title: Regenerated pulp tissue; A2-cd24-pos-vivo

description: Library name: A2-cd24-pos-vivo


title: MDAMB231_WT_H4_Input_rep1

status: Public on Apr 26 2026

type: SRA

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

country: USA

institute: Dana-Farber Cancer Institute

description: Library name: Sample15

library_source: genomic

data_processing:
ChIP-seq and ATAC-seq data processing were based on chips pipeline (Qiu et al., 2021; Taing et al., 2021). Peak calling was performed using MACS2 v2.1.2 with FDR<0.01 as the cutoff (Feng et al., 2012).
Reads were aligned to hg19 genome using BWA-MEM aligner (Li, 2013) and bigwig files were called after normalization to the corresponding input control.
Assembly: hg19
Supplementary files format and content: .bw files

molecule: genomic DNA

organism: Homo sapiens

source_name: Human breast cancer

growth_protocol: SUM149 cells were cultrued in DMEM-F12 medium +5% FBS, 10 mM HEPES pH7.4, 1 μg/ml hydrocortisone, 5 μg/ml insulin and 100U/ml Penicillin-Streptomycin. MDA-MB-231 and MDA-MB-468 cells were cultured in DMEM medium with 10% FBS and 100U/ml Penicillin-Streptomycin.

extract_protocol:
For ChIP-seq, 150 mm plates tissue culture plates were fixed in 1% formaldehyde (Electron Microscopy Sciences, 15714) containing fixing buffer (50 mM HEPESKOH pH7.5, 100 mM NaCl, 1 mM EDTA pH8 and 0.5 mM EGTA pH8) for 10 min at 37°C.  Crosslinking was quenched by adding glycine to a final concentration of 0.125 M and further rocking the plates for 5 min. Cell monolayers were washed twice with ice-cold PBS and scrapped off the plate in 10 ml PBS, spun at 200g for 5 min, and flash frozen after removing the supernatant. Frozen pellets were resuspended in 1 ml of Cell Lysis Buffer (50 mM HEPES pH8, 140 mM NaCl, 1 mM EDTA pH8, 10 % glycerol, 0.5% NP-40, 0.25% Triton X-100 and PPI) and incubated for 10 min at 4°C with gentle rotation. Nuclei were then centrifuged at 1,700g for 5 min at 4°C. Pelleted nuclei were washed twice with 1 ml Wash Buffer (10 mM Tris-HCl pH8, 200 mM NaCl, 1mM EDTA pH8, 0.5 mM EGTA pH8 and PPI) and then resuspended in 1 ml of Shearing Buffer (10 mM Tris-HCl pH7.4, 1 mM EDTA pH8, 0.1% SDS, 1% Triton-X100, 0.1% Sodium Deoxycholate, 0.25% NLauroylsarcosine, 1 mM DTT and PPI) and sonicated in a Covaris E220 focused-ultrasonicator (peak intensity: 140, 5% duty cycle, 200 cycles per burst, 10-12 min) using 1 ml AFA fiber tubes. An equivalent of 5 x 106 cells was sonicated in each tube and used for each ChIP. Lysates were centrifuged for 15 min at 10,000g in a refrigerated centrifuge. Cleared supernatants were transferred to new tubes and NaCl was added to a final concentration of 150 mM. Samples were then incubated with Dynabeads Protein G (LifeTechnologies,10003D, 40 µl/ml of lysate) for 1 hour at 4°C, with constant rotation (pre-clearing). After magnetic separation of the beads, the appropriate primary antibody was added to each tube for an overnight immunoprecipitation, at 4°C, with gentle rotation. Antibody-bound cross-linked chromatin was precipitated with prewashed Dynabeads Protein G for 2 h at 4°C and with constant rotation. Beads were then washed sequentially with low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS), high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS), LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) and twice with 1X TE buffer. Each wash was performed for 5 min at 4°C with gentle rotation. DNA was eluted from the beads with 300 µl of 100 mM sodium bicarbonate and 1% SDS for 30 min at RT with constant shaking. Crosslinking was reversed overnight at 65°C and RNA and protein were then sequentially digested by adding 0.2 mg/ml RNase A for 30 min at 37°C followed by 0.2 mg/ml Proteinase K for 1 h at 55°C. DNA was extracted with 300 µl of phenol/chloroform/isoamyl-alcohol (Calbiochem, #516726) and centrifuged at 20,000g for 5 min at RT. DNA in the upper layer was then precipitated with 1 volume isopropanol, 1/3 volume of 2 M sodium perchlorate and 5 µl glycogen and centrifuged at 20,000g for 10 min at RT. Pelleted DNA was washed twice with 70% ethanol and resuspended in 20 µl low TE. For ATAC-seq: Fifty thousand cells were resuspended in 1ml of cold ATAC-seq resuspension buffer (RSB) (10mM Tris-HCl (pH 7.4), 10mM NaCl and 3mM MgCl2 in water). Cells were centrifuged at maximum speed for 10min in a prechilled (4 °C) fixed-angle centrifuge. After centrifugation, supernatant was carefully aspirated. Cell pellets were then resuspended in 50μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin by pipetting up and down three times and incubated on ice for 3min. After lysis, 1ml of ATAC-seq RSB containing only 0.1% Tween-20 was added and the tubes were inverted to mix. Nuclei were then centrifuged for 5min at max speed in a prechilled fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50μl of transposition mix (25μl 2X TD buffer, 2.5μl transposase (100nM final), 16.5μl PBS, 0.5μl 1% digitonin, 0.5μl 10% Tween20 and 5μl water46) by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Qiagen MinElute columns.
ChIP-seq/Hi-ChIP: Libraries were prepared using the ThruPLEX DNA-seq Kit (Rubicon Genomics, R400427) according to the manufacturer’s protocol. Library fragments were size-selected by PAGE within a 150kb and 700kb range. ATAC-seq: Libraries were amplified as previously described (Buenrostro et al., 2015).

treatment_protocol: For in vitro experiment, cells were profield under three different designs: 1) baseline charaterization without any treatment; 2) 0,1% DMSO (vehicle) or 1μM A196 treatment for 5 days; 3) wiuth or without pretreatment of 1μM A196 treatment for 5 days and further in the presence or absence of 1μM Tunicamycin treatment for 12 hours.

tag: tissue

value: Human breast cancer

tag: cell line

tag: cell type

value: Human breast cancer epithelial cell

tag: genotype

value: Wild-type

tag: treatment

value: No treatment


title: MDAMB468_H4K20me3_rep1

description: Library name: Sample13


title: DN1_Primary human T cells_AIRMUT-HA_DMSO

city: san francisco

first: Jeremy

last: Bjelajac

state: CA

address: 2190 grove st

department: Pediatrics

institute: Stanford University

description:
Library name: Sample_2
Column name in raw_counts.txt: DN1_AIR-MUT

library_source: transcriptomic

data_processing:
Raw reads were assessed for quality using FastQC. Adapter trimming and quality filtering were performed.
Reads were aligned to the human reference genome (GRCh38/hg38) using STAR aligner.
Gene-level read counts were quantified using featureCounts or HTSeq against a GENCODE/Ensembl GTF annotation. (verify — check your counts.txt file header for the tool used)
Differential expression analysis was performed using DESeq2 or edgeR. Genes with adjusted p-value < 0.05 and |Log2 Fold Change| > 1 were considered differentially expressed.
PCA was performed using the top variable genes. Hierarchical clustering was performed on the top 100 genes driving PC1 variance.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text file (raw_counts.txt): raw gene-level read counts per sample, with Ensembl gene IDs as rows and sample names as columns.

molecule: total RNA

source_name: T cells (DN1)

growth_protocol: Primary human T cells were isolated from healthy donor PBMCs and activated with anti-CD3/CD28 magnetic beads (Dynabeads). T cells were lentivirally transduced with HA.28ζ, AIR-HA.28ζ, or mutAIR-HA.28ζ CAR constructs and expanded in T cell media (RPMI + 10% FBS + IL-2).

extract_protocol:
Total RNA was extracted from CAR T cells using a standard RNA isolation kit (e.g., RNeasy Mini Kit, Qiagen). RNA quality and quantity were assessed prior to library preparation.
Bulk RNA-seq libraries were prepared from total RNA using a poly(A) selection for paired-end sequencing. Libraries were sequenced by Novogene on an Illumina platform.

treatment_protocol: On Day 7 of culture, cells were treated with either DMSO (vehicle control) or Dasatinib (1 μM) for 7 days. Cells were derived from three healthy donors. After treatment, cells were harvested for RNA extraction.

value: T cells (DN1)

value: AIRMUT-HA

value: DMSO

tag: batch


title: YCC-6

city: 강남구

first: Inho

last: Park

state: 서울특별시

address: Dept. of Pathology, Gangnam Severance Hospital, 20, Eonjuro 63gil

department: Yonsei University College of Medicine

country: South Korea

institute: Yonsei University College of Medicine

description:
Library name: TN1404R0746
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-6

data_processing:
Sequencing reads were quality-checked using FastQC and trimmed with Trimmomatic. Clean reads were aligned to the human reference genome (hg19) using STAR (v2.7). Gene-level raw counts were generated with featureCounts (Subread v2.0.1) based on GENCODE gene annotation (release 38). No further normalization was applied before submission.
Assembly: hg19
Supplementary files format and content: excel file includes raw counts for each Sample

molecule: polyA RNA

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen), quality-assessed with NanoDrop and Bioanalyzer.
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA integrity was assessed using the Agilent 2100 Bioanalyzer. Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit, including poly(A) mRNA enrichment, fragmentation, cDNA synthesis, adaptor ligation, and PCR amplification. Final libraries were quantified, pooled, and sequenced on an Illumina HiSeq 2500 platform (2 x 100 bp).


title: EMT6_A196_Tumor3

description:
Library name: sample 12
10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, feature counting and aggregation was done using cellranger v7.0.1.
Assembly: mm10
Supplementary files format and content: barcode, feature and matrix file of each sample

organism: Mus musculus

source_name: primary breast tumor

growth_protocol: Primary tumors were induced by injecting cells into mammary fat pads of Balb/c mice.

extract_protocol:
Whole tumors were disrupted using micropestles and digested for 1h at 37C on a shaker with digestion medium (2% w/v collagenase IV, 2% w/v hyaluronidase and 2% w/v BSA in DMEM). Cells were filtered through 500 µm meshes, washed with PBS and stored in freezing medium. Immediately before library preparation, dead cells and debris was removed using percoll purification (50%/40%/20% layers).
About 26,000 single cells were loaded onto a 10x Genomics ChromiumTM instrument (10x Genomics) according to the manufacturer’s recommendations. The scRNAseq libraries were generated using Chromium Next GEM Single Cell 5' HT Kit v2 (10x Genomics).

treatment_protocol: Exponentially growing cells (4T1 and EMT6) were resuspended in ice cold PBS and 50% Matrigel (BD Biosciences) and orthotopically injected into the inguinal mammary fat pads in a 50 μl volume of 6-week-old female Balb/c mice. Mice were randomized after all mice developed palpable tumors to ensure no pre-treatment tumor volume differences. Compounds were administered as below: Vehicle (90% corn oil+10% DMSO) and A-196 (25mg/kg daily oral gavage). Animals were euthanized, and tumors were harvested when tumors in the control group reached ~ 2 cm3 size.

value: primary breast tumor

value: Murine mammary tumor

value: WGD+

value: MFP injection


title: EMT6_A196_Tumor2

description:
Library name: sample 11
10x Genomics


title: YCC-34

description:
Library name: TN1407R1651
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-34


title: YCC-38

description:
Library name: TN1406R1470
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-38


title: MDAMB468_H4K20me1_rep1

description: Library name: Sample11


title: VRDTreated

city: Pamplona

first: Itziar

last: Cenzano

state: Navarra

address: Avenida de Pio XII, 55

country: Spain

institute: CIMA Universidad de Navarra

description:
Library name: Bic_VRD_20w
10X Genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v6.1.1 (10x Genomics) with the mouse genome mm10. Downstream analysis, including quality control, clustering, differential expression, and pathway analysis, was conducted in R using Seurat.
Assembly: Mouse mm10
Supplementary files format and content: HDF5 files

source_name: Bone marrow

extract_protocol:
Mice were euthanized by CO₂ asphyxiation, and bones (humerus, radius, iliac crests, femurs, tibia) were collected in PBS 1X with 2% FBS and 2 mM EDTA on ice. Bone marrow (BM) cells were obtained by crushing, filtered (70 μm), and red blood cells lysed with ACK buffer. Bone fragments were digested with collagenase I (0.3%) and dispase (5 U/ml) for 15 min at 37 °C, stopped with FBS, and filtered. Live cell concentration and viability were determined using AO/PI staining on a Cellometer K2. Cells underwent negative selection with a biotinylated lineage cocktail and streptavidin magnetic beads (Miltenyi LD columns). The negative fraction was stained with antibodies against CD45, Ter119, streptavidin, and viability dyes (Vybrant Dye Orange, 7AAD, Annexin V-FITC). BM non-hematopoietic cells and GFP+ plasma cells (PC) were FACS-sorted on a BD FACSAria II and collected in PBS 1X with 0.05% BSA. Viability of sorted cells was confirmed on a Cellometer.
Libraries were prepared according to the manufacturer’s instructions (10x Genomics, Single Cell 3′ Reagent Kits v3.1). Briefly, ~15,000 cells per sample were loaded onto a Chromium Controller to generate single-cell gel bead-in-emulsions (GEMs). Poly-A RNA from each cell was reverse transcribed to cDNA containing Illumina Read 1 primer sequences, 16 bp 10x barcodes, and 12 bp Unique Molecular Identifiers (UMIs). Barcoded cDNA was amplified by PCR, size-selected using SPRIselect (Beckman Coulter), enzymatically fragmented, and subjected to end repair, A-tailing, adaptor ligation, and PCR indexing. Libraries were quantified using a Qubit 3.0 Fluorometer and Agilent 4200 TapeStation, and sequenced on an Illumina NextSeq 2000 (Read 1: 28 cycles; i7: 10; i5: 10; Read 2: 90).

treatment_protocol: In BIcγ1 mice carrying humanized CRBN, a VRd treatment arm (bortezomib, lenalidomide, dexamethasone; oral gavage, 20 consecutive weeks) was included

value: Bone marrow

value: non-hematopoietic cells and plasma cells

tag: age

value: 366 days


title: EMT6_A196_Tumor1

description:
Library name: sample 10
10x Genomics


title: DN1_Primary human T cells_HA_DMSO

description:
Library name: Sample_1
Column name in raw_counts.txt: DN1_HA

value: HA


title: YCC-36

description:
Library name: TN1407R1652
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-36


title: YCC-33

description:
Library name: TN1406R1469
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-33


title: MMMic

description:
Library name: mouse_MM_mic
10X Genomics

value: 263 days


title: EMT6_DMSO_Tumor3

description:
Library name: sample 9
10x Genomics

value: WGD-


title: MDAMB468_H4K16ac_rep2

description: Library name: Sample10

value: Human breast cancer


title: MDAMB468_H4K20me1_rep2

description: Library name: Sample12

value: Human breast cancer epithelial cell


title: YCC-32

description:
Library name: TN1407R1650
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-32


title: MGUSMic

description:
Library name: MGUS_MIC_withPC
10X Genomics

value: 140 days


title: MDAMB468_H4K16ac_rep1

description: Library name: Sample9

value: Wild-type

value: No treatment


title: EMT6_DMSO_Tumor2

description:
Library name: sample 8
10x Genomics


title: MDAMB468_H4K12ac_rep2

description: Library name: Sample8


title: YCC-31

description:
Library name: TN1407R1649
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-31


title: EMT6_DMSO_Tumor1

description:
Library name: sample 7
10x Genomics


title: MMBic

description:
Library name: MM_BIC
10X Genomics

value: 314 days


title: YCC-30

description:
Library name: TN1407R1648
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-30


title: MDAMB468_H4K12ac_rep1

description: Library name: Sample7


title: 4T1_A196_Tumor3

description:
Library name: sample 6
10x Genomics


title: MGUSBic

description:
Library name: MGUS_BIC
10X Genomics

value: 180 days


title: 4T1_A196_Tumor2

description:
Library name: sample 5
10x Genomics

value: primary breast tumor


title: YCC-29

description:
Library name: TN1407R1647
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-29


title: Control

description:
Library name: Control_miceMM
10X Genomics

value: YFP

value: 284 days


title: MDAMB468_H4K8ac_rep2

description: Library name: Sample6


title: YCC-28

description:
Library name: TN1407R1646
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-28


title: 4T1_A196_Tumor1

description:
Library name: sample 4
10x Genomics

value: Murine mammary tumor

value: WGD+

value: MFP injection


title: 4T1_DMSO_Tumor3

description:
Library name: sample 3
10x Genomics


title: YCC-27

description:
Library name: TN1407R1645
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-27


title: YCC-26

description:
Library name: TN1407R1644
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-26


title: MDAMB468_H4K5ac_rep1

description: Library name: Sample3


title: MDAMB468_H4K5ac_rep2

description: Library name: Sample4


title: 4T1_DMSO_Tumor2

description:
Library name: sample 2
10x Genomics


title: Household contact 1200524 (L4, Persistently_uninfected)

city: Nijmegen

first: Todia Pediatama

last: Setiabudiawan

state: Gelderland

address: Geert Grooteplein Zuid 10, 6525 GA Nijmegen, Netherlands

department: Internal Medicine

country: Netherlands

institute: Radboudumc

description:
Library name: INFECT_1200524
INFECT_1200524

data_processing:
Sequencing reads (single-end, 101 bp) from run 150622_SN163_0653_BC6D3JACXX were aligned to the human reference genome GRCh37 (hg19, Ensembl annotation GRCh37.71) using HISAT v0.1.5-beta. PCR duplicates were marked using Picard MarkDuplicates v1.130. Reads spanning splice junctions were split using GATK SplitNCigarReads v3.4-46. The submitted BAM files contain uniquely mapped, deduplicated, and split-trimmed alignments to GRCh37. Read counts per gene were quantified using HTSeq-count v0.5.4p3 (default union-counting mode) based on Ensembl annotation GRCh37.71. Globin genes were excluded (HBA1, HBA2, HBB, HBD, HBG1, HBG2, HBM, HBQ1, HBZ). An additional gene (ENSG00000230417) was excluded due to non-standard annotation. Genes were retained if they had BioMart annotation in GRCh37 and at least 10 reads in at least 10 samples. Normalization was performed using DESeq2 in R (v4.4.1) with a design formula including age and IGRA outcome status as covariates. Assembly: GRCh37 (hg19, NCBI build 37). Supplementary_files_format_and_content: Tab-delimited text files; INFECT_Beijing_L2vsL4_raw_counts.txt contains raw integer read counts per gene (34,927 genes x 39 samples); INFECT_Beijing_L2vsL4_normalized_counts.txt contains DESeq2 size-factor normalized counts (14,809 genes x 39 samples, after low-count filtering). Columns are sample IDs matching the Sample name field.
Assembly: hg19 (GRCh37, NCBI build 37)
Supplementary files format and content: Tab-delimited text with gene-level read counts (raw) and DESeq2-normalized counts

source_name: whole blood

growth_protocol: not applicable (primary human blood samples)

extract_protocol:
Venous blood (2.5 mL) was collected at index patient TB diagnosis into PAXgene Blood RNA Tubes (PreAnalytiX), before initiation of TB treatment. Total RNA was extracted using the PAXgene blood miRNA kit (Qiagen) with semi-automated extraction on the QIAcube (Qiagen). RNA quality and quantity were assessed using the LabChip GX HiSens RNA system (PerkinElmer).
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Preparation Kit v2 (Illumina) at the University Medical Center Groningen (UMCG), Groningen, the Netherlands. Samples were sequenced on an Illumina HiSeq 2000 (instrument ID SN163, run 653, flowcell BC6D3JACXX) as single-end 101 bp reads. Samples were demultiplexed by barcode and distributed across 6 lanes of a single flowcell, with approximately 10 samples per lane.

value: whole blood

tag: mtb lineage of index case

tag: igra status

tag: Sex

value: Male

tag: age (years)

tag: bcg scar

value: present


title: Household contact 1200525 (L2, Persistently_uninfected)

description:
Library name: INFECT_1200525
INFECT_1200525

value: Female


title: YCC-23

description:
Library name: TN1404R0757
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-23


title: Household contact 1200519 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200519
INFECT_1200519


title: MDAMB468_Input_rep2

description: Library name: Sample2

value: Human breast cancer


title: MDAMB468_Input_rep1

description: Library name: Sample1

value: Human breast cancer epithelial cell


title: Household contact 1200520 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200520
INFECT_1200520


title: YCC-25

description:
Library name: TN1406R1468
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-25


title: 4T1_DMSO_Tumor1

description:
Library name: sample 1
10x Genomics

value: WGD-


title: YCC-22

description:
Library name: TN1404R0756
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-22


title: MDAMB468_H4K8ac_rep1

description: Library name: Sample5

value: Wild-type


title: feces, αPD-L1 + TSME group, mouse6

city: Wuhan

first: xiaoting

last: Su

state: Hubei

address: Tongji Hospital, No. 1995, Jiefang Avenue, Wuhan, Hubei

country: China

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: The columns of ASV_table_tax.txt file include: (1) ‘ASV_ID’, represents the ID of Amplicon Sequence Variant (ASV); (2) the 2nd – 25th columns represent four intervention groups, each group comprising six mice. Specifically, ‘Com-1’ to ‘Com-6’, represents the combinational therapy group (i.e., TSME + aPDL1); ‘Control1’ to ‘Control6’, represents the control group; ‘TSE-1’ to ‘TSE-6’, represents the TSME only group; ‘aPDL1-1’ to ‘aPDL1-6’, represents aPDL1 only group; (3) ‘taxonomy’, provides a hierarchical classification of the detected enterobacterium, up to the genus level.

data_processing:
Cutadapt software was used to cut out the primer sequence and DADA2 was used to process raw data to obtained representative sequences and ASV abundance tables.
Specy annotation: all AVS representative sequences were compared with Silva (version138) database using QIIME 2 software package. compare them with standard databases for annotatioin results with the reference genome.
Community diversity analysis: the Qiime2 software was applied to calculate α and β diversity indices.
Inter-group difference analysis: Linear discriminant analysis Effect Size( LEfSe) was to identify the species characteristics that best explain the differences between two or more groups of samples, as well as the extent of their impact on the differences between groups.
STAMP differential analysis was used to compare the abundance of species among multiple groups of samples (using Kruskal Wallis test).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes 16S rDNA expression (ASV) of enterobacteria in mouse feces
Library strategy: 16S rDNA

source_name: feces

extract_protocol:
DNA was extracted from mouse feces using the OMEGA Soil DNA Kit (D5625-01) (Omega Bio-Tek, Norcross, GA, USA)
Following manufacturer's protocols, the V3-V4 variable region of the microbial 16S rDNA was amplified using specific primers: 338F (F terminal: ACTCCTACGGGAGGCAGCA) and 806R (R terminal: GGACTACHVGGGTWTCTAAT)

value: feces

value: WT

value: Amplified using 338F and 806R primers


title: Household contact 1200533 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200533
INFECT_1200533


title: YCC-21

description:
Library name: TN1404R0755
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-21


title: feces, αPD-L1 + TSME group, mouse5


title: YCC-20

description:
Library name: TN1404R0754
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-20


title: Household contact 1200477 (L2, Converter)

description:
Library name: INFECT_1200477
INFECT_1200477

value: Converter

value: absent


title: feces, αPD-L1 + TSME group, mouse3


title: SUM149_Xenograft_Combination_Tumor3

description: Library name: Sample22

data_processing:
RNA-seq data were processed using VIPER pipeline (Cornwell et al., 2018).  Briefly, fastq files were aligned to the human reference mm10 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b) (Dobin et al., 2013).
Genes with 0 counts across all samples were filtered out. The gene-level counts from all studies were then normalized using TMM with edgeR  (Robinson et al., 2010). Log2 transformed TMM-normalized counts per million [log2(TMM-CPM + 1)] were used for analysis.
Assembly: hg19
Supplementary files format and content: Gene-level matrix table (in .csv format) with Log2 transformed TMM-normalized counts per million [log2(TMM-CPM + 1)]

source_name: xenograft tumor

growth_protocol: SUM149 cells were cultrued in DMEM-F12 medium +5% FBS, 10 mM HEPES pH7.4, 1 μg/ml hydrocortisone, 5 μg/ml insulin and 100U/ml Penicillin-Streptomycin.

extract_protocol:
Total RNA were extracted following manufacturer's protocol pf Qiagen Rneasy Mini Kit. (Qiagen, #74106)
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols.

treatment_protocol: For in vitro experiment, SUM149 cells were treated with or without 1μM A196 for 5 days and subjected for 1μM Tunicamycin treatment for 12 hours. For in vivo xenograft experiment, exponentially growing cells were resuspended in ice cold PBS and 50% Matrigel (BD Biosciences) and orthotopically injected into the inguinal mammary fat pads in a 50 μl volume of 6-week-old female female NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice. Mice were randomized after all mice developed palpable tumors to ensure no pre-treatment tumor volume differences. Compounds were administered as below:  A-196 (25mg/kg daily oral gavage),  17AAG (12.5mg/kg, 5 days/week intraperitoneal injection) or their combination. All compounds were dissolved in 90% corn oil + 10% DMSO. Animals were euthanized, and tumors were harvested when tumors in the control group reached ~ 2 cm3 size

value: xenograft tumor

value: human breast cancer cell line

value: wild-type


title: feces, αPD-L1 + TSME group, mouse4


title: SUM149_Xenograft_Combination_Tumor2

description: Library name: Sample21


title: SUM149_Xenograft_Combination_Tumor1

description: Library name: Sample20


title: Household contact 1200486 (L2, Persistently_uninfected)

description:
Library name: INFECT_1200486
INFECT_1200486


title: Household contact 1200473 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200473
INFECT_1200473


title: feces, αPD-L1 + TSME group, mouse2


title: SUM149_Xenograft_17AAG_Tumor3

description: Library name: Sample19


title: Household contact 1200469 (L2, Converter)

description:
Library name: INFECT_1200469
INFECT_1200469


title: YCC-19

description:
Library name: TN1404R0753
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-19


title: feces, αPD-L1 + TSME group, mouse1


title: SUM149_Xenograft_17AAG_Tumor2

description: Library name: Sample18


title: Household contact 1200467 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200467
INFECT_1200467


title: Household contact 1200461 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200461
INFECT_1200461


title: YCC-18

description:
Library name: TN1406R1466
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-18


title: Household contact 1200459 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200459
INFECT_1200459


title: feces, αPD-L1 group, mouse6


title: YCC-11

description:
Library name: TN1404R0749
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-11


title: Household contact 1200457 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200457
INFECT_1200457


title: SUM149_Xenograft_A196_Tumor4

description: Library name: Sample16


title: feces, αPD-L1 group, mouse5


title: SUM149_Xenograft_A196_Tumor3

description: Library name: Sample15


title: feces, αPD-L1 group, mouse4


title: SUM149_Xenograft_A196_Tumor2

description: Library name: Sample14


title: SUM149_Xenograft_17AAG_Tumor1

description: Library name: Sample17


title: YCC-17

description:
Library name: TN1404R0751
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-17


title: YCCEL1/YCC-10

description:
Library name: TN1404R0748
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCCEL1/YCC-10


title: feces, αPD-L1 group, mouse3

description: The columns of ASV_table_tax.txt file include: (1) ‘ASV_ID’, represents the ID of Amplicon Sequence Variant (ASV); (2) the 2nd – 25th columns represent four intervention groups, each group comprising six mice. Specifically, ‘Com-1’ to ‘Com-6’, represents the combinational therapy group (i.e., TSME + aPDL1); ‘Control1’ to ‘Control6’, represents the control group; ‘TSE-1’ to ‘TSE-6’, represents the TSME only group; ‘aPDL1-1’ to ‘aPDL1-6’, represents aPDL1 only group; (3) ‘taxonomy’, provides a hierarchical classification of the detected enterobacterium, up to the genus level.


title: YCC-1

description:
Library name: TN1404R0743
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-1


title: feces, αPD-L1 group, mouse2


title: YCC-2

description:
Library name: TN1404R0744
Column name in raw_counts_gene_49GC_cell_lines.xlsx: YCC-2


title: Household contact 1200446 (L4, Converter)

description:
Library name: INFECT_1200446
INFECT_1200446


title: feces, αPD-L1 group, mouse1


title: Household contact 1200429 (L2, Persistently_uninfected)

description:
Library name: INFECT_1200429
INFECT_1200429


title: SNU-719

description:
Library name: TN1412R4309
Column name in raw_counts_gene_49GC_cell_lines.xlsx: SNU719


title: SUM149_Xenograft_A196_Tumor1

description: Library name: Sample13


title: SUM149_Xenograft_Vehicle_Tumor3

description: Library name: Sample11

value: Vehicle


title: Household contact 1200416 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200416
INFECT_1200416

value: whole blood


title: Household contact 1200411 (L4, Converter)

description:
Library name: INFECT_1200411
INFECT_1200411

value: Male


title: SUM149_Xenograft_Vehicle_Tumor4

description: Library name: Sample12


title: SNU-668

description:
Library name: TN1412R4308
Column name in raw_counts_gene_49GC_cell_lines.xlsx: SNU668


title: SNU-638

description:
Library name: TN1412R4322
Column name in raw_counts_gene_49GC_cell_lines.xlsx: SNU638


title: feces, TSME group, mouse4


title: SUM149_Xenograft_Vehicle_Tumor2

description: Library name: Sample10


title: feces, TSME group, mouse6


title: SUM149_Xenograft_Vehicle_Tumor1

description: Library name: Sample9


title: Household contact 1200395 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200395
INFECT_1200395


title: SNU-5

description:
Library name: TN1412R4305
Column name in raw_counts_gene_49GC_cell_lines.xlsx: SNU5


title: feces, TSME group, mouse3


title: feces, TSME group, mouse2


title: SUM149_A196_Tunicamycin_1

description: Library name: Sample7

source_name: breast cancer derived cell line

value: breast cancer derived cell line


title: feces, TSME group, mouse1


title: feces, TSME group, mouse5


title: Household contact 1200390 (L4, Converter)

description:
Library name: INFECT_1200390
INFECT_1200390

value: Female

value: present


title: SNU-601

description:
Library name: TN1412R4321
Column name in raw_counts_gene_49GC_cell_lines.xlsx: SNU601


title: SNU-620

description:
Library name: TN1404R0763
Column name in raw_counts_gene_49GC_cell_lines.xlsx: SNU620


title: SNU-216

description:
Library name: TN1412R4307
Column name in raw_counts_gene_49GC_cell_lines.xlsx: SNU216


title: Household contact 1200407 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200407
INFECT_1200407


title: Household contact 1200368 (L2, Persistently_uninfected)

description:
Library name: INFECT_1200368
INFECT_1200368


title: SNU-484

description:
Library name: TN1412R4320
Column name in raw_counts_gene_49GC_cell_lines.xlsx: SNU484


title: SUM149_A196_Tunicamycin_2

description: Library name: Sample8


title: Household contact 1200343 (L2, Converter)

description:
Library name: INFECT_1200343
INFECT_1200343


title: SUM149_Tunicamycin_2

description: Library name: Sample4

value: Tunicamycin


title: Household contact 1200409 (L4, Converter)

description:
Library name: INFECT_1200409
INFECT_1200409


title: Household contact 1200362 (L2, Persistently_uninfected)

description:
Library name: INFECT_1200362
INFECT_1200362


title: feces, control group, mouse6

description: The columns of ASV_table_tax.txt file include: (1) ‘ASV_ID’, represents the ID of Amplicon Sequence Variant (ASV); (2) the 2nd – 25th columns represent four intervention groups, each group comprising six mice. Specifically, ‘Com-1’ to ‘Com-6’, represents the combinational therapy group (i.e., TSME + aPDL1); ‘Control1’ to ‘Control6’, represents the control group; ‘TSE-1’ to ‘TSE-6’, represents the TSME only group; ‘aPDL1-1’ to ‘aPDL1-6’, represents aPDL1 only group; (3) ‘taxonomy’, provides a hierarchical classification of the detected enterobacterium, up to the genus level.


title: SUM149_A196_2

description: Library name: Sample6


title: Household contact 1200342 (L2, Persistently_uninfected)

description:
Library name: INFECT_1200342
INFECT_1200342

value: not available


title: SUM149_A196_1

description: Library name: Sample5


title: SNU-16

description:
Library name: TN1412R4306
Column name in raw_counts_gene_49GC_cell_lines.xlsx: SNU16


title: feces, control group, mouse5


title: feces, control group, mouse3


title: SNU-1

description:
Library name: TN1412R4304
Column name in raw_counts_gene_49GC_cell_lines.xlsx: SNU1


title: Household contact 1200340 (L2, Persistently_uninfected)

description:
Library name: INFECT_1200340
INFECT_1200340


title: SUM149_Vehicle_1

description: Library name: Sample1


title: NUGC-4

description:
Library name: TN1412R4315
Column name in raw_counts_gene_49GC_cell_lines.xlsx: NUGC4


title: OCUM-1

description:
Library name: TN1412R4324
Column name in raw_counts_gene_49GC_cell_lines.xlsx: OCUM1


title: feces, control group, mouse4


title: SUM149_Vehicle_2

description: Library name: Sample2


title: NCI-N87

description:
Library name: TN1412R4317
Column name in raw_counts_gene_49GC_cell_lines.xlsx: NCI-N87


title: NUGC-3

description:
Library name: TN1412R4314
Column name in raw_counts_gene_49GC_cell_lines.xlsx: NUGC3


title: SUM149_Tunicamycin_1

description: Library name: Sample3


title: Household contact 1200331 (L2, Persistently_uninfected)

description:
Library name: INFECT_1200331
INFECT_1200331


title: feces, control group, mouse2


title: Household contact 1200337 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200337
INFECT_1200337


title: subcutaneous tumor, αPD-L1 + TSME group, mouse 1

description: In the “gene_fpkm.txt” file, columns ‘NC3’, ‘NC13’, ‘NC26’ represent the results of three mice from the control group; columns ‘TSE7’, ‘TSE28’, ‘TSE29’ are from the TSME-only intervention group; columns ‘PDL1TSE1’, ‘PDL1TSE18’, ‘PDL1TSE23’ from the combinational intervention group (PDL1+TSME); columns ‘PDL14’, ‘PDL117’, ‘PDL115’ from the PD-L1-only intervention group.

data_processing:
GraphPad Prism 8.0.2 software was used for data processing and mapping.
Hisat2 software was used to compare the results with the reference genome.
featureCounts software was used for quantitative analysis.
DESeq2 software was used for variance analysis.
ClusterProfiler software was used for enrichment analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene expression of tumor tissue

source_name: tumor tissue

growth_protocol: Six-week-old female BALB/c mice were housed in the SPF Barrier Center of the Animal Center of the Scientific Research Building, Tongji Hospital, with unrestricted access to food and water.

extract_protocol:
There were four treatment regimen groups: control, TSME only, αPD-L1 only, and αPD-L1 + TSME
Tumor tissue samples were processed to enrich mRNA using Oligo(dT) beads. The polyA-tailed mRNA was then fragmented using divalent cations in NEB Fragmentation Buffer.
RNA libraries were prepared using the library construction kit NEBNext®Ultra™RNA from Illumina®, following the common protocols of NEB library construction.

value: tumor tissue

value: Enrichment via Oligo(dT) beads


title: subcutaneous tumor, αPD-L1 + TSME group, mouse 3

value: WT


title: A549_TSA_48h_rep1

city: Beijing

first: Lifei

last: Ma

address: 5 Dong Dan San Tiao

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
Quality control was conducted using FastQC software (version v0.11.9), and low-quality reads with an average quality score of less than 20 were discarded.
Adapter sequences and low-quality bases were trimmed using trim-galore (version 0.6.7).
The aligned sample sequences were mapped to the GRCh38 genome using STAR (version 2.5.2a).
Gene expression (transcripts per million, TPM) was quantified using RSEM (version v1.3.3).
Protein-coding genes were identified using the BiomaRt R package (version 2.46.3).
Assembly: GRCh38
Supplementary files format and content: raw_tpm_normalized.txt: Tab-delimited text file includes TPM values for each sample.

growth_protocol: Human LUAD epithelial A549 cells were purchased form the American Type Culture Collection (Manassas, VA, USA) and cultured in RPMI-1640 medium (Gibco, Grand Island, USA) supplemented with 10% fetal bovine serum (Gibco), 100 U/mL penicillin (Gibco), and 100 μg/mL streptomycin (Gibco) in a humidified 5% CO2 incubator at 37 °C.

extract_protocol:
Total RNA was extracted from A549 cells using the TRIzol method (Invitrogen, Carlsbad, CA, USA) and treated with RNase-free DNase I (Takara) according to the manufacturer’s instructions.
A cDNA library with paired-end reads was constructed and sequenced on a NovaSeq 6000 system.

treatment_protocol: A549 cells were exposed to growth medium containing TSA (300 nM) under different conditions (Control, 6, 12, 24, and 48 h).

value: Human lung cancer epithelial cells

value: TSA

tag: time point


title: Household contact 1200336 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200336
INFECT_1200336


title: Household contact 1200330 (L2, Persistently_uninfected)

description:
Library name: INFECT_1200330
INFECT_1200330


title: subcutaneous tumor, αPD-L1 + TSME group, mouse 2


title: A549_TSA_24h_rep2


title: MKN-45

description:
Library name: TN1412R4312
Column name in raw_counts_gene_49GC_cell_lines.xlsx: MKN45


title: A549_TSA_12h  [ATAC-seq]

data_processing:
Trim_galore (version 0.6.7) was used to remove poor-quality reads and adapter sequences of raw sequence reads.
Then, clean data were aligned to the human reference genome (hg38) using Bowtie2 (version 2.3.4.2). Uniquely mapped paired reads were retained, and SAM files were sorted and converted to the BAM format using Samtools (version 1.3.1).
Subsequently, peak calling was performed using MACS2 (version 2.2.7.1) to identify the significant peaks in each sample.
Peak regions of the genome were annotated using the ChIPseeker R package (version 1.26.2). The Integrative Genomics Viewer tool was used to convert the viewable bigwig files from DeepTools (version 3.5.1).
To identify DARs, the treatment and control groups were compared in separate cell lines using DESeq2 (version 1.30.1) with a threshold of P < 0.05.
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: lung cancer cells

extract_protocol:
Following exposure to drugs for different durations, live cultured A549 cells were scraped and placed in cold 1× phosphate-buffered saline (PBS). Purified nuclei were isolated from 50,000 cells and used for Tn5 enzyme transposition reaction and open area fragmentation of chromatin using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme Biotech Co., Ltd.) and incubated at 37 °C for 30 min. The DNA was purified using a DNA purification kit (Qiagen), following the manufacturer’s instructions. DNA libraries were generated by performing nine cycles of PCR amplification using the NEBNext High-Fidelity 2 PCR Master Mix (New England Biolabs).
After size selection to remove non-target fragments, the generated DNA libraries were sequenced on an Illumina NovaSeq 6000 platform, generating 150 bp paired-end reads for the ATAC-seq libraries.

value: lung cancer cells


title: A549_TSA_48h_rep2


title: feces, control group, mouse1

value: feces

value: Amplified using 338F and 806R primers


title: A549_TSA_Control [ATAC-seq]

value: Control


title: subcutaneous tumor, αPD-L1 group, mouse 2


title: Household contact 1200327 (L4, Converter)

description:
Library name: INFECT_1200327
INFECT_1200327

value: Converter


title: Household contact 1200332 (L2, Persistently_uninfected)

description:
Library name: INFECT_1200332
INFECT_1200332

value: whole blood


title: MKN-7

description:
Library name: TN1412R4311
Column name in raw_counts_gene_49GC_cell_lines.xlsx: MKN7


title: MKN-28

description:
Library name: TN1404R0770
Column name in raw_counts_gene_49GC_cell_lines.xlsx: MKN28


title: subcutaneous tumor, αPD-L1 group, mouse 3


title: MKN-74

description:
Library name: TN1412R4313
Column name in raw_counts_gene_49GC_cell_lines.xlsx: MKN74


title: A549_TSA_24h_rep1


title: A549_TSA_12h_rep2


title: MKN-1

description:
Library name: TN1404R0768
Column name in raw_counts_gene_49GC_cell_lines.xlsx: MKN1


title: Household contact 1200318 (L2, Persistently_uninfected)

description:
Library name: INFECT_1200318
INFECT_1200318

value: Male


title: subcutaneous tumor, αPD-L1 group, mouse 1


title: Household contact 1200321 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200321
INFECT_1200321


title: subcutaneous tumor, TSME group, mouse 3


title: KATOIII

description:
Library name: TN1412R4323
Column name in raw_counts_gene_49GC_cell_lines.xlsx: KATOIII

source_name: KATOIII

value: KATOIII


title: A549_TSA_12h_rep1


title: subcutaneous tumor, TSME group, mouse 2


title: Household contact 1200315 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200315
INFECT_1200315

value: Female


title: Household contact 1200316 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200316
INFECT_1200316

value: present


title: Hs-746T

description:
Library name: TN1412R4318
Column name in raw_counts_gene_49GC_cell_lines.xlsx: Hs746T


title: IM-95.m

description:
Library name: TN1412R4319
Column name in raw_counts_gene_49GC_cell_lines.xlsx: IM95m


title: subcutaneous tumor, TSME group, mouse 1

description: In the “gene_fpkm.txt” file, columns ‘NC3’, ‘NC13’, ‘NC26’ represent the results of three mice from the control group; columns ‘TSE7’, ‘TSE28’, ‘TSE29’ are from the TSME-only intervention group; columns ‘PDL1TSE1’, ‘PDL1TSE18’, ‘PDL1TSE23’ from the combinational intervention group (PDL1+TSME); columns ‘PDL14’, ‘PDL117’, ‘PDL115’ from the PD-L1-only intervention group.


title: subcutaneous tumor, control group, mouse 3


title: AGS

description:
Library name: TN1412R4316
Column name in raw_counts_gene_49GC_cell_lines.xlsx: AGS

source_name: AGS

value: AGS


title: A549_TSA_6h_rep1


title: Household contact 1200313 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200313
INFECT_1200313


title: Household contact 1200314 (L4, Persistently_uninfected)

description:
Library name: INFECT_1200314
INFECT_1200314


title: A549_TSA_6h_rep2


title: subcutaneous tumor, control group, mouse 2


title: Household contact 1200311 (L2, Persistently_uninfected)

description:
Library name: INFECT_1200311
INFECT_1200311


title: subcutaneous tumor, control group, mouse 1


title: A549_TSA_Control_rep1


title: LV SCI 12w rep5

status: Public on Apr 25 2026

city: Kelowna

first: Christopher

middle: Roy

last: West

state: BC

address: Reichwald Health Sciences Centre, 1088 Discovery Ave

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

description:
Library name: 87_12W_5
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 12W_5

data_processing:
FastQ files obtained from the sequencing centre underwent quality control via FastQC (version 0.12.1). No fastQ files were removed from downstream alignment and analysis.
Assembly: Using high-performance computing (Compute Canada, Cedar), the paired-end reads were aligned with the Rattus Norvegicus genome (index using mRatBN7.2 files; Ensembl 29) using STAR (version 2.7.11a 30) and a count matrix was generated using featureCounts (version 2.0.6 31). All above-mentioned computing was enabled in part by support provided by the University of British Columbia, Simon Fraser University and the Digital Research Alliance of Canada (alliancecan.ca).
Supplementary files format and content: csv file contains raw counts for each sample (protein coding)

organism: Rattus norvegicus

source_name: left ventricle, free wall, mid-ventricular level

extract_protocol:
Frozen heart tissues were homogenized for 20s at 5000 revolutions per minute on the Precellys Evolution homogenizer (Bertin Technologies SAS, Montigny-le-Bretonneux, France) using the 2 mL soft tissue homogenizing ceramic beads CK14 (Bertin Technologies SAS, Cat No. P000912-LYSK0-A). Total RNA was isolated from the extracts using the Maxwell RSC simplyRNA Tissue Kit (Promega Cat. No. AS1340) on the Maxwell RSC instrument (Promega) according to the manufacturer’s instructions. Extracted RNA was treated with DNase1 and its quality was analyzed using the High Sensitivity RNA Assay (Agilent Technologies, Cat No. 5067-5579 and 5067-5580) on the TapeStation 4200 (Agilent Technologies, Cat. No. G2991BA). RNA concentrations are measured using the Qubit RNA HS assay (ThermoFisher; Cat No. Q32852) on the Qubit 4 Fluorometer (ThermoFisher).  RNA quality metrics for RNA include the RNA integrity number (RIN) and DV200.
Samples meeting pre-specified quality thresholds were advanced to library preparation. 100ng of total RNA was used as input for ribosomal RNA depletion using the DNBSEQ rRNA Depletion kit (Complete Genomics, Cat No. 940-001811-00).  Strand-specific libraries were prepared using the DNBSEQ Fast RNA Library Prep kit (Complete Genomics, Cat No. 940-000963-00). Library quality and size were assessed with the TapeStation 4200 (Agilent Technologies; D1000 Assay Cat No. 5067-5582), and libraries were quantified using the Qubit dsDNA HS Assay (Thermo Fisher; Cat No. Q32854). Libraries were sequenced on a DNBSEQ-G400RS sequencer using paired-end 100 bp reads (PE100).

value: SCI

tag: collection post-surgery

value: 12 weeks


title: LV SCI 12w rep1

description:
Library name: 83_12W_1
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 12W_1

value: left ventricle, free wall, mid-ventricular level


title: A549_TSA_Control_rep2


title: LV SCI 3d rep6

description:
Library name: 62_3D_6
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 3D_6

value: 3 days


title: Control-day14

city: Edinburgh

first: Du

last: ninghui

address: Old College, South Bridge, Edinburgh, EH8 9YL, UK

country: United Kingdom

institute: School of Science and Engineering，University of Edinburgh

description: Library name: Sample 1

data_processing:
CLC Genomics Workbench v 20.0.1
Data preprocessing (adapter / low-quality filtering) is carried out using the CLC Genomics Workbench tool, with a quality limit set at 0.05, and reads containing adapters are removed. The trimmed FASTQ format reads are output.
The trimmed sequences are processed through the CLC Genomics Workbench platform. The mismatch cost (parameters - mismath cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8) is set.
The read count extraction and normalization process is carried out using the same CLC Genomics Workbench platform. Firstly, the original read count is generated from the alignment data, and then normalization processing is performed through the built-in algorithm.
Supplementary files format and content: tab-delimited tex fle includes raw counts for each Sample
Supplementary files format and content: csv files include FPK values for each Sample

organism: Bos

source_name: skin

extract_protocol:
Total RNA was extracted from skin tissue using the RNeasy Blood & Tissue Kit (Qiagen, Germany).  1.3 ug oftotal RNA was used for theconstruction ofsequencing libraries.
RNA libraries for RNA-seg were prepared using GENESEED mRNA-Seg Library Prep Kit followingmanufacturer's protocols

treatment_protocol: The Holsteins in the high-temperature group were maintained at a temperature of 35°C ± 1°C in an environment with 60% humidity, while the Holsteins in the control group were set at a temperature of 20°C ± 2°C and 50% humidity.

value: skin

value: wt

value: temperature :20°C ± 2°C;humidity:50%


title: LV SCI 12w rep4

description:
Library name: 86_12W_4
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 12W_4


title: LV SCI 12w rep2

description:
Library name: 84_12W_2
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 12W_2


title: LV SCI 3d rep5

description:
Library name: 61_3D_5
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 3D_5


title: LV SCI 12w rep3

description:
Library name: 85_12W_3
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 12W_3


title: LV SCI 3d rep4

description:
Library name: 60_3D_4
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 3D_4


title: heat-tolerance-day14

description: Library name: Sample 2

value: temperature :35°C ± 1°C;humidity:60%


title: LV SCI 3d rep2

description:
Library name: 58_3D_2
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 3D_2


title: Head_5: Homeostatic head RNA-seq, replicate 5, DMSO

city: Davis

first: Sergio

middle: Esteban

last: Campos

address: One Shields Ave

department: Molecular and Cellular Biology

institute: University of California Davis

description: Library name: Head_5

data_processing:
Raw reads were trimmed with Trimmomatic v0.39 to remove adapter sequences and low quality reads, with the following parameters: PE -threads 16 -phred33 / ILLUMINACLIP: TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 \         SLIDINGWINDOW:4:15 MINLEN:32
Resulting reads were mapped to a reference transcriptome using rsem with the following parameters: rsem-calculate-expression --num-threads 16 --no-bam-output \         --bowtie2 --paired-end
Assembly: GCA_004118135.1
Supplementary files format and content: comma delimited text files including raw counts and FPKM

organism: Hydra oligactis

source_name: Hypostome and tentacles ring

growth_protocol: Hydra oligactis strain innsbruck 12 polyps were cultured according to standard protocol (Lenhoff, 1983) at 18˚C and fed 3 times weekly with Artemia nauplii.

extract_protocol:
30 tissue segments adjacent to the wound site were collected per sample, put in Trizol and homogeneized with a vortex. Trizol:chloroform protocol was used to extract total nucleic acids. After treatment with DNAse I, samples were passed through RNA purification columns (Zymo Research).
mRNA libraries were prepared by Novogene

treatment_protocol: For alsterpaullone treatment, Hydra were incubated in 5 uM alsterpaullone for 3 hours after amputation. Following, this incubation Hydra polyps were washed and put in Hydra media until tissue was collected.

value: Hypostome and tentacles ring

value: DMSO


title: LV SCI 12w rep6

description:
Library name: 88_12w_6
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 12W_6


title: Head_4: Homeostatic head RNA-seq, replicate 4, DMSO

description: Library name: Head_4


title: LV SCI 1d rep6

description:
Library name: 82_1D_6
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 1D_6

value: 1 day


title: WPMY1_control

type: RNA

city: Minato-ku

first: Takahashi

last: Sayuri

state: Tokyo

address: 4-6-1 Shirokanedai

country: Japan

institute: The University of  Tokyo

description: Gene expression in sh-luc transduced WPMY1 cells

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: WPMY1, luciferase shRNA control

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Cell were grown and maintained in a 37°C incubator with 5% CO2. RPMI1640 mefdium with 10%FBS penicillin/streptmycin.

extract_protocol: RNA was extracted according to the manufacturer's protocol, purified using RNeasy kit (Qiagen)

tag: transduction

value: non-targeting control shRNA


title: WPMY1_WNT5AshRNA

description: Gene expression in sh-WNT5A transduced WPMY1 cells

source_name: WPMY1, WNT5A shRNA

value: shRNA targeting WNT5A


title: LV SCI 1d rep4

description:
Library name: 80_1D_4
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 1D_4


title: Foot_4: Homeostatic foot RNA-seq, replicate 4, DMSO

description: Library name: Foot_4

source_name: Foot and peduncle

value: Foot and peduncle


title: LV SCI 1d rep3

description:
Library name: 79_1D_3
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 1D_3


title: LV SCI 1d rep5

description:
Library name: 81_1D_5
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 1D_5


title: aFR_24hpa_2: Foot regeneration RNA-seq, 24 hours post amputation, replicate 2, Alsterpaullone

description: Library name: aFR_24hpa_2

source_name: Body column

value: Body column

value: Alsterpaullone 5 uM


title: LV SCI 3d rep1

description:
Library name: 57_3D_1
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 3D_1


title: aFR_24hpa_3: Foot regeneration RNA-seq, 24 hours post amputation, replicate 3, Alsterpaullone

description: Library name: aFR_24hpa_3


title: Foot_5: Homeostatic foot RNA-seq, replicate 5, DMSO

description: Library name: Foot_5


title: LV SCI 1d rep1

description:
Library name: 77_1D_1
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 1D_1


title: LV SCI 3d rep3

description:
Library name: 59_3D_3
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 3D_3


title: aFR_24hpa_1: Foot regeneration RNA-seq, 24 hours post amputation, replicate 1, Alsterpaullone

description: Library name: aFR_24hpa_1


title: LV SHAM rep6

description:
Library name: 68_SHAM_6
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: SHAM_6

value: SHAM

value: 7 days


title: LV SCI 1d rep2

description:
Library name: 78_1D_2
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: 1D_2

value: SCI


title: FR_24hpa_3: Foot regeneration RNA-seq, 24 hours post amputation, replicate 3, DMSO

description: Library name: FR_24hpa_3


title: HR_24hpa_1: Head regeneration RNA-seq, 24 hours post amputation, replicate 1, DMSO

description: Library name: HR_24hpa_1


title: FR_24hpa_1: Foot regeneration RNA-seq, 24 hours post amputation, replicate 1, DMSO

description: Library name: FR_24hpa_1


title: LV SHAM rep4

description:
Library name: 66_SHAM_4
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: SHAM_4

value: left ventricle, free wall, mid-ventricular level


title: HR_0hpa_7: Head regeneration RNA-seq, 0 hours post amputation, replicate 7, DMSO

description: Library name: HR_0hpa_7


title: HR_24hpa_3: Head regeneration RNA-seq, 24 hours post amputation, replicate 3, DMSO

description: Library name: HR_24hpa_3


title: HR_24hpa_2: Head regeneration RNA-seq, 24 hours post amputation, replicate 2, DMSO

description: Library name: HR_24hpa_2


title: LV SHAM rep5

description:
Library name: 67_SHAM_5
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: SHAM_5


title: LV SHAM rep1

description:
Library name: 63_SHAM_1
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: SHAM_1


title: RNA-seq of endometrial organoid treated with Lactobacillus crispatus, rep1

city: Chongqing

first: Shen

last: Zhang

address: No. 288 Tianwen avenue, Nanan district

department: Obstetrics and Gynecology Department

institute: The Second Affiliated Hospital of Chongqing Medical University

description: Library name: L_cris1

data_processing:
Raw sequencing reads were trimmed for adapters and low-quality bases using fastp (v0.23.2). Clean reads were aligned to the GRCh38 human reference genome using HISAT2 (v2.2.1) with strand-specific parameters. Transcript abundances were quantified as transcripts per million (TPM) using RSEM (v1.3.3).
Assembly: GRCh38
Supplementary files format and content: The processed data file is an Excel spreadsheet containing normalized transcript expression levels in Transcripts Per Million (TPM). Each row corresponds to a transcript and TPM values for each sample.

source_name: Endometrium

extract_protocol:
Total RNA was extracted from endometrial organoids using TRIzol® Reagent (Thermo Fisher Scientific, Waltham, MA, USA) and purified with the RNA Purification Kit (MajorBio Technology Co., Ltd, Shanghai, China).
Stranded mRNA libraries were prepared using the Illumina® Stranded mRNA Prep, Ligation Kit (Illumina, San Diego, CA, USA). The process included poly(A) selection to isolate mRNA, fragmentation to achieve an average insert size of 300 bp, and ligation of sequencing adapters.

value: Endometrium

value: endometrial organoid

value: epithelial cells

value: wild type

value: Lactobacillus crispatus


title: RNA-seq of endometrial organoid treated with Lactobacillus crispatus, rep3

description: Library name: L_cris3


title: HR_0hpa_5: Head regeneration RNA-seq, 0 hours post amputation, replicate 5, DMSO

description: Library name: HR_0hpa_5


title: RNA-seq of endometrial organoid treated with Lactobacillus iners, rep3

description: Library name: L_iners3

value: Lactobacillus iners


title: FR_24hpa_2: Foot regeneration RNA-seq, 24 hours post amputation, replicate 2, DMSO

description: Library name: FR_24hpa_2

value: DMSO


title: LV SHAM rep2

description:
Library name: 64_SHAM_2
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: SHAM_2


title: Head_3: Homeostatic head RNA-seq, replicate 3, DMSO

description: Library name: Head_3

value: Hypostome and tentacles ring


title: FR_0hpa_5: Foot regeneration RNA-seq, 0 hours post amputation, replicate 5, DMSO

description: Library name: FR_0hpa_5


title: RNA-seq of endometrial organoid treated with Lactobacillus crispatus, rep2

description: Library name: L_cris2


title: FR_0hpa_6: Foot regeneration RNA-seq, 0 hours post amputation, replicate 6, DMSO

description: Library name: FR_0hpa_6


title: FR_0hpa_7: Foot regeneration RNA-seq, 0 hours post amputation, replicate 7, DMSO

description: Library name: FR_0hpa_7


title: LV SHAM rep3

description:
Library name: 65_SHAM_3
In Fossey_Bulk_RNA_count_data_protein-coding.csv; colum: SHAM_3


title: RNA-seq of endometrial organoid treated with Prevotella disiens, rep2

description: Library name: L_pre2

value: Prevotella disiens


title: HR_0hpa_6: Head regeneration RNA-seq, 0 hours post amputation, replicate 6, DMSO

description: Library name: HR_0hpa_6


title: Head_1: Homeostatic head RNA-seq, replicate 1, DMSO

description: Library name: Head_1


title: RNA-seq of endometrial organoid treated with Lactobacillus iners, rep2

description: Library name: L_iners2


title: Head_2: Homeostatic head RNA-seq, replicate 2, DMSO

description: Library name: Head_2


title: Foot_3: Homeostatic foot RNA-seq, replicate 3, DMSO

description: Library name: Foot_3


title: RNA-seq of endometrial organoid treated with none, rep2

description: Library name: NC2


title: RNA-seq of endometrial organoid treated with Prevotella disiens, rep3

description: Library name: M_pre3


title: RNA-seq of endometrial organoid treated with none, rep3

description: Library name: NC3


title: Foot_2: Homeostatic foot RNA-seq, replicate 2, DMSO

description: Library name: Foot_2


title: RNA-seq of endometrial organoid treated with none, rep1

description: Library name: NC1


title: aFR_48hpa_4: Foot regeneration RNA-seq, 48 hours post amputation, replicate 4, Alsterpaullone

description: Library name: aFR_48hpa_4

source_name: body column

value: body column


title: RNA-seq of endometrial organoid treated with Prevotella disiens, rep1

description: Library name: L_pre1


title: RNA-seq of endometrial organoid treated with Lactobacillus iners, rep1

description: Library name: L_iners1


title: aFR_48hpa_2: Foot regeneration RNA-seq, 48 hours post amputation, replicate 2, Alsterpaullone

description: Library name: aFR_48hpa_2


title: aFR_48hpa_3: Foot regeneration RNA-seq, 48 hours post amputation, replicate 3, Alsterpaullone

description: Library name: aFR_48hpa_3


title: Foot_1: Homeostatic foot RNA-seq, replicate 1, DMSO

description: Library name: Foot_1

value: Foot and peduncle


title: aFR_48hpa_1: Foot regeneration RNA-seq, 48 hours post amputation, replicate 1, Alsterpaullone

description: Library name: aFR_48hpa_1


title: control rep2 (from 3 technical replicates)

city: Basel

first: Knut

last: Drescher

state: BS

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

data_processing:
Sequencing of the cDNA libraries was performed by the LAFUGA service unit (Gene Center, munich, Blum group)
cDNA reads were imported into CLC Genomics Workbench v11.0 and analysed using mostly standard parameters.
3'adaptor- and quality trimming was performed using the trim reads command with the following settings: Sequence = TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, Strand = Minus, Action = Remove adapter, Scores = Mismatch: 2, Gapcost: 3, Cutoff: 10, Cutoff at end: 4
The trimmed reads were checked for quality and mapped to the V.cholerae reference genome: NCBI Acc.number: NC_002505, NC_002506 using the following settings: Mismatch cost =  2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = Yes, Strand specific = Reverse, Maximum number of hits for a read = 1
Reads mapping in CDS were counted, and genes with a total count cutoff of >15 in all samples were considered for analysis. Read counts were normalized (CPM), and transformed (log2). Differential expression was tested using the built in tool corresponding to edgeR in exact mode with tagwise dispersions. Genes with a fold-change of > 3.0 in either condition and a FDR adjusted p-value < 0.05 were considered to be differentially expressed.
Genome_build: NC_002505, NC_002506
Supplementary_files_format_and_content: Read count table and edgeR (exact mode) analysis

organism: Vibrio cholerae

source_name: whole bacterial cells

growth_protocol: Vibrio cholerae C6706 biofilms were grown in microfluidic chambers under constant flow of M9 media with 0.5% glucose at 25° C.

extract_protocol:
RNA was isolated using Tri-reagent according to standard protocols. Prepared RNA was DNAse digested and cleaned up using standard nucleic acid precipitation procedures. Depletion of ribosomal RNA was performed using Ribo-Zero kits (Epicentre) for Gram-negative bacteria. Integrity of the prepared RNA was tested using a Bioanalyzer.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Libary Prep Kit for Illumina (NEB E7760) according to the manufacturers instructions. Quality of the prepared libraries was tested using a Bioanalyzer.

treatment_protocol: Dispersal was triggered by taking out glucose from supplied media. Samples were collected from 1h glucose starved biofilms. Control samples were collected from biofilms which were not treated for glucose starvation.

tag: strain

value: Wild type

tag: growth phase

value: Biofilm under flow

value: no treatment


title: treated rep2 (from 3 technical replicates)

value: glucose starvation


title: HR_48hpa_3: Head regeneration RNA-seq, 48 hours post amputation, replicate 3, DMSO

description: Library name: HR_48hpa_3

tag: tissue


title: treated rep1 (from 3 technical replicates))


title: HR_48hpa_1: Head regeneration RNA-seq, 48 hours post amputation, replicate 1, DMSO

description: Library name: HR_48hpa_1


title: control rep1 (from 3 technical replicates)


title: HR_48hpa_2: Head regeneration RNA-seq, 48 hours post amputation, replicate 2, DMSO

description: Library name: HR_48hpa_2


title: HASMC, TCF7L2 IP, rep3

city: Ann arbor

first: Yongjie

last: Deng

address: 2800 Plymouth Rd. NCRC blg26, Rm355s

institute: University of Michigan

description: Library name: HASMC_TCF7L2_rep3

data_processing:
Raw sequencing reads were assessed for quality using FastQC.
Reads were aligned to the human reference genome GRCh38 using Bowtie2.
Peak calling was performed using MACS2 with parameters -f BAMPE -g hs -B -q 0.01.
Reproducibility across replicates was assessed by IDR analysis with a threshold of 0.05.
Peak visualization and annotation, including transcription start site distance analysis, were performed using deepTools and ChIPseeker.
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: human primary aortic smooth muscle cell

growth_protocol: Human primary aortic smooth muscle cells were maintained in SMC growth medium 2 (Lonza, CC-3182) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were crosslinked with 1% formaldehyde, quenched with glycine, and lysed prior to chromatin preparation.
Approximately 2 ng of immunoprecipitated chromatin per sample was used for library preparation with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645). Sequencing was performed on a NovaSeq X platform to generate 151 bp paired-end reads, with approximately 50 million reads per sample.

value: human primary aortic smooth muscle cell

tag: chip antibody


title: HASMC, TCF7L2 IP, rep2

description: Library name: HASMC_TCF7L2_rep2

tag: cell type


title: HASMC, IgG control, rep3

description: Library name: HASMC_IgG_rep3

value: IgG


title: FR_48hpa_3: Foot regeneration RNA-seq, 48 hours post amputation, replicate 3, DMSO

description: Library name: FR_48hpa_3


title: HASMC, TCF7L2 IP, rep1

description: Library name: HASMC_TCF7L2_rep1


title: HASMC, IgG control, rep2

description: Library name: HASMC_IgG_rep2


title: HASMC, IgG control, rep1

description: Library name: HASMC_IgG_rep1


title: human primary aortic smooth muscle cells, TCF7L2 knockdown, rep4

description:
Library name: TCF7L2 knockdown_rep4
Column name in gene_TPM.txt: 8270-YD-8

data_processing:
Cutadapt was used to trim adaptor sequences from raw reads.
Read quality was assessed using the FastQC and Fastq Screen.
Trimmed reads were aligned to the human reference genome GRCh38 using STAR following ENCODE guidelines.
gene expression levels were quantified using RSEM to generate raw counts and TPM values.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing TPM value for each sample.

extract_protocol:
Total RNA was isolated from HASMCs using the RNeasy Mini Kit (QIAGEN, #74106). RNA quality was assessed using an Aigilent Bioanalyzer. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared with the NEBNext Ultra RNA Library Prep Kit (NEB, #E7770).

treatment_protocol: Prior to experiments, HASMCs were serum-starved for 24 hours in Opti-MEM I. HASMCs were transfected with 20 nM siTCF7L2 (D-003816-01, GAUGGAAGCUUACUAGAUU) and 20nM siITGB1 (L-004506-00-0005) or 20 nM Silencer Select Negative Control siRNA (siControl, D-001206-14, UAAGGCUAUGAAGAGAUAC) from Horizon Discovery for 48 hours, using jetPRIME transfection reagent (Polyplus, 55-133) according to the manufacturer’s protocol.


title: human primary aortic smooth muscle cells, TCF7L2 knockdown, rep2

description:
Library name: TCF7L2 knockdown_rep2
Column name in gene_TPM.txt: 8270-YD-6


title: FR_48hpa_2: Foot regeneration RNA-seq, 48 hours post amputation, replicate 2, DMSO

description: Library name: FR_48hpa_2


title: human primary aortic smooth muscle cells, TCF7L2 knockdown, rep3

description:
Library name: TCF7L2 knockdown_rep3
Column name in gene_TPM.txt: 8270-YD-7


title: FR_48hpa_1: Foot regeneration RNA-seq, 48 hours post amputation, replicate 1, DMSO

description: Library name: FR_48hpa_1


title: human primary aortic smooth muscle cells, TCF7L2 knockdown, rep1

description:
Library name: TCF7L2 knockdown_rep1
Column name in gene_TPM.txt: 8270-YD-5


title: human primary aortic smooth muscle cells, control, rep4

description:
Library name: siControl_rep4
Column name in gene_TPM.txt: 8270-YD-4

value: siControl


title: U-2 OS cells, SRSF1 S-A-2

city: Xiamen

first: Fan

last: Wu

address: 4221 Xiang'an South Road

institute: Xiamen University

description:
Library name: SRSF1 S-A-2
Column name in DEseq_result.xlsx: SRSF1 S-A-2 (FPKM), SRSF1 S-A-2 (Count)

data_processing:
For the quantitative analysis of RNA-seq results, the fastp software (https://github.com/OpenGene/fastp, version fastp-V0.20.1) was used to remove adapters and low-quality sequences from the raw data. The filtered data was aligned against the Homo sapiens genome GRCh38.112 by HISAT2 (https://daehwankimlab.github.io/hisat2/, version v2.2.1). Use the StringTie (https://github.com/gpertea/stringtie, version V2.0.4) to perform preliminary assembly and merge genes or transcripts. The final assembly annotation results were obtained by comparing transcripts with reference annotations by gffcompare (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml) and quantitative analysis was then performed. Use DEseq2 (http://www.bioconductor.org/packages/release/bioc/html/DESeq.html) to carry out significant difference analysis between samples. Alternative splicing events were identified using rMATS (version v3.2.5) with the criteria FDR < 0.05 and |Δψ| ≥ 0.05.  GO enrichment analysis on all differentially expressed genes associated with alternative splicing.
Assembly: GRCh38
Supplementary files format and content: Xlsx file including FPKM and Read counts for each sample
Supplementary files format and content: Xlsx file including differential mRNA splicing events
Supplementary files format and content: Xlsx file including GO enrichment analysis for differential mRNA splicing events with |ΔPSI (percentage spliced in)| > 0.1

source_name: Bone

extract_protocol:
Total RNA was extracted by AG RNAex Pro Reagent (Accurate Biology; AG21102).
To enrich PCR products of 200–500 bps in length, library preparation was carried out using the KCTM Digital mRNA Library Preparation Kit (SeqhealthTech Co., Ltd., Wuhan, China). Following quantification, sequencing was performed using the DNBSEQ-T7 sequencing platform (MGI).

value: Bone

tag: cell line

value: U-2 OS

value: Human osteosarcoma cells

tag: genotype

value: SRSF1 S-A


title: aFR_12hpa_3: Foot regeneration RNA-seq, 12 hours post amputation, replicate 3, Alsterpaullone

description: Library name: aFR_12hpa_3

tag: treatment

value: Alsterpaullone 5 uM

tag: batch


title: HeLa-Cas9 cells untransfected

city: Heidelberg

first: Marie

last: Buck-Wiese

address: Im Neuenheimer Feld 267

department: BioQuant

country: Germany

institute: Universität Heidelberg

description: Gene expression data from HeLa-Cas9 cells 48h untreated control

hyb_protocol: 5,5 ug of fragmented and labeled ss-cDNA were hybridized for 17 hr at 45°C on Applied Biosystems™ human Clariom™ S Array, according to Affymetrix WT PLUS Reagent Kit user manual.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: The data were normalised using quantile normalisation with R using function normalize.quantiles from Bioconductor package preprocessCore

label: biotin

source_name: HeLa-Cas9 cells 48h post-solid-phase reverse transfection

label_protocol: The Applied Biosystems™ WT PLUS Reagent Kit is used to generate labeled ss-cDNA from input amounts of 100ng total RNA

growth_protocol: 50,000 Hela-Cas9 cells were seeded per well on 24-well plates in DMEM growth medium (1g/l Glucose, 110mg/l Sodium Pyruvate, 2% L-Glutamine, 10%FCS, 1%Pen/Strep)

extract_protocol: total RNA was extracted via a Qiagen RNeasy Kit according to the manufacturer's instructions with DNAse treatment

treatment_protocol: 24-well plate wells were pre-coated with solid-phase reverse transfection mix

value: HeLa (THP SCL-03-CA3)


title: HeLa-Cas9 cells mock transfected 2

description: Gene expression data from HeLa-Cas9 cells 48h transfection mock control


title: aFR_12hpa_2: Foot regeneration RNA-seq, 12 hours post amputation, replicate 2, Alsterpaullone

description: Library name: aFR_12hpa_2


title: U-2 OS cells, SRSF1 S-A-1

description:
Library name: SRSF1 S-A-1
Column name in DEseq_result.xlsx: SRSF1 S-A-1 (FPKM), SRSF1 S-A-1 (Count)


title: human primary aortic smooth muscle cells, control, rep3

description:
Library name: siControl_rep3
Column name in gene_TPM.txt: 8270-YD-3


title: human primary aortic smooth muscle cells, control, rep2

description:
Library name: siControl_rep2
Column name in gene_TPM.txt: 8270-YD-2


title: aFR_12hpa_1: Foot regeneration RNA-seq, 12 hours post amputation, replicate 1, Alsterpaullone

description: Library name: aFR_12hpa_1


title: U-2 OS cells, SRSF1 WT-1

description:
Library name: SRSF1 WT-1
Column name in DEseq_result.xlsx: SRSF1 WT-1 (FPKM), SRSF1 WT-1 (Count)

value: SRSF1 WT


title: U-2 OS cells, SRSF1 WT-3

description:
Library name: SRSF1 WT-3
Column name in DEseq_result.xlsx: SRSF1 WT-3 (FPKM), SRSF1 WT-3 (Count)


title: U-2 OS cells, SRSF1 WT-2

description:
Library name: SRSF1 WT-2
Column name in DEseq_result.xlsx: SRSF1 WT-2 (FPKM), SRSF1 WT-2 (Count)


title: HR_12hpa_3: Head regeneration RNA-seq, 12 hours post amputation, replicate 3, DMSO

description: Library name: HR_12hpa_3

value: DMSO


title: HR_12hpa_1: Head regeneration RNA-seq, 12 hours post amputation, replicate 1, DMSO

description: Library name: HR_12hpa_1

value: body column


title: U-2 OS cells, SRSF1 S-A-3

description:
Library name: SRSF1 S-A-3
Column name in DEseq_result.xlsx: SRSF1 S-A-3 (FPKM), SRSF1 S-A-3 (Count)


title: HCC4006_detached_7 day_rep1.

city: Shimotsuke

first: Toshiro

last: Niki

state: Tochigi

department: Department of Pathology

institute: Jichi Medical University

description:
Library name: PR1960_12_a
Column name for Gene_expression.txt : PR1960_12_a.TPM

data_processing:
Raw reads were mapped to the human reference genome (GRCh38), and gene-level read counts were obtained.
Gene-level expression values were normalized to TPM (Transcripts Per Million) to account for gene length and sequencing depth differences across samples.
Assembly: GRCh38
Supplementary files format and content: Processed data files contain gene-level expression matrices including raw read counts and TPM values for each sample.
Supplementary files format and content: Each tab-delimited text file includes the following information for each gene:  Gene ID (Ensembl Gene ID)  TPM values for each sample  Raw read counts for each sample  Genomic annotation (Chromosome, Start, End, Gene Length, Strand)  Gene symbol and gene type  Transcript ID  Entrez Gene ID  Functional annotations (Gene description, Gene Ontology terms, KEGG pathway information)  Genes are arranged in rows and samples in columns.

growth_protocol: Cells were maintained in RPMI-1640 medium, supplemented with 10% FBS, 100 U/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit.
SMART-Seq v4 PLUS Kit was used to prepare library construction.

treatment_protocol: Trypsinized cells were plated onto ultra-low attachment culture plate (Corning), and RNA was extracted at indicated time points.

value: lung adenocarcinoma

value: Detachment


title: HeLa-Cas9 cells transfected with non-targeting antibody

description: Gene expression data from HeLa-Cas9 cells 48h after non-targeting antibody transfection


title: HR_12hpa_2: Head regeneration RNA-seq, 12 hours post amputation, replicate 2, DMSO

description: Library name: HR_12hpa_2


title: human primary aortic smooth muscle cells, control, rep1

description:
Library name: siControl_rep1
Column name in gene_TPM.txt: 8270-YD-1


title: Case G

city: Fuzhou

first: Zhiren

last: Liu

state: Fujian

address: 20 Chazhong Road

institute: the First Affiliated Hospital of Fujian Medical University

description: Library name: Case G

data_processing:
The raw sequencing reads underwent quality control and trimming processes using FastQC and Trimmomatic software.
Clean reads were mapped to GRCh38 using BWA. Samblaster was utilized for deduplication, while the Genome Analysis Toolkit (GATK) was employed for variant calling and subsequent annotation using Annovar and snpEff.
Assembly: GRCh38
Supplementary files format and content: Variants were inclued in the Case_G_variants_annotation

source_name: Peripheral Blood

extract_protocol:
Genomic DNA was extracted from peripheral blood samples
The sequencing library was prepared using a Fast Library Prep Kit (iGeneTech, Beijing, China).

value: Peripheral Blood


title: HCC4006_detached_1 day_rep1.

description:
Library name: PR1960_11_a
Column name for Gene_expression.txt : PR1960_11_a.TPM


title: HeLa-Cas9 cells transfected with antibody targeting TLN1

description: Gene expression data from HeLa-Cas9 cells 48h after TLN1-targeting antibody transfection


title: HeLa-Cas9 cells transfected with antibody targeting KD2

description: Gene expression data from HeLa-Cas9 cells 48h after KD2-targeting antibody transfection


title: FR_12hpa_3: Foot regeneration RNA-seq, 12 hours post amputation, replicate 3, DMSO

description: Library name: FR_12hpa_3


title: HeLa-Cas9 cells transfected with siRNA targeting KD2

description: Gene expression data from HeLa-Cas9 cells 48h after KD2 knock-down


title: FR_12hpa_2: Foot regeneration RNA-seq, 12 hours post amputation, replicate 2, DMSO

description: Library name: FR_12hpa_2


title: HCC4006_attached (control)_rep1.

description:
Library name: PR1960_10_a
Column name for Gene_expression.txt : PR1960_10_a.TPM


title: HeLa-Cas9 cells mock transfected 1


title: HeLa-Cas9 cells transfected with siRNA targeting TLN1

description: Gene expression data from HeLa-Cas9 cells 48h after TLN1 knock-down


title: HeLa-Cas9 cells transfected non-targeting siRNA

description: Gene expression data from HeLa-Cas9 cells 48h after knock-down negativ control


title: 4T1 Cmas KO, TILs

city: Vienna

first: Stefan

last: Mereiter

address: Dr. Bohr-Gasse 3, IMBA

country: Austria

institute: IMBA

description: Library name: Sample 2

data_processing:
Sequencing was performed using NovaSeq S4 lane PE150 (Illumina) with a target of 15,000 reads per cell. Alignment of the samples was perfomed with the 10x Genomics Cell Ranger 7.1.0 multi pipeline. The reads were trimmed to a length of 28bp read1 and 92bp read2 and aligned to the mouse reference genome (refdata-gex-mm10-2020-A) and probeset (Probe_Set_v1.0.1_mm10-2020-A.csv) with default parameters using cellranger multi. The four per sample count outputs were combined with cellranger aggr. The cellranger output files for each sample (filtered barcodes, features and count matrix files) were then used for custom analysis in R using the Seurat package (version 4.2.0).
Assembly: mm10-2020-A
Supplementary files format and content: h5

source_name: Mammary tumor

growth_protocol: 4T1 cells were orthotopically injected into the right inguinoabdominal mammary fat pad of BALB/c mice. For this purpose, cells were cultured in monolayer, harvested by trypsin, and washed with PBS. 100 μl of a 1:1 PBS and Matrigel (Corning Inc., Corning, NY) cell suspension (250,000 cells) were injected per mouse. Tumors were monitored and measured every second day starting from day 4 after injection.

extract_protocol:
Tumors were resected at day 15 post injection and immediately dissociated using a tumor dissociation kit and GentleMACS dissociator (both Miltenyi). CD45 positive cells were then isolated with anti-CD45 microbeads (Miltenyi) following a previously described protocol. Cells were counted using NucleoCounter NC250 (Chemometec) following the manufacturer instructions and CD45 positivity and viability measured on a BD Fortessa instrument (BD); more than 90% cells were viable and 95% of the cells were confirmed to express CD45. For each sample, one million cells were fixed for 22 hours at 4°C, quenched and stored at -80°C according to 10X genomic Fixation of Cells & Nuclei for Chromium Fixed RNA profiling (CG000478) using the Chromium Next GEM Single Cell Fixed RNA Sample preparation kit (PN-1000414, 10X Genomics, Pleasanton, CA).
250,000 cells per sample were used for probe hybridization using the Chromium Fixed RNA Kit, Mouse Transcriptome, 4rxn x 4BC (PN-1000496, 10X Genomics), pooled at equal numbers and washed following the Pooled Wash Workflow following the Chromium Fixed RNA Profiling Reagent kit protocol (CG000527, 10X Genomics). GEMs were generated on Chromium X (10X Genomics) with a target of 10,000 cells recovered and libraries prepared according to the manufacturer instructions (CG000527, 10X Genomics).

treatment_protocol: No treatment

value: Mammary tumor

value: Cmas KO

value: no treatment


title: HeLa-Cas9 cells transfected non-targeting sgRNA

description: Gene expression data from HeLa-Cas9 cells 48h after knock-out negativ control


title: Case E

data_processing:
The raw sequencing reads underwent quality control and trimming processes using FastQC and Trimmomatic software.
Clean reads were mapped to GRCh38 using BWA. Samblaster was utilized for deduplication, while the Genome Analysis Toolkit (GATK) was employed for variant calling and subsequent annotation using Annovar and snpEff.
Supplementary files format and content: Variants were inclued in the Case *-significant.snp_indel
Library strategy: whole-exome sequencing

source_name: human peripheral blood samples

value: human peripheral blood samples

value: MI oocytes with an agar-like ZP


title: NCI-H2228_detached_7 day_rep1.

description:
Library name: PR1960_09_a
Column name for Gene_expression.txt : PR1960_09_a.TPM


title: FR_12hpa_1: Foot regeneration RNA-seq, 12 hours post amputation, replicate 1, DMSO

description: Library name: FR_12hpa_1


title: 4T1 Ctrl tumor, TILs

description: Library name: Sample 1

value: Ctrl


title: VbdR rep3

data_processing:
Sequencing of the cDNA libraries was performed by MPGC
cDNA reads were imported into CLC Genomics Workbench v11.0 and analysed using mostly standard parameters.
The reads were checked for quality and mapped to the V.cholerae reference genome: NCBI Acc.number: NC_002505, NC_002506 using the following settings: Mismatch cost =  2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = Yes, Strand specific = Reverse, Maximum number of hits for a read = 1
Reads mapping in CDS were counted, and genes with a total count cutoff of >15, in all samples were considered for analysis. Read counts were normalized (TPM), and transformed (log2). Differential expression was tested using the built in tool with CLC Genomics Workbench v11.0. Genes with a fold-change of > 1.5 in either condition and a FDR adjusted p-value < 0.001 were considered to be differentially expressed.
Genome_build: NC_002505, NC_002506
Supplementary_files_format_and_content: Read count table by TPM normalization

extract_protocol:
RNA was isolated by the hot phenol method (Fröhlich et al., Nucleic Acids Res. 2018). Prepared RNA was DNase-digested and cleaned up using RNACleanXP. Depletion of ribosomal RNA was performed using Ribo-Zero kits (Epicentre) for Gram-negative bacteria. Integrity of the prepared RNA was tested using a Bioanalyzer.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Libary Prep Kit for Illumina (NEB E7760) according to the manufacturers instructions. Quality of the prepared libraries was tested using a Bioanalyzer.

treatment_protocol: The 21hr grown biofilm cells were treated with 1mM IPTG. After 1hr of treatment cells were harvested in tubes containing 1/5 vol. "stop-mix" (95% ethananol, 5% phenol) and snap frozen in liquid nitrogen until further processing.

value: WT + ptac-vbdR

value: Biofilm under flow

value: 1mM IPTG


title: aFR_3hpa_3: Foot regeneration RNA-seq, 3 hours post amputation, replicate 3, Alsterpaullone

description: Library name: aFR_3hpa_3

value: Alsterpaullone 5 uM


title: aFR_3hpa_2: Foot regeneration RNA-seq, 3 hours post amputation, replicate 2, Alsterpaullone

description: Library name: aFR_3hpa_2


title: Case F

data_processing:
The raw sequencing reads underwent quality control and trimming processes using FastQC and Trimmomatic software.
Clean reads were mapped to GRCh38 using BWA. Samblaster was utilized for deduplication, while the Genome Analysis Toolkit (GATK) was employed for variant calling and subsequent annotation using Annovar and snpEff.
Assembly: GRCh38
Supplementary files format and content: Variants were inclued in the Case I.significant.snp_indel

value: Case I with agar-like ZP ooctyes


title: LC-2/ad_detached_7 day_rep1.

description:
Library name: PR1960_06_a
Column name for Gene_expression.txt : PR1960_06_a.TPM


title: NCI-H2228_attached (control)_rep1.

description:
Library name: PR1960_07_a
Column name for Gene_expression.txt : PR1960_07_a.TPM


title: Case D


title: NCI-H2228_detached_1 day_rep1.

description:
Library name: PR1960_08_a
Column name for Gene_expression.txt : PR1960_08_a.TPM


title: Case 1

data_processing:
The raw sequencing reads underwent quality control and trimming processes using FastQC and Trimmomatic software.
Clean reads were mapped to GRCh38 using BWA. Samblaster was utilized for deduplication, while the Genome Analysis Toolkit (GATK) was employed for variant calling and subsequent annotation using Annovar and snpEff.
processed data files format and content: Variants were inclued in the Case *-significant.snp_indel
Library strategy: whole-exome sequencing

source_name: MI oocytes with a normal ZP


title: HeLa-Cas9 cells transfected with sgRNA targeting TLN1

description: Gene expression data from HeLa-Cas9 cells 48h after TLN1 knock-out

value: HeLa (THP SCL-03-CA3)


title: HeLa-Cas9 cells transfected with sgRNA targeting KD2

description: Gene expression data from HeLa-Cas9 cells 48h after KD2 knock-out


title: Case B

source_name: MI oocytes with an agar-like ZP


title: aFR_3hpa_1: Foot regeneration RNA-seq, 3 hours post amputation, replicate 1, Alsterpaullone

description: Library name: aFR_3hpa_1


title: Case C


title: VbdR rep1


title: Case A


title: LC-2/ad_attached (control)_rep1.

description:
Library name: PR1960_04_a
Column name for Gene_expression.txt : PR1960_04_a.TPM


title: control rep3

value: WT + ptac-ctr


title: VbdR rep2


title: HR_3hpa_2: Head regeneration RNA-seq, 3 hours post amputation, replicate 2, DMSO

description: Library name: HR_3hpa_2

value: body column

value: DMSO


title: HR_3hpa_1: Head regeneration RNA-seq, 3 hours post amputation, replicate 1, DMSO

description: Library name: HR_3hpa_1


title: HR_3hpa_3: Head regeneration RNA-seq, 3 hours post amputation, replicate 3, DMSO

description: Library name: HR_3hpa_3


title: LC-2/ad_detached_1 day_rep1.

description:
Library name: PR1960_05_a
Column name for Gene_expression.txt : PR1960_05_a.TPM

value: lung adenocarcinoma

value: Detachment


title: NCI-H2009_detached_7 day_rep1.

description:
Library name: PR1960_03_a
Column name for Gene_expression.txt : PR1960_03_a.TPM


title: control rep1


title: SIILC3_Cnot3CKO_3

city: Akita

first: Megumi

last: Tatematsu

department: Department of Medical Biology

institute: Akita University Graduate School of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (v. 0.23.2) (parameters - Quality >= Q15, N base limit = 10)
Trimmed sequence reads were mapped to GRCm39 using STAR aligner (v. 2.7.11a) with default parameters
Read count exxtraction were performed using featureCounts (v. 2.0.3)
Read count normalization were caliculated by R (v. 4.1.3)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Small intestine

extract_protocol:
Cells were isolated and directly brought into First-Strand cDNA Synthesis step using SMART-Seq® Stranded Kit (Takara).
Libraries were generated using SMART-Seq® Stranded Kit according to manufacturer's instruction

value: Small intestine

value: Cnot3f/f Il7r-Cre Rorgt-GFP


title: NCI-H2009_detached_1 day_rep1.

description:
Library name: PR1960_02_a
Column name for Gene_expression.txt : PR1960_02_a.TPM


title: NCI-H2009_attached (control)_rep1.

description:
Library name: PR1960_01_a
Column name for Gene_expression.txt : PR1960_01_a.TPM


title: FR_3hpa_3: Foot regeneration RNA-seq, 3 hours post amputation, replicate 3, DMSO

description: Library name: FR_3hpa_3


title: control rep2


title: SIILC3_Cnot3CKO_2


title: FR_3hpa_2: Foot regeneration RNA-seq, 3 hours post amputation, replicate 2, DMSO

description: Library name: FR_3hpa_2


title: SIILC3_control_3

value: Cnot3f/f Rorgt-GFP


title: SIILC3_Cnot3CKO_1


title: KG-1 HDAC8i 10μM 12h rep2

city: MONROVIA

first: Yahuei

last: Kuo

address: 1218 S 5TH AVE

department: Hem Malignancies Trans Sci

institute: City of Hope National Medical Center

description:
Library name: COHP_57010_KG-1_HDAC8i_10uM_12h_rep2
KG-1 treated

data_processing:
Quality control of raw FASTQ files using FastQC.
Adapter trimming and low-quality base removal using Trim Galore.
Alignment to the human reference genome (GRCh38) using STAR.
Gene-level quantification using featureCounts to generate count matrices.
Normalization and QC using DESeq2 or edgeR.
Assembly: Homo sapiens GRCh38/hg38
Supplementary files format and content: Gene-level raw count matrix in txt format for all samples.

growth_protocol: Cells (MV4-11, Kasumi-1, KG-1) were cultured in RPMI-1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C with 5% CO₂.

extract_protocol:
Total RNA was extracted using the Zymo Research Direct-zol RNA Microprep Kit according to the manufacturer's instructions.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s protocol.

treatment_protocol: Cells were treated with 10 μM HDAC8 inhibitor (compound 22d) or DMSO (control) for 12 hours.

value: Leukemia

value: HDAC8i 10μM 12h


title: KG-1 HDAC8i 10μM 12h rep3

description:
Library name: COHP_57011_KG-1_HDAC8i_10uM_12h_rep3
KG-1 treated


title: HR_0hpa_4: Head regeneration RNA-seq, 0 hours post amputation, replicate 4, DMSO

description: Library name: HR_0hpa_4

data_processing:
Raw reads were trimmed with Trimmomatic v0.39 to remove adapter sequences and low quality reads, with the following parameters: PE -threads 16 -phred33 / ILLUMINACLIP: TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 \         SLIDINGWINDOW:4:15 MINLEN:32
Resulting reads were mapped to a reference transcriptome using rsem with the following parameters: rsem-calculate-expression --num-threads 16 --no-bam-output \         --bowtie2 --paired-end
Assembly: GCA_004118135.1
Supplementary files format and content: comma delimited text files including raw counts and FPKM


title: KG-1 HDAC8i 10μM 12h rep1

description:
Library name: COHP_57009_KG-1_HDAC8i_10uM_12h_rep1
KG-1 treated


title: FR_3hpa_1: Foot regeneration RNA-seq, 3 hours post amputation, replicate 1, DMSO

description: Library name: FR_3hpa_1


title: SIILC3_control_1


title: SIILC3_control_2


title: KG-1 DMSO 12h rep3

description:
Library name: COHP_57008_KG-1_DMSO_rep3
KG-1 control

value: DMSO 12h


title: HR_0hpa_3: Head regeneration RNA-seq, 0 hours post amputation, replicate 3, DMSO

description: Library name: HR_0hpa_3


title: SIILC2_Cnot3CKO_3


title: HR_0hpa_1: Head regeneration RNA-seq, 0 hours post amputation, replicate 1, DMSO

description: Library name: HR_0hpa_1


title: SIILC2_Cnot3CKO_2


title: H441-FL_attached_rep1

description: Gene expression of H441-FL in detached conditions.

hyb_protocol: The labeled cRNA was fragmented and hybridized to an array, using Gene Expression Hybridization Kit.

data_processing:
The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: Lung adenocarcinoma cell subline H441-FL, attached

label_protocol: RNA was reverse-transcribed using an oligo(dT) primer to generate double-stranded cDNA, followed by in vitro transcription to produce Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit, one-color.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit.

value: NCI-H441-FL (subline of NCI-H441)

value: attached


title: HR_0hpa_2: Head regeneration RNA-seq, 0 hours post amputation, replicate 2, DMSO

description: Library name: HR_0hpa_2


title: SIILC2_Cnot3CKO_1


title: KG-1 DMSO 12h rep2

description:
Library name: COHP_57007_KG-1_DMSO_rep2
KG-1 control


title: H441-FL_detached_rep1

source_name: Lung adenocarcinoma cell subline H441-FL, detached

value: detached


title: KG-1 DMSO 12h rep1

description:
Library name: COHP_57006_KG-1_DMSO_rep1
KG-1 control


title: H441_detached_7 days_rep1

description: Gene expression of H441 at day 7 in detached condition, i.e., day 7 after replating cells onto ultra-low attachment culture plate.

source_name: Lung adenocarcinoma cell line H441, detached for 7 days

value: detached for 7 days


title: MV4-11 HDAC8i 10μM 12h rep2

description:
Library name: COHP_56998_MV4-11_HDAC8i_10uM_12h_rep2
MV4-11 treated


title: FR_0hpa_4: Foot regeneration RNA-seq, 0 hours post amputation, replicate 4, DMSO

description: Library name: FR_0hpa_4


title: H441_detached_1 day_rep1

description: Gene expression of H441 at day 1 in detached condition, i.e., day 1 after replating cells onto ultra-low attachment culture plate.

source_name: Lung adenocarcinoma cell line H441, detached for 1 day

value: detached for 1 day


title: SIILC2_control_3


title: SIILC2_control_1


title: H441_attached_rep1

description: Gene expression of H441 in attached conditions.

source_name: Lung adenocarcinoma cell line H441, attached


title: MV4-11 HDAC8i 10μM 12h rep3

description:
Library name: COHP_56999_MV4-11_HDAC8i_10uM_12h_rep3
MV4-11 treated


title: LungILC2_Cnot3CKO_3

source_name: lung

value: lung

value: Cnot3f/f Il7r-Cre


title: A549-FL_attached_rep1

description: Gene expression of A549-FL in detached conditions.

source_name: Lung adenocarcinoma cell subline A549-FL, attached

value: A549-FL (subline of A549)


title: A549-FL_detached_rep1

source_name: Lung adenocarcinoma cell subline A549-FL, detached


title: SIILC2_control_2