title: S-2P- B cell v2D14 Rep1 - GEX

description: 10x Genomics


title: ChIP_DIV12_Ctrl-sh_Input_biorep2

status: Public on Jul 07 2023

type: SRA

city: Saint Louis

first: Nicole

last: Hamagami

state: MO

address: 4487 McPherson Ave. Unit C

department: Neuroscience

country: USA

institute: Washington University in St. Louis

library_source: genomic

data_processing:
ChIP-seq reads were mapped to the mm9 genome using bowtie2 alignment and reads were extended based on library sizes and deduplicated.
Bedtools coverage -counts parameter was used to quantify ChIP signal
To generate bigWig files, bedtools genomecov parameter was used to convert ChIP-seq reads to a bedgraph format and then were renormalized (to counts per million, cpm). Bedgraphs were subsequently converted to bigWigs.
Assembly: mm9
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: cultured cortical neurons

growth_protocol: Neurobasal medium supplemented with 5% fetal bovine serum, GlutaMAX, B27 Supplement and Antibiotic-Antimycotic. Cells were maintained at 37oC with 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico sonicator (Diagenode) for 30 cycles of 30s on/ 30s off.
ChIP-seq libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) and complemented with the Accel-NGS 2S Set A adapters. Up to 4ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 12-16 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent DNA D5000 Screentape Assay Kit.

treatment_protocol: Cells were treated with lentivirally expressed shRNAs at MOI of 3 on days in vitro (DIV) 1. Cells were grown in vitro until DIV 12.

tag: strain

tag: cell type

value: cultured cortical neurons

tag: biological replicate

tag: chip antibody

tag: treatment

value: Ctrl sh


title: Cd206_hi_0h_4

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

description:
Cd206_hi_0h
Mhc2_Cd206_baseline_raw_expression_matrix.csv

library_source: transcriptomic single cell

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v3.1.1). Then, low quality cells (expressing less than 500 genes or more than 9000 genes), potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for dural Cd206_hi cells and Mhc2_hi cells at base line condition.

molecule: total RNA

source_name: mouse dural cd206_hi cell

growth_protocol: Smart-Seq3 single-cell RNA libraries

extract_protocol:
FACS sorted dural Cd206_hi cells and Mhc2_hi cells were processed by Smart-Seq3 protocol
Libraries were generated following Smart-Seq3 protocol (Hagemann-Jensen M et al.,Single-cell RNA counting at allele and isoform resolution using Smartseq3. Nat Biotechnol 2020)

value: mouse dural cd206_hi cell

value: FACS sorted

tag: molecule type

value: single cell RNA


title: Cd206_hi_0h_3


title: Cd206_hi_0h_5


title: S-2P+ B cell v2D14 Rep2 - ADT

city: Bethesda

first: Susan

last: Moir

state: Maryland

address: 9000 Rockville Pike

department: NIAID

institute: NIH

description: 10x Genomics

data_processing:
The GEX and ADT libraries were mapped to the GRCh38 human reference genome using CellRanger version 6.0.1. Data were further processed using Seurat version 4.1.0 running in R v4.1.0.
B cell receptor V(D)J data processing, B cell receptor (BCR) V(D)J repertoire data processing and analysis were carried out using tools in the Immcantation framework (www.immcantation.org). V(D)J genes were re-assigned from CellRanger output using IgBLAST v.1.15.0. Cells with multiple IGH V(D)J sequences were assigned to the most abundant IGH V(D)J sequence by UMI count. Following V(D)J gene annotation, non-functional sequences were removed from further analysis, and functional V(D)J sequences were assigned into clonal groups using Change-O v.1.0.0. Then, the immune repertoire information was added into Seurat object as meta data integrated to the transcriptome information at a per-cell level.
Assembly: hg38
Supplementary files format and content: Tab-separated values files, matrix files, antibody feature reference csv files

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
B cells of three vaccinees were isolated from thawed cryopreserved peripheral blood mononuclear cells (PBMC) by negative magnetic bead-based selection using a B cell enrichment cocktail (StemCell Technologies). The isolated B cells were stained with PE-Cy7-conjugated anti-human CD19 (ThermoFisher, cat# 25-0198-42) and APC-H7-conjugated anti-human CD20 (BD Biosciences, cat# 560734). SARS-CoV-2-specific B cells were identified using biotinylated spike protein (S-2P) tetramerized with PE-Cy5.5-labeled streptavidin (SA) (ThermoFisher, cat# SA1018) at a molar ratio of 4:1. Three B cell populations were sorted, (1) CD20+S-2P+ B cell, (2) CD20+S-2P-  B cell, and (3) CD20- B cell (plasmablast) populations, using a BD FACSAria Fusion instrument (BD Biosciences).
Isolated B cells from different donors were pooled evenly before cell sorting. Cells from each donor were demultiplexed in silico using donor-specific single nucleotide polymorphism (SNP) information collected during data analysis. Multiple cell pools were prepared, such that cells from the same donors but different time points were in different pools. After cell sorting, cell pools from v2D28 and v2M6 timepoints were Fc blocked (Human TruStain FcX, BioLegend), CITE-seq and hashtag stained with custom TotalSeq-C cocktail antibodies, (including RBD and S1 oligo-tagged tetramers, and washed 3x with staining buffer (2% BSA in PBS). Due to the lower frequency of S-2P+ B cells at earlier time points, pools from v1D14 to v2D14 timepoints were CITE-seq and hashtag (HTO) stained before cell sorting to avoid cell loss during washes. No RBD and S1 oligo-tagged tetramers could be added due to technical reasons. Final cell pools were suspended in 0.04% BSA in PBS and then counted before being immediately processed by the single cell partitioning step. Cell pools were mixed with a reverse transcription (RT) mix and partitioned into single cell Gel-Bead in Emulsion (GEM) using the 10x Chromium Single Cell Immune Profiling Next GEM v2 Chemistry Kit (10x Genomics, Pleasanton, CA). The RT step was conducted using a C1000 touch Thermo Cycler (BioRad, Hercules, CA). Single-cell gene expression (GEX), cell surface protein (ADT) and B cell receptor (BCR) libraries were prepared as instructed by 10x Genomics Single Cell Immune Profiling kit v.2 user guide. A total of 84 libraries were quality control tested using a TapeStation 4200 (Agilent, Santa Clara, CA) and quantified using the KAPA Library Quantification kit (Roche, Wilmington, MA). These libraries were then pooled and sequenced on Illumina NovaSeq platform (Illumina, San Diego, CA) using the sequencing parameters recommended by the 10x Genomics user guide. The minimum sequencing depths were 50,000 read pairs/cell for the GEX library, 5,000 read pairs/cell for the BCR library, and 5,000 read pairs/cell for the ADT library. Sequencing saturation of the libraries was 80% for the GEX and 10% for the BCR and ADT libraries.

value: S-2P+ B cell

tag: timepoint


title: DMS454_DMSO_4h_rep1

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

library_source: transcriptomic

data_processing:
Multiplexed samples were sequenced on an Illumina HiSeq 2500 system. Base-calling was performed using the Real-Time Analysis (RTA) software version 2.4.11. Conversion of the raw bcl2 output files to gzipped FASTQ files was performed using the bcl2fastq2 software version 2.20.0 provided by Illumina.
Data was processed with a pipeline building upon the implementation of the ENCODE "Long RNA-seq" pipeline: In brief, paired-end sequencing reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (source 1000 Genomes Project - GRCh38_full_analysis_set_plus_decoy_hla.fa,  excluding alternate contigs, chromosome mapping via grch38_ucsc2ensembl.txt) using the STAR (v2.5.2b) aligner allowing for soft clipping of adapter sequences. For quantification, transcript annotation files from Ensembl version 86 were used. Samples were quantified with the above annotations using featureCount (v1.5.1). Quality controls were implemented using FastQC (v0.11.5), picardmetrics (v0.2.4), and dupRadar (v1.0.0) at the respective steps. Finally, differential expression analysis was performed on the counts derived from featureCount using limma/voom.
Assembly: GRCh38
Supplementary files format and content: Processed data files contain sample-wise results produced by FeaturesCounts and include raw count values for each gene.

source_name: DMS 454 cancer cell line

growth_protocol: The cell lines were grown in the media recommended by the vendor.

extract_protocol:
Cells were lysed in TRI lysis reagent (Qiagen, #79306) according to the manufacturer's instructions. Total RNA was isolated with RNAeasy Mini Kit (Qiagen, #73404).
RNA-seq libraries were prepares using the TruSeq RNA Library Preparation Kit v2 according to manufacturer's instructions.

treatment_protocol: See samples section.

tag: cell line

value: DMS 454

tag: disease

value: small cell lung cancer

tag: replicate

tag: ID


title: ChIP_DIV12_Ctrl-sh_Input_biorep1


title: DMS454_BI00894999_100nM_4h_rep2


title: DMS454_BI00894999_100nM_4h_rep1


title: ChIP_DIV12_Ctrl-sh_DNMT3A_biorep2

value: DNMT3A (abcam, #ab2850)


title: Cd206_hi_0h_1


title: S-2P+ B cell v2D14 Rep2 - GEX

description: 10x Genomics


title: COR-L95_DMSO_4h_rep2

source_name: COR-L95 cancer cell line


title: DMS454_DMSO_4h_rep2


title: ChIP_DIV12_Ctrl-sh_H3K36me2_biorep2


title: ChIP_DIV12_Ctrl-sh_H3K36me2_biorep1


title: S-2P+ B cell v2D14 Rep1 - ADT

description: 10x Genomics


title: S-2P+ B cell v2D14 Rep1 - GEX

description: 10x Genomics


title: CD140+/PDGFRa+_GR_IP

city: nanjing

first: yifan

last: lv

state: jiangsu

address: 300 Guangzhou Road

department: Department of Geriatrics

country: China

institute: the First Affiliated Hospital to Nanjing Medical University

data_processing:
Raw sequence reads were initially processed by FastQC for quality control,
For each sample, 20 million fixed cells were lysed to prepare nuclear extracts. After chromatin shearing by sonication, lysates were incubated overnight at 4°C with protein A Dynabeads coupled with 5 μg of antibody. After immunoprecipitation, beads were recovered using a magnet and washed. DNA was eluted and cross􀏋links reverted at 65􀁥C for 4 hours then purified with QIAGEN Kit. DNA was quantitated using the Qubit® dsDNA HS assay and a Qubit® 2.0 Fluorimeter (Invitrogen). For ChIP-Seq, 5ng of purified ChIP DNA were used to generate the sequencing library using a NEB kit and sequenced with the Illumina HiSeq X Ten. ChIP-seq reads were aligned to mm10 using Bowtie2. Only unique mapped reads were considered for further analysis. Aligned reads from biological replicates were pooled together. Afterward, peaks were merged together using BEDTools(2.17.0), and then resized to 200 bp.
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 was used to call peaks with the sonicated input as a control and an initial threshold q-value of 0.01 as cutoff.
Supplementary_files_format_and_content: Sam files were converted to Bam format using Samtools and used for peak calling.

source_name: PDGFRa+ adipocyte progenitor subgroup with DEX treatment

growth_protocol: CD137+ and PDGFRα+ cells were isolated from SAT or VAT by MACS. Cells were cultured in cultured under growth condition and then exposed toadipogenesis cocktail.

extract_protocol:
After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
Lysates were clarified from sonicated nuclei GR-DNA were isolated with antibody.

treatment_protocol: Differentiated CD137+ and PDGFRα+ cells were treated with Dexamethasone(DEX,1μM).

tag: tissue

value: adipose

value: adipose progenitors

value: DEX treatment


title: COR-L95_BI00894999_100nM_4h_rep2


title: CD140+/PDGFRa+_Input


title: COR-L95_BI00894999_100nM_4h_rep1


title: CD137+_Input

source_name: CD137+ adipocyte progenitor subgroup with DEX treatment


title: ChIP_DIV12_Ctrl-sh_DNMT3A_biorep1


title: Cd206_hi_0h_2


title: CD137+_GR_IP


title: TBI 6 hpi mouse brain legacy

city: Spring Hill

first: Duy

middle: Truong

last: Pham

state: Queensland

address: 391 Wichkham Terrace

country: Australia

institute: The University of Queensland

description: 10x Genomics legacy

data_processing:
Raw BCL files were processed by bcl2fastq V2.7.0, and the fastq reads mapped to the mouse reference genome GRCm38
Assembly: GRCm38
Supplementary files format and content: count_matrix.tsv: Count matrix of legacy data
Supplementary files format and content: spatial.tsv: Spatial information of legacy data
Supplementary files format and content: image.jpg: H&E image file

source_name: Brain

extract_protocol:
Additional TBI samples (6 hours and 3 days post-injury) were independently prepared with the Legacy ST kit, an earlier version of 10x Genomics' ST platform. Mouse TBI samples were obtained as described above and prepared for ST analysis following the Library Preparation Manual Version 190219 (10x Genomics, USA). Briefly, ipsilateral brain hemisphere samples were collected at 6 hours and 3 days post-TBI and embedded in O.C.T. Next, 10 μm cryosections were collected onto the Legacy ST library preparation slide, fixed with 4% paraformaldehyde at room temperature and then stained with haematoxylin for 10 minutes, blueing buffer for 1 minute, and eosin Y for 3 minutes in an RNase-Free environment. High-resolution H&E images were again captured using the Zeiss Axio Imager.
ST sequencing libraries were prepared as per the manufacturer’s instructions, with pre-permeabilisation and permeabilisation performed at 20 minutes and 7 minutes, respectively. On-slide cDNA synthesis, tissue removal, probe cleavage, and final library preparation were all performed as per the manual. High-quality cDNA libraries with sizes ranging between 660-780bp were obtained and sequenced on the Illumina Nextseq500, using a 150 cycles kit with read configuration as read 1 (26 bp) and read 2 (124 bp).
Spatial transcriptomics Legacy platform

value: Brain

value: multiple cell types


title: Type 2 Diabetic Retinopathy above 15 years - Clustering group C - #3

type: RNA

city: Taichung

first: Fuu-Jen

last: Tsai

address: No.2, Yude Rd., North Dist.

department: Department of Medical Research

country: Taiwan

institute: China Medical University Hospital

hyb_protocol: The hydridization was performed against the GeneChip™ miRNA 4.0 Array (Catalog number: 902413) by following the Affymetrix protocol for 17 hours at 45°C and 60 rpm.

scan_protocol: The arrays were subsequently washed (Affymetrix Fluidics Station 450) and stained with streptavidin-phycoerythrin(GeneChip® Hybridization, Wash, and Stain Kit, 900720), and were scanned on an Affymetrix GeneChip® Scanner 3000 7G.

data_processing:
The scanning-output data, which was stored in CEL files, was analyzed by using Transcriptome Analysis Console (TAC) software of the Affymetrix company with default parameters. Moreover, uploaded CHP files were generated from the CEL files by the software.
The levels of miRNA expression were determined with the Tukey biweight average scores, which was compared with eBayes, which is one of ANOVA methods, which was performanced by the TAC suite (version 4.0.2.15).

label: Biotin

source_name: Type-2 diabetic patient, with DR complication within 15 years, was assigned to group C by hierarchical clustering on principal components.

label_protocol: 300 ng of each sample was amplified and labeled using the GeneChip™ WT Sense Target Labeling and Control Reagents (Catalog number: 900652).

growth_protocol: According to medical records of China Medical University Hospital and Changhua Christian Hospital, the selected candidates were diagnosed and classified into detailed groups non-diabetes as control, type-2 diabetes without DN/DR complications (T2D), type-2 diabetes with nephropathy (T2DN), and type-2 diabetes with retinopathy (T2DR). Based on the classifications, the blood samples of them were collected individually. Next, whole cells in the samples was accumulated by centrifugation and homogenized to prepare mixtures for RNA extraction.

extract_protocol: Total RNA was subsequently isolated by RNeasy Mini Kit (P/N: 74104, QIAGEN) according to the manufacturer's instructions. Then, RNA quantity and purity were assessed at 260 nm and 280nm using a Nanodrop (ND-1000; Labtech. International).

value: Blood

tag: gender

value: Male

tag: age

value: 54 years old

tag: t2d duration

value: 15 years

tag: hba1c (%) of the sample

tag: bmi

tag: sampling in t2d stage

value: T2D with retinopathy

tag: reference

value: Changhua Christian Hospital


title: Type 2 Diabetic Nephropathy above 15 years - Clustering group C - #1

source_name: Type-2 diabetic patient, with DN complication within 15 years, was assigned to group C by hierarchical clustering on principal components.

value: 81 years old

value: 21 years

value: T2DN stage II (30 ≤ ACR < 300 mg/g)


title: Type 2 Diabetic Nephropathy above 15 years - Clustering group C - #2

value: Female

value: 62 years old

value: 24 years


title: TBI 3 dpi mouse brain legacy

description: 10x Genomics legacy

tag: cell type


title: Input-2wk_GTCCGC

source_name: cerebral cortex

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using the S220 Ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) and complemented with the Accel-NGS 2S Set A adapters. Up to 4ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 12-16 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent DNA D5000 Screentape Assay Kit.

tag: strain

value: C57/BL6 (wildtype)

value: cerebral cortex

tag: time

value: 2 week

tag: biological replicate

tag: chip antibody


title: InputB1


title: Input_A2


title: InputB2


title: SL_31

city: Toronto

first: Shahrzad

last: Ghazisaeidi

state: Ontario

address: 250 College Street

department: Krembil Centre for Neuroinformatics

country: Canada

institute: Centre for Addiction and Mental Health

data_processing:
Quality control check for fastq files
The filtered reads are aligned to a reference genome using STAR
Trimmed sequences were alligned to genome assemblies
Assembly: Mus musculus (GRCm38-mm10.0) and Rattus Norvegicus assembly (Rnor_6.0)
Supplementary files format and content: raw counts- text file csv

organism: Rattus norvegicus

source_name: L4:L5- Spinal cord dorsal horn-ipsi

extract_protocol:
RNA was extracted from the tissue using Rneasy kit Qiagen and preserved in RNALater
cDNA library was prepared using High Capacity RNA-to cDNA kit, ThermoFisher according to manufactorer's instructions and sequenced at TCAG at The Hospital for Sick Children.

treatment_protocol: Spared nerve injury (SNI) and Sham Surgery , Post operative day 7.

value: L4:L5- Spinal cord dorsal horn-ipsi

tag: genotype

value: WT

value: Sprague-Dawley

tag: Sex

tag: treatment

value: SHAM


title: S-2P- B cell v2D28 - GEX

description: 10x Genomics

value: S-2P- B cell

tag: timepoint


title: Input_A1

tag: tissue


title: S-2P- B cell v2D28 - ADT

description: 10x Genomics


title: S-2P+ B cell v2D28 Rep2 - ADT

description: 10x Genomics

value: S-2P+ B cell


title: SL_32

source_name: L4:L5- Spinal cord dorsal horn-contra

value: L4:L5- Spinal cord dorsal horn-contra


title: SL_30

value: SNI


title: S-2P+ B cell v2D28 Rep2 - GEX

description: 10x Genomics


title: Type 2 Diabetic Retinopathy above 15 years - Clustering group C - #2

value: Blood

tag: gender

value: Male

value: 69 years old

value: 17 years

value: T2D with retinopathy

value: Changhua Christian Hospital


title: SL_29

value: Female


title: ChIP_cortex_2week_H3K4me2_1

value: C57/BL6 (wildtype)

value: cerebral cortex

value: H3K4me2 (abcam, #ab7766)


title: Type 2 Diabetic Retinopathy above 15 years - Clustering group C - #1

tag: age

value: 76 years old

value: 22 years


title: ChIP_cortex_2week_H3K4me1_2

value: 2 week

value: H3K4me1 (abcam, #ab8895)


title: S-2P+ B cell v2D28 Rep1 - ADT

description: 10x Genomics

value: S-2P+ B cell


title: Type 2 Diabetic Retinopathy above 15 years - Clustering group B - #2

source_name: Type-2 diabetic patient, with DR complication within 15 years, was assigned to group B by hierarchical clustering on principal components.

value: 66 years old

tag: t2d duration

value: 26 years

value: T2DN stage II (30 ≤ ACR < 300 mg/g)


title: SL_28

value: L4:L5- Spinal cord dorsal horn-contra

value: WT

value: Sprague-Dawley

value: Male

value: SHAM


title: ChIP_cortex_2week_H3K4me1_1


title: SL_27

value: L4:L5- Spinal cord dorsal horn-ipsi


title: Type 2 Diabetic Nephropathy above 15 years - Clustering group B - #2

source_name: Type-2 diabetic patient, with DN complication within 15 years, was assigned to group B by hierarchical clustering on principal components.

value: Blood

value: 42 years old

value: around 15 years

tag: hba1c (%) of the sample

value: Changhua Christian Hospital


title: Type 2 Diabetic Nephropathy above 15 years - Clustering group B - #1

value: Female

value: 74 years old

tag: bmi


title: ChIP_cortex_2week_DNMT3A_2

description: Gabel_Chip_DNMT3AB2_NEBNext_Index_22_CGTACGTAAT_S8_R1_001.fastq.gz

value: C57/BL6 (wildtype)

value: cerebral cortex

value: 2 week

value: DNMT3A (abcam, #ab2850)


title: SL_25

value: SNI


title: ChIP_cortex_2week_H3K4me2_2

value: H3K4me2 (abcam, #ab7766)


title: MAIT cells, Healthy donor 4, Influenza virus

city: London

first: Patricia

last: Barral

address: London

country: United Kingdom

institute: King's College London

data_processing:
STAR (1.3.1)
Differential expression assessment by DESeq2 version 1.32.0
GRCh38, Ensembl release-95
Supplementary files format and content: RSEM output tables

source_name: Blood

growth_protocol: streptomycin during 20h in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using NucleoSpin RNA XS kit (Macherey-Nagel) following the manufacturer’s instructions
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional PolyA mRNA kit (New England Biolabs) following manufacturer's protocols.

treatment_protocol: mL, Sigma-Aldrich) or H1N1 PR8 influenza virus (MOI 1). Then, MAIT cells were sorted as Zombie-CD14-CD19-CD3ε+CD8α+CD161+Vα7.2+ cells directly in Extraction Buffer of the RNA extraction kit

tag: cell line

value: Primary cells

value: MAIT cells

value: Influenza virus


title: SL_24

value: L4:L5- Spinal cord dorsal horn-contra

value: WT

value: Sprague-Dawley

value: SHAM


title: SL_26

value: Male


title: ChIP_cortex_2week_H3K36me2_2


title: ChIP_cortex_2week_DNMT3A_1

description: Gabel_Chip_DNMT3AB1_NEBNext_Index_9_GATCAGATCT_S4_R1_001.fastq.gz


title: ChIP_cortex_2week_H3K36me2_3


title: Type 2 Diabetes without complications above 15 years - Clustering group C - #5

source_name: Type-2 diabetic patient, without DN and DR complications within 15 years, was assigned to group C by hierarchical clustering on principal components.

value: Blood

value: 67 years old

value: 11 years

tag: sampling in t2d stage

value: T2D without complications (T2D duration ≥ 10 years & HbA1c ≥ 7%)

tag: reference

value: Changhua Christian Hospital


title: MAIT cells, Healthy donor 4, IFNα2A

tag: cell type


title: Type 2 Diabetes without complications above 15 years - Clustering group C - #3

value: 60 years old


title: ChIP_cortex_2week_H3K36me2_1

tag: strain

value: C57/BL6 (wildtype)

value: cerebral cortex

tag: time

value: 2 week


title: MAIT cells, Healthy donor 4, Control

value: Primary cells

value: Control (PBS)


title: SL_23

value: L4:L5- Spinal cord dorsal horn-ipsi

value: Female


title: Type 2 Diabetes without complications above 15 years - Clustering group C - #4

value: 61 years old

value: 12 years

value: T2D without complications (T2D duration ≥ 10 years & HbA1c < 7%)


title: B16_Day9_S4

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

description: cancer.mouse.counts.txt

data_processing:
bcl2fastq2 v2.20 was used to convert BCL files generated by Illumina NextSeq to standard FASTQ file formats
Alignment to GRCm38.p5 was done using STAR v2.5.3a with default settings except for the following ones: --sjdbOverhang 74 --quantMode GeneCounts.
The resulting gene counts were further processed and normalised using DESeq2 R package v1.20.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: raw counts

source_name: B16 melanoma

growth_protocol: Cancer cell lines were kept in growth medium DMEM (GIBCO) supplemented with 10% (v/V) FBS (Hyclone), GlutaMAX™ (Gibco), sodium pyruvate (GIBCO) and penicillin-streptomycin (Hyclone). All cells were grown at 37ºC, 5% (v/V) CO2.

extract_protocol:
Reprogrammed cancer cells were sorted through co-expression of eGFP, CD45+ and MHC-II+ at day 3, 5, 7 and 9 post-transductions. LLC co-expressing eGFP and CD45+ were sorted at day 7 and day 9 for mRNA-seq analysis. eGFP transduced cells were stained normally for CD45 and MHC-II and confirmed for null expression of both markers before purification based on eGFP expression. Total RNA from 3000-5000 pre-sorted cells was extracted following TRIzol™ manufacturer’s protocol (Invitrogen).
cDNA was generated with the SMARTSeq v4 Ultra low input RNA kit (Takara) and amplified with 8 cycles followed by purification by AMPure XP beads. cDNA was analyzed using the Agilent High sensitivity DNA kit on an Agilent Bioanalyzer 2100 (Agilent). Library preparation was performed using the Nextera XT DNA library preparation kit (Illumina) according to the manufacturer’s protocol. Following tagmentation of cDNA, forward and reverse indexes were added by 12 cycles of PCR. Normalization was performed by normalizing beads according to manufacturer’s protocol and libraries were mixed in equal volumes and sequenced on an Illumina NextSeq 500 (75-bp paired-end).

treatment_protocol: Cell lines used for reprogramming were seeded at a density of 6x104 cells/mL in six-well plates. Cells were transduced with 2x104 viral copy numbers/cell.  On day 3 of reprogramming, cells were seeded 1:6 in 100mm2 dishes and media changed every 2-3 days until fluorescently activated cell sorting for eGFP+; eGFP+ CD45+ MHC-II+ or eGFP+ CD45+.

tag: strain background

value: CD45+ MHC-II+


title: MAIT cells, Healthy donor 3, Influenza virus

value: Blood

value: MAIT cells

tag: genotype

value: Influenza virus


title: Type 2 Diabetic Retinopathy above 15 years - Clustering group B - #1

value: Male

value: 63 years old

value: 21 years

value: T2D with retinopathy


title: SL_22

value: L4:L5- Spinal cord dorsal horn-contra

value: WT

value: Sprague-Dawley

tag: Sex

value: SNI


title: S-2P+ B cell v2D28 Rep1 - GEX

description: 10x Genomics

value: S-2P+ B cell


title: Type 2 Diabetes without complications above 15 years - Clustering group C - #2

value: 51 years old

value: T2D without complications (T2D duration ≥ 10 years & HbA1c ≥ 7%)

value: Changhua Christian Hospital


title: MAIT cells, Healthy donor 4, Klebsiella

value: Primary cells

tag: treatment

value: Klebsiella pneumoniae


title: SL_21

value: L4:L5- Spinal cord dorsal horn-ipsi

value: Female


title: B16_Day9_S3

description: cancer.mouse.counts.txt

value: CD45+ MHC-II+


title: Type 2 Diabetes without complications above 15 years - Clustering group C - #1

value: Blood

value: 61 years old

value: 15 years

value: T2D without complications (T2D duration ≥ 10 years & HbA1c < 7%)


title: MAIT cells, Healthy donor 3, IFNα2A

value: MAIT cells


title: MAIT cells, Healthy donor 3, Control

value: Control (PBS)


title: MAIT cells, Healthy donor 2, Influenza virus

value: Influenza virus


title: B16_Day9_S2

description: cancer.mouse.counts.txt


title: MAIT cells, Healthy donor 3, Klebsiella


title: SL_20

value: L4:L5- Spinal cord dorsal horn-contra

value: WT

value: Sprague-Dawley

value: Male

value: SHAM


title: Type 2 Diabetes without complications above 15 years - Clustering group B - #4

source_name: Type-2 diabetic patient, without DN and DR complications within 15 years, was assigned to group B by hierarchical clustering on principal components.

value: 73 years old

value: 19 years

value: T2D without complications (T2D duration ≥ 10 years & HbA1c ≥ 7%)

value: Changhua Christian Hospital


title: Type 2 Diabetes without complications above 15 years - Clustering group B - #3

value: 63 years old

value: around 15 years


title: SL_19

value: L4:L5- Spinal cord dorsal horn-ipsi


title: SL_18

value: SNI


title: B16_Day9_S1

description: cancer.mouse.counts.txt

value: CD45+ MHC-II+


title: MAIT cells, Healthy donor 2, IFNα2A

value: Blood

value: Primary cells

value: MAIT cells


title: Type 2 Diabetes without complications above 15 years - Clustering group B - #2

value: 66 years old

value: 17 years


title: Type 2 Diabetes without complications above 15 years - Clustering group B - #1

value: 56 years old

value: 20 years

value: T2D without complications (T2D duration ≥ 10 years & HbA1c < 7%)


title: MAIT cells, Healthy donor 2, Klebsiella

value: Klebsiella pneumoniae


title: B16_Cnt_S1

description: cancer.mouse.counts.txt

value: unsorted cells


title: SL_16

value: L4:L5- Spinal cord dorsal horn-contra

value: WT

value: Sprague-Dawley

value: Male

value: SHAM


title: B16_Cnt_S2

description: cancer.mouse.counts.txt


title: LLC_Day9_S3

description: cancer.mouse.counts.txt

source_name: Lewis Lung Carcinoma (LLC)

value: LLC


title: SL_15

value: L4:L5- Spinal cord dorsal horn-ipsi


title: SL_14

value: SNI


title: MAIT cells, Healthy donor 2, Control

value: Blood

value: Primary cells

value: Control (PBS)


title: Type 2 Diabetic Retinopathy within 5 years - Clustering group C - #3

source_name: Type-2 diabetic patient, with DR complication within 5 years, was assigned to group C by hierarchical clustering on principal components.

value: Female

value: 43 years old

value: 1 year

value: T2D with retinopathy

value: Changhua Christian Hospital


title: Type 2 Diabetic Nephropathy within 5 years - Clustering group C - #1

source_name: Type-2 diabetic patient, with DN complication within 5 years, was assigned to group C by hierarchical clustering on principal components.

value: 57 years old

value: 4 years

value: T2DN stage III (300 ≤ ACR < 2000 mg/g)


title: LLC_Day9_S2

description: cancer.mouse.counts.txt

value: CD45+ MHC-II+


title: Type 2 Diabetic Nephropathy within 5 years - Clustering group C - #2

value: Male

value: 62 years old

value: 5 years


title: SL_13

value: L4:L5- Spinal cord dorsal horn-ipsi

value: WT

value: Sprague-Dawley


title: MAIT cells, Healthy donor 1, Klebsiella

value: Blood

value: Primary cells

value: MAIT cells

value: Klebsiella pneumoniae


title: MAIT cells, Healthy donor 1, Influenza virus

value: Influenza virus


title: MAIT cells, Healthy donor 1, IFNα2A


title: SL_12

value: L4:L5- Spinal cord dorsal horn-contra

value: Female

value: SHAM


title: SL_17

value: SNI


title: Type 2 Diabetic Retinopathy within 5 years - Clustering group C - #1

value: 59 years old

value: T2D with retinopathy

value: Changhua Christian Hospital


title: Type 2 Diabetic Retinopathy within 5 years - Clustering group C - #2

value: 63 years old

value: less than 1 year


title: SL_11

value: L4:L5- Spinal cord dorsal horn-ipsi


title: LLC_Day7_S2

description: cancer.mouse.counts.txt

value: LLC

value: CD45+ MHC-II+


title: LLC_Day7_S1

description: cancer.mouse.counts.txt


title: LLC_Day7_S3

description: cancer.mouse.counts.txt


title: LLC_Day9_S1

description: cancer.mouse.counts.txt


title: MM27_AlisertibTrametinib_rep3

city: Milano

first: Marine

last: Melixetian

address: via Adamello 16

country: Italy

institute: European Institute of Oncology

data_processing:
Basecalls performed using CASAVA version 1.9
Data were filtered using the Illumina quality control flag
Reads were aligned to the homo sapiens genome build hg38 using tophat (v2.0.8), which uses Bowtie (2.1.0) and Samtools (v0.1.18) using default parameters and --transcriptome H. sapiens index, UCSC hg38 gtf.
Raw read counts were summarised using HTSeq (v0.5.3p9), then normalized for library size differences using estimateSizeFactors function from DESeq package (v1.10.1).
Differential expression of genes was calculated with the same R package, using three biological replicas for each  condition (Alisertib treated, Trametinib treated   and  treated with combination of both MM27 PDX cells   vs non treated  control).
Assembly: hg38
Supplementary files format and content: raw HT counts  tab delimited file

source_name: metastasis of cutaneous melanoma

extract_protocol:
Total RNA was extracted with Quick-RNA MiniPrep (cat#R1055, Zymo Research), according to manufacturer protocol
Libraries were constructed using Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) starting from 1µg of total RNA

treatment_protocol: Cells isolated from PDXs (passage 2) were treated in vitro with DMSO (control), Alisertib (500nM), Trametinib (100 nM) or combination of both for 72 hours and then harvested

value: patient derived xenograft cells

tag: passage

tag: melanoma mutation

tag: drug treated pdx cells

value: Alisertib (500nM) and Trametinib (100nM) treated


title: MAIT cells, Healthy donor 1, Control

tag: tissue

value: Blood

value: Primary cells

value: MAIT cells

value: Control (PBS)


title: SL_9

value: WT

value: Sprague-Dawley

value: Female


title: Type 2 Diabetic Retinopathy within 5 years - Clustering group B - #2

source_name: Type-2 diabetic patient, with DR complication within 5 years, was assigned to group B by hierarchical clustering on principal components.

tag: gender

tag: age

value: 77 years old

tag: t2d duration

value: 2 years


title: MM27_AlisertibTrametinib_rep2


title: SL_8

value: L4:L5- Spinal cord dorsal horn-contra

value: Male

value: SNI


title: Type 2 Diabetic Nephropathy within 5 years - Clustering group B - #2

source_name: Type-2 diabetic patient, with DN complication within 5 years, was assigned to group B by hierarchical clustering on principal components.

value: 49 years old

value: 1 year

tag: hba1c (%) of the sample

tag: bmi

value: T2DN stage II (30 ≤ ACR < 300 mg/g)

value: Changhua Christian Hospital


title: MM27_AlisertibTrametinib_rep1

value: patient derived xenograft cells

value: Alisertib (500nM) and Trametinib (100nM) treated


title: LLC_Day5_S1

description: cancer.mouse.counts.txt

tag: cell line

value: LLC

value: CD45+ MHC-II+


title: LLC_Day3_S3

description: cancer.mouse.counts.txt

tag: cell type


title: LLC_Day5_S2

description: cancer.mouse.counts.txt


title: LLC_Day3_S4

description: cancer.mouse.counts.txt


title: MM27_Alisertib_rep3

value: Alisertib treated (500 nM)


title: SL_6

value: WT

tag: strain

value: SHAM


title: SL_10

value: Sprague-Dawley

value: Female


title: MM27_Alisertib_rep2


title: Type 2 Diabetic Nephropathy within 5 years - Clustering group B - #1

value: Blood

value: 72 years old

value: 5 years

tag: sampling in t2d stage

tag: reference


title: Type 2 Diabetic Retinopathy within 5 years - Clustering group B - #1

value: 57 years old

value: less than 1 year

value: T2D with retinopathy


title: SL_7

value: L4:L5- Spinal cord dorsal horn-ipsi

tag: genotype

value: Male

value: SNI


title: Type 2 Diabetes without complications within 5 years - Clustering group C - #4

source_name: Type-2 diabetic patient, without DN and DR complications within 5 years, was assigned to group C by hierarchical clustering on principal components.

value: 66 years old

value: 6 years

value: T2D without complications (5years ≤ T2D duration < 10 years)

value: Changhua Christian Hospital


title: NCI-H1048_BI00894999_100nM_4h_rep1

source_name: NCI-H1048 cancer cell line

tag: disease

value: small cell lung cancer

tag: replicate

tag: ID


title: LLC_Day3_S2

description: cancer.mouse.counts.txt

tag: strain background

value: LLC

value: CD45+ MHC-II+


title: SL_3

value: WT

value: Sprague-Dawley

tag: Sex

value: Female

tag: treatment


title: SL_4

tag: tissue

value: L4:L5- Spinal cord dorsal horn-contra


title: LLC_Day3_S1

description: cancer.mouse.counts.txt


title: Type 2 Diabetes without complications within 5 years - Clustering group C - #3

value: Blood

tag: gender

tag: age

value: 49 years old

value: 5 years


title: MM27_Trametinib_rep1

value: patient derived xenograft cells

tag: passage

tag: melanoma mutation

tag: drug treated pdx cells

value: Trametinib treated (100 nM)


title: Type 2 Diabetes without complications within 5 years - Clustering group C - #2

value: Male

value: 40 years old

tag: t2d duration

value: 4 years

tag: hba1c (%) of the sample

tag: bmi

value: T2D without complications (T2D duration < 5 years)


title: SL_5

value: L4:L5- Spinal cord dorsal horn-ipsi

tag: strain

value: SHAM


title: MM27_Untreated_rep3

tag: cell type

value: DMSO treated control


title: Type 2 Diabetes without complications within 5 years - Clustering group C - #5

value: 62 years old

value: 6 years

tag: sampling in t2d stage

value: T2D without complications (5years ≤ T2D duration < 10 years)

tag: reference

value: Changhua Christian Hospital


title: LLC_Cnt_S3

description: cancer.mouse.counts.txt

tag: cell line

value: LLC

value: unsorted cells


title: LLC_Cnt_S2

description: cancer.mouse.counts.txt

tag: strain background


title: MM27_Untreated_rep2


title: SL_1

tag: genotype

value: WT

value: Sprague-Dawley

tag: Sex

value: Female


title: COR-L95_DMSO_4h_rep1

source_name: COR-L95 cancer cell line

tag: disease

value: small cell lung cancer

tag: treatment

tag: replicate

tag: ID


title: Type 2 Diabetes without complications within 5 years - Clustering group C - #1

tag: tissue

value: Blood

tag: gender

tag: age

value: 55 years old

value: 3 years


title: Type 2 Diabetes without complications within 5 years - Clustering group B - #4

source_name: Type-2 diabetic patient, without DN and DR complications within 5 years, was assigned to group B by hierarchical clustering on principal components.

value: Male

value: 44 years old

tag: t2d duration

value: 1 year

tag: hba1c (%) of the sample

value: T2D without complications (T2D duration < 5 years)


title: LLC_Cnt_S1

description: cancer.mouse.counts.txt


title: MM27_Alisertib_rep1

value: patient derived xenograft cells

tag: passage

tag: melanoma mutation

tag: drug treated pdx cells

value: Alisertib treated (500 nM)


title: Syn3A cells, colony A3_S, endpoint evolution

city: La Jolla

first: Christopher

last: Dalldorf

state: CA

address: 9500 Gilman Dr

department: Bioengineering

institute: UCSD

description: GenBank ID: CP016816.2

data_processing:
Reads counted using HTSeq
Libarires normalized using transciptos per million (TPM)
Assembly: GenBank ID: CP016816.2
Supplementary files format and content: csv
Supplementary files format and content: comma seperated value containing log TPM values of each gene expression levels

organism: synthetic bacterium JCVI-Syn3A

source_name: synthetic bacterium

growth_protocol: ALE experiments were conducted with automated devices that  serially propagated batch cultures of JCVI-syn3A between growth tubes with 15 mL of  SP4-KO medium (containing 17% v/v KnockOut™ Serum Replacement [GIBCO] in lieu  of fetal bovine serum in SP4), well aerated through mixing and kept at 37°C. Ten  replicate lineages were started from the JCVI-syn3A ancestor and for each lineage 150  ul of culture was passed to a fresh tube once daily (6.6 generations/day), switching to  30 ul passage volume (9 generations/day) after 200 generations and continuing for a  total of 400 generations

extract_protocol:
Genomic DNA was isolated using bead agitation in 96-well plates
Total RNA isolation, rRNA removal, and sequencing library preparation was performed as previously described  (Chen et al. 2021)  removal, and sequencing library preparation was performed as previously described  (Chen et al. 2021)
Libraries were run on an Illumina NextSeq, raw sequencing reads were mapped using Bowtie

value: synthetic bacterium

tag: cell type

value: synthetic

value: evolution endpoint


title: MM27_Untreated_rep1

value: DMSO treated control


title: MM27_Trametinib_rep2

value: Trametinib treated (100 nM)


title: Shoot, salt treated, rep 3 [21050R-01-12V1]

city: NEWCASTLE UPON TYNE

first: Norah

middle: Abdullah

last: Alyahya

address: Drummond WEB REQ Tyne

institute: Newcastle University

description:
Salt_treated_Shoot_vs_Control_Shoot.txt
Salt_treated_Root_vs_Salt_treated_Shoot.txt
count_table_normalized.txt

data_processing:
Quality of FASTQ files was assessed with FastQC (version 11.8)
Contaminating adaptor sequences were removed using ‘trimmomatic’ (version 0.36)
Reads were quantified against transcripts using Salmon (version 0.12.0)
Assembly: Ensembl Triticum aestivum genome (version 51)
Supplementary files format and content: Text files include quantitative data from expression profiling analysis

organism: Triticum aestivum

source_name: Plant shoot

growth_protocol: Plants were maintained under controlled conditions; 16 h light at 20 °C, 8 h dark at 15 °C and 70% humidity.

extract_protocol:
Total RNA was extracted using Plant/Fungi Total RNA Purification Kit (Cat. 25800; Norgen, Canada) and treated with RNase-Free DNase I Kit (Cat. 25710, Norgen)
Library construction was done according to the NEBNext® Ultra™ II Non-Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA).

treatment_protocol: Control plants were irrigated with tap water (0 mM NaCl) and salt-treated plants were watered with 200 mM NaCl solution after seed sowing

value: Plant shoot

value: Najran wheat cultivar

value: 200 mM NaCl


title: Syn3A cells, colony A3_1Plus, endpoint evolution

description: GenBank ID: CP016816.2

tag: cell line


title: Type 2 Diabetes without complications within 5 years - Clustering group B - #3

value: Blood

value: Female

tag: bmi

tag: sampling in t2d stage

tag: reference

value: Changhua Christian Hospital


title: Type 2 Diabetes without complications within 5 years - Clustering group B - #2

value: Male

value: 54 years old

value: less than 1 year


title: Shoot, salt treated, rep 1 [21050R-01-10V1]

tag: genotype


title: Type 2 Diabetes without complications within 5 years - Clustering group B - #1

value: 63 years old

value: 1 year

value: T2D without complications (T2D duration < 5 years)


title: Control - Clustering group A - #9

source_name: Non-diabetic patient was assigned to group A or control group by hierarchical clustering on principal components.

value: 40 years old

value: Not applicable

value: Between 4.0% and 5.6%

value: China Medical University Hospital


title: Syn3A cells, colony A1L, endpoint evolution

description: GenBank ID: CP016816.2

value: synthetic bacterium

value: synthetic

tag: treatment

value: evolution endpoint


title: Root, salt treated, rep 2 [21050R-01-08V1]

description:
Salt_treated_Root_vs_Control_Root.txt
Salt_treated_Root_vs_Salt_treated_Shoot.txt
count_table_normalized.txt

source_name: Plant root

value: Plant root

value: Najran wheat cultivar

value: 200 mM NaCl


title: Root, salt treated, rep 3 [21050R-01-09V1]


title: Syn3A cells, colony A1_S, endpoint evolution

description: GenBank ID: CP016816.2


title: Root, salt treated, rep 1 [21050R-01-07V1]


title: Syn3A cells, colony A1_L, endpoint evolution

description: GenBank ID: CP016816.2


title: Shoot, control, rep 3 [21050R-01-06V1]

description:
Salt_treated_Shoot_vs_Control_Shoot.txt
Control_Shoot_vs_Control_Root.txt
count_table_normalized.txt

value: Plant shoot

value: 0 mM NaCl


title: Syn3A cells, colony A7, endpoint evolution

description: GenBank ID: CP016816.2


title: Shoot, salt treated, rep 2 [21050R-01-11V1]


title: Control - Clustering group A - #8

value: Blood

value: Female

value: 46 years old


title: Control - Clustering group A - #7

value: Male

value: 41 years old


title: Shoot, control, rep 1 [21050R-01-04V1]


title: Control - Clustering group A - #3

value: 43 years old


title: SL_2

source_name: L4:L5- Spinal cord dorsal horn-contra

value: L4:L5- Spinal cord dorsal horn-contra

value: WT

tag: strain

value: Sprague-Dawley

tag: Sex

value: SHAM


title: Syn3A cells, colony A6 Plus, endpoint evolution

description: GenBank ID: CP016816.2

value: synthetic bacterium

value: synthetic


title: Syn3A cells, wildtype normal

description: GenBank ID: CP016816.2

value: evolution endpoint


title: Control - Clustering group A - #1

tag: tissue

value: 47 years old

value: Not applicable

value: Between 4.0% and 5.6%

value: China Medical University Hospital


title: Control - Clustering group A - #4

value: Blood

tag: gender

value: 42 years old


title: Shoot, control, rep 2 [21050R-01-05V1]

value: Plant shoot

value: Najran wheat cultivar

value: 0 mM NaCl


title: Root, control, rep 3 [21050R-01-03V1]

description:
Salt_treated_Root_vs_Control_Root.txt
Control_Shoot_vs_Control_Root.txt
count_table_normalized.txt

value: Plant root


title: Control - Clustering group A - #2

value: Female

tag: age

value: 54 years old


title: Syn3A cells, colony A8, endpoint evolution

description: GenBank ID: CP016816.2


title: Syn3A cells, colony A2, endpoint evolution

description: GenBank ID: CP016816.2


title: Syn3A cells, colony A4, endpoint evolution

description: GenBank ID: CP016816.2


title: Syn3A cells, colony A5, endpoint evolution

description: GenBank ID: CP016816.2


title: Root, control, rep 2 [21050R-01-02V1]


title: Syn3A cells, wildtype stationary

description: GenBank ID: CP016816.2


title: Control - Clustering group A - #6

value: 43 years old

tag: t2d duration


title: Control - Clustering group A - #5

tag: hba1c (%) of the sample


title: Root, control, rep 1 [21050R-01-01V1]


title: E14 mGFP hindgut 3

status: Public on Jul 06 2023

city: Boston

first: Hasreet

last: Gill

state: MA

address: 77 Avenue Louis Pasteur, NRB 360

department: Genetics

institute: Harvard Medical School

data_processing:
Reads were quasi-mapped to the Gallus gallus transcriptome using Salmon and transcript abundance estimates were calculated
QC was performed on count data using qualimap
PCA analysis indicated potential sample swap for 1 replicate per condition at E14, and samples in question were excluded from downstream processing (Samples 16, 18, 24 above)
DESeq2 was used to perform read count normalization and differential gene expression analyses
Unsupervised clustering was performed to identify genes commonly differentially expressed in the Hoxd13 midgut and mGFP hindgut relative to mGFP midgut
Assembly: GRCg6a
Supplementary files format and content: tab-delimited text file includes raw counts for each sample at e12
Supplementary files format and content: tab-delimited text file includes raw counts for each sample at e14

organism: Gallus gallus

source_name: Intestinal mesoderm

growth_protocol: Chicken embryos were incubated at 38 degrees Celsius

extract_protocol:
RNA was extracted using QIAGEN RNeasy Micro Kit following the manufacturer's protocol
RNA-seq libraries were constructed using TruSeq Stranded mRNA kit, following the manufacturer's protocol

treatment_protocol: in ovo electroporation of retroviral constructs--RCAS-mGFP and RCAS-Hoxd13--into midgut-level splanchnic lateral plate mesoderm at HH17

value: Intestinal mesoderm

tag: tissue location

value: hindgut

value: RCAS-mGFP

value: RCAS-mGFP electroporation into splanchnic LPM at HH17


title: E14 mGFP hindgut 4


title: E14 Hox midgut 2

value: midgut

value: RCAS-Hoxd13 electroporation into splanchnic LPM at HH17


title: E14 Hox midgut 4


title: E14 mGFP hindgut 1


title: E14 Hox midgut 3


title: E14 mGFP midgut 4


title: E14 mGFP midgut 3


title: E14 mGFP hindgut 2


title: E14 Hox midgut 1


title: E14 mGFP midgut 2


title: E12 Hox midgut 1


title: E12 Hox midgut 4


title: E14 mGFP midgut 1


title: E12 Hox midgut 3


title: E12 mGFP hindgut 4


title: E12 mGFP hindgut 3


title: E12 mGFP hindgut 2


title: E12 mGFP hindgut 1


title: E12 mGFP midgut 4


title: WT_total_OE scRNA

city: SAN FRANCISCO

first: Lea

last: Kiefer

address: 1651 4th Street, Weill Neurosci RM 471A

institute: UCSF

description: 10x scRNA-seq

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment: All samples were aligned to mm10. For paired-end data sets, only read 1 was used for alignment and downstream analysis. RNA-seq samples were aligned with STAR (v2.5.3a) with the following parameters:  --outFilterIntronMotifs RemoveNoncanonical --outFilterType BySJout --outFilterMultimapNmax 20. HiC samples were aligned and processed using HiC-Pro (Servant et al. 2015 Genome Biology). 10x single cell RNA-seq was processed using cellranger.
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1).
For RNA-Seq, bigWig files were generated with RSeQC (2.6.4).
10x scRNAseq data were analyzed using 10x Genomics Cell Ranger 6.0.1 with a recovery of 4000-8000 cells per experiment. Data analysis was performed using Seurat(55–58) and custom scripts.
Assembly: mm10
Supplementary files format and content: bigWig files at base pair resolution normalized to a library size of 10,000,000 reads

source_name: Olfactory epithilium

extract_protocol:
For RNA-seq: RNA  was  isolated  from  tissue  using  TRIzol.  Cell  lysate  was  extracted  with  bromo-chloropropane and RNA was precipitated with 100% isopropanol supplemented with 10 μg of glycobluefor 10 min at room temperature and then pelleted at 16,000 x g for 30 min at  4°C.  The  RNA  pellet  was  washed  once  with  75%  ethanol  and  then  resuspended  in RNase-free water to a maximal concentration of 200 ng/μl. Genomic DNA contaminants were   removed   by   Turbo   DNase.   Removal   of   Turbo   DNase   was   performed   by phenol:chloroform  extraction  and  RNA  was  precipitated  as  described  above  and resuspended in RNase-free water and stored at -80°C.  For Raphe RNA-seq: RNA  was  isolated  from  coronal  sections  of  the  Raphe  (20  μm  thick)  obtainedfrom paraformaldehyde-fixed   brain   (described   in   more   detail   below,   see   paragraph “Preparation of Mouse Brain Tissue Sections”). After 3x 5 minutes washes of the slides with 1X PBS, a small portion of each section containing approximately the Raphe region was extracted. Then, the RNA was isolated using  RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Invitrogen) as instructed by the manufacturer.  For in situ HiC was carried out according to Rao et al. 2014. For ChIP-seq: Cells were crosslinked with 1% formaldehyde for  10 minutes  at room  temperature. Formaldehyde  was  quenched  by  adding  glycine to  a  final concentration of 0.125 M for 5 minutes at room temperature. Cells were then washed with 1X cold PBS with protein inhibitors twice and pelleted. Cell pellets were stored at -80°C till use. Cells were lysed in lysis buffer (50 mM Tris pH 7.5, 140 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) for 10 minutes. Nuclei were spun for 10 minutes at 1000 x g and resuspended in the sonication buffer (10 mM Tris pH 7.5, 0.5% SDS) as 5million nuclei per 300 μl sonication buffer. Chromatin was sheared by Covaris (Peak power 105.0; Duty Factor 2.0; Cycle/Burst 200; Treatment 960 sec; Temperature 4-8°C). Following a spin at 13,000 x g for 10 minutes to remove debris, the sheared chromatin was diluted such that the final binding buffer concentration was 15 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS) and incubated for 2 hours with dynabeads G pre-equilibrated in the binding buffer for pre-clearing of the chromatin. Post-cleared chromatin was then incubated with the specific antibody overnight (1 μg of antibody was used per 5 million nuclei). The next day, dynabeads G were added to the chromatin-antibody mix for 2 hours. A total of four washes with 1X wash buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate) and one wash with TE buffer (10 mM Tris pH 7.5, 1 mM EDTA) were performed. The elution was performed at65°C for 1 hour in the elution buffer (1% SDS, 250 mM NaCl, 2 mM DTT).  All steps, with the exception of the elution, were performed at 4°C. All buffers, with the exception of the TE and elution buffer contained 1X protease inhibitors. The eluted chromatin was reverse-crosslinked overnight at 65°C and the DNA was purified with AMPure  XP  beads  (Beckman  Coulter).
For RNA-Seq experiments, raw FASTQ files were aligned with either Tophat or STAR using hg19 or mm10 reference genomes. When libraries were made following the SMARTer Stranded Total RNA-Seq, the initial 4 base pairs of both paired reads were trimmed prior to alignment.  For single cell RNA-seq, raw FASTQ files were analyzed using cellranger.  For in situ Hi-C experiments, raw FASTQ files were analyzed using HiC-Pro and hic files were generated (Servant et al. 2015).

treatment_protocol: Mice were sacrificed using CO2 followed by cervical dislocation. The main olfactory epithelium (MOE) was dissected and transferred to ice-cold PBS. The MOE was cut in to small pieces with a razor blade, and then dissociated with a papain dissociation system (Worthington Biochemical). For RNA-seq, dissociated cells were washed once with sort media (PBS + 2% Fetal Bovine Serum) and then resuspended in sort media supplemented with 100 U/mL DNase I (Worthington Biochemical)  and 500ng/mL DAPI (Invitrogen). For  HiC samples, cells were fixed prior to sorting. For fixation, dissociated cells were resuspended in PBS + 1% methanol-free formaldehyde (Pierce). Cells were fixed at room temperature for 10 minutes, and then fixation was quenched by adding 1/10th volume of 1.25M glycine. Fixed cells were pelleted (500 rcf, 5 minutes, room temperature), washed once with PBS + 2% FBS, and then resuspended in sort media. All cells were passed through a 40uM cell strainer prior to sorting.

value: Olfactory epithilium

value: WT


title: Cut_Run_TCF1_TCF1KO_LSK_L1_DN1_rep2B_S11

city: Philadelphia

first: Naomi

last: Goldman

state: PA

address: 324 BRB II/III, 421 Curie Blvd

institute: University of Pennsylvania

data_processing:
CUT&RUN data analysis: The FASTQ files of CUT&RUN experiments were aligned to the bam file using BWA (version 0.7.17-r1188). In this process, minor chromosomes such as mitochondrial chromosome or chrY were removed using samtools (version 1.11). Next, duplicated reads were removed using Picard (version 2.26.7) and then the bam files were indexed using samtools. BigWig files were generated using bamCoverage (version 3.3.2) with parameters ‘normalizedUsing=CPM, binsize=30, smoothLength=300, p=5, extendReads=200’. For peak calling, macs2 (version 2.1.4) was used with following commands: ‘macs2 callpeak -t input_file -c control -g mm -n output_path –nomodel -f BAMPE -B –keep-dup all –broad –broad-cutoff 0.25 -q 0.25’. For the background (control), the bam file of IgG CUT&RUN data was used. CUT&RUN peaks from two conditions and both replicates were merged and the number of fragments in each peak were counted with bedtools. The count data of each peak was then fed to DESeq2 for differential analysis.
Assembly: mm10
Library strategy: CUT&RUN

source_name: BM derived CD44+ CD25- DN1

extract_protocol:
Transduction of Tcf7 KO scid.adh cells was accomplished by addition of retroviral supernatants to culture medium supplemented with polybrene (8mg/ml) and spinfected at 1,750 RPM for 25 minute. 72hrs after transduction, live transduced cells were sorted for downstream experiments. Cells from co-cultures were stained with L/D APCef780, and fluorescent antibodies to B220, CD44, CD45, Thy1.2, Ckit, CD25, and CD11b. Sorting was performed on a BD FACSAria after 7 days to isolate DN1 (CD45+c-KithiCD44hI CD25low) and DN2 cells (CD45+c-KitlowCD44low CD25high). CUT&RUN was performed using CUTANA™ ChIC/CUT&RUN Kit (EpiCypher, Cat#14-1048), using manufacturer’s recommendation. Briefly, from live sorted cells, nuclei were extracted, washed, and allowed to adsorb onto activated ConA beads. Cells were then resuspended in recommended buffer, 0.5 mg of antibody was added, mixed well, and allowed to incubate at 4°C overnight on a nutator. TCF1/TCF7 (C63D9) Rabbit mAb #2203 was used along with positive and negative controls. Subsequently, the reactions were washed with cell permeabilization buffer and incubated with pAG-MNase, and DNA was isolated for the antibody-bound regions. At least two biological replicates were generated for each experiment. Library preparation was carried out using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and were paired-end sequenced (38bp+38bp) on a NextSeq 550 (Illumina) or 61bp+61bp on Novaseq 6000 (Illumina).
Libraries were validated for quality and size distribution using Qubit dsDNA HS Assay Kit (Invitrogen, cat# Q32851) and TapeStation 2200 (Agilent). Libraries were paired-end sequenced (66bp+66bp) on NovaSeq 6000 (Illumina).

value: BM derived CD44+ CD25- DN1

value: Tcf7eGFP fl/fl Cre+

value: Cultured on OP9-DLL1


title: Cut_Run_TCF1_TCF1KO_LSK_P45_DN2_50Kcells_rep1B

source_name: BM derived CD44+ CD25+ DN2

value: BM derived CD44+ CD25+ DN2


title: Cut_Run_TCF1_TCF1KO_LSK_L1_DN1_rep1B_255035832_S2


title: Cut_Run_TCF1_TCF1KO_LSK_EV_DN1_rep1B


title: Cut_Run_TCF1_TCF1KO_LSK_EBF1_CTD_L1_swap_DN1_rep1B


title: E12 mGFP midgut 3


title: E12 mGFP midgut 1


title: Cut_Run_TCF1_TCF1KO_LSK_L1_DN2_rep2B


title: Cut_Run_TCF1_TCF1KO_LSK_P45_DN3_rep2B

source_name: BM derived CD44- CD25+ DN3

value: BM derived CD44- CD25+ DN3


title: Cut_Run_TCF1_DN3-KO_p45_Rep1

source_name: Scid.adh cell line

value: Scid.adh cell line

value: WT TCF-1 RV


title: multiplexed different protocols

first: Rory

middle: James

last: Maizels

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
data processed with dynast, outputted into separate adatas for each cell
data then collated into one adata object with replicate, treatment, and other informations stored in metadata
cells with fewer than 1000 reads removed to exclude ambient RNA
Assembly: mm10
Supplementary files format and content: h5ad, anndata

source_name: mESC HM1

growth_protocol: mESC neural tube differentiation protocol. Grown in N2B27 with supplements. D0: FGF, D2: FGF+CHIR, D3-8: RA+SAG, collected cells from D4

extract_protocol:
methanol fixation with DEPC, stored at -80°C for under a month
chemical conversion protocol with IAA, followed by custom optimised sci-RNA-seq protocol
combinatorial indexing, two rounds of 384 barcodes

value: mESC HM1

value: differentiating HM1s


title: E12 Hox midgut 2

value: Intestinal mesoderm


title: Cut_Run_TCF1_TCF1KO_LSK_P45_DN3_rep1B


title: Cut_Run_TCF1_DN3-KO_L1_Rep1

value: {delta}L1 TCF-1 RV


title: Cut_Run_TCF1_DN3-KO_L1_Rep2


title: Cut_Run_FLAG_DN3-KO_p45_Rep2


title: Cut_Run_TCF1_TCF1KO_LSK_P45_DN1_rep2B_S7


title: Cut_Run_TCF1_TCF1KO_LSK_P45_DN1_rep1B_255035832_S1


title: Cut_Run_TCF1_TCF1KO_LSK_P45_DN1_rep2B_255035832_S5


title: LLC_Cnt_S4

description: cancer.mouse.counts.txt

source_name: Lewis Lung Carcinoma (LLC)

tag: strain background

value: LLC

value: unsorted cells


title: Cut_Run_TCF1_TCF1KO_LSK_L1_DN1_rep2B_255035832_S6


title: replicate 1, sample collected days 3,4,5,6,7,8

description:
processed_data_counting.h5ad
processed_data_estimate.h5ad
processed_data_splicing.h5ad

data_processing:
data processed with dynast, outputted into separate adatas for each cell
data then collated into one adata object with replicate, timepoint, and other informations stored in metadata
cells with fewer than 1000 reads removed to exclude ambient RNA
Assembly: mm10
Supplementary files format and content: h5ad, anndata containing all data: split into objects containing new/total based on dynast counting, (processed_data_counting.h5ad), new/total based on dynast estimation (processed_data_estimate.h5ad), and unspliced/spliced reads (processed_data_estimate.h5ad)

growth_protocol: mESC neural tube differentiation protocol. Grown in N2B27 with supplements. D0: FGF, D2: FGF+CHIR, D3-8: RA+SAG

treatment_protocol: 4sU labelling 2 hours 500µM

value: differentiating embryonic stem cells


title: E12 mGFP midgut 2

value: midgut

value: RCAS-mGFP

value: RCAS-mGFP electroporation into splanchnic LPM at HH17


title: replicate 2, sample collected days 3,4,5,6,7,8


title: background data with no 4sU, cells from D3 through to D8

data_processing:
data processed with dynast in 'control' mode
output snps and p_e only elements used for analysis
Assembly: mm10
Supplementary files format and content: csvs detailing snps and background mutation rate

extract_protocol:
methanol fixation with DEPC, stored at -80°C for under a month
custom optimised sci-RNA-seq protocol
combinatorial indexing, two rounds of 384 barcodes

value: differentiating ES cells


title: Cut_Run_TCF1_TCF1KO_LSK_L1_DN1_rep1B_S5

value: BM derived CD44+ CD25- DN1

value: Tcf7eGFP fl/fl Cre+


title: Cut_Run_TCF1_TCF1KO_LSK_P45_DN2_50Kcells_rep2B

value: BM derived CD44+ CD25+ DN2

value: Cultured on OP9-DLL1


title: Cut_Run_TCF1_TCF1KO_LSK_EV_DN1_rep2B


title: Cut_Run_FLAG_DN3-KO_p45_Rep1

value: Scid.adh cell line


title: Cut_Run_TCF1_TCF1KO_LSK_P45_DN1_rep1B_S1


title: Cut_Run_FLAG_DN3-KO_L1_Rep1


title: Cut_Run_TCF1_DN3-KO_p45_Rep2

value: WT TCF-1 RV


title: Cut_Run_TCF1_TCF1KO_LSK_L1_DN2_rep1B


title: Cut_Run_TCF1_TCF1KO_LSK_EBF1_CTD_L1_swap_DN1_rep2B


title: 6F_M_2864

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: 6F_M_2863


title: 6F_M_2856


title: 6F_M_2862


title: 6F_M_2861


title: 6F_M_2854


title: 6F_M_2852


title: 6F_M_2853


title: 6F_M_2866


title: Cut_Run_FLAG_DN3-KO_L1_Rep2

tag: cell type


title: 6F_M_2851


title: 6F_M_2850


title: replicate 4, sample collected days 3.2, 3.4, 3.6, 3.8

tag: cell line

value: mESC HM1


title: replicate 3, sample collected days 3,4,5,6,7,8


title: 6F_M_2844


title: 6F_M_2868


title: 6F_M_2860


title: 6F_M_2841


title: 6F_M_2839


title: 6F_M_2843


title: 6F_M_2842


title: 6F_M_2836


title: 6F_M_2859


title: 6F_M_2840


title: 6F_M_2837


title: 6F_M_2838


title: 6F_M_2867


title: 6F_M_2832


title: 6F_M_2833


title: 6F_M_2865


title: 6F_M_2858


title: 6F_M_2855


title: 6F_M_2849


title: 6F_M_2847


title: 6F_M_2846


title: 6F_M_2848


title: 6F_M_2857


title: 6F_M_2827


title: 6F_M_2835


title: 6F_M_2830


title: 6F_M_2831


title: 6F_M_2829


title: 6F_M_2834


title: 6F_M_2826


title: 6F_M_2816


title: 6F_M_2824


title: 6F_M_2814


title: 6F_M_2812


title: 6F_M_2818


title: 6F_M_2811


title: 6F_M_2809


title: 6F_M_2828


title: 6F_M_2822


title: 6F_M_2825


title: 6F_M_2808


title: 6F_M_2807


title: 6F_M_2821


title: 6F_M_2817


title: 6F_M_2820


title: 6F_M_2819


title: 6F_M_2823


title: 6F_M_2804


title: 6F_M_2815


title: 6F_M_2806


title: 6F_M_2805


title: 6F_M_2813


title: 6F_M_2802


title: 6F_M_2803


title: 6F_M_2799


title: 6F_M_2800


title: 6F_M_2798


title: 6F_M_2797


title: 6F_M_2794


title: 6F_M_2796


title: 6F_M_2810


title: 6F_M_2795


title: 6F_M_2793


title: 6F_M_2792


title: 6F_M_2791


title: 6F_M_2789


title: 6F_M_2788


title: 6F_M_2787


title: 6F_M_2784


title: 6F_M_2785


title: 6F_M_2790


title: 6F_M_2786


title: 6F_M_2801


title: 6F_M_2780


title: 6F_M_2782


title: 6F_M_2778


title: 6F_M_2783


title: 6F_M_2774


title: 6F_M_2779


title: 6F_M_2775


title: 6F_M_2773


title: 6F_M_2772


title: 6F_M_2771


title: 6F_M_2776


title: 6F_M_2777


title: 6F_M_2770


title: 6F_M_2766


title: 6F_M_2768


title: 6F_M_2765


title: 6F_M_2763


title: 6F_M_2764


title: 6F_M_2769


title: 6F_M_2760


title: 6F_M_2759


title: 6F_M_2758


title: 6F_M_2757


title: 6F_M_2754


title: 6F_M_2761


title: 6F_M_2762


title: 6F_M_2751


title: 6F_M_2753


title: 6F_M_2755


title: 6F_M_2756


title: 6F_M_2750


title: 6F_M_2767


title: 6F_M_2748


title: 6F_M_2749


title: 6F_M_2752


title: 6F_M_2746


title: 6F_M_2744


title: 6F_M_2747


title: 6F_M_2745


title: 6F_M_2740


title: 6F_M_2735


title: 6F_M_2743


title: 6F_M_2742


title: 6F_M_2741


title: 6F_M_2738


title: 6F_M_2736


title: 6F_M_2739


title: 6F_M_2730


title: 6F_M_2734


title: 6F_M_2731


title: 6F_M_2733


title: 6F_M_2724


title: 6F_M_2726


title: 6F_M_2725


title: 6F_M_2729


title: 6F_M_2781


title: 6F_M_2722


title: 6F_M_2727


title: 6F_M_2723


title: 6F_M_2728


title: 6F_M_2732


title: 6F_M_2717


title: 6F_M_2720


title: 6F_M_2721


title: 6F_M_2716


title: 6F_M_2737


title: 6F_M_2719


title: 6F_M_2712


title: 6F_M_2713


title: 6F_M_2711


title: 6F_M_2710


title: 6F_M_2708


title: 6F_M_2709


title: 6F_M_2714


title: 6F_M_2715


title: 6F_M_2707


title: 6F_M_2702


title: 6F_M_2701


title: 6F_M_2705


title: 6F_M_2703


title: 6F_M_2706


title: 6F_M_2700


title: 6F_M_2697


title: 6F_M_2695


title: 6F_M_2698


title: 6F_M_2696


title: 6F_M_2718


title: 6F_M_2693


title: 6F_M_2690


title: 6F_M_2689


title: 6F_M_2688


title: 6F_M_2692


title: 6F_M_2694


title: 6F_M_2687


title: 6F_M_2683


title: 6F_M_2682


title: 6F_M_2685


title: 6F_M_2684


title: 6F_M_2681


title: 6F_M_2680


title: 6F_M_2679


title: 6F_M_2678


title: 6F_M_2611


title: 6F_M_2612


title: 6F_M_2608


title: 6F_M_2610


title: 6F_M_2704


title: 6F_M_2609


title: 6F_M_2691


title: 6F_M_2606


title: 6F_M_2607


title: 6F_M_2605


title: 6F_M_2686


title: 6F_M_2601


title: 6F_M_2604


title: 6F_M_2603


title: 6F_M_2602


title: 6F_M_2600


title: 6F_M_2597


title: 6F_M_2599


title: 6F_M_2595


title: 6F_M_2596


title: 6F_M_2594


title: 6F_M_2592


title: 6F_M_2593


title: 6F_M_2677


title: 6F_M_2590


title: 6F_M_2589


title: 6F_M_2591


title: 6F_M_2587


title: 6F_M_2588


title: 6F_M_2585


title: 6F_M_2580


title: 6F_M_2583


title: 6F_M_2581


title: 6F_M_2582


title: 6F_M_2584


title: 6F_M_2579


title: 6F_M_2578


title: 6F_M_2573


title: 6F_M_2577


title: 6F_M_2574


title: 6F_M_2598


title: 6F_M_2576


title: 6F_M_2571


title: 6F_M_2570


title: 6F_M_2699


title: 6F_M_2566


title: 6F_M_2567


title: 6F_M_2569


title: 6F_M_2568


title: 6F_M_2565


title: 6F_M_2563


title: 6F_M_2564


title: 6F_M_2562


title: 6F_M_2586


title: 6F_M_2561


title: 6F_M_2558


title: 6F_M_2557


title: 6F_M_2553


title: 6F_M_2552


title: 6F_M_2556


title: 6F_M_2555


title: 6F_M_2484


title: 6F_M_2551


title: 6F_M_2554


title: 6F_M_2549


title: 6F_M_2482


title: 6F_M_2479


title: 6F_M_2550


title: 6F_M_2480


title: 6F_M_2483


title: 6F_M_2478


title: 6F_M_2559


title: 6F_M_2476


title: 6F_M_2481


title: HNRNPK_P_Nuc_PARCLIP

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

data_processing:
bcl2fastq/2.20.0 was used to convert bcl to fastq
For RNA-Seq fastq files were aligned using star/2.7.2b or TopHat(2)
differential expression was done using cuffdiff (cufflinks/2.2.1)
PARCLIP was analysed using Parpipes (https://github.com/ohlerlab/PARpipe)
Assembly: hg38

source_name: Triple-negative breast cancer

growth_protocol: MDA-MB-231 cells were authenticated by short-tandem repeat profiling, performed by ATCC. MDA-MB-231 KRT19 KO cells generated using the CRISPR/Cas9 system and cells stably expressing GFP or GFP-KRT19 generated using the lentiviral system, Cells were grown in Dulbecco’s modified essential medium (DMEM; Gibco, Grand Island, NY) supplemented with 10% Fetal Bovine Serum (GE Healthcare, Logan, UT) and 1% penicillin/streptomycin (Gibco) in a humidified incubator at 5% CO2 and 37°C.

extract_protocol:
For RNA-seq analysis, total RNAs from three biological replicates each of untransfected parental and KRT19 KO cells, transfected with siHNRNPK, control siRNA, HNRNPK ∆NLS or vector.
Ribosomal RNA was depleted of using the NEBNext® rRNA Depletion Kit and cDNA libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA).
RNA was barcoded using the NEBNext Multiplex Oligos for Illumina (NEB).

treatment_protocol: For siRNA, RNAimax lipofectamine (Invitrogen, Waltham, MA) was used to transfect HNRNPK smartpool siRNA (Dharmacon) or non-targeting siRNA (Qiagen) according to the manufacturer’s protocol. For overexpression plasmids, jetOptimus DNA transfection reagent (Polyplus, Illkirch, France) was used according to the manufacturer’s protocol.

value: parental

tag: rip antibody

value: anti-HNRNPK/J (Santa Cruz, #sc-32307)


title: 6F_M_2560


title: HNRNPK_KO_Nuc_PARCLIP

value: K19 KO


title: 6F_M_2572


title: HNRNPK_KO_Cyt_PARCLIP


title: MDA-MB-231_P2__sihnRNP_K


title: MDA-MB-231_P3__sihnRNP_K


title: MDA-MB-231_P1__sicontrol

value: sicontrol


title: HNRNPK_P_Cyt_PARCLIP


title: MDA-MB-231_KO3__sihnRNP_K


title: MDAMB231_Imi_2

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: Breast cancer cell-line MDA-MB-231

growth_protocol: Cells were maintained in complete medium (DMEM high glucose media supplemented with 10% FBS and 1% Anti-Anti).

extract_protocol:
Total RNA was extracted  from control and MCF7 Imipramine samples (96 hours after treatment),  using RNeasy mini kit (Qiagen)
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

treatment_protocol: Cells were plated in 6 well plates in complete media. After 24hrs, cells were treated with DMSO or 40µM Imipramine for 96 hours.

tag: cell-line

value: MDA-MB-231 Imipramine

tag: rna harvest

value: 96 hours after treatment


title: MDAMB231_Imi_3


title: MDA-MB-231_KO1__sihnRNP_K

institute: NIH

tag: genotype


title: 6F_M_2477


title: MDAMB231_C3

tag: treatment

value: MDA-MB-231 Vehicle


title: MDA-MB-231_KO1__sicontrol


title: MDAMB231_Imi_1


title: MDA-MB-231_KO3__sicontrol


title: MDAMB231_C1


title: MCF7_C4

source_name: Breast cancer cell-line MCF7

value: MCF7 Vehicle


title: MDA-MB-231_P2__sicontrol


title: MDA-MB-231_P3__sicontrol


title: MDAMB231_C2


title: 6F_M_2473

tag: strain


title: MCF7_40_4

value: MCF7 Imipramine


title: MCF7_40_1


title: MDA-MB-231_P1__sihnRNP_K


title: 6F_M_2474


title: 6F_M_2475


title: 6F_M_2472


title: 6F_M_2471


title: 6F_M_2469


title: 6F_M_2470


title: MDA-MB-231_KO2__sicontrol


title: 6F_M_2463


title: 6F_M_2464


title: 6F_M_2462


title: MCF7_C1


title: 6F_M_2461


title: 6F_M_2458


title: 6F_M_2460


title: 6F_M_2457


title: 6F_M_2456


title: 6F_M_2459


title: 6F_M_2454


title: 6F_M_2451


title: 6F_M_2452


title: 6F_M_2450


title: 6F_M_2448


title: 6F_M_2466


title: 6F_M_2446


title: 6F_M_2447


title: 6F_M_2449


title: 6F_M_2445


title: 6F_M_2465


title: 6F_M_2441


title: 6F_M_2440


title: 6F_M_2439


title: 6F_M_2443


title: 6F_M_2438


title: 6F_M_2437


title: 6F_M_2455


title: 6F_M_2453


title: 6F_M_2434


title: 6F_M_2433


title: 6F_M_2435


title: 6F_M_2431


title: 6F_M_2436


title: 6F_M_2428


title: 6F_M_2429


title: 6F_M_2427


title: 6F_M_2430


title: 6F_M_2424


title: 6F_M_2423


title: 6F_M_2426


title: 6F_M_2421


title: 6F_M_2444


title: 6F_M_2358


title: 6F_M_2422


title: 6F_M_2442


title: 6F_M_2468


title: 6F_M_2356


title: 6F_M_2354


title: 6F_M_2355


title: 6F_M_2432


title: 6F_M_2351


title: 6F_M_2353


title: 6F_M_2349


title: 6F_M_2352


title: 6F_M_2348


title: 6F_M_2347


title: 6F_M_2346


title: 6F_M_2344


title: 6F_M_2345


title: 6F_M_2343


title: 6F_M_2341


title: 6F_M_2340


title: 6F_M_2357


title: 6F_M_2335


title: 6F_M_2342


title: 6F_M_2337


title: 6F_M_2336


title: 6F_M_2425


title: 6F_M_2334


title: 6F_M_2331


title: 6F_M_2329


title: 6F_M_2338


title: 6F_M_2333


title: 6F_M_2339


title: 6F_M_2328


title: 6F_M_2327


title: 6F_M_2332


title: 6F_M_2350


title: 6F_M_2330


title: 6F_M_2326


title: 6F_M_2323


title: 6F_M_2324


title: 6F_M_2322


title: 6F_M_2321


title: 6F_M_2319


title: 6F_M_2320


title: 6F_M_2317


title: 6F_M_2316


title: 6F_M_2314


title: 6F_M_2318


title: 6F_M_2312


title: 6F_M_2311


title: 6F_M_2307


title: 6F_M_2304


title: 6F_M_2309


title: 6F_M_2308


title: 6F_M_2305


title: 6F_M_2310


title: 6F_M_2306


title: 6F_M_2299


title: 6F_M_2300


title: 6F_M_2298


title: 6F_M_2302


title: 6F_M_2301


title: 6F_M_2296


title: 6F_M_2295


title: 6F_M_2297


title: 6F_M_2325


title: 6F_M_2103


title: 6F_M_2101


title: 6F_M_2102


title: 6F_M_2100


title: 6F_M_2313


title: 6F_M_2099


title: 6F_M_2098


title: 6F_M_2096


title: 6F_M_2094


title: 6F_M_2095


title: 6F_M_2093


title: 6F_M_2092


title: 6F_M_2091


title: 6F_M_2090


title: 6F_M_2084


title: 6F_M_2085


title: 6F_M_2089


title: 6F_M_2087


title: 6F_M_2088


title: 6F_M_2081


title: 6F_M_2078


title: 6F_M_2077


title: 6F_M_2086


title: 6F_M_2083


title: 6F_M_2072


title: 6F_M_2076


title: 6F_M_2079


title: 6F_M_2070


title: 6F_M_2069


title: 6F_M_2073


title: 6F_M_2071


title: 6F_M_2074


title: 6F_M_2097


title: 6F_M_2066


title: 6F_M_2068


title: 6F_M_2067


title: 6F_M_2082


title: 6F_M_2075


title: 6F_M_2065


title: 6F_M_2063


title: 6F_M_2064


title: 6F_M_2080


title: 6F_M_2061


title: 6F_M_2062


title: 6F_M_2057


title: 6F_M_2060


title: 6F_M_2058


title: 6F_M_2056


title: 6F_M_2052


title: 6F_M_2054


title: 6F_M_2053


title: 6F_M_2049


title: 6F_M_2050


title: 6F_M_2043


title: 6F_M_2045


title: 6F_M_2044


title: 6F_M_2046


title: 6F_M_2047


title: 6F_M_2055


title: 6F_M_2051


title: 6F_M_2041


title: 6F_M_1975


title: 6F_M_1974


title: 6F_M_2042


title: 6F_M_1972


title: 6F_M_1970


title: 6F_M_2040


title: 6F_M_2059


title: 6F_M_1969


title: 6F_M_1968


title: 6F_M_1971


title: 6F_M_1973


title: 6F_M_1967


title: 6F_M_1964


title: 6F_M_1965


title: 6F_M_2048


title: 6F_M_1966


title: 6F_M_1963


title: 6F_M_1961


title: 6F_M_1960


title: 6F_M_1958


title: 6F_M_1957


title: 6F_M_1959


title: 6F_M_1962


title: 6F_M_1954


title: 6F_M_1951


title: 6F_M_1953


title: 6F_M_1949


title: 6F_M_1956


title: 6F_M_1950


title: 6F_M_1947


title: 6F_M_1955


title: 6F_M_1952


title: 6F_M_1944


title: 6F_M_1943


title: 6F_M_1942


title: 6F_M_1941


title: 6F_M_1940


title: 6F_M_1939


title: 6F_M_1938


title: 6F_M_1937


title: 6F_M_1936


title: 6F_M_1935


title: 6F_M_1934


title: 6F_M_1932


title: 6F_M_1928


title: 6F_M_1933


title: 6F_M_1924


title: 6F_M_1926


title: 6F_M_1927


title: 6F_M_1931


title: 6F_M_1948


title: 6F_M_1929


title: 6F_M_1923


title: 6F_M_1946


title: 6F_M_1930


title: 6F_M_1925


title: 6F_M_1945


title: 6F_M_1920


title: 6F_M_1919


title: 6F_M_1916


title: 6F_M_1921


title: 6F_M_1922


title: 6F_M_1915


title: 6F_M_1914


title: 6F_M_1780


title: 6F_M_1782


title: 6F_M_1912


title: 6F_M_1783


title: 6F_M_1913


title: 6F_M_1776


title: 6F_M_1781


title: 6F_M_1773


title: 6F_M_1778


title: 6F_M_1772


title: 6F_M_1774


title: 6F_M_1769


title: 6F_M_1763


title: 6F_M_1918


title: 6F_M_1766


title: 6F_M_1779


title: 6F_M_1767


title: 6F_M_1762


title: 6F_M_1775


title: 6F_M_1759


title: 6F_M_1761


title: 6F_M_1770


title: 6F_M_1768


title: 6F_M_1765


title: 6F_M_1764


title: 6F_M_1760


title: 6F_M_1917


title: 6F_M_1758


title: 6F_M_1777


title: 6F_M_1771


title: 6F_M_1757


title: 6F_M_1756


title: 6F_M_1753


title: 6F_M_1755


title: 6F_M_1751


title: 6F_M_1750


title: 6F_M_1752


title: 6F_M_1749


title: 6F_M_1748


title: 6F_M_1743


title: 6F_M_1745


title: 6F_M_1746


title: 6F_M_1740


title: 6F_M_1738


title: 6F_M_1739


title: 6F_M_1737


title: 6F_M_1735


title: 6F_M_1741


title: 6F_M_1731


title: 6F_M_1733


title: 6F_M_1734


title: 6F_M_1730


title: 6F_M_1729


title: 6F_M_1728


title: 6F_M_1754


title: 6F_M_1726


title: 6F_M_1727


title: 6F_M_1724


title: 6F_M_1725


title: 6F_M_1722


title: 6F_M_1721


title: 6F_M_1742


title: 6F_M_1744


title: 6F_M_1656


title: 6F_M_1732


title: 6F_M_1736


title: 6F_M_1723


title: 6F_M_1652


title: 6F_M_1720


title: 6F_M_1651


title: 6F_M_1654


title: 6F_M_1646


title: 6F_M_1649


title: 6F_M_1648


title: 6F_M_1643


title: 6F_M_1641


title: 6F_M_1642


title: 6F_M_1655


title: 6F_M_1640


title: 6F_M_1636


title: 6F_M_1637


title: 6F_M_1633


title: 6F_M_1635


title: 6F_M_1653


title: 6F_M_1631


title: 6F_M_1629


title: 6F_M_1638


title: 6F_M_1632


title: 6F_M_1628


title: 6F_M_1626


title: 6F_M_1650


title: 6F_M_1645


title: 6F_M_1630


title: 6F_M_1627


title: 6F_M_1644


title: 6F_M_1621


title: 6F_M_1639


title: 6F_M_1620


title: 6F_M_1622


title: 6F_M_1618


title: 6F_M_1619


title: 6F_M_1634


title: 6F_M_1616


title: 6F_M_1617


title: 6F_M_1615


title: 6F_M_1614


title: 6F_M_1612


title: 6F_M_1610


title: 6F_M_1608


title: 6F_M_1609


title: 6F_M_1613


title: 6F_M_1604


title: 6F_M_1624


title: 6F_M_1625


title: 6F_M_1603


title: 6F_M_1602


title: 6F_M_1599


title: 6F_M_1606


title: 6F_M_1607


title: 6F_M_1601


title: 6F_M_1598


title: 6F_M_1623


title: 6F_M_1600


title: 6F_M_1596


title: 6F_M_1595


title: 6F_M_1594


title: 6F_M_1592


title: 6F_M_1593


title: 6F_M_1591


title: 6F_M_1611


title: 6F_M_1589


title: 6F_M_1590


title: 6F_M_1605


title: 6F_M_1588


title: 6F_M_1584


title: 6F_M_1586


title: 6F_M_1583


title: 6F_M_1582


title: 6F_M_1580


title: 6F_M_1597


title: 6F_M_1581


title: 6F_M_1579


title: 6F_M_1578


title: 6F_M_1570


title: 6F_M_1571


title: 6F_M_1572


title: 6F_M_1573


title: 6F_M_1577


title: 6F_M_1569


title: 6F_M_1576


title: 6F_M_1575


title: 6F_M_1568


title: 6F_M_1567


title: 6F_M_1564


title: 6F_M_1565


title: 6F_M_1562


title: 6F_M_1566


title: 6F_M_1563


title: 6F_M_1587


title: 6F_M_1561


title: 6F_M_1560


title: 6F_M_1559


title: 6F_M_1585


title: 6F_M_1574


title: 6F_M_1558


title: 6F_M_1556


title: 6F_M_1557


title: 6F_M_1555


title: 6F_M_1553


title: 6F_M_1554


title: 6F_M_1552


title: 6F_M_1551


title: 6F_M_1550


title: 6F_M_1549


title: 6F_M_1547


title: 6F_M_1548


title: 6F_M_1545


title: 6F_M_1544


title: 6F_M_1540


title: 6F_M_1538


title: 6F_M_1543


title: 6F_M_1541


title: 6F_M_1537


title: 6F_M_1542


title: 6F_M_1546


title: 6F_M_1536


title: 6F_M_1533


title: 6F_M_1535


title: 6F_M_1534


title: 6F_M_1539


title: 6F_M_1531


title: 6F_M_1530


title: 6F_M_1532


title: 6F_M_1528


title: 6F_M_1526


title: 6F_M_1529


title: 6F_M_1527


title: 6F_M_1525


title: 6F_M_1524


title: 6F_M_1522


title: 6F_M_1523


title: 6F_M_1521


title: 6F_M_1516


title: 6F_M_1517


title: 6F_M_1515


title: 6F_M_1519


title: 6F_M_1518


title: 6F_M_1513


title: 6F_M_1511


title: 6F_M_1514


title: 6F_M_1512


title: 6F_M_1510


title: 6F_M_1509


title: 6F_M_1505


title: 6F_M_1508


title: 6F_M_1503


title: 6F_M_1504


title: 6F_M_1499


title: 6F_M_1501


title: 6F_M_1498


title: 6F_M_1500


title: 6F_M_1496


title: 6F_M_1502


title: 6F_M_1520


title: 6F_M_1495


title: 6F_M_1506


title: 6F_M_1497


title: 6F_M_1492


title: 6F_M_1494


title: 6F_M_1507


title: 6F_M_1491


title: 6F_M_1490


title: 6F_M_1489


title: 6F_M_1487


title: 6F_M_1486


title: 6F_M_1485


title: 6F_M_1488


title: 6F_M_1481


title: 6F_M_1482


title: 6F_M_1483


title: 6F_M_1477


title: 6F_M_1478


title: 6F_M_1479


title: 6F_M_1476


title: 6F_M_1480


title: 6F_M_1471


title: 6F_M_1474


title: 6F_M_1468


title: 6F_M_1475


title: 6F_M_1467


title: 6F_M_1493


title: 6F_M_1469


title: 6F_M_1466


title: 6F_M_1400


title: 6F_M_1470


title: 6F_M_1401


title: 6F_M_1399


title: 6F_M_1397


title: 6F_M_1398


title: 6F_M_1484


title: 6F_M_1396


title: 6F_M_1472


title: 6F_M_1393


title: 6F_M_1394


title: 6F_M_1395


title: 6F_M_1392


title: 6F_M_1391


title: 6F_M_1388


title: 6F_M_1386


title: 6F_M_1390


title: 6F_M_1384


title: 6F_M_1385


title: 6F_M_1382


title: 6F_M_1389


title: 6F_M_1377


title: 6F_M_1381


title: 6F_M_1387


title: 6F_M_1380


title: 6F_M_1378


title: 6F_M_1379


title: 6F_M_1373


title: 6F_M_1371


title: 6F_M_1376


title: 6F_M_1368


title: 6F_M_1375


title: 6F_M_1367


title: 6F_M_1374


title: 6F_M_1372


title: 6F_M_1357


title: 6F_M_1370


title: 6F_M_1359


title: 6F_M_1358


title: 6F_M_1366


title: 6F_M_1355


title: 6F_M_1364


title: 6F_M_1365


title: 6F_M_1383


title: 6F_M_1363


title: 6F_M_1350


title: 6F_M_1348


title: 6F_M_1362


title: 6F_M_1356


title: 6F_M_1346


title: 6F_M_1360


title: 6F_M_1340


title: 6F_M_1343


title: 6F_M_1361


title: 6F_M_1345


title: 6F_M_1352


title: 6F_M_1354


title: 6F_M_1339


title: 6F_M_1349


title: 6F_M_1351


title: 6F_M_1344


title: 6F_M_1342


title: 6F_M_1336


title: 6F_M_1333


title: 6F_M_1338


title: 6F_M_1347


title: 6F_M_1331


title: 6F_M_1327


title: 6F_M_1329


title: 6F_M_1341


title: 6F_M_1328


title: 6F_M_1330


title: 6F_M_1334


title: 6F_M_1332


title: 6F_M_1326


title: 6F_M_1325


title: 6F_M_1323


title: 6F_M_1324


title: 6F_M_1321


title: 6F_M_1322


title: 6F_M_1318


title: 6F_M_1319


title: 6F_M_1317


title: 6F_M_1320


title: 6F_M_1316


title: 6F_M_1337


title: 6F_M_1311


title: 6F_M_1335


title: 6F_M_1314


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title: 6F_M_1315


title: 6F_M_1308


title: 6F_M_1313


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title: 6F_M_1307


title: 6F_M_1304


title: 6F_M_1305


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title: 6F_M_1301


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title: 6F_M_1302


title: 6F_M_1298


title: 6F_M_1295


title: 6F_M_1297


title: 6F_M_1291


title: 6F_M_1294


title: 6F_M_1290


title: 6F_M_1293


title: 6F_M_1287


title: 6F_M_1292


title: 6F_M_1286


title: 6F_M_1285


title: 6F_M_1288


title: 6F_M_1283


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title: 6F_M_1289


title: 6F_M_1278


title: 6F_M_1280


title: 6F_M_1279


title: 6F_M_1282


title: 6F_M_1277


title: 6F_M_1276


title: 6F_M_1281


title: 6F_M_1208


title: 6F_M_1209


title: 6F_M_1296


title: 6F_M_1275


title: 6F_M_1210


title: 6F_M_1206


title: 6F_M_1204


title: 6F_M_1203


title: 6F_M_1202


title: 6F_M_1201


title: 6F_M_1200


title: 6F_M_1198


title: 6F_M_1197


title: 6F_M_1195


title: 6F_M_1192


title: 6F_M_1194


title: 6F_M_1193


title: 6F_M_1205


title: 6F_M_1191


title: 6F_M_1187


title: 6F_M_1186


title: 6F_M_1183


title: 6F_M_1180


title: 6F_M_1184


title: 6F_M_1178


title: 6F_M_1177


title: 6F_M_1188


title: 6F_M_1181


title: 6F_M_1199


title: 6F_M_1176


title: 6F_M_1175


title: 6F_M_1196


title: 6F_M_1174


title: 6F_M_1172


title: 6F_M_1173


title: 6F_M_1169


title: 6F_M_1189


title: 6F_M_1167


title: 6F_M_1170


title: 6F_M_1168


title: 6F_M_1179


title: 6F_M_1165


title: 6F_M_1182


title: 6F_M_1163


title: 6F_M_1207


title: 6F_M_1166


title: 6F_M_1160


title: 6F_M_1159


title: 6F_M_1158


title: 6F_M_1155


title: 6F_M_1156


title: 6F_M_1171


title: 6F_M_1154


title: 6F_M_1153


title: 6F_M_1152


title: 6F_M_1151


title: 6F_M_1148


title: 6F_M_1149


title: 6F_M_1145


title: 6F_M_1146


title: 6F_M_1147


title: 6F_M_1144


title: 6F_M_1164


title: 6F_M_1142


title: 6F_M_1162


title: 6F_M_1190


title: 6F_M_1141


title: 6F_M_1161


title: 6F_M_1138


title: 6F_M_1140


title: 6F_M_1139


title: 6F_M_1136


title: 6F_M_1135


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