title: MEF mock 0x sRNA

city: Solna

first: Wenjing

last: Kang

address: SciLifeLab, Tomtebodavägen 23

country: Sweden

institute: SciLifeLab

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
MEF_R1_mock_0x_30ng_FACS.sRNA

data_processing:
Basecalls were performed using bcl2fastq v2.17.1 with the option --barcode-mismatches 0
The small RNA sequencing data were quality control (QC) checked using miRTrace v 1.0.1 qc mode. Human (miRTrace option -s hsa) databases were used as references for HEK-293T and HeLa samples and mouse (-s mmu) databases were used as references for NIH-3T3 and MEF samples. Illumina 3’ adapter sequence TGGAATTCT was provided for 3’ adapter trimming.
For MapToCleave data, The QC qualified reads of each sample were then aligned to the prepared reference sequences, which contained the sequences from the MapToCleave library and the endogenous human (for HEK-293T and HeLa sample) or mouse (for NIH-3T3 and MEF sample) miRNA hairpin sequences that are excluded from the MapToCleave library but are included in miRbase v 21. The alignment was performed using bowtie v 1.1.2 without allowing mismatches (-v 0). The reads that were uniquely mapped to the forward strand of the reference sequences were considered for the hairpin expression measurement.
For validation data, the QC qualified reads were used to quantify expression of the human miRNA hairpins and the modified hairpins (see Supplementary Data 10 of the linked publication) using miRDeep2 v 2.0.0.8 quantifier.pl with allowing 0 mismatches (-g 0) and allowing multi-mapping. The human miRNA hairpin sequences downloaded from miRBase v21 and the modified hairpin sequences were used as the precursor reference (-p). The corresponding human miRNA sequences from miRBase v21 and the manually curated miRNA sequences of the modified hairpins (see Supplementary Data 10 of the linked publication) are used as the mature reference (-m). The hairpin sequence counts are measured by summing up the number of small RNA reads that mapped to an interval 2 nucleotides upstream and 5 nucleotides downstream of the 5p or/and 3p miRNA sequence from the hairpin.
Supplementary_files_format_and_content: tab-delimited text file includes raw counts of MapToCleave sequences for each sample.
Supplementary_files_format_and_content: tab-delimited text file includes raw counts and normalized counts of the modified hairpins and the endogenous human miRNA hairpins for each sample.

source_name: MEF mock cells

extract_protocol:
For MapToCleave samples, total RNA and DNA were isolated using TRIzol reagent (Ambion). For validation samples, total RNA was extracted using a Zymo quick-RNA microprep kit (Zymo Research).
For MapToCleave samples, 1 ug of HEK-293T total RNA was used for standard small RNA library preparation using TruSeq small RNA kit v2 (Illumina). 1 ug of NIH-3T3 total RNA was used for preparation of small RNA libraries. 30 ng of the total RNA extracted from FACS-isolated MEF cells were used for preparation of small RNA libraries. The small RNA cDNA libraries were PCR-amplified in 15 cycles; the 75-bp single-end sequencing was carried out on a NextSeq500 (Illumina). DNA libraries were prepared in two steps: i) the DNA isolated from the HEK-293T and NIH-3T3 transfected cells was pre-amplified using custom primers compatible with Illumina TruSeq adapter sequences, ii) pre-amplified DNA fragments were multiplexed by PCR using Illumina TruSeq universal forward and single-indexed reverse PCR primers. The DNA libraries were resolved on a 6% Novex TBE gel (Invitrogen), and the 280 – 300 bp fraction was isolated. The 150-bp single-end sequencing was carried out using Illumina NextSeq500. For validation samples, RNA libraries were prepared using TruSeq small RNA kit v2 (Illumina).

value: MEF

tag: treatment

value: mock


title: P2_PA14_P2644_N728.S522

status: Public on Nov 16 2021

type: SRA

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

description:
processed data file: P2644.tsv
CCYYKANXX_8_N728-S522-NX-xt

library_source: transcriptomic

data_processing:
Reads were then demultiplexed according to the cell barcodes
Sequenced reads were filtered for low-complexity or low-quality sequence.
High quality reads were mapped according to the GEM pipeline
Genome_build: Human:  GRCh38
Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing gene expression values as read counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: SCC-25 (ATCCR CRL-168TM) were grown in keratinocyte serum-free media (KSFM, Gibco) supplemented with 5 μg ml–1 penicillin/streptomycin, 0.025 mg ml–1 bovine pituitary extract and 0.2 μg ml–1 hEGF.

extract_protocol:
Live SCC-25 sorted cells were lysed using lysis buffer (0.2% Triton-100, 1U/ul RNase inhibitor). Reverse transcription was performed using SuperScript II (ThermoFisher Scientific) in the presence of 1 μM oligo-dT30VN (IDT), 1 μM template-switching oligonucleotides (QIAGEN), and 1 M betaine.
Libraries were prepared according to the Nextera XT (Illumina) instructions.

treatment_protocol: Cells growing in serum–free media were treated in vitro with 300 μM palmitic acid for 96 h (4 days) and after palmitic acid withdrawal cells were passaged normally (when reaching 80% confluence) for 14 days and collected for sorting of live SCC-25 cells into 96 well sorting plates.

tag: cell line

tag: cell type

value: oral squamous cell carcinoma (OSCC) cell line

tag: shRNA

value: control pLKO.1

tag: protocol

value: Smart-seq2; full-length RNA-seq


title: CT+1

type: RNA

description: CD36-bright FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneChip scanner GSC3000 (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method as implemented in affy Bioconductor R package

label: biotin

source_name: CD36-bright cells / PLKO / VDH15 oral carcinoma cell line / control diet

label_protocol: 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Cells were grown in an orthotopic xenograft model in NOD-SCIDγ mice (NSG)

extract_protocol: RNA was isolated using magnetic beads. Library preparation and amplification were performed as described by Gonzalez et al., 2010.

tag: sample id

tag: hybridization batch

tag: scan batch

tag: biological replicate

tag: technical replicate

tag: diet

value: control diet

value: PLKO

value: VDH15 oral carcinoma cell line


title: P2_PA14_P2644_N728.S521

description:
processed data file: P2644.tsv
CCYYKANXX_8_N728-S521-NX-xt


title: NIH-3T3 mock 0x rep5 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
NIH3T3_R5_mock_0x_1000ng_NOR.sRNA

organism: Mus musculus

source_name: NIH-3T3 mock cells


title: NIH-3T3 mock 0x rep4 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
NIH3T3_R4_mock_0x_1000ng_NOR.sRNA


title: NIH-3T3 mock 0x rep3 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
NIH3T3_R3_mock_0x_1000ng_NOR.sRNA


title: sample.m1_r172h_3 [RNA-seq]

city: St Louis

first: Joshua

middle: B

last: Rubin

state: Missouri

address: 660 South Euclid Ave

department: Pediatrics

country: USA

institute: Washington University In St Louis

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount vsersion 1.4.6-p5.
Genome_build: Ensemble R76
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

molecule: polyA RNA

source_name: Primary cortical astrocytes_m1_r172h

growth_protocol: Cells were grown in DMEM/F12 supplemented with 10% FBS.

extract_protocol:
Qiagen RNAeasy mini kit
Clontech SMRTr

tag: strain background

tag: genotype

value: Trp53:R172H Overexpression

tag: passages

tag: Sex

value: male

value: Primary postnatal day 1 cortical astorcytes


title: NIH-3T3 mock 0x rep1 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
NIH3T3_R1_mock_0x_1000ng_NOR.sRNA


title: sample.f1_r172h_2 [RNA-seq]

source_name: Primary cortical astrocytes_f1_r172h

value: female


title: QC-034628

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

hyb_protocol: Labeled cDNA was hybridized at 48°C to Affymetrix Human Gene ST 2.1 array plates, which were then washed, stained and scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515) with the assistance of the University of Michigan DNA Sequencing Core.

data_processing: R bioconduct was used to process the data, and RMA was used to summarize and normalize the expression values

source_name: Skin

label_protocol: Complementary DNA was prepared and biotinylated using the NuGEN Encore Biotin Module (Encore Biotin Module Manual, P/N M01111 v6).

extract_protocol: RNA was isolated from 10μm sections of formalin-fixed paraffin embedded blocks of identified skin biopsies. RNA was extracted using the E.N.Z.A. FFPE RNA Kit (Omega Bio-tek).

tag: disease state

value: ACLE


title: sample.f1_r172h_1 [RNA-seq]


title: QC-034634

scan_protocol: Labeled cDNA was hybridized at 48°C to Affymetrix Human Gene ST 2.1 array plates, which were then washed, stained and scanned using the Affymetrix GeneTitan system (software version 3.2.4.1515) with the assistance of the University of Michigan DNA Sequencing Core.


title: P2_PA14_P2644_N728.S518

description:
processed data file: P2644.tsv
CCYYKANXX_8_N728-S518-NX-xt


title: sample.f1_r172h_3 [RNA-seq]


title: CT+2


title: P2_PA14_P2644_N728.S517

description:
processed data file: P2644.tsv
CCYYKANXX_8_N728-S517-NX-xt


title: P2_PA14_P2644_N728.S516

description:
processed data file: P2644.tsv
CCYYKANXX_8_N728-S516-NX-xt


title: QC-034625

value: DLE


title: P2_PA14_P2644_N728.S520

description:
processed data file: P2644.tsv
CCYYKANXX_8_N728-S520-NX-xt


title: mixed sample (non-demultiplexed)

city: Rehoboth

first: Dotan

last: Hoffman

address: Herzel St 234, Biological regulation

department: Biological regulation

country: Israel

institute: Weizmann institute of science

description: Sample 1

data_processing:
Read-1 files were mapped to the mm9 genome assembly using Bowtie2 (default parameters)
.Demultiplexing and UMI counting were based on 4bp pool barcodes for each sample and 8bp of UMI with 7bp of cell-barcodes for the cells in Read-2, and performed using the pipeline described in Jaitin et al. 2014
Cells with lower than 150 UMI's were excluded from the data sets
Genome_build: mm9
Supplementary_files_format_and_content: Expression data sets: Text files include UMI counts table for each gene in each cell in the sample. Sc_meta_data: Xls file contains the pool barcodes per eac sample and barcodes and coordinates of each cell needed for MARSseq pipeline (Jaitin et al. 2014)

source_name: Splenocytes

extract_protocol:
24 hours post infection spleens were removed squashed against 70 um strainer followed by red blood lysis and stained with antibodies.  Single cells were sorted to 384 well plate containing lysis solution (UPW, 8nM poly-dT barcodes, 0.1%triton and RNAse inhibitors.)
RNA-seq libraries were prepared according to MARS-seq libraries protocol (Jaitin et al Science 2014)

treatment_protocol: 8 weeks old female mice were intravenously inculated with 1X10^7 S.Tm (either WT or DSPI-2) or PBS

tag: strain

tag: infection status

value: 24 hpi or no infection

value: WT or {delta}SPI-2

tag: tissue

value: Spleen

value: Splenocytes

tag: markers


title: sample.m1_y202c_2 [RNA-seq]

source_name: Primary cortical astrocytes_m1_y202c

value: Trp53:Y202C Overexpression

tag: cell type


title: sample.m1_y202c_3 [RNA-seq]


title: QC-034626


title: P2_PA14_P2644_N728.S513

description:
processed data file: P2644.tsv
CCYYKANXX_8_N728-S513-NX-xt

tag: cell line

value: oral squamous cell carcinoma (OSCC) cell line

tag: shRNA

tag: protocol


title: QC-034627


title: QC-034629


title: QC-034621

value: SCLE


title: sample.f1_y202c_1 [RNA-seq]

source_name: Primary cortical astrocytes_f1_y202c


title: P2_PA14_P2644_N727.S522

description:
processed data file: P2644.tsv
CCYYKANXX_8_N727-S522-NX-xt

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: CT-1

description: CD36-dim FACS sorted cells from PLKO orthotopic VDH15 oral carcinoma cell line xenografts exposed to control diet

source_name: CD36-dim cells / PLKO / VDH15 oral carcinoma cell line / control diet

tag: sample id

tag: hybridization batch

tag: scan batch

value: control diet

value: PLKO


title: sample.f1_y202c_2 [RNA-seq]


title: QC-034620


title: P2_PA14_P2644_N727.S521

description:
processed data file: P2644.tsv
CCYYKANXX_8_N727-S521-NX-xt


title: Mouse liver WCE ChIP-Seq WT PTU+T3 sample 140 seq-rep 1

city: new york

first: arturo

last: mendoza

state: ny

address: 1 east loop 15a

department: Division of Endocrinology, Diabetes and Metabolism

institute: weill cornell medicine

description: ChIP-Seq_WCE_Mm_liver_WT_PTU_T3_140_001.bw

library_source: genomic

data_processing:
ChIP-seq data were aligned to the mm10 mouse genome using Bowtie2 (Langmead and Salzberg, 2012).
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were processed using samtools (Li et al., 2009)
Peaks were called by MACS2 (Zhang et al., 2008), and low peaks (4<fold higher coverage than whole cell extract (WCE)) were removed.
Reads were assigned to peaks, normalized and quantified using EdgeR. Low signal peaks (log2 CPM<2) were removed, and differential peaks were defined at log2 FC≥1 and log2 FDR≤0.05.
For ChIP-seq track visualization, reads were processed to the BigWig file format using bedtools (Quinlan and Hall, 2010) and bedGraphToBigWig (Kent et al., 2010).
Processed Bigwig files were viewed in WashU Epigenome Browser (Zhou and Wang, 2012).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: Liver

growth_protocol: Wt mice or liver specific ChREBPKO mice were used

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with Anti-ChREBP
Affinity-bound chromatin fragments were reverse-crosslinked, purified and used to construct DNA libraries for sequencing using the Illumina TruSeq ChIP Library Preparation Kit (Illumina)

treatment_protocol: mice were rendered hypothyroid by a PTU/LowIodine Diet for 21 days, hyperthyroid mice were on same diet and injected by T3 5micrograms/100gbodyweight daily during las four days of diet. Then, livers were harvest and frozend in liquid nitrogen

value: liver

value: WT

tag: treatment

tag: condition

value: hyperthyroidism

tag: chip antibody


title: Mouse liver WCE ChIP-Seq WT PTU+T3 sample 136 seq-rep 1

description: ChIP-Seq_WCE_Mm_liver_WT_PTU_T3_136_001.bw

tag: genotype


title: Mouse liver WCE ChIP-Seq WT PTU sample 201 seq-rep 2

value: PTU

value: hypothyroidism


title: Mouse liver WCE ChIP-Seq WT PTU+T3 sample 136 seq-rep 2


title: sample.m1_y202c_1 [RNA-seq]

tag: strain background

tag: passages

tag: Sex

value: male

value: Primary postnatal day 1 cortical astorcytes


title: Mouse liver WCE ChIP-Seq WT PTU sample 201 seq-rep 1

tag: strain


title: sample.f1_y202c_3 [RNA-seq]

value: female


title: QC-034624

tag: disease state

value: DLE


title: P2_PA14_P2644_N727.S520

description:
processed data file: P2644.tsv
CCYYKANXX_8_N727-S520-NX-xt


title: sample.m1_y217c_1 [RNA-seq]

source_name: Primary cortical astrocytes_m1_y217c

value: Trp53:Y217C Overexpression


title: Mouse liver WCE ChIP-Seq WT PTU sample 200 seq-rep 2

tag: tissue


title: sample.m1_y217c_2 [RNA-seq]

tag: cell type


title: Mouse liver WCE ChIP-Seq WT PTU sample 200 seq-rep 1


title: P2_PA14_P2644_N727.S518

description:
processed data file: P2644.tsv
CCYYKANXX_8_N727-S518-NX-xt

tag: cell line


title: P2_PA14_P2644_N727.S517

description:
processed data file: P2644.tsv
CCYYKANXX_8_N727-S517-NX-xt

tag: shRNA


title: Mouse liver WCE ChIP-Seq WT PTU+T3 sample 140 seq-rep 2


title: P2_PA14_P2644_N727.S516

description:
processed data file: P2644.tsv
CCYYKANXX_8_N727-S516-NX-xt

tag: protocol


title: Mouse liver WCE ChIP-Seq KO PTU+T3 sample 54 seq-rep 1

description: ChIP-Seq_WCE_Mm_liver_KO_PTU_T3_054_001.bw

value: liver specific ChREBPKO


title: Mouse liver WCE ChIP-Seq KO PTU+T3 sample 54 seq-rep 2


title: Mouse liver WCE ChIP-Seq KO PTU+T3 sample 53 seq-rep 2

description: ChIP-Seq_WCE_Mm_liver_KO_PTU_T3_053_001.bw


title: P2_Empty_P2644_N727.S513

description:
processed data file: P2644.tsv
CCYYKANXX_8_N727-S513-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line


title: Mouse liver ChREBP ChIP-Seq WT PTU+T3 sample 140 seq-rep 2

description: ChIP-Seq_ChREBP_Mm_liver_WT_PTU_T3_140_001.bw

value: ChREBP (NB400-135 - Novus Biologicals)


title: sample.m1_y217c_3 [RNA-seq]


title: P2_PA14_P2644_N727.S515

description:
processed data file: P2644.tsv
CCYYKANXX_8_N727-S515-NX-xt

value: control pLKO.1


title: sample.f1_y217c_3 [RNA-seq]

source_name: Primary cortical astrocytes_f1_y217c


title: sample.f1_y217c_2 [RNA-seq]


title: m1_y217c.rep1 [ChIP-seq]

data_processing:
Sequence reads were processed using the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline v1.1.6 (http://github.com/ENCODE-DCC/chip-seq-pipeline2).
Reads were filtered and mapped to the Mus musculus genome (mm10) using the pipeline.
Signal strength relative to the control samples were generated using MACS2.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwig

source_name: Primary cortical astrocytes

growth_protocol: Astrocytes were growth in DMEM/F12 supplemented with 10% FBS.

extract_protocol:
Astrocytes were fixed for chromatin isolation per Schmidl et l., Nature Methods 10:963.
Chipmentation - Chromatin isolation with the indicated antibody followed by tagmentation with Tn5 as per Schmidl et l., Nature Methods 10:963.

tag: antibody

value: Primary cortical astrocytes

tag: age

value: post natal day 1


title: P2_UN14_P2644_N726.S521

description:
processed data file: P2644.tsv
CCYYKANXX_8_N726-S521-NX-xt

value: Smart-seq2; full-length RNA-seq


title: sample.f1_y217c_1 [RNA-seq]


title: P2_PA14_P2644_N728.S515

description:
processed data file: P2644.tsv
CCYYKANXX_8_N728-S515-NX-xt


title: m1_y217c.rep2 [ChIP-seq]


title: Mouse liver WCE ChIP-Seq KO PTU+T3 sample 53 seq-rep 1

value: liver


title: P2_UN14_P2644_N726.S522

description:
processed data file: P2644.tsv
CCYYKANXX_8_N726-S522-NX-xt


title: Mouse liver ChREBP ChIP-Seq WT PTU+T3 sample 140 seq-rep 1

value: WT


title: m1_y217c_input.rep1 [ChIP-seq]

value: Input Control


title: P2_UN14_P2644_N726.S520

description:
processed data file: P2644.tsv
CCYYKANXX_8_N726-S520-NX-xt


title: Mouse liver ChREBP ChIP-Seq WT PTU+T3 sample 136 seq-rep 2

description: ChIP-Seq_ChREBP_Mm_liver_WT_PTU_T3_136_001.bw

value: hyperthyroidism


title: P2_UN14_P2644_N726.S517

description:
processed data file: P2644.tsv
CCYYKANXX_8_N726-S517-NX-xt


title: P2_UN14_P2644_N726.S518

description:
processed data file: P2644.tsv
CCYYKANXX_8_N726-S518-NX-xt


title: Mouse liver ChREBP ChIP-Seq WT PTU+T3 sample 136 seq-rep 1


title: m1_y202c.rep3 [ChIP-seq]

value: Trp53:Y202C Overexpression


title: m1_y202c.rep2 [ChIP-seq]

value: male


title: QC-034617


title: Mouse liver ChREBP ChIP-Seq WT PTU sample 201 seq-rep 2

description: ChIP-Seq_ChREBP_Mm_liver_WT_PTU_201_001.bw

value: PTU

value: hypothyroidism


title: QC-034623

value: DLE


title: P2_UN14_P2644_N726.S516

description:
processed data file: P2644.tsv
CCYYKANXX_8_N726-S516-NX-xt


title: m1_y202c.rep1 [ChIP-seq]


title: Mouse liver ChREBP ChIP-Seq WT PTU sample 201 seq-rep 1


title: QC-034611


title: Mouse liver ChREBP ChIP-Seq WT PTU sample 200 seq-rep 2

description: ChIP-Seq_ChREBP_Mm_liver_WT_PTU_200_001.bw


title: QC-034622


title: P2_UN14_P2644_N726.S515

description:
processed data file: P2644.tsv
CCYYKANXX_8_N726-S515-NX-xt


title: m1_y202c_input.rep1 [ChIP-seq]


title: QC-034616

value: ACLE


title: P2_UN14_P2644_N726.S513

description:
processed data file: P2644.tsv
CCYYKANXX_8_N726-S513-NX-xt


title: QC-034603


title: m1_r172h.rep3 [ChIP-seq]

value: Trp53:R172H Overexpression


title: QC-034607

value: SCLE


title: Mouse liver ChREBP ChIP-Seq WT PTU sample 200 seq-rep 1

value: ChREBP (NB400-135 - Novus Biologicals)


title: m1_r172h.rep2 [ChIP-seq]


title: P2_UN14_P2644_N724.S522

description:
processed data file: P2644.tsv
CCYYKANXX_8_N724-S522-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1


title: Mouse liver ChREBP ChIP-Seq KO PTU+T3 sample 54 seq-rep 2

description: ChIP-Seq_ChREBP_Mm_liver_KO_PTU_T3_054_001.bw

value: liver specific ChREBPKO


title: m1_r172h.rep1 [ChIP-seq]

value: Primary cortical astrocytes

value: post natal day 1


title: Mouse liver ChREBP ChIP-Seq KO PTU+T3 sample 54 seq-rep 1

value: liver


title: m1_r172h_input.rep1 [ChIP-seq]

value: Input Control


title: Mouse liver ChREBP ChIP-Seq KO PTU+T3 sample 53 seq-rep 2

description: ChIP-Seq_ChREBP_Mm_liver_KO_PTU_T3_053_001.bw

value: hyperthyroidism


title: QC-034605


title: HEK-293T mock rep2 sRNA batch 2

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R2_mock_CRG_1004.sRNA

source_name: HEK-293T mock cells

value: mock


title: m1_cre.rep3 [ChIP-seq]

value: Trp53 KO

value: male


title: Mouse liver ChREBP ChIP-Seq KO PTU+T3 sample 53 seq-rep 1


title: HEK-293T mock rep1 sRNA batch 2

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R1_mock_CRG_1003.sRNA


title: HeLa mock rep1 sRNA batch 2

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
Hela_R1_mock_CRG_1007.sRNA

source_name: HeLa mock cells

value: HeLa


title: HeLa mock rep2 sRNA batch 2

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
Hela_R2_mock_CRG_1008.sRNA


title: m1_cre.rep2 [ChIP-seq]


title: m1_cre.rep1 [ChIP-seq]


title: QC-034600


title: P2_UN14_P2644_N724.S517

description:
processed data file: P2644.tsv
CCYYKANXX_8_N724-S517-NX-xt

value: Smart-seq2; full-length RNA-seq


title: P2_UN14_P2644_N724.S516

description:
processed data file: P2644.tsv
CCYYKANXX_8_N724-S516-NX-xt


title: P2_UN14_P2644_N724.S521

description:
processed data file: P2644.tsv
CCYYKANXX_8_N724-S521-NX-xt


title: P2_UN14_P2644_N724.S520

description:
processed data file: P2644.tsv
CCYYKANXX_8_N724-S520-NX-xt


title: P2_UN14_P2644_N724.S515

description:
processed data file: P2644.tsv
CCYYKANXX_8_N724-S515-NX-xt


title: P2_UN14_P2644_N724.S513

description:
processed data file: P2644.tsv
CCYYKANXX_8_N724-S513-NX-xt


title: P2_UN14_P2644_N724.S518

description:
processed data file: P2644.tsv
CCYYKANXX_8_N724-S518-NX-xt


title: QC-034613

value: NN


title: m1_cre_input.rep1 [ChIP-seq]


title: f1_y217c.rep3 [ChIP-seq]

value: Trp53:Y217C Overexpression

value: female


title: QC-034614


title: f1_y217c.rep2 [ChIP-seq]


title: P2_UN14_P2644_N723.S522

description:
processed data file: P2644.tsv
CCYYKANXX_8_N723-S522-NX-xt


title: P2_UN14_P2644_N723.S521

description:
processed data file: P2644.tsv
CCYYKANXX_8_N723-S521-NX-xt


title: P2_UN14_P2644_N723.S520

description:
processed data file: P2644.tsv
CCYYKANXX_8_N723-S520-NX-xt


title: f1_y217c_input.rep1 [ChIP-seq]


title: f1_y217c.rep1 [ChIP-seq]


title: P2_UN14_P2644_N723.S518

description:
processed data file: P2644.tsv
CCYYKANXX_8_N723-S518-NX-xt


title: f1_y202c.rep3 [ChIP-seq]

value: Trp53:Y202C Overexpression


title: f1_y202c.rep2 [ChIP-seq]


title: QC-034599

value: ACLE


title: QC-034618

value: DLE


title: Donor2 LPS BCG 3mo

city: Cambridge

first: Lingjia

last: Kong

state: MA

address: 415 Main St.

department: Infectious Disease and Microbiome

institute: Broad Institute

data_processing:
Demultiplexing with bcl2fastq
Alignment with BWA
Counting of transcripts with custom python script
Downstream analysis with the Seurat (v3.1.0) R package
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Monocytes

extract_protocol:
TCL plus 2% of 2M DTT buffer in 96 well plates
384 single cells per plate tagged and multiplexed with 5' digital gene expression strategy

tag: individual

value: cd14 monocytes from pbmcs

value: LPS+BCG

tag: time

value: 3 months after day0

tag: number of cells

value: 95 single cells

tag: total volume

tag: collection buffer

value: TCL 1% BME

tag: sample type

value: single cell lysate


title: Donor2 RPMI BCG 3mo

tag: treatment

value: RPMI+BCG


title: Donor3 RPMI BCG 2wk

value: 2 weeks after day0


title: Donor3 LPS BCG 3mo


title: Donor3 LPS

value: LPS


title: Donor3 RPMI

value: RPMI


title: Donor3 RPMI BCG 3mo


title: Donor3 LPS BCG 2wk


title: f1_y202c.rep1 [ChIP-seq]

value: Primary cortical astrocytes

tag: genotype

value: post natal day 1

tag: Sex


title: Donor2 RPMI BCG 2wk


title: P2_UN14_P2644_N723.S515

description:
processed data file: P2644.tsv
CCYYKANXX_8_N723-S515-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: P2_UN14_P2644_N723.S517

description:
processed data file: P2644.tsv
CCYYKANXX_8_N723-S517-NX-xt


title: Donor2 LPS BCG 2wk


title: f1_r172h.rep3 [ChIP-seq]

value: Trp53:R172H Overexpression

value: female


title: P2_UN14_P2644_N723.S516

description:
processed data file: P2644.tsv
CCYYKANXX_8_N723-S516-NX-xt


title: f1_y202c_input.rep1 [ChIP-seq]

value: Input Control

value: Trp53:Y202C Overexpression


title: Donor2 LPS

value: cd14 monocytes from pbmcs


title: f1_r172h.rep2 [ChIP-seq]


title: f1_cre.rep3 [ChIP-seq]

value: Trp53 KO


title: Donor2 RPMI

value: 95 single cells

value: TCL 1% BME


title: Donor1 RPMI BCG 2wk

value: RPMI+BCG

value: single cell lysate


title: f1_r172h_input.rep1 [ChIP-seq]


title: f1_cre.rep2 [ChIP-seq]


title: Donor1 LPS BCG 3mo

value: LPS+BCG

value: 3 months after day0


title: f1_cre.rep1 [ChIP-seq]

value: Primary cortical astrocytes


title: Donor1 LPS BCG 2wk

value: 2 weeks after day0


title: parotid gland 1

city: Chengdu

first: Weimin

last: Lin

state: Sichuan

address: Wuhou strict, People South Street

country: China

institute: Sichuan University

data_processing:
Cellranger
Genome_build: hg19

source_name: human parotid gland

extract_protocol:
Tissue was digested with 2mg/ml collagenase I and 2mg/ml dispase II. Single cells were suspended in Ca2+ and Mg2+ free PBS containing 0.04% BSA and loaded to Chronmium platform.
RNA libraries were prepared with Chromium single cell 3' Reagent v3 Kits according to the manufacturer's protocol

tag: gender

value: Male


title: P2_PA4_P2644_N722.S522

description:
processed data file: P2644.tsv
CCYYKANXX_8_N722-S522-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1


title: P2_PA4_P2644_N722.S517

description:
processed data file: P2644.tsv
CCYYKANXX_8_N722-S517-NX-xt

value: Smart-seq2; full-length RNA-seq


title: P2_PA4_P2644_N722.S516

description:
processed data file: P2644.tsv
CCYYKANXX_8_N722-S516-NX-xt


title: P2_Empty_P2644_N723.S513

description:
processed data file: P2644.tsv
CCYYKANXX_8_N723-S513-NX-xt


title: P2_PA4_P2644_N722.S521

description:
processed data file: P2644.tsv
CCYYKANXX_8_N722-S521-NX-xt


title: P2_PA4_P2644_N722.S518

description:
processed data file: P2644.tsv
CCYYKANXX_8_N722-S518-NX-xt


title: P2_PA4_P2644_N722.S520

description:
processed data file: P2644.tsv
CCYYKANXX_8_N722-S520-NX-xt


title: Donor1 RPMI BCG 3mo


title: f1_cre_input.rep1 [ChIP-seq]

value: post natal day 1

value: female


title: Donor1 RPMI

value: RPMI


title: Donor1 LPS

value: cd14 monocytes from pbmcs

value: LPS


title: G-Smo tumor POx-palbo #2

city: Atanta

first: Tim

last: Gershon

state: GA

address: Emory University School of Medicine

institute: Emory University

data_processing:
Raw sequence data were processed in a Linux environment to generate a digital expression (DGE) matrices, using Drop-seq Tools V1.13.
https://github.com/broadinstitute/Drop-seq/releases
alignment: Star aligner was used version 2.5.4a
DGE creation: We first convert Fastq to BAM/SAM format and merge samples that were sequenced across multiple lanes.
full downstream pipeline code:
https://github.com/malawsky/Gershon_single-cell
 all alignment and quantification was done using cell ranger version v6.2.1
Genome_build: GrCh38 human genome
Supplementary_files_format_and_content: Generic data matrices in csv format with cell barcodes/UMI as column headers

source_name: mouse medulloblastoma

extract_protocol:
Brains were cut in half sagittally and drop-fixed in 4% paraformaldehyde for IHC, and half cerebellum or tumor collected for Drop-Seq.Cells were dissociated using the Papain Dissociation System (Worthington Biochemical) according to the manufacturer’s protocol, as in our prior studies. https://www.nature.com/articles/s41467-019-13657-6#Sec18.
Cell-indexed, 3' biased cDNA libraries were prepared according to the Drop-seq protocol V3.1, full details available online (http://mccarrolllab.com/dropseq/). Cell and bead concentrations were both set to between 95 and 110/μL. cDNA libraries were prepared for sequencing using standard Illumina protocols . All samples were balanced based on cDNA content so that there would be equal representation across lanes during the nova-seq run and then tagged with a unique primer prior to sequencing.

tag: strain background

value: 5 daily doses of palbociclib 25mg/kg delvered as POx-palbo via IP injection, starting at P10

tag: age at harvest


title: G-Smo tumor POx-palbo #1


title: G-Smo tumor POx-palbo #3


title: QC-034596

tag: disease state

value: SCLE


title: P2_PA4_P2644_N722.S515

description:
processed data file: P2644.tsv
CCYYKANXX_8_N722-S515-NX-xt

tag: cell line

tag: cell type

tag: shRNA


title: P2_PA4_P2644_N722.S513

description:
processed data file: P2644.tsv
CCYYKANXX_8_N722-S513-NX-xt

tag: protocol


title: PROseq_Untreated_14D_rep2

data_processing:
Library strategy: PRO-seq
Pro-seq: FASTQ data were trimmed by Cutadapt 1.14 and Trimmomatic v0.32.
Pro-seq: Reads were aligned on hg19 or dm3 genome by bowtie 1.1.2 26. Strand-specific single nucleotide ends of aligned reads were generated by Bedtools v2.26 with genomecov as bedgraph format. Bedgraph data were normalized by the number of reads mapped to spike-in dm3 genome, and then converted to bigwig files.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: The processed data files are in bigWig format: Pro-seq: bigwigs were with Bedtools v2.26 with genomecov.

source_name: OSCC cells

extract_protocol:
PRO-seq experiments were performed as described previously (Mahat, D. B. et al. 2016). Nuclei were isolated by Dounce homogenizer with loose pestle. 1x10^7 nuclei were subjected to nuclear run-on (30oC, 3min) in the presence of 25 μM Biotin-11-ATP/GTP/CTP/UTP (PerkinElmer). Total RNA was extracted and hydrolyzed in 0.2 M NaOH (on ice, 10 min).
PRO-seq libraries used biotinylated nascent RNAs were purified by Dynabeads M-280 streptavidin (Invitrogen). Following adaptor ligation as described in previously (Mahat, D. B. et al. 2016), cDNA synthesis, and PCR amplification 140–350 bp libraries were size-selected by Pippin HT with 2% gel cassette 20B (Sage Science).

treatment_protocol: SCC cells growing in serum–free media were treated in vitro with 300 μM palmitic acid for 96 h (4 days) and after palmitic acid withdrawal cells were passaged normally (when reaching 80% confluence) for 14 days and collected for chromatin fixation.

value: Untreated 14D


title: PROseq_Untreated_14D_rep1


title: P2_PA4_P2644_N721.S521

description:
processed data file: P2644.tsv
CCYYKANXX_8_N721-S521-NX-xt


title: P2_PA4_P2644_N721.S520

description:
processed data file: P2644.tsv
CCYYKANXX_8_N721-S520-NX-xt


title: P2_PA4_P2644_N721.S517

description:
processed data file: P2644.tsv
CCYYKANXX_8_N721-S517-NX-xt


title: PROseq_Treated_14D_rep2

value: post-PA 14D


title: P2_PA4_P2644_N721.S518

description:
processed data file: P2644.tsv
CCYYKANXX_8_N721-S518-NX-xt


title: PROseq_Treated_14D_rep1


title: QC-034612

value: NN


title: PROseq_Untreated_4D_rep2

value: Untreated 4D


title: P2_PA4_P2644_N721.S522

description:
processed data file: P2644.tsv
CCYYKANXX_8_N721-S522-NX-xt


title: P2_PA4_P2644_N721.S516

description:
processed data file: P2644.tsv
CCYYKANXX_8_N721-S516-NX-xt


title: PROseq_Untreated_4D_rep1


title: PROseq_Treated_4D_rep2

value: PA 4D


title: P2_PA4_P2644_N721.S515

description:
processed data file: P2644.tsv
CCYYKANXX_8_N721-S515-NX-xt


title: PROseq_Treated_4D_rep1


title: QC-034615


title: brain rJ2.2.8b rep5

city: taian

first: yuming

last: li

state: shandong

address: 2 Yingsheng Dong Road

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

data_processing:
RNAseq reads were mapped to the mouse transcriptome (mm10) with Kallisto (version 1.15.0)
Transcript abundances were normalized with Transcripts Per Million (TPM) mapped reads.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values

source_name: brain

extract_protocol:
brain total RNA was harvested using Trizol reagent. mRNA was enriched by magnetic beads with Oligo (dT), RNAseq libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530L, NEB). Libraries were sequenced on an Illumina Hiseq machine to obtain 150 bp paired-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: brain

tag: age

value: wild type

value: IC rJ2.2.8b virus


title: brain rJ2.2.8b-KO rep5

value: IC rJ2.2.8b-KO virus


title: brain rJ2.2.8b-KO rep2


title: brain rJ2.2.8b-KO rep3


title: brain rJ2.2.8b-KO rep4


title: QC-034610


title: QC-034608


title: QC-034592

value: DLE


title: P2_PA4_P2644_N720.S522

description:
processed data file: P2644.tsv
CCYYKANXX_8_N720-S522-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: HEK-293T mock 0x rep4 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R4_mock_0x_1000ng_NOR.sRNA

value: mock


title: HEK-293T mock 0x rep3 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R3_mock_0x_1000ng_NOR.sRNA


title: QC-034602

value: ACLE


title: P2_PA4_P2644_N720.S521

description:
processed data file: P2644.tsv
CCYYKANXX_8_N720-S521-NX-xt


title: HEK-293T mock 0x rep2 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R2_mock_0x_1000ng_NOR.sRNA


title: brain rJ2.2.8b-KO rep1


title: QC-034595


title: QC-034606


title: P2_PA4_P2644_N720.S520

description:
processed data file: P2644.tsv
CCYYKANXX_8_N720-S520-NX-xt


title: QC-034597


title: P2_PA4_P2644_N721.S513

description:
processed data file: P2644.tsv
CCYYKANXX_8_N721-S513-NX-xt


title: Splenic B cells, 165KO_B_3

city: St. Louis

first: Xiao

last: Huang

address: 4940 Parkview Place, CSRB 7766, Department of Pathology and Immunology

department: Pathology and Immunology

institute: Washington University in St. Louis, School of Medicine

description: Splenic B cells from Zeb2 -165-/-  mouse

hyb_protocol: Following fragmentation and labeling, 2.5 ug of cDNA were hybridized onto the Gene 1.0 ST arrays and placed in GeneChip Hybridization Oven 640 for 18 hr at 45C. Gene Chip’s were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 7G 3000 Scanner.

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

source_name: Splenic B cells from Zeb2 -165-/-  mouse

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico reagent kit from 100pg-2ng total RNA.

extract_protocol: Column extraction of total RNA was performed acording to the manufacturer's instructions.

treatment_protocol: Splenic B cells sort-purifed from WT or  Zeb2 -165-/- mice.

value: Spleen

value: B cells


title: HEK-293T mock 0x rep1 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R1_mock_0x_1000ng_NOR.sRNA


title: brain rJ2.2.8b rep4


title: brain rJ2.2.8b rep2


title: brain rJ2.2.8b rep3


title: P2_PA4_P2644_N720.S518

description:
processed data file: P2644.tsv
CCYYKANXX_8_N720-S518-NX-xt


title: P2_PA4_P2644_N720.S517

description:
processed data file: P2644.tsv
CCYYKANXX_8_N720-S517-NX-xt


title: Basophil_Subject_25_CR_Day1

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

data_processing:
For analysis of the miR-Seq data, raw reads were de-multiplexed and FASTQ files for each sample were generated using Illumina bcl2fastq software. FASTQ data were checked using the FastQC tool. Reads and UMI counts were generated using QIAGEN GeneGlobe pipeline. During the QIAseq miRNA Library Kit construction process, each individual miRNA molecule was tagged with an UMI. Following sequencing and trimming, reads were analyzed for the presence of UMIs. All reads containing identical insert sequence and UMI sequence (insert-UMI pair) were collapsed into a single read. These reads were passed into the analysis pipeline. Additionally, reads containing partial UMI were also passed into the analysis pipeline to allow for true quantification of the miRNAs by eliminating library amplification bias. Cutadapt (version 1.11) was used to remove the adapter sequences and output adapter-free sequences.
The UMI counts for each miRNA were read into R (r-project.org) using the Bioconductor edgeR package and filtered to remove miRNAs that were either unexpressed or expressed at a consistent, unreliably low level. Samples were normalized using a trimmed mean of M-values and then counts were converted to log counts/million (logCPM) using the voomWithQualityWeights function57 from the Bioconductor limma package.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI counts/miRNA

source_name: Basophils

extract_protocol:
Exosomes were isolated from the plasma of the study participants using Invitrogen’s Total Exosome Precipitation Reagent (Thermo Fisher Scientific, Inc., Waltham, MA). miRNAs were then isolated from the exosomes using the QIAGEN miRNeasy Serum/Plasma Kit (QIAGEN Sciences, Germantown, MD). For basophils, peripheral blood samples were collected in EDTA tubes.  Human nucleated cells were separated from red blood cells using HetaSep reagent (Stemcell Technologies, Vancouver, Canada).  Basophils were isolated from nucleated cells using the Stemcell Technologies EasySep Human Basophil Enrichment Kit (isolation purity, mean ± SD, 94.0 ± 2.5%). Purified basophils were centrifuged at 1,500 rpm for 10 minutes. The pellet was resuspended in 200L of PBS, 1 mL of Trizol was added, and the purified basophils were stored at -80oC until RNA was isolated. Total RNA from basophils was isolated using the QIAGEN miRNeasy Micro extraction kit. The integrity of the total RNA samples was evaluated using a 2100 Bioanalyzer instrument (Agilent Technologies, Inc., Palo Alto, CA).  A Thermo Fisher Scientific NanoDrop™ 1000 Spectrophotometer was used to determine purity of RNA samples by measuring OD260/280 and OD260/230 ratios.  Only samples with RNA Integrity Number (RIN)s of ≥7 and OD260/280 and OD260/230 ratios >1.8 were used for further analysis.  Total RNA concentrations were determined using Thermo Fisher Scientific Qubit RNA HS Assay Kit.
miRNA sequencing libraries prepared with the QIAseq miRNA Library Kit were sequenced using a NextSeq 500 instrument (Illumina, Inc., San Diego, CA). Libraries were quantified, adjusted to 4 nM each and pooled. The pooled libraries were further diluted down to 1.8 pM and loaded into a flow cell on an Illumina NextSeq 500. The sequencing specifications were 1x76 bases and 12 million targeted reads per sample.

tag: response

value: Complete responder

value: Basophils

tag: patient diagnosis

value: chronic spontaneous urticaria (CSU)

tag: subject number


title: P2_PA4_P2644_N720.S516

description:
processed data file: P2644.tsv
CCYYKANXX_8_N720-S516-NX-xt


title: Splenic B cells, 165KO_B_2


title: Basophil_Subject_17_CR_Day1


title: Basophil_Subject_24_NR_Day1

value: Non-responder


title: Retina Adult OrJ

city: Memphis

first: Victoria

last: Honnell

state: Tennessee

address: 262 Danny Thomas

institute: St. Jude Children's Research Hospital

description:
OrJ
Retina Adult OrJ RNA-Seq
Honnell et al. Table S2 REVISED.xls

data_processing:
scRNA-sequencing data was processed individually then aggregated using cellranger v3.0.2
Genome_build: mm10
Supplementary_files_format_and_content: For scRNA-seq tab delimited features(genes) and barcodes file and matrix file.
Supplementary_files_format_and_content: RNA-seq: FPKM

source_name: retina

extract_protocol:
Retinas were removed, dissociated with papain, and run through a 4% BSA cushion. Cells were processed using the 10x genomics protocols. For bulk RNA, RNA was extracted from retina through trizol method
Library construction was completed using the 10x RNA(v3) single cell kits

value: retina

value: OrJ


title: Retina Adult R0 KO

description:
R0 Δ/Δ
Retina Adult R0 KO RNA-Seq
Honnell et al. Table S2 REVISED.xls

value: R0 delta/delta


title: Mutu3 Olaparib treated

city: Camden

first: Jozef

last: Madzo

state: NJ

address: 403 Haddon Avenue

department: Bioinformatics

institute: Coriell Institute

description:
Mutu3_olap
Olaparib treated biological replicate

data_processing:
Illumina HiSeq2500 single end sequencing
Sequenced reads were aligned to the ebv genome assembly using the Star software suite
ht-seq-count  with default settings to generate counts of each gene
Genome_build: EBV
Supplementary_files_format_and_content: The processed files are in csv text file. The first column is gene name.  The next columns are the gene counts  of the individual samples.

source_name: MUTU

growth_protocol: Lymphoblastoid cell lines (LCLs) were cultured in suspension in RPMI 1640 medium supplemented with 15% fetal bovine serum and antibiotics in 5% CO2 at 37°C.

extract_protocol:
RNA was extracted from 5 × 106 cells using a Qiagen RNeasy Plus Mini Kit according to the manufacturer’s protocol. Total RNA was depleted of the ribosomal RNA component using RiboZero (Epicentre).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Olaparib was dissolved in DMSO and cells were treated with 1 μM olaparib for 72 hrs in the appropriate media.

value: B-cells

tag: agent

value: Olaparib


title: P2_PA4_P2644_N720.S515

description:
processed data file: P2644.tsv
CCYYKANXX_8_N720-S515-NX-xt


title: Mutu1 Olaparib treated

description:
Mutu1_olap
Olaparib treated


title: P2_PA4_P2644_N720.S513

description:
processed data file: P2644.tsv
CCYYKANXX_8_N720-S513-NX-xt


title: Basophil_Subject_16_CR_Day1


title: brain rJ2.2.8b rep1

value: brain

tag: genotype

value: wild type

tag: treatment

value: IC rJ2.2.8b virus


title: Mutu3 DMSO control

description:
Mutu3_cont
Control biological replicate

value: Control


title: Basophil_Subject_12_CR_Day1


title: Retina Adult R0 KO scRNA-seq Rep2

description:
R0 Δ/Δ
Retina Adult R0 KO scRNA-seq Rep2


title: Retina Adult R0 KO scRNA-seq

description:
R0 Δ/Δ
Retina Adult R0 KO scRNA-seq


title: Splenic B cells, 165KO_B_1


title: Retina Adult OrJ scRNA-seq

description:
OrJ
Retina Adult OrJ scRNA-seq


title: P2_UN4_P2644_N719.S522

description:
processed data file: P2644.tsv
CCYYKANXX_8_N719-S522-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: Basophil_Subject_11_NR_Day1


title: Mutu1 DMSO control

description:
Mutu1_cont
Control


title: Retina Adult R1 KO scRNA-seq Rep2

description:
R1 Δ/Δ
Retina Adult R1 KO scRNA-seq Rep2

value: R1 delta/delta


title: P2_UN4_P2644_N719.S521

description:
processed data file: P2644.tsv
CCYYKANXX_8_N719-S521-NX-xt


title: Basophil_Subject_10_CR_Day1

value: Complete responder


title: Splenic B cells, WT_B_3

description: Splenic B cells from WT B6 mouse

source_name: Splenic B cells from WT B6 mouse

value: Spleen

value: B cells

value: WT


title: P2_UN4_P2644_N719.S520

description:
processed data file: P2644.tsv
CCYYKANXX_8_N719-S520-NX-xt


title: LCL3 Olaparib treated

description:
LCL3_olap
Olaparib treated biological replicate

source_name: LCL


title: Splenic B cells, WT_B_1

description: Splenic B cells from WT B6 mouse


title: Splenic B cells, WT_B_2

description: Splenic B cells from WT B6 mouse


title: Basophil_Subject_9_NR_Day1

value: Non-responder

value: Basophils

value: chronic spontaneous urticaria (CSU)


title: LCL2 DMSO control

description:
LCL2_cont
Control biological replicate

value: B-cells


title: Retina Adult R0 WT scRNA-seq

description: Retina Adult R0 WT scRNA-seq

value: retina


title: LCL1 Olaparib treated

description:
LCL1_olap
Olaparib treated

value: Olaparib


title: LCL1 DMSO control

description:
LCL1_cont
Control


title: Basophil_Subject_3_NR_Day1


title: OPN-KO E. coli 3

city: Madison

first: Petra

last: Popovics

state: WI

department: Department of Urology

institute: University of Wisconsin-Madison

description: edgeRglm_GENE_WTinflamed-OPNKOinflamed.xlsx, edgeRglm_GENE_OPNKOcontrol-OPNKOinflamed.xlsx

data_processing:
Libraries were sequenced on a NovaSeq 6000 platform as paired-end, 150bp reads and fastq files were generated with bcl2fastq2 conversion software v2.20 using reads meeting Q30 in >80% of reads.
The trimming software Skewer80 (v0.1.123) was used to trim Illumina adaptors from the fastq files.
Trimmed reads were aligned to the mouse genome GRCm38.p5 (accession NCBI:GCA_000001635.7) using the splice-junction aware read aligner STAR (v2.5.3a). Based on ensembl version 88 annotation (March 2017), mapped paired-end reads for genes were counted in each sample using RSEM v1.3.0 (RNASeq by Expectation Maximization), described by Li and Dewey. Samples were normalized by the method of trimmed mean of M-values (TMM), where the product of this factor and the library sizes defines the effective library size. Independent filtering was performed prior to differential expression analysis, requiring a threshold of least 1 transcript count per million in at least 3 samples, ignoring any prior group assignment.
Supplementary_files_format_and_content: Analysis of differentially expressed genes was performed using EdgeR package (v3.16.5). Statistical significance of the negative-binomial regression test was adjusted with a Benjamini-Hochberg FDR correction at the 5% level. Processed files contain contrasts of WT inflamed vs OPN-KO inflamed, WT inflamed vs WT control, OPN-KO control vs. WT control, OPN-KO control vs. OPN-KO inflamed and raw counts.

source_name: ventral prostate lobe

extract_protocol:
Ventral lobes were thawed and the RNA was stabilized in RNAlater (Thermo Fisher Scientific) for 1 hour. Total RNA was isolated from ventral lobes using the Qiagen RNeasy Micro kit with on-column DNAse digestion (Germantown, MD).
RNA quantity was measured with NanoDrop and assayed on an Agilent 2100 Bioanalyzer. The cDNA library was prepared by the TruSeq Stranded Total RNA (Gold) Library Prep with after polyA enrichment and rRNA reduction. Libraries were quantified using Qubit DNA HS kit and assayed on Agilent Tapestation DNA 1000 system.

treatment_protocol: The UTI89 uropathogenic Escherichia coli strain used for transurethral instillation was isolated from a patient with cystisis and transformed with a PCOMGFP plasmid providing kanamycin resistance and green fluorescent protein expression.  One colony of UTI89 E. coli was used to inoculate 100 ml Luria-Bertani (LB) broth and incubated by shaking at 200 rpm at 37°C for 16 hours. Cells were harvested by centrifugation at 1400g for 15 min. and resuspended in sterile PBS. Optical density (OD) was adjusted to 0.8. UTI89 or PBS was instilled via a transurethral catheter (OD 0.8, 100 ul) two times, 3 days apart, to 8-week-old WT or OPN-KO mice. Necropsy was performed and tissues were collected one or 8 weeks after the first instillation. Free catch urine was collected 24 hours after the second instillation and colony forming units (CFU) were determined as described earlier.

value: transurethral E.coli instillation


title: OPN-KO E. coli 2


title: P2_UN4_P2644_N719.S517

description:
processed data file: P2644.tsv
CCYYKANXX_8_N719-S517-NX-xt

data_processing:
Reads were then demultiplexed according to the cell barcodes
Sequenced reads were filtered for low-complexity or low-quality sequence.
High quality reads were mapped according to the GEM pipeline
Genome_build: Human:  GRCh38
Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing gene expression values as read counts

extract_protocol:
Live SCC-25 sorted cells were lysed using lysis buffer (0.2% Triton-100, 1U/ul RNase inhibitor). Reverse transcription was performed using SuperScript II (ThermoFisher Scientific) in the presence of 1 μM oligo-dT30VN (IDT), 1 μM template-switching oligonucleotides (QIAGEN), and 1 M betaine.
Libraries were prepared according to the Nextera XT (Illumina) instructions.


title: P2_UN4_P2644_N719.S515

description:
processed data file: P2644.tsv
CCYYKANXX_8_N719-S515-NX-xt


title: P2_UN4_P2644_N719.S518

description:
processed data file: P2644.tsv
CCYYKANXX_8_N719-S518-NX-xt


title: P2_UN4_P2644_N719.S513

description:
processed data file: P2644.tsv
CCYYKANXX_8_N719-S513-NX-xt


title: P2_UN4_P2644_N719.S516

description:
processed data file: P2644.tsv
CCYYKANXX_8_N719-S516-NX-xt


title: Basophil_Subject_8_CR_Day1


title: OPN-KO saline 3 control

description: edgeRglm_GENE_OPNKOcontrol-WTcontrol.xlsx, edgeRglm_GENE_OPNKOcontrol-OPNKOinflamed.xlsx

value: transurethral saline instillation


title: OPN-KO saline 2 control


title: Basophil_Subject_1_CR_Day1


title: Exosomes_Subject_24_NR_Day1

source_name: Plasma exosomes

value: Plasma exosomes


title: P2_UN4_P2644_N718.S522

description:
processed data file: P2644.tsv
CCYYKANXX_8_N718-S522-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line


title: Exosomes_Subject_25_CR_Day1


title: OPN-KO saline 1 control


title: P2_UN4_P2644_N718.S521

description:
processed data file: P2644.tsv
CCYYKANXX_8_N718-S521-NX-xt

value: control pLKO.1


title: WT E. coli 2

description: edgeRglm_GENE_WTinflamed-OPNKOinflamed.xlsx, edgeRglm_GENE_WTinflamed-WTcontrol.xlsx


title: Exosomes_Subject_11_NR_Day1


title: P2_UN4_P2644_N718.S517

description:
processed data file: P2644.tsv
CCYYKANXX_8_N718-S517-NX-xt

value: Smart-seq2; full-length RNA-seq


title: P2_UN4_P2644_N718.S518

description:
processed data file: P2644.tsv
CCYYKANXX_8_N718-S518-NX-xt


title: P2_UN4_P2644_N718.S520

description:
processed data file: P2644.tsv
CCYYKANXX_8_N718-S520-NX-xt


title: Exosomes_Subject_12_CR_Day1


title: Exosomes_Subject_10_CR_Day1


title: WT saline 3 control

description: edgeRglm_GENE_WTinflamed-WTcontrol.xlsx, edgeRglm_GENE_OPNKOcontrol-WTcontrol.xlsx


title: P2_UN4_P2644_N718.S516

description:
processed data file: P2644.tsv
CCYYKANXX_8_N718-S516-NX-xt


title: WT saline 2 control


title: MEF transfection 1x sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
MEF_R1_sh-lib_1x_30ng_FACS.sRNA

data_processing:
Basecalls were performed using bcl2fastq v2.17.1 with the option --barcode-mismatches 0
The small RNA sequencing data were quality control (QC) checked using miRTrace v 1.0.1 qc mode. Human (miRTrace option -s hsa) databases were used as references for HEK-293T and HeLa samples and mouse (-s mmu) databases were used as references for NIH-3T3 and MEF samples. Illumina 3’ adapter sequence TGGAATTCT was provided for 3’ adapter trimming.
For MapToCleave data, The QC qualified reads of each sample were then aligned to the prepared reference sequences, which contained the sequences from the MapToCleave library and the endogenous human (for HEK-293T and HeLa sample) or mouse (for NIH-3T3 and MEF sample) miRNA hairpin sequences that are excluded from the MapToCleave library but are included in miRbase v 21. The alignment was performed using bowtie v 1.1.2 without allowing mismatches (-v 0). The reads that were uniquely mapped to the forward strand of the reference sequences were considered for the hairpin expression measurement.
For validation data, the QC qualified reads were used to quantify expression of the human miRNA hairpins and the modified hairpins (see Supplementary Data 10 of the linked publication) using miRDeep2 v 2.0.0.8 quantifier.pl with allowing 0 mismatches (-g 0) and allowing multi-mapping. The human miRNA hairpin sequences downloaded from miRBase v21 and the modified hairpin sequences were used as the precursor reference (-p). The corresponding human miRNA sequences from miRBase v21 and the manually curated miRNA sequences of the modified hairpins (see Supplementary Data 10 of the linked publication) are used as the mature reference (-m). The hairpin sequence counts are measured by summing up the number of small RNA reads that mapped to an interval 2 nucleotides upstream and 5 nucleotides downstream of the 5p or/and 3p miRNA sequence from the hairpin.
Supplementary_files_format_and_content: tab-delimited text file includes raw counts of MapToCleave sequences for each sample.
Supplementary_files_format_and_content: tab-delimited text file includes raw counts and normalized counts of the modified hairpins and the endogenous human miRNA hairpins for each sample.

organism:
Mus musculus
synthetic construct

source_name: MEF transfected cells

extract_protocol:
For MapToCleave samples, total RNA and DNA were isolated using TRIzol reagent (Ambion). For validation samples, total RNA was extracted using a Zymo quick-RNA microprep kit (Zymo Research).
For MapToCleave samples, 1 ug of HEK-293T total RNA was used for standard small RNA library preparation using TruSeq small RNA kit v2 (Illumina). 1 ug of NIH-3T3 total RNA was used for preparation of small RNA libraries. 30 ng of the total RNA extracted from FACS-isolated MEF cells were used for preparation of small RNA libraries. The small RNA cDNA libraries were PCR-amplified in 15 cycles; the 75-bp single-end sequencing was carried out on a NextSeq500 (Illumina). DNA libraries were prepared in two steps: i) the DNA isolated from the HEK-293T and NIH-3T3 transfected cells was pre-amplified using custom primers compatible with Illumina TruSeq adapter sequences, ii) pre-amplified DNA fragments were multiplexed by PCR using Illumina TruSeq universal forward and single-indexed reverse PCR primers. The DNA libraries were resolved on a 6% Novex TBE gel (Invitrogen), and the 280 – 300 bp fraction was isolated. The 150-bp single-end sequencing was carried out using Illumina NextSeq500. For validation samples, RNA libraries were prepared using TruSeq small RNA kit v2 (Illumina).

value: MEF

value: 1x of the MapToCleave library


title: WT saline 1 control


title: P2_UN4_P2644_N718.S515

description:
processed data file: P2644.tsv
CCYYKANXX_8_N718-S515-NX-xt


title: Exosomes_Subject_8_CR_Day1

value: Complete responder


title: Exosomes_Subject_3_NR_Day1


title: EB6_mESC_lncMN2_KO2

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

data_processing:
FASTQ reads were aligned, filtered and counted through the Cell Ranger pipeline (v4.0) using standard parameters
Genome_build: mm10
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every cell in each sample of the dataset.

growth_protocol: HB9::GFP mESC were cultured and differentiated into MN as described in Wichterle et al., 2008 and Capauto et al., 2018

extract_protocol:
10X Single Cell Protocol for transcriptome determination through droplet-based single-cell RNA-seq methodology (10X Genomics Chromium, Chromium Single Cell 3’ Solution V3.1, Klein and Macosko., 2017)
libraries were prepared according to the Single Cell 3' Reagent Kits User Guide (V3.1)

treatment_protocol: CRISPR/Cas9 methodolgy was used to produce lncMN2 DeltaSP and KO clones.

tag: differentiation stage

value: Embryoid bodies from mESC differentiation at day6


title: NIH-3T3 transfection 1x rep1 DNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
NIH3T3_R1_sh-lib_1x_1000ng_NOR.DNA

molecule: other

source_name: NIH-3T3 transfected cells

tag: molecule type

value: plasmid DNA


title: P2_UN4_P2644_N718.S513

description:
processed data file: P2644.tsv
CCYYKANXX_8_N718-S513-NX-xt


title: Exosomes_Subject_16_CR_Day1


title: NIH-3T3 transfection 1x rep4 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
NIH3T3_R4_sh-lib_1x_1000ng_NOR.sRNA


title: WT E. coli 3


title: EB6_mESC_lncMN2_KO1


title: Exosomes_Subject_1_CR_Day1


title: NIH-3T3 transfection 1x rep3 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
NIH3T3_R3_sh-lib_1x_1000ng_NOR.sRNA


title: NIH-3T3 transfection 1x rep1 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
NIH3T3_R1_sh-lib_1x_1000ng_NOR.sRNA


title: WT E. coli 1


title: EB6_mESC_lncMN2_DeltaSP2


title: EB6_mESC_lncMN2_DeltaSP1


title: Exosomes_Subject_9_NR_Day1

value: Non-responder


title: Human hepatocytes RNA-Seq ctrl sample 3

description:
translating mRNA
RNA-Seq_Hs_hepatocytes_ctrl_003.bw
RNA-Seq_mRNA_cpms.tsv

data_processing:
RNA-seq data were aligned to the hg38 human genome using TopHat2 (Kim et al., 2013).
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were assigned to transcripts, normalized and quantified using featureCounts (Liao et al., 2014) and EdgeR (Robinson et al., 2010).
Low expressed genes (log2 CPM≥2) were filtered out, and differentially expressed genes were defined at log2 fold-change (FC) ≥1 and log2 false discovery rate (FDR)≤0.05
Gene set enrichment analysis was performed using DAVID Bioinformatics Resources 6.8 (Huang da et al., 2009) and summarized by REVIGO (Supek et al., 2011).
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts for reads aligning to genes (cpm)

source_name: Hepatocytes

growth_protocol: Undifferentiated iPSCs BU-3-strain were adapted to feeder-free conditions, maintained on Matrigel (Corning) coated dishes in mTeSR1 media (Stem Cell Technologies), and dissociated for passaging with Gentle Cell Dissociation Reagent (Stem Cell Technologies). iPSCs were differentiated to the hepatic lineage as follows. On “Day 0”, cells were dissociated and approximately 40,000/cm2 were seeded in mTeSR containing 10 mM Y-27632 (Tocris). The following day (Day 1), media was changed and endodermal differentiation initiated using the STEMdiff Definitive Endoderm Kit (Stem Cell Technologies). Cells were cultured in media according to the manufacturer’s instructions for 96 hours (Days 1-5). On Day 5, cells were dissociated with Gentle Cell Dissociation Reagent and split into new matrigel-coated wells at a ratio of approximately 1:3 in complete serum-free differentiation media containing 0.05ug/ml Activin A (R&D 338-AC), 0.01ug/ml BMP4 (R&D 314-BP), 0.01ug/ml FGF2 (R&D 233-FB), 0.01ug/ml VEGF (R&D 293VE), and 10 mM Y-27632. On Day 6, cells were refed with this same media in the absence of Y-27632. Cells were then differentiated in media conditions as previously described (Wilson et al., 2015. Stem Cell Reports, 4(5), 873-885) for days 7-20.

extract_protocol:
total RNA extracted using an miRNeasy kit (Qiagen). Quality of directed differentiation was confirmed by quantification of expression of markers of definitive endoderm (CKIT/CXCR4) on Day 5 of directed differentiation.
Nextera XT DNA Library Preparation Kit (Illumina FC-131)

treatment_protocol: On Day 20, cells were refed with hepatic differentiation media containing T3 at a concentration of either 10nM or 100nM or control vehicle. 24 hours later, cells were harvested

value: hepatocytes

value: ctrl

tag: chip antibody


title: Human hepatocytes RNA-Seq ctrl sample 4

description:
translating mRNA
RNA-Seq_Hs_hepatocytes_ctrl_004.bw
RNA-Seq_mRNA_cpms.tsv


title: S24: tagged mir-16, tagged mir-30a variant 3, tagged mir-125a (rep2)

description:
count_table_for_experimental_validation.txt
sample_24.sRNA

organism:
Homo sapiens
synthetic construct

source_name: HEK-293T transfected cells

value: Equimolar abundances of tagged mir-16, tagged mir-30a variant 3 and tagged mir-125a


title: P2_UN4_P2644_N716.S518

description:
processed data file: P2644.tsv
CCYYKANXX_8_N716-S518-NX-xt


title: Human hepatocytes RNA-Seq ctrl sample 2

description:
translating mRNA
RNA-Seq_Hs_hepatocytes_ctrl_002.bw
RNA-Seq_mRNA_cpms.tsv


title: EB6_mESC_WT2

value: wild type


title: P2_UN4_P2644_N716.S522

description:
processed data file: P2644.tsv
CCYYKANXX_8_N716-S522-NX-xt


title: P2_UN4_P2644_N716.S517

description:
processed data file: P2644.tsv
CCYYKANXX_8_N716-S517-NX-xt


title: P2_UN4_P2644_N716.S521

description:
processed data file: P2644.tsv
CCYYKANXX_8_N716-S521-NX-xt


title: OPN-KO E. coli 1

description: edgeRglm_GENE_WTinflamed-OPNKOinflamed.xlsx, edgeRglm_GENE_OPNKOcontrol-OPNKOinflamed.xlsx


title: S22: tagged mir-16, tagged mir-30a variant 1, tagged mir-125a (rep2)

description:
count_table_for_experimental_validation.txt
sample_22.sRNA

value: Equimolar abundances of tagged mir-16, tagged mir-30a variant 1 and tagged mir-125a


title: S23: tagged mir-16, tagged mir-30a variant 2, tagged mir-125a (rep2)

description:
count_table_for_experimental_validation.txt
sample_23.sRNA

value: Equimolar abundances of tagged mir-16, tagged mir-30a variant 2 and tagged mir-125a


title: Human hepatocytes RNA-Seq T3 sample 13

description:
translating mRNA
RNA-Seq_Hs_hepatocytes_T3_013.bw
RNA-Seq_mRNA_cpms.tsv


title: NIH-3T3 transfection 1x rep5 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
NIH3T3_R5_sh-lib_1x_1000ng_NOR.sRNA


title: S21: tagged mir-16 variant 4, tagged mir-30a, tagged mir-125a (rep2)

description:
count_table_for_experimental_validation.txt
sample_21.sRNA

value: Equimolar abundances of tagged mir-16 variant 4, tagged mir-30a and tagged mir-125a


title: Human hepatocytes RNA-Seq ctrl sample 1

description:
translating mRNA
RNA-Seq_Hs_hepatocytes_ctrl_001.bw
RNA-Seq_mRNA_cpms.tsv


title: 6wwdox-rep3

city: Vienna

first: Julia

last: Arand

address: Schwarzspanierstr. 16

country: Austria

institute: Medical University of Vienna

description:
dataset2
E18

data_processing:
Obtained reads were mapped to mouse reference genome mm10 with STAR2.5.1b using default settings. Genes from the Refseq database that have at least 10 reads in more than 50% of all samples of one condition, were used for further analysis. Differentially expressed genes were obtained using DEseq2 (p.adj.<0.05, absolute log2FC>1)
Genome_build: mm10
Supplementary_files_format_and_content: txt - FPM values from DEseq2 analysis

source_name: pituitary

extract_protocol:
Harvested pituitaries were immediately snap frozen in dry ice and stored at -80°C
RNA isolation, mRNA library preparation and sequencing on a NovaSeq6000 in a paired-end 150bp run was performed by Novogene Co., Ltd.
mRNA library preparation (dataset1: by rRNA depletion, dataset2: by PolyA enrichment)

value: 6w +dox

tag: mouse strain

value: shRB

tag: Sex

value: female


title: 6wwdox-rep2

description:
dataset2
E17


title: P2_UN4_P2644_N716.S516

description:
processed data file: P2644.tsv
CCYYKANXX_8_N716-S516-NX-xt

tag: cell line

tag: cell type

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: P2_UN4_P2644_N716.S520

description:
processed data file: P2644.tsv
CCYYKANXX_8_N716-S520-NX-xt

tag: shRNA

tag: protocol


title: Human hepatocytes RNA-Seq T3 sample 12

description:
translating mRNA
RNA-Seq_Hs_hepatocytes_T3_012.bw
RNA-Seq_mRNA_cpms.tsv

tag: strain


title: S20: tagged mir-16 variant 2, tagged mir-30a, tagged mir-125a (rep2)

city: Solna

first: Wenjing

last: Kang

institute: SciLifeLab

description:
count_table_for_experimental_validation.txt
sample_20.sRNA

value: Equimolar abundances of tagged mir-16 variant 2, tagged mir-30a and tagged mir-125a


title: EB6_mESC_WT1

value: Embryoid bodies from mESC differentiation at day6


title: P2_UN4_P2644_N716.S513

city: Sabadell

first: Antoni

last: Berenguer-LLergo

institute: Parc Taulí Research and Innovation Institute (I3PT)

description:
processed data file: P2644.tsv
CCYYKANXX_8_N716-S513-NX-xt


title: Human hepatocytes RNA-Seq T3 sample 11

description:
translating mRNA
RNA-Seq_Hs_hepatocytes_T3_011.bw
RNA-Seq_mRNA_cpms.tsv


title: S19: tagged mir-16 variant 3, tagged mir-30a, tagged mir-125a (rep2)

description:
count_table_for_experimental_validation.txt
sample_19.sRNA

value: Equimolar abundances of tagged mir-16 variant 3, tagged mir-30a and tagged mir-125a


title: Human hepatocytes RNA-Seq T3 sample 10

description:
translating mRNA
RNA-Seq_Hs_hepatocytes_T3_010.bw
RNA-Seq_mRNA_cpms.tsv


title: P1_PA14_P2633_N715.S522

description:
processed data file: P2633.tsv
CCYYKANXX_7_N715-S522-NX-xt


title: P1_PA14_P2633_N715.S521

description:
processed data file: P2633.tsv
CCYYKANXX_7_N715-S521-NX-xt


title: Human hepatocytes RNA-Seq T3 sample 9

description:
translating mRNA
RNA-Seq_Hs_hepatocytes_T3_009.bw
RNA-Seq_mRNA_cpms.tsv


title: P1_PA14_P2633_N715.S518

description:
processed data file: P2633.tsv
CCYYKANXX_7_N715-S518-NX-xt


title: P1_PA14_P2633_N715.S517

description:
processed data file: P2633.tsv
CCYYKANXX_7_N715-S517-NX-xt


title: S17: WT mir-16, WT mir-30a, tagged mir-125a (rep2)

description:
count_table_for_experimental_validation.txt
sample_17.sRNA

value: Equimolar abundances of WT mir-16, WT mir-30a and tagged mir-125a


title: S16: tagged mir-16, WT mir-30a, WT mir-125a (rep2)

description:
count_table_for_experimental_validation.txt
sample_16.sRNA

value: Equimolar abundances of tagged mir-16, WT mir-30a and WT mir-125a


title: Exosomes_Subject_17_CR_Day1

value: Complete responder

tag: tissue

value: Plasma exosomes

value: chronic spontaneous urticaria (CSU)


title: S15: WT mir-16, tagged mir-30a, WT mir-125a (rep2)

description:
count_table_for_experimental_validation.txt
sample_15.sRNA

value: Equimolar abundances of WT mir-16, tagged mir-30a and WT mir-125a


title: 12wwdox-rep4

description:
dataset2
E5

value: 12w +dox

value: male


title: S14: tagged mir-16, tagged mir-30a, tagged mir-125a (rep2)

description:
count_table_for_experimental_validation.txt
sample_14.sRNA

value: Equimolar abundances of tagged mir-16, tagged mir-30a and tagged mir-125a


title: P1_PA14_P2633_N715.S520

description:
processed data file: P2633.tsv
CCYYKANXX_7_N715-S520-NX-xt


title: 6wwdox6wndox-rep2

description:
dataset2
E9

value: 6w +dox, 6w-dox

value: shRB


title: 6wwdox6wndox-rep3

description:
dataset2
E11

value: female


title: P1_PA14_P2633_N715.S515

description:
processed data file: P2633.tsv
CCYYKANXX_7_N715-S515-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1


title: S13: WT mir-16, WT mir-30a, WT mir-125a (rep2)

description:
count_table_for_experimental_validation.txt
sample_13.sRNA

value: Equimolar abundances of WT mir-16, WT mir-30a and WT mir-125a


title: 6wwdox6wndox-rep5

description:
dataset2
E13


title: 6wwdox6wndox-rep1

description:
dataset2
E8


title: 12wwdox-rep3

description:
dataset2
E4


title: S18: tagged mir-16 variant 1, tagged mir-30a, tagged mir-125a (rep2)

description:
count_table_for_experimental_validation.txt
sample_18.sRNA

value: Equimolar abundances of tagged mir-16 variant 1, tagged mir-30a and tagged mir-125a


title: P1_PA14_P2633_N715.S513

description:
processed data file: P2633.tsv
CCYYKANXX_7_N715-S513-NX-xt

value: Smart-seq2; full-length RNA-seq


title: S12: tagged mir-16, tagged mir-30a variant 3, tagged mir-125a (rep1)

description:
count_table_for_experimental_validation.txt
sample_12.sRNA

value: Equimolar abundances of tagged mir-16, tagged mir-30a variant 3 and tagged mir-125a


title: S11: tagged mir-16, tagged mir-30a variant 2, tagged mir-125a (rep1)

description:
count_table_for_experimental_validation.txt
sample_11.sRNA

value: Equimolar abundances of tagged mir-16, tagged mir-30a variant 2 and tagged mir-125a


title: 6wwdox6wndox-rep4

description:
dataset2
E12


title: S10: tagged mir-16, tagged mir-30a variant 1, tagged mir-125a (rep1)

description:
count_table_for_experimental_validation.txt
sample_10.sRNA

value: Equimolar abundances of tagged mir-16, tagged mir-30a variant 1 and tagged mir-125a


title: P1_PA14_P2633_N714.S522

description:
processed data file: P2633.tsv
CCYYKANXX_7_N714-S522-NX-xt


title: 12wwdox-rep1

description:
dataset2
E1


title: P1_PA14_P2633_N714.S521

description:
processed data file: P2633.tsv
CCYYKANXX_7_N714-S521-NX-xt


title: 16w+dox-5d-dox-rep3

description:
dataset1
H17

value: 16w +dox, 5d -dox


title: P1_PA14_P2633_N715.S516

description:
processed data file: P2633.tsv
CCYYKANXX_7_N715-S516-NX-xt


title: P2_UN4_P2644_N716.S515

description:
processed data file: P2644.tsv
CCYYKANXX_8_N716-S515-NX-xt


title: S09: tagged mir-16 variant 4, tagged mir-30a, tagged mir-125a (rep1)

description:
count_table_for_experimental_validation.txt
sample_9.sRNA

value: Equimolar abundances of tagged mir-16 variant 4, tagged mir-30a and tagged mir-125a


title: P1_PA14_P2633_N714.S520

description:
processed data file: P2633.tsv
CCYYKANXX_7_N714-S520-NX-xt


title: P1_PA14_P2633_N714.S518

description:
processed data file: P2633.tsv
CCYYKANXX_7_N714-S518-NX-xt


title: S08: tagged mir-16 variant 2, tagged mir-30a, tagged mir-125a (rep1)

description:
count_table_for_experimental_validation.txt
sample_8.sRNA

value: Equimolar abundances of tagged mir-16 variant 2, tagged mir-30a and tagged mir-125a


title: 16w+dox-3d-dox-rep3

description:
dataset1
H13

value: 16w +dox, 3d -dox


title: P1_PA14_P2633_N714.S517

description:
processed data file: P2633.tsv
CCYYKANXX_7_N714-S517-NX-xt


title: S06: tagged mir-16 variant 1, tagged mir-30a, tagged mir-125a (rep1)

description:
count_table_for_experimental_validation.txt
sample_6.sRNA


title: 16w+dox-5d-dox-rep2

description:
dataset1
H16


title: 16w+dox-5d-dox-rep1

description:
dataset1
H15


title: P1_PA14_P2633_N714.S516

description:
processed data file: P2633.tsv
CCYYKANXX_7_N714-S516-NX-xt


title: 12wwdox-rep2

description:
dataset2
E2

value: 12w +dox


title: 16w+dox-3d-dox-rep1

description:
dataset1
H11

value: male


title: 16w+dox-1d-dox-rep4

description:
dataset1
H10

value: 16w +dox, 1d -dox


title: S05: WT mir-16, WT mir-30a, tagged mir-125a (rep1)

description:
count_table_for_experimental_validation.txt
sample_5.sRNA

value: Equimolar abundances of WT mir-16, WT mir-30a and tagged mir-125a


title: P1_PA14_P2633_N714.S515

description:
processed data file: P2633.tsv
CCYYKANXX_7_N714-S515-NX-xt


title: P1_PA14_P2633_N712.S521

description:
processed data file: P2633.tsv
CCYYKANXX_7_N712-S521-NX-xt


title: 16w+dox-3d-dox-rep2

description:
dataset1
H12

value: shRB


title: 16w+dox-1d-dox-rep3

description:
dataset1
H9

value: female


title: S04: tagged mir-16, WT mir-30a, WT mir-125a (rep1)

description:
count_table_for_experimental_validation.txt
sample_4.sRNA

value: Equimolar abundances of tagged mir-16, WT mir-30a and WT mir-125a


title: Retina Adult R3 KO scRNA-seq

description:
R3 Δ/Δ
Retina Adult R3 KO scRNA-seq

value: retina

value: R3 delta/delta


title: S01: WT mir-16, WT mir-30a, WT mir-125a (rep1)

description:
count_table_for_experimental_validation.txt
sample_1.sRNA

value: Equimolar abundances of WT mir-16, WT mir-30a and WT mir-125a


title: 16w+dox-1d-dox-rep1

description:
dataset1
H7


title: P1_PA14_P2633_N712.S520

description:
processed data file: P2633.tsv
CCYYKANXX_7_N712-S520-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: S03: WT mir-16, tagged mir-30a, WT mir-125a (rep1)

description:
count_table_for_experimental_validation.txt
sample_3.sRNA

value: Equimolar abundances of WT mir-16, tagged mir-30a and WT mir-125a


title: P1_PA14_P2633_N712.S522

description:
processed data file: P2633.tsv
CCYYKANXX_7_N712-S522-NX-xt


title: 16w+dox-rep3

description:
dataset1
H3

value: 16w +dox


title: S02: tagged mir-16, tagged mir-30a, tagged mir-125a (rep1)

description:
count_table_for_experimental_validation.txt
sample_2.sRNA

value: Equimolar abundances of tagged mir-16, tagged mir-30a and tagged mir-125a


title: 16w+dox-rep2

description:
dataset1
H2


title: HEK-293T transfection 10x rep2 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R2_sh-lib_10x_1000ng_NOR.sRNA

value: 10x of the MapToCleave library


title: 16w+dox-rep1

description:
dataset1
H1


title: P1_PA14_P2633_N714.S513

description:
processed data file: P2633.tsv
CCYYKANXX_7_N714-S513-NX-xt


title: HEK-293T transfection 10x rep4 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R4_sh-lib_10x_1000ng_NOR.sRNA


title: 16w+dox-1d-dox-rep2

description:
dataset1
H8


title: HEK-293T transfection 10x rep3 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R3_sh-lib_10x_1000ng_NOR.sRNA


title: P1_PA14_P2633_N712.S515

description:
processed data file: P2633.tsv
CCYYKANXX_7_N712-S515-NX-xt


title: P1_PA14_P2633_N712.S517

description:
processed data file: P2633.tsv
CCYYKANXX_7_N712-S517-NX-xt


title: Empty_P2633_N712.S513

description:
processed data file: P2633.tsv
CCYYKANXX_7_N712-S513-NX-xt

source_name: Empty


title: HEK-293T transfection 1x rep4 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R4_sh-lib_1x_1000ng_NOR.sRNA

value: 1x of the MapToCleave library


title: P1_UN14_P2633_N711.S522

description:
processed data file: P2633.tsv
CCYYKANXX_7_N711-S522-NX-xt


title: Retina Adult Vsx2SE WT

description:
Wildtype littermate Vsx2SE
Vsx2SE_FPKM_master.xlsx

data_processing:
scRNA-sequencing data was processed individually then aggregated using cellranger v3.0.2
scATAC-sequencing data was processed using cellranger-atac v1.0.1
Genome_build: mm10
Supplementary_files_format_and_content: For scRNA-seq tab delimited features(genes) and barcodes file and matrix file.
Supplementary_files_format_and_content: For scATAC-seq tab delimited fragments and barcodes file, matrix file, peaks bed file, and tab delimited peak_annotation

extract_protocol:
Retinas were removed, dissociated with papain, and run through a 4% BSA cushion. Cells were processed using the 10x genomics protocols. For bulk RNA, RNA was extracted from retina through trizol method. For ChIP, retina were removed and immediately place on dry ice.
Library construction was completed using the 10x RNA(v3) and ATAC-seq(v1) single cell kits

tag: age

value: adult

value: Vsx2SE Wildtype

value: RNA


title: HEK-293T transfection 1x rep3 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R3_sh-lib_1x_1000ng_NOR.sRNA


title: Retina Adult Vsx2SE KO

description:
Kknockout littermate Vsx2SE
Vsx2SE_FPKM_master.xlsx

value: Vsx2SE delta/delta


title: Retina Adult Vsx2SE HET

description:
Heterozygous littermate Vsx2SE
Vsx2SE_FPKM_master.xlsx

value: Vsx2SE +/delta


title: P1_PA14_P2633_N712.S516

description:
processed data file: P2633.tsv
CCYYKANXX_7_N712-S516-NX-xt


title: P1_PA14_P2633_N712.S518

description:
processed data file: P2633.tsv
CCYYKANXX_7_N712-S518-NX-xt


title: P1_UN14_P2633_N711.S520

description:
processed data file: P2633.tsv
CCYYKANXX_7_N711-S520-NX-xt


title: HEK-293T transfection 1x rep2 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R2_sh-lib_1x_1000ng_NOR.sRNA


title: HEK-293T transfection 1x rep1 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R1_sh-lib_1x_1000ng_NOR.sRNA


title: P1_UN14_P2633_N711.S521

description:
processed data file: P2633.tsv
CCYYKANXX_7_N711-S521-NX-xt


title: Retina Adult R1 KO scRNA-seq

description: Retina Adult R1 KO scRNA-seq

value: R1 delta/delta

value: 3’ RNA


title: P1_UN14_P2633_N711.S518

description:
processed data file: P2633.tsv
CCYYKANXX_7_N711-S518-NX-xt


title: Retina Adult Vsx2 input

description: ChIP-seq input

value: retina

value: DoubleConsensus delta/delta

value: DNA


title: Retina Adult Vsx2 ab2

description: ChIP-seq on DoubleConsensus KO retina with ab2 (Vsx2)

value: Vsx2 ab2 (Exalpha Biologicals Inc. catalog number X1180P)


title: HEK-293T transfection 10x rep1 sRNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R1_sh-lib_10x_1000ng_NOR.sRNA


title: Retina Adult Vsx2 ab1

description: ChIP-seq on DoubleConsensus KO retina with ab1 (Vsx2)

value: Vsx2 ab1 (Exalpha Biologicals Inc. catalog number X1179P)


title: shFEV-4

city: Suzhou

first: Jubin

last: Zhang

state: Jiangsu

address: Shizi street

institute: Soochow University

data_processing:
FastQC softwae was used to filter the raw data and then got the clean data.
Hisat2 was used to map the clean data to the reference genome sequences
Stringtie software was used  to the assembly the reads that mapped the genome.
Stringtie software was used to calculate the expression amount readcount. Then calculate the FPKM of the gene and transcript.
Genome_build: Homo_sapiens.GRCh38.92.gtf
Supplementary_files_format_and_content: Excel file include p-value or q-value and FPKM  for each Sample.

source_name: peripheral blood

growth_protocol: MV4-11 cells were cultured in RPMI medium supplemented with 10% FBS.

extract_protocol:
The total RNA was extracted  for libraries construction by the Triozol kit according the standard protocol. NEBNext Ultra RNA Library Prep Kit for Illumina (Cat#E7530S ) was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MV4-11 cells were sorted after transfected with NC-GFP or sh-FEV-GFP  for 3 days

tag: disease

value: acute monocytic leukemia

value: macrophage

tag: transfected with

value: shFEV


title: P1_UN14_P2633_N711.S516

description:
processed data file: P2633.tsv
CCYYKANXX_7_N711-S516-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: NC-1

value: NC-GFP


title: NC-2


title: Retina Adult DC KO

description:
Knockout Double Consensus
Vsx2SE_FPKM_master.xlsx

value: adult

value: RNA


title: shFEV-2


title: shFEV-3


title: Retina Adult R1 WT scRNA-seq

description: Retina Adult R1 WT scRNA-seq

value: R1 Wildtype


title: P1_UN14_P2633_N710.S520

description:
processed data file: P2633.tsv
CCYYKANXX_7_N710-S520-NX-xt


title: P1_UN14_P2633_N711.S515

description:
processed data file: P2633.tsv
CCYYKANXX_7_N711-S515-NX-xt


title: Retina Adult Cb KO

description:
Knockout Consensus B
Vsx2SE_FPKM_master.xlsx

value: ConsensusB delta/delta


title: Retina Adult R2 KO

description:
Knockout Region2
Vsx2SE_FPKM_master.xlsx

value: R2 delta/delta


title: P1_UN14_P2633_N710.S522

description:
processed data file: P2633.tsv
CCYYKANXX_7_N710-S522-NX-xt


title: P1_UN14_P2633_N711.S513

description:
processed data file: P2633.tsv
CCYYKANXX_7_N711-S513-NX-xt


title: Retina Adult R1 KO

description:
Knockout Region1
Vsx2SE_FPKM_master.xlsx

value: retina

value: R1 delta/delta


title: Retina Adult R3 KO

description:
Knockout Region3
Vsx2SE_FPKM_master.xlsx

value: R3 delta/delta


title: P1_UN14_P2633_N710.S518

description:
processed data file: P2633.tsv
CCYYKANXX_7_N710-S518-NX-xt


title: P1_UN14_P2633_N711.S517

description:
processed data file: P2633.tsv
CCYYKANXX_7_N711-S517-NX-xt


title: P1_UN14_P2633_N710.S517

description:
processed data file: P2633.tsv
CCYYKANXX_7_N710-S517-NX-xt


title: Retina Adult DC HET

description:
Heterozygous littermate Double Consensus
Vsx2SE_FPKM_master.xlsx

value: +/delta


title: P1_UN14_P2633_N710.S516

description:
processed data file: P2633.tsv
CCYYKANXX_7_N710-S516-NX-xt


title: shFEV-1


title: P1_UN14_P2633_N710.S521

description:
processed data file: P2633.tsv
CCYYKANXX_7_N710-S521-NX-xt


title: ko28-2 [snRNA-seq]

first: David

last: Beier

address: 1900 9th Avenue

department: CDBRM

institute: Seattle Children's Research Institute

data_processing:
Cell Ranger (for snRNA-seq experiments) or Cell Ranger ATAC (for snATAC-seq experiments) was used to demultiplex input files and generate feature-barcode matrices, which were then further analyzed via Seurat (RNA) or ArchR (ATAC). Specific details including software versions and parameters are described in Thomas, et al bioRxiv 2021.07.31.454254.
Genome_build: hg38
Supplementary_files_format_and_content: .tsv; fragment/feature/barcode matrices for each sample

source_name: Human induced pluripotent stem cell derived organoid

growth_protocol: Human induced pluripotent stem cells (hiPSCs) and Retinal Organoids were generated according to Olemacher et al., (2015) doi:10.1002/9780470151808.sc01h08s32 ; Gantner et al., (2020) doi:10.1056/NEJMoa1815111

extract_protocol:
Nuclear isolation from flash frozen tissue described in Thomas et al. bioRxiv 2021.07.31.454254; doi: https://doi.org/10.1101/2021.07.31.454254
10X Genomics scATAC-Seq and scRNA-Seq protocols. Detail described in Thomas et al. bioRxiv 2021.07.31.454254; doi: https://doi.org/10.1101/2021.07.31.454254
single-nucleus (sn)ATAC-Seq and snRNA-Seq

treatment_protocol: Enhancer knockout iPSCs generated as described in Thomas et al. bioRxiv 2021.07.31.454254; doi: https://doi.org/10.1101/2021.07.31.454254

tag: donor apparent sex

value: Female

tag: donor age

value: 58 years

tag: donor apparent race

value: caucasian

tag: postmortem interval

tag: molecule subtype

value: single nucleus RNA

tag: library type

value: Chromium Next GEM Single Cell 3’ GEM, Library & Gel  Bead Kit v3.1


title: wt28-3 [snRNA-seq]


title: Retina Adult Ca KO

description:
Knockout Consensus A
Vsx2SE_FPKM_master.xlsx

tag: genotype

value: ConsensusA delta/delta

tag: molecule type


title: ko28-3 [snRNA-seq]


title: ko28-1 [snRNA-seq]


title: Retina Adult Cb HET

description:
Heterozygous littermate Consensus B
Vsx2SE_FPKM_master.xlsx


title: P1_UN14_P2633_N710.S515

address: Parc del Taulí, 1

description:
processed data file: P2633.tsv
CCYYKANXX_7_N710-S515-NX-xt

tag: cell line

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: wt28-1 [snRNA-seq]


title: NckH_female_15wk_pathogenicCD4_rep5

city: Dallas

first: Eva Marie

last: Moresco

state: TX

address: 5323 Harry Hines Boulevard

department: Center for the Genetics of Host Defense

institute: University of Texas Southwestern Medical Center

description: Gene expression in female NOD/NckH mouse spleen CD4+CD25- T cells recovered at 15 weeks of age. This population is depleted of regulatory T cells (CD4+CD25+FoxP3+) and enriched in CD4+ pathogenic lymphocytes (CD4+CD62L-).

hyb_protocol: Sample hydridization (Agilent whole mouse genome oligo microarrays) was performed by Miltenyi Biotech (Cologne, Germany).

scan_protocol: Microarray probe fluorescence signals produced by the Agilent Feature Extraction (AFE) image analysis software were converted to expression values using Bioconductor Agi4x44PreProcess package with a custom annotation package. All the steps were performed by Miltenyi Biotech (Cologne, Germany).

source_name: Pathogenic Cd4

label_protocol: Preparation of RNA, amplification of RNA, sample labeling, sample hydridization (Agilent whole mouse genome oligo microarrays) scanning and data acquisition were performed by Miltenyi Biotech (Cologne, Germany).

growth_protocol: Not applicable

extract_protocol: Cell and islet pellets and tissues were lysed using SuperAmpTMlysis buffer (Miltenyi Biotech, Waldbronn, Germany) and stored at -80°C until all samples were collected. RNA quality and purity were assessed on the Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Islets of Langerhans: NOD/NckH and NOD/NckL male mice pancreata were perfused with a solution of collagenase P (0.6 mg/mL; Roche), dissected free from surrounding tissues and then digested at 37°C for 13 minutes. After extensive washes, islets were purified by hand-picking. NOD/NckH and NOD/NckL male mice spleen CD4+CD25- T cells recovered at 6 and 15 weeks of age. This population was depleted of regulatory T cells (CD4+CD25+FoxP3+) as previously described (You S, Belghith M, Cobbold S, Alyanakian MA, Gouarin C, Barriot S, et al. Autoimmune diabetes onset results from qualitative rather than quantitative age-dependent changes in pathogenic T-cells. Diabetes 2005; 54:1415-1422)

value: NOD/NckH

value: 15 weeks

tag: Sex


title: P1_UN14_P2633_N710.S513

description:
processed data file: P2633.tsv
CCYYKANXX_7_N710-S513-NX-xt

tag: cell type

tag: shRNA


title: wt28-2 [snRNA-seq]


title: ko20-3 [snRNA-seq]


title: Retina Adult R3 HET

description:
Heterozygous littermate Region3
Vsx2SE_FPKM_master.xlsx

tag: strain

value: adult

value: RNA


title: S07: tagged mir-16 variant 3, tagged mir-30a, tagged mir-125a (rep1)

address: SciLifeLab, Tomtebodavägen 23

description:
count_table_for_experimental_validation.txt
sample_7.sRNA

tag: treatment

value: Equimolar abundances of tagged mir-16 variant 3, tagged mir-30a and tagged mir-125a


title: Retina Adult R2 HET

description:
Heterozygous littermate Region2
Vsx2SE_FPKM_master.xlsx

value: retina

tag: age


title: NckH_female_15wk_pathogenicCD4_rep4

data_processing: Microarray probe fluorescence signals produced by the Agilent Feature Extraction (AFE) image analysis software were converted to expression values using Bioconductor Agi4x44PreProcess package with a custom annotation package. All the steps were performed by Miltenyi Biotech (Cologne, Germany).


title: P1_UN14_P2633_N707.S522

description:
processed data file: P2633.tsv
CCYYKANXX_7_N707-S522-NX-xt

tag: protocol


title: P1_UN14_P2633_N707.S521

description:
processed data file: P2633.tsv
CCYYKANXX_7_N707-S521-NX-xt


title: ko20-2 [snRNA-seq]


title: Retina Adult DC WT

description:
Wildtype littermate Double Consensus
Vsx2SE_FPKM_master.xlsx

value: Wildtype


title: ko20-1 [snRNA-seq]


title: P1_UN14_P2633_N707.S520

description:
processed data file: P2633.tsv
CCYYKANXX_7_N707-S520-NX-xt


title: wt20-3 [snRNA-seq]


title: P1_UN14_P2633_N707.S518

description:
processed data file: P2633.tsv
CCYYKANXX_7_N707-S518-NX-xt


title: Retina Adult Ca HET

description:
Heterozygous littermate Consensus A
Vsx2SE_FPKM_master.xlsx

value: +/delta


title: NckH_female_15wk_pathogenicCD4_rep2

value: Female


title: Retina Adult Cb WT

description:
Wildtype littermate Consensus B
Vsx2SE_FPKM_master.xlsx


title: 6wwdox-rep1

description:
dataset2
E16

value: 6w +dox

tag: mouse strain

value: shRB

value: female


title: P1_UN14_P2633_N707.S517

description:
processed data file: P2633.tsv
CCYYKANXX_7_N707-S517-NX-xt


title: Retina Adult Ca WT

description:
Wildtype littermate Consensus A
Vsx2SE_FPKM_master.xlsx


title: NckH_female_15wk_pathogenicCD4_rep3


title: wt20-2 [snRNA-seq]

tag: donor apparent sex

value: 58 years

value: caucasian

value: single nucleus RNA

value: Chromium Next GEM Single Cell 3’ GEM, Library & Gel  Bead Kit v3.1


title: Retina Adult R3 WT

description:
Wildtype littermate Region3
Vsx2SE_FPKM_master.xlsx


title: NckH_female_15wk_pathogenicCD4_rep1


title: P1_UN14_P2633_N707.S516

description:
processed data file: P2633.tsv
CCYYKANXX_7_N707-S516-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: P1_UN14_P2633_N707.S515

description:
processed data file: P2633.tsv
CCYYKANXX_7_N707-S515-NX-xt


title: Retina Adult R2 WT

description:
Wildtype littermate Region2
Vsx2SE_FPKM_master.xlsx

value: adult


title: ko12-3 [snRNA-seq]

tag: donor age


title: Retina Adult R1 HET

description:
Heterozygous littermate Region1
Vsx2SE_FPKM_master.xlsx

value: RNA


title: Empty_P2633_N707.S513

description:
processed data file: P2633.tsv
CCYYKANXX_7_N707-S513-NX-xt


title: NckH_female_6wk_pathogenicCD4_rep4

description: Gene expression in female NOD/NckH mouse spleen CD4+CD25- T cells recovered at 6 weeks of age. This population is depleted of regulatory T cells (CD4+CD25+FoxP3+) and enriched in CD4+ pathogenic lymphocytes (CD4+CD62L-).

value: NOD/NckH

value: 6 weeks


title: NckH_female_6wk_pathogenicCD4_rep2


title: NckH_female_6wk_pathogenicCD4_rep3


title: Retina Adult R1 WT

description:
Wildtype littermate Region1
Vsx2SE_FPKM_master.xlsx

value: retina

value: Wildtype


title: P1_PA4_P2633_N706.S522

description:
processed data file: P2633.tsv
CCYYKANXX_7_N706-S522-NX-xt


title: ko12-1 [snRNA-seq]

value: Female

tag: donor apparent race


title: wt12-3 [snRNA-seq]

tag: postmortem interval


title: Retina Adult WT scATAC-seq

description: Retina Adult Wildtype scATAC-seq

value: DNA


title: Retina E14.5 WT scATAC-seq, rep1

description: Retina E14.5 Wildtype scATAC-seq Rep1


title: P1_PA4_P2633_N706.S521

description:
processed data file: P2633.tsv
CCYYKANXX_7_N706-S521-NX-xt


title: NckH_male_15wk_pathogenicCD4_rep5

description: Gene expression in male NOD/NckH mouse spleen CD4+CD25- T cells recovered at 15 weeks of age. This population is depleted of regulatory T cells (CD4+CD25+FoxP3+) and enriched in CD4+ pathogenic lymphocytes (CD4+CD62L-).

value: 15 weeks

value: Male


title: wt20-1 [snRNA-seq]

value: 58 years

tag: molecule subtype


title: NckH_female_6wk_pathogenicCD4_rep5


title: NckH_male_15wk_pathogenicCD4_rep4


title: P1_PA4_P2633_N706.S520

description:
processed data file: P2633.tsv
CCYYKANXX_7_N706-S520-NX-xt


title: Retina E14.5 WT scATAC-seq, rep2

description: Retina E14.5 Wildtype scATAC-seq Rep2


title: wt12-2 [snRNA-seq]

value: caucasian

tag: library type


title: NckH_female_6wk_pathogenicCD4_rep1


title: wt12-1 [snRNA-seq]

value: single nucleus RNA


title: NckH_male_15wk_pathogenicCD4_rep3


title: P1_PA4_P2633_N706.S517

description:
processed data file: P2633.tsv
CCYYKANXX_7_N706-S517-NX-xt


title: ko5-2 [snRNA-seq]

value: Chromium Next GEM Single Cell 3’ GEM, Library & Gel  Bead Kit v3.1


title: P1_PA4_P2633_N706.S516

description:
processed data file: P2633.tsv
CCYYKANXX_7_N706-S516-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line


title: NckH_male_15wk_pathogenicCD4_rep2


title: ko5-1 [snRNA-seq]


title: Retina Adult WT scRNA-seq

description: Retina Adult Wildtype scRNA-seq

tag: genotype

value: Vsx2SE Wildtype;Nrl-GFP

value: 3’ RNA


title: Retina E14.5 SE KO scRNA-seq

description: Retina E14.5 SE KO scRNA-seq

value: Vsx2SE delta/delta

tag: molecule type


title: NckH_male_6wk_pathogenicCD4_rep4

description: Gene expression in male NOD/NckH mouse spleen CD4+CD25- T cells recovered at 6 weeks of age. This population is depleted of regulatory T cells (CD4+CD25+FoxP3+) and enriched in CD4+ pathogenic lymphocytes (CD4+CD62L-).


title: NckH_male_6wk_pathogenicCD4_rep5


title: Retina E14.5 WT scRNA-seq

description: Retina E14.5 Wildtype scRNA-seq


title: P1_PA4_P2633_N706.S515

description:
processed data file: P2633.tsv
CCYYKANXX_7_N706-S515-NX-xt

tag: cell line

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: Retina E14.5 SE KO RNA-seq

description:
Retina E14.5 Vsx2SE KO bulk RNA-seq
DE_single_subject_protein_coding_ko_vs_wt.txt

value: RNA


title: P1_PA4_P2633_N706.S513

description:
processed data file: P2633.tsv
CCYYKANXX_7_N706-S513-NX-xt


title: P1_PA4_P2633_N706.S518

description:
processed data file: P2633.tsv
CCYYKANXX_7_N706-S518-NX-xt


title: wt5-1 [snRNA-seq]


title: NckH_male_6wk_pathogenicCD4_rep3

value: NOD/NckH

value: 6 weeks

tag: Sex


title: HEK-293T transfection 1x rep4 DNA

description:
count_table_of_MapToCleave_sequences_in_HEK_NIH3T3_MEF_HeLa_cells.txt
HEK_R4_sh-lib_1x_1000ng_NOR.DNA

tag: cell type

value: 1x of the MapToCleave library

value: plasmid DNA


title: Retina Adult SE KO scRNA-seq

description: Retina Adult SE KO scRNA-seq

value: retina

value: adult

value: Vsx2SE delta/delta;NRL-GFP


title: P1_PA4_P2633_N705.S522

description:
processed data file: P2633.tsv
CCYYKANXX_7_N705-S522-NX-xt

tag: shRNA


title: wk28-2 [snATAC-seq]

value: Female

value: 58 years

value: caucasian

value: single nucleus ATAC

value: Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1


title: ko12-2 [snRNA-seq]

value: single nucleus RNA

value: Chromium Next GEM Single Cell 3’ GEM, Library & Gel  Bead Kit v3.1


title: NckH_male_6wk_pathogenicCD4_rep2

tag: strain

value: Male


title: wk28-1 [snATAC-seq]


title: P1_PA4_P2633_N705.S521

description:
processed data file: P2633.tsv
CCYYKANXX_7_N705-S521-NX-xt

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1

value: Smart-seq2; full-length RNA-seq


title: NckH_male_15wk_pathogenicCD4_rep1

value: NOD/NckH

value: 15 weeks


title: wt5-2 [snRNA-seq]


title: NckH_male_6wk_pathogenicCD4_rep1

value: 6 weeks


title: wk20-2 [snATAC-seq]


title: NckL_female_15wk_pathogenicCD4_rep5

description: Gene expression in female NOD/NckL mouse spleen CD4+CD25- T cells recovered at 15 weeks of age. This population is depleted of regulatory T cells (CD4+CD25+FoxP3+) and enriched in CD4+ pathogenic lymphocytes (CD4+CD62L-).

value: NOD/NckL


title: NckL_female_15wk_pathogenicCD4_rep4


title: P1_PA4_P2633_N705.S520

description:
processed data file: P2633.tsv
CCYYKANXX_7_N705-S520-NX-xt


title: NckL_female_15wk_pathogenicCD4_rep3


title: wk20-1 [snATAC-seq]


title: P1_PA4_P2633_N705.S518

description:
processed data file: P2633.tsv
CCYYKANXX_7_N705-S518-NX-xt


title: P1_PA4_P2633_N705.S517

description:
processed data file: P2633.tsv
CCYYKANXX_7_N705-S517-NX-xt


title: wk5-2 [snATAC-seq]


title: P1_PA4_P2633_N705.S516

description:
processed data file: P2633.tsv
CCYYKANXX_7_N705-S516-NX-xt


title: iPSC-2 [snATAC-seq]

source_name: Human induced pluripotent stem cells


title: wk5-1 [snATAC-seq]


title: 25-shGAL #73_4 PALM  #3

description: Neural fraction cells from strom derived from shGAL orthotopic SCC25 oral carcinoma cell line xenografts exposed to PA-rich diet

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method as implemented in affy Bioconductor R package

source_name: shGAL / SCC25 oral carcinoma cell line / PA-rich diet

extract_protocol: RNA was isolated using magnetic beads. Library preparation and amplification were performed as described by Gonzalez et al., 2010.

tag: sample id

tag: scan batch

tag: diet

value: PA-rich diet

tag: sh

value: shGAL

value: SCC25 oral carcinoma cell line


title: P1_PA4_P2633_N705.S515

description:
processed data file: P2633.tsv
CCYYKANXX_7_N705-S515-NX-xt

tag: protocol


title: iPSC-1 [snATAC-seq]

tag: donor apparent sex

tag: donor age

value: 61 years


title: NckL_female_15wk_pathogenicCD4_rep2

tag: age

value: Female


title: P1_PA4_P2633_N705.S513

description:
processed data file: P2633.tsv
CCYYKANXX_7_N705-S513-NX-xt


title: P1_PA4_P2633_N704.S522

description:
processed data file: P2633.tsv
CCYYKANXX_7_N704-S522-NX-xt


title: NckL_female_15wk_pathogenicCD4_rep1


title: 25-shGAL #73_4 CT  #3

description: Neural fraction cells from strom derived from shGAL orthotopic SCC25 oral carcinoma cell line xenografts exposed to control diet

source_name: shGAL / SCC25 oral carcinoma cell line / control diet

value: control diet


title: 25-shGAL #73_4 PALM  #2


title: NckL_female_6wk_pathogenicCD4_rep3

description: Gene expression in female NOD/NckL mouse spleen CD4+CD25- T cells recovered at 6 weeks of age. This population is depleted of regulatory T cells (CD4+CD25+FoxP3+) and enriched in CD4+ pathogenic lymphocytes (CD4+CD62L-).


title: NckL_female_6wk_pathogenicCD4_rep5


title: P1_PA4_P2633_N704.S521

description:
processed data file: P2633.tsv
CCYYKANXX_7_N704-S521-NX-xt


title: 25-shGAL #73_4 PALM  #1


title: 25-shGAL #73_4 CT  #1


title: NckL_female_6wk_pathogenicCD4_rep2


title: 25-shGAL #73_4 CT  #2


title: Hu37 [snRNA-seq]

source_name: Adult human retina

value: 25 years

tag: donor apparent race

value: caucasian

tag: postmortem interval

tag: molecule subtype


title: NckL_female_6wk_pathogenicCD4_rep4


title: Hu8  [snATAC-seq]

value: 52 years

value: single nucleus ATAC

tag: library type

value: Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1


title: P1_PA4_P2633_N704.S520

description:
processed data file: P2633.tsv
CCYYKANXX_7_N704-S520-NX-xt

tag: cell line

value: oral squamous cell carcinoma (OSCC) cell line

value: control pLKO.1


title: Hu7 [snRNA-seq]

value: 50 years

value: black

value: single nucleus RNA

value: Chromium Next GEM Single Cell 3’ GEM, Library & Gel  Bead Kit v3.1


title: NckL_female_6wk_pathogenicCD4_rep1

value: NOD/NckL

value: 6 weeks

tag: Sex