title: R03_RNASeq1_RM38.R1

status: Public on Jul 31 2025

type: SRA

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

country: USA

institute: University of Illinois

library_source: transcriptomic

data_processing:
Illumina pipeline for demultiplexing and adaptor removal
Sequenced reads were aligned to 88,647 Glyma1 cDNA soybean gene models determined by the Soybean Genome Project (Schmutz et al. 2010) using Bowtie (Langmead et al. 2009). Bowtie parameters allowed up to three mismatches and up to 25 alignments per read.
Reads per kilobase of gene model per million mapped reads (RPKM) were calculated according to Mortazavi et al. (2008).
Assembly: Glycine max cv. Williams 82 Wm82.a2 at https://phytozome-next.jgi.doe.gov/
Supplementary files format and content: Excel file of the RPKM (reads per million per kilobase) of RNA-seq hits to each soybean Glyma transcript model for each library.

molecule: total RNA

organism: Glycine max

source_name: immature seed coat

growth_protocol: Plants were grown under optimal greenhouse conditions. The developing seed were harvested at the stated mg fresh weight ranges. Whole seeds were dissected by hand into cotyledons and seed coats. Other tissues as seedling cotyledons, vegetative buds, or shoots tips, were extracted from germinating seedlings or 1 month-old plants.

extract_protocol:
Total RNA was extracted from tissues using phenol:chloroform, lithium chloride precipitation, and ethanol precipitation.
Libraries were constructed with Illumina Tru Seq or Stranded Tru Seq kits by the University of Illinois DNA Services Laboratory and sequenced using Illumina machines.

treatment_protocol: Standard greenhouse conditions unless otherwise noted in each sample.

tag: tissue

value: immature seed coat

tag: stage or_seed_fresh_wt

tag: cultivar

value: Clark i isoline with brown seed coats

tag: lab names

tag: phenotype descriptors

value: stable brown seed coat

tag: genotype

value: i r T  W1

tag: other

tag: grin l_number_(or_other_designation)

tag: grin pi_number


title: P031 tumor, de novo

city: Milwaukee

first: Abdullah

middle: A.

last: Memon

state: Wisconsin

address: 9200 W Wisconsin Ave

department: Department of Otolaryngology and Communication Sciences

institute: Medical College of Wisconsin

description:
Library name: P031_tumor
no-RT_P031

data_processing:
Raw data were first processed using FastQC to assess parameters such as the total number of reads, base quality scores, and GC content. Trimmomatic was then used to ensure high quality reads by filtering out low-quality bases and adapter sequences. BAM files were then generated by aligning trimmed reads to the reference human genome GRCh38 using STAR. These BAM files were subsequently processed with featureCounts to quantify gene-level expression.
Assembly: GRCh38
Supplementary files format and content: Gene expression matrix (raw counts): .txt

molecule: polyA RNA

organism: Homo sapiens

source_name: Tumor

extract_protocol:
Total RNA was extracted from tumor tissues using the Qiagen RNeasy Mini Kit according to the manufacturer’s protocol. RNA concentration and purity were assessed using NanoDrop, and integrity was evaluated using the Agilent Fragment Analyzer 5200 to obtain RIN scores.
Library preparation and sequencing were performed by the MCW Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine. Poly(A)-enriched mRNA libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep Kit, and sequencing was conducted on the Illumina NovaSeq 6000 platform with paired-end 100 bp reads.

value: Tumor

tag: treatment

value: De novo


title: P033 tumor, radiation-recurrent

description:
Library name: P033_tumor
RT_P033

value: Radiation-recurrent


title: P034 tumor, de novo

description:
Library name: P034_tumor
no-RT_P034


title: P028 tumor, de novo

description:
Library name: P028_tumor
no-RT_P028


title: P030 tumor, de novo

description:
Library name: P030_tumor
no-RT_P030


title: P029 tumor, radiation-recurrent

description:
Library name: P029_tumor
RT_P029


title: P027 tumor, de novo

description:
Library name: P027_tumor
no-RT_P027


title: P024 tumor, de novo

description:
Library name: P024_tumor
no-RT_P024


title: P026 tumor, radiation-recurrent

description:
Library name: P026_tumor
RT_P026


title: P019 tumor, de novo

description:
Library name: P019_tumor
no-RT_P019


title: P021 tumor, de novo

description:
Library name: P021_tumor
no-RT_P021


title: P022 tumor, de novo

description:
Library name: P022_tumor
no-RT_P022


title: P018 tumor, radiation-recurrent

description:
Library name: P018_tumor
RT_P018


title: P017 tumor, de novo

description:
Library name: P017_tumor
no-RT_P017


title: P015 tumor, radiation-recurrent

description:
Library name: P015_tumor
RT_P015


title: P013 tumor, de novo

description:
Library name: P013_tumor
no-RT_P013


title: P016 tumor, de novo

description:
Library name: P016_tumor
no-RT_P016


title: P012 tumor, de novo

description:
Library name: P012_tumor
no-RT_P012


title: PBMC-MCAR-iNKT

city: Los Angeles

first: Yichen

last: Zhu

state: California

address: 610 Charles E Young Drive S

institute: University of California, Los Angeles

description:
Library name: Sample_03
10x Genomics

library_source: transcriptomic single cell

data_processing:
For cell clustering and annotation, the merged digital expression matrix generated by Cellranger was analyzed using an R package Seurat (v.4.0.0) following the guidelines. Briefly, after filtering the low-quality cells, the expression matrix was normalized using NormalizeData function, followed by selecting variable features across datasets using FindVariableFeatures and SelectIntegrationFeatures functions. To correct the batch effect, FindIntegrrationAnchors and IntegrateData functions were used based on the selected feature genes. The corrected dataset was subjected to standard Seurat workflow for dimension reduction and clustering. In this study, clusters of therapeutic cells were manually merged and annotated based on gene signatures reported from Human Protein Atlas (proteinatlas.org) and previous studies. AddModuleScore was used to calculate module scores of each list of gene signatures, and FeaturePlot function was used to visualize the expression of each signature in the UMAP plots.
Assembly: Human (GRCh38) 2024-A
Supplementary files format and content: matrix.mtx.gz: Matrix Market Format, with rows representing genes and columns representing cells.
Supplementary files format and content: barcode.tsv.gz: Tab-separated values, where each row represents a unique identifier for a cell.
Supplementary files format and content: features.tsv.gz: Tab-separated values, where each row represents a gene.

source_name: In vitro

extract_protocol:
Therapeutic cell products (Pre-infusion) were subjected to FACS sorting for isolating live cells including MCAR-T, Allo15MCAR-NKT  and PBMC-MCAR-iNKTcells.
Cells were quantified using a Cell Countess II automated cell counter (Invitrogen/Thermo Fisher Scientific). A total of 10,000 cells from each experimental group were loaded on the Chromium platform (10X Genomics), and libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v3.1 and the Chromium Next GEM Chip G Single Cell Kit (10X Genomics), according to the manufacturer’s instructions. Library quality was assessed using the D1000 ScreenTape on a 4200 TapeStation System (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq using the NovaSeq S4 Reagent Kit (100 cycles; Illumina).

value: In vitro

tag: time

value: Pre-infusion

tag: cell type

value: T cells


title: P014 tumor, de novo

description:
Library name: P014_tumor
no-RT_P014


title: P036 tumor, de novo

description:
Library name: P036_tumor
no-RT_P036


title: P011 tumor, radiation-recurrent

description:
Library name: P011_tumor
RT_P011


title: P010 tumor, de novo

description:
Library name: P010_tumor
no-RT_P010


title: P009 tumor, de novo

description:
Library name: P009_tumor
no-RT_P009


title: P032 tumor, de novo

description:
Library name: P032_tumor
no-RT_P032


title: P008 tumor, de novo

description:
Library name: P008_tumor
no-RT_P008


title: P035 tumor, de novo

description:
Library name: P035_tumor
no-RT_P035


title: P007 tumor, radiation-recurrent

description:
Library name: P007_tumor
RT_P007


title: P006 tumor, de novo

description:
Library name: P006_tumor
no-RT_P006


title: BAL, SSc 09

city: Chicago

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior St

department: Pulmonary and Critical Care

institute: Northwestern University

description: Library name: SSc_09

data_processing:
Data were processed using Cell Ranger 3.1.0 (10x Genomics), reads were mapped to GRCh38.84 reference genome (10x Genomics Cell Ranger Human 1.2.0 GRCh38 reference). Data were processed using Scanpy 1.7.2, and multisample integration was performed with scvi-tools 0.14.0. The scVI models was constructed on 1000 HVGs with the hyperparameters n_layers = 2, dropout_rate = 0.2, and n_latent = 10, and were trained using the settings max_epochs = 400, check_val_every_n_epoch = 2, and early_stopping = True. Default hyperparameters and settings were used otherwise.
Assembly: GRCh38.84
Supplementary files format and content: gene expression count matrices

source_name: BAL

extract_protocol:
Bronchoscopic BAL was performed in patients and healthy volunteers in the bronchoscopy suite at Northwestern Memorial Hospital or Yale New Haven Hospital. Patients or healthy volunteers were given sedation and topical anesthesia at the discretion of the physician performing the bronchoscopy. Lavage was directed to lobes with higher GGO and fibrosis scores; 90–120 ml of saline was instilled into the segment of interest and aspirated back, with the first 5 ml of return discarded. BALF collected at Northwestern was processed fresh within 2 hours after collection. BALF samples collected at Yale were filtered through a 70-μm cell strainer, and mixed with HypoThermosol solution (Biolife Solutions, cat #101104) at 1:1 ratio and shipped overnight for further processing on wet ice to Northwestern University. BALF samples were processed using either “no FACS” or “FACS” protocol. BALF sample processing for scRNA-seq using “no FACS” protocol: BALF samples were filtered through a 70-μm cell strainer, pelleted by centrifugation at 400 rcf for 10 min at 4°C, followed by hypotonic erythrocyte lysis using 1 ml of PharmLyse solution (BD) for 2 min, followed by another wash with 10 ml of 0.5% BSA in PBS and centrifugation. Cell pellet was resuspended in 0.5% BSA in PBS at the final concentration ~1000 cells/ul. Cell concentration and viability were determined using K2 Cellometer (Nexcelom) with AO/PI reagent and cells were loaded on 10x Genomics Chip A with Chromium Single Cell 3′ V2 gel beads and reagents (10x Genomics) aiming to capture 5,000–7,000 cells per library. Libraries were prepared according to the manufacturer’s protocol (10x Genomics, CG000052_RevB). BALF sample processing for scRNA-seq using “FACS” protocol: BAL fluid samples were filtered through a 70-μm cell strainer, pelleted by centrifugation at 400 relative centrifugal force (rcf) for 10 min at 4 °C, followed by hypotonic lysis of red blood cells with 2 ml of PharmLyse (BD Biosciences) reagent for 2 min. Lysis was stopped by adding 13 ml of MACS buffer (Miltenyi Biotech). Cells were pelleted again and resuspended in 100 μl of a 1:10 dilution of Human TruStain FcX (BioLegend) in MACS buffer and a 10-μl aliquot was taken for counting using a K2 Cellometer (Nexcelom) with Acridine Orange (AO)/Propidium Iodide (PI) reagent. The cell suspension volume was adjusted so the concentration of cells was always <5 × 107 cells ml−1 and the fluorophore-conjugated antibody cocktail was added in a 1:1 ratio. A full list of antibodies can be found in the methods section of the respective publication. After incubation at 4 °C for 30 min, cells were washed with 5 ml of MACS buffer, pelleted by centrifugation and resuspended in 500 μl of MACS buffer with 2 μl of SYTOX Green viability dye (Thermo Fisher Scientific). Cells were sorted on a FACS Aria III SORP instrument using a 100-μm nozzle. Cells were sorted into 300 μl of 2% bovine serum albumin (BSA) in Dulbecco’s phosphate-buffered saline (DPBS) and immediately after sorting pelleted by centrifugation at 400 rcf for 5 min at 4 °C, resuspended in 0.5 BSA in DPBS to ~1,000 cells μl−1 concentration. Concentration was confirmed using a K2 Cellometer (Nexcelom) with AO/PI reagent using the ‘Immune cells low RBC’ program with default settings and cells were immediately used for scRNA-seq.
Libraries were prepared with 10x Genomics 3' V3 gene expression (GEX) reagents according to the manufacturer protocol (CG000331_RevA).

value: BAL

tag: age

tag: Sex

value: female

tag: protocol

value: FACS

tag: condition

value: SSc


title: P005 tumor, radiation-recurrent

description:
Library name: P005_tumor
RT_P005


title: P023 tumor, de novo

description:
Library name: P023_tumor
no-RT_P023


title: P004 tumor, de novo

description:
Library name: P004_tumor
no-RT_P004


title: P002 tumor, de novo

description:
Library name: P002_tumor
no-RT_P002


title: BAL, SSc 08

description: Library name: SSc_08


title: BAL, SSc 06

description: Library name: SSc_06

value: male


title: BAL, SSc 04

description: Library name: SSc_04


title: BAL, SSc 07

description: Library name: SSc_07


title: BAL, SSc 02-2

description: Library name: SSc_02-2


title: BAL, SSc 03

description: Library name: SSc_03


title: BAL, SSc 02-1

description: Library name: SSc_02-1

value: no FACS


title: BAL, SSc 05

description: Library name: SSc_05


title: BAL, Healthy Volunteer 12

description: Library name: HV_12

value: control


title: BAL, SSc 01

description: Library name: SSc_01


title: BAL, Healthy Volunteer 10

description: Library name: HV_10


title: BAL, Healthy Volunteer 9

description: Library name: HV_09


title: BAL, Healthy Volunteer 13

description: Library name: HV_13


title: BAL, Healthy Volunteer 6

description: Library name: HV_06

extract_protocol:
Bronchoscopic BAL was performed inhealthy volunteers in the bronchoscopy suite Duke University Hospital. Healthy volunteers were given sedation and topical anesthesia at the discretion of the physician performing the bronchoscopy. Lavage was directed to lobes with higher GGO and fibrosis scores; 90–120 ml of saline was instilled into the segment of interest and aspirated back, with the first 5 ml of return discarded. BALF samples were filtered through a 70-μm cell strainer, and mixed with HypoThermosol solution (Biolife Solutions, cat #101104) at 1:1 ratio and shipped overnight for further processing on wet ice to Northwestern University. BAL fluid samples were filtered through a 70-μm cell strainer, pelleted by centrifugation at 400 relative centrifugal force (rcf) for 10 min at 4 °C, followed by hypotonic lysis of red blood cells with 2 ml of PharmLyse (BD Biosciences) reagent for 2 min. Lysis was stopped by adding 13 ml of MACS buffer (Miltenyi Biotech). Cells were pelleted again and resuspended in 100 μl of a 1:10 dilution of Human TruStain FcX (BioLegend) in MACS buffer and a 10-μl aliquot was taken for counting using a K2 Cellometer (Nexcelom) with Acridine Orange (AO)/Propidium Iodide (PI) reagent. The cell suspension volume was adjusted so the concentration of cells was always <5 × 107 cells ml−1 and the fluorophore-conjugated antibody cocktail was added in a 1:1 ratio. The following antibodies were used (antigen, clone, fluorochrome, manufacturer, catalog no., final dilution): CD4, RPA-T4, BUV395, BD, 564724, 1:40; CD19, HIB19, BUV395, BD, 740287, 1:40; CD25, 2A3, BUV737, BD, 564385, 1:20; CD56, NCAM16.2, BUV737, BD, 612766, 1:20; HLA-DR, L243, eFluor450, Thermo Fisher Scientific, 48-9952-42, 1:40; CD45, HI30, BV510, BioLegend, 304036, 1:20; CD15, HI98, BV786, BD, 563838, 1:20; CD3, SK7, PE, Thermo Fisher Scientific, 12-0036-42, 1:20; CD127, HIL-7R, PECF594, BD, 562397, 1:20; CD206, 19.2, PECy7, Thermo Fisher Scientific, 25-2069-42, 1:40; CD8, SK1, APC, BioLegend, 344721, 1:40; CD14, M5E2, APC, BioLegend, 301808, 1:40; and EpCAM, 9C4, APC, BioLegend, 324208, 1:40. After incubation at 4 °C for 30 min, cells were washed with 5 ml of MACS buffer, pelleted by centrifugation and resuspended in 500 μl of MACS buffer with 2 μl of SYTOX Green viability dye (Thermo Fisher Scientific). Cells were sorted on a FACS Aria III SORP instrument using a 100-μm nozzle. Cells were sorted into 300 μl of 2% bovine serum albumin (BSA) in Dulbecco’s phosphate-buffered saline (DPBS) and immediately after sorting pelleted by centrifugation at 400 rcf for 5 min at 4 °C, resuspended in 0.5 BSA in DPBS to ~1,000 cells μl−1 concentration. Concentration was confirmed using a K2 Cellometer (Nexcelom) with AO/PI reagent using the ‘Immune cells low RBC’ program with default settings and cells were immediately used for scRNA-seq.
Libraries were prepared with 10x Genomics 3' V3 gene expression (GEX) reagents according to the manufacturer protocol (CG000331_RevA).

value: FACSorted


title: BAL, Healthy Volunteer 7

description: Library name: HV_07


title: BAL, Healthy Volunteer 8

description: Library name: HV_08


title: P003 tumor, de novo

description:
Library name: P003_tumor
no-RT_P003


title: BAL, Healthy Volunteer 4

description: Library name: HV_04


title: BAL, Healthy Volunteer 5

description: Library name: HV_05


title: BAL, Healthy Volunteer 2

description: Library name: HV_02


title: BAL, Healthy Volunteer 1

description: Library name: HV_01


title: Caco2WT3

city: Charleston

first: Antonis

last: Kourtidis

state: SC

address: 173 Ashley Avenue

department: Regenerative Medicine and Cell Biology

institute: Medical University of South Carolina

description:
Library name: Caco2 WT sample 3
S1

data_processing:
Sequenced reads were first processed using Cutadapt (v1.15) to trim the 3′ adapter sequence (5′-AGATCGGAAGAGCACACGTCT-3′). Reads from three independent replicates for each condition were catenated prior to further analysis. Adapter-trimmed reads were analyzed using the piPipes small RNA pipeline to quantify transposon-mapped reads and normalize sense and antisense counts as counts per million (CPM) uniquely mapped to the hg19 genome(Han et al., 2015b). In parallel, reads were aligned to Repbase and known piRNA clusters using Bowtie2(Langmead and Salzberg, 2012, Langmead et al., 2019) and only successfully aligned reads were retained. These reads were then assessed for size distribution and 5′ nucleotide signature using the TBr2_basicanalyses.pl script (Rosenkranz et al., 2015).
Assembly: hg19
Supplementary files format and content: Normalized counts (counts per million) of sense and anti-sense reads mapping to RefSeq genes. Since the replicates were catenated, one processed file is being submitted for all the samples.

source_name: colon epithelial Caco2 cell line

extract_protocol:
RNA from Caco2 WT and PIWIL2 KO cells was isolated by adding 1ml of Trizol (Invitrogen # 15596018), incubating the sample at RT for 5 minutes then using the PureLink RNA mini kit (Invitrogen #12183018A) for total RNA, using the whole transcriptome protocol of the kit. Final RNA concentrations and purity were determined by using a NanoDrop spectrophotometer.
Short RNA sequencing was performed using the NovaSeq SE50 strategy.

value: colon epithelial Caco2 cell line

tag: cell line

value: epithelial

value: WT


title: Caco2WT1

description:
Library name: Caco2 WT sample 1
S1

tag: tissue


title: PIWIL2KO1

description:
Library name: Caco2 PIWIL2 knckout sample 1
S2

value: PIWIL2 knckout


title: PIWIL2KO3

description:
Library name: Caco2 PIWIL2 knckout sample 3
S2


title: Caco2WT2

description:
Library name: Caco2 WT sample 2
S1


title: PIWIL2KO2

description:
Library name: Caco2 PIWIL2 knckout sample 2
S2


title: TSA treatment iPSC-derived cortical neurons well 3

city: Indianapolis

first: Madeline

last: Peyton

state: IN

address: 410 W 10th St

institute: Indiana University

description:
Library name: TSA_well3
TSA treatment (60 ng/ml, Sigma-Aldrich T1952), iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 3

data_processing:
Raw FASTQ files quality assessed and processed
Reads aligned to human reference genome (GRCh38/hg38)
Gene-level read counts quantified using featureCounts
Individual sample count files merged into combined count matrix
Technical replicates assessed for correlation and final count matrix (counts_matrix_GEO.csv) generated
Assembly: GRCh38/hg38
Supplementary files format and content: Raw count matrix (counts_matrix_GEO.csv) - gene-level read counts for all samples with Ensembl gene IDs as rows and sample names as columns

source_name: iPSC-derived cortical neurons

growth_protocol: Human cortical neurons derived from iPSCs (Fujifilm R1061) cultured in BrainPhys media in 24-well plates with poly-D-ornithine and Matrigel coating, half medium exchanged daily

extract_protocol:
Total RNA extracted using Total RNA Purification Kit (Stem Cell Tech, Catalog #79040) according to manufacturer's protocol
Total RNA libraries were prepared using Clontech SMARTer RNA Pico Kit v3 (catalog #634487) following manufacturer's protocols. rRNA depletion was included in the kit.

treatment_protocol: Four treatment conditions: (1) Control - untreated neurons maintained in standard culture conditions, (2) TSA - 60 ng/ml TSA (Sigma-Aldrich T1952) for 24h at DIV 4, (3) Aβ oligomers - 5 μM Aβ oligomers (StressMarq SPR-488) for 24h at DIV 4, (4) Combined - TSA pre-treatment (60 ng/ml for 24h) followed by Aβ oligomers (5 μM for 24h) at DIV 4

value: iPSC-derived cortical neurons

value: TSA 60 ng/ml


title: TSA+Aβ combination treatment iPSC-derived cortical neurons well 2

description:
Library name: TSAplusAlphaBeta_well2
Combined treatment: TSA pre-treatment (60 ng/ml for 24h) followed by Aβ oligomers (5 μM), iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 2

value: TSA 60 ng/ml + Aβ oligomers 5 μM


title: TSA treatment iPSC-derived cortical neurons well 4

description:
Library name: TSA_well4
TSA treatment (60 ng/ml, Sigma-Aldrich T1952), iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 4


title: TSA+Aβ combination treatment iPSC-derived cortical neurons well 4

description:
Library name: TSAplusAlphaBeta_well4
Combined treatment: TSA pre-treatment (60 ng/ml for 24h) followed by Aβ oligomers (5 μM), iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 4


title: TSA+Aβ combination treatment iPSC-derived cortical neurons well 1 extra

description:
Library name: TSAplusAlphaBeta_well1_extra
Combined treatment: TSA pre-treatment (60 ng/ml for 24h) followed by Aβ oligomers (5 μM), iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 1, extra sample


title: TSA treatment iPSC-derived cortical neurons well 1 extra

description:
Library name: TSA_well1_extra
TSA treatment (60 ng/ml, Sigma-Aldrich T1952), iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 1, extra sample


title: TSA+Aβ combination treatment iPSC-derived cortical neurons well 1

description:
Library name: TSAplusAlphaBeta_well1
Combined treatment: TSA pre-treatment (60 ng/ml for 24h) followed by Aβ oligomers (5 μM), iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 1


title: BAL, Healthy Volunteer 3

description: Library name: HV_03


title: TSA treatment iPSC-derived cortical neurons well 1

description:
Library name: TSA_well1
TSA treatment (60 ng/ml, Sigma-Aldrich T1952), iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 1


title: Aβ oligomer treatment iPSC-derived cortical neurons well 3

description:
Library name: AlphaBeta_well3
Aβ oligomer treatment (5 μM, StressMarq SPR-488), iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 3

value: Aβ oligomers 5 μM


title: Aβ oligomer treatment iPSC-derived cortical neurons well 4

description:
Library name: AlphaBeta_well4
Aβ oligomer treatment (5 μM, StressMarq SPR-488), iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 4


title: Aβ oligomer treatment iPSC-derived cortical neurons well 1 extra

description:
Library name: AlphaBeta_well1_extra
Aβ oligomer treatment (5 μM, StressMarq SPR-488), iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 1, extra sample


title: Aβ oligomer treatment iPSC-derived cortical neurons well 1

description:
Library name: AlphaBeta_well1
Aβ oligomer treatment (5 μM, StressMarq SPR-488), iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 1


title: Aβ oligomer treatment iPSC-derived cortical neurons well 2

description:
Library name: AlphaBeta_well2
Aβ oligomer treatment (5 μM, StressMarq SPR-488), iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 2


title: Control iPSC-derived cortical neurons well 4

description:
Library name: FGM_Control_well4
Untreated control condition, iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 4

value: Control (untreated)


title: Control iPSC-derived cortical neurons well 2

description:
Library name: FGM_Control_well2
Untreated control condition, iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 2


title: Control iPSC-derived cortical neurons well 3

description:
Library name: FGM_Control_well3
Untreated control condition, iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 3


title: Control iPSC-derived cortical neurons well 1

description:
Library name: FGM_Control_well1
Untreated control condition, iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 1


title: TSA+Aβ combination treatment iPSC-derived cortical neurons well 3

description:
Library name: TSAplusAlphaBeta_well3
Combined treatment: TSA pre-treatment (60 ng/ml for 24h) followed by Aβ oligomers (5 μM), iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 3


title: Control iPSC-derived cortical neurons well 1 extra

description:
Library name: FGM_Control_well1_extra
Untreated control condition, iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 1, extra sample


title: TSA treatment iPSC-derived cortical neurons well 2

description:
Library name: TSA_well2
TSA treatment (60 ng/ml, Sigma-Aldrich T1952), iPSC-derived cortical neurons (Fujifilm R1061), DIV 4, well 2


title: patient No.23

city: Suzhou

first: Mengyao

last: Wu

state: Jiangsu

address: No.899 Pinghai Road

country: China

institute: The First Affiliated Hospital of Soochow University

description: Library name: Sample 6

data_processing:
The raw sequencing data was processed by Fastp to trim primer sequence and low quality bases. And then cellranger was used to process sequence data and aligned to human GRCh38 in order to obtain gene expression matrix. We used Seurat (version 4.0.0) to filter low quality cells, cells with number of detected genes <200 or >5000 were omitted, and use MAD variance normal to remove cells affected by mitochondrial genes. After quality control and filtering, library-size normalization to each cell was performed by NormalizeData of Seurat. The variable genes were calculated by FindVariableGenes. Then, all libraries were combined together using FindIntegrationAnchors and IntegrateData with default parameters, and using ScaleData to regress out the variability of the numbers of UMIs. Then the RunPCA and RunUMAP was used to reduce dimensions. FindClusters was used to cluster cells using the 20 dims at a resolution of 0.8.
Assembly: mouse mm10
Assembly: GRCh38
Supplementary files format and content: Cell Ranger software output H5 file

source_name: BTC

extract_protocol:
The tissue is washed with preconfigured PBS solution, sterilized mechanically spliced, and digested with preconfigured digestion solution for 30-60 minutes (depending on the type of tissue). After digestion is terminated, centrifugation, supernatant removal, and resuspension are performed. The suspension is collected by centrifugation through a 70 nm sieve and subjected to cell lysis red (depending on the type of tissue, lysis red treatment is selected). After lysis red is completed, centrifugation and resuspension are performed through a 40 nm sieve. Finally, counting cell number and viability to observe and judge whether the cell suspension was qualified. After collection of cells, centrifuge at a speed not exceeding 400rcf (adjust the speed and centrifugation time according to the cell types). Carefully discard the supernatant and retain the cell precipitation. The cell pellet was resuspended by 1mL 1x PBS containing 0.04% BSA and the washing procedure was repeated twice. After washing, appropriate volume PBS was added to the cell precipitation to obtain single-cell dispersion suspension with a concentration close to the goal number. A type of wide-bore pipette tip was used in cell resuspension for a lower cell damage. If necessary, cell filter should be applied to remove cell debris and clusters (eg.30µm MACS SmartStrainers and 40µm FlowmiTM Cell Strainer). Automatic cytometry was used to determine the cell concentration. And the sample volume was calculated based on the optimal cell sampling concentration supplied by 10X official website and the target capture number. If the calculated concentration is too high, adjust the liquid volume to the appropriate concentration and repeat counting once more. Once the desired cell suspension was obtained, immediately place the samples on ice for subsequent GEMs preparation and reverse transcription.
After cell counts and viability were determined, cell suspensions were adjusted to a concentration of 1,000 cells/ml in PBS supplemented with 0.04% BSA. The 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 was used according to the manufacturer's instructions. Agilent 4200 TapeStation was used to detect the fragment length distribution of the library. Also, Qubit HS DNA Kit was used to accurately quantify the effective concentration of the library ( > 10nmol/L).The qualified library was sequenced on the DNBSEQ T7 platform at the illumina NovaSeq 6000 with PE150 read length.

value: BTC


title: patient No.20

description: Library name: Sample 5


title: Cevimeline treatment for 1 hour, total RNA was extracted at 24 hours rep1

city: Chongqing

first: Yang

last: Yang

address: No. 30, Gaotanyan Street

institute: Southwest Hosptial

description: Library name: BCe24h_1

data_processing:
The raw data was aligned to the GRCh38 genome using HISAT2, and gene expression counts were generated using HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

source_name: Cev 24h biol rep 1

extract_protocol:
RNA was hanvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used forthe construction of sequencing libraries.
RNA library preparation was conducted by using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs)

value: Primary glioma cell


title: Glutmate treatment for 1 hour, total RNA was extracted at 24 hours rep1

description: Library name: BAMPA24h_1

source_name: Glu 24h biol rep 1


title: Combination treatment of Cevimeline and glutmate, total RNA was extracted at 24 hours rep3

description: Library name: BCeAMPA24h_3

source_name: Cev+Glu 24h biol rep 3


title: Combination treatment of Cevimeline and glutmate, total RNA was extracted at 24 hours rep2

description: Library name: BCeAMPA24h_2

source_name: Cev+Glu 24h biol rep 2


title: Combination treatment of Cevimeline and glutmate, total RNA was extracted at 3 hours rep3

description: Library name: BCeAMPA2h_3

source_name: Cev+Glu 3h biol rep 3


title: Combination treatment of Cevimeline and glutmate, total RNA was extracted at 3 hours rep1

description: Library name: BCeAMPA2h_1

source_name: Cev+Glu 3h biol rep 1


title: Cevimeline treatment for 1 hour, total RNA was extracted at 24 hours rep3

description: Library name: BCe24h_3

source_name: Cev 24h biol rep 3


title: Glutmate treatment for 1 hour, total RNA was extracted at 24 hours rep3

description: Library name: BAMPA24h_3

source_name: Glu 24h biol rep 3


title: Glutmate treatment for 1 hour, total RNA was extracted at 3 hours rep1

description: Library name: BAMPA2h_1

source_name: Glu 3h biol rep 1


title: Glutmate treatment for 1 hour, total RNA was extracted at 3 hours rep3

description: Library name: BAMPA2h_3

source_name: Glu 3h biol rep 3


title: Cevimeline treatment for 1 hour, total RNA was extracted at 3 hours rep2

description: Library name: BCe2h_2

source_name: Cev 3h biol rep 2


title: Glutmate treatment for 1 hour, total RNA was extracted at 3 hours rep2

description: Library name: BAMPA2h_2

source_name: Glu 3h biol rep 2


title: Vehicle treatment rep3

description: Library name: Bcon12h_3

source_name: Con biol rep 3


title: Vehicle treatment rep1

description: Library name: Bcon12h_1

source_name: Con biol rep 1


title: Cevimeline treatment for 1 hour, total RNA was extracted at 3 hours rep1

description: Library name: BCe2h_1

source_name: Cev 3h biol rep 1


title: Vehicle treatment rep2

description: Library name: Bcon12h_2

source_name: Con biol rep 2


title: SCID NKG2Aneg, rep2, WGBS

city: Memphis

first: Tian

last: Mi

state: TN

address: 262 Danny Thomas Pl MS351

department: Immunology

institute: St. Jude Children's Research Hospital

description:
Library name: 2-1427932
WGBS

library_source: genomic

data_processing:
Basecalling was performed using Illumina Casava 1.7
Sequencing reads were aligned to the hg19 genome using the BSMAP v.2.90 software
CpG methylation levels were determined by methratio.py script from BSMAP
Assembly: hg19
Supplementary files format and content: txt files with columns of chr, loc, cov, meth

molecule: genomic DNA

source_name: Blood

extract_protocol:
DNA was extracted from the sorted cells and then bisulfite treated using an EZ DNA Methylation-Direct kit (Zymo Research).
Bisulfite-modified DNA sequencing libraries were generated using the EpiGenome kit (Epicentre) according to the manufacturer’s instructions. Bisulfite-modified DNA libraries were sequenced using Illumina NovaSeq 6000 systems

value: Blood

value: CD8 T cells

tag: donor

value: SCID patient


title: HD NKG2Aneg, rep1, WGBS

description:
Library name: 2-1319044
WGBS

value: Healthy Donor


title: SCID NKG2Apos, rep2, WGBS

description:
Library name: 2-1427931
WGBS


title: HD NKG2Apos, rep1, WGBS

description:
Library name: 2-1319043
WGBS


title: SCID NKG2Apos, rep1, WGBS

description:
Library name: 2-1319041
WGBS


title: Glutmate treatment for 1 hour, total RNA was extracted at 24 hours rep2

description: Library name: BAMPA24h_2

source_name: Glu 24h biol rep 2


title: SCID NKG2Aneg, rep1, WGBS

description:
Library name: 2-1319042
WGBS


title: Combination treatment of Cevimeline and glutmate, total RNA was extracted at 24 hours rep1

description: Library name: BCeAMPA24h_1

source_name: Cev+Glu 24h biol rep 1


title: Combination treatment of Cevimeline and glutmate, total RNA was extracted at 3 hours rep2

description: Library name: BCeAMPA2h_2

source_name: Cev+Glu 3h biol rep 2


title: Cevimeline treatment for 1 hour, total RNA was extracted at 24 hours rep2

description: Library name: BCe24h_2

source_name: Cev 24h biol rep 2


title: 12month, replicate 4, scRNAseq

description:
Library name: A30_E10
10x Genomics 5' kit

data_processing:
The demultiplexing, barcoded processing, mapping, counting and aggregation were done by Cell Ranger 6.0.0 software.
Assembly: hg38
Supplementary files format and content: Tab separated files of genes
Supplementary files format and content: Tab separated files of cell barcodes
Supplementary files format and content: MEX file of gene-barcode matrix

extract_protocol:
CD3+ T cells were FACS-purified from blood obtained from SCID-X1 patients at 14-weeks and 12-months post gene therapy.  Purified CD3+ T  cells were washed with PBS and 0.04% BSA before loading into a Chromium Next GEM Chip G (10X Genomics). GEM generation, cDNA amplification and library construction were performed following the protocol of Chromium Next GEM Single Cell 5′ Reagent Kits v2 (Dual Index, 10X Genomics) with target recovery of 5000-10000 cells per library/sample. The final 4 libraries were sequenced on the Illumina NovaSeq platform using 100bp paired-end with target reads of 500 million per sample.
GEM generation, cDNA amplification and library construction were performed following the protocol of Chromium Next GEM Single Cell 5′ Reagent Kits v2 (Dual Index, 10X Genomics) with target recovery of 5000-10000 cells per library/sample

tag: cells loaded

value: CD3 T cells

tag: timepoint


title: 14week, replicate 3, scRNAseq

description:
Library name: pt7_14w_2
10x Genomics 5' kit


title: 12month, replicate 1, scRNAseq

description:
Library name: pt7_12m
10x Genomics 5' kit


title: KYSE30 cells, control3,0Gy

city: Nanjing

first: Jian

last: Lu

address: 87 Dingjiaqiao Road,

institute: Zhongda Hospital, Southeast University

description:
Library name: control3
control3_Clean_Data

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: grch38
Supplementary files format and content: FPKM.xlsx

growth_protocol: KYSE30 esophageal squamous cell carcinoma cells were cultured in RPMI - 1640 medium containing 10% fetal bovine serum (FBS) and antibiotics in a humidified environment with 5% CO₂ at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Esophageal squamous cell carcinoma


title: 12month, replicate 2, scRNAseq

description:
Library name: pt8_12m
10x Genomics 5' kit


title: Cevimeline treatment for 1 hour, total RNA was extracted at 3 hours rep3

description: Library name: BCe2h_3

source_name: Cev 3h biol rep 3


title: KYSE30 cells, shP4HA2_3,4Gy

description:
Library name: sh_125I3
sh_125I3_Clean_Data

value: brachytherapy


title: 14week, replicate 2, scRNAseq

description:
Library name: pt8_14w
10x Genomics 5' kit


title: KYSE30 cells,control2,0Gy

description:
Library name: control2
control2_Clean_Data


title: KYSE30 cells, shP4HA2_2,4Gy

description:
Library name: sh_125I2
sh_125I2_Clean_Data


title: 12month, replicate 3, scRNAseq

description:
Library name: pt8_12m_2
10x Genomics 5' kit


title: 14week, replicate 1, scRNAseq

description:
Library name: pt7_14w
10x Genomics 5' kit


title: human naive ES, HNES1

city: Otsu

first: Takako

last: Hoshiyama

state: Shiga

address: Seta tsukinowacho

department: Department of Obstetrics and Gynecology

country: Japan

institute: Shiga University of Medical Science

description: Library name: HNES1

data_processing:
The reads were mapped on human genome (GRCh38/Hg38) using HISAT2 with a transcript assembly to guide mapping.
Reads from all samples were counted and assigned to genes in the assembled genome model using featureCounts.
Assembly: GRCh38/Hg38
Supplementary files format and content: featureCounts

source_name: embryo

growth_protocol: HNES1 and HNES3 were maintained on irradiated mouse embryonic fibroblasts (iMEFs) in PXGL medium (Guo et al., 2016). Finally, HNES cells were cultured under feeder-free conditions. hDF cells were seeded on 0.1% gelatin-coated plates and cultured in DMEM/F12 supplemented with 10% FBS and 0.5% penicillin–streptomycin.

extract_protocol:
Total RNA was extracted using TRI Reagent.
cDNA libraries were constracted by SignAC at WPI-ASHBi, Kyoto University.

value: embryo

value: human naive ES

value: PXGL medium


title: BE(2)-C cells, DpC, repeat 2

city: Brisbane

first: Zhao

last: Deng

state: QLD

address: U131/79 Moray st, New Farm, QLD

country: Australia

institute: Griffith University

description: Library name: Sample 26

data_processing:
Data filtering: The data with adapter contamination was removed from raw reads and the reads with uncertain nucleotides constitute more than 10% of either read were also removed. Then remove the reads when low quality nucleotides (Base Quality less than 5) constitute more than 50% of the read
Alignment: HISAT2 2.0.5, default parameters, code: hisat2 -x 参考基因组 -p 4 --dta -t --phred33 -1   xxx_1.fq.gz -2 xxx_2.fq.gz --un-conc-gz xxxunmap.fq.gz 2> xxx_align.log | samtools sort -O BAM --threads 4 -o xxx.bam - Quantification: featureCounts 1.5.0-p3, default parameters, code: featureCounts -a genom.gtf -t exon -g gene_id -o counts.txt  sample1.bam sample2.bam sample3.bam
Differential Analysis: DESeq2 1.20.0, parameter |log2(FoldChange)| >= 1 & padj <= 0.05
Assembly: GRCh38/hg38
Supplementary files format and content: Table-delimit text file includes raw counts for each sample
Supplementary files format and content: Text file include FPKM values for each sample

growth_protocol: SH-SY5Y and Kelly cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 1% penicillin/streptomycin, 1% sodium pyruvate solution, and 1% MEM non-essential amino acid solution. The BE(2)-C cells were cultured in Ham’s F12/MEM (50% Ham’s F12 and 50% MEM medium) with the same supplements required for RPMI above. All the cells were incubated under 5% CO2 at 37°C

extract_protocol:
Treated cells were collected in 1ml of TRI reagent (Sigma-Aldrich) and the RNA was extracted as per the manufacturer's instructions
The library preparation kit, NEBNext Ultra II RNA Library Prep Kit for Illumina(Cat No. 7770), was used to purify messenger RNA from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dTTP. The library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.  The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platform NovaSeq 6000 with sequencing strategy PE150 and generated at least 50 Mb of paired-end raw reads per sample.

treatment_protocol: All the cells were first seeded to a 60x15 mm petri dish plate and incubated under 5% CO2 at 37°C overnight to let them attach. Then the cells were incubated with a normal growth medium or this medium containing 100µM DFO, or 5µM DpC.

value: Neuroblastom cells

value: Wild type

value: DpC


title: BE(2)-C cells, DFO, repeat 3

description: Library name: Sample 24

value: DFO


title: BE(2)-C cells, DpC, repeat 1

description: Library name: Sample 25


title: BE(2)-C cells, DpC, repeat 3

description: Library name: Sample 27


title: human naive ES, HNES3

description: Library name: HNES3

value: WT


title: Kelly cells, DpC, repeat 3

description: Library name: Sample 18

source_name: Kelly

value: Kelly


title: BE(2)-C cells, Control, repeat 3

description: Library name: Sample 21

value: Control


title: BE(2)-C cells, Control, repeat 2

description: Library name: Sample 20


title: Kelly cells, DpC, repeat 2

description: Library name: Sample 17


title: Kelly cells, DpC, repeat 1

description: Library name: Sample 16


title: BE(2)-C cells, Control, repeat 1

description: Library name: Sample 19


title: BE(2)-C cells, DFO, repeat 1

description: Library name: Sample 22


title: Kelly cells, DFO, repeat 3

description: Library name: Sample 15


title: KYSE30 cells, shP4HA2_1,4Gy

description:
Library name: sh_125I1
sh_125I1_Clean_Data


title: KYSE30 cells, control1,0Gy

description:
Library name: control1
control1_Clean_Data


title: human dermal fibroblast, P5

description: Library name: hDF

source_name: dermal tissue

value: dermal tissue

value: human dermal fibroblast, P5

value: human dermal fibroblast

value: 10% FBS/DMEM


title: Kelly cells, DFO, repeat 1

description: Library name: Sample 13


title: Kelly cells, Control, repeat 2

description: Library name: Sample 11


title: Kelly cells, Control, repeat 1

description: Library name: Sample 10


title: BE(2)-C cells, DFO, repeat 2

description: Library name: Sample 23


title: SH-SY5Y cells, DFO, repeat 3

description: Library name: Sample 6


title: SH-SY5Y cells, DpC, repeat 1

description: Library name: Sample 7


title: Kelly cells, Control, repeat 3

description: Library name: Sample 12


title: SH-SY5Y cells, DFO, repeat 1

description: Library name: Sample 4


title: SH-SY5Y cells, Control, repeat 3

description: Library name: Sample 3


title: SH-SY5Y cells, Control, repeat 2

description: Library name: Sample 2


title: OCY_D12_ZNF93_Rep4

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

description:
Library name: L_62
RNAseq on OCI LY7 transducedWith pLKO_ZNF93

data_processing:
Raw reads were mapped with hisat2 with -k5 optino to the human hg19 genome
Gene summaziation performed with featureCounts using -Q 10 as option
Assembly: hg19
Supplementary files format and content: countTable raw unique read counts

source_name: OCY LI 7

growth_protocol: Cells were grown in appropriate media supplemented with FCS and PSG

extract_protocol:
NucleoSpin RNA Plus, Mini kit for RNA purification with DNA removal column MACHEREY-NAGEL Item number: 740984.50
We performed a "Illumina stranded mRNA ligation" (ISML) prep starting from 250ng of RNA (see table below), according to Illumina protocol 1000000124518 v01 (internal exp code RPX129 and LPX614). We quantified the libraries by qubit DNA HS and performed profile analysis by TapeStation TS4200. All libraries look good and have sufficient yields.

value: OCY LI 7

value: Lymphoid Cancer Cell Line


title: OCY_D12_ZNF93_Rep2

description:
Library name: L_60
RNAseq on OCI LY7 transducedWith pLKO_ZNF93


title: OCY_D12_ZNF93_Rep1

description:
Library name: L_59
RNAseq on OCI LY7 transducedWith pLKO_ZNF93


title: OCY_D12_Scr_Rep3

description:
Library name: L_57
RNAseq on OCI LY7 transducedWith pLKO_scr


title: OCY_D12_Scr_Rep2

description:
Library name: L_56
RNAseq on OCI LY7 transducedWith pLKO_scr


title: OCY_D12_Scr_Rep4

description:
Library name: L_58
RNAseq on OCI LY7 transducedWith pLKO_scr


title: SH-SY5Y cells, Control, repeat 1

description: Library name: Sample 1


title: OCY_D12_Scr_Rep1

description:
Library name: L_55
RNAseq on OCI LY7 transducedWith pLKO_scr


title: U2932_D12_ZNF93_Rep4

description:
Library name: L_54
RNAseq on U2932 transducedWith pLKO_ZNF93


title: U2932_D12_ZNF93_Rep3

description:
Library name: L_53
RNAseq on U2932 transducedWith pLKO_ZNF93


title: U2932_D12_ZNF93_Rep1

description:
Library name: L_51
RNAseq on U2932 transducedWith pLKO_ZNF93


title: Kelly cells, DFO, repeat 2

description: Library name: Sample 14


title: U2932_D12_Scr_Rep4

description:
Library name: L_50
RNAseq on U2932 transducedWith pLKO_scr


title: U2932_D12_Scr_Rep3

description:
Library name: L_49
RNAseq on U2932 transducedWith pLKO_scr


title: U2932_D12_ZNF93_Rep2

description:
Library name: L_52
RNAseq on U2932 transducedWith pLKO_ZNF93


title: SH-SY5Y cells, DpC, repeat 2

description: Library name: Sample 8


title: SH-SY5Y cells, DpC, repeat 3

description: Library name: Sample 9


title: SH-SY5Y cells, DFO, repeat 2

description: Library name: Sample 5


title: SW480_D6_ZNF93_Rep4

description:
Library name: L_38
RNAseq on SW480 transducedWith pLKO_ZNF93

value: Colorectal cancer Cell Line


title: OCY_D12_ZNF93_Rep3

description:
Library name: L_61
RNAseq on OCI LY7 transducedWith pLKO_ZNF93


title: SW480_D6_ZNF93_Rep3

description:
Library name: L_37
RNAseq on SW480 transducedWith pLKO_ZNF93


title: SW480_D6_ZNF93_Rep2

description:
Library name: L_34
RNAseq on SW480 transducedWith pLKO_ZNF93


title: SW480_D6_Scr_Rep3

description:
Library name: L_35
RNAseq on SW480 transducedWith pLKO_scr


title: U2932_D12_Scr_Rep1

description:
Library name: L_47
RNAseq on U2932 transducedWith pLKO_scr


title: SW480_D6_Scr_Rep2

description:
Library name: L_32
RNAseq on SW480 transducedWith pLKO_scr


title: SW480_D6_Scr_Rep1

description:
Library name: L_31
RNAseq on SW480 transducedWith pLKO_scr


title: RF040_ZNF93_D_Rep1

description:
Library name: L_16
RNAseq on K562 overexpressing ZNF93 upon DOX _ treated with DOX for 5 days

growth_protocol: K562 were grown in RPMI supplemented with FCS and PSG

extract_protocol:
NucleoSpin RNA Plus, Mini kit for RNA purification with DNA removal column MACHEREY-NAGEL Item number: 740984.50
Illumina stranded mRNA
We performed a "Illumina stranded mRNA ligation" (ISML) prep starting from 200 ng of RNA (see table below), according to Illumina protocol 1000000124518 v03 (internal exp code LPX760). We quantified the libraries by qubit DNA HS and performed profile analysis by TapeStation TS4200. All libraries look good and have sufficient yields.

treatment_protocol: Cells were treated with DOX during 5 Days

value: Myeloid

value: Dox


title: RF040_ZNF93_NoD_Rep2

description:
Library name: L_14
Control RNAseq on K562 overexpressing ZNF93 upon DOX _ NoDox

value: NoDox


title: RF040_ZNF93_NoD_Rep1

description:
Library name: L_13
Control RNAseq on K562 overexpressing ZNF93 upon DOX _ NoDox


title: RF040_ZNF93_NoD_Rep3

description:
Library name: L_15
Control RNAseq on K562 overexpressing ZNF93 upon DOX _ NoDox


title: Cav3.2KO

city: Charlottesville

first: Collin

last: Dube

state: Virginia

address: 21 Hospital Drive

institute: University of Virginia

description: 10X Genomics

data_processing:
Sample alignment was done by 10X Cell Ranger (v7.1.0)
Quality control was performed using Seurat (v5.0.2) by the following criteria: nUMI/cell threshold > 200, gene/cell threshold > 250, mitochondria ratio < 0.25
Cells were identified using SingleR, Findmarkers via Seurat and InferCNV
Assembly: mm10
Supplementary files format and content: Tab separated value files and matrix files

organism: Mus musculus

source_name: Brain

extract_protocol:
Tissue was dissociated using MACs neural dissociation kit.
Illumina sequencing libraries were prepared by Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics)

value: Brain

value: GBM + TME


title: U2932_D12_Scr_Rep2

description:
Library name: L_48
RNAseq on U2932 transducedWith pLKO_scr


title: RF040_ZNF93_D_Rep3

description:
Library name: L_18
RNAseq on K562 overexpressing ZNF93 upon DOX _ treated with DOX for 5 days


title: RF040_GFP_D_Rep3

description:
Library name: L_10
RNAseq on K562 overexpressing GFP upon DOX _ treated with DOX for 5 days


title: Wild Type

description: 10X Genomics

value: C57BlL6 WT


title: RF040_GFP_D_Rep1

description:
Library name: L_02
RNAseq on K562 overexpressing GFP upon DOX _ treated with DOX for 5 days


title: R247_W43R2.R1

source_name: immature seed coat

extract_protocol:
Total RNA was extracted from tissues using phenol:chloroform, lithium chloride precipitation, and ethanol precipitation.
Libraries were constructed with Illumina Tru Seq or Stranded Tru Seq kits by the University of Illinois DNA Services Laboratory and sequenced using Illumina machines.

value: immature seed coat

tag: stage or_seed_fresh_wt

tag: cultivar

value: Williams, W43

tag: lab names

tag: phenotype descriptors

value: yellow seed coat, black hilum

value: i-i RT w1


title: RF040_GFP_D_Rep2

description:
Library name: L_06
RNAseq on K562 overexpressing GFP upon DOX _ treated with DOX for 5 days

tag: genotype


title: RF040_GFP_NoD_Rep3

description:
Library name: L_09
Control RNAseq on K562 overexpressing GFP upon DOX _ NoDox

tag: treatment


title: embryoE7, cYAPKO, bio rep1

city: Philadelphia

first: Naiara

last: Akizu

state: PA

address: 3501 Civic Center Blvd

department: Pathology And Lab Medicine

institute: Children's Hospital of Philadelphia

data_processing:
The demultiplexing, barcoded processing and gene counting were made using Cell Ranger v7.1.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
E7 embryos were isolated and placed in DMEM/10% FBS on ice. Once genotypes were confirmed, embryos were pooled and dissociated using trypsin for 5 minutes at 37°C. After dissociation, trypsin was neutralized with three times the amount of DMEM/10% FBS.
The 10x Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 was used to perform single cell and library preparations. Generation of gel beads in emulsion, barcoding, GEM-RT clean-up, complementary DNA amplification, and library construction were all performed as per the manufacturer’s protocol.

value: embryo

tag: time

value: female

value: cYAPKO


title: RF040_GFP_NoD_Rep2

description:
Library name: L_05
Control RNAseq on K562 overexpressing GFP upon DOX _ NoDox

tag: cell type


title: embryoE7, WT, bio rep1

description: 10x Chromium Next GEM Single Cell 3’ GEM

value: WT


title: R252_RichYL.R1

source_name: young leaf

value: young leaf

value: 4 wk GH plants

value: Richland

value: Rich

value: yellow seed coat

value: I R t

tag: other

tag: grin l_number_(or_other_designation)

tag: grin pi_number


title: R253_T157YL.R1

value: T157, i mutation

value: imperfect black seed coat

value: i R t


title: SW480_D6_ZNF93_Rep1

description:
Library name: L_33
RNAseq on SW480 transducedWith pLKO_ZNF93

value: Colorectal cancer Cell Line


title: RF040_ZNF93_D_Rep2

description:
Library name: L_17
RNAseq on K562 overexpressing ZNF93 upon DOX _ treated with DOX for 5 days

value: Myeloid

value: Dox


title: R254_W54Root.R1

source_name: young root

value: young root

value: Williams, W54

value: W54, same as W43

value: yellow seed coat, black hilum

value: i-i RT w1


title: R255_W55Root.R1

value: Williams 55, i mutation

value: black seed coat

value: iRT w1

value: 138 kb i deletion


title: RF040_GFP_NoD_Rep1

description:
Library name: L_01
Control RNAseq on K562 overexpressing GFP upon DOX _ NoDox

value: NoDox


title: WNV capsid expressing cells, Rep3

city: Columbu

first: Manu

last: Sanjeev

state: OH

address: 484 W 12th Ave

institute: The Ohio State University

description:
Library name: Wcap_3
Wcap_3

data_processing:
Total RNA-seq:12nt UMIs at the start of Read 1 extracted using UMItools. Adapter trimming carried out with Cutadapt for the sequences AGATCGGAAGAGCACAC-GTCTGAACTCCAGTCAC and N{12}AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
RIP-seq:5nt random sequence, 5nt identifier & CC removed from 5' end and miRCat22 sequence trimmed from 3' end using Cutadapt
Trimmed reads aligned to genome using STAR
Total RNA-seq: Mapped Bam files indexed with samtools and PCR deduplicated using UMItools. Deduplicated bam files converted to fastq for transcript quantification by Kallisto.
Bam files counted using FeatureCounts for all samples.
Assembly: GRCh38, Ensembl release 100
Supplementary files format and content: Text file including raw counts calculated by Featurecounts.

source_name: Kidney

growth_protocol: Cells grown in DMEM with 10% FBS, 1% Pen-Strep antibiotic at 37C with 5% CO2

extract_protocol:
RNA extracted with Trizol for all samples. Total RNA samples Ribodepleted with Lexogen RiboCoprRNA depletion kit
Total RNA Libraries constructed with Lexogen CORALL RNA-Seq V2 library prep kit with UDIs. RIP-seq RNA libraries constructed as described in Mabin et al., 2018.

treatment_protocol: Cells transfected with siRNA/expression plasmid for 3 days for RNA seq.

value: Kidney

value: Flp-In ZeoR

value: WNV capsid

value: WNV capsid transient transfection


title: WNV capsid expressing cells, Rep2

description:
Library name: Wcap_2
Wcap_2


title: WNV capsid expressing cells, Rep1

description:
Library name: Wcap_1
Wcap_1


title: goose embryonic stem cells rep1, p57

city: Pasadena

first: Xi

last: Chen

address: 1200 E. California Blvd

institute: California Institute of Technology

description: Library name: sample3

data_processing:
STAR alignment, RSEM quantification, DESeq for differential expression
Assembly: quail reference genome (Ensembl Coturnix_japonica.Coturnix_japonica_2.0.113), goose reference genome (Ensembl Anser_cygnoides.GooseV1.0.113), Ostrich reference genome (Ensembl Struthio_camelus_australis.ASM69896v1.113)
Supplementary files format and content: txt format, including raw counts, gene length, etc

organism: Anser cygnoides

source_name: freshly laid EGK.X embryo

growth_protocol: Freshly laid avian fertile eggs at EGK.X-XII stages were kept at 16 °C before extraction. To harvest cells from yolk, a filter paper-based method was applied (Chapman et al., 2001). Filter paper with a hole at center was placed on top of the embryo. The outer edge of the filter paper was cut together with the vitelline membranes. Embryo were then released from yolk together with the filter paper and washed in PBS solution. Next, embryo was transferred into a 15ml tube free of the paper ring and dissociated by pipetting inside N2B27 medium. Dissociated cells were cultured in tissue plates coated with irradiated mouse embryonic fibroblast (MEF) cells as feeder layer. Basal medium used for routine ESC maintenance was N2B27 medium composed of DMEM/F12:Neuralbasal (1:1) plus 0.5x N2, 0.5x B27 supplement and 20ng/ml ovotransferrin with the addition of 1x penicillin-streptomycin. Avian ESC self-renewal was kept with 2µM IWR-1, 2.5µM Gö6983, 2µM SB431542. Quail and goose ESCs were treated with additional chicken LIF at 10ng/ml. ESCs were cultured at 38 °C in 5% CO2 with daily medium change. To passage, TrypLE was used to incubate the cells for 5 min and neutralized with basal medium in triple amount. Cells were handled with 5ml pipette all the time to avoid dissociation into singles.

extract_protocol:
Total RNA of in-vitro expanded cells was extracted using the RNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions.
RNA-seq

value: freshly laid EGK.X embryo

value: gES p57

value: embryonic stem cells

value: WT/GFP


title: goose embryonic stem cells rep2, p57

description: Library name: sample4


title: DENV capsid expressing cells, Rep3

description:
Library name: Dcap_3
Dcap_3

value: DENV capsid

value: DENV capsid transient transfection


title: DENV capsid expressing cells, Rep2

description:
Library name: Dcap_2
Dcap_2


title: EV HeLa, DMSO, FLAG(CUT&RUN)

city: Rochester

first: Jake

middle: A

last: Kloeber

state: MN

address: 200 First Street SW

department: Oncology

institute: Mayo Clinic

description: Library name: EV, DMSO

data_processing:
basecalls were performed using bcl2fastq
ChIP-seq reads were aligned to hg38 using BWA-MEM
Peaks were called using Macs2 v2.1.1 with a significance cutoff of <= 0.05
Sequencing depth in peaks were normalized into RPKM using deepTools 'bamCoverage' function.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

source_name: HeLa

growth_protocol: DMEM, 10% fetal bovine serum, cultured at 37C 5%CO2

extract_protocol:
CUT&RUN was performed as previously described (Skene PJ and Henikoff. Elife. 2017). Cells were incubated with ConA magnetic beads for 10 min at room temperature. Samples were incubated in primary antibody overnight at 4 C with rotation. Samples incubated  with pA/G-MNase for 1 h at 4 C and then digested on ice for 1 h. Solubilized chromatin was released and DNA was extracted with phenol-chloroform isoamyl alcohol and ethanol precipitation.
CUT&RUN libraries were prepared by NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: cells were treated with ICRF193 (100 nM) or DMSO for 4 h at 37C

value: HeLa

value: human cervical cancer cell

tag: vector

value: pLVX-FLAG-EV

value: DMSO

tag: chip antibody

value: FLAG (Sigma, #F1804)


title: Nluc expressing cells, Rep2

description:
Library name: Nluc_2
Nluc_2

tag: tissue

tag: cell line

value: Nluc

value: Nluc transient transfection


title: DENV capsid expressing cells, Rep1

description:
Library name: Dcap_1
Dcap_1

value: Kidney


title: Nluc expressing cells, Rep3

description:
Library name: Nluc_3
Nluc_3

value: Flp-In ZeoR


title: Nluc expressing cells, Rep1

description:
Library name: Nluc_1
Nluc_1


title: PYM1deltaN stable transfection, Rep3

description:
Library name: MS22_12
Column in processed file:MS22_12

value: PYM1 deltaN Overexpression

value: piggybac-HA-PYM1 deltaN transfection


title: FL-KCTD10 HeLa, DMSO, rep2, FLAG(CUT&RUN)

description: Library name: FL-KCTD10, DMSO, rep2


title: FL-KCTD10 HeLa, DMSO, rep1, FLAG(CUT&RUN)

description: Library name: FL-KCTD10, DMSO, rep1


title: SW480_D6_Scr_Rep4

description:
Library name: L_36
RNAseq on SW480 transducedWith pLKO_scr

value: Colorectal cancer Cell Line

value: WT


title: PYM1deltaN stable transfection, Rep2

description:
Library name: MS22_11
Column in processed file:MS22_11


title: Wildtype_MicroC_ring_C22

city: Parul

first: Parul

last: Singh

address: 25-28, rue du Docteur Roux

country: France

institute: Institut Pasteur

description:
Library name: Wildtype_MicroC_ring_C22
Wt_2_ring
WT_12hpi_all.mcool

data_processing:
Library strategy: Micro-C
Micro-C paired-end reads were mapped to the P. falciparum genome and processed into pairs and multi-resolution normalized contact matrix .mcool file using hicstuff
Assembly: P. falciparum genome (plasmoDB.org, version 3, release 55)
Supplementary files format and content: high resolution interaction matrice in .mcool format

organism: Plasmodium falciparum

growth_protocol: Blood stage NF54 P. falciparum parasites were cultured in human RBCs supplemented with 10% v/v Albumax I (Thermo Fisher 11020), hypoxanthine (0.1 mM final concentration, C.C.Pro Z‐41‐M) and 10 mg gentamicin (Sigma G1397) at 4% hematocrit and under 5% O2, 5% CO2 at 37 °C.

extract_protocol:
Parasites were cross-linked by adding methanol-free formaldehyde to 1% final concentration. The reaction was quenched by adding 1 M Tris-HCl pH 7.5. Parasites were washed with DPBS at 25°C, resuspended in the second cross-linking solution - 3 mM DSG in DPBS and incubated for 45 minutes. The reaction was quenched with 1 M Tris-HCl pH 7.5. The cell pellet was lysed and digested with the chosen concentration of MNase. Each pellet was resuspended in end-chewing mix [1X NEB Buffer 2.1, 2 mM ATP, 5 mM DTT, 0.5 U/μl T4 PNK] and incubated for 15 minutes. Klenow fragment was added, followed by 25 μl of end-labeling mix [0.2 mM Biotin-dATP, 0.2 mM Biotin-dCTP, 0.2 mM dTTP, 0.2 mM dGTP, 0.1 mg/ml BSA]. 500 mM EDTA was added and incubated for 30 minutes. Biotinylated DNA fragments were then covalently linked by proximity ligation by resuspending the pellet in ligation mix [1X T4 DNA ligase buffer, 0.1 mg/ml BSA, 33 U/μl T4 DNA ligase)]. The biotin-dNTPs were removed from unligated ends, the DNA was purified and decrosslinked. The DNA contained in the supernatant was recovered using the DNA Clean & Concentrator. The ligated DNA was loaded onto a 2% TAE agarose gel to separate dimers from monomers, and DNA was extracted. The biotinylated dimers were isolated with Dynabeads MyOne Streptavidin C1.
The library prep was performed with the samples on beads using the NEBNext® Ultra II Directional DNA Library Prep Kit (NEB E7645), with several modifications.

tag: strain

value: wild type


title: FL-KCTD10 HeLa, ICRF193, rep1, FLAG(CUT&RUN)

description: Library name: FL-KCTD10, ICRF193, rep1


title: Wildtype_MicroC_ring_C23

description:
Library name: Wildtype_MicroC_ring_C23
Wt_3_ring
WT_12hpi_all.mcool


title: PYM1deltaN stable transfection, Rep1

description:
Library name: MS22_10
Column in processed file:MS22_10


title: Wildtype_MicroC_ring_C21

description:
Library name: Wildtype_MicroC_ring_C21
Wt_1_ring
WT_12hpi_all.mcool


title: FL-KCTD10 HeLa, ICRF193, rep2, FLAG(CUT&RUN)

description: Library name: FL-KCTD10, ICRF193, rep2


title: PYM1 stable transcfection, Rep1

description:
Library name: MS22_07
Column in processed file:MS22_07

value: PYM1 Overexpression

value: piggybac-HA-PYM1 transfection


title: PYM1 stable transcfection, Rep3

description:
Library name: MS22_09
Column in processed file:MS22_09


title: PYM1 stable transcfection, Rep2

description:
Library name: MS22_08
Column in processed file:MS22_08


title: siPYM1 treated cells, Rep3

description:
Library name: MS22_06
Column in processed file:MS22_06

value: PYM1 knockdown

value: siPYM1 transfection


title: MORC_ChIPSeq_schizont_rep2_input4

description: Library name: MORC_ChIPSeq_schizont_rep2_input4

data_processing:
Sequenced reads were mapped to the P. falciparum genome (plasmoDB.org, version 3, release 56) using bowtie. PCR duplicates were filtered using samtools’ fixmate and markdup commands and only alignments with a mapping quality ≥ 30 were retained (samtools view -q 30). The paired end deduplicated ChIP and input BAM files were used as treatment and control, respectively, for peak calling with the MACS2 subcommand.
Assembly: P. falciparum genome (plasmoDB.org, version 3, release 56)
Supplementary files format and content: IP/Input enrichment ratio in .bw format

growth_protocol: Clonal population of MORC-3HA-glmS parasites was tightly synchronized and harvested at 36 hpi in human RBCs supplemented with 10% v/v Albumax I, hypoxanthine (0.1 mM final concentration) and 10 mg gentamicin under 5% O2, 5% CO2 at 37 °C.

extract_protocol:
For MORC-3HA-glmS parasites, the supernatant was removed and MgCl2 was added. 80 μL of ChIP Cross-link Gold were added and sample was incubated for 30 min with gentle agitation. The parasites were resuspended in DPBS at 4°C and were further cross-linked by adding methanol‐free formaldehyde (final concentration 1%) and incubated for 15 minutes. The cross-linking reaction was quenched by adding glycine. The parasites were lysed, and the lysates were sonicated in a Diagenode Pico Bioruptor.
Libraries were prepared with the NEB kit (E7645S).

value: Input sample


title: siPYM1 treated cells, Rep2

description:
Library name: MS22_05
Column in processed file:MS22_05


title: WT 16DPA rep1

city: Lubbock

first: Pallavi

last: Dhiman

address: 1006 Canton Avenue

institute: Texas Tech University

description: Library name: W.16.R1

data_processing:
All data processing was carried out on the High-Performance Computing Cluster (HPCC) at Texas Tech University
Initial quality control of raw reads was performed using FastQC
Low-quality reads and adapters were removed using Trimmomatic.
Clean reads were aligned to the Sorghum bicolor reference genome using STAR aligner.
Transcript assembly and abundance estimation were performed using Cufflinks (Trapnell et al., 2012) to generate FPKM values.
Assembly: Sorghum bicolor reference genome v3.2 BTx623 from Phytozome
Supplementary files format and content: FPKMs_allSamples.txt file contains FPKM values of all genes in all the samples

organism: Sorghum bicolor

source_name: Seed Endosperm

extract_protocol:
Total RNA was extracted using RiboPure™ RNA Purification Kit. 2ug was used for library prepration
cDNA library construction and sequencing were performed following the DNBSEQ eukaryotic transcriptome protocols

value: Seed Endosperm


title: MORC_ChIPSeq_schizont_rep2_chip4

description: Library name: MORC_ChIPSeq_schizont_rep2_chip4

value: ChIP sample


title: siPYM1 treated cells, Rep1

description:
Library name: MS22_04
Column in processed file:MS22_04


title: waxy mutant 6DPA rep1

description: Library name: M.6.R1


title: WT 6DPA rep2

description: Library name: W.6.R2


title: siNC treated cells, Rep3

description:
Library name: MS22_03
Column in processed file:MS22_03

value: Control siNC transfection


title: WT 11DPA rep2

description: Library name: W.11.R2


title: waxy mutant 21DPA rep1

description: Library name: M.21.R1


title: siNC treated cells, Rep1

description:
Library name: MS22_01
Column in processed file:MS22_01


title: WT 21DPA rep1

description: Library name: W.21.R1


title: waxy mutant 6DPA rep2

description: Library name: M.6.R2


title: ZYHT3

city: Wuhan

first: qingqing

last: li

address: No. 238 Jiefang Road, Wuchang District

department: Department of Respiratory and Critical Care Medicine

institute: Renmin Hospital of Wuhan University

description:
Library name: library 6
ZYHT group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes featurecounts counts for each sample

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

value: ZYHT


title: waxy mutant 11DPA rep1

description: Library name: M.11.R1


title: ZYHT2

description:
Library name: library 5
ZYHT group, replicate biosample 2


title: ZYHT1

description:
Library name: library 4
ZYHT group, replicate biosample 1


title: waxy mutant 21DPA rep2

description: Library name: M.21.R2


title: NC2

description:
Library name: library 2
control group, replicate biosample 2

value: control


title: NC3

description:
Library name: library 3
control group, replicate biosample 3


title: waxy mutant 16DPA rep1

description: Library name: M.16.R1


title: WT 16DPA rep2

description: Library name: W.16.R2


title: NC1

description:
Library name: library 1
control group, replicate biosample 1


title: waxy mutant 11DPA rep2

description: Library name: M.11.R2


title: WT 6DPA rep1

description: Library name: W.6.R1


title: waxy mutant 16DPA rep2

description: Library name: M.16.R2


title: MDA-MB-231, Untreated (INPUT)

city: Milan

first: Tiziana

last: Bonaldi

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: Library name: MDA-MB-231 UNTREATED, INPUT

data_processing:
ChIP-seq reads were mapped to UCSC hg38 genome using Bowtie, keeping only uniquely mapping reads and allowing for no more than two mismatches per read. The options “—best” and “–strata” were enabled. The maximum insert size for valid paired-end alignments was set to 700bp. ChIP-seq of sample with Drosophila spike-in were proccessed through the SpikeFlow pipeline with default parameters.
Peaks were called using MACS2, enabling the –BROAD option and setting both the q-value and the BROAD-CUTOFF parameter to 0.001.
bigWig files were generated starting from BAM files with the bamCoverage function of deepTools with the following parameters: -- ignoreDuplicates --centerReads –bin-size 10bp --normalizeUsing RPGC (reads per genomic content) --effectiveGenomeSize 2701495761.
For the identification of differentially bound regions featureCounts was used to count reads mapped to the list of peaks called from the untreated MDA-MB-231, and the obtained count matrix was supplied to DESeq2. Normalization of count matrix was performed using scaling factors computed by dividing the ratio of reads mapped to the human genome in the IP and reads mapped to Drosophila in the IP by the ratio of reads mapped to human in the input and reads mapped to Drosophila in the input. The inverse of the scaling factors was supplied to DESeq2 as size factors. Regions with an FDR < 0.05 were deemed as differentially bound regions.
Assembly: hg38, dm6
Supplementary files format and content: bigWig for the IP of the untreated MDA-MB-231. txt raw count table used as input for the differential binding analysis.

growth_protocol: MDA-MB-231 were grown in Dulbecco modified Eagle medium DMEM (Euroclone Spa, ECM0103L) supplemented with stable Glutamine and 10% Fetal Bovine Serum of North American origin (FBS_NA, Euroclone Spa, CHA1115L)

extract_protocol:
The chromatin was prepared from 1-5 x107 cells.The samples were fixed in 1% v/v formaldehyde (Sigma, F8775) at room temperature for 10 minutes, followed by the addition of 125 mM Glycine (Serva, SE39004) for 5 min. The samples were washed twice in PBS and then resuspended in ChIP SDS lysis buffer (100 mM NaCl, 50 mM Tris-Cl pH 8.1, 5 mM EDTA pH 8, 0.2% NaN3, and 0.5% SDS). Nuclei were pelleted for 6 minutes at 1200 rpm. The samples were resuspended in 3 ml icecold IP buffer (100mM Tris-Cl pH 8.6, 100mM NaCl, 5mM EDTA pH 8.0, 0.2 % NaN3, 5% (v/v) Triton 100X) and sonicated with a Branson Digital Sonifier 250, with a large tip for cell lines (30% amplitude, 15 second on/15 second off).
DNA libraries were prepared from 5-10 ng of input and IP DNA through an in-house protocol (PMID: 23429716).

treatment_protocol: OICR-9429 was purchased from MedChemExpress and Target Mol and resuspended in DMSO for in vitro experiments. MDA-MB-231 cells were treated with DMSO or OICR-9429 for 24-96 hours.

value: Triple Negative Breast Cancer


title: MDA-MB-231, OICR-9429, biol rep3, H3K4me2 (ChIP)

description:
Library name: MDA-MB-231 OICR-9429 R3, ChIP
IP_OICR-rep4" is the column name in "count231.txt


title: MDA-MB-231, Untreated, H3K4me2 (ChIP)

description: Library name: MDA-MB-231 UNTREATED, ChIP


title: MDA-MB-231, OICR-9429, biol rep2, H3K4me2 (ChIP)

description:
Library name: MDA-MB-231 OICR-9429 R2, ChIP
IP_OICR-rep3" is the column name in "count231.txt


title: WT 11DPA rep1

description: Library name: W.11.R1


title: siNC treated cells, Rep2

description:
Library name: MS22_02
Column in processed file:MS22_02

value: Kidney

value: Flp-In ZeoR


title: MDA-MB-231, OICR-9429, biol rep1, H3K4me2 (ChIP)

description:
Library name: MDA-MB-231 OICR-9429 R1, ChIP
IP_OICR-rep2" is the column name in "count231.txt


title: Sucralose + Anti-PD1 alone tumor gene expression

city: Pittsburgh

first: Drew

middle: Nicholas

last: Wilfahrt

address: 5535 Kamin Street

institute: University of Pittsburgh

description: Library name: sucralose + anti-PD1 treated mice, tumor, day 14, gene expression

data_processing:
Bulk RNA-Seq: All data were analyzed using Partek Flow build version 11.0.24.0226
Unaligned reads were aligned to genome using STAR
Raw Gene count values were calculated using "Quantify to annotation model (Partek E/M)"
Features where filtered to exclude features where the maximum among all samples is <= 1.0
Gene counts were normalized to Median Ratio
Differential expression analysis determined using DESeq2 with cutoffs of 2 fold and p value<0.05
Assembly: mm10
Supplementary files format and content: csv file contains Reads per kilo base of transcript per million mapped reads (RPKM)
Single-Cell RNA-Seq
Cell Ranger-7.0.0 was used to process the raw reads. . Subsequent data processing, filtering, clustering and reduced dimensionality projections were all carried out using Seurat package version 4.4.0(80) in R 4.3.0. Both the dLN and tumor data were processed using the same pipeline. Processing of the data sets involved the filtering of cells with fewer than 100 genes expressed and cells with % of mitochondrial genes greater than 20%. Genes were also filtered based on the percentage of cells in which they were expressed. Finally, doublets and negatives, as identified by the Seurat function HTODemux, were taken out of the data set. Overall, for subsequent analyses, we used 34954 dLN cells and 41850 tumor cells.
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: csv file contains Reads per kilo base of transcript per million mapped reads (RPKM),
Supplementary files format and content: single cell sequencing outputs are submitted as the cellranger output files.

source_name: tumor

growth_protocol: To expand OT-I mouse CD8+ T cells in vitro, bulk splenocytes were plated in the presence of the T cells’ cognate peptide (250ng/mL SIINFEKL) at a concentration of 1e7 cells/mL in RPMI supplemented with 10% FBS (v/v) and 50U/mL mouse IL-2 at 37°C with 5% CO2 for 24 hours. After 24 hours, cells were washed with fresh RPMI and plated at a concentration of 1e6/mL with 50ug/mL IL-2. Cultures were fed daily and kept at this concentration for the duration of expansion.

extract_protocol: Bulk RNA-Seq: RNEasy Plus Mini Kit, Illumin Stranded mRNA prep Single Cell RNA-Seq: cell suspensions were labeled with TotalSeq-C hastags as supplied by the University of Pittsburgh Sequencing Core as explained in the protocol provided by 10X genomics.

treatment_protocol:
For Bulk RNA-Seq: Sucralose was added to the fresh culture media daily at a final concentration of 0.22g/L for indicated timepoints. For "Sucralose Whole Time", cells were grown in RPMI supplemented with sucralose for the entire 7 days of culture; for "Sucralose During Activation", cells were cultured in RPMI supplemented with sucralose for the first 24 hours of culture, and then cultured in control RPMI for the remaining 6 days; For "Sucralose during expansion", cells were cultured in control RPMI during the initial 24 hours of activation, and then cultured in RPMI supplemented with sucralose for the final 6 days of culture.
For scRNA-Seq: C57BL/6 mice from Taconic consumed sucralose in the drinking water (0.09mg/mL) for 2 weeks prior to tumor injection and for the duration of the experiment. Mice were injected with 2.5x105 MC38 cells subcutaneously and treated with 200µg anti-PD1 on days 9, and 12. CD45+ cells were isolated from the tumor and tumor draining lymph node (dLN) prior to single-cell RNA sequencing on day 14 post tumor injection.

value: tumor

value: Bulk Tumor

value: C57/Bl6 wild type

value: sucralose + anti-PD1


title: MDA-MB-231, OICR-9429, biol rep3 (INPUT)

description: Library name: MDA-MB-231 OICR-9429 R3, INPUT


title: Sucralose + Anti-PD1 alone tumor TCR

description: Library name: sucralose + anti-PD1 treated mice, tumor, day 14, TCR sequencing


title: MDA-MB-231, OICR-9429, biol rep2 (INPUT)

description: Library name: MDA-MB-231 OICR-9429 R2, INPUT


title: Sucralose + Anti-PD1 alone tumor feature barcode

description: Library name: sucralose + anti-PD1 treated mice, tumor, day 14, feature barcodes


title: anti-PD-1 alone tumor TCR

description: Library name: anti-PD1 treated mouse, tumor, day 14, TCR sequencing


title: MDA-MB-231, DMSO, biol rep2, H3K4me2 (ChIP)

description:
Library name: MDA-MB-231 DMSO R2, ChIP
IP_DMSO-rep3" is the column name in "count231.txt

value: DMSO


title: anti-PD-1 alone tumor gene expression

description: Library name: anti-PD1 treated mouse, tumor, day 14, gene expression


title: BAL, Healthy Volunteer 11

city: Chicago

first: Alexander

last: Misharin

address: 303 E Superior St

institute: Northwestern University

description: Library name: HV_11

data_processing:
Data were processed using Cell Ranger 3.1.0 (10x Genomics), reads were mapped to GRCh38.84 reference genome (10x Genomics Cell Ranger Human 1.2.0 GRCh38 reference). Data were processed using Scanpy 1.7.2, and multisample integration was performed with scvi-tools 0.14.0. The scVI models was constructed on 1000 HVGs with the hyperparameters n_layers = 2, dropout_rate = 0.2, and n_latent = 10, and were trained using the settings max_epochs = 400, check_val_every_n_epoch = 2, and early_stopping = True. Default hyperparameters and settings were used otherwise.
Assembly: GRCh38.84
Supplementary files format and content: gene expression count matrices

source_name: BAL

extract_protocol:
Bronchoscopic BAL was performed in patients and healthy volunteers in the bronchoscopy suite at Northwestern Memorial Hospital or Yale New Haven Hospital. Patients or healthy volunteers were given sedation and topical anesthesia at the discretion of the physician performing the bronchoscopy. Lavage was directed to lobes with higher GGO and fibrosis scores; 90–120 ml of saline was instilled into the segment of interest and aspirated back, with the first 5 ml of return discarded. BALF collected at Northwestern was processed fresh within 2 hours after collection. BALF samples collected at Yale were filtered through a 70-μm cell strainer, and mixed with HypoThermosol solution (Biolife Solutions, cat #101104) at 1:1 ratio and shipped overnight for further processing on wet ice to Northwestern University. BALF samples were processed using either “no FACS” or “FACS” protocol. BALF sample processing for scRNA-seq using “no FACS” protocol: BALF samples were filtered through a 70-μm cell strainer, pelleted by centrifugation at 400 rcf for 10 min at 4°C, followed by hypotonic erythrocyte lysis using 1 ml of PharmLyse solution (BD) for 2 min, followed by another wash with 10 ml of 0.5% BSA in PBS and centrifugation. Cell pellet was resuspended in 0.5% BSA in PBS at the final concentration ~1000 cells/ul. Cell concentration and viability were determined using K2 Cellometer (Nexcelom) with AO/PI reagent and cells were loaded on 10x Genomics Chip A with Chromium Single Cell 3′ V2 gel beads and reagents (10x Genomics) aiming to capture 5,000–7,000 cells per library. Libraries were prepared according to the manufacturer’s protocol (10x Genomics, CG000052_RevB). BALF sample processing for scRNA-seq using “FACS” protocol: BAL fluid samples were filtered through a 70-μm cell strainer, pelleted by centrifugation at 400 relative centrifugal force (rcf) for 10 min at 4 °C, followed by hypotonic lysis of red blood cells with 2 ml of PharmLyse (BD Biosciences) reagent for 2 min. Lysis was stopped by adding 13 ml of MACS buffer (Miltenyi Biotech). Cells were pelleted again and resuspended in 100 μl of a 1:10 dilution of Human TruStain FcX (BioLegend) in MACS buffer and a 10-μl aliquot was taken for counting using a K2 Cellometer (Nexcelom) with Acridine Orange (AO)/Propidium Iodide (PI) reagent. The cell suspension volume was adjusted so the concentration of cells was always <5 × 107 cells ml−1 and the fluorophore-conjugated antibody cocktail was added in a 1:1 ratio. A full list of antibodies can be found in the methods section of the respective publication. After incubation at 4 °C for 30 min, cells were washed with 5 ml of MACS buffer, pelleted by centrifugation and resuspended in 500 μl of MACS buffer with 2 μl of SYTOX Green viability dye (Thermo Fisher Scientific). Cells were sorted on a FACS Aria III SORP instrument using a 100-μm nozzle. Cells were sorted into 300 μl of 2% bovine serum albumin (BSA) in Dulbecco’s phosphate-buffered saline (DPBS) and immediately after sorting pelleted by centrifugation at 400 rcf for 5 min at 4 °C, resuspended in 0.5 BSA in DPBS to ~1,000 cells μl−1 concentration. Concentration was confirmed using a K2 Cellometer (Nexcelom) with AO/PI reagent using the ‘Immune cells low RBC’ program with default settings and cells were immediately used for scRNA-seq.
Libraries were prepared with 10x Genomics 3' V3 gene expression (GEX) reagents according to the manufacturer protocol (CG000331_RevA).

value: BAL

tag: age

tag: Sex

value: female

tag: protocol

value: no FACS

tag: condition


title: Sucralose + Anti-PD1 alone lymph node TCR

description: Library name: sucralose + anti-PD1 treated mice, lymph node, day 14, TCR sequencing

source_name: tumor-draining lymph node

value: tumor-draining lymph node

value: Bulk LN


title: WT 21DPA rep2

description: Library name: W.21.R2

value: Seed Endosperm


title: anti-PD-1 alone tumor feature barcode

description: Library name: anti-PD1 treated mouse, tumor, day 14, feature barcodes


title: MDA-MB-231, DMSO, biol rep3 (INPUT)

description: Library name: MDA-MB-231 DMSO R3, INPUT


title: MDA-MB-231, DMSO, biol rep3, H3K4me2 (ChIP)

description:
Library name: MDA-MB-231 DMSO R3, ChIP
IP_DMSO-rep4" is the column name in "count231.txt


title: MDA-MB-231, DMSO, biol rep2 (INPUT)

description: Library name: MDA-MB-231 DMSO R2, INPUT


title: Sucralose + Anti-PD1 alone lymph node feature barcode

description: Library name: sucralose + anti-PD1 treated mice, lymph node, day 14, feature barcodes


title: MDA-MB-231, DMSO, biol rep1, H3K4me2 (ChIP)

description:
Library name: MDA-MB-231 DMSO R1, ChIP
IP_DMSO-rep2" is the column name in "count231.txt


title: Sucralose + Anti-PD1 alone lymph node gene expression

description: Library name: sucralose + anti-PD1 treated mice, lymph node, day 14, gene expression


title: MDA-MB-231, DMSO, biol rep1 (INPUT)

description: Library name: MDA-MB-231 DMSO R1, INPUT


title: anti-PD-1 alone lymph node gene expression

description: Library name: anti-PD1 treated mouse, lymph node, day 14, gene expression


title: IMR90 cells treated with exosomes from mutant MEF cells #2

city: Tsukuba

first: Motohiro

last: Sekiya

address: 1-1-1 Tennodai

institute: University of Tsukuba

data_processing:
The quality of the raw paired-end reads was assessed with FastQC (ver 0.11.7). After trimming, the reads were aligned to the GRCh38 human reference genome using HISAT2 (ver 2.1.0). Sam files were converted into bam files with Samtools (ver 1.9) and the bam files were used to estimate the abundance of uniquely mapped reads with featureCounts (ver 1.6.3). The raw read counts were normalized with transcripts per million (TPM) and clustered with Wald method based on Eucidean distances of the normalized counts using stats (ver 3.6.1) and gplots (ver 3.0.1.1) R packages
Assembly: GRCh38
Supplementary files format and content: BigWig

source_name: IMR90 fibroblast cell

growth_protocol: IMR90 fibroblast cells were maintained in Eagle’s minimum essential medium (Sigma) supplemented with 1% MEM non-essential amino acids (Sigma), 100 U/ml penicillin, 100 μg/ml streptomycin sulfate and 10% fetal bovine serum (FBS)

extract_protocol:
MEF cells were cultured in DMEM 10% exosome-depleted FBS. Exosomes were isolated with a kit (total exosome isolation kit, Thermo). Exosomes were dissolved in PBS and the protein concentrations were determined with a BCA assay. After treatment of cells, total RNA was isolated using Sepazol Reagent (Nacalai) .
The sequencing library was constructed with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and sequencing was performed using NovaSeq 6000 (Illumina). The following procedures such as quality check of the raw paired-end reads, trimming, and alignment to the mm10 mouse reference genome were performed

treatment_protocol: Cells were treated with DMEM 10% exosome depleted serum with 200 microg/ml of exosomes from either wild-type MEF cells or mutant MEF cells for 1.5 days

value: IMR90 fibroblast cell

value: exosomes from mutant MEF cells


title: IMR90 cells treated with exosomes from mutant MEF cells #3


title: anti-PD-1 alone lymph node TCR

description: Library name: anti-PD1 treated mouse, lymph node, day 14, TCR sequencing


title: IMR90 cells treated with exosomes from mutant MEF cells #4


title: anti-PD-1 alone lymph node feature barcode

description: Library name: anti-PD1 treated mouse, lymph node, day 14, feature barcodes


title: IMR90 cells treated with exosomes from mutant MEF cells #1


title: IMR90 cells treated with exosomes from wild-type MEF cells #4

value: exosomes from wild-type MEF cells


title: DEX_hTh17_rep4

city: Kyoto

first: Koichi

last: Ikuta

state: Kyoto

address: 53 Shogoin-Kawaharamacho, Sakyo-ku

department: Department of Virus Research

institute: Institute for Frontier Life and Medical Sciences, Kyoto University

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNA sequencing reads were trimmed using Trimmomatic (version 0.33) to remove poor quality reads.
Read data was then aligned to the mouse genome (mm10) with Hisat2 (version 2.1.0)
The aligned reads were used for the transcript quantification by using featureCounts from the subread package (version 1.6.5)
Assembly: hg38
Supplementary files format and content: Csv file includes raw counts for each sample.

source_name: peripheral blood

growth_protocol: CD4 T cells isolated from human PBMC were cultured with 5 ug/ml plate-bound anti-CD3 antibody and 5 ug/ml plate-bound anti-CD28 antibody in the presence of IL-6 (20 ng/ml), TGF-b (2 ng/ml), IL-23 (30 ng/ml), and anti-IL-4 antibody (5 ng/ml) for seven days.  CD4 T cells were also stimulated with or without dexamethasone. After culture, After culture, 10000 small intestinal Th17 cells (TCRb+CD4+CCR6+)  were sorted by BD Aria II.

extract_protocol:
Sorted cells were lasated by Buffer RLT (QIAGEN).
Then total RNA was harvested using Agencourt AMPure XP (Beckman Coulter) size selection beads. Takara SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Cat#634890) was used with all extracted RNA for cDNA library.  Illumina Nextera XT DNA Library Preparation Kit (Cat#FC-131-1024) and Nextera XT Index Kit (Cat#FC-131-1001) were used with 1 ng of cDNA for the construction of sequencing libraries.

value: peripheral blood

value: CCR6+CD4+TCRb+ human T cells

value: human Th17 cells

value: healthy donors

value: dexamethasone


title: MDA-MB-231, OICR-9429, biol rep1 (INPUT)

description: Library name: MDA-MB-231 OICR-9429 R1, INPUT

value: Triple Negative Breast Cancer


title: DEX_hTh17_rep3


title: C-DRG

city: wuhan

first: Jian

last: Jiang

address: jiefang avenue

institute: hospital

description: Library name: sample1

data_processing:
All libraries were sequenced using the Illumina NovaSeq platform. The raw sequencing reads were processed by Cell Ranger (v.2.1.0) with the default parameter. The reference genome was mm10.
Assembly: mouse mm10
Supplementary files format and content: Helicobacter pylori ASM2599845v1
Supplementary files format and content: Tab-separated values files and matrix files

source_name: DRG

extract_protocol:
Freshly dissected C3-C5 DRG was first homogenized in cold calcium and magnesium-free Hanks’ balanced salt solution. DRGs were digested with Collagenase A (0.2mg/ml) and Dispase ®II (1.5mg/ml) in the oxygenated DMEM for 120 min at 37 °C. After filtering through a cell strainer (70 μm), the cell homogenate was mixed with 10% Percoll (Cytiva, #17089101) for myelin removal and enrichment.
The cellular suspensions were further processed with Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v2 (PN- 120237) or v3 (PN-1000094) according to the manufacturer’s instructions to construct the scRNA-seq library.

value: DRG

value: control


title: I -DRG

description: Library name: sample2

value: IMQ for 5days


title: IMR90 cells treated with exosomes from wild-type MEF cells #2


title: DEX_hTh17_rep2


title: IMR90 cells treated with exosomes from wild-type MEF cells #1


title: DEX_hTh17_rep1


title: IMR90 cells treated with exosomes from wild-type MEF cells #3


title: 274_G2

data_processing:
Raw reads mapped with bowtie2 using --sensitive-local parmeter
Bigwigs were computed using bamCoverage from deeptools with parameters  --normalizeUsing CPM --scaleFactor 100 --binSize 50000 --smoothLength 250000
Assembly: hg19
Supplementary files format and content: Bigwigs files containing normliazed counts (CPM)

growth_protocol: HEK293T were grown in DMEM supplemented with FCS and PSG

extract_protocol:
According to protocol from Zhao et al ., 2020
BrdU-Seq (NEBNext UltraII DNA Library Prep for Illumina)
NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, cat. no. E7370)

treatment_protocol: No

value: Fibroblast

value: D™ Purified Mouse Anti-BrdU Ref :347580


title: Control_hTh17_rep4


title: T2DM_HUMAN

city: 杭州

first: XING

last: JI

state: State

address: 余杭塘路866号

institute: zhejiang university

description: 10x Genomics

data_processing:
Library sequencing was carried out on an Illumina NovaSeq PE150 platform
Aligned reads and gene-barcode matrices were generated from FASTQ files, which included Read 1, Read 2, and the i7 index, using the Cell Ranger software package (version 3.0) with default parameters.
Assembly: mm10/hg38
Supplementary files format and content: barcodes.tsv.gz files contain unique identifiers for each cell, which are typically used to track and identify individual cells.
Supplementary files format and content: features.tsv.gz files contain unique identifiers for genes, such as gene names or gene IDs, that correspond to the columns in the count matrix.
Supplementary files format and content: matrix.mtx.gz files contain matrixs where the rows represent genes, the columns represent cells, and the values in the cells indicate the expression level of a specific gene in a specific cell.

source_name: periosteum

extract_protocol:
murine tibias and femurs were digested in alpha Minimum Essential Media (αMEM) with 3 mg/ml collagenase and 4 mg/ml dispase
Human periosteum samples were prepared from surgical discard specimens obtained from patient with T2DM undergoing surgery
A single-cell library was created using the Chromium Single Cell 3' Library Kit v3 (10x Genomics)

value: periosteum


title: Control_hTh17_rep3


title: Control_hTh17_rep1


title: 274_S2


title: 274_S1


title: 274_G1


title: Control_hTh17_rep2


title: WT_S2


title: WT_S1


title: WT_G1


title: A_8_tumor_INPUT

city: Guangzhou

last: Zhen

address: 651 Dongfeng East Road

department: State Key Laboratory of Oncology in South China

institute: Sun Yat-sen University Cancer Center

description: Input sample of MeRIP-seq

data_processing:
Reads were first mapped to the human reference genome (GRCh38) by BWA (v0.7.15) and the annotation file obtained from the GENCODE database (https://www.gencodegenes.org/). Circm6A was applied to detect the circRNAs and their m6A modifications from all our PDAC tissue and normal tissue samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read count files of circRNAs for each sample

source_name: pancreas tissue

extract_protocol:
Total RNA from pancreatic cancer 8 tumor tissue samples were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
Total RNA from  tissue samples of PDAC patients were digested with DNase I and then subjected to two rounds of treatment with RiboMinus (Illumina) to reduce rRNA content.
A total amount of 1.5 μg RNA sample was used as Input. We next used Magna MeRIP m6A Kit (Millipore) for m6A immunoprecipitation (m6A-IP). Briefly, 20 μg of Ribo-off RNA was sheared to about 100 nucleotides in length by metal-ion-induced fragmentation and then purified and incubated with 10 μg anti-m6A antibody (Synaptic Systems, 202003) conjugated beads in 500 μl 1 × immunoprecipitation buffer supplemented with RNase inhibitors at 4 °C overnight. The m6A modified RNA was eluted from the beads with N6-methyladenosine (Sigma-Aldrich) and then purified and resuspended in RNase free H2O. The m6A modified RNA was recovered by treatment with proteinase K, acidic phenol/chloroform extraction and ethanol precipitation. Sequencing libraries for m6A-IP and Input were prepared and sequenced using Illumina HiSeq2500 SE50 and Illumina HiSeqX Ten PE150, respectively.

value: tumor

tag: disease

value: pancreatic cancer