title: CTCF_Input

city: Pasadena

first: Jimmy

middle: K

last: Guo

address: 1200 E California Blvd

institute: Caltech

data_processing:
Paired-end RNA sequencing reads were trimmed to remove adaptor sequences using Trim Galore! v0.6.2 and assessed with FastQC v0.11.8. Read pairs were then aligned to a combined genome reference containing the sequences of repetitive and structural RNAs (ribosomal RNAs, snRNAs, snoRNAs, 45S pre-rRNAs, tRNAs) using Bowtie2. The remaining reads were then aligned to a combined genome reference containing the mouse (mm10) and human (hg38) genomes using STAR aligner181. PCR duplicates were removed using the Picard MarkDuplicates function. For mixing experiments, only reads that mapped uniquely in the genome and unambiguously to the human or mouse genomes were kept for further analysis. For experiments done in a single species, the appropriate reference genome and alignments were used (mm10 for mouse and hg38 for human). These reads were then used for downstream analysis.  For computing enrichments, all human (hg38) and mouse (mm10) annotated genes (RefSeq, downloaded from UCSC GRCh38 and GRCm38, respectively) were used as a reference set except for the genes encoding the transfected proteins. We treated exonic regions and intronic regions of each annotated gene as separate reference genes for computing enrichment. For each reference gene, we enumerated 100 nucleotide windows that span across the gene; for each window, we calculated: (i) the number of reads overlapping the window in the protein elution sample (e.g., CLIP or CLAP) and (ii) the maximum of either the number of observed reads over the window or the median read count over all windows within the gene in the input sample. Because all windows overlapping a gene should have the same expression level in the input sample, this approach provides a conservative estimation of the input coverage because it prevents windows from being scored as enriched if the input values over a given window are artificially low due to stochastic fluctuation, while at the same time accounting for any non-random issues that lead to increases in read counts over a given window (i.e., alignment artifacts leading to non-random assignment or pileups). To directly compare the number of reads within each window between sample and input, we normalized each window count by the total number of reads sequenced and the overall complexity within each sample. For example, if one sample was sequenced twice as deeply as another, then we would expect to observe – on average – twice as many reads over a given window for that sample. To account for the differences in the number of mapped (aligned) reads between samples, we scaled the total number of sequenced reads by the proportion of aligned reads within each sample. For each window, we computed enrichment by dividing the normalized sample counts by the normalized input counts. Nominal p-values were calculated for each window using a binomial test where k (number of successes) is defined as the number of reads in the protein elution samples within the window, N (number of trials) is the sum of the number of reads in the protein elution and input samples, and p (probability of success) is the expected number of reads in the elution sample divided by the sum of the expected number of reads per window in elution and input samples. (The expected number of reads is defined as the total number of reads scaled by the proportion of aligned reads within each sample). For plotting and reporting purposes, we considered all regions with a nominal binomial p-value < 10-6 as significant. However, the overall results reported are robust to the precise p-value cutoff used.
Assembly: mm10, hg38
Supplementary files format and content: tab-delimited text file includes gene window enrichment calculations

extract_protocol: Cells were lysed in 1 mL lysis buffer (50mM Tris pH 7.5, 100mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 1X Promega PIC). For CLIP samples, RNA was digested with Ambion RNase I (1:3,000 dilution) to achieve a size range of 100-500 nucleotides in length. We used a fixed RNase condition for all experiments to enable comparison between proteins. Lysates were precleared by mixing with Protein G beads (Dynabeads) for 30 minutes at 4°C. Target proteins were immunoprecipitated overnight at 4°C from 10 million cells with 5 μg of antibody coupled to 40 μL of Protein G beads in 100 μL lysis buffer. Antibodies were pre-coupled to beads for 1 hour at room temperature with mixing, followed by 3 washes with lysis buffer to remove unbound protein. After immunoprecipitation, beads were washed four times with high salt wash buffer (50 mM TrisHCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) and four times with wash buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, 0.2% Tween-20). RNA and protein were eluted by incubating in NLS elution buffer (20 mM Tris-HCl pH 7.5, 10 mM EDTA, 2% N-lauroylsacrosine, 2.5 mM TCEP) supplemented with 100 mM DTT at 50°C for 20 minutes. Samples were then run through an SDS-PAGE gel and transferred to a nitrocellulose membrane using the iBlot transfer system. The region 70 kDa above the molecular weight of the protein of interest was isolated and treated with Proteinase K (NEB), followed by purification with RNA Clean & Concentrate-5 (Zymo). Anti-V5 antibody (Bethyl, A190-120A) was used for all CLIP experiments.  For CLAP samples, cells were resuspended in 1 mL of cold lysis buffer (50 mM HEPES pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) supplemented with 1X Protease Inhibitor Cocktail (Promega), 200 U of RiboLock (NEB), 20 U of TURBO DNase (Ambion), and 1X manganese/calcium mix (0.5mM CaCl2, 2.5 mM MnCl2). Samples were incubated on ice for 10 minutes and then at 37°C for 10 minutes at 1150 rpm shaking on a ThermoMixer (Eppendorf). Lysates were cleared by centrifugation at 15000g for 2 minutes and the supernatant was collected for capture to HaloLink Resin (Promega). For each CLAP capture, 200 μL of 25% HaloLink Resin (50 μL of HaloLink Resin total) was used per 10 million cells. Resin was washed three times with 2 mL of 1X TBS (50 mM Tris pH 7.5, 150 mM NaCl) and incubated in 1X Blocking Buffer (50 mM HEPES, pH 7.5, 10 μg/mL Random 9-mer, 100 μg/mL BSA) for 20 minutes at room temperature with continuous rotation. After the incubation, resin was washed three times with 1X TBS. Cleared lysate was mixed with 50 μL of HaloLink Resin and incubated at 4°C overnight with continuous rotation. The captured protein bound to resin was washed three times with lysis buffer at room temperature and then three times at 90°C for 3 minutes while shaking at 1200 rpm with each of the following buffers: 1X ProK/NLS buffer (50 mM HEPES, pH 7.5, 2% NLS, 10 mM EDTA, 0.1% NP-40, 10 mM DTT), high salt buffer (50 mM HEPES, pH 7.5, 10 mM EDTA, 0.1% NP-40, 1M NaCl), 8M urea buffer (50 mM HEPES, pH 7.5, 10 mM EDTA, 0.1% NP-40, 8 M Urea), and Tween buffer (50 mM HEPES, pH 7.5, 0.1% Tween 20, 10 mM EDTA). After the last wash, samples were centrifuged at 7500g for 30 seconds and supernatant was discarded. For elution, HaloLink Resin was resuspended in 100 μL of ProK/NLS buffer + 10 μL of Proteinase K (NEB) and incubated at 50°C for 20 minutes while shaking at 1200 rpm. Elutions were then transferred to microspin cups (Pierce, Thermo Fisher), centrifuged at 2000g for 30 seconds, and purified with RNA Clean and Concentrate-5 (Zymo).

treatment_protocol: Cells were washed once with PBS and then crosslinked on ice using 0.25 J cm-2 (UV 2.5k) of UV at 254 nm in a Spectrolinker UV Crosslinker. Cells were then scraped from culture dishes, washed once with PBS, pelleted by centrifugation at 1500g for 4 min, and flash-frozen in liquid nitrogen for storage at -80 °C.

value: Human embryonic kidney cells


title: TAS19_total, replicate 1_Fale FXD

status: Public on Oct 30 2024

type: SRA

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

country: USA

institute: Stowers Institute for Medical Research

library_source: transcriptomic

data_processing:
Samples were sequenced by CSHL on a PacBio Sequel II sequencer. Pacbio long reads were analyzed using Iso-Seq (v 3) starting with the generation of consensus sequences from subreads. Subsequently, poly-A tails were trimmed, and the resulting full-length isoforms were then clustered to generate unpolished isoforms, which were further polished using subreads. The polished isoforms were aligned to the hg38 reference genome using pbmm2 (v 1.7.0) and collapsed based on genomic alignments
The transcripts generated from Iso-Seq were characterized using SQANTI (v3.4.2) with gene models retrieved from Ensembl release 102. Unannotated isoforms, Isoforms mapped to Antisense strand of an annotated gene, fusion genes and novel genes were removed for downstream analysis.
Assembly: hg38
Supplementary files format and content: SQANTI Annotations of pacbio Isoforms in TSV format

molecule: total RNA

organism: Homo sapiens

source_name: lymphoblastoid cell lines

growth_protocol: LCLs were cultured in Roswell Park Memorial Institute Medium 1640 with 2mM L-glutamine or equivalent, 15 % fetal bovine serum (Heat Inactivated) at 37C under 5% CO2.

extract_protocol:
Total RNA was extrcated using TRIzol (Invitrogen).
For polyA tail Iso-sequencing, total RNA was treated with ribosomal RNA depletion. SMRTbell Express Template Prep Kit 2.0 (PacBio, Cat# 100-938-900) was used for library construction. For nomal Iso-sequencing,  (without ribosomal RNA depletion), SMRTbell Express Template Prep Kit 2.0 (PacBio, Cat# 100-938-900) was used for library construction.
RNA-sequencing using Sequel II Sequencing Kit 2.0 (PacBio#101-820-200).

tag: tissue

value: lymphoblastoid cell lines

tag: cell type

value: B-cells

tag: Sex

value: female

tag: disease state

value: FXD

tag: genotype

value: affected

tag: treatment


title: TAS49 replicate 1_Female ALL, Ribosomal RNA depletion

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.20. Reads were aligned to UCSC genome hg38 with STAR aligner (version 2.7.3a ), using Ensembl 102 gene models. TPM values were generated using RSEM (version v1.3.0 )
Assembly: hg38
Supplementary files format and content: star_count.txt: Text file of Gene read counts, RSEM_TPM_table.txt: Text file of Transcripts per Million (TPM) of each gene

extract_protocol:
Total RNA was extrcated using TRIzol (Invitrogen).
Total RNA was used for library  construction. Library construction was performed using TruSeq Stranded RNA LT Kit Ribo-Zero Gold (48) (illumina, Cat # RS-122-2302 ).

value: ALL


title: TAS48 replicate 1_Male ALL, Ribosomal RNA depletion

value: male


title: TAS43 replicate 3_Female Healthy, Ribosomal RNA depletion

value: healthy donor

value: Apparently healthy


title: TAS42 replicate 3_Male Healthy, Ribosomal RNA depletion


title: TAS41 replicate 3_Male Healthy, Ribosomal RNA depletion


title: TAS43 replicate 1_Female Healthy, Ribosomal RNA depletion


title: TAS42 replicate 1_Male Healthy, Ribosomal RNA depletion


title: TAS1_total, replicate 1_Male FXD


title: TAS41 replicate 2_Male Healthy, Ribosomal RNA depletion


title: TAS41 replicate 1_Male Healthy, Ribosomal RNA depletion


title: TAS42 replicate 2_Male Healthy, Ribosomal RNA depletion


title: TAS39 replicate 1_Male FXD, Ribosomal RNA depletion


title: TAS39 replicate 2_Male FXD, Ribosomal RNA depletion


title: TAS36 replicate 3_Male FXD, Ribosomal RNA depletion


title: TAS36 replicate 2_Male FXD, Ribosomal RNA depletion


title: TAS39 replicate 3_Male FXD, Ribosomal RNA depletion


title: TAS49 replicate 2_Female ALL, Ribosomal RNA depletion


title: TAS36 replicate 1_Male FXD, Ribosomal RNA depletion


title: TAS48 replicate 3_Male ALL, Ribosomal RNA depletion


title: TAS23 replicate 3_Male Healthy, Ribosomal RNA depletion


title: TAS29 replicate 1_Fale FXD, Ribosomal RNA depletion

value: No data


title: TAS29 replicate 3_Fale FXD, Ribosomal RNA depletion


title: TAS30 replicate 1_Female Healthy, Ribosomal RNA depletion


title: TAS29 replicate 2_Fale FXD, Ribosomal RNA depletion


title: TAS48 replicate 2_Male ALL, Ribosomal RNA depletion


title: TAS22 replicate 3_Female Healthy, Ribosomal RNA depletion


title: TAS23 replicate 1_Male Healthy, Ribosomal RNA depletion


title: TAS43 replicate 2_Female Healthy, Ribosomal RNA depletion


title: TAS22 replicate 1_Female Healthy, Ribosomal RNA depletion


title: TAS30 replicate 3_Female Healthy, Ribosomal RNA depletion


title: TAS21 replicate 2_Fale FXD, Ribosomal RNA depletion


title: TAS20 replicate 1_Male FXD, Ribosomal RNA depletion


title: TAS19 replicate 3_Fale FXD, Ribosomal RNA depletion


title: TAS20 replicate 3_Male FXD, Ribosomal RNA depletion


title: TAS20 replicate 2_Male FXD, Ribosomal RNA depletion


title: TAS19 replicate 2_Fale FXD, Ribosomal RNA depletion


title: TAS30 replicate 2_Female Healthy, Ribosomal RNA depletion


title: TAS11 replicate 1_Female Healthy, Ribosomal RNA depletion


title: TAS10 replicate 3_Male Healthy, Ribosomal RNA depletion


title: TAS1 8 replicate 2_Male FXD, Ribosomal RNA depletion


title: TAS18 replicate 1_Male FXD, Ribosomal RNA depletion


title: TAS10 replicate 1_Male Healthy, Ribosomal RNA depletion


title: TAS19 replicate 1_Fale FXD, Ribosomal RNA depletion


title: TAS10 replicate 2_Male Healthy, Ribosomal RNA depletion


title: TAS23 replicate 2_Male Healthy, Ribosomal RNA depletion


title: TAS2 replicate 3_Fale FXD, Ribosomal RNA depletion


title: TAS11 replicate 3_Female Healthy, Ribosomal RNA depletion


title: TAS2 replicate 2_Fale FXD, Ribosomal RNA depletion


title: TAS1 replicate 3_Male FXD, Ribosomal RNA depletion


title: TAS11 replicate 2_Female Healthy, Ribosomal RNA depletion


title: TAS21 replicate 1_Fale FXD, Ribosomal RNA depletion


title: Baboon, male subject2, left hemisphere, sublibrary1

city: St. Louis

first: Lite

last: Yang

address: 4922 Parkview Place

institute: Washington University in St. Louis

data_processing:
Raw sequencing data from individual libraries were processed and mapped to the reference genome and the gene-cell counts matrices from all snRNA-seq libraries of the same species were concatenated using 10X Genomics cellranger-v6.1.2 or cellranger-v7.0.1
Assembly: mouse: mm10, baboon: Panubis1.0, and macaque: Mmul_10
Supplementary files format and content: Gene matrix.rds contains gene-cell counts for all libraries, metadata.csv contains meta data for all libraries

molecule: polyA RNA

organism: Papio anubis

source_name: Ventral pallidum

extract_protocol:
Nuclear extraction for both mice and primates was performed with density gradient centrifugation according to the protocol described previously with modifications to scale down the reaction volume (85). Samples were moved from -80 ̊C and thawed on ice for 2 minutes. Tissues were transferred to a dounce homogenizer (Millipore Sigma, D8938-1SET) in homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl, pH 8.0, 5 µg/mL actinomycin, 1% BSA, and 0.08 U/µl RNase inhibitor, 0.01% NP40) on ice. Samples were homogenized for 10 strokes with the loose pestle in a total volume of 1 mL, followed by 10 additional strokes with the tight pestle. The tissue homogenate was then passed through a 50 µm filter and diluted 1:1 with working solution (50% iodixanol, 25 mM KCl, 5 mM MgCl2, and 10 mM Tris-HCl, pH 8.0). Nuclei were layered onto an iodixanol gradient after homogenization and ultracentrifuged as described previously. After ultracentrifugation, nuclei were collected between the 30 and 40% iodixanol layers and diluted with resuspension buffer (1xPBS with 1% BSA, and 0.08 U/µl RNase inhibitor). Nuclei were centrifuged at 500 g for 10 min at 4°C and resuspended in resuspension buffer with 5 ng/µl of 7-AAD. FACS was carried out to further remove cellular debris. 7-AAD+ events were collected using a 100 µm nozzle on a BD FACSAria III instrument into a 1.5 mL microcentrifuge tube.
Nuclei were processed according to the manufacturer’s manual of 10X Genomics Chromium Single Cell Gene Expression 3’ V3.1 Assay.

value: Ventral pallidum


title: Baboon, male subject2, left hemisphere, sublibrary2


title: Baboon, male subject2, left hemisphere, sublibrary3


title: TAS2 replicate 1_Fale FXD, Ribosomal RNA depletion


title: TAS22 replicate 2_Female Healthy, Ribosomal RNA depletion


title: TAS1 replicate 2_Male FXD, Ribosomal RNA depletion


title: Baboon, male subject1, left hemisphere, sublibrary1


title: TAS21 replicate 3_Fale FXD, Ribosomal RNA depletion


title: TAS1 replicate 1_Male FXD, Ribosomal RNA depletion


title: TAS18 replicate 3_Male FXD, Ribosomal RNA depletion


title: Baboon, male subject2, right hemisphere, sublibrary1


title: H460.4D4

type: RNA

city: Incheon

first: Jae-Seon

last: Lee

address: Inha-ro

country: South Korea

institute: Inha University

description: H460 IR treated 4 day-rep4

hyb_protocol: Labeled, amplified cRNA (1.5 μg per array) was hybridized to a ver. 2 of the Illumina Human-6 BeadChip (48 K) according to the manufacturer’s instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc.).

data_processing: Array data processing was performed using Illumina BeadStudio software (ver 3.1).

label: biotin

source_name: H460 cells

label_protocol: Biotin-labelled cRNA samples for hybridization were prepared according to the Illumina recommended sample labeling procedure. Briefly, 500 ng of total RNA was used for cDNA synthesis, followed by an amplication/labeling step (in vitro transcription) to synthesize biotin-labelled cRNA according to the Illumina® TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX).

growth_protocol: Human lung cancer H460 cells were purchased from the American Type Culture Collection and cultured in RPMI 1640 medium (WelGENE Inc., Daegu, Korea) supplemented with 10% FBS (WelGENE, Daegu, Korea), and 1% penicillin/streptomycin solution at 37˚C in a 5% CO2 incubator.

extract_protocol: Total RNA from H460 cells was isolated using the TRIzol reagent (Invitrogen, CA) according to the manufacturer’s instruction. The quality of total RNA was checked by gel electrophoresis and RNA concentrations were determined using the Ultrospec 3100 pro spectrophotometer (Amersham Bioscience, Buckinghamshire, UK).

treatment_protocol: H460 cells were exposed to IR 6 Gy. The cells were irradiated with a 2-mm Al filter, 150 kV accelerating voltage, and a dosage rate of 0.72 Gy/min using an X-RAD iR160 X-ray irradiator (North Branford, CT., USA, Precision X-ray (PXi) Inc.).

tag: ir treatment

value: IR 6 Gy


title: H460.4.2

description: H460 control 4 day-rep4

value: Con


title: H460.3.2

description: H460 control 4 day-rep3


title: H460.3.D4

description: H460 IR treated 4 day-rep3


title: H460.2.2

description: H460 control 4 day-rep2


title: H460.2.D4

description: H460 IR treated 4 day-rep2


title: H460.1.2

description: H460 control 4 day-rep1


title: H460.1.D4

description: H460 IR treated 4 day-rep1


title: H460.4

description: H460 control 3 day-rep4


title: H460.4.D3

description: H460 IR treated 3 day-rep4


title: H460.3.D3

description: H460 IR treated 3 day-rep3


title: H460.3

description: H460 control 3 day-rep3


title: H460.2

description: H460 control 3 day-rep2


title: H460.2.D3

description: H460 IR treated 3 day-rep2


title: H460.1

description: H460 control 3 day-rep1


title: H460.1.D3

description: H460 IR treated 3 day-rep1


title: mCCDcl1 cells, vehicle 2h, rep6

city: Erlangen

first: Alexandr

middle: V

last: Ilyaskin

address: Waldstr. 6

department: Institute of Cellular and Molecular Physiology

country: Germany

description:
248643
rlogcounts2021.txt

data_processing:
quality trimming using cutadapt v3
alignment to GRCm38 using STAR v2.7
feature counting with subRead featureCounts v2.0.1 and Ensembl annotation 102
differential expression analysis using DESeq2
Assembly: GRCm38.102
Supplementary files format and content: tab-separated text containing rlog-normalized counts

organism: Mus musculus

growth_protocol: Wildtype mCCDcl1 cells were seeded on permeable supports (Millicell PCF membrane inserts; Merck-Millipore) in a standard culture medium (phenol-red free DMEM/F12 medium supplemented with 2% fetal bovine serum, 1 nM triiodothyronine, 60 nM sodium selenite, 5 µg/ml apotransferrin, 10 ng/ml epidermal growth factor, 5 µg/ml insulin, 50 nM dexamethasone, 100 units/ml penicillin, 100 µg/ml streptomycin) and maintained in a 5% CO2 atmosphere at 37 °C. After five days, cells were fed with modified medium lacking apotransferrin, epidermal growth factor, and fetal bovine serum. 24 h before experiments, dexamethasone was removed from the supplemented medium, and medium was exchanged for the last time.

extract_protocol:
RNA was isolated from cells harvested from each individual permeable support using the NucleoSpin RNA kit (Machery-Nagel).
mRNA libraries were prepared using the Illumina Truseq Stranded mRNA kit according to the manufacturer's instructions.

treatment_protocol: mCCDcl1 cells were treated with 3 nM aldosterone or vehicle (0.9% NaCl) for 2 h.

tag: cell line

value: renal cortical collecting duct cells

value: WT

value: vehicle (0.9% NaCl), 2 h


title: mCCDcl1 cells, vehicle 2h, rep5

description:
248642
rlogcounts2021.txt


title: mCCDcl1 cells, vehicle 2h, rep4

description:
248641
rlogcounts2021.txt


title: mCCDcl1 cells, vehicle 2h, rep3

description:
248640
rlogcounts2021.txt


title: Baboon, male subject1, right hemisphere, sublibrary1


title: mCCDcl1 cells, vehicle 2h, rep1

description:
248638
rlogcounts2021.txt


title: mCCDcl1 cells, aldosterone 2h, rep6

description:
248634
rlogcounts2021.txt

value: aldosterone, 3 nM, 2 h


title: mCCDcl1 cells, vehicle 2h, rep2

description:
248639
rlogcounts2021.txt


title: mCCDcl1 cells, aldosterone 2h, rep3

description:
248626
rlogcounts2021.txt


title: mCCDcl1 cells, aldosterone 2h, rep2

description:
248625
rlogcounts2021.txt


title: mCCDcl1 cells, aldosterone 2h, rep4

description:
248627
rlogcounts2021.txt


title: mCCDcl1 cells, aldosterone 2h, rep1

description:
248624
rlogcounts2021.txt


title: OGD_A_485_3

city: 成都

first: Lu

last: He

address: WUHAN

country: China

institute: TONGJI

data_processing:
CLC Genomics Workbench v 11.0.1
sequence  reads were trimmed for adaptor sequence/low-quality sequcence using CLCgenomic benchwork(parameter-Quanlity limit:0.05)
trimmed sequence reads were mapped to GrCM38/MM10 using CLC genomic benchwork (parameters-mismath cost:2 insertion cost: 3 length fraction:0.8 similarity fraction:0.8)
read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen).1.3ug of total RNA was used for  the construction of sequencing libraries
RNA libraries for RNA-seq were prepares using SMARTER mRNA-seq library prep kit following manufacture's protocols


title: OGD_A_485_2


title: OGD_3

value: OGD


title: OGD_1


title: Ctrl_2

value: normal


title: Ctrl_1


title: OGD_A_485_1


title: LLC1 cells, EV3

city: Nanjing

first: yijian

last: zhang

state: None Selected

address: Baiziting 42, Nanjing, P.R. China, 210009

institute: NanJing Medical University

data_processing:
Sequencing data were quality controlled using "fastqc" software and rRNA sequencing was removed using "SortMeRNA".
Using CIRI (CircRNA Identifier) tools to identification circRNA
Aligning to Genome with STAR-aligner and Summarizing Gene Counts with featureCounts.
Generating analysis report with multiQC.
Assembly: mm10, hg19
Supplementary files format and content: Csv files with FPKM data.

source_name: LLC1 cells

extract_protocol:
RNA degradation and contamination, especially DNA contamination, was monitored on 1.5% agarose gels. RNA concentration and purity was measured using the NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA).
A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer （ 5X）. First strand cDNA was synthesized using random hexamer primer and Reverse Transcriptase. Second-strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select insert fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP Beads (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 and qPCR.

value: LLC1 cells

value: Mouse non-small cell lung cancer

value: EV


title: LLC1 cells, EV2


title: OGD_2


title: Ctrl_3


title: LLC1 cells, EV1


title: LLC1 cells, cEmsy OE1

value: cEmsy overexpression


title: LLC1 cells, cEmsy OE2


title: LLC1 cells, Pemetrexed+Cisplatin2

description: All.DEG.Expression

value: Pemetrexed (2.5uM)+Cisplatin (2.5uM) for 48h


title: LLC1 cells, (R)-crizotinib+Cisplatin3

description: All.DEG.Expression

value: (R)-crizotinib (10uM)+Cisplatin (50uM) for 48h


title: LLC1 cells, cEmsy OE3


title: LLC1 cells, Pemetrexed+Cisplatin1

description: All.DEG.Expression


title: LLC1 cells, Pemetrexed+Cisplatin3

description: All.DEG.Expression


title: LLC1 cells, (R)-crizotinib+Cisplatin2

description: All.DEG.Expression


title: LLC1 cells, (R)-crizotinib+Cisplatin1

description: All.DEG.Expression


title: LLC1 cells, Dactinomycin3

description: All.DEG.Expression

value: Dactinomycin (1uM) for 48h


title: mCCDcl1 cells, aldosterone 2h, rep5

description:
248630
rlogcounts2021.txt


title: LLC1 cells, Dactinomycin2

description: All.DEG.Expression


title: LLC1 cells, Dactinomycin1

description: All.DEG.Expression


title: LLC1 cells, Oxaliplatin2

description: All.DEG.Expression

value: Oxaliplatin (500uM) for 48h


title: LLC1 cells, Oxaliplatin1

description: All.DEG.Expression


title: LF1 cells, proliferating, replicate 1

city: Providence

first: Nicola

last: Neretti

state: RI

address: 225 Dyer St.

institute: Brown University

library_source: genomic

data_processing:
>60X coverage worth of nanopore long sequencing reads were fed to the “TLDR” program
Extra chromosomal insertion “patches” were appended to the T2T-HS1 reference, which were comprised of the full private insert sequence plus 500 base pairs of flanking sequence on either side of the insert-breakpoint.
Custom gene transfer file annotations were subsequently produced to document the presence of these private insertions. All reference and private L1HS and L1PA2 elements were inspected for the presence of intact (full length ORF1p and ORF2p) protein coding potential.
Sequences were extracted from our custom reference using bedtools getfasta in addition to the private insert augmented T2T-HS1 RepeatMasker gtf annotation. Open reading frames were detected using the R package “Orfik” and filtered on the basis of length. Elements which passed these criteria were denoted as “intact”.
Reference and private intact L1HS coordinates were lifted over to hg38 with the liftOver tool from the Broad Institute for use in Hi-C analyses which had reads aligned to this reference.
Assembly: hg38
Supplementary files format and content: list of L1 reference and novel
Library strategy: Long read DNA-Seq

molecule: genomic DNA

growth_protocol: Cells were passaged in regular growth media (HAMS F10, 15% FBS, and 1x of Penicillin Streptomycin and Glutamine) and maintained at 37 degrees Celsius at 5% CO2 and 2.5% O2.

extract_protocol:
All conditions (proliferating, quiescent, RS) had genomic DNA extracted using the Monarch genomic DNA purification kit from NEB. The standard protocol for DNA extraction from cells was followed with no modifications.
Sequencing libraries were prepared using the Oxford Nanopore Ligation Sequencing Kit V14 and its associated protocol. Long-fragment buffer was used to enrich for long DNA fragments.

treatment_protocol:
Proliferating cells were harvested at 60 - 80% confluency.
Replicative senescent (RS) cells were passaged in regular growth media until replicative exhaustion. These cells were maintained in the senescent state for 3-4 months.

value: lung fibroblasts


title: LF1 cells, senescent, replicate 1

value: Replicative Exhaustion


title: LLC1 cells, Oxaliplatin3

description: All.DEG.Expression


title: LLC1 cells, Bortezomib2

description: All.DEG.Expression

value: Bortezomib (100nM) for 48h


title: LLC1 cells, Bortezomib3

description: All.DEG.Expression


title: LLC1 cells, Bortezomib1

description: All.DEG.Expression


title: LLC1 cells, Doxorubicin3

description: All.DEG.Expression

value: Doxorubicin (4 mM) for 48h


title: DSI+DOX_1

city: Shiyan City, Hubei Province

first: yijun

last: pan

address: 30 Renmin South Road, Shiyan City, Hubei Province

institute: Hubei university of medicine

data_processing:
The raw data was processed by trimming adaptors and filtering out low-quality reads using Trimmomatic. The quality of the clean reads was then checked using Fastp software.
Trimmed sequence reads were aligned to the latest Rattus norvegicus genome assembly using Hisat2.
Read counts were further processed by the featureCounts software to generate count data of gene transcripts.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Rattus norvegicus

source_name: H9c2 cells

growth_protocol: H9c2 cardiomyocyte cells were cultured in high-glucose DMEM medium, supplemented with 10% fetal bovine serum and 10,000 U/ml penicillin-streptomycin at a predetermined cell density. The cultures were maintained in a 5% CO2 incubator at 37℃.

extract_protocol:
Total RNA from H9c2 cells were extracted with TRIzol reagent.
Qualified RNA samples were used for library preparation by NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s recommendations.

treatment_protocol: The cells were seeded onto 6-well plates and divided intofive groups: a control group treated with PBS, a model group exposed to 2μM DOX, a treatment group subjected to 2μM DOX in combination with 50μL DSI diluted 1/20 in culture volume, a treatment group subjected to 2μM DOX in combination with 5μM AXT and a treatment group subjected to 2μM DOX in combination with 10μM DMT. Each group consisted of three samples, with DOX added after 4 hours of DSI, AXT an DMT  treatment. The cells were harvested 24 hours after DOX treatment.

value: H9c2 cells

value: cardiomyocyte cells

value: DSI+DOX


title: kidney glomerulus, WT and I-mfa knock out

city: Fort Worth

first: Rong

last: Ma

state: TX

address: 3500 Camp Bowie Blvd

department: Integrative Physiology

institute: University of North Texas Health Science Center

description:
10x Genomics
kidney glomerulus, WT replicate1 (sample Y1)
kidney glomerulus, WT replicate2 (sample Y3)
kidney glomerulus, WT replicate3 (sample Y5)
kidney glomerulus, I-mfa knock out replicate1 (sample B2)
kidney glomerulus, I-mfa knock out replicate2 (sample B4)
kidney glomerulus, I-mfa knock out replicate3 (sample B6)

library_source: transcriptomic single cell

data_processing:
A cell density of approximately 6000 cells per sample was achieved for the reverse transcription master mix.Sc-RNA-seq data were processed with a custom pipeline.Raw read sequences were mapped to mouse transcriptome (mm10-2020-A) by Cell Ranger (v7.0.0), with  more than 95% reads mapped for cell type identification and analysis of differential gene expression.The raw gene expression matrices were collected for each sample, and subsequently analyzed using the Seurat package (v4.1.0), and integrated by Harmony (v0.1.0). Cells were preprocessed by removing barcodes as< 500 UMIs, < 200 expressed genes, > 8000 expressed genes or > 10% of reads were associated with mitochondrial genes.
Assembly: mm10/cell ranger
Supplementary files format and content: singlecell sparse matrix

source_name: kidney (glomerulus)

extract_protocol:
Mice were sacrificed with intraperitoneal injection of ketamine (60 mg/kg) and xylazine (20 mg/kg). HBSS solutoin (Cacium and Magnesium free) and dynabead solution were used for trancradial perfusion.Both kidneys were then removed immediately for isolation of glomeruli. Whole kidneys were dissociated by digestive buffer solution I (1.5 U/ml Liberase TM and 100U/ml DNase in HBSS solution, 2ml/mouse) for glomeulus dissociation.Glomerulus were isolated by magenetic seperator. Purified glomerulus were further digested to single cell suspension by digestive solution II (0.5% (wt/vol) Trypsin, 2.0 U/ml Dispase II, 2.0 U/ml Collagenase D and 10 U/ml DNAse I, 750 µl per mouse).Samples went through Syringe and 27 1/2, and 29 1/2 gauge needles twice for better dissociation into single cell suspension.Once cells are thoroughly dissociated to a single-cell suspension, stop digestion by adding 10 ml ice-cold PBS with 10% FBS. magnetic dynabeads were removed using a magnetic separator.
library preparation, and sequencing for scRNA-seq was performed by 10X genomics (Pleasanton, CA 94588).

value: kidney (glomerulus)

value: podocytes, mesangial cells, endothelial cells, renal tubular cells, vascular smooth muscle cells

value: mixed sample (wild type and I-mfa knock out _

tag: age

value: 12-13 weeks

value: male

tag: strain


title: LLC1 cells, Doxorubicin2

description: All.DEG.Expression

value: LLC1 cells

value: Mouse non-small cell lung cancer

value: WT


title: Whole blood, RNAseq, Control, subj2

city: Saint-Petersburg

first: Aleksandr

last: Tkachenko

address: Mendeleyevskaya line, 3

country: Russia

institute: D. O. Ott Research Institute of Obstetrics and Gynecology

data_processing:
RNA sequencing data was pseudoaligned to the human GENCODE v46 reference with kallisto v.0.46.0
Differential expression was analyzed using DESeq2 package v. 1.44.0
Enrichment of GO terms in differential expression data was calculated using the GSEA method with clusterProfiler v. 4.12.6
Assembly: GRCh38
Supplementary files format and content: TPM values for all samples and raw counts from kallisto pseudoalignment
Supplementary files format and content: Column names: ENSEMBL, SYMBOL, K_O, K12, K21, K22, K24, K25, K4, K7, T2D_D, T2D102, T2D106, T2D11, T2D3, T2D61, T2D66, T2D93

source_name: Whole blood

extract_protocol:
Whole blood samples were retrieved from cryostorage and thawed at room temperature. The total RNA was isolated from 300 μL of whole blood using a TRIzol reagent (Invitrogen, Carlsbad, CA, USA) with chloroform, purificated with PureLink Total RNA Blood Kit (Invitrogen™, Carlsbad, CA, USA) following the manufacturer’s instructions, and eluted with 45 μL RNase-free water. Total RNA was tested for purity using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and quantified with Qubit™ RNA High Sensitivity Assay Kit and Qubit 2.0 Fluorometer (both Invitrogen™, Carlsbad, CA, USA).
Libraries were constructed from 150 ng of previously extracted total RNA using TruSeq Stranded Total RNA library preparation kit (Illumina, Inc., San Diego, California) according to the manufacturer’s protocol. Briefly, after ribosomal RNA depletion and RNA fragmentation, first and second strand cDNA were synthesized, and 3’ ends were adenylated, followed by adapter ligation and enrichment of DNA fragments. The library’s size distribution was analyzed with Agilent 2200 TapeStation and Agilent High Sensitivity D1000 ScreenTape (both Agilent Technologies, Inc., Waltham, MA, USA).

value: Whole blood

tag: subject status

value: Control

value: female


title: Whole blood, RNAseq, Control, subj18


title: LLC1 cells, Control3

description: All.DEG.Expression

value: DMSO for 48h


title: LLC1 cells, Control2

description: All.DEG.Expression


title: Whole blood, RNAseq, Control, subj15


title: Whole blood, RNAseq, Control, subj14


title: Whole blood, RNAseq, Control, subj16


title: RPF Eif2d shRNA2 replicate 3

city: Lausanne

first: Romane

last: Meurs

state: Vaud

address: Genopode

department: Center for Integrative Genomics

country: Switzerland

institute: Universite de Lausanne

description:
RP143
ribo_counts.csv
RP_TPM.csv

data_processing:
Sequencing adapters were trimmed using Cutadapt (Martin 2011) then reads were size filtered by a custom Python script (26-35 nt for RPF and 21-60nt for RNA)
The reads were then aligned subsequently to mouse rRNA, human rRNA, mouse tRNA and mouse cDNA from Ensembl mouse database release 100 using Bowtie2 (Langmead and Salzberg 2012)
The mapped reads were counted on 5’ UTR or CDS of the protein coding genes using a custom Python script. The location of the putative A-site of RPFs were estimated as 5’ position +16 for reads shorter than or equal to 31 nt and 17 for reads longer than 31 nt.
The transcripts for which there were less than 10 counts in total of all samples were filtered out of the further analysis. Read counts were normalized using the upper quartile normalization method (Robinson and Oshlack 2010) from edgeR (Robinson, McCarthy, and Smyth 2010) then transformed to transcripts per million (TPM) to normalize for transcript length.
Translation efficiencies were calculated as the log2 transformed ratio of normalized CDS RPF counts to normalized CDS RNA counts and averaged over replicates. Transcripts were classified following their change in TE and in RNA abundance upon Denr knock-down using the DeltaTE method (Chothani et al., 2019).
Assembly: mm10
Supplementary files format and content: Comma-delimited csv files
Library strategy: RPF-seq

growth_protocol: NIH3T3 cells were cultured under standard conditions (DMEM; 10% FCS, 1% penicillin/streptomycin, all from Invitrogen) at 37°C with 5% CO2.

extract_protocol:
One 15 cm dish of confluent NIH3T3 cells was used per replicate. Cells were immediately harvested and flash frozen. For the generation of ribosome-protected fragments, cell lysates were treated with 5 units RNase I (ART-Seq) per OD260 for 45 min at RT, and monosomes were purified in MicroSpin S-400 columns (GE Healthcare) . RNA was extracted using miRNeasy MiniKit (Qiagen).
RPF-seq and RNA-seq libraries were prepared following previously reported protocols (Arpat et al., 2020; PMID 32703885 and McGlincy and Ingolia, 2017; PMID 28579404) with minor modifications. For both RPF- and RNA-seq, 2µg of RNA was used for rRNA depletion following the RiboCop rRNA Depletion Kit V1.2 instructions from Lexogen (Cat. No. 037.24). Libraries were amplified using 10 to 14 PCR cycles, and sequenced (HiSeq2500 platform).

treatment_protocol: NIH3T3 cells were selected with puromycin at 5μg/ml for 4 days after transduction with shRNA lentiviruses. Production of lentiviral particles in HEK293FT cells using envelope pMD2.G and packaging psPAX2 plasmids was performed following published protocols (Salmon and Trono 2007)

value: embryonic fibroblasts

value: Eif2d knock-down

value: Eif2d shRNA4


title: Whole blood, RNAseq, Control, subj13


title: LLC1 cells, Control1

description: All.DEG.Expression


title: Whole blood, RNAseq, Control, subj12


title: RPF Eif2d shRNA2 replicate 1

description:
RP141
ribo_counts.csv
RP_TPM.csv


title: Whole blood, RNAseq, T2D, subj11


title: RPF Eif2d shRNA2 replicate 2

description:
RP142
ribo_counts.csv
RP_TPM.csv


title: Whole blood, RNAseq, T2D, subj10


title: Whole blood, RNAseq, T2D, subj9


title: RPF Eif2d shRNA1 replicate 2

description:
RP139
ribo_counts.csv
RP_TPM.csv

value: Eif2d shRNA3


title: RPF Eif2d shRNA1 replicate 3

description:
RP140
ribo_counts.csv
RP_TPM.csv


title: RPF Eif2d shRNA1 replicate 1

description:
RP129
ribo_counts.csv
RP_TPM.csv


title: Whole blood, RNAseq, T2D, subj4


title: Whole blood, RNAseq, T2D, subj8


title: RPF Eif2d nf shRNA replicate 3

description:
RP128
ribo_counts.csv
RP_TPM.csv

value: EIf2d nf shRNA


title: RPF Denr shRNA2 replicate 3

description:
RP127
ribo_counts.csv
RP_TPM.csv

value: Denr knock-down

value: Denr shRNA2


title: Whole blood, RNAseq, Control, subj17


title: Whole blood, RNAseq, T2D, subj5


title: LLC1 cells, Doxorubicin1

description: All.DEG.Expression

value: Doxorubicin (4 mM) for 48h


title: RPF Scramble shRNA replicate 3

description:
RP126
ribo_counts.csv
RP_TPM.csv

value: scramble shRNA


title: Whole blood, RNAseq, T2D, subj7


title: RPF Eif2d nf shRNA replicate 2

description:
RP118
ribo_counts.csv
RP_TPM.csv


title: Whole blood, RNAseq, T2D, subj6

value: male


title: RPF Denr shRNA2 replicate 2

description:
RP117
ribo_counts.csv
RP_TPM.csv


title: PBMC, diabetes, scRNAseq, subj4

description:
D_S4
10X Genomics

data_processing:
Read data was aligned to the GRCh38 human reference and quantified using CellRanger v. 8.0.0
Resulting data was analyzed with Seurat v. 5.1.0
Cells with more than 200 and less than 5000 features and less than 10% mitochondrial reads were kept for further analysis. A LogNormalize function with a scaling factor of 10,000 was applied to normalize the count matrices and identify variable features. First 2000 most variable features were used for PCA. Clusters were found using the Louvain algorithm with 0.5 resolution. The Harmony method was used to integrate datasets. Cells were assigned cell-type annotations with Azimuth v. 0.5 using pbmcref as a reference
Differential cell composition between diabetes and control samples was calculated using DCATS v. 1.2.0
Assembly: GRCh38
Supplementary files format and content: Processed data contains filtered CellRanger output (barcodes, features, matrix) for every sample

source_name: PBMC

extract_protocol:
PBMCs were isolated from whole blood samples within 2 hours by Ficoll-Paque medium density gradient centrifugation for 30 min at 500 g. The cells were resuspended in 1X phosphate-buffered saline containing 0.04% filtered bovine serum albumin to achieve the required cell concentration (700–1200 cells per 1 μL). The final cell concentration and viability were determined using a Countess II Automated Cell Counter (Thermo Fisher Scientific, Waltham, MA, USA).
Cell suspension with a concentration of 1000 cells per µl was used to achieve a targeted cell recovery up to 9000 cells. Gel beads-in-emulsion (GEMs) containing uniquely barcoded gel beads and suspended cells were generated using a 10×Genomics Chromium Controller device followed by reverse transcription. Single-cell libraries were constructed using Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 according to the manufacturer’s instruction. The main steps of library preparation included breaking GEMs, pooled cDNA fractions recovery, purification, and amplification, followed by enzymatic fragmentation, end-repair, A-tailing, adapter ligation, and final amplification. The quality of the single-cell libraries was assessed with Agilent 2200 TapeStation and Agilent High Sensitivity D1000 ScreenTape (both Agilent Technologies, Inc., Waltham, MA, USA).

value: PBMC


title: PBMC, control, scRNAseq, subj2

description:
O_S2
10X Genomics


title: RPF Eif2d nf shRNA replicate 1

description:
RP115
ribo_counts.csv
RP_TPM.csv


title: PBMC, diabetes, scRNAseq, subj3

description:
B_S3
10X Genomics


title: RPF Scramble shRNA replicate 1

description:
RP113
ribo_counts.csv
RP_TPM.csv


title: RPF Denr shRNA2 replicate 1

description:
RP114
ribo_counts.csv
RP_TPM.csv


title: H358 cells, EV3

source_name: H358 cells

value: H358 cells

value: Human non-small cell lung cancer

value: EV


title: H358 cells, EV2

value: WT


title: RNA Eif2d shRNA2 replicate 3

description:
TR143
rna_counts.csv
TR_TPM.csv

data_processing:
Sequencing adapters were trimmed using Cutadapt (Martin 2011) then reads were size filtered by a custom Python script (26-35 nt for RPF and 21-60nt for RNA)
The reads were then aligned subsequently to mouse rRNA, human rRNA, mouse tRNA and mouse cDNA from Ensembl mouse database release 100 using Bowtie2 (Langmead and Salzberg 2012)
The mapped reads were counted on 5’ UTR or CDS of the protein coding genes using a custom Python script. The location of the putative A-site of RPFs were estimated as 5’ position +16 for reads shorter than or equal to 31 nt and 17 for reads longer than 31 nt.
The transcripts for which there were less than 10 counts in total of all samples were filtered out of the further analysis. Read counts were normalized using the upper quartile normalization method (Robinson and Oshlack 2010) from edgeR (Robinson, McCarthy, and Smyth 2010) then transformed to transcripts per million (TPM) to normalize for transcript length.
Translation efficiencies were calculated as the log2 transformed ratio of normalized CDS RPF counts to normalized CDS RNA counts and averaged over replicates. Transcripts were classified following their change in TE and in RNA abundance upon Denr knock-down using the DeltaTE method (Chothani et al., 2019).
Assembly: mm10
Supplementary files format and content: Comma-delimited csv files


title: RNA Eif2d shRNA2 replicate 2

description:
TR142
rna_counts.csv
TR_TPM.csv


title: H358 cells, EV1


title: H358 cells, cEMSY OE3

value: cEMSY overexpression


title: RNA Eif2d shRNA2 replicate 1

description:
TR141
rna_counts.csv
TR_TPM.csv


title: H358 cells, cEMSY OE1


title: RNA Eif2d shRNA1 replicate 3

description:
TR140
rna_counts.csv
TR_TPM.csv


title: H358 cells, cEMSY OE2


title: adipose tissue from_EJ17_preexercise_0min_subject I_female

city: Stockholm

first: Hakan

middle: Claes

last: Rundqvist

state: Huddinge

address: Alfred Nobels ale 8

department: Department of Laboratory Medicine

country: Sweden

institute: Karolinska institutet

hyb_protocol: cDNA was fragmented, biotin-labeled and hybridized to the Human Gene 1.0 ST. Arrays were hybridized for 16 hours at 45°C in a Gene Chip Oven 640 (Affymetrix) followed by washing and staining using the Gene Chip Fluidics Station 450 according to the protocol described in WT Sense Target Labeling Assay Manual

scan_protocol: Scanning was carried out using the Affymetrix Gene Chip Scanner 3000 7G

data_processing: Raw intensity data (CEL files) were processed by using Affymetrix Expression Console Software (v.1.0). Background correction (PM-6CBG), global median normalization and summarization of probe intensity (Plier) were performed

source_name: Subcutaneous abdominal adipose tissue at rest in female subject

label_protocol: 100 ng of total RNA were amplified and labeled using Whole Transcript (WT) Sense Target Labeling protocol

extract_protocol: total RNA

value: adipose tissue

tag: gender

value: female


title: RNA Eif2d shRNA1 replicate 2

description:
TR139
rna_counts.csv
TR_TPM.csv

value: embryonic fibroblasts

value: Eif2d knock-down


title: adipose tissue from_EJ18_postexercise_15min_subject I_female

source_name: Subcutaneous abdominal adipose tissue after exercise in female subject


title: RPF Scramble shRNA replicate 2

description:
RP116
ribo_counts.csv
RP_TPM.csv


title: PBMC, control, scRNAseq, subj1

description:
G_S1
10X Genomics

value: Control


title: RNA Eif2d shRNA1 replicate 1

description:
TR129
rna_counts.csv
TR_TPM.csv

value: Eif2d shRNA3


title: RNA Eif2d nf shRNA replicate 3

description:
TR128
rna_counts.csv
TR_TPM.csv

value: EIf2d nf shRNA


title: hiPSC-EC2, shSND1, 48Hr

city: Chicago

first: Jordan

last: Jousma

state: Illinois

address: 909 South Wolcott

department: Pharmacology and Regenerative Medicine

institute: University of Illinois

data_processing:
Raw Fastq files were uploaded to the cloud based analysis suite, BioJupies, and analyzed using the default parameters
Supplementary files format and content: Raw read counts in processed data file are listed in a tab delimited .txt file

source_name: iPSC-EC

extract_protocol:
Cells were lysed in Trizol, and total RNA extracts were isolated and submitted for sequencing.
Prepared according to manufactures specificaitons

value: iPSC-EC

value: Endothelial Cell

tag: time

value: 48 hours


title: adipose tissue from_EJ14_postexercise_15min_subject G_female


title: adipose tissue from_EJ16_postexercise_15min_subject H_male

source_name: Subcutaneous abdominal adipose tissue after exercise in male subject

value: male


title: adipose tissue from_EJ15_preexercise_0min_subject H_male

source_name: Subcutaneous abdominal adipose tissue at rest in male subject


title: hiPSC-EC1, shSND1, 48Hr


title: adipose tissue from_EJ13_preexercise_0min_subject G_female


title: adipose tissue from_EJ11_preexercise_0min_subject F_female


title: adipose tissue from_EJ12_postexercise_15min_subject F_female


title: adipose tissue from_EJ09_preexercise_0min_subject E_male


title: adipose tissue from_EJ10_postexercise_15min_subject E_male


title: RNA Denr shRNA2 replicate 3

description:
TR127
rna_counts.csv
TR_TPM.csv

value: Denr knock-down

value: Denr shRNA2


title: adipose tissue from_EJ07_preexercise_0min_subject D_female


title: hiPSC-EC3, shScramble, 48Hr

value: shScramble


title: adipose tissue from_EJ04_postexercise_15min_subject B_female


title: adipose tissue from_EJ05_preexercise_0min_subject C_male


title: adipose tissue from_EJ06_postexercise_15min_subject C_male


title: RNA Scramble shRNA replicate 3

description:
TR126
rna_counts.csv
TR_TPM.csv

value: scramble shRNA


title: Cluster_Wt_3

first: Shiyuan

middle: (Cynthia)

last: Chen

department: Computational Biology

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq. Reads were aligned to UCSC genome mm10 with Tophat2 aligner, using Ensembl 84 gene models. Count file was generated using htseq-count.
Assembly: mm10
Supplementary files format and content: Read count file in csv format for each sample

source_name: Bone Marrow

extract_protocol:
Mouse bone marrow whole cell extract standard protocols
Clontech(poly A)/Nextera Non-stranded RNA-Seq Kit standard construction protocol
Followed Nextera XT library kit standard protocols and six samples pooled together for sequencing

value: Bone Marrow

value: Wildtype


title: hiPSC-EC2, shScramble, 48Hr


title: Cluster_Wt_2


title: hiPSC-EC3, shSND1, 48Hr


title: RNA Eif2d nf shRNA replicate 2

description:
TR118
rna_counts.csv
TR_TPM.csv

value: WT


title: Cluster_KO_3

value: Mutant


title: adipose tissue from_EJ02_postexercise_15min_subject A_female

value: adipose tissue

value: female


title: Cluster_Wt_1


title: hiPSC-EC1, shScramble, 48Hr


title: RNA Denr shRNA2 replicate 2

description:
TR117
rna_counts.csv
TR_TPM.csv

value: embryonic fibroblasts


title: adipose tissue from_EJ08_postexercise_15min_subject D_female


title: Cluster_KO_2


title: Cluster_KO_1


title: RNA Scramble shRNA replicate 2

description:
TR116
rna_counts.csv
TR_TPM.csv


title: adipose tissue from_EJ03_preexercise_0min_subject B_female


title: RNA Eif2d nf shRNA replicate 1

description:
TR115
rna_counts.csv
TR_TPM.csv


title: RNA Denr shRNA2 replicate 1

description:
TR114
rna_counts.csv
TR_TPM.csv


title: CortexEntorhinalis_rTg4510_T24

city: Exeter

first: Emma

last: Walker

address: RILD Barrack Rd

country: United Kingdom

institute: University of Exeter

data_processing:
Sequencing quality was assessed using FastQC (version v0.11.7) with all samples characterized by high quality and thus passing QC
Sequences were trimmed using TrimGalore (version 0.4.4_dev), with a quality score of 20 and an error rate of 0.2 used to remove poor quality bases at the ends of reads
Reads with fewer than 20 base pairs after trimming were then removed
Reads were aligned to the mm10 (GRCm38) mouse genome using Bismark v0.19.0 with default parameters, which implements SAMtools 1.8 and Bowtie2 v2.3.4.1
Assembly: GRCm38
Supplementary files format and content: Matrices containing methylation values (csv)

source_name: Entorhinal Cortex

growth_protocol: Animals were housed under standard conditions (constant temperature and humidity) with a 12h light/dark cycle in individually ventilated cages, with free access to food (Teklad irradiated global rodent diet (Envigo, United Kingdom)) and water.

extract_protocol:
Genomic DNA from all samples was isolated from the entorhinal cortex or hippocampus using the AllPrep DNA/RNA Mini Kit (Qiagen)
RRBS libraries were prepared using the Premium RRBS kit (Diagenode) with some modifications. Libraries were checked using the High Sensitivity D1000 Screentape and 2200 TapeStation System (Agilent Technologies). Final library pools were distributed across thirty-two HiSeq2500 (Illumina) lanes and subjected to 50 bp single-end sequencing

treatment_protocol: Mice were terminally anaesthetized with pentobarbital (intraperitoneal injection) and transcardially perfused with phosphate-buffered saline (PBS). The entorhinal cortex was dissected from the left brain hemisphere on wet ice and snap-frozen on dry ice for subsequent analysis

value: Entorhinal Cortex

tag: histology

tag: group id

value: TG

tag: age months


title: CortexEntorhinalis_rTg4510_T23


title: RNA Scramble shRNA replicate 1

description:
TR113
rna_counts.csv
TR_TPM.csv


title: CortexEntorhinalis_rTg4510_T21


title: CortexEntorhinalis_rTg4510_T22


title: TCCSUP- ε (siRNA treated) [8B]

city: New Delhi

first: DEEPIKA

last: TREHAN

state: Delhi

address: ICMR- National Institute of Pathology, Safdarjung Hospital Campus, Ansari Nagar

country: India

institute: ICMR-NATIONAL INSTITUTE OF PATHOLOGY

description: Gene expression after knockdown with siRNA PKCε

hyb_protocol: 5µg of Cyanine 3-labeled, linearly amplified cRNA was mixed with 50µl of 10× Gene Expression Blocking Agent and 10µl of 25× Fragmentation buffer at 60°C, 30mins. Immediate cooling was done followed by treatment with 250µl 2× Hi-RPM Hybridization Buffer at 65°C, 17hrs and loading on array (cat no:G2534-60014).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for Agilent HD array slides (61 × 21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.1.0.3 (Agilent) using default parameters (protocol GE1_1200 and Grid: 072363_D_F_20200924) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: TCCSUP- ε (siRNA treated)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 25 ug  RNA Spike-In Kit, One-Color (Agilent, cat no:5188-5282) according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN, cat no: 74536).  Dye incorporation and cRNA yield were checked with NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: The T24 cells, 5637 cells, TCCSUP cells, and HT-1376 cells were grown in Mc Coy's 5a, RPMI-1640, Minimal Essential Growth medium respectively at 5% CO2, 37°C.

extract_protocol: The  RNA was extracted through Qiagen RNA extraction kit (cat no: 74536) according to the manufacturer protocol. Cells were lysed and ethanol was added to ensure complete lysis. The lysate was loaded onto the RNeasy column followed by elution into the elution buffer. The concentration was calculated through a bioanalyzer and nanodrop reading (ng/μl).

treatment_protocol: 10 million cells were grown upto 70-90% confluency followed by transfection of siRNA mixed with lipofectamine 2000 in 1:1 ratio.

tag: cell lines

value: Urinary bladder

value: bladder grade IV carcinoma

value: Female

tag: treatment/time point

value: after knockdown with siRNA PKCε


title: TCCSUP-ζ (siRNA treated) [9B]

description: Gene expression after knockdown with siRNA PKCζ

source_name: TCCSUP-ζ (siRNA treated)

tag: cell type

value: after knockdown with siRNA PKCζ


title: TCCSUP-ζ (siRNA treated) [9A]


title: TCCSUP- ε (siRNA treated) [8A]


title: adipose tissue from_EJ01_preexercise_0min_subject A_female

tag: tissue


title: CortexEntorhinalis_rTg4510_T20


title: TCCSUP-Control [7B]

description: Gene expression after 24hrs confluency of tumor cells

source_name: TCCSUP-Control

value: after 24hrs confluency of tumor cells


title: TCCSUP-Control [7A]


title: 5637-ζ (siRNA treated) [6B]

source_name: 5637-ζ (siRNA treated)

value: bladder grade II carcinoma

value: Male


title: 5637-ζ (siRNA treated) [6A]


title: 5637- ε (siRNA treated) [5B]

source_name: 5637- ε (siRNA treated)


title: CortexEntorhinalis_rTg4510_T19


title: CortexEntorhinalis_rTg4510_T17


title: CortexEntorhinalis_rTg4510_T18


title: 5637- Control [4B]

source_name: 5637- Control


title: 5637- Control [4A]


title: 5637- ε (siRNA treated) [5A]


title: T24-ζ (siRNA treated) [3A]

source_name: T24-ζ (siRNA treated)

value: bladder transitional cell carcinoma Grade I


title: T24-ζ (siRNA treated) [3B]


title: CortexEntorhinalis_rTg4510_S24


title: CortexEntorhinalis_rTg4510_S23


title: T24- ε (siRNA treated) [2B]

source_name: T24- ε (siRNA treated)


title: CortexEntorhinalis_rTg4510_S22


title: NonClassicalMonocytes_SLE_Visit2_9

type: genomic

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: iDATs were analyzed using a standard pipeline, with the shinyepico package (1.0.0) of the Bioconductor project and custom code with limma and minfi packages

label: Cy5 and Cy3

source_name: SLE

label_protocol: Standard Illumina Protocol

growth_protocol: Monocyte subsets were isolated from SLE and healthy donor PBMCs by sorter using CD15, CD56, CD19 and CD3 negative selection and CD14 and CD16 positive selectin

extract_protocol: Total DNA was isolated using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to manufacturer’s instruction


title: IntermediateMonocytes_SLE_Visit1_9


title: ClassicalMonocytes_SLE_Visit2_9


title: NonClassicalMonocytes_SLE_Visit1_8


title: CortexEntorhinalis_rTg4510_S21


title: T24- ε (siRNA treated) [2A]


title: IntermediateMonocytes_SLE_Visit2_6


title: IntermediateMonocytes_SLE_Visit2_9


title: IntermediateMonocytes_SLE_Visit1_7


title: T24-Control [1B]


title: CortexEntorhinalis_rTg4510_S20


title: IntermediateMonocytes_SLE_Visit1_8


title: ClassicalMonocytes_SLE_Visit1_9


title: ClassicalMonocytes_SLE_Visit2_7


title: NonClassicalMonocytes_SLE_Visit1_9


title: ClassicalMonocytes_SLE_Visit1_7


title: IntermediateMonocytes_SLE_Visit2_8


title: T24-Control [1A]


title: CortexEntorhinalis_rTg4510_S19


title: ClassicalMonocytes_SLE_Visit1_8


title: CortexEntorhinalis_rTg4510_S18


title: ClassicalMonocytes_SLE_Visit2_5


title: ClassicalMonocytes_SLE_Visit2_8


title: NonClassicalMonocytes_SLE_Visit1_7


title: HT-1376-ζ (siRNA treated) [12A]

source_name: HT-1376-ζ (siRNA treated)

value: bladder grade III carcinoma


title: NonClassicalMonocytes_SLE_Visit1_6


title: IntermediateMonocytes_SLE_Visit2_7


title: HT-1376-ζ (siRNA treated) [12B]


title: ClassicalMonocytes_SLE_Visit2_6


title: CortexEntorhinalis_rTg4510_S17

value: WT


title: CortexEntorhinalis_rTg4510_Q24


title: NonClassicalMonocytes_SLE_Visit2_6


title: HT-1376- ε (siRNA treated) [11B]

source_name: HT-1376- ε (siRNA treated)


title: IntermediateMonocytes_SLE_Visit1_5


title: HT-1376-Control [10B]


title: NonClassicalMonocytes_SLE_Visit1_5


title: HT-1376- ε (siRNA treated) [11A]


title: IntermediateMonocytes_SLE_Visit1_6


title: IntermediateMonocytes_SLE_Visit2_4


title: HT-1376-Control [10A]


title: CortexEntorhinalis_rTg4510_Q22


title: IntermediateMonocytes_SLE_Visit2_5


title: CortexEntorhinalis_rTg4510_Q21


title: ClassicalMonocytes_SLE_Visit1_6


title: CortexEntorhinalis_rTg4510_Q23


title: ClassicalMonocytes_SLE_Visit1_5


title: hippocampal tissues, TMAO-3

city: nanjing

first: Rui

last: Duan

address: Yanshan road 139

institute: Nanjing First hospital

description: 2VO rats were given TMAO (120 mg/kg) for 8 consecutive weeks

data_processing:
Sequencing was according to the PE150 mode of Illumina novaseq 6000.  Raw reads containing splice or low-quality bases were filtered by fastp (version 0.18.0).  Ribosomal RNA (rRNA) was removed using the comparison tool bowtie2, and clean reads of paired ends were compared to a reference genome (Rattus norvegicus Ensembl_release106) using HISAT2 (version 2.1.0).  StringTie software was used to perform quantitative analysis of lncRNA.  Genes differential expression analysis was performed by DESeq2 software.  Parameter |log2(Foldchange)| ≥ 1 and P-value <  0.05 were defined as significantly differentially expressed lncRNAs.
Assembly: rn6
Supplementary files format and content: count and fpkm values for all samples, lncRNA_Expression.xlsx, lncRNA_Differential_Expression_Summary.xlsx

source_name: hippocampal tissues

extract_protocol:
RNA was isolated from hippocampal tissues of rats using Trizol
RNA library was prepared with 1 μg of DNase-treated total RNA as input, and quantified with ABI StepOnePlus Real-Time PCR System

value: brain

tag: disease state

value: 2VO rats

value: TMAO


title: CortexEntorhinalis_rTg4510_Q20

tag: genotype


title: CortexEntorhinalis_rTg4510_Q19


title: NonClassicalMonocytes_SLE_Visit1_4


title: ClassicalMonocytes_SLE_Visit2_4


title: hippocampal tissues, TMAO-2

tag: treatment


title: CortexEntorhinalis_rTg4510_Q18


title: hippocampal tissues, 2VO-3

description: 2VO rats were given sterile water for 8 consecutive weeks

value: control


title: hippocampal tissues, 2VO-2


title: CortexEntorhinalis_rTg4510_Q17

value: Entorhinal Cortex


title: CortexEntorhinalis_rTg4510_P24

value: TG


title: hippocampal tissues, 2VO-1


title: NonClassicalMonocytes_SLE_Visit2_3


title: CortexEntorhinalis_rTg4510_P23


title: hippocampal tissues, TMAO-1


title: IntermediateMonocytes_SLE_Visit1_3


title: NonClassicalMonocytes_SLE_Visit1_2


title: S508 96h

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

institute: University of Warwick

data_processing:
Sequencing reads were mapped to the hg38 human genome assembly using STAR2 v2.5.3a using default settings.
Peaks were called on a merged mapped file using MACS-2.1.0. HTSeq-0.6.1 was used to assign reads to peaks.
Assembly: hg38
Supplementary files format and content: Decidualization_timecourse_ATACseq_counts_matrix.txt: counts matrix in .TXT format

source_name: Endometrial stromal cells

extract_protocol:
ATAC-seq was implemented as outlined previously (Corces et al 2017). After thawing on ice, 50,000 cells were washed, chemically lysed (1% Digitonin, 10% Tween-20 & 10% NP-40) and pelleted. 50ul of transposition reaction mix (Tn5 transposase, Tagment DNA buffer, Tween-20, & Digitonin) was added to the pellet and incubated at 37 ˚C for 30 minutes. DNA was then isolated using Qiagen MinElute Reaction Cleanup kit.
Libraries were generated using the Ad1 noMX and Ad2.1–2.20 barcoded primers by Illumina before purification with AMPure beads to remove primer dimers. Amplified libraries were quantified Using Qubit HS DNA Assay (Thermo Fisher Scientific, Paisley, United Kingdom). Library sizes were assessed on an Agilent Technologies 2100 Bioanalyzer before sequencing on the Illumina Nextseq platform paired-end reads (35 bp (R1) and 40 bp (R2)). One cartridge was used per 2 patients i.e. 20 multiplexed samples per cartridge.

treatment_protocol: Endometrial biopsies were collected in DMEM-F12 media and processed for primary EnSC culture as described (Brosens 1999). Monolayers of stromal cells were cultured (in DMEM-F12 media, 10 % dextra-coated charcoal-stripped FBS, 1× Antibiotic-Antimycotic, L-Glutamine, Insulin and E2, at 37 ˚C with 5 % CO2) until confluent. Confluent cells were incubated for 12 hours in differentiation base media (phenol red-free DMEM/F-12, 2 % dextran-coated charcoal-stripped FBS, 1× Antibiotic-Antimycotic, L-Glutamine) before the addition of 0.5 mM 8-bromo-cAMP and 1M medroxyprogesterone acetate (MPA) to induce decidualization.

value: Endometrial stromal cells

tag: batch

value: Batch 2


title: ClassicalMonocytes_SLE_Visit2_2

value: Female


title: ClassicalMonocytes_SLE_Visit1_3


title: ClassicalMonocytes_SLE_Visit1_4


title: IntermediateMonocytes_SLE_Visit2_2


title: CortexEntorhinalis_rTg4510_P22


title: NonClassicalMonocytes_SLE_Visit2_22


title: ClassicalMonocytes_SLE_Visit1_2


title: CortexEntorhinalis_rTg4510_P21


title: ClassicalMonocytes_SLE_Visit2_22


title: S508 36h

tag: cell line


title: IntermediateMonocytes_SLE_Visit2_3

tag: age


title: IntermediateMonocytes_SLE_Visit1_2


title: CortexEntorhinalis_rTg4510_P20


title: S508 24h


title: CortexEntorhinalis_rTg4510_P19


title: ClassicalMonocytes_SLE_Visit1_22


title: S508 48h


title: CortexEntorhinalis_rTg4510_P18


title: IntermediateMonocytes_SLE_Visit1_22


title: IntermediateMonocytes_SLE_Visit2_21


title: S508 12h


title: IntermediateMonocytes_SLE_Visit1_4


title: ClassicalMonocytes_SLE_Visit1_21


title: S508 9h


title: ClassicalMonocytes_SLE_Visit2_3


title: S508 18h


title: IntermediateMonocytes_SLE_Visit2_22


title: CortexEntorhinalis_rTg4510_P17


title: CortexEntorhinalis_rTg4510_O24


title: NonClassicalMonocytes_SLE_Visit1_22


title: S508 6h


title: IntermediateMonocytes_SLE_Visit1_21


title: NonClassicalMonocytes_SLE_Visit2_20


title: CortexEntorhinalis_rTg4510_O23


title: IntermediateMonocytes_SLE_Visit2_20


title: ClassicalMonocytes_SLE_Visit2_20


title: CortexEntorhinalis_rTg4510_O22


title: S508 3h


title: CortexEntorhinalis_rTg4510_O21


title: CortexEntorhinalis_rTg4510_O20


title: IntermediateMonocytes_SLE_Visit1_20


title: S508 0h


title: S506 96h


title: NonClassicalMonocytes_SLE_Visit2_21


title: CortexEntorhinalis_rTg4510_O19


title: IntermediateMonocytes_SLE_Visit2_1


title: ClassicalMonocytes_SLE_Visit2_21


title: NonClassicalMonocytes_SLE_Visit1_1


title: IntermediateMonocytes_SLE_Visit2_19


title: NonClassicalMonocytes_SLE_Visit1_21


title: NonClassicalMonocytes_SLE_Visit2_1


title: ClassicalMonocytes_SLE_Visit1_1


title: CortexEntorhinalis_rTg4510_N24


title: IntermediateMonocytes_SLE_Visit1_1


title: S506 24h


title: S506 48h


title: ClassicalMonocytes_SLE_Visit1_20


title: ClassicalMonocytes_SLE_Visit2_1


title: CortexEntorhinalis_rTg4510_O18


title: CortexEntorhinalis_rTg4510_M24


title: ClassicalMonocytes_SLE_Visit2_19


title: S506 18h


title: S506 36h


title: S506 12h


title: CortexEntorhinalis_rTg4510_M23


title: S506 9h


title: NonClassicalMonocytes_SLE_Visit2_19


title: IntermediateMonocytes_SLE_Visit2_18


title: IntermediateMonocytes_SLE_Visit1_19


title: S506 6h


title: CortexEntorhinalis_rTg4510_M21


title: ClassicalMonocytes_SLE_Visit2_17


title: S506 3h


title: ClassicalMonocytes_SLE_Visit1_19


title: CortexEntorhinalis_rTg4510_M20


title: NonClassicalMonocytes_SLE_Visit2_17


title: IntermediateMonocytes_SLE_Visit1_18


title: IntermediateMonocytes_SLE_Visit2_17


title: CortexEntorhinalis_rTg4510_M19


title: NonClassicalMonocytes_SLE_Visit1_19


title: ClassicalMonocytes_SLE_Visit1_17


title: ClassicalMonocytes_SLE_Visit1_18


title: S170 96h

value: Batch 1


title: CortexEntorhinalis_rTg4510_M22


title: NonClassicalMonocytes_SLE_Visit1_17


title: CortexEntorhinalis_rTg4510_M18


title: ClassicalMonocytes_SLE_Visit2_18


title: NonClassicalMonocytes_SLE_Visit2_16


title: S506 0h


title: CortexEntorhinalis_rTg4510_M17


title: S170 48h


title: IntermediateMonocytes_SLE_Visit1_17


title: S170 36h


title: ClassicalMonocytes_SLE_Visit1_16


title: CortexEntorhinalis_rTg4510_L24


title: S170 18h


title: ClassicalMonocytes_SLE_Visit2_16


title: CortexEntorhinalis_rTg4510_L22


title: S170 24h


title: IntermediateMonocytes_SLE_Visit2_16


title: CortexEntorhinalis_rTg4510_L21


title: S170 9h


title: ClassicalMonocytes_SLE_Visit1_15


title: CortexEntorhinalis_rTg4510_L23


title: NonClassicalMonocytes_SLE_Visit2_15


title: S170 12h


title: CortexEntorhinalis_rTg4510_L19


title: CortexEntorhinalis_rTg4510_L18


title: S170 6h


title: IntermediateMonocytes_SLE_Visit1_16


title: ClassicalMonocytes_SLE_Visit2_15


title: IntermediateMonocytes_SLE_Visit1_15


title: NonClassicalMonocytes_SLE_Visit1_15


title: CortexEntorhinalis_rTg4510_L17


title: IntermediateMonocytes_SLE_Visit2_15


title: S170 3h


title: ClassicalMonocytes_SLE_Visit2_14


title: S170 0h


title: IntermediateMonocytes_SLE_Visit2_14


title: CortexEntorhinalis_rTg4510_K23


title: NonClassicalMonocytes_SLE_Visit2_14


title: S169 96h


title: IntermediateMonocytes_SLE_Visit1_14


title: CortexEntorhinalis_rTg4510_K21


title: ClassicalMonocytes_SLE_Visit2_13


title: S169 48h


title: CortexEntorhinalis_rTg4510_K20


title: ClassicalMonocytes_SLE_Visit1_14


title: IntermediateMonocytes_SLE_Visit2_13


title: CortexEntorhinalis_rTg4510_K19


title: S169 36h


title: IntermediateMonocytes_SLE_Visit1_13


title: IntermediateMonocytes_SLE_Visit1_10


title: S169 24h


title: ClassicalMonocytes_SLE_Visit1_13


title: ClassicalMonocytes_SLE_Visit1_10


title: NonClassicalMonocytes_HealthyDonor_23

source_name: HD


title: ClassicalMonocytes_SLE_Visit2_10


title: CortexEntorhinalis_rTg4510_K18


title: NonClassicalMonocytes_SLE_Visit2_10


title: S169 18h


title: CortexEntorhinalis_rTg4510_K17


title: IntermediateMonocytes_HealthyDonor_23


title: S169 12h


title: NonClassicalMonocytes_SLE_Visit1_10


title: NonClassicalMonocytes_SLE_Visit2_13


title: IntermediateMonocytes_SLE_Visit2_10


title: CortexEntorhinalis_J20_J24


title: S169 9h


title: S169 6h


title: CortexEntorhinalis_J20_J23


title: CortexEntorhinalis_J20_J22


title: NonClassicalMonocytes_SLE_Visit1_13


title: CortexEntorhinalis_J20_J21


title: ClassicalMonocytes_HealthyDonor_23


title: S169 0h


title: S169 3h


title: NonClassicalMonocytes_HealthyDonor_20


title: ClassicalMonocytes_HealthyDonor_21


title: DMT+DOX_3

source_name: H9c2 cells

value: H9c2 cells

value: cardiomyocyte cells

value: DMT+DOX


title: NonClassicalMonocytes_HealthyDonor_22


title: ClassicalMonocytes_HealthyDonor_22


title: CortexEntorhinalis_J20_J20


title: DMT+DOX_1


title: AXT+DOX_2

value: AXT+DOX


title: CortexEntorhinalis_J20_J17


title: DSI+DOX_3

value: DSI+DOX


title: AXT+DOX_3


title: AXT+DOX_1


title: CortexEntorhinalis_J20_H24


title: CortexEntorhinalis_J20_J19


title: CortexEntorhinalis_J20_I20


title: DSI+DOX_2


title: DOX_2

value: DOX


title: IntermediateMonocytes_HealthyDonor_22


title: DOX_1


title: con_3

value: WT


title: IntermediateMonocytes_HealthyDonor_19


title: CortexEntorhinalis_J20_H22


title: IntermediateMonocytes_HealthyDonor_21


title: con_1


title: NonClassicalMonocytes_HealthyDonor_23

data_processing:
fastq files were aligned to hg38 and normalized using Kallisto
Differentially expressed genes (³1-fold and £5% false discovery rate) were identified with Ashr shrinkage algorithm using lfcShrink function from DESeq2 package
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample

extract_protocol:
Total RNA was isolated using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to manufacturer’s instruction
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

tag: background strain


title: con_2


title: CortexEntorhinalis_J20_H23


title: CortexEntorhinalis_J20_H21


title: ClassicalMonocytes_HealthyDonor_23


title: NonClassicalMonocytes_HealthyDonor_22


title: IntermediateMonocytes_HealthyDonor_22


title: ClassicalMonocytes_HealthyDonor_18


title: NonClassicalMonocytes_HealthyDonor_15


title: NonClassicalMonocytes_HealthyDonor_21


title: CortexEntorhinalis_J20_H17


title: IntermediateMonocytes_HealthyDonor_23


title: IntermediateMonocytes_HealthyDonor_18


title: ClassicalMonocytes_HealthyDonor_15


title: DMT+DOX_2


title: NonClassicalMonocytes_HealthyDonor_28


title: CortexEntorhinalis_J20_G23


title: NonClassicalMonocytes_HealthyDonor_18


title: ClassicalMonocytes_HealthyDonor_28


title: CortexEntorhinalis_J20_H18


title: CortexEntorhinalis_J20_G22


title: NonClassicalMonocytes_HealthyDonor_27


title: CortexEntorhinalis_J20_G21


title: ClassicalMonocytes_HealthyDonor_19


title: ClassicalMonocytes_HealthyDonor_27


title: NonClassicalMonocytes_HealthyDonor_26


title: IntermediateMonocytes_HealthyDonor_26


title: DOX_3


title: CortexEntorhinalis_J20_G20


title: ClassicalMonocytes_HealthyDonor_16


title: ClassicalMonocytes_HealthyDonor_22


title: CortexEntorhinalis_J20_G19


title: IntermediateMonocytes_HealthyDonor_15


title: IntermediateMonocytes_HealthyDonor_14


title: IntermediateMonocytes_HealthyDonor_17


title: IntermediateMonocytes_HealthyDonor_20


title: ClassicalMonocytes_HealthyDonor_24


title: CortexEntorhinalis_J20_G17


title: ClassicalMonocytes_HealthyDonor_26


title: IntermediateMonocytes_HealthyDonor_24


title: CortexEntorhinalis_J20_F24


title: ClassicalMonocytes_SLE_22_Visit1


title: IntermediateMonocytes_SLE_22_Visit1


title: NonClassicalMonocytes_SLE_21_Visit1


title: NonClassicalMonocytes_HealthyDonor_15


title: IntermediateMonocytes_SLE_21_Visit1


title: ClassicalMonocytes_SLE_21_Visit1


title: ClassicalMonocytes_HealthyDonor_14


title: NonClassicalMonocytes_SLE_22_Visit1


title: IntermediateMonocytes_HealthyDonor_16


title: ClassicalMonocytes_HealthyDonor_20


title: NonClassicalMonocytes_HealthyDonor_16


title: NonClassicalMonocytes_SLE_19_Visit1


title: CortexEntorhinalis_J20_F20


title: ClassicalMonocytes_SLE_19_Visit1


title: CortexEntorhinalis_J20_F21


title: NonClassicalMonocytes_HealthyDonor_24


title: IntermediateMonocytes_HealthyDonor_15


title: NonClassicalMonocytes_SLE_17_Visit1

value: Male


title: IntermediateMonocytes_SLE_17_Visit1


title: ClassicalMonocytes_SLE_17_Visit1


title: IntermediateMonocytes_SLE_19_Visit1


title: IntermediateMonocytes_SLE_13_Visit1


title: NonClassicalMonocytes_SLE_13_Visit1


title: CortexEntorhinalis_J20_G24


title: CortexEntorhinalis_J20_F19


title: ClassicalMonocytes_SLE_13_Visit1


title: CortexEntorhinalis_J20_F17


title: CortexEntorhinalis_J20_F18


title: NonClassicalMonocytes_SLE_9_Visit1


title: NonClassicalMonocytes_HealthyDonor_17


title: ClassicalMonocytes_SLE_9_Visit1


title: IntermediateMonocytes_SLE_9_Visit1


title: CortexEntorhinalis_J20_E22


title: CortexEntorhinalis_J20_F22


title: IntermediateMonocytes_SLE_8_Visit1


title: NonClassicalMonocytes_SLE₈_Visit1


title: ClassicalMonocytes_SLE_7_Visit1


title: NonClassicalMonocytes_SLE_7_Visit1


title: ClassicalMonocytes_SLE_8_Visit1


title: IntermediateMonocytes_SLE_7_Visit1


title: IntermediateMonocytes_HealthyDonor_28


title: CortexEntorhinalis_J20_E20


title: CortexEntorhinalis_J20_E21


title: CortexEntorhinalis_J20_D23


title: CortexEntorhinalis_J20_E18


title: ClassicalMonocytes_SLE_5_Visit1


title: IntermediateMonocytes_SLE_6_Visit1


title: NonClassicalMonocytes_SLE_6_Visit1


title: ClassicalMonocytes_SLE_6_Visit1


title: CortexEntorhinalis_J20_E19


title: CortexEntorhinalis_J20_D20


title: IntermediateMonocytes_SLE_5_Visit1


title: NonClassicalMonocytes_SLE_5_Visit1


title: NonClassicalMonocytes_SLE_2_Visit1


title: ClassicalMonocytes_HealthyDonor_17


title: IntermediateMonocytes_SLE_2_Visit1


title: B-Mo-TSN-siCD93

city: Guangzhou

first: Da

last: Jiang

state: Guangdong

address: No. 135 West Xingang Road Guangzhou City

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
The FPKM of each gene was calculated based on the length of the gene and number of reads count mapped to this gene was calculated.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: blood

extract_protocol:
four polyA mRNA-seg libraries, include two from si-NC monocyte samples and two from si-CD93 monocyte samples. RNA was harvested using Trizol reagent. DNBSEQ stamdard kits was used with 3 ug of total RNA for the construction of Sequencing.
RNA libraries were prepared for sequencing using standard DNBSEQ-T7 protocols.

value: blood

value: monocyte

value: myeloid


title: ClassicalMonocytes_HealthyDonor_15


title: ClassicalMonocytes_SLE_2_Visit1


title: CortexEntorhinalis_J20_D19

source_name: Entorhinal Cortex

value: Entorhinal Cortex


title: B-Mo-TSN-NC

value: siNC


title: CortexEntorhinalis_J20_E17


title: A-Mo-TSN-siCD93


title: CortexEntorhinalis_J20_D18

value: TG


title: IntermediateMonocytes_SLE_1_Visit1


title: CortexEntorhinalis_J20_D17


title: RNA-seq_oocyte_Ell3_KD_1

first: Jingjing

state: 2 Sipailou

address: 2 Sipailou

department: School of Life Science and Technology

institute: Southeast University

data_processing:
Fastq files were checked for quality using fastqc (v0.11.5) .Fastq files were mapped to mouse genome using Hisat2 (v2.2.1.0).Read counts were generated using featureCounts  for coding genes from genomes.
Assembly: mm10
Supplementary files format and content: *.bw: bigWig files; *.count: reads count files

source_name: oocyte

extract_protocol:
We followed the methods described previously for smart-seq2 with some modifications.Briefly, oocytes were rinsed in 0.2% BSA/PBS without Ca2+ and Mg2+ and placed in 0.2 ml PCR tube, immediately transferred into cell lysis buffer.After incubation at 72 °C for 3 min, reverse transcription for first-strand cDNA was performed using SuperScript III Reverse Transcriptase.After second-strand cDNA synthesis, the cDNA library was amplified with KAPA Hifi HotStart for 16 cycles.
After fragmentation, the sequence libraries were generated using the KAPA Hyper Prep Kit for the Illumina platform, following the manufacturer’s instructions. Paired-end 150-bp sequencing was performed on NovaSeq (Illumina) platform.

value: oocyte

value: Ell3 KD


title: A-Mo-TSN-NC


title: RNA-seq_oocyte_Ctrl_2

value: Ctrl


title: GB-d1-CEACAM6+Dox_rep4

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
Assembly: GRCh38.p13
Supplementary files format and content: TPM abundance estimates, generated with kallisto quant 0.4.6
Supplementary files format and content: normalized values created with voom of the limma package in R

growth_protocol: GB-d1 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin (100 IU/mL and 100 g/mL).

extract_protocol:
Total RNA was extracted from cells with NucleoSpin RNA Kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols, strand specific mRNA sequencing on DNBSEQ platform PE100bp

treatment_protocol: CEACAM6 protein expression was induced with 2 µg/ml doxycycline (Dox)

value: gallblader cancer cells

value: CEACAM6 overexpression


title: GB-d1-CEACAM6_rep4


title: RNA-seq_oocyte_Ctrl_1

last: He


title: lumbar spinal cord, 444.37

city: Baltimore

first: Joseph

last: Mankowski

address: 733 N Broadway

institute: Johns Hopkins University

data_processing:
Following quality checking with the software Fastqc, RNA-seq reads were mapped to a reference Macaca mulatta genome (e.g., Mmul_10) with the spliced alignment tool STAR v 2.7.6a
Gene and transcript expression levels in each sample were computed with DESeq222, using as reference the ENSEMBL v.99 gene annotations for M. mulatta.
R version /Bioconductor software packages were used for principal components analysis and data visualization.
Gene and transcript expression levels in each sample were computed and differentially expressed genes determined for each comparison with DESeq222.
Pathway analysis of differentially expressed genes was performed using Enrichr and Gene Set Enrichment Analysis.
SeqSeek, a harmonized atlas of cell types in the mouse spinal cord, was used to evaluate individual spinal cord cell type expression of the genes upregulated in SIV and SIV+ART.
Assembly: Mmul_10
Supplementary files format and content: Excel file includes normalized counts for each sample

organism: Macaca nemestrina

source_name: Spinal cord

extract_protocol:
RNA was isolated from 100 mg frozen lumbar spinal cord samples using RNA-STAT60 reagent followed by cleaning with Promega RQ1 DNase set (M6101) and Qiagen RNeasy Mini Kit (74104). For the transcriptome sequence sample preparation, the NEBNext rRNA Depletion Kit (E6310) was used to purify isolated 1 ug RNA samples according to the manufacturer’s recommendations.
cDNA libraries were prepared with the NEBNext Ultra II Directional Library Prep with Sample Purification Beads (E7765) according to the manufacturer’s recommendations. cDNA libraries were submitted to the Johns Hopkins University Genetic Resources Core Facility for sequencing.

value: Spinal cord

value: PNS uninfected


title: CortexEntorhinalis_J20_C21


title: lumbar spinal cord, 443.37


title: CortexEntorhinalis_J20_C22


title: GB-d1-CEACAM6+Dox_rep3


title: ClassicalMonocytes_SLE_1_Visit1

value: Female


title: CortexEntorhinalis_J20_C23


title: KO5_LV

first: Lan

last: Tang

address: 1838  Guangzhou North Ave,

department: School of Pharmaceutical Science

institute: Southern Medical University

data_processing:
Illumina Casava1.8 software used for base-calling.
Reads containing adapter, reads containing ploy-N and low quality reads were trimmed.
HISAT2 v2.0.5 was used for alignment.
StringTie was used for assembly.
The counts and Fragments Per Kilobase of exon per Megabase of library size (FPKM) of genes were calculated and normalized by DESeq2 1.16.1.
Genome_build: mm10
Supplementary_files_format_and_content: count or log2FPKM values for each Sample.

extract_protocol:
Kidney and liver tissues were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: Sex

value: male

tag: genotype/variation

value: Lxralphs KO

value: liver


title: CortexEntorhinalis_J20_C20

tag: histology


title: lumbar spinal cord, 401.37

value: SIV+ART+MVC


title: NonClassicalMonocytes_SLE_1_Visit1

tag: gender


title: RNA-seq_oocyte_Ell3_KD_2


title: KO4_LV


title: KO5_Kn

value: kidney


title: lumbar spinal cord, 400.37


title: CortexEntorhinalis_J20_C19

tag: group id

value: WT

tag: age months


title: IntermediateMonocytes_HealthyDonor_27


title: KO4_Kn


title: GB-d1-CEACAM6+Dox_rep2


title: CortexEntorhinalis_J20_C18

value: Entorhinal Cortex


title: GB-d1-CEACAM6_rep2


title: CortexEntorhinalis_J20_F23


title: KO3_LV


title: lumbar spinal cord, 393.37

value: SIV+ART


title: CortexEntorhinalis_J20_C17


title: KO3_Kn


title: GB-d1-CEACAM6+Dox_rep1


title: GB-d1-CEACAM6_rep1


title: CortexEntorhinalis_J20_B24

value: TG


title: lumbar spinal cord, 391.37


title: KO2_LV


title: GB-d1-CEACAM6_rep3


title: lumbar spinal cord, 389.37


title: KO2_Kn


title: CortexEntorhinalis_J20_B22


title: SNU308_siCEACAM6_3_rep3

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
Assembly: GRCh38.p13
Supplementary files format and content: TPM abundance estimates, generated with kallisto quant 0.4.6
Supplementary files format and content: normalization method with voom of the limma package

growth_protocol: SNU308 cells were cultured in RPMI medium supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin (100 IU/mL and 100 g/mL).

treatment_protocol: SNU308 cells were transfected using siRNAs (final concentration 25nM) for 3 days prior to total RNA isolation. Oligofectamine (Thermo Fisher Scientific, Waltham, MA, USA) was used as transfection reagent according to the manufacturee's protocol.

value: CEACAM6 knockdown


title: KO1_LV


title: lumbar spinal cord, 375.37

value: Uninfected


title: CortexEntorhinalis_J20_B21


title: SNU308_siCEACAM6_3_rep2


title: lumbar spinal cord, 394.37


title: KO1_Kn


title: lumbar spinal cord, 374.37


title: CortexEntorhinalis_J20_G18


title: CortexEntorhinalis_J20_B20


title: SNU308_siCEACAM6_3_rep1


title: CT6_LV

source_name: wild type_liver

value: wild type


title: CortexEntorhinalis_J20_B18


title: CortexEntorhinalis_J20_B23


title: lumbar spinal cord, 373.37


title: lumbar spinal cord, 392.37


title: CT6_Kn

source_name: wild type_kidney


title: SNU308_siCEACAM6_2_rep4

value: gallblader cancer cells


title: SNU308_siCEACAM6_3_rep4


title: SNU308_siCEACAM6_2_rep3


title: SNU308_siCEACAM6_2_rep2


title: lumbar spinal cord, 334.37


title: CT5_Kn


title: CortexEntorhinalis_J20_A24


title: CortexEntorhinalis_J20_A23


title: SNU308_siCEACAM6_2_rep1


title: CT4_LV


title: CT4_Kn


title: SNU308_NTC_rep4


title: CortexEntorhinalis_J20_A22


title: lumbar spinal cord, 332.37


title: lumbar spinal cord, 333.37


title: CortexEntorhinalis_J20_A20


title: CortexEntorhinalis_J20_A21


title: SNU308_NTC_rep3


title: CortexEntorhinalis_J20_B17


title: lumbar spinal cord, 350.37

value: SIV infected


title: SNU308_NTC_rep2


title: CT3_Kn


title: lumbar spinal cord, 300.37

value: Spinal cord


title: lumbar spinal cord, 349.37


title: lumbar spinal cord, 320.37


title: CortexEntorhinalis_J20_A19


title: SNU308_NTC_rep1


title: CT5_LV


title: CT1_LV


title: CortexEntorhinalis_J20_A18


title: CT1_Kn


title: lumbar spinal cord, 293.37


title: CortexEntorhinalis_J20_A17


title: hippocampi, sevoflurane, 6h, rep3

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: 10x Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria: Ø MT% < 30%;  Ø Cell Gene Number < Median Gene Number * 2; Ø Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: ASM275486v1
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

organism: Callithrix jacchus

source_name: hippocampi

extract_protocol:
Each sample was placed in a sterile Petri dish on ice. Fat, fibrous and necrotic areas were removed, and the tissue was subsequently minced to smaller pieces of less than 3 mm. Samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase Ⅱ (Worthington) for 60 min at 37°C, with agitation. Subsequently, the sample was filtered using a 70-mm nylon mesh (Miltenyi #130-095-823). 10 ml of this cell suspension was counted by Trypan Blue to determine the concentration of live cells. The sample was then centrifuged at 300g and 4℃ for 5 min, and the supernatant was discarded. The cell pellet was resuspended in 1 ml freezing media (Gibco) for long term cryopreservation in liquid nitrogen. Throughout the dissociation procedure, cells were maintained on ice whenever possible, and the entire procedure was completed in less than 1 hr.
Cryopreserved single-cell suspensions were promptly thawed and prepared as outlined by the 10x Genomics Single Cell 3 v3.1 Reagent Kit user guide.

value: hippocampi

value: sevoflurane


title: lumbar spinal cord, 291.37


title: hippocampi, sevoflurane, 6h, rep2

description: 10x Genomics


title: lumbar spinal cord, 268.37


title: CT3_LV

value: male


title: hippocampi, oxygen, 6h, rep3

description: 10x Genomics

value: control


title: lumbar spinal cord, 297.37


title: lumbar spinal cord, 203.37


title: hippocampi, oxygen, 6h, rep2

description: 10x Genomics


title: hippocampi, oxygen, 6h, rep1

description: 10x Genomics


title: TIM-3 tumor 3

first: Payton

last: De La Cruz

state: Rhode Island

address: 200 Chestnut St

department: Division of Biology and Medicine

institute: Brown University

hyb_protocol: The reporter code set and capture probe set tubes were removed from -80C and thawed on ice, prior to mixing by tapping and pulse centrifugation. 70 µl hybridization buffer was added to the tube containing the reporter probe set and mixed by tapping, followed by pulse centrifugation. 8 µl of the diluted reporter probe was added to a PCR tube. Each RNA sample was diluted in water to 25 ng/µl and 2 µl final volume for 50 ng total input per sample. 5 µl RNA sample was added to each tube containing the reporter probe set and mixed by tapping, followed by pulse centrifugation. 2 µl Capture Probe Set was added to each tube, mixed by tapping, and the sample was collected by pulse centrifugation and then immediately placed in a pre-heated PCR machine, with the lid set to 70 °C and the block set to 65 °C. The hybridization was performed for 18 h at 65 °C. Samples were cooled to 4 °C and any condensation was collected by pulse centrifugation. Each sample was diluted with 18 µl hybridization buffer.

scan_protocol: An nCounter Sprint cartridge was calibrated to room temperature for 15 min prior to injection of 33 µl of each sample into one of the 12 injection ports of the cartridge, followed by the introduction of an air seal. The sample injection cartridge was sealed with provided tape and the reagent supply ports were unsealed prior to loading on the nCounter Sprint profiler. The analysis run was started immediately after loading.

data_processing:
The resulting data file in RCC format was used for data analysis in the nSolver analysis platform. Raw data in RCC format was uploaded to nSolver for automated normalization, background subtraction, and quality control (QC) check.
low count genes were filtered out for a total of 750 genes detected on the panel

label: fluorescent barcode

source_name: tumor derived from E0771 cells

growth_protocol: E0771 cells were cultured in Dulbecco Modified Eagle Medium supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin. 5x10^5 cells were injected with matrigel into the 4th mammary pad of female eight week old C57Bl/6J mice. Tumors were allowed to grow for 14 days. Mice were allocated into treatment groups once tumors were palpable.

extract_protocol: RNA extraction from flash frozen on-treatment tumors (n=3 per group) was performed using the Quick-RNA MiniPrep Kit (Zymo Research, R1054) with the manufacturer’s instructions.

treatment_protocol: Mice received 200 μg doses of mouse anti-PD-1 (clone: 29F.1A12), anti-LAG-3 (clone: C9B7W), anti-TIM-3 (clone: RMT3-23), or rat IgG2a isotype control (clone: 2A3) every 4 days via intraperitoneal injection, with treatments stopping after the third dose.

value: mouse tumor


title: TIM-3 tumor 2


title: IgG control tumor 2

value: IgG control


title: IgG control tumor 3


title: TIM-3 tumor 1


title: patient3_chd_sample2

city: San Francisco

first: Michael

middle: A

last: Smith

state: CA

address: 550 16th St, 5th Floor

department: Pediatrics

institute: UC San Francisco

data_processing:
The workflow “QIAseq miRNA Quantification” of CLC Genomics Server with standard parameters is used to map the reads to miRBase version 22.
Assembly: miRBase version 22
Supplementary files format and content: CSV file containing raw read counts for all samples

source_name: Peripheral blood

extract_protocol:
RNA was isolated from 200 ul using the miRNeasy Serum/Plasma Advanced (QIAGEN) according to manufacturer’s instructions with an elution volume of 20 ul.
The library preparation was done using the QIAseq miRNA Library Kit (QIAGEN).

value: Peripheral blood

value: CHD


title: patient14_cdh_sample2

value: CDH


title: patient27_idiohered_sample2

value: Idiohered


title: patient32_idiohered_sample2


title: patient13_chd_sample2


title: patient29_chd_sample2


title: hippocampi, sevoflurane, 6h, rep1

description: 10x Genomics


title: patient21_other_sample2

value: Other


title: LN-229 MGMT-transfected cells exposed to solvent-control (1x), rep3

city: Zurich

first: Shana

middle: J.

last: Sturla

address: Schmelzbergstrasse 9

department: D-HEST

institute: ETH Zurich

data_processing:
After demultiplexing of sequencing data, each sample was represented by two fastq.gz files containing 151-nucleotide-long genomic reads. The quality of the raw sequencing data was checked via FastQC version 0.12.1.
Low-quality reads and adapter-containing reads were removed via trimmomatic version 0.39 with the following parameters: PE ILLUMINACLIP:/cluster/home/jabueche/programs/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:151.
Reads containing the AD1B sequence, which were not removed by subtractive hybridization, were discarded using cutadapt version 4.4 and the following settings: -b "GACTGGTTCCAATTGAAAGTGCTCTTCCGATCT;e=0.1;min_overlap=15" -B "AGATCGGAAGAGCACTTTCAATTGGAACCAGTC;e=0.1;min_overlap=15" --pair-filter=any --discard-trimmed. 12 base pairs of the 5’ end of all R2 reads (not containing the site of interest) were cropped due to low quality and suboptimal per base sequence content, increasing alignment rate.
The paired reads were mapped to human reference genome GRCh38 via bowtie2 version 2.5.1, using pre-built bowtie2 index from https://genome-idx.s3.amazonaws.com/bt/GRCh38_noalt_as.zip and applying the following additional settings: --no-mixed --no-discordant.
Read duplicates were removed by gatk (version 4.2.0.0) MarkDuplicatesSpark.
Samtools version 1.17 were employed to sort, index, and generate statistics of bam files.
Bedtools2 version 2.31 were used to retrieve the coordinates of mapped and deduplicated reads and extract the sequence context of the modified nucleotides from the reference genome, while the -1 position of the read start was the modification site.
Assembly: hg38
Supplementary files format and content: The processed .tsv files are tab-separated lists of all found modification sites. Headers "Chr", "Position", "Strand", "Base", "MAPQ" are included. It contains all found sites, not only guanines.
Library strategy: O6‑MeG‑seq, a novel sequencing strategy to map O6‑methylguanine in the human genome

growth_protocol: Cells were cultured in GlutaMAX™ DMEM supplemented with 10% FBS and 1% Penicillin-Streptomycin at 5% CO2 and 37°C.

extract_protocol:
Cells were detached with 0.25% Trypsin-EDTA and DNA was extracted using the QIAamp® DNA Mini Kit according to manufacturer's instructions.
Briefly, the extracted DNA was sheared, end-repaired with NEBNext Ultra II DNA Library Prep Kit and custom adapters were ligated. Fragments containing O6‑methylguanine were enriched with immunopercipitation and stalling of a high-fidelity polymerase was used to mark the site of O6‑methylguanine. Subtractive hybridisation was used to remove unwanted fragments and the library was indexed and amplified using dual indexing primers for Illumina.

treatment_protocol: LN-229 WT and MGMT-transfected cells were exposed to 1mM temozolomide in growth medium, or 1% DMSO as solvent control, once (1x) or repetitively every 4 h (3x) and DNA was extracted 24 h after first exposure. Naked DNA was allowed to react with temozolomide for 24h.

value: glioblastoma

value: MGMT-transfected

value: solvent-control (1x)


title: Naked genomic DNA from LN-229 MGMT-transfected cells exposed to 1mM TMZ,  rep3

value: 1 mM TMZ on naked DNA (1x)


title: Naked genomic DNA from LN-229 WT cells exposed to 1mM TMZ,  rep3

value: WT


title: LN-229 WT cells exposed to solvent-control (1x), rep3


title: patient18_idiohered_sample2


title: LAG-3 tumor 3

city: Providence


title: LN-229 MGMT-transfected cells exposed to 100 μM TMZ (1x), rep3

value: 100 μM TMZ (1x)


title: LAG-3 tumor 2


title: IgG control tumor 1


title: LN-229 WT cells exposed to 100 μM TMZ (1x), rep3


title: patient37_idiohered_sample2