title: EC_2ug_3

city: Harbin

first: Rui

last: Sui

address: Department of Microbiology, Harbin Medical University, 194 Xuefu Road, Nangang District, Harbin, China, 150086

department: Microbiology

institute: Harbin medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to NC_000913.3 whole genome using  Bowtie2-2.2.3 with parameters -p 8 -x index -1reads1.fq -2 reads2.fq -S out.sam
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then  FPKM  of  each  gene  was  calculated  based  on  the  length  of  the  gene  and reads  count  mapped  to  this  gene.  FPKM, expected  number  of  Fragments  Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time,and   is   currently   the   most   commonly   used   method   for   estimating   gene expression levels.
(For DESeq with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0).
Picard-tools v1.96 and samtools v0.1.18 were used to sort, mark duplicated reads and reorder the bam alignment results of each sample. GATK2 software   was used to perform SNP calling
Genome_build: NC_000913.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Samples

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli K12 strain MG1655

growth_protocol: E. coli K12 strain MG1655 was grown in 250 mL flasks with Luria-Bertani (LB) medium in a shaking incubator at 37 ℃ and 250 rpm overnight.

extract_protocol:
Total RNA isolation from E. coli cells was performed using the Qiagen RNA protect bacterial reagent (Qiagen, Hilden, Germany) and purification was conducted using Qiagen RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instruction. After assessment of RNA purity and integrity, RNA samples were treated using Epicentre Ribo-zero rRNA Removal Kit (Epicentre, Madison, WI, USA), followed by RNA fragmentation, synthesis of the first and second strands DNA, and appendence of sequencing adapter. Then the selected fragments by Agencourt AMPure XP Beads (Illumina Inc , San Diego, CA, USA) were amplified, followed by library purification, enrichment and quality determination. Accordingly, 6 cDNA libraries (3 from ciprofloxacin-treated E. coli, and 3 from non-ciprofloxacin-treated E. coli) were constructed and subjected to Illumina Hiseq 2500 sequencing platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: treated with 2 μg/mL ciprofloxacin for 20min

tag: treatment

value: treated with 2 microg/mL ciprofloxacin for 20min


title: FOXA1_NKI_13_T

status: Public on Jun 16 2020

type: SRA

city: Boston

first: Matthew

last: Freedman

state: Massachusetts

address: 450 Brookline Avenue

country: USA

institute: Dana Faber Cancer Institute

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

molecule: genomic DNA

organism: Homo sapiens

source_name: Patient localized prostate tissue

extract_protocol:
One (histone ChIP) or three (transcription factor ChIP) 2 mm2 frozen cores were pulverized using the Covaris CryoPrep system. Tissue was fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced using 75-bp reads on the Illumina platform at the Dana-Farber Cancer Institute.

tag: tissue

value: Patient localized prostate tissue

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.#

tag: chip antibody lot/batch#


title: EC_2ug_2

country: China

library_source: transcriptomic

molecule: total RNA


title: FOXA1_NKI_7_N


title: FOXA1_NKI_13_N


title: FOXA1_NKI_5_N


title: FOXA1_NKI_1_N


title: FOXA1_NKI_23_N


title: FOXA1_DF_2030_N

value: localized prostate tissue


title: EC_2ug


title: EC_0_3

value: untreated


title: FOXA1_DF_2484_N


title: EC_0


title: EC_0_2


title: FOXA1_DF_2483_N


title: AR_UW_PDX_189-4

source_name: CRPC PDX

value: CRPC pdx

value: AR

value: Santa Cruz Biotechnology


title: RBFOX2 1100nM

city: Cambridge

first: Bridget

middle: E

last: Begg

state: MA

address: 31 Ames St

department: Biology

institute: Massachusetts Institute of Technology

description: 3' UTR 110-nt synthetic oligonucleotides

data_processing:
Reads were aligned to the designed library.
Perfectly-mapping reads only were assigned to each oligonucleotide.
Only oligonucleotides with 100 or more attributable reads in the input RNA library were considered for further analyses.
Genome_build: 3' UTR nsRBNS library: hg19, mm9
Supplementary_files_format_and_content: Each processed data file contains the perfectly mapping reads attributable to each oligonucleotide in that sample.

organism: synthetic construct

source_name: predesigned sequence library using 3' UTRs from H. sapiens/M. musculus

extract_protocol:
RBP:RNA:bead complexes were pulled down with a magnet and washed gently 2X. RNA was eluted by two incubations with biotin for 30m at RT. RNA eluate was purified with Ampure beads.
RNA was reverse transcribed. The cDNA was amplified for 6-16 cycles and gel-purified to produce the final library.

treatment_protocol: Recombinantly-expressed, tagged RBFOX2 RRM was incubated at varied concentrations with 250nM synthetic RNA oligonucleotide library to equilibrium (1h 4C).

tag: protein concentration

value: RBFOX2 1100nM


title: AR_UW_PDX_189-3


title: AR_UW_PDX_170-3


title: AR_UW_PDX_170-2


title: AR_UW_PDX_167


title: ce117_13

city: La jolla

first: Jerel

middle: Adam

last: Fields

address: 9500 Gilman Dr., BSB 3009

institute: UCSD

data_processing:
Quality of the sequencing reads were assessed using FASTQC v0.11.8. Adapters and low-quality reads were trimmed using a kmer approach as implemented in BBDuk v38.62 using default settings.
Transcripts were quantified using quasi-mapping mode of Salmon v0.14.1, using paameters -validateMappings -gcBias -sseqBias -numGibbsSamples 100
Transcripts were summarized to gene counts for downstream analysis using the tximport v1.10.0  package. Technical replicates were collpased. Genes were retained in the analysis if they achieved counts per million (cpm) > 1 in at least half of the brain samples.
For the log-transformed expression data with precision weights, per-gene linear regression models were fit to account for the effects of cognitive impairment status after adjustment for unmodeled variation sources.
Test for statistical significance was achieved by implementation of a Bayesian strategy of Lönnstedt and Speed as implemented in R package limma v3.38.3
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Frontal Cortex

extract_protocol:
Total RNA was isolated from 50 mg of postmortem brain tissues from Broddmann Area 46 using the Qiagen RNeasy Lipid Tissue Kit per manufacturer’s instructions (Qiagen; cat no. 74804)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Frontal Cortex

tag: age

tag: Sex

value: Male

tag: neurocognitive status

value: MND

tag: arv status


title: ce117_S4


title: CE116_S6

value: Female

value: HAART


title: CE150_S6


title: ce144_S7


title: CE135_S7


title: CE116_S7


title: ce125_S11

value: Normal


title: cc295_S6

value: ANI


title: AR_UW_PDX_136


title: AR_UW_PDX_92


title: AR_UW_PDX_141


title: AR_UW_PDX_86-2


title: cc196_S13

value: Naïve


title: AR_UW_PDX_81


title: cc202_S14


title: CE150_S5


title: FOXA1_DF_2480_N


title: cc196_S15


title: AR_UW_PDX_58


title: FOXA1_DF_2078_N


title: cc128_S5

value: normal


title: AR_UW_PDX_77


title: cc128_S4


title: AR_UW_PDX_70


title: AR_UW_PDX_35


title: cc125_S10


title: cc202_S16


title: cc106_S9


title: cb194_S14


title: AR_NKI_23_T

value: Patient localized prostate tissue

value: Millipore


title: AR_NKI_19_T


title: AR_NKI_7_T


title: cb194_S5


title: AR_NKI_27_T


title: AR_NKI_29_T


title: ca295_S11


title: ca237_S1


title: AR_UW_PDX_78


title: CB164_S0


title: AR_NKI_1_T


title: CA195_S2


title: AR_NKI_5_T


title: ca209_S15


title: AR_DF_4024_T

value: localized prostate tissue


title: AR_DF_2815_T


title: ca184_S16

value: HAD


title: CA195_S1


title: AR_DF_2752_T


title: ca176_S8


title: AR_DF_1592_T


title: 7472_S3


title: AR_DF_1853_T


title: AR_DF_1816_T


title: 7472_S12


title: ca295_S2


title: AR_NKI_13_T


title: 4170_S9

value: MALE


title: AR_DF_1798_T

value: AR


title: 4170_S8


title: 4151_S9


title: AR_DF_1730_T

value: Santa Cruz Biotechnology


title: AR_NKI_25_N


title: AR_NKI_27_N


title: AR_NKI_19_N


title: 4077_S2


title: AR_NKI_7_N


title: 4109_S3


title: 4067_S10


title: AR_DF_1239_T


title: AR_DF_1636_T


title: 4077_S3


title: AR_NKI_1_N


title: AR_NKI_13_N


title: 4067_S11


title: ngn-1_10_S8_rep4

city: Kennesaw

first: Martin

middle: Lyn

last: Hudson

state: GA

address: 370 Paulding Avenue, Suite SC507, MD1201

department: Molecular and Cellular Biology

institute: Kennesaw State University

data_processing:
Read quality was determined using FastQC ver.0.11.7
Read files were converted to sanger files and groomed for read quality using FASTQ Groomer ver.1.1.1
Reads were aligned back to the C. elegans reference genome (wbcel235) using Hisat2 ver.2.1.0 with (Samtools 1.4)
Aligned reads were assembled and transcripts were quantified using Stringtie 1.3.3.2 (with Samtools 1.6)
Differential expression analysis performed using DESeq2 ver.3.4.1 (galaxy.org ver.2.11.40.2)
Genome_build: wbcel235
Supplementary_files_format_and_content: tab-delimited text files in .tsv and .gtf formats (note that the gene abundance estimates are .tsv files but have a .gtf file tag)

organism: Caenorhabditis elegans

growth_protocol: Embryos were isolated by alkaline lysis from gravid worms grown in liquid culture.

extract_protocol:
Total RNA was extracted using RiboZol (AMRESCO) and followed the vendor’s protocol. Embryonic tissue was added to 1 mL of RiboZol and 500 uL aliquoted into two 5 PRIME Phase Lock Gel Tubes. At the isopropanol stage, 3uL of 20ng/ml glycogen was added to improve RNA pellet visualization.
Illumina TruSeq RNA v2 kit, according to manufacturer's protocol

treatment_protocol: Embryos were snap frozen in liquid nitrogen, ground to a fine powder and transferred to an RNase-free microfuge tube

tag: strain background

tag: genotype/variation

value: embryo


title: ngn-1_9A_S7_rep3


title: ngn-1_8_S6_rep2


title: ngn-1_7B_S5_rep1


title: N2_11A_S4_rep4

value: wild type


title: WIBR3 tdhTSC Line 1 Rep 2

city: Haining

first: Yixin

last: Guo

address: 718 East Haizhou Rd.

institute: Zhejiang University

data_processing:
FASTQ files were mapped to hg19 using the STAR aligner with default parameters.
Bam files were analyzed by RNA-SeQC to confirm library quality.
Read counts were calculated with htseq-count and RPKM was calculated using cufflinks with default settings.
Genome_build: hg37
Supplementary_files_format_and_content: readcount file

source_name: WIBR3 tdhTSC Line 1

growth_protocol: hTSCs were cultured according to published protocol(Okae et al., 2018) with the following alterations. 0.5-1 x 105 cells were plated on each well of a six-well plate, and cells were passaged every 5-7 days. Cells were grown at 5% O2 5% CO2

extract_protocol:
RNA extraction was performed using Qiagen RNeasy micro kit
mRNA was enriched from 500ng total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module kit and libraries were generated using Swift RNA library kit

treatment_protocol: Naïve hESCs were passaged to Matrigel (Corning) coated plates at 20-30% confluency into trophoblast stem cell culture media. Cells were grown on collagen-coated plates in subsequent passages, akin to control hTSCs.

tag: cell type

value: Transdifferentiated human trophoblast stem cells


title: WIBR3 tdhTSC Line 1 Rep 1


title: UCLA1 tdhTSC Line 1 Rep 2

source_name: UCLA1 tdhTSC Line 1


title: WIBR3 tdhTSC Line 2 Rep 2

source_name: WIBR3 tdhTSC Line 2


title: WIBR3 tdhTSC Line 3 Rep 1

source_name: WIBR3 tdhTSC Line 3


title: UCLA1 tdhTSC Line 1 Rep 1


title: 4151_S10

value: Frontal Cortex

value: MND


title: N2_6_S3_rep3


title: 4109_S4


title: WIBR3 Naive hESCs Rep 2

source_name: WIBR3 Naive hESCs

growth_protocol: Naïve hESCs were cultured in PXGL maintenance medium (24.5 ml DMEM F-12, 24.5 ml Neurobasal media, 0.25 ml N2, 0.5 ml B27, 1xGlutamax, 150 μM L-ascorbic acid, 0.1mM β-mercaptoethanol, 1μM PD0325901, 2μM Gö6983, 10μM ROCKi, 2μM XAV939 and 10ng/ml recombinant hLIF)

treatment_protocol: hESCs were reverted to naïve state using a one-step induction adapted from published protocols(Guo et al., 2017)

value: Human embryonic stem cells


title: WIBR3 Primed hESCs Rep 4

source_name: WIBR3 Primed hESCs

growth_protocol: Primed hESCs were routinely cultured with TeSR-E8 (StemCell Technologies) on hESC Qualified Matrigel (Corning).


title: CT3 hTSCs Rep4

source_name: CT3 hTSCs

value: Human trophoblast stem cells


title: N2_5_S2_rep2


title: N2_4_S1_rep1


title: CT3 hTSCs Rep3


title: CT1 hTSCs Rep6

source_name: CT1 hTSCs


title: CT1 hTSCs Rep7


title: BT2 hTSC Rep4

source_name: BT2 hTSC


title: BT2 hTSC Rep3


title: WIBR3 tdhTSC Line 2

description: WGBS library for transdifferentiated human trophoblast stem cells line 2

data_processing:
The adaptor sequences of paired end 150bp WGBS raw reads were first trimmed based on the FastQC(v0.11.8)(Andrews, 2010) report using Cutadapt(v1.9.1)(Martin, 2011).
Then the last 15 bp of read1 and first 15 bp of read2 were cut according to Swift kits manual using Cutadapt(v1.9.1)(Martin, 2011).
Trimmed paired end reads were then aligned to human reference genome (GRCh38) using BSMAP (v2.7.4)(Xi and Li, 2009) allowing 2 mismatches.
Methylation level over each cytosine were then calculated using BSMAP (v2.7.4) methratio.py scripts.
Potential unconverted reads were removed as described before with customized function incorporated in the methratio.py script(Cokus et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: Fomat: txt; Content: CG methratio

source_name: Transdifferentiated human trophoblast stem cells

extract_protocol:
Genomic DNA was collected using Qiagen Blood and Tissue kit. An RNase A treatment step was included according to manufacturer’s protocol. DNA concentration was measured using Nanodrop.
500ng of DNA was fragment using Covaris M202 instrument and 250ng was processed with a Zymogen Bisulfite conversion kit. The equivalent of 50ng-100ng of starting DNA used for library prep, which was conducted using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences) and Unique Dual Index adaptors according to manufacturer protocols.


title: WIBR3 tdhTSC Line 1

description: WGBS library for transdifferentiated human trophoblast stem cells line 1


title: V39-MF

type: RNA

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

hyb_protocol: none provided by submitter

scan_protocol: 50-100 ng of RNA was analysed for the expression of 770 genes related to the innate immune system with the nCounter® Human Myeloid Innate Immunity Panel v2 utilizing the NanoString platform, using the CodeSet-Plus/Panel-Plus nCounter XT Gene Expression Assay.

data_processing: Raw data were quality checked in the nSolver software followed by normalization. Normalization factors were calculated based on 40 reference genes included in the myeloid innate immunity panel.

label: Nanostring

source_name: skin biopsy, FFPE

label_protocol: standard Nanostring protocol

extract_protocol: Total RNA was isolated from ten 10-μm sections of FFPE samples using the Roche high pure RNA FFPE isolation kit.

tag: condition

value: MF

tag: cohort

value: validation


title: V40-MF


title: WIBR3 Primed hESC

description: WGBS library for WIBR3 Primed hESC

source_name: Human embryonic stem cells

value: embryonic stem cells


title: V1-D

value: D


title: CT1 hTSC

description: WGBS library for CT1 human trophoblast stem cells

source_name: Human trophoblast stem cells

value: trophoblast stem cells


title: CT3 hTSC

description: WGBS library for CT3 human trophoblast stem cells


title: V44-MF


title: V41-MF


title: V43-MF


title: V42-MF


title: V35-MF


title: V38-MF


title: V37-MF


title: V36-MF


title: V34-MF


title: V33-MF


title: CT1 hTSCs Rep5


title: V32-MF


title: V31-MF


title: V30-MF


title: V29-MF


title: HepaRG_cell_nefazodone_30µM_bile_acid_mix_3

city: Jette

first: Eva

middle: Anne D

last: Gijbels

state: Brussels

address: Laarbeeklaan 103, Building G, 2th floor, Department IVTD

country: Belgium

institute: VUB

description: Gene expression of human hepatoma HepaRG cells treated with 30µM nefazodone and the 50 times concentrated bile acid mixture during 72 hours

hyb_protocol: 12.5 μg of fragmented amplified RNA was hybridized to Affymetrix Human genome U133 plus 2.0 GeneChip and Affymetrix Mouse Genome 430 2.0 GeneChip. Subsequently, the chips were placed in a GeneChip Hybridization Oven 645 (Affymetrix, Germany). After incubation, the arrays were washed with GeneChip Fluidics Station 450 (Affymetrix, Germany) and stained with Affymetrix HWS kit.

scan_protocol: Stained arrays were scanned via an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Robust Multichip Average (RMA) Express was utilized for normalization and summarization.
Background adjustment, quantile normalization and summarization using median polish was executed via RMA Expression Software.

label: Biotin

source_name: Cell lysates of HepaRG cells treated with 30µM nefazodone and the bile acid mix

label_protocol: 100 ng total RNA per sample was amplified using a GeneChip 3′IVT Express Kit following manufacturer’s instructions (Affymetrix, Germany). Amplified RNA was purified with magnetic beads and 15 mg biotin-amplified RNA was treated with fragmentation reagent.

growth_protocol: Sv129 were housed in the animal facility of the Faculty of Medicine and Health Sciences at Ghent University, Belgium, and allowed to acclimatize at least 1 week prior to the experiments under controlled conditions. Cryopreserved differentiated HepaRG cells (Biopredic International, France) were thawed and seeded following manufacturer’s instructions with basal hepatic cell medium (Williams’ E basal medium with GlutaMAX containing phenol red, Biopredic International, France) supplemented with thaw seed and general purpose medium (Biopredic International, France). Hereafter, HepaRG cells were maintained in basal hepatic cell medium supplemented with maintenance and metabolism medium (Biopredic International, France) and refreshed every 2–3 days. Cells were treated from day 7 after seeding.

extract_protocol: Total RNA was extracted using the Rneasy mini kit (Qiagen, Belgium)

treatment_protocol: Sv129 mice were subjected to common bile duct ligation surgery and HepaRG cells were treated with cholestatic drugs atazanavir, cyclosporin A and nefazodone in absence or presence of a 50 times concentrated bile acid mixture.

tag: cell line

value: HepaRG cells


title: HepaRG_cell_nefazodone_30µM_bile_acid_mix_1

tag: treatment

value: 30µM nefazodone and the 50 times concentrated bile acid mixture


title: HepaRG_cell_nefazodone_30µM_2

description: Gene expression of human hepatoma HepaRG cells treated with 30µM nefazodone during 72 hours

source_name: Cell lysates of HepaRG cells treated with 30µM nefazodone

value: 30µM nefazodone


title: HepaRG_cell_nefazodone_30µM_bile_acid_mix_2


title: HepaRG_cell_nefazodone_30µM_3


title: V27-MF


title: HepaRG_cell_cyclosporinA_20µM_bile_acid_mix_3

description: Gene expression of human hepatoma HepaRG cells treated with 20µM cyclosporin A and the 50 times concentrated bile acid mixture during 72 hours

source_name: Cell lysates of HepaRG cells treated with 20µM cyclosporin A and the bile acid mix


title: V28-MF


title: V25-MF


title: V24-MF


title: V21-MF


title: V23-MF


title: HepaRG_cell_cyclosporinA_20µM_bile_acid_mix_2

value: 20µM cyclosporin A and the 50 times concentrated bile acid mixture


title: V26-MF


title: HepaRG_cell_cyclosporinA_20µM_3

description: Gene expression of human hepatoma HepaRG cells treated with 20µM cyclosporin A during 72 hours

source_name: Cell lysates of HepaRG cells treated with 20µM cyclosporin A

value: 20µM cyclosporin A


title: HepaRG_cell_cyclosporinA_20µM_2


title: V20-MF


title: HepaRG_cell_nefazodone_30µM_1


title: V19-MF


title: HepaRG_cell_atazanavir_60µM_bile_acid_mix_2

description: Gene expression of human hepatoma HepaRG cells treated with 60µM atazanavir and the 50 times concentrated bile acid mixture during 72 hours

source_name: Cell lysates of HepaRG cells treated with 60µM atazanavir and the bile acid mix


title: HepaRG_cell_atazanavir_60µM_bile_acid_mix_1

value: 60µM atazanavir and the 50 times concentrated bile acid mixture


title: HepaRG_cell_cyclosporinA_20µM_bile_acid_mix_1


title: HepaRG_cell_atazanavir_60µM_bile_acid_mix_3


title: HepaRG_cell_atazanavir_60µM_3

description: Gene expression of human hepatoma HepaRG cells treated with 60µM atazanavir during 72 hours

source_name: Cell lysates of HepaRG cells treated with 60µM atazanavir

value: 60µM atazanavir


title: V22-MF


title: V18-MF


title: D83-HS

value: HS

value: Discovery


title: D82-HS


title: D84-HS


title: D80-HS


title: D81-HS


title: D78-HS


title: D79-HS


title: HepaRG_cell_atazanavir_60µM_2


title: HepaRG_cell_bile_acid_mix_2

description: Gene expression of human hepatoma HepaRG cells treated with a 50 times concentrated bile acid mixture during 72 hours

source_name: Cell lysates of HepaRG cells treated with the bile acid mix


title: HepaRG_cell_atazanavir_60µM_1


title: HepaRG_cell_cyclosporinA_20µM_1


title: HepaRG_cell_bile_acid_mix_1

value: a 50 times concentrated bile acid mixture


title: HepaRG_cell_control_2

description: Gene expression of human hepatoma HepaRG cells treated with the vehicle control during 72 hours

source_name: Cell lysates of HepaRG cells treated with the vehicle control

value: the vehicle control


title: HepaRG_cell_control_3


title: 0_10_A_1

city: Seoul

first: Doyoung

last: Kim

address: 50-1 Yonsei-ro Seodaemun-gu

department: Dermatology

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: Excel format with RPKM raw data for each sample

source_name: primary dermal papilla cells

growth_protocol: The hDP cells were cultured in Dulbecco's modified Eagle's medium (DMEM; Hyclone, Logan, UT, USA) supplemented with 10% fetal bovine serum (FBS; Hyclone) and antibiotic/antimycotic solution (Gibco BRL, Gaithersburg, MD, USA) containing penicillin and streptomycin. Cells were incubated at 37°C in a 5% CO2 incubator. All cultures used for experiments were in the third passage

extract_protocol:
Extraction of total RNA was performed using an RNeasy plus mini kit (Qiagen, Hilden, Germany) following the nanufacturer's instructions.
Sequencing libraries were prepared using the SMARTer Stranded RNA-Seq Kit (Clontech Laboratories, Inc., USA) and the Poly(A) RNA Selection Kit (LEXOGEN, Inc., Austria) by the manufacturer’s recommendation. Quantification was performed using the library quantification kit using a StepOne Real-Time PCR System (Life Technologies, Inc., USA). High-throughput sequencing was performed as paired-end 100 sequencing using HiSeq2500 (Illumina, Inc., USA).

treatment_protocol: In order to expose NTAPP on cells, 6.5 × 104 cells were seeded in a 35-mm culture dish and incubated for 24 h. The cells were exposed to 4.2 kV of NTAPP for 1 min, the NTAPP-exposed cells were further incubated for 24 h before harvesting. The distance between the device and cells was fixed to 1 cm, and 1. 5 ml of medium was used.

tag: source tissue

value: anagen hair follicles

tag: passages

tag: plasma

value: exposed


title: E1WT rep4

city: Columbus

first: Zihai

last: Li

state: OH

address: 460 W 12th Ave

department: Institute for Immuno-Oncology

institute: Ohio State University

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

organism: Mus musculus

source_name: CD4+ T cells

extract_protocol:
Total naive CD4+ T cells isolated from the spleen of wild-type and Pcbp1fl/flCd4-Cre male mice using the naïve T cell isolation kit (Miltenyi, USA). Total RNA was extracted from the cells using the Rneasy kit (Qiagen).
Libraries were prepared using 50 ng of total RNA using the NEB Next Ultra RNA Library Kit for Illumina (Cat# E7530) and sequenced on HiSeq3000 at 75bp paired-end.

tag: strain

tag: tissue

value: spleen

value: 6-8 weeks old

tag: genotype

value: Pcbp1fl/flCd4-Cre (KO)

value: CD4+ T cells


title: E1WT rep2

tag: age


title: D77-HS


title: E1WT rep1


title: E1WT rep3


title: cont_1

value: unexposed


title: T47D_repl1

city: Solna

first: Henrik

middle: J

last: Johansson

state: Stockholm

address: Tomtebodavägen 23A

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

description:
4_151001_AC7HMTANXX_P2662_118
3_151001_AC7HMTANXX_P2662_118

data_processing:
1. Mapping: Reads were mapped with Tophat/2.0.4 to the Human genome assembly, build GRCh37. 2. Merging: Bamfiles from samples run on different lanes were merged with samtools. 3. Sorting and Marking duplicates: Merged bam files were sorted and duplicates removed using picard-tools/1.29. 4. Counts for genes: Gene counts were generated using htseq/0.6.1 on bam files with duplicates included. 5. FPKMs for genes and transcripts: FPKMs for genes and transcripts were generated using cufflinks/2.1.1 on bamfiles with duplicates included. 6. Mapping statistics: Mapping statistics were calculated from numbers obtained by running bam_stat.py (included in rseqc/2.3.6) on bam files with and without duplicates. 7. Readdistribution: read_distribution.py (included in rseqc/2.3.6) was run on bam files with duplicates. 8. Genebodycovarage: geneBody_coverage.py (included in rseqc/2.3.6) was run on bam files with duplicates. 9. Strandedness: infer_experiment.py (included in rseqc/2.3.6) was run on bam files with duplicates. 10. Library complexity: The complexity plot is generated by running preseq/0.1.0 on bam files with duplicates. 11. Corelation heatmap: The correlation heatmap is generated using the R-package pheatmap on the FPKM table for genes.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Cell line

growth_protocol: Panel of breast cancer cell lines consisting of HCC1419, MCF7, CAMA, HCC1428, T47D, HCC38, HCC70, HCC1569, MDA-MB-157, HCC1143, BT20, MDA-MB-231, MDA-MB-468, BT549, SUM159PT, Cal51 were purchased from the American Type Culture Collection (ATCC). Cell lines were maintained in RPMI1640 (Gibco, Thermo Fisher) supplemented with 10% FBS (Gibco, Thermo Fisher) and 2 mM L-glutamine (Gibco, Thermo Fisher), 10 mM HEPES (Gibco, Thermo Fisher), and 1 mM Sodium Pyruvate (Gibco, Thermo Fisher).

extract_protocol:
RNA was first isolated using Trizol reagent (Invitrogen, Life technologies), followed by RNeasy Mini Kit (Qiagen)
Illumina TruSeq Stranded total RNA, Illumina RiboZero

treatment_protocol: Untreated

value: Breast cancer cell line

value: Untreated


title: T47D_repl3


title: D75-HS


title: T47D_repl2


title: D76-HS


title: E1KO rep3

value: Pcbp1+/+Cd4-Cre (WT)


title: D74-HS


title: D72-D

value: D


title: SUM149PT_repl3


title: HepaRG_cell_bile_acid_mix_3

value: HepaRG cells


title: HepaRG_cell_control_1


title: D71-D


title: E1KO rep4


title: D73-HS


title: E1KO rep1


title: SUM149PT_repl2

description:
6_151001_AC7HMTANXX_P2662_135
5_151001_AC7HMTANXX_P2662_135


title: D70-D


title: SUM149PT_repl1

description:
4_151001_AC7HMTANXX_P2662_117
3_151001_AC7HMTANXX_P2662_117


title: SKBR3_repl3


title: SKBR3_repl2

description:
6_151001_AC7HMTANXX_P2662_134
5_151001_AC7HMTANXX_P2662_134


title: SKBR3_repl1

description:
4_151001_AC7HMTANXX_P2662_116
3_151001_AC7HMTANXX_P2662_116


title: D68-D


title: D69-D


title: E1KO rep2


title: D67-D


title: D66-D


title: MDAMB157_repl1

description:
4_151001_AC7HMTANXX_P2662_115
3_151001_AC7HMTANXX_P2662_115


title: MDAMB157_repl2

description:
6_151001_AC7HMTANXX_P2662_133
5_151001_AC7HMTANXX_P2662_133


title: D65-D


title: MCF7_HJ_repl3

description:
8_151001_AC7HMTANXX_P2662_150
7_151001_AC7HMTANXX_P2662_150


title: D64-D


title: MCF7_HJ_repl2

description:
6_151001_AC7HMTANXX_P2662_132
5_151001_AC7HMTANXX_P2662_132


title: D63-D


title: D61-D


title: D62-early-MF

value: early-MF


title: TN sample 2

city: Jeddah

first: Hans-Juergen

last: Schulten

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

hyb_protocol: Following fragmentation, 6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip HuGene-1.0-st arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
Data were generated using the Affymetrix Expression Console Software using Affymetrix default analysis settings.
Data were RMA normalized and analyzed with Partek Genomics Suite 6.6 and other bioinformatics softwares.

label: biotin

source_name: Thyroid, normal histology

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA from biospecimens was extracted using the Quagen RNeasy mini kit according to the manufacturer's instructions and integrity of RNA was assessed using the Agilent Bioanalyzer.

tag: gender

value: not available

tag: sample type

value: normal thyroid samples (TN)


title: TN sample 3


title: MDAMB157_repl3

description:
8_151001_AC7HMTANXX_P2662_151
7_151001_AC7HMTANXX_P2662_151


title: mPTC sample mPTC-6R-THY

source_name: mPTC histology (stage I)

value: F

value: micro PTC (mPTC)


title: TN sample 1


title: mPTC sample mPTC-3R-THY


title: MCF7_repl1

description:
4_151001_AC7HMTANXX_P2662_113
3_151001_AC7HMTANXX_P2662_113


title: MCF7_repl2

description:
6_151001_AC7HMTANXX_P2662_131
5_151001_AC7HMTANXX_P2662_131


title: mPTC sample mPTC-2R-THY


title: mPTC sample mPTC-5R-THY


title: mPTC sample mPTC-4R-THY

value: M


title: D59-D

value: Discovery


title: D58-early-MF


title: D57-early-MF


title: PTC sample PTC w/o HT-6R-THY

source_name: PTC histology (stage I) without HT in background

value: PTC without HT in background


title: mPTC sample mPTC-1R-THY


title: PTC sample PTC w/o HT-4R-THY


title: LCC2_repl2

description:
6_151001_AC7HMTANXX_P2662_130
5_151001_AC7HMTANXX_P2662_130


title: MCF7_repl3

description:
8_151001_AC7HMTANXX_P2662_149
7_151001_AC7HMTANXX_P2662_149


title: LCC2_repl3

description:
8_151001_AC7HMTANXX_P2662_148
7_151001_AC7HMTANXX_P2662_148


title: D60-D

source_name: skin biopsy, FFPE


title: MCF7_HJ_repl1

description:
4_151001_AC7HMTANXX_P2662_114
3_151001_AC7HMTANXX_P2662_114


title: PTC sample PTC w/o HT-5R-THY

source_name: PTC histology (stage II) without HT in background


title: D56-early-MF


title: LCC2_repl1

description:
2_151001_AC7HMTANXX_P2662_112
1_151001_AC7HMTANXX_P2662_112


title: HCC70_repl2

description:
6_151001_AC7HMTANXX_P2662_129
5_151001_AC7HMTANXX_P2662_129


title: PTC sample PTC w/o HT-2R-THY


title: HCC70_repl1

description:
2_151001_AC7HMTANXX_P2662_111
1_151001_AC7HMTANXX_P2662_111


title: D52-early-MF


title: PTC sample PTC w/o HT-3R-THY


title: HCC70_repl3

description:
8_151001_AC7HMTANXX_P2662_147
7_151001_AC7HMTANXX_P2662_147


title: D53-early-MF


title: D50-early-MF


title: D54-early-MF


title: HCC38_repl2

description:
6_151001_AC7HMTANXX_P2662_128
5_151001_AC7HMTANXX_P2662_128


title: HCC38_repl1

description:
2_151001_AC7HMTANXX_P2662_110
1_151001_AC7HMTANXX_P2662_110


title: D51-early-MF


title: PTC sample PTC w/ HT-6R-THY

source_name: PTC histology (stage I) with HT in background

value: papillary thyroid carcinoma (PTC) with HT in background


title: PTC sample PTC w/ HT-5R-THY


title: HCC1954_repl3

description:
8_151001_AC7HMTANXX_P2662_145
7_151001_AC7HMTANXX_P2662_145


title: HCC1954_repl2

description:
6_151001_AC7HMTANXX_P2662_127
5_151001_AC7HMTANXX_P2662_127


title: PTC sample PTC w/ HT-7R-THY


title: HCC1954_repl1

description:
2_151001_AC7HMTANXX_P2662_109
1_151001_AC7HMTANXX_P2662_109


title: PTC sample PTC w/ HT-4R-THY


title: D46-D


title: PTC sample PTC w/ HT-2R-THY


title: PTC sample PTC w/ HT-3R-THY


title: PTC sample PTC w/o HT-1R-THY


title: D49-early-MF


title: HT sample HT-13R-THY

source_name: HT histology

value: Hashimoto's thyroiditis (HT), papillary thyroid carcinoma (PTC) with HT in background, PTC without HT in background, micro PTC (mPTC), and three normal thyroid samples (TN).


title: D48-D


title: D55-early-MF


title: HT sample HT-12R-THY


title: D47-D


title: PTC sample PTC w/ HT-8R-THY


title: HCC1397_repl2

description:
6_151001_AC7HMTANXX_P2662_126
5_151001_AC7HMTANXX_P2662_126


title: HCC1397_repl1

description:
2_151001_AC7HMTANXX_P2662_108
1_151001_AC7HMTANXX_P2662_108


title: D44-D


title: D45-D


title: PTC sample PTC w/ HT-1R-THY


title: HCC1569_repl2

description:
4_151001_AC7HMTANXX_P2662_125
3_151001_AC7HMTANXX_P2662_125


title: HCC1569_repl3

description:
8_151001_AC7HMTANXX_P2662_143
7_151001_AC7HMTANXX_P2662_143


title: HT sample HT-11R-THY


title: D42-D


title: HCC1397_repl3

description:
8_151001_AC7HMTANXX_P2662_144
7_151001_AC7HMTANXX_P2662_144


title: D41-D


title: D40-D


title: HCC1569_repl1

description:
2_151001_AC7HMTANXX_P2662_107
1_151001_AC7HMTANXX_P2662_107


title: D39-D


title: HCC1419_repl3

description:
8_151001_AC7HMTANXX_P2662_142
7_151001_AC7HMTANXX_P2662_142


title: HCC1419_repl2

description:
4_151001_AC7HMTANXX_P2662_124
3_151001_AC7HMTANXX_P2662_124


title: D43-D


title: D38-early-MF


title: HT sample HT-9R-THY


title: HCC1419_repl1

description:
2_151001_AC7HMTANXX_P2662_106
1_151001_AC7HMTANXX_P2662_106


title: HT sample HT-8R-THY


title: HT sample HT-10R-THY


title: HCC1187_repl2

description:
4_151001_AC7HMTANXX_P2662_123
3_151001_AC7HMTANXX_P2662_123


title: HT sample HT-5R-THY


title: HT sample HT-6R-THY


title: HT sample HT-7R-THY


title: HCC1187_repl1

description:
2_151001_AC7HMTANXX_P2662_105
1_151001_AC7HMTANXX_P2662_105


title: D36-early-MF


title: HCC1187_repl3


title: D34-early-MF


title: D37-early-MF


title: HCC1143_repl3

description:
8_151001_AC7HMTANXX_P2662_140
7_151001_AC7HMTANXX_P2662_140


title: stage 40 rep 2

city: Beijing

first: Yongjie

last: Liu

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology

data_processing:
Adapters were removed using Trimmomatic(version 0.36)
Mapping by Bowtie( version 2.3.4.1) under the parameters -X 2000 --very-sensitive --qc-filter
PCR duplicates reads were removed using Picard
Peak calling was performed with macs2 2.1.2 using ‘macs2 callpeak -f BAMPE --keep-dup all -g 7.34e8’
Peak reads counts were calculated by multicov function from BEDTools
Genome_build: medaka ASM223467v1
Supplementary_files_format_and_content: wig files were generated using bamCoverage; Scores represent reads counts

organism: Oryzias latipes

source_name: whole embryo

growth_protocol: Embryos were incubated at 28 ◦C fresh water for all time course and processed for ATAC-seq at the indicated times

extract_protocol:
Medaka embryos were grown to the indicated times and chorions were removed by incubating in 1mg/mL Pronase.After removed yorks using deyork buffer,embryo tissues were triturated to homogeneity in 1 mL 1X TrypLE™ Express.
ATAC-Seq libraries were prepared using Omni-ATAC protocol and DNA fragments were recovered using mini-ATAC protocol

value: offspring of d-rR-Tg(olvas-GFP) and Qurt

tag: developmental stage

value: stage 40


title: D32-early-MF


title: HT sample HT-3R-THY


title: D35-early-MF


title: HT sample HT-4R-THY


title: D33-early-MF


title: HCC1143_repl2

value: Breast cancer cell line


title: stage 38 rep 2

value: stage 38


title: D31-early-MF


title: HT sample HT-2R-THY


title: stage 32 rep 2

value: stage 32


title: CAL51_repl3

description:
8_151001_AC7HMTANXX_P2662_139
7_151001_AC7HMTANXX_P2662_139

value: Untreated


title: stage 32 rep 1


title: CAL51_repl2

description:
4_151001_AC7HMTANXX_P2662_121
3_151001_AC7HMTANXX_P2662_121


title: D30-early-MF


title: HCC1143_repl1

description:
2_151001_AC7HMTANXX_P2662_104
1_151001_AC7HMTANXX_P2662_104


title: CAL51_repl1

description:
2_151001_AC7HMTANXX_P2662_103
1_151001_AC7HMTANXX_P2662_103


title: D28-early-MF


title: BT549_repl3

description:
6_151001_AC7HMTANXX_P2662_138
5_151001_AC7HMTANXX_P2662_138


title: stage 25 rep 2

value: stage 25


title: D27-early-MF

value: early-MF


title: BT549_repl2

description:
4_151001_AC7HMTANXX_P2662_120
3_151001_AC7HMTANXX_P2662_120


title: HT sample HT-1R-THY


title: stage 29 rep 1

value: stage 29


title: stage 25 rep 1


title: stage 36 rep 2

value: stage 36


title: BT549_repl1

description:
2_151001_AC7HMTANXX_P2662_102
1_151001_AC7HMTANXX_P2662_102


title: D26-early-MF


title: D25-early-MF


title: BT20_repl3

description:
6_151001_AC7HMTANXX_P2662_137
5_151001_AC7HMTANXX_P2662_137


title: BT20_repl2

description:
3_151001_AC7HMTANXX_P2662_119
4_151001_AC7HMTANXX_P2662_119


title: D24-early-MF


title: BT20_repl1

description:
1_151001_AC7HMTANXX_P2662_101
2_151001_AC7HMTANXX_P2662_101


title: stage 11 rep 2

value: stage 11


title: D29-early-MF


title: stage 15 rep 2

value: stage 15


title: st41-2_RNA

first: Qiang

last: Tu

address: No.1 West Beichen Road,Chaoyang District

description: Illumina TruSeq stranded  RNA-seq

data_processing:
for TPM.tab file: genome mapping using hisat2(2.1.0), default parameters
for TPM.tab file: gene expression quantification using stringtie(v1.3.3b), default parameters
for fasta file: gene model built from pacbio data and generate transcript sequance
Genome_build: medaka ASM223467v1
Supplementary_files_format_and_content: Two TPM.tab files are plain text(quantification count matrix  by TPM, rows are genes and columns  are samples), fasta file is transcript sequence use for quantification.

extract_protocol:
RNA extraction using both TRIzol and Qiagen RNeasy Micro Kit
Illumina TruSeq stranded mRNA library preparation protocol for RNA-seq samples

value: d-rR / Qurt

value: embryo

tag: developmental stages


title: D23-early-MF

value: Discovery


title: D22-early-MF


title: D21-early-MF


title: stage 29 rep 2


title: D20-early-MF


title: st40-2_RNA

description: Illumina TruSeq stranded  RNA-seq


title: HEK293-Trex cells, Control_2_IP

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

description:
NYNs_vs_Controls_intersect_peaks.tsv
NYN2_IPvsControl2_peaks.narrowPeak

data_processing:
library strategy: iCLIP
RNA sequencing reads were trimmed using Trimmomatic (v0.32). removing adaptor and other Illumina-specific sequences, and low-quality bases at the end of each read, using a 4bp sliding window to trim where average window quality fell below 30 (phred33 < 30). Trimmed reads with less than 15 bases were discarded.
The resulting clean set of reads were then aligned to the hg19 (GRCh37) reference genome using STAR (v2.3.0e) with default parameters. Reads mapping to more than 10 locations in the genome (MAPQ < 1) were discarded.
Secondary alignment reads were removed using samtools (v1.9) and duplicates were removed using Picard (v2.10.7) MarkDuplicates.
Peaks were then called on the resulting bam files using macs2 (v2.1.1) callpeak using the nomodel option and an extension size of 100.
The list of final peaks is then created by taking the intersection of the peaks found comparing NYN1 vs control1 and NYN2 vs control2. Peaks were then annotated with HOMER (v4.10) annotatePeaks using the hg19 reference.
Genome_build: hg19
Supplementary_files_format_and_content: tsv file containing annotation of the peaks called by macs2 and annotated by HOMER

source_name: HEK293-Trex cells

growth_protocol: cell culture growth media

extract_protocol:
Lysates were clarified from sonicated UV-crosslinked cells and MARF1-RNA complexes were isolated with FLAG antibody.
Crosslink immunoprecipitation experiments were conducted using a modified single-end (se)CLIP approach  (Van Nostrand et al., 2017).  All experiments were conducted using HEK293 cells (negative control), or HEK293 cells that express FLAG-tagged MARF-NYN.  Briefly, FLAG-tagged MARF1-NYN expression was induced in a 15 cm dish of HEK293 cells with 100ng/mL of doxycycline for 12 hours.  Following induction, 2x10e7 cells were lysed in iCLIP lysis buffer and sonicated (BioRuptor).  Lysates were treated with RNAseI (Thermo) to shear RNA, after which FLAG-tagged MARF1-NYN-RNA complexes were immunoprecipitated with FLAG antibody.  Stringent washes were performed, during wish RNA was dephosphorylated with FastAP (Thermo) and T4 PNK (NEB).  Following dephosphorylation, a 3’ RNA adaptor was ligated onto the RNA with T4 RNA ligase (NEB).  Protein-RNA complexes were resolved by SDS-PAGE, transferred to nitrocellulose membranes, and RNA was isolated from the membrane region corresponding to the migration of MARF1 and 75kDa above.  Isolated RNA was subsequently reverse transcribed with AffinityScript (Agilent) and the 3’ DNA adaptor was ligated onto the cDNA with T4 RNA ligase (NEB).  Libraries were then amplified with Q5 PCR mix (NEB).

treatment_protocol: 400 mJ cm2- UV 254 nm treatment

tag: expressing

value: negative control

tag: rip antibody

value: FLAG antibody


title: HEK293-Trex cells, Control_1_IP

description:
NYNs_vs_Controls_intersect_peaks.tsv
NYN1_IPvsControl1_peaks.narrowPeak


title: Vc_self_4

city: Swansea

first: Daniel

last: Eastwood

address: Singleton Park

country: United Kingdom

institute: Swansea University

data_processing:
Initial quality filtering of raw sequence reads was performed at CGR using Cutadapt v1.2.1 (Martin, 2011). The option -O 3 was used, so the 3' end of any reads which matched the adapter sequence for 3 bp. or more were trimmed.
The reads were further trimmed using Sickle v1.200 with a minimum window quality score of 20. Reads shorter than 10 bp. after trimming were removed.
De novo assembly of the V. comedens transcriptome was conducted using all combined sequence reads with Trinityv2.1.1(Grabherr et al. 2011), using default parameters and specifying a minimum contig length of 200 bp.
All transcripts were annotated against a custom database comprised of all available transcripts in NCBI Nucleotide for Trametes versicolor, Moniliophthora roreri, Saccharomyces cerevisiae, Punctularia strigozonata and Stereum hirsutum, using Blastn with an e-value cutoff < 1e-5.
Sequence reads from each independent replicate were then aligned against the final transcriptome assembly using Bowtie2 (v.2.2.6; Langmead et al. 2012), specifying –k 1 to report a single best hit for each read.
Raw count data for each transcript was extracted using idxstats in samtools (v. 0.1.19; Li et al. 2009) and used to calculate normalised FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values for each replicate.
Genome_build: De novo assembly.
Supplementary_files_format_and_content: abundance measurements as txt file (Five columns: transcript name, transcript length, abundance for rep1, rep2 and rep3)

organism: Vuilleminia comedens

source_name: Beech wood (Fagus sylvaticus) colonised with Vuilleminia comedens

growth_protocol: Beech wood blocks of 2 cm3 were pre-soaked in sterile distilled water, autoclaved three times, and then added to 0.5% malt extract plates colonised by V. comedens (strain VcWVJH1).  The wood blocks were incubated for approximately 8 weeks at 20oC in the dark. The external fungal biomass was scraped from the surface and two blocks placed together with their vessels aligned on perlite at 20oC for 7 days. The blocks were initially held together with a sterile elastic band, which was removed after 3 days. At the end of the incubation, the blocks were frozen under liquid nitrogen, freeze dried and stored at -80oC.

extract_protocol:
The half of each wood block which was in contact with the other block was ground into sawdust using a block plane. Total RNA was extracted using the RNA Powersoil kit from MoBio (California, USA), according to the manufacturer’s instructions. Samples were quality controlled and quantified using the Nanodrop (ThermoFisher Scientific, Massachusetts, USA) and the Agilent Bioanalyzer (California, USA). Dynabeads mRNA purification kit (Ambion, Massachusetts, USA) was used to isolate mRNA from the extracted total RNA.
The cDNA library was generated and amplified using the SMARTer stranded RNA-seq kit from Clontech (California, USA) according to the manufacturer’s instructions, followed by purification using the Agencourt AMPure PCR purification kit (California, USA). The library preparation was validated using the High Sensitivity DNA kit for the Agilent Bioanalyzer. The 3 independent libraries were kept at -80oC before sequencing by the Centre for Genomic Research (CGR) at Liverpool University. Paired-end sequencing (2x125 bp) of indexed libraries was conducted using the Illumina HiSeq 2500 platform, sequenced with SBS V4 chemistry.

tag: length of incubation

value: 7 days

tag: temperature


title: HEK293-Trex cells, NYN2_IP

tag: cell line

value: a doxycycline (Dox)-inducible FLAG-tagged MARF1


title: st38-2_RNA

description: Illumina TruSeq stranded  RNA-seq

value: Hd-rR


title: stage 19 rep 2

value: offspring of d-rR-Tg(olvas-GFP) and Qurt

value: stage 19


title: D19-early-MF

tag: condition

tag: cohort


title: HEK293-Trex cells, NYN1_IP


title: st32-2_RNA

description: Illumina TruSeq stranded  RNA-seq


title: st29-2_RNA

description: Illumina TruSeq stranded  RNA-seq


title: E20

city: Vestec by Prague

first: Radek

last: Šindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

data_processing:
Ribosomal RNA sequences were removed using sortmerna (version 2.1b) and the SILVA rRNA database (version 119). Low quality reads and adaptor sequences were removed using Trimmomatic PE (version 0.36). A de novo transcriptome was created using Trinity (v2.3.2) with default parameters and SS_lib_type specification as RF. We created a genome guided de novo transcriptome using an in-lab sequenced draft genome of A. ruthenus. The reads were first aligned using STAR (v.2.5.2b) and then the genome guided de novo transcriptome was generated using Trinity. These two transcriptomes were merged using EvidentialGene (v17mar10) script tr2aacds.pl. A count table was generated using kallisto (v. v0.43.1) and the numbers were rounded to the nearest whole number.
Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on the NormQ method.
Genome_build: Draft genome. FASTA of transcriptome sequences included on series record.
Supplementary_files_format_and_content: Tab-delimited text files include non-normalized and DESeq2 normalized number of reads for each Sample

organism: Acipenser ruthenus

source_name: Oocyte

extract_protocol:
One egg was mounted to OCT medium and sliced using a cryostat. RNA was isolated using TRIzol and reprecipitated using 2.5M Lithium Chloride. 200 ng of total RNA was used for rRNA depletion using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat, Illumina). Agilent SureSelect Strand-Specific RNA Library Prep Kit was used with the rRNA depleted RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: oocyte

tag: Stage

value: Stage 1

tag: section (a-e, animal-vegetal)

value: E

tag: oocyte #


title: Vc_self_2

tag: strain


title: D18-early-MF

value: early-MF


title: dxo1-2_3 [cDNA]

city: HONG KONG

first: Huan

last: ZHONG

state: HONG KONG

address: T1012 CHA CHI-MING SCIENCE TOWER

department: BIOLOGY

country: Hong Kong

institute: HKBU

description:
20171120dxo_all_fpkm.csv
d2-C.

data_processing:
TopHat 2.1.0 software (Trapnell, Pachter and Salzberg, 2009) was used to map the reads to the Arabidopsis genome (TAIR10). RSEM 2.1.30 (Anders, Pyl and Huber, 2015) was used for statistical analysis of the read counts for each gene.
Genome_build: A. thaliana Ensemble 41
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values for each Sample

organism: Arabidopsis thaliana

growth_protocol: To grow seedlings on solid media, surface-sterilized seeds were placed on half-strength Murashige and Skoog (MS) Basal Salts (M5524, Sigma-Aldrich) containing 1% (w/v) sucrose (15503-022, Invitrogen) and 0.6% agar (A1296, Sigma-Aldrich), with a pH of 5.8 adjusted by 1 M KOH.The plates with seeds were stratified in the dark at 4 ºC for three days and then placed in a growth chamber (Percival Scientific) at 22 ºC with 50% humidity and a light intensity of 125 mol m-2 sec-1 under a 16-h light/8-h dark photoperiod for 5 days. The seedlings in plates were then transferred to soil growing in a walk-in growth room at 22 ºC (± 2 ºC) with 50% humidity and a light intensity of 125 mol m-2 sec-1 provided by cold, white fluorescent lamps under a 16-h light/8-h dark photoperiod.

extract_protocol:
Total RNA for RNA-seq and real-time PCR were extracted using the Agilent Plant RNA Isolation Mini Kit (5188-2780, Agilent Technologies) following the manufacturer's instruction.
The mRNA libraries were prepared by Novogene Incorporation (Beijing, China) using reagents for Illumina

tag: tissue

value: rosette leaves


title: dxo1-2_2 [cDNA]

description:
20171120dxo_all_fpkm.csv
d2-B,

tag: age


title: D17-early-MF


title: dxo1-2_1 [cDNA]

description:
20171120dxo_all_fpkm.csv
d2-A,


title: st25-2_RNA

description: Illumina TruSeq stranded  RNA-seq


title: D16-early-MF


title: C20

value: C


title: D15-early-MF


title: dxo1-1_3 [cDNA]

description:
20171120dxo_all_fpkm.csv
d1-C


title: B20

value: B


title: dxo1-1_2 [cDNA]

description:
20171120dxo_all_fpkm.csv
d1-B,


title: st36-2_RNA

description: Illumina TruSeq stranded  RNA-seq


title: st15-2_RNA

description: Illumina TruSeq stranded  RNA-seq


title: Vc_self_3


title: A20

value: A


title: D14-early-MF


title: st11-2_RNA

description: Illumina TruSeq stranded  RNA-seq

value: embryo


title: D13-early-MF

value: Discovery


title: E18


title: D12-early-MF


title: dxo1-1_1 [cDNA]

description:
20171120dxo_all_fpkm.csv
d1-A,


title: st06-2_RNA

description: Illumina TruSeq stranded  RNA-seq


title: D11-early-MF


title: D20

value: D


title: HCC38_repl3

description:
8_151001_AC7HMTANXX_P2662_146
7_151001_AC7HMTANXX_P2662_146

tag: cell type

value: Breast cancer cell line

tag: treatment

value: Untreated


title: Col-0_2 [cDNA]

description:
20171120dxo_all_fpkm.csv
d0-B,


title: st19-2_RNA

description: Illumina TruSeq stranded  RNA-seq


title: Col-0_3 [cDNA]

description:
20171120dxo_all_fpkm.csv
d0-C


title: D18


title: C18


title: stage 40 rep 1

data_processing:
Adapters were removed using Trimmomatic (version 0.36).
Mapping by Bowtie (version 2.3.4.1) under the parameters -X 2000 --very-sensitive --qc-filter.
PCR duplicates reads were removed using Picard.
Peak calling was performed with macs2 2.1.2 using ‘macs2 callpeak -f BAMPE --keep-dup all -g 7.34e8’.
Peak reads counts were calculated by multicov function from BEDTools.
Genome_build: medaka ASM223467v1
Supplementary_files_format_and_content: bigWig files were generated using bamCoverage; Scores represent reads counts.

growth_protocol: Embryos were incubated at 28 ◦C fresh water for all time course and processed for ATAC-seq at the indicated times.

extract_protocol:
Medaka embryos were grown to the indicated times and chorions were removed by incubating in 1mg/mL Pronase. After removed yorks using deyork buffer, embryo tissues were triturated to homogeneity in 1 mL 1X TrypLE™ Express.
ATAC-Seq libraries were prepared using Omni-ATAC protocol and DNA fragments were recovered using mini-ATAC protocol.

tag: strain/background

value: Whole embryo

tag: developmental stage

value: stage 40


title: Col-0_1 [cDNA]

description:
20171120dxo_all_fpkm.csv
d0-A,


title: stage 38 rep 1

value: offspring of d-rR-Tg(olvas-GFP) and Qurt

value: stage 38


title: D10-early-MF


title: stage 36 rep 1

value: stage 36


title: B18

value: oocyte

value: Stage 1


title: dxo1-2_3

description:
dxo small RNA analysis.xlsx
sample12

data_processing:
The 18-26 nt clean reads were mapped to structural RNA (rRNAs, tRNAs, snoRNAs, and snRNAs) database (http://rfam.xfam.org/) to remove the structural RNA. Then the unmapped reads were aligned to TAIR10 genome using bowtie program with following parameters: -v 0 -a -M 3 --best --strata
Genome_build: A. thaliana Ensemble 41
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values for each Sample

extract_protocol:
Small RNAs (<200 nt) for small RNA-seq were isolated from 10-day-old seedlings using miRNeasy Mini Kit (217004, QIAGEN) according to the manufacturer's instruction.
The sRNA libraries were prepared by Novogene Incorporation using reagents for Illumina


title: stage 19 rep 1

value: stage 19


title: D9-early-MF

value: early-MF


title: A18


title: E10

value: E


title: dxo1-2_2

description:
dxo small RNA analysis.xlsx
sample11

value: rosette leaves


title: dxo1-2_1

description:
dxo small RNA analysis.xlsx
sample10


title: D10


title: D7-early-MF


title: D6-D


title: dxo1-2dcl4-2_3

description:
dxo small RNA analysis.xlsx
sample9


title: stage 11 rep 1

value: stage 11


title: D5-D


title: C10

value: C


title: B10

value: B


title: HBCx95_m43

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

description:
H3K27me3_scChIPseq
R1 fastq file: nucleosomal sequence. R2 fastq file: single-cell barcode sequence (0 – 91bp) and cell type specific sequence

data_processing:
scChIP-seq: Each #Read 2 was first separated into two parts – a cell barcode part composed of the first 91 nucleotides and the last 10 nucleotides composed of genomic DNA.
scChIP-seq: Full #Read 1 and genomic DNA of #Read 2 were mapped in paired-end mode to hg38 whole genome using STAR v2.6.0c with parameters --alignEndsType EndToEnd --outFilterMultimapScoreRange 2 --winAnchorMultimapNmax 1000 --alignIntronMax 1 --peOverlapNbasesMin 10 --alignMatesGapMax 450 --limitGenomeGenerateRAM 25000000000 --outSAMunmapped Within
scChIP-seq: Barcodes were extracted from the 91bp of Reads #2 by retrieving the three 20-mer indices (respectively located at positions 1-20, 25-44, 49-68 on Read #2). Each index was independently aligned on the 96 possibles indexes of it’s respective set of indices using Bowtie2 2.2.9 (produced by splitting Barcode_indexes.fasta into indexes B,C,D and building index with bowtie2-build) with options ‘-N 1 -L 10 --rdg 0,7 --rfg 0,7 --mp 7,7 --ignore-quals --score-min L,0,-1 -t --no-unal –no-hd’, allowing up to two mismatches / indels on the entire sequence. Full non redundant barcodes were then reconstructed for reads mapping all of the three indexes.
scChIP-seq: For each barcode, aligned reads were deduplicated by removing successively:  1. PCR duplicates, identified if #Read1 + #Read 2 mapped at the same position, 2. RT duplicates, identified if #Read 1 mapped at the same postion and  3. Window duplicates : all the reads falling in the same 50 bp window were stacked into one as reads possibly originating from PCR duplicates or from the same nucleosome. Then, reads were binned in non-overlapping 50 kb for H3K27me3 spanning the genome to generate a n x m coverage matrix with n barcodes and m genomic bins used in downstream analysis
scChIP-seq: Single cells with a total number of uniquely mapped reads within the upper percentile were considered as outliers and removed. Genomic regions not represented in at least 1% of all cells were filtered out. The coverage matrix was then normalized by dividing counts by the total number of reads per cell and multiplying by the average number of reads across all cells.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read count for each cell genomic bins (scChIP-seq). First column is genomic bin in format ‘chr:start-end’.

growth_protocol: Human MDA-MB-468 cell lines were grown in RPMI medium supplemented with 10% heat inactivated bovine serum and 1% Penicillin-Streptomycin.

extract_protocol:
Prior to scChIP-seq cells were  individualized and re-suspended in PBS/0.04% BSA (ThermoFisher Scientific, # AM2616).
After immunoprecipitation targeting H3K27me3, scChIP-seq libraries were prepared as following: barcoded-nucleosomes were amplified by in vitro transcription using the T7 MegaScript kit (ThermoFisher Scientific). The resulting amplified RNA was purified using 1x RNAClean XP beads (Beckman) and reverse transcribed by random priming in cDNA. After RNA digestion, DNA was amplified by PCR using with Illumina Primers for 12 cycles and library fragments ranging from 300 to 600 bp (single-cell barcode plus nucleosomal sequence + PCR primer sequence) were size-selected on an agarose gel. Single-cell ChIP-seq libraries were sequenced on Illumina NextSeq 500 MidOutput 150 cycles
scChIP-Seq

value: Patient-Derived-Xenograft

tag: antibody


title: D4-D

value: D

value: Discovery


title: dxo1-2dcl4-2_1

description:
dxo small RNA analysis.xlsx
sample7


title: MDAMB468

description:
H3K27me3_scChIPseq
R1 fastq file: nucleosomal sequence. R2 fastq file: single-cell barcode sequence (0 – 91 bp) and cell type specific sequence

value: MDAMB468 cell line


title: D8-early-MF


title: D3-D


title: A10

value: A


title: D2-D


title: RNA-seq of mus musculus: adult male testis6

city: Nanjing

first: Mengjie

address: No. 12, Xuefu Road, Pukou District

institute: Nanjing university

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5.
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis was performed using the DESeq2 R package (1.16.1)
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: testis

extract_protocol:
RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA degradation and contamination was monitored on 1% agarose gels.RNA purity was checked using the NanoPhotometer® spectrophotometer(IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer(Life Technologies, CA, USA).  RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the  Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently  performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: genotype

value: PCGF6 KO


title: D1-D


title: stage 15 rep 1

value: offspring of d-rR-Tg(olvas-GFP) and Qurt

value: Whole embryo

value: stage 15


title: WIBR3 tdhTSC Line 2 Rep1

data_processing:
FASTQ files were mapped to hg19 using the STAR aligner with default parameters.
Bam files were analyzed by RNA-SeQC to confirm library quality.
Read counts were calculated with htseq-count and RPKM was calculated using cufflinks with default settings.
Genome_build: hg37
Supplementary_files_format_and_content: readcount file

source_name: WIBR3 tdhTSC Line 2

extract_protocol:
RNA extraction was performed using Qiagen RNeasy micro kit
mRNA was enriched from 500ng total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module kit and libraries were generated using Swift RNA library kit

value: Transdifferentiated human trophoblast stem cells


title: dcl4-2_1

description:
dxo small RNA analysis.xlsx
sample4


title: Hec116

growth_protocol: Cultured in DMEM F12 containing 10% bovine calf serum and 1xPen/Strep. Passaging is performed by treatment with 0.05% Trypsin

value: Endometrial epithelium cell line


title: FT190

value: Fallopian tube epithelium cell line


title: dcl4-2_2

description:
dxo small RNA analysis.xlsx
sample5


title: RNA-seq of mus musculus: adult male testis5


title: RNA-seq of mus musculus: adult male testis4


title: WIBR3 Naive hESCs Rep 1

source_name: WIBR3 Naive hESCs

value: Human embryonic stem cells


title: WIBR3 Primed hESCs Rep 3

source_name: WIBR3 Primed hESCs


title: V16-D

data_processing: Raw data were quality checked in the nSolver software followed by normalization. Normalization factors were calculated based on 40 reference genes included in the myeloid innate immunity panel.

extract_protocol: Total RNA was isolated from ten 10-μm sections of FFPE samples using the Roche high pure RNA FFPE isolation kit.

value: validation


title: Col-0_3

description:
dxo small RNA analysis.xlsx
sample3

value: rosette leaves


title: V15-D


title: Col-0_2

description:
dxo small RNA analysis.xlsx
sample2


title: RNA-seq of mus musculus: adult male testis3

value: WT


title: dxo1-2dcl4-2_2

description:
dxo small RNA analysis.xlsx
sample8


title: WIBR3 Primed hESCs Rep 2


title: dcl4-2_3

description:
dxo small RNA analysis.xlsx
sample6


title: Col-0_1

description:
dxo small RNA analysis.xlsx
sample1


title: RNA-seq of mus musculus: adult male testis2


title: RNA-seq of mus musculus: adult male testis1


title: V14-D


title: WIBR3 Primed hESCs Rep 1


title: ey>lilac[4]

city: Cologne

first: Mirka

last: Uhlirova

state: NRW

address: Joseph-Stelzmann Str. 26

department: Institute for Genetics

country: Germany

institute: CECAD Research Center  Cologne

description: Stankovic et al_Dataset S1

data_processing:
Data was processed using the QuickNGS pipeline of the Bioinformatics facility of CECAD, University of Cologne
initial quality check was performed using FastQC
Reads were aligned to the Drosophila reference genome BDGP Release 6 (dm6) using Tophat2 v2.0.10
The transcriptome was assembled with Cufflinks2 2.1.1
Differential gene expression determined by DESeq2
The GO category enrichment analysis of differentially regulated genes was performed with DAVID
Genome_build: dm6 (D. melanogaster)
Supplementary_files_format_and_content: .xlsx

organism: Drosophila melanogaster

source_name: Eye-Antennal Imaginal Disc

growth_protocol: Virgins of ey-Gal4 were crossed to male flies carrying RP-associated mutant Prp8 constructs, and the crosses were kept at 25 °C until dissection

extract_protocol:
Eye-antennal discs of third instar larvae were dissected in ice cold PBS and immediately covered in TRI Reagent and extracted according to manufacturer's protocol.
Libraries were prepared using the Illumina TruSeq kit according to manufacturer's instructions

value: Ey-Gal4 (EAD)

tag: uas

value: L3, 7 day AEL, 25 °C


title: UCLA1 Primed hESCs Rep3

source_name: UCLA1 Primed hESCs


title: ey>lilac[3]

description: Stankovic et al_Dataset S1


title: V17-D

value: D


title: RNA-seq of mus musculus: adult male brain5

source_name: brain


title: V12-D


title: RNA-seq of mus musculus: adult male brain6


title: ey>lilac[2]

description: Stankovic et al_Dataset S1


title: V13-D


title: UCLA1 Primed hESCs Rep2


title: UCLA1 Primed hESCs Rep1


title: RNA-seq of mus musculus: adult male brain4


title: ey>fuchsia[4]

description: Stankovic et al_Dataset S1


title: V11-D


title: CT3 hTSCs Rep2

source_name: CT3 hTSCs

value: Human trophoblast stem cells


title: V10-D


title: RNA-seq of mus musculus: adult male brain2


title: ey>fuchsia[3]

description: Stankovic et al_Dataset S1


title: V9-D


title: CT3 hTSCs Rep1


title: RNA-seq of mus musculus: adult male brain1


title: CT1 hTSCs Rep4

source_name: CT1 hTSCs


title: ey>fuchsia[2]

description: Stankovic et al_Dataset S1


title: ey>russet[4]

description: Stankovic et al_Dataset S1


title: CT1 hTSCs Rep3


title: V7-D

source_name: skin biopsy, FFPE


title: V8-D


title: RNA-seq of mus musculus: adult male liver6

source_name: liver


title: V6-D


title: ey>russet[3]

description: Stankovic et al_Dataset S1


title: RNA-seq of mus musculus: adult male liver5


title: CT1 hTSCs Rep2


title: RNA-seq of mus musculus: adult male liver4


title: RNA-seq of mus musculus: adult male brain3


title: V5-D


title: ey>russet[2]

description: Stankovic et al_Dataset S1


title: ey>WT[5]

description: Stankovic et al_Dataset S1


title: V4-D


title: RNA-seq of mus musculus: adult male liver3


title: ey>WT[3]

description: Stankovic et al_Dataset S1


title: RNA-seq of mus musculus: adult male liver2


title: ey>WT[2]

description: Stankovic et al_Dataset S1


title: BT2 hTSC Rep1

source_name: BT2 hTSC


title: RNA-seq of mus musculus: adult male liver1


title: V3-D


title: JQ1 RNApolII ser2 ChIP-Seq

status: Public on Jun 15 2020

city: Cambridge

first: Michael

middle: B

last: Yaffe

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
Illumina bcl2fastq  software was used for basecalling and fastq file generation.
ChIP-seq reads were aligned to the hg19 genome assembly using the Burroughs-Wheeler Aligner BWA-MEM v. 0.7.12-r1039 with flag –t 4 and otherwise default parameters [bio-bwa.sourceforge.net]
The resulting bam files were sorted and indexed using samtools v. 1.5, and duplicates were marked using Picard v. 2.9.0-1-gf5b9f50-SNAPSHOT  MarkDuplicates MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false    REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json . Bam files with duplicate reads marked were sorted and indexed again
Wig files were prepared for each libraries using igvtool’s count function, with –e matching the mode of the insert size of the library and -w 25 , which were converted to BigWig using UCSC’s wigToBigWig tool with default parameters and hg19’s chromosome sizes as an input.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files are provided for each library, recapitulating read densities across the genome.

source_name: HeLa cells

growth_protocol: HeLa cells were grown on 15cm plates in 10% FBS + DMEM until they were 80% confluent, upon which time they were subjected to drug treatment, fixed and harvested for Ch-IP.

extract_protocol: The ChIP protocol has been adapted from previous studies (Library preparation for Illumina NextSeq was performed using the NEBNext Ultra II DNA library prep kit (NEB) as per manufacturer’s protocol. ) with the following modification. Diagenode Bioruptor was used to sonicate with 30 cycles of 30 sec on, 30 sec off. The samples were sonicated in 15ml polystyrene tubes at 4°C while samples were immersed in ice cold water. Antibodies used for ChIP include:  ~200 ng of DNA was submitted to SPRI-works Fragment Library System I (Beckman Coulter) for each library prepared. Briefly, the DNA is subjected to size selection (200-400bp) with magnetic beads, end repaired, then a single adenine nucleotide is added to allow for directional ligation of adaptors. For this study, a 1:100 dilution of Single End read adapters (Illumina) was used in the ligation reaction. Each sample was then amplified for 19 cycles, using the Illumina protocol, adding additional bases from the PCR primers that aid sequences to anneal to the Illumina Genome Analyzer flow cell. The samples were then purified on a Qiagen MinElute column, and libraries were quantified by Quant-it DNA Assay (Invitrogen, Q-33120), and examined for proper size and structure by Bioanalyzer (Agilent) and qPCR.

treatment_protocol: HeLa cells were treated with either DMSO or 500nM JQ1 for 16hours before harvesting.

value: HeLa cells

value: Human cervical cancer epithelial cells

tag: passages

tag: chip antibody

value: RNAPII Ser2, Abcam, ab5095


title: JQ1 BRD4 ChIP-Seq

tag: cell line


title: V2-D

tag: condition

tag: cohort


title: CT1 hTSCs Rep1

first: Yixin


title: DMSO gH2AX ChIP-Seq

value: DMSO

value: gH2AX, Millipore Sigma, 05-636


title: DMSO RNApolII ser2 ChIP-Seq


title: DMSO BRD4 ChIP-Seq


title: JQ1 Input


title: DMSO IgG ChIP-Seq

value: Rabbit IgG, EMD Millipore, 12-370


title: Human HGSC cell line OVCAR8

city: Omaha

first: Adam

middle: R

last: Karpf

state: NE

address: S 42nd &, Emile St

institute: UNMC

data_processing:
Aligning Fastq files to the human genome hg19
Imputing transcript dropout using scImputer R package from https://github.com/Vivianstats/scImpute
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include transcript counts (imputed).  Rows represeting isolated cells and columns representing genes

molecule: polyA RNA

source_name: OVCAR8 cells

growth_protocol: Growth in standard cell culture conditions with cell harvest during log growth phase

extract_protocol:
Droplet-based capture and lysis of single cells followed by reverse transcription to generate full-length, barcoded cDNA
Chromium™ Single Cell 3’ v2 Protocol
scRNA-seq, gel bead in emulsions, 10x Genomics

value: high-grade serous ovarian cancer (HGSC) cells


title: Human immortalized FTE cell line FT282-C11

source_name: FT282-C11 cells

value: fallopian tube epitheilal (FTE) cells


title: BT2 hTSC Rep2

city: Haining

last: Guo

address: 718 East Haizhou Rd.

institute: Zhejiang University


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, auxin treated for 2h, S4U 2h_replicate 3

city: Bethesda

first: Alexei

last: Arnaoutov

state: MD

address: 49 Convent Dr, Bldg 49 Room 5A10

department: PCRM

institute: NICHD

description: Replicate 3

data_processing:
The SLAM-seq data were processed with a SLAM-DUNK pipeline. The reads were aligned to the human genome GRCh38.p10.
Differential expression analysis of TcReadCounts was performed with DESeq2 (version 1.26.0) using R 3.5.1, padj was FDR-adjusted. For global normalization sizeFactors were used based on total ReadCounts.
Genome_build: Human reference genome GRCh38.p10.
Supplementary_files_format_and_content: Tab-limited files have human gene names as well as TotalReadCounts and TcReadCounts

source_name: DLD-1 cells

growth_protocol: The human colorectal cancer cell line DLD-1 was cultured in DMEM supplemented with heat-inactivated 10% FBS, antibiotics, and 2 mM GlutaMAX in 5% CO2 atmosphere at 37°C. From 75 to 100K of AID-tagged cells were plated on each well of 6-well plate dishes for RNA isolation.

extract_protocol:
Total RNA from triplicates was collected in 1 ml of TRIzol Reagent (Invitrogen), stored at -800C, and further purified according to Lexogen manufacturing protocol. Five micrograms of total RNA were alkylated with freshly prepared 100 mM Iodoacteamide (IAA). RNA quality and concentration were measured using Qubit 4 RNA IQ and RNA BR assay kit (ThermoFisher Scientific).
QuantSeq 3’ mRNA-seq Libraries were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina (FWD) and sequenced by Lexogen company, and a total of 8 to 24 million reads were generated per sample.

treatment_protocol: All AID-tagged cell lines were treated with 1 mM auxin (I5148, Sigma Aldrich) for Tpr nucleoporin loss for 2 hours. Nex, for chasing, cells were treated with media containing 300 µM S4U or 300 µM S4U supplemented with 1 mM auxin for 0 min, 30 min, 60 min, or 2 hours.

value: cell line

value: AID-NeonGreen-TPR

tag: treatments

value: S4U, auxin

tag: incubation time

value: 2h auxin 1mM, 2h S4U


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, S4U 2h_replicate 3

description: Replicate 3


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, S4U 2h_replicate 2

description: Replicate 2


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, S4U 1h_replicate 2

description: Replicate 2


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, auxin treated for 2h, S4U 1h_replicate 3

description: Replicate 3

value: 2h auxin 1mM, 1h S4U


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, S4U 2h_replicate 1

description: Replicate 1


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, auxin treated for 2h, S4U 1h_replicate 2

description: Replicate 2


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, auxin treated for 2h, S4U 2h_replicate 2

description: Replicate 2


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, auxin treated for 2h, S4U 1h_replicate 1

description: Replicate 1


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, auxin treated for 2h, S4U 2h_replicate 1

description: Replicate 1


title: JQ1 gH2AX ChIP-Seq


title: JQ1 IgG ChIP-Seq


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, auxin treated for 2h, S4U 30 min_replicate 3

description: Replicate 3

value: 2h auxin 1mM, 30 min S4U


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, S4U 1h_replicate 1

description: Replicate 1


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, auxin treated for 2h, S4U 30 min_replicate 1

description: Replicate 1


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, auxin treated for 2h, S4U 30 min_replicate 2

description: Replicate 2


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, S4U 30 min_replicate 1

description: Replicate 1

value: 30 min


title: DMSO Input


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, S4U 30 min_replicate 2

description: Replicate 2


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR_replicate 3

description: Replicate 3


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR_replicate 1

description: Replicate 1


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, auxin treated for 2h_replicate 2

description: Replicate 2

value: 2h auxin 1mM, 0h S4U


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR_replicate 2

description: Replicate 2


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, S4U 1h_replicate 3

description: Replicate 3


title: hiPSC_PAX7_2

city: Boston

first: Jyoti

last: Rao

address: 60 Fenwood road

department: Pathology/Genetics

institute: Brigham and Women’s Hospital/Harvard Medical School

description: Single-cell RNA-Seq (inDrops)

data_processing:
Single-cell RNA-seq data were generated using inDrop version 3. Raw sequencing FASTQ files were demultiplexed and processed using a custom python pipeline as previously described (see Zilionis et al., Nature Protocols 2017) Also available at github.com/indrops/indrops. Default parameters were applied (for Trimmomatic, LEADING: "28", SLIDINGWINDOW: "4:20", MINLEN: "16"; for UMI quantification, m: 10, u: 1, d: 600, split-ambigs: False, min_non_polyA: 15; for low complexity filter, max_low_complexity_fraction: 0.50; for output: output_unaligned_reads_to_other_fastq: False, filter_alignments_to_softmasked_regions: False).
Sequencing reads were first sorted according to sample of origin.  Each library is associated with 4 reads - R1, R2, R3 and R4.  R1 is the biological read, R2 carries the first half of the hydrogel bead barcode (8 bp), R3 carries the library index (8 bp), and R4 carries the second half of the hydrogel bead barcode (8 bp), followed by the UMI (6 bp).
Cell-specific barcodes for each cDNA read were then matched against a set of pre-determined barcodes, hiPSC_PAX7_1 = CTTAATAG , hiPSC_PAX7_2 = TCGCATAA.
cDNA reads were then aligned to a reference transcriptome using Bowtie (version 1.2.2, parameters: -n 1 -l 15 -e 100 -m 200 -best -strata -a).  Reference transcriptomes were built from human GRCh38.p12 (GCF_000001405.38) genome assembly. Mapped reads were then processed into counts of UMI-filtered transcripts per gene.
UMI counts matrices were filtered to exclude cell barcodes associated with low numbers of reads.  This determination was made by inspecting a weighted histogram of UMI counts for each cell barcode and thresholds were set manually for each sample. We excluded the cells with less than 250 genes expressed, and exclude the genes if they were expressed in less than 3 cells. Fraction of counts due to mitochondrial genes (n) was determined and cells with n= 0.2 were removed. Cells with less than 250 genes expressed were removed. Genes expressed in less than 3 cells were filtered out. Fraction of counts due to mitochondrial genes (n) was determined and cells with n= 0.2 were removed.
Genome_build: GRCh38.p12 (GCF_000001405.38)
Supplementary_files_format_and_content: X.csv: Raw UMI-filtered counts.  Matrix columns are transcripts, rows are single cells.
Supplementary_files_format_and_content: CellData.csv: Identifiers for single cells corresponding to the rows of X.csv.  Unique cell identifiers are in the following format: LibraryName_CellBarcodePart1_CellBarcodePart2.  Numbers of UMIS and genes detected and clustering assignments are included for each cell
Supplementary_files_format_and_content: GeneData.csv: Gene names corresponding to the columns of X.csv

source_name: human iPSC NCRM1

extract_protocol:
For generating cell suspensions from NCRM1 human iPSC derived PAX7-Venus positive cells, PAX7-Venus reporter line was differentiated as described (Chal et al., 2016). On day 27, cells were dissociated and captured using inDrops technique. For dissociation, cells were incubated in 2.5mg/ml Type IV Collagenase and 0.05% Trypsin EDTA for 15 minutes at 37 ºC. After mechanical dissociation using a wide bore pipette, cells were added to 5% FBS in DMEM and passed through a 70mm nylon Cell Strainer, spun down at 300g for 5 min and resuspended in 0.1% FBS in PBS. Cells were filtered through a 30mm filter and Venus expressing cells were collected using flow cytometry. Cell density was quantified manually and was adjusted to 150,000 cells/ml for encapsulation. The dissociation method and flow cytometry were optimized to achieve >90% viable cells and minimize cell doublets. Cells were collected from two independent experiments. Library construction was performed according to custom inDrops protocol as in Zilionis et al. Nature Protocols 2017.
Single-cell RNA-Seq libraries were prepared using a protocol customized for the inDrops platform (see Zilionis et al., Nature Protocols 2017)

value: human iPSC derived PAX7 cells

value: PAX7-Venus reporter

tag: library name


title: hiPSC_PAX7_1

description: Single-cell RNA-Seq (inDrops)


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, S4U 30 min_replicate 3

description: Replicate 3


title: MACE_FFPE_Pap_patient_5

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

description:
data_MACE_FFPE_time.csv
BH0011_R1.MACE.cleaned2.fastq_trimmed.fastqsanger

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human reference genome (hg38, gencode release 31) with RNA STAR Galaxy Version 2.7.2b (default parameters) using the Gencode annotation file (Gencode 31, release June 2019
Reads mapped to the human reference genome were counted using featureCounts Galaxy Version 1.6.4 (default parameters) using the aforementioned annotation file.
The outputs of featureCounts or DESeq2 were imported to RStudio (Version 1.2.1335, R Version 3.5.3) for further analysis. Gene symbols and gene types were determined based on ENSEMBL release 97 (July 2019) (Human genes, GRCh38.p12, download on 12/09/2019) 20. Differentially expressed genes were defined by log2 fold change >2 or <-2 and by an adjusted p-value <0.05.
Genome_build: hg38
Supplementary_files_format_and_content: normalized and raw comma seperated values

source_name: Conjunctival Papilloma

extract_protocol:
Total RNA was isolated from formalin-fixed and paraffin-embedded sections of all specimens using the Quick-RNA FFPE Kit (Zymo Research, USA). Following DNAse I digestion using the Baseline-ZERO kit (Epicentre, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorometer (Life Technologies, USA). RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, USA).
Standard RNA-Seq libraries were prepared by GenXPro GmbH. The rRNA depletion and mRNA enrichment were performed via poly(A) selection and purification. All samples were sequenced strand-specific on the HiSeq2500 (Illumina, USA).   MACE libraries were constructed by GenXPro GmbH. Briefly, poly-adenylated mRNA was isolated from 1 μg of total RNA. 28 barcoded libraries comprising unique molecule identifiers (UMIs) were sequenced on the NextSeq 500 (Illumina, USA) with 1×75 bp, followed by TrueQuant PCR bias elimination using UMIs.

tag: disease

value: Conjunctival Papilloma


title: MACE_FFPE_Pap_patient_6

description:
data_MACE_FFPE_time.csv
BH0012_R1.MACE.cleaned2.fastq_trimmed.fastqsanger


title: MACE_FFPE_SCC_patient_4

description:
data_MACE_FFPE_time.csv
BH27_R1.MACE.cleaned.fastq_trimmed

source_name: Conjunctival SCC

value: Conjunctival SCC


title: MACE_FFPE_Pap_patient_3

description:
data_MACE_FFPE_time.csv
BH0009_R1.MACE.cleaned2.fastq_trimmed.fastqsanger


title: MACE_FFPE_Pap_patient_7

description:
data_MACE_FFPE_time.csv
BH23_R1.MACE.cleaned.fastq_trimmed


title: MACE_FFPE_SCC_patient_5

description:
data_MACE_FFPE_time.csv
BH28_R1.MACE.cleaned.fastq_trimmed


title: MACE_FFPE_SCC_patient_6

description:
data_MACE_FFPE_time.csv
BH29_R1.MACE.cleaned.fastq_trimmed


title: MACE_FFPE_SCC_patient_7

description:
data_MACE_FFPE_time.csv
BH30_R1.MACE.cleaned.fastq_trimmed


title: MACE_FFPE_healthy_tissue_patient_10

description:
data_MACE_FFPE_time.csv
data_MACE_fixed_unfixed.csv
BH31_R1.MACE.cleaned.fastq_trimmed.fastqsanger

source_name: Healthy conjuncitva

value: Healthy conjuncitva


title: MACE_FFPE_SCC_patient_2

description:
data_MACE_FFPE_time.csv
BH24_R1.MACE.cleaned.fastq_trimmed


title: MACE_FFPE_Pap_patient_4

description:
data_MACE_FFPE_time.csv
BH0010_R1.MACE.cleaned2.fastq_trimmed.fastqsanger


title: MACE_FFPE_Pap_patient_2

description:
data_MACE_FFPE_time.csv
BH0008_R1.MACE.cleaned2.fastq_trimmed.fastqsanger


title: MACE_FFPE_healthy_tissue_patient_9

description:
data_MACE_FFPE_time.csv
data_MACE_fixed_unfixed.csv
BH21_R1.MACE.cleaned.fastq_trimmed.fastqsanger


title: MACE_FFPE_SCC_patient_3

description:
data_MACE_FFPE_time.csv
BH25_R1.MACE.cleaned.fastq_trimmed


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, auxin treated for 2h_replicate 1

description: Replicate 1


title: MACE_FFPE_Pap_patient_1

description:
data_MACE_FFPE_time.csv
BH0007_R1.MACE.cleaned2.fastq_trimmed.fastqsanger


title: MACE_FFPE_healthy_tissue_patient_6

description:
data_MACE_FFPE_time.csv
BH0006_R1.MACE.cleaned.fastq_trimmed.fastqsanger


title: MACE_FFPE_SCC_patient_1

description:
data_MACE_FFPE_time.csv
BH0014_R1.MACE.cleaned2.fastq_trimmed.fastqsanger


title: MACE_FFPE_healthy_tissue_patient_5

description:
data_MACE_FFPE_time.csv
BH0005_R1.MACE.cleaned.fastq_trimmed.fastqsanger


title: MACE_FFPE_healthy_tissue_patient_1

description:
data_MACE_FFPE_time.csv
BH0001_R1.MACE.cleaned.fastq_trimmed.fastqsanger


title: MACE_FFPE_healthy_tissue_patient_2

description:
data_MACE_FFPE_time.csv
BH0002_R1.MACE.cleaned.fastq_trimmed.fastqsanger


title: MACE_FFPE_healthy_tissue_patient_4

description:
data_MACE_FFPE_time.csv
BH0004_R1.MACE.cleaned.fastq_trimmed.fastqsanger


title: MACE_FFPE_healthy_tissue_patient_8

description:
data_MACE_FFPE_time.csv
data_MACE_fixed_unfixed.csv
BH20_R1.MACE.cleaned.fastq_trimmed.fastqsanger


title: MACE_fresh_healthy_tissue_patient_8

description:
data_MACE_FFPE_time.csv
data_MACE_fixed_unfixed.csv
BH20LB_R1.MACE.cleaned.fastq_trimmed


title: MACE_fresh_healthy_tissue_patient_10

description:
data_MACE_FFPE_time.csv
data_MACE_fixed_unfixed.csv
BH31LB_R1.MACE.cleaned.fastq_trimmed


title: MACE_fresh_healthy_tissue_patient_9

description:
data_MACE_FFPE_time.csv
data_MACE_fixed_unfixed.csv
BH21LB_R1.MACE.cleaned.fastq_trimmed


title: MACE_fresh_healthy_tissue_patient_7

description:
data_MACE_FFPE_time.csv
data_MACE_fixed_unfixed.csv
BH19LB_R1.MACE.cleaned.fastq_trimmed


title: MACE_FFPE_healthy_tissue_patient_7

description:
data_MACE_FFPE_time.csv
data_MACE_fixed_unfixed.csv
BH19_R1.MACE.cleaned.fastq_trimmed.fastqsanger


title: DC-180727-00358: Donor 3627_3a

first: Ying-Lin Stefanie

last: Tan

address: 1 Portland St

institute: Pfizer

data_processing:
Transcriptional data was aligned using STAR (https://github.com/alexdobin/STAR) aligner.
Gene counts from resulting bam files were generated using featurecounts using GTF file from UCSC (http://bioinf.wehi.edu.au/featureCounts/).
Elucidata
Genome_build: hg38

source_name: Donor 3627_3a

growth_protocol: Primary human CD4+ T cells were isolated from frozen hPBMCs

extract_protocol:
RNA was extracted from frozen cell pellets using the Qiagen RNAeasy mini isolation kit, and 400ng RNA used in the construction of libraries.
Sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep (cat.20020594) according to standard protocols.

treatment_protocol: Cell were activated for 24 hr in the presence of indicated treatment regimens, then washed and frozen.

tag: tissue

value: T Lymphocytes;CD4+

tag: activation state

value: Non-activated

value: Water


title: RNA_Seq_fresh_healthy_tissue_patient_9

description:
data_RNASeq_MACE.csv
BH21_cleaned_R1.fastq


title: DC-180727-00304: Donor 3627_3b

source_name: Donor 3627_3b

tag: treatment


title: DC-180727-00315: Donor 3926_1c

source_name: Donor 3926_1c


title: DC-180727-00347: Donor 0380_2a

source_name: Donor 0380_2a


title: RNA_Seq_fresh_healthy_tissue_patient_10

description:
data_RNASeq_MACE.csv
BH31_cleaned_R1.fastq


title: DC-180727-00280: Donor 3926_1b

source_name: Donor 3926_1b


title: DC-180727-00308: Donor 3627_15c

value: Anti-CD3/anti-CD28 activated

value: Metformin, 2-Deoxyglucose


title: DC-180727-00329: Donor 3627_15a


title: DC-180727-00273: Donor 3627_15b


title: RNA_Seq_fresh_healthy_tissue_patient_8

description:
data_RNASeq_MACE.csv
BH20_cleaned_R1.fastq


title: DC-180727-00345: Donor 3627_6b

source_name: Donor 3627_6b


title: DC-180727-00292: Donor 0380_2b

source_name: Donor 0380_2b


title: DC-180727-00334: Donor 0380_5b

source_name: Donor 0380_5b


title: DC-180727-00336: Donor 3926_1a

source_name: Donor 3926_1a


title: DC-180727-00326: Donor 0380_2c

source_name: Donor 0380_2c


title: DC-180727-00312: Donor 3627_6a

source_name: Donor 3627_6a


title: MACE_FFPE_healthy_tissue_patient_3

description:
data_MACE_FFPE_time.csv
BH0003_R1.MACE.cleaned.fastq_trimmed.fastqsanger


title: DC-180727-00340: Donor 3926_13b


title: DC-180727-00323: Donor 3926_4b

source_name: Donor 3926_4b


title: DC-180727-00318: Donor 0380_14a


title: DC-180727-00302: Donor 3627_6c

source_name: Donor 3627_6c


title: DC-180727-00301: Donor 0380_5a

source_name: Donor 0380_5a


title: DC-180727-00290: Donor 0380_5c

source_name: Donor 0380_5c


title: DC-180727-00289: Donor 3926_4a

source_name: Donor 3926_4a


title: DC-180727-00348: Donor 3627_3c

source_name: Donor 3627_3c


title: 1097D-ENDO

city: New York

first: Natalia

last: Teleshova

state: NY

address: 1230 York Avenue

institute: Population Council

description: counts.matrix" column "1097D.ENDO

data_processing:
Input adapter trimming using Cutadapt version 1.9.1 with -a AAAAAAAAAAAAA -a TTTTTTTTTTTTT -a AGATCGGAAGAG -a CTCTTCCGATCT
Aligning the input reads to reference genome using STAR_2.4.2a
Quality assesment on aligned data using FastQC v0.11.5
Quality assesment on aligned data using QualiMap  v.2.2
Count reads on exon level (-f exon) and gene level (default no -f) using featureCounts v1.5.0-p2
Genome_build: GRCh37
Supplementary_files_format_and_content: .counts summarizing count information of gene presented after aligning samples to the reference genome

source_name: tissue

extract_protocol:
Tissue RNA was extracted using total RNAase Fibrous Tissue Mini Kit (Qiagen, Valencia, CA). The concentration and purity of the extracted RNA were assessed by the Agilent Bioanalyzer (Agilent, Santa Clara, CA). RNA was labeled and sequenced at the RU Genomics center by using Illumina TruSeq technology (75bp, >30M coverage).
100 ng of total RNA was used to generate RNA-Seq libraries using Illumina TruSeq stranded mRNA LT kit (Cat# RS-122-2101).

treatment_protocol: Tissue from subjects undergoing hysterectomies for non-malignant conditions were stored in RNAlater at -80°C before RNA extraction

value: endocervix

tag: cell type

value: mucosa

tag: e2 levels


title: 1093Z-ENDO

description: counts.matrix" column "1093Z.ENDO


title: 1077J-ECTO

description: counts.matrix" column "1077J.ECTO

value: ectocervix


title: 1073F-ENDO

description: counts.matrix" column "1073F.ENDO


title: 1068A-ENDO

description: counts.matrix" column "1068A.ENDO


title: 1086S-ENDO

description: counts.matrix" column "1086S.ENDO


title: 1059R-ENDO

description: counts.matrix" column "1059R.ENDO


title: 1063V-ENDO

description: counts.matrix" column "1063V.ENDO


title: 1043B-ENDO

description: counts.matrix" column "1043B.ENDO


title: 1068A-ECTO

description: counts.matrix" column "1068A.ECTO


title: 1076I-ECTO

description: counts.matrix" column "1076I.ECTO


title: 1043B-ECTO

description: counts.matrix" column "1043B.ECTO


title: 1059R-ECTO

description: counts.matrix" column "1059R.ECTO


title: 1040Y-ECTO

description: counts.matrix" column "1040Y.ECTO


title: P4_G6_C5_x1_33

city: London

first: Marcela

last: Lipovsek

address: 18-20 Newcomen Street - New Hunt's House

department: Centre for Developmental Neurobiology

institute: King's College London

data_processing:
Paired-end read fastq files were demultiplexed, quality controlled using FastQC and trimmed using Trim Galore. Reads were pseudoaligned and quantified using kallisto against a reference transcriptome from Ensembl Release 89 (Gencode Release M17 GRCm38.p6) with sequences corresponding to the ERCC spike-ins and the Cre recombinase and tdT genes added to the index. Transcripts were collapsed into genes using the sumAcrossFeatures function in scater (v1.12.2).
Cell level quality control and cell filtering was performed in scater (v1.12.2). Cells with <1000 genes, <100,000 reads, >75% reads mapping to ERCC spike-ins, >10% reads mapping to mitochondrial genes or low library complexity were discarded from downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing kallisto estimated counts or tpm (transcripts per million) collapsed to genes

source_name: Olfactory bulb dopaminergic neuron

growth_protocol: Mice of either gender were used and housed under a 12 h light:dark cycle in an environmentally controlled room with access to water and food ad libitum.

extract_protocol:
For manual sorting of fluorescently labelled dopaminergic neurons we adapted the protocol described in Hempel, et al. 2007.
Sequencing libraries were generated following a modified Smart-Seq2 protocol. Briefly, 1 µl of a 1:2,000,000 dilution of ERCC spike-ins (Invitrogen. Cat. no. 4456740) was added to each sample and mRNA was captured using modified oligo-dT biotinylated beads (Dynabeads – Invitrogen). PCR amplification was performed for 22 cycles. Amplified cDNA was cleaned with a 0.8:1 ratio of Ampure-XP beads (Beckman Coulter). cDNAs were quantified on Qubit using HS DNA reagents (Invitrogen) and selected samples were run on a Bioanalyzer HS DNA chip (Agilent) to evaluate size distribution. For generating the sequencing libraries, individual cDNA samples were normalised to 0.2ng/µl and 1µl was used for one-quarter standard-sized Nextera XT (Illumina) tagmentation reactions, with 12 amplification cycles. Sample indexing was performed using index sets A and D (Illumina). At this point, individual samples were pooled according to their index set. Pooled libraries were cleaned using a 0.6:1 ratio of Ampure beads and quantified on Qubit using HS DNA reagents and with the KAPA Library Quantification Kits for Illumina (Roche). Samples were sequenced on two separate rapid-runs on HiSeq2500 (Illumina), generating 100bp paired-end reads. An additional 5 samples were sequenced on MiSeq (Illumina).

treatment_protocol: 24 hours prior to cell collection, mice were subjected to olfactory sensory deprivation by unilateral naris occlusion. Briefly, mice were anesthetised with isoflurane and a custom made plug, coated in petroleum jelly, was inserted into the right naris. Sham controls were obtained by similarly inserting a plug into the right naris and immediately removing it.

tag: strain

value: Olfactory bulb

tag: sample type

value: Single cell


title: P4_H9_C6_X10_55

source_name: Positive control

value: Positive control


title: P4_H6_C6_x1_8


title: DC-180727-00278: Donor 3926_4c

source_name: Donor 3926_4c


title: P4_H1_C6_x1_6


title: P4_H4_C4_x1_26


title: P4_H7_O2_x1_84


title: 1040Y-ENDO

description: counts.matrix" column "1040Y.ENDO


title: P4_G5_O5_x1_77


title: P4_G3_O3_x1_39


title: P4_G4_O6_x1_64


title: P4_G10_O6_x1_86


title: P4_G2_C5_x1_28


title: 1076I-ENDO

description: counts.matrix" column "1076I.ENDO


title: P4_G1_O5_x1_69


title: P4_F11_C6_X10_72


title: 1063V-ECTO

description: counts.matrix" column "1063V.ECTO


title: P4_F10_O5_x1_16


title: P4_F9_C3_x1_95


title: P4_F6_O6_x1_9


title: P4_F8_C5_x1_2


title: P4_F7_C7_x1_58


title: P4_F3_O2_x1_81


title: P4_F2_C5_x1_41


title: P4_F1_C4_x1_70


title: P4_E11_O4_x1_62


title: P4_E6_O4_x1_80


title: DLD-1 cells with endogenously modified AID-NeonGreen-TPR, auxin treated for 2h_replicate 3

description: Replicate 3

source_name: DLD-1 cells

tag: developmental stage

value: cell line

tag: genotype

value: AID-NeonGreen-TPR

value: S4U, auxin

value: 2h auxin 1mM, 0h S4U


title: P4_E4_C3_x1_63


title: P4_E3_C3_x1_45


title: P4_D9_O6_x1_88


title: P4_D2_O3_x1_44


title: P4_D6_O2_x1_54


title: P4_E2_O4_x1_25


title: P4_E12_C6_x1_34


title: P4_C12_O3_x1_75


title: P4_C6_O2_x1_7


title: P4_D8_C3_x1_90


title: P4_B11_C7_x1_32


title: P4_D1_C6_x1_71


title: P4_C2_C7_x1_73


title: P4_C3_O3_x1_22


title: P4_D3_O6_x1_23


title: P4_C4_C7_x1_82


title: P4_D12_O5_x1_4


title: P4_B12_C4_x1_14


title: P4_C11_C5_x1_59


title: P4_B7_C6_x1_24


title: P4_B8_O5_x1_61


title: P4_B1_O4_x1_50


title: P4_A12_O4_x1_56


title: P4_B4_O3_x1_30


title: P4_A9_O2_x1_96


title: P4_A7_O4_Neg_52

source_name: Negative control

value: Negative control


title: P4_A1_C3_x1_13


title: P3_H9_C6_x1_76


title: P3_H8_C6_x1_54


title: P3_H7_O6_x1_61


title: P3_H6_C3_x1_2


title: P3_G8_O5_x1_5


title: P3_G5_C6_x1_19


title: P3_G7_C3_x1_23


title: P3_H3_C7_x1_71


title: P3_F11_C5_x1_42


title: P3_G1_O2_x1_89


title: P3_H5_O4_Neg_44


title: P3_H1_O4_x1_14


title: P3_G3_O3_x1_29


title: P3_F6_O4_x1_49


title: P3_F4_O3_x1_11


title: P3_F9_C5_x1_3


title: P3_E10_O5_x1_36


title: P4_A10_C4_x1_48


title: P3_F2_C3_x1_15


title: P3_E11_O2_x1_31


title: P3_E7_C5_x1_75


title: P3_E5_C6_x1_88


title: P4_A5_C7_x1_27


title: P4_A6_C6_x0_66

source_name: No_cell control

value: No_cell control


title: P3_H12_O3_x1_40


title: P3_D12_O5_x10_45


title: P3_E2_C3_x1_6


title: P3_E3_O4_x1_84


title: P3_H4_O5_x1_22


title: P3_D9_C4_x1_58


title: P3_D11_O3_x1_25


title: P3_D6_O5_x1_33


title: P3_D4_O6_x1_60


title: P3_C6_C7_x1_43


title: P3_E8_O5_x10_52


title: P3_C7_C4_x1_93


title: P3_D3_C3_x1_62


title: P3_D2_O4_x1_39


title: P3_C8_C7_x1_20