title: 569T

city: Kaohsiung

first: Shu-Chi

last: Wang

address: No.100, Shin-Chuan 1st Road, Sanmin Dist.,

department: Department of Medical Laboratory Science and Biotechnology.

country: Taiwan

institute: Kaohsiung Medical University.

data_processing:
The reads were aligned with TopHat 2.0.13 to GRCh37 with default parameters and then were assembled by Cufflink 2.2.1, using Ensembl v75 annotations.
Transcript abundance was measured in fragments per kb of exon per million fragments mapped (FPKM).
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: NBNC-HCC

extract_protocol:
Total RNA was extracted from T/ANT tissues using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA) following the recommendations of the manufacturer. The quality of the total RNA was evaluated in an Agilent 2100 bioanalyzer (Agilent, Palo Alto, CA, USA) using an RNA 6000 Nano LabChip kit (Agilent, Palo Alto, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: section

value: Tumor

tag: etiology

value: NBNC

tag: bclc stage


title: 565T

status: Public on Jul 22 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: B


title: 569N

value: Non-tumor


title: 450N


title: 475T

source_name: HCV-HCC

value: HCV


title: 565N


title: 519T

value: A


title: 519N


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , DMSO treated, S2 infected, replicate 3

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description:
polyA RNA extracted from whole cells
Hsp90_gene_counts.tsv.gz

data_processing:
PolyA-RNA and total-RNA sequencing reads were mapped to the hg38 version of the human genome using STAR (version 2.7.1a) combined with the GENCODE (v30) annotation and the non-standard parameters (--sjdbOverhang 300 --twopassMode Basic --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 200000 --alignIntronMax 200000).
Small-RNA sequencing reads were preprocessed using cutadapt (version 2.9) in two passes, first trimming i) the Illumina TruSeq adaptor at the 3’ end, ii) all 3’ end bases with mean Phred score below 30 and iii) the three 5’end overhang nucleotides associated with the Clonetech library preparation protocol. In the second pass, poly(A)-tails were trimmed. Trimmed reads were mapped to hg38 using bowtie (version 1.2.2) and the non-standard parameters (-q -n 1 -e 80 -l 18 -a -m 5 --best --strata). The expression of known miRNAs (miRBase 22 annotation) was estimated using mirdeep2 (version 2.0.0.7) and standard parameters. Gene expression was estimated using FeatureCounts (version 1.5.1) and the non-standard parameters (-F GTF -t exon -g gene_id -C -M --fraction -p -s 2 -O -T 16 -B -Q 4).
For scRNA-seq, data was processed using the pigx pipeline version 1.1.4 (http://bioinformatics.mdc-berlin.de/pigx/, Wurmus et al. 2018 doi: 10.1093/gigascience/giy123). Genomes used were hg19, AY310120 (SARS-CoV-1) and MN908947 (SARS-CoV-2)
Genome_build: hg38, hg19
Supplementary_files_format_and_content: tab separated values

molecule: polyA RNA

source_name: Calu3 cells

growth_protocol: H1299, Caco-2 and Calu-3 cells were grown in DMEM/10%FCS/PenStrep/non-essential amino acids/L-glutamine/pyruvate

extract_protocol:
For polyA/total/small RNA-seq, cells were lysed in Trizol and RNA extracted using standard methods. For single-cell RNA-sequencing, cells were fixed in methanol and stored at -80 degrees until further processing. Rehydration was done as described in Alles et al. 2017 (doi: 10.1186/s12915-017-0383-5)
PolyA and total RNA-seq libraries were constructed using the NEB Ultra II Directional RNA Library Prep Kit. SmallRNA-seq libraries were constructed using the Clontech SMARTer smRNA-Seq Kit. Single-cell libraries were constructed using a a Nadia device (Dolomite Bio) according to version 1.8 of the manufacturer's protocol, except that the second-strand synthesis step as described in Hughes et al. 2019 (doi: doi.org/10.1101/689273) was included after the exonuclease step.

treatment_protocol: Infections were done by adding the appropriate amount of virus stock solution (produced in Vero E6 cells) at an MOI of 0.3  directly to the cells. For mock infections, supernatant from non-infected Vero E6 cells was used.

tag: infection

tag: moi

tag: time point


title: 475N


title: 450T


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , DMSO treated, S2 infected, replicate 1


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , DMSO treated, mock infected, replicate 2

value: mock


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , 800 nM Onalespib treated, S2 infected, replicate 2


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , 800 nM Ganetespib treated, S2 infected, replicate 2


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , 800 nM Ganetespib treated, S2 infected, replicate 3


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , 800 nM Ganetespib treated, S2 infected, replicate 1


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , 800 nM 17-AAG treated, S2 infected, replicate 2


title: H2228_H1975_A549_H838_HCC827_Mixture_10X_90percent_sample

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Basecalling for the Illumina short-read data was performed using RTA 2.4.11 and fastq files were generated using Cell Ranger (3.1). Fastq files for the PromethION long-read data were generated by Guppy (3.1.5).
Illumina short reads were aligned to the mouse genome using Rsubread (1.29.6). Long reads were aligned using minimap2 (2.17) with default parameters.
Short read data were analysed using scPipe (1.4.0) to generate a gene count matrix. Nanopore long-read data were analysed by FLAMES (0.1.0) to generate an isoform count matrix along with isoform annotation.
Genome_build: GRCh38 patch 10
Supplementary_files_format_and_content: Lib10.csv: 1000 most abundant cell barcodes with cell ids, barcode sequence and counts on the Lib10 sample
Supplementary_files_format_and_content: gene_count_Lib10.csv: Count matrix with samples along the columns and genes along the rows for the Lib10 sample
Supplementary_files_format_and_content: Lib90.csv: 3000 most abundant cell barcodes with cell ids, barcode sequence and counts on the Lib90 sample
Supplementary_files_format_and_content: gene_count_Lib90.csv: Count matrix with samples along the columns and genes along the rows for the Lib90 sample
Supplementary_files_format_and_content: isoform_annotated.filtered.gff3: Isoform annotation derived from long-read data (Lib10 sample)
Supplementary_files_format_and_content: transcript_count.csv: Transcript counts from long-read data (Lib10 sample)

source_name: lung adenocarcinoma

growth_protocol: The human lung adenocarcinoma cell lines H2228, H1975, A549, H838 and HCC827 were retrieved from ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum (FCS) and 1% Penicillin-Streptomycin.  The cells were grown independently at 37C  with 5% carbon dioxide until near 100% confluency.

extract_protocol:
The cells were counted using Chamber Slide and roughly 2 million cells from each cell line were mixed and processed by 10X.
Cell isolation and library construction was performed using a Chromium 10X v3 protocol that was adapted to accommodate both Illumina and Nanopore sequencing. The 90% sample was sequenced by Illumina short-read sequencing only and the 10% sample was sequenced by both Illumina short-read and Oxford Nanopore Technologies long-read sequencing according to the protocol at dx.doi.org/10.17504/protocols.io.8d9hs96.

tag: barcode coordinate

value: bases 1 to 16 on R1

tag: umi coordinate

value: bases 17 to 28 on R1


title: H2228_H1975_A549_H838_HCC827_Mixture_10X_10percent_sample


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , 800 nM 17-AAG treated, S2 infected, replicate 3


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , DMSO treated, S2 infected, replicate 2


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , DMSO treated, S2 infected, replicate 2


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , DMSO treated, mock infected, replicate 3


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , 800 nM 17-AAG treated, S2 infected, replicate 1


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , DMSO treated, S2 infected, replicate 1


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , DMSO treated, mock infected, replicate 3


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 2 , DMSO treated, mock infected, replicate 1


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , 800 nM Onalespib treated, S2 infected, replicate 1


title: 7002v2A-A_run7

city: NEW YORK

first: Miriam

last: Merad

state: New York

address: 1470 Madison Ave, Room 5-301

department: Oncological Sciences

country: USA

institute: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI

data_processing:
Library strategy: CITE-seq
Transcriptomic and TCR library reads were aligned and quantified using Cellranger v3.1.0 (10x Genomics). CITEseq ADT and CITEseq HTO reads were queried for antibody- and cell-specific oligonucleotide sequence barcodes in the designated read positions, including antibody sequences within a Hamming distance of 1 from the reference, using the feature-indexing function of Cellranger. TCR data was aligned using Cellranger vdj function with default parameters.
Genome_build: GRCh38/84
Supplementary_files_format_and_content: Raw feature-barcode matrices, containing UMI counts in Market Exchange Format. Also contains tsv files with feature and barcode sequences to row and column indices, respectively.

source_name: lung

extract_protocol: Cell suspensions were split and barcoded using “hashing antibodies” staining beta-2-microglobulin and CD298 and conjugated to “hash-tag” oligonucleotides (HTOs). Hashed samples were pooled and stained with CITEseq antibodies that had been purchased either from the Biolegend TOTALseq catalog or conjugated using the Thunder-Link PLUS Oligo Conjugation kit (Expedeon). Stained cells were then encapsulated for single-cell reverse transcription using the 10X Chromium platform and libraries were prepared as previously described (Stoeckius, Marlon, et al. "Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics." Genome biology 19.1 (2018): 1-12.).

value: lung

tag: tissue type

value: Normal, Tumor, PBMC, spiked mouse cells

tag: patient id

tag: libraryname

tag: Sex

value: male

tag: library type

value: ADT

tag: 10x chromium encapsulation kit


title: 7002T5-T_run12

data_processing:
Library strategy: TCR
Transcriptomic and TCR library reads were aligned and quantified using Cellranger v3.1.0 (10x Genomics). CITEseq ADT and CITEseq HTO reads were queried for antibody- and cell-specific oligonucleotide sequence barcodes in the designated read positions, including antibody sequences within a Hamming distance of 1 from the reference, using the feature-indexing function of Cellranger. TCR data was aligned using Cellranger vdj function with default parameters.
Genome_build: GRCh38/84
Supplementary_files_format_and_content: Raw feature-barcode matrices, containing UMI counts in Market Exchange Format. Also contains tsv files with feature and barcode sequences to row and column indices, respectively.

extract_protocol: TCRseq was performed using the Chromium Single Cell 5’ VDJ kit, following manufacturer’s instructions.

value: TCR


title: Tkod_65deg_mock_rep2

status: Public on Jul 23 2020

city: Tel Aviv

first: Aldema

last: Sas-Chen

state: Israel

address: Tel Aviv University

department: Shmunis School of Biomedicine and Cancer Research

country: Israel

institute: Tel Aviv University

data_processing:
Library strategy: ac4C-seq
alignment using STAR (V. 2.5.3a)
base-calling using JACUSA v2.0.0 under default parameters
calculation of misincorporation rates per base
Genome_build: ASM996v1 for Thermococcus kodakarensis, ASM27560v1 for Pyrococcus furiosus, ASM15120v2 was used for Thermococcus sp. AM4, ASM700v1 for Sulfolobus solfataricus and ASM9166v1 for Methanocaldococcus jannaschii. For human GRCh37/hg19 with UCSC Genes annotations. For Saccharomyces cerevisiae samples the sacCer3 assembly.
Supplementary_files_format_and_content: TableS2_SasChen.xlsx an excel file detailing ac4C sites identified in each organism including the level of modification of each site.

organism: Thermococcus kodakarensis

source_name: archaeal cells

growth_protocol: T. kodakarensis and T. sp AM4 strains – TS559 can derivatives thereof – were grown as previously described (Santangelo et al. 2007; Hileman and Santangelo 2012; Gehring et al. 2017) in artificial sea water (ASW) medium supplemented with vitamins and trace minerals. Pyrococcus furiosus strain COM1 was cultured at 75-95˚C in an artificial sea water based medium supplemented with cellobiose, maltose, yeast extract, S˚, trace minerals, cysteine and sodium tungstate as previously described (Lipscomb et al, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Apr. 2011, p. 2232–2238).

extract_protocol:
Total RNA was isolated from T. kodakarensis using TRIZOL according to manufacturer’s protocol. For the indicated samples of T. kodakarensis ,rRNAs were depleted according to  Morlan et al.(Morlan et al. 2012) using reagents provided in the NEBNext® rRNA Depletion Kit (NEB #E6310). For indicated samples purifications of T. kodakarensis ribosomes of the wild-type and TkNat10 knockout were conducted similar to previously documented procedures (Matzov et al. 2017).
Fragmentation, 3' adapter ligation, cDNA synthesis, second adapter ligation and enrichment

treatment_protocol: growth at various temperatures

tag: genetic background

value: WT

tag: treatment

tag: growth condition

value: 65 degrees


title: IN190329

description: patient did not consent to sharing of raw reads

data_processing:
Transcriptomic and TCR library reads were aligned and quantified using Cellranger v3.1.0 (10x Genomics). CITEseq ADT and CITEseq HTO reads were queried for antibody- and cell-specific oligonucleotide sequence barcodes in the designated read positions, including antibody sequences within a Hamming distance of 1 from the reference, using the feature-indexing function of Cellranger. TCR data was aligned using Cellranger vdj function with default parameters.
Genome_build: GRCh38/84
Supplementary_files_format_and_content: Raw feature-barcode matrices, containing UMI counts in Market Exchange Format. Also contains tsv files with feature and barcode sequences to row and column indices, respectively.

extract_protocol: 10,000 cells were loaded onto a 10X Chromium single-cell encapsulation chip according to manufacturer instructions. Libraries were prepared according to manufacturer instructions. QC of cDNA and final libraries was performed using CyberGreen qPCR library quantification assay. Sequencing was performed on Illumina sequencers to a depth of at least 80 million reads per library.

value: Normal

value: female

value: GEX


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , DMSO treated, S2 infected, replicate 3


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , DMSO treated, mock infected, replicate 1


title: IT190329

value: Tumor


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , 800 nM Onalespib treated, S2 infected, replicate 3


title: 5TEST1N-T_run329


title: 5TEST1T-T_run329


title: 5TEST1N_run330


title: polyA RNA from Calu3 cells, Hsp90 Inhibitors Exp. 1 , DMSO treated, mock infected, replicate 2


title: 7002N5-T_run12


title: 7002v2A_run7


title: lib40_HCCC7BGX2


title: 7001v2D-H_run1

value: HTO


title: 7001T5-T_run5


title: 714N_run590


title: 7001v2B-H_run1


title: 714T_run590


title: 7001v2A-H_run1


title: 5TEST1T_run330


title: 7001v2A-A_run1


title: SK1_ecm11Δ_1

city: New York

first: Hajime

last: Murakami

state: NY

address: 1275 york ave

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: Spo11-associated DNA oligonucleotides

library_source: genomic

data_processing:
Base calls perfomed using HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were clipped from reads using fastx_clipper, part of the FASTX Toolkit 0.0.13.2, with parameters -l 15 -n -v -Q33 -i
First five bases (diffusion primer added in library prep) in each sequence were trimmed and trimmed sequence was recorded in the FASTQ ID tag for downstream tracking
Clipped reads were mapped using SHRiMP 2.1.1b with parameters -N 15 -U -g -1000 -q -1000 -m 10 -i -20 -h 100 -r 50% -n 1 -s 1111111111,11110111101111,1111011100100001111,1111000011001101111 -o 1001 -Q -E --sam-unaligned --strata
Sequences clipped from a read during mapping should be polyC on the 3' end or polyG on the 5' end. If clipped bases were not polyC or polyG the alignment score was corrected by deducting the mismatch score for each non-C,G base in the clipped sequence.
Maps of 5' ends of sequence reads were compiled and analyzed in R (RStudio version 0.98.1091, R version 3.0.1)
Genome_build: For wild-derived S. cerevisiae strains YPS128 and UWOPS03-461.4, reads were mapped to the SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645; for S. paradoxus YPS138, reads were mapped to the strain's genome assembly from SGRP (Saccharomyces Genome Resequencing Project, Wellcome Trust Sanger Institute); for S. mikatae IFO1815 and S. kudriavzevii ZP591, reads were mapped to the strains' genome assemblies from Scannell et al. 2011 G3 1: 11-25, available on http://www.saccharomycessensustricto.org.
Supplementary_files_format_and_content: tab delimited text files include Spo11-oligo hitcount at each nucleotide position in the genome

molecule: genomic DNA

organism: Saccharomyces cerevisiae SK1

source_name: Saccharomyces cerevisiae

growth_protocol: For samples 1-8: Cells were grown in two stages of SPS (0.5% yeast extract, 2% peptone, 2% glucose) pre-growth culturing beofre transfeering into sporulation medium. For samples 9-10:  Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 13.5–14 hr at 30ºC, harvested, resuspended in 2% potassium acetate, and sporulated at 30ºC.

extract_protocol:
Based on Pan et al. 2011 Cell 144:719-731. Whole cell extracts were prepared by grinding frozen cells in a bead mill and resuspending powder in 10%TCA. Pellets were then extracted with SDS and soluble protein was subjected to affinity purification of Spo11-Flag fusion with Protein-G Dynabeads (for samples 1-8) or PrA fusion with IgG Sepharose Fast Flow beads (for samples 9-11). Protein was digested with proteinase K and Spo11-associated oligonucleotides were recovered by ethanol precipitation.
Based on Pan et al. 2011 Cell 144:719-731. Oligonucleotides were tailed with ribo-G using rGTP and terminal transferase, then ligated to duplex DNA adaptors with a dC overhang using T4 RNA ligase 2. Complementary strands were synthesized with Klenow, then purified by denaturing polyacrylamide electrophoresis. Purified complementary strands were subjected to 3' tailing with ribo-G using rGTP and terminal transferase, then another duplex adaptor was ligated using T4 RNA ligase 2. Ligated material was amplified with 16 cycles of PCR to add Illumina HiSeq adaptors. For sample 5, a spike-in oligonucleotides were added during library preparation to increase DNA amount, sequece is: TGGATCCGTGGAATAATGCACAATT

tag: strain

tag: epitope tag

value: epitope tag:Spo11-Flag

tag: meiotic time-point

value: meiotic time-point:5 hr in meiosis

value: meiotic Saccharomyces cerevisiae culture


title: 630TN_run449

tag: tissue

value: Normal, Tumor


title: lib39_HCCC7BGX2


title: 7002v2A-H_run7


title: 596TN2_run420


title: 626TN1-H_run438


title: 7001T5_run0


title: 626TN2-H_run438


title: 7001N5-T_run5


title: 7001v2C-H_run1


title: 7001v2C-A_run1


title: 596TN1_run420


title: 593TN-A_run404


title: 626TN1_run507


title: 593TN_run402


title: 7001N5_run4


title: 626TN2-A_run513


title: 7001v2D-A_run1


title: 7001N5_run0


title: 626TN2_run508


title: 584TN2-H_run404


title: 626TN1-A_run513


title: 596TN2-H_run420


title: 584TN2_run406


title: 596TN2-A_run411


title: 630TN-H_run447


title: 584TN1-A_run405


title: 596TN1-H_run404


title: 7001v2B-A_run1


title: 630TN-A_run448


title: 578T


title: 584TN2-A_run405


title: 581T_run406


title: 584TN2_run407


title: 572N_run394


title: 584TN1_run407


title: 578N


title: 572T_run394


title: 584TN1-H_run402


title: 593TN-H_run404


title: 596TN1-A_run411


title: 584TN1_run406


title: 572N_run395


title: 581N_run406


title: 581TN-H_run393


title: 581TN_run393


title: 581T_run407


title: 572T_run395


title: 570T_run395


title: 581TN-A_run393


title: 581N_run407


title: 564T


title: 571T_run394


title: 571T_run395


title: 570T_run394


title: 564N


title: 569N_run393


title: 558T_run378


title: 532T_run344


title: BM174N_run332


title: 464T


title: 514N_run323


title: 460T_run276


title: 460N_run278


title: 458T


title: 460T_run278


title: 570N_run395


title: 532N_run344


title: BM174T_run332


title: 570N_run394


title: 514T_run323


title: 464N


title: tumor_410_H3TWNBGX3


title: 569T_run393


title: 460N_run276


title: 458N


title: normal_408_H3TWNBGX3


title: tumor_408_H3TWNBGX3


title: normal_410_H3TWNBGX3


title: 406N_run214


title: 403T_run214


title: 403N_run214


title: 178_run338


title: 378N_run199


title: normal_377_HGKWGBGX2


title: tumor_377_HGKWGBGX2


title: tumor_371_HYJJ7BGXY


title: tumor_370_HYJJ7BGXY


title: normal_371_HYJJ7BGXY


title: BE2C_Flag-LIN28Bmut_yDox_input

city: Hangzhou

first: Ting

last: Tao

state: Zhejiang

address: 3333 Binsheng Road

country: China

institute: Children's Hospital, Zhejiang University School of Medicine

data_processing:
ChIP-Seq reads were aligned to the hg19 revision of the human reference genome using Bowtie with parameters -k 2 -m 2 –best and -l set to the read length.
WIG files were made using MACS 1.4 with parameters -w -S –space=50 –nomodel –shiftsize=200 and subsequently normalized for the millions of mapped reads in each sample.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Neuroblastoma

growth_protocol: The BE2C, CHP134 or Kelly neuroblastoma cells were maintained in RPMI 1640 Medium (GIBCO) supplemented with 10% fetal bovine serum (Sigma) and 1X penicillin-streptomycin (GIBCO).

extract_protocol:
Lysates were clarified from sonicated nuclei and target bound fragments were isolated with antibody.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: Cells were treated (yDox) with doxycycline at 50 ng/ml for 3 days.

tag: cell line

tag: cell type

value: Neuroblastoma cells


title: LIN28Bmut_yDox_2

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were aligned to the hg19 revision of the human reference genome using TopHat with parameters –library-type fr-firststrand –no-novel-juncs and -G set to a GTF of Refseq genes downloaded 7/5/2017.
Counts of reads covering genes were quantified using HTSeq-count with parameters -I gene_id –stranded=reverse -f bam -m intersection-strict and a GTF of Refseq genes downloaded 7/5/2017.
Differentially expressed genes were called by the R Bioconductor package DESeq2.
Genome_build: hg19

growth_protocol: The BE2C neuroblastoma cells were maintained in RPMI 1640 Medium (GIBCO) supplemented with 10% fetal bovine serum (Sigma) and 1X penicillin-streptomycin (GIBCO).

extract_protocol:
Total RNA was depleted of ribosomal RNA with the SMARTer Universal Low Input RNA Kit (Clontech). Enriched mRNA was then applied to library preparation according to manufacturer’s protocol (NEBNext Ultra). After repeated quality control for average DNA input size of 300 bp, the samples were sequenced on a Illumina NextSeq 500 with 75bp single-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were untreated (nDox) or treated (yDox) with doxycycline at 50 ng/ml for 3 days.

tag: genotype/variation

value: doxycycline-inducible overexpression of mutant LIN28B

value: treated (yDox) with doxycycline


title: LIN28Bmut_yDox_3


title: 406T_run214

value: lung


title: BE2C_ZNF143

tag: chip antiboy


title: LIN28Bmut_yDox_1


title: Kelly_input

value: Kelly


title: CHP134_LIN28B

value: LIN28B (Cell Signaling #11976, Lot #1)


title: BE2C_Flag-LIN28Bwt_yDox_Flag

value: Flag (SIGMA #F1804, Lot #SLBT7654)


title: CHP134_input


title: BE2C_LIN28B


title: BE2C_Flag-LIN28Bwt_yDox_input


title: Kelly_LIN28B


title: LIN28Bmut_nDox_3

value: untreated (nDox)


title: BE2C_input


title: BE2C_Flag-LIN28Bmut_yDox_Flag


title: LIN28Bwt_yDox_1

value: doxycycline-inducible overexpression of wild-type LIN28B


title: LIN28Bmut_nDox_1


title: 378T_run199

tag: tissue type

value: female


title: LIN28Bwt_yDox_3


title: LIN28Bwt_yDox_2


title: LIN28Bwt_nDox_2


title: WT_009 nILC2 (ISO)

city: Los Angeles

first: Pedram

last: Shafiei Jahani

state: CA

address: 1450 Biggy Street NRT 5509

department: MMI

institute: USC

data_processing:
Illumina Casava1.7 software used for basecalling, algorithm: bcl2fastq-v2.17.1.14
RNAseq data were analyzed using Partek® Flow® software, version 7.0 Copyright ©; 2018
Raw reads were first trimmed based on Quality Score (min quality level 20, trim from both ends, min read length 25)
Trimmed reads were aligned to mm10 with Gencode M19 as guidance using STAR 2.5.3a
Aligned reads were quantified to Gencode M16 genes using Partek E/M. Normalized reads counts were tested for differential expression using Partek's GSA algorithm.
Genome_build: mm10

organism: Mus musculus

source_name: visceral adipose tissue

extract_protocol:
Total RNA was isolated using MicroRNAeasy (Qiagen). 10ng of input RNA was used to produce cDNA for downstream library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Freshly sorted naïve or activated ILC2s were incubated (5 x 104 per mL) with rm-IL-2, rm-IL-7, with  DR3 agonist  or ISO control for 24 h.

value: BALB/cByJ

tag: age

value: 8 weeks

value: type 2 innate lymphoid cells

value: ISO control


title: normal_370_HYJJ7BGXY

value: Normal

tag: patient id

tag: libraryname

value: GEX


title: LIN28Bwt_nDox_3


title: LIN28Bwt_nDox_1


title: WT_008 nILC2 (Agonist)

value: DR3 agonist


title: WT_007 nILC2 (Agonist)


title: WT_006 aILC2 (ISO)


title: WT_005 aILC2 (ISO)


title: WT_001 aILC2 (Agonist)


title: WT_002 aILC2 (Agonist)


title: WT_004 aILC2 (ISO)


title: WT_010 nILC2 (ISO)


title: male_Atf3-KO_Crush_168_rep1

city: Boston

first: Will

last: Renthal

state: MA

address: 60 Fenwood Rd.

institute: Brigham and Women's Hospital

description:
processed data file:
Atf3_WT_KO_Raw_counts.RDS.gz

data_processing:
Raw fastq files are prepared by demultiplexing Illumina Nextseq runs using v3 indrops python scripts (github/indrops). Barcoded nuclei in a biological sample are divided into 2-3 tubes and their libararies are prepared and sequenced separately, which are then added together for each sample informatically after mapping.
All  subsequent processing steps from fastq files to count matrixes were performed using a custom pipeline for inDrops data analysis (github.com/indrops), using the default version 3 parameters.
inDrops.py first filters reads based on information present in read files 2,3, and 4, for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index. inDrops.py demultiplexes by Illumina library index (read 3).  For read 3, the library indices provided to the indrop.py custom pipeline are given in the yaml files. Libraries called "not_included_in_study_*" were not included in the study, but their indexes should be specified when using the indrop.py pipeline for demultiplexing.
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes (revealed by Read 2 and 4) against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 70 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.81 or GRCh38.85) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes). The reference index is assembled using inDrops.py as described in the manual.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene. Resulting raw count files are provided and called  *.counts.tsv.gz.
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw counts tables from each sample were then combined by their respective experiment into the RDS files available in GEO and analyzed in the Seurat single-cell analysis pipeline as described in the manuscript (Renthal et al. 2020)

extract_protocol:
Mouse dorsal root ganglia were dissociated into a single nuclei suspension as described in Renthal et al. Nat. Neurosci 2018 and Renthal et al. 2020. Briefly, tissue was dissociated by dounce homogenization and clarified by ultracentrifugation through a Optiprep gradient based on a protocol (Mo et al. Neuron 2015) and modified in Renthal et al. 2020. Nuclei were encapsulated using the inDrops platform, into droplets on ice and lysed in the 3 nL microfluidic droplets using a final concentration of 0.4% w/v Igepal-CA630. Single-nuclei lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015 and Zilionis et al., Nat. Protoc. 2017). Libraries were prepared as in Zilionis et al., Nat. Protoc. 2017, with modifications summarized in the associated manuscript (Renthal et al. 2020)
inDrops libraries were constructued as described in Zilionis et al., Nat. Protoc. 2017; single-nucleus RNA-seq

tag: Sex

value: male

tag: injury

value: Crush

tag: time after injury(h)

tag: tissue/cell type

value: Dorsal root ganglion


title: male_Atf3-WT_Crush_168_rep2


title: male_Atf3-KO_Crush_36_rep1


title: male_Atf3-KO_Naive_0_rep1

value: Naive


title: male_Atf3-KO_Naive_0_rep2


title: male_Atf3-KO_Crush_168_rep2


title: male_Atf3-WT_Crush_168_rep1


title: male_Atf3-KO_Naive_0_rep3


title: male_Atf3-WT_Crush_36_rep1


title: male_Atf3-WT_Naive_0_rep3


title: 42. Sow 3 Uterus SRF1 24h

type: RNA

city: Girona

first: Isabel

last: Barranco

state: CATALUñA

address: Calle Maria Aurèlia Campany, 69, Facultad de Ciencias

country: Spain

institute: University of Girona

description:
miRNA
miRNA expression in explant culture media
Uterus SRF, Sow 3

hyb_protocol: The biotin-labelled RNA samples were hybridized to the GeneChip miRNA 4.0 arrays for 18 h at 48 °C with 60 rpm rotation in Affymetrix® Oven 455 (Thermo Fisher Scientific). Upon hybridization, arrays were washed and stained using the Affymetrix® GeneChipTM Hybridization Wash and Stain Kit (Thermo Fisher Scientific) and Affymetrix® Fluidic Station 450 (Thermo Fisher Scientific).

scan_protocol: Arrays were scanned using Affymetrix® GeneChip Scanner 3000 7G (Thermo Fisher Scientific).

data_processing: The raw data were produced with the Affymetrix® GeneChip Command Console Software (version 4.0, Thermo Fisher Scientific), and further analysed using the Affymetrix® Transcriptome Analysis Console software (version 4.0, Thermo Fisher Scientific).

label: Biotin

organism: Sus scrofa

source_name: Culture medium from uterus mucosal explants exposure to M199 with SP-SRF

label_protocol: Biotin-labelled RNA was synthesized using Affymetrix® FlashTagTM Biotin HSR RNA Labelling Kit (Thermo Fisher Scientific).

growth_protocol: Mucosal explants from the uterus, UTJ and isthmus from each oestrus sow and were initially cultured in Medium 199 (M199) at 38 °C in 5% CO2 in air in a humidified incubator (CO₂ Incubator C60, Labotect Labor-Technik-Göttingen GmbH, Göttingen, Germany) under continuous gentle shaking (Orbit™ P2 Digital Shaker, Labnet International Inc., Edison, NJ, USA) for 60 min.

extract_protocol: RNA was obtained using a commercially kit designed to isolate cell-free small RNAs in fluids (miRNeasy serum/plasma kit, Qiagen, Hilden, Germany), following manufacturer instructions.

treatment_protocol: Mucosal explants from uterus, UTJ and isthmus were separately subjected to the following treatments (as described below): M199 alone (Control, C-), and M199 supplemented (1:40 v/v) with pooled SP from the SRF, the post-SRF or the recomposed EE. After a 16 h-incubation period, the media were harvested and replaced with 2 mL of fresh M199 and incubated under the same conditions for further 24 h, to finally collect the medium, which was frozen in liquid nitrogen and stored at −80 °C (Ultra Low Freezer; Haier Inc., Qingdao, China) until examined for miRNA analysis profiling.

tag: sow number

value: mucosal explant from sow genital tract

tag: explant source

value: uterus

tag: treatment

value: M199 with SP-SRF


title: 39. Sow 3 UTJ Post-SRF 24h

description:
miRNA
miRNA expression in explant culture media
UTJ Post-SRF, Sow 3

source_name: Culture medium from utero-tubal junction mucosal explants exposure to M199 with SP-post-SRF

value: utero-tubal junction

value: M199 with SP-post-SRF


title: 44. Sow 3 Uterus Post-SRF 24h

description:
miRNA
miRNA expression in explant culture media
Uterus Post-SRF, Sow 3

source_name: Culture medium from uterus mucosal explants exposure to M199 with SP-post-SRF


title: 40. Sow 3 UTJ EE 24h

description:
miRNA
miRNA expression in explant culture media
UTJ EE, Sow 3

source_name: Culture medium from utero-tubal junction mucosal explants exposure to M199 with SP-EE

value: M199 with SP-EE


title: male_Atf3-WT_Naive_0_rep1

tag: strain


title: 36. Sow 3 UTJ C- 24h

description:
miRNA
miRNA expression in explant culture media
UTJ C-, Sow 3

source_name: Culture medium from utero-tubal junction mucosal explants exposure to M199 alone

tag: tissue

value: M199 alone


title: 41. Sow 3 Uterus C- 24h

description:
miRNA
miRNA expression in explant culture media
Uterus C-, Sow 3

source_name: Culture medium from uterus mucosal explants exposure to M199 alone


title: 37. Sow 3 UTJ SRF1 24h

description:
miRNA
miRNA expression in explant culture media
UTJ SRF, Sow 3

source_name: Culture medium from utero-tubal junction mucosal explants exposure to M199 with SP-SRF


title: 38. Sow 3 UTJ SRF2 24h


title: 43. Sow 3 Uterus SRF2 24h


title: 35. Sow 3 Isthmus EE 24h

description:
miRNA
miRNA expression in explant culture media
Isthmus EE, Sow 3

source_name: Culture medium from isthmus mucosal explant exposure to M199 with SP-EE

value: isthmus


title: 33. Sow 3 Isthmus SRF2 24h

description:
miRNA
miRNA expression in explant culture media
Isthmus SRF, Sow 3

source_name: Culture medium from isthmus mucosal explant exposure to M199 with SP-SRF


title: 32. Sow 3 Isthmus SRF1 24h


title: WT_003 aILC2 (Agonist)

value: BALB/cByJ

value: 8 weeks

value: type 2 innate lymphoid cells


title: 45. Sow 3 Uterus EE 24h

description:
miRNA
miRNA expression in explant culture media
Uterus EE, Sow 3

source_name: Culture medium from uterus mucosal explants exposure to M199 with SP-EE


title: 30. Sow 2 Uterus EE 24h

description:
miRNA
miRNA expression in explant culture media
Uterus EE, Sow 2


title: 29. Sow 2 Uterus Post-SRF 24h

description:
miRNA
miRNA expression in explant culture media
Uterus Post-SRF, Sow 2


title: 34. Sow 3 Isthmus Post-SRF 24h

description:
miRNA
miRNA expression in explant culture media
Isthmus Post-SRF, Sow 3

source_name: Culture medium from isthmus mucosal explant exposure to M199 with SP-post-SRF


title: 31. Sow 3 Isthmus C- 24h

description:
miRNA
miRNA expression in explant culture media
Isthmus C-, Sow 3

source_name: Culture medium from isthmus mucosal explant exposure to M199 alone


title: male_Atf3-WT_Naive_0_rep2


title: male_Mrgprd-cre_Crush_1440_rep1

description:
processed data file:
C57_Raw_counts.RDS.gz


title: male_Mrgprd-cre_Crush_1440_rep2


title: male_Mrgprd-cre_Naive_0_rep3


title: male_Mrgprd-cre_Crush_168_rep1


title: male_C57_CFA_48_rep1

value: CFA


title: male_Mrgprd-cre_Naive_0_rep2


title: male_Mrgprd-cre_Naive_0_rep1


title: male_C57_Paclitaxel_168_rep1

value: Paclitaxel


title: male_C57_Paclitaxel_168_rep2

value: male


title: male_C57_ScNT_1440_rep2

value: ScNT


title: male_C57_ScNT_672_rep1

value: Dorsal root ganglion


title: male_C57_ScNT_672_rep2


title: male_C57_ScNT_168_rep2


title: male_C57_ScNT_72_rep2


title: 24. Sow 2 UTJ Post-SRF 24h

description:
miRNA
miRNA expression in explant culture media
UTJ Post-SRF, Sow 2


title: 27. Sow 2 Uterus SRF1 24h

description:
miRNA
miRNA expression in explant culture media
Uterus SRF, Sow 2


title: 26. Sow 2 Uterus C- 24h

description:
miRNA
miRNA expression in explant culture media
Uterus C-, Sow 2


title: male_C57_ScNT_72_rep1


title: 21. Sow 2 UTJ C- 24h

description:
miRNA
miRNA expression in explant culture media
UTJ C-, Sow 2


title: male_C57_ScNT_24_rep1


title: 28. Sow 2 Uterus SRF2 24h


title: 16. Sow 2 Isthmus C- 24h

description:
miRNA
miRNA expression in explant culture media
Isthmus C-, Sow 2


title: male_C57_ScNT_12_rep2


title: 18. Sow 2 Isthmus SRF2 24h

description:
miRNA
miRNA expression in explant culture media
Isthmus SRF, Sow 2


title: male_C57_ScNT_168_rep1


title: 20. Sow 2 Isthmus EE 24h

description:
miRNA
miRNA expression in explant culture media
Isthmus EE, Sow 2


title: 22. Sow 2 UTJ SRF1 24h

description:
miRNA
miRNA expression in explant culture media
UTJ SRF, Sow 2


title: 15. Sow 1 Uterus EE 24h

description:
miRNA
miRNA expression in explant culture media
Uterus EE, Sow 1


title: male_C57_ScNT_1440_rep1


title: 23. Sow 2 UTJ SRF2 24h


title: male_C57_Crush_2160_rep2

value: Crush


title: male_C57_ScNT_12_rep1


title: 19. Sow 2 Isthmus Post-SRF 24h

description:
miRNA
miRNA expression in explant culture media
Isthmus Post-SRF, Sow 2

value: mucosal explant from sow genital tract


title: 17. Sow 2 Isthmus SRF1 24h


title: male_C57_Crush_2160_rep1


title: male_C57_Crush_1440_rep1


title: male_C57_Crush_1440_rep2


title: male_C57_ScNT_6_rep1


title: 13. Sow 1 Uterus SRF2 24h

description:
miRNA
miRNA expression in explant culture media
Uterus SRF, Sow 1

value: uterus


title: 14. Sow 1 Uterus Post-SRF 24h

description:
miRNA
miRNA expression in explant culture media
Uterus Post-SRF, Sow 1


title: male_C57_Crush_672_rep1


title: 11. Sow 1 Uterus C- 24h

description:
miRNA
miRNA expression in explant culture media
Uterus C-, Sow 1


title: 10. Sow 1 UTJ EE 24h

description:
miRNA
miRNA expression in explant culture media
UTJ EE, Sow 1


title: 8. Sow 1 UTJ SRF2 24h

description:
miRNA
miRNA expression in explant culture media
UTJ SRF, Sow 1

value: M199 with SP-SRF


title: male_C57_Crush_336_rep2


title: 7. Sow 1 UTJ SRF1 24h

value: utero-tubal junction


title: 25. Sow 2 UTJ EE 24h

description:
miRNA
miRNA expression in explant culture media
UTJ EE, Sow 2


title: 12. Sow 1 Uterus SRF1 24h


title: male_C57_Crush_336_rep1

description:
processed data file:
C57_Raw_counts.RDS.gz


title: male_C57_Crush_168_rep2


title: male_C57_Crush_168_rep1


title: male_C57_Crush_672_rep2


title: 9. Sow 1 UTJ Post-SRF 24h

description:
miRNA
miRNA expression in explant culture media
UTJ Post-SRF, Sow 1

value: M199 with SP-post-SRF


title: 4. Sow 1 Isthmus Post-SRF 24h

description:
miRNA
miRNA expression in explant culture media
Isthmus Post-SRF, Sow 1


title: 6. Sow 1 UTJ C- 24h

description:
miRNA
miRNA expression in explant culture media
UTJ C-, Sow 1


title: 5. Sow 1 Isthmus EE 24h

description:
miRNA
miRNA expression in explant culture media
Isthmus EE, Sow 1

value: M199 with SP-EE


title: male_C57_Crush_72_rep1


title: 3. Sow 1 Isthmus SRF2 24h

description:
miRNA
miRNA expression in explant culture media
Isthmus SRF, Sow 1


title: male_C57_Crush_24_rep1


title: male_C57_Crush_24_rep2


title: male_C57_Crush_6_rep1


title: 1. Sow 1 Isthmus C- 24h

description:
miRNA
miRNA expression in explant culture media
Isthmus C-, Sow 1

source_name: Culture medium from isthmus mucosal explant exposed to M199 alone

value: M199 alone


title: male_C57_Crush_6_rep2


title: 2. Sow 1 Isthmus SRF1 24h

value: isthmus


title: male_C57_SpNT_168_rep3

value: SpNT


title: male_C57_Crush_72_rep2


title: Tet_A3A_IFNa_72h_22

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

description:
Cell culture
Tet_A3A_IFNa_72h_22

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

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

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

source_name: A3A expressor in presence of IFNalpha

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

growth_protocol: HepaRG cells and derivates were cultured similar to described procedures (Lucifora et al., 2010).

extract_protocol: Total RNA was extracted from cell line pellets using the Qiagen Allprep kit.

treatment_protocol: Cells with and without transfected A3A were grown without or in presence of TNFalpha.

tag: cell line

value: HepaRG


title: male_C57_SpNT_168_rep4


title: male_C57_SpNT_72_rep4


title: male_C57_SpNT_72_rep5


title: Tet_A3A_IFNa_72h_23

description:
Cell culture
Tet_A3A_IFNa_72h_23


title: Tet_A3A_IFNa_72h_21

description:
Cell culture
Tet_A3A_IFNa_72h_21


title: Tet_A3A_72h_20

description:
Cell culture
Tet_A3A_72h_20

source_name: A3A expressor


title: Tet_A3A_72h_18

description:
Cell culture
Tet_A3A_72h_18


title: Tet_A3A_72h_17

description:
Cell culture
Tet_A3A_72h_17


title: Tet_A3A_IFNa_6h_12

description:
Cell culture
Tet_A3A_IFNa_6h_12


title: Tet_A3A_IFNa_6h_10

description:
Cell culture
Tet_A3A_IFNa_6h_10


title: mock_72h_15

description:
Cell culture
mock_72h_15

source_name: control


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_ParB_chimera_D_rep1

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

data_processing:
For analysis of ChIP-seq data, Hiseq 2500 Illumina short reads (50 bp) were mapped back to the Caulobacter NA1000 reference genome (NCBI Reference Sequence: NC_011916.1) using Bowtie 1 and the following command: bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NA1000-bowtie --sam *.fastq > output.sam. Subsequently, the sequencing coverage at each nucleotide position was computed using BEDTools using the following command: bedtools genomecov -d -ibam output.sorted.bam -g NA1000.fna > coverage_output.txt. For analysis of E. coli ChIP-seq data, the same procedure as above was applied, except that short reads were map to the reference genome of the E. coli MG1655 (NCBI Reference Sequence: NC_000913.3). Finally, ChIP-seq profiles were plotted with the x-axis representing genomic positions and the y-axis is the number of reads per base pair per million mapped reads (RPBPM) using custom R scripts.
Genome_build: NC_011916.1 (C. crescentus)
Genome_build: NC_000913.3 (E. coli)
Supplementary_files_format_and_content: *_coverage_output.txt: The processed data files for ChIP-seq are tab-delimited files containing three fields: the genome build, the nucleotide position, and the coverage at that position.

organism: Escherichia coli

source_name: Escherichia coli AB1157

growth_protocol: For E. coli ChIP-seq, cells harboring pUT18C-1xFLAG-ParB were grown in LB (25 mL) at 28oC to mid-exponential phase (OD600 ~0.4) before 1 mM IPTG was added for 1-3 hours. The induction time (either 1, 2 or 3 hours) was chosen so that all ParB variants were produced to a similar protein level as judged by an α-FLAG immunoblot. Subsequently, formaldehyde was added to a final concentration of 1% to fix the cells. For C. crescentus ChIP-seq, MT148 cells harboring van::Pvan-FLAG-ParB (WT)/mutants were grown in PYE (25 mL) + 0.3% glucose + 0.5 mM vanillate to mid-exponential phase (OD600 ~0.4) before formaldehyde was added to a final concentration of 1% to fix the cells.

extract_protocol:
For ChIP-seq, DNA was isolated using Qiagen PCR purification columns.
For ChIP-seq libraries, a standard library construction procedure (using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina sequencing) was employed.

treatment_protocol: FLAG-ParB were produced by addition of 1mM IPTG before formaldehyde to 1% (final concentration) was added to fix cells for ChIP-seq.

tag: strain/background

tag: genotype

value: TLE3200 (ygcE::parS) + pUT18C::1xFLAG-ParB_chimera_D

tag: developmental stage

value: mixed population, exponential phase

tag: chip-seq antibody

value: FLAG


title: Tet_A3A_IFNa_6h_11

description:
Cell culture
Tet_A3A_IFNa_6h_11


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_ParB_Chimera_C_rep1

value: TLE3200 (ygcE::parS) + pUT18C::1xFLAG-ParB_Chimera_C


title: male_C57_SpNT_72_rep2

value: male


title: Tet_A3A_6h_5

description:
Cell culture
Tet_A3A_6h_5


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_ParB_chimera_D_rep2


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_ParB_chimera_B_rep1

value: TLE3200 (ygcE::parS) + pUT18C::1xFLAG-ParB_chimera_B


title: male_C57_SpNT_36_rep1

value: Dorsal root ganglion


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_ParB_chimera_A_rep2

value: TLE3200 (ygcE::parS) + pUT18C::1xFLAG-ParB_chimera_A


title: male_C57_SpNT_168_rep2


title: male_C57_SpNT_36_rep2


title: male_C57_SpNT_168_rep1


title: male_C57_SpNT_24_rep1


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_Pseudomonas_aeruginosa_ParB

value: TLE3200 (ygcE::parS) + pUT18C::1xFLAG-Pseudomonas_aeruginosa_ParB


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_ParB_chimera_B_rep2


title: mock_72h_13

description:
Cell culture
mock_72h_13


title: Tet_A3A_6h_7

description:
Cell culture
Tet_A3A_6h_7


title: male_C57_SpNT_6_rep2


title: male_C57_SpNT_6_rep3


title: male_C57_SpNT_6_rep1


title: male_C57_Naive_0_rep5

value: Naive


title: male_C57_SpNT_72_rep3


title: Tet_A3A_6h_8

description:
Cell culture
Tet_A3A_6h_8


title: mock_6h_2

description:
Cell culture
mock_6h_2


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_Dechloromonas_aromatica_ParB

value: TLE3200 (ygcE::parS) + pUT18C::1xFLAG-Dechloromonas_aromatica_ParB


title: male_C57_SpNT_72_rep1


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_Caulobacter_crescentus_ParB

value: TLE3200 (ygcE::parS) + pUT18C::1xFLAG-Caulobacter_crescentus_ParB


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_ParB_Chimera_C_rep2


title: male_C57_SpNT_48_rep2


title: male_C57_Naive_0_rep1


title: male_C57_SpNT_48_rep1


title: mock_6h_3

description:
Cell culture
mock_6h_3


title: male_C57_SpNT_24_rep2


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_Xanthomonas_campestris_ParB

value: TLE3200 (ygcE::parS) + pUT18C::1xFLAG-Xanthomonas_campestris_ParB


title: male_C57_SpNT_12_rep2


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_Thermus_thermophilus_ParB

value: TLE3200 (ygcE::parS) + pUT18C::1xFLAG-Thermus_thermophilus_ParB


title: d4-Atg7 KO

city: Wuhan

first: Jing-Jing

last: Zhang

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

institute: Huazhong Agricultural University

description: WGBS

data_processing:
All the WGBS paired-end reads were mapped to the mouse mm10 reference genome using Bismark software and the methylation level of genome-wide cytosine was called.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files were generated using deepTools.

source_name: Embryonic Stem Cells (ESCs)

growth_protocol: ESCs were routinely cultivated on mitotically inactivated mouse embryonic fibroblasts (MEFs) in Knockout DMEM supplemented with 20% Knockout Serum Replacement, 1× Glutamine Max, 1× NEAA, 1× Pen/Strep, 0.1 mM 2-mercaptoethanol, 1000 U ml-1 LIF, 1 μM PD0325901 and 3 μM CHIR99021. MEFs were grown in DMEM high glucose supplemented with 15% FBS and 1× Pen/Strep.

extract_protocol: Libraries were constructed with TruSeq DNA library preparation kit (Illumina).

treatment_protocol: The EpiLCs induction were performed by seeding 1.0×10e5 ESCs into a well of a 12-well plate coated with 16.7 mg/ml human plasma fibronectin in N2B27 medium containing 20 ng/ml Activin A, 12 ng/ml bFGF, and 20% KSR. The culture medium was changed every day.

tag: genotype/variation

value: Atg7 KO

value: ESC to EpiLC transition

tag: time point


title: d4-Control

description: WGBS

value: Control


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_ParB_chimera_A_rep1


title: male_C57_SpNT_12_rep1

value: SpNT


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_Myxococcus_xanthus_ParB

value: TLE3200 (ygcE::parS) + pUT18C::1xFLAG-Myxococcus_xanthus_ParB

value: mixed population, exponential phase


title: WT Intestinal stromal single cell_rep2

city: Daejeon

first: Hyunsoo

last: Cho

address: Yuseonggu

country: South Korea

institute: IBS/KAIST

data_processing:
Cell Ranger (v3.0.2) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mouse reference genome.
Aligned reads were then read by Seurat (v3.0.1) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 1000 genes) and potential doublets (expressing more than 6000 genes) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control, expression matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Cell-gene expression matrix of log normalized UMI counts for WT and LATS1/2 KO datasets

extract_protocol:
FACS sorted stromal cells were processed on the 10X chromium system following the manufacturer's protocols.
Using Chromium Single cell 3' v3 Reagent Kit (10X genomics), cDNA libraries were constructed

tag: strain background

tag: age

value: Adult

value: wild type

tag: cell preparation

value: FACS sorted

tag: cell type

value: PDGFRb+ intestinal stromal single cells


title: female_C57_Naive_0_rep1

tag: Sex

value: female

tag: injury

tag: time after injury(h)

tag: tissue/cell type

value: Dorsal root ganglion


title: WT Intestinal stromal single cell_rep1


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_Moorella_thermoacetica_ParB

value: TLE3200 (ygcE::parS) + pUT18C::1xFLAG-Moorella_thermoacetica_ParB

value: FLAG


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_Lawsonia_intracellularis_ParB

value: TLE3200 (ygcE::parS) + pUT18C::1xFLAG-Lawsonia_intracellularis_ParB


title: LATS1/2 KO intestinal stromal single cell

data_processing:
Cell Ranger (v2.2.0) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mouse reference genome.
Aligned reads were then read by Seurat (v2.3.4) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 200 genes) and potential doublets (expressing more than 3000 genes) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control, expression matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Cell-gene expression matrix of log normalized UMI counts for WT and LATS1/2 KO datasets (column headers are the cell barcodes)

source_name: PDGFRb+ intestinal stromal single cells

extract_protocol:
FACS sorted stromal cells were processed on the 10X chromium system following the manufacturer's protocols.
Using Chromium Single cell 3' v2 Reagent Kit (10X genomics), cDNA libraries were constructed

tag: strain

tag: sorting method


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_Helicobacter_pylori_ParB

value: TLE3200 (ygcE::parS) + pUT18C::1xFLAG-Helicobacter_pylori_ParB


title: male_C57_Naive_0_rep4

value: male

value: Naive


title: N05_C2

city: Leuven

first: Bart

last: De Strooper

address: O&N4 Herestraat 49

department: Centre for Brain and Disease research

country: Belgium

institute: VIB - KU Leuven

data_processing:
Spatial Transcriptomics Pipeline (ST pipeline)
Genome_build: Mus Musculus genome mm10, ensemble version 88
Supplementary_files_format_and_content: raw_counts.txt.gz:  Raw gene  expression counts per ST spot in a gzipped tab separated values file.
logCPM_counts.txt.gz:  log-CPM normalized count table in gzipped tab separated value file.

source_name: coronal section bregma: - 2.0 to -2.2

extract_protocol:
OCT-embedded hemispheres were cryosectioned coronally to a thickness of 10 μm (bregma: - 2.0 to -2.2) using a CryoStar NX70 cryostat (ThermoFisher).
Spatial Transcriptomics Library Preparation protocol.

value: APPNL-G-F

value: TG

tag: tissue

value: brain


title: N04_E1


title: N05_D2


title: male_C57_Naive_0_rep3


title: WT Intestinal stromal single cell


title: N04_D1


title: B04_E1

value: WT


title: Wildtype control 1

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

description:
Col10a1Cre;Rosa26-Tdtomato
bulk RNAseq of chondrocytes
Wt1

data_processing:
The fastq read-pairs were aligned to mouse reference genome (mm10) using the HISAT2 aligner
The resulting SAM files were sorted and re-formatted as BAM files using SAMTOOLS (0.1.18)
The BAM files were quantified to mouse gene model by GENCODE (v19) using Cufflinks and HTSeq-count
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample for all genes

source_name: proximal tibia

growth_protocol: The mice grow under normal condition.

extract_protocol:
RNA extraction from dissociated cells was done according to Smartseq2 protocol (Picelli et al., 2014)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No special treatment is applied.

tag: number of genes detected


title: B04_D1

tag: genotype


title: b-cat GoF mutant 1

description:
Col10a1Cre;Rosa26-Tdtomato;Ctnnb1-exon3 Δ/+
bulk RNAseq of chondrocytes
G1


title: b-cat LoF mutant 4

description:
Col10a1Cre;Rosa26-Tdtomato;Ctnnb1Δ/Δ (LoF mutant)
bulk RNAseq of chondrocytes
C4

value: Col10a1Cre;Rosa26-Tdtomato;Ctnnb1delta /delta  (LoF mutant)


title: male_C57_Naive_0_rep2


title: female_C57_Crush_168_rep2

value: Crush


title: female_C57_Crush_168_rep1


title: b-cat LoF mutant 2

description:
Col10a1Cre;Rosa26-Tdtomato;Ctnnb1Δ/Δ (LoF mutant)
bulk RNAseq of chondrocytes
C2


title: B06_E1


title: LATS1/2 KO intestinal stromal single cell_2w

value: Adult

value: LATS1/2 KO


title: b-cat LoF mutant 1

description:
Col10a1Cre;Rosa26-Tdtomato;Ctnnb1Δ/Δ (LoF mutant)
bulk RNAseq of chondrocytes
C1


title: LeLab_ChIP_seq_TLE3002_pUT18C_1xFLAG_Bacillus_subtilis_ParB

tag: strain/background

value: TLE3200 (ygcE::parS) + pUT18C::1xFLAG-Bacillus_subtilis_ParB

tag: developmental stage

value: mixed population, exponential phase


title: female_C57_Naive_0_rep2

value: female

value: Dorsal root ganglion


title: N03_D2


title: N03_C2


title: N02_D1


title: LATS1/2 KO intestinal stromal single cell_1w

tag: genotype/variation

value: FACS sorted

value: PDGFRb+ intestinal stromal single cells


title: N02_C1


title: Wildtype control 2

description:
Col10a1Cre;Rosa26-Tdtomato
bulk RNAseq of chondrocytes
Wt2


title: B03_C2


title: B05_E2


title: mice_9month-old-APP/PS1_rep1 [9-4]

city: Beijing

first: li

last: zeng

state: Beijing

address: Institute of Medical Biotechnology, Tiantan Xili, Dongcheng District, Beijing

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College

hyb_protocol: 0.6 ug of Cy3-labelled linearly amplified cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 22.5 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Microarrays (G4858A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1(Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data.  Raw data were normalized in quantile algorithm with genespring 13.0(Agilent). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 5 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: ll the mice were given food and water ad libitum and kept in a constant temperature and humidity environment according to the Guide for the Care and Use of Laboratory Animals.

extract_protocol: RNA was extracted by Invitrogen’s Trizol reagent (Thermo Fisher Scientific, Waltham, MA, USA). following the manufacturer's recommendations.

treatment_protocol: The mice were then sacrificed by cervical dislocation and their brains were quickly removed and preserved via flash freezing in liquid nitrogen.

value: APP/PS1 mouse model

tag: gender

tag: molecule subtype

value: lncRNA


title: B05_D2

tag: age


title: b-cat GoF mutant 2

description:
Col10a1Cre;Rosa26-Tdtomato;Ctnnb1-exon3 Δ/+
bulk RNAseq of chondrocytes
G2


title: mice_9month-old-APP/PS1_rep1 [9-2]

tag: strain background

value: male


title: N06_D2

value: APPNL-G-F


title: mice_9month-old-APP/PS1_rep1 [9-3]


title: b-cat LoF mutant 3

description:
Col10a1Cre;Rosa26-Tdtomato;Ctnnb1Δ/Δ (LoF mutant)
bulk RNAseq of chondrocytes
C3


title: N07_C1

value: TG


title: B07_C2

value: brain


title: B03_D2

value: WT


title: mice_6month-old-APP/PS1_rep1 [6-3]


title: mice_6month-old-APP/PS1_rep1 [6-2]


title: mice_6month-old-APP/PS1_rep1 [6-4]


title: Ribo-seq_het-2 (STHdhQ7/Q111)

city: Jupiter

first: Srinivasa

last: Subramaniam

state: FL

address: 130 Scripps Way

institute: The Scripps Research Institute

description:
Ribosome footprints
262-5

data_processing:
Library strategy: Ribo-seq
We used an Illumina NextSeq 500 system and a HIGH output 75 Kit with 1x50 bp read length. Base-calling was performed online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.2.0.
For Riboseq reads, 3’ adapters were trimmed using Cutadapt with the following parameters : -a TGGAATTCTCGGGTGCCAAGG --minimum-length 23. The reads were further trimmed using Cutadapt to remove 4 bases from either side of each read accordingly to the NEXTflex™ Small RNA Trimming Instructions (cutadapt -u 4 -u -4).
Mouse rRNA sequences were retrieved from NCBI (37) with the following accessions: NR_003279, NR_003278, NR_003280, NR_030686. Ribo-seq and RNA-seq reads aligning to these sequences were removed using bowtie (version 1.0.1) with the following command: bowtie -v 3 --norc <path_to_rRNA_indices> -q <input>.fastq --un <output>.fastq. The remaining reads were then mapped using bowtie to the RefSeq mouse transcriptome downloaded from  ftp://ftp.ncbi.nlm.nih.gov/refseq/M_musculus/mRNA_Prot/ on 9th October 2018. The following command was used: bowtie -a -m 100 -l 25 -n 2 -S --norc <path_to_transcriptome_indices> -q <input>.fastq <output>.sam.
The command line version of the PausePred software was run with the following parameters for each replicate (control, HD-het and HD-homo): fold change : 5; window size: 1000 nucleotides; read lengths: 26-32 nucleotides; window coverage: 5. Individual offset values were assigned according to metagene analysis for each read length (26-32 nucleotides) accounting for mismatches at the 5' ends of the reads. For genes with detected pauses, the center of ribosome density was determined using an in-house python script
The raw data files are in fastq format and need to be 3' adapter trimmed with cutadapt using the following: -a TGGAATTCTCGGGTGCCAAGG -o FILE_NAME.trim1.fq --minimum-length 23 FILE_NAME.fastq.gz. This command excludes any inserts less than 15 bases (where the minimum length of 23 refers to 8 randomized bases and a minimum 15-base insert). The trimmed insert should be further trimmed to remove 4 bases from either end (these are 4 random bases introduced by the adapters to reduce ligation bias) using: cutadapt -u 4 -u -4 -o FILE_NAME.trim2.fq FILE_NAME.trim1.fq
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene counts are provided in a matrix table for all samples in a .csv spreadsheet.

source_name: Striatal cells

growth_protocol: Mouse immortalized striatal cells (i.e. control, HD-het, and HD-homo cells) were plated in 15 cm dishes at a confluency of 70%. The following day the mediums were changed and after 2 hours the cells were incubated with cycloheximide (CHX, 100 mg/ml) for 10 min. The cell then scraped and washed with cold PBS (containing 100 mg/ml CHX) twice

extract_protocol:
80S monosome fraction RNA was purified using Qiagen miRNeasy mini kit.
To isolate the 26-32nt ribosome-protected footprints, 20ug of RNA from each sample was run on 15% TBE-Urea gel (Novex) along with 26 and 32 nt RNA markers. RNA was extracted from the excised gel bands using crush and soak with nuclease-free water overnight at 4C and precipitated using RNase-free isopropanol. T4 Polynucleotide Kinase (NEB) was used to catalyze the addition of 5' monophosphate and removal of the 3’ phosphate in the RNA fragments to leave a 3’ hydroxyl terminal needed for adapter ligation. RNA was purified using the Zymo clean and conc-5 kit (Zymo Research, Cat. # R1013). Ribosomal RNA was depleted from the samples using TruSeq total RNA rRNA-depletion protocol (Illumina, Cat. #RS-122-2201. Purified RNA was directly processed with the Perkin Elmer NextFlex small RNA kit V3 and converted into libraries.

value: Expressing knock-in mutant Htt exon 1 with 111 Glu repeats, Heterozygote

tag: cell type

value: Striatal


title: Ribo-seq_control-2 (STHdhQ7/Q7)

description:
Ribosome footprints
262-4

value: Expressing knock-in wild-type Htt exon 1 with 7 Glu repeats


title: Ribo-seq_homo-2 (STHdhQ111/Q111)

description:
Ribosome footprints
262-6

value: Expressing knock-in mutant Htt exon 1 with 111 Glu repeats, Homozygote


title: Ribo-seq_homo-3 (STHdhQ111/Q111)

description:
Ribosome footprints
262-9


title: Ribo-seq_het-3 (STHdhQ7/Q111)

description:
Ribosome footprints
262-8


title: B02_D1


title: A26 HuR KO BAT

city: Columbus

first: Michael

last: Tranter

state: OH

address: 2255 Kenny Road

department: Molecular Medicine and Therapeutics

institute: The Ohio State University

data_processing:
All read mapping and analysis was performed using the CLC Genomics Workbench v20.0.2 (CLC Bio-Qiagen).
Reads were mapped using the following parameters:  min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Expression value= Total counts.
Supplementary_files_format_and_content: Transcripts-COUNTS.xls

source_name: interscapular brown adipose

extract_protocol:
Brown adipose tissue was removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 28 weeks

value: adipo-HuR-/-


title: B02_E1


title: RNA-seq_homo-3 (STHdhQ111/Q111)

description:
264-9
homo3_RNA

data_processing:
We used an Illumina NextSeq 500 system and a HIGH output 75 Kit with 2x40 bp read length. Base-calling was performed online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.2.0.
RNAseq reads were trimmed using Cutadapt with the following parameters : -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --minimum-length=15 –pair-filter=any.
Reads were mapped to the mouse genome using Bowtie v1.1.2. Any reads mapping to rRNA and tRNA were filtered out.
Reads were aligned to the mouse transcriptome with RSEM v1.3.0 using the GRCm38.p5 genome annotation.
Differential gene expression analysis was performed using Deseq2.
Genome_build: mm10
Supplementary_files_format_and_content: The raw data files are in the fastq format and need to be need to be trimmed to remove the Illumina TruSeq adapters. -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Supplementary_files_format_and_content: Raw gene counts are provided in a matrix table for all samples in a .csv spreadsheet.

extract_protocol:
Total RNAs of these samples were isolated using miRNeasy Mini Kit (Qiagen)
NEBNext Ultra II directional library prep with poly(A) mRNA Magnetic isolation module

value: Expressing knock-in mutant Htt exon 1 with 111 Glu repeats, Homozygous

value: striatal


title: mice_3month-old-APP/PS1_rep1 [3-5]

value: female


title: RNA-seq_homo-2 (STHdhQ111/Q111)

description:
264-8
homo2_RNA


title: RNA-seq_homo-1 (STHdhQ111/Q111)

description:
264-7
homo1_RNA


title: A24 HuR KO BAT


title: mice_3month-old-APP/PS1_rep1 [3-3]


title: A8 WT BAT

value: wild-type


title: mice_3month-old-APP/PS1_rep1 [3-1]

value: APP/PS1 mouse model


title: RNA-seq_het-1 (STHdhQ7/Q111)

description:
264-4
het1_RNA

value: Expressing knock-in mutant Htt exon 1 with 111 Glu repeats, Heterozygous


title: mice_1month-old-APP/PS1_rep1 [1-5]

value: lncRNA


title: RNA-seq_control-3 (STHdhQ7/Q7)

description:
264-3
control3_RNA


title: RNA-seq_control-2 (STHdhQ7/Q7)

description:
264-2
control2_RNA


title: OSKMD5 FLAG #2 (ATAC-seq)

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

data_processing:
Reads were aligned to the mouse mm10 genome using bowtie2 v2.2.0
Peaks were discovered using Dfilter (v1.6)
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are peak bed files

source_name: Mouse MEFs, OSKM day 5

growth_protocol: MEFs were maintained in DMEM/high glucose (Hyclone) containing 10% fetal bovine serum (FBS, PAA), Glutamax (Invitrogen), nonessential amino acids (Invitrogen), and penicillin/streptomycin (Hyclone). Mouse ESCs and iPSCs were cultured on feeder layer (MEF treated with mitomycin-C) in ESC medium containing DMEM/high glucose (Hyclone) supplemented with 15% FBS (GIBCO), Glutamax, nonessential amino acids, sodium pyruvate, penicillin/streptomycin, beta-mercaptoethanol and leukaemia inhibitory factor (LIF). Reprogramming of MEFs was performed either in mES medium. Vitamin C was purchased from Sigma and used at concentration of 50 µg/ml.

extract_protocol:
ATAC-seq and analysis. A total of 50,000 cells were washed once with cold PBS and re-suspended in 50 μl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2, 0.1% IGEPAL CA-630). The suspension was then centrifuged at 500 g for 10 minutes at 4°C, followed by addition of 50 μl transposition reaction mix of TruePrep DNA Library Prep Kit (Vazyme, TD502). Samples were then incubated at 37°C for 30 minutes. Transposition reactions were cleaned up using a MinElute PCR Purification Kit (QIAGEN, 28004). ATAC-seq libraries were subjected to five cycles for pre-amplification and amplified by PCR for an appropriate number of cycles. The amplified libraries were purified with a QIAquick PCR Purification Kit (QIAGEN, 28104). Library concentration was measured using VAHTSTM Library Quantification Kit (Vazyme, NQ101). Libraries were sequenced by Vazyme Co., Ltd, China. All sequencing data were mapped onto the mm10 mouse genome assembly using bowtie2 (–very-sensitive). Low quality mapped reads were removed using samtools (view –q 30) and only unique reads mapping to a single genomic location and strand were kept. We removed mitochondrial sequences using ‘grep –v ‘chrM’.
Standard Illumina protocols

treatment_protocol: Plat-E cells were transfected with pMXs vectors for OSKM to produce virus. Plat-E cells were maintained in DMEM/high glucose containing 10% FBS.  MEFs within 3 passages were plated at 4000-5000 per square centimetre and infected with retrovirus. We marked the first infection time point as day0, after 2 rounds of 24h infection, the medium was changed to ESC medium, including Vitamin C.

tag: day

tag: transfection

value: OSKM retroiviral transfection

tag: overexpression

value: FLAG

tag: knockout

value: Wildtype

tag: presumed cell type

value: Intermediate pluripotent reprogrammed cells


title: OSKMD10 FLAG #2 (ATAC-seq)

source_name: Mouse MEFs, OSKM day 10

tag: strain


title: MEF #2 (ATAC-seq)

source_name: MEFs

value: mouse embryonic fibroblast


title: A25 HuR KO BAT


title: mice_1month-old-APP/PS1_rep1 [1-1]

value: male

tag: tissue

value: brain


title: OSKMD5 FLAG #1 (ATAC-seq)


title: mice_Wild Type_rep1  [N-5]

source_name: mice,Wild Type

value: wild type


title: OSKMD10 FLAG #1 (ATAC-seq)


title: E11.5 Mut HL 2

city: Storrs

first: Rahul

middle: N

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

data_processing:
Reads were mapped using Hisat2
Expression calls were made using IsoEM
Differential expression was determined with IsoDE2
Genome_build: mm10
Supplementary_files_format_and_content: tab delimeted text files with gene TPM for each sample

source_name: Hindlimb bud

extract_protocol:
Limb buds were dissected and placed into Trizol. RNA was extracted using Direct-zol RNA Miniprep Plus Kit.
RNA libraries were generated for sequencing through standard Illumina recommended protocols

value: Hindlimb bud


title: A31 HuR KO BAT

value: 28 weeks

value: adipo-HuR-/-


title: Ribo-seq_homo-1 (STHdhQ111/Q111)

description:
Ribosome footprints
262-3

value: Expressing knock-in mutant Htt exon 1 with 111 Glu repeats, Homozygote

value: Striatal


title: mice_Wild Type_rep1  [N-2]


title: mice_Wild Type_rep1  [N-4]

value: female


title: mice_1month-old-APP/PS1_rep1 [1-6]

value: APP/PS1 mouse model


title: E11.5 Mut FL 3

source_name: Forelimb bud

value: Forelimb bud


title: ESC #1 (ATAC-seq)

source_name: ESCs

value: embryonic stem cells


title: A29 HuR KO BAT


title: E11.5 Mut FL 1


title: OGT KO BMDMs; IL-4-stimulated (M2) [F73]

city: New Haven

first: Xiaoyong

last: Yang

address: 375 Congress Ave

department: Comparative Medicine

institute: Yale University

data_processing:
Sequencing reads were aligned against the mouse mm10 reference genome using the TopHat2 software version 2.1.0 with the default parameters.
Mapped reads were assigned to gene features and quantified using the HTSeq software version 0.9.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include HTSeq raw abundance values for each sample.

source_name: BMDMs

extract_protocol: Total RNA was isolated by using the RNeasy Plus Mini Kit (QIAGEN).

value: OGT KO

value: 12 weeks

value: Bone marrow-derived macrophages

tag: treatment

value: IL-4-stimulated (M2)


title: OGT KO BMDMs; IL-4-stimulated (M2) [F63]


title: Ribo-seq_control-3 (STHdhQ7/Q7)

description:
Ribosome footprints
262-7

tag: genotype

value: Expressing knock-in wild-type Htt exon 1 with 7 Glu repeats


title: E11.5 WT HL 3


title: Ribo-seq_control-1 (STHdhQ7/Q7)

description:
Ribosome footprints
262-1


title: RNA-seq_control-1 (STHdhQ7/Q7)

description:
264-1
control1_RNA

value: striatal


title: A12 WT BAT

value: wild-type


title: RNA-seq_het-3 (STHdhQ7/Q111)

description:
264-6
het3_RNA

value: Expressing knock-in mutant Htt exon 1 with 111 Glu repeats, Heterozygous


title: Ribo-seq_het-1 (STHdhQ7/Q111)

description:
Ribosome footprints
262-2

value: Expressing knock-in mutant Htt exon 1 with 111 Glu repeats, Heterozygote


title: RNA-seq_het-2 (STHdhQ7/Q111)

description:
264-5
het2_RNA


title: E11.5 WT HL 2

value: Hindlimb bud


title: WT BMDMs; IL-4-stimulated (M2) [F33]

tag: strain/background

value: WT


title: A7 WT BAT

value: 28 weeks


title: WT BMDMs; IL-4-stimulated (M2) [F23]


title: E11.5 Mut HL 3


title: ESC #2 (ATAC-seq)

value: Wildtype


title: OGT KO BMDMs; LPS-stimulated (M1) [F82]

value: LPS-stimulated (M1)


title: E10.5 Mut HL 1

description: 3nt were trimmed from terminal 3' end using fastx


title: OGT KO BMDMs; LPS-stimulated (M1) [F62]


title: MEF #1 (ATAC-seq)

value: mouse embryonic fibroblast


title: E11.5 Mut HL 1


title: E11.5 Mut FL 2

value: Forelimb bud


title: OGT KO BMDMs; LPS-stimulated (M1) [F52]


title: OGT KO BMDMs; IL-4-stimulated (M2) [F83]


title: WT BMDMs; LPS-stimulated (M1) [F32]


title: E11.5 WT FL 2


title: WT BMDMs; LPS-stimulated (M1) [F12]


title: WT BMDMs; IL-4-stimulated (M2) [F43]


title: OGT KO BMDMs; IL-4-stimulated (M2) [F53]


title: WT BMDMs; IL-4-stimulated (M2) [F13]


title: E11.5 WT FL 1


title: E11.5 WT FL 3


title: E10.5 Mut HL 2


title: E10.5 Mut HL 3


title: OGT KO BMDMs; Unstimulated (M0) [F71]

value: Unstimulated (M0)


title: E10.5 WT FL 3


title: E10.5 WT FL 2


title: OGT KO BMDMs; LPS-stimulated (M1) [F72]

value: OGT KO


title: E10.5 Mut FL 3


title: WT BMDMs; LPS-stimulated (M1) [F42]

value: 12 weeks


title: E10.5 Mut FL 2


title: E11.5 WT HL 1


title: E10.5 Mut FL 1


title: WT BMDMs; LPS-stimulated (M1) [F22]

value: Bone marrow-derived macrophages


title: E10.5 WT HL 3


title: patch93

city: Cambridge

first: Joshua

last: Levin

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description:
nuclear RNA
TPM.patch.tsv
cell760_C7_S29_L004

data_processing:
RSEM v1.2.87 was run on raw fastq fileswith default parameters on alignments created by Bowtie on UCSC gene annotation
TPM estimates were tranformed to log space by taking log TPM +1
TopHat2 v2.0.10 was used to map fastq files to mm10 reference
RNASeq-QC was run on the TopHat2 bamfiles to get QC metrics
For TRN and patch-seq samples, cells were removed if they had less than 40% genome mapping rate or or less than 1500 detected genes
Clustering and DE analysis of TRN samples was perfomed with biSNE software (https://github.com/yinqingl/nucseq_analysis), including normalizing the log TPM data to a normalized log TPM
For non-TRN samples, nuclei expressing <1500 genes were removed
Seurat v2.2.0 was used for clustering of the non-TRN samples
Genome_build: mm10
Supplementary_files_format_and_content: Formatted expression matrix (tab deliminated text file) with cells as columns, genes as rows, and TPM values as entries

source_name: TRN

extract_protocol:
Sucrose gradient nuclei isolation followed by FACS sorting for Violet+, Violet+ GFP+ or Violet+ NeuN+ nuclei
Modified SMARTseq2 single nuclei RNA-Seq

tag: sample type

value: sNuc-seq

tag: used for patch-seq

value: Yes

tag: facs sorting signal

tag: plate type

value: Patch-Seq


title: E10.5 WT HL 2

tag: age


title: WT BMDMs; Unstimulated (M0) [F21]

tag: genotype/variation


title: patch92

description:
nuclear RNA
TPM.patch.tsv
M460_F6_S59_L004


title: E10.5 WT HL 1


title: patch91

description:
nuclear RNA
TPM.patch.tsv
M459_C6_S28_L004


title: OGT KO BMDMs; Unstimulated (M0) [F61]

tag: cell type


title: OGT KO BMDMs; Unstimulated (M0) [F51]


title: patch87

description:
nuclear RNA
TPM.patch.tsv
M455_B5_S16_L004


title: Species Mixing - 350 cells/ul - SC_CA

city: Chicago

first: Ryan

middle: Patrick

last: Dohn

state: IL

address: 5841 S. Maryland Ave.

department: Department of Medicine

institute: University of Chicago

description:
Sample 10
Candida cells not diluted 4 hours prior to experiment
Requires processed files from samples 12 and 13 to filter out misaligned genes.

data_processing:
A Snakemake protocol called dropRunner was used to create an expression matrix corresponding to the UMI of each gene in a cell. https://github.com/aselewa/dropseqRunner
STARsolo (STAR 2.7.0a) was used for sequence alignment to the respective yeast genomes
Genome_build: sacCer3_s288c (S. cerevisiae); A21-s02-m09-r10 (C. albicans)
Supplementary_files_format_and_content: Matrix table with raw UMI counts for every gene and every cell, cell barcode file, and gene id file.
Supplementary_files_format_and_content: Tab delimited raw count table with gene and barcode ids (Samples 3 and 4).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene (Samples 14 and 15)

organism:
Saccharomyces cerevisiae
Candida albicans

source_name: S. cerevisiae and C. albicans cells

growth_protocol: Yeast cells were grown in suspension in rich YEPD media over night and diluted 4 hours prior to experiment to obtain log phase growth.

extract_protocol:
Cells encapsulation into nL droplets using a microfluidic device along with oligo poly-dT beads and zymolyase containing lysis buffer. Cells were then incubated at 37°C for 15-25 minutes for lysis. mRNA was captured by the poly-dT oligo beads.
Reverse tracnription to cDNA was performed using a template switch oligo. Beads then underwent exonuclease treatment and PCR amplification. A Illumina Nextera (cat#FC-131-1096) was used with 500-600 pg cDNA for construction of sequencing libraries.

treatment_protocol: Heat Shock Cells incubated in 42°C thermomixer for 20 minutes prior to microfluidic encapsulation.

value: untreated


title: patch95

description:
nuclear RNA
TPM.patch.tsv
cell762_F7_S60_L004


title: WT BMDMs; Unstimulated (M0) [F41]


title: patch94

description:
nuclear RNA
TPM.patch.tsv
cell761_D7_S40_L004


title: WT BMDMs; Unstimulated (M0) [F31]


title: RB_MG_2

city: Jinan

first: jianhua

last: zhang

address: gongyebei street No. 23788

institute: Shandong Academy of Agricultural Sciences

description: RBSDV infection in Laodelphax striatellus (Fallén) midgut

data_processing:
circRNA-Seq: Firstly, Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined
circRNA-Seq: We used Bowtie2 and Tophat2 to map reads to the genome of species. Remaining reads (unmapped reads) were still mapped to genome using tophat-fusion
circRNA-Seq: CIRCExplorer was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion and CIRCExplorer.
Genome_build: https://www.ncbi.nlm.nih.gov/genome/?term=Laodelphax+striatellus
Supplementary_files_format_and_content: excel,expression profiles

organism: Laodelphax striatellus

source_name: midgut

growth_protocol: Laodelphax striatellus was reared in an incubator with rice plants at the tillering stage at 27 ± 1°C, humidity 70%–80% and 16 h light: 8 h dark photoperiod.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina HiSeq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The 3rd-instar L. striatellus nymphs were reared on RBSDV-infected rice plants for two days. Then, the nymphs were transferred to healthy rice seedlings. After two days later, the nymph was collected as RBSDV-infected samples. Meanwhile, the 3rd-instar L. striatellus was reared on healthy rice seedlings for four days, and the nymph was collected as virus free samples.

value: midgut

tag: condition

value: reared on RBSDV infected rice


title: patch83

description:
nuclear RNA
TPM.patch.tsv
X748_G6_S69_L004


title: patch85

description:
nuclear RNA
TPM.patch.tsv
X8_H10_S82_L004


title: WT_MG_2

description: virus free (VF)  Laodelphax striatellus (Fallén) midgut

value: reared on uninfected rice


title: RB_MG_3


title: patch82

description:
nuclear RNA
TPM.patch.tsv
X747_E6_S49_L004


title: patch88

description:
nuclear RNA
TPM.patch.tsv
M456_D5_S38_L004


title: patch84

description:
nuclear RNA
TPM.patch.tsv
X7_G10_S73_L004


title: OGT KO BMDMs; Unstimulated (M0) [F81]


title: WT BMDMs; Unstimulated (M0) [F11]

value: WT


title: patch79

description:
nuclear RNA
TPM.patch.tsv
X744_A6_S6_L004


title: Species Mixing - 700 cells/ul - SC

description:
Sample 11
Candida cells not diluted 4 hours prior to experiment
Requires processed files from samples 12 and 13 to filter out misaligned genes.


title: OTTA2014_3798_REPB1

city: Vancouver

middle: S

last: Anglesio

state: BC

department: Obstetrics and Gynecology

country: Canada

institute: University of British Columbia

description: single-sample normalized data

hyb_protocol: NanoString Gene Expression protocol using 500ng of Total RNA as measured by NanoDrop spectrophotmeter. RNA is combined with capture and reporter codesets, and hybridization buffer. Reaction mixtures are hybridized in a thermal cycler at 65C for either short (16H) or long (20H) hybridization. Samples are then washed and fixed to cartridges using the nCounter Prep Station (high-sensitivity mode) for imaging.

scan_protocol: imaging on nCounter Digital Analyzer at maximum FOV

data_processing: Samples data is processed and normalized following protocols described in Talhouk et al (PMID: 27096160) using PrOTYPE. Briefly: Count data is Log2 transformed, the mean of housekeeping genes (ACTB, RPL19, SDHA, POLR1B, and PGK1) subtracted on a per-sample basis, and then normalized relative to reference samples (denoted as Pool1, Pool2, and Pool3). Code available at https://github.com/AlineTalhouk/PrOType

source_name: primary high-grade serous tubo-ovarian carcinoma

label_protocol: NanoString probe-specific unique barcode

extract_protocol: Total RNA extracted with the Qiagen miRNeasy FFPE kit (modified protocol)

tag: diagnosis

value: HGSOC

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

value: unknown

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

tag: vital status

value: dead

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

value: presumed adnexal

tag: experiment site

value: USC

tag: site id

value: BRO


title: patch90

description:
nuclear RNA
TPM.patch.tsv
M458_H5_S78_L004

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: RB_MG_1

tag: tissue

tag: condition


title: E10.5 WT FL 1

description: 3nt were trimmed from terminal 3' end using fastx

tag: strain

value: Forelimb bud

tag: age

tag: genotype


title: WT_MG_3


title: patch75

description:
nuclear RNA
TPM.patch.tsv
X740_A5_S5_L004


title: OTTA2014_3764_REPB1

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

tag: year of diagnosis

value: adnexal


title: patch81

description:
nuclear RNA
TPM.patch.tsv
X746_D6_S39_L004

tag: sample type

tag: used for patch-seq


title: WT_MG_1


title: patch86

description:
nuclear RNA
TPM.patch.tsv
X8_H1_S74_L004

tag: facs sorting signal

tag: plate type


title: OTTA2014_2451_REPB1

description: single-sample normalized data

tag: vital status

tag: overall survival time

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

tag: experiment site

value: VAN

tag: site id


title: OTTA2014_2437_REPB1

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: high

value: any

value: alive


title: patch70

description:
nuclear RNA
TPM.patch.tsv
X3_C10_S32_L004

value: sNuc-seq

value: Yes

value: Patch-Seq


title: OTTA2014_2428_REPB1

description: single-sample normalized data

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity


title: patch89

description:
nuclear RNA
TPM.patch.tsv
M457_F5_S58_L004

tag: sample type

tag: used for patch-seq

tag: facs sorting signal


title: OTTA2014_3807_REPB1

description: single-sample normalized data

tag: year of diagnosis

tag: vital status

tag: overall survival time


title: patch66

description:
nuclear RNA
TPM.patch.tsv
X336_E9_S52_L004

tag: plate type


title: OTTA2014_3791_REPB1

description: single-sample normalized data

tag: progression-free survival time

tag: study entry delay

tag: anatomical site

tag: experiment site


title: patch80

description:
nuclear RNA
TPM.patch.tsv
X745_B6_S17_L004


title: OTTA2014_2335_REPB1

description: single-sample normalized data

tag: diagnosis

tag: sample region cellularity

tag: sample region necrosis

tag: site id


title: OTTA2014_2328_REPB1

description: single-sample normalized data

tag: age at diagnosis

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status


title: OTTA2014_3778_REPB1

description: single-sample normalized data

tag: race/ethnicity


title: patch77

description:
nuclear RNA
TPM.patch.tsv
X742_E5_S48_L004

tag: sample type

tag: used for patch-seq

tag: facs sorting signal


title: patch76

description:
nuclear RNA
TPM.patch.tsv
X741_C5_S27_L004

tag: plate type


title: OTTA2014_3785_REPB1

description: single-sample normalized data

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time


title: OTTA2014_3769_REPB1

description: single-sample normalized data

tag: diagnosis

tag: study entry delay

tag: anatomical site

tag: experiment site


title: patch74

description:
nuclear RNA
TPM.patch.tsv
X6_F10_S63_L004


title: patch73

description:
nuclear RNA
TPM.patch.tsv
X5_E10_S53_L004


title: patch72

description:
nuclear RNA
TPM.patch.tsv
X4_D10_S43_L004


title: OTTA2014_2446_REPB1

description: single-sample normalized data

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: site id


title: OTTA2014_2452_REPB1

description: single-sample normalized data

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity


title: patch78

description:
nuclear RNA
TPM.patch.tsv
X743_G5_S68_L004

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_2445_REPB1

description: single-sample normalized data

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time


title: patch71

description:
nuclear RNA
TPM.patch.tsv
X3_C11_S33_L004


title: patch63

description:
nuclear RNA
TPM.patch.tsv
X333_B9_S20_L004


title: OTTA2014_2274_REPB1

description: single-sample normalized data

tag: diagnosis

tag: study entry delay

tag: anatomical site

tag: experiment site


title: patch62

description:
nuclear RNA
TPM.patch.tsv
X332_A9_S9_L004


title: patch68

description:
nuclear RNA
TPM.patch.tsv
X338_G9_S72_L004


title: OTTA2014_2266_REPB1

description: single-sample normalized data

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: pathogenic BRCA2 mutation

tag: site id


title: patch69

description:
nuclear RNA
TPM.patch.tsv
X339_H9_S81_L004


title: OTTA2014_2426_REPB1

description: single-sample normalized data

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity


title: OTTA2014_2435_REPB1

description: single-sample normalized data


title: patch67

description:
nuclear RNA
TPM.patch.tsv
X337_F9_S62_L004

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_2296_REPB1

description: single-sample normalized data

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time


title: OTTA2014_2181_REPB1

description: single-sample normalized data

tag: diagnosis

tag: study entry delay

tag: anatomical site

tag: experiment site


title: patch60

description:
nuclear RNA
TPM.patch.tsv
X330_G8_S71_L004


title: patch59

description:
nuclear RNA
TPM.patch.tsv
X32_H4_S77_L004


title: OTTA2014_2385_REPB1

description: single-sample normalized data

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: site id


title: patch64

description:
nuclear RNA
TPM.patch.tsv
X334_C9_S31_L004


title: patch56

description:
nuclear RNA
TPM.patch.tsv
X327_D8_S41_L004


title: OTTA2014_2148_REPB1

description: single-sample normalized data

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity


title: OTTA2014_2173_REPB1

description: single-sample normalized data


title: patch55

description:
nuclear RNA
TPM.patch.tsv
X326_C8_S30_L004

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_1425_REPB1

description: single-sample normalized data

value: white

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: LAX


title: patch65

description:
nuclear RNA
TPM.patch.tsv
X335_D9_S42_L004


title: patch61

description:
nuclear RNA
TPM.patch.tsv
X331_H8_S80_L004


title: patch52

description:
nuclear RNA
TPM.patch.tsv
X323_H7_S79_L004


title: OTTA2014_2287_REPB1

description: single-sample normalized data

tag: diagnosis

value: HGSOC

value: unknown

tag: study entry delay

tag: anatomical site

tag: experiment site


title: patch57

description:
nuclear RNA
TPM.patch.tsv
X328_E8_S51_L004


title: patch58

description:
nuclear RNA
TPM.patch.tsv
X329_F8_S61_L004


title: patch50

description:
nuclear RNA
TPM.patch.tsv
X320_E7_S50_L004


title: OTTA2014_2082_REPB1

description: single-sample normalized data

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: dead

tag: site id


title: OTTA2014_2103_REPB1

description: single-sample normalized data

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity


title: patch47

description:
nuclear RNA
TPM.patch.tsv
X2_B11_S22_L004

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_1421_REPB1

description: single-sample normalized data

value: low

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: presumed adnexal

value: USC


title: OTTA2014_1419_REPB1

description: single-sample normalized data

tag: diagnosis

tag: study entry delay

tag: anatomical site

tag: experiment site


title: patch53

description:
nuclear RNA
TPM.patch.tsv
X324_A8_S8_L004


title: OTTA2014_2063_REPB1

description: single-sample normalized data

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: adnexal

tag: site id


title: OTTA2014_1416_REPB1

description: single-sample normalized data

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

value: all wildtypes

tag: race/ethnicity


title: OTTA2014_1424_REPB1

description: single-sample normalized data

value: high


title: OTTA2014_1422_REPB1

description: single-sample normalized data

value: pathogenic BRCA1 mutation


title: patch48

description:
nuclear RNA
TPM.patch.tsv
X316_A7_S7_L004

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: patch51

description:
nuclear RNA
TPM.patch.tsv
X322_G7_S70_L004


title: patch49

description:
nuclear RNA
TPM.patch.tsv
X317_B7_S18_L004


title: OTTA2014_1420_REPB1

description: single-sample normalized data

value: hispanic

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time


title: OTTA2014_1418_REPB1

description: single-sample normalized data

tag: diagnosis

tag: study entry delay

tag: anatomical site

tag: experiment site


title: patch46

description:
nuclear RNA
TPM.patch.tsv
X2_B10_S21_L004

value: sNuc-seq


title: patch54

description:
nuclear RNA
TPM.patch.tsv
X325_B8_S19_L004

value: Yes


title: OTTA2014_1412_REPB1

description: single-sample normalized data

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: alive

tag: site id


title: patch41

description:
nuclear RNA
TPM.patch.tsv
patchseq_170204_9_S201

value: Patch-Seq


title: OTTA2014_1417_REPB1

description: single-sample normalized data

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: white


title: patch44

description:
nuclear RNA
TPM.patch.tsv
X1_A11_S11_L004

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: patch40

description:
nuclear RNA
TPM.patch.tsv
patchseq_170204_8_S284


title: OTTA2014_1409_REPB1

description: single-sample normalized data

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time

value: LAX


title: patch39

description:
nuclear RNA
TPM.patch.tsv
patchseq_170204_7_S272


title: patch45

description:
nuclear RNA
TPM.patch.tsv
X24_H3_S76_L004


title: OTTA2014_1410_REPB1

description: single-sample normalized data

tag: diagnosis

value: HGSOC

value: any

tag: study entry delay

tag: anatomical site

tag: experiment site


title: OTTA2014_1415_REPB1

description: single-sample normalized data

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

value: pathogenic BRCA2 mutation

value: dead

tag: site id


title: patch42

description:
nuclear RNA
TPM.patch.tsv
X16_H2_S75_L004


title: OTTA2014_1411_REPB1

description: single-sample normalized data

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity

value: presumed adnexal


title: OTTA2014_1407_REPB1

description: single-sample normalized data

value: USC


title: OTTA2014_1414_REPB1

description: single-sample normalized data


title: patch36

description:
nuclear RNA
TPM.patch.tsv
patchseq_170204_4_S236

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: OTTA2014_1408_REPB1

description: single-sample normalized data

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time


title: patch37

description:
nuclear RNA
TPM.patch.tsv
patchseq_170204_5_S248


title: OTTA2014_1406_REPB1

description: single-sample normalized data

tag: diagnosis

tag: study entry delay

tag: anatomical site

tag: experiment site


title: OTTA2014_1403_REPB1

description: single-sample normalized data

tag: sample region cellularity

tag: sample region necrosis

tag: age at diagnosis

tag: site id


title: OTTA2014_1402_REPB1

description: single-sample normalized data

tag: Stage

tag: residual disease status

tag: brca1 and brca2 germline mutation status

tag: race/ethnicity


title: patch33

description:
nuclear RNA
TPM.patch.tsv
patchseq_170204_33_S204

tag: sample type

tag: used for patch-seq

tag: facs sorting signal

tag: plate type


title: patch31

description:
nuclear RNA
TPM.patch.tsv
patchseq_170204_31_S275


title: OTTA2014_1401_REPB1

description: single-sample normalized data

tag: year of diagnosis

tag: vital status

tag: overall survival time

tag: progression-free survival time