title: clsy4-1_smRNA-seq

status: Public on Dec 05 2021

city: La Jolla

first: Julie

middle: Ann

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: PLANT MOLECULAR AND CELLULAR BIOLOGY LABORATORY

institute: The Salk Institute for Biological Studies

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering, Mapping, and cluster calling: The adapters were removed from the de-multiplexed reads using cutadapt (v1.9.1) and trimmed reads longer that 15nt were mapped to the TAIR10 genome using ShortStack (v3.8.1) with the following options: --mismatches 1 and either --mmap f, to include multi-mapping reads, or --mmap n, to include only unique mapping reads. Only perfectly matched read or reads with a single 3’ mismatch were used to call smRNA clusters using ShortStack with the --mincov 20, --pad 100, --dicermin 21 and dicermax 24 options, to generate Tag Directories using the using the makeTagDirectory script from the HOMER with the -format sam -mis 1 and -keepAll options, and to make genome browser tracks specifically for the 24nt sized smRNAs using the makeUCSCfile script from HOMER with the -fragLength 24 and -norm 10000000 options.
TAIR10
Supplementary_files_format_and_content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

source_name: stage 12 and younger flower buds (Fl)

growth_protocol: Growth conditions and tissue collection for 15 day old aerial rosettes (Ar) and 25 day old leaves (Lv) for all genotypes were as follows: seeds were sterilized with bleach and plated on half strength Linsmaier and Skoog medium (1/2 LS) supplemented with 1% agar. After three days stratification in the dark at 4℃, plants were grown in the Percival growth chamber (GCU-36L5) under 16h-light and 8h-dark cycle at 22℃ for 7 days and then were transplanted onto soil in Salk’s green house with long day conditions. At day 15 and day 25 of total growth, aerial rosette tissue (whole seedling without roots) or the first and second true leaves (without petioles) were collected from~40 plants as the Ar and Lv samples, respectively, immediately frozen in liquid nitrogen, and kept at -80°C until use. Growth conditions and tissue collection for mature, unfertilized ovules (Ov) were as follows: seeds were grown from soil in Salk’s greenhouse with long day conditions and un-opened flower buds (stage 10-12) were dissected to obtain carpels using a tweezer and then fixed on a double-side tape on a glass slide. Subsequently, carpels were dissected under dissection microscope using a needle and ovules were collected with the vacuum-based micro-aspiration device as detailed below. After collection, ovules for RNA extraction were quickly mixed with 100 µL trizol (Invitrogen, Cat# 15596018), flash frozen in liquid nitrogen and preserved at -80℃ until use, while ovules for DNA preparation were preserved in the same way without trizol. For each genotype, > 300 carpels were dissected and over 10,000 ovules were collected.

extract_protocol:
Total RNAs were isolated using Trizol reagent (Life Tech, Cat# 15596018) following the manual and dissolved in 250μL RNase-free water. 2.0 µg of total RNA from Ar and Lv tissues, or ~0.5ug of total RNA from Ov, were used for smRNA enrichment through a polyethylene glycol (PEG) precipitation step. One volume of a 20% PEG 8000/2M NaCl solution was added to each RNA sample, mixed well and kept on ice for more than 30 minutes (min) and then centrifuged at 13,000rpm for 15min at 4°C. The supernatant, containing the small RNAs, was collected and precipitated with 1 volume of cold isopropanol, mixed and incubated on ice for 30min. Then the small RNA samples were recovered by centrifuged at 13,000rpm for 30min at 4°C. The resulting small RNA samples were run on 15% polyacrylamide-8M urea gels and performed size-selection of fragments from 17-29 nucleotide (nt) following the ZR-small RNA ladder (zymo research, Cat# R1090). The small RNAs in the gels were recovered by incubating with 0.3M NaCl overnight, filtering the gels and add 2.5 volumes of 100% ethanol and 3μL of glycogen for precipitation over 2 hours (h) at -80°C.
The small RNAs were used for library preparation with the NEBnext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Cat# E7300) following the user’s manual. The final library products were further purified using an 8% polyacrylamide gel to excise 130-160nt products relative to the pBR322 DNA-MspI Digest ladder (New England Biolabs, Cat# E7323AA). The purified libraries were pooled and sequenced (single end 50 bp, SE50) on a HiSeq 2500 machine (Illumina).

tag: ecotype

value: Columbia

tag: tissues

value: stage 12 and younger flower buds (Fl)

tag: genotype


title: WT_rep2_smRNA-seq

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Arabidopsis thaliana

value: wild-type


title: clsy3-1_smRNA-seq


title: AK1 a

status: Public on Aug 18 2021

city: Phoenix

first: Eric

last: Alsop

state: AZ

address: 445 N 5th St

institute: TGen

description:
Cell lysate
AK1_a_15_S35

data_processing:
cutadapt for quality filtering
sRNABench for small RNA
normalization in DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: miRNA_ALL_norm_counts.txt

organism: Mus musculus

source_name: Peritoneal macrophages isolated from Akita mice

extract_protocol:
Qiagen miRNeasy Mini Kit
NextFlex v3

tag: cell type

value: Peritoneal macrophages

value: Akita


title: WT_rep1_smRNA-seq


title: AK3 a

description:
Cell lysate
AK3_a_17_S37


title: AK6 b

description:
Cell lysate
AK6_b_14_S34


title: lPEG10_OE3

status: Public on Dec 25 2021

city: Beijing

first: Fengjie

last: Liu

address: No.8 Xishiku Street, Xi Cheng District

department: Dermatology and Venereology

country: China

institute: Peking University First Hospital

data_processing:
MF skin-biopsy sequencing data produced by Illumina HiSeq 4000 and cell line sequencing data produced by BGISEQ-500 called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
After filtering raw reads via SOAPnuke,clean reads were mapped to the human hg38 reference genome via HISAT.
For sequence data of skin-biopsy samples, gene expression levels were calculated by summarizing the transcript levels belonging to the same gene estimated by Kallisto,which was quantified by TPM（transcripts per million）.
For sequence data of cell lines,clean reads were aligned to the reference gene sequence using Bowtie2 and gene expression levels were calculated by RSEM,which was normalized as FPKM（fragments per kilobase million）.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM/FPKM values for 49 MF skin-biopsy samples and 14 CTCL cell-line samples

organism: Homo sapiens

source_name: CTCL cell line(Myla)

growth_protocol: HH  and Myla cells were cultured in RPMI 1640 medium with 10% fetal bovine serum , containing 100 U/mL penicillin and 0.1 mg/mL streptomycin

extract_protocol:
200ng total RNA samples were extracted from lesional skin biopsies obtained from 49 patients with MF (26 LCT, 23 NLCT) using Trizol reagent; from control HH cells and PEG10-silienced HH cells , control Myla cells and  PEG10-overexpressed Myla cells  using EZNA total RNA kit II (Omega Bio-tek) ,respectively.
RNA libraries were prepared for sequencing using standard Illumina and BGISEQ protocols

treatment_protocol: HH cells  were subjected with lentivirus-mediated transfection of vectors expressing PEG10-shRNA(shPEG10-1 and shPEG10-2)  or scrambled shRNA(sh0), and then cultured  to produce stable PEG10 knockdown cell line.  Myla cells  were subjected with lentivirus-mediated transfection of empty vetors and PEG10 expression vectors ( RF1b, RF1b/2, RF1b/2+CNF) , and then cultured  to produce stable PEG10 overexpression cell line.

tag: tumor

value: MF

tag: tissue

value: skin

tag: dissease state

value: stage IIA


title: AK5b

description:
Cell lysate
AK5b_13_S33


title: AK3 b

description:
Cell lysate
AK3_b_11_S31


title: AK1 b

description:
Cell lysate
AK1_b_9_S29


title: WT_rep3_smRNA-seq


title: wt3a

description:
Cell lysate
wt3a_8_S28

source_name: Peritoneal macrophages isolated from WT mice

value: WT


title: sPEG10_OE1


title: AK4 b

description:
Cell lysate
AK4_b_12_S32


title: AK2 b

description:
Cell lysate
AK2_b_10_S30


title: wt1a

description:
Cell lysate
wt1a_6_S26


title: wt5b

description:
Cell lysate
wt5b_5_S25


title: wt4b

description:
Cell lysate
wt4b_4_S24


title: stz3 mono hi

description:
Cell lysate
stz3_mono_hi_S96

source_name: Monocytes Ly-6Chi sorted from WT mice treated with STZ

value: Monocytes Ly-6Chi

tag: agent

value: STZ


title: wt1b

description:
Cell lysate
wt1b_1_S22


title: wt3b

description:
Cell lysate
wt3b_3_S23


title: ctl 4 mono hi

description:
Cell lysate
ctl_4_mono_hi_S89

source_name: Monocytes Ly-6Chi sorted from WT mice treated with citrate buffer

value: citrate buffer


title: stz0 mono hi

description:
Cell lysate
stz0_mono_hi_S109


title: AK2 a

description:
Cell lysate
AK2_a_16_S36


title: ctl 3 mono hi

description:
Cell lysate
ctl_3_mono_hi_S88


title: A5+6 hi

description:
Cell lysate
A5_6_hi_10_11_2017_S61

source_name: Monocytes Ly-6Chi sorted from Akita mice


title: A3+4 hi

description:
Cell lysate
A3_4_hi_10_11_2017_S59


title: A1+2 hi

description:
Cell lysate
A1_2_hi_10_11_2017_S60


title: A1 hi

description:
Cell lysate
A1_hi_10_04_2018_S56


title: A5 hi

description:
Cell lysate
A5_hi_10_04_2017_S58


title: WT3+4 hi 10.11.2017

description:
Cell lysate
WT3_4_hi_10_11_2017_10_11_2018_S55

source_name: Monocytes Ly-6Chi sorted from WT mice


title: WT3+4 hi

description:
Cell lysate
WT3_4_hi_10_04_2017_S54


title: WT1+2  hi

description:
Cell lysate
WT1_2_hi_10_11_2018_S53


title: WT2 hi

description:
Cell lysate
WT2_hi_10_04_2017_S50


title: HG-media-6

description:
Cell lysate
HG_media_20_S38

source_name: BMDM cultured in 25mM glucose

value: BMDM cultured in 25mM glucose

value: 25mM glucose


title: wt2a

description:
Cell lysate
wt2a_7_S27


title: WT4 hi

description:
Cell lysate
WT4_hi_10_04_2017_S52


title: WT5 hi

description:
Cell lysate
WT5_hi_10_11_2018_S51


title: HG-media-4

description:
Cell lysate
HG_media_19_S42


title: HG-media-2

description:
Cell lysate
HG_media_18_S28


title: HG-media-1

description:
Cell lysate
HG_media_17_S30


title: LG media-5

description:
Cell lysate
LG_media_15_S37

source_name: BMDM cultured in 5.5mM glucose

value: BMDM cultured in 5.5mM glucose

value: 5.5mM glucose


title: LG media-3

description:
Cell lysate
LG_media_14_S29


title: stz 2 mono hi

description:
Cell lysate
stz_2_mono_hi_S82


title: LG media-1

description:
Cell lysate
LG_media_13_S34


title: HG exo 12.11.19

description:
Exosomes
HG_exo_26_S31

source_name: Exosomes produced by BMDM cultured in 25mM glucose

value: Exosomes


title: LG exo 12.18.19

description:
Exosomes
LG_exo_27_S33

source_name: Exosomes produced by BMDM cultured in 5.5mM glucose


title: HG exo 12.18.19

description:
Exosomes
HG_exo_28_S40


title: ctl 2 mono hi

description:
Cell lysate
ctl_2_mono_hi_S87


title: LG exo 12.11.19

description:
Exosomes
LG_exo_25_S39


title: HG exo 01.08.20

description:
Exosomes
HG_exo_24_S32


title: LG exo 01.08.20

description:
Exosomes
LG_exo_23_S35


title: HG exo 01.15.20

description:
Exosomes
HG_exo_22_S43


title: LG exo 01.15.20

description:
Exosomes
LG_exo_21_S41


title: HG-media-6 [RNA-Seq]

data_processing:
cutadapt for quality filtering
STAR alignment to genome
FeatureCounts for gene counting from BAM
Genome_build: GRCm38.88
Supplementary_files_format_and_content: genecounts_renamed_normalized.txt

source_name: Cell lysate

extract_protocol:
Qiagen miRNeasy Mini Kit
SMARTer HI

value: Bone marrow-derived macrophage

tag: treatment

value: 25 mM Glucose


title: HG-media-2 [RNA-Seq]


title: HG-media-1 [RNA-Seq]


title: HG-media-4 [RNA-Seq]


title: LG media-3 [RNA-Seq]

value: 5.5mM Glucose + 19.5mM Mannitol


title: LG media-5 [RNA-Seq]


title: LG media-6

description:
Cell lysate
LG_media_16_S36


title: LG media-1 [RNA-Seq]


title: BMDM stim HGexo 01-15-20 [RNA-Seq]

value: BMDM-HG-exo


title: BMDM stim HGexo 12-18-19 [RNA-Seq]


title: BMDM stim HGexo 12-11-19 [RNA-Seq]


title: BMDM stim LGexo 01-15-20 [RNA-Seq]

value: BMDM-NG-exo


title: BMDM stim LGexo 12-11-19 [RNA-Seq]


title: BMDM stim LGexo 12-18-19 [RNA-Seq]


title: A3 hi

description:
Cell lysate
A3_hi_10_04_2017_S57

value: Akita


title: BMDM stim LGexo 01-08-20 [RNA-Seq]


title: Unstim 12-18-19 [RNA-Seq]

value: PBS


title: Unstim 01-08-2020 [RNA-Seq]


title: SAMPLE 14: Aorta EES-2

status: Public on Apr 30 2021

type: RNA

city: New York

first: Shiqi

last: Hu

state: NY

address: 3960 Broadway Rm 430

institute: Columbia University

data_processing:
For the normalization it uses the average of five housekeeping genes: ACTB, GAPDH and LDHA
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., mature DC/immature DC) ratios.

label: SYBR Green

organism: Rattus norvegicus

source_name: Rat aorta

label_protocol: PCR assays were performed using ScienCell's GeneQuery Rat Macrophage Polarization Markers qPCR Array Kit following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the iScript™ cDNA Synthesis Kit (Bio-Rad). Quantitative real-time PCR were performed (Light Cycler 480, Roche) using SsoAdvanced Universal SYBR Green Supermix (Bio-Rad).

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: Rat aorta

value: EES

tag: time

value: Day 7


title: SAMPLE 16: Aorta EES-4


title: SAMPLE 13: Aorta EES-1


title: Unstim 12-11-19 [RNA-Seq]


title: SAMPLE 10: Aorta DES-2

value: DES


title: SAMPLE 12: Aorta DES-4


title: SAMPLE 11: Aorta DES-3


title: LG media-6 [RNA-Seq]


title: SAMPLE 9: Aorta DES-1


title: SAMPLE 8: Aorta BMS-4

value: BMS


title: SAMPLE 7: Aorta BMS-3


title: SAMPLE 5: Aorta BMS-1


title: SAMPLE 6: Aorta BMS-2


title: SAMPLE 3: Aorta Control-3

value: Sham


title: SAMPLE 4: Aorta Control-4


title: BMDM stim HGexo 01-08-20 [RNA-Seq]


title: SAMPLE 2: Aorta Control-2


title: Input rep2

status: Public on Apr 06 2021

city: Jupiter

first: Joseph

last: Kissil

state: FL

address: 130 Scripps Way #2C1

department: Department of Cancer Biology

institute: The Scripps Research Institute, Scripps Florida

library_source: genomic

data_processing:
Adapter sequences and low quality read ends were trimmed using cutadapt v1.8.1
Reads were aligned to the hg19 genome build using bowtie2 v2.2.9
Post-alignment filtering was performed according to the AQUAS pipeline (github.com/kundajelab/chipseq_pipeline).
Peaks were called using macs2 v2.1.1.20160309 using the shift size values calculated from the run_spp.R script from the SPP peak caller (5, 6).
High-quality peaks were then identified using the idr1 pipeline, selecting peaks with an idr score of less than or equal to 0.02.
Genome_build: hg19
Supplementary_files_format_and_content: The narrowPeak files are the idr-passed peaks called in each of the three ChIP conditions

molecule: genomic DNA

growth_protocol: Human Schwann cells (hSC2λ) cells were maintained in low glucose Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco) supplemented with 10% fetal bovine serum (Atlas Biologicals) and antibiotics (100 units/ml penicillin and 100 μg/ml Streptomycin) (Gibco), at 37°C in a humidified atmosphere of 5% CO2 (v/v).

extract_protocol:
20 million cells were fixed with 1% formaldehyde for 10’ at R.T. Fixation was halted with 125 mM glycine for 5’ at RT. Fixed cells were washed 2x with cold PBS. Cell pellets were then resuspended in ChIP lysis buffer and chromatin was sheared with Misonix S-3000 bath sonicator for 15min sonication at 280W, 30” ON and 30” OFF to obtain 0.3–0.5 kb DNA fragments. Antibody (5μg) and Dynabeads Protein A were added to the cell lysate and incubated overnight at 4°C. Beads were washed with buffer 1 (150 mM NaCL, 20 mM TrisCl pH 8.0, 5 mM EDTA, 65% w/v sucrose, 10% Triton-X-100, 20% SDS) and then washed with TE buffer. DNA was eluted by resuspending the beads in TE/1%SDS. ChIP DNA and Input were treated with RNase A (5 μg) for 1 hr at 37°C. Proteinase K (0.5 mg/mL) was added and incubated overnight at 65°C to reverse crosslinking. DNA was then purified in phenol:chloroform and resuspended in a 30 μL of elution buffer.
ChIP-Seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (Cat No. E7645S) from New England Biolabs Inc. (Ipswich, MA). 1ng of fragmented DNA was used as input. The following steps were followed for library preparation: End repair, 5’ phosphorylation, dA-tailing, adapter ligation, U excision, clean up of adaptor-ligated DNA without size selection, and library amplification. 12 to 13 cycles followed by clean-up with 1 X Agencourt AMPure XP. The quality of the libraries was assessed using the Agilent High Sensitivity DNA kit (Cat No. 5067-4626) on the Agilent 2100 Bioanalyzer (Agilent Technologies) and were quantified using the NEBNext Library Quant kit for Illumina (Cat No. E7630S) by New England Biolabs Inc. The libraries were sequenced using the NextSeq 500 High Output v2 kit (75 cycles) (Cat No. FC-404-2005) on the NextSeq 500 platform from Illumina (San Diego, CA).

tag: chip antibody

value: input


title: HumanANNUBP_SingleCellRNAseq

status: Public on Apr 07 2021

city: New Brunswick

first: Xiyuan

last: Zhang

state: NJ

address: 195 Little Albany St.

department: Pediatric Hematology/Oncology

institute: Rutgers Cancer Institute

data_processing:
10X Genomics cellranger (version 3.1.0) was used to extract fastq
Sequenced reads were aligned to the 10x Genomics provided Human reference sequence (refdata-cellranger-GRCh38-3.0.0)
Count matrix was processed in Seurat v3.0 for cell clustering and cell type annotation
Supplementary file is the annotated RDS object used in the publication
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrix

source_name: ANNUBP

extract_protocol:
Surgicallly removed primary ANNUBP was enzymatically dissociated into single cell suspension. Three thousand four hundred and sixty seven live cells were captured for single-cell library preparation with 10X 3' v3.0 reagent.
All subsequent steps of library preparation and Quality Control were performed as described in the 10X Genomics 3’ v3.0 Single Cell User Guide.

value: atypical neurofibromatosis neoplasms of uncertain biologic potential

value: Enzymatically dissociated single cell suspension


title: Unstim 01-15-20 [RNA-Seq]


title: Input rep1


title: EZH2_ChIPseq rep3

value: EZH2 active motif #39901


title: EZH2_ChIPseq rep2


title: SAMPLE 15: Aorta EES-3


title: EZH2_ChIPseq rep1


title: YY1_ChIPseq rep3

value: Anti-YY1 antibody-ChIP Grade (ab38422)


title: YY1_ChIPseq rep1


title: YY1_ChIPseq rep2


title: YAP_ChIPseq rep2

value: YAP Cell Signaling (#4912)


title: YAP_ChIPseq rep1


title: D42_w118-VG-2

status: Public on Mar 31 2021

data_processing:
qualtity trimming with cutadapt (v.1.14)
Alignment to the fly genome with STAR (v.2.5.3a)
Generating raw counts tables for genes using feature counts (v.1.5.3)
Genome_build: dmel r6.27
Supplementary_files_format_and_content: counts table of raw gene counts

organism: Drosophila melanogaster

growth_protocol: Drosophila genotypes were raised at 25*C.

extract_protocol:
RNA was extracted from the samples using a RNEAsy kit by Qiagen
SMART-seq v4 Ultra Low Input RNA Kit by Clontech
Samples were sequenced by the Bejing Genomics Institute using a HiSeq4000.

treatment_protocol: At the 3rd instar larvae stage, larvae were either subjected to immunoprecipiation (100 larvae, IP and INPUT samples) or Ventral ganglion dissections (15 larvae, VG samples)

tag: genotype/variation

tag: developmental stage/tissue

value: 3rd instar larvae

tag: sample type

value: VG


title: D42_TDP43WT-VG-2


title: D42_w118-VG-1


title: D42_TDP43WT-VG-3


title: D42_TDP43WT-VG-1


title: D42_w118-VG-3


title: D42_TDP43WT-IP-4

value: IP


title: D42_TDP43WT-INPUT-4

value: INPUT


title: D42_TDP43WT-INPUT-3


title: D42_TDP43WT-IP-3


title: D42_TDP43WT-IP-2


title: SAMPLE 1: Aorta Control-1


title: D42_TDP43WT-INPUT-2


title: D42_RPL10-VG-2

data_processing:
library strategy: Translating ribosome affinity purification (TRAP)-seq
qualtity trimming with cutadapt (v.1.14)
Alignment to the fly genome with STAR (v.2.5.3a)
Generating raw counts tables for genes using feature counts (v.1.5.3)
Genome_build: dmel r6.27
Supplementary_files_format_and_content: counts table of raw gene counts


title: D42_RPL10TDP43WT-VG-3


title: D42_RPL10-VG-1


title: D42_RPL10-VG-3


title: D42_RPL10TDP43WT-VG-2


title: D42_RPL10TDP43WT-INPUT-4


title: D42_RPL10TDP43WT-VG-1


title: D42_RPL10TDP43WT-IP-3


title: D42_RPL10TDP43WT-INPUT-1


title: D42_RPL10-IP-2


title: D42_RPL10TDP43WT-INPUT-3


title: D42_RPL10-IP-1


title: D42_RPL10TDP43WT-IP-4


title: D42_RPL10G298S.9-VG-3


title: D42_RPL10-INPUT-1


title: D42_RPL10G298S.9-IP-3


title: D42_RPL10G298S.9-VG-2


title: D42_RPL10G298S.9-INPUT-4


title: D42_RPL10G298S.9-IP-2


title: D42_RPL10G298S.9-IP-4


title: D42_RPL10G298S.9-INPUT-3


title: D42_G298S.9-VG-3


title: D42_RPL10G298S.9-INPUT-2


title: D42_G298S.9-VG-1


title: D42_RPL10TDP43WT-IP-1


title: D42_G298S.9-IP-4


title: D42_G298S.9-INPUT-2


title: D42_G298S.9-INPUT-4


title: D42_G298S.9-IP-1


title: D42_G298S.9-VG-2


title: ER+ tumour Lymph-node cells from Patient 0068

status: Public on Mar 19 2021

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Read alignment and count summarization were performed using CellRanger v3.0.2 using the Illumina BCL files as input.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx files contain genewise read counts for all cells in the space-efficient matrix market format. The supplementary file features.tsv.gz contains the corresponding Ensembl IDs and gene symbols as tab-delimited text. The barcode.tsv files contain the 10X barcodes used to identify cells. Each matrix market file can be read into R, together with features.tsv.gz, using the read10X function of the edgeR software package.

molecule: polyA RNA

source_name: Mammary gland

extract_protocol:
A 10X Genomics Chromium machine was used for single cell capture and cDNA was prepared using the Single Cell 3’ Protocol recommended by the manufacturer.
The 10X Genomics Chromium machine partitions cells into Gel Bead-In-EMulsions (GEMs), where all generated cDNA share a common 10x Genomics barcode but uses a pool of about 750,000 barcodes to separately index each cell’s transcriptome. The R1 primers were added during the GEM incubation and the P5, P7, a sample index and R2 during library construction via end repair, A-tailing, adaptor ligation and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The sequencing was carried out on an Illumina NextSeq 500.

tag: patient

tag: gender

value: Male

tag: menopause

tag: parity

tag: cancer type

value: ER+ tumour

tag: cell population

value: Involved lymph node

tag: number of cells


title: D42_RPL10-INPUT-2


title: ER+ tumour Lymph-node cells from Patient 0173

value: Female


title: ER+ tumour Total cells from Patient 0173

value: Total


title: ER+ tumour Total cells from Patient 0167


title: ER+ tumour Lymph-node cells from Patient 0167


title: D42_RPL10G298S.9-VG-1


title: ER+ tumour Lymph-node cells from Patient 0064


title: ER+ tumour Total cells from Patient 0064


title: ER+ tumour Lymph-node cells from Patient 0056


title: ER+ tumour Total cells from Patient 0056


title: D42_G298S.9-IP-2


title: ER+ tumour Lymph-node cells from Patient 0043


title: ER+ tumour Total cells from Patient 0029-7C


title: ER+ tumour Total cells from Patient 0040


title: ER+ tumour Lymph-node cells from Patient 0040


title: ER+ tumour Total cells from Patient 0043


title: ER+ tumour Total cells from Patient 0029-9C


title: D42_G298S.9-INPUT-1


title: ER+ tumour Total cells from Patient 0163


title: ER+ tumour Total cells from Patient 0032


title: ER+ tumour Total cells from Patient 0114


title: ER+ tumour Total cells from Patient 0360


title: ER+ tumour Total cells from Patient 0178


title: ER+ tumour Total cells from Patient 0042


title: ER+ tumour Total cells from Patient 0068


title: PR+ tumour Total cells from Patient 0319

value: PR+ tumour


title: ER+ tumour Total cells from Patient 0001


title: HER2+ tumour Total cells from Patient 0069

value: HER2+ tumour


title: HER2+ tumour Total cells from Patient 0161


title: HER2+ tumour Total cells from Patient 0031


title: ER+ tumour Total cells from Patient 0125


title: HER2+ tumour Total cells from Patient 0337


title: HER2+ tumour Total cells from Patient 0308


title: Triple negative BRCA1 tumour Total cells from Patient 0554

value: Triple negative BRCA1 tumour


title: HER2+ tumour Total cells from Patient 0176


title: Triple negative BRCA1 tumour Total cells from Patient 0177


title: Triple negative BRCA1 tumour Total cells from Patient 0131


title: ER+ tumour Total cells from Patient 0151


title: Triple negative tumour Total cells from Patient 0114

value: Triple negative tumour


title: ER+ tumour Total cells from Patient 0025


title: Triple negative tumour Total cells from Patient 0135


title: Triple negative tumour Total cells from Patient 0106


title: BRCA1 pre-neoplastic Total cells from Patient 0090

value: Post (oophorectomy)

value: Parous

value: BRCA1 pre-neoplastic


title: BRCA1 pre-neoplastic Total cells from Patient 0023


title: Triple negative tumour Total cells from Patient 0126


title: Normal Total cells from Patient 0372

value: Post

value: Normal


title: BRCA1 pre-neoplastic Total cells from Patient 0894

value: Pre

value: Nulliparous


title: Normal Epithelial cells from Patient 0372

value: Epithelial


title: Normal Total cells from Patient 0169


title: Normal Total cells from Patient 0021


title: Normal Epithelial cells from Patient 0275

value: Post (hysterectomy)


title: Normal Total cells from Patient 0064


title: Normal Total cells from Patient 0288


title: Normal Epithelial cells from Patient 0342


title: Normal Total cells from Patient 0233


title: Normal Total cells from Patient 0123


title: Normal Total cells from Patient 0275


title: Normal Epithelial cells from Patient 0408


title: Normal Epithelial cells from Patient 1469


title: Normal Total cells from Patient 0342


title: Normal Epithelial cells from Patient 0230.16


title: Normal Total cells from Patient 0230.17


title: Normal Epithelial cells from Patient 0064


title: Normal Epithelial cells from Patient 0123


title: Normal Total cells from Patient 0093


title: Normal Epithelial cells from Patient 0093


title: Triple negative BRCA1 tumour Total cells from Patient 4031


title: Gastric cancer cell line SNU484 (Short-read RNA-seq)

status: Public on Dec 10 2020

city: Singapore

first: Kie Kyon

last: Huang

state: Select State/Province

address: 8 College Road

country: Singapore

institute: Duke-NUS Graduate Medical School

description: Short-read RNA-seq

data_processing:
We used CCS module of IsoSeq3 program (https://github.com/PacificBiosciences/IsoSeq3) to generate circular consensus sequence (CCS) reads from the sub-reads generated from the sequencing run.
Reads that were identified as full length were considered for de-novo clustering of reads using cluster module of IsoSeq3 to identify unique isoforms.
Isoforms were mapped to human genome (version hg38) using GMAP and only high-quality isoforms (supported by at least two FLNC reads) were considered for further analysis.
Isoforms identified across all cell lines were merged into a single non-redundant transcriptome using gffcompare (https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) and annotated using SQANTI2.
Transcript-level expression in the unit of transcript per million (tpm) were estimated for each identified isoform using Kallisto applied on short-read sequencing data and reference transcriptome defined using Iso-seq.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: gtf file containing the merged, non-redundant gastric cancer transcriptome.
Supplementary_files_format_and_content: Matrix table with tpm value for every isoform and every sample.

source_name: Gastric cancer cell line

extract_protocol:
Total RNA was extracted from 10 gastric cell-lines using RNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions.
For long-read Iso-seq, amplified cDNA products were made into SMRTbell template libraries according to the Iso-Seq protocol by Pacific Biosciences.
For short-read RNA-seq, two micrograms of total RNA was used to create libraries with Illumina TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, California, USA) according to manufacturer’s instructions.

tag: cell line

tag: cell type

value: Gastric cancer cell line


title: Gastric cancer cell line NCC59 (Short-read RNA-seq)

description: Short-read RNA-seq


title: Normal Epithelial cells from Patient 1105


title: Normal Total cells from Patient 0092


title: Normal Epithelial cells from Patient 0280


title: BRCA1 pre-neoplastic Total cells from Patient 0033


title: Normal Total cells from Patient 0019


title: Gastric cancer cell line SNU1967 (Short-read RNA-seq)

description: Short-read RNA-seq


title: Gastric cancer cell line SNU719 (Short-read RNA-seq)

description: Short-read RNA-seq


title: Gastric cancer cell line MKN1 (Short-read RNA-seq)

description: Short-read RNA-seq


title: Hyalocytes sample 5 lane 3

status: Public on Oct 05 2020

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human reference genome (hg38, gencode, release 31) with RNA STAR Galaxy Version 2.6.0b-2 (default parameters) using the Gencode annotation file (Gencode 31, release June 2019)
Samples were then checked for contamination with rRNA using SortMeRNA Galaxy Version 2.1b.6 as well as with non-human reads (bacteria, virus, funghi, arachea and protozoa) using RNA STAR Galaxy Version 2.6.0b-2. Reference genomes were downloaded from NCBI FTP server (ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/, Download between 6th and 13th July 2019).
Three BAM files for each sample (one for each lane) were combined in one BAM file per sample using Convert, Merge, Randomize BAM datasets Galaxy Version 2.4.0
Reads mapped to the human reference genome were counted using featureCounts Galaxy Version 1.6.4 (default parameters) using the aforementioned annotation file.
Samples with less than 10 mio. assigned reads were excluded from further analysis.
Differential gene expression was analyzed using DESeq2 Galaxy Version 2.11.40.6 (default parameters)
The output of DESeq2 was imported to RStudio (Version 1.2.1335, R Version 3.5.3). Genesymbols and genetypes were determined based on ENSEMBL (download: 22.09.2019). Genes without a hit in the ENTREZ Gene (NCBI) search were removed from analysis.
Genome_build: hg38

extract_protocol:
Vitreous tissue samples collected in vitrectomy collection bags were immediately placed on ice in the operating theatre and processed for cell isolation within two hours of surgical resection. The content of each vitrectomy bag was centrifuged for 10 min at 250x g at 15°C. After removing the supernatant, the pellet was transferred to FACS tubes by washing with phosphate-buffered saline (PBS) buffer (PAN) and Hank’s balanced salt solution (HBSS, Gibco) and again centrifuged for 10 min at 250x g at 15°C. The vitreous pellet was digested with Collagenase D (5 mg/mL, Roche) and DNase I (1 mg/mL, Roche) in HBSS for 20 min at 37°C. Cells were then filtered through a 70 µm cell strainer. Following another centrifugation step (7 min at 250x g at RT), 0.5 µL of Fixable Viability Dye (eFluor™ 780, eBioscience™) per 1 mL of cells was added. The pellet was stained for CD45 BV421 (anti-human, 1:100, BioLegend®), CD11b FITC (anti-human, 1:100, BioLegend®), CX3CR1 PE-Cy7 (anti-human, 1:200, BioLegend®). To exclude any potential contamination with blood-derived monocytes due to possible surgically induced micro bleedings which may influence the results, we further used the Anti-Human Mature Macrophages (MatMac) Antibody, an ED2-like (ectodermal dysplasia 2) marker for resident macrophages, which is absent in monocytes 8 (eFluor660, anti-human, 1:100, eBioscience™). After an incubation step of 20 min at 4°C the cells were re-suspended in FACS buffer and processed for sorting on the MoFlo Asrios EQ Cytometer (Beckman Coulter). Sorted cells were stored in RNAprotect Cell Reagent (QIAGEN) at 2-8 °C until sequencing was performed.  RNA extraction, library preparation and RNA sequencing were performed at the Genomics Core Facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (University of Regensburg, Regensburg, Germany; www.kfb-regensburg.de). In brief, total RNA was extracted from isolated hyalocytes and stabilized in RNAprotect Cell Reagent according to the RNeasy Plus Micro Kit protocol (QIAGEN). After pelleting, the RNAprotect buffer was removed and replaced by RLT Plus and the samples homogenized by vortexing for 30 sec. Genomic DNA contamination was eliminated using gDNA Eliminator spin columns. Next, ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally, total RNA was eluted in 12 μl of nuclease-free water.
In total 13 samples were analyzed using RNA-sequencing. The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc.) was used to generate first strand cDNA from 750 pg total-RNA. Double-stranded cDNA was amplified by LD PCR (12 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc.). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc.). Equimolar amounts of each library were pooled, and the pools then used for cluster generation on the cBot with the Illumina TruSeq SR Cluster Kit v3. The sequencing run was performed on a HiSeq 1000 instrument using the indexed, 50 cycles single-read (SR) protocol and TruSeq SBS v3 Reagents according to the Illumina HiSeq 1000 System User Guide. Image analysis and base calling resulted in bcl files, which were converted into fastq files with the bcl2fastq v2.18 software. The sequence data have been submitted to the Gene Expression Omnibus database under accession number GSE147449. The password is available from the corresponding author upon request.

value: Hyalocyte


title: Hyalocytes sample 3 lane 2


title: Hyalocytes sample 3 lane 1


title: Hyalocytes sample 5 lane 1


title: Hyalocytes sample 4 lane 1


title: Hyalocytes sample 8 lane 1


title: Hyalocytes sample 3 lane 3


title: Hyalocytes sample 1 lane 2


title: extracellular exosome, WT_04_05_2018_168

status: Public on Aug 06 2020

description: small RNA

data_processing:
NEXTFLEX smallRNA kit adapter trimming with cutadapt
smallRNA alignment and counts table generation with sRNABench (v. 0514)
collapsing miRNA counts into single counts table
Genome_build: mm10
Supplementary_files_format_and_content: miRNA raw counts table

source_name: bone marrow

extract_protocol:
Cell culture supernatant was harvested and centrifuged to remove debris. OptiPrep density gradient was used to purify exosomes
libraries were prepared using the PerkinElmer NextFlex smallRNA seq kit

value: extracellular exosome

value: control (wild type)

tag: tissue

value: Excised bone


title: cell lysate, WT_3_21_18_12

description: small RNA

value: cell lysate


title: Hyalocytes sample 1 lane 1


title: extracellular exosome, WT_03_16_2018_106

description: small RNA


title: Gastric cancer cell line NCC24 (Short-read RNA-seq)

description: Short-read RNA-seq


title: extracellular exosome, IL4_12_29_2017_101

description: small RNA

value: stimulated macrophages


title: cell lysate, WT_1_23_18_78

description: small RNA


title: cell lysate, IL4_3_14_18_2

description: small RNA


title: Hyalocytes sample 2 lane 1


title: extracellular exosome, IL4_04_05_2018_167

description: small RNA


title: Gastric cancer cell line OCUM1 (Short-read RNA-seq)

description: Short-read RNA-seq


title: Hyalocytes sample 8 lane 3


title: Gastric cancer cell line IM95 (Short-read RNA-seq)

description: Short-read RNA-seq


title: Hyalocytes sample 7 lane 1


title: Hyalocytes sample 7 lane 3


title: Hyalocytes sample 8 lane 2


title: Hyalocytes sample 7 lane 2


title: cell lysate, IL4_1_23_18_74

description: small RNA


title: Gastric cancer cell line NCC19 (Short-read RNA-seq)

description: Short-read RNA-seq


title: Hyalocytes sample 4 lane 3


title: Hyalocytes sample 4 lane 2


title: Hyalocytes sample 5 lane 2


title: Hyalocytes sample 2 lane 3


title: Hyalocytes sample 2 lane 2


title: Hyalocytes sample 1 lane 3


title: Day 1 Input

status: Public on Jul 13 2020

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

description: DAY 1 INPUT

data_processing:
Alignment was performed with Bowtie (1.0.0)
Filtering of low quality reads and multi-mapped reads was done with samtools and rmdup command
MACS 1.4.2 was used for peak calling
Genome_build: MM9 for mouse
Supplementary_files_format_and_content: bed files for OSKM binding

source_name: MEF cells 1 day reprogrammed

growth_protocol: MEFs were cultured and reprogrammed as described (Hussein SMI et al., 2014 & Polo JM et al., 2012)

extract_protocol:
MEFs undergoing reprogramming and control cells (naïve MEFs, mESCs, miPSCs) were cultured under optimum conditions and were fixed at a high-confluence stage at room temperature for 10 minutes using 1% formaldehyde in fixing buffer, followed by quenching with 0.125M glycine at room temperature for 5 minutes. Upon extensive washes, cells were resuspended in Lysis [50mM Hepes (pH 7.9), 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100] and then in sonication buffer [0.1% SDS, 1mM EDTA, 10mM Tris (pH 8.1)]. Chromatin shearing was carried out in the Covaris S2 sonicator using the Covaris TC12x12mm tubes (Tube AFA Fiber and Cap, Covaris) for 12 min (200 cycles per burst) allowing the shearing of chromatin within a range of 250-500 bps DNA fragments. Triton X-100 and NaCl were then added in the sheared chromatin to final concentrations of 1% and 150 mM, respectively. The chromatin was then centrifuged and the harvested supernatants were filtered throughout a 0.2 m syringe. ChIPs were carried out by incubating 75 μg of chromatin (corresponding to approximately 5x107 cells) with 2-10μg of antibody per ChIP reaction [Anti-mOct4 (19857, Abcam), Anti-mSox2 (2748S, Cell Signaling), Anti-mKlf4 (H-180, SC-20691, Santa-Cruz), Anti-mc-Myc (N-262, SC-764, Santa-Cruz) and rabbit IgG (crude serum)] overnight at 4°C. Next, Protein G-Dynabeads (10004D, Thermo Fisher Scientific) pre-equilibrated in IP buffer [0.1% SDS, 1mM EDTA, 10mM Tris (pH 8.1), 1% Triton X-100, 150mM NaCl], were incubated with the chromatin-antibody solution in an orbital mixer at 4°C for 2 hours. The recovered resin was subsequently washed with low and high salt buffers and LiCl buffer and the captured chromatin fragments were subjected to Proteinase K (03115828001, Roche Life Sciences) digestion at 50°C for 15 minutes, followed by overnight incubation with RNase A at 65°C. All DNA present in each sample was purified with AMPure XP beads and eluted in TE buffer.
Next Generation Sequencing (NGS) libraries were prepared using 1-15 ng of ChIP DNA and TruSeq adapters. DNA was blunt ended by End Repair Enzyme Mix (T4 DNA Polymerase, Klenow Fragment, T4 DNA Polynucleotide kinase) followed by “A” tailing of 3’ ends and ligation with the annealed TruSeq Adapters (Illumina). Conversion of the Y-shaped adapters to dsDNA occurred prior to the library size selection through 2.5% Metaphor/SeaKem LE (3:1 ratio) agarose gel electrophoresis. Each library was purified using miniElute columns (Qiagen) and then subjected to pre-amplification. The final quantification of DNA libraries was carried out according to the Quantification Standards of Illumina on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: ~500,000 of C57BL/6 early-passage MEFs (Passage 1-3) were co-transduced overnight with lenti-supernatants of FUW-M2rtTA and TetO-FUW-OSKM followed by medium change [MEF medium (High-Glucose DMEM, 15% FBS, Glutamax, P/S, NEAA)] and recovery of the culture for an additional day. The transduced cells were expanded and then passaged in 0.1% gelatin pre-coated 6 cm dishes. The induction of OSKM overexpression was initiated 24 hours later by the addition of doxycycline (DOX) at 2 g/ml final concentration. Half of the dishes were treated with doxycycline (+DOX), while the other half was left untreated (-DOX). Cells were harvested at selected time points during reprogramming course

value: mouse embryonic fibroblasts

value: DOX


title: ChIPseq of KLF4 in MEFs

source_name: MEF cells

tag: antibody

value: Anti-mKlf4 (H-180, SC-20691, Santa-Cruz)


title: Mef Input

description: MEF INPUT

tag: treatment


title: ChIPseq of OCT4 at Day 1 of reprogramming

description: ChIPseq of OCT4 at Day1 of reprogramming

value: Anti-mOct4 (19857, Abcam)


title: ChIPseq of SOX2 at Day 1 of reprogramming

description: ChIPseq of SOX2 at Day1 of reprogramming

value: Anti-mSox2 (2748S, Cell Signaling)


title: ChIPseq of KLF4 at Day 1 of reprogramming

description: ChIPseq of KLF4 at Day1 of reprogramming


title: extracellular exosome, WT_12_29_2017_104

description: small RNA


title: extracellular exosome, IL4_01_25_2018_102

description: small RNA


title: cell lysate, WT_3_14_18_9

description: small RNA


title: ChIPseq of KLF4 in iPSCs

source_name: iPSCs

value: induced pluripotent stem cells


title: ChIPseq of SOX2 at Day 5 of reprogramming

description: ChIPseq of SOX2 at Day5 of reprogramming

source_name: MEF cells 5 days reprogrammed


title: cell lysate, IL4_3_21_18_5

description: small RNA


title: extracellular exosome, IL4_03_16_2018_103

description: small RNA


title: ESC Input

description: ESC INPUT

source_name: mESCs

value: mouse embryonic stem cells


title: ChIPseq of SOX2 at Day 3 of reprogramming

description: ChIPseq of SOX2 at Day3 of reprogramming

source_name: MEF cells 3 days reprogrammed


title: ChIPseq of MYC at Day 5 of reprogramming

description: ChIPseq of MYC at Day5 of reprogramming

value: Anti-mc-Myc (N-262, SC-764, Santa-Cruz)


title: ChIPseq of KLF4 at Day 5 of reprogramming

description: ChIPseq of KLF4 at Day5 of reprogramming


title: extracellular exosome, WT_01_25_2018_105

description: small RNA


title: iPSCs Input

description: IPSC INPUT


title: Day 5 Input

description: DAY 5 INPUT


title: ChIPseq of MYC at Day 3 of reprogramming

description: ChIPseq of MYC at Day3 of reprogramming


title: ChIPseq of KLF4 at Day 3 of reprogramming

description: ChIPseq of KLF4 at Day3 of reprogramming


title: ChIPseq of MYC in MEFs


title: Day 3 Input

description: DAY 3 INPUT


title: G583 H3K27ac input

status: Public on Jun 06 2019

city: Houston

first: Marco

last: Gallo

state: TX

address: 1102 Bates Avenue

department: Pediatrics

institute: Baylor College of Medicine

data_processing:
Fastq files were aligned with bwa 0.7.17 to the hg38 reference genome to generate SAM files. Parameters: bwa mem -t 12
SAM files filtered using grep to remove alignments to alternative contigs, unlocalized sequence, or unplaced sequence. Samtools view -hS <input.sam> | Grep -v chrUn | grep -v random | grep -v _alt
SAM files filtered using samtools to filter out reads with mapping quality < 30. samtools view -bS -q 30
SAM files filtered to exclude high-signal artifact regions. Bedtools intersect -v -abam stdin <input.sam>  hg38.blacklist.bed.gz
SAM files sorted and converted to BAM using samtools sort. Default parameters used.
MACS2 callpeak was used to call ChIP-Seq peaks from the filtered, sorted BAM alignments using the following parameters: -f BAMPE -g hs -q 0.05 -B --SPMR. The parameter --broad was included for H3K27ac but not for CTCF.
Fold Enrichment traces were generated from output of macs2 callpeak using macs2 bdgcmp -t <input>_treat_pileup.bdg -c <input>_control_lambda.bdg -m FE
Fold Enrichment traces were sorted using igvtools sort <input>_FE.bdg <input>_FE.sorted.bdg hg38
TDF files were generated for IGV display using igvtools toTDF -z 10 <input>_FE.sorted.bdg <input>_FE.tdf hg38
ROSE was used to call superenhancers from H3K27ac ChIP data using the following command: "python ROSE_main.py -g HG38 -i <h3k27ac broad peak bed> -r <h3k27ac ip bam> -o <ROSE output directory> -s 6000 -t 2500 -c <h3k27ac input bam>"
Calls from biological replicates of the same sample were joined using 'bedtools merge' to make "union" bed files for ChIP peaks and superenhancer calls.
Genome_build: hg38
Supplementary_files_format_and_content: .narrowPeak files: bed6+4 containing peak calls from macs2
Supplementary_files_format_and_content: .broadPeak files: bed6+4 containing broad peak calls from macs2
Supplementary_files_format_and_content: .tdf files: IGV compressed files containing fold enrichment tracks. Generated from MACS2 output using IGVtools.
Supplementary_files_format_and_content: .bed files - union peak call regions from MACS2 or superenhancer calls generated by ROSE

source_name: primary GBM cell culture

growth_protocol: Glioma cells were grown in Neurocult NS-A media with supplement, EGF and FGF, on poly-L-ornithine and laminin coated plates, and harvested at 80% confluence with Accutase.

extract_protocol:
Cells were either treated with media containing 1% formaldehyde for 10 minutes at room temperature followed by quenching, wash and snap-freezing (CTCF) or by snap-freezing of native samples (H3K27Ac).Chromatin from 3 million cells was used to perform ChIP with 1 uL of CTCF antibody (CST #3418; lot 1) or with 1 ug of H3K27Ac antibody (Active Motif #39133, lot # 31814008)
Libraries were size selected and amplified using the NEBNext Ultra II DNA kit (New England Biolabs).

tag: culture

tag: digestion protocol

value: MNase digest

value: primary glioblastoma


title: G567 H3K27ac IP, replicate 2


title: G583 H3K27ac IP, replicate 1


title: ChIPseq of MYC in iPSCs


title: ChIPseq of MYC at Day 1 of reprogramming

description: ChIPseq of MYC at Day1 of reprogramming


title: ESC Input 1

description: ESC INPUT 1


title: ChIPseq of SOX2 in iPSCs


title: G523 H3K27ac IP, replicate 2


title: G523 H3K27ac input


title: G583 CTCF IP, replicate 2

value: crosslinked


title: ChIPseq of OCT4 at Day 5 of reprogramming

description: ChIPseq of OCT4 at Day5 of reprogramming


title: ChIPseq of OCT4 at Day 3 of reprogramming

description: ChIPseq of OCT4 at Day3 of reprogramming


title: G583 CTCF IP, replicate 1


title: ChIPseq of OCT4 in iPSCs


title: ChIPseq of MYC in ESCs


title: ChIPseq of SOX2 in ESCs


title: G583 H3K27ac IP, replicate 2


title: G567 H3K27ac IP, replicate 1


title: G567 H3K27ac input


title: G523 H3K27ac IP, replicate 1


title: G583 CTCF input


title: ChIPseq of KLF4 in ESCs


title: G567 CTCF input


title: G523 CTCF IP, replicate 1


title: G523 CTCF IP, replicate 2


title: ChIPseq of OCT4 in ESCs


title: G523 CTCF input


title: G567 CTCF IP, replicate 1


title: G567 CTCF IP, replicate 2


title: FL197

status: Public on Feb 19 2019

city: Toronto

first: Anjali

last: Silva

state: ON

address: 610 University Ave

department: Lymphoid Cancer Research

country: Canada

institute: Princess Margaret Cancer Centre - University Health Network

description:
Patient sample
FL197

hyb_protocol: labeled PCR products were hybridized to HT-12v4 BeadChips and washed following Illumina's standard protocols

scan_protocol: beadchips were scanned using the Illumina BeadArray System

data_processing: These are raw and normalized data. Normalization was performed using the quantile normalization setting in the normaliseIllumina function from the beadarray R package.

source_name: Follicular lymphoma

label_protocol: 400ng of FFPET total RNA was converted to cDNA, followed by an amplification step using the Illumina Human Whole-Genome DASL HT Assay kit (catalogue #DA-905-0096, San Diego, CA, US)

growth_protocol: primary patient samples, formalin-fixed and paraffin-embedded

extract_protocol: Roche High Pure RNA Paraffin kit

value: Follicular lymphoma

tag: patient treatment

value: rituximab+chemotherapy

tag: codeffs

tag: ffs

tag: codeos

tag: os

value: NEG

tag: modified gene-expression profiling (mgep) score


title: FL185

description:
Patient sample
FL185


title: FL195

description:
Patient sample
FL195

value: POS


title: FL194

description:
Patient sample
FL194


title: FL192

description:
Patient sample
FL192


title: FL171

description:
Patient sample
FL171


title: FL183

description:
Patient sample
FL183


title: FL181

description:
Patient sample
FL181


title: FL174

description:
Patient sample
FL174


title: FL193

description:
Patient sample
FL193


title: FL173

description:
Patient sample
FL173


title: FL189

description:
Patient sample
FL189


title: FL167

description:
Patient sample
FL167


title: FL190

description:
Patient sample
FL190


title: FL180

description:
Patient sample
FL180


title: FL168

description:
Patient sample
FL168


title: FL196

description:
Patient sample
FL196


title: FL191

description:
Patient sample
FL191


title: FL166

description:
Patient sample
FL166


title: FL178

description:
Patient sample
FL178


title: FL179

description:
Patient sample
FL179


title: FL162

description:
Patient sample
FL162


title: FL187

description:
Patient sample
FL187


title: FL172

description:
Patient sample
FL172


title: FL159

description:
Patient sample
FL159


title: FL163

description:
Patient sample
FL163


title: FL161

description:
Patient sample
FL161


title: FL184

description:
Patient sample
FL184


title: FL169

description:
Patient sample
FL169


title: FL160

description:
Patient sample
FL160


title: FL152

description:
Patient sample
FL152


title: FL150

description:
Patient sample
FL150


title: FL132

description:
Patient sample
FL132


title: FL140

description:
Patient sample
FL140


title: FL156

description:
Patient sample
FL156


title: FL138

description:
Patient sample
FL138


title: FL151

description:
Patient sample
FL151


title: FL127

description:
Patient sample
FL127


title: FL148

description:
Patient sample
FL148


title: FL135

description:
Patient sample
FL135


title: FL139

description:
Patient sample
FL139


title: FL130

description:
Patient sample
FL130


title: FL134

description:
Patient sample
FL134


title: FL137

description:
Patient sample
FL137


title: FL129

description:
Patient sample
FL129


title: FL131

description:
Patient sample
FL131


title: FL128

description:
Patient sample
FL128


title: FL153

description:
Patient sample
FL153


title: FL124

description:
Patient sample
FL124


title: FL126

description:
Patient sample
FL126


title: FL149

description:
Patient sample
FL149


title: FL114

description:
Patient sample
FL114


title: FL118

description:
Patient sample
FL118


title: FL115

description:
Patient sample
FL115


title: FL120

description:
Patient sample
FL120


title: FL119

description:
Patient sample
FL119


title: FL116

description:
Patient sample
FL116


title: FL122

description:
Patient sample
FL122


title: FL101

description:
Patient sample
FL101


title: FL103

description:
Patient sample
FL103


title: FL123

description:
Patient sample
FL123


title: FL117

description:
Patient sample
FL117


title: FL121

description:
Patient sample
FL121


title: FL112

description:
Patient sample
FL112


title: FL110

description:
Patient sample
FL110


title: FL106

description:
Patient sample
FL106


title: FL111

description:
Patient sample
FL111


title: FL097

description:
Patient sample
FL097


title: FL107

description:
Patient sample
FL107


title: FL084

description:
Patient sample
FL084


title: FL086

description:
Patient sample
FL086


title: FL102

description:
Patient sample
FL102


title: FL099

description:
Patient sample
FL099


title: FL088

description:
Patient sample
FL088


title: FL100

description:
Patient sample
FL100


title: FL096

description:
Patient sample
FL096


title: FL095

description:
Patient sample
FL095


title: FL080

description:
Patient sample
FL080


title: FL078

description:
Patient sample
FL078


title: FL094

description:
Patient sample
FL094


title: FL105

description:
Patient sample
FL105


title: FL071

description:
Patient sample
FL071


title: FL069

description:
Patient sample
FL069


title: FL070

description:
Patient sample
FL070


title: FL089

description:
Patient sample
FL089


title: FL092

description:
Patient sample
FL092


title: FL090

description:
Patient sample
FL090


title: FL083

description:
Patient sample
FL083


title: FL058

description:
Patient sample
FL058


title: FL087

description:
Patient sample
FL087


title: FL076

description:
Patient sample
FL076


title: FL059

description:
Patient sample
FL059


title: FL074

description:
Patient sample
FL074


title: FL082

description:
Patient sample
FL082


title: FL073

description:
Patient sample
FL073


title: FL075

description:
Patient sample
FL075


title: FL077

description:
Patient sample
FL077


title: FL056

description:
Patient sample
FL056


title: FL054

description:
Patient sample
FL054


title: FL144

description:
Patient sample
FL144


title: FL067

description:
Patient sample
FL067


title: FL065

description:
Patient sample
FL065


title: FL064

description:
Patient sample
FL064


title: FL062

description:
Patient sample
FL062


title: FL060

description:
Patient sample
FL060


title: FL068

description:
Patient sample
FL068


title: FL057

description:
Patient sample
FL057


title: FL039

description:
Patient sample
FL039


title: FL038

description:
Patient sample
FL038


title: FL028

description:
Patient sample
FL028


title: FL034

description:
Patient sample
FL034


title: FL055

description:
Patient sample
FL055


title: FL031

description:
Patient sample
FL031


title: FL053

description:
Patient sample
FL053


title: FL048

description:
Patient sample
FL048


title: FL021

description:
Patient sample
FL021


title: FL052

description:
Patient sample
FL052


title: FL049

description:
Patient sample
FL049


title: FL046

description:
Patient sample
FL046


title: FL051

description:
Patient sample
FL051


title: FL045

description:
Patient sample
FL045


title: FL019

description:
Patient sample
FL019


title: FL018

description:
Patient sample
FL018


title: FL042

description:
Patient sample
FL042


title: FL050

description:
Patient sample
FL050


title: FL047

description:
Patient sample
FL047


title: FL016

description:
Patient sample
FL016


title: FL041

description:
Patient sample
FL041


title: FL040

description:
Patient sample
FL040


title: hepatocytes 72 hours with dox

status: Public on Feb 14 2019

description: Gene expression data from mHEPs reprogramming

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430A 2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

label: biotin

source_name: Hepatocytes 72 hours with dox

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

growth_protocol: ~500,000 of C57BL/6 early-passage MEFs (P1-P3) were co-transduced overnight with lenti-supernatants of FUW-M2rtTA and TetO-FUW-OSKM followed by medium change [MEF medium (High-Glucose DMEM, 15% HI FBS, Glutamax, P/S, NEAA)] and recovery of the culture for an additional day. The transduced cells were expanded in 10 cm dishes and then passaged in 0.1% gelatin pre-coated 6 cm dishes. The induction of OSKM expression was initiated 24 hours later by the addition of doxycycline (DOX) at 2 mg/ml. Half of the dishes were treated with doxycycline (+DOX), while the other half was left untreated (-DOX). Cells were harvested at selected timepoints during reprogramming course followed by total RNA extraction and Microarray hybridization assays . Similar to the kinetic studies employed in MEFs, lentiviral transductions and reprogramming setup were performed in mHeps.

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

treatment_protocol: The reprogramming of human fibroblasts (P1-P3) was performed as previously described (Pliatska et al., 2018) by transducing ~500,000 cells with a lentiviral supernatant mixture of FUW-M2rtTa and TetO-FUW-OSKM in a ratio of 1:1 in the presence of 6μg/ml polybrene. After the induction of the OSKM expression by the addition of DOX (Day 0), cells were harvested at the selected time points followed by total RNA extraction and qPCR assays.

tag: cells

value: mHeps

tag: time point

tag: dox

value: yes


title: hepatocytes 72 hours no dox

source_name: Hepatocytes 72 hours with no dox

value: no


title: esc cell

description: Gene expression data from ESC cells

source_name: ESC cells

value: mouse ESC


title: mef 72 hours with dox

description: Gene expression data from MEF reprogramming

source_name: MEF 72 hours with dox

value: mouse embryonic fibroblasts


title: mef 144 hours with dox

source_name: MEF 144 hours with dox


title: FL024

description:
Patient sample
FL024


title: FL027

description:
Patient sample
FL027


title: FL035

description:
Patient sample
FL035


title: FL036

description:
Patient sample
FL036


title: FL029

description:
Patient sample
FL029


title: mef 48 hours with dox

source_name: MEF 48 hours with dox


title: FL020

description:
Patient sample
FL020


title: mef 60 hours with dox

source_name: MEF 60 hours with dox


title: mef 36 hours with dox

source_name: MEF 36 hours with dox


title: mef 432 hours with dox

source_name: MEF 432 hours with dox


title: hepatocytes 144 hours with dox

source_name: Hepatocytes 144 hours with dox


title: hepatocytes 144 hours no dox

source_name: Hepatocytes 144 hours with no dox


title: ipsc cells

description: Gene expression data from iPSC cells

source_name: iPSC cells

value: mouse iPSC


title: FL011

description:
Patient sample
FL011


title: hepatocytes 0 hours

source_name: Hepatocytes


title: FL002

description:
Patient sample
FL002


title: mef 72 hours no dox

source_name: MEF 72 hours with no dox


title: mef 12 hours with dox

source_name: MEF 12 hours with dox


title: mef 48 hours no dox

source_name: MEF 48 hours with no dox


title: mef 60 hours no dox

source_name: MEF 60 hours with no dox


title: mef 288 hours with dox

source_name: MEF 288 hours with dox


title: mef 36 hours no dox

source_name: MEF 36 hours with no dox


title: mef 432 hours no dox

source_name: MEF 432 hours with no dox


title: mef 144 hours no dox

source_name: MEF 144 hours with no dox


title: mef 24 hours with dox

source_name: MEF 24 hours with dox


title: mef 288 hours no dox

source_name: MEF 288 hours with no dox


title: 2a_man_HH1862 [T00338933]

status: Public on Dec 26 2018

city: Lyon

first: Anne

last: Wierinckx

state: select a state

address: 8, av Rockefeller

country: France

institute: University Lyon1

hyb_protocol: Ten micrograms of biotin-labelled aRNA was fragmented using 5 μl of fragmentation buffer in a final volume of 20 µl and was then mixed with 240 µl of Amersham hybridization solution (GE Healthcare Europe GmbH, Freiburg, Germany) and injected onto CodeLink Uniset Human Whole Genome bioarrays containing 55000 human oligonucleotide gene probes (GE Healthcare Europe GmbH, Freiburg, Germany)

scan_protocol: The slides were scanned using a Genepix 4000B scanner (Axon, Union City, USA) and Genepix software, with the laser set at 635 mm, the laser power at 100%, and the photomultiplier tube voltage at 60%.

data_processing:
The scanned image files were analyzed using CodeLink expression software, version 4.2 (GE Healthcare), which produces both a raw and a normalized hybridization signal for each spot on the array. CodeLink software was used to normalize the raw hybridization signal on each array to the median of the array (median intensity is 1 after normalization) for better cross-array comparison. The threshold of detection was calculated using the normalized signal intensity of the 100 negative control samples in the array: spot with signal intensity below this threshold was referred as ‘absent’. The quality of processing was evaluated by generating scatter plots of positive signal distribution.
The complete_data.txt contains raw (SIGNAL_RAW), normalized data (VALUE) and quality flag data.

source_name: male_frozen lactotrop tumor_2a

label_protocol: Total RNA (2 µg) was amplified and biotin-labeled by a round of in vitro transcription with a Message Amp aRNA kit (Ambion, Austin, Texas, USA) following the manufacturer’s protocol

growth_protocol: All included tumors were resected between 1989 and 2005 by the transsphenoidal route and were further shown to be positive for prolactin expression by immunohistochemistry. The tumors were rapidly frozen after resection

extract_protocol: Total RNA was extracted from pituitary tumors using Trizol (Invitrogen), according to the manufacturer’s protocol (Invitrogen, Carlsbad, California, USA)

treatment_protocol: no treatment before resection

tag: gender

value: male

tag: classification

value: lactotroph pituitary tumor

tag: response to treatment

value: Responsive


title: 2a_man_HH1619 [T00338927]

tag: tissue


title: 1a_man_HH1357 [T00338931]

source_name: male_frozen lactotrop tumor_1a


title: 1a_woman_HH1546 [T00337597]

source_name: female_frozen lactotrop tumor_1a

value: female


title: mef 0 hours

source_name: MEF


title: 2a_woman_HH1710 [T00338932]

source_name: female_frozen lactotrop tumor_2a


title: 2a_man_HH1136 [T00338924]


title: 1b_man_HH0946 [T00337600]

source_name: male_frozen lactotrop tumor_1b


title: mef 12 hours no dox

source_name: MEF 12 hours with no dox


title: mef 24 hours no dox

source_name: MEF 24 hours with no dox


title: 2b_man_HH0915 [T00338934]

source_name: male_frozen lactotrop tumor_2b


title: 2b_woman_HH1430 [T00337576]

source_name: female_frozen lactotrop tumor_2b


title: 2a_man_HH1183 [T00338925]


title: 1a_man_HH1837 [T00337575]


title: 2b_man_HH1152 [T00337590]

value: Resistant


title: 1b_woman_HH1561 [T00337596]

source_name: female_frozen lactotrop tumor_1b


title: 1a_woman_HH1794 [T00338935]


title: 1a_woman_HH1536 [T00337589]


title: 2a_man_HH2348 [T00279480]


title: EPN, MPE, sample 297 [validation set]

status: Public on Jan 18 2018

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

description:
SAMPLE 297
Methylation data from brain tumor sample.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'.

label: biotin/DNP

source_name: brain tumor

label_protocol: Illumina protocol.

extract_protocol: Illumina protocol.

treatment_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

value: brain tumor

tag: methylation class

value: EPN, MPE

tag: material


title: 1a_woman_HH1512 [T00337593]


title: YCC-21 [RNA-seq]

status: Public on Sep 28 2016

first: Aditi

last: Qamra

address: 60 Biopolis Street, Genome, #02-01

institute: GIS

data_processing:
RNA-seq reads were aligned to the human genome (hg19) using TopHat2-2.0.12
Transcript abundances at the gene level were estimated by cufflinks
Gene expression from primary samples showing variation greater than zero were corrected for potential batch effects using ComBat
Genome_build: hg19
Supplementary_files_format_and_content: the genomic intervals followed by sequencing coverage.

source_name: Gastric cancer cell line

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit according to the manufacturer’s protocol.
Sequencing libraries were prepared using Illumina TruSeq RNA Sample Prep Kit v2 according to manufacturer’s protocol.

tag: tissuetype

value: Gastric cancer cell line

tag: histology

value: Adenocarcinoma


title: 1a_woman_HH2806 [T00279484]


title: 1a_woman_HH1838 [T00337591]


title: 1a_man_HH1615 [T00337594]


title: 2a_man_HH1697 [T00338928]


title: 2b_man_HH1804 [T00337577]


title: 2b_man_HH2182 [T00279476]


title: KATOIII [RNA-seq]

value: SRCC


title: 2b_woman_HH2376 [T00279473]


title: 2b_man_HH1539 [T00279472]


title: 2a_man_HH2495 [T00279478]


title: 2b_man_HH1599 [T00279474]


title: SNU16 [RNA-seq]

value: gastric carcinoma; poorly differentiated


title: 2a_man_HH1782 [T00337573]


title: 2b_man_HH2611 [T00279479]


title: 1a_man_HH2171 [T00279475]


title: Down syndrome heart CDH6

status: Public on Nov 21 2004

city: Napoli

first: Lucio

last: Nitsch

address: Via Pansini 5

department: Biologia e Patologia Cellulare e Molecolare

country: Italy

institute: Unversity of Naples Federico II

description:
The heart tissue was explanted from a human fetus with chromosome 21 trisomy and atrio-ventricular septal defects, following therapeutic abortion. The posterior half representing all the four heart chambers was dissected by a longitudinal cut. Total RNA was extracted and PolyA+ mRNA was obtained to prepare biotinilated target cRNA according to Affymetrix protocols (http://www.affymetrix.com/support/technical/manuals/expression_manual.affx). Target cRNA was hybridized to Affymetrix HG-U133A chip using an Affymetrix GeneChip Instrument System according to the procedures described at http://www.affymetrix.com/support/downloads/manuals/expression_s2_manual.pdf.
Image data were analyzed using the Affymetrix expression analysis software. The Affymetrix software Microarray Suite (MAS 5.0) assigned to each probe set of the chip an average difference value corresponding to the expression level of the gene it represents and an absolute call that indicates whether the transcript is present in the sample. Data sets were scaled to a total targeted fluorescence of 100.
Keywords = Down syndrome
Keywords = heart gene expression

data_processing: Affymetrix CEL files were imported into GeneSping 7.2 software (Agilent Technologies Inc.) and normalized by MAS5 algorithm

label: Biotin

source_name: Fetal heart at 20 weeks of gestation

label_protocol: In vitro transcription was performed to obtain biotin labeled cRNA according to Affymetrix protocols described at http://www.affymetrix.com/support/technical/manuals.affx

extract_protocol: Total RNA was extracted by Trizol

value: Heart from fetus with Down syndrome and septal defects.

tag: age

value: 20 gestation weeks


title: Down syndrome heart CDH5

hyb_protocol: according to Affymetrix protocols described at http://www.affymetrix.com/support/technical/manuals.affx

source_name: Fetal heart at 18 weeks of gestation

tag: Heart tissue from fetus with Down syndrome and septal defects.

value: 18 gestation weeks


title: Down syndrome heart CDH2

description:
The heart tissue was explanted from a human fetus with chromosome 21 trisomy and atrio-ventricular septal defects at 20 weeks of gestation, following therapeutic abortion. The posterior half representing all the four heart chambers was dissected by a longitudinal cut. Total RNA was extracted and PolyA+ mRNA was obtained to prepare biotinilated target cRNA according to Affymetrix protocols (http://www.affymetrix.com/support/technical/manuals/expression_manual.affx). Target cRNA was hybridized to Affymetrix HG-U133A chip using an Affymetrix GeneChip Instrument System according to the procedures described at http://www.affymetrix.com/support/downloads/manuals/expression_s2_manual.pdf.
Image data were analyzed using the Affymetrix  expression analysis software. The Affymetrix software Microarray Suite (MAS 5.0) assigned to each probe set of the chip an average difference value corresponding to the expression level of the gene it represents and an absolute call that indicates whether the transcript is present in the sample.  Data sets were scaled to a total targeted fluorescence of 100.
Keywords = Down syndrome
Keywords = heart gene expression

scan_protocol: according to Affymetrix protocols described at http://www.affymetrix.com/support/technical/manuals.affx

source_name: Fetal heart at 20 week of gestation

value: heart from fetus with Down syndrome and septal defects.


title: Down syndrome heart CDH4

description:
The heart tissue was explanted from a human fetus with chromosome 21 trisomy and atrio-ventricular septal defects at 21 weeks of gestation, following therapeutic abortion. The posterior half representing all the four heart chambers was dissected by a longitudinal cut. Total RNA was extracted and PolyA+ mRNA was obtained to prepare biotinilated target cRNA according to Affymetrix protocols (http://www.affymetrix.com/support/technical/manuals/expression_manual.affx). Target cRNA was hybridized to Affymetrix HG-U133A chip using an Affymetrix GeneChip Instrument System according to the procedures described at http://www.affymetrix.com/support/downloads/manuals/expression_s2_manual.pdf.
Image data were analyzed using the Affymetrix expression analysis software. The Affymetrix software Microarray Suite (MAS 5.0) assigned to each probe set of the chip an average difference value corresponding to the expression level of the gene it represents and an absolute call that indicates whether the transcript is present in the sample. Data sets were scaled to a total targeted fluorescence of 100.
Keywords = Down syndrome
Keywords = heart gene expression

source_name: Fetal heart at 21 weeks of gestation

extract_protocol: Total RNA was extract by Trizol

tag: Age 21 gestation weeks