title: NipblKO_Kat6bKO_rep2

description: Library name: NipblKO_Kat6bKO_rep2

data_processing:
ChIP-seq sequencing data was trimmed and aligned to mm10 by bowtie2. Unmapped, multimapped and PCR duplicates were removed.
Relevant comparisons were made by using "test" function within the MaGeCK tools
The RNA-Seq alignment and quantification pipeline is available at https://github.com/ren-lab/rnaseq-pipeline. Briefly, reads were aligned to mm10 (GRCm38) and GENCODE GTF version M25 with rnaSTAR77. PCR duplicates were removed using Picard. Raw reads for each gene were quantified using featureCounts. RPKM values were calculated for each gene Particularly, we created two extra chromosomes for the two tagged Sox2 alleles. Reads uniquely mapped to egfp and mCherry sequences were counted using samtools. Expression level of Sox2 gene from CAST and 129 allele was calculated by RPKM values of the egfp and mCherry gene, respectively.
Assembly: mm10
Supplementary files format and content: Signal tracks were generated by bamCoverage with parameters "--normalizeUsingRPKM -bs 50 --smoothLength 150" (deepTools)
Supplementary files format and content: Gene comparison summary files in "txt" format
Supplementary files format and content: tab-delimited text files include raw counts matrix for each sample

extract_protocol:
Crosslinked cells were processed by Covaris truChIP Chromatin Shearing kit and chromatin were sonicated to 300-500bp by Covaris M220.
After cell harvesting genomic DNA was isolated as described before (Sanjana et al., 2014 and Shalem et al., 2014).
Total RNA from cells was extracted using the TRIzol Plus RNA purification kit (Thermo Fisher Scientific, Catlog: 12183555).
ChIP DNA and Input DNA were constucted into illumina Tru-seq libraries using VAHTS Universal DNA Prep Kit for Illumina V4 (ND610-01)
CRISPR libraries were prepared on sorted populations according to previously described protocol mainly consisting of two-step PCRs (Sanjana et al., 2014 and Shalem et al., 2014)
RNA-Seq libraries were prepared from 4 µg total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit Set A (RS-122-2101; Illumina) or Set B (RS-122-2102; Illumina). RNA-seq libraries were sequenced on illumina Next-seq 2000  (100-bp paired ends).

value: 4CBS insertion, NipblKO + Kat6bKO


title: 17SD06149_002

status: Public on Mar 31 2025

type: protein

city: LYON

first: Julie

last: CARAMEL

address: 28 Rue Laennec

country: France

institute: Cancer Research Center of Lyon

hyb_protocol: not provided

scan_protocol: not provided

data_processing: The nCounter digital barcode counts for each antibody and ROI sample were first normalized using internal spike-in controls, then using the mean expression of house-keeping proteins

molecule: protein

organism: Homo sapiens

source_name: melanoma

label_protocol: not provided

extract_protocol: NanoString GeoMx Digital Spatial Profiler (Human Immuno-Oncology Protein Assay) was used on FFPE tissues. Tissue sections were incubated with a cocktail of 32 unique oligonucleotide-conjugated antibodies and counterstained with a nuclear stain .

tag: tissue

value: melanoma

tag: tissue preparaation

value: FFPE


title: PA1380-1

type: SRA

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

library_source: genomic

data_processing:
Raw reads were trimmed by Trim Galore with default parameters.
ChIP-seq reads were mapped to the P. aeruginosa genomes (NC_002516) using Bowtie2 (Version 2.3.4.1). Only the uniquely mapped reads were kept for the subsequent analyses.
Binding peaks (q < 0.05) were identified using MACS2 software (version 2.1.1.20160309).
Assembly: P. aeruginosa genomes (NC_002516)
Supplementary files format and content: narrowPeak

molecule: genomic DNA

organism: Pseudomonas aeruginosa PAO1

source_name: bacterial cell

extract_protocol:
P. aeruginosa  was cultured in LB medium until mid-log phase (OD600 = 0.6), then treated with 1% formaldehyde for 10 min at 37℃. After quenching and lysis, cells were subjected to sonication to produce 100–300 bp DNA fragments.
ChIP-seq libraries were constructed using NEXTflex ChIP-Seq kit (Bio Scientific), and agarose gel was used to cut DNA fragments between 150 and 250 bp.

tag: strain

tag: cell type

value: bacterial cell

tag: chip antibody

value: Anti-vsv

tag: genotype

value: WT


title: NipblKO_rep2

city: San Diego

first: Melodi

last: Tastemel

address: 9500, Gilman drive

department: CMME

country: USA

institute: UCSD

description: Library name: NipblKO_rep2

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

source_name: F123 ESC

growth_protocol: Cells were cultured on feeder-free, serum free 2i condition (Serum free mouse ES medium supplemented with 1uM PD03259010, 3uM CHIR99021, 2mM glutamine, 0.15uM Monothioglycerol, 1000U/ml LIF). The growth medium was changed every day. Cells were dissociated by Accutase (AT104) and passaged to onto 0.2% gelatin-coated plates every 2-3 days.

tag: cell line

value: F123 ESC

value: F1 hybrid (castaneus x S129/SvJae)

value: 4CBS insertion, NipblKO

tag: treatment


title: 17SD06149_003


title: NipblKO_rep1

description: Library name: NipblKO_rep1


title: NipblKO_Kat6bKO_rep1

description: Library name: NipblKO_Kat6bKO_rep1


title: PA1312-2


title: 17SD06149_004


title: PA1312-1


title: 4CBS_control_rep2

description: Library name: 4CBS_control_rep2

value: 4CBS insertion


title: NipblKO_D_Dot1lKO_rep2

description: Library name: Nipbl_Dot1lKO_rep2

value: 4CBS insertion, NipblKO + Dot1lKO


title: NipblKO_D_Dot1lKO_rep1

description: Library name: Nipbl_Dot1lKO_rep1


title: 17SD06149_005


title: 4CBS_control_rep1

description: Library name: 4CBS_control_rep1


title: 17SD06149_006


title: 17SD06149_009


title: 17SD06149_008


title: PA1285-1


title: NipblKO_D_rep1

description: Library name: NipblKO_D_rep1


title: Ctcf_2ildtag6h_rep1

description: Library name: Ctcf_2ildtag6h_rep1

value: 4CBS insertion, CTCF-FKBP36V

value: 6h 2uM dtag13


title: PA1182-2


title: Ctcf_diffdtag_rep1

description: Library name: Ctcf_diffdtag_rep1

value: 24h 2uM dtag13 + diff media


title: NipblKO_D_rep2

description: Library name: NipblKO_D_rep2


title: Ctcf_diffdtag_rep2

description: Library name: Ctcf_diffdtag_rep2


title: PA1182-1


title: PA1285-2


title: Ctcf_2ildtag24h_rep2

description: Library name: Ctcf_2ildtag24h_rep2

value: 24h 2uM dtag13


title: 17SD06149_011


title: Ctcf_2ildtag6h_rep2

description: Library name: Ctcf_2ildtag6h_rep2


title: Ctcf_diff_rep1

description: Library name: Ctcf_diff_rep1

value: 24h diff media


title: PA0217-2


title: 17SD06149_012


title: 17SD06149_007


title: PA0217-1


title: Ctcf_2il_rep1

description: Library name: Ctcf_2il_rep1


title: 17SD06149_010


title: Rad21_2ildtag6h_rep1

description: Library name: Rad21_2ildtag6h_rep1

value: 4CBS insertion, Rad21-FKBP36V


title: Rad21_2ildtag6h_rep2

description: Library name: Rad21_2ildtag6h_rep2


title: PA5116-1


title: Rad21_diffdtag_rep2

description: Library name: Rad21_diffdtag_rep2


title: Ctcf_diff_rep2

description: Library name: Ctcf_diff_rep2


title: Ctcf_2ildtag24h_rep1

description: Library name: Ctcf_2ildtag24h_rep1


title: PA5116-2


title: Ctcf_2il_rep2

description: Library name: Ctcf_2il_rep2


title: 17SD06291_013


title: Rad21_diffdtag_rep1

description: Library name: Rad21_diffdtag_rep1


title: 17SD06291_001


title: Rad21_diff_rep1

description: Library name: Rad21_diff_rep1


title: Rad21_2ildtag24h_rep2

description: Library name: Rad21_2ildtag24h_rep2


title: Rad21_diff_rep2

description: Library name: Rad21_diff_rep2


title: PA4147-2


title: PA4147-1


title: Rad21_2ildtag24h_rep1

description: Library name: Rad21_2ildtag24h_rep1


title: 17SD06291_002


title: 17SD06291_003


title: PA3965-2


title: Rad21_2il_rep2

description: Library name: Rad21_2il_rep2


title: Rad21_2il_rep1

description: Library name: Rad21_2il_rep1


title: 17SD06291_004


title: PA3965-1


title: Ctrl_screen_gfp_low_rep1

description: Library name: Ctrl_screen_gfp_low_rep1

value: 4CBS insertion outside Sox2 locus


title: Ctrl_screen_gfp_high_rep1

description: Library name: Ctrl_screen_gfp_high_rep1


title: 4CBS_screen_gfp_high_rep2

description: Library name: 4CBS_screen_gfp_high_rep2


title: 17SD06291_006

value: melanoma


title: 17SD06291_007

value: FFPE


title: PA3948-1

value: bacterial cell


title: 17SD06291_005


title: 4CBS_screen_gfp_low_rep2

description: Library name: 4CBS_screen_gfp_low_rep2


title: PA3932-2

value: Anti-vsv


title: 4CBS_screen_gfp_low_rep1

description: Library name: 4CBS_screen_gfp_low_rep1


title: 4CBS_screen_gfp_high_rep1

description: Library name: 4CBS_screen_gfp_high_rep1


title: PA3948-2

value: WT


title: rad21_input_rep2

description: Library name: rad21_input_rep2

value: F123 ESC

tag: batch


title: rad21_input_rep1

description: Library name: rad21_input_rep1

value: F1 hybrid (castaneus x S129/SvJae)


title: 17SD06291_008


title: ctcf_input_rep2

description: Library name: ctcf_input_rep2


title: PA3932-1


title: flag_kat6b_nt20_rep2

description: Library name: flag_kat6b_nt20_rep2

value: 4CBS insertion, Flag-tagged Kat6b

value: anti-Flag (sigma F3165)


title: PA3714-2


title: ctcf_input_rep1

description: Library name: ctcf_input_rep1


title: 17SD06291_0010


title: 17SD06291_0011


title: PA3604-2


title: ctcf_dtag9hrArec_k27ac_rep2

description: Library name: ctcf_dtag9hrArec_k27ac_rep2

value: 12h 1uM A485,2uM dtag13+ 9hr only 2uM dtag13

value: anti-H3K27ac (active motif 39685)


title: ctcf_dtag6hrArec_k27ac_rep2

description: Library name: ctcf_dtag6hrArec_k27ac_rep2

value: 4CBS insertion, CTCF-FKBP36V

value: 12h 1uM A485,2uM dtag13+ 6hr only 2uM dtag13


title: PA3604-1


title: ctcf_dtag3hrArec_k27ac_rep2

description: Library name: ctcf_dtag3hrArec_k27ac_rep2

value: 12h 1uM A485,2uM dtag13+ 3hr only 2uM dtag13


title: 17SD06291_012


title: ctcf_12hdtagA_k27ac_rep2

description: Library name: ctcf_12hdtagA_k27ac_rep2

value: 12h 1uM A485,2uM dtag13


title: PA3174-2


title: 16SD08442_001


title: ctcf_12hdtag_k27ac_rep2

description: Library name: ctcf_12hdtag_k27ac_rep2

value: 12h 2uM dtag13


title: ctcf_3hrArec_k27ac_rep2

description: Library name: ctcf_3hrArec_k27ac_rep2

value: 12h 1uM A485 + 3hr washout


title: PA3174-1


title: 17SD06291_009

value: melanoma


title: 16SD08442_014

value: FFPE


title: PA3714-1

value: bacterial cell


title: ctcf_6hrArec_k27ac_rep2

description: Library name: ctcf_6hrArec_k27ac_rep2

value: 12h 1uM A485 + 6hr washout


title: PA3122-2

value: Anti-vsv

value: WT


title: 16SD08442_013


title: PA3122-1


title: flag_kat6b_nt20_rep1

description: Library name: flag_kat6b_nt20_rep1

value: F123 ESC

value: F1 hybrid (castaneus x S129/SvJae)


title: input_nt20_rep2

description: Library name: input_nt20_rep2

value: 4CBS insertion, Flag-tagged Kat6b


title: 16SD08442_012


title: ctcf_dtag9hrArec_k27ac_rep1

description: Library name: ctcf_dtag9hrArec_k27ac_rep1

value: 12h 1uM A485,2uM dtag13+ 9hr only 2uM dtag13


title: ctcf_dtag6hrArec_k27ac_rep1

description: Library name: ctcf_dtag6hrArec_k27ac_rep1

value: anti-H3K27ac (active motif 39685)


title: input_nt20_rep1

description: Library name: input_nt20_rep1


title: PA2848-2


title: 16SD08442_011


title: ctcf_dtag3hrArec_k27ac_rep1

description: Library name: ctcf_dtag3hrArec_k27ac_rep1

value: 4CBS insertion, CTCF-FKBP36V


title: ctcf_12hdtagA_k27ac_rep1

description: Library name: ctcf_12hdtagA_k27ac_rep1


title: PA2848-1


title: ctcf_12hdtag_k27ac_rep1

description: Library name: ctcf_12hdtag_k27ac_rep1


title: PA2718-1


title: ctcf_12hA_k27ac_rep2

description: Library name: ctcf_12hA_k27ac_rep2


title: 16SD08442_007


title: PA2601-2


title: ctcf_2i_control_k27ac_rep1

description: Library name: ctcf_2i_control_k27ac_rep1


title: ctcf_diffdtag_k27ac_rep2

description: Library name: ctcf_diffdtag_k27ac_rep2

value: 24h 2uM dtag13 + diff media


title: ctcf_diff_k27ac_rep2

description: Library name: ctcf_diff_k27ac_rep2

value: 24h diff media


title: PA2547-2


title: rad21_diffftag_k27ac_rep2

description: Library name: rad21_diffftag_k27ac_rep2

value: 4CBS insertion, Rad21-FKBP36V


title: 16SD08442_006


title: 16SD08442_005


title: 16SD08442_010


title: ctcf_2ildtag_k27ac_rep2

description: Library name: ctcf_2ildtag_k27ac_rep2

value: 24h 2uM dtag13


title: ctcf_9hrArec_k27ac_rep1

description: Library name: ctcf_9hrArec_k27ac_rep1

value: 12h 1uM A485 + 9hr washout


title: PA2547-1


title: 16SD08442_009

value: melanoma


title: PA2718-2


title: ctcf_6hrArec_k27ac_rep1

description: Library name: ctcf_6hrArec_k27ac_rep1


title: ctcf_3hrArec_k27ac_rep1

description: Library name: ctcf_3hrArec_k27ac_rep1

value: 12h 1uM A485 + 3hr washout


title: 16SD08442_004

value: FFPE


title: ctcf_12hA_k27ac_rep1

description: Library name: ctcf_12hA_k27ac_rep1


title: 16SD08442_008


title: 16SD08442_003


title: PA2449-1

value: bacterial cell


title: PA2601-1

value: Anti-vsv


title: ctcf_2il_k27ac_rep2

description: Library name: ctcf_2il_k27ac_rep2


title: rad21_2il_k27ac_rep1

description: Library name: rad21_2il_k27ac_rep1


title: rad21_diff_k27ac_rep2

description: Library name: rad21_diff_k27ac_rep2


title: 16SD08442_015


title: ctcf_diffdtag_k27ac_rep1

description: Library name: ctcf_diffdtag_k27ac_rep1


title: rad21_2ildtag_k27ac_rep2

description: Library name: rad21_2ildtag_k27ac_rep2


title: rad21_2il_k27ac_rep2

description: Library name: rad21_2il_k27ac_rep2


title: 15SD06506_001


title: PA2447-1

value: WT


title: ctcf_2ildtag_k27ac_rep1

description: Library name: ctcf_2ildtag_k27ac_rep1

value: F123 ESC


title: PA2417-2


title: 15SD06506_002


title: PA2449-2


title: Kat6bKo_Rad21_rep2

description: Library name: Kat6bKo_Rad21_rep2

value: F1 hybrid (castaneus x S129/SvJae)

value: 4CBS insertion, Kat6b KO

value: anti-Rad21 (ab992)


title: 15SD06506_003


title: rad21_diff_k27ac_rep1

description: Library name: rad21_diff_k27ac_rep1

value: anti-H3K27ac (active motif 39685)


title: 16SD08442_002


title: 4CBS_Rad21_rep2

description: Library name: 4CBS_Rad21_rep2

value: 4CBS insertion


title: rad21_diffftag_k27ac_rep1

description: Library name: rad21_diffftag_k27ac_rep1

value: 24h 2uM dtag13 + diff media


title: Kat6bKo_Rad21_rep1

description: Library name: Kat6bKo_Rad21_rep1


title: PA2417-1


title: rad21_2ildtag_k27ac_rep1

description: Library name: rad21_2ildtag_k27ac_rep1


title: 4CBS_Rad21_rep1

description: Library name: 4CBS_Rad21_rep1


title: PA1853-2


title: WT, 6mo SM, 3

city: Pittsburgh

first: Justin

last: Sui

state: PA

address: 200 Lothrop Street

institute: University of Pittsburgh School of Medicine

description: Library name: WT6moSM3

library_source: transcriptomic single cell

data_processing:
Raw data were demultiplexed using Cell Ranger 5.0.1 and the mkfastq function and then aligned to 10X Genomics’ mouse reference genome mm10-2020-A using cellranger count.
Assembly: mm10-2020-A
Supplementary files format and content: processed files contained outputs from CellRanger including barcodes, features, and matrix

molecule: total RNA

source_name: whole lung

extract_protocol:
left lung lobe from each mouse was further processed to isolate single cell suspensions. Lung tissue was first minced into small pieces and placed in 0.5mL Dispase solution (50U/mL, Sigma) in a conical tube. The tissue was incubated at room temperature on a gentle rocker for 45 minutes. The tissue was then placed in a petri dish with 7mL complete media with 10ml DNase-I solution (1mg/mL, Sigma), teased apart, and placed on a rocker for 12 minutes to liberate adherent cells. Liberated cells were then passed through a 70mm strainer into a conical tube with subsequent washing of the strainer with 5mL of media. This process was repeated with a 40mm strainer. Cells were spun down at 400g for 10minutes at 4 degrees. Cells were resuspended in 6mL of red blood cell lysis buffer, incubated for 5 minutes, and spun down.  Cell pellets were resuspended in 0.5mL PBS with 0.4% bovine serum albumin (BSA, Albuminx from ThermoFisher), filtered a final time through a 40mm FloMi filter tip (Bel-Art), and kept on ice. Cells were counted and 5,000 cells were processed. Individual cells were barcoded with library preparation using 3primeV2 reagents by 10X Genomics Chromium System per the manufacturer’s protocol.
Next generation RNA sequencing was performed on the libraries using an Illumina NextSeq-500 by the UPMC Genome Center (Pittsburgh, PA).

value: whole lung

tag: age

value: 10-12wks age

tag: Sex

value: female

value: Smoke 4 cigarettes/day 6 months tx


title: 15SD06506_004

value: melanoma


title: PA2447-2


title: ctcf_diff_k27ac_rep1

description: Library name: ctcf_diff_k27ac_rep1

value: 4CBS insertion, CTCF-FKBP36V

value: 24h diff media


title: PA1853-1

value: bacterial cell


title: WT, 6mo SM, 1

description: Library name: WT6moSM1


title: WT, 6mo Air, 3

description: Library name: WT6moAir3

value: room air 6 months tx


title: WT, 6mo Air, 2

description: Library name: WT6moAir2

value: WT


title: PA1653-2

value: Anti-vsv


title: ctcf_2il_k27ac_rep1

description: Library name: ctcf_2il_k27ac_rep1

value: F123 ESC

value: F1 hybrid (castaneus x S129/SvJae)


title: 15SD06506_006

value: FFPE


title: WT, 6mo Air, 1

description: Library name: WT6moAir1


title: Ant1KO, 6mo Smoke, 3

description: Library name: Ant1KO6moSM3

value: Ant1 null


title: 15SD06506_007


title: PA1653-1


title: Ant1KO, 6mo Smoke, 1

description: Library name: Ant1KO6moSM1


title: 15SD06506_008


title: Ant1KO, 6mo Smoke, 2

description: Library name: Ant1KO6moSM2


title: PA1403-2


title: Ant1KO, 6mo Air, 2

description: Library name: Ant1KO6moAir2


title: Ant1KO, 6mo Air, 3

description: Library name: Ant1KO6moAir3


title: WT, 6mo SM, 2

description: Library name: WT6moSM2


title: WT, 2mo SM, 2

description: Library name: WT2moSM2

source_name: whole lung, 10-12wks age, WT, female, Smoke 4 cigarettes/day 2 months tx

value: cigarette smoke 2 months


title: PA0873-1


title: PA1403-1


title: PA0873-2


title: Stionary phase, colony 3

city: Milwaukee

first: Madhusudan

last: Dey

state: WI

address: 3209 N Maryland Ave

department: Biological Sciences

institute: UW-Milwaukee

description: Library name: Dey-7

data_processing:
The raw sequencing data were pre-processed using the FASTP program to ensure quality control, trim adapters, and prune reads. The resulting FASTQ files were aligned with the Xenorhabdus szentirmaii genome (NIBV01000001.1 and NIBV01000002.1) using the STAR (Spliced Transcripts Alignment to a Reference) aligner tool with default parameters and the "alignIntronMax" parameter set to 1. Across all replicates, the uniquely mapped read fraction exceeded 70%, with absolute mapped reads ranging from 1.57 to 3.61 million. We used the gene-wise counts from the STAR to perform differential gene expression analysis via the DESeq2 program (v1.38.3). In this process, genes with a cumulative count of less than 10 across replicates were excluded. The remaining genes were analyzed using DESeq2 default parameters. A gene was deemed differentially expressed if its adjusted p-value was below 0.05 and it exhibited an absolute log2-fold change exceeding 1. To conduct principal component analysis (PCA), we utilized variance-stabilized gene expression values obtained via the “vst” function and derived the principal components using the “plotPCA” function of DESeq2 program.
Assembly: NIBV01000001.1 and NIBV01000002.1
Supplementary files format and content: RNA_seq_raw_counts and TPM

organism: Xenorhabdus szentirmaii

source_name: colony

growth_protocol: Bacterium Xenorhabdus szentirmaii was grwon in LB medium containing 50 ug/ml ampicillin

extract_protocol:
Total RNA was prepared by standard protocol using PureLink RNA isolation kit (Invitrogen, USA)
Sequencing libraries were prepared from 1mg of total RNA from each sample using Illumina Stranded Total RNA Prep with Ribo-Zero (20040525) and IDT for Illumina DNA/RNA UD INdexes (Illumina, 20026121).

treatment_protocol: Nothing

value: strain DSM16338

value: colony


title: WT, 2mo SM, 3

description: Library name: WT2moSM3

value: whole lung, 10-12wks age, WT, female, Smoke 4 cigarettes/day 2 months tx


title: 15SD06506_005


title: PA0831-2


title: WT, 2mo Air, 3

description: Library name: WT2moAir3

source_name: whole lung, 10-12wks age, WT, female, room air 2 months tx

value: room air 2 months


title: WT, 2mo SM, 1

description: Library name: WT2moSM1


title: Stionary phase, colony 2

description: Library name: Dey-6


title: PA0831-1


title: WT, 2mo Air, 2

description: Library name: WT2moAir2

value: whole lung, 10-12wks age, WT, female, room air 2 months tx


title: WT, 2mo Air, 1

description: Library name: WT2moAir1


title: Ant1KO, 2mo Smoke, 3

description: Library name: Ant1KO2moSM3

source_name: whole lung, 10-12wks age, Ant1 null, female, Smoke 4 cigarettes/day 2 months tx


title: Stionary phase, colony 1

description: Library name: Dey-5


title: Ant1KO, 2mo Smoke, 1

description: Library name: Ant1KO2moSM1

value: whole lung, 10-12wks age, Ant1 null, female, Smoke 4 cigarettes/day 2 months tx


title: PA0533-2


title: Stionary phase, colony 4

description: Library name: Dey-8


title: Ant1KO, 2mo Air, 3

description: Library name: Ant1KO2moAir3

source_name: whole lung, 10-12wks age, Ant1 null, female, room air 2 months tx


title: Ant1KO, 2mo Smoke, 2

description: Library name: Ant1KO2moSM2


title: Log phase, colony 4

description: Library name: Dey-4


title: Ant1KO, 6mo Air, 1

description: Library name: Ant1KO6moAir1

value: whole lung

value: 10-12wks age

value: female


title: PA0533-1

value: bacterial cell


title: Log phase, colony 3

description: Library name: Dey-3

value: WT


title: PA0527-2

value: Anti-vsv


title: Ant1KO, 2mo Air, 1

description: Library name: Ant1KO2moAir1

value: whole lung, 10-12wks age, Ant1 null, female, room air 2 months tx


title: 462iflox

city: Durham

first: HAMED

last: BOSTAN

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

data_processing:
Trim sequences using trim_galore to obtain high quality clean reads
Trimmed reads alignment versus the reference genome using STAR aligner v.020201
Reads count cuantification using featurcounts v.2.16.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file including counts per each sample

source_name: Ileum

extract_protocol:
RNA was extracted from the ileum and colon with QIAzol. Purification of total RNA was performed with the QIAGEN RNeasy RNA isolation kit (Redwood City, CA) according to the manufacturer’s protocol.
RNA-seq libraries were generated with 1 microgram of RNA as input using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) with poly(A)-enrichment according to the TruSeq protocol.

treatment_protocol: Nine-month old Flox control and SIRT1 PKO female mice were challenged with a chronic colitis model by feeding mice with two cycles of 7-day 2.5% DSS drinking water separated by a 14-day regular water break. Body weights and rectal bleeding were monitored daily during the DSS treatment and one week immediately after DSS treatment. According to the animal protocol, mice with more than 20% loss of their initial body mass were sacrificed during the experiments.

value: Ileum

value: Flox


title: Ant1KO, 2mo Air, 2

description: Library name: Ant1KO2moAir2

value: Ant1 null


title: Log phase, colony 2

description: Library name: Dey-2


title: 440iflox

value: two cycles of 7-day 2.5% DSS drinking water separated by a 14-day regular water break


title: Log phase, colony 1

description: Library name: Dey-1

value: strain DSM16338


title: PA0527-1


title: 473ipko

value: SIRT1 PKO


title: v3.9.7

city: Bethesda

first: Daniel

middle: S

last: Reich

state: Maryland

address: 10 Center Drive Bldg 10 Rm 5C103

department: NINDS

institute: NIH

data_processing:
Single nucleus transcriptomic data analysis pipeline
Alignment. The raw snRNA-seq reads were aligned to a marmoset genome assembly, ASM275486v1 (GCA_002754865.1) with a reference package built as described in (34). CellRanger (version 3.1.0, 10x Genomics) software was used to align reads for snRNA-seq samples to generate cell barcode-to-gene feature matrix for downstream analysis, and automatic estimation of cell number was applied for most of the snRNA-seq samples unless otherwise specified (TableS3).
Preprocessing and quality control. Preprocessing and quality control parameters were applied as described (42). Briefly, a Seurat v3 object was created for individual samples, and DoubletFinder (142) was applied to estimate and remove putative doublets to mitigate technical confounding artifacts. In addition, cells with gene numbers 200–5000 and less than 5% mitochondrial genes were kept, and genes observed in more than 5 cells were kept. In parallel, SoupX (143) was applied to correct ambient RNA background, through which ambient RNA from empty droplets that contained <10 unique molecular identifiers (UMI) were analyzed, and the “soup” contamination fraction was calculated and removed for each cluster. Next, the cell barcodes that passed the DoubletFinder and additional QC were used as index to subset the SoupX-corrected matrix to generate a new matrix subset as downstream analysis input. For individual samples, post-QC Seurat object was created, and the index labels: IL01_uniqueID, IL02_species, IL03_source, IL04_sex, IL05_ageDays, IL06_tissue.1 (coarse category), IL06_tissue.2 (developmental category), IL06_tissue.3 (fine category), IL07_location, IL08_condition (diseased condition), IL09_illumina, IL10_chemistry, IL11_batch, IL12_LMinDays (minimum lesion age in days), IL13_LMaxDays (maximum lesion age in days), IL14_dataset, IL15_annotation were added to the metadata as cell attributes.
Clustering and visualization. As described in (34), hierarchical level 1 (L1) and level 2 (L2) analyses were employed for snRNA-seq dataset to facilitate cluster tracking and result interpretation. Briefly, a merged Seurat object was created from 43 snRNA-seq samples, log-normalized and scaled, and the top 3000 variable genes calculated and used in Principal Component Analysis (PCA). Harmony (144) was applied to integrate different samples over IL01_uniqueID attribute, and the top 5 Harmony-corrected embeddings (H5) were used for Seurat to learn UMAP and annotate L1 cell classes. Canonical cell-type markers (PTPRC for immune cells, PDGFRA for OPC, MAG for oligodendrocytes, GFAP and SLC1A2 for astrocytes, LEPR and CEMIP for vasculature and meningeal cells, and CNTN5 and NRG1 for neurons) annotated 6 of the classes unambiguously. Low-quality cells with high percentage of reads mapped to the mitochondrial genome, low RNA counts and features, and/or expressed genes that mapped to multiple cell class canonical markers, were removed. Nuclei that passed L1 QC were divided into 5 partitions (IMM, OPC, OLI, VAS/AST, NEU) for L2 analysis. Additional rounds of QC were applied to IMM and VAS/AST partitions prior to L2 analysis to facilitate artifact identification among similar cell classes. The IMM partition was further split into FLT1high microglia (MIC) and FLT1low peripheral immune cells (P.IMM) cell classes (34), and VAS/AST mixed partition was separated into ALDH1L1high astrocytes (AST) and ALDH1L1low vascular/meningeal/ventricular cells (VAS). As a result, a total of 7 partitions (AST, OPC, OLI, MIC, P.IMM, VAS, NEU) were parsed for L2 analysis. As detailed in (34), rounds of supervised QC, differentially expressed gene (DEG) search, and unsupervised clustering were performed to yield a total of 133 clusters in this study. The following compound naming conversion was created to label clusters: general cell class category in numeric order, followed by major tissue type or diseased condition contributor. If a cluster found in the current report was similar to the transcription profile of a cluster previously reported (34), the same numerical name was followed.
Preparation of objects for cross-cluster and analysis. To facilitate downstream analysis and comparison, several annotated object subsets were created after the clustering and UMAP embedding were finalized for each cell class. An object (EAE200) containing up to 200 nuclei per cluster for all 133 clusters was prepared by random sampling (median genes per cell: ~1550) to facilitate global and local unique gene selection and comparison. An object (EAEwm) containing nuclei sampled from “WM” (fWM, tWM, pWM, pCC, and OpT) was prepared to analyze the relative prevalence of each cluster across WM lesional states to create the centered and z-scored heatmap (Fig3B). The same EAEwm object was used to analyze the dominant clusters during lesional states transition using the scProportionTest (v0.0.0.9000) package. To infer and compare cellular interactions at the WM between control and marmoset EAE with CellChat (145), a nuclei number-balanced object (EAEwm200) between naïve control and EAE samples was prepared from the same “WM” sampling sites stated above to mitigate outlier biases. More specifically, clusters within each condition with fewer than 50 nuclei were disregarded from further analysis, clusters with many nuclei were down-sampled to 200, and an equal number (50–200) of nuclei were sampled from the matching cluster found in control and EAE samples.
See manuscript
Assembly: ASM275486v1
Supplementary files format and content: CellRanger (version 3.1.0, 10x Genomics)
Supplementary files format and content: Rdata for merged data

molecule: nuclear RNA

organism: Callithrix jacchus

source_name: pCTX

extract_protocol:
Tissue dissection for cryosection and nuclei isolation: Before the day of tissue harvest, a custom-made brain holder was generated for each marmoset brain by 3D printing (Ultimaker 2+) to guide tissue sampling (141). Tissue dissection was carried out as described (34). Briefly, marmosets were deeply anesthetized with 5% isoflurane until no signs of breathing, then were transcardially perfused with ice-cold artificial cerebrospinal fluid (aCSF) for 5 min. After skull and meninges removal, each brain was quickly positioned into the designated brain holder submerged in ice-cold aCSF solution within 10 min post-perfusion. The brain was sectioned into 12–13 slabs at 3 mm with a homemade blade-separator set submerged in aCSF solution. Each brain slab was transferred into a tissue cassette (70078-15, Electron Microscopy Sciences) with the anterior side of the brain slab facing the biopsy foam pad (62325-06, Electron Microscopy Sciences). The cassettes were then submerged into a jar full of RNAlater (RNAlater™ Stabilization Solution, AM7021, Invitrogen) and stored at 4°C overnight. The following day, brain slabs were transferred to 25 x 20 x 5 mm3 molds (Tissue-Tek® Cryomold®, 4557, Sakura Finetek) on ice to facilitate targeted sampling. Slabs were matched to terminal MRI and informed by marmoset 3D MRI atlases (139,140) for region annotation. For nuclei dissociation, a cylinder of tissue 2 mm in diameter and 3 mm in height for each area was collected with a tissue punch (EMS-core sampling tool, 69039-20, EMS), and ejected into PCR tubes filled with 100 µL of RNAlater and kept at −80°C for long-term storage. For cryosection, a 6.5 x 6.5 x 3 mm3 block of tissue per region of interest (ROI) was prepared by a customized 3D-printed brain cutter and stored in cryomold filled with RNAlater at −80°C or proceeded immediately to OCT (Tissue-Tek® O.C.T. Compound, 4583, Sakura) embedding. The quality of RNAlater-preserved tissue was assessed by measuring RNA Integrity Number (RIN) on the Agilent 2100 Bioanalyzer (G2939BA, Agilent). Bulk RNA was isolated with TRIzol™ Reagent (15596026, Invitrogen) and measured with Agilent RNA 6000 Pico Kit (5067-1513, Agilent); samples with RIN >8.5 were used in the study.
10x Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1

value: pCTX

value: tissue

tag: il01 uniqueid

tag: il02 species

value: cjacchus

tag: il03 source

tag: il04 sex

value: F

tag: il05 agedays

tag: il06 tissue

tag: il06 tissue.coarse

value: GM

tag: il06 tissue.dev

value: Telencephalon

tag: il06 tissue.fine

tag: il07 location

tag: il08 condition

tag: il08 condition.status

value: EAE

tag: il08 condition.range

tag: il08 condition.maxday

tag: il08 condition.status.maxdays

tag: il08 condition.tissue.status

tag: il08 condition.tissue.maxdays

tag: il09 illumina

tag: il10 chemistry

tag: il11 batch

tag: il12 lmindays

tag: il13 lmaxdays

tag: il14 dataset


title: PA0403-2

tag: strain

tag: cell type

value: bacterial cell

tag: chip antibody

tag: genotype


title: 491cflox

source_name: Colon

tag: tissue

value: Colon

tag: treatment


title: 462cflox


title: 454cflox


title: v3.9.6

source_name: fWM

value: fWM

tag: cell line

tag: il01 uniqueid

tag: il02 species

tag: il03 source

tag: il04 sex

tag: il05 agedays

tag: il06 tissue

tag: il06 tissue.coarse

value: WM

tag: il06 tissue.dev

tag: il06 tissue.fine

tag: il07 location

tag: il08 condition

tag: il08 condition.status

tag: il08 condition.range


title: PA0367-2

tag: strain

tag: cell type

tag: chip antibody

value: Anti-vsv

tag: genotype

value: WT


title: PA0403-1


title: 490cpko

tag: tissue

tag: treatment


title: 439pko


title: v3.9.5

source_name: LGN

value: LGN

tag: cell line

tag: il01 uniqueid

tag: il02 species

tag: il03 source

value: other

value: Diencephalon

tag: il08 condition.maxday

tag: il08 condition.status.maxdays

tag: il08 condition.tissue.status

tag: il08 condition.tissue.maxdays

tag: il09 illumina

tag: il10 chemistry

tag: il11 batch

tag: il12 lmindays

tag: il13 lmaxdays

tag: il14 dataset


title: ATAC_AECII_IAV_2

city: Braunschweig

first: Andreas

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

country: Germany

institute: Helmholtz Center for Infection Research

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality ≥ 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Analysis was conducted using the following soft-ware: bcl2fastq2 (v2.20) for processing of Illumina base-call data and demultiplexing, Samtools (v0.1.19) for processing of BAM files, BEDtools (v2.25.0) for processing of BED files, wigToBig-Wig (v4) for generation of bigWIG files and Subread (v1.5.2) for counting of reads in BAM files.
Assembly: mm10
Supplementary files format and content: bw: bigWig files contain fragment densities for 32-nt bins along the genome

source_name: lung

growth_protocol: Female C57BL/6JOlaHsd mice of age 10 - 14 weeks maintained under specific-pathogen-free conditions

extract_protocol:
FACS-sorted AECII (pooled from 5 - 6 mice/experimental group) were frozen in culture medium containing FBS and 5 % (v/v) DMSO. Cryo-preserved cells were sent to Active Motif Inc. for ATAC-sequencing. Cells were thawed in a 37 °C water bath, pelleted, washed with cold PBS, and tagmented as previously described (doi:10.1038/nmeth.2688), with some modifications based on Corces et al. (doi:10.1038/nmeth.4396). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina).
Tagmented DNA was purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AM-Pure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quan-tification Kit for Illumina platforms (KAPA Biosystems) and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).

treatment_protocol: If indicated, mice were intranasally infected with 7.9 TCID50 IAV (H1N1, PR/8/34, mouse-adapted) in 25µL of PBS following ketamine/xylazine anesthesia. 14 days post IAV infection AECII cell from lungs were FACS-sorted. If indicated, control mice were treated with matching volumes of PBS via the same application method.

value: lung

tag: cell type

value: AECII

tag: genotype

tag: Sex

value: female

value: Influenza A Virus, day 14


title: PA0367-1

tag: strain

tag: chip antibody


title: 438cpko

tag: tissue

value: SIRT1 PKO

tag: treatment

value: two cycles of 7-day 2.5% DSS drinking water separated by a 14-day regular water break


title: v3.9.4

tag: cell line

value: tissue

tag: il01 uniqueid

tag: il02 species

value: cjacchus

tag: il03 source

tag: il04 sex

value: F

tag: il05 agedays

tag: il06 tissue

tag: il06 tissue.coarse

tag: il06 tissue.dev

tag: il06 tissue.fine

tag: il07 location

tag: il08 condition

tag: il08 condition.status

tag: il08 condition.range

tag: il08 condition.maxday


title: ATAC_AECII_PBS_2

tag: tissue

tag: cell type

tag: genotype

tag: Sex

value: PBS control


title: v3.9.2

value: fWM

tag: cell line

tag: il01 uniqueid

tag: il02 species

value: Telencephalon

value: EAE

tag: il08 condition.status.maxdays

tag: il08 condition.tissue.status

tag: il08 condition.tissue.maxdays

tag: il09 illumina

tag: il10 chemistry

tag: il11 batch

tag: il12 lmindays

tag: il13 lmaxdays

tag: il14 dataset


title: ATAC_AECII_PBS_1

tag: treatment


title: PA0233-2

tag: strain

value: bacterial cell

tag: chip antibody

value: Anti-vsv

value: WT


title: ATAC_AECII_IAV_1

tag: tissue

tag: cell type

tag: genotype


title: PA0233-1


title: Glomeruli MCTO rep3 [LAB-177-14]

city: Tsukuba

first: Akihiro

last: Kuno

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

data_processing:
Sequencing reads were mapped to the Ensembl mouse genome (release GRCm38.102) using subread (version 2.0.1) (PMID:23558742) and the read counts aligning to known genes were generated by featureCounts (PMID: 24227677).
The read counts were normalized with the iDEGES/edgeR method implemented in TCC (version 1.34.0) (PMID:12770646), and pairwise comparisons of gene expression between livers from WT control and Lmln KO were conducted with the edgeR (version 3.36.0) (PMID:19910308). The false discovery rate (FDR) adjustments (DOI:http://www.jstor.org/stable/2346101) were applied to correct for multiple testing, and differentially expressed genes (DEGs) were identified with an FDR cutoff of 0.05.
Assembly: GRCm38.102
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Glomeruli

extract_protocol:
RNA-seq was applied for transcriptome analysis. RNA was extracted from glomeruli from 3 control (Mafb MCTO/ MCTO) and 3 wild-type mice. Briefly, total RNA was isolated using TRIZOL reagent (ThermoFisher Scientific). RNA quality was controlled using an RNA 6000 Pico kit (Agilent, Santa Clara, CA, USA). A total amount of 250 ng total RNA was used for RNA-seq library preparation using the NEBNext rRNA Depletion Kit and NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA); 2×36 base paired-end sequencing was performed with NextSeq500 (Illumina, San Diego, CA) by Tsukuba i-Laboratory LLP (Tsukuba, Ibaraki, Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Glomeruli

tag: age

value: 10 week

value: MCTO


title: v3.8.7

tag: cell line

tag: il01 uniqueid

tag: il02 species

tag: il03 source

tag: il04 sex

tag: il05 agedays

tag: il06 tissue

tag: il06 tissue.coarse

value: WM

tag: il06 tissue.dev

tag: il06 tissue.fine

tag: il07 location

tag: il08 condition

tag: il08 condition.status

tag: il08 condition.range

tag: il08 condition.maxday


title: PA0207-2

tag: strain

tag: cell type

tag: chip antibody

tag: genotype


title: v3.8.6

tag: tissue

tag: cell line

tag: il01 uniqueid

tag: il02 species

tag: il08 condition.status.maxdays

tag: il08 condition.tissue.status

tag: il08 condition.tissue.maxdays

tag: il09 illumina

tag: il10 chemistry

tag: il11 batch

tag: il12 lmindays

tag: il13 lmaxdays

tag: il14 dataset


title: Glomeruli MCTO rep2 [LAB-177-13]

tag: strain

tag: age


title: ctcf_2i_control_k27ac_rep2

description: Library name: ctcf_2i_control_k27ac_rep2

value: F123 ESC

value: F1 hybrid (castaneus x S129/SvJae)

value: 4CBS insertion, CTCF-FKBP36V

tag: treatment

tag: batch

value: anti-H3K27ac (active motif 39685)


title: Glomeruli MCTO rep1 [LAB-177-12]

tag: tissue

tag: genotype


title: Glomeruli WT rep2 [LAB-177-10]

value: wild type


title: Glomeruli WT rep3 [LAB-177-11]


title: PA0207-1

tag: cell type

tag: chip antibody


title: v3.8.5

source_name: tWM

value: tWM

tag: cell line

value: tissue

tag: il01 uniqueid

tag: il02 species

value: cjacchus

tag: il03 source

tag: il04 sex

value: F

tag: il05 agedays

tag: il06 tissue

tag: il06 tissue.coarse

tag: il06 tissue.dev

tag: il06 tissue.fine

tag: il07 location

tag: il08 condition

tag: il08 condition.status

tag: il08 condition.range

tag: il08 condition.maxday

tag: il08 condition.status.maxdays


title: PA0167-2

tag: strain

tag: cell type

tag: chip antibody

tag: genotype


title: Glomeruli WT rep1 [LAB-177-09]

tag: tissue

tag: age


title: v3.8.4

tag: cell line

tag: il01 uniqueid

tag: il02 species

tag: il03 source

tag: il04 sex

tag: il05 agedays

value: Telencephalon

value: EAE

tag: il08 condition.tissue.status

tag: il08 condition.tissue.maxdays

tag: il09 illumina

tag: il10 chemistry

tag: il11 batch

tag: il12 lmindays

tag: il13 lmaxdays

tag: il14 dataset


title: Tbx4 lineage - -37

city: Los Angeles

first: ting

last: Xie

state: CA

address: 127 San Vicente Blvd

department: Pulmonary

institute: Cedars-Sinai Medical Center

description:
Tbx4-2-A3-1-C01_S3
GEO C1 Tbx4 lineage neg

data_processing:
Raw reads were aligned to the transcriptome using Bowtie (version 1.1.1) (Langmead et al., 2009) / RSEM (version 1.2.20) (Li and Dewey, 2011) with default parameters, using a custom reference containing both 92 ERCC sequences and the mouse transcriptome GRCm38 reference downloaded from http://www.gencodegenes.org, containing all protein coding and long non-coding RNA genes based on Release M3 annotation.
Expression counts for each gene in all samples were normalized by the total number of reads mapped to the transcriptome in order to account for sequencing depth (transcripts per million; TPM) with the correction of size factors derived from ERCC spike-in. We imposed additional quality control criteria to remove low quality cells: 1) total number of raw sequencing reads <1M; 2) among all sequencing reads, percentage of total mapped read is <50%; 3) among mapped reads, percentage of exonic reads <50% and 4) percentage of ERCC spike-in reads>40% to eliminating majority of the dying or dead cell.
The resultant 54 Tbx4 lineage+ cells and 39 Tbx4 lineage- cells passed quality control and were included for the subsequent analysis. The expression counts were transformed into log scale.
To identify the subpopulation among the samples in an unsupervised way, principle component analysis (PCA) was performed to select most varied genes across all single cells based on their eigenvectors (Pollen et al., 2014; Trapnell et al., 2014) with FactoMineR v1.31 in R/Bioconductor v3.2.
The top 250 most varied genes from PCA was clustered with Euclidean distance matrix with ggplots2 v1.0.1 in R/Bioconductor.
Genome_build: mm9
Supplementary_files_format_and_content: Read Count Table

extract_protocol:
Tbx4 lineage+ and Tbx4 lineage- cells within epcam+ CD31- CD45- 7AAD- cells were sorted from Tbx4cre;RosaTm mouse lung, and run on the C1 chip (Fluidigm). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq on Fluidigm C1 Single-Cell Auto Prep System following the manufacturer’s protocol. Medium sized C1 mRNA- Seq chips were used to capture each cell-cycle fraction. The C1 Auto-prep system captured the dissociated single cells across 96 wells and performed cell lysis, cDNA synthesis with reverse transcription and PCR reaction using the SMARTer Ultra Low Input RNA Kit. Cells captured across the 96 wells are manually inspected as a quality control measure to remove empty well, doublets or debris containing wells. 92 ERCC spike-ins of known concentration were added during the lysis step to assess and quantify technical variation. cDNA from several representative cells were checked by High Sensitivity DNA chips using Fragment Analyzer (Advanced Analytical).
Libraries for each of the 96 captured cells were prepared using the Illumina Nextera XT DNA sample preparation kit with 96 dual barcoded indices. Single cell libraries were multiplexed and sequenced across 4 lanes of a NextSeq 500 platform (Illumina) using 75 single-end sequencing. On average, about 6-7 million reads would be generated from each single cell library.

tag: strain

value: lung

value: adult mouse

tag: cell type

value: Tbx4 lineage-


title: Tbx4 lineage - -39

description:
Tbx4-2-A11-1-C53_S21
GEO C1 Tbx4 lineage neg

tag: tissue

tag: age


title: Tbx4 lineage - -38

description:
Tbx4-2-A12-1-C54_S26
GEO C1 Tbx4 lineage neg


title: v3.8.3

tag: cell line

tag: il01 uniqueid

tag: il06 tissue

tag: il06 tissue.coarse

tag: il06 tissue.dev

tag: il06 tissue.fine

tag: il07 location

tag: il08 condition

tag: il08 condition.status

tag: il08 condition.range

tag: il08 condition.maxday

tag: il08 condition.status.maxdays


title: PA0167-1

value: bacterial cell

tag: chip antibody

value: Anti-vsv

tag: genotype

value: WT


title: Tbx4 lineage - -36

description:
Tbx4-2-A4-1-C49_S23
GEO C1 Tbx4 lineage neg

tag: strain

tag: cell type


title: PA5438-2


title: v3.8.1

tag: tissue

tag: il02 species

tag: il03 source

tag: il04 sex

value: M

tag: il05 agedays

value: WM

tag: il08 condition.tissue.status

tag: il08 condition.tissue.maxdays

tag: il09 illumina

tag: il10 chemistry

tag: il11 batch

tag: il12 lmindays

tag: il13 lmaxdays

tag: il14 dataset


title: PA5438-1

tag: chip antibody


title: Tbx4 lineage - -35

description:
Tbx4-2-A6-1-C51_S4
GEO C1 Tbx4 lineage neg

tag: age


title: ctcf_9hrArec_k27ac_rep2

description: Library name: ctcf_9hrArec_k27ac_rep2

tag: cell line

value: F123 ESC

tag: strain

value: F1 hybrid (castaneus x S129/SvJae)

tag: genotype

value: 4CBS insertion, CTCF-FKBP36V

tag: treatment

value: 12h 1uM A485 + 9hr washout

tag: batch


title: v3.7.8

source_name: pWM

tag: tissue

value: pWM

value: tissue

tag: cell type

tag: il01 uniqueid

tag: il02 species

tag: il03 source

tag: il04 sex

tag: il06 tissue

tag: il06 tissue.coarse

tag: il06 tissue.dev

tag: il06 tissue.fine

tag: il07 location

tag: il08 condition

tag: il08 condition.status

tag: il08 condition.range

tag: il08 condition.maxday

tag: il08 condition.status.maxdays


title: Tbx4 lineage - -33

description:
Tbx4-2-B5-1-C56_S33
GEO C1 Tbx4 lineage neg

tag: strain

tag: age


title: PA5431-2

source_name: bacterial cell

tag: cell type

tag: chip antibody

tag: genotype


title: Tbx4 lineage - -31

description:
Tbx4-2-C12-1-C66_S31
GEO C1 Tbx4 lineage neg

tag: tissue


title: Tbx4 lineage - -34

description:
Tbx4-2-A9-1-C04_S35
GEO C1 Tbx4 lineage neg


title: Tbx4 lineage - -32

description:
Tbx4-2-B7-1-C12_S14
GEO C1 Tbx4 lineage neg


title: PA5431-1


title: v3.7.7

tag: cell line

tag: il01 uniqueid

tag: il02 species

value: cjacchus

tag: il03 source

tag: il04 sex

value: F

tag: il05 agedays

tag: il08 condition.tissue.status

tag: il08 condition.tissue.maxdays

tag: il09 illumina

tag: il10 chemistry

tag: il11 batch

tag: il12 lmindays

tag: il13 lmaxdays

tag: il14 dataset


title: v3.7.6

value: pCTX

tag: cell type

tag: il06 tissue

tag: il06 tissue.coarse

value: GM

tag: il06 tissue.dev

value: Telencephalon

tag: il06 tissue.fine

tag: il07 location

tag: il08 condition

tag: il08 condition.status

value: EAE

tag: il08 condition.range

tag: il08 condition.maxday

tag: il08 condition.status.maxdays


title: Tbx4 lineage - -30

description:
Tbx4-2-C3-1-C13_S8
GEO C1 Tbx4 lineage neg

tag: strain

tag: tissue

value: lung

tag: age

value: adult mouse

value: Tbx4 lineage-


title: PA5382-2

value: bacterial cell

tag: chip antibody

value: Anti-vsv

tag: genotype

value: WT


title: Tbx4 lineage - -28

description:
Tbx4-2-C7-1-C18_S19
GEO C1 Tbx4 lineage neg


title: v3.7.5

tag: cell line

tag: il01 uniqueid

tag: il02 species

tag: il03 source

tag: il04 sex

tag: il05 agedays

tag: il08 condition.tissue.status

tag: il08 condition.tissue.maxdays

tag: il09 illumina

tag: il10 chemistry

tag: il11 batch

tag: il12 lmindays

tag: il13 lmaxdays

tag: il14 dataset


title: Tbx4 lineage - -27

description:
Tbx4-2-C8-1-C17_S5
GEO C1 Tbx4 lineage neg

tag: strain

tag: tissue

tag: age

tag: cell type


title: Tbx4 lineage - -26

description:
Tbx4-2-D1-1-C21_S1
GEO C1 Tbx4 lineage neg


title: PA5382-1

tag: chip antibody

tag: genotype


title: Tbx4 lineage - -25

description:
Tbx4-2-D5-1-C68_S38
GEO C1 Tbx4 lineage neg


title: 472ipko

value: Ileum

value: SIRT1 PKO

tag: treatment

value: two cycles of 7-day 2.5% DSS drinking water separated by a 14-day regular water break


title: Tbx4 lineage - -23

description:
Tbx4-2-E1-1-debris-C25_S2
GEO C1 Tbx4 lineage neg


title: PA5356-2


title: v3.7.4

value: pWM

tag: cell line

tag: il01 uniqueid

tag: il02 species

tag: il03 source

tag: il04 sex

tag: il06 tissue

tag: il06 tissue.coarse

value: WM

tag: il06 tissue.dev

tag: il06 tissue.fine

tag: il07 location

tag: il08 condition

tag: il08 condition.status

tag: il08 condition.range

tag: il08 condition.maxday

tag: il08 condition.status.maxdays


title: PA5356-1

tag: strain

tag: cell type

tag: chip antibody

tag: genotype


title: v3.7.3

tag: tissue

tag: cell line

value: tissue

tag: il01 uniqueid

tag: il02 species

value: cjacchus

tag: il05 agedays

tag: il08 condition.tissue.status

tag: il08 condition.tissue.maxdays

tag: il09 illumina

tag: il10 chemistry

tag: il11 batch

tag: il12 lmindays

tag: il13 lmaxdays

tag: il14 dataset


title: Tbx4 lineage - -24

description:
Tbx4-2-D8-1-C23_S10
GEO C1 Tbx4 lineage neg

tag: strain

tag: age


title: Tbx4 lineage - -22

description:
Tbx4-2-E2-1-C26_S22
GEO C1 Tbx4 lineage neg

tag: cell type


title: Tbx4 lineage - -21

description:
Tbx4-2-E7-1-C28_S24
GEO C1 Tbx4 lineage neg


title: Tbx4 lineage - -29

description:
Tbx4-2-C4-1-C61_S28
GEO C1 Tbx4 lineage neg


title: v3.7.1

value: tWM

tag: il03 source

tag: il04 sex

value: M

tag: il06 tissue

tag: il06 tissue.coarse

tag: il06 tissue.dev

tag: il06 tissue.fine

tag: il07 location

tag: il08 condition

tag: il08 condition.status

tag: il08 condition.range

tag: il08 condition.maxday

tag: il08 condition.status.maxdays


title: PA5283-2

tag: chip antibody

tag: genotype


title: v3.6.8

source_name: pCC

tag: tissue

value: pCC

tag: cell line

tag: il01 uniqueid

tag: il02 species

value: F

tag: il05 agedays

value: Telencephalon

tag: il08 condition.tissue.status

tag: il08 condition.tissue.maxdays

tag: il09 illumina

tag: il10 chemistry

tag: il11 batch

tag: il12 lmindays

tag: il13 lmaxdays

tag: il14 dataset


title: Tbx4 lineage - -20

description:
Tbx4-2-E8-1-C29_S15
GEO C1 Tbx4 lineage neg

tag: strain

value: lung

tag: age

value: adult mouse

tag: cell type


title: Tbx4 lineage - -19

description:
Tbx4-2-E9-1-C30_S40
GEO C1 Tbx4 lineage neg

value: Tbx4 lineage-


title: PA5283-1

value: bacterial cell

tag: chip antibody

value: Anti-vsv

tag: genotype


title: Tbx4 lineage - -16

description:
Tbx4-2-F6-1-C79_S9
GEO C1 Tbx4 lineage neg

tag: tissue


title: Tbx4 lineage - -18

description:
Tbx4-2-F1-1-C31_S7
GEO C1 Tbx4 lineage neg


title: Tbx4 lineage - -17

description:
Tbx4-2-F2-1-C32_S27
GEO C1 Tbx4 lineage neg


title: v3.6.5

source_name: OpT

value: OpT

tag: cell line

tag: il01 uniqueid

tag: il03 source

tag: il04 sex

tag: il06 tissue

tag: il06 tissue.coarse

tag: il06 tissue.dev

value: Diencephalon

tag: il06 tissue.fine

tag: il07 location

tag: il08 condition

tag: il08 condition.status

value: EAE

tag: il08 condition.range

tag: il08 condition.maxday

tag: il08 condition.status.maxdays


title: Tbx4 lineage - -14

description:
Tbx4-2-F8-1-C35_S20
GEO C1 Tbx4 lineage neg

tag: strain

tag: age

tag: cell type


title: PA5218-2

tag: chip antibody

tag: genotype

value: WT


title: PA5218-1


title: PA5179-2


title: Tbx4 lineage - -15

description:
Tbx4-2-F7-1-C34_S29
GEO C1 Tbx4 lineage neg

tag: tissue


title: v3.6.4

tag: cell line

tag: il01 uniqueid

tag: il02 species

tag: il03 source

tag: il04 sex

tag: il05 agedays

value: WM

tag: il08 condition.tissue.status

tag: il08 condition.tissue.maxdays

tag: il09 illumina

tag: il10 chemistry

tag: il11 batch

tag: il12 lmindays

tag: il13 lmaxdays

tag: il14 dataset


title: v3.6.3

value: tissue

tag: cell type

tag: il06 tissue

tag: il06 tissue.coarse

tag: il06 tissue.dev

tag: il06 tissue.fine

tag: il07 location

tag: il08 condition

tag: il08 condition.status

tag: il08 condition.range

tag: il08 condition.maxday

tag: il08 condition.status.maxdays


title: Tbx4 lineage - -12

description:
Tbx4-2-G1-1-C37_S12
GEO C1 Tbx4 lineage neg

tag: strain

tag: tissue

tag: age


title: Tbx4 lineage - -11

description:
Tbx4-2-G10-1-C90_S16
GEO C1 Tbx4 lineage neg


title: Tbx4 lineage - -10

description:
Tbx4-2-G2-1-C38_S32
GEO C1 Tbx4 lineage neg


title: v3.3.7

value: pWM

tag: cell line

tag: il01 uniqueid

tag: il02 species

value: cjacchus

tag: il03 source

tag: il04 sex

tag: il05 agedays

tag: il08 condition.tissue.status

tag: il08 condition.tissue.maxdays

tag: il09 illumina

tag: il10 chemistry

tag: il11 batch

tag: il12 lmindays


title: v3.3.4

tag: cell type

tag: il06 tissue

tag: il06 tissue.coarse

tag: il06 tissue.dev

tag: il06 tissue.fine

tag: il07 location

tag: il08 condition

tag: il08 condition.status

tag: il08 condition.range

tag: il08 condition.maxday

tag: il13 lmaxdays

tag: il14 dataset


title: PA5157-2

tag: strain

tag: chip antibody

tag: genotype


title: Tbx4 lineage - -9

description:
Tbx4-2-G3-1-C39_S13
GEO C1 Tbx4 lineage neg

tag: tissue

tag: age


title: Tbx4 lineage - -8

description:
Tbx4-2-G7-1-C40_S34
GEO C1 Tbx4 lineage neg

tag: cell type


title: Tbx4 lineage - -13

description:
Tbx4-2-F9-1-C36_S6
GEO C1 Tbx4 lineage neg


title: PA5179-1


title: Tbx4 lineage - -7

description:
Tbx4-2-G8-1-C41_S25
GEO C1 Tbx4 lineage neg


title: Tbx4 lineage - -6

description:
Tbx4-2-G9-1-C42_S11
GEO C1 Tbx4 lineage neg


title: v3.3.3

tag: cell line

tag: il01 uniqueid

tag: il02 species

tag: il03 source

tag: il04 sex

tag: il05 agedays

tag: il06 tissue

tag: il08 condition.status.maxdays

tag: il08 condition.tissue.status

tag: il08 condition.tissue.maxdays

tag: il09 illumina

tag: il10 chemistry

tag: il11 batch

tag: il12 lmindays


title: PA5157-1

tag: strain

tag: chip antibody

tag: genotype


title: Tbx4 lineage - -4

description:
Tbx4-2-H2-1-C44_S37
GEO C1 Tbx4 lineage neg

tag: tissue

tag: age

tag: cell type


title: PA5032-2


title: Tbx4 lineage - -3

description:
Tbx4-2-H3-1-C45_S18
GEO C1 Tbx4 lineage neg


title: v3.3.1

value: tWM

tag: cell line

tag: il01 uniqueid

tag: il02 species

tag: il03 source

tag: il06 tissue.coarse

tag: il06 tissue.dev

tag: il06 tissue.fine

tag: il07 location

tag: il08 condition

tag: il08 condition.status

tag: il08 condition.range

tag: il08 condition.maxday

tag: il13 lmaxdays

tag: il14 dataset


title: Tbx4 lineage - -2

description:
Tbx4-2-H7-1-C46_S39
GEO C1 Tbx4 lineage neg

tag: strain

tag: tissue


title: PA5032-1

tag: cell type

tag: chip antibody

tag: genotype


title: Tbx4 lineage - -1

description:
Tbx4-2-H8-1-C47_S30
GEO C1 Tbx4 lineage neg

tag: age


title: Tbx4 lineage +-53

description:
7m-Lung-A2-1-C02_S50
GEO C1 Tbx4 lineage pos

value: Tbx4 lineage+


title: Tbx4 lineage +-54

description:
7m-Lung-A1-1-C03_S1
GEO C1 Tbx4 lineage pos


title: PA4381-2


title: Mouse_WT_E14.5_Pinna

city: Guangzhou

first: Xu

last: Xiaopeng

address: 96 Xingdao South Road, Guangzhou International Bio Island, Haizhu District

country: China

institute: Guangzhou National Laboratory

description: Library name: Mouse_WT_E14.5_Pinna

data_processing:
The scRNA-seq reads were processed using the CeleScope pipeline, details of which are available at https://github.com/singleron-RD/CeleScope. This processing generated a 10x Genomics-like raw feature-barcode matrix suitable for downstream filtering and data integration using Seurat (version 4.3.0). For cell filtering, we assumed that both the log10-transformed gene counts and UMI counts per cell for each sample followed a normal distribution. We calculated the mean ± 1.96 times the standard deviation, defining the 95% confidence interval, to determine the lower and upper thresholds. These thresholds were then converted back to the original scale (as the power of 10 of the log values) to establish criteria for excluding low-quality cells. Furthermore, cells exhibiting a mitochondrial gene expression ratio exceeding 5% were also categorized as low quality.
Data integration was accomplished using the CCA2-based pipeline of Seurat package. The SelectIntegrationFeatures function was utilized to identify variable features across datasets for integration. Subsequently, the FindIntegrationAnchors function was employed to identify anchor pairs between datasets, followed by the IntegrateData function to create an integrated assay, which included the newly integrated expression profiles. Based on the results of integration, we performed PCA dimensionality reduction using RunPCA on the variable features employed for integration. This was followed by UMAP dimensionality reduction using RunUMAP with parameters -dims 1:20, -n.neighbors 50. For unsupervised clustering, we executed the FindNeighbors function using default parameters, and FindClusters with -resolution 0.4.
Assembly: GRCm39
Supplementary files format and content: Tab-separated value files and matrix files

source_name: pinna

extract_protocol:
Micro-dissected forming pinna prominences from Hmx1wt/EGFP embryos were enzymatically dissociated using 0.5% trypsin/1× EDTA for 10 minutes at 37 °C (for E10.5 and E12.5 stages) and papain digestion mix for 7 minutes (for E14.5 stage). The treated tissues were then rinsed in ice-cold 1× DMEM, filtered, and GFP+ cells were enriched using FACS (Sony, MA900). These collected cells were resuspended and diluted in 1× DPBS (Cytiva) to a concentration of 1×106 cells per ml
Gene expression libraries were prepared using GEXSCOPE Single Cell RNA Library Kits v.2 (Singleron, catalog no. SD-4180022). The single-cell suspensions were loaded onto the GEXSCOPE microchip, which facilitates automated single cell capture, cell lysis, cellular mRNA capture, and molecular labeling via the Singleron Matrix instrument. The barcoded cDNA was amplified and utilized for constructing single cell NGS libraries. The quality and quantity of the resulting libraries were assessed using Qubit 4.0 (Thermo Fisher Scientific) and Qseq100 (Bioptic)

value: pinna


title: Tbx4 lineage +-51

description:
7m-Lung-A5-1-C50_S52
GEO C1 Tbx4 lineage pos


title: PA4381-1


title: Tbx4 lineage +-52

description:
7m-Lung-A4-1-C49_S31
GEO C1 Tbx4 lineage pos


title: Mouse_KI_E14.5_Pinna

description: Library name: Mouse_KI_E14.5_Pinna


title: PA4341-2


title: mESC-TT_Figure4_R2

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: Library name: sample 27

library_source: other

data_processing:
Read processing was performed using an adapted nf-core/clipseq pipeline with Nextflow. Read demultiplexing was performed using Ultraplex with parameters “--phredquality 15--min_length0” . Adaptor trimming was performed using Cutadapt with parameters “--minimum-length 20”. Bowtie2 was used for premapping to ribosomal and small RNAs. Genome mapping was performed using STAR, for mouse samples with GRCm38 (mm10) release-89 annotation, and for S288C samples with S. cerevisiae Ensembl R64-1-1 release-90 annotation. UMI-tools was used for deduplication. BedTools was used to identify the 5’-most nucleotide (tag) and for genome-wide comparative analyses.
Assembly: mouse samples with GRCm38 (mm10) release-89 annotation, and for yeast S288C samples with S. cerevisiae Ensembl R64-1-1 release-90 annotation
Supplementary files format and content: bedGraph

molecule: other

growth_protocol: Yeast growth conditions S. cerevisiae BY4741 strain background (derived from S288C) was used for the analysis of the yeast part of the manuscript. Cells were grown in liquid cultures (YPD (1.0% (w/v) yeast extract, 2.0% (w/v) peptone, 2.0% (w/v) glucose, and supplemented with uracil (2.4 mg/l) and adenine (1.2 mg/l))) in incubator/shaker (30°C, 300 rpm) till the exponential phase.   mESCs culturing mESCs (HM1) were grown in 2i/LIF [49% DMEM/F12-/- (Gibco), 49% Neurobasal (Gibco), 1X N2 (Gibco), 1X B27 (Gibco), 0.05 mM 2-Mercaptoethanol (Gibco), 2mM L-Glutamine (Gibco), Recombinant mouse 50,000 units LIF (ESGRO), 1 µM PD03259010 (Stemgent), 3 µM CHIR 99021 (TOCRIS), 1% Penicillin/Streptomycin]]. Cell culture surfaces were coated with 0.15% gelatin in PBS, for a minimum of 10 minutes at 37°C for mESC culture. mESCs were maintained at 37°C, 5% CO2, and confirmed to be negative for mycoplasma. mESCs were passed every 2-3 days depending on colony size, with media change occurring in the intermediate days. To pass cells, one wash with PBS was performed, before incubating the cells with Accutase (Gibco) at 37ºC for exactly 3 minutes.

extract_protocol:
RNA was extracted from yeast as previously detailed (Chia et al. 2021). For RNA extraction from yeast grown in YPD, 24 optical density (OD) units for TSS-seq were collected by centrifugation, and snap-frozen in liquid nitrogen. Per 10 OD units, RNA was extracted with 1 ml Tris-EDTA-SDS (TES) buffer (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.5% SDS) and 1 ml Acid Phenol:Chloroform:Isoamyl alcohol (125:24:1, Ambion), by shaking at 65°C for 45 minutes at 1400 rpm. After centrifugation at 4°C, max speed, 10 minutes, the aqueous phase was transferred to cold ethanol with 0.3 M sodium acetate. Precipitation was carried out overnight at 4°C, before centrifugation at 4°C, max speed, 20 minutes. The pellet was washed once with 80% v/v ethanol, dried, and reconstituted in DEPC-treated sterile water. rDNase (Machery-Nagel) treatment was carried out for 20 minutes at 37°C, before spin column purification (Machery-Nagel).  RNA was extracted from mammalian cells using TRIzol (Thermo Fisher). For TRIzol RNA extraction, 1 ml of TRIzol was added per 10-cm dish. Chloroform (0.2 volume, Thermo Fisher) was added, and the mixture was shaken for 30 seconds before centrifugation was performed. The aqueous phase was mixed with 1.1 volumes of isopropanol (Thermo Fisher), and RNA was precipitated overnight at 4°C. After centrifugation, the pellet was washed with 85% (v/v) ethanol, dried, and reconstituted in DEPC-treated sterile water. rDNase (Qiagen) digestion was carried out at 37°C for 1 hour before purification by spin column (Qiagen) or by phenol:chloroform and ethanol precipitation.  For small RNA size selection, Monarch RNA Cleanup with a 1:3 ratio of sample: ethanol volume was used.                                                                                4SU RNA labelling 4SU labelling was carried out as detailed previously (Gregersen et al. 2020), with few modifications. Cell culture media was removed, and filtered, and 1 mM 4SU (Glentham Life Sciences) was added. The cells were returned to the incubator, and labelled with 4SU for 15 minutes before medium aspiration and TRIizol addition. 1/5 volume of chloroform was added, mixed, and then centrifuged at 12,000g for 15 minutes at 4°C. 1.1 volumes of isopropanol and 1 µl of glycoblue were mixed with the upper aqueous layer, precipitation then occurred overnight at -20°C. The pellet was washed once with 85% ethanol, dried, and resuspended.  RNA integrity was checked for a selection of samples using Bioanalyser (Agilent Technologies). 4SU incorporation was assessed using slot blot. Here, 5 µg of total RNA was mixed with 3 µl biotin buffer (833 mM Tris-HCl, pH 7.4, and 83.3 mM EDTA) and 50 µl of 0.1 mg/ml MTSEA biotin-XX linker (Biotium, dissolved in dimethylformamide; Sigma-Aldrich) to a total volume of 200 µl, and incubated in the dark for 30 minutes. RNA clean-up was performed by adding an equal volume of phenol/chloroform/isoamyl alcohol (25:24:1 (vol/vol/vol)), mixing, and centrifuging at 12,000g for 5 minutes at 4°C. The aqueous phase was mixed with 1.1 volumes of isopropanol, 1/10 volume of 5 M NaCl and 1 µl of glycoblue and precipitated at -20°C for at least 2 hours. The pellet was washed once with 85% ethanol, dried, and resuspended to 10 µl.
The TSS-seq protocol: total RNA was dephosphorylated with quickCIP (NEB, 1.2 U/µg RNA) 37°C, with RNasin Plus before heat inactivation. RNA was extracted using phenol/chloroform/isoamyl alcohol as before. RNA was treated with mRNA decapping enzyme (NEB, 0.7 U/µg RNA) at 37°C with RNasin Plus. RNA was extracted using phenol/chloroform/isoamyl alcohol as before. RNA and the 5’ adaptor (10 µM) were denatured for 2 minutes at 70°C, then cooled on ice for 2 minutes. Ligation was performed, 16°C using and T4 RNA ligase I (30 U), with RNasin Plus. RNAClean XP (1.8X ratio, Beckman Coulter) was used to remove unligated adaptors, according to the manufacturer’s instructions. The concentration of the samples was measured using Qubit RNA BR assay, and samples were multiplexed. polyA+ RNA was enriched using Dynabeads Oligo(dT)25 (Thermo Fisher). Yeast RNA was fragmented with alkaline fragmentation reagent (Ambion). RNeasy MinElute Clean-up columns, with 1.5x volume of Ethanol, were used to purify the samples. The 3’ ends were fixed by CIP treatment (NEB,30 U).  Ligation was carried out by T4 Rnl2tr (NEB,200 U) for 2 hours, 25°C then 16 hours, 16°C. RNAClean XP (1.8X ratio) was used to remove unligated adaptors. RNA, RT oligo (0.5 pmol) and dNTP (10 mM each) were denatured at 65°C, then cooled on. Reverse transcription was carried out by SuperScript III (2 µl), with RNasin Plus with the following conditions: 25°C for 5 minutes, 42°C for 20 minutes, 50°C for 40 minutes, 80°C for 5 minutes. Template RNA was removed by RNase H (10 U) for 37°C, 30 minutes. AMPure XP beads (Agencourt, Beckman Coulter) were used to clean up the cDNA. 3X beads and 1.7x isopropanol added to the reverse transcription reaction, and incubated for 5 minutes. Beads were washed twice with 85% ethanol, dried, and eluted twice in nuclease-free water. cDNA pre-amplification was performed with i5_s and i7_s (300 nM each) primers and Phusion HF PCR Mastermix (Thermo Fisher). 6 PCR cycles were carried out (98°C for 10 seconds, 65°C for 30 seconds, 72°C for 30 seconds, with 3 minutes at 72°C final extension). ProNex beads (Promega) with a 1:2.95 ratio to sample were used to remove sequences less than 55 nt (including primer dimers). Final amplification was carried out with NEBNext i50 and i70 primers (500 nM each) and Phusion HF PCR Mastermix, for 8 cycles. Amplification was checked by using Novex 6% TBE (Tris/Borate/EDTA) gel and staining with SYBR green. ProNex beads (Promega) with a 1:2.3 ratio to sample were used for purification. Library concentration was measured using Qubit High Sensitivity D1000. Libraries were sequenced with Illumina NovaSeq 6000 using 100 nt paired-end reads, with 50 million reads minimum per sample.

tag: cell line

value: mESC


title: CTRL

city: Yangsan

first: Hansong

last: Lee

address: 49 Busandaehak-ro

country: South Korea

institute: Pusan National University

description: Library name: SET2-CONT

data_processing:
The raw sequences were converted into a feature-barcode matrix using the 10X Genomics Cell Ranger v3.1.0 pipeline. The BCL file obtained from the Illumina sequencer was processed into FASTQ file using Cell Ranger’s ‘mkfastq’ module (bcl2fastq v2.20.0). The reads were aligned to the mouse reference Alignment STAR version 2.7.3a.
Assembly: STAR (v2.7.3a) with mouse reference genome
Supplementary files format and content: features.tsv.gz: feature information
Supplementary files format and content: matrix.mtx.gz: sparse count matrix
Supplementary files format and content: barcodes.tsv.gz: cell barcode information

source_name: mouse small intestinal organoid

extract_protocol:
Single cells from three independent organoid lines were pooled for the control- and melatonin-treated group on culture day 3.
Chromium controller constructed libraries for scRNA-seq according to the Chromium Single Cell 3’ RNA library v3 protocol (10X Genomics). The cDNA library underwent amplification and sequencing using the Illumina NovaSeq 6000 platform.

value: mouse small intestinal organoid

tag: treatment

value: control


title: Tbx4 lineage +-49

description:
7m-Lung-A7-1-C06_S18
GEO C1 Tbx4 lineage pos

value: lung

value: adult mouse


title: mESC-TT_Figure4_R1

description: Library name: sample 26


title: MLT

description: Library name: SET2-M500

value: melatonin-treated


title: Tbx4 lineage +-47

description:
7m-Lung-A9-1-C04_S20
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-48

description:
7m-Lung-A8-1-C05_S19
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-50

description:
7m-Lung-A6-1-C51_S4
GEO C1 Tbx4 lineage pos


title: PA4341-1

value: bacterial cell

value: Anti-vsv


title: Tbx4 lineage +-46

description:
7m-Lung-B11-1-C59_S28
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-45

description:
7m-Lung-B2-1-C08_S2
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage - -5

description:
Tbx4-2-H1-1-C43_S17
GEO C1 Tbx4 lineage neg

value: Tbx4 lineage-


title: PA4296-1

value: WT


title: Tbx4 lineage +-44

description:
7m-Lung-B7-1-C12_S25
GEO C1 Tbx4 lineage pos


title: PA4296-2


title: mESC-polyA-Figure4_R2

description: Library name: sample 25


title: mESC-polyA-Figure4_R1

description: Library name: sample 24


title: Tbx4 lineage +-43

description:
7m-Lung-B8-1-C11_S26
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-42

description:
7m-Lung-B9-1-C10_S27
GEO C1 Tbx4 lineage pos


title: PA4157-2


title: mESC-TT_decap_R1

description: Library name: sample 23


title: Tbx4 lineage +-41

description:
7m-Lung-C1-1-C15_S8
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-40

description:
7m-Lung-C2-1-C14_S9
GEO C1 Tbx4 lineage pos


title: PA4157-1


title: Tbx4 lineage +-39

description:
7m-Lung-C3-1-C13_S44
GEO C1 Tbx4 lineage pos


title: mESC-TT_control_R1

description: Library name: sample 22


title: PA4094-2


title: Tbx4 lineage +-37

description:
7m-Lung-C8-1-C17_S33
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-38

description:
7m-Lung-C7-1-C18_S32
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-36

description:
7m-Lung-D1-1-C21_S15
GEO C1 Tbx4 lineage pos


title: PA4094-1


title: mESC_scaRNA_FigureS2_R2

description: Library name: sample 21


title: Tbx4 lineage +-34

description:
7m-Lung-D2-1-C20_S16
GEO C1 Tbx4 lineage pos


title: mESC_scaRNA_R1

description: Library name: sample 19


title: mESC_scaRNA_FigureS2_R1

description: Library name: sample 20


title: PA3973-2


title: PA3973-1


title: Tbx4 lineage +-35

description:
7m-Lung-D12-1-C72_S42
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-31

description:
7m-Lung-D8-1-C23_S40
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-30

description:
7m-Lung-D9-1-C22_S34
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-32

description:
7m-Lung-D7-1-C24_S39
GEO C1 Tbx4 lineage pos


title: PA3927-2


title: Tbx4 lineage +-33

description:
7m-Lung-D3-1-C19_S51
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-28

description:
7m-Lung-E11-1-C77_S35
GEO C1 Tbx4 lineage pos


title: mESC-polyA_control_R1

description: Library name: sample 17


title: mESC-polyA_decap_R1

description: Library name: sample 18


title: Tbx4 lineage +-29

description:
7m-Lung-E1-1-C25_S22
GEO C1 Tbx4 lineage pos


title: PA3927-1


title: Tbx4 lineage +-27

description:
7m-Lung-E2-1-C26_S23
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-26

description:
7m-Lung-E3-1-C27_S3
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-25

description:
7m-Lung-E4-1-C75_S38
GEO C1 Tbx4 lineage pos


title: Mo_C57B6_Ctl_H20Vap_Pool_M_F_DorStri_Nuclei_NCellPlex301_302_305_306

city: Baltimore

first: Seth

middle: A

last: Ament

state: MD

address: 670 W Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

description:
Library name: Replication 2.3, 2.4
10X Genomics

data_processing:
We demultiplexed the male vs. female cells within each pooled sample based on the universally expressed female-specific marker gene Xist. First, we performed zeropreserving imputation of read counts with ALRA87 to reduce dropouts. Then, cells with normalized Xist expression values greater than the median were assigned as female, and cells with expression values below the median were assigned as male. We validated that Y chromosome genes were expressed near-exclusively in cells assigned as male.
: Genome alignment (mm10), cell calling, and read counting were performed with cellranger count (v7.1.0), Doublets were detected and removed via scDblFinder.8
Assembly: mm10
Supplementary files format and content: Seurat rds and rdata objects

source_name: Dorsal Striatum

extract_protocol:
Distinct nuclei isolation protocols were used in the discovery dataset and in each of the two replication datasets. For the discovery dataset, cellular nuclei were isolated from frozen dorsal striatal tissue following a 10x Genomics Demonstrated Protocol (CG000124.RevE) with modifications. One hemisphere, dorsal striatum 1 mm punch, was used for 150ul lysis buffer for nuclei extraction. To remove cellular debris and large clumps, an Iodixanol density gradient was used. An 8.5% iodixanol (OptiPrepTM Density Gradient, Millipore) buffer serves as a cushion to remove membranes at 1000xg/10 min at 4C. Clean nucleus was collected in the pellet. Propidium iodide was used to determine the nuclei concentration using a bench cytometer MoxiGoII (Orflo) and nuclei aggregation and clumping were evaluated under 60X magnification in a fluorescent microscope and brightfield. For both replication datasets, nuclei were isolated from frozen brain tissue following a published protocol with our slight modifications.82,83 Briefly, frozen brain tissue was disaggregated by pipetting up and down in chilled extraction buffer consisting of Poly(1- 22 vinylpyrrolidone-co-vinyl acetate) (Sigma #190845), 0.1% TritonX-100, and 1% bovine serum albumen (BSA) in dissociation buffer (DB; 82 mM Na2SO4, 30mM K2SO4, 10mM Glucose, 2.5mM MgCl2,10mM Hepes pH7.4, and RNase inhibitor [Protector, Roche]). Pellets containing nuclei were resuspended in DB and filtered with 70 um and 40 um strainers. To separate nuclei from debris, the nuclei suspension was mixed in a 25% (final) iodixanol layer over a 27% iodixanol cushion, followed by centrifugation (13000g x 20min, 4° C), then nuclei were washed twice in DB.
Nuclei from one male mouse and one female mouse of the same ethanol treatment group were pooled. Approximately 20,000 nuclei per pooled sample were loaded into a Chromium X microfluidics controller (10x Genomics, Pleasanton, CA). 10x Genomics NextGEM 3’ GEX sequencing libraries were prepared from each sample following manufacturer’s instructions and sequenced at depth of 50M/sample on HiSeq4000 Sequencer. In the second replication dataset, nuclei were labeled with sample-specific oligonucleotide tag using CellPlex reagents, following a validated protocol (CG000391). Finally, nuclei were counted using a MoxiGoII (Orflo) cytometer, and the concentration was adjusted to 365 nuclei/ul in phosphate buffered saline with 2% BSA. 17,000 nuclei were loaded in each well of a Chromium Controller (10x Genomics). Nuclei from four male and four female mice were pooled in each sample. Sequencing libraries were prepared using NextGEM 3’ Gene Expression reagents (10x Genomics), following manufacturer’s instructions and sequenced on HiSeq4000 (Replication Dataset 1) and NovaSeq6000 (Replication Dataset 2) sequencers

value: Dorsal Striatum

value: Air


title: PA3571-2


title: Mo_C57B6_ETOHVap_Pool_M_F_DorStr_Nuclei_NCellPlex_303_304_307_308

description:
Library name: Replication 2.1, 2.2
10X Genomics

value: EtOH


title: Tbx4 lineage +-24

description:
7m-Lung-E7-1-C28_S46
GEO C1 Tbx4 lineage pos


title: PA3571-1


title: Tbx4 lineage +-23

description:
7m-Lung-E8-1-C29_S47
GEO C1 Tbx4 lineage pos


title: Kat6bKO_hic_rep1

description: Library name: Kat6bKO_hic_rep1

data_processing:
ChIP-seq sequencing data was trimmed and aligned to mm10 by bowtie2. Unmapped, multimapped and PCR duplicates were removed.
Relevant comparisons were made by using "test" function within the MaGeCK tools
The RNA-Seq alignment and quantification pipeline is available at https://github.com/ren-lab/rnaseq-pipeline. Briefly, reads were aligned to mm10 (GRCm38) and GENCODE GTF version M25 with rnaSTAR77. PCR duplicates were removed using Picard. Raw reads for each gene were quantified using featureCounts. RPKM values were calculated for each gene Particularly, we created two extra chromosomes for the two tagged Sox2 alleles. Reads uniquely mapped to egfp and mCherry sequences were counted using samtools. Expression level of Sox2 gene from CAST and 129 allele was calculated by RPKM values of the egfp and mCherry gene, respectively.
Hi-C reads were aligned to mm10 using bwa-mem for each read separately and then paired. For chimeric reads, only 5′ end-mapped locations were kept. Duplicated read pairs mapped to the same location were removed to leave only one unique read pair. The output bam files were transformed into juicer file format for visualization in Juicebox. Contact matrices were normalized using the Knight–Ruiz matrix balancing method
Assembly: mm10
Supplementary files format and content: Signal tracks were generated by bamCoverage with parameters "--normalizeUsingRPKM -bs 50 --smoothLength 150" (deepTools)
Supplementary files format and content: Gene comparison summary files in "txt" format
Supplementary files format and content: tab-delimited text files include raw counts matrix for each sample
Supplementary files format and content: juicer hic files that can be visualized in Juicebox

source_name: F123 ESC

extract_protocol:
Crosslinked cells were processed by Covaris truChIP Chromatin Shearing kit and chromatin were sonicated to 300-500bp by Covaris M220.
After cell harvesting genomic DNA was isolated as described before (Sanjana et al., 2014 and Shalem et al., 2014).
Total RNA from cells was extracted using the TRIzol Plus RNA purification kit (Thermo Fisher Scientific, Catlog: 12183555).
Hi-C experiments were performed in biological replicates using MboI, following the protocol described by Rao et al., Cell 2014 (PMID: 25497547)
ChIP DNA and Input DNA were constucted into illumina Tru-seq libraries using VAHTS Universal DNA Prep Kit for Illumina V4 (ND610-01)
CRISPR libraries were prepared on sorted populations according to previously described protocol mainly consisting of two-step PCRs (Sanjana et al., 2014 and Shalem et al., 2014)
RNA-Seq libraries were prepared from 4 µg total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit Set A (RS-122-2101; Illumina) or Set B (RS-122-2102; Illumina). RNA-seq libraries were sequenced on illumina Next-seq 2000  (100-bp paired ends).
Hi-C libraries were prepared following the protocol described by Rao et al., Cell 2014 (PMID: 25497547)

value: F123 ESC

value: F1 hybrid (castaneus x S129/SvJae)

value: 4CBS insertion, Kat6b KO


title: Tbx4 lineage +-21

description:
7m-Lung-F1-1-C31_S29
GEO C1 Tbx4 lineage pos

value: Tbx4 lineage+


title: Tbx4 lineage +-19

description:
7m-Lung-F2-1-C32_S30
GEO C1 Tbx4 lineage pos


title: PA2696-2


title: PA2834-1


title: Tbx4 lineage +-18

description:
7m-Lung-F3-1-C33_S10
GEO C1 Tbx4 lineage pos


title: Male germ cells, CSDS, replicate 2

city: Fujisawa

first: Shu

last: Aizawa

state: Kanagawa

address: 1866 Kameino

department: Department of Zoological Science

institute: Nihon University College of Bioresource Sciences

description: Library name: CSDS_2

data_processing:
Sequence reads were trimmed using Trim Galore (Version 0.5.0, q = 20, Phred scores 30) to remove low quality bases (> 20) and adaptor sequences.
The trimmed reads were aligned to the reference genome (GRCm38) using Bismark (Version 0.20.0) with the "-non_directional" option.
The read counts were calculated and normalized using the methyKit (Version 1.16.0).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include read counts and methylation percentage of each sample

source_name: Male germ cells

extract_protocol:
DNA was extracted from germ cells using DNeasy Blood & Tissue Kit (Qiagen).
The libraries for RRBS were prepared using Zymo-Seq RRBS Library Kit (Zymo Research).

value: Male germ cells


title: Tbx4 lineage +-15

description:
7m-Lung-F8-1-C35_S54
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-17

description:
7m-Lung-F4-1-C81_S45
GEO C1 Tbx4 lineage pos


title: Male germ cells, Control, replicate 3

description: Library name: Cont_3


title: Male germ cells, CSDS, replicate 3

description: Library name: CSDS_3


title: Tbx4 lineage +-20

description:
7m-Lung-F10-1-C84_S14
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-14

description:
7m-Lung-F9-1-C36_S48
GEO C1 Tbx4 lineage pos


title: PA2488-2


title: Tbx4 lineage +-13

description:
7m-Lung-G1-1-C37_S36
GEO C1 Tbx4 lineage pos


title: Male germ cells, Control, replicate 2

description: Library name: Cont_2


title: Tbx4 lineage +-12

description:
7m-Lung-G2-1-C38_S37
GEO C1 Tbx4 lineage pos


title: PA2696-1


title: Tbx4 lineage +-16

description:
7m-Lung-F7-1-C34_S53
GEO C1 Tbx4 lineage pos


title: Male germ cells, CSDS, replicate 1

description: Library name: CSDS_1


title: PA2488-1


title: Male germ cells, Control, replicate 1

description: Library name: Cont_1


title: Tbx4 lineage +-10

description:
7m-Lung-G7-1-C40_S5
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-9

description:
7m-Lung-G8-1-C41_S6
GEO C1 Tbx4 lineage pos


title: PA2281-2


title: Tbx4 lineage +-22

description:
7m-Lung-E9-1-C30_S41
GEO C1 Tbx4 lineage pos


title: Anterior claustro-insular tissue in Nurr1 deficeint brains

city: Berlin

first: Andrew

last: Newman

address: Charitéplatz 1

department: Institute for Cell and Neurobiology

institute: Charité Universitätsmedizin Berlin

description: Library name: P3023_SP090_012_Nurr_Ko_P0_S37

data_processing:
Reads were aligned to mm10 using Cellranger 7.0.1 using --include-introns
Data was read into R and quality filtered to remove cells with > 5% mitochrondrial gene content and more than 400 genes detected per cell.
Doublets were removed using DoubletFinder with an optimal pK determined to be 0.2
Samples were integrated using the standard Seurat workflow and cell types annotated using the mouse cerebral cortex set from Azimuth
Assembly: mm10 (refdata-gex-mm10-2020-A)
Supplementary files format and content: RDS file of integrated seurat object (all cells)

source_name: claustro-insular tissue

extract_protocol:
The claustro-insular portions of mouse cerebral cortices were isolated and dissociated using ‘Neural Tissue Dissociation Kit (P)’ (Miltenyi Biotec) containing 1x protease inhibitors (SIGMA) according to the manufacter's instruction. The cell suspension was then incubated in ‘nuclei EZ lysis buffer’ (SIGMA) containing 1x protease inhibitors for 5 min on ice and quickly passed through single cell strainers (pore size 70 mm, Miltenyi).
Library was constructed according to the manufacter's instructions (single cell 3' v3 protocol, 10x Genomics).

value: claustro-insular tissue

value: In vivo cerebral tissue

value: neurons

tag: batch


title: Tbx4 lineage +-8

description:
7m-Lung-G9-1-C42_S55
GEO C1 Tbx4 lineage pos

value: lung

value: adult mouse


title: PA2834-2

value: bacterial cell


title: PA2281-1

value: Anti-vsv


title: Tbx4 lineage +-7

description:
7m-Lung-H1-1-C43_S43
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-5

description:
7m-Lung-H3-1-C45_S24
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-6

description:
7m-Lung-H10-1-C96_S21
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-4

description:
7m-Lung-H6-1-C91_S11
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-2

description:
7m-Lung-H8-1-C47_S13
GEO C1 Tbx4 lineage pos


title: Tbx4 lineage +-11

description:
7m-Lung-G3-1-C39_S17
GEO C1 Tbx4 lineage pos


title: Control mouse 3

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

description: Library name: B6 57S Ctl

data_processing:
Reads generated were mapped to the mouse genome (mm10) by gSNAP, expression (FPKM) derived by Cufflinks and differential expression analyzed with ANOVA in R. Genes significant at a p < 0.05 were submitted to pathway analysis using R, and genes significant p < 0.05 were submitted to KEGG pathway analysis using Enrichr.
Assembly: MM10
Supplementary files format and content: Microsoft Excel format

source_name: Platelet

growth_protocol: Whole blood was drawn from three TNFdARE mice and three  littermates of 8-12 weeks.

extract_protocol:
RNA was extracted from isolated washed platelets of mice (healthy littermattes and the TNFdARE, n4 each). The extraction was performed with the TRIzol reagent (Invitrogen). Then, RNA was treated with DNase (Qiagen), and purified with columns (Qiagen).
Libraries from extracted RNA were then sequenced as dual pass 150 bp reads on the Illumina NovaSeq 6000 sequencer by the University of Colorado Medical Campus Cancer Center Genomics Shared Resource Core Facility (RRID:SCR_021984).

treatment_protocol: 5.2 month old male mice were euthanized, humeri was extracted.

value: Platelet

value: Male

value: Hematopoietic cell

value: TNFdAre -

value: Baseline


title: Control mouse 2

description: Library name: B6 C57 Ctl


title: Tbx4 lineage +-1

description:
7m-Lung-H9-1-C48_S7
GEO C1 Tbx4 lineage pos


title: ChIP-Seq_H3K27Ac_Brains_NHS_rep2

city: Moscow

first: Nadezhda

middle: E

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
ChIP-seq, FAIRE-Seq and RNA-Seq reads were aligned to the dm6 genome by HISAT2 (using UseGalaxy.eu online tools)
Assembly: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary files format and content: Aligned reads were sorted to have MAPQ>5. BigWig files were generated using  bamCoverage 3.0.2. Scores represent number of reads normalized by the size of the library. Final BigWIgs were generated The final bigwig files (representing the protein binding profiles) were obtained using bigwigcompare tool by computing a ratio between the ChIP signal and the Input (all Inputs were preliminary smoothed over a 1 kb window). For the H3K27Ac ChIP-Seqs the Input was substracted from the signal. FAIRE-Seq data were not normalized by Input and presented as a number of reads. The final bigwig files (representing the protein binding profiles) were obtained using bigwigcompare tool by computing a ratio between the ChIP signal and the Input (all Inputs were preliminary smoothed over a 1 kb window). For the H3K27Ac ChIP-Seqs the Input was substracted from the signal. FAIRE-Seq data were not normalized by Input and presented as a number of reads.

organism: Drosophila melanogaster

source_name: Brains/eye-antennal discs were dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation

growth_protocol: The Drosophila melanogaster of hsp-GAL4 7-1,CyO/IF;10UAS-3xFLAG-E23,w+  stock (=hsp-e23; capable of expressing E23 after treatment with the heat shock) and Oregon-R-modENCODE (corresponds to Bloomington stock 25211) stock were used. All flies were raised at 25°C on standard agar medium.

extract_protocol:
ChIP protocol: crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine. After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 5 ug of antibodies and 8 uL of MabSelect sepharose (GE healthcare) were taken. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 uL per 500 uL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 uL of proteinase K and 5 uL of 0.5M EDTA per 500 uL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation. Total RNA was extracted with the TRI reagent (Ambion). PolyA comprising RNA fraction was isolated with the NEBNext UltraTM II Directional RNA Library Prep Kit. FAIRE-Seq protocol was perfomed exactly as previously described in Simon et al (2012) Nat protocols, 7:256-267.
DNA and RNA-Seq libraries were prepared for sequencing using standard Illumina NEBNext protocols

treatment_protocol:
no treatment
For the RNA-Seq and ChIP-Seq experiments, hsp-e23 larvae (or Oregon-R larvae) of L3 stage 20-22h before puparium formation were subjected to double 1-hour heat shocks at 37°C with a 1-hour rest period between at RT. For dissection, wandering larvae were used approximately 4-6 hours before the puparium formation. Dissections were performed manually in PBS/0.1% NP-40. Tissues targeted for RNA-Seqs were collected directly into TRI-reagent. Dissected salivary glands and brains (brains were taken with eye/antennal discs) aimed for ChIP-Seqs and FAIRE-Seqs were accumulated in tubes containing PBS/0.1% NP-40 and placed on ice. Dissected tissues were stored on ice not more than 1 hour. After the dissection, tissues were warmed to room temperature and fixated by addition of FA up to 1% for 10 min. The fixation was stopped by addition of 1/20V 2.5M Gly to the reaction for 5 min. After the fixation, the Sonication buffer (ChIP lysis buffer) containing 0.1% SDS and PIC (Roche) was added to the tissues and they were stored at -70°C. The sonication step was performed after the thawing.

value: hsp-GAL4 7-1,CyO/IF;10UAS-3xFLAG-E23,w+  stock (described in a current study)

tag: chip antibodies

value: Active motif antibodies against Histone H3K27Ac (39133)

value: no treatment


title: ChIP-Seq_CBP_Nejire_Brains_NHS_rep2

value: Brains/eye-antennal discs were dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation

value: anti-CBP/p300/Neijre  (125–310 aa) antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189. )


title: ChIP-Seq_Rpb3_Brains_NHS_rep2

value: anti-Rpb3 (1–275 aa) antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189. )


title: ChIP-Seq_CBP_Nejire_Salivary_glands_HS_rep3

source_name: Salivary glands were dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation

treatment_protocol:
hsp-e23 larvae of L3 stage 20-22h before puparium formation were subjected to double 1-hour heat shocks at 37°C with a 1-hour rest period between at RT. For dissection, wandering larvae were used approximately 4-6 hours before the puparium formation.
For the RNA-Seq and ChIP-Seq experiments, hsp-e23 larvae (or Oregon-R larvae) of L3 stage 20-22h before puparium formation were subjected to double 1-hour heat shocks at 37°C with a 1-hour rest period between at RT. For dissection, wandering larvae were used approximately 4-6 hours before the puparium formation. Dissections were performed manually in PBS/0.1% NP-40. Tissues targeted for RNA-Seqs were collected directly into TRI-reagent. Dissected salivary glands and brains (brains were taken with eye/antennal discs) aimed for ChIP-Seqs and FAIRE-Seqs were accumulated in tubes containing PBS/0.1% NP-40 and placed on ice. Dissected tissues were stored on ice not more than 1 hour. After the dissection, tissues were warmed to room temperature and fixated by addition of FA up to 1% for 10 min. The fixation was stopped by addition of 1/20V 2.5M Gly to the reaction for 5 min. After the fixation, the Sonication buffer (ChIP lysis buffer) containing 0.1% SDS and PIC (Roche) was added to the tissues and they were stored at -70°C. The sonication step was performed after the thawing.

value: heat shock


title: ChIP-Seq_EcR-full_Brains_NHS_rep2

value: EcR-full antibodies against full-length EcR-A isoform NM_165461 were obtained in our lab and described in this manuscript for the first time.


title: WT-6-2

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

institute: City University of Hong Kong

data_processing:
Raw reads were trimmed by Trim Galore with default parameters.
ChIP-seq reads were mapped to the P. aeruginosa genomes (NC_002516) using Bowtie2 (Version 2.3.4.1). Only the uniquely mapped reads were kept for the subsequent analyses.
Binding peaks (q < 0.05) were identified using MACS2 software (version 2.1.1.20160309).
Assembly: P. aeruginosa genomes (NC_002516)
Supplementary files format and content: narrowPeak

extract_protocol:
P. aeruginosa  was cultured in LB medium until mid-log phase (OD600 = 0.6), then treated with 1% formaldehyde for 10 min at 37℃. After quenching and lysis, cells were subjected to sonication to produce 100–300 bp DNA fragments.
ChIP-seq libraries were constructed using NEXTflex ChIP-Seq kit (Bio Scientific), and agarose gel was used to cut DNA fragments between 150 and 250 bp.

value: WT


title: ChIP-Seq_CBP_Nejire_Brains_NHS_rep1

tag: sample id


title: ChIP-Seq_CBP_Nejire_Salivary_glands_NHS_rep3

value: Salivary glands were dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation


title: Anterior claustro-insular tissue in Cre-negative control brains

description: Library name: P3023_SP090_011_Nurr_WT_P0_S36

value: claustro-insular tissue

value: In vivo cerebral tissue

value: neurons


title: PA0701-2

value: bacterial cell

value: Anti-vsv


title: Control mouse 4

description: Library name: B6 Ctl 18F

value: Platelet

value: Female

value: Hematopoietic cell

value: TNFdAre -


title: TNFdARE mouse 2

description: Library name: dARE 07/13/21

value: TNFdAre +

value: Baseline


title: Tbx4 lineage +-3

description:
7m-Lung-H7-1-C46_S12
GEO C1 Tbx4 lineage pos

value: lung

value: adult mouse

value: Tbx4 lineage+


title: WT-8-2


title: PA0701-1


title: WT-6-1


title: WT-8-1


title: FAIRE-Seq_Brains_NHS_rep2

value: Brains/eye-antennal discs were dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation

value: hsp-GAL4 7-1,CyO/IF;10UAS-3xFLAG-E23,w+  stock (described in a current study)

value: no treatment


title: Control mouse 1

description: Library name: B6 25-BR


title: TNFdARE mouse 1

description: Library name: dARE 25-BL

value: Male


title: ChIP-Seq_Rpb3_Salivary_glands_HS_rep2

value: Salivary glands were dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation

value: anti-Rpb3 (1–275 aa) antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189. )

value: heat shock


title: ChIP-Seq_Rpb3_Salivary_glands_HS_rep1


title: WT-7-2

value: bacterial cell

value: Anti-vsv

value: WT