title: Ileum, morphine, 24 hrs, replicate 4

city: Miami

first: Udhghatri

last: Kolli

state: Fl

address: 1501 Nw 15th street

department: Surgery

institute: University of Miami

data_processing:
Mapping STAR V2
Quantification HTSeq v0.6.1
Differential Analysis DESeq2 v2_1.6.3
Enrichment Analysis ClusterProfiler v2.4.3, TOPPcluster, clueGo
Assembly: mm10
Supplementary files format and content: Text file includes FPKM, differential gene expression and statistics

source_name: ileum

growth_protocol: Eight-week-old, pathogen free, C57/B6 male mice (Jackson laboratories) Animals were maintained in a 12-h light/dark cycle, with constant temperature (72 ± 1°F) and 50% humidity with food and tap water provided ad libitum

extract_protocol:
RNA was extracted from flash frozen terminal ileum RNeasy plus Universal Kit from Qiagen (73404)
NEBNext Ultra RNA library prep kit

treatment_protocol: The animals were lightly anesthetized using isoflurane (Pivetal®) and a 25 mg slow-release Morphine pellet or placebo pellet was implanted subcutaneously.

value: ileum

value: Wild type

value: Morphine, 25mg pellet, 24 hrs


title: young seurm infusion, chorolid plexus, 13

status: Public on Aug 30 2023

type: SRA

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto St

department: Environmental and Occupational Health

country: USA

institute: University of Pittsburgh

description:
C418
YS-infusion-CP.xlsx

library_source: transcriptomic

data_processing:
FASTQ TO BAM
FEATURECOUNTS
EDGER
Assembly: mm10
Supplementary files format and content: raw expresison counts from featurecounts

molecule: total RNA

organism: Mus musculus

source_name: choroid plexus

growth_protocol: All animal experiments were performed in accordance with the NIH Guide for Care and Use of Animals and approved by the University of Pittsburgh Institutional Animal Care and Use Committee.

extract_protocol:
Mice were anesthetized by intraperitoneal injection using Avertin (250 mg/kg of body weight). Blood was collected from the right ventricle, followed by trans-cardiac perfusion through the left ventricle with 20 mL of cold 0.1 M phosphate buffered saline (PBS), pH 7.4. Brain was removed and divided into hemispheres. One hemisphere was dissected into the hippocampus and choroid plexus and flash frozen on dry ice for bulk RNA-seq.
RNA was isolated from cortex and purified using RNeasy mini kit (Qiagen) per the manufacturer’s protocol. RNA quality was assessed using 2100 Bioanalyzer (Agilent Technologies) and samples with RIN > 8 were further used for sequencing. Sequencing libraries were generated by Novogene.

treatment_protocol: Mice were anesthetized by isoflurane and blood was collected via cardiac puncture of the right ventricle with 25-gauge 5/8-inch 1 mL needle. Blood was incubated at room temperature for 60 min and centrifuged for 20 min at 16,000 g. The serum was aliquoted into 1.5 mL centrifuge tubes and stored at -20°C. For the young serum infusion, aged WT male mice received 100µL of young serum. Animals were injected every three days over a 25-day period.

tag: tissue

value: choroid plexus

tag: genotype

value: WT


title: Ileum, morphine, 24 hrs, replicate 5

tag: strain

tag: treatment


title: Ileum, morphine, 24 hrs, replicate 3


title: Liver_4MU_rep2

city: Moscow

first: Noreen

last: Halimani

address: Bol'shoy Bul'var, 30, стр 1

department: Faculty of Life Sciences

country: Russia

institute: Skolkovo Institute of Science and Technology

description:
4MU.2
_raw_counts.csv.gz

data_processing:
Raw reads were preprocessed as follows: trimmed with Trimmomatic (v0.39) to remove the adapters. The processed reads were aligned to the Mus musculus genome (assembly GRCm39.105) using the HISAT2 algorithm. Following analysis was performed in R version 3.4.2. Gene read counts were calculated using Rsubread package, function featureCounts (with parameters count MultiMap-pingReads = F, isPairedEnd = TRUE) Genes with less than 10 reads on average for per sample were filtered out. To check the data for self-consistency, the following analysis was carried out: correlation analysis and MDS using the Spearman correlation and PCA using normalised gene counts as CPM (count per million). DEGs were identified using DESeq2 R package in comparisons between samples. Gene ontology analysis of DEGs was performed using the ClusterProfiler package with all significant genes as background. Pathway enrichment analyses were done across Bioplanet 2019, GO Molecular function, MSigDB_Hellmark_2020 and KEGG_Pathways_2019 CHEA 2016 databases were used to annotate differences in molecular functions, biological processes, and signalling pathways between experimental groups with Enrich
Supplementary files format and content: _raw_counts.csv.gz : a tab delineated txt file containing raw counts for each sample

source_name: Healthy_total liver homogenate

extract_protocol:
PolyA mRNA was isolated from liver samples using Trizol(15596018, Thermo Fisher Scientific), following manufacturer's protocol
A measure of 1 μg RNA was reverse-transcribed to cDNA using the QuantiTect Reverse Transcription Kit (Qiagen, Hilden, Germany). Illumina cDNA libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs, MA, USA) following the manufacturer’s protocol. cDNA libraries were sequenced using the NextSeq500 (Illumina, San Diego, CA USA) instrument. Sequencing was carried out with a read length of at least 85bp in the paired-end mode, with an average number of reads per sample not less than 30 million

tag: Sex

value: Female

value: Balb/c

value: liver

tag: condition

value: Healthy

value: IP olive oil injection plus 4MU gavage

value: 4MU gavage everyday for a fortnight


title: ccRCC_ExtendedOpioid_3

city: Rockville

first: Alexis

middle: L

last: Norris

state: MD

address: 7500 Standish Place

institute: US FDA

data_processing:
Base calling with bcl2fastq2 version 2.19.0
Sequencing reads were trimmed using trimmomatic (version 0.36.6; parameters: SLIDINGWINDOW:4:20 MINLEN:50)
Trimmed reads were aligned to GRCh38/hg38 using HISAT2 (version 2.1.0; parameters: --n-ceil L,0.0,0.15 --mp 6,2 --no-softclip --np 1 --rdg 5,3 --rfg 5,3 --sp 2,1 --score-min L,0.0,-0.2 --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --min-intronlen 20 --max-intronlen 500000).
Gene counts were estimated using featureCounts (version 1.6.3; parameters: -s 1 -t 'exon' -g 'gene_id' -J -Q 12 --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0) with GENCODE gene annotation (GENCODE version 33; Ensembl version 99).
Assembly: hg38
Supplementary files format and content: tab-delimited text file include gene counts for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Advanced clear cell renal cell carcinoma - tumor FFPE

extract_protocol:
Total RNA was extracted using the RNeasy FFPE Kit from Qiagen according to the manufacturer instructions and assessed for quality using the Agilent Bioanalyzer Total RNA Nano Chip. Samples with DV200 > 20 were selected to proceed for the RNA-Seq.
100 ng of total RNA was used to generate the RNA-seq paired end library through the Illumina RNA Prep with Enrichment Kit. RNA was reverse-transcribed into cDNA, followed by fragmentation, probes hybridization, and individual indexing. The indexed cDNAs were enriched by exome probes and followed by 14 PCR cycles amplification. After obtaining the sequencing libraries, 0.6 nM of the pooled library was subjected to sequencing on an Illumina NovaSeq instrument with SP capacity. Following the instruction provided by the manufacturer, paired end 2x75 cycles sequencing was performed.

value: Extended opioid exposure


title: LASPC_Veh_24h_1

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

description: LASCPC01 cell line 24h Vehicle rep 1

data_processing:
Sequencing was performed on Illumina HiSeq 2500 for MR42D and LASCPC-01 cell lines. For the rest, sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Paired-end alignments were obtained using STAR v2.5.2a as the aligner (Dobin et al. Bioinformatics. 2013.) using the following options (--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outSAMtype BAM Unsorted --outReadsUnmapped Fastx --outSAMstrandField intronMotif). Samtools (v 1.5) was used to sort and index the bam file. featureCounts function from the subread program (v1.6.1) was used to compute gene and isoform counts.
Differential expression was performed using DESeq2 v4.1.0 using ranked shrunkLFC (shrunk Log Fold Change) values
Assembly: hg38
Supplementary files format and content: The columns of the counts.txt files are: (1) refgeneGene; (2) entrez; (3) symbol; (4) gene  coordinates (5) sample read count

growth_protocol: LNcaP-NMyc cells were grown in RPMI with 10% FBS. MR42D cells were grown in RPMI with 10% FBS and 10µM Enzalutamide. LASCPC-01 cells were grown in modified HITES media as recommended by ATCC (CRL-3356).

extract_protocol:
After the indicated treatments, RNA was extracted from cells using the RNeasy Plus Mini Kit (Qiagen cat# 74034) according to the manufacturer’s protocol.
Libraries were prepared using the Illumina TruSeq stranded kit.

treatment_protocol: LASCPC-01 cells were treated with 300 nM SP2509 for 24 hours. LNCaP-NMyc and MR42D cells were treated with 600 nM SP2509 fro 48hours.

tag: cell line

tag: agent

value: Veh

tag: time point


title: Ileum, morphine, 24 hrs, replicate 2


title: Liver_4MU_rep1

description:
4MU.1
_raw_counts.csv.gz


title: young seurm infusion, chorolid plexus, 10

description:
C412
YS-infusion-CP.xlsx


title: ccRCC_OpioidNaive_3

value: Advanced clear cell renal cell carcinoma - tumor FFPE

value: Opioid naive


title: ccRCC_ExtendedOpioid_2


title: Liver_control_rep4

description:
CNTRL.4
_raw_counts.csv.gz

value: IP olive oil injection plus PBS tail vein injection

value: IP and tail vein injection twice a week for a fortnight


title: young seurm infusion, chorolid plexus, 9

description:
C411
YS-infusion-CP.xlsx


title: ccRCC_OpioidNaive_2


title: Ileum, morphine, 24 hrs, replicate 1

value: ileum


title: ccRCC_ExtendedOpioid_1


title: young seurm infusion, chorolid plexus, 8

description:
C410
YS-infusion-CP.xlsx


title: Liver_control_rep2

description:
CNTRL.2
_raw_counts.csv.gz


title: young seurm infusion, chorolid plexus, 7

description:
C409
YS-infusion-CP.xlsx


title: young seurm infusion, chorolid plexus, 12

description:
C417
YS-infusion-CP.xlsx


title: ileum, Control, 24 hrs, replicate 4

value: Wild type

value: control


title: ccRCC_OpioidNaive_1


title: young seurm infusion, chorolid plexus, 11

description:
C415
YS-infusion-CP.xlsx

value: choroid plexus


title: ileum, Control, 24 hrs, replicate 3


title: Liver_control_rep1

description:
CNTRL.1
_raw_counts.csv.gz


title: young seurm infusion, chorolid plexus, 6

description:
C408
YS-infusion-CP.xlsx

value: WT


title: ileum, Control, 24 hrs, replicate 2


title: young seurm infusion, chorolid plexus, 4

description:
C404
YS-infusion-CP.xlsx


title: CCS 2 human ileal organoid

city: Houston

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

description:
3D
I206D_B2

data_processing:
Fastq files were trimmed using Trim Galore!.
Trimmed reads were aligned to the GRCh38 genome using HISAT2.
Aligned reads were quantified using featureCounts.
Assembly: GRCh38
Supplementary files format and content: raw count comma separated file

source_name: intestine

growth_protocol: Organoids were generated from tissue biopsies using standard protocols. Organoids were then grown in standard organoid growth media during proliferation.

extract_protocol:
RNA was isolated with the Qiagen RNeasy Micro kit according to the manufacturer's protocol. A Qiashredder was used to account for the 3D and matrigel.
Sequencing and library preparation was performed by Novogene

treatment_protocol: CCS and Non-CCS organoids were not treated in any way. Growth factors were removed for 3 days to allow cells to differentiate prior to RNA extraction. NGN3 over expressing organoids were treated with doxycycline for 5 days to induce expression. Uninduced cells did not receive doxicycline.

value: intestine

tag: segment

tag: organoid

value: ileal organoid

tag: status

value: CCS


title: CN,SMC1_NMDA_Input_2

city: Dalals

first: Morgan

last: Crewe

address: 2201 Inwood Road

department: Psychiatry

institute: University of Texas Southwestern Medical Center

library_source: genomic

data_processing:
Raw FASTQ sequencing reads were analyzed for quality control using FastQC, trimmed using Trimmomatic, and aligned to the mm10 reference genome (GRCm38.p6 assembly) using BWA-MEM.
BAM files were marked and filtered for duplicate reads using Sambamba and Samtools, respectively.
Peaks were called using MACS2 from biological duplicates and pseudo-replicates where each ChIP sample was normalized to input DNA.
MACS2-generated bedGraph files were converted to bigWig files using Kent Utils for individual replicates and pooled replicates
IDR (irreproducible discovery rate thresholding was performed on MACS2 peak calls using an IDR threshold of 0.05.
Assembly: mm10
Supplementary files format and content: BED - IDR thresholded peaks

molecule: genomic DNA

source_name: Mouse Cortical Neurons

growth_protocol: Dissociated cortical neurons from E16 Swiss-Webster mice (Charles River) were plated at a density of 5 million cells/plate in 10 cm plates. The plates were pre-coated with poly-D-lysine (0.5 mg/ml) overnight at 37°C, followed by washing twice with dH2O. Neurons were maintained in neurobasal media (GIBCO) supplemented with L-glutamine, penicillin/streptomycin, and B27. Etoposide (ETP, 50µM, Sigma E1383) was dissolved in DMSO. Cells were treated by adding drug directly to the culture media 30 minutes prior to collection

extract_protocol:
SMC1 ChIP was performed for two biological replicates using a ChIP assay kit (MilliporeSigma) as described by the manufacturer. Briefly, DIV13 primary cortical neurons (~15M cells per replicate) were crosslinked with 1% formaldehyde for 10 minutes at 37°C, washed twice with ice-cold PBS, scraped, and resuspended in SDS lysis buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS, protease and phosphatase inhibitor cocktail). Cells were sonicated to shear DNA to 200-500 bp using a bioruptor (Diagenode; high power, 30 seconds on/30 seconds off for 40 cycles). Samples were then centrifuged at 13,000 RPM for 10 minutes at 4°C to remove cellular debris, and the supernatant was diluted up to 2 mL in ChIP dilution buffer (16.7 mM Tris-HCl pH 8, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS). Prior to immunoprecipitation, 1% of each sample transferred to a clean tube to be used for input normalization. Samples were then incubated with anti-SMC1 antibody (1:1000, Bethyl, A300-055A) overnight at 4°C followed by incubation with ChIP-grade protein A/G magnetic beads (Thermo) for 3 hours at 4°C. Antibody-conjugated beads were washed with low salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 150 mM NaCl), high salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 500 mM NaCl), LiCl buffer (10 mM Tris-HCl pH 8, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 0.25 M LiCl), and twice with TE buffer (50 mM Tris-HCl pH 8, 1 mM EDTA) for 5 minutes each with agitation at room temperature. Immunoprecipitated CTCF-DNA complexes were eluted from the magnetic beads in 500 µl ChIP elution buffer (1% SDS, 0.1 M NaHCO3). DNA-protein crosslinks for immunoprecipitated samples and input DNA were reversed via incubation with an additional 20 mM NaCl for 4 hours at 37°C and residual protein was digested with Proteinase K (NEB) for 1 hour at 45°C. DNA was precipitated using phenol/chloroform isolation and ethanol precipitation, washed with 70% ethanol, and resuspended in 50 µl TE buffer.
Samples were prepared for sequencing using a paired-end library preparation kit compatible with Illumina sequencing instruments (KAPA biosciences) according to the manufacturer’s instructions. Following library amplification, DNA fragment size was assessed via Tapestation (Agilent) to ensure a final library size of 350-450 bp. DNA concentration was quantified by fluorometry (dsDNA high sensitivity Qubit assay, Thermo) to ensure equal DNA concentration for each replicate before replicates were pooled and sequenced on an Illumina NextSeq 500 instrument using V2.5 reagents to an average depth of 25-35 million reads per replicate.

treatment_protocol: DIV13 primary cortical neurons were bath stimulated with 50 micromolar NMDA for 10 minutes followed by washout and recovery in drug-free media for 50 minutes prior to collection

tag: cell type

value: Mouse Cortical Neurons

value: NMDA


title: ileum, Control, 24 hrs, replicate 1


title: CN,SMC1_NMDA_Input_1


title: NGN3 Induced Overexspressing Organoid

description:
3D
NGN3_B2

value: jejunum

value: J2 NGN3

value: NGN3 Induced Overexspressing Organoid

value: Induced (+Dox)


title: young seurm infusion, chorolid plexus, 5

description:
C406
YS-infusion-CP.xlsx


title: ileum, Control, 24 hrs, replicate 5


title: NGN3 Uninduced Overexpressing Organoid

description:
3D
UINGN3_B2

value: NGN3 Uninduced Overexpressing Organoid

value: Uninduced (-Dox)


title: CN,SMC1_NMDA_ChIP_2

tag: antibody

value: anti-SMC1 antibody (1:1000, Bethyl, A300-055A)


title: CCS 1 human ileal organoid

description:
3D
I206D

value: ileum


title: young seurm infusion, chorolid plexus, 2

description:
C402
YS-infusion-CP.xlsx


title: Liver_control_rep3

description:
CNTRL.3
_raw_counts.csv.gz

value: Female

value: Balb/c

value: liver

value: Healthy

value: IP olive oil injection plus PBS tail vein injection

value: IP and tail vein injection twice a week for a fortnight


title: young seurm infusion, chorolid plexus, 3

description:
C403
YS-infusion-CP.xlsx

value: choroid plexus

value: WT


title: spleen, PBS inoculated, rep3

city: Hangzhou

first: Haiguang

last: Mao

state: Zhejiang

address: Yuhangtang Road 866

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: spleen

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: PBS inoculated


title: CN,SMC1_NMDA_ChIP_1

value: Mouse Cortical Neurons

value: NMDA


title: CN,SMC1_CON_Input_2


title: spleen, PBS inoculated, rep1


title: spleen, PBS inoculated, rep2


title: young seurm infusion, chorolid plexus, 1

description:
C401
YS-infusion-CP.xlsx


title: Non-CCS human ileal organoid

description:
3D
I109D

value: intestine

value: ileal organoid

value: healthy


title: Non-CCS human ileal organoid repeat

description:
3D
I109D_B2


title: young seurm infusion, hippocampus, 38

description:
H440
YS-infusion-H.xlsx

source_name: hippocampus

value: hippocampus


title: spleen, MPV-ACYW135 inoculated, rep3

value: MPV-ACYW135 inoculated


title: CN,SMC1_CON_Input_1


title: CCS 2 human colonic organoid

description:
3D
HJK_B2

value: colon

value: HJK

value: colonic organoid

value: CCS


title: young seurm infusion, hippocampus, 37

description:
H439
YS-infusion-H.xlsx


title: CN,SMC1_CON_ChIP_2

value: anti-SMC1 antibody (1:1000, Bethyl, A300-055A)


title: CCS 1 human colonic organoid repeat

description:
3D
C206D_B2


title: spleen, MPV-ACYW135 inoculated, rep2


title: young seurm infusion, hippocampus, 36

description:
H438
YS-infusion-H.xlsx


title: CN,SMC1_CON_ChIP_1


title: CCS 1 human colonic organoid

description:
3D
C206D


title: CN,CTCF_NMDA_Input_2

extract_protocol:
CTCF ChIP was performed for two biological replicates using a ChIP assay kit (MilliporeSigma) as described by the manufacturer. Briefly, DIV13 primary cortical neurons (~15M cells per replicate) were crosslinked with 1% formaldehyde for 10 minutes at 37°C, washed twice with ice-cold PBS, scraped, and resuspended in SDS lysis buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS, protease and phosphatase inhibitor cocktail). Cells were sonicated to shear DNA to 200-500 bp using a bioruptor (Diagenode; high power, 30 seconds on/30 seconds off for 40 cycles). Samples were then centrifuged at 13,000 RPM for 10 minutes at 4°C to remove cellular debris, and the supernatant was diluted up to 2 mL in ChIP dilution buffer (16.7 mM Tris-HCl pH 8, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS). Prior to immunoprecipitation, 1% of each sample transferred to a clean tube to be used for input normalization. Samples were then incubated with anti-CTCF antibody (1:200, CST, #3418) overnight at 4°C followed by incubation with ChIP-grade protein A/G magnetic beads (Thermo) for 3 hours at 4°C. Antibody-conjugated beads were washed with low salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 150 mM NaCl), high salt buffer (20 mM Tris-HCl pH 8, 1% Triton-X-100, 2 mM EDTA, 0.1% SDS, 500 mM NaCl), LiCl buffer (10 mM Tris-HCl pH 8, 1% IGEPAL-CA630, 1% deoxycholic acid (sodium salt), 1 mM EDTA, 0.25 M LiCl), and twice with TE buffer (50 mM Tris-HCl pH 8, 1 mM EDTA) for 5 minutes each with agitation at room temperature. Immunoprecipitated CTCF-DNA complexes were eluted from the magnetic beads in 500 µl ChIP elution buffer (1% SDS, 0.1 M NaHCO3). DNA-protein crosslinks for immunoprecipitated samples and input DNA were reversed via incubation with an additional 20 mM NaCl for 4 hours at 37°C and residual protein was digested with Proteinase K (NEB) for 1 hour at 45°C. DNA was precipitated using phenol/chloroform isolation and ethanol precipitation, washed with 70% ethanol, and resuspended in 50 µl TE buffer.
Samples were prepared for sequencing using a paired-end library preparation kit compatible with Illumina sequencing instruments (KAPA biosciences) according to the manufacturer’s instructions. Following library amplification, DNA fragment size was assessed via Tapestation (Agilent) to ensure a final library size of 350-450 bp. DNA concentration was quantified by fluorometry (dsDNA high sensitivity Qubit assay, Thermo) to ensure equal DNA concentration for each replicate before replicates were pooled and sequenced on an Illumina NextSeq 500 instrument using V2.5 reagents to an average depth of 25-35 million reads per replicate.


title: CN,CTCF_NMDA_Input_1


title: Non-CCS  human colonic organoid repeat

description:
3D
C109D_B2


title: young seurm infusion, hippocampus, 34

description:
H436
YS-infusion-H.xlsx


title: spleen, MPV-ACYW135 inoculated, rep1


title: Non-CCS  human colonic organoid

description:
3D
C109D


title: D5_IL6_6022

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

state: CA

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie against the human genome assembly GRCh38.
Assembly: GRCh38
Supplementary files format and content: TSV count matrices

source_name: monocyte

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

value: monocyte

tag: subject id

value: donor 5

value: IL6 10ng/ml + 18.7ng/ml IL6R


title: D4_IL6_6018

value: donor 4


title: young seurm infusion, hippocampus, 35

description:
H437
YS-infusion-H.xlsx

value: WT


title: D5_Control_6021

value: Control


title: young seurm infusion, hippocampus, 33

description:
H435
YS-infusion-H.xlsx


title: CN,CTCF_NMDA_ChIP_2

value: Mouse Cortical Neurons

value: NMDA

value: anti-CTCF antibody (1:200, CST, #3418)


title: CN,CTCF_NMDA_ChIP_1


title: EV168

city: PORTLAND

first: Hyun Ji

last: Kim

state: Oregon

address: 3181 SW Sam Jackson Park Rd.

institute: Oregon Health and Science University

data_processing:
STAR version 2.5.3a for alignment with --twopassMode Basic flag
Samtools version 1.15.1 for bam file sorting and indexing
deeptools v3.5.1 for generating bigwigs
Assembly: hg38 (ensembl v94)
Supplementary files format and content: bigwig files generated from aligned bam files

source_name: Human lung cancer plasma

extract_protocol:
Plasma/Serum Circulating and Exosomal RNA Purification Kit (Slurry Format)
SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian

tag: fraction

tag: age

tag: gender

value: Male


title: young seurm infusion, hippocampus, 32

description:
H434
YS-infusion-H.xlsx

tag: tissue

value: hippocampus

tag: genotype


title: D4_Control_6017

tag: treatment


title: CN,CTCF_CON_Input_2


title: EV166


title: young seurm infusion, hippocampus, 31

description:
H433
YS-infusion-H.xlsx


title: CN,CTCF_CON_Input_1


title: young seurm infusion, hippocampus, 30

description:
H432
YS-infusion-H.xlsx


title: EV165


title: D3_Control_6013

value: donor 3


title: CN,CTCF_CON_ChIP_2


title: D2_IL6_6010

value: donor 2


title: EV164


title: young seurm infusion, hippocampus, 27

description:
H429
YS-infusion-H.xlsx


title: EV163


title: young seurm infusion, hippocampus, 28

description:
H430
YS-infusion-H.xlsx


title: D2_Control_6009


title: CN,CTCF_CON_ChIP_1


title: D1_IL6_6006

value: donor 1


title: EV167


title: D1_Control_6005


title: D3_IL6_6014


title: SOC Day P16 3

city: Tel Aviv

first: Karen

last: Avraham

country: Israel

institute: TAU

data_processing:
Sequenced reads were mapped to the Mus musculus genome (mm10), using STAR v2.5.3a_modified.
Genes were identified using a .gtf obtained from GENCODE release 27. Per gene reads were counted using HTSeq.
Normalization and detection of differentially expressed genes were done using DEseq2.
Assembly: mm10
Supplementary files format and content: RNA-seq-SOC_coch_counts.txt: Tab-delimited text file includes counts for each Sample.

source_name: superior olivary complex

extract_protocol:
SOC - innuPrep miRNA Kit (Isolation of miRNAs and total RNA). SE - Direct-zolTM RNA Miniprep kit (Zymo Research, CA, USA).
SOC - Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Human/Mouse/Rat. SE - The NEBNext® Ultra II Directional RNA Library Prep Kit (Illumina) with NEBNext rRNA Depletion Kit v2.

value: superior olivary complex

value: neuronal

value: Day P16


title: EV161

source_name: Human multiple myeloma plasma


title: young seurm infusion, hippocampus, 26

description:
H428
YS-infusion-H.xlsx


title: SOC Day P16 1


title: EV162


title: young seurm infusion, hippocampus, 25

description:
H427
YS-infusion-H.xlsx


title: SOC Day P16 2


title: young seurm infusion, hippocampus, 24

description:
H426
YS-infusion-H.xlsx


title: HEB-3

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: Hypoxia Myr-EBIN-treated sample 3. The cells were cultured until endothelial monolayer was formed and then subjected to treatment with 1 µM Myr-EBIN for 3 h under 0.1% hypoxia growth conditions.

data_processing:
Raw reads were aligned to reference genome hg38 using STAR (Dobin et al., 2013). ENSEMBL gene expression was quantified using FeatureCounts (Liao et al., 2014).
Assembly: hg38
Supplementary files format and content: Tab-delimited text of gene expression counts (unnormalized)

source_name: human retinal microvascular endothelial cells in cell culture

growth_protocol: Human retinal microvascular endothelial cells were grown in endothelial growth media supplemented with commercial supplement packs and 10% FBS. Cells were maintained at 37 °C and 5% CO2.

extract_protocol:
Total RNA from HRECs challenged with normoxia or acute (3 h) hypoxia treated with vehicle or EBIN were isolated by RNeasy Plus kit (Qiagen, 74034). Concentrations of isolated RNA samples were measured using the Nanodrop 1000 (Thermo Fisher) at 260 nm. The quality of the isolated RNA was assessed by 260/280 optical density ratio to check for purity. Lastly, the RNA samples were reverse transcribed to cDNAs using a high-capacity cDNA reverse transcription kit (Thermo Fischer, 4368814). The resulting cDNAs were sent to the University of Chicago for bulk RNA sequencing.
The RNA quality and quantity was assessed using the Agilent bio-analyzer. All samples showed RNA integrity number > 8. Strand-specific RNA-SEQ libraries were prepared using a TruSEQ mRNA RNA-SEQ library protocol (Illumina provided). Library quality and quantity was assed 32 using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000 (Illumina provided reagents and protocols).

treatment_protocol: Human retinal microvascular endothelial cells were treated with 1 µM Myr-EBIN or Myr-control peptides once prior to incubation under either normoxic or acute hypoxia.

tag: hypoxia

value: hypoxia

value: peptide


title: HEB-2

description: Hypoxia Myr-EBIN-treated sample 2. The cells were cultured until endothelial monolayer was formed and then subjected to treatment with 1 µM Myr-EBIN for 3 h under 0.1% hypoxia growth conditions.

value: human retinal microvascular endothelial cells in cell culture


title: SOC Day P0 4

value: Day P0


title: EV160


title: EV159


title: young seurm infusion, hippocampus, 23

description:
H425
YS-infusion-H.xlsx

value: WT


title: young seurm infusion, hippocampus, 29

description:
H431
YS-infusion-H.xlsx


title: HEB-1

description: Hypoxia Myr-EBIN-treated sample 1. The cells were cultured until endothelial monolayer was formed and then subjected to treatment with 1 µM Myr-EBIN for 3 h under 0.1% hypoxia growth conditions.

value: vehicle


title: EV158


title: SOC Day P0 3


title: young seurm infusion, hippocampus, 22

description:
H424
YS-infusion-H.xlsx


title: Pool of 3 brain lesions from 482N1

city: Madrid

first: Manuel

last: Valiente

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIO

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
STARSolo
Assembly: GRCm39
Supplementary files format and content: Data matrices form STARSolo output

source_name: Brain

extract_protocol:
Resected brain lesions were processed with the Brain Tumor Dissociation Kit (Miltenyi, ref. 130-095-942) using gentleMACS C Tubes (Miltenyi, ref. 130-093-237) and the gentleMACS™ Octo Dissociator (Miltenyi, ref.  130-096-427). For myelin removal and red cells lysis, reagents from the Adult Brain Dissociation Kit (Miltenyi, ref. 130-107-677) were used. To isolate cancer cells, single cell suspension was sorted based on GFP expression.
Cell sample was processed with the "Chromium Next GEM Single Cell 3' Reagent Kits v3.1" (10xGenomics PN-1000268). Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, cDNA amplification and library construction were all performed as recommended by the manufacturer.

value: cancer cells

value: Brain

tag: strain

value: 14 weeks old


title: EV157

value: Male


title: SOC Day P0 2


title: HCo-3

description: Hypoxia control sample 3. The cells were cultured until endothelial monolayer was formed and then subjected to treatment with 1 µM control peptide (2T-A mutant of EBIN) for 3 h under 0.1% hypoxia growth conditions.


title: HCo-2

description: Hypoxia control sample 2. The cells were cultured until endothelial monolayer was formed and then subjected to treatment with 1 µM control peptide (2T-A mutant of EBIN) for 3 h under 0.1% hypoxia growth conditions.


title: young seurm infusion, hippocampus, 21

description:
H423
YS-infusion-H.xlsx

value: hippocampus


title: young seurm infusion, hippocampus, 20

description:
H422
YS-infusion-H.xlsx


title: SOC Day P0 1


title: EV149

source_name: Human liver cancer plasma


title: SOC Day E16 4

value: Day E16


title: EB-2

description: Normoxia Myr-EBIN-treated sample 2. The cells were cultured until endothelial monolayer was formed and then subjected to treatment with 1 µM Myr-EBIN for 3 h under normal growth normoxia conditions.

value: normoxia


title: EV150


title: SOC Day E16 3


title: young seurm infusion, hippocampus, 18

description:
H419
YS-infusion-H.xlsx


title: SOC Day E16 2


title: EV147


title: Co-2

description: Normoxia control sample 2. The cells were cultured until endothelial monolayer was formed and then subjected to treatment with 1 µM control peptide (2T-A mutant of EBIN) for 3 h under normal growth normoxia conditions.


title: EV148


title: EB-1

description: Normoxia Myr-EBIN-treated sample 1. The cells were cultured until endothelial monolayer was formed and then subjected to treatment with 1 µM Myr-EBIN for 3 h under normal growth normoxia conditions.


title: young seurm infusion, hippocampus, 17

description:
H418
YS-infusion-H.xlsx


title: young seurm infusion, hippocampus, 16

description:
H417
YS-infusion-H.xlsx


title: SOC Day E16 1


title: Cochlea Day P16 3

source_name: cochlea

value: cochlea

value: inner ear sensory epithelium


title: Co-1

description: Normoxia control sample 1. The cells were cultured until endothelial monolayer was formed and then subjected to treatment with 1 µM control peptide (2T-A mutant of EBIN) for 3 h under normal growth normoxia conditions.


title: young seurm infusion, hippocampus, 15

description:
H416
YS-infusion-H.xlsx


title: EV144

value: Female


title: HCo-1

description: Hypoxia control sample 1. The cells were cultured until endothelial monolayer was formed and then subjected to treatment with 1 µM control peptide (2T-A mutant of EBIN) for 3 h under 0.1% hypoxia growth conditions.


title: Cochlea Day P16 2

value: Day P16


title: young seurm infusion, hippocampus, 19

description:
H421
YS-infusion-H.xlsx


title: Cochlea Day P16 1


title: Cortical epithelial cells

city: London

first: Paola

last: Bonfanti

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts for each library
Features were annotated using the cellranger count pipeline.
Assembly: GRCh38/hg19
Supplementary files format and content: Raw read count matrix for each sample in form of the Cell Ranger matrix, features and barcodes files.

source_name: Thymus donor

growth_protocol: Tissue was processed fresh after cardiothoracic surgery

extract_protocol:
Thymic tissue was dissociated to single cells by enzymatic treatment . Single cell suspension was depleted of CD45 and CD235ab (red blood) expressing cells by immunomagnetic separation. The enriched fraction was stained for cortical (EpCAMlowCD205Pos) and medullary  (EpCAMhighCD205neg) thymic epithelial cells (TEC) and further separated based on CD49f expression
RNA libraries were prepared for sequencing using Chromium Single Cell 3' v3 protocol; cDNA amplification involved 12 PCR cycles

treatment_protocol: Tissue was digsted with collagenase and dispase at single-cell level, stained form epithlial markers and 4 epithelial populations separated by FACS analysis based on surface markers expression

tag: Stage

value: paediatric

tag: Sex

value: female

value: Cortical epithelial cells


title: young seurm infusion, hippocampus, 14

description:
H415
YS-infusion-H.xlsx


title: EV143


title: young seurm infusion, hippocampus, 13

description:
H413
YS-infusion-H.xlsx


title: EV142


title: EV146


title: Cochlea Day P0 3

value: Day P0


title: young seurm infusion, hippocampus, 12

description:
H412
YS-infusion-H.xlsx

value: WT


title: Medullary epithelial cells CD49f+

value: Medullary epithelial cells CD49f+


title: Cochlea Day P0 1


title: EV140


title: EV145


title: Cochlea Day P0 2


title: Bulk thymic progenitor and stem cells Replicate 2

source_name: Thymus donor 2

growth_protocol: thymic and skin epithelial progenitor and stem cells have been expanded for 4 passages on feeder layer

extract_protocol:
Cells have been trypsinised subconfluent at day 5 after mechanical removal of mouse feeder layer
RNA libraries were prepared for sequencing using Chromium Single Cell 3' v3 protocol

value: Bulk thymic progenitor and stem cells


title: Bulk thymic progenitor and stem cells Replicate 1

source_name: Thymus donor 1

value: male


title: Cochlea Day E16 3


title: young seurm infusion, hippocampus, 11

description:
H411
YS-infusion-H.xlsx


title: EV139


title: Bulk skin keratinocyte progenitor and stem cells Replicate 1

source_name: Skin donor 1

value: adult


title: EV138

source_name: Human healthy control plasma

value: Male


title: young seurm infusion, hippocampus, 10

description:
H410
YS-infusion-H.xlsx

value: hippocampus


title: Cortical epithelial cells CD49f+

value: Cortical epithelial cells CD49f+


title: Medullary epithelial cells

value: Medullary epithelial cells


title: young seurm infusion, hippocampus, 8

description:
H408
YS-infusion-H.xlsx


title: Cochlea Day E16 2

value: cochlea

value: Day E16


title: EV137


title: EV136


title: Medullary derived thymic progenitor and stem cells Replicate 1


title: PT12_27 GFP_H_3

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

data_processing:
FastQC + Trimming (trimagalore v0.5.0)
reads alignment with STAR (v2.7.0d)
featurecounts v1.6.3 (min overlap 10 + nochimera + uniquely mapping)
Assembly: GRCh38 gencodegenes primary assembly
Supplementary files format and content: tab-delimited file

source_name: Xenograft BALL blasts

extract_protocol:
PDX`s bm derived GFPhigh(miR-126low) and GFPlow(miR-126high) cells were freshly sorted andprocessed for transcriptomic analysis by RNAseq
Sequencing libraries were produced with SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Mountain View, CA, USA), as per manufacturer’s instructions

tag: cell population

value: Xenograft BALL blasts

tag: donor


title: Medullary derived thymic progenitor and stem cells Replicate 2


title: EV141

value: Female


title: Cortical derived thymic progenitor and stem cells Replicate 2

value: paediatric


title: PT12_27 GFP_L_3


title: young seurm infusion, hippocampus, 6

description:
H406
YS-infusion-H.xlsx


title: young seurm infusion, hippocampus, 5

description:
H405
YS-infusion-H.xlsx


title: EV135


title: PT12_27 GFP_H_2


title: young seurm infusion, hippocampus, 9

description:
H409
YS-infusion-H.xlsx


title: young seurm infusion, hippocampus, 4

description:
H404
YS-infusion-H.xlsx


title: EV134


title: PT12_27 GFP_L_2


title: cultivated skin epithelial progenitor and stem cells

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts for each library
Assembly: GRCh38/hg19
Supplementary files format and content: Raw read count matrix for each sample in form of the Cell Ranger matrix, features and barcodes files.

source_name: healthy adult donor

growth_protocol: epithelial progenitor and stem cells from airways and skin have been expanded for 3 passages on feeder layer

extract_protocol:
Cells have been trypsinised subconfluent at day 7 and stained to be FACS sorted and separated from mouse feeder layer
RNA libraries were prepared for sequencing using Chromium Single Cell 3' v3 protocol

value: female

tag: culture method

value: 2D culture on feeder layer


title: Cortical derived thymic progenitor and stem cells Replicate 1


title: EV126


title: cultivated airways epithelial progenitor and stem cells

description: NHBE-A


title: Cochlea Day E16 1

value: inner ear sensory epithelium


title: PT12_27 GFP_H_1


title: young seurm infusion, hippocampus, 7

description:
H407
YS-infusion-H.xlsx

extract_protocol:
Mice were anesthetized by intraperitoneal injection using Avertin (250 mg/kg of body weight). Blood was collected from the right ventricle, followed by trans-cardiac perfusion through the left ventricle with 20 mL of cold 0.1 M phosphate buffered saline (PBS), pH 7.4. Brain was removed and divided into hemispheres. One hemisphere was dissected into the hippocampus and choroid plexus and flash frozen on dry ice for bulk RNA-seq.
RNA was isolated from cortex and purified using RNeasy mini kit (Qiagen) per the manufacturer’s protocol. RNA quality was assessed using 2100 Bioanalyzer (Agilent Technologies) and samples with RIN > 8 were further used for sequencing. Sequencing libraries were generated by Novogene.

value: WT


title: young seurm infusion, hippocampus, 2

description:
H402
YS-infusion-H.xlsx


title: cultivated thymic epithelial progenitor and stem cells from Replicate 2

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts for each library
Features were annotated using the cellranger count pipeline. The two independent sequencing runs for HuTEC135 and HuTEC136 were merged using cellrnager aggregate.
Assembly: GRCh38/hg19
Supplementary files format and content: Raw read count matrix for each sample in form of the Cell Ranger matrix, features and barcodes files.

growth_protocol: thymic epithelial progenitor and stem cells have been expanded for 3 passages on feeder layer


title: PT12_27 GFP_L_1


title: young seurm infusion, hippocampus, 1

description:
H401
YS-infusion-H.xlsx


title: EV125


title: PT10_395 GFP_L_3


title: EV124


title: cultivated thymic epithelial progenitor and stem cells from Replicate 1


title: WT, young, 4

description:
Wty4
klotho-ko-het.xlsx

source_name: brain

value: brain


title: PT10_395 GFP_H_3


title: EV123


title: young seurm infusion, hippocampus, 3

description:
H403
YS-infusion-H.xlsx

source_name: hippocampus


title: WT, young, 3

description:
Wty3
klotho-ko-het.xlsx


title: PT10_395 GFP_L_2


title: Calycosin and Tanshinone IIA 3

city: 济南市

first: 燕云

last: 江

state: 山东省

address: 山东省济南市长清区

institute: 山东中医药大学

description: Rat renal artery endothelial cells, maodan, 3

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mRatBN7.2

organism: Rattus norvegicus

source_name: Rat renal artery endothelial cells

growth_protocol: RRAECs were cultured in Dulbecco's modified Eagle medium (DMEM, Cat. No. C11995500CP, Gibco, Thermo Fisher Scientific, Inc.) supplemented with 10% fetal bovine serum (FBS, Cat. No. 2123971P, Gibco, Thermo Fisher Scientific, Inc.) and 1% penicillin and streptomycin (P/S, Cat. No.S110VJ, Shanghai Yuanpei Biotechnology Co., Ltd) at a temperature of 37 °C in a 5% CO2, water-saturated atmosphere. Once the cells reached a dense monolayer with a coverage rate of 75%-85%, they were digested using 0.25% trypsin-EDTA (Cat. No. ma0233, meilunbio) and routinely passaged every 2-3 days. Cells from the 2nd to 8th passage were utilized for subsequent experiments.

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen, Germany). Strand-specific libraries were generated using the TruSeq® Stranded Total RNA Sample Preparation kit (Illumina, USA) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Rat renal artery endothelial cells

value: endothelial cells

tag: condition

value: Calycosin and Tanshinone IIA treatment


title: Calycosin and Tanshinone IIA 2

description: Rat renal artery endothelial cells, maodan, 2

tag: cell type


title: WT, young, 2

description:
Wty2
klotho-ko-het.xlsx

data_processing:
FASTQ TO BAM
FEATURECOUNTS
EDGER
Assembly: mm10
Supplementary files format and content: raw expresison counts from featurecounts


title: Calycosin and Tanshinone IIA 1

description: Rat renal artery endothelial cells, maodan, 1


title: EV122

source_name: Human lung cancer plasma


title: EV133

value: Male


title: Model 3

description: Rat renal artery endothelial cells, Moxing, 3

value: Model


title: EV121


title: PT10_395 GFP_L_1


title: EV120


title: Model 2

description: Rat renal artery endothelial cells, Moxing, 2


title: PT10_395 GFP_H_2


title: WT, old, 4

description:
Wto5
klotho-ko-het.xlsx


title: PT10_395 GFP_H_1


title: WT, old, 3

description:
Wto3
klotho-ko-het.xlsx


title: WT, young, 1

description:
Wty1
klotho-ko-het.xlsx


title: EV118


title: EV119


title: H1650 siMena replicate 2

city: Rome

first: Lorenzo

last: D'Ambrosio

address: Via Elio Chianesi 53

department: Dept. Of Research, Advanced Diagnostic, and Technological Innovation

institute: Regina Elena National Cancer Institute, IRCCS

data_processing:
ATAC profiles were aligned to the reference genome hg19. Reads were quality controlled with FastQC v0.11.5 and aligned to the reference genome using bowtie 2.3.4.2 [30] with default parameters. The generated sequence alignments were converted into binary files (BAM), then sorted and indexed using the SAMtools V1.7 [34]. ATAC-seq peaks were generated using MACS v2.2.5 [35] with parameters ‘--nomodel --shift -100 --extsize 200 -B --SPMR --call-summits -q 0.01’.
Assembly: hg19
Supplementary files format and content: Narrow peaks in bed format

growth_protocol: Human lung H1650 cells were maintained in RPMI 1640 Medium (Euroclone), supplemented with 10% fetal bovine serum (Euroclone), 1% Glutamine, 1% Penicillin/Streptomycin (Euroclone), and incubated at 37°C in a 5% CO2 air-humidified atmosphere.

extract_protocol:
Total RNA was harvested using Qiazol (Qiagen), purified from DNA contamination through DNase I (Qiagen) and enriched by  RNeasy (Qiagen) columns for gene expression profiling. Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies, DE) and by Agilent 2100 Bioanalyzer (Agilent Technologies, CA), respectively.
To investigate chromatin accessibility dynamics, the ATAC-seq protocol developed by Buenrostro et al. was used, with minor modifications

treatment_protocol: 3 × 10^5 cells/well in exponential growth phase were plated in 6-well plates. The next day, cells were transfected with 20 nmol/L of hMENA(t)-specific pooled siRNA duplexes (siGENOME SMARTpool Human ENAH), or 20 nmol/L of mix of three siRNAs each matching 21 nucleotides within the 11a exon sequences (51) or 20nmol/l of ON-TARGETplus Nontargeting Control Pool (GEHealthcare, Dharmacon, Lafayette, CO, USA) using Lipofectamine® RNAiMAX Transfection Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.

value: Human Non-Small Cell Lung Cancer

value: hMena siRNA


title: WT, old, 2

description:
Wto2
klotho-ko-het.xlsx


title: Normal 3

description: Rat renal artery endothelial cells, zhengchang, 3

value: Normal


title: EV117


title: Model 1

description: Rat renal artery endothelial cells, Moxing, 1


title: H1650 siMena replicate 1


title: Klotho ko, young, 4

description:
Klko4
klotho-ko-het.xlsx

value: Klko


title: WT, old, 1

description:
Wto1
klotho-ko-het.xlsx


title: EV116


title: Normal 1

description: Rat renal artery endothelial cells, zhengchang, 1


title: H1650 siMena11a replicate 2

value: hMena11a siRNA


title: Normal 2

description: Rat renal artery endothelial cells, zhengchang, 2


title: WT

city: Beijing

first: Shuyan

last: Yang

address: 2# Yabao Road

institute: Children's Hospital of Capital Institute of Pediatrics

data_processing:
For gene expression analysis, the matched reads were calculated and then normalized to RPKM using RESM software
The significance of the differential expression of genes was defined by the bioinformatics service of BGI according to the combination of the absolute value of log2 Ratio ≥1 and FDR ≤ 0.001.
Library construction and sequencing were performed on a BGISEQ-500.
Assembly: GRCz10.81
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

organism: Danio rerio

source_name: erythroblast

extract_protocol:
Total RNA was isolated using SMART-Seq® HT Kit.
Library construction and sequencing were performed on a BGISEQ-500 by CapitalBio Technology (www.capitalbiotech.com, Beijin, China). Clean-tags were mapped to the reference genome and genes available at the Zebrafish Genome.

value: erythroblast

value: wildtype


title: H1650 siMena11a replicate 1


title: Klotho ko, young, 3

city: Pittsburgh

first: Iliya

last: Lefterov

institute: University of Pittsburgh

description:
Klko3
klotho-ko-het.xlsx


title: MT

value: add1 knockout


title: H1650 siControl replicate 1

value: Control siRNA


title: EV114

source_name: Human multiple myeloma plasma

value: Female


title: EV112


title: YUC9oe, infected, biol rep 3

city: Pozuelo de Alarcón

first: Stephan

last: Pollmann

state: Madrid

address: Campus de Montegancedo, Autovia M-40 (km 38)

institute: CBGP (UPM-INIA/CSIC)

data_processing:
Novogene Novogene Co., LTD Genomics Service (Cambridge, UK)
Original image data files from the Illumina platform were transformed to sequenced reads by CASAVA base recognition.
Sequence reads were trimmed for the adaptor sequence/low-quality reads were deleted using a Novogene in-house script (quality parameter limit: 0.05)
Trimmed sequence reads were mapped against the TAIR10 Arabidopsis genome using hisat2 v2.0.5.
Read count extraction and normalization was performed using the featureCounts v1.5.0-p3 application.
Assembly: TAIR10 Arabidopsis genome
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: Roots

growth_protocol: Seedlings were grown vertically for seven days on 0.5x MS medium. Then, they were transferred to solidified Plant Nutrition Medium. Root tissue was harvested after teen days.

extract_protocol:
DNA-free total RNA was extracted by employing the phenol/chloroform method described by Oñate-Sánchez & Vicente-Carbajosa, 2008, BMC Res. Notes.
Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s recommendations.

treatment_protocol: Each seedling was either mock-infected (50 µl water) or inoculated with 50 µl of a solution containing 2 x 105 spores ml-1.

value: Roots

value: YUC9 overexpressor

value: S. indica infected


title: EV111


title: EV113


title: Klotho ko, young, 1

address: 130 De Soto St

description:
Klko1
klotho-ko-het.xlsx

value: brain


title: H1650 untreated replicate 2

value: Untreated


title: H1650 siControl replicate 2


title: YUC9oe, infected, biol rep 1


title: Klotho het, old, 5

description:
HET7
klotho-ko-het.xlsx

value: Klhet


title: Klotho het, old, 4

description:
HET6
klotho-ko-het.xlsx


title: EV115

value: Male


title: EV110


title: SiMENA11a rep 3

data_processing:
All data processing was conducted through RNA-Seq Analysis Pipeline (RAP) webtool  (D’Antonio et al. BMC Genomics, 2015), with default parameters.
Assembly: hg19
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

extract_protocol:
Total RNA was harvested using Qiazol (Qiagen), purified from DNA contamination through DNase I (Qiagen) and enriched by  RNeasy (Qiagen) columns for gene expression profiling. Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies, DE) and by Agilent 2100 Bioanalyzer (Agilent Technologies, CA), respectively.
RNA libraries for sequencing were generated  using 500ng of RNA for each sample according to the Illumina TruSeq Stranded Total RNA kit with an initial ribosomal depletion step using Ribo Zero Gold (Illumina, CA). Libraries were quantified by qPCR and sequenced in paired-end mode (2x75 bp) with NextSeq 500 (Illumina, CA).

value: Human Non-Small Cell Lung Cancer

value: transfection with hMENA11a siRNA pool

tag: time

value: Day 3


title: Klotho het, old, 3

description:
HET5
klotho-ko-het.xlsx


title: YUC9oe, mock, biol rep 3

value: Control


title: Klotho het, old, 2

description:
HET3
klotho-ko-het.xlsx


title: EV109

tag: fraction


title: SiMENA11a rep 2


title: SiMENA11a rep 1


title: EV101

tag: age


title: Klotho ko, young, 2

description:
Klko2
klotho-ko-het.xlsx

value: Klko


title: EV102

tag: gender


title: Klotho het, old, 1

description:
HET2
klotho-ko-het.xlsx

tag: tissue


title: YUC9oe, mock, biol rep 1

tag: genotype


title: YUC9oe, infected, biol rep 2

tag: treatment


title: H1650 untreated replicate 1


title: EV100


title: SiMENA rep 2

value: transfection with hMENA(t) siRNA pool


title: SiMENA rep 1


title: Vehicle, mRNA-derived cDNA

city: Birmungham

first: Vipul

last: Sheth

state: AL

address: 2173 highland ave drive

institute: UAB

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and ADT barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT sequences were concatenated and treated as Custom library with default settings (v7.0.0) and aligning to the mm10 genome build.
Assembly: mm10
Supplementary files format and content: 10X Genomics output files: *_barcodes.tsv.gz, *_features.tsv.gz, *_matrix.mtx.gz

source_name: Bone marrow

extract_protocol:
LSK (Lin-FLT3-C-kit+Sca-1+) were freshly isolated(FACS) from the BM of vehicle/Nilotinib/Hifi/Hifi+Nilotinib treated CML mice (4 replicates per group)
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Bone marrow

value: LSK cells

value: transgenic SCL-tTA/BCR-ABL (BA) mouse model

value: CML vehicle 14 days

tag: library type

value: mRNA

tag: antibodies/tags

value: Vehicle_1/TotalSeq-B0301 ; Vehicle_2/TotalSeq-B0302 ; CD16/32/TotalSeq-B0109 ; CD48/TotalSeq-B0429 ; CD150/TotalSeq-B0203 ; CD34/TotalSeq-B0857 ; CD135/TotalSeq-B0098 ; CD201/TotalSeq-B0439


title: Vehicle2, ADT-derived cDNA

description: Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

library_source: other

molecule: protein

value: ADT

value: Vehicle2_1/TotalSeq-B0301 ; Vehicle2_2/TotalSeq-B0302 ; CD16/32/TotalSeq-B0109 ; CD48/TotalSeq-B0429 ; CD150/TotalSeq-B0203 ; CD34/TotalSeq-B0857 ; CD135/TotalSeq-B0098 ; CD201/TotalSeq-B0439


title: EV099


title: WT, infected, biol rep 3

value: Roots

value: S. indica infected


title: WT, infected, biol rep 2


title: WT, infected, biol rep 1


title: EV098

value: Male


title: YUC9oe, mock, biol rep 2

value: YUC9 overexpressor


title: EV097


title: Vehicle2, mRNA-derived cDNA


title: Control rep 3

value: Human Non-Small Cell Lung Cancer

value: Control:transfection with non-targeting RNA pool


title: Control rep 2

value: Day 3


title: WT, mock, biol rep 3

value: Control


title: TK1, ADT-derived cDNA

value: CML TKI 14 days

value: TK1_1/TotalSeq-B0301 ; TK1_2/TotalSeq-B0302 ; CD16/32/TotalSeq-B0109 ; CD48/TotalSeq-B0429 ; CD150/TotalSeq-B0203 ; CD34/TotalSeq-B0857 ; CD135/TotalSeq-B0098 ; CD201/TotalSeq-B0439


title: WT, mock, biol rep 2


title: WT, mock, biol rep 1


title: TK1, mRNA-derived cDNA

value: Bone marrow

value: LSK cells


title: EV095

source_name: Human liver cancer plasma


title: Control rep 1


title: TK1_2, ADT-derived cDNA

value: transgenic SCL-tTA/BCR-ABL (BA) mouse model

value: TK1_2_1/TotalSeq-B0301 ; TK1_2_2/TotalSeq-B0302 ; CD16/32/TotalSeq-B0109 ; CD48/TotalSeq-B0429 ; CD150/TotalSeq-B0203 ; CD34/TotalSeq-B0857 ; CD135/TotalSeq-B0098 ; CD201/TotalSeq-B0439


title: SiMENA rep 3

value: transfection with hMENA(t) siRNA pool


title: EV094


title: Vehicle, ADT-derived cDNA

value: CML vehicle 14 days

value: ADT

value: Vehicle_1/TotalSeq-B0301 ; Vehicle_2/TotalSeq-B0302 ; CD16/32/TotalSeq-B0109 ; CD48/TotalSeq-B0429 ; CD150/TotalSeq-B0203 ; CD34/TotalSeq-B0857 ; CD135/TotalSeq-B0098 ; CD201/TotalSeq-B0439


title: Transcriptional BIK treatment

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

description: Cotyledon tissue of 5-d-old-seedlings Arabidopsis thaliana Col-0, TMMpro:GFP line, treated with 50 µM BIK for 2h

data_processing:
Demultiplexing; Cell Ranger mkfastq; version 3.1.0
Read alignment + counting; Cell Ranger count; version 3.1.0
Genome_build: TAIR 10; Ensembl Plants, release 40
Supplementary_files_format_and_content: h5 file containing filtered count matrix (output Cell Ranger count)

source_name: cotyledon

growth_protocol: All seeds were surface sterilized, sown on solid 1⁄2 MS plates without sucrose, and stratified for 24h at 4°C two days before they were grown at 22°C in a 16 h light/8 h dark photoperiod.

extract_protocol:
The whole aerial tissue of the Arabidopsis seedlings was harvested and incubated in protoplasting solution (1.5% (wt/vol) cellulose YC, 0.15% (wt/vol) pectolyase, 0.4 M mannitol, 20 mM KCl, 10 mM CaCl2, 0.1% (wt/vol) BSA, 20 mM MES, pH 5.7). After 1 h gentle shaking, cells were filtered through a 70 μm cell strainer and spun down at 100 × g for 6 min. Pelleted protoplasts were resuspended with washing solution (0.4 M mannitol, 20 mM KCl, 10 mM CaCl2, 0.1% (wt/vol) BSA, 20 mM MES, pH 5.7), and filtered through a 40 μm cell strainer. The protoplasts were then sorted on a BD FACSAria II based on the GFP signal.
Sorted cells were centrifuged at 400g at 4ºC for 5 minutes and resuspended in washing solution to yield an estimated concentration of 1,000 cells/µl. Cellular suspensions were loaded on either a GemCode Single Cell 3′ Gel Bead and Library Kit (V2 chemistry, 10X Genomics) for the control experiment, or a Chromium Single Cell 3’ GEM, Library & Gel Bead Kit (V3 chemistry, 10X Genomics) for the treatment experiment according to the manufacturer’s instructions.
scRNA-seq

treatment_protocol: 5 dpg Arabidopsis seedlings expressing TMMpro::GFP were immersed in liquid ½ MS medium supplemented with 1 μM BL, 50 μM BIK or 0.1% DMSO for 2 h.

tag: ecotype

tag: line

value: 50 µM BIK


title: HIF, ADT-derived cDNA

value: CML HIFi 14 days

value: HIF_1/TotalSeq-B0303 ; HIF_2/TotalSeq-B0304 ; CD16/32/TotalSeq-B0109 ; CD48/TotalSeq-B0429 ; CD150/TotalSeq-B0203 ; CD34/TotalSeq-B0857 ; CD135/TotalSeq-B0098 ; CD201/TotalSeq-B0439


title: Transcriptional DMSO control

description: Cotyledon tissue of 5-d-old-seedlings Arabidopsis thaliana Col-0, TMMpro:GFP line, treated with 0.1% DMSO for 2h

value: 0.1% DMSO


title: EV093

value: Male


title: TK1_2, mRNA-derived cDNA

value: mRNA


title: EV092


title: EV090

value: Female


title: HIF, mRNA-derived cDNA


title: Translational control

description: Cotyledon tissue of 5-d-old-seedlings Arabidopsis thaliana Col-0, TMMpro:TMM-GFP line in control conditions


title: HIF_2, ADT-derived cDNA

value: HIF_2_1/TotalSeq-B0303 ; HIF_2_2/TotalSeq-B0304 ; CD16/32/TotalSeq-B0109 ; CD48/TotalSeq-B0429 ; CD150/TotalSeq-B0203 ; CD34/TotalSeq-B0857 ; CD135/TotalSeq-B0098 ; CD201/TotalSeq-B0439


title: Transcriptional BL treatment

description: Cotyledon tissue of 5-d-old-seedlings Arabidopsis thaliana Col-0, TMMpro:GFP line, treated with 1 µM BL for 2h

value: 1 µM BL


title: HIF_2, mRNA-derived cDNA

value: Bone marrow


title: EV089


title: Neonatal Shank3(+/+) skeletal muscle (4)

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

country: Germany

institute: University of Ulm

data_processing:
Raw reads were mapped to the UCSC mouse  genome version 10 (mm10) using HISAT2  (Kim et al., 2015, 2019; Pertea et al., 2016; http://daehwankimlab.github.io/hisat2/; version 2.2.1).
Count matrix generated using  featureCounts (Liao et al., 2014;  https://subread.sourceforge.net; version 2.0.1).
Assembly: mm10 / GRCm38, Ensembl
Supplementary files format and content: Count matrix (text file matrix containing counts for all samples); Count_matrix.txt

extract_protocol: RNA extraction, library preparation,  cluster generation and sequencing were  executed at the Eurofins Genomics  Germany GmbH. Initially, 1 ng/µl of RNA  per sample was used for RNA sampling

value: gastrocnemius muscle at postnatal day 0-1

tag: strain background

value: skeletal muscle

value: postnatal day 0-1


title: HUVECs, siCD44-2

type: RNA

city: Zhengzhou

first: Lu

last: Zhang

state: Henan

address: Henan University of Technology, Lianhua Street, Zhengzhou

institute: Henan University of Technology

description: RMA expression value derived from Affymetrix Gene X.0 ST array Serviceanalysis

hyb_protocol: Samples were hybridized with  GeneChip® Gene1.0 ST Arrays (Affymetrix) and scanned at the UCLA Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with Affymetrix Gene X.0 ST array Service  for background correction and normalization.  Genes with >    twofold changes and both the false discovery rate (FDR, q) and the Wilcoxon rank-sum test significance level (p) <0.05 were considered significantly regulated.

label: biotin

source_name: Human umbilical vein endothelial cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: HUVECs cells were maintained in ECM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen, 15596-018) according to the manufacturer's instructions from the HUVECs.  1.5μg of total RNA was used for the Microarray assays.

treatment_protocol: The cells in the logarithmic growth stage were evenly spread in the plate. After the cell growth reached 70%, the cells were transfected with 50nM sicontorl RNA or siCD44 RNA (invitrogen) for 24h.

value: Human umbilical vein endothelial cells


title: EV091

data_processing:
STAR version 2.5.3a for alignment with --twopassMode Basic flag
Samtools version 1.15.1 for bam file sorting and indexing
deeptools v3.5.1 for generating bigwigs
Assembly: hg38 (ensembl v94)
Supplementary files format and content: bigwig files generated from aligned bam files

extract_protocol:
Plasma/Serum Circulating and Exosomal RNA Purification Kit (Slurry Format)
SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian


title: Combo, ADT-derived cDNA

value: LSK cells

value: transgenic SCL-tTA/BCR-ABL (BA) mouse model

value: CML TKI+HIFi 14 days

value: Combo_1/TotalSeq-B0303 ; Combo_2/TotalSeq-B0301 ; CD16/32/TotalSeq-B0109 ; CD48/TotalSeq-B0429 ; CD150/TotalSeq-B0203 ; CD34/TotalSeq-B0857 ; CD135/TotalSeq-B0098 ; CD201/TotalSeq-B0439


title: EV088


title: Neonatal Shank3Δ11(-/-) skeletal muscle (5)


title: HUVECs, siControl

value: siControl


title: HUVECs, siCD44-1


title: EV096


title: Combo, mRNA-derived cDNA


title: Neonatal Shank3(+/+) skeletal muscle (1)


title: EV087


title: Neonatal Shank3(+/+) skeletal muscle (2)


title: fibroblast 4

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

hyb_protocol: Hybridisation and washing of slides was carried out according to Agilent's protocol for gene expression microarrays.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Raw intensities were imported into R using the Biocinductor package Agi4x44PreProcess. Data were quality filtered using default parameters followed by quantile normalization.

source_name: fibroblast

label_protocol: Labelling of samples was carried out according to Agilent's protocol (low input).

extract_protocol: Simultaneous DNA and RNA extraction using the AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. Isolated DNA was quantified using the Qubit 2.0 fluorometer.

value: fibroblast


title: Neonatal Shank3(+/+) skeletal muscle (3)


title: fibroblast 3


title: Neonatal Shank3Δ11(-/-) skeletal muscle (4)


title: Combo2, ADT-derived cDNA

value: ADT

value: Combo2_1/TotalSeq-B0303 ; Combo2_2/TotalSeq-B0304 ; CD16/32/TotalSeq-B0109 ; CD48/TotalSeq-B0429 ; CD150/TotalSeq-B0203 ; CD34/TotalSeq-B0857 ; CD135/TotalSeq-B0098 ; CD201/TotalSeq-B0439


title: Combo2, mRNA-derived cDNA

value: mRNA


title: fibroblast 2


title: fibroblast 1


title: EV085

value: Female


title: Neonatal Shank3Δ11(-/-) skeletal muscle (2)


title: vascular wall-derived stem cell 4

source_name: mesenchymal stem cell

value: mesenchymal stem cell


title: Neonatal Shank3Δ11(-/-) skeletal muscle (1)


title: EV084


title: vascular wall-derived stem cell 2


title: vascular wall-derived stem cell 3


title: Control R1

city: St. Louis

first: Spencer

middle: G.

last: Willet

state: MO

address: 660 S. Euclid Avenue, Campus Box 8103

department: Department of Developmental Biology

institute: Washington University in St. Louis

data_processing:
Quality control of reads was performed using FastQC v.0.10.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.33.
Trimmed sequence reads were mapped to GrCM38/mm10 using Salmon v.1.8.0 with default parameters.
Read count extraction and normalization were performed using EdgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw gene counts for each Sample

source_name: Gastric Corpus

extract_protocol:
RNA was harvested using Rneasy midi kit (Qiagen). 0.5 to 1ug of total RNA was used for the construction of sequencing libraries.
Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt-ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired-end reads extending 150 bases.

value: Gastric Corpus

value: TetOSox9/+ ; ROSA26rtTA/rtTA

value: control


title: SOC Day P16 3

description: small RNA

data_processing:
Sequenced reads were mapped to the Mus musculus genome (mm10), using Bowtie (version 2.2.5).
miRs were identified by mapping to reference mouse mature miRNA sequences downloaded from miRBase (version 22).
Normalization and detection of differentially expressed miRs were done using DEseq2.
Assembly: mm10
Supplementary files format and content: miR-seq_SOC_coch_counts.txt: Tab-delimited text file includes counts for each Sample.

source_name: superior olivary complex

extract_protocol:
SOC - innuPrep miRNA Kit (Isolation of miRNAs and total RNA). SE - Direct-zolTM RNA Miniprep kit (Zymo Research, CA, USA).
SOC - Illumina TruSeq Small RNA library. SE - SMARTer smRNA-Seq Kit (Takara Bio Inc.)

value: superior olivary complex

value: neuronal

value: WT

value: Day P16


title: A056 NRKF cells, pH 6.0, sample group: 6

city: Halle (Saale)

first: Virginie

last: Dubourg

address: Magdeburger Str. 6

department: Julius Bernstein Institute for Physiology

institute: Martin Luther University - Halle-Wittenberg

data_processing:
Read alignment (HISAT2 2.1.0)
Read counting (featureCounts - 2.0.0)
Annotation with biomaRt and Ensembl 104
Assembly: rn6
Supplementary files format and content: .csv file including annotation raw counts (output of featureCounts) for each sample

source_name: NRKF

growth_protocol: NRKE and NRKF were cultivated with DMEM medium (10% FCS, 1.5g/L NaHCO3), at 37°C, 5% CO2

extract_protocol:
Total RNA was isolated with BluZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
polyA enrichment (performed by Novogene Europe)

treatment_protocol: Cells were synchronized for 24h with medium without FCS. The incubation with pH 7.4 or 6.0 (reached with HCl) was then started and was maintained for 48h

value: NRKF

tag: sample group


title: EV083

city: PORTLAND

first: Hyun Ji

last: Kim

address: 3181 SW Sam Jackson Park Rd.

institute: Oregon Health and Science University


title: CreCre Sox9 R2

value: Fgf20Cre/Cre ; TetOSox9/+ ; ROSA26rtTA/rtTA

value: Sox9 misexpression


title: SOC Day P16 2

city: Tel Aviv

first: Karen

last: Avraham

institute: TAU

description: small RNA


title: Neonatal Shank3Δ11(-/-) skeletal muscle (3)

value: gastrocnemius muscle at postnatal day 0-1

value: skeletal muscle

value: postnatal day 0-1


title: CreCre Sox9 R1


title: EV082


title: Ileum, Abx+morphine, 24 hrs, replicate 7

city: Miami

first: Udhghatri

last: Kolli

address: 1501 Nw 15th street

institute: University of Miami

data_processing:
Mapping STAR V2
Quantification HTSeq v0.6.1
Differential Analysis DESeq2 v2_1.6.3
Enrichment Analysis ClusterProfiler v2.4.3, TOPPcluster, clueGo
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM, differential gene expression and statistics

source_name: ileum

extract_protocol:
RNA was extracted from flash frozen terminal ileum RNeasy plus Universal Kit from Qiagen (73404)
NEBNext Ultra RNA library prep kit

treatment_protocol: For depletion of the gut microbiota, a pan-antibiotics + antifungal cocktail [vancomycin 32 (mg/kg), bacitracin (80mg/kg), metronidazole (80mg/kg), neomycin (320mg/kg), and Pimaricin (0.192mg/kg)] was prepared every day in drinking water and an oral gavage was given to mice for 7 daysThe animals were lightly anesthetized using isoflurane (Pivetal®) and a 25 mg slow-release Morphine pellet or placebo pellet was implanted subcutaneously.

value: ileum

tag: strain

value: Wild type

value: Antibiotics cocktail (7days) + Morphine, 25mg pellet, 24 hrs


title: EV086

value: Female


title: EV081


title: SOC Day P0 4

description: small RNA

value: Day P0


title: vascular wall-derived stem cell 1

value: mesenchymal stem cell


title: A054 NRKF cells, pH 6.0, sample group: 6

tag: cell line

value: fibroblast


title: SOC Day P0 3

description: small RNA

value: superior olivary complex


title: EV080


title: Control R2

value: Gastric Corpus

value: TetOSox9/+ ; ROSA26rtTA/rtTA

value: control


title: A055 NRKF cells, pH 6.0, sample group: 6

value: NRKF


title: EV079


title: A053 NRKF cells, pH 7.4, sample group: 6


title: SOC Day P16 1

description: small RNA

value: neuronal

value: WT

value: Day P16


title: SOC Day P0 2

description: small RNA


title: A052 NRKF cells, pH 7.4, sample group: 6


title: A051 NRKF cells, pH 7.4, sample group: 6


title: Ileum, Abx+morphine, 24 hrs, replicate 4


title: Ileum, Abx+morphine, 24 hrs, replicate 3


title: SOC Day E16 4

description: small RNA

value: Day E16


title: EV078


title: SOC Day E16 3

description: small RNA


title: A041 NRKF cells, pH 7.4, sample group: 4


title: SOC Day P0 1

description: small RNA


title: EV074


title: EV077


title: EV076


title: Ileum, Abx+morphine, 24 hrs, replicate 5


title: SOC Day E16 2

description: small RNA


title: A040 NRKF cells, pH 7.4, sample group: 4


title: EV075


title: Ileum, Abx+morphine, 24 hrs, replicate 2


title: Ileum, Abx+morphine, 24 hrs, replicate 1


title: A042 NRKF cells, pH 6.0, sample group: 4


title: A043 NRKF cells, pH 6.0, sample group: 4


title: A039 NRKF cells, pH 7.4, sample group: 4


title: ileum, Morphine, 24 hrs, replicate 5

value: Morphine, 25mg pellet, 24 hrs


title: Cochlea Day P16 4

description: small RNA

source_name: cochlea

value: cochlea

value: inner ear sensory epithelium


title: ileum, Morphine, 24 hrs, replicate 3

value: ileum

value: Wild type


title: EV073

value: Female


title: EV065

value: Male


title: SOC Day E16 1

description: small RNA


title: ileum, Morphine, 24 hrs, replicate 4


title: EV066


title: A037 NRKE cells, pH 6.0, sample group: 3

source_name: NRKE

value: NRKE

value: epithelial


title: Cochlea Day P16 2

description: small RNA


title: Cochlea Day P16 3

description: small RNA


title: ileum, Morphine, 24 hrs, replicate 2


title: ileum, Morphine, 24 hrs, replicate 1


title: A038 NRKE cells, pH 6.0, sample group: 3


title: A036 NRKE cells, pH 6.0, sample group: 3


title: EV064


title: A035 NRKE cells, pH 7.4, sample group: 3


title: EV062


title: A034 NRKE cells, pH 7.4, sample group: 3


title: E14 cells, Haspin KO, rep1

city: shanghai

first: ying

middle: ying

last: Gao

address: Siping Road Street

institute: Tongji University

data_processing:
In order to remove adaptor sequence/low-quality sequence , pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1)
HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

growth_protocol: mouse embryonic stem cells were maintained in knockout-DMEM supplemented with 15% fetal bovine serum (FBS), Lif and2i in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol Reagent.
1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: No special treatment

value: mouse embryonic stem cell

value: Haspin knockout


title: E14 cells, Haspin KO, rep2


title: Cochlea Day P0 3

description: small RNA

value: Day P0


title: Cochlea Day P0 4

description: small RNA


title: E14 cells, WT, rep2


title: EV063


title: A033 NRKE cells, pH 7.4, sample group: 3


title: EV061


title: E14 cells, WT, rep1


title: EV060

source_name: Human healthy control plasma


title: EV059


title: A026 NRKE cells, pH 6.0, sample group: 1


title: Cochlea Day P0 2

description: small RNA


title: Cochlea Day P0 1

description: small RNA


title: A025 NRKE cells, pH 6.0, sample group: 1


title: Ileum, Abx+morphine, 24 hrs, replicate 6

growth_protocol: Eight-week-old, pathogen free, C57/B6 male mice (Jackson laboratories) Animals were maintained in a 12-h light/dark cycle, with constant temperature (72 ± 1°F) and 50% humidity with food and tap water provided ad libitum

value: Antibiotics cocktail (7days) + Morphine, 25mg pellet, 24 hrs


title: T4

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger count software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
LSK (Lin-FLT3-C-kit+Sca-1+) were freshly isolated(FACS) from the BM of vehicle or Nilotinib treated SCL-tTA-BCR-ABL mice or wild type C57BL/6 mice (2 replicates per group)
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Bone marrow

value: LSK cells

tag: cell markers

value: transgenic SCL-tTA/BCR-ABL (BA) mouse model

value: CML Nilotinib 2w


title: Cochlea Day E16 2

description: small RNA

tag: cell type

value: WT

value: Day E16


title: Cochlea Day P16 1

description: small RNA

value: cochlea

value: inner ear sensory epithelium

value: Day P16


title: T3

description: 10X Genomics


title: A024 NRKE cells, pH 6.0, sample group: 1


title: EV057

value: Female


title: Cochlea Day E16 1

description: small RNA


title: A023 NRKE cells, pH 7.4, sample group: 1


title: A022 NRKE cells, pH 7.4, sample group: 1


title: EV056


title: T1

description: 10X Genomics

value: CML Nilotinib 2d


title: EV055


title: A021 NRKE cells, pH 7.4, sample group: 1

value: NRKE


title: EV054

source_name: Human lung cancer plasma


title: C34.D.M

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description:
R34
Duck_RNAseq.xlsx

data_processing:
Quality of sequenced CAGE reads was checked by using FastQC v0.11.5 and then trimmed with fastx_trimmer -Q33 -l 75 (FASTX Toolkit 0.0.14). Moirai removeN script was applied to remove reads with “N” nucleotides. CAGE reads matching to adapters or rRNA (Moirai defined rRNA for galGal3) were removed with Trimmomatic-0.38 and RNAdust 1.06, respectively.
Trimmed CAGE reads were aligned with BWA 0.7.10-r789 and unmapped reads realigned with Hisat2 v2.1.0
Alignments were processed into CTSS (CAGE transcription start sites) and CAGE peaks with PromoterPipeline (https://github.com/Population-Transcriptomics/C1-CAGE-preview) with default threshold of at least 10 TPM (tags per million) in one of the samples.
CAGE peaks were associated with nearby transcripts located on the same strand by using ChIPseeker v1.32.0 package for R.
Quality of sequenced RNAseq reads was checked by using FastQC v0.11.5 and then trimmed with Trimmomatic-0.38
Trimmed RNAseq reads were aligned to reference genome assemblies by using Hisat2 v2.1.0, counted with HTSeq v2.0.1, and normalized by library size and exon length in edgeR v3.42.2.
Assembly: galGal6 (GCF_000002315.6)
Assembly: Coturnix_japonica_2.1 (GCF_001577835.2)
Assembly: MGAL_WU_HG_1.0 (GCA_905368555.1)
Assembly: GT_SO_6221 (http://gigadb.org/dataset/100559)
Assembly: ZJU1.0 (GCF_015476345.1)
Assembly: bTaeGut2.pat.W.v2 (GCF_008822105.2)
Assembly: ZJU1.0 (GCA_016128335.1)
Supplementary files format and content: xlsx files with CAGE peaks coordinates, TSS position, associated genes, tag per million normalized counts
Supplementary files format and content: xlsx files with RNAseq raw and FPKM counts

organism: Anas platyrhynchos

source_name: embryonic fibroblasts P5

growth_protocol: Embryonic fibroblast cells were isolated from eggs incubated for ~10 days at 38.5 °C to reach stage HH36. Embryos were then treated by resection of head and neck, limb, skin and fat deposit, and internal developing organs. The remained trunk portion was trypsinized at 37°C, followed by neutralization and centrifugation to obtain digested cell pellet. Cell pellet was resuspended with DMEM/10%FBS and seeded in DMEM/10%FBS or DMEM/F12/10%FBS for expansion.

extract_protocol:
Total RNA was prepared using commercial reagents (TRIzol, Invitrogen) from each sample of avian embryonic fibroblast cells at the fifth passage (P5).
5ug of RNA from each fibroblast sample was used for nAnTi-CAGE and polyA RNAseq libraries preparation and subsequent sequencing using the Illumina HiSeq2500 platform (K. K. DNAForm, Yokohama, Japan)

value: embryonic fibroblasts P5

tag: Sex

value: male

tag: medium

value: DMEM/10percent FBS


title: V3

description: 10X Genomics

value: CML vehicle 2w


title: C32.D.F

description:
R32
Duck_RNAseq.xlsx

value: female


title: Cell line Exon3, Olaparib, Replicate 2

city: Frederick

first: Shyam

last: Sharan

address: Building 560, Room 32-33

institute: Mouse Cancer Genetics Program

description: Sahu et al_Suppl file 2.xlsx

data_processing:
The reads were demultiplexed using bcl2fastq (Illumina) and fastq files were generated. The paired end reads were merged using FLASH and reads were aligned to the reference amplicon with a global sequence alignment algorithm using Needleman-Wunsch Alignment.
The total number of aligned reads were quantified using CRISPResso2 http://crispresso.pinellolab.org/submission  (63) and individual unique alignments were annotated with a custom-made variant caller modified from ANNOVAR (64) (release 2019-10-21) and the R/Bioconductor Biostrings package in R version 4.1.2 https://bioconductor.org/packages/Biostrings. Merged reads containing “N” bases were removed from the analysis.
Abundances of SNVs were quantified when the reads contained the synonymous PAM modification (HDR marker) and no other substitution or indels were present. The variants generated at a low frequency (less than 1 in 105 reads in any one of the replicates) were excluded from further analysis to prevent erroneous variant categorization. A pseudo count of 1 was added to all reads and for every sample and at all the conditions. Read counts for each SNVs were then normalized to the total read coverage of the sequencing library.
Dropout or enrichment scores were calculated by taking the ratio of frequency of the variants at day 14 in DMSO or cisplatin or olaparib over day 3. The scores were expressed in Log2 scale, which we define as function scores of SNVs in DMSO, cisplatin and olaparib.
The FSs, averaged over two independent replicates, were fit using a probit regression model for statistical modelling to calculate the probabilities of impact on function
Assembly: GRCh38
Supplementary files format and content: xlsx: Excel files include PIF, function scores, and additional annotations for all variants.
Library strategy: Amplicon sequencing

extract_protocol:
Genomic DNA was extracted from the cell pellets using Zymo Genomic DNA Extraction kit
DNA libraries were prepared using TruSeq Nano DNA Library Prep kit

value: Embryonic stem cell


title: Cell line Exon3, Olaparib, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: Cell line Exon3, Cisplatin, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: Cell line Exon3, Cisplatin, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: EV052

tag: fraction

tag: age


title: Cell line Exon3, DMSO, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: EV058

tag: gender


title: V2

description: 10X Genomics

tag: tissue

value: Bone marrow

value: LSK cells

tag: genotype

value: CML vehicle 2d


title: V1

description: 10X Genomics

value: transgenic SCL-tTA/BCR-ABL (BA) mouse model

tag: treatment


title: Duck-EF 2020-03 High P5 [C36]

description:
C36
Duck_CAGE.xlsx


title: EV051


title: EV053


title: T2

description: 10X Genomics


title: PSTOL2_Crown_50DAS_LP_3

city: Riverside

first: Julia

last: Bailey-Serres

state: California

address: 900 University Ave

department: Department of Botany and Plant Sciences

institute: UC Riverside

data_processing:
Quality reports of raw reads were generated with the FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapter sequences were trimmed using Cutadapt (Martin et al. 2011).
Sequences were aligned to the  IWGSC v1.1 reference genome using hisat2 (Kim et al. 2015). The OsPSTOL1 K-allele CDS was added as a separate chromosome.
Read count data in terms of RPKM (reads per kilobase per million) were calculated for exons on gene ( Genomic features exonsby). For samples with both single end and paired end reads, single end and paired end reads were aligned and counted seperately as described above. The counts were then added from the two alignments
Genome_build: IWGSC v1.1
Supplementary_files_format_and_content: Normalized RPKM for each sample. P-values for comparisons are given only for genes with 5 counts per million in at least three samples.

organism: Triticum aestivum

source_name: 50 days after sowing crowns

growth_protocol: For evaluation of growth under low P conditions, seeds of transgenic and null segregant plants were germinated as described above, except seeds were sterilized prior to being imbibed by incubating seeds in 50% (v/v) ethanol for 15 minutes, followed by incubating in 2% (w/v) sodium perchlorate for 10 minutes, and washing 5 times with sterile ddH2O. Seeds were pre-germinated on wet filter paper on sealed petri dishes in a growth chamber at 22°C, with 16 h light (115 µE info and dark cycle for 3 days. Five to six germinated seedlings of average size and similar developmental stage were transplanted into each pot containing a mix of 70% (v/v) #20 silica sand (Gillibrand) and 30% (v/v) Green Grades Profile™. Profile™ contains 10% (v/v) aluminum oxide which acts as a solid-state buffer for phosphate77. Prior to transplanting, the growth medium of each pot was pre-washed 16 times with 0.75 L Industrial H2O, with at least 4 hours between each wash to reduce the starting phosphate content to 25 μM. For the first 14 days after sowing (DAS), plants were sub-irrigated (from pot base) with unfertilized industrial water containing negligible amounts of phosphate and nitrogen. At 14 DAS, pots were sub-irrigated with 3 L of industrial water supplemented with the following nutrients: 2.3 mM NH4NO3, 2 mM KNO3, 0.00007 mM (NH4)Mo7O24, 0.01148 mM H3BO3, 0.002 mM CuSO4, 0.0094 mM Iron-EDTA, 0.003 mM MnSO4, and 0.0035 mM ZnSO4. For high phosphate (HP), the solution contained 436 µM KH2PO4, and for low phosphate (LP) this was substituted with 440 µM KCl. The industrial water used contains 1625 µM Ca2+, 375 µM Mg2+, and 656 µM SO42-.

extract_protocol:
Total RNA was extracted using TRizol reagent (Invitrogen) according to the manufacturer’s instructions. Following quantitation with a NanoDrop (Wilmington, DE), 15 µg of total-RNA was used to isolate mRNA using Dynabeads™ Oligo(dT)25 (Invitrogen) following the manufacture’s instructions.
mRNA-seq Libraries were produced using the non-strand specific Brad’s Rapid Ravi-seq procedure (Kumar et al. 2012).

value: 50 DAS

tag: organ

value: Crowns

value: Low Phosphate

tag: cultivar

value: Fielder


title: Cell line Exon3, DMSO, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: Duck-EF 2020-02 High P5 [C34]

description:
C34
Duck_CAGE.xlsx


title: PSTOL2_Crown_50DAS_LP_2

treatment_protocol: For high phosphate (HP), the solution contained 436 µM KH2PO4, and for low phosphate (LP) this was substituted with 440 µM KCl.

tag: line


title: Duck-EF 2020-03 F12 P5 [C35]

description:
C35
Duck_CAGE.xlsx

value: DMEM/F12/10percent FBS


title: V4

description: 10X Genomics


title: EV049

value: Female


title: Duck-EF 2020-02 F12 P5 [C33]

description:
C33
Duck_CAGE.xlsx


title: EV042

value: Male


title: Cell line Exon3, Day3, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: PSTOL2_Crown_50DAS_LP_1


title: Cell line Exon19, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: PSTOL2_Crown_50DAS_HP_3

value: High Phosphate


title: EV041


title: Cell line Exon19, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: PSTOL2_Crown_50DAS_HP_2


title: PSTOL2_Crown_50DAS_HP_1


title: EV039


title: Cell line Exon19, Olaparib, Replicate 38

description: Sahu et al_Suppl file 2.xlsx


title: EV040


title: Cell line Exon19, Olaparib, Replicate 39

description: Sahu et al_Suppl file 2.xlsx


title: RNAseq_7VIA12_VEGF_MAB_7d

city: Leuven

first: Bernard

middle: Klaas

last: van der Veer

state: Vlaams-Brabant

address: Herestraat 49 - box 804

department: Department of Development and Regeneration

institute: KU Leuven

description:
normalized count file
GC1003559

data_processing:
ea-utils was used for adapter trimming
Hisat2 was used for splice-aware alignment
HT-seq Count was used for coutning reads
Assembly: Rnor6.0
Supplementary files format and content: normalized.counts.csv

source_name: Urethra

extract_protocol:
TRIPURE Isolation Reagent
LexoGen Quantseq 3' library prep

value: Urethra

value: VEGF OE

value: day 7 - VEGF MAB


title: PSTOL1_Crown_50DAS_LP_3


title: EV050


title: Cell line Exon3, Day3, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: RNAseq_7VIA11_VEGF_MAB_7d

description:
normalized count file
GC1003558


title: Cell line Exon19, Negative Control

description: Sahu et al_Suppl file 2.xlsx

value: Negative Control


title: Cell line Exon19, DMSO, Replicate 2

description: Sahu et al_Suppl file 2.xlsx

value: Embryonic stem cell


title: PSTOL1_Crown_50DAS_LP_2


title: PSTOL1_Crown_50DAS_LP_1


title: EV037


title: EV030

source_name: Human multiple myeloma plasma


title: RNAseq_7VIA6_VEGF_MAB_7d_recovery

description:
normalized count file
GC1003556

value: day 7 - VEGF MAB recovery


title: PSTOL1_Crown_50DAS_HP_3


title: Cell line Exon19, DMSO, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: RNAseq_7HIA13_MAB_7d

description:
normalized count file
GC1003555

value: WT

value: day 7 - MAB


title: Duck-EF 2020-01 High P5 [C32]

description:
C32
Duck_CAGE.xlsx

value: embryonic fibroblasts P5

value: female

value: DMEM/10percent FBS


title: EV029


title: PSTOL1_Crown_50DAS_HP_2

value: 50 DAS

value: Crowns


title: Cell line Exon19, Cisplatin, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: RNAseq_7HIA11_MAB_7d

description:
normalized count file
GC1003554


title: EV038


title: EV027


title: RNAseq_7HIA7.2_MAB_7d

description:
normalized count file
GC1003552


title: EV028


title: PSTOL1_Crown_50DAS_HP_1

value: Fielder


title: Cell line Exon18b, Olparib, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: RNAseq_7HIA9_MAB_7d

description:
normalized count file
GC1003553


title: Null_Crown_50DAS_LP_3

value: Null Segregant

value: Low Phosphate


title: EV026

value: Male


title: Cell line Exon18b, Olparib, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: Null_Crown_50DAS_LP_1


title: Null_Crown_50DAS_LP_2


title: EV024

source_name: Human liver cancer plasma

value: Female


title: Cell line Exon18b, DMSO, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: Null_Crown_50DAS_HP_1

value: High Phosphate


title: Cell line Exon18b, Cisplatin, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: EV025


title: RNAseq_7VIA7_VEGF_MAB_7d_recovery

description:
normalized count file
GC1003557

value: Urethra

value: VEGF OE


title: RNAseq_3VIA4_VEGF_MAB_3d

description:
normalized count file
GC1003547

value: day 3 - VEGF MAB


title: Null_Crown_50DAS_HP_3


title: Cell line Exon19, Cisplatin, Replicate 1

description: Sahu et al_Suppl file 2.xlsx

value: Embryonic stem cell


title: Null_Crown_50DAS_HP_2


title: EV022


title: Cell line Exon18b, Cisplatin, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: Cell line Exon18b, Day3, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: Cell line Exon18b, DMSO, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: EV023


title: EV021


title: RNAseq_7SIA5_saline_7d

description:
normalized count file
GC1003551

value: WT

value: day 7 - saline


title: RNAseq_7SIA1_saline_7d

description:
normalized count file
GC1003548


title: RNAseq_3VIA3_VEGF_MAB_3d

description:
normalized count file
GC1003546


title: Cell line Exon18a, Olaparib, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: PSTOL2_Root_50DAS_LP_3

source_name: 50 days after sowing roots

value: Roots


title: RNAseq_7SIA3_saline_7d

description:
normalized count file
GC1003550


title: EV018


title: Cell line Exon18b, Day3, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: RNAseq_7SIA2_saline_7d

description:
normalized count file
GC1003549


title: EV020


title: RNAseq_3VIA2_VEGF_MAB_3d

description:
normalized count file
GC1003545


title: EV019


title: PSTOL2_Root_50DAS_LP_1


title: RNAseq_0.5HIA4_MAB_3d

description:
normalized count file
GC1003543

value: day 3 - MAB


title: RNAseq_3VIA1_VEGF_MAB_3d

description:
normalized count file
GC1003544


title: Cell line Exon18a, Olaparib, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: PSTOL2_Root_50DAS_HP_3


title: EV015


title: EV017


title: Cell line Exon18a, Cisplatin, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: EV016


title: RNAseq_0.5HIA3_MAB_3d

description:
normalized count file
GC1003542


title: RNAseq_0.5HIA1_MAB_3d

description:
normalized count file
GC1003540


title: Cell line Exon18a, Cisplatin, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: PSTOL2_Root_50DAS_HP_2


title: PSTOL1_Root_50DAS_LP_3


title: PSTOL2_Root_50DAS_HP_1


title: Cell line Exon18a, DMSO, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: EV014


title: Cell line Exon18a, Day3, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: RNAseq_3SIA10_saline_3d

description:
normalized count file
GC1003539

value: day 3 - saline


title: PSTOL1_Root_50DAS_LP_1

value: 50 DAS


title: PSTOL1_Root_50DAS_LP_2


title: RNAseq_3SIA8_saline_3d

description:
normalized count file
GC1003537


title: EV013


title: RNA: Adipose Tissue Biopsy, P5963_CW3

city: Nashville

first: Samuel

last: Bailin

address: 1161 21st Avenue South, MCN A-2200

institute: Vanderbilt Universit Medical Center

data_processing:
Indiviudal samples were input into Cellranger v6.0.0 with default parameters
Reads were mapped to hg38 and UMI count matrices were computed by Cellranger with default parameters
Assembly: hg38
Supplementary files format and content: Cellranger output with all samples aggregated together after quality control and doublet removal

source_name: subcutaneous adipose tissue

extract_protocol:
Custom adipose tissue dissociation.
10X 5' Gene Expression (GEX) and Antibody Expression (ADT) Library Construction

tag: disease state

value: HIV- diabetic

value: subcutaneous adipose tissue

tag: number of donors


title: RNAseq_3SIA9_saline_3d

description:
normalized count file
GC1003538


title: RNAseq_0.5HIA2_MAB_3d

description:
normalized count file
GC1003541


title: RNAseq_3SIA6_saline_3d

description:
normalized count file
GC1003536


title: Cell line Exon13.23, Day3, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: PSTOL1_Root_50DAS_HP_3

value: Fielder


title: PSTOL1_Root_50DAS_HP_2


title: Cell line Exon18a, DMSO, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: Cell line Exon13.23, Day3, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: PSTOL1_Root_50DAS_HP_1


title: ADT: Adipose Tissue Biopsy, P5963_CW2

value: HIV+ diabetic


title: RNA: Adipose Tissue Biopsy, P5963_CW2


title: ADT: Adipose Tissue Biopsy, P5963_CW1

value: HIV+ non-diabetic and HIV+ prediabetic


title: Cell line Exon13.23, Olaparib, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: Null_Root_50DAS_LP_3

value: Null Segregant

value: Low Phosphate