title: placenta (588184_oxBS)

city: Atlanta

first: Carmen

last: Marsit

state: GA

address: 1518 Clifton Road

department: Environmental Health

institute: Rollins School of Public Health at Emory University

hyb_protocol: bisulphite and oxidative bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

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

data_processing:
Signal intensities files were extracted using the minfi Bioconductor package. Normalization was performed using the Functional Normalization function implemented in minfi
[MatrixProcessed.txt]  minfi-normalized Average Beta values

source_name: human placenta, oxidative bisulfite converted

extract_protocol: Genomic DNA was extracted from placenta samples, collected near term-equivalent age USA) and aliquoted into a standardized concentration for subsequent analyses

tag: infant sex

tag: maternal age (years)

tag: birthweight (grams)

tag: gestational age (weeks)

tag: mother education

value: Any post graduate schooling

tag: tissue

value: placenta


title: A11-CTRL-MNP technical replicate 3

status: Public on Jan 04 2021

type: SRA

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description: MNP, CTRL, Animal A11, technical replicate 3

library_source: transcriptomic

data_processing:
Illumina bcl2fastq 2.18.0.12 software used for demultiplexing.
tab-delimited text files include gene counting for each sample
Genome_build: ss102 (Ensembl 91)
Supplementary_files_format_and_content: reads counts

molecule: total RNA

organism: Sus scrofa

source_name: MNP

extract_protocol:
Total RNA from sorted cells was extracted using the Arcturus PicoPure RNA Isolation kit (ThermoFisher Scientiﬁc, St Aubin, France) according to the manufacturer’s instructions. The RNase-Free DNase Set (Qiagen, France) was used to remove contaminating DNA. RNA integrity was assessed using an RNA 6000 Pico kit on a Bioanalyzer 2100 (Agilent Technologies).
1 to 3 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech). Afterwards 150 pg of amplified cDNA was used to prepare library following Nextera XT DNA kit (Illumina).

tag: strain

value: Large White

tag: cell type

value: MNP

tag: infected

value: no

tag: virus

tag: original name (to remove)

tag: animal id


title: A11-FL-MNP technical replicate 2

description: MNP, FL, Animal A11, technical replicate 2

value: yes

value: FL


title: placenta (588312_BS)

type: genomic

country: USA

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: human placenta, bisulfite converted

label_protocol: Standard Illumina Protocol

value: Female

value: College graduate


title: placenta (588172_BS)

value: Male


title: placenta (588184_BS)


title: A11-CTRL-MNP technical replicate 4

description: MNP, CTRL, Animal A11, technical replicate 4


title: placenta (588172_oxBS)


title: placenta (588312_oxBS)


title: A11-CTRL-MNP technical replicate 2

description: MNP, CTRL, Animal A11, technical replicate 2


title: A11-LENA-MNP technical replicate 2

description: MNP, LENA, Animal A11, technical replicate 2

value: LENA


title: placenta (588160_BS)


title: A3-FL-AM technical replicate 12

description: AM, FL, Animal A3, technical replicate 12

source_name: AM

value: AM


title: placenta (588160_oxBS)


title: A11-CTRL-MNP technical replicate 1

description: MNP, CTRL, Animal A11, technical replicate 1


title: A3-FL-AM technical replicate 11

description: AM, FL, Animal A3, technical replicate 11


title: A3-FL-AM technical replicate 10

description: AM, FL, Animal A3, technical replicate 10


title: HeartPos1_ATACSeq

city: PHILADELPHIA

first: Arndt

last: Siekmann

state: Pennsylvania

address: 421 Curie Boulevard, 1114 Biomedical Research Building II/III

department: Perelman School of Medicine

institute: UNIVERSITY OF PENNSYLVANIA

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ATACSeq reads were aligned to the mm10 genomes using Bowtie2 (v 2.3.5.1) maximum insert size  set to 2000 (-X 2000)
Resulting SAM file from Bowtie2 were filtered for quality and converted to BAM using samtools v1.19 (samtools view -h -F 4 -q 10 -bS). Duplicate reads were removed using picard tools (https://broadinstitute.github.io/picard/)
NarrowPeak file were generated using Genrich peak caller (https://github.com/jsh58/Genrich), excluding chrM and chrY for peak identification (genrich -j -v -y  -r  -e chrM, chrY -E $BLACKLIST). BLACKLIST regions file for mm10 was downloaded from https://github.com/Boyle-Lab/Blacklist/tree/master/lists
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated from bedGraph files generated by generich.

organism: Mus musculus

extract_protocol:
NuTRAP/Cdh5-Cre (NuTRAP from Roh, 2017, Cell Reports) animals were generated to GFP tag endothelial cell nuclei. Total nuclei were isolated from whole hearts of 8-12week old male animals. Endothelial cell nuclei (GFP+) were isolated by flow cytometry in addition to non-endothelial nuclei (GFP-).
100-50,000 purified  GFP+ ("Pos") and GFP- ("Neg") nuclei were processed for ATACSeq, using the protocol outlined in Buenrostro, et al 2013, using 2.5uL of Tn5 per 50,000 nuclei.

tag: strain background

tag: genotype/variation

tag: age

value: 8-12 weeks

value: heart

value: endothelial cell (GFP+) nuclei

value: 2.5uL per 50,000 nuclei


title: A11-FL-MNP technical replicate 1

description: MNP, FL, Animal A11, technical replicate 1


title: placenta (588108_BS)

value: Junior college graduate or equivalent


title: A3-FL-AM technical replicate 9

description: AM, FL, Animal A3, technical replicate 9


title: HeartNeg1_ATACSeq

value: non-endothelial cell (GFP-) nuclei


title: A3-FL-AM technical replicate 8

description: AM, FL, Animal A3, technical replicate 8


title: placenta (588148_oxBS)

value: placenta


title: placenta (588108_oxBS)


title: A3-FL-AM technical replicate 7

description: AM, FL, Animal A3, technical replicate 7

value: Large White


title: A3-FL-AM technical replicate 6

description: AM, FL, Animal A3, technical replicate 6


title: placenta (588092_BS)

value: Any post graduate schooling


title: placenta (588092_oxBS)


title: A3-FL-AM technical replicate 5

description: AM, FL, Animal A3, technical replicate 5


title: A3-FL-AM technical replicate 4

description: AM, FL, Animal A3, technical replicate 4


title: placenta (588088_oxBS)


title: A3-FL-AM technical replicate 3

description: AM, FL, Animal A3, technical replicate 3


title: placenta (588088_BS)


title: placenta (588148_BS)


title: A3-FL-AM technical replicate 2

description: AM, FL, Animal A3, technical replicate 2


title: placenta (588048_oxBS)


title: A3-FL-AM technical replicate 1

description: AM, FL, Animal A3, technical replicate 1


title: placenta (588036_BS)


title: A2-FL-AM technical replicate 12

description: AM, FL, Animal A2, technical replicate 12


title: placenta (588032_oxBS)


title: placenta (588036_oxBS)


title: A2-FL-AM technical replicate 10

description: AM, FL, Animal A2, technical replicate 10


title: A2-FL-AM technical replicate 9

description: AM, FL, Animal A2, technical replicate 9


title: A2-FL-AM technical replicate 8

description: AM, FL, Animal A2, technical replicate 8


title: placenta (588032_BS)


title: placenta (588008_oxBS)


title: placenta (587916_BS)


title: A2-FL-AM technical replicate 7

description: AM, FL, Animal A2, technical replicate 7


title: placenta (587844_oxBS)


title: placenta (587844_BS)


title: placenta (587916_oxBS)


title: A2-FL-AM technical replicate 2

description: AM, FL, Animal A2, technical replicate 2


title: A2-FL-AM technical replicate 5

description: AM, FL, Animal A2, technical replicate 5


title: A2-FL-AM technical replicate 1

description: AM, FL, Animal A2, technical replicate 1


title: A2-FL-AM technical replicate 3

description: AM, FL, Animal A2, technical replicate 3


title: placenta (587808_oxBS)


title: placenta (588048_BS)


title: placenta (587824_BS)


title: A1bis-FL-AM technical replicate 11

description: AM, FL, Animal A1bis, technical replicate 11


title: A1bis-FL-AM technical replicate 12

description: AM, FL, Animal A1bis, technical replicate 12


title: Ifnar1ko-1

city: Iowa City

first: Scott

middle: Matthew

last: Lieberman

state: IA

address: 500 Newton Road, 2191A ML

institute: University of Iowa

data_processing:
Reads were demultiplexed and converted from the native Illumina BCL format to fastq format using an in-house python wrapper to Illumina’s ‘bcl2fastq’ conversion utility.
FASTQ data were processed with ‘bcbio’, a best-practices pipeline available at the open-source ‘bcbio-nextgen’ project (https://github.com/chapmanb/bcbio-nextgen; version 1.0.8)
Reads were aligned to mm10 (genome FASTA and annotations derived from ftp://ftp.ensembl.org/pub/release-97/fasta/mus_musculus/) reference genomes using the ultra-rapid ‘hisat2’ aligner (ver 2.1.0)
Concurrently, reads were also quantified against the transcriptome using the ‘salmon’ aligner (ver 0.9.1), yielding estimated counts and values in length-normalized TPM (transcripts per million).
Transcript-level abundances were converted to gene-level counts using the ‘tximport’ package from Bioconductor
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with the counts that have been adjusted for library size factors and gene lengths
Supplementary_files_format_and_content: Matrix table with the raw counts

source_name: lacrimal gland

extract_protocol:
Qiagen Rneasy Plus Mini kit
RNA was prepared for sequencing using Illumina HiSeq 4000

value: NOD

tag: genotype

value: Ifnar1 knockout

tag: Sex

value: male

value: lacrimal gland


title: placenta (588008_BS)

tag: infant sex


title: placenta (587808_BS)

tag: maternal age (years)

value: College graduate


title: placenta (587784_BS)

value: Male

tag: birthweight (grams)


title: placenta (587752_BS)

tag: gestational age (weeks)


title: placenta (587784_oxBS)

tag: mother education


title: A2-FL-AM technical replicate 6

description: AM, FL, Animal A2, technical replicate 6

value: yes

value: FL


title: Def6 WT cOB Og0 rep2

city: NEW YORK

first: Kazuki

last: Inoue

state: New York

address: 535 E70TH STREET, S building 8th floor

institute: HOSPITAL FOR SPECIAL SURGERY

data_processing:
fastp(https://github.com/OpenGene/fastp) was used to evaluate quality of sequenced reads and trim contaminated adaptor portions of sequenced reads.
RNA-seq reads were aligned to the mouse genome (mm10) using HISAT2. HTseq was subsequently used to count reads in features and then edgeR was used to estimate the transcript abundances as CPM (counts per million) values.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample.

source_name: Calvaial bone

growth_protocol: osteoblastic cells were isolated from the calvarial bone of newborn (0-3d) mice by enzymatic digestion in α-MEM with 0.1% collagenase and 0.2% dispase and were cultured in α-MEM medium (ascorbic acid free, Invitrogen)  with 10% FBS (Invitrogen).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions.
NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB) was used to purify poly-A+ transcripts and generate libraries with multiplexed barcode adaptors following the manufacturer’s instructions.

treatment_protocol: Calvarial cells were cultured in osteogenic medium containing α-MEM with 10% FBS supplemented with 100 μg/mL ascorbic acid and 10 mM β-glycerophosphate to induce osteoblast differentiation. The osteogenic media were exchanged every two days.

value: WT


title: A2-FL-AM technical replicate 4

description: AM, FL, Animal A2, technical replicate 4

value: AM


title: A1bis-FL-AM technical replicate 8

description: AM, FL, Animal A1bis, technical replicate 8


title: A1bis-FL-AM technical replicate 9

description: AM, FL, Animal A1bis, technical replicate 9


title: A1bis-FL-AM technical replicate 7

description: AM, FL, Animal A1bis, technical replicate 7


title: placenta (587752_oxBS)

tag: tissue


title: placenta (587732_BS)


title: A1bis-FL-AM technical replicate 6

description: AM, FL, Animal A1bis, technical replicate 6

tag: strain


title: placenta (587716_BS)


title: placenta (587824_oxBS)


title: A1bis-FL-AM technical replicate 5

description: AM, FL, Animal A1bis, technical replicate 5

tag: cell type


title: placenta (587732_oxBS)


title: placenta (587716_oxBS)


title: A1bis-FL-AM technical replicate 3

description: AM, FL, Animal A1bis, technical replicate 3

tag: infected


title: A1bis-FL-AM technical replicate 2

description: AM, FL, Animal A1bis, technical replicate 2

tag: virus


title: A1bis-FL-AM technical replicate 10

description: AM, FL, Animal A1bis, technical replicate 10

tag: original name (to remove)


title: placenta (587708_BS)

value: Female


title: A1bis-FL-AM technical replicate 1

description: AM, FL, Animal A1bis, technical replicate 1

tag: animal id


title: placenta (587708_oxBS)


title: placenta (587692_oxBS)


title: A2-FL-AM technical replicate 11

description: AM, FL, Animal A2, technical replicate 11


title: A3-CTRL-AM technical replicate 12

description: AM, CTRL, Animal A3, technical replicate 12

value: no


title: placenta (587692_BS)

value: Junior college graduate or equivalent


title: placenta (587656_BS)


title: A3-CTRL-AM technical replicate 10

description: AM, CTRL, Animal A3, technical replicate 10


title: placenta (587656_oxBS)


title: A3-CTRL-AM technical replicate 9

description: AM, CTRL, Animal A3, technical replicate 9


title: A3-CTRL-AM technical replicate 8

description: AM, CTRL, Animal A3, technical replicate 8


title: placenta (587644_oxBS)

value: High school graduate


title: A3-CTRL-AM technical replicate 7

description: AM, CTRL, Animal A3, technical replicate 7


title: A1bis-FL-AM technical replicate 4

description: AM, FL, Animal A1bis, technical replicate 4


title: A3-CTRL-AM technical replicate 6

description: AM, CTRL, Animal A3, technical replicate 6


title: placenta (587644_BS)

value: placenta


title: placenta (587640_oxBS)

value: Less than 11th grade


title: A3-CTRL-AM technical replicate 11

description: AM, CTRL, Animal A3, technical replicate 11

value: Large White


title: placenta (587632_BS)

value: Any post graduate schooling


title: A3-CTRL-AM technical replicate 5

description: AM, CTRL, Animal A3, technical replicate 5


title: placenta (587628_oxBS)


title: placenta (587632_oxBS)


title: placenta (587628_BS)


title: A3-CTRL-AM technical replicate 3

description: AM, CTRL, Animal A3, technical replicate 3


title: placenta (587640_BS)


title: A3-CTRL-AM technical replicate 1

description: AM, CTRL, Animal A3, technical replicate 1


title: placenta (587608_oxBS)


title: A2-CTRL-AM technical replicate 10

description: AM, CTRL, Animal A2, technical replicate 10


title: A2-CTRL-AM technical replicate 12

description: AM, CTRL, Animal A2, technical replicate 12


title: A3-CTRL-AM technical replicate 2

description: AM, CTRL, Animal A3, technical replicate 2


title: A3-CTRL-AM technical replicate 4

description: AM, CTRL, Animal A3, technical replicate 4


title: placenta (587608_BS)


title: placenta (587600_BS)


title: A2-CTRL-AM technical replicate 11

description: AM, CTRL, Animal A2, technical replicate 11


title: A2-CTRL-AM technical replicate 9

description: AM, CTRL, Animal A2, technical replicate 9


title: placenta (587588_oxBS)


title: A2-CTRL-AM technical replicate 8

description: AM, CTRL, Animal A2, technical replicate 8


title: placenta (587600_oxBS)


title: placenta (587588_BS)


title: placenta (587516_oxBS)


title: placenta (587516_BS)


title: A2-CTRL-AM technical replicate 6

description: AM, CTRL, Animal A2, technical replicate 6


title: A2-CTRL-AM technical replicate 5

description: AM, CTRL, Animal A2, technical replicate 5


title: placenta (587504_oxBS)


title: A2-CTRL-AM technical replicate 3

description: AM, CTRL, Animal A2, technical replicate 3


title: placenta (587504_BS)


title: placenta (587496_oxBS)


title: placenta (587496_BS)


title: A2-CTRL-AM technical replicate 1

description: AM, CTRL, Animal A2, technical replicate 1


title: placenta (587492_BS)


title: A1-CTRL-AM technical replicate 12

description: AM, CTRL, Animal A1, technical replicate 12


title: placenta (587492_oxBS)


title: placenta (587436_oxBS)


title: A1-CTRL-AM technical replicate 9

description: AM, CTRL, Animal A1, technical replicate 9


title: A2-CTRL-AM technical replicate 7

description: AM, CTRL, Animal A2, technical replicate 7


title: placenta (587428_BS)


title: placenta (587428_oxBS)


title: A1-CTRL-AM technical replicate 6

description: AM, CTRL, Animal A1, technical replicate 6


title: A2-CTRL-AM technical replicate 4

description: AM, CTRL, Animal A2, technical replicate 4


title: A1-CTRL-AM technical replicate 7

description: AM, CTRL, Animal A1, technical replicate 7


title: placenta (587376_oxBS)


title: placenta (587368_BS)


title: A2-CTRL-AM technical replicate 2

description: AM, CTRL, Animal A2, technical replicate 2


title: A1-CTRL-AM technical replicate 5

description: AM, CTRL, Animal A1, technical replicate 5


title: placenta (587368_oxBS)


title: A1-CTRL-AM technical replicate 4

description: AM, CTRL, Animal A1, technical replicate 4


title: A1-CTRL-AM technical replicate 3

description: AM, CTRL, Animal A1, technical replicate 3


title: placenta (587340_BS)


title: A1-CTRL-AM technical replicate 2

description: AM, CTRL, Animal A1, technical replicate 2


title: A1-CTRL-AM technical replicate 1

description: AM, CTRL, Animal A1, technical replicate 1


title: A3-FL-cDC1 technical replicate 12

description: cDC1, FL, Animal A3, technical replicate 12


title: placenta (587340_oxBS)


title: placenta (587436_BS)


title: A3-FL-cDC1 technical replicate 11

description: cDC1, FL, Animal A3, technical replicate 11


title: A1-CTRL-AM technical replicate 11

description: AM, CTRL, Animal A1, technical replicate 11


title: A1-CTRL-AM technical replicate 8

description: AM, CTRL, Animal A1, technical replicate 8


title: placenta (587304_oxBS)


title: placenta (587300_BS)


title: A3-FL-cDC1 technical replicate 10

description: cDC1, FL, Animal A3, technical replicate 10


title: placenta (587300_oxBS)


title: A3-FL-cDC1 technical replicate 9

description: cDC1, FL, Animal A3, technical replicate 9


title: placenta (587376_BS)


title: A3-FL-cDC1 technical replicate 8

description: cDC1, FL, Animal A3, technical replicate 8


title: placenta (587260_BS)


title: A3-FL-cDC1 technical replicate 7

description: cDC1, FL, Animal A3, technical replicate 7


title: A1-CTRL-AM technical replicate 10

description: AM, CTRL, Animal A1, technical replicate 10


title: A3-FL-cDC1 technical replicate 6

description: cDC1, FL, Animal A3, technical replicate 6


title: placenta (587256_BS)


title: A3-FL-cDC1 technical replicate 5

description: cDC1, FL, Animal A3, technical replicate 5


title: placenta (587220_oxBS)


title: A3-FL-cDC1 technical replicate 3

description: cDC1, FL, Animal A3, technical replicate 3


title: placenta (587220_BS)


title: A3-FL-cDC1 technical replicate 2

description: cDC1, FL, Animal A3, technical replicate 2


title: placenta (587304_BS)


title: A3-FL-cDC1 technical replicate 1

description: cDC1, FL, Animal A3, technical replicate 1


title: A3-FL-cDC1 technical replicate 4

description: cDC1, FL, Animal A3, technical replicate 4


title: A2-FL-cDC1 technical replicate 12

description: cDC1, FL, Animal A2, technical replicate 12


title: placenta (587176_BS)


title: A2-FL-cDC1 technical replicate 11

description: cDC1, FL, Animal A2, technical replicate 11


title: placenta (587176_oxBS)


title: placenta (587212_oxBS)


title: placenta (587160_BS)


title: A2-FL-cDC1 technical replicate 10

description: cDC1, FL, Animal A2, technical replicate 10


title: placenta (587260_oxBS)


title: placenta (587160_oxBS)


title: placenta (587144_BS)


title: A2-FL-cDC1 technical replicate 9

description: cDC1, FL, Animal A2, technical replicate 9


title: placenta (587144_oxBS)


title: placenta (587256_oxBS)


title: placenta (587236_oxBS)


title: A2-FL-cDC1 technical replicate 8

description: cDC1, FL, Animal A2, technical replicate 8


title: placenta (587236_BS)


title: Chromatin_fraction_unlabeled_52R

city: Goettingen

first: Anna

last: Sawicka

address: Am Fassberg 11

department: Dep. of Molecular Biology

country: Germany

institute: Max Planck Institure for Biophysical Chemistry

description:
U2OS cells expressing RPB1-CTD with 52 repeats (Boehning et al 2018), no treatment
chromatin associated polyA-RNA

data_processing:
Long-read sequencing:Direct RNA Nanopore sequencing reads were obtained one replicate of RPB1-52R cells and RPB1-25R cells.  FAST5 files were base-called using Guppy 3.1.5 (Oxford Nanopore Technologies) with the following parameters: guppy_basecaller -i fast5 -s basecalled --num_callers 1 --cpu_threads_per_caller 12 -c rna_r9.4.1_70bps_hac.cfg -r --fast5_out --calib_detect --u_substitution on -q 0. Direct RNA nanopore sequencing reads were mapped with minimap2 2.10 (Li, 2016) to the GRCh38/hg38 genome assembly (Human Genome Reference Consortium) with the following parameters: minimap2 -ax splice -k14 --secondary=no. SAMtools 1.3.1 (Li et al, 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 20 (-q 20) were skipped.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigWig coverage files

source_name: U2OS osteosarcoma cells

growth_protocol: Human osteosarcoma U2OS cells (wild-type) were obtained from the Darzacq laboratory (Boehning et al, 2018). U2OS cells expressing CTD mutants were generated in the Darzacq laboratory (Boehning et al, 2018). RPB1-52R cells stably express RPB1 protein containing N-terminal HALO tag, N792D mutation conferring a-amanitin resistance and 52 CTD repeats present in the endogenous, wild type RPB1.  RPB1-25R mutant cells express only 25 repeats present in the wild type RPB1, which correspond to repeats 1-21 and 49-52. The cells are grown in DMEM(1X)+GlutaMAX-I medium (Gibco, #21885-025) with 10% FBS (Gibco, #10500-064) in the presence 100 U/ml of Penicillin-Streptomycin (Thermo Fisher, #15140122) in a humidified incubator with 5% CO2 at 37oC. Mutant cells we cultured with 1 ug/ml of a-Amanitin (Sigma-Aldrich, #A2263)

extract_protocol:
Isolation of chromatin associated RNA was performed as described (Conrad & Ørom, 2017) using  6 x 107 U2OS cells per replicate. One biological replicate was prepared. RNA isolated from the chromatin fraction was subject to purification of polyadenylated RNA using Dynabeads mRNA Purification kit (Thermo Fisher, #61006) according to manufacturer’s instructions. Two increase the purity of mRNA, two rounds of purification were performed for each sample. 500 ng of mRNA was converted into a sequencing library using Direct RNA Sequening kit (Oxford Nanopore, #SQK-RNA002) according to manufacturer’s instructions. Reverse transcription reaction step was omitted. The libraries were loaded onto previously primed SpotON flowcells and sequenced using MinION device (Oxford Nanopore).
Direct RNA Sequening kit (Oxford Nanopore, #SQK-RNA002)
direct RNA-seq of polyadenylated RNA

value: RPB1-CTD with 52 repeats


title: placenta (587108_BS)


title: placenta (587132_BS)


title: A2-FL-cDC1 technical replicate 7

description: cDC1, FL, Animal A2, technical replicate 7


title: iMoP_sorted1

type: RNA

city: Freiburg

first: Anne

last: Loesslein

address: Breisacherstr. 115

department: CCI

institute: Universität Freiburg

description: mouse bone marrow, iMoP

hyb_protocol: Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip Pico Reagent Kit User Guide (Affymetrix, Inc., Santa Clara, CA, USA).

scan_protocol: Fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.1.3 software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the GCCN-SST-RMA algorithm with the Affymetrix GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P values were calculated. Probe sets with a fold change above 2.0 fold and a student’s t test P value lower than 0.05 were considered as significantly regulated.

label: biotin

source_name: mouse bone marrow, iMoP

label_protocol: Purified ds cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the dUTP residues followed by a terminal labeling with biotin.

growth_protocol: animal facilities of the University of Freiburg under specific pathogen-free conditions

extract_protocol: Bones were flushed with full medium. Cells were extracted from bone marrow by magnetic cell separation and fluorescence-activated cell sorting. Total RNA was extracted from sorted cells with the Rneasy Micro Kit (Qiagen) as per manufacturer's instructions.

treatment_protocol: no treatment


title: placenta (587212_BS)


title: iMoP_sorted2

description: mouse bone marrow, iMoP


title: placenta (587108_oxBS)


title: A2-FL-cDC1 technical replicate 6

description: cDC1, FL, Animal A2, technical replicate 6


title: Chromatin_fraction_unlabeled_25R

description:
U2OS cells expressing RPB1-CTD with 25 repeats (Boehning et al 2018) , no treatment
chromatin associated polyA-RNA

value: RPB1-CTD with 25 repeats


title: placenta (587080_oxBS)


title: cMoP_sorted1

description: mouse bone marrow, cMoP

source_name: mouse bone marrow, cMoP


title: cMoP_sorted2

description: mouse bone marrow, cMoP


title: Co-THP1_II

city: Ribeirão Preto

first: Ana

middle: Lucia

last: Fachin

state: SP

address: Av. Costabile Romano, 2201

department: Biotechonology  Unit

country: Brazil

institute: Unaerp

description: miRNA

data_processing:
FastQC v0.11.2 was used to visualize the libraries quality before and after trimming.
TRIM GALORE! was used to remove adapters, low quality regions and sequences of less than 17 nucleotides.
Filtered reads were mapped onto the human genome (hg38) using the Bowtie.
HTSeq was used to obtain read counts. A GTF containing pre-miRNAs annotations (mirBase - Release 22.1) was used.
Differentially expressed genes were determined with EdgeR in R using HTSeq counts from the all reads analysis and a FDR < 0.05 as the significance cutoff.
Target genes of miRNAs were obtained from the recorded pairs in miRTarBase database.
In order to discuss the relationship between miRNAs from modulated macrophages and the pathogenicity of T.rubrum, the databases miRBase, miRTarBase and PantherDB were used.
Genome_build: Human genome (hg38), Broad T. rubrum strain CBS118892 genome.
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each sample and EdgeR output in TXT format containing logFC, logCPM, LR and p value.

organism:
Trichophyton rubrum
Homo sapiens

source_name: Co-culture, replicate II

growth_protocol: The Trichophyton rubrum strain CBS 118892 was cultured on Sabouraud dextrose agar for 15 days at 28ºC. Keratinocytes were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS) at 37ºC in a humidified atmosphere containing 5% CO2.

extract_protocol:
RNA extraction of T. rubrum and  THP-1 were performed using an Illustra RNAspin Mini RNA Isolation according to GE Healthcare guidelines.
Micro RNA libraries were prepared for sequencing according to Illumina guidelines.

treatment_protocol: Pre-cultured conidia and heat inactive of T. rubrum were added to THP-1 cell line and the co-culture was incubated for 24 h at 37ºC in a humidified atmosphere containing 5% CO2.

tag: human cell line


title: Co-THP1_III

description: miRNA

source_name: Co-culture, replicate III


title: placenta (587044_oxBS)


title: placenta (587028_BS)


title: A2-FL-cDC1 technical replicate 5

description: cDC1, FL, Animal A2, technical replicate 5


title: placenta (587132_oxBS)


title: placenta (587080_BS)


title: placenta (587028_oxBS)


title: Co-THP1_I

description: miRNA

source_name: Co-culture, replicate I


title: placenta (586968_BS)


title: A2-FL-cDC1 technical replicate 3

description: cDC1, FL, Animal A2, technical replicate 3


title: placenta (586968_oxBS)


title: A2-FL-cDC1 technical replicate 2

description: cDC1, FL, Animal A2, technical replicate 2


title: NOPRIMARY TSA-seq Pulldown Replicate2

city: Philadelphia

first: Katherine

middle: A

last: Alexander

address: Smilow Center for Translational Research

institute: University of Pennsylvania

data_processing:
Library strategy: SON TSA-seq
Demultiplexed paired-end fastq files were aligned to the hg19 genome using Bowtie2 with a maximum fragment length of 1000 base pairs (-X 1000) and otherwise default conditions.
SAM files were converted to BAM files using samtools-1.1 function samtools view, BAM files were sorted using samtools sort (samtools sort -n -@ 4 -m 1G -O bam -o sorted.bam -T prefix bamFile), and duplicate reads were removed using Picard MarkDuplicates (with REMOVE_DUPLICATES=True and ASSUME_SORT_ORDER=queryname)
Input-subtracted SON TSA-seq signal was quantified and significance was determined across sliding windows of different sizes (25kb, 50kb, 100kb, and 500kb) using DiffBind (https://github.com/katealexander/TSAseq-Alexander2020/tree/master/genomicBins_DiffBind)
Significant domains with various adjusted p-values were extracted from DiffBind results, and domains were merged using bedtools sort and bedtools merge (https://github.com/katealexander/TSAseq-Alexander2020/tree/master/genomicBins_DiffBind). The text file, genes_sigUp_25to100_padj0.01.txt contains a list of genes that were within significantly increasing SON bins between Nutlin and DMSO with an adjusted p-value of less than 0.01 from sliding windows of 25kb, 50kb, and 100kb
A list of genes with transcription start sites within significantly changing domains was extracted using python (https://github.com/katealexander/TSAseq-Alexander2020/tree/master/genomicBins_DiffBind).
Genome_build: hg19
Supplementary_files_format_and_content: DiffBind results text files (starting with "DiffBindResults_") of 9 sliding 25kb, 50kb, 100kb, and 500kb windows
Supplementary_files_format_and_content: Gene list text files (starting with "genes_") containing the genes that increase SON signal from 25kb, 50kb, and 100kb merged DiffBind binds at different adjusted p-value cutoffs designated at the end of the file name, before ".txt"
Supplementary_files_format_and_content: Text file list of IMR90 p53 targets (defined using https://github.com/katealexander/TSAseq-Alexander2020/tree/master/IMR90_p53targets)
Supplementary_files_format_and_content: Text file lists of IMR90 p53 targets that do ("IMR90_p53targs_upSONpadj0.01.txt") or do not ("IMR90_p53targs_nsSONpadjOver0.1.txt") increase SON signal upon Nutlin treatment.
Supplementary_files_format_and_content: bigWig files (ending in ".bw") for USCS genome browser veiwing of input-subtracted SON TSA-seq and no primary experiments.
Supplementary_files_format_and_content: BED files (ending in ".bed") of merged domains that increase SON signal upon Nutlin treatment called at 25kb, 50kb, and 100kb window sizes with different DiffBind adjusted p-value cutoffs

growth_protocol: Proliferative IMR90 cells were grown in 3% oxygen at 37C in DMEM media with 10% FBS

extract_protocol:
Pulldown and input DNA was prepared using the SON TSA-seq protocol according to Condition E from https://www.biorxiv.org/content/10.1101/824433v2.full, with DNA sheared to an average 250bp size using a Covaris S220 as in ChIP-seq protocols.
Libraries were prepared from sheared DNA using the NEBnext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: Cells were treated at 1:1000 with DMEM or Nutlin-3a for 6 hours for a final concentration of 5uM Nutlin from a 5mM DMSO-dissolved stock solution.

tag: treatment

value: Untreated


title: placenta (586932_BS)


title: placenta (586932_oxBS)


title: NOPRIMARY TSA-seq Input Replicate2


title: A2-FL-cDC1 technical replicate 1

description: cDC1, FL, Animal A2, technical replicate 1


title: placenta (586912_oxBS)

value: College graduate


title: placenta (586912_BS)


title: A1-FL-cDC1 technical replicate 12

description: cDC1, FL, Animal A1, technical replicate 12


title: placenta (586868_oxBS)

value: Male


title: NOPRIMARY TSA-seq Pulldown Replicate1


title: placenta (587044_BS)


title: placenta (586868_BS)


title: NOPRIMARY TSA-seq Input Replicate1


title: placenta (586796_BS)


title: A2-FL-cDC1 technical replicate 4

description: cDC1, FL, Animal A2, technical replicate 4

value: yes


title: NUTLIN SON TSA-seq Pulldown Replicate2

value: NUTLIN


title: A1-FL-cDC1 technical replicate 11

description: cDC1, FL, Animal A1, technical replicate 11

value: FL


title: NUTLIN SON TSA-seq Input Replicate2


title: placenta (586788_BS)


title: placenta (586788_oxBS)


title: placenta (586796_oxBS)


title: placenta (586780_BS)


title: NUTLIN SON TSA-seq Pulldown Replicate1


title: NUTLIN SON TSA-seq Input Replicate1


title: placenta (586748_oxBS)


title: placenta (586748_BS)


title: placenta (586780_oxBS)


title: placenta (586744_BS)


title: DMSO SON TSA-seq Pulldown Replicate2

value: DMSO


title: DMSO SON TSA-seq Pulldown Replicate1


title: DMSO SON TSA-seq Input Replicate2


title: A1-FL-cDC1 technical replicate 5

description: cDC1, FL, Animal A1, technical replicate 5


title: A1-FL-cDC1 technical replicate 6

description: cDC1, FL, Animal A1, technical replicate 6


title: A1-FL-cDC1 technical replicate 9

description: cDC1, FL, Animal A1, technical replicate 9


title: A1-FL-cDC1 technical replicate 7

description: cDC1, FL, Animal A1, technical replicate 7


title: A1-FL-cDC1 technical replicate 10

description: cDC1, FL, Animal A1, technical replicate 10


title: A1-FL-cDC1 technical replicate 4

description: cDC1, FL, Animal A1, technical replicate 4


title: A1-FL-cDC1 technical replicate 8

description: cDC1, FL, Animal A1, technical replicate 8


title: DMSO SON TSA-seq Input Replicate1


title: placenta (586628_oxBS)


title: placenta (586744_oxBS)

value: Female


title: placenta (586628_BS)


title: placenta (586700_BS)


title: placenta (586516_BS)


title: placenta (586532_oxBS)


title: placenta (586700_oxBS)


title: DG-S22_S31

city: University Park

first: David

middle: Asher

last: Galbraith

address: 19a Chemical Ecology Lab

institute: Penn State University

data_processing:
We removed adaptor sequences, reads composed of more than 5% unknown nucleotides, and reads with more than 20% of the base qualities under 10.
The transcriptome sequencing reads were aligned to the Amel_4.5 honey bee genome assembly using Hisat2
The data was normalized using a trimmed mean of M-values (TMM) method.
The LIMMA package in R was used to identify significantly differentially expressed genes.
The transcriptome sequencing reads were also aligned to pseudo-parent genomes (reference genome with parental SNPs included, one for paternal and one for maternal) allowing 0 mismatches with Hisat2 to look at parent specific gene expression.  This data can be found in PSGE_Sterile_reads.txt and PSGE_Reproductive_reads.txt
Genome_build: Amel4.5
Supplementary_files_format_and_content: PSGE_gene_expression.txt contains the gene expression data for each individual. PSGE_sterile.txt contains read counts for each sterile individual at each parental snp. PSGE_reproductive.txt contains read counts for each reproductive  individual at each parental snp.

molecule: polyA RNA

organism: Apis mellifera

source_name: Honey bee brain

growth_protocol: Individuals from reciprocal crosses of Africanized and European honey bees were raised in queenless colonies for ~18 days, allowing time for the workers to activate the ovaries and become reproductively active.

extract_protocol:
Brains from individual bees were lyophilized and dissected in RNAlater® (Qiagen, Valencia, CA) on dry ice and excess RNAlater® was removed from the samples.  RNA was isolated using TRIzol® Reagent (Invitrogen, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: reproductive status

value: Sterile

tag: lineage

tag: genotype (maternal x paternal)

value: Afr x Eur

tag: block

value: B


title: A1-FL-cDC1 technical replicate 1

description: cDC1, FL, Animal A1, technical replicate 1


title: A1-FL-cDC1 technical replicate 2

description: cDC1, FL, Animal A1, technical replicate 2


title: DG-S23_S32


title: DG-S24_S33


title: A1-FL-cDC1 technical replicate 3

description: cDC1, FL, Animal A1, technical replicate 3


title: A3-CTRL-cDC1 technical replicate 12

description: cDC1, CTRL, Animal A3, technical replicate 12

value: no


title: DG-S21_S30

value: Reproductive


title: DG-S20_S29


title: A3-CTRL-cDC1 technical replicate 11

description: cDC1, CTRL, Animal A3, technical replicate 11

value: Large White


title: A3-CTRL-cDC1 technical replicate 10

description: cDC1, CTRL, Animal A3, technical replicate 10


title: placenta (586464_oxBS)

tag: infant sex

tag: maternal age (years)

value: placenta


title: placenta (586404_BS)

tag: birthweight (grams)

tag: gestational age (weeks)

value: Junior college graduate or equivalent


title: placenta (586480_oxBS)

tag: mother education

value: Any post graduate schooling

tag: tissue


title: placenta (586496_BS)


title: placenta (586404_oxBS)


title: placenta (586496_oxBS)


title: placenta (586460_BS)


title: placenta (586516_oxBS)


title: placenta (586452_oxBS)


title: placenta (586464_BS)


title: placenta (586452_BS)


title: placenta (586460_oxBS)


title: DG-S18_S27

value: Eur x Afr


title: A3-CTRL-cDC1 technical replicate 9

description: cDC1, CTRL, Animal A3, technical replicate 9

tag: strain

tag: cell type


title: placenta (586480_BS)


title: A3-CTRL-cDC1 technical replicate 8

description: cDC1, CTRL, Animal A3, technical replicate 8

tag: infected

tag: virus


title: placenta (586396_oxBS)


title: placenta (586532_BS)

value: College graduate


title: placenta (586396_BS)

value: Male


title: placenta (586392_BS)


title: DG-S17_S26


title: DG-S16_S25


title: placenta (586388_oxBS)


title: DG-S15_S24


title: A3-CTRL-cDC1 technical replicate 7

description: cDC1, CTRL, Animal A3, technical replicate 7

tag: original name (to remove)

tag: animal id


title: A3-CTRL-cDC1 technical replicate 4

description: cDC1, CTRL, Animal A3, technical replicate 4


title: A3-CTRL-cDC1 technical replicate 3

description: cDC1, CTRL, Animal A3, technical replicate 3


title: DG-S11_S20

value: A


title: DG-S13_S22


title: A3-CTRL-cDC1 technical replicate 5

description: cDC1, CTRL, Animal A3, technical replicate 5


title: placenta (586372_BS)

value: High school graduate


title: placenta (586380_oxBS)


title: DG-S14_S23


title: A3-CTRL-cDC1 technical replicate 6

description: cDC1, CTRL, Animal A3, technical replicate 6


title: DG-S10_S19


title: DG-S12_S21


title: placenta (586364_oxBS)


title: placenta (586292_BS)


title: placenta (586292_oxBS)


title: placenta (586336_BS)


title: placenta (586364_BS)


title: placenta (586380_BS)


title: placenta (586392_oxBS)


title: A3-CTRL-cDC1 technical replicate 1

description: cDC1, CTRL, Animal A3, technical replicate 1


title: placenta (586336_oxBS)


title: A3-CTRL-cDC1 technical replicate 2

description: cDC1, CTRL, Animal A3, technical replicate 2


title: placenta (586388_BS)


title: DG-S9_S18


title: placenta (586280_oxBS)


title: A2-CTRL-cDC1 technical replicate 12

description: cDC1, CTRL, Animal A2, technical replicate 12


title: A2-CTRL-cDC1 technical replicate 11

description: cDC1, CTRL, Animal A2, technical replicate 11


title: placenta (586372_oxBS)


title: placenta (586228_oxBS)


title: DG-S8_S17


title: placenta (586228_BS)


title: placenta (586220_BS)


title: A2-CTRL-cDC1 technical replicate 9

description: cDC1, CTRL, Animal A2, technical replicate 9


title: DG-S6_S15


title: A2-CTRL-cDC1 technical replicate 8

description: cDC1, CTRL, Animal A2, technical replicate 8


title: DG-S5_S14


title: placenta (586268_BS)


title: placenta (586220_oxBS)


title: A2-CTRL-cDC1 technical replicate 10

description: cDC1, CTRL, Animal A2, technical replicate 10


title: DG-S7_S16


title: placenta (586156_BS)


title: A2-CTRL-cDC1 technical replicate 7

description: cDC1, CTRL, Animal A2, technical replicate 7


title: placenta (586268_oxBS)


title: DG-S4_S13


title: placenta (586156_oxBS)


title: placenta (586280_BS)


title: placenta (586148_oxBS)


title: placenta (586148_BS)


title: placenta (586144_oxBS)


title: DG-S3_S12


title: placenta (586144_BS)


title: A2-CTRL-cDC1 technical replicate 5

description: cDC1, CTRL, Animal A2, technical replicate 5


title: DG-S2_S11


title: A2-CTRL-cDC1 technical replicate 4

description: cDC1, CTRL, Animal A2, technical replicate 4


title: placenta (586120_BS)


title: placenta (586140_oxBS)


title: DG-S1_S10


title: A2-CTRL-cDC1 technical replicate 3

description: cDC1, CTRL, Animal A2, technical replicate 3


title: placenta (586120_oxBS)


title: Embryonic Day 13 Murine Fetal Lung

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

data_processing:
The sample was processed using the standard Cellranger v.3 pipeline
Reads were mapped to GRCm38
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Genome_build: GRCm38
Supplementary_files_format_and_content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

source_name: Wild Type C57/BL6 Mice

extract_protocol:
Cell sorting was conducted on a Beckman MoFlo Coulter Astrios. Isolated primary cells were stained with CD41-APC and resuspended in a sort buffer (2% BSA in PBS) containing Calcein Blue AM (1:1000). Live-singlets and the top 1% of CD41-APC+ events were sorted into sort buffer. Cells counts and viability after sorting was confirmed by hemocytometer using trypan blue.
Isolated cells were single cell captured using the 10X Genomics Chromium platform and prepared using the Single Cell 3’ v3 kit. Library preparation and sequencing was done using the Illumina NextSeq 500 instrument.

tag: developmental stage

value: Embryonic Day 13

tag: genotype

value: Wild Type

tag: isolation method

value: enriched for live-CD41+ cells by flow cytometry


title: placenta (586096_BS)


title: placenta (586096_oxBS)


title: Embryonic Day 13 Murine Fetal Liver


title: A2-CTRL-cDC1 technical replicate 2

description: cDC1, CTRL, Animal A2, technical replicate 2


title: placenta (586024_oxBS)

value: Female


title: placenta (586060_BS)


title: placenta (586024_BS)


title: Week 10 Murine Adult Lung

value: Week 10


title: placenta (586012_oxBS)


title: A1-CTRL-cDC1 technical replicate 12

description: cDC1, CTRL, Animal A1, technical replicate 12


title: placenta (586140_BS)


title: Week 10 Murine Adult Bone Marrow


title: A2-CTRL-cDC1 technical replicate 6

description: cDC1, CTRL, Animal A2, technical replicate 6


title: DG-S19_S28

tag: reproductive status

tag: lineage

tag: genotype (maternal x paternal)

value: Afr x Eur

value: B


title: placenta (585944_BS)

tag: infant sex

tag: maternal age (years)


title: placenta (585944_oxBS)

tag: birthweight (grams)

tag: gestational age (weeks)


title: Sample 40_Single Cells_10xGenomics_IEL

city: New York

first: Tiago

last: Castro

address: 1230 York Avenue

institute: The Rockefeller University

description:
Gene Expression
IEL_S3_L003

data_processing:
The raw bulk ATAC-Seq files were processed using the ENCODE-DCC pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) automated through Cromwell (https://github.com/broadinstitute/cromwell). Shortly, adapter sequences were trimmed (Cutadapt) prior to genome map with Bowtie2. Subsequently, mapped reads were filtered with Samtools. Next, sequencing enriched regions, associated to chromatin accessible peaks were called with MACS2 and filtered by running IDR, Irreproducible Discovery Rate, algorithm with a 10% threshold. Later, filtered peak regions were annotated by using HOMER software tools.
The raw bulk ChIP-Seq files were processed using the ENCODE-DCC pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2) automated through Cromwell (https://github.com/broadinstitute/cromwell). Shortly, adapter sequences were trimmed by Cutadapt prior to the genome mapping with BWA and filtered subsequently using Samtools. Next, sequencing enriched regions associated to the transcription factor binding sites were called with SPP and filtered by running IDR, Irreproducible Discovery Rate, algorithm with a 5% threshold. Later, filtered peak regions were annotated by the HOMER software suite of tools. Comprehensive motif screening was performed with MEME-ChIP by using promoter originated, length-normalized reads to a 500 kb.
The raw fastq sequencing files were processed together with the gencode mouse annotation database (v. M21), by running kallisto (v. 0.46.0) to calculate the transcript abundances. Next, the abundance files were submitted to the sleuth (v. 0.30.0) pipeline based on R, for transcript abundance normalization, gene expression analysis and statistics. The quantified transcripts were combined into genes for the downstream analysis. Batch effects were evaluated through principal component analysis and removed with Limma. To capture significantly expressed genes we performed a likelihood ratio test between a null model and our experimental design using an adjusted p-value of 0.05 as threshold. The selected features were clustered using k-means and represented as a heatmap to define group gene signatures. Pairwise comparisons between groups were performed using the Wald-test and significant genes were considered for downstream analysis by having an adjusted p-value smaller than 0.05 and a log2 foldchange of 1.
The single cell RNA-Seq fastq files originated from the Chromium 10x libraries were processed with Cell Ranger (v. 3.0.2) for cell barcode aggregation, genome alignment, and UMI transcript quantification. The matrix of gene counts was analyzed with the Seurat (v. 3.1.2) package for the R environment. For downstream analysis, the top 3000 genes containing the highest standardized variance and expression were pre-selected. The detected cell clusters were visualized by performing Uniform Manifold Approximation and Projection (UMAP) algorithm. Cluster signatures were determined by the Wilcoxon Rank Sum test and genes containing adjusted p-values smaller than 0.01 were considered significant. For pseudotime trajectory analysis, the Seurat dataset was converted into a ‘SingleCellExperiment’ object and used within Slingshot and Monocle.
Genome_build: mm10
Supplementary_files_format_and_content: tsv: kallisto abundances
Supplementary_files_format_and_content: h5: kallisto abundances and bootstrap estimates for sleuth
Supplementary_files_format_and_content: 10x mtx: UMI counts
Supplementary_files_format_and_content: 10x features.tsv: feature names
Supplementary_files_format_and_content: 10x barcodes.tsv: single cell barcodes
Supplementary_files_format_and_content: bb:  Indexed binary files containing annotated peaks
Supplementary_files_format_and_content: narrowpeak: text (BED6+4) files containing annotated peaks
Supplementary_files_format_and_content: bed: interval file containing annotated chip peaks
Supplementary_files_format_and_content: bigwig: Indexed binary files containing dense continuous data of read mapping

source_name: Single Cells_10xGenomics_IEL

extract_protocol:
Atac-Seq: ATAC-Seq was performed on 5,000-40,000 FACS-purified cells from 2-9 mice. In brief, cells were lysed in lysis buffer for 1 minute and transposed with Tagment DNA Enzyme 1 (Illumina) for 30 minutes. DNA was cleaned up using a MinElute DNA purification Kit (Qiagen), followed by barcoding and library preparation by the Nextera DNA Library preparation kit (Illumina) according to manufacturer’s guidelines and sequenced on an Illumina Illumina NextSeq 500.
ChIP-Seq: Cells were fixed in 1% formaldehyde for 20min, quenched with 0.15M glycine and washed in PBS. 2x106 were then sorted and lysed for 30min at 4ºC. Cells were then sonicated for 22 minutes at 30 seconds on/off using the Bioruptor sonicator (Diagenode) and spun down. 10% was frozen for input, the remaining 90% was incubated with anti-ThPOK antibody bound to goat anti-rabbit M280 magnetic beads (Invitrogen) overnight at 4ºC prior to washing with RIPA buffer and overnight decrosslinking at 65ºC. DNA was then eluted off beads into TE buffer and, along with input, purified using the Zymogen DNA clean & concentrator kit. DNA was sequenced using NextSeq2500. To obtain Tregs, Foxp3RFP reporter mice were injected with IL-2/aIL-2 complex as previously described for 3 consecutive days for Treg expansion. CD4+ T cells were isolated from the spleen and mLNs and sorted as Thy1+TCRb+CD4+CD8a–RFP+.
RNA-Seq: Sorted cells (300-800) were lysed in TCL buffer (Qiagen, 1031576) supplemented with 1% βmercaptoethanol. RNA was isolated using RNAClean XP beads (Agentcourt, A63987), reversibly transcribed, and amplified. Uniquely barcoded libraries were prepared using Nextera XT kit (Illumina) following manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq 550.
Single Cell Sequencing: Lymphocytes were sorted, counted for viability and immediately subjected to library preparation. The scRNA-Seq library was prepared using the 10x Single Cell Chromium system, according to the manufacturer’s instructions at the Genomics core of Rockefeller University and was sequenced on an Illumina NextSeq 550 to a minimum sequencing depth of 50,000 reads per cell using read lengths of 26 bp read 1, 8 bp i7 index, 98 bp read 2.

tag: strain background

tag: mouse id

tag: Sex

value: Single cells from intestinal epithelium


title: placenta (585868_BS)

tag: mother education

tag: tissue


title: A1-CTRL-cDC1 technical replicate 11

description: cDC1, CTRL, Animal A1, technical replicate 11

tag: strain

value: Large White

tag: cell type

tag: infected

value: no

tag: virus

tag: original name (to remove)


title: A2-CTRL-cDC1 technical replicate 1

description: cDC1, CTRL, Animal A2, technical replicate 1

tag: animal id


title: Sample 39_Single Cells_10xGenomics_LPL

description:
Gene Expression
LPL_S2_L002

source_name: Single Cells_10xGenomics_LPL

tag: genotype

value: Single cells from intestinal lamina propria


title: placenta (586012_BS)

value: placenta


title: placenta (585868_oxBS)

value: Any post graduate schooling


title: placenta (585864_BS)


title: A1-CTRL-cDC1 technical replicate 9

description: cDC1, CTRL, Animal A1, technical replicate 9


title: placenta (585832_BS)

value: Junior college graduate or equivalent


title: placenta (585864_oxBS)

value: Male


title: Sample 38_Single Cells_10xGenomics_MLN

description:
Gene Expression
MLN_S1_L001

source_name: Single Cells_10xGenomics_MLN

value: Single cells from mesenteric lymph node


title: A1-CTRL-cDC1 technical replicate 8

description: cDC1, CTRL, Animal A1, technical replicate 8


title: placenta (585860_BS)

value: College graduate


title: A1-CTRL-cDC1 technical replicate 7

description: cDC1, CTRL, Animal A1, technical replicate 7


title: placenta (585828_BS)


title: placenta (585800_oxBS)

source_name: human placenta, oxidative bisulfite converted


title: A1-CTRL-cDC1 technical replicate 6

description: cDC1, CTRL, Animal A1, technical replicate 6


title: A1-CTRL-cDC1 technical replicate 4

description: cDC1, CTRL, Animal A1, technical replicate 4


title: A1-CTRL-cDC1 technical replicate 10

description: cDC1, CTRL, Animal A1, technical replicate 10


title: placenta (585800_BS)


title: placenta (585796_BS)

value: High school graduate


title: Sample 23_RNASeq_iTreg-MLN

description:
Gene Expression
C*.mLN_iTreg_16WT_m1

value: iTreg-MLN


title: placenta (585828_oxBS)


title: Sample 24_RNASeq_iTreg-MLN

description:
Gene Expression
C*.mLN_iTreg_17WT_m3


title: Sample 22_RNASeq_iTreg-IEL

description:
Gene Expression
C*.IEL_iTreg_4WT_m1

value: iTreg-IEL


title: placenta (585796_oxBS)


title: Sample 25_RNASeq_iTreg-MLN

description:
Gene Expression
WT_mLN_iTreg21_S3

value: Female


title: placenta (585792_BS)


title: A1-CTRL-cDC1 technical replicate 5

description: cDC1, CTRL, Animal A1, technical replicate 5


title: placenta (585860_oxBS)


title: Sample 26_RNASeq_FFiexTreg-IEL

description:
Gene Expression
C*.exTregIEL_2FF_m4

value: exTreg-IEL


title: Sample 21_RNASeq_iTreg-IEL

description:
Gene Expression
C*.IEL_iTreg_9WT_m3


title: placenta (586060_oxBS)


title: A1-CTRL-cDC1 technical replicate 3

description: cDC1, CTRL, Animal A1, technical replicate 3


title: placenta (585792_oxBS)


title: placenta (585832_oxBS)


title: A1-CTRL-cDC1 technical replicate 2

description: cDC1, CTRL, Animal A1, technical replicate 2


title: Sample 20_RNASeq_iTreg-IEL

description:
Gene Expression
WT_IE_iTreg1_S5


title: placenta (585756_oxBS)


title: Sample 19_RNASeq_exTreg-IEL

description:
Gene Expression
WT_exTregIEL7_S2


title: placenta (585760_oxBS)


title: placenta (585756_BS)


title: A1-CTRL-cDC1 technical replicate 1

description: cDC1, CTRL, Animal A1, technical replicate 1


title: Sample 18_RNASeq_exTreg-IEL

description:
Gene Expression
C*.exTregIEL_3WT_m3


title: Sample 17_RNASeq_Pre-IEL

description:
Gene Expression
WT_preIEL6_S1

value: preIEL


title: placenta (585684_oxBS)


title: placenta (585732_BS)


title: Sample 16_RNASeq_Pre-IEL

description:
Gene Expression
WT_preIEL2_S4


title: placenta (585716_oxBS)


title: placenta (585716_BS)


title: placenta (585732_oxBS)


title: placenta (585684_BS)


title: A3-FL-cDC2 technical replicate 11

description: cDC2, FL, Animal A3, technical replicate 11

value: yes

value: FL


title: A3-FL-cDC2 technical replicate 10

description: cDC2, FL, Animal A3, technical replicate 10

value: Large White


title: A3-FL-cDC2 technical replicate 8

description: cDC2, FL, Animal A3, technical replicate 8


title: placenta (585672_BS)


title: placenta (585596_oxBS)

value: Less than 11th grade


title: placenta (585672_oxBS)


title: A3-FL-cDC2 technical replicate 9

description: cDC2, FL, Animal A3, technical replicate 9


title: placenta (585596_BS)


title: A3-FL-cDC2 technical replicate 7

description: cDC2, FL, Animal A3, technical replicate 7


title: placenta (585576_oxBS)


title: Sample 13_RNASeq_CD4-IEL

description:
Gene Expression
C*.CD4IEL_2WT_m1


title: Sample 15_RNASeq_CD4-IEL

description:
Gene Expression
C*.CD4IEL_7aWT_m3


title: A3-FL-cDC2 technical replicate 12

description: cDC2, FL, Animal A3, technical replicate 12


title: placenta (585576_BS)


title: Sample 14_RNASeq_CD4-IEL

description:
Gene Expression
WT_CD4IEL4_S6


title: A3-FL-cDC2 technical replicate 6

description: cDC2, FL, Animal A3, technical replicate 6


title: Sample 12_ATAC_FFiTreg-IEL

description:
Accessible chromatin
FFATAC_iTreg12_S11

value: pooled male and female

tag: pooled sample info.

value: iTreg


title: placenta (585568_BS)

tag: infant sex

value: Any post graduate schooling

value: placenta


title: A3-FL-cDC2 technical replicate 5

description: cDC2, FL, Animal A3, technical replicate 5


title: placenta (585540_oxBS)

tag: maternal age (years)


title: Sample 11_ATAC_FFiTreg-IEL

description:
Accessible chromatin
Treg-1_S2


title: placenta (585760_BS)

tag: birthweight (grams)

value: Junior college graduate or equivalent


title: placenta (585540_BS)

tag: gestational age (weeks)


title: Sample 10_ATAC_FFextreg-IEL

description:
Accessible chromatin
FFATAC_exTregIEL12_S12

tag: strain background


title: placenta (585524_oxBS)


title: A3-FL-cDC2 technical replicate 4

description: cDC2, FL, Animal A3, technical replicate 4


title: placenta (585504_BS)


title: placenta (585504_oxBS)


title: A3-FL-cDC2 technical replicate 3

description: cDC2, FL, Animal A3, technical replicate 3


title: Sample 9_ATAC_FFextreg-IEL

description:
Accessible chromatin
exTreg-IEL1_S3

tag: mouse id


title: placenta (585484_BS)


title: placenta (585484_oxBS)


title: placenta (585568_oxBS)

value: Male


title: A3-FL-cDC2 technical replicate 1

description: cDC2, FL, Animal A3, technical replicate 1


title: Sample 8_ATAC_Pre-IEL

description:
Accessible chromatin
WTATAC_preIEL_S8

tag: Sex

value: male


title: placenta (585476_BS)

tag: mother education


title: A3-FL-cDC2 technical replicate 2

description: cDC2, FL, Animal A3, technical replicate 2


title: placenta (585476_oxBS)

tag: tissue


title: placenta (585468_BS)

value: College graduate


title: A2-FL-cDC2 technical replicate 11

description: cDC2, FL, Animal A2, technical replicate 11

tag: strain


title: placenta (585524_BS)


title: Sample 6_ATAC_iTreg-IEL

description:
Accessible chromatin
WTATAC_iTreg_S7

tag: cell type


title: placenta (585472_BS)


title: placenta (585448_oxBS)

value: High school graduate


title: Sample 5_ATAC_iTreg-IEL

description:
Accessible chromatin
Treg_S6


title: placenta (585448_BS)


title: Sample 4_ATAC_CD4-IEL

description:
Accessible chromatin
WTATAC_CD4IELa_S10


title: placenta (585424_BS)


title: A2-FL-cDC2 technical replicate 9

description: cDC2, FL, Animal A2, technical replicate 9

tag: infected


title: placenta (585424_oxBS)


title: Sample 7_ATAC_Pre-IEL

description:
Accessible chromatin
preIEL_S7


title: placenta (585472_oxBS)


title: placenta (585420_oxBS)


title: A2-FL-cDC2 technical replicate 8

description: cDC2, FL, Animal A2, technical replicate 8

tag: virus


title: placenta (585420_BS)


title: Sample 3_ATAC_CD4-IEL

description:
Accessible chromatin
IEL_S5


title: placenta (585404_oxBS)


title: A2-FL-cDC2 technical replicate 12

description: cDC2, FL, Animal A2, technical replicate 12

tag: original name (to remove)


title: placenta (585404_BS)


title: Sample 2_ATAC_exTreg-IEL

description:
Accessible chromatin
WTATAC_exTregIEL_S9

value: ExTreg-IEL


title: placenta (585380_BS)

value: Female


title: placenta (585372_BS)


title: A2-FL-cDC2 technical replicate 6

description: cDC2, FL, Animal A2, technical replicate 6

tag: animal id


title: A2-FL-cDC2 technical replicate 5

description: cDC2, FL, Animal A2, technical replicate 5


title: A2-FL-cDC2 technical replicate 10

description: cDC2, FL, Animal A2, technical replicate 10


title: placenta (585380_oxBS)


title: Sample 1_ATAC_exTreg-IEL

description:
Accessible chromatin
exTreg_IEL_S8

tag: genotype


title: A2-FL-cDC2 technical replicate 7

description: cDC2, FL, Animal A2, technical replicate 7


title: placenta (585372_oxBS)


title: CASP1::shy2-2/slr-1_8hr_10µMNAA_rep2

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.3)
Reads were further filtered for low complexity with seq_crumbs (v. 0.1.8)
Reads were aligned against Arabidopsis thaliana genome (build TAIR 10) using STAR (v. 2.4.0a)
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7)
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1) using Ensembl Plants gene annotation (v. 21)
Genome_build: Arabidopsis thaliana genome (build TAIR 10)
Supplementary_files_format_and_content: Tab-separated .txt files with gene-level read count estimates, computed by the htseq-count software package

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis thaliana ecotype Col-0 was grown at 22 Celsius degree under continous light, vertically on solid half-strength Murashige-Skoog medium for 6 days in the same growth chamber after 2-day startification at 4 degrees Celsius .

extract_protocol:
RNA was extracted using a Trizol-mediated RNA extraction and total RNA was treated with RNA-free Dnase (Qiagen) and cleaned-up with an RNAeasy minElute kit (Qiagen).
RNA quality was assessed on a Fragment Analyzer (Advanced Analytical Technologies, Inc., Ankeny, IA, USA).  RNA-seq libraries were prepared using 1000 ng of total RNA  and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA) on a Sciclone liquid handling robot (PerkinElmer; Waltham, Massachusetts, USA)   using a PerkinElmer-developed automated script. Cluster generation was performed with the resulting libraries using the Illumina TruSeq SR Cluster Kit v4 reagents and  sequenced on the Illumina HiSeq 2500 using TruSeq SBS Kit v4 reagents. Sequencing data were processed using the Illumina Pipeline Software version 2.20.

treatment_protocol: 6 day-old seedlings were transferred to control plates or to plates containing 10µM NAA at designated time points, 0, 2, 4, 8, 16 and 24 hrs, to ensure that all plants were 7 day-old prior to harvesting. For harvesting, the root tip (~3mm) and the shoot including hypocotyl were removed and root sections were flash-frozen in liquid nitrogen and stored at -80 degrees Celcius untill processed.

value: root

tag: ecotype

tag: treatment

value: 10 microMolar NAA for 480 min


title: CASP1::shy2-2/slr-1_8hr_10µMNAA_rep3


title: placenta (585468_oxBS)

tag: infant sex

tag: maternal age (years)


title: placenta (585364_BS)

tag: birthweight (grams)

tag: gestational age (weeks)


title: placenta (585360_BS)


title: A2-FL-cDC2 technical replicate 3

description: cDC2, FL, Animal A2, technical replicate 3

value: yes


title: A2-FL-cDC2 technical replicate 2

description: cDC2, FL, Animal A2, technical replicate 2

value: FL


title: CASP1::shy2-2/slr-1_control_rep1

value: no treatment


title: CASP1::shy2-2/slr-1_control_rep2


title: placenta (585352_oxBS)


title: placenta (585352_BS)


title: placenta (585344_BS)


title: A1-FL-cDC2 technical replicate 12

description: cDC2, FL, Animal A1, technical replicate 12

value: Large White


title: A2-FL-cDC2 technical replicate 1

description: cDC2, FL, Animal A2, technical replicate 1


title: placenta (585340_BS)


title: A1-FL-cDC2 technical replicate 11

description: cDC2, FL, Animal A1, technical replicate 11


title: placenta (585328_BS)


title: placenta (585328_oxBS)


title: A1-FL-cDC2 technical replicate 10

description: cDC2, FL, Animal A1, technical replicate 10


title: placenta (585364_oxBS)


title: placenta (585308_BS)


title: placenta (585304_oxBS)


title: placenta (585344_oxBS)


title: A1-FL-cDC2 technical replicate 9

description: cDC2, FL, Animal A1, technical replicate 9


title: CASP1::shy2-2/slr-1_4hr_10µMNAA_rep2

value: 10 microMolar NAA for 240 min


title: A2-FL-cDC2 technical replicate 4

description: cDC2, FL, Animal A2, technical replicate 4


title: CASP1::shy2-2/slr-1_4hr_10µMNAA_rep3


title: CASP1::shy2-2/slr-1_4hr_10µMNAA_rep1


title: placenta (585340_oxBS)


title: CASP1::shy2-2/slr-1_8hr_10µMNAA_rep1


title: placenta (585308_oxBS)


title: placenta (585304_BS)


title: placenta (585360_oxBS)


title: CASP1::shy2-2/slr-1_control_rep3


title: placenta (585300_oxBS)


title: placenta (585300_BS)


title: placenta (585296_oxBS)

value: Less than 11th grade


title: CASP1::shy2-2/slr-1_24hr_10µMNAA_rep3

value: 10 microMolar NAA for 1440 min


title: placenta (585292_oxBS)

value: placenta


title: placenta (585280_BS)

value: Any post graduate schooling


title: placenta (585292_BS)

value: Male


title: CASP1::shy2-2/slr-1_24hr_10µMNAA_rep1


title: placenta (585284_oxBS)


title: CASP1::shy2-2/slr-1_2hr_10µMNAA_rep2

value: 10 microMolar NAA for 120 min


title: A1-FL-cDC2 technical replicate 6

description: cDC2, FL, Animal A1, technical replicate 6


title: placenta (585284_BS)

value: College graduate


title: CASP1::shy2-2/slr-1_2hr_10µMNAA_rep3


title: placenta (585280_oxBS)


title: CASP1::shy2-2/slr-1_24hr_10µMNAA_rep2


title: placenta (585296_BS)


title: placenta (585276_BS)


title: placenta (585276_oxBS)


title: A1-FL-cDC2 technical replicate 5

description: cDC2, FL, Animal A1, technical replicate 5


title: CASP1::shy2-2/slr-1_2hr_10µMNAA_rep1


title: A1-FL-cDC2 technical replicate 4

description: cDC2, FL, Animal A1, technical replicate 4


title: A1-FL-cDC2 technical replicate 3

description: cDC2, FL, Animal A1, technical replicate 3


title: placenta (585264_oxBS)


title: placenta (585264_BS)


title: CASP1::shy2-2/slr-1_16hr_10µMNAA_rep2

value: 10 microMolar NAA for 960 min


title: A1-FL-cDC2 technical replicate 2

description: cDC2, FL, Animal A1, technical replicate 2


title: A1-FL-cDC2 technical replicate 1

description: cDC2, FL, Animal A1, technical replicate 1


title: placenta (585252_BS)


title: CASP1::shy2-2/slr-1_16hr_10µMNAA_rep1


title: A1-FL-cDC2 technical replicate 7

description: cDC2, FL, Animal A1, technical replicate 7


title: placenta (585252_oxBS)


title: A1-FL-cDC2 technical replicate 8

description: cDC2, FL, Animal A1, technical replicate 8


title: CASP1::shy2-2/slr-1_16hr_10µMNAA_rep3


title: A3-CTRL-cDC2 technical replicate 12

description: cDC2, CTRL, Animal A3, technical replicate 12

value: no


title: placenta (585244_BS)


title: placenta (585228_oxBS)

value: Female


title: placenta (585228_BS)


title: A3-CTRL-cDC2 technical replicate 10

description: cDC2, CTRL, Animal A3, technical replicate 10


title: A3-CTRL-cDC2 technical replicate 11

description: cDC2, CTRL, Animal A3, technical replicate 11


title: placenta (585220_oxBS)


title: placenta (585208_BS)


title: slr-1_8hr_10µMNAA_rep2

value: root

value: solitairy root 1 (slr-1)


title: placenta (585244_oxBS)


title: slr-1_8hr_10µMNAA_rep1

value: 10 microMolar NAA for 480 min


title: slr-1_4hr_10µMNAA_rep3


title: placenta (585216_oxBS)


title: A3-CTRL-cDC2 technical replicate 9

description: cDC2, CTRL, Animal A3, technical replicate 9


title: slr-1_8hr_10µMNAA_rep3


title: slr-1_4hr_10µMNAA_rep2


title: slr-1_4hr_10µMNAA_rep1


title: placenta (585216_BS)


title: A3-CTRL-cDC2 technical replicate 8

description: cDC2, CTRL, Animal A3, technical replicate 8


title: slr-1_control_rep3


title: placenta (585220_BS)


title: placenta (585204_BS)

value: Junior college graduate or equivalent


title: placenta (585204_oxBS)


title: slr-1_24hr_10µMNAA_rep3


title: A3-CTRL-cDC2 technical replicate 6

description: cDC2, CTRL, Animal A3, technical replicate 6


title: A3-CTRL-cDC2 technical replicate 5

description: cDC2, CTRL, Animal A3, technical replicate 5


title: A3-CTRL-cDC2 technical replicate 7

description: cDC2, CTRL, Animal A3, technical replicate 7


title: placenta (585196_BS)


title: placenta (585192_BS)


title: placenta (585208_oxBS)


title: placenta (585196_oxBS)


title: placenta (585180_BS)


title: A3-CTRL-cDC2 technical replicate 4

description: cDC2, CTRL, Animal A3, technical replicate 4


title: placenta (585180_oxBS)


title: A3-CTRL-cDC2 technical replicate 3

description: cDC2, CTRL, Animal A3, technical replicate 3


title: placenta (585172_BS)

value: High school graduate


title: slr-1_24hr_10µMNAA_rep2


title: placenta (585172_oxBS)


title: A3-CTRL-cDC2 technical replicate 2

description: cDC2, CTRL, Animal A3, technical replicate 2

value: Large White


title: slr-1_24hr_10µMNAA_rep1


title: placenta (585136_BS)


title: A3-CTRL-cDC2 technical replicate 1

description: cDC2, CTRL, Animal A3, technical replicate 1


title: placenta (585120_BS)


title: placenta (585116_oxBS)


title: placenta (585116_BS)


title: placenta (585120_oxBS)


title: placenta (585136_oxBS)


title: A2-CTRL-cDC2 technical replicate 12

description: cDC2, CTRL, Animal A2, technical replicate 12


title: A2-CTRL-cDC2 technical replicate 11

description: cDC2, CTRL, Animal A2, technical replicate 11


title: placenta (585088_oxBS)


title: slr-1_2hr_10µMNAA_rep3


title: placenta (585088_BS)


title: placenta (585084_oxBS)


title: placenta (585084_BS)


title: slr-1_2hr_10µMNAA_rep2


title: placenta (585192_oxBS)


title: slr-1_2hr_10µMNAA_rep1


title: A2-CTRL-cDC2 technical replicate 10

description: cDC2, CTRL, Animal A2, technical replicate 10


title: placenta (585080_BS)


title: slr-1_control_rep2

value: no treatment


title: placenta (585080_oxBS)


title: slr-1_16hr_10µMNAA_rep3


title: placenta (585076_oxBS)


title: placenta (585076_BS)


title: A2-CTRL-cDC2 technical replicate 8

description: cDC2, CTRL, Animal A2, technical replicate 8


title: placenta (585072_BS)

value: Less than 11th grade


title: A2-CTRL-cDC2 technical replicate 7

description: cDC2, CTRL, Animal A2, technical replicate 7


title: A2-CTRL-cDC2 technical replicate 6

description: cDC2, CTRL, Animal A2, technical replicate 6


title: placenta (585064_BS)


title: placenta (585072_oxBS)


title: placenta (585064_oxBS)


title: placenta (585056_oxBS)


title: A2-CTRL-cDC2 technical replicate 9

description: cDC2, CTRL, Animal A2, technical replicate 9


title: slr-1_16hr_10µMNAA_rep2


title: placenta (585056_BS)


title: Bin67_BRG1_IgG_JR591

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

description:
Bin67 BRG1 transfected IgG CUT&RUN Rep 2
None
JR591

data_processing:
FASTQ Files were trimmmed using trim_galore (version 0.6.2) and QC peformed using fastqc (0.11.8).
trimmed files were aligned using bowtie2 (version 2.3.4.1) to hg38 using the "--very-sensitive-local" "--no-dovetail" "--no-discordant" "--no-mixed" and "--no-unal" flags
aligned files were sorted using samtools (v 1.9) and duplicate reads were removed using Picard (v2.20.0)
sorted and duplicate removed files were used to genreate bigwig tracks using bamCoverage in deeptools (v 3.2.0) using a binSize of 30 and a smoothLenght of 60. Additionally, read were normalzed using CPM (counts per million) and reads were extended to fragment length . Enrichment relative to IgG was then calculated by dividing the IP track by the IgG track using bigWigCompare in deeptools. Final bigwig files were then generated using wiggletools to average individual replicates.
Peaks were called using MACS2 (v2.1.2) on pooled replicates using the bam file of the antibody of interst as the treatment and the IgG from that sample as control.
Genome_build: hg38
Supplementary_files_format_and_content: Format: BigWig - Normalized, averaged, signal tracks of each antibody in each cell line
Supplementary_files_format_and_content: Format: Bed  - Peak locations from MACS2 analysis

source_name: Bin67 Ovarian Cancer Cell Line

growth_protocol: BIN67 cells were cultured in RPMI-1640 (Gibco #11875-093) supplemented with 10% FBS and maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Samples were processed for CUT&RUN following protocol from https://dx.doi.org/10.17504/protocols.io.zcpf2vn . Antibodies were used at 1:25 dilution .
Libraries were construct using Kapa Hyperprep DNA kit and Kapa dual index adapters per manufacturers instructions.

treatment_protocol: BIN67 cells were co-transfected (FuGENE 6, Promega #E269A) with either control (pCMV-neo or pCDNA3-neo) or BRG1 (PBJ5-BRG1) plasmids at a 10:1 ratio to a plasmid containing puromycin resistance (pBABE-puro). Twenty-four hours after transfection, cells were placed on 2 µg/ml puromycin for 3 days and then harvested for RNA-seq analysis.

tag: cell line

tag: transfected vector

tag: antibody

value: IgG


title: placenta (585052_BS)

source_name: human placenta, bisulfite converted

tag: mother education

tag: tissue

value: placenta


title: placenta (585048_BS)

value: Any post graduate schooling


title: A2-CTRL-cDC2 technical replicate 4

description: cDC2, CTRL, Animal A2, technical replicate 4

tag: strain

tag: cell type


title: Bin67_CTRL_IgG_JR587

description:
Bin67 Control Transfected IgG CUT&RUN Rep 2
None
JR587

value: Control


title: A2-CTRL-cDC2 technical replicate 3

description: cDC2, CTRL, Animal A2, technical replicate 3

tag: infected

tag: virus


title: placenta (585052_oxBS)

value: Male


title: Bin67_BRG1_Brg1_JR588

description:
Bin67 BRG1 transfected BRG1  CUT&RUN Rep 2
Bin67_BRG1_Brg1.mean.relIgg.bw
JR588


title: Bin67_CTRL_Brg1_JR584

description:
Bin67 Control Transfected BRG1 CUT&RUN Rep 2
Bin67_CTRL_Brg1.mean.relIgg.bw
JR584


title: placenta (585048_oxBS)


title: placenta (585040_BS)

value: College graduate


title: A2-CTRL-cDC2 technical replicate 2

description: cDC2, CTRL, Animal A2, technical replicate 2

tag: original name (to remove)

tag: animal id


title: slr-1_16hr_10µMNAA_rep1

tag: ecotype

tag: genotype

value: 10 microMolar NAA for 960 min


title: Bin67_BRG1_IgG_JR742

description:
Bin67 BRG1 Transfected IgG CUT&RUN Rep 1
None
JR742


title: placenta (585040_oxBS)

tag: infant sex


title: slr-1_control_rep1

tag: treatment


title: A2-CTRL-cDC2 technical replicate 1

description: cDC2, CTRL, Animal A2, technical replicate 1

value: no


title: Bin67_BRG1_Jun_JR741

description:
Bin67 BRG1 Transfected c-Jun CUT&RUN Rep 2
Bin67_BRG1_Jun.mean.relIgg.bw
JR741

value: c-Jun


title: placenta (585032_BS)

tag: maternal age (years)

tag: birthweight (grams)


title: A2-CTRL-cDC2 technical replicate 5

description: cDC2, CTRL, Animal A2, technical replicate 5


title: placenta (585032_oxBS)

tag: gestational age (weeks)


title: A1bis-CTRL-cDC2 technical replicate 12

description: cDC2, CTRL, Animal A1bis, technical replicate 12


title: placenta (585016_BS)

value: Female


title: placenta (585016_oxBS)


title: placenta (584992_BS)


title: Bin67_BRG1_Jun_JR740

description:
Bin67 BRG1 Transfected c-Jun CUT&RUN Rep 1
Bin67_BRG1_Jun.mean.relIgg.bw
JR740

tag: cell line

tag: transfected vector


title: A1bis-CTRL-cDC2 technical replicate 11

description: cDC2, CTRL, Animal A1bis, technical replicate 11


title: placenta (584992_oxBS)

tag: mother education


title: A1bis-CTRL-cDC2 technical replicate 10

description: cDC2, CTRL, Animal A1bis, technical replicate 10


title: placenta (584988_oxBS)

tag: tissue


title: placenta (584988_BS)


title: placenta (584984_oxBS)


title: placenta (584984_BS)


title: A1bis-CTRL-cDC2 technical replicate 9

description: cDC2, CTRL, Animal A1bis, technical replicate 9

tag: strain


title: Bin67_CTRL_Jun_JR737

description:
Bin67 Control Transfected c-Jun CUT&RUN Rep 2
BIn67_CTRL_Jun.mean.relIgg.bw
JR737

tag: antibody


title: Bin67_CTRL_Jun_JR736

description:
Bin67 Control Transfected c-Jun CUT&RUN Rep 1
BIn67_CTRL_Jun.mean.relIgg.bw
JR736


title: Bin67_BRG1_Brg1_JR739

description:
Bin67 BRG1 Transfected Brg1  CUT&RUN Rep 1
Bin67_BRG1_Brg1.mean.relIgg.bw
JR739


title: placenta (584980_oxBS)


title: placenta (584980_BS)


title: A1bis-CTRL-cDC2 technical replicate 8

description: cDC2, CTRL, Animal A1bis, technical replicate 8

tag: cell type

tag: infected


title: A1bis-CTRL-cDC2 technical replicate 7

description: cDC2, CTRL, Animal A1bis, technical replicate 7

tag: virus

tag: original name (to remove)


title: placenta (584972_BS)


title: placenta (584972_oxBS)


title: placenta (584960_oxBS)


title: placenta (584964_oxBS)


title: A1bis-CTRL-cDC2 technical replicate 6

description: cDC2, CTRL, Animal A1bis, technical replicate 6

tag: animal id


title: A1bis-CTRL-cDC2 technical replicate 5

description: cDC2, CTRL, Animal A1bis, technical replicate 5


title: placenta (584960_BS)


title: HT1_BRG1_Brg1_JR596

description:
SCCOHT-1 BRG1 Transfected Brg1  CUT&RUN Rep 2
HT1_BRG1_Brg1.mean.relIgg.bw
JR596

source_name: SCCOHT-1 Ovarian Cancer Cell Line


title: Bin67_CTRL_IgG_JR738

description:
Bin67 Control Transfected IgG CUT&RUN Rep 1
None
JR738


title: placenta (584948_BS)


title: placenta (584964_BS)


title: A1bis-CTRL-cDC2 technical replicate 4

description: cDC2, CTRL, Animal A1bis, technical replicate 4


title: HT1_CTRL_T7_JR595

description:
SCCOHT-1 Control Transfected T7 antibody CUT&RUN Rep 2
None
JR595


title: placenta (584944_BS)


title: placenta (584944_oxBS)


title: HT1_CTRL_Brg1_JR592

description:
SCCOHT-1 control transfected BRG1 CUT&RUN Rep 2
HT1_CTRL_Brg1.mean.relIgg.bw
JR592


title: A1bis-CTRL-cDC2 technical replicate 3

description: cDC2, CTRL, Animal A1bis, technical replicate 3


title: HT1_BRG1_c-Jun_JR646

description:
SCCOHT-1 BRG1 Transfected BRG1 CUT&RUN Rep 2
HT1_BRG1_c-Jun.mean.relIgg.bw
JR646


title: placenta (584928_BS)


title: placenta (584924_BS)


title: Bin67_CTRL_Brg1_JR735

description:
Bin67 Control Transfected Brg1 CUT&RUN Rep 1
Bin67_CTRL_Brg1.mean.relIgg.bw
JR735


title: placenta (584924_oxBS)


title: A1bis-CTRL-cDC2 technical replicate 2

description: cDC2, CTRL, Animal A1bis, technical replicate 2


title: HT1_BRG1_T7_JR599

description:
SCCOHT-1 BRG1 Transfected T7 antibody CUT&RUN Rep 2
None
JR599


title: placenta (584928_oxBS)


title: HT1_BRG1_T7_JR639

description:
SCCOHT-1 BRG1 Transfected T7 antibody CUT&RUN Rep 1
None
JR639


title: HT1_CTRL_c-Jun_JR642

description:
SCCOHT-1 Control Transfected c-Jun CUT&RUN Rep 2
HT1_CTRL_c-Jun.mean.relIgg.bw
JR642


title: A1bis-CTRL-cDC2 technical replicate 1

description: cDC2, CTRL, Animal A1bis, technical replicate 1


title: A3-FL-AM-like technical replicate 12

description: AM-like, FL, Animal A3, technical replicate 12

source_name: AM-like

value: AM-like

value: yes

value: FL


title: placenta (584920_oxBS)

value: Junior college graduate or equivalent


title: placenta (584916_BS)


title: HT1_BRG1_c-Jun_JR638

description:
SCCOHT-1 BRG1 Transfected c-Jun   CUT&RUN Rep 1
HT1_BRG1_c-Jun.mean.relIgg.bw
JR638


title: placenta (584916_oxBS)


title: A3-FL-AM-like technical replicate 11

description: AM-like, FL, Animal A3, technical replicate 11

value: Large White


title: A3-FL-AM-like technical replicate 10

description: AM-like, FL, Animal A3, technical replicate 10


title: placenta (584912_oxBS)

value: High school graduate


title: placenta (584900_BS)


title: placenta (584948_oxBS)


title: HT1_BRG1_Brg1_JR636

description:
SCCOHT-1 BRG1 Transfected Brg1  CUT&RUN Rep 1
HT1_BRG1_Brg1.mean.relIgg.bw
JR636


title: HT1_CTRL_T7_JR635

description:
SCCOHT-1 Control Transfected T7 antibody CUT&RUN Rep 1
None
JR635


title: placenta (584900_oxBS)


title: A3-FL-AM-like technical replicate 8

description: AM-like, FL, Animal A3, technical replicate 8


title: placenta (584896_oxBS)


title: placenta (584892_BS)


title: placenta (584892_oxBS)


title: HT1_CTRL_Brg1_JR632

description:
SCCOHT-1 Control Transfect BRG1 CUT&RUN-Rep1
HT1_CTRL_Brg1.mean.relIgg.bw
JR632


title: A3-FL-AM-like technical replicate 7

description: AM-like, FL, Animal A3, technical replicate 7


title: placenta (584920_BS)


title: A3-FL-AM-like technical replicate 6

description: AM-like, FL, Animal A3, technical replicate 6


title: placenta (584888_BS)


title: HT1_CTRL_c-Jun_JR634

description:
SCCOHT-1 Control Transfect c-Jun CUT&RUN Rep 1
HT1_CTRL_c-Jun.mean.relIgg.bw
JR634


title: A3-FL-AM-like technical replicate 5

description: AM-like, FL, Animal A3, technical replicate 5


title: placenta (584876_BS)

value: Less than 11th grade


title: placenta (584876_oxBS)


title: placenta (584888_oxBS)


title: placenta (584872_BS)


title: placenta (584912_BS)


title: A3-FL-AM-like technical replicate 4

description: AM-like, FL, Animal A3, technical replicate 4


title: A3-FL-AM-like technical replicate 3

description: AM-like, FL, Animal A3, technical replicate 3


title: T_52R_30D_Rep2

data_processing:
TT-seq and RNA-seq: Paired-end reads with additional 6 bp of barcodes were obtained for each group of samples. Two replicates were treated for each condition. Reads were aligned to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium) using STAR 2.6.0 (Dobin et al., 2013), with the following specifications: outFilterMismatchNmax 2, outFilterMultimapScoreRange 0 and alignIntronMax 500000. Bam files were filtered with Samtools (Li et al., 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f2) were selected. Read counts for different features were calculated with HTSeq (Anders et al., 2015). Further data processing was carried out using the R/Bioconductor environment. Expressed transcripts were defined as possessing more than 50 read counts per kilobase (RPK) in two summarized replicates of TT-seq solvent control (DMSO). Prior to quantification, data was normalized by using added RNA spike-in as described previously (Schwalb et al., 2016). Normalized coverage was exported to the bigwig format using R/Bioconductor rtracklayer package.
PRO-seq: PRO-seq data were trimmed with cutadapt version 1.11 (Martin, 2011) using the following parameters: sample PROseq_25R_Rep1: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACATCGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; sample PROseq_25R_Rep2: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGGTCAATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; sample PROseq_52R_Rep1: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCTGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; and sample PROseq_52R_Rep: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGACGGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20 . The reads were mapped to the human genome (Genome Reference Consortium version GRCh38) of the human genome (from April 2014) and to the Drosophila melanogaster genome version BDGP6.28 with STAR (v2.6.1) (Dobin et al, 2013) using the following parameters: --outFilterMismatchNmax 3 --outFilterMultimapScoreRange 0 --alignIntronMax 500000. Resulting bam files were filtered using SAMTOOLS (v1.9) (Li et al, 2009) to remove alignments with mapping quality lower than 7 (-q 7). Only proper pairs (-f2) were retained. In order to calculate normalization factors for PRO-seq, HTSeq (v0.6.0) (Anders et al, 2015) with intersection-strict mode and --stranded=reverse parameter was used to calculate reads mapping to D.melanogaster transcripts (Drosophila_melanogaster.BDGP6.28.100.gtf.gz from Ensembl.org) followed by calculation of size factors with DESeq2 Bioconductor package (Love et al, 2014). PRO-seq sequencing Read1 mapping to the human genome was converted to reverse complement sequence and the last nucleotide incorporated by the RNAPII was determined (RNAPII position) - last base of the reversely complemented Read 1 for the “+” strand, and first base of the reversely complemented Read 1 for the “-” strand. Coverage for RNAPII position was calculated using coverage function from GRanges R Bioconductor package (Lawrence et al, 2013) and normalized using size factors determined with DESeq2 for D.melanogaster transcripts.  Normalized coverage was exported to the bigwig format using R/Bioconductor rtracklayer package.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigWig coverage files

extract_protocol:
TT-seq, RNA-seq (Schwalb et al, 2016; Wachutka et al., 2019)
TruSeq Stranded Total RNA Library Prep Gold (Illumina, #20020598)

treatment_protocol: For activation experiments with TPA, the cells were treated with 200 nM TPA (12-O-Tetradecanoylphorbol 13-acetate) (Sigma Aldrich, #P1585) or DMSO (solvent control). DMSO was diluted 1:20000 in the culturing medium to prevent its possible side-effects on transcription (Verheijen et al, 2019)

value: U2OS osteosarcoma cells

tag: rna fraction

value: Total fragmented RNA

tag: genotype

value: U2OS cells expressing RPB1-CTD with 52 repeats (Boehning et al 2018)

value: DMSO for 30 min


title: placenta (584856_oxBS)

tag: infant sex

value: Any post graduate schooling

value: placenta


title: T_52R_30TPA_Rep2

tag: treatment

value: 200 nM TPA for 30 min


title: placenta (584856_BS)

tag: maternal age (years)

tag: birthweight (grams)


title: placenta (584852_BS)

value: Male

tag: gestational age (weeks)


title: T_52R_30D_Rep1

tag: cell line


title: A3-FL-AM-like technical replicate 9

description: AM-like, FL, Animal A3, technical replicate 9


title: A3-FL-AM-like technical replicate 2

description: AM-like, FL, Animal A3, technical replicate 2


title: placenta (584896_BS)

tag: mother education

value: College graduate


title: T_52R_15TPA_Rep2

value: 200 nM TPA for 15 min


title: placenta (584852_oxBS)

tag: tissue


title: A3-FL-AM-like technical replicate 1

description: AM-like, FL, Animal A3, technical replicate 1

tag: strain

value: AM-like


title: T_52R_30TPA_Rep1


title: placenta (584840_BS)


title: placenta (584836_oxBS)

value: Female


title: T_52R_15TPA_Rep1


title: placenta (584840_oxBS)


title: A2-FL-AM-like technical replicate 12

description: AM-like, FL, Animal A2, technical replicate 12

value: yes

value: FL


title: A2-FL-AM-like technical replicate 11

description: AM-like, FL, Animal A2, technical replicate 11

value: Large White


title: placenta (584836_BS)

value: High school graduate


title: T_52R_15D_Rep2

value: DMSO for 15 min


title: placenta (584812_BS)

value: Junior college graduate or equivalent


title: placenta (584812_oxBS)


title: placenta (584804_oxBS)


title: placenta (584792_BS)


title: A2-FL-AM-like technical replicate 10

description: AM-like, FL, Animal A2, technical replicate 10


title: placenta (584792_oxBS)


title: placenta (584788_BS)


title: placenta (584784_oxBS)


title: placenta (584872_oxBS)

value: Less than 11th grade


title: placenta (584804_BS)


title: T_25R_30TPA_Rep2

value: U2OS osteosarcoma cells

value: Total fragmented RNA

value: U2OS cells expressing RPB1-CTD with 25 repeats (Boehning et al 2018)


title: A2-FL-AM-like technical replicate 9

description: AM-like, FL, Animal A2, technical replicate 9


title: A2-FL-AM-like technical replicate 6

description: AM-like, FL, Animal A2, technical replicate 6


title: placenta (584780_BS)

value: placenta


title: T_25R_15TPA_Rep1


title: placenta (584768_oxBS)


title: placenta (584700_BS)


title: T_25R_30TPA_Rep1

value: 200 nM TPA for 30 min


title: T_25R_15D_Rep2


title: T_25R_30D_Rep2

value: DMSO for 30 min


title: A2-FL-AM-like technical replicate 8

description: AM-like, FL, Animal A2, technical replicate 8


title: placenta (584788_oxBS)

value: College graduate


title: A2-FL-AM-like technical replicate 7

description: AM-like, FL, Animal A2, technical replicate 7


title: placenta (584784_BS)

value: Any post graduate schooling


title: T_25R_30D_Rep1


title: placenta (584780_oxBS)

value: Male


title: placenta (584632_BS)

value: Female


title: T_25R_15TPA_Rep2

value: 200 nM TPA for 15 min


title: placenta (584768_BS)


title: placenta (584624_oxBS)


title: A2-FL-AM-like technical replicate 5

description: AM-like, FL, Animal A2, technical replicate 5

value: AM-like

value: yes

value: FL


title: L_52R_30TPA_Rep1

data_processing:
Library strategy: TT-seq
TT-seq and RNA-seq: Paired-end reads with additional 6 bp of barcodes were obtained for each group of samples. Two replicates were treated for each condition. Reads were aligned to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium) using STAR 2.6.0 (Dobin et al., 2013), with the following specifications: outFilterMismatchNmax 2, outFilterMultimapScoreRange 0 and alignIntronMax 500000. Bam files were filtered with Samtools (Li et al., 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f2) were selected. Read counts for different features were calculated with HTSeq (Anders et al., 2015). Further data processing was carried out using the R/Bioconductor environment. Expressed transcripts were defined as possessing more than 50 read counts per kilobase (RPK) in two summarized replicates of TT-seq solvent control (DMSO). Prior to quantification, data was normalized by using added RNA spike-in as described previously (Schwalb et al., 2016). Normalized coverage was exported to the bigwig format using R/Bioconductor rtracklayer package.
PRO-seq: PRO-seq data were trimmed with cutadapt version 1.11 (Martin, 2011) using the following parameters: sample PROseq_25R_Rep1: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACATCGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; sample PROseq_25R_Rep2: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGGTCAATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; sample PROseq_52R_Rep1: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCTGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; and sample PROseq_52R_Rep: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGACGGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20 . The reads were mapped to the human genome (Genome Reference Consortium version GRCh38) of the human genome (from April 2014) and to the Drosophila melanogaster genome version BDGP6.28 with STAR (v2.6.1) (Dobin et al, 2013) using the following parameters: --outFilterMismatchNmax 3 --outFilterMultimapScoreRange 0 --alignIntronMax 500000. Resulting bam files were filtered using SAMTOOLS (v1.9) (Li et al, 2009) to remove alignments with mapping quality lower than 7 (-q 7). Only proper pairs (-f2) were retained. In order to calculate normalization factors for PRO-seq, HTSeq (v0.6.0) (Anders et al, 2015) with intersection-strict mode and --stranded=reverse parameter was used to calculate reads mapping to D.melanogaster transcripts (Drosophila_melanogaster.BDGP6.28.100.gtf.gz from Ensembl.org) followed by calculation of size factors with DESeq2 Bioconductor package (Love et al, 2014). PRO-seq sequencing Read1 mapping to the human genome was converted to reverse complement sequence and the last nucleotide incorporated by the RNAPII was determined (RNAPII position) - last base of the reversely complemented Read 1 for the “+” strand, and first base of the reversely complemented Read 1 for the “-” strand. Coverage for RNAPII position was calculated using coverage function from GRanges R Bioconductor package (Lawrence et al, 2013) and normalized using size factors determined with DESeq2 for D.melanogaster transcripts.  Normalized coverage was exported to the bigwig format using R/Bioconductor rtracklayer package.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigWig coverage files

value: 4sU-labeled RNA

value: U2OS cells expressing RPB1-CTD with 52 repeats (Boehning et al 2018)


title: placenta (584616_BS)


title: L_52R_30D_Rep2


title: placenta (584700_oxBS)

value: Junior college graduate or equivalent


title: A2-FL-AM-like technical replicate 4

description: AM-like, FL, Animal A2, technical replicate 4

value: Large White


title: placenta (584656_BS)


title: A2-FL-AM-like technical replicate 2

description: AM-like, FL, Animal A2, technical replicate 2


title: T_52R_15D_Rep1

value: U2OS osteosarcoma cells

value: Total fragmented RNA

value: DMSO for 15 min


title: placenta (584632_oxBS)

value: placenta


title: T_25R_15D_Rep1

value: U2OS cells expressing RPB1-CTD with 25 repeats (Boehning et al 2018)


title: placenta (584624_BS)

value: College graduate


title: A2-FL-AM-like technical replicate 1

description: AM-like, FL, Animal A2, technical replicate 1


title: L_52R_30D_Rep1

value: DMSO for 30 min


title: placenta (584584_BS)


title: placenta (584584_oxBS)


title: A1bis-FL-AM-like technical replicate 9

description: AM-like, FL, Animal A1bis, technical replicate 9


title: L_52R_30TPA_Rep2

value: 200 nM TPA for 30 min


title: placenta (584560_oxBS)

value: Male


title: A1bis-FL-AM-like technical replicate 12

description: AM-like, FL, Animal A1bis, technical replicate 12


title: A1bis-FL-AM-like technical replicate 11

description: AM-like, FL, Animal A1bis, technical replicate 11


title: placenta (584656_oxBS)

value: Female

value: Any post graduate schooling


title: A1bis-FL-AM-like technical replicate 10

description: AM-like, FL, Animal A1bis, technical replicate 10

value: AM-like

value: yes


title: placenta (584612_BS)


title: A1bis-FL-AM-like technical replicate 8

description: AM-like, FL, Animal A1bis, technical replicate 8

value: FL


title: placenta (584612_oxBS)


title: A1bis-FL-AM-like technical replicate 7

description: AM-like, FL, Animal A1bis, technical replicate 7


title: placenta (584464_BS)


title: placenta (584528_BS)

value: High school graduate


title: L_52R_15D_Rep1

value: 4sU-labeled RNA

value: U2OS cells expressing RPB1-CTD with 52 repeats (Boehning et al 2018)


title: L_52R_15TPA_Rep1

value: U2OS osteosarcoma cells

value: 200 nM TPA for 15 min


title: L_52R_15TPA_Rep2


title: placenta (584616_oxBS)


title: placenta (584440_BS)


title: L_52R_15D_Rep2

value: DMSO for 15 min


title: A1bis-FL-AM-like technical replicate 6

description: AM-like, FL, Animal A1bis, technical replicate 6

value: Large White


title: placenta (584464_oxBS)

value: placenta


title: placenta (584416_oxBS)

value: Junior college graduate or equivalent


title: L_25R_30TPA_Rep2

value: U2OS cells expressing RPB1-CTD with 25 repeats (Boehning et al 2018)


title: placenta (584416_BS)


title: placenta (584412_BS)


title: A2-FL-AM-like technical replicate 3

description: AM-like, FL, Animal A2, technical replicate 3


title: placenta (584440_oxBS)


title: A1bis-FL-AM-like technical replicate 3

description: AM-like, FL, Animal A1bis, technical replicate 3


title: A1bis-FL-AM-like technical replicate 5

description: AM-like, FL, Animal A1bis, technical replicate 5


title: placenta (584560_BS)

value: College graduate


title: placenta (584528_oxBS)

value: Male


title: A1bis-FL-AM-like technical replicate 4

description: AM-like, FL, Animal A1bis, technical replicate 4


title: L_25R_30D_Rep1

value: DMSO for 30 min


title: L_25R_30D_Rep2


title: placenta (584388_oxBS)


title: L_25R_30TPA_Rep1

value: 200 nM TPA for 30 min


title: A1bis-FL-AM-like technical replicate 2

description: AM-like, FL, Animal A1bis, technical replicate 2

value: AM-like


title: L_25R_15TPA_Rep2


title: A1bis-FL-AM-like technical replicate 1

description: AM-like, FL, Animal A1bis, technical replicate 1

value: yes


title: L_25R_15TPA_Rep1


title: placenta (584300_BS)

value: Female


title: placenta (584320_oxBS)


title: placenta (584300_oxBS)


title: L_25R_15D_Rep2


title: A3-CTRL-AM-like technical replicate 12

description: AM-like, CTRL, Animal A3, technical replicate 12

value: no


title: placenta (584276_BS)

value: Any post graduate schooling


title: placenta (584320_BS)


title: placenta (584240_BS)


title: placenta (584276_oxBS)


title: A3-CTRL-AM-like technical replicate 11

description: AM-like, CTRL, Animal A3, technical replicate 11


title: L_25R_15D_Rep1

value: 4sU-labeled RNA


title: placenta (584260_oxBS)


title: placenta (584388_BS)


title: A3-CTRL-AM-like technical replicate 10

description: AM-like, CTRL, Animal A3, technical replicate 10


title: placenta (584412_oxBS)


title: placenta (584172_oxBS)


title: placenta (584216_oxBS)


title: placenta (584172_BS)


title: PROseq_52R2

data_processing:
Library strategy: PRO-seq
TT-seq and RNA-seq: Paired-end reads with additional 6 bp of barcodes were obtained for each group of samples. Two replicates were treated for each condition. Reads were aligned to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium) using STAR 2.6.0 (Dobin et al., 2013), with the following specifications: outFilterMismatchNmax 2, outFilterMultimapScoreRange 0 and alignIntronMax 500000. Bam files were filtered with Samtools (Li et al., 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f2) were selected. Read counts for different features were calculated with HTSeq (Anders et al., 2015). Further data processing was carried out using the R/Bioconductor environment. Expressed transcripts were defined as possessing more than 50 read counts per kilobase (RPK) in two summarized replicates of TT-seq solvent control (DMSO). Prior to quantification, data was normalized by using added RNA spike-in as described previously (Schwalb et al., 2016). Normalized coverage was exported to the bigwig format using R/Bioconductor rtracklayer package.
PRO-seq: PRO-seq data were trimmed with cutadapt version 1.11 (Martin, 2011) using the following parameters: sample PROseq_25R_Rep1: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACACATCGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; sample PROseq_25R_Rep2: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACTGGTCAATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; sample PROseq_52R_Rep1: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGATCTGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20; and sample PROseq_52R_Rep: cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACGGACGGATCT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGT -m 20 . The reads were mapped to the human genome (Genome Reference Consortium version GRCh38) of the human genome (from April 2014) and to the Drosophila melanogaster genome version BDGP6.28 with STAR (v2.6.1) (Dobin et al, 2013) using the following parameters: --outFilterMismatchNmax 3 --outFilterMultimapScoreRange 0 --alignIntronMax 500000. Resulting bam files were filtered using SAMTOOLS (v1.9) (Li et al, 2009) to remove alignments with mapping quality lower than 7 (-q 7). Only proper pairs (-f2) were retained. In order to calculate normalization factors for PRO-seq, HTSeq (v0.6.0) (Anders et al, 2015) with intersection-strict mode and --stranded=reverse parameter was used to calculate reads mapping to D.melanogaster transcripts (Drosophila_melanogaster.BDGP6.28.100.gtf.gz from Ensembl.org) followed by calculation of size factors with DESeq2 Bioconductor package (Love et al, 2014). PRO-seq sequencing Read1 mapping to the human genome was converted to reverse complement sequence and the last nucleotide incorporated by the RNAPII was determined (RNAPII position) - last base of the reversely complemented Read 1 for the “+” strand, and first base of the reversely complemented Read 1 for the “-” strand. Coverage for RNAPII position was calculated using coverage function from GRanges R Bioconductor package (Lawrence et al, 2013) and normalized using size factors determined with DESeq2 for D.melanogaster transcripts.  Normalized coverage was exported to the bigwig format using R/Bioconductor rtracklayer package.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigWig coverage files

extract_protocol:
PRO-seq (Mahat et al, 2016)
PRO-seq (Mahat et al, 2016)

value: U2OS osteosarcoma cells

value: Biotin-labeled RNA PolII-associated RNA

value: U2OS cells expressing RPB1-CTD with 52 repeats (Boehning et al 2018)

value: no treatment