title: Normal Muscle, ctrl muscle F539-A

city: Los Angeles

first: Safiyyah

last: Ziyad

address: 621 Charles E. Young Drive, South

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description:
piece 2
IL19

data_processing:
Fastq files were aligned to mm10 genome using STAR version 20201
Read counts per gene was quantified by STAR using Ensembl GRCm38.88  gtf file
Read counts normalized by voom were calculated using R package Limma.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file reporting voom normalized log cpm

source_name: Normal Muscle

extract_protocol:
Lesions were disected, transferred to microcentrifuge tubes, snap frozen immediately in liquid nitrogen, and stored at -80C until RNA extraction.  RLT buffer containing beta-mercaptoethanol was was used to lyse tissues, which were then homogenized.  Qiagen RNeasy kit was used to isolate total RNA.
Illumina TruSeq unstranded poly-A selection kit (Cat# RS-122-2001) was used to make library from 1ug of RNA.

value: SB Transposase; onc3

tag: phenotype

value: Normal Muscle

value: muscle


title: Male EAE CysCKO rep 3

status: Public on Sep 09 2020

type: SRA

city: Calgary

first: Shalina

last: Ousman

state: Alberta

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

library_source: transcriptomic

data_processing:
bcl2fastq v2.20.0.422 (default params)
kallisto 0.42.4 (quant -b 100 --single -l 180 -s 20 -i /export/common/dbs/kallisto/mm10.refMrna)
raw counts rounded to integer
Genome_build: Mouse RefSeq mRNA July 2017 (mm10)
Supplementary_files_format_and_content: Raw Mapped Read Counts vs RefSeq transcripts

molecule: total RNA

organism: Mus musculus

source_name: CD11b+ cells

extract_protocol:
CD11b+ cells were isolated by positive selection from spleens and RNA retrieved with an RNeasy Mini Kit. All samples were subjected to reverse transcription and Multiple Displacement Amplification with REPLI-g SensiPhi DNA Polymerase and oligo-dT primers as per the QIAGEN REPLI-g Single Cell RNA Library preparation kit and the manufacturer’s protocol. Libraries were prepared with 1 ug of total RNA using the QIAGEN GeneRead Adaptor I Set A 12-plex index adapters as per the REPLI-g single cell RNA library prep kit’s protocol and subjected to on-board cluster formation and sequencing on an Illumina NextSeq 500 sequencer with a high-output v2 75 cycle sequencing kit as per the standard Illumina protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: Spleen-derived

tag: disease

value: EAE

tag: Sex

value: Male

tag: genotype

value: CysC knockout


title: Normal Muscle, ctrl muscle F539-B

state: CA

country: USA

description:
piece 1
IL18


title: HT29-shctrl-rep2

type: RNA

city: Xiamen

first: Wanyun

last: Lee

state: Fujian

address: Xiang'an South Road, Xiang'an District

country: China

institute: Xiamen University

description: gene expression

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 500ul containing 1x Agilent fragmentation buffer and 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan  (Scan Area 61 x 21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 4 out of 8 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method.

organism: Homo sapiens

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All cell lines were cultured in DMEM medium supplemented with 10% fetal bovine serum.They were incubated for 24 hours  at 37 ºC in a humidified incubator with 5% CO2

extract_protocol: RNA was prepared using the RNasey Mini Kit(Qiagen p/n 74104) following the manufacturer's recommendations.   RNA was quantified and qualitied using a NanoDrop-1000 spectrophotometer .

tag: tumor

value: colon cancer


title: SC_VitC_1_Genomic_Input

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

description:
Genomic Input
Counts of reads in each peak

library_source: genomic

data_processing:
Library strategy: hMeDIP-Seq
Basecalls performed using CASAVA version 1.4
Bases were quality trimmed to q20 and adaptors were removed using Trim_Galore!
RNA-seq reads were aligned to the RN6 transcriptome using STAR or to RN6 genome using BWA
For hMeDIP samples, peaks were called using the Irreproducible Discovery Rate
Genome_build: RN6
Supplementary_files_format_and_content: Count files were generated using HTSeq-count.

molecule: genomic DNA

organism: Rattus norvegicus

source_name: SC_VitC_Genomic Input

extract_protocol:
Qiagen RNEasy or Qiagen DNA Mini
Epicentre RiboZero or Active Motif hMeDIP

treatment_protocol: Cells were taken upon passage 3

tag: cell type

value: Primary Schwann Cells

tag: passage

value: Passage 3

tag: treatment

value: VitC


title: Male EAE CysCKO rep 2


title: HT29-shNRP1-rep1

description: gene expression


title: HT29-shNRP1-rep2

description: gene expression


title: MDA-MB-231-shNRP1-rep2

description: gene expression

value: breast cancer


title: HT29-shctrl-rep1

description: gene expression


title: Normal Muscle, ctrl muscle M536-A

description:
piece 2
IL16


title: G. lacustris, 12 degrees C, sample 2

city: Leipzig

first: Polina

last: Lipaeva

address: Permoserstraße 15

department: Biotox

country: Germany

institute: Helmholtz Centre for Environmental Research - UFZ

description:
lat_long:
51° 54’11.67”N, 105° 4’7.61”E
Pooled sample of approx. 11 individuals of G. lacustris were acclimated at 6 degrees C for 14 days, then the temperature was gradually increased to 12 °C by 1-1.5 °C/day over about 6 days, and animals were kept at 12 degrees C for 1 month.

data_processing:
Raw reads were mapped onto transcriptome assemblies with the align_and_estimate_abundance.pl script from the Trinity v2.9.1 toolkit. We used salmon v1.1.0 as an abundance estimation method.
Differential expression was performed with DESeq2 v1.26.0. In-house scripts for data analysis are available at GitHub, see https://github.com/PolinaLip/Amphipods_ColdAdaptation_RNA.
Genome_build: de novo transcriptome assembly of the corresponding species (FASTA files on series record)
Supplementary_files_format_and_content: Salmon output files as TPM (transcript per million counts, tab-delimited text files) and DESeq2 output files (tab-delimited text files)

organism: Gammarus lacustris

source_name: whole body

extract_protocol:
Frozen coarse powder of amphipods was homogenized in 1 ml of Qiazol Reagent (Qiagen) using an MM400 mixer mill (Retsch). Total RNA of amphipods was manually isolated using an RNeasy Mini kit (Qiagen). All samples were treated with DNase (TURBO DNA-free Kit).
mRNA purification from total RNA was performed using an Oligotex mRNA Mini Kit. RNA concentration and quality were evaluated using Qubit 2.0 fluorometer and Agilent Bioanalyzer 2100. Twenty-four RNA-seq libraries were prepared from 20 ng of mRNA using ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, SSV21124).

treatment_protocol: Animals were acclimated at 6 degrees C for 14 days before the experiment. Please refer to description of individual samples for species- and sample-specific details. After the temperature expositions, animals were frozen in liquid nitrogen. The frozen animals were ground to coarse powder in a mortar, which was stored at -80 degrees C until further sample processing.

value: whole body

value: rocky littoral zone

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village

tag: depth

value: adult

tag: condition

value: 12 degree C


title: MDA-MB-231-shNRP1-rep1

description: gene expression


title: Normal Muscle, ctrl muscle M536-B

description:
piece 1
IL15

value: SB Transposase; onc3


title: total mRNA siSCR U251 cells from 2nd experiment

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

description: Biological replicate 2 of 4. Cytoplasmic RNA; siScr treated U251 cells

hyb_protocol: Oligoarray  hybridization was performed in Agilent chambers according to the manufacturer’s instructions

scan_protocol: Scanned on an Ion Proton (Lifetechnologies) according to the manufacturer’s instructions

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

label_protocol: labelling with Cy3 was performed with 100 ng of  RNA

growth_protocol: Human glioblastoma cell lines  U251 (obtained from C. Simon’s laboratory, UPENN, Philadelphia, PA, USA) were used and routinely maintained in Dulbecco’s Modified Eagle Medium (Lonza, Portsmouth, NH, USA) supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin at 37C° in 5% CO2-humidified incubators as previously described.

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

treatment_protocol: Human U251  glioblastoma cells were transfected with 20 nmol/L of siScramble (siScr, Qiagen, Venlo, Limburg, The Netherlands) or 20 nmol/L of siRNA against human INT6/eIF3e (si3e: SI02662499, FlexiTube EIF3E siRNA, 20 nmol, 5'-CCCAAAGGUCGCGAUAAUAUU-3', Qiagen; or si3e#2: Dharmacon ON-TARGET plus SMART pool EIF3E siRNA 3646, 10 nmol) for 72h

tag: cell line

tag: tissue/cell type

value: Human glioblastoma cell line

tag: genotype/variation

value: siRNA Scramble/control (siSCR)

tag: molecule subtype

value: Cytoplasmic RNA


title: Normal Muscle, ctrl muscle F544-A

description:
piece 2
IL14

value: Normal Muscle

value: muscle


title: SC_Control_3_Genomic_Input

value: control


title: Female naïve WT rep 1

value: Spleen-derived

value: naive

value: Female

value: wildtype


title: Male EAE CysCKO rep 1

value: EAE

value: Male

value: CysC knockout


title: SC_VitC_2_RNA

description:
Ribodepleted RNA
Counts of reads in each gene

data_processing:
Basecalls performed using CASAVA version 1.4
Bases were quality trimmed to q20 and adaptors were removed using Trim_Galore!
RNA-seq reads were aligned to the RN6 transcriptome using STAR or to RN6 genome using BWA
For hMeDIP samples, peaks were called using the Irreproducible Discovery Rate
Genome_build: RN6
Supplementary_files_format_and_content: Count files were generated using HTSeq-count.

value: Primary Schwann Cells

value: Passage 3

value: VitC


title: Normal Muscle, ctrl muscle F544-B

description:
piece 1
IL13

value: SB Transposase; onc3


title: Male EAE WT rep 3


title: Male EAE WT rep 4


title: SC_VitC_1_hMeDIP

description:
5hmc-precipitated DNA
Counts of reads in each peak


title: SC_VitC_1_RNA


title: SC_VitC_3_RNA


title: SC_Control_2_Genomic_Input


title: MDA-MB-231-shctrl-rep1

description: gene expression

value: breast cancer


title: Male EAE WT rep 2


title: SC_Control_3_hMeDIP


title: SC_Control_3_RNA


title: Muscle Vascular Anomaly, 5f-B

description:
piece 2
IL12

source_name: Muscle Vascular Anomaly

value: VEC-Cre;SB Transposase; onc3

value: Muscle Vascular Anomaly


title: SC_Control_1_hMeDIP


title: Male EAE WT rep 1


title: Male naïve CysCKO rep 3


title: SC_Control_1_Genomic_Input


title: Muscle Vascular Anomaly, 5f-A

description:
piece 1
IL7


title: SC_Control_2_hMeDIP


title: Muscle Vascular Anomaly, F347#1

description:
lesion 1
IL5


title: Male naïve CysCKO rep 2


title: SC_Control_1_RNA


title: HepG2_siSFPQ2_rep1

city: Aarhus C

first: Thomas

middle: B

last: Hansen

state: State...

address: C.F. Moellers Alle 3, build 1130

country: Denmark

institute: MBG, Aarhus University

description:
HepG2_featureCounts.txt
HepG2_ciri2.txt
HepG2_find_circ.txt

data_processing:
Reads were mapped onto hg19 with STAR (v2.7) and quantified with featureCounts (v2.0.0) using gencode annotations (v28lift37 for hg19).
CircRNAs were predicted and quantified using ciri2 v2.0.6 and find_circ v1.2 adhering to default settings
Quantseq reads were mapped onto hg19 using STAR (v2.7). The resulting bam-files were merged and divided into plus and minus-strand alignments. Then, using MACS2 peakcall  (v2.2.6, https://github.com/macs3-project/MACS) with parameters [--nomodel --shift 0 –g 2.9e9], quantseq peaks were extracted. Each peak was then subsequently quantified using featureCounts (v2.0.0).
Genome_build: hg19
Supplementary_files_format_and_content: Merged raw counts provided by ciri2, find_circ or featureCounts

source_name: Knockdown in HepG2 using siSFPQ2, rep1

growth_protocol: HEK293T cells (Invitrogen), HepG2 (ATCC) were cultured in Dulbecco’s modified Eagle’s media (DMEM) with GlutaMAX (Thermo Fisher Scientific) supplemented with 10% foetal bovine serum (FBS) and 1% penicillin/streptomycin sulphate (P/S). All cells were kept at 37°C in a humidified chamber with 5% CO2.

extract_protocol:
RNA was extracted using TriZOL
For total RNA sequencing of HEK293T, RNA from SFPQ, NONO, and CTRL KD were rRNA depleted using RiboCop rRNA Depletion Kit V1.2 (Lexogen) according to manufacturer’s protocol. Subsequent cDNA libraries were prepared using SENSE Total RNA-Seq Library Prep Kit (Lexogen) following manufacturer’s protocol. For 3’end sequencing, cDNA libraries from HEK293T were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen). Total RNAseq was done as 100nt paired-end sequencing and performed using the Illumnia platform (HiSEQ4000, BGI, Copenhagen), while for 3’end sequencing, 75nt single-end sequencing was performed at MOMA (Aarhus University Hospital) on a NextSeq500. For total RNA sequencing of HepG2 cells, library preparation and sequencing was performed at BGI (Copenhagen) using BGIseq.

treatment_protocol: Knockdown of SFPQ and NONO were carried out using transient transfections of siRNAs accordingly: For HEK293T, approximately 250.000 cells were plated in a 6-well dish and transfected with a final concentration of 22.5 nM siRNA using siLentFect Lipid Reagent (Bio-Rad) accordingly to manufacturer’s protocol. 48 hours post transfection, the cells were replenished with new media and re-transfected using Lipofectamine 2000 (Thermo Fisher Scientific). After additional 48 hrs, cells were harvested. For HepG2, approximately 400.000 cells were plated in a 6-well dish and reverse transfected with a final siRNA concentration of 50 nM using Lipofectamine RNAiMax (Thermo Fisher Scientific). 48 hrs post transfection, the cells were trypsinized before reverse transfected for the second hit using Lipofectamine 2000 (Thermo Fisher Scientific). After 48 hrs, the cells were harvested

value: Knockdown using siSFPQ2

tag: library kit

value: Prepared by BGI (Copenhagen)

tag: ribodepleted

value: Yes


title: Male naïve CysCKO rep 1

tag: strain

value: Spleen-derived


title: Muscle Vascular Anomaly, F349 B

description:
piece 2
IL4

tag: phenotype

tag: tissue

value: muscle


title: HepG2_siSFPQ1_rep2

source_name: Knockdown in HepG2 using siSFPQ1, rep2

value: Knockdown using siSFPQ1


title: Male naïve WT rep 3

tag: disease

value: naive

tag: Sex

value: wildtype


title: MDA-MB-231-shctrl-rep2

description: gene expression

tag: tumor


title: Muscle Vascular Anomaly, F349 A

description:
piece 1
IL2

tag: genotype


title: Male naïve WT rep 1

value: Male


title: Normal Adipose, ctrl fat M2

source_name: Normal Adipose

extract_protocol:
Lesions were disected, transferred to microcentrifuge tubes, snap frozen immediately in liquid nitrogen, and stored at -80C until RNA extraction.  QIAzol was was used to lyse tissues, which were then homogenized.  Qiagen RNeasy Lipid Tissue kit was used to isolate total RNA.
Illumina TruSeq unstranded poly-A selection kit (Cat# RS-122-2001) was used to make library from 1ug of RNA.

value: Normal Adipose

value: adipose


title: Normal Adipose, ctrl fat M602


title: SC_Control_2_RNA

tag: cell type

value: Primary Schwann Cells

tag: passage

value: Passage 3

value: control


title: HepG2_siSFPQ2_rep2

source_name: Knockdown in HepG2 using siSFPQ2, rep2

tag: treatment


title: HepG2_siSFPQ1_rep1

source_name: Knockdown in HepG2 using siSFPQ1, rep1


title: Muscle Vascular Anomaly, F347#2

description:
lesion 2
IL6


title: Normal Adipose, ctrl fat M5

value: SB Transposase; onc3


title: HepG2_siNONO1_rep2

source_name: Knockdown in HepG2 using siNONO1, rep2

value: Knockdown using siNONO1


title: DN-PC_Rep3

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

data_processing:
Reads were mapped on GRCm38/mm10 mouse reference genome and quantified using CLC Genomics Workbench version 12.0 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: Dominant negative form of p38α_BLM treatment

growth_protocol: Anesthesia: Anesthesia for mouse was induced by 3% isoflurane in air through a nose cone which was assisted by the mechanical ventilation (stroke volume 200 µl at 150 strokes/min), and mouse was kept on a heating pad with monitoring rectal temperature. After a tracheal intubation, anesthesia was maintained by 1.5% isoflurane in air with the mechanical ventilation. Operation: The neck skin of each mouse was cut longitudinally, and the trachea was exposed. A single intratracheal injection of BLM hydrochloride (3 mg/kg) dissolved in PBS using a repeating syringe dispenser (Hamilton). Then, the skin was sutured. As a sham operation, PBS was injected in substitution for BLM.

extract_protocol:
Tissue-derived total RNA was prepared according to the manufacturer’s protocol of ISOGEN plus (TAKARA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Eight days post operation, mouse was deeply anesthetized and intracardially infused with ice-cold PBS, and the left upper lobe was dissected out and placed on ice in the ISOGEN solution.

tag: strain background

tag: age

value: 3 months

value: male

value: Transgenic:human surfactant protein C promoter-driven M2 flag-p38alpha dominant negative

value: bleomycin-injected (BLM)

value: Lung


title: DN-PC_Rep2


title: smcKlf5-/--2808

city: Tangshan

first: Dong

last: Ma

state: Hebei

address: No. 21 Bohai Avenue, Caofeidian New Town, Tangshan, Hebei Province

department: School of public health

institute: North China University of Science and Technology

description: This sample is of AngII-induced smcKlf5-/- mouse abdominal aneurysm. It is the first of three smcKlf5-/-type biological replicates used in this experiment, each from separate mouse.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185),

source_name: smcKlf5-/- aortas 28 d AngII replicate 1

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

treatment_protocol: To generate an Ang II-induced AAA model, eight-week-old wild-type or smcKlf5-/- male mice were administered saline or Ang II (1000 ng/kg/min) via mini-osmotic pumps (Model 1004, Alzet, CA, USA) for 28 d to induce suprarenal aneurysms. After 28 d, all animals were anesthetized and perfused with cold 0.9% NaCl, and the abdominal arteries were harvested for analysis of total RNA extraction.

value: abdominal aorta

tag: gender

value: 8 weeks


title: HepG2_siNONO1_rep1

source_name: Knockdown in HepG2 using siNONO1, rep1

tag: cell line

value: Prepared by BGI (Copenhagen)

value: Yes


title: smcKlf5-/-2783


title: DN-PC_Rep1

tag: genotype/variation


title: Normal Adipose, ctrl fat F539


title: smcKlf5-/--2807


title: control-1974

description: This sample is of AngII-induced wild-type mouse abdominal aneurysm. It is the first of three wild-type biological replicates used in this experiment, each from separate mouse.

source_name: WT aortas 28 d AngII replicate 1

value: WT


title: Adipose Vascular Anomaly, M605 subQ

source_name: Adipose Vascular Anomaly

value: VEC-Cre;SB Transposase; onc3

value: Adipose Vascular Anomaly


title: HepG2_siCTRL1_rep2

source_name: Knockdown in HepG2 using siCTRL1, rep2

value: Knockdown using siCTRL1

tag: library kit


title: Hep.hu102516

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Alignment-independent quantification using Salmon
Genome_build: hg38
Supplementary_files_format_and_content: TPM as txt file

growth_protocol: Human hepatocytes and EpCAM+ biliary cells were isolated from cadaveric livers. Hepatocytes were transplanted into FRG/N mouse livers.

extract_protocol:
RNA was isolated by trizol based method.
RNA libraries were generated with Illumina HiSeq library prepare kit 2.0 following standard protocols.

treatment_protocol: Humanized livers were treated with 0.1% DDC for eight weeks, then human hepatocytes and human EpCAM+ samples were isolated and sequenced, along with the human biliary cells.

value: Hepatocyte


title: control-1699


title: Male naïve WT rep 2

value: Spleen-derived

value: naive

value: Male

value: wildtype


title: HepG2_siNONO2_rep2

source_name: Knockdown in HepG2 using siNONO2, rep2

value: Knockdown using siNONO2

tag: ribodepleted


title: Hep.huHC


title: Adipose Vascular Anomaly, M278 fat

tag: strain

value: adipose


title: HepG2_siNONO2_rep1

source_name: Knockdown in HepG2 using siNONO2, rep1


title: HepG2_siCTRL1_rep1

source_name: Knockdown in HepG2 using siCTRL1, rep1


title: HepG2_siCTRL2_rep2

source_name: Knockdown in HepG2 using siCTRL2, rep2

value: Knockdown using siCTRL2


title: Adipose Vascular Anomaly, M610 subQ

tag: phenotype


title: DN-NC_Rep2

source_name: Dominant negative form of p38α_control (Sham)

value: 3 months

value: male

value: Transgenic:human surfactant protein C promoter-driven M2 flag-p38alpha dominant negative

value: control (sham)

tag: tissue

value: Lung


title: Hep.HLV91712-HC


title: Adipose Vascular Anomaly, F578 subQ


title: CA-PC_Rep3

source_name: Constitutive active form of MKK6_BLM treatment

value: transgenic:human surfactant protein C promoter-driven 3HA-MKK6 constitutive active

value: bleomycin-injected (BLM)


title: DN-NC_Rep1


title: Rep.huDDC_Epplus44minus_526_b1t1

value: human hepatocytes reprogrammed into biliary cells


title: HepG2_siCTRL2_rep1

source_name: Knockdown in HepG2 using siCTRL2, rep1

value: Prepared by BGI (Copenhagen)

value: Yes


title: Adipose Vascular Anomaly, M566 arm subQ

value: VEC-Cre;SB Transposase; onc3

value: Adipose Vascular Anomaly


title: Hep.huHCQIE

value: Hepatocyte


title: CA-PC_Rep1


title: control-2576

value: abdominal aorta

value: 8 weeks

value: WT


title: DN-NC_Rep3


title: Rep.huDDC_Epplus44minus_714_b1t1


title: CA-PC_Rep2


title: Rep.huDDC_Epplus_317_b1t1


title: Adipose Vascular Anomaly, 18f fat

value: adipose


title: Rep.huDDC_Epplus_62_b1t1


title: Bil.KHH057-4A10posi

value: Biliary cell


title: Adipose Vascular Anomaly, M566 leg subQ


title: Adipose Vascular Anomaly, M580 lg subQ


title: Sgg_PD_caspase_2

city: Cambridge

first: Steve

last: Russell

address: Downing Street

department: Genetics

country: United Kingdom

institute: University of Cambridge

description: all

data_processing:
Fastq reads were aligned using tophat (v2.1.1) with Bowtie (version:  2.3.4.0) using the default parameters.
Gene counts tables across samples were created with Rsubread (1.22.3) using dmel_r6.20.gtf and options GTF.featureType="exon" and GTF.attrType="gene_id" and default parameters.
Read counts were imported into edgeR (3.14.0) and filtered using the filterByExpr function with the default parameters (10526 genes were retained).
The data was then normalised in limma (3.28.21) using limma-voom. Significant genes were identified fitting a linear model (lmFit) and empirical Bayes method (eBayes). Genes were considered significant differential expressed with fdr <= 0.05 and logFC >= |0.7|.
Genome_build: FlyBase dmel_r6.20
Supplementary_files_format_and_content: GeneCounts.txt is a tab delimited file containing the raw counts created by Rsubread per sample (columns) for each gene (row). The DSgg_RNAseq_limma-voom_result_master.txt file contains the filtered raw counts, normalised logCPM and the limma stats columns.

organism: Drosophila melanogaster

growth_protocol: 10-15hr embryos from a homozygous sggisoD-cI-DS-SFS and control sggisoD-DS-SFS  were collected and processed for RNA-seq .

extract_protocol:
Tissue was homogenised in 300 µL TRIzol with a motorised pellet pestle for 30 seconds. The sample volume was then increased to 1 mL, then 200 µL of Choloroform was added and vortexed. Samples were centrifuged at max speed for 15 minutes at room temperature and the upper phase transfered to a new 1.5 mL tube. The RNA was then precipitated with 0.8 volumes of Isopropanol and incubated at -20°C for 2 hours. The samples were then centrifuged at 4°C at maxmium speed for 30 minutes to pellet the RNA. The pellet was then washed with 1 mL 70% ethanol and centrifuged cold for another 5 minutes. After complete removal of the ethanol the RNA was dried for 5 minutes and re-supended in 20 µL DEPC-treated water. The concentration of the samples were measured using the Qubit RNA HS Assay Kit and sample quality assess with the Bioanalyzer and or 1% agarore gel.
Libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina. For each sample 100ng total RNA were processed with the NEBNext Poly(A) mRNA Magnetic Isolation Module. For all reactions half reactions/volumnes were used throughout the protocol, with exception for the AMPure bead cleanup step where washes were performed used the standard 200 µL 80% fresh Ethanol. Samples were barcoded and PCR amplification were performed for 12 cycles. After Bioanalyzer quality control equal amount of samples were pooled and submitted for Illumina single-end sequencing.

treatment_protocol: Embryos frozen in liquid nitrogen and stored at minus 80 degree Celsius untill processing

tag: fly stock

value: sggisoD-CI-DS-SFS

tag: developmental stage

value: embryos


title: CA-NC_Rep2

source_name: Constitutive active form of MKK6_control (Sham)

value: 3 months

tag: Sex

value: male

value: control (sham)


title: Hetero_M3

city: Daejeon

first: Sangrak

last: Jin

address: 291 Daehak-ro, Yuseong-gu

department: Department of Biological Science

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
CLC Genomics workbench 6.5 (CLC bio) was used for data trimming and read mapping.
Raw reads were mapped to PhiX control sequence (NCBI Genbank accession number : NC_001422) to eliminate the PhiX control reads with the following parameters; Mismatch cost : 2, Insertion cost : 3, Deletion cost : 3, Length fraction : 0.9, Similarity fraction 0.9, non-specific matches were randomly mapped.
After eliminating the Phix mapped reads, unmapped reads were trimmed with the following parameters; Ambiguous limit : 2, Quality limit : 0.05, Minimum number of nucleotides in reads : 15
After trimming low quality reads, remaining reads were aligned to the genome of C. autoethanogenum DSM 1006 obtained from NCBI (NC_022592.1) with the following parameters: mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.9, and similarity fraction = 0.9. Only uniquely mapped reads were retained.
The expression of the genes was normalized using the DESeq2 package in R.
Genome_build: NC_022592.1
Supplementary_files_format_and_content: RNA_seq_readcounts.txt

organism: Clostridium autoethanogenum DSM 10061

source_name: Whole cell from liquid culture

growth_protocol: Cells were cultivated anaerobically at 37 °C in 100 mL of PETC medium. Cells were grown heterotrophic (5 g/L of fructose and headspace pressure of 200 kPa under 100% N2 gas) or autotrophic (headspace pressure of 200 kPa under 80% H2 with 20% CO2 gas) or CdS-treatment (2 mM of CdS-NPs and headspace pressure of 200 kPa 100% CO2 gas under 100 intensity of 450 nm blue light LED).

extract_protocol:
The cultured microbes were sampled at 44 h (mid-exponential) by centrifugation immediately at 6000 g at 4 °C for 10 min. The pellets were resuspended by the 500 mL of lysis buffer (20 mM Tris-HCl pH 7.4, 140 mM NaCl, 5 mM MgCl2, and 20% of Triton X-100) and were rapidly frozen in liquid nitrogen, followed by grinding the frozen cells using a mortar and pestle. Total RNA was then isolated using TRIzol reagent (Thermo Scientific).
To remove fragmented DNA in the isolated RNA samples, rDNase I (Ambion) was treated to RNA samples for 30 min at 37 °C. Ribosomal RNAs (rRNAs) were eliminated through the Ribo-ZeroTM rRNA Removal Kit for Meta-bacteria (Epicentre). The RNA-Seq libraries were constructed from rRNA depleted RNA samples using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and then sequenced by a 100-bp single-end sequencing recipe in an Illumina Hi-Seq 2500 instrument (Rapid-Run mode).

tag: sampling time

value: Mid-exponential phase_48h

tag: culture condition

value: PETC_media(pH5.5) treated with 5 g/L of fructose


title: CA-NC_Rep3

value: transgenic:human surfactant protein C promoter-driven 3HA-MKK6 constitutive active

value: Lung


title: Sgg_PD_caspase_1

description: all


title: Hetero_M2


title: Bil.KHH034_4A10nega

tag: cell type


title: CA-NC_Rep1

tag: treatment


title: Sgg_PD_WT_3

description: all

value: sggisoD-DS-SFS


title: Sgg_PD_caspase_3

description: all


title: WT-PC_Rep3

source_name: Wild-type_BLM treatment

tag: strain background

value: wild type

value: bleomycin-injected (BLM)


title: Bil.KHH034_4A10posi


title: Hetero_M1


title: Sgg_PD_WT_2

description: all

tag: age


title: Bil.KHH029-4A10posi


title: WT-PC_Rep2


title: H2M3

value: Mid-exponential phase_44h

value: PETC_media(pH5.5) charged H2/CO2 (80:20)


title: Bil.KHH029-4A10nega


title: H2M2


title: Sgg_PD_WT_1

description: all


title: Bil.KHH028-4A10nega


title: H2M1


title: WT-PC_Rep1


title: WT-NC_Rep3

source_name: Wild-type_control (Sham)


title: Bil.KHH028-4A10posi


title: CLM3

value: PETC_media(pH5.5) treated with 20 mg of CdS


title: WT-NC_Rep1


title: E. verrucosus, 1.5 degrees C, sample 2

description:
lat_long:
51° 54’11.67”N, 105° 4’7.61”E
Pooled sample of 3 individuals of E. verrucosus were acclimated at 6 degrees C for 14 days, gradually cooled down to 1.5 °C at a rate of 1-1.5 °C/d over about 6 days. Afterwards animals were kept at 1.5 degrees C for 1 month.

organism: Eulimnogammarus verrucosus

source_name: whole body

value: whole body

value: rocky littoral zone

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village

tag: depth

value: adult

tag: condition

value: 1.5 degree C


title: Bil.1915-4D9

value: Biliary cell


title: Bil.1919-4D9


title: E. verrucosus, 1.5 degrees C, sample 1


title: CLM1


title: WT-NC_Rep2

value: 3 months

value: male

tag: genotype/variation

value: control (sham)


title: E. verrucosus, 1.5 degrees C, sample 4


title: CLM2


title: E. verrucosus, 12 degrees C, sample 3

description:
lat_long:
51° 54’11.67”N, 105° 4’7.61”E
Pooled sample of 3 individuals of E. verrucosus were acclimated at 6 degrees C for 14 days, then the temperature was gradually increased to 12 °C by 1-1.5 °C/day over about 6 days, and animals were kept at 12 degrees C for 1 month.

value: 12 degree C


title: IFI16-/- A549-12h rep2

city: Bei jing

first: zhimin

last: jiang

address: No.2 Yuanmingyuan West Road, Haidian District, Beijing

department: college of Veterinary medicine

institute: China agriculture university

data_processing:
raw data of fastq format were firstly processed through in-house perl scripts.
index of the reference genome was built using bowtie v2.0.6 and paired-end reads were aligned to the reference genome using topHat v2.0.12.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: All expression excel file includes FPKM values of every sample

source_name: IFI16 knockout A549 cells

extract_protocol:
these cells were collected and the total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: we infected IFI16+/+ and IFI16-/- A549 cells with PR8 virus at an MOI of 1 for 0h or 12h.

value: lung

tag: cell line

value: A549 cells

tag: genotype

value: IFI16 knockout

tag: infection

value: the cells were inoculated with PR8/H1N1 virus at an MOI of 1 for 12 hours


title: IFI16-/- A549-12h rep1


title: E. verrucosus, 12 degrees C, sample 2


title: E. verrucosus, 12 degrees C, sample 4


title: Caudate Nucleus [SI32C]

city: Davis

first: Smita

last: Iyer

address: county rd 98 & hutchison, ccm room 2075

department: Center for Immunology and Infectious Disease

institute: University of California-Davis

description:
SI32C
44032
3′-Tag-Seq
counts_all.out

data_processing:
The raw read data was filtered using HTStream (version 1.3.1) which included screening for contaminants (such as PhiX and rRNA), quality-based trimming, and adapter trimming. (https://github.com/s4hts/HTStream)
STAR (version 2.7.3a) was used to align the processed data to the rhesus genome (Mmul_10). Dobin, Alexander, et al. "STAR: ultrafast universal RNA-seq aligner." Bioinformatics 29.1 (2013): 15-21.
MultiQC (custom version) was then used for read and alignment quality assessment. https://github.com/s4hts/MultiQC
Differential expression analyses were conducted using the limma-voom Bioconductor pipeline, using edgeR version 3.30.3 and limma version 3.44.3 in R 4.0.1  The model used in limma included effects for brain region, infection status, and their interaction, and standard errors of log fold changes were adjusted for within-animal correlations.
Genome_build: Mmul_10
Supplementary_files_format_and_content: counts_all.out.txt: Table of normalized counts per gene.
Supplementary_files_format_and_content: Comparison between tissue types and characteristics.

organism: Macaca mulatta

source_name: Brain Tissue

extract_protocol:
Different parts of brain tissues were collected from perfused animals. Collected cells were flash frozen in RLT buffer and extracted using the Qiagen mini lipid RNA isolation kit according to manufacturer's instructions.
The libraries were constructed following the 3' TagSeq protocol using Lexogen kit (QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina). 500ng of total RNA was used as input.

value: Caudate Nucleus

tag: gender

value: Female

value: SHIV infected- Perfused


title: PFC A46 (w) [SI32P]

description:
SI32P
44032
3′-Tag-Seq
counts_all.out

tag: tissue

value: PFC A46 (w)


title: E. verrucosus, 1.5 degrees C, sample 3

value: whole body

value: rocky littoral zone


title: IFI16+/+ A549-12h rep2

source_name: wildtype A549 cells

value: wildtype


title: IRI F PTs rep 2 [2_tub_IR_F]

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

description:
processed data file:
tub.IR.M_vs_F.txt
tub.IR_vs_SHAM.F.txt
2-2

data_processing:
Reads quantified against transcripts from the GENCODE vM19 assembly using salmon v0.13.1 (flags --gcBias --validateMappings)
Fold change analsyis performed using DESeq2
Transcript quantification data read using the tximport library. Count matrix filtered to retain only genes with 5+ reads in at least two samples.
Separate DESeqDataSet objects constructed for endothelial and proximal tubule cells. Technical replicates for sample 9_tub_SHAM_M combined using collapseReplicates(). Calculation of size factors and differential expression using the model '~condition' where condition is the combination of AKI or No Injury plus sex
Fold changes calculated between IRI and uninjured for Male and Female animals, and between male and female animals in uninjured and IRI conditions using the lfcShrink() function with the 'apeglm' method.
pvalue and padj recalculated without outlier detection (call to results() with cooksCutoff=F), and substituted for pvalue and padj calculated with lfcShrink. Values of pvalue and padj from lfcShrink added to results as pvalue.cooks and padj.cooks respectively
Genome_build: GRCm38
Supplementary_files_format_and_content: Salmon transcript quantification: tab-delimited text
Supplementary_files_format_and_content: DESeq2 differential expression results: tab-delimited text

extract_protocol:
RNA was isolated from PTs or renal endothelial cells from 3 male and 3 female mice in each experimental group, using the RNeasy Plus Micro Kit (Qiagen Inc., Toronto, Ontario, Canada). RNA quality was assessed using the Fragment Analyzer (Advanced Analytical Technologies, Inc., Ames, LA, USA). Only RNA with RQN scores of >7 was selected for further analysis
Library construction was performed with the NEB Next Ultra II RNA Library Prep Kit for Illumina using the polyA mRNA workflow (New England Biolabs Ltd., Ipswich, MA, USA). For each sample, 20 ng of total RNA was used as input for the library preparation. Following library construction, the samples were pooled to minimize potential sequencing bias and run on NextSeq 500 (Illumina, San Diego, CA, USA). A total of six 75 cycle high output flow cells were run to achieve approximately 40 million reads per sample.

treatment_protocol: Endothelial an proximal tubular cells were isolated from kidneys after enzymatic digestion, CD31+ microbeads were used to obtain endothelial cells and proximal tubular cell were collected by microdissection.

tag: strain

value: FVB

value: Acute Kidney injury

value: kidney

value: Proximal tubular cells


title: IFI16+/+ A549-12h rep1


title: PFC A46 (w) [SI04P]

description:
SI04P
44104
3′-Tag-Seq
counts_all.out


title: E. verrucosus, 12 degrees C, sample 1

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village

value: adult


title: IFI16-/- A549-0h rep2

value: lung

value: the cells were inoculated with PR8/H1N1 virus at an MOI of 1 for 0 hour


title: Caudate Nucleus [SI04C]

description:
SI04C
44104
3′-Tag-Seq
counts_all.out


title: Hippocampus [SI04H]

description:
SI04H
44104
3′-Tag-Seq
counts_all.out

value: Hippocampus


title: IFI16-/- A549-0h rep1

value: A549 cells

value: IFI16 knockout


title: E. cyaneus, 1.5 degrees C, sample 3

description:
lat_long:
51° 54’11.67”N, 105° 4’7.61”E
Pooled sample of approx. 13 individuals of E. cyaneus were acclimated at 6 degrees C for 14 days, gradually cooled down to 1.5 °C at a rate of 1-1.5 °C/d over about 6 days. Afterwards animals were kept at 1.5 degrees C for 1 month.

organism: Eulimnogammarus cyaneus

value: 1.5 degree C


title: IFI16+/+ A549-0h rep2


title: E. cyaneus, 1.5 degrees C, sample 1


title: Bil.1930-4D9

value: Biliary cell


title: Superior Temporal Sulcus [SI04S]

description:
SI04S
44104
3′-Tag-Seq
counts_all.out

value: Superior Temporal Sulcus

value: Female

value: SHIV infected- Perfused


title: IRI F PTs rep 3 [8_tub_IR_F]

description:
processed data file:
tub.IR.M_vs_F.txt
tub.IR_vs_SHAM.F.txt
8-2


title: Hippocampus [SI32H]

description:
SI32H
44032
3′-Tag-Seq
counts_all.out


title: E. cyaneus, 12 degrees C, sample 4

description:
lat_long:
51° 54’11.67”N, 105° 4’7.61”E
Pooled sample of approx. 13 individuals of E. cyaneus were acclimated at 6 degrees C for 14 days, then the temperature was gradually increased to 12 °C by 1-1.5 °C/day over about 6 days, and animals were kept at 12 degrees C for 1 month.

value: whole body

value: rocky littoral zone

value: 12 degree C


title: PFC A46 (w) [SI64P]

description:
SI64P
44164
3′-Tag-Seq
counts_all.out

value: PFC A46 (w)


title: IFI16+/+ A549-0h rep1

value: wildtype


title: E. cyaneus, 12 degrees C, sample 3

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village


title: patient3, chidamide, BMMCs, CE1706020269LR01

city: Shanghai

first: Yifeng

last: Sun

institute: Zhongshan Hospital, Fudan University

description: CE1706020269LR01 is the RNA sample of bone marrow mononuclear cells (BMMCs) of patient3 which was cultured in 6μM chidamide for 24 hours.

data_processing:
After removing the adapter sequences and reads with poor quality by Trim Galore (v0.5.0, www.bioinformatics.babraham.ac.uk/projects/trim_galore), the qualified reads were mapped to the reference genome (hg19) and the expression level of genes were measured by RSEM (v1.3.1) with the reference annotation file obtained from Ensemble GRCh37.
The expression level of genes was calculated in the form of Fragments per Kilobase of transcript per Million Mapped Reads (FPKM). Genes whose expression level was not detected in all samples (FPKM<1) were excluded in the following analysis.
Differentially expressed genes (DEGs) were defined as genes with fold change >2 or <0.5 and Benjamini and Hochberg (BH) adjusted p-value < 0.05.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files; counts, FPKM values were determined using custom scripts.

source_name: bone marrow mononuclear cells

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and contaminant DNA was removed by the RNase-Free DNase Set (Qiagen). RNA integrity was verified with the Agilent 2100 Bioanalyzer automated electrophoresis system (Agilent Technologies). mRNA was isolated using the Poly(A) mRNA Magnetic Isolation Module (NEB).
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: BMMCs derived from three initial MM patients were culture in 10% FBS 1640 medium for 24h treated with DMSO or 6μM chidamide.

tag: individual

value: bone marrow mononuclear cells (BMMCs)

value: 6μM chidamide for 24 hours


title: Superior Temporal Sulcus [SI32S]

description:
SI32S
44032
3′-Tag-Seq
counts_all.out


title: E. cyaneus, 1.5 degrees C, sample 4

value: adult


title: IRI F PTs rep 1 [1_tub_IR_F]

description:
processed data file:
tub.IR.M_vs_F.txt
tub.IR_vs_SHAM.F.txt
1-2

value: FVB

tag: Sex

value: Acute Kidney injury

value: kidney

value: Proximal tubular cells


title: Caudate Nucleus [SI64C]

description:
SI64C
44164
3′-Tag-Seq
counts_all.out

value: Caudate Nucleus


title: Sham F PTs rep 3 [13_tub_SHAM_F]

description:
processed data file:
tub.SHAM.M_vs_F.txt
tub.IR_vs_SHAM.F.txt
13-2

value: No injury


title: patient3, DMSO, BMMCs, CE1706020268LR01

description: CE1706020268LR01 is the RNA sample of bone marrow mononuclear cells (BMMCs) of patient3 which was cultured in DMSO for 24 hours.

value: DMSO for 24 hours


title: Sham F PTs rep 2 [11_tub_SHAM_F]

description:
processed data file:
tub.SHAM.M_vs_F.txt
tub.IR_vs_SHAM.F.txt
11-2

value: Female


title: Hippocampus [SI64H]

description:
SI64H
44164
3′-Tag-Seq
counts_all.out

value: Hippocampus

value: SHIV infected- Perfused


title: E. cyaneus, 12 degrees C, sample 1

value: whole body

value: rocky littoral zone

value: 12 degree C


title: E. cyaneus, 1.5 degrees C, sample 2

value: Russia:Irkutsk region, Lake Baikal, Bolshie Koty village

value: 1.5 degree C


title: Sham F PTs rep 1 [10_tub_SHAM_F]

description:
processed data file:
tub.SHAM.M_vs_F.txt
tub.IR_vs_SHAM.F.txt
10-2


title: patient2, chidamide, BMMCs, CE1706020267LR01

description: CE1706020267LR01 is the RNA sample of bone marrow mononuclear cells (BMMCs) of patient2 which was cultured in 6μM chidamide for 24 hours.

value: bone marrow mononuclear cells (BMMCs)

value: 6μM chidamide for 24 hours


title: GDC-R_Input

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

data_processing:
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using bowtie2 with defautl parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated by bedGraphToBigWig, and peaks were called by Macs2

source_name: prostate

growth_protocol: Cells were maintained at 37°C and 5% CO2 in RPMI 1640 containing 10% fetal bovine serum (FBS) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).FGF-2 (NS expansion medium).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: PC-3-control and PC-3-GDC-R cells were treated with DMSO, or iCBP112, or SAHA for 24 hours

value: prostate cancer

tag: passages

tag: chip antibody


title: Caudate Nucleus [SI88C]

description:
SI88C
44288
3′-Tag-Seq
counts_all.out

value: Control- Perfused


title: control_Input

tag: cell type


title: patient1, DMSO, BMMCs, CE1706020264LR01

description: CE1706020264LR01 is the RNA sample of bone marrow mononuclear cells (BMMCs) of patient1 which was cultured in DMSO for 24 hours.

tag: treatment


title: patient2, DMSO, BMMCs, CE1706020266LR01

description: CE1706020266LR01 is the RNA sample of bone marrow mononuclear cells (BMMCs) of patient2 which was cultured in DMSO for 24 hours.


title: E. cyaneus, 12 degrees C, sample 2

value: adult


title: patient1, chidamide, BMMCs, CE1706020265LR01

description: CE1706020265LR01 is the RNA sample of bone marrow mononuclear cells (BMMCs) of patient1 which was cultured in 6μM chidamide for 24 hours.


title: GDC-R_SAHA_BRD4_rep2

value: Rabbit monoclonal anti-BRD4 Abcam ab128874


title: GDC-R_SAHA_BRD4_rep1


title: H929 cells, CHI, input

data_processing:
The raw sequencing reads from ChIP-seq were aligned to human reference genome (UCSC GRCh37, hg19) using Bowtie 2.
Peak calling was performed using MACS2 (version 2.1.1) using the following settings: B --nomodel --SPMR -g hs --extsize 147. The resulting normalized (per million reads) bedgraph files were converted to bigWig files using bdg2bw.
Normalized read density (RPKM) was calculated from pooled replicates using bamCoverage function in Deeptools
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: The number of fragments in each bin is stored in a bigWig file.

source_name: H929 cells

growth_protocol: CON:H929 cell line treated with DMSO for 24h; CHI:H929 cell line treated with 6μM chidamide for 24h

extract_protocol: Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cross-linked chromatin was sheared by sonication and immunoprecipitated with indicated antibodies. DNA was purified by phenol/chloroform extraction and ethanol precipitation.

value: H929 cells

value: 6μM chidamide for 24h


title: Superior Temporal Sulcus [SI88S]

description:
SI88S
44288
3′-Tag-Seq
counts_all.out

value: Superior Temporal Sulcus


title: IRI F endo rep 3 [8_endo_IR_F]

description:
processed data file:
endo.IR.M_vs_F.txt
endo.IR_vs_SHAM.F.txt
8-1

value: FVB

value: Female

value: Acute Kidney injury

value: kidney

value: endothelial cells


title: H929 cells, CHI, IP

value: Anti-Histone H3 (acetyl K27) antibody, AbCam, Cat# ab4729


title: Superior Temporal Sulcus [SI64S]

description:
SI64S
44164
3′-Tag-Seq
counts_all.out

value: SHIV infected- Perfused


title: GDC-R_iCBP_BRD4_rep2


title: H929 cells, CON, input

value: DMSO for 24h


title: IRI F endo rep 1 [1_endo_IR_F]

description:
processed data file:
endo.IR.M_vs_F.txt
endo.IR_vs_SHAM.F.txt
1-1


title: GDC-R_iCBP_BRD4_rep1


title: PFC A46 (w) [SI03P]

description:
SI03P
44003
3′-Tag-Seq
counts_all.out

value: PFC A46 (w)


title: H929 cells, CON, IP


title: GDC-R_vehicle_BRD4_rep2


title: PFC A46 (w) [SI88P]

description:
SI88P
44288
3′-Tag-Seq
counts_all.out


title: Superior Temporal Sulcus [SI03S]

description:
SI03S
44003
3′-Tag-Seq
counts_all.out


title: Caudate Nucleus [SI03C]

description:
SI03C
44003
3′-Tag-Seq
counts_all.out

value: Caudate Nucleus


title: GDC-R_vehicle_BRD4_rep1

value: prostate cancer


title: PFC A46 (w) [SI21P]

description:
SI21P
45821
3′-Tag-Seq
counts_all.out

value: Control- Perfused


title: control_vehicle_BRD4_rep2


title: Hippocampus [SI03H]

description:
SI03H
44003
3′-Tag-Seq
counts_all.out

value: Hippocampus


title: MLL4 Q4092X/wt (C6) 8h ATRi [C6_8H_S10]

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

data_processing:
Sequenced reads quality was assessed using fastQC
Reads were trimmed using Trimmomatic v0.39.
Reads were aligned to the human genome (GRCh38/hg38) using STAR v2.71a.
reads per Kilobase per Megabase of library size (RPKM)  were calculated using HOMER v4.10 with the command analyzeRepeats.pl rna hg38 -count 3utr  -rpkm -condenseGenes
Rpkm normalized bigwig files created using DeepTools3.1.2.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: rpkm-normalized reads per sample are presented in the bigwig-format. RPKM for each gene in all samples are presented in a .txt file.

source_name: MLL4 Q4092X/wt (C6) 8h ATRi

growth_protocol: hTERT-immortalized human mesenchymal stem cells (iMSCs) were cultured at 37°C and 5% CO2 in 1:1 DMEM/F-12 medium (Gibco #11320-074) supplemented with 10% Fetal Bovine Serum (Euroclone #ECS0180L). iMSCs expressing Cas9WT were generated by transducing iMSCs with lentiviral vector generated using the plasmid pCW-Cas9WT (Addgene # 50661). Transduced cells were selected with 1μg/ml of puromycin. The expression of sgRNAs were obtained by transducing iMSCs-Cas9WT with lentiviral vectors generated using the plasmid pLX-sgRNA (Addgene #50662). Transduced cells were selected with 2μg/ml of blasticidin.

extract_protocol:
Wild type and MLL4 Q4092X MSCs  were extracted collected by centrifuging cell cultures, either untreated or at 8 and 24 hours after ATR inhibition. Cellular pellets were resuspended with TRIzol (Thermo Fisher cat. #15596026Ambion #15596018), and total RNA was extracted according to the manufacturer’s instructions. Contaminating genomic DNA was removed by DNase (Qiagen cat. #79254) digestion. RNA quality and concentration were assed with the 2100 Bioanalyzer (Agilent cat. #G2939BA) and the Qubit fluorometer (Thermo Fisher cat. # Q33226), respectively.
3’-RNA-seq libraries were prepared by using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen cat. #015.24) and starting from 500 ng of total RNA. Libraries were sequenced as single reads of 50 bp with the Illumina HiSeq2500.

treatment_protocol: Prior to harvest, cells were treated with 0.2 μM ATR inhibitor for 8 and 2 hours or left untreated, respectively.

value: 8 hour ATRi treatment


title: MLL4 Q4092X/wt (C6) 24h ATRi [C6_24H_S11]

source_name: MLL4 Q4092X/wt (C6) 24h ATRi

value: hTERT-immortalized human mesenchymal stem cells (iMSCs)

value: 24 hour ATRi treatment


title: Hippocampus [SI21H]

description:
SI21H
45821
3′-Tag-Seq
counts_all.out


title: IRI F endo rep 2 [2_endo_IR_F]

description:
processed data file:
endo.IR.M_vs_F.txt
endo.IR_vs_SHAM.F.txt
2-1


title: MLL4 Q4092X /wt (C6) 8h ATRi [C6_8H_S9]

source_name: MLL4 Q4092X /wt (C6) 8h ATRi


title: MLL4 Q4092X/wt (C6) untreated [C6_UT_S8]

source_name: MLL4 Q4092X/wt (C6) untreated

value: untreated


title: Hippocampus [SI88H]

description:
SI88H
44288
3′-Tag-Seq
counts_all.out


title: MLL4 Q4092X/wt (C6) untreated [C6_UT_S7]


title: PFC A46 (w) [SI61P]

description:
SI61P
43361
3′-Tag-Seq
counts_all.out

value: Male


title: Sham F endo rep 1 [10_endo_SHAM_F]

description:
processed data file:
endo.SHAM.M_vs_F.txt
endo.IR_vs_SHAM.F.txt
10-1

value: FVB

value: Female

value: No injury


title: GDC-R_SAHA_H3K27ac_rep1

value: Rabbit polyclonal anti-Histone H3K27-ac Abcam ab4729


title: Sham F endo rep 2 [11_endo_SHAM_F]

description:
processed data file:
endo.SHAM.M_vs_F.txt
endo.IR_vs_SHAM.F.txt
11-1

treatment_protocol: Endothelial and proximal tubular cells were isolated from kidneys after enzymatic digestion, CD31+ microbeads were used to obtain endothelial cells and proximal tubular cells were collected by microdissection.

value: kidney

value: endothelial cells


title: GDC-R_SAHA_H3K27ac_rep2


title: GDC-R_iCBP_H3K27ac_rep1


title: GDC-R_iCBP_H3K27ac_rep2


title: Caudate Nucleus [SI61C]

description:
SI61C
43361
3′-Tag-Seq
counts_all.out


title: wildtype 24h ATRi [WT_24H_S5]

source_name: wildtype 24h ATRi

value: wildtype


title: wildtype 24h ATRi [WT_24H_S6]


title: wildtype 8h ATRi [WT_8H_S3]

source_name: wildtype 8h ATRi


title: GDC-R_vehicle_H3K27ac_rep2


title: wildtype untreated [WT_UT_S2]

source_name: wildtype untreated


title: wildtype untreated [WT_UT_S1]


title: Superior Temporal Sulcus [SI61S]

description:
SI61S
43361
3′-Tag-Seq
counts_all.out

value: Superior Temporal Sulcus


title: wildtype 8h ATRi [WT_8H_S4]


title: GDC-R_vehicle_H3K27ac_rep1


title: PC-3_GDC-R_Rep3

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Reads aligned to human reference genome (hg19) using Tophat (v2.0.6) with default parameters
Raw count and RPKM were calcualted using RSeQC (v2.3.6) on hg19.refseq.bed12
Genome_build: hg19
Supplementary_files_format_and_content: xls file for raw count and FPKM

growth_protocol: Cells were maintained at 37°C and 5% CO2 in RPMI 1640 containing 10% fetal bovine serum (FBS) and 1% antibiotic/antimycotic (Thermo Fisher Scientific).

extract_protocol:
RNAs were extracted using RNeasy Mini Kit.
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.

treatment_protocol: PC-3-GDC-R cells were maintained by continuous treatment of GDC-0068. Control cells PC-3-control were generated in parallel by treating cells with vehicle (DMSO).

value: continuous treatment of GDC-0068


title: PC-3_GDC-R_Rep2

value: prostate cancer


title: PC-3_GDC-R_Rep1


title: control_vehicle_H3K27ac_rep2


title: control_vehicle_H3K27ac_rep1


title: PC-3_control_Rep3

value: control


title: PC-3_control_Rep1


title: A549 cells processed with SNARE-seq2 protocol (RNAseq)

city: La Jolla

first: Kun

last: Zhang

address: 9500 Gilman Dr Mailcode: 0412

department: Bioengineering

institute: University of California, San Diego

data_processing:
Library strategy: SNARE-seq2
R1/R2 reads and R1/R2/R3 reads.  For R1/R2/R3 reads: R1 = biological, R2 = technical, R3 = biological. R2 contains cellular barcodes sequences.
Deindexer was used to demultiplex reads according to sample barcodes from first round of barcoding for both ATAC and RNA libraries
snaptools 1.4.8 and Minimap2 2.11-r797 to map ATAC libraries
STAR-2.5.1b to map RNA libraries
dropest 0.8.6 to generate RNA count matrices and dropestr to filter cells
ArchR 0.9.4 to generate peak calls and cell by peak matrices
Genome_build: hg38/mm10
Supplementary_files_format_and_content: gz compressed tar archive of features-barcodes matrix

source_name: A549 cells

growth_protocol: GM12878 cell line was grown in RPMI-1640 culture medium supplemented with 15% FBS and 2 mM L-glutamine at 37 ºC in a 5% CO2 humidified incubator. A549 cell line was grown in F-12K medium supplemented with 10% FBS at 37 ºC in a 5% CO2 humidified incubator.  NIH/3T3 was grown in Dulbecco’s Modified Eagle’s Medium supplemented with 10% FBS at 37 ºC in a 5% CO2 humidified incubator.

extract_protocol: 1-3 M cells were spun down at 300 g for 5 min at 4C and then washed twice with chilled 1x PBS. Cells were resuspended in 1.2 mL of 1x PBS with RNase Inhibitors (0.04 U/uL SUPERase In RNase Inhibitor, 0.04 U/uL Enzymatics RNase Inhibitors) and filtered through 30 uM CELLTRICS strainers. GM12878 nuclei were extracted from cells with ATAC lysis buffer with 0.1% NP-40 resuspended in 1x PBS with RNase Inhibitors then fixed with 1% formaldehyde. 3T3/A549/GM12878 cells without nuclei extraction were fixed by adding 3 mL of 1.33% formaldehyde and mixed by pipetting followed by incubation on ice for 10 min. GM12878 cells were pelleted at 500 g for 5 min at 4C then resuspended in a resuspension buffer (10 mM Tris-HCl, 10 mM sodium chloride, 3 mM magnesium chloride, 0.04 U/uL SUPERase In RNase Inhibitor, 0.04 U/uL Enzymatics RNase Inhibitors, 0.1% wt/vol BSA) and permeabilized with lysis buffer (10 mM Tris-HCl, 10 mM sodium chloride, 3 mM magnesium chloride, 0.04 U/uL SUPERase In RNase Inhibitor, 0.04 U/uL Enzymatics RNase Inhibitors, 0.1% wt/vol BSA, 0.1% v/v NP-40) for 3 min on ice. 3T3/A549 cells were frozen after fixation in 1x PBS with 10% (v/v) DMSO and 0.1% (wt/vol) BSA for three weeks then washed and permeabilized as described for fresh GM12878 cells. Post permeabilization (or fixation in the case of nuclei), sample were processed using SNARE-seq2 starting from tagmentation step.

treatment_protocol: 3T3 cells amd A549 cells were fixed with 1% formaldehyde and cryopreserved in 1x PBS with 10% (vol/vol) DMSO and 0.1% (wt/vol) BSA for three weeks. GM12878 cells were freshly fixed with 1% formaldeyhyde and ran in two separate experiments. GM12878 nuclei were lysed in cell lysis buffer with RNase Inhibitors (10 mM Tris pH 7.4, 10 mM sodium chloride, 3 mM magnesium chloride, 0.1% v/v NP-40, Superase RNase Inhibitors, Enzymatics RNase Inhibitors) then fixed with 1% formaldehyde. Fixed samples were processed with SNARE-seq2 protocol.

value: A549 cells

value: fixed and cryopreserved for 3 weeks


title: A549 cells processed with SNARE-seq2 protocol (ATACseq)


title: Caudate Nucleus [SI21C]

description:
SI21C
45821
3′-Tag-Seq
counts_all.out

value: Caudate Nucleus

value: Control- Perfused


title: PC-3_control_Rep2


title: Hippocampus [SI61H]

description:
SI61H
43361
3′-Tag-Seq
counts_all.out

value: Hippocampus


title: OP_MM565 replicate 2

status: Public on Sep 08 2020

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
[read trimming / clipping]  cutdapt
[read mapping]  READemption 0.3.5
[gene quantification ]  READemption 0.3.5
[coverage calcutation]  READemption 0.3.5
[differential gene expression analysis]  DESeq2 1.6.3
Genome_build: NC_003901.1
Supplementary_files_format_and_content: Gene-wise read quantifications and nucleotide wise read coverages

organism: Methanosarcina mazei Go1

source_name: cell culture

growth_protocol: Cells of M. mazei vector control strain and MM565 overproducing strain were grown under optimal growth conditions (with puromycin in the media) and harvested at mid exponential growth phase

extract_protocol:
RNA isolation was performed using TRI reagent following the manufacturer´s protocol followed by DNaseI treatment and phenol-chloroform precipitation
cDNA libraries for Illumina sequencing  were constructed by vertis Biotechnologie AG, Germany (http://www.vertis‐biotech.com/) as described previously for eukaryotic microRNA (Berezikov et al., 2006) but omitting the RNA size‐fractionation step prior to cDNA synthesis. In brief, equal amounts of RNA samples were poly(A)‐tailed using poly(A) polymerase. Then, the 5'PPP structures were removed using tobacco acid pyrophosphatase (TAP). Afterwards, an RNA adapter was ligated to the 5 ́‐phosphate of the RNA. First‐strand cDNA was synthesis by an oligo(dT)‐adapter primer and the M‐MLV reverse transcriptase. In a PCR‐based amplification step using a high fidelity DNA polymerase the cDNA concentration was increased to 20‐30 ng/μl. A library‐specific barcode for multiplex sequencing was part of a 3'‐sequencing adapter.

value: MM565 overproduction


title: OP_MM565 replicate 1


title: MLL4 Q4092X/wt (C6) 24h ATRi [C6_24H_S12]

value: hTERT-immortalized human mesenchymal stem cells (iMSCs)

value: 24 hour ATRi treatment


title: pWM321 replicate 1


title: pWM321 replicate 2


title: Tissue associated B cells

city: St Louis

first: Luigi

last: Adamo

state: Missouri

address: 660 South Euclid Ave

department: Internal Medicine - Cardiovascular Division

institute: Washington University In St Louis

data_processing:
Generation of fastq files via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Alignment to mm10 genome build via https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Heart,Blood,Lung,Liver

extract_protocol:
Heart, blood, lung, and liver were isolated from the same mice. B cells were isolated by flow sorting using a FACS Aria-II Cell Sorter. Doublets and dead cells were excluded. Flow-sorted B cells from each tissue/organ were all labelled with Hashtag-C antibodies. Blood was labelled with Hashtag-C #1, lung with Hashtag-C #2, liver with Hashtag-C #3, heart with Hashtag-C #4. Blood, heart, lung and liver were submitted to the same digestion protocol and B cells were sorted on the same day.
10x Genomcis Chromium single cell preparation

value: 10 weeks old

value: Male


title: Superior Temporal Sulcus [SI21S]

description:
SI21S
45821
3′-Tag-Seq
counts_all.out

value: Female


title: MBAB-Mouse_15_days-CD21-Cd23-CD11b

source_name: B cells flow-sorted from the heart

extract_protocol:
Myocardial-associated B cells were isolated by flow sorting using a FACS Aria-II Cell Sorter. Doublets and dead cells were excluded. Neonatal and adult samples were submitted to the same digestion protocol and B cells were sorted on the same day.
10x Genomcis Chromium single cell preparation

value: 2 weeks old

value: pooled male and female

value: cardiac B cells


title: MBAB-Mouse_8_weeks-CD21-Cd23-CD11b

value: 8 weeks old

value: male


title: WT_PGC (whs v17)

city: Tianjin

first: wang

middle: hua

last: song

address: Tianjin city, China

institute: nankai university

description: WT_PGC-VS-T2KO_PGC.PossionDis_Method.GeneDiffExp.txt

data_processing:
we analysed the raw data of fq.gz files by Hisat2,samtools  and featurecounts to get the raw counts.
Genome_build: mm10
Supplementary_files_format_and_content: The reads counts of 133 samples, containg young WT, young Tet2-/-, old WT and old Tet2-/-, and some of Tet1 samples.

source_name: Primordial germ cell

extract_protocol:
For oocyte sequence, we obtained 133 ovulated oocytes; for PGC sequence, we purified E13.5 PGC from 4-6 embryos each group
oocyte library were prepared using standard  Illumina protocols; PGC library were prepared according to micro RNA construction

value: wild type

value: Purified PGC from E13.5


title: Aortic_isograft_4wk 4

city: London

first: Jiacheng

last: Deng

address: James Black Centre, 125 Coldharbour Lane

institute: King's College London

data_processing:
Data were processed following standard protocols using Cell Ranger version 3.1.0.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting,  UMI counting, and to generate  feature-barcode matices.
Genome_build: mm10
Supplementary_files_format_and_content: H5 files includes tdTomato-labeled c-Kit lineage cells from 2-week and 4-week aortic isografts.

source_name: Aortic isograft

extract_protocol:
Aortic isografts were harvested from the mice. Adventitial layer of the grafts was first dissected from the medial and neointimal layers. After three times washes of PBS, grafts were cut into fine pieces and digested in digestion solutions (which consist of 1 mg/ml papain, 0.5 mg/ml 1,4-Dithioerythritol, 0.156 mg/ml Taurine; 0.25 mg/ml bovine serum albumin in PBS) at 37 °C with reciprocal shaking for a total 40 min. Detached cells were then collected through a 40 μm cell strainer and suspended in DMEM with 10% FBS. Cells were further stained with LIVE/DEAD ™ Fixable Near-IR Dead Cell Stain Kit and Hoechst 33342 for 20 mins. After PBS washing, cells were resuspended in PBS and single nucleated live cells (Hoechst+/Dead Cell Stain-) were sorted into PBS with 0.04% BSA using a Flow Cytometer. Cells were then analyzed on a 10x Chromium instrument using Chromium Single Cell 3' Reagent Kit v3 chemistry (10X Genomics), following a standard protocol.
Library was generated and sequenced on a NovaSeq platform (Illumina) with paired-end 150 bp (PE 150) sequencing strategy.

value: BALB/c

value: Aortic isograft

tag: time point


title: H1cTKO;Vav-iCre  CD8+ splenocyte, Rep.1

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

data_processing:
Sequencing and base calling was performed by NYU Center for Health Informatics and Bioinformatics (https://genome.med.nyu.edu). The sequencing libraries were multiplexed and clustered on a flowcell. After clustering, the flowcell were loaded on the Illumina Novaseq 6000 according to manufacturer’s instructions.  The samples were sequenced using a 2x51 Paired End (PE) configuration.  Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq instrument.  Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and de-multiplexed using Illumina bcl2fastq v. 2.17 program. One mis-match was allowed for index sequence identification.
Hi-C reads from separate lines were concatenated and aligned to mm10 and processed with HiC-Pro (v.2.11.3-beta) using default parameters and genomic bin sizes of 25 and 100 kb.
Replicates were pooled to for A/B compartment analysis with CscoreTool (v. 1.1; https://doi.org/10.1093/bioinformatics/btx802). This program was compiled from https://github.com/scoutzxb/CscoreTool, and Cscores of 100 kb bins were calculated from the intrachromosomal contact matrices.
Genome_build: mm10 (GENCODE Release M20 (GRCm38.p6))
Supplementary_files_format_and_content: HiC-Pro-generated contact matrix and associated genome bed file at 25 kb and 100 kb resolution; Cscore bedGraph track at 25 and 100 kb resolution showing A/B chromatin compartments.

source_name: CD8+ splenic T cells

extract_protocol:
Splenocytes from two pairs of wildtype and two pairs of H1cTKO;Vav-iCre mice were pooled and T cells were isolated by affinity column depletion. 1.7-2.0 x106 CD8+ T cells were further purified by flow cytometry. Cells were subjected to crosslinking at a concentration of 1x106 cells/mL in PBS, 10% FBS, 2% formaldehyde (final concentration) at room temperature for 10 minutes, before the reaction was quenched by adding 2.5M glycine to a final concentration of 0.2M and the cells were pelleted and flash frozen.
Libraries were prepared using the Arima-HiC+ kit (Arima Genomics) according to the manufaturer’s protocol, and subjected to sequencing.

value: spleen

value: CD8+ T cells

value: M


title: H1cTKO;Vav-iCre  CD8+ splenocyte, Rep.2

value: F


title: WT CD8+ splenocyte, Rep.2

value: WT


title: WT CD8+ splenocyte, Rep.1


title: Aortic_isograft_4wk 3


title: 08_2_AF_9689: KBM5 the combination

city: Saga

first: Kazuharu

last: Kamachi

department: Hematology and Oncology

institute: Saga university

hyb_protocol: According to the manufacturer’s instructions.

data_processing: Using GeneSpring GX (Agilent Technologies, Inc., CA). Normalized to expression of housekeeping gene controls using GeneSpring GX (Agilent Technologies, Inc., CA). Gene expression levels between samples were compared and expressed as -fold changes.

label: biotin

source_name: KBM5, OR21 nM, IM 1000nM

growth_protocol: K562 and KBM5 cells were maintained in RPMI-1640 medium (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% foetal bovine serum (FBS, Sigma-Aldrich, St. Louis, MO, USA).

extract_protocol: Total RNA was isolated using a Direct-zol RNA MiniPrep kit (Zymo Research, Orange, CA).

treatment_protocol: K562 and KBM5 cells were pre-treated with OR21 100nM for 3 consecutive days, then followed by IM 1000nM treatment. Total RNA of each treated cells in each cell line was extracted 24 hours after IM exposure and gene expressions were compared among 4 groups; control (no exposure), OR21, IM, and the combination.

value: chronic myeloid leukemia (CML)

value: OR21 nM, IM 1000nM


title: 07_2_AF_9689: KBM5 IM

scan_protocol: According to the manufacturer’s instructions.

source_name: KBM5, IM 1000nM

value: IM 1000nM


title: 05_2_AF_9689: KBM5 control

source_name: KBM5, No treatment

label_protocol: According to the manufacturer’s instructions.

value: No treatment


title: 06_2_AF_9689: KBM5 OR21

source_name: KBM5, OR21 100nM


title: Aortic_isograft_4wk 1


title: 03_2_AF_9689: K562 IM


title: 01_1_AF_9689: K562 control

source_name: K562, No treatment


title: Aortic_isograft_2wk 3


title: Aortic_isograft_2wk 4


title: 02_2_AF_9689: K562 OR21


title: Aortic_isograft_2wk 2


title: 04_2_AF_9689: K562 the combination


title: Aortic_isograft_2wk 1


title: NICHE_VC

city: Nanjing

first: Shentong

last: Fang

address: Longmian Avenue

institute: China Pharmaceutical University

data_processing:
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
We used the Seurat R package (v3.1) for QC, filtering and analysis of the aggregated data (Butler et al. Nature Biotechnology 2018)
Cells were filtered based on the number of genes and the percentage of mitochondrial genes.
For further analysis, Seurat R package was used.
Genome_build: mm10

molecule: polyA RNA

source_name: bone marrow LepR+ cells and Ecs

extract_protocol:
the mice were injected intravenously with VE-Cadherin A647 (BioLegend, CA). WBM plug was obtained by flushing tibias and digestion with Collagenase I (Worthington Biochemical Corporation, NJ), Dispase II (Roche Applied Science, Swizerland) and DNase I (Sigma-Aldrich) in HBSS with calcium and magnesium. The digested marrow was pooled with staining buffer (HBSS +2% FBS +2mM EDTA) to stop the enzymatic reaction. The red cell-depleted WBM cells were stained with antibodies against CD45 eFluor 450, Ter119 eFluor 450, and biotinylated LepR (1:100, R&D Systems, CA) on ice for 30 minutes followed by streptavidin PE-Cy5 on ice for 15 minutes.
use the Chromium Single-Cell 3′RNA-sequencing system (10x Genomics, Pleasanton, CA) with the Reagent Kit v3.1 according to the manufacturer’s instructions
Sample libraries were sequenced on the Illumina NovaSeq 6000 system using S2 flow cell (Illumina)

treatment_protocol: For sample 1-3, mice received tamoxifen via gavage.

value: bone marrow

value: Cdh5CreERT2;Vegfc flox/flox


title: NRS neutrophils

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

description: NRS treated

data_processing:
Cell Ranger Single Cell Software Suite was used to perform sample de-multiplexing, barcode processing, and single cell gene counting (Alignment, Barcoding and UMI Count) at the University of Michigan Biomedical Core Facilities DNA Sequencing Core
Genome_build: GRCh38
Supplementary_files_format_and_content: Seurat R package was used to perform unsupervised clustering and identification of cell-type specific markers. Used only  cells with > 500 genes and < 20% mitochondrial read content.

source_name: NRS treated

extract_protocol:
Eyes were dissected, and the vitreous fluid was collected
Retinas were rinsed with 200 ul of PBS and cells collected from rinse. Neutrophils were purified by MACS Ly6G bead purification. Cell purity and viability was confirmed by flow cytometry.
The cDNA libraries were constructed using the 10x ChromiumTM Single cell 3’ Library Kit according to the manufacturer’s original protocol.
Libraries were sequenced on an Illumina Novaseq paired-end kits using the following read length: 26bp Read1 for cell barcode and UMI, 8bp I7 index for sample index and 98bp Read2 for transcript.

value: vitreous fluid

value: Ly6G+ cells


title: Mono2_PM_32_2

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to mouse genome release mm10 using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: TSV text file containing FPKM for all samples and genes

source_name: Lung tissue

growth_protocol: Alveolar macrophages and monocytes were flow sorted from FA and PM2.5 exposed mice

extract_protocol:
RNA was extracted using RNeasy Micro Kit from Qiagen
SMART-Seq Stranded mRNA Library Kit (Takara)

value: lung

value: Monocyte

value: PM


title: Mono2_PM_32_0


title: Mono2_PM_32_1


title: Mono2_FA_32_2

value: FA


title: T2KO_PGC (whs v17)

tag: age

value: Tet2 knock out

value: Purified PGC from E13.5


title: Mono2_FA_32_1


title: Aortic_isograft_4wk 2

value: BALB/c

value: Aortic isograft

value: wild type


title: MF2_FA_32_1

value: Macrophage


title: Mono_FA_4_0


title: Mono_PM_4_1


title: Mono1_FA_32_1


title: Mono1_FA_32_2


title: NICHE_WT

value: WT


title: Mono_FA_4_2


title: Mono_FA_4_1


title: Mono2_FA_32_0


title: Mono1_PM_32_2


title: Mono1_FA_32_0


title: Mono1_PM_32_0


title: NICHE_FLOX

value: Vegfc flox/flox


title: MF2_PM_32_1


title: Mono1_PM_32_1


title: MF2_PM_32_0


title: MF1_PM_32_2


title: MF1_PM_32_0


title: MF2_FA_32_0


title: MF1_FA_32_2


title: MF1_FA_32_0


title: MF_PM_4_2


title: MF_PM_4_1


title: Mono_PM_4_0


title: Mono_PM_4_2


title: MF2_PM_32_2


title: MF_FA_4_1


title: MF1_PM_32_1


title: MF_FA_4_2


title: MF_PM_4_0


title: Aortic_graft_4wk

data_processing:
Data were processed following standard protocols using Cell Ranger version 2.2.0.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting,  UMI counting, and to generate  feature-barcode matices.
Genome_build: mm10
Supplementary_files_format_and_content: H5 files for cells from 2-week and 4-week mouse aortic grafts

source_name: Aortic graft

extract_protocol:
Aortic grafts were harvested from the mice. Adventitial layer of the grafts was first dissected from the medial and neointimal layers. After three times washes of PBS, grafts were cut into fine pieces and digested in digestion solutions (which consist of 1 mg/ml papain, 0.5 mg/ml 1,4-Dithioerythritol, 0.156 mg/ml Taurine; 0.25 mg/ml bovine serum albumin in PBS) at 37 °C with reciprocal shaking for a total 40 min. Detached cells were then collected through a 40 μm cell strainer and suspended in DMEM with 10% FBS. Cells were further stained with LIVE/DEAD ™ Fixable Near-IR Dead Cell Stain Kit and Hoechst 33342 for 20 mins. After PBS washing, cells were resuspended in PBS and single nucleated live cells (Hoechst+/Dead Cell Stain-) were sorted into PBS with 0.04% BSA using a Flow Cytometer. Cells were then analyzed on a 10x Chromium instrument using Chromium Single Cell 3' Reagent Kit v2 chemistry (10X Genomics), following a standard protocol.
Library was generated and sequenced on a NovaSeq platform (Illumina) with paired-end 150 bp (PE 150) sequencing strategy.
single-cell RNA seq

value: Aortic graft

value: wildtype


title: Aortic_graft_2wk


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H9_ad004

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: CP

value: male


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H9_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H9_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H9_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H9_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H9_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H8_ad002


title: MF_FA_4_0


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H8_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H8_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H8_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H7_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H8_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H7_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H9_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H8_ad006


title: MF1_FA_32_1


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H7_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H7_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H7_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H7_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H6_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H6_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H7_ad001


title: MF2_FA_32_2


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H5_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H6_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H5_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H5_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H4_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H4_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H4_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H4_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H4_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H4_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H2_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H2_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H4_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H2_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H12_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H12_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H12_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H5_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H12_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H5_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H12_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H7_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H11_ad006


title: control_vehicle_BRD4_rep1

source_name: prostate

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: prostate cancer

value: Rabbit monoclonal anti-BRD4 Abcam ab128874


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H11_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H12_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H2_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H4_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H10_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H2_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H11_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H10_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H2_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H10_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H1_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H10_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H1_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H1_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H1_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H1_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H1_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G9_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G9_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H1_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G9_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G9_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G9_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H10_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G9_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G8_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G9_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G8_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G8_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H10_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G7_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H10_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G8_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G8_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H10_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G8_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G7_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G7_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G7_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G6_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G7_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G7_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G7_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_H1_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G6_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G6_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G6_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G6_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G5_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G5_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G5_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G6_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G5_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G5_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G5_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G4_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G4_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G4_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G3_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G4_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G4_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G3_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G4_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G3_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G3_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G3_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G2_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G2_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G3_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G2_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G2_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G2_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G12_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G12_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G12_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G12_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G12_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G4_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G11_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G11_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G11_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G11_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G10_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G10_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G10_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G11_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G11_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G3_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G1_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G1_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G5_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G1_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G10_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F9_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G1_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G2_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F9_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F9_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F9_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F8_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F8_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F8_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F7_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F7_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F7_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_G1_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F7_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F8_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F6_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F6_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F6_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F6_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F5_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F5_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F5_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F6_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F5_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F5_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F7_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F5_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F6_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F9_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F4_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F4_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F4_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F4_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F4_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F7_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F3_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F3_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F3_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F3_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F3_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F3_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F2_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F2_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F2_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F12_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F2_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F2_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F12_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F5_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F12_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F12_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F12_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F11_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F4_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F11_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F11_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F11_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F11_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F10_ad007


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F10_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F10_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F10_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F10_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F2_ad001


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F10_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F1_ad012


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F12_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F1_ad002


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F11_ad006


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F1_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_F1_ad004


title: CEMBA180910_5J_3_CEMBA180910_5J_4_E9_ad010


title: CEMBA180910_5J_3_CEMBA180910_5J_4_E9_ad008


title: CEMBA180910_5J_3_CEMBA180910_5J_4_E9_ad001


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