title: DSP-1001660011989-A-H02

city: Seattle

first: Jie

last: An

state: WA

address: 750 Republican Street

institute: University of Washington

description:
Library name: Sample86
Column P

data_processing:
For spatial analysis, fixed tissue was stained with antibodies to CD45 and cytokeratin (CK) to mark immune cells and keratinocytes respectively and processed on the GeoMx digital spatial profiler.  GeomxTools was used to process and quality control the GeoMX data. Only segments that achieve these requirements were used, including minimum # of reads =1,000; >80% aligned reads; with>75% saturation; >80% stitched. In addition, segments with <20 nuclei were also removed. Low-performing probes were removed before summarizing the data into gene-level count. Upper quartile (i.e. Q3) normalization was applied. Finally, linear mixed model was used to model the GeoMx gene level data and to conduct differential expression analysis (Zollinger et al., 2020)
Assembly: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA: MW0R30722
Supplementary files format and content: Processed data files format: DCC, PKC
Library strategy: Spatial Transcriptomics

source_name: Skin

growth_protocol: Mice used in this study were 12-16 week old C57BL/6 (B6, wild type) females.

extract_protocol:
For GeoMx DSP sample collection, we followed GeoMx DSP instrument user manual (MAN-10088-03). Briefly, tissue slides were loaded to GeoMx DSP instrument and then scanned to visualize whole tissue images. For each tissue sample, we placed ROIs and segmented them into two regions: PanCK+ and CD45+ regions.
Each GeoMx DSP sample was uniquely indexed using Illumina’s i5 × i7 dual-indexing system. In all, 4 μL of a GeoMx DSP sample was used in a PCR reaction with 1 μM of i5 primer, 1 μM i7 primer, and 1× NSTG PCR Master Mix. Thermocycler conditions were 37 °C for 30 min, 50 °C for 10 min, 95 °C for 3 min, 18 cycles of 95 °C for 15 s, 65 °C for 60 s, 68 °C for 30 s, and final extension of 68 °C for 5 min. PCR reactions were purified with two rounds of AMPure XP beads (Beckman Coulter) at 1.2× bead-to-sample ratio. Libraries were paired-end sequenced.

treatment_protocol: Mice were anesthetized with isoflurane and a single dose of UVB (500 mJ/cm2) was delivered to the shaved whole back using FS40T12/UVB bulbs (National Biological Corporation). The narrow band UVB light energy (290-320 nm) at the dorsal surface was measured with Photolight IL1400A radiometer with a SEL240/UVB detector (International Light Technologies). Biopsies were taken at times 0, 6 and 24 hours. All animal experiments were approved by the Institutional Animal Care and Use Committee of the University of Washington, Seattle.

value: Skin

value: adipose

value: 0 h

value: Mouse 219_scan 2


title: DSP-1001660011989-A-H01

status: Public on Dec 08 2025

type: SRA

country: USA

description:
Library name: Sample85
Column P

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

tag: treatment

value: 6 h

tag: batch


title: Pericyte transwell Mock 8hr infection rep. 2

city: Cambridge

first: Rudolf

last: Jaenisch

state: MA

address: 455 Main St.

institute: Whitehead Institute for Biomedical Research

description: Library name: PC8 Mock 2

data_processing:
Counts were tabulated for human protein coding genes, lncRNAs (ENSEMBL release 93 annotations) and viral genes (MN988713.1) using featureCounts.
Assembly: GRCh38, ENSEMBL release 93, GenBank MN988713.1
Supplementary files format and content: Raw feature counts per sample as tab delimited text.

organism: Homo sapiens

growth_protocol: Differentiation of hPSC-derived cell types or culture of primary cells using standard tissue culture techniques

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plus Micro Kit
Libraries for samples shown on lines 34-60 were prepared using SWIFT RNA Library Kit. Libraries for samples shown on lines 62-85 were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit.

treatment_protocol: Exposure to WNV (Nea Santa strain obtained from BEI, expanded on Vero cells) for 1 hour in minimum volume of serum-free culture media. Mock infection was done by exposing cells to a matched volume of Vero conditioned media.

tag: cell line

value: hPSC-derived pericytes

value: Mock infection 8 hours


title: Pericyte transwell WNV 8hr infection rep. 3

description: Library name: PC8 WNV 3

value: WNV infection 8 hours


title: Pericyte transwell Mock 8hr infection rep. 1

description: Library name: PC8 Mock 1


title: DSP-1001660011989-A-G11

description:
Library name: Sample83
Column P

value: panCK

value: deep dermis


title: Pericyte transwell WNV 8hr infection rep. 2

description: Library name: PC8 WNV 2


title: Failed AVF 5

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

description:
Library name: T626
10X Genomics

library_source: transcriptomic single cell

data_processing:
FASTQ files were generated with Cell Ranger's mkfastq pipeline (version 6.0.2).
The Cell Ranger's count pipeline (version 6.0.2) was used to generate raw gene-barcode matrices from alignment to the 10X Genomics pre-built Cell Ranger human reference package (version 2020-A), from GRCh38 Ensembl build 98/GENCODE v32 gene annotations.
Assembly: GRCh38 Ensembl build 98
Supplementary files format and content: barcodes.tsv.gz is a gzipped text file listing individual cell barcodes included in the sample analysis
Supplementary files format and content: features.tsv.gz is a gzipped tab-delimited file of the gene features included in the gene quantification for each sample
Supplementary files format and content: matrix.mtx.gz is a gzipped tab-delimited file of the counts per feature per cell barcode for each sample

source_name: AVF

extract_protocol:
Upper arm veins or venous AVF segments 0.5-1 cm in length were cut longitudinally with a sterile scalpel and then into 1-2 mm square sections. Samples were enzymatically digested for 90 minutes at 37°C with shaking using a combination of collagenase type II, soybean trypsin inhibitor, elastase, Dispase, DNAse I, collagenase type XI, hyaluronidase type I, and HEPES in HBSS with Ca2+ and Mg2+. After 90 minutes, an equal volume of Accumax was added to the dissociation mix and incubated for an additional 5 minutes. Single cells were filtered through a 40 μM strainer, washed with HBSS twice, and incubated with red blood cell lysis buffer for 5-10 min. Cells were washed once again with HBSS and resuspended in 0.1% BSA in PBS for counting and RNA sequencing.
Samples were run using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10X Genomics) with a target capture of 10,000 cells. Each sample was processed on an independent Chromium Single Cell A Chip (10X Genomics) and subsequently run on a thermocycler (Eppendorf). Sequencing libraries were evaluated for quality on the Agilent Tape Station (Agilent Technologies, Palo Alto, CA) and quantified using a Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and qPCR before sequencing on the Illumina NovaSeq 6000.

value: AVF

tag: Sex

value: Female

tag: age

tag: race/ethnicity

value: Black


title: Mature AVF 2

description:
Library name: T618
10X Genomics


title: Mature AVF 6

description:
Library name: T637
10X Genomics

value: Male

value: Hispanic


title: Failed AVF 2

description:
Library name: T614
10X Genomics


title: Pre-access vein 3

description:
Library name: V833
10X Genomics

source_name: Pre-access vein

value: Pre-access vein


title: Pre-access vein 4

description:
Library name: V834
10X Genomics


title: Early AVF resection 1A

description:
Library name: T632A
10X Genomics


title: Mature AVF 4

description:
Library name: T635
10X Genomics


title: Pre-access vein 1

description:
Library name: V821
10X Genomics


title: Mature AVF 3

description:
Library name: T622
10X Genomics


title: Pre-access vein 6

description:
Library name: V843
10X Genomics


title: DSP-1001660011989-A-G10

description:
Library name: Sample82
Column P


title: Mature AVF 5

description:
Library name: T636
10X Genomics


title: Failed AVF 4

description:
Library name: T625
10X Genomics


title: Failed AVF 3

description:
Library name: T619
10X Genomics


title: Early AVF resection 1B

description:
Library name: T632B
10X Genomics


title: Pre-access vein 2

description:
Library name: V822
10X Genomics


title: Failed AVF 6

description:
Library name: T628
10X Genomics


title: Failed AVF 1

description:
Library name: T611
10X Genomics


title: Mature AVF 1

description:
Library name: T615
10X Genomics


title: Pre-access vein 5

description:
Library name: V840
10X Genomics


title: DSP-1001660011989-A-G12

description:
Library name: Sample84
Column P


title: Pericyte transwell WNV 8hr infection rep. 1

description: Library name: PC8 WNV 1


title: DSP-1001660011989-A-G09

description:
Library name: Sample81
Column P

value: epidermis


title: Pericyte transwell Mock 48hr infection rep. 3

description: Library name: PC Mock 3

value: Mock infection 48 hours


title: Pericyte transwell Mock 48hr infection rep. 2

description: Library name: PC Mock 2


title: DSP-1001660011989-A-G07

description:
Library name: Sample79
Column P

value: Skin


title: Pericyte transwell Mock 48hr infection rep. 1

description: Library name: PC Mock 1


title: Pericyte transwell WNV 48hr infection rep. 3

description: Library name: PC WNV 3

value: WNV infection 48 hours


title: DSP-1001660011989-A-G06

description:
Library name: Sample78
Column P

value: Mouse 219_scan 2


title: BMEC w/ Pericyte transwell WNV 8hr infect rep. 3

description: Library name: BMEC8 WNV 3

value: hPSC-derived BMECs


title: DSP-1001660011989-A-G01

description:
Library name: Sample73
Column P

value: 6 h


title: DSP-1001660011989-A-G03

description:
Library name: Sample75
Column P


title: DSP-1001660011989-A-F08

description:
Library name: Sample68
Column P


title: DSP-1001660011989-A-G02

description:
Library name: Sample74
Column P


title: BMEC w/ Pericyte transwell mock 8hr infect rep. 2

description: Library name: BMEC8 Mock 2

value: Mock infection 8 hours


title: Pericyte transwell WNV 48hr infection rep. 1

description: Library name: PC WNV 1

value: hPSC-derived pericytes


title: BMEC w/ Pericyte transwell WNV 8hr infect rep. 2

description: Library name: BMEC8 WNV 2

value: WNV infection 8 hours


title: BMEC w/ Pericyte transwell WNV 48hr infect rep. 2

description: Library name: BMEC WNV 2


title: DSP-1001660011989-A-F09

description:
Library name: Sample69
Column P

value: panCK


title: DSP-1001660011989-A-G05

description:
Library name: Sample77
Column P


title: Pericyte transwell WNV 48hr infection rep. 2

description: Library name: PC WNV 2


title: BMEC w/ Pericyte transwell WNV 8hr infect rep. 1

description: Library name: BMEC8 WNV 1


title: BMEC w/ Pericyte transwell mock 8hr infect rep. 3

description: Library name: BMEC8 Mock 3


title: DSP-1001660011989-A-F11

description:
Library name: Sample71
Column P

value: deep dermis


title: DSP-1001660011989-A-F12

description:
Library name: Sample72
Column P


title: BMEC w/ Pericyte transwell WNV 48hr infect rep. 1

description: Library name: BMEC WNV 1


title: DSP-1001660011989-A-F06

description:
Library name: Sample66
Column P

value: 0 h


title: DSP-1001660011989-A-G08

description:
Library name: Sample80
Column P


title: BMEC w/ Pericyte transwell mock 48hr infect rep. 3

description: Library name: BMEC Mock 3


title: BMEC w/ Pericyte transwell WNV 48hr infect rep. 3

description: Library name: BMEC WNV 3


title: DSP-1001660011989-A-F05

description:
Library name: Sample65
Column P


title: DSP-1001660011989-A-F07

description:
Library name: Sample67
Column P


title: DSP-1001660011989-A-F03

description:
Library name: Sample63
Column P


title: BMEC w/ Pericyte transwell mock 48hr infect rep. 2

description: Library name: BMEC Mock 2


title: DSP-1001660011989-A-F04

description:
Library name: Sample64
Column P


title: DSP-1001660011989-A-F10

description:
Library name: Sample70
Column P


title: DSP-1001660011989-A-F02

description:
Library name: Sample62
Column P


title: BMEC w/ Pericyte transwell mock 48hr infect rep. 1

description: Library name: BMEC Mock 1


title: H1 hPSC-derived PCs rep. 3

description: Library name: P1 PC 3

value: hPSC-derived mesoderm pericytes


title: H1 hPSC-derived PCs rep. 2

description: Library name: H1 PC 2


title: H1 hPSC-derived NCC-PCs rep. 3

description: Library name: H1 NCC-PC 3

value: hPSC-derived nerual crest pericytes


title: DSP-1001660011989-A-E12

description:
Library name: Sample60
Column P


title: DSP-1001660011989-A-E11

description:
Library name: Sample59
Column P


title: H1 hPSC-derived PCs rep. 1

description: Library name: H1 PC 1


title: DSP-1001660011989-A-E09

description:
Library name: Sample57
Column P

value: adipose

value: Mouse 210_scan 2


title: H1 hPSC-derived NCC-PCs rep. 2

description: Library name: H1 NCC-PC 2


title: H1 hPSC-derived NCCs rep. 2

description: Library name: H1 NCC 2

value: hPSC-derived neural crest cells


title: DSP-1001660011989-A-F01

description:
Library name: Sample61
Column P


title: H1 hPSC-derived NCC-PCs rep. 1

description: Library name: H1 NCC-PC 1


title: DSP-1001660011989-A-E07

description:
Library name: Sample55
Column P


title: DSP-1001660011989-A-E08

description:
Library name: Sample56
Column P


title: H1 hPSC-derived NCCs rep. 3

description: Library name: H1 NCC 3


title: H1 hPSC-derived NCCs rep. 1

description: Library name: H1 NCC 1


title: DSP-1001660011989-A-E06

description:
Library name: Sample54
Column P

value: epidermis


title: DSP-1001660011989-A-G04

description:
Library name: Sample76
Column P

value: Skin


title: H1 hPSCs rep. 3

description: Library name: H1 STEM 3

value: hPSCs


title: DSP-1001660011989-A-E05

description:
Library name: Sample53
Column P


title: H1 hPSCs rep. 2

description: Library name: H1 STEM 2


title: DSP-1001660011989-A-E04

description:
Library name: Sample52
Column P


title: BMEC w/ Pericyte transwell mock 8hr infect rep. 1

description: Library name: BMEC8 Mock 1


title: H1 hPSCs rep. 1

description: Library name: H1 STEM 1


title: iPS11 hPSC-derived PCs rep. 3

description: Library name: iPS11 PC 3


title: iPS11 hPSC-derived PCs rep. 2

description: Library name: iPS11 PC 2


title: DSP-1001660011989-A-E02

description:
Library name: Sample50
Column P


title: DSP-1001660011989-A-E03

description:
Library name: Sample51
Column P


title: DSP-1001660011989-A-E10

description:
Library name: Sample58
Column P

value: Mouse 219_scan 2


title: DSP-1001660011989-A-E01

description:
Library name: Sample49
Column P


title: DSP-1001660011989-A-D11

description:
Library name: Sample47
Column P


title: iPS11 hPSC-derived NCC-PCs rep. 2

description: Library name: iPS11 NCC-PC 2


title: iPS11 hPSC-derived NCC-PCs rep. 3

description: Library name: iPS11 NCC-PC 3


title: DSP-1001660011989-A-D09

description:
Library name: Sample45
Column P


title: DSP-1001660011989-A-D10

description:
Library name: Sample46
Column P


title: iPS11 hPSC-derived NCC-PCs rep. 1

description: Library name: iPS11 NCC-PC 1


title: iPS11 hPSC-derived NCCs rep. 3

description: Library name: iPS11 NCC 3


title: iPS11 hPSC-derived NCCs rep. 2

description: Library name: iPS11 NCC 2


title: DSP-1001660011989-A-D07

description:
Library name: Sample43
Column P


title: iPS11 hPSC-derived NCCs rep. 1

description: Library name: iPS11 NCC 1


title: DSP-1001660011989-A-D05

description:
Library name: Sample41
Column P


title: DSP-1001660011989-A-D12

description:
Library name: Sample48
Column P


title: iPS11 hPSCs rep. 2

description: Library name: iPS11 STEM 2


title: iPS11 hPSCs rep. 1

description: Library name: iPS11 STEM 1


title: DSP-1001660011989-A-D03

description:
Library name: Sample39
Column P


title: Primary brain pericytes rep. 3

description: Library name: Primary PC 3

source_name: Primary brain pericytes (ScienCell Cat#1200)


title: Primary brain pericytes rep. 2

description: Library name: Primary PC 2

value: Primary brain pericytes (ScienCell Cat#1200)


title: DSP-1001660011989-A-D02

description:
Library name: Sample38
Column P

value: 6 h


title: DSP-1001660011989-A-D01

description:
Library name: Sample37
Column P


title: DSP-1001660011989-A-C11

description:
Library name: Sample35
Column P


title: DSP-1001660011989-A-C12

description:
Library name: Sample36
Column P


title: ATG7 KO 20 min pulse, 2 h chase, 28 h chase with Torin1 IP rep 2

first: Graham

middle: Jordan

last: Ray

address: 77 Massachusetts Ave

department: Biology

institute: Massachusetts Institute of Technology

description: Library name: ATG7_IP_28hrTorin_2

data_processing:
Fastq files from multiple lanes were concatenated and them trimmed using fastp69 with the command: fastp -i R1.fq.gz -I R2.fq.gz -o trimmed.R1.fq.gz -O trimmed. R2.fq.gz -U --umi_loc=read2 --umi_len=10 --adapter_sequence=GATCGTCGGACTGTAGAACTCTGAACGTGTAG --adapter_sequence_r2=AAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Reads were then mapped using STAR successively such that unmapped reads were then remapped to the next “genome” in the following order: rRNA, tRNA, mitochondrial RNA, ncRNA, and the whole transcriptome with the spike-in RNAs added. Then featurecounts74 was used with the following command for rRNA, mitochondrial RNAs, and the whole transcriptome with spike-in RNAs: featureCounts -p -d 15 -s 2 -T 16 -t exon -B -C. Because many RNAs are highly similar for tRNA and ncRNAs, reads were allowed to multimap so the following command was used: featureCounts -M --fraction -p -d 15 -s 2 -T 16 -t exon -B -C. In this instance a multimapping read was counted as 1/number of locations that it maps to. Using R, reads were then combined from all mappings and filtered for distinct geneids keeping the first instance such that redundant genes in multiple datasets were removed and the one first mapped to was retained. Then reads were normalized to their length /1000 to get read per kilobase (RPK) values.   For lysosomal enrichment experiments, ERCC and SIRV spike in values were filtered for either having 18/24 or 16/16 samples having 10+ reads. Then reads for each sample and the corresponding known spike-in concentrations from Lexogen were fit with a linear regression model. Then RPK values were divided by the slope value from the linear regression, and subsequently also multiplied by the values below to account for both differences in lysosomal capture, as quantified by LAMP2 western intensities, as well as normalizations for how much material was input into the IP versus taken for whole-cell and if RNA was diluted prior to spike-in addition. Normalization factors for the WT, KO, tKO lysosomal enrichment experiment were as follows. Whole cell samples: 14285, tKO lysoIP reps 1 & 2: 1025 & 775, KO lysoIP reps 1 & 2: 45 & 57, WT lysoIP reps 1 & 2: 47 & 46, tKO Torin lysoIP reps 1 & 2: 859 & 1000, KO Torin lysoIP reps 1 & 2: 295 & 459, and WT Torin lysoIP reps 1 & 2: 41 & 66. Normalization factors for the ATG7, FIP200, and LARP1 KO lysosomal enrichment experiment were as follows. Whole cell samples: 1800, control KO LysoIP reps 1 & 2: 112 & 90, ATG7 KO LysoIP reps 1 & 2: 89 & 104, FIP200 KO LysoIP reps 1 & 2: 100 & 97, and LARP1 KO LysoIP reps 1 & 2: 83 & 93. To calculate lysosomal enrichment for each genotype, the average normalized lysosomal reads of the 2 biological replicates was divided by the average normalized whole cell reads of the 2 biological replicates. For the WT, KO, tKO lysosomal enrichment experiment the replicates used are from independently generated clonal cell lines. To define the role of ATG7 in lysosomal RNA localization, we calculated the average lysosomal enrichment in tKO cells that express ATG7 targeting guide RNAs and Cas9, and divide that by the average lysosomal enrichment in tKO cells that express control targeting guide RNAs and Cas9. The same analysis was applied to FIP200 and LARP1.
Mapping and analysis of RNA sequencing was done as above, except that samples were not normalized by length, and samples were normalized to a nLuc spike-in RNA by dividing by the counts for all other genes by the counts for nLuc in each sample. Then, for each gene the reads at each time-point were normalize to timepoint 0 such that all RNAs started at 1.  The data was then fit in R using nlsLM to the following equation for each replicate: y= log2(C*(exp(-k *x))+z). y is the log2 number of normalized counts at time x. z is a background metric that is the max value of any of the 4 mock IP samples or 0.000005 divided by the spike-normalized reads at timepoint 0(pre-normalization to nLuc). When fitting for each gene, C and k were bound from 0 to infinity, with starting values of 2^(max(y)) and 1 respectively. For Torin1 treated samples C was fixed as the C value of the untreated sample since C value represents an initial value that should be independent of the treatment. The half-life was calculated as ln(2)/k with a maximum of 50 h. Only half-lives where the Pr(>|t|) <.05 for k and C where recorded. A synthesis rate S was calculated as C*k. Downstream analyses are the average of independently calculated half-lives for each replicate.
Assembly: The rRNA “genome” was built with the following command: STAR --runMode genomeGenerate --genomeSAindexNbases 6 --genomeDir STAR_rRNA --genomeFastaFiles 5S.fasta 5_8S.fasta 18S.fasta 28S.fasta --sjdbGTFfile rRNA.gtf --sjdbOverhang 39 --runThreadN 16. Fasta files are from NCBI and rRNA.gtf was created using biopython70 to create a gff file from a fasta and gffread71 to make a gtf from a gff file.  The tRNA “genome” was built with the following command: STAR --runMode genomeGenerate --genomeSAindexNbases 5 --genomeDir STAR_tRNA --genomeFastaFiles CCA_hg38-tRNAs.fasta --sjdbGTFfile CCA_hg38-tRNAs.gtf --sjdbOverhang 39 --runThreadN 16. A tRNAs fasta of sequences was from the genomic tRNA database72 but had CCAs added to their 3′ using biopython such that mature tRNAs were not discarded for containing sequence that does not match the reference. GTF files were created as above.  The mitochondrial RNA “genome” was built with the following command: STAR --runMode genomeGenerate --genomeSAindexNbases 8 --genomeDir STAR_mito --genomeFastaFiles mito.fasta --sjdbGTFfile mito.gtf --sjdbOverhang 39 --runThreadN 16. The fasta and gff files are from NCBI reference NC_012920.1. GTF files were created as above.  The ncRNA “genome” was built with the following command: STAR --runMode genomeGenerate --genomeSAindexNbases 13 –genomeDir STAR_ncRNA --genomeFastaFiles Min_Nc_RNA_Fasta_transcripts.fasta --sjdbGTFfile Min_Nc_RNA_Fasta_transcripts.gtf --sjdbOverhang 39 --runThreadN 16. Here, we wanted to map to abundant ncRNAs that may have homologs or pseudogenes throughout the genome. To do so we used biopython to first only look at RNAs not annotated as pseudogenes and then filtered for any RNAs with the biotype snRNA, snoRNA, or scaRNA as well as the RNAs RNY1, RNY3, RNY4, RN7SL1, RN7SL2, RN7SL3, VTRNA1, VTRNA2 and RPPH1. GTF files were created as above.  The “genome” for the whole transcriptome with the spike-in RNAs was built with the following command: STAR --runMode genomeGenerate  --genomeDir STAR_hg38_ERCC_SIRV --genomeFastaFiles hg38_Gencode_v43_primary_ERCC_SIRV.fa --sjdbGTFfile hg38_Gencode_v43_primary_ERCC_SIRV.gtf --sjdbOverhang 39 --runThreadN 16. Fasta and GTF files for the primary GRCh38 version 43 human genome were downloaded from Gencode and concatenated with ERCC_SIRV fasta and GTF files downloaded from Lexogen. For the 5EU experiment fastas and GTFs with the sequences of nLUC and GFP were also included.
Supplementary files format and content: excel files including normailzed counts and caluclated values used throughout the manuscript

extract_protocol:
RNA isolation for lysosomal enrichment experiments Samples were purified using Trizol LS (Invitrogen 10296010) and the RNA clean and concentrator (Zymo R1015 or R1017). Briefly, 750 uL Trizol LS was mixed with 250 uL of sample (if the sample was less than 250 uL, water was added to 250 uL). Samples were homogenized by pipetting and frozen at -80°C if the RNA purification was not done the same day. After thawing, 200 uL chloroform was added per 750 uL of Trizol LS. Samples were mixed by shaking for 15 s and incubated at room temperature for 3 min. Then, samples were centrifuged for 15 min at 12,000 x g at 4°C. 500 uL of the upper aqueous phase was transferred to a new tube, 500 uL of 100% ethanol was added to the sample, and they were mixed by pipetting. 700 uL of this sample was then transferred to zymo-spin IC or IICR column in a collection tube and centrifuged at 10,000 x g for 30 s. The flow through was discarded. Additional sample was transferred to the same column and centrifuged at 10,000 x g for 30 s. Flow through was again discarded. 400 uL of RNA prep buffer was added to the column and centrifuged at 10,000 x g for 30 s. Flow through was discarded. 700 uL of RNA wash buffer was added to the column and centrifuged at 10,000 x g for 30 s. Flow through was discarded. 400 uL of RNA wash buffer was added to the column and centrifuged at 10,000 x g for 30 s. Flow through was discarded. The column was transferred to a new tube for elution. 15 or 25 uL of water was added to the column matrix and the sample was centrifuged at 10,000 x g for 30 s.  5EU labeling and isolation of labeled RNA 150 mL of cells were incubated with 0.5 mM 5EU for 10 min shaking at 37°C, then spun at 300 x g for 3 min, and resuspended in 50 mL of media with 1 mM uridine (~20 min until 5EU was removed). Cells were then spun 2 more times as above resuspending in 50 mL media with 1 mM uridine, and then 200 mL media with 1 mM uridine.  Then cells were incubated at for 2 h post initial wash, with shaking at 37°C. At this point Torin1 (Selleck Chemicals S2827) treatment was started on half of the samples. Timepoints were collected by spinning down 15 mL cells at 300 x g for 3 min and resuspending in 4 mL of Tri reagent (Thermo Fisher Scientific AM9738) and freezing at -80°C.  Cells in tri-reagent were thawed and had 1 ng GFP and 5 ng of nLuc spike-in RNAs added to them. Spike-in RNAs were made by in vitro transcription as in Eisen et al.21. RNAs were then precipitated by adding 100 uL BCP for each 1 mL of tri reagent, mixing by shaking for 15 s, incubation at room temperature for 5 to 15 min, and then centrifugation at 12,000 x g for 15 min at 4°C. The aqueous phases (490-500 ul) were transferred to a fresh tube and 1 uL of 5 mg/mL linear acrylamide was added to each sample. 500 ul of isopropanol was then added per 1 mL of Tri reagent solution used for the sample. The samples were then mixed by vortexing and incubated at -20°C overnight. Samples were centrifuged at 12,000 x g for 8 min at 4°C, and the supernatant was removed without disturbing the pellet. Samples were washed with 1 mL cold 75% ethanol, then centrifuged at 12,000 x g for 5 min at 4°C. Ethanol was removed, and samples were centrifuged again briefly to remove any residual ethanol. Samples were air dried for 5 min and then dissolved in 100 ul water or 150ul water for the four untreated 28 h timepoints.  Biotinylation reactions were done as Eisen et al. 21. Briefly, half of the isolated RNA from above was incubated in a 50 mM HEPES, pH 7.5, 4 mM disulfide biotin azide (Click Chemistry Tools), 2.5 mM CuSO4, 2.5 mM Tris(3-hydroxypropyltriazolylmethyl)amine (THPTA, Sigma-Aldrich), and 10 mM sodium ascorbate (Sigma-Aldrich) in a final volume of 180 uL for 1 h at room temperature protected from light. Reactions were stopped by adding EDTA to a final concertation of 5 mM, brought to 300 uL with water, and then had 300 uL phenol:chloroform:isoamyl alcohol (25:24:1,Sigma P2069-100ML) added. Samples were mixing by vortexing for 20 s, incubated at room temperature for 10 min, and centrifuged at 21,000 x g for 10 min at 4°C. The upper aqueous phase (280 uL) was transferred to a new tube, and 18 uL of 5 M NaCl, 2 uL 5 mg/mL linear acrylamide, and 900 uL ethanol were added, mixed, and incubated at -20°C overnight. Samples were then centrifuged at 21,000 x g for 10 min at 4°C and the supernatant was removed without disturbing the pellet. Samples were washed with 1 mL cold 75% ethanol, then centrifuged at 21,000 x g for 5 min at 4°C. Ethanol was removed, and samples were centrifuged again briefly to remove any residual ethanol. Samples were air dried for 5 min and then dissolved in 100 ul water.  RNA was fragmented for 7 min at 94°C using the NEB RNA fragmentation module (E6150S) in a final volume of 110 uL, and 10 uL of 3M pH 5.5 sodium acetate, 2 uL 5 mg/mL linear acrylamide, and 325 uL ethanol were added, mixed, and incubated at -20°C overnight. Samples were then centrifuged at 21,000 x g for 15 min at 4°C and supernatant was removed without disturbing the pellet. Samples were washed with 1 mL cold 70% ethanol, then centrifuged at 21,000 x g for 10 min at 4°C. Ethanol was removed, and samples were centrifuged again briefly to remove any residual ethanol. Samples were air dried for 5 min and then resuspended in 100ul 1X HSWB (10 mM Tris pH 7.5, 1 mM EDTA, 100 mM NaCl, 0.01% Tween-20).  Purification of biotinylated RNAs were done as Eisen et al. 21. Dynabeads MyOne Streptavidin C1 beads (Invitrogen 65002) for each set of samples were combined and batch washed, with 200 μL of beads per reaction. Beads were washed twice with 1X B&W buffer (5 mM Tris-HCl, pH 7.5, 0.5 mM EDTA, 1 M NaCl and 0.005% Tween-20), twice with solution A (0.1 M NaOH, 50 mM NaCl), twice with solution B (0.1 M NaCl), and then twice with water, using for each wash a volume equal to that of the initial bead suspension. Following the last wash, beads were resuspended in an initial bead volume of 1X high salt wash buffer (HSWB, 10 mM Tris-HCl, pH 7.4, 1 mM EDTA, 0.1 M NaCl, 0.01% Tween-20) supplemented with 0.5 mg/mL yeast RNA (Thermo Fisher) and incubated at 23°C on a thermal mixer, shaking in a cycle of 15 s 1400 RPM on and 1 min 45 s off, for 30 min, again using a volume equal to that of the initial bead suspension. Beads were then washed three times with 1X HSWB per reaction and split for each reaction during the last wash. After the wash was removed, sample RNA previously resuspended in 100 μL 1X HSWB was added to blocked beads and incubated at 23°C on a thermal mixer, shaking in a cycle of 15 s 1400 RPM on and 1 min 45 s off, for 30 min. Beads were washed twice with 400 μL water at 50°C, incubating at 50°C for 2 min for each wash, and then twice with 400 μL 10X HSWB, incubating at 50°C for 2 min for each wash. RNA was eluted from beads by incubating with 180 μL 0.5 M tris(2-carboxyethyl)phosphine (TCEP, Sigma-Aldrich) at 50°C shaking on a thermal mixer in a cycle of 15 s 1400 RPM on and 1 min 45 s off, for 30 min. The initial eluate was collected, and beads were resuspended in 150 μL water and eluted again, combining the two eluates for each sample. RNA from the eluate was then mixed with 22 uL 5 M NaCl, 3 uL 5 mg/mL linear acrylamide and 1 mL ethanol and incubate at -20°C overnight. Samples were then centrifuged at 21,000 x g for 30 min at 4°C and supernatant was removed without disturbing the pellet. Samples were washed with 1 mL cold 75% ethanol, then centrifuged at 21,000 x g for 10 min at 4°C. Ethanol was removed, and samples were centrifuged again briefly to remove any residual ethanol. Samples were air dried for 5 min and then resuspended in 20 ul water.  Samples were then PNK treated as done above for lysosomal enrichment RNA sequencing, brought up to 350 uL with water, and mixed with 350 uL of phenol:chloroform:isoamyl alcohol (25:24:1,Sigma P2069-100ML). Samples were mixing by vortexing for 20 s, incubated at room temperature for 10 min, and centrifuged at 21,000 x g for 10 min at 4°C. The upper aqueous phase (340 uL) was transferred to a new tube, and 340ul chloroform was mixed in before incubating at room temperature for 10 min and centrifugation at 21,000 x g for 10 min at 4°C. The upper aqueous phase (280 uL) was transferred to a new tube, and 18 uL of 5M NaCl, 2 uL 15 mg/mL glycoblue, and 900 uL ethanol were added, mixed, and incubated at -20°C overnight. Samples were then centrifuged at 21,000 x g for 30 min at 4°C and supernatant was removed without disturbing the pellet. Samples were washed with 1 mL cold 75% ethanol, then centrifuged at 21,000 x g for 10 min at 4°C. Ethanol was removed, and samples were centrifuged again briefly to remove any residual ethanol. Samples were air dried for 5 min and then dissolved in 20ul water. 50 ng of RNA, or 10ul for mock IP samples, were then input into the TGIRT RNA sequencing protocol outlined above.
Purified RNA (ranging from 100 to 2000 ng) from whole-cell and lysosomal samples had equal amounts of SIRV-Set 3 (Iso Mix E0/ERCC) (Lexogen 051.01) spike-ins added to them such that spike-ins would represent ~0.01 to ~0.2% of reads. They were then treated with DNAse I (Zymo E1010) according to Zymo’s instructions. RNA was then purified using Trizol LS and zymo-RNA clean and concentrators kits as above. Then, RNA was fragmented for 7 min at 94°C using NEB RNA fragmentation module (E6150S), before again purifying RNA using Trizol LS and zymo-RNA clean and concentrators kits as above. Then, to remove any 3′ cyclic phosphates from fragmentation, 30 uL of RNA was PNK treated with 50 U T4 PNK (Biosearch technologies P0503K) in a final volume of 60 uL prior to again purifying RNA using Trizol LS and zymo-RNA clean and concentrators kits as above. RNA was then quantified and checked for proper fragmentation by bioanalyzer as outlined above.  RNA sequencing libraries from these samples were prepared based on Xu et al.38 with some modifications. Briefly, reverse transcription was done using TGIRT-III from the Lambowitz lab using an annealed R2 RNA (rArArGrArUrCrGrGrArArGrArGrCrArCrArCrGrUrCrUrGrArArCrUrCrCrArGrUrCrArC/3SpC3/) / R2R DNA (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTN) mix. DNA was cleaned up using MinElute reaction cleanup kits (Qiagen 28204). Then cDNA was ligated to adenylated (NEB E2610S) R1R DNA (/5Phos/NNNNNNNNNNGATCGTCGGACTGTAGAACTCTGAACGTGTAG/3SpC3/) using Thermostable 5′ AppDNA/RNA ligase (NEB M0319S). DNA was cleaned up using MinElute reaction cleanup kit.  cDNA was amplified using Phusion (Thermo Fisher F531S) and the following primers: P5 barcode primer: AATGATACGGCGACCACCGAGATCTACAC-BARCODE-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTT, P7 barcode primer: CAAGCAGAAGACGGCATACGAGAT-BARCODE- CTACACGTTCAGAGTTCTACAGTCCGACGATC. A cycle course of (6, 9, 12, 15, or 18 cycles) or (8, 10, 12, 14, or 16 cycles) was performed on half of the cDNA to determine the fewest amount of cycles necessary for library amplification (established by the PCR product being visible on an ethidium bromide stained agarose gel). Note, that here the primers used are different than those in the Lambowitz protocol. This is for two reasons. One is to use the non-truncated p5 sequence, and the other is to invert the reads such that the base biased sequence near the barcode is read second. If this is not done, sequencing quality is dramatically diminished, because NovaSeq is highly sensitive to base bias in the first 26 cycles.  PCR products were cleaned up to remove primers using 2 rounds of ampure xp bead (Beckman Coulter A63880) with a 1.4 x ratio of beads to PCR volume prior to submission for paired end 50nt sequencing on NovaSeq. As a result of the differences in primer design outlined above, sequencing was done with custom oligos. Read 1 primer was oGJR992: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTT. Read 2 primer was oGJR993: CTACACGTTCAGAGTTCTACAGTCCGACGATC. i7 sequencing primer was oGJR994: GATCGTCGGACTGTAGAACTCTGAACGTGTAG. i5 sequencing primer was oGJR995: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC.

value: ATG7 KO

value: IP


title: iPS11 hPSC-derived PCs rep. 1

description: Library name: iPS11 PC 1


title: ATG7 KO 20 min pulse, 2 h chase, 28 h chase IP rep 2

description: Library name: ATG7_IP_28hrNT_2

value: 20 min pulse, 2 h chase, 28 h chase


title: DSP-1001660011989-A-D08

description:
Library name: Sample44
Column P

value: panCK


title: WT 20 min pulse, 2 h chase, 28 h chase with Torin1 IP rep 2

description: Library name: WT_IP_28hrTorin_2

value: WT


title: Primary brain pericytes rep. 1

description: Library name: Primary PC 1


title: DSP-1001660011989-A-C10

description:
Library name: Sample34
Column P

value: 0 h


title: DSP-1001660011989-A-C06

description:
Library name: Sample30
Column P


title: iPS11 hPSCs rep. 3

description: Library name: iPS11 STEM 3


title: WT 20 min pulse, 2 h chase, 28 h chase IP rep 2

description: Library name: WT_IP_28hrNT_2


title: DSP-1001660011989-A-C03

description:
Library name: Sample27
Column P

value: Mouse 208_scan 2


title: ATG7 KO 20 min pulse, 2 h chase, 8 h chase IP rep 2

description: Library name: ATG7_IP_8hrNT_2

value: 20 min pulse, 2 h chase, 8 h chase


title: DSP-1001660011989-A-C05

description:
Library name: Sample29
Column P


title: DSP-1001660011989-A-C08

description:
Library name: Sample32
Column P

value: deep dermis


title: WT 20 min pulse, 2 h chase, 8 h chase with Torin1 IP rep 2

description: Library name: WT_IP_8hrTorin_2


title: DSP-1001660011989-A-D06

description:
Library name: Sample42
Column P

value: Mouse 210_scan 2


title: WT 20 min pulse, 2 h chase, 8 h chase IP rep 2

description: Library name: WT_IP_8hrNT_2


title: DSP-1001660011989-A-C07

description:
Library name: Sample31
Column P


title: ATG7 KO 20 min pulse, 2 h chase, 8 h chase with Torin1 IP rep 2

description: Library name: ATG7_IP_8hrTorin_2


title: DSP-1001660011989-A-C02

description:
Library name: Sample26
Column P

value: adipose


title: DSP-1001660011989-A-C01

description:
Library name: Sample25
Column P

value: PanCK


title: WT 20 min pulse, 2 h chase, 4 h chase IP rep 2

description: Library name: WT_IP_4hrNT_2

value: 20 min pulse, 2 h chase, 4 h chase


title: ATG7 KO 20 min pulse, 2 h chase, 4 h chase with Torin1 IP rep 2

description: Library name: ATG7_IP_4hrTorin_2


title: ATG7 KO 20 min pulse, 2 h chase, 2 h chase with Torin1 IP rep 2

description: Library name: ATG7_IP_2hrTorin_2


title: DSP-1001660011989-A-B12

description:
Library name: Sample24
Column P

value: Skin


title: DSP-1001660011989-A-B11

description:
Library name: Sample23
Column P

value: epidermis


title: WT 20 min pulse, 2 h chase, 2 h chase with Torin1 IP rep 2

description: Library name: WT_IP_2hrTorin_2


title: ATG7 KO 20 min pulse, 2 h chase, 2 h chase IP rep 2

description: Library name: ATG7_IP_2hrNT_2

value: 20 min pulse, 2 h chase, 2 h chase


title: DSP-1001660011989-A-B09

description:
Library name: Sample21
Column P


title: WT 20 min pulse, 2 h chase, 2 h chase IP rep 2

description: Library name: WT_IP_2hrNT_2


title: DSP-1001660011989-A-D04

description:
Library name: Sample40
Column P

value: 6 h


title: DSP-1001660011989-A-B08

description:
Library name: Sample20
Column P


title: DSP-1001660011989-A-C09

description:
Library name: Sample33
Column P


title: DSP-1001660011989-A-C04

description:
Library name: Sample28
Column P


title: WT 20 min pulse, 2 h chase, 4 h chase with Torin1 IP rep 2

description: Library name: WT_IP_4hrTorin_2


title: DSP-1001660011989-A-B07

description:
Library name: Sample19
Column P


title: ATG7 KO 20 min pulse, 2 h chase, 1 h chase with Torin1 IP rep 2

description: Library name: ATG7_IP_1hrTorin_2

value: ATG7 KO


title: ATG7 KO 20 min pulse, 2 h chase, 4 h chase IP rep 2

description: Library name: ATG7_IP_4hrNT_2

value: IP


title: ATG7 KO 20 min pulse, 2 h chase, 1 h chase IP rep 2

description: Library name: ATG7_IP_1hrNT_2

value: 20 min pulse, 2 h chase, 1 h chase


title: DSP-1001660011989-A-B05

description:
Library name: Sample17
Column P


title: DSP-1001660011989-A-B04

description:
Library name: Sample16
Column P


title: DSP-1001660011989-A-B02

description:
Library name: Sample14
Column P


title: WT 20 min pulse, 2 h chase, 1 h chase IP rep 2

description: Library name: WT_IP_1hrNT_2


title: WT 20 min pulse, 2 h chase, 1 h chase with Torin1 IP rep 2

description: Library name: WT_IP_1hrTorin_2


title: WT 20 min pulse, 2 h chase, 0 h chase IP rep 2

description: Library name: WT_IP_0hr_2

value: 20 min pulse, 2 h chase, 0 h chase


title: WT no label IP rep 2

description: Library name: WT_mock_2

value: WT

value: no label


title: DSP-1001660011989-A-B03

description:
Library name: Sample15
Column P

value: Mouse 208_scan 2


title: ATG7 KO 20 min pulse, 2 h chase, 0 h chase IP rep 2

description: Library name: ATG7_IP_0hr_2


title: DSP-1001660011989-A-B06

description:
Library name: Sample18
Column P


title: DSP-1001660011989-A-B10

description:
Library name: Sample22
Column P


title: ATG7 KO no label IP rep 2

description: Library name: ATG7_mock_2


title: ATG7 KO 20 min pulse, 2 h chase, 28 h chase with Torin1 WC rep 2

description: Library name: ATG7_WC_28hrTorin_2

value: WC


title: ATG7 KO 20 min pulse, 2 h chase, 28 h chase WC rep 2

description: Library name: ATG7_WC_28hrNT_2

value: 20 min pulse, 2 h chase, 28 h chase


title: DSP-1001660011989-A-A10

description:
Library name: Sample10
Column P


title: DSP-1001660011989-A-A09

description:
Library name: Sample9
Column P

value: deep dermis

value: 0 h


title: WT 20 min pulse, 2 h chase, 28 h chase with Torin1 WC rep 2

description: Library name: WT_WC_28hrTorin_2


title: DSP-1001660011989-A-A12

description:
Library name: Sample12
Column P


title: WT 20 min pulse, 2 h chase, 28 h chase WC rep 2

description: Library name: WT_WC_28hrNT_2


title: DSP-1001660011989-A-A08

description:
Library name: Sample8
Column P


title: DSP-1001660011989-A-A07

description:
Library name: Sample7
Column P

value: PanCK


title: WT no label WC rep 2

description: Library name: WT_WC_noLabel_2


title: DSP-1001660011989-A-A06

description:
Library name: Sample6
Column P


title: ATG7 KO 20 min pulse, 2 h chase, 28 h chase with Torin1 IP rep 1

description: Library name: ATG7_IP_28hrTorin_1


title: DSP-1001660011989-A-A05

description:
Library name: Sample5
Column P


title: WT 20 min pulse, 2 h chase, 28 h chase with Torin1 IP rep 1

description: Library name: WT_IP_28hrTorin_1


title: ATG7 KO 20 min pulse, 2 h chase, 28 h chase IP rep 1

description: Library name: ATG7_IP_28hrNT_1


title: DSP-1001660011989-A-A04

description:
Library name: Sample4
Column P


title: DSP-1001660011989-A-B01

description:
Library name: Sample13
Column P


title: DSP-1001660011989-A-A03

description:
Library name: Sample3
Column P


title: DSP-1001660011989-A-A11

description:
Library name: Sample11
Column P


title: WT 20 min pulse, 2 h chase, 28 h chase IP rep 1

description: Library name: WT_IP_28hrNT_1


title: DSP-1001660011989-A-A02

description:
Library name: Sample2
Column P


title: DSP-1001660011989-A-A01

description:
Library name: Sample1
Column P

source_name: No Template Control

value: No Template Control


title: ATG7 KO 20 min pulse, 2 h chase, 8 h chase IP rep 1

description: Library name: ATG7_IP_8hrNT_1

value: 20 min pulse, 2 h chase, 8 h chase


title: ESC Ctl Kdm6a

city: Solna

first: Jasper

last: Panten

address: Tomtebodavägen 23

country: Sweden

institute: SciLifeLab

description: Library name: Utx_WT

library_source: genomic

data_processing:
Library strategy: Capture Hi-C
Allele-specific Capture Hi-C analysis was performed using the Hi-C Pro pipeline (v2.11.4). Paired-end reads were first independently aligned using bowtie2 to the same N-masked genome reference. Read pairs were then assigned to either C57BL-6J or CAST-EiJ genomes and allele-specific BAM files for downstream analysis are generated. Low-quality reads, multiple hits, singletons and read pairs which do not map to the same genotype were then removed. Further filtering for valid interactions, which excludes reads outside of the captured region, was performed and only valid pairs were used to build the normalized contact maps at a 10kb resolution with the cooler package (v0.8.9)
Assembly: mm10
Supplementary files format and content: mcool files contains the contact maps at various resolution for visualization

molecule: genomic DNA

source_name: ES cell

growth_protocol: ESCs were cultured on gelatine-coated (0.1 % gelatine in 1X-PBS) cell culture dish in 2i-containing ESC media (DMEM, 15% FBS, 0.1 mM β-mercaptoethanol, 1,000 U/mL−1 leukaemia inhibitory factor (LIF), CHIR99021 (3 µM), and PD0325901 (1 µM)). NPCs were cultured on gelatine-coated (0.1 % gelatine in 1X-PBS) cell culture dish in NPC media (N2B27 media supplemented with with FGF2 (10 ng/mL) and EGF (10 ng/mL, both Peprotech)).

extract_protocol:
Capture Hi-C was performed as described in Hauth et. al 2022. Three arrays of biotinylated RNA probes were designed to tile 3 Mb targets on the mouse X chromosome (Hcfc1-Mecp2 cluster; ChrX:72,590,000 - 75,430,000; Kdm5c cluster; ChrX:150,210,000 - 153,045,000, Kdm6a cluster: ChrX:15,725,000-18,725,000).
Capture Hi-C libraries were constructed using the SureSelect XT Library Prep Kit

treatment_protocol: Xist expression was induced by addition of doxycycline (1 µg/mL) to the media. Culture media supplemented with doxycycline was renewed every 24h if applicable. For doxycycline wash-out, doxycycline-containing media was removed, and cells were refreshed with doxycycline-free culture media. Auxin-mediated depletion of SPEN was achieved by supplementing the culture media with Auxin (Sigma) at the concentration of 500 µM, as previously described [Dossin et al. 2020]. Auxin-containing media was renewed every 24h.

tag: strain

value: C57BL6/J x CAST/EiJ

value: ES cell

value: Xptet / R26rtTA

value: Control

tag: experiment


title: ATG7 KO 20 min pulse, 2 h chase, 4 h chase with Torin1 IP rep 1

description: Library name: ATG7_IP_4hrTorin_1

value: ATG7 KO

value: IP


title: ESC Dox Kdm6a

description: Library name: Utx_Dox

value: Dox (24h)


title: WT 20 min pulse, 2 h chase, 8 h chase with Torin1 IP rep 1

description: Library name: WT_IP_8hrTorin_1

value: WT


title: ESC Ctl Kdm5c

description: Library name: Jarid_WT


title: WT 20 min pulse, 2 h chase, 8 h chase IP rep 1

description: Library name: WT_IP_8hrNT_1


title: WT 20 min pulse, 2 h chase, 4 h chase with Torin1 IP rep 1

description: Library name: WT_IP_4hrTorin_1


title: ESC Dox Kdm5c

description: Library name: Jarid_Dox


title: ATG7 KO 20 min pulse, 2 h chase, 4 h chase IP rep 1

description: Library name: ATG7_IP_4hrNT_1

value: 20 min pulse, 2 h chase, 4 h chase


title: WT 20 min pulse, 2 h chase, 4 h chase IP rep 1

description: Library name: WT_IP_4hrNT_1


title: E6 Dox (7d) - washout (4d) Kdm5c

source_name: neural progenitor cell

value: neural progenitor cell

value: Dox (7d) - washout (4d)


title: ATG7 KO no label WC rep 2

description: Library name: ATG7_WC_noLabel_2

value: no label

value: WC


title: E6 Dox (21d) – washout (7d) Mecp2

description: Library name: Mecp2_E6_21dox_wo

value: Dox (21d) - washout (7d)


title: E6 Dox (21d) Mecp2

value: Dox (21d)


title: ATG7 KO 20 min pulse, 2 h chase, 2 h chase with Torin1 IP rep 1

description: Library name: ATG7_IP_2hrTorin_1


title: E6 Dox (7d) - washout (4d) Mecp2


title: WT 20 min pulse, 2 h chase, 2 h chase with Torin1 IP rep 1

description: Library name: WT_IP_2hrTorin_1


title: ATG7 KO 20 min pulse, 2 h chase, 1 h chase with Torin1 IP rep 1

description: Library name: ATG7_IP_1hrTorin_1


title: E6_7d_Dox_Washout

description: short_treat_washout_rep1.sorted.genome*.bismark.cov.gz

data_processing:
Library strategy: EM-Seq
Processing of DNA methylation was performed using the methylseq nextflow pipeline with the --emseq option (v2.3.0, NextFlow v22.10.6). Reads were trimmed using TrimGalore! (v0.6.7) and aligned to the same N-masked genome (GRCm38) using bismarck (v0.24.0), and used SNP_split (v0.5.0) to assign mapped reads to parental genomes, similar to the RNA-Seq data. We finally used bismark_methylation_extractor from the bismarck software to generate base-level methylation counts for both haplotypes.
Assembly: GRCm38
Supplementary files format and content: Bismarck coverage file

growth_protocol: NPCs were cultured on gelatine-coated (0.1 % gelatine in 1X-PBS) cell culture dish in NPC media (N2B27 media supplemented with with FGF2 (10 ng/mL) and EGF (10 ng/mL, both Peprotech)).

extract_protocol:
Genomic DNA (gDNA) from >1M NPC was extracted using column-based DNeasy Blood & Tissue Kit (Qiagen).
DNA integrity was tested on a 0.8% agarose gel and 200 ng of high-quality gDNA was used to prepare libraries according to the NEBNext® Enzymatic Methyl-seq Kit following the section for large insert libraries with minor modifications. A total of 55-100 ng of DNA was used per library, including a spike-in of pUC and Lambda DNA as a control for methylation efficiency. Samples were fragmented using the Covaris S2 System to achieve an average fragment size of 350-400 bp and barcoded using 5 PCR cycles for 100 ng input and 6 PCR cycles for 55 ng input.

treatment_protocol: Xist expression in TX1072 was induced by addition of doxycycline (1 µg/mL) to the NPC media. Culture media supplemented with doxycycline was renewed every 24h. For doxycycline wash-out, doxycycline-containing media was removed, and cells were refreshed with doxycycline-free culture media.

value: Dox (7d) - washout

tag: enrichment

value: Untargeted


title: CL30.7 Dox (21d) Mecp2

value: C57BL6/J x CAST/EiJ

value: Xptet / R26rtTA / SPEN-AID


title: WT 20 min pulse, 2 h chase, 2 h chase IP rep 1

description: Library name: WT_IP_2hrNT_1

value: 20 min pulse, 2 h chase, 2 h chase


title: CL30.7 Dox (21d) Aux (23d) Mecp2


title: ATG7 KO 20 min pulse, 2 h chase, 8 h chase with Torin1 IP rep 1

description: Library name: ATG7_IP_8hrTorin_1


title: WT 20 min pulse, 2 h chase, 1 h chase with Torin1 IP rep 1

description: Library name: WT_IP_1hrTorin_1


title: CL30.7 Ctrl  Mecp2

value: Control


title: E6_21d_Dox_Washout

description: long_treat_washout_rep1.sorted.genome*.bismark.cov.gz

value: Xptet / R26rtTA

value: Dox (21d) - washout


title: ATG7 KO 20 min pulse, 2 h chase, 2 h chase IP rep 1

description: Library name: ATG7_IP_2hrNT_1

value: ATG7 KO

value: IP


title: WT 20 min pulse, 2 h chase, 1 h chase IP rep 1

description: Library name: WT_IP_1hrNT_1

value: WT

value: 20 min pulse, 2 h chase, 1 h chase


title: ATG7 KO no label IP rep 1

description: Library name: ATG7_mock_1


title: CL30.7 October2023 Dox (21d)

data_processing:
Reads were trimmed using trim_galore (v0.6.6). To construct reference genomes for allele-specific mapping, genomes in which known heterozygous variants (https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.vcf.gz) were masked by the ambiguous base N were constructed using SNPsplit (SNPsplit_genome_preparation script, v0.5.0) and converted to STAR references (STAR v2.5.3a). For the E6, CL30/CL30.7 and CL31/CL31.16, the mm10 genome was used (GRCm38). Reads were aligned to the N-masked genomes using the options --sjdbOverhang 99 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType. Reads mapping to the mitochondrial genome were removed and split into parental genotypes using SNPsplit and known heterozygous variants. Gene-level read counts for each haplotype and without allelic resolution were derived using featureCounts (v2.0.1).
Allele-specific expression per gene was calculated from genotype-assigned read counts. First, lowly expressed genes with an average allelic read count < 10 were excluded (summing both haplotypes). Escape of an X-linked gene was generally quantified as the fraction of read counts on the inactivated X against the total read count across both active and inactive X (Xi / (Xi + Xa), allelic ratio, also known as d-score).
Assembly: GRCm38
Supplementary files format and content: delimited text file

extract_protocol:
RNA was extracted from > 1M NPCs using the RNeasy kit and on-column DNAse digestion (Qiagen). RNA integrity was measured using the Bioanalyzer Nano Kit.
Only high-quality RNA was used for subsequent library preparation using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490L) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L, New England Biolabs (NEB), Ipswich, MA, USA) implemented on the liquid handling robot Beckman i7. Obtained libraries that passed the QC step were pooled in equimolar amounts; and the pools were loaded on the Illumina sequencer NextSeq 500 or NextSeq 2000 and sequenced bi-directionally, generating ~500 million paired-end reads, each 75 bases long.

treatment_protocol: Xist expression in TX1072 was induced by addition of doxycycline (1 µg/mL) to the NPC media. Culture media supplemented with doxycycline was renewed every 24h. For doxycycline wash-out, doxycycline-containing media was removed, and cells were refreshed with doxycycline-free culture media. Auxin-mediated depletion of SPEN was achieved by supplementing the culture media with Auxin (Sigma) at the concentration of 500 µM, as previously described [Dossin et al. 2020]. Auxin-containing media was renewed every 24h.

value: neural progenitor cell

tag: experiment id


title: ATG7 KO 20 min pulse, 2 h chase, 0 h chase IP rep 1

description: Library name: ATG7_IP_0hr_1

value: 20 min pulse, 2 h chase, 0 h chase


title: E6 October2023 Dox (21d) - washout (7d)


title: WT no label IP rep 1

description: Library name: WT_mock_1

value: no label


title: E6_21d_Dox


title: ATG7 KO 20 min pulse, 2 h chase, 1 h chase IP rep 1

description: Library name: ATG7_IP_1hrNT_1


title: E6_7d_Dox

value: Dox (7d)


title: WT 20 min pulse, 2 h chase, 0 h chase IP rep 1

description: Library name: WT_IP_0hr_1


title: WT 20 min pulse, 2 h chase, 28 h chase with Torin1 WC rep 1

description: Library name: WT_WC_28hrTorin_1

value: WC


title: E6 October2023 Dox (21d)

value: Dox (21d)


title: WT 20 min pulse, 2 h chase, 28 h chase WC rep 1

description: Library name: WT_WC_28hrNT_1

value: 20 min pulse, 2 h chase, 28 h chase


title: E6 October2023 Dox (7d)

value: C57BL6/J x CAST/EiJ


title: E6 October2023 Dox (7d) - washout (7d)

value: Dox (7d) - washout (7d)


title: ATG7 KO no label WC rep 1

description: Library name: ATG7_WC_noLabel_1


title: E6 October2023 Control


title: E6 April2023 Dox (21d) - washout (7d)

value: Dox (21d) - washout (7d)


title: WT no label WC rep 1

description: Library name: WT_WC_noLabel_1


title: E6_No_Dox

value: Control

value: Untargeted


title: RNASET2 PLD3 RNASE4 tKO no serum + LARP1 gRNA LysoIP rep 2

description: Library name: Lyso_LARP1_2

value: RNASET2 PLD3 RNASE4 tKO no serum

value: LARP1 gRNA 2

value: LysoIP


title: CL31.16 April2023 Dox (3d)

value: Xptet / R26rtTA / SPEN-AID

value: Dox (3d)


title: RNASET2 PLD3 RNASE4 tKO no serum + control gRNA LysoIP rep 2

description: Library name: Lyso_Control_2

value: control gRNA 2


title: RNASET2 PLD3 RNASE4 tKO no serum + LARP1 gRNA LysoIP rep 1

description: Library name: Lyso_LARP1_1

value: LARP1 gRNA 1


title: E6 April2023 Dox (21d)

value: neural progenitor cell

value: Xptet / R26rtTA


title: E6 October2022 Dox (14d) - washout (7d)

value: Dox (14d) - washout (7d)


title: CL31.16 April2023 Dox (7d)

value: Dox (7d)


title: ATG7 KO 20 min pulse, 2 h chase, 28 h chase with Torin1 WC rep 1

description: Library name: ATG7_WC_28hrTorin_1

value: ATG7 KO

value: WC


title: E6 October2022 Dox (7d) - washout (14d)

value: C57BL6/J x CAST/EiJ

value: Dox (7d) - washout (14d)


title: RNASET2 PLD3 RNASE4 tKO no serum + ATG7 gRNA LysoIP rep 1

description: Library name: Lyso_ATG7_1

value: ATG7 gRNA 1


title: E6 October2022 Dox (3d)


title: RNASET2 PLD3 RNASE4 tKO no serum + FIP200 gRNA LysoIP rep 2

description: Library name: Lyso_FIP200_2

value: FIP200 gRNA 2


title: E6 October2022 Dox (7d) - washout (7d)

value: Dox (7d) - washout (7d)


title: RNASET2 PLD3 RNASE4 tKO no serum + control gRNA LysoIP rep 1

description: Library name: Lyso_Control_1

value: RNASET2 PLD3 RNASE4 tKO no serum

value: control gRNA 1


title: E6 October2022 Dox (14d)

value: Dox (14d)


title: CL31.16 October2022 Aux (2d)

value: Xptet / R26rtTA / SPEN-AID

value: Aux (2d)


title: RNASET2 PLD3 RNASE4 tKO no serum + ATG7 gRNA LysoIP rep 2

description: Library name: Lyso_ATG7_2

value: ATG7 gRNA 2

value: LysoIP


title: CL30.7 October2022 Dox (3d), Aux (5d)

value: neural progenitor cell

value: Dox (3d), Aux (5d)


title: CL30.7 October2022 Control

value: Control


title: RNASET2 PLD3 RNASE4 tKO no serum + FIP200 gRNA whole cell rep 2

description: Library name: WC_FIP200_2

value: whole cell


title: RNASET2 PLD3 RNASE4 tKO no serum + LARP1 gRNA whole cell rep 1

description: Library name: WC_LARP1_1

value: LARP1 gRNA 1


title: CL30.7 April2023 Dox (7d)

value: C57BL6/J x CAST/EiJ

value: Dox (7d)


title: CL31.16 October2022 Dox (3d), Aux (5d)


title: RNASET2 PLD3 RNASE4 tKO no serum + FIP200 gRNA whole cell rep 1

description: Library name: WC_FIP200_1

value: FIP200 gRNA 1


title: CL30.7 April2023 Dox (3d)

value: Dox (3d)


title: CL30.7 October2022 Dox (7d), Aux (9d)

value: Dox (7d), Aux (9d)


title: CL31.16 October2022 Control


title: RNASET2 PLD3 RNASE4 tKO no serum + FIP200 gRNA LysoIP rep 1

description: Library name: Lyso_FIP200_1

value: RNASET2 PLD3 RNASE4 tKO no serum


title: CL30.7 October2022 Aux (2d)


title: RNASET2 PLD3 RNASE4 tKO no serum + ATG7 gRNA whole cell rep 1

description: Library name: WC_ATG7_1

value: ATG7 gRNA 1


title: RNASET2 PLD3 RNASE4 tKO no serum + LARP1 gRNA whole cell rep 2

description: Library name: WC_LARP1_2

value: LARP1 gRNA 2


title: WT LysoIP Torin1 rep 2

description: Library name: WT_Lyso_Torin_2

value: WT


title: E6 September2022 Control

value: Xptet / R26rtTA


title: E6 October2022 Dox (7d) - washout (4d)

value: Dox (7d) - washout (4d)


title: RNASET2 KO Torin1 LysoIP rep 2

description: Library name: KO_Lyso_Torin_2

value: RNASET2 KO

value: LysoIP


title: CL31.16 October2022 Dox (7d), Aux (9d)

value: neural progenitor cell

value: Xptet / R26rtTA / SPEN-AID


title: E6 September2022 Dox (7d) - washout (7d)

value: Dox (7d) - washout (7d)


title: WT LysoIP Torin1 rep 1

description: Library name: WT_Lyso_Torin_1


title: RNASET2 PLD3 RNASE4 tKO no serum + ATG7 gRNA whole cell rep 2

description: Library name: WC_ATG7_2

value: ATG7 gRNA 2

value: whole cell


title: RNASET2 PLD3 RNASE4 tKO no serum Torin1 LysoIP rep 1

description: Library name: tKO_Lyso_Torin_1

value: RNASET2 PLD3 RNASE4 tKO

value: no serum Torin1


title: E6 September2022 Dox (7d)

value: C57BL6/J x CAST/EiJ

value: Dox (7d)


title: RNASET2 PLD3 RNASE4 tKO no serum Torin1 LysoIP rep 2

description: Library name: tKO_Lyso_Torin_2


title: WT LysoIP rep 2

description: Library name: WT_Lyso_2


title: WT LysoIP rep 1

description: Library name: WT_Lyso_1


title: RNASET2 KO Torin1 LysoIP rep 1

description: Library name: KO_Lyso_Torin_1


title: RNASET2 PLD3 RNASE4 tKO no serum + control gRNA whole cell rep 2

description: Library name: WC_Control_2

value: RNASET2 PLD3 RNASE4 tKO no serum

value: control gRNA 2


title: E6 March2022 Dox (7d)


title: E6 March2022 Dox (7d) - washout (4d)


title: E6 March2022 Dox (3d)

value: Dox (3d)


title: RNASET2 KO LysoIP rep 2

description: Library name: KO_Lyso_2


title: RNASET2 KO LysoIP rep 1

description: Library name: KO_Lyso_1


title: RNASET2 PLD3 RNASE4 tKO no serum LysoIP rep 2

description: Library name: tKO_Lyso_2

value: no serum


title: CL31 December2021 Dox (7d)


title: RNASET2 PLD3 RNASE4 tKO no serum + control gRNA whole cell rep 1

description: Library name: WC_Control_1

value: control gRNA 1


title: CL30 December2021 Dox (7d)


title: WT Torin1 whole cell rep 1

description: Library name: WT_WC_Torin_1

value: WT


title: CL30 December2021 Dox (3d)


title: WT Torin1 whole cell rep 2

description: Library name: WT_WC_Torin_2


title: CL31 December2021 Dox (3d)


title: CL31 December2021 Control

value: Control


title: E6 March2022 Control

value: Xptet / R26rtTA


title: Embryo41

description: AAFCTG2M5_E45doxSept23_23s002684-1-2_loda_lane1H2

data_processing:
Reads were trimmed using trim_galore (v0.6.6). To construct reference genomes for allele-specific mapping, genomes in which known heterozygous variants (https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.vcf.gz) were masked by the ambiguous base N were constructed using SNPsplit (SNPsplit_genome_preparation script, v0.5.0) and converted to STAR references (STAR v2.5.3a). Reads were aligned to the N-masked genomes using the options --sjdbOverhang 99 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 500000 --alignMatesGapMax 500000 --alignEndsType EndToEnd. Reads mapping to the mitochondrial genome were removed and split into parental genotypes using SNPsplit and known heterozygous variants. Gene-level read counts for each haplotype and without allelic resolution were derived using featureCounts (v2.0.1). The embryo RNA-Sequencing data was pre-processed as described above (Allele-specific preprocessing of RNA-Sequencing data), using the SNPs between C57BL/6J and JF1 mice (https://ftp.ebi.ac.uk/pub/databases/mousegenomes/REL-2112-v8-SNPs_Indels/mgp_REL2021_snps.vcf.gz). To confirm the annotated genotypes of the embryos, the rtTA transgene was included in the reference genome, and any embryo with >150 mapped transgene reads was considered rtTA-positive. For developmental staging, principal component analysis (prcomp, stats v4.2.0) was performed on total read counts after size-factor normalization (estimateSizeFactors, DESeq2, v1.36.0) and subsetting on highly variable genes (getTopHVGs, scran, v1.24.1). The first principal component separated embryo stages as determined by morphological staging and was used as a developmental pseudotime.
Assembly: GRCm39
Supplementary files format and content: delimited text files

source_name: whole embryo

extract_protocol:
Single embryos were picked and washed three times with transfer buffer (1X- PBS, 0.4% BSA) and transferred into 0.2 ml PCR tubes containing 2μl of lysis buffer (0.7% Triton X-100, 2U/μl RNasin (Promega), 1μl of oligo-dT30VN primer (10 μM 5'-aagcagtggttatcaacgcagagtact30vn-3') and 1 μl of 10 mM dNTP mix (Thermo Fisher).
Illumina libraries were prepared by using a modified smart-seq2 protocol [Picelli 2014] using SuperScript IV RT and tagmentation procedure as previously described [Henning 2018]. The RT reaction mix was as follows: 2 μl SSRT IV 5x buffer; 0.5 μl 100 mM DTT; 2 μl 5 M betaine; 0.1 μl 1 M MgCl2; 0.25 μl 40 U/μl RNAse inhibitor; 0.25 μl SSRT IV; 0.1 μl 100 uM TSO, 1.15 μl RNase-free H2O. RT thermal conditions: 52 °C 15 min, 80 °C 10 min. cDNA was generated using 16 PCR cycles. The cDNA cleanup (0.6x SPRI ratio) was carried out omitting the ethanol wash steps and the elution volume was 13 μl of H2O. For tagmentation, the sample input was normalized to 0.2 ng/μl. Obtained libraries that passed the QC step were pooled in equimolar amounts.
Libraries were sequenced at 50 bp paired-end on NextSeq 2000 platform.

treatment_protocol: Embryos were derived from natural mating between C57BL/6 TX males Xptet/Y; R26rtTA/WT (whole embryo RNA-seq) or Xptet/Y; R26rtTA/rtTA  with wild type JF1 females. Embryos were harvested at E2.5 and E3.5 and cultured in vitro in the presence of Doxycycline for 24 hours.

value: JF1 x C57BL6/J (Xptet/Y; R26rtTA/WT)

value: whole embryo

value: embryonic cells

value: Xptet

value: 24h doxycycline

tag: experiment number

tag: embryo stage


title: RNASET2 KO Torin1 whole cell rep 1

description: Library name: KO_WC_Torin_1

value: RNASET2 KO

value: whole cell


title: RNASET2 PLD3 RNASE4 tKO no serum Torin1 whole cell rep 2

description: Library name: tKO_WC_Torin_2

value: RNASET2 PLD3 RNASE4 tKO

value: no serum Torin1


title: Embryo40

description: AAFCTG2M5_E45doxSept23_23s002684-1-2_loda_lane1G4


title: CL30 December2021 Control

value: C57BL6/J x CAST/EiJ

value: neural progenitor cell

value: Xptet / R26rtTA / SPEN-AID


title: Embryo39

description: AAFCTG2M5_E45doxSept23_23s002684-1-2_loda_lane1G2


title: RNASET2 KO Torin1 whole cell rep 2

description: Library name: KO_WC_Torin_2


title: WT whole cell rep 1

description: Library name: WT_WC_1


title: Embryo38

description: AAFCTG2M5_E45doxSept23_23s002684-1-2_loda_lane1F4


title: Embryo37

description: AAFCTG2M5_E45doxSept23_23s002684-1-2_loda_lane1E1


title: WT whole cell rep 2

description: Library name: WT_WC_2


title: Embryo36

description: AAFCTG2M5_E45doxSept23_23s002684-1-2_loda_lane1D1


title: RNASET2 KO whole cell rep 2

description: Library name: KO_WC_2


title: Embryo35

description: AAFCTG2M5_E45doxSept23_23s002684-1-2_loda_lane1C6


title: RNASET2 PLD3 RNASE4 tKO no serum whole cell rep 2

description: Library name: tKO_WC_2

value: no serum


title: RNASET2 KO whole cell rep 1

description: Library name: KO_WC_1


title: Embryo34

description: AAFCTG2M5_E45doxSept23_23s002684-1-2_loda_lane1A6


title: RNASET2 PLD3 RNASE4 tKO no serum whole cell rep 1

description: Library name: tKO_WC_1


title: Embryo33

description: AACYJJ7M5_E45doxSept23_23s002684-1-1_loda_lane1B41H5


title: MT3

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

country: South Korea

institute: University of Ulsan College of Medicine

description: Library name: 4_MT200

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: hg19
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Mesenchymal stem cell

growth_protocol: MSCs derived from H9 human embryonic stem (hES) cells were maintained in endothelial cell medium (ECM; ScienCell Research Laboratories) on rat tail collagen typeⅠ-coated plates in a humidified and heated atmosphere of 5% CO₂ and 37℃.

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: The hES-MSCs were plated at a density of 2 × 10⁵ cells/mL in medium supplemented with 200 µM of melatonin (Sigma) for 24 hours before further evaluations.

value: Mesenchymal stem cell

value: Melatonin primed


title: RNASET2 PLD3 RNASE4 tKO no serum LysoIP rep 1

description: Library name: tKO_Lyso_1

value: LysoIP


title: NT3

description: Library name: 3_NT

value: non-treatment


title: Embryo32

description: AACYJJ7M5_E45doxSept23_23s002684-1-1_loda_lane1B39H2

value: JF1 x C57BL6/J (Xptet/Y; R26rtTA/WT)


title: Embryo31

description: AACYJJ7M5_E45doxSept23_23s002684-1-1_loda_lane1B35G2

value: whole embryo


title: NT2

description: Library name: 2_NT1


title: MT2

description: Library name: 3_MT200


title: Embryo30

description: AACYJJ7M5_E45doxSept23_23s002684-1-1_loda_lane1B34G1

value: embryonic cells

value: Xptet / R26rtTA


title: Embryo28

description: AACYJJ7M5_E45doxSept23_23s002684-1-1_loda_lane1B23D5

value: 24h doxycycline


title: Embryo26

description: AACYJJ7M5_E45doxSept23_23s002684-1-1_loda_lane1A1A1


title: MT1

description: Library name: 2_MT200


title: J.gamma1 shELOVL5_rep2

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

country: China

institute: Children’s Hospital of Soochow University

description: Library name: Sample 4

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Transcripts per Kilobase of exon model per Million mapped reads (TPM) were calculated using a methodology adapted from the StringTie software. In brief, all isoforms of a gene were assembled and merged to generate a composite transcript model. The number of reads mapped to the exonic regions of this composite transcript model was tallied and subsequently normalized. Normalization was achieved by dividing the read count by the length of the composite transcript model (in kilobases) and then scaling the result by the size of the total mapped library (in millions of reads).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample.

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: T-ALL cells


title: J.gamma1 shELOVL5_rep1

description: Library name: Sample 3


title: NT1

description: Library name: 1_NT


title: J.gamma1 shNC_rep2

description: Library name: Sample 2

value: shNC


title: Embryo27

description: AACYJJ7M5_E45doxSept23_23s002684-1-1_loda_lane1A6A6

value: Xptet


title: Embryo23

description: AACYJJ7M5_E45doxSept23_23s002684-1-1_loda_lane1A10B4


title: J.gamma1 shNC_rep1

description: Library name: Sample 1


title: Embryo24

description: AACYJJ7M5_E45doxSept23_23s002684-1-1_loda_lane1A12B6


title: Human PDAC tumor, patient 06, multiome (ATAC)

city: Stanford

first: Chuner

last: Guo

state: CA

address: 257 Campus Dr

department: Surgery

institute: Stanford University

description: Library name: PDAC06_ATAC

library_source: genomic single cell

data_processing:
Cell Ranger ARC (v2.0.2) was used to perform alignment, barcode processing, peak calling, and counting of both ATAC and GEX molecules.
Assembly: GRCh38
Supplementary files format and content: cell Ranger ARC (v2.0.2) was used to perform alignment, barcode processing, peak calling, and counting of both ATAC and GEX molecules.

source_name: pancreas

extract_protocol:
Single nuclei were extracted as previously described (Foster DS, Griffin M, Januszyk M, Delitto D, Norton JA, Longaker MT. Optimized Nuclei Isolation from Fresh and Frozen Solid Tumor Specimens for Multiome Sequencing. J Vis Exp. 2023. doi: 10.3791/65831. PMID: 37902368).
Libraries were made following the 10x Genomics Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide.

value: pancreas


title: Embryo25

description: AACYJJ7M5_E45doxSept23_23s002684-1-1_loda_lane1A18C6


title: Human PDAC tumor, patient 06, multiome (GEX)

description: Library name: PDAC06_GEX

molecule: polyA RNA


title: Embryo20

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s7A


title: Embryo19

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s6B


title: Embryo21

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s7B


title: Human PDAC tumor, patient 05, multiome (ATAC)

description: Library name: PDAC05_ATAC


title: Human PDAC tumor, patient 04, multiome (ATAC)

description: Library name: PDAC04_ATAC


title: Human PDAC tumor, patient 05, multiome (GEX)

description: Library name: PDAC05_GEX


title: Human PDAC tumor, patient 04, multiome (GEX)

description: Library name: PDAC04_GEX


title: Embryo17

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s5B


title: Embryo18

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s6A


title: Embryo16

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s5A


title: Embryo15

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s4B


title: Human PDAC tumor, patient 03, multiome (GEX)

description: Library name: PDAC03_GEX


title: Embryo29

description: AACYJJ7M5_E45doxSept23_23s002684-1-1_loda_lane1B33F5


title: Human PDAC tumor, patient 03, multiome (ATAC)

description: Library name: PDAC03_ATAC


title: Human PDAC tumor, patient 02, multiome (ATAC)

description: Library name: PDAC02_ATAC


title: RNASET2 PLD3 RNASE4 tKO no serum Torin1 whole cell rep 1

description: Library name: tKO_WC_Torin_1

value: RNASET2 PLD3 RNASE4 tKO

value: no serum Torin1

value: whole cell


title: Embryo14

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s3A


title: Embryo13

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s2B


title: Human PDAC tumor, patient 02, multiome (GEX)

description: Library name: PDAC02_GEX


title: Human PDAC tumor, patient 01, multiome (GEX)

description: Library name: PDAC01_GEX


title: Embryo11

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s20B


title: Embryo22

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s9B


title: Adiopicyte, OO, biol rep 3

city: Berkeley

first: Yuchen

last: He

state: California

address:
344 Morgan Hall, University of California
 Berkeley

department: Department of Nutritional Science and Toxicology

institute: University of California Berkeley

description:
OO3
counts_heterochronic_WAT_MPS.xlsx

data_processing:
FASTQ file generation was performed by Novogene using Illumina NovaSeq 6000
Original image data file from the high-throughput sequencing platform was transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files.
Alignment were performed with HISAT2
Gene expression level analysis, including PCA, hierarchical clustering
Differential expression analysis using pyDESeq2
Assembly: Homo_sapiens_Ensembl_94
Supplementary files format and content: .xlsx files includes raw gene counts info
Supplementary files format and content: .xlsx files includes sample metadata of each batch of experiments

source_name: G15.AO iPSC

extract_protocol:
Cells were exposed by cutting and exfoliating the cell chamber slab off the device then lysed in Trizol (#15596026, Invitrogen)
Library construction was performed by Novogene. The polyA enrichment library preparation procedure was used and resulted in the construction of 250-300 bp insert cDNA library.

value: G15.AO iPSC

value: Adipocyte

value: WT

value: MSC and adipogenic differentiation, PPARG lentivius transduction

tag: group

value: OO


title: Embryo9

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s1A

value: JF1 x C57BL6/J (Xptet/Y; R26rtTA/WT)


title: Adiopicyte, OO, biol rep 2

description:
OO2
counts_heterochronic_WAT_MPS.xlsx


title: Embryo10

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s1B

value: whole embryo


title: Embryo8

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s18A

value: embryonic cells


title: Embryo6

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s12B

value: Xptet / R26rtTA


title: Adiopicyte, OY, biol rep 3

description:
OY3
counts_heterochronic_WAT_MPS.xlsx

value: OY


title: Adiopicyte, OY, biol rep 2

description:
OY2
counts_heterochronic_WAT_MPS.xlsx


title: Embryo7

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s17A

value: 24h doxycycline


title: Embryo5

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s12A


title: Adiopicyte, OY, biol rep 1

description:
OY1
counts_heterochronic_WAT_MPS.xlsx


title: Embryo4

description: AACKYJCM5_E35_dox_Feb23_23s000758-1-1_loda_lane1s11

value: Morula


title: Adiopicyte, YO, biol rep 3

description:
YO3
counts_heterochronic_WAT_MPS.xlsx

value: YO


title: Embryo3

description: AACKYJCM5_E35_dox_Feb23_23s000758-1-1_loda_lane1s10

value: Xptet


title: Embryo2

description: AACKYJCM5_E35_dox_Feb23_23s000758-1-1_loda_lane1s8


title: Adiopicyte, YO, biol rep 2

description:
YO2
counts_heterochronic_WAT_MPS.xlsx


title: Adiopicyte, YO, biol rep 1

description:
YO1
counts_heterochronic_WAT_MPS.xlsx


title: Human PDAC tumor, patient 01, multiome (ATAC)

description: Library name: PDAC01_ATAC

value: pancreas


title: Embryo1

description: AACKYJCM5_E35_dox_Feb23_23s000758-1-1_loda_lane1s1


title: Embryo12

description: AACMTNTM5_EmbryoJF1Rtta2_23s001680-1-1_Kneuss_lane1s22B


title: Adiopicyte, YY, biol rep 3

description:
YY3
counts_heterochronic_WAT_MPS.xlsx

value: YY


title: S.aureus IMQ 3

city: San Diego

first: Eduardo

last: Ansaldo

address: 15550 Torrey Pines Rd

department: IMM

institute: Scripps Research

description: Library name: GEX 10x Lane 6

data_processing:
The initial processing of the expression data involved generating fastq files and count matrices using Cell Ranger v7.1.0 **[@zheng2017]** (10X Genomics, Pleasanton, CA) that was run with the “Include introns=True” option and the mm10-2020-A transcriptome reference. Processing of the expression data was performed with the 'cellranger count' and 'cellranger aggr' functions. After processing and aggregation, the estimated number of cells and mean reads per cell for each library were as follows: 48107 estimated number of cells, 21369 mean reads per cell (from 6 GEX libraries). The overall sequencing quality was high in the 6 mRNA libraries: \>90.3% of bases in the RNA reads had Q30 or above. Furthermore, across the 6 GEX libraries the median gene count per cell range was 708-819, the sequencing saturation ranged between 72-87%, and 61-71% of the reads mapped confidently to the transcriptome
The downstream analysis of the expression data was performed in R 4.4.2, the on expression matrix for each lane (filtered_feature_bc_matrix ) was loaded into Seurat version 4.4.0 **[@hao2021]** using the CreateSeuratObject function with min.cells=3. For filtering out low-quality nuclei, we established stringent thresholds for gene and UMI counts (1000 \< nCount_RNA \< 50000, 1000 \< nFeature_RNA \< 7500), and a maximum threshold for percentage mitochondrial content (percent.mt \< 6).
Log-normalization (LogNormalize) of the RNA count data for each lane was carried out using the NormalizeData function. The top 2000 variable features were determined with the VariableFeatures function, expression data was scaled with ScaleData, and dimensionality reduction was performed with the RunPCA function on the variable features, followed by determining the dimensionality of the dataset on an elbow plot (ElbowPlot function), which was determined to be 35. Subsequently, FindNeighbors, FindClusters, and RunUMAP were run on 35 dimensions and a resolution of 0.5.
Data for the different lanes was integrated using the SelectIntegrationFeatures, FineIntegrationAnchors, and IntegrateData functions. Subsequently, on the integrated dataset, FindVariableFeatures (nFeatures=2000) was run, data was scaled with ScaleData, RunPCA was run (npcs=100) and the top 32 dimensions were used to run FindNeighbors, FindClusters (with a range of resolutions and a final chosen resolution of 0.25), and RunUMAP.
Clusters were annotated using cell type specific markers, cluster specific differentially expressed genes, and gene signatures obtained from published datasets (Usokin et al, Renthal et al, Sharma et al). Gene signatures were computed with UCell **[@andreatta2021]**.
Assembly: mm10
Supplementary files format and content: The filtered_feature_bc_matrix.h5 file contains the gene expression output of the cellranger (10x Genomics) count commands.
Supplementary files format and content: The .rds file contains the final Seurat object, product of the analysis described in the processing step section.

source_name: Dorsal root ganglion

extract_protocol:
Single nuclei were isolated from dorsal root ganglion as described in the manuscript's methods section.
10000 nuclei per lane isolated from dorsal root ganglion of mice (total of 6 lanes, 3 Control and 3 S. aureus IMQ) were loaded on a Chromium Single Cell Controller (10X Genomics) to encapsulate the nuclei into droplets. The gene expression (GEX) library was prepared using Chromium Single Cell 5’ v2 reagent kits following the manufacturer’s instructions, and sequenced on an Illumina Nextseq2000 platform

value: Dorsal root ganglion


title: Adiopicyte, YY, biol rep 1

description:
YY1
counts_heterochronic_WAT_MPS.xlsx

value: G15.AO iPSC


title: Adiopicyte, YY, biol rep 2

description:
YY2
counts_heterochronic_WAT_MPS.xlsx

value: Adipocyte


title: Adiopicyte, OY, biol rep 4

description:
OY3_1
counts_heterochronic_WAT_MPS.xlsx

value: WT


title: Control 3

description: Library name: GEX 10x Lane 3


title: Adiopicyte, Not treated, biol rep 3

description:
Ctrl3
counts_heterochronic_WAT_MPS.xlsx

value: MSC and adipogenic differentiation, PPARG lentivius transduction

value: Not treated


title: Adiopicyte, Not treated, biol rep 2

description:
Ctrl2
counts_heterochronic_WAT_MPS.xlsx


title: S.aureus IMQ 1

description: Library name: GEX 10x Lane 4


title: S.aureus IMQ 2

description: Library name: GEX 10x Lane 5


title: Adiopicyte, female YCM 2, biol rep 3

description:
FY2_3
counts_OCM_YCM_treated_WAT_MPS.xlsx

value: female YCM 2


title: Adiopicyte, Not treated, biol rep 1

description:
Ctrl1
counts_heterochronic_WAT_MPS.xlsx


title: Adiopicyte, female YCM 2, biol rep 1

description:
FY2_1
counts_OCM_YCM_treated_WAT_MPS.xlsx


title: Control 2

description: Library name: GEX 10x Lane 2


title: Adiopicyte, Control sample for OF2

description:
OF2_ctrl
counts_OCM_YCM_treated_WAT_MPS.xlsx

value: Control sample for OF2


title: Adiopicyte, female OCM 2, biol rep 4

description:
OF2_4
counts_OCM_YCM_treated_WAT_MPS.xlsx

value: female OCM 2


title: Adiopicyte, female OCM 2, biol rep 2

description:
OF2_2
counts_OCM_YCM_treated_WAT_MPS.xlsx


title: Adiopicyte, female OCM 2, biol rep 1

description:
OF2_1
counts_OCM_YCM_treated_WAT_MPS.xlsx


title: Adiopicyte, Control sample for OF1 and FY2

description:
OF1_FY2_ctrl
counts_OCM_YCM_treated_WAT_MPS.xlsx

value: Control sample for OF1 and FY2


title: Adiopicyte, female OCM 1, biol rep 1

description:
OF1_1
counts_OCM_YCM_treated_WAT_MPS.xlsx

value: female OCM 1


title: M200_IP_Bp-females

city: Baltimore

first: Julie

last: Dunning Hotopp

state: MD

address: 670 W Baltimore St

institute: University of Maryland, Baltimore

description: Library name: IL100190689

data_processing:
Read adapters were trimmed with Trimmomatic
Reads were aligned to the Brugia pahangi genome using HiSAT2
Read counts were generated using htseq-count
Assembly: Brugia pahangi FR3 ASM1207055v1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: edgeR DGEList object containing the counts and samples object, the DGELRT object with pvalues, and the TPM values per sample

organism: Brugia pahangi

source_name: Whole organism

extract_protocol:
RNA was isolated using NEB Biolabs Monarch Total RNA Miniprep kit (T2010)
polyA libraries were constructed with the NEBNext Ultra II Directional RNA for Library Prep kit

value: Whole organism


title: M055_SQ_Bp-females

description: Library name: IL100190659


title: M200_IP_Bp-males

description: Library name: IL100208181


title: Adiopicyte, female OCM 1, biol rep 4

description:
OF1_4
counts_OCM_YCM_treated_WAT_MPS.xlsx


title: Adiopicyte, Control sample for YF1

description:
YF1_Ctrl
counts_OCM_YCM_treated_WAT_MPS.xlsx

value: Control sample for YF1


title: M055_SQ_Bp-mf

description: Library name: IL100190666


title: M057_SQ_Bp-males

description: Library name: IL100190680


title: Adiopicyte, male OCM 1, biol rep 3

description:
Fat_OM1_3
counts_OCM_YCM_treated_WAT_MPS.xlsx

value: male OCM 1


title: Adiopicyte, male OCM 1, biol rep 2

description:
Fat_OM1_2
counts_OCM_YCM_treated_WAT_MPS.xlsx


title: M057_SQ_Bp-mf

description: Library name: IL100190671


title: Control 1

description: Library name: GEX 10x Lane 1


title: Adiopicyte, female YCM 1, biol rep 1

description:
YF1_1
counts_OCM_YCM_treated_WAT_MPS.xlsx

value: female YCM 1


title: Adiopicyte, male OCM 1, biol rep 1

description:
Fat_OM1_1
counts_OCM_YCM_treated_WAT_MPS.xlsx


title: Adiopicyte, Control sample for MY1 and Fat_OM1

description:
MY1_ctrl
counts_OCM_YCM_treated_WAT_MPS.xlsx

value: Control sample for MY1 and Fat_OM1


title: M069_SQ_Bp-females

description: Library name: IL100208180


title: Adiopicyte, male YCM 1, biol rep 3

description:
MY1_3
counts_OCM_YCM_treated_WAT_MPS.xlsx

value: male YCM 1


title: M069_SQ_Bp-mf

description: Library name: IL100190675


title: NC_3

type: RNA

city: Jinan

first: Lan

address: jingsi

institute: Shandong University

description: Gene expression of human blood-derived exocrine

hyb_protocol: The biotinylated cRNA targets were then hybridized with the slides.

scan_protocol: After hybridization, slides were scanned on the Agilent Microarray Scanner G5761A (Agilent technologies, Santa Clara, CA, US).

data_processing: Data were extracted with Feature Extraction software 12.0.3.1 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm. The microarray experiments were performed by following the protocol of Agilent technologies at LC Sciences Corporation （Hangzhou，China）

source_name: Exosomes derived from peripheral blood

label_protocol: RNA samples of each group were then used to generate biotinylated cRNA targets for the LC Human ceRNA array V1.0（4*180K, Design ID:085202）.

extract_protocol: Total RNA was isolated using RNA Isolation Kit #58000(Norgen, Canada) according to the manufacturer’s instructions, and purified by using a RNeasy Mini Kit (Qiagen, Germany) .Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: gender

value: female

value: whole blood


title: Adiopicyte, male YCM 1, biol rep 2

description:
MY1_2
counts_OCM_YCM_treated_WAT_MPS.xlsx

value: G15.AO iPSC

value: Adipocyte


title: NC_2

tag: tissue


title: NC_1


title: F006_IP_Bp-males

description: Library name: IL100190658


title: APS_2


title: Adiopicyte, male YCM 1, biol rep 1

description:
MY1_1
counts_OCM_YCM_treated_WAT_MPS.xlsx

tag: cell type

value: WT

value: MSC and adipogenic differentiation, PPARG lentivius transduction


title: APS_3


title: 505_STA123A172

city: Pittsburgh

first: Laura

middle: P

last: Stabile

state: Pennsylvania

address: 5117 Centre Avenue

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh, PA, USA

data_processing:
stats4    splines   grid      parallel  stats     graphics  grDevices utils     datasets  methods   base
Assembly: grch38
Supplementary files format and content: excel file with name: processed_data.xlsx

source_name: Brain metastasis

extract_protocol:
RNA was harvested using  Zymo Quick RNA FFPE Extraction Kit according to the manufacturer’s protocol.
RNA libraries for RNAseq were prepared using Illumina RNA Exome Kit following manufacture's protocol.

tag: disease

value: lung adenocarcinoma

value: Brain metastasis


title: 86_STA123A100


title: F012_IP_Bp-females

description: Library name: IL100190661


title: F006_IP_Bp-mf

description: Library name: IL100190691


title: 500_STA123A169


title: F012_IP_Bp-mf

description: Library name: IL100190673


title: F015_SQ_Bp-males

description: Library name: IL100190656


title: 19_0051_2_STA123A147

source_name: Lung tumor

value: Lung tumor


title: M057_SQ_Bp-females

description: Library name: IL100190681


title: F009_IP_Bp-females

description: Library name: IL100190660


title: 228_STA123A163


title: APS_1


title: F015_SQ_Bp-females

description: Library name: IL100190657


title: 19_0050_2_STA123A146


title: 19_0049_2_STA123A145


title: M204_IP_Bp-males

description: Library name: IL100198854


title: 19_0048_2_STA123A144


title: 19_0047_2_STA123A143


title: F022_SQ_Bp-females

description: Library name: IL100190669


title: F022_SQ_Bp-males

description: Library name: IL100190668


title: 19_0045_2_STA123A141


title: 19_0046_2_STA123A142


title: 19_0044_2_STA123A140


title: 19_0040_2_STA123A138


title: WT, t60 alpha-factor Rep2

city: Bethesda

first: Hernan

middle: A

last: Lorenzi

state: Maryland

address: 8 Center Dr, Bldg 8A

department: National Institutes of Diabetes and Digestive and Kidney Diseas

institute: National Institutes of Health

description: Library name: VM-4

data_processing:
Fastq files from sequencing were trimmed of remaining sequencing adaptors and low-quality sequences using bbtools.
The resulting fastq files were aligned to the sacCer3 reference genome using STAR
Duplicate reads were removed and a table of read counts per gene per sample were generated using featureCounts
Assembly: sacCer3
Supplementary files format and content: Tabulated file with read counts per sample per gene

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown overnight at 30ºC in YPGal (1% yeast extract, 2% peptone, and 2% galactose) to mid-log phase and then centrifuged and resuspended in YPD (1% yeast extract, 2% peptone, and 2% glucose) for 3 hours in order to arrest cells in G1 (Figure 1A).

extract_protocol:
Total RNA was prepared using SDS, hot acid phenol, and chloroform
Libraries for RNA-sequencing were prepared using "Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus" kits (with 50-nt sequencing) from total RNA. During the reverse-transcription step of library preparation, removal of cytoplasmic and mitochondrial rRNA was done using the QIAseq FastSelect -rRNA Yeast Kit.

treatment_protocol: After the 3-hour synchronization, half of the culture was pelleted, the YPD was removed, and the pellet was flash frozen in liquid nitrogen for RNA extraction. To the second half of the culture, alpha-factor (10mM in 0.1 M sodium acetate pH 5.2, Zymo Research) was added at a 1:500 ratio (20 µM final concentration) for 60 minutes before the same freezing process was done.

value: MATa

tag: genotype

value: MATa ade1 bar1 cln1 cln2 cln3 his2 leu2:LEU2::GAL-CLN3 trp1 ura3

tag: treatment

value: alpha-factor


title: F024_SQ_Bp-males

description: Library name: IL100210465

value: Whole organism


title: WT, t60 no alpha-factor, Rep2

description: Library name: VM-3

tag: cell line

tag: batch


title: 40_STA123A151


title: F006_IP_Bp-females

description: Library name: IL100190692


title: 96_STA123A154


title: WT, t60 alpha-factor Rep1

description: Library name: VM-2


title: 87_STA123A152


title: 231_STA123A164


title: F015_SQ_Bp-mf

description: Library name: IL100190667


title: M069_SQ_Bp-males

description: Library name: IL100190679


title: F009_IP_Bp-mf

description: Library name: IL100190676


title: F024_SQ_Bp-females

description: Library name: IL100208175


title: 19_0037_2_STA123A135


title: WT, t60 no alpha-factor, Rep1

description: Library name: VM-1


title: F012_IP_Bp-males

description: Library name: IL100190685


title: F022_SQ_Bp-mf

description: Library name: IL100208177


title: 19_0036_2_STA123A134


title: F024_SQ_Bp-mf

description: Library name: IL100208176


title: 19_0035_2_STA123A133


title: M204_IP_Bp-females

description: Library name: IL100198853


title: 19_0024_2_STA123A124


title: 19_0039_2_STA123A137


title: ime4, alpha-factor, Rep4

description: Library name: AY65

value: MATa ade1 bar1 cln1 cln2 cln3 his2 leu2:LEU2::GAL-CLN3 trp1 ura3 ime4::KanMX


title: 19_0022_2_STA123A123


title: 19_0038_2_STA123A136


title: M204_IP_Bp-mf

description: Library name: IL100208182


title: 19_0018_2_STA123A119


title: 19_0020_2_STA123A121


title: 19_0017_2_STA123A118


title: ime4, alpha-factor, Rep2

description: Library name: AY57


title: 19_0016_2_STA123A117


title: ime4, alpha-factor, Rep1

description: Library name: AY56


title: 19_0014_2_STA123A116


title: M206_IP_Bp-females

description: Library name: IL100190655


title: 19_0010_2_STA123A112


title: 19_0009_2_STA123A111


title: M206_IP_Bp-mf

description: Library name: IL100190677


title: ime4, None, Rep4

description: Library name: AY63


title: 18_0422_2_STA123A149


title: ime4, None, Rep2

description: Library name: AY55


title: M055_SQ_Bp-males

description: Library name: IL100190664


title: 18_0421_2_STA123A148


title: 172_STA123A101


title: ime4, None, Rep3

description: Library name: AY62


title: 170_STA123A160


title: ime4, None, Rep1

description: Library name: AY54


title: 169_STA123A159


title: ime4, alpha-factor, Rep3

description: Library name: AY64


title: 116_STA123A156


title: M206_IP_Bp-males

description: Library name: IL100190654


title: CAR22/41BB/CD3z-short linker, BACH2 CRISPR KO, end of manufacturing, rep 3

city: St. Louis

first: Nathan

last: Singh

address: 660 S Euclid Ave

institute: Washington University School of Medicine in St Louis

description: Library name: M_BBs(BACH2 KO)-3

data_processing:
In brief, paired-end reads were trimmed for adapters and low-quality bases and aligned to hg38 using Bowtie version 2.5.4. PCR duplicates were removed and for CUT&RUN fragments were truncated to 120 base pairs to enrich mononucleosome-sized fragments.  Sorted BAM files were used for peak calling with MACS2, and resulting narrow peaks were filtered against the ENCODE blacklist. Peak sequences were extracted for downstream motif and footprinting analyses. Differential binding analysis was performed using DiffBind (v3.18.0) with DESeq2 (1.48.2) framework and default settings after resizing peaks to 500 bp around summits. Genomic annotation of peaks and nearest-gene mapping were performed using ChIPseeker (v1.44.0) with the default settings.
Assembly: hg38
Supplementary files format and content: narrowPeak

source_name: Peripheral blood mononuclear cells

growth_protocol: Primary Human T cells  were grown in RPMI media with 10% FBS, 1% Pen/Strep, 1% HEPES, 1% L-glutamine in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
ATAC library preparation was done by standard methods(45). 50,000 CAR T cells were used per reaction and index primers for sequencing acquired were from IDT for Illumina DNA/RNA UD Indexes plate A (Illumina 20027213), then size selection of fragments (< 600bp) was done using SPRIselect Beads (Beckman Coulter, Inc.).
ATAC library preparation was done by standard methods(45). 50,000 CAR T cells were used per reaction and index primers for sequencing acquired were from IDT for Illumina DNA/RNA UD Indexes plate A (Illumina 20027213), then size selection of fragments (< 600bp) was done using SPRIselect Beads (Beckman Coulter, Inc.).

treatment_protocol: Cells were stimulated on CD3/CD28 dynabeads at a ratio of 3 beads : 1 T cell. The following day, different lentiviral vectors encoding CAR or BACH2 were co-transduced into T cells. Beads were removed on day 6 after bead stimulation and cells were expanded for 8 more days prior to collection for genomic DNA purification. For chronic stimulation, CAR+ T cells with truncated CD34 were magnetically sorted with CD34-PE and anti-PE microbeads, and BACH2-overexpressed CAR+ T cells with truncated EGFR were magnetically sorted with EGFR-PE and anti-PE microbeads. Absolute count of CD34+ T cells and GFP+ Nalm6 were evaluated by flow cytometry and combined with an targeted E:T ratio. The absolute count of T cell and Nalm6 in this co-culture were re-evaluated every 2-3 days by flow cytometry and fresh cancer cells were added to maintain an targeted E:T ratio. On day 7 after co-culture, dead cells were removed, then CAR+ T cells were magnetically sorted again.

value: Peripheral blood mononuclear cells

value: primary human T cells

value: CAR22-short linker/41BB/CD3z with BACH2 KO


title: CAR22/41BB/CD3z-short linker, BACH2 CRISPR KO, end of manufacturing, rep 2

description: Library name: M_BBs(BACH2 KO)-2


title: SG_HCT_SOG_Control_seq_rep2

city: Boston

first: Jarrett

last: Smith

address: 455 Main st, Room 627

institute: Whitehead Institute

description:
RNA seq of SG purified fraction
cts_SGseq.csv

data_processing:
DESeq2
Assembly: hg38
Supplementary files format and content: Comma-delimited files containing read counts for all samples.
Supplementary files format and content: Supplemental Excel tables that summarize the sequencing data.

growth_protocol: All cells were cultured at 37°C with 5% CO2 using McCoy’s 5A medium supplemented with 10% fetal bovine serum (FBS) and 2mM L-glutamine

extract_protocol:
Ribosome profiling and matched RNA seq libraries were then prepared according to previously established protocol, a detailed version of which is available at http://bartellab.wi.mit.edu/ protocols.html.
Ribosome profiling and matched RNA seq libraries were then prepared according to previously established protocol, a detailed version of which is available at http://bartellab.wi.mit.edu/ protocols.html.

treatment_protocol: Cells were either treated with 500 μM IAA (depletion), 500 μM sodium arsenite for 1 hr (oxidative stress), or 45°C incubation for 25 min (heatshock)

value: oxidative stress


title: WT, alpha-factor, Rep2

description: Library name: AY53


title: CAR22/41BB/CD3z-short linker, BACH2 CRISPR KO, end of manufacturing, rep 1

description: Library name: M_BBs(BACH2 KO)-1


title: M200_IP_Bp-mf

description: Library name: IL100190690


title: 504_STA123A171


title: CAR22/41BB/CD3z-short linker, end of manufacturing, rep 3

description: Library name: M_BBs-3

value: CAR22-short linker/41BB/CD3z


title: 168_STA123A158


title: F009_IP_Bp-males

description: Library name: IL100190684


title: Cyto_HCT_SOG_Control_seq_rep2

description:
RNA seq of total cytoplasmic RNA
cts_SGseq.csv


title: SG_HCT_OG_Control_seq_rep2

value: dox; oxidative stress


title: CAR22/41BB/CD3z-short linker, end of manufacturing, rep 2

description: Library name: M_BBs-2


title: Cyto_HCT_OG_Control_seq_rep2


title: WT, alpha-factor, Rep3

description: Library name: AY60


title: SG_HCT_WT_SOG_seq_rep2

value: dox; oxidative stress; blue light


title: WT, alpha-factor, Rep1

description: Library name: AY52


title: SG_HCT_WT_OG_seq_rep2

value: dox; blue light


title: WT, None, Rep4

description: Library name: AY59


title: Cyto_HCT_WT_OG_seq_rep2


title: WT, alpha-factor, Rep4

description: Library name: AY61


title: 133_STA123A157


title: CAR22/41BB/CD3z-long linker, end of manufacturing, rep 3

description: Library name: M_BBL-3

value: WT

value: CAR22-long linker/41BB/CD3z


title: WT, None, Rep2

description: Library name: AY51


title: Cyto_HCT_SOG_Control_seq_rep1


title: WT, None, Rep3

description: Library name: AY58


title: CAR22/41BB/CD3z-long linker, end of manufacturing, rep 2

description: Library name: M_BBL-2


title: SG_HCT_OG_Control_seq_rep1


title: Cyto_HCT_OG_Control_seq_rep1


title: CAR22/41BB/CD3z-long linker, end of manufacturing, rep 1

description: Library name: M_BBL-1


title: SG_HCT_OG_seq_rep1


title: Cyto_HCT_SOG_seq_rep1


title: CAR22/CD28/CD3z-short linker, end of manufacturing, rep 3

description: Library name: M_28s-3

value: CAR22-short linker/CD28/CD3z


title: ∆Ste12, alpha-factor, 1hs, Rep4, batch_2

description: Library name: AY38

value: MATa ade1 bar1 cln1 cln2 cln3 his2 leu2:LEU2::GAL-CLN3 trp1 ura3 ste12::KanMX


title: SG_HCT_SOG_seq_rep1


title: Cyto_HCT_OG_seq_rep1


title: WT, None, Rep1

description: Library name: AY50

value: MATa