title: APE34

description:
Library name: 525
column name in E3_processed_counts.csv: 525

value: y w; apnull/apGAL4; P{UASap}


title: 235-BL

status: Public on May 12 2025

type: SRA

city: Dallas

first: David

last: Gerber

state: Texas

address: 5323 Harry Hines Blvd.

country: USA

institute: UT Southwestern Medical Center

description: Library name: Sample_00000000000064

library_source: transcriptomic

data_processing:
Raw paired‑end FASTQ files were processed with MiXCR (vX.X) to assemble BCR heavy‑chain sequences, call clonotypes, and quantify clone counts and frequencies
Assembly: Not applicable—reads were not aligned to a whole‑genome assembly but instead processed for V(D)J annotation using the built‑in MiXCR IMGT reference.
Supplementary files format and content: Tab‑delimited text (.tsv) files, one per sample, with one row per BCR clonotype

molecule: polyA RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
Total RNA was isolated via poly‑A mRNA enrichment using oligo‑dT magnetic beads as part of the TruSeq Stranded mRNA kit workflow (oligo‑dT capture, wash, and elution)
Illumina TruSeq® Stranded mRNA Library Preparation protocol (poly‑A selection, mRNA fragmentation, first‑ and second‑strand cDNA synthesis, end repair and A‑tailing, UMI adapter ligation, two rounds of AMPure XP bead clean‑up, PCR amplification)

tag: tissue

value: Blood

tag: cell type

value: PBMCs

tag: treatment

value: pembrolizumab

tag: time

value: BL


title: 235-3W

description: Library name: Sample_00000000000063


title: APE32

city: London

first: Gabriella

middle: Alves

last: Sidhu

state: Ontario

address: The Laurene O. Paterson Building, Western Science Centre

department: Biology

country: Canada

institute: Western University

description:
Library name: 522
column name in E3_processed_counts.csv: 522

data_processing:
RNAseq reads were aligned to the BDGP6 assembly of the Drosophila melanogaster genome using HISAT2 (version 2.2.1)
Gene count data was extracted with featureCounts (version 2.0.1) with the BDGP6.46.110 genome assembly
Differentially expressed genes were detected with DEseq2 (version 1.40.2).
Salmon (version 1.10.1) estimated the number of transcripts expressed from the endogenous transcription factor loci and UAS transcription factor constructs using the BDGP6 assembly of the Drosophila melanogaster transcriptome supplemented with files of the UAS constructs used (Supplemental data S1).
Assembly: BDGP6 assembly of Drosophila melanogaster genome.
Supplementary files format and content: csv files include raw counts for each Sample

molecule: total RNA

organism: Drosophila melanogaster

source_name: wing imaginal disc

extract_protocol:
Total RNA was extracted from the tissues using the Quagen RNeasy mini kit.
Sequencing services were executed with the DNBseq sequencing technology, featuring cPAS and DNA Nanoballs (DNBTM) technology.

value: wing imaginal disc

tag: developmental stage

value: early third larval

tag: genotype

tag: batch


title: 233-BL

description: Library name: Sample_00000000000062

value: nivolumab


title: 228-BL

description: Library name: Sample_00000000000061


title: APE33

description:
Library name: 523
column name in E3_processed_counts.csv: 523


title: ConE35

description:
Library name: 120
column name in E3_processed_counts.csv: 120

value: y w; apnull/apGAL4


title: 223-BL

description: Library name: Sample_00000000000058

value: durvalumab


title: ConE34

description:
Library name: 110
column name in E3_processed_counts.csv: 110


title: 222-BL

description: Library name: Sample_00000000000056


title: ConE33

description:
Library name: 74
column name in E3_processed_counts.csv: 74


title: 228-6W

description: Library name: Sample_00000000000060


title: 224-BL

description: Library name: Sample_00000000000059

value: pembrolizumab+other


title: ConE32

description:
Library name: 73
column name in E3_processed_counts.csv: 73


title: 222-6W

description: Library name: Sample_00000000000055


title: 220-BL

description: Library name: Sample_00000000000054


title: WTE35

description:
Library name: 119
column name in E3_processed_counts.csv: 119

value: y w


title: 220-6W

description: Library name: Sample_00000000000053


title: WTE34

description:
Library name: 118
column name in E3_processed_counts.csv: 118


title: WTE33

description:
Library name: 66
column name in E3_processed_counts.csv: 66


title: ConE31

description:
Library name: 72
column name in E3_processed_counts.csv: 72


title: 217-6W

description: Library name: Sample_00000000000051


title: WTE32

description:
Library name: 65_AP_WT
column name in E3_processed_counts.csv: 65_AP_WT


title: 216-BL

description: Library name: Sample_00000000000050

value: ipilimumab+nivolumab


title: WTE31

description:
Library name: 64
column name in E3_processed_counts.csv: 64


title: 215-BL

description: Library name: Sample_00000000000048


title: APE31

description:
Library name: 521
column name in E3_processed_counts.csv: 521


title: 216-6W

description: Library name: Sample_00000000000049


title: SQZdsx5

description:
Library name: 52_SQZ
column name in DSX_processed_counts.csv: 52_SQZ

source_name: P13-P15 abdomen

value: P13-P15 abdomen

value: w; P{UASsqz}; dsx1/dsxGAL4


title: SQZdsx4

description:
Library name: 242
column name in DSX_processed_counts.csv: 242


title: SQZdsx2

description:
Library name: 222
column name in DSX_processed_counts.csv: 222


title: 213-BL

description: Library name: Sample_00000000000047


title: 213-6W

description: Library name: Sample_00000000000046


title: SQZdsx3

description:
Library name: 232
column name in DSX_processed_counts.csv: 232


title: 223-2W

description: Library name: Sample_00000000000057


title: 212-6W

description: Library name: Sample_00000000000044


title: 212-BL

description: Library name: Sample_00000000000045


title: SQZdsx1

description:
Library name: 212
column name in DSX_processed_counts.csv: 212


title: 205-BL

description: Library name: Sample_00000000000043


title: FOXOdsx4

description:
Library name: 141
column name in DSX_processed_counts.csv: 141

value: w; P{UASfoxo}; dsx1/dsxGAL4


title: FOXOdsx5

description:
Library name: 151
column name in DSX_processed_counts.csv: 151


title: FOXOdsx3

description:
Library name: 131
column name in DSX_processed_counts.csv: 131


title: 202-BL

description: Library name: Sample_00000000000042


title: FOXOdsx2

description:
Library name: 121
column name in DSX_processed_counts.csv: 121


title: 201-BL

description: Library name: Sample_00000000000041


title: 201-6W

description: Library name: Sample_00000000000040


title: 217-BL

description: Library name: Sample_00000000000052


title: 197-BL

description: Library name: Sample_00000000000039

value: avelumab


title: 197-6W

description: Library name: Sample_00000000000038


title: ODDdsx5

description:
Library name: 57_ODD
column name in DSX_processed_counts.csv: 57_ODD

value: w; P{UASodd}; dsx1/dsxGAL4


title: ODDdsx4

description:
Library name: 47
column name in DSX_processed_counts.csv: 47


title: 196-BL

description: Library name: Sample_00000000000037

value: Blood


title: ODDdsx3

description:
Library name: 7_3
column name in DSX_processed_counts.csv: 7_3


title: ODDdsx2

description:
Library name: 7_2
column name in DSX_processed_counts.csv: 7_2


title: ODDdsx1

description:
Library name: 7_1
column name in DSX_processed_counts.csv: 7_1


title: 195-6W

description: Library name: Sample_00000000000035

value: PBMCs


title: 191-BL

description: Library name: Sample_00000000000034


title: 195-BL

description: Library name: Sample_00000000000036

value: pembrolizumab


title: 191-4W

description: Library name: Sample_00000000000033


title: 174-BL

description: Library name: Sample_00000000000032

value: BL


title: EYdsx4

description:
Library name: 49
column name in DSX_processed_counts.csv: 49

value: w; P{UASey}; dsx1/dsxGAL4


title: EYdsx3

description:
Library name: 9_3
column name in DSX_processed_counts.csv: 9_3


title: EYdsx2

description:
Library name: 9_2
column name in DSX_processed_counts.csv: 9_2


title: 174-6W

description: Library name: Sample_00000000000031


title: 155-BL

description: Library name: Sample_00000000000030


title: EYdsx1

description:
Library name: 9_1
column name in DSX_processed_counts.csv: 9_1


title: 155-9M

description: Library name: Sample_00000000000029


title: ANTPdsx5

description:
Library name: 56_ANTP
column name in DSX_processed_counts.csv: 56_ANTP

value: w; P{UASAntp}; dsx1/dsxGAL4


title: ANTPdsx4

description:
Library name: 46
column name in DSX_processed_counts.csv: 46


title: FOXOdsx1

description:
Library name: 111_FOXO
column name in DSX_processed_counts.csv: 111_FOXO


title: 155-6M

description: Library name: Sample_00000000000028


title: 155-12M

description: Library name: Sample_00000000000027


title: ANTPdsx2

description:
Library name: 6_2
column name in DSX_processed_counts.csv: 6_2


title: 153-3M

description: Library name: Sample_00000000000025

value: nivolumab


title: ANTPdsx1

description:
Library name: 6_1
column name in DSX_processed_counts.csv: 6_1


title: 143-BL

description: Library name: Sample_00000000000024


title: BAB1dsx4

description:
Library name: 78
column name in DSX_processed_counts.csv: 78

value: w; P{UASbab1}; dsx1/dsxGAL4


title: BAB1dsx5

description:
Library name: 88
column name in DSX_processed_counts.csv: 88


title: EYdsx5

description:
Library name: 59_EY
column name in DSX_processed_counts.csv: 59_EY


title: BAB1dsx3

description:
Library name: 68
column name in DSX_processed_counts.csv: 68


title: 143-6W

description: Library name: Sample_00000000000023


title: 141-6W

description: Library name: Sample_00000000000021


title: BAB1dsx1

description:
Library name: 48
column name in DSX_processed_counts.csv: 48


title: 139-6W

description: Library name: Sample_00000000000019

value: ipilimumab


title: 139-BL

description: Library name: Sample_00000000000020


title: 126-BL

description: Library name: Sample_00000000000018


title: DSXFdsx5

description:
Library name: 85
column name in DSX_processed_counts.csv: 85

value: w; dsx1, P{UASdsxF}/dsxGAL4


title: BAB1dsx2

description:
Library name: 58_BAB1
column name in DSX_processed_counts.csv: 58_BAB1


title: DSXFdsx4

description:
Library name: 75
column name in DSX_processed_counts.csv: 75


title: 126-6W

description: Library name: Sample_00000000000017


title: 125-BL

description: Library name: Sample_00000000000016


title: DSXFdsx3

description:
Library name: 65_DSXF
column name in DSX_processed_counts.csv: 65_DSXF


title: ANTPdsx3

description:
Library name: 6_3
column name in DSX_processed_counts.csv: 6_3


title: DSXFdsx2

description:
Library name: 55_DSXF
column name in DSX_processed_counts.csv: 55_DSXF


title: 125-3M

description: Library name: Sample_00000000000015


title: 153-BL

description: Library name: Sample_00000000000026


title: DSXFdsx1

description:
Library name: 45
column name in DSX_processed_counts.csv: 45


title: Condsx6

description:
Library name: 61_dsx1
column name in DSX_processed_counts.csv: 61_dsx1

value: w; dsx1/dsxGAL4


title: 122-6W

description: Library name: Sample_00000000000013


title: 141-BL

description: Library name: Sample_00000000000022


title: 122-BL

description: Library name: Sample_00000000000014


title: Condsx4

description:
Library name: 41
column name in DSX_processed_counts.csv: 41


title: Condsx5

description:
Library name: 51
column name in DSX_processed_counts.csv: 51


title: Condsx3

description:
Library name: 1_3
column name in DSX_processed_counts.csv: 1_3


title: Condsx2

description:
Library name: 1_2
column name in DSX_processed_counts.csv: 1_2


title: hESC 250 treated with Veh

city: Research Triangle Park

first: Francesco

middle: John

last: DeMayo

state: North Carolina

address: 111 T W Alexander Dr

department: DIR

institute: NIEHS

description: Library name: 250Veh

library_source: genomic

data_processing:
The HiCUP platform (Version 0.9.2) was used to process and align HiChIP samples with Arima digest and default parameters except minimum and maximum ditag length (set to 100 and 1,000 bp)
Peaks were inferred from the HiChIP data using MACS2 (Version 2.2.9.1) with a q-value threshold of 0.01 and extension size of 100 and the --nomodel and --keep-dup all flags
Loops with at least one loop anchor in a peak region were called and differential loops were identified using FitHiChIP (Version 11.0) following the author’s vignette except for bin size (set to 10 kb) and background model (set to peak-to-all; option 0)
Assembly: hg38 genome (GCF_000001405.40)
Supplementary files format and content: bigInteract files
Supplementary files format and content: bedpe files
Library strategy: HiChIP

molecule: genomic DNA

source_name: primary human endometrial stromal cells

growth_protocol: Primary human endometrial stromal cells were cultured in DMEM-F12 supplemented with 5% Fetal bovine serum (FBS) and 1X Penicillin Streptomycin. Cells were used within 6 passages.

extract_protocol: Libraries were prepared by Arima Genomics.

treatment_protocol: hESC were treated with 0.2% ethanol (vehicle) or a mixture of 10 nM 17β-estradiol (Sigma-Aldrich, St. Louis, MO, USA), 1 µM medroxyprogesterone acetate (Sigma-Aldrich, St. Louis, MO, USA) and 100 µM dibutyral cyclic AMP (Sigma-Aldrich, St. Louis, MO, USA) in media containing OptiMEM with 2% Charcoal Stripped Serum (csFBS, Gibco Thermo Fisher Scientific, Waltham, MA, USA) and 1% Penicillin-Streptomycin). Cells were treated for 3 days, with media being replaced after 2 days.

tag: cell line

value: primary human endometrial stromal cells

value: Wildtype

value: Veh


title: Female5

description:
Library name: 53_Female
column name in DSX_processed_counts.csv: 53_Female

value: P13-P15 abdomen

value: OreR


title: hESC 221 treated with Veh

description: Library name: 221Veh


title: hESC 221 treated with EPC

description: Library name: 221EPC

value: EPC


title: ESR1 gRNA E2 R3

description: Library name: Sample12

data_processing:
Adapter trimming, optical deduplication, and PCR deduplication were performed using BBMap v39.01
Reads were mapped to the hg38 genome (GCF_000001405.40) using STAR v2.6.0c
Differential expression analysis was performed using edgeR v4.2.2 in R v4.4.1
Assembly: hg38 genome (GCF_000001405.40)
Supplementary files format and content: raw_counts.csv contains the raw counts data for each sample, with genes at row titles and samples as column titles.
Supplementary files format and content: normalized_counts_log2cpm.csv contains normalized counts using the log2 of counts per million method.

source_name: THESC

growth_protocol: CRISPR engineered cells were maintained in DMEM/F-12 supplemented with 10% Fetal Bovine Serum and 4ug/mL Blasticidin. Cells were cultured and grown in a 5% CO2 and 37°C incubator. Cell media was changed every three days and cells were passaged before reaching 90% confluency.

extract_protocol:
The total RNA of the cells was isolated using Qiagen RNeasy RNA mini prep kit with Qiagen on-column DNase digestion following the manufacturer’s instructions.
Illumina Tru-seq Stranded mRNA library kit with IDT for Illumina TruSeq RNA UD-96 barcodes

treatment_protocol: Cells were treated with 10nM E2 or 0.01% EtOH (vehicle) in OptiMEM with 2% Charcoal Stripped Serumand 1% Penicillin-Streptomycin for 24 hours.

value: THESC

value: Endometrial Stromal Cells

value: ESR1 activated

value: 10nM estradiol (E2)


title: Condsx1

description:
Library name: 1_1
column name in DSX_processed_counts.csv: 1_1


title: ESR1 gRNA E2 R2

description: Library name: Sample11


title: Female4

description:
Library name: 43
column name in DSX_processed_counts.csv: 43


title: ESR1 gRNA E2 R1

description: Library name: Sample10


title: ESR1 gRNA Veh R3

description: Library name: Sample9

value: Vehicle (0.01% ethanol)


title: ESR1 gRNA Veh R2

description: Library name: Sample8


title: Female2

description:
Library name: 3_2
column name in DSX_processed_counts.csv: 3_2


title: Female1

description:
Library name: 3_1
column name in DSX_processed_counts.csv: 3_1


title: Male5

description:
Library name: 52_Male
column name in DSX_processed_counts.csv: 52_Male


title: NT gRNA E2 R2

description: Library name: Sample5

value: WT


title: Male2

description:
Library name: 2_2
column name in DSX_processed_counts.csv: 2_2


title: NT gRNA Veh R3

description: Library name: Sample3


title: hESC 250 treated with EPC

description: Library name: 250EPC


title: Male3

description:
Library name: 2_3
column name in DSX_processed_counts.csv: 2_3


title: NT gRNA E2 R1

description: Library name: Sample4


title: ESR1 gRNA Veh R1

description: Library name: Sample7


title: Male1

description:
Library name: 2_1
column name in DSX_processed_counts.csv: 2_1


title: Roots_PL4xWD_4

city: Petit-bourg

first: Leny

last: Calvez

address: Station de Roujol

country: France

institute: CIRAD

description:
Library name: Sample 56
counts_roots.csv

data_processing:
Raw sequencing read cleaning : trimmomatic software
Read aligment : MapSplice gapped alignment algorithm
Count reads : HTSeq-count Python tool
Assembly: Citrus clementina V1.0 Phytozome genome ID: 182 • NCBI taxonomy ID: 85681
Supplementary files format and content: counts_leaves.csv : file includes raw counts (RPKM) for each leaves samples
Supplementary files format and content: counts_roots.csv : file includes raw counts (RPKM) for each roots samples

organism: Citrus sinensis

source_name: Roots

growth_protocol: Plants were transplanted in 40L pots with the same substrate's amount containing (50% volcanic rock and 50% peat). The plants grown up for 2 years in an insect-proof greenhouse with natural photoperiod, day/night temperatures of 25-32°C and 22-28°C and a relative humidity between 70% and 98%. Daily irrigations and regular NPK fertilisations were applied.

extract_protocol:
Total RNA was extracted from 100 mg of leaves and roots frozen powder using the RNeasy® Plant Mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA quality and quantity were determine using a mySPEC microvolume spectrophotometer (VWR, Radnor, PA, USA). High purity RNA samples (OD260/OD280 values at 1.8-2.0) were used for library construction and sequencing. For each RNA sample, cDNA libraries were prepared for sequencing from 1 µg of total RNA using the Truseq Stranded mRNA kit (Illumina, San Diego, CA, USA) following the manufacturer’s protocol.

treatment_protocol: Trees were split in two group treatments as follow: (i) control plant set with trees under regular irrigation and (ii) and a drought stress set with trees subjected to water deficit condition by stopping the irrigation.

value: Roots

tag: scion

value: Persian lime (Citrus latifolia)

tag: rootstock

value: tetraploid Swingle citrumelo 4475 (Citrus sinensis x Poncirus trifoliata)

value: Water deficit


title: Male4

description:
Library name: 42
column name in DSX_processed_counts.csv: 42


title: NT gRNA Veh R2

description: Library name: Sample2


title: NT gRNA Veh R1

description: Library name: Sample1


title: NT gRNA E2 R3

description: Library name: Sample6


title: Roots_PL4xWD_1

description:
Library name: Sample 53
counts_roots.csv


title: GBM, Mix2-2

city: Daejeon

first: Seung Hyuck

last: Jeon

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description:
Library name: GBM, Mix2-2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The scRNA-seq data were aligned and quantified using the Cell Ranger Single-Cell Software Suite (10x Genomics) against the GRCh38 human reference genome.
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: primary

extract_protocol:
The cells were washed 3 times with PBS supplemented with 1% BSA, and the number of cells was adjusted to 700-1,200 cells/μL.
The scRNA-seq and scTCR-seq libraries were prepared using the Chromium Next GEM Single Cell 5’ Kit v1.1 (10x Genomics) according to the standard manufacturer’s instructions

value: Glioblastoma

value: CD8+ cells


title: Female3

description:
Library name: 3_3
column name in DSX_processed_counts.csv: 3_3


title: Roots_PL4xCtrl_2

description:
Library name: Sample 51
counts_roots.csv

value: Control


title: Roots_PL4xWD_3

description:
Library name: Sample 55
counts_roots.csv


title: Multiome, NCIH2170 cells, GEX

city: Chapel Hill

first: Elizabeth

last: Brunk

state: NC

address: 250 Bell Tower Dr.  4352 Genome Sciences Bldg.

department: Pharmacology, Lineberger Comprehensive Cancer Center, UNC School of Medicine

institute: University of North Carolina at Chapel Hill

description: Library name: NCIH2170_GEX_control

data_processing:
After aligning to GRCh38 genome, cells met following criteria were kept for further downstream analysis: nCount_ATAC between 1,000 and 25,000; nCount_RNA between 1,000 and 25,000; nucleosome signal less than 2; TSS.enrichment more than 1; mitochondria gene percent less than 20%; predicted to be singlet.
Assembly: GRCh38
Supplementary files format and content: RDS file containing the processed and analysis-ready scRNA & scATAC data for cell line NCIH2170

source_name: Cell line

extract_protocol:
10X single cell suspension was prepared according to the corresponding 10X protocol
Library construction was done by following the 10X corresponding protocol

value: Cell line

value: Cancer cell


title: Multiome, NCIH2170 cells, ATAC

description: Library name: NCIH2170_scATAC_control

library_source: genomic single cell


title: G39_WM, GEX

city: Campinas

first: Diogo

middle: Fernando Troggian

last: Veiga

state: SP

address: Rua Vital Brasil, 80

department: Department of Translational Medicine

country: Brazil

institute: Universidade Estadual de Campinas

description: Library name: G39_WM_GE

data_processing:
Demultiplexing, genome alignment, gene quantification, and peak accessibility analysis for single nuclei were conducted using the Cell Ranger ARC pipeline. Specifically, fastq files were generated with cellranger mkfastq, followed by processing with cellranger-arc count v.2.0.2 using the human genome GRCh38 to produce count matrices for RNA and ATAC modalities.
Assembly: GRCh38
Supplementary files format and content: outputs from 10X Cell Ranger ARC Count pipeline

source_name: subcortex

extract_protocol:
Nuclei were isolated using the Chromium Nuclei Isolation kit (10X Genomics) according to the manufacturer’s protocol (CG000505, revision A), which is compatible with the Single Cell Multiome ATAC + Gene Expression assay.  Briefly, frozen tissue samples were dissociated with a pestle in lysis buffer and passed through a nuclei isolation column. The isolated nuclei were then resuspended in a debris removal buffer, followed by washes to clear any remaining debris. Recovered nuclei were stained with Trypan blue and counted with a hemocytometer. Nuclei integrity was evaluated under a microscope at 40X or 60X magnification, and nuclei were considered viable if they were roundish and with an intact membrane.
Libraries were prepared using the Multiome ATAC + Gene Expression kit (10X Genomics) according to the manufacturer’s protocol CG000338 revision E.

value: subcortex

tag: specimen identifier

tag: donor

tag: dissection

value: WM

tag: condition

value: MOGHE

tag: Sex

value: male

tag: age at_surgery

tag: age at_onset

tag: lobe

value: Temporal

tag: side of_resection

value: Left

tag: tissue source

value: Epilepsy surgery


title: GBM, Mix2-1

description:
Library name: GBM, Mix2-1
10x Genomics

tag: tissue

tag: cell type


title: Roots_PL4xWD_2

description:
Library name: Sample 54
counts_roots.csv

tag: treatment


title: Roots_PL4xCtrl_3

description:
Library name: Sample 52
counts_roots.csv


title: Roots_PL2xWD_2

description:
Library name: Sample 41
counts_roots.csv

value: diploid Swingle citrumelo 4475 (Citrus sinensis x Poncirus trifoliata)


title: Roots_PL4xCtrl_1

description:
Library name: Sample 50
counts_roots.csv

value: Roots


title: Roots_PL2xWD_3

description:
Library name: Sample 42
counts_roots.csv

value: Persian lime (Citrus latifolia)


title: G39_WM, ATAC

description: Library name: G39_WM_ATAC


title: Roots_PL2xWD_1

description:
Library name: Sample 40
counts_roots.csv


title: G39_GM, GEX

description: Library name: G39_GM_GE

source_name: cortex

value: cortex

value: GM


title: Roots_PL2xCtrl_1

description:
Library name: Sample 36
counts_roots.csv


title: Roots_ML4xWD_4

description:
Library name: Sample 28
counts_roots.csv

value: Mexican lime (Citrus aurantiifolia)

value: tetraploid Swingle citrumelo 4475 (Citrus sinensis x Poncirus trifoliata)

value: Water deficit


title: G39_GM, ATAC

description: Library name: G39_GM_ATAC


title: Roots_PL2xCtrl_3

description:
Library name: Sample 38
counts_roots.csv

value: Control


title: Roots_PL2xCtrl_2

description:
Library name: Sample 37
counts_roots.csv


title: Roots_ML4xWD_3

description:
Library name: Sample 27
counts_roots.csv


title: G23_WM, GEX

description: Library name: G23_WM_GE

value: female

value: Frontal

value: Right


title: G23_GM, ATAC

description: Library name: G23_GM_ATAC

value: MOGHE


title: G23_WM, ATAC

description: Library name: G23_WM_ATAC

value: subcortex

value: WM


title: Roots_ML4xWD_2

description:
Library name: Sample 26
counts_roots.csv


title: GBM, Mix1-1

description:
Library name: GBM, Mix1-1
10x Genomics

value: Glioblastoma

value: CD8+ cells


title: RIbeta-L50R-mRuby2 transfected cells, biol rep 2

city: La Jolla

first: Emily

middle: H

last: Pool

state: California

address: 9500 Gilman Dr.

department: Pharmacology

institute: UCSD

data_processing:
Raw data were analyzed using the web-based platform Galaxy (https://usegalaxy.org) and open-source R software (version 4.3.2, https://www.r-project.org). High-quality raw reads were mapped to the reference human genome, hg38, using HISAT2 (version 2.2.1). Aligned reads were counted using htseq-count (version 0.9.1). The R package DESeq2 (version 1.34.0) was used to conduct differentially expressed gene (DEG) analysis. Genes with log(2) fold change (> 0.5) and p-adj < 0.05 were considered significant DEGs.
Assembly: Hg38
Supplementary files format and content: Tabular files for each sample contain total raw counts of reads mapped to the known genome.

source_name: RIalpha KO HEK293T

growth_protocol: RIalpha KO HEK293T were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% Pen/Strep in a humidified atmosphere with 5% CO2 at 37C, and transiently transfected with construct over 24 hours using PolyJet reagent.

extract_protocol:
Total RNA was extracted using TRIzol.Approximately 1 µg of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: RIalpha KO HEK293T

value: Human embryonic kidney

tag: genotype

value: PRKAR1A CRISPR knockout

value: RIbeta-L50R-mRuby2 transfected cells


title: Roots_ML4xCtrl_3

description:
Library name: Sample 24
counts_roots.csv

value: Roots


title: RIbeta-L50R-mRuby2 transfected cells, biol rep 3

tag: cell line


title: GBM, Mix1-2

description:
Library name: GBM, Mix1-2
10x Genomics


title: Roots_ML4xWD_1

description:
Library name: Sample 25
counts_roots.csv

tag: scion

value: Mexican lime (Citrus aurantiifolia)


title: Roots_ML4xCtrl_1

description:
Library name: Sample 22
counts_roots.csv

tag: rootstock

value: tetraploid Swingle citrumelo 4475 (Citrus sinensis x Poncirus trifoliata)


title: Roots_ML4xCtrl_2

description:
Library name: Sample 23
counts_roots.csv


title: RIbeta-L50R-mRuby2 transfected cells, biol rep 1


title: RIbeta-mRuby2 transfected cells, biol rep 1

value: RIbeta-mRuby2 transfected cells


title: RIbeta-mRuby2 transfected cells, biol rep 3


title: Roots_ML2xWD_4

description:
Library name: Sample 14
counts_roots.csv

value: diploid Swingle citrumelo 4475 (Citrus sinensis x Poncirus trifoliata)

value: Water deficit


title: RIbeta-mRuby2 transfected cells, biol rep 2


title: G23_GM, GEX

description: Library name: G23_GM_GE

value: cortex

tag: specimen identifier

value: GM

value: female

value: Frontal

value: Epilepsy surgery


title: Roots_ML2xWD_2

description:
Library name: Sample 12
counts_roots.csv


title: mRuby2 control cells, biol rep 2

value: mRuby2 control cells


title: mRuby2 control cells, biol rep 1


title: Roots_ML2xCtrl_3

description:
Library name: Sample 10
counts_roots.csv

value: Control


title: Huh7, Mock - rep4

city: Princeton

first: Jiayu

last: Zhang

state: NJ

address: 119 Lewis Thomas Laboratory, Washington Road

department: Molecular Biology

institute: Princeton

data_processing:
Raw Illumina sequence data were demultiplexed with fastq-multx. Reads were then mapped to the human genome hg38 with hisat2 2.1.0, and reads mapping to the comprehensive gene annotation on the primary assembly were counted with htseq-count v1.99.2 using snakemake wrapper RASflow
Assembly: human genome hg38 release 39
Supplementary files format and content: Counts matrix of genes (hg38) x 35 samples

growth_protocol: Huh7 cells were maintained in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S) in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Sorted cells were then centrifuged and subjected to RNA extraction using RecoverAll Total Nucleic Acid Isolation Kit (Thermo Scientific) according to manufacturer instructions with slight modifications. Briefly, cell pellets were resuspended in digestion buffer and incubated at 50 °C for 3 hrs with constant shaking. During column purification, in-column DNase treatment was omitted. Instead, eluted RNA were treated with TURBO™ DNase (Thermo Scientific) for 30 mins at 37 °C and cleaned up with 0.8X RNAClean XP Beads (Beckman Coulter) . The RNA integrity was assessed by Agilent TapeStation 4200 (Agilent) with High Sensitivity RNA ScreenTape (Agilent).
Total RNA samples (300ng per sample) were used as input for reverse transcription using barcoded oligo-dT primers to label each sample in the 96-well plate following the drop-seq method. The pooled barcoded cDNA samples were amplified by PCR and purified, then turned into sequencing libraries using the Tn5 transpose-based tagmentation method to include only the poly-A tail adjacent 3’ ends of transcripts.  These libraries were sequenced on Illumina NovaSeq 6000 SP 100 cycle flowcell. Raw sequencing reads were filtered by Illumina NovaSeq Control Software and only the Pass-Filter (PF) reads were used for further analysis.

treatment_protocol: Huh7 cells were plated at 1e6 cells/well in 6-well plate the day before infection. Virus were inoculated at a MOI of 0.5 and incubate at 37 °C before replacement of fresh DMEM supplemented with 10% FBS and 1% P/S. 48 hours later, cells were collected, washed, and fixed with 4% PFA supplemented with SUPERase•In™ RNase Inhibitor  for 30 mins at 4 °C. The cells were centrifuged, resuspended in sort buffer (PBS containing 0.2% (w/vol) bovine serum albumin [BSA] and SUPERase•In™ RNase Inhibitor) for FACS. High mScarlet-expressing cells were sorted for RNA extraction.

value: Human hepatoma

tag: strain

value: mock

tag: replicate


title: Roots_ML2xCtrl_2

description:
Library name: Sample 9
counts_roots.csv


title: Huh7, Mock - rep3


title: Roots_ML2xCtrl_1

description:
Library name: Sample 8
counts_roots.csv


title: Huh7, Mock - rep2


title: Huh7, Mock - rep1


title: Huh7, 17D-[Asibi-NS2A] - rep3


title: Huh7, 17D-[Asibi-NS2A] - rep2


title: Huh7, 17D-[Asibi-NS2A] - rep1


title: Huh7, Dakar-[17DEns/2A] - rep3


title: Roots_ML2xWD_3

description:
Library name: Sample 13
counts_roots.csv


title: 3_1F8

city: madison

first: Xinyu

last: Zhao

state: WI

address: 1500 Highland Ave

department: Waisman Center

institute: University of Wisconsin-Madison

description:
patch-seq, pcd99, replicate 1
SMART-seq3

data_processing:
snATAC/RNA-seq: The 10x Multiome ATAC(snATAC-seq) + Gene Expression(snRNA-seq) dataset was processed using the Cell Ranger ARC pipeline. To analyze the macaque data, we used the Cell Ranger ARC mkref to create a rheMac10 reference. Subsequently, we performed a quality check on the output of the Cell Ranger ARC pipeline, and then used it for downstream analysis.
SMART-seq:The SMART-seq3 RNA-seq reads from human were aligned to reference genome GRCh38 and the reads from rhesus macaque were aligned to reference genome rheMac10. Trim Galore was used for the adaptor trimming. We used STAR (v2.7.2b) (69) in two pass Mode for the alignment and removed PCR duplicates. STAR quantMode was used for gene counts on uniquely aligned reads, and the intergenic regions were excluded.
Assembly: rheMac10; GRCh38
Supplementary files format and content: snATAC-seq: fragments files are generated from Cell Ranger ARC pipeline. ; snRNA-seq: barcodes, features and matrix files are generated from Cell Ranger ARC pipeline. SMART-seq3: "AcuteRhesusPatchseq.csv" and "OrganotypicCHD8Patchseq.csv" are normalized gene expression data files.

molecule: nuclear RNA

organism: Macaca mulatta

source_name: dlPFC

extract_protocol:
Macaque brain specimens were collected from postconceptional day (PCD) 87 to PCD155. All experiments using non-human primates were carried out in accordance with a protocol approved by the University of Wisconsin’s Institutional Animal Care and Use Committee and NIH guidelines.
snMultiomes:The libraries were constructed in accordance with the guidelines provided in the "Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide" (10x Genomics, CG000338); SMART-seq3: follow the protocol according to publication "Single-cell RNA counting at allele and isoform resolution using Smart-seq3" (PMID: 32518404).

value: dlPFC

tag: developmental stage

value: cortical cells

value: wild type

value: no treatment


title: 3_1E8


title: 3_1H6


title: Huh7, Dakar-[17DEns/2A] - rep1


title: 3_1G7


title: 3_1F7


title: 3_1G8


title: Huh7, Dakar-[17DEns/2A] - rep2


title: Huh7, 17D-[Asibi-Ens/2A] - rep3


title: 3_1E7


title: mRuby2 control cells, biol rep 3

value: RIalpha KO HEK293T

value: Human embryonic kidney

value: PRKAR1A CRISPR knockout


title: Roots_ML2xWD_1

description:
Library name: Sample 11
counts_roots.csv

value: Roots

value: Mexican lime (Citrus aurantiifolia)

value: diploid Swingle citrumelo 4475 (Citrus sinensis x Poncirus trifoliata)

value: Water deficit


title: Huh7, 17D-[Asibi-Ens/2A] - rep2


title: Huh7, 17D-[Asibi-Ens/2A] - rep1


title: 3_1D9


title: 3_1D8


title: Huh7, 17D-[Asibi-Ens] - rep3


title: 3_1D7


title: 3_1H8


title: Huh7, 17D-[Asibi-Ens] - rep1


title: 3_1H7


title: Huh7, 17D-[Asibi-Ens] - rep2


title: 3_1C8


title: Huh7, Asibi-[17D-Ens/2A] - rep3


title: 3_1B9


title: Huh7, Asibi-[17D-Ens/2A] - rep1


title: 3_1B8


title: Huh7, Asibi-[17D-Ens/2A] - rep2


title: 3_1A9


title: 2_2C7

description:
patch-seq, pcd96, replicate 1
SMART-seq3


title: Huh7, Asibi-[17D-NS2A] - rep1


title: Huh7, Asibi-[17D-NS2A] - rep3


title: Huh7, Asibi-[17D-NS2A] - rep2


title: Huh7, Asibi-[17D-Ens] - rep2


title: Huh7, Asibi-[17D-Ens] - rep3


title: Huh7, Dakar - rep3

value: Dakar


title: 1_4C4


title: 1_4D4


title: 1_4B4


title: 3_1C9


title: 1_4A4


title: Huh7, Asibi-[17D-Ens] - rep1


title: 12CS_044, Inoculated, 21dpi, Rep2

city: Dakar

first: Darius

last: Tchoutang Nzepang

address: Route des hydrocarbures

country: Senegal

institute: IRD

description:
Library name: Sample26
colunm name in salmon.merged.gene_counts.txt: 12CS_044T21_REP2

data_processing:
nf-core/rnaseq pipeline version 3.11.2
The quality of the raw reads from the RNA-seq was analyzed using Fastqc
Adapters and low-quality sequences (Phred score < 30) were removed using Cutadapt
Clean reads were aligned to the reference sequence using STAR
The quality of the alignment was assessed using Qualimap, and gene expression was quantified using Salmon
Assembly: arahy.Tifrunner.gnm1.KYV3.genome_main.fna
Supplementary files format and content: tab-delimited text includes raw counts for each sample

organism: Arachis hypogaea

source_name: Nodulated root

growth_protocol: The plants were grown in a growth chamber at 28 °C with a photoperiod lighting 16h of light (150 mmol.m2.s-1) and 8h of darkness and  70 % humidity.

extract_protocol:
RNA was extracted from approximately 100 mg of powdered material by following the RNeasy Minikit protocol (Qiagen). 2 µg of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were constructed using Stranded mRNA Prep ligation kit (Illumina)

treatment_protocol: Two treatments were applied: one without nitrogen, and another without nitrogen + inoculated with the efficient B. vignae strain ISRA400 (1 ml). The inoculum was applied seven days after planting in growth chamber.

value: Nodulated root


title: 12CS_044, Inoculated, 21dpi, Rep3

description:
Library name: Sample27
colunm name in salmon.merged.gene_counts.txt: 12CS_044T21_REP3


title: 12CS_044, Inoculated, 21dpi, Rep1

description:
Library name: Sample25
colunm name in salmon.merged.gene_counts.txt: 12CS_044T21_REP1


title: 1_4A12


title: 12CS_051, Inoculated, 21dpi, Rep2

description:
Library name: Sample23
colunm name in salmon.merged.gene_counts.txt: 12CS_051T21_REP2


title: Huh7, Dakar - rep2


title: 12CS_051, Inoculated, 21dpi, Rep3

description:
Library name: Sample24
colunm name in salmon.merged.gene_counts.txt: 12CS_051T21_REP3


title: Huh7, Dakar - rep1


title: 12CS_051, Inoculated, 21dpi, Rep1

description:
Library name: Sample22
colunm name in salmon.merged.gene_counts.txt: 12CS_051T21_REP1


title: Fleur11, Inoculated, 21dpi, Rep3

description:
Library name: Sample21
colunm name in salmon.merged.gene_counts.txt: Fleur11T21_REP3


title: Huh7, Asibi - rep3

value: Asibi


title: 1_1H1


title: Fleur11, Inoculated, 21dpi, Rep1

description:
Library name: Sample19
colunm name in salmon.merged.gene_counts.txt: Fleur11T21_REP1


title: Fleur11, Inoculated, 21dpi, Rep2

description:
Library name: Sample20
colunm name in salmon.merged.gene_counts.txt: Fleur11T21_REP2


title: 1_1G2


title: 12CS_044, Inoculated, 12dpi, Rep3

description:
Library name: Sample18
colunm name in salmon.merged.gene_counts.txt: 12CS_044T12_REP3


title: 2_2B7


title: 12CS_044, Inoculated, 12dpi, Rep2

description:
Library name: Sample17
colunm name in salmon.merged.gene_counts.txt: 12CS_044T12_REP2


title: 3_1A8


title: Huh7, 17D - rep4


title: 12CS_051, Inoculated, 12dpi, Rep2

description:
Library name: Sample14
colunm name in salmon.merged.gene_counts.txt: 12CS_051T12_REP2


title: 1_1H2


title: Huh7, Asibi - rep1


title: 12CS_051, Inoculated, 12dpi, Rep1

description:
Library name: Sample13
colunm name in salmon.merged.gene_counts.txt: 12CS_051T12_REP1


title: Huh7, 17D - rep3


title: 1_1G1


title: 1_1F1


title: 12CS_044, Control, 0 dpi, Rep3

description:
Library name: Sample9
colunm name in salmon.merged.gene_counts.txt: 12CS_044T0_REP3

source_name: Root without nodules

value: Root without nodules

value: Control


title: 1_1E2


title: Huh7, 17D - rep2

value: Human hepatoma


title: Fleur11, Inoculated, 12dpi, Rep1

description:
Library name: Sample10
colunm name in salmon.merged.gene_counts.txt: Fleur11T12_REP1


title: Huh7, Asibi - rep2


title: Huh7, 17D - rep1


title: 12CS_051, Contro, 0dpi, Rep3

description:
Library name: Sample6
colunm name in salmon.merged.gene_counts.txt: 12CS_051T0_REP3


title: 1_1E1

description:
patch-seq, pcd96, replicate 1
SMART-seq3

value: dlPFC


title: 12CS_044, Control, 0 dpi, Rep1

description:
Library name: Sample7
colunm name in salmon.merged.gene_counts.txt: 12CS_044T0_REP1


title: 12CS_051, Contro, 0dpi, Rep2

description:
Library name: Sample5
colunm name in salmon.merged.gene_counts.txt: 12CS_051T0_REP2


title: 1_1D2

value: cortical cells


title: 12CS_051, Inoculated, 12dpi, Rep3

description:
Library name: Sample15
colunm name in salmon.merged.gene_counts.txt: 12CS_051T12_REP3


title: 12CS_044, Inoculated, 12dpi, Rep1

description:
Library name: Sample16
colunm name in salmon.merged.gene_counts.txt: 12CS_044T12_REP1


title: 12CS_051, Contro, 0dpi, Rep1

description:
Library name: Sample4
colunm name in salmon.merged.gene_counts.txt: 12CS_051T0_REP1


title: Huh7, mock, rep6

data_processing:
Raw Illumina sequence data were demultiplexed with fastq-multx. Reads were then mapped to the human genome hg38 with hisat2 2.1.0, and reads mapping to the comprehensive gene annotation on the primary assembly were counted with htseq-count v1.99.2 using snakemake wrapper RASflow
Assembly: human genome hg38 release 39
Supplementary files format and content: Counts matrix of genes (hg38) x 24 samples

value: mock


title: 1_1F2

value: wild type

value: no treatment


title: Huh7, mock, rep5


title: 1_1C2


title: Fleur11, Control, 0 dpi, Rep3

description:
Library name: Sample3
colunm name in salmon.merged.gene_counts.txt: Fleur11T0_REP3


title: 1_1C1


title: Huh7, mock, rep3


title: Fleur11, Inoculated, 12dpi, Rep3

description:
Library name: Sample12
colunm name in salmon.merged.gene_counts.txt: Fleur11T12_REP3


title: Fleur11, Control, 0 dpi, Rep2

description:
Library name: Sample2
colunm name in salmon.merged.gene_counts.txt: Fleur11T0_REP2


title: Huh7, mock, rep4


title: TE1_NC-P

city: Guangzhou

first: Jinlong

last: Lin

address: Dongfeng dong road

country: China

institute: Sun Yat-sen university cancer center

description: Library name: Sample 4

data_processing:
In PAS-seq data analysis, the genomic locations of the 3' ends of valid poly(A) reads aligned to the reference genome (the last column of Table 4) are defined as poly(A) sites. These PAS sites are filtered and statistically analyzed using CAGEr (Haberle, Forrest et al. 2015). The filtering process involves the following steps:
Calculating the TPM value for each PAS site and removing PAS sites with TPM values less than 1.
Clustering PAS sites located within a 24-nt distance from each other into poly(A) site clusters (PACs).
Discarding PACs containing only one PAS site with a TPM value less than 3.
When multiple samples are present, PACs with TPM values greater than 5 in each sample are selected. PACs located within a 500-nt distance from each other across samples are then further clustered, resulting in the final set of PACs detected across all samples.
Assembly: GRCh38.p14
Supplementary files format and content: Excel files include consensus clusters identified in all samples

source_name: esophageal cancer

extract_protocol:
Total RNA extraction using TRIZOL (15596-018, Ambion,USA). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (M6101, Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm(A260/A280) using Ultrafine spectrophotometer (N50 touch, IMPLEN, Germany).The integrity of RNA was further verified by 1.0% agarose gel electrophoresis.
For each sample, 5 μg of total RNA was treated with RQ1 DNase (M6101, Promega) to remove DNA, fragmented RNAs were used for PAS-seq library preparation. mRNAs were captured with mRNA Capture Beads kit (N401, Vazyme). Fragmented mRNAs were used for directional PAS-seq library preparation by KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (KK8544, Roche). Fragmented mRNAs were converted into double-strand cDNA. Following end repair and A tailing, the DNAs were ligated to Diluted Roche Adaptor (KK8726, Roche). After purification of the ligation product and size fractioning to 300-500 bp, the ligated products were amplified and purified, quantified, and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing.For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to the Illumina Novaseq Xplus system for 150 nt paired-end sequencing.

value: esophageal cancer

value: PBS


title: Fleur11, Inoculated, 12dpi, Rep2

description:
Library name: Sample11
colunm name in salmon.merged.gene_counts.txt: Fleur11T12_REP2


title: 12CS_044, Control, 0 dpi, Rep2

description:
Library name: Sample8
colunm name in salmon.merged.gene_counts.txt: 12CS_044T0_REP2


title: 1_1B2


title: TE1_lac-P

description: Library name: Sample 3

value: L-lactate


title: Huh7, mock, rep2


title: Huh7, mock, rep1


title: 1_1B1


title: K30_lac-P

description: Library name: Sample 1


title: 1_1A2


title: THP-1 NOFQ treatment 4

city: Leipzig

first: Alexander

last: Jais

address: Philipp-Rosenthal-Straße 27

country: Germany

institute: Helmholtz Institute for Metabolic, Obesity, and Vascular Research (HI-MAG)

data_processing:
The trimmed reads were aligned to the reference genome using HISAT2 v2.0.5, which generated a database of splice junctions from the gene model annotation file to improve alignment quality.
Gene expression levels were quantified using featureCounts v1.5.0-p3, with results expressed in FPKM (Fragments Per Kilobase of transcript per Million mapped reads) to normalize for gene length and sequencing depth.
For differential gene expression analysis, DESeq2 was employed for groups with biological replicates. Criteria for differential expression included log2 fold change > 0.5 and adjusted p-value < 0.05.
Assembly: GRCh38 (hg38)
Supplementary files format and content: xlsx (Excel file containing FPKM values and DEG analysis)

extract_protocol:
RNeasy Mini Kit
Fragmentation was followed by the synthesis of the first strand cDNA using random hexamer primers, and the second strand cDNA was synthesized using dUTP to ensure strand specificity. The resulting cDNA libraries underwent end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Library quality was confirmed using Qubit for quantification, real-time PCR, and bioanalyzer for size distribution.

treatment_protocol: PMA-differentiated THP-1 cells, untreated vs. 10 ng/ml N/OFQ for 24 hours

value: Macrophage

value: PMA + 10 ng/ml N/OFQ


title: Huh7, Dakar, rep6


title: K30_NC-P

description: Library name: Sample 2


title: Fleur11, Control, 0 dpi, Rep1

description:
Library name: Sample1
colunm name in salmon.merged.gene_counts.txt: Fleur11T0_REP1


title: THP-1 NOFQ treatment 2


title: THP-1 NOFQ treatment 3


title: Huh7, Dakar, rep5


title: THP-1 vehicle control 4

value: PMA + vehicle


title: THP-1 vehicle control 3


title: THP-1 vehicle control 2


title: Huh7, Dakar, rep4

value: Dakar


title: THP-1 NOFQ treatment 1


title: new3_4H12

description:
patch-seq, pcd91, replicate 1
SMART-seq3


title: new3_4H11


title: THP-1 vehicle control 1


title: new3_4H1


title: Huh7, Dakar, rep3


title: Huh7, Dakar, rep2


title: new3_4E7


title: U2OS cells, hour 4, replicate 2

city: Worcester

first: Michael

last: Lee

state: MA

address: 368 Plantation Street

institute: UMASS Chan Medical School

description:
Library name: U2OS_4hr_Rep2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

data_processing:
Basecalling and demultiplexing was performed using BCL Convert v4.3.6
Transcript abundance was estimated using Kallisto (0.46.1) with parameters --bootstrap-samples 30 --single-overhang --rf-stranded. The ensembl GRCh38 cdna transcriptome build was used, appended with ERCC control transcript sequences.
Gene-level counts were generated in R using the tximport package. Counts were normalized to ERCC spike-ins using DESeq2, implemented with the function "estimateSizeFactors" with the option "controlGenes" set to the identities of the 92 ERCC transcripts. Counts were filtered for protein coding genes.
Assembly: GRCh38
Supplementary files format and content: CSV file of ERCC spike-in normalized counts for each sample

growth_protocol: Cells were maintained in high glucose DMEM supplemented with 10% fetal bovine serum, penicillin/streptomycin, and glutamine in a humidified incubator with 5% CO2 at 37C

extract_protocol:
At assay endpoint cells were trypsinized, counted using a hemacytometer, pelleted, washed with PBS, and moved immediately to RNA extraction. Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, 74134) according to manufacturer protocol. To facilitate absolute RNA quantification, polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were diluted 1:100 in nuclease-free water, and added to each sample at 1 µL/100,000 cells. ERCC spike-ins were added immediately following lysis of cells in RLT-plus buffer, and prior to all subsequent total RNA extraction steps using the RNeasy Plus kit. mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490).
RNAseq libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit using the NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7765 and E7600).

treatment_protocol: Cells were seeded onto six-well plates (300,000 cells per well) and left to adhere overnight. Cells were then drugged with 1 µM triptolide the next day (hr0).

value: osteosarcoma

value: Wild-type

value: 1 µM triptolide

tag: time

value: 4 hours


title: U2OS cells, hour 8, replicate 2

description:
Library name: U2OS_8hr_Rep2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: 8 hours


title: Huh7, Dakar, rep1

value: Human hepatoma


title: U2OS cells, hour 4, replicate 1

description:
Library name: U2OS_4hr_Rep1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS cells, hour 0, replicate 2

description:
Library name: U2OS_0hr_Rep2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: 0 hours


title: new3_4D7

value: dlPFC

value: cortical cells


title: U2OS-BAX-BAK1 -/- cells, hour 24, replicate 2

description:
Library name: DKO_24hr_Rep2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number

value: BAX Knockout, BAK1 knockout

value: 24 hours


title: Huh7, Asibi, rep6

value: Asibi


title: U2OS cells, hour 0, replicate 1

description:
Library name: U2OS_0hr_Rep1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: 1_1A1

description:
patch-seq, pcd96, replicate 1
SMART-seq3

value: wild type

value: no treatment


title: new3_4B7


title: U2OS-BAX-BAK1 -/- cells, hour 24, replicate 1

description:
Library name: DKO_24hr_Rep1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: Huh7, Asibi, rep5


title: Huh7, Asibi, rep4


title: new3_4A2


title: U2OS-BAX-BAK1 -/- cells, hour 8, replicate 1

description:
Library name: DKO_8hr_Rep1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS-BAX-BAK1 -/- cells, hour 4, replicate 2

description:
Library name: DKO_4hr_Rep2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS-BAX-BAK1 -/- cells, hour 8, replicate 2

description:
Library name: DKO_8hr_Rep2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: Huh7, Asibi, rep3


title: new3_4A11


title: U2OS-BAX-BAK1 -/- cells, hour 4, replicate 1

description:
Library name: DKO_4hr_Rep1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS-BAX-BAK1 -/- cells, hour 0, replicate 2

description:
Library name: DKO_0hr_Rep2
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS-BAX-BAK1 -/- cells, hour 0, replicate 1

description:
Library name: DKO_0hr_Rep1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: U2OS cells, hour 8, replicate 1

description:
Library name: U2OS_8hr_Rep1
polyadenylated ERCC standards (Thermo Fisher Scientific, 4456740) were spiked in proportional to cell number


title: Huh7, Asibi, rep2


title: new3_3H9


title: ICANS6, VisiumHD

city: Muenster

first: I-Na

last: Lu

state: NRW

address: Domagkstraße 20

department: Department of Pediatric Hematology and Oncology

institute: University Children's Hospital Münster

description:
Library name: ICANS6
fatal ICANS

data_processing:
Sequencing was performed on the NextSeq 2000 with a 43-10-10-50 read setup. Flow cells were demultiplexed using the mkfastq command in Space Ranger v3.0.1 (10X Genomics), and FASTQs were aligned to the human (GRCh38) reference.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files, matrix files, and images.
Library strategy: Spatial Transcriptomics

source_name: brain

extract_protocol:
5 µm FFPE serial sections were placed on standard glass slides and H&E-stained and processed following the manufacturer’s instructions (Visium HD by 10X Genomics). The CytAssist instrument was used to facilitate the transfer of transcriptomic probes from the standard glass slide to the Visium HD Spatial Gene Expression slide with 6.5 x 6.5 mm capture area.
The library was processed using VisiumHD kit (10x Genomics).

treatment_protocol: The post-mortem ICANS patient received treatment utilizing commercially available CAR-T cell products and developed ICANS (grade 4) within 7 days of infusion.

value: brain

value: brain cells

value: anti-CD19 CAR T-cell therapy


title: Huh7, Asibi, rep1


title: UNCseq2091-H05_ROI_Non nuclear

first: Andrew

middle: B

last: Gladden

address: 160 N. Medical Drive

department: Pathology & Laboratory Medicine

institute: The University of North Carolina at Chapel Hill

description: FFPE spatial transcriptomic sequencing

data_processing:
Raw BCL files converted to FASTQ by illumina BCL-Convert 3.9.3
Assembly: FASTQ files processed into DCC files by geomxngspipeline build 2.3.3.10
Supplementary files format and content: Matched_UNCseq_LGeoMx_Results_Summary_20221020.txt: corresponds DCC files to sample names
Supplementary files format and content: Hs_R_NGS_WTA_v1.0.pkc: associates GeoMx barcodes with RNA targets
Supplementary files format and content: Annotation template file.txt: denotes which samples have nuclear or non-nuclear beta-catenin
Supplementary files format and content: PSC-AG-1785_Broaddus_WTA_20221003T1451_GNP_config: assists with reading fastq files
Library strategy: Spatial Transcriptomics

source_name: Endometrium

growth_protocol: Tumors were in formalin-fixed and paraffin embedded blocks and serial sections were cut to 5 uM thickness with a microtome

extract_protocol:
The GeoMx DSP uses UV cleavable light to obtain 95 ROI's and transfer them to a 96 well plate for downstream sequencing.
Libraries were created using NanoString GeoMx Seq Code prep kits following the manufacturer's protocol.

treatment_protocol: Serially sectioned slide was stained with Beta-Catenin antibody and visualized with DAB.

value: Endometrium

value: Exon 3 CTNNB1 mutant


title: UNCseq2091-H04_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2091-H06_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2091-H03_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: new3_3H12


title: new3_3H11


title: new3_3H1


title: new3_4A7


title: UNCseq2091-H02_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2714-H12_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2091-H01_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: Huh7, 17D, rep5


title: UNCseq2714-H09_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2714-H08_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: Huh7, 17D, rep2


title: Huh7, 17D, rep3


title: UNCseq2714-H07_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: new3_3D7


title: Huh7, 17D, rep4


title: UNCseq2453-D06_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: new3_3C6


title: UNCseq2714-H10_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: Huh7, 17D, rep6


title: UNCseq2453-D05_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2453-D04_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: new3_3A12


title: Huh7, 17D, rep1


title: UNCseq2453-D03_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: RUES02, TIRN+iDUX4 (LIF-3i + dox), RNAseq, batch 02, replicate 003

city: Baltimore

first: Ludovic

last: Zimmerlin

email: lzimme14@jhmi.edu, ludovicz@gmail.com

state: MD

address: 733 N. Broadway

department: Pediatric Oncology

institute: Johns Hopkins University

data_processing:
Sequence reads were generated from stranded mRNA libraries using an Illumina Novaseq 6000 instrument (S1, 100 cycle, paired end, 2x50bp run configurations).
Reads were aligned to GRCh38 genome assembly using STAR (v2.70a) using Ensembl release 109 fastq and gtf files with parameters: -outSAMtype BAM Unsorted SortedByCoordinate -quantMode TranscriptomeSAM GeneCounts.
Read counts were calculated using summarizeOverlaps (GenomicAlignements R package) using parameters features=exonsbyGene, mode="Union", singleEnd=FALSE, ignore-strand=FALSE, fragments=TRUE and stored as a RangedSummarizedExperiment object. A raw count matrix was extracted using the function assay().
Normalized read counts were calculated from the SummarizedExperiment object using Deseq2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files includes raw and normalized (rlog) counts for each sample.
Supplementary files format and content: Bigwig files were created from the STAR-generated sorted BAM files using bamCoverage (Deeptools).

growth_protocol: RUES02 hESC were maintained in either E8 (primed) or LIF5i -> LIF-3i (TIRN)

extract_protocol:
RUES02 hESC were prepared in E8 (primed; primed +iDUX4 after 24 hours supplementation with 2mg/mL doxycycline) or LIF-3i/MEF (TIRN; TIRN +iDUX4 after 24 hours supplementation with 2mg/mL doxycycline). Cells were gently collected using a mixture 1:1 Versene/Accutase (5 min) and pass through a 70um cell strainer. PolyA mRNA libraries were prepared  using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer's instructions.
PolyA mRNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB#E7490) following manufacturer's protocols .

treatment_protocol: For the primed+iDUX4 and TIRN+iDUX4 condition, transgenic RUES02 hESC were treated for 24 hours with doxycycline to activate DUX4 expression.

value: human embryonic stem cells (hESC)

tag: lentiviral transduction

tag: condition

tag: culture method

value: LIF5i -> LIF-3i

value: 24 hours 2ug/mL doxycycline

tag: passage

tag: batch


title: new3_1H2

tag: tissue


title: UNCseq2453-D02_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: new3_1H12

tag: cell type


title: UNCseq2714-H11_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2446-D12_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: RUES02, TIRN+iDUX4 (LIF-3i + dox), RNAseq, batch 02, replicate 002

tag: treatment


title: UNCseq2446-D11_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing

tag: genotype


title: RUES02, TIRN+iDUX4 (LIF-3i + dox), RNAseq, batch 02, replicate 001

tag: cell line


title: UNCseq2446-D10_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2446-D09_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: RUES02, TIRN (LIF-3i), RNAseq, batch 02, replicate 003

value: TIRN


title: new3_1H1


title: UNCseq2446-D08_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2446-D07_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: new3_1G3


title: RUES02, TIRN (LIF-3i), RNAseq, batch 02, replicate 002


title: new3_3A1


title: new3_1G12


title: RUES02, TIRN (LIF-3i), RNAseq, batch 02, replicate 001


title: UNCseq1706-B04_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq1706-B06_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq1706-B03_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: RUES02, primed+iDUX4 (E8 + dox), RNAseq, batch 02, replicate 003


title: new3_1G1


title: UNCseq1706-B02_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: new3_1D1


title: UNCseq1706-C01_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: new3_1C7


title: RUES02, primed+iDUX4 (E8 + dox), RNAseq, batch 02, replicate 002


title: UNCseq2138-B12_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2138-B11_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: RUES02, primed+iDUX4 (E8 + dox), RNAseq, batch 02, replicate 001


title: new3_1C1


title: UNCseq2138-B10_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2138-B09_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: new3_1B1


title: RUES02, primed (E8), RNAseq, batch 02, replicate 003

value: primed


title: UNCseq2138-B08_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: RUES02, primed (E8), RNAseq, batch 02, replicate 002


title: UNCseq1706-B05_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: new3_1A7

value: dlPFC


title: UNCseq2500-C06_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2500-C05_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: RUES02, primed (E8), RNAseq, batch 02, replicate 001


title: new3_1A2

value: cortical cells


title: UNCseq2500-C03_ROI_Non-nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2500-C02_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: RUES02, TIRN+iDUX4 (LIF-3i + dox), RNAseq, batch 01, replicate 003


title: new3_1A12


title: UNCseq2500-D01_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: 4_1B1


title: UNCseq2127-C12_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: RUES02, TIRN+iDUX4 (LIF-3i + dox), RNAseq, batch 01, replicate 001


title: 4_1A1


title: RUES02, TIRN+iDUX4 (LIF-3i + dox), RNAseq, batch 01, replicate 002


title: UNCseq2127-C10_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2127-C11_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2127-C09_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: 2_2E8

description:
patch-seq, pcd87, replicate 1
SMART-seq3


title: UNCseq2138-B07_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: RUES02, TIRN (LIF-3i), RNAseq, batch 01, replicate 002


title: UNCseq2127-C07_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: RUES02, TIRN (LIF-3i), RNAseq, batch 01, replicate 003


title: UNCseq1034-A06_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: 2_2D8


title: UNCseq2127-C08_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq2500-C04_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: 2_2C8


title: 2_2B8


title: RUES02, TIRN (LIF-3i), RNAseq, batch 01, replicate 001


title: UNCseq1034-A02_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq1034-B01_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq1034-A05_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq1034-A04_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq1992-A12_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: RUES02, primed (E8), RNAseq, batch 01, replicate 002


title: 2_2A8


title: UNCseq1992-A11_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq1992-A10_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: RUES02, primed (E8), RNAseq, batch 01, replicate 001


title: Sample73_Flight.M2.2_human_serum

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

data_processing:
Our processing pipeline consists of the following elements: (1) base calls generated in real-time on the NovaSeq6000 instrument (RTA 3.1.5); (2) demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4); (3) sequence read and base quality are checked using the FASTX-toolkit (v0.0.13); (4) sequences are aligned to GRCh38 with reference transcriptome GENCODE release 30 using STAR (v2.6.1d).
Gene level expression quantification is generated with RNA-SeQC (v2.3.3) and RSEM (v1.3.1). RPKM and TPM for transcript isoforms are quantitated on the merged lane-level data with RSEM (v1.3.1). Gene-level RPKMs are quantitated with RNA-SeQC (v2.3.3) on a standard collapsed reference annotation.
RSEM transcript abundances were read into R using the Bioconductor tximeta package and summarized at the gene level.
Assembly: Gencode v30 (GRCh38)
Supplementary files format and content: Counts per gene

source_name: Kidney

growth_protocol: Deidentified human cortical kidney samples were collected through the Northwest Biotrust at the University of Washington Medical Center with local IRB approval (UW IRB Study 1297). Primary human proximal tubule epithelial cells were isolated by mechanical and enzymatic dissociation and cultured as previously described.38,39 Serum-free tubular cell cultures were maintained in PTEC maintenance media consisting of DMEM/F12 (Gibco, 11330-032) supplemented with 1x insulin-transferrin-selenium-sodium pyruvate (ITS-A, Gibco, 51300044), 50 nM hydrocortisone (Sigma, H6909), and 1x Antibiotic-Antimycotic (Gibco, 15240062). Upon reaching 70-80% confluence, PTECs were passaged by enzymatic digestion with 0.05% trypsin EDTA (Gibco, 25200056) and manual cell scraping to obtain a single-cell suspension that was subsequently neutralized with defined trypsin inhibitor (Gibco, R007100). Cells were pelleted by centrifugation at 200 x g for 6 minutes, resuspended in maintenance media, and plated in cell culture-treated flasks at >30% confluency. PTECs were used at passage number 2-3 from all donors in these experiments.

extract_protocol:
RNA was isolated from devices fixed with RNALater by injecting 100 µL of RLT lysis buffer (Qiagen, 79216) into the injection port using a 1 mL syringe outfitted with a 22-gauge needle. The cell lysate was collected at the outlet, 400 µL of RLT lysis buffer was added to each tube, and the samples were stored at -80°C until extraction. RNA was extracted using the RNeasy Micro Kit (Qiagen, 74004) and converted to cDNA with 20 the SMART-Seq v4 Ultra Low Input RNA Kit (Takara, 634891). Sequencing libraries were constructed using the SMARTer ThruPlex DNA-Seq Kit (Takara, R400676) and sequenced on a NovaSeq 6000 instrument (Illumina, San Diego, CA). Sequencing reads were aligned to GRCh38.p12 with reference transcriptome GENCODE human release 30 (with additional ERCC spike-in sequences) using STAR (v2.6.1d).
Total RNA was normalized to 2ng/ul in a total volume of 9ul and then transcribed to cDNA in a dedicated PCR clean workstation using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio, Moutain View, CA).  Sequencing libraries were constructed from cDNA using the SMARTer ThurPLEX DNA-Seq kit (Takara Bio).  Final libraries were quantified and library insert size distribution was checked using the Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples were normalized and pooled prior to treatment to block free adapters in the sequencing reaction.  Final pools were normalized to 10nM prior to sequencing.

treatment_protocol: Triplex microfluidic devices were purchased from Nortis, Inc (Bothell, WA) and prepared as previously described.40 Triplex microfluidic devices contain three fluidic circuits, which enables generation of three PTEC tubules on a single device that can be continuously perfused with media. 19 Maintenance, treatment, and fixation of devices in BioServe perfusion platform: The BioServe perfusion platform was developed to house three Triplex devices in a self-contained, hermetically sealed system to meet the levels of containment required by NASA and reduce the space required to perfuse the Triplex devices. A flow rate of 0.5 µL/min was used for cell maintenance and treatment. The treatments conditions were control (PTEC maintenance media), vitamin D, or 2% human serum.19 To prepare 2% human serum treatment media, normal human serum (Valley Biomedical, HS1021) was diluted in PTEC maintenance media to a final concentration of 2%. Vitamin D treatment media consisted of PTEC maintenance media supplemented with 1.5 µM 25(OH)D3 (Toronto Research Chemicals, C125700) and 3 µM DBP (Athens Research, 16-16-070307). To prepare vitamin D treatment media, stock 25(OH)D3 was solubilized with molecular biology grade ethanol to 5 mM. DBP was reconstituted to 3 µM in PTEC maintenance media to create PTEC-DBP media. 25(OH)D3 was then diluted into PTECDBP media to 1.5 µM. Vitamin D media was allowed to equilibrate at room temperature for 30 minutes prior to filling the treatment cassette to ensure binding of 25(OH)D3 to DBP. The final concentration of ethanol in the vitamin D treatment media was 0.02%. In order to preserve the tubules at the end of treatment for analyses, the devices were fixed for 2 hours with either 10% neutral buffered formalin (Thermo, 5725) or RNALater (ThermoFisher, AM7024) at a flow rate of 10 µL/min

value: Kidney

value: Primary cells

tag: Sex

value: Male

tag: environment

value: Flight

tag: donor


title: UNCseq1992-A09_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq1992-A08_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: 1_4G12

value: wild type

value: no treatment


title: 1_4H4


title: UNCseq1992-A07_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: Sample72_Flight.M2.2_human_serum


title: UNCseq0495-E06_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq0495-E04_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: Sample71_Flight.F1.2_human_serum

value: Female


title: 1_1H5


title: UNCseq0495-E05_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq1034-A03_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: 1_4A5


title: UNCseq0495-E02_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: RUES02, primed (E8), RNAseq, batch 01, replicate 003


title: Sample70_Flight.F1.2_human_serum


title: UNCseq0495-E03_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq0495-E01_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: 1_1G5


title: UNCseq1813-E11_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: Sample68_Flight.M1.2_human_serum


title: UNCseq1813-E08_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq1813-E12_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq1813-E09_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: Sample67_Flight.M1.2_human_serum


title: 1_1F5


title: UNCseq1813-E07_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: 1_1A6


title: 4_1C4

description:
patch-seq, pcd155, replicate 4
SMART-seq3


title: UNCseq1481-F04_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq1481-F05_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq1481-F06_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: Sample65_Flight.F2.Vitamin_D


title: Sample69_Flight.F1.2_human_serum


title: UNCseq1481-F03_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: 4_1H3

description:
patch-seq, pcd155, replicate 3
SMART-seq3


title: Sample64_Flight.F2.Vitamin_D


title: UNCseq1481-F01_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq1481-F02_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq0980-F12_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq0980-F11_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: 1_1E5


title: 4_1G2


title: 4_1G3


title: Sample62_Flight.M1.Vitamin_D


title: Sample63_Flight.M1.Vitamin_D


title: UNCseq0980-F10_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq0980-F08_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq0980-F09_ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: Sample61_Flight.M1.Vitamin_D


title: UNCseq0980-F07_ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: 4_1F3


title: Sample66_Flight.M1.2_human_serum


title: Sample60_Flight.F1.Media

value: Media


title: UNCseq1479-G06 ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing

value: Endometrium


title: 4_1E2


title: Sample59_Flight.F1.Media


title: UNCseq1479-G03 ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing

value: Exon 3 CTNNB1 mutant


title: UNCseq1479-G04 ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: 4_1D2


title: 4_1A4


title: UNCseq1479-G02 ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: Sample58_Flight.M1.Media


title: UNCseq1479-G01 ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: Sample57_Flight.M2.2_human_serum


title: 4_1C2


title: UNCseq0482-G12 ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: UNCseq0482-G10 ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: Sample56_Flight.M2.2_human_serum


title: UNCseq0482-G09 ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: 4_1G1

description:
patch-seq, pcd155, replicate 2
SMART-seq3


title: UNCseq0482-G07 ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing


title: 4_1F1


title: No template control

description: FFPE spatial transcriptomic sequencing

value: control


title: UNCseq1479-G05 ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: 4_1E1


title: ICANS5, scRNA-seq

data_processing:
To process the sequencing data, a customized reference was constructed by incorporating the previously characterized CAR gene sequences for both Yescarta and Tecartus, which originated from msgv-fmc63-28z, into the GRCh38 reference genome. This custom reference was prepared using Cellranger mkref (version 7.2.0) adhered to the manufacturer’s instructions. Raw bcl files were then de-multiplexed using the cellranger mkfastq pipeline. Subsequent read alignments and transcript counting were done individually for each sample using the cellranger count pipeline using the custom reference.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: TCR.csv: TCR_filtered_contig_annotations files

source_name: CSF

extract_protocol:
All lumbar punctures were conducted under strict sterile conditions and performed for clinical reasons. CSF samples were meticulously collected in sterile tubes utilizing the Sprotte spinal needle, with processing within a 2-hour window post lumbar puncture to uphold sample integrity. Upon collection, CSF was carefully transferred into round-bottom polypropylene tubes and subsequently centrifuged at 300x g for 10 minutes. The resulting cell-free supernatants were delicately withdrawn using a pipette, then preserved at -80°C for subsequent proteomic analysis. The CSF-cell pellet was resuspended in autologous CSF and gently diluted into 500μL of RPMI-1640 supplemented with 40% FBS. For cryopreservation, the CSF-cell suspension was slowly diluted dropwise with 500μL of pre-chilled freezing medium comprising RPMI-1640 supplemented with 40% FBS and 20% DMSO. Subsequently, the CSF sample was expeditiously placed within a freezing container (Mister Frosty, Thermo Fisher) and stored overnight in a -80°C freezer prior to transfer to liquid nitrogen (LN) storage. For the thawing of cryopreserved CSF cells, the samples were carefully retrieved from the LN and thawed at 37°C for 1–2 minutes, allowing for the presence of a tiny ice crystal within the cryotube. The cells were then diluted 1:10 in PBS supplemented with 10% FBS and subjected to centrifugation at 300g for 10 minutes at 4°C. After discarding the supernatant, the cells were resuspended in 50μL of PBS, with 10μL reserved for cell counting purposes. The remaining cells were then processed for 5'-single cell RNA sequencing.
The scRNA-seq libraries were processed using Chromium single-cell 5′ library and gel bead kit v.2 (10x Genomics).

treatment_protocol: All participants received treatment utilizing commercially available CAR-T cell products.

value: CSF

value: CSF cells

value: ICANS

value: anti-CD19 CAR T-cell therapy


title: Sample55_Flight.F1.2_human_serum


title: ICANS3, scRNA-seq


title: ICANS4, scRNA-seq


title: Sample54_Flight.F1.2_human_serum


title: 2_2H3

description:
patch-seq, pcd155, replicate 1
SMART-seq3

value: dlPFC


title: Sample53_Flight.F1.2_human_serum


title: Sample52_Flight.M1.2_human_serum


title: ICANS2, scRNA-seq


title: ICANS1-3, scRNA-seq

value: post-ICANS remission


title: 2_2B10

value: cortical cells


title: ICANS1-2, scRNA-seq


title: 4_1B3


title: Sample51_Flight.M1.2_human_serum

value: Kidney

value: Primary cells


title: UNCseq0482-G11 ROI_Nuclear

description: FFPE spatial transcriptomic sequencing


title: ICANS1-1, scRNA-seq

value: pre-CART infusion

value: Non


title: Sample50_Flight.M1.2_human_serum

value: Male

value: Flight


title: 2_2A10

value: wild type

value: no treatment


title: IIH1, IIH2, IIH3, scRNA-seq

value: Controls


title: IIH4, scRNA-seq


title: 1_4H9


title: UNCseq0482-G08 ROI_Non nuclear

description: FFPE spatial transcriptomic sequencing

value: Endometrium

value: Exon 3 CTNNB1 mutant


title: Sample49_Flight.F1.Vitamin_D

value: Female


title: 1_4F9


title: Sample48_Flight.F1.Vitamin_D


title: 1_4E9


title: 1_4C10


title: 1_4B10


title: Sample45_Flight.M2.Media

value: Media


title: 1_4A10


title: Sample44_Flight.M2.Media


title: 1_3H4


title: Sample43_Flight.F1.Media


title: Liver MP F4/80 - PH+SE 7d 3

type: RNA

city: Moscow

first: Polina

last: Vishnyakova

address: Oparina 4

country: Russia

institute: National Medical Research Center for Obstetrics, Gynecology and Perinatology

description: Liver MP F4/80 - PH+SE 7d

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip™ Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affimetrix GeneChip Scanner 3000 7g

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) Software version 4.0.2 using Affymetrix default analysis settings and RMA algorithm

label: Biotin

organism: Mus musculus

source_name: Liver MP F4/80 - PH+SE 7d

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: After sorting RNA was extracted from isolated F4/80+ macrophages with MagZOL reagent according to manufacturer’s recommendations.

treatment_protocol: The mouse liver  was dissected, minced and incubated in 0.1% solution of type I and IV collagenases (PanEco, Russia) at 37° C and horizontal shaking for 30 minutes. The suspension was passed through a 100 µm nylon strainer (SPL Life Sciences, Korea) and washed twice from the enzymes (300 g at 20 °С for 10 minutes). The cells were resuspended in 30 mL of phosphate-buffered saline and centrifuged at 50 g for 3 minutes. As a result, parenchymal cells of the liver (hepatocytes) were sedimented and the non-parenchymal cell types (including liver macrophages, the Kupffer cells) remained in the supernatant.  To enrich the stromal cell fraction with macrophages, the supernatant was mixed with Lympholyte®-M density separation medium (Cedarlane, Canada) and centrifuged at 400g and 20 °C for 30 minutes. The obtained fraction predominantly consisted of Kupffer cells. Cell number and viability were assessed in a TC20 analyzer (Bio-Rad). The suspension underwent immunomagnetic sorting on a manual MidiMACS™ Separator using LS Columns (Miltenyi Biotec, Germany) with Anti-F4/80 MicroBeadsUltraPure magnetic microparticles (Miltenyi Biotec) in accordance with the manufacturer’s recommendations.

value: macrophages F4/80+


title: Sample46_Flight.M2.Media


title: Sample42_Flight.F1.Media


title: Liver MP F4/80 - PH 3d 3

description: Liver MP F4/80 - PH 3d

source_name: Liver MP F4/80 - PH 3d


title: Liver MP F4/80 - PH 7d 3

description: Liver MP F4/80 - PH 7d

source_name: Liver MP F4/80 - PH 7d


title: Liver MP F4/80 - PH+SE 3d 2

description: Liver MP F4/80 - PH+SE 3d

source_name: Liver MP F4/80 - PH+SE 3d


title: Liver MP F4/80 - PH 7d 2

description: Liver MP F4/80 - PH 7d


title: Liver MP F4/80 - PH 7d 1

description: Liver MP F4/80 - PH 7d


title: Liver MP F4/80 - PH+SE 3d 3

description: Liver MP F4/80 - PH+SE 3d


title: Liver MP F4/80 - PH+SE 24h 3

description: Liver MP F4/80 - PH+SE 24h

source_name: Liver MP F4/80 - PH+SE 24h


title: Liver MP F4/80 - PH+SE 7d 2

description: Liver MP F4/80 - PH+SE 7d


title: Liver MP F4/80 - PH+SE 3d 1

description: Liver MP F4/80 - PH+SE 3d


title: 1_3G4

value: dlPFC


title: Sample47_Flight.M1.Vitamin_D


title: Liver MP F4/80 - PH+SE 24h 2

description: Liver MP F4/80 - PH+SE 24h


title: Liver MP F4/80 - PH 24h 1

description: Liver MP F4/80 - PH 24h

source_name: Liver MP F4/80 - PH 24h


title: Liver MP F4/80 - PH 24h 2

description: Liver MP F4/80 - PH 24h


title: Liver MP F4/80 - PH 3d 1

description: Liver MP F4/80 - PH 3d


title: 1_3E4


title: Liver MP F4/80 - PH 24h 3

description: Liver MP F4/80 - PH 24h


title: Sample40_Flight.M1.Media


title: Liver MP F4/80 - PH 3d 2

description: Liver MP F4/80 - PH 3d


title: Sample41_Flight.M1.Media


title: 1_3F4


title: Liver MP F4/80 - PH+SE 7d 1

description: Liver MP F4/80 - PH+SE 7d


title: 1_3D4


title: Sample39_Ground.F2.2_human_serum

value: Ground


title: 1_3C4

value: cortical cells


title: Sample38_Ground.F2.2_human_serum

value: Kidney


title: 1_3B4


title: morc-HiChIP-6B-1

city: Wuhan

first: Qingxiao

last: Jia

state: Hubei

address: No.1,Shizishan Street

institute: HZAU

description: Library name: morc-HiChIP-6B-1

data_processing:
Hi-ChIP raw data were processed with the HiC-pro pipeline v.2.8.0
The valid read pairs were used for loop-calling. H3K27me3-HiChIP loops were called based on valid pairs with > 8 kb genomic span using ChIA-PET v3.
The contact matrices were built and normalized according to the library size before ICE correction by HiCExplorer. The matrices were compared and visualized using the hicCompareMatrices and hicPlotMatrix functions in HiCExplorer62, respectively. The TADs were determined by hicFindTADs in HiCExplorer63, 64 with parameters "--minDepth 50000 --maxDepth 100000 --step 10000 --delta 0.1". HiCExplorer application for TAD identification has been reported in several studies, including those related to plant 3D genomes
TAD boundaries were identified using TAD-separation score method
genome assembly: MSU version 7.0 rice genome
processed data files format and content: mcool
Library strategy: HiChIP

organism: Oryza sativa Japonica Group

source_name: seedling

extract_protocol:
Briefly, nuclei were isolated from rice leaves (14-day-old), digested with Dpn II (New England Biolabs, R0543T), immuno-precipitated with the anti-H3K27me3 and anti-OsMORC6b antibody. The precipitated chromatin DNA fragments were recovered for constructing Hi-ChIP-seq libraries.
The beads were directly subjected to Vazyme TruePrep DNA Library Prep Kit (TD501) for library construction.

value: seedling

value: MORC1/6a/b knockout

tag: chip antibody


title: Liver MP F4/80 - K SE 2

description: Liver MP F4/80 - K SE

source_name: Liver MP F4/80 - K SE


title: ZH11-HiChIP-6B-2

description: Library name: ZH11-HiChIP-6B-2

value: WT


title: ZH11-HiChIP-6B-1

description: Library name: ZH11-HiChIP-6B-1


title: Liver MP F4/80 - K SE 3

description: Liver MP F4/80 - K SE


title: Sample35_Ground.F1.2_human_serum

value: Primary cells


title: Liver MP F4/80 - K intact 3

description: Liver MP F4/80 - K intact

source_name: Liver MP F4/80 - K intact


title: morc-A1-2

description: Library name: morc-A1-2

data_processing:
the adaptors were trimmed from the raw reads with Trimmomatic version 0.36 (Bolger et al., 2014) with the arguments: ILLUMINACLIP:FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15.
The ChIP clean reads were mapped to the MSU7.0 genome with Bowtie2 (version 2.4.2) using default parameters.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
The DESeq2 method imple_x0002_mented in DiffBind was used to test the differential peak
genome assembly: MSU version 7.0 rice genome
processed data files format and content: bigWig
Library strategy: Cut&Tag

extract_protocol:
Seedling were cut into small pieces and the nuclei were separated. Nuclei were obtained per sample for subsequent experiments, washed with wash buffer, and immobilized to concanavalin A-coated beads (Vazyme, TD903) with incubation at room temperature for 10 min. The bead-bound nuclei were incubated in 200 μL of primary antibody buffer with 1:50 anti-EMF2b or anti-ALKBH1 antibody dilution at 4 °C by rotating overnight. The next day, the primary antibody buffer was removed and cells were washed with 800 μL of dig-wash buffer. After washing, antibody-incubated nuclei were resuspended in 200 µL of dig-wash buffer with a 1:100 dilution of secondary antibody (Vazyme, TD903) and incubated at room temperature with gentle rotation for 1 h. To eliminate binding antibodies, nuclei were washed three times with 800 µL dig-wash buffer. After a brief wash with dig-wash buffer, nuclei were resuspended in 200 µL of dig-300 buffer and incubated at room temperature for 1 h with gentle rotation. pA-Tn5-bound nuclei were washed with 800 µL of dig-300 buffer three times, then tagmentated at 37 °C for 1 h. 15 mM EDTA, 500 µg/ml proteinase K, and 0.1% SDS were added after tagmentation to terminate tagmentation and degrade protein. Genomic DNA was extracted and purified with VAHTS DNA Clean Beads (Vazyme, N411-01).
Purified genomic DNA was amplified using the universal i5 primer and barcoded i7 primer (Vazyme, TD202) using Vazyme Master Mix (Vazyme, TD903). The library PCR products were cleaned with Agencourt AMPure XP beads (Beckman Coulter, A63881).


title: Liver MP F4/80 - K intact 2

description: Liver MP F4/80 - K intact


title: Liver MP F4/80 - K SE 1

description: Liver MP F4/80 - K SE


title: Liver MP F4/80 - PH+SE 24h 1

description: Liver MP F4/80 - PH+SE 24h


title: 2_2G8

description:
patch-seq, pcd112, replicate 1
SMART-seq3

source_name: dlPFC


title: ZH11-A1-2

description: Library name: ZH11-A1-2


title: ZH11-A1-1

description: Library name: ZH11-A1-1


title: morc-2B-2

description: Library name: morc-2B-2


title: Sample34_Ground.M1.2_human_serum

value: Male


title: Sample33_Ground.M1.2_human_serum


title: Liver MP F4/80 - K intact 1

description: Liver MP F4/80 - K intact


title: morc-2B-1

description: Library name: morc-2B-1


title: ZH11-2B-2

description: Library name: ZH11-2B-2


title: 1_4E5

value: wild type


title: morc-HiChIP-6B-2

description: Library name: morc-HiChIP-6B-2


title: Sample37_Ground.F1.2_human_serum


title: 1_3A5

value: no treatment


title: morc-A1-1

description: Library name: morc-A1-1


title: ZH11-2B-1

description: Library name: ZH11-2B-1


title: Sample32_Ground.M1.2_human_serum


title: 1_3A4


title: Sample31_Ground.F2.Vitamin_D


title: morc-ATAC-2

description: Library name: morc-ATAC-2

data_processing:
the adaptors were trimmed from the raw reads with Trimmomatic version 0.36 (Bolger et al., 2014) with the arguments: ILLUMINACLIP:FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15.
The clean reads were mapped to the MSU7.0 genome with Bowtie2 (version 2.4.2) using default parameters.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
The DESeq2 method imple_x0002_mented in DiffBind was used to test the differential peak
genome assembly: MSU version 7.0 rice genome
processed data files format and content: bigWig

growth_protocol: Seedlings were grown in one-half-strength Murashige and Skoog medium under 16-h light/8-h dark cycles at 30 °C

extract_protocol:
Seedling were cut into small pieces and the nuclei were separated. 1× 105 nuclei were incubated with 50 µL transposition mix containing 2 µL Tn5 transposase (Vazyme, TD711) at 37 °C for 30 min. The mixture was further incubated at 55 °C for 30 min, and the fragmentation products were then subjected to DNA extraction using ATAC DNA Extract Beads.  fragments were sorted using ATAC DNA Clean Beads (Vazyme, TD711), and precipitated by cold ethanol.
Purified genomic DNA was amplified using the universal i5 primer and barcoded i7 primer (Vazyme, TD202) using Vazyme Master Mix (Vazyme, TD711). The library PCR products were cleaned with Agencourt AMPure XP beads (Beckman Coulter, A63881).


title: 2_2F8


title: Sample30_Ground.F2.Vitamin_D


title: ZH11-ATAC-1

description: Library name: ZH11-ATAC-1


title: 1_4C5


title: morc-ATAC-1

description: Library name: morc-ATAC-1


title: NCIH2170_ONT_long_read_ECdna_rapid

description: Library name: NCIH2170_ONT_long_read_ECdna_rapid

data_processing:
The software Guppy was used for base calling. The software Flye was used for de novo assembly.
Assembly: GRCh38
Supplementary files format and content: graphical fragment assembly (gfa) file representing the assembled dominant ecDNA structure in NCIH2170 cell line using the ONT long-read data.

source_name: Cell line

extract_protocol:
The DNA was extracted according to the ONT standard protocol
The two libraries were prepared using the ligation sequencing kit and rapid sequencing kit

value: Cell line

value: Cancer cell


title: 1_4D5


title: 1_1G6


title: 1_1H6


title: morc-HiCHIP-2

data_processing:
none provided
Assembly: MSU version 7.0 rice genome

extract_protocol: none provided

tag: type

value: H3K27me3 HiChIP


title: Sample29_Ground.F1.Vitamin_D

value: Female


title: NCIH2170_ONT_long_read_ECdna_ligation

description: Library name: NCIH2170_ONT_long_read_ECdna_ligation


title: Sample28_Ground.F1.Vitamin_D


title: ZH11-HIChIP-2


title: 1_1F6

data_processing:
snATAC/RNA-seq: The 10x Multiome ATAC(snATAC-seq) + Gene Expression(snRNA-seq) dataset was processed using the Cell Ranger ARC pipeline. To analyze the macaque data, we used the Cell Ranger ARC mkref to create a rheMac10 reference. Subsequently, we performed a quality check on the output of the Cell Ranger ARC pipeline, and then used it for downstream analysis.
SMART-seq:The SMART-seq3 RNA-seq reads from human were aligned to reference genome GRCh38 and the reads from rhesus macaque were aligned to reference genome rheMac10. Trim Galore was used for the adaptor trimming. We used STAR (v2.7.2b) (69) in two pass Mode for the alignment and removed PCR duplicates. STAR quantMode was used for gene counts on uniquely aligned reads, and the intergenic regions were excluded.
Assembly: rheMac10; GRCh38
Supplementary files format and content: snATAC-seq: fragments files are generated from Cell Ranger ARC pipeline. ; snRNA-seq: barcodes, features and matrix files are generated from Cell Ranger ARC pipeline. SMART-seq3: "AcuteRhesusPatchseq.csv" and "OrganotypicCHD8Patchseq.csv" are normalized gene expression data files.

tag: developmental stage


title: morc-HiCHIP-1


title: Sample27_Ground.F1.Vitamin_D


title: Female KO MTECs, HDM, biol rep 2

city: Orlando

first: Justine

middle: T.

last: Tigno-Aranjuez

state: FL

address: 6900 Lake Nona Blvd., BSBS Bldg, Rm 370

department: BSBS, Immunity and Pathogenesis Division

institute: University of Central Florida

description: Library name: Sample 16

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an FDR 0.1 and min fold change > 2 were called as differentially expressed genes for each comparison.
For k-means clustering, data was transformed and genes were ranked by standard deviation. Only to the top 2000 are used for clustering (3 clusters were used). Enrichment analysis was performed for each cluster using KEGG pathways. Enrichment p-value are calculated based on one-sided the hypergeometric test, which is then adjusted for multiple testing using the Benjamini-Hochberg procedure and converted to FDR(false discovery rate). FDR tells us how likely to observe the enrichment by chance. Due to increased statistical power, large pathways tend to have smaller FDRs. Fold Enrichment is defined as the percentage of genes in the list belonging to a pathway, divided by the corresponding percentage in the background. As a measure of effect size, Fold Enrichment indicates how drastically genes of a certain pathway is overrepresented. The background genes are filtered genes from the original gene list. The filtered genes are those that are passed a low filter in RNA-seq. A total of 343 gene sets are obtained from KEGG ( Kyoto Encyclopedia of Genes and Genomes ). Dabase version/date is Release 104.0 . For details on this KEGG type of database, please refer to: Kanehisa M, et al. , KEGG: kyoto encyclopedia of genes and genomes , Nucleic Acids Res. 2000 Jan 1;28(1):27-30 ( PubMed ID: 10592173 ). After the analysis is done, pathways are first filtered based on a FDR cutoff (0.05). Then the significant pathways are sorted by. FDR . Only the top 10 pathways are shown.
Assembly: Mus musculus GRCm38 reference genome
Supplementary files format and content: *.csv file contains raw counts for each sample

source_name: Murine tracheal airway epithelium cultures

growth_protocol: Murine tracheal airway epithelial cell cultures were generated as in Lauer et al. J Biol Chem. 2008 Sep 19;283(38):26283-96.

extract_protocol:
Rneasy mini kit as directed by manufacturer (Qiagen)
A. mRNA enrichment, mRNA fragmentation and random priming; B. First and second strand cDNA synthesis; C. End repair, 5' phosphorylation and dA-tailing; D. Adaptor ligation, PCR enrichment and sequencing

treatment_protocol: untreated or treated with 20 ug/ml house dust mite extract overnight

value: Primary

value: airway epithelial cells

value: LMAN1 KO

value: HDM


title: 1_1E6

extract_protocol:
Macaque brain specimens were collected from postconceptional day (PCD) 87 to PCD155. All experiments using non-human primates were carried out in accordance with a protocol approved by the University of Wisconsin’s Institutional Animal Care and Use Committee and NIH guidelines.
snMultiomes:The libraries were constructed in accordance with the guidelines provided in the "Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide" (10x Genomics, CG000338); SMART-seq3: follow the protocol according to publication "Single-cell RNA counting at allele and isoform resolution using Smart-seq3" (PMID: 32518404).

value: dlPFC

value: cortical cells


title: ZH11-HIChIP-1

value: seedling


title: 1_1D6


title: Female KO MTECs, HDM, biol rep 1

description: Library name: Sample 15

value: Murine tracheal airway epithelium cultures


title: Sample26_Ground.M1.Vitamin_D

value: Kidney

value: Ground