title: Ch12 Klf16,Maz,Sp1,Zbtb7a KO biotag Smad7 rep1

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad7AntiSmad7S3R1

value: Klf16, Maz, Sp1, Zbtb7a Knockout


title: Expression, patient 25

status: Public on Jul 21 2022

type: SRA

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

country: Japan

institute: Chiba univercity

library_source: transcriptomic single cell

data_processing:
Basecalls and mapping performed using Cell Ranger ver 6.0
Assembly: GRCh38
Supplementary files format and content: TCR and BCR VDJ, barcodes, features and matrix tsv files

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
PBMC samples recovered from COVID-19 patients at admission (n=13) or within 10 days after admission (n=8), were stained with anti-human CD45 antibody. Propidium iodine was also added to samples to remove dead cells. Live CD45+ cells were sorted using a SONY SH800S (4,000-10,000 cells each, cell viability >98%) and then encapsulated into droplets.
Libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3.1 following the manufacturer’s protocol (10X Genomics, CA, USA). The generated scRNA-seq libraries were sequenced using a total of 127 cycles (paired-end reads) with a NovaSeq 6000 (Illumina, Inc., CA, USA)
Single cell RNA-seq, Single cell TCR and BCT V(D)J segments (scVDJ-seq)

tag: cell type

value: PBMC

tag: method

value: Expression

tag: individual

value: patient 25

tag: admission

value: admission

tag: disease state


title: cat8 YPGal 48h lane7777_GGCTAC_E56_11_CAT8_48h

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description:
cat8 YPGal 48h
Annotated Probe Report for All Probes - main paper datasets.txt

library_source: transcriptomic

data_processing:
bcl2fastq version 1.8.4 was used for demultiplexing
Assembly: R64-1-1
After adapter and quality trimming using Trim Galore (v0.6.6), RNA-seq data was mapped to yeast genome R64-1-1 using HISAT2 v2.1.0 (Kim et al., 2019) by the Babraham Institute Bioinformatics Facility. Mapped data was imported into SeqMonk v1.47.0
Quantified for log2 total reads mapping to the antisense strand of annotated open reading frames (opposite strand specific libraries) including probes to the rDNA intergrenic regions. Read counts were adjusted by Size Factor normalisation for the full set of quantified probes.
Supplementary files format and content: Tab-separated file (Annotated SeqMonk Probe report) where the first columns are information about the gene (name, strand, start, end, chromosome, …), and the remaining columns are the samples (log2RPM counts).

organism: Saccharomyces cerevisiae

source_name: MEP diploid

growth_protocol: All cells were grown in YPx media (2% peptone, 1% yeast extract, 2% sugar) at 30°C with shaking at 200 rpm. Media components were purchased from Formedium and media was sterilised by filtration. MEP experiments were performed as described with modifications (Cruz et al., 2018): cells were inoculated in 4 ml YPx (where x is the sugar) and grown for 6-8 hours then diluted in 25 ml YPx and grown for 16-18 hours to 0.2-0.6x107 cells/ml in 50 ml Erlenmeyer flasks. 0.125x107 cells per aged culture were harvested by centrifugation (15 s at 13,000 g), washed twice with 125 µl PBS and re-suspended in 125 µl of PBS containing ~3 mg/ml Biotin-NHS (Pierce 10538723). Cells were incubated for 30 min on a wheel at room temperature, washed once with 125 µl PBS and re-suspended in 125 µl YPx then inoculated in 125 ml YPx at 1x104 cells/ml in a 250 ml Erlenmeyer flask (FisherBrand FB33132) sealed with Parafilm. 1 µM β-estradiol (from stock of 1 mM Sigma E2758 in ethanol) was added after 2 h (glucose, fructose), 3 h (galactose, sucrose) or 4 h (potassium acetate). An additional 0.125x107 cells were harvested from the log phase culture while biotin labelling reactions were incubating at room temperature. Cells were harvested by centrifugation for 1 min, 4600 rpm, immediately fixed by resuspension in 70% ethanol and stored at -80°C.

extract_protocol:
Cells were re-suspended in 50 µl Lysis/Binding Buffer (from mirVANA kit, Life Technologies AM1560), and 50 µl 0.5 µm zirconium beads (Thistle Scientific 11079105Z) added. Cells were lysed with 5 cycles of 30 s 6500 ms-1 / 30 s ice in an MP Fastprep bead beater or for 3 min at power 12 in a Bullet Blender (ThermoFisher) in cold room, then 250 µl Lysis/Binding buffer added followed by 15 µl miRNA Homogenate Additive and cells were briefly vortexed before incubating for 10 minutes on ice. 300 µl acid phenol : chloroform was added, vortexed and centrifuged 5 min at 13,000 g, room temperature before extraction of the upper phase. 400 µl room temperature ethanol and 2 µl glycogen (Sigma G1767) were added and mixture incubated for 1 hour at -30 °C before centrifugation for 15 minutes at 20,000 g, 4 °C. The pellet was washed with cold 70% ethanol and re-suspended in 10 µl water. 1 µl RNA was glyoxylated and analysed on a BPTE mini-gel, and RNA was quantified using a PicoGreen RNA kit (Life Technologies R11490) or Qubit® RNA HS Assay Kit.
150 ng RNA was used to prepare libraries using the NEBNext Ultra II Directional mRNAseq kit with poly(A)+ purification module (NEB E7760, E7490) as described with modifications: Reagent volumes for elution from poly(T) beads, reverse transcription, second strand synthesis, tailing and adaptor ligation were reduced by 50%; libraries were amplified for 13 cycles using 2 µl each primer per 50 µl reaction before two rounds of AMPure bead purification at 0.9x and elution in 11 µl 0.1x TE prior to quality control using a Bioanalyzer HS DNA ChIP (Agilent) and quantification using a KAPA Library Quantification Kit (Roche).

treatment_protocol: Percoll gradients (1-2 per sample depending on harvest density) were formed by vortexing 1 ml Percoll (Sigma P1644) with 110 µl 10x PBS in 2 ml tubes and centrifuging 15 min at 15,000 g, 4 °C. Ethanol fixed cells were defrosted and washed once with 1 volume of cold PBSE (PBS + 2 mM EDTA) before resuspension in ~100 µl cold PBSE per gradient and layering on top of the pre-formed gradients. Gradients were centrifuged for 4 min at 2,000 g, 4 °C, then the upper phase and brown layer of cell debris removed and discarded. 1 ml PBSE was added, mixed by inversion and centrifuged 1 min at 2,000 g, 4 °C to pellet the cells, which were then re-suspended in 1 ml PBSE per time point (re-uniting samples where split across two gradients). 25 µl Streptavidin microbeads (Miltenyi Biotech 1010007) were added and cells incubated for 5 min on a wheel at room temperature. Meanwhile, 1 LS column per sample (Miltenyi Biotech 1050236) was loaded on a QuadroMACS magnet and equilibrated with cold PBSE in 4 °C room. Cells were loaded on columns and allowed to flow through under gravity, washed with 1 ml cold PBSE and eluted with 1 ml PBSE using plunger. Cells were re-loaded on the same columns after re-equilibration with ~500 µl PBSE, washed and re-eluted, and this process repeated for a total of three successive purifications. After addition of Triton X-100 to 0.01% to aid pelleting, cells were split into 2 fractions in 1.5 ml tubes, pelleted 30 s at 20,000 g, 4 °C, frozen on N2 and stored at -70 °C.

value: MEP diploid

tag: strain

tag: media

value: YPGal

tag: age


title: Mock_n1 A549 ATAC-Seq

city: Philadelphia

first: Erica

last: Korb

state: PENNSYLVANIA

address: 3400 Civic Center Boulevard

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
Fastq files were aligned by Bowtie2
IGVtools was used to generate TDF files
NGSplot was used to generate genome-wide analysis plots
Genome_build: hg38
Supplementary_files_format_and_content: bam files aligned by bowtie2

molecule: genomic DNA

extract_protocol:
Transfected cells were isolated by FACS and lysed in cell lysis buffer (10mM TrisHCl ph7.5, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween20, 0.1% Digitonin
Transposition reactionx mix from Nextera Library Prep kit was used (Tagment DNA Enzyme 1 and Tagment DNA Buffer)
Nextera primer sets with NEBNext Master Mix was used to generate libraries with Ampure beads used for cleanup

tag: treatment

value: Mock infection


title: Mock_n2 A549 ATAC-Seq


title: Expression, patient 29

value: patient 29


title: cat8 YPGal 24h lane7777_GATCAG_E56_9_CAT8_24h

description:
cat8 YPGal 24h
Annotated Probe Report for All Probes - main paper datasets.txt


title: Expression, patient 24

value: patient 24

value: within 10 days after admission


title: Ch12 Klf16,Maz,Sp1,Zbtb7a KO biotag Smad3 rep3

city: Bethesda

first: Yongbing

last: Zhao

state: Maryland

address: 10 Center Drive RooM 13C101A

department: NIAMS

institute: National Institutes of Health

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad3AntiSmad3S3R3

data_processing:
Base calling: Illumina CASAVA 1.8.2
ChIP-Seq: Align raw reads to the reference genome with bowtie2 (default parameters).
ChIP-Seq: Remove duplicates with picard.
ChIP-Seq: Keep high-quality reads with MAPQ>=30.
ChIP-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
ChIP-Seq: Call peak with MACS2.
Genome_build: mm10

organism: Mus musculus

source_name: Ch12 cell line

growth_protocol: CH12 B lymphoma cells were cultured in RPMI-1640 media supplemented with 10% FBS (Gemini), 1% Penicillin-Streptomycin and 50 µM of b-mercaptoethanol (Thermo Fisher Scientific).

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and stored at −80°C until further processing or resuspended in 800 uL of RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1 × Complete Mini EDTA free proteinase inhibitor (Roche)). Sonication was performed using Bioruptor sonicator, 30 cycles of 30” sonication and 30” of pause. Five microgram of respective antibody was incubated with 40 μL of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μL of sonicated chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/mL Proteinase K. ChIP DNA was purified by ChIP DNA clean and concentrator column (Zymo research).
ChIP-Seq: Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on Illumina HiSeq 3000.

treatment_protocol: CRISPR Cas9 engineering of CH12 B-cells: For complete deletion of respective transcription factor gene, two sgRNA were used per target gene. (a)sgRNA design: sgRNA targets were dresigned by the sgRNA online tool (https://crispr.zhaopage.com). Selected sgRNAs were cloned into px458 (Addgene #48138). (b) Nucleofection and cell sorting: Cultured CH12 B cells were nucleofected with 1 ug of plasmid per 1 million cells, using the SF Cell line 4D-Nucleofector X kit with the 4D-Nucleofector device (Pulse code: CM150). Cells were single cell-sorted for GFP expression into 96-well plates and allowed to recover for 7-10 days. Grown colonies were genotyped using respective primers, and clones with homozygous deletion were expanded for further experiments and analysis.

value: Ch12 cell line

tag: genotype

tag: experimental type

value: ChIP-Seq


title: Expression, patient 26

value: patient 26


title: Del_n1 A549 ATAC-Seq

value: Orf8 deletion SARS-CoV-2 infection


title: Ch12 Klf16,Maz,Sp1,Zbtb7a KO biotag Smad3 rep1

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad3AntiSmad3S3R1


title: Expression, patient 23

value: patient 23


title: cox9 gal80 YPGal 48h lane7777_CTTGTA_E56_12_COX9_GAL80_48h

description:
cox9 gal80 YPGal 48h
Annotated Probe Report for All Probes - main paper datasets.txt

value: cox9 gal80


title: Ch12 Klf16,Maz,Sp1,Zbtb7a KO BirA only input rep2

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagBirAInputS4

value: Klf16, Maz, Sp1, Zbtb7a Knockout


title: Expression, patient 22

value: PBMC

value: patient 22


title: hap4 YPD log lane7777_CGTACG_E57_2_HAP4_log

description:
hap4 YPD log
Annotated Probe Report for All Probes - mutants not in paper.txt

value: YPD

value: log


title: Ch12 Klf16,Maz,Sp1,Zbtb7a KO BirA only input rep1

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagBirAInputS3


title: Ch12 Klf16,Maz,Sp1,Zbtb7a KO BirA only rep2

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagBirAAntiBirAS4


title: Expression, patient 19

value: Expression

value: patient 19

value: admission


title: Expression, patient 20

value: patient 20


title: gcn4 YPD 48h lane7777_GAGTGG_E57_3_GCN4_48h

description:
gcn4 YPD 48h
Annotated Probe Report for All Probes - mutants not in paper.txt

value: MEP diploid


title: Ch12 Maz

description: library: ChIPch12_EGS_FA_MAZ_Bethyl

value: WT


title: Ch12 Klf16,Maz,Sp1,Zbtb7a KO BirA only rep1

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagBirAAntiBirAS3

value: Ch12 cell line


title: Ch12 Klf16,Maz,Sp1,Zbtb7a KO biotag Smad3 rep2

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad3AntiSmad3S3R2

value: ChIP-Seq


title: cox9 gal80 YPGal log lane7777_CGATGT_E56_2_COX9_GAL80_log

description:
cox9 gal80 YPGal log
Annotated Probe Report for All Probes - main paper datasets.txt

value: YPGal


title: snf4 YPGal log lane7777_CCGTCC_E56_16_SNF4_log

description:
snf4 YPGal log
Annotated Probe Report for All Probes - main paper datasets.txt


title: cat8 YPGal log lane7777_CAGATC_E56_7_CAT8_log

description:
cat8 YPGal log
Annotated Probe Report for All Probes - main paper datasets.txt


title: Ch12 Yy1

description: library: ChIPCh12WtAntiYY1S1R2


title: wild type YPGal 48h lane7777_ATGTCA_E56_15_Wt_GAL_48h

description:
wild type YPGal 48h
Annotated Probe Report for All Probes - main paper datasets.txt

value: wild type


title: hap4 YPD 48h lane7777_ATTCCT_E57_4_HAP4_48h

description:
hap4 YPD 48h
Annotated Probe Report for All Probes - mutants not in paper.txt


title: A549_siP62

type: RNA

city: London

first: John

last: Di Guglielmo

state: ON

address: 1151 Richmond Street

department: Physiology and Pharmacology

country: Canada

institute: UWO

description: Gene expression in siP62 transfected A549 cells

hyb_protocol: Following fragmentation, 5.5 ug of ss cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Probe level data was generated using Applied Biosystems Transcriptome Analysis Console v4.0.2.15. Probes were summarized to gene level data using the RMA algorithm.

label: SAPE

source_name: a549 cells

label_protocol: Biotinylated ds cDNA were prepared according to the Affymetrix Whole Transcript protocol from 100 ng total RNA.

growth_protocol: standard growth conditions; 37 degrees C; 5% CO2

extract_protocol: Trizol

treatment_protocol: siRNA transfected

tag: cell line

value: adenocarcinoma


title: A549_siCONTROL

description: Gene expression in siCONTROL transfected A549 cells

value: siCONTROL


title: Expression, patient 18

value: patient 18


title: Expression, patient 21

value: PBMC

value: patient 21


title: Ch12 Sp1

description: library: ChIPCh12WtAntiSP1S1R2


title: cat8 YPGal log lane7777_ATCACG_E56_1_CAT8_log


title: undiff_5hr_Compl

city: Yokohama

first: nobuaki

last: shiraki

address: 4259-B-25 Nagatsuta-cho, Midori-ku

department: School of Life Science and Technology

institute: Tokyo Institute of Technology

description: undifferentiated hiPSCS cultured with complete medium for 5hr

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Transcriptome Analysis console (TAC) software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (WT Expression kit for Affymetrix Whole Transcript Expression Arrays, P/N 4411973, Affymetrix).

growth_protocol: For differentiation into pancreatic endocrine cells, undifferentiated hiPSCs were dissociated and cultured in pluripotent cell maintenance medium to allow the cells to form spheres for 24 h.After the formation of spheres, hiPSCs were treated for 5 h with the same medium deprived of methionine (ΔMet) or control complete medium. Initiation of differentiation was induced by switching to differentiation media

extract_protocol: Total RNA was extraced using RNeasy Mini Kit, according to the manufacturer's instructions.

treatment_protocol: Initiation of differentiation was done after 5 h complete or methionine deprivation pretreatment. The media used for the 5-stage β cell differentiation protocol followed that reported previously (Shahjalal et al.2014; Nakashima et al. 2016), with minor modifications

tag: tissue

value: human iPS cells, Toe


title: Expression, patient 16

value: patient 16


title: Human islet

description: Human islet (HP-14341-01, PRODO)

source_name: Human islet

value: Human islet


title: undiff_5hr_deltaMet

description: undifferentiated hiPSCS cultured with methionine deprived medium for 5hr


title: Day25_Compl

description: hiPSCS derived EG cells differentiated using pancreatic diff. media for 25 days after 5 h complete pretreatment.

source_name: hiPSCS derived EC cells_Compl


title: Day13_Compl

description: hiPSCS derived EP cells differentiated using pancreatic diff. media for 13 days after 5 h complete pretreatment.

source_name: hiPSCS derived EP cells_Compl


title: Day25_deltaMet

description: hiPSCS derived EG cells differentiated using pancreatic diff. media for 25 days after 5 h methionine deprivation pretreatment.

source_name: hiPSCS derived EC cells_deltaMet


title: Day13_deltaMet

description: hiPSCS derived EP cells differentiated using pancreatic diff. media for 13 days after 5 h methionine deprivation pretreatment.

source_name: hiPSCS derived EP cells_deltaMet


title: Expression, patient 15

value: Expression

value: patient 15

value: within 10 days after admission


title: Ch12 biotag Zbtb7a

description: library: ChIPCh12BiotagZbtb7aAntiZbtb7a


title: Expression, patient 13

value: patient 13


title: Expression, patient 17

value: patient 17


title: cox9 gal80 YPGal log lane7777_ACTTGA_E56_8_COX9_GAL80_log

value: MEP diploid

value: cox9 gal80

value: log


title: Expression, patient 14

value: patient 14

value: admission


title: P7_GNPs_ATAC_rep1

city: Beijing

first: Du

last: Yi

state: Beijing

address: No. 1 West Beichen Road

country: China

institute: Institute of Genetics and Developmental Biology Chinese Academy of Sciences

data_processing:
ATAC-seq reads were trimed using fastp  (0.21.0).
Pair-end ATAC-seq reads were aligned to the mouse genome (mm10) by Bowtie2 (2.4.4) with the parameters --end-to-end.
Mapped reads were sorted using Samtools (1.12) and duplicated reads were removed with the Picard MarkDuplicates function (2.25.5). Only primary aligned reads with MAPQ greater than 30  were used for further analysis.
Unique reads were shifted by ATACseqQC R package.
Peak calling was performed by MACS2 (2.2.7.1) with following parameters: -f BAMPE -q 0.05 --shift -100 --extsize 200 --nomodel -B --SPMR -g mm. Blacklisted regions identified by ENCODE(Amemiya et al., 2019) from mm10 were removed from the peak file with the bedtools (2.30.0) subtract module.
read counts were normalized using bamCoverage in the Deeptools2 (3.5.1) suite to compute the counts per million reads sequenced (CPM) on a 10-bp window.
Genome_build: mm10
Supplementary_files_format_and_content: Narrow Peaks format includes peak coordinates, length, summit, -log(pvalue) and fold enrichment

source_name: cerebellar GNP

extract_protocol:
Atoh1 positive GNPs were FACS purified from the P7 cerebellum. Cells were lysised in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.5%NP-40) for 10 min on ice. After lysis, the nuclear lysis were incubate with Tn5 transposome and 5×TTBL (Vazyme Biotech, TD502) at 37 ℃ for 30 min. 5×TS was added to stop the tagmentation reaction. DNA was purified by phenol-chloroform extraction with the presence of 40 ng carrier RNA followed by ethanol precipitation and then amplified by PCR
Sequencing library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina. PCR was preformed to amplified the library for 15-20 cycles according to the DNA amount. After the PCR reaction, libraries were size selected by 0.5×SPRI beads and purified with additional 1×SPRI beads.  The libraries were then sequenced on a NovaSeq sequencer.

value: cerebellum

value: granule neuron progenitor


title: wild type YPGal log lane7777_AGTCAA_E56_13_Wt_GAL_log

description:
wild type YPGal log
Annotated Probe Report for All Probes - main paper datasets.txt

value: wild type

value: YPGal


title: Day11_deltaMet

description: hiPSCS derived PP cells differentiated using pancreatic diff. media for 11 days after 5 h methionine deprivation pretreatment.

source_name: hiPSCS derived PP cells_deltaMet

value: human iPS cells, Toe


title: Ch12 biotag Klf13

description: library: ChIPCh12BiotagKLF13AntiKLF13

value: Ch12 cell line

value: WT

value: ChIP-Seq


title: P7_GNPs_ATAC_rep2


title: Expression, patient 11

value: PBMC

value: Expression

value: patient 11


title: Day11_Compl

description: hiPSCS derived PP cells differentiated using pancreatic diff. media for 11 days after 5 h complete pretreatment.

source_name: hiPSCS derived PP cells_Compl


title: wild type YPD->YPGal log lane7777_ATGAGC_E53_3_5_GLU-GAL

description:
wild type YPD->YPGal log
Annotated Probe Report for All Probes - media shifts.txt

value: YPD->YPGal


title: P1_cochlearHC_ATAC_rep2

data_processing:
Files from same library (P1_cochlearHC_ATAC_rep1 and P1_cochlearHC_ATAC_rep1_add) were combined together using cat command. ATAC-seq reads were trimed using fastp  (0.21.0).
Pair-end ATAC-seq reads were aligned to the mouse genome (mm10) by Bowtie2 (2.4.4) with the parameters --end-to-end.
Mapped reads were sorted using Samtools (1.12) and duplicated reads were removed with the Picard MarkDuplicates function (2.25.5). Only primary aligned reads with MAPQ greater than 30  were used for further analysis.
Unique reads were shifted by ATACseqQC R package.
Peak calling was performed by MACS2 (2.2.7.1) with following parameters: -f BAMPE -q 0.05 --shift -100 --extsize 200 --nomodel -B --SPMR -g mm. Blacklisted regions identified by ENCODE(Amemiya et al., 2019) from mm10 were removed from the peak file with the bedtools (2.30.0) subtract module.
read counts were normalized using bamCoverage in the Deeptools2 (3.5.1) suite to compute the counts per million reads sequenced (CPM) on a 10-bp window.
Genome_build: mm10
Supplementary_files_format_and_content: Narrow Peaks format includes peak coordinates, length, summit, -log(pvalue) and fold enrichment

source_name: cochlear hair cell

extract_protocol:
Atoh1 positive hair cells were FACS purified from the P1 cochlea. Cells were lysised in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.5%NP-40) for 10 min on ice. After lysis, the nuclear lysis were incubate with Tn5 transposome and 5×TTBL (Vazyme Biotech, TD502) at 37 ℃ for 30 min. 5×TS was added to stop the tagmentation reaction. DNA was purified by phenol-chloroform extraction with the presence of 40 ng carrier RNA followed by ethanol precipitation and then amplified by PCR
Sequencing library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina. PCR was preformed to amplified the library for 15-20 cycles according to the DNA amount. After the PCR reaction, libraries were size selected by 0.5×SPRI beads and purified with additional 1×SPRI beads.  The libraries were then sequenced on a NovaSeq sequencer.

value: cochlea

value: hair cell


title: Day5_Compl

description: hiPSCS derived PG cells differentiated using pancreatic diff. media for 5 days after 5 h complete pretreatment.

source_name: hiPSCS derived PG cells_Compl


title: Expression, patient 9

value: patient 9


title: Day3_deltaMet

description: hiPSCS derived DE cells differentiated using pancreatic diff. media for 3 days after 5 h methionine deprivation pretreatment.

source_name: hiPSCS derived DE cells_deltaMet


title: wild type YPD 24h lane7752_TTAGGC_E53_3_GLU_24h

description:
wild type YPD 24h
Annotated Probe Report for All Probes - media shifts.txt

value: MEP diploid

value: YPD


title: wild type YPGal 24h lane7777_AGTTCC_E56_14_Wt_GAL_24h

description:
wild type YPGal 24h
Annotated Probe Report for All Probes - main paper datasets.txt


title: Expression, patient 10

value: patient 10

value: admission


title: Day3_Compl

description: hiPSCS derived DE cells differentiated using pancreatic diff. media for 3 days after 5 h complete pretreatment.

source_name: hiPSCS derived DE cells_Compl


title: P1_cochlearHC_Atoh1_C_R_ctrl

data_processing:
Library strategy: CUT&RUN
CUT&RUN reads were trimed using fastp  (0.21.0).
Pair-end CUT&RUN reads were aligned to the mouse genome (mm10) by Bowtie2 (2.4.4) with the parameters --end-to-end.
Mapped reads were sorted using Samtools (1.12) and duplicated reads were removed with the Picard MarkDuplicates function (2.25.5). Only primary aligned reads with MAPQ greater than 30  were used for further analysis.
Peak calling was performed by MACS2 (2.2.7.1) with following parameters: -f BAMPE -q 0.05 -B --SPMR -g mm.
read counts were normalized using bamCoverage in the Deeptools2 (3.5.1) suite to compute the counts per million reads sequenced (CPM) on a 10-bp window.
Genome_build: mm10
Supplementary_files_format_and_content: Narrow Peaks format includes peak coordinates, length, summit, -log(pvalue) and fold enrichment

extract_protocol:
Cochlear sensory regions from Atoh1-EGFP/+ and Atoh1-EGFP/Atoh1-EGFP mice at P1 were dissected and directly treated with EGFP antibody (experimental group, 2 replicates) or IgG (control, 1 replicate). Bio-Mag Plus Concanavalin A coated beads (Co-A beads) were equilibrated and washed by binding buffer (20 mM HEPES pH7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) three times and resuspended by binding buffer. Fresh cochleae were transferred to 45 ?l wash buffer (20 mM HEPES pH7.5, 150 mM NaCl, 0.5 mM spermidine, 1×proteinase inhibitor cocktail). Cochlear tissues were added the resuspended Co-A beads and incubated at room temperature for 10 min. Samples were separated from the buffer through magnetic stand. Samples were further incubated with rabbit anti-GFP (Abcam, Cat#: ab290) or rabbit anti-mouse IgG (Abcam, Cat#: ab46540) antibodies with a 1:100 dilution in antibody incubation buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.02% digitonin, 2 mM EDTA, 1× protease-inhibitor cocktails) at 4?°C for 2 h. After washing out the unbound antibodies, samples were incubated with pA-MNase for an additional hour at 4 °C. Soluble target DNA (180 ml) was released after Ca2+ activation, stopped by adding 20 ml 10×DRSTOP buffer (1.7 M NaCl, 100 mM EDTA, 20 mM EGTA, 0.02% digitonin, 0.25 mg/ml glycogen). The target DNA was purified through phenol-chloroform extraction with the presence of 40 ng carrier RNA followed by ethanol precipitation overnight at -20°C. NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, E7645S) was used for library construction, and then SPRI beads (Beckman coulter, Cat#: B23318) were used to perform size selection to enrich 200 bp-500 bp libraries.
NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, E7645S) was used for library construction. The library was size selected by 0.65× and another 0.75× beads.

tag: antibody

value: rabbit anti-mouse IgG (ab46540)


title: cat8 YPGal 48h lane7777_ACAGTG_E56_5_CAT8_48h

description:
cat8 YPGal 48h
Annotated Probe Report for All Probes - main paper datasets.txt

value: YPGal


title: P1_cochlearHC_ATAC_rep1


title: P1_cochlearHC_Atoh1_C_R_rep2

value: rabbit anti-GFP (ab290)


title: wild type YPD->YPD log lane7752_TGACCA_E53_4_GLU-GLU

description:
wild type YPD->YPD log
Annotated Probe Report for All Probes - media shifts.txt

value: wild type

value: YPD->YPD

value: log


title: wild type YPD->YPD log lane7777_GGTAGC_E53_3_4_GLU-GLU


title: Day5_deltaMet

description: hiPSCS derived PG cells differentiated using pancreatic diff. media for 5 days after 5 h methionine deprivation pretreatment.

source_name: hiPSCS derived PG cells_deltaMet

value: human iPS cells, Toe


title: Expression, patient 8

source_name: PBMC

value: PBMC

value: Expression

value: patient 8

value: within 10 days after admission


title: Expression, patient 12

value: patient 12


title: f10n (E8.5 Mef2c-F10N-LacZ)

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

description: 3 embryos out of the 6 collected from Mef2c-F10N-LacZ contained the Mef2c-F10N-LacZ construct

data_processing:
fastq files were generated from bcl files using bcl2fastq2 v2.20 and 10x cellranger version 3.0.0. Data was aligned to the mm10 genome from UCSC with annotations from Ensembl 98. Sequences for lacZ and pEYFP were included in the gene annotation.
Data was read into R (3.6.1) and analyzed using Seurat (3.1.5.9003)
Data was filtered to remove cells with less than 500 genes, greater than 10,000 genes, or a mitochondrial percentage higher than the 75th percentile of the f10n sample.
Data was normalized using SCTransform in Seurat. 46 Principal components were used for further analysis. The two data sets were integrated using Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data is the integrated data from both experiments (from the SCT assay, data slot). "eyfp" and "f10n" were prepended to each cell id. The file is tab delimited text. The IDs are ensembl ids and gene symbols from Ensembl 98. The metadata.txt file is the metadata table from the Seurat object showing the cluster identity and other metadata about the cells.

extract_protocol:
Cranial tissues successfully isolated from each set of 6 embryos were quickly transferred into a 1.5ml Eppendorf tube on ice. Tissues were then incubated in 500ul 0.25% Trypsin+EDTA in 37C water bath for 1min and dissociated through gentle repetitive pipetting about 10 times. The tube was then incubated again in 37C water bath for another minute prior to the addition of 250ul cold FBS to stop tissue reaction with Trypsin. Tissues were dissociated further through the same pipetting motion while avoiding the formation of any bubbles. Samples were then centrifuged at 1600rcf at 15C for 4 mins. Supernatant was removed and cells were resuspended in 200ul PBS+2% FBS. Cells were centrifuged again and resuspended in 40ul PBS
Dissociated cells were loaded on a Chromium Single Cell Controller (10x Genomics), based on live cell concentration, with a target of 4,000-10,000 cells per sample. Libraries were prepared using the Chromium Next GEM Chip G Single Cell Kit (10x Genomics) according to manufacturer’s directions. Resulting short fragment libraries were checked for quality and quantity using an Bioanalyzer 2100 (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: No treatment. Pregnant female was sacrificed by cervical dislocation. All embryo dissection and dissociation were carried out in DEPC Tyrode and RNase-free solutions

value: Mouse embryo

tag: developmental stage

value: FVB


title: P1_cochlearHC_Atoh1_C_R_rep1

value: cochlea

value: hair cell


title: Expression, patient 7

value: patient 7

value: admission


title: wild type YPD 24h lane7752_GTTTCG_E53_3_3_GLU_24h

source_name: MEP diploid

value: MEP diploid

value: YPD


title: wild type YPGal log lane7752_GTGGCC_E53_3_2_GAL_log

description:
wild type YPGal log
Annotated Probe Report for All Probes - media shifts.txt

value: wild type

value: YPGal


title: eyfp (E8.5 Wnt1-Cre;R26R-eYFP)

description: 4 embryos out of the 6 collected from Wnt1-Cre;R26R-YFP were positive for YFP signal

value: Mixed background:B6/129/FVB


title: wild type YPGal log lane7752_TAGCTT_E53_2_2_GAL_log

value: log


title: wild type YPD log lane7752_GTCCGC_E53_3_1_GLU_log

description:
wild type YPD log
Annotated Probe Report for All Probes - media shifts.txt


title: control kd, rep2

city: Toledo

first: Robert

middle: J

last: Trumbly

state: OH

address: 3000 Arlington Avenue

department: Biochemistry and Cancer Biology

institute: University of Toledo

hyb_protocol: Standard hybridization conditions recommended by Affymetrix for the Mouse Gene 2.0 ST chip.

scan_protocol: Standard Affymetrix protocol for the Mouse Gene 2.0 ST chip.

data_processing: The CEL files were analyzed using the Oligo package from Bioconductor. The rma function performed background subtraction, normalization and summarization using median-polish in a single step.

source_name: beast cancer cell line

label_protocol: The cRNA was labeled with biotinylated ribonucleotide analog.

growth_protocol: 168FARN cells were cultured in 5% FBS/5% newborn calf serum.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) from three independent samples of RKIP or control knockdown 168FARN cells

treatment_protocol: For RNAi-based silencing of expression of RKIP, we prepared stable knockdown cells expressing the corresponding small interfering RNAs (siRNAs) or a firefly luciferase-specific siRNA as control from the short hairpin RNA (shRNA) expression vectors pSUPER.retro-puro (Oligoengine).

value: breast cancer cell

tag: sirna

value: control luciferase


title: Expression, patient 4

value: PBMC

value: Expression

value: patient 4


title: RKIP kd, rep3

value: RKIP


title: Expression, patient 6

value: patient 6


title: C57BL/6 resting B cell WGS

description: library: WGSC57Bl6GENOME

data_processing:
Base calling: Illumina CASAVA 1.8.2
Whole genome sequencing: Align raw reads to the reference genome with bwa (default parameters).
Whole genome sequencing: Remove mitochondria reads.
Whole genome sequencing: Keep high-quality reads with MAPQ>=30.
Whole genome sequencing: Extract all variants with bcftools .
Genome_build: mm10

source_name: resting B cells

extract_protocol:
Whole genome sequencing: B cells were isolated from spleen of respective mouse strain using EasySep™ Mouse B Cell Isolation Kit (#19854, Stemcell Technologies). Genomic DNA was extracted using DNeasy Blood and tissue kit according to the manufacturer’s instructions (#69506, Qiagen).
Whole genome sequencing: PCR-free whole genome sequencing library was prepared using TruSeq DNA PCR-Free High Throughput Library Prep Kit (#20015963, Illumina) using 1 ug as input genomic DNA, according to manufacturer’s instructions. 100 cycles of sequencing data were acquired on the Illumina NovaSeq 6000 (Illumina).

value: resting B cells

value: Whole genome sequencing


title: wild type YPGal->YPD log lane7752_GTAGAG_E53_3_8_GAL-GLU

description:
wild type YPGal->YPD log
Annotated Probe Report for All Probes - media shifts.txt

value: YPGal->YPD


title: control kd, rep3


title: Expression, patient 3

value: patient 3

value: within 10 days after admission


title: control kd, rep1


title: BALB/c resting B cell WGS

description: library: WGSBalbcGENOME


title: day 2 rep 2

city: New Delhi

first: Jyothish

middle: Madambikattil

last: Sasi

state: Delhi

address: BenitoJuarez Marg

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi

description: small RNA profiling

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequencing data was filtered through a pipeline of UEA small RNA workbench 3.0 with default parameters (Stocks et al. 2012). The sequences without 3’ adaptor and those trimmed sequences not lying between the specified sequence lengths were discarded and sequences with the length specified by the user (16-35 nt) were extracted. Further, low complexity sequences (sequences containing less than 3 distinct nucleotides), invalid tags with ‘N’ nucleotides, degradation products and other non-small RNAs were discarded. The fragments of rRNA, tRNA, snRNA or snoRNA were removed after being mapped on plant t/rRNAs sequences from “Rfam” (except miRNA), Arabidopsis tRNAs from “The Genomic tRNA Database”, and plant t/rRNA sequences from “EMBL” release 95.
For identification of miRNAs and their precursors, the clean putative small RNA reads obtained after filtration through elimination pipeline were aligned to rice reference genome dataset with no mismatch by using miRCat pipeline of UEA sRNA tool kit with set parameters (Stocks et al. 2012).
Assembly: Rice genome  MSU7.0
Supplementary files format and content: The .txt files report abundance measurements of small RNA reads

organism: Oryza sativa

source_name: Coleoptile

growth_protocol: Rice seeds were surface sterilized and submerged for seven days in sterile water.

extract_protocol:
Total RNA was isolated using modified guanidinium isothiocyanate (GITC) method (Chomzynski and Sacchi, 1987). Quantity and quality of RNA was assessed using a spectrophotometer (Bio-Rad, USA) followed by checking on MOPS-formaldehyde-agarose gel.
Low molecular weight RNA fraction was extracted from the total RNA by resolving on a TBE-urea-PAGE gel and excising 15-30 nt portion. The Low molecular weight RNA was ligated with 5’ and 3’ RNA adapters using T4 RNA ligase. First strand cDNA was synthesized from the adapter ligated low molecular weight fraction and cDNA library was enriched using adapter-specific primers. The enriched libraries were purified, and the quality of the same was evaluated using Bioanalyzer (Agilent Technologies, USA). High-throughput sequencing of libraries was performed using Illumina GA IIx sequencing platform.

treatment_protocol: The seeds with coleoptile was transferred to aerobic condition

value: Coleoptile

value: 9 days post germination

value: submergence


title: Expression, patient 2

value: patient 2

value: admission


title: day 2 rep 1

description: small RNA profiling

value: wild type


title: Control rep 2

description: small RNA profiling

value: 7 days post germination


title: Expression, patient 5

value: PBMC

value: patient 5


title: wild type YPD 24h lane7752_GGCTAC_E53_2_3_GLU_24h

value: MEP diploid

value: YPD


title: Ch12 Sp4 Sp1het Ko H2

description: library: RNAch12Sp4Sp1hetH2

data_processing:
Base calling: Illumina CASAVA 1.8.2
mRNA-Seq: Align raw reads to the reference genome with STAR.
mRNA-Seq: Quantify transcript and gene abundances with RSEM.
mRNA-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
Genome_build: mm10

source_name: Ch12 cell line

extract_protocol:
mRNA-seq: Total RNA was extracted from 0.5 million cultured cells using RNAqueous™ Total RNA Isolation Kit (AM1912). mRNA was then isolated using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB E7490).
mRNA-seq: Standard RNA-Seq library preparation was performed following Illumina's RNA-Seq protocol v2. 50 cycles of sequencing data were acquired on HiSeq 3000 (Illumina).

value: Ch12 cell line

value: Sp4 Sp1het Knockout

value: mRNA-Seq


title: Ch12 Sp4 Sp1het Ko G2

description: library: RNAch12Sp4Sp1hetG2


title: wild type YPD log lane7752_GATCAG_E53_2_1_GLU_log

value: log


title: RKIP kd, rep2

value: breast cancer cell

value: RKIP


title: RKIP kd, rep1


title: wild type YPGal 24h lane7752_GCCAAT_E53_6_GAL_24h

description:
wild type YPGal 24h
Annotated Probe Report for All Probes - media shifts.txt

value: YPGal


title: Ch12 Sp4 Sp1het Ko C4

description: library: RNAch12Sp4Sp1hetC4


title: Expression, patient 1

value: Expression

value: patient 1


title: Control rep 1

description: small RNA profiling

value: Coleoptile

value: submergence


title: CAST/EiJ resting B cell WGS

description: library: WGSCastGENOME

value: resting B cells

value: Whole genome sequencing


title: granulosa cells_4h

city: Ube

first: Yuichiro

last: Shirafuta

state: Yamaguchi

address: 1-1-1, minami-kogushi

institute: Yamaguchi university

data_processing:
Basecalls performed using CASAVA version 1.8
Tophat version 2.1.1 with the default parameters was used to map onto the human mm10 assembly
Cufflinks version 2.2.1 with -G option was used to quantify the gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values file with FPKM values

source_name: mouse granulosa cells

growth_protocol: C57BL/6 female mice were injected intraperitoneally with 4 IU of eCG to promote follicular growth followed by 5 IU of hCG injection to induce ovulation and luteinization.

extract_protocol:
Total RNA was isolated from the granulosa cells from three different mice at each time point, respectively, with an RNeasy® Mini Kit (QIAGEN).
The library for mRNA-seq was generated by the modified Illumina protocol using a mRNAseq preparation kit (Illumina).

treatment_protocol: The ovaries were obtained before hCG (0), and 4, 12 hours (h) after hCG injection.  The follicles were punctured to isolate GCs.

value: wild type

value: post natal day 21-28

tag: treatment/time point

value: 4 hours after hCG injection

value: ovary

value: mouse granulosa cells


title: wild type YPGal log lane7752_CGATGT_E53_2_GAL_log

tag: cell type

value: MEP diploid


title: granulosa cells_12h

value: 12 hours after hCG injection


title: granulosa cells_12h_H3K4me3

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie version 2.2.3 with the default parameters
Data were filtered using the following specifications…
peaks were called using MACS version 2.0.9 with the following setting: effective genome size = 1.87x10^9 (Mus musculus); upper and lower limit for model building = 5 and 50; q-value cutoff = 0.05; bandwidth = 300; broad mode = “off” ; nolambda=”on”.
Genome_build: mm10
Supplementary_files_format_and_content: peak BED file

extract_protocol:
Lysates were clarified from sonication/enzymatic digested nuclei and histone-DNA complexes were isolated with antibody.  The ChIP DNA and the Input DNA ends were repaired using T4 DNA polymerase, Klenow enzyme, and T4 polynucleotide kinase(PNK) (New England Biolabs), followed by treatment with Klenow exo- to add an A base to the 3’ end. After ligation of the Solexa adaptor using TaKaRa ligation Mix (TaKaRa), the adaptor-ligated DNAs were amplified using Solexa PCR primers for 18 cycles, and the amplified library was isolated from an agarose gel. The samples were purified using the QIAquick MinElute kit (Qiagen) at each preparation step.
The purified library was used for cluster generation and sequencing analysis using the Genome Analyzer GAIIx (Illumina).

tag: chip antibody

value: H3K4me3 (generous gifts from Dr. H. Kimura, Osaka University, Osaka, Japan)


title: Ch12 Sp2 Sp3 Ko G2r2

description: library: RNAch12Sp2Sp3G2r2

value: Ch12 cell line

value: Sp2 Sp3 Knockout

value: mRNA-Seq


title: granulosa cells_4h_H3K4me3


title: P300

city: Tianjin

first: Heng

last: Zhang

address: 38 Rd.Tongyan

institute: Nankai University

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR)  primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format  were processed by Cutadapt[1]（version 1.9.1）to be high quality clean data.
Mapping: Firstly, hg38 reference genome sequences and gene model annotation files were  downloaded from UCSC. Secondly, bowtie2-build  is used to index reference genome sequence. Finally, clean data is aligned to reference genome via  software Bowtie2 (version 2.2.6).
Peaks analysis: Use MACS[2](V2) to analyze peaks quality control, peaks calling and peaks annotation.
Assembly: hg38
Supplementary files format and content: bw

growth_protocol: PLC-PRF-5 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum and 100 U/mL penicillin, 100 mg/mL streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and H3K4me3-DNA, H3K4me1-DNA, H3K27ac DNA or P300-DNA complexes were isolated with antibody.
For each sample, ChIP product was used for library preparation. The ChIP product was treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dA-tailing in one reaction, followed by ligation to adaptors with a “T” base overhang. Adaptorligated DNA was then recovered using Beads. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flowcell to perform bridge PCR and P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 3.0 Fluorometer.

value: Alexander Hepatoma cell


title: wild type YPD->YPD log lane7752_CTTGTA_E53_2_4_GLU-GLU

value: YPD->YPD

value: log


title: Ch12 Sp2 Sp1het Ko F2

description: library: RNAch12Sp2Sp1hetF2

value: Sp2 Sp1het Knockout


title: H3K27ac


title: Ch12 Sp2 Sp3 Ko G2r3

description: library: RNAch12Sp2Sp3G2r3


title: wild type YPGal->YPD log lane7752_CCGTCC_E53_2_8_GAL-GLU

value: YPGal->YPD


title: H3K4me1


title: granulosa cells_0h_H3K4me3

value: before hCG (0) injection


title: H3K4me3


title: Ch12 Sp2 Sp3 Ko G2r1

description: library: RNAch12Sp2Sp3G2r1


title: Ch12 Sp2 Sp1het Ko C7

description: library: RNAch12Sp2Sp1hetC7


title: wild type YPGal->YPGal log lane7752_CAGATC_E53_7_GAL-GAL

description:
wild type YPGal->YPGal log
Annotated Probe Report for All Probes - media shifts.txt

value: wild type

value: YPGal->YPGal


title: HUVEC, Gsα, rep3

city: Jinan,

first: Lifan

last: He

state: Shandong

address: No. 107, Wen Hua Xi Rd,

institute: Shandong University

data_processing:
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions
the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated
Reads Count for each gene in each sample was counted by HISAT v2.1.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DESeq2 was designed for differential gene expression analysis between two samples with biological replicates. Genes with q≤0.05 and |log2_Foldchange|≥1 are identified as differentially expressed genes.
Assembly: Home_sapiens.GRCh38.94.chr
Supplementary files format and content: expression profiles

source_name: endothelium

growth_protocol: HUVECs were cultured by ECM supplemented with 5% FBS and 1% ECGF

extract_protocol:
RNA was harvested using Trizol (Thermo Fisher). Total RNA > 10nM was used for the construction of sequencing libraries.
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: HUVECs were transfected with GFP and Gsα adenovirus for 48 hours

value: endothelium

value: HUVEC

value: endothelial cells

value: Gsalpha overexpression


title: wild type YPGal->YPGal log lane7752_ATGTCA_E53_2_7_GAL-GAL

data_processing:
bcl2fastq version 1.8.4 was used for demultiplexing
Assembly: R64-1-1
After adapter and quality trimming using Trim Galore (v0.6.6), RNA-seq data was mapped to yeast genome R64-1-1 using HISAT2 v2.1.0 (Kim et al., 2019) by the Babraham Institute Bioinformatics Facility. Mapped data was imported into SeqMonk v1.47.0
Quantified for log2 total reads mapping to the antisense strand of annotated open reading frames (opposite strand specific libraries) including probes to the rDNA intergrenic regions. Read counts were adjusted by Size Factor normalisation for the full set of quantified probes.
Supplementary files format and content: Tab-separated file (Annotated SeqMonk Probe report) where the first columns are information about the gene (name, strand, start, end, chromosome, …), and the remaining columns are the samples (log2RPM counts).

extract_protocol:
Cells were re-suspended in 50 µl Lysis/Binding Buffer (from mirVANA kit, Life Technologies AM1560), and 50 µl 0.5 µm zirconium beads (Thistle Scientific 11079105Z) added. Cells were lysed with 5 cycles of 30 s 6500 ms-1 / 30 s ice in an MP Fastprep bead beater or for 3 min at power 12 in a Bullet Blender (ThermoFisher) in cold room, then 250 µl Lysis/Binding buffer added followed by 15 µl miRNA Homogenate Additive and cells were briefly vortexed before incubating for 10 minutes on ice. 300 µl acid phenol : chloroform was added, vortexed and centrifuged 5 min at 13,000 g, room temperature before extraction of the upper phase. 400 µl room temperature ethanol and 2 µl glycogen (Sigma G1767) were added and mixture incubated for 1 hour at -30 °C before centrifugation for 15 minutes at 20,000 g, 4 °C. The pellet was washed with cold 70% ethanol and re-suspended in 10 µl water. 1 µl RNA was glyoxylated and analysed on a BPTE mini-gel, and RNA was quantified using a PicoGreen RNA kit (Life Technologies R11490) or Qubit® RNA HS Assay Kit.
150 ng RNA was used to prepare libraries using the NEBNext Ultra II Directional mRNAseq kit with poly(A)+ purification module (NEB E7760, E7490) as described with modifications: Reagent volumes for elution from poly(T) beads, reverse transcription, second strand synthesis, tailing and adaptor ligation were reduced by 50%; libraries were amplified for 13 cycles using 2 µl each primer per 50 µl reaction before two rounds of AMPure bead purification at 0.9x and elution in 11 µl 0.1x TE prior to quality control using a Bioanalyzer HS DNA ChIP (Agilent) and quantification using a KAPA Library Quantification Kit (Roche).

value: MEP diploid


title: A549 cells with Orf8 deletion, CoV2 infection, H3K9ac IP, replicate r3

first: Karl

middle: Michael

last: Glastad

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: CDB

data_processing:
raw reads demultiplexed with bcl2fastq
reads quality and adapter trimmed with cutadapt
aligned to GRCh38 using bowtie2
peaks were called with macs2
Assembly: GRCh38
Supplementary files format and content: bed files with all peaks called using given approach for each replicate hPTM

source_name: A549 cells

extract_protocol:
For histone PTM ChIP-sequencing, 4-10M cells were resuspended in 1mL of lysis buffer 1 (50mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol,0.5% NP-40, 0.25% Triton X-100) and rotated at 4C for 10min, followed by centrifugation removal of supernatant. Cells were then re-suspended in 1mL lysis buffer 2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA), rotated for 10min at 4C, followed by centrifugation removal of supernatant.Cells were then resuspended in 1mL of lysis buffer 3 (10mM Tris-HCl pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and rotated again for 10min at 4C. This was followed by sonication with a Covaris S220 sonicator for 35 minutes (peak incident power: 140; duty factor: 5 %; cycles/burst: 200). This was followed by addition of 110uL Triton X-100, and centrifugation for 15minutes at maximum speed (20kg) at 4C to clear lysate. Lysate chromatin concentration was then equalized according to DNA content (as measured with a qubit flourometer). Following this, 5% of equivalently-treated chromatin from C. floridanus pupae were added to all samples according to chromatin concentration, and 50uL of lysate saved as input shearing control. 250uL of equalized lysate were then added to washed, antibody-conjugated protein A/G Dynabeads (2ug antibody conjugated to 15uL/15uL A/G dynabeads, resuspended in 50uL per IP) and IPs were rotated overnight at 4C in a final volume of 300uL. The following day, IPs were washed 5x in RIPA wash buffer (50mM HEPES-KOH pH 7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and once in TE pH 8.0. Washes were followed by two elutions into 75   l of elution buffer (50 mM Tris-HCl pH 8.0; 10 mM EDTA; 1% SDS) at 65  C for 45 min with shaking(1,100 RPM). DNA was purified via phenol:chloroform:isoamyl alcohol (25:24:1) followed by ethanol precipitation. Pelleted DNA was resuspended in 25 ul TE.
Libraries for sequencing were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina  (NEB E7645), as described by the manufacturer but using half volumes of all reagents and starting material. For PCR amplification optimal number of PCR cycles was determined using a qPCR side-reaction using 10% of adapter-ligated, size-selected DNA. 8 cycles of PCR were used for hPTM libraries and 5 cycles were used for Inputcontrols. Samples were sequenced on a NextSeq 500 instrument (42bp read length, paired end).

value: Orf8 deletion, CoV2 infection

tag: chip target

value: H3K9ac IP (Active Motif, cat# 39137)


title: A549 cells with Orf8 deletion, CoV2 infection, H3K9ac IP, replicate r2


title: HUVEC, GFP, rep3

value: WT


title: wild type YPGal 24h lane7752_AGTTCC_E53_2_6_GAL_24h

value: YPGal


title: Ch12 Sp2 Sp1 Ko E10r3

description: library: RNAch12Sp2Sp1E10r3

value: Ch12 cell line

value: Sp2 Sp1 Knockout

value: mRNA-Seq


title: wild type YPD->YPGal log lane7752_AGTCAA_E53_2_5_GLU-GAL

value: YPD->YPGal

value: log


title: wild type YPGal->YPGal log lane7752_ATTCCT_E53_3_7_GAL-GAL


title: HUVEC, Gsα, rep2


title: Ch12 Sp2 Sp1 Ko E10r2

description: library: RNAch12Sp2Sp1E10r2


title: Ch12 Sp2 Sp1het Ko E2

description: library: RNAch12Sp2Sp1hetE2

value: Sp2 Sp1het Knockout


title: A549 cells with Orf8 deletion, CoV2 infection, H3K9ac IP, replicate r1


title: HUVEC, Gsα, rep1


title: wild type YPD log lane7752_ATCACG_E53_1_GLU_log

value: wild type

value: YPD


title: A549 cells with CoV2 infection, H3K9ac IP, replicate r3

value: CoV2 infection


title: Ch12 Sp2 Sp1 Ko E10r1

description: library: RNAch12Sp2Sp1E10r1


title: HUVEC, GFP, rep2

value: endothelium

value: HUVEC


title: A549 cells with CoV2 infection, H3K9ac IP, replicate r1


title: T47D from T47D+HS27a Co-Culture Sample 5

city: Ann Arbor

first: Gary

last: Luker

state: MI

address: 109 Zina Pitcher Place  A710 Biomedical Sciences Research Building

department: Radiology

institute: University of Michigan

description:
2151-JB-9
Counts_Raw_2151.txt
CPM_2151.txt

data_processing:
Trimmed using Trim_Galore (v 0.5.0) https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Aligned using STAR (v 2.6.0) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/
UMI collapsed using Lexogen’s supplied collapse_UMI_bam binary.
Counted using Bioconductor R package Rsubread and featureCounts function:
Genome_build: Reference and Annotation: GRCh38 from ENSEMBL

source_name: ER+ Breast Cancer Cells

growth_protocol: We grew cells for 24 hours in 10cm polystyrene, cell culture-treated dishes in full medium (DMEM (#11995, Gibco, Thermo Fisher, Grand Island, NY, USA) with 10% FBS (HyClone, ThermoScientific, Waltham, MA, USA), 1% GlutaMAX (#35050, Gibco), and 1% Penicillin-Streptomycin (P/S, #15140, Gibco)). We seeded cells either by themselves (monoculture) or in co-culture at a ratio of 10% cancer cells with 90% MSCs. After 24 hours, we changed medium to low glucose, phenol-red free DMEM (LG/LF, #11054, Gibco) with 1% FBS, 1% GlutaMAX, 1% P/S, and 10 nM β-Estradiol (#E2758, Sigma-Aldrich, Millipore Sigma, Saint Louis, MO, USA). We waited 48 hours after changing media to harvest cells.

extract_protocol:
To separate cancer cells from stromal cells in co-culture conditions, we used human CD326 (EpCAM) Microbeads (#130-061-101, Miltenyi, Auburn, California, USA) and LS columns (#130-042-401, Miltenyi) and followed the manufacturer’s recommendations for separation.
We extracted RNA using the RNeasy Mini Kit following manufacturer’s instructions (#74104, Qiagen, Hilden, Germany)
We prepared RNA libraries for sequencing using standard Illumina protocols

tag: source condition

value: T47D+HS27a Co-Culture

tag: batch

tag: biological replicate

tag: replicate (of biological replicate)

value: A


title: Ch12 Sp1 Ko G7r3

description: library: RNAch12Sp1KOG7r3

value: Sp1 Knockout


title: HUVEC, GFP, rep1

value: endothelial cells


title: granoulosa cells_0h

tag: strain

tag: age

value: post natal day 21-28

value: before hCG (0) injection

value: ovary

value: mouse granulosa cells


title: wild type YPGal->YPD log lane7752_ACTTGA_E53_8_GAL-GLU

value: MEP diploid

tag: media

value: YPGal->YPD


title: wild type YPGal 24h lane7752_ACTGAT_E53_3_6_GAL_24h

value: YPGal


title: HS27a from T47D+HS27a Co-Culture Sample 5

description:
2151-JB-8
Counts_Raw_2151.txt
CPM_2151.txt

source_name: Bone Marrow Stromal/Stem Cells


title: A549 cells with Mock infection, H3K9ac IP, replicate r3

tag: treatment

value: Mock infection

value: H3K9ac IP (Active Motif, cat# 39137)


title: Ch12 Sp1 Ko G7r1

description: library: RNAch12Sp1KOG7r1

value: Ch12 cell line

tag: genotype

tag: experimental type

value: mRNA-Seq


title: A549 cells with Mock infection, H3K9ac IP, replicate r2


title: wild type YPD->YPGal log lane7752_ACAGTG_E53_5_GLU-GAL

description:
wild type YPD->YPGal log
Annotated Probe Report for All Probes - media shifts.txt

value: wild type

value: YPD->YPGal

value: log


title: A549 cells with Mock infection, H3K9ac IP, replicate r1


title: T47D from T47D+HS27a Co-Culture Sample 4

description:
2151-JB-7
Counts_Raw_2151.txt
CPM_2151.txt

tag: cell line

value: T47D+HS27a Co-Culture

value: A


title: HS27a from T47D+HS27a Co-Culture Sample 4

description:
2151-JB-6
Counts_Raw_2151.txt
CPM_2151.txt


title: Ch12 Maz Sp1 Ko C10r3

description: library: RNAch12MazSp1C10r3

value: Maz Sp1 Knockout


title: snf4 YPD log lane7662_TTAGGC_E51_03_snf4_log

description:
snf4 YPD log
Annotated Probe Report for All Probes - mutants not in paper.txt

value: YPD


title: T47D from T47D+HS5 Co-Culture Sample 4

description:
2151-JB-5
Counts_Raw_2151.txt
CPM_2151.txt

value: T47D+HS5 Co-Culture


title: tec1 YPD log lane7662_TGACCA_E51_04_tec1_log

description:
tec1 YPD log
Annotated Probe Report for All Probes - mutants not in paper.txt


title: A549 cells with ARKSAP deletion, CoV2 infection, H3K9ac IP, replicate r3

value: ARKSAP deletion, CoV2 infection


title: HS5 from T47D+HS5 Co-Culture Sample 7

description:
2151-JB-4
Counts_Raw_2151.txt
CPM_2151.txt


title: A549 cells with ARKSAP deletion, CoV2 infection, H3K9ac IP, replicate r2


title: Ch12 Maz Sp1 Ko C10r1

description: library: RNAch12MazSp1C10r1


title: clb5 YPD 48h lane7662_TAGCTT_E51_5_clb5_48h

description:
clb5 YPD 48h
Annotated Probe Report for All Probes - mutants not in paper.txt


title: sip4 YPD 48h lane7662_GTCCGC_E51_8_sip4_48h

description:
sip4 YPD 48h
Annotated Probe Report for All Probes - mutants not in paper.txt


title: Ch12 Wt S6

description: library: ATACCh12WtS6

data_processing:
Base calling: Illumina CASAVA 1.8.2
ATAC-Seq: Align raw reads to the reference genome with bowtie2 (default parameters).
ATAC-Seq: Remove duplicates with picard.
ATAC-Seq: Remove mitochondria reads.
ATAC-Seq: Keep high-quality reads with MAPQ>=30.
ATAC-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
ATAC-Seq: Call peak with MACS2.
Genome_build: mm10

extract_protocol:
ATAC-seq: To prepare nuclei for tagmentation, 100,000 cells were centrifuged at 500 × g for 5 minutes, then washed with 50 μL of cold 1x PBS and centrifugated at 500 × g for 5 minutes. Cells were lysed using cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were centrifuged at 500 × g for 10 minutes using a refrigerated centrifuge. Immediately following the nuclei prep, the pellets were resuspended in the transposase reaction mix (25 μL 2x TD buffer, 2.5 μL Transposase (Illumina) and 22.5 μL of nuclease free water). The transposition reaction was carried out for 30 minutes at 37 °C. Directly following transposition the sample was purified using a Zymo Clean and Concentrator kit. After purification, library fragments were amplified using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers, using the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by 4 cycles at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. To reduce GC and size bias in our PCR, the PCR reaction was monitored using qPCR in order to stop amplification prior to saturation. A 5 μl aliquot of the PCR reaction was mixed with 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6x, and a 20-cycles qPCR was run to determine the additional number of cycles needed for the remaining 45 μL reaction. The libraries were then purified using the Zymo Clean and Concentrator kit.
ATAC-seq: DNA was prepared for single-end Illumina sequencing. 50 cycles of sequencing data were acquired on the Illumina NovaSeq 6000.

value: wt

value: ATAC-Seq


title: Ch12 Sp1 Ko G7r2

description: library: RNAch12Sp1KOG7r2

value: Sp1 Knockout


title: A549 cells with Orf8 deletion, CoV2 infection, Input control, replicate r3

value: Orf8 deletion, CoV2 infection

value: Input control


title: cat8 YPD 48h lane7662_GTGGCC_E51_9_cat8_48h

description:
cat8 YPD 48h
Annotated Probe Report for All Probes - mutants not in paper.txt

value: MEP diploid


title: HS5 Monoculture Sample 5

description:
2151-JB-2
Counts_Raw_2151.txt
CPM_2151.txt

value: Mono-Culture


title: HS27a Monoculture Sample 5

description:
2151-JB-3
Counts_Raw_2151.txt
CPM_2151.txt


title: T47D Monoculture Sample 5

description:
2151-JB-1
Counts_Raw_2151.txt
CPM_2151.txt


title: Ch12 Maz Sp1 Ko C10r2

description: library: RNAch12MazSp1C10r2

value: Ch12 cell line

value: mRNA-Seq


title: A549 cells with Orf8 deletion, CoV2 infection, Input control, replicate r2


title: Ch12 Wt S5Rep2

description: library: ATACCh12WtS5Rep2


title: Ch12 Wt S5Rep1

description: library: ATACCh12WtS5Rep1


title: adr1 YPD 48h lane7662_GTAGAG_E51_10_adr1_48h

description:
adr1 YPD 48h
Annotated Probe Report for All Probes - mutants not in paper.txt


title: mig1 YPD 48h lane7662_GGTAGC_E51_11_mig1_48h

description:
mig1 YPD 48h
Annotated Probe Report for All Probes - mutants not in paper.txt


title: T47D from T47D+HS27a Co-Culture Sample 3

description:
1454-JB-30
Counts_Raw_1454.txt
CPM_1454.txt

value: C


title: A549 cells with Orf8 deletion, CoV2 infection, Input control, replicate r1


title: dot6 tod6 YPD log lane7662_GGCTAC_E51_06_dot6_tod6_log

description:
dot6 tod6 YPD log
Annotated Probe Report for All Probes - mutants not in paper.txt

value: dot6 tod6

value: log


title: A549 cells with CoV2 infection, Input control, replicate r3

value: CoV2 infection


title: Ch12 Wt S5R2

description: library: ATACCh12WtS5R2


title: T47D from T47D+HS27a Co-Culture Sample 2

description:
1454-JB-29
Counts_Raw_1454.txt
CPM_1454.txt

value: T47D+HS27a Co-Culture

value: B


title: A549 cells with ARKSAP deletion, CoV2 infection, H3K9ac IP, replicate r1

value: H3K9ac IP (Active Motif, cat# 39137)


title: rox1 YPD 48h lane7662_GCCAAT_E51_1_rox1_48h

description:
rox1 YPD 48h
Annotated Probe Report for All Probes - mutants not in paper.txt

value: YPD


title: T47D from T47D+HS27a Co-Culture Sample 1

description:
1454-JB-28
Counts_Raw_1454.txt
CPM_1454.txt

value: A


title: Ch12 Wt S5R1

description: library: ATACCh12WtS5R1

value: wt

value: ATAC-Seq


title: A549 cells with CoV2 infection, Input control, replicate r1


title: tec1 YPD 48h lane7662_GATCAG_E51_4_tec1_48h

description:
tec1 YPD 48h
Annotated Probe Report for All Probes - mutants not in paper.txt


title: Ch12 Wt S4R2

description: library: ATACCh12WtS4R2


title: HS27a from T47D+HS27a Co-Culture Sample 3

description:
1454-JB-27
Counts_Raw_1454.txt
CPM_1454.txt


title: Ch12 Wt S4R1

description: library: ATACCh12WtS4R1


title: A549 cells with Mock infection, Input control, replicate r3

value: Mock infection


title: pmr1 YPD log lane7662_CGATGT_E51_02__pmr1_log

description:
pmr1 YPD log
Annotated Probe Report for All Probes - mutants not in paper.txt


title: HS27a from T47D+HS27a Co-Culture Sample 2

description:
1454-JB-26
Counts_Raw_1454.txt
CPM_1454.txt


title: A549 cells with Mock infection, Input control, replicate r2

value: Input control


title: T47D from T47D+HS5 Co-Culture Sample 3

description:
1454-JB-24
Counts_Raw_1454.txt
CPM_1454.txt

value: T47D+HS5 Co-Culture


title: HS27a from T47D+HS27a Co-Culture Sample 1

description:
1454-JB-25
Counts_Raw_1454.txt
CPM_1454.txt


title: A549 cells with Mock infection, Input control, replicate r1


title: yak1 YPD 48h lane7662_CCGTCC_E51_7__yak1_48h

description:
yak1 YPD 48h
Annotated Probe Report for All Probes - mutants not in paper.txt

value: MEP diploid


title: Ch12 Zfp580 KO Rep1

description: library: ATACCh12Zfp580KoRep1

value: Ch12 cell line

value: Zfp580 Knockout


title: yak1 YPD log lane7662_CTTGTA_E51_07__yak1_log

description:
yak1 YPD log
Annotated Probe Report for All Probes - mutants not in paper.txt


title: Ch12 Zfp580 KO Rep2

description: library: ATACCh12Zfp580KoRep2


title: pmr1 YPD 48h lane7662_CAGATC_E51_2__pmr1_48h

description:
pmr1 YPD 48h
Annotated Probe Report for All Probes - mutants not in paper.txt


title: Ch12 Zbtb7a KO S2Rep3

description: library: ATACCh12Zbtb7aKoS2Rep3

value: Zbtb7a Knockout


title: A549 cells with ARKSAP deletion, CoV2 infection, Input control, replicate r3

value: ARKSAP deletion, CoV2 infection


title: A549 cells with ARKSAP deletion, CoV2 infection, Input control, replicate r2


title: Ch12 Zbtb7a KO S2Rep2

description: library: ATACCh12Zbtb7aKoS2Rep2


title: T47D from T47D+HS5 Co-Culture Sample 2

description:
1454-JB-23
Counts_Raw_1454.txt
CPM_1454.txt


title: T47D from T47D+HS5 Co-Culture Sample 1

description:
1454-JB-22
Counts_Raw_1454.txt
CPM_1454.txt


title: mig1 YPD log lane7662_ATTCCT_E51_011_mig1_log

description:
mig1 YPD log
Annotated Probe Report for All Probes - mutants not in paper.txt

value: log


title: dot6 tod6 YPD 48h lane7662_ATGTCA_E51_6_dot6_tod6_48h

description:
dot6 tod6 YPD 48h
Annotated Probe Report for All Probes - mutants not in paper.txt

value: dot6 tod6


title: HS5 from T47D+HS5 Co-Culture Sample 6

description:
1454-JB-21
Counts_Raw_1454.txt
CPM_1454.txt

value: C


title: rox1 YPD log lane7662_ATCACG_E51_01_rox1_log

description:
rox1 YPD log
Annotated Probe Report for All Probes - mutants not in paper.txt


title: HS5 from T47D+HS5 Co-Culture Sample 5

description:
1454-JB-20
Counts_Raw_1454.txt
CPM_1454.txt

value: B


title: A549 cells with CoV2-Orf8 deletion infection infection - K9m3, replicate r2

data_processing:
raw reads demultiplexed with bcl2fastq
reads quality and adapter trimmed with cutadapt
aligned to GRCh38 using bowtie2
peaks were called with macs2 (H3K9ac) or SICER (H3K9me3 and H3K27me3) using default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: bed files with all peaks called using given approach for each replicate hPTM

extract_protocol:
For histone PTM ChIP-sequencing, 4-10M cells were resuspended in 1mL of lysis buffer 1 (50mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and rotated at 4C for 10min, followed by centrifugation removal of supernatant. Cells were then re-suspended in 1mL lysis buffer 2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA), rotated for 10min at 4C, followed by centrifugation removal of supernatant. Cells were then resuspended in 1mL of lysis buffer 3 (10mM Tris-HCl pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and rotated again for 10min at 4C. This was followed by sonication with a Covaris S220 sonicator for 35 minutes (peak incident power: 140; duty factor: 5 %; cycles/burst: 200). This was followed by addition of 110uL Triton X-100, and centrifugation for 15minutes at maximum speed (20kg) at 4C to clear lysate. Lysate chromatin concentration was then equalized according to DNA content (as measured with a qubit flourometer). Following this, 5% of equivalently-treated chromatin from C. floridanus pupae were added to all samples according to chromatin concentration, and 50uL of lysate saved as input shearing control. 250uL of equalized lysate were then added to washed, antibody-conjugated protein A/G Dynabeads (2ug antibody conjugated to 15uL/15uL A/G dynabeads, resuspended in 50uL per IP) and IPs were rotated overnight at 4C in a final volume of 300uL. The following day, IPs were washed 5x in RIPA wash buffer (50mM HEPES-KOH pH 7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and once in TE pH 8.0. Washes were followed by two elutions into 75 µl of elution buffer (50 mM Tris-HCl pH 8.0; 10 mM EDTA; 1% SDS) at 65˚C for 45 min with shaking (1,100 RPM). DNA was purified via phenol:chloroform:isoamyl alcohol (25:24:1) followed by ethanol precipitation. Pelleted DNA was resuspended in 25 µl TE.
Libraries for sequencing were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645), as described by the manufacturer but using half volumes of all reagents and starting material. For PCR amplification optimal number of PCR cycles was determined using a qPCR side-reaction using 10% of adapter-ligated, size-selected DNA. 7-10 cycles of PCR were used for hPTM libraries and 5 cycles were used for Input controls. Samples were sequenced on a NextSeq 550 instrument (42bp read length, paired end).

value: CoV2-Orf8 deletion infection infection

value: H3K9me3 IP


title: Ch12 Zbtb7a KO Rep2

description: library: ATACCh12Zbtb7aKoRep2


title: Ch12 Zbtb7a KO S2Rep1

description: library: ATACCh12Zbtb7aKoS2Rep1


title: cat8 YPD log lane7662_AGTTCC_E51_09_cat8_log

description:
cat8 YPD log
Annotated Probe Report for All Probes - mutants not in paper.txt

value: YPD


title: Ch12 Zbtb7a KO Rep1

description: library: ATACCh12Zbtb7aKoRep1


title: HS5 from T47D+HS5 Co-Culture Sample 4

description:
1454-JB-19
Counts_Raw_1454.txt
CPM_1454.txt

value: A


title: Ch12 Sp3 Zfp580 KO S1R2

description: library: ATACCh12Sp3Zfp580KoS1R2

value: Sp3,Zfp580 Knockout

value: ATAC-Seq


title: A549 cells with CoV2 infection - K9m3, replicate r3

value: CoV2 infection


title: Ch12 Sp3 Zfp580 KO S1R1

description: library: ATACCh12Sp3Zfp580KoS1R1


title: HS27a from MCF7+HS27a Co-Culture Sample 5

description:
1454-JB-17
Counts_Raw_1454.txt
CPM_1454.txt

value: MCF7+HS27a Co-Culture


title: A549 cells with CoV2 infection - K9m3, replicate r2


title: A549 cells with CoV2-Orf8 deletion infection infection - K9m3, replicate r1


title: sip4 YPD log lane7662_AGTCAA_E51_08_sip4_log

description:
sip4 YPD log
Annotated Probe Report for All Probes - mutants not in paper.txt

value: MEP diploid


title: Ch12 Sp3 KO Rep2

description: library: ATACCh12Sp3KoRep2

value: Ch12 cell line

value: Sp3 Knockout


title: snf4 YPD 48h lane7662_ACTTGA_E51_3_snf4_48h

description:
snf4 YPD 48h
Annotated Probe Report for All Probes - mutants not in paper.txt


title: MCF7 from MCF7+HS5 Co-Culture Sample 5

description:
1454-JB-16
Counts_Raw_1454.txt
CPM_1454.txt

value: MCF7+HS5 Co-Culture


title: adr1 YPD log lane7662_ACTGAT_E51_010_adr1_log

description:
adr1 YPD log
Annotated Probe Report for All Probes - mutants not in paper.txt


title: Ch12 Sp3 KO Rep1

description: library: ATACCh12Sp3KoRep1


title: clb5 YPD log lane7662_ACAGTG_E51_05_clb5_log

description:
clb5 YPD log
Annotated Probe Report for All Probes - mutants not in paper.txt


title: HS5 from MCF7+HS5 Co-Culture Sample 4

description:
1454-JB-15
Counts_Raw_1454.txt
CPM_1454.txt


title: Ch12 Sp1 Zfp580 KO S1R2

description: library: ATACCh12Sp1Zfp580KoS1R2

value: Sp1,Zfp580 Knockout


title: A549 cells with ARKSAP deletion, CoV2 infection, Input control, replicate r1

value: ARKSAP deletion, CoV2 infection

value: Input control


title: A549 cells with CoV2 infection - K9m3, replicate r1


title: A549 cells with CoV2-Orf8 deletion infection infection - K9m3, replicate r3


title: A549 cells with Mock infection - K9m3, replicate r3

value: Mock infection


title: T47D HS27a Conditioned Media Sample 3

description:
1454-JB-14
Counts_Raw_1454.txt
CPM_1454.txt

value: Addition of HS27a Conditioned Media

value: C


title: MCF7 from MCF7+HS27a Co-Culture Sample 5

description:
1454-JB-18
Counts_Raw_1454.txt
CPM_1454.txt


title: T47D HS27a Conditioned Media Sample 2

description:
1454-JB-13
Counts_Raw_1454.txt
CPM_1454.txt

value: B


title: A549 cells with Mock infection - K9m3, replicate r2

value: H3K9me3 IP


title: wild type YPGal log lane6854_TAGCTT_02_GAL_log

description:
wild type YPGal log
Annotated Probe Report for All Probes - main paper datasets.txt

value: wild type

value: YPGal

value: log


title: Ch12 Sp1 Zfp580 KO S1R1

description: library: ATACCh12Sp1Zfp580KoS1R1

value: ATAC-Seq


title: wild type YPD 48h lane6854_GTGAAA_11_GLU_48h

description:
wild type YPD 48h
Annotated Probe Report for All Probes - main paper datasets.txt

value: YPD


title: Ch12 Sp1 Zbtb7a Zfp580 KO S1R2

description: library: ATACCh12Sp1Zbtb7aZfp580KoS1R2

value: Sp1,Zbtb7a,Zfp580 Knockout


title: A549 cells with CoV2-Orf8 deletion infection infection - K9ac, replicate r3

value: CoV2-Orf8 deletion infection infection

value: H3K9ac IP


title: wild type YPRaffinose+Galactose 24h lane6854_GTAGAG_09_RAF_GAL_24h

description:
wild type YPRaffinose+Galactose 24h
Annotated Probe Report for All Probes - main paper datasets.txt

value: MEP diploid

value: YPRaffinose+Galactose


title: Ch12 Sp1 Zbtb7a Zfp580 KO S1R1

description: library: ATACCh12Sp1Zbtb7aZfp580KoS1R1

value: Ch12 cell line


title: A549 cells with Mock infection - K9m3, replicate r1


title: T47D HS27a Conditioned Media Sample 1

description:
1454-JB-12
Counts_Raw_1454.txt
CPM_1454.txt

value: A


title: A549 cells with CoV2-Orf8 deletion infection infection - K9ac, replicate r2


title: T47D HS5 Conditioned Media Sample 3

description:
1454-JB-11
Counts_Raw_1454.txt
CPM_1454.txt

value: Addition of HS5 Conditioned Media


title: T47D HS5 Conditioned Media Sample 2

description:
1454-JB-10
Counts_Raw_1454.txt
CPM_1454.txt


title: wild type YPRaffinose+Galactose 48h lane6854_GGTAGC_14_RAF_GAL_48h

description:
wild type YPRaffinose+Galactose 48h
Annotated Probe Report for All Probes - main paper datasets.txt


title: Ch12 Sp1 Zbtb7a KO S1R1

description: library: ATACCh12Sp1Zbtb7aKoS1R1

value: Sp1,Zbtb7a Knockout


title: Ch12 Sp1 Zbtb7a KO S1R2

description: library: ATACCh12Sp1Zbtb7aKoS1R2


title: wild type YPFructose log lane6854_GGCTAC_03_FRU_log

description:
wild type YPFructose log
Annotated Probe Report for All Probes - main paper datasets.txt

value: YPFructose


title: wild type YPD log lane6854_GATCAG_01_GLU_log

description:
wild type YPD log
Annotated Probe Report for All Probes - main paper datasets.txt


title: T47D HS5 Conditioned Media Sample 1

description:
1454-JB-9
Counts_Raw_1454.txt
CPM_1454.txt


title: A549 cells with CoV2 infection - K9ac, replicate r3

value: CoV2 infection


title: A549 cells with CoV2 infection - K9ac, replicate r2


title: wild type YPFructose 48h lane6854_GAGTGG_13_FRU_48h

description:
wild type YPFructose 48h
Annotated Probe Report for All Probes - main paper datasets.txt


title: Ch12 Sp1 Sp2 Sp3Het KO S1R2

description: library: ATACCh12Sp1Sp2Sp3HetKoS1R2

value: Sp1,Sp2,Sp3Het Knockout


title: wild type YPRaffinose+Galactose log lane6854_CTTGTA_04_RAF_GAL_log

description:
wild type YPRaffinose+Galactose log
Annotated Probe Report for All Probes - main paper datasets.txt

value: wild type


title: T47D Monoculture Sample 4

description:
1454-JB-8
Counts_Raw_1454.txt
CPM_1454.txt

value: Mono-Culture


title: Ch12 Sp1 Sp2 Sp3Het KO S1R1

description: library: ATACCh12Sp1Sp2Sp3HetKoS1R1


title: MCF7 HS27a Conditioned Media Sample 2

description:
1454-JB-6
Counts_Raw_1454.txt
CPM_1454.txt

value: Addition of HS27a Conditioned Media

value: B


title: A549 cells with Mock infection - K9ac, replicate r3

value: Mock infection


title: Ch12 Sp1 KO Rep2

description: library: ATACCh12Sp1KoRep2

value: Sp1 Knockout

value: ATAC-Seq


title: Ch12 Sp1 KO Rep1

description: library: ATACCh12Sp1KoRep1


title: A549 cells with CoV2 infection - K9ac, replicate r1

value: H3K9ac IP


title: wild type YPGal 48h lane6854_CGTACG_12_GAL_48h

description:
wild type YPGal 48h
Annotated Probe Report for All Probes - main paper datasets.txt

value: MEP diploid

value: YPGal


title: MCF7 HS27a Conditioned Media Sample 3

description:
1454-JB-7
Counts_Raw_1454.txt
CPM_1454.txt

value: C


title: MCF7 HS27a Conditioned Media Sample 1

description:
1454-JB-5
Counts_Raw_1454.txt
CPM_1454.txt

value: A


title: wild type YPFructose 24h lane6854_CCGTCC_08_FRU_24h

description:
wild type YPFructose 24h
Annotated Probe Report for All Probes - main paper datasets.txt


title: A549 cells with CoV2-Orf8 deletion infection infection - K9ac, replicate r1

value: CoV2-Orf8 deletion infection infection


title: Ch12 Maz KO Rep1

description: library: ATACCh12MazKoRep1

value: Ch12 cell line

value: Maz Knockout


title: MCF7 HS5 Conditioned Media Sample 2

description:
1454-JB-3
Counts_Raw_1454.txt
CPM_1454.txt

value: Addition of HS5 Conditioned Media


title: wild type YPD 24h lane6854_AGTTCC_06_GLU_24h

description:
wild type YPD 24h
Annotated Probe Report for All Probes - main paper datasets.txt

value: YPD


title: A549 cells with CoV2-Orf8 deletion infection infection - K27m3, replicate r3

value: H3K27me3 IP


title: C4-2_input

city: Dallas

first: Xu

last: Li

state: Texas

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

data_processing:
Demultiplexing by CASAVA
Bowtie2 for Genomic Mapping
Remove duplicates by PICARD
peak-calling by MACS2
HOMER for Annotate Peaks
Assembly: hg19
Supplementary files format and content: BAM

source_name: C4-2 Cells

extract_protocol:
Qiagen PCR kit
KAPA Kit

value: none (input)


title: C4-2_TEAD

value: anti-TEAAD


title: C4-2_H3K27ac


title: MCF7 Monoculture Sample 5

description:
1454-JB-1
Counts_Raw_1454.txt
CPM_1454.txt

value: Mono-Culture


title: A549 cells with Mock infection - K9ac, replicate r2

value: Mock infection


title: wild type YPGal 24h lane6854_ATGTCA_07_GAL_24h

description:
wild type YPGal 24h
Annotated Probe Report for All Probes - main paper datasets.txt

value: wild type


title: HS5 from T47D+HS5 Co-Culture Sample 3

description:
285-JB-30
Counts_Raw_285.txt
CPM_285.txt

value: T47D+HS5 Co-Culture


title: Ch12 Maz KO Rep2

description: library: ATACCh12MazKoRep2

value: ATAC-Seq


title: HS5 from T47D+HS5 Co-Culture Sample 2

description:
285-JB-29
Counts_Raw_285.txt
CPM_285.txt

value: B


title: A549 cells with Mock infection - K9ac, replicate r1

value: H3K9ac IP


title: A549 cells with CoV2 infection - K27m3, replicate r3

value: CoV2 infection


title: A549 cells with CoV2 infection - K27m3, replicate r2


title: MCF7 HS5 Conditioned Media Sample 3

description:
1454-JB-4
Counts_Raw_1454.txt
CPM_1454.txt

value: C


title: A549 cells with CoV2 infection - K27m3, replicate r1


title: Ch12 Klf16 Sp1 Zbtb7a Zfp580 KO S1R2

description: library: ATACCh12Klf16Sp1Zbtb7aZfp580KoS1R2

value: Klf16,Sp1,Zbtb7a,Zfp580 Knockout


title: HS27a from MCF7+HS27a Co-Culture Sample 4

description:
285-JB-24
Counts_Raw_285.txt
CPM_285.txt

value: MCF7+HS27a Co-Culture


title: MCF7 HS5 Conditioned Media Sample 1

description:
1454-JB-2
Counts_Raw_1454.txt
CPM_1454.txt

value: A


title: Ch12 Klf16 Zbtb7a Zfp580 KO S1R2

description: library: ATACCh12Klf16Zbtb7aZfp580KoS1R2

value: Ch12 cell line

value: Klf16,Zbtb7a,Zfp580 Knockout


title: 778, PLA2G10

city: West Haven

first: Tianxiang

state: Connecticut

address: 600 West Campus Drive, MIC 319

institute: Yale University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (v0.5.0).
Trimmed reads were mapped to the human reference genome (hg38) using HISAT2 (v2.1.0) (Kim et al., 2015).
Gene expression levels were quantified using StringTie (v1.3.3b) (Pertea et al., 2015), with the gene models (v27) from the GENCODE project.
Differentially expressed genes were identified using DESeq2 (v 1.22.1) (Love et al., 2014).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: T lymphocyte

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Activated human peripheral blood T lymphocyte

value: WT

tag: individual id


title: Ch12 Klf16 Sp1 Zbtb7a Zfp580 KO S1R1

description: library: ATACCh12Klf16Sp1Zbtb7aZfp580KoS1R1


title: Ch12 Klf16 Zbtb7a Zfp580 KO S1R1

description: library: ATACCh12Klf16Zbtb7aZfp580KoS1R1


title: A549 cells with Mock infection - K27m3, replicate r3

value: H3K27me3 IP


title: Ch12 Klf16 Sp1 Zbtb7a KO S1R2

description: library: ATACCh12Klf16Sp1Zbtb7aKoS1R2

value: Klf16,Sp1,Zbtb7a Knockout


title: A549 cells with CoV2-Orf8 deletion infection infection - K27m3, replicate r2

value: CoV2-Orf8 deletion infection infection


title: A549 cells with CoV2-Orf8 deletion infection infection - K27m3, replicate r1


title: Ch12 Klf16 Zbtb7a KO S1R2

description: library: ATACCh12Klf16Zbtb7aKoS1R2

value: Klf16,Zbtb7a Knockout


title: 518, PLA2G10

value: ITAC


title: C4-2_AR

value: anti-AR


title: Ch12 Klf16 Zbtb7a KO S1R1

description: library: ATACCh12Klf16Zbtb7aKoS1R1

value: ATAC-Seq


title: A549 cells with Mock infection - K27m3, replicate r2

value: Mock infection


title: Ch12 Klf16 Sp1 Zbtb7a KO S1R1

description: library: ATACCh12Klf16Sp1Zbtb7aKoS1R1


title: HS27a from MCF7+HS27a Co-Culture Sample 2

description:
285-JB-22
Counts_Raw_285.txt
CPM_285.txt


title: HS27a from MCF7+HS27a Co-Culture Sample 3

description:
285-JB-23
Counts_Raw_285.txt
CPM_285.txt

value: B


title: 518, ITAC+PLA2G10


title: 778, ITAC+PLA2G10


title: MCF7 from MCF7+HS27a Co-Culture Sample 4

description:
285-JB-21
Counts_Raw_285.txt
CPM_285.txt

value: C


title: 778, PBS

value: PBS


title: HS5 from T47D+HS5 Co-Culture Sample 1

description:
285-JB-28
Counts_Raw_285.txt
CPM_285.txt

value: T47D+HS5 Co-Culture


title: Ch12 Klf16 Maz Sp1 Zbtb7a KO S1R2

description: library: ATACCh12Klf16MazSp1Zbtb7aKoS1R2

value: Klf16,Maz,Sp1,Zbtb7a Knockout


title: 518  PLA2G10


title: Ch12 Klf16 Maz Sp1 Zbtb7a KO S1R1

description: library: ATACCh12Klf16MazSp1Zbtb7aKoS1R1

value: Ch12 cell line


title: A549 cells with Mock infection - K27m3, replicate r1


title: A549 cells with CoV2-Orf8 deletion infection infection - Input, replicate r3

value: Input control


title: A549 cells with CoV2-Orf8 deletion infection infection - Input, replicate r2


title: MCF7 from MCF7+HS27a Co-Culture Sample 3

description:
285-JB-20
Counts_Raw_285.txt
CPM_285.txt

value: MCF7+HS27a Co-Culture


title: 518, ITAC

value: Activated human peripheral blood T lymphocyte

value: WT


title: A549 cells with CoV2-Orf8 deletion infection infection - Input, replicate r1


title: MCF7 from MCF7+HS27a Co-Culture Sample 2

description:
285-JB-19
Counts_Raw_285.txt
CPM_285.txt

value: A


title: 518, PBS


title: Ch12 Klf16 KO Rep1

description: library: ATACCh12Klf16KoRep1

value: Klf16 Knockout


title: 501, ITAC+PLA2G10


title: HS5 from MCF7+HS5 Co-Culture Sample 2

description:
285-JB-17
Counts_Raw_285.txt
CPM_285.txt

value: MCF7+HS5 Co-Culture


title: Ch12 Klf13 KO Rep2

description: library: ATACCh12Klf13KoRep2

value: Klf13 Knockout


title: 501, PLA2G10


title: A549 cells with CoV2 infection - Input, replicate r2

value: CoV2 infection


title: A549 cells with CoV2 infection - Input, replicate r1


title: MCF7 from MCF7+HS5 Co-Culture Sample 4

description:
285-JB-15
Counts_Raw_285.txt
CPM_285.txt


title: Ch12 Klf13 KO Rep1

description: library: ATACCh12Klf13KoRep1

value: ATAC-Seq


title: 501, ITAC

value: ITAC


title: Ch12 Egr1 KO Rep2

description: library: ATACCh12Egr1KoRep2

value: Egr1 Knockout


title: A549 cells with Mock infection - Input, replicate r3

value: Mock infection


title: MCF7 from MCF7+HS5 Co-Culture Sample 2

description:
285-JB-13
Counts_Raw_285.txt
CPM_285.txt


title: MCF7 from MCF7+HS5 Co-Culture Sample 3

description:
285-JB-14
Counts_Raw_285.txt
CPM_285.txt

value: B


title: Ch12 Egr1 KO Rep1

description: library: ATACCh12Egr1KoRep1


title: Ch12 Klf16 KO Rep2

description: library: ATACCh12Klf16KoRep2


title: 501, PBS

value: PBS


title: A549 cells with Mock infection - Input, replicate r2


title: SKA-T0_S42

city: Créteil

first: cecile

last: lefebvre

address: 51 Avenue du Marechal De Lattre de Tassigny

country: France

institute: INSERM U955_VRI

data_processing:
Base calls were performed using Illumina CASAVA 1.8.2
Sequenced reads were trimmed for low-quality sequence, then mapped to hg19 whole genome using Star 2.5.3 with performed using Partek® Flow® software, Copyright ©; 2019 Partek Inc.
Aligned reads were quantified to annotation model hg19 - GENCODE Genes - release 19, with Partek E/M and counts normalized by the counts per million (CPM + 0.0001) method with performed using Partek® Flow® software, Copyright ©; 2019 Partek Inc.
Genome_build: hg19
Supplementary_files_format_and_content: LANGERHANS_MigratedvsSteadyState_Normalized_counts. 12 samples

source_name: Steady state LCs

growth_protocol: RNAseq analysis on primary skin LC. Epidermal LC of 6 healthy donors were isolated either at steady state or after 3 days of migration in culture.

extract_protocol:
Total RNA was purified from normal skin with the RNeasy Plus Micro Kit (Qiagen)
Libraries were prepared with the NEBNext UltraII directional RNA Library Prep kit. Sequencing : Single read of 101 bp, performed on the Illumina HiSeq 2500 at Vaccine Research Institute genomics Platform

tag: tissue

value: Skin

value: Steady state Langerhans cells (LCs)


title: ATAC1905C|CH12 B cells

data_processing:
Base calling: Illumina CASAVA 1.8.2
ATAC-Seq: Align raw reads to the reference genome with bowtie2 (default parameters).
ATAC-Seq: Remove duplicates with picard.
ATAC-Seq: Remove mitochondria reads.
ATAC-Seq: Keep high-quality reads with MAPQ>=30.
ATAC-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
ATAC-Seq: Call peak with MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: CH12 B cells

growth_protocol: CH12 B lymphoma cells were cultured in RPMI-1640 media supplemented with 10% FBS (Gemini), 1% Penicillin-Streptomycin and 50 µM of b-mercaptoethanol (Thermo Fisher Scientific).  Mature B cells were isolated from C57BL/6J mouse spleen by negative selection (StemCell Technologies). Mouse ES cells (E14) were cultured in Knock-out DMEM (Thermo Fisher Scientific) supplemented with 10% FBS (ES Cell qualified, ATCC), 1% Penicillin-Streptomycin, 1% Glutamax, 1% Non-Essential Amino Acids and 1% b-mercaptoethanol (Thermo Fisher Scientific).

extract_protocol:
ATAC-seq: To prepare nuclei for tagmentation, 100,000 cells were centrifuged at 500 × g for 5 minutes, then washed with 50 μL of cold 1x PBS and centrifugated at 500 × g for 5 minutes. Cells were lysed using cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were centrifuged at 500 × g for 10 minutes using a refrigerated centrifuge. Immediately following the nuclei prep, the pellets were resuspended in the transposase reaction mix (25 μL 2x TD buffer, 2.5 μL Transposase (Illumina) and 22.5 μL of nuclease free water). The transposition reaction was carried out for 30 minutes at 37 °C. Directly following transposition the sample was purified using a Zymo Clean and Concentrator kit. After purification, library fragments were amplified using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers, using the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by 4 cycles at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. To reduce GC and size bias in our PCR, the PCR reaction was monitored using qPCR in order to stop amplification prior to saturation. A 5 μl aliquot of the PCR reaction was mixed with 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6x, and a 20-cycles qPCR was run to determine the additional number of cycles needed for the remaining 45 μL reaction. The libraries were then purified using the Zymo Clean and Concentrator kit.
ATAC-seq: DNA was prepared for single-end Illumina sequencing. 50 cycles of sequencing data were acquired on the HiSeq 3000 or Illumina NovaSeq 6000 (Illumina).

value: CH12 B cells


title: HS27a Monoculture Sample 4

description:
285-JB-12
Counts_Raw_285.txt
CPM_285.txt

value: Mono-Culture

value: C


title: ATAC1105|B cells LPS+IL4+aCD180-activated

source_name: B cells LPS+IL4+aCD180-activated

value: B cells LPS+IL4+aCD180-activated


title: A549 cells with CoV2 infection - Input, replicate r3

value: Input control


title: HS5 from MCF7+HS5 Co-Culture Sample 3

description:
285-JB-18
Counts_Raw_285.txt
CPM_285.txt


title: Ins2Cre-Hetero3

city: Jung-gu

first: hyunjung

last: hong

state: Daejeon

address: Munhwaro 222

department: biomedical

country: South Korea

institute: Chungnam national university

data_processing:
FastQC v0.11.7 software used for quality check
Trimmomatic 0.38 performs trimming with various parameters for illumina paired-end or single-end.
HISAT2 quickly and accurately maps high-throughput sequencing data to the reference genome to produce aligned reads.
The transcript assembly through the StringTie program is performed using the information of the aligned reads based on the reference.
The expression profile obtained by transcript quantification of each sample is extracted with FPKM or RPKM, which is the normalization value considering read count and transcript length and depth of coverage.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: pancreatic islet

extract_protocol:
Islets were isolated from the pancreas, and RNA was harvested using Trizol reagent.  TruSeq Stranded mRNA LT Sample Prep Kit was used with 1ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Sample Preparation Guide (Part # 15031047 Rev. E)

value: pancreatic islet

value: 14 weeks old


title: HS27a Monoculture Sample 2

description:
285-JB-10
Counts_Raw_285.txt
CPM_285.txt

value: A


title: HS27a Monoculture Sample 3

description:
285-JB-11
Counts_Raw_285.txt
CPM_285.txt


title: A549 cells with Mock infection - Input, replicate r1


title: LBD-T0_S36


title: LBD-migrated_S35

source_name: Migrated LCs

value: Migrated Langerhans cells (LCs)


title: HS5 Monoculture Sample 4

description:
285-JB-9
Counts_Raw_285.txt
CPM_285.txt


title: Passage 2 organoid derived from murine salivary glands at 90 days post IR, rep2

city: Groningen

first: Rob

last: Coppes

address: Ant. Deusinglaan 1

department: Biomedical Sciences of Cells and Systems

country: Netherlands

institute: University Medical Center Groningen

data_processing:
Base-calling: bcl2fastq software (Illumina Inc.) version 2.20.0.422.
QuantSeq 3′ mRNA-Seq analysis: Bluebee (Lexogen) version 015UG108V0311
Assembly: GRCm39
Supplementary files format and content: A tab-delimited text file containing read counts

source_name: salivary gland stem/progenitor cells

growth_protocol: Organoids were cultured in Matrigel, complete growth medium consisting of DMEM-12 (Gibco/Invitrogen, 11320-074), 1x Pen/Strep antibiotics (Gibco), 2mM Glutamax (ThermoFischer Scientific, 35050038), 1x N2 (Gibco, 17502-048), 20 ng/ml EGF (Sigma-Aldrich, E9644), 20 ng/ml FGF2 (PeproTech, 100-18B), 10 μg/ml insulin (Sigma-Aldrich, I6634), 1 μM dexamethasone (Sigma-Aldrich, d4902) and 10 μM Y-27632 (Abcam, ab120129).

extract_protocol:
RNA was isolated with the RNeasy Mini Kit (Qiagen, 74104) according to manufacturer’s instructions including DNase I treatment
QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen)

value: salivary gland stem/progenitor cells

value: Passage 2 organoid

value: IR

tag: time

value: 90 days


title: Ins2Cre-Hetero2


title: Passage 2 organoid derived from murine salivary glands at 90 days post IR, rep1

tag: cell type


title: HS5 Monoculture Sample 3

description:
285-JB-8
Counts_Raw_285.txt
CPM_285.txt

value: B


title: Passage 2 organoid derived from murine salivary glands at 90 days post sham-IR, rep3

value: sham-IR


title: Ins2Cre-Cont3

value: control


title: LAL-migrated_S29

value: Skin


title: DBE-T0_S24

value: Steady state Langerhans cells (LCs)


title: Ins2Cre-Cont2


title: HS5 Monoculture Sample 2

description:
285-JB-7
Counts_Raw_285.txt
CPM_285.txt

value: Mono-Culture


title: Passage 2 organoid derived from murine salivary glands at 90 days post sham-IR, rep2


title: SKA-migrated_S41


title: Passage 1 organoid derived from murine salivary glands at 90 days post IR, rep3

value: Passage 1 organoid


title: Passage 2 organoid derived from murine salivary glands at 90 days post IR, rep3


title: DBE-migrated_S23


title: ALX-T0_S18


title: T47D Monoculture Sample 2

description:
285-JB-5
Counts_Raw_285.txt
CPM_285.txt


title: Passage 2 organoid derived from murine salivary glands at 90 days post sham-IR, rep1


title: Ins2Cre-Cont1


title: MCF7 Monoculture Sample 4

description:
285-JB-3
Counts_Raw_285.txt
CPM_285.txt

value: C


title: T47D Monoculture Sample 3

description:
285-JB-6
Counts_Raw_285.txt
CPM_285.txt


title: ALX-migrated_S17


title: Passage 1 organoid derived from murine salivary glands at 90 days post IR, rep2


title: T47D Monoculture Sample 1

description:
285-JB-4
Counts_Raw_285.txt
CPM_285.txt


title: Lung, wild type

city: Shanghai

first: Yan

last: Gu

address: 800 Xiangyin Road

department: Immunology

institute: Second Miilitary Medical University

data_processing:
Sequencing depth was normalized by using CellRanger (version v3.0.1).
We used Seurat package (version v3.0.2)  in R (version 3.5.3) to perform data filtering (both gene and cell), normalization, PCA and t-SNE.
Cells defined as type I and II epithelial cells, endothelial cells, ciliated cells, clara cells and alveolar biopotent progenitor cells.
We constructed single-cell trajectory of lung epithelial cells  by using reversed graph embedding method implemented in R Monocle package  (version 3.5.3)
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

molecule: polyA RNA

source_name: Lung

extract_protocol:
1×10^6 luciferase-labeled LLC cells were subcutaneously injected on the dorsum of mice to construct spontaneous lung metastatic models. The murine tissues in this study were prepared from mice sacrificed by cervical dislocation at day 14 after tumor-bearing. For the isolation of lung epithelial cells, Lung tissues were collected, cut into small pieces and incubated in dissociation solution with 2 mg/ml Collagenase type I, 2 mg/ml Collagenase type IV and 25 mg/ml DNase (Sigma). The solution was pipetting every 10 minutes during the incubation and suspension was dispersed through a 70 mm cell strainer. To purify AT-II lung epithelial cells, single-cell suspensions from lungs were stained with antibodies, and CD45- SftpC+ cells were sorted using a MoFlo XDP flow cytometer (Beckman-Coulter) with purities of >95%, followed by 10× library preparation and sequencing.
All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 RevD).

treatment_protocol: In spontaneous lung metastatic models, 1×10^6 luciferase-labeled LLC cells were subcutaneously injected on the dorsum of mice. Lung tissues were digested into single-cell suspensions and Sftpc+ epithelial cells were purified by FASC, followed by 10× library preparation and sequencing. wild type mouse without tumor-bearing was as a control.

value: Lung

value: Lung epithelial cells

value: wild type

value: non-treated


title: Passage 1 organoid derived from murine salivary glands at 90 days post IR, rep1


title: Lung, tumor

value: 14 days after LLC tumor subcutaneous injection


title: Ins2Cre-Hetero1

value: pancreatic islet

value: 14 weeks old


title: MB011B_ban_spg_biol_Rep2_exp

city: Waltham

first: Leslie

middle: C

last: Griffith

state: MA

address: 415 South St.

department: Volen National Center for Complex Systems/ Neuroscience

institute: Brandeis University

description: Brains diseccted at ZT12-ZT13.5 from female flies that were mated and aged 3-4 days post-eclosion.

data_processing:
Reads were mapped to the dm6 Drosophila genome using STAR (Dobin et al., 2013). PCR duplicates were removed using Picard
HTseq-count was used to generate raw read counts for individual genes. This was used as the input for EdgeR differential gene expression analysis (Robinson et al., 2010), performed on three biological replications.
Assembly: dm6
Supplementary files format and content: Comma-delineated EdgeR output with logFC (fold-change), logCPM(counts per million) and P-Value for each gene, comparing relative change in expression in experimental (MB011B>bantam-spg, GFP) compared to control (MB011B>scramble, GFP) neurons.

organism: Drosophila melanogaster

source_name: gamma5Beta'2a/Beta'2mp/Beta'2mp_bilateral Mushroom Body Output Neurons

extract_protocol:
Dynabead mRNA purification kit used on FACS isolated neurons
Smartseq 2 with NEXTERA XT (Illumina)

treatment_protocol: FACS isolation of Drosophila γ5β′2a/β′2mp/β′2mp_bilateral Mushroom Body Output Neurons

value: 3-4 days post-eclosion

tag: Sex

value: female

value: FACS isolated neurons


title: ALR-T0_S12


title: MCF7 Monoculture Sample 3

description:
285-JB-2
Counts_Raw_285.txt
CPM_285.txt

value: B


title: LAL-T0_S30


title: MB011B_ban_spg_biol_Rep1_exp

value: gamma5Beta'2a/Beta'2mp/Beta'2mp_bilateral Mushroom Body Output Neurons


title: Passage 1 organoid derived from murine salivary glands at 90 days post sham-IR, rep3

value: salivary gland stem/progenitor cells

value: sham-IR

value: 90 days