title: tsc_nuclear_RNA_rep2

description: Library name: tsc_nuclear_RNA_rep2

data_processing:
We first created a version of the GENCODE vM25 basic transcriptome that for each gene, included one representative intron-containing (i.e. nascent) transcript that began at the gene’s first annotated transcription start and the last annotated transcription end 36. We used kallisto 103 with the options “--single -s 300 -l 100 --rf-stranded” to align RNA-Seq data from total cellular RNA, as well as TSC cytoplasmic and chromatin- associated fractions.
Assembly: mm39
Supplementary files format and content: Wiggle density files were created using github.com/CalabreseLab/seekr2.0_update_manuscript/blob/main/wiggles/

growth_protocol: TSCs were cultured as in (Quinn et al. 2006). Briefly, TSCs were cultured on gelatin-coated, pre-plated irradiated mouse embryonic fibroblast (irMEF) feeder cells in TSC media (RPMI [Gibco 11875093], 20% qualified FBS [Gibco 26140079], 0.1mM penicillin-streptomycin [Gibco 15140122], 1mM sodium pyruvate [Gibco 11360070], 2mM L-glutamine [Gibco 25030081], 100uM beta-mercaptoethanol [Sigma-Aldrich 63689]) supplemented with 25ng/mL FGF4 (Gibco PHG0154) and 1ug/mL Heparin (Sigma-Aldrich H3149) just before use, at 37°C in a humidified incubator at 5% CO2. At passage, TSCs were trypsinized with 0.125% Trypsin-EDTA in PBS solution (Gibco 25200-072) for ~4 minutes at room temperature and gently dislodged from the plate with a sterile, cotton-plugged Pasteur pipette. To deplete irMEFs from TSCs prior to all harvests, TSCs were pre-plated for 45 minutes at 37°C, transferred to a fresh culture plate, and then cultured for three days in 70% irMEF-conditioned TSC media supplemented with growth factors as above.

extract_protocol:
To isolate chromatin-associated, soluble nuclear, and cytoplasmic RNA, we performed a cellular fractionation as described in 65 with a few exceptions. TSCs were passaged once off irMEFs with 40 minutes of pre-plating and cultured in conditioned media on a 10cm plate. Once the 10-cm plate was 50% confluent, cells were washed twice with cold PBS and scraped in 1 mL PBS. Cells were centrifuged at 1500 x g for 5 min, and resuspended in 200 μL cold cell lysis buffer (10 mM Tris-HCl pH 7.5, 0.05% IGEPAL CA-630, 150 mM NaCl), incubating on ice for 5 min. The cell lysate was then layered over 2.5 volumes of chilled sucrose cushion (24% sucrose in cell lysis buffer) and centrifuged at 15,000 x g for 10 min at 4°C. The supernatant was removed and became the cytoplasmic fraction. The resulting pellet of nuclei was washed with PBS (pH 7.5) containing 1 mM EDTA. The pellet was then resuspended in 100 μL of cold glycerol buffer (20 mM Tris-HCl pH 7.5, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM dithiothreitol [DTT], 0.125 mM 30 phenylmethylsulfonyl fluoride [PMSF], 50% glycerol) by gently flicking the tube. Then 100 μL of cold nuclei lysis buffer (10 mM HEPES pH 7.5, 1 mM DTT, 7.5 MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M urea, 1% IGEPAL CA-630) was added and the sample was vortexed for four seconds. After 2 min on ice, the nuclear lysate was spun at 15,000 x g for 2 min. The supernatant was removed and became the soluble nuclear (nucleoplasm) fraction. The remaining pellet (chromatin fraction) was washed with PBS containing 1 mM EDTA. To the chromatin pellet, 1 mL of TRIzol was added and vigorously resuspended by vortex and pipetting. 100 μL of cytoplasmic and nucleoplasm fractions were added to 1 mL of TRIzol and vortexed. The samples (in TRIzol) were then heated at 55°C for 10 min. The samples were then incubated on ice for 2 min. The samples were vortexed again and 200 μL CHCl3 was added. After a final vortex, samples were spun at 12,000 x g for 15 min at 4°C. The aqueous phase was extracted, and one volume of 100% ethanol was added. Samples were vortexed and RNA was extracted using Zymo-Spin IC Columns (from Zymo #R1013). RNA was eluted in 50 μL of RNase-free water. RNA concentrations were measured via Qubit 2.0 fluorometer (RNA high sensitivity kit, Thermo Fisher Q32852), and integrity of RNA was confirmed by visualizing rRNA bands  on an agarose gel, also confirming an absence of rRNA in the nucleoplasm and chromatin fractions. RNA samples were stored at -80°C.
Libraries for RNA sequencing were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche 08098140702) and KAPA Unique Dual-Indexed Adapters (Roche 08861919702) or TruSeq adapters, with each library’s input consisting of 9μL 100ng/μL total RNA (900 ng) mixed with 1μL of a 1:250 dilution of ERCC RNA spike-in controls (Thermo Fisher 4456740). RNA fragmentation was performed at 94°C for 6min. Libraries were pooled and sequenced on an Illumina NextSeq500 platform with a 75-cycle NextSeq 500/550 High Output Kit v2.5 (Illumina 20024906) or  on an Illumina NextSeq1000 platform with a 100-cycle NextSeq 1000/2000 P2 Reagents v3 kit (Illumina 20046811).

value: Cellular Fractionation


title: 3-day 10ng/mL dox-treated Xist-RMCE clone 1 Suz12

status: Public on Feb 21 2025

type: SRA

city: Chapel Hill

first: Joseph

middle: Mauro

last: Calabrese

state: NC

address: 120 Mason Farm Road

country: USA

institute: UNC Chapel Hill

description: Library name: X1_10ng_Suz12

library_source: genomic

data_processing:
ChIP-Seq reads were aligned using bowtie2 with default parameters.
Aligned reads that had a mapping quality greater than or equal to 30 were extracted with samtools 28, and allele-specific read retention (i.e., reads that overlap at least one B6 or CAST SNP) was performed as in 30,31 using a custom Perl script (intersect_reads_snps16.pl).
Assembly: mm10
Supplementary files format and content: WIG files were created using a custom perl script. Total, non-allelic read counts are divided by total aligned reads to mm10 of the dataset in million (i.e. RPM).

molecule: genomic DNA

organism: Mus musculus

source_name: RMCE Embryonic Stem Cells

growth_protocol: B6/CAST F1-hybrid Rosa26-RMCE ESCs from 12 were grown on gelatin-coated plastic dishes in a humidified Thermo Fisher Forma Series II water-jacketed incubator at 37°C and under 5% CO2. Cells were grown in DMEM high glucose plus sodium pyruvate (Gibco 11995-065), 15% ESC-qualified fetal bovine serum (Gibco 26140-079), 0.1mM non-essential amino acids (Gibco 11140-050), 100U/mL penicillin-streptomycin (Gibco 15140-122), 2mM L-glutamine (Gibco 25030-081), 0.1mM β-mercaptoethanol (Sigma-Aldrich 63689), and 1:500 LIF conditioned media produced from Lif-1Cα (COS) cells (kind gift of N. Hathaway).

extract_protocol:
ChIP beads were resuspended in Elution buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) and placed on a 65°C heat block for 17 minutes with frequent vortexing. ChIP DNA was then reverse crosslinked in 0.5% SDS and 100mM NaCl overnight at 65°C, followed by a 1-h RNaseA (3L; Thermo Scientific EN0531) treatment at 37°C and a 2.5-h Proteinase K (10L; Invitrogen 25530015) treatment at 56°C. DNA was then extracted with 1 volume of phenol:chloroform:isoamyl alcohol (Sigma-Aldrich P3803) and precipitated with 2 volumes 100% ethanol, 1/10 volume 3M sodium-acetate pH 5.4, and 1/1000 volume linear acrylamide (Invitrogen AM9520) overnight at -20°C. Precipitated DNA was then extracted with a 30-minute max speed spin at 4°C, washed once with ice-cold 80% ethanol, and resuspended in TE.
ChIP-Seq libraries were prepared with NEBNext End Repair Module (NEB, cat #: E6050S), A-tailing by Klenow Fragment (3’--5’ exo-; NEB, cat #: M0212S), and TruSeq 6-bp index adaptor ligation by Quick ligase (NEB, cat #: M2200S), and NEBNext High-Fidelity 2X PCR Master Mix (NEB, cat #: M0541S). All DNA clean-up steps were performed with AMPure XP beads (Beckman Coulter, cat #: A63880). Single-end, 100-bp sequencing was performed using an Illumina NextSeq 500/550 High Output v2.5 kit (Illumina, cat #: 20024906) on a NextSeq 500 System on an Illumina NextSeq1000 platform with a 100-cycle NextSeq 1000/2000 P2 Reagents v3 kit (Illumina 20046811)

treatment_protocol: Prior to crosslinking, RMCE cell lines (with rtTA) were treated with 0-1000ng/mL doxycycline (1000ng/mL if not otherwise specified) for 72 hours (or longer, 7 days). Adhered cells were crosslinked with 0.6% formaldehyde (Fisher Scientific BP531-500) in DMEM media with 5% FBS for 10min at room temperature, then quenched with 125mM glycine for 5min at room temperature. Crosslinked cells were then washed twice with ice-cold PBS and scraped with ice-cold PBS with 0.05% Tween (Fisher Scientific EW-88065-31) and PIC (Sigma Aldrich P8340). The cells were then spun at 1,200 x g at 4°C to remove PBS, followed by resuspension in ice-cold PBS with PIC and divided into 10-million cell aliquots.

tag: cell line

value: RMCE Embryonic Stem Cells

tag: treatment

value: 3 days with 10ng/mL doxycycline

tag: genotype

value: Xist-RMCEs

tag: chip antibody

value: Suz12 (D39F6) (Cell Signaling, cat #:3737)


title: d3 IRF6 sg1 ATAC

city: Stanford

first: Vanessa

last: Lopez-Pajares

state: CA

address: 269 Campus Dr., CCSR 2150

department: Dermatology

institute: Stanford University

description: d3 IRF6 sg1 ATAC

data_processing:
Raw reads were mapped to hg19 and counts were obtained using STAR with the following settings (--runThreadN 16 --outSJfilterReads Unique --outFilterType BySJout --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --alignIntronMin 20 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outSAMtype BAM SortedByCoordinate --outBAMcompression 10 --limitBAMsortRAM 60000000000 --quantMode TranscriptomeSAM GeneCounts --quantTranscriptomeBAMcompression 10 –outSAMstrandField intronMotif)37.
ATAC-seq read alignment, quality filtering, duplicate removal, transposase shifting, peak calling, and signal generation were all performed through the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline). Briefly, adapter sequences were trimmed, sequences were mapped to the hg19 reference genome using Bowtie2 (-X2000), poor quality reads were removed, PCR duplicates were removed (Picard Tools MarkDuplicates), chrM reads were removed, and read ends were shifted +4 on the positive strand or -5 on the negative strand to produce a set of filtered high-quality reads. These reads were put through MACS2 to get peak calls and signal files. Finally, IDR analysis was run on the two replicate peak files to produce an IDR peak file that is the reproducible set of peaks across both replicates. The full pipeline can be found on the ENCODE portal.
Differential analysis was performed using DESeq2 with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: peak files of significantly called peak

organism: Homo sapiens

source_name: keratinocyte

extract_protocol:
keratinocytes transduced with Cas9 then non-targeting or IRF6 targeting sgRNA, differentiated for 3d
Viable cells were lysed with digitonin as a detergent and pelleted by centrifugation at 500 RCF for 5 minutes at 4C. The nuclei pellet was resuspended in 50 uL of transposase mixture (25 uL 2x TD buffer, 2.5 uL of TDE1, 16.5 uL PBS, 0.5 uL 1% digitonin,  0.5 uL 10% Tween-20, 5 uL nuclease-free water). Transposition reactions were incubated at 37°C for 30 minutes in an Eppendorf ThermoMixer with agitation at 1000 RPM. Transposed DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (cat# D4014) and purified DNA was eluted in 20 ul elution buffer (10 mM Tris-HCl, pH 8).
Transposed fragments were amplified and purified with modified primers according to Buenrostro 2015. Libraries were quantified using qPCR prior to sequencing. All Fast-ATAC libraries were sequenced using paired-end, dual-index sequencing on an Illumina HiSeq 4000 at a depth of 50 million reads per sample.

treatment_protocol: Keratinocytes were grown in 50/50 growth media to maintain progenitor state or in differentiation media supplemented with normal (4.5g/L) glucose or low (0.5g/L) glucose. For IRF6 KO, keratinocytes were first transduced with Cas9 and subsequently with non-targeting or IRF6 targeting sgRNA.

value: IRF6 sg1

tag: cell type

value: keratinocyte

tag: age

value: neonatal

tag: time

value: day 3


title: 3-day 1000ng/mL dox-treated Airn-RMCE clone 2 Suz12

description: Library name: Airn2_Suz12

value: 3 days with 1000ng/mL doxycycline

value: Airn-RMCEs


title: d3 NT1 ATAC

description: d3 NT1 ATAC


title: 3-day 1000ng/mL dox-treated Empty-RMCE clone 2 Suz12

description: Library name: E2_Suz12

value: Empty-RMCEs


title: Normal glucose replicate 2 Input

data_processing:
Sequencing reads were uniquely aligned to hg19 with Bowtie2 (Langmead and Salzberg, 2012)
Reads that were unmapped, duplicate, or had less than 10 mapping quality were filtered out. ChIP signals were normalized to 10 million mapped reads with peaks called using MACS2 (p-value<10-5, FDR<0.3, fold-enrichment>5) (Zhang et al., 2008) on the filtered bam files, controlling ChIP samples to input samples, using the default parameters plus -f BAMPE --bdg.
Peak regions across all samples were merged using bedtools (Quinlan and Hall, 2010). Reads in peak regions were determined using bedtools multicov, passing the bam files and the merged peak file as parameters. Further analysis was performed using the ChIPpeakAnno (Zhu et al., 2010) R package , DESeq2 (Love et al., 2014)  and the annotation dataset TxDb.Hsapiens.UCSC.hg19.knownGene.
Genome_build: hg19
Supplementary_files_format_and_content: called peaks for each treatment condition in bed file format

source_name: Human keratinocytes

extract_protocol:
ChIP samples were crosslinked with 1% formaldehyde, lysed in nuclear lysis buffer and sheared using a Diagenode Bioruptor at high power 30sec on/off for 4 hours to achieve ~250bp. Lysates were then clarified by centrifugation for 15 minutes at 16100 rcf at 4° C. We used 8 ug of IRF6 antibody per 60ug chromatin and captured the chromatin-antibody complex with 80 uL Protein G beads (Thermo Fisher). ChIP DNA was then quantified by Qubit.
Libraries were constructed using the NEBNext Ultra II DNA library prep kit using 10ng of input material. ChIP libraries were size selected by PAGE purification (300-700 bp) for effective paired-end tag mapping and where therefore removed of all primer contamination. All libraries were sequenced on the Illumina HiSeq 4000 instrument to an average read depth of 300 million total reads.

treatment_protocol: Differentiated keratinocytes were grown in normal (4.5g/L) glucose media or low (0.5g/L) glucose media and harvested at d3 of differentiation.

value: Normal glucose


title: 3-day 10ng/mL dox-treated Xist-RMCE clone 3 H2AK119ub

description: Library name: xist_fl_cl3_10d_h2ak119ub

value: Ubiquityl-Histone H2A (Lys119) (D27C4) (H2AK119ub) (Cell Signaling, cat #:8240)


title: d6 Low ATAC

description: d6 Low ATAC

extract_protocol:
keratinocytes grown at full confluence and supplemented with 0.5g/L glucose in differentiation media for 6d
Viable cells were lysed with digitonin as a detergent and pelleted by centrifugation at 500 RCF for 5 minutes at 4C. The nuclei pellet was resuspended in 50 uL of transposase mixture (25 uL 2x TD buffer, 2.5 uL of TDE1, 16.5 uL PBS, 0.5 uL 1% digitonin,  0.5 uL 10% Tween-20, 5 uL nuclease-free water). Transposition reactions were incubated at 37°C for 30 minutes in an Eppendorf ThermoMixer with agitation at 1000 RPM. Transposed DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (cat# D4014) and purified DNA was eluted in 20 ul elution buffer (10 mM Tris-HCl, pH 8).
Transposed fragments were amplified and purified with modified primers according to Buenrostro 2015. Libraries were quantified using qPCR prior to sequencing. All Fast-ATAC libraries were sequenced using paired-end, dual-index sequencing on an Illumina HiSeq 4000 at a depth of 50 million reads per sample.

value: low glucose

value: day 6


title: 3-day 1000ng/mL dox-treated Empty-RMCE clone 4 H2AK119ub

description: Library name: empty_cl4_h2ak119ub


title: d6 Normal ATAC

description: d6 Normal ATAC

extract_protocol:
keratinocytes grown at full confluence and supplemented with 4.5g/L glucose in differentiation media for 6d
Viable cells were lysed with digitonin as a detergent and pelleted by centrifugation at 500 RCF for 5 minutes at 4C. The nuclei pellet was resuspended in 50 uL of transposase mixture (25 uL 2x TD buffer, 2.5 uL of TDE1, 16.5 uL PBS, 0.5 uL 1% digitonin,  0.5 uL 10% Tween-20, 5 uL nuclease-free water). Transposition reactions were incubated at 37°C for 30 minutes in an Eppendorf ThermoMixer with agitation at 1000 RPM. Transposed DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (cat# D4014) and purified DNA was eluted in 20 ul elution buffer (10 mM Tris-HCl, pH 8).
Transposed fragments were amplified and purified with modified primers according to Buenrostro 2015. Libraries were quantified using qPCR prior to sequencing. All Fast-ATAC libraries were sequenced using paired-end, dual-index sequencing on an Illumina HiSeq 4000 at a depth of 50 million reads per sample.

value: normal glucose


title: d3 Normal ATAC

description: d3 Normal ATAC

extract_protocol:
keratinocytes grown at full confluence and supplemented with 4.5g/L glucose in differentiation media for 3d
Viable cells were lysed with digitonin as a detergent and pelleted by centrifugation at 500 RCF for 5 minutes at 4C. The nuclei pellet was resuspended in 50 uL of transposase mixture (25 uL 2x TD buffer, 2.5 uL of TDE1, 16.5 uL PBS, 0.5 uL 1% digitonin,  0.5 uL 10% Tween-20, 5 uL nuclease-free water). Transposition reactions were incubated at 37°C for 30 minutes in an Eppendorf ThermoMixer with agitation at 1000 RPM. Transposed DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (cat# D4014) and purified DNA was eluted in 20 ul elution buffer (10 mM Tris-HCl, pH 8).
Transposed fragments were amplified and purified with modified primers according to Buenrostro 2015. Libraries were quantified using qPCR prior to sequencing. All Fast-ATAC libraries were sequenced using paired-end, dual-index sequencing on an Illumina HiSeq 4000 at a depth of 50 million reads per sample.


title: 3-day 1000ng/mL dox-treated Airn-RMCE clone 5 H2AK119ub

description: Library name: airn_cl5_h2ak119ub


title: 3-day 1000ng/mL dox-treated X872-Airn-RMCE clone 1 H2AK119ub

description: Library name: xist_airn_cl1_h2ak119ub


title: PG ATAC

description: PG ATAC

extract_protocol:
keratinocytes grown in 50/50 media
Viable cells were lysed with digitonin as a detergent and pelleted by centrifugation at 500 RCF for 5 minutes at 4C. The nuclei pellet was resuspended in 50 uL of transposase mixture (25 uL 2x TD buffer, 2.5 uL of TDE1, 16.5 uL PBS, 0.5 uL 1% digitonin,  0.5 uL 10% Tween-20, 5 uL nuclease-free water). Transposition reactions were incubated at 37°C for 30 minutes in an Eppendorf ThermoMixer with agitation at 1000 RPM. Transposed DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (cat# D4014) and purified DNA was eluted in 20 ul elution buffer (10 mM Tris-HCl, pH 8).
Transposed fragments were amplified and purified with modified primers according to Buenrostro 2015. Libraries were quantified using qPCR prior to sequencing. All Fast-ATAC libraries were sequenced using paired-end, dual-index sequencing on an Illumina HiSeq 4000 at a depth of 50 million reads per sample.

value: PG


title: 3-day 1000ng/mL dox-treated X872-Airn-RMCE clone 2 H2AK119ub

description: Library name: xist_airn_cl2_h2ak119ub

value: RMCE Embryonic Stem Cells


title: 3-day 1000ng/mL dox-treated Airn-RMCE clone 2 H2AK119ub

description: Library name: airn_cl2_h2ak119ub

value: 3 days with 10ng/mL doxycycline


title: 3-day 10ng/mL dox-treated Xist-RMCE clone 3 H3K27me3

description: Library name: xist_fl_cl3_10d_h3k27me3

value: Xist-RMCEs

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) (H3K27me3) (Cell Signaling, cat #:9733)


title: LR_SN_192

city: Worcester

first: Ryan

last: Logan

state: MA

address: 366 Plantation Street

institute: University of Massachusetts Chan Medical School

description: Library name: LR_SN_192

library_source: transcriptomic

data_processing:
For Rattus norvegicus samples: Quality control was performed by FastQC, cutadapt was used to trim low quality and over-represented sequences. STAR was used for alignment with ensembl reference (release 104) and RSEM is used for expression calculation.
For Mus musculus samples: Quality control was performed by Fastqc. Perform trimming by trimmomatic, allign the sequence using Hisat2 with Ensembl reference and read count with Hiseq
Assembly: Mus musculus:GRCm38 ; Rattus norvegicus: Rnor_6.0(Ensembl release 104)
Supplementary files format and content: mouse_raw_counts.csv: processed count data for Mus musculus samples.
Supplementary files format and content: rat_raw_counts_all.csv: processed count data for Rattus norvegicus samples.

molecule: total RNA

organism: Rattus norvegicus

source_name: brain

extract_protocol:
RNA extraction was performed from 0.5 mm punches of coronal sections using RNeasy Micro kits (Qiagen, Inc.). Briefly, tissue samples were homogenized in Buffer RLT, RNA lysis buffer, before being centrifuged in a QIAshredder column at full speed for 3 min. The flow-through was mixed with an equal volume of 70% ethanol and transferred to a MinElute spin column before being washed with Buffer RW1, RNA wash buffer, to free membrane-bound RNA. DNA was removed with on column treatment using DNAse I. The flow-through was washed again with Buffer RW1, and two times with Buffer RPE, a secondary RNA wash buffer in ethanol, to remove trace salts. The spin column was cleaned with 80% ethanol and centrifuged at full speed for 5 min to dry the column matrix. Total RNA was eluted in RNAse-free water. Concentration and purity were quantified using a Nanodrop.
Illumina Total RNAseq Paired End 75bp

tag: tissue

value: brain

value: neuron

tag: strain

value: Heterogeneous Stock

value: Withdrawal

tag: batch

value: bSCN

tag: Sex

value: female

tag: region

value: SCN


title: LR_SN_189

description: Library name: LR_SN_189


title: LR_SN_188

description: Library name: LR_SN_188


title: LR_SN_187

description: Library name: LR_SN_187


title: d3 Low ATAC

description: d3 Low ATAC

extract_protocol:
keratinocytes grown at full confluence and supplemented with 0.5g/L glucose in differentiation media for 3d
Viable cells were lysed with digitonin as a detergent and pelleted by centrifugation at 500 RCF for 5 minutes at 4C. The nuclei pellet was resuspended in 50 uL of transposase mixture (25 uL 2x TD buffer, 2.5 uL of TDE1, 16.5 uL PBS, 0.5 uL 1% digitonin,  0.5 uL 10% Tween-20, 5 uL nuclease-free water). Transposition reactions were incubated at 37°C for 30 minutes in an Eppendorf ThermoMixer with agitation at 1000 RPM. Transposed DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (cat# D4014) and purified DNA was eluted in 20 ul elution buffer (10 mM Tris-HCl, pH 8).
Transposed fragments were amplified and purified with modified primers according to Buenrostro 2015. Libraries were quantified using qPCR prior to sequencing. All Fast-ATAC libraries were sequenced using paired-end, dual-index sequencing on an Illumina HiSeq 4000 at a depth of 50 million reads per sample.

value: keratinocyte

value: neonatal

value: day 3


title: LR_SN_190

description: Library name: LR_SN_190


title: LR_SN_181

description: Library name: LR_SN_181

value: Naive


title: 3-day 1000ng/mL dox-treated Airn-RMCE clone 2 H3K27me3

description: Library name: airn_cl2_h3k27me3

value: 3 days with 1000ng/mL doxycycline

value: Airn-RMCEs


title: 3-day 1000ng/mL dox-treated Airn-RMCE clone 5 H3K27me3

description: Library name: airn_cl5_h3k27me3

value: RMCE Embryonic Stem Cells


title: 3-day 1000ng/mL dox-treated Empty-RMCE clone 1 H3K27me3

description: Library name: empty_cl1_h3k27me3

value: Empty-RMCEs


title: T1a_NEP_2B

city: BETHESDA

first: Cihan

last: Oguz

state: MD

address: NIHBC 29B BG RM 1NN20, 9000 ROCKVILLE PIKE

institute: NIH

description: Library name: DSP-1001250002850-B-H12

data_processing:
Fastqs for each ROI were converted to Digital Count Conversion (DCC) files using NanoString’s GeoMx NGS Pipeline v.2.3.3.10. 18677 genes passed the recommended LOQ (level of quantification) of 2.0, which is the default setting for high confidence detection. Targets were further filtered to 10% higher than the LOQ of 2.0 for higher confidence level, therefore the analyzed targets were reduced to 11681 after quality control and count normalization.
Assembly: hg38
Supplementary files format and content: DCC files contain raw read counts along with RTS_IDs (probe barcodes), whereas the PKC file includes probe metadata for the targets associated with the RTS_IDs in the DCC files.
Library strategy: GeoMx-Seq

extract_protocol:
The formalin-fixed, paraffin-embedded (FFPE) tissue blocks were cut at 5μm thickness onto APEX treated slides to improve attachment. After incubating at 60°C overnight, deparaffinization, and antigen retrieval was performed on Leica BOND RX autostainer using HIER2 (EDTA-based antigen retrieval solution for 20min) and proteinase K (15min at 37°C, 1μg/ml). RNA probes (NanoString GeoMx WTA Human RNA probes catalog number 121401102) were added for hybridization at 37°C for 16h per protocol. Slides were then washed 2X with stringent wash (50% formamide in 2XSSC for 25min) followed by 2X wash with 2XSSC (2min). Slides were blocked with W buffer for 30min and incubated for 60min at RT with the antibody cocktail containing PanCK-532 RRID:AB_2935724 (1:40), CD45-AF594 RRID:AB_3169472 (1:40), aSMA-AF647(1:200) and Syto 13 (10mM, nuclear stain). Slides were washed with SSC buffer 2X and scanned on the GeoMx DSP machine for selection of ROIs, using FITC/525nm filter to detect nuclei stained with Syto 13 (150msec), Cy3/568 nm channel to detect PanCK (200msec), Texas Red/615 nm to detect CD45 (200msec) and Cy5/666nm to detect aSMA (200msec). Based on tissue morphology, ROIs for EP, SRC, and DGC were selected using polygons, with masking for panCK positive cells. The combined surface area of ROIs was 7699256.57mm2 containing 57880 nuclei.
Oligonucleotide barcodes from each ROI were UV-photocleaved, collected into 96-well plates, followed by library preparation and sequencing. Extracted mRNA barcodes were prepared and sequenced on a NextSeq2000 instrument using either a P2 or P3 flow cell kit.


title: 3-day 1000ng/mL dox-treated X872-Airn-RMCE clone 2 H3K27me3

description: Library name: xist_airn_cl2_h3k27me3


title: LR_SN_184

description: Library name: LR_SN_184


title: LR_SN_182

description: Library name: LR_SN_182


title: LR_SN_177

description: Library name: LR_SN_177

value: Intox


title: 3-day 1000ng/mL dox-treated Empty-RMCE clone 4 H3K27me3

description: Library name: empty_cl4_h3k27me3

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) (H3K27me3) (Cell Signaling, cat #:9733)


title: 3-day 1000ng/mL dox-treated X872-Airn-RMCE clone 1 H3K27me3

description: Library name: xist_airn_cl1_h3k27me3


title: T1a_NEP_2A

description: Library name: DSP-1001250002850-B-H11


title: LR_SN_183

description: Library name: LR_SN_183

value: brain


title: LR_SN_191

description: Library name: LR_SN_191

value: neuron


title: 3-day 1000ng/mL dox-treated Empty-RMCE clone 1 H2AK119ub

description: Library name: empty_cl1_h2ak119ub

value: Ubiquityl-Histone H2A (Lys119) (D27C4) (H2AK119ub) (Cell Signaling, cat #:8240)


title: GC_sup_2H

description: Library name: DSP-1001250002850-B-H08


title: LR_SN_185

description: Library name: LR_SN_185

value: Heterogeneous Stock


title: LR_SN_180

description: Library name: LR_SN_180

value: bSCN


title: GC_sup_2I

description: Library name: DSP-1001250002850-B-H09


title: LR_SN_179

description: Library name: LR_SN_179

value: female


title: GC_sup_2E

description: Library name: DSP-1001250002850-B-H05


title: GC_sup_2A

description: Library name: DSP-1001250002850-B-H10


title: GC_sup_2G

description: Library name: DSP-1001250002850-B-H07


title: GC_sup_2F

description: Library name: DSP-1001250002850-B-H06


title: LR_SN_178

description: Library name: LR_SN_178

value: SCN


title: GC_sup_2B

description: Library name: DSP-1001250002850-B-H02


title: LR_SN_171

description: Library name: LR_SN_171

value: Abstinence


title: LR_SN_170

description: Library name: LR_SN_170


title: GC_deep_2E

description: Library name: DSP-1001250002850-B-G09


title: LR_SN_175

description: Library name: LR_SN_175


title: LR_SN_166

description: Library name: LR_SN_166

value: Withdrawal

value: male


title: LR_SN_174

description: Library name: LR_SN_174


title: GC_sup_2D

description: Library name: DSP-1001250002850-B-H04


title: LR_SN_176

description: Library name: LR_SN_176


title: GC_deep_2A

description: Library name: DSP-1001250002850-B-G06


title: LR_SN_164

description: Library name: LR_SN_164


title: GC_deep_2B

description: Library name: DSP-1001250002850-B-G07


title: GC_sup_2C

description: Library name: DSP-1001250002850-B-H03


title: KYSE150 with si-nc

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: NO. 199 Renai Road

country: China

institute: Soochow University

description: Library name: Sample 6

data_processing:
All libraries were sequenced on the Illumina Novaseq 6000 instrument, and 150 bp paired-end reads were generated.
Sequencing reads were aligned back to the human genome (version: GRCh38) by TopHat 2 software.
Read count extraction was performed using StringTie software.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads count for each Sample

source_name: KYSE150 with si-nc

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen).
RNA-seq libraries were generated and sequenced by CapitalBio Technology (Beijing, China).

value: Poorly differentiated squamous carcinoma cell line from human esophageal cancer


title: LR_SN_163

description: Library name: LR_SN_163


title: LR_SN_173

description: Library name: LR_SN_173


title: LR_SN_168

description: Library name: LR_SN_168


title: LR_SN_172

description: Library name: LR_SN_172


title: GC_NEP_2C

description: Library name: DSP-1001250002850-B-H01


title: GC_NEP_2B

description: Library name: DSP-1001250002850-B-G12


title: KYSE150 with siRNAs targeting ZC3H18_1

description: Library name: Sample 4

source_name: KYSE150 with siRNAs targeting ZC3H18 (sequence: GGGGTGAGGGCTTCTGATCT)


title: ECA109 with si-nc

description: Library name: Sample 3

source_name: ECA109 with si-nc


title: GC_NEP_2A

description: Library name: DSP-1001250002850-B-G11


title: LR_SN_169

description: Library name: LR_SN_169


title: LR_SN_167

description: Library name: LR_SN_167


title: T1a_NEP_1C

description: Library name: DSP-1001250002850-B-G02


title: GC_deep_2G

description: Library name: DSP-1001250002850-B-G10


title: patient 529, tumor tissue, never smoker

city: New Haven

first: Xiting

last: Yan

state: Connecticut

address: 300 Cedar Street, Ste S441D

department: Internal Medicine

institute: Yale School of Medicine

description: Library name: 529T

data_processing:
The raw sequencing reads were trimmed using CutAdapt and mapped to human genome (UCSC hg38) using STAR V2.5.1 as paired-end reads. The Rsubread R package was used to calculate the raw read counts for every sample separately. Raw counts for all samples were merged into one single matrix in rawcounts_all.txt
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: T

growth_protocol: Lung tissue and NSCLC tumors were collected from the Department of Surgical Pathology (Yale New Haven Hospital) on ice in chilled RPMI media with 10% Fetal Bovine serum. About 5mm pieces of tissues were resuspended in 1ml Trizol and stored at -80 until RNA extraction.

extract_protocol:
Total RNAs were extracted from 5mm lung tissue or tumor using Trizol (phenol-chloroform extraction, Qiagen kit). Extracted RNAs were resuspended in 50ul of DEPC-treated water and stored in -80 C until library preparation
mRNAs were purified from approximately 200ng of total RNA with oligo-dT beads and sheared by incubation at 94C in the presence of Mg. Following first-strand synthesis with random primers, second-strand synthesis and A-tailing were performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs was ligated to library insert fragments.  Library amplification amplified fragments carrying the appropriate adapter sequences at both ends.  Strands marked with dUTP were not amplified. Indexed libraries were quantified by qRT-PCR using a commercially available kit (Roch KAPA Biosystems Cat# KK4854) and insert size distribution was determined by either the Agilent Bioanalyzer. Samples with a yield of ≥ 0.5 ng/ul and a size distribution of 150-300bp were used for sequencing.

treatment_protocol: Tumor and lung tissues were collected from smokers and non-smokers. No further treatment was performed on those tissues.

value: T

tag: smoking

value: never

tag: tumor tissue

value: tumor


title: GC_deep_2C

description: Library name: DSP-1001250002850-B-G08


title: LR_SN_165

description: Library name: LR_SN_165


title: T1a_SRC_1C

description: Library name: DSP-1001250002850-B-G05


title: KYSE150 with siRNAs targeting ZC3H18_2

description: Library name: Sample 5

source_name: KYSE150 with siRNAs targeting ZC3H18 (sequence: TCGTCGGAGTGATTATCTTCCT)


title: T1a_SRC_1B

description: Library name: DSP-1001250002850-B-G04


title: LR_SN_162

description: Library name: LR_SN_162

value: Naive


title: ECA109 with siRNAs targeting ZC3H18_2

description: Library name: Sample 2

source_name: ECA109 with siRNAs targeting ZC3H18 (sequence: TCGTCGGAGTGATTATCTTCCT)


title: T1a_SRC_1A

description: Library name: DSP-1001250002850-B-G03


title: ECA109 with siRNAs targeting ZC3H18_1

description: Library name: Sample 1

source_name: ECA109 with siRNAs targeting ZC3H18 (sequence: GGGGTGAGGGCTTCTGATCT)


title: LR_SN_160

description: Library name: LR_SN_160


title: patient 532, normal tissue, never smoker

description: Library name: 532N

source_name: N

value: N

value: normal


title: patient 532, tumor tissue, never smoker

description: Library name: 532T


title: LR_SN_159

description: Library name: LR_SN_159

value: brain


title: patient 529, normal tissue, never smoker

description: Library name: 529N


title: GC_sup_1D

description: Library name: DSP-1001250002850-B-F10


title: LR_SN_155

description: Library name: LR_SN_155

value: neuron

value: Intox


title: patient 417,normal tissue, former smoker

description: Library name: 417N

value: former


title: GC_sup_1C

description: Library name: DSP-1001250002850-B-F09


title: T1a_NEP_1B

description: Library name: DSP-1001250002850-B-G01


title: LR_SN_154

description: Library name: LR_SN_154

value: Heterogeneous Stock

value: bSCN


title: patient 411, normal tissue, never smoker

description: Library name: 411N


title: GC_sup_1B

description: Library name: DSP-1001250002850-B-F08


title: T1a_NEP_1A

description: Library name: DSP-1001250002850-B-F12


title: patient 452, tumor tissue, current smoker

description: Library name: 452T

value: current


title: LR_SN_158

description: Library name: LR_SN_158

value: SCN


title: patient 452, normal tissue, current smoker

description: Library name: 452N


title: LR_SN_156

description: Library name: LR_SN_156


title: LR_SN_153

description: Library name: LR_SN_153


title: GC_sup_1E

description: Library name: DSP-1001250002850-B-F11


title: LR_SN_157

description: Library name: LR_SN_157


title: patient 411, tumor tissue, never smoker

description: Library name: 411T


title: patient 397, normal tissue, current smoker

description: Library name: 397N


title: patient 406, normal tissue, current smoker

description: Library name: 406N


title: patient 387, tumor tissue, former smoker

description: Library name: 387T


title: GC_sup_1A

description: Library name: DSP-1001250002850-B-F07


title: patient 417, tumor tissue, former smoker

description: Library name: 417T


title: patient 395, tumor tissue, former smoker

description: Library name: 395T


title: GC_NEP_1B

description: Library name: DSP-1001250002850-B-F05


title: patient 397, tumor tissue, current smoker

description: Library name: 397T


title: LR_SN_149

description: Library name: LR_SN_149

value: Abstinence


title: GC_NEP_1A

description: Library name: DSP-1001250002850-B-F04


title: proband (family 2) rep 3

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description:
Library name: proband_5
10x Genomics

library_source: transcriptomic single cell

data_processing:
Illumina 10X Genomics scRNAseq base-call files were converted to FASTQ, which aligned to the hg38 genome and transcriptome using the CellRanger v3.0.2 pipeline, for a gene–cell expression matrix.
The count matrices were processed for filtering and downstream analysis using Partek Flow software.
Assembly: hg38
Supplementary files format and content: tab-delimited values files and matrix files

source_name: cortical organoid

extract_protocol:
Sample was pooled together with three cortical organoids for RNA extraction. Dissociated cells were filtered through a 40 µm cell strainer, and centrifuged at 300G for 5 mins, papain removed and resuspended in 1% FBS in PBS.
Using the Chromium Single Cell 3’ Reagent Kits v3.1 (10X Genomics), 4000-7000 cells were captured per lane, single-cell libraries were sequenced on a NovaSeq S2 flow cell

value: cortical organoid

value: 100 days


title: patient 395, normal tissue, former smoker

description: Library name: 395N


title: LR_SN_148

description: Library name: LR_SN_148

value: male


title: LR_SN_152

description: Library name: LR_SN_152


title: GC_NEP_1C

description: Library name: DSP-1001250002850-B-F06


title: LR_SN_146

description: Library name: LR_SN_146


title: patient 406, tumor tissue, current smoker

description: Library name: 406T

value: T


title: HCT116, sh-NC-2

city: Nanjing

first: Yaya

last: Sun

address: No. 87 Dingjiaqiao, Hunan Road, Gulou District

institute: Southeast University

description:
Library name: Sample 2
sh_NC_2

data_processing:
The sequencing fragments were converted into sequence data (reads) through base calling using the CASAVA software, after being obtained as image data from the high-throughput sequencing instrument.
The quality of the sequencing data was represented by Qphred scores.
Reads with sequencing adapters were removed, as well as reads containing N (representing undetermined base information). Low-quality reads were also excluded, defined as those in which more than 50% of the bases have a Qphred score ≤ 20.
Assembly: GRCh38
Supplementary files format and content: tsv file includes fpkm values for each sample.
Supplementary files format and content: tsv file includes raw counts values for each sample.

extract_protocol:
Total RNA was extracted from cell lysate samples using Trizol. The concentration and purity of the extracted RNA were assessed using a Nanodrop 2000 spectrophotometer. RNA integrity was evaluated by agarose gel electrophoresis, and the RNA Integrity Number (RIN) was determined using an Agilent 2100 Bioanalyzer. For library preparation, the RNA samples were required to meet the following criteria: a total RNA amount of at least 1 μg, a concentration of at least 35 ng/μL, an OD260/280 ratio of at least 1.8, and an OD260/230 ratio of at least 1.0.
Library construction for the sequencing experiment was performed using the Illumina TruSeq™ RNA Sample Prep Kit method.

value: colon cancer cell

value: negative control


title: GC_deep_1C

description: Library name: DSP-1001250002850-B-F02


title: patient 387, normal tissue, former smoker

description: Library name: 387N

value: N


title: LR_SN_150

description: Library name: LR_SN_150


title: HCT116, sh-IGF2BP3-3

description:
Library name: Sample 6
sh_IGF2BP3_3

value: IGF2BP3 knockdown


title: LR_SN_151

description: Library name: LR_SN_151

value: brain


title: proband (family 2) rep 2

description:
Library name: proband_4
10x Genomics


title: HCT116, sh-NC-1

description:
Library name: Sample 1
sh_NC_1


title: HCT116, sh-IGF2BP3-2

description:
Library name: Sample 5
sh_IGF2BP3_2


title: proband (family 2) rep 1

description:
Library name: proband_3
10x Genomics


title: GC_deep_1D

description: Library name: DSP-1001250002850-B-F03


title: Palbo_2

city: Durham

first: KUO

last: DU

address: 905 SOUTH LASALLE STREET, Room 1063

department: Medicine

institute: Duke Universty

description: Library name: Sample23

data_processing:
RNA-seq data were processed using the fastp toolkit to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads. Only reads that were ≥20nt after trimming were kept for further analysis. Reads were mapped to mice genome reference combining the GRCm38. STAR v2.7.5 was used to align reads to reference genome. Gene count was quantified by featureCounts v2.0.1.
Assembly: GRCm38 and mm10
Supplementary files format and content: tsv and txt

extract_protocol:
RNA was harvested using Trizol (Invitrogen)
RNA samples were sequenced by Novogene Corporation following standard construction protocol. In brief, RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using a NanoPhotometer Spectrophotometer (IMPLEN). RNA integrity and quantity were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies). Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Clustering of index-coded samples was performed on an Illumina NovaSeq sequencer

value: Hepatocyte

value: Palbo


title: Palbo_3

description: Library name: Sample24


title: LR_SN_144

description: Library name: LR_SN_144

value: neuron

value: Withdrawal

value: female

value: NAc Core


title: HCT116, sh-IGF2BP3-1

description:
Library name: Sample 4
sh_IGF2BP3_1


title: HCT116, sh-NC-3

description:
Library name: Sample 3
sh_NC_3


title: GC_deep_1B

description: Library name: DSP-1001250002850-B-F01


title: GC_deep_1A

description: Library name: DSP-1001250002850-B-E12


title: LR_SN_145

description: Library name: LR_SN_145

value: Heterogeneous Stock

value: bSCN

value: SCN


title: Palbo_1

description: Library name: Sample22


title: Huh7_Dp44mT_4

description: Library name: Sample18


title: T1a_SRC_3B

description: Library name: DSP-1001250002850-B-E10


title: LR_SN_142

description: Library name: LR_SN_142


title: Huh7_Dp44mT_3

description: Library name: Sample17


title: Control_3

description: Library name: Sample21

value: Ctrl


title: T1a_SRC_3C

description: Library name: DSP-1001250002850-B-E11


title: T1a_SRC_3A

description: Library name: DSP-1001250002850-B-E09


title: Huh7_Dp44mT_1

description: Library name: Sample15


title: Control_2

description: Library name: Sample20


title: LR_SN_143

description: Library name: LR_SN_143


title: Huh7_Veh_4

description: Library name: Sample14

value: Vehicle


title: Huh7_Dp44mT_2

description: Library name: Sample16


title: T1a_NEP_3a

description: Library name: DSP-1001250002850-B-E08


title: LR_SN_141

description: Library name: LR_SN_141


title: T1a_NEP_3c

description: Library name: DSP-1001250002850-B-E07


title: Huh7_Veh_1

description: Library name: Sample11


title: Huh7_Veh_2

description: Library name: Sample12


title: GC_sup_3H

description: Library name: DSP-1001250002850-B-E05


title: Huh7_Veh_3

description: Library name: Sample13


title: LR_SN_137

description: Library name: LR_SN_137

value: Naive


title: LR_SN_139

description: Library name: LR_SN_139


title: LR_SN_136

description: Library name: LR_SN_136


title: LR_SN_140

description: Library name: LR_SN_140


title: Control_1

description: Library name: Sample19


title: GC_sup_3C

description: Library name: DSP-1001250002850-B-E04


title: 9_Mluc6_Con_P

city: Rochester

first: Fathima

last: Athar

state: New York

address: 500 Joseph C Wilson Blvd.

department: Biology

institute: University of Rochester

data_processing:
Fastp (0.23.4): Default parameters Salmon (v1.5.1): salmon quant --gcBias -l A
Assembly: GCA_003508835.1 (Eonycteris spelaea), EptFus1.0_HiC (DNA Zoo Consortium, Eptesicus fuscus), GCA_004027435.1 (Artibeus jamaicensis), Myoluc2.0_HiC (DNA Zoo Consortium, Myotis lucifugus), GCF_000001635.27 (Mus musculus), and GCA_000001405.29 (Homo sapiens)
Supplementary files format and content: Row count and matrix

molecule: polyA RNA

organism: Myotis lucifugus

source_name: Fibroblast

extract_protocol:
Total RNA was extracted from irradiated or non-irradiated fibroblasts from four bat species, laboratory mice, wild-caught mice and humans using PureLinkTM RNA Mini Kit (Thermo Fisher Scientific) following manufacturer’s instructions.
NGS-TruSeq Stranded mRNA libraries were generated and sequenced with Illumina NovaSeq 6000 single-end 75 bp sequencing at the University of Rochester Genomics Research Center.

value: Fibroblast

value: wildtype


title: 9_24h_Mluc6_20Gy


title: 8_24h_Mluc6_10Gy


title: GC_sup_3B

description: Library name: DSP-1001250002850-B-E03


title: 8_12d_Mluc5_20Gy


title: 7_24h_Mluc6_Con


title: GC_sup_3J

description: Library name: DSP-1001250002850-B-E02


title: 6_24h_Mluc5_20Gy


title: LR_SN_134

description: Library name: LR_SN_134


title: GC_sup_3G

description: Library name: DSP-1001250002850-B-D12


title: 7_12d_Mluc5_10Gy


title: 5_24h_Mluc5_10Gy


title: LR_SN_135

description: Library name: LR_SN_135


title: GC_sup_3D

description: Library name: DSP-1001250002850-B-D09


title: GC_sup_3I

description: Library name: DSP-1001250002850-B-E01


title: LR_SN_138

description: Library name: LR_SN_138


title: T1a_NEP_3b

description: Library name: DSP-1001250002850-B-E06


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D98

city: Suwon-si

first: yeojin

last: Kim

address: 164 World cup-ro

country: South Korea

institute: ajou Univ.

description: Library name: SAMPLE 84

data_processing:
Trimmomatic v0.39: Sequence reads were trimmed for adapter sequences and low-quality bases using Trimmomatic (parameters: sliding window = 4, mean quality = 15, base quality threshold = 3, minimum length = 36 bp).
HISAT2 v2.2.1: Trimmed sequence reads were mapped to the GRCh38 reference genome using HISAT2 (parameters: --dta, mismatch penalty = 2, insertion penalty = 3, deletion penalty = 3, alignment score minimum = 0.8).
StringTie v2.1.4: Read count extraction and transcript assembly were performed using StringTie. Normalization was applied to estimate FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million) values.
DESeq2 v1.30.1: Differentia  expression analysis was performed using DESeq2 with default parameters. Genes with |fold change| ≥ 2 and a p-value < 0.05 were considered differentially expressed.
Assembly: GRCh38
Supplementary files format and content: Excel file includes TPM values for each Sample

source_name: patient-derived fibroblast

growth_protocol: Patient-derived dermal fibroblast were matintained in DMEM supplemented with 10% Fetal Bovine Serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37˚C

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Germany) following the manufacturer’s guidelines.
RNA libraries for RNA-seq were prepared using TruSeq Standard mRNA Library Prep Kit following manufacturer's protocols

treatment_protocol: ER stress was induced by treatment of 10nM Thapsigargin for 24h in 70% confluency

tag: disease state

value: Alzheimer's Disease

value: patient-derived fibroblast

value: WT

value: Thapsigargin


title: 5_Mluc5_Con_P


title: LR_SN_131

description: Library name: LR_SN_131

value: brain

value: Intox


title: LR_SN_129

description: Library name: LR_SN_129

value: neuron


title: LR_SN_132

description: Library name: LR_SN_132

value: female


title: GC_sup_3F

description: Library name: DSP-1001250002850-B-D11


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D96

description: Library name: SAMPLE 82


title: 4_24h_Mluc5_Con


title: LR_SN_130

description: Library name: LR_SN_130

value: NAc Core


title: GC_sup_3E

description: Library name: DSP-1001250002850-B-D10


title: 3_12d_Mluc1_10Gy


title: 4_12d_Mluc1_20Gy


title: GC_NEP_3B

description: Library name: DSP-1001250002850-B-D06


title: GC_sup_3A

description: Library name: DSP-1001250002850-B-D08


title: LR_SN_133

description: Library name: LR_SN_133

value: Heterogeneous Stock


title: 2_24h_Mluc1_10Gy


title: GC_NEP_3C

description: Library name: DSP-1001250002850-B-D07


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D98

description: Library name: SAMPLE 83

value: N


title: LR_SN_128

description: Library name: LR_SN_128


title: 3_24h_Mluc1_20Gy


title: LR_SN_125

description: Library name: LR_SN_125

value: Abstinence


title: LR_SN_127

description: Library name: LR_SN_127


title: 2_12d_Mluc1_Con_P


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D96

description: Library name: SAMPLE 81


title: LR_SN_126

description: Library name: LR_SN_126


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D90

description: Library name: SAMPLE 79


title: 1_Mluc1_Con_P


title: GC_deep_3N

description: Library name: DSP-1001250002850-B-D03


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D245

description: Library name: SAMPLE 78


title: GC_NEP_3A

description: Library name: DSP-1001250002850-B-D05


title: LR_SN_122

description: Library name: LR_SN_122


title: LR_SN_121

description: Library name: LR_SN_121


title: 15_12d_Mluc10_10Gy


title: LR_SN_124

description: Library name: LR_SN_124


title: 1_24h_Mluc1_Con


title: LR_SN_119

description: Library name: LR_SN_119

value: Withdrawal

value: male


title: GC_deep_3M

description: Library name: DSP-1001250002850-B-D02


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D90

description: Library name: SAMPLE 80


title: LR_SN_123

description: Library name: LR_SN_123


title: 14_12d_Mluc10_Con_P


title: GC_deep_3K

description: Library name: DSP-1001250002850-B-C12


title: GC_deep_3L

description: Library name: DSP-1001250002850-B-D01


title: 16_12d_Mluc10_20Gy


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D244

description: Library name: SAMPLE 76


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D245

description: Library name: SAMPLE 77


title: LR_SN_118

description: Library name: LR_SN_118


title: GC_deep_3O

description: Library name: DSP-1001250002850-B-D04


title: LR_SN_120

description: Library name: LR_SN_120


title: 12_12d_Mluc6_20Gy


title: 12_24h_Mluc10_20Gy


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D244

description: Library name: SAMPLE 75


title: 13_12d_Mluc10_Con_P


title: GC_deep_3I

description: Library name: DSP-1001250002850-B-C11


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D233

description: Library name: SAMPLE 74


title: GC_deep_3H

description: Library name: DSP-1001250002850-B-C10


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D233

description: Library name: SAMPLE 73


title: GC_deep_3G

description: Library name: DSP-1001250002850-B-C09


title: GC_deep_3E

description: Library name: DSP-1001250002850-B-C07


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D230

description: Library name: SAMPLE 72


title: GC_deep_3F

description: Library name: DSP-1001250002850-B-C08


title: 11_12d_Mluc6_10Gy


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D229

description: Library name: SAMPLE 70


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D229

description: Library name: SAMPLE 69


title: 10_Mluc6_Con_P


title: LR_SN_113

description: Library name: LR_SN_113

value: Naive


title: LR_SN_116

description: Library name: LR_SN_116


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D225

description: Library name: SAMPLE 68


title: LR_SN_112

description: Library name: LR_SN_112


title: LR_SN_115

description: Library name: LR_SN_115


title: skin of animal p6

city: Bochum

first: Arne

last: Sahm

address: Universitätsstr. 150

country: Germany

institute: Ruhr-Universität Bochum

description: Library name: skin.p6

data_processing:
Reads were trimmed for adaptor sequence/low-quality sequence using cutadapt and trimmomatic.
Preprocessed reads were mapped against the transcriptome assembly using bwa mem.
Quantification was performed using featureCounts.
Assembly: The transcriptome shotgun assembly that was used for mapping was uploaded to NCBI (SUB14991774). It is currently processed. This field will be updated when NCBI provides a TSA ID.
Supplementary files format and content: Excel/CSV matrix with gene expression data per sample.

organism: Proteus anguinus

source_name: skin

extract_protocol:
RNA was extracted using the Norgen RNA Purification Kit.
RNA-seq libraries were prepared using the NEBNext Ultra II Kit.

value: skin


title: GC_deep_3D

description: Library name: DSP-1001250002850-B-C06


title: LR_SN_117

description: Library name: LR_SN_117


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D220

description: Library name: SAMPLE 66


title: LR_SN_114

description: Library name: LR_SN_114


title: LR_SN_111

description: Library name: LR_SN_111


title: GC_deep_3C

description: Library name: DSP-1001250002850-B-C05


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D220

description: Library name: SAMPLE 65


title: 11_24h_Mluc10_10Gy

value: Fibroblast

value: wildtype


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D225

description: Library name: SAMPLE 67

value: Alzheimer's Disease

value: patient-derived fibroblast


title: GC_deep_3A

description: Library name: DSP-1001250002850-B-C03


title: skin of animal p4

description: Library name: skin.p4


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D217

description: Library name: SAMPLE 64

value: WT

value: Thapsigargin


title: GC_deep_3B

description: Library name: DSP-1001250002850-B-C04


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D230

description: Library name: SAMPLE 71


title: T1a_NEP_4B

description: Library name: DSP-1001250002850-B-C02


title: lung of animal p4

description: Library name: lung.p4

source_name: liver

value: liver


title: lung of animal p6

description: Library name: lung.p6


title: T1a_SRC_4D

description: Library name: DSP-1001250002850-B-C01


title: T1a_SRC_4C

description: Library name: DSP-1001250002850-B-B12


title: LR_SN_108

description: Library name: LR_SN_108

value: brain

value: neuron

value: Intox


title: LR_SN_107

description: Library name: LR_SN_107

value: Heterogeneous Stock

value: NAc Core


title: T1a_SRC_4A

description: Library name: DSP-1001250002850-B-B10


title: LR_SN_106

description: Library name: LR_SN_106


title: liver of animal p6

description: Library name: liver.p6

source_name: lung

value: lung


title: liver of animal p5

description: Library name: liver.p5


title: 10_24h_Mluc10_Con


title: LR_SN_109

description: Library name: LR_SN_109


title: T1a_SRC_4B

description: Library name: DSP-1001250002850-B-B11


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D207

description: Library name: SAMPLE 61

value: N


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D178

description: Library name: SAMPLE 59


title: LR_SN_110

description: Library name: LR_SN_110

value: male


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D178

description: Library name: SAMPLE 60


title: T1a_NEP_4C

description: Library name: DSP-1001250002850-B-B09


title: heart of animal p6

description: Library name: heart.p6

source_name: gut

value: gut


title: LR_SN_105

description: Library name: LR_SN_105


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D217

description: Library name: SAMPLE 63


title: GC_sup_4E

description: Library name: DSP-1001250002850-B-B07


title: liver of animal p4

description: Library name: liver.p4


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D166

description: Library name: SAMPLE 58


title: T1a_NEP_4A

description: Library name: DSP-1001250002850-B-B08


title: LR_SN_103

description: Library name: LR_SN_103


title: GC_sup_4D

description: Library name: DSP-1001250002850-B-B06


title: heart of animal p4

description: Library name: heart.p4


title: GC_sup_4C

description: Library name: DSP-1001250002850-B-B05


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D150

description: Library name: SAMPLE 56


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D207

description: Library name: SAMPLE 62


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D166

description: Library name: SAMPLE 57


title: LR_SN_102

description: Library name: LR_SN_102

value: Abstinence


title: GC_sup_4A

description: Library name: DSP-1001250002850-B-B03


title: brain of animal p6

description: Library name: brain.p6


title: lung of animal p5

description: Library name: lung.p5


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D149

description: Library name: SAMPLE 54


title: gut of animal p5

description: Library name: gut.p5

source_name: heart

value: heart


title: LR_SN_99

description: Library name: LR_SN_99

source_name: brain


title: LR_SN_104

description: Library name: LR_SN_104


title: gut of animal p4

description: Library name: gut.p4


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D149

description: Library name: SAMPLE 53


title: GC_NEP_4B

description: Library name: DSP-1001250002850-B-B01


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D142

description: Library name: SAMPLE 52


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D150

description: Library name: SAMPLE 55


title: LR_SN_100

description: Library name: LR_SN_100


title: brain of animal p4

description: Library name: brain.p4


title: GC_NEP_4C

description: Library name: DSP-1001250002850-B-B02


title: LR_SN_98

description: Library name: LR_SN_98


title: GC_NEP_4A

description: Library name: DSP-1001250002850-B-A12


title: GC_deep_4J

description: Library name: DSP-1001250002850-B-A11


title: GC_sup_4B

description: Library name: DSP-1001250002850-B-B04


title: wta_d3

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

institute: Technical University of Munich

description: scRNA-Seq WTA + Sample Tag (BD Rhapsody)

data_processing:
The pipeline BD Rhapsody™ Sequence Analysis Pipeline r16 available on SevenBridges platform (BD Biosciences) was used for sample demultiplexing, read mapping and counting. The reference RhapRef_Mouse_WTA_2023-02 was used.
Assembly: GRCm38 (release 98) - GENCODE Release M24
Supplementary files format and content: Compressed files contain the filtered UMI counts matrix (Market Exchange Format for sparse matrices), TSV files with genes and barcode sequences (corresponding to row and column indices respectively).

source_name: spleen

extract_protocol:
Spleens were harvested from infected mice and cut into small pieces. These pieces were the exposed to a medium containing digestive enzymes (Dnase, Liberase) for 1h hour at 37°C shaking at 240rpm. The digested tissue was then macerated through a 100µm Nytex filter, washed with DMEM and erythrocyte lysis was performed using a hypotonic ACK medium. Lysis was stopped by adding DMEM containing 10% FCS. Cells were counted using a Neubauer counting chamber and a CD90.2 MACS enrichment (Miltneyi) was performed accoring to the manufacurteres instructions. Finally, cells were stained with flurorescently labelled antibodies against CD8a, CD45.1 and CD44 as well as a fixable live/dead dye. Single, live CD8a+CD45.1+ cells were sorted and subsequently used to prepare scRNA-Seq libraries
Single-cell RNA libraries were prepared using the BD Rhapsody system (BD Biosciences). First, sample tags were added to individual cell samples (BD Ms Single Cell Sample multiplexing kit, protocol 23-21340(02)). Sample tags 5 to 8 were used for replicates 1 to 4, respectively. Next, single cells of the pooled samples were captured using the BD Rhapsody HT Xpress system and an 8-lane cartridge, followed by reverse transcription and cDNA amplification (BD Rhapsody cDNA kit, protocol 23-24252(01)). Sequencing libraries were constructed using the BD Rhapsody whole transcriptome analysis and TCR/BCR approach (BD Rhapsody Whole Transcriptome Analysis Amplification Kit, BD Rhapsody Mouse TCR/BCR Amplification Kit, protocol 23-24365(01)). QC of libraries was done with Bioanalyzer 2100 using the High Sensitivity DNA Kit (Agilent) and Qubit 2.0 fluorometer with the Qubit 1X dsDNA HS Assay-Kit (Invitrogen). Libraries were sequenced on a NovaSeq X Plus (Illumina) with paired-end 2x150bp reads.

value: spleen

value: P14 T cells

value: CD8+ T cells

tag: time point

value: LCMV Armstrong

tag: material

value: mixed samples (all replicates)


title: LR_SN_95

description: Library name: LR_SN_95

value: Withdrawal

value: female

value: NAc Shell


title: LR_SN_94

description: Library name: LR_SN_94

value: brain

value: neuron


title: GC_deep_4H

description: Library name: DSP-1001250002850-B-A09


title: wta_tcf

extract_protocol:
Spleens were harvested from infected mice and cut into small pieces. The digested tissue was then macerated through a 100µm Nytex filter, washed with DMEM and erythrocyte lysis was performed using a hypotonic ACK medium. Lysis was stopped by adding DMEM containing 10% FCS. Cells were counted using a Neubauer counting chamber and a CD90.2 MACS enrichment (Miltenyi) was performed accoring to the manufacurteres instructions. Finally, cells were stained with flurorescently labelled antibodies against CD8a, CD45.1 and CD44 as well as a fixable live/dead dye. Single, live CD8a+CD45.1+ cells were sorted into PD1hi and PD1low and subsequently used to prepare scRNA-Seq libraries.
Single-cell RNA libraries were prepared using the BD Rhapsody system (BD Biosciences). First, sample tags were added to individual cell samples (BD Ms Single Cell Sample multiplexing kit, protocol 23-21340(02)). Sample tags 1 to 5 were used for PD1lo replicates 1 to 5, respectively, and sample tags 6 to 10 were used for PD1hi replicates 1 to 5, respectively. Next, single cells of the pooled samples were captured using the BD Rhapsody Xpress system, followed by reverse transcription and cDNA amplification (BD Rhapsody cDNA kit, protocol 23-22951(02)). Sequencing libraries were constructed using the BD Rhapsody whole transcriptome analysis approach (BD Rhapsody Whole Transcriptome Analysis Amplification Kit, protocol 23-24119 (02)). QC of libraries was done with Bioanalyzer 2100 using the High Sensitivity DNA Kit (Agilent) and Qubit 2.0 fluorometer with the Qubit 1X dsDNA HS Assay-Kit (Invitrogen). Libraries were sequenced on a NovaSeq X Plus (Illumina) with paired-end 2x150bp reads.

tag: cell line

value: CD45.1 TCF7-GFP-mCherry

tag: phenotype

value: d15 pi

value: mixed samples (all replicates from PD1hi and PD1lo samples)


title: Lung adenocarcinoma cell_siRNA BCL3_biological replicate 2

city: Sharjah

first: Rifat

last: Hamoudi

state: Sharjah

address: M32 Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, , Sharjah

department: Clinical Sciences

country: United Arab Emirates

institute: University of Sharjah

description: column M

data_processing:
Ion Torrent Suite software version 5.12.1
Fragments per kilobase million (FPKM) normalization
Burrows-Wheeler Aligner (BWA)-short, BWA-long, Sequence Search and Alignment by Hashing Algorithm (SSAHA) and Super-maximal Exact Matching (SMEM), within the TMAP suite were implemented
Assembly: hg19_AmpliSeq_Transcriptome_21K_v1
Supplementary files format and content: tab-delimited read counts in one file

extract_protocol:
RNA was extracted using RNAeasy mini kit
100 ng of RNA was used to prepare library using Ion Ampliseq Human gene expression kit

value: lung adenocarcinoma cells

tag: sirna


title: LR_SN_97

description: Library name: LR_SN_97

value: Heterogeneous Stock

tag: treatment

value: male

value: NAc Core


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D142

description: Library name: SAMPLE 51

value: Alzheimer's Disease

tag: cell type

value: patient-derived fibroblast

tag: genotype

value: WT

value: N


title: LR_SN_96

description: Library name: LR_SN_96


title: LR_SN_101

description: Library name: LR_SN_101

value: Abstinence


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D114

description: Library name: SAMPLE 46

value: Thapsigargin


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D135

description: Library name: SAMPLE 48


title: Lung adenocarcinoma cell_siRNA BCL3_biological replicate 1

description: column L


title: LR_SN_91

description: Library name: LR_SN_91

value: Withdrawal

value: female


title: Human Dermal Fibroblast, Alzheimer's Disease, treat, D137

description: Library name: SAMPLE 50


title: GC_deep_4I

description: Library name: DSP-1001250002850-B-A10


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D137

description: Library name: SAMPLE 49


title: bronchial asthmatic cells_BCL3_biological replicate 1

description: column H

source_name: DHBE

value: DHBE

value: bronchial asthmatic epithelial cells


title: LR_SN_93

description: Library name: LR_SN_93

value: brain

value: neuron

value: NAc Shell


title: Lung adenocarcinoma cell_scrambled_biological replicate 2

description: column K

value: lung adenocarcinoma cells

value: empty vector


title: LR_SN_90

description: Library name: LR_SN_90

value: Heterogeneous Stock

value: Naive


title: GC_deep_4D

description: Library name: DSP-1001250002850-B-A05


title: Lung adenocarcinoma cell_scrambled_biological replicate 1

description: column J


title: bronchial asthmatic cells_vector_biological replicate 2

description: column G


title: GC_deep_4G

description: Library name: DSP-1001250002850-B-A08


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D135

description: Library name: SAMPLE 47

value: Alzheimer's Disease


title: LR_SN_92

description: Library name: LR_SN_92


title: Normal bronchial epithelial cells_BCL3_biological replicate 2

description: column E

value: normal brocnhial epithelial cells


title: bronchial asthmatic cells_BCL3_biological replicate 2

description: column I


title: LR_SN_87

description: Library name: LR_SN_87


title: Normal bronchial epithelial cells_BCL3_biological replicate 1

description: column D


title: GC_deep_4A

description: Library name: DSP-1001250002850-B-A02


title: GC_deep_4F

description: Library name: DSP-1001250002850-B-A07


title: GC_deep_4B

description: Library name: DSP-1001250002850-B-A03


title: Human Dermal Fibroblast, healthy control, untreat, C247

description: Library name: SAMPLE 41

value: healthy control

value: patient-derived fibroblast

value: WT


title: Normal bronchial epithelial cells_vector_biological replicate 2

description: column C


title: GC_deep_4E

description: Library name: DSP-1001250002850-B-A06


title: Normal bronchial epithelial cells_vector_biological replicate 1

description: column B


title: Human Dermal Fibroblast, healthy control, treat, C250

description: Library name: SAMPLE 44

value: Thapsigargin


title: bronchial asthmatic cells_vector_biological replicate 1

description: column F


title: Human Dermal Fibroblast, Alzheimer's Disease, untreat, D114

description: Library name: SAMPLE 45

value: N


title: LR_SN_89

description: Library name: LR_SN_89

value: female


title: Human Dermal Fibroblast, healthy control, untreat, C250

description: Library name: SAMPLE 43


title: LR_SN_84

description: Library name: LR_SN_84

value: Intox


title: LR_SN_85

description: Library name: LR_SN_85


title: GC_deep_4C

description: Library name: DSP-1001250002850-B-A04


title: LR_SN_88

description: Library name: LR_SN_88


title: Human Dermal Fibroblast, healthy control, treat, C247

description: Library name: SAMPLE 42


title: control_no_template

description: Library name: DSP-1001250002850-B-A01

source_name: control

value: control


title: Input, NIPBLwt, rep2

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

data_processing:
Sequenced reads were aligned to the human genome build hg38 and mouse genome build mm10 using Bowtie version 1.2.2 with the options “-n2 -m1” and the uniquely mapped reads were used for subsequent analysis.
BigWig files (100-bp bin) were generated by DROMPA version 3.7.2. The read distribution is normalized based on the number of reads derived from the mouse spike-in.
Assembly: UCSC hg38
Supplementary files format and content: BigWig files (100-bp bin) of the normalized read distribution.

growth_protocol: 293FT cells were maintained in DMEM supplemented with penicilline-streptomycin-L-glutamine solution (Wako) and 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Chromatin immunoprecipitation was performed as detailed in Nakato et al. (Nature Communications (2023)14:5647). Briefly, human culture cells were crosslinked with 1 % formaldehyde for 10 minutes at room temperature. Chromatin was then sheared by sonication (Branson Sonifier 250D) and combined with mouse spike-in chromatin. The immunoprecipitation was performed overnight at 4°C with an antibody conjugated to Dynabeads Protein A or B (Thermo Fisher Scientific, 10002D or 10004D). After completing the immunoprecipitation and reversing crosslinks, the DNA was purified.
Sequencing library was prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, E7645) according to manufacturer's instructions.

value: NIPBLwt

tag: target protein

value: Input

tag: chip antibody


title: Input, NIPBLmut, rep2

value: NIPBLmut


title: Blood, Immune cells, PLX5622, 14 dpi, rep2

city: Hangzhou

first: Xiaotao

last: Zhang

state: Zhejiang

address: 88 Jiefang Road

institute: 2nd Affiliated Hospital,ZJU

description: Library name: plx_14d_BL2

data_processing:
We use FastQC to perform basic statistics on the quality of the raw reads. Generally, celltanger count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file.
Raw read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software which can be summarized as below: (1)Remove low-quality reads: scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 10 (SLIDINGWINDOW: 4:10)(2)Remove trailing low quality or N bases (below quality 3) (TRAILING:3)(3)Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence, the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30, removed non-overlapping portions (ILLUMINACLIP: adapter.fa: 2: 30: 7)(4)Drop reads below the 26 bases long(5)Discard those reads that can not form pairedThe remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last, we use FastQC to perform basic statisticson the quality of the cleanreads
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat unless mentioned specifically.
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz: gene-barcode counts
Supplementary files format and content: genes.tsv.gz: gene files
Supplementary files format and content: barcodes.tsv.gz: cell barcode files

source_name: Blood

extract_protocol:
Mice were euthanized and subjected to ice-cold saline perfusion at either 5- or 14-days post MCAO. Ischemic hemispheres were collected, excluding meninges, the olfactory bulb, or cerebellum. For the scRNA-seq analysis of entire brain cells, brain homogenates were created using the Adult Brain Dissociation Kit (T) with a gentle MACS dissociator with heaters (Miltenyi Biotec), following the provided guidelines. In the case of scRNA-seq for CD45high immune cells, brain homogenates were generated using the Neural Tissue Dissociation Kit (T), and CD45high immune cells were isolated through FACS using the anti-CD45-PE-Cy5 antibody (Thermo Fisher Scientific, 15-0451-81). For PBMC specimens, peripheral blood was collected from the right atrium, followed by two rounds of red blood cell lysis (eBioscience, 1X RBC lysis buffer, 00-4333057).
Libraries for 10X Genomics were prepared using the 10X Genomics Chromium Single Cell 3’ v3 chemistry, in accordance with the manufacturer's instructions.Subsequently, the mixture containing captured and barcoded mRNAs was retrieved from the Chromium instrument, followed by reverse transcription. The cDNA samples were fragmented and amplified per the 10X protocol. The libraries were then purified, quantified, and sequenced utilizing the Illumina NovaSeq sequencer.

tag: tissue

value: Blood

value: 14 dpi

tag: age

value: 8-12 weeks old


title: Human Dermal Fibroblast, healthy control, treat, C243

description: Library name: SAMPLE 40


title: NELFC ChIP, NIPBLmut

value: NELF-C

value: anti-NELF-C (12265, Cell Signaling Technology)


title: Human Dermal Fibroblast, healthy control,untreat, C240

description: Library name: SAMPLE 37


title: NELFC ChIP, NIPBLwt


title: LR_SN_82

description: Library name: LR_SN_82

value: brain

value: neuron

tag: strain

value: Heterogeneous Stock

tag: batch

tag: Sex

value: NAc Shell


title: Blood, Immune cells, PLX5622, 14 dpi, rep1

description: Library name: plx_14d_BL1

value: WT


title: Human Dermal Fibroblast, healthy control, untreat, C243

description: Library name: SAMPLE 39

value: healthy control

value: patient-derived fibroblast

value: N


title: LR_SN_83

description: Library name: LR_SN_83

value: Intox

value: female

tag: region


title: Human Dermal Fibroblast, healthy control, treat, C240

description: Library name: SAMPLE 38

tag: disease state

value: Thapsigargin


title: LR_SN_86

description: Library name: LR_SN_86

value: Naive


title: LR_SN_81

description: Library name: LR_SN_81


title: Human Dermal Fibroblast, healthy control, untreat, C238

description: Library name: SAMPLE 35


title: Blood, Immune cells, Control, 14 dpi, rep2

description: Library name: Bld14d_2

value: Blood

value: Control

tag: time point


title: Blood, Immune cells, Control, 14 dpi, rep1

description: Library name: Bld14d_1

value: 14 dpi

value: 8-12 weeks old


title: LR_SN_80

description: Library name: LR_SN_80


title: Human Dermal Fibroblast, healthy control, treat, C234

description: Library name: SAMPLE 34


title: LR_SN_79

description: Library name: LR_SN_79


title: AFF4 ChIP, NIPBLwt

value: NIPBLwt

value: anti-AFF4 (A302-538A, BETHYL)


title: Blood, Immune cells, PLX5622, 5 dpi, rep1

description: Library name: Plx_5D_PB1

value: 5 dpi


title: C3

city: Uxbridge

first: Rubén

last: de Dios

state: Middlesex

address: Kingston Lane

department: Life Sciences

country: United Kingdom

institute: Brunel University London

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.0.3)
Read mapping was performed with HISAT
Differential expression analysis was performed using edgeR’s exact test for differences between two groups of negative-binomial counts with an estimated dispersion value of .1.
Read quantification was performed using Subread’s featureCounts functionality.
Read counts loaded into R and were normalized using edgeR’s Trimmed Mean of M values algorithm.  Subsequent values were then converted to counts per million (cpm).
Assembly: U00096.3
Supplementary files format and content: raw_counts.tsv includes a tab-delimited matrix with headers with the raw read values for each gene in each sample and condition
Supplementary files format and content: normalised_counts.tsv includes a tab-delimited matrix with headers with the normalised read values for each gene in each sample and condition

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli culture

growth_protocol: Three biological replicates  of saturated E. coli K12 cultures were diluted 1/100 in 25 mL LB medium (in duplicate, to obtain 3 treated cultures and 3 mock controls). The cultures were grown (37 ºC, 180 rpm) to approximately OD600 0.3 and they were treated with a final concentration of 1.4% saccharin or a water control. The cultures were further incubated until reacing OD600 0.8.

extract_protocol:
Cultures were harvested by centrifugation and washed in RNAlater to preserve RNA integrity. RNA was isolated using athe Qiagen RNAeasy Kit with on-column DNAase digestion (Qiagen). RNA quality was assessed using a Bioanalyzer.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.

treatment_protocol: The treatment (1.4% saccharin or a water control) was applied when cultures reachedOD600 0.3 and lasted until cultures reached OD600 0.8 (approximately 50-60 minutes).

value: E. coli culture

value: water control


title: Human Dermal Fibroblast, healthy control, untreat, C234

description: Library name: SAMPLE 33

value: WT


title: C2


title: LR_SN_78

description: Library name: LR_SN_78

extract_protocol:
RNA extraction was performed from 0.5 mm punches of coronal sections using RNeasy Micro kits (Qiagen, Inc.). Briefly, tissue samples were homogenized in Buffer RLT, RNA lysis buffer, before being centrifuged in a QIAshredder column at full speed for 3 min. The flow-through was mixed with an equal volume of 70% ethanol and transferred to a MinElute spin column before being washed with Buffer RW1, RNA wash buffer, to free membrane-bound RNA. DNA was removed with on column treatment using DNAse I. The flow-through was washed again with Buffer RW1, and two times with Buffer RPE, a secondary RNA wash buffer in ethanol, to remove trace salts. The spin column was cleaned with 80% ethanol and centrifuged at full speed for 5 min to dry the column matrix. Total RNA was eluted in RNAse-free water. Concentration and purity were quantified using a Nanodrop.
Illumina Total RNAseq Paired End 75bp

value: brain

value: neuron

value: Heterogeneous Stock

value: Abstinence

value: NAc Shell


title: LR_SN_77

description: Library name: LR_SN_77

value: female


title: Human Dermal Fibroblast, healthy control, treat, C214

description: Library name: SAMPLE 32

value: healthy control

value: patient-derived fibroblast

value: Thapsigargin


title: Blood, Immune cells, Control, 5 dpi, rep2

description: Library name: MCAO_5D_BL2

value: Blood

value: Control


title: Blood, Immune cells, PLX5622, 5 dpi, rep2

description: Library name: Plx_5D_PB2

value: 8-12 weeks old


title: C1


title: Human Dermal Fibroblast, healthy control, treat, C238

description: Library name: SAMPLE 36


title: Blood, Immune cells, Control, 5 dpi, rep1

description: Library name: MCAO_5D_BL1


title: LR_SN_76

description: Library name: LR_SN_76


title: sac3

value: 1.4% saccharin


title: Brain, CD45high, Old, 14 dpi, rep2

description: Library name: MCAO_14D_O3

source_name: Brain

value: Brain

value: 14 dpi

value: 20 months old


title: Human Dermal Fibroblast, healthy control, treat, C208

description: Library name: SAMPLE 30

value: WT


title: LR_SN_75

description: Library name: LR_SN_75

value: brain


title: AFF4 ChIP, NIPBLmut

value: NIPBLmut

value: anti-AFF4 (A302-538A, BETHYL)


title: LR_SN_74

description: Library name: LR_SN_74

value: neuron

value: Heterogeneous Stock

value: Abstinence


title: Brain, Brain cells, PLX5622, 14 dpi, rep2

description: Library name: plx14D_W2


title: sac1

value: E. coli culture


title: Human Dermal Fibroblast, healthy control, treat, C203

description: Library name: SAMPLE 28

value: healthy control

value: patient-derived fibroblast


title: LR_SN_73

description: Library name: LR_SN_73

value: female

value: NAc Shell


title: sac2


title: Brain, CD45high, Old, 14 dpi, rep1

description: Library name: MCAO_14D_O2

value: Control


title: Human Dermal Fibroblast, healthy control, untreat, C208

description: Library name: SAMPLE 29

value: N


title: OVCAR4 cells, chemo-resistant, ATAC, rep2

city: Chicago

first: Harun

last: Ozturk

state: Illinois

address: 303. E. Superior, Lurie cancer center

institute: Northwestern University

description: Library name: Sample2

data_processing:
Data were quality checked using FASTQC.
Reads were aligned to T2T genome assembly using Bowtie2 software (settings: --local --very-sensitive).
PCR duplicates and blacklisted regions were removed using Picard and Bedtools, respectively.
Peak calling was performed using MACS2 (settings: -f BAMPE --call-summits --keep-dup all). Mitochondrial reads were remove using Samtools.
BigWig files were generated using deeptools (settings: --binSize 1 --normalizeUsing CPM).
Assembly: T2T
Supplementary files format and content: BigWig files

source_name: ovarian

growth_protocol: OVCAR4 cells were cultured in RPMI-1640 supplemented with 10% Fetal Bovine Serum and 1% Pen-Strep.The cells were maintained in a humidified incubator at 37 °C.

extract_protocol:
Transposed DNA was eluted using the Qiagen MinElute kit (28004, Qiagen) according to the manufacturer's instructions.
Libraries were constructed using the custom oligos.

value: ovarian

value: high-grade sereous ovarian cancer cell line


title: LR_SN_72

description: Library name: LR_SN_72

value: Withdrawal

value: male


title: Brain, Brain cells, PLX5622, 14 dpi, rep1

description: Library name: plx14d_w1

value: Brain

value: WT

value: 14 dpi

value: 8-12 weeks old


title: Brain, CD45high, PLX5622, 14 dpi, rep2

description: Library name: plx14D_CD452


title: LR_SN_70

description: Library name: LR_SN_70

value: brain

value: neuron

value: Heterogeneous Stock


title: Human Dermal Fibroblast, healthy control, untreat, C198

description: Library name: SAMPLE 25

value: healthy control


title: Human Dermal Fibroblast, healthy control, untreat, C203

description: Library name: SAMPLE 27

value: patient-derived fibroblast


title: LR_SN_68

description: Library name: LR_SN_68


title: LR_SN_71

description: Library name: LR_SN_71


title: OVCAR4 cells, chemo-resistant, ATAC, rep1

description: Library name: Sample1


title: Human Dermal Fibroblast, healthy control, untreat, C214

description: Library name: SAMPLE 31


title: Human Dermal Fibroblast, healthy control, treat, C198

description: Library name: SAMPLE 26

value: Thapsigargin


title: Brain, CD45high, PLX5622, 5 dpi, rep1

description: Library name: plx_5D_1

value: 5 dpi


title: Human Dermal Fibroblast, healthy control, treat, C186

description: Library name: SAMPLE 22


title: Human Dermal Fibroblast, healthy control, treat, C187

description: Library name: SAMPLE 24


title: Brain, CD45high, PLX5622, 5 dpi, rep2

description: Library name: plx_5D_2


title: LR_SN_69

description: Library name: LR_SN_69

value: NAc Shell


title: BMDMs treated with Control-lentivirus, rep1

description: Library name: L_1

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (ftp://ftp.ensembl.org/pub/release-112/fasta/mus musculus/dna/) to map reads to the reference genome of mus musculus Ensembl_v112. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCm39
Supplementary files format and content: fpkm_expression.xlsx: tab-delimited text files include FPKM for each sample

source_name: bone marrow-derived macrophages

growth_protocol: BMDMs were isolated from the femora of adult mice.Briefly, the mice were sacrificed and disinfected with 70% alcohol. The hip bones were carefully removed, excluding skin and muscle tissues, and the bone ends were trimmed. Subsequently, the marrow was flushed into a 15 mL centrifuge tube using a 1 mL syringe. After centrifugation at 600×g and 4°C for 5 minutes, the resulting cells were diluted to a concentration of 1 × 106 cells/mL. These cells were then cultured in DMEM with 1% penicillin/streptomycin and 10% fetal bovine serum at 37 °C with 5% CO2. M-CSF (Thermo Fisher Invitrogen, PMC2044) was introduced at a final concentration of 20 ng/mL for 6 days to induce BMDM differentiation.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >8.5, and confirmed by electrophoresis with denaturing agarose gel.
mRNA was purified from total RNA (5μg) using Dynabeads Oligo (dT) (Thermo Fisher) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, e6150) under 94℃ 5-7 minutes). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, 1896649), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, m0209), RNase H (NEB, m0297) and dUTP Solution (Thermo Fisher, R0133). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, m0280) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA libraries were 300±50 bp. At last, we performed the 2×150 bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Mafb-lentivirus infection was conducted to achieve overexpression of Mafb in BMDMs according to the documented protocol75. In short, BMDMs were transduced with Mafb-lentivirus at M.O.I of 30 and polybrene (6mg/ml), using mCherry-lentivirus as control. BMDMs were then incubated at 37 °C with 5% CO2 for 48 h. Thereafter, the medium containing lentivirus and polybrene were carefully aspirate and replaced with DMEM containing M-CSF for 6 days to induce Mafb overexpression.

value: bone marrow-derived macrophages

value: Control-lentivirus


title: RNA-seq KO_Batf_4

city: Montréal

first: Nathalie

last: Labrecque

state: QC

address: 110, avenue des Pins O

department: Unité de recherche en immunobiologie des lymphocytes T

country: Canada

institute: Institut de recherches cliniques de Montréal

description: Library name: Sample 44

data_processing:
Sequenced reads were trimmed for sequencing adapters and low-quality 3′ bases using Trimmomatic version 0.35 (Bolger et al., 2014) and then aligned to the reference mouse genome version GRCm38 (or mm10 gene annotation from Gencode version M13, based on Ensembl 88) using STAR version 2.5.1b (Dobin et al., 2013). Gene expression was obtained both as read count directly from STAR as well as computed using RSEM (Li and Dewey, 2011) to obtain gene and transcript level expression, either in transcripts per kilobase million or fragments per kilobase per million mapped reads values, for these stranded RNA libraries. DESeq2 version 1.16.1 was then used to normalize gene read counts and compute differential expression between different experimental conditions (Love et al., 2014). Gene Ontology term (GO-term) enrichment analysis of differentially expressed genes was performed using DAVID (Huang et al., 2009) and determination of relevant upstream regulators was done with QIAGEN’s Ingenuity Pathway Analysis (IPA). GSEA enrichment analysis was performed using the Broad Institute’s software and Molecular Signature Database (MSigDB) (https://www.gsea-msigdb.org/gsea/index.jsp) (Subramanian et al., 2005). For experiments evaluating the impact of BATF overexpression, sequences were trimmed with Trimmomatic version 0.39 (Bolger et al., 2014) and aligned to reference genome GRCm38 using STAR version 2.7.8a (Dobin et al., 2013). Gene counts were determined with featureCounts (Liao et al., 2014). Robust principal component analysis (Chen et al., 2020) was used to detect outlier samples and two samples (one KO-empty and one KO-BATF sample) were therefore excluded from differential expression analysis. DESeq2 v1.24.0 was used to determine differential expression (Love et al., 2014).
Assembly: GRCm38
Supplementary files format and content: Read counts (.xlsx)

source_name: Spleen

extract_protocol:
Cells were FACS-sorted directly into TRIzol reagent, frozen at −80°C and RNA was extracted usind a TRIzol protocol.
Library preparation was done with the KAPA RNA HyperPrep PolyA library preparation kit (Roche) using 150 ng of RNA.

value: Spleen

value: Activated OT-I CD8+ T cell

value: Notch1/2 KO

tag: infection

value: Listeria monocytogenes

tag: timepoint

value: Day 3

value: Female


title: Human Dermal Fibroblast, healthy control, treat, C175

description: Library name: SAMPLE 20

value: WT


title: RNA-seq KO_Batf_2

description: Library name: Sample 42


title: RNA-seq KO_Batf_3

description: Library name: Sample 43


title: Brain, CD45high, PLX5622, 14 dpi, rep1

description: Library name: plx14D_CD451

value: Brain

value: 14 dpi

value: 8-12 weeks old


title: RNA-seq KO_Empty_3

description: Library name: Sample 39


title: Human Dermal Fibroblast, healthy control, untreat, C187

description: Library name: SAMPLE 23

value: healthy control

value: N


title: BMDMs treated with Control-lentivirus, rep3

description: Library name: L_3


title: RNA-seq KO_Batf_1

description: Library name: Sample 41


title: Human Dermal Fibroblast, healthy control, untreat, C175

description: Library name: SAMPLE 19

value: patient-derived fibroblast


title: LR_SN_67

city: Worcester

first: Ryan

last: Logan

address: 366 Plantation Street

institute: University of Massachusetts Chan Medical School

description: Library name: LR_SN_67

data_processing:
For Rattus norvegicus samples: Quality control was performed by FastQC, cutadapt was used to trim low quality and over-represented sequences. STAR was used for alignment with ensembl reference (release 104) and RSEM is used for expression calculation.
For Mus musculus samples: Quality control was performed by Fastqc. Perform trimming by trimmomatic, allign the sequence using Hisat2 with Ensembl reference and read count with Hiseq
Assembly: Mus musculus:GRCm38 ; Rattus norvegicus: Rnor_6.0(Ensembl release 104)
Supplementary files format and content: mouse_raw_counts.csv: processed count data for Mus musculus samples.
Supplementary files format and content: rat_raw_counts_all.csv: processed count data for Rattus norvegicus samples.

value: brain

value: neuron

value: Heterogeneous Stock

value: Withdrawal

value: male


title: BMDMs treated with Mafb-lentivirus, rep3

description: Library name: M_3

value: bone marrow-derived macrophages

value: Mafb-lentivirus


title: LR_SN_66

description: Library name: LR_SN_66

value: Naive

value: NAc Shell


title: RNA-seq KO_Empty_2

description: Library name: Sample 38

value: Spleen

value: Activated OT-I CD8+ T cell

value: Notch1/2 KO

value: Listeria monocytogenes

value: Day 3

value: Female


title: Human Dermal Fibroblast, healthy control, untreat, C186

description: Library name: SAMPLE 21

value: healthy control

value: WT

value: N


title: LR_SN_64

description: Library name: LR_SN_64

value: brain

value: neuron


title: RNA-seq WT_Batf_4

description: Library name: Sample 36


title: Human Dermal Fibroblast, healthy control, untreat, C170

description: Library name: SAMPLE 17

value: patient-derived fibroblast


title: Human Dermal Fibroblast, healthy control, treat, C170

description: Library name: SAMPLE 18

value: Thapsigargin


title: RNA-seq KO_Empty_4

description: Library name: Sample 40


title: LR_SN_63

description: Library name: LR_SN_63

value: Heterogeneous Stock

value: male


title: LR_SN_65

description: Library name: LR_SN_65

value: Naive


title: Human Dermal Fibroblast, healthy control, treat, C168

description: Library name: SAMPLE 16


title: LR_SN_61

description: Library name: LR_SN_61

value: NAc Shell


title: BMDMs treated with Mafb-lentivirus, rep2

description: Library name: M_2

value: bone marrow-derived macrophages

value: Mafb-lentivirus


title: Human Dermal Fibroblast, healthy control, untreat, C168

description: Library name: SAMPLE 15


title: LR_SN_62

description: Library name: LR_SN_62


title: RNA-seq WT_Batf_2

description: Library name: Sample 34

value: Spleen

value: Activated OT-I CD8+ T cell


title: E1A/HrasG12V MEFs, Zmat3 + Trp53-KO 3

city: Stanford

first: Laura

middle: D

last: Attardi

address: 269 Campus Drive

institute: Stanford University

description:
Library name: Sample 19
Column name in CPM_all_samples.txt: P53G1

data_processing:
Reads were aligned to the GRCm38 mouse genome using HISAT2 (v 2.0.4; RRID:SCR_015530).
Sorted BAM files were generated using Samtools (v 1.3.1; RRID:SCR_002105).
The number of reads mapping to each gene in the mouse Ensembl database (v 87; RRID:SCR_002344) was counted using HTSeq-count (v 0.6.1; RRID:SCR_011867).
Differential gene expression analysis was performed using DESeq2 (v 1.24.0; RRID:SCR_015687).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes CPM for each sample

source_name: E1A/HrasG12V-expressing murine embryonic fibroblast

growth_protocol: Cells were maintained in DMEM + 10% FBS and incubated at 37°C in a carbon dioxide incubator held at 5% oxygen.

extract_protocol:
RNA was extracted from cells using the RNeasy midi kit (Qiagen, Cat#75144).
NEBNext Ultra II RNA Library Prep by Illumina


title: Human Dermal Fibroblast, healthy control, treat, C162

description: Library name: SAMPLE 14

source_name: patient-derived fibroblast


title: E1A/HrasG12V MEFs, Zmat3 + Trp53-KO 2

description:
Library name: Sample 18
Column name in CPM_all_samples.txt: P53A2

value: E1A/HrasG12V-expressing murine embryonic fibroblast


title: BMDMs treated with Control-lentivirus, rep2

description: Library name: L_2

value: Control-lentivirus


title: RNA-seq WT_Batf_3

description: Library name: Sample 35

value: Listeria monocytogenes

value: Day 3

value: Female


title: RNA-seq WT_Empty_4

description: Library name: Sample 32

value: WT


title: RNA-seq KO_Empty_1

description: Library name: Sample 37

value: Notch1/2 KO


title: Human Dermal Fibroblast, healthy control, untreat, C162

description: Library name: SAMPLE 13

value: healthy control

value: patient-derived fibroblast

value: N


title: LR_SN_58

description: Library name: LR_SN_58

value: brain

value: neuron

value: Heterogeneous Stock

value: Intox

value: male


title: E1A/HrasG12V MEFs, Zmat3 + Trp53-KO 1

description:
Library name: Sample 17
Column name in CPM_all_samples.txt: P53A1


title: RNA-seq WT_Batf_1

description: Library name: Sample 33

value: Spleen


title: LR_SN_59

description: Library name: LR_SN_59

value: NAc Shell


title: BMDMs treated with Mafb-lentivirus, rep1

description: Library name: M_1

value: bone marrow-derived macrophages

value: Mafb-lentivirus


title: E1A/HrasG12V MEFs, Zmat3 + Trp53-KO 4

description:
Library name: Sample 20
Column name in CPM_all_samples.txt: P53G2

value: E1A/HrasG12V-expressing murine embryonic fibroblast


title: E1A/HrasG12V MEFs, Zmat3 + Cdkn1a-KO 4

description:
Library name: Sample 16
Column name in CPM_all_samples.txt: Z2P2

value: Zmat3 + Cdkn1a-KO


title: LR_SN_60

description: Library name: LR_SN_60


title: E1A/HrasG12V MEFs, Zmat3 + Cdkn1a-KO 3

description:
Library name: Sample 15
Column name in CPM_all_samples.txt: Z2P1


title: RNA-seq WT_Empty_3

description: Library name: Sample 31

value: Activated OT-I CD8+ T cell

value: Listeria monocytogenes

value: Day 3

value: Female


title: Human Dermal Fibroblast, healthy control, treat, C156

description: Library name: SAMPLE 12

value: healthy control

value: patient-derived fibroblast

value: WT

value: Thapsigargin


title: RNA-seq WT_Empty_2

description: Library name: Sample 30


title: LR_SN_57

description: Library name: LR_SN_57

value: brain

value: neuron

value: Heterogeneous Stock


title: LR_SN_56

description: Library name: LR_SN_56

value: Intox

value: male


title: E1A/HrasG12V MEFs, Zmat3 + Cdkn1a-KO 2

description:
Library name: Sample 14
Column name in CPM_all_samples.txt: Z1P2


title: RNA-seq WT_Empty_1

description: Library name: Sample 29

value: Spleen


title: Human Dermal Fibroblast, healthy control, untreat, C156

description: Library name: SAMPLE 11

value: N


title: E1A/HrasG12V MEFs, Zmat3 + Cdkn1a-KO 1

description:
Library name: Sample 13
Column name in CPM_all_samples.txt: Z1P1

value: E1A/HrasG12V-expressing murine embryonic fibroblast