_OSS_IgG_1_ChIP

description: Library name: Dmel_OSS_IgG_1_ChIP

value: OSS


title: Dmel_OSS_H3K4me3_siTj_CutRun

description: Library name: Dmel_OSS_H3K4me3_siTj_CutRun


title: OVCAR3 cells, 30μM Atovaquone treated, 48 hours, batch C, replicate 2

description: Library name: IC50_48_C_2


title: Dmel_OSS_Input_1_ChIP

description: Library name: Dmel_OSS_Input_1_ChIP


title: X2Kpa_R2.FPKM

value: 2kpa hardness medium culture


title: X2Kpa_R3.FPKM


title: PIEZO2FF mouse 2, Cre+, HFD

description:
Library name: lof_03
lof.tar

value: inguinal adipose tissue

value: PIEZO2 f/f

value: Cre+, HFD


title: OVCAR3 cells, untreated, 24 hours, batch B, replicate 1

description: Library name: NT_24_B_1


title: X2Kpa_R1.FPKM

value: Human Colorectal Cancer Cell Line

value: Human Colorectal Cancer Cell


title: OVCAR3 cells, DMSO treated, 48 hours, batch C, replicate 1

description: Library name: D_48_C_1

value: WT

value: DMSO


title: OVCAR3 cells, DMSO treated, 48 hours, batch C, replicate 2

description: Library name: D_48_C_2

value: High-grade serous ovarian adenocarcinoma


title: ZR01-Jak2VF+Zrsr2-m5

data_processing:
Reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned  to the GRCm38 assembly using the gene, transcript, and exon features of Ensembl (release 67) gene model. Expression was estimated using RSEM (version 1.2.30).
Assembly: GRCm38
Supplementary files format and content: comma-delimited text files include RSEM expected read count values for each sample

source_name: Bone marrow

extract_protocol:
Total RNA was extracted from sorted Lineage- Sca1+ Kit+ (LSK) cells using Arcturus PicoPure RNA Isolation Kit (Applied Biosystems)
Following RNA isolation and quantification, 5 ng of total RNA was used to prepare the cDNA libraries as per the manufacturer’s protocol (NEB Next Ultra II RNA Library Prep Kit for Illumina, New England BioLabs). Briefly, polyA RNA was isolated, fragmented and primed prior to cDNA synthesis, end repair/dA tailing and Illumina adaptor ligation. The resulting products were PCR enriched /indexed with size selection and quantitation before sequencing.

value: Bone marrow

value: Lineage- Sca1+ Kit+

value: tamoxifen


title: OVCAR3 cells, 45μM Atovaquone treated, 24 hours, batch B, replicate 1

description: Library name: IC75_24_B_1

value: 45μM Atovaquone

value: Hour 24


title: OVCAR3 cells, 45μM Atovaquone treated, 24 hours, batch A, replicate 1

description: Library name: IC75_24_A_1

value: A


title: NHR gene WPS series main plate - even columns - replicate 2

city: Worcester

first: Xuhang

state: Massachusetts

address: 55 N Lake Ave

department: Department of Systems Biology

institute: University of Massachusetts Medical School

description:
NHR_rep2_even_lib
Multiplexed RNA-seq library generated by Worm Perturb-seq (WPS) technology. Contains samples for 44 NHR gene RNAi knockdowns and two empty vector control treatment. To analyze the data, refer to our publication and supplementary files for the metadata (barcode) table and WPS data processing pipeline. Samples with bad quality were not included in the metadata table. This library was sequenced three times because the first two runs had low yield.

data_processing:
As part of the WPS data processing pipeline, raw reads were processed using an in-house dolphinNext pipeline to generate a gene-by-sample read count matrix.
Raw reads were demultiplexed by a homemade python script that extracts the barcode information from read 1 and combines that with read 2.
The processed reads were passed to Trimmomatic (v0.32) to remove polyA and adaptor sequences.
Next, reads were aligned to the C. elegans genome (WormBase WS279) by STAR (parameter: --runThreadN 4 --alignIntronMax 25000 --outFilterIntronMotifs RemoveNoncanonicalUnannotated).
Finally, the output bam file was processed by ESAT to obtain the read counts of genes. In ESAT, we used an extension window of 1000 bp and the ‘proper’ method of multiple mappings. Unique Molecular Identifier (UMI) features were not used by setting umiMin = 1. Read counts, rather than UMI counts, were used as the gene expression quantity. We did not observe significant PCR duplicates during the development of our method (i.e., read counts highly correlate with UMI counts, data not shown), which is consistent with the low number of PCR cycles for library construction. Therefore, we directly used the read counts regardless of the presence of UMI in our library.
Assembly: WormBase WS279
Supplementary files format and content: a comma-separated values (CSV) file for the gene-by-sample read count matrix
Supplementary files format and content: a comma-separated values (CSV) file detailed annotation of sample barcode and sample information for all libraries included here

organism: Caenorhabditis elegans

source_name: Whole animal (excluding eggs)

growth_protocol: The N2 strain was used as the wild-type strain. Animals were maintained at 20°C on nematode growth media (NGM) and fed with E. coli HT115 containing the empty RNAi vector L4440. In WPS experiments, animals were fed with the RNAi bacteria from first larval (L1) stage, followed by incubation at 20°C for approximately 63 hours to collect gravid adults. In cases where RNAi feeding led to developmental delays, synchronized L1 animals were initially fed with vector control RNAi-containing bacteria and animals were transferred to the corresponding RNAi plates at 17 hours (L2 stage) to circumvent RNAi-associated developmental delays. By delayed RNAi exposure, animals typically developed to gravid adult stage at similar stage as control. The animal culture for developmental stage dataset followed the same procedure as described above, including the induction of dsRNA expression using empty vector control bacteria. The supplementary metadata table includes condition-specific growth information (i.e., seeding stages).

extract_protocol:
Animals were transferred to 96-well plates for high-throughput RNA extraction following protocol described in the WPS method paper. Importantly, this method only extracts total RNA from adult animal tissues and leaves any eggs intact.
Extracted total RNA was barcoded during reverse transcription to enable early pooling of samples. Multiplexed RNA-seq libraries each containing ~50 samples were constructed following a protocol adapted from the CEL-seq2 single-cell RNA-seq library construction method (Hashimshony, Genome Biology, 2016). For detailed protocols, refer to our WPS method paper. This library construction method produces a multiplexed RNA-seq library comprising ~50 samples. The sample pooling strategy differs from standard WPS due to historical reasons. Specifically, samples from the main plate were pooled by replicates, i.e., samples in the same biological replicate were pooled together. Samples from the supplementary plates were pooled in a mixed manner: the supplementary plate - lib1 contains samples from up to three replicates; the supplementary plate - lib2 contains samples only from replicate #1, except for vector control samples.

treatment_protocol: See "growth protocol".

value: Whole animal (excluding eggs)

tag: developmental stage

value: Gravid adult (63-66 hours post L1 seeding)

tag: Sex

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for 44 NHR  genes


title: ZR01-Jak2VF+Zrsr2-m2


title: ZR01-Jak2VF+Zrsr2-m1


title: OVCAR3 cells, DMSO treated, 48 hours, batch C, replicate 3

description: Library name: D_48_C_3

value: Hour 48

value: C


title: OVCAR3 cells, 30μM Atovaquone treated, 24 hours, batch B, replicate 1

description: Library name: IC50_24_B_1

value: 30μM Atovaquone

value: B


title: OVCAR3 cells, 30μM Atovaquone treated, 24 hours, batch B, replicate 2

description: Library name: IC50_24_B_2

value: WT


title: Mus musculus Macrophage CD11cCre Casp8flox/flox Female Young, Replicate 5

city: Chicago

first: Deborah

middle: R

last: Winter

state: IL

address: 240 E. Huron Street, M300

institute: Northwestern University

description:
Library name: Mac_Y_CreCOM5
CD11cC8_Y_F5_MACS

data_processing:
Raw sequencing files were de-multiplexed using bcl2fastq.
Adapter sequences and low-quality bases were trimmed using bbduk.
Trimmed reads were aligned to the mouse genome (mm10) using STAR aligner.
Gene expression counts were quantified using HTSeq with GRCm38 gene reference.
Normalized expression values were calculated as counts per million (CPM).
Assembly: mm10
Supplementary files format and content: tab-delimited table of RNA counts across all samples
Supplementary files format and content: tab-delimited table of CPM values across all samples

source_name: brain

growth_protocol: Mice were housed in a barrier/specific-pathogen-free facility with controlled temperature and humidity. Female mice aged 5-6 months (young cohort) and 11-12 months (old cohort) were used for all experiments.

extract_protocol:
Brain tissues were harvested immediately following perfusion with ice-cold HBSS. Brains were dissociated using a combination of mechanical and enzymatic digestion (Liberase TL and DNase I), and cell populations were sorted by FACS based on surface markers. RNA was extracted from FACS-purified populations using the PicoPure RNA Isolation Kit following the manufacturer’s protocol.
RNA-seq libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina (Lexogen Inc.). Libraries were indexed and amplified according to the manufacturer's instructions. Samples were excluded based on experimental and technical factors that impact their quality.

tag: age

value: Young:5 - 6 months

value: brain

value: macrophage

value: CD11ccre Casp8flox/flox


title: Mus musculus Macrophage CD11cCre Casp8flox/flox Female Young, Replicate 3

description:
Library name: Mac_Y_CreCOM3
CD11cC8_Y_F3_MACS


title: Mus musculus Macrophage CD11cCre Casp8flox/flox Female Young, Replicate 4

description:
Library name: Mac_Y_CreCOM4
CD11cC8_Y_F4_MACS


title: Mus musculus Macrophage CD11cCre Casp8flox/flox Female Old, Replicate 3

description:
Library name: Mac_O_CreCOM3
CD11cC8_O_F3_MACS

value: Old:11 - 12 months


title: OVCAR3 cells, DMSO treated, 24 hours, batch B, replicate 2

description: Library name: D_24_B_2

value: High-grade serous ovarian adenocarcinoma

value: DMSO

tag: time


title: ZR01-Jak2VF+EV-m5

value: Bone marrow

value: Lineage- Sca1+ Kit+

value: tamoxifen


title: Mus musculus Macrophage CD11cCre Casp8flox/flox Female Old, Replicate 4

description:
Library name: Mac_O_CreCOM4
CD11cC8_O_F4_MACS


title: ZR01-Jak2VF+Zrsr2-m3


title: TWT3

city: Baltimore

first: Michael

last: Wolfgang

state: MD

address: 855 N. Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: Johns Hopkins University School of Medicine

description: Library name: Sample 11

data_processing:
RNA-seq raw reads were filtered to remove reads containing adapters or reads of low quality.
Clean reads were mapped to the reference genome (GRCm38/mm10) using the HISAT2 software.
Gene counts were extracted and gene expression levels were estimated by the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM).
Pairwise comparisons of differential gene expression analysis was performed by read count normalization, model dependent p-value estimation, and FDR value estimation based on multiple hypothesis testing by Novogene's standard procedures.
Assembly: GRCm38/mm10
Supplementary files format and content: gene_count.txt includes raw readcount list with the annotation of each gene for each sample. Tab-delimited text file.
Supplementary files format and content: gene_fpkm.txt includes the FPKM list with the annotation of each gene for each sample.Tab-delimited text file.
Supplementary files format and content: Cpt2Atf3DKOvsCpt2KO_deg.txt includes the differential analysis results of all genes when comparing Atf3;Cpt2 liver-specific DKO to Cpt2 liver-specific KO livers. Tab-delimited text file.
Supplementary files format and content: Cpt2Atf3DKOvsControl_deg.txt includes the differential analysis results of all genes when comparing Atf3;Cpt2 liver-specific DKO to control livers. Tab-delimited text file.
Supplementary files format and content: Cpt2KOvsControl_deg.txt includes the differential analysis results of all genes when comparing Cpt2 liver-specific KO to control livers. Tab-delimited text file.

extract_protocol:
Total RNA was extracted from flash frozen liver tissue using TRIzol reagent (Invitrogen for Thermo Fisher Scientific, 15596026) with additional purification using RNeasy Mini Kit (Qiagen, 74106), as per manufacturers’ instructions. RNA quality was assessed by nanodrop and independently by Novogene Corporation Inc (https://en.novogene.com/services/research-services/transcriptome-sequencing/).
RNA libraries for RNA-seq were prepared by Novogene following Novogene's standard protocols.

value: liver

value: CPT1A/1B/2 triple floxed control

value: 24hr fast


title: TWT4

description: Library name: Sample 12


title: OVCAR3 cells, 30μM Atovaquone treated, 24 hours, batch A, replicate 1

description: Library name: IC50_24_A_1

value: Hour 24

value: A


title: TWT2

description: Library name: Sample 10


title: CPT24

description: Library name: Sample 8

value: CPT2 liver-specific KO


title: ZR01-Jak2VF+EV-m4


title: ZR01-Jak2VF+EV-m3


title: NHR gene WPS series main plate - odd columns - replicate 2

description:
NHR_rep2_odd_lib
Multiplexed RNA-seq library generated by Worm Perturb-seq (WPS) technology. Contains samples for 45 NHR gene RNAi knockdowns and two empty vector control treatment. To analyze the data, refer to our publication and supplementary files for the metadata (barcode) table and WPS data processing pipeline. Samples with bad quality were not included in the metadata table. This library was sequenced three times because the first two runs had low yield.

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for 45 NHR  genes


title: OVCAR3 cells, 45μM Atovaquone treated, 24 hours, batch B, replicate 2

description: Library name: IC75_24_B_2

value: WT

value: 45μM Atovaquone

value: B


title: Mus musculus Macrophage CD11cCre Casp8flox/flox Female Old, Replicate 1

description:
Library name: Mac_O_CreCOM1
CD11cC8_O_F1_MACS

value: Old:11 - 12 months

value: brain

value: macrophage

value: CD11ccre Casp8flox/flox


title: OVCAR3 cells, DMSO treated, 24 hours, batch B, replicate 1

description: Library name: D_24_B_1

value: High-grade serous ovarian adenocarcinoma

value: DMSO


title: CPT23

description: Library name: Sample 7

value: liver

value: 24hr fast


title: Mus musculus Macrophage Casp8flox/flox Female Young, Replicate 6

description:
Library name: Mac_Y_WT6
C8_Y_F6_MACS

value: Young:5 - 6 months


title: TWT1

description: Library name: Sample 9

value: CPT1A/1B/2 triple floxed control


title: CPT22

description: Library name: Sample 6

value: CPT2 liver-specific KO


title: A3C2DKO4

description: Library name: Sample 4

value: ATF3;CPT2 liver-specific double KO


title: CPT21

description: Library name: Sample 5


title: Mus musculus Macrophage Casp8flox/flox Female Young, Replicate 2

description:
Library name: Mac_Y_WT2
C8_Y_F2_MACS


title: OVCAR3 cells, 45μM Atovaquone treated, 8 hours, batch A, replicate 1

description: Library name: IC75_8_A_1

value: Hour 8

value: A


title: A3C2DKO3

description: Library name: Sample 3


title: OVCAR3 cells, 45μM Atovaquone treated, 8 hours, batch B, replicate 2

description: Library name: IC75_8_B_2

value: WT


title: kalta4, 6 dpf, rep8

first: Summer

last: Thyme

address: 364 Plantation St

institute: UMass Chan Medical School

description: Library name: Sample 8

data_processing:
Single-end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner (2.7.3a-GCC-6.4.0-2.28).
The raw counts files from STAR, in this record, were normalized using the rlog method in DESeq2 for subsequent published analysis.
Assembly: GRCz11
Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.

organism: Danio rerio

source_name: head with eyes, 3-5 heads combined

extract_protocol:
RNA was extracted using the MicroElute Total RNA Kit (Omega Bio-Tek R6834-02), with a 15-min incubation with Dnase I.
Libraries were constructed using an in-house protocol based on SMART-Seq2, followed by Nextera XT Library Preparation (FC-131-1096).

value: head with eyes, 3-5 heads combined

value: elavl3:kalta4 wildtype siblings


title: OVCAR3 cells, 30μM Atovaquone treated, 8 hours, batch B, replicate 2

description: Library name: IC50_8_B_2

value: 30μM Atovaquone

value: B


title: OVCAR3 cells, 45μM Atovaquone treated, 8 hours, batch B, replicate 1

description: Library name: IC75_8_B_1

value: 45μM Atovaquone


title: kalta4, 6 dpf, rep6

description: Library name: Sample 6


title: kalta4, 6 dpf, rep7

description: Library name: Sample 7


title: Mus musculus Macrophage Casp8flox/flox  Female Old, Replicate 4

description:
Library name: Mac_O_WT4
C8_O_F4_MACS

value: Old:11 - 12 months

value: brain

value: macrophage


title: Mus musculus Macrophage Casp8flox/flox Female Young, Replicate 1

description:
Library name: Mac_Y_WT1
C8_Y_F1_MACS


title: Mus musculus Macrophage Casp8flox/flox  Female Old, Replicate 2

description:
Library name: Mac_O_WT2
C8_O_F2_MACS


title: OVCAR3 cells, 30μM Atovaquone treated, 8 hours, batch B, replicate 1

description: Library name: IC50_8_B_1

value: High-grade serous ovarian adenocarcinoma


title: A3C2DKO2

description: Library name: Sample 2

value: liver

value: 24hr fast


title: ZR01-Ja2kVF+EV-m2

value: Bone marrow

value: Lineage- Sca1+ Kit+

value: tamoxifen


title: OVCAR3 cells, 30μM Atovaquone treated, 8 hours, batch A, replicate 1

description: Library name: IC50_8_A_1

value: Hour 8


title: A3C2DKO1

description: Library name: Sample 1

value: ATF3;CPT2 liver-specific double KO


title: kalta4, 6 dpf, rep4

description: Library name: Sample 4

value: elavl3:kalta4 heterozygous transgenic


title: Mus musculus Microglia CD11cCre Casp8flox/flox  Female Old, Replicate 5

description:
Library name: Microglia_O_CreCOM5
CD11cC8_O_F5_MIC

value: microglia

value: CD11ccre Casp8flox/flox


title: OVCAR3 cells, DMSO treated, 24 hours, batch A, replicate 1

description: Library name: D_24_A_1

value: WT

value: DMSO

value: Hour 24

value: A


title: kalta4, 6 dpf, rep3

description: Library name: Sample 3

value: head with eyes, 3-5 heads combined


title: ZR01-Jak2VF+EV-m1


title: cKO - Nestin-Cre; TDP-43 homozygous conditional knockout mouse, Thalamus, ID-154

first: Shuo-Chien

last: Ling

state: Singapore

address: 12 Science Drive 2, MD1, 16-03-H

department: Physiology

institute: National University of Singapore

description: Library name: THL_154

data_processing:
The RNA-seq reads were pseudoaligned and quantified using kallisto v.46.1 with default parameters and 100 bootstraps.
Assembly: GRCm39 GENCODE vM29 Ensembl 106
Supplementary files format and content: abundance.h5: HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length.
Supplementary files format and content: abundance.tsv.gz: plaintext file of the abundance estimates (estimated counts, TPM and effective length of transcript). These files do not contain bootstrap estimates.

source_name: Thalamus

growth_protocol: The mice were maintained at C57BL/6J background and housed in groups with individually ventilated cages under a 12:12-hour light/dark cycle and access to food/water ad libitum. Conditional TDP-43 (Tardbp-fl/fl) mice (stock number 017591) and Nestin-Cre (stock number 003771) were purchased from the Jackson Laboratory.

extract_protocol:
Cortex and thalamus tissues were dissected from 14.5 days old embryonic mice brains and flash frozen under liquid nitrogen. The RNA was harvested using Trizol reagent
RNA-Seq libraries were contructed using the Illumina TruSeq Sample Prep Kit

value: Thalamus

value: Nestin-Cre; TDP-43 f/f

value: female


title: OVCAR3 cells, DMSO treated, 8 hours, batch B, replicate 2

description: Library name: D_8_B_2

value: High-grade serous ovarian adenocarcinoma

value: B


title: Mus musculus Microglia CD11cCre Casp8flox/flox  Female Old, Replicate 4

description:
Library name: Microglia_O_CreCOM4
CD11cC8_O_F4_MIC

value: Old:11 - 12 months

value: brain


title: kalta4, 6 dpf, rep5

description: Library name: Sample 5

value: elavl3:kalta4 wildtype siblings


title: kalta4, 6 dpf, rep2

description: Library name: Sample 2


title: Mus musculus Microglia CD11cCre Casp8flox/flox  Female Old, Replicate 3

description:
Library name: Microglia_O_CreCOM3
CD11cC8_O_F3_MIC


title: kalta4, 6 dpf, rep1

description: Library name: Sample 1


title: OVCAR3 cells, DMSO treated, 8 hours, batch A, replicate 1

description: Library name: D_8_A_1

value: Hour 8


title: OVCAR3 cells, 45μM Atovaquone treated, 1 hour, batch B, replicate 2

description: Library name: IC75_1_B_2

value: 45μM Atovaquone

value: Hour 1


title: Mus musculus Microglia CD11cCre Casp8flox/flox  Female Old, Replicate 1

description:
Library name: Microglia_O_CreCOM1
CD11cC8_O_F1_MIC

value: microglia

value: CD11ccre Casp8flox/flox


title: cKO - Nestin-Cre; TDP-43 homozygous conditional knockout mouse, Thalamus, ID-104

description: Library name: THL_104

value: male


title: cKO - Nestin-Cre; TDP-43 homozygous conditional knockout mouse, Thalamus, ID-128

description: Library name: THL_128


title: Mus musculus Macrophage Casp8flox/flox  Female Old, Replicate 7

description:
Library name: Mac_O_WT7
C8_O_F7_MACS

value: macrophage


title: cKO - Nestin-Cre; TDP-43 homozygous conditional knockout mouse, Thalamus, ID-108

description: Library name: THL_108


title: OVCAR3 cells, 45μM Atovaquone treated, 1 hour, batch B, replicate 1

description: Library name: IC75_1_B_1

value: WT


title: Control - TDP-43 floxed mouse, Thalamus, ID-147

description: Library name: THL_147

value: TDP-43 f/f


title: Mus musculus Microglia Casp8flox/flox Female Old, Replicate 3

description:
Library name: Microglia_O_WT3
C8_O_F3_MIC

value: Young:5 - 6 months


title: OVCAR3 cells, 45μM Atovaquone treated, 1 hour, batch A, replicate 1

description: Library name: IC75_1_A_1

value: A


title: Mus musculus Microglia Casp8flox/flox Female Old, Replicate 2

description:
Library name: Microglia_O_WT2
C8_O_F2_MIC


title: OVCAR3 cells, DMSO treated, 8 hours, batch B, replicate 1

description: Library name: D_8_B_1

value: DMSO


title: Control - TDP-43 floxed mouse, Thalamus, ID-125

description: Library name: THL_125

value: Thalamus


title: NHR gene WPS series main plate - odd columns - replicate 3

description:
NHR_rep3_odd_lib
Multiplexed RNA-seq library generated by Worm Perturb-seq (WPS) technology. Contains samples for 45 NHR gene RNAi knockdowns and two empty vector control treatment. To analyze the data, refer to our publication and supplementary files for the metadata (barcode) table and WPS data processing pipeline. Samples with bad quality were not included in the metadata table.

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for 45 NHR  genes


title: OVCAR3 cells, 30μM Atovaquone treated, 1 hour, batch B, replicate 2

description: Library name: IC50_1_B_2

value: High-grade serous ovarian adenocarcinoma

value: 30μM Atovaquone

value: B


title: NHR gene WPS series supplementary plate - lib2

description:
NHR_supp_lib2
Multiplexed RNA-seq library generated by Worm Perturb-seq (WPS) technology. Contains samples for 41 NHR gene RNAi knockdowns and three empty vector controls collected in three biological replications. Specially, the 41 NHR RNAi samples were collected only in the replicate #1. Two vector control samples from the other two replicates were also included in the data, regardless of being from other replicates. To analyze the data, refer to our publication and supplementary files for the metadata (barcode) table and WPS data processing pipeline. Samples with bad quality were not included in the metadata table. We recommend referring to the Supplementary Methods of  WPS paper for proper handling of this library.

value: Including empty vector controls and single gene RNAi knockdown for 41 NHR  genes


title: NHRgeneWPSseriessupplementaryplate-lib1

description:
NHR_supp_lib1
Multiplexed RNA-seq library generated by Worm Perturb-seq (WPS) technology. Contains samples for one or more biological replicates (max 3) of 18 NHR gene RNAi knockdowns and three empty vector controls collected in the three biological replications. To analyze the data, refer to our publication and supplementary files for the metadata (barcode) table and WPS data processing pipeline. Samples with bad quality were not included in the metadata table. We recommend referring to the Supplementary Methods of  WPS paper for proper handling of this library.

value: Including empty vector controls and single gene RNAi knockdown for 18 NHR  genes


title: Control - TDP-43 floxed mouse, Thalamus, ID-120

description: Library name: THL_120

value: male


title: Mus musculus Microglia Casp8flox/flox Female Old, Replicate 1

description:
Library name: Microglia_O_WT1
C8_O_F1_MIC

value: brain

value: microglia


title: NHR gene WPS series main plate - even columns - replicate 3

description:
NHR_rep3_even_lib
Multiplexed RNA-seq library generated by Worm Perturb-seq (WPS) technology. Contains samples for 28 NHR gene RNAi knockdowns and one empty vector control treatment. To analyze the data, refer to our publication and supplementary files for the metadata (barcode) table and WPS data processing pipeline. Samples with bad quality were not included in the metadata table.

value: Including empty vector controls and single gene RNAi knockdown for 28 NHR  genes


title: Mus musculus Microglia CD11cCre Casp8flox/flox Female Young, Replicate 5

description:
Library name: Microglia_Y_CreCOM5
CD11cC8_Y_F5_MIC

value: Old:11 - 12 months

value: CD11ccre Casp8flox/flox


title: OVCAR3 cells, 30μM Atovaquone treated, 1 hour, batch B, replicate 1

description: Library name: IC50_1_B_1

value: WT

value: Hour 1


title: Mus musculus Microglia Casp8flox/flox Female Old, Replicate 5

description:
Library name: Microglia_O_WT5
C8_O_F5_MIC

value: Young:5 - 6 months


title: Fxr cko NEC pups_3

city: Tianjin

first: yuchao

last: Jing

address: No.22, Meteorological Tai Road, Tianjin

institute: Tianjin Medical University

description: Library name: sample4

data_processing:
RNA-Seq fastq files were first processed by fastp to remove adaptor and low-quality reads, then aligned to the reference genome using Hisat2 (v2.0.5). DEGs were identified by edgeR (v3.22.5). P values were adjusted using the Benjamini & Hochberg method. p<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression. Pathway analysis was performed using Metascape. For analysis of ferroptosis signatures, GSEA was performed by using the Broad Institute’s GSEA program.
Assembly: Hisat2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Intestinal

extract_protocol:
RNA-Seq library preparation and sequencing were conducted by Novogene (Beijing, CN) on a NovaSeq 6000 machine for small intestine,
The end reading of 150bp pairing was generated. RNA-Seq fastq files were first processed by fastp to remove adaptor and low-quality reads, then aligned to the reference genome using Hisat2 (v2.0.5).

value: Intestinal

value: mouse intestinal

value: Fxr cko

value: NEC model


title: OVCAR3 cells, 30μM Atovaquone treated, 1 hour, batch A, replicate 1

description: Library name: IC50_1_A_1

value: High-grade serous ovarian adenocarcinoma

value: 30μM Atovaquone

value: A


title: NHR gene WPS series main plate - odd columns - replicate 1

last: Li

description:
NHR_rep1_odd_lib
Multiplexed RNA-seq library generated by Worm Perturb-seq (WPS) technology. Contains samples for 42 NHR gene RNAi knockdowns and two empty vector control treatment. To analyze the data, refer to our publication and supplementary files for the metadata (barcode) table and WPS data processing pipeline. Samples with bad quality were not included in the metadata table.

value: Whole animal (excluding eggs)

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including empty vector controls and single gene RNAi knockdown for 42 NHR  genes


title: Mus musculus Microglia CD11cCre Casp8flox/flox Female Young, Replicate 4

description:
Library name: Microglia_Y_CreCOM4
CD11cC8_Y_F4_MIC

value: brain

value: microglia


title: Regular RNA-seq profile of N2 C. elegans at 64 hours post L1 seeding

description:
Library name: WT_64hph_regular_RNA_seq
Regular bulk RNA-seq library of gravid adult C. elegans. The total RNA sample from one replicate of the developmental stage time-course experiment (64 hour post L1) was sent to BGI for Transcriptome Resequencing Pure-sequencing service, which is a commonly used commercial RNA-seq service similar to Illumina TruSeq RNA. Data were processed using standard RSEM processing pipeline (v1.7.0) in Via Foundry platform (PMID: 32306927), which aligns the reads to genome by Bowtie and estimate gene-level counts using RSEM.

data_processing:
As part of the WPS data processing pipeline, raw reads were processed using an in-house dolphinNext pipeline to generate a gene-by-sample read count matrix. For the regular RNA-seq library, data were processed using standard RSEM processing pipeline (v1.7.0) in Via Foundry platform (PMID: 32306927), which aligns the reads to genome by Bowtie and estimate gene-level counts using RSEM. The following descriptions are only for WPS library processing.
Raw reads were demultiplexed by a homemade python script that extracts the barcode information from read 1 and combines that with read 2.
The processed reads were passed to Trimmomatic (v0.32) to remove polyA and adaptor sequences.
Next, reads were aligned to the C. elegans genome (WormBase WS279) by STAR (parameter: --runThreadN 4 --alignIntronMax 25000 --outFilterIntronMotifs RemoveNoncanonicalUnannotated).
Finally, the output bam file was processed by ESAT to obtain the read counts of genes. In ESAT, we used an extension window of 1000 bp and the ‘proper’ method of multiple mappings. Unique Molecular Identifier (UMI) features were not used by setting umiMin = 1. Read counts, rather than UMI counts, were used as the gene expression quantity. We did not observe significant PCR duplicates during the development of our method (i.e., read counts highly correlate with UMI counts, data not shown), which is consistent with the low number of PCR cycles for library construction. Therefore, we directly used the read counts regardless of the presence of UMI in our library.
Assembly: WormBase WS279
Supplementary files format and content: a comma-separated values (CSV) file for the gene-by-sample read count matrix
Supplementary files format and content: a comma-separated values (CSV) file detailed annotation of sample barcode and sample information for all libraries included here

extract_protocol:
Animals were transferred to 96-well plates for high-throughput RNA extraction following protocol described in the WPS method paper. Importantly, this method only extracts total RNA from adult animal tissues and leaves any eggs intact.
Extracted total RNA was barcoded during reverse transcription to enable early pooling of samples. Multiplexed RNA-seq libraries each containing ~50 samples were constructed following a protocol adapted from the CEL-seq2 single-cell RNA-seq library construction method (Hashimshony, Genome Biology, 2016). For detailed protocols, refer to our WPS method paper. This library construction method produces a multiplexed RNA-seq library comprising ~50 samples. The sample pooling strategy differs from standard WPS due to historical reasons. Specifically, samples from the main plate were pooled by replicates, i.e., samples in the same biological replicate were pooled together. Samples from the supplementary plates were pooled in a mixed manner: the supplementary plate - lib1 contains samples from up to three replicates; the supplementary plate - lib2 contains samples only from replicate #1, except for vector control samples. For regular RNA-seq (WT_64hph_regular_RNA_seq), library construction was performed using BGI Transcriptome Resequencing Pure-sequencing service.

value: gravid adult stage (64 hours post L1 seeding)

value: hermaphrodite

value: Animals were fed on HT115 bacteria expressing empty vector control (L4440), i.e., the dsRNA expression was induced as in regular WPS experiments.


title: NHR gene WPS series main plate - even columns - replicate 1

description:
NHR_rep1_even_lib
Multiplexed RNA-seq library generated by Worm Perturb-seq (WPS) technology. Contains samples for 45 NHR gene RNAi knockdowns and two empty vector control treatment. To analyze the data, refer to our publication and supplementary files for the metadata (barcode) table and WPS data processing pipeline. Samples with bad quality were not included in the metadata table.

value: Including empty vector controls and single gene RNAi knockdown for 45 NHR  genes


title: Mus musculus Microglia CD11cCre Casp8flox/flox Female Young, Replicate 3

description:
Library name: Microglia_Y_CreCOM3
CD11cC8_Y_F3_MIC

value: Old:11 - 12 months

value: CD11ccre Casp8flox/flox


title: Fxr cko NEC pups_1

description: Library name: sample3

value: Intestinal

value: mouse intestinal

value: Fxr cko


title: C. elegans developmental stage time course library - Superscript III

description:
dev_SS3
Multiplexed RNA-seq library generated by Worm Perturb-seq (WPS) technology. Contains the triplicate samples for C. elegans animals collected in various developmental stages. To analyze the data, refer to our publication and supplementary files for the metadata (barcode) table and WPS data processing pipeline. Specially, this library was constructed with SuperScript III as the reverse transcriptase. This library was generated during our method optimization.

value: Time course samples from L2 to gravid adult stage (17-69 hours post L1 seeding)


title: Fxr fl/fl  NEC pups_2

description: Library name: sample2

value: Fxrfl/fl

value: NEC model


title: Mus musculus Microglia CD11cCre Casp8flox/flox Female Young, Replicate 2

description:
Library name: Microglia_Y_CreCOM2
CD11cC8_Y_F2_MIC


title: C. elegans developmental stage time course library - Superscript II

description:
dev_SS2
Multiplexed RNA-seq library generated by Worm Perturb-seq (WPS) technology. Contains the triplicate samples for C. elegans animals collected in various developmental stages. To analyze the data, refer to our publication and supplementary files for the metadata (barcode) table and WPS data processing pipeline. Specially, this library was constructed with SuperScript II as the reverse transcriptase. This library was generated during our method optimization.

value: Whole animal (excluding eggs)


title: Fxr fl/fl  NEC pups_1

description: Library name: sample1


title: OVCAR3 cells, DMSO treated, 1 hour, batch A, replicate 1

description: Library name: D_1_A_1

value: High-grade serous ovarian adenocarcinoma

value: WT

value: DMSO

value: Hour 1

value: A