title: mESC to CM Day 15 rep1

city: Chicago

first: Megan

middle: J

last: Rowton

state: IL

address: 900 East 57th Street

department: Human Genetics and Genetic Medicine

institute: University of Chicago

description:
transposase-accessible genomic DNA
D15_FE.bw
D15_peaks.narrowPeak

data_processing:
Mapping reads to mm10; Adapter sequences were clipped from reads using Cutadapt version 2.10 (cutadapt  -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 4 -m 10) , then aligned to UCSC mouse genome mm10 with bowtie2 version 2.3.2 with default settings.
Filtering for quality reads; Low quality reads ( q < 30 ) and reads mapping to blacklisted regions were removed using samtools version 1.5. Duplicated reads were marked and removed with picard tool MarkDuplicates version 2.8.1.
Peak calling; Accessible regions were identified using MACS2 version 2.1.1 grouping replicates together. (macs2 callpeak -f BAMPE -g mm –keep-dup all -B --SPMR ).
Generating fold enrichment tracks; Fold enrichment tracks were generated with MACS2 bdgcmp ( -m FE). Bedgraph files from MACS2 were converted to bigwig format with UCSC tool bedGraphToBigWig version 4.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files are aligned to the mm10 genome. NarrowPeak files are called ATAC-seq peaks in the mm10 genome.

source_name: A2lox.cre mouse embryonic stem cell line under cardiac differentiation

extract_protocol:
Nuclei were extracted by deteregent lysis. Transposition was carried out at 37C for 30 minutes.
Libraries were prepared with Illumina’s Nextera DNA Library Prep kit (Illumina 15028212).

value: cardiomyocyte


title: mESC to CM Day 15 rep2

status: Public on Sep 02 2024

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell line

tag: cell type


title: SAC, P11G10, ON, rep59

city: Baltimore

first: Rebecca

last: James

state: MD

address: 725 N. Wolfe Street

department: Neuroscience

institute: Johns Hopkins University

description:
P11a_58
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

library_source: transcriptomic single cell

data_processing:
Single-cell RNA sequencing FASTQ files were aligned to the GRCm38.p6 (mm10) mouse reference genome using HISAT2 v2.1.0. SAM files were converted to BAM files using SAMtools v1.3.1. Transcript abundance estimation and normalization were performed using the Cuffquant and Cuffnorm tools, respectively, in Cufflinks v2.2.1. Downstream analyses were performed using Monocle2 in RStudio.
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: Cuffnorm matrix containing FPKM values for each gene for each cell Supplementary files format and content: Cuffnorm matrix containing annotations for each gene Supplementary files format and content: Cuffnorm matrix containing annotations for each sample
Supplementary files format and content: Some processed data files without data - they are empty files because the supplied reference annotation GTF file we used in Cufflinks to assemble the transcriptomes did not contain TSS/ CDS gene attributes. I

molecule: polyA RNA

source_name: starburst amacrine cell

extract_protocol:
Retinas from ChatCre/+; ROSA-LSL-TD-Tomato mice were isolated at P1, P4, P8, P11 and P16 in ice cold HBSS, and the retinal pigmented epithelium and inner limiting membranes were removed. Retinas were digested with papain, triturated slowly 15-20 time with a P1000 pipet tip, strained into a 50 mL conical tube, and pelleted for 3 minutes at 1.3k rpm. The pellet was gently resuspended and cells were washed three times in ice cold Hibernate A media lacking Ca2+, Mg2+, and phenol red, with pelleting between the washes. Care was taken to tap the tube gently to dislodge the pellet before adding media and resuspending the pellet, to prevent cell lysis and subsequent accumulation of DNA and cellular debris, which forms as a sticky gel-like substance in the supernatant. Washed and resuspended cells in ice cold Hibernate A were subjected to FACS to isolate single cells in cell lysis buffer before proceeding with Smart-seq2 mRNA sequencing as in Chevee et al., 2018.
A modified Smart-seq2 mRNA sequencing protocol was used to construct libraries, described in Chevee et al., 2018.

tag: tissue type

value: retina

value: starburst amacrine cell

tag: genotype/strain

tag: age

value: Postnatal day 11


title: T-AQP4_01 [L49813_Track-90407]

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

description:
RawExpressionCountTable.csv
TCR_data.csv

data_processing:
library strategy: Plate base Single cell RNA seq (SMARTseq2)
Fragments were aligned to the human reference genome hg38 with support of Ensembl 98 splice sites using the aligner gsnap (v2019-06-10).
Counts per gene and cell were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl annotation using featureCounts (v2.0.1)
T-cell receptor sequences were assembled per cell using TraCeR (v0.5)
Assembly: hg38
Supplementary files format and content: Counts per gene per cell, CSV
Supplementary files format and content: T-cell receptor sequences, CSV

organism: Homo sapiens

source_name: Blood

growth_protocol: 2.5-5x10^7 PBMCs were plated in 2 ml RPMI-1640 medium (GIBCO), supplemented with 5% (v/v) human AB-serum (Sigma Aldrich, Schnelldorf, Germany) in 6-well cell culture plates.

extract_protocol:
CD154+ memory cells were isolated by MACS and further purified by FACS sorting on a FACS Aria Fusion (BD Bioscience, San Jose, CA, USA) based on dual expression of CD154 and CD69 and expression of CD45RO. Cells were directly sorted into skirted 96-well PCR plates which were equipped with 2 µl lysis buffer (nuclease-free water with 0.2% Triton-X 100 solution (Roche Diagnostics GmbH, Mannheim, Germany) with 4 U/µL RNase Inhibitor (New England Biolabs)) in advance. After FACS sorting plates were shortly centrifuged (30 sec, 200xg) and immediately frozen at -80°C until shipment.
Library preparation and sequencing was performed at the DRESDEN-concept Genome Center (DcGC, TU Dresden, Germany). The workflow was based on the previously described SMARTseq2 protocol 81. After thawing the samples, 2 ul of a primer mix was added (5 mM dNTP (Invitrogen), 0.5 uM dT-primer*, 4 U RNase Inhibitor (NEB)). RNA was denatured for 3 minutes at 72°C and the reverse transcription was performed at 42°C for 90 min after filling up to 10 ul with RT buffer mix for a final concentration of 1X superscript II buffer (Invitrogen), 1 M betaine, 5 mM DTT, 6 mM MgCl2, 1 uM TSO-primer*, 9 U RNase Inhibitor and 90 U Superscript II. After synthesis, the reverse transcriptase was inactivated at 70°C for 15 min. The cDNA was amplified using 2X Kapa HiFi HotStart Readymix (Roche) at a final 1X concentration and 0.1 uM UP-primer* under following cycling conditions: initial denaturation at 98°C for 3 min, 22 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. The amplified cDNA is purified using 0.6X volume of hydrophobic Sera-Mag Beads (Cytvia: GE24152105050250,) and DNA was eluted in 12 ul nuclease free water. The cDNA quality and concentration of a few representative samples was determined with the Fragment Analyzer (Agilent). For library preparation, 2 µl amplified cDNA was tagmented in 1X Tagmentation Buffer using 0.8 µl bead-linked transposome (Illumina DNA Prep, (M) Tagmentation, Illumina) at 55°C for 15 min in a total volume of 4 µL. The reaction was stopped by adding 1 µl of 0.1 % SDS (37°C, 15 min). Magnetic beads were bound to a magnet, the supernatant was removed, beads were resuspended in 4 µl indexing PCR Mix containing 1x KAPA Hifi HotStart Ready Mix (Roche). After adding 700 nM unique dual indexing primers (i5 and i7) using Echo Acoustic Liquid Handler (Echo 525, Beckman Coulter), the reaction mixture was subjected to a PCR (72°C 3 min, 98°C 30 sec, 12 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min). After PCR, libraries are quantified with a Tecan plate reader Infinite 200 pro in 384 well black flat bottom low volume plates (Corning) using AccuBlue Broad range chemistry (Biotium) and equimolarly pooled using Echo Acoustic Liquid Handler (Echo 525, Beckman Coulter GmbH). The pooled libraries were then purified with 0.9x volume Sera-Mag SpeedBeads, followed by a double size selection with 0.6x and 0.9x volume of beads. Re-double size selection with 0.6x and 0.9x volume of beads was performed if needed.

treatment_protocol: PBMC were stimulated for 7 h in presence of 1 µg/ml CD40 pure antibody (Miltenyi Biotec, Bergisch Gladbach, Germany) with AQP4, Influenza A H1N1 (HA) and C.albicans MP65 peptide pools or PMA/Ionomycin

tag: tissue

value: Blood

value: CD4 T cell

value: T cell

tag: treatment

value: AQP4 peptide pool


title: mESC to CM Day 10 rep2

description:
transposase-accessible genomic DNA
D10_FE.bw
D10_peaks.narrowPeak


title: mouse mOSNs, 19d, scATACseq

city: Guangzhou

first: Jin

last: Xu

state: Guangdong

address: No. 135 Xingang Xi Road

country: China

institute: Sun Yat-sen University

description: 10x Genomics V1.1

library_source: genomic single cell

data_processing:
For each scATAC-seq dataset, raw reads were preprocessed using CellRanger ATAC version 2.0.0, including read filtering, alignment to Mus musculus reference genome mm10 provided by 10X Genomics, peak calling, cell calling, and peak-barcode count matrices. Count data and fragment files were loaded into R (Version 4.1.3) and further processed using the R package Siganc. For each scATAC-seq data, we calculated the nucleosome signal (the ratio of mononucleosomal to nucleosome-free fragments), TSS enrichment score, and the percentage of reads in peaks for each cell. High-quality cells with 5000-40000 fragments, TSS enrichment score >= 4, nucleosome signal <2, and the percentage of reads in peaks >= 40 were retained for downstream analysis. Next, scATAC-seq datasets across two different time points were integrated using the integration workflow (https://stuartlab.org/signac/articles/integrate_atac.html). Cell identity is annotated by gene activity scores of canonical marker genes and cross-modality label transfer.  Cells in the olfactory neuronal lineage (HBCs, GBCs, INPs, Immature OSNs and mature OSNs) and mature OSNs were extracted  for further subclustering analysis.
Assembly: mm10
Supplementary files format and content: *.filtered_peak_bc_matrix.h5, *.fragments.tsv.gz, *.singlecell.csv, *.peaks.bed: cell-by-peak count matrix, fragments in each cell, cellular quality control information and called peaks output by CellRanger
Supplementary files format and content: combined_mouse_OE_scATAC_metadata.csv.gz: Metadata for high-quality cells in all scATAC-seq datasets

source_name: FACS-enriched mature OSNs

growth_protocol: All mice were housed in barrier facilities in a 12 h light/dark cycle with free access to standard mouse diet and water.

extract_protocol:
Mice were deeply anesthetized and perfused transcardially with 20 ml of ice-cold phosphate buffered saline (PBS). Mice were then rapidly decapitated, and turbinate tissues were washed and immersed in ice-cold PBS. Tissues were minced into small pieces and disaggregated in 0.25% Trypsin-EDTA (1x) (GIBCO) with gentle agitation at 37 °C for 20 min. After adequate disaggregation, adding equal volume DMEM containing 10% Fetal Bovine Serum (FBS, GIBCO) to stop the disaggregation reaction then the disaggregated cells were washed with ice-cold PBS and filtered through a 40 μm strainer. 7-AAD (Invitrogen) was added to exclude dead cells. For fluorescent reporter-expressing mouse lines (PWK/PhJ*129P2/OlaHsd (OMP-ChR2-YFP), fluorescence-positive cells (mOSNs) were sorted. Cells were sorted into DMEM containing 10% FBS and centrifuged for 5 minutes at 300 g and resuspended with PBS.
Single-cell sequencing libraries were prepared using the Chromium Single Cell ATAC Reagent Kit V1.1 (10x Genomics) according to the manufacturer’s guidelines. Sequencing library fragments were examined using the Agilent High Sensitivity DNA kit (Agilent) and quantified via qPCR by the KAPA library quantification kit (Roche).

value: FACS-enriched mature OSNs

tag: genotype

value: F1 of PWK/PhJ and OMP-ChR2-YFP (OCY58)

value: 19 days


title: Control ChIP-seq (input DNA) on embryonic 16.5 day mouse forebrain, biological replicate 2

city: Cleveland

first: Ming

last: Hu

state: OH

address: 9500 Euclid Avenue

institute: Cleveland Clinic

data_processing:
The fastq files of CTCF ChIP-seq data were mapped to mouse genome (mm10) and processed using the ENCODE uniform processing pipeline for ChIP-seq data (https://github.com/ENCODE-DCC/chip-seq-pipeline) with default parameters.
Assembly: mm10

source_name: forebrain

extract_protocol:
~30 mg fixed tissues were thawed on ice and the nuclei preparation was performed using truChIP® Chromatin Shearing Kit (Covaris) following the manufacturer’s instruction. The lysed nuclei were sheared using Covaris M220 with following setting: Setting: power, 75 W; duty factor, 8%; cycle per burst, 200; time, 12 min; temp, 7 °C. The sheared chromatins were cleared by centrifugation at 15,000×g for 12 min. The supernatant was collected and incubated with M-280 sheep anti-rabbit magnetic beads (Thermo Fisher, 11203D) for 3 hours at 4°C with slow rotation for preclearing. ~5% of precleared cell lysate was saved as input control after the incubation was done. The rest of precleared lysate was mixed M-280 sheep anti-rabbit magnetic beads that coupled with 0.9 μg of CTCF antibody (3418, Cell Signaling) and rotate at 4°C for 16 hours. On the next day, the beads were collected using magnetic stand and the supernatant was discarded. The beads are then washed with RIPA buffer three times, high-salt RIPA buffer (10 mM Tris, pH 8.0, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) twice, LiCl buffer (10 mM Tris, pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% IGEPAL CA-630, 0.1% sodium deoxycholate) once, TE buffer (10 mM Tris, pH 8.0, 0.1 mM EDTA) twice. Washed beads were treated with 10 μg Rnase A in extraction buffer (10 mM Tris, pH 8.0, 350 mM NaCl, 0.1 mM EDTA, 1% SDS) for 1 hours at 37°C, followed by reverse crosslinking in the presence of proteinase K (20 μg) overnight at 65°C. After reverse crosslinking the DNA was purified and quantified. The input control DNA was reverse crosslinked and purified in the same way as ChIPed DNA as described above.
Library preparation was performed using QIAseq Ultralow Input Library Kit (Qiagen) starting from 10–100 ng ChIPed DNA or input DNA. After PCR the amplified libraries were purified with SPRI Beads to extract fragments between 200-600bp for sequencing.

value: forebrain

tag: developmental stage

value: embryonic 16.5 day

tag: chip antibody


title: SAC, P11F4, OFF, rep53

description:
P11a_52
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: mESC to CM Day 10 rep1


title: T-AQP4_01 [L49811_Track-90387]


title: SAC, P11F9, OFF, rep58

description:
P11a_57
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_01 [L49812_Track-90447]


title: SAC, P11F3, OFF, rep52

description:
P11a_51
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: unknown, P11F7, filtered out, rep56

description:
P11a_55
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Control ChIP-seq (input DNA) on embryonic 16.5 day mouse forebrain, biological replicate 1


title: mESC to CM Day 8 rep2

description:
transposase-accessible genomic DNA
D8_FE.bw
D8_peaks.narrowPeak

value: intermediate of cardiac differentiation


title: SAC, P11F2, ON, rep51

description:
P11a_50
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Control ChIP-seq (input DNA) on embryonic 14.5 day mouse forebrain, technical replicate 2

value: embryonic 14.5 day


title: mESC to CM Day 8 rep1


title: Control ChIP-seq (input DNA) on embryonic 13.5 day mouse forebrain, biological replicate 2

value: embryonic 13.5 day


title: Control ChIP-seq (input DNA) on embryonic 14.5 day mouse forebrain, technical replicate 1


title: mESC to CM Day 7 rep1

description:
transposase-accessible genomic DNA
D7_FE.bw
D7_peaks.narrowPeak


title: T-AQP4_01 [L49808_Track-90364]


title: SAC, P11F12, OFF, rep50

description:
P11a_49
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Control ChIP-seq (input DNA) on embryonic 12.5 day mouse forebrain, biological replicate 2

value: embryonic 12.5 day


title: T-AQP4_01 [L49804_Track-90383]


title: SAC, P11E8, OFF, rep46

description:
P11a_45
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: SAC, P11E9, ON, rep47

description:
P11a_46
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: mESC to CM Day 7 rep2


title: mESC to CM Day 5 rep2

description:
transposase-accessible genomic DNA
D5_FE.bw
D5_peaks.narrowPeak


title: T-AQP4_01 [L49805_Track-90535]


title: Control ChIP-seq (input DNA) on embryonic 12.5 day mouse forebrain, biological replicate 1


title: mESC to CM Day 6 rep1

description:
transposase-accessible genomic DNA
D6_FE.bw
D6_peaks.narrowPeak


title: T-AQP4_01 [L49807_Track-90376]


title: SAC, P11F11, OFF, rep49

description:
P11a_48
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Control ChIP-seq (input DNA) on embryonic 12.5 day mouse neural tube, biological replicate 2

source_name: neural tube

value: neural tube


title: T-AQP4_01 [L49803_Track-90385]


title: SAC, P11E7, OFF, rep45

description:
P11a_44
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: retina


title: T-AQP4_01 [L49802_Track-90473]


title: SAC, P11E6, OFF, rep44

description:
P11a_43
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: starburst amacrine cell


title: mESC to CM Day 5 rep1


title: Control ChIP-seq (input DNA) on embryonic 12.5 day mouse neural tube, biological replicate 1


title: T-AQP4_01 [L49801_Track-90545]

description:
RawExpressionCountTable.csv
TCR_data.csv


title: T-AQP4_01 [L49810_Track-90515]


title: mESC to CM Day 4 rep2

description:
transposase-accessible genomic DNA
D4_FE.bw
D4_peaks.narrowPeak


title: SAC, P11F10, OFF, rep48

description:
P11a_47
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: Postnatal day 11


title: mESC to CM Day 6 rep2


title: T-AQP4_01 [L49806_Track-90534]

value: Blood


title: Control ChIP-seq (input DNA) on embryonic 13.5 day mouse forebrain, biological replicate 1


title: T-AQP4_01 [L49800_Track-90453]

value: CD4 T cell


title: SAC, P11E4, ON, rep42

description:
P11a_41
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Control ChIP-seq (input DNA) on embryonic 12.5 day mouse craniofacial prominence, biological replicate 2

source_name: craniofacial prominence

value: craniofacial prominence


title: Control ChIP-seq (input DNA) on embryonic 12.5 day mouse craniofacial prominence, biological replicate 1


title: T-AQP4_01 [L49798_Track-90541]

value: T cell

value: AQP4 peptide pool


title: Control ChIP-seq (input DNA) on embryonic 12.5 day mouse limb, biological replicate 1

source_name: limb

value: limb


title: mESC to CM Day 4 rep1


title: SAC, P11E1, ON, rep39

description:
P11a_38
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: Control ChIP-seq (input DNA) on embryonic 12.5 day mouse midbrain, biological replicate 2

source_name: midbrain

value: midbrain


title: mESC to CM Day 3 rep1

description:
transposase-accessible genomic DNA
D3_FE.bw
D3_peaks.narrowPeak


title: S.lycopersicum rep3, parasitized

city: Galaneika – Lamia

first: Vasiliki

last: Kotsira

address: Papasiopoulou 2-4

country: Greece

institute: Department of Computer Science and Biomedical Informatics

library_source: transcriptomic

data_processing:
Read quality was assessed with FastQC from the Babraham Institute. In order to remove adapter sequences and trim low-quality reads from the raw sequencing data, Cutadapt tool was utilized. Pre-processed reads were subjected to splice-aware genomic alignment and quantification, using STAR (v2.7.10) and RSEM (v1.3.1), respectively. Differential expression analysis was performed using the programming language R (version 4.2.2) and the R package edgeR. The limma R package was used for pathway enrichment analysis, employing the kegga() function and the KEGG database.
Assembly: GCF_000188115.5_SL3.1_genomic.fna, GCF_001406875.1_SPENNV200_genomic.fna
Supplementary files format and content: RSEM output files

molecule: total RNA

organism: Solanum lycopersicum

source_name: Roots

extract_protocol:
Total RNA was extracted from tomato roots, using the NucleoSpin RNA kit (MACHEREY-NAGEL, Germany) according to the manufacturer’s instructions. Thermo Scientific NanoDrop ND-1000 Spectrophotometer UV/Vis was used to determine the concentration and quality of the RNA.
Samples were subjected to cDNA library preparation (poly-A selection) and sequenced (150nt paired-end reads) on an Illumina NovaSeq 6000 system (Novogene Europe, Cambridge, UK). On average 13.9 million reads were obtained per library.

value: Roots

value: Formula

value: Orobanche ramosa-parasitized


title: unknown, P11E12, filtered out, rep38

description:
P11a_37
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: SAC, P11E2, OFF, rep40

description:
P11a_39
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_01 [L49794_Track-90429]


title: SAC, P11E11, OFF, rep37

description:
P11a_36
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: S.lycopersicum rep2, parasitized


title: S.lycopersicum rep1, parasitized


title: mESC to CM Day 2 rep1

description:
transposase-accessible genomic DNA
D2_FE.bw
D2_peaks.narrowPeak

value: intermediate of cardiac differentiation


title: SAC, P11E5, OFF, rep43

description:
P11a_42
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: SAC, P11E3, OFF, rep41

description:
P11a_40
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_01 [L49799_Track-90402]


title: mESC to CM Day 1 rep2

description:
transposase-accessible genomic DNA
D1_FE.bw
D1_peaks.narrowPeak


title: mESC to CM Day 1 rep1


title: SAC, P11E10, OFF, rep36

description:
P11a_35
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: S.lycopersicum rep3, control

value: non treated (control)


title: T-AQP4_01 [L49793_Track-90510]


title: mESC to CM Day 3 rep2


title: T-AQP4_01 [L49796_Track-90396]


title: mESC to CM Day 2 rep2


title: SAC, P11D9, OFF, rep35

description:
P11a_34
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: mESC to CM Day 0 rep1

description:
transposase-accessible genomic DNA
D0_FE.bw
D0_peaks.narrowPeak


title: T-AQP4_01 [L49795_Track-90434]


title: T-AQP4_01 [L49791_Track-90548]


title: T-AQP4_01 [L49792_Track-90359]


title: mESC 2i rep2

description:
transposase-accessible genomic DNA
2i_FE.bw
2i_peaks.narrowPeak

source_name: A2lox.cre mouse embryonic stem cell line

value: mouse embryonic stem cell


title: mESC to CM Day 0 rep2


title: S.lycopersicum rep2, control


title: SAC, P11D8, OFF, rep34

description:
P11a_33
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_01 [L49789_Track-90420]

description:
RawExpressionCountTable.csv
TCR_data.csv


title: T-AQP4_01 [L49790_Track-90397]


title: mESC 2i rep1


title: CxCC_99_HPV16

city: St. Louis

last: Zhang

address: 4511 Forest Park Parkway

department: Radiation Oncology

institute: Washington University School of Medicine

data_processing:
Sequenced reads were aligned to human reference genome GRCh38 (r90) using STAR v2.7.0f.
The aligned reads were sorted and indexed using sambamba v0.6.9.
Gene expression was characterized using featureCounts v1.6.4 to obtain read counts and cufflinks v2.2.1 to obtain normalized FPKM.
Assembly: GRCh38 (r90)
Supplementary files format and content: FPKM of all genes for the sample
Supplementary files format and content: Tab-delimited matrix of FPKM values for all genes of all samples

source_name: primary cervical cancer

extract_protocol:
Total RNA was extracted using the TRIzol method, and prepared using Rneasy Mini and Micro Kit following manufacturer's instructions.
Library preparation was performed with 10ug of total RNA. Sample quality was assessed with Agilent bioanalyzer or tapestation. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in buffer containing 40mM Tris Acetate pH 8.2, 100mM Potassium Acetate and 30mM Magnesium Acetate and heating to 94 degrees for 150 seconds. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies) 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 cycles using primers incorporating unique index tags.

value: primary cervical cancer

tag: figo 2009_stage

tag: hpv genotype


title: T-AQP4_01 [L49788_Track-90497]


title: SAC, P11D5, OFF, rep31

description:
P11a_30
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: retina


title: CxCC_97_HPV16


title: adipose, combined rep 5

city: Madrid

first: Cristina

last: Ovilo

address: Ctra Coruña km 7.5

country: Spain

institute: INIA-CSIC

data_processing:
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of raw sequencing data.
TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to quality trim data with default settings and to remove the sequencing adaptors and poly A and T tails (stringency of 6 bp, -s 6) keeping only paired-end reads where both pairs were longer than 40 bp.
Filtered reads were mapped against the pig reference genome (Sscrofa11.1) using HISAT2 applying default settings except that reads were first aligned to the ENSEMBL (11.1.90) transcriptome annotation (-G option), and the distance between both pairs was set to 100 bp (inner-mean distance) and the standard deviation to 150 bp.
HTseq-counts was used to calculate transcript abundances. Differential expression was analysed with Deseq2
Assembly: Sscrofa 11.1
Supplementary files format and content: Processed data file includes read counts for all genes in all 24 samples

organism: Sus scrofa

source_name: adipose

growth_protocol: Subcutaneous adipose tissue was collected within 15 min postmortem, snap-frozen in liquid nitrogen, and then stored at -80° C until processing.

extract_protocol:
Total RNA was extracted from 50-100mg samples of adipose tissue using the RiboPure TM of High Quality total RNA kit (Ambion, Austin, TX, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-100 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The quality of the RNA was evaluated using the RNA Integrity Number (RIN) value from the Agilent 2100 Bioanalyzer device (Agilent technologies, Santa Clara, CA, USA).
Sequencing libraries were made using the mRNA-Seq sample preparation kit (Illumina Inc., Cat. # RS-100-0801) according to manufacturer’s protocol. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode with the read length 2x76bp on a on a NovaSeq 6000 (Illumina, Inc). Images from the instrument were processed using the manufacturer’s software to generate FASTQ sequence files.

treatment_protocol: 50-100 mg samples of each tissue were ground in liquid nitrogen with mortar and pestle.

value: adipose

value: Iberian pig

value: VEHT


title: T-AQP4_01 [L49787_Track-90454]

value: Blood

value: CD4 T cell


title: SAC, P11D4, OFF, rep30

description:
P11a_29
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: starburst amacrine cell

value: Postnatal day 11


title: adipose, combined rep 4


title: CxCC_96_HPV16

value: IVa


title: T-AQP4_01 [L49786_Track-90358]

value: T cell

value: AQP4 peptide pool


title: adipose, combined rep 3


title: SAC, P11D3, ON, rep29

description:
P11a_28
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: S.lycopersicum rep1, control

value: Roots

value: Formula


title: T-AQP4_01 [L49784_Track-90379]


title: CxCC_94_HPV16


title: adipose, combined rep 2


title: SAC, P11D2, ON, rep28

description:
P11a_27
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: SAC, P11D1, OFF, rep27

description:
P11a_26
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: adipose, combined rep 1


title: adipose, combined rep 6


title: CxCC_93_HPV45

value: IIb


title: SAC, P11D6, OFF, rep32

description:
P11a_31
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: adipose, vitamin E rep 6

value: VE


title: SAC, P11D12, OFF, rep26

description:
P11a_25
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_01 [L49781_Track-90469]


title: T-AQP4_01 [L49782_Track-90438]


title: SAC, P11D11, ON, rep25

description:
P11a_24
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: CxCC_92_HPV16

value: IVb


title: T-AQP4_01 [L49780_Track-90512]


title: adipose, vitamin E rep 4


title: SAC, P11D10, ON, rep24

description:
P11a_23
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_01 [L49779_Track-90440]


title: SAC, P11C9, ON, rep23

description:
P11a_22
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: CxCC_90_HPV16

value: primary cervical cancer


title: adipose, vitamin E rep 3


title: CxCC_89_HPV16


title: T-AQP4_01 [L49778_Track-90405]


title: T-AQP4_01 [L49783_Track-90421]


title: SAC, P11C8, ON, rep22

description:
P11a_21
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: retina


title: CxCC_88_HPV16


title: adipose, vitamin E rep 2

value: adipose


title: SAC, P11C7, OFF, rep21

description:
P11a_20
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_01 [L49777_Track-90521]


title: adipose, hydroxytyrosol rep 6

value: Iberian pig

value: HT


title: SAC, P11C6, ON, rep20

description:
P11a_19
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: CxCC_86_HPV16

value: IIIb


title: adipose, vitamin E rep 1


title: CxCC_87_HPV16


title: CxCC_91_HPV16


title: T-AQP4_01 [L49776_Track-90384]

value: Blood

value: CD4 T cell


title: adipose, hydroxytyrosol rep 5


title: T-AQP4_01 [L49775_Track-90425]


title: CxCC_85_HPV52


title: SAC, P11C5, ON, rep19

description:
P11a_18
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: starburst amacrine cell

value: Postnatal day 11


title: adipose, vitamin E rep 5


title: CxCC_84_HPV31


title: SAC, P11C3, ON, rep17

description:
P11a_16
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: adipose, hydroxytyrosol rep 4


title: CxCC_83_HPV16


title: T-AQP4_01 [L49772_Track-90542]

value: T cell


title: SAC, P11C4, OFF, rep18

description:
P11a_17
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: adipose, hydroxytyrosol rep 3


title: T-AQP4_01 [L49774_Track-90540]

description:
RawExpressionCountTable.csv
TCR_data.csv

value: AQP4 peptide pool


title: T-AQP4_01 [L49771_Track-90547]


title: SAC, P11C2, ON, rep16

description:
P11a_15
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: SAC, P11D7, OFF, rep33

description:
P11a_32
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: CxCC_82_HPV16


title: adipose, hydroxytyrosol rep 2


title: T-AQP4_01 [L49770_Track-90436]


title: SAC, P11C1, OFF, rep15

description:
P11a_14
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: adipose, hydroxytyrosol rep 1


title: CxCC_81_HPV16


title: CxCC_80_HPV16


title: adipose, control rep 6

value: C


title: CxCC_98_HPV16


title: SAC, P11C12, OFF, rep14

description:
P11a_13
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_01 [L49769_Track-90441]


title: SAC, P11C11, OFF, rep13

description:
P11a_12
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: CxCC_79_HPV52


title: T-AQP4_01 [L49767_Track-90527]


title: adipose, control rep 5


title: T-AQP4_01 [L49768_Track-90445]


title: CxCC_78_HPV16


title: unknown, P11C10, filtered out, rep12

description:
P11a_11
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: adipose, control rep 4


title: T-AQP4_01 [L49766_Track-90368]


title: CxCC_77_HPV16


title: adipose, control rep 3


title: T-AQP4_01 [L49765_Track-90506]


title: SAC, P11B9, ON, rep11

description:
P11a_10
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: SAC, P11B8, OFF, rep10

description:
P11a_9
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_01 [L49764_Track-90457]


title: adipose, control rep 2


title: adipose, control rep 1


title: CxCC_75_none


title: SAC, P11B7, OFF, rep9

description:
P11a_8
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_01 [L49763_Track-90478]


title: CxCC_74_HPV16


title: unknown, P11B5, filtered out, rep7

description:
P11a_6
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: CxCC_73_HPV18


title: T-AQP4_01 [L49762_Track-90403]


title: IL6-3 rep3, parasitized

organism: Solanum lycopersicum x Solanum pennellii

value: Roots

value: Orobanche ramosa-parasitized


title: IL6-3 rep2, parasitized


title: unknown, P11B2, filtered out, rep6

description:
P11a_5
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: T-AQP4_01 [L49760_Track-90526]


title: SAC, P11B6, OFF, rep8

description:
P11a_7
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: SAC, P11B12, ON, rep5

description:
P11a_4
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: IL6-3 rep1, parasitized


title: CxCC_71_HPV73


title: T-AQP4_01 [L49759_Track-90505]


title: CxCC_70_HPV16


title: T-AQP4_01 [L49758_Track-90543]


title: SAC, P11B10, ON, rep3

description:
P11a_2
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: CxCC_69_HPV16


title: CxCC_76_HPV18

value: IIb


title: T-AQP4_01 [L49757_Track-90458]


title: IL6-3 rep1, control

value: non treated (control)


title: SAC, P11B11, ON, rep4

description:
P11a_3
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt


title: CxCC_72_HPV16

value: primary cervical cancer


title: IL6-3 rep2, control


title: T-AQP4_01 [L49756_Track-90537]


title: Clone B P30 +GLN

first: Luke

middle: B

last: Morina

address: 3400 N Charles St; CLARK HALL Rm118a

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using Cell Ranger version 6.0.2
Assembly: CHOK1GS_HD (GCA_900186095.1)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Cricetulus griseus

source_name: CHO K1GS

growth_protocol: These cells were cultured with imMEDIAte ADVANTAGE 87093C (SAFC) media, a serum-free custom made medium by Milipore Sigma, in 125 mL shake flasks (Fisher Scientific) with a working volume of 30mL. Incubation was done in a humidified orbital shaking incubator set at 37C, 80% humidity, 5% CO2 and 125 rpm shaking. The two clonal cell lines were thawed and seeded at 0.3 x 106 cells/mL.

extract_protocol:
Chromium Single Cell 3’ library construction kit
Chromium Single Cell 3’ library construction kit

treatment_protocol: The cells were passaged every 3 days with viable cell density (VCD) and viability was determined by hemocytometer using trypan blue dye exclusion. The cells were then seeded in fresh media at 0.3 x 106 cells/mL. Cells were passaged for a total of 30 passages over 90 days during the aging process.

value: CHO K1GS

value: Chinese Hamster Ovary

value: Clone B

value: 6mM L-Glutamine


title: SAC, P11A8, OFF, rep2

description:
P11a_1
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: retina


title: IL6-2 rep2, parasitized


title: Clone B P0 -GLN

description: 10X Genomics

value: L-Glutamine free


title: T-AQP4_01 [L49753_Track-90485]

description:
RawExpressionCountTable.csv
TCR_data.csv

value: Blood

value: CD4 T cell


title: IL6-2 rep3, parasitized


title: Clone B P30 -GLN

description: 10X Genomics


title: T-AQP4_01 [L49752_Track-90399]


title: IL6-2 rep1, parasitized


title: IL6-3 rep3, control


title: CTCF ChIP-seq on embryonic 16.5 day mouse forebrain, biological replicate 2

data_processing:
The fastq files of CTCF ChIP-seq data were mapped to mouse genome (mm10) and processed using the ENCODE uniform processing pipeline for ChIP-seq data (https://github.com/ENCODE-DCC/chip-seq-pipeline) with default parameters.
bigwig file represents the signal track for fold change over control from each replicate. Peak files are in narrowPeak format. Replicated peaks are the set of peak calls from the pooled replicates that are either observed in both biological/technical replicates, or are observed in two pseudoreplicates (https://www.encodeproject.org/chip-seq/histone/).
Assembly: mm10

value: forebrain

value: embryonic 16.5 day

value: CTCF (Cell Signaling, 3418, lot 3&4)


title: T-AQP4_01 [L49751_Track-90500]

value: T cell

value: AQP4 peptide pool


title: CTCF ChIP-seq on postnatal 0 day mouse forebrain

description: The library was sequenced twice on different machines.

value: postnatal 0 day


title: Clone A P30 -GLN

description: 10X Genomics

value: Clone A


title: Clone A P30 +GLN

description: 10X Genomics


title: T-AQP4_01 [L49750_Track-90536]


title: Clone A P0 -GLN

description: 10X Genomics


title: CTCF ChIP-seq on embryonic 14.5 day mouse forebrain, technical replicate 2

value: embryonic 14.5 day


title: IL6-2 rep1, control

value: Roots

value: non treated (control)


title: T-AQP4_01 [L49755_Track-90465]


title: SAC, P11A7, ON, rep1

description:
P11a_0
cds.attr_table.txt
cds.count_table.txt
cds.fpkm_table.txt
genes.attr_table.txt
genes.count_table.txt
genes.fpkm_table.txt
isoforms.attr_table.txt
isoforms.count_table.txt
isoforms.fpkm_table.txt
tss_groups.attr_table.txt
tss_groups.count_table.txt
tss_groups.fpkm_table.txt

value: starburst amacrine cell

value: Postnatal day 11


title: NF54 Day5 rep2

status: Public on Sep 01 2024

city: Silver Spring

first: Riette

last: Van Biljon

address: 10903 New Hampshire Avenue

institute: US FDA

data_processing:
Fastq files generated from Illumina Miseq software were subject to adaptor trimming using Trimmomatic v 0.39 to a final quality score >20 and adding an adaptor trimming step (Illuminaclip)
RNA-sequencing results were analyzed using Kallisto v. 0.48.0 to perform pseudoalignment and relative quantifications  (estimated counts and TPM) of reads against the PF3D7_transcriptome version 58.0.
Kallisto estimated counts were used to identify differentially expressed transcripts using DEseq2 v. 2.11.40.7
Assembly: PlasmoDB-58_Pfalciparum3D7_transcriptome
Supplementary files format and content: tabular tab delimited txt files contain Kallisto quantification results of estimated counts and transcript per million basepairs (TPMs) for each gene in each condition

organism: Plasmodium falciparum

growth_protocol: P. falciparum NF54e with PfMD3 C-terminal 3xHA tag was grown in under stationary conditions and heparin was added following appearance of gametocyte to deplete asexual parasites.

extract_protocol:
RNA was harvested using an RNeasy mini Kit (Qiagen) using 1.4 micrograms of RNA for the construction of RNA-sequencing libraries
RNA libraries for RNA-seq were prepared using Illumina Truseq stranded mRNA library preparation kit according to manufacturer's instructions

value: Stage II gametocytes


title: ZnKO clone A5 Day5 rep2


title: CTCF ChIP-seq on embryonic 16.5 day mouse forebrain, biological replicate 1


title: ZnKO clone A5 Day11 rep1

value: Stage V gametocytes


title: ZnKO clone A5 Day8 rep1

value: Stage IV gametocytes


title: ZnKO clone A5 Day8 rep2


title: NF54 Day8 rep1


title: IL6-2 rep3, control


title: NF54 Day11 rep2


title: NF54 Day5 rep1


title: ZnKO clone A5 Day11 rep2


title: Young

first: Siyuan

last: Zhu

address: 1838 North Guangzhou Avenu

institute: Nanfang Hospital, Southern Medical University

data_processing:
Alignment of 3’ end counting libraries from scRNA-seq analyses was completed utilizing 10× Genomics Cell Ranger 4.0.0. Each library was aligned to an indexed mm38 genome using Cell Ranger Count. “Cell Ranger Aggr” function was used to normalize the number of confidently mapped reads per cell across the two libraries.
Assembly: mm38
Supplementary files format and content: Processed data files are tab delimited .txt files of counts expression matrices corresponding to each sample, old  or young, of this study.

source_name: Bone marrow

extract_protocol:
Three aged mice and three young mice were sacrificed by cervical dislocation. And then detachd the femur from the tibia. Cut the proximal and distal ends of the bones, the bone marrow was flushed from mouse tibias and femurs using a 25G × 5/8" needle and plastic syringe and then kept in phosphate buffer saline (PBS) with 5% fetal bovine serum (FBS) on ice. Bone marrow cells were centrifuged at 400×g at 4℃ for 10 min. Resuspend the cells in 2 ml NH4Cl2 (pH: 7.2-7.6) for 5 min at room temperature (RT) to lyse the erythrocytes. Then centrifuge for 10 min, at 400×g, at 4℃ and resuspend the cells in 1 ml of 5% PBS/FBS. For fluorescence-activated cellsorting, cells were blocked with anti-mouse CD16/32 (BioLegend, 101302) on ice for at least 10min. Cells were then incubated for 30 min at 4℃with preconjugated fluorescence-labeled antibodies with the following combinations: APC anti-mouse Ly-6G/Ly-6C (Gr-1) Antibody (BioLegend, 108412), FITC anti-mouse/human CD11b Antibody (BioLegend, 101206). Fixable Viability Dye eFluor™ 450 (eBioscience, 65-0863) was used to stain cells to assay for viability. Cells were sorted with BD FACSAria III and the selected populations were isolated for next experiments.
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: Cd11b+ Gr1+ Myeloid cells


title: ZnKO clone A5 Day5 rep1


title: NF54 Day11 rep1


title: Old


title: IL6-2 rep2, control


title: SGBS_Day4_Replicate2

city: La Jolla

first: Amit

last: Majithia

address: 9500 Gilman Dr

institute: UCSD

data_processing:
Raw reads were aligned using Kallisto with default paramenters
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: SGBS preadipocyte cells

extract_protocol:
Total RNA was extracted (Qiagen #74104) from cells at days 0, 4, 8, and 15
RNA libraries for RNA-seq were prepared using Illumina TruSeq according to the manufacturers’ protocol to a depth of at least 50 million reads per sample with paired-end 100bp reads.

value: SGBS preadipocyte cells

tag: time point


title: SGBS_Day4_Replicate3


title: SGBS_Day0_Replicate3


title: SGBS_Day8_Replicate2


title: SGBS_Day0_Replicate2


title: SGBS_Day15_Replicate3


title: SGBS_Day15_Replicate2


title: SGBS_Day15_Replicate1


title: SGBS_Day8_Replicate1


title: SGBS_Day4_Replicate1


title: NF54 Day8 rep2


title: SGBS_Day0_Replicate1


title: SGBS_Day8_Replicate3


title: EXP2

city: Xuancheng City

first: Zhiming

last: Cui

state: ANHUI

address: Anhui province

institute: The Second Affiliated Hospital of Nantong University

description: Exp

data_processing:
The data provided by the company underwent batch effect removal, standardization, and correction for intra-group differences, resulting in an expression matrix.
Assembly: NCBI
Supplementary files format and content: The data provided by the company underwent batch effect removal, standardization, and correction for intra-group differences, resulting in an expression matrix.

organism: Rattus norvegicus

growth_protocol: Replacement of the medium occurred 24 h post-plating and continued every 2 days. To enhance the neuron purity, Ara-C at a concentration of 0.05 mg/mL was added 24 h after plating.

extract_protocol:
Routine experimental steps for extracting total RNA from cultured cells
ribo-depletion (RD)

treatment_protocol: For the nerve injury model, after 3 days of cell culture, the experimental group was stimulated with a culture solution containing 10 μM Glutamate for 1 h, while the control group received an equal volume of phosphate buffer saline. Subsequently, both groups were cultured for an additional 16 h in a Neurobasal-A culture medium for glutamate-free neurons.

value: spinal cord neurons

tag: strain

value: Sprague-Dawley

value: neonatal

value: treated with glutamate and GAL3 knockout transfection


title: EXP3

description: Exp


title: EXP1

description: Exp


title: CON3

description: CON

value: treated with saline and control transfection


title: CON1

description: CON


title: CON2

description: CON


title: scrambled siRNA supernatant replicate 2

type: RNA

city: Philadelphia

first: Stephanie

last: Daws

state: PA

address: 3500 N Broad St

institute: Temple University

description:
Biological replicate 2 of 3
S2(Sup,Normalized)

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to Arraystart Rat mRNA and lncRNA Epitranscriptomic Arrays (8 X 60k, Arraystar) at 65 degrees celsius for 17 hours in an Agilent Hybridization Oven.

scan_protocol: Scanned on Agilent Scanner G205C.

data_processing:
Agilent Feature Extraction Software (version 11.0.1.1) was used to analyze array images. Raw intensities of immuneprecipitated (IP, Cy-5 labelled) and supernatent (Sup, Cy-3 labelled) were normalized with the average of log2-scaled Spike-In RNA intensities. Probe signals have present (P) or marginal (M) QC flags in at least 3 out of 12 samples were retained for further m6A quantity analyses. m6A quantities was calculated for m6A methulation based on the IP (Cy-5) normalized intensities.
m6A quantity = IPCy5 normalized intensity where IPCy5 normalized intensity = log2 (IPCy5 raw) - Average [log2 (IPspike-in_Cy5 raw)]
SupCy3 normalized intensity = log2(SupCy3 raw) - Average [log2 (Supspike-in_Cy3 raw)]

source_name: primary neuronal culture

label_protocol: Total RNA was immuneprecipitated with anti-N6-methyladenosine (m6A) antibody. The immuneprecipitated (IP) fraction contained enriched m6A methylated RNAs and the supernatent (Sup) contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively, using the Arraystar Super RNA labeling kit.

growth_protocol: Cells were collected from the frontal cortex of P0 Sprague Dawley rat pups and grown for 7 days in vitro in 6 well plates. Plates were coated with poly-D lysine and neurons were plated at a density of 500,000 per well. Cells were cultured with primary neuron media (DMEM containing L-glutamine, 2% B-27 supplement, 25mM HEPES and 7.8g/L dextrose).

extract_protocol: RNA was extracted using the miRNeasy Mini Kit from Qiagen according to manufacturer's protocol.

treatment_protocol: For morphine exposure, cells were treated with 20uM morphine or vehicle for 72 hours and harvested after 10 days in vitro. For Alkbh5 knockdown, cells were transfected with an ON-TARGET plus Non-targeting scrambled siRNA or rat Alkbh5 siRNA using RNAiMax transfection reagent. 5ul of 20uM siRNA was mixed with 250ul OPTI-MEM media and then combined 3ul RNAiMax transfection reagent dissolved in 250ul OPTI-MEM. Transfection mixture was incubated for 10 minutes at room temperature and added to primary neurons for 6 hours. Following 6 hours, 50% of the media was replaced with primary neuron media. Cells were harvested 72 hours after transfection on the 10th day in vitro

value: frontal cortex

value: Sprague Dawley

value: scrambled siRNA

value: primary neuronal culture

tag: fraction

value: supernatent

tag: molecule type

value: unmodified RNA


title: vehicle supernatant replicate 2

description:
Biological replicate 2 of 3
V2(Sup,Normalized)

value: vehicle control


title: vehicle supernatant replicate 1

description:
Biological replicate 1 of 3
V1(Sup,Normalized)


title: Morphine supernatant replicate 2

description:
Biological replicate 2 of 3
M2(Sup,Normalized)

value: chronic morphine exposure for 3 days


title: scrambled siRNA supernatant replicate 1

description:
Biological replicate 1 of 3
S1(Sup,Normalized)


title: Morphine supernatant replicate 1

description:
Biological replicate 1 of 3
M1(Sup,Normalized)


title: Morphine supernatant replicate 3

description:
Biological replicate 3 of 3
M3(Sup,Normalized)


title: vehicle IP replicate 2

description:
Biological replicate 2 of 3
V2(IP,Normalized)

value: immuneprecipitated fraction

value: m6A methylated RNA


title: Morphine IP replicate 3

description:
Biological replicate 3 of 3
M3(IP,Normalized)


title: scrambled siRNA IP replicate 3

description:
Biological replicate 3 of 3
S3(IP,Normalized)


title: vehicle IP replicate 3

description:
Biological replicate 3 of 3
V3(IP,Normalized)


title: vehicle IP replicate 1

description:
Biological replicate 1 of 3
V1(IP,Normalized)


title: scrambled siRNA supernatant replicate 3

description:
Biological replicate 3 of 3
S3(Sup,Normalized)


title: scrambled siRNA IP replicate 2

description:
Biological replicate 2 of 3
S2(IP,Normalized)


title: vehicle supernatant replicate 3

description:
Biological replicate 3 of 3
V3(Sup,Normalized)


title: 9-RNA5

city: Palma

first: Josep

last: Muncunill Farreny

address: Carretera de Valldemossa, 79. Hospital Universitario Son Espases

institute: IdISBa

description: Gene expression data from lung resident mesenchymal stem cells from control subject

hyb_protocol: ss-cDNA samples (2.3 µg) were hybridized to GeneChip Human Gene 1.0 ST Arrays (Affymetrix, Thermo Fisher Scientific) by rotating for 16 hours at 45ºC  and subsequently washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: Array scanning was performed at the IdISBa Genomic Core Facility by using the GeneChip Scanner 3000 7G according to the manufacturer's instruction (Affymetrix, Thermo Fisher Scientific).

data_processing: Preprocessing was performed in R/Bioconductor using the oligo package. Raw CEL files were summarized and normalized through RMA (Robust Multichip Average) and quantile normalization (oligo::rma).  Quality control analys were performed with arrayQualityMetrics package. Probes were annotated with  packages pd.clariom.s.human, clariomshumantranscriptcluster.db  and  annotation file form affymetrix (Clariom S Array, human Transcript Cluster Annotations, CSV, Release 36) .

label: biotin

source_name: Lung resident mesenchymal stem cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA (15 µg) with the GeneChip WT Plus Reagent Kit (Affymetrix, Thermo Fisher Scientific) and then fragmented and biotin-labeled with the WT Terminal Labeling Kit (Affymetrix, Thermo Fisher Scientific).

growth_protocol: Cells were cultured in αMEM medium supplemented with 10% FCS and 1% penicillin/streptomycin inside a 37ºC, 5% CO2, 98% humidity incubator

extract_protocol: RNA was isolated from cultured cells using the Extractme Total RNA kit (Blirt, EM09.1) following the manufacturer's protocol

treatment_protocol: Non-adhered cells were removed by changing the media and adhered cells were maintained in culture for 4-6 days

tag: disease state

value: Control

value: Lung resident mesenchymal stem cells


title: 7-RNA(10) BA134 LSD

description: Gene expression data from lung resident mesenchymal stem cells from IPF patient

value: IPF


title: 5-RNA(5) BA130 LSE FIB_(HuGene-1_0-st-v1).CEL


title: Alkbh5 siRNA supernatant replicate 1

description:
Biological replicate 1 of 3
A1(Sup,Normalized)

value: siRNA knockdown of Alkbh5


title: Alkbh5 siRNA IP replicate 3

description:
Biological replicate 3 of 3
A3(IP,Normalized)


title: Alkbh5 siRNA supernatant replicate 2

description:
Biological replicate 2 of 3
A2(Sup,Normalized)


title: Alkbh5 siRNA IP replicate 2

description:
Biological replicate 2 of 3
A2(IP,Normalized)


title: Morphine IP replicate 1

description:
Biological replicate 1 of 3
M1(IP,Normalized)


title: Morphine IP replicate 2

description:
Biological replicate 2 of 3
M2(IP,Normalized)


title: scrambled siRNA IP replicate 1

description:
Biological replicate 1 of 3
S1(IP,Normalized)


title: Alkbh5 siRNA supernatant replicate 3

description:
Biological replicate 3 of 3
A3(Sup,Normalized)


title: 2-RNA4


title: WT_18273_8424

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

data_processing:
Partek Flow platform used for data processing
Low quality sequence trimmed; 5.7-9.2% of sequences had an average of 2 bp trimmed.
Tophat 2 was used to align reads to the mm10 genome build
Reads were quantified to mm10 using the Partek E/M annotation model
Reads were normalized to counts per million (CPM) with 0.0001 added to the result.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file including CPM for each sample (in columns) and gene (in rows)

source_name: WT fed 15 ppm hydroxy-complexed zinc

extract_protocol:
Gut was removed immediately upon sacrifice and flash frozen, and RNA extracted using a Qiagen RNEasy kit, RNA was stored at -80° C until use.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole small intestine

value: WT

tag: diet

value: 15 ppm hydroxy-complexed zinc

value: 221 days

tag: Sex

value: male


title: KO_18273__8359

source_name: Zip4 KO fed 40 ppm hydroxy-complexed zinc

value: Zip4 KO

value: 40 ppm hydroxy-complexed zinc

value: 240 days


title: WT_18273_8353

value: 237 days


title: Het_18273_8725

source_name: Zip4 het fed 15 ppm hydroxy-complexed zinc

value: Zip4 het

value: 143 days


title: 1-RNA1

tag: cell type


title: KO_18273_8355


title: 6-RNA(4) BA121 LSD


title: HET_18273_8040

value: 338 days


title: patient 33

city: Buffalo

first: Jianxin

last: Wang

state: NY

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

description: archival colorectal cancer tissue

data_processing:
Raws fastq files are processed with nf-core/rnaseq: 3.13.2 pipeline under Nexflow 23.10.1.
Assembly: GRCh38
Supplementary files format and content: comma separated text file

source_name: colorectal

extract_protocol:
SureSelect XT HS2 RNA Target Enrichment System (Agilent Inc)
200ng of RNA was fragmented and converted to cDNA followed by end repair, duplex UMI adaptor ligation, and 11 cycles of PCR to complete the dual- index adapters. Unique dual-indexed, molecular-barcoded libraries were purified with AMPureXP beads (Beckman Coulter) and validated for appropriate size (225-275bp) on a Tapestation 4200 DNA1000 screentape (Agilent Inc.). 200ng of purified library was then hybridized to the SureSelectXT Human All Exon V8+UTR Capture library (Agilent Inc.). The hybridized regions were then bound to streptavidin magnetic beads and washed to remove any non-specific bound products. Eluted library underwent a second 13 cycle PCR amplification to generate enough material for sequencing. Final libraries were purified, measured by Tapestation 4200 DNA1000 screentape (250-350bp), and quantitated using KAPA qPCR (KAPA Biosystems). Individual libraries were pooled in equimolar 2nM final concentration. Each pool is denatured and diluted to 200pM with 1% PhiX control library added. The resulting pool is then loaded into the appropriate NovaSeq Reagent cartridge, as determined by the number of sequencing cycles desired, and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

value: colorectal


title: patient 34

description: archival colorectal cancer tissue


title: 15-BA125 LSD


title: Het_18271_8728

source_name: Zip4 het fed 15 ppm amino-complexed zinc

value: 15 ppm amino-complexed zinc

value: 141 days


title: HET_18271_7844

value: 363 days


title: Alkbh5 siRNA IP replicate 1

description:
Biological replicate 1 of 3
A1(IP,Normalized)

value: frontal cortex

value: Sprague Dawley

value: siRNA knockdown of Alkbh5

value: primary neuronal culture

value: immuneprecipitated fraction

value: m6A methylated RNA


title: patient 30

description: archival colorectal cancer tissue


title: patient 31

description: archival colorectal cancer tissue


title: WT_18271_8499

source_name: WT fed 15 ppm amino-complexed zinc

value: whole small intestine

value: WT

value: 218 days

value: male


title: patient 27

description: archival colorectal cancer tissue


title: patient 28

description: archival colorectal cancer tissue


title: KO_18271_8519

source_name: Zip4 KO fed 40 ppm amino-complexed zinc

value: Zip4 KO

value: 40 ppm amino-complexed zinc

value: 228 days

value: Female


title: patient 26

description: archival colorectal cancer tissue

value: colorectal


title: patient 29

description: archival colorectal cancer tissue


title: patient 32

description: archival colorectal cancer tissue


title: patient 23

description: archival colorectal cancer tissue


title: KO_18271_8351

value: 198 days


title: patient 25

description: archival colorectal cancer tissue


title: 10-RNA16 DLung

value: Control

value: Lung resident mesenchymal stem cells


title: WT_18271_8438

value: 15 ppm amino-complexed zinc

value: 210 days


title: patient 24

description: archival colorectal cancer tissue


title: patient 22

description: archival colorectal cancer tissue


title: patient 18

description: archival colorectal cancer tissue


title: patient 21

description: archival colorectal cancer tissue


title: patient 20

description: archival colorectal cancer tissue


title: patient 16

description: archival colorectal cancer tissue


title: patient 15

description: archival colorectal cancer tissue


title: patient 19

description: archival colorectal cancer tissue


title: patient 14

description: archival colorectal cancer tissue


title: h.CD34+, shBCL11A + Hydro C, Day 10

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

state: WA

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

data_processing:
RNA-seq mapping, demultiplexing and quantification were performed with STARsolo using GENCODEv25 for annotation, featureCounts for gene counts and DESeq2 to identify differentially expressed genes (DEGs) between groups.
Assembly: hg38
Supplementary files format and content: summary stats per sample, txt format
Supplementary files format and content: gene counts per sample, csv format

extract_protocol:
Total RNA was isolated from 106 cells using Trizol and reverse transcribed with RNase OUT kits. Quantitative real-time PCR was performed. To assess BCL11A knockdown, RNA was extracted with the Qiagen RNeasy Micro Kit and reverse transcribed with the iScript Reverse Transcription Supermix. mRNA levels and expression ratios were calculated.
RNAseq of BCL11A-microdeletion patients was performed. The day 3 and day 5 progeny of CD34+ cells were profiled with the Illumina libraries constructed using Prime-seq and sequenced at read lengths 28x8x94.

value: hematopoietic pluripotent stem cells

tag: cell line

value: Cells treated with shBCL11A+ Hydro C D10 +H

tag: time

value: Day 10


title: patient 13

description: archival colorectal cancer tissue

tag: tissue


title: h.CD34+, shBCL11A + Hydro B, Day 10

tag: treatment

value: Cells treated with shBCL11A+ Hydro B D10 +H


title: h.CD34+, shLuc + Hydro B, Day 10

value: Cells treated with shLuc + Hydro B D10 +H


title: h.CD34+, shControl + Hydro C, Day 10

value: Non Treated Cells + Hydro C D10 +H


title: h.CD34+, shControl + Hydro B, Day 10

value: Non Treated Cells + Hydro B D10 +H


title: h.CD34+, shLuc + Hydro A, Day 10

value: Cells treated with shLuc + Hydro A D10 +H


title: h.CD34+, shControl + Hydro A, Day 10

value: Non Treated Cells + Hydro A D10 +H


title: h.CD34+, shBCL11A + Hydro A, Day 10

value: Cells treated with shBCL11A+ Hydro A D10 +H


title: h.CD34+, shLuc + Hydro C, Day 10

value: Cells treated with shLuc + Hydro C D10 +H


title: h.CD34+, shBCL11A - Hydro C, Day 10

value: Cells treated with shBCL11A- Hydro C D10 -H


title: h.CD34+, shBCL11A - Hydro B, Day 10

value: Cells treated with shBCL11A- Hydro B D10 -H


title: h.CD34+, shLuc - Hydro A, Day 10

value: Cells treated with shLuc - Hydro A D10 -H


title: h.CD34+, shLuc - Hydro C, Day 10

value: Cells treated with shLuc - Hydro B D10 -H


title: h.CD34+, shControl - Hydro C, Day 10

value: Non Treated Cells - Hydro C D10 -H


title: h.CD34+, shControl - Hydro B, Day 10

value: Non Treated Cells - Hydro B D10 -H


title: h.CD34+, shControl - Hydro A, Day 10

value: hematopoietic pluripotent stem cells

value: Non Treated Cells - Hydro A D10 -H


title: h.CD34+, shBCL11A - Hydro B, Day 5

value: Cells treated with shBCL11A- Hydro B D5

value: Day 5


title: patient 17

description: archival colorectal cancer tissue

value: colorectal


title: h.CD34+, shBCL11A - Hydro C, Day 5

value: Cells treated with shBCL11A- Hydro C D5


title: h.CD34+, shBCL11A + Hydro C, Day 5

value: Cells treated with shBCL11A+ Hydro C D5


title: h.CD34+, shLuc - Hydro B, Day 5

value: Cells treated with shLuc - Hydro B D5


title: h.CD34+, shLuc + Hydro C, Day 5

value: Cells treated with shLuc + Hydro C D5


title: h.CD34+, shLuc - Hydro A, Day 5

value: Cells treated with shLuc - Hydro A D5


title: h.CD34+, shLuc + Hydro B, Day 5

value: Cells treated with shLuc + Hydro B D5


title: h.CD34+, shControl - Hydro B, Day 5

value: Non Treated Cells - Hydro B D5


title: h.CD34+, shControl - Hydro C, Day 5

value: Non Treated Cells - Hydro C D5


title: h.CD34+, shControl - Hydro A, Day 5

value: Non Treated Cells - Hydro A D5


title: h.CD34+, shBCL11A - Hydro A, Day 10

value: Cells treated with shBCL11A- Hydro A D10 -H

value: Day 10


title: h.CD34+, shControl + Hydro B, Day 5

value: Non Treated Cells + Hydro B D5


title: h.CD34+, shLuc - Hydro B, Day 10

value: hematopoietic pluripotent stem cells

value: Cells treated with shLuc - Hydro B D10 -H


title: h.CD34+, shBCL11A - Hydro A, Day 3

value: Cells treated with shBCL11A- Hydro A D3

value: Day 3


title: h.CD34+, shControl + Hydro C, Day 5

value: Non Treated Cells + Hydro C D5

value: Day 5


title: h.CD34+, shBCL11A - Hydro B, Day 3

value: Cells treated with shBCL11A- Hydro B D3


title: h.CD34+, shControl + Hydro A, Day 5

value: Non Treated Cells + Hydro A D5


title: CxCC_95_HPV82

value: primary cervical cancer

value: IIIb


title: h.CD34+, shBCL11A + Hydro B, Day 3

value: Cells treated with shBCL11A+ Hydro B D3


title: h.CD34+, shBCL11A + Hydro A, Day 3

value: Cells treated with shBCL11A+ Hydro A D3


title: h.CD34+, shLuc - Hydro C, Day 3

value: Cells treated with shLuc - Hydro C D3


title: h.CD34+, shLuc - Hydro B, Day 3

value: Cells treated with shLuc - Hydro B D3


title: h.CD34+, shLuc + Hydro C, Day 3

value: Cells treated with shLuc + Hydro C D3


title: h.CD34+, shLuc + Hydro B, Day 3

value: Cells treated with shLuc + Hydro B D3


title: h.CD34+, shControl - Hydro C, Day 3

value: Non Treated Cells - Hydro C D3


title: h.CD34+, shBCL11A + Hydro A, Day 5

value: hematopoietic pluripotent stem cells

value: Cells treated with shBCL11A+ Hydro A D5


title: h.CD34+, shBCL11A + Hydro B, Day 5

value: Cells treated with shBCL11A+ Hydro B D5


title: h.CD34+, shLuc - Hydro C, Day 5

value: Cells treated with shLuc - Hydro C D5


title: h.CD34+, shControl - Hydro B, Day 3

value: Non Treated Cells - Hydro B D3

value: Day 3


title: h.CD34+, shControl + Hydro C, Day 3

value: Non Treated Cells + Hydro C D3


title: h.CD34+, shControl + Hydro B, Day 3

value: Non Treated Cells + Hydro B D3


title: h.CD34+, shControl + Hydro A, Day 3

value: Non Treated Cells + Hydro A D3


title: h.CD34+, shLuc + Hydro A, Day 5

value: Cells treated with shLuc + Hydro A D5

value: Day 5


title: ZAP-HA in MT4, rep2

city: London

first: Daniel

last: Goncalves-Carneiro

address: Sir Alexander Fleming Building, Imperial College Rd

country: United Kingdom

institute: Imperial College London

data_processing:
Adapter Sequence removed by cutadapt in FASTX-toolkit. Reads sorted by barcoded using fastx_collapser in FASTX-toolkit. Nine nucleotides trimed using fastx_trimmer in FASTX-toolkit. Bowtie and Samtools used for alignement. Reads per nucleotide determined using mpileup and mpileup_To_counts.
Assembly: GRCh38 - hg38
Supplementary files format and content: File: BCBC1_col_trim.txt, sorted and cleaned reads for rep1. Text fileFile: BCBC3_col_trim.txt, sorted and cleaned reads for rep1. Text file.

growth_protocol: Cells were culture in RPMI supplemented with 10%FBS and gentamicin, at 37˚C with 5% CO2.

extract_protocol:
ZAP:RNA complexes were crossedlinked by exposure to UV radiation for 1min. Cells were lysed and ZAP was purified by immunoprecipitation. RNA bound to ZAP was released by proteinase K digestion and phenol:chloroform:isoamyl alcohol extraction.
A 3’ adapter was ligated to the RNA, gel purified and subsequently ligated to a 5'adapter. Resulting nucleic acids were reversed transcribed and amplified using Illumina primers.

treatment_protocol: At 48h after doxycycline treatment, 4-thiouridine was added to the culture mediam and incubated for 18h at 37˚C with 5% CO2.

value: T lymphocyte

value: Doxycycline-treatment to induce ZAP expression


title: MKL-2 ALTO 3

city: Seattle

first: Denise

last: Galloway

address: 1100 Fairview Ave N

department: Human Biology/Pathogen-Associated Malignancies IRC

institute: Fred Hutch Cancer Center

data_processing:
Image analysis and basecalling was performed using Illumina's Real Time Analysis v3.4.4 software, followed by demultiplexing of indexed reads and generation of FASTQ files with Illumina's bcl2fastq-2.20 software.
Sequenced reads were aligned to a  custom GRCh38 reference (with an added contig for Merkel cell polyomavirus isolate MKL2) using STAR2 aligner v2.7.7a in the two-pass mode.
STAR2's internal quantification method was used to generate gene-level raw counts using edited gencode v38 gene definitions (with MKL2 ST and LT genes added)
Assembly: GRCh38 (custom)
Supplementary files format and content: tab-separated file containing raw gene counts

growth_protocol: cells were cultured in RPMI 1640 HEPES media containing 10% FBS and pen/strep in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
total RNA was extracted using RNeasy mini plus kit (Qiagen).
RNA-seq libraries were constructed from 500ng total RBA using the stranded TruSeq RNA library prep kit according to the manufacturer's protocol.

treatment_protocol: cells were treated with 0.5 ug/mL doxycycline for 48 h prior to harvest

value: skin cancer cell line

value: ALTO

tag: genotype

value: 0.5 ug/mL doxycycline


title: MKL-2 RFP 3

value: RFP


title: ZAP-HA in MT4, rep1


title: PSEN.aged.4

city: Baltimore

first: Peter

middle: C

last: Searson

address: 3400 North Charles Street

institute: Johns Hopkins University

data_processing:
alignment and quantification to GRCh38 using Rsubread
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) was calculated for each gene as outlined in Trapnell et al., Nature Biotechnology, 2010.
Normalization using variance stabilizing regularized logarithm transformation (rlog) using DESeq2
Assembly: hg38
Supplementary files format and content: .txt file containing FPKM values for all of the above conditions across three biological replicates each

source_name: PSEN1(M146V) mutant

growth_protocol: Cell culture was conducted at 5% CO2 and 37 °C.  iBMECs were co-differentiated with neural cells that provide relevant cues, including Wnt/beta-catenin signaling and then purified. iBMECs were seeded into a 150 µm diameter cylinder suspended in a bulk collagen I hydrogel at a density of 80 million cells/mL and maintained in human endothelial serum-free medium supplemented with 1% human serum from platelet-poor plasma (PDS), 1% penicillin-streptomycin, 2 ng/mL human recombinant basic fibroblast growth factor, and 10 µM all-trans retinoic acid. After the first 24 h, microvessels were maintained in human endothelial serum-free medium supplemented with 1% PDS and 1% penicillin-streptomycin.

extract_protocol:
Microvascular models were washed with 1x PBS and perfused with RLT buffer; downstream lysate was collected and supplemented with β-mercaptoethanol, before isolating RNA using a RNeasy Mini Kit (Qiagen) with DNase I digestion (Qiagen).
RNA libraries were prepared with the Takara SMART-seq v4 kit following QC of purified lysates.

treatment_protocol: When supplemented with young or aged human serum, the 1% PDS volume in iBMEC maintenance media was replaced with a 1% volume of human serum pooled equally from 50 male donors with an average age of 25 (young) or 65 (aged).

value: PSEN1(M146V) mutant

value: induced iPSC-derived brain microvascular endothelial-like cell

value: aged serum


title: MKL-2 RFP 2


title: MKL-2 ALTO 2


title: PSEN.aged.5


title: PSEN.aged.3


title: h.CD34+, shLuc - Hydro A, Day 3

value: hematopoietic pluripotent stem cells

value: Cells treated with shLuc - Hydro A D3


title: PSEN.aged.6


title: MKL-2 ALTO 1


title: PSEN.aged.2


title: MKL-2 RFP 1


title: PSEN.aged.1


title: PSEN.young.6

value: young serum


title: PSEN.young.4


title: PSEN.young.5


title: PSEN.young.2


title: h.CD34+, shControl - Hydro A, Day 3

value: Non Treated Cells - Hydro A D3

value: Day 3


title: h.CD34+, shLuc + Hydro A, Day 3

value: Cells treated with shLuc + Hydro A D3


title: PSEN.young.1


title: PSEN.young.3


title: PSEN.control.5

value: control media


title: PSEN.control.4


title: PSEN.control.6


title: PSEN.control.3


title: PSEN.control.1


title: PSEN.control.2


title: APP.aged.6

source_name: APP(Swe) mutant

value: APP(Swe) mutant


title: APP.aged.5


title: APP.aged.4


title: APP.aged.3


title: APP.young.5


title: APP.young.3


title: APP.aged.2


title: APP.young.1


title: APP.aged.1


title: APP.young.6


title: APP.control.2


title: APP.control.5


title: APP.control.1


title: APP.young.2


title: WT.aged.4

source_name: WT control

value: WT control


title: WT.aged.6


title: WT.aged.3


title: APP.control.6


title: WT.aged.5


title: WT.aged.2


title: WT.young.5


title: APP.control.3


title: WT.young.6


title: WT.young.4


title: WT.young.3


title: WT.aged.1


title: WT.young.1


title: WT.young.2


title: WT.control.6


title: APP.young.4


title: APP.control.4


title: WT.control.1


title: LNCaP, ETV5OE, rep2

city: Pohang

first: Jongeun

last: Lee

address: 77 Cheongam-ro

country: South Korea

institute: POSTECH

description:
LNCaP_ETV5_2
50E-1R

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated.
Artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed to reduce biases using Trimmomatic. (parameters - base quality >= 3, window size: 4, mean quality:15, min length >= 36 bp).
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner.
The aligned reads were assembled using StringTie.
Expression profiles are represented as read count and normalization value, based on the transcript length and depth of coverage. The FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value is used as a normalization value.
Assembly: hg38
Supplementary files format and content: List of differentially expressed genes (DEGs) between control and ETV5-overexpressing LNCaP cells are presented in data2_LNCaP.xlsx file. ETV5-overexpression versus Control fold change, p-value, mean, sd, FPKM and read count for each sample are also shown in data2_LNCaP.xlsx file.

source_name: LNCaP

extract_protocol:
Total RNA was extracted using TRIzol Reagent (GeneAll, Seoul, Republic of Korea) according to the manufacturer's protocol.
The DNA library for mRNA sequencing was generated using the TruSeq RNA Sample Prep Kit Gold (Illumina). The DNA libraries were multiplexed and pooled for sequencing on the NovaSeq 6000 platform with paired-end reads.

value: LNCaP

value: Prostate carcinoma cells

value: ETV5 overexpression


title: WT.control.2


title: LNCaP, Control, rep2

description:
LNCaP_CON_2
con-2

value: WT


title: LNCaP, ETV5OE, rep1

description:
LNCaP_ETV5_1
50E-1


title: U937_NCG_TH

city: Shanghai

first: Haobin

last: Ye

address: 2005 Songhu Rd

institute: Fudan University

data_processing:
Basecalling was performed using CASAVA version 1.8
Reads were aligned to the hg38 genome assembly using hisat2 version 2.0.5.

growth_protocol: Leukemia cell lines were cultured in RPMI-1640 (roswell park memorial institute 1640 with 10% foetal bovine serum, 100 U/ml penicillin, and 100 mg/ml streptomycin) at 37℃ in an atmosphere of 5.0% CO2.

extract_protocol:
Cells were collected and flash frozen on -80℃. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For alexidine treatment: leukemia cell lines were treated with alexidine (1 μM), and control were treated with DMSO at the same volumes. For mitochondrial membrane potential high (MMP-high) or low (MMP-low) cells: leukemia cell lines, AML patient sample or bone marrow derived MOLM-13 cells were stained with TMRM fluorescence probe (15nM, 100nM, 15nM respectively) at 37℃ cell incubator, after incubation, staining was stop by addition of cold FACS buffer, cells were then washed and sorted by FACSARIA III.


title: U937_NCG_TL


title: THP1_TL


title: LNCaP, Control, rep1

description:
LNCaP_CON_1
con-1R


title: MV411_TL


title: HL60_NCG_TH


title: M13_NCG_TL


title: U937_TL


title: THP1_-TH


title: M13_TL


title: HL60_NCG_TL


title: M13_NCG_TH


title: HL60_TH


title: HL6-_TL


title: MV411_TH


title: U937_TH


title: ZXL_TL

source_name: Peripheral Blood

value: Peripheral Blood

value: leukemia cell


title: WT.control.5

value: induced iPSC-derived brain microvascular endothelial-like cell


title: ZXL_TH


title: M13_TH


title: WT.control.4


title: SJT_TL


title: WT.control.3


title: SJT_TH


title: LMH_BM_TL

value: Bone marrow


title: KHT_TL


title: LMH_BM_TH


title: KHT_TH


title: HXP_TL


title: U937_C

value: DMSO


title: HXP_TH


title: U937_A

value: Alexidine


title: THP1_C


title: MV411_C


title: THP1_A


title: MOLT4_C


title: MOLT4_A


title: KU812_A


title: MOLM-13_A


title: MV411_A


title: K562_C


title: KU812_C


title: MOLM-13_C


title: HL60_A


title: K562_A


title: HEL_C

source_name: HEL

value: HEL


title: HL60_C


title: HEL_A


title: n-1

city: Qingdao

first: Hanqing

last: Xia

address: No.1677, Wutai Mountain, Huangdao District

department: The department of urology

institute: Affiliated Hospital of Qingdao University

data_processing:
Correlation analysis was performed by R. Correlation of two parallel experiments provides the evaluation of the reliability of experimental results as well as operational stability. The correlation coefficient between two replicas was calculated to evaluate repeatability between samples. The closer the correlation coefficient gets to 1, the better the repeatability between two parallel experiments.
RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts.
Principal component analysis (PCA) was performed with R package gmodels (http://www.r-project.org/) in this experience. PCA is a statistical procedure that converts hundreds of thousands of correlated variables (gene expression) into a set of values of linearly uncorrelated variables called principal components. PCA is largely used to reveal the structure/relationship of the samples/datas.
Assembly: hg38
Supplementary files format and content: all.genes.expression.annot.xls

source_name: kidney

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB#7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chainreaction (PCR) amplified.
The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: kidney

value: Clear Cell Renal Cell Carcinoma

tag: group

value: adjacent normal


title: n-2


title: q-1

value: tumor


title: 75y_M7

city: Beijing

first: xin

last: gao

address: dongcheng street

department: The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics

institute: Beijing Hospital

data_processing:
To obtain clean, high-quality reads, we used Cutadapt (version 1.9) to filter reads by removing adapters and poly-A and poly-G sequences, reads with more than 5% unknown nucleotides (N), and low-quality reads with more than 20% of bases with a quality value (Q) ≤ 20.
After quality checks using FastQC (version 0.11.9), the HISAT2 (version 2.2.1) software package was used to align the reads to the reference genome (hg38).
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: WBC

extract_protocol:
Fresh peripheral blood collected in EDTA tubes was mixed with three volumes of red blood cell lysis buffer (Solarbio, R1010) and gently vortexed for 15 minutes on ice to lyse the red blood cells. After centrifugation at 4°C and 450 × g for 10 minutes, the leukocytes were separated. Total RNA was extracted from the leukocytes using TRIzol reagent (Thermo Fisher, 15596018).
Whole-transcriptome sequencing library preparation and sequencing were performed by Lianchuan Biotechnology Co., Ltd. (Hangzhou, China).

value: WBC

value: white blood cell

value: healthy

tag: age (years)


title: n-3


title: q-2


title: 75y_M6


title: 75y_M3


title: 75y_M5


title: 75y_M4


title: 75y_M2


title: 75y_M1


title: 75y_F7


title: 60y_M5


title: 75y_F3


title: 75y_F1


title: 60y_M4


title: 75y_F2


title: 75y_F4


title: 60y_M3


title: 75y_F6


title: 60y_F4


title: 60y_F3


title: 60y_F2


title: q-3


title: 60y_F5


title: 60y_M2


title: 60y_M1


title: 60y_F1


title: 30y_M6


title: 30y_M5


title: 75y_F5


title: Escherichia coli DH5a, TCMV0120 TCMV0084 TCMV0086 replicate 1

city: Norwich

first: Thomas

middle: Cameron

last: McLean

state: Norfolk

address: Norwich Research Park

department: Molecular Microbiology

institute: John Innes Centre

data_processing:
Reads were mapped to the DH5a + plasmid genome fasta using Bowtie2 giving the BAM and BAI files
Perbase command line tool (https://github.com/sstadick/perbase) was used on the BAM files in "only-depth" mode to count read coverage per base for each BAM file giving the xyle#.csv files
Custom python script was used to calculate the average read depth from the Perbase output file for each region: DH5a chromosome, plasmid 1, plasmid 2 and plasmid 3 giving the xyle#_regions.csv files. This was then used to create a normalised plasmid copy number per chromosome for each sample
Assembly: GenBank: CP026085.1
Supplementary files format and content: CSV files: comma-seperated value files with read-depth per base of each sample
Supplementary files format and content: CSV files: comma-seperated value files with average read-depth per genomic loci of each sample
Library strategy: Deep-sequencing

organism: Escherichia coli

growth_protocol: E. coli DH5a cells containing relevant expression plasmids were grown to a logarithmic phase from a 1:100 dilution of overnight culture. Induction of KorB WT expression was achieved with 0.2% arabinose. Induction of KorA WT required no additional IPTG. 5 mL of culture was pelleted for deep-sequencing.

extract_protocol:
Cultures for deep-sequencing prepared as for xylE reporter gene assays with 5 mL of culture resuspended in 300 µL Puregene cell lysis solution (Qiagen, UK) before being incubated at 50°C for 10 min. 2 µL RNase A (20 mg/mL) was added and the samples were mixed by inversion 25 times before incubation at 37°C for 60 min. The samples were cooled to room temperature and 100 µL Puregene protein precipitation solution (Qiagen, UK) was added. Samples were briefly vortex, incubated on ice for 10 min and protein precipitate removed via centrifugation. The supernatant was removed to a fresh microcentrifuge tube containing 600 µL isopropanol and mixed via inversion 50 times. DNA was pelleted via centrifugation, supernatant removed and pellet washed with 600 µL 70% ethanol before a final centrifugation. The supernatant was carefully removed and the DNA resuspended in 100 µL distilled water
Illumina sequencing libraries were prepared using the tagmentation-based and PCR-based Illumina DNA Prep kit and custom IDT 10bp unique dual indices (UDI) with a target insert size of 280 bp. Not additional DNA fragmentation or size selection steps were performed.

value: KorA +, KorB +

value: 0.2% arabinose


title: Escherichia coli DH5a, TCMV0120 pDM2.1 TCMV0086 replicate 3

value: KorB +


title: Escherichia coli DH5a, TCMV0120 TCMV0084 TCMV0086 replicate 2


title: 30y_M3


title: Escherichia coli DH5a, TCMV0120 TCMV0084 pBAD33 replicate 3

value: KorA +


title: 30y_M2


title: 30y_F5


title: Escherichia coli DH5a, TCMV0120 pDM2.1 TCMV0086 replicate 2


title: Escherichia coli DH5a, TCMV0120 TCMV0084 pBAD33 replicate 2


title: Escherichia coli DH5a, TCMV0120 pDM2.1 TCMV0086 replicate 1


title: Escherichia coli DH5a, TCMV0120 TCMV0084 pBAD33 replicate 1


title: 30y_F4


title: 30y_F2


title: Escherichia coli DH5a, TCMV0120 pDM2.1 pBAD33 replicate 1

value: Control


title: 30y_F3


title: Escherichia coli DH5a, TCMV0120 pDM2.1 pBAD33 replicate 3


title: Escherichia coli DH5a, TCMV0120 TCMV0084 TCMV0086 replicate 3


title: CUTRUN_FOXO1_SUDHL4_HA_FOXO1_FKBP_24hB

first: Scott

last: Hiebert

state: Tennessee

address: 2220 Pierce Ave, Hiebert Lab PRB 512

data_processing:
Adaptor trimming: Adaptors were trimmed using Trimmomatic with flollowing settings ILLUMINACLIP:adaptorfile:2:30:7, LEADING:15, TRAILING:15, MINLEN:15
File conversion and read filtering: SAM fies were converted to BAM files using samtools view with the options -S -b. Low quality reads were removed using samtools view with the following options -F 4 and -q 10. Filtered BAM files were sorted and indexed using samtools sort and samtools index respectively.
Spike-in quantication and removal: Spike-in reads were quantified using samtools idxstats to quantify reads aligned to each chromosome. Reads aligned to dm3 chromosomes were summed in R to calculate the total number of spike-in reads. A bam file containing only hg19 reads was created using samtools view with the following options -bh and the names of the hg19 chromosomes. These files were resorted and indexed as described in the previous step.
Differential analysis: Peaks were called using MACS2, reads were quantified with DiffBind, and differential analysis was performed with DEseq2.
Visualization files (bedgraph) are included as negative data.  Did not perform any peak calling or differential expression.
Assembly: hg19/dm3 (ChiP) hg19/Ecoli (C&R)
Supplementary files format and content: Visualization files (bedgraph)
Library strategy: CUT&RUN

source_name: DLBCL Cell Line

growth_protocol: NU-DUL-1 and SU-DHL-4 cells were cultured in RPMI 1640 + 10% Fetalplex +1% L-Glutamine + 1% PenStrep. OCI-LY1 cells were cultured in IDMDM + 10% FetalPlex +1% L-Glutamine + 1% PenStrep. Cells were subcultured the day before the experiment, incubated at 37C with 5% CO2, and harvested while in log phase growth.

extract_protocol:
CUT&RUN experients were performed using the EpiCypher CUTANA CUT&RUN Kit according to the manufacturer's reccommendations using anti HA (CST C29F4) at 1:800.
Libraries were constucted using the NEBNext Ultra II DNA Library Prep kit according to the manufacturer's protocol.

treatment_protocol: dTAG-47 was added to culture medium to a final concentration of 500 nm at the indicated timepoints.

value: GC-DLBCL

value: 24h dTAG-47

tag: chip antibody

value: HA


title: CUTRUN_FOXO1_HA_SUDHL4_FOXO1_FKBP_24hA


title: 30y_F1


title: 30y_M4


title: CUTRUN_FOXO1_SUDHL4_HA_FOXO1_FKBP_0hB

value: 0h (untreated)


title: CUTRUN_FOXO1_HA_OCILY1_FOXO1_FKBP_24B


title: CUTRUN_FOXO1_HA_OCILY1_FOXO1_FKBP_24hA


title: CUTRUN_FOXO1_HA_OCILY1_FOXO1_FKBP_0hA


title: 30y_M1


title: D-Allose_6

city: Itami

first: Akane

last: Kanasaki

state: Hyogo

address: 5-3 Kita-Itami

country: Japan

institute: Matsutani Chemical Industry Co., Ltd.

description: Gene expression data from the hippocampus of aged mice continuously fed a diet with D-alloset.

hyb_protocol: Biotin-labeled cDNA was injected onto the microarray and hybridized with the probes using a GeneChip hybridization apparatus (Hybridazation oven 645).

scan_protocol: Arrays were scanned in the GCS 3000 7G scanner.

data_processing: All microarray datasets were analyzed using Affymetrix default analysis settings and global scaling as a normalization method.

source_name: mouse fed a diet with D-allose

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol.

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

value: hippocampus

value: continuously fed a diet with D-alloset.