title: A3B6

value: Female


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

status: Public on Jun 25 2024

type: SRA

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description:
55B
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv

library_source: transcriptomic

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

molecule: polyA RNA

organism: Mus musculus

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

tag: tissue

value: spleen

tag: cell type

value: CD19+ (B cells)

tag: genotype

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


title: Patient 04, Kidney

city: Hamburg

first: Christian

last: Krebs

state: Hamburg

address: Martinistraße 52

institute: UKE

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

organism: Homo sapiens

source_name: Kidney

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: Kidney

tag: treatment


title: Patient 05, Kidney

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


title: A3B5

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

source_name: Human Donor Islet Cell

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

value: Human Donor Islet Cell

tag: Sex

tag: disease state

tag: patched

value: Yes


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

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 V821E (GTG-GAA) L823T (ACC-CTA) (C) 3F-V5

tag: antibody


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

description:
54B
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv

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


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

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

value: FLAG, Sigma F1804


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


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

description:
57B
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv


title: MAPS EE-KO-Pachytene rep2

city: Hong Kong

first: Dongliang

last: LI

state: Hong Kong S.A.R. of China

address: 21 SASSOON ROAD, POKFULAM

department: Obstetrics & Gynaecology Department

country: Hong Kong

institute: The University of Hong Kong

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLCgenomic benchwork (parameter - Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters - mismath cost: 2 insertion cost: 3 deletion cost: 3 length fracton: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM valuesfor each sample

source_name: testis

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

value: testis

value: primary cell

value: pachytene cell

value: MAPS overexpression in KO background

value: purify by STA-PUT


title: A3B2

value: Female


title: A3B12

value: Male


title: A3B3


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

description:
53B
salmon_raw_counts.tsv
kallisto_normalized_abundances.tsv

value: spleen

value: CD19+ (B cells)


title: RETcoh_MAYO_BM_22

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: MAYO

tag: patientid

tag: tumour location

value: BRAIN METASTATIC TUMOUR


title: Patient 03, Kidney

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

value: FACS-sorted CD3+ cells

value: Kidney


title: MAPS EE-KO-Pachytene rep1


title: A3B11

value: Human Donor Islet Cell

value: Yes


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

value: hybrid 129-C57BL/6

value: embryonic stem (ES) cells

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


title: Patient 02, Kidney

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


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


title: A3B4


title: MAPS KO-Pachytene rep2

value: testis

value: primary cell

value: pachytene cell

value: MAPS KO


title: WT-Pachytene rep1

value: WT

value: purify by STA-PUT


title: A3B10

value: Male


title: HaCaT cells, IFN-γ and TNF-α, 24h

city: Incheon

first: Youn-Jung

last: Kim

address: Academyro 119

country: South Korea

institute: Incheon National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19(UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
The read count data were processed based on the quantile-normalization method using EdgeR within R (R development Core Team, 2016) using Bioconductor
Gene classification was based on searches performed by DAVID
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: HaCaT

growth_protocol: HaCaT cells were cultured in DMEM supplemented with 10% fetal bovine serum and penicillin-streptomycin (100 U/mL; Gibco). Cells were grown at 37 °C in 100 mm dishes in a humidified atmosphere containing 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: After treatment with 60 μg/mL of PAB (Polyopes affinis extract) with TNF-α and IFN-γ (10 ng/mL each) or without, the cells were incubated for 24 h.

value: HaCaT

value: Keratinocyte

value: IFN-γ and TNF-α


title: Patient 01, Kidney

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

value: FACS-sorted CD3+ cells


title: A3A9


title: HaCaT cells, PAB + IFN-γ and TNF-α, 24h

value: PAB(Polyopes affinis extract) + IFN-γ and TNF-α


title: RETcoh_MAYO_BM_8

description: Raw data are available via DUA

value: BREAST CANCER

value: MAYO

value: BRAIN METASTATIC TUMOUR


title: MAPS KO-Pachytene rep1


title: A3B1

value: Human Donor Islet Cell

value: Female

value: Yes


title: HaCaT cells, Control, 24h

value: DMSO


title: RETcoh_MAYO_BM_2

description: Raw data are available via DUA


title: RETcoh_BM62

description: Raw data are available via DUA

value: PITT-RCSI


title: RETcoh_MAYO_BM_20

description: Raw data are available via DUA


title: RETcoh_BM72

description: Raw data are available via DUA


title: Leydig cells, Negative_siRNA_2

city: Fuzhou

first: sun

middle: jian

last: dong

address: 1 North Road, Xuefu

country: China

institute: Fujian medical university

data_processing:
Sequencing reads were mapped to a reference mouse genome (GRCm38/mm10) with  HISAT2 (default parameters)
Gene expression was counted using featureCounts
DEGs were further processed with DEGSeq
Genome_build: mm10
Supplementary_files_format_and_content: DEG.txt

source_name: mouse Leydig cell

extract_protocol:
mouse primary Leydig cells were divided into two groups: Negative siRNA and Trps1 siRNA (n = 2 per group). Cells were collected and subjected to RNA extraction (E.Z.N.A. Total RNA Kit I)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: 6-month-old mouse

value: Negative siRNA

value: Leydig cell


title: Leydig cells, Trps1_siRNA_2

value: Trps1 siRNA


title: Leydig cells, Trps1_siRNA_1


title: Ramos TFEB KO #B-24 6h_2

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 hg38 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in hg38 version 97
Assembly: hg38 gene version 97
Supplementary files format and content: Tab-delimited gene counts

source_name: Burkitt lymphoma

growth_protocol: Ramos 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: Burkitt lymphoma

value: Ramos

value: B lymphocyte

value: TFEB knockout #B-24

value: anti-IgM stimulation 6h


title: A3A7

value: Male


title: RETcoh_BM51

description: Raw data are available via DUA

value: BREAST CANCER


title: RETcoh_MAYO_BM_3

description: Raw data are available via DUA

value: MAYO

value: BRAIN METASTATIC TUMOUR


title: WT-Pachytene rep2

value: testis

value: primary cell

value: pachytene cell

value: WT

value: purify by STA-PUT


title: Leydig cells, Negative_siRNA_1

value: 6-month-old mouse

value: Negative siRNA


title: A3A6

value: Human Donor Islet Cell

value: Female

value: Yes


title: RETcoh_BM47

description: Raw data are available via DUA

value: PITT-RCSI


title: Ramos TFEB KO #A-31 18h_2

value: Burkitt lymphoma

value: Ramos

value: B lymphocyte

value: TFEB knockout #A-31

value: anti-IgM stimulation 18h


title: Ramos TFEB KO #B-24 0h_2

value: TFEB knockout #B-24

value: unstimulated control


title: RETcoh_BM17

description: Raw data are available via DUA

value: BREAST CANCER

value: BRAIN METASTATIC TUMOUR


title: A3A8

value: Male


title: A3A5


title: Ramos TFEB KO #B-24 18h_2


title: A3A4


title: Ramos TFEB KO #A-31 6h_2

value: anti-IgM stimulation 6h


title: A3A3


title: Ramos TFEB KO #A-31 0h_2


title: Ramos wt 18h_2

value: WT


title: A3A2


title: Tcell, ZNF460, resting, rep3

city: New York

middle: S

last: Silva Santos

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

data_processing:
ATAC-Seq reads were mapped to the UCSC hg38 genome using bowtie2 vx.1.0 with the parameters --local --very-sensitive-local
Duplicated reads were removed with Picard MarkDuplicates
Peaks were called using macs2 vx.1.z with the parameters --nomodel –nolambda --cutoff-analysis
bigWig files were generated using bamCoverage v1.x.1 with the parameter --normalizeUsing CPM
Assembly: hg38 + HIV inserts
Supplementary files format and content: bigwig, narrowPeak, HIV_construct_inserts_coordinates.csv

source_name: Peripheral Blood Mononuclear Cells (PBMCs)

growth_protocol: Primary T cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), antibiotics, 50 U/mL of human IL-2 and 5,000 Gy-irradiated NK and CD8 T cell depleted PBMCs, in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Genomic DNA was collected, tagmented and purified using the ATAC-Seq Kit (Active Motif)
PCR amplification of tagmented DNA and library preparation were performed using the ATAC-Seq Kit (Active Motif)

treatment_protocol: Cells were stimulated with 0.1 µg/mL of anti-CD3 and anti-CD28 monoclonal antibodies in above culture medium for 1 week (activated conditions) then cultured with 10 ng/mL of human IL-7 for an additional week (resting conditions).

value: T cell

value: cultured IL7


title: Tcell, ZNF460, resting, rep2

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: Ramos wt 6h_2


title: Tcell, ZNF460, resting, rep1


title: A3A12

value: Human Donor Islet Cell

value: Yes


title: A3A10


title: Tcell, ZNF460, activated, rep3

value: anti CD3/CD38 activation


title: Ramos wt 0h_2

value: Burkitt lymphoma

value: Ramos


title: A3A1

value: Female


title: Tcell, ZNF460, activated, rep2


title: Tcell, ZNF460, activated, rep1


title: human_neuron_RNAseq_rep3

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)

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: Neurons derived from neural stem cells

tag: cut &_run_antibody


title: Ramos TFEB KO #B-24 6h_1

value: B lymphocyte

value: TFEB knockout #B-24


title: Tcell, ZNF140, resting, rep3


title: human_neuron_RNAseq_rep2


title: Tcell, ZNF140, resting, rep2


title: Ramos TFEB KO #B-24 0h_1

value: unstimulated control


title: human_neuron_RNAseq_rep1


title: Ramos TFEB KO #A-31 18h_1

value: TFEB knockout #A-31

value: anti-IgM stimulation 18h


title: hNSC_RNAseq_rep4

value: Neural Stem Cells derived from IPSCs


title: Ramos TFEB KO #B-24 18h_1


title: Tcell, ZNF140, resting, rep1


title: Tcell, ZNF140, activated, rep3


title: hNSC_RNAseq_rep3


title: Ramos TFEB KO #A-31 6h_1

value: anti-IgM stimulation 6h


title: Ramos TFEB KO #A-31 0h_1


title: Tcell, ZNF140, activated, rep2

value: T cell


title: S_6_R5_1

type: RNA

city: Hannover

first: Matthias

middle: M

last: Wehr

address: Nikolai-Fuchs-Str. 1

institute: Fraunhofer ITEM

hyb_protocol: GeneChip™ Human Clariom™ D Arrays according to the manufacturer’s recommendation (ThermoFisher).

scan_protocol: Affymetrix GeneChip™ Command Console Software with .cel files as data output.

data_processing: Array data were analyzed with the Transcriptome Analysis Console (TAC) Software 4.0 (ThermoFisher).

label: biotin

label_protocol: Affymetrix GeneChip™ Whole Transcript (WT) PLUS Reagent Kit according to the manufacturer’s recommendation (ThermoFisher).

growth_protocol: The A549 cell line was purchased from a commercial supplier (ATCC; LGC Promochem). Cells were routinely taken from a stock pool and grown in 75cm2 flasks by use of Dulbecco´s MEM medium (Seromed, Berlin) supplemented with 10% FCS and antibiotics. Cells were passaged every 3 to 4 days. During each passage beside continuous microscopic observation, cell quality and quantity were checked by use of an electronic cell counter (CASY® Cell Counter + Analyser System; Schärfe System, Reutlingen, Germany).

extract_protocol: RNA was isolated and purified using the RNeasy MiniKit (Qiagen) and treated with DNase (Qiagen). RNA concentration (A260) and purity (A260/A280 ratio) were measured by spectrophotometry (NanoDrop™ 2000 Spectrophotometer, software version 1.6.198, ThermoFisher Scientific). RNA integrity number (RIN) was evaluated using an Agilent 2100 Bioanalyzer® (Agilent Technologies). All RNA samples showed very good quality as indicated by high RIN values between 9.0 and 10.0.

treatment_protocol: To mimic the exposure situation of the epithelium in the in vivo lung the most common approach used is the air-liquid-interface (ALI) technique based on cell cultures on microporous membranes. Therefore, cells were initially cultivated under their cell type specific conditions in 75cm² culture flasks using submerged conditions. Culture medium was changed every to 2-3 days. Before reaching 80% confluence, cells were subcultivated. During a cell passage an aliquot of the cells was then seeded on microporous membranes (Inserts, BD Falcon; 0.4µm pore size; growth area ~1cm²). Cells were further cultivated on the membranes for approximately 72hrs until they reached a confluent monolayer as inspected by light microscopy. Serum was removed from the culture during a medium change 18hrs before exposure. Previous to the exposure with the model substances, residual liquid from the apical side of each cell monolayer was gently removed. During the treatment, cells were nutrified by culture media from beneath the membrane solely while being exposed to the test substances from the top.

value: clean air

tag: concentration

value: 0 ppm

tag: replicate

tag: exposure plate

tag: group

value: CA


title: S_6_R6_1


title: hNSC_RNAseq_rep2

tag: cell type


title: Ramos wt 18h_1

tag: tissue

tag: genotype

value: WT


title: Tcell, ZNF140, activated, rep1

value: Peripheral Blood Mononuclear Cells (PBMCs)

tag: treatment

value: anti CD3/CD38 activation


title: S_6_R1_1


title: Ramos wt 6h_1

value: Burkitt lymphoma

value: Ramos


title: Tcell, KDM2A, resting, rep3

value: cultured IL7


title: S_6_NEC6_1

value: non exposed control

value: NEC


title: S_6_NEC1_1


title: S_6_NEC5_1


title: Ramos wt 0h_1

value: B lymphocyte

value: unstimulated control


title: human_neuron_C&R_POLII_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)

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: Neurons derived from neural stem cells

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


title: Tcell, KDM2A, resting, rep2


title: human_neuron_C&R_POLII_rep1

description: Kit and protocol from Epicypher Ltd


title: Tcell, KDM2A, resting, rep1


title: S_6_B6_3

value: Dimethylamine

value: HD


title: S_6_B6_2


title: S_6_B6_1


title: hNSC_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)

value: Neural Stem Cells derived from IPSCs


title: genomic DNA input

city: Madison

first: Jeffrey

last: Dilworth

state: Wisconsin

address: 1111 Highland Ave

institute: University of Wisconsin

data_processing:
The reads were aligned to the human hg38 genome using bowtie2 (v2.3.5.1).
Peak calling: MACS2 using a q value cutoff = 0.05
Genome_build: hg38

source_name: Immortalized non-FSHD human myoblast cell line WS234 (donor 15VBic)

growth_protocol: Cells were cultured in LHCN medium on 0.1% (w/v) gelatin coated plates at 37oC in 5% CO2 incubator.

extract_protocol:
Cells were rinsed with PBS, collected using cell scrapers, centrifuged at 500 x g for 5 minutes and resuspended in swelling buffer (50 mM Tris pH 8, 2.5 mM EDTA and 30% (v/v) glycerol). Cells were then incubated for 30 minutes in swelling buffer at 4oC, sonicated using Bioruptor (Diagenode) for 2 cycles (HI power, cycles of 30 sec on / 1 min off). Nuclei were spun down at 1000 x g for 5 mins at 4oC, resuspended in sonication buffer (50 mM Hepes pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and 1% SDS), and sonicated for 13 cycles using the same settings as the previous step. 7.5 ug of SMCHD1 antibody (Abcam # ab31865) was added to 250 ug of precleared chromatin and incubated for 3 hours at RT.
Library was constructed using KAPA HyperPrep Kit (Roche #07962363001).

treatment_protocol: Proliferating myoblasts were fixed in 1% (v/v) formaldehyde for 20 minutes at RT and quenched with 125 mM glycine for 10 minutes at RT.

tag: chip antibody

tag: cell tpye

value: human myoblast cell line WS234 (donor 15VBic, female non-FSHD sample)


title: hNSC_RNAseq_rep1

tag: cell line


title: S_6_B5_3

value: MD


title: hNSC_C&T_POLII_rep1

description: Kit and protocol from ActiveMotif Ltd


title: RNAseq of parental strain, 6h with NSF, rep 2

data_processing:
Raw data were demultiplexed and converted to fastq format using bcl2fastq2 (v1.17) Illumina. Fastq files were aligned using STAR (v2.7.3a) with the parameters --runMode alignReads --outFilterType BySJout --outFilterMultimapNmax 100 --outFilterMismatchNoverLmax 0.05 --outSAMmultNmax 1 --outMultimapperOrder Random --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI NM MD AS nM --outSAMunmapped Within. STAR sam output was converted to bam using samtools (v1.9). Bam files were used to calculate strand-specific coverage using bedtools genomeCoverageBed (v2.27.1), resulting bedgraph files were normalized to 1 million genome mapping reads (RPM), and converted to bigWig format using bedGraphToBigWig (v4).
Assembly: Spombe.ASM294v2.24
Supplementary files format and content: bigWig files containing normalized read counts (to 1 mio genome mapping reads per library) split by plus and minus strand for visualization in UCSC or IGV genome browser.

organism: Schizosaccharomyces pombe

source_name: S. pombe cell culture

growth_protocol: S. pombe cell cultures were grown in standard YES medium (OD = 1, exponential phase) at 30 degrees celsius. At time point 0, cells were diluted to OD = 0.01 and shifted to EMM(187mM NH4Cl) with MeOH or NSF at 30 degrees celsius.

extract_protocol:
Total RNA was extracted with the MasterPure RNA Purification Kit from epicenter (MPY03100).
Total RNA libraries were prepared with TruSeq Stranded Total RNA kit (Illumina, 20020599) according to manufacturer’s instructions.

treatment_protocol: 2, 4, 6 h growth at low density (OD=0.01) either with NSF or MeOH as control.

value: S. pombe cell culture

tag: strain

value: h+ orf{del}::ade6-M216 ura4-D18 leu1-32

value: 6h NSF


title: Tcell, KDM2A, activated, rep3

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: T cell

value: anti CD3/CD38 activation


title: SMCHD1 CHIP pull down

value: SMCHD1 antibody (Abcam #ab31865)


title: shSMCHD1 C

data_processing:
Reads are mapped to the hg38 genome using STAR.
Counts were summarized using featureCounts function in Rsubread.
DESeq2 was used to identify the differentially expressed genes.
Genome_build: hg38
Supplementary_files_format_and_content: FeatureCount Table

extract_protocol:
5 days after SMCHD1 and non-silencing lentiviral transduction, RNA was collected using a PureLink RNA mini kit (Thermo Fisher Scientific #12183018A) according to the manufacturer’s protocol.
rRNA depletionwas performed with a Ribo-Zero Magnetic Gold Kit (Illumina cat. No. MRZG12324). RNA library was prepared with a KAPA stranded RNA-seq kit (roche #07962169001).

treatment_protocol: For preparing the lentivirus, HEK293T cells were transfected with the pMD2.G, psPAX2, and shRNA vector plasmids using polyethylenimine. Lentivirus-containing medium supernatant  was centrifuged at 126086 x g for 2.5 hours at 4 oC using Optima L-100 XP ultracentrifuge, and the pellet was resuspended in LHCN medium. To transduce the cells, purified lentivirus was added to culture medium for 16 hours and fresh LHCN medium was replaced.


title: RNAseq of parental strain, 6h with NSF, rep 3


title: RNAseq of parental strain, 6h with NSF, rep 1


title: Tcell, KDM2A, activated, rep2


title: S_6_B5_2


title: S_6_B5_1


title: human_neuron_C&R_RAD21_rep2

description: Kit and protocol from Epicypher Ltd

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


title: shSMCHD1 B


title: S_6_B1_2

value: LD


title: human_neuron_C&R_RAD21_rep1

description: Kit and protocol from Epicypher Ltd


title: RNAseq of parental strain, 6h with methanol, rep 2

value: 6h MeOH


title: S_6_B1_3


title: Tcell, KDM2A, activated, rep1


title: RNAseq of parental strain, 6h with methanol, rep 3


title: Tcell, KCNA3, resting, rep3

value: cultured IL7


title: hNSC_C&R_RAD21_rep2

description: Kit and protocol from Epicypher Ltd


title: non-silencing scramble shRNA control replicate 1

value: non-silencing scramble shRNA control


title: non-silencing scramble shRNA control replicate 2


title: S_6_B1_1

value: Dimethylamine


title: hNSC_C&R_RAD21_rep1

description: Kit and protocol from Epicypher Ltd


title: Tcell, KCNA3, resting, rep1


title: Tcell, KCNA3, resting, rep2


title: RNAseq of parental strain, 4h with NSF, rep 3

value: 4h NSF


title: Tcell, KCNA3, activated, rep3


title: human_neuron_C&R_CTCF_rep1

description: Kit and protocol from Epicypher Ltd

value: Neurons derived from neural stem cells

value: CTCF (EpiCypher # 13-2014)


title: Root,  32-B2150

city: Lubbock

first: Mostafa

middle: ABDELWAHED NOURELDEIN

last: ABDELRAHMAN

state: TX

address: 3120 4th Street, Lubbock, TX, USA

institute: TEXAS TECH UNIVERSITY

data_processing:
STAR
The paired-end raw sequences obtained from RNA-seq of WT and C4 grown under both normal (0 mM NaCl) and salt-stress (150 mM NaCl) conditions were checked using FastQC v0.12.1, then trimmed using fastp
High quality reads were aligned to Athaliana_447_TAIR10.fa reference genome (phytozome-next.jgi.doe.gov/) using STAR 2.7.11a (
Read coutn calculated
Assembly: Arabidopis TAIR11
Supplementary files format and content: tab-delimited txt file contatins raw counts for each Sample
Supplementary files format and content: tab-delimited txt file contatins raw counts for each Sample

organism: Arabidopsis thaliana

source_name: root

growth_protocol: We used our previously developed A. thaliana ISPS-transgenic lines (Zuo et al., 2019). The full complementary ISPS DNA sequence including native transit peptide sequence from Eucalyptus globulus was placed under the Arabidopsis rubisco small subunit promoter rbcS-1A (At1g67090) to generate the transgenic, IE lines. After the ISPS sequence, an octopine synthase gene was placed as a transcriptional terminator of the transgene. The construct without EgISPS was also transformed with the vector to generate a NE EV control. After successful transformation, seven transgenic lines and three empty vector lines were characterized. Among the transgenic lines, B2 and C4 showed highest level of isoprene emission (Zuo et al., 2019). Thus, we selected B2 and C4 transgenic lines as IE, together with EV-B3 (referred as EV hereafter) as NE for the current study.  The A. thaliana seeds were surface sterilized with 70% ethanol and 5% bleach solution for 5 and 10 min, respectively, followed by washing with sterilized milli-Q water for five times. Seeds were placed on germination medium (GM) plates containing ½ Murashige and Skoog (MS) solid medium (0.8% agar and 1% sucrose), supplemented with Gamborg’s vitamins solution (SigmaAldrich, Germany). After stratification for three days at 4°C in the dark, the plates were vertically placed in the growth chamber under a 16 h: 8 h, light: dark photoperiod, 120 mol m−2 s−1 photosynthetically active radiation (PAR), 23/20°C day/night temperatures, and 60% relative humidity. To simulate salt stress, EV, B2, and C4 seedlings were exposed to different 16 433 The copyright holder for this preprint bioRxiv preprint doi: https://doi.org/10.1101/2024.02.09.579703 ; this version posted February 14, 2024. (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license  .

extract_protocol:
Total RNA from frozen root samples was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany). The RNA concentration, integrity, and quality were determined with a Qubit RNA Broad-Range Assay Kit (Invitrogen, Waltham, MA, USA) and a Qubit 4 benchtop fluorometer (Invitrogen, Waltham, MA, USA). RNA integrity was further assessed with a 2100 Bioanalyzer
mRNA sequencing was performed at the Michigan State University Research Technology Support Facility Genomics Core (https://rtsf. natsci.msu.edu/genomics/). Libraries were prepared using the Illumina Stranded mRNA Library Preparation, Ligation Kit with IDT for Illumina Unique Dual Index adapters following the manufacturer’s recommendations except that half volume reactions were used. Completed libraries were quality checked and quantified using a combination of Qubit dsDNA high sensitivity (HS) and Agilent 4200 Tape Station HS DNA1000 assays. The libraries were pooled in equimolar proportions and the pool quantified using the Invitrogen Collibri Quantification qPCR kit. The pool was combined with other pools of Illumina Stranded RNA libraries prepared by the Genomics Core to make use of a shared S4 lane. This combined pool was likewise quantified using the Invitrogen Collibri Quantification qPCR kit. The combined pool was loaded onto one lane of an Illumina S4 flow cell and sequencing was performed in a 2x150 bp paired end format using a NovaSeq 6000 v1.5, 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis (RTA) v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.

treatment_protocol: Concentrations of sodium chloride (NaCl). For root phenotype analyses and isoprene emission measurements, five-day-old seedlings were treated with 0, (mock), 50 (mild stress) or 100 (severe stress) mM NaCl for five days in solid MS medium. To study the primary root growth in soil rather than in an artificial substrate, NE (EV) and IE (B2 and C4) Arabidopsis plants were planted in homemade Rhizoboxes, special pots where root growth can be monitored. Plants were germinated and grown for two weeks in sterile Suremix soil (Michigan Grower Products Inc, Galesburg, MI, USA) and kept in the same controlled growth chambers used for plates.

value: root

value: 150 mM NaCl


title: Root,  34-B2150


title: RNAseq of parental strain, 4h with NSF, rep 1

value: S. pombe cell culture

value: h+ orf{del}::ade6-M216 ura4-D18 leu1-32


title: RNAseq of parental strain, 6h with methanol, rep 1


title: Root,  15-B20_S12

value: 0 NaCl


title: hNSC_C&R_CTCF_rep2

description: Kit and protocol from Epicypher Ltd

value: Neural Stem Cells derived from IPSCs


title: Tcell, KCNA3, activated, rep2

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: T cell

value: anti CD3/CD38 activation


title: RNAseq of parental strain, 4h with methanol, rep 3

value: 4h MeOH


title: Tcell, KCNA3, activated, rep1


title: hNSC_C&R_CTCF_rep1

description: Kit and protocol from Epicypher Ltd


title: Tcell, control, resting, rep4


title: human_neuron_C&R_H3K27me3_rep2

description: Kit and protocol from Epicypher Ltd

value: H3K27me3 (ThermoFisher # MA511198)


title: RNAseq of parental strain, 4h with methanol, rep 2


title: Tcell, control, resting, rep3

value: cultured IL7


title: human_neuron_C&R_CTCF_rep2

description: Kit and protocol from Epicypher Ltd


title: Root,  12-B20_S9


title: RNAseq of parental strain, 2h with NSF, rep 3

value: 2h NSF


title: RNAseq of parental strain, 2h with NSF, rep 2


title: RNAseq of parental strain, 4h with NSF, rep 2


title: Root,  39-C4150_S31


title: human_neuron_C&R_H3K27me3_rep1

description: Kit and protocol from Epicypher Ltd


title: hNSC_C&R_H3K27me3_rep2

description: Kit and protocol from Epicypher Ltd


title: RNAseq of parental strain, 2h with NSF, rep 1


title: Tcell, control, resting, rep1


title: Root,  37-C4150_S30


title: Tcell, control, resting, rep2


title: Root,  31-B2150


title: Root,  36-C4150_S29


title: hNSC_C&R_H3K27me3_rep1

description: Kit and protocol from Epicypher Ltd


title: human_neuron_C&R_H3K27ac_rep2

description: Kit and protocol from Epicypher Ltd

value: H3K27ac (EpiCypher # 13-0045)


title: RNAseq of parental strain, 2h with methanol, rep 3

value: 2h MeOH


title: Root,  14-B20_S11


title: Root,  21-WT150_S17

value: WT


title: Root,  25-WT150_S20


title: Tcell, control, activated, rep3


title: RNAseq of parental strain, 2h with methanol, rep 2


title: Tcell, control, activated, rep1


title: RNAseq of parental strain, 2h with methanol, rep 1


title: Root,  17-C40_S14


title: Root,  20-C40_S16


title: human_neuron_CHiC_rep2

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.

value: Neurons derived from neural stem cells


title: RNAseq of parental strain, 0h, rep 1


title: RNAseq of parental strain, 0h, rep 3


title: RNAseq of parental strain, 0h, rep 2


title: MOLM13_sgBOD1L_243_Dox_4d_rep2

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: MOLM-13 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was collected using Rneasy Mini Kit with DNase (QIAGEN).
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Doxycycline was treated for 4 days. DMSO or dTAG-13 were treated for 24 hours.

value: leukemia

value: 1µg/mL Doxycycline 4d


title: MOLM13_sgBOD1L_437_Dox_4d_rep2


title: MOLM13_sgBOD1L_437_Dox_4d_rep1


title: hNSC_C&R_H3K27ac_rep1

description: Kit and protocol from Epicypher Ltd


title: Root,  16-C40_S13

value: root


title: human_neuron_CHiC_rep1


title: hNSC_CHiC_rep3


title: MOLM13_sgBOD1L_243_Dox_4d_rep1


title: Root,  3-WT0_S3


title: Tcell, control, activated, rep2


title: human_neuron_C&R_H3K27ac_rep1

description: Kit and protocol from Epicypher Ltd


title: ChIPseq of Reb1-FLAG, 2h with NSF, FLAG-IP, rep 3

data_processing:
Raw data were demultiplexed and converted to fastq format using bcl2fastq2 (v1.17) and mapped using STAR with the following parameters: –alignIntronMax 1–alignEndsType EndToEnd–outFilterType Normal–seedSearchStartLmax 30–outFilterMultimapNmax 10000–outSAMattributes NH HI NM MD AS nM–outMultimapperOrder Random–outSAMmultNmax 1–outSAMunmapped Within. For bigwig track generation bedtools (version 2.26.0) and bedGraphToBigWig (from UCSC binary utilities) were used and read coverage was normalized to 1 million genome mapping reads (RPM).
Assembly: Spombe.ASM294v2.24
Supplementary files format and content: bigWig files containing normalized read counts (to 1 mio genome mapping reads per library) for visualization in UCSC or IGV genome browser.

extract_protocol:
Cells were fixed with 1% formaldehyde and lysed by beat-beating. Chromatin was sheared with a Bioruptor (Diagenode). 1% of chromatin was used as input contol and  the IP was performed for 2h at 4°C. ChIPs were decrosslinked overnight at 65°C and cleaned up using AMPure XP beads. For a detailed protocol, see Kuzdere et al, 2022.
ChIP-seq libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L) according to the manufacturer's instructions.

treatment_protocol: 2h growth at low density (OD=0.01) either with NSF or MeOH as control.

value: S. pombe cell culture

value: h- leu1-32 ura4-D18 ade6-704 reb1-6xGly-3xFlag::kanMX

value: NSF


title: MOLM13_sgCCR5_255_Dox_4d_rep2


title: hNSC_CHiC_rep2

value: Neural Stem Cells derived from IPSCs


title: hNSC_C&R_H3K27ac_rep2

description: Kit and protocol from Epicypher Ltd


title: MOLM13_sgCCR5_255_Dox_4d_rep1


title: Root,  1-WT0_S1

value: 0 NaCl


title: Root,  2-WT0_S2


title: ChIPseq of Reb1-FLAG, 2h with methanol, FLAG-IP, rep 3

value: MeOH


title: Root,  4-WT0_S4


title: MOLM13_sgAAVS_2_Dox_4d_rep2

value: sgAAVS


title: ChIPseq of Reb1-FLAG, 2h with methanol, FLAG-IP, rep 2


title: ChIPseq of Reb1-FLAG, 2h with methanol, FLAG-IP, rep 1


title: FL-Fc-DM1

city: Shenzhen

first: Dengyang

last: Zhang

state: Guangdong

address: Zhenmei road, guangming district

department: Scientific research center

institute: Seventh affiliated hospital, Sun Yat-sen University

data_processing:
Reads obtained from the sequencing machines, including raw reads were further filtered by fastp (version 0.18.0). Reads containing adapters, containing more than 10% of unknown nucleotides, and low-quality reads containing more than 50% of low-quality bases were removed.
rRNA-mapped reads were also removed. The paired-end clean reads were mapped to the human reference genome using HISAT2.2.4. The mapped reads of each sample were assembled using StringTie v1.3.1 in a reference-based approach. The FPKM method was used to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).  The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥2 were considered differentially expressed genes/transcripts.
Assembly: rRNA-mapped reads were also removed. The paired-end clean reads were mapped to the human reference genome using HISAT2.2.4. The mapped reads of each sample were assembled using StringTie v1.3.1 in a reference-based approach. The FPKM method was used to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).  The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥2 were considered differentially expressed genes/transcripts.
Supplementary files format and content: RAW data

source_name: THP-1 cells, treated by cytarabine (20 µM) for 3 days, and then treated with FL-Fc-DM1 (5 nM) for 1 day in the absence of cytarabine

growth_protocol: THP-1 cells were cultured in RPMI 1640 medium supplemented with 10% FBS, in a 5% CO2, 37 °C incubator.

extract_protocol:
Cells from each group were extracted by using the Trizol method. RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA) and checked using RNase-free agarose gel electrophoresis.
Total mRNA was enriched by Oligo(dT) beads. Then, the enriched mRNA was fragmented and reverse-transcripted into cDNA with random primers. Second-strand cDNA was synthesized by DNA polymerase I. The cDNA fragments were purified with the QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size-selected by agarose gel electrophoresis, PCR amplified and sequenced using Illumina HiSeq2500 by Gene Denovo Biotechnology Co. (China).

treatment_protocol: In the control group, THP-1 cells were cultured for 4 days. In the cytarabine group, THP-1 cells were treated with 20 µM cytarabine for 4 days. In the FL-Fc-DM1 treatment group, THP-1 cells were treated by cytarabine for 3 days and then treated with FL-Fc-DM1 (5 nM) for another 24 hours in the absence of cytarabine. In the FL-Fc treatment group, THP-1 cells were treated by cytarabine for 3 days and then treated with FL-Fc (5 nM) for another 24 hours in the absence of cytarabine.

value: THP-1 is a monocyte isolated from peripheral blood from an acute monocytic leukemia patient.

value: wild type

value: cytarabine (20 uM) for 3 days, and then treated with FL-Fc-DM1 (5 nM) for 1 day in the absence of cytarabine


title: FL-Fc

source_name: THP-1 cells, treated by cytarabine (20 µM) for 3 days, and then treated with FL-Fc (5 nM) for 1 day in the absence of cytarabine

value: treated by cytarabine (20 uM) for 3 days, and then treated with FL-Fc (5 nM) for 1 day in the absence of cytarabine


title: Ara-C

source_name: THP-1 cells, treated by cytarabine (20 µM) for 4 days

value: cytarabine (20 uM) for 4 days


title: MOLM13_FKBP-BOD1L_dTAG13_1h_CTDpS5

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie2.3.3.1.
Duplication reads were removed from aligned file by using picard-tools-2.18.2
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER v4.7 makeUCSCfile command and comberted to bigwig by bedGraphToBigWig. BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
Cells were fixed with 2mM DSG and 1% formaldehyde, and samples from sonicated nuclear fraction were incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.

treatment_protocol: Doxycycline were treated for 4 days. DMSO or 500 nM dTAG-13 were treated for 1 h or 24 h before fixation.

value: 500nM dTAG-13 1h

value: Phospho-Rpb1 CTD (Ser5) (Cell Signaling, #13523)


title: MOLM13_FKBP-BOD1L_DMSO_24h_rep2

value: leukemia

value: DMSO 24h


title: MOLM13_FKBP-BOD1L_dTAG13_24h_rep2


title: MOLM13_FKBP-BOD1L_DMSO_1h_CTDpS5

value: DMSO 1h


title: MOLM13_FKBP-BOD1L_DMSO_24h_rep1


title: Ctrl

source_name: THP-1 cells, control, cultured for 4 days

value: untreated


title: ChIPseq of Reb1-FLAG, 0h, FLAG-IP, rep 2

value: S. pombe cell culture

value: h- leu1-32 ura4-D18 ade6-704 reb1-6xGly-3xFlag::kanMX


title: ChIPseq of Reb1-FLAG, 2h with NSF, FLAG-IP, rep 2

value: NSF


title: ChIPseq of Reb1-FLAG, 2h with NSF, FLAG-IP, rep 1


title: hNSC_CHiC_rep1

value: Neural Stem Cells derived from IPSCs


title: RETcoh_2449M

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

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: BRAIN METASTATIC TUMOUR


title: MOLM13_FKBP-BOD1L_dTAG13_1h_RNAP2NTD

value: Rpb1 NTD (Cell Signaling, #14958)


title: ChIPseq of Reb1-FLAG, 0h, FLAG-IP, rep 1


title: MOLM13_FKBP-BOD1L_DMSO_1h_RNAP2NTD


title: RETcoh_914M

description: Raw data are available via DUA

tag: patientid


title: ChIPseq of Fil1-FLAG, 2h with NSF, FLAG-IP, rep 3

value: h- leu1-32 ura4-D18 ade6-704 fil1-6xGly-3xFlag::kanMX


title: RETcoh_796M

description: Raw data are available via DUA

tag: tumour location


title: MOLM13_FKBP-BOD1L_dTAG13_1h_SETD1A

value: SETD1A (Cell Signaling, #61702)


title: MM12_H3K27ac HiChIP

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

description: Paired-end HiChIP

data_processing:
Dovetail HiChIP data were aligned and processed using bwa-mem, and the reads in the fastq files were aligned to the human reference genome (GRCh37/hg19) using BWA mem function.
The aligned bam file were further analyzed using pairtools v1.0.2 parse module to find ligation junctions with following criteria --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30
The parsed pairs are then sorted using pairtools sort module and the PCR duplication were tags using pairtools dedup module. Pairtools split module were use to split the pairsam file into individual mapped pairs file. The mapped pairs were further format  to HiC-Pro valid pairs format for hichip loop call.
Hichipper version 2.7.9 was used to extract the valid interactions from the HiC-Pro data format from pairtools output and generate the bedpe interaction file by utilizing anchors from peaks called by MACS2 broadPeak using the dangling-end and self-cycle Hi-ChIP read pairs with the following parameters: --keep-dup=1.
Hichipper used to process interactions using the following parameters: -l 50 -mi 5000 -ma 2000000.
Assembly: hg19
Supplementary files format and content: *_mapped.pairs.gz: txt file output from pairtools
Supplementary files format and content: *.intra.loop_counts.bedpe: bedpe file output from hichipper
Supplementary files format and content: *.anchors.bed: anchor used by hichipper
Library strategy: HiChIP

source_name: Multiple myeloma Patient Sample

growth_protocol: Multiple myeloma cell lines were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol: The sequencing libraries were prepared using Kapa Hyper Prep Kit (KAPA) and indexed using Dual Index Primer Set #1 for Illumina. The HiChIP libraries were sequenced with 75 bp paired-end reads on HiSeq 2500 platform (Illumina).

treatment_protocol: All MM cells were cross-linked with formaldehyde and chromatin was digested within intact nuclei using MNase. Cells were then lysed with RIPA buffer and H3K27ac-DNA complexes were isolated with the antibody. After biotin end filling ligation and crosslink reversal, HiChIP DNA was purified with SPRIselect Beads.

value: Multiple myeloma Patient Sample

value: MMPT

value: multiple myeloma

value: MM

value: Cell Signaling Technology, #8173


title: MM13_H3K27ac HiChIP

description: Paired-end HiChIP


title: MOLM13_FKBP-BOD1L_dTAG13_24h_rep1

value: leukemia


title: MOLM13_sgAAVS_2_Dox_4d_rep1

value: sgAAVS

value: 1µg/mL Doxycycline 4d


title: MM11_H3K27ac HiChIP

description: Paired-end HiChIP


title: ChIPseq of Fil1-FLAG, 2h with NSF, FLAG-IP, rep 2

value: S. pombe cell culture


title: RETcoh_681M

description: Raw data are available via DUA


title: ChIPseq of Reb1-FLAG, 0h, FLAG-IP, rep 3

value: h- leu1-32 ura4-D18 ade6-704 reb1-6xGly-3xFlag::kanMX


title: MOLM13_FKBP-BOD1L_DMSO_1h_SETD1A

value: DMSO 1h


title: NPC2_H3K27ac HiChIP

description: Paired-end HiChIP

source_name: Normal plasma cell

value: Normal plasma cell

value: NPC

value: Control


title: ChIPseq of Fil1-FLAG, 2h with NSF, FLAG-IP, rep 1

value: NSF


title: MOLM13_sgBOD1L_243_Dox_4d_H3K36me3

value: H3K36me3 (abcam, ab9050)


title: Participant 603 10x RNA Replicate2 - Resting

description: 5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
The demultiplexing, barcoded processing, TCR assembly and gene counting and aggregation were made using the Cell Ranger software v7.2  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
CD4+ T cells harboring intact latent HIV-1 proviruses were enriched using their T cell receptors (Weymar et al., 2022). CD4+ T cells from participants 603 (Rockefeller University IRB-approved Protocols MCA-0866/TSC-0910) and 5104 (Protocols MCA-0965/TSC-0910) were isolated by magnetic separation using CD4+ T Cell Isolation Kit, human (Miltenyi Biotec, cat. 130-091-155) and CD45RA MicroBeads, human (Miltenyi Biotec, cat. 130-045-901) and prepared for cell sorting exactly as described (Weymar et al., 2022). Cells from 603 (CD4+TRBC1+TRBV19+) and 5104 (CD3+CD4+TRBC1+TRBV) were sorted into 96 well “U” bottom plates (5 cells per well) containing 200 µL of activation media (composition described above), plus feeder cells, supplemented with the following ARVs: 1µM Tenofovir, 1µM Emtricitabine, 1nM Nevirapine and 10 µM T-20. Cell sorting was performed on FACSymphony S6 using FACSDiva software (version 9.5.1, BD Biosciences) and data was analyzed using FlowJo (version 10.10.0, BD Biosciences). The culture media was replaced twice a week to replenish ARVs and avoid new infections. Three weeks after sorting, cells were screened for the presence of the HIV clone of interest by Env PCR and sequencing (Salazar-Gonzalez et al., 2008). Cell lines containing clones of interest were expanded in a T25 culture flask in 10 mL of activation medium. The frequency of latent cells in the cultures was determined three weeks after expansion by sorting single cells into 10 µL of RLT buffer (Qiagen, cat 79216) using Agencourt RNAClean XP and magnetic beads (Beckman Coulter, cat. A63987) for DNA preparation and Env PCR.
10X Genomics gene expression and V(D)J libraries were generated with the Chromium Single Cell 5′ Library & Gel Bead Kit (10X Genomics, cat. PN-1000014) and Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (10X Genomics, cat. PN-1000005) as described in the 10X Genomics protocol. The 5’ expression library and the V(D)J library were sequenced with NovaSeq 6000 S1 (100 cycles) (Illumina, cat. 20012865).

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: CD4+ T cells

value: cultured IL7


title: ChIPseq of Fil1-FLAG, 2h with methanol, FLAG-IP, rep 3

value: h- leu1-32 ura4-D18 ade6-704 fil1-6xGly-3xFlag::kanMX

value: MeOH


title: MOLM13_sgAAVS_2_Dox_4d_H3K36me3


title: Participant 603 10x VDJ Replicate1 - Resting


title: U266_H3K27ac HiChIP

description: Paired-end HiChIP

source_name: Multiple myeloma cell line U266

value: Multiple myeloma cell line U266

value: multiple myeloma

value: MM

value: Cell Signaling Technology, #8173


title: Participant 603 10x VDJ Replicate2 - Resting


title: RPMI8226_H3K27ac HiChIP

description: Paired-end HiChIP

source_name: Multiple myeloma cell line RPMI8226

value: Multiple myeloma cell line RPMI8226


title: ChIPseq of Fil1-FLAG, 2h with methanol, FLAG-IP, rep 2

value: S. pombe cell culture


title: ChIPseq of Fil1-FLAG, 2h with methanol, FLAG-IP, rep 1


title: MM1S_H3K27ac HiChIP

description: Paired-end HiChIP

source_name: Multiple myeloma cell line MM.1S

value: Multiple myeloma cell line MM.1S


title: MOLM13_FKBP-BOD1L_HA

value: leukemia

value: HA-Tag (Cell Signaling, #3724)


title: MOLM13_sgBOD1L_243_Dox_4d_CTDpS2

value: 1µg/mL Doxycycline 4d

value: Phospho-Rpb1 CTD (Ser2) (Cell Signaling, #13499)


title: Participant 603 10x RNA Replicate1 - Resting


title: ChIPseq of Fil1-FLAG, 0h, FLAG-IP, rep 3


title: MOLM13_sgAAVS_2_Dox_4d_CTDpS2


title: NAT2895-rep2

description: HiChIP Lib+Seq (H3k27Ac)_H929_sample1-rep2

data_processing:
Sequencing data of H3K27ac Hi-ChIP were processed with fastp to remove adapter sequence (CTGTCTCTTATACACA) and phred quality >=Q15. Then the sequenced reads were aligned, paired, and removed of duplicates using the pairtools pipeline version (1.0.0) where the fastq files were aligned to hg19 genome using bwa mem
The aligned data were further processed using hichipper to call the interactions with either H929 or KMS28BM. Hichipper version 2.7.9 processed the valid interactions from pairtools and generate the interaction bedpe file. The reads were undergo deduplication using pairtools pipeline and merge using samtools merge.
Hichipper processed the interactions using parameters as shown -l 100 -mi 5000 -ma 2000000 -mg 12500.
Assembly: hg19
Supplementary files format and content: txt file output from pairtools
Supplementary files format and content: bedpe file output from hichipper
Supplementary files format and content: anchor used by hichipper
Library strategy: HiChIP

source_name: Multiple myeloma cell line KMS28BM

extract_protocol:
The sequencing libraries were prepared using Kapa Hyper Prep Kit (KAPA) and indexed using Dual Index Primer Set #1 for Illumina. The HiChIP libraries were sequenced with 75 bp paired-end reads on HiSeq 2500 platform (Illumina).
Paired-end HiChIP


title: ChIPseq of Fil1-FLAG, 0h, FLAG-IP, rep 2


title: MOLM13_sgBOD1L_243_Dox_4d_CTDpS5

value: Phospho-Rpb1 CTD (Ser5) (Cell Signaling, #13523)


title: NAT2895-rep1

description: HiChIP Lib+Seq (H3k27Ac)_H929_sample1-rep1


title: ChIPseq of Fil1-FLAG, 0h, FLAG-IP, rep 1


title: MOLM13_sgAAVS_2_Dox_4d_CTDpS5


title: Participant 603 10x RNA Replicate1 - Activated

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: anti CD3/CD38 activation


title: NAT2896-rep2

description: HiChIP Lib+Seq (H3k27Ac)_H929_sample2-rep2


title: Participant 5104 10x VDJ Replicate1 - Resting

value: CD4+ T cells

value: cultured IL7


title: ChIPseq of Reb1-FLAG, 2h with NSF, input, rep 3

value: h- leu1-32 ura4-D18 ade6-704 reb1-6xGly-3xFlag::kanMX

value: NSF


title: NPC1_H3K27ac HiChIP

description: Paired-end HiChIP

value: Normal plasma cell

value: NPC

value: Control


title: Participant 5104 10x RNA Replicate1 - Resting


title: MOLM13_sgBOD1L_243_Dox_4d_RNAP2NTD

value: Rpb1 NTD (Cell Signaling, #14958)


title: NAT2896-rep1

description: HiChIP Lib+Seq (H3k27Ac)_H929_sample2-rep1

value: Cell Signaling Technology, #8173


title: ChIPseq of Reb1-FLAG, 2h with NSF, input, rep 2

value: S. pombe cell culture


title: NAT2897-rep2

description: HiChIP Lib+Seq (H3k27Ac)_KMS28BM_sample4-rep2

source_name: Multiple myeloma cell line H929 (NCI-H929)


title: Participant 5104 10x VDJ Replicate1 - Activated


title: MOLM13_sgAAVS_2_Dox_4d_RNAP2NTD

value: leukemia


title: MOLM13_sgBOD1L_243_Dox_4d_NELFE

value: NELFE (abcam, ab170104)


title: ChIPseq of Reb1-FLAG, 2h with methanol, input, rep 3

value: MeOH


title: Participant 603 10x VDJ Replicate1 - Activated


title: ChIPseq of Reb1-FLAG, 2h with NSF, input, rep 1


title: Participant 5104 10x RNA Replicate1 - Activated


title: MOLM13_sgAAVS_2_Dox_4d_NELFE

value: 1µg/mL Doxycycline 4d


title: NAT2897-rep1

description: HiChIP Lib+Seq (H3k27Ac)_KMS28BM_sample4-rep1


title: S_6_R6_1

data_processing:
Read alignments were done using the TempO-SeqR software package according to manufacturer´s recommendation (BioClavis).
CPM normalization and DESeq2-software package was used to derive differentially expressed genes.
Assembly: hg38

extract_protocol:
RNA was isolated and purified using the RNeasy MiniKit (Qiagen) and treated with DNase (Qiagen). RNA concentration (A260) and purity (A260
A280 ratio) were measured by spectrophotometry (NanoDrop™ 2000 Spectrophotometer, software version 1.6.198, ThermoFisher Scientific). RNA integrity number (RIN) was evaluated using an Agilent 2100 Bioanalyzer® (Agilent Technologies). All RNA samples showed very good quality as indicated by high RIN values between 9.0 and 10.0.
TempO-SeqR software package according to manufacturer´s recommendation (BioClavis)

value: clean air

value: 0 ppm

value: CA


title: Jurkat, ZNF407, rep3

data_processing:
ATAC-Seq reads were mapped to the UCSC hg38 genome using bowtie2 vx.1.0 with the parameters --local --very-sensitive-local
Duplicated reads were removed with Picard MarkDuplicates
Peaks were called using macs2 vx.1.z with the parameters --nomodel –nolambda --cutoff-analysis
bigWig files were generated using bamCoverage v1.x.1 with the parameter --normalizeUsing CPM
Assembly: hg38 + HIV inserts
Supplementary files format and content: bigwig, narrowPeak, HIV_construct_inserts_coordinates.csv

extract_protocol:
Genomic DNA was collected, tagmented and purified using the ATAC-Seq Kit (Active Motif)
PCR amplification of tagmented DNA and library preparation were performed using the ATAC-Seq Kit (Active Motif)

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: Jurkat


title: Jurkat, ZNF407, rep2


title: NAT2898-rep2

description: HiChIP Lib+Seq (H3k27Ac)_KMS28BM_sample3-rep2


title: ChIPseq of Reb1-FLAG, 2h with methanol, input, rep 2

value: h- leu1-32 ura4-D18 ade6-704 reb1-6xGly-3xFlag::kanMX


title: S_6_R5_1


title: NAT2898-rep1

description: HiChIP Lib+Seq (H3k27Ac)_KMS28BM_sample3-rep1


title: RNAseq of parental strain, 6h with NSF, experiment 2, rep 3

value: h+ orfdelta::ade6-M216 ura4-D18 leu1-32

value: 6h NSF


title: ChIPseq of Reb1-FLAG, 2h with methanol, input, rep 1


title: S_6_R1_1


title: Jurkat, ZNF407, rep1


title: ChIPseq of Reb1-FLAG, 0h, input, rep 3


title: Jurkat, ZNF460, rep3


title: ChIPseq of Reb1-FLAG, 0h, input, rep 2


title: RNAseq of parental strain, 6h with NSF, experiment 2, rep 2


title: S_6_NEC6_1

value: non exposed control

value: NEC


title: Jurkat, ZNF460, rep2


title: S_6_NEC5_1


title: ChIPseq of Reb1-FLAG, 0h, input, rep 1


title: RNAseq of parental strain, 6h with NSF, experiment 2, rep 1


title: RNAseq of parental strain, 6h with methanol, experiment 2, rep 3

value: 6h MeOH


title: S_6_NEC1_1


title: ChIPseq of Fil1-FLAG, 2h with NSF, input, rep 3

value: h- leu1-32 ura4-D18 ade6-704 fil1-6xGly-3xFlag::kanMX

value: NSF


title: Jurkat, ZNF140, rep3


title: RNAseq of parental strain, 6h with methanol, experiment 2, rep 2

value: S. pombe cell culture


title: S_6_B6_3

value: Dimethylamine

value: HD


title: RNAseq of parental strain, 6h with methanol, experiment 2, rep 1


title: ChIPseq of Fil1-FLAG, 2h with NSF, input, rep 1


title: Jurkat, ZNF460, rep1


title: ChIPseq of Fil1-FLAG, 2h with NSF, input, rep 2


title: S_6_B6_2


title: S_6_B6_1


title: Jurkat, ZNF140, rep2


title: Jurkat, ZNF140, rep1


title: ChIPseq of Fil1-FLAG, 2h with methanol, input, rep 3

value: MeOH


title: ChIPseq of Fil1-FLAG, 2h with methanol, input, rep 2


title: RNAseq of parental strain, 4h with NSF, experiment 2, rep 3

value: 4h NSF


title: Jurkat, KDM2A, rep3


title: S_6_B5_3

value: MD


title: RNAseq of parental strain, 4h with NSF, experiment 2, rep 2


title: Jurkat, KDM2A, rep2


title: ChIPseq of Fil1-FLAG, 2h with methanol, input, rep 1


title: S_6_B5_2


title: RNAseq of parental strain, 4h with NSF, experiment 2, rep 1


title: RNAseq of parental strain, 4h with methanol, experiment 2, rep 3

value: 4h MeOH


title: Jurkat, KDM2A, rep1

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: S_6_B5_1


title: ChIPseq of Fil1-FLAG, 0h, input, rep 2


title: Jurkat, KCNA3, rep3

value: Jurkat


title: RNAseq of parental strain, 4h with methanol, experiment 2, rep 2


title: S_6_B1_3

value: LD


title: S_6_B1_2


title: Jurkat, KCNA3, rep1


title: Jurkat, KCNA3, rep2


title: ChIPseq of Php3-FLAG, 2h with NSF, FLAG-IP, rep 3

value: h- leu1-32 ura4-D18 ade6-704 php3-6xGly-3xFlag::kanMX


title: RNAseq of parental strain, 4h with methanol, experiment 2, rep 1

value: h+ orfdelta::ade6-M216 ura4-D18 leu1-32


title: ChIPseq of Fil1-FLAG, 0h, input, rep 1


title: RNAseq of parental strain, 2h with NSF, experiment 2, rep 3

value: 2h NSF


title: S_6_B1_1


title: Jurkat, chr13, rep2


title: Jurkat, chr13, rep1


title: RNAseq of parental strain, 2h with methanol, experiment 2, rep 3

value: 2h MeOH


title: Jurkat, chr13, rep3


title: RNAseq of parental strain, 2h with NSF, experiment 2, rep 1


title: ChIPseq of Php3-FLAG, 2h with NSF, FLAG-IP, rep 1


title: ChIPseq of Php3-FLAG, 2h with methanol, FLAG-IP, rep 3


title: ChIPseq of Fil1-FLAG, 0h, input, rep 3


title: Tcell, chr13, resting, rep3

value: T cell

value: cultured IL7


title: ChIPseq of Php3-FLAG, 2h with methanol, FLAG-IP, rep 2


title: Tcell, chr13, resting, rep2


title: ChIPseq of Php3-FLAG, 2h with NSF, FLAG-IP, rep 2

value: NSF


title: RNAseq of parental strain, 2h with NSF, experiment 2, rep 2

value: S. pombe cell culture


title: ChIPseq of Php3-FLAG, 2h with methanol, FLAG-IP, rep 1


title: Tcell, chr13, activated, rep3

value: anti CD3/CD38 activation


title: Tcell, chr13, resting, rep1


title: Derlin-2_KO_1

city: Miyazaki

first: Naoya

last: Murao

department: Medical Sciences

institute: University of Miyazaki

description: Gene expression

hyb_protocol: 600 ng of Cy3-labeled cRNA was fragmented and hybridized onto the Agilent SurePrint G3 mouse GE 8 × 60K slide (design ID-074809), with rotating incubation at 65˚C for 17 h.

scan_protocol: Slides were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation, and scanned by the Agilent DNA Microarray scanner (G2505C).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 028282_D_F_20110531) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.  The data files were subjected to the GeneSpring (ver. 14.9) for analysis.

source_name: mouse dentate gyrus

label_protocol: For RNA amplification and labeling, we used Agilent Low-Input QuickAmp labeling kit (Agilent) according to the manufacture’s guidance.  150 ng of total RNA of each sample was amplified T7-RNA polymerase and simultaneously incorporated Cy3-labeled CTP.

growth_protocol: C57BL/6 mice were raised under specific pathogen-free conditions.

extract_protocol: Total RNA from mouse dentate gyrus were extracted using NucleoSpin RNA kit (TaKaRa Bio) according to the instructions. This included an on-column DNase digestion with the RNase-free Dnase (TaKaRa Bio)

treatment_protocol: Derlin-1_control was Derlin-1flox/flox, and Derlin-2_control was Derlin-2flox/flox. Mice expressing Cre recombinase driven by the nestin promoter were intercrossed with Derl1flox/flox mice and Derl2flox/flox mice respectively to generate Derlin-1_KO and Derlin-2_KO mice.

value: Dentate gyrus

tag: gender

value: male


title: RNAseq of parental strain, 2h with methanol, experiment 2, rep 1


title: RNAseq of parental strain, 0h, experiment 2, rep 2


title: ChIPseq of Php3-FLAG, 0h, FLAG-IP, rep 3


title: Derlin-2_control_2

description: Gene expression

value: Derlin-2 control


title: Tcell, chr13, activated, rep2


title: ChIPseq of Php3-FLAG, 0h, FLAG-IP, rep 1


title: RNAseq of parental strain, 0h, experiment 2, rep 1


title: ChIPseq of Hsr1-FLAG, 2h with NSF, FLAG-IP, rep 3

value: h- leu1-32 ura4-D18 ade6-704 hsr1-6xGly-3xFlag::kanMX


title: Tcell, chr13, activated, rep1


title: AR3

city: Suita

first: Ryuya

last: Edahiro

institute: Osaka University

library_source: other

data_processing:
Raw reads were trimmed and filtered using SOAPnuke and then aligned to reference using Bowtie2 (v2.2.9).
The small RNA expression level was calculated by counting absolute numbers of molecules using unique molecular identifiers.
Assembly: GRCm38
Supplementary files format and content: raw counts

molecule: other

source_name: serum

growth_protocol: Mice were housed in box cages, maintained on a 12-hour light / 12-hour dark cycle, and fed a normal-fat chow diet (Oriental Yeast, MF). The ambient temperature and humidity were 23°C ± 1.5°C and 45% ± 15%, respectively. All animal experiments were approved by the Animal Research Committee of Osaka University and complied with the Japanese Animal Protection and Management Law (No. 25). We complied with all relevant ethical regulations.

extract_protocol:
A MagCapture™ Exosome Isolation Kit PS Ver.2 (Fujifilm Wako, 290-84103) was used to isolate exosomes. Small RNA with a size of 18–30 nt was isolated by gel electrophoresis.
Small RNA Library Prep Kit (940-000196-00, MGI), and quality and quantity were assessed at all steps by capillary electrophoresis (Agilent Bioanalyzer). Libraries were sequenced on a DNBSEQ-G400 with cPAS chemistry (DNBSEQ-G400RS High-throughput Sequencing Set, FCL SE50, 1000016941, MGI).

treatment_protocol: Whole-body Rubicon-KO mice on a C57BL/6 background were generated as described previously.

value: serum

value: cell-free (purified EVs)

value: Rubicon -/-

tag: age


title: Jurkat, ATP2B, rep3

first: Gabriela

source_name: Peripheral Blood Mononuclear Cells (PBMCs)

value: Jurkat


title: AR2


title: RNAseq of parental strain, 0h, experiment 2, rep 3


title: ChIPseq of Php3-FLAG, 0h, FLAG-IP, rep 2

value: h- leu1-32 ura4-D18 ade6-704 php3-6xGly-3xFlag::kanMX


title: RNAseq of parental strain, 2h with methanol, experiment 2, rep 2

value: h+ orfdelta::ade6-M216 ura4-D18 leu1-32


title: ChIPseq of Hsr1-FLAG, 2h with NSF, FLAG-IP, rep 2


title: surface epithelium_H3K27me3_rep1

city: Guangzhou

first: Huaxing

last: Huang

address: 7 Jinsui Road

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

data_processing:
Reads were trimmed by trimmomatic tool and then aligned to human hg19 reference genome using BWA software (version 0.7.17). Duplicated reads were removed by Picard Markduplicates (version 2.18.16) and only uniquely mapping reads were retained for further analysis. MACS2 (version 2.1.1) was used to call peak.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: surface epithelium

growth_protocol: For surface epithelium differentiation, H1 hESCs were digested into colonies of 100 to 200 μm in diameter and seeded onto Matrigel-coated plates. The next day, mTeSR1 medium was changed to Essential 6 medium supplemented with recombinant human BMP4 (5 ng/ml) and 1 μM RA.

extract_protocol:
Cells were cross-linked with 1% formaldehyde (Thermo Fisher Sci_x0002_entific, 28906) in Dulbecco’s Modified Eagle Medium for 10min at room temperature. Formaldehyde was then quenched with 125 mM glycine (Sigma-Aldrich, 50046) for 5min at room temperature. Cells were lysed in sonication buffer [50 mM Hepes-NaOH (pH 7.5), 500 mM NaCl, 1 mM EDTA, 0.1% Na-deoxycholate, 1% Triton X-100, and 0.1% SDS]. Chromatin was sheared with Covaris M220 focused-ultrasonicator to an average DNA fragment length of 200 to 500base pairs (bp). Chromatin was then diluted in lysis buffer without SDS and immunoprecipitated with primary antibodies overnight at 4°C. The immunocomplexes were captured with Protein A and Protein G magnetic beads (1:1, Invitrogen). After three washes with sonication buffer, two washes with low-salt wash buffer [10 mM tris-HCl (pH 8.0), 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, and 0.5% Na-deoxycholate], and one wash with TE buffer [10 mM tris-HCl (pH 8.0) and 1 mM EDTA], chromatin was then eluted from beads and de–cross-linked with 1% SDS in TE for 4 hours. After 1-hour digestion at 37°C with proteinase K (Invitrogen) and ribonuclease A (Invitrogen), DNA was purified using the MinElute PCR Purification Kit (QIAGEN)
Purified DNA was used to prepare ChIP-seq DNA libraries for Illumina sequencing by KAPA Hyper Prep Kit (KAPABIOSYSTEMS).

value: surface epithelium


title: surface epithelium_H3K27me3_rep2


title: Derlin-1_KO_2

description: Gene expression


title: Derlin-2_KO_2

description: Gene expression


title: Derlin-2_control_1

description: Gene expression


title: Derlin-1_KO_1

description: Gene expression


title: Jurkat, ATP2B, rep2

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: AR1


title: Derlin-1_control_2

description: Gene expression

value: Derlin-1 control


title: Derlin-1_control_1

description: Gene expression


title: surface epithelium_H3K4me3_rep2


title: ChIPseq of Hsr1-FLAG, 2h with methanol, FLAG-IP, rep 3

source_name: S. pombe cell culture

value: MeOH


title: Tcell, ATP2B, resting, rep2

value: T cell

value: cultured IL7


title: ChIPseq of Hsr1-FLAG, 2h with methanol, FLAG-IP, rep 1

value: S. pombe cell culture


title: AC3

value: Rubicon +/+


title: R3


title: surface epithelium_H3K4me3_rep1


title: R2


title: Tcell, ATP2B, resting, rep3


title: surface epithelium_H3K4me1_rep2


title: Tcell, ATP2B, activated, rep3

value: anti CD3/CD38 activation


title: R1


title: Tcell, ATP2B, resting, rep1


title: surface epithelium_H3K27ac_rep2


title: ChIPseq of Hsr1-FLAG, 0h, FLAG-IP, rep 2


title: ChIPseq of Hsr1-FLAG, 0h, FLAG-IP, rep 3


title: surface epithelium_H3K4me1_rep1


title: Tcell, ATP2B, activated, rep2


title: ChIPseq of Hsr1-FLAG, 2h with NSF, FLAG-IP, rep 1

value: NSF


title: Jurkat, ATP2B, rep1


title: surface epithelium_H3K27ac_rep1


title: AC2


title: ChIPseq of Hsr1-FLAG, 2h with methanol, FLAG-IP, rep 2

value: h- leu1-32 ura4-D18 ade6-704 hsr1-6xGly-3xFlag::kanMX


title: AC1

value: serum


title: C3

value: cell-free (purified EVs)


title: Tcell, ATP2B, activated, rep1


title: surface epithelium_GATA3_rep1


title: Jurkat, control, rep3


title: ChIPseq of Adn2-FLAG, 2h with NSF, FLAG-IP, rep 3

value: h- leu1-32 ura4-D18 ade6-704 adn2-6xGly-3xFlag::kanMX


title: ChIPseq of Hsr1-FLAG, 0h, FLAG-IP, rep 1


title: C2


title: surface epithelium_GRHL2_rep2


title: ChIPseq of Adn2-FLAG, 2h with NSF, FLAG-IP, rep 1


title: C1


title: ChIPseq of Adn2-FLAG, 2h with methanol, FLAG-IP, rep 3


title: surface epithelium_GRHL2_rep1


title: G-MDSCs,after FACS sorting, 90days, rep7

city: Gui Yang

first: MING

last: NI

address: 28 Guiyi St., Yunyan District

department: Department of Hematology

institute: Affiliated Hospital of Guizhou Medical University,

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by  Removing reads containing sequencing adapter, Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;  Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set;
The expression level of gene was calculated by RSEM.
Assembly: GRCh38.p13
Supplementary files format and content: Tab-delimited text file includes row counts for each sample
Supplementary files format and content: Tab-delimited text file includes fpkm for each sample

source_name: Blood

extract_protocol:
Total RNA was extracted using Trizol
RNA transcriptome profiles were generated by the Beijing Genomics Institute (BGI) using the DNA Nanoball sequence (DNBSEQ) platform.

value: Blood


title: G-MDSCs,after FACS sorting, 90days, rep6