title: GC-JC-7819-B02_S10

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_8


title: Armi FAST-iCLIP from Control-KD rep2

status: Public on Mar 28 2019

type: SRA

city: Tokyo

first: Hirotsugu

last: Ishizu

address: 35 Shinanomachi

country: Japan

institute: Keio University

description:
IndexCHKPEI85216100038_Control_rep2_1
processed data file:
Armi_iCLIP_RNAi_RPM.txt

library_source: transcriptomic

data_processing:
Reads were filtered for quality, and PCR duplicates removed using the random barcode. 3' adaptor sequences were trimmed using Cutadapt, and reads were mapped to the Drosophila genome (dm6) using STAR. 3' adapter sequence is "TGGAATTCTCGGGTGCCAAGG".
RIP-seq: Piwi associated small RNA sequencing data was analyzed as described previously (PMID: 27425411). 3' adapter sequence is "TGGAATTCTCGGGTGCCAAGG".
Armi-CLIPPARE* samples: Reads were filtered for quality, and PCR duplicates removed using the random barcode. 3' adaptor sequences were trimmed using Cutadapt, and reads were mapped to the Drosophila genome (dm6) using STAR. 3' adapter sequence is "TGGAATTCTCGGGTGCCAAGG".
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

molecule: total RNA

organism: Drosophila melanogaster

source_name: Armi FAST-iCLIP from Control-KD

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase T1 (Roche) and immunoprecipitation of RNA-protein complexes with an anti-Armi antibody (PMID: 20966047). After dephosphorylation with T4 PNK (NEB), a preadenylated DNA adapter was ligated to the 3’ end with T4 RNA Ligase2, truncated KQ (NEB). Ligations were performed on-bead. Samples were then run on NuPAGE gels (Life Technologies) and transferred to nitrocellulose membranes. After cutting out the region of nitrocellulose containing RNA–protein complexes, RNAs were removed from the membrane by Proteinase K (Roche) digestion.
Samples were processed for reverse transcription, cDNA purification, and cDNA circularization as previously described in (PMID: 25411354). Libraries were then amplified with Q5 DNA polymerase (NEB) and size-selected via polyacrylamide gel electrophoresis. Each sequencing read conatins 5 random bases (N) at the 5’ end "NNNGGTTNN".

treatment_protocol: OSCs were crosslinked with UV (254 nm, 200 mJ/cm2). Cells were then isolated with cell scrapers and precipitated by centrifugation for 2 min at 10000 rpm.

tag: cell type

value: Ovarian Somatic Cells (OSC)

tag: genotype/variation

value: EGFP RNAi

tag: ip antibody

value: anti-Armi antibody (PMID:20966047)


title: U1_HACA_siCTRL_PARN_02

city: Stanford

first: Caitlin

middle: M

last: Roake

state: California

address: CCSR 1150, 269 Campus Drive

country: USA

institute: Stanford

data_processing:
Paired-end joining using fastq-join (Galaxy Version 1.1.2-806.1)
Isolated 3' sequence ends with custom python scripts ()
Binned 3' ends into categories with custom python scripts ()
Supplementary_files_format_and_content: csv files were generated using custom python scripts ()

organism: Homo sapiens

source_name: cell line

extract_protocol:
Trizol extraction of RNA
Kapa hyper-prep (KK8502) of RACE amplicons using illumina TruSeq (RS-122-2001, RS-122-2002) barcodes. Briefly, RACE amplicons of different RNAs from the same sample were pooled into one index, and libraries were prepared according to manufacturer protocol.

tag: cell line

value: PARN CRISPR KO HeLa with transfected U1 chimera


title: U1_HACA_SiDKC1_02

value: HeLa with transfected U1 chimera; siDKC1


title: P170694_S12: HEK293_MeBP_TKO_G16_+Aza_RNA-seq_rep_1

city: Oxford

first: Skirmantas

last: Kriaucionis

address: Old Road Campus Research Building

country: United Kingdom

institute: Ludwig Institute for Cancer Research

description: RNA-seq using ribo-RNA depleted total RNA

data_processing:
RNA-Seq: Base calls performed using X. The reads from each lane were merged for each sample and aligned to the hg19 genome using STAR (v2.4.2), allowing for uniquely mapped reads only ( --outFilterMultimapNmax 1). The number of reads overlapping each gene (on each strand) were counted using multiBamSummary from deeptools (v3.0.2). Only those genes with at least one read were kept. The count tables were converted into GRanges objects (GenomicRanges v1.34.0) in R (v3.5.1) and split according to strand into sense and antisense. We used DESeq2 (v1.22.1) with default parameters to calculate differential expression between conditions with "design = ~ Sample + Condition", where Sample is the batch. We used "apeglm" shrinkage when generating the results tables.
genome_build: hg19
processed_data_files_format_and_content: A DESeq2 result table for each comparison is output in tab-delimited format into separate sheets in an Excel document. AS indicates analyses on the antisense strand. For RNA-Seq there are 4 grouped Excel files in total: Supplementary Table 1 (TET1-CD effect in HEK293 cells), Supplementary Table 2 (5-aza-2'-deoxycytidine and TET1-CD effect in U2OS cells), Supplementary Table 3 (5-aza-2'-deoxycytidine, UVA, and 4-Thio-2'-deoxythymidine effect in HEK293 cells), Supplementary Table 6 (MeBP analyses in HEK293 cells).

growth_protocol: all cells were cultured in DMEM (high glucose) containing antibiotics, L-glutamine, 10% FBS at 37°C, 5%CO2

extract_protocol:
RNeasy Mini kit with DNase I treatment, Ribo-Zero rRNA Removal Kit
TruSeq Stranded Total RNA kit (Illumina)

tag: treatment

value: 880 nM 5-aza-2'-deoxycytidine for 48 hours

value: TET-CD-GFP


title: P170694_S16: HEK293_MeBP_TKO_G16_Untreated_RNA-seq_rep_3


title: Armi FAST-iCLIP from Control-KD rep1

description:
IndexCHKPEI85216100038_Control_rep1_1
processed data file:
Armi_iCLIP_RNAi_RPM.txt


title: U1_HACA_siCTRL_PARN_01


title: ChIPseq mouse LUC/LUC#2-H3K4me3

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

library_source: genomic

data_processing:
Basecalls performed using RTA 1.7 or Illumina Casava1.7
ChIP-seq reads were mapped to the mouse genome (mm9) using Bowtie2. The reads with MAPQ <=10 or redundant reads were removed for further analysis in each library.
We identified Enriched-ChIP regions using SLICER
Genome_build: mm9
Supplementary_files_format_and_content: txt: plan text file. Each line is a peak region. The five columns are chrom, chrom_index, start position, end position, peak position.

molecule: genomic DNA

organism: Mus musculus

source_name: NIH/3T3 tet-on 3G cells

extract_protocol: Libraries were prepared according to Illumina's instructions. The ChIP DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Taq polymerase to generate a protruding 3 A base used for adaptor ligation. Following ligation of a pair of Solexa adaptors to the repaired ends, the ChIP DNA was amplified using the adaptor primers for 17 cycles and the fragments around 220 bp (mononucleosome + adaptors) isolated from agarose gel. Libraries were sequenced on the Hi-seq following the manufacturer's protocols. As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).

tag: antibody

value: Histone H3 trimethyl Lys4 antibody (Millipore, cat no. 17-614)


title: Armi FAST-iCLIP rep2

description:
IndexCHKPEI85216100038_Armi_rep2_1
processed data file:
Armi_iCLIP_RPM.txt

source_name: Armi FAST-iCLIP

value: untreated


title: GC-JC-7819-A05_S33

city: London

first: Vlatka

last: Antolovic

address: Gower Street

department: MRC Laboratory for Molecular Cell Biology

institute: University College London

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_5

data_processing:
Paired-end reads were mapped to the Dictyostelium genome (version obtained from Gareth Bloomfield, masking the duplication on chromosome 2) using Tophat version 2.0.9 (parameters: -r 300 -p 4 -g 1).
Reads for each gene were counted with htseq-count (parameters: -m union -s no -a 0).
Insert size was calculated with picard 1.119 (CollectInsertSizeMetrics)
Genome_build: dicty_2.7
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each replicate.

molecule: polyA RNA

organism: Dictyostelium discoideum

source_name: mound stage cell

growth_protocol: Cells were cultured in petri dishes in HL5 media (Formedium). For development, cells were washed in KK2 (20mM KPO4 pH 6.2) then plated on KK2/1.5% agar in 35mm petri dishes with 1-5 x 106 cells. The dishes were incubated at 22°C for 14h. Aggregates were disaggregated to single cells by taking them up in 1ml KK2/10mM EDTA and repeatedly passing the structures through a 20G needle.

extract_protocol:
Cells were loaded onto Integrated Fluidic Circuit chips (IFC; Fluidigm).  We identified capture of multiple cells and empty wells using brightfield illumination, with validation of single cell capture also carried out using a genetically-encoded red fluorescent nuclear marker. Cell lysis, reverse transcription and cDNA pre-amplification were performed in the C1 Single-Cell Auto Prep IFC using the SMARTer PCR cDNA Synthesis Kit (Clontech) and the Advantage 2 PCR Kit, as specified by the manufacturer (protocol 100-7168 A2). ERCC RNA spike-in control mix (92 transcripts; ThermoFisher) was added to the chambers at a 1:1000 ratio.
cDNA was harvested and the libraries were prepared using the Nextera XT DNA Sample Preparation Kit and the Nextera Index Kit (Illumina), according to the manufacturer's recommendations (protocol 100-7168 A2). Libraries from one chip were pooled, and paired-end 75bp sequencing was performed on 4 lanes of an Illumina NextSeq500.

tag: strain

value: AX3 with H2B-mCherry inserted in the rps30 locus

tag: replicate number

tag: developmental stage

value: mound


title: U1_HACA_siDKC1_01


title: U1_HACA_siCTRL_02

value: HeLa with transfected U1 chimera


title: GC-JC-7819-A04_S25

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_4


title: P170694_S13: HEK293_MeBP_TKO_G16_Untreated_RNA-seq_rep_2


title: GC-JC-7819-A06_S41

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_6


title: P170694_S10: HEK293_MeBP_TKO_G16_Untreated_RNA-seq_rep_1


title: Armi FAST-iCLIP rep1

description:
IndexCHKPEI85216100038_Armi_rep1_1
processed data file:
Armi_iCLIP_RPM.txt


title: DKO_10_T24

description: 3' RACE: TERC, U2

value: HeLa PARN/PAPD5 DKO

tag: 4su pulse time

value: 1 hr 250 uM

tag: 4su chase time

tag: molecule subtype

value: nascent RNA


title: P170694_S08: HEK293_MeBP_TET_WT_+Dox_RNA-seq_rep_3

value: 1 μg/mL Doxycycline for 48 hours

value: TETMut-CD-GFP


title: U1_HACA_siCTRL_01


title: GC-JC-7819-A02_S9

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_2


title: DKO_08_T24

description: 3' RACE: TERC, U2


title: P170694_S05: HEK293_MeBP_TET_WT_+Dox_RNA-seq_rep_2


title: DKO_10_T8

description: 3' RACE: TERC, U2


title: GC-JC-7819-A01_S1

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_1


title: P170694_S02: HEK293_MeBP_TET_WT_+Dox_RNA-seq_rep_1


title: AM-CH3CS89_S27

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_46


title: DKO_08_T8

description: 3' RACE: TERC, U2


title: AM-CH3CS87_S28

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_45


title: P170694_S06: HEK293_MeBP_TET_WT_+Aza_RNA-seq_rep_2


title: P170694_S09: HEK293_MeBP_TET_WT_+Aza_RNA-seq_rep_3


title: Mated_M3_abdomen (run 2)

city: Columbia

first: Brian

last: Hollis

state: SC

address: 715 Sumter Street

department: Department of Biological Sciences

institute: University of South Carolina

description:
run2_iv_abd_mated_m3
18 total libraries were sequenced twice.

data_processing:
Trimming and filtering of reads was performed with Trimmomatic version 0.33. TruSeq adapters were removed from read ends; additionally bases with a quality score smaller than 20 (less than 99 % base call accuracy) were removed from both read ends and further quality trimming was done using a 5 bp wide sliding window requiring an average quality score of 20. Finally, only reads of a length of at least 50 bp after trimming were retained.
Reads were mapped to the D. melanogaster transcriptome with TopHat2 2.1.0 (default parameters) using genome assembly BDGP6 and genome annotation BDGP6.84
Reads were counted using HTSeq 0.6.1 with options as follows: mode = "union", stranded = "reverse", alignment quality minimum = 10, and nonunique = "none".
Genome_build: BDGP6
Supplementary_files_format_and_content: tab-delimited text file includes counts for each sample, where "run1" corresponds to samples from the first flow cell (filenames beginning with 170213) and "run2" corresponds to samples from the second flow cell (filenames beginning with 170607)

source_name: Female abdomen

growth_protocol: Females from the IV base population were collected as virgins and either mated at 3 days of age (mated samples) to males from each of the six experimental evolution populations or not mated (virgin samples). Females were then flash frozen at 4 days of age (i.e. 24 hours after mating). Female heads and abdomens were then dissected on ice and stored at -80C until RNA extraction. Twenty female heads or abdomens were pooled for each sample.

extract_protocol: Stranded libraries were generated using TruSeq Stranded Total RNA Library Prep kit (Illumina).

treatment_protocol: Six populations with a census size of 200 individuals were established from the IV population of D. melanogaster in 2007: three (M1, M2, and M3) were held under enforced monogamy by randomly pairing one male and one virgin female, whereas the other three (P1, P2, and P3) experienced mating in polygamous groups of five females and five males. After two days of sexual interactions, males were discarded and females were allowed to lay eggs for three days in groups of 50, which assured similar degree of non-sexual competition. The populations had undergone 182 generations of experimental evolution and one subsequent generation of common garden rearing when males from each population were mated to standard females. The standard females' gene expression was then measured. For further details, see paper.

tag: gender

value: female

tag: mating status

value: mated

tag: male mate population

tag: tissue

value: abdomen


title: Mated_M2_abdomen (run 2)

description:
run2_iv_abd_mated_m2
18 total libraries were sequenced twice.


title: Mated_P2_abdomen (run 2)

description:
run2_iv_abd_mated_p2
18 total libraries were sequenced twice.


title: Mated_P3_abdomen (run 2)

description:
run2_iv_abd_mated_p3
18 total libraries were sequenced twice.


title: Mated_P1_abdomen (run 2)

description:
run2_iv_abd_mated_p1
18 total libraries were sequenced twice.


title: GC-JC-7819-A03_S17

description:
processed data file:
Dd_Mound_Rep3.txt
14h3_3


title: P170694_S03: HEK293_MeBP_TET_WT_+Aza_RNA-seq_rep_1

description: RNA-seq using ribo-RNA depleted total RNA


title: human white blood cells single cells H3K4me3 Ab-Mnase-18

data_processing:
Raw Sequence reads were aligned to the reference human genome (UCSC, hg18) by Bowtie2 (bowtie2 -D 20 -R 3 -N 1 -L 16 -i S,1,0.5 -X 1000  -p 20 -q -5 0 -3 30). The reads with mapping quality (MAPQ ≤10) or redundant reads that mapped to the same location with the same orientation were removed from further analysis in each single cell library. For scH3K4me3,  To avoid the possibility of doublet (or triplet) outliers, four cells were removed. A cell is defined as a doublet outlier if it satisfies the following two requirements.    1. The log-library size of the cell is larger the averaged the log-library size over all cells.    2. Cells are sorted based on their log-library size. With any of the selected window sizes, the log-library size of the cell is larger than three local scaled median absolute deviation (MAD) from the local median within the sliding window. A number of window sizes are tested. Finally, the remaining 281 cells are used for genome browser visualization and identification of peaks for pooled cells.
Peaks/Enriched regions for the 281 pooled single cell H3K4me3 data were identified using SICER (gap size = 200 bp, window size =200bp and frag size= 150bp). 22293 peaks are identified for the pooled H3K4me3 scChIC-seq data. Peaks/Enriched regions for the 106  pooled single cell H3K4me3 data were identified using SICER (gap size = 600 bp, window size =200bp and frag size= 150bp). 21,465 peaks are identified for the pooled H3K27me3 scChIC-seq data.
For each single cell library (both scH3K4me3 and scH3K27me3), we filtered the reads that are not located in the identified peak regions (22,293 peaks and 21,465 peaks for scH3K4me3 and scH3K27me3 libraries, respectively). Therefore, the *filtered.txt files are obtained for the downstream analysis.
Genome_build: hg18
Supplementary_files_format_and_content: *filtered.txt: bed 6 file. Each line is a peak region. The six columns are chrom, start position, end position, end position-start position, mapq, strand
Supplementary_files_format_and_content: bed: Bed 6 file. Each line is a read. The six columns are chrom, start position, end position, end position-start position, mapq, strand
Supplementary_files_format_and_content: bedgraph: bed 4 file. Each line is a bin, with bin size = 200bp. The four columns are chrom, start position, end position,read density.
Library strategy: scChIC-seq

source_name: white blood cells

extract_protocol:
The DNAs were end-repaired using the End-It™ DNA End-Repair Kit (Lucigen, Radnor, PA, USA). The reaction was done in 10 µL reaction volume according to the manufacturer’s instruction. The reaction was terminated by adding 115 µL 10 mM Tris-Cl buffer (pH7.5) containing 1 mM EDTA, and the DNAs were extracted by the phenol-chloroform extraction, followed by the ethanol precipitation as described above. The precipitate is re-suspended in 5 µL Qiagen Buffer EB (10 mM Tris-Cl buffer (pH 8.5)). The addition of 3’ A overhangs to the end-repaired DNA fragments was done using the Klenow fragment (3’→5’ exo-) (New England BioLabs, Ipswich, MA, USA) and 1 mM deoxyadenosine triphosphate in the reaction buffer. The DNA fragments were incubated at 37°C for 20 min and the enzymes were inactivated at 75°C for 20 min. The Illumina Adaptor Oligo Mix (Illumina, San Diego, CA, USA) was ligated to the 3’ A overhangs of the DNA fragments using the T4 DNA ligase (New England BioLabs) by incubating at room temperature for 3 hr.
The DNA fragment with the adaptors bound was PCR amplified using the Phusion High-Fidelity PCR Master Mix (New England BioLabs) and the 125 nM PE PCR Primer 1.0 (Illumina). The PCR was done under the following condition: 98°C for 10 min, followed by a cycle of 30 sec at 68°C and 30 sec at 72°C (repeat 18 cycles in the case of 3,000 cells or 25 cycles in the case of a single cell). The 2% [w/v] agarose gel electrophoresis was done to isolate the 140-350 bp fragments and purify using the QIAquick Gel Extraction kit (Qiagen). The concentration of the purified DNAs was measured using Qubit dsDNA HS kit (Thermo Fisher Scientific). The paired-end sequencings were run using the Illumina MiSeq and HiSeq2000.

value: white blood cells

tag: antibody-mnase

value: H3K4me3 Ab-MNase


title: Virgin_3_abdomen (run 2)

description:
run2_iv_abd_virgin_3
18 total libraries were sequenced twice.

value: virgin


title: Total_DKO_08

description: 3' RACE: TERC

value: total RNA


title: Total_DKO_10

description: 3' RACE: TERC


title: P170694_S04: HEK293_MeBP_TET_WT_Untreated_RNA-seq_rep_2


title: AM-CH3CS80_S31

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_42


title: Virgin_2_abdomen (run 2)

description:
run2_iv_abd_virgin_2
18 total libraries were sequenced twice.


title: HopX_P3_1

city: Philadelphia

first: Yijing

last: Su

state: PA

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

data_processing:
Basecalls performed using BCl2fastq
ATAC-seq reads were aligned to the mm9 genome assembly using Bowtiw with the default setting
peaks were called using MACS, with p < 0.05 as cutoff.
Genome_build: mm9
Supplementary_files_format_and_content: bed

source_name: HopX+ cells

extract_protocol: ADD

tag: cell type

value: neural progenitor cells

tag: chip antibody


title: AM-CH3CS78_S32

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_41


title: Virgin_1_abdomen (run 2)

description:
run2_iv_abd_virgin_1
18 total libraries were sequenced twice.


title: AM-CH3CS75_S33

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_40


title: P170694_S01: HEK293_MeBP_TET_WT_Untreated_RNA-seq_rep_1

tag: genotype/variation


title: P170694_S07: HEK293_MeBP_TET_WT_Untreated_RNA-seq_rep_3

tag: cell line


title: DKO_10_T0

description: 3' RACE: TERC, U2


title: AM-CH3CS86_S29

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_44


title: Mated_M1_abdomen (run 2)

description:
run2_iv_abd_mated_m1
18 total libraries were sequenced twice.


title: PAPD5_04_T24

description: 3' RACE: TERC, U2

value: HeLa PAPD5 CRISPR KO


title: Mated_P3_head (run 2)

description:
run2_iv_head_mated_p3
18 total libraries were sequenced twice.

source_name: Female head

value: head


title: AM-CH3CS72_S35

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_38

value: AX3 with H2B-mCherry inserted in the rps30 locus

value: mound


title: P170424_S27: HEK293_TET_mut_+Dox_RNA-seq_rep_3

tag: treatment


title: Mated_P2_head (run 2)

description:
run2_iv_head_mated_p2
18 total libraries were sequenced twice.


title: AM-CH3CS82_S30

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_43


title: AM-CH3CS74_S34

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_39


title: PAPD5_04_T8

description: 3' RACE: TERC, U2


title: PAPD5_06_T8

description: 3' RACE: TERC, U2


title: Mated_P1_head (run 2)

description:
run2_iv_head_mated_p1
18 total libraries were sequenced twice.


title: P170424_S19: HEK293_TET_mut_+Dox_RNA-seq_rep_1


title: P170424_S23: HEK293_TET_mut_+Dox_RNA-seq_rep_2


title: PAPD5_06_T0

description: 3' RACE: TERC, U2


title: DKO_08_T0

description: 3' RACE: TERC, U2

value: HeLa PARN/PAPD5 DKO


title: AM-CH3CS69_S36

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_37


title: P170424_S26: HEK293_TET_mut_Untreated_RNA-seq_rep_3


title: Mated_M3_head (run 2)

description:
run2_iv_head_mated_m3
18 total libraries were sequenced twice.


title: AM-CH3CS68_S37

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_36


title: PAPD5_06_T24

description: 3' RACE: TERC, U2

value: 1 hr 250 uM


title: PAPD5_04_T0

description: 3' RACE: TERC, U2

value: nascent RNA


title: P170424_S22: HEK293_TET_mut_Untreated_RNA-seq_rep_2

description: RNA-seq using ribo-RNA depleted total RNA


title: AM-CH3CS67_S38

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_35


title: Total_PAPD5_06

description: 3' RACE: TERC


title: Mated_M2_head (run 2)

description:
run2_iv_head_mated_m2
18 total libraries were sequenced twice.


title: P170424_S18: HEK293_TET_mut_Untreated_RNA-seq_rep_1


title: Mated_M1_head (run 2)

description:
run2_iv_head_mated_m1
18 total libraries were sequenced twice.


title: Total_PAPD5_04

description: 3' RACE: TERC


title: Virgin_3_head (run 2)

description:
run2_iv_head_virgin_3
18 total libraries were sequenced twice.


title: P170424_S21: HEK293_TET_WT_+Dox_RNA-seq_rep_2

value: 1 μg/mL Doxycycline for 48 hours

value: TET-CD-GFP


title: Virgin_2_head (run 2)

description:
run2_iv_head_virgin_2
18 total libraries were sequenced twice.

value: female


title: P170424_S25: HEK293_TET_WT_+Dox_RNA-seq_rep_3


title: P170424_S17: HEK293_TET_WT_+Dox_RNA-seq_rep_1


title: Virgin_1_head (run 2)

description:
run2_iv_head_virgin_1
18 total libraries were sequenced twice.


title: AM-CH3CS57_S41

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_31


title: PARN_L4_T24

description: 3' RACE: TERC, U2, E1, U68

value: HeLa PARN CRISPR KO


title: AM-CH3CS6_S3

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_32


title: PARN_A2_T24

description: 3' RACE: TERC, U2, E1, U68


title: Mated_P3_abdomen (run 1)

description:
run1_iv_abd_mated_p3
18 total libraries were sequenced twice.

value: mated

value: abdomen


title: P170424_S24: HEK293_TET_WT_Untreated_Dox_RNA-seq_rep_3


title: AM-CH3CS55_S42

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_30


title: PARN_A2_T8

description: 3' RACE: TERC, U2, E1, U68


title: Mated_P2_abdomen (run 1)

description:
run1_iv_abd_mated_p2
18 total libraries were sequenced twice.


title: PARN_L4_T8

description: 3' RACE: TERC, U2, E1, U68


title: Mated_P1_abdomen (run 1)

description:
run1_iv_abd_mated_p1
18 total libraries were sequenced twice.


title: AM-CH3CS54_S43

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_29


title: P170424_S16: HEK293_TET_WT_Untreated_Dox_RNA-seq_rep_1


title: AM-CH3CS61_S39

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_34


title: PARN_A2_T0

description: 3' RACE: TERC, U2, E1, U68


title: AM-CH3CS53_S44

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_28


title: Mated_M3_abdomen (run 1)

description:
run1_iv_abd_mated_m3
18 total libraries were sequenced twice.


title: PARN_L4_T0

description: 3' RACE: TERC, U2, E1, U68


title: P170424_S10: HEK293_TET_WT_+UVA+Thio_RNA-seq_rep_2

description: RNA-seq using ribo-RNA depleted total RNA

value: 25 µM 4-Thio-2'-deoxythymidine for 48 hours with irradiation with 10 kJ/m^2 365 nm UV (UVA) every 8 hours for 4 times


title: AM-CH3CS60_S40

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_33


title: AM-CH3CS51_S45

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_27


title: Mated_M2_abdomen (run 1)

description:
run1_iv_abd_mated_m2
18 total libraries were sequenced twice.


title: AM-CH3CS50_S46

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_26


title: PARN_L4_elute

description: 3' RACE: TERC

value: TERT IP'd RNA


title: P170424_S08: HEK293_TET_WT_+UVA+Thio_RNA-seq_rep_1


title: Mated_M1_abdomen (run 1)

description:
run1_iv_abd_mated_m1
18 total libraries were sequenced twice.


title: PARN_A2_input

description: 3' RACE: TERC

value: total RNA


title: AM-CH3CS47_S26

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_25


title: P170424_S11: HEK293_TET_WT_+UVA_RNA-seq_rep_3

value: irradiation with 10 kJ/m^2 365 nm UV (UVA) every 8 hours for 4 times


title: P170424_S20: HEK293_TET_WT_Untreated_Dox_RNA-seq_rep_2


title: AM-CH3CS43_S24

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_23


title: PARN_L4_input

description: 3' RACE: TERC


title: P170424_S09: HEK293_TET_WT_+UVA_RNA-seq_rep_2


title: Virgin_2_abdomen (run 1)

description:
run1_iv_abd_virgin_2
18 total libraries were sequenced twice.

value: virgin


title: Total_PARN_L4

description: 3' RACE: TERC


title: AM-CH3CS46_S25

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_24


title: P170424_S07: HEK293_TET_WT_+UVA_RNA-seq_rep_1


title: AM-CH3CS42_S23

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_22


title: Mated_P3_head (run 1)

description:
run1_iv_head_mated_p3
18 total libraries were sequenced twice.

value: head


title: P170424_S15: HEK293_TET_WT_+Thio_RNA-seq_rep_3

value: 25 µM 4-Thio-2'-deoxythymidine for 48 hours


title: Virgin_1_abdomen (run 1)

description:
run1_iv_abd_virgin_1
18 total libraries were sequenced twice.


title: P170424_S12: HEK293_TET_WT_+UVA+Thio_RNA-seq_rep_3


title: AM-CH3CS4_S2

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_21

value: AX3 with H2B-mCherry inserted in the rps30 locus

value: mound


title: PARN_rescue

description: 3' RACE: TERC

value: HeLa PARN CRISPR KO +lentiPARN


title: PARN_A2_elute

description: 3' RACE: TERC


title: P170424_S14: HEK293_TET_WT_+Thio_RNA-seq_rep_2


title: Mated_P2_head (run 1)

description:
run1_iv_head_mated_p2
18 total libraries were sequenced twice.


title: AM-CH3CS39_S22

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_20


title: hES_unbound2

description: 3' RACE: TERC, E1, U2, U68, U3, U8

value: H1 hES passage 68

value: 4 hr 50 uM

value: depleted RNA


title: PARN_GFP

description: 3' RACE: TERC

value: HeLa PARN CRISPR KO +lentiGFP


title: Mated_P1_head (run 1)

description:
run1_iv_head_mated_p1
18 total libraries were sequenced twice.

value: female


title: P170424_S13: HEK293_TET_WT_+Thio_RNA-seq_rep_1

description: RNA-seq using ribo-RNA depleted total RNA

value: TET-CD-GFP


title: Virgin_3_abdomen (run 1)

description:
run1_iv_abd_virgin_3
18 total libraries were sequenced twice.

value: abdomen


title: AM-CH3CS37_S20

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_18


title: P170424_S06: HEK293_TET_WT_+Aza_RNA-seq_rep_3

value: 880 nM 5-aza-2'-deoxycytidine for 48 hours


title: AM-CH3CS38_S21

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_19


title: hES_unbound1

description: 3' RACE: TERC, E1, U2, U68, U3, U8


title: hES_nascent2

description: 3' RACE: TERC, E1, U2, U68, U3, U8

value: nascent RNA


title: P170424_S04: HEK293_TET_WT_+Aza_RNA-seq_rep_2


title: Mated_M3_head (run 1)

description:
run1_iv_head_mated_m3
18 total libraries were sequenced twice.

value: mated


title: Mated_M2_head (run 1)

description:
run1_iv_head_mated_m2
18 total libraries were sequenced twice.


title: HeLa_unbound2_4hr

description: 3' RACE: TERC, E1, U2, U68, U3, U8

value: parental HeLa


title: P170424_S02: HEK293_TET_WT_+Aza_RNA-seq_rep_1


title: hES_nascent1

description: 3' RACE: TERC, E1, U2, U68, U3, U8


title: P170424_S05: HEK293_TET_WT_Untreated_Aza_RNA-seq_rep_3


title: HeLa_unbound1_4hr

description: 3' RACE: TERC, E1, U2, U68, U3, U8


title: P170424_S03: HEK293_TET_WT_Untreated_Aza_RNA-seq_rep_2


title: Virgin_2_head (run 1)

description:
run1_iv_head_virgin_2
18 total libraries were sequenced twice.

value: virgin


title: AM-CH3CS32_S17

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_15


title: Virgin_3_head (run 1)

description:
run1_iv_head_virgin_3
18 total libraries were sequenced twice.

value: head


title: HeLa_unbound2_1hr

description: 3' RACE: TERC, E1, U2, U68, U3, U8

value: 1 hr 250 uM


title: P170424_S01: HEK293_TET_WT_Untreated_Aza_RNA-seq_rep_1


title: AM-CH3CS31_S16

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_14

value: AX3 with H2B-mCherry inserted in the rps30 locus


title: AM-CH3CS29_S15

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_13

value: mound


title: HeLa_unbound1_1hr

description: 3' RACE: TERC, E1, U2, U68, U3, U8


title: Virgin_1_head (run 1)

description:
run1_iv_head_virgin_1
18 total libraries were sequenced twice.


title: MDA-MB-453_Int_4

type: RNA

first: Margaret

middle: C

last: Cam

institute: NIH

description:
MDA-MB-453 cells on 30kPa PA gels, biological replicate 4
Gene expression data from proliferating epithilial cancer cells

hyb_protocol: Fragmented samples were hybridized to Affymetrix GeneChip PrimeView Human Gene Expression array or  Affymetrix mouse Gene ST 2.0 GeneChip, for MDA-MB-453 and MMTV-PyVt tumor cells respectively, in an Affymetrix hybridization oven at 45 °C, 60 rpm for 16 hours.  Wash and staining were performed on Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip scanner 3000, and data collected using Affymetrix AGCC software.

data_processing: Affymetrix PrimeView Human Gene Expression and Mouse Gene 2.0 ST Array data were processed using the affy and limma bioconductor packages. For the human MDA-MB-453 cell assays, differentially expressed genes were detected in low and medium stiffness gels compared with glass.  For the mouse data, gene expression changes between cells immediately after isolation from the tumor were compared those same cells plated and cultured on PA gels or glass.

label: biotin

source_name: MDA-MB-453 cells, 5 days on 30 kPa PA gels

label_protocol: For the human MDA-MB-453 cells, 100 ng of RNA was reverse transcribed and labeled with biotin using Affymetrix 3’ IVT Plus kit, following manufacturer’s protocol (Affymetrix, Santa Clara, CA). For mouse tumor cells, 2 ng of RNA was reverse transcribed, amplified and sense strand cDNA was fragmented and labeled using WT Pico expression kit, following the manufacturer’s suggested protocol.

growth_protocol: MDA-MB-453 cells were cultured in a 37°C, 5% CO2 humidified environment in T75 tissue culture treated flasks, and grown in RPMI-1640 cell culture medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 0.1 vol% gentamicin. mouse mammary tumor cells were isolated by aseptically removing the tumors, mincing the tissue into 1 mm cubes, and mammary epithelial cancer cells isolated using collagenase. Cells were suspended in complete EpiCult-B media, transferred to a sterile petri dish and allowed to incubate at 37°C for 1 hour to allow for the adherence of stromal cells. The nonadherent fraction, containing mammary epithelial tumor cells, was collected and used for experimental assays.

extract_protocol: total RNA isolated using the RNeasy micro extraction kit, following the manufacturer’s instructions (Qiagen Sciences, Germantown, MD). RNA quality was checked on an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA), and all samples used in microarray analysis had a high quality score (RIN >7 for mouse, RIN > 9 for human).

treatment_protocol: Human MDA-MB-453 cells, or freshly isolated MMTV-PyVT mouse tumor cells, were seeded onto 96 well arrays containing 5kPa or 30kPa PA gels, as well as the glass control, at 25 x 103 and 50 x 103 cells/well, respectively. After 5 days of culture, the media was removed and cells collected following a 10 min. incubation with trypsin.

value: Mammary gland/breast

tag: morphology

value: epithelial


title: AM-CH3CS27_S14

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_12

tag: strain


title: AM-CH3CS36_S19

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_17

tag: replicate number


title: MDA-MB-453_Int_3

description:
MDA-MB-453 cells on 30kPa PA gels, biological replicate 3
Gene expression data from proliferating epithilial cancer cells


title: AM-CH3CS26_S13

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_11

tag: developmental stage


title: HeLa_02_T24

description: 3' RACE: TERC, U2, E1, U68

tag: 4su pulse time


title: AM-CH3CS34_S18

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_16


title: Mated_M1_head (run 1)

description:
run1_iv_head_mated_m1
18 total libraries were sequenced twice.


title: MDA-MB-453_Int_2

description:
MDA-MB-453 cells on 30kPa PA gels, biological replicate 2
Gene expression data from proliferating epithilial cancer cells


title: HeLa_01_T24

description: 3' RACE: TERC, U2, E1, U68

tag: 4su chase time


title: HeLa_02_T8

description: 3' RACE: TERC, U2, E1, U68

tag: molecule subtype


title: AM-CH3CS23_S11

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_9


title: HeLa_01_T8

description: 3' RACE: TERC, U2, E1, U68


title: MDA-MB-453_Soft_4

description:
MDA-MB-453 cells on 5kPa PA gels, biological replicate 4
Gene expression data from proliferating epithilial cancer cells

source_name: MDA-MB-453 cells, 5 days on 5 kPa PA gels

tag: gender


title: MDA-MB-453_Int_1

description:
MDA-MB-453 cells on 30kPa PA gels, biological replicate 1
Gene expression data from proliferating epithilial cancer cells


title: AM-CH3CS22_S10

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_8


title: HeLa_02_T0

description: 3' RACE: TERC, U2, E1, U68


title: MDA-MB-453_Soft_3

description:
MDA-MB-453 cells on 5kPa PA gels, biological replicate 3
Gene expression data from proliferating epithilial cancer cells


title: MDA-MB-453_Soft_2

description:
MDA-MB-453 cells on 5kPa PA gels, biological replicate 2
Gene expression data from proliferating epithilial cancer cells


title: HeLa_01_T0

description: 3' RACE: TERC, U2, E1, U68


title: AM-CH3CS20_S9

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_7


title: AM-CH3CS2_S1

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_6


title: HeLa_nascent2_4hr

description: 3' RACE: TERC, E1, U2, U68, U3, U8

value: 4 hr 50 uM


title: AM-CH3CS25_S12

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_10


title: NRF2-BaP-3_MCY

city: Medford

first: Eric

middle: R

last: Reed

state: MA

address: 419 Boston Ave.

department: Data Intensive Studies Center

institute: Tufts University

hyb_protocol: labeled fragmented DNA was generated from 100 ng of total RNA and was hybridized to the GeneChip™ Human Gene 2.0 ST Array

scan_protocol: Microarrays were scanned using Affymetrix GeneArray Scanner 3000 7G Plus

data_processing: CEL files were annotated to unique Entrez gene IDs, using a custom CDF file from BrainArray (hugene20st_Hs_ENTREZG_21.0.0) and RMA normalized in R package oligo v1.34.2

label_protocol: As described in GeneChip™ WT PLUS Reagent Kit manual and GeneChip™ WT Terminal Labeling and Controls Kit protocol (Thermo Fisher Scientific)

growth_protocol: Cells were subcultured using Clonetics ReagentPack subculture reagents (Lonza, Portsmouth NH). In preparation for exposure, cells were plated into 24-well plates and allowed to reach confluency for 24 hours.

extract_protocol: RNA was isolated using a standard Qiazol and Qiacube protocol from Qiagen (Valencia, CA). RNA purity was assessed using a NanoDrop spectrophotometer and no samples were excluded from downstream analysis.

treatment_protocol: Cell culture media was replaced, and compounds added at a concentration of 24 μg/ml CSC, 173μM BaP, 490μM NNK or DMSO. NNK and BaP compounds were obtained from Sigma-Aldrich (St. Louis MO) and CSC obtained from Murty Pharmaceuticals (Lexington, KY). Genotypic perturbations included CRISPR knockouts of FAT1, and CDKN2A, as well as overexpression of NRF2 (NFE2L2), FGFR1, NRG1 and PIK3CA. Cells transfected with a pSpCas9-EGFP (GFP) plasmid (PX458) in the absence of sgRNAs were used as controls for the CRISPR perturbations while overexpression of an empty vector containing the reporter HcRed served as control for the overexpression experiments.

value: AALE

value: immortalized human bronchial epithelial cells (AALE)

tag: genotypic perturbation

tag: genotypic perturbation type

value: overexpression

tag: chemical perturbation

value: BaP


title: NRF2-BaP-2_MCY


title: HeLa_nascent1_4hr

description: 3' RACE: TERC, E1, U2, U68, U3, U8


title: NRF2-BaP-1_MCY


title: MDA-MB-453_Soft_1

description:
MDA-MB-453 cells on 5kPa PA gels, biological replicate 1
Gene expression data from proliferating epithilial cancer cells

tag: tissue

value: female


title: HeLa_nascent2_1hr

description: 3' RACE: TERC, E1, U2, U68, U3, U8


title: AM-CH3CS15_S7

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_4


title: MDA-MB-453_Glass_4

description:
MDA-MB-453 cells on glass, biological replicate 4
Gene expression data from proliferating epithilial cancer cells

source_name: MDA-MB-453 cells, 5 days on glass


title: NRF2-CSC-3_MCY

tag: cell type

value: CSC


title: HCRED-BaP-3_MCY

value: HCRED


title: MDA-MB-453_Glass_3

description:
MDA-MB-453 cells on glass, biological replicate 3
Gene expression data from proliferating epithilial cancer cells


title: HCRED-BaP-1_MCY


title: AM-CH3CS14_S6

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_3


title: HeLa_nascent1_1hr

description: 3' RACE: TERC, E1, U2, U68, U3, U8

value: nascent RNA


title: HeLa_elute

description: 3' RACE: TERC

value: parental HeLa

value: TERT IP'd RNA


title: HCRED-BaP-2_MCY


title: AM-CH3CS12_S5

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_2


title: NRF2-CSC-1_MCY


title: HCRED-CSC-3_MCY


title: AM-CH3CS11_S4

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_1


title: NRF2-CSC-2_MCY


title: AM-CH3CS18_S8

description:
processed data file:
Dd_Mound_Rep2.txt
14h2_5


title: AM-CH2CS95_S62

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_29


title: Total_HeLa

description: 3' RACE: TERC

value: total RNA


title: HCRED-CSC-1_MCY


title: Piwi-associated smRNA from Yb-KD

description:
ishizu-2_S2_L001_R1_001
processed data file:
piRNA_RPM.txt

source_name: Piwi-associated smRNA from Yb-KD

extract_protocol:
Piwi was immunoprecipitated using anti-Piwi antibody (PMID: 16882972) from confluent OSCs in 10 cm dishes, and Piwi-associated RNA was isolated from the immunopurified complex by phenol-chloroform extraction and ethanol precipitation.
Small RNA cloning was performed as previously described (PMID: 27425411)

value: Ovarian Somatic Cells (OSC)

value: EGFP RNAi

tag: ip antibody

value: anti-c-Myc antibody 9E10 (Sigma)


title: MDA-MB-453_Glass_2

description:
MDA-MB-453 cells on glass, biological replicate 2
Gene expression data from proliferating epithilial cancer cells

value: Mammary gland/breast


title: Piwi-associated smRNA from Control-KD

description:
ishizu-1_S1_L001_R1_001
processed data file:
piRNA_RPM.txt

source_name: Piwi-associated smRNA from Control-KD

tag: genotype/variation


title: Circulating miRNAs from umbilical cord blood TNG_P_102M

city: Brno

first: Jaroslav

last: Juracek

address: Kamenice 5

country: Czech Republic

institute: CEITEC MU

description:
Circulating miRNAs from umbilical cord blood
Test
miRCURY LNA™ Universal RT microRNA PCR, Ready-to-Use Human Panels I+II V4

data_processing:
The data normalization was performed using GenEx software.
Data were recalculated using interplate calibration (IPC, UniSp3) and normalized on U6 reference gene expression level.
Target gene signals normalized to reference gene; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_RG).

label: SYBR Green

source_name: Umbilical cord blood, plasma

extract_protocol: Total RNA was extracted with miRNeasy Serum/Plasma Kit (Qiagen).

tag: age

value: <34 years

tag: bmi

tag: pregnancy weight gain

tag: blood type

value: AB

tag: rh factor

value: negative

tag: allergies

value: Yes

tag: addictive substance abuse

value: No

tag: smoking status

value: Non-smoker


title: AM-CH2CS91_S63

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_28

tag: strain

value: AX3 with H2B-mCherry inserted in the rps30 locus

tag: replicate number

tag: developmental stage

value: mound


title: Circulating miRNAs from umbilical cord blood TNG_P_081M

value: A

value: positive


title: Circulating miRNAs from umbilical cord blood TNG_P_084M

value: >34 years


title: HCRED-CSC-2_MCY

tag: cell line

value: AALE

value: immortalized human bronchial epithelial cells (AALE)

tag: genotypic perturbation

value: HCRED

tag: genotypic perturbation type

value: overexpression

value: CSC


title: MDA-MB-453_Glass_1

description:
MDA-MB-453 cells on glass, biological replicate 1
Gene expression data from proliferating epithilial cancer cells

tag: tissue

value: Mammary gland/breast

tag: morphology

value: epithelial

tag: gender

value: female


title: HeLa_input

description: 3' RACE: TERC

value: parental HeLa

tag: molecule subtype

value: total RNA


title: NRF2-DMSO-1_MCY

tag: cell type

tag: chemical perturbation

value: DMSO


title: AM-CH2CS8_S49

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_25


title: Circulating miRNAs from umbilical cord blood TNG_P_080M

tag: age

tag: bmi

tag: pregnancy weight gain

tag: blood type

value: Yes

value: No

value: Non-smoker


title: NRF2-DMSO-3_MCY


title: AM-CH2CS77_S66

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_24

value: AX3 with H2B-mCherry inserted in the rps30 locus

value: mound


title: Piwi-associated smRNA

description:
1_S1_L001_R1_001
processed data file:
Armi_iCLIP_RPM.txt

source_name: Piwi-associated smRNA

value: Ovarian Somatic Cells (OSC)

tag: genotype/variation

value: untreated

tag: ip antibody

value: anti-Piwi antibody (PMID:16882972)


title: PROseq from nxf3 KO ovaries

city: Aarhus

first: Peter

last: Andersen

state: Denmark

address: Universitetsbyen 83

department: MBG

country: Denmark

institute: Aarhus University

description: nascent RNA

data_processing:
HiSeq data was basecalled with the instruments RTA (Run time analysis version 1.18.66.3): SCS (PN:RTA DS:Controlling software on instrument VN:2.2.68)
NextSeq data was basecalled with the instruments RTA (Run time analysis version 2.4.11): SCS (PN:RTA DS:Controlling software on instrument VN:2.2.0.4)
for small RNA sequencing and PROseq fastq files were adapter 'AGATCGGAAGAGCACACGTCT' clipped using cutadapt, version 1.0, default settings and the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini)
reads were mapped with bowtie v0.12.7 or STAR (RNAseq and RIPseq data only) to D. mel. genome (dm6, r6.18)
BigWig files were generated with Homertools v4.6
Genome_build: Drosophila melanogaster dm6, release 6.18
Supplementary_files_format_and_content: The processed data files are normalized bigwig tracks with uniquely mapping reads only

source_name: Adult ovaries

growth_protocol: Flies were kept at strandard conditions at 25º C.

extract_protocol:
Lysis and sonication of formaldehyde-crosslinked ovaries
Modified from PMID: 27442863
Ovaries were hand-dissected into ice-cold PBS

tag: fly genotype

tag: antibodies used

value: Dynabeads MyOne Streptavidin C1


title: NRF2-DMSO-2_MCY

tag: cell line

value: AALE

value: immortalized human bronchial epithelial cells (AALE)

value: overexpression


title: PROseq from rhino KO ovaries

description: nascent RNA


title: Circulating miRNAs from umbilical cord blood TNG_P_077M

value: <34 years

value: A

tag: rh factor

value: positive

tag: allergies

tag: addictive substance abuse

tag: smoking status

value: Smoker


title: Circulating miRNAs from umbilical cord blood TNG_P_097M

value: negative

value: Stop-smoker


title: Circulating miRNAs from umbilical cord blood TNG_P_070M

value: >34 years

value: No

value: Yes


title: AM-CH2CS81_S65

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_26

tag: strain

value: AX3 with H2B-mCherry inserted in the rps30 locus

tag: replicate number

tag: developmental stage

value: mound


title: AM-CH2CS76_S67

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_23


title: PROseq from w1118 (wildtype) ovaries

description: nascent RNA


title: PAC010 ACF 28

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description:
mRNA-seq
PolyA RNA
PAC010@ACF@28@S24
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt

data_processing:
Preprocessing: Low quality ends and adapter sequences were trimmed off from the Illumina reads with FastX 0.0.14 and Cutadapt 1.15 (HannonLab, 2010; Martin, 2011). Subsequently, small reads (length < 35 bp), polyA-reads (more than 90% of the bases equal A), ambiguous reads (containing N), low-quality reads (more than 50 % of the bases < Q25) and artifact reads (all but three bases in the read equal one base type) were filtered using FastX 0.0.14 and ShortRead 1.36.0 (Morgan et al., 2009). With Bowtie2 2.3.3.1 we identified and removed reads that align to phix_illumina (Langmead & Salzberg, 2012).
Xenome classification: The preprocessed reads were classified into human and mouse reads using Xenome (version 1.0.0; now part of the gossamer suite) which allows segregation of mixed reads as compared to two genome references (Conway et al. 2012). The reference genomes were from EnsEMBL website (i.e. GRCh38 for Human and GRCm38 for Mouse). With Xenome, 1.2-1.9% of the reads per sample were discarded due to ambiguity (ambigous_reads), cross-mapped reads (both_reads) or unclassifiable reads (neither_reads).
Mapping: The preprocessed human reads were aligned with STAR aligner v2.5.2b to the reference genome of Homo sapiens (GRCh38) (AD et al., 2013). Default STAR aligner parameter settings were used, except for ‘--outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate’. Using Samtools 1.5, reads with a mapping quality smaller than 20 were removed from the alignments (Li et al., 2009).
Counting: The number of reads in the alignments that overlap with gene features were counted with featureCounts 1.5.3 (Liao et al., 2014). Following parameters were chosen: -Q 0 -s 2 -t exon -g gene_id. We removed genes for which all samples had less than 1 count-per-million. Raw counts were further corrected within samples for GC-content and between samples using full quantile normalization, as implemented in the EDASeq package from Bioconductor (Risso et al., 2011). One sample (PAC010@GEM@11@S17) has been identified as an outlier after summarization of the human samples and was discarded for the statistical comparisons.
Genome_build: GRCh38 (human) and GRCm38 (mouse)
Supplementary_files_format_and_content: Raw counts are in tab-delimited text files for each reference genome (RNAseqCounts_Mouse.txt for mouse and RNAseqCounts_Human.txt for human).

organism:
Homo sapiens
Mus musculus

source_name: patient-derived tumor xenografts (PDTX) model of pancreatic ductal adenocarcinoma (PDAC)

growth_protocol: The development and characterization of the PDTX model has been described in detail by Hermans et al. 2016. Endoscopy, 48: 1016-1022.

extract_protocol:
RNA from biological tissue samples was isolated with the RNeasy Kit (Qiagen, Chatsworth, CA) according to the manufacturer's instructions. The RNA quality and quantity were verified with a NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). RNA sequencing and processing were performed by VIB Nucleomics Core (www.nucleomics.be).
Per sample, an amount of 500 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version: Part # 15031047 Rev. E - October 2013) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA PolymeraseI and RNase H. The cDNA fragments were extended with a single ‘A’ base to the 3’ ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally, enrichment PCR was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library. Sequence-libraries of each sample were pooled and sequenced on an Illumina HiSeq 4000 full flow-cell (8 lanes) with a single read 50 kit (68 cycles, 2nM Pool + 1% PhiX v3) at the VIB Nucleomics core (www.nucleomics.be).

treatment_protocol: After the tumor reach a volume of 100-200 mm3, these mice were randomly divided into three groups with eight mice in each group; A) the control group that was treated with vehicle (0.9% NaCl) and the experimental groups was treated intraperitoneally for up to 28 days with B) Gemcitabine (50 mg/kg) injected twice a week. C) Acriflavine: schedule four doses of acriflavine were injected daily with a fixed dose of 5 mg/kg Monday to Thursday and single dose of 10 mg/kg on Friday for the weekend. At the end of the experiment or when the tumor volume reached the limit the tissue samples from each tumor were weighed, photographed and stored for histological analysis and molecular profiling.

tag: model

tag: treatment

value: Acriflavine


title: HCRED-DMSO-1_MCY

tag: cell type

tag: genotypic perturbation

value: HCRED

tag: genotypic perturbation type

tag: chemical perturbation

value: DMSO


title: PAC010 ACF 27

description:
mRNA-seq
PolyA RNA
PAC010@ACF@27@S23
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: HCRED-DMSO-3_MCY

value: AALE


title: Circulating miRNAs from umbilical cord blood TNG_P_067M

tag: age

tag: bmi

tag: pregnancy weight gain

tag: blood type

value: B

value: Non-smoker


title: AM-CH2CS71_S68

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_22


title: PAC010 ACF 26

description:
mRNA-seq
PolyA RNA
PAC010@ACF@26@S22
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: AM-CH2CS84_S64

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_27


title: AM-CH2CS70_S69

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_21


title: RIPseq UAP56 IP, replicate 1

extract_protocol:
Total RNA extraction from immunopurified protein complexes from ovary lysates
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
Ovaries were hand-dissected into ice-cold PBS

tag: fly genotype

tag: antibodies used

value: anti-FLAG (Sigma, M8823)


title: PAC010 GEM 29

description:
mRNA-seq
PolyA RNA
PAC010@GEM@29@S20
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt

value: Gemcitabine


title: AM-CH2CS7_S48

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_20


title: HCRED-DMSO-2_MCY

tag: cell line

value: immortalized human bronchial epithelial cells (AALE)

value: overexpression


title: Circulating miRNAs from umbilical cord blood TNG_P_064M

value: <34 years

tag: rh factor

value: positive

tag: allergies

tag: addictive substance abuse

tag: smoking status


title: PAC010 ACF 25

description:
mRNA-seq
PolyA RNA
PAC010@ACF@25@S21
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt

tag: model


title: AM-CH2CS69_S70

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_19

tag: strain

tag: replicate number

tag: developmental stage


title: RIPseq Nxf3 IP, replicate 1

value: w[1118]; ; nxf3-GFP-V5-3xFLAG[knock-in]


title: RIPseq from control IP (NLS_GFP_V5_3xFLAG), replicate 2


title: AM-CH2CS64_S71

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_18


title: PAC010 GEM 14

description:
mRNA-seq
PolyA RNA
PAC010@GEM@14@S19
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt

tag: treatment


title: PAC010 GEM 13

description:
mRNA-seq
PolyA RNA
PAC010@GEM@13@S18
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: AM-CH2CS63_S72

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_17


title: RIPseq from control IP (NLS_GFP_V5_3xFLAG), replicate 1


title: Circulating miRNAs from umbilical cord blood TNG_P_059M

description:
Circulating miRNAs from umbilical cord blood
Test
miRCURY LNA™ Universal RT microRNA PCR, Ready-to-Use Human Panels I+II V4

value: >34 years

value: AB

value: No


title: Circulating miRNAs from umbilical cord blood TNG_P_063M

value: A

value: Yes

value: Stop-smoker


title: AM-CH2CS6_S47

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_16

value: AX3 with H2B-mCherry inserted in the rps30 locus

value: mound


title: PAC010 GEM 11

description:
mRNA-seq
PolyA RNA
PAC010@GEM@11@S17
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: RIPseq UAP56 IP, replicate 2


title: Input sample of UAP56 RIP, replicate 2

extract_protocol:
Total RNA extraction from ovary lysate
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
Ovaries were hand-dissected into ice-cold PBS


title: Circulating miRNAs from umbilical cord blood TNG_P_054M


title: Circulating miRNAs from umbilical cord blood TNG_P_050M


title: PAC010 GEM 09

description:
mRNA-seq
PolyA RNA
PAC010@GEM@09@S16
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: RIPseq Nxf3 IP, replicate 2


title: Input sample of UAP56 RIP, replicate 1


title: AM-CH2CS57_S73

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_15


title: PAC010 Control 08

description:
mRNA-seq
PolyA RNA
PAC010@Cont@08@S15
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt

value: Control


title: Circulating miRNAs from umbilical cord blood TNG_P_048M

value: Non-smoker


title: AM-CH2CS55_S74

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_14


title: PAC010 Control 07

description:
mRNA-seq
PolyA RNA
PAC010@Cont@07@S14
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: Input sample of Nxf3 RIP, replicate 2


title: Circulating miRNAs from umbilical cord blood TNG_P_043M

value: B

value: negative


title: Input sample of Nxf3 RIP, replicate 1


title: AM-CH2CS48_S61

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_12


title: PAC010 Control 06

description:
mRNA-seq
PolyA RNA
PAC010@Cont@06@S13
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: Circulating miRNAs from umbilical cord blood TNG_P_046M


title: Circulating miRNAs from umbilical cord blood TNG_P_041M


title: Circulating miRNAs from umbilical cord blood TNG_P_045M

value: Smoker


title: Input sample of control RIP, replicate 2


title: PAC006 ACF 27

description:
mRNA-seq
PolyA RNA
PAC006@ACF@27@S11
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt

value: Acriflavine


title: AM-CH2CS47_S60

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_11


title: Circulating miRNAs from umbilical cord blood TNG_P_039M


title: AM-CH2CS46_S59

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_10


title: RNAseq (polyA-selected) from CG13741 KO ovaries, replicate 2

extract_protocol:
Total RNA extraction with TRIzol followed by polyA RNA purification using oligo-dT magnetic beads
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina
Ovaries were hand-dissected into ice-cold PBS


title: PAC006 ACF 26

description:
mRNA-seq
PolyA RNA
PAC006@ACF@26@S10
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: Circulating miRNAs from umbilical cord blood TNG_P_031M

value: <34 years


title: Circulating miRNAs from umbilical cord blood TNG_P_030M

value: positive


title: AM-CH2CS41_S58

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_9


title: RNAseq (polyA-selected) from nxf3 KO ovaries, replicate 2


title: PAC006 ACF 25

description:
mRNA-seq
PolyA RNA
PAC006@ACF@25@S9
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: PAC006 GEM 29

description:
mRNA-seq
PolyA RNA
PAC006@GeM@29@S8
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt

value: Gemcitabine


title: RNAseq (polyA-selected) from CG13741 KO ovaries, replicate 1


title: AM-CH2CS31_S56

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_7


title: RNAseq (polyA-selected) from rhino KO ovaries, replicate 2


title: PAC006 GEM 13

description:
mRNA-seq
PolyA RNA
PAC006@GEM@13@S6
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: PAC006 GEM 09

description:
mRNA-seq
PolyA RNA
PAC006@GEM@09@S5
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: BHS3: RNAseq of LCM microdissected ovules: sexual H. perforatum pool3

city: Legnaro

first: giulio

last: Galla

state: Padova

address: Viale dell'Universita

department: DAFNAE

country: Italy

institute: University of Padova

data_processing:
Adapter trimming was erformed with the software CLC Genomics Workbench V 7 (Qiagen)
Quality trimming based on quality scores was erformed with the software CLC Genomics Workbench V 7 (Qiagen), with default parameters
Mapping and sequence counts were performed with the software CLC Genomics Workbench V 7 (Qiagen)
Differentially expressed genes (DEGs) were identified by using the software empirical analysis of DGE (Robinson et al., 2010) implemented in the CLC Genomics Workbench V 7 (Qiagen)
Genome_build: GHFN01000000
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Hypericum perforatum

source_name: ovule nuclellus

extract_protocol:
RNA was purified with the Stratagene Absolutely RNA® Nanoprep Kit (Agilent) from 250,000 of µm2 of tissue sections.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: ovule nucellus

value: pre-meiotic

tag: reproductive strategy

value: sexual


title: AM-CH2CS54_S75

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_13


title: PAC006 GEM 14

description:
mRNA-seq
PolyA RNA
PAC006@GEM@14@S7
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: Circulating miRNAs from umbilical cord blood TNG_P_022M

description:
Circulating miRNAs from umbilical cord blood
Test
miRCURY LNA™ Universal RT microRNA PCR, Ready-to-Use Human Panels I+II V4

tag: age

tag: bmi

value: No


title: AM-CH2CS37_S57

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_8


title: AM-CH2CS30_S55

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_6


title: RNAseq (polyA-selected) from nxf3 KO ovaries, replicate 1


title: AM-CH2CS27_S54

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_5


title: RNAseq (polyA-selected) from w1118 (wildtype) ovaries, replicate 4


title: Circulating miRNAs from umbilical cord blood TNG_P_025M

tag: pregnancy weight gain

tag: blood type


title: BHS1: RNAseq of LCM microdissected ovules: sexual H. perforatum pool1


title: RNAseq (polyA-selected) from rhino KO ovaries, replicate 1

tag: fly genotype


title: AM-CH2CS20_S53

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_4


title: BHS2: RNAseq of LCM microdissected ovules: sexual H. perforatum pool2


title: Circulating miRNAs from umbilical cord blood TNG_P_024M

value: A

value: Yes


title: AM-CH2CS17_S52

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_3

value: AX3 with H2B-mCherry inserted in the rps30 locus


title: PAC010 Control 05

description:
mRNA-seq
PolyA RNA
PAC010@Cont@05@S12
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: PAC006 Control 05

description:
mRNA-seq
PolyA RNA
PAC006@Cont@05@S4
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: RNAseq (polyA-selected) from w1118 (wildtype) ovaries, replicate 3


title: PAC006 Control 03

description:
mRNA-seq
PolyA RNA
PAC006@Cont@03@S3
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: Input sample of control RIP, replicate 1


title: AM-CH2CS15_S51

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_2

value: mound


title: PAC006 Control 02

description:
mRNA-seq
PolyA RNA
PAC006@Cont@02@S2
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt

value: Control


title: BHA2: RNAseq of LCM microdissected ovules: aposporous H. perforatum pool2

value: apomictic


title: RNAseq (polyA-selected) from w1118 (wildtype) ovaries, replicate 1


title: AM-CH2CS11_S50

description:
processed data file:
Dd_Mound_Rep1.txt
14h1_1


title: RNAseq (polyA-selected) from w1118 (wildtype) ovaries, replicate 2


title: PAC006 Control 01

description:
mRNA-seq
PolyA RNA
PAC006@Cont@01@S1
processed data file: RNAseqCounts-Human.txt
processed data file: RNAseqCounts-Mouse.txt


title: BHA1: RNAseq of LCM microdissected ovules: aposporous H. perforatum pool1


title: Total_RNA_Pol2_ChIPSeq_shSPT5_EtOH_Replicate2

status: Public on Mar 27 2019

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

country: Germany

institute: Christian-Albrechts-University Kiel

data_processing:
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v2.27. and normalized to the sample with the spike in control.
Genome_build: hg19
Supplementary_files_format_and_content: bedgrpah files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).
For 4sU-seq, reads were mapped to hg19 with  Bowtie2 with -N 1 settings.
Reads per gene were counted using the summarizeOverlaps function from the R package {GenomicRanges}.
Weakly and non-expressed genes were removed (mean count over all samples <1).
Genome_build: hg19
Supplementary_files_format_and_content: bedgrpah files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

growth_protocol: U2OS cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin

extract_protocol:
Cells were treated with 1% formaldehyde for 10 min at 37°C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using a Branson sonifier. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina®. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with Qiagen gel extraction kit. DNA fragments were amplified by 16 and 17 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay

treatment_protocol: Dox - 12-16 hours (when dox is added)/48 hours

value: EtOH

tag: sirna

tag: antibody

value: Santa Cruz Biotechnology A-10, #sc-17798


title: Total_RNA_Pol2_ChIPSeq_shSPT5_Dox_Replicate2

value: Dox


title: Total_RNA_Pol2_ChIPSeq_siMYC

value: siMYC


title: Total_RNA_Pol2_ChIPSeq_shSPT5_EtOH_Replicate1


title: SPT5_ChIPSeq_DMSO

value: DMSO

value: Santa Cruz Biotechnology D-3 X, #sc-133217 X


title: SPT5_ChIPSeq_THZ1


title: 4sU_Seq_siSPT5_Minus_Strand

description: nascent RNA

data_processing:
Library strategy: 4sU Seq
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v2.27. and normalized to the sample with the spike in control.
Genome_build: hg19
Supplementary_files_format_and_content: bedgrpah files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).
For 4sU-seq, reads were mapped to hg19 with  Bowtie2 with -N 1 settings.
Reads per gene were counted using the summarizeOverlaps function from the R package {GenomicRanges}.
Weakly and non-expressed genes were removed (mean count over all samples <1).
Genome_build: hg19
Supplementary_files_format_and_content: bedgrpah files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

extract_protocol:
RNA was isolated using miRNeasy columns and biotinylated. This was followed by pulldown using streptavidin-MyOne beads and elution
NEB Ultra/Ultra Directional RNA Seq

value: 15 min 4sU


title: SPT5_ChIPSeq_MYC_ON


title: 4sU_Seq_siCTR_Plus_Strand

description: nascent RNA

value: siCTR


title: Total_RNA_Pol2_ChIPSeq_Input


title: SPT5_ChIPSeq_Myc_High


title: SPT5_ChIPSeq_Input_HighMYC_Med_MYC

description: nascent RNA


title: 4sU_Seq_siCTR_Minus_Strand

description: nascent RNA


title: Total_RNA_Pol2_ChIPSeq_shSPT5_Dox_Replicate1


title: sGT_5_mRNA-Seq_rep2

city: Debrecen

first: Lilla

last: Ozgyin

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

description:
PROTOCOLS: "RNA-Seq"
sGT_mRNA-Seq_edgeR_RPKM_matrix_table.txt

data_processing:
RNA-Seq: Base calling and quality scoring are performed by RTA v2, demultiplexing was performed using bcl2fastq v2.20.0.422.
RNA-Seq: TopHat version 2.0.7 was used for read alignment with the option --max-multihits 1.
RNA-Seq: EdgeR was used for calculating RPKM values using UCSC GRCh37/hg19 annotation track, genes having less than 5 reads per million mapped reads (CPM < 5) in all 10 RNA-Seq samples were removed, and corrected for batch effects (EdgeR).
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq: sGT_mRNA-Seq_edgeR_RPKM_matrix_table.txt: matrix file type containing gene IDs, genomic location and RPKM values for the 10 sGT samples.

source_name: B-lymphoblastoid cell line

growth_protocol: LCL cells were grown in RPMI-1640 medium supplemented with 15% FBS, 1v/v% Penicillin-Streptomycin and 2mM L-glutamine until sub-confluency (up to 0.8*10-5 cells/ml) before experiments.

extract_protocol:
RNA-Seq: Cells were resuspended in 1 ml trizol after PBS washing, vortexed for 5 min at room temperature and stored at -20°C until RNA isolation. Phase separation was performed by adding 1:5 volume of chloroform, vortexing for 5 min and subjecting to high-speed centrifugation at 4°C. RNA was precipitated from the aqueous phase using 1:1 volume of isopropanol at room temperature for 10 min. Pellets were washed twice with chilled 75% ethanol, vacuum-dried and redissolved in nulcease-free water at 65°C for 10 min.
RNA-Seq: Sequencing libraries were prepared following Illumina’s TruSeq RNA Sample Preparation v2 Guide with poly(A) selection using 1 μg total RNA as the starting material. Indexed libraries were pooled and subjected to single-end sequencing on a NextSeq 500 sequencer with 50-bp read length.

tag: cell line

value: untreated

tag: sample pairing

value: biological replicate:sample 25


title: 4sU_Seq_siSPT5_Plus_Strand

description: nascent RNA


title: sGT_4_mRNA-Seq_rep2

value: biological replicate:sample 23


title: sGT_5_mRNA-Seq_rep1

value: biological replicate:sample 26


title: BHA3: RNAseq of LCM microdissected ovules: aposporous H. perforatum pool3

value: ovule nucellus

value: pre-meiotic


title: Total_RNA_Pol2_ChIPSeq_siCTR


title: U266 control at time 24h biol replicate 1

city: Cosenza

first: Cirino

last: Botta

address: Via Migliori

department: Hematology Unit

institute: "Annunziata" Hospital of Cosenza

hyb_protocol: cDNA was hybridized on GeneChip Human Transcriptome Array 2.0  at 45C for 16-18 hours. The arrays were washed and stained on Affymetrix Fluidics Stations 450.

scan_protocol: The arrays were scanned with an Affymetrix GeneChip Scanner 3000

data_processing:
Data were processed using Affymetrix Expression Console for quality control after summarization and Robust Multi-array Average (RMA) normalization
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: U266 MM cells untreated

label_protocol: cDNA was processed for fragmentation and labeling using the Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix Inc.) according to the Affymetrix procedures

growth_protocol: U266 cells were maintained in RPMI-1640 medium supplemented with 15%FBS and  1% penicillin/streptomycin

extract_protocol: total RNA (tRNA) from MM cells was extracted  with TRIzol® Reagent (Life Technologies) according to manufacturer’s instructions

treatment_protocol: U266 MM cells were exposed to PBS or 2.5 μM of trabectedin for 24 h

tag: cell type

value: multiple myeloma (MM) cell line

value: plasma cells

value: none (untreated)


title: U266 treated at time 24h biol replicate 2

source_name: U266 MM cells treated with 2.5 nM of trabectedin

value: 2.5 nM of trabectedin


title: sGT_4_mRNA-Seq_rep1

value: biological replicate:sample 24


title: U266 treated at time 24h biol replicate 1


title: sGT_2_mRNA-Seq_rep2

value: biological replicate:sample 19


title: sGT_3_mRNA-Seq_rep1

value: biological replicate:sample 22


title: U266 control at time 24h biol replicate 2


title: sGT_1_mRNA-Seq_rep1

value: biological replicate:sample 18


title: sGT_3_mRNA-Seq_rep2

value: biological replicate:sample 21


title: sGT_4_H3K27ac_rep2

description:
PROTOCOLS/extract protocol: "ChIP-Seq_sGT"
sGT_H3K27ac_RPKM_over_sGT_consensus_peak_set_matrix_table.bed

data_processing:
ChIP-Seq: Base calling and quality scoring are performed by RTA v2, demultiplexing was performed using bcl2fastq v2.20.0.422.
ChIP-Seq: BWA 0.7.10 was used for to align ChIP-Seq reads to the hg19 (GRCh37) genomic build.
ChIP-Seq: HOMER 4.9.1. was used to predict genomic regions with H3K27ac enrichment (FindPeaks, histone)., and DiffBind was used to calculate RPKM values and we used BedTools to remove ENCODE's blacklisted genomic regions.
Supplementary_files_format_and_content: ChIP-Seq: sGT_H3K27ac_RPKM_over_sGT_consensus_peak_set_matrix_table.bed: matrix-type data file; genomic locations (chr, start, end) and RPKM values of genomic regions with H3K27ac-enrichment in at least one sample (sGT), without ENCODE blacklisted regions.
Genome_build: hg19

extract_protocol:
ChIP-Seq_sGT: 20 million cells were crosslinked at RT with 1 % methanol-free formaldehyde for 10 min. Formaldehyde was quenched for 5 min at RT using 0.125 M glycine/PBS and cells were washed with ice-cold PBS. Nuclei were isolated by thoroughly resuspending cells in ChIP Lysis Buffer followed by high-speed centrifugation at 4°C (repeated 3 times) and sonicated using a probe-type sonicator in ChIP Lysis Buffer. Nuclear debris was sedimented using high-speed centrifugation at 4°C, the top 90% of the supernatant was diluted ten-fold with ChIP Lysis Buffer, then diluted chromatin equivalent to 5 million cells were immunoprecipitated overnight at 4°C with 2.5 μg anti-histone H3 (acetyl K27) antibody (Abcam, cat. ab4729) or isotype control antibody (Santa Cruz Biotechnology, cat. sc-2027 X). Immunoprecipitation reactions were centrifuged and the top 90% of the supernatant (antibody-antigen complexes) was captured for 6 hours at 4°C using 47.5 μl Protein A-Protein G paramagnetic bead mix (1:1 ratio) (Thermo Fisher Scientific, cat. 10002D and 10004D) pe-blocked overnight with 0.5 w/v% BSA/PBS at 4°C. Capture beads were washed for 3 min on a rotating rack at 4°C once with IP Wash Buffer I, twice with IP Wash Buffer II, once with IP Wash Buffer III and finally twice with IP Wash Buffer IV, collecting beads between washes using a magnetic rack (components of in-house buffers can be found in Table S3). Antibody-antigen complexes were eluted using 200 μl Bead Elution Buffer (30 min at RT, 1000 rpm), and crosslinks were reversed by adding 0.4 M NaCl and incubating overnight at 65°C. Eluates were then treated with 20 μg RNAse A and 40 μg Proteinase K, respectively. ChIP fragments were isolated using Quiagen’s MinElute PCR purification kit (cat. 28006) as per the manufacturer’s recommendations.
ChIP-Seq (sGT and trio) Sequencing libraries were prepared following Illumina’s TruSeq RNA Sample Preparation v2 Guide with poly(A) selection from 1 μg total RNA. Indexed libraries were pooled and sequenced on the NextSeq 500 platform (75 bp, single-end).

value: biological replicate:sample 7


title: sGT_5_H3K27ac_rep1

value: biological replicate:sample 10


title: sGT_3_H3K27ac_rep2

value: untreated

value: biological replicate:sample 5


title: GM12873_H3K27ac_rep1

description:
PROTOCOLS/extract protocol: "ChIP-Seq_trio"
sGT_trio_H3K27ac_RPKM_over_sGT+trio_consensus_peak_set_matrix_table.bed

data_processing:
ChIP-Seq: Base calling and quality scoring are performed by RTA v2, demultiplexing was performed using bcl2fastq v2.20.0.422.
ChIP-Seq: BWA 0.7.10 was used for to align ChIP-Seq reads to the hg19 (GRCh37) genomic build.
ChIP-Seq: HOMER 4.9.1. was used to predict genomic regions with H3K27ac enrichment (FindPeaks, histone)., and DiffBind was used to calculate RPKM values and we used BedTools to remove ENCODE's blacklisted genomic regions.
Supplementary_files_format_and_content: ChIP-Seq: sGT_trio_H3K27ac_RPKM_over_sGT+trio_consensus_peak_set_matrix_table.bed: matrix-type data file; genomic locations (chr, start, end) and RPKM values of genomic regions with H3K27ac-enrichment in at least one sample  of the sGT and trio data set,  without ENCODE blacklisted regions
Genome_build: hg19

extract_protocol:
ChIP-Seq_trio: 20 million cells were crosslinked at RT, first with 2 mM di(N-succinimidyl) glutarate for 45 min and then with 1 % methanol-free formaldehyde for 10 min. Formaldehyde was quenched for 5 min at RT using 0.125 M glycine/PBS and cells were washed with ice-cold PBS. Nuclei were isolated by thoroughly resuspending cells in ChIP Lysis Buffer followed by high-speed centrifugation at 4°C (repeated 3 times) and sonicated using a probe-type sonicator in ChIP Lysis Buffer. Nuclear debris was sedimented using high-speed centrifugation at 4°C, the top 90% of the supernatant was diluted ten-fold with ChIP Lysis Buffer, then diluted chromatin equivalent to 5 million cells were immunoprecipitated overnight at 4°C with 2.5 μg anti-histone H3 (acetyl K27) antibody (Abcam, cat. ab4729) or isotype control antibody (Santa Cruz Biotechnology, cat. sc-2027 X). Immunoprecipitation reactions were centrifuged and the top 90% of the supernatant (antibody-antigen complexes) was captured for 6 hours at 4°C using 47.5 μl Protein A-Protein G paramagnetic bead mix (1:1 ratio) (Thermo Fisher Scientific, cat. 10002D and 10004D) pe-blocked overnight with 0.5 w/v% BSA/PBS at 4°C. Capture beads were washed for 3 min on a rotating rack at 4°C once with IP Wash Buffer I, twice with IP Wash Buffer II, once with IP Wash Buffer III and finally twice with IP Wash Buffer IV, collecting beads between washes using a magnetic rack (components of in-house buffers can be found in Table S3). Antibody-antigen complexes were eluted using 200 μl Bead Elution Buffer (30 min at RT, 1000 rpm), and crosslinks were reversed by adding 0.4 M NaCl and incubating overnight at 65°C. Eluates were then treated with 20 μg RNAse A and 40 μg Proteinase K, respectively. ChIP fragments were isolated using Quiagen’s MinElute PCR purification kit (cat. 28006) as per the manufacturer’s recommendations.
ChIP-Seq (sGT and trio) Sequencing libraries were prepared following Illumina’s TruSeq RNA Sample Preparation v2 Guide with poly(A) selection from 1 μg total RNA. Indexed libraries were pooled and sequenced on the NextSeq 500 platform (75 bp, single-end).

value: biological replicate:sample 16


title: Ser2_ChIPSeq_shSPT5

description: genomic Deoxyribose Nucleic Acid

data_processing:
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v2.27. and normalized to the sample with the spike in control.
genome build: hg19
Supplementary_files_format_and_content: bedgraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

extract_protocol:
Cells were treated with 1% formaldehyde for 10 min at 37 °C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using a Branson sonifier. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina®. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and purified with Qiagen gel extraction kit. DNA fragments were amplified by 16 and 17 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay

value: Doxycyclin, 48 hours

value: RNAPII pSer2 abcam; Lot:GR3205578-3


title: GM12872_H3K27ac_rep2

value: biological replicate:sample 13


title: sGT_2_mRNA-Seq_rep1

value: biological replicate:sample 20


title: sGT_3_H3K27ac_rep1

value: biological replicate:sample 6


title: GM12872_H3K27ac_rep1

value: biological replicate:sample 14


title: GM12864_H3K27ac_rep2

value: biological replicate:sample 11


title: sGT_5_H3K27ac_rep2

value: biological replicate:sample 9


title: GM12864_H3K27ac_rep1

value: biological replicate:sample 12


title: sGT_2_H3K27ac_rep2

value: biological replicate:sample 3


title: sGT_1_H3K27ac_rep1

value: biological replicate:sample 2


title: sGT_2_H3K27ac_rep1

value: biological replicate:sample 4


title: GM12873_H3K27ac_rep2

value: biological replicate:sample 15


title: sGT_1_mRNA-Seq_rep2

value: biological replicate:sample 17


title: Ser2_ChIPSeq_Input

description: genomic Deoxyribose Nucleic Acid

value: RNAPII pSer2 abcam; Lot:GR3205578-1


title: Ser2_ChIPSeq_EV

description: genomic Deoxyribose Nucleic Acid

value: EtOH, 48 hours

value: RNAPII pSer2 abcam; Lot:GR3205578-2


title: sGT_1_H3K27ac_rep2

value: untreated

value: biological replicate:sample 1


title: SPT5_ChIPSeq_siCTR

description: genomic Deoxyribose Nucleic Acid

value: siCTR

value: Spt5 D3 X scbt; Lot:B1310


title: SPT5_ChIPSeq_siMYC

description: genomic Deoxyribose Nucleic Acid

value: siMYC

value: Spt5 D3 X scbt; Lot:B1311


title: R3_4sU_Seq_MYC_ON_Minus_Strand

description: nascent RNA

data_processing:
Library strategy: 4sU Seq
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
Reads per gene were counted using the summarizeOverlaps function from the R package {GenomicRanges}.
Weakly and non-expressed genes were removed (mean count over all samples <1).
genome build: hg19
Supplementary_files_format_and_content: bedgraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

value: siMYC+Dox


title: R3_4sU_Seq_MYC_ON_Plus_Strand

description: nascent RNA


title: SPT5_ChIPSeq_Input

description: genomic Deoxyribose Nucleic Acid

value: Spt5 D3 X scbt; Lot:B1309


title: R3_4sU_Seq_MYC_OFF_Plus_Strand

description: nascent RNA

value: siMYC+EtOH


title: R3_4sU_Seq_MYC_OFF_Minus_Strand

description: nascent RNA


title: R2_4sU_Seq_MYC_ON_Plus_Strand

description: nascent RNA


title: R2_4sU_Seq_MYC_ON_Minus_Strand

description: nascent RNA


title: R2_4sU_Seq_MYC_OFF_Minus_Strand

description: nascent RNA


title: R2_4sU_Seq_MYC_OFF_Plus_Strand

description: nascent RNA


title: R2_4sU_Seq_HighMyc_Minus_Strand

description: nascent RNA

value: siCTR+Dox


title: 8min_release_Unperturbed_4sUDRBSeq

description: nascent RNA

data_processing:
Library strategy: 4sUDRBSeq
Fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
Reads per gene were counted using the summarizeOverlaps function from the R package {GenomicRanges}.
Weakly and non-expressed genes were removed (mean count over all samples <1).
genome build: hg19
Supplementary_files_format_and_content: bedgraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

value: DRB 2.5 Hrs, 8 min release


title: R2_4sU_Seq_HighMyc_Plus_Strand

description: nascent RNA


title: 4sU_Seq_OHT_Replicate3

data_processing:
For 4sU-Seq, fastq files were generated using Illumina's CASAVA software and overall sequencing quality was analyzed with the FastQC script.
For 4sU-seq, reads were mapped to hg19 with  Bowtie2 with -N 1 settings.
Reads per gene were counted using the summarizeOverlaps function from the R package {GenomicRanges}.
Weakly and non-expressed genes were removed (mean count over all samples <1).
Genome_build: hg19
Supplementary_files_format_and_content: Count matrix containing Ensembl gene ID, gene symbol, gene description and counts for all samples and each gene.

source_name: SH-EP-NMYCER

growth_protocol: Neuroblastoma cells were grown in RPMI-1640 (Sigma). Medium was supplemented with 10% fetal calf serum (Biochrom) and penicillin/streptomycin (Sigma).

extract_protocol:
Before harvest of RNA through Qiagen miRNEasy kit, nascent RNA was labelled by adding 200 µM of 4sU (Sigma) in RPMI media to the cells for 15 min under normal culture conditions. After extraction and quantification by Nanodrop of total RNA, equal amount was labelled with biotin (Pierce) in presence of DMF-HPDP buffer. Free biotin removal was carried out by chloroform-isoamyl alcohol extraction after which RNA was re-suspended into nuclease free water. Myone Streptavidin beads (Life Technologies) were used for enrichment of biotinylated RNA which was then eluted by 100 mM DTT and cleaned by RNAeasy MinElute cleanup kit. Nascent RNA concentration was then measured using RiboGreen RNA assay kit and equal amount was used for library preparation
Before library preparation, rRNA was depleted using NEB rRNA depletion kit and then all eluted amount was used for NEB Ultra Directional kit with 17 PCR cycles.
The libraries were then finally sequenced for 75 cycles using Illumina NextSeq 500 system.

treatment_protocol: SH-EP MYCNER cells were cultured at density of 5 million cells per plate 24 h before treatment with 4-OHT

tag: molecule

value: nascent RNA

tag: label


title: 4sU_Seq_EtOH_Replicate1

value: EtOH


title: 4sU_Seq_OHT_Replicate2


title: 4sU_Seq_EtOH_Replicate3


title: 4sU_Seq_EtOH_Replicate2


title: 4sU_Seq_OHT_Replicate1


title: 16min_release_Unperturbed_4sUDRBSeq

description: nascent RNA

value: DRB 2.5 Hrs, 16min release


title: 15min_release_MYC_OFF_4sUDRBSeq

description: nascent RNA

value: DRB 2.5 Hrs, 15min release


title: 15min_release_HighMYC_4sUDRBSeq

description: nascent RNA


title: 10min_release_MYC_OFF_4sUDRBSeq

description: nascent RNA

value: DRB 2.5 Hrs, 10min release


title: 10min_release_MYC_ON_4sUDRBSeq

description: nascent RNA


title: 4min_release_Unperturbed_4sUDRBSeq

description: nascent RNA

value: DRB 2.5 Hrs, 4min release


title: sGT_4_H3K27ac_rep1

value: untreated

value: biological replicate:sample 8


title: WT GM-CSF 24h rep1

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Reads were trimmed using Trimmomatic
Trimmed reads were aligned to the mm10  ENSEMBL genome assembly using STAR aligner
Read counts were summarised at the gene level using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: gene-wise counts for all samples

source_name: WT_GM-CSF-24h_bone marrow

growth_protocol: RPMI1640 + Pen-Strep + 10% HI-FCS

extract_protocol:
Bone marrow neutrophils were FACS sorted and subdivided into three cohorts: unstimulated (immediately post-sort), or cultured in GM-CSF-containing media for 4h or 24h. Cells were lysed in RLT buffer, RNA extracted using Rneasy Plus Mini Kit (QIAGEN). Next-generation sequencing libraries were created with 100 ng of RNA from samples with distinct 18S and 28S peaks and RNA Integrity Number (RIN) values greater 7, using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Unstimulated or cultured in GM-CSF-containing media (100 ng/mL) for 4h or 42h

value: 10 weeks

tag: genotype/variation

value: WT

value: GM-CSF 24h

value: Bone marrow


title: CIS-/- GM-CSF 24h rep1

source_name: CISKO_GM-CSF-24h_bone marrow

value: CIS-/-


title: WT GM-CSF 24h rep2


title: CIS-/- GM-CSF 24h rep2


title: CIS-/- GM-CSF 4h rep3

source_name: CISKO_GM-CSF-4h _bone marrow

value: GM-CSF 4h


title: CIS-/- GM-CSF 24h rep3


title: WT GM-CSF 4h rep3

source_name: WT_GM-CSF-4h_bone marrow


title: 15min_release_MYC_ON_4sUDRBSeq

description: nascent RNA

value: siMYC+EtOH


title: 10min_release_HighMYC_4sUDRBSeq

description: nascent RNA

value: siCTR+Dox


title: CIS-/- GM-CSF 4h rep1

source_name: CISKO_GM-CSF-4h_bone marrow


title: WT GM-CSF 4h rep2


title: CIS-/- unstimulated rep1

source_name: CISKO_unstimulated_bone marrow

value: none (unstimulated)


title: WT GM-CSF 4h rep1


title: WT unstimulated rep2

source_name: WT_unstimulated_bone marrow


title: WT unstimulated rep3

source_name: WT_unstimulated _bone marrow


title: WT unstimulated rep1


title: CIS-/- unstimulated rep2


title: WT GM-CSF 24h rep3


title: NMG_1

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

institute: VIB-University of Ghent

description: Microglia of C57BL/6JRj mice

data_processing:
FastQC v0.11.4 is used to check the quality of the samples
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.38 with parameters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35
Sequenced reads were then mapped to mm10 transcriptome using Tophat2 v2.1.0 with parameters --library-type fr-unstranded --min-intron-length 50 --no-coverage-search
The mapping files were then filtered using samtools v0.1.18 (samtools view with parameters -bq 20) and sorted using samtools sort
Reads were counted using HTSeqCount v0.6.1p1 with parameters -f bam -m intersection-strict -s no -a 10 -t exon -i gene_id
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output HTSeqCount) for each sample

source_name: Brain

extract_protocol: All Methods listed in Van Hove et al.  A single-cell atlas of non-parenchymal brain macrophages reveals unique transcriptional identities that are shaped by ontogeny and tissue environment.  Nature Neuroscience. 2019.

tag: strain

value: Microglia


title: NCPM_2

description: Choroid plexus macrophages of C57BL/6JRj mice

source_name: Choroid Plexus

value: Choroid plexus macrophages


title: PM_3

description: Peritoneal macrophages of C57BL/6JRj mice

source_name: Peritoneal cavity

value: Peritoneal macrophages


title: NMG_4

description: Microglia of C57BL/6JRj mice


title: PM_4


title: NCPM_3


title: NCPM_1


title: PM_2


title: PM_1


title: CIS-/- GM-CSF 4h rep2

tag: treatment


title: ME-MHCII-int_1

description: MHC II lo Dura of C57BL/6JRj mice

source_name: Dura

value: MHC II lo Dura


title: ME-MHCII-int_3

description: MHC II lo Dura of C57BL/6JRj mice


title: ME-MHCII-int_4

description: MHC II lo Dura of C57BL/6JRj mice


title: CIS-/- unstimulated rep3

tag: tissue


title: ME-MHCII-high_3

description: MHC II hi Dura of C57BL/6JRj mice

value: MHC II hi Dura


title: ME-MHCII-high_4

description: MHC II hi Dura of C57BL/6JRj mice


title: NMG_3

description: Microglia of C57BL/6JRj mice


title: ME-MHCII-high_2

description: MHC II hi Dura of C57BL/6JRj mice


title: ME-MHCII-high_1

description: MHC II hi Dura of C57BL/6JRj mice


title: MEP-d

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

institute: Weatheral Institute of Molecular Medicine

data_processing:
RNA-Seq:Short reads were aligned to the human genome (GRCh37 assembly (hg19)) using Tophat software.
RNA-Seq: The mapping parameter ‘-g 1’ was used to allow one alignment to the reference for a given read
RNA-Seq: The featureCounts software was used to count reads on the basis of the RefSeq gene model. CPM and RPKM expression values were calculated using a script in R
Genome_build: GRCh37 assembly (hg19)
Supplementary_files_format_and_content: CPM and RPKM values from RNA sequencing

source_name: MEP (Bulk of 100 cells)

extract_protocol:
cDNA was generated according to Smart-seq2 protocol
Illumina sequencing libraries were constructed using the Nextera XT DNA Sample Preparation kit according to manufacturer's protocol.

treatment_protocol: Cells from human bone marrow of healthy adult donors were isolated by FACS

value: MEP

tag: disease

value: healthy

tag: phenotype


title: LMPP-d

source_name: LMPP (Bulk of 100 cells)

value: LMPP

value: Lin- CD34+ CD38- CD45RA+


title: MEP-a


title: MEP-b


title: MEP-c


title: NCPM_4


title: HSC-MPP-d

source_name: HSC-MPP (Bulk of 100 cells)

value: HSC-MPP

value: Lin- CD34+ CD38- CD45RA-


title: LMPP-b

value: Bone marrow


title: LMPP-a


title: bacterial culture_32h biol rep1

city: Madison

first: Tippapha

last: Pisithkul

state: Wisconsin

address: 1550 Linden Drive

department: Bacteriology

institute: UW-Madison

description:
B. subtilis grown in a biofilm-inducing medium for 32 hours; biological replicate #1
Sample name: 32h1

data_processing:
Bacillus subtilis NCIB3610 chromosome (GenBank accession number: CP020102.1) and plasmid pBS32 (GenBank accession number: NZ_CP020103.1) were concatenated into a single FASTA file.
100 base single-end reads were aligned to the sequences in the resulting FASTA file using BWA-MEM version 0.7.15
Alignment files were prepared using SAMtools, version 1.3.1
The number of reads aligning to each coding sequence was determined using the summarize overlaps function from the R package GenomicAlignments, with the arguments ignore.strand = TRUE and mode = “IntersectionNotEmpty”.
Read count normalization and calculation of differential expression was performed using a combination of the R package edgeR and the voomWithQualityWeights function from the R package limma.
Calculation of false discovery rate was performed by the method of Benjamini and Hochberg.
Genome_build: Bacillus subtilis NCIB3610 chromosome (GenBank accession number: CP020102.1) and plasmid pBS32 (GenBank accession number: NZ_CP020103.1)
Supplementary_files_format_and_content: RPKMs

organism: Bacillus subtilis

source_name: bacterial culture

growth_protocol: Bacillus subtilis strain NCIB3610 was maintained on Luria-Bertani (LB) agar plates. Floating biofilms (pellicles) were grown in modified MSgg medium adjusted to pH 6.8 ± 0.05. The modified MSgg contains 2% (v/v) glycerol, 1% (w/v) glutamate, 5 mM potassium phosphate (pH 7), 5 mM MOPS (pH 7), 2 mM MgCl2, 700 uM CaCl2, 50 uM MnCl2, 50 uM FeCl3, 1 uM ZnCl2, and 2 uM thiamine. Pellicles were grown in a 12-well polystyrene plate format at 37°C. Each well contained 4.5 mL culture volume with a custom-made stainless-steel mesh. Samples were collected every 4 hours from 8 to 32 hours after inoculation (in a 1:1000 dilution) from a late exponential LB culture (OD600 ~ 1.0-1.5) into MSgg.

extract_protocol:
Planktonic cells and/or pellicles (4 biological replicates per sample) were washed in -20°C cold methanol (50% (v/v) final concentration) and subject to centrifugation. The supernatant was discarded while the pellet was immediately freeze-dried using liquid nitrogen and stored at -80°C until extraction. To extract RNA, the pellet (volume of approximately 100 μL) was thawed on ice and resuspended in 200 μL of lysozyme-TE (10 mM Tris-Cl, pH 7.5; 1mM EDTA, pH 8) by vortexing before a 20 min-incubation at 37°C. RNA in the resultant mixture was extracted using RNeasy Mini Kit (QIAGEN, Valencia, CA, USA) as per manufacturer’s instructions. Residual DNA was enzymatically removed using DNase (RNase-Free DNase Set; QIAGEN).
Total RNA was verified for purity and integrity via the NanoDrop2000 Spectrophotometer and Agilent 2100 BioAnalyzer, respectively. Samples that meet the Illumina sample input guidelines were then prepared according the TruSeq® RNA Preparation Guide. For each sample’s TruSeq RNA library preparation, 1 μg of total RNA was ribosomally reduced using the RiboZeroTM rRNA Removal (Bacteria) kit (Illumina, San Diego, CA, USA). rRNA-depleted samples were purified with Agencourt RNAClean XP Beads (Beckman Coulter, Indianapolis, IN, USA). Subsequently, rRNA-depleted samples were fragmented using divalent cations under elevated temperature and immediately reversed transcribed into double-stranded (ds) cDNA using SuperScript II Reverse Transcriptase (Invitrogen, Carlsbad, California, USA) and random primers. The ds cDNA was purified by paramagnetic beads, end-repaired by T4 DNA polymerase and Klenow DNA Polymerase, and phosphorylated by T4 polynucleotide kinase. The blunt ended cDNA was purified by paramagnetic beads and then incubated with Klenow DNA Polymerase to add an ‘A’ base (Adenine) to the 3’ end of the blunt phosphorylated DNA fragments. DNA fragments were ligated to Illumina adapters, which have a single ‘T’ base (Thymine) overhang at their 3’end. The adapter-ligated products were purified by paramagnetic beads. Products of the ligation were PCR-amplified with PhusionTM DNA Polymerase using Illumina's genomic DNA primer set and purified by paramagnetic beads. Quality and quantity of the finished libraries were assessed using an Agilent DNA1000 chip (Agilent Technologies, Inc., Santa Clara, CA, USA) and Qubit® dsDNA HS Assay Kit (Invitrogen, Carlsbad, California, USA), respectively. Libraries were standardized to 2μM. Cluster generation was performed using standard Cluster Kits (v3) and the Illumina cBot. Single 100bp sequencing was performed, using standard SBS chemistry (v3) on an Illumina HiSeq2000 sequencer. Images were analyzed using the standard Illumina Pipeline, version 1.8.2.

value: grown in a biofilm-inducing medium

tag: developmental stage

value: biofilm

tag: time


title: bacterial culture_32h biol rep3

description:
B. subtilis grown in a biofilm-inducing medium for 32 hours; biological replicate #3
Sample name: 32h3


title: bacterial culture_32h biol rep4

description:
B. subtilis grown in a biofilm-inducing medium for 32 hours; biological replicate #4
Sample name: 32h4


title: bacterial culture_32h biol rep2

description:
B. subtilis grown in a biofilm-inducing medium for 32 hours; biological replicate #2
Sample name: 32h2


title: HSC-MPP-a


title: bacterial culture_28h biol rep2

description:
B. subtilis grown in a biofilm-inducing medium for 28 hours; biological replicate #2
Sample name: 28h2


title: bacterial culture_28h biol rep1

description:
B. subtilis grown in a biofilm-inducing medium for 28 hours; biological replicate #1
Sample name: 28h1


title: GMP-d

source_name: GMP (Bulk of 100 cells)

value: GMP


title: HSC-MPP-b


title: bacterial culture_28h biol rep4

description:
B. subtilis grown in a biofilm-inducing medium for 28 hours; biological replicate #4
Sample name: 28h4


title: ME-MHCII-int_2

description: MHC II lo Dura of C57BL/6JRj mice


title: GMP-c


title: bacterial culture_28h biol rep3

description:
B. subtilis grown in a biofilm-inducing medium for 28 hours; biological replicate #3
Sample name: 28h3


title: bacterial culture_24h biol rep4

description:
B. subtilis grown in a biofilm-inducing medium for 24 hours; biological replicate #4
Sample name: 24h4


title: bacterial culture_24h biol rep3

description:
B. subtilis grown in a biofilm-inducing medium for 24 hours; biological replicate #3
Sample name: 24h3


title: bacterial culture_24h biol rep2

description:
B. subtilis grown in a biofilm-inducing medium for 24 hours; biological replicate #2
Sample name: 24h2


title: CMP-CD131-c

source_name: CMP-CD131 (Bulk of 100 cells)


title: GMP-b


title: GMP-a


title: bacterial culture_20h biol rep3

description:
B. subtilis grown in a biofilm-inducing medium for 20 hours; biological replicate #3
Sample name: 20h3


title: CMP-CD131-b


title: bacterial culture_24h biol rep1

description:
B. subtilis grown in a biofilm-inducing medium for 24 hours; biological replicate #1
Sample name: 24h1


title: LMPP-c