title: K. lactis Sfp1 mutant expression data [252035410018_2_1_Klac_T60_SFP1]

description:
252035410018_201105131056_S01_GE2_105_Dec08_2_1.txt
K. lactis Sfp1 mutant expression data


title: K. lactis Sfp1 mutant expression data [252035410018_2_2_Klac_T90_SFP1]

status: Public on Aug 26 2020

type: RNA

city: Cambridge

first: Carl

middle: G

last: de Boer

state: MA

address: 415 Main St

country: USA

institute: The Broad Institute

description:
252035410018_201105131056_S01_GE2_105_Dec08_2_2.txt
K. lactis Sfp1 mutant expression data

hyb_protocol: For each time point, either two or three biological replicates were hybridized. We used two-color Agilent 55- or 60-mer oligo-arrays in the 4 × 44 K or 8 × 15 K format for the S. cerevisiae strain (commercial array; four to five probes per target gene) or the custom 8 × 15 K format for all other species (two probes per target gene)

scan_protocol: After hybridization and washing per the manufacturer’s instructions, arrays were scanned using an Agilent scanner and analyzed with Agilent’s Feature Extraction software (release 10.5.1.).

data_processing:
From each set of data in the raw data the ProbeName, SystematicName, gMeanSignal, rMeanSignal, gBGMeanSignal, rBGMeanSignal features were selected for each DATA entry.
To define a value for each probe in the attached matrices, the values for gMeanSignal, rMeanSignal, gBGMeanSignal, rBGMeanSignal features were first averaged for the multiple entries for each individual probe. Then, for each probe in each data set the averaged values were background-subtracted, log-transformed. Each value in the species matrices corresponds to log(<gMeanSignal>-<gBGMeanSignal>+1) or log(<rMeanSignal>-<rBGMeanSignal>+1) for the Cy3 and Cy5 data, respectively. In cases where <gBGMeanSignal> < <gMeanSignal> or <rBGMeanSignal> < <rMeanSignal>, 0 was inserted. So it is these averaged and transformed values that appear in the attached matrices for each probe in each species dataset. For interpretability the systematic gene name mapped to each of the probes is given for each species data set.

molecule: total RNA

organism: Kluyveromyces lactis

label_protocol: Samples were quality controlled with the RNA 6000 Nano ll kit of the Bioanalyzer 2100 (Agilent, Palo Alto, CA). cDNA samples were labeled with either Cy3 or Cy5 using a modification of the protocol developed by Joe DeRisi (University of California at San Francisco) and Rosetta Inpharmatics that can be obtained at http://www.microarrays.org (Wapinski et al., 2010).

growth_protocol: We used the following strains for each species: S. cerevisiae RM11-1a and BY4741, C. glabrata CBS 138, N. castellii 4310 (MATa ho::loxp), K. lactis Say 509  (MATa ade2 leu2 metA1 trp1 uraA1 nej1::LEU2, and S. pombe SPY73h+. All species were grown in the following rich medium (termed BMW): yeast extract (1.5%), peptone (1%), dextrose (2%), SC amino acid mix (Sunrise Science) 2 g/l, adenine 100 mg/l, tryptophan 100 mg/l, uracil 100 mg/l. The medium was chosen to minimize cross-species variation in growth. All strains were grown at 30°C except for N. castellii, which was grown at 25°C. Cultures were grown exactly as described above. SFP1 was deleted from haploid strains of each specie using homologous recombination. Parent and deletion strains are listed in Table S1, and the primers used in Table S2 of the associated paper for this dataset.  For S. cerevisiae (RM11-1a), SFP1 was deleted with URA3.  The plasmid, 106,pRS406 (URA3) was used to create the transformation fragment.  URA3 was amplified from the vector with primers containing ~60 base pairs of homology to the up- and downstream sequences to SFP1. Phusion enzyme (NEB) was used with standard protocol and a gradient PCR was done to find the optimal annealing temperature. PCR fragments were pooled and cleaned up with a phenol/chloroform extraction. Transformation was done using a standard S. cerevisiae electroporation protocol. Correct integration was checked by PCR of genomic DNA isolated from deletion candidates using sequences that were up- and downstream of the gene and internal to the drug cassette.  Negative PCR controls included the PCR for the ORF and PCR running from the ORF to the up and downstream locations. Positive PCR controls included the same PCR reactions on the genomic DNA of the parent strain. S. cerevisiae (BY4741) was obtained from Open Biosystems (5312).      For N. castellii, C. glabrata, K. lactis and S. pombe, the transformation fragment was created using a fusion PCR method as described by Szewczyk et al.(Szewczyk et al., 2007)  The Pringle primers were used to amplify the drug cassette of the NAT1MX4 (pAG25) and pFA6a-KANMX6 vectors (Wach et al., 1994).  The P1/P3 and P4/P6 primer combinations were used to amplify the up and downstream sequences of SFP1 and also contained homology to the drug cassette.  The P2/P5 primers were used to fuse the three fragments together in a single PCR reaction. The basic PCR cycling parameters used were as previously described (Wach et al., 1994), except that PCRs were done using Phusion enzyme (NEB) and temperatures were adjusted accordingly. Optimal PCR cycling conditions for each species was determined using a gradient PCR. PCR fragments were pooled and cleaned up with a phenol/chloroform extraction. Transformation was done using a protocol adapted from Kooistra et al., 2004 (Kooistra, Hooykaas and Steensma, 2004). Correct integration was checked by PCR of genomic DNA isolated from deletion candidates using sequences that were up and downstream of the gene (P1 and P6 primers) and internal to the drug cassette (Pringle internal check)., For S. paradoxus, the drug cassette was amplified out of pFA6a-3HA-KANMX6 vector with ultramer primers of 200 bp length, designed to amplify this region and also to add ~180 bp of homology to the upstream and downstream regions of the S. paradoxus SFP1 ORF. Additional PCRs were carried out to add ~1kb of homology up and downstream of the SFP1 ORF and then fusion PCR was carried out as described above. Negative PCR controls included the PCR for the ORF and also PCR running from the ORF to the up and downstream locations.  Positive PCR controls included doing all of the same PCR reactions on the genomic DNA of the parent strains.

extract_protocol: RNA extraction and microarray hybridization were completed as described by Thompson et al.(Thompson et al., 2013): RNA preparation and labeling Total RNA was isolated using the RNeasy Midi or Mini Kits (Qiagen, Valencia, CA) according to the provided instructions for mechanical lysis.

treatment_protocol: On day 1, cells were grown in BMW with growth saturation times as follows: S. cerevisiae, N. castellii, C. glabrata: ~24 hours, K. lactis: ~48 hours, S. pombe: ~36 hours. On day 2, 50 ml cultures, inoculated at 1x106 cells/ml from the overnights were grown in BMW until glucose reached zero, in the New Brunswick shaker. Glucose levels were measured throughout growth, but more frequently as they were reaching zero, using the YSI 2700 Biochemistry Analyzer. When glucose levels reached zero, cells were counted using the Cellometer Auto M10, and enough cells were removed to inoculate 300 ml of BMW at 1x107 cells/ml. Samples were collected at 30 minutes, 60 minutes, 90 minutes as previously described (Thompson et al., 2013). Briefly,  50-ml conical tubes filled with the appropriate amount of 100% methanol to produce a 60/40 mixture once the sample is added. The methanol-filled tubes were stored at −80°C until ready for use. During sample collection tubes were placed in a rack in a dry-ice ethanol bath kept at approximately −40°C. Once the sample was added to the methanol, the methanol and media were separated from the cells by centrifugation and poured off. The conicals containing a cell pellet were then stored at −80°C until processed for permanent storage. For permanent storage, the cell pellets were then washed in 5 ml of nuclease-free water and spun for 5 min at 3700 rpm at 4°C. The supernatant was discarded and the pellet re-suspended in 2 ml of RNA later (Invitrogen) and transferred to 2 ml Sarstadt tubes for storage. The samples were left at 4°C for 24 hr before being moved to a −80°C freezer.

tag: genotype/varation

value: K. lactis Sfp1 mutant


title: K. lactis Sfp1 mutant expression data [252035410019_2_1_Klac_T60_SFP1]

description:
252035410019_201106301049_S01_GE2_105_Dec08_2_1.txt
K. lactis Sfp1 mutant expression data


title: K. lactis Sfp1 mutant expression data [252035410018_1_1_Klac_T30_SFP1]

description:
252035410018_201105131056_S01_GE2_105_Dec08_1_1.txt
K. lactis Sfp1 mutant expression data


title: K. lactis WT expression data [252035410018_2_1_Klac_T60_WT]

description:
252035410018_201105131056_S01_GE2_105_Dec08_2_1.txt
K. lactis WT expression data

value: K. lactis WT


title: K. lactis Sfp1 mutant expression data [252035410017_2_4_Klac_T60_SFP1]

description:
252035410017_201104071111_S01_GE2_105_Dec08_2_4.txt
K. lactis Sfp1 mutant expression data


title: K. lactis Sfp1 mutant expression data [252035410017_2_3_Klac_T30_SFP1]

description:
252035410017_201104071111_S01_GE2_105_Dec08_2_3.txt
K. lactis Sfp1 mutant expression data


title: K. lactis WT expression data [252035410019_1_1_Klac_T30_WT]

description:
252035410019_201106301049_S01_GE2_105_Dec08_1_1.txt
K. lactis WT expression data


title: K. lactis WT expression data [252035410017_2_4_Klac_T60_WT]

description:
252035410017_201104071111_S01_GE2_105_Dec08_2_4.txt
K. lactis WT expression data


title: K. lactis WT expression data [252035410018_1_3_Klac_T90_WT]

description:
252035410018_201105131056_S01_GE2_105_Dec08_1_3.txt
K. lactis WT expression data


title: K. lactis Sfp1 mutant expression data [252035410018_2_4_Klac_T60_SFP1]

description:
252035410018_201105131056_S01_GE2_105_Dec08_2_4.txt
K. lactis Sfp1 mutant expression data


title: K. lactis WT expression data [252035410018_2_3_Klac_T30_WT]

description:
252035410018_201105131056_S01_GE2_105_Dec08_2_3.txt
K. lactis WT expression data


title: K. lactis WT expression data [252035410017_2_2_Klac_T90_WT]

description:
252035410017_201104071111_S01_GE2_105_Dec08_2_2.txt
K. lactis WT expression data


title: K. lactis WT expression data [252035410017_2_3_Klac_T30_WT]

description:
252035410017_201104071111_S01_GE2_105_Dec08_2_3.txt
K. lactis WT expression data


title: K. lactis Sfp1 mutant expression data [252035410018_1_3_Klac_T90_SFP1]

description:
252035410018_201105131056_S01_GE2_105_Dec08_1_3.txt
K. lactis Sfp1 mutant expression data


title: K. lactis WT expression data [252035410017_2_1_Klac_T60_WT]

description:
252035410017_201104071111_S01_GE2_105_Dec08_2_1.txt
K. lactis WT expression data


title: K. lactis WT expression data [252035410018_2_4_Klac_T60_WT]

description:
252035410018_201105131056_S01_GE2_105_Dec08_2_4.txt
K. lactis WT expression data


title: K. lactis Sfp1 mutant expression data [252035410017_2_1_Klac_T60_SFP1]

description:
252035410017_201104071111_S01_GE2_105_Dec08_2_1.txt
K. lactis Sfp1 mutant expression data


title: K. lactis WT expression data [252035410017_1_4_Klac_T30_WT]

description:
252035410017_201104071111_S01_GE2_105_Dec08_1_4.txt
K. lactis WT expression data


title: K. lactis Sfp1 mutant expression data [252035410017_1_3_Klac_T90_SFP1]

description:
252035410017_201104071111_S01_GE2_105_Dec08_1_3.txt
K. lactis Sfp1 mutant expression data


title: K. lactis Sfp1 mutant expression data [252035410017_1_4_Klac_T30_SFP1]

description:
252035410017_201104071111_S01_GE2_105_Dec08_1_4.txt
K. lactis Sfp1 mutant expression data


title: K. lactis WT expression data [252035410018_1_2_Klac_T60_WT]

description:
252035410018_201105131056_S01_GE2_105_Dec08_1_2.txt
K. lactis WT expression data


title: K. lactis Sfp1 mutant expression data [252035410017_1_2_Klac_T60_SFP1]

description:
252035410017_201104071111_S01_GE2_105_Dec08_1_2.txt
K. lactis Sfp1 mutant expression data


title: K. lactis WT expression data [252035410017_1_2_Klac_T60_WT]

description:
252035410017_201104071111_S01_GE2_105_Dec08_1_2.txt
K. lactis WT expression data


title: K. lactis WT expression data [252035410017_1_3_Klac_T90_WT]

description:
252035410017_201104071111_S01_GE2_105_Dec08_1_3.txt
K. lactis WT expression data


title: K. lactis Sfp1 mutant expression data [252035410017_1_1_Klac_T30_SFP1]

description:
252035410017_201104071111_S01_GE2_105_Dec08_1_1.txt
K. lactis Sfp1 mutant expression data


title: N. castellii WT expression data [252035310017_2_1_Ncas_T90_WT]

description:
252035310017_201008061053_S01_GE2_105_Dec08_2_1.txt
N. castellii WT expression data

organism: Naumovozyma castellii

value: N. castellii WT


title: N. castellii WT expression data [252035310017_1_4_Ncas_T60_WT]

description:
252035310017_201008061053_S01_GE2_105_Dec08_1_4.txt
N. castellii WT expression data


title: N. castellii WT expression data [252035310017_2_2_Ncas_T90_WT]

description:
252035310017_201008061053_S01_GE2_105_Dec08_2_2.txt
N. castellii WT expression data


title: N. castellii Sfp1 mutant expression data [252035310017_1_4_Ncas_T60_551]

description:
252035310017_201008061053_S01_GE2_105_Dec08_1_4.txt
N. castellii Sfp1 mutant expression data

value: N. castellii Sfp1 mutant


title: K. lactis WT expression data [252035410017_1_1_Klac_T30_WT]

description:
252035410017_201104071111_S01_GE2_105_Dec08_1_1.txt
K. lactis WT expression data


title: N. castellii Sfp1 mutant expression data [252035310017_2_1_Ncas_T90_551]

description:
252035310017_201008061053_S01_GE2_105_Dec08_2_1.txt
N. castellii Sfp1 mutant expression data


title: N. castellii Sfp1 mutant expression data [252035310017_2_2_Ncas_T90_551]

description:
252035310017_201008061053_S01_GE2_105_Dec08_2_2.txt
N. castellii Sfp1 mutant expression data


title: N. castellii Sfp1 mutant expression data [252035310017_1_3_Ncas_T60_551]

description:
252035310017_201008061053_S01_GE2_105_Dec08_1_3.txt
N. castellii Sfp1 mutant expression data


title: K. lactis Sfp1 mutant expression data [252035410017_2_2_Klac_T90_SFP1]

description:
252035410017_201104071111_S01_GE2_105_Dec08_2_2.txt
K. lactis Sfp1 mutant expression data


title: N. castellii Sfp1 mutant expression data [252035310017_1_1_Ncas_T30_551]

description:
252035310017_201008061053_S01_GE2_105_Dec08_1_1.txt
N. castellii Sfp1 mutant expression data


title: N. castellii Sfp1 mutant expression data [252035310017_1_2_Ncas_T30_551]

description:
252035310017_201008061053_S01_GE2_105_Dec08_1_2.txt
N. castellii Sfp1 mutant expression data


title: N. castellii WT expression data [252035310017_1_3_Ncas_T60_WT]

description:
252035310017_201008061053_S01_GE2_105_Dec08_1_3.txt
N. castellii WT expression data


title: N. castellii WT expression data [252035310017_1_2_Ncas_T30_WT]

description:
252035310017_201008061053_S01_GE2_105_Dec08_1_2.txt
N. castellii WT expression data


title: N. castellii WT expression data [252035310017_1_1_Ncas_T30_WT]

description:
252035310017_201008061053_S01_GE2_105_Dec08_1_1.txt
N. castellii WT expression data


title: N. castellii WT expression data [252035310016_2_2_Ncas_T90_WT]

description:
252035310016_201008061045_S01_GE2_105_Dec08_2_2.txt
N. castellii WT expression data


title: ISPY2_pre-treatment breast cancer tumor_218503

status: Public on Sep 20 2020

city: San Francisco

first: Denise

middle: M

last: Wolf

state: CA

address: 2340 Sutter st

institute: University of California, San Francisco

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing:
gnormalized signal (log2) data, as provided in the sample data table and raw files on each patient, was extracted and aligned to the 75th quantile across arrays by Agendia. All values indicated for non-confirmity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified.  Expression data from the first ~900 I-SPY 2 patients distributed over the two platforms were combined into a single gene-level dataset over the set of common genes after batch-adjusting using ComBat [PMID:16632515].  The data matrix for this study constitutes 150 samples from this larger COMBAT-combined expression set.  Linear adjustment factors were derived from the larger ComBat operation, per platform, and can be used against these 150 samples for batch correcting on raw files.  An updated probe annotation for platform GPL16233 was used and is provided as Series supplementary file.
The platform corrected, normalized expression values (from two different platforms) are provided in the 'ExpDat_ISPY2_MK2206_n150.txt'.  Data is collapsed on the gene level as was used in the analysis.

organism: Homo sapiens

source_name: Breast cancer biopsy (pre-treatment)

label_protocol: standard Agilent protocol

extract_protocol: not provided

tag: hr

tag: pcr

tag: arm

value: MK2206 Arm


title: N. castellii Sfp1 mutant expression data [252035310016_2_2_Ncas_T90_719]

description:
252035310016_201008061045_S01_GE2_105_Dec08_2_2.txt
N. castellii Sfp1 mutant expression data


title: N. castellii Sfp1 mutant expression data [252035310016_2_1_Ncas_T90_719]

description:
252035310016_201008061045_S01_GE2_105_Dec08_2_1.txt
N. castellii Sfp1 mutant expression data


title: N. castellii Sfp1 mutant expression data [252035310016_1_3_Ncas_T60_719]

description:
252035310016_201008061045_S01_GE2_105_Dec08_1_3.txt
N. castellii Sfp1 mutant expression data


title: N. castellii Sfp1 mutant expression data [252035310016_1_4_Ncas_T60_719]

description:
252035310016_201008061045_S01_GE2_105_Dec08_1_4.txt
N. castellii Sfp1 mutant expression data


title: N. castellii WT expression data [252035310016_2_1_Ncas_T90_WT]

description:
252035310016_201008061045_S01_GE2_105_Dec08_2_1.txt
N. castellii WT expression data


title: N. castellii WT expression data [252035310016_1_3_Ncas_T60_WT]

description:
252035310016_201008061045_S01_GE2_105_Dec08_1_3.txt
N. castellii WT expression data


title: S. cerevisiae WT expression data [251507210446_1_4_Scer_RM_T90_WT]

description:
251507210446_201102091144_S01_GE2_105_Dec08_1_4.txt
S. cerevisiae WT expression data

organism: Saccharomyces cerevisiae

value: S. cerevisiae RM11-1a WT


title: N. castellii WT expression data [252035310016_1_2_Ncas_T30_WT]

description:
252035310016_201008061045_S01_GE2_105_Dec08_1_2.txt
N. castellii WT expression data


title: N. castellii Sfp1 mutant expression data [252035310016_1_2_Ncas_T30_719]

description:
252035310016_201008061045_S01_GE2_105_Dec08_1_2.txt
N. castellii Sfp1 mutant expression data


title: N. castellii WT expression data [252035310016_1_1_Ncas_T30_WT]

description:
252035310016_201008061045_S01_GE2_105_Dec08_1_1.txt
N. castellii WT expression data


title: N. castellii Sfp1 mutant expression data [252035310016_1_1_Ncas_T30_719]

description:
252035310016_201008061045_S01_GE2_105_Dec08_1_1.txt
N. castellii Sfp1 mutant expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210446_1_3_Scer_RM_T90_SFP1]

description:
251507210446_201102091144_S01_GE2_105_Dec08_1_3.txt
S. cerevisiae Sfp1 mutant expression data

value: S. cerevisiae RM11-1a Sfp1 mutant


title: S. cerevisiae WT expression data [251507210446_1_3_Scer_RM_T90_WT]

description:
251507210446_201102091144_S01_GE2_105_Dec08_1_3.txt
S. cerevisiae WT expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210446_1_2_Scer_RM_T60_SFP1]

description:
251507210446_201102091144_S01_GE2_105_Dec08_1_2.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae WT expression data [251507210446_1_1_Scer_RM_T30_WT]

description:
251507210446_201102091144_S01_GE2_105_Dec08_1_1.txt
S. cerevisiae WT expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210446_1_1_Scer_RM_T30_SFP1]

description:
251507210446_201102091144_S01_GE2_105_Dec08_1_1.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae WT expression data [251507210445_1_4_Scer_RM_T30_WT]

description:
251507210445_201102091129_S01_GE2_105_Dec08_1_4.txt
S. cerevisiae WT expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210445_1_3_Scer_RM_T90_SFP1]

description:
251507210445_201102091129_S01_GE2_105_Dec08_1_3.txt
S. cerevisiae Sfp1 mutant expression data


title: N. castellii WT expression data [252035310016_1_4_Ncas_T60_WT]

description:
252035310016_201008061045_S01_GE2_105_Dec08_1_4.txt
N. castellii WT expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210445_1_1_Scer_RM_T30_SFP1]

description:
251507210445_201102091129_S01_GE2_105_Dec08_1_1.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae WT expression data [251507210445_1_2_Scer_RM_T60_WT]

description:
251507210445_201102091129_S01_GE2_105_Dec08_1_2.txt
S. cerevisiae WT expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210445_1_2_Scer_RM_T60_SFP1]

description:
251507210445_201102091129_S01_GE2_105_Dec08_1_2.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae WT expression data [251507210445_1_1_Scer_RM_T30_WT]

description:
251507210445_201102091129_S01_GE2_105_Dec08_1_1.txt
S. cerevisiae WT expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210443_1_4_Scer_BY_T15_SFP1]

description:
251507210443_201106301041_S01_GE2_105_Dec08_1_4.txt
S. cerevisiae Sfp1 mutant expression data

value: S. cerevisiae BY4741-Sfp1 mutant


title: S. cerevisiae WT expression data [251507210443_1_3_Scer_BY_T30_WT]

description:
251507210443_201106301041_S01_GE2_105_Dec08_1_3.txt
S. cerevisiae WT expression data

value: S. cerevisiae BY4741-WT


title: S. cerevisiae Sfp1 mutant expression data [251507210443_1_3_Scer_BY_T30_SFP1]

description:
251507210443_201106301041_S01_GE2_105_Dec08_1_3.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210446_1_4_Scer_RM_T90_SFP1]

description:
251507210446_201102091144_S01_GE2_105_Dec08_1_4.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210443_1_2_Scer_BY_T15_SFP1]

description:
251507210443_201106301041_S01_GE2_105_Dec08_1_2.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae WT expression data [251507210446_1_2_Scer_RM_T60_WT]

description:
251507210446_201102091144_S01_GE2_105_Dec08_1_2.txt
S. cerevisiae WT expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210445_1_4_Scer_RM_T30_SFP1]

description:
251507210445_201102091129_S01_GE2_105_Dec08_1_4.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae WT expression data [251507210443_1_2_Scer_BY_T15_WT]

description:
251507210443_201106301041_S01_GE2_105_Dec08_1_2.txt
S. cerevisiae WT expression data


title: S. cerevisiae WT expression data [251507210436_1_4_Scer_BY_T90_WT]

description:
251507210436_201012081150_S01_GE2_105_Dec08_1_4.txt
S. cerevisiae WT expression data


title: S. cerevisiae WT expression data [251507210443_1_1_Scer_BY_T5_WT]

description:
251507210443_201106301041_S01_GE2_105_Dec08_1_1.txt
S. cerevisiae WT expression data


title: S. cerevisiae WT expression data [251507210436_1_3_Scer_BY_T90_WT]

description:
251507210436_201012081150_S01_GE2_105_Dec08_1_3.txt
S. cerevisiae WT expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210436_1_4_Scer_BY_T90_SFP1]

description:
251507210436_201012081150_S01_GE2_105_Dec08_1_4.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210443_1_1_Scer_BY_T5_SFP1]

description:
251507210443_201106301041_S01_GE2_105_Dec08_1_1.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210436_1_3_Scer_BY_T90_SFP1]

description:
251507210436_201012081150_S01_GE2_105_Dec08_1_3.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210436_1_2_Scer_BY_T60_SFP1]

description:
251507210436_201012081150_S01_GE2_105_Dec08_1_2.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae WT expression data [251507210445_1_3_Scer_RM_T90_WT]

description:
251507210445_201102091129_S01_GE2_105_Dec08_1_3.txt
S. cerevisiae WT expression data


title: S. cerevisiae WT expression data [251507210443_1_4_Scer_BY_T15_WT]

description:
251507210443_201106301041_S01_GE2_105_Dec08_1_4.txt
S. cerevisiae WT expression data


title: S. cerevisiae WT expression data [251507210435_1_4_Scer_BY_T60_WT]

description:
251507210435_201012081142_S01_GE2_105_Dec08_1_4.txt
S. cerevisiae WT expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210436_1_1_Scer_BY_T30_SFP1]

description:
251507210436_201012081150_S01_GE2_105_Dec08_1_1.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae WT expression data [251507210436_1_2_Scer_BY_T60_WT]

description:
251507210436_201012081150_S01_GE2_105_Dec08_1_2.txt
S. cerevisiae WT expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210435_1_1_Scer_BY_T30_SFP1]

description:
251507210435_201012081142_S01_GE2_105_Dec08_1_1.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210435_1_3_Scer_BY_T60_SFP1]

description:
251507210435_201012081142_S01_GE2_105_Dec08_1_3.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae WT expression data [251507210435_1_3_Scer_BY_T60_WT]

description:
251507210435_201012081142_S01_GE2_105_Dec08_1_3.txt
S. cerevisiae WT expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210435_1_2_Scer_BY_T30_SFP1]

description:
251507210435_201012081142_S01_GE2_105_Dec08_1_2.txt
S. cerevisiae Sfp1 mutant expression data


title: S. cerevisiae WT expression data [251507210435_1_1_Scer_BY_T30_WT]

description:
251507210435_201012081142_S01_GE2_105_Dec08_1_1.txt
S. cerevisiae WT expression data


title: C. glabrata WT expression data [251600210023_1_4_Cgla_T60_WT]

description:
251600210023_201103041103_S01_GE2_105_Dec08_1_4.txt
C. glabrata WT expression data

organism: Nakaseomyces glabratus

value: C. glabrata WT


title: C. glabrata Sfp1 mutant expression data [251600210023_1_3_Cgla_T90_9955]

description:
251600210023_201103041103_S01_GE2_105_Dec08_1_3.txt
C. glabrata Sfp1 mutant expression data

value: C. glabrata Sfp1 mutant


title: C. glabrata Sfp1 mutant expression data [251600210023_1_4_Cgla_T60_682]

description:
251600210023_201103041103_S01_GE2_105_Dec08_1_4.txt
C. glabrata Sfp1 mutant expression data


title: S. cerevisiae Sfp1 mutant expression data [251507210435_1_4_Scer_BY_T60_SFP1]

description:
251507210435_201012081142_S01_GE2_105_Dec08_1_4.txt
S. cerevisiae Sfp1 mutant expression data


title: C. glabrata Sfp1 mutant expression data [251600210023_1_2_Cgla_T60_682]

description:
251600210023_201103041103_S01_GE2_105_Dec08_1_2.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata WT expression data [251600210023_1_3_Cgla_T90_WT]

description:
251600210023_201103041103_S01_GE2_105_Dec08_1_3.txt
C. glabrata WT expression data


title: S. pombe WT expression data [252061310019_2_4_Spom_T90_WT]

description:
252061310019_201105131048_S01_GE2_105_Dec08_2_4.txt
S. pombe WT expression data

organism: Schizosaccharomyces pombe

value: S. pombe WT


title: S. cerevisiae WT expression data [251507210435_1_2_Scer_BY_T30_WT]

description:
251507210435_201012081142_S01_GE2_105_Dec08_1_2.txt
S. cerevisiae WT expression data


title: S. cerevisiae WT expression data [251507210436_1_1_Scer_BY_T30_WT]

description:
251507210436_201012081150_S01_GE2_105_Dec08_1_1.txt
S. cerevisiae WT expression data


title: S. pombe WT expression data [252061310019_1_4_Spom_T30_WT]

description:
252061310019_201105131048_S01_GE2_105_Dec08_1_4.txt
S. pombe WT expression data


title: C. glabrata WT expression data [251600210023_1_2_Cgla_T60_WT]

description:
251600210023_201103041103_S01_GE2_105_Dec08_1_2.txt
C. glabrata WT expression data


title: K. lactis WT expression data [252035410019_2_2_Klac_T90_WT]

description:
252035410019_201106301049_S01_GE2_105_Dec08_2_2.txt
K. lactis WT expression data


title: C. glabrata Sfp1 mutant expression data [251600210023_1_1_Cgla_T90_9955]

description:
251600210023_201103041103_S01_GE2_105_Dec08_1_1.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata WT expression data [251600210023_1_1_Cgla_T90_WT]

description:
251600210023_201103041103_S01_GE2_105_Dec08_1_1.txt
C. glabrata WT expression data


title: S. pombe Sfp1 mutant expression data [252061310019_2_4_Spom_T90_SFP1]

description:
252061310019_201105131048_S01_GE2_105_Dec08_2_4.txt
S. pombe Sfp1 mutant expression data

value: S. pombe Sfp1 mutant


title: S. pombe Sfp1 mutant expression data [252061310018_2_3_Spom_T30_SFP1]

description:
252061310018_201104071055_S01_GE2_105_Dec08_2_3.txt
S. pombe Sfp1 mutant expression data


title: S. pombe WT expression data [252061310019_2_1_Spom_T60_WT]

description:
252061310019_201105131048_S01_GE2_105_Dec08_2_1.txt
S. pombe WT expression data


title: S. pombe WT expression data [252061310018_2_2_Spom_T90_WT]

description:
252061310018_201104071055_S01_GE2_105_Dec08_2_2.txt
S. pombe WT expression data


title: S. pombe Sfp1 mutant expression data [252061310019_2_3_Spom_T30_SFP1]

description:
252061310019_201105131048_S01_GE2_105_Dec08_2_3.txt
S. pombe Sfp1 mutant expression data


title: S. pombe WT expression data [252061310019_2_3_Spom_T30_WT]

description:
252061310019_201105131048_S01_GE2_105_Dec08_2_3.txt
S. pombe WT expression data


title: S. pombe Sfp1 mutant expression data [252061310019_2_2_Spom_T90_SFP1]

description:
252061310019_201105131048_S01_GE2_105_Dec08_2_2.txt
S. pombe Sfp1 mutant expression data


title: S. pombe WT expression data [252061310019_2_2_Spom_T90_WT]

description:
252061310019_201105131048_S01_GE2_105_Dec08_2_2.txt
S. pombe WT expression data


title: S. pombe Sfp1 mutant expression data [252061310019_1_4_Spom_T30_SFP1]

description:
252061310019_201105131048_S01_GE2_105_Dec08_1_4.txt
S. pombe Sfp1 mutant expression data


title: S. pombe Sfp1 mutant expression data [252061310019_2_1_Spom_T60_SFP1]

description:
252061310019_201105131048_S01_GE2_105_Dec08_2_1.txt
S. pombe Sfp1 mutant expression data


title: S. pombe Sfp1 mutant expression data [252061310019_1_3_Spom_T90_SFP1]

description:
252061310019_201105131048_S01_GE2_105_Dec08_1_3.txt
S. pombe Sfp1 mutant expression data


title: S. pombe WT expression data [252061310018_1_4_Spom_T30_WT]

description:
252061310018_201104071055_S01_GE2_105_Dec08_1_4.txt
S. pombe WT expression data


title: S. pombe Sfp1 mutant expression data [252061310018_1_3_Spom_T90_SFP1]

description:
252061310018_201104071055_S01_GE2_105_Dec08_1_3.txt
S. pombe Sfp1 mutant expression data


title: S. pombe WT expression data [252061310019_1_3_Spom_T90_WT]

description:
252061310019_201105131048_S01_GE2_105_Dec08_1_3.txt
S. pombe WT expression data


title: S. pombe WT expression data [252061310018_1_3_Spom_T90_WT]

description:
252061310018_201104071055_S01_GE2_105_Dec08_1_3.txt
S. pombe WT expression data


title: S. pombe Sfp1 mutant expression data [252061310018_1_2_Spom_T60_SFP1]

description:
252061310018_201104071055_S01_GE2_105_Dec08_1_2.txt
S. pombe Sfp1 mutant expression data


title: S. pombe WT expression data [252061310018_2_4_Spom_T60_WT]

description:
252061310018_201104071055_S01_GE2_105_Dec08_2_4.txt
S. pombe WT expression data


title: S. pombe Sfp1 mutant expression data [252061310018_2_4_Spom_T60_SFP1]

description:
252061310018_201104071055_S01_GE2_105_Dec08_2_4.txt
S. pombe Sfp1 mutant expression data


title: S. pombe Sfp1 mutant expression data [252061310018_2_2_Spom_T90_SFP1]

description:
252061310018_201104071055_S01_GE2_105_Dec08_2_2.txt
S. pombe Sfp1 mutant expression data


title: S. pombe WT expression data [252061310018_2_3_Spom_T30_WT]

description:
252061310018_201104071055_S01_GE2_105_Dec08_2_3.txt
S. pombe WT expression data


title: S. pombe Sfp1 mutant expression data [252061310019_1_2_Spom_T60_SFP1]

description:
252061310019_201105131048_S01_GE2_105_Dec08_1_2.txt
S. pombe Sfp1 mutant expression data


title: S. pombe Sfp1 mutant expression data [252061310018_2_1_Spom_T60_SFP1]

description:
252061310018_201104071055_S01_GE2_105_Dec08_2_1.txt
S. pombe Sfp1 mutant expression data


title: S. pombe WT expression data [252061310018_2_1_Spom_T60_WT]

description:
252061310018_201104071055_S01_GE2_105_Dec08_2_1.txt
S. pombe WT expression data


title: S. pombe WT expression data [252061310019_1_1_Spom_T30_WT]

description:
252061310019_201105131048_S01_GE2_105_Dec08_1_1.txt
S. pombe WT expression data


title: S. pombe Sfp1 mutant expression data [252061310018_1_4_Spom_T30_SFP1]

description:
252061310018_201104071055_S01_GE2_105_Dec08_1_4.txt
S. pombe Sfp1 mutant expression data


title: S. pombe WT expression data [252061310019_1_2_Spom_T60_WT]

description:
252061310019_201105131048_S01_GE2_105_Dec08_1_2.txt
S. pombe WT expression data


title: S. pombe Sfp1 mutant expression data [252061310019_1_1_Spom_T30_SFP1]

description:
252061310019_201105131048_S01_GE2_105_Dec08_1_1.txt
S. pombe Sfp1 mutant expression data


title: S. pombe WT expression data [252061310018_1_2_Spom_T60_WT]

description:
252061310018_201104071055_S01_GE2_105_Dec08_1_2.txt
S. pombe WT expression data


title: S. pombe WT expression data [252061310018_1_1_Spom_T30_WT]

description:
252061310018_201104071055_S01_GE2_105_Dec08_1_1.txt
S. pombe WT expression data


title: S. pombe Sfp1 mutant expression data [252061310018_1_1_Spom_T30_SFP1]

description:
252061310018_201104071055_S01_GE2_105_Dec08_1_1.txt
S. pombe Sfp1 mutant expression data


title: C. glabrata Sfp1 mutant expression data [251983910042_2_4_Cgla_T90_682]

description:
251983910042_201102091136_S01_GE2_105_Dec08_2_4.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata Sfp1 mutant expression data [251983910042_2_3_Cgla_T30_682]

description:
251983910042_201102091136_S01_GE2_105_Dec08_2_3.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata WT expression data [251983910042_2_4_Cgla_T90_WT]

description:
251983910042_201102091136_S01_GE2_105_Dec08_2_4.txt
C. glabrata WT expression data


title: C. glabrata Sfp1 mutant expression data [251983910042_2_2_Cgla_T90_682]

description:
251983910042_201102091136_S01_GE2_105_Dec08_2_2.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata WT expression data [251983910042_2_3_Cgla_T30_WT]

description:
251983910042_201102091136_S01_GE2_105_Dec08_2_3.txt
C. glabrata WT expression data


title: C. glabrata Sfp1 mutant expression data [251983910042_1_3_Cgla_T90_682]

description:
251983910042_201102091136_S01_GE2_105_Dec08_1_3.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata Sfp1 mutant expression data [251983910042_1_2_Cgla_T60_682]

description:
251983910042_201102091136_S01_GE2_105_Dec08_1_2.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata Sfp1 mutant expression data [251983910042_1_1_Cgla_T30_682]

description:
251983910042_201102091136_S01_GE2_105_Dec08_1_1.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata WT expression data [251983910042_2_1_Cgla_T60_WT]

description:
251983910042_201102091136_S01_GE2_105_Dec08_2_1.txt
C. glabrata WT expression data


title: C. glabrata WT expression data [251983910042_1_1_Cgla_T30_WT]

description:
251983910042_201102091136_S01_GE2_105_Dec08_1_1.txt
C. glabrata WT expression data


title: C. glabrata Sfp1 mutant expression data [251983910042_2_1_Cgla_T60_682]

description:
251983910042_201102091136_S01_GE2_105_Dec08_2_1.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata Sfp1 mutant expression data [251983910042_1_4_Cgla_T30_682]

description:
251983910042_201102091136_S01_GE2_105_Dec08_1_4.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata Sfp1 mutant expression data [251983910041_2_4_Cgla_T60_9955]

description:
251983910041_201102091113_S01_GE2_105_Dec08_2_4.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata WT expression data [251983910042_1_4_Cgla_T30_WT]

description:
251983910042_201102091136_S01_GE2_105_Dec08_1_4.txt
C. glabrata WT expression data


title: C. glabrata Sfp1 mutant expression data [251983910041_2_3_Cgla_T90_9955]

description:
251983910041_201102091113_S01_GE2_105_Dec08_2_3.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata WT expression data [251983910042_2_2_Cgla_T90_WT]

description:
251983910042_201102091136_S01_GE2_105_Dec08_2_2.txt
C. glabrata WT expression data


title: C. glabrata WT expression data [251983910042_1_3_Cgla_T90_WT]

description:
251983910042_201102091136_S01_GE2_105_Dec08_1_3.txt
C. glabrata WT expression data


title: C. glabrata WT expression data [251983910041_2_1_Cgla_T60_WT]

description:
251983910041_201102091113_S01_GE2_105_Dec08_2_1.txt
C. glabrata WT expression data


title: C. glabrata Sfp1 mutant expression data [251983910041_1_3_Cgla_T90_9955]

description:
251983910041_201102091113_S01_GE2_105_Dec08_1_3.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata WT expression data [251983910041_2_4_Cgla_T60_WT]

description:
251983910041_201102091113_S01_GE2_105_Dec08_2_4.txt
C. glabrata WT expression data


title: C. glabrata WT expression data [251983910041_1_1_Cgla_T30_WT]

description:
251983910041_201102091113_S01_GE2_105_Dec08_1_1.txt
C. glabrata WT expression data


title: C. glabrata WT expression data [251983910041_2_3_Cgla_T90_WT]

description:
251983910041_201102091113_S01_GE2_105_Dec08_2_3.txt
C. glabrata WT expression data


title: C. glabrata Sfp1 mutant expression data [251983910041_2_1_Cgla_T60_9955]

description:
251983910041_201102091113_S01_GE2_105_Dec08_2_1.txt
C. glabrata Sfp1 mutant expression data


title: B16F10 cell line bulk small RNA seq [B16_bulk]

status: Public on Jul 07 2020

type: SRA

city: Beijing

first: Tao

last: Cai

address: No. 7 Science Park Road, Zhongguancun Life Science Park

country: China

institute: National Institute Of Biological Sciences, Beijing (NIBS)

library_source: transcriptomic

data_processing:
library strategy: parallel single cell small RNA sequencing (PSCSR-seq)
The PSCSR-seq analysis procedures are adapted from the method in the publication(S. Mi and T. Cai et al., Cell 133, 116, 2008). Briefly, the small RNA sequences, cell barcodes and molecules UMI are extracted from the raw reads using the customized scripts. The small RNA sequence with the length of 19nt~39nt were kept and mapped to the reference genome with no mismatch (bowtie v1.2.2). The small RNAs are annotated to according to the databases including miRbase (release v22.1), EBI RNAcenter database (release v11), EBML CDS database (ENSEMBL release v96). For certain small RNA gene, different UMIs (at least 2-base difference) were counted as the measurement of small RNA expression. The computational pipeline can be found at github (https://github.com/biocaitao/PSCSR-seq).
The single cells in PSCSR-seq were selected using TaKaRa ICell8 system protocol (“StandardCellSettings-V5” or “PBMCv4”). The cell barcodes of selected cells were exported. The valid cells were filtered from the background according to the exported barcodes (allowing 2 mismatches). Further, the cells within a ~10-fold range of UMI counts were considered high quality (GX.Zheng, JM.Terry, Nat Commun.16;8:14049 2017 or refer to https://github.com/biocaitao/PSCSR-seq ).
Single-cell RNA-seq analysis can refer to the 10X genomics "cellranger" software manual (detail can refer to Y. Wang and Z. Tang, et al., PNAS,115,2407, 2018).
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: PSCSR-seq processed files contain: plain text files for cell barcodes and estimated expression of miRNAs and all small RNAs; single cell mRNA-seq processed files contain: zipped plain text files from output of cellranger (version 3.0.1, 10X Genomics).

organism: Mus musculus

source_name: cultured cell line

growth_protocol: A549 cells were cultured in DMEM/F-12 (11320082, Gibco), Hela, 3T3, and HEK293T cells were cultured in DMEM-basic (C11965500BT, Gibco) and K562 cells were cultured in RPMI Medium 1640 basic(1X) (C22400500BT,Gibco). All the cultured media were supplemented with 10% (v/v) foetal bovine serum (26140079, Gibco) and 1% penicillin-streptomycin (15140122, Gibco). Cells were cultured at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
A549, Hela cultured cells, PBMCs, and B16F10 tumor cells were harvested and dissociated. Cells were dispensed into a ICELL8 nanowell chip for PSCSR-seq analysis.
single cell small RNA analysis used PSCSR-seq protocol, briefly, small RNAs were ligated with 3' adapters using T4 RNA Ligase 2, truncated KQ (NEB), the remained 3' adapter were removed by 5' Deadenylase (NEB) and Lambda Exonuclease (Thermo Fisher). 5'adapters were ligated to the small RNA using T4 RNA Ligase 1(NEB). The adapters carrying 8 random nucleotides (UMI) for the small RNA counting. The ligated small RNAs were reverse-transcribed using Superscript III (Thermo Fisher), and two rounds of PCRs were performed to introduce the barcodes for labeling cells and multiplexing samples. PSCSR library was size selected with Pippin Prep, and the size distribution was assessed using an Agilent 2100 BioAnalyzer; Single cell RNA-seq followed Chromium Single Cell 3' Reagent Kits User Guide (v2 Chemistry) from the 10X Genomics company.

tag: cell type

tag: passages

tag: molecule subtype

value: small RNA


title: C. glabrata Sfp1 mutant expression data [251983910041_1_4_Cgla_T30_9955]

description:
251983910041_201102091113_S01_GE2_105_Dec08_1_4.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata WT expression data [251983910041_1_4_Cgla_T30_WT]

description:
251983910041_201102091113_S01_GE2_105_Dec08_1_4.txt
C. glabrata WT expression data


title: C. glabrata Sfp1 mutant expression data [251983910041_2_2_Cgla_T30_9955]

description:
251983910041_201102091113_S01_GE2_105_Dec08_2_2.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata WT expression data [251983910041_2_2_Cgla_T30_WT]

description:
251983910041_201102091113_S01_GE2_105_Dec08_2_2.txt
C. glabrata WT expression data


title: PSCSR-seq analysis for A549, Hela, K562, HEK293T cell mixture

data_processing:
The PSCSR-seq analysis procedures are adapted from the method in the publication(S. Mi and T. Cai et al., Cell 133, 116, 2008). Briefly, the small RNA sequences, cell barcodes and molecules UMI are extracted from the raw reads using the customized scripts. The small RNA sequence with the length of 19nt~39nt were kept and mapped to the reference genome with no mismatch (bowtie v1.2.2). The small RNAs are annotated to according to the databases including miRbase (release v22.1), EBI RNAcenter database (release v11), EBML CDS database (ENSEMBL release v96). For certain small RNA gene, different UMIs (at least 2-base difference) were counted as the measurement of small RNA expression. The computational pipeline can be found at github (https://github.com/biocaitao/PSCSR-seq).
The single cells in PSCSR-seq were selected using TaKaRa ICell8 system protocol (“StandardCellSettings-V5” or “PBMCv4”). The cell barcodes of selected cells were exported. The valid cells were filtered from the background according to the exported barcodes (allowing 2 mismatches). Further, the cells within a ~10-fold range of UMI counts were considered high quality (GX.Zheng, JM.Terry, Nat Commun.16;8:14049 2017 or refer to https://github.com/biocaitao/PSCSR-seq ).
Single-cell RNA-seq analysis can refer to the 10X genomics "cellranger" software manual (detail can refer to Y. Wang and Z. Tang, et al., PNAS,115,2407, 2018).
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: PSCSR-seq processed files contain: plain text files for cell barcodes and estimated expression of miRNAs and all small RNAs; single cell mRNA-seq processed files contain: zipped plain text files from output of cellranger (version 3.0.1, 10X Genomics).

extract_protocol:
Cultured cancer cells, PBMCs, and tumor tissue were harvested and dissociated. Cells were dispensed into a ICELL8 nanowell chip for PSCSR-seq analysis.
single cell small RNA analysis used PSCSR-seq protocol, briefly, small RNAs were ligated with 3' adapters using T4 RNA Ligase 2, truncated KQ (NEB), the remained 3' adapter were removed by 5' Deadenylase (NEB) and Lambda Exonuclease (Thermo Fisher). 5'adapters were ligated to the small RNA using T4 RNA Ligase 1(NEB). The adapters carrying 8 random nucleotides (UMI) for the small RNA counting. The ligated small RNAs were reverse-transcribed using Superscript III (Thermo Fisher), and two rounds of PCRs were performed to introduce the barcodes for labeling cells and multiplexing samples. PSCSR library was size selected with Pippin Prep, and the size distribution was assessed using an Agilent 2100 BioAnalyzer; Single cell RNA-seq followed Chromium Single Cell 3' Reagent Kits User Guide (v2 Chemistry) from the 10X Genomics company.

value: mixture of A549, Hela, K562, HEK293T cells


title: F1-iMNIC rep1

status: Public on Jun 29 2020

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: replicate 1

data_processing:
Trimmed for adapter sequences using Trimmomatic-0.36 to trim overrepresented sequences.
Alignment and annotated the raw data to the Homo sapiens NCBI GRCh38 genome using HISAT2.
Assemble the mapped reads into possible transcripts and generate a transcriptome assembly with Cufflinks.
Calculation of counts with HTSeq.
Variance stabilization performed using log2 scaling.
Batch effect correction after integration with RNA-seq data from the Sequence Read Archive (SRA) database for wild type motoneurons MN wtMN-1(BJ) (SRR2038215), wtMN-2(S+P) (SRR606336) and human ESC H9 (SRR3647179)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file include log2 counts values for each sample

growth_protocol: Human adult fibroblasts were obtained from surgical resectates, which have been obtained with the informed consent. Parental fibroblasts were maintained in fibroblast medium (high-glucose DMEM (GIBCO) containing 10% fetal bovine serum (FBS) (GIBCO), 1% penicillin/streptomycin, 1 mM l-glutamine, 1% non-essential amino acids (NEAA) (GIBCO), and 0.1 mM beta-mercaptoethanol (GIBCO)). 293T cells used for virus production were maintained in high-glucose DMEM containing 10% FBS, penicillin/streptomycin, l-glutamine.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Generation of iMNs :
Human fibroblasts were seeded at 1 x 104 cells on gelatin-coated 6-well plates. On the next day, the fibroblasts were infected with lentiviral vector in fibroblast medium containing 6 microg/ml protamine sulfate. The viral supernatant was removed after 24 h of infection and replaced with fresh fibroblast medium. At 3 days post-infection, the medium was switched to neural induction medium (DMEM/F12 (GIBCO) supplemented with N2 (GIBCO), penicillin/streptomycin, 10 ng/ml bFGF (Peprotech), and 10 ng/ml epidermal growth factor (EGF, Peprotech)). Infected cells were mechanically isolated by a glass micropipette and transferred into defined MN induction medium (DMEM/F12 and neurobasal medium (GIBCO) supplemented with N2 (GIBCO), B27 (GIBCO), penicillin/streptomycin, 50 ng/ml SHH (Peprotech), and 10 ng/ml IGF-1). The floating MN aggregates were re-plated onto PDL/laminin-coated plate, and the iMN-like cells outgrew gradually.

value: Induced motor neurons (iMN)


title: F1-iMN rep1

description: replicate 1


title: C. glabrata WT expression data [251983910042_1_2_Cgla_T60_WT]

description:
251983910042_201102091136_S01_GE2_105_Dec08_1_2.txt
C. glabrata WT expression data


title: C. glabrata WT expression data [251983910041_1_3_Cgla_T90_WT]

description:
251983910041_201102091113_S01_GE2_105_Dec08_1_3.txt
C. glabrata WT expression data


title: C. glabrata Sfp1 mutant expression data [251983910041_1_2_Cgla_T60_9955]

description:
251983910041_201102091113_S01_GE2_105_Dec08_1_2.txt
C. glabrata Sfp1 mutant expression data


title: C. glabrata WT expression data [251983910041_1_2_Cgla_T60_WT]

description:
251983910041_201102091113_S01_GE2_105_Dec08_1_2.txt
C. glabrata WT expression data


title: C. glabrata Sfp1 mutant expression data [251983910041_1_1_Cgla_T30_9955]

description:
251983910041_201102091113_S01_GE2_105_Dec08_1_1.txt
C. glabrata Sfp1 mutant expression data


title: Healthy Lung autopsy_1 [HealthyLungBiopsy_1]

status: Public on Aug 11 2020

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: txt files storing raw read counts per gene per sample

source_name: Healthy Lung autopsy

growth_protocol: Protocols for maintenance of hPSCs and generation of lung organoids were slightly modified from previous studies. The hESC line RUES2 was cultured on irradiated mouse embryonic fibroblasts (Global Stem, cat. no. GSC-6001G) at a density of 20,000- 25,000 cells/cm2 in a medium of DMEM/F12, 20% knockout serum replacement (Life Technologies), 0.1 mM β-mercaptoethanol (Sigma Aldrich) and 20 ng/ml bFGF (R&D Systems), and medium was changed daily. hESC cultures were maintained in an undifferentiated state at 37 °C in a 5% CO2/air environment until stem cells reached about 90% confluence.     hESC differentiation into endoderm was performed in serum-free differentiation (SFD) medium of DMEM/F12 (3:1) (Life Technologies) supplemented with N2 (Life Technologies), B27, 50 μg/ml ascorbic acid, 2 mM Glutamax, 0.4 μM monothioglycerol, 0.05% BSA at 37 °C in a 5% CO2/5% O2/95% N2 environment. hESCs were treated with Accutase and plated onto low attachment 6-well plates (Corning Incorporated, Tewksbury MA), resuspended in endoderm induction medium containing 10 μM Y-27632, 0.5 ng/ml human BMP4, 2.5 ng/ml human bFGF, 100 ng/ml human Activin A, for 72-76 hours dependent on the formation rates of endoderm cells. On day 3 or 3.5, the endoderm bodies were dissociated into single cells using 0.05% Trypsin/0.02% EDTA and plated onto fibronectin-coated, 24-well tissue culture plates (~100,000–150,000 cells/well). For induction of anterior foregut endoderm, the endoderm cells were cultured in SFD medium supplemented with 1.5 μM dorsomorphin dihydrochloride (R&D Systems) and 10 μM SB431542 (R&D Systems) for 36 hrs, and then switched to 36 hrs of 10 μM SB431542 and 1 μM IWP2 (R&D Systems) treatment. For induction of early stage lung progenitor cells (day 6–15), the resulting anterior foregut endoderm was treated with 3 μM CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human KGF, 10 ng/ml human BMP-4 and 50-60 nM all-trans retinoic acid (ATRA), in SFD medium for 8–10 d. The day 10–15 cultures were maintained in a 5% CO2/air environment. On days 15 and 16, the lung field progenitor cells were replated after one minute trypsinization onto fibronectin-coated plates, in the presence of SFD containing either a combination of five factors (3 μM CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human FGF7, 10 ng/ml human BMP4, and 50 nM ATRA). Day 16–25 cultures of late stage lung progenitor cells were maintained in SFD media containing 3 μM CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human KGF, in a 5% CO2/air environment. For differentiation of mature lung cells (day 25 to 55) in 3D culture, cultures were re-plated and embedded in 90% Matrigel after brief trypsinization in SFD media containing maturation components containing 3 μM CHIR99021, 10 ng/ml human FGF-10; 10 ng/ml human KGF, and DCI (50 nM Dexamethasone, 0.1 mM 8-bromo-cAMP (Sigma Aldrich ) and 0.1 mM IBMX (3,7-dihydro-1-methyl-3-(2-methylpropyl)-1H-purine-2,6-dione) (Sigma Aldrich).

extract_protocol:
At 24 hpi, hPSC-LOs or hPSC-COs were washed three times in PBS and lysed in TRIzol for RNA analysis.
Libraries were prepared using Illumina TruSeq stranded mRNA Sample Preparation kit.

treatment_protocol: hPSC-LOs were infected with SARS-CoV-2 at the indicated MOI and incubated for 24 hrs at 37°C.

tag: subject status

value: healthy

tag: tissue/cell type

value: adult lung autopsy


title: Healthy Lung autopsy_2 [HealthyLungBiopsy_2]


title: PSCSR-seq analysis for A549/Hela cell mixture [AH_PSCSR]

value: A549/Hela mixture


title: PSCSR-seq analysis for A549 cell line [A549_PSCSR]


title: MEF

status: Public on Jun 24 2020

description: replicate 1

hyb_protocol: Purified and labeled cRNA was then hybridized for 18 hrs onto HumanHT-12 v4 expression BeadChips (Illumina, USA) following the manufacturer’s instructions

scan_protocol: After the recommended washing, the chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and the accompanying software.

data_processing:
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina),
background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model,
variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in MATLAB.
Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the
Unweighted Pair-Group Method using Average (UPGMA) linkage method

label: biotin

source_name: MEF

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol:
300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 18h)
The RNA samples from in vivo transplanted and FACS sorted cells
were amplified using the TargetAmp 2-Round Biotin-aRNA Amplification Kit 3.0 (Epicentre, USA) from 100 pg to 50 microg.

tag: oct family member

tag: strain


title: NSC-HA rep1

description: replicate 1

source_name: NSC-HA

value: Neural Stem Cell (NSC)


title: F1 rep1

description: replicate 1

value: Fibroblast


title: F2-iMNIC rep1

description: replicate 1


title: PSCSR-seq analysis for K562 cell line

tag: cell line


title: F2-iMN rep1

description: replicate 1


title: PSCSR-seq analysis for tumor tissue [Tumor_PSCSR]

description: The metastatic foci and the surrounding lung tissue from melanoma mouse model were collected 12 days after tail injection of B16-F10 cells and dissociated.12 days after B16F10 tail injection)

source_name: lung tissue from melanoma mouse model

value: melanoma cells and normal cells


title: PSCSR-seq analysis for PBMCs

description: Individual PBMC components were purchased from ALLCELLs, Shanghai

source_name: PBMCs purchased from ALLCELLS (Shanghai, China)

value: mixture of CD3+ Pan T Cells, CD19+ B Cells, CD14+ Monocytes, and CD56+ Natural Killer Cells


title: O7 iPS rep 2

description: replicate 2

source_name: O7 iPS


title: O7 iPS rep 1

description: replicate 1


title: O11 iPS rep 2

description: replicate 2

source_name: O11 iPS


title: O6 iPS rep 2

description: replicate 2

source_name: O6 iPS


title: O4 iPS rep 1

description: replicate 1

source_name: O4 iPS


title: O6 iPS rep 1

description: replicate 1


title: O11 iPS rep 1

description: replicate 1


title: O4 iPS rep 2

description: replicate 2


title: O8 iPS rep 2

description: replicate 2

source_name: O8 iPS


title: O9 iPS rep 1

description: replicate 1

source_name: O9 iPS


title: H1 ESC rep1

description: replicate 1

data_processing:
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in MATLAB.
Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method

extract_protocol: 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 18h)

value: Human Embryonic Stem Cell (ESC)


title: O8 iPS rep 1

description: replicate 1


title: H1 ESC rep2

description: replicate 2


title: H9 ESC rep2

description: replicate 2


title: O9 iPS rep 2

description: replicate 2


title: O9 iPS#3 rep 2

description: replicate 2

source_name: O9 iPS#3

value: Human induced Pluripotent Stem (iPS) cells


title: O9 iPS#3 rep 1

description: replicate 1


title: O9 iPS#4 rep 2

description: replicate 2

source_name: O9 iPS#4


title: H9 ESC rep1

description: replicate 1


title: O8 iPS#1 rep 1

description: replicate 1

source_name: O8 iPS#1


title: O8 iPS#1 rep 2

description: replicate 2


title: O9 iPS#4 rep 1

description: replicate 1


title: F2 rep1

description: replicate 1


title: O4 iPS#2 rep 2

description: replicate 2

source_name: O4 iPS#2


title: O7 iPS#1 rep 2

description: replicate 2

source_name: O7 iPS#1


title: O7 iPS#4 rep 2

description: replicate 2

source_name: O7 iPS#4


title: O7 iPS#1 rep 1

description: replicate 1


title: O8 iPS#3 rep 2

description: replicate 2

source_name: O8 iPS#3


title: Fibs1 rep 2

description: replicate 2

value: Human fibroblast


title: Fibs2 rep 1

description: replicate 1


title: O6 iPS#2 rep 2

description: replicate 2

source_name: O6 iPS#2


title: O7 iPS#4 rep 1

description: replicate 1


title: O6 iPS#1 rep 2

description: replicate 2

source_name: O6 iPS#1


title: O6 iPS#2 rep 1

description: replicate 1


title: O8 iPS#3 rep 1

description: replicate 1


title: O4 iPS#1 rep 1

description: replicate 1

source_name: O4 iPS#1


title: O4 iPS#1 rep 2

description: replicate 2


title: Fibs2 rep 2

description: replicate 2


title: O4 iPS#2 rep 1

description: replicate 1


title: Fibs1 rep 1

description: replicate 1


title: O6 iPS#1 rep 1

description: replicate 1


title: liver51

status: Public on May 06 2020

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: liver biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array  (Affymetrix, Santa Clara, CA).

growth_protocol: All human liver biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

tag: tissue

value: liver transplant biopsy


title: liver194


title: liver235


title: liver29


title: liver114


title: liver40


title: liver42


title: liver34


title: liver107


title: liver190


title: liver193


title: liver230


title: liver43


title: liver217


title: liver115


title: liver56


title: liver127


title: liver12


title: liver69


title: liver213


title: liver221


title: liver72


title: liver36


title: liver191


title: liver225


title: liver73


title: liver196


title: liver148


title: liver13


title: liver54


title: liver4


title: liver134


title: liver183


title: liver123


title: liver129


title: liver1


title: liver10


title: liver26


title: liver75


title: liver198


title: liver53


title: liver108


title: liver199


title: liver33


title: liver133


title: liver2


title: liver215


title: liver233


title: liver119


title: ESC

description: replicate 1

source_name: ESC


title: liver20


title: liver228


title: liver207


title: liver11


title: liver65


title: liver216


title: liver96


title: liver41


title: liver192


title: liver111


title: liver80


title: liver105


title: liver155


title: liver49


title: liver59


title: liver184


title: liver68


title: liver231


title: liver159


title: liver25


title: liver76


title: liver50


title: liver95


title: liver141


title: liver94


title: liver88


title: liver142


title: liver35


title: liver161


title: liver118


title: liver210


title: liver126


title: liver77


title: liver124


title: liver102


title: liver67


title: liver169


title: liver171


title: liver47


title: liver203


title: liver202


title: liver46


title: liver136


title: liver140


title: liver19


title: liver167


title: liver120


title: liver234


title: liver163


title: liver223


title: liver156


title: liver83


title: liver137


title: liver153


title: liver112


title: liver93


title: liver186


title: liver85


title: liver8


title: liver97


title: liver157


title: liver168


title: liver214


title: liver92


title: liver82


title: liver219


title: liver122


title: liver100


title: liver116


title: liver23


title: liver15


title: liver143


title: liver32


title: liver179


title: liver31


title: liver226


title: liver5


title: liver170


title: liver218


title: liver27


title: liver151


title: liver222


title: liver90


title: liver201


title: liver173


title: liver84


title: liver89


title: liver30


title: liver38


title: liver160


title: liver37


title: liver70


title: liver57


title: liver132


title: liver64


title: liver189


title: liver154


title: liver128


title: liver195


title: liver86


title: liver220


title: liver99


title: liver130


title: liver66


title: liver39


title: liver229


title: liver74


title: liver55


title: liver81


title: liver125


title: liver135


title: liver91


title: liver165


title: liver208


title: liver172


title: liver211


title: liver52


title: liver58


title: liver103


title: liver178


title: liver212


title: liver188


title: liver104


title: liver209


title: liver232


title: liver174


title: liver206


title: liver28


title: liver22


title: liver24


title: liver79


title: liver146


title: liver78


title: liver110


title: liver62


title: liver7


title: liver113


title: liver197


title: liver14


title: liver144


title: liver224


title: liver6


title: liver175


title: liver60


title: liver71


title: liver152


title: liver17


title: liver182


title: liver180


title: liver44


title: liver162


title: liver9


title: liver106


title: liver176


title: liver63


title: liver45


title: liver158


title: liver164


title: liver101


title: liver205


title: liver16


title: liver48


title: liver139


title: liver138


title: liver21


title: liver200


title: liver147


title: liver227


title: liver185


title: liver98


title: liver61


title: liver149


title: liver18


title: liver121


title: liver109


title: liver166


title: dtog1_H2

status: Public on Apr 09 2020

city: Lisbon

first: Miguel

middle: Cacho

last: Teixeira

address: Avenida Rovisco Pais 1

department: Institute for Bioengineering and Biosciences

country: Portugal

institute: Instituto Superior Tecnico

data_processing:
Quality control of reads was assessed with FastQC
Trimming of the reads was performed with Skewer
Mapping to the reference genome was done using TopHat
Counts per gene were calculated with HTSeq
Differential gene expression analysis was calculated with DESeq2
Genome_build: CBS138
Supplementary_files_format_and_content: Counts files containing the genome's ORFs and the number of read counts for each ORF

source_name: Cell pellet

growth_protocol: Cell were grown in minimal medium until early exponential phase

extract_protocol:
Ambion Ribopure-Yeast RNA kit, according to manufacturer’s instructions.
Illumina Truseq Stranded Total RNA library prep kit with ribosomal depletion via RiboZero Gold according to the manufacturer’s protocol

treatment_protocol: Cell pellets were collected and immediately stored at -80ºC

tag: genotype

tag: treatment

value: hydrogen peroxide


title: Series15_HealthyLungBiopsy_1

status: Public on Apr 10 2020

first: Daniel

last: Blanco Melo

address: One Gustave L. Levy Place, Box 1124

department: Microbiology

institute: Icahn School of Medicine at Mount Sina

description:
Lung25220-77yearsold-male-GB1-indD11
processed data file: RawReadCounts_Human.tsv

data_processing:
cDNA libraries were sequenced using an Illumina NextSeq 500 platform
Raw sequencing reads were aligned to the human genome (hg19) or Ferret genome (MusPutFur1.0) using the RNA-Seq Alignment App (v2.0.1) on Basespace (Illumina, CA)
Differential gene expression analysis was performed using DESeq2 (implemented in the RNA Express App (v1.1.0) on Basespace (Illumina, CA)) comparing Infected samples to their correspondent mock treated sample, for each virus/cell type.
Genome_build: human (hg19), Ferret (MusPutFur1.0)
Supplementary_files_format_and_content: Tab separated value (tsv) matrix of raw read counts per gene for each sample.

molecule: polyA RNA

source_name: Lung biopsy for heatly negative control

extract_protocol:
TruSeq RNA Library Prep Kit v2
Total RNA was extracted using RNeasy Mini Kit (Qiagen)

value: No treatment - healthy 77 years old, male

value: Lung Biopsy


title: Series15_HealthyLungBiopsy_2

description:
Lunng8-22839-72yearsold-male-GB2-indD12
processed data file: RawReadCounts_Human.tsv

value: No treatment - healthy 72 years old, male


title: WT_C1

value: WT

value: control


title: WT_C2


title: liver187


title: liver3


title: liver145


title: liver204


title: dtog1_C2


title: dtog1_H1


title: liver131


title: liver177


title: liver181


title: WT_H1


title: dtog1_C1


title: WT_H2


title: HSC-1

status: Public on Mar 02 2020

city: Baltimore

first: Michael

middle: A

last: Koldobskiy

state: MD

address: 855 N. Wolfe St.

department: Center for Epigenetics

institute: Johns Hopkins University

library_source: genomic

data_processing:
base calls and demultiplexing: bcl2fastq v1.8.4
Trim Galore! v0.3.6
Bismark v0.12.3
InformME
Genome_build: hg19
Supplementary_files_format_and_content: bed format.  Tracks include mean methylation level (MML), normalized methylation entropy (NME), methylation sensitivity index (MSI), and differential quantities of the above between samples (dMML, dNME, dMSI) and Jensen Shannon Distance (JSD) to measure epigenetic discordance between samples, as well as tracks of differentially methylated regions (DMR) based on JSD.

molecule: genomic DNA

source_name: HSC

extract_protocol:
Epicentre DNA extraction kit
Whole Genome Bisulfite Sequencing; Illumina TruSeq, NEBNext

tag: tissue type

value: primary

value: HSC


title: CD34-3

source_name: CD34+ HSPC

value: CD34+ HSPC


title: L-MPP-1

source_name: L-MPP

value: L-MPP


title: CD34-2


title: CD34-1


title: GMP-1

source_name: GMP

value: GMP


title: AML-9

source_name: acute myeloid leukemia

value: acute myeloid leukemia

tag: cytogenetics

value: MLL-rearranged


title: AML-8


title: AML-7


title: AML-5


title: AML-6


title: AML-3


title: AML-4


title: Cd0 rep 3

status: Public on Apr 30 2020

type: genomic

description: replicate 3

hyb_protocol: Genomic input DNA and the IP DNA were first amplified by Genome Plex Complete WGA Kit (Sigma Aldrich, Hamburg, Germany) as described in the manufacturer protocol. Briefly, 30 ng DNA of a 3 ng/microl DNA solution were amplified by 20 PCR cycles using the Amplification Master Mix. Input DNA and IP DNA were labeled in parallel, and 1 microg of each amplified DNA sample were hybridized to NimbleGen (Roche, Basel, Switzerland) Mouse 385 K RefSeq Promoter Arrays containing all known RefSeq genes (NM prefix). Hybridization was performed using the NimbleGen Hybridization System as per the manufacturers instructions. The hybridized arrays were then washed with the NimbleGen Wash Buffer Kit, and dried with the NimbleGen Microarray Drier as per the manufacturers instructions.

scan_protocol: The hybridized arrays were scanned on an Axon 4000B microarray scanner (Molecular Devices, Sunnyvale, CA), and the images were analyzed with Axon GenePix software version 4.1. Image and data analyses were processed with NimbleScan version 2.5 and SIgnalMap version 1.9 software.

data_processing:
The methylation ratios between the IP DNA samples and the control input samples were normalized across samples using the quantile method after performing a variance stabilization using log2 scaling.
The mean of each promoter feature was determined from three different biological replicates,
Data post-processing and graphics were performed with in-house developed functions in MATLAB.
The 293792 array features that report signals across all 6 samples are reported below.

source_name: Cd0 rep 3, methylation-enriched

label_protocol:
Genomic DNA (1 microgram) from each tissue sample was sonicated in a final volume of 200 microl to produce random fragments
ranging in size from 300-1,000 bp by the Vibra Cell 75022 Ultrasonic Processor (Novodirect, Kehl, Germany) with a 2-mm tipp.
Immunoprecipitation (IP) of methylated DNA was performed with the MeDIP kit (Diagenode, Liege, Belgium) in accordance with the manufacturer instructions.
In brief, DNA samples at a final concentration of 0.1 microg/microl were denatured at 95C for 3 min,
quickly chilled on ice and finally immunoprecipitated by adding 0.3 microl of manufacturer´s bead-immobilized anti-5-methylcytosine antibody.
Control input samples contained only 20% of that DNA sample used for IP.
The bound DNA was separated from the beads by incubation at 65C for 10 min and by using 1 volume of phenol/chloroform/isoamylalcohol (25/24/1).
Input and methylation-enriched samples were labelled with Cy3 and Cy5, respectively, using the NimbleGen Dual-Colour DNA Labelling Kit.

extract_protocol:
10 to 15 mg of tissue were placed in liquid nitrogen and thoroughly grounded with a mortar.
Tissue powder was incubated at 56C for 4 hours in lysis buffer including 12 mAU proteinase K, before adding 0.4 mg RNase A at room temperature for 2 minutes.
DNA was precipitated with ethanol and separated by using QIAamp Mini spin columns to finally obtain 8 to 20 microg of high quality DNA per sample.

tag: gender

value: Female

tag: testosterone treated

value: No

value: liver

tag: methylation-enrichment

source_name: Cd0 rep 3, input


title: Td0 rep 2

description: replicate 2

source_name: Td0 rep 2, methylation-enriched

value: Yes

source_name: Td0 rep 2, input


title: Cd0 rep 2

description: replicate 2

source_name: Cd0 rep 2, methylation-enriched

source_name: Cd0 rep 2, input


title: Zfish OPCs

status: Public on Feb 18 2020

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

data_processing:
Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods 10, 1096-1098 (2013). The sequencing was done on a Illumina HiSeq 2500 instrument. Further specifications: The run was on a high-output flow cell with 50 bp single-read, clustered on a cBot with V4 kit.
Individual cell fastq files were aligned to the transcriptome with STAR.2.5.1b GRCz11 ENSEMBL94 reference genome. Gene expression for each gene was calculated with Salmon0.9.1 using the reads aligned to the transcriptome for each of the individual cells.
Expression matrix was built by combining all cells gene expressions as TPM. QC and clustering with Seurat3 allowed the annotation of 310  individual cells in specific celltypes.
The R object (.rds), consists of a Seurat v.3 object. Cells were clustered with Seurat  v.3  and filtered based on the distribution of gene expression and mitochondrial gene expression. The remaining 310 cells were log-normalized individually with a scale of factor of 10,000. The shared-nearest neighbor (SNN) graph was constructed on cell-to-cell distance matrix from top 50 PCs. The SNN graph with resolution 1 was used as an input for the smart local moving (SLM) algorithm to obtain cell clusters, and visualized with t-distributed stochastic neighbor embedding (t-SNE). The object includes in reductions, tsne, and metadata, Celltype, the embedding and clustering used in the study.
Genome_build: GRCz11
Supplementary_files_format_and_content: Final expression data matrix with 310 cells as used in the study, where columns are the cells and rows the genes. Gene expression values provided as TPM. Annotation data matrix, where columns belong to celltype and rows to cells. R object (.rds).

organism: Danio rerio

source_name: oligodendrocyte precursor cells

growth_protocol: Tg(olig1:memYFP) zebrafish were raised until  5 days post fertilization

extract_protocol:
A single-cell suspension was generated by incubation of the whole embryo in papain (30min @ 37°C), followed by manual tissue dissociation and subsequent filtration and centrifugations. The resulting single-cell suspension was sorted at a MoFlo EDP cell sorter in two steps: 1. EYFP-pos/ Propidium Iodite-neg; 2. EYFP-pos/ Vybrant DyeCycle Ruby-pos.
SmartSeq2 raw data was processed according to procedures described in S. Picelli et al., Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods 10, 1096-1098 (2013)

treatment_protocol: no treatment

tag: transgenic line

value: EYFP cells FACS sorted from dissociated whole animal

value: oligodendrocyte precursor cells

tag: age

value: 5 days post fertilization


title: AML-2

tag: cell type


title: liver_Vd11 rep 3

status: Public on Feb 10 2020

description: replicate 3

hyb_protocol: Agilent mouse whole genome 8x60K oligo microarrays (design 028005) were used for hybridizations. Each microarray displayed 39,430 Entrez Gene RNAs and 16,251 lincRNAs. The Agilent Gene Expression Hybridization Kit was used for hybridization as detailed in the Agilent processing protocol (Agilent technologies). In brief, 600 ng Cy3-labelled fragmented cRNA in hybridization buffer was hybridized overnight at 65C to the microarrays using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed with the Agilent Gene Expression Wash Buffer 1 (1 min at 23C) and then with preheated Agilent Gene Expression Wash Buffer 2 (1 min at 37C)

scan_protocol: The Agilent’s Microarray Scanner Sytem (Agilent Technologies) was used for detecting fluorescence signals on the hybridized microarrays. The microarray image files were processed with the Agilent Feature Extraction Software (FES).

data_processing: The microarray raw data were normalized using the quantile method.

source_name: Vd11 rep 3

label_protocol: Each RNA sample was used to produce Cy3-labeled cRNA. Eqivalents of 100 ng from the individual RNA samples were amplified and labeled with the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Yields of cRNA and dye-incorporation were determined with the ND-1000 Spectrophotometer (NanoDrop Technologies). The incorporations were between 18 and 23 fmol Cy3/ng cRNA.

extract_protocol: Livers were aseptically removed from sacrificed mice, rapidly frozen in liquid nitrogen and stored at -80o C until use. For isolation of total RNA, livers were individually grounded in a mortar under liquid nirogen and aliquots were subjected to the Trizol standard RNA extraction. An additional cleaning up of  RNA followed using the miRNeasy Kit (Qiagen, Hilden, Germany). Integrity and quality of RNA was checked with the Agilent 2100 Bioanalyzer platform (Agilent Technologies). RIN values of all RNA samples ranged beween 8.7 and 9.1.

value: Balb/c

tag: Sex

value: female

tag: vaccinated status

value: Vaccinated


title: Cd0 rep 1

description: replicate 1

source_name: Cd0 rep 1, methylation-enriched

source_name: Cd0 rep 1, input


title: AML-1

value: primary


title: Td0 rep 1

description: replicate 1

source_name: Td0 rep 1, methylation-enriched

source_name: Td0 rep 1, input


title: liver_Vd11 rep 1

description: replicate 1

source_name: Vd11 rep 1


title: liver_Vd8 rep 1

description: replicate 1

source_name: Vd8 rep 1


title: liver_Vd8 rep 3

description: replicate 3

source_name: Vd8 rep 3


title: Td0 rep 3

description: replicate 3

source_name: Td0 rep 3, methylation-enriched

source_name: Td0 rep 3, input


title: liver_Vd4 rep 3

description: replicate 3

source_name: Vd4 rep 3


title: liver_Vd4 rep 2

description: replicate 2

source_name: Vd4 rep 2


title: liver_Vd1 rep 2

description: replicate 2

source_name: Vd1 rep 2


title: liver_Vd8 rep 2

description: replicate 2

source_name: Vd8 rep 2


title: liver_Vd4 rep 1

description: replicate 1

source_name: Vd4 rep 1


title: liver87

source_name: liver biopsy

value: liver transplant biopsy


title: liver_Nd11 rep 3

description: replicate 3

source_name: Nd11 rep 3

value: Non-vaccinated


title: liver_Vd0 rep 3

description: replicate 3

source_name: Vd0 rep 3


title: liver117


title: liver_Vd0 rep 2

description: replicate 2

source_name: Vd0 rep 2


title: liver_Vd0 rep 1

description: replicate 1

source_name: Vd0 rep 1


title: liver_Vd11 rep 2

description: replicate 2

source_name: Vd11 rep 2


title: liver_Vd1 rep 1

description: replicate 1

source_name: Vd1 rep 1


title: liver_Nd11 rep 2

description: replicate 2

source_name: Nd11 rep 2


title: liver_Nd8 rep 2

description: replicate 2

source_name: Nd8 rep 2


title: liver_Nd8 rep 3

description: replicate 3

source_name: Nd8 rep 3


title: Microglia PBS 1

status: Public on Jan 21 2020

city: New Brunswick

first: Qi

last: Yang

state: NJ

address: 89 French St

institute: Rutgers RWJMS

data_processing:
Single-end 75 bp high throughout sequencing was performed using a NextSeq 500 (Illumina).
Raw data was converted to fastq files using bcl2fastq v2.20.0.422 and quality checked using fastqc v 1.0.0.
RNA-seq reads were aligned to mm10 genome by the STAR aligner V2.5.3a.
Reads Per Kilobase of exon per Megabase (RPKM) estimation of reference genes and transcripts using Cufflinks V2.0.
Differential expression was calculated using DEseq2 (v1.1).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: IL-5_treated_mice_final.txt: Text file includes normalized abundance measurements for all Samples.

source_name: Microglia

extract_protocol:
Microglia and brain T cells from IL-5 or PBS treated aged brains were sorted based on their surface marker expressions. Trizol-LS extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Aged mice (20-22mos) were injected with 2ug of IL-5 daily for 2 days

value: PBS


title: liver150


title: liver_Nd1 rep 2

description: replicate 2

source_name: Nd1 rep 2


title: Microglia PBS 2


title: Microglia IL-5_1


title: T cells IL-5_1

source_name: T cells

treatment_protocol: Aged mice (20-22mos) were injected with 2ug of IL-5 daily for 2 days.


title: T cells PBS 2


title: liver_Nd0 rep 1

description: replicate 1

source_name: Nd0 rep 1


title: T cells IL-5_2


title: IL-33 Aged 3 ILC2

description: 7x 400ng IL-33

data_processing:
Single-end 75 bp high throughout sequencing was performed using a NextSeq 500 (Illumina)
Raw data was converted to fastq files using bcl2fastq v2.20.0.422 and quality checked using fastqc v 1.0.0.
RNA-seq reads were aligned to mm10 genome by the STAR  aligner V2.5.3a
Reads Per Kilobase of exon per Megabase  (RPKM) estimation of reference genes and transcripts using Cufflinks V2.0
Differential expression was calculated using DEseq2 (v1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Text file for processed data file, and Fastq files for each sample

source_name: Brain ILC2

extract_protocol:
Microglia, T cells and ILC2 from aged brains were sorted based on their surface marker expressions. Trizol-LS extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Aged mice (20-22mos) were injected with 400ng of IL-33 daily for 7 days.

value: Brain ILC2


title: IL-33 Aged 2 T cells

description: 7x 400ng IL-33

source_name: Brain T cells

value: Brain T cells


title: liver_Nd4 rep 2

description: replicate 2

source_name: Nd4 rep 2


title: liver_Nd0 rep 3

description: replicate 3

source_name: Nd0 rep 3


title: T cells PBS 1


title: Microglia IL-5_2


title: IL-33 Aged 2 Microglia

description: 7x 400ng IL-33

value: Microglia


title: liver_Nd4 rep 1

description: replicate 1

source_name: Nd4 rep 1


title: IL-33 Aged 2 ILC2

description: 7x 400ng IL-33


title: liver_Nd1 rep 3

description: replicate 3

source_name: Nd1 rep 3


title: liver_Nd11 rep 1

description: replicate 1

source_name: Nd11 rep 1


title: liver_Nd4 rep 3

description: replicate 3

source_name: Nd4 rep 3


title: liver_Nd0 rep 2

description: replicate 2

source_name: Nd0 rep 2


title: liver_Nd1 rep 1

description: replicate 1

source_name: Nd1 rep 1


title: IL-33 Aged 1 ILC2

description: 7x 400ng IL-33


title: IL-33 Aged 3 T cells

description: 7x 400ng IL-33


title: IL-33 Aged 3 Microglia

description: 7x 400ng IL-33


title: Young ILC2 culture 2-weeks_1

source_name: Young brain ILC2

growth_protocol: brain ILC2 were sorted from young and aged mice based on ILC2 surface marker expressions. ILC2 are cultured in ILC2 media consisting of 20% FCS in the presence of IL7, IL2, IL33 and SCF

extract_protocol:
Trizol-LS extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Old ILC2 culture 2-weeks_1

source_name: Old brain ILC2


title: Old ILC2 culture 2-weeks_3


title: IL-33 Aged 1 T cells

description: 7x 400ng IL-33


title: Young ILC2 culture 2-weeks_3


title: IL-33 Aged 1 Microglia

description: 7x 400ng IL-33


title: liver_Nd8 rep 1

description: replicate 1

source_name: Nd8 rep 1


title: Old ILC2 culture 2-weeks_2


title: Young ILC2 culture 2-weeks_2


title: Run_2788_Mouse: iKras_3w_ON

status: Public on Jan 13 2020

city: Ann Arbor

first: Marina

last: Pasca Di Magliano

state: MI

address: 1500 E Medical Center Dr.

institute: University of Michigan

description: Whole iKras* pancreas with PanIN lesions digested to single cell suspension and submitted for single cell sequencing

data_processing:
Sample was run using paired-end 50 cycle reads on HiSeq 4000 (Illumina) to a depth of 100,000 reads. Raw data was processed and aligned by the University of Michigan Advanced Genomics Core. Files were demultiplexed into FASTQ files using cellranger mkfastq v3.0.0.
FASTQ files were aligned, filtered, and counted by cellranger count v3.0.0 and formed into feature-barcode matrices.
Feature-barcode matrices were read into R using the Seurat package v3.2.2 and were analyzed according to the Seurat pipeline, including normalizing, scaling, filtering based on read counts and mitochondrial gene percentage, and manually labelling cells according to gene expression profiles.
Genome_build: mm10

extract_protocol:
Samples were mechanically and enzymatically digested (Collagenase V; 1 mg/mlL in RPMI) under constant agitation. Single cell suspensions were obtained by filtering consecutively through 500 μm, 100 μm, and 40 μm cell strainers. Dead cells were removed using MACS Dead Cell Removal Kit (Miltenyi Biotec).
Single cell cDNA libraries were prepared and sequenced using the 10X Genomics platform at the University of Michigan Advanced Genomics Core.

treatment_protocol: Mice were fed doxycycline water to induce expression of KrasG12D (Kras*) for 3 weeks following induction of acute pancreatitis.

value: Mixed

tag: disease state

value: acute pancreatitis

tag: ikras status

value: Kras* induced

tag: time point

value: 3 weeks ON

tag: number of mice pooled

value: iKras Pancreatic Intraepithelial Neoplasia (PanIN)


title: _Rpn4_Flu_I

status: Public on Sep 27 2019

data_processing:
Sequenced reads were trimmed for adaptor sequence, low-quality base calls using Skewer v0.2.2 with parameters -m pe -l 36 -q 15 -Q 15
Reads were mapped to CBS138 whole genome using TopHat v2.1.1 with parameters -p 12 -g 1 --b2-very-sensitive --library-type fr-firststrand
Reads counts per feature (ORF) were obtained with the htseq-count script from HTSeq (v 0.7.1) using parameters -m union -s reverse -t gene -i Name
Genome_build: CBS138 (http://www.candidagenome.org/)
Supplementary_files_format_and_content: Table with read counts for each feature (ORF)

growth_protocol: Cells were grown in minimal medium and exposed to fluconazole stress for 1h or not (control). Cells were pelleted and frozen at -80ºC until RNA extraction

extract_protocol:
Ambion Ribopure-Yeast RNA kit, according to the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype/variation

value: 1h fluconazole exposure


title: _Rpn4_Flu_II

tag: treatment


title: Wt_control_II

source_name: Wild type_control

value: Wild type

value: none (control)


title: Wt_Flu_II

source_name: Wild type_Flc


title: _Rpn4_control_I


title: _Rpn4_control_II


title: Wt_Flu_I


title: Wt_control_I


title: PEB#1 iPS

status: Public on Dec 09 2019

description: replicate 1

data_processing:
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina),
background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model,
variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in MATLAB.

source_name: PEB#1 iPS

tag: type of cell

value: PEB-iPSCs


title: H1-ESC rep 1 (3D)

description: replicate 1

source_name: H1-ESC rep 1

value: ESC


title: Old 3

description:
QY-C6_6
Performed at Boston University Microarray and Sequencing Resource Core Facility, Boston, MA, USA.

data_processing:
CDF: mogene20st_Mm_ENTREZG_17.1.0
Mouse Gene 2.0 ST CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the affymetrix package (version 1.36.1). Differential expression was assessed using the moderated (empirical Bayesian) t test implemented in the limma package (version 3.14.4).

source_name: Old mouse 3 Choroid plexus

growth_protocol: The choroid plexus of young and aged mice were harvested.

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

tag: strain/background

tag: tissue

value: Choroid plexus


title: Young 1

description:
QY-C1_1
Performed at Boston University Microarray and Sequencing Resource Core Facility, Boston, MA, USA.

source_name: Young mouse 1 Choroid plexus

value: 2-3 mos


title: H1-ESC rep 2 (3D)

description: replicate 2

source_name: H1-ESC rep 2


title: Old 2

description:
QY-C5_5
Performed at Boston University Microarray and Sequencing Resource Core Facility, Boston, MA, USA.

source_name: Old mouse 2 Choroid plexus


title: Young 2

description:
QY-C2_2
Performed at Boston University Microarray and Sequencing Resource Core Facility, Boston, MA, USA.

source_name: Young mouse 2 Choroid plexus


title: Young 3

description:
QY-C3_3
Performed at Boston University Microarray and Sequencing Resource Core Facility, Boston, MA, USA.

source_name: Young mouse 3 Choroid plexus


title: Old 1

description:
QY-C4_4
Performed at Boston University Microarray and Sequencing Resource Core Facility, Boston, MA, USA.

source_name: Old mouse 1 Choroid plexus


title: liver_Vd1 rep 3

description: replicate 3

source_name: Vd1 rep 3

value: Balb/c

value: female

value: liver

value: Vaccinated


title: Nd1 rep 2

status: Public on Sep 23 2019

description:
replicate 2
replicate 2

hyb_protocol: Equal amounts of labeled IP and input DNA were combined and loaded on Agilent's Mouse CpG Island Microarray, 2x105K. The hybridization procedure was executed at 67°C for 40 hours in the Agilent's hybridization oven according the manufactures instructions. The hybridized arrays were washed thoroughly and dried using a microarray centrifuge for 1 min in dark.

scan_protocol: The hybridized arrays were washed, dried and finally scanned on an MS200 microarray scanner (Roche) at a resolution of 2 microm. The raw methylation data were extracted with the default ChIP protocol from the software Agilent Feature Extraction 12.0.3.1.

data_processing: The methylation ratios between the IP DNA samples and the control input samples were normalized across samples using the quantile method. The mean of each promoter feature was determined from three different biological replicates. Hierarchical clustering of replicates was performed with one minus correlation metric and the unweighted average distance linkage method All data processing including mapping of microarray probes to promoters, gene annotation, data post-processing, Principal Component Analysis (PCA), identification of differentially methylated regions, and all graphics were performed with in-house developed functions in Matlab.

label_protocol: A whole genome amplification of the input DNA and the IP DNA samples was  performed applying the Genome Plex Complete WGA Kit (Sigma-Aldrich) as described in the user?s guide. As template, we have used 100 ng IP DNA and 100 ng  input DNA. The amplification products were purified using QIAquick PCR Purification Kit (Qiagen, Hilden, Germany). Both input and IP DNA were labeled with Cyanine 3 and Cyanine 5, respectively, by the use of random primers and the  Klenow (3'-5' exo-) fragment. Labeling was performed using the SureTag DNA Labeling SureTag Complete DNA Labeling Kit (Santa Clara, CA). Labeled DNA was cleaned with 70% ethanol and dried using a vacuum centrifuge for few minutes.

extract_protocol: Genomic DNA (1 µg) from each tissue sample was sonicated in a final volume of 100 microl to produce random fragments ranging in size from 300-1,000 bp by the Bioruptor sonicator (Diagenode, Liege, Belgium) in TPX polymethylpentene tubes. Twenty  sonication pulses for 15 sec were given at 4C. Immunoprecipitation (IP) of methylated DNA was then performed with the magMeDIP kit (Diagenode, Liege, Belgium) according to the manufacturer´s instructions. Briefly, DNA samples at a final concentration of 0.1 microg/microl were denatured at 95C for 3 min, quickly chilled on ice and finally immunoprecipitated by adding washed 20 microl of manufacturer's magnetic bead-immobilized anti-5-methylcytosine antibody. Control input samples contained only 20% of that DNA sample used for IP. The bound DNA was separated from the beads by incubation with Proteinase K at 55C for 15 min.

tag: vaccinated

value: Non-vaccinated


title: Nd1 rep 3

description:
replicate 3
replicate 3


title: Nd0 rep 2

description:
replicate 2
replicate 2


title: Nd8 rep 3

description:
replicate 3
replicate 3


title: Vd8 rep 1

description:
replicate 1
replicate 1


title: Nd0 rep 1

description:
replicate 1
replicate 1


title: Vd1 rep 3

description:
replicate 3
replicate 3


title: Vd0 rep 2

description:
replicate 2
replicate 2


title: Vd0 rep 3

description:
replicate 3
replicate 3


title: Nd8 rep 2

description:
replicate 2
replicate 2


title: Vd8 rep 2

description:
replicate 2
replicate 2


title: Nd1 rep 1

description:
replicate 1
replicate 1


title: Vd1 rep 2

description:
replicate 2
replicate 2


title: Vd0 rep 1

description:
replicate 1
replicate 1


title: P2_Lhx2_ChIP-seq

status: Public on May 09 2019

first: Seth

last: Blackshaw

address: 733 N. Broadway Avenue

department: Department of Neuroscience

institute: Johns Hopkins University School of Medicine

description:
Lhx2 genome wide binding sites
P2 Lhx2 ChIP-Seq rep1: SRR5659474 (H0A2UDAXXs_2_1_merged)
P2 Lhx2 ChIP-Seq rep2: SRR5659475 (H13FHADXX_1_CTTGTA_1)
P2 Lhx2 ChIP-Seq rep3: SRR5659476 (H140CADXX_1_GCCAAT_1)
P2 Lhx2 ChIP-Seq Control IgG: SRR5659477 (H140CADXX_1_ACAGTG_1)
P2 Lhx2 ChIP-Seq Control Input: SRR5659478 (inpp2_HAEFKADXX_2_GTGAAA_1)

data_processing:
Bowtie2 alignment ont the mm9 genome assembly
RNA-Seq reads were aligned to the mouse transcriptome (mm9 by UCSC) by Tophat2 , and differentially expressed genes (DEGs) were identified by Cuffdiffs , imposing a cutoff q-val =  0.05 for pairwise comparison.  Bowtie2 was adopted for ChIP-Seq ChIP-Seq and ATAC-Seq reads alignment on the mouse genome (mm9)
Uniquely mappable reads from  ChIP-Seq were retained for peak calling by MACS  (band width = 300, mfold =5, 50, d = 200, max tags per position =1, min FDR q-val cutoff  = 1E-02,  lambda = 1000-10000 bp).    ATAC-Seq regions were called on MACS2 (20) (--broad).
Genome_build: mm9;  liftover to mm10 for  visual display of custom tracks

source_name: retinal cells

growth_protocol: Developmental time course analysis

extract_protocol:
Open chromatin extraction, tagmentation and profiling (ATAC-Seq) performed based on Buenrostro et al. (2013); RNA-Seq extraction performed with Qiagen RNAeasy Mini kit; chromatin extraction, crosslinking, shearing and TF / histone- DNA-complexes were isolated with antibodies (ChIP-Seq) based on (Shang et al. 2000)
ChIP-Seq; RNA-Seq; ATAC-Seq; Libraries prepared  according to the Manufacturer's protocols: TruSeq Nano DNA Library Prep Kit, TruSeq total RNA Sample preparation kit and Nextera DNA sample preparation kit, Illumina® respectively.

treatment_protocol: Lhx2 cKO at E14 (Chx10-Cre-GFP; Lhx2 fl/fl) and  P2 (P0 electroporated pCAG-Cre-GFP construct; Lhx2 fl/fl)

value: retinal progenitor cells (RPCs)

tag: developmental time point

value: post-natal day 2


title: E14_Lhx2_ChIP-seq

description:
Lhx2 genome wide binding sites
E14 Lhx2 ChIP-Seq rep1: SRR5659468 (HJGYCBCXX_1_GTGAAAC_1)
E14 Lhx2 ChIP-Seq rep2: SRR5659469 (HJGYCBCXX_1_ACAGTGA_1)
E14 Lhx2 ChIP-Seq Control IgG: SRR5659470 (HJGYCBCXX_2_GCCAATA_1)

value: embryonic day 14


title: E14_H3K27AC_ChIP-seq

description:
Enhancers
E14 H3K27Ac ChIP-Seq rep1: SRR5659471 (HVGL2BCXX_2_CGATGTA_1)
E14 H3K27Ac ChIP-Seq rep2: SRR5659472 (HVGL2BCXX_2_CAGATCA_1)
E14 H3K27Ac ChIP-Seq Control IgR for H3K27ac e14: SRR5659473 (HVGL2BCXX_2_GTGAAAC_1)


title: P2_H3K27AC_ChIP-seq

description:
Enhancers
P2 H3K27Ac ChIP-Seq rep1: SRR5659479 (H7W7TBCXX_2_TGACCA_1)
P2 H3K27Ac ChIP-Seq Control IgR: SRR5659480 (H7W7TBCXX_2_CCGTCC_1)


title: iHep rep 1

status: Public on Aug 21 2019

description: replicate 1

hyb_protocol: Samples were hybridized to Affymetrix Mouse Genome 430 2.0 chip, following the manufacturer’s instructions

scan_protocol: Data generation was controlled by the Affymetrix GeneChip Command Console AGCC Version 2.0.0.1029 software of AGCC Portal and the Expression Console Version 1.1 was used for data quality control and analysis application (Affymetrix).

data_processing: Normalyzation was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, Data post-processing and graphics were performed with in-house developed functions in MATLAB. Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method.

source_name: iHep rep 1

label_protocol: Biotinylated cRNA were prepared for Affymetrix arrays following the manufacturer's instructions.

growth_protocol:
Isolation of mouse primary hepatocytes: The experimental procedures were approved by the Animal Care and Use Committee at Ulsan National Institute of Science and Technology (Ulsan, South Korea). Primary murine hepatocytes were isolated from 6–week–old mice (C57BL/6J) by the two-step collagenase perfusion method. The isolated primary murine hepatocytes were cultured in HEP medium.
Cell culture: MEFs were maintained in DMEM (GIBCO) containing 10% Fetal Bovine Serum (FBS) (GIBCO), penicillin/streptomycin (GIBCO), L-glutamine (GIBCO), 2-Mercaptoethanol (GIBCO), MEM non-essential amino acid (GIBCO).  To generation of iHSC from somatic cells, MEFs were seeded at 1.0 x 10^4 cells on gelatin-coated dish.  On the next day, the MEFs were infected with lentivirus for 24 hr in MEF medium containing 6 ug/ml protamine sulfate.  After 3 days, the MEF medium was switched to HEP Medium [William’s E Medium (GIBCO) containing 10% FBS, N2 supplement (GIBCO),  10 mM Nicotinamide (Sigma), 10 M-7 Dexamethasone (Sigma), 20 ng/ml HGF (Peprotech) and 20 ng/ml EGF (Peprotech).  The aggregated iHSC-like cells were mechanically isolated and expanded into stable iHSC clones in HEP medium on collagen coated-dish.  We conducted further characterization of iHSC at early passage (P3) and late passage (p20).

extract_protocol: Total RNA was isolated using RNeasy mini kit (Qiagen) following the manufacturer's instructions.

value: induced Hepatic Stem Cells

tag: reprogrammed

value: Yes

tag: passage


title: Nd0 rep 3

description:
replicate 3
replicate 3


title: Vd1 rep 1

description:
replicate 1
replicate 1


title: Vd8 rep 3

description:
replicate 3
replicate 3


title: Nd8 rep 1

description:
replicate 1
replicate 1


title: MEF rep 1

description: replicate 1

source_name: MEF rep 1

tag: cell type

value: MEF (mouse embryonic fibroblast)

value: No


title: MEF rep 4

description: replicate 4

source_name: MEF rep 4


title: MEF rep 2

description: replicate 2

source_name: MEF rep 2


title: iHep rep 2

description: replicate 2

source_name: iHep rep 2


title: pHep

description: replicate 1

source_name: pHep

value: primary hepatocyte


title: MEF rep 3

description: replicate 3

source_name: MEF rep 3