title: Labeled stromal cells 2 HTO

description:
3190_SG-602_d27_inh_mCh_IGO_12437_197_sparse_counts_barcodes.csv
3190_SG-602_d27_inh_mCh_IGO_12437_197_sparse_counts_genes.csv
3190_SG-602_d27_inh_mCh_IGO_12437_197_sparse_molecule_counts.csv


title: Liver, sh959, run1 (WGBS)

status: Public on May 02 2023

type: SRA

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

library_source: genomic

data_processing:
Reads were mapped using the bowtie2 option (v 2.3.3.1) of the Bismark software (Brabraham Bioinformatics, v 0.18.1_dev) against the Syrian hamster reference genome provided by Ensembl (MesAur1.0, release 95). FastQC (Brabraham Bioinformatics, v 0.11.2) was used to assess quality of the WGBS samples, indicating good quality (both on the raw and trimmed fastq files). Trim Galore! (Brabraham Bioinformatics, v 0.1.0) was used to trim out bad quality bases (quality score < 20, default) from reads (reads trimmed shorter than 15bp were discarded). Bismark and bismark_methylation_extractor (v 0.18.0) were used to quantify CpG methylation. Finally, coverage files were compiled (bismark2bedGraph, v0.18.0) for downstream analysis.
Assembly: MesAur1.0
Supplementary files format and content: Bismark coverage files including tab seperated files on chromosome, chromosomal position, methylation percentage, methylated counts and unmethylated counts.

molecule: genomic DNA

organism: Mesocricetus auratus

source_name: Liver

extract_protocol:
Liver was flushed with physiological salt solution, removed and snap-frozen in liquid nitrogen and stored at −80 °C.
Total DNA from liver tissue samples was extracted using Machery Nagel Nucleospin tissue kit and used for whole genome bisulfite sequencing (WGBS) by NXTGNT (www.nxtgnt.com). Concentration of the extracted DNA was measured using Quant-iT PicoGreen kit (Invitrogen). DNA quality was checked on a 1% agarose gel (E-gel EX Invitrogen). 500ng DNA was used from each sample for further analysis. Fragmentation was performed using Covaris model S2 to obtain fragments with a size of approximately 400 bp, followed by bisulfite conversion with the EZ DNA methylation Gold kit (Zymo Research, Irvine, CA, USA) according to manufacturer’s protocol. For library preparation, the NEBNext Ultra II DNA library prep kit (New England Biolabs, Ipswich, MA, USA) was used according to protocol, followed by sequencing on three Hiseq3000 lanes (Illumina), generating PE2x150bp reads.

treatment_protocol: All hibernating animals were kept in darkness until euthanization. Arousal was induced at > 3 days of torpor by gentle handling. The animal's activity pattern accurately identified torpor bouts of hamsters, as evidenced by mouth temperature (Tm) at euthanization, being 9.0±0.9°C and 35.0±2.1°C for TL and AE, respectively, whereas SE animals had a Tm of 35.7±0.5°C.

tag: tissue

value: Liver

tag: sample id

tag: hibernation stage

value: torpor late

tag: hibernation stage abbrev

value: TL

tag: run


title: Labeled stromal cells 2

city: New York

first: Siting

last: Gan

state: NY

address: 417 East 68th Street

department: SKI

country: USA

institute: MSKCC

library_source: transcriptomic single cell

data_processing:
GFP+ cancer cell and GFP- non cancer cell samples were mapped to hg38 and mm38 genome references, respectively.
The SEQC pipeline performed read alignment, multi-mapping read resolution, and cell barcode and UMI correction to generate a raw UMI-based (cell × gene) count matrix per sample.
An in-house method called SHARP (https://github.com/hisplan/sharp, version 0.2.1) assigned a cell as labeled by a particular Hashtag oligo and thereby belonging to the specific mouse (bearing either MDA231-BrM metastases or HCC1954-BrM metastases) barcoded with this oligo or as a doublet or low-quality droplet.
Assembly: hg38 and mm38
Supplementary files format and content: barcode gene counts
Supplementary files format and content: gene counts
Supplementary files format and content: molecule counts

molecule: polyA RNA

organism: Mus musculus

source_name: brain

extract_protocol:
4 weeks post innoculation with cancer cells, brains were harvested from euthanized mice and processed for enzymatic tissue dissociation with the Adult Brain Dissociation kit, removal of myelin with myelin removal beads II, and removal of debris and dead cells. Single cell suspensions of each sample were incubated with an anti-human Hashtag antibody and an anti-mouse Hashtag antibody, 1:100 TruStain FeX Fc receptor blocking solution, 1:100 TruStain FeX anti-mouse CD16/32 antibody, and 1:20 APC Annexin V. Calcein Violet positive and Annexin V negative cells of each sample were sorted into 3 groups, GFP positive mCherry positive, GFP negative mCherry positive, and GFP negative mCherry negative cells.
Single-cell RNA-Seq of FACS-sorted cell suspensions was performed on the Chromium instrument (10X genomics). Droplet encapsulation was performed on the cells after sorting and viability assessment. After reverse transcription and cell barcoding within droplets, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification per user manual instruction. Resulting libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

value: brain

tag: cell type

value: non-cancer cells in mouse brain

tag: genotype

value: wild type


title: Liver, sh951, run1 (WGBS)

value: arousal early

value: AE


title: Dataset D3 lib10

city: New York City

first: Itai

last: Yanai

address: 435 East 30th Street

institute: NYU Langone Health

description: S. aureus grown to an OD600 of 1 in TSB

data_processing:
All analysis was performed using the Tavazoie lab computational pipeline (https://tavazoielab.c2b2.columbia.edu/PETRI-seq/PETRI_Seq_Computational.pdf).
Initial QC was performed using FastQC then unique molecular identifiers were extracted with UMI tools. Initial demultiplexing by cell barcode was performed iteratively using Cutadapt.
After selecting barcodes associated with the highest number of reads, reads from individual barcodes were aligned to the E. coli MG1655  and S. aureus USA300-FPR3757 reference genomes using BWA.
Numbers of reads mapping to individual genes were quantified using FeatureCounts before counts were collapsed into unique reads based on UMI and used to make the final counts matrix.
Sample annotations were extracted from the number of barcode 1, since this corresponds to the way samples were added in the initial plate during reverse transcription.
Assembly: E. coli reads were aligned to the K-12 MG1655 reference assembly (GCA_000005845.2) and S. aureus to the USA300_FPR3757 reference assembly (GCF_000013465.1).
Supplementary files format and content: Counts matrices: gzip-compressed tab-separated text files of counts by genes (columns) by cell barcode (rows) ("_counts.txt.gz")
Supplementary files format and content: Metadata files: tab-separated files containing library and sample information for each cell barcode ("_metadata.txt").

molecule: total RNA

organism: Staphylococcus aureus

source_name: Whole bacteria

growth_protocol: Bacteria were streaked out onto agar from frozen stocks overnight then grown overnight in LB or TSB as indicated. Samples were then diluted back to grow in the medium and to the densities indicated. With the exception of Datasets D3 and D4, there was an initial "back-dilution" step prior to harvesting to improve population homogeneity.

extract_protocol:
Samples were fixed and processed according to the protocol of Blattman et al. (PMID: 32451472). Briefly, cells were fixed overnight with 4% formaldehyde, permeabilized with 50% ethanol followed by enzymatic cell wall digestion (100 µg/ml, 15 min using lysozyme for E. coli and lysostaphin for S. aureus), then treated with DNase to remove genomic DNA (this step was ommited for some samples in Dataset D4).
Reverse transcription and split-pool barcode ligation were carried out in situ in fixed cells according to the protocol of  Blattman et al. (PMID: 32451472). After barcoding, cells were separated into aliquots of ~20,000 cells for further processing. After lysis and reversal of crosslinking, second strand synthesis was performed using the NebNext Second Strand Synthesis module (New England Biolabs) and tagmentation was carried out using the EZ-Tn5 transposase (Lucigen), before final amplification with multiplex indexing primers.

treatment_protocol: After growth as described, most bacteria were not subjected to further treatment with the exception of some cells in Dataset D6 that were treated with 10 mM N-acetylcysteine for 90 min, and for cells in Dataset D7 that were treated with 10 µg/ml vancomycin for variable times.

value: Whole bacteria

tag: cell line

value: USA300 LAC

value: Bacteria

value: WT

tag: treatment

value: TSB


title: Dataset D3 lib9

description: S. aureus grown to an OD600 of 1 in TSB


title: Dataset D3 lib8

description: S. aureus grown to an OD600 of 1 in TSB


title: 180801_CEMBA_mm_P56_P63_RS2_180801_P7_180801_P8_A10_AD001

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2 & 3

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x1012 to 1x1013 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: source

value: THl

tag: target

value: STR

tag: Sex

value: male


title: Liver, sh939, run1 (WGBS)


title: Labeled stromal cells 1 HTO

description:
2109_Labeled_stromal_cells_IGO_11324_9_sparse_counts_barcodes.csv
2109_Labeled_stromal_cells_IGO_11324_9_sparse_counts_genes.csv
2109_Labeled_stromal_cells_IGO_11324_9_sparse_molecule_counts.csv


title: Labeled stromal cells 1


title: Liver, sh931, run1 (WGBS)


title: Dataset D3 lib6

description: S. aureus grown to an OD600 of 1 in TSB


title: D28_WT_KIDNEY_ORGANOID_HNF1A_INPUT

city: Singapore

first: Adrian

middle: Kee Keong

last: Teo

state: Singapore

address: 61 Biopolis Drive, Proteos

department: Stem Cells and Diabetes Laboratory

country: Singapore

institute: IMCB, A*STAR

data_processing:
Sequencing adapters were trimmed using BBDuk from the BBMap toolkit [v38.59] (https://sourceforge.net/projects/bbmap)
Trimmed reads were aligned to GRCh38 with Bowtie2 version 2.2.5 and reads non-uniquely mapped were discarded.
Filtering of unmapped and duplicate aligned reads were performed using samtools 1.12 and sambamba 0.8.0
Peaks were called using MACS2 version 2 2.7.1 against input control library with default q-value (minimum FDR) cutoff of 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: peak bed files

organism: Homo sapiens

source_name: Kidney organoid cells at D28 of renal differentiation

growth_protocol: Kidney organoids derived from WT hPSCs were generated following the protocol as described in Morizane et al., 2015. (doi: 10.1038/nbt.3392)

extract_protocol:
Nuclear lysates were clarified from sonicated kidney organoids following dissociation using TrypLE. Immunoprecipitation of HNF1A protein was performed using HNF1A antibody (ab96777).
Library preparation was done using a commercially available kit, NEB# E7645 NEBNext Ultra II DNA Library Prep Kit for Illumina KIT® following the manufacturer’s protocol. During the library construction, the ChIP-ed DNA underwent End Repair, Adapter ligation, size selection (for ~150bp insert)  and 16 cycles PCR enrichment to generate the final sequencing ready library. The quality of the library was checked using Agilent D1000 ScreenTape. The final library should have a fragment size of ~270bp insert plus adaptor and PCR primer sequences). The quality of the library was checked using Agilent D1000 ScreenTape. A single peak was expected and was observed indicating that the library was good and suitable for sequencing.

value: WT-hPSC (H9) derived kidney organoid cells

tag: chip antibody

tag: age

value: Day 28 of renal differentiation


title: Dataset D3 lib7

description: S. aureus grown to an OD600 of 1 in TSB


title: D28_WT_KIDNEY_ORGANOID_HNF1A_CHIP

value: Rb anti-HNF1A (ab96777)


title: Unlabeled stromal cells 2

description:
3188_SG-602_d27_inh_eg_IGO_12437_195_sparse_counts_barcodes.csv
3188_SG-602_d27_inh_eg_IGO_12437_195_sparse_counts_genes.csv
3188_SG-602_d27_inh_eg_IGO_12437_195_sparse_molecule_counts.csv


title: Liver, sh929, run1 (WGBS)

value: Liver


title: Unlabeled stromal cells 1

description:
2110_Unlabeled_stromal_cells_IGO_11324_10_sparse_counts_barcodes.csv
2110_Unlabeled_stromal_cells_IGO_11324_10_sparse_counts_genes.csv
2110_Unlabeled_stromal_cells_IGO_11324_10_sparse_molecule_counts.csv

value: brain


title: dSVZ_P2

city: Lyon

first: Guillaume

last: Marcy

address: 8 avenue Rockefeller

country: France

institute: Universite Lyon 1

library_source: transcriptomic

data_processing:
Reads were aligned and counted using CellRanger 3.1.0 (10x Genomics) using standard parameters
Seurat version 3 was used to analyze data
Low-quality cells were filtered out of the dataset: percentage mitochondrial genes >10%, nCount >8000 genes or <2000 genes.
Assembly: mm10 3.0.0
Supplementary files format and content: Seurat Data Object rds file containing the processed data, CellRanger filtered output: sparse UMI matrix mtx file with features (rows) and cells (columns),   Cell Ranger filtered output: cell barcodes in tsv file and Cell Ranger filtered output: features/genes in tsv file.

source_name: microdissected dorsal subventricular zone

extract_protocol:
The dorsal subventricular zone (dSVZ) of 2 male mice were microdissected and pooled. During all stages of the dissociation protocol, the tissue was kept in aCSF solution containing 125 mM NaCl, 2.5 mM KCl, 1.25 mM NaH2PO4, 26 mM NaHCO3, 17 mM glucose, 1.25 mM CaCl2 and 1 MgCl2. The small dissected tissues were incubated in Papain during 20 minutes at 37°C. Following enzymatic digestion, tissues were triturated and resuspended on ice in Leibovit’z L-15 medium supplemented with 0.1% of bovine serum albumin. The cell suspension was then filtered through a 70-μm cell strainer to remove aggregated cells.
mRNA libraries were prepared according to 10x Genomics 3’ version 3 chemistry & Illumina protocols

tag: strain

value: OF1 (Charles River)

value: subventricular zone (brain)

value: Postnatal day 2

value: Male


title: Dataset D3 lib11

description: S. aureus grown to an OD600 of 1 in TSB

value: Whole bacteria


title: dSVZ_P22

value: Postnatal day 22


title: Dataset D3 lib5

description: S. aureus grown to an OD600 of 1 in TSB

value: USA300 LAC

value: Bacteria


title: HUMREC4

first: Lindsey

last: Devisscher

address: Corneel Heymanslaan 10

data_processing:
Extract UMIs, UMI-tools 1.1.1, command: umi_tools extract -I <in.fastq.gz> -S <out.fastq.gz>  --extract-method=regex  --bc-pattern='(?P<umi_1>.{{6}})(?P<discard_1>.{{4}}).*'
trim_galore --cores <threads> --stringency 3 --three_prime_clip_R1 3 -a " AGATCGGAAGAGC -a AAAAAAAAAAAA" --length 25 --output_dir <output_dir> <in.fastq.gz>
Mapping reads, STAR 2.7.9a, command: STAR --runThreadN 10 --genomeDir <index_star> --readFilesIn <in.fastq.gz> --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix <sample_> --quantMode TranscriptomeSAM
Process UMIs, UMI-tools 1.1.1, command: umi_tools dedup -I <in.bam> --output-stats=deduplicated -S <out.bam>
Quantify expression with RSEM, RSEM 1.3.1, rsem-calculate-expression -p 60 --forward-prob 1 --no-bam-output --bam <in.bam> <rsem_index> <sample_name>
Genome_build: GRCh38.p13, release 103
Supplementary_files_format_and_content: normalized counts (DESeq2)

source_name: Fresh liver tissue of a patient with recurrent cholestasis

extract_protocol:
RNA extraction from paraffin embedded liver tissue. At least 4 human liver tissue-section cuts (≤ 10 µm thick) from the human control patients (HUMN1-3) were combined in an Eppendorf tube, after which a deparaffinization solution from the Quick-RNA FFPE Kit (Zymo Research, USA) was added and incubated at 55 °C for 1 minute. Subsequently, deparaffinized tissue was digested with proteinase K and digestion buffer from the Quick-RNA FFPE Kit (Zymo Research, USA) for 1 hour at 55 °C. After digestion, the Eppendorf tube was transferred and incubated at 94°C for 20 minutes. Further RNA extraction was performed using the same Quick-RNA FFPE Kit (Zymo Research, USA) according to the manufacturer’s instructions.  RNA extraction from full liver tissue  RNA was extracted from human liver tissue preserved in RNAlater (ThermoFisher Scientific, Belgium) using the Aurum Total RNA Mini Kit (Bio-Rad Laboratories, Belgium), following manufacturer’s protocol. Quantification and purity of the isolated RNA were determined via spectrophotometric analysis with a Nanodrop spectrophotometer (ThermoFisher Scientific, Belgium).
Library construction was performed with the QuantSeq 3’ mRNA FWD kit (Lexogen) and UMI Second Strand Synthesis Module (Lexogen).

value: Liver tissue

tag: disease state

value: Recurrent cholestasis


title: Liver, sh920, run1 (WGBS)

value: torpor late

value: TL


title: Eu-TCL1, rep4

city: Leipzig

first: Marco

last: Herling

address: Johannisallee 32a

department: Department for Hematology, Cell Therapy, Hemostaseology, and Infectious Diseases

country: Germany

institute: University Clinic Leipzig

data_processing:
Illumina Casava software used for basecalling
RNA-Seq data were processed through the QuickNGS analysis pipeline  version 1.2.7, based on Ensembl 93
Sequenced reads mapped to Mouse
Fragment Per Kilobase of exon per Million (FPKM) were calculated using a Cufflinks
Genome_build: Ensembl version 93 ( mus_musculus )
Supplementary_files_format_and_content: Text file include FPKM values for each Sample

source_name: spleen

extract_protocol:
splenic mononuclear cells were isolated from leukemic mice. Tatal RNA war isolated using mirVana™ miRNA Isolation Kit (Invitrogen).
NovaSeq 6000

value: spleen

value: splenic mononuclear cells


title: HUMREC3


title: Liver, sh974, run2 (WGBS)

value: euthermic

value: EU


title: Dataset D3 lib3

description: S. aureus grown to an OD600 of 1 in TSB

value: WT

value: TSB


title: Liver, sh973, run2 (WGBS)

value: Liver


title: Eu-TCL1, rep3


title: Dataset D3 lib2

description: S. aureus grown to an OD600 of 1 in TSB


title: Dataset D3 lib4

description: S. aureus grown to an OD600 of 1 in TSB


title: HUMREC1


title: Eu-TCL1, rep2


title: Liver, sh959, run2 (WGBS)


title: Liver, sh970, run2 (WGBS)


title: Dataset D3 lib1

description: S. aureus grown to an OD600 of 1 in TSB


title: HUMAC3

source_name: Fresh liver tissue of a patient with acute cholestasis

value: Acute cholestasis


title: iKdm1a;Em, rep4


title: Eu-TCL1, rep1


title: iKdm1a;Em, rep5


title: HUMAC1


title: Liver, sh939, run2 (WGBS)

value: arousal early

value: AE


title: iKdm1a;Em, rep2


title: HUMAC2


title: HUMN3

source_name: Parrafin embedded liver tissue of a petients with liver injury (segment IV)

value: Controls, without cholestasis


title: HUMN2

source_name: Parrafin embedded liver tissue of a patient with morbid obesity


title: HUMREC2


title: Liver, sh931, run2 (WGBS)


title: Liver, sh929, run2 (WGBS)


title: Plasma exosomes_healthy control_rep3

type: RNA

city: Jinan

first: Xinyue

last: Zhang

address: 324，Jingwu Road

country: China

institute: Department of Pediatric Cardiology, Shandong Provincial Hospital, Shandong University

description:
Con 3
miRNA expression in plasma exosomes from health children

hyb_protocol: 22.5 uL 2X Hybridization buffer (Agilent) was mixed with the completed labeling reaction to a final volume of 45 uL. The mixture was heated at 100°C for 5 min and chilled immediately to 0°C. 45 uL labeled sample mix was hybridized onto a microarray at 55°C for 20 hrs. The slides were washed at room temperature in 6X SSC with 0.005% Triton X-102 for 10 min, then in 0.1X SSC with 0.005% Triton X-102 for 5 min.

scan_protocol: The slides were scanned on an Agilent G2505C microarray scanner.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. The raw intensities were log2 transformed and quantile normalized. After normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 5 out of 6 samples were retained. Multiple probes from the same small RNA (miRNA/tsRNA/pre-miRNA/tRNA/ snoRNA) were averaged and consolidated into one RNA level. Differentially expressed small RNAs between two comparison groups were identified by filtering at the indicated fold change (FC) and statistical significance (p-value) thresholds. Hierarchical clustering, scatter plots, and volcano plots were generated by R software.

source_name: Plasma exosomes, healthy control

label_protocol: For Small RNA Microarray profiling, 100 ng total RNA was firstly dephosphorylated with 3 units T4 polynucleotide kinase (T4 PNK) at 37°C for 40 min to remove both (P) and (cP) chemical groups from the 3' end of RNAs to form a 3-OH end. The reaction was terminated at 70°C for 5 min and cooled immediately to 0°C. 7 uL of DMSO was added and heated to 100°C for 3 min to denature the RNAs and chilled immediately to 0°C. RNA end labeling was performed by adding ligase buffer, BSA, final 50 mM pCp-Cy3, and 15 units T4 RNA ligase in a 28 uL reaction at 16°C overnight.

extract_protocol: total RNA was isolated using TRIzol (Invitrogen). RNA quantity was measured by using NanoDrop ND-1000 spectrophotometer and RNA integrity (quality) was assessed by Bioanalyzer 2100 or denaturing gel electrophoresis.

value: healthy control

value: plasma exosomes


title: iKdm1a;Em, rep1


title: dSVZ_P12_2

data_processing:
Reads were aligned and counted using CellRanger 3.1.0 (10x Genomics) using standard parameters
Seurat version 3 was used to analyze data
Low-quality cells were filtered out of the dataset: percentage mitochondrial genes >10%, nCount >8000 genes or <2000 genes.
Genome_build: mm10 3.0.0
Supplementary_files_format_and_content: Seurat 3 Data Object rds file containing the 2 integrated samples P12_1 and P12_2  CellRanger filtered output: sparse UMI matrix mtx file with features (rows) and cells (columns)  Cell Ranger filtered output: cell barcodes in tsv file  Cell Ranger filtered output: features/genes in tsv file

extract_protocol:
The dorsal subventricular zone (dSVZ) from P12 mice (2 males) of 2 independent experiments were dissected. During all stages of the dissociation protocol, the tissue was kept in aCSF solution containing 125 mM NaCl, 2.5 mM KCl, 1.25 mM NaH2PO4, 26 mM NaHCO3, 17 mM glucose, 1.25 mM CaCl2 and 1 MgCl2. The small dissected tissues were incubated in Papain during 20 minutes at 37°C. Following enzymatic digestion, tissues were triturated and resuspended on ice in Leibovit’z L-15 medium supplemented with 0.1% of bovine serum albumin. The cell suspension was then filtered through a 70-μm cell strainer to remove aggregated cells.
mRNA libraries were prepared according to 10x Genomics 3’ version 3 chemistry & Illumina protocols

value: OF1 (Charles River)

value: subventricular zone (brain)

value: Postnatal day 12

value: Male


title: dSVZ_P12_1


title: XII_1_02_IP, biological repeat 2

status: Public on May 01 2023

city: Wuhan

first: Bang

last: Shen

address: No. 1 SHizishan St

institute: Huazhong Agricultural University

data_processing:
To analyze the ChIP-seq results, raw sequencing data were filtered by Trimmomatic and reads contaminated with adaptor sequences were trimmed.
The clean reads were aligned to reference genome GT1 (ToxoDB) using the STAR software (version 2.5.3a) with default parameters.
The MACS2 software (Version 2.1.1) was used for peak calling.
Assembly: ToxoDB (https://toxodb.org/toxo/app/downloads/Current_Release/TgondiiGT1/fasta/)
Supplementary files format and content: bigwig

organism: Toxoplasma gondii

source_name: whole organism

growth_protocol: All Toxoplasma gondii used in this study were maintained in human foreskin fibroblasts cultured at 37 ℃ in 5% CO2 in complete Dulbecco’s Modified Eagle Medium supplemented with 10% heat-inactivated fetal bovine serum, 100 unit/mL penicillin, and 100 μg/mL streptomycin

extract_protocol:
To perform chromatin immunoprecipitation, intracellular parasites of RH iAP2XII-1 were fixed with 1% formaldehyde for 10min. A final concentration of 0.125 M glycine was added to quench the fixation. Then all samples were scraped and syringe-lysed using a 22-gauge needle, filtered by filtration through 3-µm polycarbonate membranes. The purified parasites were lysed using the ChIP lysis buffer (50 mM HEPES, 150 mM NaCl, 1 % NP40, 0.1 % SDS, 0.1 % sodium deoxycholate, 1 mM EDTA, pH 8 and Roche protease inhibitor cocktail) for 30 min and the lysates were sonicated using the bioruptor UCD-200 for 16 min at 4 ℃ with a 30 s on/off cycle.
The libraries for sequencing were constructed using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, China).

value: whole organism

tag: developmental stage

value: tachyzoites

value: HA (the clone TANA2, MBL)


title: Liver, sh951, run2 (WGBS)

tag: tissue


title: Plasma exosomes_healthy control_rep1

description:
Con 1
miRNA expression in plasma exosomes from health children


title: Plasma exosomes_healthy control_rep2

description:
Con 2
miRNA expression in plasma exosomes from health children


title: Liver, sh920, run2 (WGBS)

tag: sample id

value: torpor late

value: TL


title: Plasma exosomes_fulminant myocartidis_rep3

description:
FM 3
miRNA expression in plasma exosomes from children with fulminant myocarditis

source_name: Plasma exosomes, fulminant myocartidis

value: fulminant myocartidis


title: XII_1_02_Input, biological repeat 2


title: ME49 iKD AP2XII-1 +IAA 0h, biological repeat 3, WT

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome of Toxoplasma gondii type II strain ME49
Read count extraction and normalization were performed using Salmon (version 1.9) and edgeR
Assembly: ToxoDB (https://toxodb.org/toxo/app/downloads/Current_Release/TgondiiME49/fasta/)
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent, and 1 ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

value: merozoites

value: WT

value: IAA 0h


title: XII_1_01_IP, biological repeat 1


title: ME49 iKD AP2XII-1 +IAA 0h, biological repeat 2, WT


title: ME49 iKD AP2XII-1 +IAA 60h, biological repeat 3, AP2 XII-1 knock down 60h

value: AP2 XII-1 knock down

value: IAA 60h


title: ME49 iKD AP2XII-1 +IAA 0h, biological repeat 1, WT


title: XII_1_01_Input, biological repeat 1


title: Plasma exosomes_fulminant myocartidis_rep2

description:
FM 2
miRNA expression in plasma exosomes from children with fulminant myocarditis


title: Plasma exosomes_fulminant myocartidis_rep1

description:
FM 1
miRNA expression in plasma exosomes from children with fulminant myocarditis


title: HUMN1

source_name: Parrafin embedded liver tissue of a patient with hepatocellular adenoma (segment III), biopsy derived from healthy tissue

value: Liver tissue

value: Controls, without cholestasis


title: 2D culture condylar chondrocyte rep2

first: Yang

middle: xue

last: wen

address: No. 237, Luoyu Road, Hongshan District

institute: Wuhan University

data_processing:
1.Experimental procedure.1)mRNA enrichment and purification: Oligo dT Selection to enrich the mRNA (For total RNA extracted from human whole blood, globin mRNA are depleted ); 2)RNA fragmentation and cDNA synthesis (second-strand cDNA synthesis with dUTP instead of dTTP); 3)End repair, add A and adaptor ligation; 4)PCR; 5)Circularization and make DNB; 6) Sequencing on DNBSEQ platform
2.Sequencing data filtering:This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor(adaptor pollution);  2) Remove reads whose N content is greater than 5%;  3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  The filtered "Clean Reads" are saved in FASTQ format.SOAPnuke Version v1.5.2
3.Sequencing data filtering:This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor(adaptor pollution);  2) Remove reads whose N content is greater than 5%;  3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  The filtered "Clean Reads" are saved in FASTQ format.
4.Reference genome alignment:Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT) is software for mapping RNA-seq reads. . Compared with other software, HISAT has the advantages of high speed, high sensitivity and accuracy, and low memory consumption. HISAT's index based on Burrows-Wheeler transform and Ferragina-Manzini (FM) uses two types of indexes: whole genome indexes and partial genome indexes. See the HISAT alignment diagram for the details and statistics of genome mapping results.HISAT2,Version：v2.0.4
5.Analytical method:We used Bowtie2 to map the clean reads to the reference gene sequence (transcriptome), and then used RSEM to calculate the gene expression level of each sample.Bowtie2: Version：v2.2.5;RSEM: Version：v1.2.8.The DEseq2 method is based on the principle of negative binomial distribution. This project uses the method described in Michael I, et al.to perform differential gene, DEG, which is an abbreviation for differentially expressed genes, and refers to the genes detection of different samples with different expression.
Supplementary files format and content: fq；6G for each Sample

organism: Rattus norvegicus

source_name: chondrocyte

growth_protocol: mandibular condylar chondrocytes were maintained in DMEM supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C；condylar cartilage organoid were maintained in special chondrogenic medium with 5% CO2 at 37C

extract_protocol:
total RNA was extracted from the cells and tissues respectively using Trizol reagent (Life technologies, New York, USA)   according to manual instruction.
RNA libraries for RNA-seq were prepared using related mRNA-Seq Library Prep Kit following DNBSEQ platform's protocols.

treatment_protocol: 2D culture mandibular condylar chondrocytes and condylar cartilage organoid

value: chondrocyte


title: condylar organoid rep3

source_name: organoid

value: organoid


title: condylar organoid rep2


title: 2D culture condylar chondrocyte rep1


title: 2D culture condylar chondrocyte rep3


title: condylar organoid rep1


title: 196279

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
VDJ-Seq: The bioinformatic analysis of the VDJ-seq data was performed as described in detail in Chovanec et al., Nat. Protoc. 13, 2018. using the BabrahamLinkON pipeline: (1) preclean.py (default parameters), Includes trimming and alignment steps (BabrahamLinkOn pipeline) deduplicate.py (default parameters), based on UMI  (BabrahamLinkOn pipeline) (2) assemble_clones.py (default parameters)  (BabrahamLinkOn pipeline) (3) The resulting counts were summarized using customized scripts based on the statistical language R version 3.3.3. The relative usage of each VH gene is shown as percentage of all VDJH recombination events determined.
ChIP-Seq:  Reads were aligned against the Mus musculus genome version of July 2007 (NCBI37/mm9) with the Bowtie program version 0.12.5. Genome-wide read coverages were normalized to the number of aligned reads, per million (=RPM)., using 'bedtools' and 'kent source utilities'.
RNA-Seq: The number of reads per gene was counted using the featureCounts version 1.5.0 with default settings. Transcripts per million (TPM) values were calculated as described previously.
total RNA-Seq: Reads were aligned with STAR version 2.4.2 to the Mus musculus genome version of July 2007 (NCBI37/mm9). Read coverages were calculated with the BEDTool program, were normalized to reads per millions (RPM) using the SAMTools as well as the KentTools.
Assembly: mm9 (total RNA-Seq, RNA-Seq,ChIP-Seq), mm10 (VDJ-Seq)
Supplementary files format and content: tab-delimited text files include RPM values for each VDJ-Seq sample and TPM values for RNA-Seq samples. bigWig files include read coverage for total RNA-Seq and ChIP-Seq samples.

source_name: total RNA-Seq Pre-B cell WT

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
total RNA was isolated using a lysis step based on guanidine thiocyanate

value: bone marrow

value: Pre-B cell

value: Ex-vivo FACS sorted from bone marrow


title: ME49 iKD AP2XII-1 +IAA 60h, biological repeat 2, AP2 XII-1 knock down 60h

value: whole organism


title: ME49 iKD AP2XII-1 +IAA 60h, biological repeat 1, AP2 XII-1 knock down 60h


title: 187484

source_name: total RNA-Seq Pro-B cell WT

value: Pro-B cell


title: retinal ganglion cell, Control subject 3 replicate 3

city: Los Angeles

first: David

last: Cobrinik

address: 4546 Sunset Blvd.

department: Ophthalmology

institute: Children's Hospital Los Angeles

description: ribosomal RNA depleted RNA

data_processing:
Quality control and adapter trimming were performed using trim galore version 0.4.2
Reads were aligned to the GRCh38 genome and transcriptome using HISAT2 (version 2.0.4) with default parameters
Gene-level quantification was performed using featureCounts (v1.5.1) with parameters ‘-s 2 –p –t exon –g gene_id’
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files including length and count values for each GeneID

source_name: iPSC derived retinal organoid day 42

growth_protocol: iPSC lines were maintained in E8, Vitronectin or  mTESR,matirgel culture. Differentiation to retinal organoids used a modification of the Kuwahara et al (2015) protocol. See Aparicio et al 2022 for more details

extract_protocol:
RNA was isolated using RNeasy mini kit (Qiagen74104) from ethanol fixed and then FACS-sorted BRN3+ immunolabeled cells at day 40-43 of differentiation. For each prep at least 60 ROs were pooled.
Random primed sequencing libraries depleted of ribosomal RNA were constructed from 50 ng RNA using KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (KAPA Biosystems) according to instructions except those volumes were halved and an extra 1.2X KAPA bead library cleanup was performed to remove adapter dimers prior to 13 cycles of amplification.

value: iPSC derived retinal organoid day 42

value: retinal ganglion cell

value: Control

value: female


title: retinal ganglion cell, Control subject 3 replicate 2

description: ribosomal RNA depleted RNA

source_name: iPSC derived retinal organoid day 41

value: iPSC derived retinal organoid day 41


title: retinal ganglion cell, Control subject 2 replicate 1

description: ribosomal RNA depleted RNA

value: male


title: retinal ganglion cell, Control subject 3 replicate 1

description: ribosomal RNA depleted RNA


title: retinal ganglion cell, Control subject 2 replicate 3

description: ribosomal RNA depleted RNA

source_name: iPSC derived retinal organoid day 43

value: iPSC derived retinal organoid day 43


title: retinal ganglion cell, Control subject 2 replicate 2

description: ribosomal RNA depleted RNA


title: retinal ganglion cell, ONH subject 3 replicate 3

description: ribosomal RNA depleted RNA

value: Optic nerve hypoplasia (ONH)


title: retinal ganglion cell, Control subject 1 replicate 1

description: ribosomal RNA depleted RNA


title: retinal ganglion cell, Control subject 1 replicate 3

description: ribosomal RNA depleted RNA


title: retinal ganglion cell, ONH subject 3 replicate 1

description: ribosomal RNA depleted RNA


title: retinal ganglion cell, ONH subject 2 replicate 3

description: ribosomal RNA depleted RNA


title: Control2

city: Huai'an

first: Lingling

last: Zhong

state: Jiangsu

address: Huanghe Road West

institute: The affiliated Huai’an No. 1 People’s Hospital of Nanjing Medical University

description: circRNAs expression in plasma samples of healthy control

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Healthy control

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: All plasma samples were collected using EDTA anticoagulant tubes. Half an hour after sampling, the samples were centrifuged at 3000 rpm for 10 minutes.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: Healthy control


title: Stage1 PD1

description: circRNAs expression in plasma samples of PD

source_name: Parkinson’s Disease

value: Parkinson’s Disease


title: Stage1 PD2


title: Stage4-5 PD2


title: retinal ganglion cell, Control subject 1 replicate 2

description: ribosomal RNA depleted RNA


title: retinal ganglion cell, ONH subject 3 replicate 2

description: ribosomal RNA depleted RNA


title: retinal ganglion cell, ONH subject 2 replicate 2

description: ribosomal RNA depleted RNA


title: Stage2-3 PD3


title: retinal ganglion cell, ONH subject 1 replicate 3

description: ribosomal RNA depleted RNA


title: retinal ganglion cell, ONH subject 2 replicate 1

description: ribosomal RNA depleted RNA


title: Stage4-5 PD3


title: Stage2-3 PD1


title: Control3


title: Control1


title: retinal ganglion cell, ONH subject 1 replicate 2

description: ribosomal RNA depleted RNA


title: Stage1 PD3


title: Stage2-3 PD2


title: CD4+ CD64+ T cells patient 6

city: Tel Aviv

first: Alon

last: Richter

address: Ramat Aviv

department: Pathology

country: Israel

institute: Tel Aviv University

description: Illumina NextSeq mid output 150 cycles

data_processing:
Gene count matrix was analyzed for differential expression using DESeq2 1.24.0
Enrichment analysis was performed on differentially expressed genes (adjusted p-value < 0.05)
using clusterProfiler 3.12.0
KEGG pathway enrichment analysis was performed using GAGE 2.42.0 (27), and visualized with Pathview 1.32.0
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: CD4+ CD64+ T cells

extract_protocol:
Qiagene Rneasy micro kit
INCPM mRNA-seq

value: CD4+ CD64+ T cells

tag: disease

value: tonsillitis


title: CD4+ CD64- T cells patient 6

description: Illumina NextSeq mid output 150 cycles

source_name: CD4+ CD64- T cells

value: CD4+ CD64- T cells


title: CD4+ CD64- T cells patient 2

description: Illumina NextSeq mid output 150 cycles


title: TIL,Nonresponder3,12h coculture [NR3_2399_CD69pos]

city: Houston

first: Melisa

middle: Angela

last: Martinez-Paniagua

state: Texas

address: S222 Engg Bldg 1, 4226 Martin Luther King Blvd.

department: William A. Brookshire Department of Chemical and Biomolecular Engineering

institute: University of Houston

data_processing:
Quality control of the sequencing data was performed by using Cutadapt (1.8.3) to remove the adapter sequences from the 3’ end, followed by trimming of the first 12 bases of all reads at 5’ end to address the non-uniform distribution caused either by biased selection of reads or contamination of other sequences.
Reads shorter than 20bp were then dropped to avoid potential mapping to multiple locations on the reference genome.
Transcripts were aligned to the human reference genome UCSC hg19 using TopHat2 (v2.1.0). The mapped genes were annotated using R package “GenomicAlignments” (1.0.6) and gene annotation information in R package “TxDb.Hsapiens.UCSC.hg19.knownGene” (2.14.0).
Differentially expressed genes (DEGs) were identified using DEseq2 (1.4.5) tool that tests for differential gene expression based on a model using the negative binomial distribution.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file with normalized count of gene transcripts from each sample

growth_protocol: TILs were grown in TIL culture media as follow RPMI 1640 (Corning) supplemented with 10% human sera (AB), 1x L-glutamine (Corning), 1x HEPES(Gibco/Invitrogen), 1x Pen-Strep (Corning) 1 mmol/L Sodium pyruvate (Corning) with 6000 IU/ml IL2 (hrIL-2) (Novartis) in 24-well plates.

extract_protocol:
The cells were harvested, stained, and sorted using FACS Aria Fusion Cell Sorter (BD Bioscience). T cells CD3+CD8+CD69+ and CD3+CD8-CD69- were sorted directly into lysis buffer, and RNA was isolated using an RNA isolation kit (Macherey-Nagel, RNA-XS).
cDNA libraries were synthesized using the commercially available SMART-Seq Ultra Low Input RNA kit (Clontech). cDNA libraries were first tagmented and then barcoded by indexing primers using the Nextra XT kit (Illumina)

tag: subject status/id

value: Tumor infiltrated lymphocytes (TIL)

value: Autologous tumor cell 12 hours


title: CD4+ CD64+ T cells patient 2

description: Illumina NextSeq mid output 150 cycles


title: TIL,Nonresponder2,12h coculture [NR2_2559_CD69pos]


title: TIL,Nonresponder1,12h coculture [NR1_2373_CD69neg]


title: TIL,Nonresponder1,12h coculture [NR1_2373_CD69pos]


title: TIL,Responder3,12h coculture [R3_2508_CD69neg]


title: TIL,Responder1,12h coculture [R1_2379_CD69neg]


title: TIL,Nonresponder2,12h coculture [NR2_2559_CD69neg]


title: TIL,Nonresponder3,12h coculture [NR3_2399_CD69neg]


title: TIL,Responder2,12h coculture [R2_2357_CD69pos]


title: TIL,Responder3,12h coculture [R3_2508_CD69pos]


title: TIL,Responder2,12h coculture [R2_2357_CD69neg]


title: TIL,Responder1,12h coculture [R1_2379_CD69pos]


title: 1007MM [RNA-seq]

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

data_processing:
The libraries were sequenced as 75 bp single-end for 40 million reads per sample at Northwestern University’s NUSeq Core using the NextSeq 500 system (Illumina, San Diego, CA). The quality of DNA reads was evaluated using FastQC. Adapters were trimmed and reads of poor quality or that aligned to rRNA sequences were filtered out. The cleaned reads were aligned to the Homo sapiens Genome (hg38) using STAR aligner (v2.6.3) with default settings (86). Read counts for each gene were calculated using htseq (87). Differential gene expression was detected using DESeq2 with false discovery rate (FDR) threshold set at 0.05. Expression values were transformed using DESeq2’s regularized log transformation (rlog) before visualization using PCA.
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to hg38 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited file with read counts per gene

source_name: fresh frozn tissue

extract_protocol:
Total RNA was isolated from approximately 30 mg of frozen LM and matched MM tissues using the RNeasy Fibrous Tissue kit (Cat no: 74704, Qiagen) following the manufacturer’s instructions. RNA quality was assessed using the Agilent Bioanalyzer 2100 (Santa Clara, CA).
RNA-seq libraries were prepared using the Stranded RNA-seq kit with RiboErase (Cat no: KK8483, KAPA Biosystems, Wilmington, MA). The RNA library concentrations were measured by Qubit TM 4 Fluorometer (Cat no: Q33238, Thermo Fisher Scientific) and library quality was determined using the Agilent Bioanalyzer 2100.

value: fresh frozn tissue

value: wild type

tag: subject id

value: patient #1007

tag: tissue/cell type

value: MM


title: 1007LM [RNA-seq]

tag: genotype

value: LM


title: 1123LM [RNA-seq]

value: patient #1123


title: 1008LM [RNA-seq]

value: patient #1008


title: 1008MM [RNA-seq]


title: retinal ganglion cell, ONH subject 1 replicate 1

description: ribosomal RNA depleted RNA

source_name: iPSC derived retinal organoid day 40

value: iPSC derived retinal organoid day 40

tag: cell line

tag: cell type

value: retinal ganglion cell

value: female


title: 967MM [RNA-seq]

value: patient #967


title: 1123MM [RNA-seq]


title: 1252LM [RNA-seq]

value: patient #1252


title: 965MM [RNA-seq]

value: patient #965


title: 975LM [RNA-seq]

value: patient #975


title: 1252MM [RNA-seq]


title: 975MM [RNA-seq]


title: 858LM [RNA-seq]

value: patient #858


title: 865LM_MED12

data_processing:
The quality of DNA reads was evaluated using FastQ.The reads were then aligned to the hg38 genome using Bowtie2 with the in-house script and alignment information for each read is stored in the BAM format. Peak calling was performed using HOMER: findPeaks (-style factor) for PR or ERα ChIP-seq, and findPeaks (-style histone) for MED12 ChIP-seq. BED files were constructed from the peaks using HOMER (pos2bed function). ChIPseeker was used to annotate the BED files of each replicate to obtain the frequency of binding sites in each annotated genomic region. The BAM and BED files from replicates were used as input for the Bioconductor package DiffBind to merge the intervals of peaks and identify the consensus overlapping regions across all replicates in mut-MED12 LM, wt-MED12 LM, and their matched MM samples. The peak consensus regions in the genome were also annotated using ChIPseeker. Differentially bound sites in the consensus regions were detected using DESeq2 included in DiffBind with thresholds of FDR<0.05 and log fold ≥2 based on the read counts. Motif analyses were performed using HOMER (findMotifsGenome.pl, -size 200bp).
Assembly: hg38
Supplementary files format and content: Peak files

extract_protocol:
0.2-0.5 g of frozen LM and matched MM tissues were used for ChIP-seq. Tissue was finely grounded with mortar and pestle in liquid nitrogen, followed by fixation in 1% paraformaldehyde for 15 min and quenching with 1X glycine for 5 minutes at room temperature. Chromatin was isolated using the SimpleChIP Enzymatic Chromatin IP Kit (Cat no: 9003S, Cell Signaling Technology, Danvers, MA) following the manufacturer’s protocol. 15 µg of chromatin was incubated with 6 µg of each of the antibodies against PR, MED12, or ERα to immunoprecipitate the target protein-bound DNA, which was then purified for library preparation.
The libraries were prepared using the KAPA Hyper Prep Kit (Cat no: KK8502, KAPA Biosystems) and KAPA Single-Indexed Adapter Kit (Cat no: KK8722, KAPA Biosystems). The libraries were sequenced as 75 bp single-end for 40 million reads per sample at Northwestern University’s NUSeq Core using the NextSeq 500 system (Illumina, San Diego, CA).

value: patient #865

tag: antibody


title: 865MM_MED12


title: 910MM [RNA-seq]

value: patient #910


title: 865LM_Input

value: fresh frozn tissue

value: Input


title: 975MM_MED12

value: wild type


title: 865MM [RNA-seq]

value: MM


title: 858MM_Input


title: 858LM_Input

value: LM


title: 975MM_Input


title: 910LM [RNA-seq]


title: 865LM [RNA-seq]


title: 858MM_MED12


title: 965LM [RNA-seq]


title: 967LM [RNA-seq]


title: 967MM_MED12


title: 967LM_MED12


title: 967LM_Input


title: 967MM_Input


title: ZsGreen+ Metastasis Ingesting Macrophage Biological Replicate 4

city: Seattle

first: Mark

middle: B

last: Headley

state: WA

address: 1100 Fairview Ave N

department: TST

institute: Fred Hutch Cancer Center

data_processing:
Raw bulk RNA reads  were aligned to the Mus musculus Ensembl GRCm38 v.78 genome and those reads uniquely mapping to Ensembl IDs were tabulated using STAR_2.4.2a.
The resulting sample by gene matrix was passed to DESeq2 for downstream normalization and differential expression testing.
Assembly: Ensembl GRCm38 v.78
Supplementary files format and content: Tab-delimited text file with ensembl ID and raw counts for indicated sample.

source_name: Lung

growth_protocol: Wild Type C57/BL6 Mice were bred and housed in our facilities. All Animals were age and sex matched between experimental groups. All animal procedures were approved by the Institutional Animal Care and Use Committee of our institution

extract_protocol:
Lungs were dissected and processed into a single cell suspension using Liberase TM and DNAse containing media and processed on a GentleMACs octodissociator. Cells were stained with a cocktail of fluorescently-conjugated antibodies to identify Macrophages with or without ingestion of ZsGreen. Cells were sorted directly into Arcturus Pico Pure Lysis buffer and RNA prepared using the Arcturus PicoPure RNA Isolation Kit.
Libraries were prepared for each sample utilizing the Nugen Ovation Library Preparation Kit (Tecan). Single End 50bp sequencing was performed on an Illumina HiSeq 3000.

treatment_protocol: Wild Type C57/Bl6 mice were injected intravenously with 1 X 10^ B16-F10 Tumor Cells Expressing ZsGreen and humanely euthanized 24hrs after injection.

value: Lung

tag: treatment

value: B16-F10 ZsGreen


title: ZsGreen- Metastasis Associated Macrophage Biological Replicate 2


title: ZsGreen- Metastasis Associated Macrophage Biological Replicate 1


title: 975LM_Input


title: 858MM [RNA-seq]


title: 965LM_MED12


title: 858LM_MED12


title: 865MM_Input


title: 975LM_MED12


title: ZsGreen- Metastasis Associated Macrophage Biological Replicate 4


title: 965MM_MED12


title: ZsGreen+ Metastasis Ingesting Macrophage Biological Replicate 3


title: ZsGreen+ Metastasis Ingesting Macrophage Biological Replicate 1


title: 910LM_MED12


title: 965MM_Input


title: DS20191307Tumor

city: Ann Arbor

first: Marina

last: Pasca di Magliano

state: MI

address: 1500 E Medical Center Dr

institute: University of Michigan Medical School

data_processing:
Samples were run using 50-cycle paired-end reads on the NovaSeq 6000 (Illumina) to a depth of 100,000 reads.  Cell Ranger count version 6.0 was used with default settings, with an initial expected cell count of 10,000.  The GCH38 refererence genome was used for aligment. Ambient RNA correction was done for each sample independently using SoupX. Briefly, SoupX estimates the ambient RNA profile from the cell-free RNA, then it estimates the cell-specific contamination fraction using a set of user-specified negative markers. Then, we used Seurat’s recommended workflow for scRNASeq data processing and integration. Briefly, we removed low-quality cells with more than a 15% fraction of mitochondrial genes expression or less than 200 features (genes) detected.
Assembly: GRCH38

source_name: Pancreas Tumor

extract_protocol:
Briefly, the donor pancreas was dissected by a clinically-trained pancreatobiliary surgeon. The organ was dissected into head, body, and tail, with portions of each placed into DMEM media with 1%BSA/10μM Y27632.  Tissue was minced into 1mm3 pieces, then digested with 1 mg/mL collagenase P for 20-30 min at 37°C with gentle agitation.  Digested tissue was rinsed three times with DMEM/1%BSA/10μM Y27632, then filtered through a 40μm mesh.  Resulting cells were submitted to the University of Michigan Advanced Genomics Core for single cell sequencing using the 10x Genomics Platform.
Single-cell complementary DNA libraries were prepared and sequenced at the University of Michigan Sequencing Core using the 10× Genomics Platform.

value: Pancreas Tumor


title: 910LM_Input


title: 965LM_Input


title: DS20191299Tumor


title: DS20191296Tumor


title: DS20191306Tumor


title: DS20191302Tumor


title: DS20191294Tumor


title: ZsGreen- Metastasis Associated Macrophage Biological Replicate 3


title: rig + tpi 2 [RNA210902SA_Rig_I_2_S5]

city: Portland

first: sudarshan

last: anand

address: 2720 S Moody Ave

department: CDCB

institute: oregon health & science university

data_processing:
Data processed using the RANAseq pipeline with the DESeq2 algorithm. Wald's test was used for calculating significance between the treatment groups
Assembly: GRCh38
Supplementary files format and content: Excel spreadsheet counts for each sample, grouped by cell line and treatment group.

source_name: Umbilical Cord

growth_protocol: HUVEC and HMVEC cells were maintained inEBM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using the Eurx RNA extraction kit according to manufacturer’s instructions. 0.5 ug were used for library preparation
RNA libraries were prepared by the Illumina Truseq procotol by the OHSU Massively Parallel Sequencing Shared Resource using Poly (A)+ selection

treatment_protocol: Cells were treated with 0.1 ug/mL RIG-I or control agonist in Lyovec according to manufacturer’s instructions (Invivogen). 16 hours later, cells were treated with 10 nmol TPI in PBS or PBS as vehicle control for 24 hours.

value: Umbilical Cord

value: HUVEC

value: endothelial

value: WT

value: RIG-I Agonist + Tipiracil


title: DS20191262Tumor


title: 910MM_Input


title: rig + tpi 3 [RNA210902SA_RIG_I_3_S6]


title: cnt + tpi 3 [RNA210902SA_Control_3_S3]

value: Control Agonist + Tipiracil


title: DS20191261TumorKeller


title: ZsGreen+ Metastasis Ingesting Macrophage Biological Replicate 2


title: DS20191261Tumor


title: cnt + tpi 1 [RNA210902SA_Control_1_S1]


title: rig + tpi 1 [RNA210902SA_RIG_I_1_S4]


title: DS20191258PancNorm

source_name: Pancreas Tumor Adjacent Normal

value: Pancreas Tumor Adjacent Normal


title: DS20191314Tumor


title: hmv rig 2 [RNA201106SA_hmv_rig_2_S8]

source_name: dermal microvascular

value: dermal microvascular

value: HMVEC

value: RIG-I Agonist


title: 910MM_MED12

value: fresh frozn tissue

value: patient #910


title: hmv rig 1 [RNA201106SA_hmv_rig_1_S7]


title: DS20191238Tumor


title: DS20191246Tumor


title: DS20191229Tumor


title: hmv cnt 1 [RNA201106SA_hmv_cnt_1_S5]

value: Control Agonist


title: DS20191253Tumor


title: huv rig 1 [RNA201106SA_huv_rig_1_S3]


title: huv rig 2 [RNA201106SA_huv_rig_2_S4]


title: huv cnt 2 [RNA201106SA_huv_cnt_2_S2]


title: 181429


title: 19-227PancNorm


title: 19-732PancNorm


title: Human islets, 2% oxygen, biol_rep_3

city: Kumamoto

first: Tomonori

last: Tsuyama

state: Kumamoto

address: 1-1-1, Honjo Chuo-ku

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto university

data_processing:
Sequence reads were trimmed for universal illumina adaptors using TrimGalore.
Trimmed sequence reads were mapped to GENCODE36 genome sequence (for human) or M25 genome sequence (for mouse) using HISAT2 with default parameters setting. Mapped reads were sorted and converted to a binary alignment/map format using SAMtools.
Gene assembly and quantification were performed using Stringtie.
Assembly: GRCh38, GRCm38
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: Primary islets cells

extract_protocol:
RNA was extracted using RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit (E7765L and E7770, New England Biolabs.) following manufacturer's protocols.

value: Primary islets cells

value: Pancreatic endocrine cells

value: 2percent_oxygen (24h)


title: huv cnt 1 [RNA201106SA_huv_cnt_1_S1]


title: human milk FB

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

library_source: other

data_processing:
fastq files were generated using CellRanger v5.0.0
Gene- and protein-expression counts were generated using CellRanger v5.0.0
Assembly: GRCh38.p13 GENCODE Release 32
Supplementary files format and content: gzipped tab-delimited text files

molecule: protein

source_name: milk

extract_protocol:
Human milk samples were collected at the University Hospital Zurich from healthy women, aged 20 to 40 years [mean (SD) 32.0 (5.0)], within 4 to 63 days after delivery. For isolation of milk cells, milk was diluted in a 1:1 ratio with PBS and centrifuged at 800 g for 20 minutes at 15°C. The lipid layer and skim milk were removed, and the cell pellet was washed twice in PBS by centrifugation at 400 g for 5 minutes and resuspension in PBS.
10X GEX 3`v3.1 Single index, Paired end 28_91 With Feature Barcoding

value: milk

value: healthy

tag: Sex

value: female


title: cnt + tpi 2 [RNA210902SA_Control_2_S2]

value: Umbilical Cord

value: HUVEC

value: endothelial


title: Human islets, 2% oxygen, biol_rep_2

value: WT


title: Human islets, 20% oxygen, biol_rep_2

value: 20percent_oxygen (24h)


title: Human islets, 2% oxygen, biol_rep_1


title: human milk


title: Human islets, 20% oxygen , biol_rep_1


title: hmv cnt 2 [RNA201106SA_hmv_cnt_2_S6]

value: dermal microvascular


title: X4

city: pittsburgh

first: Leonardo

last: D'aiuto

state: pa

address: 3811 O'Hare st

department: psychiatry

institute: UPMC

data_processing:
sequenced reads were processed and aligned using CLCbio v11
Sequences were trimmed based on quality score using the modified-Mott trimming algorithm as implemented in CLC bio software, using a trim cutoff error probability of 0.05.  Ambiguous bases were trimmed using a post trim maximal ambiguous base cutoff of 2.  The trimmed reads were then mapped to the human genome GRCh38/hg38, using sequence and annotation provided by Ensembl (release 82).
Assembly: GRCh38/hg38
Supplementary files format and content: csv format file with total counts, RPKM, TPM and CPM for each sample

source_name: iPSC line

growth_protocol: Neural progenitor cells (NPCs) were derived from hiPSC-neurons as previously described (D’Aiuto et al. Organogenesis. 2014;10(4):365-77).

extract_protocol:
Total RNA cellular RNA was extracted (RNeasy Mini Kits, Qiagen) and quantified using Agilent 4200 TapeStation (Agilent Technologies).
Total RNA libraries were generated using the Illumina TruSeq Stranded Total RNA Sample Preparation Guide, Revision E. The first step involved the removal of ribosomal and mitochondrial RNA using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, remaining RNA was fragmented using divalent cations under elevated temperature, which were then copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Subsequently, a single adenosine base was added to each of the cDNA fragments, followed by ligation of an adapter. The products were purified and enriched with PCR to create the final cDNA library. The cDNA libraries were validated using KAPA Biosystems primer premix kit with Illumina-compatible DNA primers and Qubit 2.0 fluorimeter. Quality was examined using an Agilent Bioanalyzer Tapestation 2200. The cDNA libraries were pooled at a final concentration 1.8pM. Cluster generation and 100 bp paired-read dual-indexed sequencing was performed on Illumina NextSeq 500 (Children’s Hospital of Pittsburgh, University of Pittsburgh).

treatment_protocol: NPCs were cultured in StemDiff Neural progenitor Medium, containing antivirals. All assays were conducted in quadruplicate.  Cells were harvested after 72 hours and the cellular RNA was extracted (RNeasy Mini Kits, Qiagen) and quantified using Agilent 4200 TapeStation (Agilent Technologies).

value: Neural progenitor cells (NPCs)

value: treated with compund 7


title: 110474_2_S58

city: Aurora

first: Lauren

last: Vanderlinden

state: Colorado

address: 13001 E. 17th Place, Mail Stop B119

department: Department of Biostatistics and Informatics

institute: Colorado School of Public Health

data_processing:
FASTQ files for the two runs for each sample were concatenated. Reads were trimmed to remove adapters and low-quality base calls with Cutadapt (13). Reads were aligned to the reference human genome (hg19) with use of TopHat2 (14). Individual samples were quantified against the most up-to-date Ensembl reference transcriptome with the RSEM (RNA-Seq by Expectation-Maximization) algorithm (15). The expected counts were used for further processing and normalization. For removal of any technical variation, the data first were quantile normalized with DESeq2 (16) and then normalized with removal of unwanted variation (17). Based on scree plots, we adjusted for one factor, as it explained the most variability in the data. The data were then transformed with the regularized log function (16). The transformed data were used in all subsequent analyses. We filtered out genes if ≥20% of the samples did not have a read mapped to the gene (transcripts per million value of 0) or the average transcripts per million value across all samples was <1. A total of 12,477 genes passed the filtering criteria.
Assembly: hg19/Ensembl.v87
Supplementary files format and content: RSEM.RUVs.k1.rlog.Dec2020.csv  Final normalized and cleaned dataset used in analyses, each row a gene and column a sample.
Supplementary files format and content: RSEM.estCounts.geneLevel.csv Estimated counts per gene from the RSEM output.  Not normalized or cleaned.

source_name: blood

extract_protocol:
In DAISY, venous blood samples are collected at 9, 15, and 24 months and yearly thereafter. Beginning in November of 2007, RNA samples were collected from all DAISY participants with Tempus tubes (Applied Biosystems). We selected samples from two visits (termed IA-1 and IA-2) that occurred after the onset of IA for mRNA sequencing. The IA-1 visit was selected as the first available visit after the onset of IA for all groups. In the progressor group, the visit that preceded clinical onset of T1D was selected as the IA-2 visit. In the maintainer and reverter groups, the IA-2 visit was selected as the visit where age was closest to median age in the progressor group at the IA-2 visit.
Total RNA was isolated and purified from frozen (−80°C), peripheral whole blood samples ofn= 138 subjects meeting the inclusion criteria (Supplementary Material). We also included 12 control samples and 12 technical replicates. NuGEN library preparation kits were used to construct the strand-specific total RNA libraries. The Globin AnyDeplete kit was used to remove globin transcripts. RNA integrity number (RIN) scores for all samples were quantitated with use of the TapeStation (Agilent). Paired-end 150-cycle 2 × 150 sequencing was performed with the Illumina NovaSeq 6000 system. Samples were pooled together in a single flow cell and were sequenced twice to obtain the desired read depth, resulting in a median read depth of 90 million paired end reads across the samples (range 54–128 million).

value: blood

tag: ID

tag: tr n

tag: visit

value: RNA 1

tag: group

value: Maintainer

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn

tag: age ia


title: X3


title: 110591_3_S75

tag: tissue

value: RNA 2

value: Progressor

tag: age


title: 61353210-Tumor

value: Pancreas Tumor


title: 110664_2_S50


title: 110441_3_S83


title: X1


title: X2


title: W4

value: control


title: 110581_1_S81

value: Reverter


title: 110623_2_S23


title: W3


title: 110712_2_S74


title: W2


title: 110652_2_S31


title: Stage4-5 PD1

tag: disease state

value: Parkinson’s Disease


title: V4

value: treated with compund 8


title: 110614_2_S22


title: 110433_2_S30


title: 110711_2_S81

value: Control


title: V2


title: 110710_1_S55


title: W1


title: V3


title: V1


title: U4

value: treated with compund 2b


title: 110707_1_S42


title: U3


title: 110708_3_S21


title: U2


title: 110706_4_S55


title: 110654_1_S73


title: U1


title: 110705_3_S19


title: 110443_2_S66


title: 110703_4_S54


title: T2

value: treated with compund 6


title: 110702_3_S76


title: T3


title: S4

value: treated with Acyclovir


title: S3


title: S2


title: T1


title: S1


title: 110697_1_S57


title: 110700_1_S67


title: 110709_4_S68


title: 110570_1_S65


title: 110516_3_S77


title: 110482_3_S85


title: 110617_1_S59


title: T4


title: 110603_1_S12


title: 110704_2_S89


title: iTSC_M6

city: Jerusalem

first: Yosef

last: Buganim

address: Jerusalem, IMRIC-Hadassah Medical School

department: Developmental Biology and Cancer Research

institute: HUJI

description: mRNA, Poly(A) pull-down

data_processing:
Raw reads were quality-trimmed and adapters removed.
The processed fastq files were mapped to the mouse transcriptome and genome using HISAT2 (v2.1.0). The genome version was GRCm38, with annotations from Ensembl release 84.
Quantification was done using featuresCounts (v1.6.2)
Normalization was done with the DESeq2 package (version 1.24.0)

growth_protocol: hiTSC and hbdTSC cells were grown on a layer of Mitomycin C-treated mouse embryonic fibroblast (MEF) feeder cells and cultured in human TSC medium (Okae et al, 2018). HFFs were grown in DMEM containing 10%FBS, 1% L-glutamine and 1% penicillin-streptomycin. hESCs and hiPSCs were grown in human embryonic stem cell (hES) medium comprised of Knockout DMEM containing 15% KnockOut serum replacement, 0.1 mM 2-mercaptoethanol, 1% L-glutamine, 1% non-essential amino acids and 1% Penicillin-Streptomycin, supplemented with freshly added 4ng/ml bFGF.

extract_protocol:
Total RNA was isolated using the Macherey-Nagel RNA NucleoSpin kit (Ornat)
mRNA libraries were prepared using the SENSE mRNA-seq library prep kit V2 (Lexogen)

value: Human induced trophoblast stem cells, line #4


title: iTSC_M4

description: mRNA, Poly(A) pull-down

value: Human induced trophoblast stem cells, line #1


title: KEN_B

description: mRNA, Poly(A) pull-down

source_name: HFF (KEN)

value: Human foreskin fibroblasts, KEN line


title: KEN_A

description: mRNA, Poly(A) pull-down


title: iTSC_M5

description: mRNA, Poly(A) pull-down


title: 110716_3_S94

value: blood


title: 110575_1_S20

value: RNA 1


title: 110701_2_S82


title: iPSC_M1

description: mRNA, Poly(A) pull-down

source_name: hiPSC

value: Human induced pluripotent stem cell line


title: 110452_3_S86


title: iTSC_M3

description: mRNA, Poly(A) pull-down


title: iPSC_M2

description: mRNA, Poly(A) pull-down


title: 110560_3_S67

value: RNA 2

value: Maintainer


title: hES_B

description: mRNA, Poly(A) pull-down

source_name: hESC

value: Human embryonic stem cell line


title: 110555_3_S59


title: 110717_3_S93

value: Progressor


title: 110635_3_S32


title: hES_A

description: mRNA, Poly(A) pull-down


title: bdhTSC_E9_B

description: mRNA, Poly(A) pull-down

value: Human bastocyst-derived trophoblast stem cells, line #9


title: bdhTSC_E9_A

description: mRNA, Poly(A) pull-down


title: 110637_3_S40


title: 110449_1_S51

value: Reverter


title: 110425_3_S6


title: hiTSC_GMOK3_B

description: mRNA, Poly(A) pull-down

value: Human induced trophoblast stem cells, line #7


title: 110524_1_S50


title: bdhTSC_E2_A

description: mRNA, Poly(A) pull-down

value: Human bastocyst-derived trophoblast stem cells, line #2


title: bdhTSC_E2_B

description: mRNA, Poly(A) pull-down


title: 110595_3_S31


title: 110622_3_S23


title: 110600_3_S8


title: 110594_3_S16


title: 110439_1_S58


title: circMLLe9-10_rep2

city: Adelaide

first: Simon

last: Conn

state: South Australia

address: Sturt Road, Bedford Park

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

data_processing:
Library strategy: 4C-Seq
High-throughput sequencing was performed using Illumina NextSeq (SE100).
Raw reads were adaptor trimmed and filtered for short sequences using cutadapt v1.8.13, setting minimum-length option to 15, error-rate 0.2 and overlap 5.
The resulting FASTQ files were mapped against the human reference genome (hg19) using the STAR spliced alignment algorithm (version 2.7.0e)
The resulting STAR produced alignment BAM file for each sample used for counting the reads mapped to genes using featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample

source_name: HEK293T cells

growth_protocol: Cell lines were grown in DMEM with 10% FBS at 37oC, with 5% CO2

extract_protocol:
gDNA was extracted using phenol chloroform as per van de Werken et al (2012) Methods Enzymology 513: 89-112. The MLL genomic region targeted as the bait was hg38 chr11:118,484,077-118,484,578, exploiting primary and secondary restriction enzyme NlaII and BglII, respectively.
As per van de Werken et al (2012) Methods Enzymology 513: 89-112

treatment_protocol: Briefly, circMLLexon9-10 overexpression constructs (in pcDNA3.1 vector backbone) or the empty pcDNA3.1 vector were transfected into HEK 293T cells using lipofectamine 2000, with 1 x 107 cells fixed at 24 hrs post-transfection. Overexpression was confirmed by RT-PCR.

tag: cell line

value: HEK293T cells

tag: genotype/variation

value: circular RNA overexpression (circMLLe9-10)


title: EV_rep2

value: empty vector (pcDNA3.1)


title: 110672_3_S57


title: circMLLe9-10_rep1


title: EV_rep1


title: hiTSC_GMOK3_A

description: mRNA, Poly(A) pull-down


title: 110668_3_S34


title: DRIPMLLexon12_rep1

description: processed data file: DRIPMLLexon12merged.trimmed_NEB.bwa.hg19.sorted_peaks.xls

data_processing:
library strategy: DRIP-Seq
Samples were multiplexed and sequenced on the Illumina NextSeq 500 using the stranded single end protocol with a read length of 75.
Raw reads were adaptor trimmed and filtered for short sequences using cutadapt v1.8.1 3
The resulting FASTQ files were analysed and quality checked using the FastQC program
The filtered reads were mapped against the human reference genome (Hg19) using the BWA alignment algorithm 4 (version 0.7.9a-r786 with default parameters)
Enriched regions of the genome were identified using the MACS2 peak caller 5 (version 2.1.1.20160309) using default parameters and reporting only peakswith a FDR cut-off (-q) < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 peak files

growth_protocol: HEK293 cells were grown in DMEM supplemented with 10% FBS and 1X penicillin-Streptomycin-Antimycotic. These were grown at 37oC and 5% carbon dioxide

extract_protocol:
Genomic DNA was harvested by GenElute Mammalian Genomic DNA miniprep kit (Merck)
DRIP DNA (2 ng) was used to generate DRIP-0seq libraries with NEBNext Ultra II DNA library prep kit (New England Biolabs) according to manufactureres instructions. Samples were multiplexed and sequenced on the Illumina NextSeq 500 (Illumina) using the single end protocol with 75 read length (high ouotput kit).

treatment_protocol: Cell were harvested at maximum 90% confluency after transfection. Cell were transfected at 60-70% confluency in 10cm dish with 6ug of plasmid DNA, 5ul Lipofectamine 2000 with Optimem. Cells were collected 3days after transfection.

tag: passages


title: 110531_3_S42


title: DRIPMLLexon12_rep2


title: DRIPMLLexon9to10_rep1

description: processed data file: DRIPMLLexon9to10merged.trimmed_NEB.bwa.hg19.sorted_peaks.xls


title: 110618_2_S19


title: DRIPpcDNA31_rep1


title: DRIPpcDNA31_rep2


title: DRIPinput_rep1

source_name: DRIPinput


title: 110649_1_S56


title: 110468_2_S27


title: HEK293T_Nuc_rep2

data_processing:
Whole transcriptome RNA, or nuclear and cytoplasmic-fractionated RNA from ribo-depleted (total RNA-seq) or RNase R treated (circular RNA-seq) samples, respectively, were multiplexed and sequenced separately on the Illumina NextSeq 500 platform (high output mode) using the stranded, single end protocol with a read length of 150.
Raw reads were adaptor trimmed and filtered for short sequences using cutadapt v1.8.13, setting minimum-length option to 18, error-rate 0.2 and overlap 5.
The resulting FASTQ files were mapped against the human reference genome (Hg19) using the STAR spliced alignment algorithm (version 2.5.3a with default parameters and --chimSegmentMin 20)
The resulting STAR produced Chimeric.out.junction file for each sample was parsed and annotated for circRNA prediction and backsplice abundance using CIRCexplorer2
Genome_build: hg19
Supplementary_files_format_and_content: CircExplorer2 circRNA detection and abundandce estimation

extract_protocol:
RNA was harvested by Trizol (ThermoFisher Scientific) or, for nuclear/cytosolic fractionation, using the PARIS kit (ThermoFisher Scientific)
KAPA RNA HyperPrep kit with RIboErase (Roche)

treatment_protocol: Cell were harvested at maximum 90% confluency after transfection. Cell were transfected in 6-well trays with 2.5ug of plasmid DNA, 5ul Lipofectamine 2000 with Optimem. Cells were collected 24hrs after transfection

tag: molecule subtype

value: rRNA depleted, RNase R treated, nuclear RNA


title: 110606_1_S64


title: 110640_4_S62

value: RNA 3


title: HEK293T_Nuc_rep1


title: 110426_3_S49


title: 110719_3_S44


title: HEK293T_Cyto_rep2

value: rRNA depleted, RNase R treated, cytoplasmic RNA


title: 110436_3_S52

value: blood


title: HEK293T_Cyto_rep1


title: 110619_2_S7


title: 110562_4_S64

value: RNA 1


title: DRIPMLLexon9to10_rep2


title: HEK293T_pcDNA31_rep1

value: rRNA depleted, total RNA


title: HEK293T_pcDNA31_rep2


title: HEK293T_MLL_e9-10_rep2


title: HEK293T_MLL_e9-10_rep1


title: 110481_2_S33

value: RNA 2


title: 110476_3_S74


title: 110535_3_S66


title: 110427_2_S41

value: Maintainer


title: 110632_1_S49


title: 110626_1_S41


title: 110485_2_S25


title: 110548_2_S46


title: 110504_2_S38


title: 110562_2_S15


title: 110448_2_S17


title: 110478_3_S60


title: 110422_3_S68


title: 110528_2_S10


title: 110420_2_S85


title: 110522_2_S93


title: 110438_2_S2


title: 110486_3_S35


title: MDA-MB-231 MELK KO clone C3, biological rep 3

city: HOUSTON

first: Chandra

last: Bartholomeusz

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

description:
231-C3-NT-3
MDA-MB-231 MELK KO clone C3
Human breast tumors

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G.

data_processing:
Raw gene expression data were read into R using the BioC-package affy, normalized using the Robust MultiArray (RMA) algorithm, and log2-transformed.
Probes with normalized expression values exceeding log2(100) in at least 25% of the arrays were filtered for further analysis. In addition, redundancy in probes mapping to the same gene was removed by retaining only the probe with the largest reported variation in gene expression measured by standard deviation.
The Master_regulators_of_gene_expression_20221021_ORAPaths.xlsx file shows the top pathways and genes affected by MELK knockout.

label: biotin

source_name: MDA-MB-231 MELK KO clone C3

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cells were cultured in Dulbecco modified Eagle medium/F12 medium (Life Technologies Inc, Grand Island, NY, USA) supplemented with fetal bovine serum (FBS; 10%) and antibiotic/antimycotic (1%).

extract_protocol: Total RNA was extracted from the cells using the miRNeasy mini kit (Sigma-Aldrich, St. Louis, MO, USA) according to the manufacturer’s instructions.

treatment_protocol: The cells were cultured for overnight, serum-starved for 36 hours, and then subjected to RNA extraction.

tag: genotype

value: MELK KO

tag: Sex

value: Female


title: MDA-MB-231 Cas9-P15 control, biological rep 2

description:
231-P15-NT-2
MDA-MB-231 Cas9-p15 cell
Human breast tumors

source_name: MDA-MB-231 Cas9-p15 cell


title: MDA-MB-231 MELK KO clone C28, biological rep 2

description:
231-C28-NT-2
MDA-MB-231 MELK KO clone C28
Human breast tumors

source_name: MDA-MB-231 MELK KO clone C28


title: MDA-MB-231 Cas9-P15 control, biological rep 3

description:
231-P15-NT-3
MDA-MB-231 Cas9-p15 cell
Human breast tumors


title: MDA-MB-231 MELK KO clone C28, biological rep 3

description:
231-C28-NT-3
MDA-MB-231 MELK KO clone C28
Human breast tumors


title: MDA-MB-231 MELK KO clone C3, biological rep 1

description:
231-C3-NT-1
MDA-MB-231 MELK KO clone C3
Human breast tumors


title: NF cells_rep3

city: Nanjing

first: Junlong

last: Zhuang

address: 321# Zhongshan Road

institute: Institute of Urology, Drum Tower hospital

description: NFs from human bladder cancer tissues

hyb_protocol: Labeled mRNA was hybridized Target Hybridization for Cartridge Arrays and Target Hybridization for Gene 1.1 ST Array Plates Processed on the GeneTitan® Instrument as described in the protocol (GeneChip® Hybridization, Wash and Stain Kit).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G

data_processing: The data were analyzed with Robust Multi-chip Average (RMA) algorithm as normalization method.

source_name: NFs from human bladder cancer tissues

label_protocol: Per RNA sample, 1 ug were used as input into the procedure as recommended by protocol (GeneChip® WT Terminal Labeling Kit).

growth_protocol: cells were maintained in DMEM/F12 supplemented with 10% FBS, 100 units/ml penicillin and 100g/ml streptomycin at 37℃

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

tag: cell type

value: NF cells


title: 110611_3_S4

tag: ID

tag: tr n

tag: visit


title: CAF cells_rep3

description: CAFs from human bladder cancer tissues

source_name: CAFs from human bladder cancer tissues

value: CAF cells


title: MDA-MB-231 MELK KO clone C3, biological rep 2

description:
231-C3-NT-2
MDA-MB-231 MELK KO clone C3
Human breast tumors


title: ucp1 ucp3_R3 biol rep 3

city: Botucatu

first: Ivan

middle: Godoy

last: Maia

state: São Paulo

address: Rua Professor Doutor Antonio Celso Wagner Zanin, Instituto de Biociências - UNESP

department: Ciências Químicas e Biológicas (Setor Genética)

country: Brazil

institute: UNESP (Universidade Estadual Paulista "Júlio de Mesquita Filho")

data_processing:
Kallisto was used as read aligment software
DESeq2 package was used to identify differentially expressed transcripts
The normalization method of transcripts per kilobase million (TPM) was used in this study to calculate the expression level of each gene in the samples.
For tune the thresh-old p-value, the adjusted p-value (Padj) method was used.
Assembly: TAIR10 Arabidopsis reference genome
Supplementary files format and content: tab-delimited text files include counts and TPM values for each transcript in each sample

organism: Arabidopsis thaliana

source_name: vegetative tissue

extract_protocol:
Total RNA from 21-day-old plants was extracted using the RNeasy Plant Mini Kit (Qiagen, Germany)
cDNA libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, United States)

treatment_protocol: normal growth conditions in MS medium

value: vegetative tissue

tag: ecotype

value: Columbia

value: ucp1 ucp3 double mutant

tag: condition

value: mutant


title: MDA-MB-231 parental, biological rep1

description:
231-Parental-NT-1
MDA-MB-231 parental cell
Human breast tumors

source_name: MDA-MB-231 parental cell

value: parental cell


title: NF cells_rep2

description: NFs from human bladder cancer tissues


title: MDA-MB-231 parental, biological rep2

description:
231-Parental-NT-2
MDA-MB-231 parental cell
Human breast tumors


title: MDA-MB-231 Cas9-P15 control, biological rep 1

description:
231-P15-NT-1
MDA-MB-231 Cas9-p15 cell
Human breast tumors


title: CAF cells_rep2

description: CAFs from human bladder cancer tissues


title: 110688_3_S27

tag: group

value: Reverter

tag: female yn

tag: nhw yn

tag: dr34 yn

tag: fdr yn


title: MDA-MB-231 MELK KO clone C28, biological rep 1

description:
231-C28-NT-1
MDA-MB-231 MELK KO clone C28
Human breast tumors

tag: cell line


title: CAF cells_rep1

description: CAFs from human bladder cancer tissues


title: 110634_2_S16

tag: tissue

tag: age

tag: age ia


title: ucp1 ucp3_R2 biol rep 2

tag: genotype


title: 110688_1_S90


title: 110629_2_S24


title: MDA-MB-231 parental, biological rep3

description:
231-Parental-NT-3
MDA-MB-231 parental cell
Human breast tumors

tag: Sex


title: 110580_4_S67

value: RNA 3

value: Progressor


title: WT_R2 biol rep 2

value: wild-type

value: control


title: 110715_3_S80

value: blood


title: bes1-D, biological replicate #3

city: Seoul

first: DAMI

last: YANG

address: Cheonpa-ro 47 gil 100, Yongsan-gu

department: Department of Biological Sciences

country: South Korea

institute: Sookmyung Women's University

data_processing:
Tuxedo protocol (https://doi.org/10.1038/nprot.2016.095)
Filtering : The quality of the reads were checked using fastQC (v.0.10.1), helping the understanding for the basic quality for sequence quality score, GC content, N content, length distribution and duplication level. Low quality reads were filtered according to the following criteria; reads contain more than 10% of skipped bases (marked as ‘N’s), reads contain more than 40% of bases whose quality scores are less than 20 and reads whose average quality scores of each read is less than 20. The whole filtering process was performed using the in-house scripts.
Sequence alignment : Filtered reads were mapped to the Arabidopsis thaliana reference genome (Ensembl release 23) using the aligner Tophat2.
Gene expression estimation : Gene expression level was measured with Cufflinks v2.1.1 using the gene annotation database of Ensembl release 23. Non-coding gene region was removed with –mask option. To improve the accuracy of measurement, multi-read-correction and fragbias-correct options were applied. All other options were set to default values.
Assembly: TAIR10
Supplementary files format and content: Exel file including FPKM values for each Sample

source_name: Seven-day-old seedlings

growth_protocol: Seeds were sterilized with 75% ethanol containing 0.05% Tween-20 for 15 min, washed twice in 95% ethanol and once in 100% ethanol, and then placed in 1/2 Murashige & Skoog (MS; Duchefa Biochemie) plates containing 0.8% plant agar. When grown in soil, seeds were sown directly onto soil (Sunshine mix #5) top-layered with fine particles of vermiculite. After cold stratification at 4°C for 2 days in the dark condition, all plants were grown at 22°C, under long-day conditions (16 h light/8 h dark).

extract_protocol:
Total RNA was extracted from 7 days-old MS media grown seedlings using TRI Reagent® (SIGMA according to the manufacturer’s protocol)
The libraries were prepared for 100bp paired-end sequencing using TruSeq RNA Sample Preparation Kit (Illumina, CA, USA). Quality of these cDNA libraries was evaluated with the Agilent 2100 BioAnalyzer (Agilent, CA, USA). Following cluster amplification of denatured templates, sequencing was progressed as paired-end (2×100bp) using Illumina HiSeq2500 (Illumina, CA, USA).

treatment_protocol: No treatment

value: Seven-day-old seedlings

value: Enkheim (En2)


title: 110540_3_S91

value: RNA 1

value: Maintainer


title: ucp1 ucp3_R1 biol rep 1


title: 110694_1_S61

value: RNA 2


title: 110472_3_S88


title: WT_R3 biol rep 3


title: NF cells_rep1

description: NFs from human bladder cancer tissues

tag: cell type

value: NF cells


title: bes1-D, biological replicate #2


title: WT_R1 biol rep 1

value: vegetative tissue


title: bes1-D, biological replicate #1


title: 110592_1_S53

tag: ID


title: 110679_2_S62

tag: tr n


title: RAV1 over-expression, biological replicate #3


title: RAV1 over-expression, biological replicate #2


title: En2 wild type, biological replicate #3


title: 110588_2_S79

tag: visit


title: 110616_2_S54


title: RAV1 over-expression, biological replicate #1


title: 110587_1_S88


title: En2 wild type, biological replicate #1


title: 110557_2_S14


title: 110579_1_S96


title: 110568_2_S6


title: ID β Hltf KO Index604_OtC7520

city: Lubbock

first: Beverly

middle: S

last: Chilton

department: Cell Biology & Biochemistry

institute: Texas Tech University HSC

description: rRNA depleted

data_processing:
Paired-end 100 nucleotide reads were aligned to reference mouse genome C57BL/6J (GRCm38/mm10) and analyzed using the platform provided by DNAnexus, Inc. (Mountain View, CA) to generate three-way transcriptomic (RNAseq) analyses of whole pancreata from β Hltf KO IC and ID newborn mice, and wild type (Hltf +/+) controls.
Comparison of expression level (fpkm_tracking) and differential isoform expression (fpkm_tracking).
The analysis included alternative splicing analysis in control (Hltf +/+) pancreata.
Exon quantification was performed to show the relative expression of all known Hltf isoforms.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text files of RPKM values for each gene; RPKM values for alternative splicing.

source_name: Newborn pancreas

extract_protocol:
Because pancreata are ribonuclease-rich, trunks of decapitated newborn mice were perfused in situ with RNAlater by insertion of a 20g-1-inch needle attached to a 5 ml syringe into the abdomen via the crural (posterior) attachment of the diaphragm . RNA stabilization occurred concomitant with the initial stretching of the pancreas. Pancreata were stored in RNA later at -70C until total RNA was isolated. RNA integrity and purity were assessed (Agilent Bioanalyzer) for 10 samples, i.e. 3 from β Hltf KO IC mice with low (<15 mg/dL) blood sugar, 3 from Hltf +/+ controls, and 4 from β Hltf KO ID mice.
cDNA was generated from Ribo-Zero Plus rRNA-depleted samples and subjected to Illumina library preparation.
Libraries were sequenced utilizing Illumina sequencing technology.

value: pancreas

tag: strain

value: immunodeficient (ID) beta cell specific Hltf-/- mouse

tag: developmental stage

value: newborn


title: 110589_2_S5

tag: group


title: 110583_3_S14

tag: female yn


title: Parietal cells, isolated, noggin, Bio Replicate 3

first: Andrea

last: Todisco

address: 1150 West Medical Center Dr.

department: Internal Medicine

institute: University of Michigan

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.  The reads files were downloaded from the Sequencing Core’s storage at the University of Michigan Bioinformatics Core, and concatenated into a single.fastq file for each sample. The quality of the raw reads data for each sample was checked using FastQC (version 0.10.0) to identify features of the data that may indicate quality problems.  Three bases at the 5’ ends were trimmed to remove Clonetech adapter sequences and also trimmed for low quality sequences. The Tuxedo Suite software package was used for alignment, differential expression analysis, and post-analysis diagnostics.
genome build: UCSC mm10

source_name: Stomach

extract_protocol: Total RNA quality was assessed using the TapeStation 2200 (Agilent).  At least 1ng of DNase-treated total was used to generate indexed mRNA libraries using SMART-Seq Ultra Low Input RNA-seq V3 kits (Takara). Library quality was assessed using the TapeStation 2200 (Agilent) and libraries were quantitated using KAPA Library Quantification Kits (Roche). Pooled libraries were subjected to 50 bp single-end sequencing according to the manufacturer’s protocol (Illumina HiSeq2500).

value: Stomach

value: Primary cell

value: Parietal cell

value: Transgenic-Tom-nog

tag: treatment

value: Noggin


title: ID β Hltf KO Index602_OtC7518

description: rRNA depleted


title: 110583_2_S13

value: Reverter

tag: nhw yn

tag: dr34 yn


title: 110663_3_S79

value: blood

value: Progressor

tag: fdr yn


title: 110444_3_S71

tag: tissue


title: Parietal cells, isolated, noggin, Bio Replicate 1

tag: cell line


title: ID β Hltf KO Index601_OtC7517

description: rRNA depleted


title: 110682_3_S39

tag: age

tag: age ia


title: 110598_3_S47


title: Parietal cells, isolated, control, Bio Replicate 3

tag: genotype

value: Transgenic-Tom

value: Control


title: Parietal cells, isolated, control, Bio Replicate 2

tag: cell type


title: 110553_3_S1

tag: ID


title: Parietal cells, isolated, control, Bio Replicate 1


title: 110501_2_S87

tag: tr n

value: RNA 1

value: Maintainer


title: 110503_3_S9

tag: visit


title: IC β Hltf KO Index 19 OtC0458

description: rRNA depleted

data_processing:
Paired-end 100 nucleotide reads were aligned to genomic assembly mm10 and analyzed using the platform provided by DNAnexus, Inc.
Comparison of expression level (fpkm_tracking) and differential isoform expression (fpkm_tracking)
Exon quantification was performed to show the relative expression of all known Hltf isoforms
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of RPKM values for each gene; RPKM values for alternative splicing

source_name: pancreas

extract_protocol:
Pancreata were perfused in situ with RNAlater using a 1 CC syringe and a 26g ½ needle, and snap frozen prior to rRNA-depletion.
cDNA was generated from rRNA-depleted samples [3 biological replicates for control and 3 biological replicates for rIPCre fl/fl (beta cell-specific Hltf-deleted)] and subjected to Illumina library preparation.
Libraries were sequenced utilizing Illumina sequencing technology

tag: strain

value: beta cell specific Hltf-/-


title: IC β Hltf KO Index 18 OtC0456

description: rRNA depleted

tag: developmental stage


title: 110605_1_S76

source_name: blood

value: RNA 2

tag: group


title: 110602_1_S68

tag: female yn


title: ID β Hltf KO Index603_OtC7519

description: rRNA depleted

value: pancreas


title: En2 wild type, biological replicate #2

value: Seven-day-old seedlings

value: Enkheim (En2)


title: 110563_3_S81


title: Hltf +/+ Index 9 OtB9942

description: rRNA depleted

value: control Hltf +/+

value: newborn


title: 110491_3_S89


title: 110424_4_S63


title: 110471_3_S22


title: IC β Hltf KO Index 16 OtC0450

description: rRNA depleted


title: Parietal cells, isolated, noggin, Bio Replicate 2

value: Stomach

value: Primary cell

value: Parietal cell

tag: treatment


title: Hltf +/+ Index 8 OtB9935

description: rRNA depleted


title: 9592

city: Vienna

first: Moritz

last: Gaidt

address: Campus-Vienna-Biocenter 1

institute: IMP

data_processing:
VDJ-Seq: The bioinformatic analysis of the VDJ-seq data was performed as described in detail in Chovanec et al., Nat. Protoc. 13, 2018. using the BabrahamLinkON pipeline: (1) preclean.py (default parameters), Includes trimming and alignment steps (BabrahamLinkOn pipeline) deduplicate.py (default parameters), based on UMI  (BabrahamLinkOn pipeline) (2) assemble_clones.py (default parameters)  (BabrahamLinkOn pipeline) (3) The resulting counts were summarized using customized scripts based on the statistical language R version 3.3.3. The relative usage of each VH gene is shown as percentage of all VDJH recombination events determined.
ChIP-Seq:  Reads were aligned against the Mus musculus genome version of July 2007 (NCBI37/mm9) with the Bowtie program version 0.12.5. Genome-wide read coverages were normalized to the number of aligned reads, per million (=RPM)., using 'bedtools' and 'kent source utilities'.
RNA-Seq: The number of reads per gene was counted using the featureCounts version 1.5.0 with default settings. Transcripts per million (TPM) values were calculated as described previously.
total RNA-Seq: Reads were aligned with STAR version 2.4.2 to the Mus musculus genome version of July 2007 (NCBI37/mm9). Read coverages were calculated with the BEDTool program, were normalized to reads per millions (RPM) using the SAMTools as well as the KentTools.
Assembly: mm9 (total RNA-Seq, RNA-Seq,ChIP-Seq), mm10 (VDJ-Seq)
Supplementary files format and content: tab-delimited text files include RPM values for each VDJ-Seq sample and TPM values for RNA-Seq samples. bigWig files include read coverage for total RNA-Seq and ChIP-Seq samples.

source_name: E2A AB ChIP-Seq Pro-B cell Rag2(-/-)

extract_protocol:
ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols
ChIP DNA Clean and Concentrator kit (Zymo Research)

value: bone marrow

tag: chip antibody

value: E2A Ab (homemade; clone 9296)

value: Pro-B cell

value: 5-days in-vitro expansion


title: Hltf +/+ Index 7 OtB9933

description: rRNA depleted


title: 110487_1_S9

value: blood

tag: nhw yn

tag: dr34 yn


title: 110536_3_S92

tag: tissue

tag: fdr yn


title: 110458_1_S1

value: RNA 1

tag: age


title: 110440_3_S84

value: Maintainer

tag: age ia


title: 110495_1_S84


title: 110671_1_S92


title: 110499_1_S26

value: Progressor


title: 110651_2_S9

value: RNA 2


title: 110424_3_S30


title: 110669_1_S45

value: Reverter


title: 110465_2_S3


title: 110661_3_S10


title: 110463_1_S37


title: 110574_2_S1


title: 110647_1_S34


title: 110564_3_S2


title: 110643_4_S58