title: Replicate 1 L1 F4+3 fed

description:
Table 2 Transcriptome Analysis Control vs F4+3 – All Genes and Groups
S3_N2_L1_SF


title: ACCLM_NICDKD_3A

status: Public on Mar 09 2023

type: SRA

city: peking

first: kong

last: lu

address: capital medical university

country: China

institute: ccmu

library_source: transcriptomic

data_processing:
A total of 18 samples were tested using the DNBSEQ platform, with an average yield of 1.19G data per sample. The average alignment ratio of the sample comparison genome was 94.90%, which was comparative The average alignment of the gene set was 80.35%; a total of 18782 genes were detected.
Reference Genome Version：GCF_000001405.39_GRCh38.p13
The raw data for sequencing contains reads of low quality, adaptor contamination, and excessively high levels of unknown base N. These reads need to be removed before data analysis to ensure the reliability of the results. For the quality index of filtered reads, see the filtered reads quality statistics table and the raw data filtering component statistics chart. For the base content distribution and quality distribution, see the base content distribution chart of clean reads and the base quality distribution chart of clean reads.
After getting clean reads, we used HISAT to align the clean reads to the reference genome. The alignment results are shown as follows.Align clean reads to the reference genes by using Bowtie2 to get the alignment result.

molecule: total RNA

organism: Homo sapiens

source_name: salivary adenoid cystic carcinoma

extract_protocol: RNA extracted from 1×10^7 cells in 1 mL TRIZOL reagen

tag: tissue

value: salivary adenoid cystic carcinoma

tag: genotype

value: NICD knockdown


title: ACCLM_NICDKD_1A


title: Replicate 1 L1 Control starved

city: New YorK

first: Columbia

middle: Carlotta

last: University

state: NEW YORK

address: 1212 Amsterdam Avenue

department: Biological Sciences

country: USA

institute: HHMI/Columbia University

description:
Table 2 Transcriptome Analysis Control vs F4+3 – All Genes and Groups
S2_N2_L1_FS

data_processing:
Alignment to WS220 using subread package and featurecounts
differential gene expression analysis was done using DESeq2
Assembly: WS220
Supplementary files format and content: Table 1 Transcriptome Analysis Parental Control vs F4 – All Genes and Groups contains all transripts with normalized counts for each sample from the D1 adults. Statistics for all comparisons are included
Supplementary files format and content: Table 2 Transcriptome Analysis Control vs F4+3 – All Genes and Groups contains all transripts with normalized counts for each sample from the L1 animals. Statistics for all comparisons are included

organism: Caenorhabditis elegans

source_name: whole worm (n~10000)

extract_protocol:
Animals were collected at the respective stage as described above. At the time of collection, animals were washed off the plate with M9, washed 3x with M9, mechanically homogenized in TRIzolusing disposable tissue grinder  ).  Total RNA was isolated using RNeasy Minelute kit according to manufacturer (Qiagen).
RNA-seq libraries were prepped using the Ovation Universal RNA-seq kit (Nugen) according to manufacters instructions

tag: strain

value: strain N2

tag: developmental stage

tag: current nutritional status

value: starved

tag: own or ancestral l1 experience

value: fed (ancestral)


title: PBS-10-4

city: New York

first: David

middle: C

last: Lyden

state: NY

address: 413 East 69th Street, Room BB1228

department: Cell and Developmental Biology

institute: Weill Cornell Medicine

description: This PBS group was used as control for the B16F10_exomeres,  B16F10_Exo-S, and B16F10_Exo-L group, respectively

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing
RNA reads were aligned and mapped to the mm9 mouse reference genome by TopHat2 (Version2.0.11)
Transcriptome reconstruction was performed by Cufflinks (Version 2.1.1), and the abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM)
Gene expression profiles were constructed for differential expression, cluster, and principal component analyses with the DESeq2 package
For differential expression analysis, pairwise comparisons between two or more groups using parametric tests where read-counts follow a negative binomial distribution with a gene-specific dispersion parameter. Corrected p-values were calculated based on the Benjamini-Hochberg method to adjusted for multiple testing.
Assembly: mm9
Supplementary files format and content: Excel file with Log2FC, p-value and q-value for each gene expressed in the livers from tumor-bearing or EVP-educated mice, compared to their respective controls.

organism: Mus musculus

source_name: Liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen. Total RNA was extracted using TRIzol reagent, and RNA was further purified using RNeasy Mini kit including a DNase digest following the manufacturer’s instructions
RNA libraries were prepared using TruSeq Stranded mRNA Library Preparation (Illumina) following the manufacturer’s instructions

value: Liver

tag: treatment

value: Intravenous injection of 100 ul of PBS every other day for 4 weeks


title: PBS-10-3


title: PBS-10-2


title: Replicate 3 Day1Adult L1 starved sterile

description:
Table 1 Transcriptome Analysis Parental Control vs F4 – All Genes and Groups
S9_N2_D1Ad_F4_noEggs

source_name: whole worm (n~100)

value: Developmental stage Day 1 Adult

value: fed

value: starved (own)


title: ACCLM_MYB_KD_3A

value: MYB knockdown


title: Replicate 1 L1 Control fed

description:
Table 2 Transcriptome Analysis Control vs F4+3 – All Genes and Groups
S1_N2_L1_FF


title: B16F10_Exo-L-4

value: Intravenous injection of 10 ug of B16F10_Exo-L in 100 ul of PBS every other day for 4 weeks


title: ACCLM_MYB_KD_2A


title: RNA_seq_Sham_2

city: Shanghai

first: Zengyu

last: Zhang

state: Shanghai

address: Dong'an Road

department: Neurology

institute: Fudan University

data_processing:
Raw data were first evaluated by FastQC for quality control to determine whether the sequencing data were suitable for subsequent analyses.
Adapter sequences, low-quality reads, and too short reads were removed from raw data with Trim-galore to obtain clean data.
Sequencing reads were aligned to annotated RefSeq genes in the mouse reference genome (UCSC mm10) with HISAT2. And Samtools v1.9 was used to sort and build the alignment file index.
A gene count matrix that contained raw transcript counts for each annotated gene were generated using the featureCounts v1.6.3.
To determine the most appropriate threshold for removing genes with low counts, we relied on the automatic and independent filtering performed by DESeq2 R package (1.16.1). And raw transcript counts were normalized, log2 transformed, and analyzed using the default procedures in DESeq2 to identify genes that were differentially regulated following CCH.
Assembly: mm10
Supplementary files format and content: raw gene counts text files

source_name: brain

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water

extract_protocol:
RNA was harvested using the TRIzol Reagent (Life technologies, California, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol:
The control group was exposed to sham operation
The experimental group was exposed to bilateral carotid artery stenosis (BCAS) operation

tag: cell line

value: brain

tag: cell type

value: right cerebral cortex

value: WT

value: Sham operation

tag: time

value: 3 weeks


title: 41C [0_Yu_YL60_051909]

type: RNA

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

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

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

data_processing: The data were normalized by RMA with Partek Genomics Suite 6.6.

label: biotin

label_protocol:
mRNA is converted to cDNA and amplified using NuGEN pico amplification kit.
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Cell lines were compared under four conditions (16 C, 24C, 40C, 41C).

value: Melanoma cell line

tag: condition


title: Replicate 3 Day1Adult L1 starved fertile

description:
Table 1 Transcriptome Analysis Parental Control vs F4 – All Genes and Groups
S8_N2_D1Ad_F4_withEggs


title: Replicate 3 Day1Adult Control always fed

description:
Table 1 Transcriptome Analysis Parental Control vs F4 – All Genes and Groups
S7_N2_D1Ad_Ctrl

value: fed (own)


title: ACCLM_MYB_KD_1A

value: salivary adenoid cystic carcinoma


title: 24C [0_Yu_YL57_051909]


title: ACCLM_Double_KD_2A

value: MYB knockdown and NICD knockdown


title: 41C [0_Yu_YL58_051909]


title: Replicate 2 Day1Adult L1 starved sterile

description:
Table 1 Transcriptome Analysis Parental Control vs F4 – All Genes and Groups
S6_N2_D1Ad_F4_noEggs

value: strain N2


title: B16F10_Exo-L-2

value: Liver


title: ACCLM_Double_KD_1A


title: Replicate 2 Day1Adult L1 starved fertile

description:
Table 1 Transcriptome Analysis Parental Control vs F4 – All Genes and Groups
S5_N2_D1Ad_F4_withEggs


title: B16F10_Exo-L-1


title: 24C [0_Yu_YL56_051909]


title: Replicate 2 Day1Adult Control always fed

description:
Table 1 Transcriptome Analysis Parental Control vs F4 – All Genes and Groups
S4_N2_D1Ad_Ctrl


title: PBS-10-1

value: Intravenous injection of 100 ul of PBS every other day for 4 weeks


title: B16F10_Exo-S-4

value: Intravenous injection of 10 ug of B16F10_Exo-S in 100 ul of PBS every other day for 4 weeks


title: ACC83_WT_3A


title: 24C [0_Yu_YL55_051909]


title: 41C [0_Yu_YL59_051909]


title: ACCLM_Double_KD_3A


title: 40c [0_Yu_YL51_051909]


title: 40c [0_Yu_YL50_051909]


title: ACC83_WT_2A


title: B16F10_Exo-S-3


title: B16F10_Exo-L-3


title: 16C [0_Yu_YL30_011509]


title: B16F10_Exo-S-2


title: 40c [0_Yu_YL49_051909]


title: ACC83_WT_1A


title: Replicate 1 Day1Adult L1 starved sterile

description:
Table 1 Transcriptome Analysis Parental Control vs F4 – All Genes and Groups
S3_N2_D1Ad_F4_noEggs

value: Developmental stage Day 1 Adult

value: fed


title: Replicate 1 Day1Adult Control always fed

description:
Table 1 Transcriptome Analysis Parental Control vs F4 – All Genes and Groups
S1_N2_D1Ad_Ctrl


title: 16C [0_Yu_YL29_011509]


title: ACC83_MYBCDNA_3A

value: MYB OE


title: B16F10_Exo-S-1


title: ACC83_MYBCDNA_1A


title: ACC83_MYBCDNA_2A


title: B16F10_exomeres-3

value: Intravenous injection of 10 ug of B16F10_exomeres in 100 ul of PBS every other day for 4 weeks


title: B16F10_exomeres-2


title: RNAseq, regeneration tips 24hrs, DMSO, Rep3

city: Pune

first: Sanjeev

last: Galande

state: Maharashtra

address: Dr. Homi bhabha road, Pashan

department: Biology

country: India

institute: IISER Pune

data_processing:
Sequences were trimmed using trimmomatic
Trimmed sequences were aligned using the hisat2 aligner to the Hydra 2.0 genome (available at https://research.nhgri.nih.gov/hydra/download/assembly/Hm105_Dovetail_Assembly_1.0.fa.gz)
Read counts were extracted using htseq-count.

organism: Hydra vulgaris

source_name: regenerating tips

growth_protocol: A clonal culture of Hydra vulgaris Ind-Pune was maintained at 18°C in Hydra medium (HM) (100 µM KCl, 100 µM MgSO4.7H2O, 1 mM CaCl2.2H2O, 1 mM Tris (pH-8.0), 1 mM NaCl) using standard protocols described previously (Horibata et al. 2004). Hydra polyps were fed with freshly hatched Artemia nauplii larvae daily and cleaned 6–8 h post-feeding.

extract_protocol:
The polyps were decapitated, and the regenerating tips were collected at 0 hpa, 3 hpa, 8 hpa, 12 hpa, and 24 hpa. RNA was isolated using Trizol.
The isolated RNA was used to perform 3’ mRNA sequencing using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Austria) according to the manufacturer’s instructions.

treatment_protocol: Control set polyps were treated with 0.2% DMSO and treament set was done in 150 mM UNC0379 inhibitor.

value: regenerating tips

value: Ind-Pune

value: DMSO


title: RNAseq, regeneration tips 24hrs, DMSO, Rep2


title: Replicate 1 Day1Adult L1 starved fertile

description:
Table 1 Transcriptome Analysis Parental Control vs F4 – All Genes and Groups
S2_N2_D1Ad_F4_withEggs

value: starved (own)


title: PBS-8-5

description: This PBS group was used as control for the B16F10-CL-EVPs group


title: PBS-8-4


title: A375_RAC1P29S_2

city: Iowa City

first: Eliot

last: Zhu

state: IA

address: 376 Newton Road

department: Anatomy and Cell Biology

institute: The University of Iowa

data_processing:
Transcript alignment/quantification was performed with Kallisto using default settings
Ensembl annotation v86 was used to annotate transcripts using tximport R package
Deseq2 with default settings was used to generated normalized counts
Assembly: GRch38 Ensembl 86
Supplementary files format and content: text files contain Deseq2 normal transformed counts

source_name: tumor

growth_protocol: DMEM, 10% FBS, Penn/Strep

extract_protocol:
monarch Total RNA miniprep kit
Illumina TruSeq

value: tumor

value: melanoma cells

value: empty vector


title: A375_RAC1P29S_3


title: A375_RAC1P29S_1


title: RNAseq, regeneration tips 12hrs, DMSO, Rep3


title: RNAseq, regeneration tips 12hrs, DMSO, Rep2


title: A375_E_3


title: PBS-8-3


title: RNAseq, regeneration tips 24hrs, DMSO, Rep1


title: B16F10_exomeres-4


title: 16C [0_Yu_YL28_011509]

value: Melanoma cell line


title: UM-Chor1 cells, sg-ADAR-1

city: Cambridge

first: Tanaz

last: Sharifnia

state: MA

address: 415 Main Street

department: Chemical Biology and Therapeutics Science Program

institute: Broad Institute

data_processing:
Sequenced reads were aligned to the UCSC hg38 reference genome assembly, and gene counts were quantified using STAR (v2.7.3a).
Assembly: hg38
Supplementary files format and content: Comma-separated files containing read counts and transcript-per-million (TPM) values per gene for all samples.

growth_protocol: UM-Chor1 cells were maintained in IMDM/RPMI (4:1) media + 10% fetal bovine serum (FBS) and 1X non-essential amino acids.

extract_protocol:
Total RNA was extracted from cells using an RNeasy kit (Qiagen).
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200 ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7. The finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance. The final pool was sequenced on an Illumina NovaSeq 6000 targeting 40 million 100-base pair read pairs per library.

treatment_protocol: UM-Chor1 cells stably expressing Cas9 were seeded at a density of 300,000 cells/well in 6-well collagen I-coated plates. The next day, media was replaced with media containing lentivirus corresponding to the lentiGuide-Puro plasmid (Addgene #52963), encoding the sgRNA of interest (sg-EGFP, sg-ADAR-1, or sg-ADAR-2), in the presence of 8 µg/mL polybrene. Cells were spin-infected at 2,000 rpm for 30 min at 30°C. Following spin-infection, media was replaced with standard growth media and cells were incubated at 37°C overnight. The next day (at least 24 h post-infection), media was replaced with selective media containing 1 µg/mL puromycin. Following selection for infected cells, selective growth media was replaced with standard growth media. One day post-media-change (6 d post-transduction), cells were harvested.

value: chordoma cell line


title: UM-Chor1 cells, sg-ADAR-2


title: A375_E_2


title: PBS-8-2


title: UM-Chor1 cells, sg-EGFP

value: sg-EGFP-expressing


title: A375_E_1


title: PBS-8-1

value: Liver


title: CAR-T dataset, sort CD3, T cell subset bone marrow [CART_9_P1883]

city: Calgary

first: Nizar

last: Bahlis

state: Alberta

address: 3330 Hospital Dr NW HMRB328

department: Divisions of Hematology and Oncology

country: Canada

institute: University of Calgary

description:
10x Genomics 3' scRNA
CART_9_P1883

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1
Assembly: GRCh38
Supplementary files format and content: Filtered_feature_bc_matrix.h5 for bam files

molecule: polyA RNA

source_name: T cells

extract_protocol:
Serial blood samples and BM aspirates were collected from patients treated with anti-BCMA TCE or CAR T at variable time points, prior and post initiation of therapy and at relapse. Bone marrow mononuclear fractions were isolated through Ficoll density gradients coupled with magnetic sorting of CD3+ T cells.
Library was performed according to the manufacter’s instructions (TCE samples: 5' single cell RNA/VDJ v1.1, 10x Genomics; CAR-T samples: 3' scRNA version 3.1,  10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: human bone marrow mononuclear cells

value: T cells

value: relapsed-refractory multiple myeloma


title: RNAseq, regeneration tips 8hrs, DMSO, Rep3


title: CAR-T dataset, sort CD3, T cell subset bone marrow [CART_7_P1895]

description:
10x Genomics 3' scRNA
CART_7_P1895


title: RNAseq, regeneration tips 8hrs, DMSO, Rep2


title: A375_VAV1_SRCi_3

value: VAV1 overexpression

value: saracatinib


title: B16F10_exomeres-1

value: Intravenous injection of 10 ug of B16F10_exomeres in 100 ul of PBS every other day for 4 weeks


title: B16F10-CL-EVPs-5

value: Intravenous injection of 10 ug of B16F10-CL-EVPs in 100 ul of PBS every other day for 4 weeks


title: CAR-T dataset, sort CD3, T cell subset bone marrow [CART_5_P1759]

description:
10x Genomics 3' scRNA
CART_5_P1759


title: CAR-T dataset, sort CD3, T cell subset bone marrow [CART_8_P2164]

description:
10x Genomics 3' scRNA
CART_8_P2164


title: A375_VAV1_SRCi_2


title: RNAseq, regeneration tips 12hrs, DMSO, Rep1

value: regenerating tips

value: Ind-Pune


title: B16F10-CL-EVPs-4


title: B16F10-CL-EVPs-3


title: CAR-T dataset, sort CD3, T cell subset bone marrow [CART_4_P2334]

description:
10x Genomics 3' scRNA
CART_4_P2334


title: A375_VAV1_SRCi_1


title: CAR-T dataset, sort CD3, T cell subset bone marrow [CART_3_P2106]

description:
10x Genomics 3' scRNA
CART_3_P2106


title: RNAseq, regeneration tips 3hrs, DMSO, Rep2

value: DMSO


title: A375_VAV1_VEH_3

value: tumor

value: vehicle


title: RNAseq, regeneration tips 3hrs, DMSO, Rep3


title: A375_VAV1_VEH_2

value: melanoma cells


title: CAR-T dataset, sort CD3, T cell subset bone marrow [CART_2_P1907]

description:
10x Genomics 3' scRNA
CART_2_P1907


title: RNAseq, regeneration tips 3hrs, DMSO, Rep1


title: A375_VAV1_VEH_1


title: CAR-T dataset, sort CD3, T cell subset bone marrow [CART_1_P1912]

description:
10x Genomics 3' scRNA
CART_1_P1912


title: CAR-T dataset, sort CD3, T cell subset bone marrow [CART_6_P1705]

description:
10x Genomics 3' scRNA
CART_6_P1705


title: RNAseq, regeneration tips 8hrs, DMSO, Rep1


title: A375_E_VEH_3

value: empty vector


title: B16F10-CL-EVPs-2


title: PT19_late_relapse,non_responder,  sort CD3, T cell subset bone marrow, scVDJseq [PT19_P2202_VDJ]

description:
10x Genomics 5' VDJ
PT19_P2202_VDJ

tag: subject id/time_point

tag: subject group


title: RNAseq, regeneration tips 0hr, DMSO, Rep2


title: RNAseq, regeneration tips 0hr, DMSO, Rep3


title: PBS-7-3

description: This PBS group was used as control for the K7M2-TE-EVPs and K7M2-CL-EVPs group, respectively

value: BALB/c

value: Intravenous injection of 100 ul of PBS every other day for 4 weeks


title: A375_E_VEH_2


title: RNAseq, regeneration tips 0hr, DMSO, Rep1


title: PT19_late_relapse, non_responder,sort CD3, T cell subset bone marrow, scRNAseq [PT19_P2202_RNA]

description:
10x Genomics 5' scRNA
PT19_P2202_RNA


title: A375_E_VEH_1


title: K7M2-CL-EVPs-2

value: Liver

value: Intravenous injection of 10 ug of K7M2-CL-EVPs in 100 ul of PBS every other day for 4 weeks


title: K7M2-CL-EVPs-3


title: PT19_pre, non_responder, sort CD3, T cell subset bone marrow, scRNAseq [PT19_P1950_RNA]

description:
10x Genomics 5' scRNA
PT19_P1950_RNA

value: human bone marrow mononuclear cells

value: T cells


title: PBS-7-1


title: PT19_pre, non_responder, sort CD3, T cell subset bone marrow, scVDJseq [PT19_P1950_VDJ]

description:
10x Genomics 5' VDJ
PT19_P1950_VDJ

value: relapsed-refractory multiple myeloma


title: HCT116-shSCR-2

city: Wuhan

first: xie

last: ting

address: Donghu road

institute: Wuhan University

description: RNA-seq

data_processing:
RNA-seq reads quality was evaluated using FastQC and mapped to the human genome reference assembly (hg38) using HISAT2. Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q<0.01), log2foldchange > 0.5 using DEseq2 software. The heatmap was generated using pHeatmap software.
Assembly: hg38
Supplementary files format and content: Library normalized bigWig files were provided for all samples

source_name: HCT116 cell line

growth_protocol: Human colon cancer cell lines (HCT116, RKO) were grown in Dulbecco’s modified Eagle’s medium (DMEM; Hyclone) containing 10% FBS and 1% penicillin/streptomycin at 37°C in the presence of 5% CO2. All cell lines were authenticated by short tandem repeat (STR) analysis.

extract_protocol:
For RNA-seq, total RNA was extracted using Trizol.
Total cellular RNA were extracted using TRIzol (Thermo Fisher Scientific). RNA libraries were constructed using TruSeq RNA Library Prep Kit v2 (Illumina) and sequenced as 150 bp paired-end reads by NovaSeq 6000.

treatment_protocol: HCT116 or RKO cells were infected with shCDK13 or scrambled control (shSCR) lentiviruses and cultured for 72 h.

value: HCT116 cell line

value: shSCR


title: HCT116-shSCR-1

description: RNA-seq


title: HCT116-shCDK13-2

description: RNA-seq


title: RNAseq, regeneration tips 12hrs, UNC, Rep3


title: RNAseq, regeneration tips 24hrs, UNC, Rep1


title: RNAseq, regeneration tips 24hrs, UNC, Rep3


title: RNAseq, regeneration tips 12hrs, UNC, Rep2


title: K7M2-TE-EVPs-2

value: Intravenous injection of 10 ug of K7M2-TE-EVPs in 100 ul of PBS every other day for 4 weeks


title: K7M2-CL-EVPs-1


title: PT18_late, non_responder, sort CD3, T cell subset bone marrow, scVDJseq [PT18_P1846_VDJ]

description:
10x Genomics 5' VDJ
PT18_P1846_VDJ


title: RNAseq, regeneration tips 24hrs, UNC, Rep2

value: regenerating tips


title: RNAseq, regeneration tips 12hrs, UNC, Rep1

value: Ind-Pune


title: PT18_late, non-responder, sort CD3, T cell subset bone marrow, scRNAseq [PT18_P1846_RNA]

description:
10x Genomics 5' scRNA
PT18_P1846_RNA

value: non-responder


title: PT17_late_relapse, responder, sort CD3, T cell subset bone marrow, scVDJseq [PT17_P2918_VDJ]

description:
10x Genomics 5' VDJ
PT17_P2918_VDJ

value: responder


title: K7M2-TE-EVPs-3


title: PBS-7-2


title: PT18_pre, non_responder, sort CD3, T cell subset bone marrow, scVDJseq [PT18_P1814_VDJ]

description:
10x Genomics 5' VDJ
PT18_P1814_VDJ


title: RKO-shSCR-2

description: RNA-seq

source_name: RKO cell line

value: RKO cell line


title: HCT116-shCDK13-1

description: RNA-seq


title: PT17_late_relapse, responder,  sort CD3, T cell subset bone marrow, scRNAseq [PT17_P2918_RNA]

description:
10x Genomics 5' scRNA
PT17_P2918_RNA


title: RNAseq, regeneration tips 8hrs, UNC, Rep2


title: PT17_pre, responder, sort CD3, T cell subset bone marrow, scVDJseq [PT17_P2552_VDJ]

description:
10x Genomics 5' VDJ
PT17_P2552_VDJ


title: PT18_pre, non-responder, sort CD3, T cell subset bone marrow, scRNAseq [PT18_P1814_RNA]

description:
10x Genomics 5' scRNA
PT18_P1814_RNA


title: PBS-6-3

description: This PBS group was used as control for the B16F10-TE-EVPs group


title: PBS-6-2


title: PT17_pre, responder, sort CD3, T cell subset bone marrow, scRNAseq [PT17_P2552_RNA]

description:
10x Genomics 5' scRNA
PT17_P2552_RNA


title: B16F10-CL-EVPs-1

value: Intravenous injection of 10 ug of B16F10-CL-EVPs in 100 ul of PBS every other day for 4 weeks


title: RNAseq, regeneration tips 8hrs, UNC, Rep3


title: RKO-shSCR-1

description: RNA-seq


title: PBS-6-5


title: PBS-6-4


title: RKO-shCDK13-3

description: RNA-seq


title: RNAseq, regeneration tips 3hrs, UNC, Rep2


title: RNAseq, regeneration tips 8hrs, UNC, Rep1


title: RKO-shSCR-3

description: RNA-seq


title: RNAseq, regeneration tips 0hr, UNC, Rep2


title: PT16_pre, responder, sort CD3, T cell subset bone marrow, scVDJseq [PT16_P2024_VDJ]

description:
10x Genomics 5' VDJ
PT16_P2024_VDJ


title: PT16_pre, responder,  sort CD3, T cell subset bone marrow, scRNAseq [PT16_P2024_RNA]

description:
10x Genomics 5' scRNA
PT16_P2024_RNA


title: TAPBPR library sorted for rescue of surface HLA-A2 expression in tapasin-KO cells (Replicate 2)

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois at Urbana Champaign

data_processing:
Data was analyzed using python scripts in the Enrich package: http://depts.washington.edu/sfields/software/enrich/
Fuser command (Fragment A): python3 Paired_read_fuser.py --path directory_A/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq.gz --read2 sample_R2.fastq.gz --wtseq GGGAAGGAGGTGACCTGTGAGATCTCCCGCTACTTTCTCCAGATGACAGAGACCACTGTTAAGACAGCAGCTTGGTTCATGGCCAACGTGCAGGTCTCTGGAGGGGGACCTAGCATCTCCTTGGTGATGAAGACTCCCAGGGTCGCCAAGAATGAGGTGCTCTGGCAC --read1_overlap_start 20 --read1_overlap_end 188 --read2_overlap_start 61 --read2_overlap_end 229 --mode B
Fuser command (Fragment B): python3 Paired_read_fuser.py --path directory_B/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq.gz --read2 sample_R2.fastq.gz --wtseq CCCCAGGGGACTGTGCGAACTGCAGTGGAGTTCCAGGTGATGACACAGACCCAATCCCTGAGCTTCCTGCTGGGGTCCTCAGCCTCCTTGGACTGTGGCTTCTCCATGGCACCGGGCTTGGACCTCATCAGTGTGGAGTGGCGACTGCAGCACAAGGGCAGGGGT --read1_overlap_start 21 --read1_overlap_end 186 --read2_overlap_start 65 --read2_overlap_end 230 --mode B
Fuser command (Fragment C): python3 Paired_read_fuser.py --path directory_C/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq.gz --read2 sample_R2.fastq.gz --wtseq GCAGGGCAGGGGCAGGCTGTGCGGAAGGGCGCTACCCTGGAGCCTGCACAACTGGGCATGGCCAGGGATGCCTCCCTCACCCTGCCCGGCCTCACTATACAGGACGAGGGGACCTACATTTGCCAGATCACCACCTCTCTGTACCGAGCTCAGCAGATCATCCAGCTCAACATCCAAGCTTCCCCTAAAGTACGACTGAGCTTGGCAAACGAAGCTCTGCTGCCC  --read1_overlap_start 24 --read1_overlap_end 249 --read2_overlap_start 2 --read2_overlap_end 227 --mode B
Fuser command (Fragment D): python3 Paired_read_fuser.py --path directory_D/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq.gz --read2 sample_R2.fastq.gz --wtseq CTCATCTGCGACATTGCTGGCTATTACCCTCTGGATGTGGTGGTGACGTGGACCCGAGAGGAGCTGGGTGGATCCCCAGCCCAAGTCTCTGGTGCCTCCTTCTCCAGCCTCAGGCAAAGCGTGGCAGGCACCTACAGCATCTCCTCCTCTCTCACCGCAGAACCTGGCTCTGCAGGTGCCACTTACACCTGCCAGGTCACACACATCTCTCTGGAGGAGCCC --read1_overlap_start 25 --read1_overlap_end 247 --read2_overlap_start 2 --read2_overlap_end 229 --mode B
Fuser command (Fragment E): python3 Paired_read_fuser.py --path directory_D/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq.gz --read2 sample_R2.fastq.gz --wtseq GGTGCGCACCGTGGAGCTCTCGCCAGCAGTGAGGAC --read1_overlap_start 22 --read1_overlap_end 58 --read2_overlap_start 134 --read2_overlap_end 170 --mode B
Aligner command (Fragment A): python3 Fused_read_aligner.py --path directory_A/ --infile sample_R1.fast_B_qc1 --referenceDNA GGGAAGGAGGTGACCTGTGAGATCTCCCGCTACTTTCTCCAGATGACAGAGACCACTGTTAAGACAGCAGCTTGGTTCATGGCCAACGTGCAGGTCTCTGGAGGGGGACCTAGCATCTCCTTGGTGATGAAGACTCCCAGGGTCGCCAAGAATGAGGTGCTCTGGCAC --referenceAA GKEVTCEISRYFLQMTETTVKTAAWFMANVQVSGGGPSISLVMKTPRVAKNEVLWH  --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment B): python3 Fused_read_aligner.py --path directory_B/ --infile sample_R1.fast_B_qc1 --referenceDNA CCCCAGGGGACTGTGCGAACTGCAGTGGAGTTCCAGGTGATGACACAGACCCAATCCCTGAGCTTCCTGCTGGGGTCCTCAGCCTCCTTGGACTGTGGCTTCTCCATGGCACCGGGCTTGGACCTCATCAGTGTGGAGTGGCGACTGCAGCACAAGGGCAGGGGT --referenceAA PQGTVRTAVEFQVMTQTQSLSFLLGSSASLDCGFSMAPGLDLISVEWRLQHKGRG --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment C): python3 Fused_read_aligner.py --path directory_C/ --infile sample_R1.fast_B_qc1 --referenceDNA GCAGGGCAGGGGCAGGCTGTGCGGAAGGGCGCTACCCTGGAGCCTGCACAACTGGGCATGGCCAGGGATGCCTCCCTCACCCTGCCCGGCCTCACTATACAGGACGAGGGGACCTACATTTGCCAGATCACCACCTCTCTGTACCGAGCTCAGCAGATCATCCAGCTCAACATCCAAGCTTCCCCTAAAGTACGACTGAGCTTGGCAAACGAAGCTCTGCTGCCC --referenceAA AGQGQAVRKGATLEPAQLGMARDASLTLPGLTIQDEGTYICQITTSLYRAQQIIQLNIQASPKVRLSLANEALLP  --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment D): python3 Fused_read_aligner.py --path directory_D/ --infile sample_R1.fast_B_qc1 --referenceDNA CTCATCTGCGACATTGCTGGCTATTACCCTCTGGATGTGGTGGTGACGTGGACCCGAGAGGAGCTGGGTGGATCCCCAGCCCAAGTCTCTGGTGCCTCCTTCTCCAGCCTCAGGCAAAGCGTGGCAGGCACCTACAGCATCTCCTCCTCTCTCACCGCAGAACCTGGCTCTGCAGGTGCCACTTACACCTGCCAGGTCACACACATCTCTCTGGAGGAGCCC --referenceAA LICDIAGYYPLDVVVTWTREELGGSPAQVSGASFSSLRQSVAGTYSISSSLTAEPGSAGATYTCQVTHISLEEP --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
Aligner command (Fragment E): python3 Fused_read_aligner.py --path directory_D/ --infile sample_R1.fast_B_qc1 --referenceDNA GGTGCGCACCGTGGAGCTCTCGCCAGCAGTGAGGAC --referenceAA GAHRGALASSED --gap_max 250 --unresolvable_max 250 --maxmutrun 250 --avg_quality 30 --chaste 1 --Ncount_max 250 --use_N 0 --mode B
MapCounts command: python mapCounts.py --path directory/ --infile sample_R1.fast_B_qc1_PRO_qc2
MapRatios command Example: python mapRatios.py --path directory/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts command: python mapParts.py --path directory/ --infile mapratios_sorted_library --mode mutations:1
Unlink script:  python mapUnlink.py --path directory/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size number_of_residues_in_fragment
In Excel, the log(base2) enrichment ratio of the wildtype sequence was subtracted from the log(2) enrichment ratios for all single mutations.
Assembly: Not applicable
Supplementary files format and content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution.  Also includes the frequency of each mutation in the naïve plasmid library.

source_name: Synthetic coding sequences

extract_protocol:
Total RNA was extracted from FACS sorted cells using a GeneJet kit (Thermo Scientific), and cDNA was synthesized using high fidelity Accuscript (Agilent) primed from a gene-specific primer.  The TAPBPR cDNA was PCR amplified as four overlapping fragments for full coverage by Illumina sequencing.  In a first round of PCR, primer overhangs added sequences for annealing to the Illumina sequencing primers. In a second round of PCR, primer overhangs added unique barcodes and Illumina adaptors.  To determine the frequencies of mutations in the naive library, the library plasmid DNA was used as the template for PCR amplification and Illumina sequencing.
Primer pair for 1st round of PCR (Fragment A): Illumina_TAPBPR_273_for (TCTTTCCCTACACGACGCTCTTCCGATcttgctccatgctgactgca) and Illumina_TAPBPR_483_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCAGTGGCAAGTTCAGCGTTG)
Primer pair for 1st round of PCR (Fragment B): Illumina_TAPBPR_466_for (TCTTTCCCTACACGACGCTCTTCCGATCTacgctgaacttgccactgag) and Illumina_TAPBPR_671_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGTCCAGCTGTACACCAACTG)
Primer pair for 1st round of PCR (Fragment C): Illumina_TAPBPR_649_for (TCTTTCCCTACACGACGCTCTTCCGATCTggtcagttggtgtacagctg) and Illumina_TAPBPR_920_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCCAGCAATGTCGCAGATGAG)
Primer pair for 1st round of PCR (Fragment D): Illumina_TAPBPR_875_for (TCTTTCCCTACACGACGCTCTTCCGATCtggcaaacgaagctctgctg) and Illumina_TAPBPR_1148_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGGACAACCTGGGTGCTG)
Primer pair for 1st round of PCR (Fragment E): Illumina_TAPBPR_111_for (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGACTGTTTCCTGGTGAAGG) and Illumina_TAPBPR_229_rev (TCTTTCCCTACACGACGCTCTTCCGATCTCCTTGGAAATCGGTGAAGTC)
Primer pair for 2nd round of PCR (added I5 and I7 Illumina adaptors): MiSeq_Start_Adaptamer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and MiSeq_Index_Adaptamer (CAAGCAGAAGACGGCATACGAGAT-6nt-barcode-GTGACTGGAGTTCAGACGTGTGCTCTTC)
Amplicons were deep sequenced on a NovaSeq 6000 using a 2x250 nt paired end protocol.

treatment_protocol: Tapasin-KO Expi293F cells were transfected with a plasmid library encoding variants of chimeric TAPBPR-CT, where the TAPBPR C-terminus is replaced with the equivalent residues of tapasin.  Library DNA was diluted with a large excess of carrier DNA to ensure that cells typically acquired no more than one TAPBPR variant, maintaining a tight genotype-to-phenotype link.  24 h post-transfection, cells with the highest surface HLA-A2 (the top 0.5% of fluorescent cells after staining with PE-conjugated anti-HLA-A2) were collected by FACS.

tag: protein

value: TAPBPR

tag: sort gate

value: Top 0.5% of cells for surface HLA-A2 expression


title: K7M2-TE-EVPs-1

value: BALB/c


title: RNAseq, regeneration tips 3hrs, UNC, Rep3


title: RKO-shCDK13-2

description: RNA-seq


title: RKO-shCDK13-1

description: RNA-seq


title: B16F10-TE-EVPs-3

value: Liver

value: Intravenous injection of 10 ug of B16F10-TE-EVPs in 100 ul of PBS every other day for 4 weeks


title: RNAseq, regeneration tips 0hr, UNC, Rep1


title: PBS-6-1

value: Intravenous injection of 100 ul of PBS every other day for 4 weeks


title: C1: lung metastses

description: 10x Genomics

data_processing:
Illumina sequencing, Sequencing raw data, Valid barcodes, Valid UMI, Alignment with STAR, Gene-barcode Matrix, Detected Genes, UMI Normalization, PCA, t - SNE, k-means clustering, Subgroup correlation, Multiples and P values of gene expression differences in subpopulations, top20 significant genes
Use cell Ranger Single Cell V3 software to process data.The raw data contains a small number of articulated, repetitive, low-quality Reads that affect the quality of the comparison and subsequent analysis and are filtered during Cell Ranger processing.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung metastses

extract_protocol:
The tissue Dissociation Kit (Tumor Dissociation Kit, Human) is used. Mechanical Dissociation and enzymatic hydrolysis are carried out according to the Dissociation operation steps. The cell suspension is first filtered through 70um and then filtered through 30um, if the number of red blood cells in the single cell suspension is large, Red blood cells need to be removed with RBC lysate to prepare a single cell suspension.After the tissue samples were made into single-cell suspension, luna-FL automatic cell counting apparatus was used to count and measure cell viability. The activity of cultured cells was higher than 90% (the activity of primary cells was higher than 70%). If the cell activity could not meet the standard, the dead cells should be removed with the desiccated cell kit to improve cell viability. The cell concentration was adjusted to the ideal concentration of 700-1200 cells /μL
After the amplification products were qualified, the sequencing library was constructed.The cDNA is first chemically broken to 200 to 300bp   The left and right fragments, cDNA fragmentation, terminal repair and addition of A, cDNA fragment screening, P7 Adaptor connector connection and PCR amplification to introduce sample Index, finally the fragment screening to obtain the cDNA library.

value: lung metastses


title: RNAseq, regeneration tips 3hrs, UNC, Rep1


title: B16F10-TE-EVPs-4


title: RNAseq, regeneration tips 0hr, UNC, Rep3


title: F: adjacent normal lung tissue

description: 10x Genomics

source_name: adjacent normal lung tissue

value: adjacent normal lung tissue


title: B1: lung metastses

description: 10x Genomics


title: TAPBPR library sorted for rescue of surface HLA-A2 expression in tapasin-KO cells (Replicate 1)


title: Library of TAPBPR variants

library_source: genomic

molecule: genomic DNA


title: PT16_late, responder, sort CD3, T cell subset bone marrow, scVDJseq [PT16_P2287_VDJ]

description:
10x Genomics 5' VDJ
PT16_P2287_VDJ

value: human bone marrow mononuclear cells

value: T cells

value: relapsed-refractory multiple myeloma


title: PT15_late_relapse, non_responder,sort CD3, T cell subset bone marrow, scVDJseq [PT15_P2251_VDJ]

description:
10x Genomics 5' VDJ
PT15_P2251_VDJ


title: PBS-4-5

description: This PBS group was used as control for the B16F1-Tb group

value: Three weeks post  subcutaneous injection of 100 ul of PBS


title: PT7_late, responder,  sort CD3, T cell subset bone marrow, scVDJseq [PT7_P2232_VDJ]

description:
10x Genomics 5' VDJ
PT7_P2232_VDJ


title: B16F10-TE-EVPs-2


title: A1: lung metastses

description: 10x Genomics


title: PT15_late_relapse,non_responder, sort CD3, T cell subset bone marrow, scRNAseq [PT15_P2251_RNA]

description:
10x Genomics 5' scRNA
PT15_P2251_RNA


title: H4K20me1, 12hrs, Rep2

data_processing:
1.5 pM of the denatured libraries were used as an input to obtain sequencing reads. The DNA was loaded onto a NextSeq 500/550 High-Output v2.5 Kit (75 cycles) (Cat # 20024906, Illumina) and sequenced using 35 cycles for read1, 8 cycles for indexes and 35 cycles for read2 on Nextseq 550 (Illumina) at IISER Pune.
.bcl files were converted to .fastq files using bcl2fastq command. The fastq files from the lanes specific to the sample were concatenated using cat command. Quality of reads were checked by FastQC.
The fastq files were aligned to reference genome using bowtie2 and aligned sam files were converted to bam files using Samtools. Bam files were sorted and indexed.
The sorted bam files were used to generate bigwig files using deeptools (Ramirez et al., 2016). The bam files for the H4K20me1 ChIP samples were normalized against the respective input bam file. The combinatorial occupancy matrices were generated using the computeMatrix tool and the plots were generated using the plotHeatmap tool in the deeptools package.
Assembly: Hydra_2.0_assembly

extract_protocol:
Two thousand Hydra polyps per time point were decapitated and the regenerating tips were collected and cross-linked with 1% methanol free formaldehyde. The fixation reaction was quenched with 150 mM Glycine. The fixed regenerating tips were resuspended in Swelling Buffer (25 mM Tris-HCl pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT, 0.5 mM PMSF, 1X Protease inhibitor cocktail/PIC) and homogenized using a Dounce homogenizer (35 strokes) to lyse the cells and release the nuclei. The nuclei were pelleted, resuspended in sonication buffer (50 mM Tris-HCl pH 7.9, 140 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 1% SDS, 0.1% Sodium deoxycholate, 0.5 mM PMSF, 1X PIC), and incubated for 30 min on ice. They were then sonicated to obtain an average chromatin size of 300 bp. Chromatin was pre-cleared using 50 μl of a 50% protein A sepharose (GE healthcare) slurry for 1 h at 4°C with gentle inverting. Immunoprecipitations were carried out in ChIP buffer (16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton-X 100, 0.01% SDS, 1X PIC) with Anti-H4K20me1. An appropriate IgG control was also used with inverting at 4°C for 14–16 h. The samples were then incubated with 50 μl of a 50% Protein A sepharose slurry (saturated with 0.5% BSA and 10 mg/ml yeast tRNA) for 3 h at 4°C with gentle inverting. ChIP samples were reverse-crosslinked, and the DNA was purified using Phenol:Chloroform:Isomamyl alcohol based precipitation method. Input chromatin was obtained after pre-clearing, by de-crosslinking and purifying input DNA Phenol:Chloroform:Isoamyl alcohol based precipitation method. Purified DNA was subjected to library preparation for sequencing
A total of 1 ng of purified ChIPped DNA for each sample was used for library preparation using Ultra II DNA kit (NEB) as per the manufacturer’s instructions. All library samples were amplified for 9-10 cycles depending on cycle number estimation by qPCR. Amplified libraries were subjected to double-sided bead purification using one round of 0.5X volume of Hi-prep PCR purification kit (Magbio Genomics, USA) to remove the primer dimers and one round of 1.8X volume to remove the fragments larger than 1000 bp. Library concentration was determined using Qubit (Thermo scientific, USA), and average fragment size was estimated using DNA HS assay on Bioanalyzer 2100 (Agilent Technologies, USA) before pooling libraries at equimolar ratio.

treatment_protocol: The polyps were decapitated, and the regenerating tips were collected at 0 hpa, 3 hpa, 8 hpa, 12 hpa, and 24 hpa to perform ChIP.

value: regenerating tips

value: Ind-Pune

tag: chip antibody


title: B16F10-TE-EVPs-1


title: H4K20me1, 24hrs, Rep2


title: PT15_pre, non_responder, sort CD3, T cell subset bone marrow, scVDJseq [PT15_P2117_VDJ]

description:
10x Genomics 5' VDJ
PT15_P2117_VDJ


title: PT16_late, responder, sort CD3, T cell subset bone marrow, scRNAseq [PT16_P2287_RNA]

description:
10x Genomics 5' scRNA
PT16_P2287_RNA

value: responder


title: PT15_pre, non_responder, sort CD3, T cell subset bone marrow, scRNAseq [PT15_P2117_RNA]

description:
10x Genomics 5' scRNA
PT15_P2117_RNA


title: B16F10-TE-EVPs-5


title: AP: adjacent normal tissue

description: 10x Genomics

source_name: adjacent normal tissue

value: adjacent normal tissue


title: H4K20me1, 24hrs, Input


title: ACC001-input001

data_processing:
Data filtering: This project uses the filtering software SOAPnuke developed by BGI independently for raw data filtering: Remove low quality tags as well as contaminants to get clean reads
Sequences mapping: After filtering, SOAPaligner/SOAP2(v 2.21t),which allows up to two mismatches in the alignment, is used to align clean data to the reference genome. The unique mapped reads are used for downstream bioinformatic analysis.
Parameter：Clean Parameter: soap_mm_gz -p 4 -v 2 -s 35
Peak calling is a tool to identify regions which are enriched. MACS (Model-based Analysis of  ChIP-Seq)  software applied in our workflow uses Dynamic Possion Distribution to calculate p-value of the specific region based on the unique mapped reads. The region would be defined as a peak when p-value< le-5. Thus, MACS assigns each enriched region (Peak) with set of numerical values which are the number of summits, tags, normalized p-value as well as fold enrichment information. The more enriched these regions are, the more likely they are transcription factor binding sites. The score is positively correlated to transcription factor binding intensity.
MACS14 is mainly used to calculate peaks of transcription factors or narrow peak proteins.
Parameter：Calling Parameter: macs14 -s 50 -g 3.25e9 -p 1e-5 -w --space 50 -m 10,30
MACS2 (version: 2.1.2) is mainly used to calculate peaks of histones or broad peak proteins. By default, other unknown proteins are used this software as well.
Parameter：Calling Parameter: --bw 200 -g XXX -s 50 -p 1e-5 -m 10 30 --broad -B --trackline' was used.
SICER (version:1.1) is mainly used to calculate peaks of histones.
Parameter：Reference 1 200 0.8 600 0.01([Species] [redundancy threshold] [window size (bp)] [effective genome fraction] [gap size (bp)] [Statistic threshold value])
Peak annotation
MAnorm(v1.1) is used to build different enriched peaks of different samples. The significant regions are picked up if |M| ≥ 1 and p-value ≤ 10-5. The gene element annotation of peak or different enrichment peak from different samples is carried out by bedtools intersect mode with overlap 50].
Assembly: hg19

source_name: Human tumor salivary gland (MYB-NFIB fusion)

extract_protocol: Fresh tissue samples were homogenized and crosslinked with 1% formaldehyde. Extracted DNA was fragmented by ultrasonication. The supernatant was collected and divided into two groups, the input and MYB groups. MYB antibodies (5 μg) were used in the immunoprecipitation.The DNA fragments isolated from the immune complex were purified by a DNA purification kit and then analysed by BGI. Peak values were acquired in a 2-kb region. Data processing and gene annotation were completed in the Dr.Tom system.

treatment_protocol: According to the results of the previous experiments, it is suggested that MYB antibodies have good specificity, so this experiment is divided into two groups, input and MYB groups

tag: disease state

value: salivary adenoid cystic carcinoma

value: none (input)


title: PT7_pre, responder, sort CD3, T cell subset bone marrow, scRNAseq [PT7_P2085_RNA]

description:
10x Genomics 5' scRNA
PT7_P2117_RNA


title: PT7_late, responder, sort CD3, T cell subset bone marrow, scRNAseq [PT7_P2232_RNA]

description:
10x Genomics 5' scRNA
PT7_P2232_RNA


title: B16F1-Tb-5

tag: tissue

value: Three weeks post  subcutaneous injection of 5×105 of  B16F1 cells in 100 ul of PBS


title: PBS-4-4


title: A: primary salivary gland ACC

description: 10x Genomics

source_name: primary salivary gland ACC

value: primary salivary gland ACC


title: PBS-4-2

value: Liver


title: H4K20me1, 24hrs, Rep1


title: H4k20me1, 8hrs, Rep1


title: H4K20me1, 12hrs, Rep1


title: ACC001-MYB

value: Human tumor salivary gland (MYB-NFIB fusion)

value: MYB


title: PBS-4-3


title: PT7_pre, responder, sort CD3, T cell subset bone marrow, scVDJseq [PT7_P2085_VDJ]

description:
10x Genomics 5' VDJ
PT7_P2085_VDJ


title: PT6_late, responder, sort CD3, T cellsubset bone marrow, scVDJseq [PT6_P2216_VDJ]

description:
10x Genomics 5' VDJ
PT6_P2216_VDJ


title: MDAT41_S127A_NoDox

first: Mahesh

last: Saqcena

address: 1275 York Ave, Box 296

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina Bcl2fastq v2.2 software was used for basecalling.
Sequence reads were aligned to hg38 genome assembly using STAR aligner v2.7.3a, and aligned reads were quantified using Partek E/M annotation model and hg38 ensembl release 91.
Transcripts Per Million (TPM) was used for normalization and 0.0001 was added to obtain non-zero noramlized gene expression counts matrix.
Assembly: hg38
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

source_name: Thyroid cancer cell line

extract_protocol:
The cells were collected into TRIzol LS (Invitrogen, #10296010) for RNA-sequencing
The total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102) with 8 cycles of PCR, barcoded, and run on a NovaSeq 6000 in a PE50 run using the NovaSeq 6000 SP Reagent Kit (Illumina).

treatment_protocol: The cells were incubated for 3 days in medium with/without doxycycline in 1%FBS.

value: Lentivirally transduced dox-inducible vector for YAP S127A expression

value: No dox control


title: MDAT41_S127A_wDox

value: Dox-induced YAP S127A expression


title: H4K20me1, 12hrs, Input


title: PT6_late, responder, sort CD3, T cell subset bone marrow, scRNAseq [PT6_P2216_RNA]

description:
10x Genomics 5' scRNA
PT6_P2216_RNA

value: human bone marrow mononuclear cells

value: T cells


title: B16F1-Tb-3


title: H4K20me1, 8hrs, Input


title: PBS-4-1

value: Three weeks post  subcutaneous injection of 100 ul of PBS


title: B16F1-Tb-2


title: MDAT32_S127A_wDox


title: MDAT32_S127A_NoDox


title: H4K20me1, 8hrs, Rep2

value: regenerating tips


title: B16F1-Tb-1


title: PT6_pre, responder, sort CD3, T cell subset bone marrow, scRNAseq [PT6_P2081_RNA]

description:
10x Genomics 5' scRNA
PT6_P2081_RNA

value: relapsed-refractory multiple myeloma


title: H4K20me1, 3hr, Rep2

value: Ind-Pune


title: KTC2_S127A_wDox


title: PT3_late, responder, sort CD3, T cell subset bone marrow, scVDJseq [PT3_P2125_VDJ]

description:
10x Genomics 5' VDJ
PT3_P2125_VDJ

value: responder


title: PBS-2-5

description: This PBS group was used as control for the K7M2-Tb group

value: BALB/c

value: Four weeks post intratibia injection of 10 ul of PBS


title: B16F1-Tb-4

value: Three weeks post  subcutaneous injection of 5×105 of  B16F1 cells in 100 ul of PBS


title: H4K20me1, 3hr, Input


title: BHT101_S127A_wDox


title: PT3_pre, responder, sort CD3, T cell subset bone marrow, scVDJseq [PT3_P1924_VDJ]

description:
10x Genomics 5' VDJ
PT3_P1924_VDJ


title: H4K20me1, 0hr, Rep2


title: PT3_late, responder, sort CD3, T cell subset bone marrow, scRNAseq [PT3_P2125_RNA]

description:
10x Genomics 5' scRNA
PT3_P2125_RNA


title: KTC2_S127A_NoDox


title: PBS-2-4


title: PBS-2-3


title: SW1736_shYAP_wDox

value: Lentivirally transduced dox-inducible miRE vector for YAP knockdown

value: Dox-induced YAP1 shRNA


title: H4K20me1, 0hr, Rep1


title: PT6_pre, responder, sort CD3, T cell subset bone marrow, scVDJseq [PT6_P2081_VDJ]

description:
10x Genomics 5' VDJ
PT6_P2081_VDJ


title: BHT101_S127A_NoDox


title: H4K20me1, 0hr, Input


title: H4K20me1, control, Input

source_name: whole polyps

extract_protocol:
The polyps in each treatment set were collected and cross-linked with 1% methanol free formaldehyde. The fixation reaction was quenched with 150 mM Glycine. The fixed regenerating tips were resuspended in Swelling Buffer (25 mM Tris-HCl pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT, 0.5 mM PMSF, 1X Protease inhibitor cocktail/PIC) and homogenized using a Dounce homogenizer (35 strokes) to lyse the cells and release the nuclei. The nuclei were pelleted, resuspended in sonication buffer (50 mM Tris-HCl pH 7.9, 140 mM NaCl, 1 mM EDTA, 1 % Triton X-100, 1% SDS, 0.1% Sodium deoxycholate, 0.5 mM PMSF, 1X PIC), and incubated for 30 min on ice. They were then sonicated to obtain an average chromatin size of 300 bp. Chromatin was pre-cleared using 50 μl of a 50% protein A sepharose (GE healthcare) slurry for 1 h at 4°C with gentle inverting. Immunoprecipitations were carried out in ChIP buffer (16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton-X 100, 0.01% SDS, 1X PIC) with Anti-H4K20me1. An appropriate IgG control was also used with inverting at 4°C for 14–16 h. The samples were then incubated with 50 μl of a 50% Protein A sepharose slurry (saturated with 0.5% BSA and 10 mg/ml yeast tRNA) for 3 h at 4°C with gentle inverting. ChIP samples were reverse-crosslinked, and the DNA was purified using Phenol:Chloroform:Isomamyl alcohol based precipitation method. Input chromatin was obtained after pre-clearing, by de-crosslinking and purifying input DNA Phenol:Chloroform:Isoamyl alcohol based precipitation method. Purified DNA was subjected to library preparation for sequencing
A total of 1 ng of purified ChIPped DNA for each sample was used for library preparation using Ultra II DNA kit (NEB) as per the manufacturer’s instructions. All library samples were amplified for 9-10 cycles depending on cycle number estimation by qPCR. Amplified libraries were subjected to double-sided bead purification using one round of 0.5X volume of Hi-prep PCR purification kit (Magbio Genomics, USA) to remove the primer dimers and one round of 1.8X volume to remove the fragments larger than 1000 bp. Library concentration was determined using Qubit (Thermo scientific, USA), and average fragment size was estimated using DNA HS assay on Bioanalyzer 2100 (Agilent Technologies, USA) before pooling libraries at equimolar ratio.

treatment_protocol: Two thousand polyps in each treatment set were used. Control polyps were treated with 0.2% DMSO and experimental set was treated with 5 µM ALP. Polyps were treated for 24 hrs after which the treatment was stopped and Hydra medium was added.

value: whole polyps


title: PBS-2-1

value: Liver


title: PT3_pre, responder, sort CD3, T cell subset bone marrow, scRNAseq [PT3_P1924_RNA]

description:
10x Genomics 5' scRNA
PT3_P1924_RNA


title: PBS-2-2


title: H4K20me1, control, rep2


title: PT2_late, responder, sort CD3, T cell subset bone marrow, scVDJseq [PT2_P1879_VDJ]

description:
10x Genomics 5' VDJ
PT2_P1879_VDJ


title: PT2_late, responder, sort CD3, T cell subset bone marrow, scRNAseq [PT2_P1879_RNA]

description:
10x Genomics 5' scRNA
PT2_P1879_RNA


title: Hth104_shYAP_wDox


title: K7M2-Tb-4

value: Four weeks post intratibia injection of 1×106 of  K7M2 cells in 10 ul of PBS


title: PT2_pre, responder, sort CD3, T cell subset bone marrow, scVDJseq [PT2_P1860_VDJ]

description:
10x Genomics 5' VDJ
PT2_P1860_VDJ


title: H4K20me1, control, rep1


title: K7M2-Tb-2


title: H4K20me1, 3hr, Rep1


title: K7M2-Tb-5


title: 8505C_shYAP_NoDox

value: No dox control


title: PT2_pre,responder, sort CD3, T cell subset bone marrow, scRNAseq [PT2_P1860_RNA]

description:
10x Genomics 5' scRNA
PT2_P1860_RNA


title: SW1736_shYAP_NoDox


title: Input_mSp_ChIPseq

city: Imabari-shi

first: Koji

last: Hayakawa

state: Ehime

address: 1-3 Ikoino-oka

department: Department of Toxicology, Faculty of Veterinary Medicine

country: Japan

institute: Okayama University of Science

data_processing:
In this study, all of data processing for ChIP-seq was performed by using Galaxy platform (https://usegalaxy.org/).
Same fastq files were concatenated by using program “Concatenate datasets tail-to-head (Galaxy Version 1.0.0)”
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie (version 1.1.2).
Peaks were called using MACS (ver 1.0.1) with the following setting: Tag size (100), Band width (125), Pvalue cutoff for peak detection (1e-5).
Genome_build: mm10
Supplementary_files_format_and_content: Bed files were generated using MACS (ver1.0.1) with the following setting: Extend tag from its middle point to a wigextend size fragment (-1), Resolution for saving wiggle files (10).

source_name: mouse spermatogenic cells

growth_protocol: Spermatogenic cells were isolated from the testes of 6-week-old ICR mice, following the previous report (Y.F. Chang, J.S. Lee-Chang, S. Panneerdoss, J.A. MacLean, M.K. Rao, Isolation of Sertoli, Leydig, and spermatogenic cells from the mouse testis, Biotechniques 51 (2011) 341-342, 344.).

extract_protocol:
ChIP-enriched DNA was obtaind by using ChIP-IT Express Enzymatic (Active Motif, 53009) and H1T specific antibody (R. Tani, K. Hayakawa, S. Tanaka, K. Shiota, Linker histone variant H1T targets rDNA repeats, Epigenetics 11 (2016) 288-302.).
The libraries for ChIP-seq of mouse spermatogenic cells were prepared using the KAPA Hyper Prep Kit (KAPA, KK8504) according to the manufacturer's instructions.

value: ICR

value: Germ cell

tag: antibody


title: Sample 3 - biol rep 2

status: Public on Mar 08 2023

city: Louisville

middle: Albert

last: Scott

state: KY

address: 501 S Preston St

department: OIID

institute: University of Louisville

description: Depleted RNA

data_processing:
Downloaded Filifactor alocis: ATCC 35896 GenBank and FASTA files from NCBI. Generated PTT and RNT files using gbkToPttAnd Rnt
Removed genes with incomplete coordinates
Read QC. Removed potential adapter contamination using Trimmomatic v0.39
Assessed trimmed read quality using FastQCv0.11.7 and MultiQC v1.1
Read alignment and counting.  Aligned the trimmed reads against the reference using EDGE-Pro v1.3.1.  EDGE-Pro also counted reads on each gene included in the PTT and RNT files
Assembly: Filifactor alocis: ATCC 35896 GenBank and FASTA files from NCBI: NC_016630.1
Supplementary files format and content: tab-delimited text file containing raw gene counts per sample

organism: Filifactor alocis

source_name: Bacterial

growth_protocol: Anaerobic conditions. BHIY or BHIY/CSE media

extract_protocol:
Pellet under anaerobic conditions.  Resuspend in Qiagen RLT and lyse in MP fast prep.  Supernatant prepared with Qiagen Rneasy kit
NEBNext Ultra II Directional RNA kit (#7760) and NEB UDI plate 1 adapters (#6440) using 220 ng input and 11 cycle PCR

treatment_protocol: Passage at mid-log from BHIY to BHIY and BHIY/CSE.  RNA extraction at mid-log

tag: group

value: (BHIY/CSE media) - passage 2

tag: strain

value: Bacterial


title: Sample 3 - biol rep 3

description: Depleted RNA


title: Hth104_shYAP_NoDox


title: H4K20me1, ALP, Input

value: ALP


title: Sample 1 - biol rep 1

description: Depleted RNA

value: (BHIY media) - passage 1


title: K7M2-Tb-3

source_name: Liver


title: H4K20me1, ALP, rep2

value: Ind-Pune


title: H1t_mSp_ChIPseq

value: H1T (rabbit polyclonal antibody, prepared in-house)


title: 8505C_shYAP_wDox


title: Patient38R

city: London

first: Findlay

last: Bewicke-Copley

address: John Vane Science Centre, Barts Cancer Institute

country: United Kingdom

institute: Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London

data_processing:
Automatic data analysis was carried out using the AmpliSeq™ RNA plugin on the Torrent Suite™ (Thermo Fisher) platform
The Torrent Mapping Alignment Program (TMAP) was used for alignment
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files containing all read counts for all samples.

source_name: Right Testicle

extract_protocol:
RNA was extracted from 2-4 x10µm sections of FFPE tissue using the Ambion RecoverAll total nucleic acid isolation kit (Life Technologies) according to the manufacturer’s instructions.
The gene expression profiles (GEP) of the biopsies were assessed using the Ion AmpliSeq™ Human Gene Expression assay, which uses a single multiplexed panel targeting 20,802 genes. The library preparation and sequencing were performed by a designated certified service provider (Fasteris SA, Switzerland)

tag: batch

value: Batch 7

tag: timepoint

value: Relapse

value: ABC

tag: patid

value: RCHOP + IT MTX

tag: response

value: CR

tag: age

tag: Sex

value: M

value: Right Testicle


title: Patient37R

source_name: Right Tonsil

value: GCB

tag: treatment

value: RCHOP

value: F

value: Right Tonsil


title: Patient37D

source_name: Left Tonsil

value: Diagnosis

value: Left Tonsil


title: H4K20me1, ALP, rep1

value: whole polyps

value: ALP


title: Sample 2 - biol rep 2

description: Depleted RNA

value: (BHIY media) - passage 2

tag: cell type

value: Bacterial


title: K7M2-Tb-1

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen. Total RNA was extracted using TRIzol reagent, and RNA was further purified using RNeasy Mini kit including a DNase digest following the manufacturer’s instructions
RNA libraries were prepared using TruSeq Stranded mRNA Library Preparation (Illumina) following the manufacturer’s instructions

value: Liver

value: BALB/c

value: Four weeks post intratibia injection of 1×106 of  K7M2 cells in 10 ul of PBS


title: Sample 2 - biol rep 3

description: Depleted RNA


title: Sample 3 - biol rep 1

description: Depleted RNA

value: (BHIY/CSE media) - passage 2


title: Patient29R

source_name: Skin Bx

value: Batch 4

value: Relapse

value: ABC

value: RCHOP X3 + IT MTX AND IFRT

value: CR

value: Skin Bx


title: Patient30R

source_name: Lymph Node

value: Batch 2

value: UNC

value: RCHOP

value: M

value: Lymph Node


title: Sample 1 - biol rep 3

description: Depleted RNA

value: (BHIY media) - passage 1


title: Sample 2 - biol rep 1

description: Depleted RNA

value: (BHIY media) - passage 2

value: Bacterial


title: Patient32D

source_name: Stomach

value: Batch 5

value: Diagnosis

value: GCB

value: F

value: Stomach


title: Sample 1 - biol rep 2

description: Depleted RNA


title: Patient38D

source_name: Left Testicle

value: Batch 7

value: RCHOP + IT MTX

value: Left Testicle


title: Patient36R

value: Relapse

value: RCHOP X3 + RADIOTHERAPY

value: CR


title: Patient27D

source_name: Left Breast

value: Batch 4

value: ABC

value: Left Breast


title: Patient35R

value: Batch 1

value: R-CEOP + RADIOTHERAPY

value: M

value: Lymph Node


title: Patient36D

value: Batch 5

value: Diagnosis


title: Patient35D

source_name: Submandibular Gland

value: Submandibular Gland


title: Patient34D

source_name: Inguinal Lymph Node

value: UNC

value: R-CEOP

value: F

value: Inguinal Lymph Node


title: Patient33R

source_name: Skin

value: Batch 2

value: Relapse

value: RCHOP + IT MTX

value: Skin


title: Patient34R

value: Batch 4

value: CR


title: Patient33D


title: Patient32R

value: GCB

value: RCHOP


title: Patient23D

source_name: Abdominal Mass

value: Abdominal Mass


title: Patient23R

source_name: Left Para-Aortic Node

value: Left Para-Aortic Node


title: Patient31D

source_name: Soft Tissue

value: ABC

value: Soft Tissue


title: Patient31R

source_name: Axillary Lymph Node

value: Axillary Lymph Node


title: Patient19R

source_name: Lymph Node (recurrence)

value: Batch 3

value: Lymph Node (recurrence)


title: Patient20D

source_name: Generalised Lymphadenopathy

value: Diagnosis

value: DAC

value: M

value: Generalised Lymphadenopathy


title: Patient30D

value: Batch 2

value: Lymph Node


title: Patient29D

source_name: Oral-Soft Tissue

value: Batch 4

value: RCHOP X3 + IT MTX AND IFRT

value: Oral-Soft Tissue


title: Patient28R

source_name: Left Para Aortic

value: Relapse

value: RCHOP

value: CR

value: F

value: Left Para Aortic


title: Patient28D

source_name: Retroperitoneal/Renal

value: ABC

value: Retroperitoneal/Renal


title: Patient17R

source_name: Right Inguinal Lymph Node

value: Batch 3

value: GCB

value: Right Inguinal Lymph Node


title: Patient16R

value: Left Breast


title: Patient16D

source_name: Breast Biopsy And Nodes

value: Diagnosis

value: Breast Biopsy And Nodes


title: Patient27R

value: RCHOP + IT MTX


title: Patient21D

source_name: Mesenteric Nodes

value: Batch 4

value: PR

value: M

value: Mesenteric Nodes


title: Patient14R

source_name: Orbturator Mass. Piriformis Mass

value: Relapse

value: RCHOP

value: Orbturator Mass. Piriformis Mass


title: Patient26D

source_name: Left Groin

value: CR

value: F

value: Left Groin


title: Patient26R

source_name: Retroperitoneal

value: ABC

value: Retroperitoneal


title: Patient25R

source_name: Right Elbow Lump

value: Right Elbow Lump


title: Patient14D

source_name: Lumps Left Thigh, Mediastinal And Abdominal Nodes

value: Batch 3

value: GCB


title: Patient25D

source_name: Gingival Mucosa

value: Diagnosis

value: Gingival Mucosa


title: Patient12D

source_name: Lymph Node

value: Lymph Node


title: Patient13D

source_name: Left Neck Mass

value: PR

value: Left Neck Mass


title: Patient24R

source_name: Right Axilla

value: Batch 4

value: RCHOP + LOCALISED RT

value: M

value: Right Axilla


title: Patient24D


title: Patient22D

source_name: Anterior Mediastinal Mass

value: RCHOP

value: Anterior Mediastinal Mass


title: Patient22R

source_name: Right Cervical Lymph Node

value: Relapse

value: F

value: Right Cervical Lymph Node


title: Patient11D

source_name: Cervical Nodes And Nasal Obstruction

value: ABC

value: CR

value: Cervical Nodes And Nasal Obstruction


title: Patient21R

source_name: Nodes Both Groins

value: Nodes Both Groins


title: Patient8R

source_name: Right Cervical Lymph Node Bx

value: Batch 5

value: GCB

value: Right Cervical Lymph Node Bx


title: Patient8D

source_name: Oesophageal Bx

value: Diagnosis

value: Oesophageal Bx


title: Patient18R

source_name: Subcutaneous Lumps

value: Batch 3

value: PR

value: Subcutaneous Lumps


title: Patient7D

source_name: Right Tonsil

value: Batch 6

value: RCHOP

value: Right Tonsil


title: Patient18D

source_name: Cervical Lymph Node

value: DAC

value: F

value: Cervical Lymph Node


title: Patient6D

source_name: Retroperitoneal Masscore Bx

value: ABC

value: CR

value: M

value: Retroperitoneal Masscore Bx


title: Mc1-Untr-3

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

data_processing:
demultiplexed Fasq reads generated from Novogene were analyzed using Partek® Flow® software, v10.0
Reads were trimmed for Phred score of 20, adapters removed using cutadapt
Trimmed reads were aligned using STAR 2.7.3 using and annotated with Ensembl EquCab3.0.107. Feature counts were generated with Htseq
Differential analysis was computed using counts normalized to CPM, using DESeq
Pathway analysis was performed with GSEA (Gene Set Enrichment Analysis) v4.2.1using Hallmark pathways
Assembly: EquCab3.0
Supplementary files format and content: txt file of cpm normalized counts filtered for protein coding genes

organism: Equus caballus

source_name: monoocyte derived macrophage

growth_protocol: To generate macrophage cultures, equine peripheral blood mononuclear cells were isolated from whole blood of two horses by density gradient centrifugation (Ficoll- Paque TM plus, GE Healthcare Bio-Sciences) and cultured in macrophage media (Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum, non-essential amino acids, and penicillin/streptomycin antibiotics; SigmaAldrich) with human M-CSF (PeproTech, Rocky Hill, NJ USA 80553) at 30 ng/mL to stimulate differentiation into macrophages in five days, as previously described [332].

extract_protocol:
Qiagen Rneasy
mRNA was enriched using oligo(dT) beads, followed by cDNA library generation using TruSeq RNA Library Prep Kit

treatment_protocol: Equine monocyte-derived macrophages were stimulated with IL-1ß (10 ng/mL) and OTs (MSC-CM, PRP lysate, ACS) were added at the same time to macrophage culture media at a ratio of 1:3 OT to complete growth media in culture (i.e., 25% OT in culture media) Following transient addition of treatments for 24 hours in culture, macrophages were washed three times with phosphate buffered saline (PBS) , collected in RNA lysis buffer (350 L/sample) and frozen at -20C until RNA isolation was performed.

value: monoocyte derived macrophage

value: Untreated


title: Patient17D

source_name: Mesenteric Lymph Node Mass

value: Diagnosis

value: GCB

value: Mesenteric Lymph Node Mass


title: Patient15R

source_name: Left Neck Node

value: Batch 3

value: Relapse

value: PR

value: Left Neck Node


title: Patient5D

source_name: Left Tonsil Excision

value: Batch 6

value: RCHOP

value: Left Tonsil Excision


title: Patient15D


title: Mc1-IL1b-3


title: Mc1-IL1b-1


title: Patient3R

source_name: Lymph Node Right Axilla Core Bx

value: Batch 5

value: Lymph Node Right Axilla Core Bx


title: Patient10R

source_name: Right Neck Node

value: ABC

value: F

value: Right Neck Node


title: Patient10D

source_name: Upper Neck Nodes

value: Upper Neck Nodes


title: Patient9R

source_name: Right Breast And Infra-Clavicular Fossa

value: DAC

value: CR

value: Right Breast And Infra-Clavicular Fossa


title: Patient2R

source_name: Testis

value: Batch 2

value: M

value: Testis


title: Patient9D

source_name: Axillary Lymph Node

value: Batch 3

value: Diagnosis

value: GCB

value: Axillary Lymph Node


title: Patient7R

source_name: Right Supraclavicular Lymph Node

value: Batch 6

value: Relapse

value: RCHOP

value: Right Supraclavicular Lymph Node


title: Patient2D

source_name: Lymph Node

value: ABC

value: Lymph Node


title: Mc1-MSC-1

value: monoocyte derived macrophage

value: MSC


title: Patient1R

source_name: Salivary Gland

value: Batch 4

value: CR

value: Salivary Gland


title: Mc1-IL1b-2


title: Patient6R

source_name: Left Neck Lymph Node Core Bx

value: M

value: Left Neck Lymph Node Core Bx


title: Patient13R

value: Batch 3

value: PR

value: F

value: Right Neck Node


title: Patient20R

source_name: Cervical Node Biopsy

value: GCB

value: DAC

value: Cervical Node Biopsy


title: Patient12R

source_name: Lymph Node - Left Arm

value: Relapse

value: RCHOP

value: Lymph Node - Left Arm


title: Liver 8:00pm rep2

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

description:
immunoprecipitated genomic DNA
DRMR7

data_processing:
Raw data were analyzed by the Illumina CASAVA 1.8.2
The reads were aligned to the mm9 revision of the mouse reference genome using only annotated chromosomes 1-19, chrX, chrY and chrM. Alignment was performed using Bowie (Langmead et al., 2009) with parameters -m 1 –strata –best-y-S - 40.
Genome_build: mm9
Supplementary_files_format_and_content: Normalized Bigwig files were generated using homer make UCSC file v4.9.1 (Heinz et al., 2010) with the following parameters ‘-norm 1e7’

source_name: Immunoprecipitated DNA using 5-methyl cytosine antibody

extract_protocol:
MeDIP assay was performed using freshly isolated liver from wild type mice at 8:00am (ZT02) and 8:00 pm( ZT14). Genomic DNA was prepared using phenol chloroform extraction method, purified and sonicated. The sonicated DNA was used for immunoprecipitation using 5 methyl cytosine antibody. The immunoprecipitated DNA was used for MeDIP-seq and analysis.
MeDIP libraries were prepared using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions.

value: Liver

tag: genotype

value: wild type

tag: time point


title: Patient5R

source_name: Left Tonsil Biopsy

value: Batch 6

value: Left Tonsil Biopsy


title: Patient11R

source_name: Unknown

value: ABC

value: CR

value: Unknown


title: Liver 8:00pm rep1

description:
immunoprecipitated genomic DNA
DRMR9


title: Mc1-Untr-1

source_name: monoocyte derived macrophage

value: monoocyte derived macrophage

value: Untreated


title: Mc1-PRP-2

value: PRP


title: Liver 8:00am rep2

description:
immunoprecipitated genomic DNA
DRMR11


title: Mc1-IRAP-LIB

value: ACS


title: Mc1-PRP-1


title: Patient4R

source_name: Omental Nodule

value: Batch 7

value: UNC

value: F

value: Omental Nodule


title: Mc1-MSC-2

value: MSC


title: Mc1-MSC-3


title: Patient3D

source_name: Skin Bx

value: Batch 5

value: Diagnosis

value: RCHOP

value: M

value: Skin Bx


title: human ventricular cardiac organoid chamber [N-COC_S1_L004]

city: Sha Tin

first: Shangli

last: Cheng

address: No. 15 Science Park West Avenue

department: Ming Wai Lau Centre for Reparative Medicine

country: Hong Kong

institute: Karolinska Institutet

description:
hIPSC-hvCOC
hiPSC_UMIcounts.txt

data_processing:
The unique molecular identifier (UMI) counts of each barcode were analysed by using Cell Ranger following the pipeline with default parameters..
The low-quality cells with total UMI counts of less than 1,000 or more than 50,000 or with mitochondrial genes accounting for more than 15% out of the total UMI counts were excluded from the analysis. The cells expressing less than 1,000 or more than 7,500 features were also disregarded.
All analyses were carried out with R (version 4.1.1).
The analysis of maturation state was carried out by using Cellular Trajectory Reconstruction Analysis (CytoTRACE, version 0.3.3).
The differentially expressed genes were calculated using the DESeq2 (version 1.32.0).
Assembly: hg38
Supplementary files format and content: UMI count matrices of hPSCs with sample information in the column names.

source_name: hPSC

growth_protocol: All hPSCs were cultured in a 6-well tissue culture plate coated with Matrigel, using mTeSR1 medium

extract_protocol:
All tissue constructs were washed with PBS without Ca2+ and Mg2+ and incubated in a solution containing 10 unit/mL of papain (Sigma, 76220) and 1 mM of EDTA (Roth, 8043.2) for 45 min at 37°C. The cells were then gently triturated for ~1 min until a single-cell suspension was obtained. Medium with 10% fetal calf serum (FCS, Merck-Milipore, S 0615) was added to inhibit the digestion process. The cells were then washed in PBS and counted.
Single Cell 3’ Reagent Kit v2 (Chromium Single Cell 3’ Library & Gel Bead Kit v2, Chromium Single Cell A Chip Kit, 48 runs, 10x Genomics) and Chromium Controller (10x Genomics)

treatment_protocol: All hPSCs were differentiated in a 6-well low-attachment culture plate using the embryoid body suspension method in two induction stages: stage 1 with the addition of BMP4 and Activin A for mesodermal induction and stage 2 with the addition of IWR-1 to inhibit Wnt signaling pathways for cardiac specification.

tag: cell line

value: hiPSC

tag: tissue configuration

value: hvCOC


title: Mc1-IRAP-Cheyto


title: Mc1-IRAP-PC


title: human ventricular cardiac organoid chamber [N-COC_S1_L001]

description:
hIPSC-hvCOC
hiPSC_UMIcounts.txt


title: human ventricular cardiac organoid chamber [hES2-COC_S1_L004]

description:
hvCOC-03
hESC_UMIcounts.txt

value: hESC


title: B3

city: Chengdu

first: Jin

last: XIAO

address: No.37, Twelve Bridges Road, Jinniu District, Chengdu, Sichuan Province

institute: Chengdu University of TCM

description: 2100 biochip analyzer

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: Colon tissue

growth_protocol: The rats were housed in standard class II animal rooms, quiet and noiseless, with circulating ventilation in the experimental environment. The room temperature was 22±2℃, the room humidity was 50±10%, and the light-to-dark ratio was 1/1. after 1 week of acclimatization feeding.

extract_protocol:
The skin and subcutaneous tissues and the greater omentum were cut along the midline of the rat's abdomen using scissors, and the terminal tissues of the colon and rectum were exposed and separated, and the tissues of the intestinal segment 6 cm from the end of the anus were removed for the next step of testing.
RNA libraries for RNA-seq were prepared using small RNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The IBS-D animal model was established using a combination of the colorectal dilatation method + chronic restraint stress method in the model rats. The rats were gently touched on the anal region before the experiment to induce them to evacuate feces. The homemade colorectal dilatation balloon coated with paraffin oil was gently inserted into the rectum of the rat about 7 cm, and the catheter was fixed at the tail of the rat, about 1 cm from the anus, after which the rat was fixed in a transparent observation chamber (20*6*8 cm) so that it could only move back and forth, and the colorectal dilatation was performed after waiting for the rat to calm down, and the dilatation pressure was 80 mmHg once/day for 2 weeks; meanwhile, the blank control group only stroked the perineum with the same frequency.

value: Colon tissue

value: Blank control

tag: molecule type

value: miRNAs


title: B2

description: 2100 biochip analyzer

tag: tissue


title: human ventricular cardiac organoid chamber [hES2-COC_S1_L003]

description:
hvCOC-03
hESC_UMIcounts.txt


title: B1

description: 2100 biochip analyzer


title: Patient4D

source_name: Left Ovary

value: ABC

value: CR

value: Left Ovary


title: human ventricular cardiac organoid chamber [hES2-COC_S1_L002]

description:
hvCOC-03
hESC_UMIcounts.txt


title: Mc1-PRP-3

value: monoocyte derived macrophage

value: PRP


title: M3

description: 2100 biochip analyzer

value: IBS-D


title: Liver 8:00am rep1

description:
immunoprecipitated genomic DNA
DRMR5

value: Liver

value: wild type


title: human ventricular cardiac anisotropic sheet  [hES2-CAS_S1_L004]

description:
hvCAS-02
hESC_UMIcounts.txt

value: hvCAS


title: human ventricular cardiac organoid chamber [N-COC_S1_L003]

description:
hIPSC-hvCOC
hiPSC_UMIcounts.txt


title: M2

description: 2100 biochip analyzer


title: human ventricular cardiac anisotropic sheet  [hES2-CAS_S1_L002]

description:
hvCAS-02
hESC_UMIcounts.txt


title: human ventricular cardiac organoid chamber [N-COC_S1_L002]

description:
hIPSC-hvCOC
hiPSC_UMIcounts.txt


title: human ventricular cardiac anisotropic sheet  [hES2-CAS_S1_L001]

description:
hvCAS-02
hESC_UMIcounts.txt


title: Patient1D

source_name: Submandibular Lymph Node

value: Batch 1

value: Diagnosis

value: GCB

value: RCHOP

value: M

value: Submandibular Lymph Node


title: M1

description: 2100 biochip analyzer

value: Colon tissue


title: human ventricular cardiac anisotropic sheet  [hES2-CAS_S1_L003]

description:
hvCAS-02
hESC_UMIcounts.txt

value: hESC


title: human ventricular cardiac organoid chamber [hES2-COC_S1_L001]

description:
hvCOC-03
hESC_UMIcounts.txt

value: hvCOC


title: Fuji ZSTK 0 μM 24h

city: Tokyo

first: Sho

last: Isoyama

state: Tokyo

address: 3-8-31 Ariake, Koto-ku

department: Cancer Chemotherapy Center

institute: Japanese foundation for cancer research

description: Gene expression data from non-treated synovial sarcoma cells

hyb_protocol: Biotin-labelled and fragmented cRNAs were hybridized with Affymetrix Hybridization, Wash, and Stain Kit to the Human Genome U133 Plus 2.0 Array.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Microarray data were analyzed using MAS5.0 and GeneSpring v14.9.1 software.

label: Biotin

source_name: Human synovial sarcoma cell line Fuji treated with ZSTK474 0 μM for 24h

label_protocol: Biotinylated cRNA was prepared with Affymetrix GeneChip 3'IVT expression kit according to the manufactuer's instruction.

growth_protocol: Human synovial sarcoma cell lines were grown in RPMI-1640 medium supplemented with 5% Fetal Bovine Serum in a humidified incubator at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using the Qiagen kit following manufacturer's instructions.

treatment_protocol: Human synovial sarcoma cells were treated with vehicle or a pan-PI3K inhibitor ZSTK474 at 0, 0.3 or 3 μM for 24h.

value: control

value: Synovial Sarcoma

value: Fuji


title: Fuji ZSTK 0.3 μM 24h

description: Gene expression data from synovial sarcoma cells treated with a pan-PI3K inhibitor ZSTK474

source_name: Human synovial sarcoma cell line Fuji treated with ZSTK474 0.3 μM for 24h

value: ZSTK474 0.3 μM for 24h


title: Yamato-SS ZSTK 0.3 μM 24h

source_name: Human synovial sarcoma cell line Yamato-SS treated with ZSTK474 0.3 μM for 24h

value: Yamato-SS


title: Fuji ZSTK 3 μM 24h

source_name: Human synovial sarcoma cell line Fuji treated with ZSTK474 3 μM for 24h

value: ZSTK474 3 μM for 24h


title: Yamato-SS ZSTK 3 μM 24h

source_name: Human synovial sarcoma cell line Yamato-SS treated with ZSTK474 3 μM for 24h


title: Yamato-SS ZSTK 0 μM 24h

source_name: Human synovial sarcoma cell line Yamato-SS treated with ZSTK474 0 μM for 24h


title: BINGRENZU5

city: guangzhou

first: cuicui

last: wang

state: guangdong

address: 1 Pan Fu Road

department: rheumatology

institute: Guangzhou First People’s Hospital, The Second Affiliated Hospital of South China University of Technology

data_processing:
To get high quality clean reads, reads were further filtered by fastp(version 0.18.0)
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2(version 2.1.0)
The reconstruction of transcripts was carried out with software Stringtie (version 1.3.4)
Transcripts abundances were quantified by software StringTie in a reference-based approach
RNAs and lncRNAs differential expression analysis was performed by DESeq2 software
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: Peripheral venous blood

extract_protocol:
The RNA of  peripheral blood mononuclear cells(PBMCs) was harvested using Trizol reagent. RNA quality was assessed on an Agilent 2100 Bioanalyzer(Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
Total RNA was extracted, rRNAs were removed to retain mRNAs and ncRNAs. The enriched mRNAs and ncRNAs were fragmented into short fragments by using fragmentation buffer and reverse transcribed into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP (dUTP instead of dTTP) and buffer.The cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen,Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. Then UNG (Uracil-N-Glycosylase) was used to digest the second-strand cDNA. The digested products were size selected by agarose gel electrophoresis,PCR amplified, and sequenced using Illumina HiSeqTM 4000 (or other platforms) by Gene Denovo Biotechnology Co. (Guangzhou, China)

value: Peripheral venous blood

tag: diagnosis

value: SLE

value: Peripheral Blood Mononuclear Cell


title: BINGRENZU3


title: DUIZHAOZU3

value: healthy control


title: Individual tibialis anterior myofiber from Smn1deltaSKM+AFS mouse 2, replicate 3 [Smn1deltaSKM+AFS-7]

city: Padova

first: Caterina

last: Millino

address: Ugo Bassi 58

country: Italy

institute: University of Padova

description: Gene expression of individual tibialis anterior myofiber from Smn1deltaSKM+AFS mouse

hyb_protocol: 800 ng of labeled cDNA were mixed with 5 µl of 10X Blocking Agent (Agilent Technologies) and water to a final volume of 25 µl. Samples were denatured at 95°C for 2 min. and added to 25 µl of 2X GEx Hybridization Buffer HI-RPM (Agilent Technologies). 40 µl of mix was dispensed onto one array of the SurePrint G3 Mouse Gene Expression 8x60K microarray. Slides were loaded into the Agilent SureHyb chambers and hybridization was performed in a hybridization oven at 65°C for 17 hours with 10 rpm rotation. Finally, slides were washed using Wash Buffer Kit (Agilent Technologies) and dried at room temperature.

scan_protocol: Microarrays were scanned using the Agilent Technologies Scanner G2505C US22502723 (ChipScan software version A.8.5.1), scan region 61 x 21.6 mm, scan resolution 3 micron single pass, Green PTM 100%, no extended dynamic range (NO XDR).

data_processing: Data was extracted from the scanned image using the Agilent Feature Extraction Software version 10.7.3.1 (protocol GE1_107_Sep09). Quantile inter-arrays normalization was performed with the Expander software (Bioinformatics 2003; 19:1787-99) on the gProcessedSignal column of the result table and normalized data is reported in the VALUE column. Probes with Found or Well Above Background value of zero were disregarded and labeled as “null”. Mean values were calculated for multiple probes with the same Agilent Probe ID.

label_protocol: RNA was exponentially amplified using the TransPlex WholeTranscriptome Amplification 2 Kit (Sigma-Aldrich) in accordance with the manufacturer’s instructions, using 18 cycles of amplification. Amplification product was purified with the GenElute PCR Clean-up columns (Sigma-Aldrich). Resulting cDNA was quantified with Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific). 2 µg of amplified-purified cDNA were labeled using the Genomic DNA Enzymatic Labeling Kit (Agilent Technologies), as suggested by manufacturer, and purified using the Amicon 30kDa filters (Millipore). On average, cDNA yield was about 4 µg and the specific activity of 30 pmol Cy3 per µg cDNA.

growth_protocol: Mice were housed in a normal environment provided with ad libitum food and water and were killed by rapid cervical dislocation to minimize suffering.

extract_protocol: A single myofiber was lysed in 250 µl of TRIzol Reagent (Thermo Fisher Scientific) following the manufacturer’s instructions. After phases separation the upper aqueous phase containing RNA was added with 70% ethanol before column purification with RNeasy Micro Kit (Qiagen). Total RNA quality was monitored using the RNA Pico LabChip on a 2100 Bioanalyzer (Agilent Technologies).

tag: gender

value: Male

value: 3 months

value: Tibialis anterior


title: Individual tibialis anterior myofiber from Smn1deltaSKM+AFS mouse 1, replicate 1 [Smn1deltaSKM+AFS-1]


title: Aska-SS ZSTK 0.3 μM 24h

source_name: Human synovial sarcoma cell line Aska-SS treated with ZSTK474 0.3 μM for 24h

value: Aska-SS


title: SYO-1 ZSTK 3 μM 24h

source_name: Human synovial sarcoma cell line SYO-1 treated with ZSTK474 3 μM for 24h


title: Aska-SS ZSTK 0 μM 24h

source_name: Human synovial sarcoma cell line Aska-SS treated with ZSTK474 0 μM for 24h


title: Aska-SS ZSTK 3 μM 24h

source_name: Human synovial sarcoma cell line Aska-SS treated with ZSTK474 3 μM for 24h


title: DUIZHAOZU1


title: Individual tibialis anterior myofiber from Smn1deltaSKM+AFS mouse 1, replicate 4 [Smn1deltaSKM+AFS-4]


title: BINGRENZU6


title: Individual tibialis anterior myofiber from Smn1deltaSKM+AFS mouse 2, replicate 2 [Smn1deltaSKM+AFS-6]


title: SYO-1 ZSTK 0 μM 24h

source_name: Human synovial sarcoma cell line SYO-1 treated with ZSTK474 0 μM for 24h


title: Individual tibialis anterior myofiber from Smn1deltaSKM+AFS mouse 2, replicate 1 [Smn1deltaSKM+AFS-5]


title: B3

city: nanchang

first: chao

last: zhu

address: Yongwai Main Street

institute: The First Affiliated Hospital of Nanchang University, Donghu District, Nanchang City, Jiangxi Province

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1)
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: UMUC3 cells

extract_protocol:
UMUC3 cells were washed by PBS for 3 times and then lysed by Trizol at 4℃ for 10 minutes . Next, samples were sent to GeneChem on dry ice.
RNA libraries were prepared for sequencing using lliumina protocols.

value: infect PLVX-IRES-Zsgreen


title: SYO-1 ZSTK 0.3 μM 24h

source_name: Human synovial sarcoma cell line SYO-1 treated with ZSTK474 0.3 μM for 24h


title: BINGRENZU1


title: BINGRENZU2


title: DUIZHAOZU2


title: Individual tibialis anterior myofiber from Smn1deltaSKM mouse 3, replicate 3 [Smn1deltaSKM-11]

description: Gene expression of individual tibialis anterior myofiber from Smn1deltaSKM mouse


title: Individual tibialis anterior myofiber from Smn1deltaSKM mouse 2, replicate 1 [Smn1deltaSKM-5]


title: Individual tibialis anterior myofiber from Smn1deltaSKM+AFS mouse 1, replicate 2 [Smn1deltaSKM+AFS-2]


title: Individual tibialis anterior myofiber from Smn1deltaSKM mouse 2, replicate 3 [Smn1deltaSKM-7]


title: Individual tibialis anterior myofiber from Smn1deltaSKM mouse 2, replicate 2 [Smn1deltaSKM-6]


title: Individual tibialis anterior myofiber from Smn1deltaSKM mouse 3, replicate 4 [Smn1deltaSKM-12]


title: Individual tibialis anterior myofiber from Smn1deltaSKM mouse 3, replicate 2 [Smn1deltaSKM-10]


title: Individual tibialis anterior myofiber from Smn1deltaSKM mouse 3, replicate 1 [Smn1deltaSKM-9]


title: Individual tibialis anterior myofiber from Smn1deltaSKM mouse 2, replicate 4 [Smn1deltaSKM-8]


title: A1

value: infect TIM-1-PLVX-IRES-zsgreen


title: Patient19D

source_name: Bilateral Cervical Lymphadenopathy

value: Batch 3

value: Diagnosis

value: ABC

value: RCHOP

value: CR

value: F

value: Bilateral Cervical Lymphadenopathy


title: Individual tibialis anterior myofiber from Smn1deltaSKM+AFS mouse 1, replicate 3 [Smn1deltaSKM+AFS-3]


title: B2


title: K562 CEBPA reporter cell line, Stress and Proteostasis Sublibrary, Far Right bin

city: Berkeley

first: Nicholas

middle: T

last: Ingolia

address: 1 Barker Hall #3202

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
fr
stress_proteostasis_sgRNA_raw_counts.txt

data_processing:
Sequencing reads were first trimmed to remove adapter sequences using Cutadapt.
Trimmed sgRNA reads were then counted using MAGeCK.
Assembly: hCRISPRiv2 sgRNA sequence reference
Supplementary files format and content: tab-delimited text file containing raw, unnormalized read counts for each sample per sublibrary screen.
Library strategy: CRISPRi

growth_protocol: Human K562 cells were grown in RPMI-1640 with L-glutamine (ThermoFisher Scientific) supplemented with 10% FBS, 1% sodium pyruvate, 100 units/mL penicillin and 100 mg/mL streptomycin and grown at 37C and 5% CO2.

extract_protocol:
Genomic DNA was harvested with DNeasy Blood and Tissue kit (Qiagen, 69504).
sgRNA fragments from genomic DNA were isolated by SbfI (New England Biolabs) restriction digestion and Ampure bead size selection then amplified by PCR for deep sequencing using custom primers.

value: myeloid leukemia cells

value: CRISPRi

tag: bin

value: fr


title: K562 CEBPA reporter cell line, Stress and Proteostasis Sublibrary, Far Left bin

description:
fl
stress_proteostasis_sgRNA_raw_counts.txt

value: fl


title: K562 CEBPA reporter cell line, Stress and Proteostasis Sublibrary, Near Right bin

description:
nr
stress_proteostasis_sgRNA_raw_counts.txt

value: nr


title: K562 CEBPA reporter cell line, Stress and Proteostasis Sublibrary, Near Left bin

description:
nl
stress_proteostasis_sgRNA_raw_counts.txt

value: nl


title: A3


title: Individual tibialis anterior myofiber from Smn1deltaSKM mouse 1, replicate 4 [Smn1deltaSKM-4]

value: Male

value: 3 months

value: Tibialis anterior


title: Individual tibialis anterior myofiber from Smn1deltaSKM mouse 1, replicate 3 [Smn1deltaSKM-3]


title: Individual tibialis anterior myofiber from Smn1deltaSKM mouse 1, replicate 1 [Smn1deltaSKM-1]


title: K562 CEBPA reporter cell line, Cancer and Apoptosis Sublibrary, Near Right bin

description:
nr
cancer_apoptosis_sgRNA_raw_counts.txt


title: Mc1-Untr-2

source_name: monoocyte derived macrophage

value: monoocyte derived macrophage

value: Untreated


title: Individual tibialis anterior myofiber from Smn1deltaSKM mouse 1, replicate 2 [Smn1deltaSKM-2]


title: AoV_DKO3

city: Tsukuba

first: Hiromi

last: Yanagisawa

state: Ibaraki

address: 1-1-1 Tennodai

department: TARA Center

institute: University of Tsukuba

data_processing:
Sequencing was done in MiSeq (illumina) to generate 6 gz fastq files per mouse model
Reads (FASTQ files) were analyzed by using CLC Genomics Workbench (Version 22.0, QIAGEN) and trimmed sequences were mapped on the mouse genome (GRCm39.105).
Gene expression values were presented in total read counts and TPM values
Differentially expressed genes were analyzed using the Differential Expression tool in RNA-seq and small RNA analysis on CLC Genomics Workbench. Differentially expressed genes were filtered using 2 fold change and p value < 0.05.
Assembly: GRCm39.105
Supplementary files format and content: tab-delimited text files include gene name; identifier; fold change and p value for differential expressed genes comparison between DKO vs CTRL, DKO vs ECKO and DKO vs SMKO; total read counts and TPM values in each sample.

source_name: aortic valve

extract_protocol:
Hearts and aortic valves were harvested from CTRL, ECKO, SMKO, and DKO mice after perfusion with 5 ml of 1xPBS. The tissues were immediately fixed with 4% paraformaldehyde, then washed with 20% sucrose and embedded in OCT (SAKURA Finetek USA Inc., #4583) to make frozen tissue samples. Cross-sections of the aortic valves (20 μm thickness) were mounted onto PEN-Membrane slides (Leica, #11600288) and stored at -80ºC until the LMD process. The aortic valve sections on the slide were replaced at room temperature and dried up with a handy circulator. The sections were fixed briefly with 100% ethanol and stained with hematoxylin solution (Muto Pure Chemicals Co., LTD, #30141) for 3 min, then incubated in a water bath at 30ºC for 15 min. After that, the sections were cleaned with 100% ethanol and dried up completely at room temperature. Whole aortic valve leaflets were captured using LMD7 (Leica) under the 10x magnification and collected into MaxyClear (low adhesion) microtube (Corning, PCR-02-L-C) with 20 µL 99.5% ethanol and stored at -80ºC until cDNA library preparation.
cDNA library was prepared from LMD-captured aortic valves by the Nextera XT DNA library prep kit (illumina, FC-131-1024) as previously described. The amplified 0.25 ng cDNA was used for RNA-seq library preparation and sequenced on the MiSeq (illumina) with paired-end 75-base read option..

tag: strain

value: DKO

value: aortic valve leaflets

value: 2 months old


title: Individual tibialis anterior myofiber from WT mouse 2, replicate 2 [WT-6]

description: Gene expression of individual tibialis anterior myofiber from WT mouse

value: wild type


title: B1

value: infect PLVX-IRES-Zsgreen


title: Individual tibialis anterior myofiber from WT mouse 1, replicate 4 [WT-4]


title: Individual tibialis anterior myofiber from WT mouse 2, replicate 4 [WT-8]


title: Individual tibialis anterior myofiber from WT mouse 1, replicate 3 [WT-3]


title: A2

value: infect TIM-1-PLVX-IRES-zsgreen


title: K562 CEBPA reporter cell line, Kinases, Phosphatases, and Drug Targets Sublibrary, Far Left bin

description:
fl
kinases_sgRNA_raw_counts.txt

value: myeloid leukemia cells


title: K562 CEBPA reporter cell line, Cancer and Apoptosis Sublibrary, Near Left bin

description:
nl
cancer_apoptosis_sgRNA_raw_counts.txt

value: CRISPRi


title: Individual tibialis anterior myofiber from WT mouse 2, replicate 3 [WT-7]


title: Individual tibialis anterior myofiber from WT mouse 2, replicate 1 [WT-5]


title: K562 CEBPA reporter cell line, Cancer and Apoptosis Sublibrary, Far Left bin

description:
fl
cancer_apoptosis_sgRNA_raw_counts.txt


title: K562 CEBPA reporter cell line, Cancer and Apoptosis Sublibrary, Far Right bin

description:
fr
cancer_apoptosis_sgRNA_raw_counts.txt

value: fr


title: K562 CEBPA reporter cell line, Kinases, Phosphatases, and Drug Targets Sublibrary, Near Right bin

description:
nr
kinases_sgRNA_raw_counts.txt


title: AoV_DKO1


title: AoV_DKO2


title: AoV_ECKO2

value: ECKO


title: AoV_SMKO3

value: SMKO


title: K562 CEBPA reporter cell line, Gene Expression Sublibrary, Near Left bin

description:
nl
gene_expression_sgRNA_raw_counts.txt

value: nl


title: K562 CEBPA reporter cell line, Kinases, Phosphatases, and Drug Targets Sublibrary, Far Right bin

description:
fr
kinases_sgRNA_raw_counts.txt


title: AoV_ECKO1


title: AoV_SMKO2


title: iHEP RWV ORG + MTG Ri_3 [I3DRiM_3]

city: San francisco

first: Tammy

last: Chang

state: CA

address: 513 parnassus Ave.

institute: UCSF

description: Processed data files_stem cells full list.xlsx

data_processing:
Raw reads in FASTQ format were processed by removing the adaptor reads or poly-N and low-quality reads.
Error rate distribution and Q20, Q30, and GC content of the cleaned data were calculated.
Quality-controlled reads were mapped to the human reference genome (hg19) with STAR alignment software
Raw reads were normalized by DESeq2 algorithm
Assembly: hg19
Supplementary files format and content: DESeq2 output

source_name: liver

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plus Mini Kit, and 1μg of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated by NEBNext Ultra Directional RNA Library Prep Kit for Illumina following the manufacturer’s protocols.

value: liver

value: AICS-0023 iPSC

value: Induced Pluripotent Stem Cells

value: iHEP RWV ORG + MTG Ri


title: AoV_CTRL2

value: CTRL


title: Individual tibialis anterior myofiber from WT mouse 1, replicate 1 [WT-1]

value: Male

value: 3 months

value: Tibialis anterior


title: iHEP RWV ORG + MTG Ri_1 [I3DRiM_1]


title: Individual tibialis anterior myofiber from WT mouse 1, replicate 2 [WT-2]

value: wild type


title: AoV_SMKO1

value: aortic valve leaflets

value: 2 months old


title: K562 CEBPA reporter cell line, Kinases, Phosphatases, and Drug Targets Sublibrary, Near Left bin

description:
nl
kinases_sgRNA_raw_counts.txt

value: myeloid leukemia cells


title: K562 CEBPA reporter cell line, Gene Expression Sublibrary, Near Right bin

description:
nr
gene_expression_sgRNA_raw_counts.txt

value: CRISPRi

value: nr


title: AoV_ECKO3

value: ECKO


title: K562 CEBPA reporter cell line, Gene Expression Sublibrary, Far Right bin

description:
fr
gene_expression_sgRNA_raw_counts.txt

value: fr


title: K562 CEBPA reporter cell line, Gene Expression Sublibrary, Far Left bin

description:
fl
gene_expression_sgRNA_raw_counts.txt

value: fl


title: iHEP RWV ORG + MTG Ri_2 [I3DRiM_2]

value: liver


title: iHEP MTG ORG + Ri_3 [I2DRi_3]

value: AICS-0023 iPSC

value: iHEP MTG ORG + Ri


title: iHEP RWV ORG + Ri_3 [I3DRi_3]

value: Induced Pluripotent Stem Cells

value: iHEP RWV ORG + Ri


title: AoV_CTRL1

value: CTRL


title: iHEP MTG ORG + Ri_2 [I2DRi_2]


title: iHEP MTG ORG + Ri_1 [I2DRi_1]