title: IECs_Input

data_processing:
ChIP-seq reads were aligned to the mm10 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control
Assembly: GRCm38
Supplementary files format and content: bigwig files were generated using Deeptools(3.5.0)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: IEC

value: epithelial cell

tag: chip antibody


title: Clam SC135P-0946

status: Public on Feb 26 2025

type: genomic

city: Stony Brook

first: Denis

last: Grouzdev

address: 100 Nicolls Rd

country: USA

institute: Stony Brook University

description: SC Phase II

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: Genotyping was performed at Neogen (Lincoln, Nebraska) on the Axiom 384HT arrays (Axiom HD Array [60K] Clam) following protocols outlined in the Axiom Assay 384HT Array Format Automated Workflow User Guide.

data_processing:
The raw genotyping data in CEL format was downloaded from the CAT website after the service and genotype annotation was analyzed using the Axiom software (v 5.4, Thermo Fisher) following the Best Practices Workflow with recommended threshold settings (DishQC ≥ 0.82, QC call rate ≥ 97%).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

molecule: genomic DNA

organism: Mercenaria mercenaria

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Adults M. mercenaria (12-14 months old) were collected from three farms in Cedar Key, Florida with one whole bag from each farm (1000-1200 clams). The clam seeds of each farm were originally sourced from different hatcheries. After purchase, the quahogs from each bag were cleaned at the farms using fresh water to remove sediment before being transported to the laboratory in a cooler (1 hr driving). After arriving at the laboratory, all quahogs were maintained in an indoor recirculating artificial seawater system equipped with a bead filter (Endurance 4000, Aquaculture Systems Technologies, Baton Rouge, LA) at 24 ± 0.55°C, 25 ppt salinity, and pH = 8.35. Quahogs were fed daily with a combination of microalgae, including Tetraselmis spp., Isochrysis spp., and Chaetoceros spp., at 50,000 cells/ml supplemented with commercial algal paste (Instant algae, Reed Mariculture, San Jose, CA, USA). System water quality was checked daily using a saltwater combination kit (AQ-4, Lamotte, Maryland, USA) for ammonia (< 0.01 mg/L), nitrite (< 0.01 mg/L), and nitrate levels (< 10 mg/L).

extract_protocol: The quahogs that died earliest (n = 330) were categorized as “dead” under the dichotomous phenotype, and the quahogs that died latest (n = 144) and survivors (n =231) were considered as “survived”. Genotyping of samples was performed on the previously described SNP microarray chip (Grouzdev et al., 2024). Fixed samples were shipped to the Center for Aquaculture Technologies (CAT, https://aquatechcenter.com, San Diego, CA) for this service. The total genomic DNA was extracted from sample sources (adductor muscle or hemocytes) using a magnetic bead-based extraction protocol. Briefly, fixed tissues (~10-15 mg) were subsampled and processed using mag-bind blood and tissue DNA kits (Omega BioTek, Norcross, GA) according to the manufacturer’s guidelines. Automated processing and liquid handling steps associated with the extraction protocol were performed using PurePrep 96 units (Molgen, San Diego, CA) according to kit and instrument-specific guidelines. Extracted gDNAs were assessed for yields and quality by spectrophotometry (Nanodrop, ThermoFisher) and 2% agarose gels targeting a minimum of 35 µl at >20 ng/µl of largely intact DNA (minimum 5KB).

treatment_protocol: The heat shock challenge was applied by increasing water temperature at 1°C per day from 24°C to a final temperature of 35°C using a heat pump with a temperature controller (Model No. DC24S, Aqualogic, San Diego, CA, USA). When the total dead quahog numbers reached about 50% of the total initial clam number, the temperature decreased from 35°C to 27°C within 24 hr and gradually to 24°C within another 24 hr. For easy reading, the heat challenge was separated into three phases (Figure 1): Phase I (13 days) – temperature increased from 24°C to 35°C and stayed at 35°C; Phase II (9 days) – temperature decreased from 35°C to 24°C with more clams died, and Phase III – temperature was maintained at 24°C and no quahog mortality was found in two days. Two HOBO pendant temperature loggers (UA-001–64, Onset, MA, USA) were submerged in the tank to record the temperature changes. No feeding was conducted after the temperature reached 28°C, and water quality was monitored twice a day.

tag: tissue

value: Adductor muscle


title: hiPSC_NPCs_rep1

type: SRA

city: Kyoto

first: Kenji

last: Osafune

address: Shogoin-Kawahara-cho 53

department: Center for iPS Cell Research and Application (CiRA)

country: Japan

institute: Kyoto University

library_source: transcriptomic

data_processing:
Raw reads were trimmed and quality-filtered using Trim Galore! (version 0.4.4), Trimmomatic (version 0.36), and cutadapt (version 1.16).
Trimmed reads were mapped to the human GRCh38 genome using STAR (version 2.7.2b).
Read counts on annotated genes were quantified using featureCounts (version 1.6.1), and FPKM values were calculated by normalizing to total counts and transcript length.
Differential expression and Gene Ontology (GO) enrichment analysis were performed using iDEP (version 0.96).
Assembly: GRCh38.p13 (hg38)
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was extracted from hiPSC-NPCs and hiPSC-FS-NPCs using the RNeasy Mini Kit (Qiagen), and the quality of the RNA was assessed using a Bioanalyzer (Agilent) to ensure that the RNA integrity number (RIN) was above 7.0.
After poly(A)+ enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs), double-stranded cDNA libraries were prepared using the SMARTer Stranded Total RNA Sample Prep Kit-HI Mammalian (Clontech).

tag: cell line

tag: cell type

value: Induced pluripotent stem cells

tag: genotype

value: wild type

tag: treatment

value: differentiation into nephron progenitor cells


title: U-2OS Clone#12 cells, G1 DOX REP1

city: Munich

first: Stephan

last: Hamperl

state: Bayern

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz-Zentrum Munich

library_source: genomic

data_processing:
Paired-end reads were trimmed using trim_galore (version 0.6.10) (Krueger et al., 2023) with the parameter --quality 28
Reads were mapped to the genome using bowtie2 (version 2.5.1) with the parameters --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --dovetail -I 10 -X 700
Aligned reads were filtered by samtools (version 1.17) with the parameter -q 12
Duplicated reads were removed using picard MarkDuplicates (version 3.0.0) with the parameter -REMOVE_DUPLICATES TRUE
Genome coverages were created using deeptools bamCoverage (version 3.5.2) (Ramírez et al., 2016) with parameters --blackListFileName hg38-blacklist.v2.bed --ignoreForNormalization MT --binSize 20 --smoothLength 60 –extendReads --maxFragmentLength 700 --normalizeUsing "CPM"
Assembly: hg38
Supplementary files format and content: bigWig with normalized BrdU-seq coverage
Library strategy: BrdU-IP-seq

source_name: U-2OS Clone#12

growth_protocol: U-2OS Clone#12 cells were grown in DMEM (GIBCO) containing 10% FBS, 2mM L-glutamine, and penicillin/streptomycin, in a 5% CO2 environment at 37°C

extract_protocol:
Genomic DNA was isolated by phenol-chloroform extraction. 20 µg/sample of DNA were sonicated on a Covaris E220 focused sonicator for 10 min.
Libraries were constructed using NEBNext Ultra II DNA Library Kit with Purification Beads (E7103S, E7103L) and NEBNext Multiplex Oligos for Illumina (E6440S) according to manufacturer's instructions

treatment_protocol: U-2OS Clone#12 cells were synchronized by double thymidine block. Cells were released into S-phase by replacing thymidine containing medium by fresh culturing medium or kept in thymidine containing medium for G1 conditions. Simultaneous to S-phase release  0 or 1 µg/mL Doxycycline was added.

value: U-2OS Clone#12

value: U-2OS Tet-ON

tag: antibody

value: BrdU (BD Biosciences #347580)


title: Clam SC134D-0798

description: SC Phase I


title: Clam SC140D-0736

description: SC Phase I


title: Clam SC133D-0791

description: SC Phase I


title: 618_H2122-SMARCA4KO-CON-4,rep4

city: HOUSTON

first: Yonathan

last: Lissanu

state: TEXAS

address: 1515 Holcombe Blvd

department: Cardiovascular and Thoracic Surgery

institute: md anderson cancer centre

data_processing:
Raw sequencing reads were aligned to human reference genome hg38 and transcriptome gene annotation GENCODE V44 using TopHat2 v2.1.1. HTseq-count v0.11.0 was used to count the expression level of each gene.
Assembly: hg38
Supplementary files format and content: Text file containing gene expression

source_name: xenograft

growth_protocol: The cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin–streptomycin at 37 °C with 5% CO2.

extract_protocol:
Total RNA was isolated from cells using the RNAeasy Mini kit (Qiagen) followed by purification using the RNeasy Mini Kit according to manufacturer’s instructions.
Libraries were constructed using the NEBNext Ultra II DNA Library prep kit according to manufacturer’s instructions

value: xenograft

value: Lung cancer

value: SMARCA4 KO

value: vehicle


title: Clam SC132D-0771

description: SC Phase I


title: U-2OS Clone#12 cells, G1 REP2


title: U-2OS Clone#12 cells, 2h REP2


title: HFD-Saline-4

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
10X Chromium 3′ v3.1
Universal Mix v1.0 - 195 ADT Panel

library_source: transcriptomic single cell

data_processing:
Resulting FASTQ files processed using the Cell Ranger V7.0.1 workflow to the mm10-2.1.0 genome to obtain filtered_matrix sparse matrix files for further analysis in the software AltAnalyze version 2.1.4.  To identify cell populations from combined sample sets for each separate tissue, an unsupervised analysis was performed with the software ICGS2 in AltAnalyze.
Assembly: Mm10
Supplementary files format and content: .h5 Cell Ranger filtered sparse matrix files

organism: Mus musculus

source_name: Lung

extract_protocol:
Single cell RNA-sequencing of lung and eWAT immune cells was performed on CD45+ immune cells using FACS. Sorted cells from two independent biological replicates were pooled and assessed for viability with a live dead stain (Zombie - UV).
Approximately 10,000 cells were loaded into separate ports of a 10X Genomics Chromium 3′ version 3.1 kit. Emulsion, Gel Bead-In Emulsions (GEM) collection, clean-up and cDNA amplification were performed according to 10x Genomics protocols. Library preparation was performed according to manufacturer instructions.
The 10x Genomics libraries were sequenced on Illumina S4 flow cells with PE150 +10 +10 setting (Illumina).  BCL files were demultiplexed into FASTQ files for CellRanger input.

value: Lung

value: Immune

value: WT

value: Saline-High Fat Diet


title: HINI-EWAT-CD45pos

description:
10X Chromium 3′ v3.1
Epididymal White Adipose CD45 positive immune cells with infection

source_name: Epididymal White Adipose

value: Epididymal White Adipose

value: Chow


title: 615_H2122-SMARCA4KO-CON-3,rep3


title: U-2OS Clone#12 cells, G1 REP1


title: 614_H2122-SMARCA4KO-CON-2,rep2


title: HFD-Saline-3


title: Clam SC131D-0734

description: SC Phase I

value: Adductor muscle


title: hiPSC_NPCs_rep3

value: Induced pluripotent stem cells


title: HFD-Flu-8

description:
10X Chromium 3′ v3.1
High fat diet mice with flu infection


title: HIO-20-Macs-ETYA-LPS_S89

city: Ramat Gan

first: Tzipi

last: Braun

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center at Tel Hashomer

data_processing:
Reads were quantified by kallisto version 42.5, using Gencode v24 as the reference genome
Assembly: Gencode v24
Supplementary files format and content: tab-delimited text files include estimates counts values for each Sample

molecule: polyA RNA

source_name: iPSC-derived macrophages

growth_protocol: Macrophages were generated from iPSPC using the STEMdiff™ Hematopoietic Kit (Stemcell Tech) and differentiation protocol

extract_protocol:
Qiagen AllPrep RNA/DNA Mini Kit
TruSeq RNA sample library preparation

treatment_protocol: iPSC-derived macrophages were assayed under basal conditions or following LPS (100 ng/mL for 72 hours) ± ETYA (50 mM for 72 hours) stimulation

value: iPSC-derived macrophages

tag: group

value: Macs-ETYA-LPS


title: Clam SC130D-0746

description: SC Phase I


title: HFD-Flu-7

value: Flu-High Fat Diet


title: Clam SC128D-0711

description: SC Phase I


title: HIO-18-Macs-ETYA_S86

value: Macs-ETYA


title: U-2OS Clone#12 cells, G1 DOX REP2

value: U-2OS Clone#12

value: U-2OS Tet-ON

value: BrdU (BD Biosciences #347580)


title: 601A_H2122PAR-CON-5,rep4

value: xenograft

value: Lung cancer


title: EWAT-CD45pos

description:
10X Chromium 3′ v3.1
Epididymal White Adipose CD45 positive immune cells without infection


title: IECs_NSD2_F_F,ChIP

city: Shanghai

first: Yue

last: Xu

address: 上海市徐汇区华山路

country: China

institute: 上海交通大学

source_name: colon

value: colon

value: IEC

value: epithelial cell


title: 568_H2122PAR-CON-3,rep3

value: WT

value: vehicle


title: Clam SC127D-0797

description: SC Phase I


title: 565_H2122PAR-CON-2,rep2


title: HIO-16-Macs-ETYA_S85


title: Chow-Saline-2

description:
10X Chromium 3′ v3.1
Chow fed mice with Saline injection

value: Lung

value: Immune

value: Saline


title: Clam SC124D-0813

description: SC Phase I

value: Adductor muscle


title: HIO-16-Macs-ETYA_S49

value: iPSC-derived macrophages


title: Chow-Saline-1

value: Saline-Chow


title: Chow-Flu-6

description:
10X Chromium 3′ v3.1
Chow fed mice with Flu infection

value: Flu


title: 604_H2122-SMARCA4KO-CON1,rep1

value: SMARCA4 KO


title: HIO-20-Macs-ETYA-LPS_S53

value: Macs-ETYA-LPS


title: PFOS, S2, scRNAseq

city: Amherst

first: Kruuttika

last: Satbhai

state: MA

address: 637 N. Pleasant St.

department: Environmental Health Science

institute: University of Massachusetts Amherst

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using 10x Cloud Analysis Cell Ranger Pipeline (Version cellranger-v7.0.1)
(https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: Danio_rerio.GRCz11.108.gtf
Supplementary files format and content: Tab separated value files and matrix files

organism: Danio rerio

source_name: whole body cells

extract_protocol:
Whole body cells from zebrafish larvae (72 hpf) were isolated using dispase solution, homogenized, FBS added, solution filtered using 70 µm and 40 µm filters, washed with BSA in PBS
Library was performed according to the manufacturer’s instructions (10x Chromium Single cell 3’ Library Kit v3.1 (dual index)

treatment_protocol: Zebrafish embryos (3 hpf - 72 hpf) were expsoed to DMSO (0.01%) and PFOS (16 µM)

value: whole body cells

tag: strain background

value: AB wildtype background

tag: age

value: 72 hpf


title: Chow-Flu-5

value: Flu-Chow


title: Clam SC120D-0745

description: SC Phase I


title: Clam SC123D-0719

description: SC Phase I


title: HIO-13-ETYA_S47

value: ETYA


title: DMSO, S1, scRNAseq

description: 10x Genomics


title: HIO-13-ETYA_S83


title: Clam SC11D-0769

description: SC Phase I

source_name: Clam SC11D-0769


title: paneth cells, zinc depleted diet, replicate 4

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Reads were subjected to QC with fastqc (v0.12.0)
reads were mapped to the mm39 reference genome using the STAR (v2.7.0a) aligner with the --quantMode GeneCounts option to immediatly obtain counts per genes for each sample
Differential expressed genes were obtained with DESeq2 with standard analysis settings
Assembly: mm39
Supplementary files format and content: A tab delimited text file with raw counts for each sample

source_name: small intestine

extract_protocol:
The small intestine was isolated and a single cell suspension was prepared from the material. Cells were sorted using FACS and paneth cells were collected for RNA isolation. RNA was isolated using an aurum total RNA mini kit accorting to the manufacturers instructions
library preparation was done with the illumina truseq stranded mRNA library kit according to the manufacturers instructions

treatment_protocol: Mice were iven standard chow or zinc depleted chow at libitum for 7 weeks

value: small intestine

value: purified paneth cells

value: zinc depletion


title: HIO-08-Macs-LPS_S81

value: Macs-LPS


title: Clam SC113D-0721

description: SC Phase I


title: Gene expression of Control, ICI, ICI-dexa10 and ICI-dexa200, scRNAseq

city: Taipei City

first: Nai-Wen

last: Chang

address: 2F., No.7, Zhongshan S. Rd., Zhongzheng Dist.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v6.0.0(https://support.10xgenomics.com/)
Assembly: mm10
Supplementary files format and content: Tab-seprated values files and matrix files

source_name: Tumor-infiltrating T cells

extract_protocol:
Subcutaneous Hepa1-6 and orthotopic BNL 1MEA.7R.1 syngeneic HCC models were used. Low-dose (LD; 10 μg) or high-dose (HD; 200 μg) dexamethasone (Dexa) was intraperitoneally administered before each dose of anti-CTLA-4 and anti-PD-1. Tumor shrinkage, T cell priming, cytokine quantitation, as well as cytotoxicity and single-cell RNA-sequencing (scRNA-seq) of tumor-infiltrating T cells were assessed.
Single-cell gene expression library was prepared by the Chromium Next GEM Single Cell 5ʹ Kit v2 (10x Genomics) following the manufacturer’s instructions.

value: Tumor-infiltrating T cells

tag: library type

value: Gene expression


title: feature reference of Control, ICI, ICI-dexa10 and ICI-dexa200, scRNAseq

description: 10x Genomics

value: Feature reference


title: paneth cells, zinc depleted diet, replicate 3


title: HIO-08-Macs-LPS_S45

value: iPSC-derived macrophages


title: paneth cells, zinc depleted diet, replicate 2


title: HIO-18-Macs-ETYA_S50

value: Macs-ETYA


title: P13P5 placebo E13.5

city: Beaverton

first: Lisa

last: Vrooman

state: OR

address: 505 NW 185th Ave.

institute: Oregon Health and Sciences University

data_processing:
Raw reads were aligned to the mouse mm10 reference genome using STAR
Aligned reads with mapping quality score greater than 20 were assigned to genes using featureCounts
Differentially expressed genes were called using DESeq2
Assembly: mm10
Supplementary files format and content: raw read counts

source_name: oocytes

extract_protocol:
RNA was isolated using PicoPure RNA Isolation Kit (Arcturus) according to manufacturer's instructions
Libaries were prepared using SmartSeq Plus (Takara Bio) according to manufacturer's instructions

value: oocytes

value: placebo E13.5


title: Clam SC126D-0790

description: SC Phase I

value: Adductor muscle


title: 561_H2122PAR-CON-1,rep1

value: xenograft

value: Lung cancer

value: WT

value: vehicle


title: Clam SC111S-0988

description: SC Phase III

value: Hemocytes in ethanol


title: HIO-07-Macs-LPS_S80


title: P13P4 placebo E13.5


title: paneth cells, zinc depleted diet, replicate 1

value: small intestine


title: Clam SC110D-0809

description: SC Phase I


title: Clam SC10S-0963

description: SC Phase III

source_name: Clam SC10S-0963


title: HIO-06-Macs_S79

value: Macs


title: P13P3 placebo E13.5


title: P13P2 placebo E13.5


title: paneth cells, standard diet, replicate 4

value: purified paneth cells

value: control


title: paneth cells, standard diet, replicate 3


title: P13P1 placebo E13.5


title: paneth cells, standard diet, replicate 2


title: Clam SC108D-0743

description: SC Phase I


title: Clam SC105S-0987

description: SC Phase III


title: P13A4 placebo E13.5


title: paneth cells, standard diet, replicate 1


title: HIO-04-Macs_S42


title: P13A5 placebo E13.5


title: Clam SC100D-0796

description: SC Phase I


title: paneth cells, zinc supplemented water, replicate 4

treatment_protocol: Mice wre put on Milli-Q or zinc supplemented (25mM ZnSO4) water for 7 days

value: 25 mM ZnSO4


title: P13A3 placebo E13.5


title: P13A2 placebo E13.5


title: paneth cells, zinc supplemented water, replicate 2


title: paneth cells, zinc supplemented water, replicate 3


title: Clam CK95P-0240

description: CK Phase II

source_name: Clam CK95P-0240


title: P13A1 placebo E13.5


title: Clam CK93S-0274

description: CK Phase III

source_name: Clam CK93S-0274


title: niPSCs, on feeder, scRNAseq

city: Minato-ku

first: Hideki

last: Masaki

state: Tokyo

address: 4-6-1 Shirokanedai

department: Institute of Medical Science

institute: University of Tokyo

data_processing:
For bulk RNAseq, reads were trimmed using Fastp to remove sequencing adapters and low quality (<Q22) bases from the 3’ end, reads shorter than 75bp were discarded. Trimmed reads were then aligned to the ENSEMBL Mouse and Chimp references (ENSEMBL_Mus_musculus.GRCm39.109 and ENSEMBL_Pan_troglodytes.Pan_tro_3.0-rel109) using STAR Dobin et al. (2013) version=2.7.9a. The aligned reads were processed by XenofilteR Kluin et al. (2018) version 1.6 to remove suspected mouse related transcripts.
For scRNAseq datasets, raw Illumina data were processed using 10x Genomics Cell Ranger 7.1.0.Cell Ranger mkfastq to demultiplex into cellplex pools (utilising bcl2fastq v2.20.0.422 Illumina). Cellranger multi to demultiplex the cellplex pools align and produce count matrices.
Assembly: Chimpanzee: Pan_tro_3.0-rel109; Mouse:GRCm39.109; Human: GRCh38-2020-A
Supplementary files format and content: For bulk RNAseq samples, tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: For scRNAseq samples, each element of the feature-barcode matrix is the number of UMIs associated with a feature (row) and a barcode (column).

source_name: niPSCs

growth_protocol: Chimpanzee primed or capacitated iPSCs were cultured with AFX medium (N2B27 basal medium supplemented with 20ng/ml Activin-A, 20ng/ml bFGF, and 2-5μM XAV939). Chimp naive iPSCs were cultured with AE6 medium (N2B27 supplemented with 1μM PD032590, 2μM XAV939, 2μM Gö6983, 10ng/ml human LIF, 20 ng/mL Activin-A, 20 ng/mL IL6, and 0.5-1 μM EPZ-6438). Capacitated iPSCs were originated from naïve iPSCs following culture with N2B27 supplemented with 2 μM XAV. For TE induction, naive iPSCs were cultured with N2B27 supplemented with 3μM PD032590 and 3μM A83-01. Human naive ESCs, HNES1, was cultured with PXGL medium (N2B27 supplemented with 1μM PD032590, 2μM XAV939, 2μM Gö6983, 10ng/ml human LIF, 20 ng/mL) on MEF feeder, or with AE6 on feeder-free.

extract_protocol:
For bulk RNAseq, total RNA was extracted from cultures using TRIzol/chloroform, followed by RNA precipitation with isopropanol. Genomic DNA was depleted using TurboDNase and clean-up was performed using Zymogen Clean and Concentrator kit.
For bulk RNAseq, sequencing libraries were prepared using the NEB Next Ultra Library prep kit for Illumina.
For scRNAseq, cells were dissociated and labelled using the 3' CellPlex kit Set A, then multiplexed and single cells were isolated using the Chromium Next Gem Chip G Single Cell kit on the Chromium X.
For scRNAseq, libraries were prepared using the Chromium Next GEM Single Cell 3' v3.1 kit with 3' Feature Barcode Kit.

value: niPSCs

tag: condition

value: on feeder


title: B13P3 bisphenol A E13.5

value: bisphenol A E13.5


title: Clam SC109D-0744

description: SC Phase I


title: paneth cells, zinc supplemented water, replicate 1


title: HIO-04-Macs_S78

value: iPSC-derived macrophages


title: HNES1 cells, feeder-free, scRNAseq

source_name: HNES1 cells

value: HNES1 cells

value: feeder-free


title: Clam CK98D-0069

description: CK Phase I

source_name: Clam CK98D-0069

value: Adductor muscle


title: HIO-07-Macs-LPS_S44

value: Macs-LPS


title: B13P2 bisphenol A E13.5

value: oocytes


title: paneth cells, Milli-Q water, replicate 4

value: Milli-Q water


title: Clam CK91P-0254

description: CK Phase II

source_name: Clam CK91P-0254


title: Clam CK90D-0086

description: CK Phase I

source_name: Clam CK90D-0086


title: HIO-02-Ctrl_S76

value: Ctrl


title: paneth cells, Milli-Q water, replicate 3


title: B13P1 bisphenol A E13.5


title: paneth cells, Milli-Q water, replicate 2


title: niPSCs, feeder-free, scRNAseq


title: hPSC-derived Monocyte/Macrophages, Day 28, scRNA-seq

first: Daniel

middle: O.

last: Kechele

address: 3333 Burnet Ave Location R3.034

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

description: 10x Genomics

data_processing:
Standard 10x Genomics Cell Ranger (v3.0.2) pipeline to generate FASTQ and generate filtered matrices.
Assembly: hg38 for Day 35 HIOs with and without Macrophages and Day 28 Monocyte/Macrophage
Supplementary files format and content: tab seperated value files and matrix files

source_name: hPSC-derived monocyte/macrophages

extract_protocol:
For Day 35 HIOs with and without Macrophages and Day 28 Macrophages: Organoid were washed with cold Cell Recovery solution and minced in HBSS with Mg2+ and Ca2+ 1% BSA. Original supernatants collected and spun down and readded into the sample. HIOs were mechanically and enzymatically digested enzymes from Neural Tissue Dissociation Kit as recommended by Manufacturer's instructions for 45-60 minutes at 37C. Samples were shaken and fluxed through a P1000 then P200 tip every 10 mins. Dissociated cells were washed and filtered through a BSA coated 70um follow 40um cell strainer, centrifuged at 300 RPM for 5 minutes, and resuspended in 2% FBS in HBSS with y-27632 and 1% BSA. Day 28 Macrophages were subjected to the same mechanical and enzymatic manipulations as the dissociated HIOs.
Library was performed according to the manufacter’s instructions (single cell Chromium 3’ v3 GEM protocol, 10x Genomics) loading 12,800 cell for approximately 8,000 captured cells. Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: hPSC-derived monocyte/macrophages

value: WA01 hESC

value: hematopoietic

value: 28 days post-hPSC


title: paneth cells, Milli-Q water, replicate 1

value: small intestine

value: purified paneth cells


title: Clam CK88P-0223

description: CK Phase II

source_name: Clam CK88P-0223


title: hPSC-derived HIO w/Macrophages, Day 35, biol rep 2, scRNA-seq

description: 10x Genomics

source_name: hPSC-derived intestinal organoids with added macrophages

value: epithelial, mesenchymal, hematopoietic

value: 35 days post-hPSC


title: B13A2 bisphenol A E13.5

value: bisphenol A E13.5


title: HIO-02-Ctrl_S40

source_name: iPSC-derived macrophages

value: iPSC-derived macrophages


title: hPSC-derived HIO w/Macrophages, Day 35, biol rep 1, scRNA-seq

description: 10x Genomics

value: hPSC-derived intestinal organoids with added macrophages


title: KO 4 Day 8 after C. rodentium infection

city: PARIS

first: Béatrice

last: ROMAGNOLO

address: 24 rue du Fb St Jacques 75014

department: CANCER

country: France

institute: INSERM-Institut Cochin

data_processing:
STAR (v2.7.6a)
STAR --genomeDir /path/to/STAR/reference/directory --sjdbGTFfile /path/to/gtf --runThreadN 20 --readFilesIn /path/to/fastq/R1 /path/to/fastq/R2 --outFileNamePrefix $echantillon --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
RSEM (v1.3.1)
rsem-calculate-expression -p 20 --paired-end --bam --no-bam-output /path/to/AlignedToTranscriptome/file /path/to/rsem-prepare-reference/files [sample-rsem-suffix]
DESeq2_1.38.1
Assembly: Ensembl release 101, GRCm38
Supplementary files format and content: Tabulated files with raw count from RSEM

source_name: Intestine

growth_protocol: Mice were provided ad libitum access to a standard laboratory diet. Tamoxifen injections were administered to mice aged two to three months. Both male and female mice were included in the study, with intraperitoneal injections of 1 mg tamoxifen per day for 5 consecutive days.

extract_protocol:
Distal colon RNA was extracted using Trizol reagent following the manufacturer's protocol for RNA sequencing.
Library preparation and sequencing were conducted by the Genom’IC platform at Institut Cochin. Libraries were prepared using the TruSeq Stranded messenger RNA protocol from Illumina, starting with 800 ng high-quality total RNA (RNA Integrity Number > 8). Paired-end sequencing (2 x 75bp) was performed on an Illumina Nextseq 500 platform, utilizing 20-40 million paired-end reads for subsequent analysis.

treatment_protocol: The C. rodentium strain ICC180 was cultured overnight in Luria-Bertani broth supplemented with kanamycin at 37°C in a shaking incubator. An oral administration of 5.109 colony-forming units (cfu) in 200 µl of PBS was given to each mouse.

value: Intestine

tag: strain

tag: infection

tag: time

value: Day 8


title: Clam CK85P-0227

description: CK Phase II

source_name: Clam CK85P-0227

value: Adductor muscle


title: B13A1 bisphenol A E13.5

value: oocytes


title: WT 4 Day 8 after C. rodentium infection

value: Control


title: HNES1 cells, on feeder, scRNAseq

value: HNES1 cells

value: on feeder


title: WT Unifected

value: No infection

value: Day 0


title: Clam CK81D-0041

description: CK Phase I

source_name: Clam CK81D-0041


title: hPSC-derived HIO, Day 35, biol rep 2, scRNA-seq

description: 10x Genomics

source_name: hPSC-derived intestinal organoids

value: hPSC-derived intestinal organoids

value: WA01 hESC

value: epithelial, mesenchymal


title: Ang_II_tdT

city: Hangzhou

first: Hong

last: Wu

address: 79 Qingchun Road

department: Department of Cardiology

institute: the First Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Data were processed following standard protocols using Cell Ranger version 6.0.0.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting, UMI counting, and to generate feature-barcode matices.
Assembly: mm10
Supplementary files format and content: TSV data for genes and barcodes; MTX data for gene expression matrix

source_name: abdominal aorta

extract_protocol:
Mice were euthanized and perfused with PBS and aortas were harvested and placed in a petri dish containing DMEM with 10% fetal bovine serum (FBS) on ice. Perivascular adipose tissues and connective tissues were carefully removed. After collecting all grafts, to obtain single cell suspensions, arteries were washed with PBS for three times, cut into fine pieces and incubated with 1 mg/ml papain digesting solution [1 mg/ml papain (Sigma, P4762), 0.5 mg/ml 1,4-Dithioerythritol (Sigma, D8255), 0.156 mg/ml Taurine (Sigma, T8691), 0.25 mg/ml bovine serum albumin in PBS]. The digestion was performed at 37 ℃ water bath with reciprocal shaking. Detached cells in the supernatant were collected and suspended in DMEM with 10% FBS. Vascular allografts were then incubated with fresh digestion solutions every 10 min. After 3-4 digestions, the remaining tissues were incubated with 1 mg/ml papain digesting solution and 2 mg/ml collagenase I (Gibco, 17018029) and 1 mg/ml dispase II (Sigma, D4693) in Hank’s balanced salt solution containing calcium and magnesium. Detached cells were collected and fresh digestion solutions were added until the tissues dissolved completely. All digested cells from one sample were pooled together at the end of the digestion process. After sufficient digestion, cells were filtered through a 40-μm cell strainer, and the collected cells were centrifuged 8 min at 500 g speed at 4 ℃. Subsequently, cell pellet was suspended in PBS and stained with LIVE/DEAD ™ Fixable Near-IR Dead Cell Stain Kit, Hoechst 33342, CD45  for 30 mins on ice. After PBS washing, cells were resuspended in PBS and single nucleated live cells (Hoechst+ & Dead Cell Stain- & tdTomato+ ) were sorted into PBS with 0.04% BSA using a Flow Cytometer. Samples were subjected to scRNA-seq. A ChromiumTM Single Cell 3' Reagent Kit v2 or V3 chemistry (10x Genomics) was used and a standard protocol was followed. The library was generated and sequenced on a Novaseq6000 PE150 platform (Illumina) with paired-end 150 bp sequencing strategy.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: abdominal aorta

value: nucleated living  tdTomato+CD45- cells

value: ApoE-deficient

value: 12-16 weeks old

tag: agent


title: hPSC-derived HIO, Day 35, biol rep 1, scRNA-seq

description: 10x Genomics

value: 35 days post-hPSC


title: Clam CK7S-0258

description: CK Phase III

source_name: Clam CK7S-0258

value: Hemocytes in ethanol


title: Clam CK8D-0033

description: CK Phase I

source_name: Clam CK8D-0033


title: PC9_WT_RAD21_rep2

city: New Haven

first: Eric

last: Sun

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale University

description: CUT&RUN Antibody: RAD21

data_processing:
Adapter sequences from paired-end sequencing reads were trimmed with Trimmomatic and quality control was performed using FastQC. Bowtie2 version 2.4.2 was used to align reads to the GRCh37 genome using the –very-sensitive flag and allowing for one mismatch. SAMtools version 1.16 was used to remove unmapped reads, secondary alignment reads, and reads with a Phred score of <30. Macs2 version 2.2.7.1 was used to call peaks with default peak-calling settings. Peaks were called against H2A. IgG peaks were subtracted from BED files using BEDTools v2.30. IDR was used to determine significant peaks between two biological replicates. Deeptools version 3.5.1 was used for data visualization. Plots depicting CUT&RUN signal were generated by using Deeptools bamCompare to normalize signal by CPM and to H2A, and duplicates were ignored. In all plots, the mean normalized bigWig signal between two biological replicates is plotted. Signal is Peak intersections were performed using BEDTools v2.30.
Assembly: GRCh37
Supplementary files format and content: bigWig files are mean files derived from two biological replicates that were derived from Counts Per Million normalization.
Supplementary files format and content: Files with postfix idr.txt were high-confidence, reproducible peaks identified using idr.
Library strategy: CUT&RUN

growth_protocol: Cells were cultured in RPMI-1640 medium (Thermo Fisher, 11875119) with 1% penicillin-streptomycin (pen-strep, Thermo Fisher, 15140122) and 10% fetal bovine serum (FBS).

extract_protocol:
CUT&RUN was performed using the CUTANA ChIC/CUT&RUN Kit (EpiCypher 141048) according to the manufacturer’s instructions. Approximately 5 x 10^5 cells were used per reaction. The following antibodies were used: Histone H2A (12349), PDS5A (Thermo Fisher PA5-57755), RAD21 (Active Motif 91245), H3K27ac (CST 8173) and IgG (EpiCypher 13-0042). One microliter of chromatin was analyzed via Agilent TapeStation to determine fragment size. DNA concentration was measured using Qubit (Invitrogen Q32854).
Library preparation was performed using the CUTANA CUT&RUN Library Prep Kit (EpiCypher 14-1001) using 2.5 ng chromatin as input. Pooled libraries were sequenced by Novogene with NovaSeq with 20 million paired-end reads sequenced per library.

treatment_protocol: Osimertinib-treated cells were treated with osimertinib over the course of 6-8 weeks via dose escalation starting from 100nM Osimertinib.

value: lung adenocarcinoma

value: Wild-type

value: Untreated


title: KO 2 Unifected

value: Intestine


title: KO 3 Unifected


title: B13A3 bisphenol A E13.5

source_name: oocytes

value: oocytes

value: bisphenol A E13.5


title: KO 1 Unifected

value: No infection


title: Bpool, scRNAseq

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

description: 10x Genomics

data_processing:
Raw sequencing data were processed with Cell Ranger (v6.1.2) (PMID: 28091601). Cellranger mkfastq command was used to demultiplex the different samples and cellranger count command was used to generate gene – cell expression matrices. Mouse genome mm10 was used for the alignment and gencode vM25 was used for gene annotation and coordinates (PMID: 33270111).Downstream analysis was performed in R with Seurat (v4.1.0) (PMID: 34062119) and customized R scripts.
Assembly: mm10
Supplementary files format and content: .h5

source_name: Lung

extract_protocol:
Wild type C57Bl/6 mice (10 weeks old) were treated systemically for seven days with bleomycin (100 U/kg) using subcutaneously implanted osmotic minipumps (ALZET 1007D; DURECT Corporation, Cupertino, CA; containing 100 µl, designed to deliver contents at 0.5 µl/h for 7 days). Control mice were treated with saline vehicle. Pumps were removed on day 7 per manufacturer’s instructions. On day 21, mice were sacrificed by isoflurane overdose and the lungs harvested. The rib cage was opened to expose the lungs. Mice were systemically perfused via the left ventricle with PBS. The left lobe was then tied and cut off. Lung tissue was washed in cold DMEM and minced into small pieces using fine surgical scissors. The tissue from each mouse was resuspended in 5 ml of collagenase (1 mg/ml, Roche #10103578001) and shaken at low speed for 45 min at 37°C. Digestion was stopped by addition of 10 ml of DMEM/10% FBS. The sample was passed through a 40 μm cell strainer to prepare a monodisperse cell suspension. Cells were collected by centrifugation (1200 rpm, 10 min, 4°C, Beckman GS-6R centrifuge) and the cell pellets resuspended in 1 ml ACK lysing buffer (LONZA #10-548E) for 5 min to remove red blood cells. Lung cells were then collected by centrifugation, washed with PBS, and collected again. Single-cell suspensions from six control saline-treated mice and six bleomycin-treated mice were each pooled in equal numbers prior to loading onto a 10X Genomics Next GEM Chip B and emulsified with Single Cell 3’ GEM beads using a Chromium™ Controller (10x Genomics).
Library was performed according to the manufacter's instruction.(single cell 3' protocol, 10x Genomics). Cells collected were counted; 50,000 cells from each sample were labeled in 200uL of PDB +1% BSA. Mixed well by repeated gentle pipetting. Incubated on ice for 30mins. Labeled cells washed 2X w/1.5ml PBS +1% BSA(pelleted between washes at 500 tcf x 5 min @RT). After final wash,labeled cells resuspended in ~50uL PBS + 1%BSA and counted. Processing on the 10x Genomics Single-Cell Protocol by the MUSC Translation Science Lab. Libraries were constructed using the Chromium Single Cell 3’ Library Construction Kit (10x Genomics, v3.1) and sequenced at Vanderbilt’s Next Gen Sequencing Core (Illumina NovaSeq 6000).

value: Lung

value: 10 weeks old

value: Wildtype

value: Bleomycin


title: PC9_WT_PDS5A_rep2

description: CUT&RUN Antibody: PDS5A


title: Spool, scRNAseq

description: 10x Genomics

value: Saline


title: Sham_tdT

value: abdominal aorta

value: nucleated living tdTomato+ cells

value: Sham


title: PC9_WT_RAD21_rep1

description: CUT&RUN Antibody: RAD21


title: Clam CK75S-0272

first: Denis

last: Grouzdev

address: 100 Nicolls Rd

institute: Stony Brook University

description: CK Phase III

source_name: Clam CK75S-0272


title: Clam CK74D-0074

description: CK Phase I

source_name: Clam CK74D-0074

value: Adductor muscle


title: WT 2 Unifected

value: Control

value: Day 0


title: Ad-IFNalpha_Treated_Sample_2

city: Houston

first: Ganiraju

last: Manyam

state: TX

institute: UT MD Anderson Cancer Center

description:
MB49-4
Bladder tumor cells from mouse

data_processing:
Sample preparation and sequencing were performed by the MD Anderson Cancer Center Sequencing and Microarray Facility
The raw reads were mapped to the mouse reference genome (mm10) using the cellranger count pipeline
The digital expression matrix was extracted from the filtered_feature_bc_matrix folder outputted by the cellranger count pipeline.
Assembly: mm10
Supplementary files format and content: Transcript-Level Read Count files

source_name: Bladder

extract_protocol:
72h post drug treatment, mice were euthanized, and tumor samples were subjected to single-cell dissociation for cell viabilty assessment and scRNA-seq
Samples were normalized for input onto the Chromium Single Cell Chip B Kit (10x Genomics, Pleasanton, CA), in which single cells were lysed and barcoded for reverse-transcription. The pooled single-stranded, barcoded cDNA was amplified and fragmented.

value: Bladder

value: Bladder Tumor

value: Ad-IFNα treated


title: Clam CK72S-0271

city: Stony Brook

description: CK Phase III

data_processing:
The raw genotyping data in CEL format was downloaded from the CAT website after the service and genotype annotation was analyzed using the Axiom software (v 5.4, Thermo Fisher) following the Best Practices Workflow with recommended threshold settings (DishQC ≥ 0.82, QC call rate ≥ 97%).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: Clam CK72S-0271

extract_protocol: The quahogs that died earliest (n = 330) were categorized as “dead” under the dichotomous phenotype, and the quahogs that died latest (n = 144) and survivors (n =231) were considered as “survived”. Genotyping of samples was performed on the previously described SNP microarray chip (Grouzdev et al., 2024). Fixed samples were shipped to the Center for Aquaculture Technologies (CAT, https://aquatechcenter.com, San Diego, CA) for this service. The total genomic DNA was extracted from sample sources (adductor muscle or hemocytes) using a magnetic bead-based extraction protocol. Briefly, fixed tissues (~10-15 mg) were subsampled and processed using mag-bind blood and tissue DNA kits (Omega BioTek, Norcross, GA) according to the manufacturer’s guidelines. Automated processing and liquid handling steps associated with the extraction protocol were performed using PurePrep 96 units (Molgen, San Diego, CA) according to kit and instrument-specific guidelines. Extracted gDNAs were assessed for yields and quality by spectrophotometry (Nanodrop, ThermoFisher) and 2% agarose gels targeting a minimum of 35 µl at >20 ng/µl of largely intact DNA (minimum 5KB).

value: Hemocytes in ethanol


title: PC9_WT_PDS5A_rep1

description: CUT&RUN Antibody: PDS5A

value: lung adenocarcinoma

value: Wild-type

value: Untreated


title: Clam CK87S-0273

description: CK Phase III

source_name: Clam CK87S-0273


title: WT 1 Unifected

value: Intestine

value: No infection


title: PC9_WT_osi_RAD21_rep2

description: CUT&RUN Antibody: RAD21

value: Osimertinib


title: Clam CK6S-0257

description: CK Phase III

source_name: Clam CK6S-0257


title: Clam CK69D-0067

description: CK Phase I

source_name: Clam CK69D-0067


title: PC9_WT_osi_RAD21_rep1

description: CUT&RUN Antibody: RAD21


title: Ad-Control_Sample_1

description:
MB49-1
Bladder tumor cells from mouse


title: Ad-Control_Sample_2

description:
MB49-2
Bladder tumor cells from mouse


title: Clam CK68S-0270

description: CK Phase III

source_name: Clam CK68S-0270


title: Spleen, B cells, scRNA-seq

city: Beijing

first: Shaonan

last: Wen

address: Beijing 100875, China

institute: Beijing Normal University

description: GEXSCOPE single cell RNA library

data_processing:
The demuliplexing,barcoded processing, gene counting and aggregaion were made using the Cell Ranger soware v6.1.2(https://www.10xgenomics.com/support/software/cell-ranger/downloads) e-expression/software/pipelines/latest/what-is-cell-ranger
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
The CD45+ CD3-CD19 + B220+ B cells were seperated from mouse spleen after the mice were induced by LPS.
Single-cell suspensions (2×10^5 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) (Ref). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: Spleen

value: tissue

value: B cells

value: Wild type

value: The mouse was LPS-treated, B cells were FACS sorted as live CD45+ CD3- CD19+ B220+ cells


title: PC9_WT_osi_PDS5A_rep2

description: CUT&RUN Antibody: PDS5A


title: PC9_WT_osi_PDS5A_rep1

description: CUT&RUN Antibody: PDS5A


title: Clam CK60D-0048

description: CK Phase I

source_name: Clam CK60D-0048

value: Adductor muscle


title: KO 2 Day 8 after C. rodentium infection

source_name: Intestine

value: Day 8


title: Clam CK63P-0234

description: CK Phase II

source_name: Clam CK63P-0234


title: PC9_WT_osi_H3K27Ac_rep2

description: CUT&RUN Antibody: H3K27Ac


title: WT 5 Day 18 after C. rodentium infection

value: Control

value: Day 18


title: Clam CK5D-0015

description: CK Phase I

source_name: Clam CK5D-0015


title: Ad-IFNalpha_Treated_Sample_1

description:
MB49-3
Bladder tumor cells from mouse

value: Bladder

value: Bladder Tumor

value: Ad-IFNα treated


title: Clam CK59P-0253

description: CK Phase II

source_name: Clam CK59P-0253


title: PC9_WT_osi_IgG_rep1

description: CUT&RUN Antibody: IgG

value: lung adenocarcinoma

value: Wild-type

value: IgG


title: mESCs, 0 ng/ml FGF

city: Leiden

first: Max

last: Fernkorn

address: Einsteinweg 55

department: Leiden Academic Centre for Drug Research (LACDR)

institute: University Leiden

data_processing:
Demultiplexing to the individual samples and alignment to the mouse genome mm10 (GENCODE vM23/Ensembl 98, obtained from 10x Genomics) was performed with CellRanger with default settings (version 4.0.0, 10x Genomics).
Assembly: mm10 (GENCODE vM23/Ensembl 98, obtained from 10x Genomics).
Supplementary files format and content: For every demultiplexed sample: matrix.mtx: count matrix of genes and barcodes in Market Exchange Format (MEX); features.tsv: table of corresponding Ensembl IDs (first column) and Gene IDs (second column), corresponding to rows in matrix.mtx; barcodes.tsv: table of cell barcodes, corresponding to columns in matrix.mtx.

growth_protocol: 1.5 * 10^4 Fgf4-mutant cells/cm2 were seeded in 6-well plates in ES + LIF medium.

extract_protocol:
Cells were washed with PBS and detached with trypsin or Accutase. After centrifugation (5 min at 200xg), cells were resuspended in PBS supplemented with 0.5% BSA. Before GEM generation, cells were passed through a cell strainer (FALCON, 35µm mesh). Droplet generation, lysis, mRNA capture was performed following the instructions by 10x genomics (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 with Feature Barcoding technology for CRISPR Screening, CG000205 Rev D).
Generation of the gene expression libraries was performed following the instructions by 10x genomics (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 with Feature Barcoding technology for CRISPR Screening, CG000205 Rev D). We chose 12 PCR cycles for cDNA amplification and 13 cycles for the sample index PCR.
10x Genomics single index single-cell RNA sequencing.

treatment_protocol: 24h of FGF stimulation with 0, 5, or 50ng/mL FGF4 was started in N2B27 medium with 1μg/ml Heparin and Chiron.

value: mESCs

value: 24h N2B27 + Chiron + 0 ng/ml FGF4


title: WT 1 Day 8 after C. rodentium infection

value: Intestine


title: CD44_KO_IRI2

city: Guangzhou

first: Jiewu

last: Huang

address: State Key Laboratory of Organ Failure Research

institute: Nanfang Hospital

data_processing:
Quality control: clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5)
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each samples
Supplementary files format and content: tab-delimited text files includes FPKM for each samples

source_name: kidney

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer.

value: kidney

value: CD44 knockout

value: IRI


title: Clam CK55P-0214

description: CK Phase II

source_name: Clam CK55P-0214


title: PC9_WT_osi_H3K27Ac_rep1

description: CUT&RUN Antibody: H3K27Ac

value: Osimertinib


title: KO 3 Day 8 after C. rodentium infection


title: CD44_KO_IRI3


title: WT 2 Day 8 after C. rodentium infection


title: PC9_WT_osi_IgG_rep2

description: CUT&RUN Antibody: IgG


title: WT 3 Day 8 after C. rodentium infection


title: mESCs, 5 ng/ml FGF

value: 24h N2B27 + Chiron + 5 ng/ml FGF4


title: PC9_WT_osi_H2A_rep2

description: CUT&RUN Antibody: H2A


title: Clam CK54D-0010

description: CK Phase I

source_name: Clam CK54D-0010

value: Adductor muscle


title: KO 1 Day 8 after C. rodentium infection

value: Day 8


title: IRI3

value: WT


title: CD44_KO_IRI1


title: IRI2


title: KO 5 Day 18 after C. rodentium infection

value: KO

value: Day 18


title: Clam CK53P-0226

description: CK Phase II

source_name: Clam CK53P-0226


title: WT 4 Day 18 after C. rodentium infection

value: Control


title: WT 3 Day 18 after C. rodentium infection


title: PC9_WT_H3K27Ac_rep2

description: CUT&RUN Antibody: H3K27Ac

value: lung adenocarcinoma

value: Untreated


title: mESCs, 50 ng/ml FGF

value: 24h N2B27 + Chiron + 50 ng/ml FGF4


title: Clam CK52D-0085

description: CK Phase I

source_name: Clam CK52D-0085


title: KO 4 Day 18 after C. rodentium infection


title: Clam CK50S-0268

description: CK Phase III

source_name: Clam CK50S-0268

value: Hemocytes in ethanol


title: Clam CK4S-0256

description: CK Phase III

source_name: Clam CK4S-0256


title: PC9_WT_IgG_rep2

description: CUT&RUN Antibody: IgG

value: Wild-type

value: IgG


title: IRI1

value: kidney


title: PC9_WT_H3K27Ac_rep1

description: CUT&RUN Antibody: H3K27Ac


title: PC9_WT_osi_H2A_rep1

description: CUT&RUN Antibody: H2A


title: KO 3 Day 18 after C. rodentium infection

value: Intestine


title: Clam CK49S-0267

description: CK Phase III

source_name: Clam CK49S-0267


title: Clam CK47P-0233

description: CK Phase II

source_name: Clam CK47P-0233


title: PC9_WT_IgG_rep1

description: CUT&RUN Antibody: IgG


title: KO 2 Day 18 after C. rodentium infection


title: PC9_WT_H2A_rep2

description: CUT&RUN Antibody: H2A


title: PC9_WT_H2A_rep1

description: CUT&RUN Antibody: H2A


title: Female CPT1a LKO-4 [S22]

city: Lexington

first: Robert

middle: N

last: Helsley

state: KY

address: 741 S. Limestone St.

department: Intern

institute: University of Kentucky

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Novogenes methods
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
Assembly: not provided
Supplementary files format and content: RPKM and total counts for each Sample

source_name: Liver

extract_protocol:
Total RNA was isolated from livers using the Qiagen Rneasy Mini kit. Novogene isolated mRNA from the total RNA provided by the investigators using poly-T oligo-attached magnetic beads.
mRNA libraries were constructed by Novogene using random hexamers and dUTP. The library was complete after end repair, A-tailing, adapter ligation, size selection, amplification, and purification, following Novogenes methods.

value: Liver

tag: Sex

value: Female

value: CPT1a LKO

value: HFD-fed for 15-weeks


title: KO 1 Day 18 after C. rodentium infection


title: Clam CK45D-0034

description: CK Phase I

source_name: Clam CK45D-0034

value: Adductor muscle


title: PC9_M7A_Rescue_RAD21_rep2

description: CUT&RUN Antibody: RAD21

value: METTL7A overexpression in METTL7A KO background


title: Clam CK46D-0068

description: CK Phase I

source_name: Clam CK46D-0068


title: WT 1 Day 18 after C. rodentium infection


title: Clam CK44S-0266

description: CK Phase III

source_name: Clam CK44S-0266


title: Female CPT1a LKO-2 [S20]


title: PC9_M7A_Rescue_RAD21_rep1

description: CUT&RUN Antibody: RAD21


title: Female CPT1a LKO-1 [S19]


title: Female CPT1a LKO-3 [S21]


title: Clam CK42P-0232

description: CK Phase II

source_name: Clam CK42P-0232


title: TIL EARLY TREG_4

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

description: bulk RNAseq, each sample sequenced twice then combined bioinformatically, combination shown here

data_processing:
Quality controlled FASTQ files were aligned to the Ensembl Mus musculus genome (GRCm38) using STAR aligner . We then used featureCounts to generate counts of reads uniquely mapped to annotated genes using the GRCm38 annotation gtf file. Differential gene expression analysis between the different conditions was estimated using DESeq2 based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate, and differentially expressed genes were determined at the 5% threshold. Gene set enrichment analysis was used to assess the statistical enrichment of gene ontologies, and pathways, and visualized using Clusterprofiler. All statistical analyses were performed using R.
Assembly: Ensembl Mus musculus genome (GRCm38)

source_name: tumor

growth_protocol: Mice were injected with  250,000 MC38 and sacrificied at the indicated timepoints.

extract_protocol:
Tumors were prepared for single cell suspension with in Liberase (Sigma Aldrich) at 50 mg/mL for 15 minutes at 37°C in RPMI without fetal bovine serum (FBS) and mechanical disruption. Tumor samples were negatively selected to remove CD105+ epithelial cells using CD105 Biotin (eBioscience) and Pierce Streptavidin Beads (ThermoFisher).
Libraries were constructed for SMART-seq RNA following manufacturer's instructions

treatment_protocol: We treated mice injected with two MC38 tumors with isotype (Rat IgG2a, Leinco) or anti-PD1 (Leinco) at Day 7, 10, and 13

value: tumor

tag: tumor cell_line

value: Treg


title: Female CPT1a LKO-5 [S23]

tag: tissue


title: Female Control-6 [S18]

value: Control


title: Female CPT1a LKO-6 [S24]


title: TIL NR TREG_4


title: WT 2 Day 18 after C. rodentium infection

source_name: Intestine

value: Day 18


title: PC9_M7A_Rescue_PDS5A_rep2

description: CUT&RUN Antibody: PDS5A

tag: cell line

value: lung adenocarcinoma

value: Untreated


title: Female Control-5 [S17]


title: Clam CK41D-0017

description: CK Phase I

source_name: Clam CK41D-0017


title: TIL ISO TREG_4

tag: cell type

value: Isotype


title: PC9_M7A_Rescue_osi_RAD21_rep2

description: CUT&RUN Antibody: RAD21

tag: genotype

value: Osimertinib


title: PC9_M7A_Rescue_PDS5A_rep1

description: CUT&RUN Antibody: PDS5A

tag: treatment


title: Clam CK400P-0225

description: CK Phase II


title: PC9_M7A_Rescue_osi_RAD21_rep1

description: CUT&RUN Antibody: RAD21

tag: antibody


title: Female Control-4 [S16]


title: Female Control-3 [S15]


title: TIL LATE TREG_4


title: Clam CK399P-0230

description: CK Phase II


title: PC9_M7A_Rescue_osi_PDS5A_rep2

description: CUT&RUN Antibody: PDS5A


title: Clam CK38S-0264

description: CK Phase III

source_name: Clam CK38S-0264

value: Hemocytes in ethanol


title: TIL NR CD4_4


title: Female Control-2 [S14]


title: TIL ISO CD4_4


title: TIL EARLY CD4_4


title: PC9_M7A_Rescue_osi_PDS5A_rep1

description: CUT&RUN Antibody: PDS5A


title: Clam CK40S-0265

description: CK Phase III

source_name: Clam CK40S-0265


title: PC9_M7A_Rescue_osi_H3K27Ac_rep2

description: CUT&RUN Antibody: H3K27Ac


title: Male CPT1a LKO-6 [S12]

value: Male


title: Clam CK375P-0247

description: CK Phase II


title: LN EARLY TREG_4

source_name: non-draining lymph node

value: non-draining lymph node


title: Clam CK371D-0056

description: CK Phase I


title: Male CPT1a LKO-5 [S11]

value: Liver


title: PC9_M7A_Rescue_osi_IgG_rep2

description: CUT&RUN Antibody: IgG

value: IgG


title: Clam CK366S-0348

description: CK Phase III


title: Female Control-1 [S13]

value: Female


title: Male CPT1a LKO-3 [S9]

value: CPT1a LKO

value: HFD-fed for 15-weeks


title: PC9_M7A_Rescue_osi_IgG_rep1

description: CUT&RUN Antibody: IgG

value: METTL7A overexpression in METTL7A KO background


title: LN ISO TREG_4


title: TIL LATE CD4_4

value: tumor


title: PC9_M7A_Rescue_osi_H2A_rep2

description: CUT&RUN Antibody: H2A


title: Clam CK35D-0082

description: CK Phase I

source_name: Clam CK35D-0082

value: Adductor muscle


title: Male CPT1a LKO-2 [S8]


title: Clam CK361S-0347

description: CK Phase III


title: LN LATE TREG_4

value: Treg


title: PC9_M7A_Rescue_osi_H3K27Ac_rep1

description: CUT&RUN Antibody: H3K27Ac


title: LN LATE CD4_4


title: Clam CK357P-0229

description: CK Phase II


title: Male CPT1a LKO-4 [S10]


title: Male CPT1a LKO-1 [S7]


title: PC9_M7A_Rescue_osi_H2A_rep1

description: CUT&RUN Antibody: H2A


title: LN EARLY CD4_4


title: LN NR TREG_4


title: PC9_M7A_Rescue_H3K27Ac_rep2

description: CUT&RUN Antibody: H3K27Ac


title: Clam CK350D-0060

description: CK Phase I


title: Male Control-6 [S6]

value: Control


title: LN NR CD4_4


title: PC9_M7A_Rescue_H3K27Ac_rep1

description: CUT&RUN Antibody: H3K27Ac

value: lung adenocarcinoma


title: Male Control-5 [S5]


title: LN ISO CD4_4


title: PC9_M7A_Rescue_IgG_rep2

description: CUT&RUN Antibody: IgG

value: Untreated


title: Clam CK348P-0211

description: CK Phase II


title: PC9_M7A_Rescue_IgG_rep1

description: CUT&RUN Antibody: IgG


title: TIL LATE TREG_3


title: TIL EARLY TREG_3


title: Clam CK340S-0342

description: CK Phase III


title: Clam CK342S-0343

description: CK Phase III


title: Male Control-4 [S4]


title: Clam CK344S-0344

description: CK Phase III


title: PC9_M7A_Rescue_H2A_rep1

description: CUT&RUN Antibody: H2A


title: Male Control-1 [S1]


title: Clam CK33S-0263

description: CK Phase III

source_name: Clam CK33S-0263


title: Clam CK34D-0006

description: CK Phase I

source_name: Clam CK34D-0006


title: Male Control-2 [S2]


title: TIL ISO TREG_3

value: Isotype


title: PC9_M7A_KO_PDS5A_rep2

description: CUT&RUN Antibody: PDS5A

value: METTL7A knockout


title: TIL NR TREG_3


title: TIL LATE CD4_3


title: PC9_M7A_Rescue_H2A_rep2

description: CUT&RUN Antibody: H2A


title: TIL NR CD4_3


title: PC9_M7A_KO_RAD21_rep2

description: CUT&RUN Antibody: RAD21


title: Clam CK338P-0246

description: CK Phase II


title: Male Control-3 [S3]


title: Clam CK339P-0238

description: CK Phase II


title: PC9_M7A_KO_PDS5A_rep1

description: CUT&RUN Antibody: PDS5A


title: HIO-06-Macs_S43

city: Ramat Gan

first: Tzipi

last: Braun

address: Derech Sheba 2

institute: Sheba Medical Center at Tel Hashomer

data_processing:
Reads were quantified by kallisto version 42.5, using Gencode v24 as the reference genome
Assembly: Gencode v24
Supplementary files format and content: tab-delimited text files include estimates counts values for each Sample

source_name: iPSC-derived macrophages

extract_protocol:
Qiagen AllPrep RNA/DNA Mini Kit
TruSeq RNA sample library preparation

value: iPSC-derived macrophages

tag: group

value: Macs


title: 14583 CSCs

type: RNA

city: Doha

first: Cristina

last: Maccalli

address: Doha

country: Qatar

institute: Sidra Medicine

description: The Nanostring miRNA panel V3

hyb_protocol: CodeSet Hybridization

data_processing:
The miRNA data in *.RCC (Reporter Code Count) format was analyzed using the nSolver Analysis Software to extract raw counts for all samples. Differential expression analyses were performed with the limma R package (v3.6.0) from the Bioconductor project. Linear modeling and empirical Bayes moderation in limma were applied to identify differentially expressed miRNAs, which were ranked by P-values,
Normalized data: background subtraction using the geometric mean of negative controls, normalization using the geometric mean of positive controls, and further normalization using the geometric mean of housekeeping genes across all samples,

source_name: Colorectal cancer

growth_protocol: CICs were cultured as colon-spheres in Advanced DMEM/F12 medium  containing 20 ng/ml of EGF , 50 ng/ml FGF-2. Differenciated cells were cultured in the presence of RPMI 1640 supplemented with 10% FBS

extract_protocol: RNA extraction and purification from CICs and FBS cell lines were performed using the AllPrep DNA/RNA Mini Kit  The amount and the quality of nucleic acids have been assessed by the Nanodrop 8000 and Qubit PicoGreen assay and RNA RIN threshold has been determined by the 2100 BioAnalyzer. A total of ~100 ng of total RNA was used as input for each of the samples assessed. Sample preparation, ligation, hybridization, detection, and scanning were performed as per the manufacturer’s instructions. Following hybridization, the samples were transferred to the nCounter Prep Station, where excess probes were removed, and samples were aligned and immobilized on the nCounter cartridge. The cartridge was placed on the nCounter Digital Analyzer for data collection.

value: cell line

value: CIC


title: TIL EARLY CD4_3


title: CSC 59

description: The Nanostring miRNA panel V3

label_protocol: A total of ~100 ng of total RNA was used as input for each of the samples assessed. Sample preparation, ligation, hybridization, detection, and scanning were performed as per the manufacturer’s instructions.


title: CSC 57

description: The Nanostring miRNA panel V3


title: Clam CK334D-0045

description: CK Phase I


title: PC9_M7A_KO_RAD21_rep1

description: CUT&RUN Antibody: RAD21


title: Clam CK333S-0341

description: CK Phase III

value: Hemocytes in ethanol


title: CSC 21

description: The Nanostring miRNA panel V3


title: Clam CK332S-0340

description: CK Phase III


title: PC9_M7A_KO_osi_RAD21_rep2

description: CUT&RUN Antibody: RAD21

value: Osimertinib


title: TIL ISO CD4_3


title: LN NR TREG_3

value: non-draining lymph node


title: Clam CK32S-0262

description: CK Phase III

source_name: Clam CK32S-0262


title: Clam CK330S-0339

description: CK Phase III


title: PC9_M7A_KO_osi_PDS5A_rep1

description: CUT&RUN Antibody: PDS5A


title: PC9_M7A_KO_osi_RAD21_rep1

description: CUT&RUN Antibody: RAD21


title: LN LATE TREG_3


title: CSC 20

description: The Nanostring miRNA panel V3


title: LN LATE CD4_3


title: Clam CK323S-0338

description: CK Phase III


title: LN EARLY TREG_3


title: PC9_M7A_KO_osi_H3K27Ac_rep2

description: CUT&RUN Antibody: H3K27Ac


title: Clam CK324P-0249

description: CK Phase II


title: LN EARLY CD4_3


title: PC9_M7A_KO_osi_PDS5A_rep2

description: CUT&RUN Antibody: PDS5A


title: CSC 3 R2

description: The Nanostring miRNA panel V3


title: Clam CK327D-0040

description: CK Phase I


title: PC9_M7A_KO_osi_H3K27Ac_rep1

description: CUT&RUN Antibody: H3K27Ac


title: CSC 14

description: The Nanostring miRNA panel V3


title: CSC 9

description: The Nanostring miRNA panel V3


title: CSC 13

description: The Nanostring miRNA panel V3


title: LN ISO TREG_3


title: CSC 11

description: The Nanostring miRNA panel V3


title: Clam CK322S-0337

description: CK Phase III


title: PC9_M7A_KO_osi_IgG_rep2

description: CUT&RUN Antibody: IgG

value: IgG


title: LN ISO CD4_3


title: LN NR CD4_3


title: PC9_M7A_KO_osi_H2A_rep2

description: CUT&RUN Antibody: H2A


title: PC9_M7A_KO_osi_IgG_rep1

description: CUT&RUN Antibody: IgG


title: Clam CK321D-0092

description: CK Phase I


title: Clam CK31D-0013

description: CK Phase I

source_name: Clam CK31D-0013


title: PC9_M7A_KO_osi_H2A_rep1

description: CUT&RUN Antibody: H2A


title: CSC 8

description: The Nanostring miRNA panel V3


title: TIL EARLY TREG_2


title: Clam CK318D-0018

description: CK Phase I


title: Clam CK317S-0336

description: CK Phase III


title: TIL LATE TREG_2


title: Clam CK315D-0066

description: CK Phase I


title: CSC 5

description: The Nanostring miRNA panel V3


title: PC9_M7A_KO_H3K27Ac_rep2

description: CUT&RUN Antibody: H3K27Ac


title: TIL NR TREG_2


title: CSC 2

description: The Nanostring miRNA panel V3


title: PC9_M7A_KO_H3K27Ac_rep1

description: CUT&RUN Antibody: H3K27Ac


title: TIL ISO TREG_2


title: PC9_M7A_KO_IgG_rep2

description: CUT&RUN Antibody: IgG


title: PC9_M7A_KO_IgG_rep1

description: CUT&RUN Antibody: IgG


title: 1247 col.

description: The Nanostring miRNA panel V3

value: FBS


title: 1872 col.

description: The Nanostring miRNA panel V3


title: 14583 CSC

description: The Nanostring miRNA panel V3


title: Clam CK313S-0335

description: CK Phase III


title: CSC 7

description: The Nanostring miRNA panel V3


title: TIL EARLY CD4_2

value: tumor


title: Clam CK30P-0213

description: CK Phase II

source_name: Clam CK30P-0213

value: Adductor muscle


title: PC9_M7A_KO_H2A_rep2

description: CUT&RUN Antibody: H2A


title: 1247 CSC

description: The Nanostring miRNA panel V3


title: PC9_M7A_KO_H2A_rep1

description: CUT&RUN Antibody: H2A


title: 1076 col.

description: The Nanostring miRNA panel V3


title: Clam CK306S-0333

description: CK Phase III


title: TIL ISO CD4_2


title: TIL LATE CD4_2


title: HCC827_OR_M7A_OE_MYC_tag_rep2

description: ChIP Antibody: MYC-tag

data_processing:
Adapter sequences from paired-end sequencing reads were trimmed with Trimmomatic and quality control was performed using FastQC. Bowtie2 version 2.4.2 was used to align reads to the GRCh37 genome using the –very-sensitive flag and allowing for one mismatch. SAMtools version 1.16 was used to remove unmapped reads, secondary alignment reads, and reads with a Phred score of <30. Macs2 version 2.2.7.1 was used to call peaks with default peak-calling settings. Peaks were called against input chromatin. IDR was used to determine significant peaks between two biological replicates. Deeptools version 3.5.1 was used for ChIP-seq data visualization. Plots depicting ChIP-seq signal were generated by using Deeptools bamCoverage to normalize signal by CPM and duplicates were ignored. Peak intersections were performed using BEDTools v2.30.
Assembly: GRCh37
Supplementary files format and content: bigWig files are mean count per million signal files.
Supplementary files format and content: Files with postfix idr.txt are peak files that were generated from running idr to identify highly reproducible peaks.

extract_protocol:
ChIP-seq was performed using the Active Motif ChIP-IT Express Kit (Active Motif 53008) according to the manufacturer’s instructions. Approximately 2 x 10^7 cells were used per biological replicate. Chromatin was sheared using a Covaris S220 using a peak power of 175W, duty factor of 10%, 200 cycles/burst, and 160 seconds per run. One uL of decrosslinked chromatin was analyzed via Agilent TapeStation to determine fragment size, and DNA concentration was measured using Qubit (Invitrogen Q32854). The following antibodies were used: IgG isotype control (CST 5415S) and c-MYC-tag (Cell Signaling Technologies 2276S). 20 ug of chromatin was pre-incubated with antibody overnight at 4ºC. Protein G beads were subsequently added to antibody-bound chromatin and incubated for 4 hours at 4ºC.
2.5 ng of immunoprecipitated chromatin was subject to library preparation using EpiCypher CUT&RUN Library Kit (EpiCypher 141001) according to the manufacturer’s instructions. Pooled libraries were sequenced by Novogene with NovaSeq 6000 with 20 million paired-end reads sequenced per library.

treatment_protocol: Osimertinib-resistant cells were grown in 1uM osimertinib.

value: METTL7A-MYC-tag-FLAG Overexpression

value: MYC-tag


title: Clam CK305D-0091

description: CK Phase I


title: LN LATE TREG_2

value: Treg


title: 1076 CSC

description: The Nanostring miRNA panel V3


title: HCC827_OR_M7A_OE_MYC_tag_rep1

description: ChIP Antibody: MYC-tag

value: lung adenocarcinoma


title: LN EARLY TREG_2


title: Clam CK303S-0332

description: CK Phase III


title: Clam CK301D-0065

description: CK Phase I


title: HCC827_OR_M7A_OE_Input_rep2

description: ChIP Antibody: Input


title: LN NR TREG_2


title: HCC827_OR_M7A_OE_Input_rep1

description: ChIP Antibody: Input


title: CSC 3 R1

description: The Nanostring miRNA panel V3


title: HCC827_OR_M7A_OE_IgG_rep2

description: ChIP Antibody: IgG


title: CSC 33

description: The Nanostring miRNA panel V3


title: Clam CK29D-0052

description: CK Phase I

source_name: Clam CK29D-0052


title: Control PDC028

city: London

first: Carolina

last: Barcellos Machado

address: 4-8 Maple St

country: United Kingdom

institute: BenevolentAI

description: Library name: 197191-R16

data_processing:
Reads were aligned to the GRCh38 (hg38) genome. The data were mapped to RefSeq gene model, using a professional website DNAnexus (https://dnanexus.com/).
sequencing QC was run with FastQC version 3.0.1
adaptors trimmed with Trim Galore version 0.6.0
alignment was run with STAR version 2.0.0
aligned sequencing reads were quantified with RSEM version 1.0.0
Assembly: GRCh38 (hg38)
Supplementary files format and content: csv file per sample including count, TPM and FPKM

source_name: brain tissue

extract_protocol:
Total RNA was isolated from tissue using the RNeasy Plus Universal Mini Kit (Qiagen) according to the manufacturer's protocol with an additional DNAse digestion step using DNase I, RNase-free (Roche). 1ug of Total RNA was used for the construction of sequencing libraries.
rRNA depletion was performed using the NEBNext rRNA Depletion V2 Kit (Human/Mouse/Rat) (NEB). RNA sequencing library preparation used the NEBNext Ultra II RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB).

value: brain tissue

value: fresh frozen tissue

value: brain cells

tag: batch

tag: which cingulate_gyrus

value: Anterior

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Pancreatic cancer

tag: classification of_ms

value: Non-MS control

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Clam CK307S-0334

description: CK Phase III

tag: tissue

value: Hemocytes in ethanol


title: MS MS523

description: Library name: 197191-R15

tag: cell line

tag: cell type

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Bronchopneumonia, MS

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Optic neuritis

tag: first presented_symptom_category

value: Visual

tag: history of_motor_weakness

value: Yes

tag: history of_sensory_loss

value: No

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?


title: Clam CK298S-0331

description: CK Phase III

tag: tissue


title: HCC827_OR_M7A_OE_IgG_rep1

description: ChIP Antibody: IgG

tag: cell line

tag: cell type

tag: genotype

value: METTL7A-MYC-tag-FLAG Overexpression

tag: treatment

value: Osimertinib

tag: antibody

value: IgG


title: TIL NR CD4_2

value: tumor

tag: tumor cell_line


title: MS MS517

description: Library name: 197191-R14

value: brain tissue

value: fresh frozen tissue

value: brain cells

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Chest sepsis, MS

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Sensory

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: LN EARLY CD4_2

tag: tissue

value: non-draining lymph node

tag: tumor cell_line

tag: cell type

tag: genotype

tag: treatment


title: HCC827_OR_WT_MYC_tag_rep2

description: ChIP Antibody: MYC-tag

tag: cell line

value: lung adenocarcinoma

value: Wild-Type

tag: antibody

value: MYC-tag


title: Clam CK297D-0090

description: CK Phase I

value: Adductor muscle


title: CSC 16

description: The Nanostring miRNA panel V3

value: cell line

value: CIC


title: LN NR CD4_2


title: HCC827_OR_WT_MYC_tag_rep1

description: ChIP Antibody: MYC-tag


title: Clam CK294S-0330

description: CK Phase III

value: Hemocytes in ethanol


title: LN ISO CD4_2

value: Isotype


title: LN ISO TREG_2

value: Treg


title: TIL LATE TREG_1

value: tumor


title: MS MS406

description: Library name: 197191-R12

value: brain tissue

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Chest infection, aspiration pneumonia, multiple sclerosis

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Vertigo

tag: first presented_symptom_category

value: Brainstem, Cerebellar

tag: history of_motor_weakness

value: Yes

tag: history of_sensory_loss

value: No

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion


title: Clam CK295D-0047

description: CK Phase I

tag: tissue


title: MS MS398

description: Library name: 197191-R11

tag: cell line

value: fresh frozen tissue

tag: cell type

value: brain cells

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Bronchopneumonia, multiple sclerosis

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Blurred vision, Muscle weakness

tag: first presented_symptom_category

value: Visual, Motor

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: HCC827_OR_WT_Input_rep1

description: ChIP Antibody: Input

tag: cell line

tag: cell type

value: lung adenocarcinoma

tag: genotype

value: Wild-Type

tag: treatment

value: Osimertinib

tag: antibody


title: Clam CK293D-0089

description: CK Phase I

tag: tissue

value: Adductor muscle


title: Clam CK291S-0329

description: CK Phase III

value: Hemocytes in ethanol


title: HCC827_OR_WT_IgG_rep2

description: ChIP Antibody: IgG

value: IgG


title: MS MS274

description: Library name: 197191-R10

value: brain tissue

tag: batch

tag: which cingulate_gyrus

value: Anterior

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Cancer of oesophagus

tag: classification of_ms

value: RRMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Myokymia

tag: first presented_symptom_category

value: Brainstem

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion


title: Clam CK290S-0328

description: CK Phase III

tag: tissue


title: LN LATE CD4_2

value: non-draining lymph node

tag: tumor cell_line

tag: cell type

tag: genotype

tag: treatment


title: MS MS263

description: Library name: 197191-R09

tag: cell line

value: fresh frozen tissue

value: brain cells

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Septicaemia, bronchopneumonia, urinary tract infection, small bowel obstruction, multiple sclerosis

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Numbness

tag: first presented_symptom_category

value: Sensory

tag: history of_motor_weakness

value: Yes

value: No

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: TIL EARLY TREG_1

tag: tissue

value: tumor

tag: tumor cell_line

tag: cell type

value: Treg

tag: genotype

tag: treatment


title: TIL ISO TREG_1

value: Isotype


title: MS MS231

description: Library name: 197191-R08

value: brain tissue

tag: cell line

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Bronchopneumonia, multiple sclerosis

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Sensory loss, Muscle weakness

tag: first presented_symptom_category

value: Sensory, Motor

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion


title: TIL NR TREG_1

tag: tissue

tag: tumor cell_line

tag: cell type

tag: genotype

tag: treatment


title: HCC827_OR_WT_IgG_rep1

description: ChIP Antibody: IgG

tag: cell line

value: lung adenocarcinoma

value: Wild-Type

value: Osimertinib

tag: antibody

value: IgG


title: Clam CK28S-0261

description: CK Phase III

source_name: Clam CK28S-0261

value: Hemocytes in ethanol


title: HCC827_M7A_OE_MYC_tag_rep2

description: ChIP Antibody: MYC-tag

value: METTL7A-MYC-tag-FLAG Overexpression

value: Untreated

value: MYC-tag


title: MS MS500

description: Library name: 197191-R13

value: fresh frozen tissue

value: brain cells

tag: batch

tag: which cingulate_gyrus

value: Anterior

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Urinary Sepsis

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Headache

tag: first presented_symptom_category

value: Sensory

tag: history of_motor_weakness

value: Yes

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

value: No

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: TIL LATE CD4_1

source_name: tumor

tag: tissue

value: tumor

tag: tumor cell_line

tag: cell type

tag: genotype

tag: treatment


title: HCC827_M7A_OE_MYC_tag_rep1

description: ChIP Antibody: MYC-tag

tag: cell line

value: lung adenocarcinoma

tag: antibody


title: MS MS162

description: Library name: 197191-R07

value: brain tissue

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Upper gastrointestinal bleeding due to peptic ulcer disease, multiple sclerosis

tag: classification of_ms

value: SPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion


title: HCC827_OR_WT_Input_rep2

description: ChIP Antibody: Input

tag: cell line

tag: cell type

tag: genotype

value: Wild-Type

tag: treatment

value: Osimertinib

tag: antibody


title: Clam CK288S-0326

description: CK Phase III

tag: tissue

value: Hemocytes in ethanol


title: HCC827_M7A_OE_Input_rep2

description: ChIP Antibody: Input

value: METTL7A-MYC-tag-FLAG Overexpression

value: Untreated


title: Clam CK287S-0325

description: CK Phase III


title: Clam CK289S-0327

description: CK Phase III


title: MS MS098

description: Library name: 197191-R05

value: fresh frozen tissue

value: brain cells

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Multiple sclerosis, sepsis secondary to urinary tract infection

tag: classification of_ms

value: RRMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Pain

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: TIL ISO CD4_1

tag: tissue

value: tumor

tag: tumor cell_line

tag: cell type

tag: genotype

tag: treatment

value: Isotype


title: TIL EARLY CD4_1


title: HCC827_M7A_OE_IgG_rep2

description: ChIP Antibody: IgG

tag: cell line

value: lung adenocarcinoma

tag: antibody

value: IgG


title: MS MS102

description: Library name: 197191-R06

value: brain tissue

tag: batch

tag: which cingulate_gyrus

value: Anterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Left ventricular failure, pneumonia, pleural effusion

tag: classification of_ms

value: PPMS

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

value: Sensory

tag: history of_motor_weakness

value: Yes

value: No

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion


title: MS MS049

description: Library name: 197191-R04

tag: tissue

tag: cell line

value: fresh frozen tissue

tag: cell type

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Aspiration pneumonia, cerebrovascular accident, multiple sclerosis

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

value: Blurred vision

tag: first presented_symptom_category

value: Visual

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Control C087

description: Library name: 197191-R03

tag: tissue

tag: cell line

tag: cell type

value: brain cells

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: female

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Pneumonia, valvular heart disease, atrial fibrillation, left ventricular failure

tag: classification of_ms

value: Non-MS control

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion


title: LN EARLY TREG_1

tag: tissue

value: non-draining lymph node

tag: tumor cell_line

tag: cell type

value: Treg

tag: genotype

tag: treatment


title: LN LATE TREG_1


title: Clam CK284S-0323

description: CK Phase III

value: Hemocytes in ethanol


title: HCC827_WT_MYC_tag_rep2

description: ChIP Antibody: MYC-tag

tag: cell line

value: lung adenocarcinoma

value: Wild-Type

value: Untreated

tag: antibody

value: MYC-tag


title: Clam CK285S-0324

description: CK Phase III


title: Control C039

description: Library name: 197191-R01

value: brain tissue

tag: batch

tag: which cingulate_gyrus

tag: age

tag: Sex

value: male

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: Myelodysplastic Syndrome, Rheumatoid Arthritis

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: history of_depression

tag: history of_cognitive_function_loss

tag: history of_brainstem_relapse

tag: history of_spinal_cord_episode

tag: macroscopic lesions_at_meninges

tag: any periventricular_demyelination?

tag: macroscopic lesions_at_brainstem?

tag: occipital lobe_-_presence_of_lesion

tag: cerebellum -_presence_of_lesion

tag: basal ganglion_-_presence_of_lesion

tag: cingulate gyrus_-_presence_of_lesion

tag: thalamus -_presence_of_lesion

tag: hypothalamus -_presence_of_lesion

tag: hippocampus -_presence_of_lesion

tag: spinal cord_-_presence_of_lesion

tag: optic nerve_-_presence_of_lesion


title: Control C045

description: Library name: 197191-R02

tag: tissue

tag: cell line

value: fresh frozen tissue

tag: cell type

tag: batch

tag: which cingulate_gyrus

value: Posterior

tag: age

tag: Sex

tag: brain weight_(grams)

tag: csf ph

tag: cause of_death

value: cardio pulmonary degeneration, prostate cancer, old age, Alzheimers

tag: classification of_ms

tag: age of_disease_onset

tag: age of_progressive_disease

tag: first presented_symptoms

tag: first presented_symptom_category

tag: history of_motor_weakness

tag: history of_sensory_loss

tag: history of_cerebellar_malfunction

tag: macroscopic lesions_at_cerebellar?

tag: macroscopic lesions_at_thalamus?

tag: macroscopic lesions_at_temporal_lobe?

tag: macroscopic lesions_at_spinal_cord

tag: microscopic presence_of_grey_lesion

tag: microscopic presence_of_white_lesion

tag: frontal lobe_-_presence_of_lesion

tag: temporal lobe_-_presence_of_lesion

tag: parietal lobe_-_presence_of_lesion


title: HCC827_M7A_OE_Input_rep1

description: ChIP Antibody: Input

tag: cell line

tag: cell type

tag: genotype

value: METTL7A-MYC-tag-FLAG Overexpression

tag: treatment

tag: antibody


title: Clam CK282D-0044

description: CK Phase I

tag: tissue

value: Adductor muscle


title: HCC827_WT_MYC_tag_rep1

description: ChIP Antibody: MYC-tag


title: HCC827_M7A_OE_IgG_rep1

description: ChIP Antibody: IgG

value: IgG


title: LN NR TREG_1

tag: tumor cell_line


title: h9-R2-Treated

city: Frederick

first: Colin

state: MD

department: RNA Biology Laboratory

institute: NCI

description:
Library name: modified_wt_h9_r2
in vivo SHAPE probing

data_processing:
Reads were analyzed using ShapeMapper2 (v2.2) using default parameters.
Supplementary files format and content: SHAPE reactivity
Library strategy: SHAP-MaP

source_name: Flp-In T-REx HeLa

growth_protocol: Cells were grown in Dulbecco’s modified medium (DMEM) supplemented with 10% fetal bovine serum, 2 mM L-glutamin e and maintained in a 5% CO2 humidified incubator .

extract_protocol:
Cells were pelleted and lysed using the provided buffer from Quick-RNA Miniprep Kit (Zymo, R1054) and RNA was isolated per instructions including optional steps. To ensure proper digestion of all plasmid DNA, RNA was additionally treated with 100 U of TURBO DNase I (Thermo Fisher Scientific, AM2238) with appropriate buffering conditions and was subsequently precipitated.
Libraries were generated by using error-prone reverse transcription to generate cDNA.  Then libraries underwent gene specific  amplification to adding Illumina adaptors, and a second amplification to add Illumina barcodes.

treatment_protocol: HeLa cells were plated (1 x 106) on a 10 cm plate, a day prior to SHAPE probing. On day of treatment, cells were washed twice with 10 mL of PBS, trypsinized, and spun down at 500 x g for 5 minutes. The cells were resuspended in PBS buffered with 200 mM HEPES and were divided into treated or untreated conditions. 5-Nitroisatoic anhydride (5NIA) (Sigma, S889075) was added to a final concentration of 25 mM to the treated sample and untreated cells were incubated with an equal volume of DMSO at 37˚C for 10 minutes. Reactions were quenched by adding DTT to a final concentration of 125 mM.

value: Flp-In T-REx HeLa

value: Cervical Cancer

value: WT

value: Treated with 5NIA


title: Clam CK280S-0322

description: CK Phase III

value: Hemocytes in ethanol


title: LN ISO TREG_1

value: non-draining lymph node

value: Treg

value: Isotype


title: HCC827_WT_Input_rep2

description: ChIP Antibody: Input

value: lung adenocarcinoma

value: Wild-Type

value: Untreated


title: TIL NR CD4_1

value: tumor


title: h9-R1-Treated

description:
Library name: modified_wt_h9_r1
in vivo SHAPE probing


title: LN LATE CD4_1


title: Clam CK279P-0208

description: CK Phase II


title: Clam CK286P-0245

description: CK Phase II


title: HCC827_WT_Input_rep1

description: ChIP Antibody: Input


title: h9-R2-Untreated

description:
Library name: untreated_wt_h9_r2
in vivo SHAPE probing

value: Treated with DMSO


title: Clam CK278S-0321

description: CK Phase III


title: LN EARLY CD4_1


title: h9-R1-Untreated

description:
Library name: untreated_wt_h9_r1
in vivo SHAPE probing


title: HCC827_WT_IgG_rep1

description: ChIP Antibody: IgG


title: LN NR CD4_1


title: Clam CK276D-0049

description: CK Phase I


title: Clam CK270S-0320

description: CK Phase III