title: SPT16_AID_V5_Clone1_3-IAA_Rep3 [TT-seq]

status: Public on Mar 15 2023

city: Pittsburgh

first: David

middle: Charles

last: Klein

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

description: Incubated with 4sU for 5 minutes at 37C

data_processing:
library strategy: TT-seq
Barcode adapter sequences removed
Reads mapped to mm10 genome using STAR, with options --outFilterMismatchNoverReadLmax 0.02 and --outFilterMultimapNmax 1
Aligned reads were processed in deepTools by using the bamCoverage command to generate stranded bigwig files detailing coverage genome-wide in 1 bp bins with BPM normalization
Features in aligned reads were counted using HTSeq and analyzed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

growth_protocol: Murine embryonic stem cells were grown under feeder-free conditions in DMEM, supplemented with 10% Fetal Bovine Serum, 2 mM-Glutamine, 1X non-essential amino acids, 0.129mM 2-mercaptoethanol, 1000U/mL Leukemia Inhibitory Factor (LIF), 3 µM CHIR99021 GSK inhibitor (p212121), and 1 µM PD0325091 MEK inhibitor (p212121). Cells were passaged every 48 hours using trypsin (Gibco) and split at a ratio of ~1:8 with fresh medium. Routine anti-mycoplasma cleaning was conducted (LookOut DNA Erase spray, Sigma) and cell lines were screened by PCR to confirm no mycoplasma presence.

extract_protocol: Medium was aspirated and cells were washed with DPBS. DPBS was aspirated and replaced with fresh medium containing 500 mM 4-thiouridine (4sU). Cells were incubated at 37 degrees Celsius with 5% CO2 for five minutes, then washed with DPBS and trypsinized. Cells were pelleted, washed with DPBS, and RNA was extracted with TRIzol per manufacturer's instructions.

treatment_protocol: After 48 hours of undisturbed growth on 10 cm plates, medium was aspirated and cells were washed with DPBS. DPBS was aspirated and fresh medium was added containing 500 nM 3-Indoleacetic acid (3-IAA) or an equivalent volume of 100% ethanol. Plates were then left at 37 degrees Celsius with 5% CO2 for 24 hours before extraction.

tag: cell line/type

value: E14 mES cell line

tag: tag integration

value: osTIR1 was integrated into the genome using CRISPR-directed homologous recombination; separately, Supt16 was C-terminally tagged with the 37 kDa mini-AID tag and a triple V5 tag

value: Cells were left undisturbed on 10 cm plates for 48 hours prior to treatment. Cells were treated with 500 nM 3-IAA mixed into medium for 24 hours. Cells were incubated at 37 degrees Celsius with 5% CO2 for the duration of treatment.

tag: rna extraction

value: Cells were trypsinized, quenched, pelleted, washed with cold PBS, and crosslinked with 1% formaldehyde for 15 minutes. Crosslinking was quenched with .5M glycine for 5 minutes. Fixed cells were pelleted and washed with cold PBS

tag: molecule subtype

value: 4sU-labeled RNA


title: Untagged_3-IAA_Rep3 [TT-seq]

type: SRA

country: USA

description: Incubated with 4sU for 5 minutes at 37C

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: osTIR1 was integrated into the genome using CRISPR-directed homologous recombination

tag: treatment


title: SPT16_AID_V5_Clone2_3-IAA_Rep3 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C


title: SPT16_AID_V5_Clone1_EtOH_Rep3 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C

value: Cells were left undisturbed on 10 cm plates for 48 hours prior to treatment. Cells were treated with 0.1% ethanol mixed into medium for 24 hours. Cells were incubated at 37 degrees Celsius with 5% CO2 for the duration of treatment.


title: O_67_rep2

status: Public on Mar 17 2023

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

library_source: genomic

data_processing:
Library strategy: DNA-Seq
Illumina sequencing reads (~54 million paired end reads per sample) were de-multiplexed generating compressed FASTQ files by the on-board DRAGEN informatics pipeline (Illumina DRAGEN FASTQ Generation – 3.7.4) on the NextSeq 2000.
The FASTQ files were trimmed to remove adapter sequences with cutadapt/3.0 and the qualities of the FASTQs checked by running FASTQC/0.11.9. The reads were aligned with bowtie/2-2.4.2 using the end-to-end option to the GRCm38/mm10 genome assembly
Sam output files were then filtered to retain alignments with a minimum mapping quality of 2 using samtools/1.9. Reads mapping to Encyclopedia of DNA Elements (ENCODE) blacklist regions were removed from the analysis.
The bamCoverage option in deepTools/3.5.0 was used to generate RPKM (reads per kilobase per million mapped reads) normalized bigWig files. Input reads were subtracted from the different salt fractions and pellet with bigwigCompare.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using  bamCoverage in deepTools/3.5/0; Scores represent the coverage on the genome location

molecule: genomic DNA

source_name: mouse liver

extract_protocol:
Nuclei was released from frozen tissue by douncing in TM2 buffer (10 mM Tris HCl, pH 7.4, 2 mM MgCl2 supplemented with 1X Halt protease and phosphatase inhibitor and 0.5 mM PMSF), pelleted by centrifugation and washed once to remove debris. The washed pellet was resuspended in TM2 buffer with 1 mM CaCl2 and 12000U of MNase (New England Biolabs), incubated at 23°C for 15 minutes and the reactions stopped by addition of 0.5 mM EGTA. Approximately 30% was saved for analysis (“0”) and the rest was pelleted by centrifugation. The supernatant was removed and saved as “Supernatant” fraction after clearing. The nuclei were washed once with TM2 buffer and then resuspended in 70 µl Triton buffer (10 mM Tris–HCl pH 7.4, 2 mM MgCl2, 2 mM EGTA, 0.1% Triton X-100 supplemented with 1X Halt protease and phosphatase inhibitor and 0.5 mM PMSF) and evenly divided. The first aliquot was saved as “Input” while the second was used for sequential salt extraction by using Triton buffer with either 67.5, 150, 250 or 350 mM NaCl. Each extraction was done by incubating the resuspended pellet at 4°C for 2 hours. After each extraction, the nuclei were pelleted by centrifugation and the supernatant saved as “67.5”, “150”, “250” or “350” mM fraction. Finally, the remainder pellet which corresponds to ~5–10% of chromatin, was resuspended in 35 µl of TNE buffer (10 mM Tris–HCl pH 7.4, 200 mM NaCl, 1 mM EDTA supplemented with 1X Halt protease and phosphatase inhibitor) and labeled as “Pellet” fraction. DNA was purified from each of these fractions using DNA clean and concentrator columns (Zymo Research).
Purified DNA (~10 ng) was used to make libraries using the NEBNext Ultra II kit (New England Biolabs).

treatment_protocol: Old as treated group

tag: tissue

value: liver

tag: strain

tag: salt concentration

tag: group

value: old


title: Untagged_EtOH_Rep3 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C


title: SPT16_AID_V5_Clone2_EtOH_Rep3 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C


title: Kidney allograft, non-rejection

status: Public on Mar 28 2023

city: Boston

first: Jamil

middle: R

last: Azzi

state: MA

address: 221 Longwood ave

department: Transplantation Research Center

institute: Brigham and Women's Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1
empty drops were removed using dropletUtils package
Doublets were removed using doubletfinder package
Cells with nFeature_RNA > 3500, nFeature_RNA > 4000, nFeature_RNA > 6000, for non-rejecting, TCMR and borderline, respectively. Cells with percent.mt < 20 were kept.
The three samples were integrated and the resolution of 0.3 was used for the clustering of cells
Assembly: Hg38
Supplementary files format and content: barcodes_raw_borderline_rejection.tsv, barcodes_raw_non_rejecting.tsv,barcodes_raw_TCMR.tsv contain the barcodes for each sample
Supplementary files format and content: matrix_raw_borderline_rejection.mtx, matrix_raw_non_rejecting.mtx, matrix_raw_TCMR.mtx contain sparse matrix for each sample
Library strategy: snRNA-seq

molecule: nuclear RNA

organism: Homo sapiens

source_name: Kidney allograft

extract_protocol:
Frozen kidney biopsy specimens were obtained after appropriate patient consent and in accordance with Partners Healthcare IRB and institutional guidelines. After first removing the surrounding optimal cutting temperature (OCT) embedding medium with PBS, a previously published protocol using salt Tris-based buffers was used to isolate single nuclei. 8,000 single nuclei were then loaded into each channel of the Chromium single cell 3’ chip (v3; 10x Genomics, Pleasanton, USA).
Single nuclei were partitioned into gel bead-in-emulsions (GEMs) and incubated to generate barcoded cDNA by reverse transcription. Barcoded cDNA was then amplified by PCR prior to library construction. Fragmentation, sample index, and adaptor ligation, and PCR were used to generate libraries of paired-end constructs according to the manufacturer’s recommendations (10x Genomics, Pleasanton, USA). Libraries were pooled and sequenced using the Illumina HiSeq X system (San Diego, USA).
single nuclei RNA sequencing (snRNA seq)

value: Kidney allograft


title: SPT16_AID_V5_Clone2_3-IAA_Rep2 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C


title: SPT16_AID_V5_Clone1_3-IAA_Rep2 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C


title: SPT16_AID_V5_Clone2_EtOH_Rep2 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C


title: Untagged_3-IAA_Rep2 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C


title: SPT16_AID_V5_Clone1_EtOH_Rep2 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C


title: SPT16_AID_V5_Clone2_3-IAA_Rep1 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C


title: SPT16_AID_V5_Clone1_3-IAA_Rep1 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C


title: Untagged_EtOH_Rep2 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C


title: Untagged_3-IAA_Rep1 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C


title: SPT16_AID_V5_Clone1_EtOH_Rep1 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C


title: Untagged_EtOH_Rep1 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C


title: SPT16_AID_V5_Clone2_EtOH_Rep1 [TT-seq]

description: Incubated with 4sU for 5 minutes at 37C


title: O_250_rep2


title: Untagged_IAA_Rep3 [MNase-seq]

description: Digested for 5 minutes at 37C with 30U micrococcal nuclease (TaKaRa)

data_processing:
Barcode adapter sequences removed
Reads mapped to mm10 genome using bowtie2, allowing for 1 mismatch
Duplicates were removed using Picard
Reads were filtered for quality using SAMtools (MAPQ ≥ 10)
Reads were size-selected into nucleosome (135-165), subnucleosome (100-130) and TF (1-80) size classes
Nucleosome-sized reads were processed in deepTools by using the bamCoverage command to generate bigwig files detailing coverage genome-wide in 1 bp bins with BPM normalization
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol: Medium was aspirated and cells were washed with DPBS. DPBS was aspirated and cells weretrypsinized. Cells were pelleted, washed with DPBS, crosslinked with 1% formaldehyde for 15 minutes at room temperature, and quenched with 0.5M glycine for five minutes. Crosslinked cells were pelleted, lysed in hypotonic buffer and pre-incubated with calcium, then digested with 30U MNase for five minutes and chelated with EDTA.

tag: cell ine/type

tag: extraction


title: SPT16_AID_V5_Clone2_IAA_Rep2 [MNase-seq]


title: Untagged_EtOH_Rep3 [MNase-seq]


title: Untagged_IAA_Rep2 [MNase-seq]


title: SPT16_AID_V5_Clone2_EtOH_Rep2 [MNase-seq]


title: SPT16_AID_V5_Clone1_EtOH_Rep2 [MNase-seq]


title: Untagged_EtOH_Rep2 [MNase-seq]


title: SPT16_AID_V5_Clone2_EtOH_Rep1 [MNase-seq]


title: SPT16_AID_V5_Clone1_IAA_Rep2 [MNase-seq]


title: Untagged_IAA_Rep1 [MNase-seq]


title: Untagged_EtOH_Rep1 [MNase-seq]


title: Untagged_V5_Rep3 [CUT&RUN]

data_processing:
library strategy: CUT&RUN
Barcode adapter sequences removed and reads trimmed to 25 bp
Reads mapped to mm10 genome using Bowtie2, and allowing 1 mismatch
Picard used to remove duplicates
Low quality reads were removed (MAPQ <10)
Reads divded into size classes: 1-120 bp
Aligned reads were processed in deepTools by using the bamCoverage command to generate bigwig files detailing coverage genome-wide in 1 bp bins with BPM normalization
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Untagged

extract_protocol: Unfixed nuclei were bound to ConcanavalinA beads, washed, followed by successive addition of primary antibodie followed by proteinA-Mnase. Cleavage of Mnase was initiated by Ca** addition and stopped by chelation. Fragments were released and deep sequencing libraries were prepared.

treatment_protocol: No treatment was performed on these cells.

tag: nuclear harvest

value: Cells were trypsinized, quenched, pelleted, washed with cold PBS, and nuclei were extracted

tag: primary antibody

value: anti-V5 mouse monoclonal, Invitrogen 46-0705, lot 1923773

tag: secondary antibody

value: recombinant Protein A/Protein G- MNase (pA/G-MN)


title: Untagged_Untargeted_Rep3 [CUT&RUN]


title: SPT16_AID_V5_Clone1_EtOH_Rep1 [MNase-seq]


title: SPT16_AID_V5_Clone2_Untargeted_Rep2 [CUT&RUN]


title: SPT16_AID_V5_Clone1_V5_Rep2 [CUT&RUN]

source_name: SPT16_AID_V5 Clone_1


title: SPT16_AID_V5_Clone2_V5_Rep2 [CUT&RUN]


title: Untagged_Untargeted_Rep2 [CUT&RUN]


title: SPT16_AID_V5_Clone1_IAA_Rep1 [MNase-seq]


title: SPT16_AID_V5_Clone1_Untargeted_Rep2 [CUT&RUN]


title: SPT16_AID_V5_Clone1_V5_Rep1 [CUT&RUN]


title: SPT16_AID_V5_Clone2_Untargeted_Rep1 [CUT&RUN]


title: Untagged_V5_Rep1 [CUT&RUN]


title: Untagged_Untargeted_Rep1 [CUT&RUN]


title: SPT16_AID_V5_Clone2_V5_Rep1 [CUT&RUN]


title: 24_dHET

status: Public on Feb 28 2023

city: New York

first: Laura

last: Pasqualucci

state: NY

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the mouse genome (UCSC mm10) using hisat2 with the following options: --threads 4 --add-chrname --ignore-quals -q -x mm10 -k 5.
Reads were mapped to exons using featureCounts to produce abundance tables.
Assembly: mm10
Supplementary files format and content: Tab delimited text file of read counts produced by featureCounts

source_name: spleen

growth_protocol: Mice (12 week old) were immunized with SRBC (day 0: 1X10^8 cells; d5:1X10^9 cells) and sacrificed at d12 for analysis.

extract_protocol:
Single cell suspensions prepared from the spleen of immunized mice were processed with the mouse B-cell isolation kit (Miltenyi Biotec), and germinal center B cells (B220+CD95+PNA+) were sorted from individual mouse samples by fluorescence-activated cell sorting
Total RNA was isolated using the Total RNA isolation NucleoSpin RNA XS kit (NACHEREY-NAGEL) according to the user's manual.

treatment_protocol: mice immunized

value: spleen

tag: cell type

tag: genotype

value: d12 post-SRBC immunization

tag: age

value: 12-16-wk old animal


title: SPT16_AID_V5_Clone1_Untargeted_Rep1 [CUT&RUN]

tag: cell line/type


title: 18_Kmt2d_HET

value: germinal center B cells (B220+CD95+PNA+)


title: 1_dHET


title: 26_Kmt2d_HET


title: SPT16_AID_V5_Clone2_IAA_Rep1 [MNase-seq]

value: E14 mES cell line

tag: tag integration


title: 17_Crebbp_HET


title: 25_WT


title: 23_Crebbp_HET


title: 22_dHET


title: Untagged_V5_Rep2 [CUT&RUN]


title: 12_WT


title: 19_WT


title: 13-5A' at 0 h, after 4℃ treatment, 3

status: Public on Feb 25 2023

city: shanghai

first: shi

last: yao

address: jinqi road

department: Horticultural Research Institute

country: China

institute: Shanghai Academy of Agricultural Sciences

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DHL92_v3.6.1 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: DHL92_v3.6.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Cucumis melo

source_name: Leaves

growth_protocol: two melon varieties, ‘162’ (chilling-tolerant) and ‘13-5A’ (chilling-sensitive) were used in this study.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) following the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina NovaSeq 6000 platform and 150bp paired-end reads were generated.

treatment_protocol: ‘162’(chilling-tolerant) and ‘13-5A’(chilling-sensitive) were carried out under 4℃ chilling stress at 0h and 12h.

value: Leaves

tag: cultivar

value: 4degreeC treatment

tag: time point


title: 13-5A' at 0 h, after 4℃ treatment, 2

tag: treatment


title: 13-5A' at 12 h, after 4℃ treatment, 1

tag: tissue


title: 162' at 12 h, after 4℃ treatment, 3


title: 162' at 12 h, after 4℃ treatment, 2


title: 162' at 12 h, after 4℃ treatment, 1


title: 162' at 0 h, after 4℃ treatment, 2


title: 13-5A' at 0 h, after 4℃ treatment, 1


title: sg-1-RNC.fq.gz

status: Public on Feb 16 2023

city: Guangzhou

first: Wei

last: Wei

state: -- None selected --

address: 越秀区中山二路

institute: 中山大学附属第一医院

data_processing: For the RNA-seq, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode.

molecule: polyA RNA

source_name: esophagus

growth_protocol: TE-9 cells were cultured in DMEM (Gibco, USA) with 10% fetal bovine serum (FBS, Gibco, USA), 1% streptomycin (Gibco, USA) and 1% Penicillin (Gibco, USA). Cells were cultured in a water-saturated atmosphere under 5% CO2 at 37°C.

extract_protocol:
RNA was extracted according to TRIzol protocol.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit

treatment_protocol: TE-9 cells were knocked out of NAT10 by Crispr-Cas9. TE-9 cells with normal expression of NAT10 were used as control.

value: esophagus

tag: cell line

value: esophageal epithelial

value: non


title: 162' at 0 h, after 4℃ treatment, 3


title: sg-2-RNC.fq.gz


title: NC-2-input.fq.gz

value: WT


title: NC-2-RNC.fq.gz


title: NC-1-RNC.fq.gz


title: Smaple6_ADT-derived cDNA_Symptomatic

status: Public on Feb 01 2023

first: Dr. Chiara

last: Giannarelli

address: 435 E 30th St

department: Cardiology

institute: NYU Langone Health

description: 10x Genomics

library_source: other

data_processing:
scRNA-seq used the Cell Ranger Single-Cell Software Suite (version 2.1.1, 10X Genomics) to quality control the single-cell expression data.
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v2.1.1) and aligning to the hg38 genome.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
CITE-seq used the Cell Ranger Single-Cell Software Suite (version 2.1.1, 10X Genomics) to quality control the expression data.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: human plaque isolated cells

extract_protocol: For the citeseq sample, the Chromium Single Cell 3′ Library, Gel Bead and Multiplex Kit, and Chip Kit (10X Genomics)73,74 was used. The Chromium Single Cell 3′ v2 Reagent (10X Genomics, 120237) kit was used to prepare  libraries according to the manufacturer’s instructions.

value: human plaque isolated cells

tag: library type

value: Antibody-derived oligonucleotide (ADT)


title: NC-1-input.fq.gz


title: 13-5A' at 12 h, after 4℃ treatment, 2


title: 13-5A' at 12 h, after 4℃ treatment, 3


title: Sample5_scRNAseq_Asymptomatic

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
scRNA-seq used the Cell Ranger Single-Cell Software Suite (version 2.1.1, 10X Genomics) to quality control the single-cell expression data.
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v2.1.1) and aligning to the hg38 genome.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
CITE-seq used the Cell Ranger Single-Cell Software Suite (version 2.1.1, 10X Genomics) to quality control the expression data.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol: The single-cell suspensions of scRNA-seq samples were converted to barcoded scRNA-seq libraries using the Chromium Single Cell 3′ Library, Gel Bead and Multiplex Kit, and Chip Kit (10X Genomics)73,74.


title: Sample6_HTO-derived cDNA_Symptomatic

description: 10x Genomics

value: Hashtag-derived oligonucleotide (HTO)


title: Sample3A_scRNAseq_Asymptomatic

description: 10x Genomics


title: Sample1_scRNAseq_Symptomatic

description: 10x Genomics


title: Sample2_scRNAseq_Asymptomatic

description: 10x Genomics


title: Sample6_mRNA-derived cDNA_Symptomatic

description: 10x Genomics

value: RNA


title: sg-2-input.fq.gz


title: Sample3_scRNAseq_Asymptomatic

description: 10x Genomics


title: Sample4_scRNAseq_Asymptomatic

description: 10x Genomics


title: A375_NES_Day28_R2

status: Public on Jan 16 2023

city: Washington

first: Xiaolong

last: Cheng

state: DC

address: 7144 13th Place NW

institute: Children's National

description: Pcr product from genomic DNA of cell line

data_processing:
Read count table generated by MAGeCK 0.5.9.4
MAGeCK count command was used to collect read count from the fastq file
Robust Rank Aggreation algorithm was used to rank the sgRNAs and target genes. Those sgRNAs that target non-essential genes were used as negative control.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized counts for each Sample

source_name: skin

growth_protocol: Human melanoma A375 cells was maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS). Protein-coding gene and lncRNA-targeting plasmid libraries under lentiviral pLentiCasRxDR-puro backbone were firstly transfected along with pCMV8.74 and pMD2.G packaging plasmids into cells using Lipofectamine™ 2000 Transfection Reagent to generate Cas13d sgRNA-expressing lentivirus. Harvest virus-containing media at 72 hours post-transfection, and spin down the media at 1000 g for 5 min to remove the floating cells and cell debris. Carefully collect the virus supernatant, aliquot and store them at -80°C for further use. Test the virus titer and MOI (multiplicity of infection) before proceeding to the screen.

extract_protocol:
The regions encompassing the sgRNAs were firstly PCR-amplified for around 20-23 cycles . The second round of PCR were employed to attach the illumina adaptors and index for around 10-12 cycles. These PCR products were gel purified and pooled for high-throughput sequencing to identify sgRNA abundance on illumina PE150 sequencing platform (Novogene, China).
The pooled synthesized oligos (Synbio Technologies, China) were PCR amplified and then cloned into pLentiCasRxDR-puro vector (for expressing CasRx sgRNA) via BsmBI site by Gibson Assembly. The ligated Gibson Assembly mix was transformed into self-prepared electrocompetent Stable E. coli cells by electro-transformation to reach the efficiency with at least 100X coverage representation of each clone in the designed library. The transformed bacteria were cultured directly in liquid LB medium for 16~20 hours at temperature 30°C to minimize the recombination events in E. coli. The library plasmids were then extracted with EndoFree Maxi Plasmid Kit (TIANGEN, Cat no. 4992194).
Ensembl gene and lncRNA annotations (version: GRCh38) are used to extract the sequences of corresponding genes or lncRNAs. For genes (or lncRNAs) with multiple transcripts, the transcripts that have the corresponding RefSeq ID are used. We first enumerate all possible guides (22bp) that span the entire transcript, then remove guides that (1) map to more than one location in the human genome and transcriptome (allowing up to 1 mismatch) or (2) contains BsmBI digestion sites (“CGTCTC” or “GAGACG”). The remaining guides are randomly selected if they hit the greatest number of transcripts (“common” guides) within the same gene/lncRNA. If all the guides that hit the greatest number of transcripts are selected, the remaining guides that hit the second greatest number of transcripts will be randomly selected, and so on. For essential and non-essential genes, 35 guides are designed per gene. For other genes or lncRNAs, 15 guides are designed per gene or lncRNA.

treatment_protocol: Cas13d-expressing A375 cells were firstly generated by lentiviral infection of Cas13d (pLentiCas13d-NLS-blast) and then amplified to a number around 3x107. Then, these cells were infected with Cas13d sgRNA-expressing lentiviral CRISPR library with MOI ~0.3. Two days later, select the infected cells with puromycin (1 µg/mL) for three days to get rid of any non-infected cells before changing back to normal media. At least ~300x coverage of cells were collected as Day 0 sample and stored at -80°C for later genomic DNA isolation. The rest of cells were continually cultured until Day 28 before harvesting as the end point sample.

value: skin

value: melanoma cells

tag: time

value: day 28


title: P28_CM_p300_RNA-seq_rep1

status: Public on Jan 19 2023

first: Pingzhu

last: Zhou

address: 320 Longwood Ave

institute: Boston Children's Hospital

data_processing:
For RNA-seq data, reads mapped to mm10 genome using STAR.
Sam converted to BAM using Samtools
For RNA-seq data, reads counts for all genes were done by HTSeq-count.
Genome_build: mm10
Supplementary_files_format_and_content: text files containing raw reads count of all genes in all replicates

source_name: Heart

extract_protocol: For E12.5, E16.5, P0, and P7 CMs, ventricular apexes were dissociated using the Neonatal mouse cardiomyocyte isolation kit (Cellutron Life Technologies) and purified using the mouse neonatal cardiomyocyte isolation kit (Miltenyi). P14, P28, and P42 CMs were dissociated and purified from ventricular apexes by Langendorf collagenase perfusion followed by differential sedimentation. Purified cardiomyocytes were used with three biological replicates per group for RNA-seq. RNA was purified using the Purelink RNA mini kit (Life Technologies). Ribosomal RNA was depleted using Ribo-Zero rRNA removal kits (Epicentre). RNA-seq libraries were prepared using ScriptSeq v2 library kit (Epicentre). Libraries were sequenced using an Illumina NextSeq500 with single end 75   bp reads. At least 50 M reads were obtained for each biological replicate.

tag: strain

value: ventricle cardiomyocytes

tag: developmental stage


title: P28_CM_p300_RNA-seq_rep2


title: P28_CM_p300_RNA-seq_rep3


title: A375_NES_Day28_R1


title: 162' at 0 h, after 4℃ treatment, 1


title: A375_NES_Day0_R1

value: day 0


title: sg-1-input.fq.gz


title: A375_Day35_PP020_CasRx_nls_R2

data_processing:
Library strategy: CRISPR screen
Read count table generated by MAGeCK 0.5.9.4
MAGeCK count command was used to collect read count from the fastq file
Robust Rank Aggreation algorithm was used to rank the sgRNAs and target genes. Those sgRNAs that target non-essential genes were used as negative control.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each Sample

source_name: melanoma cells

treatment_protocol: Cas13d-expressing A375 cells were firstly generated by lentiviral infection of Cas13d (pLentiCas13d-NLS-blast) and then amplified to a number around 3x107. Then, these cells were infected with Cas13d sgRNA-expressing lentiviral CRISPR library with MOI ~0.3. Two days later, select the infected cells with puromycin (1 µg/mL) for three days to get rid of any non-infected cells before changing back to normal media. At least ~300x coverage of cells were collected as Day 5 sample and stored at -80°C for later genomic DNA isolation. The rest of cells were continually cultured until Day 33 before harvesting as the end point sample.

value: Day 33


title: A375_Day35_PP020_CasRx_nls_R1


title: 21_Crebbp_HET

value: spleen

value: germinal center B cells (B220+CD95+PNA+)

value: d12 post-SRBC immunization

value: 12-16-wk old animal


title: A375_Day5_PP020_CasRx_nls_R1

value: Day 5


title: A375_Day5_PP020_CasRx_nls_R2


title: A375_NES_Day0_R2


title: SJALCL045631_D1

status: Public on Jan 02 2023

type: genomic

city: Memphis

first: Timothy

middle: Isham

last: Shaw

state: TN

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing:
The methylation score of each CpG site in the array is represented as a beta (β) value and was computed using the methylation module of the Geno meStudio software (version 1.9.0; Illumina). Beta-values were converted to M-values (39) prior to differential methylation analysis and clustering.
Processed data: Average Beta

source_name: ALCL Diagnosis

label_protocol: Illumina protocol

growth_protocol: Primary Tissue

extract_protocol: Genomic DNA (1 µg) from 37 ALCL was bisulfite converted by using the EZ DNA Methylation kit (Zymo Research Corp, Irvine, CA, USA). Converted samples were processed and hybridized to the Infinium MethylationEPIC BeadChip (850K) system (Illumina, San Diego, CA, USA).

tag: gender

value: F

tag: age at diagnosis

tag: sample source

tag: histologic subtype

value: common


title: SJALCL045634_D1

value: M


title: SJALCL045625_D1


title: SJALCL045627_D1


title: SJALCL045622_D1


title: SJALCL045614_D1

value: Mediastinum (including paratracheal)


title: SJALCL045613_D1

value: Mesenteric


title: SJALCL045616_D1

value: SCV


title: SJALCL045620_D1


title: SJALCL045612_D1


title: SJALCL045611_D1

value: Left inguinal and femoral


title: SJALCL045610_D1


title: SJALCL017858_D1

value: Small bowel


title: SJALCL017860_D1

value: Lymph node cervical


title: SJALCL017861_D1

value: Lymph node, abdominal


title: SJALCL017857_D1

value: Lymph node


title: SJALCL017862_D1


title: SJALCL017854_R1

source_name: ALCL Relapse


title: SJALCL017851_D1

value: LH


title: SJALCL017847_D1

value: Lymph node, inguinal


title: SJALCL017845_D1

value: Lymph node, axillary


title: SJALCL017844_D1


title: SJALCL017853_D1

value: Skin


title: SJALCL014728_D1

value: Lymph node, occipital


title: SJALCL014727_D1

value: Lymph node, submandibular


title: SJALCL045629_D1

value: F

value: Right neck:Cervical, supraclavicular, occipital, and pre-auricular


title: SJALCL014724_R1

value: M

value: Lymph node, neck

value: common


title: SJALCL014723_R1

value: Ascites fluid


title: SJALCL014725_D1


title: THP-1 cells, cell-pooled KO screen

status: Public on Jan 01 2023

city: Cambridge

first: Douglas

last: Yao

address: 1350 Massachusetts Ave

institute: Harvard University

description: 10X Genomics

data_processing:
The “cellranger mkfastq” command with default parameters (from the 10x CellRanger tool v6.0.1; https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) was used to generate FASTQ files.
The “cellranger count” command with default parameters was used to align the expression reads to the GRCh38 build of the human transcriptome and generate a gene expression count matrix.
Assembly: GRCh38
Supplementary files format and content: All expression counts stored as Seurat object (R data set file format). Expression counts are stored under the "RNA" assay, while cell by perturbation design matrix stored under the "perturbations" assay. Cell meta-data is stored in the Seurat metadata.
Supplementary files format and content: All expression counts stored as Anndata object (h5ad file format). Object contains expression counts and cell meta-data but not perturbation by cell design matrix.
Supplementary files format and content: Perturbation by cell design matrix (tab-delimited text file). Rows correspond to perturbations and columns correspond to cells. Entries of the matrix indicate how many unique guides the cell contains for the given perturbation (ranging from 0 to 4).
Supplementary files format and content: KO_cell_pooled_FRPerturb_effect_sizes.csv: Log fold changes and qvalues of all perturbation-on-gene effects estimated by FR-Perturb.

source_name: Cas9-expressing THP-1

growth_protocol: THP-1 cells (ATCC, TIB202) were cultured in RPMI medium (ATCC, 30-2001) supplemented with 10% FBS (ATCC, 30-2020) and 0.05mM 2-mercaptoethanol (sigma Aldrich, M7522). Cells were maintained between 0.8 and 2 million cells per milliliter.

extract_protocol:
The THP-1 cell suspension was prepared for droplet generation according to the manufacturer’s suggested protocol (10x Genomics, CG00053 Rev C).
The standard 10x single cell 3’ RNAseq protocol (Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 PN-1000121) was run according to manufacturer's recommendation.

treatment_protocol: THP-1 cell lines were infected with sgRNA libraries at a multiplicity of infection (MOI) specific for each experiment. 12 hours after spinfection, cells and media were diluted 1:10 and cells were allowed to recover for 48h. Cells were selected with puromycin (2 micrograms/mL) for four days. The selected cells were differentiated into macrophages by stimulation in 20ng/mL phorbol 12-myristate 13-acetate (Sigma Aldrich, P8139-1mg) for 24 hours. Cells were then allowed to rest in normal culture medium for 48 hours before stimulation in medium containing 100ng/mL LPS (Millipore sigma, L4391-1mg) for 3 hours.

value: Cas9-expressing THP-1

tag: cell type

value: Macrophage

value: 3 hours LPS


title: THP-1 cells, guide-pooled KD screen

description: 10X Genomics

data_processing:
The “cellranger mkfastq” command with default parameters (from the 10x CellRanger tool v6.0.1; https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) was used to generate FASTQ files.
The “cellranger count” command with default parameters was used to align the expression reads to the GRCh38 build of the human transcriptome and generate a gene expression count matrix.
Assembly: GRCh38
Supplementary files format and content: All expression counts stored as Seurat object (R data set file format). Expression counts are stored under the "RNA" assay, while cell by perturbation design matrix stored under the "perturbations" assay. Cell meta-data is stored in the Seurat metadata.
Supplementary files format and content: All expression counts stored as Anndata object (h5ad file format). Object contains expression counts and cell meta-data but not perturbation by cell design matrix.
Supplementary files format and content: Perturbation by cell design matrix (tab-delimited text file). Rows correspond to perturbations and columns correspond to cells. Entries of the matrix indicate how many unique guides the cell contains for the given perturbation (ranging from 0 to 4).
Supplementary files format and content: Effect sizes estimated by FR-Perturb for all cells in the conventional knock-out screen.
Supplementary files format and content: KD_guide_pooled_FRPerturb_effect_sizes.csv: Log fold changes and qvalues of all perturbation-on-gene effects estimated by FR-Perturb.

source_name: dCas9-KRAB-expressing THP-1

value: dCas9-KRAB-expressing THP-1


title: THP-1 cells, conventional KD screen

description: 10X Genomics

data_processing:
The “cellranger mkfastq” command with default parameters (from the 10x CellRanger tool v6.0.1; https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) was used to generate FASTQ files.
The “cellranger count” command with default parameters was used to align the expression reads to the GRCh38 build of the human transcriptome and generate a gene expression count matrix.
Assembly: GRCh38
Supplementary files format and content: All expression counts stored as Seurat object (R data set file format). Expression counts are stored under the "RNA" assay, while cell by perturbation design matrix stored under the "perturbations" assay. Cell meta-data is stored in the Seurat metadata.
Supplementary files format and content: All expression counts stored as Anndata object (h5ad file format). Object contains expression counts and cell meta-data but not perturbation by cell design matrix.
Supplementary files format and content: Perturbation by cell design matrix (tab-delimited text file). Rows correspond to perturbations and columns correspond to cells. Entries of the matrix indicate how many unique guides the cell contains for the given perturbation (ranging from 0 to 4).
Supplementary files format and content: KD_all_FRPerturb_effect_sizes.csv: Log fold changes and qvalues of all perturbation-on-gene effects estimated by FR-Perturb (conventional and pooled samples combined when inferring effects).
Supplementary files format and content: KD_conventional_FRPerturb_effect_sizes.csv: Log fold changes and qvalues of all perturbation-on-gene effects estimated by FR-Perturb.


title: RNA_MSC_CTR_OVX_1

status: Public on Dec 05 2022

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

description: RNA-seq, Primary stromal cells from bone marrow of OVX operated mice on control diet

data_processing:
RNA-seq reads were aligned to mm10 genome using STAR aligner and default settings.
Gene expression was quantified using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -count exons -condenseGenes -noCondensing -noadj. Normalization and differential expression analysis was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) taking Group (CTR_SHAM, CTR_OVX, HFD_SHAM, and HFD_OVX) into the design matrix, excluding genes which were not detected in any sample. Log 2 fold changes and FDR values were calculated with respect to CTR_SHAM.
Genome_build: mm10
Supplementary_files_format_and_content: Txt file containing raw counts and DEseq2 derived normalized andrlog transformed counts as well as p values, adjusted p values and logFC in comparison to CTR_SHAM

growth_protocol: Front and hind limbs were collected after 12 weeks of diet intervention, crushed and digested with 5% collagenase (StemCell). After filtration and washing steps with PBS/2%FBS, BMSCs were obtained as negative fraction from triple staining with antibodies against CD45, CD31 and Ter119 (Miltenyi Biotec) and passing through the magnetic columns. BMSCs were cultivated and expanded using standard tissue culture conditions and alpha-MEM supplemented with 20% FBS, 1% Penicilin-Strepotomycin 1% Glutamax, non-essential amino acids (NEAA) and pyruvate sodium (Gibco). At passage 3 cells were used for the subsequent molecular and cellular analyses.

extract_protocol:
RNA was extracted from cultured cells using Trizol combined with the Qiagen Rneasy Mini Kit (Qiagen).
RNA-seq was performed according to manufacturer’s instructions (TruSeq 2, Illumina) using 1 µg RNA for preparation of cDNA libraries.

treatment_protocol: Female C57BL/6J mice (Taconic, Rensselaer, NY, USA) at 8 weeks of age were assigned for either ovariectomy (OVX) or sham operation and afterwards fed a R-70 normal-diet (ND) (containing Kcal%: protein 14.5%, carbohydrates 60%, and fat 4.5%) or high-fat diet (HFD) (Research Diet [New Brunswick, NJ, USA] D12492, containing Kcal%: protein 20%, carbohydrates 20%, and fat 60%). Mice were anesthetized before ovariectomy by the dorsal approach using intraperitoneal injection of ketamine (100mg/kg) and xylazine (10mg/kg). Animals were fed ad libitum and housed (4 animals per cage) under standard conditions (21°C, 55% relative humidity) on a 12-hour light/dark cycle for a period of 12 weeks. All experimental procedures were approved by the Danish Animal Ethical committee (2017-15-0201-01210).

value: Primary stromal cells


title: THP-1 cells, conventional KO screen

description: 10X Genomics

data_processing:
The “cellranger mkfastq” command with default parameters (from the 10x CellRanger tool v6.0.1; https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) was used to generate FASTQ files.
The “cellranger count” command with default parameters was used to align the expression reads to the GRCh38 build of the human transcriptome and generate a gene expression count matrix.
Assembly: GRCh38
Supplementary files format and content: All expression counts stored as Seurat object (R data set file format). Expression counts are stored under the "RNA" assay, while cell by perturbation design matrix stored under the "perturbations" assay. Cell meta-data is stored in the Seurat metadata.
Supplementary files format and content: All expression counts stored as Anndata object (h5ad file format). Object contains expression counts and cell meta-data but not perturbation by cell design matrix.
Supplementary files format and content: Perturbation by cell design matrix (tab-delimited text file). Rows correspond to perturbations and columns correspond to cells. Entries of the matrix indicate how many unique guides the cell contains for the given perturbation (ranging from 0 to 4).
Supplementary files format and content: KO_all_FRPerturb_effect_sizes.csv: Log fold changes and qvalues of all perturbation-on-gene effects estimated by FR-Perturb (conventional and pooled samples combined when inferring effects).
Supplementary files format and content: KO_conventional_FRPerturb_effect_sizes.csv: Log fold changes and qvalues of all perturbation-on-gene effects estimated by FR-Perturb.


title: AdCo-07

status: Public on Nov 17 2022

city: Richmond

first: Nicholas

middle: E

last: Johnson

state: VA

address: 1101 E Marshall St

institute: Virginia Commonwealth University

data_processing:
Low quality reads and adapters were trimmed using Trim Galore! and aligned to hg38 reference genome using STAR v 2.7.2d with parameters --twopassMode Basic and sjdbGTffile with a GTF from ensembl realse 98
Gene level counts were obtained per sample using featurecounts v2.0.0
RNA splicing between any two comparisions was performed using rMATS v4.1.0 in paired mode with variable read length being specified.
Differential gene expression was quantified using edgeR.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene with Ensembl gene IDs and every sample
Supplementary files format and content: Tab delineated Case vs Control skipped exon file output by rMATS. IncLevel 1 and IncLevel2 contain psi values for case and control respectively.
Supplementary files format and content: Text file containing order of samples input in rMATs. Aslo pertains to the order of IncLevel1 and IncLevel2 psi values in skipped exon file

source_name: tibialis anterior

extract_protocol:
Muscle tissue was removed by biopsy, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
Total RNA-sequencing libraries were prepared using the NEBNext rRNA Depletion Kit in conjunction with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Deviations from the manufacturer’s protocol include modifications of the recommended 5-fold adaptor dilution to a 40-fold adaptor dilution for RNA inputs between 250ng-100ng and RNA fragmentation times based on RIN and 28S:18S ratios. Samples with a RIN ³ 7.9 were fragmented for 15 minutes, but if the 28S:18S ratio was £ 0.5, then the sample was fragmented for 12 minutes. Additionally, samples with a RIN between 7.0 – 7.8 were fragmented for 12 minutes. Samples with a RIN £ 6.9 were fragmented for 8 minutes unless they had 28S:18S ratio ³ 0.6, in which case they were fragmented for 12 minutes

value: Skeletal Muscle

tag: group

value: AdCo

tag: Sex

value: Male

tag: age


title: AdCo-05

source_name: vastus lateralis


title: AdCo-03

value: Female


title: AdCo-06


title: AdCo-01


title: PeCo-19

source_name: quadriceps femoris

value: PeCo


title: PeCo-20


title: AdCo-04


title: PeCo-16


title: PeCo-14


title: PeCo-21


title: PeCo-18


title: SJALCL017846_D1

value: Humerus


title: PeCo-13


title: PeCo-11


title: PeCo-12


title: PeCo-15


title: PeCo-10


title: PeCo-17


title: PeCo-06


title: PeCo-08


title: PeCo-05


title: PeCo-07

source_name: Skeletal Muscle


title: PeCo-04


title: PeCo-01


title: PeCo-02


title: PeCo-03


title: PeCo-09


title: DM1-22


title: AdCo-02


title: DM1-20


title: DM1-19


title: DM1-18


title: DM1-21


title: DM1-17


title: DM1-16


title: DM1-14


title: DM1-15


title: DM1-13


title: DM1-12


title: DM1-11


title: DM1-09


title: DM1-08


title: DM1-06


title: DM1-05


title: DM1-04


title: DM1-01


title: CDM-36

description: Repeat biopsy from CDM-32

value: CDM


title: CDM-35


title: DM1-02


title: CDM-33

source_name: soleus


title: CDM-31


title: CDM-30


title: CDM-29


title: CDM-28


title: CDM-26


title: CDM-25


title: CDM-27


title: CDM-24


title: CDM-22


title: DM1-07


title: CDM-20


title: CDM-21


title: CDM-23


title: DM1-10


title: CDM-18

description: Repeat biopsy from CDM-01


title: CDM-16


title: CDM-15


title: DM1-03


title: CDM-13


title: CDM-19


title: CDM-14


title: CDM-12


title: CDM-34


title: CDM-11


title: CDM-32


title: CDM-09


title: CDM-08


title: CDM-10


title: CDM-07


title: CDM-04


title: CDM-03


title: CDM-02


title: Lung section derived from Sftpc:KrasG12D sample 2

status: Public on Oct 19 2022

city: Duarte

first: Crystal

middle: N

last: Marconett

email: cmarcone@usc.edu, cmarconett@coh.org

state: CA

address: 1500 E Duarte Rd

department: Integrative Translational Sciences

institute: City of Hope

description:
Sftpc:KrasG12D Lung 2
FFPE Visium mouse

data_processing:
Paired-end sequencing (2x100) was performed on an Illumina instrument. Sequencing data was pre-processed using the Space Ranger pipelines (10x Genomics, https://cloud.10xgenomics.com/cloud-analysis).
BCL data was demultiplexed and converted to FASTQ format using the spaceranger mkfastq pipeline.
The spaceranger count pipeline was then used for read alignment to human reference genome mm10, Unique Molecular Identifier (UMI) counting, and generation of feature-spot matrices corresponding to the microscopic tissue image. The pipeline also performs automatic tissue detection and fiducial alignment from the image.
Assembly: mm10
Supplementary files format and content: UMI count matrices

source_name: Lung

growth_protocol: The Sftpc-CreERT2 mouse line has been used previously to track AT2 cell fate (65, 66). Gramd2-CreERT2 mice were generated by homologous recombination insertion of a cassette including CreERT2- downstream of the endogenous Gramd2 gene stop codon within exon 12. These were separately crossed to heterozygous KrasLSL-G12D mice (Jackson laboratory, Stock: #008179). Gramd2-CreERT2 and Sftpc-CreERT2 mice were in a B6/129 mixed strain background (129 N1), while KrasLSL-G12D mice are in a B6/129S4 mixed strain background (C57BL/6 N10).

extract_protocol:
Spatial transcriptomic profiling was performed at the Molecular Genomics Core, a part of the Norris Comprehensive Cancer Center and under manufacturer’s instructions. Briefly, two biological replicates (one block for each) of Gramd2:KrasG12D and Sftpc:KrasG12D underwent initial 10μM sectioning at the Tissue Pathology Core, part of the Norris Comprehensive Cancer Center. Sections were H&E stained (as above) and underwent pathology review. Regions of Interest (ROIs) then underwent sample preparation including test slide sample sequencing using the Visium Tissue Section Test Slide (PN-2000460, 10X Genomics, Dublin, CA, USA). RNA quality assessment of test slides was determined by first extracting RNA using the Qiagen RNeasy FFPE kit (#73504, Qiagen, Hilden, Germany) and measuring RNA concentration using a Qubit fluorometer (#Q33238, ThermoFisher Scientific, Waltham, MA, USA). To determine The percentage of total fragments >200nt in length was determined by running the samples using a 4200 Tapestation (#G2991AA, Agilent, Santa Clara, CA). Once samples were determined to be of high enough quality to continue, 5μM FFPE sections were then placed in a 42C water bath and once rehydrated adhered to the Visium Spatial Gene Expression Slide (PN-2000233, 10X Genomics). Subsequently, samples were dried at 42C for 3hrs in a desiccation chamber and underwent deparrafinization using Qiagen Deparaffinization Solution (Cat # 19093) at 60C for 2 hr. Subsequently H&E staining (#MHS16, #HT110116 Millipore Sigma, Burlington MA, USA) was performed according to Visium technical parameters (CG000409) and images were captured with a Zeiss Axioscan2 microscope using a 10x objective. Decrosslinking was performed according to 10X standard protocol (CG000407) and immediately hybridized to the Visium Mouse Transcriptome probe set V1.0, which contained 20,551 genes targeted by 20,873 probes.
Post-probe extension, sequencing library construction was performed using unique sample indices using the Dual Index Kit TS, Set A (PN-1000251) for Illumina-compatible sequencing.

treatment_protocol: Tamoxifen (Sigma, CAS: 10540-29-1) powder was first dissolved in 100% ethanol (SHBJ8384, Sigma-Aldrich) and then diluted to a final concentration of 40 mg/mL with corn oil (Sigma, CAS: 8001-30-7). To ensure that tamoxifen was fully dissolved, the mixture was gently shaken in a shaking incubator (SHEL LAB, model: SSI5R; cat: #33-804R) at 55℃ for 2 hours. Six-week-old mice were injected with tamoxifen via intraperitoneal injection. For Gramd2-CreERT2; Sftpc-CreERT2, KrasLSL-G12D and WT mice, 40 mg/mL tamoxifen was injected via intraperitoneal injection. The dosage of tamoxifen was 200 mg/Kg according to the body weight of each mouse. Tamoxifen was given three times over a period of one week. For Sftpc::KrasLSL-G12D mice, 40mg/mL tamoxifen was injected via intraperitoneal injection. The dosage of tamoxifen was 100 mg/Kg according to the body weight of each mouse. Tamoxifen was given twice over a period of one week.

value: Lung

tag: genotype

value: C57BL/6 Sftpc-CreERT2;Kras-LSL-G12D

value: 2x100 ug/kg Tamoxifen


title: Lung section derived from Gramd2:KrasG12D sample 1

description:
Gramd2:KrasG12D Lung 1
FFPE Visium mouse

value: C57BL/6 Gramd2-CreERT2;Kras-LSL-G12D

value: 3x 150 ug/kg Tamoxifen


title: CDM-05


title: CDM-17


title: CDM-01


title: Lung section derived from Sftpc:KrasG12D sample 1

description:
Sftpc:KrasG12D Lung 1
FFPE Visium mouse


title: R1_HCC827_PacBio

status: Public on Jul 20 2022

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
MinKNOW PromethION Release 19.12.9 (ONT)
Base calling and quality scoring (Illumina): Real-Time Analysis on board software v2.4.6. Base calling (ONT): Guppy 4.2.2, with the PromethION model, in high-accuracy mode.
Circular consensus sequence generation (PacBio): ccs 4.0.0 (commit SL-release-8.0.0).
FASTQ file generation and de-multiplexing (Illumina): bcl2fastw conversion software v2.15.0.4. De-multiplexing (PacBio): lima 1.10.0 (commit SL-release-8.0.0).
Refining and clustering (PacBio): isoseq3 3.2.2 (commit SL-release-8.0.0)
Sequenced reads were mapped to the GRCh38 reference genome and RNA Sequin decoy chromosome combined sequences using the align function in the Rsubread package (version 1.34.7, Liao et al. Nucleic Acids Research, 2013) with default parameters (Illumina),  minimap2 version 2.17 with arguments -ax splice -uf -k14 -L (ONT) and pbmm2 1.1.0 (commit SL-release-8.0.0) (PacBio).
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.34.7) using the GENCODE v33 annotation and RNA sequin annotation 2.4 combined GTF file (Illumina) and the GENCODE v29 annotation and RNA sequin annotation 2.4 combined GTF file (ONT, PacBio) .
Genome_build: GrCh38 and RNA sequin decoy chromosome 2.4 combined sequences
Supplementary_files_format_and_content: Tab-delimited text files with columns representing Ensembl IDs and the number of reads mapping to that gene.

source_name: Human lung cancer cell line HCC827

growth_protocol: The cell lines were retrieved from the ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum and 1% penicillin-streptomycin. The cells were grown independently at 37°C with 5% carbon dioxide until near 100% confluency.

extract_protocol:
The mRNA was extracted using a Qiagen RNA miniprep kit and purified using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490).
3.75ng purified mRNA spiked with sequins were used for the NEBNext Ultra II Directional RNA Library Prep Kit (Illumina). Fragmentation was done for 15 minutes at 94°C, and final amplification with 11 PCR cycles. The libraries were sequenced in 75PE on NextSeq 500. The cRNA-PCR Barcoding (SQK-PCS109 with SQK-PBK004) kit was used with the supplied protocol (ONT). Amplication for 1.5ng purified mRNA spiked with sequins was done with 14 PCR cycles with a 2 minutes and 30 seconds extension step. Pooled barcoded libraries were sequenced on 5 PromethION R9 flow cells. Iso-Seq libraries were prepared and sequenced by Novogene on Sequel II (PacBio). Libraries were prepared according to the manufacturer's specifications from total RNA spiked in with sequins. Size selection was performed for the standard ~2kb target. The total number of PCR cycles is 12.

treatment_protocol: Cells were dissociated into single cell suspensions in FACS buffer, centrifuged and frozen at -80 °C.

value: Lung adenocarcinoma

tag: replicate


title: R1_H1975_PacBio

source_name: Human lung cancer cell line NCI-H1975


title: R2_HCC827_PacBio


title: Enteric E16.5 Sox10-CreERT2 SS2_20_089

status: Public on Apr 28 2022

first: Louis

last: Faure

address: 321 E 61st Street

institute: Memorial Sloan Kettering Cancer Center

description:
Enteric E16.5 Sox10-CreERT2
corresponding raw files include SS2_20_089 in the filename

data_processing:
The samples were analyzed by first demultiplexing the fastq files using deindexer (http://github.com/ws6/deindexer) using the nextera index adapters and the 384 well layout.
Individual fastq files were then mapped to the relevant genome assembly using the STAR aligner (Dobin et al. Bioinformatics 2013) using 2-pass alignment to have improved performance of de novo splice junction reads, filtered for only uniquely mapping reads that are saved in the BAM  file.
The expression values were computed per gene as described in Ramsköld et al. (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. 2013 PLoS ONE).
BAM files from each plate were processed using python command-line velocity tool, using run-smartseq2 command with GENCODE M21 genome and repeat masker annotation files
count matrix was pre-processed using scanpy and scFates python packages, which includes normalization, clustering of cells, and projection on low embedding for visualization
Assembly: mm10
Supplementary files format and content: raw_counts.csv contains compiled count data from all plates, plate id is mentioned in cell name. files starting with 'p2w' are pagoda2 web objects, that can be opened on http://adameykolab.srv.meduniwien.ac.at/pagoda2/ (BIN format). Files starting with 'adata' are anndata object that can be read by scanpy or scFates.
Supplementary files format and content: adata_assigned.h5ad contains precise cell annotation as represented in figure 1 of the associated publication.
Supplementary files format and content: adata_glia_focus.h5ad contains a subset of the dataset containing a specific cell type, related to figure 7 of the associated publication.

source_name: Enteric

extract_protocol:
Collection and dissection of embryonic and postnatal traced tissue were carried out using a stereotactic microscope equipped with a fluorescent light source to enrich the tissue in relevant cells. Dissected tissue was collected in 1xPBS on ice, and either 0.05% Trypsin/0.02% EDTA or 2 mg/mL collagenase P was used for enzymatic digestion of embryonic or postnatal tissue, respectively, incubated at 37°C for 5-20 min depending on the developmental stage. Following enzymatic digestion, the tissue was triturated with a P-1000 and then P-200 pipette until dissociation, and cold 10% FBS was added to quench the enzymes. The cell suspension was spun down, 300xg, 5 min, 4°C and washed three times with 1xPBS. Finally, the cellular suspension was filtered through a 40 µm-pore size cell strainer and collected into a FACS tube on ice. Single TOMATO+ cells were sorted into 384-well plates prefilled with lysis buffer according to the previously published SmartSeq2 protocol (Picelli, Faridani et al. 2014) using a BD FACSAria Fusion Cell Sorter B5/R3/V3 system with a three-laser configuration (488nm, 633nm, and 405nm) and 16 fluorescence detectors. Single-cell transcriptomic sequencing was performed as previously described (Picelli, Faridani et al. 2014).
RNA libraries were prepared according to Smart-seq2 protocol.

value: Sox10-CreERT2; R26-Tomato

value: Enteric


title: Limb E13.5 Sox10-CreERT2 SS2_20_085

description:
Limb E13.5 Sox10-CreERT2
corresponding raw files include SS2_20_085 in the filename

source_name: Limb

value: Limb


title: Trunk E13.5 Sox10-CreERT2 SS2_20_087

description:
Trunk E13.5 Sox10-CreERT2
corresponding raw files include SS2_20_087 in the filename

source_name: Trunk

value: Trunk


title: R3_H1975_PacBio


title: R3_HCC827_PacBio


title: R2_H1975_PacBio


title: CDM-06

value: Skeletal Muscle


title: Sympathoadrenal system Adult Wnt1-Cre SS2_19_374

description:
Sympathoadrenal system Adult Wnt1-Cre
corresponding raw files include SS2_19_374 in the filename

source_name: Sympathoadrenal system

value: Wnt1-Cre; R26-Tomato

value: Adult

value: Sympathoadrenal system


title: Enteric E13.5 Sox10-CreERT2 SS2_20_079

description:
Enteric E13.5 Sox10-CreERT2
corresponding raw files include SS2_20_079 in the filename


title: Trunk E10.5 Sox10-CreERT2 SS2_19_372

description:
Trunk E10.5 Sox10-CreERT2
corresponding raw files include SS2_19_372 in the filename


title: Limb P0 Sox10-CreERT2 SS2_19_364

description:
Limb P0 Sox10-CreERT2
corresponding raw files include SS2_19_364 in the filename


title: Limb P10 Sox10-CreERT2 SS2_19_366

description:
Limb P10 Sox10-CreERT2
corresponding raw files include SS2_19_366 in the filename


title: Sympathoadrenal system E18.5 Wnt1-Cre SS2_19_358

description:
Sympathoadrenal system E18.5 Wnt1-Cre
corresponding raw files include SS2_19_358 in the filename


title: Trunk E11.5 Plp1-CreERT2 SS2_19_352

description:
Trunk E11.5 Plp1-CreERT2
corresponding raw files include SS2_19_352 in the filename

value: Plp1-CreERT2; R26-Tomato


title: Lung section derived from Gramd2:KrasG12D sample 2

description:
Gramd2:KrasG12D Lung 2
FFPE Visium mouse

tag: treatment


title: Sympathoadrenal system P2 Wnt1-Cre SS2_19_362

description:
Sympathoadrenal system P2 Wnt1-Cre
corresponding raw files include SS2_19_362 in the filename

tag: tissue


title: Limb E14.5 Wnt1-Cre SS2_19_350

description:
Limb E14.5 Wnt1-Cre
corresponding raw files include SS2_19_350 in the filename


title: Sympathoadrenal system E14.5 Wnt1-Cre SS2_19_346

description:
Sympathoadrenal system E14.5 Wnt1-Cre
corresponding raw files include SS2_19_346 in the filename


title: Sympathoadrenal system E16.5 Wnt1-Cre SS2_19_344

description:
Sympathoadrenal system E16.5 Wnt1-Cre
corresponding raw files include SS2_19_344 in the filename


title: Trunk E11.5 Plp1-CreERT2; R26-YFP SS2_19_340

description:
Trunk E11.5 Plp1-CreERT2; R26-YFP
corresponding raw files include SS2_19_340 in the filename

value: Plp1-CreERT2; R26-YFP


title: Sympathoadrenal system E14.5 Wnt1-Cre SS2_19_342

description:
Sympathoadrenal system E14.5 Wnt1-Cre
corresponding raw files include SS2_19_342 in the filename


title: Limb E16.5 Wnt1-Cre SS2_19_338

description:
Limb E16.5 Wnt1-Cre
corresponding raw files include SS2_19_338 in the filename


title: Trunk E10.5 Sox10-CreERT2 SS2_20_083

description:
Trunk E10.5 Sox10-CreERT2
corresponding raw files include SS2_20_083 in the filename


title: Enteric E14.5 Sox10-CreERT2 SS2_20_081

description:
Enteric E14.5 Sox10-CreERT2
corresponding raw files include SS2_20_081 in the filename


title: DRG E12.5 PV-cre SS2_19_324

description:
DRG E12.5 PV-cre
corresponding raw files include SS2_19_324 in the filename

source_name: DRG

value: PV-cre; R26-Tomato

value: DRG


title: Trunk E10.5 Wnt1-Cre SS2_18_109

description:
Trunk E10.5 Wnt1-Cre
corresponding raw files include SS2_18_109 in the filename


title: DRG E12.5 PV-cre SS2_19_322

description:
DRG E12.5 PV-cre
corresponding raw files include SS2_19_322 in the filename


title: Trunk E9.5 Sox10-CreERT2 SS2_17_552

description:
Trunk E9.5 Sox10-CreERT2
corresponding raw files include SS2_17_552 in the filename


title: Trunk E10.5 Wnt1-Cre SS2_18_108

description:
Trunk E10.5 Wnt1-Cre
corresponding raw files include SS2_18_108 in the filename


title: Trunk E9.5 Sox10-CreERT2 SS2_17_528

description:
Trunk E9.5 Sox10-CreERT2
corresponding raw files include SS2_17_528 in the filename


title: Trunk E10.5 Wnt1-Cre SS2_18_107

description:
Trunk E10.5 Wnt1-Cre
corresponding raw files include SS2_18_107 in the filename


title: Sympathoadrenal system P2 Wnt1-Cre SS2_19_360

description:
Sympathoadrenal system P2 Wnt1-Cre
corresponding raw files include SS2_19_360 in the filename


title: DRG E10.5 Isl1-cre SS2_16_769

description:
DRG E10.5 Isl1-cre
corresponding raw files include SS2_16_769 in the filename

value: Isl1-cre; R26-Tomato


title: DRG E10.5 Isl1-cre SS2_17_432

description:
DRG E10.5 Isl1-cre
corresponding raw files include SS2_17_432 in the filename


title: DRG E10.5 Isl1-cre SS2_17_433

description:
DRG E10.5 Isl1-cre
corresponding raw files include SS2_17_433 in the filename


title: DRG E12.5 TrkC-cre SS2_16_384

description:
DRG E12.5 TrkC-cre
corresponding raw files include SS2_16_384 in the filename

value: TrkC-cre; R26-Tomato


title: Sympathoadrenal system E13.5 Wnt1-Cre SS2_16_258-2

description:
Sympathoadrenal system E13.5 Wnt1-Cre
corresponding raw files include SS2_16_258-2 in the filename


title: Incisor Adult Plp1-CreERT2; R26-YFP SS2_16_634

description:
Incisor Adult Plp1-CreERT2; R26-YFP
corresponding raw files include SS2_16_634 in the filename

source_name: Incisor

value: Incisor


title: DRG E10.5 Isl1-cre SS2_16_688

description:
DRG E10.5 Isl1-cre
corresponding raw files include SS2_16_688 in the filename


title: Cranial E9.5 Sox10-CreERT2+Plp1-CreERT2 SS2_16_032

description:
Cranial E9.5 Sox10-CreERT2+Plp1-CreERT2
corresponding raw files include SS2_16_032 in the filename

source_name: Cranial

value: Sox10-CreERT2; R26-Tomato and Plp1-CreERT2; R26-Tomato

value: Cranial


title: Sympathoadrenal system E12.5 Wnt1-Cre SS2_16_249-2

description:
Sympathoadrenal system E12.5 Wnt1-Cre
corresponding raw files include SS2_16_249-2 in the filename


title: Cranial E10.5 Sox10-CreERT2+Plp1-CreERT2 SS2_16_026

description:
Cranial E10.5 Sox10-CreERT2+Plp1-CreERT2
corresponding raw files include SS2_16_026 in the filename


title: Sympathoadrenal system E16.5 Wnt1-Cre SS2_19_348

description:
Sympathoadrenal system E16.5 Wnt1-Cre
corresponding raw files include SS2_19_348 in the filename


title: Cranial E9.5 Sox10-CreERT2+Plp1-CreERT2 SS2_16_027

description:
Cranial E9.5 Sox10-CreERT2+Plp1-CreERT2
corresponding raw files include SS2_16_027 in the filename


title: Limb E18.5 Sox10-CreERT2 SS2_15_0171

description:
Limb E18.5 Sox10-CreERT2
corresponding raw files include SS2_15_0171 in the filename

value: Sox10-CreERT2; R26-Tomato


title: Cranial E9.5 Wnt1-Cre SS2_15_0088-2

description:
Cranial E9.5 Wnt1-Cre
corresponding raw files include SS2_15_0088-2 in the filename


title: Trunk E9.5 Wnt1-Cre SS2_15_0087

description:
Trunk E9.5 Wnt1-Cre
corresponding raw files include SS2_15_0087 in the filename


title: Limb E12.5 Plp1-CreERT2 SS2_15_0168

description:
Limb E12.5 Plp1-CreERT2
corresponding raw files include SS2_15_0168 in the filename


title: Trunk E9.5 Wnt1-Cre SS2_15_0086

description:
Trunk E9.5 Wnt1-Cre
corresponding raw files include SS2_15_0086 in the filename


title: Enteric E12.5 Plp1-CreERT2 SS2_15_0170

description:
Enteric E12.5 Plp1-CreERT2
corresponding raw files include SS2_15_0170 in the filename

value: Enteric


title: Cranial E12.5 Plp1-CreERT2 SS2_15_0073

description:
Cranial E12.5 Plp1-CreERT2
corresponding raw files include SS2_15_0073 in the filename


title: Trunk E9.5 Wnt1-Cre SS2_15_0085

description:
Trunk E9.5 Wnt1-Cre
corresponding raw files include SS2_15_0085 in the filename


title: MII_smart_rep2

status: Public on Apr 19 2022

city: Beijing

first: Zhuqing

last: Xiong

state: FOREIGN

address: Haidian District

institute: School of Life Science, Tsinghua Univers

data_processing:
Ribo-lite reads were trimmed with cutadapt v1.14 with parameters: cutadapt --trim-n -a GATCGGAAGAGCACACGTCTG -a AGAGCACACGTCTG <input.file> | cutadapt -u 3 -a A{100} --no-indels -e 0.16666666666666666 - | cutadapt -O 8 --match-read-wildcards -g GTTCAGAGTTCTACAGTCCGACGATCSSS -m 18 - -o <output.file> , and the trimmed reads were sequentially mapped to mouse/human rRNAs sequences (mm9/hg19) using Bowtie2 v2.2.2 with parameters --seedlen=23. Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of mm9/hg19 using STAR v2.5.3a with parameters --outFilterMismatchNmax 2 --outFilterMultimapNmax 20 --outFilterMatchNmin 16 --alignEndsType EndToEnd. The gene expression level was then calculated by Cufflinks v2.2.1 based on the annotation of CDS region。
All mRNA-seq data were trimmed by Trim Galore v0.4.2 then mapped to transcriptome of mm9/hg19 by STAR v2.5.3a with parameters --outFilterMultimapNmax 20 --outSAMstrandField intronMotif. The gene expression level was calculated by Cufflinks v2.2.1.
Genome_build: mm9

source_name: Oocyte

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/31 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

value: WT

value: MII oocyte

tag: molecule

value: polyA RNA


title: Sympathoadrenal system E13.5 Wnt1-Cre SS2_16_250-2

description:
Sympathoadrenal system E13.5 Wnt1-Cre
corresponding raw files include SS2_16_250-2 in the filename

value: Wnt1-Cre; R26-Tomato


title: Colon-Left-Epithelium-Z0000043C

status: Public on Mar 02 2022

city: Jerusalem

first: Tommy

last: Kaplan

address: Givat Ram Campus

department: School of Computer Science and Engineering

country: Israel

institute: Hebrew University

data_processing:
Paired-end FASTQ files were mapped to the human (hg19 -or- hg38), lambda, pUC19 and viral genomes using bwa-meth (V 0.2.0), with default parameters (Pedersen et al., 2014), then converted to BAM files using SAMtools (V 1.9) (Li et al., 2009).
Duplicated reads were marked by Sambamba (V 0.6.5), with parameters “-l 1 -t 16 --sort-buffer-size 16000 --overflow-list-size 10000000” (Tarasov et al., 2015).
Reads with low mapping quality, duplicated, or not mapped in a proper pair were excluded using SAMtools view with parameters -F 1796 -q 10.
Reads were stripped from non-CpG nucleotides and converted to BETA files using wgbstools (V 0.2.0) (Loyfer and Kaplan).
Genome_build: hg19
Supplementary_files_format_and_content:
beta files were generated using wgbstools (https://github.com/nloyfer/wgbs_tools) with default parameteres
bigwig files were generated from beta files using wgbstools beta2bw with default parameteres
blocks file (bed) was generated using wgbstools segment, and then compressed and indexed using tabix (samtools)

source_name: Colon

extract_protocol:
DNA was extracted using the DNeasy Blood and Tissue kit (#69504 Qiagen; Germantown, MD) according to the manufacturer’s instructions, and stored at -20°C for bisulfite conversion and whole genome sequencing.
Up to 75 ng of sheared gDNA was subjected to bisulfite conversion using the EZ-96 DNA Methylation Kit (Zymo Research; Irvine, CA), with liquid handling on a Hamilton MicroLab STAR (Hamilton; Reno, NV). Dual indexed sequencing libraries were prepared using Accel-NGS Methyl-Seq DNA library preparation kits (Swift BioSciences; Ann Arbor, MI) and custom liquid handling scripts executed on the Hamilton MicroLab STAR. Libraries were quantified using KAPA Library Quantification Kits for Illumina Platforms (Kapa Biosystems; Wilmington, MA). Four uniquely dual indexed libraries, along with 10% PhiX v3 library (Illumina; San Diego, CA), were pooled and clustered on a Illumina NovaSeq 6000 S2 flow cell followed by 150-bp paired-end sequencing.

treatment_protocol: Fresh tissue obtained at the time of surgery was trimmed to remove extraneous tissue. Cells were dispersed using enzyme-based protocols optimized for each tissue type. The resulting single-cell suspension was incubated with the relevant antibodies and FACS sorted to obtain the desired cell type. Purity of live sorted cells was determined by mRNA analysis for key known cell-type specific genes whereas purity of cells that were fixed prior to sorting was determined using previously validated cell-type specific methylation signals

value: Colon

value: Epithelium

tag: lab

value: Had-HU

value: F

tag: race

value: White


title: Cranial E12.5 Plp1-CreERT2 SS2_15_0169

description:
Cranial E12.5 Plp1-CreERT2
corresponding raw files include SS2_15_0169 in the filename

tag: strain

value: Plp1-CreERT2; R26-Tomato


title: Small-int-Epithelium-Z000000RT

source_name: Small intestine

value: Small intestine

value: M


title: Small-int-Epithelium-Z0000042V

source_name: Jejunum

value: Jejunum


title: Colon-Left-Endocrine-Z0000044T

value: Endocrine


title: Colon-Right-Epithelium-Z000000V8


title: Colon-Left-Epithelium-Z0000043B


title: Small-int-Epithelium-Z000000UW


title: Colon-Right-Epithelium-Z000000V0


title: Gastric-antrum-Endocrine-Z00000438

source_name: Gastric

value: Gastric


title: Colon-Left-Epithelium-Z000000VA


title: Enteric E18.5 Sox10-CreERT2 SS2_15_0173

description:
Enteric E18.5 Sox10-CreERT2
corresponding raw files include SS2_15_0173 in the filename

value: Sox10-CreERT2; R26-Tomato

tag: developmental stage


title: Gastric-antrum-Epithelium-Z000000SR

source_name: Gastric antrum

value: Gastric antrum


title: Gastric-antrum-Epithelium-Z000000SP


title: Gastric-body-Epithelium-Z000000ST

source_name: Gastric body

value: Gastric body


title: Gastric-body-Epithelium-Z000000SM


title: Gastric-antrum-Epithelium-Z000000SF


title: MII_smart_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/28 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

value: WT

value: MII oocyte


title: Gastric-body-Epithelium-Z000000SD


title: Gastric-fundus-Epithelium-Z000000SV

source_name: Gastric fundus

value: Gastric fundus


title: Gastric-fundus-Epithelium-Z000000SK


title: Gastric-fundus-Epithelium-Z000000RX


title: Lung-Alveolar-Epithelium-Z000000VE

source_name: Lung alveolar

value: Lung alveolar


title: Gastric-antrum-Endocrine-Z00000437


title: Lung-Pleura-Z0000042B

source_name: Lung pleural

value: Lung pleural

value: Epithelium


title: Colon-Right-Endocrine-Z0000044S

value: Colon

value: Had-HU

value: F


title: Lung-Alveolar-Epithelium-Z000000VC

value: White


title: Lung-Alveolar-Epithelium-Z000000T1

value: M


title: Breast-Basal-Epithelium-Z0000043E

source_name: Breast

value: Breast

value: Basal epithelial


title: Breast-Luminal-Epithelium-Z000000VN

value: Luminal epithelial


title: Breast-Basal-Epithelium-Z000000VG


title: Colon-Left-Endocrine-Z0000044J

value: Endocrine


title: Breast-Basal-Epithelium-Z000000VL


title: Breast-Luminal-Epithelium-Z000000V2


title: Breast-Basal-Epithelium-Z000000V6


title: Bladder-Epithelium-Z0000044L

source_name: Bladder

value: Bladder


title: Bladder-Epithelium-Z0000043F


title: Breast-Luminal-Epithelium-Z000000VJ


title: Bladder-Epithelium-Z000000QP


title: Bladder-Epithelium-Z000000QM


title: Prostate-Epithelium-Z0000045G

source_name: Prostate

value: Prostate


title: Prostate-Epithelium-Z0000045F


title: Gallbladder-Epithelium-Z00000432

source_name: Gallbladder

value: Gallbladder


title: Prostate-Epithelium-Z000000S3


title: Prostate-Epithelium-Z000000RV


title: Lung-Bronchus-Epithelium-Z000000S5

source_name: Lung bronchus

value: Lung bronchus


title: Esophagus-Epithelium-Z00000426

source_name: Esophagus

value: Esophagus


title: Esophagus-Epithelium-Z000000PZ


title: Tongue_base-Epithelium-Z0000044B

source_name: Tongue

value: Tongue


title: Lung-Bronchus-Epithelium-Z000000RZ


title: Larynx-Epithelium-Z000000QB

source_name: Larynx

value: Larynx


title: Lung-Bronchus-Epithelium-Z000000QD

value: Epithelium


title: Tongue-Epithelium-Z00000449


title: Tongue-Epithelium-Z000000QV


title: Tongue-Epithelium-Z0000044F


title: Bladder-Epithelium-Z00000450


title: Tonsil-Pharyngeal-Epithelium-Z000000S1

source_name: Tonsil pharyngeal

value: Tonsil pharyngeal


title: Tonsil-Palatine-Epithelium-Z000000RR

source_name: Tonsil palatine

value: Tonsil palatine

value: Had-HU


title: Tonsil-Pharyngeal-Epithelium-Z000000Q9

value: F

value: White


title: Tonsil-Palatine-Epithelium-Z000000QF

value: M


title: Epidermal-Keratinocytes-Z00000424

source_name: Skin

value: Skin

value: keratinocyte

value: Lonza


title: Blood-B-Mem-Z0000041J

source_name: Blood

value: Blood

value: Memory B cells


title: Tonsil-Palatine-Epithelium-Z000000RP


title: Blood-B-Mem-Z0000041K


title: Blood-B-Z000000UR

value: B cells


title: Blood-B-Z000000TX


title: Blood-B-Z000000UB


title: Pharynx-Epithelium-Z0000044A

source_name: Pharynx

value: Pharynx


title: Blood-Granulocytes-Z000000UT

value: Granulocytes


title: Blood-Granulocytes-Z000000TZ


title: Lung-Interstitial-Macrophages-Z0000044E

source_name: Lung interstitial

value: Lung interstitial

value: Macrophages


title: Blood-Granulocytes-Z000000UD


title: Lung-Interstitial-Macrophages-Z0000044D


title: Lung-Alveolar-Macrophages-Z0000044C

value: Lung alveolar


title: Lung-Alveolar-Macrophages-Z00000448


title: Colon-Macrophages-Z00000444

source_name: Colon

value: Colon


title: Blood-Monocytes-Z000000TP

value: Monocytes


title: Blood-Monocytes-Z000000UH

value: Had-HU


title: Colon-Macrophages-Z00000446

value: F


title: Blood-NK-Z000000UF

value: NK

value: White


title: Blood-NK-Z000000U1

value: M


title: Liver-Macrophages-Z0000043P

source_name: Liver

value: Liver

value: Sigma


title: Blood-Monocytes-Z000000U3

value: Blood


title: Blood-T-Naive-CD8-Z0000041B

value: Naive T cells CD8


title: Blood-T-Naive-CD8-Z0000041H


title: Blood-NK-Z000000TM


title: Blood-T-EffMem-CD4-Z00000416

value: T effector memory CD4


title: Blood-T-EffMem-CD4-Z0000041C


title: Blood-T-Eff-CD8-Z0000041F

value: T effector cell CD8


title: Blood-T-Naive-CD4-Z0000041E

value: Naive T cells CD4


title: Blood-T-EffMem-CD8-Z0000041G

value: T effector memory CD8


title: Blood-T-Eff-CD8-Z0000041Q


title: Blood-T-CenMem-CD4-Z0000041N

value: T central memory CD4


title: Blood-T-EffMem-CD8-Z0000041A


title: Blood-T-Eff-CD8-Z00000419


title: Lung-Interstitial-Macrophages-Z00000447

value: Lung interstitial

value: Macrophages


title: Blood-T-CenMem-CD4-Z0000041D


title: Blood-T-CD8-Z000000U5

value: T cytotoxic (CD8+) cells


title: Blood-T-CenMem-CD4-Z00000417

value: Had-HU


title: Blood-T-CD8-Z000000UK

value: F


title: Blood-T-CD8-Z000000TR


title: Blood-T-CD4-Z000000U7

value: T helper(CD4+) cells


title: Blood-T-CD4-Z000000TT

value: White


title: Blood-T-CD3-Z000000TV

value: T (CD3+) cells


title: Bone_marrow-Erythrocyte_progenitors-Z000000RH

source_name: Bone marrow

value: Bone marrow

value: Erythrocyte progenitors


title: Blood-T-CD4-Z000000UM

value: Blood


title: Blood-T-EffMem-CD4-Z0000041M

value: M


title: Endometrium-Epithelium-Z0000043S

source_name: Endometrium

value: Endometrium

value: Epithelium


title: Endometrium-Epithelium-Z00000435


title: Bone_marrow-Erythrocyte_progenitors-Z000000RF


title: Bone_marrow-Erythrocyte_progenitors-Z000000RK


title: Thyroid-Epithelium-Z0000042T

source_name: Thyroid

value: Thyroid


title: Thyroid-Epithelium-Z0000042U


title: Kidney-Glomerular-Podocytes-Z00000441

source_name: Kidney glomerular

value: Kidney glomerular

value: Podocyte


title: Fallopian-Epithelium-Z000000UV

source_name: Fallopien tubes

value: Fallopien tubes


title: Fallopian-Epithelium-Z000000S9


title: Kidney-Tubular-Epithelium-Z00000440

source_name: Kidney tubular

value: Kidney tubular


title: Kidney-Glomerular-Podocytes-Z0000042W


title: Kidney-Tubular-Epithelium-Z000000QH


title: Kidney-Tubular-Epithelium-Z0000043Z


title: Kidney-Glomerular-Epithelium-Z0000045L


title: Pancreas-Alpha-Z00000456

source_name: Pancreas

value: Pancreas

value: Alpha

value: UA


title: Endometrium-Epithelium-Z00000434

value: Had-HU

value: F


title: Blood-T-CD3-Z000000UP

value: T (CD3+) cells

value: White


title: Ovary-Epithelium-Z000000QT

source_name: Ovary

value: Ovary


title: Pancreas-Alpha-Z00000459

value: IIDP


title: Pancreas-Beta-Z00000458

value: Beta


title: Pancreas-Delta-Z00000457

value: Delta


title: Kidney-Glomerular-Epithelium-Z0000045K

value: Epithelium

value: M


title: Pancreas-Delta-Z00000454


title: Fallopian-Epithelium-Z000000Q7


title: Kidney-Glomerular-Podocytes-Z00000442

value: Kidney glomerular


title: Pancreas-Beta-Z00000455


title: Pancreas-Delta-Z00000451


title: Pancreas-Alpha-Z00000453


title: Pancreas-Acinar-Z0000043X

value: Acinar


title: Pancreas-Acinar-Z0000043Y


title: Pancreas-Acinar-Z000000QX

value: OHSU


title: Pancreas-Duct-Z0000043V

value: Duct


title: Pancreas-Duct-Z0000043T

value: Pancreas


title: Pancreas-Acinar-Z0000043W


title: Pancreas-Duct-Z000000QZ


title: Pancreas-Duct-Z0000043U


title: Liver-Hepatocytes-Z0000044M

value: Liver

value: Hepatocyte


title: Liver-Hepatocytes-Z0000044H

value: Had-HU


title: Liver-Hepatocytes-Z000000R3


title: Cerebellum-Neuron-Z000000TB

description: not sorted

source_name: Brain

value: Brain

value: Neuronal

value: KI


title: Liver-Hepatocytes-Z00000431

value: Lonza

value: F

value: White


title: Cortex-Neuron-Z0000042K


title: Cortex-Neuron-Z000000TD

description: not sorted


title: Pancreas-Beta-Z00000452

value: Beta

value: UA


title: Cortex-Neuron-Z0000042M

value: M


title: Liver-Hepatocytes-Z0000043Q


title: Cortex-Neuron-Z0000042P


title: Cortex-Neuron-Z0000042J


title: Cortex-Neuron-Z000000TF

description: not sorted


title: Neuron-Z000000TH


title: Oligodendrocytes-Z0000042N

value: Oligodendrocytes


title: Thyroid-Epithelium-Z0000042S

value: Thyroid

value: Epithelium


title: Cortex-Neuron-Z0000042H


title: Cortex-Neuron-Z0000042F


title: Oligodendrocytes-Z0000042L


title: Oligodendrocytes-Z0000042E


title: Oligodendrocytes-Z000000TK


title: Liver-Hepatocytes-Z000000T3

value: OHSU


title: Heart-Cardiomyocyte-Z0000044N

source_name: Heart

value: Heart

value: Cardiomyocyte


title: Heart-Cardiomyocyte-Z0000044K


title: Heart-Cardiomyocyte-Z0000044P


title: Bone-Osteoblasts-Z0000042Z

source_name: Bone

value: Bone

value: Osteoblasts

value: Hisp


title: Heart-Cardiomyocyte-Z0000044Q

value: Had-HU


title: Bladder-Smooth-Muscle-Z0000041Z

source_name: Bladder

value: Bladder

value: Smooth muscle

value: Black


title: Aorta-Smooth-Muscle-Z0000041U

source_name: Aorta

value: Aorta

value: Lonza

value: White


title: Lung-Bronchus-Smooth-Muscle-Z00000421

source_name: Bronchial

value: Bronchial

value: M


title: Skeletal-Muscle-Z00000427

description: not sorted

source_name: Skeletal muscle

value: Skeletal muscle

value: Striated muscle

value: F


title: Heart-Fibroblasts-Z0000041X

value: Heart

value: Fibroblast


title: Heart-Fibroblasts-Z0000043R


title: Heart-Cardiomyocyte-Z0000044G

value: Cardiomyocyte


title: Coronary-Artery-Smooth-Muscle-Z00000420

source_name: Cornary artery

value: Cornary artery


title: Prostate-Smooth-Muscle-Z0000041Y

source_name: Prostate

value: Prostate


title: Skeletal-Muscle-Z00000429

description: not sorted

value: Had-HU


title: Heart-Fibroblasts-Z0000041W


title: Dermal-Fibroblasts-Z00000423

source_name: Ad-dermal

value: Ad-dermal


title: Heart-Fibroblasts-Z0000041V


title: Heart-Cardiomyocyte-Z0000044R


title: Pancreas-Endothelium-Z0000042X

value: Pancreas

value: Endothelium

value: UA


title: Lung-Alveolar-Endothelium-Z0000045H

source_name: Lung alveolar

value: Lung alveolar


title: Lung-Alveolar-Endothelium-Z000000Q1

value: White


title: Pancreas-Endothelium-Z0000042D


title: Colon-Fibroblasts-Z0000042A

source_name: Colon

value: Colon


title: Lung-Alveolar-Endothelium-Z000000QK


title: Pancreas-Endothelium-Z00000430


title: Kidney-Tubular-Endothelium-Z000000Q3

value: Kidney tubular

value: M


title: Pancreas-Islet-Endothelium-Z0000042Y


title: Kidney-Tubular-Endothelium-Z0000042R


title: Kidney-Tubular-Endothelium-Z000000PX


title: Saphenous-Vein-Endothelium-Z000000SB

source_name: Vascular saphenous

value: Vascular saphenous


title: Kidney-Glomerular-Endothelium-Z00000443

source_name: Kidney glomerular

value: Kidney glomerular


title: Saphenous-Vein-Endothelium-Z000000S7

value: F


title: Kidney-Glomerular-Endothelium-Z0000045J


title: Liver-Endothelium-Z000000RB

source_name: Liver

value: Liver

value: OHSU


title: Kidney-Glomerular-Endothelium-Z000000Q5


title: Colon-Fibroblasts-Z0000042C

value: Fibroblast


title: TGFB1 + miR_5

status: Public on Feb 28 2022

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of LX-2 cells treated with human recombinant TGF beta and trasfected with mimic miR34b and with mimic miR34c, biological rep5

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq; Trimming and cleaning with bbduk; Alignment was performed with STAR 2.6.0a. The expression levels of genes were determined with HTseq-counts 0.9.1.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files including raw counts.

growth_protocol: LX-2 cells were cultured in DMEM/2% FBS

extract_protocol:
RNA was quantified and mixed at 10ng/µl.
NEGEDIA Digital mRNA-seq: Total RNA was quantified using the Qubit 4.0 fluorometric Assay (Thermo Fisher Scientific). Libraries were prepared from 125 ng of total RNA using the NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl) which included library preparation, quality assessment and sequencing on a NovaSeq 6000 sequencing system using a single-end, 100 cycle strategy (Illumina Inc.).

treatment_protocol: LX-2 cells were treated with 2ng/ml of human recombinant TGF beta. The cells were trasfected with mimic universal control or mimic miR34b and mimic miR34c. After 6 hours, the cells were treated with 2ng/ml of TGF beta. The LX-2 cells were treated with 2ng/ml of TGF beta and after 24 hours we extracted the total RNA.


title: Adipocytes-Z000000T7

source_name: Abdominal Subcut.

value: Abdominal Subcut.

value: Adipocytes

value: KI


title: Saphenous-Vein-Endothelium-Z000000RM

value: Had-HU


title: TGFB1 + miR_3

description: Transcriptome profile of LX-2 cells treated with human recombinant TGF beta and trasfected with mimic miR34b and with mimic miR34c, biological rep3


title: Aorta-Endothelium-Z0000043G

value: Aorta

value: Endothelium


title: Adipocytes-Z000000T9


title: Aorta-Endothelium-Z00000422

value: Lonza


title: TGFB1 + miR_1

description: Transcriptome profile of LX-2 cells treated with human recombinant TGF beta and trasfected with mimic miR34b and with mimic miR34c, biological rep1


title: Adipocytes-Z000000T5


title: TGFB1 + miR_4

description: Transcriptome profile of LX-2 cells treated with human recombinant TGF beta and trasfected with mimic miR34b and with mimic miR34c, biological rep4


title: TGFB1 + miR_2

description: Transcriptome profile of LX-2 cells treated with human recombinant TGF beta and trasfected with mimic miR34b and with mimic miR34c, biological rep2


title: TGFB1 + NC_5

description: Transcriptome profile of LX-2 cells treated with human recombinant TGF beta and trasfected with mimic universal negative control, biological rep5


title: TGFB1 + NC_4

description: Transcriptome profile of LX-2 cells treated with human recombinant TGF beta and trasfected with mimic universal negative control, biological rep4


title: TGFB1 + NC_3

description: Transcriptome profile of LX-2 cells treated with human recombinant TGF beta and trasfected with mimic universal negative control, biological rep3


title: TGFB1 + NC_2

description: Transcriptome profile of LX-2 cells treated with human recombinant TGF beta and trasfected with mimic universal negative control, biological rep2


title: miR_4

description: Transcriptome profile of LX-2 cells trasfected with mimic miR34b and with mimic miR34c, biological rep4


title: miR_3

description: Transcriptome profile of LX-2 cells trasfected with mimic miR34b and with mimic miR34c, biological rep3


title: miR_1

description: Transcriptome profile of LX-2 cells trasfected with mimic miR34b and with mimic miR34c, biological rep1


title: miR_5

description: Transcriptome profile of LX-2 cells trasfected with mimic miR34b and with mimic miR34c, biological rep5


title: TGFB1_4

description: Transcriptome profile of LX-2 cells treated with human recombinant TGF beta, biological rep4


title: TGFB1_3

description: Transcriptome profile of LX-2 cells treated with human recombinant TGF beta, biological rep3


title: TGFB1_5

description: Transcriptome profile of LX-2 cells treated with human recombinant TGF beta, biological rep5


title: NC_4

description: Transcriptome profile of LX-2 cells trasfected with mimic universal negative control, biological rep4


title: TGFB1_1

description: Transcriptome profile of LX-2 cells treated with human recombinant TGF beta, biological rep1


title: NC_1

description: Transcriptome profile of LX-2 cells trasfected with mimic universal negative control, biological rep1


title: NT_5

description: Transcriptome profile of LX-2 cells untreated , biological rep5

value: LX-2 cells untreated


title: NT_2

description: Transcriptome profile of LX-2 cells untreated , biological rep2


title: genomic DNA from ENKTL125

status: Public on Jan 12 2022

city: Columbus

first: Christopher

last: OAKES

state: OH

address: 400 W. 12th Avenue, Wiseman Hall, Suite 455

institute: The Ohio State University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan using standard recommended settings

data_processing:
Data were processed using the RnBeads software, using BMIQ normalization
Average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Tumor

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was isolated using the Gentra Puregene Blood/cell DNA isolation kit (Qiagen) from fresh-frozen samples or the QIAamp FFPE tissue DNA isolation kit (Qiagen) as indicated according to standard instructions

tag: disease state

value: Tumor

tag: sample type

value: ENKTL

tag: dna isolation type

value: FFPE

tag: pdx-derived

value: No

tag: pdx treatment

tag: sorted population


title: genomic DNA from ENKTL123


title: NT_1

description: Transcriptome profile of LX-2 cells untreated , biological rep1


title: NT_4

description: Transcriptome profile of LX-2 cells untreated , biological rep4


title: TGFB1_2

description: Transcriptome profile of LX-2 cells treated with human recombinant TGF beta, biological rep2


title: genomic DNA from ENKTL121


title: genomic DNA from ENKTL119


title: NC_3

description: Transcriptome profile of LX-2 cells trasfected with mimic universal negative control, biological rep3


title: genomic DNA from ENKTL111


title: genomic DNA from ENKTL110


title: genomic DNA from ENKTL103


title: genomic DNA from ENKTL108


title: genomic DNA from ENKTL101


title: genomic DNA from ENKTL102


title: genomic DNA from ENKTL62


title: genomic DNA from ENKTL100


title: genomic DNA from ENKTL64


title: genomic DNA from ENKTL59


title: genomic DNA from ENKTL57


title: NC_2

description: Transcriptome profile of LX-2 cells trasfected with mimic universal negative control, biological rep2


title: genomic DNA from ENKTL120


title: genomic DNA from ENKTL51


title: genomic DNA from ENKTL122


title: genomic DNA from ENKTL124


title: genomic DNA from ENKTL54


title: genomic DNA from ENKTL114


title: genomic DNA from ENKTL50


title: genomic DNA from ENKTL39


title: genomic DNA from ENKTL47


title: genomic DNA from ENKTL37


title: genomic DNA from ENKTL48


title: genomic DNA from ENKTL36


title: genomic DNA from ENKTL34


title: genomic DNA from ENKTL113


title: genomic DNA from ENKTL35


title: genomic DNA from ENKTL30


title: genomic DNA from ENKTL31


title: genomic DNA from ENKTL21


title: genomic DNA from ENKTL32


title: genomic DNA from ENKTL29


title: genomic DNA from ENKTL18


title: genomic DNA from ENKTL16


title: genomic DNA from ENKTL9


title: genomic DNA from ENKTL20


title: genomic DNA from ENKTL56


title: genomic DNA from ENKTL5


title: genomic DNA from ENKTL55


title: genomic DNA from ENKTL3


title: genomic DNA from ENKTL2


title: genomic DNA from ENKTL26


title: genomic DNA from ENKTL13


title: Donor 1 - whole genome bisulfite sequencing- D6 (AT1-like) cells

status: Public on Oct 27 2021

data_processing:
For DNA, Fastq files were aligned to the bisulfite hg19 genome by the USC Epigenome Center core. For RNA and ChIPseq, Reads were aligned to the canonical Hg19 genome using Bowtie 2.
For DNA, Bis-SNP was used for methylation and SNPtype calling (Liu et al., Genome Biology, 2012). For RNA, TopHat2 was used to assemble transcripts using Gencode. For ChIPseq, peaks were called using SICER with gap spacing of 600 for H3K27me3 and H3K79me2, gap spacing of 200 for other marks. MACS2 was also used to call enhancer regions for ROADMAP/ENCODE comparisons.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RNA and ChIPseq have aligned bigwig files.
Supplementary_files_format_and_content: DNA files have peak domains in R files for processed UMR, LMR, and PMR regions.
Supplementary_files_format_and_content: UMRsLMRs.gr.D0.rds: Unmethylated and low-methylation domains R file.
Supplementary_files_format_and_content: UMRsLMRs.gr.D4.rds: Unmethylated and low-methylation domains R file.
Supplementary_files_format_and_content: UMRsLMRs.gr.D6.rds: Unmethylated and low-methylation domains R file.
Supplementary_files_format_and_content: PMDs.D0dna.rds: partially methylated domains R file.
Supplementary_files_format_and_content: PMDs.D4dna.rds: partially methylated domains R file.
Supplementary_files_format_and_content: PMDs.D6dna.rds: partially methylated domains R file.
Supplementary_files_format_and_content: UMRsLMRs.D0.tab: Unmethylated and low-methylation domains tab-delimited file.
Supplementary_files_format_and_content: UMRsLMRs.D4.tab: Unmethylated and low-methylation domains tab-delimited file.
Supplementary_files_format_and_content: UMRsLMRs.D6.tab: Unmethylated and low-methylation domains tab-delimited file.
Supplementary_files_format_and_content: PMDs.D0dna.tab: partially methylated domains tab-delimited file.
Supplementary_files_format_and_content: PMDs.D4dna.tab: partially methylated domains tab-delimited file.
Supplementary_files_format_and_content: PMDs.D6dna.tab: partially methylated domains tab-delimited file.

source_name: In vitro differentiated AT1-like cells

growth_protocol: Primary AT2 cells were extracted as described previously and differentiated in vitro for six days (Marconett et al., PLoS Genetics, 2013).

extract_protocol:
DNA, RNA, and ChIP material were prepared as previously published (Zuber et al., JNCI, 2016).
Library construction was performed at the USC Epigenome Center core, as previously described (Zuber et al., JNCI, 2016).
WGBS Indexes were included on Donor 1 samples. Donor 1 D0 Index : TGACCA, Donor 1 D2 Index: CAGTG, Donor 1 D4 Index: GCCAAT, Donor 1 D6 Index: CAGATC. ChIPseq samples were multiplexed on Illumina HiSeq2000 lanes, the indicated adapters on FASTQ files were used to de-multiplex.

treatment_protocol: Purified DNA underwent bisulfite treatment as described previously (Zuber et al., JNCI, 2016). RNA underwent polyA selection and library preparation as previously described (Zuber at al., 2016). ChIP material underwent adapter ligation, library preparation, and multiplexed sequencing as previously described (Zuber et al., 2016).

tag: cell type

value: In vitro differentiated AT1-like cells

tag: time point

tag: donor

tag: material type

value: WGBS:Bisulfite-treated DNA


title: Donor 3 - Total RNA ribozero treated - D4 (AT1-like) cells

value: Ribozero depleted total RNA


title: Donor 3 - Total RNA ribozero treated - D0 (AT2) cells

source_name: purified primary AT2 cells

value: purified primary AT2 cells


title: Donor 3 - Total RNA ribozero treated - D2 (AT intermediate) cells

source_name: Differentiating intermediate AT cells

value: Differentiating intermediate AT cells


title: Donor 1 - whole genome bisulfite sequencing- D4 (AT1-like) cells


title: Donor 2 - Total RNA ribozero treated - D6 (AT1-like) cells


title: Donor 2 - Total RNA ribozero treated - D4 (AT1-like) cells


title: Donor 3 - Total RNA ribozero treated - D6 (AT1-like) cells


title: Donor 1 - whole genome bisulfite sequencing- D0 (AT2) cells


title: Donor 2 - Total RNA ribozero treated - D2 (AT intermediate) cells


title: Donor 2 - Total RNA ribozero treated - D0 (AT2) cells


title: Donor 1 - Total RNA ribozero treated - D6 (AT1-like) cells


title: sample 35, PPMS 7

status: Public on Dec 14 2021

type: RNA

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

country: Germany

institute: University of Rostock

description: Gene expression data for a patient with PPMS

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 °C on Clariom D Arrays (Applied Biosystems). The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in a GeneChip Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Thermo Fisher Scientific.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console software version 4.0. The signal intensities of the >6 million oligonucleotide probes were further processed using the Transcriptome Analysis Console (TAC) version 4.0.2 (Applied Biosystems) in the default configuration. The signal space transformation robust multi-array average (SST-RMA) algorithm was applied for background adjustment, quantile normalization, probe set summarization and log2 transformation. The TAC software was also utilized for differential gene expression analysis.
Exon-level processed data are available on the series record.

label: Biotin

source_name: B cells from the peripheral blood

label_protocol: According to the GeneChip Whole Transcript (WT) manual, cRNA was prepared from 100 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

growth_protocol: Twenty ml of peripheral blood were taken from MS patients during regular clinical visits as well as from healthy donors at the Rostock University Medical Center.

extract_protocol: Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll density gradient separation (Histopaque-1077, Sigma-Aldrich). Untouched B cells were then enriched from the PBMC by negative selection using the Pan B Cell Isolation Kit (Miltenyi Biotec). Total RNA was isolated using the miRNeasy Mini Kit (Qiagen) in combination with the RNase-free DNase set (Qiagen).

treatment_protocol: The patients were treated with different therapies according to the approved labels and the guidelines and recommendations of the German Society of Neurology.

tag: subject identifier

tag: group

value: PPMS patient

tag: therapy

value: glucocorticosteroids

tag: Sex

value: female

tag: age (years)

tag: disease duration (years)

tag: edss score

tag: relapses in previous year


title: Donor 1 - Total RNA ribozero treated - D4 (AT1-like) cells


title: sample 34, PPMS 6

value: male


title: sample 33, PPMS 5


title: sample 26, healthy control 26

description: Gene expression data for a healthy individual

value: healthy control


title: Donor 1 - Total RNA ribozero treated - D2 (AT intermediate) cells


title: sample 37, PPMS 9


title: Donor 1 - Total RNA ribozero treated - D0 (AT2) cells


title: Donor 2 - ChIPseq using H3K27Ac antibody - D6 (AT1-like) cells

tag: chip antbody

value: ChIP DNA