title: ATAC_shHMGA1+RIS_Rep5

data_processing:
Mapped to the human reference (hg19) with BWA (version 0.7.12)
Low quality reads (mapping quality less than 20) as well as known adapter contamination were filtered out using Cutadapt (version 1.10.0)
Average fragment size was determined using the ChIPQC Bioconductor package, and peak calling was performed with MACS2 (version 2.1.0), using fragment size as an extension size (--extsize parameter)
Coverage files were generated using MACS2 (version 2.1.0).
Genome_build: hg19
Supplementary_files_format_and_content: .bedgraph = coverage files
Supplementary_files_format_and_content: .narrowPeak = peak files

extract_protocol:
ATAC-seq performed using 100,00 cells and 13 cycles of PCR amplification. Otherwise, as previously described (Buenrostro et al., 2015).
Libraries prepared using 13 cycles of PCR following nuclei transposition using the Nextera DNA library preperation kit (Illumina, FC-121-1030). Samples were size selected between 170 and 400bp (in order to isolate ‘nucleosome free’ and ‘mono-nucleosome’ fragments) using SPRIselect beads (B23319, Beckman Coulter)

treatment_protocol: For RIS samples, cells are treated for 6 days with 4OHT. For co-cultures, IMR90 ER:HRAS(G12V) cells expressing mRFP are cultured for 6 days in the presence of 4OHT before flow sorting of red cells.

tag: vector 2

value: MSCV shHMGA1

value: Yes


title: CASC15_004_Sph_Sh1

status: Public on Apr 24 2018

type: SRA

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

country: Sweden

institute: Gothenburg university

description:
processed data file:
CASC15_Sphere_hg19_combined_rpkm.txt.gz

library_source: transcriptomic

data_processing:
The samples from ILLUMINA  system were aligned using Tophat
All alignments were made using hg19 as reference genome assembly
The reads are quantified using featureCounts (subRead)
Normalization of reads performed as Reads Per Kilobase Million  (RPKM)
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements
CASC15_KD_hg19_combined_rpkm.txt.gz: 'GeneID' followed by normalized counts, RPKM from samples,"Csh_Batch1_D0", "Csh_Batch1_D7", "Csh_Batch2_D0", "Csh_Batch2_D7", "Csh_Batch3_D0", "CASC15-003 sh1_Batch3_D0", "CASC15-003 sh1_Batch2_D7", "CASC15-003 sh2_Batch1_D0", "CASC15-003 sh2_Batch1_D7", "CASC15-003 sh2_Batch2_D0", "CASC15-003 sh2_Batch2_D7", "CASC15-004 sh1_Batch2_D0", "CASC15-004 sh1_Batch2_D7", "CASC15-004 sh2_Batch2_D0", "CASC15-004 sh2_Batch2_D7", "Length"
CASC15_Sphere_hg19_combined_rpkm.txt.gz: 'GeneID' followed by normalized counts, RPKM from samples,"CASC15_Sph_Csh1", "CASC15_003_Sph_Sh1", "CASC15_003_Sph_Sh2", "CASC15_004_Sph_Sh1_rep1", "CASC15_004_Sph_Sh2"

molecule: total RNA

organism: Homo sapiens

source_name: SHSY5Y cells

growth_protocol: SH-SY5Y cells were routinely cultured in DMEM media supplemented with 10% FBS. For differentiation cells were treated with 10 mM RA for 7 days in DMEM/F12 media (1:1) supplemented with 10% FBS. Sphere formation was carried out in sphere forming media.

extract_protocol:
Cells were collected 48 hours post-transfection and RNA extraction was carried out using ReliaPrep RNA Cell Miniprep System
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA with Ribo-Zero from Illumina (Cat #  RS-122-2201)

treatment_protocol:
cells were cultured in sphere forming media
stable shRNA cells were generated after lentival transduction of the shRNA particle followed by puromycin selection.

tag: cell line

tag: shRNA sequence

value: CAGGCTGTTCCCAGGGATTTA

tag: culture status

value: sphere culture


title: Rif1-MNase 10''

city: Geneva

first: Lukas

last: Hafner

state: Geneva

address: 30 quai Ernest-Ansermet

department: Molecular Biology

country: Switzerland

institute: University of Geneva

description: ChEC-seq

library_source: genomic

data_processing:
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "--end-to-end --sensitive -k 20"
Data were filtered to retain only the mapped reads with at most 5 hits in the reference.
reads were extended by read length (50bp)
for ChEC-seq: ChrM was ommited from reference genome
Genome_build: Saccer3
Supplementary_files_format_and_content: .bw

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: whole organism

growth_protocol: 50 ml of cells were grown in YPAD to OD600=0.7

extract_protocol:
DNA was extracted with MasterPure Yeast DNA purification Kit (Epicentre), dissolved in 50ul and treated with RNAse RNAse A 200ug/ml for 20min at 37°C. ChEC DNA was subjected to Ampure XP beads (Agencourt) size selection (amount of beads: 2.5:1 v/v). The un-bound fraction (supernatant) containing the small fragments was recovered
Library preparation was carried out using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina protocol kit (Biolabs)

treatment_protocol: Cells were washed three times with 1 ml of Buffer A (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA, 0.2 mM spermine, 0.5 mM spermidine, 1X complete EDTA-free mini protease inhibitors, Roche, 1 mM PMSF). Cells were permealized in 1ml of Buffer A with 0.1% digitonin at 30°C for 5 min, then MNase activated adding 5mM CaCl2. At each time point, 200μl aliquot was taken and reaction stopped by adding 250 mM EGTA.

tag: strain

tag: genotype

value: W303 RAD5+, MAT::loxP, ADE2::loxP, LEU2::pGAL-HO, LYS2::loxP, MNT2::TG80-HO-CA80-ADE2-LYS2, RIF1-MNase-3xFLAG-KANMX4

tag: phase

value: unsynchronized

tag: time point

tag: treatment

value: Chromatin endogenous cleavage


title: CASC15-004 sh2_Batch2_D7

description:
processed data file:
CASC15_KD_hg19_combined_rpkm.txt.gz

treatment_protocol:
cells were differentiated to neuronal lineage for 7 days with 10 mM RA in 1% FBS media
stable shRNA cells were generated after lentival transduction of the shRNA particle followed by puromycin selection.

value: TAGGAATACCTTACATCCAAT

value: differentiated


title: CASC15_004_Sph_Sh2


title: CASC15_003_Sph_Sh1

value: CTAGCACTGACCTCCTTCATT


title: CASC15_003_Sph_Sh2

value: CTTTCCATCAGCCAACAATAT


title: Csh_sph

tag: shRNA

value: scrambled non-mammalian target control


title: ATAC_shHMGA1+RIS_Rep3

city: London

first: Shamith

last: Samarajiwa

address: ICTEM Building, Hammersmith Campus, Du Cane Road,

department: Genetics and Genomics Section  Department of Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

tag: vector 1

tag: passage


title: ATAC_shHMGA1+RIS_Rep2


title: CASC15-004 sh1_Batch2_D0

treatment_protocol:
culture in 10%FBS media
stable shRNA cells were generated after lentival transduction of the shRNA particle followed by puromycin selection.

value: non-differentiated


title: CASC15-003 sh2_Batch2_D7


title: ATAC_shHMGA1+RIS_Rep1


title: ATAC_CoCulture_RIS_Hep3B_Rep1

value: pLPC mRFP


title: CASC15-003 sh2_Batch1_D7


title: GGD49 DCL4-6:FHA

city: Strasbourg

first: Patrice

last: Dunoyer

state: Alsace

address: 12 rue du général Zimmer

department: Ibmp

country: France

institute: CNRS

description:
Immunoprecipited RNA
IR71_seeds_RPM.txt
IR2039_seeds_RPM.txt
miR822_seeds_RPM.txt
TAS1a_seeds_RPM.txt
TAS1b_seeds_RPM.txt
TAS1c_seeds_RPM.txt
TAS2_seeds_RPM.txt
TAS3a_seeds_RPM.txt
TAS3b_seeds_RPM.txt
TAS4_seeds_RPM.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were mapped using Hisat2 (v.2.0.5) (55), with the default parameters, to   the TAIR10 assembly,
Genome coverage of the loci of interest were made with genomeCoverageBed from bedtools suite (v.2.25.0)
Coordinates of miR (miRBase, v23), EndoIR-siRNAs (Montavon et. al., A specific dsRNA-binding protein complex selectively sequesters endogenous inverted-repeat siRNA precursors and inhibits their processing, Nucleic Acids Res. 2017), tasiRNA producing loci given by tasiRNAdb (last update September 1 2013)
normalisation : Data were normalized with the total output number of reads obtained for each corresponding library (coverage normalized per library size)
Genome_build: Col-0 TAIR10
Supplementary_files_format_and_content: tab-delimited text files include raw and normalised coverage of loci of interest

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Plant seeds were stratified for 2–4 days at 4°C before growth in soil under standard conditions at 22◦ C with a 16 h light/ 8 h dark cycle

extract_protocol:
Immunoprecipitated RNA from Col-0, pDCL4-DCL4-6:FHA/dcl4-2 and pDCL4-DCL4-8:FHA/dcl4-2 seedlings or flowers was extracted with Tri-Reagent (Sigma) and used for library preparation.
The libraries were constructed using the TruSeq SBS kit V3 from Illumina following manufacturer's  instructions and the libraries were sequenced as single-end 50 nt reads using an Illumina HiSeq 2500  (Fasteris, Switzerland)

tag: ecotype

value: Columbia

tag: tissue

value: Seedlings


title: ATAC_CoCulture_RIS_A549_Rep1


title: CASC15-003 sh2_Batch1_D0


title: ATAC_CoCulture_RIS_Hep3B_Rep2


title: ATAC_shHMGA1+RIS_Rep4


title: CASC15-003 sh1_Batch2_D7


title: CASC15-003 sh2_Batch2_D0


title: CASC15-004 sh1_Batch2_D7


title: Csh_Batch3_D0


title: ATAC_CoCulture_RIS_A549_Rep2


title: ATAC_N+RIS_Rep2

value: pWZL N1ICD


title: ATAC_CoCulture_RIS_MCF7_Rep2


title: ATAC_N+RIS_Rep3


title: Csh_Batch2_D7


title: Csh_Batch2_D0


title: Csh_Batch1_D7


title: Csh_Batch1_D0

data_processing:
The samples from ILLUMINA  system were aligned using Tophat
All alignments were made using hg19 as reference genome assembly
The reads are quantified using featureCounts (subRead)
Normalization of reads performed as Reads Per Kilobase Million  (RPKM)
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements
CASC15_KD_hg19_combined_rpkm.txt.gz: 'GeneID' followed by normalized counts, RPKM from samples,"Csh_Batch1_D0", "Csh_Batch1_D7", "Csh_Batch2_D0", "Csh_Batch2_D7", "Csh_Batch3_D0", "CASC15-003 sh1_Batch3_D0", "CASC15-003 sh1_Batch2_D7", "CASC15-003 sh2_Batch1_D0", "CASC15-003 sh2_Batch1_D7", "CASC15-003 sh2_Batch2_D0", "CASC15-003 sh2_Batch2_D7", "CASC15-004 sh1_Batch2_D0", "CASC15-004 sh1_Batch2_D7", "CASC15-004 sh2_Batch2_D0", "CASC15-004 sh2_Batch2_D7", "Length"
CASC15_Sphere_hg19_combined_rpkm.txt.gz: 'GeneID' followed by normalized counts, RPKM from samples, "CASC15_Sph_Csh1", "CASC15_003_Sph_Sh1", "CASC15_003_Sph_Sh2", "CASC15_004_Sph_Sh1_rep1", "CASC15_004_Sph_Sh2"


title: ATAC_NIS_Rep3

value: No


title: ATAC_NIS_Rep2


title: ATAC_RIS_Rep3

value: Yes


title: HNSCC sensitive cell line SCC25 baseline 2

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

country: USA

institute: University of Maryland, Baltimore

data_processing:
TCGA RSEM V2 normalization pipeline
MapSplice_multi_threads_2.0.1.9_unix --all-chromosomes-files HG19.fasta  --pairend -X 2 -Q fq   --chromosome-dir indv_chr/ -x HG19.index
picard-tools-1.93/AddOrReplaceReadGroups.jar RGPL=illumina RGPU=illumina  VALIDATION_STRINGENCY=SILENT SO=coordinate
samtools flagstat
samtools index
samtools 0.1.19 sort_bam_by_reference_and_name.pl
ubu-1.2-jar-with-dependencies.jar sam-xlate  --bed unc_hg19.bed   --order hg19_M_rCRS_ref.transcripts.fa --xgtags --reverse
ubu-1.2-jar-with-dependencies.jar sam-filter --strip-indels --max-insert 10000 --mapq 1
1.2.9/rsem-calculate-expression  --paired-end --bam --estimate-rspd -p 8 hg19_M_rCRS_ref  rsem
Genome_build: hg19
Supplementary_files_format_and_content: text file containing normalized read counts from RSEM

molecule: polyA RNA

source_name: cell line SCC25, parental cell line 2

extract_protocol:
RNA isolation and sequencing were performed for the parental SCC25 (C0) and each of the cetuximab and PBS generations (C1 to C11) at the Johns Hopkins Medical Institutions (JHMI) Deep Sequencing & Microarray Core Facility. Total RNA was isolated from a total of 1x106 cells using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following manufacturer’s instructions. The RNA concentration was determined by the spectrophotometer Nanodrop (Thermo Fisher Scientific, Waltham, MA) and quality was assessed using the 2100 Bioanalyzer (Agilent, Santa Clara, CA) system. An RNA Integrity Number (RIN) of 7.0 was considered as the minimum to be used in the subsequent steps for RNAseq.
Library was constructed using TrueSeq Stranded Total RNA seq Poly A1 Gold Kit (Illumina, San diego,CA) according to manufacturer's recommendations, followed by mRNA enrichment using poly(A) enrichment for ribosomal RNA removal.

tag: sample type

value: SCC25 parental cell line

tag: generations

tag: cetuximab resistant clone

tag: scc25 batch


title: Cetuximab resistant clones derived from SCC25, CTXR12

source_name: SCC25 clone, PBS, CTXR12

value: SCC25 cetuximab resistant clone 12


title: ATAC_RIS_Rep2

tag: vector 2


title: Cetuximab resistant clones derived from SCC25, CTXR10

source_name: SCC25 clone, PBS, CTXR10

value: SCC25 cetuximab resistant clone 10


title: Cetuximab resistant clones derived from SCC25, CTXR9

source_name: SCC25 clone, PBS, CTXR9

value: SCC25 cetuximab resistant clone 9


title: ATAC_Growing_Rep4

value: pWZL Vector


title: ATAC_RIS_Rep1


title: ATAC_Growing_Rep3


title: ATAC_CoCulture_RIS_MCF7_Rep1


title: Cetuximab resistant clones derived from SCC25, CTXR11

source_name: SCC25 clone, PBS, CTXR11

value: SCC25 cetuximab resistant clone 11


title: Cetuximab resistant clones derived from SCC25, CTXR8

source_name: SCC25 clone, PBS, CTXR8

value: SCC25 cetuximab resistant clone 8


title: Cetuximab resistant clones derived from SCC25, CTXR7

source_name: SCC25 clone, PBS, CTXR7

value: SCC25 cetuximab resistant clone 7


title: CASC15-003 sh1_Batch3_D0

tag: cell line

tag: shRNA sequence

value: CTAGCACTGACCTCCTTCATT


title: ATAC_N+RIS_Rep1


title: Fezf2 knockout_P14

city: Minato-ku, Tokyo

first: Sumiko

last: Watanabe

address: 4-6-1 Shirokane-dai

department: Institute of Medical Science

country: Japan

institute: University of Tokyo

data_processing:
CASAVA-1.8.2 was used for basecalling with default parameters
The sequence reads were aligned to the mouse reference genome assembly (NCBI37/mm9) using TopHat (v2.0.8b) with the option (--coverage-search --max-multihits 50)
fragments per kilobase of exon per million mapped fragments (FPKM) was calculated from the aligned reads by using CuffLinks (v2.1.1) with the default option
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: retina

growth_protocol: SPF with normal feeding

extract_protocol:
total RNA was extracted using RNeasy Plus Micro Kit (Qiagen), and RNA quality was confirmed using a 2100 Bioanalyzer (Agilent Technologies)
The first-strand cDNA was synthesized using random primers and SuperScript II (Invitrogen), and the second-strand cDNA was synthesized using RNaseH and DNA pol I (Illumina). Illumina GA sequencing adaptors were ligated to the cDNA ends. Double-stranded cDNA was size-fractionated by 6% PAGE, and cDNAs of 200 bp were recovered. cDNAs were amplified by 15 PCR cycles using Phusion DNA Polymerase (Finnzymes). Thirty-six-base-pair single-end-read RNA Seq tags were generated using an Illumina GA sequencer according to the standard protocol.

tag: age

value: postnatal day 14

value: retina

tag: background strain


title: ATAC_NIS_Rep1


title: control littermate_P14

tag: genotype

value: wildtype


title: ATAC_Growing_Rep1


title: Cetuximab resistant clones derived from SCC25, CTXR5

source_name: SCC25 clone, PBS, CTXR5

value: SCC25 cetuximab resistant clone 5


title: Cetuximab resistant clones derived from SCC25, CTXR3

source_name: SCC25 clone, PBS, CTXR3

value: SCC25 cetuximab resistant clone 3


title: Fezf2 knockout_P7

value: postnatal day 7


title: Cetuximab resistant clones derived from SCC25, CTXR2

source_name: SCC25 clone, PBS, CTXR2

value: SCC25 cetuximab resistant clone 2


title: iExo [ncRNA-Seq]

city: Incheon Metropolitan City

first: Yong Seung

last: Lee

address: SimGokro 100gil 25

department: College of Medicine

country: South Korea

institute: Catholic Kwandong University

data_processing:
SMARTer Stranded RNA-seq adapter sequence that may included in raw reads were trimmed by CutAdapt (https://pypi.python.org/pypi/cutadapt).
Adapter trimmed reads were mapped by TopHat2 (http://tophat.cbcb.umd.edu) with bowtie2 (http://bowtie-bio.sourceforge.net).
Counting sequence reads to genomic features by HTSeq (http://www-huber.embl.de/HTSeq).
Genome_build: Human reference genome build hg19 (R19, GRCh37.p13) from GENCODE (https://www.gencodegenes.org/releases/19.html)
Supplementary_files_format_and_content: Excel file include read count in read mapping for each sample

source_name: dermal fibroblast

growth_protocol: HDF cells were maintained in Dulbecco’s modified Eagle’s media (DMEM, Gibco) contained with 10% FBS (Gibco), and 1% penicillin/streptomycin (Gibco). UHDF (ultrasound treated HDF cells) were cultured in hNSC media of StemPro® NSC SFM (Gibco) supplemented with 2 mM GlutaMAX™-I Supplement (Gibco), 6 U/mL heparin (Sigma-Aldrich, St. Louis, MO, USA), 200 µM ascorbic acid (Sigma) and exosome (released exosome from ultrasound stimulus HDF cells). All cells were cultured at 37 oC in an atmosphere of 5% CO2.

extract_protocol:
Exosme was extracted from each culture medium of the ultrasound treated HDF cell by miRCURYTM Exosome isolation kit. Total RNA of exosome was extracted by miRCURYTM RNA isolation kit (Exiqon. Inc.). The isolated RNA from exosome and cells were quantificated by Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).
The exosomal RNAs were performed to library using NEBNext Multiplex Small RNA library prep kit (New England BioLabs, MA, USA)

treatment_protocol: Exosome isoltion method : 1x106 HDFs were directly exposed to ultrasound stimulus (20 KHz) for 5 sec (UHDF) using an ultrasonic processor. And then, 2 x 105 UHDFs were cultured on a 35-mm petri dish with ultrasound-treated hNSC medium (20 KHz, for 10 min) for 1 day.  Exosomes were isolated from cultured medium of UHDFs as previously described method. The culture medium was centrifuged at 3,000 x g for 20 min to remove cellular debris and dead cell, and the supernant was passed through a 0.22-mm filter (Minisart® Syringe Filter, Sartorius, 37070 Goettingen, Germany). The filtered medium was transferred to an Amicon® Ultra-15 100,000 kDa device (Millipore, Billerica, MA, USA) and exosome concentrated by centrifuge at 14,000 x g for 20 min.

value: skin


title: Cetuximab resistant clones derived from SCC25, CTXR1

source_name: SCC25 clone, PBS, CTXR1

value: SCC25 cetuximab resistant clone 1


title: nExo [WTS]

growth_protocol: HDF cells were maintained in Dulbecco’s modified Eagle’s media (DMEM, Gibco) contained with 10% FBS (Gibco), and 1% penicillin/streptomycin (Gibco). All cells were cultured at 37 oC in an atmosphere of 5% CO2.

extract_protocol:
Exosme was extracted from each culture medium of HDF cell by miRCURYTM Exosome isolation kit. Total RNA of exosome was extracted by miRCURYTM RNA isolation kit (Exiqon. Inc.). The isolated RNA from exosome and cells were quantificated by Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).
The exosomal RNAs were performed to library using SMARTer Stranded RNA-seq kit (Clontech, Madison, WI, USA).

treatment_protocol: Exosome isoltion method : Exosomes were isolated from cultured medium of HDF cell. The culture medium was centrifuged at 3,000 x g for 20 min to remove cellular debris and dead cell, and the supernant was passed through a 0.22-mm filter (Minisart® Syringe Filter, Sartorius, 37070 Goettingen, Germany). The filtered medium was transferred to an Amicon® Ultra-15 100,000 kDa device (Millipore, Billerica, MA, USA) and exosome concentrated by centrifuge at 14,000 x g for 20 min.


title: rNPC-P1 [RNA-seq]

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 Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Dermal fibroblast cells

growth_protocol: HDF cells were maintained in Dulbecco’s modified Eagle’s media (DMEM, Gibco) contained with 10% FBS (Gibco), and 1% penicillin/streptomycin (Gibco). rNPCs were cultured in hNSC media of StemPro® NSC SFM (Gibco) supplemented with 2 mM GlutaMAX™-I Supplement (Gibco), 6 U/mL heparin (Sigma-Aldrich, St. Louis, MO, USA), 200 µM ascorbic acid (Sigma) and exosome (released exosome from ultrasound stimulus HDF cells). All cells were cultured at 37 oC in an atmosphere of 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Exosome isoltion method : 1x106 HDFs were directly exposed to ultrasound stimulus (20 KHz) for 5 sec (UHDF) using an ultrasonic processor. And then, 2 x 105 UHDFs were cultured on a 35-mm petri dish with ultrasound-treated hNSC medium (20 KHz, for 10 min) for 1 day.  Exosomes were isolated from cultured medium of UHDFs as previously described method1. The culture medium was centrifuged at 3,000 x g for 20 min to remove cellular debris and dead cell, and the supernant was passed through a 0.22-mm filter (Minisart® Syringe Filter, Sartorius, 37070 Goettingen, Germany). The filtered medium was transferred to an Amicon® Ultra-15 100,000 kDa device (Millipore, Billerica, MA, USA) and exosome concentrated by centrifuge at 14,000 x g for 20 min. Generation of HDFs : 1x105 HDFs were seeded and cultured on 35mm cultured dish for 1 day. After 1 day, the medium was replaced with hNSC medium include isolated exosome and culture for 5 days. The culture medium was replaced every two days.


title: HNSCC sensitive cell line SCC25 baseline

source_name: cell line SCC25, parental cell line 1

value: SCC25 parental cell line


title: rNPC-P5 [RNA-seq]


title: hNSC [RNA-seq]

source_name: neural stem cells

value: brain


title: ATAC_Growing_Rep2

value: No


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 11

source_name: cell line SCC25,cetuximab,week 11

value: CTX generation 11 for SCC25 cetuximab resistant generations

value: 100nM Cetuximab


title: HNSCC sensitive cell line SCC25 treated with PBS, week 11

source_name: cell line SCC25,PBS,week 11

value: PBS generation 11 for SCC25 cetuximab resistant generations

value: PBS


title: HDF [RNA-seq]


title: HNSCC sensitive cell line SCC25 treated with PBS, week 10

source_name: cell line SCC25,PBS,week 10

value: PBS generation 10 for SCC25 cetuximab resistant generations


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 10

source_name: cell line SCC25,cetuximab,week 10

value: CTX generation 10 for SCC25 cetuximab resistant generations


title: Cetuximab resistant clones derived from SCC25, CTXR4

source_name: SCC25 clone, PBS, CTXR4

value: SCC25 cetuximab resistant clone 4


title: caco21D_ctrl3

city: Ramat Gan

first: Tzipi

last: Braun

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center at Tel Hashomer

data_processing:
Reads were quantified by kallisto v42.5
Abundance was summed to the gene level using a in-house script.
Genome_build: Gencode v24
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Caco-2 human colon carcinoma cell line

extract_protocol:
RNA was isolated using Tri Reagent-LS (Sigma, T9424). , RNA quality and concentration were measured by Agilent Bioanalyzer 2100 using the RNA 6000 Nano Assay
RNA sequencing (RNA-seq) libraries were prepared using the Illumina TruSeq RNA preparation kit and sequenced on the Illumina HiSeq 2000 with paired-end 75-bp reads (Illumina, San Diego, CA).

tag: cell type

value: 21 days differentiated caco-2 cells


title: caco21D_ctrl2


title: HNSCC sensitive cell line SCC25 treated with PBS, week 9

source_name: cell line SCC25,PBS,week 9

value: PBS generation 9 for SCC25 cetuximab resistant generations

tag: treatment


title: caco21D_ctrl4


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 8

source_name: cell line SCC25,cetuximab,week 8

value: CTX generation 8 for SCC25 cetuximab resistant generations


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 9

source_name: cell line SCC25,cetuximab,week 9

value: CTX generation 9 for SCC25 cetuximab resistant generations


title: control littermate_P7

source_name: retina

value: postnatal day 7

value: retina

value: wildtype


title: HNSCC sensitive cell line SCC25 treated with PBS, week 8

source_name: cell line SCC25,PBS,week 8

value: PBS generation 8 for SCC25 cetuximab resistant generations


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 7

source_name: cell line SCC25,cetuximab,week 7

value: CTX generation 7 for SCC25 cetuximab resistant generations


title: HNSCC sensitive cell line SCC25 treated with PBS, week 7

source_name: cell line SCC25,PBS,week 7

value: PBS generation 7 for SCC25 cetuximab resistant generations


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 5

source_name: cell line SCC25,cetuximab,week 5

value: CTX generation 5 for SCC25 cetuximab resistant generations


title: HNSCC sensitive cell line SCC25 treated with PBS, week 5

source_name: cell line SCC25,PBS,week 5

value: PBS generation 5 for SCC25 cetuximab resistant generations


title: HNSCC sensitive cell line SCC25 treated with PBS, week 4

source_name: cell line SCC25,PBS,week 4

value: PBS generation 4 for SCC25 cetuximab resistant generations


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 3

source_name: cell line SCC25,cetuximab,week 3

value: CTX generation 3 for SCC25 cetuximab resistant generations

value: 100nM Cetuximab


title: HNSCC sensitive cell line SCC25 treated with PBS, week 2

source_name: cell line SCC25,PBS,week 2

value: PBS generation 2 for SCC25 cetuximab resistant generations

value: PBS


title: HNSCC sensitive cell line SCC25 treated with PBS, week 3

source_name: cell line SCC25,PBS,week 3

value: PBS generation 3 for SCC25 cetuximab resistant generations


title: HNSCC sensitive cell line SCC25 treated with100nM cetuximab, week 1

source_name: cell line SCC25,cetuximab,week 1

value: CTX generation 1 for SCC25 cetuximab resistant generations


title: HDF [MBD-seq]

data_processing:
Illumina bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate methylation levels, the MBD Seq reads were mapped to the genome of Homo sapiens(hg19) using Bowtie 1.1.1.
PCR duplicates were removed with Picard Mark Duplicates (version 1.118).
Raw data (the reads for mapped in genome) were normalized by RMS (Relative Methylayion Score) each ROI region using MEDIPS package (version 1.16.0).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include RMS values for each Sample and ROI
Supplementary_files_format_and_content: CGI_PROMOTER.rms.txt: Relative Methylation Score matrix txt

source_name: Dermal fibroblast cells

extract_protocol:
1ug of gDNA was sheared to 200~400bp using the Covaris LE220 sonicator (Covaris Inc. Woburn, MA). The fragmented products were immunoprecipitated using the MethylMiner Methylated DNA Enrichment Kit (Invitrogen) following the manufacture’s recommended protocol. Briefly, Methylated DNA was isolated from fragmented whole genomic DNA by binding to the methyl-CpG binding domain of human MBD2 protein, which is coupled to paramagnetic Dynabeads® M-280 Streptavidin via a biotin linker. The methylated fragments were eluted as a single enriched population with a 2000 mM NaCl elution buffer.
DNA libraries were prepared for sequencing using MethylMiner Methylated DNA Enrichment Kit (Invitrogen).

value: skin


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 2

source_name: cell line SCC25,cetuximab,week 2

value: CTX generation 2 for SCC25 cetuximab resistant generations


title: HNSCC sensitive cell line SCC25 treated with PBS, week 1

source_name: cell line SCC25,PBS,week 1

value: PBS generation 1 for SCC25 cetuximab resistant generations


title: HNSCC sensitive cell line SCC25, baseline for cetuximab resistant generations

source_name: cell line SCC25, parental cell line, baseline for generations

value: Baseline for SCC25 cetuximab resistant generations


title: rNPC-p5 [MBD-seq]


title: LTAD DHT treated siControl

status: Public on Apr 23 2018

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
The SOLiD-generated RNA-Seq reads was in 50 bp length and an initial filtering process was taken to remove any non-desirable contamination sequences.
The reads were mapped to the human RefSeq mRNA database.
The expression levels of mapped transcripts were normalized into Reads Per Kilobase of exon per Million mapped reads (RPKM) to faciliate comparison among different samples.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file of RPKM values for each Sample

source_name: prostate cancer cells

growth_protocol: LNCaP cells were cultures in RPMI 1640 containing 10% FBS. LTAD cells were treated with phenol-red free RPMI1640 containing 10% charcoal/dextran treated FBS. Before hormone treatment, cells were incubated in phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol:
Total RNA was extracted using ISOGEN reagent.
RNA sequencing (RNA-seq) library construction and sequencing was performed according to the manufacturer’s protocol for the Applied Biosystems SOLiD 4 System (Applied Biosystems).

treatment_protocol: Cells were transfected with siRNA for 48 h and treated with vehicle or DHT 10 nM for 24 h.

value: LTAD cells

value: DHT 10 nM 24 h siControl


title: LNCaP Ethanol treated siCTBP1-AS

value: LNCaP cells

value: ethanol 24h siCTBP1-AS treated


title: SKOV3 Wild Type Replicate 1 (SKOV3_WT_701)

city: Washington

first: Wenge

last: Zhu

state: DC

address: 800 22nd Street NW, , Science & Engineering Hall 8480

department: School of Medicine and Health Sciences

institute: George Washington University

description: SKOV3 wild type ovarian cancer cell line

data_processing:
Alignment of paired end reads was performed using the STAR Aligner v. 2.5.1a, default parameters.
Read Counting of bam alignment files was performed using HTSeq (htseq-count) to generate raw per-gene read counts.
DESeq, R package, was used to generate normalized reads, Log2FoldChange, and differential expression statistics
Genome_build: Ensembl Human: GRCh38.p7, and corresponding GTF file.
Supplementary_files_format_and_content: Two matrix files are provided, one containing raw read counts and the other containing normalized read counts.

source_name: ovarian cancer cell line

growth_protocol: WT cells was treat with cisplatin for 4 hours, followed by release to cisplatin free medium for three weeks, we repeated the cisplatin treatment in the medium with the increased concentration of cisplatin. After 5 months treatment (six cycles), we identified cells that were able to grow in the medium with high concentration of cisplatin and named these cisplatin resistant cells as SKOV3 CR

extract_protocol:
RNA isolation was completed using the Qiagen miRNeasy Mini Kit according to the manufacturer’s protocol
RNA samples are converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina # RS-122-2103).  Briefly, Total RNA samples are concentration normalized, and poly-adenylated RNA is purified using oligo-dT attached to magnetic beads.  Purified mRNA is fragmented using heat in the presence of divalent cations. Fragmented RNA is converted into double-stranded cDNA, with dUTP utilized in place of dTTP in the second strand master mix.  A single 'A' base is added to the cDNA and forked adaptors that include index, or barcode, sequences are attached via ligation. The resulting molecules are amplified via polymerase chain reaction (PCR). During PCR the polymerase stalls when a dUTP base is encountered in the template. Since only the second strand includes the dUTP base, this renders the first strand the only viable template, thereby preserving the strand information. Final libraries are quantified, normalized and pooled.  Pooled libraries are bound to the surface of a flow cell, and each bound template molecule is clonally amplified up to 1000-fold to create individual clusters.  Four fluorescently labeled nucleotides are then flowed over the surface of the flow cell and incorporated into each nucleic acid chain.  Each nucleotide label acts as a terminator for polymerization, thereby ensuring that a single base is added to each nascent chain during each cycle.  Fluorescence is measured for each cluster during each cycle to identify the base that was added to each cluster. The dye is then enzymatically removed to allow incorporation of the next nucleotide during the next cycle.

treatment_protocol: Both SKOV3 WT or SKOV3 CR cells were collected in narmal growth medium in log growth phase and without any treatment.

value: ovarian cancer

tag: phenotype

value: Cisplatin Susceptible

tag: uid


title: LTAD DHT treated siCOBLL1

value: DHT 10 nM 24 h siCOBLL1 treated


title: LNCaP DHT treated siPSF

value: DHT 10 nM 24 h siPSF treated


title: LNCaP Ethanol treated siPSF

value: ethanol 24h siPSF treated


title: SKOV3 Cisplatin Resistant Replicate 2 (SKOV3_CR_704)

description: SKOV3 cisplatin resistant ovarian cancer cell line

value: Cisplatin Resistant


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 4

source_name: cell line SCC25,cetuximab,week 4

value: CTX generation 4 for SCC25 cetuximab resistant generations

value: 100nM Cetuximab


title: SKOV3 Cisplatin Resistant Replicate 1 (SKOV3_CR_703)


title: LNCaP DHT treated siControl

value: DHT 10 nM 24 h siControl treated


title: LTAD siControl DHT ChIPed by AR

data_processing:
Basecalls performed using CASAVA-1.8.2
ChIP-seq reads were aligned to the hg18 or hg19 genome assembly using Bowtie version 0.12.8 with parameters -a --best --strata -m 1 -v 2.
Generate alignments in the SAM format given single-end reads. Convert SAM to BAM files using samtools view command. samtools version is 0.1.16.
Signal scores were calculated using Model-based analysis of ChIP-seq (MACS; P-value < 10xE-4 or -5)
Genome_build: hg18 or hg19 (as appended to filenames)
Supplementary_files_format_and_content: Bed files can be visualized by Integrative genomic viewer ver 2.2 (IGV ver 2.2)

growth_protocol: LNCaP cells were cultured in RPMI 1640 containing 10% FBS. Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.  LTAD cells were treated with phenol-red free RPMI1640 containing 10% charcoal/dextran treated FBS. VCaP-LTAD cells were  cultured in DMEM containing 10% charcoal/dextran treated FBS.

extract_protocol:
Cells were fixed with 1% formaldehyde. Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The Chromatin immunoprecipitated DNA fragments (approx.10 ng in 30 µl water) are end repaired by using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase in the presence of dNTPs. And an ‘A’ base is added to the 3’end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment. Then, adaptors (Adaptor oligo mix, Illumina) are ligated to the ends of the DNA fragments. The resulting DNA fragments are purified by MinElute column (QIAGEN).  300 ~ 500 bp DNA fragments are purified by using E-Gel SizeSelect agarose Gels (Invitrogen) according to manufacturer’s instruction.Size selected adaptor-modified DNA fragments are amplified by 18 cycles of PCR using Phusion polymerase and PCR primer 1.1 and 2.1 (Illumina). The resulting PCR products are purified by MinElute column (QIAGEN).

treatment_protocol: LNCaP, LTAD and VCaP-LTAD cells were treated with vehicle, DHT 1nM or DHT 10 nM for 24 h.

value: 24h DHT 10 nM siControl treated

tag: chip antibody

value: AR (santacruz H-280)


title: SKOV3 Wild Type Replicate 2 (SKOV3_WT_702)


title: HNSCC sensitive cell line SCC25 treated with PBS, week 6

source_name: cell line SCC25,PBS,week 6

value: PBS generation 6 for SCC25 cetuximab resistant generations

value: PBS


title: LTAD Ethanol treated siCOBLL1

value: LTAD cells

value: ethanol 24h siCOBLL1 treated


title: LTAD Ethanol treated siControl

value: ethanol 24h siControl


title: NSC [MBD-seq]

source_name: neural stem cells

value: brain


title: LNCaP DHT treated siCTBP1-AS

value: LNCaP cells

value: DHT 10 nM 24 h siCTBP1-AS treated


title: LNCaP Ethanol treated siControl

value: ethanol 24h siControl treated


title: HNSCC sensitive cell line SCC25 treated with 100nM cetuximab, week 6

source_name: cell line SCC25,cetuximab,week 6

value: CTX generation 6 for SCC25 cetuximab resistant generations


title: LTAD siCOBLL1 DHT ChIPed by AR

value: 24h DHT 10 nM siCOBLL1 treated


title: LTAD siCOBLL1 DHT input

value: input


title: VCaP-LTAD DHT 1nM ChIPed by AR

value: VCaP-LTAD cells

value: 24h DHT 1 nM


title: rhesus_950807_muscle

city: Beijing

first: Jia-Yu

last: Chen

address: No.5 Yiheyuan Road Haidian District

department: Institute of Molecular Medicine

country: China

institute: Peking University

data_processing:
raw reads were aligned by Tophat v1.2.0
only uniquely-mapped reads are retained
RPKM values were calculated by in-house perl scripts
Genome_build: rheMac2
Supplementary_files_format_and_content: chromsome, start,end, gene ID, RPKM value, strand information, the longest transscript, reads number, transcipt length

organism: Macaca mulatta

extract_protocol:
Total RNA was extracted from rhesus monkey tissues using the Trizol method and analyzed by an Agilent 2100 bio-analyzer (Agilent Technologies). Poly (A)-positive RNA was purified with the Dynabeads mRNA purification kit (Invitrogen) from 5μg of total RNA with high quality (RNA integrity number >7.5), following the manufacturer's instructions.
A strand-specific RNA-Seq library preparation on the basis of the incorporation of deoxy-UTP was performed.

tag: sample group

value: case (with extreme high insulin level)

tag: gender

value: male

value: muscle

tag: library type

value: strand-specific, dUTP protocal


title: rhesus_950509_muscle

value: control

tag: tissue


title: VCaP-LTAD DHT ChIPed by AR

value: 24h DHT 10 nM

value: AR (santacruz H-280)


title: rhesus_950509_fat

value: fat


title: rhesus_950807_fat


title: HFE-145-YAP5SA-1

city: Daejeon

first: Wonyoung

last: Choi

address: 291 Daehak-ro

institute: KAIST

description: library constructed with multiple Small RNA library Prep kit (NEB)

data_processing:
Quality filtering with FastQC
Aligned to reference genome (UCSC hg19)
Read counts were quantile normalized
Genome_build: hg19
Supplementary_files_format_and_content: excel file includes read counts of mature miRNAs

extract_protocol:
Total RNA was isolated from each set of samples using easy-BLUE (Intron).
For library construction, we used multiple Small RNA library Prep kit (NEB).

tag: gene overexpression


title: LTAD DHT ChIPed by K9me2

value: LTAD cells


title: LTAD DHT input


title: rhesus_940313_fat


title: rhesus_940129_muscle


title: VCaP-LTAD input


title: HFE-145-vector-1

value: vector


title: LTAD siControl DHT input

value: 24h DHT 10 nM siControl treated


title: HFE-145-YAP5SA-2


title: LTAD DHT ChIPed by AcH3

value: AcH3 (Millipore #06-599)


title: rhesus_940129_fat


title: HFE-145-vector-2


title: LTAD DHT 1nM input


title: rhesus_920401_muscle


title: LNCaP DHT 1nM ChIPed by AR

value: LNCaP cells


title: LTAD siCTBP1-AS DHT ChIPed by PSF

value: 24h ethanol siCTBP1-AS treated

value: PSF (sigma#WH0006421M2)


title: rhesus_920401_fat


title: LNCaP DHT 1nM input

value: input


title: LTAD siCTBP1-AS Et ChIPed by PSF

value: 24h DHT 10 nM siCTBP1-AS treated


title: LTAD DHT ChIPed by PSF


title: LTAD DHT ChIPed by COBLL1

value: COBLL1 (Abcam#64465)


title: rhesus_940313_muscle

value: male


title: LTAD DHT input2


title: LTAD Et ChIPed by COBLL1

value: 24h ethanol


title: LNCaP DHT ChIPed by K9me2


title: LTAD ChIPed by AcH3


title: LTAD Et input2


title: Fig5C_DDDAAA_Smc1PK_IP

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

department: Biochemistry

institute: University of Oxford

description: Exponentially growing strain K26757 (expressing smc1 DDD mutant from an ectopic locus and smc3AAA mutant from the endogenous locus)

data_processing:
Library sequencing was carried out on the Ion Torrent Proton
The quality of the raw sequence data was examined using FastQC (Galaxy tool version 1.0.0) and trimming of reads was carried out using “trim sequences” (Galaxy tool version 1.0.0)
Any reads smaller than 50bp were removed using ‘Filter FASTQ’
The final reads were aligned to the Saccharomyces cerevisiae genome (sacCer3, SGD) or Candida glabrata genome (CBS138, genolevures) using Bowtie2 (Galaxy tool version 0.2) with the default (--sensitive) parameters
To generate an alignment in which all the sequences exclusively align to the Saccharomyces cerevisiae genome, the whole reads were first aligned to Candida glabrata genome and the unaligned reads were retrieved as a separate Fastq file. Subsequently, these unaligned reads were re-aligned to Saccharomyces cerevisiae genome and the resulting aligned BAM file therefore contained reads that were unique to Saccharomyces cerevisiae. A same strategy was used to generate alignments unique to Candida glabrata.
Genome_build: SacCer3 or Candida glabrata (ASM254v2)
Supplementary_files_format_and_content: bigwig files

source_name: Saccharomyces cerevisiae cells

growth_protocol: Yeast cells were grown in YPD to reach a density of 0.3-0.6 OD600.

extract_protocol:
To crosslink cells, 45ml of yeast culture was mixed with 4.2ml of fixation solution (50mM Tris-HCl pH 8.0, 100mM NaCl, 0.5mM EGTA, 1mM EDTA, 30% Formaldehyde) and incubated at 18°C for 30 minutes. The crosslinking reaction was quenched by incubating with 2ml of 2.5M Glycine for 5 min. Fixed cells were harvested, washed with ice-cold PBS and re-suspended in 1ml of ChIP lysis buffer (50mM Hepes-KOH pH 8.0, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF, Roche protease inhibitor). For each ChIP, 10 OD600 units of Saccharomyces cerevisiae cells mixed with 5 OD600 units of Candida glabrata cells were pelleted and re-suspended in 0.3ml of ChIP lysis buffer. Cells were mixed with glass beads and disrupted by FastPrep®-24 (MP Biomedicals, USA). The entire lysis was collected and sonicated at 4°C for 40 minutes using a Bioruptor (Diagenode, Belgium). The cell debris were removed by centrifugation and supernatants containing sheared chromatin with a size range from 100-800bp were adjusted to a final volume of 1ml with ChIP lysis buffer. Extracts were pre-cleared for 1 hour at 4°C with 30µl of Protein G Dynabeads (Invitrogen). 80µl of supernatant was taken as whole cell extract (W) and stored at -80°C. Five µg of anti-PK antibody (Bio-Rad) and 50 µl of Protein G Dynal beads (Invitrogen) was used for immunoprecipitation (6 hours-overnight, rotation at 4°C). The beads were subsequently washed for 5 minutes with the following buffers: 2Ã—ChIP lysis buffer; 3x ChIP high-salt lysis buffer (50mM Hepes-KOH pH 8.0, 500mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF); 2Ã—ChIP wash buffer (10mM Tris-HCl pH 8.0, 0.25M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1mM EDTA, 1mM PMSF) and 1x TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 50mM NaCl). The immunoprecipitated chromatin was eluted by incubation of beads with 120µl of TES buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 1% SDS) at 65°C for 15 minutes. The supernatants were collected and termed the IP sample. The whole cell extract sample (W) was mixed with 40µl of TES3 buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 3% SDS). Both samples were de-crosslinked at 65°C overnight. RNA was degraded by incubating with 2-µl of RNAse A (10mg/ml, Roche) at 37°C for 1 hour and protein was subsequently removed by incubation with 10µl of Proteinase K (18mg/ml, Roche) at 65°C for 2 hours. DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research, USA).
NEBNext Fast DNA Library Prep set for Ion Torrent, E6270

tag: sac_cer strain

tag: can_gla strain

tag: antibody

value: anti-PK antibody (Bio-Rad)

tag: growth

value: exponentially growing


title: Fig5C_DDDAAA_Smc1PK_WCE

value: none (input)

value: strain K26757 (expressing smc1 DDD mutant from an ectopic locus and smc3AAA mutant from the endogenous locus)


title: LTAD Et ChIPed by PSF

tag: cell line

value: PSF


title: LNCaP DHT ChIPed by AcH3 - 2

value: 24h DHT 10 nM


title: Fig5C_DDDKKK_Smc1PK_WCE

description: Exponentially growing strain K26756 (expressing the wild type Smc3 from the endogenous locus and the smc1DDD mutant from an ectopic locus)


title: LNCaP DHT ChIPed by AcH3 - 1


title: LNCaP DHT input


title: LTAD  input

value: LTAD cells


title: LTAD DHT 1nM ChIPed by AR

value: 24h DHT 1 nM

value: AR (santacruz H-280)


title: LTAD Et ChIPed by AR


title: FigS2C_WT_Smc3HA_WCE

description: Exponentially growing strain K26983, expressing wild type Smc3-HA and wild type Smc1 from ectopic loci and containing the deletion of the SMC1 gene


title: FigS2C_WT_Smc3HA_IP

value: anti-HA atibody (3F10, Roche)

value: strain K26983, expressing wild type Smc3-HA and wild type Smc1 from ectopic loci and containing the deletion of the SMC1 gene


title: FigS2C_DDAAA_Smc3HA_WCE

description: Exponentially growing strain K26982, expressing smc1 K554D K661D and Smc3AAA-HA mutant from ectopic loci and containing the deletion of the SMC1 gene


title: LNCaP input

value: LNCaP cells


title: Fig5C_DDDKKK_Smc1PK_IP

value: strain K26756 (expressing the wild type Smc3 from the endogenous locus and the smc1DDD mutant from an ectopic locus)


title: LTAD Et  input

value: input


title: FigS2C_DDAAA_Smc3HA_IP

value: strain K26982, expressing smc1 K554D K661D and Smc3AAA-HA mutant from ectopic loci and containing the deletion of the SMC1 gene


title: LNCaP Et ChIPed by AcH3

value: AcH3 (Millipore #06-599)


title: Fig4C_K650D_K661D_Smc1PK_WCE

description: exponentially growing strain K15226 containing a deletion of the endogenous SMC1 gene and expressing the smc1 K650D,K661D mutant from an ectopic locus


title: Fig4C_K650D_K661D_Smc1PK_IP

value: strain K15226 containing a deletion of the endogenous SMC1 gene and expressing the smc1 K650D,K661D mutant from an ectopic locus


title: CASC15-004 sh2_Batch2_D0

source_name: SHSY5Y cells

tag: shRNA sequence

value: TAGGAATACCTTACATCCAAT

tag: time point

tag: culture status

value: non-differentiated


title: Lats1/2iΔLgr5 2

data_processing:
Raw sequencing data were aligned to the reference genome (GRCm38) using TopHat (2.1.1)
Sequence reads were counted with HTSeq
Differential gene expression was statistically determined using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes differentially expressed genes processed with DESeq2 for all samples

source_name: Pyloric epithelium

extract_protocol:
Mouse stomachs were harvested, cut open, and pinned flat on a thick sheet of paper. They were snap-frozen in vapor-phase liquid nitrogen, and mounted with frozen sectioning media (Leica). The samples were then sectioned in a cryostat, with five to seven 10 μm sections collected beginning with the first observed epithelial structures. RNA was isolated from each set of samples using easy-BLUE (Intron).
For library construction, we used Truseq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA). Briefly, the steps of the strand-specific protocol are as follows: first strand cDNA synthesis; second strand synthesis using dUTPs instead of dTTPs; end repair, A-tailing and adaptor ligation; PCR amplification. Then, each library was diluted to 8 pM for 76 cycles of paired-read sequencing (2 X 75 bp) on an Illumina NextSeq 500 following the manufacturer’s recommended protocol.

tag: strain

value: stomach

tag: cell type

value: Pyloric epithelium

tag: genotype


title: Fig5A_DDDEQ_Scc2PK_WCE

description: exponentially growing strain K26840 (ectopic smc1DDD E1158Q) containing Scc2-PK6

value: none (input)

value: exponentially growing


title: Fig5A_DDDEQ_Scc2PK_IP

value: anti-PK antibody (Bio-Rad)

value: strain K26840 (ectopic smc1DDD E1158Q) containing Scc2-PK6


title: Lats1/2iΔLgr5 1


title: Fig5A_EQ_Scc2PK_WCE

description: exponentially growing strain K25646 (ectopic smc1 E1158Q) containing Scc2-PK6


title: Fig5A_EQ_Scc2PK_IP

value: strain K25646 (ectopic smc1 E1158Q) containing Scc2-PK6


title: WT 2


title: Fig5A_WT_Scc2PK_IP

description: exponentially growing strain K26839 (ectopic Smc1) containing Scc2-PK6


title: e14.5_LatsCKO

city: Houston

first: Yang

last: Xiao

state: Texas

address: One Baylor Plaza,  Room 509E, Baylor College of Medicine, Department of Molecular Physiology

institute: Baylor College of Medicine

data_processing:
Drop-seq data was processed as described in Shekhar et. al. (2016).
FastQ files were converted to BAMs with Picard tools (FastqToSam) and then used is input for STAR alignment, cell barcode correction, and digital gene expression (DGE) matrix generation via the Drop-seq tools software (available at http://mccarrolllab.com/dropseq/).
Genome_build: mm10
Supplementary_files_format_and_content: Digital gene expression matrix of raw integer read values processed according to Macosko et. al., 2015 (Dropseq_tools_1.12).

source_name: cardiac tissue

extract_protocol:
Lysis in droplets
Illumina Nextera XT

value: heart

tag: developmental stage

tag: genotype/variation

value: Wt1 CreERT2/+; Lats1/2 F/F; Rosa26mTmG/+


title: Fig4C_K554D_K661D_Smc1PK_IP

description: exponentially growing strain K14324 containing a deletion of the endogenous SMC1 gene and expressing the wild type Smc1 from an ectopic locus


title: WT 1


title: Fig5A_WT_Scc2PK_WCE

value: strain K26839 (ectopic Smc1) containing Scc2-PK6


title: Fig4ES3B_DDD_Smc1PK_WCE

description: exponentially growing K24327 (ectopic Smc1)

value: K24327 (ectopic Smc1)


title: e13.5_LatsCKO


title: Fig4ES3B_DDD_Smc1PK_IP


title: Fig4ES3B_5C_WT_Smc1PK_WCE

description: exponentially growing K26756 (ectopic Smc1DDD)

value: K26756 (ectopic Smc1DDD)


title: Fig4ES3B_untagged_WCE

description: exponentially growing K699 (untagged control)

value: K699 (untagged control)


title: Fig4C_WT_Smc1PK_WCE

description: exponentially growing strain K15322 containing a deletion of the endogenous SMC1 gene and expressing the smc1 K554D,K661D mutant from an ectopic locus


title: e13.5_control

value: Wt1 CreERT2/+; Rosa26mTmG/+


title: Fig4ES3B_5C_WT_Smc1PK_IP


title: Fig4C_K554D_K661D_Smc1PK_WCE

value: strain K14324 containing a deletion of the endogenous SMC1 gene and expressing the wild type Smc1 from an ectopic locus


title: Fig4ES3B_untagged_IP


title: Fig3CS3A_DDAAA_Smc3HA_IP

description: Strain K26611 (containing 3XminiAID tagged-smc3 and smc1DD in their respective endogenous locus, and smc3AAA mutant expressed from an ectopic locus) was arrested in G1, synthetic auxin (indole-3-acetic acid) was added to 1 mM 30 min before release. The culture was released into YPD containing 1mM auxin and nocodazole to arrest the cultures in G2 and analyzed by calibrated ChIP-sequencing

value: anti-HA atibody (3F10, Roche)


title: Fig3CS3A_DDAAA_Smc3HA_WCE

value: Strain K26611 (containing 3XminiAID tagged-smc3 and smc1DD in their respective endogenous locus, and smc3AAA mutant expressed from an ectopic locus)

value: arrested in G1, synthetic auxin (indole-3-acetic acid) was added to 1 mM 30 min before release. The culture was released into YPD containing 1mM auxin and nocodazole to arrest the cultures in G2


title: Fig4C_WT_Smc1PK_IP

value: strain K15322 containing a deletion of the endogenous SMC1 gene and expressing the smc1 K554D,K661D mutant from an ectopic locus


title: Fig3CS3A_WT_Smc3HA_WCE

description: Strain K26797 (containing 3XminiAID-tagged smc3 in the endogenous locus and Smc3 wild type expressed from an ectopic locus) was arrested in G1, synthetic auxin (indole-3-acetic acid) was added to 1 mM 30 min before release. The culture was released into YPD containing 1mM auxin and nocodazole to arrest the cultures in G2 and analyzed by calibrated ChIP-sequencing

value: none (input)


title: CXCR4 12G5 affinity sort replicate 1

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

institute: University of Illinois

description:
Deep mutational scan of CXCR4 for surface expression and affinity for antibody 12G5 in Expi293F cells
enrichment_ratios_CXCR4.xlsx
CXCR4_12G5_Affinity1
Synthetic coding sequences

data_processing:
Data was analyzed using Enrich: http://depts.washington.edu/sfields/software/enrich/
Fuser script: CCR5 fragment A read 1: python Paired_read_fuser.py --path directory_fragA_R1/ --read1 CCR5_R1.fastq.bz2 --read2 CCR5_R1.fastq.bz2 --wtseq GCCGATTATCAAGTGTCAAGTCCAATCTATGACATCAATTATTATACATCGGAGCCCTGCCAAAAAATCAATGTGAAGCAAATCGCAGCCCGCCTCCTGCCTCCGCTCTACTCACTGGTGTTCATCTTTGGTTTTGTGGGCAACATGCTGGTCATCCTCATCCTGATAAACTGCAAAAGGCTGAAGAGCATGACTGAC --read1_overlap_start 46 --read1_overlap_end 244 --mode R1
Fuser script: CCR5 fragment A read 2: python Paired_read_fuser.py --path directory_fragA_R2/ --read1 CCR5_R2.fastq.bz2 --read2 CCR5_R2.fastq.bz2 --wtseq GTCACCTTTGGGGTGGTGACAAGTGTGATCACTTGGGTGGTGGCTGTGTTTGCGTCTCTCCCAGGAATCATCTTTACCAGATCTCAAAAAGAAGGTCTTCATTACACCTGCAGCTCTCATTTTCCATACAGTCAGTATCAATTCTGGAAGAATTTCCAGACATTAAAGATAGTCATCTTGGGGCTGGTCCTGCCGCTGCTTGTAATGGTC --read2_overlap_start 19 --read2_overlap_end 229 --mode R2
Fuser script: CCR5 fragment B read 1: python Paired_read_fuser.py --path directory_fragB_R1/ --read1 CCR5_R1.fastq.bz2 --read2 CCR5_R1.fastq.bz2 --wtseq ATCTACCTGCTCAACCTGGCCATCTCTGACCTGTTTTTCCTTCTTACTGTCCCCTTCTGGGCTCACTATGCTGCCGCCCAGTGGGACTTTGGAAATACAATGTGTCAACTCTTGACAGGGCTCTATTTTATAGGCTTCTTCTCTGGAATCTTCTTCATCATCCTCCTGACAATCGATAGGTACCTGGCTGTCGTCCATGCTGTGTTTGCTTTAAAA --read1_overlap_start 22 --read1_overlap_end 238 --mode R1
Fuser script: CCR5 fragment B read 2: python Paired_read_fuser.py --path directory_fragB_R2/ --read1 CCR5_R2.fastq.bz2 --read2 CCR5_R2.fastq.bz2 --wtseq ATCTGCTACTCGGGAATCCTAAAAACTCTGCTTCGGTGTCGAAATGAGAAGAAGAGGCACAGGGCTGTGAGGCTTATCTTCACCATCATGATTGTTTATTTTCTCTTCTGGGCTCCCTACAACATTGTCCTTCTCCTGAACACCTTCCAGGAATTCTTTGGCCTGAATAATTGCAGTAGCTCTAACAGGTTGGACCAAGCTATGCAGGTGACAGAGACTCTTGGG --read2_overlap_start 6 --read2_overlap_end 231 --mode R2
Fuser script: CCR5 fragment C read 1: python Paired_read_fuser.py --path directory_fragC_R1/ --read1 CCR5_R1.fastq.bz2 --read2 CCR5_R1.fastq.bz2 --wtseq TTAAAAGCCAGGACGGTCACCTTTGGGGTGGTGACAAGTGTGATCACTTGGGTGGTGGCTGTGTTTGCGTCTCTCCCAGGAATCATCTTTACCAGATCTCAAAAAGAAGGTCTTCATTACACCTGCAGCTCTCATTTTCCATACAGTCAGTATCAATTCTGGAAGAATTTCCAGACATTAAAGATAGTCATCTTGGGGCTGGTCCTGCCGCTGCTTGTA --read1_overlap_start 19 --read1_overlap_end 238 --mode R1
Fuser script: CCR5 fragment C read 2: python Paired_read_fuser.py --path directory_fragC_R2/ --read1 CCR5_R2.fastq.bz2 --read2 CCR5_R2.fastq.bz2 --wtseq ATGACGCACTGCTGCATCAACCCCATCATCTATGCCTTTGTCGGGGAGAAGTTCAGAAACTACCTCTTAGTCTTCTTCCAAAAGCACATTGCCAAACGCTTCTGCAAATGCTGTTCTATTTTCCAGCAAGAGGCTCCCGAGCGAGCAAGCTCAGTTTACACCCGATCCACTGGGGAGCAGGAAATATCTGTGGGCTTGTGA --read2_overlap_start 12 --read2_overlap_end 213 --mode R2
Fuser script: CXCR4 fragment A read 1: python Paired_read_fuser.py --path directory_fragA_R1/ --read1 CXCR4_R1.fastq.bz2 --read2 CXCR4_R1.fastq.bz2 --wtseq GAGGGGATCAGTATATACACTTCAGATAACTACACCGAGGAAATGGGCTCAGGGGACTATGACTCCATGAAGGAACCCTGTTTCCGTGAAGAAAATGCTAATTTCAATAAAATCTTCCTGCCCACCATCTACTCCATCATCTTCTTAACTGGCATTGTGGGCAATGGATTGGTCATCCTGGTCATGGGT --read1_overlap_start 51 --read1_overlap_end 240 --mode R1
Fuser script: CXCR4 fragment A read 2: python Paired_read_fuser.py --path directory_fragA_R2/ --read1 CXCR4_R2.fastq.bz2 --read2 CXCR4_R2.fastq.bz2 --wtseq AAGGTGGTCTATGTTGGCGTCTGGATCCCTGCCCTCCTGCTGACTATTCCCGACTTCATCTTTGCCAACGTCAGTGAGGCAGATGACAGATATATCTGTGACCGCTTCTACCCCAATGACTTGTGGGTGGTTGTGTTCCAGTTTCAGCACATCATGGTTGGCCTTATCCTGCCTGGTATTGTCATCCTGTCCTGCTATTGCATT --read2_overlap_start 24 --read2_overlap_end 228 --mode R2
Fuser script: CXCR4 fragment B read 1: python Paired_read_fuser.py --path directory_fragB_R1/ --read1 CXCR4_R1.fastq.bz2 --read2 CXCR4_R1.fastq.bz2 --wtseq GGTTACCAGAAGAAACTGAGAAGCATGACGGACAAGTACAGGCTGCACCTGTCAGTGGCCGACCTCCTCTTTGTCATCACGCTTCCCTTCTGGGCAGTTGATGCCGTGGCAAACTGGTACTTTGGGAACTTCCTATGCAAGGCAGTCCATGTCATCTACACAGTCAACCTCTACAGCAGTGTCCTCATCCTGGCCTTCATCAGTCTGGACCGCTAC --read1_overlap_start 20 --read1_overlap_end 236 --mode R1
Fuser script: CXCR4 fragment B read 2: python Paired_read_fuser.py --path directory_fragB_R2/ --read1 CXCR4_R2.fastq.bz2 --read2 CXCR4_R2.fastq.bz2 --wtseq ATTATCATCTCCAAGCTGTCACACTCCAAGGGCCACCAGAAGCGCAAGGCCCTCAAGACCACAGTCATCCTCATCCTGGCTTTCTTCGCCTGTTGGCTGCCTTACTACATTGGGATCAGCATCGACTCCTTCATCCTCCTGGAAATCATCAAGCAAGGGTGTGAGTTTGAGAACACTGTGCACAAGTGGATTTCCATCACCGAG --read2_overlap_start 25 --read2_overlap_end 229 --mode R2
Fuser script: CXCR4 fragment C read 1: python Paired_read_fuser.py --path directory_fragC_R1/ --read1 CXCR4_R1.fastq.bz2 --read2CXCR4_R1.fastq.bz2 --wtseq GACCGCTACCTGGCCATCGTCCACGCCACCAACAGTCAGAGGCCAAGGAAGCTGTTGGCTGAAAAGGTGGTCTATGTTGGCGTCTGGATCCCTGCCCTCCTGCTGACTATTCCCGACTTCATCTTTGCCAACGTCAGTGAGGCAGATGACAGATATATCTGTGACCGCTTCTACCCCAATGACTTGTGGGTGGTTGTGTTCCAGTTTCAGCACATC --read1_overlap_start 21 --read1_overlap_end 237 --mode R1
Fuser script: CXCR4 fragment C read 2: python Paired_read_fuser.py --path directory_fragC_R2/ --read1 CXCR4_R2.fastq.bz2 --read2 CXCR4_R2.fastq.bz2 --wtseq ACCGAGGCCCTAGCTTTCTTCCACTGTTGTCTGAACCCCATCCTCTATGCTTTCCTTGGAGCCAAATTTAAAACCTCTGCCCAGCACGCACTCACCTCTGTGAGCAGAGGGTCCAGCCTCAAGATCCTCTCCAAAGGAAAGCGAGGTGGACATTCATCTGTTTCCACTGAGTCTGAGTCTTCAAGTTTTCACTCCAGC --read2_overlap_start 12 --read2_overlap_end 210 --mode R2
Aligner script: CCR5 fragment A read 1: python Fused_read_aligner.py --path directory_fragA_R1/ --infile CCR5_R1.fast_R1_qc1 --referenceDNA GCCGATTATCAAGTGTCAAGTCCAATCTATGACATCAATTATTATACATCGGAGCCCTGCCAAAAAATCAATGTGAAGCAAATCGCAGCCCGCCTCCTGCCTCCGCTCTACTCACTGGTGTTCATCTTTGGTTTTGTGGGCAACATGCTGGTCATCCTCATCCTGATAAACTGCAAAAGGCTGAAGAGCATGACTGAC --referenceAA ADYQVSSPIYDINYYTSEPCQKINVKQIAARLLPPLYSLVFIFGFVGNMLVILILINCKRLKSMTD --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: CCR5 fragment A read 2: python Fused_read_aligner.py --path directory_fragA_R2/ --infile CCR5_R2.fast_R2_qc1 --referenceDNA GTCACCTTTGGGGTGGTGACAAGTGTGATCACTTGGGTGGTGGCTGTGTTTGCGTCTCTCCCAGGAATCATCTTTACCAGATCTCAAAAAGAAGGTCTTCATTACACCTGCAGCTCTCATTTTCCATACAGTCAGTATCAATTCTGGAAGAATTTCCAGACATTAAAGATAGTCATCTTGGGGCTGGTCCTGCCGCTGCTTGTAATGGTC --referenceAA VTFGVVTSVITWVVAVFASLPGIIFTRSQKEGLHYTCSSHFPYSQYQFWKNFQTLKIVILGLVLPLLVMV --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: CCR5 fragment B read 1: python Fused_read_aligner.py --path directroy_fragB_R1/ --infile CCR5_R1.fast_R1_qc1 --referenceDNA ATCTACCTGCTCAACCTGGCCATCTCTGACCTGTTTTTCCTTCTTACTGTCCCCTTCTGGGCTCACTATGCTGCCGCCCAGTGGGACTTTGGAAATACAATGTGTCAACTCTTGACAGGGCTCTATTTTATAGGCTTCTTCTCTGGAATCTTCTTCATCATCCTCCTGACAATCGATAGGTACCTGGCTGTCGTCCATGCTGTGTTTGCTTTAAAA --referenceAA IYLLNLAISDLFFLLTVPFWAHYAAAQWDFGNTMCQLLTGLYFIGFFSGIFFIILLTIDRYLAVVHAVFALK --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: CCR5 fragment B read 2: python Fused_read_aligner.py --path directroy_fragB_R2/ --infile CCR5_R2.fast_R2_qc1 --referenceDNA ATCTGCTACTCGGGAATCCTAAAAACTCTGCTTCGGTGTCGAAATGAGAAGAAGAGGCACAGGGCTGTGAGGCTTATCTTCACCATCATGATTGTTTATTTTCTCTTCTGGGCTCCCTACAACATTGTCCTTCTCCTGAACACCTTCCAGGAATTCTTTGGCCTGAATAATTGCAGTAGCTCTAACAGGTTGGACCAAGCTATGCAGGTGACAGAGACTCTTGGG --referenceAA ICYSGILKTLLRCRNEKKRHRAVRLIFTIMIVYFLFWAPYNIVLLLNTFQEFFGLNNCSSSNRLDQAMQVTETLG --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: CCR5 fragment C read 1: python Fused_read_aligner.py --path directroy_fragC_R1/ --infile CCR5_R1.fast_R1_qc1 --referenceDNA TTAAAAGCCAGGACGGTCACCTTTGGGGTGGTGACAAGTGTGATCACTTGGGTGGTGGCTGTGTTTGCGTCTCTCCCAGGAATCATCTTTACCAGATCTCAAAAAGAAGGTCTTCATTACACCTGCAGCTCTCATTTTCCATACAGTCAGTATCAATTCTGGAAGAATTTCCAGACATTAAAGATAGTCATCTTGGGGCTGGTCCTGCCGCTGCTTGTA --referenceAA LKARTVTFGVVTSVITWVVAVFASLPGIIFTRSQKEGLHYTCSSHFPYSQYQFWKNFQTLKIVILGLVLPLLV --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: CCR5 fragment C read 2: python Fused_read_aligner.py --path directroy_fragC_R2/ --infile CCR5_R2.fast_R2_qc1 --referenceDNA ATGACGCACTGCTGCATCAACCCCATCATCTATGCCTTTGTCGGGGAGAAGTTCAGAAACTACCTCTTAGTCTTCTTCCAAAAGCACATTGCCAAACGCTTCTGCAAATGCTGTTCTATTTTCCAGCAAGAGGCTCCCGAGCGAGCAAGCTCAGTTTACACCCGATCCACTGGGGAGCAGGAAATATCTGTGGGCTTGTGA --referenceAA MTHCCINPIIYAFVGEKFRNYLLVFFQKHIAKRFCKCCSIFQQEAPERASSVYTRSTGEQEISVGL* --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: CXCR4 fragment A read 1: python Fused_read_aligner.py --path directroy_fragA_R1/ --infile CXCR4_R1.fast_R1_qc1 --referenceDNA GAGGGGATCAGTATATACACTTCAGATAACTACACCGAGGAAATGGGCTCAGGGGACTATGACTCCATGAAGGAACCCTGTTTCCGTGAAGAAAATGCTAATTTCAATAAAATCTTCCTGCCCACCATCTACTCCATCATCTTCTTAACTGGCATTGTGGGCAATGGATTGGTCATCCTGGTCATGGGT --referenceAA EGISIYTSDNYTEEMGSGDYDSMKEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVILVMG --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: CXCR4 fragment A read 2: python Fused_read_aligner.py --path directroy_fragA_R2/ --infile CXCR4_R2.fast_R2_qc1 --referenceDNA AAGGTGGTCTATGTTGGCGTCTGGATCCCTGCCCTCCTGCTGACTATTCCCGACTTCATCTTTGCCAACGTCAGTGAGGCAGATGACAGATATATCTGTGACCGCTTCTACCCCAATGACTTGTGGGTGGTTGTGTTCCAGTTTCAGCACATCATGGTTGGCCTTATCCTGCCTGGTATTGTCATCCTGTCCTGCTATTGCATT --referenceAA KVVYVGVWIPALLLTIPDFIFANVSEADDRYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCI --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: CXCR4 fragment B read 1: python Fused_read_aligner.py --path directroy_fragB_R1/ --infile CXCR4_R1.fast_R1_qc1 --referenceDNA GGTTACCAGAAGAAACTGAGAAGCATGACGGACAAGTACAGGCTGCACCTGTCAGTGGCCGACCTCCTCTTTGTCATCACGCTTCCCTTCTGGGCAGTTGATGCCGTGGCAAACTGGTACTTTGGGAACTTCCTATGCAAGGCAGTCCATGTCATCTACACAGTCAACCTCTACAGCAGTGTCCTCATCCTGGCCTTCATCAGTCTGGACCGCTAC --referenceAA GYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVNLYSSVLILAFISLDRY --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: CXCR4 fragment B read 2: python Fused_read_aligner.py --path directroy_fragB_R2/ --infile CXCR4_R2.fast_R2_qc1 --referenceDNA ATTATCATCTCCAAGCTGTCACACTCCAAGGGCCACCAGAAGCGCAAGGCCCTCAAGACCACAGTCATCCTCATCCTGGCTTTCTTCGCCTGTTGGCTGCCTTACTACATTGGGATCAGCATCGACTCCTTCATCCTCCTGGAAATCATCAAGCAAGGGTGTGAGTTTGAGAACACTGTGCACAAGTGGATTTCCATCACCGAG --referenceAA IIISKLSHSKGHQKRKALKTTVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHKWISITE --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
Aligner script: CXCR4 fragment C read 1: python Fused_read_aligner.py --path directroy_fragC_R1/ --infile CXCR4_R1.fast_R1_qc1 --referenceDNA GACCGCTACCTGGCCATCGTCCACGCCACCAACAGTCAGAGGCCAAGGAAGCTGTTGGCTGAAAAGGTGGTCTATGTTGGCGTCTGGATCCCTGCCCTCCTGCTGACTATTCCCGACTTCATCTTTGCCAACGTCAGTGAGGCAGATGACAGATATATCTGTGACCGCTTCTACCCCAATGACTTGTGGGTGGTTGTGTTCCAGTTTCAGCACATC --referenceAA DRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEADDRYICDRFYPNDLWVVVFQFQHI --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R1
Aligner script: CXCR4 fragment C read 2: python Fused_read_aligner.py --path directroy_fragC_R2/ --infile CXCR4_R2.fast_R2_qc1 --referenceDNA ACCGAGGCCCTAGCTTTCTTCCACTGTTGTCTGAACCCCATCCTCTATGCTTTCCTTGGAGCCAAATTTAAAACCTCTGCCCAGCACGCACTCACCTCTGTGAGCAGAGGGTCCAGCCTCAAGATCCTCTCCAAAGGAAAGCGAGGTGGACATTCATCTGTTTCCACTGAGTCTGAGTCTTCAAGTTTTCACTCCAGC --referenceAA TEALAFFHCCLNPILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 25 --chaste 1 --Ncount_max 3 --use_N 0 --mode R2
MapCounts script: Example: python mapCounts.py --path directory_fragA_R1/ --infile CCR5_R1.fast_R1_qc1_PRO_qc2
MapRatios script: Example: python mapRatios.py --path ratios_directory/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts script: Example: python mapParts.py --path ratios_directory/ --infile mapratios_sorted_library --mode mutations:1
Unlink script: Example: python mapUnlink.py --path ratios/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size ##
In Excel, the log(base2) enrichment ratio of the wildtype sequence was subtracted from the log(2) enrichment ratios for all single mutations.
Data was then assembled from the different fragments/reads to span the full sequence in Excel.  Where there was overlap, real enrichment ratios were averaged and converted back to log(base2). Maximum depletion was set to log(base2) enrichment ratio = -5.
Genome_build: Not applicable
Supplementary_files_format_and_content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution.  Also includes the number of reads for each mutation in the naïve plasmid library.

source_name: CXCR4 12G5 affinity sort

growth_protocol: Expi293F cells cultured in Expi293 Expression Medium (Life Technologies)

extract_protocol:
Total RNA was harvested from sorted cells using GeneJet RNA Purification Kit (Thermo Scientific) and cDNA prepared using Accuscript Hi-Fi (Agilent Genomics) primed with a gene-specific primer (EBV_reverse).
In the first round of PCR (18 cycles), the CCR5 and CXCR4 coding sequences were amplified as three overlapping fragments of ~800 bp each.
Primer pair: CCR5 fragment A: MiSeq_CCR5_myctag_F (TCTTTCCCTACACGACGCTCTTCCGATCTCGAGCAAAAGCTGATCTCAG) and MiSeq_CCR5_652_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTAGGATTCCCGAGTAGCAG)
Primer pair: CCR5 fragment B: MiSeq_CCR5_176_F (TCTTTCCCTACACGACGCTCTTCCGATCTAAGGCTGAAGAGCATGACTG) and MiSeq_CCR5_875_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTGATGCAGCAGTGCGTCAT)
Primer pair: CCR5 fragment C: MiSeq_CCR5_388_F (TCTTTCCCTACACGACGCTCTTCCGATCTCGTCCATGCTGTGTTTGCT) and MiSeq_pCEP4_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTATCATGTCTGGATCCGG)
Primer pair: CXCR4 fragment A: MiSeq_CXCR4_myctag_F (TCTTTCCCTACACGACGCTCTTCCGATCTGCCGAGCAGAAATTGATCAG) and MiSeq_CXCR4_682_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGTGTGACAGCTTGGAGATG)
Primer pair: CXCR4 fragment B: MiSeq_CXCR4_169_F (TCTTTCCCTACACGACGCTCTTCCGATCTGATTGGTCATCCTGGTCATG) and MiSeq_CXCR4_882_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACAGTGGAAGAAAGCTAGGG)
Primer pair: CXCR4 fragment C: MiSeq_CXCR4_375_F (TCTTTCCCTACACGACGCTCTTCCGATCTATCCTGGCCTTCATCAGTCT) and MiSeq_pCEP4_R (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTATCATGTCTGGATCCGG)
In a second round of PCR (15 cycles), Illumina adaptors and experiment-specific barcodes were added.
Primer pair for adding I5 and I7 Illumina adaptors: MiSeq_Start_Adaptamer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and MiSeq_Index_Adaptamer (CAAGCAGAAGACGGCATACGAGAT-6nt-barcode-GTGACTGGAGTTCAGACGTGTGCTCTTC)
Amplicons were deep sequenced with MiSeq v3 and HiSeq 2500 instruments using a 2x250 nt paired end protocol, though data is analyzed as single reads.

treatment_protocol: Cells expressing DNA libraries of CXCR4 or CCR5 mutants (cloned into pCEP4, Invitrogen) were FACS sorted for receptor surface expression and binding to different protein ligands.

value: Expi293F cells (a HEK293 derivative)

tag: protein

tag: sort gate 1

value: Top 50% expression (anti-myc FITC staining); square gate in FCS-vs-FITC plot

tag: sort gate 2

value: Top 10% for binding signal (0.15 ug/ml 12G5-APC); sloped gate in FITC-vs-APC plot

tag: # collected cells


title: CXCR4 12G5 affinity sort replicate 2

description:
Deep mutational scan of CXCR4 for surface expression and affinity for antibody 12G5 in Expi293F cells
enrichment_ratios_CXCR4.xlsx
CXCR4_12G5_Affinity2
Synthetic coding sequences


title: CXCR4 Surface Expression Sort (anti-myc-FITC) Replicate 2

description:
Deep mutational scan of CXCR4 for surface expression in Expi293F cells
enrichment_ratios_CXCR4.xlsx
CXCR4_antimycFITC_Expression2
Synthetic coding sequences


title: CXCR4 SSM Library

description:
plasmid DNA
CXCR4 SSM library
enrichment_ratios_CXCR4.xlsx
CXCR4_library
Synthetic coding sequences

molecule: other

source_name: CXCR4 SSM Library


title: Fig3CS3A_WT_Smc3HA_IP

tag: sac_cer strain

value: Strain K26797 (containing 3XminiAID-tagged smc3 in the endogenous locus and Smc3 wild type expressed from an ectopic locus)


title: e14.5_control

tag: tissue

value: heart


title: CXCR4 CXCL12 affinity sort replicate 1

description:
Deep mutational scan of CXCR4 for surface expression and affinity for CXCL12 in Expi293F cells
enrichment_ratios_CXCR4.xlsx
CXCR4_CXCL12_Affinity1
Synthetic coding sequences

source_name: CXCR4 CXCL12 affinity sort

value: Top 50% expression (anti-myc Alexa647 staining); square gate in FCS-vs-FITC plot

value: Top 10% for binding signal (5 uM CXCL12-sfGFP); sloped gate in FITC-vs-APC plot


title: CXCR4 CXCL12 affinity sort replicate 2

description:
Deep mutational scan of CXCR4 for surface expression and affinity for CXCL12 in Expi293F cells
enrichment_ratios_CXCR4.xlsx
CXCR4_CXCL12_Affinity2
Synthetic coding sequences


title: CCR5 gp120-CD4 affinity sort replicate 1

description:
Deep mutational scan of CCR5 for surface expression and binding to HIV-1(BaL) gp120-CD4 in Expi293F cells
enrichment_ratios_CCR5.xlsx
CCR5_gp120CD4_Affinity1
Synthetic coding sequences

source_name: CCR5 gp120-CD4 affinity sort

value: Top 40% expression (anti-myc Alexa647 staining); square gate in FCS-vs-FITC plot

value: Top 10% for binding signal (gp120-CD4 conditioned medium); sloped gate in FITC-vs-APC plot


title: Fig6BS3C_Smc3_Scc1FusionPK_IP

description: exponentially growing Smc3-Scc1 fusion strain (K24838).

tag: can_gla strain

tag: antibody

value: anti-PK antibody (Bio-Rad)

value: Smc3-Scc1 fusion strain (K24838)

value: exponentially growing


title: CXCR4 Surface Expression Sort (anti-myc-Alexa647) Replicate 1

description:
Deep mutational scan of CXCR4 for surface expression in Expi293F cells
enrichment_ratios_CXCR4.xlsx
CXCR4_antimycAlexa647_Expression1
Synthetic coding sequences


title: CCR5 gp120-CD4 affinity sort replicate 2

description:
Deep mutational scan of CCR5 for surface expression and binding to HIV-1(BaL) gp120-CD4 in Expi293F cells
enrichment_ratios_CCR5.xlsx
CCR5_gp120CD4_Affinity2
Synthetic coding sequences


title: CCR5 Surface Expression Sort (anti-myc-Alexa647) Replicate 2

description:
Deep mutational scan of CCR5 for surface expression in Expi293F cells
enrichment_ratios_CCR5.xlsx
CCR5_antimycAlexa647_Expression2
Synthetic coding sequences


title: CXCR4 Surface Expression Sort (anti-myc-Alexa647) Replicate 2

description:
Deep mutational scan of CXCR4 for surface expression in Expi293F cells
enrichment_ratios_CXCR4.xlsx
CXCR4_antimycAlexa647_Expression2
Synthetic coding sequences


title: Fig6BS3C_Scc1PK_WCE

description: exponentially growing wild type strain (K23889)

value: wild type strain (K23889)

tag: growth


title: CCR5 Surface Expression Sort (anti-myc-Alexa647) Replicate 1

description:
Deep mutational scan of CCR5 for surface expression in Expi293F cells
enrichment_ratios_CCR5.xlsx
CCR5_antimycAlexa647_Expression1
Synthetic coding sequences


title: CCR5 Revised Library

description:
plasmid DNA
Revised CCR5 SSM library with missing mutants spiked in; used for anti-myc-Alexa647 expression sorts and gp120-CD4 affinity sorts
enrichment_ratios_CCR5.xlsx
CCR5_RevisedLibrary
Synthetic coding sequences

source_name: CCR5 Revised Library


title: CCR5 2D7 affinity sort replicate 2

description:
Deep mutational scan of CCR5 for surface expression and binding to antibody 2D7 in Expi293F cells
enrichment_ratios_CCR5.xlsx
CCR5_2D7_Affinity2
Synthetic coding sequences

source_name: CCR5 2D7 affinity sort

value: Top 10% for binding signal (1.5 ug/ml 2D7-APC); sloped gate in FITC-vs-APC plot


title: CXCR4 Surface Expression Sort (anti-myc-FITC) Replicate 1

description:
Deep mutational scan of CXCR4 for surface expression in Expi293F cells
enrichment_ratios_CXCR4.xlsx
CXCR4_antimycFITC_Expression1
Synthetic coding sequences


title: Fig6BS3C_Scc1PK_IP


title: CCR5 Surface Expression Sort (anti-myc-FITC) Replicate 2

description:
Deep mutational scan of CCR5 for surface expression in Expi293F cells
enrichment_ratios_CCR5.xlsx
CCR5_antimycFITC_Expression2
Synthetic coding sequences


title: CCR5 2D7 affinity sort replicate 1

description:
Deep mutational scan of CCR5 for surface expression and binding to antibody 2D7 in Expi293F cells
enrichment_ratios_CCR5.xlsx
CCR5_2D7_Affinity1
Synthetic coding sequences


title: CCR5 Surface Expression Sort (anti-myc-FITC) Replicate 1

description:
Deep mutational scan of CCR5 for surface expression in Expi293F cells
enrichment_ratios_CCR5.xlsx
CCR5_antimycFITC_Expression1
Synthetic coding sequences


title: mRNA-seq_Col/C24_Rep2

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

description: polyA RNA isolated

data_processing:
RNA-sequencing reads for Col and C24 were mapped to TAIR10 genome and  C24 genome using Tophat software respectively. For hybrid RNA sequencing data analysis, we aligned the reads to both of the TAIR10 genome and C24 genome. Reads were assigned to an allele based upon the highest quality alignment and were further used to calculated allelic expression divergence.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for mRNA seq samples

source_name: seedling shoot

growth_protocol: Wild-type hybrid was generated by crossing Arabidopsis thaliana ecotype Col and C24.   The shoots of 14-day-old seedlings were used for RNA-seq. All seedlings were grown under short-day condition (8 hours light at 22℃ and 16 hours dark at 18℃).

extract_protocol: Total RNA was extracted from shoots of 14-day-old Arabidopsis seedling using the Rneasy plant mini kit (Qiagen). mRNAs were extracted from the total RNAs by Dynabeads oligo(dT) (Invitrogen Dynal). First- and second-strand cDNAs were obtained using random hexamer primers and SuperScript II reverse transcriptase (Invitrogen). RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: age

value: 14 day old

tag: ecotype


title: mRNA-seq_C24_Rep2

description: polyA RNA isolated


title: mRNA-seq_C24/Col_Rep1

description: polyA RNA isolated


title: mRNA-seq_C24/Col_Rep3

description: polyA RNA isolated


title: mRNA-seq_Col/C24_Rep3

description: polyA RNA isolated


title: mRNA-seq_C24_Rep3

description: polyA RNA isolated


title: mRNA-seq_C24/Col_Rep2

description: polyA RNA isolated


title: mRNA-seq_Col/C24_Rep1

description: polyA RNA isolated


title: Fig6BS3C_Smc3_Scc1FusionPK_WCE


title: mRNA-seq_C24_Rep1

description: polyA RNA isolated


title: mRNA-seq_Col_Rep2

description: polyA RNA isolated

value: Col


title: mRNA-seq_Col_Rep3

description: polyA RNA isolated


title: WT_control_2

status: Public on Apr 22 2018

city: Darlinghurst

first: Saskia

last: Reibe

state: NSW

address: 384 Victoria Street

department: Diabetes & Metabolism

country: Australia

institute: Garvan Institute of Medical Research

description: rep 2

data_processing:
The sequenced sample libraries were trimmed with Trim Galore (v.0.2.8),
mapped to the mouse genome and transcriptome with STAR (v.2.4.0d)
counted with RSEM (v.1.2.12)
The counts reported with RSEM were normalized with R package DESeq2
Genome_build: Gencode mouse, v.M5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample (countdata.txt)

source_name: BMDM

extract_protocol:
Qiagen RNeasy extraction kit
TruSeq Stranded mRNA Sample Preparation Kit (Illumina)

treatment_protocol: see treatment

value: WT

tag: treatment

value: 5% FBS and 2% BSA


title: WT_untreated_1

description: rep 1

tag: strain

value: untreated


title: WT_untreated_2

description: rep 2


title: KO_untreated_1

description: rep 1


title: mRNA-seq_Col_Rep1

description: polyA RNA isolated


title: WT_control_1

description: rep 1


title: KO_PolyIC_1

description: rep 1

value: pre-treated Poly(I:C)


title: KO_PolyIC_2

description: rep 2


title: KO_untreated_2

description: rep 2


title: KO_control_1

description: rep 1


title: healthy donor CTRL2

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Gene and transcript intensities were computed using STAR/RSEM software using Gencode Release 19 (GRCh37.p13) as a reference, using the “stranded” option. Differential expression analysis for mRNA was performed using R package EBSeq2.
Genome_build: HG19
Supplementary_files_format_and_content: RSEM output: transcript_id, gene_id, length, effective_length, expected_count, TPM, FPKM, IsoPct

source_name: blood

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were prepared by centrifugation. Peripheral blood was layered (density=1.077) and centrifuged at 950g for 30 min. After isolation on a Ficoll-Histopaque layer (Sigma, Italy), cell viability was assayed by a trypan blue exclusion test and the cells were used for RNA extraction.  Samples were homogenized and total RNA was isolated by Trizol® reagent (Life Science Technologies, Italy) following the manufacturer’s specifications. RNAs were quantified using a Nanodrop ND-100 Spectrophotometer (Nanodrop Technologies, Wilmington, USA) and a 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit, Waldbronn, Germany); RNAs with a 260:280 ratio of ≥1.5 and an RNA integrity number of ≥8 were subjected to deep sequencing.
Sequencing libraries were prepared by the Illumina TruSeq Stranded RNA Library Prep, version 2, Protocol D, using 500-ng total RNA (Illumina). The qualities of the libraries were assessed by 2100 Bioanalyzer with a DNA1000 assay. Libraries were quantified by qPCR using the KAPA Library Quantification kit for Illumina sequencing platforms (KAPA Biosystems); RNA processing has been carried out using Illumina NextSeq 500 Sequencing.

value: blood

tag: diagnosis

value: healthy donor


title: healthy donor CTRL3


title: healthy donor CTRL1


title: SLA TARDBP mutated patient TARDBP-m2

value: SLA TARDBP mutated patient


title: SLA SOD1 mutated patient SOD1-m2

value: SLA SOD1 mutated patient


title: CCR5 Original Library

description:
plasmid DNA
Original CCR5 SSM library; used for anti-myc-FITC expression sorts and 2D7 affinity sorts
enrichment_ratios_CCR5.xlsx
CCR5_OriginalLibrary
Synthetic coding sequences

source_name: CCR5 Original Library

tag: cell type

value: Expi293F cells (a HEK293 derivative)


title: SLA sporadic patient ALS-s9

value: SLA sporadic patient


title: SLA TARDBP mutated patient TARDBP-m1


title: SLA FUS mutated patient FUS-m1

value: SLA FUS mutated patient


title: SLA sporadic patient ALS-s7


title: SLA sporadic patient ALS-s10


title: SLA FUS mutated patient FUS-m2


title: SLA sporadic patient ALS-s8


title: SLA sporadic patient ALS-s11


title: SLA SOD1 mutated patient SOD1-m1


title: SLA sporadic patient ALS-s6


title: SLA sporadic patient ALS-s4


title: SLA sporadic patient ALS-s5


title: SLA sporadic patient ALS-s2


title: SLA sporadic patient ALS-s3


title: KO_control_2

description: rep 2

tag: genotype


title: H9-WT-4_smallRNA-seq

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

institute: BMC

description: RNA < 200nt

data_processing:
cutadapt -a TGGAATTCTCGGGTGCCAAGG -o <infile_trim1.fastq.gz> --minimum-length 23 <infile>
cutadapt -u 4 -u -4 -o <infile_trim2.fastq.gz> <infile_trim1.fastq.gz>
bowtie -m 500 -v2 --best --strata -p 10 –sam hg38_tRNA  <infile_trim2.fastq> > <outfile_bowtie.sam>
samtools view -Sb <outfile_bowtie.sam> | samtools sort -@ 9 -o <outfile_bowte.sorted.bam>  -
samtools idxstats <outfile_bowte.sorted.bam>
MINTmap.pl -f <infile_trim2.fastq>  -p  <prefixPath>
MINTmerge.pl -files <all expression.txt MINTmap files>  -outfile 'MINT_tRNA_summary.xls'
Genome_build: hg38
Supplementary_files_format_and_content: MINT norm to total tRNA reads: *sorted.bam.txt
Supplementary_files_format_and_content: hg38_tRNA bowtie number of mapped reads: *reads.txt

source_name: ES cell line

growth_protocol: hESCs (H9 line) were plated on Matrigel (Corning) and cultured in mTeSR (Stem Cell Technology) according to manufacturer instructions. One well of a 6-well plate was used per replicate.

extract_protocol:
RNA was extracted using Trizol reagent (Thermo Scientific). Total RNA was extracted and treated with Turbo Dnase (Thermo Scientific). Small RNAs (< 200nt) were isolated using RNA clean and concentrator -25 (Zymo Research). rRNAs were removed using Ribo-Zero Gold rRNA removal kit (Illumina).
Libraries were constructed starting from 100ng of small RNA fraction, rRNA-depleted. Libraries were built using NEXTflex Small RNA-Seq Kit v3 (Bioo Scientific) following manufacturer instructions. In order to capture all small RNAs no size selection step was performed. Libraries were sequenced on NextSeq platform (Illumina), 75 cycles, single end.

tag: cell line

value: ES cell line

tag: genotype/variation

tag: passage


title: SLA sporadic patient ALS-s1


title: H9-PUS7KO-1_smallRNA-seq

description: RNA < 200nt

value: PUS7 KO


title: H9-PUS7KO-2_smallRNA-seq

description: RNA < 200nt


title: H9-WT-2_smallRNA-seq

description: RNA < 200nt


title: H9-WT-1_smallRNA-seq

description: RNA < 200nt


title: H9-WT-3_smallRNA-seq

description: RNA < 200nt


title: H9-PUS7KO-3_smallRNA-seq

description: RNA < 200nt


title: CRPC RP62_plus

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

institute: Korea Research Institutue of Bioscience & Biotechnology

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data from Homo sapiens were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).
Tophat2 was applied to tissue samples for mapping reads to reference genome. The fragments
per
kilobase
 of
transcript
 per
million
 fragments
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text format with FPKM values of transcripts

source_name: CRPC

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.

tag: biopsy site

value: prostate

tag: progression step

value: CRPC

tag: normal/tumor

value: tumor


title: CRPC RP680


title: advanced CaP RP621

source_name: advanced CaP

value: advanced CaP


title: CRPC RP627


title: advanced CaP RP588


title: CRPC RP542_plus


title: advanced CaP RP553


title: advanced CaP RP62


title: advanced CaP RP542


title: BdC3

city: Grand Rapids

first: Jeremy

last: Van Raamsdonk

state: Michigan

address: 333 Bostwick Ave

department: Center For Neurodegenerative Science

institute: Van Andel Research Institute

data_processing:
All 6 libraries (3 treatment and 3 controls) were combined into a single pool. This pool was loaded on one lane of an Illumina HiSeq 2500 Rapid Run flow cell (v2). Sequencing was performed in a PE100 format with HiSeq Rapid SBS reagents. Base calling was done by Illumina Real Time Analysis (RTA) v1.18.64 and output of RTA was de-multiplexed and converted to Fastq format with Illumina Bcl2fastq v1.8.4.
Read quality was assessed using FASTQC v. 0.11.3
Reads were aligned to the B. distachyon v2.1 genome using Subread v. 1.4.3.
Raw read counts to known exons were obtained using FeatureCounts v 1.4.3 using strand specific read counting. Counts per million (CPM) were calculated and log2 transformed using voom.
Transformation and differential expression analyses were conducted using the limma package v 3.28.7 in R
Genome_build: Brachypodium distachyon v2.1
Supplementary_files_format_and_content: MUA_20150814_RNA_Counts.txt

organism: Brachypodium distachyon

source_name: Untreated Root

growth_protocol: Brachypodium seeds from reference line Bd21 were surface-sterilized in 2% (v/v) sodium hypochlorite solution for 15 minutes, rinsed five times with distilled water and then allowed to imbibe in the distilled water for 24 hours. Following the 24-hour period, the seeds were transferred under sterile conditions to 9-cm petri plates (#633185, Greiner bio-one, North Carolina, USA) lined with germination paper (Anchor Paper, Minnesota, USA). Plates were sealed with parafilm (L-2020-1, BioExpress, Utah, USA), wrapped completely in aluminum foil, and then allowed to germinate at room temperature (25°C) for approximately 72–96 hours. Germinated seedlings were transferred to 15-cm petri plates (#639102, Greiner bio-one, North Carolina, USA) containing low-N2 Fahraeus medium and allowed to grow for 7 days in a Percival growth chamber (#CU-22L, Iowa, USA) with a 16-h, 22°C day and 8-h, 24°C night cycle and 150 to 200 μmol m–2s–1 light intensity, and relative humidity of 65% prior to hormone treatment.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy® Plant Mini Kit (Cat #74904, California, USA) per manufacturer’s protocol. RNA was extracted from both control and NLS containing plant roots 7 days post treatment with auxin.
Sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit LT.

treatment_protocol: For hormone treatments of Brachypodium seedlings, we used the synthetic auxin, 2,4-Dichlorophenoxyacetic acid (2,4-D) (CAS# 94-75-7, Caisson Laboratories Inc., Utah, USA). Seven-day-old whole plants were soaked in 50μM of 2,4-D solution for one hour under sterile conditions. Ten ml of 2,4-D solution was used per plant for treatment solution. Following this treatment, the plants were transferred to 15-cm petri plates (#639102, Greiner bio-one, North Carolina, USA) containing low-N2 Fahraeus medium. All plants were grown in a Percival growth chamber (Model #: CU-22L, Iowa, USA) with a 16-h, 22°C day and 8-h, 24°C night cycle and 150 to 200 μmol m–2s–1 light intensity at 65% relative humidity. Plants were phenotypically scored for NLS formation after seven and fourteen days post treatment using a Leica MZ6 stereomicroscope (Leica Microsystems Inc., Illinois, USA).

value: Untreated


title: CRPC RP516_plus


title: H9-PUS7KO-4_smallRNA-seq

description: RNA < 200nt


title: BdT1

source_name: Nodule-Like Structures


title: CRPC RP537


title: BdT2


title: BdC2


title: BdC1


title: iClip.H9.PUS7KO.1

data_processing:
fastq_trim_and_split.pl -fastq <input summary fasta.gz> -outpath <path to splitted fastq.gz> -barcodes  "TTGT" "GGTT" "TGGC" "CGGA" "GGTC" "GGCA" -linker 'AGATCGGAAGAGCGGTTCAG'
gunzip  <path to splitted fastq.gz>*.gz
bowtie -m 500 -v2 --best --strata –sam hg38_tRNA <fastq file>  > <outfile.sam>
samtools view -Sb <outfile.sam> | samtools sort -o youtfile.sorted.bam> -
IDXstats_4_bams.pl -bams <sorted.bam#1> <sorted.bam#2> <...> <sorted.bam#n>  -outfile <outfile.xls>  -n 5
merge_codons_in_tRNA_summary.pl -infile <outfile.xls>  -outfile <outfile_collapsed.xls>
bamToBed -i <data.bam> > <data.bed>
Piranha -s -p 0.05 -b 200  <data.bed> -i 200 -l <control.bed> -d ZeroTruncatedNegativeBinomialRegression -n >  <data.peaks>
Genome_build: http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Hsapi38/hg38-tRNAs.fa
Supplementary_files_format_and_content: tRNA quantified bowtie mapped: *txt
Supplementary_files_format_and_content: quantified piranja peaks: *peaks.txt

source_name: H9 cell line

growth_protocol: hESCs (H9 line) were plated on Matrigel (Corning) and cultured in mTeSR (Stem Cell Technology) according to manufacturer instructions. HEK 293T were grown in DMEM (Life Technologies), 10% FBS, 1%P/S.  2x15cm plates were used per replicate

extract_protocol:
Samples were processed following iCLIP protocol (Huppertz et al., 2014). Briefly, lysates were cleared by sonication and digested with Rnase I (Ambion). PUS7-RNA complexes were immunoprecipitated using anti-FLAG M2 magnetic-beads (Sigma) for 2h at 4°C. PUS7-RNA complexes were run on a gel and isolated. PUS7 protein was digested by Proteinase K (Thermo Scientific) treatment and RNA was purified by phenol-chloroform precipitation.
Library were constructed as described in Huppertz et al., 2014. Briefly read 1 is set up as follow: NNNXXXXNN where N are random nucleotides and X are replicate unique barcodes. Libraries were sequenced on MiSeq platform (Illumina) for 50 cycles, single-end read.

treatment_protocol: Cells were irradiated using UV at 254nm with 200mJ/cm2 as described in iCLIP protocol.

tag: barcode

value: AATA

value: Anti-Flag M2 magnetic beads (sigma M8823)


title: iClip.H9.PUS7KO.FlagPUS7.1

value: CGGA


title: advanced CaP RP516


title: iClip.H9.PUS7KO.FlagPUS7.2

value: GGTT


title: iClip.H9.PUS7KO.2

value: TTGT


title: CaP RP499

source_name: CaP

value: CaP


title: iClip.293T.PUS7KO.3

source_name: 293T cell line

value: HEK 293T


title: iClip.293T.PUS7KO.1

value: GGTC


title: iClip.293T.PUS7KO.FlagPUS7.3


title: CaP RP496


title: iClip.293T.PUS7KO.FlagPUS7.2

value: GGCA


title: iClip.293T.PUS7KO.FlagPUS7.1


title: BdT3


title: CaP RP482


title: CaP RP436


title: CaP RP461


title: E17.5Srg170dcKO_M_3

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

country: Germany

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Reads were mapped to mouse genome mm10.
In ChIP-Seq reads were filtered leaving only high quality reads (MAPQ != (0, 2, 3, 4)).
In RNA-Seq reads were counted using FeaturesCount. In ChIP-Seq peaks were called using MACS2 with q-value < 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files and count files.

source_name: embryonic cortex

extract_protocol:
RNA was isolated using Rneasy kit from Qiagen. Chromatin immunoprecipitation was performed using home-made protocol.
Libraries for ChIP-Seq were prepared using NEBNext Ultra DNA Library Preparation Kit for Illumina. Libraries for RNA-Seq were prepared using Illumina TruSeq RNA Sample Preparation v2 Kit.

value: BAF dcKO_hGFAP-Cre


title: CaP RP432


title: E17.5Srg170dcKO_M_4


title: E17.5Srg170dcKO_M_2


title: E17.5Srg170dcKO_C_4


title: CRPC RP407


title: advanced CaP RP484


title: E17.5Srg170dcKO_C_3


title: E17hGFAPSrg170Input_K_1

tag: chip antibody

value: Input


title: E17.5Srg170dcKO_C_2


title: CaP RP342


title: E17.5Srg170dcKO_C_1


title: E17hGFAPSrg170H3K4me2_K_4

value: H3K4me2 (Millipore 07-449)


title: iClip.293T.PUS7KO.2

value: TGGC

tag: antibody


title: CaP RP395

value: prostate


title: CRPC RP308

value: CRPC

value: tumor


title: E17hGFAPSrg170H3K4me2_K_2


title: E17hGFAPSrg170H3K4me2_K_1


title: E17hGFAPSrg170Input_C_1


title: CaP RP463


title: CaP RP286


title: CaP RP437


title: E17hGFAPSrg170H3K4me2_C_4


title: E17hGFAPSrg170H3K27me3_K_4

value: H3K27me3 (Millipore 07-030)


title: E17hGFAPSrg170H3K4me2_C_1


title: E17hGFAPSrg170H3K4me2_C_2


title: E17hGFAPSrg170H3K4me2_C_3


title: CaP RP280


title: CRPC RP256


title: E17hGFAPSrg170H3K27me3_K_3


title: advanced CaP RP264

value: advanced CaP


title: E17hGFAPSrg170H3K27me3_C_4


title: CRPC RP226


title: E17hGFAPSrg170H3K27me3_K_1


title: E17hGFAPSrg170H3K27me3_C_3


title: E17hGFAPSrg170H3K27me3_C_2


title: E17hGFAPSrg170H3K27me3_C_1


title: CaP RP194


title: E17.5WTVeh_V_4

value: wild type

value: Vehicle


title: E17.5WTVeh_V_3


title: advanced CaP RP160


title: E17.5WTVeh_V_1


title: CaP RP166


title: CRPC RP170


title: E17.5Srg170dcKOWNTi_I_4

value: Wnt inhibitor


title: E17.5Srg170dcKOWNTi_I_3


title: E17.5WTVeh_V_2


title: T26R3

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

institute: The University of Queensland

data_processing:
The quality of raw data from each library was controlled by CLC Genomic Workbench version 7.5.1.  Raw data were stripped of adapters and reads with quality score above 0.05 and less than 2 ambiguous nucleotides were retained. Reads without 3’ adapters and also reads with less than 16 nt were discarded from the libraries. Clean data considered as mappable reads for further analysis.
Tab separated files with the read sequences and their counts were used as input file for homologous miRNA analysis CLC genomic workbench.

organism: Plutella xylostella

source_name: High dose- 6 hrs Expossed - Replicate 3

growth_protocol: We obtained an insecticide susceptible population of DBM from the Waite campus at the University of Adelaide.

extract_protocol: Total RNA was extracted from larvae using Triazol® following the manufacturer’s protocol (Life Technologies). RNA concentrations were measured using a spectrophotometer and integrity was ensured through analysis of RNA on a 1% (w/v) agarose gel. The small RNA libraries were generated from all samples with three biological replicates using the Illumina Truseq small RNA preparation kit at the Australian Genome Research Facility (AGRF-Melbourne, Australia). The purified cDNA libraries were sequenced on Illumina HiSeq and raw sequencing reads (50 nt) were obtained using Illumina’s Sequencing Control Studio software.

treatment_protocol: To determine P. xylostella miRNA responses to a xenobiotic stress, we exposed the susceptible DBM larvae to two doses of Chlorantraniliprole (0.01 and 0.1 ppm). Total RNA samples were collected from surviving larvae 6 and 24 h post-treatment. This included 16 samples (three replicates for each time and dose of treatment plus two replicates of control larvae at both times).

value: Waite

tag: tissue

value: Whole body

tag: developmental stage

value: 3rd Instar larvae


title: CaP RP106

value: CaP


title: T26R2

source_name: High dose- 6 hrs Expossed - Replicate 2


title: E17.5Srg170dcKOWNTi_I_2

tag: age


title: E17.5Srg170dcKOWNTi_I_1

tag: treatment


title: CaP RP097


title: E17hGFAPSrg170H3K27me3_K_2

tag: strain


title: T224R3

source_name: High dose- 24 hrs Expossed - Replicate 3


title: BPH H750

source_name: BPH

value: BPH

value: nomal


title: E17.5Srg170dcKOVeh_V_4

value: BAF dcKO_hGFAP-Cre


title: BPH H747


title: T224R2

source_name: High dose- 24 hrs Expossed - Replicate 2


title: E17.5Srg170dcKOVeh_V_3


title: E17.5Srg170dcKOVeh_V_1


title: BPH H736


title: T16R3

source_name: Low dose- 6 hrs Expossed - Replicate 3


title: CRPC RP160_plus


title: T224R1

source_name: High dose- 24 hrs Expossed - Replicate 1


title: BPH H735


title: BPH H732


title: BPH H731


title: T124R2

source_name: Low dose- 24 hrs Expossed - Replicate 2


title: BPH H726


title: T26R1

source_name: High dose- 6 hrs Expossed - Replicate 1


title: T124R1

source_name: Low dose- 24 hrs Expossed - Replicate 1