title: C12

city: Philadelphia

first: Yijing

last: Su

state: PA

address: Levy 326

department: Department of Oral Medicine

institute: University of Pennsylvania

data_processing:
Basecalls performed using BCL2fastq
Read 1 contains the biological read.
Read 2 contains the UMI and barcode: 1-10 UMI, 11-18 Round3; 49-56 round2; 87-94 round1 for barcodes.
RNAseq reads were aligned to the hg38 genome assembly using STAR 2.5
Data processing was preprocessed using Drop-seq-1.13
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: day150 organoid in single cell level

growth_protocol: Generation of forebrain organoids from iPSCs was performed as previously described (Qian et al., 2018; Qian et al., 2016). First, iPSC colonies were detached with Collagenase Type IV 7 days after passage and washed with fresh stem cell medium in a 15 ml conical tube. On Day 0, detached iPSC colonies were transferred to an ultra-Low attachment 6-well plate (Corning Costar), containing 3 ml of stem cell medium (without FGF-2), plus 2 µM Dorsomorphine and 2 µM A83-01. On Day 5 and Day 6, half of the medium was replaced with induction medium consisting of DMEM:F12, 1X N2 Supplement, 1X Penicillin/Streptomycin, 1X Non-essential Amino Acids, 1X GlutaMax, 1 µM CHIR99021, and 1 µM SB-431542. On Day 7, organoids were embedded in Matrigel and cultured in the induction medium for 7 more days. On Day 14, embedded organoids were mechanically dissociated from Matrigel by manual pipetting in a 5 ml pipette tip. Typically, 20 organoids were transferred to each well of a 12-well spinning bioreactor (SpinΩ) (Qian et al., 2016) containing differentiation medium consisting of DMEM:F12, 1X N2 and B27 Supplements, 1X Penicillin/Streptomycin, 1X 2-Mercaptoenthanol, 1X Non-essential Amino Acids, 2.5 µg/ml human Insulin. From Day 35 to Day 70, extracellular matrix (ECM) proteins was supplemented in differentiation medium by dissolving Matrigel at 1% (v/v). At Day 70, differentiation medium was exchanged with maturation medium consisting of Neurobasal medium, 1X B27 Supplement, 1X Penicillin/Streptomycin, 1X 2-Mercaptoenthanol, 0.2 mM Ascorbic Acid, 20 ng/ml BDNF, 20 ng/ml GDNF, and 1 µM cAMP. Detailed step-by-step procedures for generating forebrain organoids, building SpinΩ bioreactor and required 3D printing files can be found in reference (Qian et al., 2018). For comparison between unsliced forebrain organoids with SNOs over long-term culture, forebrain organoids were transferred to ultra-Low attachment 6-well plate placed on a CO2 resistant orbital shaker (ThermoFisher) rotating at 120 rpm in the incubator after Day 45.

extract_protocol:
Tissue were minced with a razor blade and homogenized using a tissue grinder in a 1 ml of HB buffer (1 mM DTT), 0.15 mM spermine, 0.5 mM spermidine, EDTA-free protease inhibitor, 0.3% IGEPAL-630, 0.25 M sucrose, 25 mM MgCl2, 20 mM Tricine-KOH) for 5 to 10 strokes, then filtered through a 40 mm strainer, underlayer with a cushion buffer (0.5 mM MgCl2, 0.5 mM DTT, EDTA-free protease inhibitor, 0.88 M sucrose) and centrifuged at 2800g for 10 minutes in a swinging bucket centrifuge at 4 ºC. Nuclei were collected as pellets. Nuclei were then centrifuged for 3 mins at 500g at 4 ˚C. The pellet was resuspended in 1 ml of cold PBS-RI (1x PBS + 0.05U/μl RNase Inhibitor). The nuclei were passed through a 40 μm strainer. 3 ml of cold 1.33% formaldehyde solution was then added to 1 ml of cells. Nuclei were fixed for 10 mins before adding 160 μl of 5% Triton X-100. Nuclei were then permeabilized for 3 mins and centrifuged at 500g for 3 mins at 4 ˚C. Nuclei were resuspended in 500 μl of PBS-RI before adding 500 μl of cold 100 mM Tris-HCl pH 8. Then, nuclei were spun down at 500g for 3 mins at 4 ˚C and resuspended in 300 μl of cold 0.5 X PBS-RI. Finally, nuclei were again passed through a 40 μm strainer and then counted on a hemocytometer, diluted to 1,000,000 cells/ml.
mRNA from single nuclei were tagged 3 rounds with barcoded primers, with in-cell ligations using T4 DNA ligase. Plates were incubated for 30 mins at 37 ºC with gentle sharking (50 rpm) to allow hybridization and ligation to occur. The ligation products were purified with Dynabeads MyOne Streptavidin C1 beads. After washing beads once with 10 mM Tris and 0.1% Tween-20 solution and once with water, beads were resuspended into a solution containing 110 μl of 2X Kapa HiFi HotStart Master Mix, 8.8 μl of 10 μM stocks of primers BC_0062 and BC_0108, and 92.4 μl of water. PCR thermocycling was performed as follows: 95 °C for 3 mins, then five cycles at 98 °C for 20 seconds, 65 °C for 45 seconds, 72 °C for 3 mins. After these five cycles, Dynabeads beads were removed from PCR solution and EvaGreen dye was added at a 1X concentration. Samples were again placed in a qPCR machine with the following thermocycling conditions: 95 °C for 3 mins, cycling at 98 °C for 20 seconds, 65 °C for 20 seconds, and then 72 °C for 3 mins, followed by a single 5 mins at 72 °C after cycling. Once the qPCR signal began to plateau, reactions were removed.
PCR reactions were purified using a 0.8X ratio of KAPA Pure Beads and cDNA concentration was measured using a qubit. For tagmentation, a Nextera XT Library Prep Kit was used. 600 pg of purified cDNA was diluted in water to a total volume of 5 μl. 10 μl of Nextera TD buffer and 5 μl of Amplicon Tagment enzyme were added to bring the total volume to 20 μl. After mixing by pipetting, the solution was incubated at 55°C for 5 mins. A volume of 5 μl of neutralization buffer was added and the solution was mixed before incubation at room temperature for another 5 minutes. PCR was then performed with the following cycling conditions: 95 °C for 30 seconds, followed by 12 cycles of 95 °C for 10 seconds, 55 °C for 30 seconds, 72 °C for 30 seconds, and 72 °C for 5 mins after the 12 cycles. 40 μl of this PCR reaction was removed and purified with a 0.7X ratio of SPRI beads to generate an Illumina-compatible sequencing library.

treatment_protocol: Forebrain organoid at Day 45 were collected from SpinΩ bioreactor using a cut P1000 pipette tip and immersed in melted 3% low melting point agarose dissolved in DMEM:F12 kept at 37 °C in a custom cubic mold of 1.5 cm sides. Typically, up to 10 organoids were embedded in one agarose block. Before the agarose solidify, multiple organoids were spread evenly and arranged in the same horizontal plane, with minimal spacing of 1 mm in between. The agarose blocks were placed on ice for 5-10 mins to solidify. Slicing was performed using a Leica VT 1200S vibratome in ice-cold DMEM:F12 medium at 0.1 mm/s speed and 1 mm vibration amplitude. 500 µm-thick sections from the middle of an organoid were collected, while sections from the top and bottom ends were discarded. The organoid sections were transferred to 6-well plate with differentiation medium supplemented with 1% Matrigel (v/v), left to equilibrate for 1 hr in stationary culture and placed on a CO2 resistant orbital shaker rotating at 120 rpm in the incubator. After Day 70, the medium was switched to maturation medium and organoids can be maintained for up to a year with medium change every 2 days. Repeated slicing was performed every 4 weeks after initial slicing to prevent disk-shaped SNOs from growing back to spherical or oval shape. During embedding, SNOs were carefully oriented in the agarose mold to ensure that the x-y horizontal plane is parallel to the previous slicing plane, and when necessary, the positions and orientation of SNOs were adjusted under a stereo microscope (Zeiss Discovery V8). After slicing, only one 500 µm-thick section in the middle were collected and cultured following the procedures described above. After Day 35, the time schedule for SNO cultures was followed with a flexibility range of ± 3 days. SNOs were collected using a cut P1000 pipette tip when used for analyses on the indicated age (± 3 days).

value: fore brain organoid

tag: passages


title: S54_Healthy donor 3

status: Public on Mar 05 2020

type: SRA

city: Cambridge

first: Ce

last: Gao

state: MA

address: 400 Technology Square

country: USA

institute: Ragon Institute of MGH, MIT and Harvard

library_source: transcriptomic

data_processing:
FASTQ files were obtained by Illumina demultiplexing pipeline.
STAR and RSEM were used to align to HG38 and to calculate the raw counts for genes, respectively.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts and TPM in csv

molecule: total RNA

organism: Homo sapiens

source_name: healthy donor_Uninfected_24h_pDC

growth_protocol: patient 1-6 without any treatment.for in vitro experiment.the cells were cultured in RPMI with 10% FBS medium.

extract_protocol:
Total RNA was extracted from the 7 cell populations using a commercial PicoPure RNA Isolation Kit
RNA-Seq libraries were generated as described in a previous study. Briefly, whole transcriptome amplification (WTA) and tagmentation-based library preparation was performed using SMART-seq2, followed by sequencing with a 75-cycle kit on a NextSeq 500 instrument (Illumina, CA). The quantification of transcript abundance was conducted using RSEM software (v1.2.22) supported by the STAR aligner software (STAR_2.4.2a). The raw reads were aligned to the Hg38 human genome database and the ZIKV sequence (ZIKV strain PRVABC59, GenBank: KU501215.1).

treatment_protocol: there is no treatment for patient 1-6; and for in vitro experiment, the cells were infected with ZIKV at MOI=1 for either 24h or 48h

tag: subject id

value: Healthy donor 3

tag: infection status

value: Uninfected

tag: tissue

value: peripheral blood

tag: time point

tag: environment

value: in vitro

tag: cell subtype

value: pDC


title: S53_Healthy donor 3

source_name: healthy donor_Uninfected_48h_pDC


title: Liver, C57BL6/J, Control Water + 20% Glucose, 6h (JC038)

city: Bronx

first: Jeffrey

middle: E

last: Pessin

state: NY

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

description:
group 12, rep 2
JC038a

data_processing:
Illumina Casava was used for basecalling.
Raw reads were filtered by removing read which:  (1) contained adaptors; (2) contained N > 10% (N represents base that could not be determined); and (3) The Qscore (Quality value) of over 50% bases of the read was <= 5.
STAR v2.5 was used to align clean data to mm10 reference genome with parameter mismatch = 2
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. Then FPKM of each gene was calculated.
Differential expression analysis between two conditions/groups was performed using the DESeq2 R package (2_1.6.3).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: csv files including raw counts, FPKM values for each sample, and FPKM values for each group

organism: Mus musculus

source_name: Liver

extract_protocol:
Completely dissolve approximately 5mg of frozen liver tissue powder in 500 uL of Trizol reagent at room temperature; Add 100uL of chloroform to the Trizol-liver mixture and incubate the mixture at RT for 2 min; Spin down at 12krpm for 15 minutes at 4°C; Isolate the top layer (aqueous) and mix it with 100% ethanol at 1:1 ratio and load the mixture to the RNeasy mini column from the Qiagen kit (catalogue No. 74106); Thereafter follow the protocol part 1 step 3 from the same kit to finish the extraction of total RNA.
Standard Illumina protocol using NEBNext Library Prep Kit for Illumina
Illumina NovaSeq 6000 paired with an S4 flowcell

treatment_protocol: Mice at 8 weeks of age were purchased and trained for 1 week for regulated fasting (from 10 pm to 7 pm) and feeding of regular chow (10 % of calories from fat and 64.5% of calories from carbohydrates) (from 7 pm to 10 pm). On the day of the experiment, mice were fasted from 10 pm the day before to 7 pm on the day of the experiment. They were deprived of water from 4 pm to 7 pm only on the day of the experiment. At 7 pm, they were provided with regular chow and water with or without 20% of glucose or sucrose or fructose. Mice were sacrificed at 7 pm as controls and 3, 6 or 12 hours following feeding.

tag: strain

tag: gender

value: male

tag: age

value: 8 weeks

tag: genotype

value: wild type

tag: treatment (drink)

value: Control Water + 20% Glucose

tag: time (feed duration)


title: Low_51

city: New York

first: Saghi

last: Ghaffari

address: One Gustave L. Levy Place, Box 1496

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Single end sequencing were carried out using Illumina HighSeq 4000
fastq file was generated using Illumina's bcl2fastq v2.17.1.14 with 1 mismatch barcode
Alignment was done using Star v2.5.2b to mm10

source_name: Hematopoietic Stem Cells

extract_protocol:
FACS sorted cells in 35% suspension reagent at 600 cells/µL were loaded into the 5-10 μm Fluidigm IFC and visually inspected to confirm one cell per capture site at 20X with a fluorescent microscope. Debris, multiple cells, and dead cells (Calcein negative) were excluded for subsequent library preparation.
Single cell cDNA libraries were generated from FACS-purified MMP-low and -high HSCs with the SMART-Seq v4 Ultra Low Input RNA kit, the Fluidigm C1 system and the Nextera XT library preparation kit (Illumina) following the manufactures’ protocols. The captured cells were then subjected to cDNA synthesis on the C1 system and quantified the next day using the Quant-iT Picogreen dsDNA Assay kit. cDNA was tagmented, amplified, pooled, and cleaned up with the Nextera XT kit. Single-cell cDNA libraries were then quantified with the Bioanalyzer (Agilent) and subjected to sequencing on the Illumina High-Seq. 254 single-cell cDNA libraries were multiplexed over 3 lanes (~84 samples/lane) with 100 nt single-end sequencing.

tag: flow purified

tag: fluidigm c1 platform

value: single cell


title: S52_Healthy donor 3

source_name: healthy donor_ZIKV Infected_24h_pDC

value: ZIKV Infected


title: imb_koenig_2018_12_sutandy_RNAseq_U2AF65mut_03_control_03

city: Mainz

first: Stefanie

last: Ebersberger

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

data_processing:
RNA sequencing (RNA-seq) libraries were sequenced on Illumina NextSeq500 (160-nt single-end), yielding 44.4-49.6 million reads per sample. Many reads show adapter pieces at the 3’ end, which need to be trimmed, Thus, reads were trimmed at the 3’ end to a total length of 100bp since downstream splicing analysis requires reads of equal length rather than individually adapter trimmed reads. Sequencing qualities were checked using FastQC (version 0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). All reads were mapped to the human genome (assembly version hg38/GRCh38) and its annotation (GENCODE release 25) (Harrow et al., 2012) with the splice-aware aliger STAR (version 2.5.4b) (Dobin et al., 2013) with up to 4% allowed mismatches and an overhang of at most 159 base pairs at each splice junction. Reads were sorted using SAMtools (version 1.5) (Li et al., 2009). Uniquely mapped reads were summarized per gene using featureCounts from the subread package (version 1.5.1) (Liao et al., 2014).
Genome_build: hg38

source_name: control replicate 3

extract_protocol:
Hela was lysed in 1ml lysis buffer followed by immunoprecipitation as described on previously published protocol (Huppertz et al., 2014; Sutandy et al., 2016)
in vivo iCLIP libraries were prepared from HeLa cells under U2AF65 KD and wild-type conditions according to the previously published protocol (Huppertz et al., 2014; Sutandy et al., 2016). For immunoprecipitation, we used 7.5 µg monoclonal anti-U2AF65 antibody produced in mouse (Sigma cat. no. U4758) per sample. Each iCLIP library was done in triplicates. The libraries were sequenced as single-end reads on an Illumina HiSeq 2500 and NextSeq 500 sequencing system.

tag: cell line

value: Hela

tag: technique

value: RNA-Seq

tag: barcode

value: ACTTGA


title: 170406_p1_a3

city: Solna

first: Leonard

last: Hartmanis

address: Solnavägen 9

department: Cell & Molecular Biology

country: Sweden

institute: Karolinska Institutet

data_processing:
raw sequencing data was converted to fastq files using Bcl2fastq (version 2.20)
reads were mapped against the reference genome (mm10) using STAR (version 2.4.2a)
gene expression levels were quantified using rpkmforgees (Ramsköld 2019)
Genome_build: mm10
Supplementary_files_format_and_content: Expression matrix gene-/sample-wise for raw counts

extract_protocol:
Electrophysiological properties were recorded by patch clamping. The cytosols of the cells were extracted and transferred into lysis buffer and converted to cDNA libraries for sequencing.
Patch-seq (Cadwell 2016)

tag: brain region

value: brain


title: 170406_p1_a1


title: Liver, BALB/c, Control Water + 20% Fructose, 3h (JC036)

description:
group 10, rep 2
JC036a

value: BALB/c

value: Control Water + 20% Fructose


title: Liver, BALB/c, Control Water + 20% Sucrose, 3h (JC035)

description:
group 9, rep 2
JC035a

value: Control Water + 20% Sucrose


title: Low_75


title: S50_Healthy donor 2

tag: subject id

value: Healthy donor 2

tag: infection status

value: Uninfected


title: S51_Healthy donor 3

source_name: healthy donor_ZIKV Infected_48h_pDC

value: Healthy donor 3

tag: tissue

value: peripheral blood

tag: time point

value: in vitro


title: 170406_p1_a2


title: Liver, C57BL6/J, Control Water + 20% Sucrose, 6h (JC039)

description:
group 13, rep 2
JC039

value: male

value: 8 weeks


title: S49_Healthy donor 2

tag: environment

tag: cell subtype

value: pDC


title: Low_59

value: single cell

tag: strain


title: S48_Healthy donor 2

value: ZIKV Infected


title: Liver, BALB/c, Control Water, 3h (JC033)

description:
group 7, rep 2
JC033

tag: gender

tag: age

value: wild type

value: Control Water


title: Liver, BALB/c, Control Water + 20% Glucose, 3h (JC034)

description:
group 8, rep 2
JC034a

tag: genotype

tag: treatment (drink)

value: Control Water + 20% Glucose


title: Low_11

tag: flow purified


title: Low_19

tag: fluidigm c1 platform


title: Liver, C57BL6/J, Control Water, 6h (JC037)

description:
group 11, rep 2
JC037a

tag: time (feed duration)


title: S47_Healthy donor 2


title: Low_43


title: Low_3


title: Low_35


title: Low_27


title: Liver, C57BL6/J, Control Water + 20% Glucose, 3h (JC030)

description:
group 4, rep 2
JC030a


title: Liver, C57BL6/J, Control Water + 20% Sucrose, 3h (JC031)

description:
group 5, rep 2
JC031


title: S45_Healthy donor 1

value: Healthy donor 1


title: Liver, C57BL6/J, Control Water, 3h (JC029)

description:
group 3, rep 2
JC029a


title: Low_74


title: Liver, BALB/c, Control Water, 0h (JC028)

description:
group 2, rep 2
JC028

value: BALB/c


title: S43_Healthy donor 1


title: Low_58


title: non-PCOS granulosa cells C007

type: RNA

city: Guangzhou

first: Yudong

last: Liu

state: Guangdong

address: NO.1838 GuangZhou Northern Road

department: Center for Reproductive Medicine, Department of Gynecology and Obstetrics

country: China

institute: Nanfang Hospital, Southern Medical University

description: About 30,586 LncRNAs and 26,109 coding transcripts can be detected by the LncRNA microarray. The LncRNAs are carefully constructed using the most highly-respected public transcriptome databases (Refseq, UCSC knowngenes, Gencode, etc), as well as landmark publications. Each transcript is represented by a specific exon or splice junction probe which can identify individual transcript accurately. Positive probes for housekeeping genes and negative probes are also printed onto the array for hybridization quality control.

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

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: ovary of woman with normal ovarian reserve

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a mixture of oligo(dT) and random primers (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: The granulosa cells were isolated and prepared from follicular aspirates after the removal of oocytes. The samples were then centrifuged at 400 × g for 10 min to separate the fluid from cells. The cell pellets were resuspended in phosphate-buffered saline (PBS; Hyclone), layered on 50% Percoll density gradient media (GE Healthcare, USA) and then centrifuged at 400 × g for 20 min to remove maximum red blood cells. The granulosa cells at the interface were collected and contaminating erythrocytes were removed completely by erythrocyte lysis buffer (Sigma, placed in an ice bath at 4℃ for 15min). At last, granulosa cells were washed with PBS.

treatment_protocol: Subjects included 7 infertile women with PCOS, and 7 infertile women with tubal blockage who served as controls in this study. The diagnosis of PCOS was based on the 2003 Rotterdam criteria. The antagonist protocol for controlled ovarian hyperstimulation (COH)  was used. Briefly, COH was performed on Day 2 of withdrawal bleeding with recombinant FSH (rFSH; Gonal F, Merck Serono, Modugno, Italy) or highly purified FSH (HP-FSH; Lishenbao, Livzon, Guangdong, China). The dosages of gonadotrophins were individualized according to according to age, body mass index (BMI), antral follicle count (AFC) and previous ovarian response. Cetrorelix (Cetrotide, Merck Serono, Halle, Germany) of 0.25 mg per day was initiated when at least one of the following criteria was reached: (i) the presence of at least one follicle measuring ≥14 mm, (ii) serum E2 ≥600 pg/ml or (iii) serum LH level ≥10 IU/l (Lainas et al., 2010) and was continued until and including the day of trigger. When at least three follicles reached 17 mm or two follicles reached 18 mm in diameter, individualized dosages of triptorelin (Diphereline, IPSEN, Signes, France) and HCG(Libao Biochemistry Co, Zhuhai, China) were administered for triggering final oocyte maturation and the follicles were aspirated 34 to 36 hours later. Follicular fluid was sampled by transvaginal ultrasoundguided puncture and aspiration of follicles ≥10 mm in diameter.

value: 27 years


title: Liver, C57BL6/J, Control Water, 0h (JC027)

description:
group 1, rep 2
JC027a


title: S44_Healthy donor 1


title: Low_50


title: non-PCOS granulosa cells C006

value: ovary of woman with normal ovarian reserve


title: Low_66


title: non-PCOS granulosa cells C004

value: 30 years


title: non-PCOS granulosa cells C005


title: S46_Healthy donor 1

value: Uninfected


title: non-PCOS granulosa cells C002

value: 33 years


title: Liver, BALB/c, Control Water + 20% Sucrose, 12h (JC025)

description:
group 25, rep 1
JC025

value: Control Water + 20% Sucrose


title: Low_42


title: Liver, BALB/c, Control Water + 20% Fructose, 12h (JC026)

description:
group 26, rep 1
JC026

value: Control Water + 20% Fructose


title: Liver, BALB/c, Control Water + 20% Glucose, 12h (JC024)

description:
group 24, rep 1
JC024

value: male


title: Low_34


title: Liver, C57BL6/J, Control Water + 20% Fructose, 3h (JC032)

description:
group 6, rep 2
JC032

value: 8 weeks


title: non-PCOS granulosa cells C003

value: 29 years


title: Liver, BALB/c, Control Water, 12h (JC023)

description:
group 23, rep 1
JC023


title: PCOS granulosa cells A007

source_name: ovary of PCOS patient

value: ovary of PCOS patient

value: 28 years


title: Low_26

value: single cell


title: non-PCOS granulosa cells C001

value: 35 years


title: Low_18


title: Liver, C57BL6/J, Control Water + 20% Fructose, 12h (JC022)

description:
group 22, rep 1
JC022

value: wild type


title: Low_82


title: Low_10


title: Liver, C57BL6/J, Control Water + 20% Sucrose, 12h (JC021)

description:
group 21, rep 1
JC021


title: Liver, C57BL6/J, Control Water + 20% Glucose, 12h (JC020)

description:
group 20, rep 1
JC020

value: Control Water + 20% Glucose


title: Low_81


title: Low_2


title: D11

city: nanjign

first: yi

middle: xuan

last: fan

address: No 1 weigang

institute: nanjing agricultural university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using Oar_v3.1  and paired-end clean reads were aligned to the reference genome using TopHat 2
FPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: tab-delimited text files include counts and FPKM values for each Sample

organism: Ovis aries

source_name: 55% energy level_testis

extract_protocol:
testis samples were collected and immediately frozen in liquid nitrogen, then total RNA was isolated with TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Hu sheep

tag: dietary energy level

value: 55% energy levels

tag: issue

value: testis


title: PCOS granulosa cells A006

value: 36 years


title: Low_73


title: D10


title: A16

source_name: maintenance energy level_testis

value: maintenance energy


title: PCOS granulosa cells A004

value: 26 years


title: PCOS granulosa cells A005

value: 30 years


title: PCOS granulosa cells A003

value: 27 years


title: Low_65


title: Liver, BALB/c, Control Water + 20% Fructose, 6h (JC018)

description:
group 18, rep 1
JC018

value: BALB/c

value: male

value: Control Water + 20% Fructose


title: PCOS granulosa cells A002

value: ovary of PCOS patient


title: Liver, BALB/c, Control Water + 20% Sucrose, 6h (JC017)

description:
group 17, rep 1
JC017

value: 8 weeks

value: Control Water + 20% Sucrose


title: D9


title: A15


title: A13


title: Low_49

value: single cell


title: Liver, BALB/c, Control Water + 20% Glucose, 6h (JC016)

description:
group 16, rep 1
JC016

value: wild type


title: Liver, C57BL6/J, Control Water + 20% Fructose, 6h (JC014)

description:
group 14, rep 1
JC014


title: imb_koenig_2014_03_16_JKRS25_U2AF65Nx_GS_2

data_processing:
Multiplexed iCLIP libraries were sequenced on an Illumina MiSeq sequencing system as 76bp single-end reads.  Basic sequencing quality checks were applied to all reads using FastQC (version 0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Afterwards, reads were filtered based on sequencing qualities (Phred score) of the barcode region. Only reads with at most one position with a sequencing quality < 20 in the experimental barcode (positions 4 to 7) and without any position with a sequencing quality < 17 in the random barcode (positions 1 to 3 and 8 to 9) were kept for further analysis. Remaining reads were de-multiplexed based on the experimental barcode on positions 4 to 7 using Flexbar (version 3.0.0) (Dodt et al., 2012) without allowing mismatches.  All following steps of the analysis were performed on all individual samples after de-multiplexing. Remaining adapter sequences were trimmed from the right end of the reads using Flexbar (version 3.0.0) allowing up to one mismatch in 10bp, requiring a minimal overlap of 1bp of read and adapter. After trimming off the adapter, the barcode is trimmed off of the left end of the reads (first 9bp) and added to the header of the read, such that the information is kept available for downstream analysis. Reads shorter than 15 bp were removed from further analysis.   Trimmed and filtered reads were mapped to the human genome (assembly version hg38/GRCh38) and its annotation based on GENCODE release 25 (Harrow et al., 2012) using STAR (version 2.5.4b) (Dobin et al., 2013). When running STAR, up to two mismatches were allowed, soft-clipping was prohibited and only uniquely mapping reads were kept for further analysis.   Following mapping, all samples were reduced to 100,000 randomly selected uniquely mapped reads each. Afterwards, duplicate reads were marked using the dedup function of bamUtil (version 1.0.13), which defines duplicates as reads whose 5' ends map to the same position in the genome (https://github.com/statgen/bamUtil). Subsequently, marked duplicates with identical random barcodes were removed since they are considered technical duplicates, while biological duplicates showing unequal random barcodes were kept.  Resulting bam files were sorted and indexed using SAMtools (version 1.5) (Li et al., 2009). Based on the bam files, bedgraph files were created using bamToBed of the BEDTools suite (version 2.25.0) (Quinlan and Hall, 2010), considering only the position upstream of the 5' mapping position of the read, since this nucleotide is considered as the crosslinked nucleotide. bedgraph files were then transformed to bigWig file format using bedGraphToBigWig of the UCSC tool suite (Kent et al., 2010). Processed data files were further normalized for sequencing depth by the number of reads mapping to a spike-in.
Genome_build: hg38

source_name: U2AF65  GS replicate 4

extract_protocol:
The in vitro iCLIP protocol was developed by modifying the early steps of the standard iCLIP protocol (Huppertz et al., 2014; Sutandy et al., 2016). Briefly, beads were prepared by twice washing 40 µl of protein-G Dynabeads per sample with dilution buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium deoxycholate; corresponding to the lysis buffer in the in vivo iCLIP protocol). After the second wash, 40 µl of dilution buffer was added to resuspend the beads and then followed by mixing with 3 µg of anti-U2AF65 antibody. The beads were rotated at room temperature for 30-60 min. One-time high-salt buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% Igepal CA-630, 0.1% SDS, 0.5% sodium deoxycholate) and twice dilution buffer washes were applied to wash the beads before proceeding with immunoprecipitation.  The in vitro transcripts were preheated for 5 min at 70°C to reduce large-scale RNA secondary structures. Titrated concentrations (30 nM, 50 nM, 150 nM, 250 nM, 450 nM, 750 nM, 1.5 µM, 3 µM, 5 µM, 15 µM) of U2AF65RRM12 and 2.2 nM in vitro transcript mix (eleven transcripts) were used for the Kd measurements. For the initial hnRNPC1 titration experiment, 1 µM U2AF65RRM12 was mixed with 6.75 nM in vitro transcript mix (nine transcripts; excluding MALAT1 and MIRLET7A2) and different concentrations of recombinant hnRNPC1 (200 nM, 500 nM, and 1 µM) in binding buffer. For the co-factor experiments, 500 nM U2AF65RRM12 was mixed with 6.75 nM in vitro transcript mix (nine transcripts) and different concentrations of eleven recombinant RBPs in binding buffer. In addition, 500 nM BSA was added to 500 nM U2AF65RRM12 and 6.75 nM in vitro transcript mix as a control for in vitro iCLIP co-factor assays.    All in vitro mixtures were incubated for 10 min at 37°C. After the incubation, the mixtures were placed on top of a parafilm-coated plate and UV-irradiated with 5 mJ/cm2 250 nm UV wavelength (Stratalinker 2400). The irradiated in vitro mixtures were pooled back to the tubes, and dilution buffer was added to fill the samples to a volume of 1 ml. To normalize the final in vitro iCLIP libraries, 10 µl of crosslinked mixture containing 250 nM U2AF65RRM12 and 6 nM NUP133 in vitro transcript was spiked in to each sample. Partial RNase digestion was performed by adding 10 µl of 1:1500 diluted RNase I (Ambion) to each sample. In addition, 2 µl of TURBO DNase was added to each sample to avoid DNA contamination. The sample mixtures were incubated for 3 min at 37°C, added to the prepared beads, and incubated for 2 h at 4°C. Beads were washed twice with high-salt buffer and twice with wash buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, 0.2% Tween-20).   Henceforth, we followed the steps of the standard iCLIP protocol. Briefly, 3' end RNA dephosphorylation was performed by resuspending the beads in 20 µl of mixture containing 4 µl of 5x PNK buffer (350 mM Tris-HCl pH 6.5, 50 mM MgCl2, 5 mM DTT), 0.5 µl of PNK (NEB), 0.5 µl RNasin Ribonuclease Inhibitor (Promega), and 15 µl water, followed by incubation for 20 min at 37°C. The beads were washed once with wash buffer, once with high-salt buffer and twice with wash buffer.  For the linker ligation, pre-adenylated L3 linker (5’-App-AGATCGGAAGAGCGGTTCAG-dideoxycytidine-3') was ligated by resuspending the beads in the ligation mixture containing 5 µl 4x ligation buffer (200 mM Tris-HCl pH 7.8, 40 mM MgCl2, 4 mM DTT), 1 µl T4 RNA ligase (NEB), 0.5 µl RNasin, 1.5 µl pre-adenylated L3 linker (20 µM), 4 µl PEG400, and 8 µl water. The samples were incubated at 16°C overnight. The next day, the samples were washed twice with high-salt buffer and twice with wash buffer.   Interacting RNAs were radioactively labeled by resuspending the beads in hot PNK mix (0.2 µl PNK [NEB], 0.4 µl 10x PNK buffer [NEB], 0.4 µl 32P-γ-ATP, and 3 µl water). The beads were incubated at 1,100 rpm for 5 min at 37°C. Supernatants were removed and the beads were boiled in 20 µl 1x NuPAGE loading buffer (Invitrogen) for 5 min at 70°C. Boiled beads were placed on a magnetic rack. The supernatants were then loaded into the 4-12% NuPAGE Bis-Tris gel (Invitrogen) and run in 1x MOPS buffer for 50 min at 180 V. Protein-RNA complexes from the gel were transferred to a nitrocellulose membrane for 1 h at 30 V.  To extract the interacting RNAs, the membrane was cut into pieces and digested with 10 µl proteinase K (Roche) in 200 µl PK buffer (100 mM Tris-HCl pH 7.4, 50 mM NaCl, 10 mM EDTA) for 20 min at 37°C. Another 200 µl PK buffer containing 7 M urea were added for further 20 min incubation at 37°C. The RNA-containing mixtures were transferred to Phase Lock Gel Heavy tubes and mixed with 400 µl phenol/chloroform by shaking with 1,100 rpm for 5 min at 30°C. RNAs were extracted by centrifugation for 5 min at 16,000 xg to separate the phases followed by transferring the top aqueous phase containing RNAs to new tubes. The samples were then mixed with 0.75 µl glycoblue (Ambion), 40 µl 3 M sodium acetate pH 5.5 and 1 ml ethanol absolute, and incubated overnight at -20°C. To precipitate the RNAs, the samples were centrifuged with 21,000 xg for 20 min at 4°C, washed with 80% ethanol, and resuspended in 5 µl water.
cDNA synthesis was performed by adding 1 µl dNTP mix and 1 µl RT primers containing different barcode sequences to each sample, and incubating them for 5 min at 70°C. The reaction was started by adding RT mixture (4 µl 5x RT buffer [Invitrogen], 1 µl 0.1 M DTT, 0.5 µl RNasin, 0.5 µl Superscript III [Invitrogen], 7 µl water) to the samples and incubating them for 5 min at 25°C, 20 min at 42°C, 40 min at 50°C, 5 min at 80°C, and hold at 4°C. To hydrolyze hot RNA templates, 1.65 µl 1 M NaOH was added, followed by 20 min incubation at 98°C. After the incubation, 20 µl 1 M Hepes-NaOH was added to neutralize the samples’ pH. The cDNA libraries were mixed with 0.75 µl glycoblue, 40 µl 3 M sodium acetate pH 5.5 and 1 ml ethanol absolute, and incubated overnight at -20°C. The next day, the cDNA libraries were precipitated by spinning the samples with 21,000 xg for 20 min at 4°C, washing with 80% ethanol, and resuspension in 6 µl water.   cDNA libraries were mixed with 6 µl 2x TBE-urea loading buffer (Invitrogen), heated for 5 min at 80°C, and then loaded and run in a 6% TBE-urea gel for 40 min at 180 V. DNA low molecular weight size marker (NEB) was used as the ladder. The libraries were size-selected by cutting out the gel within the range of 80-100 nt based on the ladder. Each piece of the gel was then crushed into smaller pieces and mixed with 400 µl diffusion buffer (0.5 M ammonium acetate, 10 mM magnesium acetate, 1 mM EDTA, 0.1% SDS). The mixtures were incubated for 30 min at 50°C, and moved to a Costar SpinX column (Corning) prepared with two 1 cm glass pre-filters (Whatman). To extract the cDNA libraries, the mixtures were spun at 16,000 xg for 5 min, and the eluates were added together with 400 µl phenol/chloroform into a Phase Lock Gel Heavy tube. The samples were incubated for 5 min at 30°C, and spun at 16,000 xg for 5 min to separate the phases. The aqueous top layers containing the libraries were moved to new tubes, mixed with 1 µl glycoblue, 40 µl 3 M sodium acetate pH 5.5 and 1 ml ethanol absolute, and then stored at -20°C overnight.  For circularization, libraries were centrifuged with 21,000 xg for 20 min at 4°C, washed with 80% ethanol, and resuspended in 8 µl of ligation mixture (0.8 µl 10x CircLigase buffer II [Epicentre], 0.4 µl 50 mM MnCl2, 0.3 µl CircLigase II [Epicentre], and 6.5 µl water). The libraries were transferred into PCR tubes and incubated for 1 h at 60°C. To re-linearize the libraries, 30 µl oligo annealing mix containing 3 µl FastDigest buffer (Thermo Fischer), 1 µl 10 µM cut_oligo (5’-GTTCAGGATCCACGACGACGACGCTCTTCaaaa-3'), and 26 µl water were added. The annealing program was performed by running the samples in succ

tag: technique

value: in vitro iCLIP

tag: iped-protein

value: U2AF65RRM12 GS

tag: barcode

value: CGCC


title: Liver, BALB/c, Control Water, 6h (JC015)

description:
group 15, rep 1
JC015

value: Control Water


title: Low_33


title: Liver, C57BL6/J, Control Water, 12h (JC019)

description:
group 19, rep 1
JC019


title: Liver, C57BL6/J, Control Water + 20% Sucrose, 6h (JC013)

description:
group 13, rep 1
JC013


title: Liver, C57BL6/J, Control Water + 20% Glucose, 6h (JC012)

description:
group 12, rep 1
JC012

value: Control Water + 20% Glucose


title: Low_25


title: imb_koenig_2014_03_15_JKRS23_nxRRM12_MUT_1

source_name: U2AF65  GS replicate 1

value: CGAG


title: Low_17


title: Low_9


title: Liver, C57BL6/J, Control Water, 6h (JC011)

description:
group 11, rep 1
JC011


title: Low_41


title: Liver, BALB/c, Control Water + 20% Sucrose, 3h (JC009)

description:
group 9, rep 1
JC009


title: Low_1


title: Liver, BALB/c, Control Water + 20% Glucose, 3h (JC008)

description:
group 8, rep 1
JC008


title: imb_koenig_2014_03_15_JKRS23_nxRRM12_MUT_2

source_name: U2AF65  GS replicate 2

value: CACA


title: ATACseq_KPG_rep1

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

description:
ATAC_consensus_peaks.splitbysummit.counts.txt
KPG_ATAC_merge.RPKM.bw
ATAC_consensus_peaks.splitbysummit.bed

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were trimmed of adapters using Trimmomatic v0.32
Trimmed reads were aligned using Bowtie2 v2.3.4.3 to mm10 using standard parameters and a maximum fragment length of 2000
Duplicate reads were determined using Picard tools v2.18.21
Bam files were filtered using samtools -F 1804
Reads were then processed where only the most 5' base pair for each read was kept and forward strand reads were shifted +4bp, and reverse strand reads were shifted -5bp.
For a consensus peak set, all bam files were merged using samtools and used for peak calling
Peak calling was performed using macs2 with parameters --nomodel --keep-dup all -s 1 --shift -75 --extsize 150 --call-summits. Peaks were then split evenly using summits.
featureCounts was used to count reads from replicates that fall within the consensus peak set using default parameters
DEseq2 was used to determine differential accessibility using counts
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (Merged rep1, rep2 of ATACseq_KP or KPG), bed (all ATAC peaks KP and KPG), txt (DESeq2 results comparing KPG and KP), txt (raw counts)

molecule: genomic DNA

source_name: Murine cell line

growth_protocol: Cells were grown in monolayer in RPMI + 10% FBS + Penicillin-streptomycin and amphotericin at 37ºC, 5% CO2 for 3 days

extract_protocol:
50.000 cells were treated with Transposase. Protocol as previously described in Corces et al (Nat.Methods 2017).
DNA libraries were prepared using ThruPlex Kit

tag: tissue

value: Lung

value: KrasG12D p53-/- Gata6-/-

tag: cell line

value: KPG


title: imb_koenig_2014_03_16_JKRS25_U2AF65Nx_1

source_name: U2AF65  WT replicate 3

value: TTAA


title: imb_koenig_2014_03_15_JKRS23_nxRRM12_WT_2

source_name: U2AF65  WT replicate 2

value: AGAA


title: Low_57


title: imb_koenig_2014_03_16_JKRS25_U2AF65Nx_2

source_name: U2AF65  WT replicate 4


title: imb_koenig_2014_03_16_JKRS25_U2AF65Nx_GS_1

source_name: U2AF65  GS replicate 3

value: GAAA


title: imb_koenig_2014_03_15_JKRS23_nxRRM12_WT_1

source_name: U2AF65  WT replicate 1


title: ATACseq_KP_rep2

description:
ATAC_consensus_peaks.splitbysummit.counts.txt
KP_ATAC_merge.RPKM.bw
ATAC_consensus_peaks.splitbysummit.bed

value: KrasG12D p53-/-

value: SPC-Cre KP


title: Liver, BALB/c, Control Water, 3h (JC007)

description:
group 7, rep 1
JC007

source_name: Liver

value: BALB/c

value: male

value: 8 weeks


title: Liver, C57BL6/J, Control Water + 20% Sucrose, 3h (JC005)

description:
group 5, rep 1
JC005

value: wild type

value: Control Water + 20% Sucrose


title: Liver, C57BL6/J, Control Water + 20% Fructose, 3h (JC006)

description:
group 6, rep 1
JC006

value: Control Water + 20% Fructose


title: Liver, C57BL6/J, Control Water + 20% Glucose, 3h (JC004)

description:
group 4, rep 1
JC004

value: Control Water + 20% Glucose


title: Atopic march, human T cell

city: Seoul

first: Bomi

last: Kim

address: 50-1, Yonsei-Ro

country: South Korea

institute: Yonsei University college of medicine

description: replicate 1

hyb_protocol: Labeled cRNA was hybridized to each Human HT-12 v4.0 Expression Beadchip for 17 h at 58°C according to the manufacturer’s instructions (Illumina Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina bead array reader confocal scanner.

data_processing: Raw data were extracted using the manufacturer-provided software (Illumina GenomeStudio v2011.1; Gene Expression Module v1.9.0). All data analysis and visualization of differentially expressed genes was performed using R 3.1.2 (www.r-project.org).

label: biotin

source_name: human T cell

label_protocol: Total RNA was amplified and purified using a TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (Epicentre, Madison, WI, USA) for biotinylated cRNA according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from T cells derived from human blood(PBMC) by the Qiagen RNeasy Mini Kit (Hilden, Germany). T cells were harvested using ficoll gradient separation and CD4 T-cell isolation kit (Miltenyi Biotec), in order.

tag: Sex

value: Male=9, Female=7


title: Liver, C57BL6/J, Control Water, 3h (JC003)

description:
group 3, rep 1
JC003

tag: strain

value: Control Water


title: ChIPseq_KPG_H3K27ac_rep2

description:
KPG_H3K27ac_merge.center.RPKM.bw
H3K27ac_consensus_peaks.bed
H3K27ac_consensus_peaks.blacklist.counts.txt

data_processing:
Basecalls performed using CASAVA version 1.8.2
For each read, we trimmed the first six nucleotides and the last nucleotides at the point where the Phred score of an examined base fell below 20 using in-house scripts. If, after trimming, the read was shorter than 45 bp, the entire pair was discarded.
Trimmed reads were mapped to the mouse reference genome (mm10) using BWA-MEM v0.7.17 using default parameters. For consensus peak calling, fastq files from multiple samples were mapped together (e.g. ChIPseq_KP_H3K4me3_rep1, ChIPseq_KP_H3K4me3_rep2, ChIPseq_KPG_H3K4me3_rep1, and ChIPseq_KPG_H3K4me3_rep2).
Peak and motif finding was performed using HOMER v4.10 (Heinz et al). For Gata6 peak finding, we used transcription factor mode with default parameters. For histone modifications we used -region -size 200 -minDist 1000
Reads that fell within consensus peaks were determined using featureCounts
DESeq2 was used to determine differential histone signal
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (merge of replicates for each IP and input), bed (consensus peak for each IP), txt (DESeq2 results and raw counts)

extract_protocol:
Cells were fixed in 1% formaldehyde. Pellet was resuspended in complete sonication buffer (20mM Tris pH 8.0, 2mM EDTA, 0.5mM EGTA, 1x protease inhibitors (Roche), 0.5% SDS and 0.5mM PMSF) in 1mL for 1x108 cells
DNA libraries were prepared using ThruPlex Kit

tag: antibody

value: Lung


title: ATACseq_KP_rep1


title: ATACseq_KPG_rep2

value: KrasG12D p53-/- Gata6-/-


title: Liver, C57BL6/J, Control Water, 0h (JC001)

description:
group 1, rep 1
JC001

tag: gender

tag: age


title: Liver, BALB/c, Control Water, 0h (JC002)

description:
group 2, rep 1
JC002

tag: genotype

tag: treatment (drink)


title: Scla_Term_ETLS_2

city: Daejeon

first: Soonkyu

last: Hwang

address: 291 Daehakro, Yuseong-gu

department: Biological Sciences

institute: KAIST

data_processing:
Library strategy: Term-seq
CLC Genomics workbench 6.5 (CLC bio) was used for data trimming and read mapping.
The adaptor sequence was trimmed from reads of the term-seq libraries before being aligned to the genome.
The reads were aligned to the S. clavuligerus genome and megaplasmid with the following parameters: mismatch cost 2, deletion cost 3, insertion 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.
The 5' end position of term-seq reads were counted as transcription 3' end position (TEP) peak raw counts. From the term-seq peak raw counts, the TEPs were selected by a machine learning algorithm (K-nearest neighbor classifier) with the input of positive and negative control sets that were enriched and not enriched peaks among adjecent peaks, respectively.
Genome_build: CP027858, CP027859
Supplementary_files_format_and_content: Scla_TEP.gff : tab-lelimited gff file that is finally determined and categorized TEP list. TEP position, strand, TEP name were represented

organism: Streptomyces clavuligerus

source_name: Mycelium cells from liquid culture

growth_protocol: Streptomyces clavuligerus ATCC 27064 cells were inoculated from its 20% glycerol stock of spores to 50 ml of R5- liquid complex medium with 8 g of glass beads (3 ± 0.3 mm diameter) in 250 ml of a baffled flask, and grown at 30 °C, 250 rpm

extract_protocol:
Lysate for all samples were prepared by resuspended at polysome buffer and grinding in liquid nitrogen
Term-seq libraries were constructed by enrichment of 3' termini of rRNA-depleted total RNAs through the ligation of 3' DNA adapter, fragmentation, and cDNA amplification using the primer complement to the adapter.

tag: sampling time

value: Pooling of the samples from early-exponential phase (E), transition phase (T), late-exponential phase (L), and stationary phase (S)

tag: cell sample

tag: treatment


title: ChIPseq_KPG_INPUT_rep1

value: none, INPUT

value: KPG


title: ChIPseq_KPG_INPUT_rep2


title: Sham 6 weeks [123]

city: Melboune

first: Saeedeh

last: Darzi

state: VIC

address: 27-31 Wright Street, Clayton

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Data were analysed using Fluidigm Real-Time PCR analysis software (V4.1.1) to obtain Ct values. The average of CT values were normalised to house keeping gene 18sRNA to provide delta CT values (delta CT test-delta CT 18sRNA). The delta delta CT was calculated as (delta CT test-delta CT sham) and fold change was calculated using formula 2^-delta delta CT.
Fold-change table reports test/control.

label: FAM

source_name: mouse skin

label_protocol:
100ng of RNA was used for cDNA synthesis using Superscript III kit.
Assays and Samples were combined in a 96.96 Dynamic array IFC according to Fluidigm® 96.96 Real-Time PCR Workflow Quick Reference PN 6800088. 5 µL of each assay at a final concentration of 10x was added to each assay inlet port and 5 µL of diluted sample to each sample inlet port according to the Chip Pipetting Map.

extract_protocol: Total RNA was extracted using RNeasy mini kit.

value: NSG

value: Female

value: Skin

value: Sham

tag: time point

value: 6 weeks

tag: sample type

value: Control


title: Atopic march2

description:
replicate 1
SAMPLE 5

source_name: human skin

extract_protocol: Total RNA was extracted from human skin using the Qiagen RNeasy Mini Kit (Hilden, Germany).

tag: disease

value: Atopic march

value: Male=2, Female=2


title: Scla_Term_ETLS_1


title: ChIPseq_KP_Gata6_rep2

description:
KP_GATA6_M.center.RPKM.bw
GATA6_peaks.bed

value: SPC-Cre KP

value: KrasG12D p53-/-


title: Atopic march3

description:
replicate 1
SAMPLE 6

value: Male=2, Female=1


title: ChIPseq_KPG_H3K27ac_rep1


title: Atopic march1

description:
replicate 1
SAMPLE 4

value: Male=1, Female=2


title: Atopic dermatitis2

description:
replicate 1
SAMPLE 3

value: Atopic dermatitis


title: ChIPseq_KP_Gata6_rep1

value: Lung


title: Sham 6 weeks [2346]


title: ChIPseq_KP_H3K27ac_rep2

description:
KP_H3K27ac_merge.center.RPKM.bw
H3K27ac_consensus_peaks.bed
H3K27ac_consensus_peaks.blacklist.counts.txt


title: ChIPseq_KP_H3K27ac_rep1


title: NCI-N87 in a mouse xenograft model, no treatment

city: Tsukuba

first: Hiroki

last: Irie

state: Ibaraki

address: Okubo 3

country: Japan

institute: Taiho Pharmaceutical Co., Ltd.

description:
A mixture of equal amounts of total RNA extracted from N87 xenografts of 5 animals in the control group.
PR1254_01_a

data_processing:
Basecalls performed using bcl2fastq2 v2.20
Sequenced reads were mapped to reference sequences(GRCh37/hg19 and refFlat.txt.gz by UCSC) using STAR v2.5.3a.
STAR parameters: -twopassMode true, -outFilterIntronMotifs RemoveNoncanonical, -sjdbOverhang 149, -sjdbGTFfile hg19 gtf file (UCSC), Others are default.
Number of read counts and Fragments per kilobase of exon per million reads mapped (FPKM) were calculated using Genedata Profiler Genome v11.0.11.
Gene expression fold changes and p-values were calculated using R package edgeR version 3.26.8.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text file includes read counts and FPKM values for each sample, and fold changes and p-values.

source_name: mouse xenograft

growth_protocol: The tumor cells were cultured in a CO2 incubator set at 37°C, 5% CO2, and passaged once a week or twice a week. The cell suspension was implanted subcutaneously in the vicinity of the right hindmost rib of nude mice.

extract_protocol:
Tumor tissues were removed,immersed into RNAlater® liquid solution(QIAGEN) and stored in a refrigerator for 24hr, and then transffered in a -20°C freezer until RNA extraction.RNA was extracted using AllPrep® DNA/RNA/Protein Mini kit(Qiagen). 3 µg of each RNA collected from 5 animals in each group was mixed to prepare 15 µg of RNA for the construction of sequencing libraries.
Libraries were prepared using the TruSeq Stranded mRNA Sample Kit according to the TruSeq Standrd mRNA Refference Guide v00.

treatment_protocol: The dose of each 20 mg/kg of Trastuzumab and pertuzumab were intraperitoneally administered to the nude mice bearing NCI-N87 tumor once weekly for 12 weeks.

tag: tumor cells

value: HER2-positive human gastric cancer cells

value: No treatment


title: Sham 6 weeks [408]


title: COMB_48h_3

city: Los Angeles

first: Frank

last: Pajonk

state: CA

address: 10833 Le Conte Ave

institute: UC Los Angeles

description:
readcount_13to24.txt
KB_H_24

data_processing:
Novogene Standard RNA-Seq pipeline
Genome_build: Homo_sapiens_hg19
Supplementary_files_format_and_content: standard BAM files

growth_protocol: HK-374 cells were grown in DMEM containing 10% FBS, 1% pen/strep media at 37°C in a 5% CO2 incubator. Cells were grown as monolayers, sorted for zsGreen-negative cells by purging all ZsGreen-positive cells. The sorted cells were grown overnight at 50,00 cells/well density in a 6-well plate with complete media.

extract_protocol:
Total RNA was isolated using Trizol reagent. The treated cells were lysed in 1 ml of Trizol reagent, rocked for 5 min to obtain a homogenous mixture and then transferred to RNAeasy mini kit (Qiagen) colimns for RNA isolation by following manufacturer's protocol.
The RNA sequencing library was generated using NEBNext® Ultra RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols. The library concentration was quantified using a Qubit 3.0 fluorometer (Life Technologies), and then diluted to 1 ng/uL before checking insert size on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany) and quantifying to greater accuracy by quantitative Q-PCR (library molarity >2 nM). The library was sequenced on Illumina NovaSeq6000 with an average of 20M reads per RNA sample.

treatment_protocol: The following day the sorted cells were treated with either saline or TFP (10 uM) 1 hour before irradiation. After 1 hour, the cells were treated again with saline or tFP and then irradiated at 4 Gy (using an experiemntal X-ray irradiator at a dose rate of 5.519 Gy/min. The X-ray beam was operated st 300 kV and hardened using a 4 mm Be, a 3 mm Al, and a 1.5 mm cu filter and calibrated using NIST-traceable dosimetry). Corresponding control cells were sham irradiated. The cells were then incubated and the RNA samples extracted at 1 and 48 hours post irradiation.

value: Glioblastoma

tag: source

value: patient-derived

value: 4 Gy + Trifluoperazine at 10uM


title: COMB_48h_2

description:
readcount_13to24.txt
KB_H_23

tag: tissue


title: ChIPseq_KP_H3K4me3_rep2

description:
KP_H3K4me3_merge.center.RPKM.bw
H3K4me3_consensus_peaks.bed
H3K4me3_consensus_peaks.blacklist.counts.txt

tag: cell line


title: Sham 6 weeks [2277]

value: NSG

value: Female

value: Skin


title: COMB_48h_1

description:
readcount_13to24.txt
KB_H_22


title: Atopic dermatitis1

description:
replicate 1
SAMPLE 2

tag: Sex


title: TFP_48h_3

description:
readcount_13to24.txt
KB_H_21

value: Trifluoperazine at 10uM


title: Sham 1 week [400]

tag: strain

value: Sham

value: 1 week

value: Control


title: ChIPseq_KP_INPUT_rep2

tag: antibody

value: none, INPUT

value: SPC-Cre KP

value: KrasG12D p53-/-


title: TFP_48h_2

description:
readcount_13to24.txt
KB_H_20


title: ChIPseq_KP_INPUT_rep1


title: Normal

description:
replicate 1
SAMPLE 1

value: Normal

value: Male=1, Female=3


title: Sham 1 week [119]

tag: gender


title: IR_48h_3

description:
readcount_13to24.txt
KB_H_18

value: 4 Gy


title: Sham 1 week [120]


title: Gene_Matrix

city: Stanford

first: Madeleine

last: Scott

address: 729 Lagunita Dr

institute: Stanford

description: Processed matrix of gene expression. Features (gene names, rows) and cell barcodes (columns) are available as supplementary files. Relevant phenotypic information for each cell such as animal of origin and QC metrics are available in "cell_information.csv".

data_processing:
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing)
RNA Reads were aligned to the macque reference genome (Mmul8).
Antibody Tags and cell barcodes were directly extracted from the reads in the ADT fastq files.
Genome_build: Mmul8
Supplementary_files_format_and_content: abundance; tsv files with cell barcodes and feature names for each sample, csv of phenotypic information for each barcoded cell including tSNE dimension reduction

organism: Macaca mulatta

source_name: vaginal epithelium

extract_protocol:
10x Cell Surface Protein Kit
Library was constructed as described in the 10x Genomics Single Cell Feature Barcoding Technology: Cell Surface Protein protocol. (https://www.10xgenomics.com/solutions/single-cell/)

value: vaginal epithelium


title: Sham 1 week [125]


title: PCOS granulosa cells A001

source_name: ovary of PCOS patient

value: ovary of PCOS patient

tag: age

value: 33 years


title: IR_48h_1

description:
readcount_13to24.txt
KB_H_16

value: Glioblastoma

value: patient-derived


title: Sham 1 week [2269]

value: NSG

value: Female


title: Sham 1 week [2354]

value: Skin


title: Activated (CD44+) T cells, Control

first: Warren

last: Pear

address: 556 BRB II/III 421 Curie Blvd.

data_processing:
FASTQ file generation and alignment to GRCm38 were performed using Cell Ranger v3.0.2 with default arguments.
Genome_build: GRCm38
Supplementary_files_format_and_content: Cell x gene unnormalized count matrices in matrix market format.

source_name: Activated (CD44+) T cells

extract_protocol:
Activated (CD44+) T cells (TCRb+) were FACS sorted from spleens of control or Trib1 cKO mice at day 15 post-clone 13 infection. Two biological replicates were pooled for each genotype. Cells were washed twice with RPMI, counted and single-cell RNA-seq was performed according to 10X Genomics protocols, targeting 5000 cells for loading.
Library construction was performed using the Chromium Single Cell 5' Library and Gel Bead Kit according to the manufacturer's protocol. The final pooled library (control and Trib1 cKO samples) was sequenced on a NextSeq 550 using paired-end sequencing on one 300 cycle high output FlowCell (Illumina).

value: spleen

tag: days post-infection

value: 7-8 weeks

tag: genotype

value: CD4-cre+ Trib1 +/+


title: Sham 1 week [126]

value: Sham

value: 1 week

value: Control


title: CNT_48h_3

description:
readcount_13to24.txt
KB_H_15

value: control


title: Activated (CD44+) T cells, Trib1 cKO

value: CD4-cre+ Trib1 F/F


title: CNT_48h_2

description:
readcount_13to24.txt
KB_H_14


title: IR_48h_2

description:
readcount_13to24.txt
KB_H_17

value: 4 Gy


title: ADT_Matrix

description: Processed matrix of cell surface marker expression. Features (protein name, rows) and cell barcodes (columns) are available as supplementary files.

value: vaginal epithelium


title: P nano-mesh +eMSC 6 weeks [2351]

value: P nano-mesh +eMSC

value: 6 weeks

value: Test


title: CNT_48h_1

description:
readcount_13to24.txt
KB_H_13

value: Glioblastoma

value: patient-derived


title: COMB_1h_3

description:
readcount_1to12.txt
KB_H_12

value: 4 Gy + Trifluoperazine at 10uM


title: 29siYAPerastin3: RCC4 cells treated with siRNA targeting YAP and erastin

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive

institute: Duke University

hyb_protocol: cDNA was amplified using Ambion MessageAmp™ Premier RNA Amplification Kit (Life Technologies) from 200ng total RNA, hybridized to GeneChip U133A 2.0 arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450

scan_protocol: scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

data_processing: The data were analyzed with Expression Console and normalized by the RMA (Robust Multi-Array)

source_name: Human RCC4 cells with YAP silenced by siRNA and erastin

label_protocol: not provided

growth_protocol: Renal cell carcinoma cell line, RCC4 cells, were cultured in DMEM (Thermo-11995) plus 10% heat-inactivated FBS (Hyclone #SH30070.03HI) in humidified incubator, 37°C with 5% CO2

extract_protocol: RNA was extracted by RNAeasy kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Renal cell carcinoma cell line, RCC4 cells, were treated with siRNA control, non-targeting (siNT) or siRNA targeting YAP for two days. Later, the cells were treated with either vehicle (DMSO) or 1 µM erastin for 7 hours.

value: clear cell renal caricnoma cell line

tag: genotype/variation

value: low YAP and erastin treatment


title: P nano-mesh +eMSC 6 weeks [2317]

value: NSG

value: Female

value: Skin


title: 27siYAPerastin2: RCC4 cells treated with siRNA targeting YAP and erastin


title: COMB_1h_2

description:
readcount_1to12.txt
KB_H_11


title: 25siYAPmock3: RCC4 cells treated with siRNA targeting YAP and DMSO

source_name: Human RCC4 cells with YAP silenced by siRNA and DMSO

value: low YAP


title: P nano-mesh +eMSC 6 weeks [2210]


title: P nano-mesh +eMSC 6 weeks [60]


title: P nano-mesh +eMSC 6 weeks [2400]


title: 23siYAPmock2: RCC4 cells treated with siRNA targeting YAP and DMSO


title: NCI-N87 in a mouse xenograft model, treated with Trastuzumab plus pertuzumab

description:
A mixture of equal amounts of total RNA extracted from N87 xenografts (ie. trastuzumab and pertuzumab-refractory tumor) of 5 animals in the combined treatment group with trastuzumab plus pertuzumab.
PR1254_02_a

value: HER2-positive human gastric cancer cells

value: Trastuzumab plus pertuzumab


title: WT, rep 6

city: Burlington

first: SABIKUNNAHAR

last: SABIKUNNAHAR

state: Vermont

address: 318 Rowell, 106 Carrigan Dr

department: Biomedical and Health Sciences

institute: The University of Vermont

hyb_protocol: Mouse Clariom D arrays were incubated in the Affymetrix® GeneChip® Hybridization Oven 645 at 45° C / 60 RPM for 16-18 hours.

scan_protocol: GeneChips were scanned with the 7G Affymetrix® GeneChip® Scanner 3000

data_processing: Raw intensity CEL files were imported into Expression Console software (Affymetrix, USA), and CHP files were generated for gene level analysis. CHP files were imported into Transcriptome Analysis Console (TAC software v4.0.0.25 (Affymetrix, USA), and gene level expression analysis was performed using the default ANOVA settings

label: Biotin

source_name: WT_BMDM_4h LPS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymatrix protocol from 5.5 ug total RNA

growth_protocol: Bone marrow cells were harvested from each mice and differentiated until day 7, with recombinant M-CSF to generate BMDMs

extract_protocol: Total RNA was extracted by RNEasy miniprep kit (Qiagen, USA) according to manufacturer's protocol

treatment_protocol: BMDMs were treated with LPS (100ng/ml) for 4 hours

tag: strain background

value: WT

tag: cell type

value: BMDMs

value: LPS (100ng/ml) for 4 hrs


title: Sham 6 weeks [122]

tag: treatment

value: Sham

tag: time point

value: Control


title: WT, rep 5


title: P nano-mesh +eMSC 6 weeks [529]

value: P nano-mesh +eMSC

value: 6 weeks

tag: sample type

value: Test


title: TFP_1h_3

description:
readcount_1to12.txt
KB_H_9

value: Glioblastoma

value: patient-derived

value: Trifluoperazine at 10uM


title: P nano-mesh +eMSC 1 week [2309]

value: NSG

value: 1 week


title: P nano-mesh +eMSC 6 weeks [2399]

value: Female

value: Skin


title: COMB_1h_1

description:
readcount_1to12.txt
KB_H_10

value: 4 Gy + Trifluoperazine at 10uM


title: 10siNTerastin3: RCC4 cells treated with siRNA control and erastin

source_name: Human RCC4 cells with non-targeting siRNA control and erastin

value: clear cell renal caricnoma cell line

value: erastin treatment


title: TFP_1h_2

description:
readcount_1to12.txt
KB_H_8


title: TFP_1h_1

description:
readcount_1to12.txt
KB_H_7


title: 09siNTerastin2: RCC4 cells treated with siRNA control and erastin


title: P nano-mesh +eMSC 1 week [2350]


title: IR_1h_3

description:
readcount_1to12.txt
KB_H_6

value: 4 Gy


title: p38 KO, rep 3

source_name: p38 conditional KO_BMDM_4h LPS

value: p38 conditional KO

value: BMDMs

value: LPS (100ng/ml) for 4 hrs


title: WT, rep 4

value: WT


title: 26siYAPerastin1: RCC4 cells treated with siRNA targeting YAP and erastin

value: low YAP and erastin treatment


title: 21siYAPmock1: RCC4 cells treated with siRNA targeting YAP and DMSO

value: low YAP


title: IR_1h_2

description:
readcount_1to12.txt
KB_H_5

value: Glioblastoma


title: P nano-mesh +eMSC 1 week [532]

value: P nano-mesh +eMSC

value: Test


title: p38 KO, rep 4


title: ChIPseq_KPG_H3K4me3_rep2

description:
KPG_H3K4me3_merge.center.RPKM.bw
H3K4me3_consensus_peaks.bed
H3K4me3_consensus_peaks.blacklist.counts.txt

source_name: Murine cell line

value: Lung

value: KPG

value: KrasG12D p53-/- Gata6-/-


title: 03siNTmock3: RCC4 cells treated with siRNA control and DMSO

source_name: Human RCC4 cells with non-targeting siRNA control and DMSO

value: control


title: 08siNTerastin1: RCC4 cells treated with siRNA control and erastin


title: P nano-mesh +eMSC 1 week [78]

value: NSG

value: Female

value: Skin

value: 1 week


title: IR_1h_1

description:
readcount_1to12.txt
KB_H_4

value: patient-derived

value: 4 Gy


title: Sham 6 weeks [401]

value: Sham

value: 6 weeks

value: Control


title: Liver, BALB/c, Control Water + 20% Fructose, 3h (JC010)

description:
group 10, rep 1
JC010

data_processing:
Illumina Casava was used for basecalling.
Raw reads were filtered by removing read which:  (1) contained adaptors; (2) contained N > 10% (N represents base that could not be determined); and (3) The Qscore (Quality value) of over 50% bases of the read was <= 5.
STAR v2.5 was used to align clean data to mm10 reference genome with parameter mismatch = 2
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. Then FPKM of each gene was calculated.
Differential expression analysis between two conditions/groups was performed using the DESeq2 R package (2_1.6.3).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: csv files including raw counts, FPKM values for each sample, and FPKM values for each group

extract_protocol:
Completely dissolve approximately 5mg of frozen liver tissue powder in 500 uL of Trizol reagent at room temperature; Add 100uL of chloroform to the Trizol-liver mixture and incubate the mixture at RT for 2 min; Spin down at 12krpm for 15 minutes at 4°C; Isolate the top layer (aqueous) and mix it with 100% ethanol at 1:1 ratio and load the mixture to the RNeasy mini column from the Qiagen kit (catalogue No. 74106); Thereafter follow the protocol part 1 step 3 from the same kit to finish the extraction of total RNA.
Standard Illumina protocol using NEBNext Library Prep Kit for Illumina
Illumina NovaSeq 6000 paired with an S4 flowcell

value: BALB/c

value: male

value: 8 weeks

value: wild type

tag: treatment (drink)

value: Control Water + 20% Fructose

tag: time (feed duration)


title: CNT_1h_3

description:
readcount_1to12.txt
KB_H_3

tag: tissue

value: Glioblastoma

tag: source


title: P nano-mesh +eMSC 1 week [61]

value: P nano-mesh +eMSC

value: Test


title: P nano-mesh +eMSC 1 week [10]

value: NSG


title: P nano-mesh +eMSC 1 week [2358]

value: Female


title: CNT_1h_2

description:
readcount_1to12.txt
KB_H_2

value: control


title: P nano-mesh 6 weeks [2307]

value: Skin

value: P nano-mesh


title: CNT_1h_1

description:
readcount_1to12.txt
KB_H_1

value: patient-derived


title: P nano-mesh 6 weeks [121]


title: 02siNTmock2: RCC4 cells treated with siRNA control and DMSO

tag: cell line

value: clear cell renal caricnoma cell line


title: 01siNTmock1: RCC4 cells treated with siRNA control and DMSO


title: PAN GEnC derived EVs3 [RNA-seq]

city: Nashville

first: Danielle

middle: L

last: Michell

state: TN

address: 2220 Pierece Ave

department: Department of Medicine

institute: Vanderbilt Univ. Medical Center

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v1.16
Reads were aligned to the human b37 genome using STAR v2.5.3a. Ensembl v75 gene annotations were provided to STAR to improve the accuracy of mapping.
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC
featureCounts v1.15.29 was used to count the number of mapped reads to each gene.
Significantly differential expressed genes with p-value < 0.05 and absolute fold change > 1.5 were detected by DESeq2 (v1.18.1)
Genome_build: human b37 genome

source_name: Podocytes

growth_protocol: GEnCs were incubated at 33℃ in 5% CO2 to proliferate in microvascular cell growth kit, then thermoswitched at 37℃, 5% CO2 in attachment factor coated plates. Podocytes were incubated at 33℃ in 5% CO2 in RPMI supplemented with 10% PS, 25% FCS, 5% L-glutamine, and 5% ITS. Cells were induced to differentiate at 37℃ in 5% CO2.

extract_protocol:
RNA from 2x10^5 podocytes incubated for 24h with EVs derived from GEnCs was isolated using the Total RNA Purification Kit (Norgen Biotec) according to the manufacturer's instructions.
Libraries were prepared using the Nugen Ovation Human FFPE RNA-Seq Library Systems kit

treatment_protocol: GENCs were incubated in microvascular cell growth kit media supplemented with 5% exosome depleted FBS. GEnCs were either unstimulated (steady state, SS), or stimulated with glucose (Glu, 30mmol), or puromycin aminonucleoside (PAN, 100ug/mL) for 24hr. Cell supernatants were spun at 300g for 10 min, then 2,000g for 15min, and then ultracentrifuged for 10,000g for 30min to remove cell debris and large EVs. Equal supernatant volumes were then ultracentrifuged at 100,000g for 70min at 4℃. EV pellets were resuspended in 300uL of podocyte media plus 5% exosome depleted FBS. 2x10^5 podocytes were untreated (UT) or treated with EVs from GEnCs from SS, GLu or PAN conditions for 24hr.

tag: podocyte treatment

value: GEnC derived EVs

tag: genc treatment

value: PAN


title: P nano-mesh 6 weeks [2267]

tag: strain

tag: gender

value: 6 weeks


title: PAN GEnC derived EVs2 [RNA-seq]


title: WT, rep 1

value: WT

value: BMDMs

value: LPS (100ng/ml) for 4 hrs


title: WT, rep 2


title: PAN GEnC derived EVs1 [RNA-seq]


title: p38 KO, rep 1

value: p38 conditional KO


title: Glucose GEnC derived EVs3 [RNA-seq]

value: Glucose


title: p38 KO, rep 2


title: P nano-mesh 6 weeks [52]


title: P nano-mesh 6 weeks [437]


title: ko4

city: Shanghai

first: Qinglei

last: Yin

address: Ruijin Second Road No.197

institute: Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine

hyb_protocol: Array hybridization and washing was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and a Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US). Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings.

data_processing: Raw data were normalized by Expression Console using MAS 5.

source_name: KO_β cells

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix  WT PLUS Reagent Kit(Cat#902280， Affymetrix, Santa Clara, CA, US)/ Ovation FFPE WTA System (Cat#3403， NuGEN, San Carlos, CA, US) / Ovation® Pico WTA System V2(Cat#3302， NuGEN, San Carlos, CA, US)and FL-Ovation™ cDNA Biotin Module V2(Cat#4200， NuGEN, San Carlos, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

extract_protocol: Total RNA was extracted and purified using RNeasy micro kit(Cat#74004, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: age

value: 2-week-old mice

value: Raptor knockout

value: islet

value: beta cells


title: P nano-mesh 6 weeks [438]

value: NSG

value: Female

value: Test


title: double KO, rep 2

source_name: p38-ESR1 double KO_BMDM_4h LPS

value: p38-ESR1 double KO


title: double KO, rep 1


title: double KO, rep 3


title: Glucose GEnC derived EVs2 [RNA-seq]


title: double KO, rep 4


title: P nano-mesh 6 weeks [53]

value: Skin

value: P nano-mesh


title: Steady state GEnC derived EVs3 [RNA-seq]

value: GEnC derived EVs

value: Steady state


title: Glucose GEnC derived EVs1 [RNA-seq]


title: ChIPseq_KP_H3K4me3_rep1

tag: antibody

value: Lung

value: SPC-Cre KP

tag: genotype

value: KrasG12D p53-/-


title: P nano-mesh 6 weeks [2356]

value: 6 weeks


title: P nano-mesh 1 week [2396]

value: 1 week


title: Steady state GEnC derived EVs2 [RNA-seq]


title: Steady state GEnC derived EVs1 [RNA-seq]


title: wt3

source_name: WT_β cells

tag: strain background

value: 2-week-old mice

tag: genotype/variation

value: wild type


title: Untreated 3 [RNA-seq]

value: Untreated


title: P nano-mesh 1 week [2308]

source_name: mouse skin

tag: treatment


title: Untreated 1 [RNA-seq]


title: P nano-mesh 1 week [2268]

tag: time point


title: Untreated 2 [RNA-seq]


title: P nano-mesh 1 week [132]

tag: sample type


title: RNAseq_A431_shdeltaNp63_rep3

status: Public on Mar 04 2020

city: Würzburg

first: Markus

last: Diefenbacher

address: Am Hubland

department: Chair of Biochemistry and Molecular Biology

institute: University Würzburg

data_processing:
Fastq files were generated using Illuminas base calling software GenerateFASTQ v1.1.0.64 and overall sequencing quality was analyzed using the FastQC script.
Reads were aligned to the human genome (hg19) using Tophat v2.1.1 (Kim et al., 2013) and Bowtie2 v2.3.2 (Langmead et al., 2012) and samples were normalized to the number of mapped reads in the smallest sample.
For differential gene expression analysis, reads per gene (Ensembl gene database) were counted with the “summarizeOverlaps” function from the R package “GenomicAlignments” using the “union”-mode and non- or weakly expressed genes were removed (mean read count over all samples <1).
Differentially expressed genes were called using edgeR (Robinson et al., 2010) and resulting p-values were corrected for multiple testing by false discovery rate (FDR) calculations.
Genome_build: hg19
Supplementary_files_format_and_content: .txt file containing gene names, gene description, log2FC, log2CPM, p-value, Benjamini-Höchberg-adjusted p-value

source_name: A431 cells

growth_protocol: A-431 cells were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (FCS) and 1% Pen-Strep.

extract_protocol:
RNA was isolated using ReliaPrep™ RNA Cell Miniprep System Promega kit, following the manufacturer’s instruction manual.
mRNA was purified with NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB) and the library was generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina, following the manufacturer’s instructions. For the size-selection of the libraries, Agencourt AMPure XP Beads (Beckman Coulter) were used. Library quantification and size determination was performed using Fragment Analyzer (Agilent formerly Advanced Analytical). Libraries were sequenced on an Illumina NextSeq500.

treatment_protocol: For DNA infection, Lentiviruses (MOI=10) were added to the cell medium in the presence of polybrene (5μg/ml) and incubated at 37°C for 96h. After incubation, infected cells were selected with 2.5 μg/ml Puromycin (72h) or sorted for GFP expression.


title: wt2

value: islet

tag: cell type

value: beta cells


title: RNAseq_A431_shdeltaNp63_rep1


title: RNAseq_A431_shUSP28_rep3


title: RNAseq_A431_shdeltaNp63_rep2


title: ko1

value: Raptor knockout


title: RNAseq_A431_shUSP28_rep1


title: RNAseq_A431_shUSP28_rep2


title: ko2


title: ko3


title: ChIPseq_KPG_H3K4me3_rep1

value: KPG

value: KrasG12D p53-/- Gata6-/-


title: PROseq_preCond_K562_shHSF1_HS60_rep1

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

institute: KTH Royal Institute of Technology

description:
nascent RNA
Normalized_PROseq_preCond_K562_shHSF1_HS60_minusStrand.bigWig
Normalized_PROseq_preCond_K562_shHSF1_HS60_plusStrand.bigWig

data_processing:
Adapters (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC) were removed using cutadapt (Marcel, 2011)
The reads were trimmed and filtered, and complements of reads were generated using fastx (http://hannonlab.cshl.edu/fastx_toolkit/).
The reads were aligned to combined hg19-dm3 genome using Bowtie2 (Langmead et al., 2009).
Reads that uniquely mapped to hg19 were processed to bed, bedgraph and bigWig files. The number of uniquely mapping reads to Drosophila genome (whole-genome invariant spike-in) was used for sample normalization.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized and (where applicable) replicate-combined bigWig files. Since PRO-seq reports positions of transcription complexes strand-specifically, the plus strand and minus strand are given in separate bigWig files.

growth_protocol: Human K562 erythroleukemia cells were maintained at 37°C in a humidified 5% CO2 atmosphere and cultured in RPMI medium (Sigma), containing 10% fetal calf serum, 2 mM L-glutamate, 100 μg/ml streptomycin, and 100 U/ml penicillin. The cells were grown below 5x10^5 cells/ml confluency.

extract_protocol:
After treatments, the cells were harvested by centrifugation, and washed twice with PBS. Nuclei were isolated and run-on reactions were performed with biotinylated nucleotides as described by Kwak H, Fuda NJ, Core LJ, Lis JT. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 2013 Feb 22;339(6122):950-3. The run-on reaction was conducted in the presence of nuclei from S2 cells, which provides an invariant whole-genome spike-in control between samples.
The libraries were generated using TruSeq small-RNA adaptors, amplified 11 cycles, gel-purified and size-selected to 125-400 bp fragments. The libraries were sequenced using NextSeq 500 (Illumina).
PRO-seq

treatment_protocol: Preconditioning of K562 cells was conducted by submerging cells in a 175 mL flask into a 42°C heat bath. Nine 1-hour heat treatments were conducted in total, divided to three heat treatments per day for three consecutive days. Recovery from stress was conducted by placing the cells into a 37°C incubator for two hours (between the 1h heat shocks within the day) or over night (between the days). After nine heat shock treatments, the cells were allowed to recover for 48h in 37°C incubator prior to an additional, single heat shock was introduced. The single additional heat shock was conducted by concentrating 1x10^7 cells in a 10 mL media and placing the sample either into 37°C incubator (0 min) or submerging into 42°C water bath for 30 min (HS30) or 60 min (HS60). Transfections of cells (scrambled sequence or short hairpin targeting HSF1 mRNA) was conducted 24 h prior to initiating the preconditioning.

tag: hsf1 depletion

value: HSF1 depleted (HSF1 mRNA targeting shRNA transfected)

tag: preconditioning

value: 9 x 1h heat shock at 42°C (divided to 3 consecutive days), followed by 48 h recovery at 37 °C

tag: heat shock (additional to preconditioning)

value: 60 min at 42°C water bath


title: wt1

tag: tissue


title: RNAseq_A431_DMSO_rep2

value: DMSO


title: PROseq_preCond_K562_shHSF1_HS30_rep1

description:
nascent RNA
Normalized_PROseq_preCond_K562_shHSF1_HS30_minusStrand.bigWig
Normalized_PROseq_preCond_K562_shHSF1_HS30_plusStrand.bigWig

value: 30 min at 42°C water bath


title: h2a.z.1 MO_sox10:GFP cells_Rep2

city: Delhi

first: Vivek

middle: T

last: Natarajan

state: Delhi

address: Mathura Road

country: India

institute: CSIR-IGIB

description: Gene expression in h2a.z.2 morpholino injected sox10:GFP positive cells replicate 2

hyb_protocol: Labeled cRNA sample were fragmented at 60oC and hybridized on to Agilent Zebrafish Gene  Expression Microarray 8X60K. Fragmentation of labeled cRNA and hybridization were done  using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit,    Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65o C  for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers  (Agilent Technologies, Part Number 5188-5327)

scan_protocol: The hybridized slides were scanned using the Agilent Microarray  Scanner (Agilent Technologies, Part Number G2600D). Raw data extraction from Images was  obtained using Agilent Feature Extraction software.

data_processing: Images were quantified using Feature Extraction Software (Version-11.5 Agilent). Feature  extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of  the data was done in GeneSpring GX using the 75th percentile shift (Percentile shift  normalization is a global normalization, where the locations of all the spot intensities in an array  are adjusted. [This normalization takes each column in an experiment independently, and  computes the percentile of the expression values for this array, across all spots (where n has  a range from 0-100 and n=75 is the median). It subtracts this value from the expression value of  each entity) and fold expression values were obtained with respect to Specific control Samples].  Differential expression patterns were identified among the samples. Significant genes up  regulated fold> 0.6 (logbase2) and down regulated <-0.6 (logbase2) in the test samples with  respect to control sample were identified. Statistical student T-test p-value among the replicates  was calculated based on volcano plot algorithm. Differentially regulated genes were clustered  using hierarchical clustering based on Pearson coefficient correlation algorithm to identify  significant gene expression patterns. Biological analysis was performed for the differentially  expressed genes based on their functional category and pathways using Biological Analysis tool  DAVID (http://david.abcc.ncifcrf.gov/).

organism: Danio rerio

source_name: zebrafish sox10:GFP positive cells

label_protocol: The microarray hybridization and scanning were performed at the Agilent certified microarray  facility of Genotypic Technology, Bengaluru, India. The samples for Gene expression were  labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Synthesized double stranded cDNA were used as template for cRNA  generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was  incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried  out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No:  74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Zebrafish were bred, raised and maintained at 28.5 0C according to standard protocols (Westerfield M, 2000) and were housed at the CSIR-Institute of Genomics and Integrative Biology (IGIB), Mathura Road New Delhi, India. Embryos were staged both using timing (hours post fertilization (hpf); days post fertilization (dpf)) and morphological features according to (Kimmel, 1995)

extract_protocol: Control MO and Z2 MO were injected in 1 cell stage Tg(sox10:GFP) embryos and allowed to develop till 15 hpf. Briefly, Embryos were dechorinated using pronase (5mg/ml) (Sigma, P8811) for 10-15 mins and collected in microfuge tubes. The embryos were deyolked in ice cold ringer’s solution using micropipette tip and spun at 100g for 2 minutes at cooled table top centrifuge at 40C (Eppendorf® centrifuge 5418R). The supernatant was discarded and the embryo bodies were trypsinized using TrypLE Express (Thermoscientific®, 12604039) for 15 or 30 minutes for 24hpf or 48 hpf embryos respectively at room temperature. The cell suspension was passed through 70μm cell strainer and washed twice with ice cold phosphate buffered saline + 10% Fetal bovine serum and subjected to FACS (BD Bioscience FACSAriaTM III). The GFP positive cells were sorted and collected in RP1 buffer and RNA was isolated using Nucleospin RNA XS kit (Macherey Nagel, 740902) according to manufacturer’s protocol.

treatment_protocol: Morpholinos for blocking translational initiation or splicing of RNA were designed by GeneTools®. Minimum effective concentration was determined for each morpholino (MOs) using dosage titration experiments. Concentrations of various MOs used in this study are as follows: 3 - 3.5 ng of h2a.z.2 translation block (Z2 MO), 4 - 4.5 ng of h2a.z.2 splice block (Z2 SB MO), 2 ng of h2a.z.1 splice block (Z1 MO) (Ref 4) and 0.8ng of double targeting (h2a.z.1 and h2a.z.2) translational block (Z1 + Z2 MO). Standard control morpholino from gene tools was used as a control and dosed accordingly.

value: sox10:GFP neural crest cells

tag: developmental stage

value: h2a.z.2 morpholino injected


title: h2a.z.1 MO_sox10:GFP cells_Rep1

description: Gene expression in h2a.z.2 morpholino injected sox10:GFP positive cells replicate 1


title: Control MO_sox10:GFP cells_Rep2

description: Gene expression in control morpholino injected sox10:GFP positive cells replicate 2

value: control


title: TFP_48h_1

description:
readcount_13to24.txt
KB_H_19

value: Glioblastoma

tag: source

value: patient-derived

value: Trifluoperazine at 10uM


title: Control MO_sox10:GFP cells_Rep1

description: Gene expression in control morpholino injected sox10:GFP positive cells replicate 1


title: PROseq_preCond_K562_scr_HS0_rep2

description:
nascent RNA
Normalized_PROseq_preCond_K562_scr_HS0_minusStrand.bigWig
Normalized_PROseq_preCond_K562_scr_HS0_plusStrand.bigWig

value: no depletion (scrambled sequence transfected)

value: no additional heat stress applied


title: PROseq_unCond_K562_scr_HS60_rep1

description:
nascent RNA
Normalized_PROseq_unCond_K562_scr_HS60_minusStrand.bigWig
Normalized_PROseq_unCond_K562_scr_HS60_plusStrand.bigWig


title: RNAseq_A431_DMSO_rep1


title: P nano-mesh 1 week [133]

tag: strain

value: NSG

value: Female

value: Skin

value: P nano-mesh

value: 1 week

value: Test


title: PROseq_preCond_K562_scr_HS0_rep1

value: 9 x 1h heat shock at 42°C (divided to 3 consecutive days), followed by 48 h recovery at 37 °C


title: PROseq_unCond_K562_scr_HS30_rep2

description:
nascent RNA
Normalized_PROseq_unCond_K562_scr_HS30_minusStrand.bigWig
Normalized_PROseq_unCond_K562_scr_HS30_plusStrand.bigWig


title: PROseq_preCond_K562_scr_HS30_rep2

description:
nascent RNA
Normalized_PROseq_preCond_K562_scr_HS30_minusStrand.bigWig
Normalized_PROseq_preCond_K562_scr_HS30_plusStrand.bigWig


title: LNCAP-siAR-rep2

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

description: Sample 12

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (GRCh38.p7) by STAR (version 2.5.2).
The number of fragments in each known gene from GENCODE (version 25) was enumerated using STAR QuantMode (GeneCounts) function.
The normalized fragment count for each gene was calculated by R/Bioconductor package DESeq2 (version 1.18.1).
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are normalized expression values (estimated by DESeq2) for all the samples.

source_name: LNCaP

growth_protocol: Early passage of LNCaP cells (obtained from ATCC) were grown in RPMI1640 mediun supplemented with 7% serum.

extract_protocol:
LNCaP cells treated with various regimens that manipulate endogenous AR signaling are subject to total RNA extraction by RNeasy mini kit (Qiagen, Valencia, CA). Illumina TruSeq Stranded Total RNA Preparation Kit (Illumina, cat#: RS-122-2301) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LNCaP cells treated for 4 days with various regimens to manipulate endogenous AR signaling.

value: Prostate cancer cell line

tag: cancer type

value: Prostate cancer

tag: cell line

value: LNCaP

tag: ar status

value: AR+

tag: growth condition

value: FBS+ siAR


title: PROseq_unCond_K562_shHSF1_HS60_rep1

description:
nascent RNA
Normalized_PROseq_unCond_K562_shHSF1_HS60_minusStrand.bigWig
Normalized_PROseq_unCond_K562_shHSF1_HS60_plusStrand.bigWig

value: HSF1 depleted (HSF1 mRNA targeting shRNA transfected)

value: 60 min at 42°C water bath


title: PROseq_preCond_K562_scr_HS60_rep1

description:
nascent RNA
Normalized_PROseq_preCond_K562_scr_HS60_minusStrand.bigWig
Normalized_PROseq_preCond_K562_scr_HS60_plusStrand.bigWig


title: PROseq_unCond_K562_shHSF1_HS0_rep1

description:
nascent RNA
Normalized_PROseq_unCond_K562_shHSF1_HS0_minusStrand.bigWig
Normalized_PROseq_unCond_K562_shHSF1_HS0_plusStrand.bigWig

value: no heat stress applied


title: PROseq_preCond_K562_scr_HS30_rep1

value: no depletion (scrambled sequence transfected)

value: 30 min at 42°C water bath


title: PROseq_preCond_K562_shHSF1_HS0_rep1

description:
nascent RNA
Normalized_PROseq_preCond_K562_shHSF1_HS0_minusStrand.bigWig
Normalized_PROseq_preCond_K562_shHSF1_HS0_plusStrand.bigWig

value: no additional heat stress applied


title: LNCAP-siNC-rep2

description: Sample 10

value: FBS+ siNC


title: LNCAP-siAR-rep1

description: Sample 11


title: LNCAP-AI+DHT-rep2

description: Sample 8

value: CDSS+DHT


title: LNCAP-AI+DHT-rep1

description: Sample 7


title: LNCAP-siNC-rep1

description: Sample 9


title: LNCAP-MDV-rep2

description: Sample 6


title: PROseq_unCond_K562_scr_HS30_rep1


title: LNCAP-MDV-rep1

description: Sample 5


title: LNCAP-AI-rep1

description: Sample 3

value: CDSS


title: PROseq_unCond_K562_shHSF1_HS30_rep1

description:
nascent RNA
Normalized_PROseq_unCond_K562_shHSF1_HS30_minusStrand.bigWig
Normalized_PROseq_unCond_K562_shHSF1_HS30_plusStrand.bigWig


title: LNCAP-AI-rep2

description: Sample 4


title: LNCAP-AD-rep2

description: Sample 2

value: FBS


title: LNCAP-AD-rep1

description: Sample 1


title: S5P-RNAPII_b_rep3

city: Illkirch-Graffenstaden

first: Jules

last: Deforges

address: Boulevard Gonthier d'Andernach

country: France

institute: Transgene SA

data_processing:
Reads trimmed with trimmomatic
Mapping against Arabidopsis thaliana reference genome
Readcount with Htseq-count
Genome_build: TAIR10
Supplementary_files_format_and_content: Raw read count: contains raw readcount from HTSeq-counts for each locus, for TSS > TES region, TSS > +500nt or genebody (+500nt > TES regions)

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Plants were cultivated on MS medium in the plant incubator (Percival Scientiﬁc) under long-day (LD) conditions (16 h light and 8 h dark) at 22 °C with light intensity 100 µmol m-2 s-1.

extract_protocol:
Plant material was harvested in the amount of 1 g and subjected to DNA crosslinking with 1% formaldehyde as described in Pfab et al., 2017. Immunoprecipitated DNA was obtained as described in Pfab et al., 2017 with minor modifications.
DNA SMART ChIP-Seq kit (Clontech)

treatment_protocol: Exposure to 2 mM b-estradiol ("b") or EtOH (mock, "m") for 24 h prior to material harvesting.

tag: ecotype

value: Columbia

tag: age

value: 10 DAS

tag: genetic backroung

tag: treatment (24 hours)

value: 2 mM b-estradiol

tag: inducibly expressed protein

value: GFP-TFIISmut (AT2G38560)

tag: antibody


title: S2P-RNAPII_b_rep2

value: GFP-TFIIS (AT2G38560)


title: S5P-RNAPII_b_rep2


title: S2P-RNAPII_b_rep1


title: S5P-RNAPII_m_rep1

value: EtOH


title: S5P-RNAPII_m_rep2


title: S2P-RNAPII_b_rep3


title: S2P-RNAPII_m_rep1


title: WT, rep 3

tag: strain background

tag: genotype/variation

value: WT

tag: cell type

value: BMDMs

tag: treatment

value: LPS (100ng/ml) for 4 hrs


title: S2P-RNAPII_m_rep3


title: S5P-RNAPII_b_rep1


title: S2P-RNAPII_m_rep2


title: ATACseq_day20_2

first: Zhana

last: Duren

address: 318 Campus Drive

institute: Stanford university

description: Retinoic-acid induction

data_processing:
RNA-seq: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using SRAR.
RNA-seq: Fregments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using RSEM.
ATAC-seq: Reads are mapped to mm9 by ATAC-seq pipeline described in https://www.encodeproject.org/atac-seq/.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include openess values for each Sample on union peaks

source_name: mouse embryonic stem cell

growth_protocol: mESC cells R1 were grown in mESC medium supplemented with 15% Knockout Serum Replacement and 1,000 U/ml of LIF. mESCs were differentiated using the handing drop method for 48 hours. Then, embryoid bodies (EBs) were collected for further treatment.

extract_protocol:
Total RNA were extracted using Qiagen RNeasy mini kit.
RNA-seq library were constructed using the NEBNext Ultra RNA Library Prep kit for Illumina. ATAC-seq library were constructed using Tn5 transposase, followed by PCR amplification.

treatment_protocol: EBs were placed in the well of a 6-well ultra-low attachment plate with fresh differentiation medium containing 0.5 mM retinoic acid (RA) for up to 20 days, with the medium being changed daily.

tag: time point


title: ATACseq_day20_6

description: Retinoic-acid induction


title: ATACseq_day4_9

description: Retinoic-acid induction


title: ATACseq_day20_3

description: Retinoic-acid induction


title: ATACseq_day20_1

description: Retinoic-acid induction


title: ATACseq_day20_5

description: Retinoic-acid induction


title: Control [LHb_H2_S2]

city: Seattle

first: Koichi

last: Hashikawa

state: WA

address: 1959 NE Pacific St. HSB J135

institute: University of Washington

data_processing:
Nextseq v2.5 following standard illumina protocols.
fastq files were aligned to mouse genome using Cell ranger pipeline (v2, 10x genomics)
Genome_build: mm10
Supplementary_files_format_and_content: barcode.tsv, genes.tsv and matrix.mtx to generate genexcells matrix. Txt files showing non-doublets barcodes.

source_name: habenula

extract_protocol:
Immediately after the shock session, mice were deeply anesthetized with intraperitoneal injection of 0.2 mL of stock solution containing sodium pentobarbital (39 mg/mL) and phenytoin sodium (5mg/mL) and transcardially perfused with ice-old NMDG-aCSF containing inhibitor cocktails which was used throughout procedures unless noted. NMDG-aCSF: 96 mM NMDG, 2.5 mM KCl, 1.35 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 2 mM thiourea, 5 mM Na+ ascorbate, 3 mM Na+ pyruvate, 0.6 mM glutathione-ethyl-ester, 2 mM N-acetyl-cysteine, 0.5 mM CaCl2, 10 mM MgSO4; pH 7.35-7.40, 300-305 mOsm, oxygenated with 95% O2 and 5% CO2. Inhibitor cocktails: 500 nM TTX, 10 uM APV, 10 uM DNQX, 5 µM actinomycin, 37.7 µM anysomycin. Mice in the control group were removed directly from the home cage. Brains were extracted and coronal sections containing the habenula were prepared at 300 µm using a vibratome (Leica, VT1200). Slices including the habenula (3-4 slices/animal) were recovered in a chamber for 30 min on ice. Habenula samples were then punched (0.75 mm diameter, EMS) from 4 animals/group (6-8 punches/animal) were pooled and enzymatically digested with 1 mg/mL pronase (Roche) for 45 min at room temperature, followed by mechanical trituration with fire-polished glass capillaries (tip diameter 200-300 µm) and filtered through strainers (pore size 40 µm) to remove cellular aggregates. Dead and dying cells in the cell suspension were then removed using a dead cell removal kit (Miltenyi Biotec). After centrifugation, cell concentration was manually counted using a hemocytometer and final cell concentration was adjusted to 1,000 cells/µL.
cDNA libraries were constructed following manufacture's instruction (Chronium Single Cell 3' Reagents Kits V2 User Guide, 10x Genomics). Briefly, ~17,000 dissociated cells were mixed with reverse transcription mix and loaded into the chip. The mRNAs of single cells were captured by barcoded beads using a Chromium controller. Reverse transcribed cDNAs were then PCR amplified, fragmented, and ligated with adaptors followed by sample index PCR.  cDNA libraries were sequenced on an Illumina Nextseq 500 (v2.5) and the alignment of raw sequencing reads to the mouse genome was conducted using the 10x Genomics Cell Ranger pipeline (V2) to obtain cell by gene matrices for subsequent downstream analysis.

treatment_protocol: Shock (n=4) and Control (n=4) groups were handled 5 min/day for 7 days. Mice in the Shock group were habituated to the shock chamber (Med Associates Inc.) 10 min/day for 7 days prior to the behavior experiment. On the shock day, mice in the Shock group received 30 foot-shocks (0.3 mA, 1 s duration, mean inter shock intervals: 116 s) in 60 min.

tag: tissue

value: habenula


title: S5P-RNAPII_m_rep3


title: ATACseq_day4_8

description: Retinoic-acid induction


title: N3 SW480 colon adenocarcinoma cells transfected with Stealth Negative Control Medium GC siRNAs

city: Budapest

first: Wichmann

last: Barna

address: Szentkirály

country: Hungary

institute: SOTE

description: Whole transcriptome expression data from SW480 colon adenocarcinoma cells

hyb_protocol: For sscDNA synthesis 15 µg cRNA was used and 5.5 µg fragmented and labeled sscDNA sample was hybridized to HTA 2.0 microarrays (Affymetrix) for 16 hours at 45°C with 60 rpm rotation in the Hybridization Oven (Affymetrix).

scan_protocol: Scanning was performed with GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were preprocessed by the function SST-RMA- by Gene Expression Console

source_name: SW480 colon adenocarcinoma cells

label_protocol: standard Affymetrix protocol

extract_protocol: 100 ng input total RNA samples were applied as staring material according to the manufacturer instructions

value: SW480 colon adenocarcinoma cells transfected with Stealth Negative Control Medium GC siRNAS


title: ATACseq_day4_7

description: Retinoic-acid induction


title: L2 SW480 colon adenocarcinoma cells transfected with LINC00152 Stealth siRNAs


title: L3 SW480 colon adenocarcinoma cells transfected with LINC00152 Stealth siRNAs


title: L1 SW480 colon adenocarcinoma cells transfected with LINC00152 Stealth siRNAs


title: P nano-mesh 1 week [2355]

first: Saeedeh

last: Darzi

address: 27-31 Wright Street, Clayton

data_processing:
Data were analysed using Fluidigm Real-Time PCR analysis software (V4.1.1) to obtain Ct values. The average of CT values were normalised to house keeping gene 18sRNA to provide delta CT values (delta CT test-delta CT 18sRNA). The delta delta CT was calculated as (delta CT test-delta CT sham) and fold change was calculated using formula 2^-delta delta CT.
Fold-change table reports test/control.

extract_protocol: Total RNA was extracted using RNeasy mini kit.

tag: strain

value: NSG

tag: gender

value: Female

value: Skin

value: P nano-mesh

value: 1 week

tag: sample type

value: Test