title: BMDM, Bmal1-KO, CCM, rep3

value: 100uM CCM/DMSO


title: CBO-MOK20001-WT1, WT

status: Public on Feb 03 2025

type: SRA

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: DMRTA1_WT_1_GT24-02321_CAATTAAC-ATATCTCG_S194_L005
KOLF2.2J differentiated to cortical brain organoid

library_source: transcriptomic

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

molecule: total RNA

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

tag: cell line

tag: cell type

value: iPSC

tag: editing strategy

value: Termination codon

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 6

tag: model system

value: Cortical brain (dorsal forebrain patterning)

tag: parental cell_line


title: NUGC-3 cells, PC14586, 16h, bio rep 2

city: Princeton

first: Lizhong

last: Xu

state: NJ

address: 400 Alexander Park Drive, Suite 301

country: USA

institute: PMV Pharmaceuticals, Inc.

data_processing:
DESeq2 (version 1.34.0)
Paired-end reads were aligned to the human genome GRCh38 using STAR aligner (version 2.7.7a).
Fragments were assigned to the genes (GENCODE annotation) using featureCounts (version 1.4.6-p5).
Differential expression analysis was performed using R (version 4.1.3) package DESeq2 (version 1.34.0) testing for the fold change significantly >1.5 to identify differentially expressed genes (DEGs).
Fragments per kilobase of transcript per million mapped reads (FPKM) values were computed using edgeR package (version 3.36.0) using the TMM normalization method. Transcripts per million (TPM) values were computed from FPKM values assuming that the abundance of each transcript is proportional to its FPKM value.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values (TSV) files include TPM values for each Sample.

growth_protocol: Cells were maintained in RPMI-1640 (for NUGC-3, NUGC-3 KO, and SJSA-1) or DMEM/F12, 1:1 mixture (for T3M-4) supplemented with 10% fetal bovine serum in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted immediately from the cells after treatments for 5 or 16 h as indicated and purified by using QIAcube (Qiagen) with DNase I digestion, following the manufacturer's protocols.
After rRNA depletion by using Fastselect HMR kit (Qiagen), strand-specific RNA sequencing libraries were prepared by using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB), following manufacturers’ instructions.

treatment_protocol: Cells were treated on the second day after seeding, with either DMSO or PC14586 (5 µM) for 5 h or 16 h as indicated.

value: Gastric adenocarcinoma

tag: genotype

tag: treatment


title: MLL34dKO_Naive1_eS

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

department: Urology

institute: UCSF

description: MLL34dKO.naive.merged.bw AND MLL34dKO.eS.n.merged.bw

library_source: genomic

data_processing:
library strategy: BioRepli-seq
Bowtie2 mapping to mm10
BamtoBed
Bin into 50kb genome bins
Calculate RT
Quantile normalization
Bedgraph to bigwig
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: NEBNext Ultra II (on-bead custom protocol)

tag: culture conditions

value: Naive

value: mESC cell line

tag: treatment time


title: BMDM, Bmal1-KO, LPS, rep3

city: Oxford

first: Laura

last: Bailey

address: Radcliffe Department of Medicine

department: Oxford Centre for Diabetes, Endocrinology and Metabolism

institute: University of Oxford

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. Index of the reference genome (mm10) was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: mm10
Supplementary files format and content: gene_couint.txt = Tab-delimited file with read-count for each sample with annotation of each gene

molecule: polyA RNA

source_name: Bone-marrow derived macrophage

growth_protocol: Tibiae and femurae dissected from C57BL/6 mice, and the single-cell suspension from bone marrow was cultured on non-tissue culture treated dishes with complete DMEM, 20% FBS, MCSF for 7 days.

extract_protocol:
Cells were lysed in Trizol reagent and RNA extracted using chloroform, followed by Zymo RNA Clean & Concentrator.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Cells were treated with one of the four conditions for 6 hours before lysis for RNA extraction.

tag: tissue

value: Bone-marrow derived macrophage

tag: strain

value: LysM-Cre;Bmal1 flox/flox

value: 100nM LPS/DMSO


title: NUGC-3 cells, PC14586, 16h, bio rep 1


title: CBO-MOK20001P-C11, KO

description:
Library name: DMRTA1_PTC_C11_GT24-02319_ACTCGTGT-GTTCCAAT_S182_L005
KOLF2.2J derived knockout cell line, DMRTA1 PTC, differentiated to cortical brain organoid


title: NUGC-3 cells, DMSO, 16h, bio rep 3

value: DMSO Control


title: BMDM, Wild-type, Vehicle control, rep2

value: Bmal1 flox/flox

value: DMSO (vehicle control),


title: MLL3KO_Naive3_lS


title: BMDM, Bmal1-KO, Vehicle control, rep3


title: BMDM, Wild-type, LPS + CCM, rep2

value: 100nM LPS/100uM CCM


title: CBO-MOK20001P-B11, KO

description:
Library name: DMRTA1_PTC_B11_GT24-02318_ATTGTGAA-GCAATGCA_S193_L005
KOLF2.2J derived knockout cell line, DMRTA1 PTC, differentiated to cortical brain organoid


title: BMDM, Wild-type, CCM, rep2


title: NUGC-3 cells, DMSO, 16h, bio rep 2


title: CBO-MOK20001-WT4, WT

description:
Library name: DMRTA1_WT_4_GT24-02323_AGTACTCC-AACAGGTT_S201_L005
KOLF2.2J differentiated to cortical brain organoid


title: MLL3KO_Naive3_eS

description: MLL3KO.naive.merged.bw AND MLL3KO.eS.n.merged.bw


title: CBO-MOK20007-WT3-Day8, WT

description:
Library name: FEZF2_WT_3_GT24-01200_GATTCTGC-CTCTCGTC_S216_L007_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: Not applicable

value: day 8


title: MLL3KO_Naive2_lS


title: BMDM, Wild-type, LPS, rep2


title: NUGC-3 cells, DMSO, 16h, bio rep 1


title: MLL3KO_Naive2_eS


title: BMDM, Wild-type, Vehicle control, rep1


title: CBO-MOK20007-WT2-Day8, WT

description:
Library name: FEZF2_WT_2_GT24-01199_AGCCTCAT-TCTCTACT_S212_L007_R1_001
KOLF2.2J differentiated to cortical brain organoid


title: CBO-MOK20007-WT1-Day8, WT

description:
Library name: FEZF2_WT_1_GT24-01198_CGTTAGAA-GACCTGAA_S214_L007_R1_001
KOLF2.2J differentiated to cortical brain organoid


title: SJSA-1 cells, PC14586, 5h, bio rep 3

value: Osteosarcoma

value: TP53 WT

value: 5 h


title: CBO-MOK20007P-D09-Day8, KO

description:
Library name: FEZF2_PTC_D09_GT24-01197_TACCGAGG-AGTTCAGG_S209_L007_R1_001
KOLF2.2J derived knockout cell line,FEZF2 PTC, differentiated to cortical brain organoid

value: iPSC

value: Termination codon


title: CBO-MOK20001P-F09, KO

description:
Library name: DMRTA1_PTC_F09_GT24-02320_GTCTACAC-ACCTTGGC_S188_L005
KOLF2.2J derived knockout cell line, DMRTA1 PTC, differentiated to cortical brain organoid

value: day 6

value: Cortical brain (dorsal forebrain patterning)


title: MLL3KO_Naive1_eS

value: Naive

value: mESC cell line


title: CBO-MOK20007P-B11-Day8, KO

description:
Library name: FEZF2_PTC_B11_GT24-01196_AATGCCTC-TGGATCGA_S211_L007_R1_001
KOLF2.2J derived knockout cell line,FEZF2 PTC, differentiated to cortical brain organoid


title: BMDM, Wild-type, LPS, rep1

value: Bone-marrow derived macrophage


title: SJSA-1 cells, PC14586, 5h, bio rep 1


title: CBO-MOK20007P-A09-Day8, KO

description:
Library name: FEZF2_PTC_A09_GT24-01195_GGCATTCT-CAAGCTAG_S210_L007_R1_001
KOLF2.2J derived knockout cell line,FEZF2 PTC, differentiated to cortical brain organoid


title: MLL3KO_Naive1_lS


title: BMDM, Bmal1-KO, Vehicle control, rep2

value: LysM-Cre;Bmal1 flox/flox


title: SJSA-1 cells, DMSO, 5h, bio rep 2

value: DMSO Control


title: CBO-MOK20007C-F09-Day8, KO

description:
Library name: FEZF2_CE_F09_GT24-01194_TTACAGGA-GCTTGTCA_S213_L007_R1_001
KOLF2.2J derived knockout cell line,FEZF2 CE, differentiated to cortical brain organoid

value: Critical exon


title: SJSA-1 cells, DMSO, 5h, bio rep 3


title: SJSA-1 cells, DMSO, 5h, bio rep 1


title: CBO-MOK20007C-D09-Day8, KO

description:
Library name: FEZF2_CE_B09_GT24-01193_CCGTGAAG-ATCCACTG_S215_L007_R1_001
KOLF2.2J derived knockout cell line,FEZF2 CE, differentiated to cortical brain organoid


title: SJSA-1 cells, PC14586, 5h, bio rep 2


title: BMDM, Bmal1-KO, LPS + CCM, rep2


title: BMDM, Bmal1-KO, CCM, rep2

value: 100uM CCM/DMSO


title: BMDM, Bmal1-KO, LPS, rep2

value: 100nM LPS/DMSO


title: CBO-MOK20007C-A11-Day8, KO

description:
Library name: FEZF2_CE_A11_GT24-01192_TCCAACGC-AAGTCCAA_S155_L005_R1_001
KOLF2.2J derived knockout cell line,FEZF2 CE, differentiated to cortical brain organoid


title: BMDM, Wild-type, LPS + CCM, rep1

value: Bmal1 flox/flox

value: 100nM LPS/100uM CCM


title: NUGC-3 KO cells, PC14586, 5h, bio rep 2

source_name: NUGC-3 KO

value: NUGC-3 KO

value: Gastric adenocarcinoma

value: TP53 KO


title: NUGC-3 KO cells, PC14586, 5h, bio rep 1

value: 5 h


title: BMDM, Bmal1-KO, Vehicle control, rep1

value: DMSO (vehicle control),


title: CBO-MOK20007W-D04-Day8, KO

description:
Library name: FEZF2_KO_D04_GT24-01190_GTCGGAGC-TTATAACC_S157_L005_R1_001
KOLF2.2J derived knockout cell line,FEZF2 KO, differentiated to cortical brain organoid

value: iPSC

value: Full coding region

value: day 8


title: NUGC-3 KO cells, DMSO, 5h, bio rep 3


title: BMDM, Bmal1-KO, LPS + CCM, rep1


title: CBO-MOK20007W-B09-Day8, KO

description:
Library name: FEZF2_KO_B09_GT24-01189_ACTAAGAT-CCGCGGTT_S156_L005_R1_001
KOLF2.2J derived knockout cell line,FEZF2 KO, differentiated to cortical brain organoid

value: Cortical brain (dorsal forebrain patterning)


title: NUGC-3 KO cells, DMSO, 5h, bio rep 2


title: BMDM, Bmal1-KO, CCM, rep1

value: Bone-marrow derived macrophage


title: NUGC-3 KO cells, PC14586, 5h, bio rep 3


title: NUGC-3 KO cells, DMSO, 5h, bio rep 1


title: DLD1_IRI-R+CURC_rep1

type: RNA

city: Cluj-Napoca

first: Simona

last: Visan

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute “Prof Dr. Ion Chiricuta”,

description: Gene expression of the irinotecan-resistant DLD1 cell line after treatment with curcumin at IC50 concentration

hyb_protocol: The probes were hybridized for 17 h at 65oC on Agilent SurePrint G3 Human GE v3 8x60k arrays

scan_protocol: The slides were scanned with Agilent G2505C Microarray Scanner at 3 µm resolution

data_processing: Microarray images were processed with Agilent Feature Extraction software v. 11.5.1.1.

source_name: CL65,breast biopsy,mammosphere formation M0

label_protocol: Microarray probes labeled with Cy3 were synthesized from 100 ng of total RNA with Low Input Quick Amp Labeling Kit and checked for quality and quantity with NanoDrop ND-1000 (Thermo Fischer Scientific)

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin–streptomycin and 1% glutamine.

extract_protocol: Total RNA was extracted using the phenol-chloroform method following cell lysis with TriReagent solution

value: Resistant

tag: treated/untreated with curcumin (ic50)

value: treated


title: DLD1_IRI-R_rep2

description: Gene expression of the irinotecan-resistant DLD1 cell line

value: untreated


title: BMDM, Bmal1-KO, LPS, rep1

value: LysM-Cre;Bmal1 flox/flox


title: DLD1_IRI-R_rep3


title: CBO-MOK20007P-D09-Day7, KO

description:
Library name: FEZF2_PTC_D09_Day7_GT23-05992_CCGTGAAG-ATCCACTG_S23_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 PTC, differentiated to cortical brain organoid

value: Termination codon

value: day 7


title: T3M-4 cells, PC14586, 5h, bio rep 3

value: Pancreatic ductal adenocarcinoma


title: DLD1_IRI-R+CURC_rep3


title: BMDM, Wild-type, CCM, rep1

value: Bmal1 flox/flox

value: 100uM CCM/DMSO


title: DLD1_IRI-R+CURC_rep2


title: DLD1_IRI-R_rep4


title: DLD1_IRI-R+CURC_rep4


title: T3M-4 cells, PC14586, 5h, bio rep 2


title: CBO-MOK20007P-B11-Day7, KO

description:
Library name: FEZF2_PTC_B11_Day7_GT23-05991_TCCAACGC-AAGTCCAA_S21_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 PTC, differentiated to cortical brain organoid


title: Total RNA from DRN_2

city: New York

first: Alexander

middle: R

last: Nectow

state: New York

address: 630 W 168th St., Physicians and Surgeons

department: Medicine

institute: Columbia University

data_processing:
RTA (Illumina) is used for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
Pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Human:GRCh38.p12; Mouse:GRCm38.p6) is performed using kallisto (0.44.0).
Differentially expressed genes are tested using DESeq2 R package designed to test differential expression between two groups from RNA-seq counts data.
Assembly: Mouse:GRCm38.p6
Supplementary files format and content: CSV file with differential expression output from DESeq2

source_name: Brain

extract_protocol:
RNA was extracted using the Agilent Nanoprep kit.
Clontech Ultra Low v4 kit was used for cDNA synthesis followed by NexteraXT for library preparation.

value: Brain

value: CCK-IRES-Cre

value: Total RNA


title: CBO-MOK20007W-G09-Day8, KO

description:
Library name: FEZF2_KO_G09_GT24-01191_CTTGGTAT-GGACTTGG_S154_L005_R1_001
KOLF2.2J derived knockout cell line,FEZF2 KO, differentiated to cortical brain organoid

value: iPSC


title: Total RNA from DRN_1


title: DLD1_IRI-S_rep3

description: Gene expression of the parental DLD1 cell line

value: Sensitive


title: CBO-MOK20007P-A09-Day7, KO

description:
Library name: FEZF2_PTC_A09_Day7_GT23-05990_CTTGGTAT-GGACTTGG_S34_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 PTC, differentiated to cortical brain organoid


title: Zebrafish heart, REN +/+, regenerating (7dpi), replicate 3

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

data_processing:
Demultiplexed and quality-filtered reads, were aligned to the Danio rerio reference genome GRCz10 using Hierarchical Indexing for Spliced Alignment of Transcripts 2 (HISAT2)
Read counts for each gene were quantified using featureCounts software
Assembly: Danio rerio reference genome GRCz10
Supplementary files format and content: tab separated feature counts output, text file

organism: Danio rerio

source_name: Heart

growth_protocol: Adults less than 1 year old were used for all the experiments. Males and females were mixed in similar proportions in each of the conditions.

extract_protocol:
Total RNA was extracted using Trizol method
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.
Bulk RNA sequencing

value: Heart

value: delta REN +/-


title: T3M-4 cells, PC14586, 5h, bio rep 1

value: 5 h


title: CBO-MOK20007-WT-Day7, WT

description:
Library name: FEZF2_WT_Day7_GT23-05993_TTACAGGA-GCTTGTCA_S1_L001_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: Not applicable

value: Cortical brain (dorsal forebrain patterning)


title: DLD1_IRI-R_rep1

value: Resistant

value: untreated


title: DLD1_IRI-S_rep2


title: CBO-MOK20007C-D09-Day7, KO

description:
Library name: FEZF2_CE_D09-2_Day7_GT23-05989_GTCGGAGC-TTATAACC_S36_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 CE, differentiated to cortical brain organoid

value: Critical exon


title: GFP IP from CCK neurons_1

value: Immunoprecipitate


title: T3M-4 cells, DMSO, 5h, bio rep 3

value: Pancreatic ductal adenocarcinoma

value: DMSO Control


title: Zebrafish heart, REN +/+, regenerating (7dpi), replicate 2


title: GFP IP from CCK neurons_2


title: CBO-MOK20007C-A12-Day7, KO

description:
Library name: FEZF2_CE_A12-2_Day7_GT23-05988_ACTAAGAT-CCGCGGTT_S14_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 CE, differentiated to cortical brain organoid

value: day 7


title: AP2-control fasting 6, eWAT

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: eWAT

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: eWAT

value: control

value: Overnight Fasting


title: T3M-4 cells, DMSO, 5h, bio rep 2


title: CBO-MOK20007C-A11-Day7, KO

description:
Library name: FEZF2_CE_A11-2_Day7_GT23-05987_ATGAGGCC-CAATTAAC_S47_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 CE, differentiated to cortical brain organoid

value: iPSC


title: T3M-4 cells, DMSO, 5h, bio rep 1


title: Zebrafish heart, REN +/+, uninjured, replicate 3

value: Untreated (uninjured)


title: NUGC-3 cells, PC14586, 5h, bio rep 3

value: Gastric adenocarcinoma


title: Zebrafish heart, REN +/+, uninjured, replicate 1

value: Heart

value: delta REN +/-


title: Zebrafish heart, REN -/-, regenerating (7dpi), replicate 3

value: delta REN -/-


title: AP2-control fasting 5, eWAT


title: AP2-control fasting 4, eWAT


title: NUGC-3 cells, PC14586, 5h, bio rep 2

value: 5 h


title: Zebrafish heart, REN +/+, uninjured, replicate 2


title: CBO-MOK20007W-C12-Day7, KO

description:
Library name: FEZF2_KO_C12-2_Day7_GT23-05985_AACGTTCC-AGTACTCC_S29_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 KO, differentiated to cortical brain organoid

value: Full coding region

value: Cortical brain (dorsal forebrain patterning)


title: AP2-control fasting 3, eWAT


title: NUGC-3 cells, PC14586, 5h, bio rep 1


title: AP2-control fasting 2, eWAT


title: CBO-MOK20007W-B09-Day7, KO

description:
Library name: FEZF2_KO_B09-2_Day7_GT23-05984_GGTACCTT-GACGTCTT_S10_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 KO, differentiated to cortical brain organoid


title: Zebrafish heart, REN -/-, regenerating (7dpi), replicate 2


title: DLD1_IRI-S_rep1

value: Sensitive

value: untreated


title: CBO-MOK20007-WT-Day6, WT

description:
Library name: FEZF2_WT_Day6_GT23-05983_GCACGGAC-TGCGAGAC_S13_L001_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: Not applicable

value: day 6


title: Zebrafish heart, REN +/+, regenerating (7dpi), replicate 1


title: AP2-control fasting 1, eWAT


title: NUGC-3 cells, DMSO, 5h, bio rep 3

value: DMSO Control


title: NUGC-3 cells, DMSO, 5h, bio rep 2


title: Zebrafish heart, REN -/-, regenerating (7dpi), replicate 1


title: NUGC-3 cells, DMSO, 5h, bio rep 1


title: CBO-MOK20007P-D09-Day6, KO

description:
Library name: FEZF2_PTC_D09_Day6_GT23-05982_ATGTAAGT-CATAGAGT_S24_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 PTC, differentiated to cortical brain organoid

value: Termination codon


title: AP2-HuR fasting 5, eWAT

value: eWAT


title: CBO-MOK20007P-B11-Day6, KO

description:
Library name: FEZF2_PTC_B11_Day6_GT23-05981_CGGCGTGA-ACAGGCGC_S31_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 PTC, differentiated to cortical brain organoid


title: AP2-HuR fasting 6, eWAT

value: Overnight Fasting


title: CBO-MOK20007W-D04-Day7, KO

description:
Library name: FEZF2_KO_D04-2_Day7_GT23-05986_GCAGAATT-TGGCCGGT_S30_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 KO, differentiated to cortical brain organoid

value: iPSC

value: day 7


title: input_wt_NLRP3_rep3

city: La Jolla

first: Johannes

last: Schlachetzki

address: 9500 Gilman Drive

institute: UCSD

description: Library name: input_wt_NLRP3_rep3

data_processing:
Peaks were called using HOMER findPeaks for each tag directory with relaxed peak finding parameters ‘-L 0 -C 0 -fdr 0.9’.
Merged ATAC-seq peaks were then annotated with raw H3K27ac tag counts from each sample with HOMER’s annotatePeaks using parameters -noadj and -size 800.
Subsequently, DESeq2 was used to identify the differential H3K27ac signal with the cutoffs of FC>2 and p.adj<0.05 using getDiffExpression.pl.
Assembly: mm10
Supplementary files format and content: annotated peaks with raw and normalzied counts

source_name: Forebrain

extract_protocol:
Brains were  dissociated using the Neural Tissue Dissociation kit (P) (Miltenyi Biotec), followed by removal of myelin and then MACS isolation of CD11b+ microglia following the manufacturer’s guidelines (Miltenyi Biotec). For H3K27ac ChIP-seq, fixed (1% formaldehyde for 10 min) nuclei were quickly thawed on ice and resuspended in ice-cold LB3 buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and 1x protease inhibitor cocktail. Chromatin was sheared by sonication using a PIXUL Multi-Sample Sonicator (Active Motif) set at default parameters for a processing time of 48 min. The lysates were adjusted to 250 μl with LB3 and further diluted with 25 μl 10% Triton X-100 (final concentration 1%). Samples were spun down at maximum speed at 4℃ for 10 minutes. For DNA input control, 3 μl of the lysate was taken and volume adjusted to 25 μl with TT (10 mM Tris-HCl pH 8, 0.05% Tween-20) and stored at 4℃ until library preparation. For immunoprecipitation, 20 μl of Dynabeads Protein A and Protein G (ThermoFisher Scientific, 10001D and 10003D, respectively) and H3K27ac antibody (2 μl serum; ActiveMotif, 39135) was added to the diluted lysates and rotated overnight at 4°C. Beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA), wash buffer III (10 mM Tris/HCl pH 7.4, 250 mM LiCl, 1% Triton X-100, 0.7% Na-Deoxycholate, 1 mM EDTA), twice with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20), twice with IDTET (10mM Tris-HCl pH 8.0, 0.1mM EDTA, 0.2% Tween-20) and finally resuspended in 25 μl TT.
For H3K27ac ChIP-seq, fixed (1% formaldehyde for 10 min) nuclei were quickly thawed on ice and resuspended in ice-cold LB3 buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and 1x protease inhibitor cocktail. Chromatin was sheared by sonication using a PIXUL Multi-Sample Sonicator (Active Motif) set at default parameters for a processing time of 48 min. The lysates were adjusted to 250 μl with LB3 and further diluted with 25 μl 10% Triton X-100 (final concentration 1%). Samples were spun down at maximum speed at 4℃ for 10 minutes. For DNA input control, 3 μl of the lysate was taken and volume adjusted to 25 μl with TT (10 mM Tris-HCl pH 8, 0.05% Tween-20) and stored at 4℃ until library preparation. For immunoprecipitation, 20 μl of Dynabeads Protein A and Protein G (ThermoFisher Scientific, 10001D and 10003D, respectively) and H3K27ac antibody (2 μl serum; ActiveMotif, 39135) was added to the diluted lysates and rotated overnight at 4°C. Beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA), wash buffer III (10 mM Tris/HCl pH 7.4, 250 mM LiCl, 1% Triton X-100, 0.7% Na-Deoxycholate, 1 mM EDTA), twice with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20), twice with IDTET (10mM Tris-HCl pH 8.0, 0.1mM EDTA, 0.2% Tween-20) and finally resuspended in 25 μl TT.

value: Forebrain

value: WT

tag: chip-antibody

value: input


title: CBO-MOK20007P-A09-Day6, KO

description:
Library name: FEZF2_PTC_A09_Day6_GT23-05980_TAATACAG-GTGAATAT_S20_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 PTC, differentiated to cortical brain organoid


title: AP2-HuR fasting 4, eWAT


title: Zebrafish heart, REN -/-, uninjured, replicate 1

value: Heart

value: delta REN -/-

value: Untreated (uninjured)


title: input_wt_NLRP3_rep2

description: Library name: input_wt_NLRP3_rep2


title: AP2-HuR fasting 3, eWAT


title: AP2-HuR fasting 2, eWAT


title: input_wt_NLRP3_rep1

description: Library name: input_wt_NLRP3_rep1


title: CBO-MOK20007C-D09-Day6, KO

description:
Library name: FEZF2_CE_D09-2_Day6_GT23-05979_TGACGAAT-GCCTACTG_S25_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 CE, differentiated to cortical brain organoid

value: Critical exon

value: Cortical brain (dorsal forebrain patterning)


title: CBO-MOK20007C-A11-Day6, KO

description:
Library name: FEZF2_CE_A11-2_Day6_GT23-05977_TTGGACTC-CTGCTTCC_S37_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 CE, differentiated to cortical brain organoid


title: S96_1_M

city: Aiken

first: Ethan

middle: P

last: Shealy

state: SC

address: Bldg 737-A Savannah River Site

department: Savannah River Ecology Lab

institute: University of Georgia

description:
Library name: S96
96

data_processing:
Reads were trimmed and quality-checked with Trim_Galore!, a wrapper script for CutAdapt and FastQC using a PHRED score cutoff of 20 in addition to a 4 bp hard clip on both read ends in order to reduce methylation bias
Alignment to the A. sagrei reference genome, AnoSag2.1 (Refseq: GCF_025583915.1), was conducted using Bismark with default parameters, and duplicate reads resulting from PCR bias were removed using the deduplicate_bismark tool. Alignment files were sorted and converted to .sam files using SAMtools.
Three samples were excluded from downstream analysis due to low alignment rates (<5%), leaving a total of 37 samples. SAM files were imported into R and converted to a methylation matrix using the R package methylKit.
Assembly: AnoSag2.1 (RefSEQ:  GCF_025583915.1)
Supplementary files format and content: MethylationMatrix_allSamples.tab contains a tab-seperated matrix of genomic coordinates and beta values for methylation frequencies for each of the 37 samples included after filtering. The first four column names of the matrix are for the coordinates, then subsequent column names refer to the sample's ID. This data file ws generated using MethylKit in R, and is not filtered by coverage, and not collapsed based on which strand the read originated from.
Library strategy: EM-seq

organism: Anolis sagrei

source_name: Red blood cells

growth_protocol: Animals used in this study were captive-bred descendants of stock originally collected from native A. sagrei populations near Georgetown, Great Exuma, in the Commonwealth of the Bahamas (23º29’N, 75º45’W) and imported under permits from the Bahamas Environment, Science, and Technology Commission, the Bahamas Ministry of Agriculture, and the United States Fish and Wildlife Service. Animals were housed at the University of Virginia and all procedures were approved under UVA ACUC protocol 3896. The exact hatch date of each captive-bred animal was recorded such that age was known with certainty.

extract_protocol:
DNA was isolated from the blood cell pellet (majority nucleated red blood cells) using Qiagen’s PureGene CELL extraction kit (method described in Lindsey and Schwartz 2022, "DNA Isolation from Reptile Blood using Gentra Puregene (Qiagen) DNA Isolation Kit" published on protocols.io).
Libraries were prepared using the NEBNext Enzymatic Methyl-seq kit from New England BioLabs (64) with 200 ng genomic DNA as input. Prior to enzymatic conversion, libraries were sheared to a target fragment size of 300 bp using a Covaris sonication instrument. After assessing library qualities using Bioanalyzer and Qubit instruments, 40 enzymatically converted libraries were sequenced on two lanes of an Illumina Novaseq 6000 instrument at the University of Florida’s Interdisciplinary Center for Biotechnology and Research to yield an average of ~120 million paired-end, 150bp reads per sample.

treatment_protocol: Animals were immediately euthanized by decapitation. Blood was collected from the trunk and stored on ice prior to separation of plasma and blood cells by centrifugation. All tissue samples and blood components were snap-frozen in liquid nitrogen.

value: Red blood cells

value: 1mo Male

tag: Sex

value: Male


title: AP2-HuR fasting 1, eWAT


title: CBO-MOK20007W-D04-Day6, KO

description:
Library name: FEZF2_KO_D04-2_Day6_GT23-05976_CCAAGTCT-TCATCCTT_S35_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 KO, differentiated to cortical brain organoid

tag: cell line

value: Full coding region

value: day 6


title: nput_NLRP3K0_rep2

description: Library name: nput_NLRP3K0_rep2

tag: cell type


title: Zebrafish heart, REN -/-, uninjured, replicate 3


title: AP2-control ad libitum 6, eWAT

value: eWAT

value: control

value: Ad libitum


title: S84_1_F

description:
Library name: S84
84

value: 1mo Female

value: Female


title: Zebrafish heart, REN -/-, uninjured, replicate 2


title: nput_NLRP3K0_rep1

description: Library name: nput_NLRP3K0_rep1

value: Forebrain


title: CBO-MOK20007W-B09-Day6, KO

description:
Library name: FEZF2_KO_B09-2_Day6_GT23-05974_TCTCTACT-GAACCGCG_S3_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 KO, differentiated to cortical brain organoid

value: iPSC

tag: editing strategy


title: CBO-MOK20007W-C12-Day6, KO

description:
Library name: FEZF2_KO_C12-2_Day6_GT23-05975_CTCTCGTC-AGGTTATA_S18_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 KO, differentiated to cortical brain organoid

tag: altered gene_symbol


title: H3K27ac_wt_rep3

description: Library name: H3K27ac_wt_rep3

value: WT

value: H3K27ac (ActiveMotif 39135)


title: AP2-control ad libitum 4, eWAT


title: S76_18_M

description:
Library name: S76
76

value: 18mo Male


title: S70_18_M

description:
Library name: S70
70


title: S85_1_M

description:
Library name: S85
85


title: S67_18_F

description:
Library name: S67
67

value: 18mo Female


title: AP2-control ad libitum 3, eWAT


title: S95_1_F

description:
Library name: S95
95


title: CBO-MOK20007-WT-Day5, WT

description:
Library name: FEZF2_WT_Day5_GT23-05973_GACCTGAA-CTCACCAA_S33_L001_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: Not applicable

tag: altered locus

value: day 5

value: Cortical brain (dorsal forebrain patterning)


title: H3K27ac_wt_rep2

description: Library name: H3K27ac_wt_rep2


title: CBO-MOK20007P-B11-Day5, KO

description:
Library name: FEZF2_PTC_B11_Day5_GT23-05971_TGGATCGA-TATCGCAC_S38_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 PTC, differentiated to cortical brain organoid

value: Termination codon

tag: time


title: nput_NLRP3K0_rep3

description: Library name: nput_NLRP3K0_rep3

value: input


title: CBO-MOK20007P-D09-Day5, KO

description:
Library name: FEZF2_PTC_D09_Day5_GT23-05972_AGTTCAGG-TCTGTTGG_S26_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 PTC, differentiated to cortical brain organoid

tag: model system


title: H3K27ac_wt_rep1

description: Library name: H3K27ac_wt_rep1


title: AP2-control ad libitum 1, eWAT


title: AP2-control ad libitum 2, eWAT


title: H3K27ac_NLRP3K0_rep3

description: Library name: H3K27ac_NLRP3K0_rep3


title: AP2-control ad libitum 5, eWAT


title: S66_18_F

description:
Library name: S66
66

value: Red blood cells


title: H3K27ac_NLRP3K0_rep2

description: Library name: H3K27ac_NLRP3K0_rep2


title: CBO-MOK20007P-A09-Day5, KO

description:
Library name: FEZF2_PTC_A09_Day5_GT23-05970_CAAGCTAG-CGCTATGT_S32_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 PTC, differentiated to cortical brain organoid

tag: parental cell_line


title: S62_18_M

description:
Library name: S62
62

tag: genotype

value: Male


title: CBO-MOK20007C-D09-Day5, KO

description:
Library name: FEZF2_CE_D09-2_Day5_GT23-05969_GCTTGTCA-GTATGTTC_S50_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 CE, differentiated to cortical brain organoid

value: Critical exon


title: AP2-HuR ad libitum 6, eWAT

value: eWAT

tag: treatment

value: Ad libitum


title: H3K27ac_NLRP3K0_rep1

description: Library name: H3K27ac_NLRP3K0_rep1


title: AP2-HuR ad libitum 5, eWAT


title: CBO-MOK20007C-A12-Day6, KO

description:
Library name: FEZF2_CE_A12-2_Day6_GT23-05978_CAGTAGGC-ATTCGTCA_S27_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 CE, differentiated to cortical brain organoid

value: day 6


title: S53_48_M

description:
Library name: S53
53

value: 48mo Male


title: S61_48_F

description:
Library name: S61
61

value: 48mo Female

value: Female


title: CBO-MOK20007C-A11-Day5, KO

description:
Library name: FEZF2_CE_A11-2_Day5_GT23-05967_AAGTCCAA-TACTCATA_S22_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 CE, differentiated to cortical brain organoid

value: iPSC


title: CBO-MOK20007C-A12-Day5, KO

description:
Library name: FEZF2_CE_A12-2_Day5_GT23-05968_ATCCACTG-ACGCACCT_S2_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 CE, differentiated to cortical brain organoid


title: Microglia WT replicate 4

description: Library name: WT_rep4

data_processing:
FASTQ files from ATAC-seq experiments were trimmed to 30 bp and then mapped to the mouse mm10 genome using Bowtie2 with default parameters.
HOMER was used to convert aligned reads into ‘‘tag directories’’ for further analysis.
To call peaks, we used HOMER’s findPeaks with “-style factor -size 200 -minDist 200 – L 0 – C 0 -fdr 0.9”.
We applied Irreproducibility Discovery Rate (IDR) analysis for replicates.
We used DESeq2 using HOMER’s getDIffExpression to identify differential chromatin accessibility with fold change >2 and p-adj <0.05.
Assembly: mm10
Supplementary files format and content: annotated peaks with raw and normalzied counts

extract_protocol:
Brains were  dissociated using the Neural Tissue Dissociation kit (P) (Miltenyi Biotec), followed by removal of myelin and then MACS isolation of CD11b+ microglia following the manufacturer’s guidelines (Miltenyi Biotec). Approximately 500,000 microglia were isolated from the brains of mice and centrifuged at 500 rcf for 10 minutes. Cells were resuspended in 47.5µl lysis buffer (10mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPA, CA-630 in water) at room temperature. After the addition of 2.5µl DNA enzyme I (Illumina), cells were incubated at 37°C for 30 min.
DNA was purified with Zymo ChIP DNA concentrator columns (Zymo Research), eluted with 11µl of elution buffer, and amplified using NEBNext High-fidelity 2x PCR MasterMix (New England BioLabs) with the Nextera primer Ad1 (1.25µM) and a unique Ad2.n barcoding primer (1.25µM) for 8-10 cycles. Resulting libraries were size selected by gel excision to 165-250 bp, purified, and single end sequenced using a NovaSeq 6000 (Illumina) sequencer for 51 cycles according to the manufacturer’s instructions.

value: Forebrain

value: WT


title: Microglia WT replicate 3

description: Library name: WT_rep3


title: AP2-HuR ad libitum 3, eWAT


title: CBO-MOK20007W-D04-Day5, KO

description:
Library name: FEZF2_KO_D04-2_Day5_GT23-05966_GGACTTGG-CGTCTGCG_S44_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 KO, differentiated to cortical brain organoid

value: Full coding region


title: AP2-HuR ad libitum 2, eWAT


title: Microglia WT replicate 2

description: Library name: WT_rep2


title: CBO-MOK20007W-C12-Day5, KO

description:
Library name: FEZF2_KO_C12-2_Day5_GT23-05965_TTATAACC-TCGATATC_S28_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 KO, differentiated to cortical brain organoid

value: day 5


title: S64_18_F

description:
Library name: S64
64

value: 18mo Female


title: AP2-HuR ad libitum 1, eWAT


title: S51_48_F

description:
Library name: S51
51


title: S47_48_F

description:
Library name: S47
47


title: Microglia WT replicate 1

description: Library name: WT_rep1


title: AP2-control fasting 6, iWAT

source_name: iWAT

value: iWAT

value: control

value: Overnight Fasting


title: Microglia NLRP3 knockout replicate 4

description: Library name: NLRP3KO_rep4


title: S46_48_F

description:
Library name: S46
46

value: Red blood cells


title: CBO-MOK20004-WT3-Day6, WT

description:
Library name: LHX5_WT_3-_GT24-01165_CTCTCGTC-AGGTTATA_S136_L005_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: Not applicable

value: Cortical brain (dorsal forebrain patterning)


title: Microglia NLRP3 knockout replicate 3

description: Library name: NLRP3KO_rep3


title: AP2-control fasting 5, iWAT


title: AP2-control fasting 4, iWAT


title: AP2-HuR ad libitum 4, eWAT

value: eWAT

value: Ad libitum


title: S33_36_F

description:
Library name: S33
33

value: 36mo Female


title: CBO-MOK20004-WT2-Day6, WT

description:
Library name: LHX5_WT_2-_GT24-01164_TCTCTACT-GAACCGCG_S134_L005_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: day 6


title: Microglia NLRP3 knockout replicate 2

description: Library name: NLRP3KO_rep2


title: CBO-MOK20004-WT1-Day6, WT

description:
Library name: LHX5_WT_1-_GT24-01163_GACCTGAA-CTCACCAA_S145_L005_R1_001
KOLF2.2J differentiated to cortical brain organoid


title: CBO-MOK20004P-B10-Day6, KO

description:
Library name: LHX5_PTC_B10-_GT24-01162_AGTTCAGG-TCTGTTGG_S139_L005_R1_001
KOLF2.2J derived knockout cell line,LHX5 PTC, differentiated to cortical brain organoid

value: Termination codon


title: Microglia NLRP3 knockout replicate 1

description: Library name: NLRP3KO_rep1


title: MIME28_MMouseWT_0_v1

first: MATTHEW

middle: Dae-Young

last: PARK

state: NY

address: 50 East 98th Street, 6A-1

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Sample 3
10X Genomics

library_source: transcriptomic single cell

data_processing:
Following alignment, barcodes matching cells that contained > 500 unique molecular identifiers (UMIs) were extracted.
From these cells, those with transcripts > 25% mitochondrial genes were filtered from downstream analyses.
Assembly: Gene expression reads were aligned to the mm10 reference transcriptome followed by count matrix generation using the default CellRanger 2.1 workflow, using the ‘raw’ matrix output.
Supplementary files format and content: Barcode.tsv, features.tsv, and matrix.mtx files are made available for each sample.

source_name: Lung

extract_protocol:
Immune cells were sorted and barcoded with 10x Cellplex oligos before being encapsulated using the 10X Chromium 3’ v3 chemistry kit according to manufacturer’s instructions. Cells sorted from the same genotype were barcoded and pooled into individual lanes. A total of 12,000 cells were loaded per lane from each condition. For scRNA-seq of BM of naïve, tumor- bearing and IL-4c treated mice, bone marrow myeloid cells and were sorted for sequencing. Due to their abundance in bone marrow, neutrophils were separately sorted and then recombined back with the above cells at a 1:10 ratio.
All sequencing libraries were prepared per manufacturer instructions.
After stringent cDNA and sequencing library quality control with the CybrGreen qPCR library quantification assay, samples were sequenced at a depth of 100 million reads per library with a 75-cycle kit on an Illumina Nextseq 550.

value: Lung

value: KP

value: Immune


title: AP2-control fasting 3, iWAT


title: S28_36_M

description:
Library name: S28
28

value: WT

value: 36mo Male

value: Male


title: S25_36_M

description:
Library name: S25
25


title: CBO-MOK20004P-A11-Day6, KO

description:
Library name: LHX5_PTC_A11-_GT24-01161_TGGATCGA-TATCGCAC_S142_L005_R1_001
KOLF2.2J derived knockout cell line,LHX5 PTC, differentiated to cortical brain organoid

value: iPSC


title: AP2-control fasting 1, iWAT

value: iWAT

value: control


title: MIME28_MMouseKO_0_v1

description:
Library name: Sample 2
10X Genomics

value: Axl knockout


title: S49_48_M

description:
Library name: S49
49

value: Red blood cells

value: 48mo Male


title: CBO-MOK20004P-A10-Day6, KO

description:
Library name: LHX5_PTC_A10-_GT24-01160_CAAGCTAG-CGCTATGT_S143_L005_R1_001
KOLF2.2J derived knockout cell line,LHX5 PTC, differentiated to cortical brain organoid

value: Cortical brain (dorsal forebrain patterning)


title: AP2-HuR fasting 6, iWAT

value: Overnight Fasting


title: S19_36_F

description:
Library name: S19
19

value: 36mo Female

value: Female


title: S23_36_M

description:
Library name: S23
23


title: AP2-HuR fasting 5, iWAT


title: APP/PS1.NLRP3 ko_3

city: Utrecht

first: Nathalie

last: Groen

address: Varrolaan 100

country: Netherlands

institute: Single cell discoveries

description: SORT-seq data

data_processing:
Sequencing data was mapped with BWA 0.7.15
Count tables generated with custom-written Python script (https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo2/Tablator.CELseq.py)
Seurat object and cell_metadata were generated using Seurat.
Assembly: Mus musculus mm10 (RefSeq)
Supplementary files format and content: tab separated file, CellBarcodeCounts
Supplementary files format and content: tab separated file, UMIBarcodeCounts
Supplementary files format and content: tab separated file, TranscriptCounts
Supplementary files format and content: text file, cell_metadata

extract_protocol:
Wild-type, NLRP3-/-, APP/PS1 and APP/PS1.NLRP3-/- mice were anaesthetized, sacrified and transcardially perfused with PBS.  The brains were removed and the hemispheres separated. One hemisphere was dissociated using the Neural Tissue Dissociation kit (P) (Miltenyi Biotec), and using MACS isolation the myelin was labelled and removed magnetically before the enrichment of CD11b+ microglia following the manufacturer’s guidelines (Miltenyi Biotec). The cells were then stained with LIVE/DEAD Fixable Aqua Dead Cell Stain kit (Invitrogen) and CD11b (Invitrogen), and the CD11b+ live single cells were FACS sorted at 4°C (BD FACS Aria III) into 384-well plates containing 384 primers and Mineral oil (Sigma). After sorting, plates were snap-frozen on dry ice and stored at -80°C.
Viable single cells were FACS sorted into 384-well plates, called cell capture plates, that were ordered from Single Cell Discoveries, a single-cell sequencing service provider based in the Netherlands. Each well of a cell capture plate contains a small 50 nl droplet of barcoded primers and 10 µl of mineral oil (Sigma M8410). After sorting, plates were immediately spun and placed on dry ice. Plates were stored at -80° C.  Plates were shipped on dry ice to Single Cell Discoveries, where single-cell RNA sequencing was performed according to an adapted version of the SORT-seq protocol (Muraro et al. 2016 with primers described in van den Brink et al. 2017). Cells were heat-lysed at 65° C followed by cDNA synthesis. After second-strand cDNA synthesis, all the barcoded material from one plate was pooled into one library and amplified using in vitro transcription (IVT). Following amplification, library preparation was done following the CEL-Seq2 protocol.3   to prepare a cDNA library for sequencing using TruSeq small RNA primers (Illumina). The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit (read 1: 26 cycles, index read: 6 cycles, read 2: 60 cycles)

value: Brain

value: f

value: CD11b microglia


title: APP/PS1.NLRP3 ko_2

description: SORT-seq data

value: m


title: CBO-MOK20004C-B05-Day6, KO

description:
Library name: LHX5_CE_B05-_GT24-01158_ATCCACTG-ACGCACCT_S150_L005_R1_001
KOLF2.2J derived knockout cell line,LHX5 CE, differentiated to cortical brain organoid

value: Critical exon

value: day 6


title: S15_36_F

description:
Library name: S15
15

value: WT


title: S133_60_F

description:
Library name: S133
133

value: 60mo Female


title: CBO-MOK20004C-A01-Day6, KO

description:
Library name: LHX5_CE_A01-_GT24-01157_AAGTCCAA-TACTCATA_S140_L005_R1_001
KOLF2.2J derived knockout cell line,LHX5 CE, differentiated to cortical brain organoid

value: iPSC


title: APP/PS1.NLRP3 ko_1

description: SORT-seq data


title: S132_60_F

description:
Library name: S132
132


title: AP2-HuR fasting 4, iWAT

value: iWAT


title: AP2-HuR fasting 3, iWAT


title: S131_60_M

description:
Library name: S131
131

value: 60mo Male

value: Male


title: AP2-HuR fasting 2, iWAT


title: NLRP3 ko_5

description: SORT-seq data


title: CBO-MOK20004W-E04-Day6, KO

description:
Library name: LHX5_KO_E04-_GT24-01155_TTATAACC-TCGATATC_S148_L005_R1_001
KOLF2.2J derived knockout cell line,LHX5 KO, differentiated to cortical brain organoid

value: Full coding region


title: MIME28_MMouseCre_0_v1

description:
Library name: Sample 1
10X Genomics

value: Lung

value: KP

value: Immune

value: Zbtb46-Cre x Axl-flox


title: CBO-MOK20004W-B02-Day6, KO

description:
Library name: LHX5_KO_B02-_GT24-01154_CCGCGGTT-CTAGCGCT_S153_L005_R1_001
KOLF2.2J derived knockout cell line,LHX5 KO, differentiated to cortical brain organoid

value: Cortical brain (dorsal forebrain patterning)


title: NLRP3 ko_4

description: SORT-seq data

value: Brain

value: f


title: NLRP3 ko_3

description: SORT-seq data

value: m

value: CD11b microglia


title: CBO-MOK20004C-E03-Day6, KO

description:
Library name: LHX5_CE_E03-_GT24-01159_GCTTGTCA-GTATGTTC_S135_L005_R1_001
KOLF2.2J derived knockout cell line,LHX5 CE, differentiated to cortical brain organoid

value: Critical exon

value: day 6


title: S129_60_F

description:
Library name: S129
129

value: Red blood cells

value: WT

value: 60mo Female

value: Female


title: S128_60_M

description:
Library name: S128
128

value: 60mo Male

value: Male


title: AP2-control fasting 2, iWAT

value: iWAT

value: control

value: Overnight Fasting


title: NLRP3 ko_2

description: SORT-seq data


title: CBO-MOK20004P-B10-Day5, KO

description:
Library name: LHX5_PTC_B10_Day5_GT23-07325_CCGTGAAG-ATCCACTG_S150_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 PTC, differentiated to cortical brain organoid

value: iPSC

value: Termination codon


title: AP2-control ad libitum 4, iWAT

value: Ad libitum


title: S41_48_M

description:
Library name: S41
41

value: 48mo Male


title: NLRP3 ko_1

description: SORT-seq data

value: Brain

value: m


title: S126_7_M

description:
Library name: S126
126

value: 7mo Male


title: CBO-MOK20004P-A11-Day5, KO

description:
Library name: LHX5_PTC_A11_Day5_GT23-07324_TCCAACGC-AAGTCCAA_S176_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 PTC, differentiated to cortical brain organoid

value: day 6

value: Cortical brain (dorsal forebrain patterning)


title: S125_7_M

description:
Library name: S125
125

value: Red blood cells

value: WT


title: AP2-control ad libitum 5, iWAT


title: CBO-MOK20004P-A07-Day5, KO

description:
Library name: LHX5_PTC_A7_Day5_GT23-07323_CTTGGTAT-GGACTTGG_S175_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 PTC, differentiated to cortical brain organoid


title: APP/PS1_5

description: SORT-seq data

value: f

value: CD11b microglia


title: AP2-control ad libitum 3, iWAT


title: AP2-HuR fasting 1, iWAT


title: S122_7_M

description:
Library name: S122
122

value: Male


title: AP2-control ad libitum 2, iWAT

value: iWAT


title: APP/PS1_4

description: SORT-seq data


title: CBO-MOK20004W-F01-Day6, KO

description:
Library name: LHX5_KO_F01-_GT24-01156_GGACTTGG-CGTCTGCG_S152_L005_R1_001
KOLF2.2J derived knockout cell line,LHX5 KO, differentiated to cortical brain organoid

value: Full coding region


title: AP2-control ad libitum 6, iWAT

value: control


title: CBO-MOK20004-WT-Day5, WT

description:
Library name: LHX5_WT_Day5_GT23-07326_TTACAGGA-GCTTGTCA_S167_L004_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: iPSC

value: Not applicable


title: S120_7_M

description:
Library name: S120
120


title: CBO-MOK20004C-F02-Day5, KO

description:
Library name: LHX5_CE_F2_Day5_GT23-07322_GTCGGAGC-TTATAACC_S174_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 CE, differentiated to cortical brain organoid

value: Critical exon


title: S127_60_M

description:
Library name: S127
127

value: 60mo Male


title: AP2-control ad libitum 1, iWAT

value: Ad libitum


title: CBO-MOK20004C-E03-Day5, KO

description:
Library name: LHX5_CE_E3_Day5_GT23-07321_ACTAAGAT-CCGCGGTT_S157_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 CE, differentiated to cortical brain organoid


title: AP2-HuR ad libitum 6, iWAT


title: CBO-MOK20004C-A01-Day5, KO

description:
Library name: LHX5_CE_A1_Day5_GT23-07320_ATGAGGCC-CAATTAAC_S169_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 CE, differentiated to cortical brain organoid


title: APP/PS1_1

description: SORT-seq data

value: Brain

value: m


title: APP/PS1_2

description: SORT-seq data


title: CBO-MOK20007W-B09-Day5, KO

description:
Library name: FEZF2_KO_B09-2_Day5_GT23-05964_CCGCGGTT-CTAGCGCT_S48_L001_R1_001
KOLF2.2J derived knockout cell line,FEZF2 KO, differentiated to cortical brain organoid

value: day 5


title: AP2-HuR ad libitum 5, iWAT


title: S116_7_F

description:
Library name: S116
116

value: 7mo Female

value: Female


title: CBO-MOK20004W-F01-Day5, KO

description:
Library name: LHX5_KO_F1_Day5_GT23-07319_GCAGAATT-TGGCCGGT_S151_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 KO, differentiated to cortical brain organoid

value: day 6

value: Cortical brain (dorsal forebrain patterning)


title: S111_7_F

description:
Library name: S111
111

value: Red blood cells

value: WT


title: APP/PS1_3

description: SORT-seq data

value: CD11b microglia


title: AP2-HuR ad libitum 4, iWAT

value: iWAT


title: WT_4

description: SORT-seq data


title: CBO-MOK20004W-B02-Day5, KO

description:
Library name: LHX5_KO_B2_Day5_GT23-07317_GGTACCTT-GACGTCTT_S152_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 KO, differentiated to cortical brain organoid

value: Full coding region


title: AP2-HuR ad libitum 3, iWAT


title: WT_2

description: SORT-seq data


title: S107_7_M

description:
Library name: S107
107

value: 7mo Male

value: Male


title: S110_7_F

description:
Library name: S110
110


title: S117_7_F

description:
Library name: S117
117


title: CBO-MOK20004-WT-Day4, WT

description:
Library name: LHX5_WT_Day4_GT23-07316_GCACGGAC-TGCGAGAC_S173_L004_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: iPSC

value: Not applicable

value: day 4


title: S106_7_F

description:
Library name: S106
106


title: AP2-HuR ad libitum 1, iWAT

value: Ad libitum


title: WT_1

description: SORT-seq data

value: Brain

value: f


title: FKO-HuR fasting 3, eWAT

value: eWAT

value: KO

value: Overnight Fasting


title: CBO-MOK20004P-B10-Day4, KO

description:
Library name: LHX5_PTC_B10_Day4_GT23-07315_ATGTAAGT-CATAGAGT_S161_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 PTC, differentiated to cortical brain organoid

value: Termination codon

value: Cortical brain (dorsal forebrain patterning)


title: S10_36_F

description:
Library name: S10
10

value: Red blood cells

value: WT

value: 36mo Female

value: Female


title: CBO-MOK20004P-A11-Day4, KO

description:
Library name: LHX5_PTC_A11_Day4_GT23-07314_CGGCGTGA-ACAGGCGC_S156_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 PTC, differentiated to cortical brain organoid


title: FKO-HuR fasting 2, eWAT


title: BulkSeq_Control_Hic1

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

country: Germany

institute: University Medicine Greifswald

description: pooled male and female

data_processing:
Alignment to the modified mm10 reference genome was performed using the cellranger count pipeline (10X Genomics).
The cellranger aggr pipeline was used to create aggregated library. Graphical output was generated using the cellrangerRkit R package (10X Genomics).
All datasets are processed and analyzed using the Seurat package (Satija Lab, version 3.1.2) in R.
Preliminary clustering  is performed to identify barcodes corresponding to myeloid cells based on CD45, CX3CR1, and P2RY12 expression. These cells are subsetted out, followed by quality control to remove cells expressing <200 genes and genes expressed in <3 cells. Additional quality control is performed based on sample features, including total genes expressed, total unique molecular identifiers (UMIs), and percentage mitochondrial counts to remove outliers, which may be low-quality cells and potential multiplets.
Gene expression per cell is normalized to a scale factor of 10,000. To minimize batch-associated differences in the visualization of data, datasets sequenced at similar timepoints  are merged, followed by “anchoring” of cells originating from the same biological state (Stuart et al., 2019). Expression of each gene in the harmonized data is scaled to a mean and variance of zero and one, respectively.

source_name: Control brain cells

growth_protocol: Hic1CreERT2 mice were crossed to B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J (Ai14 line, JAX stock 007914, herein referred to as Rosa26LSL-tdTomato) mice for lineage tracing.. The Hic1 gene was hence used to drive the fluorescent protein tdTomato in a Cre dependent manner. To induce Cre-ERT2 nuclear translocation timed tamoxifen injections were used (described below) leading to tdTomato expression in Hic1+ cells. This approach leads to a stable expression of tdTomato in all quiescent SPC populations which is heritable by all daughter cells proliferating of the original SPC population. The mouse line was maintained on a C57BL/6J background. Male and female mice at the age of 2-5 months were used. All mice were group housed under pathogen-free conditions (12 h light/dark cycle) and provided food and water ad libitum.

extract_protocol: Single cell suspensions were generated as described for bulk-RNA-seq with the following downstream modifications. CD45+/tdTomato- and CD45-/tdTomato+ cells were separated and enriched by FACS sorting into 0.22 μm vacuum filtered SC collection media (DMEM containing 5% FBS) with PI. Viable CD45+/tdTomato- and CD45-/tdTomato+ target cells were subsequently further purified, and debris reduced by sorting a second time. Equal numbers of each target population were collected into the same 10 μL of SC collection media. Sorted CD45+/tdTomato- cells were used as carrier cells with CD45-/tdTomato+ cells to increase the probability of successful cell capture for downstream single-cell RNA-seq protocols. Cells were counted and quality control was determined by hemocytometer. If results showed that >98% of visible objects were verified to be single cells, the suspension was put into a Chromium Controller (10X Genomics), captured and libraries are created with the Chromium single cell 3’ reagent kit v2 (10X Genomics). Suspension was put into a Chromium Controller (10X Genomics), captured and libraries are created with the Chromium single cell 3’ reagent kit v2 (10X Genomics) cDNA libraries were sequenced on a Nextseq 500 (Illumina) to a minimum depth of 50,000 reads per cell. A transgenic reference genome was generated by the concatenation of the sequences for tdTomato to the mm10 reference genome and subsequent use of the cellranger mkref pipeline.

treatment_protocol: Brains from Hic1CreERT2; Rosa26LSL-tdTomato (n=4) were pooled. A razor was used to cut the brain tissue into <1 mm3 pieces. 1.5 ml digestion buffer was added containing 1.5 U/mL Collagenase D (Roche 11 088 882 001) and 2.4 U/mL Dispase II (Roche 04 942 078 001) for 40 minutes. Digested material was subsequently triturated by pipetting and centrifuged 2200 rpm for 5 minutes. Re-suspended tissue (6 ml PBS) was again triturated by pipetting and passed through a 70 μm cell strainer. Tissue was re-suspended in 37% Percoll and centrifuged at 2200 rpm for 20 minutes at room temperature. The separated myelin and Percoll were removed followed by 5 minutes of centrifugation at 1400 rpm. To enrich for tdTomato cells from this whole brain suspension, cells were stained with a cocktail containing anti-Ter119-647d (Ablab AB00000305, 1:200), anti- CD45-488 (AbLab AB00000383, 1:1000) and anti-CD31-APC (BD Pharmingen 551262, 1:400). This mixture containing cells and antibodies was then incubated on ice for 20 minutes (in the dark). Afterwards, 3 ml FACS buffer was added to dilute the antibodies prior to centrifugation at 1400 rpm for 5 minutes. Cells were re-suspended in FACS buffer and centrifuged at 1400 rpm for 5 minutes. The pellet was re-suspended in FACS buffer containing propidium iodide (PI) and Hoechst 33342 (Sigma B2261) to a final concentration of 4 μM. Positively stained cells were then sorted using a BD Influx, and PI-negative, Hoescht positive, and forward/side scatter parameters were used to identify viable single cells for all FACS enrichments. Sorted cells were collected into sort media (DMEM, 5% FBS) in cooled siliconized microcentrifuge tubes (Fisher Scientific; 02-681-320). For isolation of RNA, cells were microfuged at 2500 rpm for 5 minutes with soft braking and the isolated cell pellet was lysed in RNAzol (Sigma R4533).

tag: genotype/variation

value: Hic1CreERT2; Rosa26LSL-tdTomato

tag: age

value: 2-5 months

tag: condition

value: control


title: SingleCell_Stroke_Rep2

description: pooled male and female

data_processing:
Alignment to the modified mm10 reference genome was performed using the cellranger count pipeline (10X Genomics).
The cellranger aggr pipeline was used to create aggregated library. Graphical output was generated using the cellrangerRkit R package (10X Genomics).
All datasets are processed and analyzed using the Seurat package (Satija Lab, version 3.1.2) in R.
Preliminary clustering  is performed to identify barcodes corresponding to myeloid cells based on CD45, CX3CR1, and P2RY12 expression. These cells are subsetted out, followed by quality control to remove cells expressing <200 genes and genes expressed in <3 cells . Additional quality control is performed based on sample features, including total genes expressed, total unique molecular identifiers (UMIs), and percentage mitochondrial counts to remove outliers, which may be low-quality cells and potential multiplets.
Gene expression per cell is normalized to a scale factor of 10,000. To minimize batch-associated differences in the visualization of data, datasets sequenced at similar timepoints  are merged, followed by “anchoring” of cells originating from the same biological state (Stuart et al., 2019). Expression of each gene in the harmonized data is scaled to a mean and variance of zero and one, respectively.

source_name: Brain ischemic area cells

growth_protocol: Single cell suspensions were generated as described for bulk-RNA-seq with the following downstream modifications. CD45+/tdTomato- and CD45-/tdTomato+ cells were separated and enriched by FACS sorting into 0.22 μm vacuum filtered SC collection media (DMEM containing 5% FBS) with PI. Viable CD45+/tdTomato- and CD45-/tdTomato+ target cells were subsequently further purified, and debris reduced by sorting a second time. Equal numbers of each target population were collected into the same 10 μL of SC collection media. Sorted CD45+/tdTomato- cells were used as carrier cells with CD45-/tdTomato+ cells to increase the probability of successful cell capture for downstream single-cell RNA-seq protocols. Cells were counted and quality control was determined by hemocytometer. If results showed that >98% of visible objects were verified to be single cells, the suspension was put into a Chromium Controller (10X Genomics), captured and libraries are created with the Chromium single cell 3’ reagent kit v2 (10X Genomics). Suspension was put into a Chromium Controller (10X Genomics), captured and libraries are created with the Chromium single cell 3’ reagent kit v2 (10X Genomics) cDNA libraries were sequenced on a Nextseq 500 (Illumina) to a minimum depth of 50,000 reads per cell. A transgenic reference genome was generated by the concatenation of the sequences for tdTomato to the mm10 reference genome and subsequent use of the cellranger mkref pipeline.

extract_protocol:
Single cell suspensions were generated as described for pop-RNA-seq with the following downstream modifications. CD45+/tdTomato- and CD45-/tdTomato+ cells were separated and enriched by FACS sorting into 0.22 μm vacuum filtered SC collection media (DMEM containing 5% FBS) with PI. Viable CD45+/tdTomato- and CD45-/tdTomato+ target cells were subsequently further purified, and debris reduced by sorting a second time. Equal numbers of each target population were collected into the same 10 μL of SC collection media. Sorted CD45+/tdTomato- cells were used as carrier cells with CD45-/tdTomato+ cells to increase the probability of successful cell capture for downstream single-cell RNA-seq protocols. Cells were counted and quality control was determined by hemocytometer. If results showed that >98% of visible objects were verified to be single cells, the suspension was put into a Chromium Controller (10X Genomics), captured and libraries are created with the Chromium single cell 3’ reagent kit v2 (10X Genomics).
suspension was put into a Chromium Controller (10X Genomics), captured and libraries are created with the Chromium single cell 3’ reagent kit v2 (10X Genomics)
cDNA libraries were sequenced on a Nextseq 500 (Illumina) to a minimum depth of 50,000 reads per cell. A transgenic reference genome was generated by the concatenation of the sequences for tdTomato to the mm10 reference genome and subsequent use of the cellranger mkref pipeline.

treatment_protocol: Brains from Hic1CreERT2; Rosa26LSL-tdTomato mice were dissected and immediately sliced into 800-µm thick coronal slices using a Vibratome (Leica VT1200S) as described above to improve visualization of the ischemic area. The ischemic area was dissected from 4 mice and pooled for FACS-sorting. Contralateral hemispheres from 4 mice were also pooled separately. A razor was used to cut the brain tissue into <1 mm3 pieces. 1.5 ml digestion buffer was added containing 1.5 U/mL Collagenase D (Roche 11 088 882 001) and 2.4 U/mL Dispase II (Roche 04 942 078 001) for 40 minutes. Digested material was subsequently triturated by pipetting and centrifuged 2200 rpm for 5 minutes. Re-suspended tissue (6 ml PBS) was again triturated by pipetting and passed through a 70 μm cell strainer. Tissue was re-suspended in 37% Percoll and centrifuged at 2200 rpm for 20 minutes at room temperature. The separated myelin and Percoll were removed followed by 5 minutes of centrifugation at 1400 rpm. To enrich for tdTomato cells from this whole brain suspension, cells were stained with a cocktail containing anti-Ter119-647d (Ablab AB00000305, 1:200), anti- CD45-488 (AbLab AB00000383, 1:1000) and anti-CD31-APC (BD Pharmingen 551262, 1:400). This mixture containing cells and antibodies was then incubated on ice for 20 minutes (in the dark). Afterwards, 3 ml FACS buffer was added to dilute the antibodies prior to centrifugation at 1400 rpm for 5 minutes. Cells were re-suspended in FACS buffer and centrifuged at 1400 rpm for 5 minutes. The pellet was re-suspended in FACS buffer containing propidium iodide (PI) and Hoechst 33342 (Sigma B2261) to a final concentration of 4 μM. Positively stained cells were then sorted using a BD Influx, and PI-negative, Hoescht positive, and forward/side scatter parameters were used to identify viable single cells for all FACS enrichments. Sorted cells were collected into sort media (DMEM, 5% FBS) in cooled siliconized microcentrifuge tubes (Fisher Scientific; 02-681-320). For isolation of RNA, cells were microfuged at 2500 rpm for 5 minutes with soft braking and the isolated cell pellet was lysed in RNAzol (Sigma R4533).

value: stroke


title: CBO-MOK20004P-A07-Day4, KO

description:
Library name: LHX5_PTC_A7_Day4_GT23-07313_TAATACAG-GTGAATAT_S155_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 PTC, differentiated to cortical brain organoid

value: iPSC

value: day 4


title: CBO-MOK20004W-E04-Day5, KO

description:
Library name: LHX5_KO_E4_Day5_GT23-07318_AACGTTCC-AGTACTCC_S166_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 KO, differentiated to cortical brain organoid

value: Full coding region

value: day 6


title: WT_3

description: SORT-seq data

tag: tissue

value: Brain

value: m

value: CD11b microglia


title: dmsABC_U3

city: Aurora

first: Andrés

last: Vázquez-Torres

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

description:
strain AV22025 ∆dmsABC
Barcode: GCAAGATC+AGTCGAAG; Mean Q-score: 35.09

data_processing:
Illumina adaptor sequences were trimmed from raw paired reads with Trim Galore (version 0.6.7) using the first 13 bp of the standard Illumina adaptor sequence, AGATCGGAAGAGC.
Reads were mapped with Bowtie2 (version 2.5.0) using the S. Typhimurium 14028s primary genome assembly GCA_000022165.1, which contains both CP001363.1 and CP001362.1, as the reference genome.
Samtools (version 1.16.1) was used to sort the alignments.
Deduplication based on UMIs was performed with UMI-tools (version 1.1.4).
Raw count files were generated with featureCounts (version 2.0.1).
Assembly: GCA_000022165.1
Supplementary files format and content: Tab-delimited matrix file with raw counts for every loci from every sample.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: bacteria

growth_protocol: Salmonella strains were cultured aerobically, overnight in LB broth at 37°C and then were diluted to 10^7 cells/ml in MOPS minimal media with 0.4% Casaminoacids and cultured anaerobically for 6 h at 37°C.

extract_protocol:
Total RNA was isolated using the High Pure RNA Isolation Kit (Roche) according to the manufacturer’s protocol.
Starting with 1 μg total RNA, ribosomal RNA was removed from the total RNA preparation using the Polaris Depletion Kit with custom rRNA depletion probes designed to target S. Typhimurium 14028s rRNA (Watchmaker Genomics). Libraries were prepared for Illumina sequencing by following the protocol accompanying the Watchmaker RNA Library Prep Kit. Samples were indexed and barcoded using full-length xGEN™ UDI-UMI Adapters (IDT, Index 1-4 and Index 9-12).

treatment_protocol: 8 mL of culture was pelleted after the 6 hrs of anaerobic growth in MOPS-CAA.

value: bacteria

tag: culture media

value: MOPS-CAA

value: 6 hrs

value: AV22025 <delta>dmsABC

value: anaerobic growth


title: CBO-MOK20004C-F02-Day4, KO

description:
Library name: LHX5_CE_F2_Day4_GT23-07312_TGACGAAT-GCCTACTG_S160_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 CE, differentiated to cortical brain organoid

value: Critical exon

value: Cortical brain (dorsal forebrain patterning)


title: FKO-HuR fasting 1, eWAT

value: eWAT

value: KO

value: Overnight Fasting


title: dmsABC_U2

description:
strain AV22025 ∆dmsABC
Barcode: ATCGATCG+TGGAAGCA; Mean Q-score: 35.22


title: AP2-HuR ad libitum 2, iWAT

value: iWAT

value: Ad libitum


title: FKO-control fasting 3, eWAT

value: Control


title: SingleCell_Control_Rep2

description: pooled male and female

source_name: Control cells 2

growth_protocol: Hic1CreERT2 mice were crossed to B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J (Ai14 line, JAX stock 007914, herein referred to as Rosa26LSL-tdTomato) mice for lineage tracing. The Hic1 gene was hence used to drive the fluorescent protein tdTomato in a Cre dependent manner. To induce Cre-ERT2 nuclear translocation timed tamoxifen injections were used (described below) leading to tdTomato expression in Hic1+ cells. This approach leads to a stable expression of tdTomato in all quiescent SPC populations which is heritable by all daughter cells proliferating of the original SPC population. The mouse line was maintained on a C57BL/6J background. Male and female mice at the age of 2-5 months were used. All mice were group housed under pathogen-free conditions (12 h light/dark cycle) and provided food and water ad libitum.

treatment_protocol: Brains from Hic1CreERT2; Rosa26LSL-tdTomato mice were dissected and hemispheres contralateral to the stroke from 4 mice were pooled. A razor was used to cut the brain tissue into <1 mm3 pieces. 1.5 ml digestion buffer was added containing 1.5 U/mL Collagenase D (Roche 11 088 882 001) and 2.4 U/mL Dispase II (Roche 04 942 078 001) for 40 minutes. Digested material was subsequently triturated by pipetting and centrifuged 2200 rpm for 5 minutes. Re-suspended tissue (6 ml PBS) was again triturated by pipetting and passed through a 70 μm cell strainer. Tissue was re-suspended in 37% Percoll and centrifuged at 2200 rpm for 20 minutes at room temperature. The separated myelin and Percoll were removed followed by 5 minutes of centrifugation at 1400 rpm. To enrich for tdTomato cells from this whole brain suspension, cells were stained with a cocktail containing anti-Ter119-647d (Ablab AB00000305, 1:200), anti- CD45-488 (AbLab AB00000383, 1:1000) and anti-CD31-APC (BD Pharmingen 551262, 1:400). This mixture containing cells and antibodies was then incubated on ice for 20 minutes (in the dark). Afterwards, 3 ml FACS buffer was added to dilute the antibodies prior to centrifugation at 1400 rpm for 5 minutes. Cells were re-suspended in FACS buffer and centrifuged at 1400 rpm for 5 minutes. The pellet was re-suspended in FACS buffer containing propidium iodide (PI) and Hoechst 33342 (Sigma B2261) to a final concentration of 4 μM. Positively stained cells were then sorted using a BD Influx, and PI-negative, Hoescht positive, and forward/side scatter parameters were used to identify viable single cells for all FACS enrichments. Sorted cells were collected into sort media (DMEM, 5% FBS) in cooled siliconized microcentrifuge tubes (Fisher Scientific; 02-681-320). For isolation of RNA, cells were microfuged at 2500 rpm for 5 minutes with soft braking and the isolated cell pellet was lysed in RNAzol (Sigma R4533).

value: Hic1CreERT2; Rosa26LSL-tdTomato

value: 2-5 months

value: control


title: CBO-MOK20004C-A01-Day4, KO

description:
Library name: LHX5_CE_A1_Day4_GT23-07310_TTGGACTC-CTGCTTCC_S172_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 CE, differentiated to cortical brain organoid

value: iPSC

value: day 4


title: dmsABC_U1

description:
strain AV22025 ∆dmsABC
Barcode: CGGCTAAT+CTCGTTCT; Mean Q-score: 35.05

value: bacteria

value: MOPS-CAA


title: DMSO_RNAseq_rep3

city: Beijing

first: Qiaoran

last: Xi

address: Haidian District

department: School of Life Sciences

country: China

institute: Tsinghua University

data_processing:
RNA reads were quality checked with FastQC v0.11.5 and trimmed to remove sequencing adaptors and low-quality reads using Trim Galore v0.6.7 with default parameters.
Trimmed sequence reads were mapped to the human (hg19) genome with Bowtie2 v2.3.3 using standard settings for paired reads. The .sam and .bam files were manipulate with samtools v1.9. On average, 80% of reads were uniquely mapped.
Uniquely mapped reads were assigned to annotated genes with featureCounts v2.0.1 using default settings.
Read counts were then normalized by library size and differential gene expression analysis based on a negative binomial distribution was conducted with DESeq2 packages in R language.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

growth_protocol: DIPG cells were cultured on Matri-gel coated plates with a serum-free DMEM medium containing B27 supplement, N2, bFGF (20 ng/mL), EGF (20 ng/mL), PDGF-AB (20 ng/mL) and 1% penicillin/streptomycin.

extract_protocol:
RNA of WT or CREB5-KD DIPG17 cells were purified using TIANGEN kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment.

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: DMSO


title: CBO-MOK20004C-E03-Day4, KO

description:
Library name: LHX5_CE_E3_Day4_GT23-07311_CAGTAGGC-ATTCGTCA_S170_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 CE, 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

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

value: Critical exon


title: FKO-control fasting 2, eWAT


title: SingleCell_Control_Rep1

description: pooled male and female

source_name: Control cells 1


title: CBO-MOK20004W-F01-Day4, KO

description:
Library name: LHX5_KO_F1_Day4_GT23-07309_CCAAGTCT-TCATCCTT_S162_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 KO, differentiated to cortical brain organoid

value: Full coding region

value: Cortical brain (dorsal forebrain patterning)


title: WT_U3

description: Barcode: TGAGCTAG+GAACGGTT; Mean Q-score: 35.16

value: 6 hrs

value: WT

value: anaerobic growth


title: FKO-HuR fasting 3, iWAT

value: iWAT

value: KO

value: Overnight Fasting


title: CBO-MOK20004W-E04-Day4, KO

description:
Library name: LHX5_KO_E4_Day4_GT23-07308_CTCTCGTC-AGGTTATA_S147_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 KO, differentiated to cortical brain organoid


title: WT_U4

description: Barcode: GAGACGAT+ACCGGTTA; Mean Q-score: 35.33


title: DMSO_RNAseq_rep2


title: dmsABC_U4

description:
strain AV22025 ∆dmsABC
Barcode: GCTATCCT+AACAGGTG; Mean Q-score: 35.2

value: AV22025 <delta>dmsABC


title: FKO-control fasting 1, eWAT

value: eWAT

value: Control


title: FKO-HuR fasting 2, iWAT


title: ABBV_RNAseq_rep3


title: FKO-HuR fasting 1, iWAT


title: WT_U1

description: Barcode: CTGATCGT+GCGCATAT; Mean Q-score: 34.83


title: SingleCell_Stroke_Rep1

description: pooled male and female

growth_protocol: Hic1CreERT2 mice were crossed to B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J (Ai14 line, JAX stock 007914, herein referred to as Rosa26LSL-tdTomato) mice for lineage tracing. The Hic1 gene was hence used to drive the fluorescent protein tdTomato in a Cre dependent manner. To induce Cre-ERT2 nuclear translocation timed tamoxifen injections were used (described below) leading to tdTomato expression in Hic1+ cells. This approach leads to a stable expression of tdTomato in all quiescent SPC populations which is heritable by all daughter cells proliferating of the original SPC population. The mouse line was maintained on a C57BL/6J background. Male and female mice at the age of 2-5 months were used. All mice were group housed under pathogen-free conditions (12 h light/dark cycle) and provided food and water ad libitum. Animals received photothrombotic stroke as described below and remained in their home cage until respective time point (Day 7 post stroke) was reached.

value: Hic1CreERT2; Rosa26LSL-tdTomato

value: 2-5 months

value: stroke


title: CBO-MOK20004-WT-Day3, WT

description:
Library name: LHX5_WT_Day3_GT23-07306_GACCTGAA-CTCACCAA_S165_L004_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: iPSC

value: Not applicable

value: day 3


title: FKO-control fasting 3, iWAT


title: CBO-MOK20004P-B10-Day3, KO

description:
Library name: LHX5_PTC_B10_Day3_GT23-07305_AGTTCAGG-TCTGTTGG_S149_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 PTC, differentiated to cortical brain organoid

value: Termination codon


title: ABBV_RNAseq_rep2

value: Diffuse intrinsic pontine glioma (DIPG) cells


title: FKO-control fasting 2, iWAT


title: WT_Form_3_eS

tag: culture conditions

value: Formative

value: mESC cell line

tag: treatment time


title: CBO-MOK20004P-A11-Day3, KO

description:
Library name: LHX5_PTC_A11_Day3_GT23-07304_TGGATCGA-TATCGCAC_S159_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 PTC, differentiated to cortical brain organoid

tag: cell line

value: Cortical brain (dorsal forebrain patterning)


title: WT_Form_2_lS

tag: cell type


title: FKO-control fasting 1, iWAT

value: iWAT


title: ABBV_RNAseq_rep1


title: DMSO_RNAseq_rep1

value: DMSO


title: DMSO_ATAC-seq_rep2

data_processing:
Raw reads were quality checked with FastQC v0.11.5 and trimmed to remove sequencing adaptors and low-quality reads using Trim Galore v0.6.7 with default parameters.
Trimmed sequence reads were mapped to the human (hg19) genome with Bowtie2 v2.3.3 using standard settings for paired reads. The .sam and .bam files were manipulate with samtools v1.9. On average, 80% of reads were uniquely mapped.
Peaks were called using macs2 2.1.4 with the default setting. Visualization of detected peaks was performed using deeptools 3.4.5.
Assembly: hg19
Supplementary files format and content: bigWig

extract_protocol:
For ATAC-seq experiment, 0.5 million cells were collected for ATAC-seq followed commercial manual ATAC kit (cat. #N248, Novoprotein Inc.).
DNA libraries were prepared through PCR using a commercial ATAC kit (cat. #N248, Novoprotein Inc.) according to the manufacture’s protocol. The sequencing libraries were qualified with Qubit 2.0 and Agilent 2100, and sequenced on an Illumina HiSeq platform for each library.


title: WT_U2

description: Barcode: ACTCTCGA+CTGTACCA; Mean Q-score: 35.14

value: bacteria

value: MOPS-CAA

value: 6 hrs

value: WT

value: anaerobic growth


title: FKO-HuR ad libitum 3, eWAT

value: eWAT

value: KO

value: Ad libitum


title: ABBV_ATAC-seq_rep2


title: ABBV_ATAC-seq_rep1


title: WT_Form_1_lS

data_processing:
library strategy: BioRepli-seq
Bowtie2 mapping to mm10
BamtoBed
Bin into 50kb genome bins
Calculate RT
Quantile normalization
Bedgraph to bigwig
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol: NEBNext Ultra II (on-bead custom protocol)


title: CBO-MOK20004C-E03-Day3, KO

description:
Library name: LHX5_CE_E3_Day3_GT23-07301_ATCCACTG-ACGCACCT_S171_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 CE, differentiated to cortical brain organoid

value: iPSC

tag: editing strategy

value: Critical exon


title: CBO-MOK20004W-B02-Day4, KO

description:
Library name: LHX5_KO_B2_Day4_GT23-07307_TCTCTACT-GAACCGCG_S154_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 KO, differentiated to cortical brain organoid

value: Full coding region

tag: altered gene_symbol

value: day 4


title: CBO-MOK20004C-A01-Day3, KO

description:
Library name: LHX5_CE_A1_Day3_GT23-07300_AAGTCCAA-TACTCATA_S163_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 CE, differentiated to cortical brain organoid

tag: altered locus

value: day 3


title: WT_Form_3_lS

value: Formative

value: mESC cell line


title: WT_Form_1_eS


title: CREB5KD_RNAseq_rep2

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: CREB5 KD


title: FKO-HuR ad libitum 2, eWAT


title: KO-control ad libitium 3, eWAT

value: Control


title: DMSO_ATAC-seq_rep1

value: DMSO


title: CREB5KD_RNAseq_rep1


title: KO-control ad libitium 2, eWAT


title: CBO-MOK20004W-F01-Day3, KO

description:
Library name: LHX5_KO_F1_Day3_GT23-07299_GGACTTGG-CGTCTGCG_S168_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 KO, differentiated to cortical brain organoid

tag: time

value: Cortical brain (dorsal forebrain patterning)


title: FKO-HuR ad libitum 1, eWAT


title: WT_Naive_3_lS

value: Naive


title: WT_Naive_3_eS


title: CBO-MOK20004W-E04-Day3, KO

description:
Library name: LHX5_KO_E4_Day3_GT23-07298_TTATAACC-TCGATATC_S148_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 KO, differentiated to cortical brain organoid

tag: model system


title: WT_RNAseq_rep2

value: WT


title: KO-control ad libitium 1, eWAT

value: eWAT


title: CBO-MOK20004P-A07-Day3, KO

description:
Library name: LHX5_PTC_A7_Day3_GT23-07303_CAAGCTAG-CGCTATGT_S153_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 PTC, differentiated to cortical brain organoid

value: Termination codon

tag: parental cell_line


title: WT_RNAseq_rep1

tag: genotype


title: CBO-MOK20004W-B02-Day3, KO

description:
Library name: LHX5_KO_B2_Day3_GT23-07297_CCGCGGTT-CTAGCGCT_S164_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 KO, differentiated to cortical brain organoid


title: WT_Form_2_eS


title: WT_Naive_2_lS


title: WT_Naive_2_eS


title: FKO-HuR ad libitum 3, iWAT

value: iWAT

value: KO

tag: treatment

value: Ad libitum


title: CBO-MOK20003-WT-Day9, WT

description:
Library name: OTX1_Day9_WT2-_GT23-15123_TTACAGGA-GCTTGTCA_S145_L003_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: iPSC

value: Not applicable

value: day 9


title: WT_Naive_1_lS


title: FKO-HuR ad libitum 2, iWAT


title: H3K27MOE_H3K27ac_rep1

data_processing:
Raw reads were quality checked with FastQC v0.11.5 and trimmed to remove sequencing adaptors and low-quality reads using Trim Galore v0.6.7 with default parameters.
Trimmed sequence reads were mapped to the human (hg19) genome with Bowtie2 v2.3.3 using standard settings for paired reads. The .sam and .bam files were manipulate with samtools v1.9. On average, 80% of reads were uniquely mapped.
Peaks were called using macs2 2.1.4 with the default setting. Visualization of detected peaks was performed using deeptools 3.4.5.
Downstream analyses were performed using DiffBind 3.2.4. The motif analysis was performed using the findMotifGenome.pl program in the HOMER suite with default parameters.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: PPC

extract_protocol:
For CUT&Tag experiment, 0.5 million cells were collected for CUT&Tag followed manuals (Yeason) to get H3K27me3, H3K27ac, H3K9me2, BRG1 or CREB5-enriched DNA.
The DNA library was prepared through PCR according to the manufacturer’s protocol (cat. #12598ES12, Yeason). The sequencing libraries were quantified and quality assessed with Qubit 2.0 and Agilent 2100. DNA fragments ranging from 200-600bp were selected for PCR-assisted library using magnetic beads. Sequencing libraries were multiplexed and run on an Illumina HiSeq platform.

value: PPC

value: Normal fetal pontine neural progenitor cells

value: H3.3K27M OE

tag: chip antibody


title: H3K27MOE_H3K27ac_rep2


title: CBO-MOK20003P-A10-Day9, KO

description:
Library name: OTX1_Day9_PTC_A10-_GT23-15116_ACTAAGAT-CCGCGGTT_S144_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 PTC, differentiated to cortical brain organoid


title: CBO-MOK20003P-A11-Day9, KO

description:
Library name: OTX1_Day9_PTC_A11-_GT23-15117_GTCGGAGC-TTATAACC_S169_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 PTC, differentiated to cortical brain organoid


title: KO-control ad libitum 3, iWAT


title: WT_Naive_1_eS

source_name: mESCs

value: mESC cell line


title: H3K27MOE_H3K27me3_rep2


title: FKO-HuR ad libitum 1, iWAT


title: Naive_K4m1_rep2

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

extract_protocol: Libraries were constructed using custom adaptors.


title: CBO-MOK20003C-B08-Day9, KO

description:
Library name: OTX1_Day9_CE_B08-_GT23-15121_CCGTGAAG-ATCCACTG_S153_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 CE, differentiated to cortical brain organoid

value: Critical exon


title: H3K27MOE_H3K27me3_rep1


title: Naive_K119ubH2A_rep2


title: KO-control ad libitum 2, iWAT

value: Control


title: KO-control ad libitum 1, iWAT


title: CBO-MOK20003C-B06-Day9, KO

description:
Library name: OTX1_Day9_CE_B06-_GT23-15120_TCCAACGC-AAGTCCAA_S159_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 CE, differentiated to cortical brain organoid

value: Cortical brain (dorsal forebrain patterning)


title: HuR KO 6h, Torin, adipocytes

source_name: adipocytes

value: adipocytes

value: treatment with Torin 6h


title: PPC_H3K27M_rep2


title: Naive_H3K9m2_rep2

value: Naive


title: CBO-MOK20004C-F02-Day3, KO

description:
Library name: LHX5_CE_F2_Day3_GT23-07302_GCTTGTCA-GTATGTTC_S158_L004_R1_001
KOLF2.2J derived knockout cell line,LHX5 CE, differentiated to cortical brain organoid

value: day 3


title: CBO-MOK20003C-A08-Day9, KO

description:
Library name: OTX1_Day9_CE_A08-_GT23-15119_CTTGGTAT-GGACTTGG_S162_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 CE, differentiated to cortical brain organoid


title: HuR KO 3h, Torin, adipocytes

value: treatment with Torin 3h


title: Naive_H3K14ac_rep2


title: CBO-MOK20003W-E06-Day9, KO

description:
Library name: OTX1_Day9_KO_E06_2-_GT23-15113_GCAGAATT-TGGCCGGT_S148_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 KO, differentiated to cortical brain organoid

value: Full coding region


title: PPC_H3K27M_rep1


title: Naive_H3.3_rep2


title: CBO-MOK20003W-D04-Day9, KO

description:
Library name: OTX1_Day9_KO_D04_2-_GT23-15112_AACGTTCC-AGTACTCC_S158_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 KO, differentiated to cortical brain organoid


title: HuR KO 12h, Torin, adipocytes

value: KO

value: treatment with Torin 12h


title: HuR KO 6h, DMSO, adipocytes

value: Control 6h


title: CBO-MOK20003P-A09-Day9, KO

description:
Library name: OTX1_Day9_PTC_A09-_GT23-15115_ATGAGGCC-CAATTAAC_S156_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 PTC, differentiated to cortical brain organoid

value: iPSC

value: Termination codon

value: day 9


title: H3K27MKD2_H3K27me3_rep2

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: H3K27M KD


title: H3K27MKD2_H3K27me3_rep1


title: Naive_H2A_rep2

value: mESC cell line


title: CBO-MOK20003W-D02-Day9, KO

description:
Library name: OTX1_Day9_KO_D02_2_GT23-15111_GGTACCTT-GACGTCTT_S155_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 KO, differentiated to cortical brain organoid


title: HuR KO 3h, DMSO, adipocytes

value: Control 3h


title: Naive_H2AZ_rep2


title: H3WT_H3K27me3_rep2

value: PPC

value: Normal fetal pontine neural progenitor cells

value: WT


title: Naive_H4K14ac_rep2

value: Naive


title: CBO-MOK20003-WT-Day8, WT

description:
Library name: OTX1_Day8_WT2-_GT23-15110_GCACGGAC-TGCGAGAC_S157_L003_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: Not applicable

value: day 8

value: Cortical brain (dorsal forebrain patterning)


title: H3K27MKD1_H3K27me3_rep2


title: H3K27MKD1_H3K27me3_rep1


title: H3WT_H3K27me3_rep1


title: HuR KO 12h, DMSO, adipocytes

value: adipocytes

value: KO

value: Control 12h


title: Naive_K4m1_rep1


title: Naive_K119ubH2A_rep1


title: WT_H3K27me3_rep2


title: CBO-MOK20003P-A10-Day8, KO

description:
Library name: OTX1_Day8_PTC_A10-_GT23-15103_CAGTAGGC-ATTCGTCA_S137_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 PTC, differentiated to cortical brain organoid

value: iPSC


title: Control 3h, Torin, adipocytes

value: Control

value: treatment with Torin 3h


title: Naive_IgG_rep1 [CT962_N1_IgG]


title: CBO-MOK20003P-A09-Day8, KO

description:
Library name: OTX1_Day8_PTC_A09-_GT23-15102_TTGGACTC-CTGCTTCC_S143_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 PTC, differentiated to cortical brain organoid

value: Termination codon


title: Control 12h, Torin, adipocytes

value: treatment with Torin 12h


title: CBO-MOK20003C-B08-Day8, KO

description:
Library name: OTX1_Day8_CE_B08-_GT23-15108_ATGTAAGT-CATAGAGT_S138_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 CE, differentiated to cortical brain organoid

value: Critical exon


title: WT_H3K27me3_rep1

value: Diffuse intrinsic pontine glioma (DIPG) cells


title: Naive_H4K14ac_rep1

value: mESC cell line


title: Control 3h, DMSO, adipocytes

value: Control 3h


title: Naive_H3K14ac_rep1


title: WT_H3K9me2_rep2

value: WT


title: CBO-MOK20003C-B06-Day8, KO

description:
Library name: OTX1_Day8_CE_B06-_GT23-15107_CGGCGTGA-ACAGGCGC_S152_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 CE, differentiated to cortical brain organoid


title: Control 6h, Torin, adipocytes

value: treatment with Torin 6h


title: Control 6h, DMSO, adipocytes

value: Control 6h


title: Naive_H3K9m2_rep1

value: Naive


title: Control 12h, DMSO, adipocytes


title: CREB5KD_H3K9me2_rep2

value: CREB5 KD


title: CBO-MOK20003W-D04-Day8, KO

description:
Library name: OTX1_Day8_KO_D04_2-_GT23-15099_CTCTCGTC-AGGTTATA_S141_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 KO, differentiated to cortical brain organoid

value: Full coding region

value: day 8

value: Cortical brain (dorsal forebrain patterning)


title: WT_H3K9me2_rep1


title: CBO-MOK20003P-A11-Day8, KO

description:
Library name: OTX1_Day8_PTC_A11-_GT23-15104_TGACGAAT-GCCTACTG_S139_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 PTC, differentiated to cortical brain organoid

value: iPSC


title: CBO-MOK20003W-G02-Day8, KO

description:
Library name: OTX1_Day8_KO_G02_2-_GT23-15101_CCAAGTCT-TCATCCTT_S166_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 KO, differentiated to cortical brain organoid


title: Naive_H3.3_rep1


title: Naive_H2AZ_rep1


title: Naive_H2A_rep1


title: CREB5KD_BRG1_rep2


title: Control 4h, Insulin, adipocytes

value: adipocytes

value: Control

value: stimulation with insulin 4h


title: CREB5KD_BRG1_rep1


title: Control 1h, Insulin, adipocytes

value: stimulation with insulin 1h


title: CBO-MOK20003W-D02-Day8, KO

description:
Library name: OTX1_Day8_KO_D02_2_GT23-15098_TCTCTACT-GAACCGCG_S136_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 KO, differentiated to cortical brain organoid


title: Form_K4m1_rep2

value: Formative


title: WT_BRG1_rep2

value: Diffuse intrinsic pontine glioma (DIPG) cells


title: Form_K119ubH2A_rep2

value: mESC cell line


title: Control 4h, DMEM, adipocytes

value: Fasting control 4h


title: CBO-MOK20003P-B10-Day7, KO

description:
Library name: OTX1_Day7_PTC_B10-_GT23-15092_GCTTGTCA-GTATGTTC_S142_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 PTC, differentiated to cortical brain organoid

value: Termination codon

value: day 7


title: CBO-MOK20003C-A08-Day8, KO

description:
Library name: OTX1_Day8_CE_A08-_GT23-15106_TAATACAG-GTGAATAT_S140_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 CE, differentiated to cortical brain organoid

value: Critical exon


title: WT_BRG1_rep1

value: WT


title: Control 2h, DMEM, adipocytes

value: Fasting control 2h


title: CBO-MOK20003P-A11-Day7, KO

description:
Library name: OTX1_Day7_PTC_A11-_GT23-15091_ATCCACTG-ACGCACCT_S163_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 PTC, differentiated to cortical brain organoid


title: Control 1h, DMEM, adipocytes

value: Fasting control 1h


title: H3K27M_rep2


title: Control 2h, Insulin, adipocytes

value: stimulation with insulin 2h


title: CBO-MOK20003P-A10-Day7, KO

description:
Library name: OTX1_Day7_PTC_A10-_GT23-15090_AAGTCCAA-TACTCATA_S161_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 PTC, differentiated to cortical brain organoid

value: Cortical brain (dorsal forebrain patterning)


title: Form_H4K14ac_rep2


title: HuR KO 4h, Insulin, adipocytes

value: KO


title: H3K27M_rep1


title: Form_H3K14ac_rep2


title: CREB5_rep2


title: CBO-MOK20003C-B08-Day7, KO

description:
Library name: OTX1_Day7_CE_B08-_GT23-15095_TGGATCGA-TATCGCAC_S149_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 CE, differentiated to cortical brain organoid

value: iPSC


title: HuR KO 2h, Insulin, adipocytes

value: adipocytes


title: CBO-MOK20003C-F07-Day7, KO

description:
Library name: OTX1_Day7_CE_F07-_GT23-15096_AGTTCAGG-TCTGTTGG_S150_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 CE, differentiated to cortical brain organoid


title: CBO-MOK20003-WT-Day7, WT

description:
Library name: OTX1_Day7_WT2-_GT23-15097_GACCTGAA-CTCACCAA_S160_L003_R1_001
KOLF2.2J differentiated to cortical brain organoid

value: Not applicable


title: HuR KO 1h, Insulin, adipocytes

value: stimulation with insulin 1h


title: CREB5_rep1


title: Form_H3.3_rep2

value: Formative


title: Form_H2AZ_rep2


title: HuR KO 4h, DMEM, adipocytes


title: CBO-MOK20003C-B06-Day7, KO

description:
Library name: OTX1_Day7_CE_B06-_GT23-15094_CAAGCTAG-CGCTATGT_S154_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 CE, differentiated to cortical brain organoid


title: CBO-MOK20003W-G02-Day7, KO

description:
Library name: OTX1_Day7_KO_G02_2-_GT23-15088_GGACTTGG-CGTCTGCG_S168_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 KO, differentiated to cortical brain organoid

value: Full coding region


title: HuR KO 2h, DMEM, adipocytes


title: Form_K4m1_rep1

value: mESC cell line


title: CREB5KD_ATACseq_rep2

value: Diffuse intrinsic pontine glioma (DIPG) cells

value: CREB5 KD


title: Form_H2A_rep2


title: CREB5KD_H3K9me2_rep1


title: CBO-MOK20003W-E06-Day7, KO

description:
Library name: OTX1_Day7_KO_E06_2-_GT23-15087_TTATAACC-TCGATATC_S164_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 KO, differentiated to cortical brain organoid

value: day 7


title: Form_H3K9m2_rep2


title: HuR KO 1h, DMEM, adipocytes


title: CREB5KD_ATACseq_rep1


title: WT_ATACseq_rep2


title: CBO-MOK20003W-D02-Day7, KO

description:
Library name: OTX1_Day7_KO_D02_2_GT23-15085_CCGCGGTT-CTAGCGCT_S146_L003_R1_001
KOLF2.2J derived knockout cell line,OTX1 KO, differentiated to cortical brain organoid


title: CBO-MOK20008-WT, WT

description:
Library name: WT-DAY7_GT23-02012_GCGCAAGC-CGGCGTGA_S204_L004_R1_001
KOLF2.2J differentiated to cortical brain organoid


title: APPPS1_12m__8_2_41, time 12m

city: Luxembourg

first: Michael T.

last: Heneka

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

country: Luxembourg

institute: University of Luxembourg

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

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.

value: CD11b+ cells

tag: age


title: WT_ATACseq_rep1

value: WT


title: stuffer 2h, adipocytes

value: Fasting control 2h


title: stuffer 4h, adipocytes

value: Fasting control 4h


title: Form_K119ubH2A_rep1


title: Form_H4K14ac_rep1


title: CBO-MOK20008P-A11, KO

description:
Library name: PAX6-A11-PTC-DAY7_GT23-02005_AGCCTCAT-TCTCTACT_S199_L004_R1_001
KOLF2.2J derived knockout cell line,PAX6 PTC, differentiated to cortical brain organoid

value: Termination codon


title: Form_H3K14ac_rep1


title: stuffer 1h, adipocytes

value: Fasting control 1h


title: Insulin 4h, adipocytes

value: stimulation with insulin 4h


title: WT_6m__8_2_16, time 6m


title: CBO-MOK20008P-D09, KO

description:
Library name: PAX6-D9-PTC-DAY7_GT23-02004_CGTTAGAA-GACCTGAA_S208_L004_R1_001
KOLF2.2J derived knockout cell line,PAX6 PTC, differentiated to cortical brain organoid

value: iPSC

value: Cortical brain (dorsal forebrain patterning)


title: APPPS1_NLRP3_6m__8_2_29, time 6m


title: Form_H3.3_rep1


title: CBO-MOK20008P-A09, KO

description:
Library name: PAX6-A9-PTC-DAY7_GT23-02003_TACCGAGG-AGTTCAGG_S205_L004_R1_001
KOLF2.2J derived knockout cell line,PAX6 PTC, differentiated to cortical brain organoid


title: Form_H2AZ_rep1


title: CBO-MOK20008C-C05, KO

description:
Library name: PAX6-C5-CE-DAY7_GT23-02011_ATATGGAT-TAATACAG_S207_L004_R1_001
KOLF2.2J derived knockout cell line,PAX6 CE, differentiated to cortical brain organoid

value: Critical exon


title: Insulin 2h, adipocytes

value: adipocytes

value: stimulation with insulin 2h


title: CBO-MOK20008C-C08, KO

description:
Library name: PAX6-C8-CE-DAY7_GT23-02010_CGGACAAC-AATCCGGA_S202_L004_R1_001
KOLF2.2J derived knockout cell line,PAX6 CE, differentiated to cortical brain organoid


title: APPPS1_6m__8_1_22, time 6m


title: NLRP3_12m__8_1_45, time 12m


title: Insulin 1h, adipocytes

value: stimulation with insulin 1h


title: CBO-MOK20008C-C07, KO

description:
Library name: PAX6-C7-CE-DAY7_GT23-02009_TAAGTGGT-GGCTTAAG_S203_L004_R1_001
KOLF2.2J derived knockout cell line,PAX6 CE, differentiated to cortical brain organoid


title: NLRP3_4m__8_1_15, time 4m


title: con 6h, adipocytes

value: Control 6h


title: Form_H3K9m2_rep1

value: Formative

value: mESC cell line


title: APPPS1_NLRP3_12m__8_2_43, time 12m


title: con 3h, adipocytes

value: Control 3h


title: Naive_RNApolS2-5p_rep2

value: Naive


title: CBO-MOK20008W-C03, KO

description:
Library name: PAX6-C3-KO-DAY7_GT23-02008_CTACGACA-TTGGACTC_S200_L004_R1_001
KOLF2.2J derived knockout cell line,PAX6 KO, differentiated to cortical brain organoid

value: Full coding region

value: day 7


title: NLRP3_12m_Mxo4_7_2_50, time 12m

value: CD11b+ cells


title: NLRP3_6m__7_2_33, time 6m


title: con 12h, adipocytes

value: WT

value: Control 12h


title: Naive_Rad21_rep1


title: Naive_Rad21_rep2


title: Naive_RNApolS2-5p_rep1


title: CBO-MOK20008W-B01, KO

description:
Library name: PAX6-B1-KO-DAY7_GT23-02006_GATTCTGC-CTCTCGTC_S206_L004_R1_001
KOLF2.2J derived knockout cell line,PAX6 KO, differentiated to cortical brain organoid