title: FoxO1, Input

data_processing:
ChIP-seq reads were locally (--local) aligned to the Ensemble GRCm39 genome using Bowtie2 v2.4.5.
BAM files converted to SAM files using samtools.
SAM files were sorted by genomics coordinates using sambamba.
Sorted SAM files were filetered using sambamba to retain only uniqely mapping reads.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 200 bp to represent sequenced fragments, renormalized (to bins per million, bpm) and reformatted in the bigWig file format. Bin size of 5 were used.
Peaks were called uing MACS v3.0.0a7.
Assembly: mm39
Supplementary files format and content: bigWig, narrowPeak

source_name: cardiomyocytes

extract_protocol:
CMs harvested from WT and C/EBP-β mice were crosslinked with 1% formaldehyde for 15 minutes, following glycerine incubation for 5 min at room temperature. Cells were washed with cold PBS twice, lysed, and sonicated to shear DNA.
C/EBP-β and FoxO1 antibodies were used to immunoprecipitate  protein/chromatin complexes. Several washing steps were followed by protein digestion  using proteinase K. Reverse crosslinking was carried out at 65 °C. DNA was subsequently  purified. ChIPSeq library preparation was performed with TruSeq ChIP Library Preparation  Kit.

treatment_protocol: The Thr250Glu (ACG to GAG) mutation was introduced into the C/EBP-β  gene  (NM_00963.4; ENSMUSG00000056501) using CRISPR/Cas9 system (Cyagen Biosciences Inc., Santa Clara, CA).

value: cardiomyocytes

value: pooled

tag: chip antibody


title: NPCs D868N ChIP SET #2

status: Public on Sep 12 2022

type: SRA

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

description:
NPCD868N_Chip_SET_2
dual index library

library_source: genomic

data_processing:
FASTQ were first quality checked to evaluate sequence output with using FastQC (Andrews, S. FastQC A Quality Control tool for High Throughput Sequence Data). Reads were then trimmed using Trimmomatic 5. Reads were then aligned to reference genome hg38 using Bowtie2 6 using the --very-sensitive option. Non canonical and M chromosomes were removed from Bam files using Samtools 7 and Picard tools (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/) was used to remove PCR optical duplicates, before proceeding with further analysis. Normalized BigWig files for genomics track visualization and for subsequent analysis were generated using deepTools (v3.5.1) 8 bamCoverage with the following parameters --normalizeUsing RPKM --binSize 10 --smoothLength 300 –effectiveGenomeSize --ignoreDuplicates  --skipNAs –exactScaling. To obtain a single merged tracks from single experimental replicates for each experimental condition UCSC bigWigMerge was used.   Peak calling was performed using MACS2 9 from preprocessed Bam files for each experimental replicate from each condition. For ChIP-seq narrow peaks (H3K27ac), the following parameters were used -f  BAMPE --nomodel --qvalue 0.01 --keep-dup all --call-summits using Input for each condition as control sample.
Genome_build: hg38
Supplementary files format and content: macs broadpeak

molecule: genomic DNA

organism: Homo sapiens

source_name: NPCs

extract_protocol:
To perform ChIP experiment 200000 cells for each experimental replicate were used. Cells were cross-linked in 1% formaldehyde for 10’ minutes at room temperature.  Cells were lysed in ChIP-lysis Buffer (10mM Tris-HCl 8.0,1% SDS, 5 mM EDTA). Sonication was performed using a Diagenode Bioruptor Pico sonicator (65 cycles, 30” ON-30” OFF, each cycle). Input were collected before precipitation. Samples (two technical replicates for each ChIP) were then incubated overnight at 4° using primary antibodies for H3K27ac, H3K27me3, H3K9me3 and SET in iC buffer from iDeal ChIP‐seq kit for Histones (Diagenode, cod. C01010051).   The next day, incubation with magnetic beads was performed on a rotator wheel for 3 hours at 4°. Beads were subsequently washed using iW1, iW2,iW3 and IW4 buffer (Diagenode). ChIP-DNA was then eluted, decrosslinked for 30’ at 37° and 4 hours at 65° and purified using.  After quantification 5 ng of DNA were used to build libraries using NebNext-UltraII kit (NEB, cod.). Samples were sequenced paired-end NovaSeq6000 by GeneWiz.
TruSeq

tag: cell type

value: NPCs

tag: genotype

value: SETBP1 D868N


title: PEM-seq_HEK293T_PlmCas12e_VEGFA-2

city: Beijing

first: Changchang

last: Xin

state: Beijing

address: No.5 Yiheyuan Road Haidian District,Beijing,P.R.China

country: China

institute: Peking University

description: The cells were transfected with gRNA-PlmCas12e plasmid targeting VEGFA-2 locus, then sorted for mCherry positive (marker on gRNA-PlmCas12e plasmid) cells on Day3.

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021
Assembly: hg38
Supplementary files format and content: tab file
Library strategy: PEM-seq

source_name: cell line

extract_protocol:
Followed the PEM-seq protocol that described in Yin et al., 2019.
Followed the PEM-seq protocol that described in Yin et al., 2019.

tag: tissue

value: cell line

tag: cell line

value: Human embryonic kidney

value: WT

tag: treatment

value: plasmid transfection


title: NPCs D868D ChIP SET #2

description:
NPCD868D_Chip_SET_2
dual index library

value: SETBP1 D868D


title: PEM-seq_HEK293T_Un1Cas12f1_VEGFA-2

description: The cells were transfected with gRNA-Un1Cas12f1 plasmid targeting VEGFA-2 locus, then sorted for mCherry positive (marker on gRNA-Un1Cas12f1 plasmid) cells on Day3.


title: NPCs D868D ChIP SET #1

description:
NPCD868D_Chip_SET_1
dual index library


title: FoxO1, KI, Ischemia

city: Stanford

first: Siavash

last: Moghadami

state: CA

address: 299 Campus Drive, Fairchild Science Building, Room D236

department: Neurobiology

country: USA

institute: Stanford University

organism: Mus musculus

value: C/EBP-Beta-T250E knock-in

value: ischemia


title: PEM-seq_HEK293T_AsCas12f1_VEGFA-2

description: The cells were transfected with gRNA-AsCas12f1 plasmid targeting VEGFA-2 locus, then sorted for mCherry positive (marker on gRNA-AsCas12f1 plasmid) cells on Day3.


title: NPCs D868D ChIP H3K27ac #2

description:
NPCD868D_Chip_H3K27ac_2
dual index library

data_processing:
FASTQ were first quality checked to evaluate sequence output with using FastQC (Andrews, S. FastQC A Quality Control tool for High Throughput Sequence Data). Reads were then trimmed using Trimmomatic 5. Reads were then aligned to reference genome hg38 using Bowtie2 6 using the --very-sensitive option. Non canonical and M chromosomes were removed from Bam files using Samtools 7 and Picard tools (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/) was used to remove PCR optical duplicates, before proceeding with further analysis. Normalized BigWig files for genomics track visualization and for subsequent analysis were generated using deepTools (v3.5.1) 8 bamCoverage with the following parameters --normalizeUsing RPKM --binSize 10 --smoothLength 300 –effectiveGenomeSize --ignoreDuplicates  --skipNAs –exactScaling. To obtain a single merged tracks from single experimental replicates for each experimental condition UCSC bigWigMerge was used.   Peak calling was performed using MACS2 9 from preprocessed Bam files for each experimental replicate from each condition. For ChIP-seq narrow peaks (H3K27ac), the following parameters were used -f  BAMPE --nomodel --qvalue 0.01 --keep-dup all --call-summits using Input for each condition as control sample.
Genome_build: hg38
Supplementary files format and content: macs narrowpeak


title: VehicleRep2

city: San Francisco

first: Cecilia

last: Noecker

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: University of California San Francisco

library_source: transcriptomic

data_processing:
Trim and quality filter using fastp v0.20.0 with the following parameters: --trim_poly_g --cut_front --cut_tail --cut_window_size 4  --cut_mean_quality 20  --length_required 15
Align reads to E. lenta DSM 2243 reference genome using Hisat2 aligner v2.2.1
Count features using NCBI RefSeq annotations and the featureCounts function in the R package Rsubread v2.6.4
Assembly: GCF_000024265.1
Supplementary files format and content: Matrix of read counts per sample and feature

molecule: total RNA

organism: Eggerthella lenta DSM 2243

source_name: bacteria

growth_protocol: E. lenta DSM 2243 glycerol stocks were plated on BHI+ and incubated anaerobically at 37°C for three days. A single colony was then inoculated into 5mLs of BHI+ liquid culture and incubated at 37°C for 48 hours. 1 mL of the resulting culture was then centrifuged, washed once, and resuspended in equal volume PBS; all in anaerobic conditions. 220 μL of this inoculum were transferred into culture flasks containing 20 mL of EDM1 (carbon source restricted version) to obtain a starting OD600 of 0.01.

extract_protocol:
Qiagen Rneasy Mini Kit, with an additional 50s bead-beating step after lysozyme digestion to better disrupt cell walls
Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit (#20040529) and 10bp IDT for Illumina indices. Supplementary oligonucleotide probes specific to E. lenta rRNA and other highly expressed noncoding RNAs were incorporated during Ribo-Zero depletion

treatment_protocol: After 20 hours of growth (early or mid-exponential phase), these cultures were treated with an additional 1.9 mL of sterile water or filter-sterilized solution containing either  arginine (to reach a final concentration of 86 mM), sodium acetate (final concentration of 14.5 mM), or agmatine sulfate (final concentration of 30 mM).

value: bacteria

value: water


title: VehicleRep1


title: ArginineRep3

value: arginine


title: ArginineRep2


title: VehicleRep3


title: ArginineRep1


title: NPCs D868N ChIP H3K27ac #2

description:
NPCD868N_Chip_H3K27ac_2
dual index library


title: FoxO1, WT, Sham

value: sham


title: FoxO1, WT, Ischemia


title: PEM-seq_HEK293T_CasMINI-ge4.1_VEGFA-2

description: The cells were transfected with gRNA-CasMINI-ge4.1 plasmid targeting VEGFA-2 locus, then sorted for mCherry positive (marker on gRNA-CasMINI-ge4.1 plasmid) cells on Day3.


title: PEM-seq_HEK293T_AsCas12a_VEGFA-2

description: The cells were transfected with gRNA-AsCas12a plasmid targeting VEGFA-2 locus, then sorted for mCherry positive (marker on gRNA-AsCas12a plasmid) cells on Day3.


title: AgmatineRep3

value: agmatine


title: JP6

type: genomic

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

country: France

institute: Aix-Marseille Université - Marseille Medical Genetics

hyb_protocol: According to Diagenode protocol

scan_protocol: According to Diagenode protocol

data_processing: Raw IDAT files were processed using R package ChAMP. Probes with missing values are removed, samples with more than 10% of probes with a detection p-value of greater than 0.01, probes with a detection p-value of greater than 0.01 in at least one sample and probes for which 5% of samples have a bead count less than 3 are filtered out.  Probes targeting CpG sites that are near SNPs, belong to X/Y chromosomes, or align with multiple locations are filtered out

label: biotin

source_name: Mesenchymal stem cells

label_protocol: According to Diagenode protocol

growth_protocol: The hIPSc were differentiated into MSC, cultivated in KO DMEM supplemented 15% FBS, 10ng Beta FGF, 1mM ascobic acid 2-P, 1X glutamax, 1X NEAA, 50 µM Beta mercaptoethanol

extract_protocol: macherey nagel nucleospin tissue kit

tag: disease

value: HGPS (huntington gilford progeria syndrome)

tag: sentrix id

tag: sentrix position


title: PEM-seq_HEK293T_CasMINI_VEGFA-2

description: The cells were transfected with gRNA-CasMINI plasmid targeting VEGFA-2 locus, then sorted for mCherry positive (marker on gRNA-CasMINI plasmid) cells on Day3.


title: NPCs I871T ATAC #3

description:
NPCI871T3
single index library

data_processing:
FASTQ were first quality checked to evaluate sequence output with using FastQC (Andrews, S. FastQC A Quality Control tool for High Throughput Sequence Data). Reads were then trimmed using Trimmomatic 5. Reads were then aligned to reference genome hg38 using Bowtie2 6 using the --very-sensitive option. Non canonical and M chromosomes were removed from Bam files using Samtools 7 and Picard tools (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/) was used to remove PCR optical duplicates, before proceeding with further analysis. Normalized BigWig files for genomics track visualization and for subsequent analysis were generated using deepTools (v3.5.1) 8 bamCoverage with the following parameters --normalizeUsing RPKM --binSize 10 --smoothLength 300 –effectiveGenomeSize --ignoreDuplicates  --skipNAs –exactScaling. To obtain a single merged tracks from single experimental replicates for each experimental condition UCSC bigWigMerge was used.   Peak calling was performed using MACS2 9 from preprocessed Bam files for each experimental replicate from each condition. For ATAC-seq peak calling was performed on the Tn5- corrected single-base insertions using the following parameters --shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all –qvalue 0.01.
Genome_build: hg38
Supplementary files format and content: macs narrowpeaks

extract_protocol:
ATAC-seq was performed using a previously described protocol 3. Briefly, 50000 of cells for each experimental replicated were resuspended in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630, Sigma aldrich) to perform crude nuclei isolation. Trasposition reaction was then performed using Tn5 transposase (Illumina).  After transposition, DNA was purified using Zymo DNA Clean & Concentrator kit (cat. D4013) and amplified by PCR (NebNext ultra II polymerase, cat. M0544S). After 5 cycles the reaction was stopped, the necessary amount of cycles needed for the final amplification were calculated with qPCR. After amplification libraires were purified using Ampure XPbeads selection fragments between 100-1000 bp. Subsequently samples were sequenced paired-end on NovaSeq6000 by GeneWiz.
NexTera

value: SETBP1 I871T


title: AgmatineRep2


title: FoxO1, KI, Sham

value: cardiomyocytes


title: PEM-seq_HEK293T_SpCas9_VEGFA-2

description: The cells were transfected with gRNA-SpCas9 plasmid targeting VEGFA-2 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: AgmatineRep1


title: C/EBP, KI, Sham

value: Santa Cruz (sc-150, #A0913)


title: AcetateRep3

value: acetate


title: NPCs D868D ChIP H3K27ac #1

description:
NPCD868D_Chip_H3K27ac_1
dual index library

value: NPCs


title: NPCs I871T ATAC #1

description:
NPCI871T1
single index library


title: C/EBP, WT, Ischemia


title: C/EBP, Input

value: pooled


title: PEM-seq_HEK293T_PlmCas12e-R1-v2_VEGFA-1

description: The cells were transfected with gRNA-PlmCas12e-R1-v2 plasmid targeting VEGFA-1 locus, then sorted for mCherry positive (marker on PlmCas12e-R1-v2 plasmid) cells on Day3.

value: cell line

value: Human embryonic kidney

value: WT


title: AcetateRep1


title: PEM-seq_HEK293T_PlmCas12e_VEGFA-1

description: The cells were transfected with gRNA-PlmCas12e plasmid targeting VEGFA-1 locus, then sorted for mCherry positive (marker on gRNA-PlmCas12e plasmid) cells on Day3.

value: plasmid transfection


title: PEM-seq_HEK293T_control_VEGFA-1

description: HEK293T wild-type cells were cultured for 3 days, and collected cells on Day3.


title: IV_7

city: Chapel Hill

first: William

last: Kim

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

data_processing:
75b paired-end reads were sequenced on a NextSeq500 using the NextSeq 500/550 Mid Output Kit v2.5
Total expected read counts were quantified using Salmon
Raw SALMON read counts for all RNAseq samples were normalized by DESeq2
Supplementary_files_format_and_content: Tab-delimited text files include Normalized count values for each sample
Genome_build: mm10

source_name: Spleen

extract_protocol:
RNA was extracted with Qiagen RNeasy Plus Mini kit
Libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina), paired-end

tag: strain

value: Spleen

tag: tumor status

value: Tumor

value: B cells


title: AcetateRep2

value: bacteria


title: NPCs I871T ATAC #2

description:
NPCI871T2
single index library


title: IV_8


title: C/EBP, WT, Sham

value: sham


title: NPCs I871I ATAC #2

description:
NPCI871I2
single index library

value: SETBP1 I871I


title: NPCs D868N ATAC #3

description:
NPCD868N3
single index library

value: SETBP1 D868N


title: NPCs D868N ATAC #2

description:
NPCD868N2
single index library


title: NPCs I871I ATAC #1

description:
NPCI871I1
single index library


title: PEM-seq_HEK293T_Un1Cas12f1_VEGFA-1

description: The cells were transfected with gRNA-Un1Cas12f1 plasmid targeting VEGFA-1 locus, then sorted for mCherry positive (marker on gRNA-Un1Cas12f1 plasmid) cells on Day3.


title: C/EBP, KI, Ischemia

value: C/EBP-Beta-T250E knock-in

value: ischemia


title: OT_8


title: PEM-seq_HEK293T_AsCas12f1_VEGFA-1

description: The cells were transfected with gRNA-AsCas12f1 plasmid targeting VEGFA-1 locus, then sorted for mCherry positive (marker on gRNA-AsCas12f1 plasmid) cells on Day3.


title: PEM-seq_HEK293T_LbCas12a_VEGFA-2

description: The cells were transfected with gRNA-LbCas12a plasmid targeting VEGFA-2 locus, then sorted for mCherry positive (marker on gRNA-LbCas12a plasmid) cells on Day3.


title: OT_7


title: NPCs D868N ATAC #1

description:
NPCD868N1
single index library


title: PEM-seq_HEK293T_CasMINI-ge4.1_VEGFA-1

description: The cells were transfected with gRNA-CasMINI-ge4.1 plasmid targeting VEGFA-1 locus, then sorted for mCherry positive (marker on gRNA-CasMINI-ge4.1 plasmid) cells on Day3.


title: NPCs I871I ATAC #3

description:
NPCI871I3
single index library


title: NPCs D868D ATAC #3

description:
NPCD868D3
single index library

value: SETBP1 D868D


title: PEM-seq_HEK293T_AsCas12a_VEGFA-1

description: The cells were transfected with gRNA-AsCas12a plasmid targeting VEGFA-1 locus, then sorted for mCherry positive (marker on gRNA-AsCas12a plasmid) cells on Day3.


title: PEM-seq_HEK293T_CasMINI_VEGFA-1

description: The cells were transfected with gRNA-CasMINI plasmid targeting VEGFA-1 locus, then sorted for mCherry positive (marker on gRNA-CasMINI plasmid) cells on Day3.


title: NPCs D868D ATAC #2

description:
NPCD868D2
single index library


title: OT_5


title: OT_4


title: OT_3


title: FAPs_Young_Tg3

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

institute: Chiba University

data_processing:
Reads were aligned to the mm9 mouse genome using STAR.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using Homer.

molecule: polyA RNA

source_name: FAP

extract_protocol:
Total RNA was extracted using Rneasy column (Qiagen) according to the manufacturer's protocol.
Poly-A mRNA was extracted from total RNA by using an NEBNext Poly(A) mRNA magnetic Isolation module (NEB), after which RNA-seq libraries were prepared using a NEBNext UltraII RNA Library Prep kit for Illumina (NEB) according to the manufacturer’s protocol.

value: fibro-adipogenic progenitor cells

value: DT


title: Neurons D868N ATAC #3

description:
NeuD868N3
single index library

source_name: NPC-derived Neurons

value: NPC-derived Neurons


title: NPCs D868D ATAC #1

description:
NPCD868D1
single index library

value: NPCs


title: Pik3caHR Kdm6afl/fl Ad-K5-Cre - Rep1

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Ave, Room 1080

country: Canada

institute: Lunenfeld- Tanenbaum Research Institute

description: F.rawCount.txt

data_processing:
Reads were aligned to mm10 using Hisat2 (2.1.0)
Raw reads obtained from bam files using featureCounts and mm10 annotation file from ensembl (Mus_musculus.GRCm38.94.gtf)
DESeq2 package in R was used to determine differentially expressed genes between samples
Genome_build: mm10
Supplementary_files_format_and_content: txt, count files

source_name: mammary tumor

extract_protocol:
Tumors were dissected and incubated with 10% collagenase in DMEM/F12 for 45 minutes followed by 10 minutes of digestion in trypsin-EDTA. GFP+,DAPI- cells sorted by flow cytometry prior to RNA extraction by Zymo RNA mini-prep kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mixed C57BL/6 x FVB/N

value: Adenoviral Krt5-Cre

tag: mouseline


title: Pik3caHR Kdm6afl/fl Ad-K5-Cre - Rep2

description: F.rawCount.txt


title: FAPs_Young_WT2

value: WT


title: Neurons D868N ATAC #2

description:
NeuD868N2
single index library


title: PEM-seq_HEK293T_LbCas12a_VEGFA-1

description: The cells were transfected with gRNA-LbCas12a plasmid targeting VEGFA-1 locus, then sorted for mCherry positive (marker on gRNA-LbCas12a plasmid) cells on Day3.

value: cell line

value: Human embryonic kidney

value: plasmid transfection


title: Neurons D868N ATAC #1

description:
NeuD868N1
single index library


title: PEM-seq_HEK293T_SpCas9_VEGFA-1

description: The cells were transfected with gRNA-SpCas9 plasmid targeting VEGFA-1 locus, then sorted for mCherry positive (marker on gRNA-SpCas9 plasmid) cells on Day3.


title: OT_6

value: Spleen

value: Tumor

value: B cells


title: SIM_PlpCreRibo_Mu_T3_4_IgG

city: Leuven

first: Gianluca

last: Matteoli

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
Data analysis was performed by using the UTAP transcriptome analysis pipeline. Raw reads were trimmed using cutadapt with the parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a ‘‘A–times 2 -u 3 -u -3 -q 20 -m 25). Reads were mapped to the genome (mm10, Gencode annotation version 10.0) using STAR (v2.4.2a) with the parameters –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No. The pipeline quantifies the 3’ of Gencode annotated genes. UMI counting was done after marking duplicates (in-house script) using HTSeq-count in union mode. Only reads with unique mapping were considered for further analysis, and genes having minimum 5 reads in at least one sample were considered. Gene expression levels were calculated and normalized using DESeq2 (1.26.0) with default parameters except alpha = 0.058.
Genome_build: mm10
Supplementary_files_format_and_content: Raw files are the fastq files. Processed files are counts files in TXT format as tab delimited files

source_name: Muscularis externae of mouse

extract_protocol:
Samples were immunoprecipitated at the Weizman Instiute (Israel) according to the published protocol4, 5. In brief, samples were homogenized in 4 mL cold homogenization buffer (50 mM Tris, pH 7.4, 100 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 1:100 protease inhibitor (Sigma), 200 U/mL RNasin (Promega) and 0.1 mg/ml cycloheximide (Sigma)) with a Dounce homogenizer (Sigma) until the suspension was homogeneous. To remove cell debris, 2 mL of the homogenate was transferred to a microcentrifuge tube and centrifuged at 10,000 g at 4°C for 10 min. Supernatants were transferred and split, and 8 μL (10 µg) of anti-HA antibody (H9658, Sigma) or 20 μL (10 µg) of mouse monoclonal IgG1 antibody (Sigma, Cat# M5284) was added to the supernatant, followed by 4h of incubation with slow rotation at 4°C. Meanwhile, Dynabeads Protein G (Thermo Fisher Scientific), were equilibrated to homogenization buffer by washing three times. At the end of 4 h of incubation with antibody, beads were added to each sample, followed by incubation overnight at 4°C. Next, samples were washed three times with high-salt buffer (50 mM Tris, 300 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 1:200 protease inhibitor, 100 U/ml RNasin and 0.1 mg/ml cycloheximide). At the end of the washes, beads were magnetized and excess buffer was removed, 150 µl lysis buffer was added to the beads and RNA was extracted with Dynabeads mRNA Direct purification kit (Thermo Fisher) according to manufacturer’s instructions. RNA was eluted in 6 μl H2O and used for RNA-seq
mRNA was captured with Dynabeads oligo(dT) (Life Technologies) according to manufacturer’s guidelines. A bulk variation of MARSseq6 was used to prepare libraries for RNA-seq. RNA was reversed transcribed with MARSseq barcoded RT primer in a 10 mL volume with the Affinity Script kit (Agilent). Reverse transcription was analyzed by qRT-PCR and samples with a similar CT were pooled (up to eight samples per pool). Each pool was treated with Exonuclease I (NEB) for 30 min at 37°C and subsequently cleaned by 1.2 x volumes of SPRI beads (Beckman Coulter). Subsequently, the cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20mL reaction, incubating for 2 h at 16°C. The product was purified with 1.4 x volumes of SPRI beads, eluted in 8 mL and in vitro transcribed (with the beads) at 37°C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37°C and the amplified RNA (aRNA) purified with 1.2 volumes of SPRI beads. The aRNA was fragmented by incubating 3 min at 70°C in Zn2+ RNA fragmentation reagents (Ambion) and purified with 2 x volumes of SPRI beads. The aRNA was ligated to the MARS-seq ligation adaptor with T4 RNA Ligase I (NEB). The reaction was incubated at 22°C for 2 h. After 1.5 x SPRI cleanup, the ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent) and a primer complementary to the ligated adaptor. The reaction was incubated for 2 min at 42°C, 45 min at 50°C, and 5 min at 85°C. The cDNA was purified with 1.5 x volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5mM of P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kappa Biosystems). The amplified pooled library was purified with 0.7 x volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument

value: injected twice intraperitoneally with 100 ul of 15 mg/ml tamoxifen (Sigma) dissolved in Miglyol 812 (Caesar & Loretz, Hilden, Germany)


title: CD206DTR_CTX_d14_2

source_name: muscle

value: whole muscle tissue


title: Neurons D868D ATAC #3

description:
NeuD868D3
single index library


title: CD206DTR_CTX_d14_1


title: CD206DTR_CTX_d7_3


title: SIM_PlpCreRibo_Mu_T3_4_HA


title: Neurons D868D ATAC #2

description:
NeuD868D2
single index library


title: CD206DTR_CTX_d7_1


title: ko-97

type: RNA

city: Shanghai

first: Houbao

last: Zhu

address: 197 Ruijin Road Ⅱ

institute: Shanghai Jiao Tong University School of Medicine

description:
gene expression in dhtkd1-/- spinal cord
dhtkd1 null 1
dhtkd1 null, 8-weeks-old, replicate 1

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: dhtkd1 null, 8-weeks-old

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Mice were raised under specific pathogen-free conditions fed by free to access water and diets

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

tag: gender

value: male

tag: age

tag: genotype/variation

value: dhtkd1 null

value: spinal cord


title: PEM-seq_HEK293T_LbCas12a_COL8A1

description: The cells were transfected with gRNA-LbCas12a plasmid targeting COL8A1 locus, then sorted for mCherry positive (marker on gRNA-LbCas12a plasmid) cells on Day3.


title: CD206DTR_CTX_d4_2

value: DT


title: wt-124

description:
gene expression in wt spinal cord
wt-1
wild-type, 8-weeks-old, replicate 1

source_name: wild-type, 8-weeks-old

value: wild-type


title: Neurons D868D ATAC #1

description:
NeuD868D1
single index library

value: NPC-derived Neurons

value: SETBP1 D868D


title: SIM_PlpCreRibo_Mu_T3_3_IgG


title: SIM_PlpCreRibo_Mu_T3_3_HA


title: wt-126

description:
gene expression in wt spinal cord
wt-3
wild-type, 8-weeks-old, replicate 3


title: RNA-seq-L-EV-bio rep 1

city: Nanjing

first: Ruxu

last: Sun

state: Jiangsu

address: 140 Hanzhong Road

institute: Nanjing medical university

data_processing:
reads were sequenced with Illumina HiSeq 2500
Sequencing reads were aligned to human genome GRCh37/hg19 using HISAT2 software
Reads per kilobase per million mapped reads values were measured in 5’-untranslated region, coding sequencing and 3’-untranslated region of all genes using deepTools software
Methylated MeRIP peaks were called with exomePeak2 software, annotated using Annovar software, and matched to motifs with Homer software.
Expression of mRNA and lncRNA was analyzed in input RNAs using Stringtie algorithm with differential expression annotated using Deseq2 software.
Assembly: hg19
Supplementary files format and content: bed, narrowPeak (except for Input sample)
Supplementary files format and content: tab-delimited text files include FPKM values for all Sample  (except for IP sample)

source_name: retinal pigment epithelium cells

extract_protocol:
extracted total RNAs with high quality were sent for rRNA depletion with human TransNGS rRNA Depletion Kit (TransGen Biotech, Beijing, China) and RNA purification using MagicPure RNA beads (TransGen Biotech). RNAs were then segmented into 60~200 nt fragmentations with 10% of total RNA removed as input control. For immunoprecipitation, RNAs were incubated with Dynabeads Protein A (Thermo Fisher Scientific) and m6A antibody at 4 °C for 2 hours.
As to MeRIP-Seq, immunoprecipitated and purified RNA fragments as well as input RNAs were then sent for library construction using the VAHTS Total RNA-Seq (H/M/R) Library Prep Kit for Illumina (Vazyme, Nanjing, China)

value: retinal pigment epithelium cells


title: ko-156

description:
gene expression in dhtkd1-/- spinal cord
dhtkd1 null 3
dhtkd1 null, 8-weeks-old, replicate 3


title: RNA-seq-L-EV-bio rep 2

value: WT


title: CD206DTR_CTX_d4_1


title: CD206ctl_CTX_d14_2


title: SIM_PlpCreRibo_Mu_T3_1_IgG


title: direct Neurons D868N ATAC #3

description:
dir_NeuD868N3
single index library

source_name: iPSC-derived Neurons

value: iPSC-derived Neurons

value: SETBP1 D868N


title: direct Neurons D868N ATAC #2

description:
dir_NeuD868N2
single index library


title: RNA-seq-L-ALKBH5-bio rep 1

value: ALKBH5 overexpression


title: ko-155

description:
gene expression in dhtkd1-/- spinal cord
dhtkd1 null 2
dhtkd1 null, 8-weeks-old, replicate 2


title: m6A-seq-L-ALKBH5-bio rep 2


title: direct Neurons D868N ATAC #1

description:
dir_NeuD868N1
single index library


title: wt-125

description:
gene expression in wt spinal cord
wt-2
wild-type, 8-weeks-old, replicate 2


title: CD206ctl_CTX_d14_1


title: SIM_PlpCreRibo_Mu_T3_1_HA


title: direct Neurons D868D ATAC #3

description:
dir_NeuD868D3
single index library


title: m6A-seq-L-ALKBH5-bio rep 1


title: SIM_PlpCreRibo_Mu_T0_4_IgG


title: CD206ctl_CTX_d7_2


title: SIM_PlpCreRibo_Mu_T0_4_HA


title: m6A-seq-L-EV-bio rep 2


title: direct Neurons D868D ATAC #2

description:
dir_NeuD868D2
single index library


title: CD206ctl_CTX_d4_2


title: CD206ctl_CTX_d7_1


title: direct Neurons D868D ATAC #1

description:
dir_NeuD868D1
single index library


title: SIM_PlpCreRibo_Mu_T0_2_IgG


title: SIM_PlpCreRibo_Mu_T0_2_HA


title: NPCs D868N Hi-C #3

description:
NPC_D868N_3
dual index library

data_processing:
To perform raw data QCs and alignment to hg38 reference Juicer pipeline was used, with default settings (Durand et al, 2016).  Contact matrices were then generated up to a resolution of 5kb. The juicer-tools were used to perform all the downstream data analysis after obtaining the contact matrices
Genome_build: hg38
Supplementary files format and content: hic contact matrices

extract_protocol:
For in situ Hi-C libraries preparation 5 milions of either NPCs or neurons were used. An already published experimental protocol was used 4. The procedures consist in different experimental steps: (i) crosslinking cells with formaldehyde at 1% concentration, (ii) digesting the DNA using a 4-cutter restriction enzyme (e.g., DpnI) within intact permeabilized nuclei, (iii) filling in and biotinylating the resulting 5′-overhangs, (iv) ligating the blunt ends, (v) shearing the DNA, (vi) pulling down the biotinylated ligation junctions with streptavidin beads, and (vii) analyzing these fragments using paired end sequencing. A first sequencing run of 5 milion reads perform to verify the experimental quality. After passing the quality check, sample were sequenced paired end on Nova-seq6000 at San Raffaele hospital omics facility.
TruSeq

value: NPCs


title: SIM_PlpCreRibo_Mu_T0_1_IgG


title: AEC_EXO_2

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats
unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Genome_build: hg18
Supplementary_files_format_and_content: processed data file is a xls file contains the miRNA id, pre-miRNA_seq ,normalized abundance

source_name: Amniotic membrane

extract_protocol:
Total RNA was isolated from the samples and RNA integrity was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The miRNA-seq library was constructed using the TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA) according to the manufacturer's instructions.

value: amniotic epithelial cell-derived extracellular vesicles


title: SIM_PlpCreRibo_Mu_T0_1_HA


title: AEC_EXO_1


title: FiTAc-seq for Input of Human SCLC Tumor_27810

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with -k 1 option
ENCODE Blacklist and repeat sequences were removed
Peak signals were generated by MACS2
Bedgraph was converted to bigwig
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bigwig

source_name: Human primary SCLC tumor

extract_protocol:
FiTAc-seq has been previously described, briefly, two sections of 50um thickness for full sections of human FFPE tumors were used for ChIP profiling. Samples were treated with xylene to remove paraffin and then rehydrated with 100% ethanol for 10 min, 70% ethanol for 10 min, and water for another 10 min. Hydrated tissues were resuspended in 200ul of 1% SDS lysis buffer with 4ul of 50× EDTA-free protease inhibitor cocktail (PIC) and 1ul of 1 M sodium butyrate, then incubated overnight at 65°C with constant agitation at 1,000 r.p.m. The homogenized tissues were sonicated with Bioruptor for 12 cycles of 30 second on and 30 second off at 4°C. The soluble chromatins were subject to ChIP assay as described above. Library preparation and sequencing were done as described above.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads.

value: formalin-fixed, paraffin-embedded (FFPE) tissues

tag: antibody


title: CD206ctl_CTX_d4_1


title: NPCs D868D Hi-C #2

description:
NPC_D868D_2
dual index library


title: NPCs D868D Hi-C #3

description:
NPC_D868D_3
dual index library


title: NPCs D868N Hi-C #2

description:
NPC_D868N_2
dual index library


title: Hippocampus tissue, cko type (Brpf1 knockdown), rep4

first: Hang

last: Zhang

address: 130 Dongan Road

institute: Medical College, Fudan University

data_processing:
The pre-processing sequence was compared with the mouse genome (release-98) by STAR software after removing the linker and low-quality fragments.
StringTie software was used to count the original sequence counts of known genes
The expression of known genes was calculated using fragments per kilobase of transcript per million fragments mapped (FPKM).
The DESeq2 software was applied to screen the differentially expressed genes (DEGs) between different groups (log2 (Fold Change)>=1 or <= -1 and p value < 0.05 was used).
The function of DEGs was analyzed by David platform11(https://david.ncifcrf.gov/, RRID: SCR_001881), including gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG).
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Hippocampus CA1

growth_protocol: All mice were fed ad libitum under a 12-h light/ 12-h dark photocycle at 23±2°C.

extract_protocol:
RNA was extracted using traditional Trizol method, 1ul qubit instrument was used for RNA quality inspection.
RNA libraries for RNA-seq were prepared using Stranded mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Total RNA was extracted from hippocampal CA1 tissue from three paires of 2-month-old mice using the Trizol method (the removed mouse hippocampal CA1 region was placed in a 1.5ml centrifuge tube and 0.7 ml Trizol was added to fast-freeze dry ice).

value: Hippocampus CA1

value: Brpf1 knockdown


title: Hippocampus tissue, cko type (Brpf1 knockdown), rep3


title: NPCs D868N Hi-C #1

description:
NPC_D868N_1
dual index library

source_name: NPCs


title: EGCs_with_LPS_Stim_2

data_processing:
Preprocessing: Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15 (HannonLab, 2010; Martin, 2011). Subsequently, small reads (length < 35 bp), polyA-reads (more than 90 % of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using using FastX 0.0.14 and ShortRead 1.40.0 (Morgan et al, 2009). With Bowtie2 2.3.3.1 we identified and removed reads that align to phix_illumina (Langmead & Salzberg, 2012).
Mapping: The preprocessed reads were aligned with STAR aligner v2.5.2b to the reference genome of Mus musculus (GRCm38.82) (AD et al, 2013). Default STAR aligner parameter settings were used, except for ‘--outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate’. Using Samtools 1.5, reads with a mapping quality smaller than 20 were removed from the alignments (Li et al, 2009).
Counting: The number of reads in the alignments that overlap with gene features were counted with featureCounts 1.5.3 (Liao et al, 2014). Following parameters were chosen: -Q 0 -s 2 -t exon -g gene_id. We removed genes for which all samples had less than 1 count-per-million. Raw counts were further corrected within samples for GC-content and between samples using full quantile normalization, as implemented in the EDASeq package from Bioconductor (Risso et al, 2011).
Genome_build: mm10
Supplementary_files_format_and_content: Raw files are the fastq files. Processed files are counts file of the in TXT format as tab delimited files

source_name: Neurospheres derived from embryonic gut

extract_protocol:
Qiagen RNEasy micro kit was used to isolate RNA according to manufacturer’s instructions.
Per sample, an amount of 1 µg of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: # 1000000040498 v00 October 2017) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNAse H. The cDNA fragments were extended with a single 'A' base to the 3' ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library.

value: LPS (100ng/ml; Sigma) for 12 hours


title: Hippocampus tissue, cko type (Brpf1 knockdown), rep1


title: FiTAc-seq for H3K27ac of Human SCLC Tumor_27810

value: acetyl-histone H3K27  (Abcam, ab4729)


title: FiTAc-seq for Input of Human SCLC Tumor_27812


title: EGCs_with_LPS_Stim_1


title: NPCs D868D Hi-C #1

description:
NPC_D868D_1
dual index library


title: m6A-seq-L-EV-bio rep 1


title: Hippocampus tissue, wild type, rep4


title: Neurons D868N Hi-C #3

description:
Neu_D868N_3
dual index library


title: NKX2-1 ChIP for H187_SOX1 gRNA3

source_name: Small cell lung cancer

growth_protocol: NCI-H345 was maintained in HITES medium (serum free) with 1% P/S. NCI-H1436 was maintained in HITES medium with 5% FBS and 1% P/S, the others Cells were maintained in RPMI-1640 with 10% fetal bovine serum and 1% penicillin–streptomycin,

extract_protocol:
For SOX1, NKX2-1 and H3K27ac ChIP, cells were cross-linked with 1% formaldehyde and lysed. Chromatin in the lysates was sonicated and histone-DNA complexes were isolated with antibodies.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads.

value: Cell line

value: NKX2-1 (Bethyl Laboratories, A300-BL4000)


title: FiTAc-seq for H3K27ac of Human SCLC Tumor_27812


title: EGCs_with_LPS_Stim_3


title: EGCs_ctrl2


title: Hippocampus tissue, cko type (Brpf1 knockdown), rep2


title: Neurons D868N Hi-C #1

description:
Neu_D868N_1
dual index library


title: NKX2-1 ChIP for H187_SOX1 gRNA2


title: EGCs_ctrl1


title: Hippocampus tissue, wild type, rep1


title: Hippocampus tissue, wild type, rep2


title: Postnatal Cre+ RNA

description:
NUCLEI_POST_NATAL_CRE_POSITIVE
NUCLEI_POST_NATAL_CRE_POSITIVE
dual index library

library_source: transcriptomic single cell

data_processing:
Genome_build: mm10
Supplementary files format and content: cellranger output files

source_name: postnatal cortex

extract_protocol:
To perform single cell Multiome experiment fresh cortical tissue was dissected from 3 different animal for each experimental condition (NESTIN::CRE + and controls) and time point (e14.5 and Postnatal day2). Cortical tissue was then digested using Adult Brain Dissociation kit, mouse and rat (Milteny Biotech, 130-107-677). Tissue was first enzymatically digested with papain and Dnase provived by the kit at 37° for 10’, then mechanically dissociated using a p1000 for 10-20 passages, then digested for another 10’ and 37°. Afterwards a final mechanical dissociation passage was perform using p200 for 10-20 times. Single cells were then filtered trough a 70nm cell strain to remove debris and centrifuge at 1500 rpm for 5’ at room temperature.   After cell counting, cells deriving from the 3 different animals for each experimental condition were pulled together and nuclei were extracted following 10x Genomics protocol for Nuclei Isolation from Embryonic Mouse Brain Single Cell Multiome. A total of 1 million cells for each experimental condition were used as a starting point for nuclei extraction. After nuclei counting single cell libraries were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, cod. FC51000285). For embryonic samples 9000 cells and 14000 cells for postnatal samples, were loaded on Chromium controller after Tn5 trasposition for single cell library preparation.   For each experimental timepoint a unique RNA-seq and ATAC-seq library was obtained and sequenced on a Nova-seq6000 platform at San Raffaele hospital omics facility
transcriptomic single cell 10x multiome

value: postnatal cortex

value: CRE+


title: Neurons D868D Hi-C #2

description:
Neu_D868D_2
dual index library

value: NPC-derived Neurons

value: SETBP1 D868D


title: Neurons D868D Hi-C #3

description:
Neu_D868D_3
dual index library


title: Postnatal Cre- RNA

description:
NUCLEI_POST_NATAL_CRE_NEGATIVE
NUCLEI_POST_NATAL_CRE_NEGATIVE
dual index library

value: CRE-


title: NKX2-1 ChIP for H187_NT gRNA1


title: 10x Single Cell RNAseq of WT Day3 Post IM 2019

description: Cd45+ cells from the muscularis externa peeled from the small intestine of WT C57BL/6J mice 72 hours after intestinal manipulation

data_processing:
Demultiplexing and basecall to fastq with cellrnager mkfastq
10x cellranger version 3.0.2 was used to perform alignment (to mouse GRCm38/mm10 genome), filtering, UMI counting and to produce gene-barcode matrices
Further using Seurat R package, cells with less than 200 genes expressed or less than 10 percent mitochondrial genes were removed from the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Raw files are the possorted bam files obtained as output from cellranger in .bam format. Processed files are counts file of the cells included in the analysis aafter QC in tab separated format

source_name: Cd45+ cells from the muscularis externae of the small intestine

extract_protocol:
10x v3 3' kit was used according to manufacturer's instruction.
Single cell RNA sequencing libraries were prepared using 10x genomics platform according to manufacturer’s instructions (Single cell 3’ solution). Sequencing libraries were loaded at 1.4 pM on an Illumina NextSeq500 with NextSeq 500/550 Mid Output v2 kit (150 cycles) (Illumina). Cell Ranger software (v3.0.2) (10x Genomics) was used to demultiplex Illumina BCL files to FASTQ files (cellranger mkfastq) to perform alignment (to mouse GRCm38/mm10 genome), filtering, UMI counting and to produce gene-barcode matrices.

value: Muscularis of small intestine

value: 12 weeks


title: EGCs_ctrl3


title: NKX2-1 ChIP for H187_Parental


title: 10x Single Cell RNAseq of KO Day1 Post IM 2019

description: Cd45+ cells from the muscularis externa peeled from the small intestine of Ccr2-/-; B6.129S4-Ccr2tm1Ifc/J mice 24 hours after intestinal manipulation


title: Embryo Cre+ RNA

description:
NUCLEI_EMBRYO_CRE_POSITIVE
NUCLEI_EMBRYO_CRE_POSITIVE
dual index library

source_name: embryonic cortex

value: embryonic cortex


title: 10x Single Cell RNAseq of WT Day1 Post IM 2019

description: Cd45+ cells from the muscularis externa peeled from the small intestine of WT C57BL/6J mice 24 hours after intestinal manipulation


title: Hippocampus tissue, wild type, rep3

value: WT


title: H3K27ac ChIP for H187_SOX1 gRNA3


title: 43_Myc_N262

description: Myc Ab N262

data_processing:
Reads were aligned to hg38 using Hisat2 (2.1.0)
Duplicate reads were removed using Picard (MarkDuplicates). Blacklist regions were removed using bedtools intersect.
ChIP peaks (.narrowPeak) were called using Macs3; using 2% input as control and q=0.01
Assembly: GRCh38
Supplementary files format and content: bed files, ChIP peaks

source_name: glioma xenograft in mouse

extract_protocol:
Qiagen tissue DNA extraction kit was used according to the manufacturer's instructions.
The Sequencing library was generated from 2 ng of fragmented DNA using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (Cat# E7645S) according to the manufacturer’s instructions.

value: glioma xenograft in mouse

value: PDX 43

value: glioma

value: IDH wildtype


title: Embryo Cre- RNA

description:
NUCLEI_EMBRYO_CRE_NEGATIVE
NUCLEI_EMBRYO_CRE_NEGATIVE
dual index library


title: 43_Myc_abcam

description: Myc Ab Abcam


title: 10x Single Cell RNAseq of WT Day3 Post IM 2018

data_processing:
Demultiplexing and basecall to fastq with cellrnager mkfastq
10x cellranger version 3.0.2 was used to perform alignment (to mouse GRCm38/mm10 genome), filtering, UMI counting and to produce gene-barcode matrices
Further Seurat R package was used to QC and further analysis of scRNA seq data using the sctransfrom pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: Raw files are the possorted bam files obtained as output from cellranger in .bam format. Processed files are counts file of the cells included in the analysis aafter QC in tab separated format

extract_protocol:
10x v2 3' kit was used according to manufacturer's instruction.
Single cell RNA sequencing libraries were prepared using 10x genomics platform according to manufacturer’s instructions (Single cell 3’ solution). Sequencing libraries were loaded at 1.4 pM on an Illumina NextSeq500 with NextSeq 500/550 Mid Output v2 kit (150 cycles) (Illumina). Cell Ranger software (v3.0.2) (10x Genomics) was used to demultiplex Illumina BCL files to FASTQ files (cellranger mkfastq) to perform alignment (to mouse GRCm38/mm10 genome), filtering, UMI counting and to produce gene-barcode matrices.


title: Postnatal Cre+ ATAC #2

description:
NUCLEI_POST_NATAL_CRE_POSITIVE
ATAC_POST_NATAL_CRE_POSITIVE
single index library

library_source: genomic single cell

extract_protocol:
To perform single cell Multiome experiment fresh cortical tissue was dissected from 3 different animal for each experimental condition (NESTIN::CRE + and controls) and time point (e14.5 and Postnatal day2). Cortical tissue was then digested using Adult Brain Dissociation kit, mouse and rat (Milteny Biotech, 130-107-677). Tissue was first enzymatically digested with papain and Dnase provived by the kit at 37° for 10’, then mechanically dissociated using a p1000 for 10-20 passages, then digested for another 10’ and 37°. Afterwards a final mechanical dissociation passage was perform using p200 for 10-20 times. Single cells were then filtered trough a 70nm cell strain to remove debris and centrifuge at 1500 rpm for 5’ at room temperature.   After cell counting, cells deriving from the 3 different animals for each experimental condition were pulled together and nuclei were extracted following 10x Genomics protocol for Nuclei Isolation from Embryonic Mouse Brain Single Cell Multiome. A total of 1 million cells for each experimental condition were used as a starting point for nuclei extraction. After nuclei counting single cell libraries were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, cod. FC51000285). For embryonic samples 9000 cells and 14000 cells for postnatal samples, were loaded on Chromium controller after Tn5 trasposition for single cell library preparation.   For each experimental timepoint a unique RNA-seq and ATAC-seq library was obtained and sequenced on a Nova-seq6000 platform at San Raffaele hospital omics facility
Chromatin accessibility single cell 10x multiome


title: H3K27ac ChIP for H187_SOX1 gRNA1


title: 43_2per_Input

description: 2% ChIP Input


title: 10x Single Cell RNAseq of KO Day3 Post IM 2019

description: Cd45+ cells from the muscularis externa peeled from the small intestine ofCcr2-/-; B6.129S4-Ccr2tm1Ifc/J mice 72 hours after intestinal manipulation


title: H3K27ac ChIP for H187_SOX1 gRNA2


title: NKX2-1 ChIP for H187_SOX1 gRNA1


title: NKX2-1 ChIP for H187_NT gRNA2


title: 10x Single Cell RNAseq of WT Day1 Post IM 2018


title: H3K27ac ChIP for H187_NT gRNA2


title: 196_Myc_N262

description: Myc Ab N262

value: PDX 196

value: IDH mutant


title: Neurons D868N Hi-C #2

description:
Neu_D868N_2
dual index library

source_name: NPC-derived Neurons

value: SETBP1 D868N


title: Neurons D868D Hi-C #1

description:
Neu_D868D_1
dual index library


title: Postnatal Cre- ATAC #2

description:
NUCLEI_POST_NATAL_CRE_NEGATIVE
ATAC_POST_NATAL_CRE_NEGATIVE
single index library


title: Postnatal Cre- ATAC #1


title: H3K27ac ChIP for H187_NT gRNA1

value: Cell line

value: acetyl-histone H3K27  (Abcam, ab4729)


title: H3K27ac ChIP for H187_Parental


title: Embryo Cre+ ATAC #2

description:
NUCLEI_EMBRYO_CRE_POSITIVE
ATAC_EMBRYO_CRE_POSITIVE
single index library

value: CRE+


title: 196_2per_Input

description: 2% ChIP Input


title: 196_Myc_abcam

description: Myc Ab Abcam


title: RNA-seq-L-ALKBH5-bio rep 2

value: retinal pigment epithelium cells

value: ALKBH5 overexpression


title: SOX1 ChIP for H187


title: Embryo Cre+ ATAC #1


title: 164_Myc_N262

description: Myc Ab N262

value: PDX 164


title: Cgset4Δ grown in CAA medium: Replicate-1

city: Hyderabad

first: Rupinder

last: Kaur

state: Telangana

address: Inner Ring road

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

description: Gene expression analysis

data_processing:
The constructed libraries were sequenced on the Hiseq 2500 Illumina platform and 2x100 bp paired-end sequence was obtained, which contained 40-60 million high-quality reads per sample.
FASTQ files were generated from Illumina RNA-seq data. Based on the FASTQ file quality report, the sequence was trimmed, and only high-quality sequences were retained for further analysis.
The pre-processed reads were aligned pairwise with the C. glabrata CBS138 genome using Hisat2 program (Version-2.0.5).
The differential expression analysis was performed using Cuffdiff program of Cufflinks package (version 2.2.1) with default settings.
Further, the number of up and down regulated genes were filtered using Cuffdiff with q-value cut off ≤ 0.05 and ≥ 1.5-fold change in expression.
Assembly: Candida glabrata CBS138 genome
Supplementary files format and content: Excel file; GeneID, FPKM values of all samples, Gene name, Aliases, Feature type, Chromosome, Start Coordinate, Stop Coordinate, Strand, Primary CGDID, Secondary CGDID, Description, Name of S. cerevisiae ortholog(s)

organism: Nakaseomyces glabratus

source_name: Cgset4-delta knockout

growth_protocol: C. glabrata wild-type and Cgset4Δ strains were inoculated in CAA medium and incubated for 16 h at 30⁰C under shaking conditions (200 rpm). These cultures were re-inoculated in the fresh CAA medium at an initial OD600 of 0.1 and grown for 4-5 h at 30⁰C to obtain logarithmic (log)-phase cultures.

extract_protocol:
Total RNA was extracted using the acid-phenol method. Briefly, caspofungin-treated and untreated cultures of C. glabrata wild-type and Cgset4Δ stains were pelleted down and washed twice with chilled DEPC-treated water. The cell pellet was suspended in 350 μl of chilled AE solution (50 mM NaOAc and 10 mM EDTA) and lysed by addition of 40 μl of 10% SDS and 400 μl of acid phenol (pH 4.3) and vortexing for 10 sec. Next, the samples were incubated at 65oC for 15 min on a thermomixer followed by incubation on ice for 5 min. The samples were centrifuged at 4oC at 13,000 rpm for 10 min, and the upper aqueous layer was collected in a new 1.5 ml microcentrifuge tube. 400 μl of chloroform was added to the aqueous layer and centrifuged at 3,000 rpm for 10 min at 4⁰C. The aqueous layer was transferred to a 1.5 ml microcentrifuge tube, and RNA was precipitated with 40 µl of 3 M sodium acetate (pH 5.3) and 400 µl of ethanol, following incubation at -20oC for 20 min. Next, RNA was pelleted down by centrifugation at 13,000 rpm for 10 min at 4oC, and the pellet was washed with chilled 70% ethanol, air dried and suspended in 100 μl DEPC-treated water. To remove DNA contamination, 1 μl of DNase I was added to 1 µg of total RNA and incubated for 20 min at 37°C.
RNA-Seq library was prepared with 1 μg of total RNA using TruSeq RNA Sample Prep Kits (Illumina), as recommended by the manufacturer. In brief, total RNA was subjected to poly-A tail-based mRNA purification using magnetic beads attached with poly-T oligos. After purification, mRNA was fragmented using divalent cations at high temperature. The cleaved RNA fragments were used to synthesize cDNA first strand using reverse transcriptase and random primers. The synthesis of the second strand cDNA was done using DNA polymerase I and RNase H. These cDNA fragments underwent to end repair process followed by addition of a single ‘A’ base and ligation of the adaptors. The product was finally purified and enriched with PCR to create final cDNA library. Bioanalyzer plots were used to assess mRNA quality, enrichment success, fragment size, and the final library size. Both qubit and qPCR methods were used to measure the quantity of library before sequencing.

treatment_protocol: Log-phase cultures of wild-type and Cgset4Δ strains were either treated with 0.25 µg/ml caspofungin for 1 h or left untreated. During caspofungin treatment, cultures were incubated at 30⁰C under shaking conditions (200 rpm).

value: Cgset4-delta knockout

value: Untreated


title: 164_Myc_abcam

description: Myc Ab Abcam


title: Postnatal Cre+ ATAC #1

value: postnatal cortex


title: Cgset4Δ grown in CAA medium: Replicate-2

description: Gene expression analysis


title: 10x Single Cell RNAseq of WT Day0 Post IM 2018

description: Cd45+ cells from the muscularis externa peeled from the small intestine of naïve WT C57BL/6J mice.

value: Muscularis of small intestine

value: 12 weeks


title: NKX2-1 ChIP for H187

value: NKX2-1 (Bethyl Laboratories, A300-BL4000)


title: 164_2per_Input

description: 2% ChIP Input

value: glioma xenograft in mouse

value: glioma


title: Embryo Cre- ATAC #2

description:
NUCLEI_EMBRYO_CRE_NEGATIVE
ATAC_EMBRYO_CRE_NEGATIVE
single index library

value: embryonic cortex

value: CRE-


title: wt grown in caspofungin-containing CAA medium: Replicate-2

description: Gene expression analysis

source_name: wild-type

value: wild-type

value: Caspofungin-treated


title: NKX2-1 ChIP for H3122

source_name: Lung adenocarcinoma

value: Cell line


title: wt grown in caspofungin-containing CAA medium: Replicate-1

description: Gene expression analysis


title: Embryo Cre- ATAC #1


title: Cgset4Δ grown in caspofungin-containing CAA medium: Replicate-1

description: Gene expression analysis


title: 14_Myc_N262

description: Myc Ab N262

value: PDX 14

value: IDH wildtype


title: ChIP input for H3122


title: wt grown in CAA medium: Replicate-2

description: Gene expression analysis


title: Cgset4Δ grown in caspofungin-containing CAA medium: Replicate-2

description: Gene expression analysis


title: 14_Myc_abcam

description: Myc Ab Abcam


title: wt grown in CAA medium: Replicate-1

description: Gene expression analysis


title: Progranulin knock out neutrophils [sample5]

city: ChongQing

first: Jiayu

last: Liu

address: No. 1 Yi xue yuan Road, Yuzhong  District，ChongQing

department: School of Medical Laboratory

institute: Chongqing Medical University

data_processing:
Quality control: The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression.
Differential expression analysis: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Enrichment analysis of differentially expressed genes: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package (3.8.1), in which gene length bias was corrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package (3.8.1) to test the statistical enrichment of differential expression genes in KEGG pathways. The Reactome database brings together the various reactions and biological pathways of human model species. Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases. DO pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DisGeNET database integrates human disease-related genes. DisGeNET pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler R package (3.8.1) to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway.
Assembly: mm10 (GRCm38)
Supplementary files format and content: gene_fpkm.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: Neutrophils isolated from mouse bone marrow

growth_protocol: Wild-type and progranulin knock out neutrophils were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Neutrophils were washed three times with pre-chilled PBS, and RNA was harvested using Trizol Regent. 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol:
Neutrophils isolated from the bone marrow of mice were plated in siliconized EP tubes according to 2*10^6 cells per tube and cultured for 2hours.
Neutrophils were challenged with resuspended Candida albicans solution at MOI=1:1(2*10^6 cfu) for 6 hours.

value: Progranulin knock out

value: Challenge with Candida albicans in vitro

tag: time

value: 6 hours


title: Progranulin knock out neutrophils [sample6]

value: Neutrophils isolated from mouse bone marrow


title: ChIP input for H2087


title: 14_2per_Input

description: 2% ChIP Input


title: WT [Illumina]

city: Frederiksberg C

first: Stephan

last: Wenkel

address: Thorvaldsensvej 40

country: Denmark

institute: University of Copenhagen

data_processing:
Read quality assessment, base calling and adapter trimming was carried out with the Guppy software (version 3.2.6)
Nanofilt (version 2.7.1) was then used to remove low quality reads (Q-value < 7) and short-length reads (<50 bp)
The clean reads were subsequently corrected using Fclmr2 (version 0.1.2)
Minimap2 (version 2.17-r941)  was used to map the clean reads to the A. thaliana genome
Alignment ratio of clean reads to the reference genes was calculated using Samtools (version 1.10)
To identify m6A sites, the Tombo software de novo model together with MINES was used for calculation
Methylkit software was then used to analyze differential methylation sites (DML)
Logistic regression test was used to detect differential methylation sites.
Assembly: Minimap2 (version 2.17-r941)  was used to map the clean reads to the A. thaliana genome
Supplementary files format and content: Expression: PNG, PDF, XLS files. Boxplot, Correlation, Density, PCA
Supplementary files format and content: DE: PNG, PDF, XLS files. Boxplot, Barplot, Volcano, MA, Heatmap, Correlation
Supplementary files format and content: Methylation: M5C and M6A. PNG, PDF, XLS files. Boxplot, Density, Barplot, Dotplot, MA, Volcano
Supplementary files format and content: PolyA length: PDF, PNG, XLS files. Violin, Dotplot.
Supplementary files format and content: Structure: Novel transcripts, AS, Fusion, lncRNA, APA. PDF, PNG, XLS, FA, DPSI files.

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Seedlings grown until 14 days old on MS media in long day conditions

extract_protocol:
Extraction was done using the kit Spectrum Plant Total RNA Kit from Sigma (STRN250-1KT)
Prepared by CD genomics byt annealing dT adapters, reverse transcription and ligation of a motor adapter (Oxford Nanopore DRS protocol - SQK-RNA002, Oxford Nanopore Technologies)
Nanoport Direct RNA sequencing

value: Seedlings

value: wildtype

value: 14 days on MS

tag: ecotype


title: WT_-6hAPF_SG_FAIRE_Rep2

first: Christopher

middle: Mitsuo

last: Uyehara

address: 413 E 69th St

department: Meyer Cancer Center

institute: Weill Cornell Medicine

description:
faire_deseq_WT_Leg_v_WT_SG.csv
faire_deseq_WT_Wing_v_EcRi_Wing.csv
faire_deseq_WT_Wing_v_WT_Leg.csv
faire_deseq_WT_Wing_v_WT_SG.csv
WT_-6hAPF_SG_FAIRE_Merge_dm6_trim_q5_dupsRemoved_150to700_peaks.narrowPeak
WT_-6hAPF_SG_FAIRE_Merge_150to700_q5_dupsRemoved_rpgcNorm_zNorm.bw

data_processing:
fastq files from technical replicates were concatenated together
Adapter sequences were removed using bbmap (v38.75) using parameters ktrim=r ref=adapters rcomp=t tpe=t tbo=t hdist=1 mink=11
Trimmed sequences were aligned to the dm6 reference genome using bowtie2 (v2.3.4.1) using paramaters --phred33 --seed123
Aligned bam files were filtered to only include reads with MAPQ > 5 using samtools (v1.9)
PCR duplicates were removed using picard (v2.2.4)
For paired-end samples, fragments between 150-700bp were split into a separate sam file using a custom awk script
For paired-end samples, 150-700bp fragments were converted to bed files using the furthest start and end coordinates of each fragment
bed files from biological replicates were merged
bigwig files were generated from merged bed files using bedtools (v2.26) genomecov with parameters -bga
z-score normalized bigwigs were generated using a custom R script using R (v3.5.2)
peaks were called on merged replicates using MACS2 (v2.1.2) using parameters  --nomodel --seed 123 -g 137547960 --extsize 125
A union peak set was generated in R
Rsubread was used to assign reads to features using parameters:  strandSpecific = 0, allowMultiOverlap = T
DESeq2 was used to identify differentially-bound regions using parameters: lfcShrink = T, type = 'ashr'
Assembly: dm6
Supplementary files format and content: narrowpeak peaks from peaks called on merged replicates
Supplementary files format and content: z-score normalized bigwigs from merged replicates
Supplementary files format and content: comma-delimted tables with DESeq2 results

organism: Drosophila melanogaster

source_name: salivary gland

growth_protocol: Animals were raised at 25C. For –30hAPF, embryos on apple juice plates were cleared of any larvae, four hours later any animals that had hatched were transferred to vials, and animals dissected 72hrs later. For the -6hAPF time point, wandering (3LW) larvae were used. For the +6hAPF time point, animals were staged at the white, pre-pupae stage.

extract_protocol:
A minimum of 40 SG, wings, or legs were individually dissected in 1xPBS
The Takara Thruplex DNAseq kit with unique dual-indexes was used following manufacturer's instructions

value: salivary gland

tag: developmental stage

tag: Sex

value: female


title: Progranulin knock out neutrophils [sample4]

tag: cell type

tag: genotype


title: Primary endothelial cells_DMOG4

city: Chicago

first: Pinelopi

last: Kapitsinou

state: Il

address: 303 East Superior Street

department: Medicine/Nephrology

institute: Northwestern University, Feinberg School of Medicine

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases
sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
HISAT2 was used  to map reads to the genome of ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/
The mapped reads of each sample were assembled using StringTie
All transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and edgeR were used to estimate the expression levels of all transcripts.
Genome_build: ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/
Supplementary_files_format_and_content: text files include FPKM values for each Sample

source_name: Primary Pulmonary artery endothelial cells

growth_protocol: Endothelial cells were grown in endothelial cell growth medium-2 (EGM-2, catalog- CC-3156) supplemented with EGM-2 SingleQuot Kit (CC-4176). in 0.1 % gelatin coated 75 cm2 flask.

extract_protocol:
RNA was isolated using RNeasy Mini Kit (catlong: 74104; Qiagen)
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.

treatment_protocol: Treatment group was treated with 1mM Dimethyloxalylglycine (DMOG) and Control group was treated with same volume of dimethyl sulfoxide (DMSO) for 24 hours.

tag: tissue

value: Pulmonary artery

tag: treatment

value: DMOG treated

tag: cell line

value: Primary cells


title: Primary endothelial cells_DMOG3


title: Primary endothelial cells_DMOG2


title: EcRGFSTF_-6hAPF_Leg_CnR_aFlag_Pel_Rep2

description:
cnr_deseq--LEG_v_SG.csv
cnr_deseq--WING_v_LEG.csv
cnr_deseq--WING_v_SG.csv
EcRGFSTF_3LW_LEG_CnR_antiFlag_Merge_Pel_dm6_trim_q5_dupsRemoved_20to120_rpgcNorm_zNorm.bw
EcRGFSTF_3LW_LEG_CnR_antiFlag_Merge_Pel_dm6_trim_q5_dupsRemoved_20to120_peaks.narrowPeak

data_processing:
fastq files from technical replicates were concatenated together
Adapter sequences were removed using bbmap (v38.75) using parameters ktrim=r ref=adapters rcomp=t tpe=t tbo=t hdist=1 mink=11
Trimmed sequences were aligned to the dm6 reference genome using bowtie2 (v2.3.4.1) using paramaters --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 5 -X 999
Aligned bam files were filtered to only include reads with MAPQ > 5 using samtools (v1.9)
PCR duplicates were removed using picard (v2.2.4)
fragments between 20-120bp were split into a separate sam file using a custom awk script
20-120bp sam files were converted to bedpe files using bedtools (v2.26)
Awk was used to convert bedpe files to bed files by using the furthest start and end coordinate of each fragment
bigwig files were generated from bed files using bedtools (v2.26) genomecov with parameters -bga
z-score normalized bigwigs were generated using a custom R script using R (v3.5.2)
bedpe files from biological replicates were merged
peaks were called on merged replicates against IgG controls using MACS2 (v2.1.2) using parameters  -f BEDPE  --nomodel --seed 123 -g 137547960
A union peak set was generated in R
Rsubread was used to assign reads to features using parameters:  strandSpecific = 0, allowMultiOverlap = T
DESeq2 was used to identify differentially-bound regions using the model: ~supPel + tissue, and parameters: lfcShrink = T, type = 'ashr'
Assembly: dm6
Supplementary files format and content: narrowpeak peaks from peaks called on merged replicates against IgG controls
Supplementary files format and content: z-score normalized bigwigs from merged replicates
Supplementary files format and content: comma-delimted tables with DESeq2 results
Library strategy: CUT&RUN

source_name: leg

extract_protocol:
A minimum of 50 SG and 90 wings or legs were individually dissected in 1xPBS
The Takara Thruplex DNAseq kit with unique dual-indexes was used following manufacturer's instructions until the amplification step. For amplification, a combined, 10s annealing / extension step at 68C was used.

value: leg

value: w; EcR-GFSTF / Df(2R)BSC313

value: abcam rabbit anti-IgG ab46540; sigma antiFlag M2


title: Wild-type neutrophils control [sample2]

value: WT


title: fio1-1 [Illumina]


title: Wild-type neutrophils control [sample3]


title: Progranulin knock out macrophages [sample6]

source_name: Macrophages recruited from mouse peritoneal cavity

growth_protocol: Wild-type and progranulin knock out macrophages were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Macrophages were washed three times with pre-chilled PBS, and RNA was harvested using Trizol Regent. 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol:
Macrophages extracted from the peritoneal cavity of mice were plated in six-well cell culture plates according to 2*10^6 cells per well and cultured overnight.
Macrophages were challenged with resuspended Candida albicans solution at MOI=1:1(2*10^6 cfu) for 6 hours.


title: Primary endothelial cells_DMOG1


title: Wild-type neutrophils control [sample1]


title: ECRi_-6hAPF_Wing_RNA_Rep2

description:
rnaCountMat.csv
ecri_time_deseq.xlsx
wt_v_ecri_deseq.xlsx

data_processing:
Adapter sequences were removed using bbmap (v38.75) using parameters ktrim=r ref=adapters rcomp=t tpe=t tbo=t hdist=1 mink=11
Sequenced reads were aligned to the genome using STAR (v2.7.3a) using parameters --alignIntronMax 50000 --alignMatesGapMax 50000.
Bam file was indexed and sorted using samtools (v1.9)
Reads with MAPQ <2 were removed using samtools (v1.9)
RSubread was used to count reads mapping to genes
Differentially expressed genes were identified using DESeq2, using the lfcShrink function to shrink log-fold changes
Normalized counts were generated using DESeq2
Assembly: dm6
Supplementary files format and content: comma-delimited table with DESeq2 normalized counts for each sample
Supplementary files format and content: xlsx tables with DESeq2 results

source_name: wing

extract_protocol:
A minimum of 60 wings or SG were individually dissected in 1XPBS.
RNAseq libraries were prepared using the Tecan Genomics Universal RNA-Seq with NuQuant, Drosophila following manufacturers instructions.

value: wing

value: yw/yw; Vg-GAL4, UAS-Flp, Tub>>CD2>>GAL4; UAS-GFP / UAS-EcR-RNAi[104]


title: Primary endothelial cells_Control3

value: untreated


title: ECRi_-6hAPF_Wing_RNA_Rep1


title: WT_-6hAPF_Wing_RNA_Rep2

description:
rnaCountMat.csv
wt_wing_sg_deseq.xlsx
wing_time_deseq.xlsx


title: WT_-6hAPF_Wing_RNA_Rep1


title: EcRGFSTF_-6hAPF_Leg_CnR_aFlag_Sup_Rep2

description:
cnr_deseq--LEG_v_SG.csv
cnr_deseq--WING_v_LEG.csv
cnr_deseq--WING_v_SG.csv
EcRGFSTF_3LW_LEG_CnR_antiFlag_Merge_Sup_dm6_trim_q5_dupsRemoved_20to120_rpgcNorm_zNorm.bw
EcRGFSTF_3LW_LEG_CnR_antiFlag_Merge_Sup_dm6_trim_q5_dupsRemoved_20to120_peaks.narrowPeak


title: EcRGFSTF_-6hAPF_Leg_CnR_aFlag_Pel_Rep1


title: Primary endothelial cells_Control2


title: EcRGFSTF_-6hAPF_Leg_CnR_aFlag_Sup_Rep1


title: Primary endothelial cells_Control4


title: ECRi_-30hAPF_Wing_RNA_Rep2


title: fio1-2 [Illumina]

description: When samples were submitted for sequencing our mutant fio1-2 was named as such. Before publishing more fio mutants had been described and therefore our mutant was in the end named fio1-5, which is then the correct genotype.


title: Progranulin knock out macrophages [sample5]

value: Macrophages recruited from mouse peritoneal cavity

value: Progranulin knock out

value: Challenge with Candida albicans in vitro

value: 6 hours


title: Wild-type macrophages control [sample3]


title: WT_-6hAPF_SG_FAIRE_Rep1


title: Progranulin knock out macrophages [sample4]


title: EcRGFSTF_-6hAPF_SG_CnR_aFlag_Pel_Rep1

description:
cnr_deseq--LEG_v_SG.csv
cnr_deseq--WING_v_LEG.csv
cnr_deseq--WING_v_SG.csv
EcRGFSTF_3LW_SG_CnR_antiFlag_Merge_Pel_dm6_trim_q5_dupsRemoved_20to120_rpgcNorm_zNorm.bw
EcRGFSTF_3LW_SG_CnR_antiFlag_Merge_Pel_dm6_trim_q5_dupsRemoved_20to120_peaks.narrowPeak


title: ECRi_-30hAPF_Wing_RNA_Rep1


title: EcRGFSTF_-6hAPF_SG_CnR_aFlag_Sup_Rep2

description:
cnr_deseq--LEG_v_SG.csv
cnr_deseq--WING_v_LEG.csv
cnr_deseq--WING_v_SG.csv
EcRGFSTF_3LW_SG_CnR_antiFlag_Merge_Sup_dm6_trim_q5_dupsRemoved_20to120_rpgcNorm_zNorm.bw
EcRGFSTF_3LW_SG_CnR_antiFlag_Merge_Sup_dm6_trim_q5_dupsRemoved_20to120_peaks.narrowPeak


title: Primary endothelial cells_Control1


title: Wild-type macrophages control [sample2]


title: EcRGFSTF_-6hAPF_SG_CnR_aFlag_Pel_Rep2


title: Multi-tissue organoids week 15_S18

city: St. Paul

first: Timothy

middle: D.

last: O'Brien

state: MN

address: 1333 Gortner Avenue

department: Veterinary Population Medicine

institute: University of Minnesota

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via Hisat (v2.1.0) using the human (GRCh38) as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood city, CA) using raw read counts.
Genome_build: human GRCg38
Supplementary_files_format_and_content: RawReadCounts

source_name: iPSC line (ATCC-BYS0110, Cat. #ACS-1024)Multi-tissue organoids week 15

growth_protocol: iPSCs (ATCC-BYS0110, Cat. #ACS-1024) were expanded in culture on vitronectin (VTN-N, Thermofisher Scientific, Cat. #A14700) in Essential 8 Medium (E8, Thermo Fisher Scientific Life Sciences). iPSCs were harvested using sodium citrate buffer, briefly centrifuged, and MTO induction initiated by resuspension in 40 µL of the fluid of hydration from Cell-Mate3D µGel 40 Kit (BRTI Life Sciences, Two Harbors, MN, USA) which was then transferred to one well of a 6-well ultra-low attachment plate (Costar™ Ultra-Low Attachment Microplates, Corning Life Sciences, Corning, NY, USA) containing 5 ml of E8 medium and incubated for 24 hrs. Cells and culture medium were then transferred to a G-Rex 100 bioreactor (Wilson Wolf, New Brighton, MN) and incubated at 37oC in 5% CO2. E8 culture medium containing 1% antibiotic-antimycotic (Gibco Thermo Fisher Scientific) was changed every 3-4 days over the entirety of MTO culture.

extract_protocol:
MTOs were lysed in RLT buffer (Qiagen, Hilden, Germany) and RNA isolated from cell lysates using the RNeasy Plus mini kit (Cat. No. / ID: 74134Qiagen, Hilden, Germany) according to manufacturer’s instructions. Extracted RNA was then quantified by RiboGreen RNA assay (Thermo Fisher Scientific, Waltham, MA) and quality/size analyzed by Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using Illumina Truseq protocols

treatment_protocol: Batches of multi-tissue organoids were harvested on weeks 8, 11, and 15 (n=2 at each time point).  MTOs were disaggregated with trypsin or collagenase or both to improve RNA yield.

value: Week 15 multi-tissue organoid


title: WT_-30hAPF_Wing_RNA_Rep1


title: Wild-type macrophages control [sample1]


title: WT_-30hAPF_Wing_RNA_Rep2


title: Multi-tissue organoids week 11_S14

value: Week 11 multi-tissue organoid


title: EcRGFSTF_-6hAPF_Wing_CnR_aFlag_Pel_Rep2

description:
cnr_deseq--LEG_v_SG.csv
cnr_deseq--WING_v_LEG.csv
cnr_deseq--WING_v_SG.csv
EcRGFSTF_3LW_WING_CnR_antiFlag_Merge_Pel_dm6_trim_q5_dupsRemoved_20to120_rpgcNorm_zNorm.bw
EcRGFSTF_3LW_WING_CnR_antiFlag_Merge_Pel_dm6_trim_q5_dupsRemoved_20to120_peaks.narrowPeak

value: female


title: EcRGFSTF_-6hAPF_SG_CnR_aFlag_Sup_Rep1

value: salivary gland


title: Multi-tissue organoids week 8_S13

value: Week 8 multi-tissue organoid


title: Inf CD103-Tom- LP Trm cells_rep2

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

data_processing:
Basecalling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and alignment (Cutadapt v2.5, STAR v2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited file (txt) for raw hit counts

source_name: lamina propria Trm cells

growth_protocol: T cells were isolated from the lamina propria for sequencing.

extract_protocol:
RNA was isolated from sorted Trm cells using a PicoPure RNA isolation kit (Thermo Fisher #KIT0204).
Illumina compatible cDNA libraries generated for polyA enriched mRNA using NEB next low input protocol (New England Biolabs). The cDNA libraries were purified using AmpureXP beads (Beckman Coulter)

treatment_protocol: Immunized mice were left unchallenged or infected with Y.pseudotuberculosis 4 days prior to cell isolation.

value: Yersinia-infected


title: Inf CD103-Tom- LP Trm cells_rep3


title: ECRi_-6hAPF_SG_RNA_Rep2


title: EcRGFSTF_-6hAPF_Wing_CnR_aFlag_Pel_Rep1


title: WT_+6hAPF_Wing_RNA_Rep1


title: Inf CD103+Tom+ LP Trm cells_rep3


title: EcRGFSTF_-6hAPF_Wing_CnR_aFlag_Sup_Rep1

description:
cnr_deseq--LEG_v_SG.csv
cnr_deseq--WING_v_LEG.csv
cnr_deseq--WING_v_SG.csv
EcRGFSTF_3LW_WING_CnR_antiFlag_Merge_Sup_dm6_trim_q5_dupsRemoved_20to120_rpgcNorm_zNorm.bw
EcRGFSTF_3LW_WING_CnR_antiFlag_Merge_Sup_dm6_trim_q5_dupsRemoved_20to120_peaks.narrowPeak


title: Inf CD103-Tom- LP Trm cells_rep1


title: ECRi_-6hAPF_SG_RNA_Rep1


title: Inf CD103+Tom+ LP Trm cells_rep2


title: EcRGFSTF_-6hAPF_SG_CnR_aIgG_Pel_Rep1


title: WT_+6hAPF_Wing_RNA_Rep2


title: FiTAc-seq for Input of Human SCLC Tumor_27814

source_name: Human primary SCLC tumor

extract_protocol:
FiTAc-seq has been previously described, briefly, two sections of 50um thickness for full sections of human FFPE tumors were used for ChIP profiling. Samples were treated with xylene to remove paraffin and then rehydrated with 100% ethanol for 10 min, 70% ethanol for 10 min, and water for another 10 min. Hydrated tissues were resuspended in 200ul of 1% SDS lysis buffer with 4ul of 50× EDTA-free protease inhibitor cocktail (PIC) and 1ul of 1 M sodium butyrate, then incubated overnight at 65°C with constant agitation at 1,000 r.p.m. The homogenized tissues were sonicated with Bioruptor for 12 cycles of 30 second on and 30 second off at 4°C. The soluble chromatins were subject to ChIP assay as described above. Library preparation and sequencing were done as described above.
Up to 10 ng of DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit. The finished double strand DNA libraries were quantified by Agilent Bioanalyzer according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with paired-end 75bp reads.

value: formalin-fixed, paraffin-embedded (FFPE) tissues


title: EcRGFSTF_-6hAPF_Wing_CnR_aFlag_Sup_Rep2

value: w; EcR-GFSTF / Df(2R)BSC313


title: Inf CD103+Tom+ LP Trm cells_rep1


title: Multi-tissue organoids week 8_S11


title: WT_-6hAPF_SG_RNA_Rep1

description:
rnaCountMat.csv
wt_wing_sg_deseq.xlsx
sg_time_deseq.xlsx


title: FiTAc-seq for Input of Human SCLC Tumor_27818


title: Multi-tissue organoids week 11_S16


title: Multi-tissue organoids week 15_S17


title: EcRGFSTF_-6hAPF_SG_CnR_aIgG_Sup_Rep1

value: abcam rabbit anti-IgG ab46540; sigma antiFlag M2


title: WT100_-6hAPF_Wing_30mCnR_aIgG_Pel_Rep1

value: abcam rabbit anti-IgG ab46540


title: ECRi_-30hAPF_SG_RNA_Rep2


title: CD103-Tom- LP Trm cells_rep2

value: immunized


title: FiTAc-seq for Input of Human SCLC Tumor_27187


title: WT20_-6hAPF_Wing_30mCnR_aIgG_Pel_Rep1

value: wing


title: FiTAc-seq for Input of Human SCLC Tumor_27622


title: ECRi_-30hAPF_SG_RNA_Rep1

value: yw/yw; Vg-GAL4, UAS-Flp, Tub>>CD2>>GAL4; UAS-GFP / UAS-EcR-RNAi[104]


title: CD103+Tom+ LP Trm cells_rep2


title: CD103+Tom+ LP Trm cells_rep1


title: FiTAc-seq for H3K27ac of Human SCLC Tumor_27814

value: acetyl-histone H3K27  (Abcam, ab4729)


title: WT20_-6hAPF_Wing_30mCnR_aIgG_Sup_Rep1


title: WT100_-6hAPF_Wing_30mCnR_aIgG_Sup_Rep1


title: WT_-30hAPF_SG_RNA_Rep1


title: FiTAc-seq for H3K27ac of Human SCLC Tumor_27818


title: WT_+6hAPF_SG_RNA_Rep2


title: FiTAc-seq for H3K27ac of Human SCLC Tumor_27622


title: CD103+Tom+ LP Trm cells_rep3


title: WT_-30hAPF_SG_RNA_Rep2


title: WT_+6hAPF_SG_RNA_Rep1


title: Neural progenitor cells - rs557 A/A- myc

data_processing:
Library strategy: 4C
Read filtering of R1 fastqs for sequences beginning with respective target primer seqs (edit distance >=2)
Processing with 4cseqpipe.pl (fastq to raw format conversion): 4cseqpipe.pl -fastq2raw -convert_qual 1 -read_length 75
Processing with 4cseqpipe.pl (mapping): 4cseqpipe.pl -map -read_length 75
Processing with 4cseqpipe.pl (visualization): 4cseqpipe.pl -nearcis -calc_from 60000000 -calc_to 64000000
Genome_build: mm10
Supplementary_files_format_and_content: text, 4Cseqpipe Outputs

source_name: Neural progenitor cells

growth_protocol:
Primary Neural stem cells were grown in Lamin/poly-L-ornithine coated plates, NeuroCult™ NS-A Basal Medium supplemented with 2mM glutamine, 75ug/ml BSA, 2ug/ml heparin, anti-anti,  N2, W21 and 10 ng/ml of both EGF and bFGF.
all samples grown in the same conditions

extract_protocol:
Cell cultures were fixed with 1% PFA for 10 minutes before glycine inactivation and PBS wash
libraries were prepared for sequencing using standard Illumina protocols

value: ES-derived neural progenitor cells

tag: anchor

value: Myc anchored

value: untreated


title: WT20_-6hAPF_Wing_2mCnR_aIgG_Pel_Rep1


title: FiTAc-seq for H3K27ac of Human SCLC Tumor_27187

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with -k 1 option
ENCODE Blacklist and repeat sequences were removed
Peak signals were generated by MACS2
Bedgraph was converted to bigwig
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bigwig


title: downshock_24h

status: Public on Sep 11 2022

city: Nagoya

first: Hakuto

last: Kageyama

state: Aichi

address: 1-501, Shiogamaguchi, Tempaku-ku

institute: Meijo University

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated.
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with Bowtie. Transcript abundances are measured with mapped read count within gene region. In case of strand specific library, sense or anti-sense read counts are extracted by strand.
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage.
In groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypothesis testing.
Assembly: Halothece sp. PCC7418 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000317635.1/)
Supplementary files format and content: Tab-delimited text files include raw read counts for each sample

organism: Halothece sp. PCC 7418

source_name: Halothece cells

growth_protocol: Halothece cells were photoautotrophically cultured at 30ºC in blue-green 11 (BG11) media plus Turk Island salt solution (TISS) containing 2.0 M NaCl under continuous cool white fluorescent light intensity of 70 µE m-2 s-1.

extract_protocol:
Total RNA was extracted utilizing TRIzol LS Reagent (Thermo Fisher Scientific), according to the manufacturer’s protocol.
RNA samples were utilized to construct the libraries, which were sequenced at Macrogen (Japan).

treatment_protocol: For salt-downshock stress treatment, the cells were cultured to the exponential growth phase (OD730 = 0.6-0.8) in BG11 media plus TISS containing 2.0 M NaCl. The cells were then harvested from 100 ml cultures by centrifugation and transferred into the same volume of fresh media containing 0.5 M NaCl. The cells were cultured for 24 h before harvesting.

value: Halothece cells

value: WT

value: NaCl upshock


title: downshock_ctr

value: control for NaCl upshock treatment

value: 0 h


title: CD103-Tom- LP Trm cells_rep1

tag: strain


title: P_24h

source_name: WT

growth_protocol: Halothece cells were photoautotrophically cultured at 30ºC in blue-green 11 (BG11) media plus Turk Island salt solution (TISS) containing 0.5 M NaCl under continuous cool white fluorescent light intensity of 70 µE m-2 s-1.

treatment_protocol: For salt stress treatment, the cells were cultured to the exponential growth phase (OD730 = 0.6-0.8) in BG11 media plus TISS containing 0.5 M NaCl. The cells were then harvested from 100 ml cultures by centrifugation and transferred into the same volume of fresh media containing 2.0 M NaCl. The cells were cultured for 24 h before harvesting.  For sucrose-induced osmotic stress and nutrient deficiencies, the same volume scale as described for the salt stress treatment was performed. In the case of osmotic stress, the cells were first cultured to the exponential growth phase in BG11 media plus TISS containing 0.5 M NaCl. The cells were then harvested by centrifugation and transferred into the BG11 media plus TISS containing 0.5 M NaCl and 1.0 M sucrose. The cells were cultured for 24 h before harvesting.   For nutrient deficiencies, the experiments were conducted by starving the cells for nitrogen (N), phosphorus (P) or sulfur (S). The cells were first cultured to the exponential growth phase in BG11 media plus TISS containing 0.5 M NaCl. The cells were then harvested by centrifugation and transferred into BG11 medium containing 0.5 M NaCl and lacking N (by removing sodium nitrate), lacking P (composition of K2HPO4 was replaced with KCl), or S deficiency (composition of MgSO4 was replaced with MgCl2, ZnSO4 with ZnCl2 and CuSO4 with CuCl2). The cells were cultured for 24 h before harvesting.

value: P starvation


title: sucrose_24h

value: sucrose stress


title: N_24h

value: N starvation


title: upshock_24h


title: S_24h

value: S starvation


title: starvation_ctr

value: control for nutrient starvation and sucrose stresses


title: upshock_ctr


title: Empty_input

city: La Jolla

first: Padma

last: Natarajan

address: 10550 N.Torrey Pines Road

department: CCBB

institute: The Scripps Research Institute

description: Sample 2(02idEMPTYINPUT_S3_R1_001.fastq.gz)

data_processing:
The nf-core/chipseq pipeline (version 1.2.2; Ewels et al.,2020) written in the Nextflow domain specific language was used to perform the primary analysis of the samples.
The ChIP-seq reads were aligned to the UCSC GRCh38  reference genome using the BWA aligner (Li and Durbin, 2009) .
Mapped reads were further converted to normalized bigWig  files scaled to 1 million mapped reads using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
The peak calling was performed using MACS2 in narrowPeak mode.
Genome_build: GRCh38

source_name: TC28a2 cells transfected with an empty vector

extract_protocol:
Cells were cross-linked with 1% formaldehyde, and after lysis of cells, chromatin was fragmented by sonication. Protein-DNA complexes were purified with anti-HA tag antibody.
Libraries were constructed with ThruPLEX DNA-seq Kit (Takara Bio), according to manufacturer’s instruction.

value: TC28a2 cells

value: none (input)

tag: transfection

value: empty vector


title: Empty_CHIP

description: Sample 1(01idEMPTYHACHIP_S1_R1_001.fastq.gz)

value: Rabbit anti-HA tag antibody (clone C29F4, Cell Signaling Technology)


title: WT20_-6hAPF_Wing_2mCnR_aIgG_Sup_Rep1

value: wing

value: female

value: abcam rabbit anti-IgG ab46540


title: HA-CHIP_2

description: Sample 2 (03KLF4HAChIP3_S98_L001_R1_001.fastq.gz)

data_processing:
The nf-core/chipseq pipeline (version 1.2.2; Ewels et al.,2020) written in the Nextflow domain specific language was used to perform the primary analysis of the samples.
The ChIP-seq reads were aligned to the UCSC hg38  reference genome using the BWA aligner (Li and Durbin, 2010) .
Mapped reads were further converted to normalised bigWig files files scaled to 1 million mapped reads using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
Th peak calling was performed using MACS2 in narrowPeak mode.
Genome_build: UCSC GRCh38
Supplementary_files_format_and_content: bigWig, narrowPeak

source_name: TC28a2 cells transfected with HA-KLF4

value: transfected with HA-KLF4


title: Input

description: Sample 4 (05HAKLF4input_S98_L001_R1_001.fastq.gz)


title: Ad-KLF4_IL-1b(+)_7 [03exp3X3HUMxsample67adKLF4ilPOSrp7-5KLF4ILPOS]

description: 03exp3X3HUMxsample67adKLF4ilPOSrp7-5KLF4ILPOS_S0

data_processing:
library strategy: DRUG-seq
High-throughput RNAseq  library was sequenced on 100 cycle P2 flowcells with an Illumina NextSeq2000 sequencing instrument using paired-end sequencing (read1: 26 bases, read2: 94 bases, i5 and i8 indexes used 8 base reads).
A two-step demultiplexing was carried out: pooled libraries were demultiplexed using dual-index 8-base Illumina barcodes; then the individual samples from the pooled libraries were separated using 5'-end 10-base and 8-base inline barcodes on read1 and read2 respectively (BBTools; https://sourceforge.net/projects/bbmap/). The 3'-end 12-base UMI sequences from read1 were extracted using UMI-tools (Smith et al 2017, PMID: 28100584) and incorporated in read2 fastq as part of sequence ID.
The alignment ready, inline-barcode trimmed read2 fastq files (from the pre-deduplictated dataset) for 42 samples (made available as raw data files) were analyzed using nf-core/RNA-seq pipeline (v1.4.2 Ewels et al 2020, PMID: 32055031) written in the Nextflow domain specific language.
Adapter trimmed read2 were aligned to the reference genome using STAR v2.6.1d and gene abundance was estimated using featureCounts v1.6.4. Raw gene counts were then used to get differentially expressed genes using Bioconductor R package DESeq2 v1.20.0. Genes with BH- adjusted P-value <0.05 found by DESeq2 were assigned as significantly differentially expressed genes.
Genome_build: Ensembl GRCh38 release98
Supplementary_files_format_and_content: raw gene counts, Transcripts per million per sample; differentially expressed genes from DESeq2

source_name: Ad-KLF4-transduced TC28a2 cells with IL-1b stimulation

extract_protocol:
Total RNA was isolated with Direct-zol RNA MicroPrep kit (Zymo Research) according to manufacturer’s protocol.
Libraries were constructed using an early access High Throughput RNAseq Prep kit (Twist Bioscience).

tag: tag

value: with IL-1b stimulation


title: HA-CHIP_1

description: Sample 1 (01KLF4HAChIP1_S98_L001_R1_001.fastq.gz)


title: Ad-KLF4_IL-1b(+)_6 [03exp3X3HUMxsample66adKLF4ilPOSrp6-5KLF4ILPOS]

description: 03exp3X3HUMxsample66adKLF4ilPOSrp6-5KLF4ILPOS_S0


title: Ad-KLF4_IL-1b(+)_5 [03exp3X3HUMxsample65adKLF4ilPOSrp5-5KLF4ILPOS]

description: 03exp3X3HUMxsample65adKLF4ilPOSrp5-5KLF4ILPOS_S0


title: Ad-KLF4_IL-1b(+)_3 [03exp3X3HUMxsample63adKLF4ilPOSrp3-5KLF4ILPOS]

description: 03exp3X3HUMxsample63adKLF4ilPOSrp3-5KLF4ILPOS_S0


title: Ad-KLF4_IL-1b(+)_4 [03exp3X3HUMxsample64adKLF4ilPOSrp4-5KLF4ILPOS]

description: 03exp3X3HUMxsample64adKLF4ilPOSrp4-5KLF4ILPOS_S0


title: WT_-6hAPF_SG_RNA_Rep2

value: salivary gland


title: Ad-KLF4_IL-1b(+)_2 [03exp3X3HUMxsample62adKLF4ilPOSrp2-5KLF4ILPOS]

description: 03exp3X3HUMxsample62adKLF4ilPOSrp2-5KLF4ILPOS_S0


title: Ad-EGFP_IL-1b(+)_7 [03exp3X3HUMxsample53adEGFPilPOSrp7-4EGFPILPOS]

description: 03exp3X3HUMxsample53adEGFPilPOSrp7-4EGFPILPOS_S0

source_name: Ad-EGFP-transduced TC28a2 cells with IL-1b stimulation

value: Ad-EGFP-transduced


title: Ad-KLF4_IL-1b(+)_1 [03exp3X3HUMxsample61adKLF4ilPOSrp1-5KLF4ILPOS]

description: 03exp3X3HUMxsample61adKLF4ilPOSrp1-5KLF4ILPOS_S0


title: Ad-EGFP_IL-1b(+)_4 [03exp3X3HUMxsample50adEGFPilPOSrp4-4EGFPILPOS]

description: 03exp3X3HUMxsample50adEGFPilPOSrp4-4EGFPILPOS_S0


title: Ad-EGFP_IL-1b(+)_6 [03exp3X3HUMxsample52adEGFPilPOSrp6-4EGFPILPOS]

description: 03exp3X3HUMxsample52adEGFPilPOSrp6-4EGFPILPOS_S0


title: Ad-EGFP_IL-1b(+)_3 [03exp3X3HUMxsample49adEGFPilPOSrp3-4EGFPILPOS]

description: 03exp3X3HUMxsample49adEGFPilPOSrp3-4EGFPILPOS_S0