title: Cell Line, Affected, Rottweiler, S4

city: East Lansing

first: Vilma

last: Yuzbasiyan-Gurkan

state: MI

address: 567 Wilson Rd

department: Small Animal Clinical Sciences

institute: Michigan State University

description:
Library name: PJ Cell Line
PJ cells
HS_BD_OD_PJ_RNAseq_rawCounts.txt

data_processing:
Raw RNA sequence files from HS and both normal tissues and blood samples were submitted to the ROSALIND® online platform for differential gene expression and pathway analysis.
Reads were trimmed using cutadapt (v3.7). Normalization of raw data, quality control, and functional analysis were performed using the ROSALIND® platform. Quality scores were assessed using FastQC (v0.11.9).
Sequencing reads were aligned to the CanFam3.1 canine reference genome using STAR (v2.7.10a). Individual sample reads were quantified using HTseq (v2.0.0) and normalized via Relative Log Expression (RLE) using the DESeq2 (v1.20) R library. DEseq2 was used to calculate log2-fold changes (log2FC) and p-values.
Assembly: CanFam3.1
Supplementary files format and content: For HS_MSU_RNAseq Analysis_rawCounts.txt: Raw gene expression counts of all tissue and blood samples.
Supplementary files format and content: For HS_BD_OD_PJ_RNAseq_rawCounts.txt: Raw gene expression counts of all tissue and blood samples.

organism: Canis lupus familiaris

source_name: Cell Line

growth_protocol: For the cell lines: RPMI 1640 media supplemented with 10% heat-inactivated fetal bovine serum, 1% antibiotic-antimycotic 100X, and 0.1% 124 gentamycin. Cells were incubated in 5% CO2 at 37 ˚C.

extract_protocol:
For tissue and blood samples: RNA was extracted using the mirVANA microRNA isolation kit.
Libraries were prepared using Illumina TruSeq Stranded Total RNA kit with Ribo-zero Globin depletion.

value: Cell Line

tag: disease state

value: Histiocytic Sarcoma


title: wt, leaves, rep1

status: Public on Mar 18 2025

type: SRA

city: Athens

first: Gerasimos

last: Daras

state: Attiki

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

library_source: transcriptomic

data_processing:
RNA-seq data were analyzed using SOAPnuke (version 1.5.2) with parameters “-l 15 -q 0.2 -n 0.05"
We used Bowtie2 to map the clean reads to the reference gene sequence (transcriptome), and then used RSEM to calculate the gene expression level of each sample. DESeq2 was used to identify differentially expressed genes.
Bowtie2 version：v2.2.5 | Parameters：-q --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
RSEM version：v1.2.8 | Parameters：-p 8 --forward-prob 0.5 --paired-end
Assembly: Arabidopsis_thaliana_NCBI_GCF_000001735.4_TAIR10.1
Supplementary files format and content: Excel file with gene expression values and log2FoldChange between samples as generated by DEseq2

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Arabidopsis thaliana seeds were surface-sterilized and sown in 120×120 mm2 Petri dishes containing 0.5×Murashige and Skoog (MS) medium (Duchefa, Haarlem, the Netherlands), pH 5.7, supplemented with 1% sucrose and solidified with 0.4% phytagel (Sigma, Gillingham, UK). After 48h of stratification at 4oC, seedlings were positioned to grow at 22oC in a Fitotron (Weiss Gallenkamp, Loughborough, UK) growth chamber under a long-day photoperiod with 16h of light and 8h of darkness per day and 75 μmol m−2s−1 light intensity. After two weeks plants were transferred to soil and grown under the same conditions.

extract_protocol:
Total RNA was extracted  from three distinct rosette leaf  stages namely green, pale green and chlorotic variation using the Direct-zol RNA Miniprep (Zymo Research, Irvine CA, USA) kit with an on-column DNase treatment according to the manufacturer’s instructions. The quantity and integrity of RNA were assessed using a NanoDrop ND-1000 spectrophotometer (Thermo Fischer Scientific, Waltham, MA, USA) and agarose gel electrophoresis.
RNA-seq libraries were generated using the polyA Strand-Specific Transcriptome Library method of BGI  for DNBSEQ platform.
Sequencing was performed on DNBSEQ-G400 platform instrument at BGI (Beijing Genomics Institute) in three biological replicates for each sample.

tag: tissue

value: leaves

tag: cell line

value: wild-type rosette leaves

tag: genotype


title: scRNA, Handling_3h_S18

city: Zürich

first: Pierre-Luc

last: Germain

address: Winterthurerstrasse 190

department: D-HEST Institute for Neuroscience

country: Switzerland

institute: ETH Zürich

description: Library name: S18

library_source: transcriptomic single cell

data_processing:
Pre-processing was performed using cellranger-arc 2.0.2 using the optimized mm10 transcriptome as described previously (Pool et al., 2023).
A RNA quantification using alevin-fry (He et al., 2022) was also performed to estimate splicing proportions. Decontamination was performed using cellbender 0.3.0 (Fleming et al., 2023) with custom initialization, and doublet identification with scDblFinder 1.19.0 (Germain et al., 2022). For the RNA modality, scDblFinder was run using standard parameters twice (i.e. with two seeds) and the scores averaged, the AMULET method was used on the ATAC modality. Cells were excluded as doublets if they were called as such using both scDblFinder runs, or if their mean doublet score was above 0.2 and their amulet q-value below 0.01. Only cells with at least 500 fragments (after decontamination), less than 60% contamination, less than 1% mitochondrial reads, more than 20% unspliced fragments (before decontamination) and less than 50% of the fragments assigned to the top 10% features were used for further analysis.
Cell annotation was performed based on the RNA modality (see publication for details).
Assembly: mm10
Supplementary files format and content: Cellranger barcodes, counts and feature files, along with a csv of cell annotations.

organism: Mus musculus

source_name: ventral hippocampus

extract_protocol:
Nuclei isolation was performed similarly as for the bulk ATAC-Seq, with the addition of RNase inhibitors as previously described (Grandi et al., 2022). All steps were performed on ice. Briefly, one vHC was homogenized in lysis buffer (26 mM Sucrose, 30 mM KCl, 10 mM MgCl2, 20 mM Tricine-KOH (pH 7.8), 1 mM DTT, 0.5 mM Spermidine, 0.15 mM Spermine, 0.3% NP-40, Complete protease inhibitor, 0.2 U/μl RNAse inhibitor in nuclease-free water) by 10 strokes with pestle A and 20 strokes with pestle B. The sample was filtered through a 70 μm Flowmi strainer and centrifuged for 5 min at 400 g at 4°C. Supernatant was removed and additional lysis buffer was added to resuspend the pellet. The sample was then mixed with 50% Iodixanol solution (30 mM KCl, 26 mM Sucrose, 10 mM MgCl2, 20mM Tricine-KOH (pH 7.8), 50% Iodixanol solution in nuclease-free water) and underlaid by 30% Iodixanol solution (50% Iodixanol solution in lysis buffer) and 40% Iodixanol (50% Iodixanol solution in lysis buffer) layers. The sample was centrifuged for 20 min at 3000 g at 4°C with brakes off. The nuclei band was collected and mixed with ATAC buffer (10 mM NaCl, 10 mMTris-HCl (pH7.5), 3 mM MgCl2, 0.1% Tween20, 0.2 U/μl RNase inhibitor in nuclease-free water) before the nuclei count was assessed. The sample was centrifuged for 5 min at 500g at 4°C and supernatant was removed. Diluted nuclei buffer (0.1 M DTT, 1 U/μl RNase inhibitor, 1X Nuclei buffer (10X) in nuclease-free water) was added to achieve the desired nuclei concentration.
10X Multiome libraries were prepared following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide (CG000338, Rev. F, 10X Genomics) with a targeted nuclei recovery of 10’000 nuclei (1 sample failed due to clogging). 7 cycles were performed for sample index PCR during ATAC library preparation. 6 cycles were used for cDNA amplification and a total of 13 cycles was performed for sample index PCR for gene expression library preparation. RNA integrity was assessed on an Agilent Tapestation, according to the manufacturer’s protocol. Samples of each library type were pooled. Both libraries (gene expressions and ATAC) were then sequenced on one Illumina X Plus 25B flow cell on individual lanes with an adjusted read configuration (150-10-24-150 bp).

value: ventral hippocampus

tag: Sex

value: Female

tag: ars timepoint

tag: treatment

value: Handling

tag: batch


title: melin, White_leaves, rep3

value: White_rosette leaves

value: melinoe, EMS mutant of FMN/FHY gene (At4g21470)


title: Cell Line, Affected, Bernese Mountain Dog, S3

country: USA

description:
Library name: OD Cell Line
OD cells
HS_BD_OD_PJ_RNAseq_rawCounts.txt

molecule: total RNA


title: scRNA, Restraint_3h_S17

description: Library name: S17


title: Cell Strain, Normal, Mongrel, S2

description:
Library name: DC3F9_unstim
DC3F9_unstim cells
HS_BD_OD_PJ_RNAseq_rawCounts.txt

source_name: Cell Strain

value: Cell Strain

value: Unaffected


title: RE_SPM_BAC+1

city: Nanning

first: Wang

last: Xi

state: Guangxi

address: 100 University East Road, Nanning City, Guangxi

department: School of Medicine

country: China

institute: Guangxi University

description: Library name: Sample10

data_processing:
Use fastqc and multiqc to check the data quality · Use fastp software to perform quality control on the fastq data, filter low-quality reads ·
Assembly: mm10
Supplementary files format and content: .gz

source_name: Peritoneal macrophages

extract_protocol:
Trizol reagent protocol
SMART-Seq_V4 Ultra Low Input RNA Kit for Sequencing Protocol

value: Peritoneal macrophages

tag: cell type

value: SPM


title: melin, White_leaves, rep2


title: melin, White_leaves, rep1


title: RE_LPM_BAC+1

description: Library name: Sample9

value: LPM


title: Ecoli_SPM_BAC-2

description: Library name: Sample7


title: melin, GreenWhite_leaves, rep3

value: Green_White rosette leaves


title: Cell Line, Affected, Bernese Mountain Dog, S1

description:
Library name: BD Cell Line
BD cells
HS_BD_OD_PJ_RNAseq_rawCounts.txt


title: melin, GreenWhite_leaves, rep2


title: Lung, Affected, Bernese Mountain Dog, S55

description:
Library name: MSU HS 53
HVTWLDSXX_18936768_S55
HS_MSU_RNAseq Analysis_rawCounts.txt

source_name: Lung

value: Lung

value: Hemophagocytic Histiocytic Sarcoma


title: Lung, Affected, Bernese Mountain Dog, S58

description:
Library name: MSU HS 52
HVTWLDSXX_18936766_S58
HS_MSU_RNAseq Analysis_rawCounts.txt


title: scRNA, Restraint_15min_S13

description: Library name: S13


title: wt, leaves, rep2


title: melin, GreenWhite_leaves, rep1


title: Spleen, Affected, Bernese Mountain Dog, S60

description:
Library name: MSU HS 51
HVTWLDSXX_18936764_S60
HS_MSU_RNAseq Analysis_rawCounts.txt

source_name: Spleen

value: Spleen


title: Ecoli_LPM_BAC-2

description: Library name: Sample6


title: scRNA, Handling_45min_S12

description: Library name: S12


title: RE_LPM_BAC-1

description: Library name: Sample11


title: Liver, Affected, Bernese Mountain Dog, S50

description:
Library name: MSU HS 50
HVTWLDSXX_18936762_S50
HS_MSU_RNAseq Analysis_rawCounts.txt

source_name: Liver

value: Liver

value: Histiocytic Sarcoma


title: melin, Green_leaves, rep3

value: leaves

value: Green rosette leaves


title: scRNA, Restraint_3h_S11

description: Library name: S11

value: ventral hippocampus

value: Female


title: Ecoli_SPM_BAC+1

description: Library name: Sample5


title: Ecoli_LPM_BAC+2

description: Library name: Sample4


title: melin, Green_leaves, rep2


title: scRNA, Handling_Control_S10

description: Library name: S10

value: Control


title: scRNA, Restraint_Control_S16

description: Library name: S16


title: Lung, Affected, Bernese Mountain Dog, S41

description:
Library name: MSU HS 47
HVTWLDSXX_18936756_S41
HS_MSU_RNAseq Analysis_rawCounts.txt


title: Ecoli_SPM_BAC-1

description: Library name: Sample3


title: scRNA, Restraint_45min_S15

description: Library name: S15


title: Ecoli_SPM_BAC+2

description: Library name: Sample8


title: melin, Green_leaves, rep1

value: melinoe, EMS mutant of FMN/FHY gene (At4g21470)


title: scRNA, Handling_3h_S14

description: Library name: S14

value: Handling


title: scRNA, Restraint_15min_S1

description: Library name: S1


title: Liver, Affected, Bernese Mountain Dog, S59

description:
Library name: MSU HS 46
HVTWLDSXX_18936754_S59
HS_MSU_RNAseq Analysis_rawCounts.txt


title: Handling_15min_S9

description: Library name: Handling_15min_S9

library_source: genomic single cell

data_processing:
Pre-processing was performed using cellranger-arc 2.0.2 using the optimized mm10 transcriptome as described previously (Pool et al., 2023).
Cell annotation was based on the RNA modality.
Assembly: mm10
Supplementary files format and content: Cellranger fragment files.

molecule: genomic DNA

extract_protocol:
Nuclei isolation was performed similarly as for the bulk ATAC-Seq, with the addition of RNase inhibitors as previously described (Grandi et al., 2022). All steps were performed on ice. Briefly, one vHC was homogenized in lysis buffer (26 mM Sucrose, 30 mM KCl, 10 mM MgCl2, 20 mM Tricine-KOH (pH 7.8), 1 mM DTT, 0.5 mM Spermidine, 0.15 mM Spermine, 0.3% NP-40, Complete protease inhibitor, 0.2 U/μl RNAse inhibitor in nuclease-free water) by 10 strokes with pestle A and 20 strokes with pestle B. The sample was filtered through a 70 μm Flowmi strainer and centrifuged for 5 min at 400 g at 4°C. Supernatant was removed and additional lysis buffer was added to resuspend the pellet. The sample was then mixed with 50% Iodixanol solution (30 mM KCl, 26 mM Sucrose, 10 mM MgCl2, 20mM Tricine-KOH (pH 7.8), 50% Iodixanol solution in nuclease-free water) and underlaid by 30% Iodixanol solution (50% Iodixanol solution in lysis buffer) and 40% Iodixanol (50% Iodixanol solution in lysis buffer) layers. The sample was centrifuged for 20 min at 3000 g at 4°C with brakes off. The nuclei band was collected and mixed with ATAC buffer (10 mM NaCl, 10 mMTris-HCl (pH7.5), 3 mM MgCl2, 0.1% Tween20, 0.2 U/μl RNase inhibitor in nuclease-free water) before the nuclei count was assessed. The sample was centrifuged for 5 min at 500g at 4°C and supernatant was removed. Diluted nuclei buffer (0.1 M DTT, 1 U/μl RNase inhibitor, 1X Nuclei buffer (10X) in nuclease-free water) was added to achieve the desired nuclei concentration.
10X Multiome libraries were prepared following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide (CG000338, Rev. F, 10X Genomics) with a targeted nuclei recovery of 10’000 nuclei (1 sample failed due to clogging). 7 cycles were performed for sample index PCR during ATAC library preparation. 6 cycles were used for cDNA amplification and a total of 13 cycles was performed for sample index PCR for gene expression library preparation. RNA integrity was assessed on an Agilent Tapestation, according to the manufacturer’s protocol. Samples of each library type were pooled. Both libraries (gene expressions and ATAC) were then sequenced on one Illumina X Plus 25B flow cell on individual lanes with an adjusted read configuration (150-10-24-150 bp). ATAC-seq reads were trimmed to 49nt for further processing.


title: Lymph Node, Affected, Bernese Mountain Dog, S37

description:
Library name: MSU HS 41
HVTWLDSXX_18936752_S37
HS_MSU_RNAseq Analysis_rawCounts.txt

source_name: Lymph Node

value: Lymph Node


title: Cryptococcus neoformans var. grubii H99, pH7, 6 h, rep2

city: Chuncheon-si

first: Jiwon

last: Bang

address: 1, Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

description: Library name: WT-pH7-2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BBDuk v 39.06.
Trimmed sequence reads were mapped to reference genome sequence using HISAT2 v 2.2.1 (default parameter)
Mapped reads were counted by featureCounts in Subread package v1.4.3
Normalization were performed using DESeq2
Assembly: Cryptococcus neoformans var. grubii H99 (GCF_000149245.1)
Supplementary files format and content: mapped counts, tsv file
Supplementary files format and content: DESeq2 normalized value, tsv file

organism: Cryptococcus neoformans H99

source_name: fungal cells

growth_protocol: The cells were grown in YPD for overnight, harvested, and reinoculated into YNB LIM pH 7.0 for overnight, and the cells were harvested and incubated to YNB LIM pH 7.0 or pH 5.0.

extract_protocol:
Total RNA was extracted by the RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
Libraries for RNA sequencing were prepared using high-quality RNA with the value of RNA integrity greater than 7.0, and TruSeq Stranded mRNA Sample Prep Kit (Illumina, US) following the manufacturer’s protocol.

treatment_protocol: The cells were harvested and incubated to YNB LIM pH 7.0 or pH 5.0 at 1×107 cells/mL for 6 hr.

value: fungal cells

value: WT

value: pH7-6 h


title: Ecoli_LPM_BAC+1

description: Library name: Sample1

value: Peritoneal macrophages

value: LPM


title: Cryptococcus neoformans var. grubii H99, pH7, 6 h, rep1

description: Library name: WT-pH7-1


title: Restraint_3h_S8

description: Library name: Restraint_3h_S8


title: Shoulder, Affected, Bernese Mountain Dog, S48

description:
Library name: MSU HS 39
HVTWLDSXX_18936750_S48
HS_MSU_RNAseq Analysis_rawCounts.txt

source_name: Shoulder

value: Shoulder


title: Cryptococcus neoformans var. grubii H99, pH5, 6 h, rep2

description: Library name: WT-pH5-2

value: pH5-6 h


title: Thorax, Affected, Bernese Mountain Dog, S57

description:
Library name: MSU HS 37
HVTWLDSXX_18936748_S57
HS_MSU_RNAseq Analysis_rawCounts.txt

source_name: Thorax

value: Thorax


title: Lung, Affected, Bernese Mountain Dog, S53

description:
Library name: MSU HS 48
HVTWLDSXX_18936758_S53
HS_MSU_RNAseq Analysis_rawCounts.txt

value: Lung

value: Histiocytic Sarcoma


title: Cryptococcus neoformans var. grubii H99, pH5, 6 h, rep1

description: Library name: WT-pH5-1


title: Small RNAs from flam-del-412-St2 ovaries - line 2 - repeat 2

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description:
Library name: Flamd412_V2-9_rep2
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (GGTAT AGATCGGAAGAGCACACGTCT).

library_source: other

data_processing:
Adapter clipped reads were trimmed by 4nt from the 5' and  6nt from the 3' end to remove random nucleotides contained in the adaptors.
Reads were mapped to the Drosophila melanogaster dm6 genome and a curated TE consensus sequence file using Bowtie (release 1.3.0) with 0 mismatches for genome wide analysis
Reads mapping to annotated rRNA, tRNA, snRNA, snoRNA loci and the mitochondrial genome were excluded from analyses
Reads were normalized to 1Mio miRNA reads for piRNA analysis
Assembly: dm6 + TE consensus sequences (in-house curated list of TE sequences)
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Table with sRNA counts quantified on TE-sequences per strand. Numbers calculated as Reads per kb TE per 1 million miRNAs
Supplementary files format and content: Curated TE-consensus file used for the TE quantification analysis

molecule: other

organism: Drosophila melanogaster

source_name: Ovary

growth_protocol: 25˚C, 12h dark/light, ovaries dissected into PBS on ice, snap frozen

extract_protocol:
Argonaute-bound sRNAs were isolated according to Grentzinger et al. (2020)
Libraries were prepared by ligation of 3' barcoded adaptors containing 6 random nucleotides and a 5 nt in-line barcode and 5' adaptors containing 4 random nucleotides at the ends to reduce ligation biases followed by reverse transcription and amplification by PCR.

value: Ovary

value: flam-del-412-St2 line #2


title: Lung, Affected, Bernese Mountain Dog, S45

description:
Library name: MSU HS 35
HVTWLDSXX_18936744_S45
HS_MSU_RNAseq Analysis_rawCounts.txt


title: Small RNAs from flam-del-412-St2 ovaries - line 2 - repeat 1

description:
Library name: Flamd412_V2-9_rep1
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (CAGTG AGATCGGAAGAGCACACGTCT).


title: Handling_15min_S4

description: Library name: Handling_15min_S4

value: ventral hippocampus

value: Female


title: Leg Mass, Affected, Bernese Mountain Dog, S47

description:
Library name: MSU HS 34
HVTWLDSXX_18936742_S47
HS_MSU_RNAseq Analysis_rawCounts.txt

source_name: Leg Mass

value: Leg Mass


title: HeLa cells, Senescent + CXCL12 (2)

type: RNA

city: Bangalore

first: Suramya

last: Asthana

state: Karnataka

address: Biological Sciences Building, Indian Institute of Science

country: India

institute: Indian Institute of Science

description: Senescent cells + CXCL12 replicate 2

hyb_protocol: 600 ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to an Agilent Custom Human Gene expression 8X60K Microarray designed by Genotypic Technology Pvt. Ltd. (AMADID: 027114). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies). Hybridization was carried out in Agilent’s Surehyb Chambers at 65ºC for 16 hours.

scan_protocol: The hybridized slides were washed using Agilent Gene Expression wash buffers and scanned using the Agilent Microarray Scanner (Agilent Technologies,).

data_processing:
Data extraction from microarray images was done using Agilent Feature Extraction software. Feature extracted raw data was analyzed using Agilent  GeneSpring GX Version 12.1 Software. Normalization of the data was done using the 75th percentile shift.  Significant genes up and down regulated showing one-fold (log base2) and  above within the samples with respect to control sample were identified.
The raw files from Agilent are not available, the raw spot intensities (ie, gProcessSignal) have been provided in the individual sample files for each replicate and sample.

organism: Homo sapiens

source_name: HeLa cells, Senescent + CXCL12

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP (Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Germany) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

extract_protocol: Total cellular RNA from cell lines was isolated using TRI reagent (Sigma, USA). The concentration and purity of the RNA extracted were evaluated using the Nanodrop Spectrophotometer (Thermo Scientific, USA; 1000). The integrity of the extracted RNA was analyzed on the Bioanalyzer (Agilent; 2100).

treatment_protocol: Cells were treated with 200ng/mL of CXCL12 for 48 hours, followed by extraction.

value: HeLa

value: epithelial-like human cervical cancer cells

tag: cell state

value: Senescent

tag: treament


title: Restraint_Control_S3

description: Library name: Restraint_Control_S3

value: Control


title: Ecoli_LPM_BAC-1

description: Library name: Sample2


title: Small RNAs from flam-del-412-St2 ovaries - line 1 - repeat 2

description:
Library name: Flamd412_V2-46_rep2
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (CGTTC AGATCGGAAGAGCACACGTCT).

value: flam-del-412-St2 line #1


title: HeLa cells, Senescent (2)

description: Senescent cells replicate 2

source_name: HeLa cells, Senescent

value: control


title: HeLa cells, Senescent + CXCL12 (1)

description: Senescent cells + CXCL12 replicate 1


title: Handling_45min_S24

description: Library name: Handling_45min_S24

value: Handling


title: Handling_15min_S23

description: Library name: Handling_15min_S23


title: Small RNAs from flam-del-412-St2 ovaries - line 1 - repeat 1

description:
Library name: Flamd412_V2-46_rep1
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (TACCA AGATCGGAAGAGCACACGTCT).


title: Handling_Control_S7

description: Library name: Handling_Control_S7


title: Handling_3h_S6

description: Library name: Handling_3h_S6


title: HeLa cells, Non-Senescent + CXCL12 (2)

description: Non-senescent cells + CXCL12 replicate 2

source_name: HeLa cells, Non-Senescent + CXCL12

value: NonSenescent


title: Restraint_45min_S5

description: Library name: Restraint_45min_S5


title: Restraint_Control_S22

description: Library name: Restraint_Control_S22


title: Thorax, Affected, Bernese Mountain Dog, S40

description:
Library name: MSU HS 14
HVTWLDSXX_18936734_S40
HS_MSU_RNAseq Analysis_rawCounts.txt


title: Small RNAs from control ovaries for flam deletion - repeat 1

description:
Library name: FRT7m8_4_rep1
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (ATGGA AGATCGGAAGAGCACACGTCT).


title: OsmoStress-A375-Recovery-R1

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: TN

address: 309 Mossman Bldg. 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

library_source: genomic

data_processing:
Sequenced reads were mapped to the hg19 or dm6 genomes using bowtie2
Mapping, filtering, iterative correction, and binning were performed using the Hi-C pro pipeline available at: https://github.com/nservant/HiC-Pro
Before mapping, Drosophila fastq files were trimmed to only the first 25 bases using trimmomatic CROP:25.  Longer reads often passed into the other ligated pair and therefore trimming increased mappability.
Assembly: hg19, dm6
Supplementary files format and content: Each .mcool file (see https://cooler.readthedocs.io/ for filetype information) contains the iteratively corrected contacts binned at multiple resolutions.  For human, resolutions include 10 kb, 20 kb, 40 kb, 100 kb, 250 kb, 1 Mb, and 2.5 Mb.  For Drosophila, resolutions include 1 kb, 2kb, 5 kb, 10 kb, 20 kb, 40 kb, 100 kb, 250 kb, 1 Mb, and 2.5 Mb for the replicates combined files, with 1 kb omitted for individual replicate files.  "RC" indicates replicates combined, where the mapped valid pairs for biological replicates 1 and 2 were pooled into the final processed contact matrices.  These .mcool files can be used for analysis with cooltools or loaded into HiGlass. See https://cooltools.readthedocs.io/ and https://github.com/higlass/higlass-docker

source_name: Melanoma (A375)

growth_protocol: S2 Cells were maintained in Schneider’s Drosophila Media (1X) (Gibco) supplemented with 10% fetal bovine serum to form complete Schneider’s Drosophila Media at 25°C.   A375 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Corning), supplemented with 10% fetal bovine serum, 1% Penicillin-Streptomycin, and 1% L-Glutamine, at 37°C in a 5% CO2 atmosphere.

extract_protocol:
For both Drosophila S2 and human A375 cells, Hi-C was performed using the Arima Hi-C (Arima Genomics) kit, following the manufacturer’s protocol A160134 v01.  The only exception is for A375 replicate 1 conditions, the Hi-C protocol from Golloshi et al., 2018 was used instead of Arima.
Library amplification was performed using the NEBNext Ultra II kit (NEB;E7645S).

treatment_protocol: 15 million S2 cells were used for each of the two replicates for each condition. Prior to the Hi-C assay, the S2 cells were pretreated with just the complete Schneider’s media and 250mM NaCl prepared in complete Schneider’s media as control and stress respectively for 1 hour. The recovery cells underwent the same stress treatment for 1 hour before a 1  hour recovery in the complete Schneider’s media. After these treatments, the cells were strained passing them through a 40µm strainer to remove clumps. We then fixed the cells with 2% formaldehyde at RT for 10 minutes. The crosslinking was quenched with 125mM glycine. Following fixation and quenching, nuclei were isolated using a 5ml cold lysis buffer  . The isolated nuclei were then snap frozen in liquid nitrogen and stored at -80°C for later Hi-C analysis.  The human A375 malignant melanoma cells were purchased from ATCC (ATCC® CRL-1619™). The cells were grown in DMEM enriched with 10% FBS, 1% Pen-strep, and 1% L-glutamine, and were sub-cultured to at a density of 80%. For salt stress experiments, A375 cells were introduced into media supplemented with 250mM NaCl for one hour, for stress samples, or subjected to 250mM NaCl for one hour followed by reintroduced to conditioned DMEM for an additional hour, for recovery samples.

value: Melanoma (A375)

tag: replicate

value: biological replicate 1

value: Return to standard media, 1 hr after Stress


title: Liver, Affected, Bernese Mountain Dog, S39

description:
Library name: MSU HS 36
HVTWLDSXX_18936746_S39
HS_MSU_RNAseq Analysis_rawCounts.txt

value: Liver

value: Histiocytic Sarcoma


title: HeLa cells, Non-Senescent + CXCL12 (1)

description: Non-senescent cells + CXCL12 replicate 1


title: HeLa cells, Senescent (1)

description: Senescent cells replicate 1


title: HeLa cells, Non-Senescent (1)

description: Non-senescent cells replicate 1

source_name: HeLa cells, Non-Senescent


title: Thoracic Mass, Affected, Bernese Mountain Dog, S51

description:
Library name: MSU HS 4
HVTWLDSXX_18936732_S51
HS_MSU_RNAseq Analysis_rawCounts.txt

source_name: Thoracic Mass

value: Thoracic Mass


title: Restraint_15min_S21

description: Library name: Restraint_15min_S21

source_name: ventral hippocampus

value: ventral hippocampus


title: HeLa cells, Non-Senescent (2)

description: Non-senescent cells replicate 2


title: polyA RNA from flam-del-412-St2 deletion - line 2 - repeat 3

description: Library name: Flam_V4-9_rep3_RNA

data_processing:
Reads have been prepared by first clipping of the 3' adaptor (AGATCGGAAGAGCACACGTCT) and 5' adaptor (AGATCGGAAGAGCGTCGTGTA - paired-end only). In addition the first 5 nucleotides have been removed from each read.
Reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
Reads were mapped to the Drosophila melanogaster genome using STAR (v.2.5.2b)
Reads mapping to rRNA, tRNA, mitoRNA were excluded
Gene expression values of genes and TEs have been determined using Salmon (using FlyBase r6.40 transcriptome sequences + curated consensus TE sequences in sense and antisense).
Differential gene-expressiona anslysis was performed using DESeq2
Assembly: dm6 + TE consensus sequences
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense
Supplementary files format and content: Differential gene-expression result tables showing fold-change and p-values
Supplementary files format and content: Gene-expression analysis results as GeTMM values

extract_protocol:
RNA was extracted with TRIzol and DNase-treated twice
polyA selection, RNA-seq
Poly(A) enrichment with magnetic Dynabeads Oligo(dT) beads followed by NEBNext Ultra II strand-specific RNA-seq libraries preparation kit

value: Ovary

value: flam-del-412-St2;iso-1/iso-1 line #2


title: OsmoStress-A375-Control-R1

description: Hi-C protocol from Golloshi et al., 2018

value: Standard media


title: Restraint_45min_S20

description: Library name: Restraint_45min_S20

value: Female


title: polyA RNA from flam-del-412-St2 deletion - line 2 - repeat 2

description: Library name: Flam_V4-9_rep2_RNA


title: OsmoStress-A375-250mMNaCl-R1

value: 250 mM NaCl, 1 hr


title: Small RNAs from control ovaries for flam deletion - repeat 2

description:
Library name: FRT7m8_4_rep2
Reads have been prepared by first clipping of the 3' adaptor sequence including a 5 nt in-line barcode (GAACG AGATCGGAAGAGCACACGTCT).


title: polyA RNA from flam-del-412-St2 deletion - line 2 - repeat 1

description: Library name: Flam_V4-9_rep1_RNA


title: Lung, Affected, Bernese Mountain Dog, S56

description:
Library name: MSU HS 27
HVTWLDSXX_18936736_S56
HS_MSU_RNAseq Analysis_rawCounts.txt

value: Lung


title: Spleen, Affected, Bernese Mountain Dog, S44

description:
Library name: MSU HS 29
HVTWLDSXX_18936738_S44
HS_MSU_RNAseq Analysis_rawCounts.txt

value: Spleen


title: Handling_3h_S18

description: Library name: Handling_3h_S18


title: RNAseq-A375-Control-R2

data_processing:
The quality of reads was checked using FastQC and adapter sequences were trimmed using BBTools (https://github.com/kbaseapps/BBTools). Additionally, quality trimming of the reads was performed and any reads with a lower than 28 quality score were discarded. Reads were then aligned to hg19 using STAR alignment (https://github.com/alexdobin/STAR).
The aligned reads were then sorted by genomic position and feature counts were performed using htseq 0.11.1 (https://github.com/simon-anders/htseq). Differential expression of genes was determined by using DESeq2.
Assembly: hg19
Supplementary files format and content: Each .tsv file contains the raw RNA counts per gene produced by HTSeq

growth_protocol: A-375 (CRL-1619) cells were procured from ATCC. A-375 are isolated from a 54-year-old female patient with malignant melanoma. They possess an epithelial morphology. The cells were resuspended in basal growth medium (DMEM medium and 10% fetal bovine serum (FBS)). Experiments were performed on cells of passage greater than 3 and less than 8. Splitting was performed only after a confluence of more than 80% was achieved.

extract_protocol:
RNA was extracted from TSA-treated and untreated A375 cells using the Qiagen RNAeasy plus mini kit (Cat. No. 74134). Cells were lysed and homogenized, spun down in gDNA eliminator columns to remove any genomic DNA. All samples were washed with ethanol and the total RNA was eluted. The quality and quantity of the RNA were quantified using Agilent Bioanalyzer Nano RNA kit. All the libraries used were characterized by a RIN value between 9 and 10.
RNA was sent to Oklahoma Medical Research Foundation for library preparation (using an rRNA depletion approach) and sequencing.

treatment_protocol: For TSA treatment, the cells were grown to >70% confluence for more than 24 hours before addition of 500 nM TSA along with basal media. These were put back into the incubator and cultured for another 2 hours. Thereafter, they were washed thrice with PBS for 5 mins each and then fixed with 1% Formaldehyde in 1xHBSS.

value: biological replicate 2


title: Handling_Control_S19

description: Library name: Handling_Control_S19

value: Control

value: Handling


title: polyA RNA from flam-del-412-St2 deletion - line 1 - repeat 3

description: Library name: Flam_V4-46_rep3_RNA

value: flam-del-412-St2;iso-1/iso-1 line #1


title: Lung, Normal, German Shepherd, S80

description:
Library name: 34660
HVTWLDSXX_18937523_S80
HS_MSU_RNAseq Analysis_rawCounts.txt

value: Unaffected


title: RNAseq-A375-Control-R1

value: Melanoma (A375)

value: biological replicate 1


title: Liver, Normal, German Shepherd, S79

description:
Library name: 34656
HVTWLDSXX_18937521_S79
HS_MSU_RNAseq Analysis_rawCounts.txt

value: Liver


title: Blood, Normal, Bernese Mountain Dog, S53

description:
Library name: 35116
HT5GWDSXX_18927808_S53
HS_MSU_RNAseq Analysis_rawCounts.txt

source_name: Blood

value: Blood


title: RNAseq-A375-TSA-R2

value: 500 nM TSA, 2 hr


title: Restraint_Control_S16

description: Library name: Restraint_Control_S16

value: ventral hippocampus


title: Spleen, Normal, German Shephard, S54

description:
Library name: 34655
HVTWLDSXX_18936778_S54
HS_MSU_RNAseq Analysis_rawCounts.txt


title: RNAseq-A375-TSA-R1


title: polyA RNA from flam-del-412-St2 deletion - line 1 - repeat 2

description: Library name: Flam_V4-46_rep2_RNA

value: Ovary


title: Restraint_3h_S17

description: Library name: Restraint_3h_S17


title: Blood, Normal, Bernese Mountain Dog, S66

description:
Library name: 35780
HT5GWDSXX_18927782_S66
HS_MSU_RNAseq Analysis_rawCounts.txt


title: Blood, Normal, Bernese Mountain Dog, S54

description:
Library name: 35779
HT5GWDSXX_18927780_S54
HS_MSU_RNAseq Analysis_rawCounts.txt


title: Restraint_45min_S15

description: Library name: Restraint_45min_S15


title: polyA RNA from control ovaries for flam deletion - repeat 4

description: Library name: FRT4_rep4_RNA


title: polyA RNA from control ovaries for flam deletion - repeat 3

description: Library name: FRT4_rep3_RNA


title: HiC-A375-Control-R2

description: Arima-HiC+ Kit (Mammalian Cell Lines A160134v01)

data_processing:
Sequenced reads were mapped to the hg19 genome using bowtie2
Mapping, filtering, iterative correction, and binning were performed using the Hi-C pro pipeline available at: https://github.com/nservant/HiC-Pro
Assembly: hg19
Supplementary files format and content: Each .mcool file (see https://cooler.readthedocs.io/ for filetype information) contains the iteratively corrected contacts binned at multiple resolutions (10 kb, 20 kb, 40 kb, 100 kb, 250 kb, 1 Mb, and 2.5 Mb).  These .mcool files can be used for analysis with cooltools or loaded into HiGlass. See https://cooltools.readthedocs.io/ and https://github.com/higlass/higlass-docker

extract_protocol:
Biological replicates of Hi-C were performed on two independent samples of A375 cells, both untreated and with 2 hr treatment of 0.5 µM TSA.  The first biological replicate was processed with the protocol described in (Golloshi et al., 2018). Briefly, 10 million cells were crosslinked with 1% formaldehyde for 10 min. Crosslinked cells were then suspended in lysis buffer to permeabilize the cell membrane and were dounce homogenized. Chromatin was then digested in-nucleus overnight using the DpnII restriction enzyme. Digested ends were filled in with biotin-dATP, and the blunt ends of interacting fragments were ligated together. DNA was then purified by phenol-chloroform extraction. For library preparation, the NEBNext Ultra II DNA Library prep kit (NEB) was used for libraries with size ranges from 200-400bp. End Prep, Adaptor Ligation, and PCR amplification reactions were carried out on bead-bound DNA libraries.  The second biological replicate was processed using the Arima-HiC+ Kit from Arima Genomics following the protocol for Mammalian Cell Lines (A160134 v01) and preparing the libraries using Arima recommendations for the NEBNext Ultra II DNA library prep kit (protocol version A16041v01).
Library amplification was performed using the NEBNext Ultra II kit (NEB;E7645S).

value: Standard media


title: HiC-A375-Control-R1


title: Handling_3h_S14

description: Library name: Handling_3h_S14

value: Female


title: Y21SS00263

city: Guangzhou

first: Tianyuan

last: Zhang

address: The First Affiliated Hospital of Jinan University

institute: Jinan university

description: 10x Genomics

data_processing:
Single cell RNA-seq raw data were processed by Cell Ranger version 3.1.0 (10X Genomics) and aligned to the GRCm38 (mm10) mouse reference genome and GRCh38 (h19) human genome reference sequence
Seurat V4.05 was used for the downstream analysis, including tSNE, heatmap, and violin plots  We used R software (version: 3.6.0) with several packages for the bioinformatics analysis.
Assembly: h19 (and mm10)
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Homo sapiens
Mus musculus

source_name: Humanized mouse with humanized T cells, MCAO, Day3

extract_protocol:
Human peripheral blood mononuclear cells (PBMCs) were transferred into immunodeficient mice to generate a mouse model with humanized T cells. Ischemic hemispheres of humanized mice were perfused with ice-cold saline and freshly harvested at 0 or 3 days after tMCAO. Single cell suspensions were prepared for flow cytometry. Single cells were incubated with FITC anti-human CD45 and APC/Cyanine7 anti-mouse CD45 for 30 minutes on ice at 4 ℃ in the dark before stained with 7-AAD for 5 minutes. The live CD45high cells (human and mouse) were sorted by FACS Aria SORP (BD Bioscience). At last, we mix human and mouse CD45high cells with equal proportion
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: mixure of humanized T cells and murine immune cells

value: Ischemic hemispheres

tag: strain

value: B-NDG mice

tag: age

value: 8-12 weeks old


title: polyA RNA from control ovaries for flam deletion - repeat 2

description: Library name: FRT4_rep2_RNA


title: Restraint_15min_S13

description: Library name: Restraint_15min_S13


title: polyA RNA from control ovaries for flam deletion - repeat 1

description: Library name: FRT4_rep1_RNA


title: Y21SS00318

description: 10x Genomics

source_name: Humanized mouse with humanized T cells, Control

value: hemispheres


title: HiC-A375-TSA-R1


title: Handling_45min_S12

description: Library name: Handling_45min_S12

value: Handling


title: Restraint_3h_S11

description: Library name: Restraint_3h_S11


title: RCAS_3R, RCAS injected, autopod, batch2

city: Shenyang

first: Bai

last: Shibin

address: 120 Dongling Road

institute: Shenyang Agriculture University

description: control

data_processing:
Reads were mapped to the NCBI Gallus gallus genome assembly (bGalGal1.mat.broiler.GRCg7b) using HISAT2 version 2.2.1.
Transcript assembly by StringTie v2.1.7
Use prepDE.py3 script of StringTie to get raw counts
Use the ComBat-seq model in the Sva package to remove the batch effect brought by the sample RCAS_3R and get the adjusted counts
Assembly: bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes adjusted counts for each Sample

organism: Gallus gallus

source_name: hindlimb autopod

extract_protocol:
Total RNA was extracted using the RNeasy micro kit (Qiagen, Hilden, Germany), with on-column DNase to remove contaminating genomic DNA. RNA concentration and purity were measured using NanoDrop 2000. (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit from the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: hindlimb autopod

value: RCAS control


title: polyA RNA from flam-del-412-St2 deletion - line 1 - repeat 1

description: Library name: Flam_V4-46_rep1_RNA

value: flam-del-412-St2;iso-1/iso-1 line #1


title: OsmoStress-Dmel-S2-Recovery-R1

description:
Arima-HiC+ Kit (Mammalian Cell Lines A160134v01)
OsmoStress-Dmel-S2-Recovery-RC.1kb.mcool

source_name: Schneider 2 (S2)

value: Schneider 2 (S2)

value: biological replicate 1

value: Return to standard media, 1 hr after Stress


title: OsmoStress-Dmel-S2-Recovery-R2

value: biological replicate 2


title: polyA RNA from somatic piRNA knockdown ovaries - repeat 3

description: Library name: ovaries_tjG4_vretGD_rep3


title: Handling_Control_S10

description: Library name: Handling_Control_S10

value: ventral hippocampus

value: Control


title: RCAS_2, RCAS injected, autopod, batch1

description: control


title: OsmoStress-Dmel-S2-Control-R2

description:
Arima-HiC+ Kit (Mammalian Cell Lines A160134v01)
OsmoStress-Dmel-S2-Control-RC.1kb.mcool

value: Standard media


title: polyA RNA from somatic piRNA knockdown ovaries - repeat 2

description: Library name: ovaries_tjG4_vretGD_rep2

value: Ovary


title: Restraint_15min_S1

description: Library name: Restraint_15min_S1

value: Female


title: polyA RNA from somatic piRNA knockdown ovaries - repeat 1

description: Library name: ovaries_tjG4_vretGD_rep1


title: HiC-A375-TSA-R2

value: Melanoma (A375)

value: 500 nM TSA, 2 hr


title: RCAS_1, RCAS injected, autopod, batch1

description: control


title: RCAS_Z3_C, RCAS-Zic3 injected, autopod, batch1

description: treatment

value: RCAS-Zic3 overexpression


title: OsmoStress-Dmel-S2-250mMNaCl-R1

description:
Arima-HiC+ Kit (Mammalian Cell Lines A160134v01)
OsmoStress-Dmel-S2-250mMNaCl-RC.1kb.mcool

value: 250 mM NaCl, 1 hr


title: OsmoStress-Dmel-S2-250mMNaCl-R2


title: polyA RNA from control ovaries for piRNA knockdown - repeat 2

description: Library name: ovaries_tjG4_arr2GD_rep2


title: RCAS_Z3_B, RCAS-Zic3 injected, autopod, batch1

description: treatment


title: polyA RNA from control ovaries for piRNA knockdown - repeat 1

description: Library name: ovaries_tjG4_arr2GD_rep1


title: RCAS_Z3_A, RCAS-Zic3 injected, autopod, batch1

description: treatment


title: Twin2

status: Public on Mar 17 2025

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

description:
Library name: T2
Twin2_0

data_processing:
All libraries were pooled and denatured following the standard normalization method described by the Illumina Denature and Dilute Libraries Guide for the NextSeq System (Illumina Part #15048776), after which denatured libraries were loaded onto an Illumina NextSeq 550. To determine transcript abundance, FASTQ outputs were aligned to the Pneumocystis jirovecii RU7 genome using EdgeR normalization.
Assembly: GCF_001477535.1, NC_020331.1
Supplementary files format and content: To determine transcript abundance, FASTQ outputs were aligned to the Pneumocystis jirovecii RU7 genome using EdgeR normalization to get the FPKM abundance text file.

organism:
Homo sapiens
Pneumocystis jirovecii RU7

source_name: Bronchoalveolar Lavage (BAL) fluid

extract_protocol:
RNA was extracted with the Trizol method from the BAL cells pellets of two patients with Bare Lymphocyte Syndrome who had clinical PCP. Prior to construction of an Illumina total RNA library, DNase treated RNA was quantitated using a Qubit RNA BR assay kit (Thermo Fisher Scientific: Guide MAN0001987 MP10210, Kit #Q10210)
Cytoplasmic, mitochondrial, and bacterial rRNA was removed from 2.5 ug of each sample as indicated by the Illumina RiboZero RNA Removal Kit Reference Guide [(Document # 15066012 v02, ScriptSeq Complete Gold (Epidemiology) Kit #BEP1206 (now obsolete)]. Illumina-compatible cDNA libraries were generated according to the instructions of the TruSeq Stranded Total RNA Sample Preparation Guide (Illumina Document #1000000040499v00, Kit #20020596).

value: Bronchoalveolar Lavage (BAL) fluid


title: Twin1

description:
Library name: T1
Twin1_0


title: testes of blue catfsh sampled at age 2, biological rep4

city: Auburn

first: Ian

last: Butts

state: Alabama

address: 203, Swingle Hall

department: School of Fisheries, Aquaculture & Aquatic Sciences

institute: Auburn University

description: Library name: AGE_Sample_16

data_processing:
Raw, demultiplexed sequence files were provided in FASTQ format. The quality of raw RNA sequencing reads was assessed by FastQC (V.0.11.9). Clean reads were obtained by removing low-quality reads and adapter sequences from the raw data using Trimmomatic (V.0.39).
The genome of blue catfish (I. furcatus) was obtained from NCBI and remaining high-quality reads were aligned to the genome using STAR aligner (V.2.7.5). Post mapping quality control was performed using MultiQC (V.1.10.1).
BAM files were used to generate a gene-level count data matrix for all samples via HTSeq-count (V. 0.11.1).
Pairwise differential gene expression analyses were performed using edgeR (V.4.4.2)
Assembly: GCF_023375685.1
Supplementary files format and content: CSV files include raw counts for each sample

organism: Ictalurus furcatus

source_name: Testis

extract_protocol:
Total RNA was extracted using Quick-RNA Miniprep Plus Kit (Zymo Research) following the manufacturer’s instructions. Total RNA was treated with DNase I and resuspended in 50 µL of nuclease-free water.
Sequencing libraries (n = 16) were prepared using a NEBNext Ultra II RNA Library Preparation Kit (NEB, Ipswich, MA, U.S.), following manufacturer’s instructions

value: Testis

value: male

value: Age 2


title: testes of blue catfsh sampled at age 2, biological rep3

description: Library name: AGE_Sample_15


title: testes of blue catfsh sampled at age 2, biological rep2

description: Library name: AGE_Sample_14


title: testes of blue catfsh sampled at age 4, biological rep3

description: Library name: AGE_Sample_11

value: Age 4


title: testes of blue catfsh sampled at age 2, biological rep1

description: Library name: AGE_Sample_13


title: testes of blue catfsh sampled at age 4, biological rep2

description: Library name: AGE_Sample_10


title: testes of blue catfsh sampled at age 4, biological rep4

description: Library name: AGE_Sample_12


title: testes of blue catfsh sampled at age 7, biological rep4

description: Library name: AGE_Sample_8

value: Age 7


title: testes of blue catfsh sampled at age 4, biological rep1

description: Library name: AGE_Sample_9


title: OsmoStress-Dmel-S2-Control-R1

value: Schneider 2 (S2)

value: biological replicate 1


title: polyA RNA from control ovaries for piRNA knockdown - repeat 3

description: Library name: ovaries_tjG4_arr2GD_rep3


title: testes of blue catfsh sampled at age 9, biological rep4

description: Library name: AGE_Sample_4

value: Age 9


title: testes of blue catfsh sampled at age 9, biological rep3

description: Library name: AGE_Sample_3


title: testes of blue catfsh sampled at age 7, biological rep1

description: Library name: AGE_Sample_5


title: testes of blue catfsh sampled at age 7, biological rep2

description: Library name: AGE_Sample_6


title: testes of blue catfsh sampled at age 9, biological rep2

description: Library name: AGE_Sample_2


title: Suc_eETS-4HA_2

city: Mumbai

first: Amitesh

last: Anand

state: Maharashtra

address: Homi Bhabha Road

department: DBS

institute: TIFR

description: Library name: Sample 40

data_processing:
Raw sequencing reads were mapped to the reference genome (NC_000913.3) using bowtie v1.1.2
Maximum insert size of 1000 and two maximum mismatches after trimming 3 bp at the 3' ends.
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments packageintersection mode
The dispersion and differential expression level of each gene were estimated using DESeq2
Transcripts per Million (TPM) were calculated by DESeq2
Assembly: NC_000913.3
Supplementary files format and content: csv, TPM counts

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Whole cell

growth_protocol: An overnight culture of strains in their respective media was inoculated at 37C, which was further used to inoculate a secondary culture, used for pellet preparation under same conditions.

extract_protocol:
RNA was isolated from the cells pelleted from the mid-log phase of the culture.
NEBNext Ultra II Directional RNA Library prep kit for Illumina (Cat. no. E7760L)

treatment_protocol: 3 ml of the secondary culture with 0.6-0.8 O.D. was suspended in 6 ml freshly prepared RNA protect reagent (4% TTAB, 200 mM tartaric acid) and vortexed. Post incubation for 5 min at RT, the mixture was centrifuged, supernatant was decanted and pellet was collected and stored at -80C for further use.

value: Whole cell


title: Suc_eETS-4HA_1

description: Library name: Sample 39


title: Suc_eETS-3HA_2

description: Library name: Sample 38


title: Suc_eETS-1HA_2

description: Library name: Sample 34


title: Suc_eETS-2HA_2

description: Library name: Sample 36


title: Suc_eETS-3HA_1

description: Library name: Sample 37


title: Suc_eETS-2HA_1

description: Library name: Sample 35


title: Suc_eETS-1HA_1

description: Library name: Sample 33


title: SMOS-A_2

description: Library name: Sample 32


title: SMOS-A_1

description: Library name: Sample 31


title: Suc_uETS-4HA_1

description: Library name: Sample 29


title: testes of blue catfsh sampled at age 7, biological rep3

description: Library name: AGE_Sample_7


title: Suc_uETS-4HA_2

description: Library name: Sample 30


title: Suc_uETS-3HA_2

description: Library name: Sample 28


title: Suc_uETS-3HA_1

description: Library name: Sample 27


title: Suc_uETS-2HA_2

description: Library name: Sample 26


title: Suc_uETS-2HA_1

description: Library name: Sample 25


title: Suc_uETS-1HA_1

description: Library name: Sample 23


title: Suc_WT_1

description: Library name: Sample 21


title: Suc_WT_2

description: Library name: Sample 22


title: Suc_uETS-1HA_2

description: Library name: Sample 24


title: testes of blue catfsh sampled at age 9, biological rep1

description: Library name: AGE_Sample_1


title: Gly_eETS-4HA_2

description: Library name: Sample 20


title: Gly_eETS-4HA_1

description: Library name: Sample 19


title: Gly_eETS-2HA_2

description: Library name: Sample 16


title: Gly_eETS-3HA_2

description: Library name: Sample 18


title: Gly_eETS-3HA_1

description: Library name: Sample 17


title: Gly_eETS-1HA_2

description: Library name: Sample 14


title: GlyMOS-A_2

description: Library name: Sample 12


title: Gly_eETS-1HA_1

description: Library name: Sample 13


title: Gly_uETS-4HA_2

description: Library name: Sample 10


title: GlyMOS-A_1

description: Library name: Sample 11


title: Gly_uETS-3HA_1

description: Library name: Sample 7


title: Gly_uETS-3HA_2

description: Library name: Sample 8


title: Gly_uETS-4HA_1

description: Library name: Sample 9


title: Gly_uETS-1HA_2

description: Library name: Sample 4


title: Gly_uETS-1HA_1

description: Library name: Sample 3


title: Gly_WT_1

description: Library name: Sample 1


title: Gly_uETS-2HA_1

description: Library name: Sample 5


title: Gly_WT_2

description: Library name: Sample 2


title: Gly_uETS-2HA_2

description: Library name: Sample 6


title: MG1655, Replicate 3, pH 6.8

city: St. Louis

first: Petra

middle: Anne

last: Levin

state: MISSOURI

address: 1 Brookings Drive, Rebstock Hall, Room 323

department: Biology

institute: Washington University in St. Louis

description:
Library name: Sample 12
Column name in raw and processed files = PAL2036-Isol3-pH6-8

data_processing:
QC and adapter trimming was performed with bcl2fastq.
Read mapping was done using HISAT2.
Read counts were loaded into R, normalized with edgeR's Trimmed Mean of M values, and then values were converted to counts per million (cpm).
Differential gene expression was calculated with edgeR's quasi-linear F-test (qlfTest) functionality against treatment groups.
Assembly: ASM395745v1; ASM584v2
Supplementary files format and content: Tab-delimited file contains raw, quantified read counts
Supplementary files format and content: tab-delimited file containing the subset of all quantified genes that meet |logFC|>1 and p <0.05.

source_name: bacterial cells

growth_protocol: Cells were cultured in LB buffered to indicated pH with MMT buffer until early exponential phase (OD600 ~= 0.2).

extract_protocol:
RNA was extracted using Invitrogen Ribopure RNA extraction kit following manufacturer's instructions.
RNA was submitted to Microbial Genome Sequencing Center for library prep and sequencing.  Libraries were generated using Illumina's Stranded Total RNA Prep with Ribo-Zero plus following manufacturer's instructions.

value: bacterial cells

value: WT

value: neutral pH


title: MG1655, Replicate 3, pH 4.8

description:
Library name: Sample 9
Column name in raw and processed files = PAL2036-Isol3-pH4-8

value: acidic pH


title: MG1655, Replicate 1, pH 6.8

description:
Library name: Sample 10
Column name in raw and processed files = PAL2036-Isol1-pH6-8


title: MG1655, Replicate 1, pH 4.8

description:
Library name: Sample 7
Column name in raw and processed files = PAL2036-Isol1-pH4-8


title: Gly_eETS-2HA_1

description: Library name: Sample 15


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - BCL6 antibody BAK212 treated - replicate 1

city: Boston

first: Kimberly

last: Stegmaier

address: 450 Brookline Ave

institute: Dana Farber Cancer Institue

description: Library name: EWS502_BCL6_BAK212_R1

data_processing:
The analysis of the spiked-in ChIP-Seq data was performed according to the ENCODE standards (https://www.encodeproject.org/chip-seq/). Quality control was performed on unmapped sequences using FastQC v.0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)  and MultiQC v.1.14 Adapters and low-quality reads were removed using Trimmomatic v0.39. Reads were mapped to the human genome (GRCh38/hg38) and to the spike-in Drosophila melanogaster (dm6) using bowtie2 v.2.5.1 Mapped reads were processed with SAMtools v0.1.19 and reads with low mapping quality (MAPQ < 5) were disregarded. Duplicate reads were removed using the Picard Mark Duplicates method implemented in the sambamba 0.7.1
bamCoverage tool from the deepTools package v.3.5.0 was used to generate normalized reads per kilobase per million (RPKM) genome-wide coverage bigwig files with specified bin sizes of 20 bp and scaled with the pre-computed spike-in scale factors
Peak calling was performed using the model-based MACS2 v.2.1.1.20160309 software against experimental inputs with a significance cutoff FDR ≤ 0.01. Bwtool software was used to compute the area under the curve (AUC) for the RPKM  normalized signal across genomic regions. MACS2 peaks were filtered by removing binding regions with low AUC coverage of [log2(AUC+1)<13] and ENCODE hg38 black-list regions (https://www.encodeproject.org/annotations/ENCSR636HFF/). Various mapping and genomic analyses including indexing, sorting, intersection, and merging were executed using SAMtools v.1.9 and Bedtools v.2.29
Assembly: hg38
Supplementary files format and content: bigWig RPKM binding signal

source_name: EWS502 FKBP(F36V)-EWS/FLI1

growth_protocol: EWS502 cells expressing exogenous FKBP12(F36V)-EWS/FLI1 concurrent with Cas9 and a guide targeting an intron/exon junction of endogenous EWS/FLI1 were grown in RPMI media supplemented with 15% FBS and 1% penicllin-streptomycin

extract_protocol:
Forty million EWS502 FKBP-EWS/FLI cells per condition (20 million cells per ChIP reaction) were collected in a 50 mL Falcon tube. Cells were pelleted at 300xg for 5 mins and then washed twice in 5 ml PBS. Cells were then crosslinked by resuspension in 10 mL PBS containing 1% methanol-free formaldehyde (Thermo Fisher Scientific, 28906) and rotated slowly by hand for 10 mins at room temperature. The reaction was quenched by addition of 1 mL of 2.5 M glycine (Sigma Aldrich, G7126). Cells were pelleted at 800xg for 5 mins at 4 oC pellets and then washed twice with 10 mL PBS at room temperature supplemented with 1 mM PMSF. After resuspending in the second wash, the cell suspension was split into two chilled 50 mL Falcon tubes (5 mL and 20 million cells each). After spinning at 800xg for 5 mins and removing the second PBS wash, cell pellets were flash frozen in liquid nitrogen.
ChIP-seq libraries were prepared using a NEBNext Ultra II DNA Library Kit for Illumina sequencing (NEB, E7645S) and NEBNext Multiplex Oligos for Illumina sequencing (NEB, E6440S). HA and BCL6 samples were PCR-amplified for 12 cycles. Library pooling and indexing was evaluated with shallow sequencing on an Illumina MiSeq.

treatment_protocol: Cells were treated for 24 hours with DMSO or 1 µM of the designated compound

value: EWS502 FKBP(F36V)-EWS/FLI1

value: Ewing sarcoma

tag: chip antibody

value: BCL6 (Thermo Fischer Scientific, PA5-27390)

tag: spike-in antibody

value: Spike-in antibody (Active Motif, 61686)

tag: time

value: 24 hours


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - BCL6 antibody DEG treated - replicate 1

description: Library name: EWS502_BCL6_DEG_R1


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - BCL6 antibody BAK212 treated - replicate 2

description: Library name: EWS502_BCL6_BAK212_R2


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - BCL6 antibody DEG treated - replicate 2

description: Library name: EWS502_BCL6_DEG_R2


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - BCL6 antibody BI treated - replicate 2

description: Library name: EWS502_BCL6_BI_R2


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - BCL6 antibody BI treated - replicate 1

description: Library name: EWS502_BCL6_BI_R1


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - HA antibody BAK212 treated - replicate 2

description: Library name: EWS502_HA_BAK212_R2

value: HA (Cell Signaling Technologies, 86124SF)


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - HA antibody BAK212 treated - replicate 1

description: Library name: EWS502_HA_BAK212_R1


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - BCL6 antibody DMSO treated - replicate 1

description: Library name: EWS502_BCL6_DMSO_R1


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - HA antibody DEG treated - replicate 2

description: Library name: EWS502_HA_DEG_R2


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - BCL6 antibody DMSO treated - replicate 2

description: Library name: EWS502_BCL6_DMSO_R2


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - HA antibody BI treated - replicate 2

description: Library name: EWS502_HA_BI_R2


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - HA antibody BI treated - replicate 1

description: Library name: EWS502_HA_BI_R1


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - HA antibody DMSO treated - replicate 1

description: Library name: EWS502_HA_DMSO_R1


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - Input DNA reference BAK212 treated - replicate 2

description: Library name: EWS502_Input_BAK212_R2


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - Input DNA reference BAK212 treated - replicate 1

description: Library name: EWS502_Input_BAK212_R1


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - HA antibody DMSO treated - replicate 2

description: Library name: EWS502_HA_DMSO_R2


title: MG1655, Replicate 2, pH 6.8

description:
Library name: Sample 11
Column name in raw and processed files = PAL2036-Isol2-pH6-8


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - Input DNA reference DEG treated - replicate 1

description: Library name: EWS502_Input_DEG_R1


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - Input DNA reference DEG treated - replicate 2

description: Library name: EWS502_Input_DEG_R2


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - Input DNA reference BI treated - replicate 2

description: Library name: EWS502_Input_BI_R2


title: MG1655, Replicate 2, pH 4.8

description:
Library name: Sample 8
Column name in raw and processed files = PAL2036-Isol2-pH4-8


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - Input DNA reference DMSO treated - replicate 2

description: Library name: EWS502_Input_DMSO_R2


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - Input DNA reference BI treated - replicate 1

description: Library name: EWS502_Input_BI_R1


title: LX2 cells: DMEM + 10 ng/ml TGF-beta then + DMEM; biol rep3

city: Galveston

first: W. Samuel

last: Fagg

state: TX

address: 301 University Blvd

department: Department of Surgery

institute: University of Texas Medical Branch

description: Library name: DTD_3

data_processing:
Raw reads were assessed using FastQC version 0.12.1 and MultiQC.
Adapter trimming was performed using Trim Galore version 0.6.7.
Reads were aligned to the reference genome (hg38) using STAR version 2.7.9a with default 2-pass mapping.
Gene-level quantification was performed using Salmon version 1.10.1 in quasi- mapping mode with GC bias correction, using a transcriptome index based on GENCODE v46 annotations.
Gene expression was normalized to TPM and raw counts were obtained using featureCounts version 2.0.1.
Assembly: hg38
Supplementary files format and content: Processed data includes gene-level read counts and normalized expression values. "counts.tsv": Raw read counts per gene from featureCounts. "tpm.tsv": Transcripts per million (TPM) values from Salmon.

growth_protocol: Cells were routinely grown at 37C in DMEM + 10% FBS (high glucose) in 5% CO2

extract_protocol:
trizol was added for cell lysis, then after ethanol precipitation and centrifugation the clarified lysate was added to a ReliaPrep RNA spin column and processed as recommended by the manufacturer (including on-column Dnase treatment
NEBNext Ultra II Directional Kit (pA selection)

treatment_protocol: serum was withdrawn overnight (DMEM only) to prime cells for myofibroblast activation, then then 10 ng/ml TGF-beta was added to those cells indicated above (or DMEM only culture continued) overnight and then media changed to continue the condition above (either fresh DMEM only or DMEM with 10 ng/ml TGF-beta) or with the addition of 1 uM A-83-01 (TGF-beta inhibitor) or 25% cell-free human amniotic fluid, or with TGF-beta then DMEM to "wash out" TGF-beta

value: hepatic stellate

value: with TGF-beta to "activate" the cells then DMEM added back ("wash out" negative control)


title: LX2 cells: DMEM + 10 ng/ml TGF-beta then + 25% cell-free amniotic fluid; biol rep2

description: Library name: DTAF_2

value: with TGF-beta to "activate" the cells then 25% cell-free amniotic fluid added to assess its effect on myofibroblast activation


title: LX2 cells: DMEM + 10 ng/ml TGF-beta then + DMEM; biol rep2

description: Library name: DTD_2


title: LX2 cells: DMEM + 10 ng/ml TGF-beta then + 25% cell-free amniotic fluid; biol rep3

description: Library name: DTAF_3


title: LX2 cells: DMEM + 10 ng/ml TGF-beta then + 25% cell-free amniotic fluid; biol rep1

description: Library name: DTAF_1


title: EWS502 cell line expressing FKBP(F36V)-EWS/FLI1 - Input DNA reference DMSO treated - replicate 1

description: Library name: EWS502_Input_DMSO_R1


title: EWS502 cell line FKBP(F36V)-EWS/FLI1 - HA antibody DEG treated - replicate 1

description: Library name: EWS502_HA_DEG_R1


title: LX2 cells: DMEM + 10 ng/ml TGF-beta then + 1 uM A-83-01; biol rep2

description: Library name: DTA83_2

value: with TGF-beta to "activate" the cells then TGF-beta inhibitor (A-83-01) added to attenuate activation (control for de-activating myofibroblast-activated hepatic stellate cells)


title: LX2 cells: DMEM + 10 ng/ml TGF-beta then + 1 uM A-83-01; biol rep1

description: Library name: DTA83_1


title: LX2 cells: DMEM + 10 ng/ml TGF-beta; biol rep3

description: Library name: DT_3

value: with TGF-beta to "activate" the cells (positive control for myofibroblast-activated hepatic stellate cells)


title: LX2 cells: DMEM + 10 ng/ml TGF-beta then + DMEM; biol rep1

description: Library name: DTD_1


title: LX2 cells: DMEM + 1 uM A-83-01; biol rep3

description: Library name: DA83_3

value: neg control + TGF-beta inhibitor


title: LX2 cells: DMEM + 10 ng/ml TGF-beta; biol rep1

description: Library name: DT_1


title: LX2 cells: DMEM + 10 ng/ml TGF-beta then + 1 uM A-83-01; biol rep3

description: Library name: DTA83_3


title: LX2 cells: DMEM + 1 uM A-83-01; biol rep2

description: Library name: DA83_2


title: LX2 cells: DMEM + 10 ng/ml TGF-beta; biol rep2

description: Library name: DT_2


title: LX2 cells: DMEM + 1 uM A-83-01; biol rep1

description: Library name: DA83_1


title: LX2 cells; control DMEM only; biol rep 2

description: Library name: D_2

value: neg control


title: LX2 cells; DMEM + 25% cell-free amniotic fluid; biol rep3

description: Library name: DAF_3

value: neg control + cell-free amniotic fluid


title: LX2 cells; DMEM + 25% cell-free amniotic fluid; biol rep2

description: Library name: DAF_2


title: LX2 cells; control DMEM only; biol rep 1

description: Library name: D_1


title: UWBCC1_sgPRAME_ATRA_biolrep2

city: Montreal

first: Brandon

last: Ramchatesingh

state: Quebec

address: 1001 Decarie Boulevard

department: Experimental Medicine

country: Canada

institute: McGill University

data_processing:
Reads were retrieved and trimmed using Trimmomatic (V0.36). The FastQC tool (V0.11.5) was used to assess read quality.
Kallisto (V0.48.0) was used to pseudo-align the reads to the GRCh38 transcriptome generated from Ensembl annotation and genome files (V110) using the gffread tool (Cufflinks V2.2.1)
The tximport package (V1.22.0) summarized kallisto count estimates at the gene level
DESeq2 (V1.34) was employed to identify Differentially Expressed Genes (DEGs)
Assembly: GRch38
Supplementary files format and content: tab separated value (tsv) file of est counts data
Supplementary files format and content: tab separated value (tsv) file of transcripts per milllion data

source_name: skin

growth_protocol: Ker-CT keratinocytes were grown in KBM Gold media with bulletkit supplements, with 1% penicillin streptomycin. CAL-27 cells were grown in DMEM media with 10% FBS and 1% penicillin streptomycin. UW-BCC1 cells were grown in DMEM media with 10% FBS and 1% penicillin streptomycin. All cells were grown in a 37C incubator with 5% CO2. Cells were grown for up to a maximum of 25 passages.

extract_protocol:
RNA was harvested using the RNEasy mini kit (Qiagen) according to the manufacturer's protocols. 250ng RNA was used for library preparation.
mRNA enrichment and library preparation were performed using the Illumina Stranded mRNA Prep Kit (Illumina), as per the manufacturer’s recommendations. Libraries were quantified using the KAPA Library Quanitification Kits - Complete kit (Universal) (Kapa Biosystems). Average size fragment was determined using a Fragment Analyzer (Agilent) instrument.

treatment_protocol: Cells were treated with all-trans retinoic acid (ATRA) or a matched volume of dimethylsulfoxide (DMSO) vehicle for 24 hours prior to RNA extraction. Ker-CT keratinocytes were treated with 1μM ATRA, CAL-27 cells were treated with 20μM ATRA, UW-BCC1 cells were treated with 10μM  ATRA.

value: skin

value: basal cell carcinoma

value: sgPRAME

value: ATRA


title: UWBCC1_sgPRAME_ATRA_biolrep1


title: UWBCC1_sgPRAME_ATRA_biolrep3


title: LX2 cells; DMEM + 25% cell-free amniotic fluid; biol rep1

description: Library name: DAF_1


title: UWBCC1_sgPRAME_DMSO_biolrep2

value: DMSO


title: UWBCC1_sgPRAME_DMSO_biolrep1


title: UWBCC1_sgPRAME_DMSO_biolrep3


title: UWBCC1_SCR_ATRA_biolrep2

value: sgSCR


title: UWBCC1_SCR_ATRA_biolrep3


title: UWBCC1_SCR_ATRA_biolrep1


title: UWBCC1_SCR_DMSO_biolrep2


title: UWBCC1_SCR_DMSO_biolrep1


title: UWBCC1_SCR_DMSO_biolrep3


title: Liver, Affected, Bernese Mountain Dog, S43

city: East Lansing

first: Vilma

last: Yuzbasiyan-Gurkan

address: 567 Wilson Rd

institute: Michigan State University

description:
Library name: MSU HS 33
HVTWLDSXX_18936740_S43
HS_MSU_RNAseq Analysis_rawCounts.txt

data_processing:
Raw RNA sequence files from HS and both normal tissues and blood samples were submitted to the ROSALIND® online platform for differential gene expression and pathway analysis.
Reads were trimmed using cutadapt (v3.7). Normalization of raw data, quality control, and functional analysis were performed using the ROSALIND® platform. Quality scores were assessed using FastQC (v0.11.9).
Sequencing reads were aligned to the CanFam3.1 canine reference genome using STAR (v2.7.10a). Individual sample reads were quantified using HTseq (v2.0.0) and normalized via Relative Log Expression (RLE) using the DESeq2 (v1.20) R library. DEseq2 was used to calculate log2-fold changes (log2FC) and p-values.
Assembly: CanFam3.1
Supplementary files format and content: For HS_MSU_RNAseq Analysis_rawCounts.txt: Raw gene expression counts of all tissue and blood samples.
Supplementary files format and content: For HS_BD_OD_PJ_RNAseq_rawCounts.txt: Raw gene expression counts of all tissue and blood samples.

source_name: Liver

extract_protocol:
For tissue and blood samples: RNA was extracted using the mirVANA microRNA isolation kit.
Libraries were prepared using Illumina TruSeq Stranded Total RNA kit with Ribo-zero Globin depletion.

value: Liver

tag: disease state

value: Histiocytic Sarcoma


title: CAL27_OE_ATRA_biolrep3

source_name: tongue

tag: tissue

value: tongue

value: oral squamous cell carcinoma (keratinocyte)

value: OE


title: CAL27_OE_ATRA_biolrep1

tag: cell line


title: CAL27_OE_DMSO_biolrep2

tag: genotype


title: CAL27_OE_DMSO_biolrep3


title: CAL27_OE_ATRA_biolrep2


title: CAL27_EV_ATRA_biolrep2

value: EV


title: CAL27_EV_ATRA_biolrep3


title: CAL27_OE_DMSO_biolrep1


title: LX2 cells; control DMEM only; biol rep 3

description: Library name: D_3

value: hepatic stellate


title: CAL27_EV_ATRA_biolrep1


title: CAL27_EV_DMSO_biolrep3


title: CAL27_EV_DMSO_biolrep2


title: CAL27_EV_DMSO_biolrep1


title: KerCT_OE_ATRA_biolrep3

value: Ker-CT

value: epidermal keratinocyte


title: 786O, shBMAL1, IP HIF2a, biol rep 3

city: SAN DIEGO

first: Rebecca

last: Mello

state: CA

address: 11093 CLAIREMONT MESA BLVD

institute: The Scripps Research Institute

description:
shBmal1_HIF2a-1091.bed
shBmal1_HIF2a.bw

data_processing:
reads underwent alignment to both the human genome hg19 and the yeast genome sacCer3 using Bowtie2 2.5.3, with the following parameters: --local --very-sensitive --fr --dovetail --no-mixed -I 10 -X 700
Alignment files (SAM) were then converted to BAM format, and subjected to filtering, and duplicate reads were removed using samtools 1.6 and sambamba 1.0
Peak calling was performed using MACS2 2.2.9.1, specifying parameters --keep-dup all --max-gap 400 –p 1e-5
Post-peak calling, filtering against the hg19 blacklist was executed using bedtools 2.31.1 with the intersect option
annotation and motif analysis of the peaks was carried out using HOMER 4.11, using annotatePeaks.pl and findMotifsGenome.pl options with the human genome hg19 reference
Peak functional annotation was directly done by Homer using -go option, or with WEB-based GEne SeT AnaLysis Toolkit -WebGestalt (https://www.webgestalt.org/) to identify gene ontologies and KEGG-related pathways after crossing peaks annotation with RNA-seq data.
Spike-in normalization with the aligned reads was achieved against the yeast genome sacCer3 with deeptools 3.5.5 using bamCoverage –scaleFactor --smoothLength 60 --extendReads 150 –centerReads to produce BigWig files. Spike-in scale factor values were calculated as described in the manufacturer protocol (CST #86652).
Profiles and heatmap were obtained by using computeMatrix –referencePoint center after spike-in normalization.  BigWig files were uploaded to the UCSC genome browser (https://genome-euro.ucsc.edu/index.html) and tracks were visualized against the human genome hg19
Assembly: hg19
Supplementary files format and content: bigWig, peak file (.bed) (except for negative control)

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium + 10% fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin (Gibco), and maintained in an atmosphere containing 5% CO2 at 37°C.

extract_protocol:
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) were performed using CUT&RUN assay kit (CST #86652) following the manufacturer protocol. DNA purification was performed by phenol/chloroform extraction followed by ethanol precipitation.
Next generation sequencing libraries were prepared using DNA Library Prep Kit for Illumina (CST #56795) and Multiplex Oligos for Illumina (CST #29580).

treatment_protocol: To generate cell lines expressing shRNA, lentiviral shRNA constructs encoded in PLKO.1 vectors were produced by transient transfection in HEK293T cells. Target cells were infected with lentivirus for 4-6 hours before selection in DMEM + 10% fetal bovine serum and 1% penicillin-streptomycin containing 2.5 µg/mL puromycin for 1 week. After initial selection, cells were maintained in DMEM containing 1.25 µg/mL.

value: Adenocarcinoma; Renal Cell

value: BMAL1 knockdown

value: HIF-2α rabbit mAb (CST #59973)


title: 786O, shBMAL1, IP HIF2a, biol rep 2

description:
shBmal1_HIF2a-1091.bed
shBmal1_HIF2a.bw


title: KerCT_OE_ATRA_biolrep1

value: skin


title: KerCT_OE_ATRA_biolrep2


title: 786O, shBMAL1, IP HIF2a, biol rep 1

description:
shBmal1_HIF2a-1091.bed
shBmal1_HIF2a.bw


title: 786O, shBMAL1, IP BMAL1, biol rep 2

description:
shBmal1_BMAL1-769.bed
shBmal1_BMAL1.bw

value: BMAL1 rabbit mAb (CST #14020)


title: KerCT_OE_DMSO_biolrep3


title: KerCT_OE_DMSO_biolrep2


title: 786O, shBMAL1, IP IgG (negative control) biol rep 2

value: rabbit mAb IgG isotype  (CST #66362)


title: 786O, shBMAL1, IP IgG (negative control) biol rep 1


title: KerCT_OE_DMSO_biolrep1

value: DMSO


title: 786O, shControl, IP HIF2a, biol rep 3

description:
shctrl_HIF2a-1207.bed
shctrl_HIF2a.bw

value: WT


title: KerCT_EV_ATRA_biolrep2

value: ATRA


title: 786O, shControl, IP HIF2a, biol rep 2

description:
shctrl_HIF2a-1207.bed
shctrl_HIF2a.bw


title: KerCT_EV_ATRA_biolrep1


title: 786O, shControl, IP HIF2a, biol rep 1

description:
shctrl_HIF2a-1207.bed
shctrl_HIF2a.bw


title: 786O, shControl, IP BMAL1, biol rep 3

description:
shctrl_BMAL1-1813.bed
shctrl_BMAL1.bw


title: KerCT_EV_DMSO_biolrep2


title: KerCT_EV_DMSO_biolrep1


title: KerCT_EV_DMSO_biolrep3


title: 786O, shControl, IP BMAL1, biol rep 1

description:
shctrl_BMAL1-1813.bed
shctrl_BMAL1.bw


title: 786O, shControl, IP BMAL1, biol rep 2

description:
shctrl_BMAL1-1813.bed
shctrl_BMAL1.bw


title: Interferon-gamma rep 2

city: Los Angeles

first: Aleksandr

last: Gorin

address: 611 Charles E Young Dr E 570C Boyer Hall

institute: UCLA

data_processing:
CUT&Tag reads were aligned to the hg38 genome using bowtie2 version 2.2.5 with default parameters except –very-sensitive and –non-deterministic options and were filtered based on mapping score (MAPQ >30) by Samtools version 1.9
Duplicated reads were removed using Picard MarkDuplicates version 2.18.29.
MACS3 version 3.0.0b1 was used to identify peaks for each sample individually with default settings except FDR of 0.01, -f BAMPE, -g hs, and –nomodel.
Peaks from all samples were merged into a single file and raw peaks quantified using featureCounts.
Assembly: hg38
Supplementary files format and content: CSV of with RPKM for peaks identified in any of the conditions.
Library strategy: CUT&Tag

source_name: monocyte-derived macrophage

growth_protocol: Monocytes were isolated from PBMC with miltenyi human pan-monocyte isolation kit and grown in RPMI supplemented with 10% FBS, Penicillin-Streptomycin, and 25ng/mL human MCSF (peprotech). MCSF was refreshed on day 5 of culture. Cells were grown for a total of 7 days prior to stimulation.

extract_protocol:
Nuclei were isolated and DNA was tagmented using the CUTANA CUT&Tag kit (epichypher) and anti-H3K4me1 antibody (abcam 8895).
Libraries were constructed as per CUTANA CUT&Tag protocol (epicypher)

treatment_protocol: Cells were stimulated with LPS 100ng/mL, interferon-beta 10u/mL, interferon-gamma 100ng/mL, Pam3CSK4 100ng/mL or left unstimulated for 8 hours. After 8 hours cells were lifted with 0.5mM EDTA/PBS and gentle scraping. Cells were used for CUT&Tag protocol as per manufacturer.

value: monocyte-derived macrophage

value: Interferon-gamma 100ng/mL


title: Interferon-gamam rep 1


title: 786O, shControl, IP IgG (negative control) biol rep 1


title: 786O, shControl, IP IgG (negative control) biol rep 2


title: Interferon-beta rep 2

value: Interferon-beta 10u/mL


title: 786O, shBMAL1, IP BMAL1, biol rep 1

description:
shBmal1_BMAL1-769.bed
shBmal1_BMAL1.bw


title: Pam3CSK4 rep 2

value: Pam3CSK4 100ng/mL


title: Pam3CSK4 rep 1


title: KerCT_EV_ATRA_biolrep3

value: EV


title: Transgenic P1 hMR 2

city: Paris

first: Daniela

last: Rodrigues-Braz

address: 15 rue de l'Ecole de Médecine

country: France

institute: Inserm

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with fastp software to retain only good quality paired reads.
Star v2.5.3a has been used to align reads on rn6 reference genome using standard options
Quantification of gene and isoform abundances has been done with rsem 1.2.28, prior to normalisation on library size with edgeR bioconductor package.
Differential analysis has been conducted with the glm framework likelihood ratio test from edgeR. Multiple hypothesis adjusted p-values were calculated with the Benjamini-Hochberg procedure to control FDR.
Data were normalized with DESeq2 (v1.26.0) or/and edgeR (v3.28.0) bioconductor packages, prior to differential analysis with glm framework likelihood ratio test from edgeR package, and/or DESeq2 workflow. Multiple hypothesis adjusted p-values were calculated with the Benjamini-Hochberg procedure to control FDR. Finally, enrichment analysis was conducted with clusterProfiler R package (v3.14.3) with over-representation analysis and/or Gene Set Enrichment Analysis, on gene ontology database, XX pathways.)
Assembly: rd6
Supplementary files format and content: Tab text file including the gene counts expression for each sample
Supplementary files format and content: Tab text file inluding the isoforms counts expression for each sample

organism: Rattus norvegicus

source_name: Cornea

growth_protocol: Six-month-old male wild-type and transgenic P1 hMR rats that overexpress the human NR3C2 gene coding for mineralocorticoid receptor (MR) were euthanized, eyes were removed and the cornea dissected for RNA sequencing.

extract_protocol:
Total RNA was isolated from tissues using the RNeasy Mini Kit inluding DNase I treatment (Qiagen, Courtaboeuf, France)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cornea

tag: Sex

value: male

tag: background strain

value: Sprague-Dawley

value: transgenic

value: six months


title: LPS rep 1

tag: treatment

value: LPS 100ng/mL


title: Transgenic P1 hMR 1


title: Unstimulated rep 2

value: unstimulated


title: Interferon-beta rep 1


title: Wild-type 3

value: wild-type


title: Unstimulated rep 1


title: sgAcat1_EV_rep2_R1

first: Chen

last: Wei

state: Guangdong

address: Dongfengdong Road No.651

institute: Sun Yat-sen university Cancer center

description: Library name: Sample 2

data_processing:
We first used Trim Galore (v0.6.10) to trim 3’ end of reads. Resulting paired end cleaned reads were then aligned to the hg38/mm10 reference genome using STAR (2.7.11a). The uniquely mapped reads were assigned to UCSC annotated genes using featureCounts (v2.0.6). DESeq2 was used to performed differential gene expression analysis. Gene set enrichment analysis was performed using R packages fgsea (v1.27.1).
Assembly: mm10 for Mus musculus and hg38 for Homo sapiens
Supplementary files format and content: tab delimited text files include raw counts for each sample

source_name: Cell line

extract_protocol:
For Smart-seq2 (switching mechanism at 5’ end of the RNA transcript), single NK cells were sorted and processed as described in previous study. Briefly, total RNA was extracted and mixed with anchored oligo-dT primer (10 µM, 5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′, where “N” is any base and “V” is either “A”, “C” or “G”) and dNTP mix (10 mM), denatured at 72 °C for 3 min and placed on ice immediately. For RNA-seq, total RNA was extracted with Trizol reagent (Invitrogen) and mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
For Smart-seq2，7 µL of the first-strand reaction mix, containing 0.50 µL SuperScript II reverse transcriptase (200 U/µL), 2 µL Superscript II First-Strand Buffer (5×), 0.25 µl RNAse inhibitor (40 U/µL), 0.9 µL MgCl2 (100 mM), 0.25 µL DTT (100 mM), 2 µl betaine (5 M), 1 µL TSO (10 µM) and 0.1 µL nuclease-free water were added for reverse transcription. After this, samples were followed by PCR preamplification with the mixture containing: 25 µL KAPA HiFi HotStart ReadyMix, 1 µL ISPCR primers (10 µM, 5′-AAGCAGTGGTATCAACGCAGAGT-3′) and 14 µL nuclease-free water (Gibco). Finally, after tagmentation reaction and PCR amplification, samples were sequenced on Illumina HiSeq 2000. For RNA-seq, Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. High-throughput sequencing was performed on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: colorectal cancer cell line

value: Acat1 KO


title: sgAcat1_EV_rep1_R1

description: Library name: Sample 1


title: Wild-type 1


title: LPS rep 2


title: sgAcat1_rAcat1_WT_rep1

description: Library name: Sample 3

value: Acat1 WT


title: Wild-type 2


title: pdhR in vitro 10x 2

first: James

last: Galagan

state: Massachusetts

address: 36 Cummington Mall

department: Biomedical Engineering

institute: Boston University

description: in vitro ChIP-Seq of 500ng pdhR with C-terminal 6xHis tag

data_processing:
For ChIP-Seq: Adapters were trimmed from reads using Cutadapt version 2.6
For ChIP-Seq: Reads were aligned to GenBank ID U00096.3 using Bowtie2 versioni 2.3.4.1
For ChIP-Seq: Peak calling was done using SPAT
For ChIP-Seq: Peaks with low shift (<45 bases) between forward and reverse coverage were filtered
For ChIP-Seq: Peaks with low enrichment compared to WT controls were filtered
For ChIP-Seq: Peaks from SPA-tagged TFs that matched NagC artifacts were filtered
For ChIP-Seq: Peaks with low overall enrichment (<4.75-fold over genomic average coverage) were filtered
For ChIP-Seq: Peaks mapped to strong tag-independent artifacts (described in manuscript) were filtered
For ChIP-Seq: Peaks mapped to weak tag-independent artifacts were filtered (described in manuscript)
For ChIP-Seq: Peaks adjacent to inducible watermarks were re-added (described in manuscript)
For Library-ChIP: Inserted sequences were counted from raw reads by identifying the anchor sequence (from the flank of the insertion site) "GGACGGATCCTCGAGCATGC", and taking the following 37 nucleotides after the anchor.
For Library-ChIP: Low abundance hits were dropped out (< 0.1% of preIP reads)
For Library-ChIP: Counts were normalized within-sample for sequencing depth by dividing counts by average counts for each insertion sequence
For Library-ChIP: Enrichment was determined as the ratio of normalized postIP:preIP counts
Assembly: U00096.3
Supplementary files format and content: ChIP-Seq: GFF file containing peak calls that passed all filtering steps
Supplementary files format and content: Library-ChIP: TSV file where first column is the inserted sequence identified in processing step 1, columns 2 and 3 are the number of times sequence was identified in R1 and R2 reads, column 4 is the identifier of the sequence from the designed insertion pool, and column 5 is the sum of R1 and R2 reads

organism: Escherichia coli K-12

growth_protocol: Cells were grown in indicated media at 30°C with shaking in vented flasks

extract_protocol:
TF-DNA complexes were fixed with formaldehyde and glycine.  For in vivo ChIP-Seq, cells were sheared via sonication; for in vitro ChIP-Seq, DNA was sheared via sonication prior to TF-DNA binding.  Sheared DNA was immunoprecipitated (IP) using anti-FLAG, anti-V5, or anti-6xHis mAb (indicated in metadata).  DNA was washed with IPP150 buffer and purified via ProteinaseK digestion and Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).  For Library-ChIP, preIP samples used sheared DNA purified via ProteinaseK digestion and Qiaquick PCR purification kit prior to addition of anti-tag antibody; postIP samples used sheared DNA that was immunoprecipitated, washed, purified, and extracted in the same way as ChIP-Seq.
ChIP-DNA was converted into NGS libraries compatible with the Illumina platform using the NEBNext Ultra DNA (NEB Cat. No. E7465).  For Library-ChIP, libraries were constructed similarly to Illumina's 16S metagenomic library prep (Illumina Ref #15044223 Rev. B).  Briefly, an initial PCR was performed on DNA with a universal primer pair targeting flanks of the insertion site on the pAMD plasmid where designed sequences were inserted.  These primers contained overhangs that could be targeted by Illumina Nextera XT Index Kit v2 (Illumina Cat. No. FC-131-2001) primers.  First PCR was cleaned up with Qiaquick PCR purification kit (Qiagen - Cat. No. 28106).  Second PCR used a unique pair of primers from the Illumina Nextera kit for each sample, and were cleaned up with AMPureXP beads (Fisher Scientific Cat. No. NC9933872).

treatment_protocol: Inducible strains were treated with arabinose prior to crosslinking, some native strains were treated with GlcNac for 5 minutes prior to crosslinking (treatments indicated in metadata).

tag: transcription factor

value: pdhR

value: anti-6xHis mAb

tag: antibody vendor/catalog#

value: Invitrogen/Cat. No. MA1-21315

tag: media

value: 1 hour


title: pdhR in vitro 10x 1


title: Vehicle 4 day 7

description: V4 D7

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with fastp software to retain only good quality paired reads.
Star v2.5.3a has been used to align reads on rn6 reference genome using standard options
Quantification of gene and isoform abundances has been done with rsem 1.2.28, prior to normalisation on library size with edgeR bioconductor package.
Differential analysis has been conducted with the glm framework likelihood ratio test from edgeR. Multiple hypothesis adjusted p-values were calculated with the Benjamini-Hochberg procedure to control FDR.
Data were normalized with DESeq2 (v1.26.0) or/and edgeR (v3.28.0) bioconductor packages, prior to differential analysis with glm framework likelihood ratio test from edgeR package, and/or DESeq2 workflow. Multiple hypothesis adjusted p-values were calculated with the Benjamini-Hochberg procedure to control FDR. Finally, enrichment analysis was conducted with clusterProfiler R package (v3.14.3) with over-representation analysis and/or Gene Set Enrichment Analysis, on gene ontology database, XX pathways.)
Assembly: rd6
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with fastp software to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on rn6 reference genome and quantification with ensembl Rnor 6.0.103 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools. Following analysis were conducted with R software.
Data were normalized with DESeq2 (v1.26.0) or/and edgeR (v3.28.0) bioconductor packages, prior to differential analysis with glm framework likelihood ratio test from edgeR package,and/or DESeq2 workflow. Multiple hypothesis adjusted p-values were calculated with the Benjamini-Hochberg procedure to control FDR.
enrichment analysis was conducted with clusterProfiler R package (v3.14.3) with over-representation analysis and/or Gene Set Enrichment Analysis, on gene HALLMARK database, XX pathways.
Assembly: rd6

extract_protocol:
Two months old male Lewis rats were treated daily with subcutaneous injection of spironolactone for three days. Rats were then euthanized, eyes were removed and the peripheral cornea and limboscleral tissues dissected for RNA sequencing.
Total RNA was isolated from tissues using the RNeasy Mini Kit inluding DNase I treatment (Qiagen, Courtaboeuf, France)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lewis

value: Systemic vehicle (90 % olive oil + 10 % DMSO)

value: day 7


title: Vehicle 2 day 7

description: V2 D7


title: Vehicle 1 day 7

description: V1 D7


title: sgAcat1_rAcat1_WT_rep2

description: Library name: Sample 4

tag: cell type

value: Acat2 WT


title: yeaT native 2

description: ChIP-Seq of native yeaT with C-terminal V5 tag

value: yeaT

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: pdhR in vitro 1x 1

description: in vitro ChIP-Seq of 50ng pdhR with C-terminal 6xHis tag


title: Spironolactone 3 day 7

description: S4 D7

value: wild-type

value: Systemic spironolactone (25mg/kg/day)


title: Spironolactone 2 day 7

description: S3 D7


title: Spironolactone 1 day 7

description: S2 D7


title: zur native 1

description: ChIP-Seq of native zur with C-terminal V5 tag

value: zur


title: Vehicle 3 day 7

description: V3 D7


title: Vehicle 3 day 3

description: V5 D3

value: day 3


title: zraR inducible 1

description: ChIP-Seq of inducible zraR with C-terminal FLAG tag

value: zraR

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: ytfH inducible 1

description: ChIP-Seq of inducible ytfH with C-terminal FLAG tag

value: ytfH


title: ytfH native 2

description: ChIP-Seq of native ytfH with C-terminal V5 tag


title: Spironolactone 3 day 3

description: S4 D3

value: Lewis


title: pdhR in vitro 1x 2

value: pdhR

value: anti-6xHis mAb

value: Invitrogen/Cat. No. MA1-21315

value: 1 hour


title: ytfH native 1

value: anti-V5 mAb

value: Sigma/Cat. No. V8012


title: yqjI native 1

description: ChIP-Seq of native yqjI with C-terminal SPA tag

value: yqjI

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: Spironolactone 1 day 3

description: S2 D3

value: wild-type

value: Systemic spironolactone (25mg/kg/day)


title: ypdC inducible 1

description: ChIP-Seq of inducible ypdC with C-terminal FLAG tag

value: ypdC


title: Spironolactone 2 day 3

description: S3 D3

value: day 3


title: ycjW native 2

description: ChIP-Seq of native ycjW with C-terminal V5 tag

value: ycjW


title: yoeB native 1

description: ChIP-Seq of native yoeB with C-terminal V5 tag

value: yoeB


title: yncC native 2

description: ChIP-Seq of native yncC with C-terminal V5 tag

value: yncC


title: ttk native 4

description: ChIP-Seq of native ttk with C-terminal V5 tag

value: ttk


title: yncC native 1


title: yoeB inducible 1

description: ChIP-Seq of inducible yoeB with C-terminal FLAG tag

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: HCT116_p50_K146Q_rep2

description: Library name: Sample 8

value: colorectal cancer cell line

value: p50 wildtype


title: HCT116_p50_K146Q_rep1

description: Library name: Sample 7


title: Hashtag Pool: Mock T cell-treated 697 B-ALL (Isogenic Variants detailed in 'Genotype')

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

institute: University of Colorado, Denver

description:
Library name: Pool2_CSP
TotalSeq-B anti-human Hashtag Antibodies: Hashtag library prepared according to manufacturers instructions: https://www.biolegend.com/nl-nl/totalseq/single-cell-rna/multiplex-samples-and-hashtags

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files; h5 files

source_name: Mixed culture: bone marrow-derived B-ALL cell line, and donor T cells

growth_protocol: RPMI 1640, 20% FBS, 2-Me, Pen/Strep, human IL-2 (4U/mL)

extract_protocol:
Single cell suspension of co-cultured cells directly added to 10X Chromium
Gene expression library prepared on co-cultured cells for 3' single cell mRNAseq compatible with TotalSeq B hashtag reagents according to 10X Genomics manufacturers instructions

treatment_protocol: Mock or CD19-directed CAR-T (1:16 E:T)

value: Mixed culture:bone marrow-derived B-ALL cell line, and donor T cells

value: E2A::PBX1+ B cell progenitor

value: TP53 wt SLC27A2 wt (GTCAACTCTTTAGCG); TP53 wt SLC27A2 mut (TGATGGCCTATTGGG); TP53 mut SLC27A2 wt (TTCCGCCTCTCTTTG); TP53 mut SLC27A2 mut (AGTAAGTTCAGCGTA)

value: Mock


title: Hashtag Pool: CAR T cell-treated 697 B-ALL (Isogenic Variants detailed in 'Genotype')

description:
Library name: Pool5_CSP
TotalSeq-B anti-human Hashtag Antibodies: Hashtag library prepared according to manufacturers instructions: https://www.biolegend.com/nl-nl/totalseq/single-cell-rna/multiplex-samples-and-hashtags

value: CAR


title: GEX Pool: Mock T cell-treated 697 B-ALL (Isogenic Variants detailed in 'Genotype')

description:
Library name: Pool2_GEX
Gene expression library prepared on co-cultured cells for 3' single cell mRNAseq compatible with TotalSeq B hashtag reagents according to 10X Genomics manufacturers instructions


title: zur native 2

value: zur

value: anti-V5 mAb

value: Sigma/Cat. No. V8012

value: M9 Minimal with 0.4% glycerol

value: Log-Phase


title: GEX Pool: CAR T cell-treated 697 B-ALL (Isogenic Variants detailed in 'Genotype')

description:
Library name: Pool5_GEX
Gene expression library prepared on co-cultured cells for 3' single cell mRNAseq compatible with TotalSeq B hashtag reagents according to 10X Genomics manufacturers instructions


title: ykgD native 2

description: ChIP-Seq of native ykgD with C-terminal V5 tag

value: ykgD


title: Vehicle 2 day 3

description: V3 D3

value: Lewis

value: wild-type

value: Systemic vehicle (90 % olive oil + 10 % DMSO)

value: day 3


title: HCT116_p50_K146R_rep2

description: Library name: Sample 6

value: colorectal cancer cell line

value: p50  mutant


title: Vehicle 1 day 3

description: V2 D3


title: ykgD native 1


title: HCT116_p50_K146R_rep1

description: Library name: Sample 5


title: yjjQ inducible 1

description: ChIP-Seq of inducible yjjQ with C-terminal FLAG tag

value: yjjQ

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804

value: Arabinose added to 0.2% final volume for TF induction 1 hour prior to crosslink


title: yjiR native 1

description: ChIP-Seq of native yjjQ with C-terminal V5 tag

value: yjiR


title: yncC inducible 1

description: ChIP-Seq of inducible yncC with C-terminal FLAG tag

value: yncC