title: Untransduced cells at time 0h, replicate 1

description: Sample name: mock_t00_1


title: Cells exposed to poly (I:C) at time 6h, replicate 2

status: Public on Jun 28 2017

type: SRA

city: Milano

first: Davide

last: Cittaro

address: via Olgettina 58

department: Center for Traslational Genomics and Bioinformatics

country: Italy

institute: Ospedale San Raffaele

description: Sample name: Poly_IC_t06_2

library_source: transcriptomic

data_processing:
Base calling was performed using CASAVA 1.8.2
Reads were aligned to reference genome using STAR v2.3.0
Features were counted using htseq-count; EnsEMBL genes v72 was used as gene model; reads were summarized at gene level
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements: raw read counts over genes

molecule: polyA RNA

organism: Homo sapiens

source_name: Bone Marrow derived CD34+

extract_protocol:
Total RNA was extracted with the RNeasy Plus Micro kit (Qiagen) according manufacturer’s indications. RNA integrity was analyzed with the Agilent 2100 Bioanalyzer
Libraries, prepared starting from 100ng of total RNA/sample with the Illumina TruSeq RNA Sample Prep kit v2 procedure, were quantified by the Qubit BR assay and the Agilent 2100

tag: cell markers

tag: tissue

value: bone marrow


title: LAN1_D14_RA_B2_2

city: Stockholm

first: Johan

last: Holmberg

address: Nobels väg 3

department: Department of Cell- and Molecular Biology, Ludwig Institute for Cancer Research

country: Sweden

institute: Karolinska Institute

description:
Sample 51
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Cage2 Mouse2 day14.
RNA-seq 50 bp single read.

data_processing:
Samples 1-54: Sequenced reads were mapped to hg19 using STAR v2.3.0 with default settings.
Samples 55-68: Sequenced reads were mapped to hg19 using Subread.
Samples 1-54: RPKM per gene were calculated using rpkmforgenes.py.
Samples 55-68: RPKM per gene were calculated using the “featureCounts” function in Subread.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include RPKM values and mapped reads for each gene (samples 1-54) or mapped reads for each gene (samples 55-68).
Supplementary_files_format_and_content: supplementary1.txt: Tab-delimited text file; Matrix table with RPKMs (samples 1-55).
Supplementary_files_format_and_content: supplementary2.txt: Tab-delimited text file; Matrix table with RPKMs (samples 56-68).

molecule: total RNA

source_name: Neuroblastoma

extract_protocol:
Mice were sacrificed and tumors were dissected and snapfrozen on dry ice.
TruSeq (Illumina) according to protocol.

treatment_protocol: Adult female Crl:Nu (Ncr)-Foxn1 nu (nude mice) were injected subcutaneous with 2x10^6 cells in the right flank (day 0) and received daily i.p. injections from day 8 with vehicle (DMSO; CTRL), 10mg/kg/day Retinoic acid (RA), 0.1mg/kg/day 5-Aza-deoxycytidine (AZA), or AZA combined with RA (AZA+RA). Tumors were harvested at day 10, day 14 or EP (1000mm3).

tag: injected cells

tag: treatment

value: AZA + RA

tag: time point

value: Tumor


title: LAN1_D14_RA_B2_0

description:
Sample 50
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Cage2 Mouse0 day14.
RNA-seq 50 bp single read.


title: Cells exposed to poly (I:C) at time 3h, replicate 3

description: Sample name: Poly_IC_t03_3


title: LAN1_D14_RA_B1_3

description:
Sample 49
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Cage1 Mouse3 day14.
RNA-seq 50 bp single read.


title: Cells exposed to poly (I:C) at time 3h, replicate 2

description: Sample name: Poly_IC_t03_2


title: LAN1_D14_RA_B1_2

description:
Sample 48
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Cage1 Mouse2 day14.
RNA-seq 50 bp single read.


title: LAN1_D14_RA_B1_1

description:
Sample 47
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Cage1 Mouse1 day14.
RNA-seq 50 bp single read.


title: LAN1_D14_CTRL_B2_3

description:
Sample 46
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Cage2 Mouse3 day14.
RNA-seq 50 bp single read.

value: DMSO (CTRL)


title: Cells transduced with purified LV at time 48h, replicate 2

description: Sample name: Clinical_LV_t48_2


title: Cells transduced with purified LV at time 48h, replicate 3

description: Sample name: Clinical_LV_t48_3


title: LAN1_D14_CTRL_B2_2

description:
Sample 45
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Cage2 Mouse2 day14.
RNA-seq 50 bp single read.


title: Cells transduced with purified LV at time 48h, replicate 1

description: Sample name: Clinical_LV_t48_1


title: Lan1_R4

description:
Sample 54
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
RA treated Tumor 4 EP.
RNA-seq 50 bp single read.

value: RA

value: EP


title: RNaseIII_ko SINV

city: New York

first: Benjamin

last: tenOever

state: NY

address: 1468 Madison Avenue

department: Microbiology

country: USA

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Libraries were run on an Illumina MiSeq
Fastq files were uploaded to Illumina's BaseSpace cloud computing environment.
Adapters were trimmed using Illumina's FASTQ Toolkit
Alignment and statistical analysis was performed using the Small RNA application on BaseSpace.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing mature miRNA name, sequence, and read counts for each sample

extract_protocol:
Total RNA was extracted from cells using Trizol reagent. Illumina TruSeq Small RNA kit was used to prepare 1 ug of total RNA for the sequencing libraries.
small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: genotype

value: RNaseIII KO


title: 293T Mock

value: Wild type


title: 293T SINV


title: RNaseIII_ko Mock


title: Cells transduced with purified LV at time 24h, replicate 3

description: Sample name: Clinical_LV_t24_3


title: LAN1_D14_CTRL_B2_0

description:
Sample 43
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Cage2 Mouse0 day14.
RNA-seq 50 bp single read.


title: Cells transduced with purified LV at time 24h, replicate 2

description: Sample name: Clinical_LV_t24_2


title: Lan1_R2

description:
Sample 52
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
RA treated Tumor 2 EP.
RNA-seq 50 bp single read.


title: NoDice GFP+pBS replicate 2

data_processing:
Libraries were run on an Illumina MiSeq
Fastq files were uploaded to Illumina's BaseSpace cloud computing environment.
Alignment and statistical analysis was performed using the RNAExpress application on BaseSpace.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing gene, status, mean read count, log2(fold change), Std. err. log2(Fold Change), and q value from BaseSpace analysis.

source_name: NoDice 293T

extract_protocol:
Total RNA was extracted from cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used to prepare 1 ug of total RNA for the sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: NoDice 293T


title: LAN1_D14_CTRL_B2_1

description:
Sample 44
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Cage2 Mouse1 day14.
RNA-seq 50 bp single read.


title: RNaseIII null SINV replicate 2

description:
processed data file: NoDice_SINV_vsRNaseIIInull_SINV_Infected.txt
processed data file: 293TSINV_InfectedvsRNaseIIInull_SINV_Infected.txt

tag: infection status

value: SINV


title: Cells transduced with purified LV at time 24h, replicate 1

description: Sample name: Clinical_LV_t24_1


title: GFP-Drosha replicate 2


title: Cells exposed to poly (I:C) at time 6h, replicate 1

description: Sample name: Poly_IC_t06_1


title: RNaseIII null SINV replicate 1


title: LAN1_D14_CTRL_B1_0

description:
Sample 42
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Cage1 Mouse0 day14.
RNA-seq 50 bp single read.


title: NoDice GFP+pBS replicate 1


title: Cells exposed to poly (I:C) at time 3h, replicate 1

description: Sample name: Poly_IC_t03_1


title: GFP-Drosha replicate 1


title: NoDice SINV replicate 2

description:
processed data file: 293TSINV_InfectedvsNoDice_SINV_Infected.txt
processed data file: NoDice_SINV_vsRNaseIIInull_SINV_Infected.txt


title: NoDice SINV replicate 1


title: Cells transduced with purified LV at time 18h, replicate 2

description: Sample name: Clinical_LV_t18_2


title: RNaseIII null Mock replicate 2

description:
processed data file: NoDicevsRNaseIIInull.txt
processed data file: 293TvsRNaseIIInull.txt

value: mock


title: RNaseIII null Mock replicate 1


title: Cells transduced with purified LV at time 18h, replicate 3

description: Sample name: Clinical_LV_t18_3


title: LAN1_D10_RA_B1_3

description:
Sample 40
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Cage1 Mouse3 day10.
RNA-seq 50 bp single read.


title: NoDice Mock replicate 2

description:
processed data file: NoDicevsRNaseIIInull.txt
processed data file: 293TvsNoDice_Mock.txt


title: LAN1_D10_RA_B2_0

description:
Sample 41
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Cage2 Mouse0 day10.
RNA-seq 50 bp single read.


title: LAN1_D10_RA_B1_2

description:
Sample 39
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Cage1 Mouse2 day10.
RNA-seq 50 bp single read.


title: Cells transduced with purified LV at time 18h, replicate 1

description: Sample name: Clinical_LV_t18_1


title: LAN1_D10_RA_B1_1

description:
Sample 38
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Cage1 Mouse1 day10.
RNA-seq 50 bp single read.


title: 293T SINV replicate 2

description:
processed data file: 293Tvs293T_SINV_Infected.txt
processed data file: 293TSINV_InfectedvsNoDice_SINV_Infected.txt
processed data file: 293TSINV_InfectedvsNoDice_SINV_Infected.txt


title: 293T Mock replicate 2

description:
processed data file: 293Tvs293T_SINV_Infected.txt
processed data file: 293TvsNoDice_Mock.txt
processed data file: 293TvsRNaseIIInull.txt


title: NoDice Mock replicate 1


title: LAN1_D10_RA_B1_0

description:
Sample 37
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Cage1 Mouse0 day10.
RNA-seq 50 bp single read.


title: 293T SINV replicate 1


title: Cells transduced with purified LV at time 6h, replicate 2

description: Sample name: Clinical_LV_t06_2


title: LAN1_D10_CTRL_B2_2

description:
Sample 35
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Cage2 Mouse2 day10.
RNA-seq 50 bp single read.


title: LAN1_D10_CTRL_B2_3

description:
Sample 36
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Cage2 Mouse3 day10.
RNA-seq 50 bp single read.


title: Cells transduced with purified LV at time 6h, replicate 1

description: Sample name: Clinical_LV_t06_1


title: Cells transduced with purified LV at time 3h, replicate 3

description: Sample name: Clinical_LV_t03_3


title: Cells transduced with purified LV at time 3h, replicate 2

description: Sample name: Clinical_LV_t03_2


title: anti-H3 T11ph Wild type culture #2 4h

city: Madrid

first: Ryan

last: Kniewel

state: Madrid

address: calle Ramiro de Maeztu, 9

department: Department of Environmental Biology

country: Spain

institute: Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CIB-CSIC)

library_source: genomic

data_processing:
Mapping and coverage determination: Paired-end 50 nt reads were mapped to the S. cerevisiae reference genome (sacCer2) and the Sanger Center’s S. pombe genome version of 7 August 2010 using BWA (version 0.7.12-r1039) MEM (LI 2013). Paired reads with an insert size more than 250 bp were filtered out and the rest were converted into coverage maps. Each coverage map was normalized per 1000 reads from S. pombe chromosomes I and II.
Genome_build: S. cerevisiae reference genome (sacCer2) and the Sanger Center’s S. pombe genome version of 7 August 2010
Supplementary_files_format_and_content: text file containing 3 tab-separated columns: Chromosome name (S. cerevisiae: chr01-chr16, chrmt; S. pombe: S.pombe_1, S.pombe_2, S.pombe_3, S.pombe_M, S.pombe_mateR), Position, Coverage value

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Wild type 4h meiotic culture

growth_protocol: Two independent wild type (MATa/MATα, ho::LYS2/”, lys2/”, leu2::hisG/”, ura3/”) and one spo11-Y135F (HO, lys2, leu2::hisG/”, ura3::hisG, spo11-Y135F-HA::URA) Saccharomyces cerevisiae SK1 meiotic cultures were prepared as follows. Saturated overnight cultures in 4 ml YPD (1% yeast extract, 2% peptone, 2% glucose) were used to inoculate 25 ml of SPS (0.5% yeast extract, 1% peptone, 0.67% yeast nitrogen base without amino acids, 1% potassium acetate, 0.05 M potassium biphtalate, pH 5.5, 0.002% antifoam 289 (Sigma)) to a density of 5 x 106 cells/ml and cultured at 30 C, 250 rpm for 7 hr. Cells were then inoculated into 600 ml of fresh SPS at a density of 4x106 cells/ml and cultured at 30 C at 250 rpm for 12–16 hr until the density reached 3-4 x 107 cells/ml. Cells were collected by centrifugation, washed with 2% potassium acetate, then resuspended at 4 x 107 cells/ml in SPM (2% potassium acetate, 0.001% polypropylene glycol) supplemented with 0.32% amino acid complementation medium (1.5% lysine, 2% histidine, 2% arginine, 1% leucine, 0.2% uracyl, 1% tryptophan). Cultures were shaken at 250 rpm at 30 C and samples of 4 x 109 cells were collected 3, 3.5 or 4h after transfer to SPM. Schizosaccharomyces pombe haploid pat1-114 sporulation cultures (standard background, h+, pat1-114, ade6-3049) were carried out as described in Hyppa and Smith 2009 (Hyppa, R. W., and G. R. Smith, 2009, Methods Mol Biol 557: 235-252). Briefly, the strain was thawed on YEDS (0.5% yeast extract, 3% dextrose, 2% agar, 100 µg/ml each of 5 supplements: adenine, histidine, leucine, lysine and uracil) and grown 4 days at 25 C. Single haploid colonies were inoculated to 5 ml YEDS and grown at 25 C until saturated. The starter culture was then diluted 1:100 into 50 ml EMM2 minimal media (14.7 mM potassium hydrogen phthalate, 15.5 mM disodium phosphate, 93.5 mM ammonium chloride, 2% dextrose, salts, vitamins and minerals) with 75 µg/ml each of 5 supplements and grown at 25 C at 250 rpm in a 250 ml unbaffeled flask until the O.D.600 was between 1.5 and 2.0. This culture was then diluted to O.D.600 0.10 in 500 ml EMM2 with 75 µg/ml each of 5 supplements in a 2 L unbaffeled flask and grown at 25 C, 250 rpm to O.D.600 of 0.3-0.4. Cells were then pelleted, washed with sterile water and resuspended in 500 ml EMM2 starvation media lacking ammonium chloride and with 10 µg/ml each of 5 supplements in a 2 L unbaffeled flask and grown at 25 C, 250 rpm for 18 to 22 h. Meiosis was initiated by adding ammonium chloride to 0.5% and 5 supplements to 75 µg/ml and moving the culture to 34 C, 250 rpm. This corresponds to hour zero of the meiotic time course.

extract_protocol:
4 x 109 cells were fixed with 1% formaldehyde for 15 min at room temperature, with mixing at 50 rpm. Crosslinking was quenched by adding glycine to 131 mM for 5 min, cells were washed with water, resuspended in ice-cold ST buffer (10 mM Tris-HCl pH 7.4, 100 mM NaCl and 1x each of Roche phosphatase and protease inhibitor cocktails). To compare different samples, we used Schizosaccharomyces pombe cells as a spike-in control. S. pombe cells (standard background, h+, pat1-114, ade6-3049) harvested at 4.5 hr in meiosis were fixed and washed with the same condition described above. An aliquot of 4 x 107 S. pombe cells (1% of the number of S. cerevisiae cells) were added to each sample.   Cells were resuspended in FA lysis buffer (50 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 10 µg/ml each of leupeptin, pepstatin A, and chymostatin, 1 mM PMSF, 1x each of Roche phosphatase and protease inhibitor cocktails) and disrupted using zirconia/silica beads (0.5 mm, Biospec Products, Inc. 11079105z) and a FastPrep-24 (MP Biomedicals) with 8 rounds of shaking at 6.5 m/s for 60 seconds. Lysates were pelleted by centrifugation at 15,000 rpm for 5 min at 4°, washed with NP-S buffer (0.5 mM spermidine, 0.075% IGEPAL CA-630, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 10 mM MgCl2, 2 mM CaCl2, 10 µg/ml each of leupeptin, pepstatin A, and chymostatin, 1 mM PMSF, 1x each of Roche phosphatase and protease inhibitor cocktails) and resuspended in 3.6 mL NP-S buffer with 1 mM 2-mercaptoethanol. The resuspended pellet (chromatin) was solubilized by digestion with 25 units/ml of micrococcal nuclease (Worthington Biochemical Corp.) at 37° for 20 min. Digestion was terminated by adding EDTA to 10 µM and SDS to 0.05%. Chromatin was further solubilized by sonication (Biorupter Standard, Diagenode) on highest setting for two rounds of 30 sec with a 30 sec intervening rest. Solubilized chromatin was isolated by centrifugation at 16,000 rpm for 10 min at 4°, pooled and divided into two equal volumes.   Twenty µg of each antibody was added to the MNase-treated chromatin samples and incubated at 4° overnight on a rotisserie mixer [Antibodies: rabbit anti-H3 pAb (Abcam 1791); rabbit anti-H3 T11ph mAb (EMD Millipore 04-789)]. Immunoprecipitation was carried out by adding 200 μl protein G Dynabeads (Life Technologies Corp.) and incubating at 4° for 90 min on a rotisserie mixer. Beads were washed with 1 ml of the following buffers: NP-S buffer, FA lysis buffer, 2x FA high salt buffer (FA lysis buffer containing 1 M NaCl), 2x FA wash 2 buffer (FA lysis buffer containing 0.5 M NaCl), 2x FA wash 3 buffer (10 mM Tris-HCl pH 8, 250 mM LiCl, 2 mM EDTA, 1% IGEPAL, 1% sodium deoxycholate) and TE wash buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 0.5% Triton X-100). All washes were performed with vigorous vortexing at room temperature using Protein LoBind tubes (Eppendorf). Washed samples were eluted by incubating with 40 µl of elution buffer (50mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) at 65 C for 15 min. The eluates were mixed with 160 µl TE containing 1% SDS. Crosslinks were reversed and RNA was digested by overnight incubation at 65 C with 50 µg/ml RNase A. Protein was subsequently digested with 750 µg/ml proteinase K at 50 C for 2 hr. DNA was purified using a PCR purification kit (Qiagen) and separated on a 1.5% agarose gel. Mononucleosome-sized DNA (~150 bp) was extracted from the gel and prepared for 50 nt paired-end sequencing on the HiSeq 2000 platform (Illumina, Inc.) following standard Illumina protocols. Sequencing was performed at the Integrated Genomics Operation of Memorial Sloan-Kettering Cancer Center.
Mononucleosome-sized DNA (~150 bp) was extracted from the gel and prepared for 50 nt paired-end multiplexed sequencing on the HiSeq 2000 platform (Illumina, Inc.) following standard Illumina protocols. Barcodes from multiplexing are the following:  H3_1_IGO_07460_1 AACGTGAT     H3_2_IGO_07460_2 AACAACCA    H3_3_IGO_07460_3  AGATCGCA    H3_4_IGO_07460_4 CCGAAGTA    H3_5_IGO_07460_5 GATAGACA    T11ph_1_IGO_07460_6 TATCAGCA   T11ph_2_IGO_07460_7 AATGTTGC    T11ph_3_IGO_07460_8 CCATCCTC T11ph_4_IGO_07460_9 AAACATCG  T11ph_5_IGO_07460_10 AACCGAGA
Mononucleosome-sized DNA (~150 bp) was gel extracted and prepared for 50 nt paired-end multiplexed sequencing on the HiSeq 2000 platform (Illumina, Inc.).

tag: strain background

value: wild type (MATa/MATalpha, ho::LYS2/", lys2/", leu2::hisG/", ura3/")

tag: biological replicate number

tag: meiotic timepoint

tag: chip antibody

value: rabbit anti-H3 T11ph mAb (EMD Millipore 04-789, lot# 2879776)


title: anti-H3 T11ph spo11yf 3.5h

source_name: spo11-Y135F mutant 3.5h meiotic culture

value: spo11-Y135F (HO, lys2, leu2::hisG/", ura3::hisG, spo11-Y135F-HA::URA)


title: LAN1_D10_CTRL_B2_0

description:
Sample 33
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Cage2 Mouse0 day10.
RNA-seq 50 bp single read.


title: Cells transduced with purified LV at time 3h, replicate 1

description: Sample name: Clinical_LV_t03_1


title: LAN1_D10_CTRL_B1_3

description:
Sample 32
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Cage1 Mouse3 day10.
RNA-seq 50 bp single read.


title: Lan1_C4

description:
Sample 31
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Tumor 4 EP.
RNA-seq 50 bp single read.


title: anti-H3 T11ph Wild type culture #2 3h

source_name: Wild type 3h meiotic culture


title: Cells transduced with research-grade LV at time 48h, replicate 2

description: Sample name: LV_t48_2


title: anti-H3 T11ph Wild type culture #1 3h


title: GLAM

first: Julia

last: Domingo

address: 101 6th Av

institute: New York Genome Center

description: from plasmid library (plasmid and cDNA)

data_processing:
library strategy: DNA-seq of PCR amplicon
Read trimming (with cutadapt)
Demultiplexing samples and replicates (custom perl and python scripts using oligos used in the library construction, Supplementary table 4)
Sequence mapping to get unique counts for each artificiall transcript (bowtie2)
Read counting, replicates and samples merging in a single file (custom perl and python scripts). Each strain independent experiment has its own unique file
Supplementary_files_format_and_content: Tabular format. Headers: header=id of the inserted genomic fragment (BAM id); seq=nucleotide sequence of the inserted fragment; following columns are unique read counts for each insert: DNA/RNA=Origin of the sample, RNA-seq or DNA-seq; 1-2=replicates 1 or 2

source_name: yeast culture

growth_protocol: After 2 days of growth at 30C cells were collected all the transformants resuspended to an OD of 0.5 in synthetic complete dropout plates lacking uracil supplemented with 2% galactose as a carbon source in order to get the GALL promoter induction. After growing overnight cells were scraped off the plates and inoculated four 500 ml flasks of the same medium to OD of 0.025 as biological replicates. The cultures were grown about 10 hours at 30°C to reach an exponential phase with an OD of 0.5.

extract_protocol:
DNA plasmid was extracted usnign the MasterPure™ Yeast DNA Purification Kit (Epicentre) and the transcribed RNA using the MasterPure™ Yeast RNA Purification Kit (Epicentre) from all the biological replicas.
A gene specific primer strategy was used to generate the cDNA from each RNA preparation (see Supplementary Table 3) using the ThermoScript RT-PCR System (Life Technologies, 11146-024). The second DNA strand was amplified with barcoded primers in order to differentiate between replicas and sample origin, in this case, DNA and RNA (for details of barcoded primers combination for the libraries see Supplementary Table 3 and Supplementary Table 4). The PCR sample were set up as 50 µl reaction of Q5 DNA polymerase (NEB, M0491S) in the following cycling conditions: 98°C for 30s; 98°C for 10s, 55-64°C (depending on primer combination for demultiplexing on technical variability and biological replicates) for 30s and 72°C for 30s (20 cycles); and 72°C for 2 min. PCR products were purified using MinElute PCR Purification Kit (Qiagen, 28004)

tag: strains

tag: molecule subtype

value: PCR amplicon


title: Cells transduced with purified LV at time 6h, replicate 3

description: Sample name: Clinical_LV_t06_3


title: anti-H3 spo11yf 3.5h

value: rabbit anti-H3 pAb (Abcam 1791, lot# GR300976-2)


title: Lan1_C2

description:
Sample 30
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Tumor 2 EP.
RNA-seq 50 bp single read.


title: Cells transduced with research-grade LV at time 48h, replicate 1

description: Sample name: LV_t48_1


title: GLA2

description:
from plasmid library (plasmid and cDNA)
processed data file:
GAL_seqcounts.mat

tag: strain


title: Lan1_C1

description:
Sample 29
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Tumor 1 EP.
RNA-seq 50 bp single read.


title: 293T Mock replicate 1


title: Cells transduced with research-grade LV at time 24h, replicate 3

description: Sample name: LV_t24_3


title: GLA1


title: LAN1_D10_CTRL_B2_1

description:
Sample 34
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Cage2 Mouse1 day10.
RNA-seq 50 bp single read.


title: anti-H3 Wild type culture #2 4h


title: Lan1_C0

description:
Sample 28
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Tumor 0 EP.
RNA-seq 50 bp single read.


title: mRNAseq_PADH1-GCN4S242L_met_rep3

city: Basel

first: Joao

middle: C

last: Guimaraes

address: Klingelbergstrasse 50 / 70

department: Biozentrum

country: Switzerland

institute: University of Basel

description:
BY4741 MATa his3Δ1 leu2Δ0 ura3Δ0 gcn4::kanMX4-promADH1-GCN4 S242L
gcn4mut_counts.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to transcriptome based on the CDS annotations from the yeast database (http://www.yeastgenome.org) and the 5’/3’UTR mappings from Ref. (Nagalakshmi et al., 2008) using segemehl v0.1.7-411 with parameters --accuracy 90
Transcript counts were calculated based on uniquely mapped reads and used to estimate differential expression by DESeq2. Ribosome density foldchange was calculated using the ratio Riboseq foldchange by mRNAseq foldchange.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files include read counts and fold-change for each strain

growth_protocol: Yeast was grown on YPD (1% yeast extract, 2% peptone and 2% glucose) medium at 30°C, 200 rpm unless otherwise stated. The cells were collected in mid-log phase at OD600 0.4-0.8.

extract_protocol:
A yeast cell pellet was resuspended in 1 ml of lysis buffer from Dynabeads® mRNA DIRECTTM Kit (61011, Life technologies) and lysed at 4°C with 1 volume of acid washed glass beads in a FastPrep instrument (Thermo Scientific) using 2 cycles with the following settings; 45 s at 6.5 speed with 3 min pause on ice between each cycle.
Libraries for mRNA sequencing were prepared using the “directional mRNAseq sample preparation” protocol from Illumina with minor modifications. Polysome profiling and sequencing of ribosome-protected mRNA fragments were performed according to protocol described in (Nedialkova and Leidel, 2015).

treatment_protocol: For ribosome profiling cells were treated with cycloheximide 100ug/ml for 1 minute.

value: BY4741 MATa his3{delta}1 leu2{delta}0 ura3{delta}0 gcn4::kanMX4-promADH1-GCN4 S242L


title: Cells transduced with research-grade LV at time 24h, replicate 2

description: Sample name: LV_t24_2

value: bone marrow


title: anti-H3 Wild type culture #2 3h


title: Cells transduced with research-grade LV at time 24h, replicate 1

description: Sample name: LV_t24_1


title: mRNAseq_PADH1-GCN4S242L_met_rep2


title: anti-H3 Wild type culture #1 4h


title: anti-H3 T11ph Wild type culture #1 4h


title: anti-H3 Wild type culture #1 3h


title: Cells transduced with research-grade LV at time 18h, replicate 3

description: Sample name: LV_t18_3


title: Cells transduced with research-grade LV at time 48h, replicate 3

description: Sample name: LV_t48_3


title: Lan1_AR4

description:
Sample 27
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Tumor 4 EP.
RNA-seq 50 bp single read.

value: AZA + RA


title: mRNAseq_PADH1-GCN4S242L_met_rep1


title: Lan1_AR3

description:
Sample 26
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Tumor 3 EP.
RNA-seq 50 bp single read.

value: Tumor


title: CAY583_G2

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

description: In the processed data file the values for each chromosome were generated by dividing by 0.6.

data_processing:
Reads were mapped to the references genome for each organisms (using the Stampy package).
Samtools view was used to filter reads, retaining uniquely mapped reads with each segment properly aligned according to the aligner (-f 2) and with high mapping quality (-q 50).
Replication timing profiles were generated by normalizing the replicating (S phase) sample to the non-replicating (G2) sample in 1 kb windows. The S. castellii profile was generated from the replicating sample only.
Windows where fewer than 250 (500 for T. blattae) reads were mapped in either sample were excluded.
The resulting absolute ratios reflect the read numbers; therefore data was normalized by dividing by an empirically determined factor.
Genome_build: C_glabrata: C_glabrata_CBS138_version_s02-m02-r12_chromosomes.fasta; N_castellii: NCBI assembly ASM251v1; T_blattae: NCBI assembly ASM31591v1; Z_rouxii: NCBI assembly ASM2636v1; K_lactis: NCBI assembly ASM251v1; L_kluyveri: NCBI assembly ASM14922v1; CAY583: sacCer3
Supplementary_files_format_and_content: Processed files (*.wig) are available as Series supplementary files.
Supplementary_files_format_and_content: C_glabrata_CBS138_version_s02-m02-r12_chromosomes.fasta: Genome assembly used for mapping sequencing reads.

source_name: genomic DNA from G2 cells enriched by FACS  from asynchronous culture

growth_protocol: Cells were harvested from mid-log phase cultures grown in YPD media.

extract_protocol:
Cells obtained from FACS were resuspended in 500 µL of 1.2 M sorbitol, 200 mM Tris-HCl (pH7.5), 20 mM EDTA, 0.1% b-mercaptoethanol. Cells were spheroplasted with Zymolyase and then treated with SDS, Proteinase K and RNase A. DNA was purified by phenol chloroform extraction.
Library preparation and sequencing was carried out according to Illumina instructions.

treatment_protocol: Cells were sorted by DNA content, selecting S phase and G2 phase cells

tag: relevant genotype

value: MATa / MATalpha, spr28::KanMX / spr28::KanMX, ars428 / ars428, ars429::TRP1 / ars429::TRP1, RAD5 / RAD5, BUD4 / BUD4 leu2 / leu2, ura3 / ura3, trp1 / trp1 ade2 / ade2, his3 / his3

tag: phase


title: Cells transduced with research-grade LV at time 18h, replicate 2

description: Sample name: LV_t18_2

tag: cell markers


title: Lan1_AR0

description:
Sample 24
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Tumor 0 EP.
RNA-seq 50 bp single read.

tag: tissue


title: Cells transduced with research-grade LV at time 18h, replicate 1

description: Sample name: LV_t18_1


title: CAY583_S

source_name: genomic DNA from S phase cells enriched by FACS  from asynchronous culture

value: S


title: Lan1_A4

description:
Sample 23
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA treated Tumor 4 EP.
RNA-seq 50 bp single read.

tag: injected cells

value: AZA

value: EP


title: Cells transduced with research-grade LV at time 6h, replicate 3

description: Sample name: LV_t06_3


title: mRNAseq_wt_ura3_rep3

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 pRS426 2μ URA3
gcn4oe_expression_profiles.csv
pgal_gst_gcn4_counts.csv

value: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 pRS426 2{mu} URA3


title: Lan1_A2

description:
Sample 22
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA treated Tumor 2 EP.
RNA-seq 50 bp single read.

tag: treatment


title: Cells transduced with research-grade LV at time 6h, replicate 2

description: Sample name: LV_t06_2


title: Lan1_A0

description:
Sample 21
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA treated Tumor 0 EP.
RNA-seq 50 bp single read.

tag: time point


title: overexpression of TCP1, replicate 2

city: Split

first: Anita

last: Krisko

address: Mestrovicevo setaliste 45

country: Croatia

institute: Mediterranean Institute for Life Sciences

description:
overexpression of TCP1, replicate  2
TCP1.2

data_processing:
Sequence mapping: Sequenced reads (Illumina 50bp single-end) were mapped to the SacCer3 reference genome (April 2001 revision, http://www.ncbi.nlm.nih.gov/assembly/285498/, genome obtained from the UCSC Genome Browser; Rosenbloom et al., 2015) using the STAR aligner (version 2.3.0e Dobin et al., 2013).
Read counting: Raw read counts were determined from the overlaps with the Ensembl yeast genes using the htseq-count version 0.6.0. from the HTSeq framework (Anders et al., 2014), with the following parameters: -a 10 –s no.
Differential expression analysis: Raw reads were analyzed for differential expression with the DeSeq2 package (Love et al., 2014) within the Bioconductor framework (Huber et al., 2015) under R statistical package (R Core Team), by previously filtering out the outlier replicates with PCA analysis on rlog transformed replicate data.
Genome_build: SacCer3 reference genome (April 2001 revision, http://www.ncbi.nlm.nih.gov/assembly/285498/, genome obtained from the UCSC Genome Browser
Supplementary_files_format_and_content: bigWig; BigWig files are a compressed, indexed, binary format for RNASeq experiments; bigWig files were created from STAR alignments using bam2wig utility from RSeQC v2.3.7 (Wang et. al, 10.1093/bioinformatics/bts356)
Supplementary_files_format_and_content: NormalizedCounts.xlsx: This file has DeSeq2 normalized counts from raw counts produced with htseq-count. Each column corresponds to one replicate, raw counts were loaded into DeSeq2 and after normalization, a set of normalized counts were saved into Excel.

source_name: overexpression of TCP1, replicate 2

growth_protocol: WT Y258 was grown on YPD medium with 2% (w/v) glucose and chaperone overexpression mutants on –URA medium with 2% (w/v) glucose, at 30oC with shaking. All experiments were performed on cells from mid-exponential phase: cells were grown until OD 0.6-0.8, harvested by 5 minute centrifugation at 4000xg, washed and treated accordingly.

extract_protocol:
Total RNA was isolated from yeast cells following the procedure of the NucleoSpin RNA kit (Macherey&Nagel) for up to 3 x 108 yeast cells, which dictates incubation with 50-100U of zymolyase for 1 hour at 30°C. The quality of resulting total mRNA was tested on 1% agarose gels.
According to EMBL GeneCore platform; standard Illumina protocol

tag: genotype/variation

value: overexpression of TCP1

tag: growth phase

value: exponential culture


title: overexpression of TCP1, replicate 3

description:
overexpression of TCP1, replicate  3
TCP1.3

source_name: overexpression of TCP1, replicate 3


title: overexpression of EGD2, replicate 2

description:
overexpression of EGD2, replicate  2
EGD2.2

source_name: overexpression of EGD2, replicate 2

value: overexpression of EGD2


title: Cells transduced with research-grade LV at time 6h, replicate 1

description: Sample name: LV_t06_1


title: overexpression of EGD2, replicate 1

description:
overexpression of EGD2, replicate  1
EGD2.1

source_name: overexpression of EGD2, replicate 1


title: mRNAseq_wt_ura3_rep1


title: mRNAseq_PGAL-GST-GCN4_ura3_rep3

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 pEGH 2μ URA3 promGAL110GSTGCN 4
gcn4oe_expression_profiles.csv
pgal_gst_gcn4_counts.csv

value: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 pEGH 2{mu} URA3 promGAL1-10-GST-GCN 4


title: Lan1_AR1

description:
Sample 25
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Tumor 1 EP.
RNA-seq 50 bp single read.


title: overexpression of TCP1, replicate 1

description:
overexpression of TCP1, replicate  1
TCP1.1

source_name: overexpression of TCP1, replicate 1


title: overexpression of SSC1, replicate 3

description:
overexpression of SSC1, replicate  3
SSC1.3

source_name: overexpression of SSC1, replicate 3

value: overexpression of SSC1


title: CHP212_R4

description:
Sample 20
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
RA treated Tumor 5 EP.
RNA-seq 50 bp single read.

value: RA


title: CHP212_R3

description:
Sample 19
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
RA treated Tumor 4 EP.
RNA-seq 50 bp single read.


title: CHP212_R2

description:
Sample 18
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
RA treated Tumor 3 EP.
RNA-seq 50 bp single read.


title: overexpression of SSC1, replicate 2

description:
overexpression of SSC1, replicate  2
SSC1.2

source_name: overexpression of SSC1, replicate 2


title: overexpression of SSC1, replicate 1

description:
overexpression of SSC1, replicate  1
SSC1.1

source_name: overexpression of SSC1, replicate 1


title: mRNAseq_PGAL-GST-GCN4_ura3_rep2


title: CHP212_R0

description:
Sample 16
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
RA treated Tumor 1 EP.
RNA-seq 50 bp single read.


title: mRNAseq_wt_met_rep3

description:
BY4741 MATa his3Δ1 leu2Δ0 ura3Δ0
gcn4oe_expression_profiles.csv
padh_gcn4_counts.csv

value: BY4741 MATa his3{delta}1 leu2{delta}0 ura3{delta}0


title: mRNAseq_wt_ura3_rep2

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 pRS426 2μ URA3
gcn4oe_expression_profiles.csv
pgal_gst_gcn4_counts.csv


title: Cells transduced with heat inactivated purified LV at time 48h, replicate 2

description: Sample name: Inact_t48_2

source_name: Bone Marrow derived CD34+


title: Cells transduced with research-grade LV at time 3h, replicate 3

description: Sample name: LV_t03_3


title: Cells transduced with heat inactivated purified LV at time 48h, replicate 3

description: Sample name: Inact_t48_3


title: Cells transduced with research-grade LV at time 3h, replicate 2

description: Sample name: LV_t03_2


title: Cells transduced with research-grade LV at time 3h, replicate 1

description: Sample name: LV_t03_1


title: overexpression of LHS1, replicate 2

description:
overexpression of LHS1, replicate  2
LHS1.2

source_name: overexpression of LHS1, replicate 2

value: overexpression of LHS1


title: mRNAseq_wt_met_rep2


title: mRNAseq_wt_met_rep1


title: Cells transduced with heat inactivated purified LV at time 24h, replicate 3

description: Sample name: Inact_t24_3


title: CHP212_C3

description:
Sample 14
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Tumor 4 EP.
RNA-seq 50 bp single read.

source_name: Neuroblastoma

value: DMSO (CTRL)


title: CHP212_C4

description:
Sample 15
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Tumor 5 EP.
RNA-seq 50 bp single read.


title: overexpression of LHS1, replicate 1

description:
overexpression of LHS1, replicate  1
LHS1.1

source_name: overexpression of LHS1, replicate 1


title: WT Y258, empty vector control, replicate 3

value: WT, empty vector control


title: Cells transduced with heat inactivated purified LV at time 48h, replicate 1

description: Sample name: Inact_t48_1

value: bone marrow


title: mRNAseq_PADH1-GCN4_met_rep3

description:
BY4741 MATa his3Δ1 leu2Δ0 ura3Δ0 gcn4::kanMX4-promADH1-GCN4
gcn4oe_expression_profiles.csv
padh_gcn4_counts.csv

value: BY4741 MATa his3{delta}1 leu2{delta}0 ura3{delta}0 gcn4::kanMX4-promADH1-GCN4


title: WT Y258, empty vector control, replicate 2


title: CHP212_C2

description:
Sample 13
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Tumor 3 EP.
RNA-seq 50 bp single read.

value: Tumor


title: Cells transduced with heat inactivated purified LV at time 24h, replicate 2

description: Sample name: Inact_t24_2


title: CHP212_C1

description:
Sample 12
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Tumor 2 EP.
RNA-seq 50 bp single read.


title: mRNAseq_PGAL-GST-GCN4_ura3_rep1

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 pEGH 2μ URA3 promGAL110GSTGCN 4
gcn4oe_expression_profiles.csv
pgal_gst_gcn4_counts.csv


title: CHP212_R1

description:
Sample 17
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
RA treated Tumor 2 EP.
RNA-seq 50 bp single read.


title: mRNAseq_PADH1-GCN4_met_rep1


title: Cells transduced with heat inactivated purified LV at time 24h, replicate 1

description: Sample name: Inact_t24_1


title: CHP212_C0

description:
Sample 11
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
Untreated (DMSO) Tumor 1 EP.
RNA-seq 50 bp single read.


title: overexpression of LHS1, replicate 3

description:
overexpression of LHS1, replicate  3
LHS1.3

source_name: overexpression of LHS1, replicate 3


title: mRNAseq_PADH1-GCN4_met_rep2


title: mRNAseq_drpl9a_rep3

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rpl9a::kanMX4
rpko_expression_profiles.csv
rpko_rnaseq_counts.csv

value: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 rpl9a::kanMX4


title: CHP212_AR4

description:
Sample 10
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Tumor 5 EP.
RNA-seq 50 bp single read.

value: AZA + RA


title: Cells transduced with heat inactivated purified LV at time 18h, replicate 3

description: Sample name: Inact_t18_3


title: Cells transduced with heat inactivated purified LV at time 18h, replicate 2

description: Sample name: Inact_t18_2


title: Cells transduced with heat inactivated purified LV at time 6h, replicate 3

description: Sample name: Inact_t06_3


title: CHP212_AR3

description:
Sample 9
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Tumor 4 EP.
RNA-seq 50 bp single read.

value: EP


title: CHP212_AR2

description:
Sample 8
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Tumor 3 EP.
RNA-seq 50 bp single read.


title: mRNAseq_drpl9a_rep1


title: Cells transduced with heat inactivated purified LV at time 18h, replicate 1

description: Sample name: Inact_t18_1


title: Cells transduced with heat inactivated purified LV at time 6h, replicate 2

description: Sample name: Inact_t06_2


title: mRNAseq_drpl9a_rep2


title: mRNAseq_drpl7a_rep2

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rpl7a::kanMX4
rpko_expression_profiles.csv
rpko_rnaseq_counts.csv

value: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 rpl7a::kanMX4


title: mRNAseq_drpl7a_rep1


title: Cells transduced with heat inactivated purified LV at time 6h, replicate 1

description: Sample name: Inact_t06_1


title: CHP212_A4

description:
Sample 5
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA treated Tumor 5 EP.
RNA-seq 50 bp single read.

value: AZA


title: CHP212_AR0

description:
Sample 6
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Tumor 1 EP.
RNA-seq 50 bp single read.


title: WT Y258, empty vector control, replicate 1

value: exponential culture


title: mRNAseq_drps27b_rep3

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rps27b::kanMX4
rpko_expression_profiles.csv
rpko_rnaseq_counts.csv

value: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 rps27b::kanMX4


title: Cells transduced with heat inactivated purified LV at time 3h, replicate 3

description: Sample name: Inact_t03_3


title: mRNAseq_drps27b_rep2


title: mRNAseq_drps27b_rep1


title: CHP212_A3

description:
Sample 4
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA treated Tumor 4 EP.
RNA-seq 50 bp single read.


title: Cells transduced with heat inactivated purified LV at time 3h, replicate 2

description: Sample name: Inact_t03_2


title: CHP212_A2

description:
Sample 3
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA treated Tumor 3 EP.
RNA-seq 50 bp single read.


title: s39-P3_HVNJMCCXX_L5

city: Beijing

first: Yan-Tao

last: Ma

address: No. 5 Yiheyuan Road

country: China

institute: Peking University

description:
chemically-induced XEN-like cells
processed data file: Neuronal cell seq03.xls
s39-P3_HVNJMCCXX_L5

data_processing:
The transcriptome reads were mapped using the TopHat2 program.
The gene expression level was calculated by using FPKM method.
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_tracking files including FPKM values for the analysis of gene expression

organism: Mus musculus

source_name: chemically-induced cells from mouse fibroblasts

extract_protocol:
Total RNA from each sample was isolated using the RNeasy Plus Mini Kit (QIAGEN).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.


title: Cells transduced with heat inactivated purified LV at time 3h, replicate 1

description: Sample name: Inact_t03_1


title: Cells transduced with Env-less LV at time 48h, replicate 2

description: Sample name: Bald_t48_2


title: mRNAseq_drpl7a_rep3


title: s39-P17_HVNJMCCXX_L5

description:
chemically-induced XEN-like cells
processed data file: Neuronal cell seq03.xls
s39-P17_HVNJMCCXX_L5

value: chemically-induced cells from mouse fibroblasts


title: s12_HH2TTALXX_L7

description:
mouse fibroblast
processed data file: Hepatic cell seq01.xls
s12_HH2TTALXX_L7

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts


title: CHP212_A1

description:
Sample 2
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA treated Tumor 2 EP.
RNA-seq 50 bp single read.


title: Cells transduced with Env-less LV at time 48h, replicate 3

description: Sample name: Bald_t48_3


title: mRNAseq_drpl15b_rep3

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rpl15b::kanMX4
rpko_expression_profiles.csv
rpko_rnaseq_counts.csv

value: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 rpl15b::kanMX4


title: Cells transduced with Env-less LV at time 24h, replicate 3

description: Sample name: Bald_t24_3


title: s12_HJM3YALXX_L2

description:
mouse hepatic tissue
processed data file: Hepatic cell seq01.xls
s12_HJM3YALXX_L2

source_name: mouse hepatic tissue

value: mouse hepatic tissue


title: mRNAseq_drpl15b_rep2


title: mRNAseq_drpl6a_rep3

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 rpl6a::kanMX4
rpko_expression_profiles.csv
rpko_rnaseq_counts.csv

value: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 rpl6a::kanMX4


title: CHP212_A0

description:
Sample 1
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA treated Tumor 1 EP.
RNA-seq 50 bp single read.


title: Patient2 SFMC sti

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

data_processing:
FASTX-Toolkit was used to trim away low-quality reads and remove adaptor sequences from raw reads. The annotation analysis was performed by mapping the clean reads to a list of datasets using Bowtie
miRNAs were annotated by mapping to human miRNAs and other miRNAs from miRBase v21 allowing zero mismatches.
The expression of miRNA was normalized by reads per million (RPM) using the formula: miRNA RPM normalized expression = (miRNA counts / the total counts of all mapped miRNAs) x106.
Supplementary_files_format_and_content: Tab delimited text files with raw miRNA counts or reads per million normalized counts

source_name: RA patients

growth_protocol: Cells were stimulated with anti-CD3/anti-CD28 for 48h. Non-stimulated cells were also cultured for 48 h. EVs  were collected by series of ultracentrifugation

extract_protocol:
Total RNA from EVs was purified using miRCURY RNA isolation kit-Cell and Plant  (Exiqon)
The small RNA library of EVs was constructed using Illumina TruSeq Small RNA Sample Prep Kit (Illumina)

tag: cell type

value: SFMC

value: Stimulated


title: mRNAseq_drpl6a_rep2


title: Patient2 SFMC unsti

value: Unstimulated


title: s15_HJM3YALXX_L2

description:
mouse hepatocyte
processed data file: Hepatic cell seq01.xls
s15_HJM3YALXX_L2

source_name: mouse hepatocyte

value: mouse hepatocyte


title: Cells transduced with Env-less LV at time 48h, replicate 1

description: Sample name: Bald_t48_1

value: bone marrow


title: mRNAseq_drpl6a_rep1


title: Cells transduced with Env-less LV at time 18h, replicate 3

description: Sample name: Bald_t18_3


title: mRNAseq_wt_rep3

description:
BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0
rpko_expression_profiles.csv
rpko_rnaseq_counts.csv

source_name: wt

value: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: Patient2 PBMC sti

value: PBMC


title: Cells transduced with Env-less LV at time 18h, replicate 2

description: Sample name: Bald_t18_2


title: Patient1 SFMC sti


title: CHP212_AR1

description:
Sample 7
2E6 cells were injected (1:1 PBS:matrigel) subcutaneous in nude mice day 0, treatment start day 8.
AZA and RA treated Tumor 2 EP.
RNA-seq 50 bp single read.

value: AZA + RA

value: EP

value: Tumor


title: Patient2 PBMC unsti


title: Cells transduced with Env-less LV at time 18h, replicate 1

description: Sample name: Bald_t18_1


title: s3_HH2TTALXX_L6

description:
chemically-induced XEN-derived hepatocyte-like cells
processed data file: Hepatic cell seq01.xls
s3_HH2TTALXX_L6


title: mRNAseq_wt_rep2


title: s10_HCNYKALXX_L5

description:
chemically-induced XEN-derived hepatocyte-like cells
processed data file: Hepatic cell seq01.xls
s10_HCNYKALXX_L5


title: s11_HH2TTALXX_L6

description:
mouse fibroblast
processed data file: Hepatic cell seq01.xls
s11_HH2TTALXX_L6


title: s9_HH2H2ALXX_L6

description:
chemically-induced XEN-derived hepatocyte-like cells
processed data file: Hepatic cell seq01.xls
s9_HH2H2ALXX_L6


title: Cells transduced with Env-less LV at time 6h, replicate 2

description: Sample name: Bald_t06_2


title: Patient1 SFMC unsti


title: Cells transduced with Env-less LV at time 24h, replicate 2

description: Sample name: Bald_t24_2


title: s13_HJM3YALXX_L2

description:
mouse hepatic tissue
processed data file: Hepatic cell seq01.xls
s13_HJM3YALXX_L2


title: Cells transduced with Env-less LV at time 3h, replicate 2

description: Sample name: Bald_t03_2


title: Patient1 PBMC unsti


title: Cells transduced with Env-less LV at time 24h, replicate 1

description: Sample name: Bald_t24_1


title: Patient3 SFMC sti


title: s14_HJM3YALXX_L2

description:
mouse hepatocyte
processed data file: Hepatic cell seq01.xls
s14_HJM3YALXX_L2


title: Patient4 SFMC sti


title: mRNAseq_drpl15b_rep1


title: N253O

city: Boston

first: Muhammad

middle: B

last: Ekram

state: MA

address: 450 Brookline Avenue, DA 740A

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Basecalls were performed using CASAVA version 1.8.2
Quality check of the called bases of the reads were performed using the FastQC tool (Babraham Bioinformatics)
The datasets were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner (version 2.5.1b) using the following modified parameters: --outSAMstrandField intronMotif, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outFilterType BySJout, --outFilterScoreMinOverLread 0.33, --outFilterMatchNminOverLread 0.33, --limitSjdbInsertNsj 1200000, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --twopassMode Basic.
The read counts for individual genes were generated using the htseq-count script of the HTSeq framework (version 0.6.1p1) using modified parameters (--stranded no) and the hg19 refGene annotation file available at the UCSC Genome Browser.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated file of the raw read counts of each samples for each gene.

source_name: resected normal breast tissue

extract_protocol:
RNA was isolated from purified CD45+CD3+ leukocytes by cell sorting using antibodies listed in Supplementary Table 6. After approximately two thousand cells were sorted into 96-well plates with 2.5 μl PBS (containing 0.5 μl RNaseOut (Life Technologies) and 0.5 μl dithiothreitol (DDT, Invitrogen), cytoplasm RNA was isolated as described previously (Pan, X., et al, Proc Natl Acad Sci USA, 2013). In brief, 2.5 μl of 2× selected cytoplasm lysis buffer (SCLB) was added and the cells were lysed by pipetting. Lysate solution was centrifuged at 8,000 rpm for 5 min at 4°C. Supernatant (~5 μl), containing the total cytoplasm RNA, was transferred to a PCR tube strip with individually attached dome caps. 5′-phosphorylated oligo-GdT24 (pGdT24) primer was used to selectively reverse transcribe mRNAs. The first strand cDNA was synthesized with Superscript Reverse Transcriptase III (Invitrogen) followed by second strand synthesis. The cDNA was purified with the Genomic DNA Clean & Concentrator kit (Zymo Research). Afterwards, several steps including DNA end-blunting, 5′-end phosphorylation and ligation were performed with the End-It DNA End-Repair Kit (Epicentre) with T4 DNA ligase (Epicentre). The product was directly amplified using REPLI-g UltraFast Mini Kit (QIAGEN) and purified using the same Genomic DNA Clean & Concentrator kit (Zymo Research Corp, Irvine, CA) column. Products were fragmented to 200-500 bp by a Bioruptor Sonicator (Diagenode). Fragment sizes were validated using the High Sensitivity DNA kit (Agilent Technologies) on an Agilent 2100 Bioanalyzer. Functional concentrations were determined by qPCR with standards for Illumina sequencing libraries.
RNAseq libraries were generated by Center for Cancer Computational Biology (CCCB) at Dana-Farber Cancer Institute following manufacture protocol.

tag: tissue of origin

value: breast (normal)

value: CD45+CD3+ T cell

tag: breast tumor subtype

value: Not applicable

tag: parity

value: Nulliparous


title: N253S


title: mRNAseq_wt_rep1


title: Patient1 PBMC sti


title: s1_HH2TTALXX_L6

description:
chemically-induced XEN-derived hepatocyte-like cells
processed data file: Hepatic cell seq01.xls
s1_HH2TTALXX_L6

value: chemically-induced cells from mouse fibroblasts


title: Cells transduced with Env-less LV at time 6h, replicate 3

description: Sample name: Bald_t06_3


title: s4001_HVNJMCCXX_L5

description:
#6 XEN-like colony (Figure S4A), #1 XEN-like colony (Figure S4B)
processed data file: Neuronal cell seq03.xls
s4001_HVNJMCCXX_L5


title: HC2 PBMC unsti

source_name: Healthy controls


title: ChIPseq_Input

description: BY4741 MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 pEGH 2μ URA3 promGAL110GSTGCN 4

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to yeast genome using segemehl v0.1.7-411 with parameters --accuracy 90
ChIP peaks were found with MACS v1.4.2 and then intersected with 1kb regions extending upstream of annotated start of yeast CDS to find the gene targets.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files include Gcn4 ChIP peaks and inferred targets

extract_protocol:
Extraction has been performed accordingly to (BlecherGonen et al., 2013).
Libraries of ChIPed and input DNA were prepared according to the instruction manual of NEBNext® ChIPSeq Library Prep Reagent Set from Illumina.

treatment_protocol: Yeast cells were crosslinked with 1% formaldehyde.

value: BY4741 MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 pEGH 2{mu} URA3 promGAL1-10-GST-GCN 4

tag: chip antibody

value: none (input)


title: HC2 PBMC sti


title: Cells transduced with Env-less LV at time 6h, replicate 1

description: Sample name: Bald_t06_1


title: HC1 PBMC sti


title: Cells transduced with Env-less LV at time 3h, replicate 3

description: Sample name: Bald_t03_3


title: HC1 PBMC unsti


title: F25-P8_HVNNLCCXX_L7

description:
chemically-induced XEN-like colony
processed data file: Neuronal cell seq03.xls
F25-P8_HVNNLCCXX_L7


title: N215S


title: F25-P5-D0_HVNJMCCXX_L5

description:
chemically-induced XEN-like colony
processed data file: Neuronal cell seq03.xls
F25-P5-D0_HVNJMCCXX_L5


title: ChIPseq_Gcn4

value: anti-GST (GE Healthcare Life Sciences, cat# 27-4577-01, lot# 316319)


title: Patient3 SFMC unsti

value: SFMC


title: Cells transduced with Env-less LV at time 3h, replicate 1

description: Sample name: Bald_t03_1


title: CeXEN-P8_HVNJMCCXX_L5

description:
chemically-derived eXEN
processed data file: Neuronal cell seq03.xls
CeXEN-P8_HVNJMCCXX_L5

source_name: mouse embryonic XEN cells

value: mouse embryonic XEN cells


title: MTY_RNA_S5_DO16051912_HJMKLALXX_L1

description:
#3 XEN-like colony (Figure S4A), #6 XEN-like colony (Figure S4B)
processed data file: Neuronal cell seq03.xls
MTY_RNA_S5_DO16051912_HJMKLALXX_L1


title: N170S


title: s4009_HVNJMCCXX_L5

description:
#7 XEN-like colony (Figure S4A), #2 XEN-like colony (Figure S4B)
processed data file: Neuronal cell seq03.xls
s4009_HVNJMCCXX_L5


title: Patient3 PBMC unsti

value: Unstimulated


title: N250S


title: F25-P13_HVNJMCCXX_L5

description:
chemically-induced XEN-like colony
processed data file: Neuronal cell seq03.xls
F25-P13_HVNJMCCXX_L5


title: Patient4 PBMC sti

value: Stimulated


title: MTY_RNA_S4_DO16051912_HJMKLALXX_L1

description:
#2 XEN-like colony (Figure S4A), #5 XEN-like colony (Figure S4B)
processed data file: Neuronal cell seq03.xls
MTY_RNA_S4_DO16051912_HJMKLALXX_L1


title: HC3 PBMC sti


title: N250O


title: N170O


title: MTY_RNA_8_DO16051912_HJMKLALXX_L1

description:
#5 XEN-like colony (Figure S4A), #8 XEN-like colony (Figure S4B)
processed data file: Neuronal cell seq03.xls
MTY_RNA_8_DO16051912_HJMKLALXX_L1


title: MTY_RNA_1_DO16051912_HJMKLALXX_L1

description:
#4 XEN-like colony (Figure S4A), #7 XEN-like colony (Figure S4B)
processed data file: Neuronal cell seq03.xls
MTY_RNA_1_DO16051912_HJMKLALXX_L1


title: N215O


title: MED_039636

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 with 1 mismatch
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: normalized RPKM

source_name: moderate dysplasia_oral mucosa

extract_protocol:
Total RNA was extracted from each tissue using TRIzol kit (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. Subsequently, the RNA samples were treated with RQ1 DNase (Promega, Madison, WI, USA) to remove both double- and single-stranded DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) on SmartSpec Plus Spectrophotometer (BioRad, Philadelphia, PA, USA). RNA integrity was further verified by 1.5% agrose gel electrophoresis.
For each sample, 10 mg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with Magnetic Beads Oligo(dT) (Invitrogen, Carlsbad, CA, USA) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95oC followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 oC until used for sequencing.

tag: source patient id

tag: subject status

value: oral moderate dysplasia

value: oral mucosa

tag: tissue type

value: tissue samples obtained from patients undergoing surgical treatment for oral moderated dysplasia


title: MTY_RNA_S3_DO16051912_HJMKLALXX_L1

description:
#1 XEN-like colony (Figure S4A), #4 XEN-like colony (Figure S4B)
processed data file: Neuronal cell seq03.xls
MTY_RNA_S3_DO16051912_HJMKLALXX_L1

tag: strain


title: MED_038038


title: MED_037926


title: N169S

value: Parous


title: Brain

description:
mouse brain
processed data file: Neuronal cell seq01.xls
Brain

source_name: mouse brain

value: mouse brain


title: Normal_038038

source_name: normal_oral mucosa

value: normal samples collected from the negative surgical margins


title: N169O

value: breast (normal)

value: CD45+CD3+ T cell


title: N166S

value: Not applicable


title: CSC

description:
chemically-induced neuronal cells by FICB
processed data file: Neuronal cell seq01.xls
CSC

value: chemically-induced cells from mouse fibroblasts


title: Normal_039636


title: N113O


title: Normal_037926


title: N166O


title: MTY_RNA_N1_DO16051912_HJMKLALXX_L1

description:
Fibroblast-1 (Figure S4A), Fibroblast-2 (Figure S4B)
processed data file: Neuronal cell seq03.xls
MTY_RNA_N1_DO16051912_HJMKLALXX_L1

value: mouse embryonic fibroblasts


title: RNAseq_CTR_rep3

city: Wuerzburg

first: Stefan

last: Gaubatz

address: Am Hubland

department: Biochemistry and Cell Biology

country: Germany

institute: University of Wuerzburg

data_processing:
RNA-seq:
Overall sequencing quality was checked with FastQC.
Reads were aligned to the mouse genome using RNA-Seq Alignement Version 1.0.0 (Basespace, Illumina) using default parameters
Using results from the RNA-Seq aligner, DESeq2 (Basespace, Illumina) was used to produce gene counts, gene FPKMs and to perform differential expression analysis
Genome_build: Mus musculus (UCSC mm10)
Supplementary_files_format_and_content: Comma-separated values (CSV) file containing log2FC, p-values and adjusted p-values from DeSeq2. Comma-separated values (CSV) file containing FPKM values from DESeq2.

source_name: embryonic heart (E18.5)

extract_protocol:
For RNA extraction, Trifast (peqLab) was added to hearts and samples were sliced two times for 30 seconds at 40.000 U/min in a Ultra-Turrax. Total RNA was additionally purified using the RNeasy kit (Qiagen) including on-column DNase I digest according to the manufacturer´s protocol.
PolyA+-RNA was isolated from total with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB). The NEBNext® Ultra™ RNA Library Prep Kit for Illumina was used for library preparation following the manufacturer’s instruction. Size selection of the libraries was performed with the AMPure XP Beads (Beckman Coulter), followed by 13 PCR cycle for amplification. Library quantification and quality was assessed using the Experion Automated Electrophoresis System (Bio-Rad).

value: embryonic heart

tag: genotype

value: wildtype

tag: developmental stage


title: RNAseq_Gas2l3KO_rep3

tag: tissue


title: RNAseq_Gas2l3KO_rep1


title: N113S


title: s_1_NI

description:
Fibroblast-1 (Figure 1G, H, Figure 4K), Fibroblast-3 (Figure S4B)
processed data file: Neuronal cell seq01.xls
s_1_NI


title: MEF-7_HVNJMCCXX_L6

description:
Fibroblast-2 (Figure 1G, H, Figure 4K, Figure S4A), Fibroblast-1 (Figure S4B)
processed data file: Neuronal cell seq03.xls
MEF-7_HVNJMCCXX_L6


title: P24_H3227ALXX_L6

description:
chemically-induced XEN-derived neuronal cells
processed data file: P24 XEN derived CiNs.xls
P24_H3227ALXX_L6


title: DCIS178

source_name: resected breast tumor

value: breast (tumor)

value: DCIS

value: Not available


title: RNAseq_CTR_rep2


title: N353S


title: RNAseq_StdDefeat6

city: Princeton

first: Catherine

middle: Jensen

last: Pena

state: NJ

address: Washington Road

department: Neuroscience

institute: Princeton University

description: Adult VTA after standard-rearing and adult chronic social defeat stress

data_processing:
RNA-seq reads were aligned to mouse genome NCBI37 (mm9) using Tophat2. Uniquely aligned short reads were counted using HTSeq-counts.
Low and non-expressed genes with less than5 reads in at least 80% of samples in a condition were omitted from the analysis.
Principal component analysis was used to detect outliers for removal, although none were identified.
ChIP-seq reads were then aligned to the mouse MM10 genome using default settings of Bowtie (v2.2.0).
Only uniquely mapped reads were retained and the alignments were subsequently filtered using the SAMtools package (v0.1.19) to remove duplicate reads.
Peak-calling was performed using MACS (v2.1.1) with a FDR cutoff of 0.05.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: A single text file with tabulated RPKM values for all RNAseq samples and genes
Supplementary_files_format_and_content: One bigWig file per ChIPseq sample

source_name: Ventral tegmental area (brain)

extract_protocol:
All tissue was taken from adult male mice during the light cycle, 24 hours after behavioral testing. RNA was purified first by TriZol extraction followed by column purification sing Rneasy micro kits (Qiagen) according to manufacturer's protocol. All samples were found to have a high RIN value (>9; BioAnalyzer, Agilent). Chromatin was briefly crosslinked in 1% formaldehyde and sonicated to 200-600bp fragments. Samples were pooled by group to immunoprecipitate 1 microgram of chromatin with ChIP-grade H3K4me1 antibody (AbCam Ab8895) overnight at 4C. DNA from ChIP or Input (5%) was de-crosslinked overnight, RNA and protein degraded enzymatically, and purified by PCR purification kit (Qiagen).
RNA-seq libraries were prepared using Illumina TruSeq unstranded kit A and B for poly-A selected transcripts, according to protocol. ChIP-seq/Input libraries were prepared by NEBNext Ultra DNA kit with Illumina adaptors according to protocol.
RNA-seq samples counterbalanced across groups for multiplexing and sequenced on an Illumina Hi-Seq machine with 100-bp single-end reads in the Mount Sinai Genomics Core Facilities. Multiplexing produced >30 million reads per sample.  ChIP and corresponding Input samples were multiplexed separately to achieve >80-million reads/sample on Illumina Hi-Seq V4 chemsitry with 100-bp single-end reads in the Mount Sinai Genomics Core Facilities.

tag: stress conditions

value: Std - CSDS


title: IDC97

value: IDC (Luminal)


title: RNAseq_CTR_rep1


title: N352S


title: PNs

description:
Primary neurons-1 (Figure 1G, H), Primary neurons (Figure 4K)
processed data file: Neuronal cell seq01.xls
PNs

source_name: mouse primary cortical neurons

value: mouse primary cortical neurons


title: CiNs

description:
TauEGFP+ colonies-1 (Figure 1G,H)
processed data file: Neuronal cell seq01.xls
CiNs


title: DCIS18


title: RNAseq_StdDefeat4


title: RNAseq_StdDefeat3


title: RNAseq_StdDefeat5


title: RNAseq_Gas2l3KO_rep2


title: MTY_RNA_T2_DO16051912_HJMKLALXX_L1

description:
TauEGFP+ colonies-2 (Figure 1G), P2 XEN derived CiNs (Figure 4k)
processed data file: Neuronal cell seq02.xls
MTY_RNA_T2_DO16051912_HJMKLALXX_L1


title: RNAseq_StdDefeat2


title: N335S


title: IDC127

value: IDC (HER2+)


title: Neuron_HVNJMCCXX_L5

description:
Primary neurons-2 (Figure 1G)
processed data file: Neuronal cell seq02.xls
Neuron_HVNJMCCXX_L5


title: DCIS17


title: DCIS15


title: N261S


title: RNAseq_StdDefeat1


title: N256S


title: 26: 5 ng/mL TGF-β1

city: Gainesville

first: Ley

middle: Cody

last: Smith

state: FL

address: 2187 Mowry Rd

institute: University of Florida

description: Sample 16

data_processing:
Base-calling: Standard Illumina pipeline
Read trimming: Trimmomatic version 0.36
Alignment to hg38 genome: STAR version 2.5.2a
Quantification: RSEM v1.2.31
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample

source_name: Bronchial epithelial cells

growth_protocol: Cells were cultured in bronchial epithelial growth medium (BEGM) consisting of bronchial epithelial basal medium (BEBM, Lonza CC-3171, Walkersville, MD) and the BEGM SingleQuot Kit Supplements & Growth Factors (Lonza CC-4175) but exchanging gentamicin for Penicillin-Streptomycin-Neomycin (PSN) Antibiotic Mixture (Gibco 15640, ThermoFisher Scientific Inc., Waltham, MA). Cells were cultured in T75 Corning™ U-Shaped Cell Culture Flasks (Corning 430641U, Fisher Scientific Co LLC, Pittsburgh, PA) coated with a matrix (4.5 mL per 75 cm2) consisting of 0.01 mg/mL fibronectin (Akron AK8350, City, State), 0.03 mg/mL bovine collagen (Gibco A10644-01), and 0.01 mg/mL BSA (Fisher BP1605) in BEBM. Cells were subcultured up to 11 times before use in exposure studies. All exposures were performed in BEGM without the supplied bovine pituitary extract (BPE) aliquot because its composition is not defined.

extract_protocol:
Cell lysates were collected in RNA STAT-60TM Reagent (Tel-Test, Inc. Cs-502, Friendswood, TX) and RNA extracted per manufacturer’s specifications. RNA was precipitated overnight at -20°C in 100% molecular biology grade isopropanol (Fisher BioReagentsTM BP26184) containing 0.067% v/v GlycoBlueTM Coprecipitant (Ambion® AM9515) and purified by washing 2X with 75% molecular biology grade absolute ethanol (Fisher BioReagentsTM BP28184). RNA pellets were reconstituted in 15 μL RNAsecure™ (Ambion® AM7010). RNA was quantified using a SynergyTM H1 plate reader (BioTek Instrument, Inc., Winooski, VT) and RNA integrity was analyzed using a Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA).
RNA library construction was performed at the Interdisciplinary Center for Biotechnology Research (ICBR) Gene Expression Core, University of Florida (UF). RNA concentration was determined on Qubit® 2.0 Fluorometer (ThermoFisher/Invitrogen, Grand Island, NY), RNA quality was assessed using the Agilent 2100 Bioanalyzer. Total RNA with 28S/18S > 1 and RNA integrity number (RIN) ≥ 7 are used for RNAseq library construction. The RINs of all the total RNA was 9.7-10]. 2 μl of 1: 2000 diluted RNA spike-in ERCC (half of amount suggested in the ERCC user guide: Cat# 4456740) spike to 1 μg of high quality of total RNA followed by mRNA isolating using NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs E7490, Ipswich, MA) and RNA library construction with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs E7530) according to the manufacturer's user guide. Briefly, 100 ng of total RNA together with 2 μl of 1:2000 diluted ERCC was used to extracted mRNA with 15ul of NEBNext Magnetic Oligo d(T)25 and fragmented in NEBNext First Strand Synthesis Buffer by heating at 94 °C for 8 min, followed by first strand cDNA synthesis using reverse transcriptase and random primers.  Synthesis of ds cDNA was done using the 2nd strand master mix provided in the kit. The resulting double-stranded cDNA was end-repaired, dA-tailing and ligated with NEBNext adaptors.  Finally, library was enriched by 13 cycles of amplification, and purified by Meg-Bind RxnPure Plus beads (Omega Biotek M1386, Norcross, GA). Barcoded libraries were sized on the bioanalyzer, quantitated by QUBIT and qPCR (Kapa Biosystems KK4824, Wilmington, MA). 17 individual libraries were pooled at equal molar at 20 nM.

treatment_protocol: BEAS-2Bs were plated at 40,000 cells/mL on matrix-coated 12-well Nunc™ Cell-Culture Treated Multidishes (ThermoFisher Scientific Inc.), allowed to adhere overnight, and subsequently exposed for 48 hours to the indicated concentrations of TGF-β1 dissolved in 0.1% BSA (Fisher BP1605) and 4 mM HCl or 10 nM Estrogen dissolved in DMSO (Mediatech Inc. MT25950CQC). For the protein expression experiments, BEAS-2Bs were plated at 60,000 cells/mL on matrix-coated 6-well Corning® Costar® cell culture plates (Costar 3516), allowed to adhere overnight, and subsequently exposed for 48 hours to the indicated concentrations of TGF-β1 in BEBM without BPE. All chemical solvent concentrations were maintained below 0.1%.

tag: passage

value: lung, bronchus

value: epithelial virus transformed

tag: exposure

value: 5 ng/mL TGF-β1


title: RNAseq_StdCtl4

description: Adult VTA after standard-rearing and control conditions in adulthood

value: Std - Ctl


title: DCIS166

value: CD45+CD3+ T cell


title: 25: Vehicle Control

description: Sample 15

value: Vehicle Control


title: RNAseq_StdCtl3


title: IDC340

value: IDC (TN)


title: 23: 10 nM Estrogen

description: Sample 14

value: 10 nM Estrogen


title: IDC256


title: RNaseIII null polyIC replicate 2

description:
NoDice vs RNaseIIIKO polyIC.txt
RNaseIII KO +_- polyIC.txt

data_processing:
Libraries were run on an Illumina HiSeq2500
Fastq files were uploaded to Illumina's BaseSpace cloud computing environment.
Alignment and statistical analysis was performed using the RNAExpress application on BaseSpace.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing gene, status, mean read count, log2(fold change), Std. err. log2(Fold Change), and q value from BaseSpace analysis.

source_name: NoDice 293T

tag: protocol

value: RNaseIII null polyIC


title: 19-27: 5 ng/mL TGF-β1 + 10 nM Estrogen

description: Sample 17

value: 5 ng/mL TGF-β1 + 10 nM Estrogen


title: IDC255

value: breast (tumor)


title: 22: 10 nM Estrogen

description: Sample 13


title: RNAseq_StdCtl2


title: 21: 10 nM Estrogen

description: Sample 12


title: RNAseq_ELSDefeat6

description: Adult VTA after early life stress and adult chronic social defeat stress

value: ELS - CSDS


title: RNAseq_StdCtl1


title: NoDice polyIC replicate 3

description:
NoDice vs RNaseIIIKO polyIC.txt
NoDice +_- polyIC.txt

value: NoDice polyIC


title: 20: 5 ng/mL TGF-β1 + 10 nM Estrogen

description: Sample 11


title: IDC251

value: Not available


title: RNaseIII null polyIC replicate 1


title: IDC249


title: RNAseq_ELSDefeat4


title: RNAseq_ELSDefeat5


title: NoDice polyIC replicate 2


title: IDC242


title: 18: 5 ng/mL TGF-β1 + 10 nM Estrogen

description: Sample 10


title: NoDice Mock replicate 2

description:
NoDice vs RNaseIIIKO.txt
NoDice +_- polyIC.txt

value: NoDice Mock


title: 17: 5 ng/mL TGF-β1 + 10 nM Estrogen

description: Sample 09


title: IDC229


title: RNAseq_ELSDefeat3


title: 16: 5 ng/mL TGF-β1

description: Sample 08


title: RNaseIII null Mock replicate 2

description:
NoDice vs RNaseIIIKO.txt
RNaseIII KO +_- polyIC.txt

value: RNaseIII null Mock


title: RNAseq_ELSDefeat2


title: RNaseIII null Mock replicate 1


title: IDC192

value: IDC (HER2+)


title: IDC180


title: 15: 5 ng/mL TGF-β1

description: Sample 07

value: lung, bronchus


title: RNAseq_ELSDefeat1


title: 14: 5 ng/mL TGF-β1

description: Sample 06

value: epithelial virus transformed


title: 13: 5 ng/mL TGF-β1

description: Sample 05

value: 5 ng/mL TGF-β1


title: DCIS336

value: DCIS


title: 12: Vehicle Control

description: Sample 04


title: RNAseq_ELSCtl2

description: Adult VTA after prior early life stress exposure and contorl adult conditions

value: ELS - Ctl


title: RNAseq_ELSCtl4


title: 11: Vehicle Control

description: Sample 03

value: Vehicle Control


title: RNAseq_ELSCtl1


title: RNAseq_ELSCtl3


title: 10: Vehicle Control

description: Sample 02


title: DCIS307

value: CD45+CD3+ T cell


title: DCIS280


title: Input_Std4

description: Adult VTA after standard-rearing

value: Std - Ctl


title: DCIS320


title: NoDice Mock replicate 1


title: 9: Vehicle Control

description: Sample 01


title: ChIPseq_Std4

description: Adult VTA after standard-rearing

value: H3K4me1 (AbCam AB8895)


title: ChIPseq_Std3

description: Adult VTA after standard-rearing


title: Input_Std3

description: Adult VTA after standard-rearing


title: Input_Std2

description: Adult VTA after standard-rearing


title: Input_Std1

description: Adult VTA after standard-rearing


title: ChIPseq_Std1

description: Adult VTA after standard-rearing


title: DCIS322


title: 59C

city: Balice near Krakow

first: Klaudia

last: Pawlina-Tyszko

address: Krakowska 1

department: Deaprtment of Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

description: microRNA

data_processing:
Demultiplexing: Casava v1.8
Trimming off the 3' adapter sequences: UEA sRNA WorkbenchV3.2
Filtering: UEA sRNA WorkbenchV3.2; parameters: 17-35 nt in length, minimum abundance of at least 3 supporting reads, tRNA and rRNA sequences excluded.
Mapping: The filtered reads were mapped to EquCab2.0 genome and miRBase 21.0, using miRCat tool embeded in UEA sRNA WorkbenchV3.2. The following parameters were applied - default animal parameters, except for: minimum abundance (3 or greater), minimum length (17 nt) and maximum length (25 nt).
Genome_build: EquCab2.0
Supplementary_files_format_and_content: FASTA files after filtering and adaptor trimming, generated with the use of UEA sRNA Workbench V3.2, for each sample. They include the number of reads of the detected sequences.

organism: Equus caballus

source_name: tumor distant skin

extract_protocol:
Total RNA was extracted using Direct-zol RNA MiniPrep Kit (Zymo Research). The obtained RNA was then additionally purified and concentrated with RNA Clean & Concentrator™-5 (Zymo Research). 1ug of total RNA was used to prepare libraries.
Libraries were prepared according to TruSeq Small RNA Sample Preparation Kit protocol (Illumina, protocol 15004197 Rev.F, February 2014). First, the samples were ligated with 3' and 5' adapters, respectively. Then, miRNA-adapter ligation products were reverse transcribed and PCR amplified (14 cycles). The amplification was carried out with the use of the universal primer and one of 12 different indexed primers for each sample. Then, the libraries' fragments of ~150bp (miRNA+adapters+PCR primer sequences) were band isolated from Novex 6% TBE PAGE gel (Invitrogen). The purified libraries were then captured and clustered on an Illumina flow cell. Finally, the obtained clustered libraries were sequenced on HiScanSQ platform (Illumina) following the manufacturer's protocols.

treatment_protocol: The collected samples were frozen at -20°C in tubes with RNAlater (Qiagen).

tag: individual

value: horse 5

value: tumor distant skin

tag: sample type

value: control


title: ChIPseq_Std2

description: Adult VTA after standard-rearing


title: 59S3

description: microRNA

source_name: sarcoid

value: sarcoid

value: tumor


title: 59S1

description: microRNA


title: 55S2

description: microRNA

value: horse 4


title: ChIPseq_ELS7

description: Adult VTA after prior early life stress exposure only


title: ChIPseq_ELS6


title: Input_ELS5


title: 59S4

description: microRNA


title: ChIP_seq_RAD21_Spr_aB

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

data_processing:
Reads were aligned to the GRCm38p2/mm10 genome assembly.
Alignment done using bowtie version 0.12.7, with the parameters:   --best --all --strata  -n 2 -m1 -l 50
ChIP-seq peaks were called againts input samples using default parameters.
Genome_build: GRCm38p2/mm10
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

organism: Mus spretus

source_name: Activated primary B cells-Spretus

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and resuspended in 2 ml of RIPA buffer (10 mM Tris [pH 7.6], 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at −80°C until further processing. Sonication was performed using the Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30 min or using the Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause. Ten microgram of respective antibody was incubated with 40 μl of Dynabeads Protein A (or G) for 15 min at room temperature. Antibody-bound beads were added to 1 ml of sonicated chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml Proteinase K. ChIP DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo). The library was prepared using the Ovation SP Ultralow library system (Nugen). 75 cycles of sequencing data were acquired on and Nextseq550 (Illumina). Antibodies for ChiP-seq were: anti-RAD21 (ab992, Abcam), anti-CTCF (07-729, Millipore), Topo IIβ Antibody (H-286) (sc13059, SantaCruz) and Topoisomerase II alpha antibody (EP1102Y) (ab52934, Abcam)
libraries were prepared and sequenced following standard Illumina protocols

tag: cell type

value: Activated primary B cells-Spretus

value: WT

value: Spretus


title: ChIPseq_ELS8


title: Input_ELS8


title: 55C

description: microRNA


title: Input_ELS7


title: Z_rouxii_G2

description: In the processed data file the values for each chromosome were generated by dividing by 0.78. Data points below 0.9 or above 2.1 were excluded.

organism: Zygosaccharomyces rouxii

source_name: genomic DNA from G2 cells enriched by FACS  from asynchronous culture

tag: relevant genotype

value: wild type

tag: phase


title: END_seq_Species_Spr_aB12h_NT

data_processing:
Library strategy: END-seq
mouse and human END-seq reads were aligned to the GRCm38p2/mm10 and  GRCh37/hg19 genome assemblies,respectively.
Alignment done using bowtie version 0.12.7, with the parameters:   --best --all --strata  -n 3 -k1 -l 50
END-seq peaks were called using the parameters: --nolambda,-- nomodel and –keep-dup=all (keep all redundant reads). For Etoposide-treated END-seq data peak calling, we used the corresponding non-treated samples as control, keeping >10 fold-enriched peaks.
Genome_build: GRCm38p2/mm10 for mouse and  GRCh37/hg19 for human
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

extract_protocol:
Single cell suspensions of B-cells (15 million per agarose plug), pre-B cells (40 million per agarose plug), T-cells (15 million per agarose plug), MEFS (4 million per agarose plug), neurons (5 million per agarose plug), MCF7 (5 million per agarose plug) and Nalm6 (15 million per agarose plug) were washed in PBS, embedded in agarose and transferred into plug molds (Bio-Rad CHEF Mammalian Genomic DNA plug kit) and processed as previously described (Canela et al., 2016). Libraries were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences) and sequenced in a NextSeq 550 system (Illumina, 75 bp single end reads).
libraries were prepared and sequenced following standard Illumina protocols


title: s4012_HVNJMCCXX_L6

description:
#8 XEN-like colony (Figure S4A), #3 XEN-like colony (Figure S4B)
processed data file: Neuronal cell seq03.xls
s4012_HVNJMCCXX_L6

source_name: chemically-induced cells from mouse fibroblasts


title: 59S2

description: microRNA


title: DCIS274

tag: tissue of origin

value: breast (tumor)

tag: breast tumor subtype

tag: parity

value: Not available


title: C_glabrata_G2

description: In the processed data file the values for each chromosome were generated by dividing by 0.6. Data points below 0.9 or above 2.1 were excluded.

organism: Nakaseomyces glabratus


title: Z_rouxii_S

source_name: genomic DNA from S phase cells enriched by FACS  from asynchronous culture

value: S


title: 55S1

description: microRNA


title: 52C

description: microRNA

value: horse 3


title: 46C

description: microRNA

value: horse 2


title: 52S

description: microRNA


title: END_seq_Nalm6_NT


title: 46S

description: microRNA


title: END_seq_Species_Spr_aB12h_ETO

description: Control: Spr_aB12h_NT


title: L_kluyveri_G2

description: In the processed data file the values for each chromosome were generated by dividing by 0.9. Data points below 0.9 or above 2.1 were excluded.

organism: Lachancea kluyveri


title: ChIP_seq_CTCF_Spr_aB


title: 43C

description: microRNA

value: horse 1


title: Input_ELS6

tag: chip antibody

value: ELS - Ctl


title: C_glabrata_S

tag: strain


title: L_kluyveri_S


title: END_seq_Nalm6_ETO

description: Control: Nalm6_NT

tag: genotype


title: 43S

description: microRNA


title: END_seq_MCF7_NT


title: K_lactis_G2

description: In the processed data file the values for each chromosome were generated by dividing by 0.92. Data points below 0.9 or above 2.1 were excluded.

organism: Kluyveromyces lactis


title: Biofilm

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

data_processing:
Basecalling was performed using Illumina CASAVA version1.8.2.
CLC genomics version 5.5.1 was used for alignment, normalization (RPKM) and for differential gene expression calculation.
Kal’s statistical test, with false discovery rate, was applied to identify statistically significant alterations in the transcriptome of biofilm as compared with the planktonic cells.
Genes with P values above 0.05 and fold changes below 2 were discarded.
Genome_build: NC_013721
Supplementary_files_format_and_content: Tab-delimited text files with gene name and respective fold change values regarding the control (planktonic cells)

organism: Gardnerella vaginalis AMD

growth_protocol: Biofilms were grown as described in Castro et al., 2015, Sci Rep 5:11640. In brief, G. vaginalis was inoculated, in 96-well plates, in to Brain Heart Infusion (BHI) supplemented with 2% (wt/wt) gelatin, 0.5% (wt/wt) yeast extract, 0.1% (wt/wt) soluble starch (sBHI) and incubated at 37ºC with 10% CO2. Following 24 hours, the culture medium covering the biofilms was removed, replaced by fresh sBHI and allowed to grow, in the same conditions, for additional 24 hours. Biofilms were then scraped in sBHI and collected. Planktonic cells were grown in sBHI for 24h at 37ºC with 10% CO2. Both biofilm and planktonic cells were harvested by centrifugation (20 min, 7197 g) and resuspended in 1 mL of RNA protect (Qiagen, diluted 2:1 in PBS).

extract_protocol:
Biofilm or planktonic cells total RNA was extracted using RNeasy mini kit (QIAGEN) with minor alterations as described in França et al., 2012, PLoS One 7 (5): e37480. In brief, bacterial cells were suspended in 500 µL of in the lysis buffer provided by the kit plus 500 µL of phenol. This suspension was transferred into BeadBug tubes (1.0 mm Zirconium beads, triple-pure, high impact, Sigma) and using a MPBio 24 (MPBio) the cells were lysed. Finally, the tubes were centrifuged and the lysate transferred into a new tube. An equal volume of 70% of ethanol was added. The suspension was transferred in to the RNeasy mini kit columns and the manufacturer's instructions were strickly followed. Total RNA, eluted in 50 µL, was treated with TURBO DNase (Ambion) and 1:5 Acid-phenol:chloroform in order to degrade and isolate, respectively, genomic DNA. Additionally, total RNA was treated with Ribo-Zero rRNA removal kit for Gram-positive bacteria (Epicentre) to remove bacterial ribosomal RNA.
Libraries were constructed using ScriptSeq RNAseq Library preparation kit (low input) and strictly following the manufacturer's indications.

treatment_protocol: No treatment was performed to either planktonic or biofilm cells.

value: AMD

tag: lifestyle

value: Biofilm


title: Planktonic

value: Planktonic


title: T_blattae_S

organism: Henningerozyma blattae


title: T_blattae_G2

description: In the processed data file the values for each chromosome were generated by dividing by 0.73. Data points below 0.9 or above 2.1 were excluded.


title: END_seq_MCF7_ETO

description: Control: Not treated &MEF - TOP2B -/-


title: ChIPseq_ELS5

value: H3K4me1 (AbCam AB8895)


title: GM12878_input_B

status: Public on Jun 27 2017

city: Istanbul

first: Ogun

last: Adebali

address: Orta Mah. Universite Cad No 27

department: Faculty of Natural Sciences and Engineering

country: Turkey

institute: Sabanci University

data_processing:
adapter discarding
alignment
filtering duplicates
damage position locating
filtering rare dinucleotides
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain genomic locaions of damages of the most common two dinucleotides at the damage sites for (6-4)PP and CPD. Each interval length is 10 nt, and the pyrimidine dimer is located at the 4-5th positions.

growth_protocol: Normal human fibroblast NHF1 was obtained from W.K. Kaufmann, UNC, Chapel Hill (1) and cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 2 mM glutamine. Human lymphocyte GM12878 was purchased from the NIGMS Human Genetic Cell Repository (Coriell Institute) and cultured in RPMI 1640 medium (no phenol red) supplemented with 15% fetal bovine serum. Cells were maintained at 37°C in a 5% CO2 humidified chamber.

extract_protocol:
Genomic DNA were extracted by PureLink Genomic DNA kit (Thermo).
Genomic DNA was sheared by sonication with Q800 Sonicator (Qsonica) to generate fragments averaging 600 bp in length and then purified by an equal volume of HighPrep PCR beads (MagBio). DNA fragments were eluted by 0.1xTE and the concentration was determined by Qubit (Thermo). Purified DNA fragments (1 µg) were used for end-repair by NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) following the manufacturer's instruction. Ad1 (100 pmol) was ligated to both ends at 16°C overnight, then purified by HighPrep PCR beads (60 µl) and eluted in 55 µL of 0.1x TE. Damaged DNA immunoprecipitation was performed as described previously with modification. DNA were denatured by adding 20 µL of 8M urea, boiling for 1 min and immediately putting in ice water for 1 min. Then 20 µg of denatured sonicated salmon sperm DNA (Thermo) and 11 µL 8x IP Buffer (1x IP Buffer: 20 mM Tris-Cl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, and 0.5% sodium deoxycholate) were added, followed by incubation with antibody-coated beads which were prepared as described previously (4) at 4°C overnight.  The beads were then washed sequentially with Wash Buffer U (20 mM Tris-Cl pH 8.0, 2 mM EDTA, 1% Triton X-100, and 2M Urea), Wash Buffer II (20 mM Tris-Cl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, and 0.1% SDS), Wash Buffer III (10 mM Tris-Cl pH 8.0, 1 mM EDTA, 150 mM LiCl, 1% NP-40, and 1% sodium deoxycholate), Wash Buffer IV (100 mM Tris-Cl pH 8.0, 1 mM EDTA, 500 mM LiCl, 1% NP-40, and 1% sodium deoxycholate) and TE (10 mM Tris-Cl pH 8.0 and 1 mM EDTA) at room temperature. The fragments containing damage were eluted by incubation with 100 µL of Elution Buffer (50 mM NaHCO3, 1% SDS) at 65°C for 10 min on a thermomixer at 1100 rpm. The eluted DNA was then isolated by phenol/chloroform extraction followed by ethanol precipitation.  Primer Bio3U was attached to IP purified DNA and extended by NEBNext Q5 DNA polymerase, followed by ExoI (New England Biolabs) treatment and  HighPrep PCR beads cleanup, then denatured and captured by Dynabeads MyOne Streptavidin C1 (Thermo) as described previously (2). After incubation at 4°C for 1 hr, the beads were washed by 1x B&W buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl) and 1x TE, followed by incubation with 2 µL of USER Enzyme (New England Biolabs) in 18 µL of 0.1x TE at 37°C on a thermomixer at 900rpm for 25 min. The supernatant was separated by the magnetic stand and transferred to a new tube. Then the beads were washed with 25 µL of 1x B&W Buffer and the supernatant was collected and combined with supernatant from the last step. For subtractive hybridization, 20 pmol of oligo SH were added, followed by boiling for 1 min and naturally cooling down to room temperature. Oligo SH was then captured by incubating with 10 µL of Dynabeads MyOne Streptavidin C1 for 1 hr at room temperature. After separating the liquid on a magnet and transferring supernatant to a new tube, the beads were washed with 35 µL of 1x B&W Buffer and the supernatant was transferred to the same tube. DNA were purified by phenol/chloroform extraction and ethanol precipitation.  The following ligation of Ad2 and PCR amplification were performed as described previously (2). Libraries were sequenced from both ends on Hiseq 2500 by the University of North Carolina High-Throughput Sequencing Facility.

treatment_protocol: UV irradiation of NHF1 cells was performed as described previously (3). Briefly, the culture medium was removed from ~80% confluent cells in one R150 dish, then cells were irradiated under a GE germicidal lamp emitting primarily 254-nm UV light (1 J/m2/s) connected with a digital timer for 20s (for (6-4)PP damage) or 10s (for CPD damage). Following irradiation, the dishes were put on ice immediately or incubated in a chamber for indicated time with culture medium. The cells were then washed once with ice-cold PBS and harvested with a cell scraper in PBS and collected by centrifugation. GM12878 cells were grown to ~8x105 cells/ml in colorless medium and 10ml of cells were transferred to one R150 dish and irradiated with 20J/ m2 UV-C as described above. Then cells were immediately transferred to a pre-chilled 15 ml tube on ice, collected by centrifugation, washed with ice-cold PBS. For UV irradiation of naked DNA, purified genomic DNA in 100 µl of 1xTE buffer were irradiated with 20J/ m2 UV-C and stored at -20°C for further use.

tag: uv product

tag: replicate

value: B

tag: treatment

value: reference

tag: uv dose

tag: cell line


title: NHF1_input_A

value: A


title: GM12878_input_A


title: NHF1_input_B


title: GM12878_CPD_20J_cell_B

value: CPD

value: cell


title: GM12878_CPD_20J_nakedDNA_C

value: C

value: nakedDNA


title: GM12878_CPD_20J_cell_A


title: GM12878_6-4_20J_cell_B


title: GM12878_6-4_20J_nakedDNA_C


title: GM12878_6-4_20J_nakedDNA_A


title: K_lactis_S

value: wild type


title: NHF1_6-4_20J_2h_B


title: NHF1_6-4_20J_4h_B


title: NHF1_6-4_20J_4h_A


title: NHF1_6-4_20J_1h_B


title: NHF1_6-4_20J_1h_A


title: NHF1_6-4_20J_2h_A


title: NHF1_6-4_20J_0h_B


title: NHF1_6-4_20J_20min_B


title: NHF1_6-4_Control_A

value: Control


title: NHF1_CPD_10J_36h_A


title: NHF1_CPD_10J_24h_B


title: NHF1_CPD_10J_48h_A


title: NHF1_CPD_10J_36h_B


title: GM12878_CPD_20J_nakedDNA_A


title: GM12878_6-4_20J_cell_A


title: NHF1_CPD_10J_8h_B


title: NHF1_6-4_20J_0h_A


title: NHF1_CPD_10J_1h_B


title: NHF1_6-4_20J_20min_A


title: NHF1_CPD_Control_B


title: NHF1_CPD_10J_1h_A


title: NHF1_CPD_10J_0h_B


title: NHF1_CPD_Control_A


title: NHF1_6-4_Control_B


title: NHF1_CPD_10J_8h_A


title: SF3B1 Q698del 1

city: Cambridge

first: Silvia

last: Buonamici

address: 300 Technology Square #5

institute: H3 Biomedicine

data_processing:
Raw data were aligned to hg19 using the STAR alignment package
Junction counts and reads across exon-intron boundaries are converted to percent spliced-in (PSI)
Genome_build: hg19
Supplementary_files_format_and_content: PSI values for each junction within each sample

source_name: chronic lymphocytic leukemia (CLL)

extract_protocol:
Total RNA was harvested and Poly A selected
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: chronic lymphocytic leukemia (CLL)

tag: genotype/variation

value: SF3B1 Q698del


title: SF3B1 WT 5


title: SF3B1 p.K700E 3

value: SF3B1 K700E


title: SF3B1 K700del

value: SF3B1 K700del


title: SF3B1 p.K700E 4


title: NHF1_CPD_10J_48h_B2


title: SF3B1 Q698del 2


title: SF3B1 p.K700E 1


title: SF3B1 WT 3


title: SF3B1 WT 1


title: NHF1_CPD_10J_24h_A