title: P04_Ctrl19_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl19_S78


title: P04_Ctrl21_single_cell_passage_04

status: Public on Jan 10 2019

type: SRA

city: BETHESDA

first: Shutong

last: Liu

state: Maryland

address: 9000 Rockville Pike

department: Clinical Center

country: USA

institute: National Institutes of Health

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl21_S76

library_source: transcriptomic

data_processing:
BCL files generated by Illumina NextSeq were converted to standard FASTQ files following Illumina’s protocol (basespace.illumina.com).
STAR - 2.4.1d for alligment
Partek E/M to generate gene counts
Genome_build: hg19-RefSeq Transcripts 2016-5-2
Supplementary_files_format_and_content: gene counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: One vial of frozen Passage 2 BMSCs was thawed and plated in T75 flasks following the SOP. During the serial culture, cells were seeded at 5000 cells per cm2 and harvested at 70-80% confluence. From passage 3 to 8, cells were passaged after 5 days of culture, and culture media was changed on day 3; from passage 9 to 10, the cells were passaged after 8 days of culture, and culture media was changed on day 3 and 6. Cells from each passage were cryopreserved in a solution containing 90% FBS and 10% DMSO for further studies.

extract_protocol:
Frozen cells from different passages were thawed and plated in T75 flasks for 5-7 days. Once they reached 70-80% confluence, cells were collected for single cell separation. Fluidigm C1 Single-Cell Auto Prep Array for mRNA-Seq (10-17um) and Fluidigm C1 system were used for cell capture following the Fluidigm protocol, then reverse transcription and cDNA amplification were performed using the SMARTer PCR cDNA Synthesis kit (Clontech, version 1) on the C1 unit.
Single-cell cDNA from validation cells were harvested for library preparation. Nextera XT DNA sample preparation kits and Index kits were used for library preparation following the manufacturer’s protocol. Single-cell cDNA libraries from each passage were pooled and cleaned up, then cDNA size distribution was examined by 2100 Bioanalyzer. This was followed by quantification and normalization with the KAPA Library Quantification Kit and BioRad CFX96 qPCR machine (BioRad). Single cell mRNA sequencing was performed on NextSeq 500 by using the NextSeq High Output v2 kit (300 cycles). PhiX Control v3 (Illumina) was used as a quality control for sequencing runs.

tag: subject status

value: healthy donor

tag: cell type

value: Bone marrow stromal cells (BMSCs)

tag: passage


title: P04_Ctrl40_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl40_S57


title: P04_Ctrl18_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl18_S79


title: P04_Ctrl16_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl16_S81


title: P04_Ctrl31_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl31_S66


title: P04_Ctrl15_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl15_S82


title: P04_Ctrl32_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl32_S65


title: P04_Ctrl30_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl30_S67


title: P04_Ctrl13_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl13_S84


title: P04_Ctrl12_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl12_S85


title: P04_Ctrl14_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl14_S83


title: P04_Ctrl11_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl11_S86


title: P04_Ctrl28_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl28_S69


title: P04_Ctrl10_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl10_S87


title: P04_Ctrl07_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl07_S90


title: P04_Ctrl08_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl08_S89


title: P04_Ctrl06_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl06_S91


title: P04_Ctrl04_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl04_S93


title: P03_Ctrl42-38439544_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl42_S42


title: P04_Ctrl09_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl09_S88


title: P03_Ctrl41-38435588_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl41_S41


title: P03_Ctrl44-38442467_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl44_S44


title: P04_Ctrl05_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl05_S92


title: P04_Ctrl03_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl03_S94


title: P03_Ctrl39-38448420_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl39_S39


title: P03_Ctrl46-38444466_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl46_S46


title: P03_Ctrl40-38439542_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl40_S40


title: P03_Ctrl43-38435589_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl43_S43


title: P03_Ctrl45-38443468_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl45_S45


title: P04_Ctrl02_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl02_S95


title: P03_Ctrl37-38433600_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl37_S37


title: P03_Ctrl36-38439541_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl36_S36


title: P03_Ctrl38-38442464_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl38_S38


title: P04_Ctrl17_single_cell_passage_04

description:
processed data file: single_cell_passage_04_processed.txt
P04_Ctrl17_S80


title: P03_Ctrl34-38440565_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl34_S34


title: P03_Ctrl35-38433599_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl35_S35


title: P03_Ctrl32-38439538_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl32_S32


title: P03_Ctrl30-38444459_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl30_S30


title: P03_Ctrl33-38445450_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl33_S33


title: P03_Ctrl31-38435586_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl31_S31


title: P03_Ctrl47-38445454_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl47_S47


title: P03_Ctrl48-38443471_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl48_S48


title: P03_Ctrl27-38442461_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl27_S27


title: P03_Ctrl24-38443461_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl24_S24


title: P03_Ctrl23-38443460_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl23_S23


title: P03_Ctrl25-38444457_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl25_S25


title: P03_Ctrl26-38433595_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl26_S26


title: P03_Ctrl21-38435583_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl21_S21


title: P03_Ctrl19-38440561_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl19_S19


title: P03_Ctrl29-38433596_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl29_S29


title: P03_Ctrl18-38433591_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl18_S18


title: P03_Ctrl14-38448410_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl14_S14


title: P03_Ctrl12-38443455_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl12_S12


title: P03_Ctrl13-38439536_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl13_S13


title: P03_Ctrl10-38444450_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl10_S10


title: P03_Ctrl11-38442454_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl11_S11


title: P03_Ctrl08-38440555_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl08_S8


title: P03_Ctrl16-38448411_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl16_S16


title: P03_Ctrl06-38445437_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl06_S6


title: P03_Ctrl07-38429883_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl07_S7


title: P03_Ctrl03-38435571_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl03_S3


title: P03_Ctrl05-38434595_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl05_S5


title: P03_Ctrl04-38444446_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl04_S4


title: P03_Ctrl01-38444443_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl01_S1


title: P03_Ctrl28-38443463_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl28_S28


title: P03_Ctrl15-38444452_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl15_S15


title: P03_Ctrl09-38442452_single_cell_passage_03


title: MO_2

city: Frankfurt

first: Tobias

last: Schmid

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry I

country: Germany

institute: Goethe University Frankfurt

data_processing:
Raw data was subjected to adapter trimming using skewer.
Reads were mapped to the human reference genome (hg38) using STAR.
Gene level quantification was performed by RSEM.
Differential analysis was performed using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include TPM for each sample.

source_name: Breast carcinoma

growth_protocol: Cells were maintained in RPMI 1640 supplemented with 10% FBS, 1% sodium pyruvate, 100U/ml penicillin and 100 µg/ml streptomycin and cultivated at 37°C in a humidified atmosphere with 5% CO2. Multicellular spheroids were generated according to the liquid overlay technique and cultured for 5 days.

extract_protocol:
RNA was harvested using RNA Clean and Concentrator-25 protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD14+ macrophages were cultured with spheroids for additional 48 hours.

value: MCF7 cells

tag: infiltration

value: MФ


title: P03_Ctrl22-38445444_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl22_S22


title: P03_Ctrl20-38443458_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl20_S20


title: P03_Ctrl02-38439524_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl02_S2


title: MO_1


title: P03_Ctrl17-38442457_single_cell_passage_03

description:
processed data file: single_cell_passage_03_processed.txt
P03-BMSC-Ctrl17_S17


title: Ctrl_2


title: Ctrl_1


title: Roundup_10ug/L Combined_RM62

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

country: United Kingdom

institute: Kings College London

description:
Roundup is a glyphosate-based herbicide
Mesnage et al. Glyphosate HepaRG FPKM Data.txt

data_processing:
The RNA-seq data analysis was performed using the new version of the Tuxedo protocol with HISAT, StringTie and Ballgown
Sequences were then aligned to the human genome (prebuilt indexes H. sapiens, GRCh38 downloaded from HISAT2 website) using the hierarchical indexing for spliced alignment of transcripts program HISAT2
StringTie was used to assemble and quantify the transcripts in each sample using the Homo_sapiens.GRCh38.89 database
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with Ballgown following the protocol described in the Tuxedo protocol publication (Nat Protoc. 2016 Sep; 11(9): 1650–1667.)
Genome_build: Homo_sapiens.GRCh38.89 database
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: HepaRGTM cells (HPR 116)

growth_protocol: Differentiated HepaRG cells (HPR 116) were purchased from Biopredic International (Rennes, France). Cells were thawed, suspended and plated in the general purpose medium (Williams’E medium + GlutaMAXTM) containing with ADD670 supplement. A total of 72,000 and 2,000,000 cells were plated in collagen-coated 96 well-plates (Greiner Bio-One, Germany), and 6 well-plates (Biopredic), respectively. All cells were grown at 37°C (5% CO2). The medium was refreshed at day 3, 5 and 7. The cells were kept in the general purpose medium until day 8, when the culture becomes well organized and includes well-delineated trabeculae and many canaliculi-like structures. At this time, the culture is composed of primitive biliary epithelial cells and mature hepatocytes with basal metabolic activities similar to fresh cells.

extract_protocol:
RNA extraction was performed using the Qiagen’s RNeasy kit according to the manufacturer's instructions.
A total of 20 ng of intact high quality total RNA (RIN>9) from each sample was then used as input to generate libraries for RNA-seq using the NEBNext Ultra II Directional kit (NEB, Cat.no: E7760S) following the manufacturer’s recommendations. This protocol involved an initial step of rRNA depletion, followed by fragmentation prior to first cDNA synthesis and barcoding second-strand cDNA synthesised with indices for illumina sequencing for final library amplification.

treatment_protocol: From day 8 to day 14, cells were switched to the test medium composed of Williams’E medium + GlutaMAXTM supplemented with 2% Fetal Bovine Serum (FBS; GE Healthcare Life Sciences, Buckinghamshire, UK) and 1% DMSO, as well as different concentrations of PCB 126, three concentrations of glyphosate, one concentration of Roundup, or the solvent control. Three concentrations of the PCB and glyphosate were tested in order to cover a wide range of biological effects, starting from low environmental exposures to high concentrations.

tag: treatment

tag: cell line

value: HepaRGTM cells (HPR 116)

value: terminally differentiated hepatic cells

tag: agent

value: Roundup


title: Glyphosate_0.1g/L Combined_RM77

description: Mesnage et al. Glyphosate HepaRG FPKM Data.txt

value: glyphosate


title: Glyphosate_1mg/L Combined_RM78


title: Roundup_10ug/L Combined_RM80


title: Glyphosate_10ug/L Combined_RM61


title: Glyphosate_0.1g/L Combined_RM41


title: Roundup_10ug/L Combined_RM44


title: Roundup_10ug/L Combined_RM26


title: Glyphosate_1mg/L Combined_RM60


title: Glyphosate_1mg/L Combined_RM42


title: Glyphosate_0.1g/L Combined_RM23


title: Glyphosate_1mg/L Combined_RM24


title: Roundup_10ug/L Combined_RM08


title: Glyphosate_10ug/L Combined_RM25


title: Glyphosate_1mg/L Combined_RM06


title: Glyphosate_0.1g/L Combined_RM05


title: Glyphosate_10ug/L Combined_RM07


title: PCB_100pM Combined_RM76

description: Mesnage et al. PCB HepaRG FPKM Data.txt

value: PCB 126


title: Control Combined_RM73

description: Mesnage et al. PCB HepaRG FPKM Data.txt

value: Control


title: PCB_10nM Combined_RM75

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: PCB_1uM Combined_RM74

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: PCB_100pM Combined_RM58

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: PCB_10nM Combined_RM57

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: PCB_1uM Combined_RM56

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: Glyphosate_10ug/L Combined_RM79


title: Control Combined_RM55

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: Glyphosate_10ug/L Combined_RM43


title: Glyphosate_0.1g/L Combined_RM59


title: PCB_10nM Combined_RM39

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: PCB_100pM Combined_RM40

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: PCB_100pM Combined_RM22

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: PCB_1uM Combined_RM38

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: Control Combined_RM37

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: PCB_1uM Combined_RM02

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: PCB_1uM Combined_RM20

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: PCB_100pM Combined_RM04

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: PCB_10nM Combined_RM21

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: PCB_10nM Combined_RM03

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: Control Combined_RM01

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: Control Combined_RM19

description: Mesnage et al. PCB HepaRG FPKM Data.txt


title: MF.PC#3

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: Peritoneal Macrophages

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

organism: Mus musculus

source_name: Peritoneal Cavity

growth_protocol: 6 week old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested at 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA

treatment_protocol: Some organisms were treated with 1k or 10k IFN

tag: gender

value: male

tag: tissue

value: Peritoneal Cavity

tag: strain

tag: age

value: 6 weeks old

tag: sorting markers

value: Macrophages


title: B.F.Sp#2_

description: Female Splenic B Cells

source_name: Spleen

value: female

value: Spleen

value: TCRB- CD19+ IgM+

value: B cells


title: B.Sp#3

description: Splenic B Cells


title: MF.F.PC#2_

description: Female Peritoneal Macrophages


title: MF.F.PC#1_

description: Female Peritoneal Macrophages


title: B.Sp#4

description: Splenic B Cells


title: Treg.6m.F.Sp#1

description: Female Splenic Treg Cells

value: 6 months old

value: TCRB+ CD4+ CD25+

value: Regulatory T Cells


title: T.4.Nve.F.Sp#2

description: Female Splenic Naïve CD4 T Cells

value: CD19- TCRB+ CD4+ CD8-

value: CD4 T Cells


title: T.4.Nve.F.Sp#1

description: Female Splenic Naïve CD4 T Cells


title: T.4.Nve.Sp#2_

description: Splenic Naïve CD4 T Cells


title: B.F.Sp#1_

description: Female Splenic B Cells


title: Treg.2m.Sp#1

description: Splenic Treg Cells

value: 2 months old


title: Treg.6m.Sp#1

description: Splenic Treg Cells


title: T.4.Nve.Sp#1_

description: Splenic Naïve CD4 T Cells


title: Treg.2m.F.Sp#1

description: Female Splenic Treg Cells


title: Treg.20m.Sp#1

description: Splenic Treg Cells

value: 20 months old


title: Treg.17m.F.Sp#1

description: Female Splenic Treg Cells

value: 17 months old


title: Tgd.6m.Sp#1

description: Splenic gd T Cells

value: TCRgd+ TCRB-

value: gd T cells


title: Tgd.6m.F.Sp#1

description: Female Splenic gd T Cells


title: Tgd.2m.F.Sp#1

description: Female Splenic gd T Cells


title: MF.PC#4

description: Peritoneal Macrophages

value: male

value: Peritoneal Cavity


title: Tgd.20m.Sp#1

description: Splenic gd T Cells


title: T.8.6m.F.Sp#1

description: Female Splenic CD4 T Cells

value: TCRB+ CD8+

value: CD8 T Cells


title: Tgd.17m.F.Sp#1

description: Female Splenic gd T Cells

value: female

value: Spleen


title: Tgd.2m.Sp#1

description: Splenic gd T Cells


title: T.8.20m.Sp#1

description: Splenic CD4 T Cells


title: T.8.2m.F.Sp#1

description: Female Splenic CD4 T Cells


title: T.8.6m.Sp#1

description: Splenic CD4 T Cells


title: T.8.17m.F.Sp#1

description: Female Splenic CD4 T Cells


title: T.4.6m.Sp#2

description: Splenic CD4 T Cells

value: TCRB+ CD4+


title: T.4.6m.Sp#1

description: Splenic CD4 T Cells

value: 6 months old


title: T.4.6m.F.Sp#2

description: Female Splenic CD4 T Cells


title: T.4.2m.F.Sp#1

description: Female Splenic CD4 T Cells


title: T.4.6m.F.Sp#1

description: Female Splenic CD4 T Cells


title: T.4.2m.Sp#1

description: Splenic CD4 T Cells


title: NKT.2m.F.Sp#1

description: Female Splenic NKT Cell

value: NK1.1+ TCRB+

value: Natural Killer T cells


title: T.4.17m.F.Sp#1

description: Female Splenic CD4 T Cells


title: NKT.2m.Sp#1

description: Splenic NKT Cell


title: NKT.6m.F.Sp#1

description: Female Splenic NKT Cell


title: NKT.20m.Sp#1

description: Splenic NKT Cell


title: NKT.17m.F.Sp#1

description: Female Splenic NKT Cell


title: NK.6m.F.Sp#1

description: Female Splenic NK Cell

value: NK1.1+ TCRB-

value: Natural Killer cells


title: ANS cells 2 days after change in medium B, absent proliferation begin differentiation, sample 3

city: Torino

first: Elena

last: Grassi

address: Via Nizza 52

department: Dept. of Molecular Biotechnology and Health Sciences

country: Italy

institute: Molecular Biotechnology Center

description: TruSeq RNA Sample Prep kit v2, and then sequenced on Illumina platform HiScanSQ. Basecalls was performed using CASAVA version 1.8

data_processing:
Basecalls with CASAVA 1.8
Alignment vs mm9 with TopHat 2.0.6/Bowtie 0.12.7.0
Read counts for single genes obtained using htseq-count 0.6.0 and gene coords from the gtf in Illumina iGenomes for mm9
DESeq2 1.0.0
Roar version 1.0.0 was used to obtain m/M and roar values to detect alternative polyadenylation - check the related article supplementary files for roar analyses results
Genome_build: mm9
Supplementary_files_format_and_content: read count files obtained using htseq-count for each sample

molecule: polyA RNA

source_name: ANS cells

growth_protocol: ANS cells were maintained and expanded in a medium (named growth medium) consisting of Euromed-N medium (Euroclone, Celbio) supplemented with 1% N2 (Invitrogen), 20 ng/ml of hrFGF2 (Peprotech) and 20 ng/ml of hrEGF (Peprotech). For differentiation to GABAergic neurons, confluent ANS cells were gently dissociated using Accutase (Sigma) and plated at 1.0 x 105 - 1.5 x 105 cells/cm2 in expansion medium, after 1 day the medium was changed with a medium (named medium D1) consisting in Euromed-N with 0.5% N2, 1% B27 (Invitrogen), 10 ng/ml hrFGF and 2 ng/ml of hrEGF for 3 days. After that, cells were again dissociated with Accutase and seeded at density of 5 x 104 - 7.5 x104 cells/ml onto Laminin-coated (2mg/ml) dishes and maintained in a medium (named medium B) consisting of a 1:3 mix of DMEM/F12 and Neurobasal media (Invitrogen) containing 0.5% N2 and 1% B27 supplements, FGF-2 (10 ng/mL) and BDNF (20 ng/mL) for 3 days.

extract_protocol:
with Trizol, according to standard procedures
TruSeq RNA Sample Prep kit v2

treatment_protocol: Different mediums as described in the growth protocol, different mediums and times were detailed for each sample in the title and in the characteristic: differentiation time

value: ANS cells

tag: differentiation time

tag: embryo age


title: NK.2m.Sp#1

description: Splenic NK Cell

value: 2 months old


title: ANS cells 2 days after change in medium D1, much reduced proliferation, sample 3


title: T.4.20m.Sp#1

description: Splenic CD4 T Cells

value: 20 months old

value: CD4 T Cells


title: ANS cells 2 days after change in medium B, absent proliferation begin differentiation, sample 4


title: NKT.6m.Sp#1

description: Splenic NKT Cell


title: ANS cells 2 days after change in medium B, absent proliferation begin differentiation, sample 2


title: ANS cells 2 days after change in medium D1, much reduced proliferation, sample 2


title: ANS cells in complete growth medium, full proliferation, sample 3


title: NK.2m.F.Sp#1

description: Female Splenic NK Cell


title: NK.17m.F.Sp#1

description: Female Splenic NK Cell

value: 17 months old


title: T.8.2m.Sp#1

description: Splenic CD4 T Cells

value: male


title: NK.20m.Sp#1

description: Splenic NK Cell


title: MF.2m.PC#1

description: Peritoneal Macrophages

value: Peritoneal Cavity

value: CD19+ IgM+ TCRB-

value: Macrophages


title: MF.6m.F.PC#1

description: Female Peritoneal Macrophages

value: female


title: ANS cells 10 days after change in medium B, overt differentiation, GAD+, sample 4


title: NK.6m.Sp#1

description: Splenic NK Cell

value: Spleen


title: BMSC Passage 08 (bulk)

type: RNA

description: Sample 4

hyb_protocol: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit and subsequently mixed with Universal Human Reference RNA (Stratagene, Santa Clara, CA, USA) and cohybridized to Agilent Chip Whole Human genome, 4x44k slides according to the protocol provided by Agilent.

scan_protocol: The slides were incubated for 17h at 65°C and then the scanned using the Agilent B Scanner.

data_processing: Raw images were obtained by scanning the slides with an Agilent Scan G2505B and Agilent Scan Control software (version 9.5). The images were extracted using the Feature Extraction Software (Agilent Technologies). Partek Genomic Suite 6.4 (Partek Inc., St. Louis, MO, USA) was used for data visualization, identification of differentially expressed transcripts and hierarchical cluster analysis. We transformed the fluorescence intensity data to log2 ratios of each sample versus the universal human RNA reference (Stratagene, Santa Clara, CA, USA).

source_name: BMSCs from one healthy subject

extract_protocol: Total RNA extractions were performed on samples from passages 2, 3, 4, 6, 8, 9, and 10 using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA was quantified using Nanodrop 8000 (Thermo Scientific, Wilmington, DE). Total RNA quality was evaluated following isolation using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Samples with an RNA Integrity Number (RIN) value ≥ 8 were used for bulk cell RNA-Seq and MicroArray for gene expression analysis.

value: healthy subject

value: Bone marrow stromal cells (BMSCs)

source_name: universal human reference RNA

tag: sample type

value: pooled whole huam RNA


title: ANS cells 2 days after change in medium B, absent proliferation begin differentiation, sample 1


title: BMSC Passage 06 (bulk)

description: Sample 3

label_protocol: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit and subsequently mixed with Universal Human Reference RNA (Stratagene, Santa Clara, CA, USA)


title: ANS cells 10 days after change in medium B, overt differentiation, GAD+, sample 1


title: ANS cells 2 days after change in medium D1, much reduced proliferation, sample 1


title: BMSC Passage 10 (bulk)

description: Sample 6


title: BMSC Passage 02 (bulk)

description: Sample 1


title: ANS cells in complete growth medium, full proliferation, sample 2


title: BMSC Passage 09 (bulk)

description: Sample 5


title: MF.2m.F.PC#1

description: Female Peritoneal Macrophages


title: BMSC Passage 04 (bulk)

description: Sample 2


title: ANS cells in complete growth medium, full proliferation, sample 1


title: MF.20m.PC#1

description: Peritoneal Macrophages


title: MF.17m.F.PC#1

description: Female Peritoneal Macrophages


title: Human breast cancer xenograft 5471

city: New York

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to hg19 STAR with default parameters
RNAseq: FPKM were obtained using CuffLinks
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values for each Refseq gene.

source_name: Human breast cancer xenograft

extract_protocol:
Total RNA was extracted from PDX samples using the RNeasy Mini kit (Life Technologies). Samples were then subject to poly(A) selection using oligo-dT beads (Life Technologies).
Illumina TruSeq

treatment_protocol: PDX tumor fragments were transplanted into the cleared fat pad of 3- to 4-week-old SCID/Beige

tag: disease state

value: Triple Negative Breast Cancer

value: TNBC Patient Derived Xenograft (PDX)

tag: subtype

value: basal


title: GN.6m.Sp#1

description: Splenic Dendritic cells

value: 6 months old

value: Neutrophils


title: Human breast cancer xenograft 5310B


title: GN.6m.F.Sp#1

description: Female Splenic Dendritic cells


title: Human breast cancer xenograft 4913


title: Human breast cancer xenograft 5998


title: MF.6m.PC#1

description: Peritoneal Macrophages


title: GN.2m.Sp#1

description: Splenic Dendritic cells

value: 2 months old


title: GN.2m.F.Sp#1

description: Female Splenic Dendritic cells


title: Human breast cancer xenograft 4664


title: Human breast cancer xenograft 4698


title: GN.17m.F.Sp#1

description: Female Splenic Dendritic cells


title: GN.20m.Sp#1

description: Splenic Dendritic cells

value: 20 months old


title: Human breast cancer xenograft 4195


title: DC.6m.F.Sp#1

description: Female Splenic Dendritic cells

value: CD11c+ MHCII+ Flt3+

value: Dendritic cells


title: DC.6m.Sp#1

description: Splenic Dendritic cells

value: male


title: DC.2m.F.Sp#1

description: Female Splenic Dendritic cells


title: DC.2m.Sp#1

description: Splenic Dendritic cells


title: DC.20m.Sp#1

description: Splenic Dendritic cells


title: Human breast cancer xenograft 3904


title: Human breast cancer xenograft 4013


title: Human breast cancer xenograft 3807


title: Human breast cancer xenograft 3887


title: Human breast cancer xenograft 4175


title: B.6m.Sp#2

description: Splenic B cells

value: B cells


title: Human breast cancer xenograft 3611


title: B.6m.Sp#1

description: Splenic B cells


title: B.6m.F.Sp#2

description: Female Splenic B cell


title: Human breast cancer xenograft 3561A


title: DC.17m.F.Sp#1

description: Female Splenic Dendritic cells

value: 17 months old


title: Human breast cancer xenograft 3204


title: Human breast cancer xenograft 3107


title: B.2m.F.Sp#1

description: Female Splenic B cell

value: female


title: Human breast cancer xenograft 2665


title: B.2m.Sp#1

description: Splenic B cells

value: Spleen


title: Human breast cancer xenograft 4272


title: Human breast cancer xenograft 2147


title: B.17m.F.Sp#1

description: Female Splenic B cell


title: B.20m.Sp#1

description: Splenic B cells


title: Human breast cancer xenograft 3936


title: B.6m.F.Sp#1

description: Female Splenic B cell


title: B1ab.2m.PC#1

description: Peritoneal B1ab cells

value: Peritoneal Cavity


title: B1ab.2m.F.PC#1

description: Female Peritoneal B1ab cells


title: young_flowsorted_mac_5

city: Houston

first: Lukas

last: Simon

address: 1 Baylor Plaza

department: THINC

institute: Baylor College of Medicine

description:
Flow-sorted bulk RNA-seq
muc7453

data_processing:
For the single-cell RNA-seq data the Drop-Seq core computational pipeline was used for processing next generation sequencing reads of the scRNA-seq data, as previously described (Pubmed ID: 26000488). For the whole lung tissue and flow-sorted bulk RNA-seq data, STAR (Pubmed ID:  23104886) was used to align the reads to reference genome mm10 followed by featureCounts (Pubmed ID: 24227677) for gene summarization.
Genome_build: mm10
Supplementary_files_format_and_content: Raw count matrix from Drop-seq experiments with 21969 genes and 14813 cells in R data object and market matrix format. Raw count matrix from whole lung tissue bulk RNA-seq with 33217 genes and 6 samples. Raw count matrix from flow-sorted bulk RNA-seq with 33217 genes and 20 samples.

source_name: Macrophages

extract_protocol:
Lung tissue was perfused with sterile saline from the right to the left ventricle of the heart and subsequently inflated via a catheter in the trachea, by an enzyme mix containing dispase (50 caseinolytic units/ml), collagenase (2 mg/ml), elastase (1 mg/ml), and DNase (30 ug/ml). After tying off the trachea, the lung was removed and immediately minced to small pieces (approx. 1 mm2). The tissue was transferred into 4 ml of enzyme mix for enzymatic digestion for 30 min at 37°C.  Enzyme activity was inhibited by adding 5 ml of PBS supplemented with 10% fetal calf serum. Dissociated cells in suspension were passed through a 70 μm strainer and centrifuged at 500 x g for 5 min at 4°C. Red blood cell lysis (Thermo Fischer 00-4333-57) was done for 2 min and stopped with 10% FCS  in PBS. After another centrifugation 5 min at 500 x g (4°C) the cells were counted using a Neubauer chamber and critically assessed for single cell separation and viability. 250.000 cells were aliquoted in 2.5 mL of PBS supplemented with 0.04% of bovine serum albumin and loaded for Drop-Seq at a final concentration of 100 cells/μL.
Single cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads. Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing. For each sample, 1 ng of pre-amplified cDNA from an estimated 1000 cells was tagmented by Nextera XT (Illumina) with a custom P5 primer (Integrated DNA Technologies). Single cell libraries were sequenced in a 100 bp paired-end run on the Illumina HiSeq4000 using 0.2 nM denatured sample and 5% PhiX spike-in. For priming of read 1, 0.5 µM Read1CustSeqB (primer sequence: GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC) was used.

value: Macrophages

value: 3 months

tag: number of cells


title: B1ab.6m.F.PC#1

description: Female Peritoneal B1ab cells

tag: cell type


title: B1ab.6m.PC#1

description: Peritoneal B1ab cells


title: old_flowsorted_epi_4

description:
Flow-sorted bulk RNA-seq
muc7455

source_name: Epithelial cells

value: Epithelial cells

value: 22 months


title: old_flowsorted_mac_7

description:
Flow-sorted bulk RNA-seq
muc7457


title: old_flowsorted_mac_5

description:
Flow-sorted bulk RNA-seq
muc7449


title: old_flowsorted_mac_6

description:
Flow-sorted bulk RNA-seq
muc7451


title: B1ab.17m.F.PC#1

description: Female Peritoneal B1ab cells


title: MG.F.CNS#2

description: Female CNS Microglia

source_name: CNS

value: CNS

value: 8 weeks old

value: lin- PI- CD45int CD11b+

value: Microglia


title: young_flowsorted_epi_4

description:
Flow-sorted bulk RNA-seq
muc7452


title: young_flowsorted_mac_4

description:
Flow-sorted bulk RNA-seq
muc7450


title: young_flowsorted_mac_3

description:
Flow-sorted bulk RNA-seq
muc7447


title: old_flowsorted_mac_3

description:
Flow-sorted bulk RNA-seq
muc7446


title: MG.F.CNS#1

description: Female CNS Microglia


title: old_flowsorted_mac_4

description:
Flow-sorted bulk RNA-seq
muc7448


title: MG.CNS#3

description: CNS Microglia


title: MG.CNS#1

description: CNS Microglia


title: MG.CNS#2

description: CNS Microglia


title: MF.RP.Sp#3_

description: Red Pulp Macrophages

value: 6 weeks old


title: young_flowsorted_mac_2

description:
Flow-sorted bulk RNA-seq
muc7445


title: MF.RP.Sp#2_

description: Red Pulp Macrophages


title: old_flowsorted_epi_3

description:
Flow-sorted bulk RNA-seq
muc7441


title: young_flowsorted_epi_3

description:
Flow-sorted bulk RNA-seq
muc7440


title: young_flowsorted_mac_1

description:
Flow-sorted bulk RNA-seq
muc7442


title: MF.RP.Sp#1_

description: Red Pulp Macrophages


title: MG.F.CNS#3

description: Female CNS Microglia


title: MF.RP.F.Sp#3

description: Female Red Pulp Macrophages


title: old_flowsorted_epi_2

description:
Flow-sorted bulk RNA-seq
muc7439


title: young_flowsorted_epi_2

description:
Flow-sorted bulk RNA-seq
muc7438


title: old_flowsorted_epi_1

description:
Flow-sorted bulk RNA-seq
muc7437


title: MF.RP.F.Sp#1

description: Female Red Pulp Macrophages


title: MF.RP.F.Sp#2

description: Female Red Pulp Macrophages


title: young_flowsorted_epi_1

description:
Flow-sorted bulk RNA-seq
muc7436


title: young_wholelung_3

description:
Bulk RNA-seq
muc7435

source_name: Whole lung

value: Whole lung


title: Treg.M.Sp#2

description: Splenic Regulatory T cells

value: TCRB+ CD4+ CD25+

value: ab T cells


title: Treg.M.Sp#1

description: Splenic Regulatory T cells

value: male


title: old_flowsorted_mac_1

description:
Flow-sorted bulk RNA-seq
muc7443


title: Treg.F.Sp#3

description: Female Splenic Regulatory T cells


title: young_wholelung_2

description:
Bulk RNA-seq
muc7434


title: old_flowsorted_mac_2

description:
Flow-sorted bulk RNA-seq
muc7444


title: Treg.F.Sp#1

description: Female Splenic Regulatory T cells


title: Tgd.M.Sp#3

description: Splenic gamma delta T cells

value: TCRgd+ TCRB-

value: gd T cells


title: young_wholelung_1

description:
Bulk RNA-seq
muc7433


title: old_whole_lung_3

description:
Bulk RNA-seq
muc7432


title: Tgd.M.Sp#2

description: Splenic gamma delta T cells

value: Spleen


title: Tgd.M.Sp#1

description: Splenic gamma delta T cells


title: Tgd.F.Sp#3

description: Female Splenic gamma delta T cells

value: female


title: old_whole_lung_1

description:
Bulk RNA-seq
muc7430


title: old_Dropseq_7

description:
Drop-seq
muc4175

value: 24 months


title: young_Dropseq_8

description:
Drop-seq
muc4657

value: 3 months


title: young_Dropseq_7

description:
Drop-seq
muc4654


title: old_whole_lung_2

description:
Bulk RNA-seq
muc7431


title: old_Dropseq_6

description:
Drop-seq
muc4174


title: Treg.M.Sp#3

description: Splenic Regulatory T cells


title: Tgd.F.Sp#1

description: Female Splenic gamma delta T cells


title: Tgd.F.Sp#2

description: Female Splenic gamma delta T cells


title: T8.M.Sp#3

description: Splenic CD8 T cell

value: TCRB+ CD8+


title: Treg.F.Sp#2

description: Female Splenic Regulatory T cells


title: T8.M.Sp#2

description: Splenic CD8 T cell


title: T8.F.Sp#3

description: Female Splenic CD8 T cell


title: young_Dropseq_5

description:
Drop-seq
muc4172


title: T8.M.Sp#1

description: Splenic CD8 T cell


title: young_Dropseq_3

description:
Drop-seq
muc4169


title: old_Dropseq_5

description:
Drop-seq
muc4168


title: B1ab.20m.PC#1

description: Peritoneal B1ab cells

value: Peritoneal Cavity

value: 20 months old

value: B cells


title: old_Dropseq_4

description:
Drop-seq
muc4167


title: T8.F.Sp#2

description: Female Splenic CD8 T cell


title: young_Dropseq_4

description:
Drop-seq
muc4170


title: old_Dropseq_3

description:
Drop-seq
muc4166


title: young_Dropseq_1

description:
Drop-seq
muc3840


title: T8.F.Sp#1

description: Female Splenic CD8 T cell


title: T4.M.Sp#2

description: Splenic CD4 T cell

value: TCRB+ CD4+


title: T4.M.Sp#1

description: Splenic CD4 T cell


title: young_Dropseq_6

description:
Drop-seq
muc4173


title: old_Dropseq_2

description:
Drop-seq
muc3839


title: old_Dropseq_1

description:
Drop-seq
muc3838


title: T4.M.10kIFN.Sp#2

description: Splenic CD4 T cell-10kIFN treatment, Sac 2hours later


title: T4.F.Sp#3

description: Female Splenic CD4 T cell


title: T4.M.10kIFN.Sp#1


title: T4.F.Sp#2

description: Female Splenic CD4 T cell


title: T4.F.10kIFN.Sp#3

description: Female Splenic CD4 T cell-10kIFN treatment, Sac 2hours later


title: T4.F.Sp#1

description: Female Splenic CD4 T cell


title: T4.F.10kIFN.Sp#2


title: T4.F.10kIFN.Sp#1


title: NKT.M.Sp#3

description: Splenic Natural Killer T cells

value: NK1.1+ TCRB+

value: Natural Killer T cells


title: NKT.M.Sp#2

description: Splenic Natural Killer T cells

value: 6 weeks old


title: T4.M.Sp#3

description: Splenic CD4 T cell


title: NKT.F.Sp#3

description: Female Splenic Natural Killer T cells


title: young_Dropseq_2

description:
Drop-seq
muc3841

value: Whole lung


title: NKT.F.Sp#2

description: Female Splenic Natural Killer T cells


title: NKT.M.Sp#1

description: Splenic Natural Killer T cells


title: NK.M.Sp#2

description: Splenic Natural Killer cells

value: NK1.1+ TCRB-

value: Natural Killer cells


title: NKT.F.Sp#1

description: Female Splenic Natural Killer T cells


title: NK.M.Sp#1

description: Splenic Natural Killer cells

value: male


title: NK.M.Sp#3

description: Splenic Natural Killer cells


title: NK.F.Sp#2

description: Female Splenic Natural Killer cells


title: NK.F.Sp#3

description: Female Splenic Natural Killer cells


title: MF.M.PC#3

description: Peritoneal macrophages

value: Macrophages


title: T4.M.10kIFN.Sp#3

value: Spleen

value: ab T cells


title: NK.F.Sp#1

description: Female Splenic Natural Killer cells

value: female


title: MF.M.PC#2

description: Peritoneal macrophages


title: MF.M.10kIFN.PC#3

description: Peritoneal macrophages-10kIFN treatment, Sac 2hours later


title: MF.M.10kIFN.PC#1


title: Hop1 ChIP for pch2Δ ndt80Δ T=6 spike-in rep1

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

institute: New York University

description:
processed data file:
AH6639spikeinHop1T6a_FE.bdg.gz

library_source: genomic

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009). SNP-ChIP library reads were aligned to concatenated genome assemblies of SK1 and S288c genomes.  Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis.
3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) and probabilistically determined PCR duplicates were removed. The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
Bedgraph files were created from pooled replicates except in the case of samples for quantitative ChIP-Seq.
Genome_build: SK1 and S288c (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Synchronous meiosis was performed by first innoculating strains at OD600 = 0.3 in BYTA medium and grown for 16.5 hours at 30°C. Then cells were washed twice with sterile water and resuspended into SPO medium at OD600 = 2.0 at 30°C (details are described in (Blitzblau et al., 2012)).

extract_protocol:
25 ml of the meiotic cells were collected at different time points and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched with 125 mM glycine. Samples were processed as described in (Blitzblau et al., 2012). For quantitative ChIP-Seq (SNP-ChIP), S288c crosslinked meiotic cells were added to respective samples at 10-20% prior to ChIP processing (Vale-Silva et al., 2018).
Libraries for ChIP sequencing were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). Quality of the libraries was checked on 2100 Bioanalyzer or 2200 Tapestation. Libraries were quantified using qPCR prior to pooling. The ChIP libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 50 or 51 bp single-end reads or 100 bp single-end reads for quantitative ChIP-seq.

value: SK1/ S288c spike-in

tag: time point

value: 6 hour

tag: genotype

tag: chip antibody


title: Hop1 ChIP for pch2Δ ndt80Δ T=3 spike-in rep2

description:
processed data file:
AH6639spikeinHop1T3b_FE.bdg.gz

value: 3 hour


title: MF.F.PC#3

description: Female Peritoneal macrophages

value: Peritoneal Cavity


title: pch2Δ ndt80Δ T=6 input spike-in rep2

description:
processed data file:
AH6639spikeinHop1T6b_FE.bdg.gz

source_name: pch2Δ ndt80Δ T=6 input spike-in rep2


title: pch2Δ ndt80Δ T=3 input spike-in rep2

source_name: pch2Δ ndt80Δ T=3 input spike-in rep2


title: Hop1 ChIP for pch2Δ ndt80Δ T=6 spike-in rep2


title: Dp r2

city: Chicago

first: Maria

middle: Paula

last: Zappia

state: IL

address: 900 S Ashland Ave

department: Biochemistry and Molecular Genetics

institute: University of Illinos at Chicago

data_processing:
Illumina bcl2fastq-1.8.3 software used for basecalling
ChIPseq data analysis: Illumina pipeline analyzed short reads were uniquely aligned using the program BOWTIE (version 2)  (Langmead 2009) allowing at most two mismatches against the Drosophila reference genome BDGP5.77. Replicates are concatenated to have more coverage.
Peak caller algorithm MACS (version 1.4.2) (Zhang 2009) was used to determine enriched peak region with parameters: --nomodel, --tsize=50, --shiftsize=160. Shift size were determined using Pyicos (Althammer S et al, 2011) strand correlation method. Other parameters were kept default.
Genome_build: BDGP5.77
Supplementary_files_format_and_content: Called Peak BED

organism: Drosophila melanogaster

source_name: flight muscles

growth_protocol: Flies were kept at 25 °C in vials containing standard cornmeal- agar medium. About 96h after pupa formation (APF), flight muscles were dissected from pharate animals

extract_protocol:
Chromatin from flight muscles was extracted using homogenizer and fixed in 1.8% formaldehyde. Then lysates were sheared using a Sonifier, and chromatin was immunoprecipitated with antibodies as in Zappia, M. P. and Frolov, M. V. Nat. Commun. 7:10509 (2016)
ChIPSeq libraries were generated using an Illumina ChIP-SEQ kit

treatment_protocol: no treatment

value: anti-DP (rabbit, #212, Dimova et al., Genes Dev. 2003;17:2308-2320)

tag: developmental stage

value: Pharate stage (96h APF at 5 degrees C)

value: flight muscles


title: Dp r1


title: MF.F.PC#2

description: Female Peritoneal macrophages


title: MF.F.10kIFN.PC#3

description: Female Peritoneal macrophages-10kIFN treatment, Sac 2hours later


title: MF.F.PC#1

description: Female Peritoneal macrophages


title: MF.F.10kIFN.PC#2


title: Hop1 ChIP for ndt80Δ T=3 spike-in rep1

description:
processed data file:
AH6179spikeinHop1T3a_FE.bdg.gz

source_name: Hop1 ChIP for ndt80Δ T=3 spike-in rep1


title: pch2Δ ndt80Δ T=3 input spike-in rep1

description:
processed data file:
AH6639spikeinHop1T3a_FE.bdg.gz

source_name: pch2Δ ndt80Δ T=3 input spike-in rep1


title: ndt80Δ T=6 input spike-in rep1

description:
processed data file:
AH6179spikeinHop1T6a_FE.bdg.gz

source_name: ndt80Δ T=6 input spike-in rep1


title: MF.F.10kIFN.PC#1


title: GN.M.Sp#3

description: Splenic Neutrophils

value: Neutrophils


title: GN.M.Sp#2

description: Splenic Neutrophils

value: 6 weeks old


title: ndt80Δ T=3 input spike-in rep1

source_name: ndt80Δ T=3 input spike-in rep1


title: MF.M.PC#1

description: Peritoneal macrophages

source_name: Peritoneal Cavity


title: GN.M.Sp#1

description: Splenic Neutrophils

source_name: Spleen


title: MF.M.10kIFN.PC#2


title: Hop1 ChIP for Ndj1-FRB ndt80Δ T=6  rep1

description: AH9098T8rapaHop1a-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009). Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis.
3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) and probabilistically determined PCR duplicates were removed. The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
The input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses.
Bedgraph files were created from pooled replicates.
Genome_build: SK1 (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph

source_name: Hop1 ChIP for Ndj1-FRB ndt80Δ T=6  rep1

extract_protocol:
25 ml of the meiotic cells were collected at different time points and fixed for 30 min in 1% formaldehyde. The formaldehyde was quenched with 125 mM glycine. Samples were processed as described in (Blitzblau et al., 2012).
Libraries for ChIP sequencing were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). Quality of the libraries was checked on 2100 Bioanalyzer or 2200 Tapestation. Libraries were quantified using qPCR prior to pooling. The ChIP libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 50 or 51 bp single-end reads.

value: 8 hour


title: Ndj1-FRB ndt80Δ T=6 input for Hop1 ChIP rep1


title: GN.M.10kIFN.Sp#3

description: Splenic Neutrophils-10kIFN treatment, Sac 2hours later


title: pch2Δ ndt80Δ T=6 input spike-in rep1

source_name: pch2Δ ndt80Δ T=6 input spike-in rep1


title: Hop1 ChIP for No tag ndt80Δ T=6  rep1

description: AH7137T8rapaHop1a-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: Hop1 ChIP for No tag ndt80Δ T=6  rep1


title: GN.M.10kIFN.Sp#2


title: GN.F.Sp#3

description: Female Splenic Neutrophils


title: Hop1 ChIP for pch2Δ ndt80Δ T=3 spike-in rep1


title: Hop1 ChIP for ndt80Δ T=6 spike-in rep1

source_name: Hop1 ChIP for ndt80Δ T=6 spike-in rep1


title: Hop1 ChIP for ndj1Δ ndt80Δ T=6  rep1

description: AH9056T6Hop1a-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: Hop1 ChIP for ndj1Δ ndt80Δ T=6  rep1


title: GN.F.Sp#2

description: Female Splenic Neutrophils


title: esc1Δ ndt80Δ T=6 input for Hop1 ChIP rep2

description: AH8913Hop1T6rep-315-439-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz


title: Hop1 ChIP for esc1Δ ndt80Δ T=6  rep2

source_name: Hop1 ChIP for esc1Δ ndt80Δ T=6  rep2


title: Hop1 ChIP for sir2Δ ndt80Δ T=6  rep2

description: AH9517Hop1T6rep-563-605-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: Hop1 ChIP for sir2Δ ndt80Δ T=6  rep2


title: GN.F.Sp#1

description: Female Splenic Neutrophils


title: sir2Δ ndt80Δ T=6 input for Hop1 ChIP rep2


title: GN.F.10kIFN.Sp#3

description: Female Splenic Neutrophils-10kIFN treatment, Sac 2hours later


title: Hop1 ChIP for sir2Δ ndt80Δ T=3  rep2

description: AH9517Hop1T3rep-561-603-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: Hop1 ChIP for sir2Δ ndt80Δ T=3  rep2


title: GN.F.10kIFN.Sp#2


title: GN.F.10kIFN.Sp#1


title: DC.M.Sp#3

description: Splenic Dendritic cells

value: CD11c+ MHC2+ Flt3+

value: Dendritic cells


title: GN.M.10kIFN.Sp#1

value: male


title: ndj1Δ ndt80Δ T=6 input for Hop1 ChIP rep1


title: DC.M.Sp#2

description: Splenic Dendritic cells


title: Hop1 ChIP for sir2Δ ndt80Δ T=6  rep1

source_name: Hop1 ChIP for sir2Δ ndt80Δ T=6  rep1


title: DC.M.Sp#1

description: Splenic Dendritic cells


title: KO B2 E16 (re-analyzed)

city: St Lucia

first: Jens

last: Bunt

state: QLD

address: QBI Building 79

department: Queensland Brain Institute

country: Australia

institute: University of Queensland

description:
Sample 12
RNA-seq of neocortex total RNA from E16 mice

data_processing:
CASAVA 1.8.2
TopHat 2.0.10
Cufflinks
TopHat 2.0.10
TRASE
CuffDiff 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: NfixKOvWT_gene_exp.diff (column sample_1: Nfix knockout samples 15-18; column sample_2: wildtype samples 1-6)

source_name: Neocortex E16

growth_protocol: All mice were housed and handled in accordance with the Australian Code of Practice for the Care and Use of Animals for Scientific Purposes and with approval from the institutional Animal Ethics Committee. To generate timed-pregnant females, male and female mice were placed together overnight. The following day, E0, the females were checked for vaginal plugs.

extract_protocol:
Embryonic neocortical tissue was microdissected snap frozen on dry ice, and RNA was isolated using Trizol reagent.
RNA libraries were prepared for sequencing with Illumina TruSeq RNA Sample Prep Kit using standard Illumina protocols

value: Neocortex

value: homozygous Nfib knockout


title: KO X1 E16

description:
Sample 15
RNA-seq of neocortex total RNA from E16 mice

value: homozygous Nfix knockout


title: KO X2 E16

description:
Sample 16
RNA-seq of neocortex total RNA from E16 mice


title: KO X3 E16

description:
Sample 17
RNA-seq of neocortex total RNA from E16 mice


title: KO B4 E16 (re-analyzed)

description:
Sample 14
RNA-seq of neocortex total RNA from E16 mice


title: KO X4 E16

description:
Sample 18
RNA-seq of neocortex total RNA from E16 mice


title: KO B3 E16 (re-analyzed)

description:
Sample 13
RNA-seq of neocortex total RNA from E16 mice


title: Hop1 ChIP for sir2Δ ndt80Δ T=3  rep1

source_name: Hop1 ChIP for sir2Δ ndt80Δ T=3  rep1


title: sir2Δ ndt80Δ T=6 input for Hop1 ChIP rep1


title: DC.F.Sp#3

description: Female Splenic Dendritic cells

value: female

value: Spleen


title: KO A4 E16 (re-analyzed)

description:
Sample 10
RNA-seq of neocortex total RNA from E16 mice

value: homozygous Nfia knockout


title: sir2Δ ndt80Δ T=3 input for Hop1 ChIP rep2

value: 3 hour


title: sir2Δ ndt80Δ T=3 input for Hop1 ChIP rep1


title: DC.F.Sp#2

description: Female Splenic Dendritic cells


title: KO A3 E16 (re-analyzed)

description:
Sample 9
RNA-seq of neocortex total RNA from E16 mice


title: total RNA from myofibroblasts ATM1 derived from patient-matched adjacent tissue

city: Liverpool

first: Hanna

last: Najgebauer

address: Crown Street

department: Cellular and Molecular Physiology

institute: University of Liverpool

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: The data were processed using the Bioconductor package lumi (version 2.18.0)

label: biotin

source_name: myofibroblasts derived from patient-matched adjacent tissue

label_protocol: standard Illumina protocol

growth_protocol: Primary myofibroblast cultures were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), 1% penicillin-streptomycin, 1% antibiotic-antimycotic and 1% non-essential amino acid solution. Medium was replaced routinely every 48–60 hours and cells were lysed at 80-90% confluence for RNA extraction.

extract_protocol: Total RNA was purified using miRNeasy Mini Kit (Qiagen, cat. no. 217004) according to manufacturer’s instructions

tag: subject id

value: Female

tag: subject status

value: patient undergoing gastric cancer surgery

tag: tissue type

value: adjacent tissue myofibroblasts (ATM)


title: KO A1 E16 (re-analyzed)

description:
Sample 7
RNA-seq of neocortex total RNA from E16 mice

tag: strain

tag: tissue


title: total RNA from gastric myofibroblasts NTM1 derived from organ donors

source_name: gastric myofibroblasts derived from organ donors

tag: gender

value: Male

value: deceased transplant donors with normal morphology

value: normal tissue myofibroblasts (NTM)


title: KO A2 E16 (re-analyzed)

description:
Sample 8
RNA-seq of neocortex total RNA from E16 mice


title: DC.F.Sp#1

description: Female Splenic Dendritic cells

tag: age

value: 6 weeks old

tag: sorting markers


title: total RNA from gastric myofibroblasts NTM3 derived from organ donors


title: WT X2 E16

description:
Sample 6
RNA-seq of neocortex total RNA from E16 mice

value: wildtype control


title: Hop1 ChIP for nup2Δ ndt80Δ T=6  rep2

description: AH9535Hop1T6rep-567-609-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: Hop1 ChIP for nup2Δ ndt80Δ T=6  rep2

value: 6 hour


title: KO B1 E16 (re-analyzed)

description:
Sample 11
RNA-seq of neocortex total RNA from E16 mice


title: WT X1 E16

description:
Sample 5
RNA-seq of neocortex total RNA from E16 mice


title: B1a.M.PC#3

description: Peritoneal B cells

value: male

value: Peritoneal Cavity

value: B cells


title: Hop1 ChIP for nup2Δ ndt80Δ T=3  rep2

description: AH9535Hop1T3rep-565-607-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: Hop1 ChIP for nup2Δ ndt80Δ T=3  rep2


title: nup2Δ ndt80Δ T=6 input for Hop1 ChIP rep2


title: total RNA from myofibroblasts ATM2 derived from patient-matched adjacent tissue


title: total RNA from gastric myofibroblasts NTM2 derived from organ donors


title: total RNA from myofibroblasts ATM3 derived from patient-matched adjacent tissue


title: total RNA from myofibroblasts CAM2 derived from gastric tumour

source_name: myofibroblasts derived from gastric tumour

value: primary gastric cancer-associated myofibroblasts (CAM)


title: total RNA from myofibroblasts CAM3 derived from gastric tumour


title: nup2Δ ndt80Δ T=3 input for Hop1 ChIP rep2


title: WT B2 E16 (re-analyzed)

description:
Sample 4
RNA-seq of neocortex total RNA from E16 mice

value: Neocortex


title: B1a.M.PC#1

description: Peritoneal B cells

source_name: Peritoneal Cavity


title: WT B1 E16 (re-analyzed)

description:
Sample 3
RNA-seq of neocortex total RNA from E16 mice


title: total RNA from myofibroblasts CAM1 derived from gastric tumour


title: B1a.M.PC#2

description: Peritoneal B cells


title: WT A1 E16 (re-analyzed)

description:
Sample 1
RNA-seq of neocortex total RNA from E16 mice


title: Hop1 ChIP for nup2Δ ndt80Δ T=6  rep1

source_name: Hop1 ChIP for nup2Δ ndt80Δ T=6  rep1


title: WT A2 E16 (re-analyzed)

description:
Sample 2
RNA-seq of neocortex total RNA from E16 mice


title: B1a.F.PC#3

description: Female Peritoneal B cells

value: female


title: nup2Δ ndt80Δ T=6 input for Hop1 ChIP rep1


title: B1a.F.PC#2

description: Female Peritoneal B cells


title: Hop1 ChIP for nup2Δ ndt80Δ T=3  rep1

source_name: Hop1 ChIP for nup2Δ ndt80Δ T=3  rep1


title: B1a.F.PC#1

description: Female Peritoneal B cells


title: nup2Δ ndt80Δ T=3 input for Hop1 ChIP rep1


title: B.M.Sp#3

description: Splenic B cells

source_name: Spleen

value: Spleen

value: CD19+ IgM+TCRb-


title: B.M.1kIFN.Sp#3

description: Splenic B cells-1kIFN treatment, Sac 2hours later


title: B.M.Sp#2

description: Splenic B cells


title: B.M.Sp#1

description: Splenic B cells


title: IL13_n1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: Gene expression data

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Data were summarized using RMA and normalized using the quantile method.

label_protocol: Total RNAs were labled using the Agilent Low input QuickAmp Labeling kit.

growth_protocol: Dissociated cells from nasal turbinates were seeded on collagen-type IV coated permeable supports

extract_protocol: Trizol extraction of total (including small) RNAs was performed according to the manufacturer's instructions.

treatment_protocol: At confluency (day 7 after seeding), cultures were switched in air-liquid interface in the differentiating medium. On fully-differentiated airway cells (ALI-D47), IL-13 was incubated at 100 ng/ml in basal side in differentiating medium for 3 days

value: nasal mucosa from turbinates

tag: days of culture

value: 47 days after ALI

tag: treatment

value: Ctrl

tag: replicate


title: B.M.1kIFN.Sp#2


title: B.M.10kIFN.Sp#3

description: Splenic B cells-10kIFN treatment, Sac 2hours later


title: B.M.1kIFN.Sp#1


title: IL13_n2

description: Gene expression data


title: Ctrl_n2

description: Gene expression data


city: Kyoto

first: Knut

last: Woltjen

address: 53 Kawahara-Cho, Shogoin, Sakyo-ku

department: Reprogramming Science

country: Japan

institute: CiRA, Kyoto University

description: The PB transposon vector (PB-TAC) employs dox-responsive reprogramming cassette expression co-incident with a mCherry reporter.

hyb_protocol: Fragmented and labelled cDNA was hybridized to GeneChip Mouse Gene 1.0 ST arrays (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 TG.

data_processing: Mouse Gene 1.0 ST arrays were normalized using RMA implemented in GeneSpring 13.1. OK+9MS Trop2- intermediate reprogramming population (day 8) and OK+9MS Trop2+ intermediate reprogramming population (day 8) were separately processed from others which include some of the published data in GSE65468 (OKMS mCherry+ intermediate reprogramming population (day 6), OK+9MS mCherry+ intermediate reprogramming population (day 6), Klf4 mCherry+ intermediate reprogramming population (day 6), Klf4+9 mCherry+ intermediate reprogramming population (day 6) and LacZ population (day 2)). The data were median transformed.

label: Biotin

source_name: MEF

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix) was used according to Affymetrix protocol.

growth_protocol: For reprogramming intermediates, ROSA-rtTA; Nanog-GFP MEFs were transfected with transposons (PB-TAC-OKMS, -OK+9MS) plus pCyL43 PB transposase plasmid using FugeneHD (Promega). After 24 hr, the media was replaced with ES cell medium with doxyclycline (1ug/mL).  ESCs and iPSCs were cultured with ES cell medium. Mouse primary keratinocytes were cultured with D-KSFM medium with supplements containing mEGF (10 µg/mL) and Cholera toxin (10-10 M).

extract_protocol: Total RNA was prepared from harvested cells using the RNeasy Mini Kit (QIAGEN). Total RNA was eluted from spin columns using 30 uL RNase-free water. To eleminate contaminating DNA in the RNA solutions, DNase digestion was carried out and the RNA solutions was cleaned up using RNA clean up protocol according to the manufacturer’s instructions.

treatment_protocol: mCherry+, Trop2- or Trop2+ cell population from the PB transfected MEFs was collected on a BD FACSAria II cell sorter (BD Biosciences).

value: Sorted Trop2+ cells (d8)

value: FACS sorted on day 8 of dox treatment


title: Ctrl_n1

description: Gene expression data


title: OK+9MS Trop2- intermediate reprogramming population (day 8)

value: Sorted Trop2- cells (d8)


title: B.M.10kIFN.Sp#2

value: 6 weeks old


title: 1A2_mESC

description: Mouse embryonic stem cell (1A2) was derived from homozygous Nanog-GFP (Okita et al., 2007) transgenic males.

source_name: mouse ESC


title: B.M.10kIFN.Sp#1


title: OK+9MS mCherry+ intermediate reprogramming population (day 8)

value: Sorted mCherry+ cells (d8)


title: H10_OK+9MS_iPSC

description: Mouse induced pluripotent stem cell (H10) was derived by the Dox-inducible PB transposon vector (PB-TAC) employs OK+9MS.

source_name: mouse iPSC


title: mouse primary keratinocyte 2

description: Primary keratinocytes were isolated from newborn pups at post-natal day 2.

source_name: mouse primary keratinocyte

value: mouse primary keratinocyte


title: B.F.Sp#3

description: Female Splenic B cells


title: B.F.Sp#2

description: Female Splenic B cells


title: mouse primary keratinocyte


title: OK+9MS mCherry+ intermediate reprogramming population (day 18)

value: Sorted mCherry+ cells (d18)

value: FACS sorted on day 18 of dox treatment


title: B.F.Sp#1

description: Splenic B cells

value: B cells


title: A10_OK+9MS_iPSC

description: Mouse induced pluripotent stem cell (A10) was derived by the Dox-inducible PB transposon vector (PB-TAC) employs OK+9MS.


title: OK+9MS mCherry+ intermediate reprogramming population (day 8) 2


title: OK+9MS mCherry+ intermediate reprogramming population (day 4)

value: Sorted mCherry+ cells (d4)

value: FACS sorted on day 4 of dox treatment


title: OK+9MS mCherry+ intermediate reprogramming population (day 2)

value: Sorted mCherry+ cells (d2)

value: FACS sorted on day 2 of dox treatment


title: OKMS mCherry+ intermediate reprogramming population (day 18)


title: A9_OKMS_iPSC

description: Mouse induced pluripotent stem cell (A9) was derived by the Dox-inducible PB transposon vector (PB-TAC) employs OKMS.


title: B.F.1kIFN.Sp#1

description: Female Splenic B cells-1kIFN treatment, Sac 2hours later

value: female

value: Spleen

value: CD19+ IgM+TCRb-


title: B.F.1kIFN.Sp#3


title: OKMS mCherry+ intermediate reprogramming population (day 8) 2


title: B.F.10kIFN.Sp#1

description: Female Splenic B cells-10kIFN treatment, Sac 2hours later


title: B.F.10kIFN.Sp#3


title: A7_OKMS_iPSC

description: Mouse induced pluripotent stem cell (A7) was derived by the Dox-inducible PB transposon vector (PB-TAC) employs OKMS.


title: OKMS mCherry+ intermediate reprogramming population (day 4)


title: B.F.10kIFN.Sp#2


title: RNAseq_KO_rep4

city: shanghai

first: Xuxu

last: Sun

address: 227 south chongqing road

department: school of medicine

country: China

institute: shanghai jiao tong university

description: countTable.fpkm.txt

data_processing:
Sequence reads were aligned to mouse  genome version mm10 using TopHat.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit RPKM (number of reads per kilo base pair per million total reads)
Differential gene expression analyses were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: text file of gene FPKM values

source_name: frozen liver tissue

extract_protocol:
Frozen liver tissues RNA was harvested using Trizol reagent and the Qiagen miRNeasy Mini kit.
RNA libraries were prepared for sequencing using standard Nugen library protocols.

treatment_protocol: Liver tissues were collected and frozen in -80.

value: C57/B6 and 129 mix

value: liver

value: postnatal day 90

tag: genotype/variation

value: Arid1a Fl/Fl; Alb-cre


title: RNAseq_KO_rep3

description: countTable.fpkm.txt


title: OKMS mCherry+ intermediate reprogramming population (day 8)

tag: cell type

value: FACS sorted on day 8 of dox treatment


title: OKMS mCherry+ intermediate reprogramming population (day 2)


title: Primary tumour, sample 3

first: marjan

last: iravani

address: 237 Fulham Road

department: Breast Cancer Now

institute: Institute of Cancer research

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol of iScan.

data_processing: The data were filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples in the dataset, probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering, the data was transformed and normalized using variance-stabilizing transformation (VST) and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization.

source_name: 4T1 cell line

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

extract_protocol: Total RNA isolated from cells grown in culture from primary tumour (P), lung metastases (L) and brain metastases (B). RNA was assessed for concentration and quality using a SpectroStar (BMG Labtech, Aylesbury, UK) and a Bioanalyser (Agilent Technologies, Cheadle, UK). Microarray experiments were performed at Cambridge Genomic Services, University of Cambridge, using the Illumina MouseWG-6 v2.0 expression BeadChip (Illumina, Chesterford, UK) according to the manufacturer's instructions.

tag: cell line

value: mammary tumour

tag: host strain/background

value: Balb/c

value: Primary tumour


title: genomic DNA from myofibroblasts ATM2 derived from patient-matched adjacent tissue A2b

type: genomic

description: adjacent tissue

data_processing: Raw DNA methylation data were processed and analysed using Bioconductor package RnBeads version 0.99.17 (Assenov, Muller et al. 2014). Prior to normalization, probes with p-value>0.01 in any sample and probes overlapping with single nucleotide polymorphisms (SNPs) in the probe sequence (Chen, Lemire et al. 2013) were removed followed by BMIQ normalization (Teschendorff, Marabita et al. 2013, Wu, Joubert et al. 2014) and methylumi.noob background subtraction (Triche, Weisenberger et al. 2013). Subsequently probes outside of CpG context as well as probes on sex chromosomes were removed.

label: Cy5 and Cy3

growth_protocol: Primary myofibroblast cultures were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), 1% penicillin-streptomycin, 1% antibiotic-antimycotic and 1% non-essential amino acid solution. Medium was replaced routinely every 48–60 hours and cells were lysed at 80-90% confluence for DNA extraction.

extract_protocol: Genomic DNA was purified using a standard phenol/chloroform extraction method.

value: Female

tag: patient

value: ATM


title: Lung metastasis, sample 3

value: Lung metastasis


title: Lung metastasis, sample 1


title: RNAseq_KO_rep2

description: countTable.fpkm.txt


title: genomic DNA from myofibroblasts CAM3 derived from oesophageal tumour C3

description: tumour

value: Male

value: CAM


title: Lung metastasis, sample 2


title: genomic DNA from myofibroblasts CAM2 derived from oesophageal tumour C2b

description: tumour


title: B.F.1kIFN.Sp#2

value: 6 weeks old

value: B cells


title: Primary tumour, sample 1


title: Brain metastasis, sample 4

value: Brain metastasis


title: genomic DNA from myofibroblasts ATM2 derived from patient-matched adjacent tissue A2a

description: adjacent tissue


title: Primary tumour, sample 2


title: genomic DNA from myofibroblasts CAM2 derived from oesophageal tumour C2a

description: tumour


title: Brain metastasis, sample 3


title: RNAseq_KO_rep1

description: countTable.fpkm.txt


title: Hop1 ChIP for sir3Δ ndt80Δ T=6  rep1

description: AH8967T6Hop1a-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: Hop1 ChIP for sir3Δ ndt80Δ T=6  rep1

tag: time point

value: 6 hour

tag: genotype

tag: chip antibody


title: RNAseq_WT_rep4

description: countTable.fpkm.txt

value: C57/B6 and 129 mix

value: Arid1a Fl/Fl


title: Brain metastasis, sample 2


title: RNAseq_WT_rep3

description: countTable.fpkm.txt

value: liver

value: postnatal day 90


title: Brain metastasis, sample 1


title: ΔC27_rep2

city: Qingdao

first: Mei

last: Wang

state: Shandong

address: Binhai road 72

institute: Shandong University

description: Gene expression data from Arabidopsis transgenic line harboring a truncated TaSIN lacking the transmembrane motif

hyb_protocol: Samples were prepared for hybridization to the ATH1 GeneChips™ using the Affymetrix GeneChip Hybridization, Wash and Stain Kit. Samples were hybridized overnight in an Affymetrix GeneChip Hybridization Oven 640. Samples were then processed on the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 3.0 (MAS 3.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (using the MessageAmp™ Premier RNA Amplification Kit (Ambion)).

growth_protocol: The transgenic plants were grown at the growth chamber with a 16 h photoperiod (120 μmol m–2 s–1 light) and ~70% relative humidity at 22 ± 1°C/16 ± 4°C.

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

treatment_protocol: 12-day-old seedlings under normal growth conditions

value: 12-day-old seedlings


title: genomic DNA from myofibroblasts CAM1 derived from oesophageal tumour C1b

description: tumour


title: ΔC27_rep1

source_name: Arabidopsis transgenic line harboring a truncated TaSIN lacking the transmembrane motif


title: 1A2_mESC 2


title: genomic DNA from myofibroblasts ATM3 derived from patient-matched adjacent tissue A3

description: adjacent tissue


title: genomic DNA from myofibroblasts CAM1 derived from oesophageal tumour C1a

description: tumour


title: FL3_rep2

description: Gene expression data from Arabidopsis transgenic line harboring full length TaSIN


title: genomic DNA from gastric myofibroblasts NTM3 derived from organ donors N3N

description: normal tissue

value: NTM


title: Hop1 ChIP for tel1Δ ndt80Δ T=6  rep1

description: AH8912T6Hop1a-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz

source_name: Hop1 ChIP for tel1Δ ndt80Δ T=6  rep1


title: RNAseq_WT_rep1

description: countTable.fpkm.txt


title: genomic DNA from gastric myofibroblasts NTM1 derived from organ donors N1N

description: normal tissue


title: ΔC26_rep2


title: esc1Δ ndt80Δ T=6 input for Hop1 ChIP rep1

description: AH8913Hop1T6rep-315-439-Reps-SK1Yue-PM_B3W3_MACS2_FE.bdg.gz


title: genomic DNA from myofibroblasts ATM1 derived from patient-matched adjacent tissue A1a

description: adjacent tissue


title: hand2_ATACseq_GFPpos_72hpf_rep1

city: Warsaw

first: Michal

last: Pawlak

address: Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology

description: tagmented genomic DNA

data_processing:
Nextera adapters removal was performed by using Trimmomatic (0.36) (Bolger et al. 2014)
Reads quality filtering was performed by SAMtools (1.4) (Li et al. 2009) with parameters -b -h -f 3 -F 3340 -q 30
ATAC-seq reads were aligned to zebrafish reference genome (GRCz10) using Bowtie2 (2.2.9) (Langmead and Salzberg 2012)
Peaks of chromatin open regions were called by using MACS2 (2.1.0) (Zhang et al. 2008) with parameters --nomodel --shift -100 --extsize 200 --broad -g 1.21e9 -q 0.05 -B --keep-dup all. Nucleosome free regions were identified as previously described (Buenrostro et al. 2013).
Genome_build: GRCz10
Supplementary_files_format_and_content: bed  files from MACS2

organism: Danio rerio

source_name: FACS-sorted embryo cells

growth_protocol: Embryos were grown in embryo medium at 28°C, staged according to standard morphological criteria (Kimmel et al. 1995), and harvested at three different developmental stages: prim-5 (24 hpf), long-pec (48 hpf) and protruding-mouth (72 hpf).

extract_protocol:
For ATAC-seq 60,000 of GFP+ cells from zebrafish embryos were sorted to Hank’s solution (1X HBSS, 2mg/mL BSA, 10 mM Hepes pH 8.0), centrifuged for 5 minutes at 500x g and prepared for chromatin tagmentation as previously described (Buenrostro et al. 2013).
NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs, USA) and custom HPLC-purified primers containing Illumina-compatible indexes were used to DNA sequencing libraries according to previously described procedures (Buenrostro et al. 2015).DNA libraries were purified with Agencourt AMPure XP PCR purification beads (Beckman Coulter, USA) and DNA fragment distribution was assessed by using D1000 ScreenTape and Agilent 2200 TapeStation system (Agilent Technologies, USA). KAPA library quantification kit (Kapa Biosystems, USA) was used for qPCR-based quantification of the libraries obtained.

value: FACS-sorted embryo cells

tag: developmental stage

value: 72 hpf

tag: gfp status

value: GFP positive

tag: genetic background


title: hand2_ATACseq_GFPpos_72hpf_rep2

description: tagmented genomic DNA

tag: tissue


title: tbx5_ATACseq_GFPpos_72hpf_rep2

description: tagmented genomic DNA


title: tbx5_ATACseq_GFPpos_72hpf_rep1

description: tagmented genomic DNA


title: RNAseq_WT_rep2

description: countTable.fpkm.txt

tag: strain

tag: age


title: tel1Δ ndt80Δ T=6 input for Hop1 ChIP rep1


title: genomic DNA from myofibroblasts CAM3 derived from gastric tumour C3N

description: tumour

tag: gender


title: sir3Δ ndt80Δ T=6 input for Hop1 ChIP rep1


title: genomic DNA from myofibroblasts ATM1 derived from patient-matched adjacent tissue A1b

description: adjacent tissue

value: ATM


title: gata5_ATACseq_GFPpos_72hpf_rep2

description: tagmented genomic DNA


title: genomic DNA from myofibroblasts CAM2 derived from gastric tumour C2N

description: tumour


title: genomic DNA from myofibroblasts ATM1 derived from patient-matched adjacent tissue A1N

description: adjacent tissue

value: Female


title: genomic DNA from gastric myofibroblasts NTM2 derived from organ donors N2N

description: normal tissue


title: genomic DNA from myofibroblasts ATM2 derived from patient-matched adjacent tissue A2N

description: adjacent tissue

value: Male


title: genomic DNA from myofibroblasts ATM3 derived from patient-matched adjacent tissue A3N

description: adjacent tissue


title: gata5_ATACseq_GFPpos_72hpf_rep1

description: tagmented genomic DNA


title: wt_ATACseq_GFPpos_72hpf_rep1

description: tagmented genomic DNA

value: wild type


title: FL3_rep1

source_name: Arabidopsis transgenic line harboring full length TaSIN


title: wt_ATACseq_GFPpos_48hpf_rep2

description: tagmented genomic DNA

value: 48 hpf


title: wt_ATACseq_GFPpos_72hpf_rep2

description: tagmented genomic DNA


title: VC_rep1

description: Gene expression data from Arabidopsis transgenic line carrying an empty vector


title: U2OS_siWDR33_Pol2_S2P_input

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

country: Netherlands

institute: Utrecht University

data_processing:
Reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using TrimGalore
Processed reads were aligned to  the hg38 genome using Bowtie directly executed from the R package QuasR with standard alignment parameters allowing up to 2 missmatches and excluding multi-mappers
Coordinates of unique reads that map only once to the human genome were converted to GenomicRanges format for further analysis and to the WIG format for visualisation.
Genome_build: hg38
Supplementary_files_format_and_content: wig track format: read coverage per consecutive 100bp windows

growth_protocol: Human U-2 OS cells were grown under standard cell culture conditions (humidified atmosphere, 5% CO2) in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (GIBCO) and penicillin-streptomycin antibiotics.

extract_protocol:
Chromain Immunoprecipitation using anti phosphoserine-2 RNA Polymerase antibodies.
Sequencing libraries were prepared using the NEB-next ChIP-seq library Kit following the manual instruction and using indexed primers.
The individual libraries were generated in paralel for all ChIPs and input samples. Libraries were pooled and sequenced on an Illumina HiSeq 4000 machine.

treatment_protocol: Transfections with siRNA were performed for 72h using Ambion Silencer Select siRNAs at a final concentration of 25nM and Lipofectamine RNAiMAX (Thermo Fisher Scientific). WDR33 was depleted using siRNA ID s30772, Neg2 from Ambion was used as non-targeting control.

value: U-2 OS

tag: sirna

value: WDR33 depletion


title: Col_rep2

description: Gene expression data fromArabidopsis wild type Col-0

source_name: Arabidopsis wild type Col-0


title: IECΔCDC42 +SFB (IL006)

first: Leandro

middle: Pires

last: Araujo

address: 701 W 168th St, 9th floor

department: Microbiology and Immunology

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0). We test for differentially expressed genes under various conditions using Sleuth, an R package designed to compute transcript and gene-level differential expression from kallisto abundance files.
Genome_build: Mouse GRCm38
Supplementary_files_format_and_content: normalized counts

source_name: Intestinal epithelial cells

extract_protocol:
For all samples we use poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry.
For all samples we use ribosomal depletion to remove rRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry.
Intestinal epithelial cels were isolated and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries are then sequenced using Illumina NovaSeq 6000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.

treatment_protocol: WT and IECΔCDC42 mice were colonized with segmented filamentous bacteria (SFB) and intestinal epithelial cells were isolated to performed RNAseq.

value: Intestinal epithelial cells

value: 14 weeks

tag: treatment

value: +SFB


title: U2OS_siWDR33_Pol2_S2P_ChIP_r1

value: Anti-RNA polymerase II CTD (Abcam, catalog# ab5095, lot# GR231750-2)


title: WT no SFB (IL007)

value: WT

value: no SFB


title: WT no SFB (IL008)


title: U2OS_siWDR33_Pol2_S2P_ChIP_r2


title: U2OS_siCtr_Pol2_S2P_ChIP_r2

value: siControl

value: control


title: Col_rep1

value: 12-day-old seedlings


title: wt_ATACseq_GFPpos_48hpf_rep1

description: tagmented genomic DNA

value: FACS-sorted embryo cells

value: GFP positive


title: WT + SFB (IL005)


title: U2OS_siCtr_Pol2_S2P_ChIP_r1


title: wt_ATACseq_GFPpos_24hpf_rep2

description: tagmented genomic DNA

value: 24 hpf


title: WT + SFB (IL004)


title: IECΔCDC42 +SFB (IL003)


title: WT no SFB (IL010)


title: IECΔCDC42 +SFB (IL002)


title: WT no SFB (IL009)


title: WT + SFB (IL001)


title: cav1-/+apcmin/+ colorectal tumor tissue

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression data from mouse intestinal tissue at an age of 6 month

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with Affymetrix Expression Console. The Gene-Level Core: RMA-Sketch option was used.

source_name: C57BL/6xB6129 mice at an age of 6 month

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Mice were bred in a biosafety level 1 SPF-animal facility under standard conditions until an age of 6 months

extract_protocol: Column-based extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: Mice were sacrificed according to animal ethics guidelines, resected tissues were rinsed in PBS and snap-frozen in liquid N2 for RNA extraction using  commercially available kits (RNAeasy, Quiagen).

value: 6 month

value: Colorectal tumor tissue


title: wt_ATACseq_GFPpos_24hpf_rep1

description: tagmented genomic DNA

value: wild type


title: genomic DNA from myofibroblasts CAM1 derived from gastric tumour C1N

description: tumour

value: Female

value: CAM


title: Hop1 ChIP for esc1Δ ndt80Δ T=6  rep1

source_name: Hop1 ChIP for esc1Δ ndt80Δ T=6  rep1

value: 6 hour


title: mut Dam1

city: Regensburg

first: Mathias

last: Rass

address: Universitätsstraße 31

department: Developmental Biology

institute: University of Regensburg

description: Processed data file: mut.gatc.average.bedgraph

data_processing:
Library strategy: DamID
.bam files are converted to .fastq files and were gunzipped
log2(DamPolII/Dam) in bedgraph format have been generated by DamIDseq_pipeline provided by Marshall and Brand (2015)
single datasets have been combined and averaged to one single log2(DamPolII/Dam) per genotype with the average_tracks script provided by Marshall and Brand (2015)
Genome_build: dm6
Supplementary_files_format_and_content: bedgraph files generated

source_name: mut Dam

growth_protocol: development at 18°C. 1-3 day old flies were shifted to 29°C for 24h.

extract_protocol:
Flies were snapfrozen in liquid nitrogen and heads were removed by vortexing and sieving. Further procedures where executed as described in Southall et al. (2016)
libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®

value: Fuss expressing neurons

value: 1-3 day old adult flies

value: pooled male and female

tag: sample composition

value: 50 males, 50 females


title: mut DamPol3

source_name: mut DamPol

tag: cell type


title: ΔC26_rep1


title: cav1-/+apcmin/+ adjacent normal colon tissue

value: Normal colon tissue


title: mut DamPol2


title: mut Dam2


title: mut Dam3


title: mut DamPol1


title: induction group3

city: Guangzhou

first: Jing

last: Li

address: Zhongshan Road

institute: Zhongshan university

data_processing:
Sequenced reads were for filtered to remove those low-complexity or low-quality sequences to get clean sequences.
After quality control using an Agilent 2100 Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA, USA), we utilized a HiSeq2500 (Illumina, CA, USA) to analyze and sequence DNA fragments.
we used FastQC software to output.
we used BWA software to iditify the sequences to the genome.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Excel. The processed data files enntitled 7.xls  included the comparison of circRNAs expressioin indentified in control and induction groups of dental follicle cells during osteogenic differentiation.

organism: Rattus norvegicus

source_name: Sprague-Dawley rats

extract_protocol:
Total RNA was extracted separately from rDFCs of the induction and control groups. DNA and linear RNA were removed from the samples for circRNAs assays. The A260/A280 ratios of RNA samples were between 1.9 and 2.1, and the RNA integrity number was greater than 8.0; thus, the samples were acceptable for the following assays.
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: 3 healthy Sprague-Dawley rats (postnatal 5-7 days) were provided by the Laboratory Animal Center of Sun Yat-sen University (This study has received permission from the institutional Animal Care and Use Committee). rDFCs were isolated from the tooth germs of the first and second mandibular molars of each rat and were cultured separately in alpha-modified Eagle medium (GIBCO-BRL Life Technologies, Guangzhou Genewindows Biotech, Ltd., Guangzhou, China) containing 10% fetal bovine serum (FBS) (GIBCO-BRL Life Technologies, Guangzhou Genewindows Biotech, Ltd., Guangzhou, China). rDFCs were incubated at 37°C with 5% CO2 (Xiao et al. 2000).  During osteogenic differentiation, rDFCs at passage 3-4 were cultured for 28 days in osteogenic induction medium, which consisted of 5% FBS, 1% osteogenic induction liquid (0.010 mmol/L dexamethasone, 0.028 mmol/L ascorbic acid, and 1.000 mol/L β-glycerophosphate) and alpha-modified Eagle medium, whereas control cells were cultured in control medium containing 5% FBS and alpha-modified Eagle medium. The medium was exchanged every 3 days.

value: dental follicle cells

value: 5-7 days old


title: mouseESC_wildtype_rep1

city: Tel Aviv

first: Carmit

last: Levy

address: Ramat Aviv

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

description: miRNAs expression

hyb_protocol: miRNA CodeSet Hybridization Setup Protocol acording to manufactuer's instructions (nanoString).

scan_protocol: Scanning was performed using nanoString analyzer instrument.

data_processing: Normalization of the data was carried out using the NanoString nSolver Analysis software.

label: nanostring probe

source_name: mouse embryonic stem cells

label_protocol: nCounter miRNA expression assay Protocol acording to manufactuer's instructions (nanoString).

growth_protocol: WT and TKO R1 cells were cultured in DMEM supplemented with 15% fetal calf serum, 0.29 mg/ml stable L-glutamine, 100 units/ml penicillin, 0.1 mg/ml streptomycin, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 100 μM beta-mercaptoethanol, and 1,000 U/ml lekumia inhibitory factor (LIF). Cells were mainteind on gelatin 0.2% coating plates. All cell culture materials accept LIF were purchased from Biological Industries, and LIF was purchased from Sigma. Cells were incubated at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol: Total RNA was isolated using miRNeasy Mini Kit (QIAGEN) according to manufacturer's instructions

treatment_protocol: The three DNA methyltransferases (DNMTs) are knocked out (TKO) as descibe in Akiko Tsumura et al, Maintenance of self‐renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b (Genes to Cell 2006). Cells were differentiated for 4 days perior of RNA isolation.


title: mouseESC_TKO_rep1

description: miRNAs expression

source_name: mouse embryonic stem cells (TKO)

value: DMNTs TKO


title: mouseESC_TKO_rep2

description: miRNAs expression


title: mouseESC_wildtype_rep2

description: miRNAs expression


title: microglia_without PGC-1α_rep 3

city: Tianjin

first: Bin

last: Han

address: 154 Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

description: Gene expression in microglia without PGC-1α overexpression

hyb_protocol: Labeled controls and test samples labeled with Cy5-dCTP were dissolved in 80 μL hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: After washing, slides were scanned immediately using G2565CA (Agilent Technologies).

data_processing: The array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13 (Agilent). To select the differentially expressed genes, we used thresholdvalues of ≥2 and ≤−2-fold change and Benjamini-Hochberg corrected p vlaue of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage. Finally, we performed tree visualization by using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA).

source_name: Microglia

label_protocol: cDNA labeled with a fluorescent dye (Cy5-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. The procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer.

extract_protocol: Total RNA was extracted from microglia by using  the Trizol reagent (Invitrogen) and purified with a NucleoSpin® RNA clean-up kit (MACHEREY- NAGEL, Germany) according to manufacter’s protocol. The purity and concentration of RNA were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000). RNA integrity was determined by capillary electrophoresis using the RNA 6000 Nano Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Only RNA extracts with RNA integrity number values >6 underwent in further analysis.

value: Microglia

value: male


title: microglia_with PGC-1α_rep 1

description: Gene expression in microglia with PGC-1α overexpression


title: microglia_without PGC-1α_rep 1


title: control group3


title: 52 hpf hearts_1

city: Bad Nauheim

first: Didier

last: Stainier

address: Ludwigstrasse 43

department: Developmental Genetics

institute: Max Planck Institute for Heart and Lung Research

hyb_protocol: For the hybridisation the Agilent Gene Expression Hybridisation Kit (Agilent Technologies)is used following the manufacture`s protocol.

scan_protocol: Fluorescence signals on microarrays are detected by the SureScan Microarray Scanner (AgilentTechnologies) at a resolution of 3 micron for SurePrint G3 Gene Expression Microarrays and 5 micron for HD Microarray formats, generating a 20 bit TIFF file respectively.

data_processing: Agilent's Feature Extraction software version 11 is used to read and process the TIFF files.

source_name: Embryonic hearts, Tg(myl7:GFP), 52 hpf

label_protocol: The Low Input QuickAmp Labeling Kit (Agilent Technologies) is used for generation of fluorescent cRNA (complementary RNA). By default cRNA is amplied by using oligo-dT primer for eukaryotic samples and a random primer for prokaryotic samples and labelled with cyanine 3-CTP following the manufacture`s protocol.

extract_protocol: Hearts were extracted from 52 hpf Tg(myl7:EGFP-Hsa.HRAS)s883 hearts using a previously established protocol (Burns and MacRae, 2006), and kept in Trizol (Thermo Fisher Scientific) at -80°C until ready to use. A pool of 150 isolated hearts, which constitutes one biological sample, was then used to extract RNA using the RNA Clean and Concentrator (Zymo Research).

value: Embryonic heart

value: 52 hpf


title: 7 dpf hearts_2

source_name: Larval hearts, Tg(myl7:GFP), 7 dpf

value: Larval heart

value: 7 dpf


title: microglia_with PGC-1α_rep 2


title: ctrl DamPol2

description: Processed data file: ctrl.gatc.average.bedgraph

source_name: ctrl DamPol

value: tubgal80ts/DamPol; fussdelds-Gal4/+


title: Heart_wildtype_1

last: Kuenne

department: Bioinformatics

hyb_protocol: The Agilent Gene Expression Hybridisation Kit (Agilent Technologies) was used following the manufacture’s protocol. cRNA was hybridised on a 8x60K microarray at 65◦ C for 17 h using Agilent‘s recommended hybridisation chamber and oven. Finally the microarray was washed once with the Agilent Gene Expression Wash Buffer 1 for one minute at ambient temperature followed by a second wash with preheated (37◦ C) Gene Expression Wash Buffer 2 for one minute.

scan_protocol: Fluorescence signals on microarrays were detected by the SureScan Microarray Scanner G2600D (Agilent Technologies) at a resolution of 3 micron for SurePrint G3 Gene Expression Microarrays, generating a 20 bit TIFF file.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities.

source_name: Whole heart pools, 96 hpf, WT

label_protocol: The Low Input QuickAmp Labeling Kit (Agilent Technologies) was used for generation of fluorescent cRNA (complementary RNA) following the manufacture’s protocol (OakLabs). For 1st strand synthesis, either oligo-dT primer or a random primer / oligo-dT primer mixture (WT primer) was used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labelled with cyanine 3-CTP was performed.

extract_protocol: 500 hearts from 96 hpf klf2 WT and mutant larvae were extracted, pooled in 1.5 ml as previously described (Burns & MacRae, 2006) and then frozen in -80°C.  RNA was isolated using TRIzol (Life Technologies) followed by phenol-chloroform extraction.  In brief, 500 hearts from 96 hpf larvae were lysed and homogenized in TRIzol using the NextAdvance Bullet Blender® Homogenizer (Scientific instrument services, inc.).  Chloroform was then added and phase separation was obtained following vortexing and centrifugation.  The top aqueous phase (containing RNA) was isolated and purified using Clean and Concentrator kit (Zymo).

value: heart

value: wild type


title: 52 hpf hearts_2


title: microglia_without PGC-1α_rep 2


title: induction group2


title: ctrl DamPol1

value: Fuss expressing neurons


title: Heart_klf2_mutant_1

source_name: Whole heart pools, 96 hpf, klf2 mutants

value: klf2 knock out


title: 7 dpf hearts_1


title: microglia_with PGC-1α_rep 3