title: cholesterol medium (0.2 mM), 2.5 μg/mL bedaquiline, biological replicate 3

first: Chuan

last: Wang

address: 131 # Dong An Road

institute: Fudan University

description:
Library name: Mtb_CHOL_BDQhigh_rep3
H37Rv grown in cholesterol-supplemented medium (0.2 mM) to OD600 ≈ 0.2 (log phase), treated with 2.5 μg/mL bedaquiline for 4 h, RNA harvested with TRIzol.

data_processing:
Adapter sequences and low-quality reads were trimmed before analysis.
Filtered reads were aligned to the H37Rv reference genome (ASM19595v2) using Bowtie2.
Alignments were processed using SAMtools and gene-level read counts were generated using HTSeq.
Differential expression analysis was performed using the limma-voom framework. Genes with adjusted P < 0.05 were considered significantly differentially expressed.
Gene set enrichment analysis (GSEA) was performed using clusterProfiler. Pathways with adjusted P < 0.1 were considered significantly enriched.
Assembly: ASM19595v2 (Mycobacterium tuberculosis H37Rv)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Mycobacterium tuberculosis

source_name: whole cell

growth_protocol: Mycobacterium tuberculosis H37Rv cultures were grown in standard Middlebrook 7H9 medium or Middlebrook 7H9 medium supplemented with 0.2 mM cholesterol. Cultures were grown to logarithmic phase and adjusted to OD600 ≈ 0.2 before treatment.

extract_protocol:
Total RNA was extracted from frozen cell pellets using TRIzol reagent following the manufacturer's protocol.
Library preparation was performed by BGI Genomics using strand-specific RNA-seq library preparation protocols. Libraries were sequenced on the DNBSEQ platform with paired-end reads.

treatment_protocol: Log-phase cultures (OD600 ≈ 0.2) were treated with DMSO (vehicle control), 0.625 μg/mL bedaquiline (low dose), or 2.5 μg/mL bedaquiline (high dose) for 4 hours. To arrest transcriptional activity, cultures were immediately mixed with stop solution (95% ethanol / 5% saturated phenol, pH 4.5 ± 0.2) at a 5:1 ratio, snap-frozen in liquid nitrogen, and stored at −80°C.

value: whole cell

value: H37Rv (wild-type)

value: 2.5 μg/mL bedaquiline


title: P. promelas larvae, UP, biological replicate UP_FIELD34, lane 1, time step = NA, analyzed on 20161108

status: Public on Aug 01 2026

type: SRA

city: Durham

first: Steven

middle: Thomas

last: Purucker

state: NC

address: 109 TW Alexander Dr

country: USA

institute: US EPA

description: Library name: 20161108_ UP_FIELD_34_ACAGTG_L001_R1_001

library_source: transcriptomic

data_processing:
Raw read quality assessment with FastQC 0.11.9 & MultiQC 1.12
Reads were processed with fastp 0.23.2 trimming with quality, length, and adapter trimming all enabled by default, and polyX trimming (flag: -x) enabled manually
Alignment with STAR 2.7.10a (--outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --outSAMheaderHD @HD VN 1.4 SO:sorted --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outSAMunmapped Within --outFilterType BySJout)
Quantification with STAR 2.7.10a (--quantMode GeneCounts TranscriptomeSAM)
Assembly: P. promelas, GCF_016745375.1_EPA_FHM_2.0
Supplementary files format and content: Tab delimited text file with gene counts: all_counts_20220629.txt uploaded separately.

molecule: total RNA

organism: Pimephales promelas

source_name: whole larvae

growth_protocol: Lab-reared individual fathead minnow larvae (Pimephales promelas) 2 days post-fertilization.

extract_protocol:
Total RNA was isolated from individual FHM using the MagMAX-96 Total RNA Isolation Kit (ThermoFisher Scientific) following manufacturer's protocols. RNA was quantified by spectrophotometric analysis with a Synergy HTX multi-mode plate reader (BioTek).
Neoprep Library Prep System (Illumina) and the TruSeq Stranded mRNA Library Prep for NeoPrep (Illumina). Library concentrations were determined using either the KAPA Library Quantification Kit (Kapa Biosystems) or Qubit dsDNA HS Assay (ThermoFisher Scientific), normalized to equimolar amounts, and then combined into pools of eight samples each. Sequencing was performed at Michigan State University’s RTSF Genomics Core on the Illumina HiSeq 2500 Rapid Run flow cell (v2) for 1x50 bp single-end reads with Rapid SBS reagents.

treatment_protocol: 48 hour lab exposures to moderately hard reconstituted water or river water grab samples collected in August 15 for 6 locations in the vicinity of a wastewater treatment plant (WWTP): upstream of WWTP, WWTP effluent discharging point, proximal location downstream WWTP outfall, distal location downstream of WWTP outfall, a downstream drinking water intake, and treated drinking water collected prior to discharge to the distribution system. Other exposures included 48 hour field fish deployments in exposure vessels secured to a minnow trap at 2 locations (upstream of a WWTP, WWTP effluent discharging point).

tag: tissue

value: whole larvae

tag: age

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location

value: UP

tag: batch


title: cholesterol medium (0.2 mM), 2.5 μg/mL bedaquiline, biological replicate 2

city: Shanghai

country: China

description:
Library name: Mtb_CHOL_BDQhigh_rep2
H37Rv grown in cholesterol-supplemented medium (0.2 mM) to OD600 ≈ 0.2 (log phase), treated with 2.5 μg/mL bedaquiline for 4 h, RNA harvested with TRIzol.

tag: cell type

tag: genotype

tag: treatment


title: N0386

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

data_processing:
Processed and selected high-quality reads using FastQC (v0.11.8), excluding any reads with low base quality
Aligned to the GRCh37 human reference genome provided by GENCODE, employing STAR v2.74a
Gene and transcript expression levels were then quantified using RSEM v1.3.3
Assembly: hg19
Supplementary files format and content: comma-delimited csv file include raw counts for each sample

organism: Homo sapiens

source_name: stomach

extract_protocol:
Total RNA was extracted from 108 paired tumor and normal tissue samples using the Qiagen AllPrep DNA/RNA Mini Kit (Cat. No. 80204, Qiagen, Germany) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: stomach

tag: Sex

value: Female

value: Normal

tag: diagnosis

value: Advanced Gastric Cancer (AGC)


title: P. promelas larvae, UP, biological replicate UP_B29, lane 2, time step = 3, analyzed on 20161108

description: Library name: 20161108_ UP_3_B29_AGTCAA_L002_R1_001


title: cholesterol medium (0.2 mM), 2.5 μg/mL bedaquiline, biological replicate 1

description:
Library name: Mtb_CHOL_BDQhigh_rep1
H37Rv grown in cholesterol-supplemented medium (0.2 mM) to OD600 ≈ 0.2 (log phase), treated with 2.5 μg/mL bedaquiline for 4 h, RNA harvested with TRIzol.


title: cholesterol medium (0.2 mM), 0.625 μg/mL bedaquiline, biological replicate 3

description:
Library name: Mtb_CHOL_BDQlow_rep3
H37Rv grown in cholesterol-supplemented medium (0.2 mM) to OD600 ≈ 0.2 (log phase), treated with 0.625 μg/mL bedaquiline for 4 h, RNA harvested with TRIzol.

value: 0.625 μg/mL bedaquiline


title: N0374

value: Male


title: cholesterol medium (0.2 mM), 0.625 μg/mL bedaquiline, biological replicate 2

description:
Library name: Mtb_CHOL_BDQlow_rep2
H37Rv grown in cholesterol-supplemented medium (0.2 mM) to OD600 ≈ 0.2 (log phase), treated with 0.625 μg/mL bedaquiline for 4 h, RNA harvested with TRIzol.


title: P. promelas larvae, UP, biological replicate UP_B29, lane 1, time step = 3, analyzed on 20161108

description: Library name: 20161108_ UP_3_B29_AGTCAA_L001_R1_001


title: N0359


title: cholesterol medium (0.2 mM), DMSO (vehicle control), biological replicate 3

description:
Library name: Mtb_CHOL_DMSO_rep3
H37Rv grown in cholesterol-supplemented medium (0.2 mM) to OD600 ≈ 0.2 (log phase), treated with DMSO (vehicle control) for 4 h, RNA harvested with TRIzol.

value: DMSO (vehicle control)


title: P. promelas larvae, UP, biological replicate UP_B16, lane 2, time step = 2, analyzed on 20161108

description: Library name: 20161108_ UP_2_B16_GCCAAT_L002_R1_001


title: cholesterol medium (0.2 mM), DMSO (vehicle control), biological replicate 2

description:
Library name: Mtb_CHOL_DMSO_rep2
H37Rv grown in cholesterol-supplemented medium (0.2 mM) to OD600 ≈ 0.2 (log phase), treated with DMSO (vehicle control) for 4 h, RNA harvested with TRIzol.


title: N0352


title: P. promelas larvae, UP, biological replicate UP_B16, lane 1, time step = 2, analyzed on 20161108

description: Library name: 20161108_ UP_2_B16_GCCAAT_L001_R1_001


title: cholesterol medium (0.2 mM), DMSO (vehicle control), biological replicate 1

description:
Library name: Mtb_CHOL_DMSO_rep1
H37Rv grown in cholesterol-supplemented medium (0.2 mM) to OD600 ≈ 0.2 (log phase), treated with DMSO (vehicle control) for 4 h, RNA harvested with TRIzol.


title: N0351


title: standard medium, 2.5 μg/mL bedaquiline, biological replicate 3

description:
Library name: Mtb_STD_BDQhigh_rep3
H37Rv grown in standard medium to OD600 ≈ 0.2 (log phase), treated with 2.5 μg/mL bedaquiline for 4 h, RNA harvested with TRIzol.


title: standard medium, 2.5 μg/mL bedaquiline, biological replicate 2

description:
Library name: Mtb_STD_BDQhigh_rep2
H37Rv grown in standard medium to OD600 ≈ 0.2 (log phase), treated with 2.5 μg/mL bedaquiline for 4 h, RNA harvested with TRIzol.


title: P. promelas larvae, TR, technical replicate TR_L2-16-TR, lane 2, time step = NA, analyzed on 20161108

description: Library name: 20161108_ TR_L2-16_GAGTGG_L002_R1_001

value: TR


title: standard medium, 2.5 μg/mL bedaquiline, biological replicate 1

description:
Library name: Mtb_STD_BDQhigh_rep1
H37Rv grown in standard medium to OD600 ≈ 0.2 (log phase), treated with 2.5 μg/mL bedaquiline for 4 h, RNA harvested with TRIzol.


title: N0346


title: P. promelas larvae, TR, technical replicate TR_L2-16-TR, lane 1, time step = NA, analyzed on 20161108

description: Library name: 20161108_ TR_L2-16_GAGTGG_L001_R1_001


title: standard medium, 0.625 μg/mL bedaquiline, biological replicate 2

description:
Library name: Mtb_STD_BDQlow_rep2
H37Rv grown in standard medium to OD600 ≈ 0.2 (log phase), treated with 0.625 μg/mL bedaquiline for 4 h, RNA harvested with TRIzol.


title: N0339


title: standard medium, 0.625 μg/mL bedaquiline, biological replicate 1

description:
Library name: Mtb_STD_BDQlow_rep1
H37Rv grown in standard medium to OD600 ≈ 0.2 (log phase), treated with 0.625 μg/mL bedaquiline for 4 h, RNA harvested with TRIzol.


title: P. promelas larvae, EFP, biological replicate EFP_FIELD49, lane 2, time step = NA, analyzed on 20161108

description: Library name: 20161108_ EFP_FIELD_49_GTTTCG_L002_R1_001

value: EFP


title: standard medium, DMSO, biological replicate 3

description:
Library name: Mtb_STD_DMSO_rep3
H37Rv grown in standard medium to OD600 ≈ 0.2 (log phase), treated with DMSO (vehicle control) for 4 h, RNA harvested with TRIzol.


title: N0337


title: P. promelas larvae, EFP, biological replicate EFP_FIELD49, lane 1, time step = NA, analyzed on 20161108

description: Library name: 20161108_ EFP_FIELD_49_GTTTCG_L001_R1_001


title: standard medium, DMSO, biological replicate 2

description:
Library name: Mtb_STD_DMSO_rep2
H37Rv grown in standard medium to OD600 ≈ 0.2 (log phase), treated with DMSO (vehicle control) for 4 h, RNA harvested with TRIzol.


title: standard medium, DMSO, biological replicate 1

description:
Library name: Mtb_STD_DMSO_rep1
H37Rv grown in standard medium to OD600 ≈ 0.2 (log phase), treated with DMSO (vehicle control) for 4 h, RNA harvested with TRIzol.


title: N0334


title: DeltayhbD vancomycin replicate 3

city: Marburg

first: Peter

last: Graumann

address: Karl-von-Frisch-Str. 14

department: Chemistry

country: Germany

institute: Marburg University

description:
Library name: R3_delta_plus
B. subtilis NCIB 3610 deltayhbD, vancomycin treated

data_processing:
1. Raw read quality was assessed using FastQC v0.12.1
2. Reads were aligned to the B. subtilis NCIB 3610 reference genome    (CP020102.1) using STAR v2.7.11a with default parameters
3. Gene-level read counts were quantified using featureCounts v2.1.1    (reverse strand specificity, paired-end mode, primary alignments    only, minimum mapping quality 10)
4. Differential expression analysis was performed in R v4.4.1 using    DESeq2 v1.44.0 with design formula ~ cell_type * condition
5. Log2 fold changes were shrunk using the adaptive shrinkage    estimator ashr v2.2.63
Assembly: Bacillus subtilis NCIB 3610 (GenBank CP020102.1)
Supplementary files format and content: *.tabular: tab-separated raw gene counts from featureCounts, rows = genes (Name attribute from GFF3), columns = gene_id and count

organism: Bacillus subtilis

source_name: bacterial cell

growth_protocol: Bacillus subtilis NCIB 3610 wild-type and delta-yhbD strains were streaked from glycerol stocks and inoculated into liquid LB medium. Overnight cultures were transferred to 250 ml fresh LB medium and incubated at 37°C, 200 rpm until OD600 = 0.1, then transferred to 250 ml fresh LB medium and grown to OD600 = 0.6.

extract_protocol:
Total RNA extraction and rRNA depletion were performed by Eurofins Genomics. rRNA was removed from total RNA to enrich for mRNA. RNA concentration minimum requirement was 135 ng/ul for bacterial samples.
Strand-specific cDNA library preparation was performed by Eurofins Genomics. mRNA was fragmented prior to strand-specific cDNA synthesis. Libraries were prepared following the Illumina standard for 2x150 bp paired-end sequencing using a minimum of 20 ng rRNA-depleted mRNA (>1.4 ng/ul). Paired-end sequencing (2x150 bp) was performed on an Illumina NovaSeq X, guaranteeing a minimum of 10 million reads (+/- 3%) per sample.

treatment_protocol: At OD600 = 0.6, cultures were treated with 4 ug/mL vancomycin for 30 min at 37°C, 200 rpm. Control cultures received no treatment. Cells were pelleted at 2500 rpm for 15 min, washed with 1x PBS, pelleted again, flash-frozen in liquid nitrogen and stored at -80°C until shipment to Eurofins Genomics on dry ice.

tag: strain

value: NCIB 3610

value: bacterial cell

value: yhbD deletion

value: 4 ug/mL vancomycin 30 min


title: P. promelas larvae, EFP, biological replicate EFP_B16, lane 2, time step = 4, analyzed on 20161108

description: Library name: 20161108_ EFP_4_B16_GTGAAA_L002_R1_001


title: N0328


title: P. promelas larvae, EFP, biological replicate EFP_B16, lane 1, time step = 4, analyzed on 20161108

description: Library name: 20161108_ EFP_4_B16_GTGAAA_L001_R1_001


title: DeltayhbD control replicate 3

description:
Library name: R3_delta_minus
B. subtilis NCIB 3610 deltayhbD, no treatment

value: control


title: N0325


title: P. promelas larvae, EFP, biological replicate EFP_B21, lane 2, time step = 3, analyzed on 20161108

description: Library name: 20161108_ EFP_3_B21_ATGTCA_L002_R1_001

value: whole larvae


title: N0322


title: DeltayhbD control replicate 1

description:
Library name: R1_delta_minus
B. subtilis NCIB 3610 deltayhbD, no treatment


title: DeltayhbD control replicate 2

description:
Library name: R2_delta_minus
B. subtilis NCIB 3610 deltayhbD, no treatment


title: WT vancomycin replicate 3

description:
Library name: R3_wt_plus
B. subtilis NCIB 3610 wild-type, vancomycin treated

value: wild-type


title: WT vancomycin replicate 2

description:
Library name: R2_wt_plus
B. subtilis NCIB 3610 wild-type, vancomycin treated


title: N0321


title: WT vancomycin replicate 1

description:
Library name: R1_wt_plus
B. subtilis NCIB 3610 wild-type, vancomycin treated


title: P. promelas larvae, EFP, biological replicate EFP_B21, lane 2, time step = 1, analyzed on 20161108

description: Library name: 20161108_ EFP_1_B21_AGTTCC_L002_R1_001

value: 2 dpf


title: N0320

value: stomach


title: WT control replicate 3

description:
Library name: R3_wt_minus
B. subtilis NCIB 3610 wild-type, no treatment


title: WT control replicate 2

description:
Library name: R2_wt_minus
B. subtilis NCIB 3610 wild-type, no treatment


title: P. promelas larvae, EFP, biological replicate EFP_B21, lane 1, time step = 1, analyzed on 20161108

description: Library name: 20161108_ EFP_1_B21_AGTTCC_L001_R1_001


title: WT control replicate 1

description:
Library name: R1_wt_minus
B. subtilis NCIB 3610 wild-type, no treatment


title: P. promelas larvae, UP, biological replicate UP_FIELD55, lane 2, time step = NA, analyzed on 20161028

description: Library name: 20161028_ UP_FIELD_55_GAGTGG_L007_R1_001

value: UP


title: bb859, intracellular to qs9

city: Waterville

first: Suegene

last: Noh

state: ME

address: 5717 Mayflower Hill

department: Biology

institute: Colby College

description:
Library name: b859_qs9
rRNA depleted

data_processing:
D. discoideum reads were aligned to the D. discoideum reference genome and GTF annotation file (downloaded Jan 2023 from dictybase). The segmental duplication in this reference genome (2: 3016083-3768654) was masked using bedtools v2.28.0 (Quinlan and Hall 2010). Paraburkholderia reads were aligned to draft genome assemblies (Noh et al 2022) and Prokka GFF annotation files. Host alignments were performed with STAR v2.7.5c and symbiont alignments were performed with Bowtie2 v2.4.2. Samtools v1.3.1 was used to sort and filter alignments, Picard v2.17.10 (downloaded from broadinstitute.github.io/picard) was used to assign read groups. Read counts were extracted from primary alignments with correct strand orientation using HTSeq v0.11.2 (Anders et al. 2015).
Assembly: The D. discdoideum reference genome was downloaded Jan 2023 from http://dictybase.org. Paraburkholderia draft genome assemblies are available from NCBI and https://github.com/noh-lab/clade_infection/tree/main/genome_files
Supplementary files format and content: Tab-delimited file of raw counts per gene for each sample

organism: Paraburkholderia bonniea

source_name: whole organism

extract_protocol:
For uninfected host samples, cells were removed from RNAlater® and processed following a standard RNA extraction protocol using Qiagen RNeasy Mini kits. For free-living symbiont samples, cells were disrupted with a lysozyme treatment prior to RNeasy extraction, then treated with illumina Ribozero according to its product protocol. Symbiont-associated (infected) host samples were obtained by taking the supernatant of the first RLN buffer treatment of associated amoebas in the RNeasy protocol. Host-associated (intracellular) symbiont samples were obtained by taking the spun-down pellet of this same RLN buffer treatment step that contains amoeba nuclei as well as intracellular Paraburkholderia. This pellet was treated with lysozyme, then the RNeasy protocol and illumina Ribozero protocol as with the free-living symbiont samples.
All samples were then prepared with the illumina TruSeq Stranded mRNA library preparation protocol but only D. discoideum samples were subjected to the polyA enrichment step.

value: whole organism

value: intracellular


title: bb859, intracellular to qs864

description:
Library name: b859_864
rRNA depleted


title: N0306

value: Female

value: Normal

value: Advanced Gastric Cancer (AGC)


title: bb859, intracellular to qs18

description:
Library name: b859_qs18
rRNA depleted


title: P. promelas larvae, UP, biological replicate UP_FIELD54, lane 2, time step = NA, analyzed on 20161028

description: Library name: 20161028_ UP_FIELD_54_GGCTAC_L007_R1_001


title: N0304

value: Male


title: bb859, freeliving, sample b

description:
Library name: b859_b
rRNA depleted

value: freeliving


title: bb859, freeliving, sample c

description:
Library name: b859_c
rRNA depleted


title: P. promelas larvae, EFP, biological replicate EFP_FIELD55, lane 2, time step = NA, analyzed on 20161028

description: Library name: 20161028_ EFP_FIELD_55_ACTGAT_L007_R1_001

value: EFP


title: bb859, freeliving, sample a

description:
Library name: b859_a
rRNA depleted


title: N0301


title: 54

city: Maastricht

first: Julian

last: Krauskopf

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

library_source: other

data_processing:
Raw sequence reads were assessed for quality using FastQC. Low-quality reads and adapter sequences were trimmed using Trimmomatic with a quality score threshold of 20.
miRNA read counts were extracted using miRge2.
Assembly: miRBase v. 22
Supplementary files format and content: comma separated text files include raw counts for each sample.

molecule: other

source_name: plasma

extract_protocol:
RNA was harvested from plasma samples using the miRNeasy Serum/Plasma kit (Qiagen). A minimum of 1 ng RNA with a distinct 21-nucleotide peak was used for library construction.
RNA libraries for small RNA sequencing were prepared using the RealSeq®-small RNA sequencing library preparation kit (Somagenics) according to the manufacturer's protocols.

value: plasma

tag: exposure

value: Medium Exposure

value: 16-25 years

tag: bmi

value: Normal Weight


title: DeltayhbD vancomycin replicate 1

description:
Library name: R1_delta_plus
B. subtilis NCIB 3610 deltayhbD, vancomycin treated

value: NCIB 3610

value: bacterial cell

value: yhbD deletion

value: 4 ug/mL vancomycin 30 min


title: DeltayhbD vancomycin replicate 2

description:
Library name: R2_delta_plus
B. subtilis NCIB 3610 deltayhbD, vancomycin treated


title: P. promelas larvae, EFP, biological replicate EFP_B23, lane 2, time step = 3, analyzed on 20161028

description: Library name: 20161028_ EFP_4_B23_GTGGCC_L007_R1_001

value: whole larvae

value: 2 dpf


title: 52

value: Low Exposure


title: N0298

value: stomach


title: 51

value: 26-39 years


title: P. promelas larvae, EFP, biological replicate EFP_B23, lane 2, time step = 2, analyzed on 20161028

description: Library name: 20161028_ EFP_3_B23_TAGCTT_L007_R1_001


title: N0295

value: Normal

value: Advanced Gastric Cancer (AGC)


title: 46

value: Female

value: 40 or Above


title: P. promelas larvae, EFP, biological replicate EFP_B16, lane 2, time step = 1, analyzed on 20161028

description: Library name: 20161028_ EFP_2_B16_ATCACG_L007_R1_001

value: EFP


title: 47

value: plasma

value: Obese


title: N0413


title: 43

value: High Exposure

value: 16-25 years

value: Normal Weight


title: P. promelas larvae, EFP, biological replicate EFP_B21, lane 1, time step = 3, analyzed on 20161108

description: Library name: 20161108_ EFP_3_B21_ATGTCA_L001_R1_001


title: N0291

value: Male


title: P. promelas larvae, DWIP, biological replicate DWIP_B17, lane 2, time step = NA, analyzed on 20161028

description: Library name: 20161028_ DWIP_B17_GTCCGC_L007_R1_001

value: DWIP


title: 39


title: 34

value: Over Weight


title: 33

value: Medium Exposure


title: N0285


title: 29

value: Low Exposure

value: Under weight


title: N0276

value: stomach


title: 26


title: 20

value: 26-39 years


title: N0273

value: Normal

value: Advanced Gastric Cancer (AGC)


title: P. promelas larvae, UP, biological replicate UP_FIELD56, lane 2, time step = NA, analyzed on 20161017

description: Library name: 20161017_ UP_FIELD_56_AGTTCC_L002_R1_001

value: whole larvae

value: 2 dpf

value: UP


title: N0319


title: 201

value: plasma


title: P. promelas larvae, UP, biological replicate UP_FIELD56, lane 1, time step = NA, analyzed on 20161017

description: Library name: 20161017_ UP_FIELD_56_AGTTCC_L001_R1_001


title: 19


title: N0265

value: Female


title: 195


title: P. promelas larvae, TRUP, technical replicate TR_FIELD2-TR, lane 2, time step = NA, analyzed on 20161017

description: Library name: 20161017_ UP_FIELD_2-TR_GCCAAT_L002_R1_001

value: TR


title: 193

value: 40 or Above


title: 192

value: Male

value: Obese


title: N0264


title: P. promelas larvae, TRUP, technical replicate TR_FIELD2-TR, lane 1, time step = NA, analyzed on 20161017

description: Library name: 20161017_ UP_FIELD_2-TR_GCCAAT_L001_R1_001


title: 191

value: High Exposure

value: 16-25 years

value: Normal Weight


title: N0262


title: 190

value: Low Exposure

value: Under weight


title: 18


title: P. promelas larvae, UP, biological replicate UP_B23, lane 2, time step = 3, analyzed on 20161017

description: Library name: 20161017_ UP_3_B23_GTTTCG_L002_R1_001


title: N0258

value: stomach


title: 187

value: 26-39 years


title: P. promelas larvae, UP, biological replicate UP_B23, lane 1, time step = 3, analyzed on 20161017

description: Library name: 20161017_ UP_3_B23_GTTTCG_L001_R1_001


title: N0252

value: Normal

value: Advanced Gastric Cancer (AGC)


title: 17

value: Medium Exposure


title: 178


title: 176

value: Over Weight


title: N0249


title: 174

value: plasma


title: P. promelas larvae, UP, biological replicate UP_B23, lane 2, time step = 2, analyzed on 20161017

description: Library name: 20161017_ UP_2_B23_GTGAAA_L002_R1_001

value: whole larvae

value: 2 dpf

value: UP


title: P. promelas larvae, UP, biological replicate UP_B23, lane 1, time step = 2, analyzed on 20161017

description: Library name: 20161017_ UP_2_B23_GTGAAA_L001_R1_001


title: 173

value: Female

value: 40 or Above


title: N0246


title: 16

value: Male


title: 169

value: High Exposure


title: N0245


title: P. promelas larvae, UP, biological replicate UP_B24, lane 2, time step = 1, analyzed on 20161017

description: Library name: 20161017_ UP_1_B24_ATGTCA_L002_R1_001


title: 161

value: Normal Weight


title: P. promelas larvae, UP, biological replicate UP_B24, lane 1, time step = 1, analyzed on 20161017

description: Library name: 20161017_ UP_1_B24_ATGTCA_L001_R1_001


title: N0242


title: 151


title: P. promelas larvae, EFP, biological replicate EFP_FIELD56, lane 2, time step = NA, analyzed on 20161017

description: Library name: 20161017_ EFP_FIELD_56_CTTGTA_L002_R1_001

value: EFP


title: 148


title: N0393


title: 160


title: N0239


title: 140

value: Low Exposure


title: N0238

value: stomach


title: 134

value: 16-25 years


title: cholesterol medium (0.2 mM), 0.625 μg/mL bedaquiline, biological replicate 1

description:
Library name: Mtb_CHOL_BDQlow_rep1
H37Rv grown in cholesterol-supplemented medium (0.2 mM) to OD600 ≈ 0.2 (log phase), treated with 0.625 μg/mL bedaquiline for 4 h, RNA harvested with TRIzol.

value: whole cell

value: H37Rv (wild-type)

value: 0.625 μg/mL bedaquiline


title: 135

value: Medium Exposure


title: P. promelas larvae, EFP, biological replicate EFP_FIELD56, lane 1, time step = NA, analyzed on 20161017

description: Library name: 20161017_ EFP_FIELD_56_CTTGTA_L001_R1_001


title: 12

value: plasma


title: 132


title: P. promelas larvae, EFP, biological replicate EFP_B28, lane 2, time step = 4, analyzed on 20161017

description: Library name: 20161017_ EFP_4_B28_AGTCAA_L002_R1_001

value: whole larvae


title: N0233

value: Normal

value: Advanced Gastric Cancer (AGC)


title: P. promelas larvae, EFP, biological replicate EFP_B28, lane 1, time step = 4, analyzed on 20161017

description: Library name: 20161017_ EFP_4_B28_AGTCAA_L001_R1_001

value: 2 dpf


title: N0232


title: 126

value: Under weight


title: 124

value: Male

value: Over Weight


title: P. promelas larvae, MHW, biological replicate MHW_B28, lane 2, time step = NA, analyzed on 20161017

description: Library name: 20161017_ 15-07_B28_ACAGTG_L002_R1_001

value: MHW


title: 115

value: High Exposure

value: Normal Weight


title: N0226

value: stomach

value: Female


title: P. promelas larvae, MHW, biological replicate MHW_B28, lane 1, time step = NA, analyzed on 20161017

description: Library name: 20161017_ 15-07_B28_ACAGTG_L001_R1_001


title: 112

value: 16-25 years


title: N0225


title: SNU449 cells, sMAD2L1-2, Day 3

city: Guangzhou

first: Xinjun

last: Lu

state: Guangdong

address: #33 Yingfeng Rd

institute: SYSU

data_processing:
Basecalling is performed by Illumina RTA software in sequencer.
Raw data (raw reads) of FASTQ format were firstly processed through fastp to generate clean reads.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Differential expression analysis of two conditions/groups (five biological replicates per condition) was performed using the DESeq2 R package (1.16.1).Genes with an  P-value <0.05 found by DESeq2 were assigned as differentially expressed.
GO and KEGG enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package.
Assembly: hg38

source_name: Liver

growth_protocol: SNU449 HCC cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted employing Trizol reagent (Invitrogen, CA, USA). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Total RNA samples were converted into cDNA libraries using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (Catalog E7530L, NEB, USA) following the manufacturer's recommendations

value: Liver

tag: cell line

value: SNU 449

value: Liver tumor cell line


title: SNU449 cells, sMAD2L1-3, Day 3


title: P. promelas larvae, UP, biological replicate UP_FIELD37, lane 2, time step = NA, analyzed on 20161014

description: Library name: 20161014_ UP_FIELD_37_GGCTAC_L002_R1_001

value: UP


title: SNU449 cells, sMAD2L1-1, Day 3


title: N0223


title: standard medium, 0.625 μg/mL bedaquiline, biological replicate 3

description:
Library name: Mtb_STD_BDQlow_rep3
H37Rv grown in standard medium to OD600 ≈ 0.2 (log phase), treated with 0.625 μg/mL bedaquiline for 4 h, RNA harvested with TRIzol.

value: whole cell

value: H37Rv (wild-type)

value: 0.625 μg/mL bedaquiline


title: SNU449 cells, siControl-3, Day 3

value: siControl


title: P. promelas larvae, UP, biological replicate UP_FIELD37, lane 1, time step = NA, analyzed on 20161014

description: Library name: 20161014_ UP_FIELD_37_GGCTAC_L001_R1_001

value: whole larvae

value: 2 dpf


title: SNU449 cells, siControl-2, Day 3


title: SNU449 cells, siControl-1, Day 3


title: N0221

value: Normal

value: Advanced Gastric Cancer (AGC)


title: P. promelas larvae, UP, biological replicate UP_FIELD36, lane 2, time step = NA, analyzed on 20161014

description: Library name: 20161014_ UP_FIELD_36_TAGCTT_L002_R1_001


title: Dami cells, mutant CYCS, Mutant biol rep3

city: Athens

first: Eleni

last: Katsantoni

state: Attiki

address: Soranou tou Efesiou 4

department: Basic Research Department

country: Greece

institute: Biomedica Research Foundation Academy of Athens

data_processing:
Fastq files containing 100bp single-end reads have been generated by all sequenced samples and have been QCed using FastQC v.0.11.9. Trimming was considered not to be essential and  alignment to the human genome (hg38) using the STAR RNA Sequencing aligner (V. 2.7.7a) has been performed
The count files for each sample were generated by the featureCounts tool (V. 2.0.1)
Assembly: Hg38
Supplementary files format and content: Csv (comma separated value) files includes raw counts for each Sample

molecule: polyA RNA

source_name: Dami

growth_protocol: Dami cells have been cultured in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with glutamine, 10% Horse serum and 1% Penicillin-Streptomycin 10.000U/ml.

extract_protocol:
RNA has been extracted using TRI Reagent according to the manufacturer’s instructions.
Approximately 1 ug of RNA has been used for library preparation with the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (New England Biolabs (NEB), Massachusetts, USA), according to the manufacturer’s instruction, after the mRNA isolation with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB)

treatment_protocol: The novel variant has been inserted in Dami cells using the CRISPR-Cas9 method. Alt-R CRISPR-Cas9 crRNA and HDR Donor oligo have been designed in the IDT Alt-R CRISPR HDR Designing Tool (Supplemental Table 1). Alt-R CRISPR-Cas9 tracrRNA, Alt-R S.p HiFi Cas9 Nuclease V3 and Alt-R HDR Enhancer V2 have been purchased from IDT. The preparation of the CRISPR reagents, the gRNA complex and the culture media have been performed according to the IDT protocol. Nucleofection of Dami cells has been performed in Nucleofector 2b Device, using the Amaxa Cell Line Nucleofector Kit V (Lonza, Switzerland). 48h after nucleofection, genomic DNA has been extracted using the Quick-gDNA MiniPrep Kit (ZymoResearch, USA) and tested by Sanger sequencing. The nucleofected Dami cells have then been sorted as single cells, using FACSAria IIu (BD Biosciences, USA) in 96-well plates, for the isolation of the heterozygous (T/C), homozygous (C/C) and wild-type (WT) clones.

value: Dami

value: Megakaryocytic

value: Cell line

value: CYCS variant ((NM_018947.6):c.292T>C (p.Tyr98His)


title: P. promelas larvae, UP, biological replicate UP_FIELD36, lane 1, time step = NA, analyzed on 20161014

description: Library name: 20161014_ UP_FIELD_36_TAGCTT_L001_R1_001


title: Dami cells, mutant CYCS, Mutant biol rep2


title: N0220

value: stomach

value: Male


title: Dami cells, mutant CYCS, Mutant biol rep1


title: N0218

value: Female


title: P. promelas larvae, EMZ, biological replicate EMZ_B17, lane 2, time step = NA, analyzed on 20161014

description: Library name: 20161014_ EMZ_B17_ACTTGA_L002_R1_001

value: EMZ


title: Dami cells, WT, Control biol rep4

value: WT


title: Dami cells, WT, Control biοl rep2


title: N0215


title: Dami cells, WT, Control biol rep2


title: Dami cells, WT, Control biol rep1


title: P. promelas larvae, EMZ, biological replicate EMZ_B17, lane 1, time step = NA, analyzed on 20161014

description: Library name: 20161014_ EMZ_B17_ACTTGA_L001_R1_001


title: N0211


title: Breast-FUS(2)

type: other

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

description:
SeuratObject.RDS
SeuratTranscript.RDS
TileDB.tar.gz
At the time of contributing this dataset we were unable to confirm the presence of a FUS-induced lesion in this sample.
CosMx SMI (NanoString/Bruker)
Sample name (Flow cell): 006-day22

hyb_protocol: The sample was submitted to an in situ hybridization overnight at 37 ºC using the 1000 plex RNA Human Universal Panel, according to the manufacturer's protocol (MAN-10184-04). The next day, the tissues were subjected to stringent washes to eliminate any unbound probes. Before loading onto the instrument, the tissues were stained with CosMx Nuclear Stain, Hs CD298/B2M, Hs PanCK/CD45, and Hs CD68 markers.

scan_protocol: The slide and coverslip constitute the flow cell, which was placed within a fluidic manifold on the SMI instrument (version 1.3) for segmentation imaging and in situ analyte readout. The instrument's analysis run was set up using Configuration C (60 s FOV pre-bleaching) and segmentation profile Configuration A. The scan was set with each reporter set containing 8 readout rounds with four different fluorophores.

data_processing:
The data was processed onto the AtoMx cloud (version 1.3.2). It was selected 1211 FOVs with 880,617 cells segmented. The Negative Probe QC = outlier P-value cutoff 0.01; Minimal counts per cell = 20; Field of View (FOV) cutoff = 100; Neg Control Quantile cutoff = 0.5, detection = 0.01. The Seurat was used to Normalization RNA (https://satijalab.org/seurat/reference/normalizedata).
All data were generated using CosMx SMI version 1.3 and analyzed in the AtoMx cloud environment version 1.3.2, following the manufacturer's protocol (MAN-10184-05, MAN-10161-09, MAN-10162-06).
FOVimages_*.tar.gz - This file contains the Global FOV position file (coordinates of each FOV center). FOV is Field of View.
RawDecodedFiles_*.tar.gz - The raw data processed to decode the oligonucleotide barcodes used to identify specific genes or proteins. This process results in encoded data, which includes transcript information and their spatial locations (X, Y coordinates).
TileDB.tar.gz - Default tertiary analysis files.
*_flatFiles.tar.gz - These contain following flatfiles:
*_tx_file.csv.gz contains Global transcripts file (global coordinates for every individual transcript on the flow cell;
*_exprMat_file.csv.gz contains expression matrix
*_metadata_file.csv.gz - Cell metadata file (local (within the FOV)/global (within the flow cell) cell coordinates, morphology marker intensities)
* _fov_positions_file.csv.gz - Global FOV position file (coordinates of each FOV center)
*-polygons.csv.gz - Global cell boundaries file (global coordinates for the vertices of the polygon that represents the cells' boundaries - a representation of the cell segmentation)
QC_metrics.xls spreadsheets are related to QC metrics for the flowcell/slide/tissue analyzed: number of FOV per flowcell, cell per FOV, transcripts per flowcell/FOV/Cell.

label: Barcode probe base

source_name: human breast cancer

label_protocol: One slice of 5 µm thickness from each selected FFPE block adhered onto Leica BOND Plus slides (Leica Biosystems, S21.2113.A) and dried overnight in RT. The tissue was deparaffinized using Xylene, Hydrated with ethanol, heat-induced epitope retrieval for 15 min at 100 °C, and permeabilized with proteinase K 3 μg ml−1 digestion buffer for 30 min at 40 °C. The fiducials were applied to the tissue in a 0.001% working concentration, followed by post-fixation and blocking using NHS-acetate.

extract_protocol: Tumor specimens were removed per standard clinical care. Leftover tumor tissue was divided into several components and allocated according to study priorities. Portions designated for CosMX spatial profiling were fixed in 10% neutral‑buffered formalin and then processed into paraffin‑embedded (FFPE) blocks using standard histopathology workflows.

tag: gender

tag: sample name

tag: location on chip

value: Only sample

tag: tumor type

tag: treatment gem

tag: treatment fus

value: FUS

tag: collection method

value: Resected

tag: collection time

value: 2 weeks post FUS treatment

tag: fus lesion

value: FUS-induced lesion(?)

tag: molecule type

value: RNA count


title: N0207

tag: tissue

tag: age

tag: genotype

value: Normal


title: Breast-FUS(1)(Above) AND Breast-FUS+GEM(1)(Below)_sample2

description:
SeuratObject.RDS
SeuratTranscript.RDS
TileDB.tar.gz
CosMx SMI (NanoString/Bruker)
Sample name (Flow cell): VBC94-VBC106

value: Below

value: Triple‑negative breast cancer (TNBC)

value: Punch Biopsies

value: 1 week before FUS treatment

value: FUS-induced lesion(-)


title: Breast-FUS(1)(Above) AND Breast-FUS+GEM(1)(Below)_sample1

description:
SeuratObject.RDS
SeuratTranscript.RDS
TileDB.tar.gz
There are 2 samples on this chip, represented as sample1 and sample2 sample records.
CosMx SMI (NanoString/Bruker)
Sample name (Flow cell): VBC94-VBC106

value: Above


title: P. promelas larvae, EFP, biological replicate EFP_FIELD40, lane 2, time step = NA, analyzed on 20161014

description: Library name: 20161014_ EFP_FIELD_40_GTCCGC_L002_R1_001

value: whole larvae

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location

value: EFP

tag: batch


title: P. promelas larvae, EFP, biological replicate EFP_FIELD40, lane 1, time step = NA, analyzed on 20161014

description: Library name: 20161014_ EFP_FIELD_40_GTCCGC_L001_R1_001


title: Breast-FUS+GEM(2)

description:
SeuratObject.RDS
SeuratTranscript.RDS
TileDB.tar.gz
Lesion in upper right-hand part of tissue was characterized as a FUS-induced lesion by a pathologist
CosMx SMI (NanoString/Bruker)
Sample name (Flow cell): TPF-38138

tag: gender

value: Female

value: Gem

value: FUS-induced lesion(+)


title: N0206

value: stomach

tag: Sex

tag: diagnosis

value: Advanced Gastric Cancer (AGC)


title: Breast-Untreated Archival Sample

description:
SeuratObject.RDS
SeuratTranscript.RDS
TileDB.tar.gz
This is an archival sample that matches the genotype of Breast-FUS+GEM(1&2)
CosMx SMI (NanoString/Bruker)
Sample name (Flow cell): MAD10-488-t2

tag: sample name

value: Breast-Untreated Archival Sample

tag: location on chip

value: Only sample

tag: tumor type

value: Resected

value: Archival Sample


title: P. promelas larvae, EFP, biological replicate EFP_FIELD39, lane 2, time step = NA, analyzed on 20161014

description: Library name: 20161014_ EFP_FIELD_39_ACTGAT_L002_R1_001


title: N0205

value: Male

value: Normal


title: Treatment_24 Hrs_rep3

city: Singapore

first: Viduthalai

last: Rasheedkhan Regina

address: 60 Nanyang Drive

country: Singapore

institute: Singapore Centre for Environmental Life Sciences Engineering

data_processing:
Quality of reads was access using FasQC v0.11.7
Ribosomal RNA reads were discarded using SortMeRNA v4.2.0 and remaining non-RNA reads were trimmed using Trimmomatic v0.38 and mapped against M. restricta MYA-4611 reference genome
Aligned data were sorted with SAMTools v1.13 and used as input for feature counts function from the Rsubread v2.4.3 to generate a matrix of annotated genes with their corresponding raw counts
The count data were subjected to DESeq2 v1.30.1 for differential gene expression levels and statistical signficance
Assembly: Malassezia restricta CBS 7877 Assembly ASM369160v1 GenBank GCA_003691605.1
Supplementary files format and content: Tab-delimited text count table for all samples  count.all.txt
Supplementary files format and content: fpkm normalized table for all samples fpkm_all.txt

organism: Malassezia restricta

growth_protocol: M. restricta cells were grown in modified dixon (MD) medium for 24 hours at 33°C with shaking at 200 rpm.

extract_protocol:
Samples were concentrated using centrifugation (10,000 xg for 10 minutes) and added with 300ul of TRIzol™(Invitrogen) with rocking for 5 minutes, resuspended in trizol and stored at -80c. For RNA extraction, thawed samples were lysed by bead beating (Lysing Matrix E, 2 mL, MP Biomedicals) with three repeated cycles at 6,.5 m/s for 45 seconds. Subsequently, 200ul of Chloroform (Merck) was added per 1ml of trizol followed by centrifugation at 12,000 xg for 10mins. RNA was extracted using chloroform: isoamyl alcohol (24:1) (Merck), followed by precipitation by isopropanol (Merck). The final RNA pellet was washed with 70% ethanol followed by air drying for 2 hrs followed by dissolving in nuclease free water (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 24 hrs

tag: treatment

value: sodium propionate


title: Treatment_24 Hrs_rep2


title: P. promelas larvae, EFP, biological replicate EFP_FIELD39, lane 1, time step = NA, analyzed on 20161014

description: Library name: 20161014_ EFP_FIELD_39_ACTGAT_L001_R1_001


title: Treatment_24 Hrs_rep1


title: N0202


title: N0201


title: Treatment_12 Hrs_rep3

value: 12 hrs


title: Treatment_12 Hrs_rep2


title: Treatment_12 Hrs_rep1


title: P. promelas larvae, EFP, biological replicate EFP_B18, lane 2, time step = 4, analyzed on 20161014

description: Library name: 20161014_ EFP_4_B18_ATCACG_L002_R1_001

value: whole larvae


title: P. promelas larvae, EFP, biological replicate EFP_B18, lane 1, time step = 4, analyzed on 20161014

description: Library name: 20161014_ EFP_4_B18_ATCACG_L001_R1_001

value: 2 dpf


title: N0200


title: Treatment_6 Hrs_rep3

value: 6 hrs


title: Treatment_6 Hrs_rep2


title: P. promelas larvae, DSP, biological replicate DSP_B11, lane 2, time step = NA, analyzed on 20161014

description: Library name: 20161014_ DSP_B11_GTGGCC_L002_R1_001

value: DSP


title: Treatment_6 Hrs_rep1


title: Treatment_3 Hrs_rep3

value: 3 hrs


title: p53_6__FOXJ1neg_Epithelium_sample14

city: Chicago

first: CRI

last: Bioinformatics

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

description: Library name: DSP-1001660008418-D-B04

data_processing:
Sequencing files were processed into DCC format using the GeoMx NGS Pipeline software v1.0. GeoMx counts were log2 transformed in preparation for statistic data analysis.
Assembly: GRCh38.p13
Supplementary files format and content: DCC files include raw read counts along with RTS_IDs for each ROI
Supplementary files format and content: PKC file includes probe metadata describing the targets and is needed to interpret RTS_IDs in the DCC files

source_name: Fallopian tube, dysplastic lesion or invasive cancer

extract_protocol:
Tissue processing began with sectioning FFPE samples to a 5 μm thickness following the Nanostring GeoMx user manual (MAN-10132-04). After deparaffinization and rehydration, protein target retrieval was performed using Tris-EDTA antigen retrieval buffer for 20 minutes in a pressure cooker. RNA targets were retrieved through proteinase K digestion for 15 minutes at 37 °C. Tissues were then post-fixed in 10% NBF and hybridized overnight at 37 °C with RNA probes (Human Whole Transcriptome Atlas, containing 18,000 protein-coding genes coupled to UV-cleavable oligonucleotide barcodes). Following hybridization, excess probes were removed by stringent washing at 37 °C and incubated in blocking buffer W (Nanostring LOT#:2-23020032). The tissue sections were subsequently stained with conjugated primary antibodies targeting pan-cytokeratin (mouse monoclonal antibody, Novus NBP2-33200AF488) and p53 (Dako primary and secondary antibodies), along with CAPS (primary and secondary antibodies) and SYTO13 nuclear stain (ThermoFisher Scientific, S7575) for one hour at room temperature. For transcriptomic data acquisition, slides were analyzed on the GeoMx Digital Spatial Profiler (DSP) at 20× magnification. Regions of interest (ROIs) were identified based on immunofluorescence images with a pathologist's (AB) supervision and matched to regions selected in DVP. Following ROI selection, RNA probes were photocleaved using UV illumination within each ROI, and oligonucleotide barcodes were collected into a 96-well plate, allowing precise separation of tissue compartments.
Sequencing libraries were prepared using Illumina TruSeq technology for adaptor ligation and amplification. The amplified libraries underwent two rounds of Ampure XP magnetic bead cleanup (1.2:1 beads ratio) (HighPrep PCR from MAGBIO, Cat#: AC-60500). Purified libraries were sequenced on an Illumina NovaSeq flowcell PE50 at a depth of 100× per μm².

tag: cell type

value: Epithelium

tag: cohort


title: P. promelas larvae, DSP, biological replicate DSP_B11, lane 1, time step = NA, analyzed on 20161014

description: Library name: 20161014_ DSP_B11_GTGGCC_L001_R1_001


title: N0191

value: stomach

value: Female


title: Treatment_0.5Hrs_rep3

value: 0.5 hrs


title: Treatment_3 Hrs_rep2


title: Treatment_3 Hrs_rep1


title: P. promelas larvae, MHW, biological replicate MHW_B22, lane 2, time step = NA, analyzed on 20161014

description: Library name: 20161014_ 15-08_B22_GAGTGG_L002_R1_001

value: MHW


title: N0189

value: Advanced Gastric Cancer (AGC)


title: Treatment_0.5Hrs_rep2


title: P. promelas larvae, MHW, biological replicate MHW_B22, lane 1, time step = NA, analyzed on 20161014

description: Library name: 20161014_ 15-08_B22_GAGTGG_L001_R1_001


title: N0187


title: Treatment_0.5Hrs_rep1


title: Control_rep3

value: 0 hrs

value: Untreated control


title: N0185

value: Male

value: Normal


title: P. promelas larvae, UP, biological replicate UP_B18, lane 2, time step = 4, analyzed on 20161014

description: Library name: 20161014_ UP_4_B18_ACAGTG_L002_R1_001

value: UP


title: Control_rep2


title: P. promelas larvae, UP, biological replicate UP_B18, lane 1, time step = 4, analyzed on 20161014

description: Library name: 20161014_ UP_4_B18_ACAGTG_L001_R1_001


title: Control_rep1


title: N0183


title: shFTO, replicate 3

city: Xi'an

first: Zhaoliang

last: Shen

state: Shaanxi

address: NO.157 Xiwu Rd

department: Department of Orthopedics

institute: the Second Affiliated Hospital of Xi’an Jiaotong University

description:
Library name: shFTO3
FTO knockdown sample, biological replicate 3

data_processing:
Raw sequencing reads in FASTQ format were quality-controlled and trimmed using Fastp (v0.24.1). Adapter sequences and low-quality bases (Q < 20) were removed. Post-trimming data quality was further evaluated using FastQC (v0.10.1).
Cleaned reads were aligned to the human reference genome GRCh38 (hg38) using HISAT2 (v2.2.1) with default parameters.
Gene expression levels (read counts) for each sample were quantified from the alignment files using HTSeq (v0.6.1) against the GENCODE gene annotation file.
Transcripts were assembled and reconstructed using StringTie (v1.3.3b).
Differential expression analysis between FTO knockdown and control groups was performed using DESeq2 (v1.50.2).
Assembly: GRCh38 (hg38)
Supplementary files format and content: Tab-delimited text file includes normalized expression values FPKM for each sample.

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. RNA quality and integrity were assessed using an Agilent 2100 Bioanalyzer (RIN value > 8.0).
poly(A) mRNA was enriched using oligo(dT) magnetic beads, fragmented, and reverse-transcribed into cDNA. The cDNA was end-repaired, A-tailed, ligated to adapters, and PCR-amplified.

tag: cell line


title: shFTO, replicate 2

description:
Library name: shFTO2
FTO knockdown sample, biological replicate 2


title: P. promelas larvae, UP, biological replicate UP_B18, lane 2, time step = 3, analyzed on 20161014

description: Library name: 20161014_ UP_3_B18_AGTTCC_L002_R1_001

tag: tissue


title: N0437

tag: age


title: N0177

tag: genotype


title: N0199


title: shNC, replicate 3

description:
Library name: shNC3
Control sample, biological replicate 3


title: P. promelas larvae, UP, biological replicate UP_B18, lane 1, time step = 3, analyzed on 20161014

description: Library name: 20161014_ UP_3_B18_AGTTCC_L001_R1_001

tag: treatment-replicate id


title: shFTO, replicate 1

description:
Library name: shFTO1
FTO knockdown sample, biological replicate 1


title: shNC, replicate 2

description:
Library name: shNC2
Control sample, biological replicate 2


title: N0176


title: shNC, replicate 1

description:
Library name: shNC1
Control sample, biological replicate 1


title: P. promelas larvae, UP, biological replicate UP_B18, lane 2, time step = 2, analyzed on 20161014

description: Library name: 20161014_ UP_2_B18_CTTGTA_L002_R1_001

tag: treatment-time


title: N0173


title: N0171


title: HAP1 WT cells, CP-DIF-3, 24 h, biological replicate 2

city: Tokorozawa-shi

first: Taichi

last: Hara

state: Saitama

address: 2-579-15 Mikajima

department: Faculty of Human Science

country: Japan

institute: Waseda university

description: Library name: CP2

data_processing:
Raw sequencing reads were filtered by removing reads containing adapter contamination, reads containing more than 10% undetermined nucleotides (N), and reads for which more than 50% of bases had a Phred quality score of 5 or lower.
Paired-end clean reads were aligned to the Homo sapiens hg38 reference genome using HISAT2 v2.0.5 with default parameters.
Gene-level read counts were generated using featureCounts v1.5.0-p3 based on a Homo sapiens GRCh38/hg38 gene annotation file. FPKM values were calculated based on gene length and the number of mapped reads.
Differential expression analysis was performed for Bu-DIF-3 versus control, CP-DIF-3 versus control, and Bu-DIF-3 versus CP-DIF-3 using DESeq2 v1.20.0 with a negative binomial model and Benjamini-Hochberg multiple-testing correction.
Differentially expressed genes used for downstream enrichment analyses were selected using an adjusted P value (padj) < 0.05 and |log2FC| > 1 for Bu-DIF-3 versus control. For CP-DIF-3 versus control, padj < 0.05 and |log2FC| > 0.585 were used.
Assembly: GRCh38/hg38
Supplementary files format and content: gene_count.xls is a tab-delimited plain-text matrix containing unfiltered gene-level raw read counts for 58,735 annotated genes across all nine samples. The file also includes Ensembl gene identifiers, gene symbols, genomic coordinates, gene length, gene biotype, and gene descriptions.

growth_protocol: HAP1 WT cells were cultured in Iscove's Modified Dulbecco's Medium (IMDM; Gibco) supplemented with 10% fetal bovine serum (FBS; Gibco), 100 U/mL penicillin, and 100 µg/mL streptomycin (Gibco) at 37°C in a humidified incubator containing 5% CO2.

extract_protocol:
Total RNA was extracted from HAP1 WT cells using the ReliaPrep RNA Cell Miniprep System (Promega, Madison, WI, USA) according to the manufacturer's instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads and fragmented. First-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. Libraries were prepared by end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification. Libraries were quantified using Qubit and real-time PCR, and size distributions were assessed using a bioanalyzer before pooling and paired-end sequencing as 2 × 150 bp reads on an Illumina NovaSeq 6000.

treatment_protocol: HAP1 WT cells were seeded at 2 × 10^5 cells/well in 6-well plates and treated with 0.1% DMSO (vehicle control), 5 µM Bu-DIF-3, or 5 µM CP-DIF-3 for 24 h. Three independent biological replicates were prepared for each condition.

value: WT

value: CP-DIF-3; 5 µM; 24 h

value: biological replicate 2


title: HAP1 WT cells, CP-DIF-3, 24 h, biological replicate 1

description: Library name: CP1

value: biological replicate 1


title: P. promelas larvae, UP, biological replicate UP_B18, lane 1, time step = 2, analyzed on 20161014

description: Library name: 20161014_ UP_2_B18_CTTGTA_L001_R1_001

value: whole larvae

value: 2 dpf

tag: treatment-location


title: HAP1 WT cells, CP-DIF-3, 24 h, biological replicate 3

description: Library name: CP3

tag: batch

value: biological replicate 3


title: P. promelas larvae, UP, biological replicate UP_B13, lane 2, time step = 1, analyzed on 20161014

description: Library name: 20161014_ UP_1_B13_AGTCAA_L002_R1_001


title: P. promelas larvae, UP, biological replicate UP_B13, lane 1, time step = 1, analyzed on 20161014

description: Library name: 20161014_ UP_1_B13_AGTCAA_L001_R1_001


title: HAP1 WT cells, Bu-DIF-3, 24 h, biological replicate 1

description: Library name: Bu1

value: Bu-DIF-3; 5 µM; 24 h


title: HAP1 WT cells, Bu-DIF-3, 24 h, biological replicate 2

description: Library name: Bu2


title: N0165

value: stomach

value: Female


title: HAP1 WT cells, vehicle control, 24 h, biological replicate 3

description: Library name: C3

value: vehicle control; 0 µM; 24 h


title: P. promelas larvae, EFP, biological replicate EFP_B08, lane 2, time step = 3, analyzed on 20161014

description: Library name: 20161014_ EFP_3_B08_GTTTCG_L002_R1_001

value: EFP


title: N0164

value: Advanced Gastric Cancer (AGC)


title: HAP1 WT cells, vehicle control, 24 h, biological replicate 2

description: Library name: C2


title: HAP1 WT cells, vehicle control, 24 h, biological replicate 1

description: Library name: C1


title: N0151


title: N0148


title: P. promelas larvae, EFP, biological replicate EFP_B08, lane 1, time step = 3, analyzed on 20161014

description: Library name: 20161014_ EFP_3_B08_GTTTCG_L001_R1_001


title: Single-cell RNA-seq of human PBMCs from patient-coded sample P5, collected before IRE

city: wuhan

first: Qi-Dong

last: Xia

address: No. 1095 Jiefang Avenue

department: Urology

institute: Tongji Hospital

description:
Library name: P5_PRE_GEX_LIB1
Whole-cell PBMC suspension from patient-coded sample P5, collected before IRE.

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files for all libraries were previously submitted to SRA under BioProject PRJNA1497318 and are linked here through the corresponding SRA run accessions.
The deposited processed files are the archived filtered feature-barcode matrices used for downstream single-cell analysis of the human PBMC libraries.
The original wet-lab workflow used 10x Genomics Chromium Single Cell 3' v3 chemistry, and the archived processed matrices are consistent with a 10x-compatible gene-expression pipeline.
The processed files deposited to GEO are compressed Matrix Exchange (MEX) files for each sample: barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.
These processed matrices were used for downstream Seurat-based quality control, integration, clustering, and annotation.
Assembly: GRCh38
Supplementary files format and content: Each sample is represented by three gzip-compressed Matrix Exchange (MEX) files: barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz.
Supplementary files format and content: barcodes.tsv.gz lists filtered cell barcodes; features.tsv.gz lists gene features; matrix.mtx.gz stores the sparse gene-by-cell UMI count matrix used for downstream analysis.

source_name: peripheral blood

growth_protocol: Peripheral blood was collected from patients with clinically localized prostate cancer treated at Tongji Hospital. Each participant contributed paired samples collected immediately before IRE and 7 days after IRE. No ex vivo stimulation was applied before PBMC isolation.

extract_protocol:
Anticoagulated blood was diluted 1:1 with Ca2+/Mg2+-free DPBS plus 2% FBS and layered onto Ficoll-Paque PLUS. Density-gradient centrifugation was performed at 400 x g for 30-40 min at 18-20 C with the brake off. The PBMC interface was collected, diluted with wash buffer, washed, and resuspended as a whole-cell PBMC suspension for library construction.
Whole-cell PBMC suspensions were processed using the Chromium Single Cell 3' Library and Gel Bead Kit v3 (10x Genomics, PN-1000075) with a Chromium Controller. Gel bead-in-emulsion reverse transcription was followed by cDNA recovery, cDNA amplification, SPRI-based cleanup, library construction, sample-index PCR, and size selection. Libraries were quantified by Qubit and assessed on an Agilent 2100 Bioanalyzer before sequencing on an Illumina NovaSeq 6000.

treatment_protocol: IRE was performed clinically using the HFMP-01 Compound Steep Pulse Therapeutic Apparatus under ultrasound guidance. Disposable electrodes were positioned to cover the lesion with a 5-10 mm margin. Paired blood samples were collected immediately before treatment and again 7 days after treatment.

value: peripheral blood

value: peripheral blood mononuclear cells

value: before IRE

value: not recorded


title: Single-cell RNA-seq of human PBMCs from patient-coded sample P5, collected 7 days after IRE

description:
Library name: P5_POST_GEX_LIB1
Whole-cell PBMC suspension from patient-coded sample P5, collected 7 days after IRE.

value: 7 days after IRE


title: N0429

value: Male

value: Normal


title: Single-cell RNA-seq of human PBMCs from patient-coded sample P4, collected 7 days after IRE

description:
Library name: P4_POST_GEX_LIB1
Whole-cell PBMC suspension from patient-coded sample P4, collected 7 days after IRE.


title: N0140


title: P. promelas larvae, EFP, biological replicate EFP_B18, lane 2, time step = 2, analyzed on 20161014

description: Library name: 20161014_ EFP_2_B18_GTGAAA_L002_R1_001


title: Single-cell RNA-seq of human PBMCs from patient-coded sample P4, collected before IRE

description:
Library name: P4_PRE_GEX_LIB1
Whole-cell PBMC suspension from patient-coded sample P4, collected before IRE.


title: Single-cell RNA-seq of human PBMCs from patient-coded sample P3, collected 7 days after IRE

description:
Library name: P3_POST_GEX_LIB1
Whole-cell PBMC suspension from patient-coded sample P3, collected 7 days after IRE.


title: P. promelas larvae, EFP, biological replicate EFP_B18, lane 1, time step = 2, analyzed on 20161014

description: Library name: 20161014_ EFP_2_B18_GTGAAA_L001_R1_001


title: N0136


title: Single-cell RNA-seq of human PBMCs from patient-coded sample P3, collected before IRE

description:
Library name: P3_PRE_GEX_LIB1
Whole-cell PBMC suspension from patient-coded sample P3, collected before IRE.


title: Single-cell RNA-seq of human PBMCs from patient-coded sample P2, collected 7 days after IRE

description:
Library name: P2_POST_GEX_LIB1
Whole-cell PBMC suspension from patient-coded sample P2, collected 7 days after IRE.


title: P. promelas larvae, EFP, biological replicate EFP_B16, lane 2, time step = 1, analyzed on 20161014

description: Library name: 20161014_ EFP_1_B16_ATGTCA_L002_R1_001


title: Single-cell RNA-seq of human PBMCs from patient-coded sample P2, collected before IRE

description:
Library name: P2_PRE_GEX_LIB1
Whole-cell PBMC suspension from patient-coded sample P2, collected before IRE.


title: N0132


title: P. promelas larvae, EFP, biological replicate EFP_B16, lane 1, time step = 1, analyzed on 20161014

description: Library name: 20161014_ EFP_1_B16_ATGTCA_L001_R1_001


title: SAS cells, siITGA7, ATAC-seq, biological replicate 4 (A2-28)

city: Dresden

first: Nils

last: Cordes

state: saxony

address: Fetscherstrasse 74 / PF 41

department: Dept. of Radiation Oncology

institute: OncoRay - National Center for Radiation Research in Oncology

description:
Library name: L103297
Original sample name: A2-28; SampleID: S109737; LibraryID: L103297; cell line: SAS; condition: siITGA7; biological replicate: BR4; ATAC-seq library fragment size: 220 bp; sequencing runs: 1 paired-end run.

library_source: genomic

data_processing:
Base calling and demultiplexing were performed using bcl2fastq2 v2.20.0. Raw paired-end reads underwent quality control and adapter trimming.
Primary ATAC-seq processing was performed with nf-core/atacseq v1.2.1 using the Singularity image atacseq_latest.sif dated 2022-03-21, the human hg38 reference genome, and Ensembl release 104 annotation. Custom settings were --mito-name 'chrM' --macs_gsize '2.7e9'.
The pipeline performed alignment, read filtering, removal of duplicate and mitochondrial reads, generation of normalized coverage tracks, peak calling, and peak annotation based on the nearest gene.
A consensus peak set was created across all libraries. Accessibility values were quantified for each consensus interval, and differential accessibility analysis was performed between siControl and siITGA7 within each cell line.
ATAC-seq peaks were visualized using the Integrated Genomics Viewer. For transcription start site analyses, regions were extended 100 kb upstream and downstream and mean peak density was expressed as reads per million per base pair.
Assembly: Homo sapiens genome build hg38 / GRCh38 with Ensembl release 104 annotation.
Supplementary files format and content: Microsoft Excel workbook (.xlsx) containing separate processed peak tables for Cal33 and SAS. Each row represents a consensus ATAC-seq interval and contains Geneid, chromosome, start, end, strand, interval length, raw accessibility counts, and pseudocount-normalized accessibility values for four siControl and four siITGA7 biological replicates.
Supplementary files format and content: Sample columns identify the cell line, siRNA condition, biological replicate, and data type so that each processed-data column maps unambiguously to one GEO Sample record.

molecule: genomic DNA

source_name: head and neck squamous cell carcinoma

growth_protocol: Cal-33 and SAS HPV-negative head and neck squamous cell carcinoma cells were cultured as three-dimensional laminin-rich extracellular matrix (3D lrECM) HNSCC cell models prior to RNA extraction. In short HNSCC cell models (Supplementary Table S1) were kindly provided by R. Grenman (Turku University Central Hospital, Turku, Finland), H. Bier (University of Düsseldorf, Germany) and T. E. Carey (University of Michigan, USA). Cells were asynchronously grown in Dulbecco’s modified Eagle’s medium (DMEM) containing glutamax-I (Sigma-Aldrich, # D5796) supplemented with 10% fetal calf serum (PAN Biotech, # P30-2206) and 1% non-essential amino acids (Gibco, # 11140-035) at 37°C in a humidified atmosphere containing 8.5% CO2 here after referred as cell culture medium or complete DMEM. For 3D cultures, cells were embedded in 1.0 mg/mL physiological 3D laminin-rich extracellular matrix (lrECM; MatrigelR Matrix; CorningR, # 354248) and grown in 1% agarose-coated 24-well plates, as described previously. All cell models were authenticated using Short Tandem Repeat (STR) DNA profiling and tested negative for mycoplasma contamination. All cell experiments were performed on cell passage 3.

extract_protocol:
Cells were centrifuged at 300 × g for 5 min and the supernatant was removed. Twice the pellet volume of Corning Cell Recovery Solution (Corning, 354253) was added and samples were incubated on ice for 1 h. Cells were centrifuged at 300 × g for 5 min, washed with ice-cold 1× PBS, and gently lysed in 45 µL ice-cold lysis buffer containing 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.01% digitonin, 0.1% Tween-20, and 0.3% BSA. Nuclei were pelleted at 500 × g for 10 min at 4°C, washed twice with 45 µL wash buffer containing 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, and 0.3% BSA, and inspected microscopically. Nuclei were resuspended in 5 µL transposition mix containing 2.5 µL 2× Tagment DNA Buffer, 0.5 µL Tagment DNA Enzyme (Illumina, 20034210), and 2 µL wash buffer, incubated at 37°C for 60 min, and DNA was purified using the MinElute Reaction Cleanup Kit (QIAGEN, 28206).
Ten microliters of tagmented DNA were pre-amplified in a 24 µL PCR containing 1× KAPA HiFi HotStart ReadyMix (Roche, 7958935001) and 0.08 µM unique dual Nextera indexing primers. Cycling conditions were 72°C for 5 min, 98°C for 30 s, and 5 cycles of 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min. One microliter of pre-amplified product was used in qPCR to determine the final amplification cycle number; eight additional cycles were applied. Libraries underwent XP bead size selection (Beckman Coulter, A63882) using first 1.55× and then 0.6× bead-to-sample ratios, were quantified using the Fragment Analyzer (Agilent), and were sequenced on an Illumina NovaSeq 6000 in 2 × 100 bp paired-end mode at an average depth of approximately 50 million read pairs per library.

treatment_protocol: Cells were transfected with siControl or siITGA7 siRNA and maintained under 3D lrECM culture conditions before RNA isolation for RNA-seq profiling. siRNA transfection was performed as previously described [Broghammer, F. et al. Resistance of HNSCC cell models to pan-FGFR inhibition depends on the EMT phenotype associating with clinical outcome. Mol Cancer 23, 39 (2024).]. Briefly, 24 hours after plating cells, ON-TARGETplus SMARTpool™ siRNA targeting specific genes or a non-targeting control siRNA (Horizon Discovery Dharmacon; Supplementary Table S1) were transfected using Lipofectamine™ RNAiMAX (Invitrogen, # 13778150) according to manufacturer’s instructions. Twenty-four hours post-transfection, cells were subjected to 3D culture.

value: head and neck squamous cell carcinoma

value: SAS

value: squamous cell carcinoma cell line


title: Single-cell RNA-seq of human PBMCs from patient-coded sample P1, collected before IRE

description:
Library name: P1_PRE_GEX_LIB1
Whole-cell PBMC suspension from patient-coded sample P1, collected before IRE.


title: Single-cell RNA-seq of human PBMCs from patient-coded sample P1, collected 7 days after IRE

description:
Library name: P1_POST_GEX_LIB1
Whole-cell PBMC suspension from patient-coded sample P1, collected 7 days after IRE.


title: P. promelas larvae, MHW, biological replicate MHW_B18, lane 2, time step = NA, analyzed on 20161014

description: Library name: 20161014_ 15-07_B18_GCCAAT_L002_R1_001

value: whole larvae

value: 2 dpf

value: MHW


title: N0119

value: stomach


title: SAS cells, siITGA7, ATAC-seq, biological replicate 3 (A2-27)

description:
Library name: L103296
Original sample name: A2-27; SampleID: S109736; LibraryID: L103296; cell line: SAS; condition: siITGA7; biological replicate: BR3; ATAC-seq library fragment size: 210 bp; sequencing runs: 1 paired-end run.


title: N0122


title: SAS cells, siITGA7, ATAC-seq, biological replicate 2 (A2-26)

description:
Library name: L103295
Original sample name: A2-26; SampleID: S109735; LibraryID: L103295; cell line: SAS; condition: siITGA7; biological replicate: BR2; ATAC-seq library fragment size: 210 bp; sequencing runs: 1 paired-end run.


title: P. promelas larvae, MHW, biological replicate MHW_B18, lane 1, time step = NA, analyzed on 20161014

description: Library name: 20161014_ 15-07_B18_GCCAAT_L001_R1_001


title: N0110


title: SAS cells, siITGA7, ATAC-seq, biological replicate 1 (A2-25)

description:
Library name: L102149
Original sample name: A2-25; SampleID: S109734; LibraryID: L102149; cell line: SAS; condition: siITGA7; biological replicate: BR1; ATAC-seq library fragment size: 220 bp; sequencing runs: 1 paired-end run.


title: Cal33 cells, siITGA7, ATAC-seq, biological replicate 4 (A2-12)

description:
Library name: L103285
Original sample name: A2-12; SampleID: S109721; LibraryID: L103285; cell line: Cal33; condition: siITGA7; biological replicate: BR4; ATAC-seq library fragment size: 225 bp; sequencing runs: 2 paired-end runs.


title: P. promelas larvae, UP, biological replicate UP_FIELD23, lane 2, time step = NA, analyzed on 20161013

description: Library name: 20161013_ UP_FIELD_23_GAGTGG_L002_R1_001

value: UP


title: Cal33 cells, siITGA7, ATAC-seq, biological replicate 3 (A2-11)

description:
Library name: L103284
Original sample name: A2-11; SampleID: S109720; LibraryID: L103284; cell line: Cal33; condition: siITGA7; biological replicate: BR3; ATAC-seq library fragment size: 205 bp; sequencing runs: 1 paired-end run.


title: N0107


title: Cal33 cells, siITGA7, ATAC-seq, biological replicate 2 (A2-10)

description:
Library name: L103283
Original sample name: A2-10; SampleID: S109719; LibraryID: L103283; cell line: Cal33; condition: siITGA7; biological replicate: BR2; ATAC-seq library fragment size: 230 bp; sequencing runs: 1 paired-end run.


title: Cal33 cells, siITGA7, ATAC-seq, biological replicate 1 (A2-9)

description:
Library name: L103282
Original sample name: A2-9; SampleID: S109718; LibraryID: L103282; cell line: Cal33; condition: siITGA7; biological replicate: BR1; ATAC-seq library fragment size: 220 bp; sequencing runs: 1 paired-end run.


title: P. promelas larvae, UP, biological replicate UP_FIELD23, lane 1, time step = NA, analyzed on 20161013

description: Library name: 20161013_ UP_FIELD_23_GAGTGG_L001_R1_001


title: N0105


title: SAS cells, siControl, ATAC-seq, biological replicate 4 (A2-22)

description:
Library name: L103293
Original sample name: A2-22; SampleID: S109731; LibraryID: L103293; cell line: SAS; condition: siControl; biological replicate: BR4; ATAC-seq library fragment size: 225 bp; sequencing runs: 1 paired-end run.

value: siControl


title: SAS cells, siControl, ATAC-seq, biological replicate 3 (A2-21)

description:
Library name: L103292
Original sample name: A2-21; SampleID: S109730; LibraryID: L103292; cell line: SAS; condition: siControl; biological replicate: BR3; ATAC-seq library fragment size: 210 bp; sequencing runs: 1 paired-end run.


title: P. promelas larvae, UP, biological replicate UP_FIELD08, lane 2, time step = NA, analyzed on 20161013

description: Library name: 20161013_ UP_FIELD_08_ACTTGA_L002_R1_001


title: SAS cells, siControl, ATAC-seq, biological replicate 2 (A2-20)

description:
Library name: L103291
Original sample name: A2-20; SampleID: S109729; LibraryID: L103291; cell line: SAS; condition: siControl; biological replicate: BR2; ATAC-seq library fragment size: 220 bp; sequencing runs: 1 paired-end run.


title: P. promelas larvae, UP, biological replicate UP_FIELD08, lane 1, time step = NA, analyzed on 20161013

description: Library name: 20161013_ UP_FIELD_08_ACTTGA_L001_R1_001


title: N0101

value: Advanced Gastric Cancer (AGC)


title: SAS cells, siControl, ATAC-seq, biological replicate 1 (A2-19)

description:
Library name: L102148
Original sample name: A2-19; SampleID: S109728; LibraryID: L102148; cell line: SAS; condition: siControl; biological replicate: BR1; ATAC-seq library fragment size: 215 bp; sequencing runs: 1 paired-end run.


title: N0104


title: Cal33 cells, siControl, ATAC-seq, biological replicate 4 (A2-6)

description:
Library name: L103281
Original sample name: A2-6; SampleID: S109715; LibraryID: L103281; cell line: Cal33; condition: siControl; biological replicate: BR4; ATAC-seq library fragment size: 215 bp; sequencing runs: 1 paired-end run.


title: P. promelas larvae, EMZ, biological replicate EMZ_B07, lane 2, time step = NA, analyzed on 20161013

description: Library name: 20161013_ EMZ_B07_GTCCGC_L002_R1_001

value: EMZ


title: Cal33 cells, siControl, ATAC-seq, biological replicate 3 (A2-5)

description:
Library name: L103280
Original sample name: A2-5; SampleID: S109714; LibraryID: L103280; cell line: Cal33; condition: siControl; biological replicate: BR3; ATAC-seq library fragment size: 215 bp; sequencing runs: 1 paired-end run.


title: N0097


title: Cal33 cells, siControl, ATAC-seq, biological replicate 1 (A2-3)

description:
Library name: L103278
Original sample name: A2-3; SampleID: S109712; LibraryID: L103278; cell line: Cal33; condition: siControl; biological replicate: BR1; ATAC-seq library fragment size: 220 bp; sequencing runs: 2 paired-end runs.


title: P. promelas larvae, EMZ, biological replicate EMZ_B07, lane 1, time step = NA, analyzed on 20161013

description: Library name: 20161013_ EMZ_B07_GTCCGC_L001_R1_001


title: Cal33 cells, siControl, ATAC-seq, biological replicate 2 (A2-4)

description:
Library name: L103279
Original sample name: A2-4; SampleID: S109713; LibraryID: L103279; cell line: Cal33; condition: siControl; biological replicate: BR2; ATAC-seq library fragment size: 215 bp; sequencing runs: 2 paired-end runs.


title: N0092

value: Female


title: SAS cells, siITGA7, biological replicate 4 (R-28)

description:
Library name: L104002
Original sample name: R-28; SampleID: S109875; LibraryID: L104002; condition: Treatment; biological replicate: BR4; cells were grown in Matrigel/3D extracellular matrix. RIN = 9.3 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 43.6 ng/µl

data_processing:
RNA sequencing was performed by the DRESDEN-concept Genome Center (Technische Universität Dresden, Germany), including quality control, library preparation, sequencing, mapping, and basic raw-data processing.
Reads were aligned to the human reference genome hg38 using Ensembl release 104 splice sites and GSNAP v2020-12-16 with custom settings: -B 5 -n1 -m 0.6 -N 0.
Gene counts per sample were obtained by overlapping uniquely mapped fragments with Ensembl annotation using featureCounts v2.0.1 with settings: -s 2 -p -Q 1.
Raw fragment counts were normalized by library size.
Assembly: hg38 / GRCh38; Ensembl release 104 annotation.
Supplementary files format and content: Tab-delimited or CSV text files include raw gene-level fragment counts for each sample generated with featureCounts.

extract_protocol:
Total RNA was prepared from the 3D lrECM HNSCC cell models using the RNeasy Kit with on-column genomic DNA digestion (Qiagen) as previously described [Broghammer, F. et al. Resistance of HNSCC cell models to pan-FGFR inhibition depends on the EMT phenotype associating with clinical outcome. Mol Cancer 23, 39 (2024).]. RNA integrity was assessed, and only RNA samples with RIN >= 9 were used for sequencing.
mRNA was isolated from 500 ng total RNA using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat; New England Biolabs, NEB #E7400X) according to the manufacturer's instructions, with final elution in 5 µL nuclease-free water. Strand-specific RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep assay (NEB #E7760L). After ligation and user digest, adaptors were depleted using XP bead purification (Beckman Coulter) at a 0.9:1 bead-to-sample ratio. Unique dual indexing was performed during PCR enrichment (12 cycles) using amplification primers carrying the same sequence for i7 and i5 indices. After two additional XP bead purifications (0.9:1), libraries were quantified using the Fragment Analyzer (Agilent), pooled equimolarly, and sequenced on an Illumina NovaSeq 6000 in 100 bp paired-end mode, generating approximately 45 million read pairs per library on average.


title: P. promelas larvae, EFP, biological replicate EFP_FIELD27, lane 2, time step = NA, analyzed on 20161013

description: Library name: 20161013_ EFP_FIELD_27_GGCTAC_L002_R1_001

value: EFP


title: SAS cells, siITGA7, biological replicate 3 (R-27)

description:
Library name: L104001
Original sample name: R-27; SampleID: S109874; LibraryID: L104001; condition: Treatment; biological replicate: BR3; cells were grown in Matrigel/3D extracellular matrix. RIN = 9.1 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 36.5 ng/µl


title: P. promelas larvae, EFP, biological replicate EFP_FIELD27, lane 1, time step = NA, analyzed on 20161013

description: Library name: 20161013_ EFP_FIELD_27_GGCTAC_L001_R1_001


title: N0090


title: SAS cells, siITGA7, biological replicate 1 (R-25)

description:
Library name: L103999
Original sample name: R-25; SampleID: S109872; LibraryID: L103999; condition: Treatment; biological replicate: BR1; cells were grown in Matrigel/3D extracellular matrix. RIN = 9.1 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 39.9 ng/µl


title: SAS cells, siITGA7, biological replicate 2 (R-26)

description:
Library name: L104000
Original sample name: R-26; SampleID: S109873; LibraryID: L104000; condition: Treatment; biological replicate: BR2; cells were grown in Matrigel/3D extracellular matrix. RIN = 9.3 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 40.6 ng/µl


title: N0089


title: Cal33 cells, siITGA7, biological replicate 4 (R-12)

description:
Library name: L103990
Original sample name: R-12; SampleID: S109859; LibraryID: L103990; condition: Treatment; biological replicate: BR4; cells were grown in Matrigel/3D extracellular matrix. RIN = 10 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 41.6 ng/µl


title: N0087


title: Cal33 cells, siITGA7, biological replicate 3 (R-11)

description:
Library name: L103989
Original sample name: R-11; SampleID: S109858; LibraryID: L103989; condition: Treatment; biological replicate: BR3; cells were grown in Matrigel/3D extracellular matrix. RIN = 10 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 36.3 ng/µl


title: P. promelas larvae, EFP, biological replicate EFP_FIELD08, lane 2, time step = NA, analyzed on 20161013

description: Library name: 20161013_ EFP_FIELD_08_GTGGCC_L002_R1_001


title: Cal33 cells, siITGA7, biological replicate 1 (R-9)

description:
Library name: L103987
Original sample name: R-9; SampleID: S109856; LibraryID: L103987; condition: Treatment; biological replicate: BR1; cells were grown in Matrigel/3D extracellular matrix. RIN = 10 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 28.8 ng/µl


title: P. promelas larvae, EFP, biological replicate EFP_FIELD08, lane 1, time step = NA, analyzed on 20161013

description: Library name: 20161013_ EFP_FIELD_08_GTGGCC_L001_R1_001


title: N0086


title: Cal33 cells, siITGA7, biological replicate 2 (R-10)

description:
Library name: L103988
Original sample name: R-10; SampleID: S109857; LibraryID: L103988; condition: Treatment; biological replicate: BR2; cells were grown in Matrigel/3D extracellular matrix. RIN = 10 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 39.1 ng/µl


title: SAS cells, siControl, biological replicate 4 (R-22)

description:
Library name: L103998
Original sample name: R-22; SampleID: S109869; LibraryID: L103998; condition: Control; biological replicate: BR4; cells were grown in Matrigel/3D extracellular matrix. RIN = 9.1 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 41.1 ng/µl


title: P. promelas larvae, EFP, biological replicate EFP_B11, lane 2, time step = 4, analyzed on 20161013

description: Library name: 20161013_ EFP_4_B11_TAGCTT_L002_R1_001


title: P. promelas larvae, EFP, biological replicate EFP_B11, lane 1, time step = 4, analyzed on 20161013

description: Library name: 20161013_ EFP_4_B11_TAGCTT_L001_R1_001


title: SAS cells, siControl, biological replicate 3 (R-21)

description:
Library name: L103997
Original sample name: R-21; SampleID: S109868; LibraryID: L103997; condition: Control; biological replicate: BR3; cells were grown in Matrigel/3D extracellular matrix. RIN = 9.3 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 46 ng/µl


title: N0064


title: N0070


title: SAS cells, siControl, biological replicate 2 (R-20)

description:
Library name: L103996
Original sample name: R-20; SampleID: S109867; LibraryID: L103996; condition: Control; biological replicate: BR2; cells were grown in Matrigel/3D extracellular matrix. RIN = 9.2 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 43.7 ng/µl


title: FR Ler +50uM MeJA

type: RNA

city: Chiayi City

first: Meng-Chun

last: Lin

address: No.300 Syuefu Rd.

department: Department of Agronomy

country: Taiwan

institute: National Chiayi University

description:
Gene expression data from 4-day-old Arabidopsis seedlings
FR Ler +50uM MeJA (normalized)
BH0331-6
 FR Ler 50

hyb_protocol: biotin-labeled cRNA

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing:
The raw data was normalized using the GeneSpring GX software.
The raw signal is calculated by Affymetrix's Microarray Suite Software (MAS5)

label: biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis Ler seedlings grown under far-red light condition with 50 micro molar of MeJA treatment

label_protocol: Libraries were prepared according to the standard Affymetrix protocol from 20 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The seeds were sterilized and sown onto a germination medium (GM) with or without 50 micro molar of MeJA.

extract_protocol: Total RNA was extracted using acidic phenol/chloroform and participated with lithium chloride..

treatment_protocol: The stratified seeds were treated with or without continuous far-red light (1.5 umol m-2 s-1) for 4 days in a 22 degree Celsius growth chamber.

value: Whole seedlings

value: Ler

value: Four-day-old seedlings

value: FR Ler +50uM MeJA


title: P. promelas larvae, EFP, biological replicate EFP_B03, lane 2, time step = 3, analyzed on 20161013

description: Library name: 20161013_ EFP_3_B03_ATCACG_L002_R1_001


title: FR hy5-1 +50uM MeJA

description:
Gene expression data from 4-day-old Arabidopsis seedlings
FR hy5-1 +50uM MeJA (normalized)
BH0331-8
 FR hy5-1 50

source_name: Arabidopsis hy5-1 seedlings grown under far-red light condition with 50 micro molar of MeJA treatment

value: Ler, hy5-1

value: FR hy5-1 +50uM MeJA


title: N0056

value: Male

value: Normal


title: N0053


title: SAS cells, siControl, biological replicate 1 (R-19)

description:
Library name: L103995
Original sample name: R-19; SampleID: S109866; LibraryID: L103995; condition: Control; biological replicate: BR1; cells were grown in Matrigel/3D extracellular matrix. RIN = 9.2 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 37.5 ng/µl

value: head and neck squamous cell carcinoma

value: SAS

value: squamous cell carcinoma cell line


title: Cal33 cells, siControl, biological replicate 4 (R-6)

description:
Library name: L103986
Original sample name: R-6; SampleID: S109853; LibraryID: L103986; condition: Control; biological replicate: BR4; cells were grown in Matrigel/3D extracellular matrix. RIN = 9.8 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 37.9 ng/µl


title: P. promelas larvae, EFP, biological replicate EFP_B03, lane 1, time step = 3, analyzed on 20161013

description: Library name: 20161013_ EFP_3_B03_ATCACG_L001_R1_001

value: whole larvae

value: 2 dpf


title: FR hy5-1 +0uM MeJA

description:
Gene expression data from 4-day-old Arabidopsis seedlings
FR hy5-1 +0uM MeJA (normalized)
BH0331-7
 FR hy5-1 0

source_name: Arabidopsis hy5-1 seedlings grown under far-red light condition without MeJA treatment

value: FR hy5-1 +0uM MeJA


title: P. promelas larvae, DWIP, biological replicate DWIP_B21, lane 2, time step = NA, analyzed on 20161013

description: Library name: 20161013_ DWIP_B21_ACTGAT_L002_R1_001

value: DWIP


title: N0048

value: stomach

value: Female

value: Advanced Gastric Cancer (AGC)


title: Cal33 cells, siControl, biological replicate 3 (R-5)

description:
Library name: L103985
Original sample name: R-5; SampleID: S109852; LibraryID: L103985; condition: Control; biological replicate: BR3; cells were grown in Matrigel/3D extracellular matrix. RIN = 10 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 41.2 ng/µl

value: siControl


title: FR Ler +0uM MeJA

description:
Gene expression data from 4-day-old Arabidopsis seedlings
FR Ler +0uM MeJA (normalized)
BH0331-5
 FR Ler 0

source_name: Arabidopsis Ler seedlings grown under far-red light condition without MeJA treatment

value: Whole seedlings

value: Ler

value: Four-day-old seedlings

value: FR Ler +0uM MeJA


title: P. promelas larvae, DWIP, biological replicate DWIP_B21, lane 1, time step = NA, analyzed on 20161013

description: Library name: 20161013_ DWIP_B21_ACTGAT_L001_R1_001


title: Dark hy5-1 +50uM MeJA

description:
Gene expression data from 4-day-old Arabidopsis seedlings
Dark hy5-1 +50uM MeJA (normalized)
BH0331-4
 Dark hy5-1 50

source_name: Arabidopsis hy5-1 seedlings grown under dark condition with 50 micro molar of MeJA treatment

value: Ler, hy5-1

value: Dark hy5-1 +50uM MeJA


title: Dark Ler +50uM MeJA

description:
Gene expression data from 4-day-old Arabidopsis seedlings
Dark Ler +50uM MeJA (normalized)
BH0331-2
 Dark Ler 50

source_name: Arabidopsis Ler seedlings grown under dark condition with 50 micro molar of MeJA treatment

value: Dark Ler +50uM MeJA


title: N0046

value: Male

value: Normal


title: Cal33 cells, siControl, biological replicate 2 (R-4)

description:
Library name: L103984
Original sample name: R-4; SampleID: S109851; LibraryID: L103984; condition: Control; biological replicate: BR2; cells were grown in Matrigel/3D extracellular matrix. RIN = 10 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 39.8 ng/µl

value: head and neck squamous cell carcinoma

value: squamous cell carcinoma cell line


title: N0040


title: Cal33 cells, siControl, biological replicate 1 (R-3)

description:
Library name: L103983
Original sample name: R-3; SampleID: S109850; LibraryID: L103983; condition: Control; biological replicate: BR1; cells were grown in Matrigel/3D extracellular matrix. RIN = 9.7 //  Cells were grown in matrigel. The concenteration SD could be 0.2 ng/uL; Qubit by DcGC after adding 2 µl NFW: 33.1 ng/µl


title: P. promelas larvae, UP, biological replicate UP_B03, lane 1, time step = 4, analyzed on 20161013

description: Library name: 20161013_ UP_4_B03_ATGTCA_L001_R1_001

source_name: whole larvae

value: whole larvae

value: 2 dpf

value: UP


title: P. promelas larvae, UP, biological replicate UP_B03, lane 2, time step = 4, analyzed on 20161013

description: Library name: 20161013_ UP_4_B03_ATGTCA_L002_R1_001


title: N0034

source_name: stomach

value: stomach

value: Female


title: THP-1, H3K27ac,V2

first: Lifei

last: Liang

address: 180 Fenglin Road

institute: Zhongshan Hospital, Fudan University

description:
Library name: Sample4
Cut&Tag

data_processing:
The raw sequence data were firstly quality trimmed by fatsp software to obtain the clean reads. Then the clean reads were aligned to the (input your reference genome and version, eg, the human genome GRCh38.p12) using Bowtie2 and subsequently analyzed by the SEACR software based the ‘stringent’parameter to detect genomic regions enriched for multiple overlapping DNA fragments (peaks) that we considered to be putative binding sites. Visualization of peak distribution along genomic regions of interested genes was performed with IGV.Peaks were then annotated using chipseeker software to obtain the genes and gene annotations about peaks. Significant Motif of peaks were analyzed by MEME and DREME software and aligned to the motif database.
Assembly: hg38
Supplementary files format and content: BigWig signal tracks generated from CUT&Tag sequencing analysis.
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag assay was performed using HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina (cat.no.TD901-TD902, Vazyme Biotech, China) according to manufacturer's instruction. Briefly, prepared concanavalin A-coated magnetic beads (ConA beads) were added to resuspended cells and incubated at room temperature to bound cells.
Non-ionic detergent Digitonin was used to permeate cell membrane. Then, primary VISTA antibody, secondary antibody and the Hyperactive pA-Tn5 Transposase were incubated with the cells that were bounded by ConA beads in order. Therefore, the Hyperactive pA-Tn5 Transposase can exactly cut off the DNA fragments that were bound with target protein. In addition, the cut DNA fragments can be ligated with P5 and P7 adaptors by Tn5 transposase and the libraries were amplified by PCR with the P5 and P7 primers. The purified PCR products were evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Finally, these libraries were sequenced on the Illumina NovaSeq6000 platform and 150bp paired-end reads were generated for the following analysis.

value: Lenti-Vsir


title: Dark Ler +0uM MeJA

description:
Gene expression data from 4-day-old Arabidopsis seedlings
Dark Ler +0uM MeJA (normalized)
BH0331-1
 Dark Ler 0

source_name: Arabidopsis Ler seedlings grown under dark condition without MeJA treatment

value: Whole seedlings

value: Dark Ler +0uM MeJA


title: P. promelas larvae, UP, biological replicate UP_B08, lane 2, time step = 3, analyzed on 20161013

description: Library name: 20161013_ UP_3_B08_ACAGTG_L002_R1_001

data_processing:
Raw read quality assessment with FastQC 0.11.9 & MultiQC 1.12
Reads were processed with fastp 0.23.2 trimming with quality, length, and adapter trimming all enabled by default, and polyX trimming (flag: -x) enabled manually
Alignment with STAR 2.7.10a (--outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --outSAMheaderHD @HD VN 1.4 SO:sorted --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outSAMunmapped Within --outFilterType BySJout)
Quantification with STAR 2.7.10a (--quantMode GeneCounts TranscriptomeSAM)
Assembly: P. promelas, GCF_016745375.1_EPA_FHM_2.0
Supplementary files format and content: Tab delimited text file with gene counts: all_counts_20220629.txt uploaded separately.

extract_protocol:
Total RNA was isolated from individual FHM using the MagMAX-96 Total RNA Isolation Kit (ThermoFisher Scientific) following manufacturer's protocols. RNA was quantified by spectrophotometric analysis with a Synergy HTX multi-mode plate reader (BioTek).
Neoprep Library Prep System (Illumina) and the TruSeq Stranded mRNA Library Prep for NeoPrep (Illumina). Library concentrations were determined using either the KAPA Library Quantification Kit (Kapa Biosystems) or Qubit dsDNA HS Assay (ThermoFisher Scientific), normalized to equimolar amounts, and then combined into pools of eight samples each. Sequencing was performed at Michigan State University’s RTSF Genomics Core on the Illumina HiSeq 2500 Rapid Run flow cell (v2) for 1x50 bp single-end reads with Rapid SBS reagents.


title: N0031

data_processing:
Processed and selected high-quality reads using FastQC (v0.11.8), excluding any reads with low base quality
Aligned to the GRCh37 human reference genome provided by GENCODE, employing STAR v2.74a
Gene and transcript expression levels were then quantified using RSEM v1.3.3
Assembly: hg19
Supplementary files format and content: comma-delimited csv file include raw counts for each sample

extract_protocol:
Total RNA was extracted from 108 paired tumor and normal tissue samples using the Qiagen AllPrep DNA/RNA Mini Kit (Cat. No. 80204, Qiagen, Germany) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Advanced Gastric Cancer (AGC)


title: Dark hy5-1 +0uM MeJA

description:
Gene expression data from 4-day-old Arabidopsis seedlings
Dark hy5-1 +0uM MeJA (normalized)
BH0331-3
 Dark hy5-1 0

source_name: Arabidopsis hy5-1 seedlings grown under dark condition without MeJA treatment

value: Four-day-old seedlings

value: Dark hy5-1 +0uM MeJA


title: THP-1, H3K27ac,CN2

description:
Library name: Sample3
Cut&Tag

value: Lenti-Con


title: P. promelas larvae, UP, biological replicate UP_B08, lane 1, time step = 3, analyzed on 20161013

description: Library name: 20161013_ UP_3_B08_ACAGTG_L001_R1_001


title: 0327-CTRL

city: Milan

first: Raffaella

last: Di Micco

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

description: Library name: 0327-CTRL

data_processing:
Reads quality control checked with FASTQC
Read alignment to reference genome with STAR
Reads per gene quantification with featurecounts
Normalization and differential analysis with DESeq2
Assembly: hg38
Supplementary files format and content: ReadsPerGene_TAZ_CTRL_allsamples.txt

source_name: bone marrow

extract_protocol:
miRNeasy Mini Kit (QIAGEN)
RNA-seq: NEBnext ultra II RNA directional library preparation kit, with respective rRNA depletion module

value: bone marrow

value: Patient-derived acute myeloid leukemia blasts

value: acute myeloid leukemia blasts

value: untreated


title: THP-1, H3K4me3,V1

description:
Library name: Sample2
Cut&Tag


title: Sinorhizobium meliloti MB1157, biological rep3

city: Stanford

first: Melanie

middle: J

last: Barnett

state: CA

address: 371 Jane Stanford Way

institute: Stanford University

description: gene expression data log phase cultures

hyb_protocol: Four micrograms of biotinylated cDNA was hybridized to each chip at 48 degrees celsius for 16 hours as described by Barnett et al. 2004. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: Chips were scanned at the Stanford PAN facility using an Affymetrix Scanner 3000 7G

data_processing: The data were analyzed using Partek Genomics Suite 6.6 software, with the following settings: RMA for background correction; quantile normalization; log base 2 transformation; median polish summarization

organism: Sinorhizobium meliloti

source_name: control strain MB1157 (carries hygromycin resistance in the SMc01380-SMc01267 intergenic region

label_protocol: cDNA was fragmented and biotinylated as described by Barnett et al. 2004.

growth_protocol: Each culture was grown from a single colony inoculated into TY medium supplemented with 500 ug ml-1 Sm, in 250 ml baffled flasks, and allowed to grow with shaking (250 rpm) at 30°C. Cells were harvested at an OD-600 ranging from 0.67 to 0.72.

extract_protocol: Total RNA was extracted using a Qiagen RNeasy kit with modifications as described by Barnett et al. 2004 Proc Natl Acad Sci USA volume 101 pages 16636 to 16641.

treatment_protocol: Stop solution (5% buffer equilibrated phenol in ethanol) was added to bacterial cultures, at one tenth the culture volume, before centrifugation at 4 degrees celsius. Bacterial cell pellets were frozen in liquid nitrogen and stored at -80 degrees celsius until RNA extraction.

tag: strain


title: Sinorhizobium meliloti MB1157, biological rep2

description: gene expression data log phase cultures


title: 0784-CTRL

description: Library name: 0784-CTRL


title: P. promelas larvae, UP, biological replicate UP_B08, lane 1, time step = 2, analyzed on 20161013

city: Durham

first: Steven

last: Purucker

address: 109 TW Alexander Dr

institute: US EPA

description: Library name: 20161013_ UP_2_B08_AGTTCC_L001_R1_001


title: P. promelas larvae, UP, biological replicate UP_B08, lane 2, time step = 2, analyzed on 20161013

description: Library name: 20161013_ UP_2_B08_AGTTCC_L002_R1_001