title: BT245 cells transduced with PRMT targeting shRNA TRCN0000379612

description: BT245 PRMT5_612


title: BT245 cells transduced with PRMT targeting shRNA TRCN0000303446

status: Public on Nov 22 2024

type: SRA

city: Aurora

first: John

last: DeSisto

state: CO

department: Pediatrics

country: USA

institute: University of Colorado

description: BT245 PRMT5_446

library_source: transcriptomic

data_processing:
Alignment to GrCh38 (gSNAP)
FPKD expression derived (Cufflinks)
Differential expression (ANOVA in R)
Assembly: GrCh38
Supplementary files format and content: Tagb-delimited text
Supplementary files format and content: Data file columns:  Ensembl ID, gene_short_name, locus, FPKM, FPKM_conf_lo, FPKM_conf_hi, FPKM_status

molecule: polyA RNA

organism: Homo sapiens

source_name: thalamus

extract_protocol:
RNA was extracted from 1e6 cells using the RNEasy Mini Kit (Qiagen)
Sequencing libraries of polyA RNA were prepared using the TruSeq Library Preparation Kit v2 (Agilent)

tag: tissue

value: thalamus

tag: cell line

tag: cell type

value: Diffuse midline glioma

tag: treatment

value: PRMT5 knockdown


title: O8b_IGO_07618_K_14_S5

city: New York

first: Mungunsarnai

last: Ganbold

state: NYC

address: 417 East 68st

department: Brain Tumor Center

institute: MSKCC

description:
T8  passage 8b
T8 passage 8b bulkRNAseq

data_processing:
Raw reads were aligned to GRCh38 human reference genome in a Linux environment using STAR (v.2.7.8a) and gene-level counts were generated with “quantMode GeneCounts" parameter.
Assembly: GRCh38
Supplementary files format and content: FASTQ PE  raw files, some multiplexed, with HTO
Supplementary files format and content: Single cell processed files come as RDS Seurat objects, bulkRNA seq - as comma-separated gene level counts

source_name: primary cells

growth_protocol: PDX primary cells. See STAR Methods, Xiex et al., 2024

extract_protocol:
PDX tumor samples were collected directly into Trizol LS reagent (Invitrogen 10296028) and submitted to Integrated Genomics Operation facility (MSKCC) for RNA extraction, followed by poly(A) selection, and subsequent Illumina TruSeq paired-end library preparation according to the manufacturer’s protocols. Sequencing was performed on the Illumina HiSeq 2500 to a depth of 30–50 million 50-bp read pairs per sample.
Single cell libraries constructed in IGO, MSKCC with a standart 10X Chromium library kits. Bulk RNAseq - with Illumina TruSeq.

treatment_protocol: Temozolomide treatment for 5 days. See STAR Methods, Xiex et al., 2024

value: human PDX

value: primary cells


title: BT245 cells transduced with PRMT targeting shRNA TRCN0000381130

description: BT245 PRMT5_130


title: O2b_IGO_07618_K_13_S1

description:
T8  passage 2b
T8 passage 2b bulkRNAseq


title: OCP_rep2

city: NEW YORK CITY

first: Kyung-Hyun

last: Park-min

state: NY

address: 535 E 70th st

institute: Hospital for Special Surgery

data_processing:
Read quality was assessed with FastQC v0.11.6
Adapters were trimmed using Cutadapt v1.15
Reads were then mapped to the human genome (hg38)
Reads in exons were counted against Gencode v27 with STAR Aligner v2.5.3a
Differential gene expression analysis was performed in R v3.5.1 using edgeR v3.20.9
Genes with low expression levels (< 3 counts per million in at least one group) were filtered from all downstream analyses
The Benjamini-Hochberg false discovery rate procedure was used to calculate q-value
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include logCPM values for each Sample

molecule: total RNA

source_name: PBMCs

extract_protocol:
Monocytes and osteoclast precursor cells were sorted from human PBMC.
Two biological replicates pooled from eleven independent donors (n=5 and n=6) were used for RNA-sequencing. Total RNA was extracted using RNeasy mini kit (Qiagen, Hilden, Germany). True-seq RNA Library preparation kits (Illumina, Inc., San Diego, CA) were used to purify poly-A+ transcripts and generate libraries with multiplexed barcode adaptors following the manufacturer’s instructions. All samples passed quality control analysis on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

value: PBMCs

value: OCP


title: BT245 cells transduced with control shRNA SHC202

description: BT245 SHC_202

value: control


title: OCP_rep1


title: MO_rep2

value: MO


title: MO_rep1


title: O19

city: Atlanta

first: Subra

last: Kugathasan

state: GA

address: 1760 Haygood Dr

institute: Emory University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
CellRanger (v.7.0.1) software was used to generate count matrices and align transcriptome to reference genome.
Filtered count matrices were processed using Seurat (v5.0.0).
Assembly: GRCh38
Supplementary files format and content: Filtered sparse matrix where rows correspond to gene name and column corresponds to cell for each sample. Contains cell-associated barcodes.
Supplementary files format and content: Tab-separated values file with list of genes that correspond to rows in the matrix file for each sample.
Supplementary files format and content: Tab-separated values file with list of barcodes that correspond to columns in the matrix file for each sample.

source_name: Rectum

growth_protocol: Organoid cultures were established from patient biopsies as previously described13 and maintained in Matrigel (Corning) with Intesticult Human Organoid Growth Media (Stem Cell Technologies).

extract_protocol:
Mucosal biopsies were immediately processed after endoscopy, minced with scissors and enzymatically digested on ice using Bacillus licheniformis protease, before filtering and determining cell viability and numbers. A single cell suspension of filtered epithelial cells was obtained from organoids after TrypLE digestion.
Cells were encapsulated with a 10X Genomics Chromium, and after rt-PCR and cDNA amplification, libraries were prepared using 10X Genomics 3’ single-cell gene expression chemistry and sequenced on Illumina’s Novaseq6000 at the Yerkes Primate Research Center Genomics Core at Emory University.

value: Rectum

tag: sample type

value: Organoid


title: O24

description: 10X Genomics


title: O18

description: 10X Genomics


title: CT3-BAP

city: Taipa, Macau

first: Siyi

last: FU

state: Taipa, Macau

address: Room 2003,  N22 Building

department: FHS

country: Macau

institute: University of Macau

data_processing:
Bulk RNA sequenced reads were trimmed for short or low-quality sequence, then mapped to hg38 whole genome using hisat2 with defalut parameters
Supplementary files format and content: hg38
Supplementary files format and content: excel files include FPKM counts for each sample of  RNA-seq

growth_protocol: hESCs grow in mTeSR™1 medium (STEMCELL Technologies, 5870) under 20% O2 and 5% CO2 at 37°C

extract_protocol:
BAP cells treated with DMEM/F12 medium (Gibco, 11330057) with 20% KnockOut™ Serum Replacement (KOSR) (Gibco, 10828028) suppled with Recombinant Human BMP-4 Protein (10 ng/mL, R&D systems, 314-BP-500/CF), A83-01 (1 μM, Sigma , SML0788), and PD173074 (0.1 μM, SELLECK, S1264 ) for 6 days.
Bulk mRNA was extracted using RNeasy mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hES-derived trophoblast cells

value: WT

value: BAP differentiation

tag: time

value: Day 6


title: H9-BAP


title: CT3-ES

value: Embryonic stem cells

value: NO

value: Day 0


title: O3a_IGO_07618_K_18_S2

description:
T8  passage 3a
T8 passage 3a bulkRNAseq


title: O17

description: 10X Genomics


title: ENVY-BAP

source_name: ENVY

value: ENVY


title: H9-ES


title: F13505_I1B10_8w

city: Edinburgh

first: Kathryn

middle: R

last: Bowles

address: 49 Little France Crescent

country: United Kingdom

institute: University of Edinburgh

data_processing:
Paired end reads were trimmed for Illumina TruSeq adapters
Reads were aligned to the hg38 genome using the STAR aligner (v2.5.2b)
Genes were filtered by expression abundance (Counts per million (CPM) >0.1 in 5 or more samples)
Library sizes were estimated by the trimmed mean of M-values normalization (TMM) using edgeR (v3.26.8)
Differential gene expression was predicted by linear mixed model analysis using the variancePartition package (v1.14.1)
Assembly: hg38
Supplementary files format and content: Tab-delimited text files of raw read counts

source_name: iPSC-neuron

growth_protocol: Neurons and astrocytes were differentiated as previously published (Bowles et al, 2019; TCW et al, 2017)

extract_protocol:
Total RNA was extracted from neuron and astrocyte cultures using the Qiagen Rneasy miniprep kit
Libraries were prepared and sequenced as paired-end 150bp reads on the Illumina HiSeq 4000

treatment_protocol: No treatment

value: iPSC-neuron

tag: genotype

tag: age

value: 8 weeks


title: O15

description: 10X Genomics


title: F13505_I1B10_6w

value: 6 weeks


title: ENVY-ES


title: O10

description: 10X Genomics


title: O11

description: 10X Genomics


title: O12

description: 10X Genomics


title: F13505_I1B10_4w

value: 4 weeks


title: O13

description: 10X Genomics


title: OU2

description: 10X Genomics


title: O21

description: 10X Genomics


title: F13505_NDG11_Astro

source_name: iPSC-astrocytes

value: iPSC-astrocytes


title: OU1

description: 10X Genomics


title: M30

description: 10X Genomics

value: Mucosa


title: M29

description: 10X Genomics


title: F13505_NDG11_4w


title: O16

description: 10X Genomics


title: F13505_NDG11_6w


title: KKU-M213:hCAFs xenograft mice treated with Crenigacestat, rep 3

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

country: Italy

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

data_processing:
Basecalling (Ion Torrent S5)
Alignment (Torrent mapping alignment program)
Quantification (Ion Torrent Ampliseq RNA plugin, unique mapping mode)
Count Normalizition (Transcriptome Analysis Console)
Assembly: hg19_Ampliseq transcriptome
Supplementary files format and content: Count Normalized in reads per million

source_name: iCCA xenograft tissue

growth_protocol: KKU-M213 cell lines or KKU-M213:hCAFs respecting the 1:1 ratio, were subcutaneously injected into the flanks of 4–5-week-old females CD1 nude mice. Tumor masses volume reached approximately 70–100 mm3.

extract_protocol:
Total RNA from explanted tumor masses was isolated with miRNeasy mini kit (Qiagen, Hilden, Germany) in combination with TissueLyser homogenizer (Qiagen, Hilden, Germany) accordingly to the manufacturer’s instructions.
Target region amplification was performed using the Ion AmpliSeq Transcriptome Human Gene Expression core panel (Thermo Fisher Scientific,Waltham, MA, USA) on the Ion Chef System.

treatment_protocol: KKU-M213 cell lines or KKU-M213:hCAFs were treated with Crenigacestat (8 mg/kg) or vehicle by oral gavage every 2 days for 20 days

value: iCCA xenograft tissue

value: KKU-M213:hCAFs xenograft tissue

tag: host strain

value: CD1 immunodeficient nude mouse

value: Crenigacestat  (8 mg/kg)


title: F13505_NDG11_8w


title: F13505_I1B10_Astro


title: M28

description: 10X Genomics

value: Rectum


title: F13505_NEA11_8w

value: WT/WT


title: KKU-M213:hCAFs xenograft mice treated with Crenigacestat, rep 2


title: F13505_NEA11_Astro


title: F13505_NEA11_6w


title: F13505_NEA11_4w


title: F13505_S2A3_Astro


title: KKU-M213:hCAFs xenograft mice treated with Crenigacestat, rep 1


title: M26

description: 10X Genomics


title: F13505_S2A3_8w


title: KKU-M213:hCAFs xenograft mice untreated with Crenigacestat, rep 3

value: 1% Na-CMC, 0.25% Tween-80, 0.05% Antifoam in ddH2O


title: M25

description: 10X Genomics


title: F13505_S2A3_6w


title: M31

description: 10X Genomics


title: GP1.1_SH1G8_Astro


title: M24

description: 10X Genomics


title: KKU-M213:hCAFs xenograft mice untreated with Crenigacestat, rep 1


title: GP1.1_SH1G8_8w


title: GP1.1_SH1G8_6w


title: M23

description: 10X Genomics


title: GP1.1_SH1G8_4w


title: M22

description: 10X Genomics


title: GP1.1_SW1B4_Astro


title: M27

description: 10X Genomics


title: GP1.1_SW1B4_8w


title: GP1.1_SW1B4_6w


title: KKU-M213 xenograft mice untreated with Crenigacestat, rep 2

value: KKU-M213 xenograft tissue


title: GP1.1_SW1D8_Astro


title: M21

description: 10X Genomics


title: GP1.1_SW1D8_8w


title: F13505_S2A3_4w


title: GP1.1_SW1B4_4w


title: KKU-M213 xenograft mice untreated with Crenigacestat, rep 1


title: pehR mutant of R. solanacearum F1C1

city: Tezpur

first: Aditya

last: Kumar

state: Assam

address: R107, Dept Of Molecular Biology & Biotechnology

department: Molecular Biology and Biotechnology

country: India

institute: Tezpur University

data_processing:
The raw reads were analyzed using FastQC for base quality assessment and adapter contamination. Further TrimGalore was used for pre-processing raw reads by removing the adapter sequences and low quality bases
FeatureCounts was used to estimate and calculate transcript abundance
DeSeq was used to calculate the differentially expressed transcripts
Assembly: R. solanacearum F1C1; Sequences_FASTA.ffn
Supplementary files format and content: tab delimited text files containing read counts of each samples

organism: Ralstonia solanacearum

source_name: Bacterial

extract_protocol:
pehR mutant was created through insertional mutation of partial fragment of the pehR gene
Total RNA was extracted from the wild type and mutant strains respectively using TRIzol (Cat. No. 15596018) and QIAgen Rneasy Mini Kit (Cat. No. 74106) and sent for RNA sequencing
Library preparation was prepared with Illumina compatible NEB Next®UltraTM II Directional RNA Library Prep Kit (New England Biolabs, MA, USA). Further quality and quantity were assessed using Agilent 2200 Tape Station system and Qubit Fluorometer

treatment_protocol: Bacterial cells were grown in complete BG medium supplemented with glucose in a bacterial growth chamber at 28 °C

tag: strain

value: R. solanacearum F1C1

value: Bacterial

value: Mutant


title: Wild type R. solanacearum F1C1

value: Wild type


title: KKU-M213:hCAFs xenograft mice untreated with Crenigacestat, rep 2


title: GP1.1_WAC11_Astro


title: M19

description: 10X Genomics


title: Healthy donor_009

type: RNA

city: Little Rock

first: Yan

last: Cheng

state: Arkansas

address: 4301 W. Markham St.

department: Internal Medicine

institute: University of Arkansas for Medical Sciences

description: Bone marrow biopsy

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: Human bone marrow biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Bone marrow biopsies were harvested from the patient's iliac crest.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Bone marrow biopsies were used directly for RNA extraction.

value: Healthy donor


title: M18

description: 10X Genomics


title: GP1.1_SW1D8_4w

value: iPSC-neuron


title: KKU-M213 xenograft mice untreated with Crenigacestat, rep 3


title: GP1.1_WAC11_6w

value: 6 weeks


title: A549 cells,infected with EV-D68 (MOI=0.1),4hpi.2

city: Changchun, Jilin

first: qingran

last: yang

address: 1 Xinmin Street, Chaoyang District

country: China

institute: First hospital of Jilin university

data_processing:
DNBSEQ RNAref Analysis Method (Version: V1-Dr. TOM I)
Assembly: Homo_sapiens  GCF_000001405.38_GRCh38.p12
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: lung

extract_protocol:
Total RNA was extracted from cells or supernatant using TRIzol reagent (Life Technologies). Subsequently, total RNA was qualified and quantified using a Fragment Analyzer or Agilent 2100 Bioanalyzer (Agilent, CA, USA), or Qseq-400 (Bioptic, Taiwan, China).
Library preparation is performed using mRNA Library Preparation (DNBSEQ) BGI-NGS-JK-RNA-001 A0 following manufacturer's protocols.

value: lung

value: epithelial cell

value: WT

value: infected with EV-D68(MOI=0.1)


title: GP1.1_WAC11_4w

value: 4 weeks


title: M17

description: 10X Genomics

value: Mucosa


title: M20

description: 10X Genomics

value: Rectum


title: M16

description: 10X Genomics


title: 75.11_IH1A4_8w

value: 8 weeks


title: A549 cells,infected with EV-D68 (MOI=0.1),4hpi.1


title: GP1.1_SW1D8_6w


title: A549 cells,mock-infected.3

value: mock-infected


title: M15

description: 10X Genomics


title: A549 cells,mock-infected.2


title: 75.11_IH1A5_Astro

value: iPSC-astrocytes


title: 75.11_IH1A4_4w


title: M14

description: 10X Genomics


title: 75.11_IH1A4_6w


title: M13

description: 10X Genomics


title: 75.11_IH1A5_8w


title: A549 cells,mock-infected.1


title: 75.11_IH1A8_8w


title: GP1.1_WAC11_8w

value: WT/WT


title: M12

description: 10X Genomics


title: A549 cells,infected with EV-D68 (MOI=0.1),4hpi.3


title: 75.11_IH1A5_6w


title: 75.11_IH1A5_4w


title: 75.11_IH1A8_6w


title: 75.11_IH1A4_Astro


title: 75.11_IH1A8_Astro


title: M11

description: 10X Genomics


title: Neural cells, leptin antagonist, 42

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

country: Poland

institute: University of Agriculture in Krakow

data_processing:
trimming and filtering was performed using Flexbar software (3.5.0)
Cleaned, good quality reads were mapped to the Mouse GRC39 assembly with STAR aligner (2.7.5c)
Htseq-count (1.99.2) was used for reads counting
Assembly: Mouse GRC39 annotation MM109
Supplementary files format and content: raw counts from Htseq-count (txt format)

organism: Mus musculus

source_name: mHypoA-2/12 (Clu177, Cedarlane, Canada)

extract_protocol:
Treated and control cells were trypsinized, transferred to 1.5 mL Eppendorf-type tubes, and centrifuged at 500xg for 7 minutes. Obtained supernatants were instantly removed, and pelleted cells were snap-frozen at −80 °C pending RNA isolation. TRI Reagent™ Solution (ThermoFisher Scientific, USA) was used to purify total RNA according to a standard procedure. RNA was assessed for quality using the TapeStation 4150 System (Agilent, USA). RNA quantification was performed using the Qubit RNA BR assay (ThermoFisher Scientific, USA).
Library was prepared from 50 ng of total RNA with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, Austria)

value: mHypoA-2/12 (Clu177, Cedarlane, Canada)

value: neural cells

value: LANTA


title: rZ4b_IGO_07618_V_25_S21

description:
T11  passage 4b
T11 passage 4b bulkRNAseq

value: human PDX

value: primary cells


title: Neural cells, leptin antagonist, 27


title: 75.11_IH1A8_4w

value: iPSC-neuron


title: 75.11_IW1A12_Astro


title: M10

description: 10X Genomics


title: Neural cells, leptin antagonist, 26


title: 75.11_IW1A12_6w

value: 6 weeks


title: 75.11_IW1A12_4w


title: 75.11_IW1A12_8w


title: Neural cells, leptin antagonist, 25


title: M9

description: 10X Genomics


title: Neural cells, Leptin, 41

value: LEPA


title: 75.11_IW1F3_Astro


title: M8

description: 10X Genomics


title: 75.11_IW1F3_6w


title: Neural cells, Leptin, 24


title: 75.11_IW1F3_8w


title: 75.11_IW1G8_8w


title: Neural cells, Leptin, 23


title: 75.11_IW1F3_4w


title: M6

description: 10X Genomics


title: M5

description: 10X Genomics


title: M7

description: 10X Genomics


title: 75.11_IW1G8_Astro


title: 75.11_IW1G8_4w


title: Neural cells, Leptin, 22


title: 300.12_HAE11_8w


title: 300.12_HAE11_6w


title: M3

description: 10X Genomics


title: Neural cells, Palmitic acid, 40

value: PA


title: Neural cells, Palmitic acid, 21


title: 300.12_HBE10_Astro


title: M4

description: 10X Genomics


title: M2

description: 10X Genomics


title: 300.12_HBE10_8w


title: 300.12_HBE10_6w


title: 75.11_IW1G8_6w


title: M1

description: 10X Genomics


title: 300.12_HBE10_4w


title: 300.12_HCB8_8w


title: Neural cells, Palmitic acid, 19


title: 300.12_HCB8_4w


title: 300.12_NH1E7_Astro


title: IPF12

city: New Brunzwick

first: Zhi

last: Yang

state: New Jersey

address: 89 French Street

department: Child Health Institute of New Jersey

institute: Rutgers, the state university of New Jersey

description: Fresh frozen tissue

data_processing:
Tissue image alignment were conducted with loupe brower(version 6).
Raw sequencing data for each sample was converted to matrices of expression counts using the Space Ranger software provided by 10X Genomics (version 2.1.1).
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: h5 file including raw gene count (output Space Ranger)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcode
Supplementary files format and content: features.tsv.gz: list of gene ID
Supplementary files format and content: matrix.mtx.gz:gene expression count in Matrix Market Exchange format
Supplementary files format and content: aligned_fiducials.jpg: aligned_fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg:iamge of tissue and spots
Supplementary files format and content: scalefactors_json.json:scale factors in json format
Supplementary files format and content: tissue_hires_image.png: high resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png:low resolution image of tissue
Supplementary files format and content: tissue_positions_list.csv:  list of spatial barcodes  and the coordinates specifying tissue spots
Library strategy: Spatial transcriptomics

source_name: Idiopathic pulmonary fibrosis

extract_protocol:
Fresh frozen tissue was OCT embeded and 10μm frozen sections were cut with cryostat. For PPFE tissues 5μm tissue sections were cut with microtome
Spatial transcriptomic libraries were constructed with Visium Spatial Gene Expression Slide & Reagent Kit and Visium CytAssist Spatial Gene Expression kit following manufacturers' instruction

value: Idiopathic pulmonary fibrosis

tag: platform

value: 10x Visium


title: Neural cells, control, 16

value: CTR


title: IPF11

description: PPFE tissue

value: 10x Visium Cytassist


title: 300.12_HAE11_4w

value: 4 weeks


title: Neural cells, control, 17


title: 300.12_HCB8_6w


title: 300.12_HAE11_Astro


title: 300.12_NH1E7_4w


title: IPF10

description: PPFE tissue


title: 300.12_NH1E7_8w

value: 8 weeks


title: 300.12_NH1E7_6w


title: 300.12-NW1B10_Astro

value: iPSC-astrocytes


title: 300.12-NW1B10_8w


title: Neural cells, Palmitic acid, 20


title: 300.12-NW1B10_6w


title: Astrovirus, mRNA-derived cDNA

city: Philadelphia

first: Ken

last: Cadwell

state: PA

address: 421 Curie Boulevard

institute: University of Pennsylvania Perelman School of Medicine

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression) was performed using the 10x genomics Cell Ranger pipeline v7.1 and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v5.1.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10/Ensembl 93
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5

source_name: Whole ileum samples

extract_protocol:
Ileum samples were harvested from 2 mock infected mice, 2 mock infected mice with cage change, 2 infected mice, and 2 infected mice with cage change. Tissue were digested with DTT and collagenase. Cells were filtered, and cells from 2 mice per condition pooled equally. Afterwards cells were subjected to debris and dead cell removal. Cell were checked for viability using a hematocytometer and 25,000 cells were loaded into a Chromium Controller (10X Genomics).
Library was prepared using Chromium Next GEM Single Cell 5' Kit v2, 16 rxns PN-1000263 according to manufacturer’s protocol and counted using a Bio-Rad TC20 automated cell counter. Single cells were then encapsulated into emulsion droplets using Chromium Controller (10x Genomics) on a Chromium Next GEM Chip K Single Cell Kit, 16 rxns PN-1000287. scRNA-seq libraries were constructed using Chromium 5' Single Cell Library Construction Kit, 16 rxns PN-1000190 according to the manufacturer’s protocol. Amplified cDNA was evaluated on a Agilent BioAnalyzer 2100 and indexed with the Dual Index Kit TT Set A, 96 rxns PN-1000215.

treatment_protocol: Mock, Cage change, Astrovirus, Astrovirus and cage change

value: Whole ileum samples

value: Immune cells, fibroblast, epithelial cells


title: Neural cells, control, 3

value: mHypoA-2/12 (Clu177, Cedarlane, Canada)

value: neural cells


title: Astrovirus + Cage Change, mRNA-derived cDNA


title: 300.12-NW1B10_4w


title: N4

description: Fresh frozen tissue

source_name: Normal human lung

value: Normal human lung


title: N5

description: Fresh frozen tissue


title: Mock, mRNA-derived cDNA


title: N3

description: PPFE tissue


title: 300.12_NW1C7_8w


title: 300.12_NW1C7_Astro


title: 300.12_NW1C7_6w


title: N2

description: PPFE tissue


title: 300.12_NW1C7_4w


title: Cage Change, mRNA-derived cDNA


title: 300.12_NWBB7_Astro

value: WT/WT


title: 300.12_NWBB7_8w

value: iPSC-neuron


title: WJ_MSC_S7_HA_39

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

data_processing:
the raw data was quality filtered and trimmed by fastx_toolkit, and adaptor sequences were removed using Cutadapt.
The reads were collapsed to remove identical UMI-containing reads. FastQC was used to ensure high-quality sequencing data.
The tRNA reads were filtered and the rest reads were mapped to miRNAs from miRBase v22 using Bowtie allowing zero mismatches but allowing for non‐templated 3′ A and T bases.
The small RNA expression profiles generated were used for differential expression analysis in R using the DESeq2 package, and volcano plots were generated using R.
Assembly: miRBase v22
Supplementary files format and content: A txt file with miRNA expression matrix showing raw read counts for every detected miRNA in each sample. Samples are columns and miRNAs are rows.

extract_protocol:
RNA was extracted by miRNeasy Mini Kit (Qiagen; 217004)
RNA samples were prepared for small RNA sequencing using QIAseq small RNA Library Prep kit (Qiagen) following the protocol.

value: Mesenchymal Stem Cells

value: Snorkel-tag expressed

value: CD81-snorkel tag overexpression


title: 300.12_NWBB7_6w

value: 6 weeks


title: Midbrain Non-Dopaminergic Neurons, FoodTrained, rep4

city: Miami

first: Alexander

middle: Ve

last: Margetts

state: FL

address: 1600 NW 10th Ave, Rosenstiel Med Sci 7014A

department: Psychiatry and Behavioral Sciences

institute: University of Miami

data_processing:
Sequenced reads were concatenated into files by lane
Concatenated reads were then trimmed using Trimgalore (v.0.6.7) and cutadapt (v.1.18) for low-quality reads, Illumina sequence adaptors were removed, the leading and tailing low-quality base-pairs were trimmed following default parameters
Pair-end reads were mapped to the mm10 genome using STAR (v.2.7.10a) with the following parameters: –outSAMtype BAM SortedByCoordinate –outSAMunmapped Within –outFilterType BySJout –outSAMattributes NH HI AS NM MD XS –outFilterMultimapNmax 20 –outFilterMismatchNoverLmax 0.3 --quantMode TranscriptomeSAM GeneCounts
Resulting bam files were then passed to StringTie (v.2.1.5) to assemble sequenced alignments into estimated transcript and gene count abundance given the NCBI RefSeq GRCm38 (mm10) transcriptome assembly.
Gene count matrices from StringTie were then passed to the R/Bioconductor DESeq2 package (v.1.38.3) for normalization and differential gene expression analyses
Assembly: mm10
Supplementary files format and content: comma separated values file includes gene count matrix output from StringTie with no normalization
Supplementary files format and content: tab-delimited text file contains normalized counts conducted by DESeq2 for differential gene expression analysis

source_name: Neuronal

growth_protocol: Mice: Male heterozygous B6.SJL-Slc6a3tm1.1(cre)Bkmm/J (DAT-Cre; 8-12 weeks old, ~25-30 g; Jackson Laboratories, Bar Harbor, ME; SN: 006660) were housed in the animal facilities at the University of Miami Miller School of Medicine. Mice were maintained on a 12:12 hour light/dark cycle (0600 hours lights on; 1800 hours lights off) and housed three to five per cage. Food and water were provided ad libitum. Mice representing each experimental group were evenly distributed among testing sessions. All animals were kept in accordance with National Institutes of Health (NIH) guidelines in accredited facilities of the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC). All experimental protocols were approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Miami Miller School of Medicine. Whenever possible, the experimenter was blind to the experimental and/or treatment groups.

extract_protocol:
After the final food training session (FT), the final cocaine maintenance session (MN), and following 21 days of forced home cage abstinence (CRV) mice were anesthetized with isoflurane, decapitated, and the brains were removed. Using a brain block, the brains were sliced coronally to reveal the VTA. Bilateral tissue punches from the VTA of 2 mice were combined for each sample. Nuclei were isolated using Nuclei Extraction Buffer (Miltenyi Biotec, 130-128-024) following manufacturer’s instructions. Nuclei were then slow frozen in a Mr. Frosty (ThermoFisher, 5100-0001) at -80o C and stored until processed for fluorescently activated nuclear sorting (FANS). Nuclear suspensions were allowed to thaw, spun down, and incubated with Alexa Fluor 647 Conjugated HA-Tag (6E2) Mouse mAb (1:50, Cell Signaling Technology, #3444) and sorted with a CytoFLEX SRT (Beckman Coulter) based on the nuclear size, complexity and a positive AF-647 and DAPI signal, and the resulting isolated populations were either AF-647+(HA+)/DAPI+ (DA) or AF-647-(HA-)/DAPI+ (nDA). Nuclei were sorted into ~700 µL RLT plus buffer (Qiagen) for the extraction and purification of RNA.
RNA input was normalized and NGS libraries were prepared using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer’s instructions.

treatment_protocol:
Stereotaxic injections: Mice were anesthetized with an isoflurane (1-3%)/ oxygen vapor mixture and were mounted at a “flat skull” position in a stereotaxic frame (Kopf Instruments, Tujunga, CA). Using aseptic technique, Bregma was exposed by making a 5 mm longitudinal incision on the skin overlying the skull. Two small circular trepanations were drilled in the skull to expose the dura superior to the VTA. Bilateral injections (0.375 µL each at 0.2 µL/min) were made using the following coordinates: VTA, anterior-posterior (AP): -2.95 mm from Bregma; medial-lateral (ML): +/- 0.5 mm from midline; dorsal-ventral (DV): -4.2 mm from dura. The 30-gauge needle was left in place for 5 minutes before retracting to ensure proper AAV5-DIO-KASH-HA viral dispersion. 14 days were alloted for viral transduction in the VTA before mice underwent cocaine intraveneous self-administration
Cocaine intraveneous self-administration: Mice were permitted to self-administer cocaine intravenous infusions during daily 1-hour sessions. Infusions of cocaine dissolved in 0.9% sterile saline were delivered through Tygon catheter tubing (Braintree Scientific, MA, USA) into an intravenous catheter by a variable speed syringe pump (Med Associates Inc, Fairfax, VT, USA). During Food Training, mice started on a fixed ratio 1 (FR1) which was slowly increased to FR5 over 7 days upon mice receiving >30 food rewards per session at a given FR. Following successful Food Training, mice underwent jugular catheter surgery. Following surgical recovery, completion of the response criteria on the active lever resulted in the delivery of an intravenous infusion (32 µL over 2 sec) of an acquistion dose of cocaine (0.3 mg/kg/infusion). After 5 consecutive days of Acquisition, mice were allowed to self-administer cocaine during 10 consecutive daily 1-hour Maintenance (1.0 mg/kg/infusion) sessions. After 15 days of cocaine self-administration, mice underwent 21 days of forced home cage abstinence.

value: Neuronal

tag: region

value: Ventral Tegmental Area

value: Non-Dopaminergic Neurons

tag: Sex

value: Male

value: Operant food training

tag: group

value: nDA-FoodTrained


title: Midbrain Non-Dopaminergic Neurons, FoodTrained, rep3


title: 20wk_human_fetal_nose_ATAC

city: Los Angeles

first: J.

middle: Gage

last: Crump

state: CA

address: 1425 San Pablo Street, BCC 406

department: Eli and Edythe Broad CIRM Center for Stem Cell and Regenerative Medicine

institute: University of Southern California

library_source: genomic

data_processing:
Cellranger Arc v2.0.0 (10X Genomics) was used for alignment and peak calling to generate a peak-by-cell and gene-by-cell count matrix.
Multi-omics data were processed by Seurat v4.3.0.1 and Signac v1.10.0 packages in Rstudio (R version 4.3.1). Cell type identification was performed based on snRNAseq data. Cell Ranger ARC-output count matrices in H5 format of individual libraries were used to create Seurat objects by “CreateSeuratObject” and “CreateChromatinAssay” functions (EnsDb.Hsapiens.v86 used to create Granges containing annotations for the human genome). For human data, nose and outer ear Seurat objects were merged using the “merge” function prior to downstream processing. Quality control on was performed by setting the thresholds of accessible region counts (nCount_ATAC) < 200000 & > 1000, transcript counts (nCount_RNA) < 50000 & > 1000 and ratio of mononucleosome to nucleosome-free region (nucleosome_signal) < 1.2. RNA data were normalized and the top 2000 most variable genes selected using FindVariableFeatures for scaling. Dimensional reduction to 50 principal compoenents was performed using RunPCA function. Data were then subjected to neighbor finding (FindNeighbors, k=30) and clustering (FindClusters, resolution=0.6). The data were visualized through UMAP with 30 principal components as input. On each cell in the merged nose and outer ear Seurat object, peak calling was repeated using CallPeaks Signac function, which uses the MACS2 algorithm. Peaks on nonstandard chromosomes and in genomic blacklist regions were removed using keepStandardChromosones (pruning.mode=”coarse”) and subsetByOverlaps (using blacklist_hg38_unified). Counts in each peak remaining in the peak set were quantified for the merged multiome dataset using FeatureMatrix function and the resulting counts were added as a “Peaks” ChromatinAssay to the Seurat object.
Assembly: GRCh38
Supplementary files format and content: Two tab delimited files representing a sparse matrix containing normalized counts per feature for each cell barcode (one for RNA and one for Peaks called by Signac CallPeaks) and one tab delimited file containing clustering information and other metadatafor each cell barcode obtained from the Seurat processing pipeline described before. Human outer ear and nose cells are from separate libraries that have been merged and can be identified by barcode prefixes.

molecule: genomic DNA

growth_protocol: Human fetal tissue estimated 20 weeks post gestational age, de-identified and from an elective abortion was obtained from ….. under institutional review board (IRB) protocol ….

extract_protocol:
Human fetal outer ears and nose were dissected and processed separately. Using scissors and a scalpel, the tissue was finely minced and dissociated by mechanical and enzymatic digestion for 4 hours: the tissue was incubated with gentle agitation at 37 oC in conical flasks containing 10 mg/mL collagenase II, 10 mg/mL dispase, 1:1000 gentamicin, 1:500 primocin, 1:1000 penicillin/streptomycin, and 10% fetal bovine serium in DMEM-12 medium. The mixture was pipetted in the sterile hood every 30 minutes. The resulting cell suspension was passed through a 70-micron filter and washed in 2% FBS/PBS solution to stop enzymatic digestion. For red blood cell lysis, the cells were incubated in a solution consisting of 1 mL 2% FBS/PBS and 9 mL ammonium chloride (Stem Cells Technologies) for 10 minutes on ice and then washed in 2% FBS/PBS. We performed negative selection by magnetic activated cell sorting (MACS), using a primary anti-CD45-PE antibody (eBioscience, 12-9459-42) and anti-PE secondary antibody (Miltenyi, 130-048-801) to remove CD45+ white blood cells. We then resuspended the remaining cells in 10% DMSO and 20% fetal bovine serum in DMEM-12 medium and cryopreserved at -80 oC for one month. Subsequently, we thawed the cells and used fluorescence activated cell sorting to isolate live cells that exclude nuclear stain DAPI into 0.04% BSA/PBS at 4 oC. Nuclei isolation was performed per manufacturer’s instructions (10X Genomics, protocol CG000038, low cell input protocol). FACS cells were pelleted for 15 min (300 g at 4oC) and incubated with lysis buffer for 6 min on ice. Isolated nuclei were washed by wash buffer and resuspended in nuclei buffer. Nuclei count was confirmed using a Countess cell counter and nuclear integrity checked with a fluorescence confocal microscope with DAPI staining before use in library construction.
For nose and outer ear samples we generated separate barcoded single-nuclei libraries with simultaneous profiling of gene expression and chromatin accessibility using 10X Genomics Chromium Single Nuclei Multiome Reagent Kit per manufacturer’s instructions.

value: 20 weeks post-gestation


title: Midbrain Non-Dopaminergic Neurons, FoodTrained, rep2


title: 20wk_human_fetal_outer_ear_ATAC


title: WJ_MSC_S7_HA_33


title: N1

description: PPFE tissue

value: 10x Visium Cytassist


title: 300.12_NWBB7_4w

value: 4 weeks


title: 20wk_human_fetal_nose_RNA

molecule: nuclear RNA


title: 20wk_human_fetal_outer_ear_RNA


title: WJ_MSC_WT_CD81_37

value: wildtype

value: Wild type


title: WJ_MSC_WT_CD81_32


title: Midbrain Non-Dopaminergic Neurons, FoodTrained, rep1


title: Midbrain Dopaminergic Neurons, Craving, rep4

value: Dopaminergic Neurons

value: Cocaine intravenous self administration

value: Craving


title: Lpolyphemus_book_gills_ATAC

data_processing:
Cellranger Arc v2.0.0 (10X Genomics) was used for alignment and peak calling to generate a peak-by-cell and gene-by-cell count matrix.
Cell Ranger ARC-output count matrices in H5 format of individual libraries were used to create Seurat objects by “CreateSeuratObject” and “CreateChromatinAssay” functions. For the latter, GCF_000517525.1_Limulus_polyphemus-2.1.2_genomic.gtf from NCBI RefSeq was used to create a custom annotation for the horseshoe crab genome. Quality control was performed by setting the thresholds of accessible region counts (nCount_ATAC) < 15000, transcript counts (nCount_RNA) < 2500 and ratio of mononucleosome to nucleosome-free region (nucleosome_signal) < 1.5. Factor level names needed to be altered in the Seurat object to remove the “_” in genome contig names. Owing to high levels of ambient RNA and ATAC fragments in the dataset, we used DecontX2 and celda (CELLular Latent Dirichilet Allocation; 1.16.1)3 packages on snRNAseq and snATACseq counts to estimate and remove contamination in individual cells and added the decontaminated counts back to our Seurat object as “decontXRNA” assay and “decontXATAC” ChromatinAssay respectively. decontXRNA data were normalized and the top 2000 most variable genes selected using “FindVariableFeatures” for scaling. Dimensional reduction to 50 principal components was performed using “RunPCA”. Data were then subjected to neighbor finding (“FindNeighbors”, k=30) and clustering (FindClusters, resolution=0.6). Peak calling was performed on the decontXATAC ChromatinAssay using “CallPeaks”, which uses the MACS2 algorithm. Counts in each peak remaining in the peak set were quantified for the multiome dataset using “FeatureMatrix” and the resulting counts were added as a “Peaks” ChromatinAssay to the Seurat object.
Assembly: GCF_000517525.1
Supplementary files format and content: Two tab delimited files representing a sparse matrix containing normalized counts per feature for each cell barcode (one for RNA, one for Peaks called by Signac CallPeaks) and one tab delimited file containing clustering information and other metadatafor each cell barcode obtained from the Seurat processing pipeline described before.

organism: Limulus polyphemus

growth_protocol: We procured a live adult male wild-caught specimen (8 inches wide and 16 inches long) of Limulus polyphemus maintained at the Marine Biological Laboratory. The specimen was shipped overnight in moist vegetation.

extract_protocol:
The specimen wwas euthanized by submerging in filtered seawater prepared at a salinity of 1.025 using Instant Ocean salt containing 1g/L Tricaine-S (Syndel) and buffered with 4.5 mM sodium carbonate at 25oC until the gills stopped moving. From the adult male horseshoe crab, the opisthoma was separated and book gills dissected out using shears. The exoskeleton was peeled off to reveal the cartilage tissue. The tissue was cut using scissors into 1 cm X 1 cm pieces. Each piece was flash frozen in isopentane cooled in a liquid nitrogen bath and immediately transferred into a cryovial. The flash frozen tissue was stored at -80oC for two weeks. Subsequently, 200 mg of tissue was weighed out and finely minced using ice-cold scissors. The minced tissue was transferred into ice-cold homogenization buffer (250 mM sucrose, 10 mM Tris pH 8.0, 25 mM KCl, 5 mM MgCl2, 0.1% Triton X-100, 0.5% RNAse inhibitor (Sigma; cat. no. 3335399001), 1X protease inhibitor (Roche; cat. no. 5056489001), and 0.1 mM dithiothreitol (DTT; Sigma cat. no. 646563)). Nuclei were released through mechanical digestion: a chilled dounce was used to release nuclei by 10 strokes of the loose pestle and 7 strokes of the tight pestle from the minced tissue. The dounced nuclei were strained, filtered, and washed by centrifugation at 1000 g for 10 min before fluorescence-activated nuclei sorting.
We generated  barcoded single-nuclei libraries with simultaneous profiling of gene expression and chromatin accessibility using 10X Genomics Chromium Single Nuclei Multiome Reagent Kit per manufacturer’s instructions.

value: Adult; 8 inches across


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 16

city: BEER SHEVA

first: Hanin

last: Wattad

state: SOUTH DISTRICT

address: DAVUD BEN GURION BLVD 1

department: Department of Life Sciences

country: Israel

institute: Ben-gurion University of The Negev

data_processing:
Genome editing sequence analysis was made using CRISPResso2 for quantification window size of 2bp and 20bp  [Clement, Kendell, et al. (2019)]
Assembly: CTTTAAAGCCGGTCCACTCTCCCACATGGCATTTGTATCAAGCCTAACCTTTCTTCTGGTGAAACACTGTTTCCCCACAACTCTTTCCACACACCAACAAATTGTGAATAAAAAATAATTAAACAAAGTTCTCTTCATGCTGCGTGGATAGCATGATTGTGGCCCACATATGACTAGCTGGCCACAGGGCGGTAGAGACAAAGGGACCCCTCAAATACAGCGGGGGCTCTCCAGAACAGAGGGGCCTCCCATCACTAACTTAGGTTCTGTCAGTAGAGCGCATC
Supplementary files format and content: PDF file inculdes alleles frequency around Mr-cofilin cut-site

organism: Macrobrachium rosenbergii

source_name: Embryos

extract_protocol:
Cells were submerged in NaOH (0.2 N) and heated to 70 °C for 20 min in a Thermocycler Life Eco (Falc). After rough pipetting to ensure lysis, 50 μL of Tris HCl (0.04 M).
The extracted DNA was used as a template for amplification by PCR with specific primers flanking the Mr-cofilin gene. PCR products were sent to the Technion–Israel Institute of Technology (Israel) for Next-generation sequencing.
(Miseq Run V2; 2 × 150 bp, assuming 4 M reads per ends per run)

value: Embryos

value: embryonic primary cell culture

value: nucleofection


title: Midbrain Dopaminergic Neurons, Craving, rep3

value: Neuronal

value: Ventral Tegmental Area


title: WJ_MSC_WT_CD81_27

value: Mesenchymal Stem Cells


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 15


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 15


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 14


title: WJ_MSC_S7_CD81_40

value: Snorkel-tag expressed

value: CD81-snorkel tag overexpression


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 14


title: Midbrain Dopaminergic Neurons, Craving, rep2

value: Male


title: Midbrain Dopaminergic Neurons, Craving, rep1


title: WJ_MSC_S7_HA_28


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 13


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 12


title: H3 WBC, rep1, scRNAseq

city: Salt Lake City

first: Xiaomeng

last: Huang

state: Utah

department: Department of Human Genetics

institute: University of Utah

description: 10X Genomics 3'

data_processing:
Raw reads were processed using the 10X cellranger pipepline (v3.0.2)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: blood

extract_protocol:
Following ammonium chloride-based red cell lysis, white blood cells (WBCs) were resuspended in phosphate buffered saline (PBS) with 0.04% bovine serum albumin, counted and assessed for viability (>70% for all samples).
The 10x Genomics Single Cell 3’ Gene Expression Library Prep v3 was used.

value: blood

value: white blood cells


title: Midbrain Dopaminergic Neurons, Maintenance, rep2

value: Maintenance


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 12


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 11


title: Midbrain Dopaminergic Neurons, FoodTrained, rep4

value: Operant food training

value: FoodTrained


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 11


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 10


title: Midbrain Dopaminergic Neurons, FoodTrained, rep3

value: Dopaminergic Neurons


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 16


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 9


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 8


title: WJ_MSC_S7_CD81_34


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 10


title: Midbrain Dopaminergic Neurons, Maintenance, rep1

value: Cocaine intravenous self administration


title: H2 WBC, rep1, scRNAseq

description: 10X Genomics 3'


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 8


title: H1 WBC, rep1, scRNAseq

description: 10X Genomics 3'


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 7


title: CMML3 WBC, rep1, scRNAseq

description: 10X Genomics 3'

value: CD14+ cells


title: Midbrain Dopaminergic Neurons, FoodTrained, rep2


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 13

value: Embryos


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 9

value: embryonic primary cell culture


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 7

value: nucleofection


title: WJ_MSC_S7_CD81_29


title: CMML1 WBC, rep1, scRNAseq

description: 10X Genomics 3'


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 6


title: Midbrain Dopaminergic Neurons, FoodTrained, rep1

value: Neuronal


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 6


title: Pt4 T3 WBC, rep1, scRNAseq

description: 10X Genomics 3'


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 5


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 5


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 4


title: Pt4 T2 WBC, rep1, scRNAseq

description: 10X Genomics 3'


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 4


title: P22_D4

city: Berkeley

first: Salwan

last: Butrus

state: California

address: Stanley Hall Rm

department: Chemical and Biomolecular Engineering

institute: UC Berkeley

data_processing:
Sample demultiplexing using Cell Ranger v7.0.1 (10X Genomics)
Sample alignment to the mm10 (GENCODE vM23/Ensembl 98) reference genome and transcriptome
Assembly: GRCm38
Supplementary files format and content: h5ad files containing all counts and metadata
Supplementary files format and content: h5ad files containing all log-normed values and metadata

source_name: barrel cortex

growth_protocol: All procedures were approved by the UC Berkeley Animal Care and Use Committee and were in accordance with NIH guidelines. C57Bl6J male mice were obtained from Charles River Laboratories. Mice were maintained on a 12 hr day/night cycle and housed with littermates and the mother in the UC Berkeley animal facility.

extract_protocol:
Mice were anesthetized with isofluorane, rapidly decapitated, and the brain was dissected out into ice-cold Hibernate A (BrainBits Cat# HACA). For each condition (P12, P22 control, P22 1d RWD, P22 10d AWD) 3 mice were used for each biological replicate of single-nucleus(sn) RNA-sequencing. Extracted brains were placed on a metal brain mold (Zivic Instruments,#5569)  and the slice containing wS1 was isolated by inserting in the 11th space on the mold (~7.5 mm from the tip of the olfactory bulb, and a second blade 2 mm further anterior ( 4 spaces on the mold). This slice was removed and lowered to Hibernate A in a 60cc petri dish, placed on a ruler under a dissecting microscope. The midline was aligned with the ruler, and the first cut was bilaterally 2 mm out from the midline in a radial direction. The second cut was 2 mm medial to the first cut. The cortex was peeled off the underlying white matter. The wS1 piece was transferred into a RNAse-free cryovial, excess liquid was removed, and the tube was rapidly frozen on dry ice. Once all dissections were complete, the tissue was transferred from dry ice into a dewar of liquid nitrogen for storage before nuclei isolation.
Nuclei were isolated using the 10X Chromium nuclei isolation kit (10X Genomics,Cat#1000494). After isolation according to the chromium protocol, cells were counted on a hemocytometer in ethidium bromide and then diluted to 700-1200 nuclei/mm3. Nuclei from each biological replicate were split into two tubes and run separately on two channels of 10X v3, targeting 10,000 cells per channel. We refer to these as library replicates. For each experiment, we performed two or three biological replicates towards a total of four to six library replicates.
10x Chromium 3’ v3 platform (10X Genomics, Pleasanton, CA)

treatment_protocol: For whisker deprivation, mice were anesthetized with isoflurane, and whiskers were carefully plucked under a dissecting microscope with forceps using slow and steady force to prevent removal of the whisker follicle. Sham mice were anesthetized for the same amount of time as deprived, but whiskers were only stroked briefly with forceps.

value: barrel cortex


title: CMML2 WBC, rep1, scRNAseq

description: 10X Genomics 3'

value: mononuclear cells


title: P22_C1


title: P22_D3


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 3


title: Pt3 T3 WBC, rep1, scRNAseq

description: 10X Genomics 3'


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 1


title: P22_D2


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 2


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 2


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Negative control, Mr-cofilin, Experiment 1


title: Pt3 T2 WBC, rep1, scRNAseq

description: 10X Genomics 3'


title: 24173X25 MCT1KO ANG/PE 5

first: Joseph

last: Visker

state: UT

address: 1245 W SIENNA WAY

department: Nora Eccles Harrison Cardiovascular Research and Training Institute

institute: The University of Utah

data_processing:
The mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 112 and a reference database was created using STAR version 2.7.9a
Reads were trimmed of adapters using cutadapt 1.16 and aligned to the reference database using STAR in two pass mode.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.42.1
Assembly: mm39
Supplementary files format and content: FeatureCount output files combined into a single tab-delimited raw count matrix

source_name: Heart

extract_protocol:
RNA was isolated from 25 mouse hearts using the QIAGEN miRNeasy mini kit (217004).
Total RNA samples (5-500 ng) were hybridized with NEBNext rRNA Depletion Kit v2 (Human, Mouse, Rat) (E7400) to substantially diminish rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L).

value: Heart

value: ANG/PE


title: 24173X23 MCT1KO ANG/PE 3


title: Pt2 T3 WBC, rep1, scRNAseq

description: 10X Genomics 3'


title: P22_S4


title: 24173X24 MCT1KO ANG/PE 4


title: P22_D1


title: P22_C2


title: Pt3 T1 WBC, rep1, scRNAseq

description: 10X Genomics 3'


title: 24173X22 MCT1KO ANG/PE 2


title: P22_S3


title: 24173X21 MCT1KO ANG/PE 1


title: Pt2 T2 WBC, rep1, scRNAseq

description: 10X Genomics 3'


title: Pt4 T1 WBC, rep1, scRNAseq

description: 10X Genomics 3'


title: Macrobrachium rosenbergii, nucleofected embryonic cells, Positive control, Mr-cofilin, Experiment 3


title: 24173X20 WT ANG/PE 3

value: WT


title: P22_S2


title: 24173X19 WT ANG/PE 2


title: Pt2 T1 WBC, rep1, scRNAseq

description: 10X Genomics 3'

value: blood


title: 24173X17 MCT1KO SALINE 4

value: SALINE


title: P22_S1


title: 24173X18 WT ANG/PE 1


title: Pt1 T3 WBC, rep1, scRNAseq

description: 10X Genomics 3'

value: white blood cells


title: 24173X16 MCT1KO SALINE 3


title: Pt1 T2 WBC, rep1, scRNAseq

description: 10X Genomics 3'


title: 24173X15 MCT1KO SALINE 2


title: P12_A1


title: Pt1 T1 WBC, rep1, scRNAseq

description: 10X Genomics 3'


title: MPRA_rna4

city: Saint Louis

first: Shiming

last: Chen

state: Missouri

address: 517 South Euclid Avenue

department: Department of Ophthalmology & Visual Sciences

institute: Washington University in St Louis

description: Four samples with internal phased indexes are pooled. The internal indexes required for demultiplex can be found in p1index_dnarna.tsv

library_source: other

data_processing:
The sequencing reads were demultiplexed using the inner phasing index within the P1 adapter sequences.
The 10bp unique cis-regulatory element (CRE) identifying barcodes were extracted and counted.
The barcode counts were further filtered and normalized to produce regulatory activity scores for each testing cis-regulatory element (CRE).
Assembly: mm10
Supplementary files format and content: Raw count table provided for individual sample.
Library strategy: Coop-seq (small amplicon library)

molecule: other

source_name: Retina

growth_protocol: DMEM/F12 1:1, 10% HI-FBS, 1xPenicillin-Streptomycin. Retina ex plants were cultured at 37°C, 5% CO2 for 8 days after electroporation before harvest.

extract_protocol:
DNA and RNA from ex plant retinas were extracted using Trizol Reagents (Invitrogen) following manufacturer's protocol.
The MPRA sequencing libraries were constructed by three rounds of PCRs following a published protocol (Friedman et al. 2021).

value: Retina


title: 24173X12 WT SALINE 5


title: 24173X14 MCT1KO SALINE 1


title: IPF9

description: 10x Visium Cytassist

source_name: PPFE tissue

value: Idiopathic pulmonary fibrosis


title: Gal-WT-QKI, rep3

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

data_processing:
Trimmomatic-0.39 quality filtering and adapter trimming
Kallisto alignment to transcriptome and quantification
STAR alignment to genome
stringtie merge gtf
Assembly: sacCer3
Supplementary files format and content: kallisto counts file in text format
Supplementary files format and content: kallisto tpm count file in text format

organism: Saccharomyces cerevisiae BY4741

extract_protocol:
1mL of yeast culture pellet was resuspended in 400 ul of AE buffer (50 mM, pH 5.2 of NaOAc, 10Mm EDTA). After the addition of 40ul of 10%SDS and 400ul of PCA, samples were incubated at 65°C for 10 minutes. After a 5 minutes incubation on ice, samples were placed on phase lock gel tubes, centrifuged at high speed for 5 minutes and centrifuged again after 400ul of ul of chloroform was added on the top phase. Samples were centrifuged once more, another 400ul of chloroform was added, and samples centrifuged one final time. The aqueous phase was transferred to a new micro centrifuge tube, 50ul of 3M sodium acetate ph5.2 was added, followed by 2 volumes of 100% ethanol. Samples were centrifuged at high speed for 15 minutes, the ethanol was removed and the pellet washed by centrifugation with 70% ethanol, centrifuged for 5 minutes, ethanol was removed, and samples were air dry. Pellet was resuspend in RNA-se free water, vortexed. To clear DNA contamination, 1ug of RNA was treated with DNAse turbo following manufacturer instructions. RNA was extracted after DNA-se treatment with phenol/chloroform.
NEBNext polyA mRNA Magnetic Isolation Module followed by NEBNext Ultra II Directional RNA Library preparation

value: Gal-WT-QKI


title: MPRA_rna3

description: Six samples with internal phased indexes are pooled. The internal indexes required for demultiplex can be found in p1index_dnarna.tsv


title: Gal-WT-QKI, rep2


title: MPRA_rna2


title: Gal-WT-QKI, rep1


title: 24173X10 WT SALINE 3


title: IPF8

description: 10x Visium Cytassist


title: Parental strain, Gal-eGFP,rep3

value: parental Gal-eGFP


title: IPF7

description: 10x Visium Cytassist


title: 24173X9 WT SALINE 2


title: P12_A2


title: MPRA_rna1


title: Parental strain, Gal-eGFP,rep2


title: 24173X13 WT SALINE 6


title: 24173X8 WT SALINE 1


title: MPRA_dna


title: IPF6

description: 10x Visium Cytassist


title: IPF5

description: 10x Visium Cytassist


title: 24173X11 WT SALINE 4


title: MPRA_plasmid

description: Two samples with internal phased indexes are pooled. The internal indexes required for demultiplex can be found in p1index_pasmid.tsv


title: 24173X7 MCT1KO NO PUMP 3

value: NO PUMP


title: liver_hepatic_adenoma_VIII_RNA

city: Turin

first: Silvia

last: Deaglio

address: Via Santena, 19

institute: University of Turin

data_processing:
Basecalls and adapter trimming were performed using GenerateFASTQWorker Version=1.37.0 for NextSeq output.
RNAseq reads were aligned to the UCSC human reference genome 19 (hg19) for calculation of expression values (read counting and TPM (Transcripts Per Million) normalized value) using the RNA-Seq Alignment software Version 2.0.2 (Illumina, Inc.) with the following options: -paired-end, -stranded, - fusion calling.
Assembly: hg19
Supplementary files format and content: comma-separated values contain TPM for each sample.

source_name: Hepatic adenoma

extract_protocol:
RNA extraction was performed with TRIzol reagent (Cat. Ns. 15596026 and 15596018, Invitrogen, Waltham, MA) following manufacturer’s protocols.
RNA quality was assessed by Bioanalyzer high sensitivity RNA analysis (Cat. N. 5067-1511, Agilent, Santa Clara, CA). Libraries were prepared using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Cat. N. 20040525, Illumina, San Diego, CA) following manufacturer’s protocol.

value: Hepatic adenoma


title: Parental strain, Gal-eGFP,rep1


title: ATAC_rhom3

data_processing:
For each sample, reads were first trimmed with Trim Galore.
The trimmed reads were then mapped to the mm10 genome using Bowtie2 with parameters -X 2000 --very-sensitive.
Only uniquely mapped and properly paired reads were retained with samtools with parameters -f 0x2 -q 30.
Mitochondria reads were removed with samtools. Duplicated reads were marked and removed with Picard.
Last, reads mapped to the mm10 blacklist regions were removed by bedtools by intersect -v.
Assembly: mm10
Supplementary files format and content: bigWig files generated with deeptools. Scores represent CPM values at 10bp binsize.
Supplementary files format and content: narrowPeak files generated by MACS2 callpeak with default parameters.

extract_protocol:
For each replicate, two retinas, one from male and one from female litter mates, were pooled, lysed, and subjected to Tn5 tagmententation following a published protocol (Buenrostro et al. 2015).
ATAC-seq libraries were prepared for sequencing using standard Illumina protocols.

value: Post-natal day 14


title: ATAC_rhom2


title: IPF4

description: 10x Visium Cytassist


title: 24173X5 MCT1KO NO PUMP 1


title: IPF3

description: 10x Visium Cytassist


title: liver_hepatic_adenoma_VII_RNA


title: IPF2

description: 10x Visium Cytassist


title: liver_hepatic_adenoma_VI_RNA


title: 24173X4 WT NO PUMP 4


title: liver_hepatic_adenoma_V_RNA


title: ATAC_khom3


title: IPF1

description: 10x Visium

source_name: Fresh frozen tissue


title: 24173X3 WT NO PUMP 3


title: SingleCell_TSC_T3-B

city: Atlanta

first: Zhexing

last: Wen

address: 100 Woodruff Circle

department: Department of Psychiatry and Behavioral Sciences

institute: Emory University

data_processing:
The Emory sequencing center provided the demultiplexed data. The raw fastq files were then processed using CellRanger (v7.0.1) from 10x Genomics.
Assembly: hg38
Supplementary files format and content: HDF files of filtered_feature_bc_matrix for each sample

source_name: cortical organoids

extract_protocol:
Organoids were dissociated into single-cell suspensions using Papain Dissociation System (Worthington Biochemical, LK003153) as directed by the manufacturer. Cell viability was higher than 95%.
The library was constructed following the manufacturer's protocol. (SingleCell 3' V3.1 dual index protocal, https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/library-prep/chromium-next-gem-single-cell-3-lt-reagent-kits-v-3-1-dual-index-user-guide)

value: cortical organoids


title: liver_hepatic_adenoma_IV_RNA


title: 24173X2 WT NO PUMP 2


title: ATAC_khom2


title: liver_hepatic_adenoma_I_RNA


title: 24173X6 MCT1KO NO PUMP 2


title: SingleCell_TSC_T3-A


title: SingleCell_TSC_T2-B


title: 24173X1 WT NO PUMP 1


title: liver_normal_parenchyma_RNA

source_name: Normal hepatic parenchyma

value: Normal hepatic parenchyma


title: ATAC_khom1


title: ATAC_rhom1


title: SingleCell_TSC_T2-A


title: SingleCell_TSC_T1-B


title: RNA-seq in 120-hour mouse gastruloids - TSA treated r3

city: Montpellier

first: Marco

last: Di Stefano

address: 141 rue de la Cardonille

country: France

institute: Institut de Génétique Humaine - CNRS

data_processing:
Data were mapped and counted using the align andg featureCounts functions of the subread package.
Assembly: mm10
Supplementary files format and content: Processed files represent raw counts for each condition and replicate.

source_name: cell line

growth_protocol: ESC were grown in FBS+LIF media with standard conditions.

extract_protocol:
For mESCs, RNA was extracted usint Rnaeasy mini Qiagen kit with RLT buffer supplemented with 2-mercaptoethanol and on-column DNaseI digestion. For gastruloids, Qiagen columns and buffer were swapped for Zymo RNA Clean & Concentrator reagents.
Total RNA-seq libraries were done by rRNA depletion and constructed by BGI Tech Solutions; polyA RNA-seq libraries were donw by polyA capture by BGI Tech Solutions.

treatment_protocol: 1) ESCs - DMSO: 0.01% DMSO for 4 hours; TSA: 100 ng/ml TSA for 4 hours; REC: 4 hours TSA (100 ng/ml) followed by 24 hours of recovery; reTSA: 4 hours TSA (100 ng/ml) re-treatment following 24 hours of recovery; reREC: 24 hours of recovery following the second round of TSA treatment. 2) Gastruloids - 48h Ctrl: 0.002% DMSO from 44h to 48h; 48h TSA: 20 ng/ul TSA from 44h to 48h; 120h Ctrl: 0.002% DMSO from 44h to 48h followed by washes and 72h recovery; 120h TSA: 20 ng/ul TSA from 44h to 48h followed by washes and 72h recovery

value: cell line

value: 120h gastruloid

value: CTCF-GFP-AID

value: 20 ng/ml TSA


title: RNA-seq in 120-hour mouse gastruloids - TSA treated r2


title: RNA-seq in 120-hour mouse gastruloids - TSA treated r1


title: SingleCell_TSC_T1-A


title: Con Day6

city: London

first: John

last: Connelly

address: 4 Newark Street

department: Centre for Cell Biology and Cutaneous Research

institute: Queen Mary University of London

description: 10X Genomics

data_processing:
De-multiplexing, barcode processing, gene counting, and aggregation were performed using the Cell Ranger software (v2.2.1)
Assembly: Hg19
Supplementary files format and content: Cell Range output files: matrix, barcodes, and features files

source_name: N/TERT keratinocytes, dermal fibroblasts, human umbilical vein endothelial cells, CD14+ monocytes

extract_protocol:
Three microfluidic HSEs containing primary CD14+ monocytes were generated per condition (Con Day1, LPS Day1, Con Day6, LPS Day6). For single-cell RNA sequencing (scRNA-seq), the samples were incubated with 300 μl of 50 FU / ml nattokinase (MedChem Express) dissolved in sterile PBS for 1 h at 37 °C 5 % CO2. After 1 h incubation, the fibrin gel had been digested and the cell suspensions from each microfluidic HSE were transferred into sterile 15 ml falcon tubes (Corning, Corning Inc). Samples were then centrifuged at 200 G for 15 min at 4 °C. After centrifugation, the supernatant was carefully pipetted and discarded and cell pellets from each sample were resuspended in 40 μl FACs of buffer and kept on ice.  A CD45 positive selection was performed according to the manufacturer’s instructions (Miltenyi Biotec), to separate monocyte-derived cells from fibroblasts, endothelial cells and keratinocytes in the samples. The CD45 positive (monocyte-derived cells) and CD45 negative (fibroblasts, endothelial cells and keratinocytes) samples were resuspended in 500 μl DPBS (Sigma Aldrich, Missouri, USA) and filtered through 70 µm pore sterile Flowmi Cell Strainers (Merck, Sigma Aldrich, Missouri, USA) into sterile Eppendorf tubes and kept on ice.  Acridine orange and propidium iodide (lot number: AP0BBC0301, Logos Bio, Allied Genetics Inc) was used to assess the viability of single cell suspensions derived from the HSEs, before the single cell suspensions were sequenced. A viability cut-off of > 80 % was set for each sample to proceed. Staining was performed according to the manufacturer's instructions. Stained samples were pipetted onto Luna cell counting slides (lot number: L201B1D2GB, Logos Bio, Allied Genetics Inc). The viability of the single cell suspensions was determined using the automated LUNA-FX7™ Dual Fluorescence Cell Counter (Logos Bio, Allied Genetics Inc). 7500 live CD45 negative cells were combined with 7500 CD45 positive live cells, from each condition, in a sterile Eppendorf tubes and kept on ice.
Single-cell RNA sequencing (scRNA-seq) was performed by the Genome Centre, Blizard Institute, Queen Mary University of London using the Chromium Next GEM Single Cell 3’ assay (10X Genomics). 15,000 cells were loaded per lane (4 lanes, 15,000 cells per condition) of the Single Cell chip (10X Genomics). A total of 35,987 cells were sequenced (14,410 cells from the Control Day 1 condition, 7516 cells from the Treated Day 1 condition, 7999 cells from the Control Day 6 condition and 6062 cells from the Treated Day 6 condition). Chromium™ 10x single cell 3’v3.1 libraries were generated and library pool QC was performed using the Qubit 2.0 Fluorometer (ThermoFisher) and the Agilent 4200 Tapestation (TapeStation Analysis Software 4.1). Final libraries were run using the Illumina NextSeq2000 sequencing system to achieve a minimum depth of 50,000 raw reads per cell. NextSeq2000 QC resulted in a quality score (% bases > Q30) of 94.91 %.

value: Control


title: LPS Day6

description: 10X Genomics

value: N/TERT keratinocytes, dermal fibroblasts, human umbilical vein endothelial cells, CD14+ monocytes

value: LPS


title: ATAC_ehom3


title: ATAC_khet1


title: Con Day1

description: 10X Genomics


title: ATAC_ehom2


title: SingleCell_CTRL_C3-B


title: LPS Day1

description: 10X Genomics


title: ATAC_khet3


title: SingleCell_CTRL_C3-A


title: RNA-seq in 120-hour mouse gastruloids - control  r1


title: ATAC_khet2


title: RNA-seq in 48-hour mouse gastruloids - TSA treated r3

value: 48h gastruloid


title: ATAC_ehet6

value: Retina


title: SingleCell_CTRL_C2-B


title: SingleCell_CTRL_C2-A


title: ATAC_ehom1


title: Midbrain Dopaminergic Neurons, Maintenance, rep3

value: Neuronal

value: Ventral Tegmental Area

value: Dopaminergic Neurons

value: Male

value: Cocaine intravenous self administration

value: Maintenance


title: ATAC_ehet5

value: Post-natal day 14


title: RNA-seq in 120-hour mouse gastruloids - control r3


title: ATAC_ehet4


title: SingleCell_CTRL_C1-A

value: cortical organoids


title: RNA-seq in 48-hour mouse gastruloids - TSA treated r1

value: cell line


title: SingleCell_CTRL_C1-B


title: RNA-seq in 120-hour mouse gastruloids - control r2

value: 120h gastruloid


title: ATAC_wt3

value: WT


title: TSC_Day126_TSC010het_126_B

data_processing:
raw fastq files were trimmed by fastp (v0.23.0)
trimmed fastq files were mapped to hg38 genome using STAR (2.7.10b)
raw read counts were extracted by subread (v2.0.6)
Assembly: hg38
Supplementary files format and content: csv text file includes raw read counts for reac sample

extract_protocol:
RNA was isolated using the Direct-zol™ RNA Miniprep Kit (Zymo, R2052). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq is a standard protocol widely utilized in our laboratory at Emory. RNA-seq libraries were generated using the NEB Next Ultra II Directional with Poly A Selection Kit. A qPCR-based KAPA library quantification kit was applied to accurately quantify library concentration.


title: TSC_Day126_TSC010het_126_A


title: ATAC_wt2


title: RNA-seq in 48-hour mouse gastruloids - control r2

value: CTCF-GFP-AID


title: Glioblastoma U251 methionine deprived culture 48h, biological rep3

city: Harbin

first: Hong

last: Hu

state: 黑龙江

address: youzheng street

institute: Harbin medical university

description: Gene expression data from glioblastoma cell line of cellularisation.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Microarray were scanned using the Agilent Microarray Scanner (Agilent p/n G2565BA).

data_processing: The scanned images were analyzed with Agilent Feature Extraction (FE) software (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Purify the labeled/amplified RNA and labeled cRNA were prepared according to the RNeasy Mini Kit (Qiagen p/n 74104) standard protocol from total RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: human tumor cell line

value: Glioblastoma cell line U251


title: GFP, CYC, Head, ChIP, REP#2

city: Beijing

first: Pengfei

last: Lv

address: No. 2, Old Summer Palace West Road

institute: China agricultural university

description: Raw data for CHIP-seq

data_processing:
Raw sequencing data were processed and quality controlled using fastp, followed by alignment to the Drosophila melanogaster (dm6) reference genome (https://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips/) using Bowtie 2 (Chen et al., 2018; Langmead and Salzberg, 2012). PCR duplicates were removed using Picard Tools (http://broadinstitute.github.io/picard/). The deepTools multiBamSummary and plotCorrelation functions were used to assess the correlation between ChIP-seq samples (Ramirez et al., 2016). The SAMtools merge function was used to merge deduplicated BAM files (Li et al., 2009). narrowPeak was called using MACS2, and peak annotation and analysis were performed with the R package ChIPseeker (Yu et al., 2015; Zhang et al., 2008).
Assembly: dm6
Supplementary files format and content: The BED file contains peaks for CLOCK and CYCLE

organism: Drosophila melanogaster

source_name: Head

extract_protocol:
The ChIP protocol was modified based on Le Thomas et al. (2014). For each biological replicate, 200 heads, 200 pairs of testes, or 200 pairs of ovaries were collected at ZT10, fixed in 1% formaldehyde for 10 minutes, quenched with 25 mM glycine for 5 minutes, and washed three times with PBS. The fixed tissues were then homogenized in RIPA buffer (20 mM Tris, pH 7.4, 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, protease inhibitor, 10 mM NaF, 0.2 mM Na₃VO₄). Chromatin was sheared by sonication to fragments of 100–500 base pairs. The sample was then centrifuged at 13,000 × g for 10 minutes at 4°C, and the supernatant was collected. The supernatant was pre-cleared with Dynabeads Protein G beads (Invitrogen) for 2 hours at 4°C. 5% of the pre-cleared sample was reserved as the Input, while the remaining sample was incubated with 5 μL anti-GFP antibody (A-11122, Invitrogen) overnight at 4°C. The immunoprecipitated (IP) sample was then incubated with Dynabeads Protein G for 5 hours at 4°C to allow bead binding. After that, beads were washed 5 times in LiCl Wash Buffer (10 mM Tris pH7.4, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate), while the Input sample was incubated with 1 μL 10 mg/mL RNase A at 37°C for 1 hours. Rinsed in TE buffer (1 mM EDTA, 10 mM Tris–HCl, pH 8), and finally resuspended in Proteinase K buffer with 100 µg of Proteinase K. Finally, both samples were incubated with 100 μg of Proteinase K in PK Buffer (200 mM Tris, pH 7.4, 25 mM EDTA, 300 mM NaCl, 2% SDS) first at 55°C for 3 hours, followed by overnight incubation at 65°C.
Illumina library preparation and sequencing were performed at the Novogene sequencing platform (https://cn.novogene.com/).

value: Head


title: Glioblastoma U251 methionine deprived culture 48h, biological rep2


title: ATAC_wt1


title: Glioblastoma U251 methionine normal culture, biological rep3

source_name: Glioblastoma U251 methionine normal culture 48h


title: Glioblastoma U251 methionine deprived culture 48h, biological rep1


title: Glioblastoma U251 methionine normal culture, biological rep1


title: BG4_IAV

city: Chicago

first: Sarah

middle: J

last: Sun

state: Illinois

address: 900 E 57th Street

institute: University of Chicago

description:
RNA-seq
BWTInf16

data_processing:
Assembly: mm10
remove adapter sequences; trimmomatic-0.36; ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
read alignment; STAR; --sjdbOverhang 100
generate count matrix; featureCounts
text file, raw counts matrix of reads overlapping each gene for each sample

extract_protocol:
RNA extracted with Qiagen RNeasy kit
Illumina TruSeq

value: neutrophil

tag: primary treatment

value: BG

tag: secondary treatment

value: IAV


title: RNA-seq in 48-hour mouse gastruloids - control r1

tag: tissue

value: 48h gastruloid


title: GFP, CYC, Head, ChIP, REP#1

description: Raw data for CHIP-seq


title: TSC_Day126_TSC010homo_126_B


title: RNA-seq mESC 24h recovery after second TSA treatment r3

tag: cell line

value: mESC wt

value: Wild type

value: 24h recovery from a second round of TSA treatment


title: TSC_Day126_TSC010homo_126_A

tag: cell type


title: BG3_IAV

description:
RNA-seq
BWTInf15


title: GFP, CYC, Testis, ChIP, REP#1

description: Raw data for CHIP-seq

source_name: Testis

value: Testis


title: GFP, CYC, Testis, ChIP, REP#2

description: Raw data for CHIP-seq


title: RNA-seq mESC 24h recovery after second TSA treatment r2

tag: treatment


title: BG1_IAV

description:
RNA-seq
BWTInf13


title: RNA-seq in 48-hour mouse gastruloids - control r3


title: BG2_IAV

description:
RNA-seq
BWTInf14


title: GFP, CYC, Ovary, ChIP, REP#2

description: Raw data for CHIP-seq

source_name: Ovary

value: Ovary


title: TSC_Day126_TSC009homo_126_B


title: Glioblastoma U251 methionine normal culture, biological rep2


title: Input, CYC, Head, ChIP, REP#2

description: Raw data for CHIP-seq


title: TSC_Day126_TSC009homo_126_A


title: C4_IAV

description:
RNA-seq
BWCInf12


title: RNA-seq mESC re-treated with TSA after recovery r2

value: 100 ng/ml TSA re-treatment following 24h recovery from TSA treatment


title: TSC_Day126_TSC010_126_B

value: cortical organoids


title: RNA-seq mESC 24h recovery after second TSA treatment r1

value: cell line


title: Input, CYC, Head, ChIP, REP#1

description: Raw data for CHIP-seq


title: RNA-seq mESC TSA-treated expt2 r3

value: 100 ng/ml TSA


title: C2_IAV

description:
RNA-seq
BWCInf10

value: WT


title: C3_IAV

description:
RNA-seq
BWCInf11


title: C1_IAV

description:
RNA-seq
BWCInf9


title: Input, CYC, Testis, ChIP, REP#1

description: Raw data for CHIP-seq


title: TSC_Day126_TSC010_126_A


title: TSC_Day126_TSC007_126_A


title: RNA-seq mESC TSA-treated expt2 r1


title: TSC_Day126_TSC007_126_B


title: RNA-seq mESC TSA-treated expt2 r2


title: BG3_uninfected

description:
RNA-seq
BWT7


title: RNA-seq mESC DMSO expt2 control r3


title: TSC_Day126_TSC009_126_A


title: Input, CYC, Testis, ChIP, REP#2

description: Raw data for CHIP-seq


title: TSC_Day126_TSC001_126_B


title: RNA-seq mESC re-treated with TSA after recovery r3


title: Input, CYC, Ovary, ChIP, REP#1

description: Raw data for CHIP-seq


title: Input, CYC, Ovary, ChIP, REP#2

description: Raw data for CHIP-seq


title: TSC_Day126_TSC009_126_B


title: RNA-seq mESC re-treated with TSA after recovery r1


title: TSC_Day126_TSC001_126_A


title: BG2_uninfected

description:
RNA-seq
BWT6


title: GFP, CLK, Head, ChIP, REP#2

description: Raw data for CHIP-seq


title: BG1_uninfected

description:
RNA-seq
BWT5


title: RNA-seq mESC DMSO expt2 control r1


title: RNA-seq mESC DMSO expt2 control r2


title: CTRL_Day126_PGP1_126_B


title: BG4_uninfected

description:
RNA-seq
BWT8


title: GFP, CLK, Head, ChIP, REP#1

description: Raw data for CHIP-seq


title: CTRL_Day126_PGP1_126_A


title: C3_uninfected

description:
RNA-seq
BWC3


title: C4_uninfected

description:
RNA-seq
BWC4


title: RNA-seq mESC 24h recovery after TSA washout r3

value: 24h recovery from TSA treatment


title: CTRL_Day126_11C1_126_B


title: GFP, CLK, Testis, ChIP, REP#2

description: Raw data for CHIP-seq


title: RNA-seq mESC 24h recovery after TSA washout r2


title: C2_uninfected

description:
RNA-seq
BWC2


title: C1_uninfected

description:
RNA-seq
BWC1


title: CTRL_Day126_C1-2_126_B


title: RNA-seq mESC TSA-treated expt1 r3


title: RNA-seq mESC 24h recovery after TSA washout r1


title: GFP, CLK, Testis, ChIP, REP#1

description: Raw data for CHIP-seq


title: CTRL_Day126_11C1_126_A


title: GFP, CLK, Ovary, ChIP, REP#1

description: Raw data for CHIP-seq


title: RNA-seq mESC TSA-treated expt1 r2


title: CTRL_Day126_C1-2_126_A


title: Input, CLK, Head, ChIP, REP#2

description: Raw data for CHIP-seq


title: RNA-seq mESC TSA-treated expt1 r1


title: F2.A.SIP.b4

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

description:
F2.A.SIP.b4
RZF246ASI

data_processing:
The quality of raw data was assessed using FastQC (v.0.11.9) and MultiQC (v.1.9) prior to processing the data.
The first 12 bases as well as low-quality bases (Phred score < 20) were trimmed from each sequence using Cutadapt (v1.18).
STAR (v.2.7.4.a) was applied to align sequences to the mouse genome (GRCm38) and to determine counts per gene.
After log2 transformation and quantile normalization, data were visualized using PCA plots to assess the quality of data after alignment and possible batch effects.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized values for each Sample

source_name: Small Intestine

growth_protocol: Intestinal organoids were maintained in Advanced DMEM/F12 (ADF) media supplemented with penicillin (100ug/ml), 5ml 200 mM Glutamax, 5ml 10mM Hepes, B27 supplement (Invitrogen) and N2 supplement (Invitrogen). In addition to ADF we also use 50ng/ml recombinant Mouse EGF (Tebu-BIO), mouse Noggin-FC supernatant (~100ng/ml) and R-Spondin-FC supernatant(~ 500ng/ml). Cultures were maintained at 37 degrees celsius and checked monthly for mycoplasma contamination.

extract_protocol:
RNA was isolated using Bioke Nucleospin RNA isolation kit (Bioke) according to the manufacturer’s protocol. DNA degradation was performed using Bioke RNase-Free DNase. We assessed the quality of our RNA samples using Agelent 2100 Bioanalyzer (Agilent Technologies) and only high quality RNA samples were selected based on RIN value.
The organoid RNAseq libraries were prepared using KAPA mRNA HyperPrep (Roche) following the manufacturer’s protocol. They were barcoded, quantified using the Qubit DNA HS kit from Thermofisher and Tapestation 4200 from Agilent, pooled and multiplex sequencing was performed on the Illumina Novaseq6000 platform.

value: Small Intestine

value: Short term in vivo organoids

value: A

tag: batch


title: TSC_Day98_TSC010het_98_B


title: F2.AP.SIP.b4

description:
F2.AP.SIP.b4
RCB242FSI

value: AP


title: Input, CLK, Head, ChIP, REP#1

description: Raw data for CHIP-seq

value: Head


title: F2.AK.CO.b2.OE

description:
F2.AK.CO.b2.OE
RZF342BCOOE

source_name: Colon

value: Colon

value: AK


title: TSC_Day98_TSC010het_98_A


title: F2.A.SIP.a2

description:
F2.A.SIP.a2
RZF331BSI


title: RNA-seq mESC DMSO control expt1 r2

value: mESC wt

value: Wild type


title: Input, CLK, Testis, ChIP, REP#1

description: Raw data for CHIP-seq

value: Testis


title: TSC_Day98_TSC010homo_98_B


title: GFP, CLK, Ovary, ChIP, REP#2

description: Raw data for CHIP-seq

value: Ovary


title: Input, CLK, Ovary, ChIP, REP#2

description: Raw data for CHIP-seq


title: RNA-seq mESC DMSO control expt1 r1


title: F2.AK.SIP.a2

description:
F2.AK.SIP.a2
RZF304ASI


title: Input, CLK, Ovary, ChIP, REP#1

description: Raw data for CHIP-seq


title: ChIP input for YY1 DMSO repeat 1

data_processing:
Data were mapped using bowtie2 against mm10 and hg19 and duplicates reads were discarded. Unique mouse and human reads were discarded and a donwsampling factor for spike-in normalisation was calulated as in Fursova et al. (2019) and bigwigs were produced directly from deduplicated bam files. For detailed protocol see the Method section of the adjoining paper.
Assembly: mm10
Supplementary files format and content: Processed files are given as a spike-in normalised mouse bigwig file of the two merged replicates. Peak files correspond to high-confidence peaks present in both replicates.

extract_protocol:
Chromatin was fixed with 1% formaldehyde for 10 min at RT. To each 12 million mouse cells 1 million HEK cells were added for spike-in calibration. Nuclei were isolated with three different lysis buffers as in Lee et al., 2006 and sonicated in the lysis buffer 3 until the chromatin was disrupted to the size between 200 and 500bp.  For detailed protocol see adjoning paper.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to manufacturer's instructions.

treatment_protocol: DMSO: 0.01% DMSO for 4 hours; TSA: 100 ng/ml TSA for 4 hours; REC: 4 hours TSA (100 ng/ml) followed by 24 hours of recovery


title: TSC_Day98_TSC010_98_B


title: F2.AK.CO.b2

description:
F2.AK.CO.b2
RZF322BCO


title: TSC_Day98_TSC010_98_A


title: F2.A.CO.a2

description:
F2.A.CO.a2
RZF331BCO


title: YY1 ChIP-seq of mESC DMSO control rep2


title: F2.AK.CO.a2

description:
F2.AK.CO.a2
RZF304ACO


title: YY1 ChIP-seq of mESC DMSO control  rep1


title: CTCF ChIP-seq of mESC TSA-treated rep2


title: F2.A.CO.b2

description:
F2.A.CO.b2
RZF246ACO


title: TSC_Day98_TSC009homo_98_B


title: RNA-seq mESC DMSO control expt1 r3


title: Input, CLK, Testis, ChIP, REP#2

description: Raw data for CHIP-seq


title: TSC_Day98_TSC009homo_98_A


title: F2.KP.SIP.a2

description:
F2.KP.SIP.a2
RKAC96BSIP

value: KP


title: TSC_Day98_TSC010homo_98_A

value: cortical organoids


title: TSC_Day98_TSC009_98_B


title: F2.KP.CO.a2

description:
F2.KP.CO.a2
RKAC96BCO


title: CTCF ChIP-seq of mESC TSA-treated rep1

value: cell line


title: normal endometrial tissue-3 Cy3

first: Chengcheng

last: Ren

address: Youzheng 23

institute: The first affiliated hospital of Harbin Medical University

description: the expression of m6A related mRNAs,lncRNAs and other ncRNAs

hyb_protocol: The cRNA mixture was fragmented by adding 5 μL 10* Blocking Agent and 1 μL of 25* Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2*Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-mRNA&lncRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

source_name: normal endometrial tissue

label_protocol: The “IP” RNAs and “Sup” RNAs were added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labeling Kit. The synthesized cRNAs were purified by RNeasy Mini Kit. The concentration and specific actitity (pmol dye/μg cRNA) were measured with NanoDrop ND-1000.  2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed.

extract_protocol: 3-5 μg total RNA and m6A spike-in control mixture were added to 300 μL 1IP buffer (50mM Tris-HCl, pH7.4, 150mM NaCl, 0.1% NP40, 40U/μL RNase Inhibitor) containing 2 μg anti-m6A rabbit polyclonal antibody (Synaptic Systems). The reaction was incubated with head-over-tail rotation at 4°C for 2 hours. 20 L Dynabeads™ M-280 Sheep Anti-Rabbit IgG suspension per sample was blocked with freshly prepared 0.5% BSA at 4°C for 2 hours, washed three times with 300 μL 1IP buffer, and resuspended in the total RNA-antibody mixture prepared above. The RNA binding to the m6A-antibody beads was carried out with head-over-tail rotation at 4°C for 2 hours. The beads were then washed three times with 500 μL 1IP buffer and twice with 500 μL Wash buffer (50 mM Tris-HCl, pH7.4, 50 mM NaCl, 0.1% NP40, 40 U/μL RNase Inhibitor). The enriched RNA was eluted with 200 μL Elution buffer (10 mM Tris-HCl, pH7.4, 1 mM EDTA, 0.05% SDS, 40U Proteinase K, 1μL RNase inhibitor) at 50°C for 1 hour. The RNA was extracted by acid phenol-chloroform and ethanol precipitated.

treatment_protocol: Fresh tissue is removed during surgery and placed in cryovials and then stored in liquid nitrogen

tag: gender

value: female

value: 46 years old

tag: disease state

value: normal tissue


title: normal endometrial tissue-3 Cy5

tag: age


title: CTCF ChIP-seq of mESC DMSO control rep2

tag: genotype


title: TSC_Day98_TSC009_98_A


title: normal endometrial tissue-2 Cy3

value: 44 years old


title: CTCF ChIP-seq of mESC DMSO control rep1


title: TSC_Day98_TSC007_98_B


title: ChIP input for 24h recovery

value: 24h recovery from TSA treatment


title: F2.KP.CO.b2

description:
F2.KP.CO.b2
RKAC102BCO

value: Short term in vivo organoids


title: TSC_Day98_TSC001_98_A


title: ChIP input for DMSO repeat 2


title: F2.KPN.SIP.a2

description:
F2.KPN.SIP.a2
RKA292GSIP

value: Small Intestine

value: KPN


title: F2.KP.SIP.b2

description:
F2.KP.SIP.b2
RKAC102BSIP


title: ChIP input for TSA

value: 100 ng/ml TSA


title: TSC_Day98_TSC007_98_A


title: F2.KPN.CO.a2

description:
F2.KPN.CO.a2
RKA292GCO

value: Colon


title: TSC_Day98_TSC001_98_B


title: normal endometrial tissue-2 Cy5


title: F2.KPN.SIP.b2

description:
F2.KPN.SIP.b2
RKA283CSIP


title: CTRL_Day98_PGP1_98_B


title: normal endometrial tissue-1 Cy3

value: 40 years old


title: ChIP input for DMSO repeat 1

value: mESC wt

value: Wild type


title: normal endometrial tissue-1 Cy5


title: F2.KPN.CO.b2

description:
F2.KPN.CO.b2
RKA283CCO


title: ovarian-endometriosis-3 Cy3

source_name: ovarian-endometriosis

value: 33 years old

value: ovarian endometriosis


title: ovarian-endometriosis-2 Cy3

value: 28 years old


title: H2AK119Ub ChIP-seq mESC 24h recovery after TSA washout rep2

value: cell line


title: CTRL_Day98_PGP1_98_A

value: cortical organoids


title: H2AK119Ub ChIP-seq mESC 24h recovery after TSA washout rep1


title: ovarian-endometriosis-3 Cy5

value: female


title: CTRL_Day98_11C1_98_B


title: F2.AP.CO.b2

description:
F2.AP.CO.b2
RCB242FCO

value: AP


title: H2AK119Ub ChIP-seq of mESC TSA-treated rep2


title: H2AK119Ub ChIP-seq of mESC TSA-treated rep1


title: CTRL_Day98_C1-2_98_B


title: CTRL_Day98_11C1_98_A


title: CTRL_Day98_C1-2_98_A


title: H2AK119Ub ChIP-seq of mESC DMSO control rep2


title: F2.AP.CO.a2

description:
F2.AP.CO.a2
RCB242ECO


title: ovarian-endometriosis-2 Cy5


title: BPten Melanoma 8835 rep3

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

institute: Cancer Research UK Scotland Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts

source_name: Melanoma

growth_protocol: Melanoma fragments from Braf V600E/+ Pten fl/+ mice were transplanted subcutaneously into the flank of C57Bl6 recipient mice, and tumours were harvested at clinical end point.

extract_protocol:
Tumour tissue was lysed using a Precellys Lysing Kit and Precellys Evolution tissue homogeniser (Bertin tecnologies), then RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol. RNA quality was assessed using an Agilent 2200 Tapestation with RNA screen tape.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq RNA LT kit, then run on an Illumina NextSeq 500 (2x36 cycles, paired end, single index).

treatment_protocol: Mice were treated with the noted treatments when a single tumour >7mm diameter was detected, then samples were collected after 72 hrs of treatment.

value: Melanoma

value: Female

tag: sample type

value: Primary Tumour

value: TyrCre BrafV600E/+ Pten fl/+


title: BPten Melanoma 6244 rep3


title: TSC_Day56_TSC010Het_56_B


title: BPten Melanoma 8186 rep3


title: F2.A.SIP.a1

description:
F2.A.SIP.a1
RZF331BSI

value: Small Intestine

value: Short term in vivo organoids

value: A


title: ovarian-endometriosis-1 Cy3

value: 42 years old


title: F2.AP.SIP.a2

description:
F2.AP.SIP.a2
RCB242ESI


title: H3K27ac ChIP-seq mESC 24h recovery after TSA washout rep2

value: mESC wt

value: 24h recovery from TSA treatment


title: F2.A.CO.a1

description:
F2.A.CO.a1
RZF331BCO

value: Colon


title: RNA-seq in 48-hour mouse gastruloids - TSA treated r2

value: 48h gastruloid

value: CTCF-GFP-AID

value: 20 ng/ml TSA


title: ovarian-endometriosis-1 Cy5

value: ovarian endometriosis


title: TSC_Day56_TSC010Het_56_A

value: cortical organoids


title: BPten Melanoma 6244/8186 rep2


title: F2.AK.CO.b1.OE

description:
F2.AK.CO.b1.OE
RZF342BCOOE

value: AK


title: F2.AK.CO.b1

description:
F2.AK.CO.b1
RZF322BCO


title: TSC_Day56_TSC010Homo_56_B


title: H3K27ac ChIP-seq mESC 24h recovery after TSA washout rep1

value: cell line

value: Wild type


title: H3K27ac ChIP-seq of mESC TSA-treated rep2

value: 100 ng/ml TSA


title: F2.AK.SIP.a1

description:
F2.AK.SIP.a1
RZF304ASI


title: F2.AK.CO.a1

description:
F2.AK.CO.a1
RZF304ACO


title: H3K27ac ChIP-seq of mESC TSA-treated rep1


title: GFP, CYC, Ovary, ChIP, REP#1

description: Raw data for CHIP-seq

value: Ovary


title: H2AK119Ub ChIP-seq of mESC DMSO control rep1


title: TSC_Day56_TSC010_56_B


title: BPten Melanoma 8186 rep2

value: Melanoma

value: Female

value: Primary Tumour

value: TyrCre BrafV600E/+ Pten fl/+


title: BPten Melanoma 6244/8186 rep3


title: H3K27ac ChIP-seq of mESC DMSO control rep2

value: mESC wt


title: BPten Melanoma 8835 rep2


title: F2.KP.SIP.a1

description:
F2.KP.SIP.a1
RKAC96BSIP

value: Small Intestine

value: Short term in vivo organoids

value: KP


title: TSC_Day56_TSC010_56_A


title: H3K27ac ChIP-seq of mESC DMSO control rep1


title: TSC_Day56_TSC009Homo_56_B


title: BPten Melanoma 8835 rep1


title: F2.KP.SIP.b1

description:
F2.KP.SIP.b1
RKAC102BSIP


title: F2.KP.CO.a1

description:
F2.KP.CO.a1
RKAC96BCO

value: Colon


title: TSC_Day56_TSC010Homo_56_A


title: BPten Melanoma 6244 rep1


title: BPten Melanoma Vehicle rep3

value: Vehicle (0.5% HPMC + 0.1% Tween-80)


title: BPten Melanoma 6244 rep2


title: TSC_Day56_TSC009Homo_56_A


title: H3K27me3 ChIP-seq mESC 24h recovery after TSA washout rep1

value: 24h recovery from TSA treatment


title: BPten Melanoma 8186 rep1


title: F2.KP.CO.b1

description:
F2.KP.CO.b1
RKAC102BCO


title: H3K27me3 ChIP-seq mESC 24h recovery after TSA washout rep2


title: H3K27me3 ChIP-seq of mESC TSA-treated rep2


title: TSC_Day56_TSC009_56_A

value: cortical organoids


title: TSC_Day56_TSC009_56_B


title: BPten Melanoma Vehicle rep2


title: F2.A.CO.b1

description:
F2.A.CO.b1
RZF246ACO

value: A


title: H3K27me3 ChIP-seq of mESC DMSO control rep2

value: cell line


title: F2.KPN.SIP.a1

description:
F2.KPN.SIP.a1
RKA292GSIP

value: KPN


title: TSC_Day56_TSC007_56_B


title: BPten Melanoma 6244/8835 rep3


title: F2.KPN.CO.a1

description:
F2.KPN.CO.a1
RKA292GCO


title: H3K27me3 ChIP-seq of mESC TSA-treated  rep1

value: Wild type

value: 100 ng/ml TSA


title: TSC_Day56_TSC007_56_A


title: BPten Melanoma 6244/8835 rep2

value: Melanoma


title: F2.KPN.CO.b1

description:
F2.KPN.CO.b1
RKA283CCO


title: TSC_Day56_TSC001_56_B


title: BPten Melanoma 6244/8186 rep1

value: Female


title: F2.KPN.SIP.b1

description:
F2.KPN.SIP.b1
RKA283CSIP


title: H3K9me3 ChIP-seq mESC 24h recovery after TSA washout rep2


title: BPten Melanoma Vehicle rep1

value: Primary Tumour


title: CTRL_Day56_PGP1_56_B


title: H3K27me3 ChIP-seq of mESC DMSO control  rep1


title: F2.AP.SIP.a1

description:
F2.AP.SIP.a1
RCB242ESI

value: AP


title: F2.AP.CO.b1

description:
F2.AP.CO.b1
RCB242FCO


title: TSC_Day56_TSC001_56_A


title: H3K9me3 ChIP-seq mESC 24h recovery after TSA washout  rep1

value: mESC wt


title: CTRL_Day56_PGP1_56_A


title: H3K9me3 ChIP-seq of mESC TSA-treated rep1


title: CTRL_Day56_11C1_56_B


title: CLPs, Notch1+/dTAD (PAJ011719-014)

first: Kostandin

middle: V

last: Pajcini

state: IL

address: 909 S Wolcott Ave.

department: Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

data_processing:
Adaptor trimming performed with FASTQ Toolkit Version: 2.2.0 on BaseSpace (Illumina)
Alignment to mm10 performed using RNA-Seq Alignment Version: 2.0.0 on BaseSpace (Illumina)
Differential expression analysis performed using RNA-Seq Differential Expression Version: 1.0.1 on BaseSpace (Illumina)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Common Lymphoid Progenitor (CLP)

extract_protocol:
4-11x10^6 adult BM CLP cells from WT, Notch1+/-, or Notch1+/ΔTAD were sorted into RNA lysis buffer (Invitrogen) and stored at -80ºC until RNA extraction. Total RNA was extracted using PicoPure™ RNA Isolation Kit (ThemoFisher Scientific, USA) with inclusion of DNase treatment step.
RNA sequencing libraries for Illumina sequencing were prepared in one batch using strand-specific QuantSeq 3’ RNAseq kit (Lexogen, FWD, Cat. No. 015) along with negative and positive controls.

tag: strain

value: Common Lymphoid Progenitor (CLP)

tag: cell source

value: bone marrow

tag: developmental stage

value: Adult

value: 6-12 weeks old

tag: sorting markers


title: CLPs, Notch1+/- (PAJ011719-013)


title: H3K9me3 ChIP-seq of mESC TSA-treated rep2


title: BPten Melanoma 6244/8835 rep1

tag: Sex

value: TyrCre BrafV600E/+ Pten fl/+


title: F2.AP.CO.a1

description:
F2.AP.CO.a1
RCB242ECO

value: Colon

value: Short term in vivo organoids


title: CTRL_Day56_11C1_56_A

value: cortical organoids


title: H3K9me3 ChIP-seq of mESC DMSO control rep2

value: cell line


title: H3K9me3 ChIP-seq of mESC DMSO control rep1


title: CLPs, Notch1+/- (PAJ011719-012)


title: CTRL_Day56_C1_2_56_A


title: H3K4me3 ChIP-seq mESC 24h recovery after TSA washout rep2

value: 24h recovery from TSA treatment