title: w1118, 4.5-5h, rep3

data_processing:
Quality check of the raw reads was done by FastQC v0.11.5, and subsequently mapped to the Drosophila melanogaster reference genome assembly dm6 using STAR v2.5.2b 2-pass mode, with guidance from the gene models of FlyBase Dmel Release 6.23.
Aligned reads were assigned to gene annotation using HTSeq-count version 0.10.
Differential gene expression was calculated using DESeq2. Genes were considered differentially expressed between genotypes and timepoints if they had an absolute log2FoldChange exceeding 1 and an adjusted p-value of less than 0.01.
Reads were normalized by scale factor using DESeq2.
Transcripts per kilobases million (TPM) were calculated by RSEM v1.3.1.
Assembly: dm6
Supplementary files format and content: tab-delimited text files include counts normalized by DESeq2 size factor; tab-delimited text files include TPM values for each sample

growth_protocol: Experimental design: Flies were raised on apple agar petri dishes in acrylic cages for 30 minutes for egg laying at 25°C, petri dishes were exchanged with new ones and embryos were further incubated at 25°C for 3.5, 4.5, 5.5 and 6.5 hours

extract_protocol:
Total RNA was prepared using Nugen Ovation Drosophila RNA-seq Systems in this process 80ng of RNA was used as input for cDNA preparation
cDNA fragmentation was performed using a Covaris S2 (duty factor 10%, cycle burst 200, intensity 5, 210s) sonicator

treatment_protocol: Embryos were washed with PBST and dechorionated in 50% bleach


title: Control fibroblast C33_biological replicate

status: Public on Dec 27 2022

type: SRA

city: Brescia

first: Nicola

last: Chiarelli

state: Lombardy

address: Viale Europa 11

department: Molecular and Translational Medicine

country: Italy

institute: University of Brescia

library_source: transcriptomic

data_processing:
Raw sequences were aligned and processed by Torrent Suite 5.12.3 according to standard analysis procedures. Output normalized counts (in read per milion) were generated (*.chp files ).   Differentially expressed genes (DEGs) were identified by using the Transcriptome Analysis Console (TAC) software (version 4.0.2) with the ampliSeqRNA plugin (Thermofisher Scientific) and applying an ANOVA test with a fold-change threshold of ±1.5 and an FDR-adjusted p-value ≤ 0.01.
Assembly: hg19_AmpliSeq_Transcriptome_21K_v1.transcript
Supplementary files format and content: Output normalized counts (in read per milion) were generated (*.chp files ).

molecule: total RNA

organism: Homo sapiens

source_name: dermis

growth_protocol: Control and patient fibroblasts were grown between 1st and 4th in vitro passage at 37 °C in a 5% CO2 atmosphere in Earle's Modified Eagle Medium supplemented with 2 mM L-glutamine, 10% FBS, and 100 µg/ml penicillin and streptomycin

extract_protocol:
Total RNA was purified from patient and control cells grown for 72 hours at 70-80% of confluency using the miRNeasy kit (Qiagen). Sample quality and quantity were evaluated with the Agilent 2100 Bioanalyzer (Agilent Technology) and the Qubit fluorometer (Thermofisher Scientific), respectively.
To improve statistical power, RNA samples from all experimental groups were sequenced twice as biological replicates (BR) (at the 2nd and 4th in vitro passage, respectively) plus 20 technical replicates (TR) for control fibroblasts and 10 for both hEDS and HSD cells. Reverse transcription and library preparation were achieved following the standard protocol of the Ion Ampliseq Transcriptome Human Gene Expression Kit (Thermofisher Scientific), which targets by multiplexed PCR 18,574 protein-coding and 2,228 non-coding RNAs (mRNAs/ncRNAs). Libraries were quantified with the Ion qPCR Library Quantification Kit, diluted to 100 pM and pooled equally, with 8 samples per pool, followed by emulsion PCR and enrichment with the Ion OneTouch2 with ES system. Libraries were then loaded onto an Ion 540 chip and sequenced on the Ion S5 instrument.
RNA-seq, targeted transcriptome sequencing

tag: tissue

value: dermis

tag: cell type

value: Skin fibroblasts

tag: disease

value: healthy donors

tag: disease state

value: unaffected


title: HisC, 4.5-5h, H3K27ac, rep2

city: Göttingen

first: Ufuk

last: Günesdogan

address: Justus-von-Liebig Weg 11

country: Germany

institute: University of Göttingen

library_source: genomic

data_processing:
Nextera Transposase adapter and low quality bases were eliminated using TrimGalore v0.6.6 and Cutadapt v1.17.
Reads were mapped to the Drosophila melanogaster reference genome dm6 (FlyBase Dmel Release 6.23) assembly using bowtie2 v2.3.4.2.
Mapped pairs were further filtered to maintain mapping quality above 10, as well as FR orientation concordant alignments, using custom scripts and samtools v1.9
PCR duplicates and mitochondrial reads were removed by sambamba v0.6.7 as well as reads blacklisted by the ENCODE project
NarrowPeak representation was used for histone marks H3K4me3, H2K27ac with following settings: -f BAMPE --keepdup all -p 5e-4 --call-summits. For histone marks enriched in broad domains including H3K36me3, H3K27me3, H2AK9ac, and H2BK16ac, the broadPeak representation was used applying following settings: -f BAMPE --keepdup all -p 5e-4 -b 0.01.
bigwig files required for coverage tracks as well as heatmaps were generated using Deeptools v3.3.1
Assembly: dm6
Supplementary files format and content: bigWig, bed containing peaks

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: whole embryo

growth_protocol: Experimental design: Flies were raised on apple agar petri dishes in acrylic cages for 30 minutes for egg laying at 25°C, petri dishes were exchanged with new ones and embryos were further incubated at 25°C for 3.5, 4.5 or 5.5 hours

extract_protocol:
Embryos were washed with PBST and dechorionated in 50% bleach, mutant embryos were identified by eYFP expression. Nuclei were extracted following Kaya-Okur et al., 2019
Libraries were constructed following Kaya-Okur et al., 2019, using the listed antibodies, libraries were generated using Epicypher 15-1017-EPC and 15-1018-EPC
CUT&Tag

treatment_protocol: Maintaining flies used for embryo collection: controlled light conditions (24h light on), new apple agar plates were provided with yeast twice a day, raised at 25°C

tag: cell line

value: whole embryo

value: Drosophila embryo 4.5-5h AEL

tag: genotype

value: Df(2L)HisC, P{GAL4-twi.2xPE}/ Df(2L)HisC, P{UAS:eYFP}AH2

tag: antibody

value: H3K27ac (Active Motif, #39134)


title: HisC, 4.5-5h, H3K27ac, rep1


title: M13-NT-Non-Targeting- rep1

city: Cambridge

first: Sarah

middle: J

last: Horton

state: Cambridgeshire

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute - Department of Haematology

country: United Kingdom

institute: University of Cambridge

data_processing:
Paired end RNA-seq reads were quality filtered and adapter sequences were trimmed using TrimGalore package.
Trimmed sequence reads were mapped using STAR version=2.7.10a against the human genome (Hg38). Uniquely-mapping, high confidence reads were retained using the following flags (NH:i:1 and MAPQ=255).
Read counts were quantified with HTSeq version 1.99.2
Assembly: hg38
Supplementary files format and content: BigWig files of uniquely mappable, high-confidence reads for display in Genome Browser created using genomeCoverageBed from BAM to bedGraph, followed by conversion to BigWig using bedGraphToBigWig
Supplementary files format and content: tab-delimited text files containing read counts for each gene (in ENSEMBL IDs)

source_name: MLL-AF9 positive MOLM13

extract_protocol:
Total RNA was extracted from cells using RNeasy Plus mini (QIAGEN) kit following manufacturer’s instructions.
libraries were prepared using Illumina kit (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, Cat# E7760S) with RiboZero depletion following manufacturer’s instructions. Libraries were sequenced on Hiseq platform with PE150 reads length.

value: MLL-AF9 positive MOLM13

value: AML cell line

tag: treatment

value: CRISPR-ko nontargeting (NT)


title: w1118, 3.5-4h, rep3

value: Drosophila embryo 3.5-4h AEL

tag: time


title: AML#4-Input

data_processing:
For ChIP-seq data, paired end reads were quality checked and adapter sequences were trimmed using TrimGalore package. CUT&RUN libraries were analysed using CUT&RUNTools v2.0 pipeline with default parameters.
ChIP-seq reads were aligned against human reference genome (Hg38) using Bowtie2.
Uniquely mapped reads were retained and peaks were called uing MACS v2 against input controls with the significance cut-off q-value (FDR) < 0.1/0.05.
Peaks were further filtered by removing blacklisted regions from Encode
Assembly: hg38
Supplementary files format and content: BigWig files of reads, normalised to counts-per-million (cpm) or scaled by library size, for display in Genome Browser created using genomeCoverageBed from BAM to bedGraph, followed by conversion to BigWig using bedGraphToBigWig.
Supplementary files format and content: narrowPeak (except for Input files) files generated by MACS2 against input controls at p-value 0.05 and FDR (q) values 0.05-0.1
Library strategy: CUT&RUN

source_name: primary AML cells

extract_protocol:
CUT&RUN was performed using CUTANA CUT&RUN kit (Epicypher) following manufacturer’s instructions. 100,000 MOLM13 cells were used for the assay for each antibody.
Libraries were prepared using 2ng of DNA using NEBNext UltraII DNA library preparation kit (Cat# E7645S, Illumina) and Dual index primer-Multiplex Oligos (Cat# E7600S, Illumina).

value: untreated

value: primary AML cells

tag: chip antibody


title: Control fibroblast C32


title: AML#5-Input

value: p53 loss


title: Control fibroblast C33


title: AML#2-Input


title: Control fibroblast C34_biological replicate


title: Control fibroblast C31_technical replicate


title: HisC, 6.5-7h, rep3

value: Drosophila embryo 6.5-7h AEL


title: Control fibroblast C31_biological replicate


title: Control fibroblast C32_biological replicate


title: AML#3-Input

value: Not available


title: w1118, 5.5-6h, H3K4me2, CUTAC, rep1

data_processing:
Nextera Transposase adapter and low quality bases were eliminated using TrimGalore v0.6.6 and Cutadapt v1.17.
Reads were mapped to the Drosophila melanogaster reference genome dm6 (FlyBase Dmel Release 6.23) assembly using bowtie2 v2.3.4.2.
Mapped pairs were further filtered to maintain mapping quality above 10, as well as FR orientation concordant alignments, using custom scripts and samtools v1.9
PCR duplicates and mitochondrial reads were removed by sambamba v0.6.7 as well as reads blacklisted by the ENCODE project
peaks were called using MACS2 v2.1.2 with following settings: -f BAMPE --keepdup all -p 5e-4
bigwig files required for coverage tracks as well as heatmaps were generated using Deeptools v3.3.1
Assembly: dm6
Supplementary files format and content: bigWig

growth_protocol: Experimental design: Flies were raised on apple agar petri dishes in acrylic cages for 30 minutes for egg laying at 25°C, petri dishes were exchanged with new ones and embryos were further incubated at 25°C for 4.5 and 5.5 hours

extract_protocol:
Embryos were washed with PBST and dechorionated in 50% bleach, mutant embryos were identified by eYFP expression. Nuclei were extracted following Henikoff et al., 2020
Libraries were constructed following Henikoff et al., 2020, using the listed antibodies, libraries were generated using Epicypher 15-1017-EPC and 15-1018-EPC
CUTAC

value: Drosophila embryo 5.5-6h AEL

value: H3K4me2(Active Motif #39142)


title: HisC, 5.5-6h, H3K4me2, CUTAC, rep2


title: HisC, 5.5-6h, rep3


title: w1118, 5.5-6h, H3K4me2, CUTAC, rep2


title: HisC, 5.5-6h, H3K4me2, CUTAC, rep1


title: AML#1-Input


title: w1118, 6.5-7h, rep3


title: w1118, 5.5-6h, rep3


title: HisC, 5.5-6h, H3K27ac, rep1


title: Control fibroblast C31

value: dermis

value: Skin fibroblasts

value: healthy donors


title: w1118, 6.5-7h, rep2

value: whole embryo


title: w1118, 4.5-5h, H3K4me2, CUTAC, rep2

value: Drosophila embryo 4.5-5h AEL


title: M13-HOXA9-Cr-rep3


title: Control fibroblast C30_biological replicate

value: unaffected


title: AML#5-SAFB

value: SAFB (Millipore)


title: w1118, 5.5-6h, rep2


title: w1118, 4.5-5h, H3K4me2, CUTAC, rep1


title: w1118, 4.5-5h, rep2


title: Control fibroblast C30


title: AML#5-HOXA9

value: HOXA9 (Atlas)


title: HisC, 4.5-5h, H3K4me2, CUTAC, rep2

value: Df(2L)HisC, P{GAL4-twi.2xPE}/ Df(2L)HisC, P{UAS:eYFP}AH2


title: HisC, 3.5-4h, rep3

value: Drosophila embryo 3.5-4h AEL


title: AML#4-MTA2

value: untreated

value: MTA2 (Bethyl)


title: Control fibroblast C29_biological replicate


title: Control fibroblast C29_technical replicate


title: AML#4-SAFB

value: primary AML cells


title: HisC, 6.5-7h, rep2

value: Drosophila embryo 6.5-7h AEL


title: HisC, 4.5-5h, H3K4me2, CUTAC, rep1


title: w1118, 3.5-4h, rep2


title: 2Cell, SER, RNA-seq, rep14

city: Boston

first: Qiangzong

last: Yin

state: MA

address: 3 Blackfan St, CLS building 440A

department: Medicine

country: USA

institute: BIDMC/Harvard Medical School

data_processing:
Raw fastq files were separated into 5′ end UMI-containing reads and internal reads based on the 11-bp tag sequence (ATTGCGCAATG). For the 5′ end reads, UMI sequence was extracted by UMI tools, followed by transcriptome alignment using STAR. Only unique mapping reads were kept, and PCR duplicates were removed by UMI tools. For the internal reads, read alignment was performed using STAR and deduplication was carried out by Picard. The resulting bam files from the 5′ end and internal reads were merged. Quantification of read counts was performed by using FeatureCounts, and batch-effect correction was performed using Combat-seq. Differential expressed genes were identified using DESeq2, using a multiple hypothesis-adjusted p value of 0.1.
Assembly: mm10
Supplementary files format and content: Raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: 2Cell embryo

growth_protocol: Mouse sperm samples were collected from 12–14-week-old C57BL/6J males (Jackson Laboratory, Farmington, CT, USA). Mouse cumulus–oocyte complexes (COCs) were collected from 8–10-week old super ovulated CD1 females (Charles River Laboratories, Wilmington, MA, USA). For superovulation, females were first injected with 7.5–10 IU of pregnant mare serum gonadotropin [PMSG] (Lee BioSolutions, cat # 493-10, Maryland Heights, MO, USA) followed by 7.5–10 IU of human chorionic gonadotrophin [hCG] (Sigma, cat #CG5, St. Louis, MO, USA) 48 h later. COCs were collected in TL-HEPES 13 h post hCG injection, then washed with IVF-TYH +/+ prior to allocating them in the insemination droplets. Insemination dishes were prepared prior (4, 90 µL droplets of IVF-TYH +/+ covered in mineral oil (Fisher Scientific, cat #0121, Waltham, MA, USA)) and equilibrated overnight at 37 °C in 5% CO2. COCs were added to a single droplet in the insemination dish. After collection and treatment of the sperm as described above, each dish was inseminated with approximately 100,000 sperm of either the control- or SER-treated sperm. Insemination dishes were placed back into the incubator and cocultured for 4 h. At 4 h postinsemination (HPI), oocytes were removed from the insemination droplets and washed through the remaining clean droplets of IVF-TYH +/+. Embryo culture dishes were prepared prior (five 50 µL droplets of KSOM covered in mineral oil) and equilibrated overnight at 37 °C in 5% CO2. Oocytes from each treatment group were moved into KSOM dishes for embryo culture. Control- and SER-generated 2Cell embryos were evaluated and collected at 32 HPI for RNA-seq.

extract_protocol:
2Cell embryos were washed with PBS and collected in lysis buffer without extraction of mRNA
Individual two-cell embryos were collected in a 1x TCL buffer (Qiagen) containing 1% beta-mercaptoethanol (Sigma). Total RNA were purified by 2.2x SPRI beads (Beckman) and the beads were resuspended in 6 µL of lysis buffer. Samples were incubated at 72 °C for 10 min and on ice afterwards. Next, 2 µL of reverse transcription mix were added to each sample. Reverse transcription and template switching were carried out at 42 °C for 90 min, then 10 cycles of 50 °C for 2 min, and 42 °C for 2 min, and 85 °C for 5 min. PCR preamplification was performed by adding 12 µL of PCR mix. PCR was conducted as follows: 3 min at 98 °C, 19 cycles of 20 s at 98 °C, 30 s at 65 °C, 6 min at 72 °C, and 5 min at 72 °C. PCR product was purified by 0.8x SPRI beads and eluted in nuclease-free water. Purified cDNA was quality checked by a bioanalyzer and quantified using Qubit 1X dsDNA HS Assay Kit (Thermo Fisher Scientific). Sequence libraries were prepared using Illumina Nextera XT DNA Library Prep kit (Illumina). Libraries were sequenced at paired end (45 bp for read 1 and 30 bp for read 2) 30-bp on an Illumina NextSeq500 instrument.

treatment_protocol: Mice were euthanized by exposure to carbon dioxide (CO2). Then, cauda epididymides were dissected and collected into corresponding IVF-TYH media according to the treatment. One cauda was added to IVF-TYH +/+ (control) and the other was added to IVF-TYH −/− (SER). Sperm were recovered in each condition obtained by the “swim-out” method for 10 min, followed by the removal of the cauda tissue. Briefly, the samples were centrifuged for 5 min at 270× g at room temperature. For each treatment, supernatant was removed, and 1 mL of the appropriate medium (either IVF-TYH +/+ or −/−) was added to the sperm pellet followed by an additional centrifugation for 5 min at 150× g at room temperature. The supernatants were removed, and 1 mL of the corresponding medium was added to each treatment (IVF-TYH +/+ or −/−). The sperm were incubated at 37 °C in 5% CO2 until motility of the sperm incubated in the IVF-TYH −/− was lost (between 15 and 45 min). Upon loss of motility, both control and starved sperm were recovered with the addition of 1 mL of IVF-TYH +/+ media (recovery step in which the IVF-TYH −/− sperm are exposed to nutrients glucose and pyruvate) and centrifuged for 5 min at 150× g at room temperature. The supernatants were removed, and each tube was resuspended to 1 mL with IVF-TYH +/+ media. Sperm were immediately used for insemination of cumulus–oocyte complexes (COCs) as detailed in the in vitro fertilization section below.

value: 2Cell embryo

value: WT

value: SER


title: 2Cell, SER, RNA-seq, rep15


title: Control fibroblast C28_biological replicate

value: dermis


title: Control fibroblast C29

value: Skin fibroblasts


title: HisC, 4.5-5h, rep2


title: 2Cell, SER, RNA-seq, rep13


title: AML#3-HP1g

value: Not available

value: CBX3 (Bethyl)


title: Control fibroblast C28

value: healthy donors


title: AML#3-GATAD2A

value: GATAD2A (Bethyl)


title: HisC, 3.5-4h, rep2

value: whole embryo


title: 2Cell, SER, RNA-seq, rep12


title: AML#3-MTA2


title: Control fibroblast C27_biological replicate

value: unaffected


title: w1118, 6.5-7h, rep1


title: 2Cell, SER, RNA-seq, rep11


title: AML#3-SAFB

value: SAFB (Millipore)


title: Control fibroblast C27


title: w1118, 5.5-6h, rep1

value: Drosophila embryo 5.5-6h AEL


title: w1118, 4.5-5h, rep1

value: Drosophila embryo 4.5-5h AEL


title: 2Cell, SER, RNA-seq, rep10


title: HisC, 5.5-6h, rep2

value: Df(2L)HisC, P{GAL4-twi.2xPE}/ Df(2L)HisC, P{UAS:eYFP}AH2


title: AML#3-HOXA9

value: untreated

value: primary AML cells

value: HOXA9 (Atlas)


title: 2Cell, SER, RNA-seq, rep9

value: 2Cell embryo

value: WT


title: AML#4-HOXA9


title: Control fibroblast C26_technical replicate

value: dermis


title: AML#2-GATAD2A

value: p53 loss


title: AML#2-HP1g


title: w1118, 3.5-4h, rep1

value: Drosophila embryo 3.5-4h AEL


title: AML#2-MTA2

value: MTA2 (Bethyl)


title: Control fibroblast C25_biological replicate

value: Skin fibroblasts

value: healthy donors


title: HisC, 6.5-7h, rep1

value: whole embryo

value: Drosophila embryo 6.5-7h AEL


title: Control fibroblast C26

value: unaffected


title: 2Cell, SER, RNA-seq, rep7

value: SER


title: HisC, 5.5-6h, rep1

value: Drosophila embryo 5.5-6h AEL


title: Control fibroblast C25


title: AML#2-SAFB

value: SAFB (Millipore)


title: HisC, 4.5-5h, rep1

value: Drosophila embryo 4.5-5h AEL

value: Df(2L)HisC, P{GAL4-twi.2xPE}/ Df(2L)HisC, P{UAS:eYFP}AH2


title: 2Cell, SER, RNA-seq, rep5


title: AML#2-HOXA9

value: untreated

value: primary AML cells

value: HOXA9 (Atlas)


title: 2Cell, SER, RNA-seq, rep6

value: 2Cell embryo

value: WT


title: Control fibroblast C24_technical replicate

value: dermis


title: Control fibroblast C24_biological replicate


title: 2Cell, SER, RNA-seq, rep8


title: Control fibroblast C26_biological replicate


title: 2Cell, SER, RNA-seq, rep4


title: HisC, 3.5-4h, rep1

value: Drosophila embryo 3.5-4h AEL


title: Control fibroblast C24

value: Skin fibroblasts


title: AML#1-HP1g

value: CBX3 (Bethyl)


title: 2Cell, SER, RNA-seq, rep3


title: AML#1-MTA2

value: MTA2 (Bethyl)


title: AML#1-SAFB


title: Control fibroblast C23

value: healthy donors


title: 2Cell, SER, RNA-seq, rep1


title: Control fibroblast C23_biological replicate

value: unaffected


title: 2Cell, SER, RNA-seq, rep2

value: SER


title: Control fibroblast C22_biological replicate


title: Control fibroblast C22_technical replicate


title: Control fibroblast C22


title: 2Cell, control, RNA-seq, rep14

value: control


title: 2Cell, control, RNA-seq, rep15


title: w1118, 7.5-7h, ATACseq, rep3

data_processing:
Nextera Transposase adapter and low quality bases were eliminated using TrimGalore v0.6.6 and Cutadapt v1.17.
Reads were mapped to the Drosophila melanogaster reference genome dm6 (FlyBase Dmel Release 6.23) assembly using bowtie2 v2.3.4.2.
Mapped pairs were further filtered to maintain mapping quality above 10, as well as FR orientation concordant alignments, using custom scripts and samtools v1.9
PCR duplicates and mitochondrial reads were removed by sambamba v0.6.7 as well as reads blacklisted by the ENCODE project
Peaks of accessible chromatin were identified for each sample using MACS2 v2.1.2 with the following settings: -f BED --nomodel --shift -100 --extsize 200 --keep-dup all after converting the bam to bed file
Assembly: dm6
Supplementary files format and content: bigWig

extract_protocol:
Embryos were washed with PBST and dechorionated in 50% bleach, mutant embryos were identified by eYFP expression. Nuclei were extracted following Buenrostro et al., 2015
Libraries were constructed following Buenrostro et al., 2015 using NEB Hifi 2x PCR master mix M0541S

value: whole embryo

value: Drosophila embryo 6.5-7h AEL


title: M13-Wt Input

value: shRNA kd-EV-pLKO

value: MLL-AF9 positive MOLM13


title: 2Cell, control, RNA-seq, rep13


title: Control fibroblast C21_technical replicate


title: M13-SAFBkd HP1g

value: shRNA kd-SAFBpLKO-4ddox


title: HisC, 7.5-7h, ATACseq, rep3

value: Df(2L)HisC, P{GAL4-twi.2xPE}/ Df(2L)HisC, P{UAS:eYFP}AH2


title: AML#1-GATAD2A

value: untreated

value: primary AML cells

value: GATAD2A (Bethyl)


title: Control fibroblast C21_biological replicate

value: dermis


title: AML#1-HOXA9

value: HOXA9 (Atlas)


title: 2Cell, control, RNA-seq, rep12

value: 2Cell embryo

value: WT


title: w1118, 7.5-7h, ATACseq, rep2


title: HisC, 7.5-7h, ATACseq, rep2


title: 2Cell, control, RNA-seq, rep10


title: M13-Wt HP1g

value: CBX3 (Bethyl)


title: M13-SAFBkd MTA2

value: MTA2 (Bethyl)


title: 2Cell, control, RNA-seq, rep16


title: Control fibroblast C20_biological replicate

value: Skin fibroblasts

value: healthy donors

value: unaffected


title: 2Cell, control, RNA-seq, rep11

value: control


title: Control fibroblast C21


title: 2Cell, control, RNA-seq, rep9


title: Control fibroblast C20


title: M13-SAFBkd Input


title: w1118, 7.5-7h, ATACseq, rep1

value: whole embryo

value: Drosophila embryo 6.5-7h AEL


title: M13-Wt MTA2

value: shRNA kd-EV-pLKO

value: MLL-AF9 positive MOLM13


title: HisC, 7.5-7h, ATACseq, rep1

value: Df(2L)HisC, P{GAL4-twi.2xPE}/ Df(2L)HisC, P{UAS:eYFP}AH2


title: M13-SAFBkd BRD4

value: shRNA kd-SAFBpLKO-4ddox

value: BRD4 (Bethyl)


title: Control fibroblast C19_biological replicate

value: dermis


title: M13-Wt BRD4


title: 2Cell, control, RNA-seq, rep8


title: w1118, 5.5-6h, ATACseq, rep3

value: Drosophila embryo 5.5-6h AEL


title: 2Cell, control, RNA-seq, rep7

value: 2Cell embryo


title: Control fibroblast C19


title: M13-SAFBkd ChIP-input

data_processing:
For ChIP-seq data, paired end reads were quality checked and adapter sequences were trimmed using TrimGalore package. CUT&RUN libraries were analysed using CUT&RUNTools v2.0 pipeline with default parameters.
ChIP-seq reads were aligned against human reference genome (Hg38) using Bowtie2.
Uniquely mapped reads were retained and peaks were called uing MACS v2 against input controls with the significance cut-off q-value (FDR) < 0.1/0.05.
Peaks were further filtered by removing blacklisted regions from Encode
Assembly: hg38
Supplementary files format and content: BigWig files of reads, normalised to counts-per-million (cpm) or scaled by library size, for display in Genome Browser created using genomeCoverageBed from BAM to bedGraph, followed by conversion to BigWig using bedGraphToBigWig.
Supplementary files format and content: narrowPeak (except for Input files) files generated by MACS2 against input controls at p-value 0.05 and FDR (q) values 0.05-0.1


title: Control fibroblast C18_technical replicate


title: M13-MEIS1

value: untreated

value: MEIS1 (Atlas)


title: 2Cell, control, RNA-seq, rep6

value: WT


title: 2Cell, control, RNA-seq, rep5


title: w1118, 5.5-6h, ATACseq, rep2


title: HisC, 5.5-6h, ATACseq, rep2


title: Control fibroblast C18_biological replicate

value: Skin fibroblasts


title: w1118, 5.5-6h, ATACseq, rep1


title: Control fibroblast C18

value: healthy donors


title: 2Cell, control, RNA-seq, rep4


title: M13-Wt ChIP-input


title: HisC, 5.5-6h, ATACseq, rep1


title: Control fibroblast C17

value: unaffected


title: Control fibroblast C17_biological replicate


title: 2Cell, control, RNA-seq, rep3

value: control


title: 2Cell, control, RNA-seq, rep2


title: M13-SAFBkd H3K27ac

value: H3K27ac (Active motif)


title: w1118, 4.5-5h, ATACseq, rep3

value: whole embryo

value: Drosophila embryo 4.5-5h AEL


title: HisC, 5.5-6h, ATACseq, rep3


title: M13-H3K9me3-rep2

value: MLL-AF9 positive MOLM13

value: H3K9me3 (Abcam)


title: M13-Input


title: Control fibroblast C16_technical replicate


title: HisC, 4.5-5h, ATACseq, rep3

value: Df(2L)HisC, P{GAL4-twi.2xPE}/ Df(2L)HisC, P{UAS:eYFP}AH2


title: M13-H3K9me2-rep1


title: Control fibroblast C16


title: M13-H3K27me3-rep1

value: H3K27me3 (CellSignaling)


title: native XX MII oocytes rep2

city: Fukuoka

first: Kenta

last: Murakami

address: 3-1-1, Maidashi, Higashi-ku

department: Stem Cell Biology and Medicine

country: Japan

institute: Kyushu University

data_processing:
Adaptor sequences and low-quality bases were trimmed with Trimmomatic v.0.38 (ILLUMINACLIP: 2: 30: 10 SLIDINGWINDOW: 4: 15 LEADING: 20 TRAILING: 20 MINLEN: 30).
The processed reads were mapped to mouse genome (mm10) using HISAT2 v.2.1.0.
The number of reads mapped to each gene was counted with featureCounts v.2.0.0.
Differential gene expression analysis was done using DESeq2 v.1.30.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each sample.

source_name: in vitro MII oocytes

growth_protocol: ESCs harboring Blimp1-mVenus (BV) and Stella-ECFP (SC) reporter transgenes were maintained under a 2i/LIF condition without feeder cells .PGCLC induction was performed as described previously (Hayashi et al., 2013). PGCLCs were purified by FACS and aggregated with embryonic day (E) 12.5 female gonadal somatic cells in a low-binding U-bottom 96-well plate (NUNC or Greiner) for two days of culture in GK 15 containing 1 µM retinoic acid (Sigma) and 10 µM Y27632 (Wako). 5,000 PGCLCs and 75,000 gonadal somatic cells were cultured to form one reconstituted ovary (rOvary). IVDi culture was performed as described previously (Hayashi et al., 2017). At day 21 of IVDi culture, individual secondary follicles were manually dissociated using a sharpened tungsten needle in IVG manipulation medium (αMEM (Gibco or nacalai tesque) supplemented with 5% FCS, 1× penicillin/streptomycin, and 20mM HEPES (Gibco)). The isolated secondary follicles on the Transwell-COL membranes were soaked in IVG medium (αMEM supplemented with 5% FCS, 2% polyvinylpyrrolidone (Sigma), 150 µM ascorbic acid, 1× GlutaMAX, 1× penicillin/streptomycin, 100 µM 2-mercapthoethanol, 55µg/ml sodium pyruvate (nacalai tesque), 0.1IU/ml FSH (Merck)) with 15 ng/ml BMP15 (R&D Systems) and 15 ng/ml GDF9 (R&D Systems)). At day 2 of culture, BMP15 and GDF9 were withdrawn from the medium and the follicles were incubated in 0.1% collagenase type I (Worthington Biochemical Corporation) for 10 min at 37°C, washed three times with αMEM supplemented with 5% FCS, and cultured in IVG medium.. At day 3 of culture, IVG medium was added to cover the follicles. In the following culture, medium was changed every other day. At day 11 of culture, cumulus-oocyte complexes (COCs) grown on the membrane were collected by a fine glass capillary and were transferred to IVM medium (αMEM supplemented with 5% FCS, 25 µg/ml sodium pyruvate, 1× penicillin/streptomycin, 0.1 IU/ml FSH, 4 ng/ml EGF and 1.2 IU/ml hCG (ASKA)) and cultured for 16h.

extract_protocol:
PolyA+ RNAs were purified from oocytes (GV: 31-158; MII: 35-58), using a Dynabeads mRNA DIRECT Micro Kit (Invitrogen). Biologically duplicated samples in each stage were prepared.
Purified RNAs were subjected to library preparation using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). cDNAs were amplified by 13-cycle PCR. The libraries were sequenced on NextSeq 500 (75 bp single, Illumina).

treatment_protocol: For GV oocytes, COCs collected at day11 of IVG were incubated in CTK (1 µM CaCl2, 0.1mg/ml collagenase type IV (MP Biomedicals), 20% KSR (Gibco) and 0.025% trypsin EDTA (Gibco)) with 0.2 mM dibutyryl-cAMP (dbcAMP) (Sigma) and 0.1mM 3-Isobutyl-1-methylxanthine (IBMX) for 20 min at 37°C and in Accutase (nacalai tesque) with dbcAMP and IBMX for 15 min at 37°C. COCs were transferred to IVG manipulation medium supplemented with dbcAMP and IBMX and cumulus cells were strictly removed using a fine glass capillary. SC-positive oocytes were collected using a fluorescent microscope.For MII oocytes, at 16 h of IVM culture, COCs were picked up and swollen cumulus cells were stripped from the oocytes by treating with hyaluronidase (Sigma) and MII oocytes were determined by first polar body. SC-positive oocytes were collected using a fluorescent microscope.

value: ES-derived MII oocytes

tag: strain


title: native XX MII oocytes rep1


title: w1118, 4.5-5h, ATACseq, rep1


title: M13-Hp1g-rep2

value: CBX3 (Bethyl)


title: M13-Wt H3K27ac

value: shRNA kd-EV-pLKO


title: sex converted XX MII oocytes rep2


title: M13-HP1g-rep1

value: untreated


title: HisC, 4.5-5h, ATACseq, rep1


title: Control fibroblast C15

value: dermis


title: sex converted XX MII oocytes rep1


title: native XX GV oocytes rep2

source_name: in vitro GV oocytes

value: ES-derived GV oocytes


title: M13-GATAD2A-rep2

value: GATAD2A (Bethyl)


title: 2Cell, control, RNA-seq, rep1

value: 2Cell embryo

value: WT


title: HisC, 3.5-4h, ATACseq, rep3

value: Drosophila embryo 3.5-4h AEL


title: M13-GATAD2A-rep1


title: Control fibroblast C14_technical replicate

value: Skin fibroblasts

value: healthy donors

value: unaffected


title: native XX GV oocytes rep1


title: Control fibroblast C14_biological replicate


title: M13-MTA2-rep2

value: MLL-AF9 positive MOLM13

value: MTA2 (Bethyl)


title: w1118, 3.5-4h, ATACseq, rep3

value: whole embryo


title: Control fibroblast C14


title: Control fibroblast C16_biological replicate


title: w1118, 4.5-5h, ATACseq, rep2

value: Drosophila embryo 4.5-5h AEL


title: HisC, 4.5-5h, ATACseq, rep2

value: Df(2L)HisC, P{GAL4-twi.2xPE}/ Df(2L)HisC, P{UAS:eYFP}AH2


title: w1118, 3.5-4h, ATACseq, rep2


title: single cell murine FTE cells and OSE cells

first: Zhe

last: Li

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

data_processing:
Sample demultiplexing, barcode processing, and single cell gene counting were performed by using the in-house pipeline of Harvard Medical School Single Cell Core and Harvard Chan Bioinformatics Core.
Genome_build: mm10
Supplementary_files_format_and_content: mtx file with genes and cell barcode sequences

source_name: Cells from the stripped ovarian surface layer and cells from the distal half of fallopian tube

extract_protocol:
To isolate fallopian tube (FT) cells, the distal portion of FT was dissected, minced, and enzymatically digested. After the enzymatic reaction, FT cells were passed through a 40 um cell strainer to achieve a single cell suspension. To isolate ovarian surface (OS) cells, ovaries were dissected and incubated with Trypsin-EDTA to strip OS cells. Stripped OS cells were then passed through 100 um and followed by 40 um cell strainers to achieve a single cell suspension.
Barcoded single cell RNA-seq library was generated by the Harvard Medical School Single Cell Core (https://singlecellcore.hms.harvard.edu/), following the instructions of the InDrop Design V3.

value: multiplexed sample:Ovary (surface layer) or Fallopian tube (Oviduct, distal half)

tag: condition

value: Adult

value: Wild-type

value: FVB genetic background


title: M13-MTA2-rep1

value: untreated


title: Control fibroblast C13_biological replicate

value: dermis


title: HisC, 3.5-4h, ATACseq, rep2


title: sex converted XX GV oocytes rep2

value: ES-derived GV oocytes


title: Control fibroblast C15_biological replicate


title: w1118, 3.5-4h, ATACseq, rep1


title: M13-SAFB-rep2

value: SAFB (Millipore)


title: Control fibroblast C13


title: sex converted XX GV oocytes rep1


title: c24.8

city: Tel-Aviv

first: Gal

last: Yankovitz

address: Haim Levanon

department: The Shmunis School of Biomedicine and Cancer Research

country: Israel

institute: Tel-Aviv University

data_processing:
bcl2fastq/2.15.0.4 software used for basecalling.
Reads were aligned using the HISAT aligner to the mouse reference genome (NCBI 37, mm9).
Expression levels of the list of mouse genes were then calculated and normalized by the total number of mapped reads per experiment, using HOMMER with the default parameters.
Recorded are those reads that were mapped to mouse gene exons (using the UCSC transcript annotation).
Reads that were mapped to multiple positions were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: The tab-delimited text file includes normalized reads by the total number of mapped reads.

source_name: Lungs

extract_protocol:
Murine lungs were harvested immediately after the time of sacrifice, sliced into small pieces, homogenized using BeadBlaster Microtube Homogenizer (90sec, 4000rpm) in the presence of QIAzol, and used for total RNA extraction using the miRNeasy Mini Kit.
For the preparation of RNA‐Seq libraries, total RNA was fragmented into average size of 300 nucleotides by chemical heat (95°C) treatment for 4:30 min (NEBNext Magnesium RNA Fragmentation Module). The 3′ polyadenylated fragments were enriched by selection on poly dT beads (Dynabeads Invitrogen). Strand‐specific cDNA was synthesized using a poly T‐VN oligo (18 T) and Affinity Script RT enzyme (Agilent). Double‐strand DNA was obtained using Second strand synthesis kit (NEB). DNA ends were repaired using T4 polynucleotide kinase and T4 polymerase (NEB‐Next). After the addition of an adenine base residue to the 5′ end using Klenow enzyme (NEB‐Next), a barcode Illumina compatible adaptor (IDT) was ligated to each fragment. The washed DNA fragment was amplified by PCR (12 cycles) using specific primers (IDT) to the ligated adaptors. The quality of each library was analyzed by TapeStation (Agilent).

value: Lungs

value: flu

tag: %weight difference


title: HisC, 3.5-4h, ATACseq, rep1

value: Drosophila embryo 3.5-4h AEL


title: M13-SAFB-rep1


title: c24.7


title: C21.2


title: M13-HOXA9-rep2

value: HOXA9 (Atlas)


title: Control fibroblast C12_biological replicate

value: Skin fibroblasts

value: healthy donors

value: unaffected


title: M13-HOXA9-rep1

value: MLL-AF9 positive MOLM13


title: Control fibroblast C12


title: Control fibroblast C11_technical replicate


title: C17.8


title: Control fibroblast C11_biological replicate


title: C17.7


title: Control fibroblast C11


title: snRNAseq_JW21_meninges_infected_RP1

city: Baltimore

first: Amir

last: Rattner

state: MD - Maryland

address: 725 North Wolfe St.

institute: Johns Hopkins University

library_source: transcriptomic single cell

data_processing:
Reads were aligned to a mm10 pre-mRNA index using Cellranger version 3.1.0.  Libraries were merged using Cellranger and data was analyzed using the Seurat R package.
Assembly: mm10

source_name: P6 meninges

extract_protocol: Postnatal day 6 FVB/JN mouse, an uninfected littermate was sacrificed. The dura and arachnoid were rapidly dissected in ice-cold DPBS. The tissue was minced with a razor blade and Dounce homogenized using a loose-fitting pestle in 5 ml of homogenization buffer supplemented with 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, and EDTA-free protease inhibitor (Roche 11 836 170 001), and 60 U/mL RNasin Plus RNase Inhibitor (Promega N2611).  A 5% IGEPAL-630 solution was added to bring the homogenate to 0.3% IGEPAL-630, and the homogenate was further homogenized with five strokes of a tight-fitting pestle.  The sample was filtered through a 50 μm filter (CellTrix, Sysmex, 04-004-2327), underlayed with solutions of 30% and 40% iodixanol in homogenization buffer (Sigma D1556), and centrifuged at 10,000 x g for 18 minutes in a swinging bucket centrifuge at 4°C.  Nuclei were collected at the 30%-40% interface, diluted with 2 volumes of homogenization buffer and concentrated by centrifugation for 10 min at 0.5 x g at 4°C.  snRNA-seq sequencing libraries were constructed using the 10X Genomics Chromium single cell 3’ v3 kit.

value: FVB

value: meninges

tag: age

value: WT

value: infected


title: snRNAseq_JW19_meninges_control_RP1

value: control


title: snRNAseq_JW23_meninges_infected_RP3


title: snRNAseq_JW22_meninges_infected_RP2


title: snRNAseq_JW20_meninges_control_RP2


title: C25.4


title: Control fibroblast C12_technical replicate


title: Control fibroblast C10_technical replicate


title: Control fibroblast C10_biological replicate


title: C25.3


title: C20.8


title: C21.1


title: Control fibroblast C9_biological replicate


title: c24.4


title: CTEPH PASMC-1, PDGF+MRE269-3

city: Kyoto

first: Kazuya

last: Kuramoto

address: 14, Nishinosho-Monguchi-cho, Kisshoin, Minami-ku

department: R&D Administration Dept.

institute: Nippon Shinyaku Co., Ltd.

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (parameter- LEADING=20, TRALING=20, SLIDINGWINDOW=4:15, MINLEN=36)
Trimmed sequence reads were mapped to hg38 using HISAT2
Read count extraction and normalization were performed using featureCounts
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: lung

growth_protocol: pulmonary arterial smooth muscle cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from the attached cells the next day using the NucleoSpin RNA or NucleoSpin RNA Plus XS (Takara Bio) according to the manufacturer’s protocol.
Libraries were then prepared using the NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: For analyzing the effect of MRE-269 on gene expression, cell growth was arrested by incubation in starvation medium for 48 h. The cells were then incubated for 24 h in starvation medium containing 0.1% dimethyl sulfoxide (DMSO), 10 ng/mL recombinant platelet derived growth factor-BB (PDGF) with 0.1% DMSO, or 10 ng/mL PDGF with 1 μmol/L MRE-269.

value: lung

value: pulmonary arterial smooth muscle cells

value: vascular smooth muscle cells

value: CTEPH

value: 10 ng/mL PDGF with 1 μmol/L MRE-269


title: CTEPH PASMC-1, PDGF+MRE269-1


title: CTEPH PASMC-1, PDGF-3

value: 10 ng/mL recombinant platelet derived growth factor-BB with 0.1% DMSO


title: CTEPH PASMC-1, PDGF-2


title: CTEPH PASMC-1, vehicle-2

value: 0.1% DMSO


title: Control fibroblast C9

value: dermis


title: CTEPH PASMC-1, PDGF+MRE269-2


title: c24.3

value: Lungs

value: flu


title: C20.7


title: CTEPH PASMC-1, vehicle-3


title: Control fibroblast C8_biological replicate

value: Skin fibroblasts

value: healthy donors

value: unaffected


title: Control fibroblast C7_technical replicate


title: CTEPH PASMC-1, vehicle-1


title: CTEPH PASMC-3

value: growth condition


title: C20.5


title: CTEPH PASMC-2

value: WT


title: CTEPH PASMC-1


title: C19.6


title: Control fibroblast C8


title: C19.5


title: normal PASMC-3

value: normal


title: CTEPH PASMC-1, PDGF-1


title: Control fibroblast C7


title: Control fibroblast C7_biological replicate


title: C23.6


title: Control fibroblast C10


title: normal PASMC-2


title: normal PASMC-1


title: Control fibroblast C6_biological replicate


title: Control fibroblast C6


title: C18.8


title: C22.6


title: C22.5


title: Control fibroblast C5_technical replicate


title: Control fibroblast C5


title: C23.5


title: Control fibroblast C5_biological replicate


title: Control fibroblast C4_technical replicate


title: scATAC-seq_KO

city: Beijing

first: Yuling

address: 30 ShuangQing Street

department: Institute for Immunology and School of Medicine,

country: China

institute: Tsinghua University

library_source: genomic single cell

data_processing:
Libraries were sequenced on an Illumina NovaSeq PE50 (Noveogene) to a depth of around 260 million reads per sample (approximately 5,000 cells per sample) with paired-end reads according to the recommendations by 10x Genomics.
Analysis performed with Cell Ranger.
Supplementary files format and content: Excel/ filtered gene score data for each cluster of the total intestinal ILC (relative to Figure S5A)

source_name: Intestinal total ILC

extract_protocol:
Cells were tested for live conditions and then washed and lysed for 3 min on ice according to the low input protocol recommendations by 10x Genomics (CG000169-Rev C).
For library preparation, the 10x Genomics Chromium Controller and the 10x Genomics Chromium Single Cell ATAC Library & Gel Bead Kit (1000111) were used according to the manufacturer’s instructions (CG000168-Rev B).

value: Vav1^cre Bcl6^fl/fl

tag: source

value: Total Intestine LP


title: Control fibroblast C4


title: KO, TNFalpha-treated, biol replicate 2, scRNAseq

city: New York

first: Judy

last: Cho

state: NY

address: 1470 Madison Avenue, 8th Fl., Box 1498;

department: Pathology, Molecular and Cell-Based Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
FASTQ were demultiplexed using Cell Ranger 3.1.0 and aligned to the mm10 mice genome
Cell barcodes and unique molecular identifiers (UMIs) were extracted and “Raw” UMI matrix generated for each sample
Extracted cell-barcodes associated with at least ,500 UMIs, and a maximum of 60000 UMIs from the “Raw” output UMI matrices of CellRanger
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Colon

growth_protocol: Mice colonoids were cultured in 37 C incubator with 5% CO2 until colonoids were subject for cell dissociation

extract_protocol:
Untreated and treated colonid were subject to cell dissociation with TrypLE to generate single cell suspension. Live cell % had to exceed 65% to load suspension into 10X Chromium gel beads
Library construction was performed according to 10X Genomics v3 chemistry kits suggested protocol.

treatment_protocol: Mice organoid were treated with or without TNF ⍺ in culture medium (25%WRN+20uM DAPT+5uM Y27632) for 48 hours.

value: Colon

value: colonoid

value: epithelial cells

value: Nox1 knockout

value: TNFalpha-treated

value: IBD inflammation model


title: C20.6


title: Control fibroblast C4_biological replicate

value: dermis


title: KO, untreated, biol replicate 2, scRNAseq

value: untreated

value: control


title: Control fibroblast C3_technical replicate

value: Skin fibroblasts


title: RIP_SW480

city: Nanjing

first: Chi

last: Jin

address: Han Zhong Road

institute: Nanjing university school

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
Cutadapt (v2.5) was used to trim adapters and filter for sequences, remaining reads were then aligned to the human Ensemble genome GRCh38 (mouse Ensemble genome GRCm38) using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”. ac4C peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include RPKM values or peaks for each sample.

growth_protocol: DLD-1 and SW480 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018). The concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). For RNA-protein immunoprecipitation, cells were lysed by IP lysis buffer according to the manufacturer's protocol.  Acetylated RNA immunoprecipitation was performed using EpiTM ac4C immunoprecipitation kit (Epibiotek, R1815). RNA immunoprecipitation was performed using EpiTM RNA immunoprecipitation kit (Epibiotek, cat. no R1819).
The library was prepared by EpiTM mini longRNA-seq kit (Epibiotek, E1802) following manufacturer's protocols.

value: Human colorectal cancer cell

tag: sample type

value: IP RNA


title: Control fibroblast C3_biological replicate

value: healthy donors

value: unaffected


title: acRIP_DLD-1

value: WT

value: ac4C RNA


title: C18.7

value: Lungs

value: flu


title: KO, TNFalpha-treated, biol replicate 1, scRNAseq

value: Colon

value: colonoid


title: Control fibroblast C2_technical replicate


title: Control fibroblast C3


title: Input_DLD-1

value: total RNA


title: WT, TNFalpha-treated, biol replicate 2, scRNAseq

value: epithelial cells

value: Nox1 wildtype

value: TNFalpha-treated


title: Control fibroblast C2_biological replicate

value: dermis


title: PDAC1 with HNF1B overxpression for ChIP-seq (H3K27ac)

city: Tokyo

first: Keisuke

last: Tateishi

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Gastroenterology

institute: Graduate School of Medicine, The University of Tokyo

data_processing:
For CTCF ChIP-seq, peaks against input control were called using MACS2 with a parameter -q 0.01.
Reads for each peak were extracted using featureCounts. Input counts were extracted from CTCF ChIP counts with negative values being set to zero. These counts were normalized by edgeR giving log2CPM.
Fold enrichment signal against input was calculated using bdgcmp command in MACS2 to create bedgraph file followed by conversion into bigwig file using bedGraphToBigwig command. Bigwig file was further adjusted using scaling factor obtained from edgeR TMM normalization.
To focus on the HNF1B induced modification in HNF1B and H3K27ac ChIP-seq experiments, reads at HNF1B peak elements were taken into account using featureCounts. These counts were normalized by edgeR giving log2 fold change signals (HNF1B and H3K27ac) of HNF1B overexpressed cells over empty control.
Assembly: hg19
Supplementary files format and content: narrowPeak, bigWig
Supplementary files format and content: txt file for ChIP signal at each peak element

source_name: PDAC1 organoid

growth_protocol: Organoids were coated in Matrigel (Corning) and cultured as described previously (PMID: 34953915).

extract_protocol:
Cells from organoids were crosslinked with 1% formaldehyde for 10 minutes at room temperature and quenched using glycine. Extracted DNA was fragmented using ultrasonication (Bioruptor UCD-250) and immunoprecipitated using antibodies denoted.
Sequencing library was prepared using SMARTer ThruPLEX Tag-seq 6S Kit (Takara) and was sequenced using NextSeq500 (Illumina) with single-end 75 bp reads.

value: PDAC1 organoid

value: Pancreatic ductal adenocarcinoma

value: HNF1B overexpression

value: H3K27ac (Abcam, ab4729)


title: acRIP_SW480

value: Human colorectal cancer cell


title: PDAC1 with HNF1B overxpression for ChIP-seq (HNF1B)

value: HNF1B (Sigma, HPA002083)


title: KO, untreated, biol replicate 1, scRNAseq

value: Nox1 knockout

value: untreated

value: control


title: C28.4

value: Lungs

value: flu


title: RIP_DLD-1

value: WT

value: IP RNA


title: C28.3


title: PDAC1 with empty vector for ChIP-seq (HNF1B)

value: Control


title: Input_SW480

value: total RNA


title: PDAC1 with empty vector for ChIP-seq (H3K27ac)


title: Control fibroblast C2

data_processing:
Raw sequences were aligned and processed by Torrent Suite 5.12.3 according to standard analysis procedures. Output normalized counts (in read per milion) were generated (*.chp files ).   Differentially expressed genes (DEGs) were identified by using the Transcriptome Analysis Console (TAC) software (version 4.0.2) with the ampliSeqRNA plugin (Thermofisher Scientific) and applying an ANOVA test with a fold-change threshold of ±1.5 and an FDR-adjusted p-value ≤ 0.01.
Assembly: hg19_AmpliSeq_Transcriptome_21K_v1.transcript
Supplementary files format and content: Output normalized counts (in read per milion) were generated (*.chp files ).

value: Skin fibroblasts

value: healthy donors

value: unaffected


title: Control fibroblast C1_technical replicate

value: dermis


title: PDAC1 with HNF1B overxpression for RNA-seq rep2

data_processing:
Fastq files were preprocessed using fastp and reads were mapped onto hg19 by HISAT2.
Mapped reads were counted using featureCounts.
Reads were normalized to transcripts per million (TPM).
Assembly: hg19
Supplementary files format and content: txt file
Supplementary files format and content: Matrix table of TPM normalized counts at respective genes in each sample.

extract_protocol:
Harvested organoids were washed and total RNA was extracted using RNeasy Micro Kit (Qiagen).
Library was prepared using TruSeq stranded mRNA Kit (Illumina) and sequenced using NovaSeq6000 (Illumina) with paired-end 150 bp reads.

value: PDAC1 organoid

value: Pancreatic ductal adenocarcinoma

value: HNF1B overexpression


title: WT, TNFalpha-treated, biol replicate 1, scRNAseq

value: Colon

value: colonoid

value: epithelial cells

value: Nox1 wildtype

value: TNFalpha-treated

value: IBD inflammation model


title: WT, untreated, biol replicate 1, scRNAseq

value: untreated

value: control


title: Tumor control 811a 24h vs Tumor RL 811a 24h [E]

type: RNA

city: Hospitalet de Llobregat

first: Eva

last: González-Suárez

state: Barcelona

address: Hospital Duran i Reynals - 3a planta -Gran Via de l'Hospitalet, 199

department: Epigenetics and Cancer Biology

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5).

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

source_name: Tumor culture_control

label_protocol: Two-color microarray-based LowInput QuickAmp Labeling (Agilent)

growth_protocol: Tumor cells were grown in DMEM F12 supplemented with 5% FBS and 1% P/S, in prescence of Cholera Toxin, Insulin and EGF

extract_protocol: Total RNA was isolated by standard procedures using TriPure (Roche, #11667165001)

treatment_protocol: 1000 ug/ml RANKL during 24 hours

tag: tumor code

value: mmtv-Pymt primary tumor culture

value: Control

source_name: Tumor culture_RANKL for 24 h

value: 1000 ug/ml RANKL for 24hrs


title: PDAC1 with HNF1B overxpression for RNA-seq rep1


title: Tumor control 815a 24h vs Tumor RL 815a 24h [G]

tag: tissue


title: IPMNinv2 for ChIP-seq (CTCF)

source_name: IPMNinv2 organoid

value: IPMNinv2 organoid

tag: cell type

value: Invasive intraductal papillary mucinous neoplasm

value: Invasive IPMN


title: Pak2-/- sample 59

city: Philadelphia

first: Michael

last: Slifker

state: PA

address: 333 Cottman Ave.

institute: Fox Chase Cancer Center

description:
Nf2-/-; cdkn2a-/-;Pak2 -/-
M59

data_processing:
Alignment with STAR (performed by Novogene)
Quantification with HTseq (performed by Novogene). Generated readcount_genename.txt used for all further analysis
Standard Novogene QC protocol
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: readcount_genename.txt: tab-delimited text file containing gene annotations and gene-level counts for each sample

source_name: Peritoneal PRIMARY TUMOR

extract_protocol:
Tumors were fine chopped and pulverized in liquid nitrogen then total RNA was extracted using Qiagen's RNAeasy kit according to manufacturer's instructions.
Standard library preparation protocol performed by Novogene
mRNA enrichment, fragmentation, Illumina adapter ligation and PCR amplification

treatment_protocol: peritoneal injection of adenocre virus in conditional mouse model

value: Peritoneal PRIMARY TUMOR

tag: storage

value: STORED -80 IN RNA LATER

value: CONDITIONAL Nf2 f/f;Cdkn2a f/f; Pak2 f/f

value: peritoneal injection of adenocre virus


title: WT, untreated, biol replicate 2, scRNAseq

value: Colon

value: colonoid

tag: disease state


title: Pak2-/- sample 61

description:
Nf2-/-; cdkn2a-/-;Pak2 -/-
M61


title: Control fibroblast C1

source_name: dermis

extract_protocol:
Total RNA was purified from patient and control cells grown for 72 hours at 70-80% of confluency using the miRNeasy kit (Qiagen). Sample quality and quantity were evaluated with the Agilent 2100 Bioanalyzer (Agilent Technology) and the Qubit fluorometer (Thermofisher Scientific), respectively.
To improve statistical power, RNA samples from all experimental groups were sequenced twice as biological replicates (BR) (at the 2nd and 4th in vitro passage, respectively) plus 20 technical replicates (TR) for control fibroblasts and 10 for both hEDS and HSD cells. Reverse transcription and library preparation were achieved following the standard protocol of the Ion Ampliseq Transcriptome Human Gene Expression Kit (Thermofisher Scientific), which targets by multiplexed PCR 18,574 protein-coding and 2,228 non-coding RNAs (mRNAs/ncRNAs). Libraries were quantified with the Ion qPCR Library Quantification Kit, diluted to 100 pM and pooled equally, with 8 samples per pool, followed by emulsion PCR and enrichment with the Ion OneTouch2 with ES system. Libraries were then loaded onto an Ion 540 chip and sequenced on the Ion S5 instrument.
RNA-seq, targeted transcriptome sequencing

value: dermis

value: Skin fibroblasts

tag: disease

value: healthy donors

value: unaffected


title: Placenta_TR_rep1

city: Shanghai

first: Liao

last: Zhaodi

address: 500, Qiangye Road

department: Institute of Neuroscience

institute: Chinese Academy of Sciences

data_processing:
The raw sequencing reads were trimmed by using fastp (version 0.23.2) with default parameters to remove low-quality bases and adapters in paired-end reads.
The remaining reads were mapped to the Macaca fascicularis genome (macFas5) using Bowtie2 with default parameters.
The sam files was converted to bam files using samtools (version 1.15.1), then the bam file were sorted and the index files were created. Raw read counts were calculated by featureCounts (version 2.0.1).
Assembly: macFas5
Supplementary files format and content: a tab-delimited text file include count values for each Sample

organism: Macaca fascicularis

source_name: placenta

extract_protocol:
Total RNA was extracted from the frozen placenta tissues using phenol-chloroform extraction method. In brief, 500 µl TRIZOL reagent was added into each tube containing a steel bead and placenta tissue. After crushing with griding mill, another 500 µl TRIZOL reagent was added into each tube and vertexing. After holding on ice for 10 min, 200 µl chloroform was added into each tube and hold on ice for another 10 min after vertexing. Then, the tubes were centrifuged with 12,000 rpm in 4 ℃ for 10 min. After centrifugation, the supernatant (500 µl) was mixed with 500 µl isopropanol and hold on ice for 10 min after vertexing. Next, another round of centrifugation was performed with 12,000 rpm in 4 ℃ for 10 min. After the sediments were washed with 75% ethyl alcohol, the tubes containing total RNA were dried in cabinet. The RNA libraries were finally diluted into proper concentration with RNase-free water.
1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail;  2. mRNA molecules were fragmented into small pieces;  3. The fragmented mRNA was synthesized into first strand cDNA using random primers;  4. The second strand cDNA was synthesized;  5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments;  6. PCR amplification and purification;  7. Library quality control;  8. Library circularization;  9. The library was amplified to make DNA nanoball (DNB);  10. Sequencing on DNBSEQ (DNBSEQ Technology) platform.

value: placenta

value: placenta cell

tag: genotype

value: wild type

value: TR


title: Pak2-/- sample 14B

description:
Nf2-/-; cdkn2a-/-;Pak2 -/-
M14B

source_name: SECONDARY TUMOR

value: SECONDARY TUMOR


title: PTBP1_2

city: Cold Spring Harbor

first: Carlos

last: Martí-Gómez

email: carlos199m1@gmail.com, martigo@cshl.edu

state: New York

address: 1 Bungtown Rd

department: Quantitative Biology

institute: Cold Spring Harbor Laboratory

data_processing:
libraries were sequenced using Illumina HiSeq 2500 paired end 101nt
Fastq was processed with vast-tools and map against mm9 genome and transcriptome
Raw gene counts were analyzed using limma-voom to test for differential gene expression between PTBP1 and control mice
Differential splicing analysis was performed using vast-tools
Genome_build: VASTDB mm9 version
Supplementary_files_format_and_content: TSV files containing vast-tools counts and PSIs, and results for differential splicing and for differential expression using limma

source_name: Left ventricle

growth_protocol: 10-12 weeks old C57BL/6 mice were raised in the animal facility in standard conditions

extract_protocol:
Total RNA was extracted from the left ventricles of mice 28 days after injection with the control or PTBP1 virus using the RNAeasy extraction kit (74104, Qiagen)
Quality and integrity of each RNA sample was checked using both a Bioanalyzer and a Nanodrop before proceeding to RNAseq protocol. 100 ng of total RNA were used to generate barcoded RNA-seq libraries using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). Prior to the library construction, ribosomal RNA was removed by using the QIAseq FastSelect RNA Removal kit (mouse, ref. 333180) following manufacturer´s instructions. After that, RNA was purified using magnetic beads followed by fragmentation and then first and second cDNA strand synthesis. Second strand was synthesized with U ribonucleotide instead of T. Next, cDNA 3’ ends were adenylated and the adapters were ligated, second strand were fragmented by USER enzyme that cut the uracils to preserve the directionality of the original RNA. Then the libraries were amplified by PCR. Quality each RNA sample library was checked using both a Bioanalyzer and a Qubit.

treatment_protocol: Mice were anesthetized with 3% sevoflurane in 100% oxygen. A total of 50 μL of saline (0.9\% NaCl), containing 10^11 VP/mL, were injected per mouse through the femoral vein.

value: 10-12 weeks old

tag: developmental stage

value: Adult

value: Left ventricle

tag: agent

value: PTBP1 virus


title: IPMN2 for Hi-C

data_processing:
Raw sequenced data were processed by juicer pipeline to produce .hic file.
Assembly: hg19
Supplementary files format and content: .hic

source_name: IPMN2 organoid

extract_protocol:
One million cells from organoids were crosslinked with 2% formaldehyde for 10 minutes at room temperature and quenched using stop solution.
Library was prepared using Arima Hi-C kit (Arima Genomics) according to the manufacturer’s instructions and sequenced by NovaSeq6000 (Illumina) with paired-end 150 bp reads.

treatment_protocol: Harvested organoids were gently digested into single cell suspension using TrypLE and DNaseI.

tag: cell line

value: IPMN2 organoid

value: Intraductal papillary mucinous neoplasm

value: IPMN


title: Placenta_SCNT_rep3

tag: treatment

value: SCNT


title: PTBP1_1

tag: strain


title: Pak2-/- sample 14A

description:
Nf2-/-; cdkn2a-/-;Pak2 -/-
M14A

value: Peritoneal PRIMARY TUMOR

value: STORED -80 IN RNA LATER

value: CONDITIONAL Nf2 f/f;Cdkn2a f/f; Pak2 f/f

value: peritoneal injection of adenocre virus


title: Placenta_SCNT_rep2

value: placenta


title: Pak2-/- sample 13

description:
Nf2-/-; cdkn2a-/-;Pak2 -/-
M13


title: Tumor RL 812a 24h vs Tumor control 812a 24h [F]

value: mmtv-Pymt primary tumor culture

value: 1000 ug/ml RANKL for 24hrs

value: Control


title: PDAC1 with HNF1B overxpression for Hi-C rep1

value: PDAC1 organoid

value: Pancreatic ductal adenocarcinoma

value: HNF1B overexpression


title: PDAC1 with HNF1B overxpression for Hi-C rep2


title: Placenta_ICSI_rep2

value: placenta cell

value: wild type

value: ICSI


title: Control2

value: 10-12 weeks old

value: Adult

value: Left ventricle

value: control


title: PDAC1 for ChIP-seq (CTCF)

value: PDAC

tag: chip antibody


title: scATAC-seq_WT

value: Total Intestine LP


title: wild-type sample 20

description:
Nf2-/-; cdkn2a-/-;Pak2 +/+
W20

value: Peritoneal PRIMARY TUMOR

value: STORED -80 IN RNA LATER

value: CONDITIONAL Nf2 f/f;Cdkn2a f/f; Pak2 wt

value: peritoneal injection of adenocre virus


title: Control1


title: PDAC1 with empty vector for Hi-C rep1

value: Control


title: Placenta_ICSI_rep1

value: placenta


title: PDAC1 with empty vector for RNA-seq rep1

value: PDAC1 organoid

value: Pancreatic ductal adenocarcinoma


title: JLat_NTC_DMSO_Pol2S5p_R2_(220401_DJ_Jl_NTC_DMSO_PolS5p_R2_0322)

status: Public on Dec 26 2022

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Automated CUT&Tag for RNA-Pol2-Ser5-Phosphorylation in the J-Lat 10.6 cell line transduced with a NTC CRISPR gRNA and treated with DMSO

data_processing:
Genome_build: hg38+HIV_masked.fasta.gz
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" on PE50 NextSeq reads. 2. We used Bowtie2 2.4.2 with parameters "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to align the clipped reads to the hg38+HIV_masked refererence sequence. This is the Homo sapiens hg38 reference sequence with attenuated HIV provirus inserted on the chromsome 10. 3. We used samtools 1.14 "view" to extract properly paired reads from the alignments. 4. We used bedtools 2.30.0 "genomecov" to make normalized count bigwig files, which are the fraction of counts at each base pair scaled by the size of the reference sequence (3099932747) so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bw).

source_name: CUT&Tag

extract_protocol:
AutoCUTnTag_protocols_io.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

tag: cut&tag antibody

value: RNA-Pol2-Ser5-Phosphorylation Cell Signaling Technologies cat# 13523

value: Jlat 10.6 cell line transduced with a NTC CRISPR gRNA and treated with DMSO


title: JLat_NTC_DMSO_Pol2S5p_R4_(220525_DJ_Jl_NTC_DMSO_Pol2S5p_R2_0506)


title: JLat_NTC_DMSO_Pol2S2p_R3_(220525_DJ_Jl_NTC_DMSO_Pol2S2p_R1_0506)

description: Automated CUT&Tag for RNA-Pol2-Ser2-Phosphorylation in the J-Lat 10.6 cell line transduced with a NTC CRISPR gRNA and treated with DMSO

value: RNA-Pol2-Ser2-Phosphorylation Cell Signaling Technologies cat# 13499


title: JLat_NTC_DMSO_Pol2S5p_R3_(220525_DJ_Jl_NTC_DMSO_Pol2S5p_R1_0506)


title: JLat_NTC_DMSO_Pol2S2p_R4_(220525_DJ_Jl_NTC_DMSO_Pol2S2p_R2_0506)


title: JLat_NTC_DMSO_Pol2S2p_R2_(220401_DJ_Jl_NTC_DMSO_Pol2S2p_R2_0322)


title: wild-type sample 127

description:
Nf2-/-; cdkn2a-/-;Pak2 +/+
W127


title: JLat_NTC_DMSO_IgG_R4_(220525_DJ_Jl_NTC_DMSO_IgG_R2_0506)

description: Automated CUT&Tag for IgG control in the J-Lat 10.6 cell line transduced with a NTC CRISPR gRNA and treated with DMSO

value: IgG Abcam cat# ab172730


title: JLat_NTC_DMSO_Pol2S2p_R1_(220401_DJ_Jl_NTC_DMSO_PolS2p_R1_0322)


title: JLat_NTC_DMSO_IgG_R3_(220525_DJ_Jl_NTC_DMSO_IgG_R1_0506)


title: JLat_NTC_DMSO_IgG_R2_(220401_DJ_Jl_NTC_DMSO_IgG_R2_0322)


title: JLat_NTC_DMSO_IgG_R1_(220401_DJ_Jl_NTC_DMSO_IgG_R1_0322)


title: JLat_NTC_DMSO_H4ac_R4_(220401_DJ_Jl_NTC_DMSO_H4ac_R2_0322)

description: Automated CUT&Tag for pan-H4ac in the J-Lat 10.6 cell line transduced with a NTC CRISPR gRNA and treated with DMSO

value: pan-H4ac Active Motif cat# 39925


title: JLat_NTC_DMSO_H4ac_R3_(220401_DJ_Jl_NTC_DMSO_H4ac_R1_0322)


title: JLat_NTC_DMSO_H4ac_R2_(220224_DJ_Hs_JLat_WT_H4ac_BT_021622)


title: Female, Serum, HDM, 30319-029

city: Reno

first: Mariam

middle: A

last: Ba

address: 1664 N. Virginia St

institute: University of Nevada, Reno

description: HDM - 30319-029 - CPM

data_processing:
All analysis were performed using CLC Genomics Workbench (version 12.0.2) and CLC Genomics Server (Version 11.0.4).
FASTQ files with quality scores (QS) > 30 were analyzed by CLC Genomics Workbench (version 12.0.2) using the QIAseq miRNA quantification workflow.
The deduplicated Unique Molecular Index (UMI) reads were grouped into unique search sequences and mapped to the miRNAs annotated in the miRbase v22
The miRNA expression was calculated via counting the number of distinctive UMI reads corresponding to each miRbase-annotated miRNA
miRNA expression was normalized to the sequencing depth (counts per million)
Assembly: The remaining reads were aligned to Mouse genome version: GRCm38 (Mouse Buid 38)
Supplementary files format and content: Matrix excel file containing CPM values for each sample

source_name: Serum

extract_protocol:
RNA was extracted from 200 ml of serum using the miRNeasy serum/plasma advanced kit, and the RNA quality control (QC) was determined by qPCR of serum endogenous miRNAs (such as miRNA-103a-3p and miR-191-5p), hemolysis markers (miR-23a and miR451a), and Spike-Ins control (UniSp6).
miRNA libraries were prepared using Qiagen's miRNA Library Kit following the manufacturer's protocol.

treatment_protocol:
Mice were sensitized and challenged with an intranasal administration of 50μL of a 25μg house dust mite, HDM, (Greer Laboratories) solution or saline.
The sensitization was performed once daily for five consecutive days, and this was followed by a daily, five successive days per week, HDM or saline challenge for three weeks.

value: BALB/c

tag: Sex

value: Female

value: Serum

value: WT

value: HDM


title: Female, Serum, HDM, 30319-028

description: HDM - 30319-028 - CPM


title: Female, Serum, HDM, 30319-030

description: HDM - 30319-030 - CPM


title: JLat_NTC_DMSO_Brd4_R6_(220525_DJ_Jl_NTC_DMSO_Brd4_R2_0506)

description: Automated CUT&Tag for Brd4 in the J-Lat 10.6 cell line transduced with a NTC CRISPR gRNA and treated with DMSO

value: BRD4 Cell Signaling Technologies cat# 13440


title: wild-type sample 19

description:
Nf2-/-; cdkn2a-/-;Pak2 +/+
W19

value: Peritoneal PRIMARY TUMOR

value: STORED -80 IN RNA LATER

value: CONDITIONAL Nf2 f/f;Cdkn2a f/f; Pak2 wt


title: Female, Serum, HDM, 30319-027

description: HDM - 30319-027 - CPM


title: JLat_NTC_DMSO_Brd4_R5_(220525_DJ_Jl_NTC_DMSO_Brd4_R1_0506)


title: JLat_NTC_DMSO_Pol2S5p_R1_(220401_DJ_Jl_NTC_DMSO_PolS5p_R1_0322)


title: JLat_NTC_DMSO_Brd4_R3_(220401_DJ_Jl_NTC_DMSO_Brd4_R1_0322)


title: JLat_NTC_DMSO_Brd4_R1_(220224_DJ_Hs_JLat_WT_Brd4_Epi_021622)


title: Female, Serum, HDM, 30319-025

description: HDM - 30319-025 - CPM


title: Female, Serum, Saline, 30319-022

description: Saline - 30319-022 - CPM

value: Saline


title: Female, Serum, HDM, 30319-023

description: HDM - 30319-023 - CPM


title: Female, Serum, HDM, 30319-026

description: HDM - 30319-026 - CPM


title: JLat_NTC_DMSO_Brd4_R2_(220224_DJ_Hs_JLat_WT_Brd4_BT_021622)


title: JLat_NTC_AZD_Pol2S5p_R4_(220525_DJ_Jl_NTC_AZD_Pol2S5p_R2_0506)

description: Automated CUT&Tag for RNA-Pol2-Ser5-Phosphorylation in the J-Lat 10.6 cell line transduced with a NTC CRISPR gRNA and treated with 10 nM AZD5582

value: Jlat 10.6 cell line transduced with a NTC CRISPR gRNA and treated with 10nM AZD5582


title: Female, Serum, Saline, 30319-021

description: Saline - 30319-021 - CPM


title: JLat_NTC_DMSO_Brd4_R4_(220401_DJ_Jl_NTC_DMSO_Brd4_R2_0322)


title: JLat_NTC_AZD_Pol2S5p_R3_(220525_DJ_Jl_NTC_AZD_Pol2S5p_R1_0506)


title: JLat_NTC_DMSO_H4ac_R1_(220224_DJ_Hs_JLat_WT_H4ac_Epi_021622)


title: Female, Serum, Saline, 30319-019

description: Saline - 30319-019 - CPM


title: JLat_NTC_AZD_Pol2S5p_R5_(220525_DJ_Jl_NTC_AZD_Pol2S5p_R3_0506)


title: JLat_NTC_AZD_Pol2S5p_R1_(220401_DJ_Jl_NTC_AZD_PolS5p_R1_0322)


title: JLat_NTC_AZD_Pol2S2p_R3_(220525_DJ_Jl_NTC_AZD_Pol2S2p_R2_0506)

description: Automated CUT&Tag for RNA-Pol2-Ser2-Phosphorylation in the J-Lat 10.6 cell line transduced with a NTC CRISPR gRNA and treated with 10 nM AZD5582


title: Female, Serum, Saline, 30319-018

description: Saline - 30319-018 - CPM


title: JLat_NTC_AZD_Pol2S5p_R2_(220401_DJ_Jl_NTC_AZD_PolS5p_R2_0322)


title: Female, Serum, Saline, 30319-020

description: Saline - 30319-020 - CPM


title: Female, Serum, Saline, 30319-016

description: Saline - 30319-016 - CPM


title: Female, Serum, Saline, 30319-017

description: Saline - 30319-017 - CPM


title: JLat_NTC_AZD_Pol2S2p_R2_(220525_DJ_Jl_NTC_AZD_Pol2S2p_R1_0506)


title: Female, Serum, HDM, 30319-024

description: HDM - 30319-024 - CPM


title: Female, Serum, Saline, 30319-015

description: Saline - 30319-015 - CPM


title: Male, Serum, HDM, 30319-014

description: HDM - 30319-014 - CPM

value: Male


title: Male, Serum, HDM, 30319-013

description: HDM - 30319-013 - CPM


title: JLat_NTC_AZD_IgG_R5_(220525_DJ_Jl_NTC_AZD_IgG_R3_0506)

description: Automated CUT&Tag for IgG control in the J-Lat 10.6 cell line transduced with a NTC CRISPR gRNA and treated with 10 nM AZD5582


title: JLat_NTC_AZD_IgG_R4_(220525_DJ_Jl_NTC_AZD_IgG_R2_0506)


title: Male, Serum, HDM, 30319-012

description: HDM - 30319-012 - CPM


title: JLat_NTC_AZD_IgG_R3_(220525_DJ_Jl_NTC_AZD_IgG_R1_0506)


title: JLat_NTC_AZD_IgG_R2_(220401_DJ_Jl_NTC_AZD_IgG_R2_0322)


title: Male, Serum, HDM, 30319-010

description: HDM - 30319-010 - CPM


title: Male, Serum, HDM, 30319-009

description: HDM - 30319-009 - CPM


title: Male, Serum, HDM, 30319-008

description: HDM - 30319-008 - CPM


title: JLat_NTC_AZD_IgG_R1_(220401_DJ_Jl_NTC_AZD_IgG_R1_0322)


title: Male, Serum, HDM, 30319-007

description: HDM - 30319-007 - CPM


title: JLat_NTC_AZD_H4ac_R4_(220525_DJ_Jl_NTC_AZD_H4ac_R2_0506)

description: Automated CUT&Tag for pan-H4ac in the J-Lat 10.6 cell line transduced with a NTC CRISPR gRNA and treated with 10 nM AZD5582


title: Male, Serum, Saline, 30319-006

description: Saline - 30319-006 - CPM


title: JLat_NTC_AZD_H4ac_R2_(220401_DJ_Jl_NTC_AZD_H4ac_R2_0322)


title: JLat_NTC_AZD_H4ac_R1_(220401_DJ_Jl_NTC_AZD_PanH4_R1_0322)


title: Male, Serum, Saline, 30319-004

description: Saline - 30319-004 - CPM


title: JLat_NTC_AZD_Brd4_R5_(220525_DJ_Jl_NTC_AZD_Brd4_R3_0506)

description: Automated CUT&Tag for Brd4 in the J-Lat 10.6 cell line transduced with a NTC CRISPR gRNA and treated with 10 nM AZD5582


title: Male, Serum, Saline, 30319-005

description: Saline - 30319-005 - CPM


title: JLat_NTC_AZD_Pol2S2p_R1_(220401_DJ_Jl_NTC_AZD_PolS2p_R2_0322)


title: JLat_NTC_AZD_Brd4_R4_(220525_DJ_Jl_NTC_AZD_Brd4_R2_0506)


title: Male, Serum, Saline, 30319-003

description: Saline - 30319-003 - CPM


title: Male, Serum, HDM, 30319-011

description: HDM - 30319-011 - CPM


title: Male, Serum, Saline, 30319-002

description: Saline - 30319-002 - CPM


title: Male, Serum, Saline, 30319-001

description: Saline - 30319-001 - CPM


title: JLat_NTC_AZD_Brd4_R3_(220525_DJ_Jl_NTC_AZD_Brd4_R1_0506)


title: Female, Lung, HDM, 30319-060

description: HDM - 30319-060 - CPM

source_name: Lung

extract_protocol:
RNA was extracted with the RNeasy mini kit (Qiagen), quantified using a Nanodrop, and the RNA integrity was assessed using the Agilent TapeStation.
miRNA libraries were prepared using Qiagen's miRNA Library Kit following the manufacturer's protocol.

value: Lung


title: JLat_NTC_AZD_Brd4_R2_(220401_DJ_Jl_NTC_AZD_Brd4_R2_0322)


title: JLat_NTC_AZD_Brd4_R1_(220401_DJ_Jl_NTC_AZD_Brd4_R1_0322)


title: JLat_NTC_AZD_H4ac_R5_(220525_DJ_Jl_NTC_AZD_H4ac_R3_0506)


title: JLat_Ing3_DMSO_Pol2S5p_R4_(220525_DJ_Jl_Ing3_DMSO_Pol2S5p_R3_0506)

description: Automated CUT&Tag for RNA-Pol2-Ser5-Phosphorylation in the J-Lat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with DMSO

value: RNA-Pol2-Ser5-Phosphorylation Cell Signaling Technologies cat# 13523

value: Jlat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with DMSO


title: JLat_NTC_AZD_H4ac_R3_(220525_DJ_Jl_NTC_AZD_H4ac_R1_0506)


title: Female, Lung, HDM, 30319-059

description: HDM - 30319-059 - CPM


title: JLat_Ing3_DMSO_Pol2S5p_R3_(220525_DJ_Jl_Ing3_DMSO_Pol2S5p_R2_0506)


title: Female, Lung, HDM, 30319-058

description: HDM - 30319-058 - CPM


title: Female, Lung, HDM, 30319-057

description: HDM - 30319-057 - CPM


title: Female, Lung, HDM, 30319-056

description: HDM - 30319-056 - CPM


title: JLat_Ing3_DMSO_Pol2S5p_R1_(220401_DJ_Jl_Ing3_DMSO_PolS5p_R1_0322)


title: JLat_Ing3_DMSO_Pol2S2p_R3_(220525_DJ_Jl_Ing3_DMSO_Pol2S2p_R2_0506)

description: Automated CUT&Tag for RNA-Pol2-Ser2-Phosphorylation in the J-Lat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with DMSO

value: RNA-Pol2-Ser2-Phosphorylation Cell Signaling Technologies cat# 13499


title: JLat_Ing3_DMSO_Pol2S5p_R2_(220401_DJ_Jl_Ing3_DMSO_PolS5p_R2_0322)


title: Female, Lung, HDM, 30319-055

description: HDM - 30319-055 - CPM


title: Female, Lung, HDM, 30319-054

description: HDM - 30319-054 - CPM


title: JLat_Ing3_DMSO_Pol2S2p_R2_(220401_DJ_Jl_Ing3_DMSO_PolS2p_R2_0322)


title: Female, Lung, HDM, 30319-053

description: HDM - 30319-053 - CPM


title: JLat_Ing3_DMSO_Pol2S2p_R1_(220401_DJ_Jl_Ing3_DMSO_PolS2p_R1_0322)


title: JLat_Ing3_DMSO_IgG_R5_(220525_DJ_Jl_Ing3_DMSO_IgG_R3_0506)

description: Automated CUT&Tag for IgG control in the J-Lat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with DMSO

value: IgG Abcam cat# ab172730


title: Female, Lung, Saline, 30319-052

description: Saline - 30319-052 - CPM

value: BALB/c


title: JLat_Ing3_DMSO_IgG_R3_(220525_DJ_Jl_Ing3_DMSO_IgG_R1_0506)


title: Female, Lung, Saline, 30319-051

description: Saline - 30319-051 - CPM

value: Female


title: JLat_Ing3_DMSO_IgG_R4_(220525_DJ_Jl_Ing3_DMSO_IgG_R2_0506)


title: Female, Lung, Saline, 30319-050

description: Saline - 30319-050 - CPM


title: Female, Lung, Saline, 30319-049

description: Saline - 30319-049 - CPM


title: Female, Lung, Saline, 30319-048

description: Saline - 30319-048 - CPM


title: JLat_Ing3_DMSO_IgG_R2_(220401_DJ_Jl_Ing3_DMSO_IgG_R2_0322)


title: JLat_Ing3_DMSO_IgG_R1_(220401_DJ_Jl_Ing3_DMSO_IgG_R1_0322)


title: Female, Lung, Saline, 30319-047

description: Saline - 30319-047 - CPM


title: JLat_Ing3_DMSO_H4ac_R4_(220525_DJ_Jl_Ing3_DMSO_H4ac_R2_0506)

description: Automated CUT&Tag for pan-H4ac in the J-Lat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with DMSO

value: pan-H4ac Active Motif cat# 39925


title: Female, Lung, Saline, 30319-046

description: Saline - 30319-046 - CPM

value: WT


title: Female, Lung, Saline, 30319-045

description: Saline - 30319-045 - CPM


title: Male, Lung, HDM, 30319-042

description: HDM - 30319-042 - CPM

value: HDM


title: JLat_Ing3_DMSO_Brd4_R5_(220525_DJ_Jl_Ing3_DMSO_Brd4_R3_0506)

description: Automated CUT&Tag for Brd4 in the J-Lat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with DMSO

value: BRD4 Cell Signaling Technologies cat# 13440


title: Male, Lung, HDM, 30319-041

description: HDM - 30319-041 - CPM


title: JLat_Ing3_DMSO_H4ac_R1_(220401_DJ_Jl_Ing3_DMSO_H4ac_R1_0322)


title: JLat_Ing3_DMSO_H4ac_R2_(220401_DJ_Jl_Ing3_DMSO_H4ac_R2_0322)


title: Male, Lung, HDM, 30319-040

description: HDM - 30319-040 - CPM


title: JLat_Ing3_DMSO_Brd4_R3_(220525_DJ_Jl_Ing3_DMSO_Brd4_R1_0506)


title: JLat_Ing3_DMSO_Brd4_R2_(220401_DJ_Jl_Ing3_DMSO_Brd4_R2_0322)


title: JLat_Ing3_DMSO_Brd4_R1_(220401_DJ_Jl_Ing3_DMSO_Brd4_R1_0322)


title: Male, Lung, HDM, 30319-039

description: HDM - 30319-039 - CPM


title: Male, Lung, HDM, 30319-038

description: HDM - 30319-038 - CPM


title: Male, Lung, HDM, 30319-037

description: HDM - 30319-037 - CPM


title: Male, Lung, Saline, 30319-036

description: Saline - 30319-036 - CPM


title: JLat_Ing3_AZD_Pol2S5p_R4_(220525_DJ_Jl_Ing3_AZD_Pol2S5p_R2_0506)

description: Automated CUT&Tag for RNA-Pol2-Ser5-Phosphorylation in the J-Lat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with 10 nM AZD5582

value: Jlat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with 10 nM AZD5582


title: JLat_Ing3_DMSO_H4ac_R5_(220525_DJ_Jl_Ing3_DMSO_H4ac_R3_0506)


title: PDAC1 with empty vector for Hi-C rep2

value: PDAC1 organoid

value: Pancreatic ductal adenocarcinoma

value: Control


title: Male, Lung, Saline, 30319-035

description: Saline - 30319-035 - CPM

value: Saline


title: Male, Lung, HDM, 30319-044

description: HDM - 30319-044 - CPM

value: Male


title: JLat_Ing3_AZD_Pol2S5p_R3_(220525_DJ_Jl_Ing3_AZD_Pol2S5p_R1_0506)


title: JLat_Ing3_DMSO_H4ac_R3_(220525_DJ_Jl_Ing3_DMSO_H4ac_R1_0506)


title: JLat_Ing3_DMSO_Brd4_R4_(220525_DJ_Jl_Ing3_DMSO_Brd4_R2_0506)


title: JLat_Ing3_AZD_Pol2S5p_R2_(220401_DJ_Jl_Ing3_AZD_PolS5p_R2_0322)


title: GM1082-2

city: tianjin

first: Yunhuan

last: Gao

address: Wei Jin Road No. 94

department: School of Medicine

institute: Nankai University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9

source_name: bone marrow cells

extract_protocol:
wild-type and GM1082-/- bone marrow cells were exposed to M-CSF for 5 days, and mRNA and lncRNA expression was evaluated using High-throughput sequencin
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow cells

value: Bone marrow derived macrophages

value: macrophages

value: GM1082 KO

value: M-CSF


title: GM1082-1


title: WT-1

value: wild type


title: WT-2


title: JLat_Ing3_AZD_Pol2S5p_R1_(220401_DJ_Jl_Ing3_AZD_PolS5p_R1_0322)

value: RNA-Pol2-Ser5-Phosphorylation Cell Signaling Technologies cat# 13523


title: SB_5 [16s rRNA-seq]

city: Yangzhou

first: Yongkang

last: Zhen

state: — Please Select —

address: Yangzhou University

institute: Yangzhou University

data_processing:
Paired-end reads generated from Illumina platforms were processed and merged using FLASH software (v1.2.7).
Quality filtering on the raw reads was then performed under specific filtering conditions to obtain the high-quality clean tags according to the Fqtrim software (v0.9.4). Chimeric sequences were filtered using VSEARCH software (v2.3.4).
Finally, the feature table and feature sequence were obtained after dereplication using DADA2 software (v1.10.1).
The V3-V4 region of the prokaryotic small-subunit (16S) rRNA gene was amplified with primers 341 F (5′-CCTACGGGNGGCWGCAG-3′) and 805 R (5′-GACTACHVGGGTATCTAATCC-3′).
Supplementary files format and content: The_processed_data_for_16S_rRNA-seq.xlsx: Excel file
Library strategy: 16s rRNA-seq

organism: Capra hircus

source_name: rumen digesta

extract_protocol:
Microbial DNA from different rumen digesta samples was extracted using TIANamp Stool DNA Kit.
SMRTbell libraries were prepared using the Pacific Biosciences SMRTbellTM Template Prep kit.

tag: breed

value: Guanzhong

value: healthy

value: rumen digesta

value: infusion of sodium butyrate

tag: time point

value: Day 13

tag: individual


title: JLat_Ing3_AZD_Pol2S2p_R3_(220525_DJ_Jl_Ing3_AZD_Pol2S2p_R2_0506)

description: Automated CUT&Tag for RNA-Pol2-Ser2-Phosphorylation in the J-Lat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with 10 nM AZD5582

value: RNA-Pol2-Ser2-Phosphorylation Cell Signaling Technologies cat# 13499+H78+H78

value: Jlat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with 10 nM AZD5582


title: SB_4 [16s rRNA-seq]

tag: tissue


title: Male, Lung, Saline, 30319-032

description: Saline - 30319-032 - CPM

value: BALB/c

value: Lung

value: WT


title: SB_3 [16s rRNA-seq]


title: Male, Lung, HDM, 30319-043

description: HDM - 30319-043 - CPM

value: Male

value: HDM


title: Male, Lung, Saline, 30319-034

description: Saline - 30319-034 - CPM

value: Saline


title: SB_6 [16s rRNA-seq]


title: PDAC1 with empty vector for RNA-seq rep2

value: PDAC1 organoid

tag: cell type

value: Pancreatic ductal adenocarcinoma

value: Control


title: Male, Lung, Saline, 30319-033

description: Saline - 30319-033 - CPM


title: PTBP1_3

tag: age

value: 10-12 weeks old

value: Adult

value: Left ventricle

value: PTBP1 virus


title: SB_1 [16s rRNA-seq]

value: Guanzhong

tag: disease state

value: healthy

value: rumen digesta

value: infusion of sodium butyrate


title: JLat_Ing3_AZD_Pol2S2p_R2_(220401_DJ_Jl_Ing3_AZD_PolS2p_R2_0322)

value: RNA-Pol2-Ser2-Phosphorylation Cell Signaling Technologies cat# 13499+H78+H78

value: Jlat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with 10 nM AZD5582


title: Control fibroblast C1_biological replicate

city: Brescia

first: Nicola

last: Chiarelli

address: Viale Europa 11

institute: University of Brescia

value: dermis

value: Skin fibroblasts

tag: disease

value: healthy donors

value: unaffected


title: Male, Lung, Saline, 30319-031

description: Saline - 30319-031 - CPM

value: BALB/c

value: Male

value: Lung

tag: genotype

value: WT

value: Saline


title: SP_6 [16s rRNA-seq]

value: infusion of sodium propionate

value: Day 13


title: Control3

value: 10-12 weeks old

tag: developmental stage

value: Adult

value: Left ventricle

value: control


title: SP_5 [16s rRNA-seq]

value: Guanzhong

value: healthy

value: rumen digesta


title: Female, Lung, HDM, 30549-030

description: 30549-030 - TPM

data_processing:
All analysis were done using CLC Genomics Workbench (version 21.0.4)
Reads were trimmed for adaptor sequences and low quality sequences
Trimmed reads with high quality scores were analyzed and mapped to the mouse genome version GRCm38, and annotated using the ENSEMBL Mus_musculus.GRCm38 version 98
Gene expression was calculated by counting number of reads mapping to the annotated gene loci,
The expression values were normalized to transcripts per million (TPM)
Assembly: Mouse genome version: GRCm38 (Mouse Buid 38)
Supplementary files format and content: Matrix excel file containing TPM values for each sample

extract_protocol:
RNA was extracted with the RNeasy mini kit (Qiagen), quantified using a Nanodrop, and the RNA integrity was assessed using the Agilent TapeStation.
cDNA libraries were prepared using QIAseq Stranded mRNA Select Kit with poly-A enrichment following manufacturer's protocols

treatment_protocol:
Mice (BALB/c, male and female, 6-8 weeks old) were sensitized and challenged with an intranasal administration of 50μL of a 25μg house dust mite, HDM, (Greer Laboratories) solution or saline.
The sensitization was performed once daily for five consecutive days, and this was followed by a daily, five successive days per week, HDM or saline challenge for three weeks.

value: Female

value: HDM


title: SP_4 [16s rRNA-seq]


title: Placenta_SCNT_rep1

value: placenta

value: placenta cell

value: wild type

value: SCNT


title: JLat_Ing3_AZD_IgG_R4_(220525_DJ_Jl_Ing3_AZD_IgG_R2_0506)

description: Automated CUT&Tag for IgG control in the J-Lat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with 10 nM AZD5582

value: IgG Abcam cat# ab172730

value: Jlat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with 10 nM AZD5582


title: SP_3 [16s rRNA-seq]

value: infusion of sodium propionate


title: Female, Lung, HDM, 30549-029

description: 30549-029 - TPM

value: BALB/c

value: Lung

value: WT


title: JLat_Ing3_AZD_IgG_R3_(220525_DJ_Jl_Ing3_AZD_IgG_R1_0506)


title: SP_1 [16s rRNA-seq]

value: Day 13


title: SA_6 [16s rRNA-seq]

value: infusion of sodium acetate


title: Female, Lung, HDM, 30549-028

description: 30549-028 - TPM


title: SB_2 [16s rRNA-seq]

value: Guanzhong

value: infusion of sodium butyrate


title: SA_5 [16s rRNA-seq]

value: healthy

value: rumen digesta


title: Female, Lung, HDM, 30549-027

description: 30549-027 - TPM

value: Female

value: HDM


title: SA_4 [16s rRNA-seq]


title: JLat_Ing3_AZD_IgG_R1_(220401_DJ_Jl_Ing3_AZD_IgG_R1_0322)


title: JLat_Ing3_AZD_IgG_R2_(220401_DJ_Jl_Ing3_AZD_IgG_R2_0322)


title: Female, Lung, HDM, 30549-025

description: 30549-025 - TPM


title: JLat_Ing3_AZD_Pol2S2p_R1_(220401_DJ_Jl_Ing3_AZD_PolS2p_R1_0322)

value: RNA-Pol2-Ser2-Phosphorylation Cell Signaling Technologies cat# 13499+H78+H78


title: NC_6 [16s rRNA-seq]

value: infusion of normal saline


title: JLat_Ing3_AZD_H4ac_R5_(220525_DJ_Jl_Ing3_AZD_H4ac_R1_0506)

description: Automated CUT&Tag for pan-H4ac in the J-Lat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with 10 nM AZD5582

value: pan-H4ac Active Motif cat# 39925


title: SA_3 [16s rRNA-seq]


title: Female, Lung, HDM, 30549-026

description: 30549-026 - TPM


title: JLat_Ing3_AZD_H4ac_R6_(220525_DJ_Jl_Ing3_AZD_H4ac_R2_0506)


title: SA_1 [16s rRNA-seq]


title: SA_2 [16s rRNA-seq]


title: NC_5 [16s rRNA-seq]


title: NC_4 [16s rRNA-seq]


title: NC_3 [16s rRNA-seq]


title: Female, Lung, HDM, 30549-024

description: 30549-024 - TPM


title: Female, Lung, HDM, 30549-023

description: 30549-023 - TPM


title: SP_2 [16s rRNA-seq]


title: NC_2 [16s rRNA-seq]


title: JLat_Ing3_AZD_H4ac_R4_(220401_DJ_Jl_Ing3_AZD_H4ac_R2_0322)


title: NC_1 [16s rRNA-seq]


title: JLat_Ing3_AZD_H4ac_R3_(220401_DJ_Jl_Ing3_AZD_H4ac_R1_0322)


title: Female, Lung, Saline, 30549-022

description: 30549-022 - TPM

value: Saline


title: JLat_Ing3_AZD_H4ac_R2_(220224_DJ_Hs_JLat_Ing3_H4ac_BT_021622)

value: Jlat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with 10 nM AZD5582


title: JLat_Ing3_AZD_H4ac_R1_(220224_DJ_Hs_JLat_Ing3_H4ac_Epi_021622)


title: Female, Lung, Saline, 30549-020

description: 30549-020 - TPM


title: RNAs from seed imbibed in KSCN for 6h - qko_KSCN [qko_4_4]

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
SOAPnuke: version：v1.5.2, parameters: -l 15 -q 0.5 -n 0.1, website: https://github.com/BGI-flexlab/SOAPnuke
Transcript mapping against Arabidopsis reference transcriptome Araport v11 using Salmon algorithm
Assembly: Araport11_genes.201606.cdna.fasta downlaoded from arabidopsis.org. and abra_mygenomebrowser_011021_mrna.fasta downloaded from GenBank number PHFN00000000 (https://www.ncbi.nlm.nih.gov/nuccore/PHFN00000000)
Supplementary files format and content: tab-delimited text files include count values for each sample

organism: Arabidopsis thaliana

source_name: entire seed

growth_protocol: Seeds were sowed in petri dishes containing 0.8% agarose (SIGMA) and cultures were incubated in a controlled growth chamber under a 16 h photoperiod (170 µmol photons m2 s-1) at 22 °C (light period)/20 °C (dark period) and a constant 70% relative humidity (Ortega-Cuadros et al. 2022)

extract_protocol:
Seeds were collected to RNA isolation using NucleoSpin® RNA Plant and Fungi kit (Macherey-Nagel, Düren, Germany). RNA quantification was obtained with a NanoDrop ND-100 (NanoDrop Technologies, DE, USA) and the RNA Integrity was measure with a 4100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
RNA samples were sent to Beijing Genomics Institute (BGI) for cDNA library construction and paired-end sequencing (PE100) using the DNBseq™ technology

treatment_protocol: Seeds were imbibed in water, nitrate KNO3 10Mm, potassium thiocyanate KSCN 8µM during 6 h and a part of seeds were left to dry (with any imbibition)

value: entire seed

tag: ecotype

value: cyp79B2 cyp79B3 myb28 myb29 - qko

value: imbibed in KSCN for 6h


title: Female, Lung, Saline, 30549-021

description: 30549-021 - TPM

value: BALB/c

value: Lung

value: WT


title: JLat_Ing3_AZD_Brd4_R5_(220525_DJ_Jl_Ing3_AZD_Brd4_R2_0506)

description: Automated CUT&Tag for Brd4 in the J-Lat 10.6 cell line transduced with an Ing3 CRISPR gRNA and treated with 10 nM AZD5582

value: BRD4 Cell Signaling Technologies cat# 13440


title: RNAs from seed imbibed in KSCN for 6h - qko_KSCN [qko_4_6]


title: RNAs from seed imbibed in KSCN for 6h - qko_KSCN [qko_4_7]


title: RNAs from seed imbibed in KNO3 for 6h - qko_KNO3 [qko_3_4]

value: imbibed in KNO3 for 6h


title: RNAs from seed imbibed in KNO3 for 6h - qko_KNO3 [qko_3_7]


title: RNAs from seed imbibed in water for 6h - qko_water [qko_2_6]

value: imbibed in water for 6h


title: Female, Lung, Saline, 30549-019

description: 30549-019 - TPM


title: JLat_Ing3_AZD_Brd4_R4_(220401_DJ_Jl_Ing3_AZD_Brd4_R2_0322)


title: RNAs from seed imbibed in water for 6h - qko_water [qko_2_4]


title: RNAs from seed imbibed in KNO3 for 6h - qko_KNO3 [qko_3_6]


title: RNAs from seed imbibed in water for 6h - qko_water [qko_2_7]


title: RNAs from seed without imbibition - qko_dry [qko_1_7]

value: dry


title: RNAs from seed without imbibition - qko_dry [qko_1_6]


title: Female, Lung, Saline, 30549-018

description: 30549-018 - TPM

value: Female


title: Female, Lung, Saline, 30549-017

description: 30549-017 - TPM


title: Female, Lung, Saline, 30549-016

description: 30549-016 - TPM


title: RNAs from seed without imbibition - qko_dry [qko_1_4]


title: JLat_Ing3_AZD_Brd4_R2_(220224_DJ_Hs_JLat_Ing3_Brd4_BT_021622)


title: RNAs from seed imbibed in KSCN for 6h - myb_KSCN [myb_4_9]

value: myb28 myb29 - myb


title: JLat_Ing3_AZD_Brd4_R1_(220224_DJ_Hs_JLat_Ing3_Brd4_Epi_021622)


title: RNAs from seed imbibed in KSCN for 6h - myb_KSCN [myb_4_8]


title: Female, Lung, Saline, 30549-015

description: 30549-015 - TPM


title: RNAs from seed imbibed in KSCN for 6h - myb_KSCN [myb_4_7]


title: RNAs from seed imbibed in KNO3 for 6h - myb_KNO3 [myb_3_9]


title: RNAs from seed imbibed in water for 6h - myb_water [myb_2_9]


title: JLat_Ing3_AZD_Brd4_R3_(220401_DJ_Jl_Ing3_AZD_Brd4_R1_0322)


title: RNAs from seed imbibed in water for 6h - myb_water [myb_2_7]


title: saline_12_Pre

city: Atlanta

first: David

last: Weinshenker

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

description: Pre-IP input, saline treated

data_processing:
Fastq files were alligned to mm10 with STAR in Galaxy
FeatureCounts were obtained using R Bioconductor
Read count filtering and normalization was completed with R Bioconductor
Assembly: mm10
Supplementary files format and content: Filtered normalized counts grouped in an Excel spreadsheet

source_name: total hindbrain

extract_protocol:
RNA was harvested using Zymo RNA Clean & Concentrator-5 kit
RNA libraries for RNA-seq were prepared by Novogene using a Library Prep Kit following manufacturer's protocols

value: total hindbrain

value: saline


title: Male, Lung, HDM, 30549-012

description: 30549-012 - TPM

value: Male

value: HDM


title: saline_5_Pre

description: Pre-IP input, saline treated


title: RNAs from seed imbibed in water for 6h - myb_water [myb_2_6]


title: RNAs from seed without imbibition - myb_dry [myb_1_9]


title: DSP4_2_Pre

description: Pre-IP input, DSP-4 treated


title: RNAs from seed without imbibition - myb_dry [myb_1_5]


title: RNAs from seed imbibed in KSCN for 6h - cyp_KSCN [cyp_4_8]

value: cyp79B2 cyp79B3 - cyp


title: RNAs from seed imbibed in KSCN for 6h - cyp_KSCN [cyp_4_6]

value: entire seed


title: DSP4_7_Pre

description: Pre-IP input, DSP-4 treated


title: Male, Lung, HDM, 30549-011

description: 30549-011 - TPM


title: RNAs from seed imbibed in KNO3 for 6h - cyp_KNO3 [cyp_3_7]


title: Male, Lung, HDM, 30549-009

description: 30549-009 - TPM


title: RNAs from seed imbibed in KNO3 for 6h - cyp_KNO3 [cyp_3_6]


title: saline_6_IP

description: IP enriched, saline treated

source_name: noradrenergic

value: noradrenergic


title: RNAs from seed imbibed in water for 6h - cyp_water [cyp_2_9]


title: saline_4_IP

description: IP enriched, saline treated


title: Male, Lung, HDM, 30549-010

description: 30549-010 - TPM


title: Male, Lung, HDM, 30549-008

description: 30549-008 - TPM


title: RNAs from seed imbibed in water for 6h - cyp_water [cyp_2_8]


title: RNAs from seed imbibed in water for 6h - cyp_water [cyp_2_7]


title: DSP4_9_IP

description: IP enriched, DSP-4 treated


title: Male, Lung, HDM, 30549-014

description: 30549-014 - TPM


title: RNAs from seed imbibed in KNO3 for 6h - myb_KNO3 [myb_3_6]


title: Male, Lung, HDM, 30549-013

description: 30549-013 - TPM


title: saline_12_IP

description: IP enriched, saline treated


title: Male, Lung, HDM, 30549-007

description: 30549-007 - TPM


title: RNAs from seed without imbibition - cyp_dry [cyp_1_9]


title: DSP4_8_IP

description: IP enriched, DSP-4 treated


title: RNAs from seed without imbibition - cyp_dry [cyp_1_7]


title: RNAs from seed without imbibition - cyp_dry [cyp_1_8]


title: Male, Lung, Saline, 30549-005

description: 30549-005 - TPM

value: Saline


title: RNAs from seed imbibed in KSCN for 6h - WT_KSCN [Col_4_6]

value: imbibed in KSCN for 6h


title: RNAs from seed imbibed in KSCN for 6h - WT_KSCN [Col_4_8]


title: RNAs from seed imbibed in KNO3 for 6h - cyp_KNO3 [cyp_3_8]


title: Male, Lung, Saline, 30549-006

description: 30549-006 - TPM

value: BALB/c

value: Lung


title: DSP4_7_IP

description: IP enriched, DSP-4 treated


title: RNAs from seed imbibed in KNO3 for 6h - WT_KNO3 [Col_3_6]

value: WT


title: DSP4_3_IP

description: IP enriched, DSP-4 treated


title: RNAs from seed imbibed in KSCN for 6h - WT_KSCN [Col_4_5]


title: DSP4_1_IP

description: IP enriched, DSP-4 treated


title: Male, Lung, Saline, 30549-002

description: 30549-002 - TPM


title: RNAs from seed imbibed in KNO3 for 6h - WT_KNO3 [Col_3_5]

value: imbibed in KNO3 for 6h


title: Male, Lung, Saline, 30549-003

description: 30549-003 - TPM


title: RNAs from seed imbibed in water for 6h - WT_water [Col_2_8]

value: imbibed in water for 6h


title: DSP4_2_IP

description: IP enriched, DSP-4 treated


title: RNAs from seed imbibed in KNO3 for 6h - WT_KNO3 [Col_3_8]


title: RNAs from seed imbibed in water for 6h - WT_water [Col_2_5]


title: RNAs from seed imbibed in water for 6h - WT_water [Col_2_9]


title: RNAs from seed without imbibition - WT_dry [Col_1_9]

value: dry


title: Pooled input

city: Santa Barbara

first: Dasol

last: Han

state: California

address: University of California Santa Barbara

institute: University of California Santa Barbara

data_processing:
fastqc to QC fastq file
Fastq files were aligned to the human reference genome hg19 using bwa-0.7.13 and samtools
Peak calling on all ChIP-Seq data was performed using MACS2  with –broad parameter and using input genomic DNA as background control
Assembly: Hg19
Supplementary files format and content: bigwig files of samples genome coverage and txt of calling peaks

source_name: H9 hESCs

growth_protocol: H9 hESCs were culutred on matrigel-coated tissue culture plates with mTeSR1 media and passaged every 4-5 days depending on confluency using ReLeSR.

extract_protocol:
Formaldehyde was treated to cross-link for 15 minutes. Cross-linking was quenched by Glycine. Cells were then harvested, snap-frozen and sent to ActiveMotif for ChIP-seq service.
Illumina sequencing libraries (a custom type, using standard Illumina paired read adapter oligonucleotides) were prepared from the ChIP and Input DNAs on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500.

treatment_protocol: H9 cells were transduced with lentiviral vectors expressing control (GFP) or ZBTB12 shRNA (shA, see manuscript). Puromycin (2μg/ml) was added to the media from 24 hr post transduction. Cells were expanded to 100mm tissue culture plate.

tag: cell line

value: H9 (WiCell)

value: hESCs

tag: passage

value: pLKO.1 GFP shRNA (Addgene #30323) + pLKO.1 ZBTB12 shRNA (Sigma TRCN0000164972)

value: No IP. Input chromatin fragments.


title: anti-HDAC1, ChIP, H9, shZBTB12

tag: treatment

value: pLKO.1 ZBTB12 shRNA (Sigma TRCN0000164972)

value: anti-H3K27ac (Active Motif, #40967)


title: Male, Lung, Saline, 30549-001

description: 30549-001 - TPM

tag: strain

value: Male


title: anti-HDAC1, ChIP, H9, shGFP

value: pLKO.1 GFP shRNA (Addgene #30323)

tag: chip antibody


title: RNAs from seed without imbibition - WT_dry [Col_1_5]

value: entire seed


title: Male, Lung, Saline, 30549-004

description: 30549-004 - TPM

tag: Sex

value: Saline