title: p53-FKBP12F36V, H1299, AceTAGp300CBP-1, 24hr, R3

description:
AceTAGp300CBP_R3_induced
10INDP300CBP24HR_S33_R1_001


title: FA34

status: Public on Aug 21 2025

type: SRA

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

country: USA

institute: University of Alabama at Birmingham

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trim_Galore v0.6.10, and masked for low-complexity or low-quality sequence, then mapped to Mus_musculus.GRCm39.107  whole genome using star2.7.1a.  Counts were generated with the subread v2.0.6 and the featureCounts -p -t expm -g gene_id -a -o
Count matrixes were then analyzed using DESeq2 v1.28.1 to caculate differentialy expressed genes and normalized counts
DeSeq2 Normalized counts were calcuated by counts divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene
Assembly: Mus_musculus.GRCm39.107
Supplementary files format and content: csv file with normalized counts for each gene

molecule: total RNA

organism: Mus musculus

extract_protocol:
Zymo Direct-Zol mini prep plus kit
Libraries were prepared for sequencing using standard Illumina protocols, and poly A selection

tag: tissue

value: Kidney

tag: Sex

value: female

tag: treatment

value: inactive


title: p53-FKBP12F36V, H1299, AceTAGp300CBP-1, 24hr, R1

city: LA JOLLA

first: Christopher

last: Parker

state: CA

address: 10550 North Torrey Pines Road SR311E

institute: Scripps Research

description:
AceTAGp300CBP_R1_induced
10INDP300CBP24HR_S31_R1_001

data_processing:
Raw data was converted to fastq files using the Element base2fastq script using default settings.
Assembly: StringTie
Supplementary files format and content: Tab-delimited text files including raw counts and DESeq2 normalized counts for each Sample.

organism: Homo sapiens

source_name: p53-FKBP12F36V-induced H1299

growth_protocol: H1299 cells were cultured in complete RPMI supplemented with 10% FBS, 1% (v/v) penicillin/streptomycin, 2 mM glutamine, 10 mM HEPES, and 1 mM sodium pyruvate. Doxycycline-inducible wild-type or mutant p53-FKBP12F36V-HA H1299 cell lines were cultured in complete RPMI supplemented with 10% FBS, 1% (v/v) penicillin/streptomycin, 2 mM glutamine, 10 mM HEPES, 1 mM sodium pyruvate, 1 mL/mL Blasticidin and 50 mg/mL G418. Cells were cultured at 37℃ with 5% CO2.

extract_protocol:
RNA samples were extracted using Quick-RNA MiniPrep Kit (Zymo Research) following manufacturer’s recommended protocol.
Total RNA samples were prepared into RNAseq libraries using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s recommended protocol.

treatment_protocol: Doxycycline-inducible wild-type p53-FKBP12F36V-HA H1299 cells were plated in 6-well plates 24 h before AceTAG treatment. Cells were treated with doxycycline following by AceTAG in complete RPMI (without Blasticidin and G418) when the cells were about 50-60% confluent.

tag: cell line

value: p53-FKBP12F36V-induced H1299

tag: cell type

value: Non-small cell lung cancer

tag: genotype

value: wt


title: Mouse heart, Rac1 cKI/cKI; Myh6-Cre; saline-treated, biol rep 3

city: Ann Arbor

first: James

middle: P

last: Teuber

state: MI

address: 1150 W Medical Center Dr

department: Pharmacology

institute: University of Michigan

description:
Library name: B3_204F
B3_204F

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
HISAT2 (2.2.1) used to build the index of the reference genome, aligning paired-end clean reads to 3 the reference genome.
featureCounts (2.0.6) was used to count the reads numbers mapped to each gene.
Prior to differential gene expression analysis, for each sequencing library, read counts were 4 adjusted using the edgeR R package (4.0.16) by scaling normalization factors to eliminate differences in sequencing depth between samples, followed by differential expression analysis. The resulting P value is adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate. The threshold of significant differential expression： padj <= 0.05 ＆ |log2(foldchange)| >= 1.
Assembly: mm39
Supplementary files format and content: .txt files include raw counts and fpkm values per sample.

source_name: Mouse heart 8-10 weeks

extract_protocol:
RNA was extracted with the Qiagen RNeasy Mini Kit (Qiagen #74104).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. Library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Mouse heart 8-10 weeks

value: Ventricular tissue

value: Rac1 cKI/cKI; Myh6-Cre

value: Saline 3 days

tag: time

value: 3 days

tag: batch


title: FA33


title: FA31


title: Mouse heart, Rac1 cKI/cKI; Myh6-Cre; saline-treated, biol rep 1

description:
Library name: B1_206M
B1_206M


title: FA29

value: active


title: p53-FKBP12F36V, H1299, AceTAGPCAFGCN5-4, 24hr, R1

description:
AceTAG-PCAFGCN5_R1_induced
11INDPCAFGCN524HR_S34_R1_001


title: Mouse heart, Rac1 cKI/cKI; --; saline treated, biol rep 3

description:
Library name: A3_207F
A3_207F

value: Rac1 cKI/cKI; --


title: FA32


title: FA30


title: Abl_2

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

description: Library name: Abl_2

library_source: genomic

data_processing:
Fastq files were aligned to human genome build hg38 using bowtie2 v2.4.2 8.
PCR duplicates were marked and removed using Picard MarkDuplicates v2.24.1 (https://broadinstitute.github.io/picard/).
Peaks were called using Genrich v0.6.1 in ATAC-Seq mode (https://github.com/jsh58/Genrich?tab=readme-ov-file#atacseq).
Called peaks had the ENCODE blacklisted regions removed.
Assembly: hg38
Supplementary files format and content: narrowPeak calls using Genrich

molecule: genomic DNA

source_name: LNCaP-Abl

extract_protocol:
Nuclei Isolation and ATACseq: Cultured cells were freshly dissociated with TrypLE at 37℃ and washed with ice-cold PBS. Nuclei isolation and transposition was performed using the OMNI-ATACseq protocol (1) with some few adjustments 7. Briefly, 200, 000 cells were pelleted at 500 rcf for 5 minutes in a pre-chilled (4°C) fixed-angle centrifuge. Supernatant was carefully discarded in a 2-step method using a P1000 pipette followed by a P200 pipette. Pelleted cells were then resuspend-ed in 100 µL ice-cold lysis buffer comprising ATACseq resuspension buffer (A-RSB; 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 in nuclease free H2O) supplemented with NP-40, tween-20 and digitonin at final concentrations of 0.1%, 0.1% and 0.01% respectively. After 3 minutes of lysis re-action on ice, 1ml of ice-cold wash buffer (A-RSB supplemented with tween-20; 0.1% final concen-tration) was added and the tubes inverted to mix. The nuclei were then pelleted by centrifugation, and suspension carefully discarded (as previously described). For transposition, nuclei were resus-pended in a 50 µL transposition mix (2x TD buffer, PBS, 0.01% digitonin, 0.1 % tween 20, nucle-ase-free H20 and TDE1Tn5 transposase enzyme). Transposition was performed at 37°C for 30 minutes in a thermomixer with shaking at 850 rpm. Transposed DNA was cleaned up using the MinElute® PCR purification kit.
Libraries were generated as previously described (2), double-sized selected using AMPure XP beads and eluted in EB buffer. For sequencing, 16 libraries were pooled together and sequenced pair-end in a NextSeq P3.

value: LNCaP-Abl

value: prostate tumor cell line


title: FA27


title: FA28


title: FA26


title: FA25


title: Mouse heart, Rac1 cKI/cKI; --; saline treated, biol rep 2

description:
Library name: A2_205M
A2_205M


title: Mouse heart, Rac1 cKI/cKI; --; saline treated, biol rep 1

description:
Library name: A1_202M
A1_202M


title: iMCs, type IV collagen, biol rep 3

city: Homburg

first: Carole

last: Luthold

state: Saarland

address: Kirrberger Straße

country: Germany

institute: Saarland University

description: Library name: D3

data_processing:
(performed by Novogene) Raw reads were processed with fastp to remove adapters and low-quality reads. Clean reads were aligned to the Mus musculus genome (GRCm39/mm39) using HISAT2, and gene expression was quantified with featureCounts and normalized as FPKM values.
Assembly: GRCm39/mm39
Supplementary files format and content: Plain text, comma-separated (.csv) file containing raw gene counts. Rows correspond to Ensembl gene IDs, and columns correspond to individual samples (and replicates). The final column includes gene names.

source_name: melanocytes

growth_protocol: iMCs were maintained in RPMI supplemented with 10% fetal bovine serum (FBS), penicillin (100 U/ml), streptomycin (100 μg/ml), 100 nM sodium pyruvate, 10 mM non-essential amino acids, 200 nM TPA (12-O-tetradecanoylphorbol-13-acetate) and 200 pM cholera toxin.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) or the RNeasy Mini Kit (QIAGEN), following the manufacturer’s instructions.
(performed by Novogene) Polyadenylated mRNAs were enriched, fragmented, and reverse-transcribed into cDNA. Strand-specific libraries were prepared and quality-checked using Qubit, real-time PCR, and a Bioanalyzer, then sequenced on Illumina platforms (2 × 150 bp), generating approximately 25 million paired-end reads per sample.

value: melanocytes


title: KPPC panKRASi early

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

library_source: transcriptomic single cell

data_processing:
This dataset was processed using Cellranger (version 7.1.0) and mm39 reference genome (Gencode M34). Quality control and downstream analyses were conducted using the R environment (version 4.3.0), and Seurat package (version 5.0.3). Low-quality cells were excluded based on the mitochondrial percentage (< 5%) and total expressed genes per cell (> 300 and < 6200). Next, the normalization, dimensionality reduction, and clustering analysis were performed using functions, ScTransform, RunPCA, and FindClusters, respectively. The principal components and clustering resolution threshold were defined as 25 PCs and 0.25. Finally, we carried out manual annotation based on multiple markers identified in prior studies 31. The gene markers gene markers evaluated through Violin Plots (VlnPlot), and DotPlot based on TOP30 differential expressed genes (FindMarkers - Wilcox Test).
Assembly: mm39
Supplementary files format and content: Feature-barcode files include UMI counts in a sparse matrix format and are the output files from CellRanger.

molecule: polyA RNA

source_name: Pancreas/tumor

extract_protocol:
Pancreas/tumors were digested in 4 mg/mL collagenase IV and 4 mg/mL dispase. Samples were stained with eFluor780 Fixable Viablity dye and live cells sorted. 10,000 cells were loaded 10x Chromium X to generate Single Cell 3' Gene Expression dual indexed libraries (10x Genomics).
The creation of Gel Bead-In-Emulsions (GEM) and subsequent cell barcoding, GEM-RT cleanup, cDNA amplification, and library assembly were performed with the Chromium Next GEM Single Cell 3’ Reagents Kits v3.1 (10x Genomics) according to manufacturer’s instructions.

value: Pancreas/tumor

value: LSL-KRASG12D; Trp53loxP/loxP; Pdx1-Cre

value: panKRASi early

tag: treatment duration

value: Treated for 2 weeks


title: Mouse heart, Rac1 cKI/cKI; --; AngII (3mg/kg/d, 3 days) treated, biol rep 1

description:
Library name: C1_221M
C1_221M

value: AngII 3mg/kg/d


title: KPPC panKRASi endpoint

value: panKRASi endpoint

value: Treated for 12 weeks


title: KPPC vehicle

value: Vehicle


title: iMCs, fibronectin, biol rep 3

description: Library name: D2


title: Mouse heart, Rac1 cKI/cKI; Myh6-Cre; saline-treated, biol rep 2

description:
Library name: B2_RM
B2_RM

value: Mouse heart 8-10 weeks

value: Ventricular tissue


title: iMCs, type I collagen, biol rep 3

description: Library name: D1


title: iMCs, type IV collagen, biol rep 2

description: Library name: B3


title: GFP+ nuclei from developing antenna of pooled time points (36, 42, 48 and 80 h APF) in control condition, sample1

city: Lausanne

first: Richard

last: Benton

address: Route Cantonale

country: Switzerland

institute: University of Lausanne

description:
Library name: Mel36_80a
10x Genomics

data_processing:
Raw snRNA-seq data was first processed through Cell Ranger (v6.1.2, 10x Genomics) with default parameters except -include introns- that was set to TRUE. A custom D. melanogaster reference genome and transcriptome from FlyBase (Drosophila_melanogaster.BDGP6.28.101) were used for mapping. Two marker genes, GFP and p35, were added to the GTF and FASTA files prior to building the custom genome reference with cellranger mkref (v6.1.2) function, following the 10x Genomics protocol.
Assembly: Drosophila_melanogaster.BDGP6.28.101
Supplementary files format and content: Demultiplexing, barcodes processing, gene counting and aggregation were made using Cell Ranger Software (V6.1.2, 10x Genomics) (https://www.10xgenomics.com/support/software/cell-ranger/latest) with default parameters except -include introns- that was set to TRUE. A custom D. melanogaster reference genome and transcriptome from FlyBase (Drosophila_melanogaster.BDGP6.28.101) were used for mapping. Two marker genes, GFP and p35, were added to the GTF and FASTA files prior to building the custom genome reference with cellranger mkref (v6.1.2) function, following the 10x Genomics protocol.

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: Developing antenna

growth_protocol: Flies were reared in vials containing standard wheat flour/yeast/fruit juice medium and in incubators with 12 h light:12 h dark cycles at 25°C

extract_protocol:
10-15 virgin peb-Gal4 females were placed in vials with 5-10 UAS-unc84:GFP or UAS-p35,UAS-un84:GFP males for 5 days, after which adults were removed. White pupae (corresponding to 0 h after puparium formation (APF)) were carefully transferred to fresh vials and aged for 18, 24, 30, 36, 42, 48, 56, 64, 72 or 80 additional hours. Developing antennae from aged pupae were dissected in ice cold Schneider’s medium (Gibco, 21720024) and immediately transferred to 1.8 ml Eppendorf tubes containing 100 µl Schneider’s medium, flash-frozen in liquid nitrogen and stored at -80°C. The numbers of antennae dissected in control (peb-Gal4/+,UAS-unc84:GFP/+) and PCD-blocked (peb-Gal4/+,UAS-p35/+,UAS-unc84:GFP/+) genotypes are as follows (time-point in h APF (n antennae control / n antennae PCD-blocked): 18 (49 / 57), 24 (72 / 52), 30 (67 / 56), 36 (52 / 51), 42 (45 / 48), 48 (45 / 55), 56 (59 / 49), 64 (48 / 60), 72 (54 / 62) and 80 (47 / 53).  Samples were thawed on dry ice and nuclear suspensions prepared as described (Li et al., 2022; McLaughlin et al., 2021). Suspensions from “early” (18/24/30 h APF), “mid” (36/42/48 h APF) and “late” (56/64/72/80 h APF) developmental time points were pooled together, with the exception of time point 80 h APF in the control genotype, which was pooled with mid time points. This latter pooling reflected the initial experimental design, but 80 h APF control cells could be effectively re-classified in the late time point for all subsequent analyses. After addition of Hoechst 33342 (Thermo Fisher Scientific, 62249), samples were loaded into a FACSAria flow cytometer.
For each pooled sample, 2 ´ 20,000 GFP-positive nuclei were sorted (20,000 for early nuclei in PCD-blocked condition), which were immediately loaded onto the Chromium Next GEM Chip (10x Genomics). Sequencing libraries were prepared with the Chromium Single Cell 3ʹ reagent kit v3.1 dual index, following the manufacturer’s recommendations. Libraries were quantified by a fluorometric method and quality was assessed on a Fragment Analyzer (Agilent Technologies). Sequencing was performed on an Illumina NovaSeq 6000 v1.5 flow cell for 100 cycles according to 10x Genomicsʹ recommendations (28 cycles read1, 10 cycles i7 index read, 10 cycles i5 index, and 90 cycles read2). Demultiplexing was performed with bcl2fastq2 Conversion Software (v2.20, Illumina).

value: Developing antenna

value: Antennal cells


title: GFP+ nuclei from developing antenna of pooled time points (18, 24 and 30 h APF) in control condition, sample1

description:
Library name: Mel18_30a
10x Genomics


title: GFP+ nuclei from developing antenna of pooled time points (56, 64 and 72 h APF) in control condition, sample2

description:
Library name: Mel56_72b
10x Genomics


title: GFP+ nuclei from developing antenna of pooled time points (18, 24 and 30 h APF) in control condition, sample2

description:
Library name: Mel18_30b
10x Genomics


title: GFP+ nuclei from developing antenna of pooled time points (56, 64 and 72 h APF) in control condition, sample1

description:
Library name: Mel56_72a
10x Genomics


title: GFP+ nuclei from developing antenna of pooled time points (36, 42, 48 and 80 h APF) in control condition, sample2

description:
Library name: Mel36_80b
10x Genomics


title: GFP+ nuclei from developing antenna of pooled time points (56, 64, 72 and 80 h APF) in PCD-blocked condition, sample2

description:
Library name: p3556_80b
10x Genomics


title: GFP+ nuclei from developing antenna of pooled time points (36, 42 and 48 h APF) in PCD-blocked condition, sample1

description:
Library name: p3536_48a
10x Genomics


title: iMCs, fibronectin, biol rep 1

description: Library name: A2


title: iMCs, type I collagen, biol rep 2

description: Library name: B1


title: sample d7: mix of flies resulting from crosses between BDSC lines 66472 x 68265, 66472 x 68322, 66472 x 68255

city: New York

first: Bogdan

last: Sieriebriennikov

state: NY

address: 100 Washington Sq E

institute: New York University

description: 10X Genomics

data_processing:
Gene- and cell-level counts were generated using Cellranger 7.0.0
Assembly: BDGP6.32
Supplementary files format and content: Tab-separated values files and matrix files

source_name: central brain

extract_protocol:
DRAQ5+,GFP+ cells were FAC-sorted to enrich the samples for Kenyon cells. mtdTomato expression was not used for sorting. Given the prior knowledge that different classes of Kenyon cells separate well during the analysis of single-cell data, the brains of flies where the subtypes of different classes were labeled (e.g. γd, α′/β′ap, and α/βs) were pooled in different combinations before the dissociation to minimize batch effects.
Following manufacturer's instructions

value: central brain

value: Kenyon cells


title: GFP+ nuclei from developing antenna of pooled time points (56, 64, 72 and 80 h APF) in PCD-blocked condition, sample1

description:
Library name: p3556_80a
10x Genomics


title: sample d6: mix of flies resulting from crosses between BDSC lines 66472 x 68267, 66472 x 68370, 66472 x 68256

description: 10X Genomics


title: GFP+ nuclei from developing antenna of pooled time points (18, 24 and 30 h APF) in PCD-blocked condition

description:
Library name: p3518_30b
10x Genomics


title: iMCs, type I collagen, biol rep 1

description: Library name: A1


title: sample d8: mix of flies resulting from crosses between BDSC lines 66472 x 68265, 66472 x 68322, 66472 x 68255

description: 10X Genomics


title: GFP+ nuclei from developing antenna of pooled time points (36, 42 and 48 h APF) in PCD-blocked condition, sample2

description:
Library name: p3536_48b
10x Genomics


title: sample d5: mix of flies resulting from crosses between BDSC lines 66472 x 68267, 66472 x 68370, 66472 x 68256

description: 10X Genomics


title: sample d4: mix of flies resulting from crosses between BDSC lines 66472 x 68267, 66472 x 68370, 66472 x 68256

description: 10X Genomics


title: sample d3: mix of flies resulting from crosses between BDSC lines 66472 x 68267, 66472 x 68370, 66472 x 68256

description: 10X Genomics


title: sample d2: mix of flies resulting from crosses between BDSC lines 66472 x 68267, 66472 x 68370, 66472 x 68256

description: 10X Genomics


title: C57BL/6J Nlrc4-/- Casp11-/- mice, EpCAM+ cells from cecum and colon, 48h post infection with Shigella flexeneri, rep6

city: Berkeley

first: Kevin

middle: D

last: Eislmayr

state: California

address: 415 Weill Hall

institute: UC Berkeley

description: Library name: SF6

data_processing:
After demultiplexing, raw data were pre-processed (including quality control as well as barcode, adaptor, and quality trimming) using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/) and cutadapt, mapped to the Mus_musculus.GRCm38.96 genome assembly using Kallisto (0.44.0 via Bioconda).
Assembly: Mus_musculus.GRCm38.96
Supplementary files format and content: tab-delimited text file includes estimated raw counts for each sample from Kallisto

source_name: cecum and colon

extract_protocol:
Cells were lysed in Trizol, Chloroform extracted and the RNA was isolated using the Monarch Total RNA Miniprep Kit (NEB #T2010S) following the manufacturer’s protocol with on-column DNase treatment
Isolated RNA was polyA enriched and further processed – including library contruction and multiplexing — by using the RNA Sequencing service from Genewiz/Azenta

treatment_protocol: Mice were cohaused for three weeks. One day before infection, they were deprived of food and water in the morning and 4-6 hours later orally gavaged with 100 µL of 250 mg/mL streptomycin sulfate dissolved in pharmaceutical grade PBS, after which mice were again given food and water. On the day of infection, food and water were removed again from the cage, and 4-6 hours later, mice were orally gavaged with 100 µL of 108 CFU/mL mid-log growing Shigella flexeneri. 48h after infection, the colon and cecum were isolated. EDTA treatment liberated epithelial cells that were further digested with Dispase and, finally, magnetic bead enriched for EpCAM+ cells using the MojoSort™ Mouse CD326 (Ep-CAM) Selection Kit.

value: cecum and colon

value: EpCAM+ cells


title: C57BL/6J Nlrc4-/- Casp11-/- mice, EpCAM+ cells from cecum and colon, 48h post infection with Shigella flexeneri, rep5

description: Library name: SF5


title: E2f2-/- DEN-HFD_13

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

data_processing:
FASTQs were trimmed for the adapters following the recommendations of the NEXTflex™ Small RNA-Seq Kit manufacturers. We used Bowtie  [1] to align the reads against the human genome (GRCh38), with a mismatch 0, to avoid false positives. We select mirbase v22 to quantify mature microRNAs employing Partek Flow application, software version 7.0. Only the miRNAs with 10 or more reads in the three replicas were considered. We carried out DESeq2 [3] a method for differential analysis of count data to compare the two groups.  1- Langmead B, Trapnell C, Pop M. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25–2009. -10-3-r25 (2009). 2. Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11:R25–2010. -11-3-r25 (2010). 3-Love MI., Huber, W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15(12):550  (2014).
Assembly: GRCh38
Supplementary files format and content: Processed data files ar *.tsv format and they content microRNA mirBase IDs and raw count numbers.

source_name: Liver

extract_protocol:
The NucleoSpin miRNA extraction kit was used for miRNA extraction
Sequencing libraries were prepared following the protocol included with the kit “NEXTflex™ Small RNA-Seq Kit v3,” (©Bioo Scientific Corp. Catalog #5132-05).

value: Liver

value: DEN-HFD


title: iMCs, fibronectin, biol rep 2

description: Library name: B2

value: melanocytes


title: C57BL/6J Nlrc4-/- Casp11-/- mice, EpCAM+ cells from cecum and colon, 48h post infection with Shigella flexeneri, rep2

description: Library name: SF2


title: E2f2-/- DEN-HFD_14


title: WT DEN-HFD_9

value: WT


title: iMCs, type IV collagen, biol rep 1

description: Library name: A3


title: E2f2-/- DEN-HFD_11


title: E2f2-/- DEN-HFD_12


title: E2f2-/- DEN-HFD_10


title: WT DEN-HFD_6


title: WT DEN-HFD_7


title: C57BL/6J Nlrc4-/- Casp11-/- mice, EpCAM+ cells from cecum and colon, 48h post infection with Shigella flexeneri, rep1

description: Library name: SF1


title: Cortex, stroke zone 5, immunoprecipitated RNA, rep 5

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include counts for each Sample

source_name: brain

extract_protocol:
Immunoprecipitation was performed according to Sanz et al, PNAS 2009. RNA was harvested using RNeasy Micro Plus kit (Qiagen)
cDNA and library preparation were prepared using Ovation RNA-Seq System V2 (NuGEN) and KAPA Hyper Prep Kit (KAPA Biosystems) following manufacturer's protocols. 500 ng of generated cDNA were first fragmented to 200bp using Covaris E210 (Covaris) and then used for library preparation following manufacturer's protocols. Libraries were pooled with equal molars for PE 50-bp sequencing on HiSeq 2500 (Illumina).

treatment_protocol: Mice were euthanized via exposure to terminal levels of isofluorane and perfused with PBS for 1min, 0.5% paraformaldehyde for 5min, and 20% sucrose for 5min; rate of 5ml/min. Brains were immediately extracted, frozen in powdered dry ice, and stored at -80C until sectioning. Brains were sectioned on a cryostat, relevant sections were mounted onto PET-membrane slides, and slides were briefly stored in 100% ethanol until laser capture. Relevant brain areas were isolated via laser capture microscopy and immediately collected in supplemented homogenization buffer and stored on ice until homogenization.

tag: brain region

value: Cortex

tag: disease state

value: Cortical stroke

tag: stroke zone

value: zone 5

tag: input or_ribosomally_loaded

value: ribosomally loaded

value: brain


title: C57BL/6J Nlrc4-/- Casp11-/- mice, EpCAM+ cells from cecum and colon, 48h post infection with Shigella flexeneri, rep3

description: Library name: SF3


title: C57BL/6J Nlrc4-/- Casp11-/- mice, EpCAM+ cells from cecum and colon, non-infected, rep5

description: Library name: NI5

value: non-infected


title: Cortex, stroke zone 5, immunoprecipitated RNA, rep 4


title: WT DEN-HFD_5


title: Cortex, stroke zone 5, immunoprecipitated RNA, rep 2


title: C57BL/6J Nlrc4-/- Casp11-/- mice, EpCAM+ cells from cecum and colon, non-infected, rep4

description: Library name: NI4


title: Cortex, stroke zone 5, immunoprecipitated RNA, rep 1


title: WT DEN-HFD_8


title: C57BL/6J Nlrc4-/- Casp11-/- mice, EpCAM+ cells from cecum and colon, non-infected, rep2

description: Library name: NI2


title: Cortex, stroke zone 5, immunoprecipitated RNA, rep 3


title: Cortex, stroke zone 4, immunoprecipitated RNA, rep 5

value: zone 4


title: C57BL/6J Nlrc4-/- Casp11-/- mice, EpCAM+ cells from cecum and colon, non-infected, rep3

description: Library name: NI3


title: Cortex, stroke zone 4, immunoprecipitated RNA, rep 3


title: C57BL/6J Nlrc4-/- Casp11-/- mice, EpCAM+ cells from cecum and colon, 48h post infection with Shigella flexeneri, rep4

description: Library name: SF4


title: Cortex, stroke zone 4, immunoprecipitated RNA, rep 2


title: C57BL/6J Nlrc4-/- Casp11-/- mice, EpCAM+ cells from cecum and colon, non-infected, rep1

description: Library name: NI1


title: Cortex, stroke zone 4, immunoprecipitated RNA, rep 1


title: Cortex, stroke zone 4, immunoprecipitated RNA, rep 4


title: pup-1; pup-2 rep. 2

city: Columbus

first: Wen

last: Tang

state: Ohio

address: 1060 Carmack Rd

department: Department of Biological Chemistry and Pharmacology

institute: The Ohio State University

description:
Library name: pup-1; pup-2 rep. 2
pup-1; pup-2 rep. 2

data_processing:
Raw reads weer trimmed of adapters and removed of poor quality sequences using TrimGalore.
Reads were aligned to the C. elegans reference genome (WS279) with Bowtie
Transcript counts were quantified using custom python scripts and Bedtools
Downstream analysis was preformed using R/Python/IGV.
Assembly: WS279
Supplementary files format and content: Unique Fasta File

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Synchronized L1 were platted and maintained at 20 C on NGM median supplemented with OP50 E. coli . Animals were then harvested when the population reached day 1 adulthood.

extract_protocol:
60,000 L1 larvae were plated to 150 mm NGM plates supplemented with 2 mL of concentrated OP50 food. Approximately 64 hours after plating L1 larvae, day 1 adults with eggs were collected from plates using M9 solution. Harvested animals were washed twice with M9 and once with water. Animals were then suspended in TRI Reagent solution (Sigma) and frozen at -80°C until RNA extraction was performed. To extract RNAs animals suspended in TRI Reagent solution were thawed and lysed using a Bead Mill (Thermo Fisher Scientific). Bromo-chloropropane (Sigma) was added to the lysed worms and centrifuged at 12,000 x g for 15 minutes. Following centrifugation, the aqueous phase was pipetted to an equal volume of cold isopropanol and placed at -20°C for 1 hour to precipitate RNAs. RNAs were pelleted by centrifugation at 20,000 x g for 15 minutes at 4°C. Total RNAs were washed with 75% EtOH twice and suspended in RNAse free water. Small RNAs were enriched using the miRVana miRNA kit.
Small RNAs were treated with RNA phosphatase PIR-1 to remove gamma and beta phosphates from the 5' triphosphorylated RNAs (50). Monophosphorylated RNAs were ligated to 3' adapters ( rAppAGATCGGAAGAGCACACGTCTGAACTCCAGTCA/3ddC/, IDT) using T4 RNA ligase 2 in 25% PEG 8000 (NEB) at 15 C overnight. A 5' adapter (rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU, IDT) was then ligated to RNAs to the product using T4 RNA ligase 1 (NEB) for 4 hours at 15 C. Ligated products were reverse transcribed using SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific) to convert RNA to cDNA libraries. cDNA libraries were amplified by PCR and subsequently sequenced on an Illumina Novaseq platform (SP2 x 50 bp) at the OSU Comprehensive Cancer Center genomics core.

value: whole animal

value: pup-1 (how53) III; pup-2 (tm4344) III


title: Cortex, stroke zone 3, immunoprecipitated RNA, rep 5

value: zone 3


title: pup-1; pup-2 rep. 1

description:
Library name: pup-1; pup-2 rep. 1
pup-1; pup-2 rep. 1


title: Cortex, stroke zone 3, immunoprecipitated RNA, rep 2


title: Cortex, stroke zone 3, immunoprecipitated RNA, rep 3


title: Cortex, stroke zone 3, immunoprecipitated RNA, rep 4


title: Cortex, stroke zone 2, immunoprecipitated RNA, rep 5

value: zone 2


title: pup-3 rep. 1

description:
Library name: pup-3 rep. 1
pup-3 rep. 1


title: pup-3 rep. 2

description:
Library name: pup-3 rep. 2
pup-3 rep. 2


title: Cortex, stroke zone 3, immunoprecipitated RNA, rep 1


title: Cortex, stroke zone 2, immunoprecipitated RNA, rep 3


title: Cortex, stroke zone 2, immunoprecipitated RNA, rep 1


title: pup-2 rep. 2

description:
Library name: pup-2 rep. 2
pup-2 rep. 2

value: pup-2 (tm4344) III


title: Cortex, stroke zone 2, immunoprecipitated RNA, rep 2


title: Cortex, stroke zone 1, immunoprecipitated RNA, rep 3

value: zone 1


title: Cortex, stroke zone 2, immunoprecipitated RNA, rep 4


title: pup-2 rep. 1

description:
Library name: pup-2 rep. 1
pup-2 rep. 1


title: Cortex, stroke zone 1, immunoprecipitated RNA, rep 5


title: Cortex, stroke zone 1, immunoprecipitated RNA, rep 1


title: disl2 rep. 2

description:
Library name: disl2 rep. 2
disl-2 rep. 2

data_processing:
Raw reads weer trimmed of adapters and removed of poor quality sequences using TrimGalore.
Reads were aligned to the C. elegans reference genome (WS279) with STAR aligner
Transcript counts were quantified using FeatureCounts. BAM files were converted to BigWig files using DeepTools with CPM normalization
Downstream analysis was preformed using R/Python/IGV.
Assembly: WS279
Supplementary files format and content: BigWig

extract_protocol:
60,000 L1 larvae were plated to 150 mm NGM plates supplemented with 2 mL of concentrated OP50 food. Approximately 64 hours after plating L1 larvae, day 1 adults with eggs were collected from plates using M9 solution. Harvested animals were washed twice with M9 and once with water. Animals were then suspended in TRI Reagent solution (Sigma) and frozen at -80°C until RNA extraction was performed. To extract RNAs animals suspended in TRI Reagent solution were thawed and lysed using a Bead Mill (Thermo Fisher Scientific). Bromo-chloropropane (Sigma) was added to the lysed worms and centrifuged at 12,000 x g for 15 minutes. Following centrifugation, the aqueous phase was pipetted to an equal volume of cold isopropanol and placed at -20°C for 1 hour to precipitate RNAs. RNAs were pelleted by centrifugation at 20,000 x g for 15 minutes at 4°C. Total RNAs were washed with 75% EtOH twice and suspended in RNAse free water.
Ribosomal RNAs (rRNAs) were depleted using the RNase H-based method. Specifically, 3 μg of total RNA was incubated with antisense DNA oligonucleotides targeting C. elegans and E. coli rRNAs, followed by digestion with Thermostable RNase H (NEB) at 45 °C for 30 min. The rRNA-depleted samples were treated with Turbo DNase (Thermo Fisher Scientific) at 37 °C for 30 min. RNAs longer than 200 nts were enriched using RNA Clean & Concentrator-5 (Zymo Research). Strand-specific mRNA sequencing libraries were constructed using Ultra II Directional RNA Library Prep Kit (NEB), according to the manufacturer’s instructions. Each library was barcoded, pooled, and sequenced on the HiSeq 4000 platform (2x150 bp, Illumina).

value: disl-2 (tm5337) III


title: disl2 rep. 1

description:
Library name: disl2 rep. 1
disl-2 rep. 1


title: White matter, stroke zone 5, immunoprecipitated RNA, rep 4

value: White matter

value: White matter stroke


title: Cortex, stroke zone 1, immunoprecipitated RNA, rep 4


title: White matter, stroke zone 5, immunoprecipitated RNA, rep 2


title: control rep. 2

description:
Library name: control rep. 2
control rep. 2

value: wild-type


title: control rep. 1

description:
Library name: control rep. 1
control rep. 1


title: White matter, stroke zone 4, immunoprecipitated RNA, rep 5


title: TOFU5_depletion_6hr disl-2(how27) rep. 2

description:
Library name: TOFU5_depletion_disl2_TP6_2
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I; disl-2(how27) III

data_processing:
Raw reads weer trimmed of adapters and removed of poor quality sequences using TrimGalore. Sequences were then collapsed and transformed into fasta files using cutsom shell scripts.
Reads were aligned to contaminating RNAs (rRNAs, tRNAs, snRNAs…) using Bowtie. Reads that failed to align were aligned to the genome using Bowtie.
Aligned reads were normalized and assigned to genomic features using custom shell scripts. Alignments were converted to BigWig files using UCSC Tools.
Downstream analysis was preformed using R/Python/IGV.
Assembly: WormBase WS279
Supplementary files format and content: Unique fasta file of collapsed reads

extract_protocol:
60,000 L1 larvae were plated to 150 mm NGM plates supplemented with 2 mL of concentrated OP50 food. Approximately 64 hours after plating L1 larvae, day 1 adults with eggs were collected from plates using M9 solution. Harvested animals were washed twice with M9 and once with water. Animals were then suspended in TRI Reagent solution (Sigma) and frozen at -80°C until RNA extraction was performed. To extract RNAs animals suspended in TRI Reagent solution were thawed and lysed using a Bead Mill (Thermo Fisher Scientific). Bromo-chloropropane (Sigma) was added to the lysed worms and centrifuged at 12,000 x g for 15 minutes. Following centrifugation, the aqueous phase was pipetted to an equal volume of cold isopropanol and placed at -20°C for 1 hour to precipitate RNAs. RNAs were pelleted by centrifugation at 20,000 x g for 15 minutes at 4°C. Total RNAs were washed with 75% EtOH twice and suspended in RNAse free water. Small RNAs were enriched from total RNAs using the MirVana miRNA isolation kit according (Thermo Fisher Scientific).
Small RNAs were treated with RNA phosphatase PIR-1 to remove gamma and beta phosphates from the 5' triphosphorylated RNAs (50). Monophosphorylated RNAs were ligated to 3' adapters ( rAppAGATCGGAAGAGCACACGTCTGAACTCCAGTCA/3ddC/, IDT) using T4 RNA ligase 2 in 25% PEG 8000 (NEB) at 15 C overnight. A 5' adapter (rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU, IDT) was then ligated to RNAs to the product using T4 RNA ligase 1 (NEB) for 4 hours at 15 C. Ligated products were reverse transcribed using SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific) to convert RNA to cDNA libraries. cDNA libraries were amplified by PCR and subsequently sequenced on an Illumina Novaseq platform (SP2 x 50 bp) at the OSU Comprehensive Cancer Center genomics core.

value: 4 mM IAA Auxin


title: White matter, stroke zone 4, immunoprecipitated RNA, rep 3


title: TOFU5_depletion_12hr disl-2(how27) rep. 2

description:
Library name: TOFU5_depletion_disl2_TP12_2
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I; disl-2(how27) III


title: White matter, stroke zone 4, immunoprecipitated RNA, rep 4


title: White matter, stroke zone 4, immunoprecipitated RNA, rep 2


title: White matter, stroke zone 4, immunoprecipitated RNA, rep 1


title: White matter, stroke zone 3, immunoprecipitated RNA, rep 4


title: TOFU5_depletion_2hr disl-2(how27) rep. 2

description:
Library name: TOFU5_depletion_disl2_TP2_2
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I; disl-2(how27) III


title: #999_N_d5_r1

first: Yago

last: Jannini-Sa

address: 8700 Beverly Blvd. AHSP Room A9401

department: Medicine / Lung Institute

institute: Cedars-Sinai Medical Center

description: Library name: 976073_counts

data_processing:
align with STAR 2.6.0b-1
raw count generated by featrueCounts 1.6.0.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes counts for each sample

source_name: Lung

extract_protocol:
Bulk RNA sequencing was performed on tissue from 4 separate PCLS. Briefly, PCLS were minced manually in 2 mm pieces in Trizol (ThermoFisherScientific) before bead homogenization for 95 seconds (40+20+15+10+10 seconds) at 50 Hz. RNA was purifiedusing a column-based workflow (Machery Nagel, 740984.250). RNA quantity and quality was assessed by RNA integrity number (RIN) via 4200 TapeStation system (Agilent).
RNAseq libraries were prepared using Truseq stranded mRNA kit (Illumina; 20020594). Sequencing libraries were pooled and submitted for next-generation sequencing of 100bp single-end reads (Illumina NovaSeq sequencer, AGCT Core; Los Angeles, CA).

treatment_protocol: LTI-03 (Sequence: FTTFTVT; Lot# AJF73B//474-33-TI344 Lonza), the inactive control peptide CP (Sequence: FAAFAVA; Lot# PD200120-1, Ambiopharm) were suspended in PCLS culture media at 0.3, 5.0, or 10 μM for treatments. Nintedanib (Boehringer Ingelheim Pharmaceuticals, Inc #S1010) was prepared in a 1mM stock solution with sterile filtered DMSO and used at 0.1 μM or 1 μM. PCLS were treated every 12hrs and supernatant was harvested 12 hours following the last of either three (day 2), seven (day 4) or nine treatments (day 5). Tissue was harvested after 9 treatments (day 5).

tag: condition

value: idiopathic pulmonary fibrosis (IPF)

value: Lung

tag: tissue format

value: Precision cut lung slices

tag: sample

value: N


title: #999_CP_d5_r1

description: Library name: 976070_counts

value: CP


title: White matter, stroke zone 3, immunoprecipitated RNA, rep 5

value: ribosomally loaded

value: brain


title: #999_CP_d5_r2

description: Library name: 976071_counts


title: TOFU5_depletion_0hr disl-2(how27) rep. 2

description:
Library name: TOFU5_depletion_disl2_TP0_2
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I; disl-2(how27) III

value: whole animal


title: TOFU5_depletion_4hr disl-2(how27) rep. 2

description:
Library name: TOFU5_depletion_disl2_TP4_2
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I; disl-2(how27) III


title: Cortex, stroke zone 1, immunoprecipitated RNA, rep 2

value: Cortex

value: Cortical stroke


title: White matter, stroke zone 5, immunoprecipitated RNA, rep 3

value: zone 5


title: White matter, stroke zone 3, immunoprecipitated RNA, rep 2

value: zone 3


title: White matter, stroke zone 3, immunoprecipitated RNA, rep 1


title: White matter, stroke zone 5, immunoprecipitated RNA, rep 5


title: White matter, stroke zone 3, immunoprecipitated RNA, rep 3


title: TOFU5_depletion_12hr disl-2(how27) rep. 1

description:
Library name: TOFU5_depletion_disl2_TP12_1
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I; disl-2(how27) III


title: White matter, stroke zone 5, immunoprecipitated RNA, rep 1


title: #999_LTI10_d5_r2

description: Library name: 976067_counts


title: White matter, stroke zone 2, immunoprecipitated RNA, rep 4

value: zone 2


title: White matter, stroke zone 2, immunoprecipitated RNA, rep 3

value: White matter


title: #999_LTI10_d5_r1

description: Library name: 976066_counts


title: TOFU5_depletion_6hr disl-2(how27) rep. 1

description:
Library name: TOFU5_depletion_disl2_TP6_1
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I; disl-2(how27) III


title: White matter, stroke zone 2, immunoprecipitated RNA, rep 2

value: White matter stroke


title: White matter, stroke zone 1, immunoprecipitated RNA, rep 5

value: zone 1


title: TOFU5_depletion_4hr disl-2(how27) rep. 1

description:
Library name: TOFU5_depletion_disl2_TP4_1
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I; disl-2(how27) III

value: 4 mM IAA Auxin


title: #999_LTI3_d5_r2

description: Library name: 976064_counts

value: idiopathic pulmonary fibrosis (IPF)


title: White matter, stroke zone 2, immunoprecipitated RNA, rep 1


title: White matter, stroke zone 1, immunoprecipitated RNA, rep 4


title: #999_LTI10_d5_r3

description: Library name: 976068_counts

value: Lung


title: TOFU5_depletion_2hr disl-2(how27) rep. 1

description:
Library name: TOFU5_depletion_disl2_TP2_1
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I; disl-2(how27) III


title: Terf1FLOX rep3

city: Madrid

first: Ruth

last: Álvarez-Díaz

address: C/ Melchor Fernández Almagro, 3

department: Molecular Oncology

institute: Spanish National Cancer Research Center (CNIO)

data_processing:
Raw images generated by the sequencer are submitted to analysis, per-cycle basecalling and quality score assignment with Illumina's RTA (Real Time Analysis) integrated primary analysis software. Conversion of BCL (base calls) binary files to FASTQ format is subsequently performed with Local Run Manager GenerateFASTQ Analysis Module (Illumina).
Fastq files were pre-processed to remove read adaptors, aligned to the mouse genome GRCmm39, and normalized counts were obtained using DESeq2
Assembly: GRCm39
Supplementary files format and content: Normalized counts were obtained using DESeq2

source_name: kidney

extract_protocol:
Mice were euthanized after 8 weeks and kidneys were extracted.  To isolate renal epithelial populations in KspCadherin -CreERT2, kidneys were collected in PBS, minced, and digested with 2.5 mg/ml type I collagenase (Thermo Fisher, 17100017), 2.5 mg/ml dispase II (Thermo Fisher, 17105041), and 50 ng/ml DNAse I (Roche, 10104159001) at 37 °C for 20 min to create a homogeneous cell suspension. Cell suspensions were passed through a 70 μm filter (Cultek, 45352350) to remove any undigested tissue. To remove erythroid cells, cell suspensions and blood samples were incubated for 10 min on ice in blood erythrocyte lysis buffer (Qiagen, 79217). Before analysis, cell suspensions were treated with PBS 0.04% Ultrapure BSA (Thermo Fisher, AM216). Cells were incubated at 4 °C for 30 min with FITC-labeled anti-mouse EpCAM (BioLegend, 118207) for renal epithelial populations. Endogenous signal for KFP+ cells was used. Isolated cells were collected on a mix of NEBNext® Cell Lysis Buffer (New England Biolabs, E6428A) and Murine RNase Inhibitor (New England Biolabs, E6429A) in DNA LoBIND tubes (Eppendorf, 0030108051), using a BD FACSAria IIu cell sorter (BD Biosciences).
RNA libraries for RNA-seq were prepared using the NEBNext Single Cell/Low Input RNA Library Prep kit (NEB #E6420) by following manufacturer instructions.

treatment_protocol: Tamoxifen (TMX) (Sigma Aldrich, T-5648-1G) was intraperitoneally (i.p.) injected to six-to eight-week-old male and female Trf1+/+ KFP+/t Cre+/t and Trf1lox/lox KFP+/t Cre+/t mice for three times a week for 8 weeks until the sacrifice.

value: kidney

value: epithelilal

value: Trf1 flox/flox


title: TOFU5_depletion_0hr disl-2(how27) rep. 1

description:
Library name: TOFU5_depletion_disl2_TP0_1
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I; disl-2(how27) III


title: #999_LTI05_d5_r2

description: Library name: 976062_counts

value: Precision cut lung slices


title: White matter, stroke zone 1, immunoprecipitated RNA, rep 3

value: ribosomally loaded

value: brain


title: #999_LTI3_d5_r1

description: Library name: 976063_counts


title: Terf1FLOX rep2

value: epithelial


title: White matter, stroke zone 2, immunoprecipitated RNA, rep 5


title: #999_UT_d2_r4

description: Library name: 976059_counts

value: UT


title: CONTROL rep2


title: Terf1FLOX rep1


title: #999_LTI3_d5_r3

description: Library name: 976065_counts


title: White matter, stroke zone 1, immunoprecipitated RNA, rep 2


title: TOFU5_depletion_12hr rep. 2

description:
Library name: TOFU5_depletion_TP12_2
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I

value: whole animal


title: TOFU5_depletion_6hr rep. 2

description:
Library name: TOFU5_depletion_TP6_2
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I


title: White matter, stroke zone 1, immunoprecipitated RNA, rep 1


title: Cortex, stroke zones 1-3, input RNA, rep 3

value: Cortex

value: Cortical stroke

value: zones 1-3

value: input


title: #999_LTI05_d5_r1

description: Library name: 976061_counts


title: #999_UT_d2_r2

description: Library name: 976057_counts


title: Cortex, stroke zones 1-3, immunoprecipitated RNA, rep 3


title: Cortex, stroke zones 1-3, immunoprecipitated RNA, rep 2


title: TOFU5_depletion_0hr rep. 2

description:
Library name: TOFU5_depletion_TP0_2
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I


title: TOFU5_depletion_2hr rep. 2

description:
Library name: TOFU5_depletion_TP2_2
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I


title: #999_UT_d2_r3

description: Library name: 976058_counts


title: #999_N_d2_r2

description: Library name: 976056_counts

value: N


title: TOFU5_depletion_12hr rep. 1

description:
Library name: TOFU5_depletion_TP12_1
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I

value: 4 mM IAA Auxin


title: Cortex, stroke zones 1-3, input RNA, rep 2


title: TOFU5_depletion_4hr rep. 2

description:
Library name: TOFU5_depletion_TP4_2
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I


title: pip2d, high humidity, rep3

city: Shanghai

first: yangxuan

last: liu

address: 300 Fenglin Road

country: China

institute: CAS Center for Excellence in Molecular Plant Science (CEMPS), Chinese Academy of Sciences

data_processing:
The raw reads were trimmed with Trimmomatic v.0.39 with parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:8:true SLIDINGWINDOW:4:20 LEADING:20 TRAILING:20 MINLEN:50.
Clean reads were then aligned to the TAIR10 transcriptome using Hisat2 v2.2.1.
Expression levels were extracted for each gene using TPMCalculator v0.0.3 and featureCounts v2.0.6.
Assembly: TAIR10.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes TPM values for each sample.

organism: Arabidopsis thaliana

source_name: inflorescence meristem

extract_protocol:
Total RNA was extracted from Arabidopsis inflorescence meristems using the RNAprep Pure Plant Plus Kit Kit (TIANGEN) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using TransNGS Fast RNA-Seq Library Prep Kit for Illumina  following the manufacturer’s instructions.

value: inflorescence meristem


title: pip2d, high humidity, rep2


title: #999_N_d2_r1

description: Library name: 976055_counts

value: idiopathic pulmonary fibrosis (IPF)

value: Lung


title: TOFU5_depletion_6hr rep. 1

description:
Library name: TOFU5_depletion_TP6_1
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I


title: Cortex, stroke zones 1-3, immunoprecipitated RNA, rep 1


title: CONTROL rep3

value: kidney


title: CONTROL rep1


title: Cortex, stroke zones 1-3, input RNA, rep 1


title: TOFU5_depletion_4hr rep. 1

description:
Library name: TOFU5_depletion_TP4_1
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I


title: pip2d, low humidity, rep3


title: Cortex, uninjured, immunoprecipitated RNA, rep 5

value: sham


title: pip2d, low humidity, rep2


title: #999_LTI10_d2_r1

description: Library name: 976050_counts

value: Precision cut lung slices


title: TOFU5_depletion_0hr rep. 1

description:
Library name: TOFU5_depletion_TP0_1
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I


title: pip2d, low humidity, rep1


title: #999_UT_d2_r1

description: Library name: 976049_counts


title: TOFU5_depletion_2hr rep. 1

description:
Library name: TOFU5_depletion_TP2_1
gfp::aid::tofu-5(how48) I; sun-1p::mcherry::tirI I


title: Cortex, uninjured, immunoprecipitated RNA, rep 4

value: ribosomally loaded


title: #999_LTI3_d2_r3

description: Library name: 976047_counts


title: col0, high humidity, rep3


title: pip2d, high humidity, rep1


title: #999_LTI3_d2_r2

description: Library name: 976046_counts


title: Cortex, uninjured, immunoprecipitated RNA, rep 3

value: brain


title: disl-2(tm5337); pup-1(how50) rep. 1

description:
Library name: pup1_disl2tm5337_1
disl-2(tm5337) III; pup-1(how50) III

value: disl-2(tm5337) III; pup-1(how50) III


title: Cortex, uninjured, input RNA, rep 4

description: Cortex, uninjured, input RNA, rep 4


title: #999_CP_d2_r2

description: Library name: 976053_counts

value: CP


title: #999_CP_d2_r1

description: Library name: 976051_counts


title: #999_LTI3_d2_r1

description: Library name: 976045_counts


title: disl-2(how27); pup-1(how20) rep. 2

description:
Library name: pup1_disl2how27_2
disl-2(how27) III; pup-1(how20) III

value: whole animal

value: disl-2(how27) III; pup-1(how20) III


title: #999_LTI05_d2_r3

description: Library name: 976044_counts


title: col0, low humidity, rep3


title: Cortex, uninjured, input RNA, rep 3

description: Cortex, uninjured, input RNA, rep 3

value: Cortex


title: Cortex, uninjured, immunoprecipitated RNA, rep 2


title: col0, low humidity, rep2


title: pup-1(tm1021) rep. 2

description:
Library name: pup1_2
pup-1(tm1021) III

value: pup-1(tm1021) III


title: disl-2(tm5337); pup-1(how50) rep. 2

description:
Library name: pup1_disl2tm5337_2
disl-2(tm5337) III; pup-1(how50) III


title: #999_LTI05_d2_r2

description: Library name: 976043_counts


title: #999_LTI05_d2_r1

description: Library name: 976042_counts


title: Cortex, uninjured, input RNA, rep 2

description: Cortex, uninjured, input RNA, rep 2

value: input


title: col0, low humidity, rep1


title: pup-1 paired control rep. 2

description:
Library name: N2_pup1_paired_control_2
pup-1 paired control

value: pup-1 paired control


title: Cortex, uninjured, immunoprecipitated RNA, rep 1


title: Cortex, uninjured, input RNA, rep 1

description: Cortex, uninjured, input RNA, rep 1


title: pup-1(tm1021) rep. 1

description:
Library name: pup1_1
pup-1(tm1021) III


title: col0, high humidity, rep2


title: pup-1 paired control rep. 1

description:
Library name: N2_pup1_paired_control_1
pup-1 paired control


title: White matter, stroke zones 1-3, immunoprecipitated RNA, rep 3

value: White matter

value: White matter stroke

value: zones 1-3


title: ChP, 82w, LV

city: Zwijnaarde

first: Roosmarijn

middle: E.

last: Vandenbroucke

state: Gent

address: Technologiepark-Zwijnaarde 71

department: VIB Center for Inflammation Research

country: Belgium

institute: VIB-UGent

data_processing:
Demultiplexing of the raw data was done with 10x Cell ranger software (v2.0.1). Obtained reads from demultiplexing were used as input for ‘cellranger count’ to align reads to the mouse reference genome using STAR and collapse them to unique molecular identifier (UMI) counts.
Assembly: mm10
Supplementary files format and content: 10x Genomics output files for each sample: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Choroid Plexus Lateral ventricle

extract_protocol:
Mice for all groups were first sedated as described above, transcardially perfused with PBS with 1% Heparin after which brain tissue was excised and lateral and fourth ventricle choroid plexus tissue were carefully microdissected and collected in serum-free RPMI at 4 °C. As choroid plexus tissue is small and does not allow for single mouse scRNA-Seq analyses, we pooled choroid plexus tissues from 8 mice to generate single pooled samples for naive 7-week-old (female), 22-week-old (male) and 82-week-old (male) mouse groups, for the lateral and fourth ventricle ChP tissue separately. After tissue collection, samples were pre-cut with small scissors and diluted and digested in 2:3 stock solution of CollagenaseI (10 U/ml, Worthington), Collagenase IV (400 U/ml, Worthington) and DNaseI (30 U/ml, Worthington). Incubation was at 37 °C for 30 min with up/down pipetting every 10 min. Samples were strained through a 70 μm filter (Falcon) and washed with a total of 700 μl RPMI. Samples were centrifuged for 7 min 300 g at 4 °C, supernatant discarded and pellet resuspended in 250 μl FACS buffer (1x HBSS without Ca 2+ /Mg 2+ , 2 mM EDTA, 2% BSA). Single live cells were sorted using the BD FACS ARIAII and loaded onto a Chromium GemCode Single Cell Instrument (10x Genomics) to generate single-cell gel beads in emulsion (GEMs).
Libraries were prepared with the GemCode Single Cell 3’ Gel Bead and Library Kit v1 (10x Genomics) and the Chromium i7 Multiplex Kit (10x Genomics) according to manufacturer’s instructions. Afterwards,10X barcoded cDNA was prepared for Illumina HiSeq4000 Next Gen Sequencing. Sequencing was performed at the VIB Nucleomics Core (VIB, Leuven).

value: Choroid Plexus Lateral ventricle

tag: strain

value: C57BL/6 J

value: M

tag: age


title: #979_UT_d5_r2

description: Library name: 976041_counts

value: idiopathic pulmonary fibrosis (IPF)

tag: tissue

value: Lung

value: Precision cut lung slices

value: UT


title: #979_N_d5_r3

description: Library name: 976038_counts

tag: treatment

value: N


title: ChP, 82w, 4V

source_name: Choroid Plexus Fourth ventricle

value: Choroid Plexus Fourth ventricle

tag: Sex


title: disl-2(tm5337); parn-1(tm869) rep. 2

description:
Library name: parn1disl2_YD_2
disl-2(tm5337) III; parn-1(tm869) V

value: whole animal

value: disl-2(tm5337) III; parn-1(tm869) V


title: White matter, stroke zones 1-3, input RNA, rep 3

value: brain


title: col0, high humidity, rep1

value: inflorescence meristem


title: White matter, stroke zones 1-3, immunoprecipitated RNA, rep 2

value: ribosomally loaded


title: parn-1(tm869) rep. 2

description:
Library name: parn1_YD_2
parn-1(tm869) V

value: parn-1(tm869) V


title: disl-2(tm5337); parn-1(tm869) rep. 1

description:
Library name: parn1disl2_YD_1
disl-2(tm5337) III; parn-1(tm869) V


title: ChP, 22w, LV


title: #979_UT_d5_r1

description: Library name: 976039_counts


title: #979_N_d5_r1

description: Library name: 976036_counts


title: ChP, 22w, 4V


title: disl-2(how27); pup-1(how20) rep. 1

description:
Library name: pup1_disl2how27_1
disl-2(how27) III; pup-1(how20) III

value: disl-2(how27) III; pup-1(how20) III


title: White matter, stroke zones 1-3, input RNA, rep 2

value: White matter

value: White matter stroke

value: zones 1-3

value: input


title: parn-1(tm869) rep. 1

description:
Library name: parn1_YD_1
parn-1(tm869) V


title: White matter, stroke zones 1-3, immunoprecipitated RNA, rep 1


title: ChP, 7w, LV

description:
LpsNegLatVentr
Specific protocol: The cellranger aggr pipeline was used to aggregate the two 7w-old samples into one feature-barcode matrix.

value: Choroid Plexus Lateral ventricle

value: C57BL/6 J

value: F


title: disl-2(tm5337) rep. 2

description:
Library name: disl2_tm5337_2
disl-2(tm5337) III

value: disl-2(tm5337) III


title: ChP, 7w, 4V

description:
LpsNegFourVentr
Specific protocol: The cellranger aggr pipeline was used to aggregate the two 7w-old samples into one feature-barcode matrix.


title: #979_CP_d5_r1

description: Library name: 976033_counts

value: idiopathic pulmonary fibrosis (IPF)

value: Lung

value: Precision cut lung slices

value: CP


title: disl-2(tm5337) rep. 1

description:
Library name: disl2_tm5337_1
disl-2(tm5337) III

value: whole animal


title: White matter, stroke zones 1-3, input RNA, rep 1

value: brain


title: White matter, uninjured, immunoprecipitated RNA, rep 5

value: sham

value: ribosomally loaded


title: #979_LTI10_d5_r2

description: Library name: 976031_counts


title: White matter, uninjured, input RNA, rep 5


title: disl-2(how27) rep. 2

description:
Library name: disl2_how27_2
disl-2(how27) III

value: disl-2(how27) III


title: #979_LTI10_d5_r1

description: Library name: 976030_counts


title: TNBC-P09_BCA15_TNBC_HighTB

city: Bangkok

first: Suparada

last: Khanaruksombat

address: 2 Wanglang

department: Immunology

country: Thailand

institute: Faculty of Medicine Siriraj Hospital, Mahidol University

description: Library name: S_TNBC_P09_IM

data_processing:
BCL files were demultiplexed and converted to FASTQ format using BCL2FASTQ software (Illumina Inc., San Diego, CA, USA).
FASTQ files were aligned to the Human Whole Transcriptome v2.0 panel (22,537 probes) using STAR aligner.
Gene expression counts were extracted using BioSpyder’s analysis pipeline and normalized for downstream analysis.
Assembly: Human Whole Transcriptome v2.0 panel.
Supplementary files format and content: A CSV file containing gene-level read counts for each sample is provided. Rows represent genes, columns represent samples.
Supplementary files format and content: Values are raw read counts mapped to each gene from the Human Whole Transcriptome v2.0 panel.

source_name: Breast

growth_protocol: Not applicable. FFPE tissue samples were obtained from clinical specimens.

extract_protocol:
The selected immune cell–enriched portion of the FFPE tissues was deparaffinized and then digested. The tissue lysate was incubated with detector oligos annealing to the targeted RNA template and ligated.
Amplification of the ligated oligonucleotides was carried out using unique primers, sample-specific barcodes, and Illumina sequencing adapters. Libraries were sequenced on an Illumina HiSeq 2500 system using the High Output v4 flow cell.

treatment_protocol: Not applicable. No treatment was applied prior to tissue collection.

value: Breast

tag: region

value: Immune

tag: disease

value: Breast Cancer

tag: subtype

value: Triple-negative breast cancer

tag: tumor budding_grade

value: high

tag: tumor staging

value: IIA

tag: pathological differentiation

value: PD


title: TNBC-P04_BCA13_TNBC_HighTB

description: Library name: S_TNBC_P04_IM


title: TNBC-P06_BCA14_TNBC_HighTB

description: Library name: S_TNBC_P06_IM

value: IIIC

value: MD


title: disl-2(how27) rep. 1

description:
Library name: disl2_how27_1
disl-2(how27) III

tag: genotype


title: White matter, uninjured, immunoprecipitated RNA, rep 4

tag: brain region

value: White matter

tag: disease state

tag: stroke zone


title: TNBC-G19_BCA12_TNBC_HighTB

description: Library name: S_TNBC_G19_IM

value: IIIB


title: White matter, uninjured, input RNA, rep 4

tag: input or_ribosomally_loaded

value: input


title: #979_LTI3_d5_r2

description: Library name: 976028_counts

tag: condition

value: idiopathic pulmonary fibrosis (IPF)

value: Lung

tag: tissue format

value: Precision cut lung slices

tag: sample

tag: time


title: disl-2 isogenic control rep. 2

description:
Library name: disl2_control_2
disl-2 isogenic control

tag: tissue

value: whole animal

value: disl-2 isogenic control

tag: treatment


title: TNBC-G03_BCA11_TNBC_HighTB

description: Library name: S_TNBC_G03_IM

value: Breast

tag: region


title: #979_LTI3_d5_r1

description: Library name: 976027_counts


title: disl-2 isogenic control rep. 1

description:
Library name: disl2_control_1
disl-2 isogenic control


title: #979_CP_d5_r2

description: Library name: 976034_counts

value: CP


title: TNBC-G01_BCA10_TNBC_HighTB

description: Library name: S_TNBC_G01_IM

value: Immune

tag: disease

value: Breast Cancer

value: IIB


title: #979_LTI05_d5_r3

description: Library name: 976026_counts


title: White matter, uninjured, immunoprecipitated RNA, rep 3

value: sham

value: ribosomally loaded

value: brain


title: PC-B-130_BCA09_TNBC_HighTB

description: Library name: S_PC_B_130_IM

tag: subtype

value: Triple-negative breast cancer

value: high

value: IIIC

value: PD


title: White matter, uninjured, input RNA, rep 3

value: White matter

value: input


title: White matter, uninjured, immunoprecipitated RNA, rep 2


title: #979_LTI05_d5_r2

description: Library name: 976025_counts

value: idiopathic pulmonary fibrosis (IPF)

value: Lung

value: Precision cut lung slices


title: #979_LTI10_d5_r3

description: Library name: 976032_counts


title: henn-1 (tm4477) rep. 2

description:
Library name: henn1_2
henn-1 (tm4477) III

value: whole animal

value: henn-1 (tm4477) III


title: PC-B-099_BCA08_TNBC_HighTB

description: Library name: S_PC_B_099_IM

value: Breast

value: Immune

tag: tumor budding_grade

value: IIIA


title: #979_LTI05_d5_r1

description: Library name: 976024_counts


title: White matter, uninjured, input RNA, rep 2

value: sham


title: B166_BCA07_TNBC_HighTB

description: Library name: S_B166_IM

value: Breast Cancer

tag: tumor staging


title: White matter, uninjured, immunoprecipitated RNA, rep 1

value: ribosomally loaded

value: brain


title: disl-2(how18); henn-1(tm4477) rep. 2

description:
Library name: henn1_disl2_2
henn-1(tm4477) III; disl-2(how18) III

value: henn-1(tm4477) III; disl-2(how18) III


title: Cortex, uninjured, input RNA, rep 5

description: Cortex, uninjured, input RNA, rep 5

value: Cortex


title: #979_UT_d2_r2

description: Library name: 976022_counts

value: UT


title: #979_UT_d2_r1

description: Library name: 976021_counts


title: henn-1 (tm4477) rep. 1

description:
Library name: henn1_1
henn-1 (tm4477) III


title: White matter, uninjured, input RNA, rep 1

value: White matter


title: B041_BCA06_TNBC_HighTB

description: Library name: S_B041_IM

value: Triple-negative breast cancer

value: high

tag: pathological differentiation

value: MD


title: disl-2(how18); henn-1(tm4477) rep. 1

description:
Library name: henn1_disl2_1
henn-1(tm4477) III; disl-2(how18) III

tag: genotype


title: #979_N_d5_r2

description: Library name: 976037_counts

value: idiopathic pulmonary fibrosis (IPF)

value: Lung

value: Precision cut lung slices

value: N


title: TNBC-G06_BCA04_TNBC_LowTB

description: Library name: S_TNBC_G06_IM

value: Breast

value: Immune

value: low

value: IIA

value: PD


title: #979_N_d2_r1

description: Library name: 976019_counts


title: #979_CP_d2_r2

description: Library name: 976016_counts

value: CP


title: T7 expression of eGFP, RBS-3, replicate 2

city: Kgs. Lyngby

first: Christoffer

last: Rode

address: Søltofts Plads, Building 220

country: Denmark

institute: Technical University of Denmark

description:
Library name: ecoli_CR_00108
Column name in log_tpm.csv: ecoli_CR_00108

data_processing:
Mapping and logtpm determined using the iModulonMiner workflow, https://doi.org/10.1371/journal.pcbi.1012546
Assembly: Genome assembly ASM584v2
Supplementary files format and content: logtpm.csv contains log-TPM values for each sample

organism: Escherichia coli

source_name: bacterial cell

growth_protocol: Cells were grown in minimal M9 growth medium with 0.2% glycerol in 250 mL shake flasks at 40 mL working volume, shaking at 37C and at 225 RPM.

extract_protocol:
Total RNA was extracted from cultures following the protocol in the RNAprotect Bacteria Reagent Handbook (Qiagen). Once main cultures reached OD600 = 2, 2.5 mL culture was added to 5 mL RNAprotect Bacteria Reagent (Qiagen), vortexed, and incubated at room temperature for 5 minutes. Sample pellets were resuspended in 400 L elution buffer and split into two aliquots which were stored at -80C. Total RNA was then extracted and purified from thawed pellets on a QIAcube Connect Instrument (Qiagen) using the RNeasy Protect Bacteria Mini Kit (Qiagen). Lysozyme was used for enzymatic lysis of cells together with Proteinase K for degrading protein and SUPERaseIn RNAse inhibitor (Thermo Fisher) for protecting RNA. A DNase treatment step was added to the protocol to remove DNA contamination. Total RNA was eluted in 30 L RNase-free water, then stored at -80 C. The extracted RNA was shipped to sequencing at Azenta Life Sciences.
Enrichment, cDNA synthesis, and adapter ligation

tag: strain

tag: cell type

value: bacterial cell

value: SDT507 (gly2 rhaBADM KO) pSD78 pSD473

value: M9 glycerol ampicillin chloramphenicol

tag: batch

value: Replicate 2


title: ChIP-seq of LNCaP cells with anti-AR antibody

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

description: Library name: CS50_IP2

data_processing:
Reads were aligned to hg19 after filtering for ENCODE blacklist regions using bwa (0.7.17) and converted to BAM format using Samtools (1.17).
Duplicate reads removed using Picard (2.27.3) and peaks identified with MACS2 (2.2.7.1) with q value cutoff of 0.01.
Input subtracted bigWig files were generated using Deeptools (3.5.1).
Assembly: hg19
Supplementary files format and content: input normalized bigWig

source_name: LNCaP

growth_protocol: LNCaP: RPMI with 10% fetal bovine serum in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells or tissues were fixed with 2 mM DSG for 10 min and 1% paraformaldehyde for 10 min followed by quenching with glycine. Chromatin was isolated and sonicated using Diagenode Pico sonicator.
ChIP-seq libraries were prepared using NEB Next Ultra II DNA Library Prep Kit for Illumina and amplified libraries purified using NEB purification beads. Libraries were validated using Agilent Tapestation.

tag: cell line

value: LNCaP

tag: antibody

value: AR

tag: serum

value: FBS


title: IBC-11B_BCA02_luminal_IM_HighTB

description: Library name: S_IBC_11B_IM

value: Breast Cancer

value: Luminal breast cancer

value: high

value: III


title: #979_LTI10_d2_r3

description: Library name: 976014_counts

tag: condition

value: idiopathic pulmonary fibrosis (IPF)

value: Lung

tag: tissue format

value: Precision cut lung slices

tag: sample


title: B168_BCA03_TNBC_IM_LowTB

description: Library name: S_B168_IM

tag: tissue

value: Breast

value: Immune

value: Triple-negative breast cancer

value: low

value: IIIB


title: T7 expression of eGFP, RBS-3, replicate 1

description:
Library name: ecoli_CR_00107
Column name in log_tpm.csv: ecoli_CR_00107

value: bacterial cell

value: SDT507 (gly2 rhaBADM KO) pSD78 pSD473

tag: treatment

value: M9 glycerol ampicillin chloramphenicol

value: Replicate 1


title: B165_BCA01_HER2_IM_LowTB

description: Library name: S_B165_IM

tag: region

tag: disease

value: HER2-positive breast cancer

value: PD


title: Expression of Thaumatin, replicate 2

description:
Library name: ecoli_CR_00106
Column name in log_tpm.csv: ecoli_CR_00106

value: SDT507 (gly2 rhaBADM KO) pSD99

value: M9 glycerol ampicillin

value: Replicate 2


title: RPE-1 hTERT FUCCI H3K9me3 rep 3 no TAPS ctrl

city: Munich

first: Christoph

last: Geisenberger

address: Thalkirchnerstr. 36

institute: Institute of Pathology

description: Library name: CG-qcChIC-RPE-exp1-k9me3-pl11

data_processing:
Illumina RPI small RNA adapters
Demultiplexing of reads and extraction of single-cell barcodes
Adapter trimming with cutadapt
Mapping to human genome with bwa -mem algorithm
Extraction of mapping statistics
genome build/assembly: GRCh38.p12 / Ensembl release 97 for Homo Sapiens
processed data files format and content: Data table containing no. of mapped reads, demultiplexed reads, reads which could be assigned to a cut site and unique reads
Library strategy: scChiC-seq

source_name: Retinal Pigment Epithelial

growth_protocol: RPE-1 hTERT FUCCI cells were maintained in DMEM/F12, 10% FCS and 1% Pen-Strep. K562 cells were cultured in RPMI 1640 GlutaMAX medium, 5% FCS, non-essential amino acids and 1% Pen/Strep .

extract_protocol:
TrypLE digestion for RPE-1 hTERT FUCCI cells
Custom library protocol. Briefly, cells were incubated with the antibodies listed above and a pA-MNase fusion protein. Next, individual cells were sorted into 384-well plate. Subsequently, MNase digestion was initiated through the addition of calcium. Next, MNase digestion was stopped and DNA released by Proteinase K digestion. DNA fragments were end-repaired by Klenow Large Fragment and PNK. Repaired ends were ligated to custom barcoded adapters containing a UMI, Illumina handle and T7 promoter. After IVT and PCR, sequencing libraries were assessed with Qubit and Bioanalyzer and normalized libraries loaded onto Illumina sequencer according to the manufacturers instructions.

value: Retinal Pigment Epithelial

value: RPE-1 hTERT FUCCI

value: WT


title: sample d1: mix of flies resulting from crosses between BDSC lines 66472 x 68265, 66472 x 68322, 66472 x 68383

description: 10X Genomics

value: central brain

value: Kenyon cells


title: RPE-1 hTERT FUCCI H3K9me3 rep 2 no TAPS ctrl

description: Library name: CG-qcChIC-RPE-exp1-k9me3-pl10


title: #979_LTI10_d2_r2

description: Library name: 976013_counts

value: idiopathic pulmonary fibrosis (IPF)

value: Lung

value: Precision cut lung slices

tag: time


title: #979_LTI10_d2_r1

description: Library name: 976012_counts


title: Expression of MT1, replicate 2

description:
Library name: ecoli_CR_00104
Column name in log_tpm.csv: ecoli_CR_00104

value: bacterial cell

value: SDT507 (gly2 rhaBADM KO) pSD472


title: T7 expression of eGFP, RBS-4, replicate 2

description:
Library name: ecoli_CR_00110
Column name in log_tpm.csv: ecoli_CR_00110

value: SDT507 (gly2 rhaBADM KO) pSD78 pSD475

value: M9 glycerol ampicillin chloramphenicol


title: LNCAP_Brunello_Rep2_DMSO

first: Brian

last: Hanratty

address: 1100 Fairview Avenue

institute: Fred Hutchinson Cancer Cancer

description: Library name: 2.B2_V

library_source: other

data_processing:
Fastq files were aligned to the brunello library using MAGeCK
Genes and guides depleted in LNCaP_FGC cells were identified using MAGECK analysis. A count table was prepared using the count function. Sample groups were then compared using the test (RRE) comparison function.
Supplementary files format and content: Gene summary table from MAGeCK

molecule: other

extract_protocol:
Infections were performed to achieve a representation of at least 500 cells per sgRNA per replicate (500X; ~40 x 10^6 cells per replicate). Cells were split upon confluence, re-seeded back in culture and maintained at a density of 500X over six population doublings (PD6). After PD6, ~40 x 10^6 cells per replicate were harvested and processed for genomic DNA extrac-tion, barcode amplification and next-generation sequencing, as described previously21.
LNCaP_FGC cells were transduced with low MOI lentivirus (~0.3) of the human Brunello CRISPR KO pooled library (Addgene # 73179) and selected with puromycin for 5 days to enrich for the positive transductants.

value: prostate tumor cell line

value: DMSO


title: B031_BCA05_TNBC_HighTB

description: Library name: S_B031_IM

value: Breast

value: Immune

value: Breast Cancer

tag: subtype

value: Triple-negative breast cancer

tag: tumor budding_grade

value: high

tag: tumor staging

value: IIIC

value: PD


title: RPE-1 hTERT FUCCI H3K36me3 rep 2 no TAPS ctrl

description: Library name: CG-qcChIC-RPE-exp1-k36me3-pl2

value: Retinal Pigment Epithelial

value: RPE-1 hTERT FUCCI

tag: genotype

value: WT


title: Expression of MT1, replicate 1

description:
Library name: ecoli_CR_00103
Column name in log_tpm.csv: ecoli_CR_00103

tag: strain

tag: cell type

value: M9 glycerol ampicillin

value: Replicate 1


title: LNCAP_Brunello_Rep2_R1881

description: Library name: 2.B2_R

tag: cell line


title: LNCaP cells chromatin input

description: Library name: CS50_IN

value: LNCaP

tag: antibody

value: Input

value: FBS


title: #979_LTI3_d2_r1

description: Library name: 976006_counts

value: idiopathic pulmonary fibrosis (IPF)

value: Lung

value: Precision cut lung slices


title: RPE-1 hTERT FUCCI H3K36me3 rep 1 no TAPS ctrl

description: Library name: CG-qcChIC-RPE-exp1-k36me3-pl1


title: LNCAP_Brunello_Rep2_ENZ

description: Library name: 2.B2_E

value: prostate tumor cell line

value: ENZ


title: #979_CP_d2_r1

description: Library name: 976015_counts

value: CP


title: RPE-1 hTERT FUCCI H3K9me3 rep 4 no TAPS ctrl

description: Library name: CG-qcChIC-RPE-exp1-k9me3-pl12


title: LNCAP_Brunello_Rep2_Day0

description: Library name: 2.B2_0


title: RPE-1 hTERT FUCCI H3K27me3 rep 4 no TAPS ctrl

description: Library name: CG-qcChIC-RPE-exp1-k27me3-pl16


title: T7 control, replicate 3

description:
Library name: ecoli_CR_00067
Column name in log_tpm.csv: ecoli_CR_00067

value: bacterial cell

value: SDT507 (gly2 rhaBADM KO) pSD78 pSD208

value: M9 glycerol ampicillin chloramphenicol

tag: batch

value: Replicate 3


title: Gi-51_UT_d5_r1

description: Library name: 976005_counts

tag: condition

value: UT


title: Gi-51_N_d5_r2

description: Library name: 976002_counts

tag: tissue format

value: N


title: LNCAP_Brunello_Rep1_DMSO

description: Library name: 1.B1_V

value: DMSO


title: LNCAP_Brunello_Rep1_R1881

description: Library name: 1.B1_R


title: RPE-1 hTERT FUCCI H3K27me3 rep 3 no TAPS ctrl

description: Library name: CG-qcChIC-RPE-exp1-k27me3-pl15

value: Retinal Pigment Epithelial

value: RPE-1 hTERT FUCCI

value: WT


title: T7 expression of eGFP, RBS-Null, replicate 2

description:
Library name: ecoli_CR_00066
Column name in log_tpm.csv: ecoli_CR_00066

value: SDT507 (gly2 rhaBADM KO) pSD344

value: Replicate 1


title: T7 expression of eGFP, RBS-4, replicate 1

description:
Library name: ecoli_CR_00109
Column name in log_tpm.csv: ecoli_CR_00109

value: SDT507 (gly2 rhaBADM KO) pSD78 pSD475


title: Expression of Thaumatin, replicate 1

description:
Library name: ecoli_CR_00105
Column name in log_tpm.csv: ecoli_CR_00105

value: SDT507 (gly2 rhaBADM KO) pSD99

value: M9 glycerol ampicillin


title: RPE-1 hTERT FUCCI H3K27me3 rep 2 no TAPS ctrl

description: Library name: CG-qcChIC-RPE-exp1-k27me3-pl14


title: T7 expression of eGFP, RBS-Null, replicate 1

description:
Library name: ecoli_CR_00065
Column name in log_tpm.csv: ecoli_CR_00065


title: Gi-51_CP_d5_r2

description: Library name: 975999_counts

value: idiopathic pulmonary fibrosis (IPF)

value: Lung

value: Precision cut lung slices

tag: sample


title: Gi-51_N_d5_r1

description: Library name: 976001_counts

tag: tissue


title: LNCAP_Brunello_Rep1_ENZ

description: Library name: 1.B1_E

value: prostate tumor cell line

tag: treatment

value: ENZ


title: Gi-51_CP_d5_r1

description: Library name: 975997_counts

value: CP


title: RPE-1 hTERT FUCCI Whole Genome Bisulfite Sequencing

data_processing:
Demultiplexing of reads and extraction of single-cell barcodes
Adapter trimming with cutadapt
Mapping to human genome with Bismark
Deduplication using Bismark
Extraction of methylation information with Bismark
GRCh38.p12 / Ensembl release 97 for Homo Sapiens
Data table containing chromosome, start position, end position, relative methylation (percentage), no. of methylated reads, no. of unmethylated reads

extract_protocol:
Extraction of gDNA from TrypLE digested cells
WGBS library contruction using Zymo PicoMethyl Kit


title: LNCAP_Brunello_Rep1_Day0

description:
Library name: 1.B1_0
sgRNA CRISPR screen


title: T7 expression of eGFP, RBS-1, replicate 2

description:
Library name: ecoli_CR_00064
Column name in log_tpm.csv: ecoli_CR_00064

value: bacterial cell

value: SDT507 (gly2 rhaBADM KO) pSD78 pSD340

value: M9 glycerol ampicillin chloramphenicol

value: Replicate 2


title: K562 H3K9me3

data_processing:
Demultiplexing of reads and extraction of single-cell barcodes
Adapter trimming with cutadapt
Mapping to human genome with bwa -mem algorithm
Custom bam tagging tool to add flags for data filtering
Extracting methylation state for each CpG covered in the data from sequencing reads with custom software and writing output to .tsv files
GRCh38.p12 / Ensembl release 97 for Homo Sapiens
Data table containing library ID, cell ID, chromosome, genomic position, methylation state, cutsite motif
Library strategy: scEpi2-seq

source_name: Bone Marrow

extract_protocol:
TrypLE digestion for RPE-1 hTERT FUCCI cells
Custom library protocol. Briefly, cells were incubated with the antibodies listed above and a pA-MNase fusion protein. Next, individual cells were sorted into 384-well plate. Subsequently, MNase digestion was initiated through the addition of calcium. Next, MNase digestion was stopped and DNA released by Proteinase K digestion. DNA fragments were end-repaired by Klenow Large Fragment and PNK. Repaired ends were ligated to custom barcoded adapters containing a UMI, Illumina handle and T7 promoter. After IVT and PCR, sequencing libraries were assessed with Qubit and Bioanalyzer and normalized libraries loaded onto Illumina sequencer according to the manufacturers instructions.
Illumina RPI small RNA adapters

value: Bone Marrow


title: T7 expression of eGFP, RBS-1, replicate 1

description:
Library name: ecoli_CR_00063
Column name in log_tpm.csv: ecoli_CR_00063


title: K562 H3K36me3

value: WT


title: T7 control, replicate 4

description:
Library name: ecoli_CR_00068
Column name in log_tpm.csv: ecoli_CR_00068

value: SDT507 (gly2 rhaBADM KO) pSD78 pSD208

value: Replicate 4


title: Gi-51_LTI10_d5_r3

description: Library name: 975996_counts


title: Gi-51_LTI10_d5_r2

description: Library name: 975995_counts


title: K562 H3K27me3


title: Gi-51_LTI10_d5_r1

description: Library name: 975994_counts


title: Control, replicate 10

description:
Library name: ecoli_CR_00060
Column name in log_tpm.csv: ecoli_CR_00060

value: SDT507 (gly2 rhaBADM KO) pSD122

value: Replicate 10


title: Gi-51_LTI3_d5_r3

description: Library name: 975993_counts


title: Control, replicate 9

description:
Library name: ecoli_CR_00059
Column name in log_tpm.csv: ecoli_CR_00059

value: M9 glycerol ampicillin

value: Replicate 9


title: RPE-1 hTERT FUCCI H3K9me3 rep 3

value: Retinal Pigment Epithelial

value: RPE-1 hTERT FUCCI


title: RPE-1 hTERT FUCCI H3K36me3 rep 4 no TAPS ctrl

description: Library name: CG-qcChIC-RPE-exp1-k36me3-pl4


title: Gi-51_LTI3_d5_r1

description: Library name: 975991_counts

value: idiopathic pulmonary fibrosis (IPF)

value: Lung

value: Precision cut lung slices


title: Expression of eGFP, RBS-Null, replicate 1

description:
Library name: ecoli_CR_00057
Column name in log_tpm.csv: ecoli_CR_00057

value: bacterial cell

value: SDT507 (gly2 rhaBADM KO) pSD343

value: Replicate 1


title: Gi-51_LTI3_d5_r2

description: Library name: 975992_counts


title: Affymetrix Exon array from patient 1038

type: RNA

description: Affymetrix Human Exon array of prostate biopsy from patient 1038

hyb_protocol: Samples were hybridized using Affymetrix kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was processed using the Affymetrix Transcriptome Analysis Console
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: biotin

source_name: prostate tissues prior to treatment with neoadjuvant ADT plus enzalutamide

label_protocol: RNA was amplified, fragmented, and biotinylated using the WT-Ovation FFPE system (NuGEN) according the manufacturer's recommendations with minor modifications.

extract_protocol: After pathologic review, tissue was harvested from formalin-fixed, paraffin-embedded slides by macrodissection under RNase-free conditions. Total RNA was extracted and purified using the RNease FFPE kit (Qiagen)

tag: gender

value: male

tag: case

value: prostate


title: Affymetrix Exon array from patient 1035

description: Affymetrix Human Exon array of prostate biopsy from patient 1035


title: Affymetrix Exon array from patient 1037

description: Affymetrix Human Exon array of prostate biopsy from patient 1037


title: RPE-1 hTERT FUCCI H3K9me3 rep 2

value: WT


title: Affymetrix Exon array from patient 1036

description: Affymetrix Human Exon array of prostate biopsy from patient 1036


title: Gi-51_LTI05_d5_r2

description: Library name: 975989_counts

tag: time


title: Affymetrix Exon array from patient 1039

description: Affymetrix Human Exon array of prostate biopsy from patient 1039


title: RPE-1 hTERT FUCCI H3K36me3 rep 3


title: RPE-1 hTERT FUCCI H3K36me3 rep 4


title: Expression of eGFP, RBS-Null, replicate 2

description:
Library name: ecoli_CR_00058
Column name in log_tpm.csv: ecoli_CR_00058

value: Replicate 2


title: RPE-1 hTERT FUCCI H3K9me3 rep 1


title: T7 expression of eGFP, RBS-2, replicate 1

description:
Library name: ecoli_CR_00061
Column name in log_tpm.csv: ecoli_CR_00061

value: SDT507 (gly2 rhaBADM KO) pSD78 pSD339

value: M9 glycerol ampicillin chloramphenicol


title: Gi-51_LTI05_d5_r3

description: Library name: 975990_counts


title: Expression of eGFP, RBS-1, replicate 2

description:
Library name: ecoli_CR_00056
Column name in log_tpm.csv: ecoli_CR_00056

value: SDT507 (gly2 rhaBADM KO) pSD335


title: T7 expression of eGFP, RBS-2, replicate 2

description:
Library name: ecoli_CR_00062
Column name in log_tpm.csv: ecoli_CR_00062


title: Gi-51_LTI05_d5_r1

description: Library name: 975988_counts


title: Expression of eGFP, RBS-2, replicate 1

description:
Library name: ecoli_CR_00053
Column name in log_tpm.csv: ecoli_CR_00053

value: SDT507 (gly2 rhaBADM KO) pSD334

value: M9 glycerol ampicillin


title: RPE-1 hTERT FUCCI H3K36me3 rep 2

value: Retinal Pigment Epithelial


title: Expression of eGFP, RBS-2, replicate 2

description:
Library name: ecoli_CR_00054
Column name in log_tpm.csv: ecoli_CR_00054


title: Affymetrix Exon array from patient 1031

description: Affymetrix Human Exon array of prostate biopsy from patient 1031


title: Affymetrix Exon array from patient 1033

description: Affymetrix Human Exon array of prostate biopsy from patient 1033


title: Gi-51_UT_d2_r3

description: Library name: 975987_counts

value: UT


title: Affymetrix Exon array from patient 1032

description: Affymetrix Human Exon array of prostate biopsy from patient 1032


title: Affymetrix Exon array from patient 1034

description: Affymetrix Human Exon array of prostate biopsy from patient 1034


title: Expression of eGFP, 5 mM choline, replicate 2

description:
Library name: ecoli_CR_00052
Column name in log_tpm.csv: ecoli_CR_00052

value: SDT507 (gly2 rhaBADM KO) pSD174

value: M9 glycerol ampicillin choline


title: RPE-1 hTERT FUCCI H3K36me3 rep 1

value: RPE-1 hTERT FUCCI


title: Gi-51_UT_d2_r2

description: Library name: 975986_counts

value: idiopathic pulmonary fibrosis (IPF)

value: Lung

value: Precision cut lung slices


title: Gi-51_N_d2_r3

description: Library name: 975984_counts

value: N


title: Affymetrix Exon array from patient 1030

description: Affymetrix Human Exon array of prostate biopsy from patient 1030

value: male

value: prostate


title: Expression of eGFP, 5 mM choline, replicate 1

description:
Library name: ecoli_CR_00051
Column name in log_tpm.csv: ecoli_CR_00051

value: bacterial cell

value: Replicate 1


title: RPE-1 hTERT FUCCI H3K27me3 rep 4

value: WT


title: RPE-1 hTERT FUCCI H3K9me3 rep 4


title: Expression of eGFP, rspAB KO, replicate 1

description:
Library name: ecoli_CR_00049
Column name in log_tpm.csv: ecoli_CR_00049

value: SDT1108 (gly2 rhaBADM rspAB KO) pSD174


title: RPE-1 hTERT FUCCI H3K27me3 rep 1


title: RPE-1 hTERT FUCCI H3K27me3 rep 3


title: RPE-1 hTERT FUCCI H3K27me3 rep 2


title: Affymetrix Exon array from patient 1027

description: Affymetrix Human Exon array of prostate biopsy from patient 1027


title: Affymetrix Exon array from patient 1029

description: Affymetrix Human Exon array of prostate biopsy from patient 1029


title: Affymetrix Exon array from patient 1028

description: Affymetrix Human Exon array of prostate biopsy from patient 1028


title: Expression of eGFP, RBS-1, replicate 1

description:
Library name: ecoli_CR_00055
Column name in log_tpm.csv: ecoli_CR_00055

value: SDT507 (gly2 rhaBADM KO) pSD335


title: Expression of eGFP, rspAB KO, replicate 2

description:
Library name: ecoli_CR_00050
Column name in log_tpm.csv: ecoli_CR_00050

value: M9 glycerol ampicillin

value: Replicate 2


title: Gi-51_N_d2_r2

description: Library name: 975983_counts


title: Expression of eGFP, rspAB co-expression, replicate 2

description:
Library name: ecoli_CR_00048
Column name in log_tpm.csv: ecoli_CR_00048

value: SDT507 (gly2 rhaBADM KO) pSD250


title: 1018_BX16A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-16

data_processing:
Base-calling was performed with CASAVA 1.9
FASTQ files were pre-processed to remove sequencing adaptors with Trimmomatic v0.36.
Paired-end trimmed FASTQ files were aligned to hg19 using STAR.
RSEM was used to estimate read counts for each genomic feature.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values, gene symbol, description, transcripts-per-million (TPM)

source_name: prostate

extract_protocol:
Total RNA was extracted from cells adhered to caps using the Qiagen RNeasy FFPE kit.
rRNA-depleted RNA was converted into cDNA and assembled into strand-specific libraries using the NEBNext Ultra II Directional RNA-Seq kit.

treatment_protocol: FFPE human prostate tissues were sectioned onto metal frame membrane slides, and regions of interest were excised onto caps using laser capture microdissection.

tag: regionofinterest


title: 1018_BX13A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-108-15


title: Gi-51_UT_d2_r1

description: Library name: 975985_counts

value: UT


title: Gi-51_N_d2_r1

description: Library name: 975982_counts


title: Gi-51_CP_d2_r2

description: Library name: 975981_counts

value: CP


title: Affymetrix Exon array from patient 1026

description: Affymetrix Human Exon array of prostate biopsy from patient 1026


title: Gi-51_CP_d2_r1

description: Library name: 975979_counts


title: 1015_BX7A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-184-6


title: Expression of eGFP, rspAB co-expression, replicate 1

description:
Library name: ecoli_CR_00047
Column name in log_tpm.csv: ecoli_CR_00047


title: Affymetrix Exon array from patient 1025

description: Affymetrix Human Exon array of prostate biopsy from patient 1025


title: Gi-51_LTI10_d2_r2

description: Library name: 975978_counts


title: Affymetrix Exon array from patient 1023

description: Affymetrix Human Exon array of prostate biopsy from patient 1023


title: 1015_BX7A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-184-5


title: T7 control, replicate 2

description:
Library name: ecoli_CR_00046
Column name in log_tpm.csv: ecoli_CR_00046

value: SDT507 (gly2 rhaBADM KO) pSD78 pSD208

value: M9 glycerol ampicillin chloramphenicol


title: Gi-51_LTI10_d2_r1

description: Library name: 975976_counts

value: idiopathic pulmonary fibrosis (IPF)

value: Lung


title: #979_LTI3_d2_r2

description: Library name: 976008_counts

value: Precision cut lung slices


title: 1015_BX6A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-184-3

value: male


title: Gi-51_LTI3_d2_r2

description: Library name: 975975_counts


title: T7 expression of BLG, replicate 2

description:
Library name: ecoli_CR_00045
Column name in log_tpm.csv: ecoli_CR_00045

value: SDT507 (gly2 rhaBADM KO) pSD78 pSD206


title: 1015_BX6A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-184-4


title: Affymetrix Exon array from patient 1022

description: Affymetrix Human Exon array of prostate biopsy from patient 1022

value: prostate


title: 1015_BX4A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-184-2


title: Expression of eGFP-BLG, delayed sampling, replicate 2

description:
Library name: ecoli_CR_00042
Column name in log_tpm.csv: ecoli_CR_00042

value: bacterial cell

value: SDT507 (gly2 rhaBADM KO) pSD178


title: Affymetrix Exon array from patient 1024

description: Affymetrix Human Exon array of prostate biopsy from patient 1024


title: T7 expression of BLG, replicate 1

description:
Library name: ecoli_CR_00043
Column name in log_tpm.csv: ecoli_CR_00043

value: Replicate 1


title: Affymetrix Exon array from patient 1020

description: Affymetrix Human Exon array of prostate biopsy from patient 1020


title: 1015_BX4A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A5-184-1


title: Gi-51_LTI3_d2_r1

description: Library name: 975974_counts


title: #975_N_d5_r2

description: Library name: 975966_counts

value: N


title: Affymetrix Exon array from patient 1021

description: Affymetrix Human Exon array of prostate biopsy from patient 1021


title: Control, delayed sampling, replicate 2

description:
Library name: ecoli_CR_00041
Column name in log_tpm.csv: ecoli_CR_00041

value: SDT507 (gly2 rhaBADM KO) pSD122

value: M9 glycerol ampicillin


title: #975_N_d5_r1

description: Library name: 975964_counts


title: Affymetrix Exon array from patient 1019

description: Affymetrix Human Exon array of prostate biopsy from patient 1019


title: Affymetrix Exon array from patient 1018

description: Affymetrix Human Exon array of prostate biopsy from patient 1018


title: 1013_BX4-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-52-8


title: 1013_BX6-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-52-9


title: Expression of eGFP-ALA, replicate 2

description:
Library name: ecoli_CR_00040
Column name in log_tpm.csv: ecoli_CR_00040

value: SDT507 (gly2 rhaBADM KO) pSD180

value: Replicate 2


title: Affymetrix Exon array from patient 1017

description: Affymetrix Human Exon array of prostate biopsy from patient 1017


title: #975_LTI10_d5_r2

description: Library name: 975960_counts


title: #975_CP_d5_r1

description: Library name: 975961_counts

value: CP


title: Expression of eGFP, replicate 2

description:
Library name: ecoli_CR_00038
Column name in log_tpm.csv: ecoli_CR_00038

value: SDT507 (gly2 rhaBADM KO) pSD174


title: Expression of eGFP-BLG, replicate 2

description:
Library name: ecoli_CR_00039
Column name in log_tpm.csv: ecoli_CR_00039


title: T7 control, replicate 1

description:
Library name: ecoli_CR_00044
Column name in log_tpm.csv: ecoli_CR_00044

value: SDT507 (gly2 rhaBADM KO) pSD78 pSD208

value: M9 glycerol ampicillin chloramphenicol


title: 1013_BX1-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-52-7


title: 1013_BX11-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-52-11


title: Control, replicate 8

description:
Library name: ecoli_CR_00037
Column name in log_tpm.csv: ecoli_CR_00037

value: Replicate 8


title: Affymetrix Exon array from patient 1015

description: Affymetrix Human Exon array of prostate biopsy from patient 1015