title: S2G8


title: S2G6

status: Public on Jun 25 2024

type: SRA

city: Edmonton

first: Patrick

middle: E

last: MacDonald

state: Alberta

address: 6-126 Li Ka Shing Centre

country: Canada

institute: University of Alberta

library_source: transcriptomic single cell

data_processing:
Mapped to Gch38 using STAR
Gene counts using htseq-count
Assembly: GRCh38
Supplementary files format and content: Combined csv count table of all cells

molecule: total RNA

organism: Homo sapiens

source_name: Human Donor Islet Cell

extract_protocol: SmartSeq2 (21X-23X PCR cycles)

tag: cell type

value: Human Donor Islet Cell

tag: Sex

value: Female

tag: disease state

value: ND

tag: patched

value: Yes


title: S2G5


title: S2H1

value: Male


title: T2A6


title: S2G4


title: S2G12


title: S2G10


title: S2G11


title: T2A11


title: S2G2


title: S2F9


title: S2F7


title: S2F8


title: S2F5


title: S2H11


title: S2F3


title: S2F12


title: S2F2


title: S2F6


title: S2F11


title: S2F10


title: S2E8


title: S2E6


title: S2E5


title: S2G3


title: S2E7


title: S2E3


title: S2E2


title: S2E12


title: S2E10


title: S2E4


title: S2D9


title: S2E11


title: S2G1


title: Psoriasis_PN_257

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
The Seurat R software package (version 3.0) in R (version 3.6.2) was utilized for analysis of scRNA seq-data. Cells with nCount_RNA > 50000, nFeature > 1500, and External RNA Control Consortium (ERCC) RNA Spike-In < 15% were included in the analysis. Normalized datasets were integrated, scaled, followed by principal component analysis. Two-dimensional map coordinates were generated using the ‘RunUMAP’ procedure. Cluster analysis was performed using the ‘FindNeighbors’ and ‘FindClusters’ functions. Marker genes for clusters were identified using the ‘FindMarkers’ function. The Wilcoxon rank-sum test was used to identify differentially expressed genes (DEGs) among clusters to define cell states and was then repeated for each resultant cell type to further characterize subpopulations. The online tool EnrichR was used to perform Gene Ontology (GO) Biological Processes (BP) analysis on the significantly DEGs extracted from different pairs of comparision21. CIM-seq analysis22, an unsupervised method to analyze direct physical cell–cell interactions, was performed on RNAseq data from identified doublets/multiplets with FSC-W values exceeding 300.
Assembly: hg38
Supplementary files format and content: count matrix

molecule: polyA RNA

source_name: Skin

extract_protocol:
Four-mm full-depth punch biopsies were obtained from lesional and non-lesional skin of five untreated psoriasis patients and three sex- and age-matched healthy donors. Skin biopsies were enzymatically digested with dispase (5 U/ML, Gibco) overnight to separate the epidermis from the dermis, followed by dissociation of the epidermis to single cells using a protocol optimized to achieve partial dissociation (0.5 % trypsin, 1 U ul−1 DNase, Gibco) for 7 min at 37 °C to obtain both single cells and multiplets. In the single-cell suspensions, cells were counted and diluted to 1 × 106 cells per 100 ul with ice-cold FACS buffer, followed by incubation with dye-conjugated antibodies, including anti-CD45 (APC, eBioscience). After sorting into 384-well plates with hypotonic lysis buffer using a SONY SH800S sorter, both CD45-positive and CD45-negative cells were sorted, excluding dead/dying cells, and stored at -80 °C.
cDNA synthesis was based on the Smart-seq2 protocol as implemented in (Andrews et al. Nat. Meth. 2021). In summary, single-cell lysates were thawed on ice in 384-well plates, followed by primer annealing at 72°C for 3 minutes. Subsequently, a reverse transcription (RT) mix of 3 ul was added (0.05 ul of Maxima H Minus Reverse Transcriptase [Thermo Scientific, EP0751], 0.125 ul of Recombinant RNase Inhibitor [Takara Bio, 2313B], 1 ul of 5x First strand buffer, 0.25 ul of 100mM DTT [Thermo Fisher 707265ML], 1 ul of 5M Betaine [Sigma-Aldrich, B0300-5VL], 0.03 ul of 1M MgCl2, 0.05 ul of 100uM TSO [IDT 5′-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3′], and 0.495 ul of H2O). The RT reaction was 42°C for 90 minutes, followed by 70°C for 5 minutes and a 4°C hold. Next, 7.5 ul of cDNA pre-amplification mix was added, consisting of 1.068 ul of H2O, 6.25 ul of 2X Kapa HiFi HotStart ReadyMix (Roche 07958927001), 0.125 ul of 10 uM IS_PCR primer (IDT 5′-AAGCAGTGGTATCAACGCAGAGT-3′), and 0.056 ul of Lambda Exonuclease (ThermoFisher EN0561). The PCR program was 37°C for 30 minutes, 95°C for 3 minutes, followed by [98°C for 20 seconds, 67°C for 15 seconds, 72°C for 4 minutes] repeated for 21 cycles, and a final step of 72°C for 5 minutes, with a 4°C hold. Post-PCR, cDNA clean-up was performed using 0.7X volume SPRI beads and a magnetic 384-well rack. For tagmentation, 1 ul of diluted cDNA (150 pg/ul) was mixed with 1.5 ul of tagmentation buffer (0.5 ul TAP-PEG buffer [50mM TAPS, 25mM MgCl2, 40% PEG 8k) with 0.75 ul H2O)] and 0.25 ul of Tn5 (Vasilios 2020), followed by incubation at 55°C for 10 minutes. Upon completion, Tn5 was inactivated by adding 1 ul of 0.1% SDS (Teknova S0287). Barcoding PCR was performed on the same plate by adding 19.5 ul of PCR mix (Roche7958846001, 13.25 ul of H2O, 5 ul of 5X buffer, 0.75 ul of dNTPs, and 0.5 ul of KAPA HiFi DNA Polymerase) and 2 ul of primers. The total volume of 25 ul underwent the following PCR cycling: 72°C for 3 minutes, 95°C for 30 seconds, [95°C for 15 seconds, 55°C for 30 seconds, 72°C for 45 seconds] repeated for 12 cycles, and a 10°C hold. Finally, 2 ul per well was pooled and subjected to SPRI bead clean-up at 0.9X volume twice. The finished libraries were sequenced on an Illumina NextSeq 550 sequence paired-end 37bp with 8bp dual index.

tag: tissue

value: Skin

tag: ncount rna

tag: nfeature rna

tag: donor

tag: diagnosis

value: Psoriasis

tag: region

value: PN

tag: class

value: singlet

tag: seurat clusters

tag: celltype

value: Basal keratinocytes III


title: S2D8


title: S2F4


title: S2E1


title: S2D7


title: S2D6


title: 11JJ-CCR5kd-plus-stroke-chronic

city: Bar Harbor

first: Mary

middle: Teena

last: Joy

state: Maine

address: 600 Main St

country: USA

institute: Jackson Laboratory

library_source: transcriptomic

data_processing:
Paired-end reads were aligned to the mouse reference transcriptome, EnsDb.Mmusculus.v79, using Kallisto. Count data expressed as transcripts per million (TPM) for each transcript was estimated by Kallisto and the abundance files generated were read into R using the txi import function and the EnsDb package to produce a count matrix of genes and TPMs. Using EdgeR, counts per million (CPM) for each gene was generated and genes with less than 1 CPM in 2 samples per condition were filtered out. The total number of genes in the datasets detected following filtering were 16,662 genes for neurons and 27,830 for microglia. Normalization factors using the trimmed mean of M-values method were calculated on log2 transformed CPM data as a scaling factor for library sizes. Any batch effects from experimental day and FACS counts from samples with low events were corrected for using the removeBatchEffect function (in-built into the limma package. The final expression data are thus expressed as TMM normalized log2CPM.
Assembly: EnsDb.Mmusculus.v79
Supplementary files format and content: Counts are available in *abundance.tsv and proceesed and filtered final data are in log2.cpm.filtered.norm_batch_corrected.df.txt for neuronal samples and log2.cpm.filtered.norm.df.microglia.txt for microglial samples.
Supplementary files format and content: .tsv and .txt

organism: Mus musculus

source_name: Brain, cortex

extract_protocol:
RNA was extracted using a Zymo RNA micro extraction kit in accordance with manufacturer’s guidelines
cDNA was generated and amplified using the SMART seq v4 ultra low input and SSv4 PLUS kits from Clonetech and libraries were prepared with Nextera XT DNA Library Preparation

value: Brain, cortex

value: Microglia

tag: genotype

value: WT

tag: treatment

value: Stroke 30d + CCR5 knockdown


title: S2F1


title: S2E9


title: 11II-CCR5kd-plus-stroke-chronic


title: 11GG-CCR5kd-plus-stroke-chronic


title: S2D5


title: S2D4


title: S2D2


title: S2D11


title: 8GG-Control-LV-plus-stroke-chronic

value: Stroke 30d + Control virus


title: 11FF-CCR5kd-plus-stroke-chronic


title: S2D3


title: 8II-Control-LV-plus-stroke-chronic


title: S2D1


title: 8HH-Control-LV-plus-stroke-chronic


title: 8FF-Control-LV-plus-stroke-chronic


title: S2C9


title: S2D12


title: S2D10


title: 7JJ-CREB-plus-stroke-chronic

value: Stroke 30d +CREB overexpression


title: 8JJ-Control-LV-plus-stroke-chronic


title: S2C5


title: S2C4


title: 6GG-CCR5kd-plus-stroke-acute

value: Stroke 7d +CCR5 knockdown


title: 6FF-CCR5kd-plus-stroke-acute


title: S2C3

value: Human Donor Islet Cell


title: 7II-CREB-plus-stroke-chronic


title: S2C7

value: Female


title: S2C8

value: ND


title: 7HH-CREB-plus-stroke-chronic


title: 7GG-CREB-plus-stroke-chronic


title: 7FF-CREB-plus-stroke-chronic


title: S2C6

value: Yes


title: S2C2

value: Male


title: S2C12


title: 6JJ-CCR5kd-plus-stroke-acute


title: 2II-Control-AAV-plus-stroke-acute

value: Stroke 7d +Control virus


title: S2C10


title: 6II-CCR5kd-plus-stroke-acute


title: 2JJ-Control-AAV-plus-stroke-acute


title: 2HH-Control-AAV-plus-stroke-acute


title: S2B9


title: S2C11


title: 2GG-Control-AAV-plus-stroke-acute


title: S2B8


title: 5HH-CREB

value: CREB over expression


title: S2C1


title: 5II-CREB


title: S2B5


title: S2B7


title: 3JJ-Naive

value: No treatment


title: 2FF-Control-AAV-plus-stroke-acute


title: 4FF-CCR5kd

value: CCR5 knockdown


title: 4GG-CCR5kd


title: S2B2


title: S2B10


title: 3HH-Naive


title: 4II-CCR5kd


title: S2B3


title: 3II-Naive


title: S2B6


title: S2B11


title: S2B4


title: S2B12


title: 11I-CCR5kd-plus-stroke-chronic

value: Neurons


title: 3GG-Naive

value: Brain, cortex


title: 11H-CCR5kd-plus-stroke-chronic


title: S2A8


title: 11G-CCR5kd-plus-stroke-chronic


title: S2B1


title: 8J-Control-LV-plus-stroke-chronic


title: S2A5


title: 11F-CCR5kd-plus-stroke-chronic


title: S2A6


title: 8H-Control-LV-plus-stroke-chronic


title: 8F-Control-LV-plus-stroke-chronic


title: 11J-CCR5kd-plus-stroke-chronic


title: 7J-CREB-plus-stroke-chronic


title: 7I-CREB-plus-stroke-chronic


title: S2A2


title: S2A3


title: S2A9


title: 8G-Control-LV-plus-stroke-chronic


title: S2A11


title: 7G-CREB-plus-stroke-chronic


title: S2A10


title: S2A7


title: 6I-CCR5kd-plus-stroke-acute


title: S2A1


title: B3H9


title: B3H8


title: 6H-CCR5kd-plus-stroke-acute


title: S2A4


title: 6G-CCR5kd-plus-stroke-acute


title: B3H6


title: B3H7


title: 2J-Control-AAV-plus-stroke-acute


title: B3H5


title: B3H4


title: B3H3


title: 2I-Control-AAV-plus-stroke-acute


title: S2A12


title: 7H-CREB-plus-stroke-chronic


title: 2G-Control-AAV-plus-stroke-acute


title: B3H2


title: 6J-CCR5kd-plus-stroke-acute


title: B3H12


title: 2H-Control-AAV-plus-stroke-acute


title: 7F-CREB-plus-stroke-chronic


title: 5I-CREB


title: 5J-CREB


title: B3H11


title: 2F-Control-AAV-plus-stroke-acute


title: B3H10


title: B3H1


title: 5H-CREB


title: B3G6


title: B3G8


title: 5F-CREB


title: B3G7


title: 4H-CCR5kd


title: 6F-CCR5kd-plus-stroke-acute


title: B3G5


title: 4I-CCR5kd


title: 3J-Naive


title: B3G4


title: 4F-CCR5kd


title: B3G2


title: B3G3


title: 3G-Naive


title: B3G11


title: 3H-Naive


title: 3F-Naive


title: 5G-CREB


title: CD11b cells from the brain, 85 wk WNV 3

city: London

first: Robyn

middle: S.

last: Klein

state: ON

address: 100 Perth Dr

institute: University of Western Ontario

description: Sample R

data_processing:
STAR Aligner 2.7.8a
Assembly: Mus musculus mm39_ensembl_release105_v2
Supplementary files format and content: Partek_CD11b_2B_Aged_Mice_RNA-Seq_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt (reads quantified to mm39 - Ensembl Transcripts release 105)

source_name: CD11b+ cells from the brain

extract_protocol:
QIAGEN RNAeasy Micro
Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags.

tag: strain

tag: age

value: 85 wk

value: CD11b+ cells from the brain

tag: infection

value: West Nile Virus E218A infection 30 days post


title: B3F9

tag: cell type

tag: Sex


title: B3G10

tag: disease state

tag: patched


title: B3G9


title: CD11b cells from the brain, 85 wk WNV 1

description: Sample O1


title: CD11b cells from the brain, 85 wk WNV 2

description: Sample O3


title: B3F8


title: B3F7


title: CD11b cells from the brain, 16 wk WNV 3

description: Sample N3

value: 16 wk


title: CD11b cells from the brain, 85 wk mock 3

description: Sample L5

value: mock infection


title: B3F6


title: CD11b cells from the brain, 85 wk mock 1

description: Sample L1


title: B3F4


title: B3F5


title: 3I-Naive

tag: tissue

value: WT


title: B3F3

value: Human Donor Islet Cell


title: CD11b cells from the brain, 16 wk WNV 1

description: Sample K5


title: CD11b cells from the brain, 16 wk mock 3

description: Sample K4


title: B3F2


title: B3G1


title: B3F12


title: B3G12


title: B3F11


title: CD11b cells from the brain, 16 wk mock 1

description: Sample K2


title: B3F10


title: Mid-Aged, Infected 3

city: Sapporo

first: Kyoko

last: Hida

address: Kita-ku, N13W7

country: Japan

institute: Hokkaido University

data_processing:
NovaSeq Control Software v 1.7.5
Assembly: mm10
Supplementary files format and content: all.fpkm.txt: Tab-delimited text file includes FPKM values and read counts for each Sample.

source_name: lung endothelial cells

extract_protocol:
RNA was harvested using ReliaPrep™ RNA Miniprep Systems (Promega).
RNA libraries for RNA-seq were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing following manufacturer's protocols.

value: lung endothelial cells

value: mid-aged


title: B3E9

value: Yes


title: B3E8

value: Male


title: Young, Infected 2

value: young


title: Mid-Aged, Infected 2


title: B3F1


title: Young, Infected 3


title: CD11b cells from the brain, 85 wk mock 2

description: Sample L2


title: Mid-Aged, Uninfected 3

value: PBS


title: CD11b cells from the brain, 16 wk WNV 2

description: Sample N2


title: B3E7


title: Mid-Aged, Uninfected 2


title: B3E6


title: B3E4


title: B3E2


title: Young, Uninfected 3


title: Young, Uninfected 2


title: B3E5


title: B3E11


title: B3E12


title: ChIPseq for H3K9me3  in ADNP2 KO mES cells, replicate 1

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

library_source: genomic

data_processing:
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
Sequenced reads were aligned using STAR 2.7.3 (STAR --runMode alignReads --outSAMtype BAM SortedByCoordinate --readFilesIn R1.fastq.gz R2.fastq.gz --readFilesCommand zcat --genomeDir mm10_hg38Spike_refSTAR --runThreadN 10 --alignIntronMax 1 --alignEndsType EndToEnd --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within --outFileNamePrefix _ --clip3pAdapterSeq CTGTCTCTTATACACATCT AGATGTGTATAAGAGACAG --outBAMsortingBinsN 100).
Assembly: mm10
Supplementary files format and content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools).

molecule: genomic DNA

source_name: hybrid 129-C57BL/6

growth_protocol: Mouse embryonic stem cells were grown under standard conditions in medium containing serum, LIF and 2i.

extract_protocol:
10-20^6 mES cells were crosslinked, chromatin was extracted and sonicated to an average size of 300bp. 5% of chromatin was set aside as Input control. The chromatin was incubated with antibody and protein A/G coupled Dynabeads, washed and de-crosslinked. Purified DNA was subsequently used for library preparation. For a detailed protocol, see Ahel,Pandey et al. 2024.
Libraries were prepared using the NEB Next Ultra II DNA library prep kit according to manufacturers instructions.

tag: cell line

value: hybrid 129-C57BL/6

value: embryonic stem (ES) cells

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 adnp (C) FKBP12F36V - 3F-Avi

value: DMSO

tag: antibody

value: H3K9me3, Abcam ab8898


title: ChIPseq for H3K9me3  in ADNP2 KO mES cells, replicate 2


title: B3E1


title: ChIPseq for H3K9me3  in 2 week ADNP-depleted ADNP2 KO mES cells, replicate 1

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 adnp (C) FKBP12F36V - 3F-Avi adnp2-/-

value: 250nM dTAG13


title: B3D9


title: ChIPseq for H3K9me3  in 2 week ADNP-depleted ADNP2 KO mES cells, replicate 2


title: ChIPseq for H3K9me3  in 2 week ADNP-depleted mES cells, replicate 2


title: CD11b cells from the brain, 16 wk mock 2

description: Sample K3

value: 16 wk

value: CD11b+ cells from the brain


title: B3E10


title: B3D6


title: B3D5


title: B3D7


title: ChIPseq for H3K9me3  in unperturbed mES cells, replicate 1


title: ChIPseq for H3K9me3  in 2 week ADNP-depleted mES cells, replicate 1


title: B3D4


title: Input for ChIPseq for H3K9me3  in 2 week ADNP-depleted ADNP2 KO mES cells, replicate 2


title: B3D8


title: B3E3


title: Input for ChIPseq for H3K9me3  in 2 week ADNP-depleted ADNP2 KO mES cells, replicate 1


title: B3D3


title: B3D2


title: Input for ChIPseq for H3K9me3  in ADNP2 KO mES cells, replicate 1


title: B3D12


title: Input for ChIPseq for H3K9me3  in 2 week ADNP-depleted mES cells, replicate 2


title: B3D11


title: Input for ChIPseq for H3K9me3  in 2 week ADNP-depleted mES cells, replicate 1


title: B3D10


title: Input for ChIPseq for H3K9me3  in unperturbed mES cells, replicate 2


title: B3D1


title: RV

city: Ottawa

first: Kyoung-Han

last: Kim

state: Ontario

address: 40 Ruskin Street

institute: University of Ottawa Heart Institute

data_processing:
This pool was subjected to 151bp paired-end sequencing according to the manufacture's protocol (Illumina NovaSeq). BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed fastq.gz files. Raw fastq.gz files were processed using Nanostring’s proprietary GeoMx NGS Pipeline (v2.0), which includes adapter trimming and aligning stitched paired-end reads to the barcodes in the reference assay before removal of PCR duplicates based on the Unique Molecular Identifier (UMI) in each read.
Assembly: Mouse Whole Transcriptome Atlas RNA v1.0
Supplementary files format and content: DCC files for each full ROI or segmented AOI were processed with the GeoMxTools package (version 3.0.1 using the corresponding Nanostring DSP configuration file and the instrument generated LabWorksheet with ROI/AOI identifiers and manually annotated group labels. Initial quality control filtering and third quartile (Q3) normalization were performed following Nanostring’s recommendations for GeoMx DSP data - with minimum average negative control measurements for ROI/AOI retention and minimum counts above background for target (gene/protein) retention
Library strategy: Nanostring GeoMx Digital Spatial Profiler (DSP)

source_name: Heart

extract_protocol:
Freshly isolated neonatal hearts were fixed in a methanol-free 4% paraformaldehyde solution (Thermo ScientificTM PierceTM, #28906) in PBS overnight at 4°C. Hearts were washed twice in PBS for 30 mins each, then were incubated in filtered 30% sucrose in PBS overnight at 4°C. Fixed cryopreserved hearts were embedded in Tissue-Tek® O.C.T compound (Sakura, #4683) and immediately frozen on powdered dry ice. Embedded hearts were sectioned using a cryostat at 8 um thickness.
Following ROI selection, DNA oligos were cleaved from RNAScope probes by directing UV light at each ROI using the digital micromirror device. Cleaved oligos were then collected into the wells of a 96-well collection plate, which were subjected to library preparation and next-generation sequencing using Manufacturer's protocol

value: Heart

value: Age:Postnatal day 4


title: B3C9

value: Human Donor Islet Cell


title: IVSA


title: ChIPseq for H3K9me3  in unperturbed mES cells, replicate 2


title: B3C8


title: B3C7


title: Input for ChIPseq for H3K9me3  in unperturbed mES cells, replicate 1


title: IVSB


title: B3C6


title: LENDO


title: RA


title: B3C4


title: RPF_2


title: LEPI


title: B3C5


title: B3C2


title: Input for ChIPseq for H3K9me3  in ADNP2 KO mES cells, replicate 2


title: B3C3


title: LPF_2


title: RPF_1


title: B3C11


title: B3C12


title: DRBB_2


title: B3C1


title: DRBB_1


title: B3C10


title: PRBB_2


title: B3B9


title: B3B8


title: DLBB_2


title: B3B7


title: B3B6


title: PRBB_1


title: DLBB_1


title: B3B5


title: PLBB_2


title: B3B4


title: OCT4-mCherry nEnd Pdgfra+ R3

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

data_processing:
The preprocessing was carried out by following cellranger workflow (scRNA-seq) and raw reads where processed with bcl2fastq (bulk RNA-seq).
Raw reads where demultiplexed and converted to FASTQ using cellranger mkfastq.
Reads were further demultiplexed and counted using cellranger multi command.
Assembly: mm10-2020-A
Supplementary files format and content: tab-delimited text file including raw counts

extract_protocol:
Samples isolated by fluorescence activated cell sorting (FACS) based on DAPI negative cells using a Sony SH800Z flow cytometer.
10x Chromium Single Cell Gene Expression (EPUc) and NEBNext Ultra II Directional RNA Library Prep Kit (O4Ch)

value: nEnd

value: no treatment


title: PLBB_1


title: OCT4-mCherry nEnd Pdgfra+ R2


title: OCT4-mCherry nEnd Oct4+ R3


title: HIS_2


title: OCT4-mCherry nEnd Pdgfra+ R1


title: B3B3

value: Male

value: Yes


title: OCT4-mCherry nEnd Oct4+ R1


title: B3B2


title: OCT4-mCherry nEnd Oct4+ R2


title: B3B12


title: OCT4-mCherry nEnd DP R1


title: LNB2


title: HIS_1


title: LPF_1


title: B3B11


title: LNB1


title: Oct4-LOF nEnd plus 4OHT

source_name: EPUc

value: EPUc


title: OCT4-mCherry nEnd DP R2


title: OCT4-mCherry nEnd DP R3


title: S2_OCT4-mCherry nEnd, TSC

data_processing:
The preprocessing was carried out by following CellPlex cellranger workflow.
Raw reads where demultiplexed and converted to FASTQ using cellranger mkfastq.
Reads were further demultiplexed and counted using cellranger multi command.
Assembly: mm10-2020-A

extract_protocol:
Samples isolated by fluorescence activated cell sorting (FACS) based on DAPI negative cells using a Sony SH800Z flow cytometer.
CellPlex
single cell RNA-seq for gene expression quantification

value: Differentiated nEnd

value: TSC differentiation


title: CAVN_1


title: SAN_2


title: Oct4-LOF nEnd minus 4OHT


title: S1_OCT4-nEnd 3D nEnd, RACL


title: S1_OCT4-mCherry nEnd, TSC


title: B3A9


title: SAN_1


title: S2_OCT4-mCherry nEnd, RACL


title: B3A8


title: S2_OCT4-mCherry ESCs, 2iLIF

value: ESC


title: S1_OCT4-mCherry nEnd, RACL


title: S1_OCT4-mCherry ESCs, 2iLIF


title: B3A7


title: cNSC_RNAseq_rep4

city: New Haven

first: Atreyo

last: Pal

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University

description: KAPA mRNA HyperPrep kit for standard input PolyA library prep

data_processing:
CHi-C: Ligated reads were truncated, mapped and filtered to DpnII digested reference genomes (generated from the GRCh38 and panTro6 reference assemblies for human and chimpanzee respectively) using the HiCUP pipeline (truncating RE site flag = ^GATC,DpnII; mapping flags for Bowtie2: --very-sensitive, --no_unal, --reorder; ditag pairing criteria: MAPQ score >= 30, XS – AS tag ID score >= 10; filtering ditag range = 50 to 800bp). Valid ditags were deduplicated using the adapter UMIs through the umitools package. All DpnII fragments containing HARs and HGEs were then merged into a single bait file and significant interactions were called using CHiCAGO after combining 3 replicates from the HiCUP pipeline. Briefly, we weighted the 4-parameter Delaporte model in CHiCAGO using parameters: weight(alpha) = 24.5, weight(beta) = -2.16, weight(gamma) = -21.2 and weight(delta) = -9.2, and this was used to compute weighted P-values for every interaction. We then set a threshold for the CHiCAGO scores as >4.5 for human and >4.4 for chimpanzee samples. CUT&RUN: Reads were trimmed for adapters using Trimmomatic and aligned to either the GRCh38 (human) or panTro6 (chimpanzee) genomes using Bowtie2 (flags: --very-sensitive, -X 2000). Aligned reads were filtered based on quality and PCR duplicates were marked using the MarkDuplicates function in Picard (courtesy the Broad Institute bioinformatic toolkit). Reads with the following flags – “reads unmapped”, “not primary alignment reads” and “failing platform duplicates” were removed and the remaining properly mapped reads were used for peak calling using the program SEACR (with the --stringent flag), which was used to call enriched regions in target data by selecting the top 0.5-1% of regions by AUC depending on the mark assayed. RNA-Seq: For the hNSC versus cNSC comparison, paired-end reads were mapped to the XSAnno whole transcriptome annotation modified to compare GRCh38 to panTro6 genomes on the GENCODEv43 annotation. Briefly, this annotation subsets out genes with exons that reciprocally liftover between both species (>98% sequence similarity), then filters out those with ambiguous annotations using BLAT [blat parameters: % ID between species = 95%, % len between species = 95%, % ID within species (paralogs) = 97%, % len within species = 97%] and finally simulates reads and filters exons that are differentially expressed in the simulation using DESeq2. Mapping was performed using the STAR aligner (flags: --outSAMunMapped Within, --twopassMode Basic, --outFilterMultimapNmax 1, --quantMode TranscriptomeSAM). Using the package RSEM we generated a counts matrix for each species’ replicate and then used DESeq2 for differential gene expression analysis. Genes with FDR-adjusted P-value < 0.01 and |log2FC| > 1 were considered differentially expressed between human and chimpanzee. For the hNSC- human neuron comparison, reads were mapped to native GRCh38 RefSeq coordinates and TPM counts from RSEM in each cell type were compared for specific gene targets.  scRNA-Seq: Reads were aligned to GRCh38 using the multi function of CellRanger 6.0.1. For quality control, cells with nFeature_RNA (number of genes) and/or nCount_RNA (number of molecules) values 2 standard deviations away from the mean were removed, alongside cells with mitochondrial reads greater than 10% of total reads. Counts were normalized using Seurat v4.3.0, via the NormalizeData function with default parameters. Human and Chimpanzee count matrices were then integrated using  the SelectIntegrationFeautres, FindIntegrationAnchors, and IntegrateData functions with default parameters. Dimensionality reduction was performed using RunPCA(params: npcs = 30) and RunUMAP on the integrated data, and Louvain clustering was performed using FindNeighbors(params: dims = 1:15) and FindClusters(params: resolution = 0.3). Cluster identities were assigned by identifying cell-type markers using FindAllMarkers(params: min.pct = 025).
Assembly: Human: GRCh38, chimpanzee: panTro6
Supplementary files format and content: C-HiC: Output txt files from HiCUP pipeline based on aligned and deduplicated Capture HiC reads linked to HARs and HGEs (one per replicate), which can be input for CHiCAGO to call significant interactions;  CUT& RUN: bigwig and bed files with signal and peak calls for each chromatin mark
Supplementary files format and content: RNA-Seq: Output txt files post transcript quantification by RSEM containing raw counts, FPKM and TPM values per replicate. hNSC and cNSC processed files are in XSAnno human-chimpanzee consensus coordinates based on GENCODEv43, human neuron processed files are in native GRCh38 RefSeq coordinates;  scRNA-Seq: txt files with feature, barcodes, matrix information for each species separately (demultiplexed)

organism: Pan troglodytes

growth_protocol: Detailed information on growth and differentiation protocols is provided in the manuscript

extract_protocol:
RNA extraction done using Qiagen RNeasy Plus Mini Kit (Cat # 74134)
Libraries were prepared and sequenced (2×150 bp) using standard Illumina protocols on an Illumina NovaSeq 6000.

value: Neural Stem Cells derived from IPSCs

tag: cut &_run_antibody


title: Total RNAseq after ADNP2 depletion ADNP2 KO mES cells, replicate 2

data_processing:
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
Sequenced reads were aligned using STAR 2.7.3 (STAR --runMode alignReads --outSAMtype BAM SortedByCoordinate --readFilesIn R1.fastq.gz R2.fastq.gz --readFilesCommand zcat –genomeDir tar2_7_3a_GRCm38.primary_assembly_gencodeM23_spliced_sjdb50  --runThreadN 10 --outFilterType BySJout --outFilterMultimapNmax 10000 --outFilterMismatchNmax 3 --winAnchorMultimapNmax 20000 --alignMatesGapMax 350 --seedSearchStartLmax 30 alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 10000 --outSAMunmapped Within).
Assembly: mm10
Supplementary files format and content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools).

extract_protocol:
RNA was collected using Absolutely RNA miniprep kit (Agilent) according to manufacturer's instructions
Libraries were prepared using TruSeq Ilumina total RNA-seq

value: hybrid 129-C57BL/6

value: embryonic stem (ES) cells


title: Total RNAseq after ADNP2 depletion ADNP2 KO mES cells, replicate 3

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 adnp (C) FKBP12F36V - 3F-Avi adnp2-/-

value: 250nM dTAG13


title: cNSC_RNAseq_rep2


title: cNSC_RNAseq_rep3


title: B3A6


title: B3A5


title: B3B10


title: cNSC_RNAseq_rep1


title: Total RNAseq in untreated ADNP2 KO mES cells, replicate 3

value: DMSO


title: Total RNAseq in untreated ADNP2 KO mES cells, replicate 2


title: B3A4


title: S2_OCT4-nEnd 3D nEnd, RACL


title: cNSC_C&T_POLII_rep2

description: Kit and protocol from ActiveMotif Ltd

data_processing:
library strategy: Cut & Tag
CHi-C: Ligated reads were truncated, mapped and filtered to DpnII digested reference genomes (generated from the GRCh38 and panTro6 reference assemblies for human and chimpanzee respectively) using the HiCUP pipeline (truncating RE site flag = ^GATC,DpnII; mapping flags for Bowtie2: --very-sensitive, --no_unal, --reorder; ditag pairing criteria: MAPQ score >= 30, XS – AS tag ID score >= 10; filtering ditag range = 50 to 800bp). Valid ditags were deduplicated using the adapter UMIs through the umitools package. All DpnII fragments containing HARs and HGEs were then merged into a single bait file and significant interactions were called using CHiCAGO after combining 3 replicates from the HiCUP pipeline. Briefly, we weighted the 4-parameter Delaporte model in CHiCAGO using parameters: weight(alpha) = 24.5, weight(beta) = -2.16, weight(gamma) = -21.2 and weight(delta) = -9.2, and this was used to compute weighted P-values for every interaction. We then set a threshold for the CHiCAGO scores as >4.5 for human and >4.4 for chimpanzee samples. CUT&RUN: Reads were trimmed for adapters using Trimmomatic and aligned to either the GRCh38 (human) or panTro6 (chimpanzee) genomes using Bowtie2 (flags: --very-sensitive, -X 2000). Aligned reads were filtered based on quality and PCR duplicates were marked using the MarkDuplicates function in Picard (courtesy the Broad Institute bioinformatic toolkit). Reads with the following flags – “reads unmapped”, “not primary alignment reads” and “failing platform duplicates” were removed and the remaining properly mapped reads were used for peak calling using the program SEACR (with the --stringent flag), which was used to call enriched regions in target data by selecting the top 0.5-1% of regions by AUC depending on the mark assayed. RNA-Seq: For the hNSC versus cNSC comparison, paired-end reads were mapped to the XSAnno whole transcriptome annotation modified to compare GRCh38 to panTro6 genomes on the GENCODEv43 annotation. Briefly, this annotation subsets out genes with exons that reciprocally liftover between both species (>98% sequence similarity), then filters out those with ambiguous annotations using BLAT [blat parameters: % ID between species = 95%, % len between species = 95%, % ID within species (paralogs) = 97%, % len within species = 97%] and finally simulates reads and filters exons that are differentially expressed in the simulation using DESeq2. Mapping was performed using the STAR aligner (flags: --outSAMunMapped Within, --twopassMode Basic, --outFilterMultimapNmax 1, --quantMode TranscriptomeSAM). Using the package RSEM we generated a counts matrix for each species’ replicate and then used DESeq2 for differential gene expression analysis. Genes with FDR-adjusted P-value < 0.01 and |log2FC| > 1 were considered differentially expressed between human and chimpanzee. For the hNSC- human neuron comparison, reads were mapped to native GRCh38 RefSeq coordinates and TPM counts from RSEM in each cell type were compared for specific gene targets.  scRNA-Seq: Reads were aligned to GRCh38 using the multi function of CellRanger 6.0.1. For quality control, cells with nFeature_RNA (number of genes) and/or nCount_RNA (number of molecules) values 2 standard deviations away from the mean were removed, alongside cells with mitochondrial reads greater than 10% of total reads. Counts were normalized using Seurat v4.3.0, via the NormalizeData function with default parameters. Human and Chimpanzee count matrices were then integrated using  the SelectIntegrationFeautres, FindIntegrationAnchors, and IntegrateData functions with default parameters. Dimensionality reduction was performed using RunPCA(params: npcs = 30) and RunUMAP on the integrated data, and Louvain clustering was performed using FindNeighbors(params: dims = 1:15) and FindClusters(params: resolution = 0.3). Cluster identities were assigned by identifying cell-type markers using FindAllMarkers(params: min.pct = 025).
Assembly: Human: GRCh38, chimpanzee: panTro6
Supplementary files format and content: C-HiC: Output txt files from HiCUP pipeline based on aligned and deduplicated Capture HiC reads linked to HARs and HGEs (one per replicate), which can be input for CHiCAGO to call significant interactions;  CUT& RUN: bigwig and bed files with signal and peak calls for each chromatin mark
Supplementary files format and content: RNA-Seq: Output txt files post transcript quantification by RSEM containing raw counts, FPKM and TPM values per replicate. hNSC and cNSC processed files are in XSAnno human-chimpanzee consensus coordinates based on GENCODEv43, human neuron processed files are in native GRCh38 RefSeq coordinates;  scRNA-Seq: txt files with feature, barcodes, matrix information for each species separately (demultiplexed)

extract_protocol:
Extraction protocol taken from Epicypher CUTANA Cut and Run kit (SKU:14-1048)
Libraries were prepared and sequenced (2×150 bp) using standard Illumina protocols on an Illumina NovaSeq 6000.

value: RNA POLII (rAb, Active Motif #91152)


title: B3B1


title: cNSC_C&T_POLII_rep1

description: Kit and protocol from ActiveMotif Ltd


title: cNSC_C&R_RAD21_rep2

description: Kit and protocol from Epicypher Ltd

data_processing:
library strategy: Cut & Run
CHi-C: Ligated reads were truncated, mapped and filtered to DpnII digested reference genomes (generated from the GRCh38 and panTro6 reference assemblies for human and chimpanzee respectively) using the HiCUP pipeline (truncating RE site flag = ^GATC,DpnII; mapping flags for Bowtie2: --very-sensitive, --no_unal, --reorder; ditag pairing criteria: MAPQ score >= 30, XS – AS tag ID score >= 10; filtering ditag range = 50 to 800bp). Valid ditags were deduplicated using the adapter UMIs through the umitools package. All DpnII fragments containing HARs and HGEs were then merged into a single bait file and significant interactions were called using CHiCAGO after combining 3 replicates from the HiCUP pipeline. Briefly, we weighted the 4-parameter Delaporte model in CHiCAGO using parameters: weight(alpha) = 24.5, weight(beta) = -2.16, weight(gamma) = -21.2 and weight(delta) = -9.2, and this was used to compute weighted P-values for every interaction. We then set a threshold for the CHiCAGO scores as >4.5 for human and >4.4 for chimpanzee samples. CUT&RUN: Reads were trimmed for adapters using Trimmomatic and aligned to either the GRCh38 (human) or panTro6 (chimpanzee) genomes using Bowtie2 (flags: --very-sensitive, -X 2000). Aligned reads were filtered based on quality and PCR duplicates were marked using the MarkDuplicates function in Picard (courtesy the Broad Institute bioinformatic toolkit). Reads with the following flags – “reads unmapped”, “not primary alignment reads” and “failing platform duplicates” were removed and the remaining properly mapped reads were used for peak calling using the program SEACR (with the --stringent flag), which was used to call enriched regions in target data by selecting the top 0.5-1% of regions by AUC depending on the mark assayed. RNA-Seq: For the hNSC versus cNSC comparison, paired-end reads were mapped to the XSAnno whole transcriptome annotation modified to compare GRCh38 to panTro6 genomes on the GENCODEv43 annotation. Briefly, this annotation subsets out genes with exons that reciprocally liftover between both species (>98% sequence similarity), then filters out those with ambiguous annotations using BLAT [blat parameters: % ID between species = 95%, % len between species = 95%, % ID within species (paralogs) = 97%, % len within species = 97%] and finally simulates reads and filters exons that are differentially expressed in the simulation using DESeq2. Mapping was performed using the STAR aligner (flags: --outSAMunMapped Within, --twopassMode Basic, --outFilterMultimapNmax 1, --quantMode TranscriptomeSAM). Using the package RSEM we generated a counts matrix for each species’ replicate and then used DESeq2 for differential gene expression analysis. Genes with FDR-adjusted P-value < 0.01 and |log2FC| > 1 were considered differentially expressed between human and chimpanzee. For the hNSC- human neuron comparison, reads were mapped to native GRCh38 RefSeq coordinates and TPM counts from RSEM in each cell type were compared for specific gene targets.  scRNA-Seq: Reads were aligned to GRCh38 using the multi function of CellRanger 6.0.1. For quality control, cells with nFeature_RNA (number of genes) and/or nCount_RNA (number of molecules) values 2 standard deviations away from the mean were removed, alongside cells with mitochondrial reads greater than 10% of total reads. Counts were normalized using Seurat v4.3.0, via the NormalizeData function with default parameters. Human and Chimpanzee count matrices were then integrated using  the SelectIntegrationFeautres, FindIntegrationAnchors, and IntegrateData functions with default parameters. Dimensionality reduction was performed using RunPCA(params: npcs = 30) and RunUMAP on the integrated data, and Louvain clustering was performed using FindNeighbors(params: dims = 1:15) and FindClusters(params: resolution = 0.3). Cluster identities were assigned by identifying cell-type markers using FindAllMarkers(params: min.pct = 025).
Assembly: Human: GRCh38, chimpanzee: panTro6
Supplementary files format and content: C-HiC: Output txt files from HiCUP pipeline based on aligned and deduplicated Capture HiC reads linked to HARs and HGEs (one per replicate), which can be input for CHiCAGO to call significant interactions;  CUT& RUN: bigwig and bed files with signal and peak calls for each chromatin mark
Supplementary files format and content: RNA-Seq: Output txt files post transcript quantification by RSEM containing raw counts, FPKM and TPM values per replicate. hNSC and cNSC processed files are in XSAnno human-chimpanzee consensus coordinates based on GENCODEv43, human neuron processed files are in native GRCh38 RefSeq coordinates;  scRNA-Seq: txt files with feature, barcodes, matrix information for each species separately (demultiplexed)

value: RAD21 (Bethyl Labs # A300-080A)


title: cNSC_C&R_RAD21_rep1

description: Kit and protocol from Epicypher Ltd


title: Total RNAseq after ADNP2 depletion ADNP2 KO mES cells, replicate 1


title: cNSC_C&R_CTCF_rep1

description: Kit and protocol from Epicypher Ltd

value: CTCF (EpiCypher # 13-2014)


title: B3A2

value: Human Donor Islet Cell


title: cNSC_C&R_CTCF_rep2

description: Kit and protocol from Epicypher Ltd


title: Total RNAseq in untreated ADNP2 KO mES cells, replicate 1


title: Total RNAseq after ADNP depletion in wt mES cells, replicate 3

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 adnp (C) FKBP12F36V - 3F-Avi


title: cNSC_C&R_H3K27me3_rep1

description: Kit and protocol from Epicypher Ltd

value: H3K27me3 (ThermoFisher # MA511198)


title: cNSC_C&R_H3K27me3_rep2

description: Kit and protocol from Epicypher Ltd


title: B3A12

value: Male

value: Yes


title: cNSC_C&R_H3K27ac_rep2

description: Kit and protocol from Epicypher Ltd

value: H3K27ac (EpiCypher # 13-0045)


title: B3A11


title: cNSC_C&R_H3K27ac_rep1

description: Kit and protocol from Epicypher Ltd


title: cNSC_CHiC_rep3

description: Custom biotinylated probes from Twist Biosciences

data_processing:
library strategy: CHiC
CHi-C: Ligated reads were truncated, mapped and filtered to DpnII digested reference genomes (generated from the GRCh38 and panTro6 reference assemblies for human and chimpanzee respectively) using the HiCUP pipeline (truncating RE site flag = ^GATC,DpnII; mapping flags for Bowtie2: --very-sensitive, --no_unal, --reorder; ditag pairing criteria: MAPQ score >= 30, XS – AS tag ID score >= 10; filtering ditag range = 50 to 800bp). Valid ditags were deduplicated using the adapter UMIs through the umitools package. All DpnII fragments containing HARs and HGEs were then merged into a single bait file and significant interactions were called using CHiCAGO after combining 3 replicates from the HiCUP pipeline. Briefly, we weighted the 4-parameter Delaporte model in CHiCAGO using parameters: weight(alpha) = 24.5, weight(beta) = -2.16, weight(gamma) = -21.2 and weight(delta) = -9.2, and this was used to compute weighted P-values for every interaction. We then set a threshold for the CHiCAGO scores as >4.5 for human and >4.4 for chimpanzee samples. CUT&RUN: Reads were trimmed for adapters using Trimmomatic and aligned to either the GRCh38 (human) or panTro6 (chimpanzee) genomes using Bowtie2 (flags: --very-sensitive, -X 2000). Aligned reads were filtered based on quality and PCR duplicates were marked using the MarkDuplicates function in Picard (courtesy the Broad Institute bioinformatic toolkit). Reads with the following flags – “reads unmapped”, “not primary alignment reads” and “failing platform duplicates” were removed and the remaining properly mapped reads were used for peak calling using the program SEACR (with the --stringent flag), which was used to call enriched regions in target data by selecting the top 0.5-1% of regions by AUC depending on the mark assayed. RNA-Seq: For the hNSC versus cNSC comparison, paired-end reads were mapped to the XSAnno whole transcriptome annotation modified to compare GRCh38 to panTro6 genomes on the GENCODEv43 annotation. Briefly, this annotation subsets out genes with exons that reciprocally liftover between both species (>98% sequence similarity), then filters out those with ambiguous annotations using BLAT [blat parameters: % ID between species = 95%, % len between species = 95%, % ID within species (paralogs) = 97%, % len within species = 97%] and finally simulates reads and filters exons that are differentially expressed in the simulation using DESeq2. Mapping was performed using the STAR aligner (flags: --outSAMunMapped Within, --twopassMode Basic, --outFilterMultimapNmax 1, --quantMode TranscriptomeSAM). Using the package RSEM we generated a counts matrix for each species’ replicate and then used DESeq2 for differential gene expression analysis. Genes with FDR-adjusted P-value < 0.01 and |log2FC| > 1 were considered differentially expressed between human and chimpanzee. For the hNSC- human neuron comparison, reads were mapped to native GRCh38 RefSeq coordinates and TPM counts from RSEM in each cell type were compared for specific gene targets.  scRNA-Seq: Reads were aligned to GRCh38 using the multi function of CellRanger 6.0.1. For quality control, cells with nFeature_RNA (number of genes) and/or nCount_RNA (number of molecules) values 2 standard deviations away from the mean were removed, alongside cells with mitochondrial reads greater than 10% of total reads. Counts were normalized using Seurat v4.3.0, via the NormalizeData function with default parameters. Human and Chimpanzee count matrices were then integrated using  the SelectIntegrationFeautres, FindIntegrationAnchors, and IntegrateData functions with default parameters. Dimensionality reduction was performed using RunPCA(params: npcs = 30) and RunUMAP on the integrated data, and Louvain clustering was performed using FindNeighbors(params: dims = 1:15) and FindClusters(params: resolution = 0.3). Cluster identities were assigned by identifying cell-type markers using FindAllMarkers(params: min.pct = 025).
Assembly: Human: GRCh38, chimpanzee: panTro6
Supplementary files format and content: C-HiC: Output txt files from HiCUP pipeline based on aligned and deduplicated Capture HiC reads linked to HARs and HGEs (one per replicate), which can be input for CHiCAGO to call significant interactions;  CUT& RUN: bigwig and bed files with signal and peak calls for each chromatin mark
Supplementary files format and content: RNA-Seq: Output txt files post transcript quantification by RSEM containing raw counts, FPKM and TPM values per replicate. hNSC and cNSC processed files are in XSAnno human-chimpanzee consensus coordinates based on GENCODEv43, human neuron processed files are in native GRCh38 RefSeq coordinates;  scRNA-Seq: txt files with feature, barcodes, matrix information for each species separately (demultiplexed)

extract_protocol:
Cells were washed with Dulbecco’s PBS and dissociated with Accutase for 5-10 minutes to obtain a single cell suspension
Libraries were prepared and sequenced (2×150 bp) using standard Illumina protocols on an Illumina NovaSeq 6000.


title: B3A10


title: B3A1


title: A3H9


title: ChIPseq for ADNP2 after SETDB1 depletion in ADNP2 PxVxL mutant mES cells, replicate 2

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5  adnp2 V1139E(GTA-GAA) L1141T(CTA-ACC) (C)Avi-3F  / V1139E(GTA-GAA) L1141T(CTA-ACC) (C)Avi-3F setdb1 (N) 2HA-FKBP12F36V

value: 500nM dTAG13

value: FLAG, Sigma F1804


title: Total RNAseq in untreated wt mES cells, replicate 3

value: hybrid 129-C57BL/6


title: cNSC_CHiC_rep2

value: Neural Stem Cells derived from IPSCs


title: A3H8


title: Total RNAseq in untreated wt mES cells, replicate 1

value: embryonic stem (ES) cells


title: B3A3


title: A3H7


title: A3H6

value: Female


title: ChIPseq for ADNP2 after SETDB1 depletion in ADNP2 PxVxL mutant mES cells, replicate 1


title: ChIPseq for ADNP2 after SETDB1 depletion in wt mES cells, replicate 2

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 adnp2 (C) Avi-3F setdb1 (N) 2HA-FKBP12F36V


title: A3H5


title: ChIPseq for ADNP2 after SETDB1 depletion in wt mES cells, replicate 1


title: NPC_p3 ,shLUC, Biol rep 8

city: Philadelphia

first: Alessandro

last: Gardini

state: PA

address: 3601 Spruce St, Room 230

institute: The Wistar Institute

description: 3' - mRNA

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment: STAR
tag density files: deepTools package was used to generate BigWiggle files
gene counts:  FeatureCounts (Liao et al., 2014)
Assembly: Genome_build: hg19
Supplementary files format and content: Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization). Tab delimited gene count files were generated with FeatureCounts.

growth_protocol: iPSCs were cultured on Geltrex-coated plates and maintained in StemMACS™ iPS-Brew XF (Miltenyi Biotec, cat#130-104-368). NPCs were differentiated from iPSCs using Neural Induction Medium (98% Neurobasal Meida (ThermoFisher, cat#21103049) and 2% Neuronal Induction Supplementd) for 7 days and maintained in Neural Expansion Medium (49% Neurobasal Meida (ThermoFisher, cat#21103049), 49% Advanced DMEM/F12 (ThermoFisher, cat#12634010) and 2% Neuronal Induction Supplement. Neurons were differentiated from NPCs neuronal differentiation medium ( Neurobasal Meida (ThermoFisher Scientific, cat#21103049), B27 (ThermoFisher Scientific,cat#A3353501), GlutaMAX (ThermoFisher Scientific, cat#35050061), nonessential animal acids (ThermoFisher Scientific, cat#11140050), 20 ng/ml brain-derived neurotrophic factor (BDNF) (Peprotech, cat#450-02) and 20 ng/ml glial cell-derived neurotrophic factor (GDNF)(Peprotech, cat#450-10) for 21 days and then mainted in this media.  SHSY5Y cells were maintained in the basal medium (45% of Minimum Essential Medium (MEM) (Corning, cat#10009CV), 45% of Nutrient Mixture F-12 Ham (Sigma-Aldrich, Cat#N4888) and 10% of fetal bovine serum (Corning, cat#35010CV)). ReNcells were maintained in ReNcell proliferation medium (5 ml of 100X Glutmax, 10 ml of B27, 1 ml of Heparin (1 mg/ml) and 484 ml of DMEM/F12) that supplemented with bFGF ( 20ng/ml) and EGF (20ng/ml). To start the differentiation, ReN cells were plated in Laminin-coated 6-well plates with ReN proliferation medium at 30-40% confluency (Day 0). On the next day (Day 1), remove the medium and feed the cells with fresh ReN differentiation medium (without bFGF and EGF). Cells were fed with fresh ReN differentiation medium every 2-3 days.

extract_protocol:
RNA was extracted using the Zymo RNA Miniprep kitand then used to make sequencing libraries.
QuantSeq 3' - mRNA Seq Library Prep Kit for Illumina (Lexogen)
QuantSeq 3' - mRNA Seq

treatment_protocol: Lentiviruses were produced in HEK293T cells by co-transfection 8 ug of pLentiCRISPR v2-INTS10 gRNA3 (Target sequence: TTCTGAGAGCTACGTTTGCT). iPSCs or SH-SY5Y were passaged into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of virus medium per well (cell medium with 4 ul of lentiviral particles per ml and 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G)) was added to replace old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours. After that, cells were selected with with 0.5 ug/ml of puromycin in fresh medium (InvivoGen, cat#ant-pr-1). 48 hours after selection with puromycin, iPSC colonies were disassociated with Accutase and passed through a 40 uM cell stainer to to generate single cells. Singel cell suspension with 10 μM of ROCK inhibitor and 0.5 ug/ml of puromycin were seeded in Geltrex-coated 10 cm dishes.  ROCK inhibitor was removed 24 hours after the seeding. Single cells were cultured in iPSC medium with 0.5 ug/ml of puromycin for the next 2-3 weeks until iPSC colonies appeared. ReN and SH-SY5Y cells after selection with puromycin for 48 hours were trypsinized and plated into 10 cm tissue culture dishes. Single cells were maintained in the basal medium supplemented with 0.5 ug/ml of puromycin for the next 2-3 weeks until cell colonies appeared. Individual microcolonies were moved to a 96-well plate for clonal expansion. Clones were screened by PCR initially ( Primers: INTS10-F, 5'- TATACCAGTGGCCTCTTGTC - 3', INTS10-R, 5' - CGTCTTCCTTTATCCATCTGCC - 3') and verified by Western Blot and Sanger sequencing.

value: neuronal progenitor cell differentated from pluripotent stem cells

value: WT (shLUC)

value: shLUC


title: NPC, WT, ZMYND8, biol rep1

description: ZMYND8 ChIP-seq in WT NPCs

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
Base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality control: FastQC
Adapter trimming: Trim Galore!
Alignment (ChIPseq): BWA-MEM
Tag density files: deepTools bamCoverage
Genome_build: GRCh37/hg19
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: strand-specific bigWig, compatible with UCSC Genome Browser, generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

source_name: NPC

growth_protocol: iPSCs were cultured on Geltrex-coated plates and maintained in StemMACS™ iPS-Brew XF (Miltenyi Biotec, cat#130-104-368). NPCs were differentiated from iPSCs using Neural Induction Medium (98% Neurobasal Meida (ThermoFisher, cat#21103049) and 2% Neuronal Induction Supplementd) for 7 days and maintained in Neural Expansion Medium (49% Neurobasal Meida (ThermoFisher, cat#21103049), 49% Advanced DMEM/F12 (ThermoFisher, cat#12634010) and 2% Neuronal Induction Supplement. Neurons were differentiated from NPCs neuronal differentiation medium ( Neurobasal Meida (ThermoFisher Scientific, cat#21103049), B27 (ThermoFisher Scientific,cat#A3353501), GlutaMAX (ThermoFisher Scientific, cat#35050061), nonessential animal acids (ThermoFisher Scientific, cat#11140050), 20 ng/ml brain-derived neurotrophic factor (BDNF) (Peprotech, cat#450-02) and 20 ng/ml glial cell-derived neurotrophic factor (GDNF)(Peprotech, cat#450-10) for 21 days and then mainted in this media.  SHSY5Y cells were maintained in the basal medium (45% of Minimum Essential Medium (MEM) (Corning, cat#10009CV), 45% of Nutrient Mixture F-12 Ham (Sigma-Aldrich, Cat#N4888) and 10% of fetal bovine serum (Corning, cat#35010CV)).

extract_protocol:
Lysates were clarified from sonicated nuclei (Covaris S220), and protein-DNA complexes were isolated with antibody-conjugated Dynabeads
NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs Inc.)

treatment_protocol: Lentiviruses were produced in HEK293T cells by co-transfection 8 ug of pLentiCRISPR v2-INTS10 gRNA3 (Target sequence: TTCTGAGAGCTACGTTTGCT). iPSCs or SH-SY5Y were passaged into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of virus medium per well (cell medium with 4 ul of lentiviral particles per ml and 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G)) was added to replace old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours. After that, cells were selected with with 0.5 ug/ml of puromycin in fresh medium (InvivoGen, cat#ant-pr-1). 48 hours after selection with puromycin, iPSC colonies were disassociated with Accutase and passed through a 40 uM cell stainer to to generate single cells. Singel cell suspension with 10 μM of ROCK inhibitor and 0.5 ug/ml of puromycin were seeded in Geltrex-coated 10 cm dishes.  ROCK inhibitor was removed 24 hours after the seeding. Single cells were cultured in iPSC medium with 0.5 ug/ml of puromycin for the next 2-3 weeks until iPSC colonies appeared. SH-SY5Y cells after selection with puromycin for 48 hours were trypsinized and plated into 10 cm tissue culture dishes. Single cells were maintained in the basal medium supplemented with 0.5 ug/ml of puromycin for the next 2-3 weeks until cell colonies appeared. Individual microcolonies were moved to a 96-well plate for clonal expansion. Clones were screened by PCR initially ( Primers: INTS10-F, 5'- TATACCAGTGGCCTCTTGTC - 3', INTS10-R, 5' - CGTCTTCCTTTATCCATCTGCC - 3') and verified by Western Blot and Sanger sequencing.

value: NPC

value: wt

value: No treatment

tag: chip antibody

value: ZMYND8 (proteintech 11633-1-AP)


title: A3H4

value: Human Donor Islet Cell

value: Yes


title: Total RNAseq after ADNP depletion in wt mES cells, replicate 2

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 adnp (C) FKBP12F36V - 3F-Avi

value: 250nM dTAG13


title: NPC_p3 ,shLUC, Biol rep 7

description: 3' - mRNA


title: NPC_p3 ,shLUC, Biol rep 5

description: 3' - mRNA


title: ChIPseq for  ADNP2 in untreated ADNP2 PxVxL mutant mES cells, replicate 2

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5  adnp2 V1139E(GTA-GAA) L1141T(CTA-ACC) (C)Avi-3F  / V1139E(GTA-GAA) L1141T(CTA-ACC) (C)Avi-3F setdb1 (N) 2HA-FKBP12F36V

value: DMSO

value: FLAG, Sigma F1804


title: NPC_p3 ,shINTS10, Biol rep 4

description: 3' - mRNA


title: Total RNAseq after ADNP depletion in wt mES cells, replicate 1

value: hybrid 129-C57BL/6

value: embryonic stem (ES) cells


title: NPC_p3 ,shLUC, Biol rep 6

description: 3' - mRNA


title: cNSC_CHiC_rep1

value: Neural Stem Cells derived from IPSCs


title: NPC_p3 ,shINTS10, Biol rep 3

description: 3' - mRNA

value: neuronal progenitor cell differentated from pluripotent stem cells


title: Total RNAseq in untreated wt mES cells, replicate 2


title: A3H2

value: Female


title: NPC_p3 ,shINTS10, Biol rep 2

description: 3' - mRNA


title: ChIPseq for  ADNP2 in untreated ADNP2 PxVxL mutant mES cells, replicate 1


title: NPC_p3 ,shINTS10, Biol rep 1

description: 3' - mRNA


title: ChIPseq for ADNP2 in untreated wt mES cells, replicate 1

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 adnp2 (C) Avi-3F setdb1 (N) 2HA-FKBP12F36V


title: ChIPseq for ADNP2 in untreated wt mES cells, replicate 2


title: dF KK18G PA14 OMV ETI

city: Hanover

first: Thomas

middle: H.

last: Hampton

state: NH

address: Dewey Field Road, HB 7550

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

data_processing:
Libraries were pooled for sequencing on a NextSeq2000 instrument targeting 10M, single-end 100bp reads per sample.
Single-end reads were trimmed using cutadapt v4., and aligned to the human genome reference GRCh38, using Hisat2 v2.1.0
Genes were quantified using FeatureCounts v2.0.1, with Human Ensembl v97 as the gene annotation reference
Alignment and quantification metrics were calculated using Samtools v1.15.1
Assembly: GRCh38
Supplementary files format and content: featurecounts.readcounts.ann.tsv is a tab separated file containing raw read counts for each gene (row) in each sample (column)

source_name: polarized primary bronchial airway epithelial cells

growth_protocol:
Human primary airway epithelial cells were grown in BronchiaLife basal medium (Lifeline Cell Technology, Frederick, MD, Cat. #LM-0007) supplemented with the BronchiaLife B/T LifeFactors Kit (Lifeline Cell Technology, Cat. #LS-1047) and penicillin (10,000 U/mL) and streptomycin (10,000 μg/mL) (Sigma-Aldrich, Cat. #P4333). 500,000 cells were seeded on 24-mm permeable supports (Corning, Corning, NY, Cat. #3407), coated with Collagen type IV (Sigma-Aldrich, Cat #C-7521) and grown in an air-liquid interface media (University of North Carolina, Chapel Hill, NC) at 37°C for 3 to 4 weeks to establish polarized monolayers.
Pseudomonas aeruginosa strain PA14 was grown in artificial sputum medium (ASM) then centrifuged, washed, and resuspended in fresh ASM before measuring the optical density at 600 nm (OD600) to determine number of bacteria.
Outer membrane vesicles (bEVs) were prepared by centrifuging cultures at 2,800 g and 4 degrees C for 1 h to pellet bacteria. Supernatants were filtered twice through 0.45 μm PVDF membrane filters (Millipore, Billerica, MA) then concentrated to approximately 200 μL by centrifugation in 30 K Amicon filters (Millipore, Billerica, MA) at 2,800 g and 4 C. Concentrates were resuspended in buffer (20 mM HEPES, 500 mM NaCl, pH 7.4) and ultracentrifuged 2 h at 39,000 g and 4 C to pellet bEVs, which were resuspended in 60% OptiPrep Density Gradient Medium (Sigma-Aldrich, Cat. No. D1556) and layered with 40%, 35%, 30%, and 20% OptiPrep diluted in buffer. bEVs in OptiPrep layers were ultacentrifuged for 16 h at 100,000 g and 4 C. Fractions (500 μL) were taken from the top of the gradient, with bEVs residing in fractions 2–3, corresponding to 25% OptiPrep. The purified bEVs were quantified by nanoparticle tracking analysis (NTA, NanoSight NS300, Malvern Panalytical Ltd, Malvern, UK)

extract_protocol:
Total RNA was isolated using the miRNeasy kit (Qiagen, Germantown, MD, Cat. #217004).
RNA for RNA-seq was quantified by qubit and integrity measured on a fragment analyzer (Agilent). 100ng RNA was used as input into the Quantseq FWD workflow (Lexogen) for library preparation following manufacturer’s instructions

treatment_protocol:
Polarized human primary airway epithelial cells from donors with wild type CFTR were conditionally exposed to either Pseudomonas aeruginosa strain PA14 at a multiplicity of infection of 20:1(~2x10^7 bacteria) or 2e10 outer membrane vesicles (bEV) isolated from Pseudomonas aeruginosa strain PA14 for 6 hours, or media only as a control.
Polarized human primary airway epithelial cells from donors homozygous for the delta F 508 CFTR mutation were conditionally exposed to elexacaftor (3 micromolar) tezacaftor (3 micromolar) ivacaftor (10 nanomolar)  dissolved in DMSO or DMSO as a control for 48 hours and then conditionally exposed to either Pseudomonas aeruginosa strain PA14 at a multiplicity of infection of 20:1 (~2x10^7 bacteria) or 2e10 outer membrane vesicles (bEV) isolated from Pseudomonas aeruginosa strain PA14 for 6 hours, or media only as a control.

value: CFTR deltaF508 homozygous

tag: cftr genotype

value: dF

tag: donor

tag: pathogen exposure

value: OMV

tag: corrector

value: ETI


title: A3H12

data_processing:
Mapped to Gch38 using STAR
Gene counts using htseq-count
Assembly: GRCh38
Supplementary files format and content: Combined csv count table of all cells

value: Human Donor Islet Cell

value: Male


title: dF KK18G Control OMV DMSO

value: polarized primary bronchial airway epithelial cells

tag: genotype

value: PC


title: dF KK18G PA14 OMV DMSO


title: dF KK18G Control OMV ETI


title: A3H11

value: Yes


title: Input of ChIPseq for ADNP2 in untreated wt mES cells, replicate 2

tag: treatment

value: DMSO


title: dF KK18G PA14 ETI


title: A3H10


title: Input of ChIPseq for ADNP2 in untreated wt mES cells, replicate 1


title: dF KK18G Control ETI

value: Control


title: dF KK18G PA14 DMSO


title: A3H3


title: ChIPseq for H3K9me3 after SETDB1 depletion in ADNP2 PxVxL mutant mES cells, replicate 2

value: hybrid 129-C57BL/6

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5  adnp2 V1139E(GTA-GAA) L1141T(CTA-ACC) (C)Avi-3F  / V1139E(GTA-GAA) L1141T(CTA-ACC) (C)Avi-3F setdb1 (N) 2HA-FKBP12F36V

value: 500nM dTAG13

value: H3K9me3, Abcam ab8898


title: dF KK18G Control DMSO


title: dF KK29H PA14 OMV ETI


title: A3G9


title: A3H1

value: Female


title: dF KK29H Control OMV ETI


title: dF KK29H PA14 OMV DMSO


title: ChIPseq for H3K9me3 after SETDB1 depletion in ADNP2 PxVxL mutant mES cells, replicate 1

value: embryonic stem (ES) cells


title: dF KK29H Control OMV DMSO

value: CFTR deltaF508 homozygous


title: ChIPseq for H3K9me3 after SETDB1 depletion in wt mES cells, replicate 2

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 adnp2 (C) Avi-3F setdb1 (N) 2HA-FKBP12F36V


title: dF KK29H PA14 ETI

value: dF


title: A3G8


title: WEHI-231 TFEB KO #B-20 18h_2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.5 was used to align the reads to the GRCm38 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in GRCm38 version 100
Assembly: GRCm38 version 100
Supplementary files format and content: Tab-delimited gene counts

source_name: B cell lymphoma

growth_protocol: WEHI-231 B cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: Cells were pelleted by centrifugation, subsequently resuspended in TRIzol reagent (Ambion) and stored at -80°C

treatment_protocol: Cells were stimulated with 10µg/ml anti-IgM F(ab')2 fragments for the indicated time periods

value: B cell lymphoma

value: B lymphocyte

value: TFEB knockout #B-20

value: anti-IgM stimulation 18h


title: A3G7

extract_protocol: SmartSeq2 (21X-23X PCR cycles)

value: Human Donor Islet Cell

value: Male


title: A3G6

value: Yes


title: dF KK29H Control ETI

value: polarized primary bronchial airway epithelial cells

value: Control

value: ETI


title: ChIPseq for H3K9me3 after SETDB1 depletion in wt mES cells, replicate 1

value: hybrid 129-C57BL/6

value: 500nM dTAG13


title: WEHI-231 TFEB KO #B-20 6h_2

value: anti-IgM stimulation 6h


title: dF KK29H Control DMSO

value: DMSO


title: dF KK29H PA14 DMSO

value: CFTR deltaF508 homozygous


title: ChIPseq for H3K9me3  in ADNP2 PxVxL mutant mES cells, replicate 2

value: embryonic stem (ES) cells

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5  adnp2 V1139E(GTA-GAA) L1141T(CTA-ACC) (C)Avi-3F  / V1139E(GTA-GAA) L1141T(CTA-ACC) (C)Avi-3F

value: H3K9me3, Abcam ab8898


title: WEHI-231 TFEB KO #B-20 0h_2

value: B cell lymphoma

value: B lymphocyte

value: unstimulated control


title: ChIPseq for H3K9me3  in ADNP2 PxVxL mutant mES cells, replicate 1


title: dF KK27H PA14 OMV ETI

value: dF

value: OMV


title: A3G3

value: Human Donor Islet Cell

value: Female

value: Yes


title: ChIPseq for H3K9me3  in wt mES cells, replicate 2

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 adnp2 (C) Avi-3F setdb1 (N) 2HA-FKBP12F36V


title: WEHI-231 TFEB KO #A-59 6h_2

value: TFEB knockout #A-59


title: A3G5


title: A3G4


title: WEHI-231 TFEB KO #A-59 0h_2


title: dF KK27H Control OMV ETI

value: polarized primary bronchial airway epithelial cells

value: PC

value: ETI


title: ChIPseq for H3K9me3  in wt mES cells, replicate 1

value: hybrid 129-C57BL/6

value: DMSO


title: A3G2


title: A3G12

value: Male


title: Input of ChIPseq for H3K9me3 in untreated wt mES cells, replicate 1

value: embryonic stem (ES) cells


title: dF KK27H PA14 OMV DMSO

value: CFTR deltaF508 homozygous


title: A3G11


title: dF KK27H Control OMV DMSO


title: WEHI-231 wt 6h_2

value: B cell lymphoma

value: B lymphocyte

value: WT

value: anti-IgM stimulation 6h


title: dF KK27H PA14 ETI

value: dF


title: WEHI-231 wt 18h_2

value: anti-IgM stimulation 18h


title: WEHI-231 wt 0h_2

value: unstimulated control


title: Input_Health_5

city: Hamburg

first: Marcel

middle: Seungsu

last: Woo

state: Hamburg

address: Falkenried 94

department: Neurology

institute: UKE

data_processing:
STAR v.2.4 alignment to genome
featurCounts v.1.5.1 for gene loci counting
DESeq2 for differential expression analysis
Assembly: GRCm38 - mm10
Supplementary files format and content: tab-delimited text file including raw gene counts of every sample

source_name: Input cortex

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using poly A enrichment with NovaSeq6000 kit according to manufacturers protocol.

treatment_protocol: We actively induced EAE using MOG35-55.

value: Input cortex

value: Glt25d2 BacTRAP

value: Healthy

tag: phase


title: Input_Health_4


title: WEHI-231 TFEB KO #A-59 18h_2

value: TFEB knockout #A-59


title: A3G1

value: Human Donor Islet Cell

value: Female

value: Yes


title: dF KK27H Control ETI

value: polarized primary bronchial airway epithelial cells

value: Control

value: ETI


title: dF KK27H PA14 DMSO

value: CFTR deltaF508 homozygous

value: DMSO


title: Input of ChIPseq for H3K9me3 in untreated wt mES cells, replicate 2

value: hybrid 129-C57BL/6

value: embryonic stem (ES) cells

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 adnp2 (C) Avi-3F setdb1 (N) 2HA-FKBP12F36V


title: A3F9

value: Male


title: Input_Health_1


title: dF KK32G PA14 OMV ETI

value: dF

value: OMV


title: Input_Chronic_4

value: Input cortex

value: Glt25d2 BacTRAP

value: EAE

value: Chronic


title: A3F8

value: Human Donor Islet Cell


title: dF KK27H Control DMSO


title: A3F7

value: Yes


title: WEHI-231 TFEB KO #A-59 18h_1

value: B cell lymphoma

value: B lymphocyte

value: TFEB knockout #A-59

value: anti-IgM stimulation 18h


title: WEHI-231 TFEB KO #A-59 6h_1

value: anti-IgM stimulation 6h


title: WEHI-231 TFEB KO #B-20 0h_1

value: TFEB knockout #B-20

value: unstimulated control


title: A3F6

value: Female


title: A3G10

value: Male


title: dF KK32G PA14 OMV DMSO

value: polarized primary bronchial airway epithelial cells

value: CFTR deltaF508 homozygous

value: dF

value: DMSO


title: Input_Chronic_3

value: Input cortex

value: Glt25d2 BacTRAP

value: EAE


title: A3F5

value: Human Donor Islet Cell

value: Yes


title: Input_Chronic_2

value: Chronic


title: A3F4


title: dF KK32G Control OMV DMSO

value: PC


title: WEHI-231 TFEB KO #B-20 18h_1

value: B cell lymphoma

value: B lymphocyte

value: anti-IgM stimulation 18h


title: dF KK32G PA14 ETI

value: ETI


title: WEHI-231 wt 18h_1

value: WT


title: A3F3

value: Female


title: Input_Chronic_1


title: WEHI-231 TFEB KO #B-20 6h_1

value: TFEB knockout #B-20

value: anti-IgM stimulation 6h


title: Input_Health_2

value: Healthy


title: Input_Health_3


title: dF KK32G Control ETI

value: polarized primary bronchial airway epithelial cells

value: CFTR deltaF508 homozygous

value: dF

value: Control


title: Input_Acute_5

value: Input cortex

value: Glt25d2 BacTRAP

value: EAE

value: Acute


title: WEHI-231 wt 6h_1

value: B cell lymphoma


title: dF KK32G Control OMV ETI

value: PC


title: A3F2

value: Human Donor Islet Cell

value: Yes


title: Input_Acute_4


title: dF KK32G PA14 DMSO

value: DMSO


title: A3F12

value: Male


title: WEHI-231 TFEB KO #A-59 0h_1

value: B lymphocyte

value: TFEB knockout #A-59

value: unstimulated control


title: Input_Acute_3


title: siDerl1_3

city: Miyazaki

first: Naoya

last: Murao

department: Medical Sciences

institute: University of Miyazaki

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic (version 0.39) (parameter- adapters:NexteraPE-PE, LEADING:20 TRAILING:20, SLIDINGWINDOW:4:15, MINLEN:50)
Trimmed sequence reads were mapped to rn6 using STAR (version 2.7.3a) (parameters- quantMode: TranscriptomeSAM)
The mapped sequences were converted to TPM (transcripts per million) using RSEM (version 1.3.2) (parameter- --paired-end --estimate-rspd)
Differential gene expression analysis was performed using edgeR (version 3.28.1) (used function- calcNormFactors(), estimateCommonDisp(), estimateTagwiseDisp(), exactTest())
Assembly: rn6
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Rattus norvegicus

source_name: HCN

extract_protocol:
Total RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent RNAScreenTape. 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Derlin-1 was knocked down by reverse transfection using Thermo's Stealth RNAi™ siRNA.Thermo's Stealth RNAi™ siRNA Control Duplex was used as a control knockdown.

value: HCN

value: Rat hippocampus-derived neural stem cells

value: Derlin-1 knockdown

value: Induction to quiescence state


title: dF KK32G Control DMSO

value: polarized primary bronchial airway epithelial cells

value: CFTR deltaF508 homozygous

value: dF

value: Control


title: A3F11


title: siDerl1_2


title: Input_Acute_2

value: Input cortex

value: Glt25d2 BacTRAP

value: EAE

value: Acute


title: A3F10

value: Human Donor Islet Cell

value: Yes


title: dF KK22F PA14 OMV ETI

value: OMV

value: ETI


title: siDerl1_1


title: Input_Acute_1


title: A3F1

value: Female


title: siControl_3

value: HCN

value: Control knockdown


title: IP_Health_5

source_name: IP neurons

value: IP neurons

value: Healthy


title: IP_Health_4


title: A3E8

value: Male


title: A3E9


title: WEHI-231 wt 0h_1

value: B cell lymphoma

value: B lymphocyte

value: WT

value: unstimulated control


title: IP_Health_3

value: Glt25d2 BacTRAP


title: siControl_1

value: Rat hippocampus-derived neural stem cells

value: Induction to quiescence state


title: A3E7

value: Human Donor Islet Cell


title: dF KK22F Control ETI

value: polarized primary bronchial airway epithelial cells

value: CFTR deltaF508 homozygous

value: dF

value: Control


title: dF KK22F Control OMV DMSO

value: PC

value: DMSO


title: dF KK22F PA14 ETI

value: ETI


title: siControl_2

value: HCN

value: Control knockdown


title: IP_Health_2

value: IP neurons

value: Healthy


title: dF KK22F PA14 DMSO


title: IP_Health_1


title: sox9b, 3TG, rep1

city: Wuhan

first: Youngnam

middle: N

last: Jin

state: Hubei

address: 115 Donghu Road, Wuchang District

department: Medical Research Institute

country: China

institute: Wuhan University

data_processing:
Trimmomatic version 0.39
Adapter sequences and low-quality reads were removed.
The resulting sequencing reads were aligned to the Danio rerio genome version GRCz11 (danRer11) using STAR version 2.7.10b.
Transcripts were quantified using Salmon v1.10.1 to determine transcript abundance in terms of TPM (Transcripts per Million).
Assembly: GRCz11
Supplementary files format and content: xlsx files include TPM values for merged gene using salmon and each file contains 6 biological replicates from 2Tg and 3Tg embryos

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish embryos were placed in zebrafish E3 medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, and 0.33 mM MgSO4) and raised in a 28.5 °C incubator with a light-dark cycle of 14 h light and 10 h dark.

extract_protocol:
Total RNA was then extracted from 4-dpf embryos using TRIzol (15596026, Invitrogen, USA) or RNAiso Plus (91085, Takara Bio, Japan) following the manufacturer's protocols. At least 1 μg total RNA of each sample was used for the construction of sequencing library.
Construction of RNA libraries was done by the sequencing company (Anoroad) following standard procedures.

treatment_protocol: Embryos underwent 1-hour heat treatment at 2 and 3 dpf to induce the expression of QFvpr which is controlled by hsp70l promotor.

value: whole embryo

value: heat shock


title: sox9b, 3TG, rep2


title: dF KK22F Control OMV ETI


title: IP_Chronic_4

value: Glt25d2 BacTRAP

value: EAE

value: Chronic


title: dF KK22F Control DMSO


title: A3E4

value: Human Donor Islet Cell

value: Female

value: Yes


title: WT DD42I PA14 OMVS

value: polarized primary bronchial airway epithelial cells

value: wild type CFTR

value: WT

value: OMV


title: IP_Chronic_3


title: A3E3


title: sox9b, 2TG, rep3


title: dF KK22F PA14 OMV DMSO

value: CFTR deltaF508 homozygous

value: dF

value: DMSO


title: sox9b, 2TG, rep2


title: A3E2


title: sox9b, 3TG, rep3


title: sox9b, 2TG, rep1


title: IP_Chronic_1

value: IP neurons


title: WT DD42I Control OMVS

value: PC


title: A3E12

value: Male


title: A3E6


title: lin28a, 3TG, rep3

value: whole embryo

value: heat shock


title: WT DD42I PA14


title: A3E5


title: IP_Acute_5

value: Glt25d2 BacTRAP

value: EAE

value: Acute


title: WT DD42I Control

value: Control


title: lin28a, 3TG, rep2


title: WT DD7E PA14 OMVS


title: WT DD7E Control OMVS


title: lin28a, 3TG, rep1


title: IP_Acute_3


title: A3E10

value: Human Donor Islet Cell

value: Yes


title: A3E1

value: Female


title: A3E11


title: WT DD7E PA14

value: polarized primary bronchial airway epithelial cells

value: wild type CFTR

value: WT


title: IP_Acute_2


title: IP_Acute_1


title: IP_Chronic_2

value: Chronic


title: lin28a, 2TG, rep3


title: A3D9


title: WT DD7E Control


title: A3D8


title: lin28a, 2TG, rep1


title: A3D7


title: tardbp, 3TG, rep3


title: IP_Acute_4


title: DRG neuron, HC-HA/PTX3 (15 µg/mL), 24h, rep3

city: Baltimore

first: Chi

last: Zhang

state: MD

address: 720 Rutland Avenue

institute: Johns Hopkins University

data_processing:
Sequencing reads were aligned to annotated RefSeq genes in the mouse reference genome (mm10) using HISAT2.
Aligned reads were filtered to remove ribosomal RNA and visualized using the Integrative Genomics Viewer.
A gene count matrix that contained raw transcript counts for each annotated gene were generated using the featureCounts function of the Subread package in R against the Ensemble mm10 transcriptome.
We filtered this matrix by removing genes with zero counts across all samples and relied on the automatic and independent filtering used by limma, and EdgeR to determine the most appropriate threshold for removing genes with low counts.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: dorsal root ganglion neuron

growth_protocol: DRG neurons were maintained in DMEM/F-12 supplemented with 10% fetal bovine serum, antibiotics, and growth factors in humidified atmosphere with 5% CO2at 37°C

extract_protocol:
Total RNA was isolated using PicoPure RNA Isolation Kit (Thermo Fisher Scientific) following the manufacturer’s manual.
100 ng total RNA was input into the Illumina Total RNA prep ligation with Ribo-Zero plus library preparation kit. Libraries were prepared following manufacturer’s instructions.

treatment_protocol: After being plated on the dish for 24 hours, DRG neurons were treated with vehicle or HC-HA/PTX3 (15 µg/mL) for another 24 hours

value: dorsal root ganglion neuron

value: HC-HA/PTX3 (15 µg/mL)


title: WT DD43J PA14 OMVS

value: OMV


title: A3D6


title: tardbp, 3TG, rep2


title: DRG neuron, HC-HA/PTX3 (15 µg/mL), 24h, rep1


title: DRG neuron, HC-HA/PTX3 (15 µg/mL), 24h, rep2


title: WT DD43J Control OMVS

value: PC


title: A3D5


title: WT DD43J PA14


title: tardbp, 3TG, rep1

value: whole embryo


title: tardbp, 2TG, rep3

value: heat shock


title: DRG neuron, vehicle, rep3

value: vehicle


title: A3D4


title: WT DD43J Control


title: A3D3


title: A3D2


title: tardbp, 2TG, rep2


title: DRG neuron, vehicle, rep1


title: lin28a, 2TG, rep2


title: WT DD55J Control OMVS


title: tardbp, 2TG, rep1


title: WT DD55J PA14


title: 2_TB

city: Shang Hai

first: Ping

middle: Ping

last: Nie

address: Songhu Road 2005

institute: Fudan University

description: 10 × Genomics

data_processing:
Sequencing depth was normalized by using CellRanger (version v3.1.0).
We used Seurat package (version 3.0)  in R (version 3.5.3) to perform data filtering (both gene and cell), normalization, PCA and t-SNE.
Cells defined as neutrophils, macrophage, monocyte, dendritic cells, natural killer cells, T cells and B cells.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Tumor

extract_protocol:
Tumor tissues were dissected into 1~2 mm pieces with scissors in PBS buffer and digested in RPMI 1640 Medium containing 1% FBS, 1% penicillin-streptomycin, 1 mg/ml Collagenase II (Sigma) and 100 μg/ml DNase I (Sigma) at 37 °C for 30 min. Subsequently,  tumor tissue cells were filtered with a 70 µm cell strainer (BD Biosciences). After a 5 min centrifugation at 500 g, cells were resuspended with red blood cell lysis buffer (Beyotime) to deplete red blood cells. Thereafter, cells were washed 2~3 times and kept in RMPI1640 medium with 1% FBS and 2mM EDTA at 4°C for cell sorting.
Libraries were constructed using the Single Cell 3’ Library Kit V2 (10× Genomics).

treatment_protocol: BALB/c mice were subcutaneous inoculated with MFC cells. The tumor- bearing mice were then treated with 50mg/kg TB on day 6 for once every other day, and mice were sacrificed on day 10.

value: Tumor

value: CD45+ immune cells

value: wild type

value: Thonzonium bromide


title: A3D12

city: Edmonton

first: Patrick

last: MacDonald

institute: University of Alberta

source_name: Human Donor Islet Cell

value: Human Donor Islet Cell

value: Male

value: Yes


title: germinal center B cells, spleen, TFEB-KO, rep6

description:
GC-KO05
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
salmon version 1.10.1 was used for selective alignment and transcript-level quantification with the parameters -l A --validateMappings
kallisto.v0.48.0 was used for quasi-mapping and transcript-level quantification with 100 bootstrap samples
Assembly: Ensembl GRCm39 version 109
Supplementary files format and content: tab-delimited text file includes raw counts generated with salmon for each sample per column
Supplementary files format and content: tab-delimited text file includes normalized transcript abundances generated with kallisto

source_name: spleen

extract_protocol:
Spleen were passed through 40µm cell strainer to generate single-cell suspensions. Subsequently, ells were were sorted according to indicated marker, pelleted by centrifugation, subsequently resuspended in TRIzol reagent (Invitrogen) and stored at -80°C. Total RNA was purified from sorted cells using the TRIzol protocol (Invitrogen)extracted with
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) with minor modifications in ligation and amplification (protocol from Schattling, B., Engler, J.B., Volkmann, C. et al. Bassoon proteinopathy drives neurodegeneration in multiple sclerosis. Nat Neurosci 22, 887–896 (2019). https://doi.org/10.1038/s41593-019-0385-4)

tag: strain

value: spleen

value: CD19+, GL7+, CD95+ (GC B cells)

value: TFEB fl/fl Mb1-Cre +/-


title: WT DD25J PA14 OMVS

tag: cell type

value: polarized primary bronchial airway epithelial cells

value: wild type CFTR

value: WT


title: A3D10

tag: Sex


title: 1_Ctrl

description: 10 × Genomics

value: PBS


title: smn1, 3TG, rep1

value: whole embryo


title: WT DD55J Control

value: Control


title: A3D11

tag: disease state


title: germinal center B cells, spleen, TFEB-WT, rep4

description:
GC-WT04
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv

value: TFEB fl/fl Mb1-Cre -/-


title: smn1, 3TG, rep3

value: heat shock


title: germinal center B cells, spleen, TFEB-KO, rep5

description:
GC-KO03
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv


title: DRG neuron, vehicle, rep2

value: dorsal root ganglion neuron

value: vehicle


title: WT DD25J Control OMVS

value: PC


title: smn1, 2TG, rep3


title: smn1, 2TG, rep2


title: A3C9

value: Human Donor Islet Cell

tag: patched


title: germinal center B cells, spleen, TFEB-WT, rep3

description:
GC-WT02
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv

tag: tissue


title: WT DD25J Control


title: smn1, 3TG, rep2


title: WT DD25J PA14


title: A3D1

value: Female


title: WT DD55J PA14 OMVS

value: OMV


title: BRD4-dTAG, input

city: New York

first: Sicong

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Pair-end reads were aligned to the human genome (hg38) with decoy sequences using Bowtie2 v2.4.4 with default settings.
Samtools v1.132 was used to generate BAM files for peak calling with MACS3 v3.0.0a63.
ChIP signal was normalized to counts per million reads by deepTools2.0 v3.5.14  with duplicates ignored. Bigwg files were generated with binSize of 10.
Regions overlapping with ENCODE Blacklist regions were excluded from analysis.
ChIP-seq from some batches were analyzed using Galaxy.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: breast

growth_protocol: To study ER-dependent effect, cells were grown in 15 cm dishes for 3-4 days in phenol red-free DMEM/F-12 supplemented with 5% charcoal-dextran-treated FBS and then treated with 10 nM estrogen for 40 min.

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 10 min. Glycine was then added to quench cross-linking. Chromatin fragments were generated by sonication (Branson sonifier).
ChIP-seq library was prepared with NEBNext Ultra™ II DNA Library Prep with Sample Purification Beads (New England Biolabs)

value: breast

tag: cell line

value: breast cancer cells

value: none (input)


title: BRD4-dTAG, dTAG, E2, ER

treatment_protocol: BRD4-dTAG cells were treated with 500 nM dTAG v1 for 2 hours prior to E2. Cells were fixed with 1% formaldehyde for 10 min at room temperature.

value: ER, Santa Cruz F-10, D-12

value: dTAG, E2


title: A3C8

address: 6-126 Li Ka Shing Centre

value: Male

value: Yes


title: smn1.2TG, rep1

value: whole embryo


title: A3C7


title: germinal center B cells, spleen, TFEB-WT, rep2

description:
57G
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv

value: spleen

value: CD19+, GL7+, CD95+ (GC B cells)


title: BRD4-dTAG, E2, ER

treatment_protocol: BRD4-dTAG cells were treated with DMSO for 2 hours prior to E2. Cells were fixed with 1% formaldehyde for 10 min at room temperature.

value: DMSO, E2


title: germinal center B cells, spleen, TFEB-WT, rep1

description:
55G
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv

value: TFEB fl/fl Mb1-Cre -/-


title: BRD4-dTAG, Veh, ER

treatment_protocol: BRD4-dTAG cells were treated with DMSO for 2 hours prior to ethanol. Cells were fixed with 1% formaldehyde for 10 min at room temperature.

value: DMSO, ethanol


title: Control 03, Blood

first: Christian

last: Krebs

address: Martinistraße 52

description: Single Cell 3' v2 (10x Genomics)

data_processing:
The Cell Ranger software (Cellranger v2.1.0 and v2.2.0, 10x Genomics) was used to demultiplex cellular barcodes and map reads to the reference genome hg19. All quality control and preprocessing steps were performed in Seurat and R.
Assembly: hg19
Supplementary files format and content: filtered_gene_bc_matrices_h5.h5 : h5 files output from CellRanger
Supplementary files format and content: .rds : Seurat Files created using the output from CellRanger

source_name: Blood

extract_protocol:
Single cell suspensions were obtained from human kidney biopsies by enzymatic digestion in RPMI 1640 medium with collagenase D at 0.4 mg/ml (Roche, 11088858001) and deoxyribonuclease I (DNase I; 10 μg/ml; Sigma-Aldrich, 10104159001) at 37°C for 30 min followed by dissociation with gentle MACS (Miltenyi Biotec). Leukocytes from blood samples were separated using Leucosep tubes (Greiner Bio-One, 10349081). Cells were stained with fluorochrome-conjugated antibodies from BioLegend and BD Biosciences, CD45 BV510 (HI30), CD3 BV785 (OKT3), CD4 BV650 (RPA-T4), CD8 APC-R700 (RPA-T8), CXCR3 Pe/Dazzle (G025H7), CCR6 PerCP-Cy5-5 (G034E3). Cells were also stained with a dead cell stain (Molecular Probes, L10119) to exclude dead cells from analysis. FACS was performed on a FACSAria Fusion cell sorter (BD Biosciences). ScRNA-seq of human samples from the kidney and peripheral blood was performed from FACS-sorted CD3 positive T cells using Single Cell 3' v2 (10x Genomics) according to manufacturer's instructions. Libraries were sequenced aiming at 50,000 reads per cell on an Illumina HiSeq4000.
libaries were constructed according to manufacturer specifications
Libraries were sequenced aiming at 50,000 reads per cell on an Illumina HiSeq4000.

value: FACS-sorted CD3+ cells

value: Blood


title: Control 02, Blood

description: Single Cell 3' v2 (10x Genomics)


title: A3C6

value: Human Donor Islet Cell

value: Female


title: MED17-dTAG, clone2, dTAG, E2, H3K27ac

data_processing:
mouse chromatin was used for spike-in control during normalization
Pair-end reads were aligned to the human genome (hg38) with decoy sequences using Bowtie2 v2.4.4 with default settings.
Samtools v1.132 was used to generate BAM files for peak calling with MACS3 v3.0.0a63.
ChIP signal was normalized to counts per million reads by deepTools2.0 v3.5.14  with duplicates ignored. Bigwg files were generated with binSize of 10.
Regions overlapping with ENCODE Blacklist regions were excluded from analysis.
ChIP-seq from some batches were analyzed using Galaxy.
Assembly: hg38
Supplementary files format and content: bigwig

treatment_protocol: MED17-dTAG cells were treated with 500 nM dTAG v1 for 2 hours prior to E2. Cells were fixed with 1% formaldehyde for 10 min at room temperature.

value: breast

value: H3K27ac, Cell Signaling Technology,8173


title: germinal center B cells, spleen, TFEB-KO, rep2

description:
54G
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv

value: TFEB fl/fl Mb1-Cre +/-


title: germinal center B cells, spleen, TFEB-KO, rep3

description:
56G
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv


title: A3C5


title: MED17-dTAG, clone2, E2, H3K27ac

treatment_protocol: MED17-dTAG cells were treated with DMSO for 2 hours prior to E2. Cells were fixed with 1% formaldehyde for 10 min at room temperature.

value: breast cancer cells


title: Patient 05, Blood

description: Single Cell 3' v2 (10x Genomics)


title: Control 01, Blood

description: Single Cell 3' v2 (10x Genomics)


title: Patient 03, Blood

description: Single Cell 3' v2 (10x Genomics)


title: A3C4


title: B cells, spleen, TFEB-WT, rep5

description:
B-WT04
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv

value: CD19+ (B cells)


title: BRD4-dTAG, dTAG, E2, DNase I

data_processing:
Pair-end reads were aligned to the human female genome (hg38) using Bowtie2 with default settings.
Signal was normalized to counts per million reads by deepTools2.0 with binSize of 10.
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: To study ER-dependent effect, cells were grown in 15 cm dishes for 3 days in phenol red-free DMEM/F-12 supplemented with 5% charcoal-dextran-treated FBS and then treated with 10 nM estrogen for 40 min.

extract_protocol:
Nuclei were isolated, quantified, and divided into three tubes for digestion with 25U, 50U, and 75U of DNase I, respectively. DNA was extracted via phenol/chloroform and selectively retained for sizes below 200 bp in a 2% agarose gel.
DNase-seq library was prepared with NEBNext Ultra™ II DNA Library Prep with Sample Purification Beads (New England Biolabs)

treatment_protocol: BRD4-dTAG cells were treated with 500 nM dTAG v1 for 2 hours prior to E2.


title: Patient 06, Blood

description: Single Cell 3' v2 (10x Genomics)


title: A3C3


title: A3C11

value: Male


title: B cells, spleen, TFEB-KO, rep5

description:
B-KO03
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv


title: germinal center B cells, spleen, TFEB-KO, rep1

description:
53G
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv


title: germinal center B cells, spleen, TFEB-KO, rep4

description:
58G
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv


title: A3C10

value: Yes


title: A3C2


title: A3C12


title: Control 03, Kidney

description: Single Cell 3' v2 (10x Genomics)

source_name: Kidney

value: Kidney


title: BRD4-dTAG, Veh, DNase I

treatment_protocol: BRD4-dTAG cells were treated with DMSO for 2 hours prior to ethanol.


title: Patient 04, Blood

description: Single Cell 3' v2 (10x Genomics)


title: A3B9


title: Patient 01, Blood

description: Single Cell 3' v2 (10x Genomics)


title: B cells, spleen, TFEB-WT, rep3

description:
B-WT01
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv

value: spleen


title: MED17-dTAG, clone2, Veh, H3K27ac

treatment_protocol: MED17-dTAG cells were treated with DMSO for 2 hours prior to ethanol. Cells were fixed with 1% formaldehyde for 10 min at room temperature.


title: B cells, spleen, TFEB-KO, rep6

description:
B-KO05
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv


title: RETcoh_3M_RCS

city: Dublin

first: Leonie

last: Young

state: Dublin

address: 31A York Street

department: Surgery

country: Ireland

institute: RCSI

description: Raw data are available via DUA

data_processing:
Salmon (v.0.91) was used to perform quasi-mapping of sequencing reads, with seqBias and gcBias corrections enabled, using a 31bp k-mer index of the GRCh38.p10 (GENCODE v.27) human reference transcripts, to estimate transcript abundance for each sample
Tximport package was used to import transcript abundance estimates from quant.sf files, generated by Salmon read mapping into R statistical programming environment for gene expression quantification. Transcript abundance estimates were collapsed to gene level gene expression counts. TXI data objects for MAYO and PITT-RCSI RNA-Seq cohort, containing unprocessed Salmon read counts, transcript per million (TPM) and gene length values were combined for subsequent downstream analysis.
Genes with little to no expression across all samples were filtered.
Filtered gene level counts were normalised with edgeR calcNormFactors() and cpm() function, where counts per million (CPM): CPM = C * 106/N (counts (C) scaled by the library depth in million units). A log2 transformation was applied to CPM: log2(CPM +1), where 1 is a pseudocount added to prevent negative value counts. Filtered log2 CPM and TPM genes were annotated using biomaRt R package to identify protein coding genes using the ENSEMBL GRCh38 p.10 database.
In order to correct for between RNA-Seq cohort (MAYO, PITT-RCSI, RCSI-Bmt18) batch driven effect, filtered protein coding gene expression counts were used as input to svaseq R package for batch effect assessment. A multiple linear regression model was fit for each surrogate variable (SV), with the following independent predictors: sequencing batch ID [1,5], disease status (primary breast (P) / brain metastases (M)), estrogen receptor (ER) IHC status (ER+/ER-) and primary tumour histological subtype (DCIS, IDC, ILC, Mixed ILC/IDC). A linear model fitted using SV1 was found to be significantly associated with sequencing batch (P < 0.01; R2 ~0.58).  As such, in order to correct for between RNA-Seq cohort (MAYO, PITT-RCSI) batch driven effect, removeBatchEffect() function in LIMMA package in R, was used with SV1, to adjust gene expression values to account for mean shifts in expression driven by the batch driven effect.
Assembly: GRCh38.p10 (GENCODE v.27)
Supplementary files format and content: .xlsx excel spread sheet containing batch corrected log2 TMM normalised CPM proteing coding gene expression values for all 16 samples

source_name: BREAST CANCER

extract_protocol:
RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue using the Qiagen AllPrep DNA/RNA FFPE kit, on a QIAcube instrument, following standard protocols. Sample quality and concentration were evaluated using 2100 Expert Software - Bioanalyzer System.
100 ng of total RNA and NUSeq's Illumina Stranded Total RNA-Seq Library Preparation protocol

value: BREAST CANCER

tag: cohort

value: PITT-RCSI

tag: patientid

tag: tumour location

value: BRAIN METASTATIC TUMOUR


title: Control 01, Kidney

description: Single Cell 3' v2 (10x Genomics)


title: Patient 02, Blood

description: Single Cell 3' v2 (10x Genomics)


title: B cells, spleen, TFEB-KO, rep4

description:
58B
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv


title: BRD4-dTAG, E2, DNase I

treatment_protocol: BRD4-dTAG cells were treated with DMSO for 2 hours prior to E2.


title: RETcoh_6M_RCS

description: Raw data are available via DUA


title: A3B8


title: B cells, spleen, TFEB-WT, rep4

description:
B-WT02
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv

value: TFEB fl/fl Mb1-Cre -/-


title: Control 02, Kidney

description: Single Cell 3' v2 (10x Genomics)

value: FACS-sorted CD3+ cells


title: A3C1


title: ChIPseq for ADNP  in wt mES cells, replicate 2

data_processing:
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
Sequenced reads were aligned using STAR 2.7.3 (STAR --runMode alignReads --outSAMtype BAM SortedByCoordinate --readFilesIn R1.fastq.gz R2.fastq.gz --readFilesCommand zcat --genomeDir mm10_hg38Spike_refSTAR --runThreadN 10 --alignIntronMax 1 --alignEndsType EndToEnd --outFilterType Normal  --seedSearchStartLmax 30 --outFilterMultimapNmax 10000 --outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax 1 --outSAMunmapped Within --outFileNamePrefix _ --clip3pAdapterSeq CTGTCTCTTATACACATCT AGATGTGTATAAGAGACAG --outBAMsortingBinsN 100).
Assembly: mm10
Supplementary files format and content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools).

source_name: hybrid 129-C57BL/6

extract_protocol:
10-20^6 mES cells were crosslinked, chromatin was extracted and sonicated to an average size of 300bp. 5% of chromatin was set aside as Input control. The chromatin was incubated with antibody and protein A/G coupled Dynabeads, washed and de-crosslinked. Purified DNA was subsequently used for library preparation. For a detailed protocol, see Ahel,Pandey et al. 2024.
Libraries were prepared using the NEB Next Ultra II DNA library prep kit according to manufacturers instructions.

value: hybrid 129-C57BL/6

value: embryonic stem (ES) cells

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 adnp (C) 3F-V5

tag: antibody

value: FLAG, Sigma F1804


title: A3B7

value: Human Donor Islet Cell


title: B cells, spleen, TFEB-KO, rep3

description:
56B
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv

value: TFEB fl/fl Mb1-Cre +/-


title: ChIPseq for ADNP in ADNP PxVxL mutant mES cells, replicate 2

value: mES159-Rosa26(tg)Cre-ERT2/(tg)BirA-V5 adnp V821E (GTG-GAA) L823T (ACC-CTA) (C) 3F-V5


title: ChIPseq for ADNP in ADNP PxVxL mutant mES cells, replicate 1


title: Patient 06, Kidney

description: Single Cell 3' v2 (10x Genomics)