title: Biopsy_CIT1_EVLP16

tag: paired samples


title: N3

status: Public on Jun 22 2020

type: RNA

city: changsha

first: Fangwen

last: Zou

state: hunan

country: China

institute: Central south univ

description:
circRNA expression data from Homo sapiens matched para-carcinoma tissues.
circRNA

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software. A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated in detail with the circRNA/miRNA interaction information.

molecule: total RNA

organism: Homo sapiens

source_name: Gastrointestinal stromal matched non-tumor tissue from terminal cancer patient

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing random primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: Gastrointestinal stromal tumor and matched non-tumor tissues.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissues from gastrointestinal stromal tumor surgery and promptly frozen in liquid nitrogen.

tag: tissue

value: Matched non-tumor tissue

tag: gender

value: Female

tag: age

value: 43 years


title: N2

value: Male

value: 61 years


title: Col-0_0.5h_avrRpm1_Rep2

type: SRA

city: Chapel Hill

first: Isai

last: Salas Gonzalez

address: 250 Bell Tower Drive, Room 4244

country: USA

institute: The University of North Carolina at Chapel Hill

library_source: transcriptomic

data_processing:
Initial quality assessment of the Illumina RNA-Seq reads was performed using FastQC version 0.11.7.
Trimmomatic version 0.36 was used to identify and discard reads containing the Illumina adaptor sequence.
The resulting high-quality reads were then mapped against the TAIR10 Arabidopsis reference genome using HISAT2 version 2.1.0 with default parameters.
The featureCounts function from the Subread package was then used to count reads that mapped to each one of the 27,206 nuclear protein-coding genes, we used these counts to construct a raw count table of expression.
Genome_build: TAIR 10
Supplementary_files_format_and_content: Tab delimited file containing the count matrix

organism: Arabidopsis thaliana

source_name: leaf disc

growth_protocol: Arabidopsis plants were grown at short day conditions (8-hour light/16-hour dark cycle at 21°C/18°C and 45% humidity. Arabidopsis sequence data for helper NLRs is available under the following AGI accession numbers: ADR1/At1g33560, ADR1-L1/At4g33300, ADR1-L2/At5g04720, NRG1.1/NRG1A/At5g66900, NRG1.2/NRG1B/At5g66910.

extract_protocol:
RNA was purified from plant tissue using the RNeasy 96 Kit (Qiagen). The plant “user developed protocol” was followed except for the addition of a 96% ethanol wash step after the second RPE wash to ensure removal of residual salts. Purified RNAs were kept at -80C.
Illumina-based mRNA-Seq libraries were prepared from 1 μg RNA following [61]. Briefly, mRNAs were selected using Sera-mag oligo(dT) magnetic beads (GE Healthcare Life Sciences). RNAs were washed and fragmented at 94°C for 6 minutes. First-strand cDNA synthesis was performed using random hexamers and reverse transcriptase (Superscript III reverse transcriptase, Invitrogen). Second-strand cDNA synthesis was done using DNA Polymerase I and RNAseH. Double-stranded cDNAs were end-repaired using T4 DNA polymerase, T4 polynucleotide kinase, and Klenow polymerase. The DNA fragments were then adenylated using Klenow exo-polymerase to allow the ligation of Illumina adapters (Kapa Dual-indexed adapter kit, Roche). Unless specified, reagents were purchased from Enzymatics.
Library quality control and quantification were performed using the 5200 Fragment Analyser and the NGS fragment kit (Agilent). Libraries were sequenced using Illumina HiSeq4000 sequencers to generate 50-bp single-end reads.

treatment_protocol: Plants for bacterial infiltration assays were grown for 6 weeks under short day conditions (8h light/16h dark at 21°C/18°C and 45% humidity). For bacterial growth curves, Pst DC3000 ∆hrcC and Pst DC3000 expressing either AvrRps4, AvrRpt2, EV, AvrRpm1, grown on KB plates containing appropriate antibiotics, were re-suspended in 10 mM MgCl2 to a final concentration of 5x105 (OD600 0.001).  Plants were hand-infiltrated with the bacterial suspension.

tag: genotype

value: wildtype (Col-0)

tag: time

tag: treatment

tag: rep


title: Biopsy_CIT1_EVLP15

city: Toronto

first: Ricardo

last: Zamel

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

hyb_protocol: According to manufacturer guidelines

scan_protocol: According to manufacturer guidelines

data_processing: Affymetrix CEL files were imported and processed using RMA in R version 3.5.1 with the affy package. We used an alternative CDF probset description file from Brainarray at the University of Michigan (Nucleic Acid Research 33 (20), e175; http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp): clariomdhumanhsentrezgcdf_22.0.0.zip

label: biotin

source_name: Biopsy_timepoint end of cold ischemia

label_protocol: According to manufacturer guidelines

extract_protocol: RNA was extracted from snap frozen samples using the RNeasy Mini Kit (Qiagen; Hilden, Germany). RNA quality was assessed using Nanodrop spectrophotometer (VWR; Radnor, PA) and Bioanalyzer (Agilent; Santa Clara, CA)

tag: timepoint

value: lung


title: MP30

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

description:
case
SAMPLE 16

data_processing:
Cq-values were called using the second-derivate maximum method. Data quality was assessed using spike-in controls to determine RNA extraction efficiency, enzymatic inhibition, and overall variability. Data normalization was performed using the global mean (i.e. average Cq-value for all endogenous microRNAs with Cq<35) to obtain delta Cq-values.
normalized data file contains global-mean normalized delta Cq-value (dCqs)
Log2 Fold Change = log2 (PLS3 MP vs MN)

label: SYBR Green

source_name: serum

growth_protocol: We have previously identified four Finnish families with X-linked PLS3 osteoporosis due to different mutations in PLS3 . The first family (Family A) has an intronic splice site mutation c.73–24T>A (p.Asp25Alafs*17) identified by exome sequencing as previously described. The second family (Family B) includes three subjects with an intragenic tandem duplication within PLS3 as identified by genomic hybridization array (array-CGH). The third family (Family C) consists of a single subject with a de novo heterozygous missense mutation c.1424A>G (p.AsnN446Ser )  in exon 12 identified by Sanger sequencing of the whole PLS3 gene as previously described. The fourth family (Family D) includes two subjects with a nonsense mutation c.766C>T (p.Arg256*) in exon 8, also identified by conventional Sanger sequencing of the whole PLS3 gene.

extract_protocol: Serum was thawed at room temperature and centrifuged at room temperature for 5 minutes at 12,000 x g in order to remove cellular debris. RNA extraction was performed using precisely 200 µl serum as previously described (8,15) using the miRNeasy Mini Kit (Qiagen, Germany) with the following modification: synthetic, non-human oligonucleotides (Qiagen, Germany) were added to the Qiazol lysis buffer, glycogen was added to the precipitation at a final concentration of 0.5 mg/mL to enhance precipitation, and columns were washed three times with Ethanol before elution in 30 µl nuclease-free water. Eluted total RNA was stored at -80°C until further analysis.

treatment_protocol: We collected serum samples from all subjects during the summer months (June–August) in 2017 to avoid seasonal bias from variable sunlight exposure. We collected all samples after an overnight fast, in the morning between 8 and 9 a.m. First, we collected venous peripheral blood to normal serum tubes, let them stand and clot in room temperature for 30–60 minutes and then centrifuged them at 2500 x g for 10 minutes. The supernatants were then transferred to 1.5 ml tubes in 250 µl aliquots and stored immediately at -80 °C until analysis.

value: serum

tag: diagnosis

value: PLS3 osteoporosis

tag: pls3 mutation status

value: PLS3 mutation-positive

value: F


title: MN37

description:
control
SAMPLE 15

value: control

value: PLS3 mutation-negative


title: MN31

description:
control
SAMPLE 17


title: Col-0_4h_avrRpt2_Rep2


title: Col-0_0.5h_avrRps4_Rep2


title: MP22

description:
case
SAMPLE 14


title: Biopsy_CIT2_EVLP14

source_name: Biopsy_timepoint end of second cold ischemia


title: MN23

description:
control
SAMPLE 18


title: MN28

description:
control
SAMPLE 13


title: Col-0_0.5h_avrRpm1_Rep1


title: Col-0_8h_avrRpt2_Rep3


title: Col-0_0.5h_EV_Rep3

value: EV


title: MP24

description:
case
SAMPLE 12

value: M


title: N1

value: 55 years


title: MN33

description:
control
SAMPLE 10


title: MP35

description:
case
SAMPLE 11


title: Biopsy_CIT2_EVLP12


title: Biopsy_CIT1_EVLP14


title: Col-0_8h_avrRpt2_Rep2


title: Col-0_8h_avrRpm1_Rep3


title: Col-0_0.5h_avrRps4_Rep1


title: Pericytes_Dermal 2

city: Baltimore

first: Jiajia

last: Xu

state: MD

address: 720 Rutland Avenue

department: Pathology-Surgical Pathology

institute: The Johns Hopkins University School of Medicine

description: Skin

hyb_protocol: 17 hours at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
Affymetrix CEL files were extracted with the Partek GS 7.0 platform and their data RMA and quantile-normalized to create log2 transcript signal values, which were used in subsequent ANOVA analysis.
Clariom_D_Human.r1.pgf
Clariom_D_Human.na36.hg38.transcript.csv

source_name: Skin tissue

label_protocol: RNA was labeled with the Affymetrix GeneChip WT PLUS Reagent Kit using the manufacturer's protocol.

growth_protocol: CD146+ periosteal cells were isolated from human periosteum or abdominoplasties via fluorescence activated cell sorting (FACS). All cells were cultured in DMEM medium ( Gibco) with 10% FBS, 50% EBM2(Lonza) and 1% penicillin/streptomycin (Life)

extract_protocol: Total RNA were extracted using Trizol and chloroform then washed and purified by isopropanol and 75% ethanol.

treatment_protocol: not applicable

value: skin tissue

tag: cell type

value: pericyte


title: Pericytes_Dermal 3

description: Skin


title: MN25

description:
control
SAMPLE 9


title: Biopsy_CIT1_EVLP13


title: Pericytes_Adipose 3

description: Fat

source_name: Human fat from liposuction patient 3

value: fat


title: Pericytes_Dermal 1

description: Skin


title: Pericytes_Adipose 2

description: Fat

source_name: Human fat from liposuction patient 2


title: Col-0_0.5h_EV_Rep2


title: Biopsy_CIT2_EVLP13


title: Biopsy_CIT2_EVLP15


title: Biopsy_CIT1_EVLP12


title: MP27

description:
case
SAMPLE 7


title: Col-0_8h_avrRpt2_Rep1


title: Biopsy_CIT2_EVLP11


title: Col-0_8h_avrRps4_Rep3


title: MN24

description:
control
SAMPLE 8


title: Pericytes_Adipose 1

description: Fat

source_name: Human fat from liposuction patient 1


title: Pericytes_Periosteal 3

description: Foot

source_name: Human foot from amputation

value: periosteum


title: MN22

description:
control
SAMPLE 6


title: Biopsy_CIT2_EVLP10


title: Biopsy_CIT2_EVLP9


title: Biopsy_CIT1_EVLP11


title: Col-0_8h_avrRpm1_Rep2


title: Col-0_8h_avrRps4_Rep2


title: MP21

description:
case
SAMPLE 3


title: Col-0_0.5h_EV_Rep1


title: Col-0_8h_avrRpm1_Rep1


title: MP33

description:
case
SAMPLE 2


title: Col-0_8h_EV_Rep3


title: Biopsy_CIT1_EVLP10


title: Biopsy_CIT2_EVLP8


title: Biopsy_CIT1_EVLP8


title: MN30

description:
control
SAMPLE 4


title: MN36

description:
control
SAMPLE 1


title: Col-0_8h_avrRps4_Rep1


title: Pericytes_Periosteal 1

description: Tibia

source_name: Human Tibia from amputation


title: Biopsy_CIT1_EVLP7


title: Col-0_4h_avrRpt2_Rep3


title: Biopsy_CIT2_EVLP6


title: Col-0_8h_EV_Rep1


title: lip1-cCM

description:
Lipedema
SAMPLE 10

data_processing:
Cq-values were called using the second-derivate maximum method. Data quality was assessed using spike-in controls to determine RNA extraction efficiency, enzymatic inhibition, and overall variability. Data normalization was performed using the global mean (i.e. average Cq-value for all endogenous microRNAs with Cq<35) to obtain delta Cq-values.
Values in the Matrix normalized are global-mean normalized delta Cq-value (dCqs).  Fold Change 1 = sEVs: Lipedema vs Control  Fold Change 2 = cCM: Lipidema/Control

source_name: cCM from supernatant from SVF cells

growth_protocol: The collection of human adipose tissue was approved by the local ethical board with written patient’s consent. Subcutaneous adipose tissue was obtained during routine outpatient liposuction procedures from the hips and outer thighs (“saddlebags”) under local tumescence anaesthesia. Tumescence solution contained one vial Volon-A 10 mg (Dermapharm), three vials Suprarenin 1 mg/mL (Sanofi), 45 mL bicarbonate 8.4% (Fresenius Kabi) and 60 mL Xylocaine 2% including Lidocaine 0.04% (Astra Zeneca). The harvesting cannulas were triport and 4 mm in diameter (MicroAire System power-assisted liposuction). Table 1 provides patient characteristics. 100 mL liposuction material was transferred to a blood bag (Macopharma, Langen, Germany) and washed with an equal volume of phosphate buffered saline (PBS) to remove blood and tumescence solution. Next, for tissue digestion PBS was replaced with 0.2 U/mL collagenase NB4 (Nordmark, Uetersen, Germany) dissolved in 100 mL PBS containing Ca2+/Mg2+ and 25 mM N-(2-hydroxyethyl)piperazine-N′-(2-ethanesulfonic acid) (HEPES; Sigma, Vienna, Austria) resulting in a final collagenase concentration of  0.1 U/mL. The blood bag was incubated at 37 °C under moderate shaking (180 rpm) for 1 h. The digested tissue was transferred into 50 mL-tubes (Greiner, Kremsmünster, Austria). After centrifugation at 1200 xg for 7 min the cell pellet was incubated with 100 mL erythrocyte lysis buffer for 5 min at 37 °C to eliminate red blood cells. The supernatant was aspirated after centrifugation for 5 min at 500 xg. The pellet was washed with PBS and ﬁltrated through a 100-µm cell strainer (Greiner). After another centrifugation step at 500 xg for 5 min the supernatant was removed. The isolated SVF was resuspended in filtrated (0.22 µm; Merck, Vienna, Austria) medium before: DMEM-low glucose (Lonza, Vienna, Austria) containing 10% fetal calf serum (FCS; Sigma, Vienna, Austria), 2 mM L-glutamine (Lonza). Cell number was determined using trypan blue exclusion and quantification in a cell counter (TC-20, Bio-Rad, Vienna, Austria).

extract_protocol: Total RNA extraction was performed using 200 µl cCM or 200 µl pooled sEV fractions together with the miRNeasy mini kit (Qiagen). Synthetic oligonucleotides obtained from the miRCURY Spike-In kit (Qiagen) were added to the Qiazol lysis buffer before homogenization of the cCM/sEV samples. Glycogen (5 mg/ml) was added to the chloroform extract at 1:100 dilution to enhance precipitation. All other steps were performed according to the recommendations of the manufacturer. Total RNA was eluted in 30 µl nuclease-free water and stored at -80°C in low-bind tubes (Eppendorf) until further analysis.

treatment_protocol: For miRNA analysis, DMEM-low glucose containing 10% FCS, 2 mM L-glutamine was filtrated using 0.22 µm filter cups to remove large EVs. 6x106 freshly isolated SVF cells were seeded in 22 mL filtrated medium in a T175 flask. The cell supernatant was collected after 24 h in a 50 ml-tube and centrifuged at 500 xg for 15 min (Eppendorf, 5804R; Vienna, Austria) to remove cellular debris. After transfer to a new tube (VWR, Vienna, Austria) and centrifugation at 14 000 xg for 15 min at 4°C (Heraeus Multifuge X3R; Thermo Fisher Scientific, Vienna, Austria) the supernatant was filtrated through a 0.8 µm strainer (VWR) to prepare clarified cell culture conditioned media (cCM), which was immediately frozen and stored at –80°C until further analysis. The frozen cCM samples were shipped on dry ice to TAmiRNA GmbH, Vienna Austria. cCM was concentrated to 1 mL using centrifugation-based ultrafiltration. Briefly, 20 mL of cCM were transferred to an Amicon 30 kDa ultrafiltration column and centrifuged at room temperature for 15 minutes. Residual volumes were measured and diluted to 1 mL using sterile PBS solution. Small extracellular vesicles (sEVs) were subsequently purified from cCM by size exclusion chromatography using qEV70s single columns (Izon): 150 µl of concentrated cCM were loaded based on recommendations from the manufacturer, and fraction 8 – 11 were collected and pooled to obtained the fraction of purified sEVs. Nanoparticle tracking analysis (NTA) was performed on all sEV samples to determine particle size and concentration.

value: SVF

tag: rna fraction

value: concentrated conditioned media (cCM)

value: 24 hours


title: Pericytes_Periosteal 2

description: Tibia


title: Col-0_4h_avrRpm1_Rep3

value: wildtype (Col-0)


title: lip3-cCM

description:
Lipedema
SAMPLE 12


title: co3-cCM

description:
control
SAMPLE 9


title: Biopsy_CIT1_EVLP6

value: lung


title: Biopsy_CIT2_EVLP5


title: co2-cCM

description:
control
SAMPLE 8


title: Biopsy_CIT1_EVLP5


title: co1-cCM

description:
control
SAMPLE 7


title: lip2-cCM

description:
Lipedema
SAMPLE 11


title: lip2-sEV

description:
Lipedema
SAMPLE 5

source_name: sEV from supernatant from SVF cells

value: small extracellular vesicles (sEV)


title: lip3-sEV

description:
Lipedema
SAMPLE 6


title: lip1-sEV

description:
Lipedema
SAMPLE 4


title: Biopsy_CIT1_EVLP3


title: E14.5_9hrs_Exp_rep4

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 6.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

organism: Mus musculus

source_name: Organ homogenate, E14.5 lung

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

growth_protocol: All mice used in this experiment come from our colony at the ZTL animal housing facility, and are maintained according to their standard housing procedures. Pregnant female mice were transferred to the Gaffkystraße animal facility on the day of doxycycline administration. After doxycycline treatment, the pregnant females were housed according to Gaffkystraße's standard housing protocol until their sacrifice 9hrs later.

extract_protocol: Lungs were harvested in PBS. The left lobe of each sample was lysed in QIAzol. Total RNA was isolated using the QIAgen miRNeasy Mini Kit according to manufacturer's instructions.

treatment_protocol: Pregnant females were injected intraperitonally with 0.0015mg doxycycline per gram mouse body weight. Females were sacrificed 9hrs post injection. Embryos were removed and placed in PBS on ice. Embryonic lungs were harvested under sterile conditions and processed for RNA isolation. Embryonic tissue was taken from each sample for genotyping.

value: Organ homogenate, E14.5 lung


title: co3-sEV

description:
control
SAMPLE 3


title: E14.5_9hrs_Ctrl_rep4


title: E14.5_9hrs_Exp_rep3


title: E14.5_9hrs_Ctrl_rep3


title: Biopsy_CIT1_EVLP4


title: Biopsy_CIT2_EVLP2


title: Biopsy_CIT2_EVLP4


title: co2-sEV

description:
control
SAMPLE 2


title: co1-sEV

description:
control
SAMPLE 1


title: E14.5_9hrs_Ctrl_rep2


title: Heat deacc t=4d replicate 3

status: Public on Jun 21 2020

city: Cerdanyola del Vallès

first: ANTONI

last: GARCIA-MOLINA

state: Barcelona

address: Campus UAB - CRAG Building

department: Plant Development and Signal Transduction

country: Spain

institute: Centre for Research in Agrigenomics

description:
FPKM_Heat
HK_4TC

data_processing:
Illumina sequencing reads were generated by Novogene Biotech (Beijing, China).
Reads were treated with Trimmomatic to remove adapter sequences, aligned to the Araport11 genome reference with Tophat 2.1.1, FPKM files created with Cufflinks and the counts and differential expression files generated with featureCounts/DESeq2.
Genome_build: Araport11
Supplementary_files_format_and_content: Excel spread sheet including FPKM counts provided according to Cufflinks.

source_name: Rossete leafs

growth_protocol: Arabidopsis thaliana Col-0 seeds were stratified at 4ºC for 2 days, sown in 9x9 cm pots in a density of appr. 50-100 seeds per pot and cultivated in LED-41 HIL2 Percival cabinets under standard long day conditions [16 h light (80 µmol photons·m-2·s-1) at 22ºC and 8 h darkness at 18ºC].

extract_protocol:
Total RNA from plants was isolated using Trizol and purified using the Direct-zol RNA MiniPrep Plus columns (Zymo Research) according to the manufacturer’s instructions.
Generation of long-non-coding RNA (lncRNA-Seq) libraries and sequencing using the paired-end mode were conducted at Novogene Biotech (Beijing, China) with standard Illumina protocols. Libraries were sequenced on an Illumina HiSeq 2500 system.
ncRNA-Seq for First Read unstranded libraries

treatment_protocol: After 14 days of growth, the light intensity was increased to 450 µmol photons·m-2·s-1  to investigate acclimation to high light. For heat and cold treatments, long day conditons with continuous 32ºC or continuous 4ºC and 35 µmol photons·m-2·s-1 were applied, respectively. Acclimation treatments were started 4 hours after light onset and applied for 4 days. Finally, the plants were brought back to standard conditions for 4 additional days to assess de-acclimation. Sampling was carried out at 1 min, 15 min, 3 h, 2 d and 4 d  for treatments by fast harvesting in liquid nitrogen. Time-points 1 min and 15 min were compared to control time point 0 min and de-acclimation 1 min to control 4 d. For 3 h, 2 d and 4 d acclimation and de-acclimation, samples were compared to the corresponding control.

tag: Stage

value: 14-d-old plants

tag: ecotype

value: Heat deacc

tag: time point

tag: replicate


title: Heat deacc t=2d replicate 3

description:
FPKM_Heat
HK_2TC


title: Heat deacc t=4d replicate 2

description:
FPKM_Heat
HK_4TB


title: Heat deacc t=2d replicate 2

description:
FPKM_Heat
HK_2TB


title: Heat deacc t=4d replicate 1

description:
FPKM_Heat
HK_4TA


title: Heat deacc t=2d replicate 1

description:
FPKM_Heat
HK_2TA


title: Heat deacc t=3h replicate 2

description:
FPKM_Heat
HK_3hB


title: Heat deacc t=3h replicate 3

description:
FPKM_Heat
HK_3hC


title: Biopsy_CIT1_EVLP2

tag: paired samples


title: Biopsy_CIT2_EVLP3

tag: tissue


title: Biopsy_CIT1_EVLP1


title: Heat deacc t=3h replicate 1

description:
FPKM_Heat
HK_3hA


title: E14.5_9hrs_Exp_rep2


title: E14.5_9hrs_Exp_rep1


title: E14.5_9hrs_Ctrl_rep1


title: Heat deacc t=1min replicate 2

description:
FPKM_Heat
HK_1B


title: Heat deacc t=15min replicate 3

description:
FPKM_Heat
HK_15C


title: Heat deacc t=15min replicate 2

description:
FPKM_Heat
HK_15B


title: Heat deacc t=15min replicate 1

description:
FPKM_Heat
HK_15A


title: Heat t=4d replicate 3

description:
FPKM_Heat
H_4TC

value: Heat


title: Heat deacc t=1min replicate 1

description:
FPKM_Heat
HK_1A


title: MP25

description:
case
SAMPLE 5

value: serum

value: PLS3 osteoporosis

value: PLS3 mutation-positive

tag: gender


title: Heat t=4d replicate 1

description:
FPKM_Heat
H_4TA


title: Biopsy_CIT2_EVLP1


title: Heat t=4d replicate 2

description:
FPKM_Heat
H_4TB


title: Heat t=2d replicate 3

description:
FPKM_Heat
H_2TC


title: Heat t=2d replicate 2

description:
FPKM_Heat
H_2TB


title: Heat t=2d replicate 1

description:
FPKM_Heat
H_2TA


title: Heat t=3h replicate 2

description:
FPKM_Heat
H_3hB


title: Heat t=15min replicate 3

description:
FPKM_Heat
H_15C


title: Heat t=3h replicate 3

description:
FPKM_Heat
H_3hC


title: Heat t=3h replicate 1

description:
FPKM_Heat
H_3hA


title: Heat t=15min replicate 1

description:
FPKM_Heat
H_15A


title: Heat t=1 min replicate 1

description:
FPKM_Heat
H_1A

value: 1 min


title: Cold deacc t=4d replicate 2

description:
FPKM_Cold
CK_4TB

value: Cold deacc


title: Cold deacc t=4d replicate 3

description:
FPKM_Cold
CK_4TC


title: Heat t=15min replicate 2

description:
FPKM_Heat
H_15B


title: Heat t=1 min replicate 2

description:
FPKM_Heat
H_1B


title: Cold deacc t=2d replicate 2

description:
FPKM_Cold
CK_2TB


title: Cold deacc t=3h replicate 3

description:
FPKM_Cold
CK_3hC


title: Cold deacc t=2d replicate 1

description:
FPKM_Cold
CK_2TA


title: Cold deacc t=4d replicate 1

description:
FPKM_Cold
CK_4TA


title: Cold deacc t=2d replicate 3

description:
FPKM_Cold
CK_2TC


title: Cold deacc t=15min replicate 3

description:
FPKM_Cold
CK_15C


title: Cold deacc t=15min replicate 2

description:
FPKM_Cold
CK_15B


title: Cold deacc t=1min replicate 1

description:
FPKM_Cold
CK_1A


title: Cold deacc t=3h replicate 2

description:
FPKM_Cold
CK_3hB


title: Cold deacc t=1min replicate 2

description:
FPKM_Cold
CK_1B


title: Cold deacc t=3h replicate 1

description:
FPKM_Cold
CK_3hA


title: Cold deacc t=15min replicate 1

description:
FPKM_Cold
CK_15A


title: Biopsy_CIT2_EVLP7


title: Cold t=2d replicate 3

description:
FPKM_Cold
C_2TC

value: Cold


title: Cold t=4d replicate 3

description:
FPKM_Cold
C_4TC


title: Cold t=4d replicate 2

description:
FPKM_Cold
C_4TB


title: Cold t=2d replicate 2

description:
FPKM_Cold
C_2TB


title: Cold t=2d replicate 1

description:
FPKM_Cold
C_2TA


title: Cold t=4d replicate 1

description:
FPKM_Cold
C_4TA


title: Cold t=3h replicate 3

description:
FPKM_Cold
C_3hC


title: Cold t=15min replicate 2

description:
FPKM_Cold
C_15B


title: Cold t=3h replicate 2

description:
FPKM_Cold
C_3hB


title: Cold t=15min replicate 3

description:
FPKM_Cold
C_15C


title: Cold t=15min replicate 1

description:
FPKM_Cold
C_15A


title: Cold t=1 min replicate 2

description:
FPKM_Cold
C_1B


title: HL deacc t=4d replicate 2

description:
FPKM_HL
HLK_4TB

value: HL deacc


title: Cold t=1 min replicate 1

description:
FPKM_Cold
C_1A


title: HL deacc t=4d replicate 1

description:
FPKM_HL
HLK_4TA


title: HL deacc t=2d replicate 3

description:
FPKM_HL
HLK_2TC


title: HL deacc t=2d replicate 1

description:
FPKM_HL
HLK_2TA


title: HL deacc t=3h replicate 3

description:
FPKM_HL
HLK_3hC


title: HL deacc t=3h replicate 1

description:
FPKM_HL
HLK_3hA


title: HL deacc t=1min replicate 2

description:
FPKM_HL
HLK_1B


title: HL deacc t=3h replicate 2

description:
FPKM_HL
HLK_3hB


title: HL deacc t=15min replicate 1

description:
FPKM_HL
HLK_15A


title: HL deacc t=15min replicate 2

description:
FPKM_HL
HLK_15B


title: HL t=2d replicate 3

description:
FPKM_HL
HL_2TC

value: HL


title: HL deacc t=1min replicate 1

description:
FPKM_HL
HLK_1A


title: HL t=4d replicate 3

description:
FPKM_HL
HL_4TC


title: Cold t=3h replicate 1

description:
FPKM_Cold
C_3hA


title: HL t=2d replicate 2

description:
FPKM_HL
HL_2TB


title: HL t=3h replicate 1

description:
FPKM_HL
HL_3hA


title: HL t=3h replicate 2

description:
FPKM_HL
HL_3hB


title: HL t=2d replicate 1

description:
FPKM_HL
HL_2TA


title: HL t=15min replicate 3

description:
FPKM_HL
HL_15C


title: HL deacc t=4d replicate 3

description:
FPKM_HL
HLK_4TC


title: CBMS1_Day7Diff_ESC_single_MidS-38

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description:
80kb resolution data
Sample from GSE108556 (GSM2905071)

library_source: genomic

data_processing:
Sequence reads were trimmed to remove adapter sequences using the cutadapt program before mapping. For WGA samples, we performed a two-step adapter trimming, first removing the Illumina adapter based on the index of each NGS library and then removing the SEQXE adapter. As the SEQXE adapter sequence was not available, we empirically estimated it as the sequence that repeatedly appeared near the 5’ end.
Trimmed reads were mapped into mm9 and CBMS1-specific (CBA/MsM) diploid genome based on mm9 genomeby using bwa (ver: 0.7.10-r789, command: bwa aln => bwa samse). CBMS1-specific diploid genome was constructed as described in Sakata et al. Development (2017) with minor modifications using CBA or MsM strain genomic reads. Duplicated reads mapped into mm9 were removed by using picard tool and the reads overlapped with mm9 black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered out. The mapped reads with MAQP>10 were used for the further analysis. For the diploid genome mapping, we defined MAPQ>16 as the allele specific reads and used the liftover tool (UCSC Genome Browser) to convert to the mm9 genome coordinates. After this, duplicate reads identified as an identical chromosome start position and strand information were filtered out.
Single-cell data (CBMS1, differentiated CBMS1, EpiSC un-resolved at 80-kb): first, we counted the reads in non-overlapping 80-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the merged G1 control. Binarization was performed using the Mappability corrected 25per-S (25% S-phase) , Mid-S (50% S-phase), 75per-S (75% S-phase) reads described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy"; options for Mid-S, 75per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy"; 1-somy, unreplicated; 2-somy, replicated]. In the processed data files, replicated bin was shown as 1, unrelicated bin was shown as -1, and no-data was shown as 0. “Repliscore” was calculated as a percentage of replicated bins in the total number of replicated and unreplicated bins.
Single-cell haplotype-resolved chrX data (d0, d2, d7): after the specific filtering steps for haplotype-resolved data, we counted the reads in non-overlapping 400-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the filtered merged G1 control. Binarization was performed as described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy" ; options for Mid-S, 75per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy"].
For paired-end reads, only "R1" (Fwd) reads were used for the analysis.
Binarized 40kb data: Sample_Name_40k_100S_MAP_2HMM2_eps0.01.binary.bedGraph
Supplementary_files_format_and_content:   We provide three types of processed data files. One is the binarized data (scRepliseq_data_884cells_G1_Sphase_binary_data_80kb.txt). Second is the sample information data (scRepliseq_data_sample_Info.txt). Third is the haplotype-resolved Mid-S binarized data of chrX (scRepliseq_d0_33_CBA_XX_chrX_only_400kb.txt, scRepliseq_d0_33_MsM_XX_chrX_only_400kb.txt ,scRepliseq_d2_27_CBA_XX_chrX_only_400kb.txt, scRepliseq_d2_27_MsM_XX_chrX_only_400kb.txt, scRepliseq_d7_36_XX_Xa_chrX_only_400kb.txt ,scRepliseq_d7_36_XX_Xi_chrX_only_400kb.txt). We also provide README file for the description of each processed file.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

molecule: genomic DNA

source_name: Day7 Differentiated CBMS1 ESC

growth_protocol: CBMS1 mESCs have been described (Murakami et al. Development, 2011) and were grown in 2i/LIF medium as described (Hayashi K et al., Nat. Protoc., 2013). EpiSCs (female) and their culture protocol have been described and were grown in Activin/FGF medium as described (Tesar et al. 2007).

extract_protocol:
For single cells samples, cells were sorted with a Sony SH800 cell sorter using the single-cell mode. Sample preparations were based on the previous study (Baslan et al., Genome Res. 2015). Extracted gDNA samples were subjected to WGA with a SeqPlex kit (Sigma, SEQXE). Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu).
NGS libraries were constructed with a NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions, with slight modifications based on the previous study (Kadota et al., Sci. Rep. 2017). For a multi-plex NGS run, a SeqCap adapter kit A/B (Roche, 07141530001/ 07141548001) and NEXTflex DNA barcode (Bio Scientific, NOVA) were used. The samples were subjected to NGS on an Illumina Hiseq 1500 system (80-bp length, single-read).

treatment_protocol: For differentiation, CBMS1 mESCs were differentiated to EpiLCs for 2 days and then switched to aggregation culture (EB/embryoid body culture) in Nunclon Sphera 96U-well plates (ThermoFisher, #174925), starting from 2,000 EpiLCs per well exactly as described (Hayashi K et al. Nat. Protoc., 2013), except for the use of plain GK15 medium (Hayashi K et al. Nat. Protoc., 2013) without any additional factors added during the aggregation culture. This process is practically identical to the SFEBq neural method of mESC differentiation (serum-free floating culture of EB-like aggregates with quick reaggregation) (Eiraku et al. Nat. Protoc., 2012) except that we started from EpiLCs instead of mESCs. In our hands, this resulted in efficient formation of neurectoderm cells based on gene expression after 7 days of differentiation (2 days to EpiLCs and then 5 additional days of EB culture).

tag: strain

value: CBA/MsM

value: day7differentiated ESCs

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

value: FALSE

tag: cell cycle phase

value: MidS


title: CBMS1_Day7Diff_ESC_single_MidS-40

description:
80kb resolution data
Sample from GSE108556 (GSM2905073)

value: XX

value: MsM

value: CBA

value: TRUE


title: HL t=15min replicate 2

description:
FPKM_HL
HL_15B

value: 14-d-old plants

tag: treatment


title: CBMS1_Day7Diff_ESC_single_MidS-37

description:
80kb resolution data
Sample from GSE108556 (GSM2905070)

tag: cell type


title: CBMS1_Day7Diff_ESC_single_MidS-36

description:
80kb resolution data
Sample from GSE108556 (GSM2905069)


title: HL t=15min replicate 1

description:
FPKM_HL
HL_15A


title: HL deacc t=2d replicate 2

description:
FPKM_HL
HLK_2TB


title: HL t=1 min replicate 2

description:
FPKM_HL
HL_1B


title: HL deacc t=15min replicate 3

description:
FPKM_HL
HLK_15C


title: CBMS1_Day7Diff_ESC_single_MidS-34

description:
80kb resolution data
Sample from GSE108556 (GSM2905067)


title: HL t=1 min replicate 1

description:
FPKM_HL
HL_1A


title: CBMS1_Day7Diff_ESC_single_MidS-32

description:
80kb resolution data
Sample from GSE108556 (GSM2905065)


title: Control deacc t=4d replicate 2

description:
FPKM_Control
KK_4TB

value: Control deacc


title: HL t=3h replicate 3

description:
FPKM_HL
HL_3hC


title: CBMS1_Day7Diff_ESC_single_MidS-27

description:
80kb resolution data
Sample from GSE108556 (GSM2905060)


title: CBMS1_Day7Diff_ESC_single_MidS-26

description:
80kb resolution data
Sample from GSE108556 (GSM2905059)


title: Control deacc t=2d replicate 2

description:
FPKM_Control
KK_2TB


title: CBMS1_Day7Diff_ESC_single_MidS-29

description:
80kb resolution data
Sample from GSE108556 (GSM2905062)


title: Control deacc t=2d replicate 1

description:
FPKM_Control
KK_2TA


title: CBMS1_Day7Diff_ESC_single_MidS-21

description:
80kb resolution data
Sample from GSE108556 (GSM2905054)


title: Control deacc t=3h replicate 2

description:
FPKM_Control
KK_3hB


title: CBMS1_Day7Diff_ESC_single_MidS-35

description:
80kb resolution data
Sample from GSE108556 (GSM2905068)


title: Control deacc t=2d replicate 3

description:
FPKM_Control
KK_2TC


title: Control deacc t=3h replicate 1

description:
FPKM_Control
KK_3hA


title: CBMS1_Day7Diff_ESC_single_MidS-17

description:
80kb resolution data
Sample from GSE108556 (GSM2905050)


title: CBMS1_Day7Diff_ESC_single_MidS-16

description:
80kb resolution data
Sample from GSE108556 (GSM2905049)


title: CBMS1_Day7Diff_ESC_single_MidS-14

description:
80kb resolution data
Sample from GSE108556 (GSM2905047)


title: Control t=4d replicate 2

description:
FPKM_Control
K_4TB

value: Control


title: Biopsy_CIT1_EVLP9

tag: timepoint

value: lung


title: CBMS1_Day7Diff_ESC_single_MidS-12

description:
80kb resolution data
Sample from GSE108556 (GSM2905045)


title: Control t=4d replicate 1

description:
FPKM_Control
K_4TA

tag: Stage


title: Control deacc t=4d replicate 3

description:
FPKM_Control
KK_4TC

tag: ecotype


title: CBMS1_Day7Diff_ESC_single_MidS-13

description:
80kb resolution data
Sample from GSE108556 (GSM2905046)


title: Control t=4d replicate 3

description:
FPKM_Control
K_4TC

tag: time point


title: CBMS1_Day7Diff_ESC_single_MidS-11

description:
80kb resolution data
Sample from GSE108556 (GSM2905044)


title: Control deacc t=4d replicate 1

description:
FPKM_Control
KK_4TA

tag: replicate


title: CBMS1_Day7Diff_ESC_single_MidS-23

description:
80kb resolution data
Sample from GSE108556 (GSM2905056)


title: Control t=2d replicate 1

description:
FPKM_Control
K_2TA


title: Control t=2d replicate 2

description:
FPKM_Control
K_2TB


title: Control t=3h replicate 3

description:
FPKM_Control
K_3hC


title: CBMS1_Day7Diff_ESC_single_MidS-06

description:
80kb resolution data
Sample from GSE108556 (GSM2905039)


title: Control t=3h replicate 1

description:
FPKM_Control
K_3hA


title: Control t=3h replicate 2

description:
FPKM_Control
K_3hB


title: CBMS1_Day7Diff_ESC_single_MidS-07

description:
80kb resolution data
Sample from GSE108556 (GSM2905040)


title: Control deacc t=3h replicate 3

description:
FPKM_Control
KK_3hC


title: CBMS1_Day7Diff_ESC_single_MidS-18

description:
80kb resolution data
Sample from GSE108556 (GSM2905051)


title: CBMS1_Day7Diff_ESC_single_MidS-04

description:
80kb resolution data
Sample from GSE108556 (GSM2905037)


title: Control t=0 min replicate 3

description:
FPKM_Control
K_0C

value: 0 min


title: CBMS1_Day7Diff_ESC_single_MidS-03

description:
80kb resolution data
Sample from GSE108556 (GSM2905036)


title: Control t=0 min replicate 1

description:
FPKM_Control
K_0A


title: CBMS1_Day7Diff_ESC_single_MidS-02

description:
80kb resolution data
Sample from GSE108556 (GSM2905035)


title: EAE_EHP_2

city: Córdoba

first: Eduardo

last: Muñoz

address: Avda Menéndez Pidal s/n

institute: Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), University of Córdoba

data_processing:
Pre-processing: Sequences were pre-processed with Trimmomatic v0.36
Alignment: Pre-processed sequences were algined to mouse genome assembly mm10 using HISAT2 v2.1.0
Counts per gene were obtained with featureCounts v1.6.1 using the in-built RefSeq annotation for mm10 genome assembly
The raw counts were then analyzed with DESeq2 v1.20.0 excluding those genes with less than 15 counts across samples
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file include raw counts obtained from featureCounts

molecule: polyA RNA

source_name: Spinal cord

extract_protocol:
Total RNA was isolated from spinal cord tissue using QIAzol lysis reagent (Quiagen, Hilden, Germany) and purified with RNAEasy Lipid Tissue Mini kit (Quiagen).
Samples were processed for high throughput sequencing using poly-A selection with the TruSeq Stranded mRNA Library Prep Kit (Cat. No. RS-122-2101, Illumina, San Diego, CA, USA). In brief, 1 µg of total RNA from each sample was used to construct a cDNA library, followed by sequencing on the Illumina HiSeq 2500 system with single end 50 bp reads and ~40 millions of reads per sample.

value: Spinal cord

tag: condition


title: EAE_EHP_1

tag: tissue


title: EAE_EHP_3


title: CBMS1_Day7Diff_ESC_single_MidS-01

description:
80kb resolution data
Sample from GSE108556 (GSM2905034)


title: CBMS1_Day7Diff_ESC_single_MidS-09

description:
80kb resolution data
Sample from GSE108556 (GSM2905042)


title: CBMS1_ESC_single_MidS-49

description:
80kb resolution data
Sample from GSE108556 (GSM3521504)

source_name: CBMS1 ESC

value: embryonic stem cell


title: CBMS1_ESC_single_MidS-48

description:
80kb resolution data
Sample from GSE108556 (GSM3521503)


title: CBMS1_Day7Diff_ESC_single_MidS-08

description:
80kb resolution data
Sample from GSE108556 (GSM2905041)


title: EAE_2

value: EAE


title: CBMS1_ESC_single_MidS-50

description:
80kb resolution data
Sample from GSE108556 (GSM3521505)

value: CBA/MsM


title: Control t=2d replicate 3

description:
FPKM_Control
K_2TC


title: CBMS1_ESC_single_MidS-47

description:
80kb resolution data
Sample from GSE108556 (GSM3521502)


title: EAE_1


title: Control3


title: CBMS1_ESC_single_MidS-46

description:
80kb resolution data
Sample from GSE108556 (GSM3521501)


title: CBMS1_ESC_single_MidS-45

description:
80kb resolution data
Sample from GSE108556 (GSM3521500)


title: Control1


title: CBMS1_ESC_single_MidS-42

description:
80kb resolution data
Sample from GSE108556 (GSM3521497)


title: CBMS1_ESC_single_MidS-44

description:
80kb resolution data
Sample from GSE108556 (GSM3521499)


title: CBMS1_ESC_single_MidS-41

description:
80kb resolution data
Sample from GSE108556 (GSM3521496)


title: CBMS1_ESC_single_MidS-51

description:
80kb resolution data
Sample from GSE108556 (GSM3521506)


title: ZR-75-1 (2)

city: Boston

first: Kartik

last: Subramanian

address: 200 Longwood Avenue

institute: Harvard Medical School

data_processing:
If a sample was run twice for increased depth, the two resulting fastq files (run1_*.fastq and run2_.fastq* and represented by separate SRRs) were merged into a single file
Reads were trimmed and clipped for quality control in cutadapt v1.12
Read quality was checked for each sample using FastQC 0.11.5
High-quality reads were then aligned against the whole genome build GRCh38  using the Bcbio-nextgen software (https://bcbio-nextgen.readthedocs.io/).
The resultant counts matrices were normalized by 3 different approaches: TPM, RPKM, or variance stabilized transfom (VST)
Genome_build: GRCh38
Supplementary_files_format_and_content: counts file (.csv) with rows as entrez gene ids (coding and non-coding) and samples (cell lines) as columns.

source_name: breast cancer cell line

growth_protocol: All cell lines were grown in their recommended growth media, and maintained at 37˚C and 5% CO2 unless otherwise specified

extract_protocol:
Cells were washed 2 x with PBS, and lysed with RLT + 1% (v/v) bME. Each lysate was passed through a Qiashredder column, and RNA was extracted using an RNeasy kit acoording to the manufacturer's instructions with a 20 minute on column DNase digestion.
Libraries were prepared using a TruSeq Stranded mRNA sample preparation kit

treatment_protocol: Cells were seeded in 10 cm plates and grown until they reached ~40-50% confluency

tag: cell line

tag: receptor status

value: ER+/PR-

tag: molecular subtype

value: Luminal A


title: ZR-75-1 (3)


title: ZR-75-1 (1)


title: ZR-75-30

value: Luminal B


title: CBMS1_ESC_single_MidS-40

description:
80kb resolution data
Sample from GSE108556 (GSM3521495)

tag: strain

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

value: MidS


title: EAE_3


title: UACC-812


title: CBMS1_ESC_single_MidS-39

description:
80kb resolution data
Sample from GSE108556 (GSM3521494)

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%


title: SUM52PE


title: CBMS1_ESC_single_MidS-37

description:
80kb resolution data
Sample from GSE108556 (GSM3521492)

tag: cell type

tag: cell cycle phase


title: CBMS1_ESC_single_MidS-38

description:
80kb resolution data
Sample from GSE108556 (GSM3521493)


title: SUM44PE

value: Luminal


title: CBMS1_ESC_single_MidS-36

description:
80kb resolution data
Sample from GSE108556 (GSM3521491)


title: CBMS1_ESC_single_MidS-23

description:
80kb resolution data
Sample from GSE108556 (GSM2905005)

value: FALSE


title: CBMS1_ESC_single_MidS-35

description:
80kb resolution data
Sample from GSE108556 (GSM3521490)


title: SUM229PE

value: TNBC

value: Basal A


title: Control2


title: SUM185PE


title: CBMS1_ESC_single_MidS-13

description:
80kb resolution data
Sample from GSE108556 (GSM2904995)

value: TRUE


title: CBMS1_ESC_single_MidS-03

description:
80kb resolution data
Sample from GSE108556 (GSM2904985)

value: XX


title: CBMS1_ESC_single_MidS-17

description:
80kb resolution data
Sample from GSE108556 (GSM2904999)


title: CBMS1_ESC_single_MidS-43

description:
80kb resolution data
Sample from GSE108556 (GSM3521498)


title: SUM190PT


title: PDX1206

value: Basal


title: MGH358

value: HR+


title: MGH312


title: CBMS1_ESC_single_MidS-02

description:
80kb resolution data
Sample from GSE108556 (GSM2904984)


title: UACC893


title: MDA-MB-415


title: UACC3199


title: MDA-MB-175VII


title: CBMS1_ESC_single_G1-12

description:
80kb resolution data
Sample from GSE108556 (GSM3521523)


title: CBMS1_ESC_single_G1-11

description:
80kb resolution data
Sample from GSE108556 (GSM3521522)


title: MDA-MB-330


title: CBMS1_ESC_single_G1-10

description:
80kb resolution data
Sample from GSE108556 (GSM3521521)


title: MCF-12A

value: NM

value: Basal B


title: CBMS1_ESC_single_G1-09

description:
80kb resolution data
Sample from GSE108556 (GSM3521520)

value: embryonic stem cell


title: CBMS1_ESC_single_G1-08

description:
80kb resolution data
Sample from GSE108556 (GSM3521484)

value: CBA/MsM


title: HCC202


title: HCC1569


title: HCC1187


title: CBMS1_ESC_single_G1-07

description:
80kb resolution data
Sample from GSE108556 (GSM3521483)


title: EVSA-T (1)

value: EVSA-T

value: ER-/PR+


title: EVSA-T (2)


title: CBMS1_ESC_single_75perS-35

description:
80kb resolution data
Sample from GSE108556 (GSM3521601)


title: CBMS1_ESC_single_75perS-34

description:
80kb resolution data
Sample from GSE108556 (GSM3521600)


title: CBMS1_ESC_single_75perS-33

description:
80kb resolution data
Sample from GSE108556 (GSM3521599)


title: EFM-19 (2)

value: ER+/PR+

value: Luminal A


title: CBMS1_ESC_single_75perS-32

description:
80kb resolution data
Sample from GSE108556 (GSM3521598)

value: Single cell


title: EFM-19 (1)


title: CBMS1_ESC_single_MidS-01

description:
80kb resolution data
Sample from GSE108556 (GSM2904983)

value: MidS


title: BT-483


title: CBMS1_ESC_single_75perS-31

description:
80kb resolution data
Sample from GSE108556 (GSM3521597)

value: FALSE


title: CBMS1_ESC_single_75perS-30

description:
80kb resolution data
Sample from GSE108556 (GSM3521596)


title: AU-565

value: Luminal


title: BT-474

value: Luminal B


title: CBMS1_ESC_single_75perS-29

description:
80kb resolution data
Sample from GSE108556 (GSM3521595)


title: 184B5


title: 184A-1 (2)


title: CBMS1_ESC_single_75perS-28

description:
80kb resolution data
Sample from GSE108556 (GSM3521594)


title: CBMS1_ESC_single_75perS-27

description:
80kb resolution data
Sample from GSE108556 (GSM3521593)


title: CBMS1_ESC_single_75perS-26

description:
80kb resolution data
Sample from GSE108556 (GSM3521592)


title: CBMS1_ESC_single_75perS-25

description:
80kb resolution data
Sample from GSE108556 (GSM3521591)


title: CBMS1_ESC_single_G1-06

description:
80kb resolution data
Sample from GSE108556 (GSM3521482)


title: T47D


title: CBMS1_ESC_single_75perS-24

description:
80kb resolution data
Sample from GSE108556 (GSM3521590)

value: TRUE


title: EFM-19 (3)


title: CBMS1_ESC_single_75perS-23

description:
80kb resolution data
Sample from GSE108556 (GSM3521589)

value: XX


title: CBMS1_ESC_single_75perS-22

description:
80kb resolution data
Sample from GSE108556 (GSM3521588)


title: CBMS1_ESC_single_75perS-21

description:
80kb resolution data
Sample from GSE108556 (GSM3521587)


title: SUM149

value: TNBC


title: CBMS1_ESC_single_75perS-20

description:
80kb resolution data
Sample from GSE108556 (GSM3521586)


title: CBMS1_ESC_single_75perS-19

description:
80kb resolution data
Sample from GSE108556 (GSM3521585)


title: CBMS1_ESC_single_75perS-18

description:
80kb resolution data
Sample from GSE108556 (GSM3521566)


title: SKBR3


title: PDXHCI002

source_name: breast cancer PDX model cell line

value: Basal


title: PDXHCI002 (2)


title: SUM1315


title: 192CS4

city: Cambridge

first: Philip

last: Wigge

address: 47 Bateman street

department: Sainsbury Laboratory

country: United Kingdom

institute: Cambridge University

data_processing:
Genome_build: TAIR10
Adapters were trimmed off from raw reads with Trimmomatic with argument "ILLUMINACLIP:$FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15". Raw reads were mapped to the genome "TAIR10" with Bowtie2 under argument:"--no-mixed --no-discordant --no-unal -k2". Any read that mapped to more than one genomic location was discarded. PCR duplicate reads were removed with Picard using default setting.
Genomic binding profile was quantified in RPKM (Reads Per Kilobase per Million mapped reads) using a bin-size of 10bp. "deeptools.bamCoverage" is used.
For each treated ChIP-Seq library, peaks were called against a control 192CS19 using MACS2 with argument "--keep-dup 1 -p 0.1".
Supplementary_files_format_and_content: *.bam: Genomic alignements that were sorted, deduplicated and filtered for uniq-mapped reads.
Supplementary_files_format_and_content: *_RPKM.bw: RPKM-normalised bigwig track at 10bp resolution
Supplementary_files_format_and_content: *.narrowPeak: containing MACS2-called peaks. as described

source_name: seedling

growth_protocol: Seedlings were grown for 10 days under SDs at either 17 or 22 ºC and shifted to 27 ºC  for 2 h at ZT8 or kept at its respective temperature.

extract_protocol:
3 g of seedlings for each treatment were fixed under vacuum for 20 min in 1xPBS (10 mM PO43−, 137 mM NaCl, and 2.7 mM KCl) containing 1% Formaldehyde (F8775 Sigma). The reaction was quenched by adding glycine to a final concentration of 62 mM. ChIP experiments were performed as described19. Anti-c-Myc agarose affinity gel antibody (Sigma, A7470), Anti-HA−Agarose (Sigma, A2095) or Anti-Flag® M2 Affinity Gel (Sigma, A2220) were used for immunoprecipitation.
Sequencing libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina, IP-202-1024) or using NEBNext® Ultra™ II DNA Library Prep Kit (New England BioLabs) and samples were sequenced on the Illumina NextSeq 500 platform.

tag: genotype

tag: cultivar

value: seedling

tag: photoperiod

value: Short day (8L/16D)

tag: temperature

value: single

tag: fragmentation method

value: sonication

tag: chip antibody

value: Anti-Flag M2 Affinity Gel (Sigma, A2220)


title: PDX1328 (2)

tag: cell line


title: 192CS3

tag: tissue

tag: replicate


title: PDX1258 (2)

tag: receptor status

tag: molecular subtype


title: 184A-1 (1)

value: NM

value: Basal B


title: PDX1328


title: PDX1258


title: CBMS1_ESC_single_75perS-17

description:
80kb resolution data
Sample from GSE108556 (GSM3521564)

tag: strain

value: CBA/MsM

value: embryonic stem cell

tag: sample state

tag: xx or xo chromosomes in single cell samples


title: CBMS1_ESC_single_75perS-16

description:
80kb resolution data
Sample from GSE108556 (GSM3521562)

value: Single cell

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%


title: MDAMB468

value: Basal A


title: SUM159


title: 192CS1

tag: genotype


title: CBMS1_ESC_single_75perS-15

description:
80kb resolution data
Sample from GSE108556 (GSM3521560)

tag: cell type

value: FALSE

tag: cell cycle phase


title: MDAMB436


title: MDAMB361

value: Luminal B


title: 192CS2

tag: cultivar

tag: photoperiod

tag: temperature


title: MDAMB231

tag: cell line


title: CBMS1_ESC_single_75perS-14

description:
80kb resolution data
Sample from GSE108556 (GSM3521558)


title: 192CS18

growth_protocol: Seedlings were grown for 10 days under SDs at either 17 or 22 ºC and shifted to 27 ºC  for 2 h at ZT8 or kept at its respective temperature

extract_protocol:
3 g of seedlings for each treatment were fixed under vacuum for 20 min in 1xPBS (10 mM PO43−, 137 mM NaCl, and 2.7 mM KCl) containing 1% Formaldehyde (F8775 Sigma). The reaction was quenched by adding glycine to a final concentration of 62 mM. ChIP experiments were performed as described19. Anti-c-Myc agarose affinity gel antibody (Sigma, A7470), Anti-HA−Agarose (Sigma, A2095) or Anti-Flag® M2 Affinity Gel (Sigma, A2220) were used for immunoprecipitation
Sequencing libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina, IP-202-1024) or using NEBNext® Ultra™ II DNA Library Prep Kit (New England BioLabs) and samples were sequenced on the Illumina NextSeq 500 platform.

value: ELF3pro::ELF3-MYC elf3-1

tag: tissue

tag: fragmentation method

tag: chip antibody


title: CBMS1_ESC_single_75perS-13

description:
80kb resolution data
Sample from GSE108556 (GSM3521556)


title: MDAMB157

tag: receptor status

tag: molecular subtype


title: MDAMB134

value: ER+/PR-

value: Luminal A


title: 192CS17

tag: replicate

value: Anti-c-Myc agarose affinity gel antibody (Sigma, A7470)


title: MCF7

value: ER+/PR+


title: MCF10A


title: CBMS1_ESC_single_75perS-11

description:
80kb resolution data
Sample from GSE108556 (GSM3521551)

tag: strain

tag: sample state

tag: xx or xo chromosomes in single cell samples


title: MCF10A (2)


title: CBMS1_ESC_single_75perS-12

description:
80kb resolution data
Sample from GSE108556 (GSM3521554)

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%


title: HS578T

value: TNBC


title: 189CS16

data_processing:
Genome_build: TAIR10
Adapters were trimmed off from raw reads with Trimmomatic with argument "ILLUMINACLIP:$FA_ADAPTER:6:30:10 LEADING:3 TRAILING:3 MINLEN:36 SLIDINGWINDOW:4:15". Raw reads were mapped to the genome "TAIR10" with Bowtie2 under argument:"--no-mixed --no-discordant --no-unal -k2". Any read that mapped to more than one genomic location was discarded. PCR duplicate reads were removed with Picard using default setting.
Genomic binding profile was quantified in RPKM (Reads Per Kilobase per Million mapped reads) using a bin-size of 10bp. "deeptools.bamCoverage" is used.
For each treated ChIP-Seq library, peaks were called against a control 176CS21 using MACS2 with argument "--keep-dup 1 -p 0.1".
Supplementary_files_format_and_content: *.bam: Genomic alignements that were sorted, deduplicated and filtered for uniq-mapped reads.
Supplementary_files_format_and_content: *_RPKM.bw: RPKM-normalised bigwig track at 10bp resolution
Supplementary_files_format_and_content: *.narrowPeak: containing MACS2-called peaks. as described

tag: genotype

value: ELF3pro::ELF3-MYC elf3-1 x ELF4-ox

value: seedling

value: short days (8L/16D)

value: single


title: HCC70


title: MDAMB453

value: Luminal


title: 189CS17

tag: cultivar

value: sonication


title: CBMS1_ESC_single_75perS-09

description:
80kb resolution data
Sample from GSE108556 (GSM3521547)

value: CBA/MsM

tag: cell type

value: embryonic stem cell

tag: cell cycle phase


title: 189CS10

tag: photoperiod

tag: temperature


title: 189CS11

tag: tissue

tag: fragmentation method


title: HME1

tag: cell line

tag: receptor status

value: NM

value: Basal


title: CBMS1_ESC_single_75perS-10

description:
80kb resolution data
Sample from GSE108556 (GSM3521549)

value: Single cell

value: FALSE


title: HCC1937

tag: molecular subtype

value: Basal A


title: 184RS8

data_processing:
Genome_build: TAIR10
Raw fastq were uploaded to Bluebee Genomics Platform and analysed with Quantseq FWD analysis pipeline (https://www.lexogen.com/quantseq-data-analysis/). Briefly, the raw reads were trimmed with BBDuk and aligned to GTF-annotated genome with STAR.
Supplementary_files_format_and_content: *.txt: TSV table containing abundance of transcripts by STAR.
Supplementary_files_format_and_content: *.bam: Genomic alignment by STAR.

growth_protocol: Arabidopsis seeds were sterilized and sown on standard half-strength Murashige and Skoog-agar (MS-agar) plates at pH 5.7. Sterilized seeds were stratified for 3 days at 4 ºC in the dark and allowed to germinate for 24 hours at 22 ºC under cool-white fluorescent light at 170 μmol m-2 s-1. The plates were then transferred to short photoperiod conditions (SDs, 8-h light and 16-h dark) at different temperatures. Seedlings were grown on plates for 10 days and harvested at the indicated time points.

extract_protocol:
70 mg of seedlings were pooled per tube and total RNA was extracted using MagMAX™-96 Total RNA Isolation Kit (ThermoFisher) according to the manufacturer‘s instruction.
Libraries were prepared using Lexogen QuantSeq 3' mRNA-Seq Library Prep FWD Kit (Illumina) according to manufacturer‘s instruction. The libraries were sequenced on the Illumina NextSeq 500 platform.

value: Short day (8L/16D)

tag: replicate

tag: chip antibody


title: HCC1806


title: HCC38

value: Basal B


title: CBMS1_ESC_single_75perS-08

description:
80kb resolution data
Sample from GSE108556 (GSM3521545)

tag: strain

tag: sample state

tag: xx or xo chromosomes in single cell samples


title: CBMS1_ESC_single_75perS-07

description:
80kb resolution data
Sample from GSE108556 (GSM3521543)

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%


title: CBMS1_ESC_single_75perS-06

description:
80kb resolution data
Sample from GSE108556 (GSM3521541)

tag: cell type


title: HCC1428

value: ER+/PR+

value: Luminal A


title: 184RS6

tag: genotype

tag: cultivar


title: HCC1419


title: HCC1395

value: TNBC


title: CBMS1_ESC_single_75perS-05

description:
80kb resolution data
Sample from GSE108556 (GSM3521489)

tag: cell cycle phase


title: HCC1143


title: 184RS18

tag: tissue

value: seedling

tag: photoperiod

tag: temperature


title: 184RS15

value: ELF3pro::ELF3-Q21 #7

tag: fragmentation method


title: CellSelex_MSC2_cycle11

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: aptamers selected in vitro against IL4 treated MSC2

data_processing: Aptamers were selected using APTANI, a computational method for the identification of target-specific aptamers from HT-SELEX data and secondary structure information. Briefly, APTANI first calculates the relative enrichment of each individual aptamer sequence produced by the HT-SELEX process and then, for each aptamer with an enrichment higher than a pre-selected threshold, predicts all secondary structures in a specific energy range and extracts the motifs represented in these structures. As a result, APTANI returns a list of aptamers, ranked by their abundance and by the presence of structural motifs. Here we used APTANI with default parameters on HT-SELEX data from cycles 1, 6, 10, and 11 and set the enrichment and motif frequency thresholds 0.01% and 0.05%, respectively.

organism: synthetic RNA

source_name: random aptamer library

extract_protocol: cDNA from library 1, 6 ,10 and 11 were amplified by PCR using primers containing truetag illumina adaptors.

tag: target cell line


title: HCC1954

tag: cell line

tag: receptor status

tag: molecular subtype


title: CAMA1

value: ER+/PR-


title: 184RS11

value: ELF3pro::ELF3-Q0 #15

tag: replicate

value: single

tag: chip antibody


title: CellSelex_MSC2_cycle10


title: HCC1500

value: Luminal


title: CBMS1_ESC_single_75perS-03

description:
80kb resolution data
Sample from GSE108556 (GSM3521487)

tag: strain

value: CBA/MsM

value: embryonic stem cell

tag: sample state

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)


title: 184RS10

tag: genotype


title: 184RS7

tag: cultivar


title: CBMS1_ESC_single_75perS-02

description:
80kb resolution data
Sample from GSE108556 (GSM3521486)

tag: cell type

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase


title: CellSelex_MSC2_cycle6


title: CAL51


title: CBMS1_ESC_single_75perS-01

description:
80kb resolution data
Sample from GSE108556 (GSM3521485)


title: CBMS1_ESC_single_25perS-43

description:
80kb resolution data
Sample from GSE108556 (GSM3521584)


title: CAL851


title: 182CS24

tag: tissue

tag: photoperiod

value: short days (8L/16D)

tag: temperature

tag: fragmentation method

value: sonication

value: Anti-HA−Agarose (Sigma, A2095)


title: 22RV1_miR1908

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

institute: National cancer center research institute

hyb_protocol: Gene Expression Hybridization Kit and Gene Expression Wash Pack (Agilent)

scan_protocol: Agilent SureScan G4900DA

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: 22RV1 transfected with miR-1908 mimic

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: Prostate cancer cell lines were cultured in RPMI-1640 (Nissui Pharmaceutical, Tokyo, Japan) supplemented with 10% heat-inactivated FBS and 1% AA at 37 °C in 5% CO2.

extract_protocol:
Total RNA extracted from prostate cancer cells, and 100 ng of RNA for analysis
Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and a Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, Calif.).

treatment_protocol: Human prostate cancer cell line, 22RV1 were transfected with miR-1908 mimic (Ambion, Thermo Fisher Scientific) or negative control #1 mimic at 10nM for 24h.

tag: cell line

tag: treatment

value: transfected with miR-1908 mimic

value: prostate cancer cell line


title: 22RV1_NC1

source_name: 22RV1 transfected with Negative control #1 mimic


title: BT549

tag: receptor status

tag: molecular subtype

value: Basal B


title: CAL120


title: CBMS1_ESC_single_25perS-42

description:
80kb resolution data
Sample from GSE108556 (GSM3521583)

tag: strain

tag: sample state

value: Single cell

value: FALSE


title: 181RS27

value: Short day (8L/16D)

tag: replicate

tag: chip antibody


title: CBMS1_ESC_single_75perS-04

description:
80kb resolution data
Sample from GSE108556 (GSM3521488)

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)


title: 181RS22

tag: genotype

tag: cultivar

value: seedling


title: brm-1_BRIP2-GFP-IP-bio1

city: Guangzhou

first: yaoguang

last: yu

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

data_processing:
The raw reads were mapped to the reference genome (Arabidopsis thaliana genome, TAIR10) with Bowtie for Illumina (Galaxy Version 1.1.2) for DNA sequencing on web https://usegalaxy.org/ with default setting, except that the paired-end was required.
MACS2 (Galaxy Version 2.1.1) was used for peak calling using the following parameters “gsize=119,667,750, bw=300, q=0.01, nomodel, extsize=200”.
The alignments were first converted to Wiggle (WIG) files and the bigwig files were generated using bamCoverage with “-bs 10”, “--normalizeUsing RPKM (reads per kilobase per million)” in DeepTools and then the data were imported into the Integrative Genomics Viewer (IGV) for visualization.
Genome_build: TAIR10
Supplementary_files_format_and_content: peaks.narrowPeak

source_name: Young seedlings

growth_protocol: Plants were grown in 1/2MS media with 22 degree in 16h light/8h dark

extract_protocol:
Lysates were clarified from sonicated protein-DNA complexes were isolated with GFP antibody.
Two ng of ChIP DNA immuoprecipitated by anti-GFP antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Novaseq was used for high-throughput sequencing of the ChIP-seq library.

value: Seedling

tag: developmental stage

tag: antibody

value: GFP (ab290, abcam)


title: BT20

value: TNBC

value: Basal A


title: CellSelex_MSC2_cycle1

tag: target cell line


title: brm-1_BRIP2-GFP-Input

tag: tissue


title: CBMS1_ESC_single_25perS-41

description:
80kb resolution data
Sample from GSE108556 (GSM3521582)

tag: cell type

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase


title: ScopeseqP60

city: Ann Arbor

first: Dogukan

last: Mizrak

state: MI

address: NCRC Building 26, 263S

department: Cardiac Surgery

institute: University of Michigan

description:
PolyA RNA
processed data file: scope_matrix.txt
processed data file: scope_cell.txt

data_processing:
Read 1 and read 2 fastq files were generated on basespace.
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were aligned to the Mus musculus genome and transcriptome annotation (GRCm38, Gencode annotation vM10) using STAR v.2.5.0 with parameters --sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted. Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. To correct for sequencing errors in cell barcodes, we then collapsed CBs that were within Hamming distance one of another cell barcode, had at least 20 unique UMI-gene pairs, and had at least 75% overlap of their UMI-gene pairs. Finally, we repeated UMI error correction and collapse using the error-corrected CBs. A digital gene expression matrix was then generated from these corrected barcode-UMI-gene triplets. We note that for any experiments conducted using the 'V' base modified Drop-seq beads, we adjusted our analytical pipeline to recognize truncated CBs by the presence of excessive 'T' bases one nucleotide downstream of the position used in the pipeline described above.
To analyze the scRNA-seq data from SCOPE-Seq, we first extract the cell-identifying barcode and UMI from Read 1. The sequences in the two sets that are combined to form each cell-identifying barcode have a Hamming distance of at least three for all sequence pairs within each set. Therefore, we correct at most one substitution error in each of the two sequences should one arise from sequencing, oligonucleotide synthesis, or other sources. We only keep reads with a complete cell-identifying barcode. Next, we align the reads from Read 2 using the STAR aligner and keep strand-specific alignments to exons as described above after removing poly(A) tails >7 bases long from the 3’-end of each read. Finally, we use the UMIs to estimate the number of molecules associated with each gene in each cell.
Genome_build: GRCm38
Supplementary_files_format_and_content: SVZGCE_matrix.txt, OBGCE_matrix.txt, SVZNESFLPO_matrix.txt, OBNESFLPO_matrix.txt, and scope_matrix.txt contain the gene expression profiles of each cell.
Supplementary_files_format_and_content: SVZGCE_cell.txt, OBGCE_cell.txt, SVZNESFLPO_cell.txt, OBNESFLPO_cell.txt, and scope_cell.txt contain the ordered cell IDs for each cell in the gene expression matrix.
Supplementary_files_format_and_content: *cell_barcodes.txt files contain ordered cell barcodes for each cell in the gene expression matrix.

source_name: Ventricular-Subventricular Zone

extract_protocol:
mRNA molecules were captured using bead-bound oligo dT(30).
Captured mRNA molecules were reverse transcribed with template switching to obtain cDNA. cDNA was amplified by PCR reactions (14 cycles for Single-cell RNA sequencing and 16 cycles for Scope-seq). Aliquots of amplified cDNA from each sample were pooled, and purified with AMPure XP beads. The purified PCR products were used as input for the Nextera XT reactions to generate the sequencing libraries.

tag: gender

value: Male

tag: age

value: 8-9 weeks

value: Ventricular-Subventricular Zone

tag: number of cells analyzed

tag: number of animals


title: CBMS1_ESC_single_25perS-40

description:
80kb resolution data
Sample from GSE108556 (GSM3521581)

tag: strain

value: CBA/MsM

value: embryonic stem cell

tag: sample state


title: 181RS17

tag: photoperiod

tag: temperature

tag: replicate

value: single

tag: fragmentation method

tag: chip antibody


title: 181RS19

tag: genotype

tag: cultivar


title: NESP70OB

description:
PolyA RNA
processed data file: OBNESFLPO_matrix.txt
processed data file: OBNESFLPO_cell.txt

source_name: Olfactory Bulb

value: 10 weeks

tag: tissue

value: Olfactory Bulb


title: brm-1_BRIP1-GFP-IP-bio1

tag: developmental stage

tag: antibody


title: 181RS16


title: CBMS1_ESC_single_25perS-39

description:
80kb resolution data
Sample from GSE108556 (GSM3521580)

tag: cell type

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase


title: NESP56OB

tag: strain

tag: gender

tag: age

value: 8 weeks

tag: number of cells analyzed

tag: number of animals


title: brm-1_BRIP1-GFP-IP-bio2


title: brm-1_BRIP1-GFP-Input


title: NESP70SVZ

description:
PolyA RNA
processed data file: SVZNESFLPO_matrix.txt
processed data file: SVZNESFLPO_cell.txt


title: brm-1_BRIP2-GFP-IP-bio2


title: 181RS13

tag: photoperiod

tag: temperature

tag: replicate

tag: fragmentation method

tag: chip antibody


title: 181RS14

tag: genotype

tag: cultivar

tag: tissue


title: CBMS1_ESC_single_25perS-38

description:
80kb resolution data
Sample from GSE108556 (GSM3521579)

tag: cell type

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)


title: BRIP2-GFP-IP-bio2

data_processing:
The raw reads were mapped to the reference genome (Arabidopsis thaliana genome, TAIR10) with Bowtie for Illumina (Galaxy Version 1.1.2) for DNA sequencing on web https://usegalaxy.org/ with default setting, except that the paired-end was required.
MACS2 (Galaxy Version 2.1.1) was used for peak calling using the following parameters “gsize=119,667,750, bw=300, q=0.01, nomodel, extsize=200”.
The alignments were first converted to Wiggle (WIG) files and the bigwig files were generated using bamCoverage with “-bs 10”, “--normalizeUsing RPKM (reads per kilobase per million)” in DeepTools and then the data were imported into the Integrative Genomics Viewer (IGV) for visualization.
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files

tag: developmental stage

tag: antibody


title: 181RS12


title: NESP56SVZ

tag: strain

tag: gender

tag: age


title: CBMS1_ESC_single_25perS-37

description:
80kb resolution data
Sample from GSE108556 (GSM3521578)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

value: FALSE

tag: cell cycle phase


title: GCEOB_P70female

description:
PolyA RNA
processed data file: OBGCE_matrix.txt
processed data file: OBGCE_cell.txt

value: Female

tag: number of cells analyzed

tag: number of animals


title: CBMS1_ESC_single_25perS-36

description:
80kb resolution data
Sample from GSE108556 (GSM3521577)


title: CBMS1_ESC_single_25perS-35

description:
80kb resolution data
Sample from GSE108556 (GSM3521576)


title: 181RS11

tag: genotype

value: seedling

tag: photoperiod

value: Short day (8L/16D)

tag: temperature

tag: replicate

tag: fragmentation method

tag: chip antibody


title: BRIP2-GFP-IP-bio1

tag: tissue

value: Seedling

value: GFP (ab290, abcam)


title: 178RS23

value: ELF3pro::ELF3-Q21 #23

tag: cultivar


title: BRIP2-GFP-Input

tag: developmental stage

tag: antibody

value: input


title: GCEOB_P56female

tag: strain

tag: gender


title: GCEOB_P70male

value: Male

tag: age


title: 178RS20

value: ELF3pro::ELF3-Q7 #6


title: BRIP1-GFP-IP-bio2


title: 178RS22

value: ELF3pro::ELF3-Q21 #7


title: CBMS1_ESC_single_25perS-34

description:
80kb resolution data
Sample from GSE108556 (GSM3521575)

value: CBA/MsM

tag: cell type

value: embryonic stem cell

tag: sample state

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%


title: CBMS1_ESC_single_25perS-33

description:
80kb resolution data
Sample from GSE108556 (GSM3521574)

tag: cell cycle phase


title: CBMS1_ESC_single_25perS-32

description:
80kb resolution data
Sample from GSE108556 (GSM3521573)


title: BRIP1-GFP-IP-bio1

tag: genotype


title: BRIP1-GFP-Input


title: GCEOB_P56male

tag: number of cells analyzed

tag: number of animals


title: CBMS1_ESC_single_25perS-31

description:
80kb resolution data
Sample from GSE108556 (GSM3521571)


title: brip1brip2 BRM-GFP-IP-bio2

tag: tissue


title: GCESVZ_P70female

description:
PolyA RNA
processed data file: SVZGCE_matrix.txt
processed data file: SVZGCE_cell.txt

value: 10 weeks

value: Ventricular-Subventricular Zone


title: CBMS1_ESC_single_25perS-30

description:
80kb resolution data
Sample from GSE108556 (GSM3521568)


title: GCESVZ_P56female

value: 8 weeks


title: 178RS17

tag: cultivar

tag: photoperiod

tag: temperature

tag: replicate

value: single

tag: fragmentation method

tag: chip antibody


title: 178RS18

value: ELF3pro::ELF3-Q0 #2


title: 178RS16

value: elf3-1 X ELF4-ox


title: CBMS1_ESC_single_25perS-29

description:
80kb resolution data
Sample from GSE108556 (GSM3521539)

tag: strain

tag: cell type

value: Single cell

value: FALSE


title: GCESVZ_P56male

tag: gender

tag: age


title: brip1brip2 BRM-GFP-Input

value: Seedling

tag: developmental stage

tag: antibody


title: 178RS15

value: seedling

value: Short day (8L/16D)


title: GCESVZ_P70male


title: CBMS1_ESC_single_25perS-28

description:
80kb resolution data
Sample from GSE108556 (GSM3521538)

tag: sample state

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase


title: BRM-GFP-IP-bio2

tag: genotype

tag: tissue

value: GFP (ab290, abcam)


title: CBMS1_ESC_single_25perS-27

description:
80kb resolution data
Sample from GSE108556 (GSM3521537)


title: HSD_E2_Tumor_3

city: Miami

first: Derek

last: Van Booven

state: FL

address: 1501 NW 10th Ave

institute: University of Miami

data_processing:
Reads were automatically trimmed for adapters
Alignment was performed against the human GRCh38 genome with the STAR aligner
Quantification of reads was performed with RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: .tsv raw count matrix

source_name: MCF7 Xenograft Tumor

extract_protocol:
RNA was isolated using
Rneasy Plus Mini Kit/for Xenograft tumor Rneasy Plus Universal Mini Kit.was used
1ug of RNA was used  to contruct the library
RNA libraries were prepared using
NEB Next  Library Preperation Kit.

tag: xenograft

value: NOD-SCIDMice

tag: treatment

value: HSD E2


title: 178RS14

tag: cultivar

tag: photoperiod

tag: temperature

tag: replicate

tag: fragmentation method

tag: chip antibody


title: 177RS8

value: elf4-2 X ELF3-ox


title: HSD_E2_Tumor_2


title: BRM-GFP-Input

tag: developmental stage

tag: antibody

value: input


title: CBMS1_ESC_single_25perS-26

description:
80kb resolution data
Sample from GSE108556 (GSM3521536)

tag: strain

value: CBA/MsM

tag: cell type

value: embryonic stem cell

tag: sample state

tag: xx or xo chromosomes in single cell samples


title: BRM-GFP-IP-bio1


title: HSD_E2_Tumor_1


title: HSD_E1_Tumor_3

value: HSD E1


title: brip1brip2 BRM-GFP-IP-bio1


title: 177RS6


title: CBMS1_ESC_single_25perS-24

description:
80kb resolution data
Sample from GSE108556 (GSM3521534)

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

tag: cell cycle phase


title: HSD_E1_Tumor_2

tag: xenograft

tag: treatment


title: CBMS1_ESC_single_25perS-25

description:
80kb resolution data
Sample from GSE108556 (GSM3521535)


title: CBMS1_ESC_single_25perS-23

description:
80kb resolution data
Sample from GSE108556 (GSM3521533)


title: 177RS5

tag: genotype

tag: cultivar

tag: tissue

tag: photoperiod


title: HSD_E1_Tumor_1


title: 177RS4

tag: temperature

tag: replicate

tag: fragmentation method

tag: chip antibody


title: E2_Tumor_3


title: 177RS3


title: CBMS1_ESC_single_25perS-21

description:
80kb resolution data
Sample from GSE108556 (GSM3521531)

tag: strain

tag: cell type


title: E2_Tumor_2


title: MSC2+IL4, biological rep4

description:
MSC2_IL4_rep4
Gene expression profile of MSC2 cells treated with IL4 for 4 days.

hyb_protocol: According to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004.

data_processing: RMA of .CEL files using Bioconductor affy library and Brainarray custom CDF MGU74Av2_Mm_ENTREZG_21.0.0. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization.

source_name: immortalized MSC2 cell line treated with IL4

growth_protocol: 5e5 MSC2 were incubated for 4 days on a T75 flask in 20ml RPMI (invitrogen) containing 10% of heat inactivated FCS, L-Glutamine (2mM), sodium pyruvate (1mM), streptomycin (150U/ml), and penicillin (200U/ml) in the presence or in the absence of IL4 (100ng/ml, peprotech).

extract_protocol: Trizol extraction of total RNA was performed according to manufacturer guidelines, with minor modifications. Extraction was followed by Qiagen RNeasy column clean-up according to manufacturer instructions.

treatment_protocol: MSC2 were treated with IL-4 (100ng/ml, peprotech) or left untreated. 4 days after treatment initiation, cells were washed twice with PBS and pellet was used for RNA extraction.

tag: strain/background

value: BALB/c syngeneic

tag: cell line

value: immortalized MDSC cell line

tag: experimental condition

value: IL4 (100ng/ml for 4 days)


title: 177RS7

value: single


title: 177RS2


title: MSC2+IL4, biological rep2

description:
MSC2_IL4_rep2
Gene expression profile of MSC2 cells treated with IL4 for 4 days.

scan_protocol: According to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004.


title: E2_Tumor_1


title: MSC2+IL4, biological rep5

description:
MSC2_IL4_rep5
Gene expression profile of MSC2 cells treated with IL4 for 4 days.

label_protocol: According to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004.


title: MSC2+IL4, biological rep3

description:
MSC2_IL4_rep3
Gene expression profile of MSC2 cells treated with IL4 for 4 days.


title: E1_Tumor_3


title: 177RS24

value: ELF3pro::ELF3-Q21 #7


title: 177RS23

value: ELF3pro::ELF3-Q7 #17


title: CBMS1_ESC_single_25perS-18

description:
80kb resolution data
Sample from GSE108556 (GSM3521528)

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

value: FALSE


title: CBMS1_ESC_single_25perS-22

description:
80kb resolution data
Sample from GSE108556 (GSM3521532)

tag: cell cycle phase


title: MSC2+IL4, biological rep1

description:
MSC2_IL4_rep1
Gene expression profile of MSC2 cells treated with IL4 for 4 days.


title: CBMS1_ESC_single_25perS-17

description:
80kb resolution data
Sample from GSE108556 (GSM3521527)


title: E1_Tumor_2

tag: xenograft

tag: treatment


title: MSC2 untreated, biological rep4

description:
MSC2_ctr_rep4
Gene expression profile of MSC2 cells.

source_name: immortalized MSC2 cell line

value: untreated


title: E1_Tumor_1


title: CBMS1_ESC_single_25perS-20

description:
80kb resolution data
Sample from GSE108556 (GSM3521530)


title: 177RS22

tag: genotype

value: ELF3pro::ELF3-Q7 #6

tag: cultivar

tag: tissue

value: seedling

tag: photoperiod

value: Short day (8L/16D)

tag: temperature


title: MSC2 untreated, biological rep3

description:
MSC2_ctr_rep3
Gene expression profile of MSC2 cells.

tag: cell type


title: CBMS1_ESC_single_25perS-15

description:
80kb resolution data
Sample from GSE108556 (GSM3521525)

tag: strain


title: HSD17B14-3

source_name: MCF7 Cell line


title: CBMS1_ESC_single_25perS-19

description:
80kb resolution data
Sample from GSE108556 (GSM3521529)


title: 177RS20

value: ELF3pro::ELF3-Q0 #2

tag: replicate

tag: fragmentation method

tag: chip antibody


title: 177RS1


title: HSD17B14-2


title: MSC2 untreated, biological rep5

description:
MSC2_ctr_rep5
Gene expression profile of MSC2 cells.

tag: strain/background

tag: cell line

tag: experimental condition


title: CBMS1_ESC_single_25perS-14

description:
80kb resolution data
Sample from GSE108556 (GSM3521524)

tag: sample state

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%


title: HSD17B14-1

tag: treatment


title: MSC2 untreated, biological rep2

description:
MSC2_ctr_rep2
Gene expression profile of MSC2 cells.


title: CBMS1_ESC_single_25perS-13

description:
80kb resolution data
Sample from GSE108556 (GSM3521519)

tag: cell cycle phase


title: 177RS10

tag: genotype

value: ELF3pro::ELF3-Q0 #15

tag: cultivar

tag: tissue

tag: photoperiod


title: CBMS1_ESC_single_25perS-16

description:
80kb resolution data
Sample from GSE108556 (GSM3521526)

tag: strain

value: CBA/MsM

tag: cell type


title: MSC2 untreated, biological rep1

description:
MSC2_ctr_rep1
Gene expression profile of MSC2 cells.


title: Control3

value: Control


title: brip1 brip2 brm-1 rep2

data_processing:
Sequencing separately at Novogene, using Illumina Hiseq X-Ten (Sequencing method: Hiseq-PE150).
Reads were mapped to the TAIR10 Arabidopsis genome using TopHat (Galaxy V2.1.1 in usegalaxy.org) with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 4,000 bp were required (Paired-end). Then, mapped reads were assembled according to TAIR10 version of genome annotation using cufflinks (version 2.1.1) with default settings.
To analyze differential expression, the assembled transcripts from three independent biological replicates in Col and other mutants were included and compared using Cuffdiff (version 2.1.1) with default settings.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for wt, brm-1,  brm-3, brip1, brip2, brip1 brip2, brip1 brip2 brm-3 and brip1 brip2 brm-1.

extract_protocol:
Total RNA was extracted using the RNAprep Pure Plant Kit (Polysaccharides & Polyphenolics-rich, Vazyme, Cat.#DP441, Lot#S7717) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brip1 brip2 brm-1

tag: condition

value: LD (long day)

value: Seedling

tag: developmental stage


title: 176CS8

value: short days (8L/16D)

tag: temperature

tag: replicate

tag: fragmentation method

value: sonication

tag: chip antibody

value: Anti-Flag M2 Affinity Gel (Sigma, A2220)


title: brip1 brip2 brm-1 rep1


title: 177RS21

value: single


title: CBMS1_ESC_single_25perS-12

description:
80kb resolution data
Sample from GSE108556 (GSM3521518)

value: embryonic stem cell

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)


title: brip1 brip2 brm-3 rep3

value: brip1 brip2 brm-3


title: brip1 brip2 brm-3 rep2


title: Control1

tag: treatment


title: brip1 brip2 brm-3 rep1


title: 176CS7


title: 176CS6


title: brip1 brip2 brm-1 rep3


title: CBMS1_ESC_single_25perS-10

description:
80kb resolution data
Sample from GSE108556 (GSM3521516)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%

value: FALSE

tag: cell cycle phase


title: CBMS1_ESC_single_25perS-11

description:
80kb resolution data
Sample from GSE108556 (GSM3521517)


title: CBMS1_ESC_single_25perS-09

description:
80kb resolution data
Sample from GSE108556 (GSM3521515)


title: brip1 brip2 rep3

tag: genotype

value: brip1 brip2

tag: tissue

tag: cultivar


title: 176CS5

value: seedling

tag: photoperiod


title: TNF_E2_2

value: TNF E2


title: 176CS4


title: CBMS1_ESC_single_25perS-08

description:
80kb resolution data
Sample from GSE108556 (GSM3521514)

tag: strain

tag: cell type


title: brip1 brip2 rep2

tag: condition

tag: developmental stage


title: CBMS1_ESC_single_25perS-07

description:
80kb resolution data
Sample from GSE108556 (GSM3521513)


title: TNF_E2_1


title: TNF_E1_3

value: TNF E1


title: 176CS3

tag: temperature

tag: replicate

tag: fragmentation method


title: TNF_E1_2


title: brip1 brip2 rep1


title: 176CS21

value: INPUT

tag: chip antibody

value: NA (INPUT sample)


title: brm-1 rep2


title: 176CS22

value: NA (Input sample)


title: CBMS1_ESC_single_25perS-06

description:
80kb resolution data
Sample from GSE108556 (GSM3521512)

value: CBA/MsM

tag: sample state

tag: xx or xo chromosomes in single cell samples

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)


title: brm-1 rep3

value: LD (long day)

value: Seedling


title: CBMS1_ESC_single_25perS-05

description:
80kb resolution data
Sample from GSE108556 (GSM3521511)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: repliscore of 40–70%


title: CBMS1_ESC_single_25perS-04

description:
80kb resolution data
Sample from GSE108556 (GSM3521510)

tag: cell cycle phase


title: 176CS20

tag: genotype

tag: tissue

value: short days (8L/16D)

value: sonication

value: Anti-HA−Agarose (Sigma, A2095)


title: TNF_E2_3

tag: treatment


title: brm-3 rep3

tag: cultivar


title: brm-1 rep1


title: TNF_E1_1


title: TNF-3

value: TNF


title: 176CS1

tag: photoperiod

value: single

value: Anti-Flag M2 Affinity Gel (Sigma, A2220)


title: CBMS1_ESC_single_25perS-03

description:
80kb resolution data
Sample from GSE108556 (GSM3521509)

tag: strain

tag: cell type

value: embryonic stem cell

value: Single cell

value: FALSE


title: TNF-2


title: brm-3 rep2

tag: condition

tag: developmental stage


title: 176CS19

value: seedling

tag: temperature

tag: replicate

tag: fragmentation method


title: TNF-1


title: CBMS1_ESC_single_25perS-01

description:
80kb resolution data
Sample from GSE108556 (GSM3521507)

tag: sample state

tag: xx or xo chromosomes in single cell samples


title: CBMS1_ESC_single_25perS-02

description:
80kb resolution data
Sample from GSE108556 (GSM3521508)

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)


title: 176CS18

growth_protocol: Seedlings were grown for 10 days under SDs at either 17 or 22 ºC and shifted to 27 ºC  for 2 h at ZT8.

tag: chip antibody


title: brm-3 rep1

tag: genotype


title: 176CS12

tag: tissue


title: LM_seq_293T_XIST_L3_BASU_dCasRx_rep1

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

institute: City University of Hong Kong

description: MGISEQ-2000 platform

data_processing:
Quality control of the raw sequencing data using FastQC version v0.11.7 with default parameters.
LM-Seq reads were aligned to the hg19 genome assembly using HISAT2 version 2.1.0 with default parameters.
Sam files were converted to bam files by using samtools version 1.9.
Gene expression was quantified using gFold version 1.1.4(Feng et al., Bioinformatics, 2012.).
Gene expression matrix merges using a customer script.
Data visualization by using the R ggplot package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample and one tab-delimited text file include gene expression matrix for all samples.

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in DMEM (Life Technologies) supplemented with 10% FBS (Life Technologies) and 1% penicillin-streptomycin (Life Technologies) at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated using MiniBEST Universal RNA Extraction Kit (TAKARA) following manufacturer’s instruction.
RNA-seq library was prepared using LM-seq library prep protocol (Hou, Z., et al. (2015). "A cost-effective RNA sequencing protocol for large-scale gene expression studies." Sci Rep 5: 9570.)

treatment_protocol: For RNA seq, transfections were performed in 6-well plates. 500,000 cells were seeded in each well one day before transfection. 1.5 μg of gRNA expressing plasmid and 1.5 μg of BASU-dCasRx constructs were co-transfected with 9 μg of PEI in each well. Forty-eight hours following transfection, the cells were harvested for total RNA extraction.

tag: cell line

value: human embryonic kidney (HEK) 293T cells

tag: transfection


title: E2_cell-1

tag: treatment


title: 176CS11

tag: cultivar

tag: photoperiod


title: LM_seq_293T_XIST_L2_BASU_dCasRx_rep3

description: MGISEQ-2000 platform


title: brip2 rep1

tag: condition


title: LM_seq_293T_XIST_L3_BASU_dCasRx_rep2

description: MGISEQ-2000 platform


title: LM_seq_293T_XIST_L2_BASU_dCasRx_rep2

description: MGISEQ-2000 platform


title: brip1 rep2

tag: developmental stage


title: E1_cell-2


title: brip1 rep3


title: LM_seq_293T_XIST_L2_BASU_dCasRx_rep1

description: MGISEQ-2000 platform


title: E1_cell-1


title: E1_cell-3


title: brip1 rep1


title: LM_seq_293T_XIST_L1_BASU_dCasRx_rep3

description: MGISEQ-2000 platform


title: MCF7cFBS-3

value: cFBS


title: LM_seq_293T_XIST_L3_BASU_dCasRx_rep3

description: MGISEQ-2000 platform


title: 176CS17

tag: temperature


title: E2_cell-3


title: brip2 rep3


title: brip2 rep2


title: Control2

value: Control


title: CD11b+ MDSC from tumor, biological rep6

description:
Cd11b_tumor_6
Gene expression profile of CD11b+ cells infiltrating a s.c. C26GM tumor 9 days after challenge.

data_processing: RMA of .CEL files using Bioconductor affy library and Brainarray custom CDF Mouse4302_Mm_ENTREZG_21.0.0. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization.

growth_protocol: Balb/c mice were challenged with 5E5 C26GM cells sc. 9 days later, CD11b+ cells were magnetically isolated (Miltenyi) from RBC lysed splenocytes or collagenase (Sigma) treated tumors. CD11b+ cells purity was higher than 95% as per flow cytometry analysis.

tag: strain/background

value: BALB/c

value: Tumor infiltrate

tag: cell type

value: CD11b+ MDSC

tag: experimental condition

value: Tumor-bearing


title: LM_seq_293T_XIST_L1_BASU_dCasRx_rep2

description: MGISEQ-2000 platform


title: E2_cell-2


title: CD11b+ MDSC from tumor, biological rep5

description:
Cd11b_tumor_5
Gene expression profile of CD11b+ cells infiltrating a s.c. C26GM tumor 9 days after challenge.


title: MCF7cFBS-2


title: CD11b+ MDSC from tumor, biological rep3

description:
Cd11b_tumor_3
Gene expression profile of CD11b+ cells infiltrating a s.c. C26GM tumor 9 days after challenge.


title: WT rep2

value: WT

value: LD (long day)

value: Seedling


title: MCF7cFBS-1


title: CD11b+ MDSC from tumor, biological rep4

description:
Cd11b_tumor_4
Gene expression profile of CD11b+ cells infiltrating a s.c. C26GM tumor 9 days after challenge.


title: Taf15_sh44_5a_rep2

data_processing:
Basecalling is performed by Illumina RTA software in sequencer
Demultiplexing is performed by Illumina bcl2fastq 2.17 software based on index information
RNA-seq reads were mapped to both 129S1/SvImJ and CAST/EiJ transcriptome reference sequences using Bowtie2 (version 2.1.0)
RNA-seq reads at SNP/indel sites were counted using samtools (version 0.1.19) depth command.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text file includes read counts at SNP/indel sites for both alleles.

organism: Mus musculus musculus x Mus musculus castaneus

extract_protocol:
Total RNA was extracted and processed to remove rRNA by NEBNext rRNA depletion kit (NEB).
RNA-seq library preparation using NEBNext UltraTM II directional RNA library prep kit for Illumina (NEB).

tag: strain background

value: 129S1/SvImJ x CAST/EiJ

value: mouse embryonic fibroblasts (MEF)

value: TAF15 knockdown + 5-aza treatment

tag: biological replicate

value: rep 2


title: WT rep1


title: LM_seq_293T_pre-gRNA_BASU_dCasRx_rep3

description: MGISEQ-2000 platform


title: LM_seq_293T_pre-gRNA_BASU_dCasRx_rep2

description: MGISEQ-2000 platform


title: WT rep3


title: LM_seq_293T_pre-gRNA_BASU_dCasRx_rep1

description: MGISEQ-2000 platform


title: CD11b+ MDSC from tumor, biological rep2

description:
Cd11b_tumor_2
Gene expression profile of CD11b+ cells infiltrating a s.c. C26GM tumor 9 days after challenge.


title: CD11b+ MDSC from spleen, biological rep6

description:
Cd11b_spleen_6
Gene expression profile of CD11b+ cells from spleen of mice 9 days after s.c. challenge with 5E5 C26GM tumor cells.

source_name: CD11b+ cells from spleen of mice 9 days after s.c. challenged with 5E5 C26GM tumor cells

value: Spleen


title: NT_5a_rep2

value: 5-aza treatment


title: CD11b+ MDSC from tumor, biological rep1

description:
Cd11b_tumor_1
Gene expression profile of CD11b+ cells infiltrating a s.c. C26GM tumor 9 days after challenge.


title: LM_seq_293T_WT_rep3

description: MGISEQ-2000 platform

value: control (WT)


title: toc1-21 prr5-1_bio1

city: Beijing

first: Lei

last: Wang

address: Nanxincun 20, Xiangshan, Haidian District

department: Key Laboratory of Plant Molecular Physiology

institute: insitute of botany, chinese academy of sciences

data_processing:
150 nt paired-end high throughput sequencing was performed on an Illumina Hiseq X ten.
Low quality sequencing reads were removed. Clean reads were mapped to the Arabidopsis reference genome (TAIR10, www.arabidopsis.org) with Tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml) software, and differential expressed genes (DEGs) was identified using edgeR in the R package (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html) if FoldChange > 2 and FDR < 0.05 between case group sample and control group sample. GO and KEGG pathway enrichment analysis was performed using TopGO in the R package (http://bioconductor.org/).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: toc1-21 prr5-1_whole seedling

growth_protocol: Plants were grown under LD conditions at 22ºC for 10 days and harvest at ZT15.

extract_protocol:
Total RNA was extracted with Trizol reagent (Ambion) and treated with DNase I (Thermo Fisher).
Sequencing libraries were prepared following the protocol of the Directional RNA library Prep Kit (NEB).

tag: genotype/variation

tag: age

tag: medium

value: MS+3% sucrose

tag: time point

value: whole seedling


title: NT_5a_rep1

value: rep 1


title: toc1-21 prr5-1_bio2

tag: tissue


title: CD11b+ MDSC from spleen, biological rep5

description:
Cd11b_spleen_5
Gene expression profile of CD11b+ cells from spleen of mice 9 days after s.c. challenge with 5E5 C26GM tumor cells.

value: BALB/c


title: Col_0_bio3

source_name: WT_whole seedling

value: Wild type


title: LM_seq_293T_WT_rep2

description: MGISEQ-2000 platform

tag: cell line

value: human embryonic kidney (HEK) 293T cells

tag: transfection


title: LM_seq_293T_XIST_L1_BASU_dCasRx_rep1

description: MGISEQ-2000 platform


title: NT_rep2

tag: treatment