title: AMB_200630_9mo_2A_3A_1_P4-6-C19-H24


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-H23

status: Public on Dec 29 2025

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: age

value: 9 months

tag: brain region

value: FC

tag: gender

value: M


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-H11


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-H12


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-G23


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-F24


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-G12


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-F23


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-G24


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-I11


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-F12


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-G11


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-E12


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-E24


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-E23


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-D24


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-E11


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-D23


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-D12


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-J12


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-C24


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-D11


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-C23


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-C12


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-C11


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-B24


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-I24


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-B23


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-B12


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-B11


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-A12


title: AMB_200630_9mo_2A_3A_1_P4-6-C19-A24


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title: AMB_200630_9mo_2A_3A_1_P4-2-B4-M3


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title: AMB_200630_9mo_2A_3A_1_P3-3-I6-B18


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title: AMB_200630_9mo_2A_3A_1_P2-6-I17-P23


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-K24


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-L23


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-K12


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-J12


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-K11


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-J23


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-I24


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-I23


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-L11


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-N11


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-J24


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-I12


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-I11


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-H23


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-J11


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-L24


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-G24


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-L12


title: AMB_200630_9mo_2A_3A_1_P2-6-I17-G11


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title: AMB_200630_9mo_2A_3A_1_P2-2-C3-G15


title: AMB_200630_9mo_2A_3A_1_P2-2-C3-F16


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title: AMB_200630_9mo_2A_3A_1_P2-2-C3-E4


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title: AMB_200630_9mo_2A_3A_1_P2-2-C3-D4


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title: AMB_200630_9mo_2A_3A_1_P2-2-C3-E16


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title: AMB_200630_9mo_2A_3A_1_P2-2-C3-A4


title: AMB_200630_9mo_2A_3A_1_P2-2-C3-B15


title: AMB_200630_9mo_2A_3A_1_P2-2-C3-A16


title: AMB_200630_9mo_2A_3A_1_P2-2-C3-A3


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title: AMB_200630_9mo_2A_3A_1_P2-1-E14-N14


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title: AMB_200630_9mo_2A_3A_1_P1-6-I13-K23


title: AMB_200630_9mo_2A_3A_1_P2-1-E14-A13


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title: AMB_200630_9mo_2A_3A_1_P1-6-I13-P24


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title: AMB_200630_9mo_2A_3A_1_P1-5-B12-I22


title: AMB_200630_9mo_2A_3A_1_P1-5-B12-H10


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title: AMB_200630_9mo_2A_3A_1_P1-5-B12-G22


title: AMB_200630_9mo_2A_3A_1_P1-5-B12-G21


title: AMB_200630_9mo_2A_3A_1_P1-5-B12-G10


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title: AMB_200630_9mo_2A_3A_1_P1-5-B12-F22


title: AMB_200630_9mo_2A_3A_1_P1-5-B12-E9


title: AMB_200630_9mo_2A_3A_1_P1-5-B12-F10


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title: AMB_200630_9mo_2A_3A_1_P1-5-B12-E21


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title: AMB_200630_9mo_2A_3A_1_P1-5-B12-D9


title: AMB_200630_9mo_2A_3A_1_P1-5-B12-D22


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title: AMB_200630_9mo_2A_3A_1_P1-5-B12-B9


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title: AMB_200630_9mo_2A_3A_1_P1-5-B12-B22


title: AMB_200630_9mo_2A_3A_1_P1-5-B12-A22


title: AMB_200630_9mo_2A_3A_1_P1-5-B12-B21


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-P8


title: AMB_200630_9mo_2A_3A_1_P1-5-B12-A21


title: AMB_200630_9mo_2A_3A_1_P1-5-B12-A10


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title: AMB_200630_9mo_2A_3A_1_P1-4-D12-N20


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-M7


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-M20


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title: AMB_200630_9mo_2A_3A_1_P1-4-D12-K8


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-L8


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-K20


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-M19


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-L7


title: AMB_200630_9mo_2A_3A_1_P1-5-B12-A9


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-J20


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-K7


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-J19


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-I7


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-I19


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-H8


title: Brain-5xFAD+/- Clec7a cKO

city: Charlottesville

first: Aman

last: Manglamurti

state: Virginia

address: 409 Lane Rd.

department: Neuroscience

institute: University of Virignia

description:
Library name: 5xFAD-Clec7aKO
10x genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger Software was used for demultiplexing, barcode processing, and count generation and aggregation
Assembly: Mouse mm10
Supplementary files format and content: tab separate values and matrix files

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Half brain samples were flash frozen on dry ice and sent to Azenta-GeneWiz for single-nuclei isolation.
Single nuclei were isolated from tissue samples and nuclei suspensions were prepared under RNase-free conditions. Libraries were generated from single nuclei using a droplet-based single-cell/nucleus RNA-seq workflow that incorporates (i) reverse transcription of captured nuclear RNA, (ii) incorporation of nucleus-specific barcodes and unique molecular identifiers (UMIs) during cDNA synthesis, and (iii) PCR amplification of full-length cDNA followed by construction of Illumina-compatible sequencing libraries. Amplified cDNA was fragmented and end-repaired, A-tailed, and ligated to Illumina sequencing adapters and indexes. Final libraries were purified (SPRI bead–based cleanup) and assessed for yield and fragment size distribution (e.g., fluorometric quantification and capillary electrophoresis). Libraries were pooled at equimolar ratios and sequenced on an Illumina HiSeq 2000 platform using paired-end sequencing.

tag: tissue

value: Brain

tag: genotype

value: 5xFAD+/- Cx3cr1ERT2Cre/+ Clec7afl/fl


title: Brain-5xFAD+/-

description:
Library name: 5xFAD
10x genomics

value: 5xFAD+/- Cx3cr1+/+ Clec7afl/fl


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-H7


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-H20


title: 221020-3-1_CD4_day7

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA47277

library_source: transcriptomic

data_processing:
Sequencing was performed on NovaSeq 6000 platform in 151+151 or 101+101 base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 v2.3.5.1.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks v2.2.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
Total RNA was extracted from human cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan). According to the SMART-Seq kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

value: blood

tag: cell type

value: T cell


title: 221020-3-2_CD8_day7

description: Library name: GA47278


title: 221020-3-3_CD14_day7

description: Library name: GA47279

value: monocyte


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-H19


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-L20


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-G8


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-I8


title: 221020-1-2_CD8_day7

description: Library name: GA47275


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-J8


title: 220909_CD14_day1

description: Library name: GA45284


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-K19


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-J7


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-G7


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-G19


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-G20


title: 220909_CD8_day1

description: Library name: GA45283


title: 221020-1-1_CD4_day7

description: Library name: GA47274


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-F8


title: 220909_CD4_day1

description: Library name: GA45282


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-I20


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-F7


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-F20


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-F19


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-E8


title: 221020-1-3_CD14_day7

description: Library name: GA47276


title: input

city: Seoul

first: Yugyeong

last: KIM

address: 84, Heukseok-ro

department: Life science

country: South Korea

institute: Chung-Ang University

description:
Library name: Input
shCDK9_EV

data_processing:
Raw FASTQ files were assessed for quality using FastQC (v0.11.7). Adapter sequences and low-quality bases were trimmed using Trimmomatic (v0.38) with default parameters.
Reads were aligned to the human reference genome (GRCh38/hg38) using Bowtie (v1.1.2) with default settings. Duplicated reads were marked and removed using Picard (v0.118).
Peak calling was performed using MACS2 (v2.1.1) with the cut-off p-value<0.01
The chromosomal distribution of ChIP-seq peaks was visualized using the ChIPseeker R package (v1.26.2).
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: colon

growth_protocol: HCT116 cells were maintained in RPMI 1640 with 10% fetal bivine serum (FBS) and 1% penicillin-streptomycin

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min, followed by addition of 125mM glycine for 5min. Cells were lysed using SDS lysis buffer and then sonicated.
ChIP-seq libraries were prepared using the TruSeq DNA sample preparation kit (Illumina).

value: colon

tag: cell line

value: Colorectal carcinoma

value: CDK9 knockdown

tag: chip antibody


title: CDK9_WT

description:
Library name: CDK9_WT
shCDK9_WT

value: ANTI-FLAG (Sigma, F3165)


title: donor S_primary NK

city: Cleveland

first: Konstantin

last: Leskov

state: OHIO

address: 2109 Adelbert Rd, Wood W200

department: Molecular Biology and Microbiology

institute: Case Western Reserve University School of Medicine

description:
Library name: CWRU006279
10X Genomics

data_processing:
Raw base call (BCL) files were demultiplexed using cellranger mkfastq (10x Genomics, v4.0.0).  Cellranger 8.0.0 was used to for mapping and generation of count tables. Count tables were analyzed using Seurat package for R. Single-cell profiles with a minimum of 500 genes per cell. Predicted doublets were removed (DoubletFinder package for R) resulting in a total of ~275,000 scRNA-Seq/ABseq profiles for the 8 samples (4 participants, 2 samples per participant). Denoising of RNA counts were performed using DecontX package for R.
Assembly: Fastq files were mapped against the GRCh38 human genome reference.
Supplementary files format and content: We used Seurat package for R for gene count normalization, scaling, identifying variable genes, principal component and cluster analysis and UMAP dimensionality reduction. Cell types were predicted by computational mapping to a reference PBMC dataset. Integrated Seurat object is saved in the .rds format.

molecule: polyA RNA

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from buffy coat preparations by density gradient centrifugation using Ficoll-Hypaque (GE Healthcare). Cells were washed with DPBS and cryopreserved in 90% fetal bovine serum (FBS) and 10% dimethyl sulfoxide (DMSO) in liquid nitrogen. Prior to library preparation, PBMCs were thawed, washed, and resuspended in DPBS with 0.04% bovine serum albumin (BSA). ***NK cells were isolated using the NK Cell isolation kit (Stemcell). Cell viability and concentration were assessed using trypan blue and Countess II FL (Thermo Fisher). Approximately 10,000 viable cells per sample were loaded onto a 10x Genomics Chromium Single Cell 3’ Chip (v3.1 chemistry) for gel bead-in-emulsion (GEM) generation and cDNA synthesis. cDNA was amplified by PCR (13 cycles), and sequencing libraries were prepared following the manufacturer's protocol.
Single-cell RNA-seq libraries were prepared according to the manufacturer's protocol (10x Genomics, Chromium Single Cell 3’ v3.1). Briefly, approximately 10,000 viable NK cells per sample were resuspended in the master mix and loaded into a Chromium Single Cell Chip alongside partitioning oil and gel beads to generate gel bead-in-emulsion (GEMs). Polyadenylated RNA from each cell was reverse-transcribed into barcoded cDNA within individual GEMs. Each cDNA molecule incorporated an Illumina R1 primer sequence, a 10x barcode, and a unique molecular identifier (UMI). After reverse transcription, emulsions were broken and the cDNA was purified with Silane DynaBeads. cDNA was then amplified by PCR (13 cycles), and sequencing libraries were prepared using SPRIselect reagent for size selection. During library construction, Illumina R2 primer sequence, P5 and P7 adapters, and a sample index were added to enable paired-end sequencing.

treatment_protocol: NK cells were expanded with C9.K562-mbIL21 aAPCs for 2 weeks.

value: Blood

value: NK cells

tag: treatment

value: not expanded NK cells


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-E7


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-E19


title: donor M_primary NK

description:
Library name: CWRU006278
10X Genomics


title: donor M_expanded NK

description:
Library name: CWRU006276
10X Genomics

value: expanded NK cells (eNK)


title: sample O liver tumor tissues

city: Qingdao

first: Xiongwei

last: Wu

state: Shandong

address: Jiangsu road

country: China

institute: the Affiliated Hospital of Qingdao University

description:
Library name: HB_O_tumor
/

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: hg38
Supplementary files format and content: tab-delimited text files include genecount values for each Sample

source_name: liver tumor

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: liver tumor

value: sample O liver tumor tissues

tag: batch


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-D8

value: 9 months

value: FC

value: M


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-D7


title: sample G liver tumor tissues

description:
Library name: HB_G_tumor
/

value: sample G liver tumor tissues


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-D19


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-D20


title: sample G adjacent non-tumor tissues

description:
Library name: HB_G_normal
/

source_name: adjacent non-tumor tissues

value: adjacent non-tumor tissues

value: sample G adjacent non-tumor tissues


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-C7


title: sample F liver tumor tissues

description:
Library name: HB_F_tumor
/

value: sample F liver tumor tissues


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-C8


title: sample C liver tumor tissues

description:
Library name: HB_C_tumor
/

value: sample C liver tumor tissues


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-C19


title: sample C adjacent non-tumor tissues

description:
Library name: HB_C_normal
/

value: sample C adjacent non-tumor tissues


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-C20


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-B8


title: sample B liver tumor tissues

description:
Library name: HB_B_tumor
/

value: sample B liver tumor tissues


title: sample B adjacent non-tumor tissues

description:
Library name: HB_B_normal
/

value: sample B adjacent non-tumor tissues


title: donor S_expanded NK

description:
Library name: CWRU006277
10X Genomics

value: Blood


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-E20


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-B7


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-B20


title: sample A adjacent non-tumor tissues

description:
Library name: HB_A_normal
/

value: sample A adjacent non-tumor tissues


title: sample A liver tumor tissues

description:
Library name: HB_A_tumor
/

value: sample A liver tumor tissues


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-B19


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-A8


title: sample O adjacent non-tumor tissues

description:
Library name: HB_O_normal
/

value: sample O adjacent non-tumor tissues


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-A7


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-A20


title: sample F adjacent non-tumor tissues

description:
Library name: HB_F_normal
/

value: sample F adjacent non-tumor tissues


title: Polysomeseq NC2

city: Nanjing

first: siyuan

last: jiang

state: Jiangsu

address: sipailou NO2

department: Zhongda Hospital

institute: Southeast University

description:
Library name: Polysome NC biol rep2
RNA-Seq of polysome
TPM of Polysome-Seq.xlsx

library_source: other

data_processing:
Assess the quality of raw reads.
Remove low-quality bases and adapter sequences.
Align trimmed reads to the reference genome.
Quantify gene expression levels.
Identify differentially expressed genes between conditions.
Assembly: hg38
Supplementary files format and content: The xlsx file contains gene counts, differential expression analysis results, including gene identifiers, fold changes, p-values, and adjusted p-values.

molecule: other

source_name: Lung

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

extract_protocol:
Total RNA was extracted using TRIzol reagent following the manufacturer's protocol. For CUT&Tag, nuclei were isolated and tagmented according to the CUT&Tag protocol.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit. CUT&Tag libraries were prepared using the Illumina

treatment_protocol: For knockdown experiments, cells were transfected with siRNA targeting ICAM1 using Lipofectamine RNAiMAX. For knockout experiments, CRISPR-Cas9 was used to generate ICAM1 knockout cell lines.

value: Lung

value: CALU-1 ICAM1 KO

value: Lung adenocarcinoma cells

value: ICAM1 KO

value: plolysome isolation


title: CDK9_K56A

description:
Library name: CDK9_K56A
shCDK9_K56A

value: colon

value: Colorectal carcinoma

value: CDK9 knockdown

value: ANTI-FLAG (Sigma, F3165)


title: Polysomeseq ICAM1 KD1

description:
Library name: Polysome ICAM1 KD biol rep1
RNA-Seq of polysome
TPM of Polysome-Seq.xlsx


title: Polysome input ICAM1 KD

description:
Library name: Polysome input KD
RNA-Seq
TPM of Polysome-Seq.xlsx


title: AMB_200630_9mo_2A_3A_1_P1-4-D12-A19

value: 9 months

value: FC

value: M


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-P6


title: Polysome input NC

description:
Library name: Polysome input NC
RNA-Seq
TPM of Polysome-Seq.xlsx


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-P5


title: Polysomeseq ICAM1 KD2

description:
Library name: Polysome ICAM1 KD biol rep2
RNA-Seq of polysome
TPM of Polysome-Seq.xlsx


title: Polysomeseq NC1

description:
Library name: Polysome NC biol rep1
RNA-Seq of polysome
TPM of Polysome-Seq.xlsx


title: KO ILF2 RIP2

description:
Library name: RIP-KO-ILF2-biol rep2
RNA-Seq of ILF2 RIP
RIP of ILF2 peaks in ICAM1 WT KO Cells.xlsx

value: HCC827 ICAM1 KO

value: Squamous-cell carcinoma

value: RIP by ILF2 antibody


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-P17


title: KO ILF2 RIP1

description:
Library name: RIP-KO-ILF2-biol rep1
RNA-Seq of ILF2 RIP
RIP of ILF2 peaks in ICAM1 WT KO Cells.xlsx


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-O6


title: WT ILF2 RIP2

description:
Library name: RIP-WT-ILF2-biol rep2
RNA-Seq of ILF2 RIP
RIP of ILF2 peaks in ICAM1 WT KO Cells.xlsx

value: wildtype


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-O5


title: KO-Input of RIP

description:
Library name: RIP-KO-Input
RNA-Seq
RIP of ILF2 peaks in ICAM1 WT KO Cells.xlsx


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-O18


title: WT ILF2 RIP1

description:
Library name: RIP-WT-ILF2-biol rep1
RNA-Seq of ILF2 RIP
RIP of ILF2 peaks in ICAM1 WT KO Cells.xlsx


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-O17


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-N5


title: ICAM1 CDS-rep2

description:
Library name: ICAM1 CDS-biol rep2
RNA-seq of ICAM1 CDS OE in ICAM1 KO CALU-1 cells
NC vs ICAM1 OE_Calu-1_fpkm.txt

value: ICAM1 CDS overexpression


title: ICAM1 CDS-rep1

description:
Library name: ICAM1 CDS-biol rep1
RNA-seq of ICAM1 CDS OE in ICAM1 KO CALU-1 cells
NC vs ICAM1 OE_Calu-1_fpkm.txt

value: Lung


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-N18


title: NC2

description:
Library name: NC-biol rep2
RNA-seq of NC KD in ICAM1 KO CALU-1 cells
NC vs ICAM1 OE_Calu-1_fpkm.txt

value: CALU-1 ICAM1 KO

value: NC


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-N17


title: NC1

description:
Library name: NC-biol rep1
RNA-seq of NC in ICAM1 KO CALU-1 cells
NC vs ICAM1 OE_Calu-1_fpkm.txt

value: Lung adenocarcinoma cells

value: ICAM1 KO


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-P18


title: ICAM1 KO-1

description:
Library name: ICAM1 KO-biol rep1
RNA-seq of ICAM1 KO CALU-1 cells
Calu-1 WT and ICAM1 KO or KOKD in KO FPKM.xlsx

value: shNC


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-M6


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-M18


title: Calu1-1-3

description:
Library name: WT-biol rep3
RNA-seq of CALU-1 cells
Calu-1 WT and ICAM1 KO or KOKD in KO FPKM.xlsx


title: ICAM1 KO-2

description:
Library name: ICAM1 KO-biol rep2
RNA-seq of ICAM1 KO CALU-1 cells
Calu-1 WT and ICAM1 KO or KOKD in KO FPKM.xlsx


title: ICAM1 KO-3

description:
Library name: ICAM1 KO-biol rep3
RNA-seq of ICAM1 KO CALU-1 cells
Calu-1 WT and ICAM1 KO or KOKD in KO FPKM.xlsx


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-L6


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-M5


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-M17


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-L5


title: Calu1-1-2

description:
Library name: WT-biol rep2
RNA-seq of CALU-1 cells
Calu-1 WT and ICAM1 KO or KOKD in KO FPKM.xlsx


title: mRNA-seq_NONO-RE_Day15_rep3

city: Shanghai

first: Feizhen

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

institute: Fudan Univ, Shanghai, China

description: Library name: hiPSC-NONO-RE in Day15  rep3

data_processing:
FASTQ format were first processed using Trim Galore (v0.6.4)
The trimmed reads were subsequently aligned to the human reference genome (UCSC hg38) using TopHat (v2.1.1)
Gene expression quantification was performed using Cufflinks (v2.2.1) with default parameters, which assigned the mapped reads to human gene annotations and generated expression abundances in FPKM
The FPKM values were then normalized to TPM
Differentially expressed genes defined as those exhibiting a fold-change greater than 1.5 and a P-value less than 0.05.
Assembly: hg38
Supplementary files format and content: FPKM

source_name: hiPSC

growth_protocol: the hiPSCs were dissociated using Accutase and were cultured on Matrigel-coated plates in mTeSRTM Plus medium.

extract_protocol:
Total RNA was extracted using Trizol (Thermo, 15596018) according to the manufacturer’s protocol
RNA-seq library preparation was performed according to the manufacturer's instructions (Vazyme, TR503-01).

treatment_protocol: the hiPSCs Upon reaching approximately 80% confluence, the cells were split at a ratio of 1:5 using Accutase (Sigma, A6964). We utilized a previously established protocol involving WNT activation and inhibition to differentiate hiPSCs into cardiomyocytes38. Briefly, hiPSCs were seeded and, at 80% confluence, treated with B27 minus insulin (Thermo, A1895601)/RPMI1640 (Thermo, 11875119) plus 7μM CHIR-99021 (Selleck, S1263). Following two days of CHIR99021 treatment, the medium was switched to B27 minus insulin/RPMI1640. After 24 hours, the medium was replaced with B27 minus insulin/RPMI1640 containing 5 μM IWR1 (Selleck, S7086) for two days. Subsequently, IWR1 was removed, and differentiation continued in CDM3 medium containing RPMI640, 50mg/ml BSA (Sigma, A1933), and 213mg/ml ascorbic acid (Sigma, A4544).

value: hiPSC

value: NONO-RE_hiPSCs-derived cardiomyocytes

tag: time

value: NONO-RE


title: Calu1-1-1

description:
Library name: WT-biol rep1
RNA-seq of CALU-1 cells
Calu-1 WT and ICAM1 KO or KOKD in KO FPKM.xlsx


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-L18

value: 9 months


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-L17

value: FC


title: WT-Input of RIP

description:
Library name: RIP-WT-Input
RNA-Seq
RIP of ILF2 peaks in ICAM1 WT KO Cells.xlsx


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-N6

value: M


title: mRNA-seq_NONO-RE_Day15_rep2

description: Library name: hiPSC-NONO-RE in Day15  rep2


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-K6


title: mRNA-seq_NONO-RE_Day15_rep1

description: Library name: hiPSC-NONO-RE in Day15  rep1


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-K5


title: mRNA-seq_NONO-RE_Day9_rep3

description: Library name: hiPSC-NONO-RE in Day9  rep3


title: mRNA-seq_NONO-RE_Day9_rep2

description: Library name: hiPSC-NONO-RE in Day9  rep2


title: mRNA-seq_NONO-RE_Day9_rep1

description: Library name: hiPSC-NONO-RE in Day9  rep1


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-J6


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-J5


title: mRNA-seq_NONO-RE_Day5_rep2

description: Library name: hiPSC-NONO-RE in Day5  rep2


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-J18


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-J17


title: mRNA-seq_NONO-RE_Day2_rep3

description: Library name: hiPSC-NONO-RE in Day2  rep3


title: mRNA-seq_NONO-RE_Day5_rep1

description: Library name: hiPSC-NONO-RE in Day5  rep1


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-I6


title: mRNA-seq_NONO-RE_Day2_rep2

description: Library name: hiPSC-NONO-RE in Day2  rep2


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-I5


title: mRNA-seq_NONO-RE_Day2_rep1

description: Library name: hiPSC-NONO-RE in Day2  rep1


title: mRNA-seq_NONO-KO_Day15_rep2

description: Library name: hiPSC-NONO-KO in Day15  rep2

value: NONO-KO_hiPSCs-derived cardiomyocytes

value: NONO-KO


title: mRNA-seq_NONO-KO_Day15_rep3

description: Library name: hiPSC-NONO-KO in Day15  rep3


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-H6


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-I17


title: mRNA-seq_NONO-KO_Day15_rep1

description: Library name: hiPSC-NONO-KO in Day15  rep1


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-H5


title: mRNA-seq_NONO-KO_Day9_rep3

description: Library name: hiPSC-NONO-KO in Day9  rep3


title: mRNA-seq_NONO-KO_Day9_rep1

description: Library name: hiPSC-NONO-KO in Day9  rep1


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-G6


title: mRNA-seq_NONO-KO_Day5_rep3

description: Library name: hiPSC-NONO-KO in Day5  rep3


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-H17


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-K18


title: mRNA-seq_NONO-KO_Day9_rep2

description: Library name: hiPSC-NONO-KO in Day9  rep2


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-H18


title: mRNA-seq_NONO-RE_Day5_rep3

description: Library name: hiPSC-NONO-RE in Day5  rep3


title: mRNA-seq_NONO-KO_Day5_rep2

description: Library name: hiPSC-NONO-KO in Day5  rep2


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-K17


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-G18


title: mRNA-seq_NONO-KO_Day5_rep1

description: Library name: hiPSC-NONO-KO in Day5  rep1


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-I18


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-G17


title: mRNA-seq_NONO-KO_Day2_rep3

description: Library name: hiPSC-NONO-KO in Day2  rep3


title: mRNA-seq_NONO-KO_Day2_rep1

description: Library name: hiPSC-NONO-KO in Day2  rep1


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-F6


title: mRNA-seq_WT_Day15_rep3

description: Library name: hiPSC-WT in Day15  rep3

value: hiPSCs-derived cardiomyocytes

value: WT


title: mRNA-seq_NONO-KO_Day2_rep2

description: Library name: hiPSC-NONO-KO in Day2  rep2


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-G5


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-F18


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-E6


title: mRNA-seq_WT_Day15_rep1

description: Library name: hiPSC-WT in Day15  rep1


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-F17


title: mRNA-seq_WT_Day9_rep3

description: Library name: hiPSC-WT in Day9  rep3


title: mRNA-seq_WT_Day9_rep2

description: Library name: hiPSC-WT in Day9  rep2


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-E17


title: mRNA-seq_WT_Day15_rep2

description: Library name: hiPSC-WT in Day15  rep2


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-D6


title: mRNA-seq_WT_Day9_rep1

description: Library name: hiPSC-WT in Day9  rep1


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-D5


title: mRNA-seq_WT_Day5_rep3

description: Library name: hiPSC-WT in Day5  rep3


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-E5


title: mRNA-seq_WT_Day5_rep1

description: Library name: hiPSC-WT in Day5  rep1


title: mRNA-seq_WT_Day2_rep3

description: Library name: hiPSC-WT in Day2  rep3


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-D17


title: mRNA-seq_WT_Day2_rep2

description: Library name: hiPSC-WT in Day2  rep2


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-C5


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-D18


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-C6


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-F5


title: mRNA-seq_WT_Day2_rep1

description: Library name: hiPSC-WT in Day2  rep1


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-C17


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-E18


title: primary CLL cells sample 3

city: Paris

first: Wail

last: Zeitouni

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description:
Library name: CLL_3
10x genomics

data_processing:
CellRanger software v7.1.0 was used with default parameters for read alignment and unique molecular identifier (UMI) quantification.
Assembly: Human GRCh38
Supplementary files format and content: raw_counts.tsv: Tab-seperated matrix file.
Supplementary files format and content: metadata.tsv: Tab-seperated values file.

growth_protocol: Viably cryopreserved (90%SVF;10%DMSO)  peripheral blood mononuclear cells (PBMCs) from CLL patients

extract_protocol:
Propidium iodide (PI)-negative cells were sorted using flow cytometry.
Single-cell library prep was realized with chromium from 10X Genomics. Chromium Next GEM Single Cell 3' GEM kit and Chip G were used, following manufacturer’s recommendations. 20000 cells were loaded on the chromium and sequenced on Novaseq 6000 ILLUMINA. Using SP-100 cycles cartridge from ILLUMINA (2*800Millions of reads), calculations are based on 40000 reads/cell per sample.

value: Blood

value: PBMC


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-B5


title: primary CLL cells sample 5

description:
Library name: CLL_5
10x genomics


title: primary CLL cells sample 2

description:
Library name: CLL_2
10x genomics


title: mRNA-seq_WT_Day5_rep2

description: Library name: hiPSC-WT in Day5  rep2


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-B18


title: T98G cells, ETC-501, rep3

city: Singapore

first: Giselle

last: Nah

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

data_processing:
RNA-seq reads were mapped by STAR to the human reference genome GRCh38 with reference gene annotation GENCODE 41. Reads with low mapping quality <20 were not used for further analysis.
PCR duplicates were removed in the paired-end alignments using SAMtools
Gene expression levels of individual genes/transcripts were generated using featureCounts
Cross-sample normalization of reads counts was based on total mappable counts using RPKM
Assembly: GRCh38
Supplementary files format and content: tab delimited text files includes gene names and normalized RPKM vaues

growth_protocol: LN229 and T98G cells were maintained in DMEM and MEM respectively, supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using the Direct-zol RNA Microprep kit (Zymo Research). 1.47 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra Directional RNA Library Prep Kit following manufacturer's protocol.

treatment_protocol: Cells were treated with DMSO or 5 µM ETC-501 for 5 hours

value: Glioblastoma


title: primary CLL cells sample 1

description:
Library name: CLL_1
10x genomics


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-A6


title: T98G cells, ETC-501, rep2


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-A5


title: T98G cells, DMSO, rep3

value: DMSO


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-A17


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-A18


title: T98G cells, ETC-501, rep1


title: T98G cells, DMSO, rep2


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-P4


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-C18


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-P16


title: LN229 cells, ETC-501, rep2


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-P3


title: LN229 cells, ETC-501, rep3


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-P15


title: T98G cells, DMSO, rep1


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-B6


title: primary CLL cells sample 4

description:
Library name: CLL_4
10x genomics


title: LN229 cells, ETC-501, rep1


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-O4


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-O3


title: LN229 cells, DMSO, rep3


title: LN229 cells, DMSO, rep2


title: AMB_200630_9mo_2A_3A_1_P1-3-C20-B17


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-O15


title: ICAM1-AS KD2-2

description:
RNA-seq of ICAM1-AS KD in ICAM1 KO CALU-1 cells
Calu-1 ICAM1 KD in KO FPKM.xlsx
ko-sg2_vs_ko-puro_diff.xls

value: Lung

value: CALU-1 ICAM1 KO

value: Lung adenocarcinoma cells

value: ICAM1-AS KD in KO cells


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-N3


title: ICAM1-AS KD2-1


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-N4


title: ICAM1 KD2-3

description:
RNA-seq of ICAM1 KD in ICAM1 KO CALU-1 cells
Calu-1 ICAM1 KD in KO FPKM.xlsx
ko-sh2_vs_ko-puro_diff.xls

value: ICAM1 KD in KO cells


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-N15


title: ICAM1 KD2-2


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-N16


title: ICAM1-AS KD1-2

description:
RNA-seq of ICAM1-AS KD in ICAM1 KO CALU-1 cells
Calu-1 ICAM1 KD in KO FPKM.xlsx
ko-sg1_vs_ko-puro_diff.xls


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-M4


title: ICAM1 KD2-1


title: ICAM1-AS KD1-1


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-M16


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-M15


title: ICAM1 KD1-3

description:
RNA-seq of ICAM1 KD in ICAM1 KO CALU-1 cells
Calu-1 ICAM1 KD in KO FPKM.xlsx
ko-sh1_vs_ko-puro_diff.xls


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-L4


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-M3


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-L3


title: ICAM1 KD1-2


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-O16


title: LN229 cells, DMSO, rep1


title: siKAT7_input-1

city: Tokyo

first: Takao

last: Fujisawa

address: 7-3-1, Hongo, Bunkyo-ku

institute: The University of Tokyo

description: Library name: sample15

data_processing:
Sequence reads were trimmed for adaptor sequence/lowquality sequence using trim-galore (parameters: default, version 0.6.7).
Raw paired-end 150 bp reads were aligned to the reference genome (hg38  or mm10) using HISAT2 (version 2.2.1).
Bigwig files were generated using deeptools(version 3.5.1)
Assembly: hg38
Supplementary files format and content: Bigwig

source_name: HeLa

extract_protocol:
Cells were fixed with 4% formaldehyde. Chromatin samples were prepared using a SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9003).
DNS libraries for ChIP-seq were prepared using NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB, E6420) and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs Set 2) (NEB, E6446S).

value: HeLa

value: siRNA KAT7


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-L16

value: 9 months

value: FC


title: siKAT7_H3K14ac-2

description: Library name: sample14


title: siKAT7_H3K14ac-1

description: Library name: sample13


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-L15

value: M


title: siKAT7_input-2

description: Library name: sample16


title: ICAM1 KD1-1


title: RNA_Nodule_10wpi_3

city: Davis

first: Patricia

last: Baldrich Gonzalez

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

description: Library name: 54

data_processing:
We sent all sRNA and RNAseq libraries for sequencing to the University of Delaware Sequencing and Genotyping Center, where they were sequenced on a NovaSeq2000 instrument using 50-bp single-end reads for sRNA and 75-bp paired-end reads for RNAseq.
For sRNA libraries we first trimmed the adaptors using Cutadapt version 1.16 using a minimum insert size of 10 nt and no maximum. We assessed sequence quality using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/ fastqc/). We aligned clean reads to the Soybean W82 genome v4 and all subsequent analyses were performed using the software Bowtie2. For miRNA analyses, we used the latest version of miRBase (version 22).
For RNA-seq libraries were analyzed using HiSat2 and Stringtie pipeline, and the Soybean W82 genome v4 annotation file.
Assembly: Soybean W82 genome v4
Supplementary files format and content: small RNA seq.: microRNA count files
Supplementary files format and content: RNAseq.: gtf count files

organism: Glycine max

source_name: Nodule

growth_protocol: All plants were cultivated in pots within the greenhouse facilities at the Donald Danforth Plant Science Center (St. Louis, Missouri, USA). They were subjected to a 14/10 hour light/dark cycle and maintained at temperatures of 25/20°C, respectively. Soybean seeds (Glycine max cv. Williams-82) were sown into 1-gallon pots (two seeds per pot) containing a pre-rinsed substrate, consisting of a three to one ratio of vermiculite:perlite (3:1). Plants were well-watered and fertilized regularly via Dosatron with reverse osmosis water and B&D nutrient solution for growing legumes (with the addition of minimal nitrogen - 0.5mM KNO3) (Broughton and Dilworth 1971). The lesser of the two plantlets was sacrificed following the seven-day germination period. Seven-day-old seedlings were then inoculated with 5ml of Bradyrhizobium diazoefficiens USDA110 diluted to 0.05 OD600nm. B. diazoefficiens USDA110 (USDA-ARS culture collection, NRRL B-4361) was grown aerobically at 28°C in HM liquid medium at 6.8 pH prior to inoculation (Tóth et al. 2016). Soybean (Glycine max cv. Williams-82) seed stocks used in this research were generated from seeds gifted by Doug Allen of the Donald Danforth Plant Science Center (St. Louis, Missouri, USA). Bradyrhizobium diazoefficiens USDA110 strain gifted by Gary Stacey of the University of Missouri – Columbia (Columbia, Missouri, USA)

extract_protocol:
Frozen nodules were manually ground using pre-chilled (liquid N2) mortar and pestles. Ground tissue was further pulverized using a MM400 tissuelyzer (Retsch, Germany): 2x 45 sec at 30 Hz. Total nodule RNA was extracted using TRIreagent (Ambion, USA), following manufacturer’s instructions plus additional isopropanol rinse to remove the remaining polysaccharides (Protocol 1: Soybean Nodule RNA Extraction).
sRNA libraries were constructed using the RealSeq-AC kit version 2 (Realseq Biosciences, Santa Cruz, CA, catalog no. 500-00048;) as per the manufacturer’s instructions. For RNAseq libraries, we used NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, catalog no. E7760L) protocol.

treatment_protocol: Soybean root nodules, aged 2 wpi to 10 wpi, were harvested weekly, typically between 9 and 10 am. Nodules were carefully collected in 2ml screw cap tubes, immersed in liquid nitrogen, and promptly stored at -80oC. Each technical replicate (TR) comprised of three nodules in close proximity to the root crown of a single plant. One biological replicate (BR) corresponded to one plant. For each BR, we collected four TRs to facilitate RNA and protein extractions.

value: Nodule

tag: weeks post_inoculation

value: Williams 82

value: Inoculated with Bdi USDA110


title: siCtrl_input-2

description: Library name: sample12

value: siRNA non-targeting


title: siCtrl_input-1

description: Library name: sample11


title: siCtrl_H3K14ac-2

description: Library name: sample10


title: RNA_Nodule_10wpi_1

description: Library name: 52


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-K4


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-K3


title: siCtrl_H3K14ac-1

description: Library name: sample9


title: RNA_Nodule_9wpi_3

description: Library name: 51


title: RNA_Nodule_9wpi_2

description: Library name: 50


title: ZD_input-2

description: Library name: sample8

value: Zinc-deficeint medium for 48 hours


title: ZD_input-1

description: Library name: sample7


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-K16


title: ZD_H3K14ac-2

description: Library name: sample6


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-K15


title: RNA_Nodule_9wpi_1

description: Library name: 49


title: ZN_input-2

description: Library name: sample4

value: Normal medium


title: RNA_Nodule_8wpi_3

description: Library name: 48


title: ZN_input-1

description: Library name: sample3


title: ZN_H3K14ac-2

description: Library name: sample2


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-J4


title: RNA_Nodule_8wpi_2

description: Library name: 47


title: RNA_Nodule_10wpi_2

description: Library name: 53


title: AMB_200630_9mo_2A_3A_1_P1-2-H14-J3


title: ZN_H3K14ac-1

description: Library name: sample1


title: RNA_Nodule_8wpi_1

description: Library name: 46