title: HFO_FP_b001_53_cbc

value: Proximal Colon

value: 3 days

tag: time (in diff media)

value: 4 days

tag: individual

value: Donor 8


title: HFO_FP_b001_54_cbc

status: Public on Feb 08 2023

type: SRA

city: Cambridge

first: Scott

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

country: USA

institute: Pfizer

library_source: transcriptomic

data_processing:
Processing of the fastq files was performed using the QuickRNAseq (https://doi.org/10.1186/s12864-015-2356-9) (pipeline utilizing Hg38 for the genome and Gencode v24 for annotation). Normalization and differential expression analyses were conducted using limma-voom(https://doi.org/10.1186/gb-2014-15-2-r29).
Genome_build: Hg38
Supplementary_files_format_and_content: Gene-count-table.txt

molecule: total RNA

organism: Homo sapiens

extract_protocol: 3’RNA sequencing was performed using linear amplification and pooling followed by paired end sequencing (Hashimshony et al., 2016).

tag: passage

tag: growth conditions

value: organoid

tag: replicate

tag: tissue

tag: disease state

value: UC (ulcerative colitis)

tag: inflamed

value: normal

tag: gender

value: Male

tag: medium

value: cCDM

tag: time (in expansion media)


title: M1 muscle cell, segment A3, animal 8, cell d306084

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
NextSeq 500 sequencing using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Gene expression was quantified using RSEM version 1.3.0 and STAR version 2.5.3a alignment to a transcriptome derived from the human BDGP6 primary assembly and a version 92 annotation.
Assembly: BDGP6 Drosophila melanogaster assembly with version 92 annotation
Supplementary files format and content: 1b1sm_isoform_intCt.txt.gz is a tab delimited text file of isoform counts
Supplementary files format and content: 1b1sm_isoform_l2tpm.txt.gz is a tab delimited text file of isoform l2tpm vaules
Supplementary files format and content: 1b1sm_l2tpm.txt.gz is a tab delimited text file of gene l2tpm vaules
Supplementary files format and content: 1b1sm_intCt.txt.gz is a tab delimited text file of gene counts

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: muscle cell

growth_protocol: Fly stocks were raised at 25°C on standard molasses food in an incubator with 12 hrs day/night cycle. Actively crawling 3rd instar larvae that are size and age matched were used for all experiments.

extract_protocol:
Cellular material was aspirated in whole-cell patch electrodes and transferred to 384 well plates followed by extraction with XXX
RNAseq libraries from single cells were prepared using a modified version of the SMART-seq2 single-cell protocol (Picelli et al., 2013, Trombetta et al., 2014). RNA from single cells was placed in Hard-Shell 384-well plates (Catalog #HSP3801) in minimal volume (<2uL). cDNA was prepared following the standard protocol using 1/3 of the recommended volumes for all reagents utilizing a Mosquito HV automated liquid handler (SPT Labtech). Amplified cDNA was purified using 0.75X SPRI beads, quantified using picogreen and spot-checked on the Fragment Analyzer (Agilent). Dual indexed Illumina libraries were prepared from cDNA using a reduced volume NexteraXT reaction (1:12) on the Mosquito HV (Hendricks et al., in preparation). Final libraries were quantified using picogreen and spot-checked on the Fragment Analyzer before pooling and final quantification using qPCR on a Roche LC480II.

value: muscle cell

tag: segment

tag: cell type

tag: animal

value: M

tag: strain

tag: genotype


title: M4 muscle cell, segment A4, animal 5, cell d306044


title: HFO_FP_b001_52_cbc


title: M4 muscle cell, segment A3, animal 5, cell d306042


title: HFO_FP_b001_51_cbc

value: eCDM


title: HFO_FP_b001_50_cbc


title: M4 muscle cell, segment A2, animal 5, cell d306041


title: M1 muscle cell, segment A4, animal 5, cell d306040


title: M1 muscle cell, segment A4, animal 8, cell d306081


title: HFO_FP_b001_5_cbc

value: (Ascending) Colon

value: WT

value: Donor 89


title: M4 muscle cell, segment A5, animal 5, cell d306039


title: HFO_FP_b001_4_cbc


title: M1 muscle cell, segment A2, animal 5, cell d306038


title: HFO_FP_b001_48_cbc

value: CNM


title: M1 muscle cell, segment A2, animal 5, cell d306037


title: HFO_FP_b001_47_cbc


title: HFO_FP_b001_46_cbc


title: M4 muscle cell, segment A5, animal 5, cell d306045


title: HFO_FP_b001_45_cbc

value: (Distal) Colon

value: Donor 7


title: M1 muscle cell, segment A4, animal 5, cell d306035


title: M1 muscle cell, segment A3, animal 5, cell d306034


title: M4 muscle cell, segment A5, animal 5, cell d306036


title: HFO_FP_b001_44_cbc

value: 3 days


title: M4 muscle cell, segment A2, animal 5, cell d306033


title: M1 muscle cell, segment A3, animal 5, cell d306043


title: HFO_FP_b001_42_cbc

value: 4 days


title: HFO_FP_b001_43_cbc


title: M1 muscle cell, segment A3, animal 11, cell d270086

value: F


title: M4 muscle cell, segment A5, animal 11, cell d270087


title: M4 muscle cell, segment A2, animal 11, cell d270085


title: HFO_FP_b001_40_cbc

value: organoid


title: HFO_FP_b001_41_cbc

value: UC (ulcerative colitis)


title: HFO_FP_b001_3_cbc

value: normal


title: HFO_FP_b001_39_cbc

value: Male


title: HFO_FP_b001_49_cbc

value: Proximal Colon

value: Donor 8


title: M4 muscle cell, segment A4, animal 11, cell d270083

value: muscle cell


title: HFO_FP_b001_38_cbc


title: M1 muscle cell, segment A4, animal 10, cell d270074


title: M4 muscle cell, segment A2, animal 10, cell d270073


title: M1 muscle cell, segment A2, animal 10, cell d270071


title: HFO_FP_b001_37_cbc


title: M4 muscle cell, segment A4, animal 10, cell d270070


title: HFO_FP_b001_35_cbc

value: Ileum

value: cCDM


title: M4 muscle cell, segment A3, animal 10, cell d270072


title: HFO_FP_b001_34_cbc

value: WT


title: M4 muscle cell, segment A2, animal 9, cell d270058


title: M4 muscle cell, segment A3, animal 9, cell d270057


title: HFO_FP_b001_32_cbc

value: eCDM

value: Donor 89


title: M4 muscle cell, segment A4, animal 9, cell d270056


title: HFO_FP_b001_33_cbc


title: SALINE 4

city: Jerusalem

first: Noy

last: Pinto

address: Refael Dela Pergula 18 Jerusalem

country: Israel

institute: Hadassah Hebrew University Jerusalem

data_processing:
Quality trimming was done at the 3’ end using cutadapt. The quality cutoff was 10, skipping all G bases (that can indicate a lack of signal in Next-Seq’s two-color chemistry). The parameter was --nextseq-trim=10. Also using cutadapt, adapter and poly-A sequences were removed. The error rate (-e parameter) was set to zero. Reads that became shorter than 28 nt were filtered out (-m parameter
The processed fastq files were aligned to the Mus musculus transcriptome and genome using TopHat. The genome version was GRCm38 with annotations from Ensembl release 99. ERCC spike-in sequences (positive controls of CEL-Seq protocol) were aligned as well to the DNA Sequence Library SRM-2374. Strand information was taken into consideration (--library-type fr-secondstrand). Alignment allowed up to 2 mismatches per read, and a total edit distance of 5.
Quantification was done using htseq-count. Reads that aligned with a quality lower than 10 were skipped. Strand information was taken into consideration (--stranded=’yes’). An annotation file that lacked information for genes of type IG, TR, Artifact, miRNA, Mt_rRNA, Mt_tRNA, ncRNA, piRNA, pre_miRNA, rRNA, ribozyme, sRNA, scRNA, scaRNA, siRNA, snRNA, snoRNA, tRNA and vaultRNA was used
Differential expression analysis was done with the DESeq2 package. Genes with a mean of counts less than 3 over all samples were filtered out, then size factors and dispersion were calculated. Normalized counts were used for several quality control assays, such as distance heatmaps and principal component analysis, which were calculated and visualized in R. Differential expression was calculated with default parameters except not using the independent Filtering algorithm. Significance threshold was taken as padj<0.1 (default). Finally, the results were combined with gene details (such as symbol, known transcripts, etc.), taken from the results of a BioMart query (Ensembl, release 99), to produce the final Excel file.

organism: Mus musculus

source_name: alveolar bone

extract_protocol:
Maxillae were pulverized in a homogenizer, and total RNA was isolated from bones lysates or from cultured cells with TriZol (1000 ul per sample; Thermo Fisher Scientific). RNA purity was detected with a Nanodrop. DNA-free RNA was obtained by using and RNeasy Mini Kit (QIAGEN) with DNase treatment according to the manufacturer’s instructions. For quality control of RNA extraction yield, an RNA Screen Tape kit (Agilent Technologies), a D1000 Screen Tape kit (Agilent Technologies), Qubit RNA HS Assay kit (Invitrogen) and a Qubit DNA HS Assay kit (Invitrogen) were used for each specific step. RNA samples from Allograft vs Spon. Healing groups were all passed quality control analysis on a Bioanalyzer 2100 (Agilent Technologies). The 3 biological replicates with the highest RNA were used for mRNA library preparation and bioinformatics analysis as described previously.
RNA concentration was measured using Qubit 4 Fluorometer (Thermo Fisher Scientific) and RNA quality was measured using Agilent 2200 Tape Station (Agilent). RNA sequencing libraries were prepared using the CEL-Seq2 protocol, as published by (29) with minor modifications. Instead of single cells as input, 2 ng purified RNA was taken as input for library preparation. The CEL-Seq2 libraries were sequenced on an Illumina NextSeq 550 sequencer (Illumina). RNA measurements, library preparation and sequencing were performed by the Technion Genome Center, Technion, Israel.

value: alveolar bone

tag: treatment

value: alveolar bone defect + allograft + saline


title: SALINE 5


title: HFO_FP_b001_31_cbc

value: 3 days

tag: time (in diff media)


title: M1 muscle cell, segment A2, animal 4, cell d270033

value: M


title: M1 muscle cell, segment A4, animal 6, cell d270039


title: SALINE 2


title: HFO_FP_b001_30_cbc

value: CNM

value: 4 days

tag: individual


title: NT 3

value: alveolar bone defect


title: HFO_FP_b001_2_cbc

tag: passage

value: organoid

value: (Ascending) Colon

value: normal


title: M1 muscle cell, segment A4, animal 1, cell d270025


title: SALINE 3


title: HFO_FP_b001_36_cbc

tag: growth conditions

value: Male


title: M1 muscle cell, segment A4, animal 3, cell d270021

value: muscle cell


title: NT 2


title: NT 4


title: HFO_FP_b001_29_cbc

tag: replicate

value: Ileum


title: SALINE 1

tag: tissue


title: HFO_FP_b001_28_cbc

tag: disease state


title: M4 muscle cell, segment A4, animal 3, cell d270020


title: Sorted tumor cells_sh_B7-H3 (2)_3

city: Haining

first: Heng-Jia

last: Liu

state: Zhejiang

address: 718 East Haizhou Road

department: International Campus

country: China

institute: Zhejiang University - University of Edinburgh

description: Sorted tumor cells_sh_B7-H3 (2)_3

data_processing:
Data was processed using the VIPER pipeline.
Assembly: mm10
Supplementary files format and content: csv include RPKM/count values for each Sample

source_name: subcutaneous tumor

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared usingIllumina Stranded mRNA Prep following manufacturer's protocols.

value: subcutaneous tumor

value: Wild-type C57BL/6J

tag: cell line

value: Tsc2-deficient 105K

value: B7-H3 shRNA (2)


title: Sorted tumor cells_sh_B7-H3 (2)_1

description: Sorted tumor cells_sh_B7-H3 (2)_1


title: M4 muscle cell, segment A5, animal 3, cell d270019

tag: gender


title: Sorted tumor cells_sh_B7-H3 (1)_3

description: Sorted tumor cells_sh_B7-H3 (1)_3

value: B7-H3 shRNA (1)


title: Sorted tumor cells_sh_B7-H3 (2)_2

description: Sorted tumor cells_sh_B7-H3 (2)_2


title: M4 muscle cell, segment A4, animal 1, cell d270002

value: F


title: Sorted tumor cells_sh_B7-H3 (1)_1

description: Sorted tumor cells_sh_B7-H3 (1)_1


title: Sorted tumor cells_sh NC_3

description: Sorted tumor cells_sh NC_3

value: control shRNA


title: Sorted tumor cells_sh_B7-H3 (1)_2

description: Sorted tumor cells_sh_B7-H3 (1)_2


title: 1B neuron, seqment A3, animal 8, cell d306096

source_name: neuron

value: neuron

value: M


title: Sorted tumor cells_sh NC_2

description: Sorted tumor cells_sh NC_2


title: HFO_FP_b001_25_cbc

value: WT

tag: inflamed

tag: medium

value: cCDM

value: 3 days

value: 4 days

value: Donor 89


title: HFO_FP_b001_24_cbc

value: organoid

value: (Ascending) Colon

value: normal

value: Male

value: eCDM

tag: time (in expansion media)


title: NT 1

value: alveolar bone

value: alveolar bone defect


title: Sorted tumor cells_sh NC_1

description: Sorted tumor cells_sh NC_1

value: subcutaneous tumor

value: Wild-type C57BL/6J

value: Tsc2-deficient 105K


title: 1B neuron, seqment A5, animal 8, cell d306093

value: neuron

tag: segment

tag: cell type


title: Bulk tumor_sh_B7-H3 (1)_2

description: Bulk tumor_sh_B7-H3 (1)_2

tag: strain

value: B7-H3 shRNA (1)


title: Bulk tumor_sh_B7-H3 (1)_3

description: Bulk tumor_sh_B7-H3 (1)_3

tag: genotype


title: Bulk tumor_sh NC_3

description: Bulk tumor_sh NC_3

value: control shRNA


title: HFO_FP_b001_23_cbc

value: WT


title: 1B neuron, seqment A6, animal 8, cell d306092

tag: animal

value: M


title: Bulk tumor_sh NC_2

description: Bulk tumor_sh NC_2


title: 1B neuron, seqment A3, animal 8, cell d306091


title: Bulk tumor_sh_B7-H3 (1)_1

description: Bulk tumor_sh_B7-H3 (1)_1


title: HFO_FP_b001_22_cbc

value: 3 days

tag: time (in diff media)

value: 4 days


title: HFO_FP_b001_27_cbc

value: organoid

value: cCDM

tag: individual

value: Donor 89


title: Bulk tumor_sh NC_1

description: Bulk tumor_sh NC_1


title: 1B neuron, seqment A8, animal 8, cell d306090


title: HFO_FP_b001_21_cbc

tag: passage

value: (Ascending) Colon

value: normal

value: Male

value: CNM


title: KO3

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
The read is aligned to GRCm38 Mouse Transcriptome using Kallisto
Assembly: GRCm38
Supplementary files format and content: Kallisto quantification results.

source_name: Astrocytes

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were constructed using an NEB Next Low input RNA kit

treatment_protocol: Induction of EAE in mice. EAE was induced by injecting 150 µg of MOG35-55 diluted in 100 µL of PBS emulsified in 100 µL of CFA per mouse.

value: EAE

tag: background strain

value: Astrocytes

value: XBP1 KO


title: KO2


title: HFO_FP_b001_26_cbc

tag: growth conditions

tag: replicate


title: WT3

tag: disease state


title: KO1


title: WT2


title: HFO_FP_b001_212_cbc

value: monolayer

tag: tissue

value: Ileum

value: CD (Crohn's disease)

value: Donor 9


title: 1B neuron, seqment A6, animal 8, cell d306095

value: neuron

tag: gender

value: M


title: 1B neuron, seqment A4, animal 8, cell d306089


title: WT1

value: WT


title: 1B neuron, seqment A7, animal 8, cell d306080


title: HFO_FP_b001_20_cbc

value: organoid

tag: inflamed

value: 3 days

value: 4 days


title: HFO_FP_b001_210_cbc

tag: medium

value: eCDM


title: 1B neuron, seqment A1, animal 8, cell d306079


title: Mike_Scrm_7

data_processing:
The sample is aligned to GRCm38 transcriptome and quantified using Kallisto
Assembly: GRCm38
Supplementary files format and content: gzipped abundance.tsv output from Kallisto

source_name: induced EAE

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).

value: induced EAE

tag: Sex

tag: age

value: astrocytes

tag: condition

value: sgScrmbl


title: Mike_Scrm_9

tag: strain

value: Male

tag: cell type


title: 1S neuron, seqment A2, animal 7, cell d306078

tag: segment

tag: animal

value: F

tag: genotype


title: Mike_NCOR2_5


title: Mike_Scrm_8


title: HFO_FP_b001_209_cbc

tag: passage

value: normal

tag: time (in expansion media)

tag: time (in diff media)

tag: individual


title: Mike_NCOR2_6

tag: disease state


title: HFO_FP_b001_208_cbc

tag: growth conditions

value: monolayer

tag: replicate

tag: tissue


title: 1S neuron, seqment A3, animal 7, cell d306077

tag: gender


title: Mike_NCOR2_4

tag: Sex


title: HFO_FP_b001_211_cbc

value: Ileum

tag: inflamed

tag: medium

value: cCDM


title: Mike_NCOR1_3

tag: strain

tag: age

tag: condition


title: 1S neuron, seqment A8, animal 7, cell d306076

tag: segment

tag: cell type

tag: animal


title: KO4_CD133_RBP1

city: Portland

first: Theresa

middle: A

last: Lusardi

state: Oregon

address: 2720 SW Moody Avenue

department: Knight Cancer Institute

institute: OHSU

description:
CUT&Tag Library
RBP1q0.01_peaks.narrowPeak

library_source: genomic

data_processing:
Library strategy: CUT&TAG
Sequencing from CUT&Tag was aligned using Bowtie2
Peaks were called using MACS2
Differential enrichment was assessed using DiffBind

molecule: genomic DNA

source_name: CD133 Purifed bone marrow cells

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2108

value: CD133 Purifed bone marrow cells

tag: genotype

value: Asxl1 -/-

tag: timepoint

value: 6 months


title: KO1_CD133_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2109


title: Submandibular Gland 12 scRNA

city: Buffalo

first: Rose-Anne

last: Romano

state: NY

address: Main Cir

institute: SUNY University at Buffalo

description: scRNA-seq Data

data_processing:
Illumina RTA 2.2.68 Basecaller
Cellranger 6 mkoutput with Bcl2Fastq 2.20.0.422
Cellranger 6 Count against GRCh38 genome to produce count matrix
Seurat 4.0 used for marker gene analysis and visualization
Assembly: GRCh38
Supplementary files format and content: H5 Matrix Files

source_name: Submandibular Gland

extract_protocol:
Chromium Single Cell 3' v2 (10X Genonics)
TruSeq Stranded RNA (illumina)

value: M


title: KO2_CD133_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2110


title: HFO_FP_b001_207_cbc

tag: passage

value: CD (Crohn's disease)

value: CNM

tag: time (in expansion media)

tag: time (in diff media)

tag: individual

value: Donor 9


title: KO3_CD133_RBP1

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2107


title: HFO_FP_b001_206_cbc

tag: growth conditions

tag: replicate

tag: tissue

tag: disease state

value: 3 days

value: 4 days


title: KO2_CD133_RBP1

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2106


title: 1S neuron, seqment A6, animal 7, cell d306074

value: neuron

tag: gender


title: 1S neuron, seqment A8, animal 7, cell d306075

tag: strain


title: KO1_CD133_RBP1

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2105


title: KO5_CD133_H2aK119Ub

description:
CUT&Tag Library
H2aK119Ub.q0.00001_peaks.narrowPeak

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2104


title: HFO_FP_b001_205_cbc

tag: inflamed

tag: medium


title: HFO_FP_b001_204_cbc

value: previously inflamed

value: Female

value: Donor 4


title: 1S neuron, seqment A2, animal 7, cell d306073

tag: segment

value: F


title: KO3_CD133_H2aK119Ub

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2102

tag: cell type


title: KO2_CD133_H2aK119Ub

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2101


title: 1S neuron, seqment A1, animal 7, cell d306071

tag: animal


title: 1S neuron, seqment A1, animal 7, cell d306072

tag: genotype


title: HFO_FP_b001_203_cbc

value: monolayer


title: KO1_CD133_H2aK119Ub

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2100

tag: timepoint


title: KO4_CD133_H2aK119Ub

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2103


title: KO4_CD133_H3K27Ac

description:
CUT&Tag Library
H3K27Ac.q0.001_peaks.narrowPeak

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2098


title: HFO_FP_b001_202_cbc

extract_protocol: 3’RNA sequencing was performed using linear amplification and pooling followed by paired end sequencing (Hashimshony et al., 2016).

tag: passage

value: Ileum


title: 1S neuron, seqment A3, animal 7, cell d306070

extract_protocol:
Cellular material was aspirated in whole-cell patch electrodes and transferred to 384 well plates followed by extraction with XXX
RNAseq libraries from single cells were prepared using a modified version of the SMART-seq2 single-cell protocol (Picelli et al., 2013, Trombetta et al., 2014). RNA from single cells was placed in Hard-Shell 384-well plates (Catalog #HSP3801) in minimal volume (<2uL). cDNA was prepared following the standard protocol using 1/3 of the recommended volumes for all reagents utilizing a Mosquito HV automated liquid handler (SPT Labtech). Amplified cDNA was purified using 0.75X SPRI beads, quantified using picogreen and spot-checked on the Fragment Analyzer (Agilent). Dual indexed Illumina libraries were prepared from cDNA using a reduced volume NexteraXT reaction (1:12) on the Mosquito HV (Hendricks et al., in preparation). Final libraries were quantified using picogreen and spot-checked on the Fragment Analyzer before pooling and final quantification using qPCR on a Roche LC480II.


title: KO3_CD133_H3K27Ac

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2097


title: KO5_CD133_H3K27Ac

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2099


title: 1S neuron, seqment A3, animal 7, cell d306069


title: KO1_CD133_H3K27Ac

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2095


title: HFO_FP_b001_200_cbc

value: eCDM

tag: time (in expansion media)


title: KO4_CD133_H3K27me3

description:
CUT&Tag Library
H3K27me3_peaks._q0.001.narrowPeak

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2093

value: CD133 Purifed bone marrow cells


title: HFO_FP_b001_1_cbc

value: organoid

value: (Ascending) Colon

value: WT

value: normal

value: Male

tag: time (in diff media)

value: Donor 89


title: KO2_CD133_H3K27Ac

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2096

value: Asxl1 -/-

value: 6 months


title: 1S neuron, seqment A5, animal 7, cell d306067

value: neuron


title: HFO_FP_b001_19_cbc

value: CNM

value: 3 days

value: 4 days

tag: individual


title: 1S neuron, seqment A4, animal 7, cell d306068

value: F


title: KO2_CD133_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2091


title: KO1_CD133_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2090


title: 1S neuron, seqment A7, animal 7, cell d306066


title: KO2_CD133_H3K4me3

description:
CUT&Tag Library
H3K4me3.q0.0001_peaks.narrowPeak

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2089


title: KO1_CD133_H3K4me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2088


title: KO1_CD133_H3K4me1

description:
CUT&Tag Library
H3K4me1.q0.00001_peaks.narrowPeak

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2086


title: HFO_FP_b001_199_cbc

tag: growth conditions

value: monolayer

value: CD (Crohn's disease)

value: previously inflamed

value: Female

value: Donor 4


title: 1B neuron, seqment A6, animal 4, cell d306030

value: M


title: HFO_FP_b001_197_cbc

tag: replicate

value: Ileum


title: HFO_FP_b001_198_cbc

tag: tissue


title: WT2_CD133_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2085

value: CD133 Purifed bone marrow cells

value: Asxl1 wild type


title: 1S neuron, seqment A6, animal 7, cell d306065


title: WT1_CD133_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2084


title: 1B neuron, seqment A5, animal 4, cell d306029


title: KO2_CD133_H3K4me1

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2087


title: WT4_CD133_RBP1

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2083


title: KO5_CD133_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2094


title: HFO_FP_b001_201_cbc

extract_protocol: 3’RNA sequencing was performed using linear amplification and pooling followed by paired end sequencing (Hashimshony et al., 2016).

tag: disease state

value: eCDM


title: KO3_CD133_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2092

value: Asxl1 -/-


title: WT2_CD133_RBP1

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2081

value: 6 months


title: WT3_CD133_RBP1

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2082


title: HFO_FP_b001_195_cbc

value: normal

tag: gender

value: cCDM

value: Donor 3


title: WT1_CD133_RBP1

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2080

tag: strain


title: WT4_CD133_H2aK119Ub

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2079


title: 1B neuron, seqment A8, animal 4, cell d306027

extract_protocol:
Cellular material was aspirated in whole-cell patch electrodes and transferred to 384 well plates followed by extraction with XXX
RNAseq libraries from single cells were prepared using a modified version of the SMART-seq2 single-cell protocol (Picelli et al., 2013, Trombetta et al., 2014). RNA from single cells was placed in Hard-Shell 384-well plates (Catalog #HSP3801) in minimal volume (<2uL). cDNA was prepared following the standard protocol using 1/3 of the recommended volumes for all reagents utilizing a Mosquito HV automated liquid handler (SPT Labtech). Amplified cDNA was purified using 0.75X SPRI beads, quantified using picogreen and spot-checked on the Fragment Analyzer (Agilent). Dual indexed Illumina libraries were prepared from cDNA using a reduced volume NexteraXT reaction (1:12) on the Mosquito HV (Hendricks et al., in preparation). Final libraries were quantified using picogreen and spot-checked on the Fragment Analyzer before pooling and final quantification using qPCR on a Roche LC480II.

value: neuron


title: WT3_CD133_H2aK119Ub

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2078


title: HFO_FP_b001_193_cbc

tag: inflamed

value: 4 days


title: WT1_CD133_H2aK119Ub

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2076


title: 1B neuron, seqment A8, animal 4, cell d306026


title: WT3_CD133_H3K27Ac

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2074


title: HFO_FP_b001_192_cbc

value: monolayer

tag: medium


title: 1B neuron, seqment A2, animal 4, cell d306024

tag: segment


title: WT4_CD133_H3K27Ac

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2075

tag: cell type


title: HFO_FP_b001_191_cbc

value: CD (Crohn's disease)


title: HFO_FP_b001_196_cbc

value: previously inflamed

value: CNM

value: 3 days


title: 1B neuron, seqment A1, animal 4, cell d306023

tag: animal

value: M


title: HFO_FP_b001_190_cbc

value: Ileum

value: Female


title: WT1_CD133_H3K27Ac

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2072

value: CD133 Purifed bone marrow cells

tag: genotype

value: Asxl1 wild type


title: WT5_CD133_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2071

tag: timepoint


title: WT4_CD133_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2070


title: 1B neuron, seqment T3, animal 4, cell d306022


title: WT3_CD133_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2069


title: HFO_FP_b001_18_cbc

tag: passage

value: organoid

value: WT

value: Male

value: Donor 89


title: 1B neuron, seqment A2, animal 4, cell d306028


title: WT1_CD133_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2067

value: 6 months


title: 1B neuron, seqment A1, animal 4, cell d306021

value: neuron


title: WT2_CD133_H2aK119Ub

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2077


title: HFO_FP_b001_194_cbc

extract_protocol: 3’RNA sequencing was performed using linear amplification and pooling followed by paired end sequencing (Hashimshony et al., 2016).

value: normal

value: cCDM

tag: time (in expansion media)

value: 4 days

value: Donor 3


title: WT2_CD133_H3K4me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2066


title: HFO_FP_b001_189_cbc

value: monolayer

value: CD (Crohn's disease)

value: CNM

tag: time (in diff media)


title: 1S neuron, seqment T3, animal 3, cell d306020

value: F


title: WT1_CD133_H3K4me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2065


title: HFO_FP_b001_188_cbc

value: Ileum

value: Female

tag: individual


title: WT2_CD133_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2068

value: CD133 Purifed bone marrow cells

value: Asxl1 wild type


title: 1S neuron, seqment T3, animal 3, cell d306019


title: WT1_CD133_H3K4me1

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2063


title: WT2_CD133_H3K4me1

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2064


title: 1B neuron, seqment A3, animal 4, cell d306025

extract_protocol:
Cellular material was aspirated in whole-cell patch electrodes and transferred to 384 well plates followed by extraction with XXX
RNAseq libraries from single cells were prepared using a modified version of the SMART-seq2 single-cell protocol (Picelli et al., 2013, Trombetta et al., 2014). RNA from single cells was placed in Hard-Shell 384-well plates (Catalog #HSP3801) in minimal volume (<2uL). cDNA was prepared following the standard protocol using 1/3 of the recommended volumes for all reagents utilizing a Mosquito HV automated liquid handler (SPT Labtech). Amplified cDNA was purified using 0.75X SPRI beads, quantified using picogreen and spot-checked on the Fragment Analyzer (Agilent). Dual indexed Illumina libraries were prepared from cDNA using a reduced volume NexteraXT reaction (1:12) on the Mosquito HV (Hendricks et al., in preparation). Final libraries were quantified using picogreen and spot-checked on the Fragment Analyzer before pooling and final quantification using qPCR on a Roche LC480II.

value: M


title: WT2_CD133_H3K27Ac

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2073


title: 1S neuron, seqment A1, animal 3, cell d306018


title: HFO_FP_b001_187_cbc

tag: growth conditions


title: KO1_PBN_IgG

description:
CUT&Tag Library
none

source_name: Ly6G Purified Peripheral Blood Neutrophils

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2060

value: Asxl1 -/-


title: KO3_PBN_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2062

value: Ly6G Purified Peripheral Blood Neutrophils


title: HFO_FP_b001_186_cbc

tag: replicate

value: 7 days

value: Donor 10


title: HFO_FP_b001_185_cbc

tag: tissue

value: normal


title: KO2_BMN_IgG

description:
CUT&Tag Library
none

source_name: FACS Sorted Bone marrow cells

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2058

value: FACS Sorted Bone marrow cells

value: 6 months


title: KO3_BMN_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2059


title: 1S neuron, seqment A8, animal 3, cell d306016

value: neuron


title: KO2_PBN_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2061


title: 1S neuron, seqment A6, animal 3, cell d306015


title: 1S neuron, seqment A8, animal 3, cell d306017


title: HFO_FP_b001_184_cbc

value: monolayer

tag: disease state

value: cCDM

value: 4 days


title: HFO_FP_b001_183_cbc

value: CD (Crohn's disease)

tag: gender

value: eCDM


title: KO3_GP_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2056

tag: strain


title: KO1_BMN_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2057


title: KO1_GP_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2054


title: KO2_GP_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2055


title: 1S neuron, seqment A7, animal 3, cell d306014

value: F


title: KO2_MP_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2053


title: KO1_MP_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2052


title: WT3_PBN_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2051


title: WT2_PBN_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2050


title: HFO_FP_b001_182_cbc

extract_protocol: 3’RNA sequencing was performed using linear amplification and pooling followed by paired end sequencing (Hashimshony et al., 2016).

value: Ileum

tag: inflamed

value: Female


title: 1S neuron, seqment A3, animal 3, cell d306012


title: WT3_BMN_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2048

value: Asxl1 wild type


title: WT1_PBN_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2049


title: 1S neuron, seqment A5, animal 3, cell d306013

extract_protocol:
Cellular material was aspirated in whole-cell patch electrodes and transferred to 384 well plates followed by extraction with XXX
RNAseq libraries from single cells were prepared using a modified version of the SMART-seq2 single-cell protocol (Picelli et al., 2013, Trombetta et al., 2014). RNA from single cells was placed in Hard-Shell 384-well plates (Catalog #HSP3801) in minimal volume (<2uL). cDNA was prepared following the standard protocol using 1/3 of the recommended volumes for all reagents utilizing a Mosquito HV automated liquid handler (SPT Labtech). Amplified cDNA was purified using 0.75X SPRI beads, quantified using picogreen and spot-checked on the Fragment Analyzer (Agilent). Dual indexed Illumina libraries were prepared from cDNA using a reduced volume NexteraXT reaction (1:12) on the Mosquito HV (Hendricks et al., in preparation). Final libraries were quantified using picogreen and spot-checked on the Fragment Analyzer before pooling and final quantification using qPCR on a Roche LC480II.


title: 1S neuron, seqment A4, animal 3, cell d306011


title: WT1_BMN_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2046


title: WT2_BMN_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2047


title: HFO_FP_b001_17_cbc

value: organoid

value: WT

value: Male

tag: medium

value: 3 days

value: Donor 89


title: HFO_FP_b001_180_cbc

value: normal

value: CNM

value: 7 days

value: Donor 10


title: 1S neuron, seqment A7, animal 3, cell d306010

value: neuron

tag: segment


title: HFO_FP_b001_179_cbc

value: monolayer

value: 4 days


title: WT3_GP_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2045

tag: cell type

value: FACS Sorted Bone marrow cells

value: 6 months


title: HFO_FP_b001_178_cbc

value: Ileum

value: CD (Crohn's disease)


title: 1B neuron, seqment A7, animal 1, cell d306006

tag: animal

value: M


title: 1S neuron, seqment A5, animal 3, cell d306009

value: F

tag: genotype


title: WT2_MP_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2042

value: Asxl1 wild type

tag: timepoint


title: WT1_GP_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2043


title: HFO_FP_b001_181_cbc

tag: passage

value: Female

value: eCDM


title: KO3_PBN_H3K27me3

description:
CUT&Tag Library
PBN-H3K27me3q0.000001_peaks.narrowPeak

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2040

value: Ly6G Purified Peripheral Blood Neutrophils

value: Asxl1 -/-


title: HFO_FP_b001_177_cbc

value: (Ascending) Colon

value: normal

tag: time (in expansion media)

value: Donor 4


title: WT1_MP_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2041


title: 1B neuron, seqment A6, animal 1, cell d306005

value: neuron


title: KO1_PBN_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2038


title: HFO_FP_b001_176_cbc

value: monolayer

tag: time (in diff media)


title: KO2_PBN_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2039


title: HFO_FP_b001_174_cbc

value: CNM

value: 4 days

tag: individual


title: KO3_BMN_H3K27me3

description:
CUT&Tag Library
BMN-H3K27me3q0.000001_peaks.narrowPeak

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2037

value: FACS Sorted Bone marrow cells

value: 6 months


title: KO3_GP_H3K27me3

description:
CUT&Tag Library
GP-H3K27me3q0.000001_peaks.narrowPeak

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2034


title: KO1_BMN_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2035


title: 1B neuron, seqment A5, animal 1, cell d306002


title: HFO_FP_b001_173_cbc

tag: growth conditions

value: CD (Crohn's disease)


title: KO1_GP_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2032


title: WT2_GP_IgG

description:
CUT&Tag Library
none

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2044


title: KO2_MP_H3K27me3

description:
CUT&Tag Library
MP-H3K27me3q0.000001_peaks.narrowPeak

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2031


title: 1B neuron, seqment A5, animal 1, cell d306001

value: M


title: HFO_FP_b001_172_cbc

extract_protocol: 3’RNA sequencing was performed using linear amplification and pooling followed by paired end sequencing (Hashimshony et al., 2016).

tag: replicate


title: 1B neuron, seqment A3, animal 12, cell d270096

extract_protocol:
Cellular material was aspirated in whole-cell patch electrodes and transferred to 384 well plates followed by extraction with XXX
RNAseq libraries from single cells were prepared using a modified version of the SMART-seq2 single-cell protocol (Picelli et al., 2013, Trombetta et al., 2014). RNA from single cells was placed in Hard-Shell 384-well plates (Catalog #HSP3801) in minimal volume (<2uL). cDNA was prepared following the standard protocol using 1/3 of the recommended volumes for all reagents utilizing a Mosquito HV automated liquid handler (SPT Labtech). Amplified cDNA was purified using 0.75X SPRI beads, quantified using picogreen and spot-checked on the Fragment Analyzer (Agilent). Dual indexed Illumina libraries were prepared from cDNA using a reduced volume NexteraXT reaction (1:12) on the Mosquito HV (Hendricks et al., in preparation). Final libraries were quantified using picogreen and spot-checked on the Fragment Analyzer before pooling and final quantification using qPCR on a Roche LC480II.

tag: tissue


title: HFO_FP_b001_171_cbc

value: (Proximal) Colon)

tag: disease state

value: UC (ulcerative colitis)

value: Male

value: cCDM

value: Donor 7


title: WT3_PBN_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2029

value: Ly6G Purified Peripheral Blood Neutrophils

value: Asxl1 wild type


title: HFO_FP_b001_175_cbc

value: (Ascending) Colon

value: normal

tag: gender

value: Female

value: eCDM


title: 1B neuron, seqment A4, animal 1, cell d306004

value: neuron

tag: strain


title: WT1_PBN_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2027


title: HFO_FP_b001_170_cbc

value: monolayer

tag: inflamed

value: 4 days


title: WT3_BMN_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2026

value: FACS Sorted Bone marrow cells

value: 6 months


title: 1B neuron, seqment A2, animal 12, cell d270094

value: M


title: KO2_BMN_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2036

value: Asxl1 -/-


title: WT2_BMN_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2025


title: 1B neuron, seqment A2, animal 12, cell d270092


title: WT1_BMN_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2024


title: 1B neuron, seqment A4, animal 1, cell d306003


title: WT3_GP_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2023


title: HFO_FP_b001_169_cbc

value: (Proximal) Colon)

value: UC (ulcerative colitis)

tag: medium


title: 1B neuron, seqment A3, animal 12, cell d270091

tag: segment


title: KO2_GP_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2033

tag: cell type


title: HFO_FP_b001_168_cbc

value: Male


title: 1B neuron, seqment A4, animal 12, cell d270090

tag: animal


title: 1B neuron, seqment A6, animal 12, cell d270089

tag: genotype


title: WT2_MP_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2020

tag: timepoint


title: HFO_FP_b001_167_cbc

tag: passage

value: Donor 7


title: KO1_MP_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2030


title: KO4_RNA

description:
Bulk RNA Seq
Bulk_ASXL_counts.filt.txt

data_processing:
Sequencing from Bulk RNA seq was aligned using STAR
Differential Expression was determined using Deseq2

extract_protocol: Libraries were prepared using a TruSeq library prep kit (Illumina)

value: CD133 Purifed bone marrow cells


title: WT2_PBN_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2028

value: Ly6G Purified Peripheral Blood Neutrophils

value: Asxl1 wild type


title: KO3_RNA

description:
Bulk RNA Seq
Bulk_ASXL_counts.filt.txt


title: HFO_FP_b001_166_cbc

value: normal

tag: time (in expansion media)


title: HFO_FP_b001_16_cbc

value: organoid

value: Ileum

value: WT

value: cCDM

value: 3 days

tag: time (in diff media)

value: Donor 89


title: 1B neuron, seqment A7, animal 12, cell d270088

value: neuron


title: KO2_RNA

description:
Bulk RNA Seq
Bulk_ASXL_counts.filt.txt

value: 6 months


title: WT4_RNA

description:
Bulk RNA Seq
Bulk_ASXL_counts.filt.txt


title: HFO_FP_b001_165_cbc

value: monolayer

value: CNM

value: 4 days

tag: individual


title: 1B neuron, seqment A3, animal 11, cell d270082

value: F


title: 1B neuron, seqment A2, animal 11, cell d270081


title: WT3_RNA

description:
Bulk RNA Seq
Bulk_ASXL_counts.filt.txt


title: WT2_GP_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2022

value: FACS Sorted Bone marrow cells


title: KO1_RNA

description:
Bulk RNA Seq
Bulk_ASXL_counts.filt.txt

value: CD133 Purifed bone marrow cells

value: Asxl1 -/-


title: WT1_RNA

description:
Bulk RNA Seq
Bulk_ASXL_counts.filt.txt

value: Asxl1 wild type


title: HRCRC2045

city: Deajeon

first: YunJae

last: Shin

state: Deajeon

address: 125, Gwahak-ro, Yuseong-gu, 34141 Daejeon, South Korea

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Quality of sequencing reads was assessed using fastQC
Sequence reads were mapped to hg38 using HISAT2 aligner.
Aligned sequence reads were counted using featurecounts.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts of sequencing reads for all samples

source_name: colon

extract_protocol:
RNA was purified from the tumor tissue samples using the AllPrep DNA/RNA Mini Kit (Qiagen, Valencia, CA). The concentration and purity of extracted RNA were measured with NanoDrop and Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries for RNA-seq were prepared using TrueSeq Stranded mRNA Sample Prep Kit following manufacturer's protocols.

value: colon

tag: age

tag: Sex

value: Male

value: Late-onset colorectal cancer


title: HFO_FP_b001_164_cbc

tag: growth conditions

tag: replicate

tag: tissue

value: (Proximal) Colon)

value: UC (ulcerative colitis)

value: normal

value: Donor 7


title: HFO_FP_b001_163_cbc

tag: disease state

tag: gender


title: WT1_MP_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2019

tag: strain


title: HRCRC3403


title: WT1_GP_H3K27me3

extract_protocol: Libraries were prepared according to published protocol Kaya-Okur et al 2021


title: HFO_FP_b001_162_cbc

extract_protocol: 3’RNA sequencing was performed using linear amplification and pooling followed by paired end sequencing (Hashimshony et al., 2016).

value: Proximal Colon

tag: inflamed

tag: medium

value: cCDM

value: Donor 8


title: HRCRC2004

value: Female


title: 1B neuron, seqment A7, animal 11, cell d270078

extract_protocol:
Cellular material was aspirated in whole-cell patch electrodes and transferred to 384 well plates followed by extraction with XXX
RNAseq libraries from single cells were prepared using a modified version of the SMART-seq2 single-cell protocol (Picelli et al., 2013, Trombetta et al., 2014). RNA from single cells was placed in Hard-Shell 384-well plates (Catalog #HSP3801) in minimal volume (<2uL). cDNA was prepared following the standard protocol using 1/3 of the recommended volumes for all reagents utilizing a Mosquito HV automated liquid handler (SPT Labtech). Amplified cDNA was purified using 0.75X SPRI beads, quantified using picogreen and spot-checked on the Fragment Analyzer (Agilent). Dual indexed Illumina libraries were prepared from cDNA using a reduced volume NexteraXT reaction (1:12) on the Mosquito HV (Hendricks et al., in preparation). Final libraries were quantified using picogreen and spot-checked on the Fragment Analyzer before pooling and final quantification using qPCR on a Roche LC480II.

value: neuron

tag: segment

tag: cell type

tag: animal


title: HRCRC2071


title: HFO_FP_b001_161_cbc

tag: passage

value: monolayer

value: 4 days


title: HRCRC3036


title: 1B neuron, seqment A6, animal 11, cell d270077

value: F

tag: genotype


title: HRCRC3013


title: WT2_RNA

description:
Bulk RNA Seq
Bulk_ASXL_counts.filt.txt

value: CD133 Purifed bone marrow cells

tag: timepoint

value: 6 months


title: HRCRC3209

value: colon


title: 1B neuron, seqment A6, animal 11, cell d270075


title: HFO_FP_b001_15_cbc

value: organoid

value: Ileum

value: WT

value: Male

value: eCDM

tag: time (in expansion media)

value: 3 days

tag: time (in diff media)

tag: individual

value: Donor 89


title: HRCRC2092

tag: age

tag: Sex

value: Late-onset colorectal cancer


title: HRCRC3425

tag: tissue


title: HRCRC3447

source_name: rectum

value: rectum

tag: disease state


title: 1B neuron, seqment A4, animal 11, cell d270080

tag: gender


title: HRCRC3946

value: Female


title: 1S neuron, seqment A3, animal 10, cell d270068

value: neuron

tag: strain


title: 1B neuron, seqment A5, animal 11, cell d270079


title: HFO_FP_b001_158_cbc

tag: growth conditions

value: monolayer

tag: replicate

value: Proximal Colon

value: UC (ulcerative colitis)

tag: inflamed

value: normal

value: Donor 8


title: 1S neuron, seqment A1, animal 10, cell d270069

tag: segment

tag: cell type

value: F


title: HRCRC3937

value: colon


title: 1S neuron, seqment A4, animal 10, cell d270067

tag: animal


title: HRCRC3861


title: HRCRC3821


title: HRCRC3817


title: 1S neuron, seqment A6, animal 10, cell d270066

tag: genotype


title: HFO_FP_b001_156_cbc

tag: passage

tag: medium

value: CNM

value: 4 days


title: HRCRC3805


title: HRCRC3777

value: Male


title: HFO_FP_b001_155_cbc

tag: time (in expansion media)

tag: time (in diff media)


title: HFO_FP_b001_160_cbc

value: cCDM

tag: individual


title: HRCRC3874

tag: age

tag: Sex


title: 1S neuron, seqment A6, animal 10, cell d270065

tag: tissue


title: 1S neuron, seqment A7, animal 10, cell d270064

tag: gender


title: HRCRC3869

tag: disease state


title: 1S neuron, seqment A8, animal 10, cell d270063

tag: strain


title: HFO_FP_b001_153_cbc

tag: growth conditions

tag: replicate

value: (Distal) Colon

value: Donor 7


title: HFO_FP_b001_154_cbc

tag: inflamed


title: HRCRC3870

value: Late-onset colorectal cancer


title: HFO_FP_b001_152_cbc


title: HFO_FP_b001_157_cbc

value: eCDM


title: HRCRC3814


title: HRCRC3696

value: rectum

value: Female


title: 1S neuron, seqment A7, animal 10, cell d270062

value: neuron

tag: segment

tag: cell type


title: 1S neuron, seqment A2, animal 10, cell d270061

tag: animal

tag: genotype


title: HRCRC3847


title: HRCRC3910


title: HFO_FP_b001_151_cbc

tag: passage

value: monolayer

tag: medium


title: HRCRC3745


title: HRCRC3663


title: 1S neuron, seqment A2, animal 10, cell d270060


title: 1S neuron, seqment A3, animal 10, cell d270059


title: HRCRC3615


title: HRCRC3620


title: HFO_FP_b001_14_cbc

value: organoid

value: Ileum

value: WT

tag: time (in expansion media)

value: 3 days

tag: time (in diff media)

value: Donor 89


title: 1B neuron, seqment A6, animal 9, cell d270055

value: F


title: HFO_FP_b001_159_cbc

value: Proximal Colon

value: UC (ulcerative colitis)

value: normal

value: 4 days

tag: individual

value: Donor 8


title: HFO_FP_b001_149_cbc

value: (Distal) Colon

value: Male

value: Donor 7


title: HRCRC3537

value: rectum

tag: age

tag: Sex

value: Late-onset colorectal cancer


title: HRCRC3864

tag: tissue

value: colon

value: Female


title: HRCRC3522

tag: disease state


title: HRCRC3555


title: 1B neuron, seqment A7, animal 9, cell d270054

value: neuron

tag: gender

tag: strain


title: HRCRC3517


title: 1B neuron, seqment A8, animal 9, cell d270053


title: HFO_FP_b001_148_cbc

tag: growth conditions

value: monolayer

tag: replicate

value: eCDM


title: HRCRC3503


title: HFO_FP_b001_147_cbc

tag: inflamed

value: CNM


title: HRCRC3483


title: HRCRC3457


title: HRCRC3450


title: HFO_FP_b001_146_cbc


title: HRCRC3796


title: HRCRC3419


title: HFO_FP_b001_150_cbc


title: 1B neuron, seqment A6, animal 8, cell d270051

tag: segment

tag: cell type

value: F


title: HFO_FP_b001_145_cbc


title: HRCRC3351


title: HRCRC3348


title: HFO_FP_b001_144_cbc

value: Ileum

value: WT

value: cCDM

value: Donor 89


title: HRCRC3337


title: 1B neuron, seqment A2, animal 8, cell d270049

tag: animal

tag: genotype


title: HFO_FP_b001_143_cbc

tag: passage

value: normal

tag: medium

value: 4 days


title: HRCRC3328


title: HRCRC3295


title: HRCRC3275


title: HRCRC3291

value: Male


title: 1B neuron, seqment A6, animal 9, cell d270052


title: HFO_FP_b001_142_cbc

tag: time (in expansion media)

tag: time (in diff media)


title: 1S neuron, seqment A6, animal 7, cell d270048


title: HRCRC3221

tag: age


title: 1S neuron, seqment A7, animal 7, cell d270047


title: HRCRC3242

tag: Sex


title: HFO_FP_b001_140_cbc

tag: tissue

tag: individual


title: HFO_FP_b001_141_cbc

tag: disease state

tag: gender


title: HRCRC3759


title: HRCRC3197


title: 1S neuron, seqment T2, animal 7, cell d270045

tag: strain


title: HFO_FP_b001_13_cbc

tag: growth conditions

value: organoid

tag: replicate

value: 3 days


title: 1S neuron, seqment A6, animal 7, cell d270043

tag: segment


title: HRCRC2100

value: Early-onset colorectal cancer


title: HFO_FP_b001_139_cbc

tag: inflamed


title: HRCRC2039

value: rectum


title: 1B neuron, seqment A4, animal 8, cell d270050

tag: cell type

tag: animal


title: 1S neuron, seqment T3, animal 7, cell d270044

tag: genotype


title: HRCRC2047

value: colon


title: 1S neuron, seqment A4, animal 7, cell d270042

value: neuron


title: HRCRC3316


title: HRCRC2049


title: HFO_FP_b001_138_cbc

tag: passage

value: monolayer

tag: medium


title: HRCRC2082

value: Female


title: HRCRC2105


title: 1S neuron, seqment A2, animal 7, cell d270041


title: HFO_FP_b001_137_cbc

value: CNM

tag: time (in expansion media)

tag: time (in diff media)


title: HRCRC3076

tag: age

tag: Sex


title: 1S neuron, seqment A1, animal 7, cell d270040

tag: tissue

value: F


title: HRCRC2074

tag: disease state


title: HFO_FP_b001_135_cbc

value: Ileum

tag: gender

tag: individual


title: HRCRC3151


title: 1B neuron, seqment A7, animal 6, cell d270038

value: M

tag: strain


title: HRCRC3080


title: HFO_FP_b001_136_cbc

tag: growth conditions

tag: replicate

value: WT


title: 1B neuron, seqment A6, animal 6, cell d270037

tag: segment


title: HRCRC3957


title: HRCRC2021


title: 1B neuron, seqment A6, animal 6, cell d270036

tag: cell type


title: HFO_FP_b001_134_cbc

tag: inflamed

value: cCDM

value: Donor 89


title: HRCRC3936


title: HRCRC3927


title: 1B neuron, seqment A5, animal 6, cell d270035

tag: animal

tag: genotype


title: HRCRC3904


title: HFO_FP_b001_133_cbc

tag: passage

value: normal

tag: medium

value: 4 days


title: HRCRC3932


title: 1B neuron, seqment A5, animal 6, cell d270034


title: HFO_FP_b001_132_cbc

value: Male

value: eCDM

tag: time (in expansion media)

tag: time (in diff media)


title: HRCRC3900

tag: age

tag: Sex

value: Early-onset colorectal cancer


title: HRCRC3898

tag: tissue

tag: disease state


title: 1S neuron, seqment A3, animal 4, cell d270032

tag: gender


title: HFO_FP_b001_131_cbc

value: 3 days

tag: individual


title: HRCRC3849

value: colon


title: HFO_FP_b001_130_cbc

tag: growth conditions


title: HRCRC3839


title: HRCRC3823

value: rectum


title: HFO_FP_b001_12_cbc

value: organoid

tag: replicate


title: 1S neuron, seqment A2, animal 4, cell d270031

value: neuron

tag: segment

tag: strain


title: HFO_FP_b001_129_cbc

value: monolayer

tag: inflamed

value: CNM


title: HRCRC3809


title: 1B neuron, seqment A8, animal 5, cell d270030

tag: cell type

tag: animal


title: HRCRC3752


title: HFO_FP_b001_128_cbc

tag: passage

value: Ileum


title: HRCRC3731

value: Female


title: HFO_FP_b001_127_cbc

value: WT

tag: medium


title: HRCRC3726


title: HRCRC3744


title: 1B neuron, seqment A8, animal 5, cell d270029

value: M

tag: genotype


title: HFO_FP_b001_126_cbc

value: (Ascending) Colon

value: cCDM

tag: time (in expansion media)

tag: time (in diff media)

value: Donor 89


title: HRCRC3717

tag: age

tag: Sex

value: Male


title: 1B neuron, seqment A5, animal 5, cell d270027

tag: tissue


title: HRCRC3677

tag: disease state


title: HRCRC3441


title: HRCRC3711


title: HFO_FP_b001_125_cbc

value: normal

tag: gender

value: 4 days

tag: individual


title: 1B neuron, seqment A3, animal 5, cell d270026


title: HRCRC3601

value: Early-onset colorectal cancer


title: 1S neuron, seqment A6, animal 4, cell d270024


title: HRCRC3792

value: colon


title: HFO_FP_b001_124_cbc

tag: growth conditions

tag: replicate


title: HRCRC3571


title: HRCRC3807


title: HRCRC3561


title: 1S neuron, seqment A5, animal 4, cell d270022

tag: segment

tag: strain


title: HRCRC3109

value: rectum


title: HFO_FP_b001_123_cbc

tag: inflamed

value: eCDM


title: HRCRC3470


title: HRCRC3462


title: HRCRC3426


title: HFO_FP_b001_122_cbc


title: HRCRC3424


title: HFO_FP_b001_121_cbc


title: 1B neuron, seqment A6, animal 3, cell d270017

value: neuron

tag: cell type

tag: animal


title: HRCRC3423


title: 1S neuron, seqment A7, animal 4, cell d270023


title: 1B neuron, seqment A5, animal 3, cell d270016


title: HRCRC3310


title: HFO_FP_b001_120_cbc

tag: passage

value: monolayer

tag: medium


title: HRCRC3391


title: 1S neuron, seqment A6, animal 2, cell d270013

tag: genotype


title: HFO_FP_b001_11_cbc

value: organoid

value: CNM

tag: time (in expansion media)

value: 3 days

tag: time (in diff media)


title: HRCRC3258

tag: age

tag: Sex

value: Female


title: HFO_FP_b001_119_cbc

tag: tissue

tag: disease state

value: WT


title: 1B neuron, seqment A7, animal 3, cell d270014

tag: gender

value: M


title: HRCRC3232


title: 1B neuron, seqment A3, animal 3, cell d270018


title: 1S neuron, seqment A7, animal 2, cell d270012


title: 1S neuron, seqment A7, animal 2, cell d270010


title: LNA-2

city: Duarte

first: Zhen

last: Chen

state: CA

address: 1500 E Duarte Rd

department: DMRI

institute: City of Hope

description: polyA RNA enriched

data_processing:
Adaptors were timmed by Trimmomatic-0.39
Trimmed data was aligned to hg38 with STAR(2.7.10a)
reads map to genomic features were counted by FeatureCounts
Assembly: hg38
Supplementary files format and content: The processed counts.txt files are tab-delimited tables which includes annotation columns (‘Geneid’) and data columns (i.e. read counts for genes) for each library.

source_name: Human Umbilical Vein Endothelial Cells transfected with LNA targeting LEENE (50 nM) and harvested after 48 hours

growth_protocol: HUVECs were grown following the manufacturer's protocol

extract_protocol:
Approximately 1 million cells were used for total RNA extraction and construction of strand-specific mRNA-seq library
The libraries were constructed using the KAPA mRNA stranded HyperPrep kit following the user manual

treatment_protocol: HUVECs were cultured in complete medium; transfected with either 50 nM scramble LNA (Scr) or LNA targeting LEENE (LNA) and then harvested after 48 hours post transfection.

tag: cell line

value: HUVEC

tag: assay

value: RNA-seq


title: HFO_FP_b001_118_cbc

tag: growth conditions

tag: replicate

value: (Ascending) Colon

value: Male

tag: individual

value: Donor 89


title: LNA-3

description: polyA RNA enriched


title: HRCRC3326

value: Early-onset colorectal cancer


title: LNA-1

description: polyA RNA enriched


title: HFO_FP_b001_117_cbc

tag: inflamed

value: normal

value: cCDM

value: 6 days

value: 4 days


title: Scr-3

description: polyA RNA enriched

source_name: Human Umbilical Vein Endothelial Cells transfected with scramble LNA (50 nM) and harvested after 48 hours


title: 1S neuron, seqment A8, animal 2, cell d270009

value: neuron

tag: segment

tag: cell type

tag: animal

tag: strain


title: HRCRC3304

value: colon


title: HFO_FP_b001_116_cbc

tag: passage

value: monolayer

tag: medium

tag: time (in expansion media)


title: HRCRC3245

tag: age

tag: Sex


title: Scr-2

description: polyA RNA enriched


title: ChIRP-IP-rep2

data_processing:
Adaptors were timmed by Trimmomatic-0.39
Trimmed data was aligned to hg38 with Bowtie2(2.3.5.1)
MACS2 was used for Peak calling
Assembly: hg38

source_name: HUVEC

extract_protocol:
Cells were fixed with 1% glutaraldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor (Diagenode).
The libraries were constructed using the KAPA HyperPrep kit following the user manual.
ChIRP-seq

treatment_protocol: HUVECs were cultured in complete medium and treated with adenovirus overexperssing Ad-LEENE. Cells were harvested after 3 days.

value: Human umbilical vein endothelial cells

tag: probes

value: LEENE-targeting probes (Biosearch Technologies)


title: 1S neuron, seqment A1, animal 2, cell d270007

tag: tissue

tag: gender

tag: genotype


title: ChIRP-input_rep1

tag: cell line


title: Scr-1

description: polyA RNA enriched

tag: assay


title: 1S neuron, seqment A3, animal 2, cell d270008


title: ChIRP-input_rep2


title: HFO_FP_b001_115_cbc

tag: growth conditions

tag: replicate

tag: disease state

value: WT

tag: time (in diff media)

tag: individual


title: 1S neuron, seqment A4, animal 2, cell d270006

tag: segment

tag: cell type

tag: animal

value: M

tag: strain


title: HFO_FP_b001_114_cbc

tag: passage

tag: inflamed

tag: medium

value: eCDM

tag: time (in expansion media)


title: shZBTB7A U87MG 2

city: Seoul

first: Ji-Hoon

last: Jeong

address: 88, Olympic-ro 43-gil, Songpa-gu

department: Biomedical Sciences

institute: University of Ulsan College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
FPKM calculation using Cufflink
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: shZBTB7A U87MG

growth_protocol: Stable scramble/shZBTB7A U87MG cells were cultured in Dulbecco's modified Eagles' medium (DMEM) with 10 % fetal bovine serum (FBS) and 1 % antibiotics.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: Stable scramble/shZBTB7A U87MG cells were cultured under puromycin selection (1.5 μg/mL)

value: Human glioblastoma cell line

tag: genotype/variation


title: 1S neuron, seqment A2, animal 2, cell d270005

tag: tissue

tag: gender

tag: genotype


title: ChIRP-IP-rep1

tag: cell line

value: HUVEC

tag: probes


title: HFO_FP_b001_112_cbc

tag: growth conditions

tag: replicate

value: (Ascending) Colon

tag: disease state

value: Male


title: HFO_FP_b001_113_cbc

tag: time (in diff media)

tag: individual

value: Donor 89


title: Scramble U87MG 3

source_name: Scramble U87MG

tag: cell type

value: scramble; control vector (pLKO)


title: shZBTB7A U87MG 3


title: shZBTB7A U87MG 1


title: Scramble U87MG 2


title: 1S neuron, seqment A6, animal 1, cell d270004

tag: segment

tag: animal

value: F

tag: strain


title: Scramble U87MG 1


title: 1S neuron, seqment A5, animal 1, cell d270003


title: HFO_FP_b001_111_cbc

tag: passage

tag: inflamed

value: normal

tag: medium

value: CNM

value: 6 days


title: 1S neuron, seqment A4, animal 1, cell d270001

tag: tissue

value: neuron


title: C_4-L2_GTGCTT_L002

city: Stanford

first: Ricardo

middle: Luiz

last: De Azevedo Pereira

address: 1201 Welch Road

department: Neurosurgery

institute: Stanford

data_processing:
Illumina Casava1.7 software used for basecalling.
Fastqc (version 0.11.4) was used for sequencing quality assessment and fastx toolkit (version 0.0.14) was used to trim the first 10 bp from both reads
The trimmed reads were then aligned to the pooled transcriptome of the human (hg19) and rat (rn5) using Bowtie (version 2.2.7) with splice junctions being defined in GTF file for both genome (obtained from UCSC)
Gene level expression was determined by calculating reads per kilo base per million aligned reads (FPKM) as well as raw count using RNA-Seq by Expectation Maximization (RSEM; version 1.2.30) with a human-rat pooled reference transcriptome.
Genome_build: hg19; rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: hNSC-invitro

extract_protocol:
In vitro and transplantation sites were removed for TRAP method and RNA isolated using RNeasy Micro Kit (Qiagen) for graft and RNeasy Mini Kit (Qiagen) for host tissue. RNA from TRAP samples and TRAPnf samples were converted to cDNA using the Ovation RNA-seq v2 (Nugen) and cDNA libraries we prepared by Ovation Ultralow System V2 (Nugen) was used with 2 ng of total RNA for the construction of sequencing libraries.
RNA sequencing was performed on an Illumina HiSeq 2500 system , with TRAP samples from engrafted tissue as single lane 125 bp paired-end read, and TRAPnf and TRAP from in vitro samples as multiplexed (4 samples per lane), 50 bp paired-end reads.

value: Fetal human neural stem cells

value: fetal cortex

tag: age

value: fetal day 13-16

value: G010 (Clive Svendsen)

tag: treatment

value: in vitro

tag: sample type

value: TRAP


title: C_3-L2_AAGCCT_L002

tag: cell line


title: C_2-L1_CGTAGA_L001


title: HFO_FP_b001_110_cbc

tag: growth conditions

value: monolayer

value: WT

tag: gender

tag: time (in expansion media)

value: 4 days


title: HFO_FP_b001_10_cbc

value: organoid

tag: replicate

value: Ileum

tag: disease state

value: Male

value: 3 days

tag: time (in diff media)


title: C_1-L1_TCAGAG_L001

tag: cell type


title: hNSC-stroke-9-L3_NoIndex_L003

description:
diffgene_DESeq2_S_vs_N
S_9

source_name: Grafted-hNSC

extract_protocol:
Transplantation sites were removed for TRAP method and RNA isolated using RNeasy Micro Kit (Qiagen) for graft and RNeasy Mini Kit (Qiagen) for host tissue. RNA from TRAP samples and TRAPnf samples were converted to cDNA using the Ovation RNA-seq v2 (Nugen) and cDNA libraries we prepared by Ovation Ultralow System V2 (Nugen) was used with 2 ng of total RNA for the construction of sequencing libraries.
RNA sequencing was performed on an Illumina HiSeq 2500 system , with TRAP samples from engrafted tissue as single lane 125 bp paired-end read, and TRAPnf and TRAP from in vitro samples as multiplexed (4 samples per lane), 50 bp paired-end reads.

value: grafted human fetal cortex

value: Ischemic-stroke


title: hNSC-stroke-16-L4_NoIndex_L004

description:
diffgene_DESeq2_S_vs_N
S_16


title: hNSC-naive19-L7_NoIndex_L007

description:
diffgene_DESeq2_S_vs_N
N_19


title: 1B neuron, seqment A6, animal 12, cell d225095

tag: segment

tag: animal

value: F

tag: genotype


title: HFO_FP_b001_108_cbc

tag: passage

value: (Ascending) Colon

tag: inflamed

value: normal

value: cCDM

value: 7 days

tag: individual

value: Donor 89


title: 1B neuron, seqment A7, animal 12, cell d225091

tag: tissue

value: neuron

tag: strain


title: HFO_FP_b001_107_cbc

tag: medium


title: 1B neuron, seqment A8, animal 12, cell d225090


title: hNSC-stroke-8-L2_NoIndex_L002

description:
diffgene_DESeq2_S_vs_N
S_8

value: Fetal human neural stem cells

tag: age

value: fetal day 13-16

tag: cell line

value: G010 (Clive Svendsen)

tag: treatment

tag: sample type

value: TRAP


title: hNSC-naive17-L5_NoIndex_L005

description:
diffgene_DESeq2_S_vs_N
N_17


title: 1B neuron, seqment A7, animal 12, cell d225089

tag: gender


title: HFO_FP_b001_105_cbc

tag: growth conditions

value: monolayer

tag: replicate

tag: disease state

value: WT

value: eCDM

tag: time (in expansion media)

value: 4 days


title: IL-3-knockout_rep5

city: Heidelberg

first: Dominik

last: Schaack

address: Im Neuenheimer Feld 420

country: Germany

institute: Heidelberg University Hospital

data_processing:
Sequenced reads were depleted from ribosomal reads using SortMeRNA v2.1b and trimmed for adaptor sequences and low-quality reads by Trimmomatic v0.36. Remaining reads were then mapped to Gencode Release M17 primary assembly reference genome utilizing STAR v2.6.0c considering read strand specificity.
After conversion to sorted binary alignment format (BAM) by SAMtools v1.8.3, sample-wise count tables were generated by htseq-count v0.9.1 with the “-s yes” option set. In case technical replicates were present, count tables were summarized per sample.
Assembly: Gencode Release M17 (GRCm38.p6)
Supplementary files format and content: Tab-delimited text files include raw count values for each gene

source_name: Whole lung tissue

extract_protocol:
RNA was extracted from whole lung tissue by RNeasy mini kit (Qiagen, Venlo, Netherlands)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole lung tissue


title: IL-3-knockout_rep1


title: IL-3-knockout_rep3


title: 1B neuron, seqment A4, animal 12, cell d225088

source_name: neuron

tag: segment

tag: cell type

tag: animal


title: HFO_FP_b001_104_cbc

tag: passage

tag: inflamed

value: Male

tag: time (in diff media)


title: IL-3-knockout_rep4

tag: tissue

tag: strain

tag: genotype


title: WT rep1

value: wild type


title: 1B neuron, seqment A5, animal 12, cell d225094

value: F


title: HFO_FP_b001_103_cbc

value: (Ascending) Colon

value: normal

tag: medium

tag: individual


title: IL-3-knockout_rep2


title: 1B neuron, seqment A3, animal 12, cell d225085


title: TCCTGAGC_GCGTAAGA

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared during microfluidic capture and Nextera XT.

value: healthy

tag: Sex

tag: age

value: astrocyte

tag: aqp4 expression

value: positive

tag: edem1  expression

value: Negative


title: 1B neuron, seqment A3, animal 12, cell d225087

value: neuron

tag: gender


title: NSC-naive18-L6_NoIndex_L006

description:
diffgene_DESeq2_S_vs_N
N_18

value: Fetal human neural stem cells

value: grafted human fetal cortex

value: fetal day 13-16

tag: cell line

value: G010 (Clive Svendsen)

tag: sample type


title: AGGCAGAA_GCGTAAGA

tag: disease state

value: WT

tag: cell type


title: HFO_FP_b001_102_cbc

tag: passage

tag: growth conditions

value: monolayer

tag: replicate

value: CNM

tag: time (in expansion media)

value: 7 days

value: 4 days

value: Donor 89


title: TAGGCATG_AGAGTAGA

tag: strain

value: Male


title: HFO_FP_b001_106_cbc

tag: tissue

value: (Ascending) Colon

tag: inflamed

value: normal

value: cCDM

tag: time (in diff media)


title: HFO_FP_b001_109_cbc

tag: medium

value: 6 days

tag: individual


title: 1B neuron, seqment A5, animal 12, cell d225084

tag: segment

tag: animal

value: F

tag: genotype


title: TAAGGCGA_GCGTAAGA

value: healthy

tag: Sex

tag: age

value: astrocyte

tag: aqp4 expression

value: positive

tag: edem1  expression

value: Negative


title: TCCTGAGC_AGAGTAGA

tag: disease state

tag: cell type

value: Positive


title: HFO_FP_b001_101_cbc

tag: passage

tag: growth conditions

tag: replicate

value: WT

tag: gender


title: AGGCAGAA_AGAGTAGA

tag: strain


title: CGTACTAG_GCGTAAGA


title: GGACTCCT_AGAGTAGA


title: H929_dBRD9A_rep3

first: Keiji

last: Kurata

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
Sequenced reads were aligned to the reference human genome (hg19) using RNA-specific STAR aligner.
Read count tables were created using FeatureCounts using UCSC refFlat gene models.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: tab-delimited text files include raw read counts and normalized counts for each sample

source_name: Multiple myeloma cell line

growth_protocol: OPM2 and H929 cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 μM L-glutamine in 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen). Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: OPM2 and H929 cells were treated with 100 nM dBRD9-A or DMSO for 24h.

tag: cell line

value: multiple myeloma cell line

tag: treatment


title: TAAGGCGA_AGAGTAGA


title: TAGGCATG_TATCCTCT

value: induced EAE


title: H929_dBRD9A_rep2


title: GGACTCCT_TATCCTCT


title: 1S neuron, seqment T1, animal 11, cell d225079

tag: tissue

value: neuron


title: H929_dBRD9A_rep1


title: TCCTGAGC_TATCCTCT


title: 1S neuron, seqment A5, animal 11, cell d225082

tag: segment


title: CGTACTAG_TATCCTCT


title: TAGGCATG_CTCTCTAT


title: TAAGGCGA_TATCCTCT


title: H929_DMSO_rep3

value: DMSO


title: GGACTCCT_CTCTCTAT


title: 1S neuron, seqment A6, animal 11, cell d225077

tag: animal


title: 1S neuron, seqment A4, animal 11, cell d225075

tag: genotype


title: TCCTGAGC_CTCTCTAT

tag: Sex


title: H929_DMSO_rep1


title: 1S neuron, seqment A5, animal 11, cell d225076


title: AGGCAGAA_CTCTCTAT

tag: age


title: HFO_FP_b001_100_cbc

value: monolayer

tag: inflamed

tag: medium

value: CNM

tag: time (in expansion media)

value: 7 days

tag: time (in diff media)

value: 4 days

tag: individual

value: Donor 89


title: 1S neuron, seqment A7, animal 11, cell d225081

tag: cell type


title: OPM2_dBRD9A_rep3


title: CGTACTAG_AGAGTAGA

tag: disease state

value: Male

tag: aqp4 expression

tag: edem1  expression


title: TAAGGCGA_CTCTCTAT

tag: strain


title: 1S neuron, seqment A8, animal 11, cell d225080

tag: gender

value: F


title: OPM2_dBRD9A_rep2

tag: cell line

tag: treatment


title: Mike_WT_3

source_name: induced EAE

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).

value: Female

value: astrocytes

tag: condition

value: sgScrmbl


title: 1S neuron, seqment A3, animal 11, cell d225074

tag: tissue

tag: segment

tag: animal

tag: genotype


title: Mike_WT_2

tag: Sex

tag: age


title: 1S neuron, seqment A2, animal 11, cell d225072


title: AGGCAGAA_TATCCTCT

value: astrocyte

value: positive


title: 1S neuron, seqment A7, animal 11, cell d225078


title: Mike_WT_1

value: WT


title: OPM2_dBRD9A_rep1

value: multiple myeloma cell line


title: Mike_NR3C2_3

value: induced EAE


title: H929_DMSO_rep2


title: 1S neuron, seqment A2, animal 10, cell d225071

value: neuron


title: Mike_NR3C2_2


title: Mike_NR3C2_1


title: CGTACTAG_CTCTCTAT

value: Positive


title: OPM2_DMSO_rep3

value: DMSO


title: 1S neuron, seqment A1, animal 10, cell d225070


title: WT EpiLCs Day3_rep2

city: Leuven

first: Frederic

last: Lluis

state: Vlaams-Brabant

address: Herestraat 49

department: Development and Regeneration

country: Belgium

institute: Stem Cell Institute Leuven

description:
wt_EPI_r2
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt

data_processing:
Illumina's bcl2fast 1.8.4 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and short reads were discarded using Cutadapt. Mapping on mouse reference genome (mm10) was performed with HISAT2 v2.1.0, with default options for mESC Tcf7l1 OE Day0, Day1, Day2, Day4 and XEN samples and with strand-specific information (Reverse) and otherwise default parameters for mESC Tcf7l1 OE Day8, WT control and WT EpiLCs Day3 samples.
FeatureCounts v2.0.1 was used for gene assignment against the mouse transcriptome (Ensembl Release M25, GRCm38.p6) and DESeq2 for Differential Gene Expression Analysis, for the genes with average count across samples greater than 5, comparing Tcf7l1 overexpressed samples to Day0 samples, for each Day(1, 2, 4 or 8) of overexpression, XEN to Day0 samples and WT EpiLCs to WT control samples.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Normalized_counts.txt: Matrix table with normalized gene counts for each sample.
Supplementary_files_format_and_content: Statistical_significance_scores_of_differential_gene_expression_analysis.txt: Matrix table with statistical significance scores (adjusted p value and log2-fold-change) for each gene for each comparison.

source_name: Epi-like stem cells

growth_protocol: WT mESCs were maintained for at least 5 passages in N2B27 plus 2i/LIF: 1:1 mixture of DMEM/F12 supplemented with N2 supplement and Neurobasal media supplemented with B27, 1μM MEK inhibitor PD0325901, 3 μM GSK3 inhibitor CHIR99021 and 1000 U/ml mouse LIF. Cells were plated at a density of 1x10^4/cm2 in fibronectin coated (16.7 mg/ml) 6-well plates in N2B27 basal medium supplemented with 20ng/ml activin A, 12.5ng/ml Fgf2 and 2μM XAV939 for 3 days.

extract_protocol:
RNA extraction was performed using GenElute™ Mammalian Total RNA Miniprep Kit using On-Column DNase I Digestion Set.
Libraries were produced using KAPA Stranded RNA-Seq Library Preparation Kit Illumina® Platforms (Cat#7962207001) with 120ng of total RNA.

value: mESC-derived EpiLCs

value: treated with ActivinA, Fgf2, XAV939 for 3 days


title: 1S neuron, seqment A5, animal 10, cell d225069


title: WT EpiLCs Day3_rep1

description:
wt_EPI_r1
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt


title: OPM2_H3K27ac

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human assembly hg19 using bowtie2 with default parameters.
Duplicate reads were removed.
BAM files were converted to bed files using a custom script, and converted to BigWig using bedtobigwig.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files containing read normalized read densities.

growth_protocol: OPM2 cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 μM L-glutamine in 5% CO2 at 37°C.

extract_protocol:
OPM2 cells were crosslinked, lysed and sonicated. For ChIP with reference exogenous genome, spike-in chromatin (Active Motif, 53083) was then added. The protein-bound DNA fragments were then immunoprecipitated with specific antibodies. After reverse-crosslinking, DNA was purified.  Libraries were prepared using ThruPLEX DNA-seq Kit (Rubicon Genomics) according to the manufacturer's instructions.
Libraries were prepared using ThruPLEX DNA-seq Kit (Rubicon Genomics) according to the manufacturer's instructions.

treatment_protocol: OPM2 cells were treated with 100 nM dBRD9-A or DMSO for 6h or 24h.

tag: chip atibody

value: H3K27ac (Cell Signaling Technology, 8173)


title: 1S neuron, seqment A2, animal 10, cell d225068

data_processing:
NextSeq 500 sequencing using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Gene expression was quantified using RSEM version 1.3.0 and STAR version 2.5.3a alignment to a transcriptome derived from the human BDGP6 primary assembly and a version 92 annotation.
Assembly: BDGP6 Drosophila melanogaster assembly with version 92 annotation
Supplementary files format and content: 1b1sm_isoform_intCt.txt.gz is a tab delimited text file of isoform counts
Supplementary files format and content: 1b1sm_isoform_l2tpm.txt.gz is a tab delimited text file of isoform l2tpm vaules
Supplementary files format and content: 1b1sm_l2tpm.txt.gz is a tab delimited text file of gene l2tpm vaules
Supplementary files format and content: 1b1sm_intCt.txt.gz is a tab delimited text file of gene counts


title: XEN_rep2

description:
XEN_r2
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt

source_name: Embryo-derived extraembryonic stem cells

value: untreated


title: XEN_rep3

description:
XEN_r3
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt

value: Embryo-derived extraembryonic stem cells


title: WT control_rep1

description:
wt_ctl_r1
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt

source_name: Mouse embryonic stem cells

value: Mouse embryonic stem cells

value: cultured in N2B27/2iL


title: XEN_rep1

description:
XEN_r1
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt


title: mESC Day8 Tcf7l1 OE_rep2

description:
Day8_r2
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt

growth_protocol: Tcf7l1-inducible ESC line was purchased from the NIA Mouse ES Cell Bank (Nishiyama, et al 2009). ES cells were cultured on feeder cells in ESC medium containing 0.2µg/ml doxycycline (Dox). Before transgene induction cells were cultured on gelatin coated dish in medium containing 0.2μg/ml Dox for 3 days. One day before transgene induction, ES cells were plated onto gelatin coated 100cm2 dishes at a density of 1x10^6 for 24 hours of transgene induction. Dox was removed by washing the cells three times with PBS at interval of 3 hours. In the absence of Dox, the recombinant locus expresses TCF7L1 and Venus YFP protein connected via a synthetic internal ribosomal entry site (IRES). Following the 24h of induction (Day 1), cells were dissociated using 0.5% trypsin-EDTA and resuspended in FACS buffer [PBS supplemented with 5% FBS]. Venus high expressing cells were sorted by fluorescence-activated cell sorting (FACS) using a BD FACSAria™ III sorter and replated in ESC medium conditions. Cells were harvested after 2, 4 and 8 Days after replating.

tag: time point

value: Day 8


title: mESC Day8 Tcf7l1 OE_rep1

description:
Day8_r1
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt

tag: cell type


title: mESC Day4 Tcf7l1 OE_rep3

description:
Day4_r3
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt

value: Day 4


title: 1B neuron, seqment A5, animal 9, cell d225065

value: M


title: 1B neuron, seqment A7, animal 9, cell d225066


title: mESC Day4 Tcf7l1 OE_rep2

description:
Day4_r2
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt


title: mESC Day4 Tcf7l1 OE_rep1

description:
Day4_r1
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt


title: OPM2_BRD4

value: BRD4 (Cell Signaling Technology, 13440)


title: OPM2_MYC

value: MYC (Cell Signaling Technology, 18583)


title: 1B neuron, seqment T1, animal 9, cell d225064


title: WT control_rep2

description:
wt_ctl_r2
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt


title: OPM2_Input_GLTSCR1_dBRD9A

value: multiple myeloma cell line


title: mESC Day2 Tcf7l1 OE_rep2

description:
Day2_r2
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt

value: Day 2


title: mESC Day2 Tcf7l1 OE_rep3

description:
Day2_r3
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt


title: OPM2_DMSO_rep2


title: OPM2_DMSO_rep1


title: mESC Day1 Tcf7l1 OE_rep2

description:
Day1_r2
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt

value: Day 1


title: 1B neuron, seqment A7, animal 9, cell d225067

value: neuron


title: mESC Day2 Tcf7l1 OE_rep1

description:
Day2_r1
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt


title: 1B neuron, seqment A3, animal 9, cell d225062


title: 1B neuron, seqment A1, animal 9, cell d225063


title: mESC Day1 Tcf7l1 OE_rep3

description:
Day1_r3
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt


title: OPM2_RNAPII

value: RNAPII (Diagenode, C15100055-100)


title: OPM2_GLTSCR1_dBRD9A_rep2

value: GLTSCR1 (Cell Signaling Technology, 45441)


title: mESC Day1 Tcf7l1 OE_rep1

description:
Day1_r1
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt


title: 1B neuron, seqment A3, animal 9, cell d225061


title: mESC Day0 Tcf7l1 OE_rep3

description:
Day0_r3
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt

value: always cultured with doxycycline

value: Day 0


title: OPM2_GLTSCR1_dBRD9A_rep1


title: mESC Day0 Tcf7l1 OE_rep1

description:
Day0_r1
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt


title: mESC Day0 Tcf7l1 OE_rep2

description:
Day0_r2
Normalized_counts.txt
Statistical_significance_scores_of_differential_gene_expression_analysis.txt


title: 1B neuron, seqment A2, animal 9, cell d225060


title: OPM2_GLTSCR1_DMSO_rep2

value: DMSO


title: sample_165_dm

city: Bethesda

first: Iago

last: Pinal-Fernandez

state: MARYLAND

address: 50 South Drive, Room 1142, Building 50, MSC 8024

department: NIAMS

institute: NIH

data_processing:
Demultiplexing with bcl2fastq/2.20.0.
Raw sequencing data was cleaned using fastp/0.21.0.
The abundance of each gene was generated using Salmon/1.5.2.
Quality control output was summarized using multiqc/1.11.
Assembly: hg38
Supplementary files format and content: anonym_counts_hg38.tsv: Tab-delimited text file includes the counts for each sample.

source_name: muscle

extract_protocol:
Trizol
NeoPrep system according to the TruSeqM Stranded mRNA Library Prep protocol (Illumina, San Diego, CA), or with the NEBNext Poly(A) mRNA Magnetic Isolation Module and UltraTM II Directional RNA Library Prep Kit for Illumina (New England BioLabs, ref. #E7490 and #E7760).

value: muscle

tag: diagnosis

value: myositis (DM)


title: 1B neuron, seqment A1, animal 9, cell d225059


title: OPM2_GLTSCR1_DMSO_rep1


title: sample_163_dm


title: sample_164_dm


title: sample_162_dm


title: OPM2_Input_GLTSCR1_DMSO


title: sample_161_dm


title: OPM2_Input_BRD9_dBRD9A


title: sample_160_dm


title: sample_159_dm


title: 1S neuron, seqment A5, animal 8, cell d225057


title: sample_157_dm


title: sample_158_dm


title: OPM2_BRD9_dBRD9A_rep2

value: BRD9 (Cell Signaling Technology, 48306)


title: OPM2_BRD9_dBRD9A_rep1


title: OPM2_Input_BRD9_DMSO


title: sample_156_dm


title: 1S neuron, seqment A5, animal 8, cell d225055


title: OPM2_BRD9_DMSO_rep2


title: 1S neuron, seqment A7, animal 8, cell d225054


title: sample_154_dm


title: sample_155_dm


title: sample_152_imnm

value: myositis (IMNM)


title: 1S neuron, seqment A1, animal 8, cell d225053


title: OPM2_BRD9_DMSO_rep1


title: sample_151_imnm


title: 1S neuron, seqment T1, animal 8, cell d225058


title: 1B neuron, seqment A6, animal 7, cell d225052


title: sample_150_imnm


title: AI-NC-5

city: Guangzhou

first: shuai

last: mao

address: Dade Road

institute: Guangzhou University of Chinese Medicine

description: extracellular vesicles-derived circRNAs-lncRNAs-mRNA

data_processing:
150 bp paired-end reads were mapped to the reference human genome build GRCh38/hg38 by using hisat2.
The reads mapped the genome were calculated using HT-seq.
Differential gene expression analysis was performed using the DESeq2 R-package.
Genome_build: hg38

source_name: plasma

extract_protocol:
extracellular vesicles RNA were isolated by affinity-based binding to spin columns using an exoRNeasy Serum/Plasma kit (Qiagen, Hilden, Germany). RNA libraries were prepared for sequencing using SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian. The RNA was then fragmented chemically into about 100 nucleotides in length using fragmentation buffer (Illumina, Inc.). The RNA was precipitated using the aqueous phase by mixing with isopropyl alcohol. The samples were incubated at 15ºC to 30℃ for 10 minutes and centrifuged at 12,000 x g for 10 minutes at 4℃.
The ribosomal RNA-depleted RNAs were then used to construct RNA libraries with TruSeq Stranded Total RNA Library Prep kit (Illumina, CA, USA). The strand-specific library construction uses dUTP instead of dTTP to label the second-strand cDNA during synthesis. Uracil-DNA glycosylase (UDG) was used to hydrolyze the strand before polymerase chain reaction (PCR) enrichment to ensure that the final sequencing data was from the first cDNA strand.

value: plasma

tag: disease state

value: myocardial infarction patient without cardiac remodeling


title: sample_149_imnm


title: 1B neuron, seqment A7, animal 7, cell d225051

value: M


title: 1S neuron, seqment A7, animal 8, cell d225056


title: sample_148_imnm


title: 1B neuron, seqment T3, animal 7, cell d225050


title: sample_146_imnm


title: AI-NC-3


title: sample_145_imnm


title: AI-NC-2


title: sample_144_imnm


title: 1B neuron, seqment A6, animal 7, cell d225048


title: sample_153_imnm


title: 1B neuron, seqment A2, animal 7, cell d225047


title: sample_141_dm


title: sample_142_dm


title: sample_138_dm


title: sample_139_dm


title: AI-NC-1


title: sample_143_dm


title: sample_140_dm


title: AI-N5

value: normal healthy people


title: sample_137_dm


title: 1B neuron, seqment A3, animal 7, cell d225045


title: 1B neuron, seqment T3, animal 7, cell d225043


title: sample_136_dm


title: AI-N3


title: sample_135_dm


title: AI-N4


title: AI-NC-4


title: AI-N2


title: sample_134_dm


title: sample_133_dm


title: sample_147_imnm


title: 1B neuron, seqment A7, animal 7, cell d225049


title: 1B neuron, seqment A1, animal 7, cell d225041


title: AI-N1


title: 1S neuron, seqment A7, animal 6, cell d225040

value: F


title: sample_131_dm


title: sample_132_dm


title: sample_126_nt

value: normal muscle


title: sample_127_nt


title: sample_125_nt


title: 1S neuron, seqment A8, animal 6, cell d225037


title: 1S neuron, seqment A8, animal 6, cell d225039


title: sample_128_nt


title: AI-C4

value: myocardial infarction patient with cardiac remodeling


title: sample_129_nt


title: AI-C2


title: sample_122_nt


title: sample_123_nt


title: AI-C1


title: AI-C3


title: sample_120_nt


title: sample_124_nt


title: sample_121_nt


title: 1B neuron, seqment A2, animal 7, cell d225042

value: neuron


title: sample_118_nt


title: sample_130_dm


title: sample_117_nt


title: 1S neuron, seqment T2, animal 6, cell d225035


title: 1S neuron, seqment T2, animal 6, cell d225034


title: 1S neuron, seqment A2, animal 6, cell d225033


title: sample_116_nt


title: 1S neuron, seqment A5, animal 6, cell d225036


title: single-cell_TLE_2

city: Nanjing

first: Dijun

state: Jiangsu

address: Xianlin

department: Life Sciences

institute: Nanjing University

data_processing:
Sample demultiplexing, barcode processing, and single cell 3’ gene counting were performed by the Cell Ranger pipelines (v6.0.2,10X Genomics).
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV files with genes and barcode sequences corresponding to row and column indices, respectively.
Supplementary_files_format_and_content: matrix.mtx: Filtered gene-barcode matrix file (demultiplexed)

source_name: Brain

extract_protocol:
Brain were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Single nuclei were captured in the 10×Genomics Chromium Single Cell 3′ Solution, and RNA-seq libraries were prepared following the manufacturer’s protocol (10×Genomics). The libraries were subjected to high-throughput sequencing on an illumina Novaseq6000 platform, and 150-bp paired-end reads were generated.

value: Brain

value: TLE patients

tag: molecule subtype

value: nuclear RNA


title: single-cell_TLE_3


title: AI-C5


title: sample_119_nt


title: 1S neuron, seqment A4, animal 6, cell d225032

tag: strain


title: 1B neuron, seqment A2, animal 5, cell d225031

tag: gender


title: single-cell_TLE_1


title: single-cell_Normal_3

value: non-epileptic control patient


title: single-cell_Normal_2


title: TLE_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

extract_protocol:
Brain were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: single-cell_Normal_1


title: TLE_2


title: TLE_1


title: Normal_3


title: 1B neuron, seqment T2, animal 5, cell d225029


title: 1B neuron, seqment A2, animal 5, cell d225027


title: 1B neuron, seqment A6, animal 5, cell d225026


title: 1B neuron, seqment A5, animal 5, cell d225025


title: 1B neuron, seqment A8, animal 5, cell d225030


title: sample_114_nt


title: sample_106_nt


title: sample_102_nt


title: sample_105_nt


title: sample_107_nt


title: sample_112_nt


title: sample_115_nt


title: sample_103_nt


title: sample_108_nt


title: sample_113_nt


title: sample_111_nt


title: sample_104_nt


title: sample_110_nt


title: sample_109_nt


title: sample_100_nt


title: Normal_2


title: sample_99_nt


title: 1B neuron, seqment A3, animal 5, cell d225024


title: Normal_1


title: 1B neuron, seqment T3, animal 5, cell d225028


title: sample_98_nt


title: 1B neuron, seqment A5, animal 5, cell d225023


title: sample_101_nt


title: 1B neuron, seqment A2 , animal 5, cell d225022


title: 1S neuron, seqment A1, animal 4, cell d225021


title: sample_95_dm


title: sample_97_nt