title: control-3-DIV6


title: ILSGR0260r_S1_BC14

status: Public on Aug 28 2018

type: SRA

city: Cambridge

first: Luyi

last: Tian

state: MA

address: 415 main st Cambridge

country: USA

institute: Broad institute

library_source: transcriptomic

data_processing:
The data was first demultiplexed by the cell barcode sequence and then aligned and counted using Rsubread (1.5.0)  and featureCounts (1.5.0) with mm10 genome annotation. Quality control was performed using scPipe to remove low quality cells.
The distance of the percentage of cells in three DC subtype between sisters were calculated, and used together with the total cell count as the input of Mahalanobis distance for outlier detection. Random permutation on sisters described in Figure 1B were used to get a null distribution and a 0.05 p-value cut-off was used to exclude sisters with different lineage output, leaving us with 98 clones.
Genome_build: mm10
Supplementary_files_format_and_content: gene counting matrix, rows repsent genes and each column is a clone. For meta data, XXX_fill_sis1/XXX_fill_sis2 represent the fate bias of filler cells in sister wells, which is considered as population control. cDC1_sis1.. E.t.c are cell count of cDCs. The cell counts are normalized using beads so they are not integers.

molecule: polyA RNA

organism: Mus musculus

source_name: hematopoietic stem and progenitor cells

growth_protocol: bone marrow cells were extracted from C57BL/6 mice and cultured at a density of 1.5 x 10^6 in 96-round bottom plates with DC culture medium and 200 ng/ml FLT3L obtained from Dr Jian-Guo Zhang (WEHI).  To generate conditioned medium that can sustain the growth and differentiation of isolated DC progenitors, medium derived from FLT3L cultures after 3.5 days was centrifuged to remove cells, then passed through a 0.22-μm filter, and frozen aliquots stored at -80°C, as described previously. This medium is referred to as DC-conditioned medium (DC-CM).

extract_protocol:
On day 2.5 after culture, each 200 μl cultured well was mixed well, then 100 µL of the contents transferred manually to a separate new well, and given approximately 30-60 minutes to settle. The 96-well plates containing sister wells derived from each single UBC-GFP LSK clone were imaged on a Nikon TiE live cell imaging system. Cells were maintained at 37 °C in a humidified atmosphere and 5% CO2. Images were acquired in DIC and fluorescence using a 4x 0.13NA plan neofluor objective, and GFP filter (FITC, ex 465-495, DM 505, em 515-555). A Z-stack of 150 μm, with interval of 50um was performed and, the best focus plane was automatically selected for analysis using an offline Metamorph software (v 7.8.2.0) licence and method for automatic segmentation and cell count. Cell count script parameters, region size and diameter, were changed per experiment, on the basis of visual inspection of the 100 single cell controls. After imaging, cell cultures were incubated in 37 °C and at 5% CO2 for 4.5 days.
Depending on cell abundance 1 – 10 cells per clone were FACS sorted for RNA sequencing. Transcriptome libraries were generated according to the CEL-Seq protocol with the exception that all column purifications were replaced by magnetic bead purifications using AMPure XP beads (Beckman Coulter A63880). Libraries were sequenced on the Illumina NextSeq500 sequencer using a 75-cycle kit.

treatment_protocol: The isolation and sorting of GFP+ progenitors was performed as described. Briefly, bone marrow from C57BL/6-TG (UBC-GFP) was extracted and cells were enriched for ckit (2B8 conjugated to APC) via magnetic activated cell sorting (MACS) positive selection. The ckit enriched fraction was subsequently stained for Sca-1 (E13 161-7conjugated to Alexa Fluor 594 or Alexa Fluor 680), IL-7R (A7R34-2.2 conjugated to biotin with streptavidin-PECy7) and FLT3 (A2F10 conjugated to Phycoerythrin). Cells with positive expression of GFP, ckit, sca-1 and FLT3, while negative for IL-7R, were deemed MPPs and sorted into FLT3L-DC "filler" cultures as single cells, with 100-cell controls in duplicate. Cells with positive expression of GFP, cKit and Sca-1 were deemed Sca1+cKit+ (SKs). Cells were sorted using the BD Influx, BD FacsARIA W and BD FacsAria L. Single SKs from UBC-GFP mice were deposited in 96 well round bottomed wells pre-seeded with 1.5 x 10^6 total C57BL/6 BM cells (filler cells) cultured in DC culture medium with and additional 200 ng/mL FLT3L 37 °C and at 5% CO2 for 2.5 days.

tag: cell type

value: hematopoietic stem and progenitor cells

tag: description

value: progenitor cells at day 2.5


title: C_Alfa Aesar_CeO2_Low_2

type: RNA

city: Durham

first: Carlton

last: Jones

address: 109 T.W. Alexander Drive

institute: U.S. Environmental Protection Agency

description:
GRC189_CAA03_2
replicate 2

hyb_protocol: The global gene expression change was analyzed by using Illumina Human HT-12 v4 Expression Beadchips following the manufacturer’s protocol.

data_processing: The data processing was performed using Bioconductor’s beadarray package (version 2.4.1) for the R language (version 2.14.0). The bead-level data were loaded into a single data object using the readIllumina function, and a log2 transformation of the intensity data was performed. A probe-level summarywas produced using the summarize function by taking the median log2 intensity for each bead type. A quantile normalization of this probe-level data was performed using the normaliseIllumina function. The illuminaHumanv4.db package (version 1.12.1) containing the Illumina HumanHT12v4 annotation data was used to annotate the normalized probe-level data [29, 30].

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: HepG2_Alfa Aesar_CeO2

growth_protocol: Human HepatocellularCarcinoma Cells, designation HepG2 (ATCC cat# HB-8065, Manassa, VA, USA) were obtained and expanded through passage seven using growth medium (Basal Medium Eagle, Gibco cat. 21010-046) containing 2 mM GlutaMAXTM (Gibco cat.35050-061; Life Technologies), 1mMsodium pyruvate (Gibco cat. 11360-070 Life; Technologies), and 10% fetal bovine serum and then frozen in liquid nitrogen. Cells were subsequently carefully thawed and expanded before experimentation at passage number 10–20. Cell cultures were maintained in a humidified incubator at 37°C and 95% air/5% CO2 during the study.

extract_protocol: At the end of 72 h of cell exposure to the treatment, the media was vacuum aspirated and the flasks rinsed with warm Dulbecco’s phosphate-buffered saline. cells were lysed with lysis buffer. RNA was extracted by acid phenol-chloroform, then precipitated  with ethanol, and purified through glass fiber columns. RNA integrity was assessed by the RNA 6000 LabChip kit using a 2100 bioanalyzer (Agilent-Technologies, Palo Alto, CA). The RNA Integrity number (RIN) of all samples were between 9.8 and 10.0.As the highest RIN number is 10 for completely intactRNA, RNA with a RIN number between 9.8 and 10 is of good quality.

treatment_protocol: Working stocks of each nanomaterial were prepared at 1.0 mg per mL and diluted using culture medium. Individual flasks were treated with 200 uL per cm2 of the appropriate nanomaterial dilution and incubated for 72 h. The final concentrations were 0.3 (low dose), 3 (medium dose), and 30 (high dose) μg/mL.

tag: cell line

value: Human Hepatocellular Carcinoma Cell Line

tag: nanomaterial vendor

value: Alfa Aesar

tag: nanoparticles

tag: concentration

value: 0.3 μg/mL


title: ILSGR0260r_S1_BC12


title: control_F_6

description:
GRC189_ctr_F
replicate 6

scan_protocol: The global gene expression change was analyzed by using Illumina Human HT-12 v4 Expression Beadchips following the manufacturer’s protocol.

source_name: HepG2_No Treatment

value: No Treatment


title: ILSGR0260r_S1_BC13


title: D_Alfa Aesar_CeO2_Mid_3

description:
GRC189_DAA3_3
replicate 3

label_protocol: The global gene expression change was analyzed by using Illumina Human HT-12 v4 Expression Beadchips following the manufacturer’s protocol.

value: 3 μg/mL


title: ILSGR0260r_S1_BC11


title: control-1-DIV6

city: Irvine

first: Vivek

last: Swarup

state: CALIFORNIA

address: 3400 Bio Sci 3

department: Neurobiology and Behavior

institute: University of California Irvine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with limma package in R

source_name: Primary Cortical Neurons

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: control

tag: time point


title: control-2-DIV10


title: control-1-DIV8


title: Genomic DNA from Melanoma brain metastasis-53

type: genomic

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-53

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 BeadChip using standard Illumina protocol.

scan_protocol: BeadChips were scanned using the Illumina iScan (Illumina Inc., San Diego, CA)

data_processing:
Data was extracted using the R package methylumi. The ‘noob’ function in the R package minfi was used to process the data and then the ‘dasen’ function in the R package wateRmelon for normalization and dye-bias correction. DNA methylation levels were reported as β-value (β= intensity of the methylated allele/(intensity of the unmethylated allele + intensity of the methylated allele)) and calculated using the signal intensity value for each CpG site.
Average Beta and Unmethylated and methylated signal intensities in Series supplementary file

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Microdissected formalin-fixed paraffin-embedded tissue from metastatic brain tumors

label_protocol: Standard protocol defined by Illumina Inc. (San Diego, CA) for HM450K Beadchips

extract_protocol: Genomic DNA was extracted and purified from formalin-fixed paraffin embedded tissue samples using ZR FFPE DNA MiniPrep (D3066; Zymo Research, Irvine, CA) according to manufacturer recommendations.

tag: gender

value: Male

tag: sample type

value: Formalin-fixed paraffin-embedded tissue

tag: disease state

value: Melanoma brain metastasis


title: control-2-DIV13


title: control-1-DIV10


title: C_Alfa Aesar_CeO2_Low_1

description:
GRC189_CAA03_1
replicate 1


title: ILSGR0260r_S1_BC10


title: Genomic DNA from Melanoma brain metastasis-52

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-52


title: Genomic DNA from Melanoma brain metastasis-51

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-51


title: ILSGR0260r_S1_BC9


title: D_Alfa Aesar_CeO2_Mid_2

description:
GRC189_DAA3_2
replicate 2


title: control_E_5

description:
GRC189_ctr_E
replicate 5


title: I_Acros_TiO2_High_2

description:
GRC189_IA30_2
replicate 2

value: Acros

value: 30 μg/mL


title: A_Degussa_TiO2_Low_4

description:
GRC189_AD03_4
replicate 4

value: Degussa


title: D_Alfa Aesar_CeO2_High_1

description:
GRC189_DAA30_1
replicate 1


title: C_Alfa Aesar_CeO2_High_1

description:
GRC189_CAA30_1
replicate 1


title: ILSGR0260r_S1_BC8


title: H4: iPSC-derived Neurons

description: iPSC derived neurons from A152T Tau (patients) or control samples were treated with indicated SAHA dosage.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using RNA-STAR v 2.2
Counts were estimated using RNA-STAR
Genes were kept if they were expressed in 80% of the samples with >10 reads. The resulting read counts were normalized for library size using cqn function of CQN R package in R to get fragments per kilobase million mapped reads (FPKM) values. Log2 transformed FPKM values were corrected for batch and sequencing biases using linear model in  R.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include Normalized log2 FPKM values for each Sample ...

source_name: iPSC-derived Neurons

extract_protocol:
Total RNA was isolated using Nucleospin RNA XS kit, Takara following manufacture's protocol
RNA libraries were prepared for sequencing using Stranded poly-A library preparation kit, Illumina
75-bp paired end Stranded RNA-Seq using HiSeq4000

tag: tissue

value: iPSC-derived Neurons

tag: diagnosis/patient

tag: saha dose

value: 2.5uM SAHA

tag: batch

value: A


title: ILSGR0260r_S1_BC6

value: hematopoietic stem and progenitor cells


title: Genomic DNA from Melanoma brain metastasis-48

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-48

value: Female


title: Genomic DNA from Melanoma brain metastasis-50

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-50


title: Genomic DNA from Melanoma brain metastasis-49

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-49


title: ILSGR0260r_S1_BC7

value: progenitor cells at day 2.5


title: H_Mknano_TiO2_Low_1

description:
GRC189_HMK03_1
replicate 1

value: Human Hepatocellular Carcinoma Cell Line

value: Mknano


title: I_Acros_TiO2_High_1

description:
GRC189_IA30_1
replicate 1


title: ILSGR0260r_S1_BC4


title: C_Alfa Aesar_CeO2_Mid_1

description:
GRC189_CAA3_1
replicate 1

value: Alfa Aesar


title: Genomic DNA from Melanoma brain metastasis-47

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-47


title: ILSGR0260r_S1_BC5


title: Genomic DNA from Melanoma brain metastasis-46

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-46


title: A_Degussa_TiO2_Low_1

description:
GRC189_AD03_1
replicate 1

value: 0.3 μg/mL


title: Genomic DNA from Melanoma brain metastasis-43

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-43


title: Genomic DNA from Melanoma brain metastasis-42

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-42


title: Genomic DNA from Melanoma brain metastasis-44

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-44


title: Genomic DNA from Melanoma brain metastasis-45

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-45


title: ILSGR0260r_S1_BC3


title: Genomic DNA from Melanoma brain metastasis-41

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-41


title: ILSGR0260r_S1_BC2


title: Genomic DNA from Melanoma brain metastasis-40

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-40


title: control_G_7

description:
GRC189_ctr_G
replicate 7

value: No Treatment


title: aorta_T4_37

city: Lübeck

first: Jens

last: Mittag

address: Ratzeburger Allee 160

department: Department of Internal Medicine I

country: Germany

institute: University of Lübeck

description: Gene expression data from abdominal aorta of 4d T4 treated C57BL/6N mice

hyb_protocol: Hybridisation was conducted in accordance to Applied Biosystems GeneChip ™ WT Pico Reagent Kit

scan_protocol: GeneChip™ Mouse Gene 2.0 ST array were scanned using GeneChip™ Scanner 3000 HR

data_processing:
the raw data was analysed using the RMA and Median Polish algorithms of the Affymetrix Transcriptome Analysis Console 4.0.1 workflow
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label_protocol: Biotinylation of cRNA was conducted in accordance to Applied Biosystems GeneChip ™ WT Pico Reagent Kit

growth_protocol: Mice were housed in groups at 22°C ± 1°C und constant 12h light/dark cycle with ad libitum access to food and water

extract_protocol: RNA isolation was performed with Qiagen RNeasy Fibrous Tissue Mini Kit in accordance to manufacturer's instructions

treatment_protocol: T4-treated mice received T4 in the drinking water (1mg/L) + 0,1% BSA while the drinking water of control animals only contained 0,1% BSA

tag: strain

tag: Sex

value: male

tag: treatment

value: 1mg/L Thyroxin in drinking water for 4 days

value: abdominal aorta


title: I_Acros_TiO2_Low_1

description:
GRC189_IA03_1
replicate 1

tag: cell type

value: Acros


title: B_Nano Amor_CeO2_Low_1

description:
GRC189_BNA03_1
replicate 1

source_name: HepG2_Nano Amor_CeO2

value: Nano Amor


title: L_Alfa Aesar_CeO2_Low_1

description:
GRC189_LAA03_1
replicate 1


title: si-CITED2_3_RNA-seq

city: Seoul

first: Seung-Hyun

last: Shin

address: 103, Daehak-ro, Jongno-gu

department: Pharmacology

country: South Korea

institute: Seoul National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: PC3 cells

growth_protocol: PC3 cells were obtained from the American Type Culture Collection (Manassas, VA). PC3 cells were cultured in RPMI1640 supplemented with 10% heat-inactivated FBS in a 5% CO2 humidified atmosphere at 37 degree.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using SMARTER mRNA-Seq Library Prep Kit standard protocols.

treatment_protocol: PC3 cells were transfected with non-targeting siRNA (si-Cont) or CITED2-targeting siRNAs (si-CITED2) at an 80nM concetration.

value: PC3 cells

tag: sirna


title: aorta_T4_35

source_name: abdominal aorta of 4d T4 treated C57BL/6N mice


title: Genomic DNA from Melanoma brain metastasis-37

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-37

value: Male

value: Formalin-fixed paraffin-embedded tissue

value: Melanoma brain metastasis


title: Genomic DNA from Melanoma brain metastasis-38

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-38


title: H_Mknano_TiO2_Mid_5

description:
GRC189_HMK3_5
replicate 5

tag: cell line

value: 3 μg/mL


title: L_Alfa Aesar_CeO2_High_2

description:
GRC189_LAA30_2
replicate 2

tag: nanomaterial vendor

value: 30 μg/mL


title: M_Nano Amor_CeO2_Mid_2

description:
GRC189_MNA3_2
replicate 3

tag: nanoparticles


title: si-CITED2_1_RNA-seq


title: aorta_control_33

description: Gene expression data from abdominal aorta of wild type C57BL/6N mice

value: Control


title: A_Degussa_TiO2_High_1

description:
GRC189_AD30_1
replicate 1

value: Human Hepatocellular Carcinoma Cell Line

value: Degussa

tag: concentration


title: aorta_T4_36


title: L_Alfa Aesar_CeO2_High_5

description:
GRC189_LAA30_5
replicate 5

value: Alfa Aesar


title: si-CITED2_2_RNA-seq


title: Genomic DNA from Melanoma brain metastasis-39

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-39


title: ILSGR0260r_S1_BC1

value: hematopoietic stem and progenitor cells

tag: description

value: progenitor cells at day 2.5


title: Genomic DNA from Melanoma brain metastasis-36

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-36

tag: gender


title: Control_3_RNA-seq


title: aorta_control_29

source_name: abdominal aorta of wild type C57BL/6N mice

value: male


title: RWPE1_HiC_rep2 (duplicate of GSM2627220)

city: Los Angeles

first: Yu

middle: (Phoebe)

last: Guo

state: California

address: 1450 Biggy Street, NRT 6514

institute: Univ. of Southern California

description:
RWPE1_comb_HiC_5k.raw.matrix.txt
RWPE1_comb_HiC_40k.raw.matrix.txt

library_source: genomic

data_processing:
The quality of each Hi-C library was checked with FastQC and HICUP version 0.5.842. Raw fastq files were processed through the HiC-Pro version 2.8.0 to make the raw contact count matrices for multiple resolutions (5kb, 10kb, 20kb, 40kb, 100kb). The matrices were normalized using the iterative correction method (iced python library). For the identification of topologically associating domains (TADs), the normalized Hi-C contact matrices, binned with 40kb resolution were used and the domains were called using the Domain caller. Intra-chromosomal significant loops (50kb-10Mb range) were selected with the 5kb resolution contact count matrices using the Fit-Hi-C (false discovery rate (FDR) < 0.05). Hi-C chromatin interaction heatmaps with 5kb resolution was visualized in the 3D Genome Browser (http://biorxiv.org/content/early/2017/02/27/112268). To increase the sequencing depth, two replicates were pooled and processed as above described.
Genome_build: GRCh37
Supplementary_files_format_and_content: Hi-C contact matrices

source_name: prostate cell line RWPE1

growth_protocol: RWPE-1 cells were cultured in Keratinocyte Serum Free Medium (Thermo Fisher Scientific, cat. no. 17005-042) without antibiotics. To passage the cells, 0.05% trypsin-0.02% EDTA solution was used and the trypsinization was stopped by adding Dulbecco's phosphate-buffered saline containing 2% FBS. Cells were grown at 37 °C with 5% CO2 for under 20 passages. The cell line identity was confirmed using the STR cell line authentication method at the Norris Comprehensive Cancer Center Media Core and was shown to be free of mycoplasma using the universal mycoplasma detection kit (ATCC 30-1012K).

extract_protocol:
In situ Hi-C experiments were performed in RWPE-1 cells following the original protocol by Rao et al with minor modifications. Hi-C was performed in duplicate and 5 x 106 cells were used for each experiment. 100U of MboI restriction enzyme (NEB, R0147) was used to digest chromatin. For ligation, 2000U T4 DNA Ligase (NEB, M0202) was added and incubated at room temperature for 4 hours with slow rotation. Hi-C material was sheared to a size of 300-500bp using a Covaris instrument (Covaris S2, Woburn, MA). Biotin-tagged DNA was pulled down using Dynabeads MyOne Streptavidin C1 beads (Life technologies, 65002) with 2X Binding Buffer (2X BB: 10mM Tris-HCl (pH 7.5), 1nM EDTA, 2M NaCl). Hi-C library was amplified with 14 cycles of PCR using Illumina primers. Each library was sequenced with 75bp paired-end for ~500M read pairs using Illumina HiSeq 2000.
In situ HiC experiments were performed in RWPE-1 cells following the original protocol by Rao et al with minor modifications. HiC was performed in duplicate and 5 x 106 cells were used for each experiment. 100U of MboI restriction enzyme (NEB, R0147) was used to digest chromatin. For ligation, 2000U T4 DNA Ligase (NEB, M0202) was added and incubated at room temperature for 4 hours with slow rotation. HiC material was sheared to a size of 300-500bp using a Covaris instrument (Covaris S2, Woburn, MA). Biotin-tagged DNA was pulled down using Dynabeads MyOne Streptavidin C1 beads (Life technologies, 65002) with 2X Binding Buffer (2X BB: 10mM Tris-HCl (pH 7.5), 1nM EDTA, 2M NaCl). HiC library was amplified with 14 cycles of PCR using Illumina primers.

tag: genotype

value: wild type


title: RWPE1_HiC_rep1 (duplicate of GSM2627219)


title: Genomic DNA from Melanoma brain metastasis-33

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-33

tag: sample type

tag: disease state


title: Genomic DNA from Melanoma brain metastasis-32

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-32

value: Female


title: Human1_002

city: La Jolla

first: Catherine

last: Hedrick

address: 9420 Athena Circle

department: Division of Inflammation Biology

institute: La Jolla Institute for Allergy and Immunology

description:
processed data file:
Zhu_SC-10X_human_annotation.txt
Zhu_SC-10X_human_raw-counts.txt

data_processing:
Reads from single-cell RNA-seq were aligned and collapsed into unique molecular identifier (UMI) counts using 10x genomics’s cell-ranger software (version 1.3.0)
Counts were normalized across libraries with the aggregate function from cellranger for human and mouse separately
Genome_build: hg19/mm10
Supplementary_files_format_and_content: tab delimited files include counts and annotations for each sample

source_name: hNeP

extract_protocol:
Single-cell RNA-seq using 10X genomics platform was performed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer’s protocol (Zheng et. al., 2017).
Libraries were constructed using Chromium™ Single Cell 3' v2 Reagent Kits following the manufacturer’s protocol
Libraries were sequenced on HiSeq2500 platform to obtain 100 and 32-bp paired end reads using the following read length; read 1, 26 cycles, read 2, 98 cycles and i7 index, 8 cycles.

treatment_protocol: human hNeP cells were FACS sorted from healthy donor's fresh bone marrow.  Mouse Cluster#C cells were FACS sorted from healthy mice fresh BM as well as B16F10 melanoma tumor-bearing mice fresh BM.

tag: subject #

value: human donor #1

tag: tissue

value: bone marrow

tag: cell type surface markers

value: human (hNeP) neutrophil progenitors


title: aorta_control_31

tag: strain

value: abdominal aorta


title: Hi-C in 22Rv1 rep2 (duplicate of GSM3335733)

description:
22Rv1_HiC_10k.raw.matrix.txt
2Rv1_HiC_40k.raw.matrix.txt
hg19_10k.bed
hg19_40k.bed

data_processing:
The quality of each Hi-C library was checked with FastQC and HICUP version 0.5.8. Raw fastq files were processed through the HiC-Pro version 2.8.0 to make the raw contact count matrices for multiple resolutions. The matrices were normalized using the iterative correction method (iced python library). Intra-chromosomal significant loops (50kb-10Mb range) were selected with the 5kb resolution contact count matrices using the Fit-Hi-C (false discovery rate (FDR) < 0.05). To increase the sequencing depth, two replicates were pooled and processed as above described.
Genome_build: GRCh37
Supplementary_files_format_and_content: *raw.matrix.txt files contain 3 columns of data: column 1 = region 1, column2 = region 2, column3  = contact frequency. *bed files include chromosome coordinates for each region. Count matrices are provided for 10kb or 40kb windows.

source_name: prostate cancer cell line 22Rv1

growth_protocol: 22Rv1 cells (CRL-2505) were obtained from ATCC. Cells were cultured according to the suggested protocols at 37ºC with 5% CO2. The media RPMI 1640 supplemented with 10% fetal bovine serum (Gibco by Thermo Fisher, #10437036) plus 1% penicillin and 1% streptomycin was used to culture cells.

extract_protocol:
In situ Hi-C experiments were performed in 22Rv1 cells following the original protocol by Rao et al with minor modifications. Hi-C was performed in duplicate and 5 x 106 cells were used for each experiment. 100U of MboI restriction enzyme (NEB, R0147) was used to digest chromatin. For ligation, 2000U T4 DNA Ligase (NEB, M0202) was added and incubated at room temperature for 4 hours with slow rotation. Hi-C material was sheared to a size of 300-500bp using a Covaris instrument (Covaris S2, Woburn, MA). Biotin-tagged DNA was pulled down using Dynabeads MyOne Streptavidin C1 beads (Life technologies, 65002) with 2X Binding Buffer (2X BB: 10mM Tris-HCl (pH 7.5), 1nM EDTA, 2M NaCl).
Libraries were prepared using Kapa Hyper prep kit (Kapa #KK8503) according to the provided protocol. HiC library was amplified with 14 cycles of PCR using Illumina primers. Each library was sequenced with 75bp paired-end for ~500M read pairs using Illumina HiSeq 2000.


title: Hi-C in 22Rv1 rep1 (duplicate of GSM3335732)


title: B_Nano Amor_CeO2_Mid_2

description:
GRC189_BNA3_2
replicate 2

value: Nano Amor


title: M_Nano Amor_CeO2_High_1

description:
GRC189_MNA30_1
replicate 1


title: Human2_002

value: human donor #2


title: aorta_T4_34

tag: Sex

value: 1mg/L Thyroxin in drinking water for 4 days


title: Control_1_RNA-seq

value: PC3 cells


title: Genomic DNA from Melanoma brain metastasis-34

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-34

value: Male

value: Formalin-fixed paraffin-embedded tissue

value: Melanoma brain metastasis


title: Human2_001


title: 7dCI_rep3

first: Hilary

last: Coller

address: 610 Charles E Young Drive E

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
Reads (phred score>10) were aligned to human genome (hg19) using TopHat.
Normalized counts for all the conditions and differential expression (log2 fold change) between proliferating and 7dCI flibroblasts were obtained using standard DESeq workflow. Gene identifiers from UCSC gene annotation were used.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separarted values file containing counts for all the samples.

source_name: human dermal fibroblasts (foreskin)

growth_protocol: Proliferating fibroblasts were grown in a complete medium (DMEM and 10% FBS) and harvested at 60-70% confluency. For 7-day contact inhibited (7dCI) fibroblasts, the cells were plated at a density of 5 x 105 cells per 10 cm dish on day 1 and the cells were harvested on day 7.

extract_protocol:
Proliferating and 7dCI fibroblasts were lysed using 1 mL of Trizol reagent (Life Technologies, Carlsbad, CA) per 10 cm plate for 5 minutes.  RNA was isolated from Trizol lysates following manufacturer instructions. RNA concentrations were determined using a Nanodrop Spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA). RNA quality was verified on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) using reagents from the RNA Nano 6000 kit (Agilent Technologies).
cDNA libraries were constructed using the Illumina TruSeq mRNA sample preparation kit according to the manufacturer’s instructions for revision A of the protocol (Illumina Part #15008136).  The low-input protocol was followed for all samples and 1 to 10 μg of total RNA input was used per library.

treatment_protocol: No treatment performed.

value: human dermal fibroblasts (foreskin)

tag: cell growth conditions

value: 7 day contact inhibited cells (quiescent)

tag: fibroblast strain


title: Control_2_RNA-seq

tag: sirna

value: Control


title: control_H_8

description:
GRC189_ctr_H
replicate 8

tag: cell line

tag: cell type

value: Human Hepatocellular Carcinoma Cell Line

value: No Treatment


title: L_Alfa Aesar_CeO2_Mid_4

description:
GRC189_LAA3_4
replicate 4

tag: nanomaterial vendor

value: Alfa Aesar

tag: nanoparticles

value: 3 μg/mL


title: 7dCI_rep2


title: D_Alfa Aesar_CeO2_Mid_5

description:
GRC189_DAA3_5
replicate 5

tag: concentration


title: I_Acros_TiO2_Mid_2

description:
GRC189_IA3_2
replicate 2

value: Acros


title: C_Alfa Aesar_CeO2_High_5

description:
GRC189_CAA30_5
replicate 5

value: 30 μg/mL


title: Human1_001

value: human donor #1

value: bone marrow

value: human (hNeP) neutrophil progenitors


title: Genomic DNA from Melanoma brain metastasis-31

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-31

tag: gender


title: Genomic DNA from Melanoma brain metastasis-29

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-29


title: 7dCI_8hr_12-3

data_processing:
The reads were trimmed to remove the polyA tail and adapter sequences. Reads were aligned to human genome (hg19) using Tophat (v2.0.14,standard parameters) to generate bam files.
To obtain the counts for polyadenylation sites at each time point, the bam files were used as input to perl code provided by Gruber et al. (PMID: 27382025): http://polyasite.unibas.ch/. PolyA site atlas by Gruber et al. was used as the annotation for polyadenylation sites.
Only the polyadenylation sites present in terminal exons (TEs) were considered.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated values (CSV) file containing counts for polyadenylation sites for all the samples at different time points

source_name: human dermal fibroblasts

growth_protocol: Proliferating fibroblasts (5 x 10^5 cells) were grown in a 10 cm plate uisng a complete medium containing DMEM and 10 % fetal bovine serum. Proliferating cells were grown to a confluency of 60-70% before treatment. For contact inhibition, the cells were plated under the same conditions as proliferating cells and allowed to grow for 7 days after plating to make the cells contact-inhibited.

extract_protocol:
Actinomycin D-treated cells were lysed using 1 ml of Trizol (Life Technologies) per 10 cm plate for 5 min at room temperature. RNA was isolated from the lysed cells using the Direct-zol™ RNA MiniPrep Plus kit (Zymo Research) by following the manufacturer's instructions.The concentration of RNA was measured using a Nanodrop 2000c (Thermo Fisher Scientific).
cDNA libraries enriched in 3' end fragrments were generated with Nextera kit using Smart-seq2 cDNA amplification method (Picelli et al., PMID: 24385147). Common forward primers were used for all samples; reverse primers with a unique barcode sequence (i5 indices) were specific for each sample. The size distribution of the cDNA library was confirmed on a Bioanalyzer 2100 Instrument (Agilent Technologies). Libraries (150-1000 bp) were subjected to gel size selection to enrich for fragments in the 180 – 280 size range. The concentration of the final library was measured on a qubit fluorometer (Thermo Fisher Scientific).

treatment_protocol: The proliferating and contact-inhibited cells were treated with actinomycin D at a concentration of 15 μg/ml. Cells were harvested at different time points (2, 4, 6, and 8 hours) after actinomycin treatment using Trizol.

value: dermal fibroblasts

tag: cell strain

value: contact-inhibited for 7 days

tag: treatment

value: Actinomycin D

tag: time

value: 8 hour


title: aorta_control_28

value: male

value: abdominal aorta


title: A_Degussa_TiO2_Mid_2

description:
GRC189_AD3_2
replicate 2

value: Degussa


title: P_rep3

value: human dermal fibroblasts (foreskin)

value: proliferating cells


title: Genomic DNA from Melanoma brain metastasis-28

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-28

value: Male

tag: sample type

value: Formalin-fixed paraffin-embedded tissue

tag: disease state

value: Melanoma brain metastasis


title: 7dCI_rep1

value: 7 day contact inhibited cells (quiescent)


title: Genomic DNA from Melanoma brain metastasis-30

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-30


title: P_8hr_12-3


title: Genomic DNA from Melanoma brain metastasis-27

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-27


title: P_rep2


title: Genomic DNA from Melanoma brain metastasis-26

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-26


title: C_Alfa Aesar_CeO2_High_3

description:
GRC189_CAA30_3
replicate 3

value: Human Hepatocellular Carcinoma Cell Line

value: Alfa Aesar

value: 30 μg/mL


title: 7dCI_8hr_12-1


title: Genomic DNA from Melanoma brain metastasis-25

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-25


title: D_Alfa Aesar_CeO2_High_5

description:
GRC189_DAA30_5
replicate 5


title: P_8hr_12-1


title: 7dCI_4hr_12-3

value: 4 hour


title: Genomic DNA from Melanoma brain metastasis-24

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-24


title: P_rep1


title: P_4hr_12-3

value: dermal fibroblasts


title: Genomic DNA from Melanoma brain metastasis-23

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-23


title: Genomic DNA from Melanoma brain metastasis-22

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-22


title: xPap_Mex67AA_ip_neg

city: Aarhus C

first: Manfred

last: Schmid

address: CF Møllers Alle bldg 1130

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description:
pA+ RNA 3' end seq
Negative control IP RNA
Background subtracted from xPap ip samples.

data_processing:
Trimming and quality control of reads using bbduk.sh script from BBMAP software v35.92 using parameters k=13; ktrim=r; useshortkmers=t; mink=5; qtrim=t; trimq=10; minlength=20; ref=/home/schmidm/annotations/common/Lexogen_adapters_with_pA.fa.gz. The Lexogen adapters file contains the common Illumina TruSeq adapter sequences 1-27 and an additional A18 sequence to trim homopolymeric A-tails often observed in that protocol.
Mapping using STAR aligner (GitHub v2016-03-14) together with samtools (v1.3) using settings --outFilterType BySJout; --outFilterMultimapNmax 20; --alignSJoverhangMin 8; --alignSJDBoverhangMin 1; --outFilterMismatchNmax 999; --alignIntronMin 20; --alignIntronMax 2000; --outSAMtype BAM SortedByCoordinate. The index file used is derived from the catenation of fasta files from yeast genomes S. cerevisiae genome release sacCer3 and S. pombe genome ENSEMBL release ASM294v1. The merged genome was indexed for STAR (GitHub v2016-03-14) using settings --runMode genomeGenerate; --sjdbGTFfile r64_2_1.gff3; --sjdbGTFtagExonParentTranscript Parent; --sjdbGTFfeatureExon CDS; --genomeSAindexNbases 11; --sjdbOverhang 49. That is, providing only splice-junction information for the S. cerevisiae genome sacCer3.
Bam files are then indexed using samtools and read 5’ end positions (marking the RNA 3’ ends) of uniquely aligned reads obtained using a custom python script using HTSeq (v0.6.0) that computes coverage of uniquely mapping 5’ ends in bedgraph format.
End positions likely derived from priming of the reverse transcription primer to endogenous A-rich sequences were removed for all analysis. Removed were positions containing more than 4 As and no Cs or Ts within 6 bp downstream and positions containing more than 12 As in a 18 bp window downstream. These positions are available in the supplementary file genomicAmask.bed.
Coverage is normalized to S. pombe spike-ins.
Background is subtracted from 4tU IP tracks using S. pombe normalized values from negative control IP (RNA not labelled with 4tU) at each single genomic position.
Genome_build: UCSC sacCer3
Supplementary_files_format_and_content: Bedgraph files, where the score represents strand specific S. pombe-normalized per base genome coverage for the S. cerevisiae genome. For 4tU IP samples, these values are after background subtraction.

organism: Saccharomyces cerevisiae

source_name: Control unlabeled IP RNA in vitro polyadenylated

growth_protocol: Saccharomyces cerevisiae cells were grown in synthetic growth medium lacking uracil at 30°C.

extract_protocol:
RNA was isolated using hot acid phenol method. For 4tU IP, 4tU residues in total RNA were biotinylated using MTSEA-biotinXX; free MTSEA-biotinXX removed and biotin-labeled RNA then purified on streptavidin beads, eluted from the column using beta-mercaptoethanol and RNA purified. An aliquot of purified RNA samples was 3' polyadenylated using E. coli poly(A) polymerase and ribo-depleted.
Libraries were prepared using Lexogen QuantSeq REV kit (Lexogen GmbH, Vienna, Austria).

treatment_protocol: Rapamycin was added to nuclear-depleted samples for 15 minutes before harvesting. 4tU added 2 minutes before harvesting, except for negative controls where 4tU was not added.

tag: labeling

tag: min rapamycin

tag: replicate


title: 7dCI_4hr_12-1

tag: cell growth conditions

value: contact-inhibited for 7 days


title: P_4hr_12-1

value: Actinomycin D


title: noPap_Mex67AA_ip_neg

description:
pA+ RNA 3' end seq
Negative control IP RNA
Background subtracted from noPap ip samples.

source_name: Control unlabeled IP RNA

tag: strain


title: xPap_Mex67AA_ip_15_3

description:
pA+ RNA 3' end seq
4tU IP RNA
Background estimated from sample xPap_Mex67AA_ip_neg.

source_name: Mex67-AA 15' depleted 2' 4tU RNA in vitro polyadenylated replicate 3

value: 2min 4tU


title: 7dCI_2hr_12-3

value: 2 hour


title: P_2hr_12-3


title: xPap_Mex67AA_ip_15_2

source_name: Mex67-AA 15' depleted 2' 4tU RNA in vitro polyadenylated replicate 2


title: Genomic DNA from Melanoma brain metastasis-19

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-19


title: Genomic DNA from Melanoma brain metastasis-18

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-18

value: Female


title: 7dCI_2hr_12-1


title: P_2hr_12-1


title: L_Alfa Aesar_CeO2_High_3

description:
GRC189_LAA30_3
replicate 3

source_name: HepG2_Alfa Aesar_CeO2


title: xPap_Mex67AA_ip_15_1

source_name: Mex67-AA 15' depleted 2' 4tU RNA in vitro polyadenylated replicate 1


title: xPap_Mex67AA_ip_0_3

source_name: Mex67-AA control 2' 4tU RNA in vitro polyadenylated replicate 3


title: Genomic DNA from Melanoma brain metastasis-17

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-17

source_name: Microdissected formalin-fixed paraffin-embedded tissue from metastatic brain tumors


title: A_Degussa_TiO2_Mid_3

description:
GRC189_AD3_3
replicate 3

value: Degussa

value: 3 μg/mL


title: control_B_2

description:
GRC189_ctr_B
replicate 2

source_name: HepG2_No Treatment

value: No Treatment


title: C_Alfa Aesar_CeO2_Mid_2

description:
GRC189_CAA3_2
replicate 2


title: B_Nano Amor_CeO2_Mid_3

description:
GRC189_BNA3_3
replicate 3

source_name: HepG2_Nano Amor_CeO2

value: Nano Amor


title: B_Nano Amor_CeO2_High_5

description:
GRC189_BNA30_5
replicate 5


title: 7dCI_0hr_12-3

value: untreated

value: 0 hour


title: P_0hr_12-3

value: proliferating cells


title: C_Alfa Aesar_CeO2_Low_3

description:
GRC189_CAA03_3
replicate 3

value: Human Hepatocellular Carcinoma Cell Line

value: 0.3 μg/mL


title: Genomic DNA from Melanoma brain metastasis-21

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-21

value: Formalin-fixed paraffin-embedded tissue

value: Melanoma brain metastasis


title: Genomic DNA from Lung cancer brain metastasis-21

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-21

value: Lung cancer brain metastasis


title: Genomic DNA from Lung cancer brain metastasis-22

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-22


title: Genomic DNA from Melanoma brain metastasis-20

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-20


title: xPap_Mex67AA_ip_0_1

source_name: Mex67-AA control 2' 4tU RNA in vitro polyadenylated replicate 1


title: xPap_Nab2AA_ip_15_3

source_name: Nab2-AA 15' depleted 2' 4tU RNA in vitro polyadenylated replicate 3


title: xPap_Mex67AA_ip_0_2

source_name: Mex67-AA control 2' 4tU RNA in vitro polyadenylated replicate 2


title: xPap_Nab2AA_ip_15_2

source_name: Nab2-AA 15' depleted 2' 4tU RNA in vitro polyadenylated replicate 2


title: P_0hr_12-1

value: dermal fibroblasts


title: Genomic DNA from Lung cancer brain metastasis-20

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-20

value: Male


title: Genomic DNA from Lung cancer brain metastasis-19

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-19


title: 7dCI_0hr_12-1

value: contact-inhibited for 7 days


title: xPap_Nab2AA_ip_15_1

source_name: Nab2-AA 15' depleted 2' 4tU RNA in vitro polyadenylated replicate 1

value: 2min 4tU


title: xPap_Nab2AA_ip_0_3

source_name: Nab2-AA control 2' 4tU RNA in vitro polyadenylated replicate 3


title: xPap_Nab2AA_ip_0_2

source_name: Nab2-AA control 2' 4tU RNA in vitro polyadenylated replicate 2


title: Genomic DNA from Lung cancer brain metastasis-15

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-15


title: Genomic DNA from Lung cancer brain metastasis-16

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-16

value: Female


title: CPSF73KD_12_3

data_processing:
The reads were trimmed to remove polyA tail and adapter sequences. Reads were aligned to human genome (hg19) using Tophat (v2.0.14, standard parameters used) to generate bam files.
To obtain the counts for polyadenylation sites, the bam files were used as input to perl code provided by Gruber et al. (PMID: 27382025): http://polyasite.unibas.ch/. PolyA site atlas by Gruber et al. was used as the annotation for polyadenylation sites.
Only the polyadenylation sites present in terminal exon (TE), exon except terminal exon (EX), and intron (IN) were considered.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated values (CSV) file containing counts for polyadenylation sites for all the samples.

source_name: human dermal fibroblasts

growth_protocol: Fibroblasts were grown in complete medium (DMEM with 10% fetal bovine serum).

extract_protocol:
Harvested cells were lysed using 1 ml of Trizol (Life Technologies) per 10 cm plate for 5 min at room temperature. RNA was isolated from the lysed cells using the Direct-zol™ RNA MiniPrep Plus kit (Zymo Research)  following the manufacturer's instructions. The concentration of RNA was measured using Nanodrop 2000c (Thermo Fisher Scientific).
cDNA libraries enriched in fragrments from 3´ ends of transcripts were generated with a Nextera kit using Smart-seq2 cDNA amplification method (Picelli et al., PMID: 24385147). Common forward primers were used for all samples; reverse primers with a unique barcode sequence (i5 indices) were specific for each sample. The size distribution of the cDNA library was confirmed on a Bioanalyzer 2100 Instrument (Agilent Technologies). Libraries (150-1000 bp) were subjected to gel size selection to enrich for 180 – 280 bp sized fragments. The concentration of the final library was measured on a qubit fluorometer (Thermo Fisher Scientific).

treatment_protocol: Proliferating fibroblasts were treated with siRNA (10 cm culture dish) using Genmute transfection reagent (Signagen® Laboratories) following the manufactuter's instructions. Cell were harvested 48 hours after transfection for RNA extraction.

tag: tissue

value: Foreskin

value: human dermal fibroblasts

value: proliferating cells treated with CPSF73 siRNA

value: siRNA treatment; cell harvested 48 hours after treatment


title: CSTF64KD_12_1

value: proliferating cells treated with CstF64 siRNA


title: CSTF64KD_12_3


title: CPSF73KD_12_1


title: CFIM25KD_12_3

value: proliferating cells treated with CFIm25 siRNA


title: xPap_Nab2AA_ip_0_1

source_name: Nab2-AA control 2' 4tU RNA in vitro polyadenylated replicate 1


title: Genomic DNA from Lung cancer brain metastasis-14

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-14


title: CFIM25KD_12_1


title: xPap_Mex67AA_input_0_1

description: pA+ RNA 3' end seq

source_name: Mex67-AA control total RNA in vitro polyadenylated


title: Genomic DNA from Lung cancer brain metastasis-12

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-12


title: Genomic DNA from Lung cancer brain metastasis-10

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-10


title: xPap_Nab2AA_input_15_1

description: pA+ RNA 3' end seq

source_name: Nab2-AA 15' depleted total RNA in vitro polyadenylated


title: Genomic DNA from Lung cancer brain metastasis-17

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-17


title: CTRL_12_3

value: proliferating cells treated with control siRNA


title: Genomic DNA from Lung cancer brain metastasis-18

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-18


title: xPap_Nab2AA_input_0_1

description: pA+ RNA 3' end seq

source_name: Nab2-AA control total RNA in vitro polyadenylated


title: dot6 vs WT - Replicate 2

city: Montreal

first: Adnane

last: Sellam

address: 5000, rue Bélanger

country: Canada

institute: Universite de Montreal

description: Arrays are organized in 48 sub-arrays spotted with 6459 70-mer oligonucleotides.

hyb_protocol: The microarray slides were pre-hybridized for1 hours at 42°C with DIGeasy hybridization buffer (Roche) containing 0.5 ug/ul of yeast tRNA (Roche) and 0.5 ug/ul of salmon sperm DNA (Invitrogen) and subsequently washed with 0.1X SSC and air dried. The slides were then hybridized with labeled cDNAs overnight at 42°C in DIGeasy hybridization buffer with yeast tRNA and salmon sperm DNA. The slides were washed twice for 10 min at 42°C with 1× SSC, 0.1% SDS, twice for 10 min at 37°C with 0.1× SSC, 0.1% SDS, and finally, with quick consecutive washes in three 0.1× SSC baths. Slides were air-dried.

scan_protocol: Slides were scanned with a ScanArray 5000 scanner (Perkin Elmer) at 10-µm resolution.

data_processing: Data were normalized as following : Signal intensity was quantified with QuantArray software (Perkin Elmer) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

organism: Candida albicans

source_name: WT elutriated G1 cells  grown in YPD medium at 30°C for 10 min

label_protocol: 20 µg of total RNA was reverse transcribed using oligo(dT)21 in the presence of either Cy3-dCTP or Cy5-dCTP (Perkin-Elmer-Cetus/NEN) and Superscript III reverse transcriptase (Invitrogen). Thereafter, template RNA was degraded by adding 2.5 units of RNase H (USB) and 1 ug of RNase A (Pharmacia) followed by incubation for 15 min at 37°C. The labeled cDNAs were purified with QIAquick PCR Purification Kit (Qiagen).

extract_protocol: Total RNA was extracted using an RNAeasy purification kit (Qiagen) and glass bead lysis in a Biospec Mini 24 bead-beater. Total RNA was eluted, assessed for integrity on an Agilent 2100 Bioanalyzer prior to cDNA labeling, microarray hybridization and analysis .

treatment_protocol: Overnight cultures of dot6 mutant and WT strains were diluted to an OD600 of 0.1 in 1 L fresh YPD-uridine medium, grown at 30°C to an OD600 of 0.8 and separated into size fractions by using the Beckman JE-5.0  elutriation system at 16°C. A total of 108 unbudded G1 phase cells were harvested, released into fresh YPD medium and grown for 10 min prior to harvesting by centrifugation and stored at -80°C.

tag: genotype

value: WT

tag: growth phase

source_name: dot6 elutriated G1 cells  grown in YPD medium at 30°C for 10 min


title: dot6 vs WT - Replicatd 3


title: dot6 vs WT - Replicate 1


title: CTRL_12_1

tag: cell type


title: xPap_Mex67AA_input_15_1

description: pA+ RNA 3' end seq

source_name: Mex67-AA 15' depleted total RNA in vitro polyadenylated


title: Genomic DNA from Lung cancer brain metastasis-08

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-08

source_name: Microdissected formalin-fixed paraffin-embedded tissue from metastatic brain tumors


title: Genomic DNA from Lung cancer brain metastasis-09

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-09


title: Q_12_3

value: quiescent cells (contact-inhibited for 7 days)

value: no treatment


title: Q_12_1


title: noPap_Mex67AA_ip_15_1

description:
pA+ RNA 3' end seq
4tU IP RNA
Background estimated from sample noPap_Mex67AA_ip_neg.

source_name: Mex67-AA 15' depleted 2' 4tU RNA


title: noPap_Mex67AA_ip_0_1

source_name: Mex67-AA control 2' 4tU RNA


title: Genomic DNA from Lung cancer brain metastasis-06

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-06

value: Formalin-fixed paraffin-embedded tissue


title: P_12_3

value: proliferating cells


title: Liver tissue  from Canertinib treated MET KO mice at Day 2 after TCPOBOP administration

city: Pittsburgh

first: George

middle: K

last: Michalopoulos

state: Pennsylvania

address: 411 SBST, 200 Lothrop Street

institute: University of Pittsburgh

description: Gene expression data at Day 2 post-TCPOBOP in canertinib-treated MET KO (MET KO + EGFRi) mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: [MET KO + EGFRi] mice liver tissue Day 2 post-TCPOBOP

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Following systemic inhibition of MET-EGFR, mice were treated with chemical mitogen TCPOBOP and liver tissues harvested at 0, 1, 2 and 5 days after TCPOBOP treatment.

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

treatment_protocol: METfl/fl: TamCre+/+ mice were injected i.p. for five consecutive days with tamoxifen (100 μl of a 10 mg/ml solution in corn oil) to obtain MET KO mice. Control group consisted of littermates injected with vehicle (corn oil) only. EGFR was inhibited in MET KO mice by adding Canertinib (EGFRi) in the diet with the aim of administrating 80 mg/kg/day.  Single dose of TCPOBOP (3 mg/ kg; prepared in corn oil from a 10 mg/ml stock solution in DMSO) was administered by oral gavage at least 5 days after last tamoxifen injection. Canertinib diet was initiated one day prior to TCPOBOP injection. Microarray analysis was performed on RNAs isolated from pooled liver samples from the control and [MET KO + EGFRi] groups (0, 1, 2 and 5 days after TCPOBOP treatment)

tag: genetic background

value: Metff/ff:ERCre+/+ mice


title: Genomic DNA from Lung cancer brain metastasis-04

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-04

value: Lung cancer brain metastasis


title: Liver tissue  from Canertinib treated MET KO mice at Day 5 after TCPOBOP administration

description: Gene expression data at Day 5 post-TCPOBOP in canertinib-treated MET KO (MET KO + EGFRi) mice

source_name: [MET KO + EGFRi] mice liver tissue Day 5 post-TCPOBOP


title: noPap_Nab2AA_ip_0_1

source_name: Nab2-AA control 2' 4tU RNA


title: Liver tissue  from corn oil treated MET flox mice at Day 2 after TCPOBOP administration

description: Gene expression data at Day 2 post-TCPOBOP in Control mice

source_name: Control mice liver tissue Day 2 post-TCPOBOP


title: noPap_Nab2AA_ip_15_1

source_name: Nab2-AA 15' depleted 2' 4tU RNA


title: P_12_1


title: Genomic DNA from Lung cancer brain metastasis-03

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-03


title: Liver tissue  from corn oil treated MET flox mice at Day 5 after TCPOBOP administration

description: Gene expression data at Day 5 post-TCPOBOP in Control mice

source_name: Control mice liver tissue Day 5 post-TCPOBOP


title: Genomic DNA from Lung cancer brain metastasis-02

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-02


title: Liver tissue  from Canertinib treated MET KO mice at Day 1 after TCPOBOP administration

description: Gene expression data at Day 1 post-TCPOBOP in canertinib-treated MET KO (MET KO + EGFRi) mice

source_name: [MET KO + EGFRi] mice liver tissue Day 1 post-TCPOBOP


title: noPap_Mex67AA_input_15_1

description: pA+ RNA 3' end seq

source_name: Mex67-AA 15' depleted total RNA


title: Liver tissue  from corn oil treated MET flox mice at Day 1 after TCPOBOP administration

description: Gene expression data at Day 1 post-TCPOBOP in Control mice

source_name: Control mice liver tissue Day 1 post-TCPOBOP


title: Genomic DNA from Lung cancer brain metastasis-01

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
LCBM-01


title: Liver tissue  from corn oil treated MET flox mice at Day 0 after TCPOBOP administration

description: Gene expression data at Day 0 post-TCPOBOP in Control mice

source_name: Control mice liver tissue Day 0 post-TCPOBOP


title: Liver tissue  from Canertinib treated MET KO mice at Day 0 after TCPOBOP administration

description: Gene expression data at Day 0 post-TCPOBOP in canertinib-treated MET KO (MET KO + EGFRi) mice

source_name: [MET KO + EGFRi] mice liver tissue Day 0 post-TCPOBOP


title: noPap_Nab2AA_input_15_1

description: pA+ RNA 3' end seq

source_name: Nab2-AA 15' depleted total RNA


title: Genomic DNA from Uncertain primary tumor brain metastasis-03

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BM-03


title: Genomic DNA from Melanoma brain metastasis-35

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
MBM-35

value: Male

value: Melanoma brain metastasis


title: Nab_ip_neg

description:
pA+ RNA 3' end seq
Negative control IP RNA
Background subtracted from Nab_ip samples.

data_processing:
Trimming and quality control of reads using bbduk.sh script from BBMAP software v35.92 using parameters k=13; ktrim=r; useshortkmers=t; mink=5; qtrim=t; trimq=10; minlength=20; ref=/home/schmidm/annotations/common/Lexogen_adapters_with_pA.fa.gz. The Lexogen adapters file contains the common Illumina TruSeq adapter sequences 1-27 and an additional A18 sequence to trim homopolymeric A-tails often observed in that protocol.
Mapping using STAR aligner (GitHub v2016-03-14) together with samtools (v1.3) using settings --outFilterType BySJout; --outFilterMultimapNmax 20; --alignSJoverhangMin 8; --alignSJDBoverhangMin 1; --outFilterMismatchNmax 999; --alignIntronMin 20; --alignIntronMax 2000; --outSAMtype BAM SortedByCoordinate. The index file used is derived from the catenation of fasta files from yeast genomes S. cerevisiae genome release sacCer3 and S. pombe genome ENSEMBL release ASM294v1. The merged genome was indexed for STAR (GitHub v2016-03-14) using settings --runMode genomeGenerate; --sjdbGTFfile r64_2_1.gff3; --sjdbGTFtagExonParentTranscript Parent; --sjdbGTFfeatureExon CDS; --genomeSAindexNbases 11; --sjdbOverhang 49. That is, providing only splice-junction information for the S. cerevisiae genome sacCer3.
Bam files are then indexed using samtools and read 5’ end positions (marking the RNA 3’ ends) of uniquely aligned reads obtained using a custom python script using HTSeq (v0.6.0) that computes coverage of uniquely mapping 5’ ends in bedgraph format.
End positions likely derived from priming of the reverse transcription primer to endogenous A-rich sequences were removed for all analysis. Removed were positions containing more than 4 As and no Cs or Ts within 6 bp downstream and positions containing more than 12 As in a 18 bp window downstream. These positions are available in the supplementary file genomicAmask.bed.
Coverage is normalized to S. pombe spike-ins.
Background is subtracted from 4tU IP tracks using S. pombe normalized values from negative control IP (RNA not labelled with 4tU) at each single genomic position.
Genome_build: UCSC sacCer3
Supplementary_files_format_and_content: Bedgraph files, where the score represents strand specific S. pombe-normalized per base genome coverage for the S. cerevisiae genome.

source_name: Nab2-AA control unlabeled IP

extract_protocol:
RNA was isolated using hot acid phenol method. For 4tU IP, 4tU residues in total RNA were biotinylated using HPDP-biotin; free HPDP-biotin removed and biotin-labeled RNA then purified on streptavidin beads, eluted from the column using beta-mercaptoethanol and RNA purified.
Libraries were prepared using Lexogen QuantSeq REV kit (Lexogen GmbH, Vienna, Austria).

treatment_protocol: Rapamycin was added to nuclear-depleted samples for 15 minutes before harvesting and 4tU added to labelled samples 10 minutes before harvesting.


title: Genomic DNA from Uncertain primary tumor brain metastasis-02

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BM-02

value: Female


title: Genomic DNA from Uncertain primary tumor brain metastasis-01

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BM-01


title: Mex_ip_neg

description:
pA+ RNA 3' end seq
Negative control IP RNA
Background subtracted from Mex_ip samples.

source_name: Mex67-AA control unlabeled IP


title: Genomic DNA from Breast cancer brain metastasis-33

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-33

source_name: Microdissected formalin-fixed paraffin-embedded tissue from metastatic brain tumors

value: Breast cancer brain metastasis


title: Mex_ip_0_3

description:
pA+ RNA 3' end seq
4tU IP RNA
Background estimated from sample Mex_ip_neg.

source_name: Mex67-AA 15' depleted 10' 4tU RNA replicate 2

value: 10min 4tU


title: noPap_Mex67AA_input_0_1

description: pA+ RNA 3' end seq

source_name: Mex67-AA control total RNA

value: 2min 4tU


title: Genomic DNA from Uncertain primary tumor brain metastasis-04

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BM-04


title: noPap_Nab2AA_input_0_1

description: pA+ RNA 3' end seq

source_name: Nab2-AA control total RNA


title: Arabidopsis_mRNA-seq

city: Walnut Creek

first: Christine

last: Shulse

address: 2800 Mitchell Drive

institute: DOE Joint Genome Institute

data_processing:
Illumina CASAVA bcl2fastq v2.17 used for basecalling.
Sequenced reads were trimmed for adaptor sequence and polyA, then mapped to a combined GRCh38-TAIR10 genome mega-reference using STAR v. 2.5.2b for Drop-seq data, or mapped to TAIR10 using HISAT for RNA-seq data.
Digital gene expression matrices were created by following the Drop-seq Core Computational Protocol version 1.0.1 (http://mccarrolllab.com/dropseq/) for Drop-seq data. For mRNA-seq data, library counts were generated use featureCounts.
Genome_build: GRCh38; TAIR10
Supplementary_files_format_and_content: digital gene expression matrices and library counts are provided as txt files

organism: Arabidopsis thaliana

source_name: whole root

growth_protocol: Seeds were sown at a density of ~125 seeds per row on sterile nylon mesh filters placed on top of plant growth media consisting of 1X Murashige and Skoog Basal Medium (Sigma-Aldrich, St. Louis, MO) supplemented with 1% sucrose (Sigma-Aldrich), 1% agar (Sigma-Aldrich), 2.6 mM 2-(N-Morpholino)ethanesulfonic acid (MES; Sigma-Aldrich), and adjusted to pH 5.7. Petri dishes were positioned vertically in an incubator (Percival Scientific, Perry, IA) under a long-day photoperiod (16 h of light) at 22°C.

extract_protocol:
Total RNA was isolated from flash frozen 5-day-old Arabidopsis root material using the Qiagen RNeasy kit (Carlsbad, CA).
An RNA library was prepared for sequencing using the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101) according to the manufacturer’s Low Sample (LS) Protocol.

value: whole root

tag: ecotype

tag: age

value: 5 day


title: Mex_ip_15_2

source_name: Mex67-AA 15' depleted 10' 4tU RNA replicate 1


title: Genomic DNA from Breast cancer brain metastasis-28

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-28

tag: gender


title: Genomic DNA from Breast cancer brain metastasis-31

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-31


title: Mex_ip_0_2

source_name: Mex67-AA control 10' 4tU RNA replicate 3


title: Mex_ip_15_3

source_name: Mex67-AA 15' depleted 10' 4tU RNA replicate 3


title: Genomic DNA from Breast cancer brain metastasis-32

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-32


title: Arabidopsis_Drop-seq_137

extract_protocol:
Cells were used at their starting concentration after protoplasting (137 cells/μl). 2.5% human cells were added to each suspension. Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads as previously described (PMID: 26000488).
The library was prepared according to Drop-seq Laboratory Protocol version 3.1 (http://mccarrolllab.com/dropseq/) using Illumina's Nextera XT DNA Library Preparation Kit. The library was uniquely indexed and then pooled and sequenced on a single lane of a HiSeq 4000.

treatment_protocol: Protoplast suspensions were prepared from 5-day-old Arabidopsis seedlings using previously described methods (PMID: 16170893).


title: Mouse Tau Tg (PS19), 12M, #5

description: Gene Expression Data from PS19 Tau Transgenic mice from hippocampus

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with affy package in R with Affymetrix default analysis settings and quantile normalization as normalization method.

source_name: hippocampus

extract_protocol: Total RNA was isolated using miRNeasy kit, Qiagen following the manufacturer's instructions.

treatment_protocol: Brain samples were dissected and hippocampi isolated in ice-cold PBS. Samples were falsh frozen in liquid nitrogen

tag: age (months)

tag: transgenic

value: Tau Tg


title: Mouse Tau Tg (PS19), 12M, #1


title: Mouse Tau Tg (PS19), 9M, #5


title: Mouse Tau Tg (PS19), 9M, #4


title: Mex_ip_15_1

source_name: Mex67-AA control 10' 4tU RNA replicate 2


title: Arabidopsis_Drop-seq_96

extract_protocol:
Cells were diluted in Solution A (PMID: 16170893) to 96 cells/ul. 2.5% human cells were added to each suspension. Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads as previously described (PMID: 26000488).
The library was prepared according to Drop-seq Laboratory Protocol version 3.1 (http://mccarrolllab.com/dropseq/) using Illumina's Nextera XT DNA Library Preparation Kit. The library was uniquely indexed and then pooled and sequenced on a single lane of a HiSeq 4000.


title: Mouse Tau Tg (PS19), 6M, #4


title: Genomic DNA from Breast cancer brain metastasis-27

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-27

extract_protocol: Genomic DNA was extracted and purified from formalin-fixed paraffin embedded tissue samples using ZR FFPE DNA MiniPrep (D3066; Zymo Research, Irvine, CA) according to manufacturer recommendations.

tag: sample type


title: Genomic DNA from Breast cancer brain metastasis-26

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-26

tag: disease state


title: Mouse Tau Tg (PS19), 9M, #3


title: Mouse Tau Tg (PS19), 9M, #1


title: Mouse Tau Tg (PS19), 12M, #2


title: Mouse Tau Tg (PS19), 9M, #2


title: Mouse Tau Tg (PS19), 6M, #3


title: Mouse Tau Tg (PS19), 6M, #5


title: Nab_ip_15_3

description:
pA+ RNA 3' end seq
4tU IP RNA
Background estimated from sample Nab_ip_neg.

source_name: Nab2-AA 15' depleted 10' 4tU RNA replicate 3

tag: labeling


title: Mex_ip_0_1

source_name: Mex67-AA control 10' 4tU RNA replicate 1

tag: min rapamycin


title: Mouse Tau Tg (PS19), 6M, #2


title: Genomic DNA from Breast cancer brain metastasis-25

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-25


title: Nab_ip_15_2

source_name: Nab2-AA 15' depleted 10' 4tU RNA replicate 1

tag: replicate


title: Genomic DNA from Breast cancer brain metastasis-24

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-24


title: Genomic DNA from Breast cancer brain metastasis-23

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-23


title: Nab_ip_0_3

source_name: Nab2-AA 15' depleted 10' 4tU RNA replicate 2


title: Nab_ip_0_2

source_name: Nab2-AA control 10' 4tU RNA replicate 3


title: Genomic DNA from Breast cancer brain metastasis-22

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-22


title: Genomic DNA from Breast cancer brain metastasis-21

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-21


title: Mouse Tau Tg (PS19), 6M, #1


title: Nab_ip_15_1

source_name: Nab2-AA control 10' 4tU RNA replicate 2


title: Nab_ip_0_1

source_name: Nab2-AA control 10' 4tU RNA replicate 1


title: Mex_in_15_3

description: pA+ RNA 3' end seq

source_name: Mex67-AA 15' depleted total RNA replicate 3


title: Genomic DNA from Breast cancer brain metastasis-17

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-17

source_name: Microdissected formalin-fixed paraffin-embedded tissue from metastatic brain tumors


title: Mex_in_0_2

description: pA+ RNA 3' end seq

source_name: Mex67-AA control total RNA replicate 3


title: Mex_in_0_3

description: pA+ RNA 3' end seq

source_name: Mex67-AA 15' depleted total RNA replicate 2


title: Genomic DNA from Breast cancer brain metastasis-19

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-19


title: Genomic DNA from Breast cancer brain metastasis-20

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-20


title: Genomic DNA from Breast cancer brain metastasis-16

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-16


title: Mex_in_15_2

description: pA+ RNA 3' end seq

source_name: Mex67-AA 15' depleted total RNA replicate 1


title: Genomic DNA from Breast cancer brain metastasis-15

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-15


title: Mouse Tau Tg (PS19), 3M, #3


title: Genomic DNA from Breast cancer brain metastasis-14

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-14


title: Mouse Tau Tg (PS19), 3M, #4


title: Mex_in_15_1

description: pA+ RNA 3' end seq

source_name: Mex67-AA control total RNA replicate 2


title: Mouse Tau Tg (PS19), 3M, #5


title: Mex_in_0_1

description: pA+ RNA 3' end seq

source_name: Mex67-AA control total RNA replicate 1


title: Genomic DNA from Breast cancer brain metastasis-13

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-13


title: Mouse WT (PS19), 12M, #5


title: Mouse Tau Tg (PS19), 3M, #2


title: Mouse WT (PS19), 12M, #3


title: Genomic DNA from Breast cancer brain metastasis-12

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-12


title: Mouse WT (PS19), 12M, #2

description: Gene Expression Data from PS19 Tau Transgenic mice from hippocampus


title: Genomic DNA from Breast cancer brain metastasis-11

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-11


title: Mouse Tau Tg (PS19), 3M, #1


title: Mouse WT (PS19), 12M, #4


title: Genomic DNA from Breast cancer brain metastasis-10

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-10


title: Nab_in_0_3

description: pA+ RNA 3' end seq

source_name: Nab2-AA 15' depleted total RNA replicate 2


title: Mouse WT (PS19), 12M, #1

source_name: hippocampus


title: Mouse WT (PS19), 9M, #4


title: Nab_in_0_2

description: pA+ RNA 3' end seq

source_name: Nab2-AA control total RNA replicate 3


title: Mouse WT (PS19), 9M, #5


title: Mouse WT (PS19), 9M, #2


title: Nab_in_15_1

description: pA+ RNA 3' end seq

source_name: Nab2-AA control total RNA replicate 2


title: Mouse WT (PS19), 9M, #3


title: Genomic DNA from Breast cancer brain metastasis-08

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-08


title: Genomic DNA from Breast cancer brain metastasis-09

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-09


title: Nab_in_15_3

description: pA+ RNA 3' end seq

source_name: Nab2-AA 15' depleted total RNA replicate 3


title: Nab_in_0_1

description: pA+ RNA 3' end seq

source_name: Nab2-AA control total RNA replicate 1


title: Genomic DNA from Breast cancer brain metastasis-07

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-07


title: Genomic DNA from Breast cancer brain metastasis-06

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-06


title: Genomic DNA from Breast cancer brain metastasis-05

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-05


title: Nab_in_15_2

description: pA+ RNA 3' end seq

source_name: Nab2-AA 15' depleted total RNA replicate 1


title: Genomic DNA from Breast cancer brain metastasis-04

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-04


title: Mouse WT (PS19), 9M, #1


title: Genomic DNA from Breast cancer brain metastasis-02

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-02


title: Genomic DNA from Breast cancer brain metastasis-01

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-01


title: Mouse WT (PS19), 6M, #5


title: Mouse WT (PS19), 6M, #3


title: MDA-MB-231-miR-200c cell culture 3

city: Guangzhou

first: baiyao

last: wang

state: Guangdong province

address: 1838 guangzhou dadaobei road

department: Department of Radiation Oncology

country: China

institute: Nanfang Hospital, Southern Medical University, Guangzhou, China

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: cell population of MDA-MB-231 stably transfected with pGIPZ-his-miR-200c plasmid, cell culture 3

label_protocol: Biotinylated cRNA was prepared according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology).

growth_protocol: Cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit according to manufacturer's instructions (Qiagen).

tag: cell line

value: breast cancer cell line

tag: transfection

value: pGIPZ-his-miR-200c plasmid


title: Mouse WT (PS19), 6M, #4

value: WT


title: Mouse WT (PS19), 3M, #4


title: Mouse WT (PS19), 3M, #3


title: Mouse WT (PS19), 6M, #1


title: Mouse WT (PS19), 3M, #5


title: Mouse WT (PS19), 3M, #2


title: Mouse WT (PS19), 6M, #2


title: MDA-MB-231-pGIPZ cell culture 3

source_name: cell population of MDA-MB-231 stably transfected with pGIPZ-his plasmid, cell culture 3

tag: tissue

value: pGIPZ-his plasmid


title: MDA-MB-231-miR-200c cell culture 1

source_name: cell population of MDA-MB-231 stably transfected with pGIPZ-his-miR-200c plasmid, cell culture 1


title: MDA-MB-231-pGIPZ cell culture 1

source_name: cell population of MDA-MB-231 stably transfected with pGIPZ-his plasmid, cell culture 1


title: Mouse WT (PS19), 3M, #1


title: MDA-MB-231-pGIPZ cell culture 2

source_name: cell population of MDA-MB-231 stably transfected with pGIPZ-his plasmid, cell culture 2


title: Genomic DNA from Breast cancer brain metastasis-03

description:
Microdissected formalin-fixed paraffin-embedded tissue from brain metastasis
BCBM-03

data_processing:
Data was extracted using the R package methylumi. The ‘noob’ function in the R package minfi was used to process the data and then the ‘dasen’ function in the R package wateRmelon for normalization and dye-bias correction. DNA methylation levels were reported as β-value (β= intensity of the methylated allele/(intensity of the unmethylated allele + intensity of the methylated allele)) and calculated using the signal intensity value for each CpG site.
Average Beta and Unmethylated and methylated signal intensities in Series supplementary file

source_name: Microdissected formalin-fixed paraffin-embedded tissue from metastatic brain tumors

value: Formalin-fixed paraffin-embedded tissue


title: MDA-MB-231-miR-200c cell culture 2

source_name: cell population of MDA-MB-231 stably transfected with pGIPZ-his-miR-200c plasmid, cell culture 2


title: hPSCs-intestinal organoid + in vitro maturation #5

status: Public on Aug 27 2018

city: Daejeon

first: Mi-Young

last: Son

address: 111 Gwahangno, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

description: Gene expression of DF treated intestinal organoid passage 2 defferentiated from hPSCs

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent-026652 Whole Human Genome Microarray 4x44K v2. The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: Data was extracted using GeneSpringGX 7.3 (Agilent Technology, USA). Raw intensity data was globally normalized (Cheadle et al.(2003).

source_name: Human pluripotent stem cell, hIO differentiation passage 2, in vitro-matured

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: The hIOs were embedded in Matrigel (BD Biosciences), cultured in hIO medium with advanced DMEM/F12 medium containing 1X B27 (Invitrogen), 500 ng/ml R-Spondin 1 (R&D Systems), 100 ng/ml EGF (R&D Systems), and 100 ng/ml Noggin (R&D Systems), and then passaged every 2 weeks.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: A Transwell polyester membrane insert (Corning, Corning, NY, USA) on which hIOs had been embedded within Matrigel (BD Biosciences) was placed in a 12-well plate where stimulated immune cells were seeded at 5X10^4/cm2 in hIO medium.

value: hPSC

tag: differentiation stage

value: Intestinal organoid


title: Adult human small intestine #1

description: Gene expression of human adult small intestine tissue

source_name: Adult human small intestine #1

value: Adult human small intestine tissue

value: Small intestine


title: Human pluripotent stem cell #1

description: Gene expression of human pluripotent stem cell

source_name: Human pluripotent stem cell #1

value: Stem cell


title: hPSCs-intestinal organoid + in vitro maturation #4


title: hPSCs-intestinal organoid + in vitro maturation #6


title: Adult human small intestine #2

source_name: Adult human small intestine #2


title: Human pluripotent stem cell #3

source_name: Human pluripotent stem cell #3


title: Human pluripotent stem cell #2

source_name: Human pluripotent stem cell #2


title: hPSCs-intestinal organoid + in vitro maturation #3

description: Gene expression of co-cultured intestinal organoid passage 2 defferentiated from hPSCs


title: hPSCs-intestinal organoid + in vitro maturation #2


title: Adult human small intestine #4

source_name: Adult human small intestine #4


title: Adult human small intestine #3

source_name: Adult human small intestine #3


title: hPSCs-intestinal organoid p2 #2

description: Gene expression of intestinal organoid passage 2 defferentiated from hPSCs

source_name: Human pluripotent stem cell, hIO differentiation passage 2


title: hPSCs-intestinal organoid p0 #2

description: Gene expression of intestinal organoid passage 0 defferentiated from hPSCs

source_name: Human pluripotent stem cell, hIO differentiation passage 0


title: hPSCs-intestinal organoid p2 #3


title: hPSCs-intestinal organoid p2 #1


title: hPSCs-intestinal organoid + in vitro maturation #1


title: FUBP1_V5_CLIP

first: Mathias

last: Munschauer

address: 415 Main Street

institute: The Broad Institute of MIT and Harvard

data_processing:
A custom script was used to perform read demultiplexing and trimming. Samples were demultiplexed based on inline barcodes (allowing for up to one mismatch per barcode) and the first 18 bases of read 1 were trimmed after demultiplexing.
Reads were mapped to hg19 using TopHat (version 2.0.8). Reads aligning to rRNA were removed from downstream analysis as described in Engreitz et al. 2014 Cell 159, 188–199. Duplicate reads were identified and removed using Picard's MarkDuplicates.
Peak calling was performed with the MACS212 algorithm to identify genomic coordinates where experimental conditions (protein-IP) were significantly enriched for reads relative to size-matched controls (input). Peak calling was performed without a shifting model and the band width to compute fragment size was set to 100 bp. Significant peaks are reported with FDR correction of q=0.05. Significant peaks were further filtered to include only regions with an average minimum depth of 2 reads in the size-matched control condition.
To compile significant peaks across replicate experiments, we intersected the intervals from the peak calling output of each replicate. Normalized coverage in the intersection peaks was first calculated separately for each replicate as the average depth at a given peak divided by the total number of reads after correcting for the observed duplication rate. The mean of the relative fold change between the two replicates was calculated for each peak and peaks that did not show a 2-fold or greater change in both replicates were excluded.
Genome_build: hg19
Supplementary_files_format_and_content: Peak table

source_name: Colon cancer

growth_protocol: We maintained HCT116 cells (ATCC) in McCoy’s 5A (Thermo Fisher Scientific) with 10% heat-inactivated FBS (HIFBS, Thermo Fisher Scientific), 1 mM Sodium Pyruvate, 2mM L-glutamine, and 100 units/ml streptomycin and 100 mg/ml penicillin. Cells were grown at 37 °C and 5 % CO2 atmosphere.

extract_protocol:
To prepare cell lysates, pellets were thawed on ice and resuspended in NP40 lysis buffer (50 mM HEPES pH 7.5, 150 mM KCl, 2 mM EDTA, 1% (v/v) NP40, 0.25 mM DTT, complete EDTA-free protease inhibitor cocktail) and incubated on ice for 10 min. We sonicated cell lysates using a Branson Digital Sonifier with a microtip set at 5 W power for a total of 1 min 30 s in intermittent pulses (0.7 s on, 2.3 s off), followed by RNase I (Thermo Fisher Scientific) digestion (0.5 U/µl, 10 min at 23 °C). Subsequently, we added 15 µl/ml Murine RNase Inhibitor (New England Biolabs), followed by DNA digestion (20 U TURBO DNase (2 U/µl; Thermo Fisher Scientific), 2.5 mM MgCl2 and 0.5 mM CaCl) for 20 min at 37 °C. We incubated samples on ice for 10 min before clearing lysates by centrifugation at 15,000g for 15 min. Insoluble material was removed and total protein concentration was determined by BCA assay. Cell lysates were flash-frozen and stored in batches of 10 mg total protein at -80 °C. For each immunoprecipitation experiment, lysates (10 mg total protein) were thawed on ice and pre-cleared by incubating with Protein A/G magnetic beads (using 30 µl/mg total protein) for 30 min at 4 °C. Immunoprecipitation reactions were performed as described in Hafner et al. 2010 Cell 141, 129–141.
Sequencing libraries were constructed as described in Zarnegar et al. 2016 Nat Meth 13, 489–492, with the exception of reverse transcription reactions, which were carried out as described in Hafner et al. 2010 Cell 141, 129–141. Size-matched input libraries were constructed as described in Van Nostrand et al. 2016 Nat Meth 13, 508–514.

treatment_protocol: For each CLIP experiment we grew 20 million HCT116 cells in media supplemented with 200 µM 4-thiouridine for 8 h. Cells were washed once with PBS and then crosslinked on ice using 0.2 J/cm2 of 365 nm UV light in a Stratalinker. Cells were then scraped from culture dishes, washed once with PBS, pelleted by centrifugation at 500g for 5 min, and flash-frozen in liquid nitrogen for storage at -80 °C.

tag: clip protein


title: FUBP3_V5_CLIP


title: PUM1_CLIP


title: hPSCs-intestinal organoid p0 #3

tag: cell type


title: hPSCs-intestinal organoid p0 #1


title: hPSCs-definitive Hindgut day4 #3

description: Gene expression of hindgut differentiation day4 from hPSCs

source_name: Human pluripotent stem cell, HG differentiation day4

value: Hindgut


title: hPSCs-definitive Hindgut day4 #2


title: RBMX_SEC_fraction20

value: RBMX


title: hPSCs-definitive endoderm day3 #1

description: Gene expression of definitive endoderm differentiation day3 from hPSCs

source_name: Human pluripotent stem cell, DE differentiation day3

value: Definitive endoderm


title: ALYREF_CLIP

value: ALYREF


title: human adult tissue derived intestinal organoid control

description: Gene expression of intestinal organoid derived from human adult intestinal tissue

source_name: Human adult tissue derived intestinal organoid, control

value: Human adult tissue-derived cell


title: hPSCs-definitive endoderm day3 #2


title: human adult tissue derived intestinal organoid + nicotinamide

description: Gene expression of nicotinamide treated intestinal organoid derived from human adult intestinal tissue

source_name: Human adult tissue derived intestinal organoid, nicotinamide


title: KD_96h_rep3

data_processing:
Reads were pseudo-aligned to hg19 using kallisto with an index of either 31 or 21 k-mers
Estimated counts were collapsed across transcripts into genes
Differential expression analysis was performed using DESeq2
Percentage spliced in (PSI) was calculated for different exons or introns using SUPPA2 based upon isoform Transcripts Per Million (TPM) estimates from kallisto
Differential PSI was calculated using diffSplice with the parameters “--area 1000 --tpm-threshold 5 --lower-bound 0.00 -gc”
Genome_build: hg19
Supplementary_files_format_and_content: Count table

extract_protocol:
We extracted RNA from 20,000-50,000 cells per experiment in RLT Buffer (Qiagen) using Dynabeads MyOne Silane beads (Thermo Fisher Scientific), treated samples with TURBO DNase (Thermo Fisher Scientific), and purified RNA with Silane beads.
We isolated polyadenylated RNA (selected using oligo d(T)25 magnetic beads, NEB) and constructed RNA sequencing libraries using a strand-specific RNA-sequencing protocol for Illumina instruments described in Engreitz et al. Cell 2014.

treatment_protocol: CRISPRi knockdown was induced by supplementing cell culture media with 0.5 µg/ml doxycycline for the indicated times.

tag: genotype/variation

value: knock down

tag: time point


title: hPSCs-definitive Hindgut day4 #1


title: RBMX_SEC_fraction6


title: RBMX_CLIP_rep2


title: RBMX_SMInput_rep2


title: RBMX_SMInput_rep1


title: RBMX_CLIP_rep1


title: KD_96h_rep2


title: KD_96h_rep1


title: KD_48h_rep3


title: KD_48h_rep2


title: KD_48h_rep1


title: WT_96h_rep2

value: wild type


title: WT_96h_rep3


title: KD_24h_rep1


title: WT_96h_rep1


title: WT_48h_rep1


title: KD_24h_rep2


title: WT_48h_rep2


title: WT_48h_rep3


title: WT_24h_rep1


title: WT_24h_rep2


title: H226 shp63, 14 days vehicle, libB replicate 2

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

description:
sgRNA cassette amplicon
NODX14B_rep2

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 2500 Real-Time Analysis (RTA) software (Illumina)
Conversion to FASTQ format was carried out using bcl2fastq (v1.8.4, Illumina)
Samples were demultiplexed using fastx_barcode_splitter from the fastx_toolkit (v0.0.13.2), allowing 2 mismatches
FASTQC v0.11.2 was used to assess sequence data quality
Sequences were trimmed using fastx_trimmer from the fastx_toolkit (v0.0.13.2), with the following options: -Q33 -f 43 -l 62. This keeps only the section of each read corresponding to the unique sgRNA sequences (positions 43-62 inclusive)
Bases with qual ≥10 were removed with fastx_quality_filter from the fastx_toolkit (v0.0.13.2), with the following options: -Q33 -q 10 -p 94.
Trimmed and filtered sequences were mapped with Bowtie2 v2.2.3 using the following options (--phred33 --end-to-end --very-sensitive)
Genome_build: A reference index was generated for Bowtie2 using only the unique sgRNA sequences from the Human GeCKOv2 library annotation available from https://media.addgene.org/cms/filer_public/7d/87/7d87eaa7-e940-41bf-bf2f-47b43c7ab905/zhang_human_geckov2_grna_sequences.zip (PMID: 24336571; PMID: 25075903)
Supplementary_files_format_and_content: Tab delimited text files containing raw sgRNA counts for each sample

source_name: H226 shp63_14 days vehicle

growth_protocol: H226 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum and were maintained at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
CRISPR screen protocol: H226 shp63 cells were transduced with the GeCKOv2 A or B libraries and propogated for 14 days to clear sgRNAs targeting essential genes. The resulting cell populations were treated in triplicate with PBS (vehicle) or doxycycline (to induce p63 knockdown) for 14 days.
Genomic DNA was extracted using a DNeasy Blood and Tissue kit (Qiagen)
Custom

treatment_protocol:
shRNA protocol: Generation of H226 cell lines expressing doxycycline-inducible control and p63-targeting short hairpin RNAs (shRNAs) was described previously (PMID: 2301912). Cells were treated with vehicle (PBS), or 1 µg/mL doxycycline to induce shRNA expression.
Cells were treated with vehicle (PBS), or 1 µg/mL doxycycline to induce shRNA expression.

value: lung squamous cell carcinoma

tag: inducible shrna construct

tag: gecko library

value: HGLibB

tag: culture condition

tag: treatment

value: vehicle


title: H226 shControl, 6 days doxycycline, replicate 1

description:
total RNA from doxycycline-treated H226 shControl cells
shControl_rep1
NonTargeting_rep1

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 2500 Real-Time Analysis (RTA) software (Illumina)
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (v1.8.4, Illumina)
FASTQC (v0.11.2) was used to assess sequence data quality
Low quality bases (Q <10) were trimmed from the 3' end of reads and short reads (<30 nt after trimming) and adaptor sequences were removed using the fastqc-mcf tool from ea-utils
FastQ Screen (v0.11.0) was used to check for common sequencing contaminants
Alignment to the Human reference genome (GRCh37/hg19) was carried out using TopHat2 (v2.0.13, --b2-sensitive --keep-fasta-order --no-coverage-search --max-multihits 10 --library-type fr-firststrand) with the UCSC hg19 GTF annotation file provided in the iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were then filtered to remove low quality mapped reads (MAPQ < 10) using SAMtools (v0.1.19)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Quality assessment of final mapped reads was performed using RSeQC (v2.6)
Raw gene-level count data was generated using HTSeq (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene --mode=intersection-nonempty) using the GTF provided in the UCSC hg19-based igenomes bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Genome_build: GRCh37/hg19; Bowtie2 index and GTF from iGenomes UCSC hg19 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html)
Supplementary_files_format_and_content: Tab delimited text files containing raw gene-level counts for each sample

source_name: H226 shControl_6 days doxycycline

growth_protocol: All cell lines were plated 24 hours prior to treatment and incubated at 37°C in a humidified atmosphere with 5% CO2

extract_protocol:
RNA was extracted using a PureLink RNA Mini kit , according to manufacturer's instructions. Total RNA quality was assessed using Bioanalyzer RNA Pico chips (Agilent) and all samples had RIN >9.
Libraries for Illumina sequencing were prepared using a TruSeq Stranded mRNA Library Prep Kit (Illumina), according to the manufacturer’s instructions.

treatment_protocol: 6 days 1 µg/mL doxycycline

value: Control

value: 1 µg/mL doxycycline

value: 37°C, 5% CO2, 6 days


title: H226 shp63, 14 days doxycycline, libB replicate 2

description:
sgRNA cassette amplicon
DX14B_rep2

source_name: H226 shp63_14 days doxycycline


title: H226 shp63, 6 days doxycycline, replicate 2

description:
total RNA from doxycycline-treated H226 shp63 cells
shp63_rep2
p63KD_rep2

source_name: H226 shp63_6 days doxycycline


title: H226 shp63, 14 days doxycycline, libA replicate 2

description:
sgRNA cassette amplicon
DX14A_rep2

value: HGLibA


title: H226 shp63, 6 days doxycycline, replicate 1

description:
total RNA from doxycycline-treated H226 shp63 cells
shp63_rep1
p63KD_rep1


title: H226 shp63, 14 days doxycycline, libA replicate 1

description:
sgRNA cassette amplicon
DX14A_rep1


title: H226 shControl, 6 days doxycycline, replicate 2

description:
total RNA from doxycycline-treated H226 shControl cells
shControl_rep2
NonTargeting_rep2


title: H226 shp63, 14 days vehicle, libA replicate 1

description:
sgRNA cassette amplicon
NODX14A_rep1


title: hPSCs-definitive endoderm day3 #3

value: hPSC


title: K24W1D

city: BeiJing

first: Yidong

last: Chen

address: Yiheyuan Road

institute: Peking University

description:
polyA RNA
K24W1D

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first organized by specific cell barcode information attached in the read 2 of pair-ended reads. Second, unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails. Subsequently, we also removed reads with adapter contaminants and low-quality bases (N>10%).
Third, the cleaned reads were aligned to the hg19 human transcriptome (UCSC) using Tophat (version 2.0.12) (Trapnell et al., 2009). Fourth, uniquely mapped reads were counted using htseq-count of the HTSeq package and grouped by cell-specific barcode (Anders et al., 2014). Based on UMI information, duplicated transcripts of each gene were removed. Finally, within a given cell, distinct UMIs of each gene were counted as the transcript number of that gene.
The expression levels TPM, where TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: hg19
Supplementary_files_format_and_content: txt files which include theTPM values of RefSeq genes.

source_name: Human Embryonic Kidney Cells

extract_protocol:
A modified Smart-seq2 protocol was applied for single-cell RNA-seq. Briefly,  single cell was picked into the lysis buffer by mouth pippete. The reverse transcription reaction was performed with a 24 oligo (dT) primer, which was  anchored with a 8 bp cell specific barcode and a 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 19 cycles. Then the amplified cDNA of the cells of the same fetal sample were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on illumina HiSeq 4000 platform (sequenced by Novogene).

treatment_protocol: With enthic approval, human fetal kidney was first cut into pieces and then tissues were transferred to 1mg/ml collagenase II and collagenase IV mixture in a single tube. The tube was incubated at 37°C with shaken at 950 rpm for 20min. Then the cell suspesion was filtered through a 40 μm nylon straniner. The filtered cell suspesion was  centrifugated at 800g for 5min. We removed the supernate and resuspended the cell pellets using 500 μl DMEM medium. Single cell was picked up by mouth pipette and transfered to 8 strip 0.2 ml PCR tubes.

tag: age

tag: gender

value: male


title: K801

description:
polyA RNA
K801


title: K24W1P

description:
polyA RNA
K24W1P


title: K22W2P32

description:
polyA RNA
K22W2P32

value: female


title: K802

description:
polyA RNA
K802


title: K22W2P31

description:
polyA RNA
K22W2P31


title: K22W2P21

description:
polyA RNA
K22W2P21


title: K22W2P22

description:
polyA RNA
K22W2P22