title: 16 Minute Vehicle-Treated NETseq Replicate 1

description:
Vehicle 16 Minutes 1
VEH_vs_BMH_sumnorm_16Minutes.csv


title: 2 Minute BMH-21-Treated NETseq Replicate 3

status: Public on May 26 2021

type: SRA

city: Birmingham

first: Abigail

last: Huffines

address: 720 20th St S

country: USA

institute: University of Alabama at Birmingham

description:
BMH-21 2 Minutes 3
VEH_vs_BMH_sumnorm_2Minutes.csv

library_source: transcriptomic

data_processing:
Library strategy: NET-seq
Base-calling was done by using bcl2fastq software (version 2.20.00).
Reads were deduplicated based on the UMI sequence with fqtrim (version 0.9.7) with the "-C" option.
Reads containing the sequence 5'-AGNNNNNNNNTG-3' at the 5' end were isolated, and cutadapt (version 1.12) was used to remove this sequence. The cutadapt parameters "-g -no-indels" were used.
Cutadapt (version 1.12) was used to remove the 3' sequence 5'-CTGTAGGCACCAT-3' from reads, with the parameters "-a -no-indels".
Alignment was performed using STAR (version 2.7.1a), and reads were aligned to the Saccharomyces cerevisiae genome assembly R64-1-1. The STAR alignIntronMax parameter was set to 1.
SAMtools (version 1.6) was used to sort and index output BAM files from alignment.
Sorted BAM files were converted to BED files using BEDTools (version 2.26.0).
BEDTools (version 2.26.0) was used to generate genome coverage files, with the genomecov function and parameters "-strand" and "+strand"
Data processing and visualization was performed using R (version 4.0.2).
Genome_build: S. cerevisiae R64-1-1
Supplementary_files_format_and_content: Processed data files are in .csv file format.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast was grown at 30ºC with nutation until the OD600 reached 0.3.

extract_protocol:
RNA extraction protocol was based on Clarke et. al., NETSeq reveals heterogeneous nucleotide incorporation by RNA polymerase I, PNAS, 2018. 115 (50), E11633-E11641. In brief, cells were treated (as described in "treatment protocol" section) and then harvested via filtration and flash frozen. Cells were lysed under cryogenic conditions for 10-one minute cycles with a mikro dismembranator II. Immunoprecipitation was done as described in previously published methods, by incubating samples with anti-HA magnetic beads at 4ºC for 3 hours. Finally, RNA was extracted from the samples by using an acidic phenol-chloroform extraction,  and was precipitated at -80ºC at least overnight with an ammonium acetate ethanol solution.
The library construction protocol was based on methods from  Huffines et. al., Spt4 Promotes Pol I Processivity and Transcription Elongation, Genes, 2021. In brief, following RNA extraction, a UMI-containing DNA linker (5’-/5rApp/CANNNNNNNNCTCCACGAGTCATCCGC /3ddC/-3’) was ligated to the 3' end of the isolated RNAs. The residual linker was enzymatically digested, and samples were precipitated. Reverse transcription was performed, and samples were gel extracted to remove any remaining reverse transcription primer. Samples were then circularized, amplified, and PCRCleanDX magnetic beads were used to remove contaminating oligos and purify libraries for sequencing.

treatment_protocol: At OD600 = 0.3, each culture was treated with either vehicle phosphate buffer or BMH-21 for the allotted treatment time. Cultures were returned to 30ºC immediately after treatment was added, and remained at 30ºC until the treatment time elapsed. At that point, cultures were quickly harvested.

tag: treatment

tag: treatment time

value: 2 minutes


title: 2 Minute BMH-21-Treated NETseq Replicate 2

description:
BMH-21 2 Minutes 2
VEH_vs_BMH_sumnorm_2Minutes.csv


title: 2 Minute BMH-21-Treated NETseq Replicate 1

description:
BMH-21 2 Minutes 1
VEH_vs_BMH_sumnorm_2Minutes.csv


title: AA12

city: Durham

first: Steve

last: Taylor

state: NC

address: 303 Research Dr

department: Division of Infectious Diseases

institute: Duke University School of Medicine

description: In vivo blood sample

data_processing:
Real Time Analysis (RTA3) was used for base calling on the NovaSeq6000
Sequenced reads were trimmed for adaptor sequence and low quality bases, then mapped to ASM276v2 transcriptome using Salmon with parameters -p 8 -g $GTF-file --validateMappings
Transcripts per kilobase of exon Per Megabase of library size (TPM) were extracted from each quantification file output by Salmon using tximport.
Genome_build: ASM276v2
Supplementary_files_format_and_content: comma-delimited text files include TPM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Plasmodium falciparum

source_name: HbAA patient 12

extract_protocol:
RNA was extracted from in vitro samples using Trizol reagent, and extracted from in vivo samples using Trizol LS. Kapa Stranded mRNA-seq library prep kit was used with at least 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Plasmodium falciparum:asexual blood stage

tag: strain

value: P. falciparum natural infection

tag: hemoglobin genotype

value: HbAA

tag: parasite stage

value: Ring

tag: hours post-invasion

tag: patient age

tag: patient sex

value: Female

tag: abo

value: B

tag: parasite density (parasites/ul)

tag: date


title: 2 Minute Vehicle-Treated NETseq Replicate 3

description:
Vehicle 2 Minutes 3
VEH_vs_BMH_sumnorm_2Minutes.csv

value: vehicle


title: AA09

description: In vivo blood sample

source_name: HbAA patient 9

value: AB


title: AA08

description: In vivo blood sample

source_name: HbAA patient 8

value: Trophozoite

value: Male

value: A


title: AA05

description: In vivo blood sample

source_name: HbAA patient 5


title: 2 Minute Vehicle-Treated NETseq Replicate 2

description:
Vehicle 2 Minutes 2
VEH_vs_BMH_sumnorm_2Minutes.csv


title: AS02

description: In vivo blood sample

source_name: HbAS patient 2

value: HbAS


title: AA06

description: In vivo blood sample

source_name: HbAA patient 6

value: O


title: AA03

description: In vivo blood sample

source_name: HbAA patient 3


title: AA04

description: In vivo blood sample

source_name: HbAA patient 4


title: GATA1_Hudep1

city: Memphis

first: Mitchell

middle: J.

last: Weiss

state: Tennessee

address: 262 Danny Thomas Place

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

description: ChIP-seq

library_source: genomic

data_processing:
BWA mem mapping to hg19
Duplicated reads were removed using samtools
Genome_build: hg19
Supplementary_files_format_and_content: bigwiggle

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HUDEP-1 cells were cultured at a density of 0.3-0.5x10e6/mL in StemSpan serum-free expansion medium (SFEM; Stemcell Technologies) supplemented with 1 μM dexamethasone, 1 μg/mL doxycycline, 50 ng/ml human SCF (R&D Systems), 3 U/mL EPO (Amgen), and 1% penicillin/streptomycin.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. The reaction was quenched for 5 minutes at room temperature with a final concentration of 125 mM glycine. Fixed cells were lysed in 1mL Cell Lysis Buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% NP-40/Igepal). Nuclei were collected and lysed in 1mL Nuclear Lysis Buffer (50mM Tris-HCl pH 8, 10mM EDTA pH 8, 1% SDS). Chromatin was sonicated at 4 degrees C using a Branson 250 micro-tip sonicator with the power settings of 100% duty cycle, 10 second pulses for 2 minutes, with 90 seconds on ice between pulses. The sonicated chromatin was pre-cleared overnight at 4°C using protein A/G agarose beads. Pre-cleared chromatin was incubated with antibody. Following elution, DNA-protein complexes were treated with RNase for 30 minutes at 37°C followed by proteinase K treatment for 30 minutes at 45°C and overnight at 60°C with shaking. DNA was purified using a Qiagen MinElute kit.
Libraries were prepared using standard reagents from New England BioLabs for Illumina sequencing

tag: cell line

tag: antibody


title: AA02

description: In vivo blood sample

source_name: HbAA patient 2


title: AA01

description: In vivo blood sample

source_name: HbAA patient 1


title: AS1916_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 48 hours post-invasion

value: FUP

value: Schizont


title: AS1915_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 45 hours post-invasion


title: AS1914_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 42 hours post-invasion


title: 2 Minute Vehicle-Treated NETseq Replicate 1

description:
Vehicle 2 Minutes 1
VEH_vs_BMH_sumnorm_2Minutes.csv


title: RS_sc_PDL_46_1

city: Boston

first: David

middle: G

last: Hendrickson

address: 725 Parsons

institute: Harvard

description:
single cell RNA-seq
sceasy_hay.h5ad

data_processing:
rnaseq: Reads generated from the Illumina HiSeq 4000 were demultiplexed with bcl2fastq based on the barcode sequence of each sample. Average read depth across samples was 50 milllion paired-end reads. Reads were pseudo-aligned and then quantified using Salmon by deploying the mapping based mode using a Salmon generated index based on Hg38 and optimized for single cell RNA-seq cellRanger v3 to ensure accurate comparison between bulk and single cell RNA-seq.
scRNAseq: The raw single cell reads were demultiplexed by sample using bcl2fastq. Alignment, cell barcode demultiplexing, transcript quantification and sample merging were carried out with CellRanger 3.0 using the hg38 CR 3.0 gene annoation (also used for bulk RNA-seq). Filtered cell by gene matrices were normalized using Seurat 3.0. and SCTransform. Dimension reductionality was carried out with PCA (n = 50). Clusters were defined using the louvain algorithm and cells were visualized with UMAP projection.
atacseq: We first trimmed the raw fastq files with Trimmomatic, then using bowtie2 to align the trimmed reads to hg38. After alignment, we used samtools flags (-f 0x02 and -q2 0) to filter for only properly paired and high quality reads. PCR duplicates are removed using picard MarkDuplicates. Finally for each bam file, we adjusted the reads ends by Tn5 offset (+4 on + strand, -5 on -strand).For peak calling, we created a condition specific peak atlas by pooling all replicates in a specific condition and applied macs2 for peak calling on the pooled bam file with options (-g hs -p 1e-1 --nomodel --shift -37 --extsize 73). In addition, we performed peak calling on each individual replicates as well. Then we performed irreproducible discovery rate analysis on each condition specific peak atlas for each pair of replicates and filter for peaks that are reproducible in at least two replicates (IDR threshold of 0.05). A single accessibility atlas is created by merging condition-specific peak atlas across all conditions. Peak is assigned to nearest gene if it is within 50kb, otherwise it is annotated as intergenic.
Genome_build: Hg38
Supplementary_files_format_and_content: h5ad
Supplementary_files_format_and_content: TPM
Supplementary_files_format_and_content: bigwig

molecule: polyA RNA

growth_protocol: RS/htert: WI-38 cells were obtained from the Coriell Institute (AG06814-N) at PDL 15. The cells were grown in Dulbecco’s modifiedEagle’s medium (DMEM, Gibco) with 1 mg/ml of glucose,supplemented with 10% dialyzed fetal bovine serum (FBS)and maintained in an incubator set to 37oC, 5% CO2, and20% O2. The cells were maintained on 10 cm collagen coatedplates (Corning) and split every four to five days until cellsslowed down in growth (PDL 37) with approach to senescenceand were split every seven days instead. No change was madeto hTERT sampling. Cells were tested every month for my-coplasma contamination every month using the MycoAlertMycoplasma Detection Kit (Lonza). A smaller subset of threePDL timepoints (PDL 45, PDL 55, PDL 56) generated in a sec-ondary time course to ensure "deep" senescence (2-4 monthsafter cell cycle cessation) was profiled as previously reported[134].4.1.2 WI-38 irradiation time courseWI-38 cells at PDL 20 were plated in DMEM supplementedwith 10% FBS with 50,000 cells per well in a 6-well collagencoated plate. Cells were allowed to settle for 2 hours and weresubsequently treated with 10 Gy of X-rays. Cells were sampledbetween 1 day and 9 days for transcriptome profiling. RNAwas extracted according to methods below.4.1.3 WI-38 cell density time courseWI-38 cells at PDL 23 were grown on 10 cm collagen coatedplates in DMEM supplemented with 10% FBS. Cells weregrown and sampled intermittently between 1 day and 10 daysfor transcriptome profiling. RNA was extracted according tomethods below.

extract_protocol:
10x library construction was performed by following manufacturer's protocol
scRNAseq: At each time point, singlet hTERT controls and experimental samples were processed with Chromium Single Cell 3’ RNAseq kit V2 (10x Genomics) through cDNA amplification cleanup, where they were frozen at -20\(^o\)C.  Once all time points were converted to cDNA, the frozen cDNAs were thawed and batched for library construction. The following modifications were made to the process: Reverse transcription reactions were brought up to volume with DMEM + 10\% FBS instead of water, each emulsion targeted 3000 cells (5200 cells loaded), and cDNA was amplified 12 cycles, with 12 cycles of index PCR. There was no hTert control for time point 3, and one of the replicates for PDL 25 dropped out during library construction. Remaining samples were pooled equimolarly and sequenced on a HiSeq4000 with the standard 26,8,0,98 run configuration.
RIS : supplemented with 10\% FBS with 50,000 cells per well in a 6-well collagen coated plate. Cells were allowed to settle for 2 hours and were subsequently treated with 10 Gy of X-rays. Cells were sampled between 1 day and 9 days for transcriptome profiling. RNA was extracted according to methods below.
CD: WI-38 cells at PDL 23 were grown on 10 cm collagen coated plates in DMEM supplemented with 10\% FBS. Cells were grown and sampled intermittently between 1 day and 10 days for transcriptome profiling. RNA was extracted according to methods below.

tag: time course

value: RS timecourse

tag: population doublings

tag: time point/day

tag: extract protocol

value: Cells were trypsinized, washed and pelleted. Cell concentration was determined and 5200 cells were loaded per sample.


title: RS_sc_PDL_33_2

description:
single cell RNA-seq
sceasy_hay.h5ad


title: RS_sc_PDL_50_2

description:
single cell RNA-seq
sceasy_hay.h5ad


title: RS_sc_PDL_50_1

description:
single cell RNA-seq
sceasy_hay.h5ad


title: RS_sc_PDL_37_1

description:
single cell RNA-seq
sceasy_hay.h5ad


title: RS_sc_PDL_46_2

description:
single cell RNA-seq
sceasy_hay.h5ad


title: AS1912_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 36 hours post-invasion

value: Plasmodium falciparum:asexual blood stage


title: AS1913_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 39 hours post-invasion


title: RS_sc_PDL_33_1

description:
single cell RNA-seq
sceasy_hay.h5ad


title: RS_sc_PDL_37_2

description:
single cell RNA-seq
sceasy_hay.h5ad


title: AS1911_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 33 hours post-invasion


title: RS_sc_PDL_25_1

description:
single cell RNA-seq
sceasy_hay.h5ad


title: RS_sc_hTert_t7

description:
single cell RNA-seq
sceasy_hay.h5ad


title: AS1910_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 30 hours post-invasion


title: RS_sc_PDL_29_2

description:
single cell RNA-seq
sceasy_hay.h5ad


title: RS_sc_PDL_29_1

description:
single cell RNA-seq
sceasy_hay.h5ad


title: AS1908_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 24 hours post-invasion


title: AS1907_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 21 hours post-invasion


title: AS1909_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 27 hours post-invasion


title: RS_sc_hTert_t6

description:
single cell RNA-seq
sceasy_hay.h5ad


title: AS1906_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 18 hours post-invasion


title: AS1905_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 15 hours post-invasion


title: RS_sc_hTert_t5

description:
single cell RNA-seq
sceasy_hay.h5ad


title: RS_sc_hTert_t4

description:
single cell RNA-seq
sceasy_hay.h5ad


title: AA07

description: In vivo blood sample

source_name: HbAA patient 7

value: P. falciparum natural infection


title: AS1816_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 48 hours post-invasion


title: RS_atac_PDL50_TP7_B

extract_protocol:
ATAC-seq libraries were made based on protocol from Corces et. al., 2017
ATACseq: Freshly harvested cells were used for all reactions. Briefly, the cell monolayer was washed with PBS, trypsinized with TrypLE (Gibco), resuspended in media, and cells were pelleted. Cells were counted and 100,000 cells were used in each reaction. Cell lysis, DNA transposition, and library construction was adapted from the Omni-ATAC protocol (Corces et al. 2017). Libraries were amplified for 13 total cycles. Sample purification and size selection was done with SPRI Ampure Beads (Beckman Coulter). Libraries were run on the Pippin HT using 2\% agarose cassettes for further size selection (Sage Science). Quality of ATAC-seq libraries were assessed with the Agilent Bioanalyzer 2100 with DNA high sensitivity chips (Agilent Technologies). Libraries were sequenced on the HiSeq4000 with paired end sequencing using 2 x 150 bp reads (Illumina)
RIS : supplemented with 10\% FBS with 50,000 cells per well in a 6-well collagen coated plate. Cells were allowed to settle for 2 hours and were subsequently treated with 10 Gy of X-rays. Cells were sampled between 1 day and 9 days for transcriptome profiling. RNA was extracted according to methods below.
CD: WI-38 cells at PDL 23 were grown on 10 cm collagen coated plates in DMEM supplemented with 10\% FBS. Cells were grown and sampled intermittently between 1 day and 10 days for transcriptome profiling. RNA was extracted according to methods below.

value: Cells were trypsinized, washed and pelleted. Cell concentration was determined and 100,000 cells were carried forward per reaction


title: RS_atac_PDL50_TP7_A


title: AS1903_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 9 hours post-invasion

value: Ring


title: AS1902_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 6 hours post-invasion


title: AS1815_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 45 hours post-invasion


title: AS1901_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 3 hours post-invasion


title: RS_atac_PDL33_TP4_C


title: RS_atac_PDL46_TP6_A


title: AS1814_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 42 hours post-invasion


title: RS_atac_PDL46_TP6_B


title: AS1811_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 33 hours post-invasion


title: RS_atac_PDL37_TP5_C


title: AS1813_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 39 hours post-invasion


title: RS_atac_PDL37_TP5_B


title: AA10

description: In vivo blood sample

source_name: HbAA patient 10

value: HbAA


title: AS1812_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 36 hours post-invasion


title: RS_atac_PDL33_TP4_B


title: AS1810_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 30 hours post-invasion


title: RS_atac_PDL33_TP4_A


title: RS_sc_hTert_t2

description:
single cell RNA-seq
sceasy_hay.h5ad


title: RS_atac_PDL30_TP3_C


title: AS1904_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep2 12 hours post-invasion


title: AS1807_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 21 hours post-invasion


title: RS_atac_PDL30_TP3_A


title: AS1809_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 27 hours post-invasion


title: RS_atac_PDL30_TP3_B


title: RS_atac_PDL25_TP2_C


title: AS1806_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 18 hours post-invasion


title: AS1805_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 15 hours post-invasion


title: RS_atac_PDL37_TP5_A


title: AS1804_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 12 hours post-invasion


title: AA1716_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 48 hours post-invasion


title: AS1802_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 6 hours post-invasion


title: AS1803_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 9 hours post-invasion


title: RS_atac_PDL25_TP2_A


title: AA1715_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 45 hours post-invasion


title: RS_atac_PDL20_TP1_C


title: RS_atac_PDL20_TP1_A


title: RS_atac_PDL20_TP1_B


title: AA1714_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 42 hours post-invasion


title: RS_atac_hTERT_TP6_A


title: RS_atac_hTERT_TP7_A


title: AS1808_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 24 hours post-invasion


title: RS_atac_hTERT_TP6_B


title: AA1713_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 39 hours post-invasion


title: RS_atac_PDL25_TP2_B


title: AA1711_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 33 hours post-invasion


title: AA1709_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 27 hours post-invasion


title: RS_atac_hTERT_TP5_B


title: RS_atac_hTERT_TP5_C


title: RS_atac_hTERT_TP4_C


title: AA1712_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 36 hours post-invasion


title: AA1708_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 24 hours post-invasion


title: RS_atac_hTERT_TP4_B


title: RS_atac_hTERT_TP4_A


title: AS1801_FUP

description: In vitro time series - FUP

source_name: FUP HbAS rep1 3 hours post-invasion


title: RS_atac_hTERT_TP5_A


title: RS_atac_hTERT_TP7_B


title: AA1707_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 21 hours post-invasion


title: RS_atac_hTERT_TP2_C


title: RS_atac_hTERT_TP2_B


title: AA1706_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 18 hours post-invasion


title: AA1705_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 15 hours post-invasion


title: AA1704_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 12 hours post-invasion


title: RS_atac_hTERT_TP2_A


title: AA1703_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 9 hours post-invasion


title: RS_atac_hTERT_TP1_C


title: RS_atac_hTERT_TP1_A


title: RIS_d9_xray_C

extract_protocol:
Illumina TruSeq Stranded mRNA Library Prep kit
RNAseq: Total RNA was extracted from cells using the Direct-zol RNA purification kit (Zymo Research) for all bulk RNA-seq time course experiments. RNA was quantified using the Fragment Analyzer Standard Sense RNA kit, 15 nt (Agilent Technologies, formerly Advanced Analytical). RNA sequencing libraries were prepared as directed using TruSeq® Stranded mRNA Library Prep Kit and the TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat Library Prep kit (Illumina), with 1000ng of input material. Samples were amplified for 12 cycles of PCR with TruSeq RNA CD Index Plate (Illumina) and pooled into two separate libraries for each method, before running 3nM libraries across 4 lanes for each set (TruSeq mRNA - 4 lanes and Total RNA - 4 lanes) on the HiSeq 4000 (Illumina).
RIS : supplemented with 10\% FBS with 50,000 cells per well in a 6-well collagen coated plate. Cells were allowed to settle for 2 hours and were subsequently treated with 10 Gy of X-rays. Cells were sampled between 1 day and 9 days for transcriptome profiling. RNA was extracted according to methods below.
CD: WI-38 cells at PDL 23 were grown on 10 cm collagen coated plates in DMEM supplemented with 10\% FBS. Cells were grown and sampled intermittently between 1 day and 10 days for transcriptome profiling. RNA was extracted according to methods below.

value: Irradiation time course

value: Day 9

value: Cells were lysed on the tissue culture plate with trizol and RNA was extracted using Zymo DirectZol Miniprep Plus Kit. Manufacturer protocol was followed exactly.


title: AA1710_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 30 hours post-invasion

value: Trophozoite


title: AA1316_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 48 hours post-invasion


title: AA1701_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 3 hours post-invasion


title: RIS_d9_xray_B


title: RS_atac_hTERT_TP1_B


title: RIS_d6_xray_C

value: Day 6


title: RIS_d9_xray_A


title: AA1314_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 42 hours post-invasion


title: AA1315_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 45 hours post-invasion


title: AA1312_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 36 hours post-invasion


title: RIS_d6_xray_B


title: RIS_d6_xray_A


title: AA1311_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 33 hours post-invasion


title: RIS_d5_xray_B

value: Day 5


title: AA1309_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 27 hours post-invasion


title: RIS_d5_xray_C


title: AA1702_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep2 6 hours post-invasion


title: AA1310_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 30 hours post-invasion


title: AA1308_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 24 hours post-invasion


title: AA1307_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 21 hours post-invasion


title: RIS_d4_xray_C

value: Day 4


title: RIS_d4_xray_A


title: RIS_d5_xray_A


title: RIS_d3_xray_C

value: Day 3


title: RIS_d3_xray_B


title: AA1306_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 18 hours post-invasion

value: FUP


title: AA1305_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 15 hours post-invasion


title: AA1302_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 6 hours post-invasion


title: AA1303_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 9 hours post-invasion


title: RIS_d3_xray_A


title: RIS_d2_no_xray_B

value: Day 2


title: AS1615_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 45 hours post-invasion

value: HbAS

value: Schizont


title: AS1616_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 48 hours post-invasion

value: Plasmodium falciparum:asexual blood stage


title: AS1614_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 42 hours post-invasion


title: CD_D4_C

value: Cell density time course


title: RIS_d2_no_xray_A


title: CD_D7_C

value: Day 7


title: CD_D3.5_C

value: Day 3.5


title: AS1613_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 39 hours post-invasion


title: CD_D3_C


title: CD_D2.75_C


title: AS1612_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 36 hours post-invasion


title: AS1611_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 33 hours post-invasion


title: AS1610_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 30 hours post-invasion


title: AA1304_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 12 hours post-invasion

value: HbAA

value: Ring


title: RIS_d4_xray_B

value: Irradiation time course


title: AA1313_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 39 hours post-invasion


title: CD_D2_C

value: Cells were lysed on the tissue culture plate with trizol and RNA was extracted using Zymo DirectZol Miniprep Plus Kit. Manufacturer protocol was followed exactly.


title: CD_D2.5_C

value: Day 2.5


title: AA1301_FUP

description: In vitro time series - FUP

source_name: FUP HbAA rep1 3 hours post-invasion


title: AS1608_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 24 hours post-invasion


title: CD_D1_C

value: Day 1


title: CD_D7_B


title: AS1607_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 21 hours post-invasion


title: AS1605_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 15 hours post-invasion


title: CD_D10_C

value: Day 10


title: CD_D4_B

value: Day 4


title: AS1603_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 9 hours post-invasion


title: CD_D3_B

value: Day 3


title: AS1601_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 3 hours post-invasion


title: CD_D3.5_B


title: AS1602_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 6 hours post-invasion


title: CD_D2.75_B


title: AS1516_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 48 hours post-invasion


title: AS1609_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 27 hours post-invasion

value: Trophozoite


title: CD_D2_B

value: Day 2


title: CD_D1.5_C

value: Day 1.5


title: AS1515_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 45 hours post-invasion

value: HbAS

value: Schizont


title: AS1514_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 42 hours post-invasion

value: Plasmodium falciparum:asexual blood stage


title: RIS_d2_no_xray_C


title: CD_D1.5_B

value: Cell density time course


title: AS1513_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 39 hours post-invasion


title: CD_D1_B


title: CD_D10_B


title: CD_D7_A

value: Day 7


title: AS1606_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 18 hours post-invasion


title: AS1510_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 30 hours post-invasion


title: AS1511_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 33 hours post-invasion


title: CD_D3.5_A

value: Day 3.5


title: AS1508_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 24 hours post-invasion

value: Ring


title: AS1509_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 27 hours post-invasion


title: AS1512_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 36 hours post-invasion


title: CD_D4_A


title: AS1604_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep2 12 hours post-invasion


title: AS1507_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 21 hours post-invasion


title: CD_D2.5_A


title: CD_D2.75_A


title: CD_D3_A


title: CD_D2.5_B


title: AS1505_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 15 hours post-invasion


title: AS1506_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 18 hours post-invasion


title: CD_D1.5_A


title: CD_D1_A


title: CD_D10_A


title: AS1503_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 9 hours post-invasion


title: AS1501_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 3 hours post-invasion


title: AS1502_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 6 hours post-invasion


title: AA1716_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 48 hours post-invasion

value: HbAA


title: RS_PDL53_TP10_C

value: RS late senescent time course

value: Cells were lysed on the tissue culture plate with trizol and RNA was extracted using Zymo DirectZol Miniprep Plus Kit. Manufacturer protocol was followed exactly.


title: RS_PDL53_TP10_B


title: AA1715_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 45 hours post-invasion


title: RS_PDL52_TP9_C


title: RS_PDL53_TP10_A


title: AA1712_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 36 hours post-invasion


title: AA1714_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 42 hours post-invasion


title: RS_PDL52_TP9_B


title: AA1711_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 33 hours post-invasion


title: RS_PDL52_TP9_A


title: AA1713_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 39 hours post-invasion


title: RS_PDL45_TP7_B


title: RS_PDL45_TP7_C


title: RS_PDL45_TP7_A


title: AA1709_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 27 hours post-invasion


title: CD_D2_A


title: AA1707_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 21 hours post-invasion


title: AA1708_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 24 hours post-invasion


title: AS1504_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAS rep1 12 hours post-invasion


title: AA1706_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 18 hours post-invasion


title: AA1705_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 15 hours post-invasion


title: AA1704_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 12 hours post-invasion


title: AA1703_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 9 hours post-invasion


title: RS_PDL50_TP8_A

value: RS timecourse


title: RS_PDL46_TP6_A


title: AA1702_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 6 hours post-invasion


title: RS_PDL46_TP6_B


title: RS_PDL46_TP6_C


title: AA1316_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 48 hours post-invasion


title: AA1701_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 3 hours post-invasion


title: RS_PDL37_TP5_C


title: AA1710_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep2 30 hours post-invasion


title: RS_PDL37_TP5_A


title: RS_PDL37_TP5_B


title: AA1315_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 45 hours post-invasion


title: RS_PDL50_TP8_C


title: AA1313_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 39 hours post-invasion


title: AA1314_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 42 hours post-invasion


title: AA1312_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 36 hours post-invasion


title: RS_PDL50_TP8_B


title: AA1310_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 30 hours post-invasion


title: AA1311_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 33 hours post-invasion


title: RS_PDL33_TP4_B


title: RS_PDL28_TP3_C


title: RS_PDL28_TP3_B


title: RS_PDL33_TP4_A


title: RS_PDL28_TP3_A


title: AA1309_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 27 hours post-invasion


title: AA1308_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 24 hours post-invasion


title: AA1307_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 21 hours post-invasion


title: AA1305_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 15 hours post-invasion


title: RS_PDL25_TP2_B


title: AA1302_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 6 hours post-invasion


title: hTERT_TP7_B

source_name: WI-38 hTERT

value: hTERT


title: RS_PDL25_TP2_A


title: hTERT_TP7_C


title: RS_PDL20_TP1_B


title: RS_PDL20_TP1_A


title: hTERT_TP6_C


title: AA1303_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 9 hours post-invasion


title: RS_PDL25_TP2_C


title: RS_PDL33_TP4_C


title: hTERT_TP6_B


title: AA1301_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 3 hours post-invasion


title: hTERT_TP5_B


title: AA1306_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 18 hours post-invasion


title: RS_PDL20_TP1_C


title: hTERT_TP7_A


title: hTERT_TP6_A


title: hTERT_TP4_A


title: hTERT_TP4_B


title: hTERT_TP5_C


title: hTERT_TP2_A


title: hTERT_TP5_A


title: hTERT_TP2_B


title: hTERT_TP1_A


title: hTERT_TP4_C


title: AA1304_3D7

description: In vitro time series - 3D7

source_name: 3D7 HbAA rep1 12 hours post-invasion


title: hTERT_TP2_C


title: hTERT_TP1_C


title: hTERT_TP1_B


title: amm35: NB4 + ATRA + TSA

city: Berkeley

first: Brian

last: Li

state: California

address: 2521 Hearst Avenue

institute: University of California, Berkeley

data_processing:
Illumina 1.9 encoding used for base calling
Transcripts pseudo-mapped and quantified using Salmon v 0.10.0
Genome_build: Ensembl GRCh38 version 86
Supplementary_files_format_and_content: Comma delimited text file with TPM per gene per sample

source_name: promyelocyte

growth_protocol: AP-1060 cells were cultured in 70% IMDM (Gibco 12440053) supplemented with 20% FBS, 1X Penicillin-Streptomycin (Gibco 15070063), and 10% conditioned medium from cell line 5637 (ATCC HTB-9). For conditioned medium from cell line 5637, cells were seeded in 10 mL of RPMI-1640 (Corning 10-040-CV) supplemented with 10% FBS and 1X Penicillin-Streptomycin (Gibco 15070063). Medium was exchanged after 24 hours, then collected at 48 hours after initial seeding. Conditioned medium was then sterilized using a 0.22 µm polyethylsufone filter (Millipore Sigma SLGPM33RS). NB4 (DSMZ ACC 207) and HL-60 (ATCC CCL-240) cells were cultured in 90% RPMI-1640 supplemented with 10% FBS and 1X Penicillin-Streptomycin. AP-1060 cells were passaged at a density of 2 million cells/mL, seeded in wells of a 24-well plate at a density of 1 million, and maintained at 37 °C in 5% CO2. NB4 and HL-60 cells were passaged at a density of 5 x 105 cells/mL, seeded in wells of a 24-well plate at a density of 1million, and maintained at 37 °C in 5% CO2.

extract_protocol:
RNA was extracted from ~1 million cells using the QIAGEN RNeasy Mini Kit (QIAGEN 74104).
Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs E7770S) and the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs E7490S) with 1 μg total RNA input.

treatment_protocol: Concentrated stock ATRA was thawed and diluted to 10 mM in dimethyl sulfoxide (DMSO) prior to use, then further diluted to 1 µM working concentration in cell-culture media. 100 nM of Trichostatin A (TSA, Fisher Scientific 14-061, Mfg. Tocris Bioscience), reconstituted in DMSO, was added to cells to inhibit histone deacetylase activity. All media with relevant treatments was changed after 48 hours. Cells were collected for polyA RNA extraction after 96 hours total.

tag: aml subtype

value: acute promyelocytic leukemia

tag: treatment

value: all-trans retinoic acid + trichostatin A

tag: treatment resistance


title: amm33: NB4 + ATRA

value: all-trans retinoic acid


title: amm36: NB4 + ATRA + TSA


title: amm31: NB4 + ATRA


title: amm32: NB4 + ATRA


title: amm34: NB4 + ATRA + TSA


title: amm30: NB4 + TSA

value: trichostatin A


title: amm29: NB4 + TSA


title: amm28: NB4 + TSA


title: amm26: NB4 untreated control

value: untreated


title: amm25: NB4 untreated control


title: amm24: HL60 + ATRA + TSA

source_name: myeloblast

value: acute myeloblastic leukemia


title: amm27: NB4 untreated control


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio089

type: genomic

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

country: Germany

institute: UK Ulm

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: Illumina GenomeStudio software ("normalization based on internal controls")

label: Cy5 and Cy3

source_name: stage IA-IIIA lung adenocarcinoma; short term survivor (<2 years)

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tissue samples (FFPE) using the Maxwell RSC DNA FFPE kit according to standard instructions

tag: disease state

value: lung adenocarcinoma

tag: gender

value: male

tag: Stage

value: stage IA-IIIA lung adenocarcinoma

tag: survival

value: short term relapse-free survivor


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio098


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio092


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio093


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio099


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio083

value: female


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio096


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio091


title: amm23: HL60 + ATRA + TSA


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio095


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio094


title: amm20: HL60 + ATRA


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio085

source_name: stage IA-IIIA lung adenocarcinoma; long term survivor (>2 years)

value: long term relapse-free survivor


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio079


title: amm19: HL60 + ATRA


title: amm22: HL60 + ATRA + TSA


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio081


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio088


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio090


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio077


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio084


title: amm17: HL60 + TSA


title: amm21: HL60 + ATRA


title: amm16: HL60 + TSA


title: amm15: HL60 untreated control


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio080


title: amm13: HL60 untreated control


title: amm14: HL60 untreated control


title: amm12: AP1060 + ATRA + TSA

value: ATRA resistant


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio075


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio078


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio074


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio082


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio087


title: amm11: AP1060 + ATRA + TSA


title: amm18: HL60 + TSA


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio086


title: amm10: AP1060 + ATRA + TSA


title: amm9: AP1060 + ATRA


title: amm8: AP1060 + ATRA


title: amm7: AP1060 + ATRA


title: amm5: AP1060 + TSA


title: lung adenocarcinoma, Angio076

source_name: excluded from further analysis

value: excluded from further analysis


title: amm6: AP1060 + TSA


title: amm4: AP1060 + TSA


title: amm3: AP1060 untreated control


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio068


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio073


title: amm1: AP1060 untreated control


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio067


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio071


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio066


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio072


title: amm2: AP1060 untreated control


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio059


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio070


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio063


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio054


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio057


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio058


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio053


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio060


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio051


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio046


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio044


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio048


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio043


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio064


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio049


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio052


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio065


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio062


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio061


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio041


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio042


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio039


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio050


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio055


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio036


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio047


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio034


title: lung adenocarcinoma, Angio035


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio027


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio026


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio031


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio029


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio023


title: lung adenocarcinoma, Angio032


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio018


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio020


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio025


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio019


title: MGHΔsoxSparB

city: Columbia

first: Sathesh

middle: K

last: Sivasankaran

state: MO

address: Bond Life Sciences Center Suite 106, 1201 Rollins Street

institute: University of Missouri

data_processing:
Segemehl V0.18 used for mapping
Read counts were calculated custom made perl script.
Reads were normalized using VOOM transformation (Log2 normalized read counts) from Limma R package
Differential gene expression was calculated using Limma in R
Mapped reads were transformed into graphical "GR" files for visualisation uding IGB
Genome_build: Klebsiella pneumoniae MGH 78578
Supplementary_files_format_and_content: normalized values for each Sample.

organism: Klebsiella pneumoniae

source_name: 30 min exposure paraquat 7.81µM MGH78578 ΔSoxS

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina HiSeq2500 RNA Sample Prep Kit was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: genotype

value: {delta}SoxS

value: paraquat


title: lung adenocarcinoma, Angio045


title: lung adenocarcinoma, Angio022


title: HPVEC0

city: New Haven

first: Jonas

last: Schupp

state: CT

address: 300 Cedar Street

department: PCCSM

institute: YALE UNIVERSITY

description:
PrimaryPulmonaryEndothelialCells.raw.counts.processed.mtx
PrimaryPulmonaryEndothelialCells.processed.genes.tsv
PrimaryPulmonaryEndothelialCells.processed.barcodes.tsv

data_processing:
Demultiplex and basecall to fastq with cellranger mkfastq
Trimming of Read 2 for TSO and poly(A) with cutadapt
filtering, alligning, and barcode collapsing with STAR (v2.7.3a)
Cells filtered with >7.5% of transcriptome from intron-spanning reads; < 20% mitochondrial origin; at least 1000 transcripts profiled
background contamination using SoupX and multiplets removed
Genome_build: GRCh38 release 31
Supplementary_files_format_and_content: WholeLungeDissociates.processed.barcodes.tsv: list of corresponding cell barcode identities for the count matrix of the whole lung dissociate samples
Supplementary_files_format_and_content: PrimaryPulmonaryEndothelialCells.processed.barcodes.tsv: : list of corresponding cell barcode identities for the count matrix of the primary pulmonary endothelial cell samples
Supplementary_files_format_and_content: PrimaryPulmonaryEndothelialCells.processed.genes.tsv: list of corresponding gene identities for the count matrix of the primary pulmonary endothelial cell samples
Supplementary_files_format_and_content: WholeLungeDissociates.processed.genes.tsv: list of corresponding gene identities for the count matrix of the  whole lung dissociate samples
Supplementary_files_format_and_content: WholeLungeDissociates.raw.counts.processed.mtx: gene expression count matrix  of the whole lung dissociate samples in sparse matrix format, generated with R package 'Matrix' and writeMM() function
Supplementary_files_format_and_content: PrimaryPulmonaryEndothelialCells.raw.counts.processed.mtx: gene expression count matrix  of the primary pulmonary endothelial cell samples in sparse matrix format, generated with R package 'Matrix' and writeMM() function

source_name: primary pulmonary microvascular cells

growth_protocol: gelatin-coated plates  in EGM2 endothelial growth medium (Lonza)

extract_protocol:
passed through 40 uM strainer
10X Genomics 3 prime v2 for whole lung dissociates and 10X Genomics 3 prime v3 für primary cells
single cell RNA-Seq

treatment_protocol: Trypsinization

tag: tissue

value: primary pulmonary microvascular cells

value: Control


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio024


title: lung adenocarcinoma, Angio021


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio013


title: MGHΔsoxSparA


title: HEK293_ANRIL KD_5

type: RNA

city: Vandoeuvre-lès-Nancy

first: Sylvain

last: Maenner

address: 9 Avenue de la Forêt de Haye

department: CNRS-UL

country: France

institute: IMoPA

description: SST-RMA expression value derived from Transcriptome Analysis Console (TAC) Software; gene-exon analysis

hyb_protocol: 5.5 µg of fragmented and labeled ss-cDNA was hybridized on GeneChip® Clariom™ D, human (ThermoFisher Scientific) and incubated at 45°C in the Genechip® Hybridization oven 640 (Affymetrix) for 16 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (Affymetrix) using Applied Biosystems™ Hybridization Wash and Stain kit according to the manufacturer’s instructions (Applied Biosystems™).

scan_protocol: Array scanning was performed using the GeneChipTM Scanner 3000 with the AutoLoader Carousel add-on in combination with the GenChipTM Command ConsoleTM software following the manufacturer’s recommendation.

data_processing: Raw intensity CEL files generated by the GeneChip™Command Console™ were imported into Transcriptome Analysis Console (TAC) 4.0 (Applied Biosystems) and CHP files were generated for gene-exon level analysis using the SST-RMA summarization method.

label: biotin

source_name: HEK293_ANRIL KD

label_protocol: Sense-strand cDNA (ss-cDNA) was synthesized from 5 ng of total RNA and then fragmented and labeled using the GeneChip WT Pico Amplification Kit according to manufacturer’s instructions (Applied Biosystems™).

growth_protocol: HEK293 cells were grown in Dulbecco’s Modified Eagle’s Medium-high glucose (DMEM) (Sigma-Aldrich) supplemented with 10% Fetal Bovine Serum (FBS) (Sigma-Aldrich), 1% penicillin/streptomycin (Sigma-Aldrich), and 1% L-glutamine (Sigma-Aldrich).

extract_protocol: Total RNAs were extracted and purified using the RNeasy mini kit (QIAGEN) following the manufacturer’s recommendation.

treatment_protocol: 500,000 HEK293 cells were seeded per well in 6 well-plates 12-16h before transfection. Transfection was performed using Lipofectamine 2000 (Invitrogen). A mix of the 4 ANRIL LNA GapmeRs or scrambled LNA GapmeRs was used for transfection at a final concentration of 25nM. All samples were collected 48h post-transfection in RLT lysis buffer (RNeasy mini kit QIAGEN) for total RNA extraction.

tag: cell type

value: Human Embryonic Kidney cells

tag: Sex

tag: genotype/variation

value: ANRIL knockdown


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio015


title: MGHparA

source_name: 30 min exposure paraquat 7.81µM MGH 78578

value: Wild type

value: Paraquat


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio040


title: MGHwtB

source_name: Wild type with no exposure

value: untreated


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio014

value: lung adenocarcinoma


title: HEK293_ANRIL KD_4

tag: cell line


title: MGHwtA


title: NDRI3

description:
WholeLungeDissociates.raw.counts.processed.mtx
WholeLungeDissociates.processed.genes.tsv
WholeLungeDissociates.processed.barcodes.tsv

source_name: Whole Lung Dissociate

treatment_protocol: Enzymatic and Mechanical Digestion; Cryopreservation in 10% DMSO

value: Whole Lung Dissociate


title: H3K9me2 - suvh2suvh9+SUVH9(Y636F) R2

city: Ottawa

first: Jean-Sebastien

last: Parent

state: Ontario

address: 960 Carling Avenue

country: Canada

institute: Agriculture and Agri-Food Canada

description: Chromatin

data_processing:
WGBS: Adaptor sequences were removed using Trimmomatic, trimmed reads were then aligned on the Arabidopsis TAIR10 genome using Bismark. Alignment files were coverted to bam files, sorted and duplicate reads were removed with Picard Tools.
ChIP-seq: Adaptor sequences were removed using Trimmomatic, trimmed reads were then aligned on the Arabidopsis TAIR10 genome using Bowtie2. Alignment files were converted to bam files using Samtools and duplicates were removed using Picard tools. Genome-wide coverage was obtained with Bedtools and put in bedGraph format.
Supplementary_files_format_and_content: bedGraph

organism: Arabidopsis thaliana

source_name: complemented suvh2suvh9 mature seeds

growth_protocol: Plants were grown under long day conditions at 22 °C. Seeds were sown directly on soil after stratification in distilled water at 4 °C for three days. For seed isolation, mature fruits were collected from the primary inflorescence after seven to eight weeks of growth.

extract_protocol:
Siliques were cut open with insulin syringe needles, whole seeds were transferred to a tube and frozen. Fixed chromatin was isolated from approximately 250 to 300 whole seeds using a scaled-down version of a protocol found elsewhere. Briefly, seed samples kept at -80 °C are thawed on ice in 1 % formaldehyde. Vacuum is applied for 10 min before adding glycine to a final concentration of 0.125 M and vacuum is applied for another 5 min. Embryos are collected at the bottom of the 1.7 mL tube by spinning 1 min at 5000 rpm and washed three times with distilled water. Once last wash is removed, tubes are put in liquid nitrogen and embryos are ground to a fine powder with pre-cooled plastic pestle and 750 uL of extraction buffer I (0.4 M Sucrose, 10 mM Tris-HCl pH 8.0, 10 mM MgCl2, 25 mM β-mercaptoethanol, 1X Halt™ Protease Inhibitors (Thermo Fisher Scientific)  and 0.1 mM PMSF). Slurry is transferred and processed in a 2 mL Dounce homogenizer (MilliporeSigma) and transferred to a 15 mL conical tube on ice. When all samples are processed, tubes are inserted in a mixer slowly rotating at 4 °C form 30 min. The slurries were then filtered through a 40 µm FalconTM cell strainer (Thermo Fisher Scientific)  into a new 50 mL FalconTM tubes and tubes and filters were rinced with 5 mL of buffer I. The new tubes were spun at 4000 rpm for 20 min at 4 °C. Supernatants are poured off and pellets are resuspended in 1.25 mL of extraction buffer II (0.25 M Sucrose, 10 mM Tris-HCl pH 8.0, 10 mM MgCl2, 1% Triton X-100, 5 mM β-mercaptoethanol, 1X Halt™ Protease Inhibitors (Thermo Fisher Scientific)  and 0.1 mM PMSF) and transferred to a new DNA Lobind 1.75 mL tubes (Eppendorf). Tubes are spun at 13,000 rpm for 10 min at 4 °C. Supernatants are discarded and pellets are resuspended in 350 µL of buffer II with repeated pipetting. The solutions are then added to new tubes on top of a 350 µL of buffer III (1.7 M Sucrose, 10 mM Tris-HCl pH 8.0, 2 mM MgCl2, 0.15% Triton X-100, 5 mM β-mercaptoethanol, 1X Halt™ Protease Inhibitors and 0.1 mM PMSF). Tubes are spun at 13,000 rpm for 45 min at 4 °C. Remove supernatants and resuspend pellets in 70 µL of Nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS, 1X Halt™ Protease Inhibitors and 0.1 mM PMSF) with repeated pipetting. Incubate tubes on ice for 30 min. Shear chromatin using a Covaris® S220 ultrasonicator at a frequency of 175 MGh for 6 min. Tubes are spun at 13,000 rpm for 10 min at 4 °C, supernatants (circa 60 µL) are transferred to new tubes.The following procedures are executed in the cold room unless indicated otherwise. 540 µL of ChIP buffer (16.7 mM Tris-HCl pH 8.0, 1.2 mM EDTA, 1.1% Triton X-100, 167 mM NaCl and 1X Halt™ Protease Inhibitors) is added to the sheared chromatin and 20 µL of pre-washed Dynabeads™ Protein A (Thermo Fisher Scientific)  is added for a 1 hour pre-clearing with rotation. Beads are separated with magnet and supernatants are transferred to new tubes. Solutions are split equally between two new tubes. 2.5 µg of antibody is added to each tube, either anti-Histone H3 di-methyl (ab1220 from Abcam) or anti-Histone H3 unmodified  (ab1791). 25 µL of pre-washed beads are added to each tube and they are incubated overnight with rotation. Beads are collected and washed consecutively with 1 mL low salt buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 1% Triton X-100,, 0.1% SDS and 150 mM NaCl), 1 mL high salt buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 1% Triton X-100, 0.1% SDS and 500 mM NaCl), 1 mL LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% Nonidet P-40, 1% sodium deoxycholate and 250 mM LiCl) and 1 mL TE (10 mM Tris-HCl pH 8.0 and 1 mM EDTA) 5min each with rotation. TE wash is repeated then beads are eluted twice with 125 µL of elution buffer (1% SDS and 100mM of NaHCO3) with vortexing and 15 min incubation at 65 °C. After combining the two elutions, 10 µL of 5 M NaCl is added and solutions are incubated at 65 °C overnight to reverse cross-linking. 10 µL of 500 mM EDTA, 20 µL of 1 M Tris-HCl pH 6.5 and 1 µL of 20 mg/mL Proteinase K are added and solutions are incubated at 45 °C for 1 hour. DNA is then purified using Zymo Research ChIP DNA Clean and Concentrator columns eluted twice with 25 µL of 10 mM Tris-HCl pH 8.0.
DNA fragments are made into libraries using the NEBNext Ultra II FS kit (New England Biolabs) according to manufacturer's instructions.
Libraries were pooled together.

value: suvh2-1 suvh9-1 + SUVH9(Y636F)

tag: ecotype

tag: chip antibody

value: H3K9me2 from Abcam (ab1220)


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio012

value: male

value: stage IA-IIIA lung adenocarcinoma


title: HEK293_ANRIL KD_3

value: female


title: H3K9me2 - suvh2suvh9+SUVH9(WT) R2

description: Chromatin

value: suvh2-1 suvh9-1 + SUVH9(WT)


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio033

value: long term relapse-free survivor


title: 026C


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio010


title: H3K9me2 - suvh2suvh9+SUVH9(WT) R1

description: Chromatin


title: HEK293_ANRIL KD_2


title: 1931C


title: HPAEC0

source_name: primary pulmonary arterial cells

growth_protocol: gelatin-coated plates in EGM2 endothelial growth medium (Lonza)

value: primary pulmonary arterial cells


title: HEK293_ANRIL KD_1


title: HEK293_WT_5

value: wild type


title: 115C

value: Control


title: H3 - suvh2suvh9+SUVH9(Y636F) R2

description: Chromatin

value: H3 from Abcam (ab1791)


title: H3K9me2 - suvh2suvh9+none R1

description: Chromatin

source_name: suvh2suvh9 mature seeds

value: suvh2-1 suvh9-1


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio017


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio005


title: SET2 OTX P/R INCB059872 2

city: Houston

first: Kapil

last: Bhalla

state: TX

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

description:
R654-13-SET2-P250nMINCB16h3_S20_L004
combined-rnaseq.stringtie-genes-R654-LSD1.xls

data_processing:
Sequencing reads were trimmed using the trimGalore software.
The reads were mapped using HISAT2 against the human genome build UCSC hg19
Quantified using StringTie against the Gencode gene model
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: sAML cultured cell line (BET inhibitor resistant)

growth_protocol: SET-2 and SET-2-OTX P/R cells were cultured in 20% FBS containing RPMI1640 media. OCI-AML5 cells were cultured in MEM Alpha media with 20% FBS and 10 ng/mL of GM-CSF.

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Libraries were constructed following standard Illumina protocols for RNA sequencing.

treatment_protocol: OCI-AML5 cells with stable expression of Cas9 were transduced with 2 sgRNAs against LSD1. Eight days post transduction, cells were collected for RNA isolation. For shRNA studies, OCI-AML5 cells were stably transduced with doxycycline-inducible shRNA (non-targeting and LSD1). Cells were treated with 100 ng/mL of doxycycline daily for 96 hours and then collected for RNA isolation. OCI-AML5 cells were transduced with lentivirus expressing sh-NT for GFI1 shRNA for 96 hours and RNA was isolated. OCI-AML5 cells were treated with 1000 nM of INCB059872 for 16 hours and then RNA was isolated. SET2 or SET2-OTX P/R cells were treated with 250 nM of INCB059872 for 16 hours and then RNA was isolated.

value: leukemia blast cells

value: LSD1 inhibitor treated


title: HEK293_WT_4

value: Human Embryonic Kidney cells


title: H3 - suvh2suvh9+SUVH9(WT) R1

description: Chromatin


title: H3 - suvh2suvh9+SUVH9(Y636F) R1

description: Chromatin


title: H3 - suvh2suvh9+SUVH9(WT) R2

description: Chromatin


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio004

value: lung adenocarcinoma


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio009


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio008


title: SET2 OTX P/R  INCB059872 1

description:
R654-12-SET2-P250nMINCB16h2_S18_L004
combined-rnaseq.stringtie-genes-R654-LSD1.xls


title: H3 - suvh2suvh9+none R2

description: Chromatin


title: HEK293_WT_3


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio007


title: WGBS - suvh2suvh9+SUVH9(Y636F)

description: Bisulfite treated DNA

extract_protocol:
Siliques were cut open with insulin syringe needles, whole seeds were transferred to a tube and frozen. DNA was isolated from 250 to 500 young seeds at the mature embryo stage using the Plant/Seed DNA Miniprep kit (Zymo Research).
5ng of DNA was converted and processed into sequencing libraries with the Zymo Pico Methyl-seq Library Prep kit, according to the manufacturer instructions.
Libraries were pooled together.


title: H3 - suvh2suvh9+none R1

description: Chromatin


title: lung adenocarcinoma, Angio003

value: excluded from further analysis


title: HEK293_WT_1


title: rh27-2_root tips_sRNA-seq_rep3

city: Beijing

first: Jing

last: Sun

address: No. 1 West Beichen Road

department: IGDB

country: China

institute: Chinese Academy of Sciences

description: high-throughput profiling of small RNA in rh27-2 (mutant) root tips

data_processing:
RNA-seq reads were aligned to the Arabidopsis genome (TAIR10) using TopHat2. Read counts of genes were counted using htseq-count. Differentially expressed genes were detected using R package edgeR.
Small RNA sequencing reads were aligned to the Arabidopsis genome (TAIR10) using Bowtie2. miRNA were aligned to mature miRNA sequence from miRBase using NCBI blast. miRNAs with RPM fold change over 1.5 were defined as differentially expressed miRNAs.
Genome_build: TAIR10
Supplementary_files_format_and_content: read count files were generated using htseq-count program. miRNA abundance files were generated using miRNA counts normalized against total mapped reads.

source_name: Root tips of 5-day old seedlings

growth_protocol: The wild-type and rh27-2 line were grown on 1/2 Murashige and Skoog plates with 1% sucrose for 5 days after germination.

extract_protocol:
The shoot apices or root tips were ground into fine powder in liquid nitrogen and processed using miRNeasy Mini Kit (217004, Qiagen).
Both small RNA-sequencing and mRNA-sequencing libraries generated from Col-0 wild-type and rh27-2 samples constructed following standard protocols (Berry Genomics).

treatment_protocol: The seedlings grown at 21-22°C under a 16 h light and 8 h dark cycle.

value: root tips

tag: developmental stage

value: 5 days after germination


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio002

value: male

value: short term relapse-free survivor


title: SET2 INCB059872 2

description:
R654-4-SET2250nMINCB16h2_S23_L004
combined-rnaseq.stringtie-genes-R654-LSD1.xls

source_name: sAML cultured cell line


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio011

value: stage IA-IIIA lung adenocarcinoma


title: WGBS - suvh2suvh9+none

description: Bisulfite treated DNA


title: SET2 OTX P/R Control 1

description:
R654-9-SET2-PControl2_S27_L004
combined-rnaseq.stringtie-genes-R654-LSD1.xls

value: control cells


title: SET2 OTX P/R Control 2

description:
R654-10-SET2-PControl3_S28_L004
combined-rnaseq.stringtie-genes-R654-LSD1.xls


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio006

value: long term relapse-free survivor


title: rh27-2_root tips_sRNA-seq_rep2


title: Delta Exon8 5

source_name: HEK293_Delta Exon8

treatment_protocol: 2 million HEK293 cells were seeded per 10 cm petridish 12-16h before transfection. The two vectors containing the sgRNAs were co-transfected using lipofectamine 2000 (Invitrogen) according to the manufacturer’s recommendations. Clonal selections were performed according to the manufacturer's recommendations.

value: female

value: CRISPRed engineered; lacking Exon8 of the lncRNA ANRIL


title: H3K9me2 - suvh2suvh9+SUVH9(Y636F) R1

description: Chromatin

value: suvh2-1 suvh9-1 + SUVH9(Y636F)

value: H3K9me2 from Abcam (ab1220)


title: SET2 INCB059872 1

description:
R654-3-SET2250nMINCB16h1_S21_L004
combined-rnaseq.stringtie-genes-R654-LSD1.xls


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio001


title: rh27-2_root tips_sRNA-seq_rep1


title: WT_root tips_sRNA-seq_rep3

description: high-throughput profiling of small RNA in Col-0 (wild type) root tips

value: wildtype


title: Delta Exon8 4


title: WT_root tips_sRNA-seq_rep2


title: SET2 Control 2

description:
R654-2-SET2Control2_S19_L004
combined-rnaseq.stringtie-genes-R654-LSD1.xls

value: leukemia blast cells


title: WT_root tips_sRNA-seq_rep1


title: Delta Exon8 2


title: Delta Exon8 3


title: SET2 Control 1

description:
R654-1-SET2Control1_S17_L004
combined-rnaseq.stringtie-genes-R654-LSD1.xls


title: rh27-2_shoot apices_sRNA-seq_rep1

description: high-throughput profiling of small RNA in rh27-2 (mutant) shoot apices

source_name: Shoot apices of 5-day old seedlings

value: shoot apices


title: Delta Exon8 1

value: Human Embryonic Kidney cells


title: rh27-2_shoot apices_sRNA-seq_rep2


title: OCI-AML5 INCB059872 3

description:
R492-12-OCI5-2INCB3_S20_L002
combined-rnaseq.stringtie-genes-R492-LSD1.xls

source_name: AML cultured cell line

value: LSD1 inhibitor treated


title: WT_shoot apices_sRNA-seq_rep3

description: high-throughput profiling of small RNA in Col-0 (wild type) shoot apices


title: WT_shoot apices_sRNA-seq_rep2


title: OCI-AML5 INCB059872 2

description:
R492-11-OCI5-2INCB2_S18_L002
combined-rnaseq.stringtie-genes-R492-LSD1.xls


title: HPMEC0

description:
PrimaryPulmonaryEndothelialCells.raw.counts.processed.mtx
PrimaryPulmonaryEndothelialCells.processed.genes.tsv
PrimaryPulmonaryEndothelialCells.processed.barcodes.tsv

source_name: primary pulmonary venous cells

value: primary pulmonary venous cells

value: Control


title: WT_shoot apices_sRNA-seq_rep1

value: 5 days after germination


title: MGHparB

value: Wild type

value: Paraquat


title: WT 5

value: WT


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio056

source_name: stage IA-IIIA lung adenocarcinoma; short term survivor (<2 years)

value: lung adenocarcinoma

value: stage IA-IIIA lung adenocarcinoma

value: short term relapse-free survivor


title: Ulox_P_3CR (PEG_Shock)

city: Rehovot

first: Tomer

last: Chen

address: P.O.box 26

department: Plant and Environmental Sciences

country: Israel

institute: Weizmann Institute of Science

description:
MARS-seq
X9H

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
MARS-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). Reads were trimmed using cutadapt, (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to genome Tair-11 using STAR,  v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Araport annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream):
We used the 3 end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode.
Genome_build: Further analysis is done for genes having minimum 5 read in at least one sample.
Supplementary_files_format_and_content: Normalization of the counts and differential expression analysis was performed using DESeq2 , with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.

source_name: Arabidopsis thaliana µlox seedling roots exposed to 30% PEG for 3h

growth_protocol: Arabidopsis (Arabidopsis thaliana; ecotype Columbia-0) and µlox seedlings (7 d old) were grown under white light in a 16-h-light/8-h-dark cycle at 21°C on Murashige and Skoog medium, supplemented with 1% (w/v) Suc and 0.8% (w/v) Phytoagar (Invitrogen).

extract_protocol:
Three replicates of Arabidopsis seedlings (30 to 50 7-d-old seedlings per biological replicate) were used for each treatment. After treatment, the roots and shoots were separated, and RNA was extracted separately from frozen tissues using a standard Trizol extraction method (Sigma-Aldrich).
Libraries were prepared with the MARS-seq protocol (Diego Adhemar Jaitin, 2017) and sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).

treatment_protocol: For osmotic stress treatment, PEG average molecular weight 8,000 powder (Sigma-Aldrich) was used. For PEG solutions, 30% (w/v), PEG was dissolved in double-distilled (dd)H2O and pH was adjusted to 5.8 using HCl and KOH osmotic pressure measured at -2.0 MPa.  Seedlings were exposed to 30% PEG  for 0, 1, 2, 3 h in aqueous solution.

value: Root

value: ulox

value: 30% PEG for 3h


title: stage IA-IIIA lung adenocarcinoma, short term survivor, Angio038

value: female


title: H3K9me2 - suvh2suvh9+none R2

description: Chromatin

value: suvh2-1 suvh9-1

value: H3K9me2 from Abcam (ab1220)


title: OCI-AML5 INCB059872 1

description:
R492-10-OCI5-2INCB1_S16_L002
combined-rnaseq.stringtie-genes-R492-LSD1.xls

value: leukemia blast cells


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio028

source_name: stage IA-IIIA lung adenocarcinoma; long term survivor (>2 years)

value: male

value: long term relapse-free survivor


title: rh27-2_shoot apices_sRNA-seq_rep3

value: shoot apices


title: lung adenocarcinoma, Angio030

source_name: excluded from further analysis

value: excluded from further analysis


title: Ulox_P_3AR (PEG_Shock)

description:
MARS-seq
X9F


title: WT 3

value: Human Embryonic Kidney cells


title: OCI-AML5 Control 3

description:
R492-3-OCI5Control3_S17_L002
combined-rnaseq.stringtie-genes-R492-LSD1.xls

value: control cells


title: WT 2

value: WT


title: OCI-AML5 Control 1

description:
R492-1-OCI5Control1_S13_L002
combined-rnaseq.stringtie-genes-R492-LSD1.xls


title: Ulox_P_2AR (PEG_Shock)

description:
MARS-seq
X9C

source_name: Arabidopsis thaliana µlox seedling roots exposed to 30% PEG for 2h

value: 30% PEG for 2h


title: Ulox_P_1CR (PEG_Shock)

description:
MARS-seq
X9B

source_name: Arabidopsis thaliana µlox seedling roots exposed to 30% PEG for 1h

value: 30% PEG for 1h


title: Ulox_P_2CR (PEG_Shock)

description:
MARS-seq
X9E


title: lung adenocarcinoma, Angio037

value: lung adenocarcinoma


title: Ulox_P_3BR (PEG_Shock)

description:
MARS-seq
X9G

value: Root


title: WT 1


title: WT 4


title: Ulox_P_1BR (PEG_Shock)

description:
MARS-seq
X9A

value: ulox


title: Ulox_P_1AR (PEG_Shock)

description:
MARS-seq
X8H


title: OCI-AML5 GFI1 shRNA 2

description:
12-OCI-5-GFI-sh-467-2_S58_L007
combined-rnaseq.stringtie-genes-OCI5-LSD1.xls

source_name: AML cultured cell line (GFI1 knock down)

value: GFI1 shRNA expressing


title: Ulox_P_0CR (PEG_Shock)

description:
MARS-seq
X8G

source_name: Arabidopsis thaliana µlox seedling roots exposed to water for 1h

value: water for 1h


title: Ulox_P_2BR (PEG_Shock)

description:
MARS-seq
X9D


title: OCI-AML5 Control 2

description:
R492-2-OCI5Control2_S15_L002
combined-rnaseq.stringtie-genes-R492-LSD1.xls


title: Ulox_P_0AR (PEG_Shock)

description:
MARS-seq
X8E


title: Ulox_P_3CS (PEG_Shock)

description:
MARS-seq
X8D

source_name: Arabidopsis thaliana µlox seedling shoot exposed to 30% PEG for 3h

value: 30% PEG for 3h


title: OCI-AML5 shNT (GFI1) 2

description:
10-OCI-5-shNT-2_S66_L007
combined-rnaseq.stringtie-genes-OCI5-LSD1.xls

value: non-targeting shRNA expressing


title: stage IA-IIIA lung adenocarcinoma, long term survivor, Angio016

value: stage IA-IIIA lung adenocarcinoma


title: Ulox_P_3BS (PEG_Shock)

description:
MARS-seq
X8C


title: WGBS - suvh2suvh9+SUVH9(WT)

description: Bisulfite treated DNA

source_name: complemented suvh2suvh9 mature seeds

value: suvh2-1 suvh9-1 + SUVH9(WT)


title: Ulox_P_3AS (PEG_Shock)

description:
MARS-seq
X8B


title: Ulox_P_2BS (PEG_Shock)

description:
MARS-seq
X7H

source_name: Arabidopsis thaliana µlox seedling shoot exposed to 30% PEG for 2h


title: Ulox_P_2AS (PEG_Shock)

description:
MARS-seq
X7G


title: Ulox_P_2CS (PEG_Shock)

description:
MARS-seq
X8A


title: OCI-AML5 LSD1 shRNA 3

description:
OCI-AML5LSD1sh713_S45_L007
WF-RNASeq-June2017.genes-AML5-LSD1.xls

source_name: AML cultured cell line (LSD1 knock down)

value: leukemia blast cells

value: LSD1 shRNA expressing


title: OCI-AML5 LSD1 shRNA 2

description:
OCI-AML5LSD1sh712_S44_L007
WF-RNASeq-June2017.genes-AML5-LSD1.xls


title: Ulox_P_0BR (PEG_Shock)

description:
MARS-seq
X8F


title: OCI-AML5 LSD1 shRNA 1

description:
OCI-AML5LSD1sh711_S43_L007
WF-RNASeq-June2017.genes-AML5-LSD1.xls


title: OCI-AML5 GFI1 shRNA 1

description:
11-OCI-5-GFI-sh-467-1_S56_L007
combined-rnaseq.stringtie-genes-OCI5-LSD1.xls


title: OCI-AML5 sh-NT (LSD1) 3

description:
OCI-AML5shNT3_S42_L007
WF-RNASeq-June2017.genes-AML5-LSD1.xls


title: Ulox_P_0CS (PEG_Shock)

description:
MARS-seq
X7C

source_name: Arabidopsis thaliana µlox seedling shoot exposed to water for 1h


title: Ulox_P_0BS (PEG_Shock)

description:
MARS-seq
X7B


title: OCI-AML5 shNT (GFI1) 1

description:
9-OCI-5-shNT-1_S64_L007
combined-rnaseq.stringtie-genes-OCI5-LSD1.xls


title: WT_P_3CR (PEG_SHOCK_II)

description:
MARS-seq
X6H

source_name: Arabidopsis thaliana seedling roots exposed to 30% PEG for 3h


title: WT_P_3BR (PEG_SHOCK_II)

description:
MARS-seq
X6G


title: OCI-AML5 sh-NT (LSD1) 2

description:
OCI-AML5shNT2_S41_L007
WF-RNASeq-June2017.genes-AML5-LSD1.xls


title: Ulox_P_1CS (PEG_Shock)

description:
MARS-seq
X7F

source_name: Arabidopsis thaliana µlox seedling shoot exposed to 30% PEG for 1h


title: Ulox_P_0AS (PEG_Shock)

description:
MARS-seq
X7A


title: Veh-Sham_041317_(Clariom_S_Mouse)

city: Lexington

first: Ivan

last: Vechetti

state: KY

address: 800 Rose St.  Medical Science Build

institute: University of Kentucky

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The data was processed through Partek software using RMA for normalization

organism: Mus musculus

source_name: epididymal adipose tissue

label_protocol: Affymetrix

extract_protocol: Total RNA was extracted using Trizol and following the fabricant instructions

treatment_protocol: Samples were treated with either DMSO (vehicle) or GW4869 (extracellular vesicle inhibitor)

value: Male

tag: agent

value: Vehicle (DMSO)


title: WT_P_3AR (PEG_SHOCK_II)

description:
MARS-seq
X6F

tag: treatment


title: Ulox_P_1BS (PEG_Shock)

description:
MARS-seq
X7E


title: Ulox_P_1AS (PEG_Shock)

description:
MARS-seq
X7D


title: OCI-AML5 LSD1 KO 3

description:
8-OCI5-LSD1-KO-3_S62_L007
combined-rnaseq.stringtie-genes-OCI5-LSD1.xls

source_name: AML cultured cell line (LSD1 knockout)

value: LSD1 knockout


title: WT_P_2BR (PEG_SHOCK_II)

description:
MARS-seq
X6D

source_name: Arabidopsis thaliana seedling roots exposed to 30% PEG for 2h

value: WT


title: WT_P_2CR (PEG_SHOCK_II)

description:
MARS-seq
X6E

value: 30% PEG for 2h


title: WT_P_1CR (PEG_SHOCK_II)

description:
MARS-seq
X6B

source_name: Arabidopsis thaliana seedling roots exposed to 30% PEG for 1h

value: 30% PEG for 1h


title: WT_P_2AR (PEG_SHOCK_II)

description:
MARS-seq
X6C


title: Veh-SA_041317_(Clariom_S_Mouse)


title: GW-Sham_041317_(Clariom_S_Mouse)

value: GW4869 (extracellular vesicle inhibitor)


title: GFM012 Pcyt2_LCMV_d3

first: Hongbo

last: Chi

state: TN

department: Immunology

institute: St Jude Children's Research Hospital

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Clariom S mouse GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

source_name: SMARTA cells sorted from the spleens

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Freshly-isolated CD45.1+ wild-type and Pcyt2-deficient SMARTA cells sorted from the spleens of CD45.2+ recipient mice

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: RNA samples were isolated from freshly-isolated CD45.1+ wild-type and Pcyt2-deficient SMARTA cells sorted from the spleens of CD45.2+ recipient mice (n = 3 biological replicates each group)

value: Pcyt2KO treated with LCMV for 3 days


title: OCI-AML5 LSD1 KO 2

description:
7-OCI5-LSD1-KO-2_S61_L007
combined-rnaseq.stringtie-genes-OCI5-LSD1.xls


title: GFM009 Pcyt2_LCMV_d3


title: GFM011 Pcyt2_LCMV_d3


title: GFM005 Control_LCMV_d3

value: Non Targerting control treated with LCVM for 3 days


title: GW-SA_041317_(Clariom_S_Mouse)


title: GFM004 Control_LCMV_d3


title: WT_P_1AR (PEG_SHOCK_II)

description:
MARS-seq
X5H

value: Root


title: OCI-AML5 LSD1 KO 1

description:
6-OCI5-LSD1-KO-1_S60_L007
combined-rnaseq.stringtie-genes-OCI5-LSD1.xls


title: WT_P_0BR (PEG_SHOCK_II)

description:
MARS-seq
X5F

source_name: Arabidopsis thaliana seedling roots exposed to water for 1h

value: water for 1h


title: WT_P_0CR (PEG_SHOCK_II)

description:
MARS-seq
X5G


title: GFM003 Control_LCMV_d3


title: WT_P_0AR (PEG_SHOCK_II)

description:
MARS-seq
X5E


title: WT_P_3CS (PEG_SHOCK_II)

description:
MARS-seq
X5D

source_name: Arabidopsis thaliana seedling shoots exposed to 30% PEG for 3h

value: Shoot

value: 30% PEG for 3h


title: WT_P_3BS (PEG_SHOCK_II)

description:
MARS-seq
X5C


title: spermatogonia_RppH_rep1

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

data_processing:
The adaptor sequence was removed from the 3’ end of the reads by cutadapt (with an option --illumina), and reads that did not contain the adaptor sequence were discarded.
The retained reads were analyzed by using RepeatMasker.
Genome_build: none provided
Supplementary_files_format_and_content: raw counts

extract_protocol:
Total testes RNA was prepared by using isogene. Six hundred nanograms of RNAs were treated (or not treated as a control) with 25 U of tobacco alkaline phosphatase (TAP) (Epigcentre) for 1.5 hours at 37 ºC, and the reaction was stopped by phenol-chloroform extraction and ethanol precipitation.  The total intact RNA was also treated with 20 U of 5' polyphosphatase (5Pase) (Epicentre) for 30 min. at 37 ºC, and the reaction was stopped by phenol-chloroform extraction and ethanol precipitation.
TruSeq small RNA library preparation kit (Illumina) was then used for constructing sequence libraries.  The libraries were run on a 2% agarose gel and DNAs of 240 to 380 bp (corresponding to insert size of 115 to 255 bp) were purified from the gel.
The libraries were sequenced on MiSeq with MiSeq Reagent Kit v2 (300 cycles) in the 300-bp single-end mode

value: spermatogonia (FACS-purified)

tag: treatment of rna

value: RppH

tag: molecule subtype

value: medium length RNA (115-255 nt)


title: spermatogonia_RppH_rep2


title: OCI-AML5 sh-NT (LSD1) 1

description:
OCI-AML5shNT1_S40_L007
WF-RNASeq-June2017.genes-AML5-LSD1.xls

source_name: AML cultured cell line

value: leukemia blast cells

value: non-targeting shRNA expressing


title: 5Pase

description: Medium length RNA (115-255 nt)

data_processing:
The adaptor sequence was removed from the 3’ end of the reads by cutadapt (with an option --illumina), and reads that did not contain the adaptor sequence were discarded.
The retained reads were analyzed by using RepeatMasker.
Genome_build: none provided
Supplementary_files_format_and_content: *_expression.txt: Tab-delimited text files include raw counts.

source_name: testis

extract_protocol:
Total testes RNA was prepared by using isogene. Six hundred nanograms of RNAs were treated (or not treated as a control) with 25 U of tobacco alkaline phosphatase (TAP) (Epigcentre) for 1.5 hours at 37 ºC, and the reaction was stopped by phenol-chloroform extraction and ethanol precipitation. The total intact RNA was also treated with 20 U of 5' polyphosphatase (5Pase) (Epicentre) for 30 min. at 37 ºC, and the reaction was stopped by phenol-chloroform extraction and ethanol precipitation.
TruSeq small RNA library preparation kit (Illumina) was then used for constructing sequence libraries. The libraries were run on a 2% agarose gel and DNAs of 240 to 380 bp (corresponding to insert size of 115 to 255 bp) were purified from the gel.
The libraries were sequenced on MiSeq with MiSeq Reagent Kit v2 (300 cycles) in the 300-bp single-end mode.

value: Testis

value: 5' polyphosphatase


title: TAP

description: Medium length RNA (115-255 nt)

value: Tobacco alkaline phosphatase


title: OCI-AML5 Cas9 1

description:
1-OCI5-Cas9-2_S63_L007
combined-rnaseq.stringtie-genes-OCI5-LSD1.xls

value: Cas9 expressing


title: Intact

description: Medium length RNA (115-255 nt)


title: WT_P_3AS (PEG_SHOCK_II)

description:
MARS-seq
X5B

value: WT


title: WT_P_2BS (PEG_SHOCK_II)

description:
MARS-seq
X4H

source_name: Arabidopsis thaliana seedling shoots exposed to 30% PEG for 2h

value: 30% PEG for 2h


title: sh-Ctrl

city: Chicago

first: Issam

last: Awad

state: IL

address: 5841 S. Maryland Avenue

department: Department of Neurology

institute: The University of Chicago

data_processing:
Raw sequencing reads were trimmed by FASTX-Toolkit (v0.0.14) to remove the adaptor sequences
The reads were aligned to Ensembl human genome reference hg19 using STAR (v2.7.3) with end-to-end alignment mode
Alignments and counting of gene bodies were conducted by featureCounts from R package Rsubread (v1.30.9) without strand information
Genome_build: hg19
Supplementary_files_format_and_content: csv file storing the raw count was generated in the data processing step

source_name: Liver Carcinoma Cell Line

extract_protocol:
Total RNA was extracted from tumor tissues, white blood cells or HCC cells, using TRIzol reagent (Invitrogen, USA).
The cDNA was synthesized using the Reverse-Transcription Ace qPCR RT Master Mix with gDNA Remover Kit (Toyobo, Japan). The expression of mRNA was evaluated in triplicates using a CFX96 Touch Real-Time PCR Detection System (Bio-Rad, USA). The gene GAPDH was used as an internal control.

tag: population

value: Chinese

tag: group

value: CTL


title: WT_P_2CS (PEG_SHOCK_II)

description:
MARS-seq
X5A


title: sh-TARBP2

value: SH


title: WT_P_2AS (PEG_SHOCK_II)

description:
MARS-seq
X4G


title: WT_P_1BR (PEG_SHOCK_II)

description:
MARS-seq
X6A

value: Root

value: 30% PEG for 1h


title: oe-TARBP2

value: OE


title: WT_P_1CS (PEG_SHOCK_II)

description:
MARS-seq
X4F

source_name: Arabidopsis thaliana seedling shoots exposed to 30% PEG for 1h

value: Shoot


title: WT_P_1BS (PEG_SHOCK_II)

description:
MARS-seq
X4E


title: Y1

first: Tingyi

state: Beijing

address: No.10 Xitoutiao, You'anmenwai, Fengtai District

institute: Capital Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures.
miRmiRNA expression levels were estimated by TPM ( transcript per million million) through the following criteria (Zhou et al., 2010):Normalization formula: Normalized expression = mapped read count/Total  reads*1000000
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited csv files include TPM values for each Sample ...

source_name: distal colon

extract_protocol: miRNA libraries were prepared for sequencing using standard Illumina protocols

value: distal colon tissues


title: Y3


title: Y2


title: oe-Ctrl

value: PCDH


title: WT_P_1AS (PEG_SHOCK_II)

description:
MARS-seq
X4D


title: OCI-AML5 Cas9 2

description:
2-OCI5-Cas9-3_S65_L007
combined-rnaseq.stringtie-genes-OCI5-LSD1.xls

value: leukemia blast cells


title: O3


title: WT_P_0CS (PEG_SHOCK_II)

description:
MARS-seq
X4C

source_name: Arabidopsis thaliana seedling shoots exposed to water for 1h

value: water for 1h


title: rh27-2_root tips_RNA-seq_rep3

description: high-throughput profiling of transcriptome in rh27-2 (mutant) root tips

source_name: Root tips of 5-day old seedlings

value: root tips

value: 5 days after germination


title: rh27-2_root tips_RNA-seq_rep2


title: S3-S-1 (sham_cont)

description:
MARS-seq
X3F

source_name: Arabidopsis thaliana seedling shoots exposed to 1mM SHAM for 3h

growth_protocol: Arabidopsis (Arabidopsis thaliana; ecotype Columbia-0) seedlings (7 d old) were grown under white light in a 16-h-light/8-h-dark cycle at 21°C on Murashige and Skoog medium, supplemented with 1% (w/v) Suc and 0.8% (w/v) Phytoagar (Invitrogen).

treatment_protocol: For osmotic stress treatment, PEG average molecular weight 8,000 powder (Sigma-Aldrich) was used. For PEG solutions, 30% (w/v), PEG was dissolved in double-distilled (dd)H2O and pH was adjusted to 5.8 using HCl and KOH osmotic pressure measured at -2.0 MPa. Solutions were supplemented with His (5 mm) or SHAM (0.1 mm) where indicated in Seedlings were exposed to 30% PEG + 1mM SHAM  for 0, 1, 2, 3 h in aqueous solution.

value: 1mM SHAM for 3h


title: rh27-2_root tips_RNA-seq_rep1


title: S3-S-3 (sham_cont)

description:
MARS-seq
X3H


title: MB liver - Input

description: Input DNA

data_processing:
Adaptor sequences and low quality sequences were removed by Trim Galore (with options, --adapter AGATCGGAAGAGCACACG --adapter2 AGATCGGAAGAGCGTCGTGT).
Sequences were mapped on the mouse genome (mm10) by hisat2.
Alignment data was converted to wig files by samtools and bam2wig.
Peaks were detected by MACS2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_peaks.narrowPeak: Peak files
Supplementary_files_format_and_content: *.rmdup.wig: Wig files

source_name: liver

extract_protocol:
Chromatin was prepared using EpiSeeker ChIP tissue (Abcam) and incubated with anti-H3K9ac antibody (ab4441, Abcam). Chromatin was recovered by Dyna beads Protein-G (Thermo Fisher Scientific), reverse cross-linked, and treated with proteinase K.
ChIP-seq libraries were made by NEBNext DNA Ultra kit (New England Biolab).
Sequencing was run on HiSeq2500 in the 50-bp paired-end mode.

treatment_protocol: Adult livers were fixed with 1% formaldehyde at room temperature for 15 min., and the fixation was stopped with glycine.

value: F1 hybrid, MSM (Mat) x B6 (Pat)

tag: age

value: Adult

value: Liver


title: S3-S-2 (sham_cont)

description:
MARS-seq
X3G

value: WT


title: WT_P_0AS (PEG_SHOCK_II)

description:
MARS-seq
X4A


title: O2


title: O1


title: WT_root tips_RNA-seq_rep2

description: high-throughput profiling of transcriptome in Col-0 (wild type) root tips

value: wildtype


title: BM liver - Input

description: Input DNA

tag: strain

value: F1 hybrid, B6 (Mat) x MSM (Pat)


title: MSM liver - Input_rep2

description: Input DNA

value: MSM/Ms


title: S3-R-3 (sham_cont)

description:
MARS-seq
X3E

source_name: Arabidopsis thaliana seedling roots exposed to 1mM SHAM for 3h

value: Root

tag: genotype


title: WT_root tips_RNA-seq_rep3

tag: tissue


title: S3-R-2 (sham_cont)

description:
MARS-seq
X3D


title: S3-R-1 (sham_cont)

description:
MARS-seq
X3C


title: S2-S-3 (sham_cont)

description:
MARS-seq
X3B

source_name: Arabidopsis thaliana seedling shoots exposed to 1mM SHAM for 2h

value: 1mM SHAM for 2h


title: S2-S-1 (sham_cont)

description:
MARS-seq
X2H

value: Shoot


title: S2-S-2 (sham_cont)

description:
MARS-seq
X3A


title: S2-R-3 (sham_cont)

description:
MARS-seq
X2G

source_name: Arabidopsis thaliana seedling roots exposed to 1mM SHAM for 2h


title: WT_P_0BS (PEG_SHOCK_II)

description:
MARS-seq
X4B


title: S2-R-2 (sham_cont)

description:
MARS-seq
X2F


title: MSM liver - Input_rep1

description: Input DNA


title: rh27-2_shoot apices_RNA-seq_rep3

description: high-throughput profiling of transcriptome in rh27-2 (mutant) shoot apices

source_name: Shoot apices of 5-day old seedlings

value: shoot apices


title: WT_root tips_RNA-seq_rep1


title: S2-R-1 (sham_cont)

description:
MARS-seq
X2E


title: S1-S-3 (sham_cont)

description:
MARS-seq
X2D

source_name: Arabidopsis thaliana seedling shoots exposed to 1mM SHAM for 1h

value: 1mM SHAM for 1h


title: B6 liver - Input_rep2

description: Input DNA


title: HEK293_WT_2

description: SST-RMA expression value derived from Transcriptome Analysis Console (TAC) Software; gene-exon analysis

tag: cell type

value: Human Embryonic Kidney cells

value: female

value: wild type


title: S1-S-2 (sham_cont)

description:
MARS-seq
X2C


title: S1-S-1 (sham_cont)

description:
MARS-seq
X2B


title: rh27-2_shoot apices_RNA-seq_rep1

value: 5 days after germination


title: B6 liver - Input_rep1

description: Input DNA


title: S1-R-2 (sham_cont)

description:
MARS-seq
X1H

source_name: Arabidopsis thaliana seedling roots exposed to 1mM SHAM for 1h


title: S1-R-3 (sham_cont)

description:
MARS-seq
X2A


title: MB liver - H3K9ac

description: ChIP DNA

value: H3K9ac (ab4441, Abcam)


title: WT_shoot apices_RNA-seq_rep3

description: high-throughput profiling of transcriptome in Col-0 (wild type) shoot apices


title: S0-S-2 (sham_cont)

description:
MARS-seq
X1E

value: water for 1h


title: BM liver - H3K9ac

description: ChIP DNA

value: Adult


title: S0-S-3 (sham_cont)

description:
MARS-seq
X1F


title: S1-R-1 (sham_cont)

description:
MARS-seq
X1G


title: WT_shoot apices_RNA-seq_rep1


title: MSM liver - H3K9ac_rep2

description: ChIP DNA

value: Liver


title: WT_shoot apices_RNA-seq_rep2


title: S0-R-3 (sham_cont)

description:
MARS-seq
X1C

source_name: Arabidopsis thaliana seedling roots exposed to water for 1h

value: WT


title: B6 liver - H3K9ac_rep2

description: ChIP DNA


title: S0-R-1 (sham_cont)

description:
MARS-seq
X1A


title: PH0-S-3 (Peg_SHAMf1_res)

description:
MARS-seq
8D


title: AVPV_E2_CRE3

city: La Jolla

first: Alexander

last: Kauffman

address: 9500 Gilman Drive

department: OBGYN and Reproductive Sciences

institute: University of California San Diego

description:
ribosome-affiliated RNA
SS_AVPV_IP_6_S12

data_processing:
Reads were trimmed using Trimmomatic 0.38 using the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:27
Trimmed reads were aligned using STAR v2.6.0a using default parameters
Reads were quantified using RSEM v1.3.0 using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts matrix for each ENSEMBL gene and sample

source_name: AVPV Kiss1 cells

extract_protocol:
Brains from ovariectomized or E2-treated Cre+ mice were removed, flash frozen on dry ice, and micropunches of the AVPV brain region collected and pooled (n=4 brains per pooled sample). Pooled AVPV samples were run through the Ribotag immunoprecipitation pulldown procedure (Sanz et al., Current Protocols in Neuroscience, 88:e77, 2019) to isolate HA-tagged ribosomes from which RNA was extracted using the Qiagen RNeasy Plus Micro Kit (#74034) per the kit instructions.
Unstranded mRNA library kits from Illumina that used polyA enrichment were used to create the library.

tag: strain background

tag: Sex

value: brain (AVPV nucleus)

tag: hormone status


title: AVPV_GDX_CRE4

description:
ribosome-affiliated RNA
SS_AVPV_IP_11_S15

value: GDX (no E2)


title: MSM liver - H3K9ac_rep1

description: ChIP DNA

value: MSM/Ms


title: rh27-2_shoot apices_RNA-seq_rep2


title: B6 liver - H3K9ac_rep1

description: ChIP DNA


title: PH0-S-2 (Peg_SHAMf1_res)

description:
MARS-seq
8C


title: PH0-S-1 (Peg_SHAMf1_res)

description:
MARS-seq
8B


title: AVPV_E2_CRE2

description:
ribosome-affiliated RNA
SS_AVPV_IP_5_S11


title: AVPV_E2_CRE1

description:
ribosome-affiliated RNA
SS_AVPV_IP_4_S10


title: S0-S-1 (sham_cont)

description:
MARS-seq
X1D


title: PH0-R-2 (Peg_SHAMf1_res)

description:
MARS-seq
7H

value: Root


title: AVPV_GDX_CRE3

description:
ribosome-affiliated RNA
SS_AVPV_IP_3_S9


title: PH0-R-1 (Peg_SHAMf1_res)

description:
MARS-seq
7G


title: PS3-S-3 (Peg_SHAMf1_res)

description:
MARS-seq
6H

source_name: Arabidopsis thaliana seedling shoots exposed to 30% PEG + 1mM SHAM for 3h

value: 30% PEG + 1mM SHAM for 3h


title: 72hrs-MDSC

first: Kai

middle: W

last: Wucherpfennig

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology and Virology

institute: Dana Farber Cancer Institute

data_processing:
De-multiplexing, alignment to the mm10 mouse genome and UMI counting were performed using Cell Ranger (version 2.0.1, 10X Genomics)
All samples were then aggregated by using the “cellranger aggr” function without depth normalization
After getting the digital cell by gene expression matrix, the cells with poor quality (cells with high percentage of mitochondrial gene reads, cells express less than 200 genes and cells which show high doublet scores determined by DoubletFinder (v2.0.2)) were filted
The Seurat package in R was then used for analyses
Genome_build: mm10
Supplementary_files_format_and_content: Each RNA sequenting sample contains a compressed tab-delimited text files including matrix.mtx (UMI count matrix in a sparse matrix format), genes.tsv (Gene names) and barcodes.tsv (Cell barcodes).

source_name: Spleen and lymph nodes

growth_protocol: Cells were cultured in RPMI-1640 supplemented with 10% FBS, 2mM L-glutamine, 100ug/mL streptomycin, and 100ug/mL penicillin

extract_protocol:
Cells were enriched by FACS and processed for 10X genomics sequencing immediately as per 10X genomics instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment is inclusion or exclusion of MDSCs

value: OT-I CD8+ T cells

tag: time point


title: 72hrs-DC


title: PS3-S-2 (Peg_SHAMf1_res)

description:
MARS-seq
6G

value: Shoot


title: 24hrs-MDSC


title: S0-R-2 (sham_cont)

description:
MARS-seq
X1B


title: PS3-S-1 (Peg_SHAMf1_res)

description:
MARS-seq
6F


title: PS3-R-3 (Peg_SHAMf1_res)

description:
MARS-seq
6E

source_name: Arabidopsis thaliana seedling roots exposed to 30% PEG + 1mM SHAM for 3h


title: AVPV_GDX_CRE2

description:
ribosome-affiliated RNA
SS_AVPV_IP_2_S8


title: 24hrs-DC


title: AVPV_GDX_CRE1

description:
ribosome-affiliated RNA
SS_AVPV_IP_1_S7


title: PS2-S-1 (Peg_SHAMf1_res)

description:
MARS-seq
5H

source_name: Arabidopsis thaliana seedling shoots exposed to 30% PEG + 1mM SHAM for 2h

value: 30% PEG + 1mM SHAM for 2h


title: PS3-R-1 (Peg_SHAMf1_res)

description:
MARS-seq
6C