title: JH0007.Day 63

source_name: Subject: JH0007; Sample Day: Day 63 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)


title: CON_12m_M_1

status: Public on Jul 25 2019

type: SRA

city: Boston

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

country: USA

institute: Brigham and Women's Hospital

description:
PolyA RNA
processed data file: Interventions_assigned_reads.txt

library_source: transcriptomic

data_processing:
HiSeq Control Software v2.2 was used for system control and base calling through an integrated primary analysis software RTA (Real Time Analysis. v1.18). The BCL (base calls) binary was converted into FASTQ utilizing Illumina package bcl2fastq (v1.8.4).
Quality filtering and adapter removal were performed using Trimmomatic version 0.32.
Reads were mapped to mm10 mouse genome using STAR (version 2.5.2b). Genes were counted via featureCounts (version 1.5).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Interventions_assigned_reads.txt: Tab-delimited text file includes gene counts for each sample.

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
After sacrifice, liver was removed and frozen on dry ice. RNA was extracted from liver tissues with PureLink RNA Mini Kit.
Sequencing libraries were prepared for sequencing using Illumina TruSeq RNA Sample Preparation v2 protocol.

treatment_protocol: Mice were kept on control diet (Purina 5LG6 for UM-HET3, GHRKO and Snell dwarf mice; 14% kcal protein, 76% kcal carbohydrate, and 10% kcal fat diet from Research Diets for C57BL/6J mice) or the same diet supplied with the certain compounds (acarbose, rapamycin, 17aE2, Protandim). In case of CR, Purina 5LG6 diet was restricted by 40%. In case of C57Bl/6J mice, controls were fed diet containing 0.86% w/w methionine whereas MR mice were fed the same diet but with 0.12% w/w methionine.

tag: strain

tag: Sex

value: Male

tag: age

value: 12 months

tag: tissue

value: Liver

tag: intervention

value: Control

tag: dose

tag: intervention duration


title: JH0007.Day 0

type: protein

city: Irvine

first: Arlo

middle: Zan

last: Randall

state: CA

address: 1 Technology Drive, Suite E309

institute: Antigen Discovery Inc

description: ALS samples were exposed to ETEC protein microarrays and bound antibody to individual protein spots was measured by fluorescence.

hyb_protocol: ALS samples were diluted 1:2 in a 3 mg mL-1 E. coli lysate solution in protein arraying buffer (Maine Manufacturing, Sanford, ME, USA) and incubated at room temperature for 30 min. Chips were rehydrated in blocking buffer for 30 min. Blocking buffer was removed, and chips were probed with pre-incubated serum samples using sealed, fitted slide chambers to ensure no cross-contamination of sample between pads. Chips were incubated overnight at 4°C with agitation. Chips were washed five times with TBS-0.05% Tween 20, followed by incubation with biotin-conjugated goat anti-human IgG (Jackson ImmunoResearch, West Grove, PA, USA) diluted 1:200 in blocking buffer at room temperature. Chips were washed three times with TBS-0.05% Tween 20, followed by incubation with streptavidin-conjugated SureLight P-3 (Columbia Biosciences, Frederick, MD, USA) at room temperature protected from light. Chips were washed three times with TBS-0.05% Tween 20, three times with TBS, and once with water. Chips were air dried by centrifugation at 1,000 x g for 4 min and dried overnight in dessicator before scanning.

scan_protocol: Probed microarrays (slides) were scanned using a GenePix 4300A High-Resolution Microarray Scanner (Molecular Devices, Sunnyvale, CA, USA) an image file (.tif) was saved for each array using GenePix Pro 7 software. The scanned image files were quantified using the Mapix software (Innopsys) auto gridding feature. For this process two input files are required: (1) a .gal file that defines the array and sub-array layout and (2) the tiff image file for an array. Once the auto-gridding is complete the overlay of the mapped array, subarray, and individual spot locations are shown in the graphical user interface (GUI). If the automatic gridding fails to map to the correct positions the mapping can be manually adjusted using the GUI. Once the gridding is confirmed to be correct the array spots are quantified and saved to an output .gpr file. For each spot on the slide the gpr file contains the foreground intensity (median of pixels inside of circle defining spot) and local background intensity (median of pixels just outside of circle defining spot).

data_processing: Foreground spot intensities were adjusted by local background by subtraction, and negative values were converted to 1. Next, all foreground values were transformed using the base 2 logarithm. The dataset was normalized to remove systematic effects by subtracting the median signal intensity of the IVTT controls for each sample. Since the IVTT control spots carry the chip, sample and batch-level systematic effects, but also antibody background reactivity to the IVTT system, this procedure normalizes the data and provides a relative measure of the specific antibody binding to the non-specific antibody binding to the IVTT controls (a.k.a. background). With the normalized data, a value of 0.0 means that the intensity is no different than the background, and a value of 1.0 indicates a doubling with respect to background

label: biotin

molecule: protein

organism: Homo sapiens

source_name: Subject: JH0007; Sample Day: Day 0 with respect to first vaccination; Replicate: 1

label_protocol: not provided

growth_protocol: Each of the three live-attenuated strains that comprise ACE527 vaccine were grown as Master (MCB) and Working Cell Banks (WCB) and were produced under Good Manufacturing Practice at the Walter Reed Army Institute of Research (WRAIR) Pilot BioProduction Facility (PBF), Silver Spring, MD, USA. Vials from the WCBs were expanded into shake flasks to prepare a starter culture which was subsequently transferred into a 30L working volume bioreactor and grown for 5–7 h. At the desired cell density, the cells were harvested by continuous flow centrifugation. The resulting pellet was washed by centrifugation and resuspended in stabilizer solution (100 mM mannitol, 50 mM sucrose), 1.2 mL volumes were aliquoted and lyophilized in 5 mL vials which were stored at −20 °C ± 5 °C. Each strain met pre-set physical, microbiological, biochemical and antigenic criteria before being released for use in the clinical trial.

extract_protocol: not provided

treatment_protocol: Vaccine doses were prepared in a research pharmacy by reconstituting individual vials of each strain and mixing to provide 3 × 10^9 cfu of each in 10 mL of PBS per subject. ≤ two hours before dosing, the mixture was added to 190 mL of CeraVacx® buffer (Cera Products Columbia, MD). For volunteers allocated to receive dmLT, individual vials were reconstituted and diluted to a concentration of 50 µg/mL, from which 0.5 mL was added to the reconstituted vaccine ≤ five minutes before dosing. Placebo preparations consisted of 10 mL of PBS mixed with 190 mL of CeraVacx®. The CeraVacx® buffer used as the placebo and to deliver the three vaccine strains in this study has been used for the same purposes in prior Phase 1 and 2b trials of ACE527 [9], [10].

tag: subject identifier

tag: treatment group

value: Ace 527 + dmLT

tag: protected

value: yes

tag: molecule

value: anti-IgA antibody


title: CON_12m_F_3

value: Female


title: CON_12m_F_2


title: JH0007.Day 28

source_name: Subject: JH0007; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: JH0007.Day 7

source_name: Subject: JH0007; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: CON_12m_M_2


title: C2Z7Z

type: RNA

city: La Jolla

first: Vahid

middle: H

last: Gazestani

state: California

address: 8110 La Jolla Shores Drive, Suite 201

institute: UCSD

hyb_protocol: Standard Illumina hyb protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Outlier samples are removed. Expression data are log2 transformed and quantile normalized for probes with detection p-value <0.05 (standard settings).

source_name: leukocyte transcriptome

label_protocol: Standard Illumina labeling protocol

extract_protocol: four to six milliliters of blood were collected into ethylenediaminetetraacetic-coated tubes from all subjects. Total RNA was extracted following standard procedures and manufacturer’s instructions (Ambion)

tag: cell type

value: leukocyte

tag: gender

value: M

tag: age (months)

tag: diagnosis

value: PDDNOS


title: JH0007.Day 56

source_name: Subject: JH0007; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: H5A4A_repB

value: ASD


title: J6X6L

value: TD


title: CON_12m_F_1


title: B8C8D


title: C8Z4P


title: H5A4A_repA


title: Y7W5K


title: H4M6T

value: LD


title: P5N8P


title: JH0007.Day 35

source_name: Subject: JH0007; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: KM_Obese_Vehicle_28wk_Vehicle_Replicate7

first: eric

last: muise

state: MA

address: 33 Ave Louis Pasteur

department: Genetics and Pharmacogenomics

institute: Merck

data_processing:
Alignment and differential gene expression analysis was performed in Omicsoft Array Studio version 10.0.0.88.
Cleaned   reads were aligned to the Rat.B6.0 genome reference using the Omicsoft Aligner with a maximum  of 2 allowed mismatches.
Gene level counts, and FPKM, were determined by the OSA algorithm as implemented in Omicsoft Array Studio and using Ensembl.R82 gene models.
Genome_build: Rat.B6.0
Supplementary_files_format_and_content: Tab-delimited text file include FPKM values for each Sample. Each column corresponds to one sample (barcode)

organism: Rattus norvegicus

source_name: Kidney Medulla

extract_protocol:
Kidneys were removed, flash frozen in liquid nitrogen, and RNA was harvested using the Qiagen RNAeasy kit. Illumina Truseq stranded total  RNA RiboZero library preparation kit (Catalog #: RS-122-2201) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Kidney Medulla

value: 20 weeks

tag: treatment

value: Vehicle

tag: treatment time

value: 28 weeks

tag: replicate group


title: KM_Obese_Vehicle_28wk_Vehicle_Replicate6

tag: strain


title: KM_Obese_Vehicle_28wk_Vehicle_Replicate5

tag: age


title: CR_12m_M_3

tag: Sex

value: Male

value: 12 months

tag: tissue

value: CR

value: 8 months


title: RNA-Seq_mm_fc_Egr1ko_rep1

city: NY

first: zhixiong

last: sun

state: NY

address: 3908 pardes building, NYSPI

department: Psychiatry

institute: Columbia University

data_processing:
Sequencing adapters in raw sequencing reads were removed by Cutadapt (v.11.2). Moreover, the bad quality of bases in either ends of reads were trimmed by a customized Perl script. After trimming, reads were mapped to mm10 by RSEM (v1.3.0) with Bowtie2 (v2.2.9). Subsequently, DESeq2 (v 1.14.1) was employed to identify differentially expressed genes (DEGs), which were defined as (1) |log2FC|>log2(1.5); (2) p-value adjusted < 0.05.
6wk_rep1, 6wk_rep2 and 6wk_rep3 processed RNA-seq data based on raw data from from existing GSM Samples, these are used as control for our RNA-seq analysis. The GSM for 6wk_rep1: GSM1173821, GSM1173822; for 6wk_rep2: GSM1173823; for 6wk_rep3: GSM1173824
Genome_build: mm10
Supplementary_files_format_and_content: BEDGRAPH

source_name: Frontal cortex from 6 week old Egr1-/- mouse brain

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
Total RNA was extracted from mouse frontal cortex tissues using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s instructions. mRNA-Seq libraries were generated from 500ng total RNA with polyA+ selection of mRNA using the TruSeq Stranded mRNA Library Preparation Kit (Cat# RS-122-2101, Illumina, San Diego, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

tag: tissue/cell type

value: brain (frontal cortex)

tag: genotype

value: male


title: CR_12m_M_2

value: Liver

tag: intervention

tag: dose

tag: intervention duration


title: KM_Obese_Vehicle_28wk_Vehicle_Replicate4


title: JH0040.Day 7.Post

source_name: Subject: JH0040; Sample Day: Day 7.Post with respect to challenge; Replicate: 1

value: antibody lymphocyte supernatants (ALS)

tag: subject identifier

tag: treatment group

value: Ace 527 + dmLT

tag: protected

value: no

tag: molecule

value: anti-IgA antibody


title: CR_12m_M_1


title: JH0026.Day 56

source_name: Subject: JH0026; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: KM_Obese_Vehicle_28wk_Vehicle_Replicate3

tag: treatment


title: N2Y9F

tag: cell type

value: leukocyte

tag: gender

value: M

tag: age (months)

tag: diagnosis

value: TD


title: CR_12m_F_3

tag: strain

tag: Sex

value: Female

tag: age


title: JH0040.Day 35

source_name: Subject: JH0040; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

tag: tissue


title: CR_12m_F_2


title: KM_Obese_MK_8722_28wk_1mpk_Replicate6

value: Kidney Medulla

value: 20 weeks

tag: treatment time

tag: replicate group


title: JH0040.Day 0

source_name: Subject: JH0040; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: Z3U4D

value: ASD


title: KM_Obese_MK_8722_28wk_1mpk_Replicate4

value: 28 weeks


title: KM_Obese_MK_8722_28wk_1mpk_Replicate7


title: CR_12m_F_1

value: 12 months

tag: intervention

value: CR

tag: dose


title: ACA_12m_M_3

value: Male

value: Acarbose

tag: intervention duration

value: 8 months


title: JH0040.Day 7

source_name: Subject: JH0040; Sample Day: Day 7 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)

tag: subject identifier

tag: treatment group


title: S4X9Y_repA


title: JH0040.Day 56

source_name: Subject: JH0040; Sample Day: Day 56 with respect to first vaccination; Replicate: 1

value: Ace 527 + dmLT

tag: protected

tag: molecule


title: J3L5W_repB

tag: cell type


title: JH0040.Day 63

source_name: Subject: JH0040; Sample Day: Day 63 with respect to first vaccination; Replicate: 1

value: no


title: W3P6A

tag: gender


title: ACA_12m_M_1

value: Liver


title: KM_Obese_MK_8722_28wk_1mpk_Replicate2

tag: treatment


title: ACA_12m_M_2


title: KM_Obese_MK_8722_28wk_1mpk_Replicate1


title: KM_Obese_MK_8722_28wk_10mpk_Replicate6


title: JH0045.Day 28

source_name: Subject: JH0045; Sample Day: Day 28 with respect to first vaccination; Replicate: 1

value: Placebo

value: yes

value: anti-IgA antibody


title: JH0045.Day 7

source_name: Subject: JH0045; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: ACA_12m_F_2

source_name: Liver

value: Female


title: JH0040.Day 28

source_name: Subject: JH0040; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: KM_Obese_MK_8722_28wk_10mpk_Replicate3

value: Kidney Medulla


title: K8G4A

value: leukocyte

value: M

tag: age (months)

tag: diagnosis

value: TD


title: ACA_12m_F_3

tag: strain

tag: Sex

value: 12 months


title: J2W9F


title: Z3W7W

value: ASD


title: JH0045.Day 63

source_name: Subject: JH0045; Sample Day: Day 63 with respect to first vaccination; Replicate: 1

tag: tissue


title: ACA_12m_F_1

tag: age


title: KM_Obese_MK_8722_28wk_10mpk_Replicate2

value: 20 weeks

tag: treatment time

value: 28 weeks

tag: replicate group


title: KM_Obese_MK_8722_28wk_10mpk_Replicate1


title: JH0045.Day 0

source_name: Subject: JH0045; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: JH0045.Day 35

source_name: Subject: JH0045; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: KM_Obese_MK_8722_28wk_10mpk_Replicate5


title: P6C6P

source_name: leukocyte transcriptome


title: KM_Obese_Enalpril_28wk_10mpk_Replicate7

source_name: Kidney Medulla

value: Enalpril


title: J3L5W_repA


title: JH0045.Day 56

source_name: Subject: JH0045; Sample Day: Day 56 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)


title: KM_Obese_Enalpril_28wk_10mpk_Replicate5


title: JH0045.Day 7.Post

source_name: Subject: JH0045; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: JH0075.Day 35

source_name: Subject: JH0075; Sample Day: Day 35 with respect to first vaccination; Replicate: 1


title: H2Q8U

value: PDDNOS


title: KM_Obese_Enalpril_28wk_10mpk_Replicate3


title: S2F4Y


title: P8G8P


title: non-metastatic PCa 19

city: Toronto

first: Yutaka

last: Amemiya

state: ON

address: 2075 Bayview Ave.

country: Canada

institute: Sunnybrook Research Institute

description:
cDNA from small RNA fraction
R657

data_processing:
Ion Torrent sequencing was performed for 160 flows on an Ion S5XL Sequencer with Ion 540 Chips.
Ion Torrent platform-specific pipeline software (Torrent Suite version 5.0.4; ThermoFisher Scientific) was used to remove polyclonal, low quality and adapter dimer reads and then separate barcoded reads for each sample.
Ion Torrent platform-specific Small RNA Analysis plug-in (v5.0.5) was used to analyze micro RNA reads.
Reads were aligned to mature micro RNAs (mirBase build 21) using bowtie2 aligners.
Unmapped reads were further aligned to the hg19 Human genome reference to rescue miRbase unaligned reads and count other RNA molecules.
Genome_build: hg19 Human genome reference
Supplementary_files_format_and_content: text files.  Raw read count and normalized reads count (RPM, reads per million).

source_name: Prostate cancer tissue

extract_protocol:
FFPE cores with a diameter of 1 mm and a maximum length of 3 mm were used for total RNA extraction. FFPE cores were manually ground in a 1.5ml conical tube using plastic pellet pestles. Total RNA was then extracted using the RecoverAll Total Nucleic Acid Isolation Kit for FFPE (ThermoFisher Scientific) in accordance with the manufacturer’s manuals.
Complementary DNA (cDNA) libraries were constructed from the enriched small RNA using the Ion Total RNA-Seq Kit v2 (ThermoFisher Scientific) in accordance with the manufacturer’s manuals.

value: Prostate cancer tissue

tag: pathologic stage

tag: gleason score on radical prostatectomy specimen

tag: psa (ng/ml)

tag: metastasis

value: N

tag: recurrent

tag: positive surgical margin


title: R6P4Y

tag: cell type


title: KM_Obese_Enalpril_28wk_10mpk_Replicate2


title: D2M2C

tag: gender


title: KM_Obese_Enalpril_28wk_10mpk_Replicate6

tag: treatment


title: Z7W4J

tag: age (months)


title: iHep-2 (3D)

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Division of Organogenesis and Regeneration

country: Japan

institute: Medical Institute of Bioreguration, Kyushu University

description: induced hepatocyte-like cells

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Mouse Gene Expression Microarray 4x44K v1; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: induced hepatocyte-like cells derived from MDFs in 3D culture

label_protocol: cRNA was amplified and labelled using a Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using RNeasy Micro Kit (QIAGEN).

tag: cell/tissue type

value: induced hepatocyte-like cells

tag: culture


title: JH0075.Day 28

source_name: Subject: JH0075; Sample Day: Day 28 with respect to first vaccination; Replicate: 1

tag: subject identifier

tag: treatment group

value: Placebo

tag: protected

value: no

tag: molecule


title: iHep-1 (3D)

description: induced hepatocyte-like cells

tag: strain


title: M8C6X

tag: diagnosis


title: E7Y4A


title: Y2W7Y


title: iHep-1+ (2D)

description: induced hepatocyte-like cells

source_name: induced hepatocyte-like cells derived from MDFs in 2D culture


title: JH0075.Day 63

source_name: Subject: JH0075; Sample Day: Day 63 with respect to first vaccination; Replicate: 1

tag: tissue

value: anti-IgA antibody


title: iHep-2+ (2D)

description: induced hepatocyte-like cells


title: A6L7X


title: KM_Lean_Vehicle_28wk_Vehicle_Replicate7

value: Kidney Medulla

tag: age

value: Vehicle

tag: treatment time

tag: replicate group


title: non-metastatic PCa 18

description:
cDNA from small RNA fraction
R589

tag: pathologic stage

tag: gleason score on radical prostatectomy specimen

tag: psa (ng/ml)

tag: metastasis

tag: recurrent

tag: positive surgical margin


title: JH0075.Day 0

source_name: Subject: JH0075; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: metastatic PCa 18

description:
cDNA from small RNA fraction
R541

value: Y


title: metastatic PCa 19

description:
cDNA from small RNA fraction
R546


title: non-metastatic PCa 17

description:
cDNA from small RNA fraction
R550


title: KM_Lean_Vehicle_28wk_Vehicle_Replicate5

tag: treatment


title: KM_Lean_Vehicle_28wk_Vehicle_Replicate3


title: non-metastatic PCa 16

description:
cDNA from small RNA fraction
R515


title: non-metastatic PCa 15

description:
cDNA from small RNA fraction
R509


title: JH0075.Day 7.Post

source_name: Subject: JH0075; Sample Day: Day 7.Post with respect to challenge; Replicate: 1

tag: subject identifier


title: KM_Lean_Vehicle_28wk_Vehicle_Replicate1


title: JH0075.Day 56

source_name: Subject: JH0075; Sample Day: Day 56 with respect to first vaccination; Replicate: 1

tag: treatment group


title: JH0075.Day 7

source_name: Subject: JH0075; Sample Day: Day 7 with respect to first vaccination; Replicate: 1

tag: protected


title: JH0033.Day 35

source_name: Subject: JH0033; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

value: Ace 527 + dmLT

value: yes

tag: molecule


title: KC_Obese_Vehicle_28wk_Vehicle_Replicate6

source_name: Kidney Cortex

tag: strain

value: Kidney Cortex


title: KM_Lean_Vehicle_28wk_Vehicle_Replicate6

value: 20 weeks


title: non-metastatic PCa 14

description:
cDNA from small RNA fraction
R503


title: metastatic PCa 17

description:
cDNA from small RNA fraction
R457


title: KC_Obese_Vehicle_28wk_Vehicle_Replicate5

value: 28 weeks


title: Q2H7B

tag: cell type

value: leukocyte

tag: gender

value: M

tag: age (months)

tag: diagnosis

value: TD


title: R2H8H


title: J2B8Q


title: JH0033.Day 7

source_name: Subject: JH0033; Sample Day: Day 7 with respect to first vaccination; Replicate: 1

tag: tissue

value: antibody lymphocyte supernatants (ALS)


title: KC_Obese_Vehicle_28wk_Vehicle_Replicate3

tag: age

tag: treatment time

tag: replicate group


title: JH0033.Day 28

source_name: Subject: JH0033; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: JH0033.Day 0

source_name: Subject: JH0033; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: V5J4N

source_name: leukocyte transcriptome


title: metastatic PCa 15

description:
cDNA from small RNA fraction
R451

value: Prostate cancer tissue

tag: pathologic stage

tag: gleason score on radical prostatectomy specimen

tag: psa (ng/ml)

tag: metastasis


title: KC_Obese_Vehicle_28wk_Vehicle_Replicate2

tag: treatment


title: H5Z7Y_repB

value: LD


title: non-metastatic PCa 13

description:
cDNA from small RNA fraction
R450

value: N

tag: recurrent

tag: positive surgical margin


title: KC_Obese_Vehicle_28wk_Vehicle_Replicate1


title: A5M2D

value: PDDNOS


title: H5Z7Y_repA


title: R3E9X_repA


title: JH0033.Day 56

source_name: Subject: JH0033; Sample Day: Day 56 with respect to first vaccination; Replicate: 1

tag: subject identifier

tag: treatment group

tag: protected

tag: molecule

value: anti-IgA antibody


title: JH0033.Day 7.Post

source_name: Subject: JH0033; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: JH0033.Day 63

source_name: Subject: JH0033; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: KC_Obese_MK_8722_28wk_1mpk_Replicate7

tag: strain


title: metastatic PCa 13

description:
cDNA from small RNA fraction
R432

source_name: Prostate cancer tissue


title: metastatic PCa 14

description:
cDNA from small RNA fraction
R433


title: metastatic PCa 16

description:
cDNA from small RNA fraction
R454


title: KC_Obese_MK_8722_28wk_1mpk_Replicate6


title: JH0031.Day 7

source_name: Subject: JH0031; Sample Day: Day 7 with respect to first vaccination; Replicate: 1

value: Ace 527


title: KC_Obese_MK_8722_28wk_1mpk_Replicate4


title: R3E9X_repB

tag: cell type

tag: gender

tag: age (months)

tag: diagnosis


title: KC_Obese_MK_8722_28wk_1mpk_Replicate2

tag: tissue

tag: age

tag: treatment time

tag: replicate group


title: JH0031.Day 7.Post

source_name: Subject: JH0031; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: JH0031.Day 63

source_name: Subject: JH0031; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: metastatic PCa 12

description:
cDNA from small RNA fraction
R407

tag: pathologic stage

tag: gleason score on radical prostatectomy specimen

tag: psa (ng/ml)

tag: metastasis


title: JH0031.Day 28

source_name: Subject: JH0031; Sample Day: Day 28 with respect to first vaccination; Replicate: 1

tag: subject identifier


title: KC_Obese_MK_8722_28wk_1mpk_Replicate1

tag: treatment


title: metastatic PCa 11

description:
cDNA from small RNA fraction
R378

tag: recurrent

tag: positive surgical margin


title: JH0031.Day 0

source_name: Subject: JH0031; Sample Day: Day 0 with respect to first vaccination; Replicate: 1

tag: treatment group

tag: protected

tag: molecule


title: KC_Obese_MK_8722_28wk_10mpk_Replicate7

tag: strain


title: R3X6V

tag: cell type

tag: gender

tag: age (months)

tag: diagnosis

value: PreemieNoDelay


title: W4U6W


title: X3P3Q


title: Y5Z3H


title: JH0031.Day 56

source_name: Subject: JH0031; Sample Day: Day 56 with respect to first vaccination; Replicate: 1

tag: tissue


title: non-metastatic PCa 10

description:
cDNA from small RNA fraction
R320

tag: pathologic stage

tag: age


title: KC_Obese_MK_8722_28wk_10mpk_Replicate5

tag: treatment time

tag: replicate group


title: non-metastatic PCa 9

description:
cDNA from small RNA fraction
R268

tag: gleason score on radical prostatectomy specimen

tag: psa (ng/ml)

tag: metastasis

value: Y


title: KC_Obese_MK_8722_28wk_10mpk_Replicate6

tag: treatment


title: JH0031.Day 35

source_name: Subject: JH0031; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

tag: subject identifier

tag: treatment group


title: non-metastatic PCa 8

description:
cDNA from small RNA fraction
R267

tag: recurrent

tag: positive surgical margin


title: JH0030.Day 63

source_name: Subject: JH0030; Sample Day: Day 63 with respect to first vaccination; Replicate: 1

value: Placebo

tag: protected

value: no

tag: molecule


title: non-metastatic PCa 7

description:
cDNA from small RNA fraction
R256


title: KC_Obese_MK_8722_28wk_10mpk_Replicate2

source_name: Kidney Cortex

tag: strain

value: Kidney Cortex


title: R7K2D

tag: cell type

tag: gender

tag: age (months)

tag: diagnosis


title: KC_Obese_MK_8722_28wk_10mpk_Replicate4

tag: tissue

tag: age

value: 20 weeks

tag: treatment time


title: JH0030.Day 28

source_name: Subject: JH0030; Sample Day: Day 28 with respect to first vaccination; Replicate: 1


title: KC_Obese_Enalpril_28wk_10mpk_Replicate7

value: Enalpril

value: 28 weeks

tag: replicate group


title: JH0030.Day 56

source_name: Subject: JH0030; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: S3D7F

value: leukocyte

value: M

value: ASD


title: metastatic PCa 10

description:
cDNA from small RNA fraction
R254

value: Prostate cancer tissue

tag: pathologic stage

tag: gleason score on radical prostatectomy specimen

tag: psa (ng/ml)

tag: metastasis


title: L9U2V


title: metastatic PCa 9

description:
cDNA from small RNA fraction
R248

tag: recurrent


title: HIP3

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: RNA derived from the pancreatic duct gland compartment in HIAPP-expressing transgenic animals (HIP)

data_processing:
Aligned to rn5 using STAR spliced read aligner
Count read using HT-seq and using rn5 RefSeq as reference
Genes with count 0 across samples were removed. Normalization (TMM), quantitation (logCPM) and differential expression analysis using edgeR and limma voom.
Genome_build: rn5
Supplementary_files_format_and_content: logCPM values

extract_protocol:
RNA was extracted using the PicoPure® RNA Isolation Kit, KIT0204
Libraries prepared using the Nugen Ultra Low Mass RNA Library Prep Kit

treatment_protocol: The PDG compartment was identified morphologically and cut into 0.5 ml tube cap filled with 10 µl of extraction buffer and 0.5 µl RNase inhibitor. To avoid RNA degradation, slides were processed one at a time, and staining and dissection from each slide was finished within 20 min. The LCM procedure was performed using a Leica LMD7000 Laser Microdissection system

value: Sprague-Dawley

tag: genotype

value: transgenic (HIAPP-expressing, or HIP)

value: pancreatic duct gland


title: KC_Obese_Enalpril_28wk_10mpk_Replicate6

tag: treatment


title: HIP2


title: metastatic PCa 8

description:
cDNA from small RNA fraction
R247

tag: positive surgical margin

value: N


title: JH0030.Day 35

source_name: Subject: JH0030; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)

tag: subject identifier

tag: treatment group

tag: protected

tag: molecule

value: anti-IgA antibody


title: JH0030.Day 7

source_name: Subject: JH0030; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: Y7H4L

source_name: leukocyte transcriptome

tag: cell type

tag: gender

tag: age (months)

tag: diagnosis

value: TD


title: KC_Obese_Enalpril_28wk_10mpk_Replicate4

tag: strain

tag: tissue

tag: age

tag: treatment time

tag: replicate group


title: HIP30


title: K9S3V


title: K4X5H


title: M8U6H


title: JH0030.Day 0

source_name: Subject: JH0030; Sample Day: Day 0 with respect to first vaccination; Replicate: 1

value: Placebo


title: K3S4A

value: LD


title: non-metastatic PCa 6

description:
cDNA from small RNA fraction
R221

tag: pathologic stage

tag: gleason score on radical prostatectomy specimen

tag: psa (ng/ml)

tag: metastasis

tag: recurrent

value: Y


title: JH0030.Day 7.Post

source_name: Subject: JH0030; Sample Day: Day 7.Post with respect to challenge; Replicate: 1

tag: subject identifier

tag: treatment group

value: no


title: WT4

description: RNA derived from the pancreatic duct gland compartment in WT animals

tag: genotype

value: WT


title: KC_Obese_Enalpril_28wk_10mpk_Replicate1

value: Kidney Cortex

value: 20 weeks

tag: treatment

value: Enalpril

value: 28 weeks


title: non-metastatic PCa 5

description:
cDNA from small RNA fraction
R212

source_name: Prostate cancer tissue

value: Prostate cancer tissue

tag: positive surgical margin


title: WT1

value: Sprague-Dawley


title: JH0023.Day 28

source_name: Subject: JH0023; Sample Day: Day 28 with respect to first vaccination; Replicate: 1

value: Ace 527 + dmLT

tag: protected

value: yes

tag: molecule


title: metastatic PCa 7

description:
cDNA from small RNA fraction
R211

value: N


title: KC_Lean_Vehicle_28wk_Vehicle_Replicate7

tag: strain

value: Vehicle


title: metastatic PCa 6

description:
cDNA from small RNA fraction
R208

tag: tissue


title: KC_Lean_Vehicle_28wk_Vehicle_Replicate6

tag: age


title: JH0023.Day 7.Post

source_name: Subject: JH0023; Sample Day: Day 7.Post with respect to challenge; Replicate: 1

value: antibody lymphocyte supernatants (ALS)

value: anti-IgA antibody


title: WT26

value: pancreatic duct gland


title: JH0023.Day 0

source_name: Subject: JH0023; Sample Day: Day 0 with respect to first vaccination; Replicate: 1


title: metastatic PCa 5

description:
cDNA from small RNA fraction
R205


title: KC_Lean_Vehicle_28wk_Vehicle_Replicate3

tag: treatment time


title: KC_Lean_Vehicle_28wk_Vehicle_Replicate2

tag: replicate group


title: JH0023.Day 7

source_name: Subject: JH0023; Sample Day: Day 7 with respect to first vaccination; Replicate: 1


title: metastatic PCa 4

description:
cDNA from small RNA fraction
R197

tag: pathologic stage


title: metastatic PCa 3

description:
cDNA from small RNA fraction
R189

tag: gleason score on radical prostatectomy specimen


title: KC_Lean_Vehicle_28wk_Vehicle_Replicate1


title: KC_Obese_Enalpril_28wk_10mpk_Replicate2


title: L_3

city: Chengdu

first: Meng-qi

last: Wang

address: Huimin street 211

country: China

institute: Sichuan 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  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: http://www.mbkbase.org/Pinku1/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Verbena bonariensis

source_name: leaves

growth_protocol: Verbena bonariensis seeds were available from Benary Manufacturer and grown in the greenhouse (16 h photoperiod, 25℃/16℃ day/night temperature)

extract_protocol:
Verbena bonariensis leaves were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 3 months old Verbena bonariensis seedlings were treated in 4℃ for 24 h, followed by -4℃ for 4 h. Control seedlings remains unchanged.  The leaves samples were immediately frozen in liquid nitrogen and stored at -80°C.It’s three biological replicates per treatment for subsequent RNA extraction and analysis.

value: Finesse

value: leaves

tag: stress

value: control


title: JH0023.Day 56

source_name: Subject: JH0023; Sample Day: Day 56 with respect to first vaccination; Replicate: 1


title: T_1

value: low temperature


title: T_2


title: JH0023.Day 63

source_name: Subject: JH0023; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: non-metastatic PCa 4

description:
cDNA from small RNA fraction
R137

tag: psa (ng/ml)

tag: metastasis

value: Y


title: L_2


title: non-metastatic PCa 3

description:
cDNA from small RNA fraction
R132

tag: recurrent


title: L_1


title: metastatic PCa 2

description:
cDNA from small RNA fraction
R109


title: RatIC_PC1_DMSO

city: Biberach

first: Christian

middle: Thaddaeus

last: Wohnhaas

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

description: Animals were either fed with choline-sufficient, l-amino acid-defined (CSAA) diet or choline-deficient, l-amino acid-defined (CDAA) diet

data_processing:
Reads: Read 1: 26 bp (cell barcode and UMI), Index read: 8, Read 2: 98 (sequence read)
Data were processed with Cell Ranger version 2.1.1. Raw base BCL files were demultiplexed using "cellranger mkfastq" and bcl2fastq v2.17.1.14. FASTQ files generated from "cellranger mkfastq" were further processed by "cellranger count"  which made use of STAR  to align the 98 bp sequence read against Rnor6.0. Filtering for valid cell barcodes and quantification of cell barcodes as well as unique molecular identifiers (UMIs) was also performed using "cellranger count".
Genome_build: Rnor6.0
Supplementary_files_format_and_content: Market Exchange format containing three files: tab-separated values files containing barcodes and annotated genes, respectively, matrix file containing UMI counts and indices for the barcode and gene tsv files

molecule: polyA RNA

source_name: immune cells

extract_protocol:
Livers were sequentially pushed through 500 µm, 200 µm and 70 µm filters and the cells were washed using chilled PBS/0.5 % FCS buffer. Erythrocytes were lysed using RBC Lysis Buffer (Invitrogen, Thermo Fisher Scientific, Waltham, MA) and the cells were resuspended in 15 mL of PBS/0.5 % FCS buffer. The cell suspension was transferred on top of 12 mL of Lymphocyte Separation Medium (Lonza, Basel, Switzerland) and centrifuged for 20 min at 400 g and 4 °C (brake set to 7) to separate the immune cells. Droplet-based single-cell partitioning of washed immune cells was performed using the 10X Genomics Chromium Controller.
Single-cell RNA-Seq libraries were generated using the Chromium Single-Cell 3′ Reagent v2 Kit (10X Genomics, Pleasanton, CA) according to the manufacturer´s instructions.

tag: timepoint

value: week 3

tag: preservation protocol

value: DMSO cryopreservation

value: Han Wistar

value: liver

tag: diet

value: CDAA


title: RatIC_PC2_DMSO


title: JH0023.Day 35

source_name: Subject: JH0023; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

tag: subject identifier

tag: treatment group

value: Ace 527 + dmLT


title: T_3


title: JH0038.Day 28

source_name: Subject: JH0038; Sample Day: Day 28 with respect to first vaccination; Replicate: 1

tag: protected

value: no

tag: molecule


title: JH0038.Day 56

source_name: Subject: JH0038; Sample Day: Day 56 with respect to first vaccination; Replicate: 1

tag: tissue


title: RatIC_NC2_DMSO

tag: strain

value: CSAA


title: salt rep3

city: Shanghai

first: Zaizhi

last: You

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Trinity was used for de novo transcriptome assembly.
Supplementary_files_format_and_content: FA files include unigene and excel file include differential expression of genes.

organism: Parachlorella kessleri

source_name: Parachlorella kessleri cells

extract_protocol:
The RNAs for RNA-seq from Parachlorella kessleri cells, were extracted by TRIzol (Invitrogen, USA) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Proton Sequencing process protocols

tag: treatment

value: cultivated under salt stress conditions


title: non-metastatic PCa 2

description:
cDNA from small RNA fraction
R094

value: Prostate cancer tissue

tag: age

value: N

tag: positive surgical margin


title: RatIC_NC1_DMSO


title: salt rep2


title: JH0038.Day 35

source_name: Subject: JH0038; Sample Day: Day 35 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)

value: anti-IgA antibody


title: RatIC_PC2_fresh

value: fresh

value: no preservation


title: JH0038.Day 7.Post

source_name: Subject: JH0038; Sample Day: Day 7.Post with respect to challenge; Replicate: 1


title: con rep3

value: cultivated under control conditions


title: cut explant [TR2]

city: Martonvásár

first: Norbert

middle: Tibor

last: Hidvégi

address: Brunszvik street 2.

department: Department of Biological Resources

country: Hungary

institute: HUN-REN Centre for Agricultural Research Agricultural Institute

description: wild type with stress conditions

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequence reads were trimmed with TrimGalore v0.5.0 and aligned to the reference genome with HISAT2 v2.1.0.
From the aligned mRNA reads the differentially expressed genes were analyzed with SeqMonk v1.42.0. We calculated the quantitated values in reads per million reads of input and were log2 transformed. To filter the list of quantitated genes for significantly differentially expressed genes with the intensity difference filter in SeqMonk, which is based on the X2 probe.
Genome_build: GCA_000226075.1 assembly from EMBL (https://www.ebi.ac.uk/ena/data/view/GCA_000226075.1)
Supplementary_files_format_and_content: SeqMonk data file in smk file format with intensity difference filter.

organism: Solanum tuberosum

source_name: wild type with stress conditions

growth_protocol: Four-week-old in vitro potato plantlets (cv. Desirée) were used for the experiment. The culture conditions, medium and vessels used were the same as in our earlier study (Dobránszki et al., 2017). Dobránszki J, Asboth G, Homoki D, Bíró-Molnár P, Teixeira da Silva JA, Remenyik J (2017) Ultrasonication of in vitro potato single node explants: activation and recovery of antioxidant defence system and growth responses. Plant Physiology and Biochemistry 121: 153–160

extract_protocol:
Total RNA was purified with Zymo Research Direct-zol kit with TRIzol reagent. We used the manufacturer”s protocol. mRNA from the samples was enriched using oligo(dT) beads. For long non-coding libraries, rRNA was removed using the Plant Ribo-Zero rRNA removal kit (Illumina, San Diego, CA, USA) using the manufacturer’s protocol, resulting in mRNA (rRNA-depleted RNA-seq).
Using the Illumina TruSeq Stranded mRNA kit, mRNA was first randomly fragmented by adding fragmentation buffer, then cDNA was synthesized with an mRNA template and a random hexamer primer, after which a custom second-strand synthesis buffer, dNTPs, RNase H and DNA polymerase I were added to initiate second-strand synthesis. The second step involved terminal repair, A ligation and sequencing adaptor ligation, after which the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: Single-node segments with a single leaf were cut from whole 4-week-old in vitro plantlets, and cutting served as the experimental treatment. Uncut plantlets served as the control.

tag: cultivar

value: cv. Desiree

tag: genotype

value: wild type

value: 4 week

tag: condition

value: cutting stress

value: leaf


title: JH0038.Day 63

source_name: Subject: JH0038; Sample Day: Day 63 with respect to first vaccination; Replicate: 1


title: non-metastatic PCa 1

description:
cDNA from small RNA fraction
R038

source_name: Prostate cancer tissue

tag: pathologic stage

tag: gleason score on radical prostatectomy specimen

tag: psa (ng/ml)

tag: metastasis


title: metastatic PCa 1

description:
cDNA from small RNA fraction
R028

value: Y

tag: recurrent


title: RatIC_PC1_fresh

tag: timepoint

tag: preservation protocol

value: Han Wistar

value: liver

tag: diet

value: CDAA


title: RatIC_NC2_fresh

value: CSAA


title: JH0038.Day 0

source_name: Subject: JH0038; Sample Day: Day 0 with respect to first vaccination; Replicate: 1

tag: subject identifier

tag: treatment group

tag: protected

value: no

tag: molecule


title: con rep2

tag: treatment


title: con rep1


title: RatIC_NC1_fresh

tag: strain

tag: tissue


title: uncut explant [TR1]

description: wild type without stress conditions

source_name: wild type without stress conditions

tag: cultivar

tag: genotype

tag: age


title: HCC.097.H

status: Public on Jul 24 2019

first: David

middle: T

last: Ting

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
The paired-end reads from the three sequencing runs were combined and aligned to the hg38 genome from http://genome.ucsc.edu using the STAR v2.4.0h aligner with default settings. Reads that did not map or mapped to multiple locations were discarded.
Duplicate reads were marked using the MarkDuplicates tool in picard-tools-1.8.4 and were removed.
The uniquely aligned reads were counted using htseq-count in the intersection-strict mode against the Homo_sapiens.GRCh38.79.gtf annotation table from http://www.ensembl.org.
Genome_build: hg38
Supplementary_files_format_and_content: Raw unnormalized counts are in the processed data file as a count table

source_name: Helper T cells

extract_protocol:
RNA extraction and isolation protocol: CEC-enriched samples were flash frozen in RNAlater and stored at -80 deg C. RNA was later extracted in batches using the RNEasy micro kit (Qiagen).
Nextera XT DNA library preparation kit (Illumina)

value: Peripheral blood

tag: cell type

value: Helper T cells

tag: diagnosis

value: Hepatocellcular carcinoma patient


title: HCC.097.M

source_name: Monocytes

value: Monocytes


title: HCC.097.N

source_name: NK cells

value: NK cells


title: HCC.074.N


title: HCC.097.G

source_name: Granulocytes

value: Granulocytes


title: HCC.074.M


title: HCC.074.H


title: HCC.097.B

source_name: B cells

value: B cells


title: HCC.063.N


title: salt rep1

value: cultivated under salt stress conditions


title: JH0038.Day 7

source_name: Subject: JH0038; Sample Day: Day 7 with respect to first vaccination; Replicate: 1

value: antibody lymphocyte supernatants (ALS)

value: anti-IgA antibody


title: HCC.063.M


title: HCC.063.H


title: HCC.063.C

source_name: Cytotoxic T cells

value: Cytotoxic T cells


title: HCC.063.B


title: HCC.074.G


title: HCC.021.N


title: HCC.097.C


title: HCC.021.M


title: HCC.021.H


title: HCC.021.C


title: HCC.105

source_name: Circulating epithelial cells

value: Circulating epithelial cells


title: Gipr +ve Hypothalamic cells replicate 2_3

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

data_processing:
Base calls were preprocessed using Cellranger mkfastq command (version 2.0) to generate fastqs
Cellranger count command was used to map reads to the mouse genome and to measure gene abundance
Cellranger aggr command was used to aggregate combine the data from the two replicates
Further analyses (TSNE, Clustering and DGE) were performed using Seurat V3.0
Genome_build: mm10
Supplementary_files_format_and_content: Raw UMI counts from cells are provided in a tab-delimted data matrix

source_name: Gipr +ve Hypothalamic cells

extract_protocol:
Hypothalamic tissue isolated from GIPREYFP mice was digested into single cells using papain. Gipr +ve cells were FACS purified based on their EYFP fluorescence. Purified Gipr +ve cells were loaded onto the 10 X Genomics platform for single cell library construction.
10X Genomics 3'GEX  V2
single cell RNAseq

tag: strain background

value: 4-6 weeks old

value: Hypothalamus

tag: replicate

value: GIPREYFP

tag: data chunk


title: Gipr +ve Hypothalamic cells replicate 2_10


title: Gipr +ve Hypothalamic cells replicate 2_2


title: Gipr +ve Hypothalamic cells replicate 2_12


title: Gipr +ve Hypothalamic cells replicate 2_8


title: Gipr +ve Hypothalamic cells replicate 2_4


title: Gipr +ve Hypothalamic cells replicate 2_11


title: Gipr +ve Hypothalamic cells replicate 2_5


title: Gipr +ve Hypothalamic cells replicate 2_1


title: HCC.104


title: HCC.063.G


title: Gipr +ve Hypothalamic cells replicate 2_7


title: Gipr +ve Hypothalamic cells replicate 1_10


title: Gipr +ve Hypothalamic cells replicate 2_6


title: HCC.102


title: HCC.101


title: Gipr +ve Hypothalamic cells replicate 1_8


title: HCC.099


title: HCC.021.B


title: HCC.098


title: Gipr +ve Hypothalamic cells replicate 1_5


title: Gipr +ve Hypothalamic cells replicate 1_11


title: Gipr +ve Hypothalamic cells replicate 1_4


title: HCC.093


title: Gipr +ve Hypothalamic cells replicate 1_3


title: Gipr +ve Hypothalamic cells replicate 1_12


title: HCC.090


title: HCC.103


title: HCC.091


title: HCC.095


title: HCC.087


title: non-metastatic PCa 11

description:
cDNA from small RNA fraction
R427

value: Prostate cancer tissue

tag: pathologic stage

tag: gleason score on radical prostatectomy specimen

tag: psa (ng/ml)

tag: metastasis

value: N

tag: recurrent

tag: positive surgical margin

value: Y


title: Gipr +ve Hypothalamic cells replicate 1_6


title: Gipr +ve Hypothalamic cells replicate 1_9


title: HCC.084_2

value: Peripheral blood


title: Gipr +ve Hypothalamic cells replicate 1_2


title: Gipr +ve Hypothalamic cells replicate 1_7


title: HCC.082

value: Hepatocellcular carcinoma patient


title: HCC.094


title: Neocortex Control 1

city: Copenhagen

first: Guido

last: Barzaghi

address: Strandlodsvej 19B, st TH

country: Denmark

institute: University of Copenhagen

data_processing:
The raw reads generated through Illumina HiSeq2500 platform were aligned using STAR to the human genome hg19/GRCh37
The tool FeatureCount from subread v1.6.2 has been employed to produce the count matrix
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: CountMatrix.tsv

source_name: Brain

extract_protocol:
RNA was extracted from flash frozen biopsies using AllPrep DNA/RNA/protein Extraction Kit (Qiagen) according to manufacturer's instructions. In brief, tissue biopsies was cut into smaller pieces and submerged in lysis buffer. Extraction was done on a QIAcube liquid handling system (Qiagen). After extraction, RNA was quantified and analyzed for purity and size distribution using a Bioanalyzer (Agilent).
For RNA sequencing, 200 ng input RNA was used for preparing RNA sequencing libraries, which was done using TruSeq Stranded Total RNA Library Prep Kit (Illumina) following manufacturer's instructions. Briefly, RNA was denatured and ribosomal RNA (rRNA) was removed using Ribominus Gold (Illumina). After cleanup, RNA was fragmented and 1st and 2nd strand synthesis performed. Finally, libraries was adaptor ligated and amplified. AMPure XP beads was used for cleaning up the prepared sequencing libraries and quantification was done using a Qubit fluorometer (Thermo Fisher). Sequencing libraries was paired-end sequenced (2x125 bp) on the Illumina HiSeq2500 platform. Sequenced reads was trimmed and mapped to hg19/GRCh37 reference genome using BWA-MEM v0.7.12 software.
Stranded Total RNA Library

tag: condition

value: without epilepsy

tag: individual

value: control patient without epilepsy

value: Neocortex


title: Hippocampus patient 17

value: mesial temporal lobe epilepsy

value: patient 17

tag: tissue

value: Hippocampus


title: Neocortex Control 2


title: Gipr +ve Hypothalamic cells replicate 1_1


title: Hippocampus patient 16

value: patient 16


title: Hippocampus patient 15

value: patient 15


title: Neocortex patient 16


title: HCC.076

value: Circulating epithelial cells


title: HCC.075


title: HCC.074


title: HCC.078


title: HCC.079


title: Neocortex patient 15


title: HCC.069


title: Neocortex patient 14

value: patient 14


title: HCC.068


title: HCC.067


title: Hippocampus patient 13

value: patient 13


title: Neocortex patient 17


title: Hippocampus patient 14


title: HCC.083


title: Hippocampus patient 12

value: patient 12


title: HCC.064


title: HCC.065


title: Gipr +ve Hypothalamic cells replicate 2_9

value: 4-6 weeks old

value: Hypothalamus

value: GIPREYFP


title: Neocortex patient 12


title: HCC.061

value: Peripheral blood


title: HCC.062

value: Hepatocellcular carcinoma patient


title: Neocortex patient 11

value: patient 11


title: Hippocampus patient 11


title: Hippocampus patient 10

value: patient 10


title: Neocortex patient 10

value: Neocortex


title: HCC.052


title: Neocortex patient 13

value: mesial temporal lobe epilepsy


title: HCC.060


title: HCC.058


title: Neocortex patient 8

value: patient 8


title: Hippocampus patient 8

value: Hippocampus


title: Hippocampus patient 7

value: patient 7


title: HCC.046


title: Hippocampus patient 6

value: patient 6


title: HCC.047

value: Circulating epithelial cells


title: Neocortex patient 6


title: Neocortex patient 7


title: Neocortex patient 9

value: patient 9


title: HCC.050


title: HCC.041_3


title: HCC.040


title: HCC.042


title: Neocortex patient 5

value: patient 5


title: HCC.035


title: HCC.030


title: Hippocampus patient 4

value: patient 4


title: HCC.097


title: HCC.029


title: Neocortex patient 4


title: Hippocampus patient 9


title: HCC.059


title: Hippocampus patient 3

value: patient 3


title: Neocortex patient 3


title: HCC.027


title: HCC.021


title: Hippocampus patient 2

value: patient 2


title: HCC.019_2


title: HCC.016_4


title: HCC.037


title: HCC.015


title: HCC.013


title: HCC.011


title: HCC.014


title: Hippocampus patient 1

value: patient 1


title: Hippocampus patient 5


title: CLD.091

value: Peripheral blood

value: Chronic liver disease patient


title: CLD.090


title: HCC.018

value: Hepatocellcular carcinoma patient


title: Normal_R11_B1

city: Pennington

first: Ron

last: Ammar

state: New Jersey

address: 311 Pennington Rocky Hill Road

institute: Bristol-Myers Squibb

description: m_20161128MN_E03P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

data_processing:
Reads were aligned to the Human genome (GRCh38) with the Omicsoft Sequence Aligner.
Gene and transcript abundance was determined with Ensembl R90 mouse gene models using RSEM.
All RNA-Seq data were processed in R with Bioconductor packages.
RNA-Seq samples were TMM normalized with the edgeR package.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files of counts and log2CPM

source_name: human subject

extract_protocol:
Total RNA was prepared using the RNeasy 96 kit (Qiagen, Germany) according to the manufacturer's instructions. cDNA synthesis was performed with high capacity RNA to cDNA kit (Life Technologies, Carlsbad, CA). Sequencing libraries were generated using Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina, San Diego, CA) following manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Lung

tag: batch

tag: diseasestatus

value: Normal

tag: samplename

tag: race

value: Caucasian

tag: gender

value: Male

tag: tobacco

value: Never smoked

tag: height

tag: weight


title: IPF_R22_B1

description: m_20161128MN_F01P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: IPF

tag: age

value: Former smoker


title: Neocortex patient 1

value: mesial temporal lobe epilepsy

value: Neocortex


title: CLD.085

tag: cell type

value: Circulating epithelial cells

tag: diagnosis


title: CLD.086


title: CLD.088


title: Normal_R3_B1

description: m_20161128MN_A05P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Unknown


title: IPF_R32_B1

description: m_20161128MN_H02P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R18_B1

description: m_20161128MN_E02P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R28_B1

description: m_20161128MN_G05P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Other


title: Normal_R17_B1

description: m_20161128MN_G02P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Female


title: CLD.084


title: Normal_R20_B1

description: m_20161128MN_H08P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R11_B1

description: m_20161128MN_C05P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R6_B1

description: m_20161128MN_B05P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.087


title: IPF_R19_B1

description: m_20161128MN_E05P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.082


title: CLD.083


title: Normal_R7_B1

description: m_20161128MN_D01P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R31_B1

description: m_20161128MN_H01P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R36_B1

description: m_20161128MN_H06P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R33_B1

description: m_20161128MN_H03P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.081


title: CLD.080


title: CLD.078


title: CLD.079


title: CLD.076


title: CLD.077


title: Normal_R13_B1

description: m_20161128MN_F03P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Active smoker


title: Normal_R1_B1

description: m_20161128MN_A01P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R14_B1

description: m_20161128MN_D03P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.073

value: Peripheral blood


title: CLD.074

value: Chronic liver disease patient


title: CLD.071


title: CLD.075


title: IPF_R8_B1

description: m_20161128MN_C01P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R2_B2

description: T_20170808MAN1_A03P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R10_B2

description: T_20170808MAN1_H02P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R34_B1

description: m_20161128MN_H04P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: African American


title: IPF_R26_B1

description: m_20161128MN_G03P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Lung


title: IPF_R4_B1

description: m_20161128MN_B01P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R8_B2

description: T_20170808MAN1_F03P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: Normal_R2_B1

description: m_20161128MN_A02P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Normal


title: CLD.065


title: IPF_R3_B2

description: T_20170808MAN1_A04P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Caucasian


title: IPF_R7_B1

description: m_20161128MN_B07P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Male


title: CLD.062


title: CLD.070


title: IPF_R23_B1

description: m_20161128MN_F02P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.089


title: non-metastatic PCa 12

description:
cDNA from small RNA fraction
R428

value: Prostate cancer tissue

tag: pathologic stage

tag: gleason score on radical prostatectomy specimen

tag: psa (ng/ml)

tag: metastasis

value: N

value: Y


title: CLD.061


title: CLD.060


title: IPF_R21_B1

description: m_20161128MN_E08P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: IPF

value: Former smoker


title: CLD.058

value: Circulating epithelial cells


title: Normal_R14_B1

description: m_20161128MN_F04P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.072


title: CLD.057


title: IPF_R12_B1

description: m_20161128MN_C07P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.056


title: CLD.046_2


title: IPF_R5_B1

description: m_20161128MN_B03P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Never smoked


title: Normal_R5_B1

description: m_20161128MN_B06P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.040


title: CLD.036


title: Neocortex patient 2

tag: condition

value: mesial temporal lobe epilepsy

tag: individual

value: patient 2

value: Neocortex


title: CLD.038

tag: tissue

value: Peripheral blood


title: CLD.055

value: Chronic liver disease patient


title: CLD.032


title: CLD.039


title: IPF_R9_B1

description: m_20161128MN_C02P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

tag: batch

tag: diseasestatus


title: Normal_R16_B1

description: m_20161128MN_F08P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

tag: samplename

tag: race

value: Active smoker


title: IPF_R10_B1

description: m_20161128MN_C03P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Lung

tag: gender

tag: tobacco


title: IPF_R3_B1

description: m_20161128MN_A08P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: African American

tag: height

tag: weight


title: IPF_R35_B1

description: m_20161128MN_H05P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

tag: age

value: Caucasian

value: Female


title: IPF_R16_B1

description: m_20161128MN_D08P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Male


title: Normal_R6_B1

description: m_20161128MN_C04P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Normal


title: CLD.037

tag: cell type

tag: diagnosis


title: IPF_R30_B1

description: m_20161128MN_G08P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.033


title: CLD.031


title: Normal_R10_B1

description: m_20161128MN_D06P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.028


title: IPF_R13_B1

description: m_20161128MN_C08P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R15_B1

description: m_20161128MN_D07P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.027


title: ALI_R4_B2

description: T_20170808MAN1_B04P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: ALI


title: CLD.026


title: CLD.034


title: CLD.029


title: IPF_R29_B1

description: m_20161128MN_G06P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: IPF


title: CLD.025


title: IPF_R17_B1

description: m_20161128MN_E01P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Former smoker


title: ALI_R7_B2

description: T_20170808MAN1_D04P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.024

value: Circulating epithelial cells


title: IPF_R9_B2

description: T_20170808MAN1_G02P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R27_B1

description: m_20161128MN_G04P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Never smoked


title: CLD.022


title: Normal_R18_B1

description: m_20161128MN_G07P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R1_B1

description: m_20161128MN_A04P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R2_B1

description: m_20161128MN_A07P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.015_2


title: CLD.023


title: ALI_R8_B2

description: T_20170808MAN1_E03P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.013


title: Normal_R15_B1

description: m_20161128MN_F05P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.011


title: IPF_R5_B2

description: T_20170808MAN1_E04P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Other


title: CLD.012


title: Normal_R9_B1

description: m_20161128MN_D04P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.019


title: ALI_R5_B2

description: T_20170808MAN1_C04P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.010


title: CLD.009


title: CLD.017


title: IPF_R25_B1

description: m_20161128MN_F07P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.008


title: IPF_R1_B2

description: T_20170808MAN1_A01P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.007


title: ALI_R3_B2

description: T_20170808MAN1_B03P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.006


title: Normal_R19_B1

description: m_20161128MN_H07P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.005


title: CLD.004


title: Normal_R4_B1

description: m_20161128MN_B04P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: ALI_R6_B2

description: T_20170808MAN1_D01P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.002


title: normal_R3_B2

description: T_20170808MAN1_C02P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.001


title: normal_R4_B2

description: T_20170808MAN1_C03P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: CLD.003


title: normal_R6_B2

description: T_20170808MAN1_D03P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R20_B1

description: m_20161128MN_E06P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: normal_R5_B2

description: T_20170808MAN1_D02P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: normal_R8_B2

description: T_20170808MAN1_H01P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: ALI_R9_B2

description: T_20170808MAN1_F04P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Unknown


title: normal_R2_B2

description: T_20170808MAN1_C01P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: IPF_R24_B1

description: m_20161128MN_F06P1_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: MLE-12, Control-2

first: Tanyalak

last: Parimon

address: 127 San Vicente

institute: Cedars-Sinai Medical Center

data_processing:
mRNA sequencing reads were aligned to the mouse reference genome (GRCm38/mm10) using Tophat2 (2.0.7);
Aligned sequences were mapped to mouse genes with Ensembl database annotation (Mus Musculus.GRCm38.82);
The relative gene expression RPKM were estimated using SAMMate (2.7.4).
Genome_build: mouse reference genome (GRCm38/mm10)
Supplementary_files_format_and_content: RPKMs

source_name: Lung epithelial cells

growth_protocol: Cells were grown in 1xDMEM plus 10% FBS plus 1% penicillin/streptomycin

extract_protocol:
Total RNAs were isolated using Trizol reagent isolation protocol
Library preparation was performed using Illumina TruSeq Stranded mRNA library preparation kit (Illumina, San Diego, CA)

treatment_protocol: Cells were treated with extracellular vesicles from bronchoalveolar lavage fluid of bleomycin-injured wild-type or syndecan-1 deficient mice or regular cell culture media

tag: strain

value: SP-C/TAg Transgenic mice

tag: passages

value: Lung tumors

tag: cell line

value: lung epithelial cell line MLE-12

tag: treatment

value: control


title: MLE-12, WTD21-3

value: bronchoalveolar lavage fluid extracellular vesicles of bleomycin-injured, wild-type mice


title: MLE-12, KOD21-1

value: bronchoalveolar lavage fluid extracellular vesicles of bleomycin-injured, syndecan-1 deficient mice


title: MLE-12, Control-3


title: MLE-12, WTD21-2


title: MLE-12, KOD21-2


title: MLE-12, KOD21-3


title: MLE-12, WTD21-1


title: normal_R1_B2

description: T_20170808MAN1_B02P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Lung

value: Caucasian


title: IPF_R6_B2

description: T_20170808MAN1_F01P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Male


title: IPF_R4_B2

description: T_20170808MAN1_E01P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: MLE-12, Control-1


title: normal_R7_B2

description: T_20170808MAN1_E02P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: Normal


title: IPF_R7_B2

description: T_20170808MAN1_F02P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017


title: ALI_R2_B2

description: T_20170808MAN1_B01P01_IPF_Lung_UPenn_P.20161128.0001_11Sep2017

value: ALI


title: CJ24_Butyrate treatment_MDBK_H3K9me3

city: Beltsville

first: George

middle: E.

last: Liu

state: Maryland (MD)

address: 10300 Baltimore Ave Bldg 306

institute: USDA-ARS

description: CL5_CJ24_USDA_C30RTACXX_GGCTAC_L005_R1_001

library_source: genomic

data_processing:
we removed contaminating adapter molecules, reads containing ploy-N, and low-quality reads using Trim_Galore (version 0.4.1)
We then mapped clean reads to the cattle reference genome (UMD3.1.1) using BWA algorithm with default settings. We only kept reads uniquely aligned with less than two mismatches for the subsequent analysis. We employed MACS2.1.1 for peak-calling with default parameter settings by looking for significant enrichment in the studied samples when compared to the input data file (i.e., random background)
Genome_build: UMD 3.1.1
Supplementary_files_format_and_content: bed

molecule: genomic DNA

organism: Bos taurus

source_name: Butyrate treatment_MDBK_H3K9me3

extract_protocol:
Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
ChIP-seq of rumen epithelial tissue and MDBK cells were performed as reported in our earlier publication 8. In short, DNA recovered from a conventional ChIP procedure was quantified using the QuantiFluor fluorometer (Promega, Madison, WI). The DNA integrity was verified using the Agilent Bioanalyzer 2100 (Agilent; Palo Alto, CA, USA). The DNA was then processed, including end repair, adaptor ligation, and size selection, using an Illumina sample prep kit following the manufacturer’s instructions (Illumina, San Diego, CA, USA). Final DNA libraries were validated and sequenced at 75-nt per sequence read, using an Illumina HiSeq 2500 platform.

tag: breed

value: Hostein

value: Butyrate treatment

value: MDBK

tag: chip antibody

value: Mouse monoclonal to H3K9me3

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: CJ23_Butyrate treatment_MDBK_RNA pol II

description: CL5_CJ23_USDA_C30RTACXX_CTTGTA_L005_R1_001

source_name: Butyrate treatment_MDBK_RNA pol II

value: Mouse monoclonalto RNApolyII


title: CJ22_Butyrate treatment_MDBK_H3K27ac

description: CL5_CJ22_USDA_C30RTACXX_TAGCTT_L005_R1_001

source_name: Butyrate treatment_MDBK_H3K27ac

value: Rabbit polyclonal to H3K27ac


title: CJ21_Butyrate treatment_MDBK_H3K9ac

description: CL5_CJ21_USDA_C30RTACXX_GATCAG_L005_R1_001

source_name: Butyrate treatment_MDBK_H3K9ac

value: Rabbit polyclonal to H3K9ac


title: 6F-iMN-2 (Single Cell)

first: Kate

middle: E

last: Galloway

department: Chemical Engineering

institute: Massachusetts Institute of Technology

data_processing:
We used the cellranger count pipeline (10x Genomics) to align and quantify single cell expression for each library.
Samples were combined into a single matrix via the aggr pipeline and normalized by read depth across the libraries.
scRNAseq datasets were imported into Monocle using cellrangerRkit in R to create a cellDataSet.
Data were normalized using estimateSizeFactors. Outliers were removed based on variance using estimateDispersion to remove 108 outlier cells. Clustering was performed using 10,300 genes with high dispersion and mean gene expression >= 0.1 on the first 10 PCs. Clusters of varying number were examined and clustering via 3 primary clusters was chosen to capture different populations (e. g. MEFs, converting cells, and iMNs). Pseudotemporal ordering was performed using identified clusters. Pseudotemporal ordering was rooted in the identified iMN endpoint.
Analysis of embryonic motor neurons and induced motor neurons from various conditions was performed using Seurat 2.2. Following alignment and processing in CellRanger, variable genes were identified using FindVariableGenes. Clustering was performed using FindClusters based on the number of PCs identified through the PCElbow plot function. Cluster markers were identified for each cluster using the FindMarkers function.
Genome_build: mm10

source_name: Induced motor neurons with 6F

growth_protocol: Cells were harvested at different points in conversion. Specific populations were identified and collected via FACS and all cells were sorted to obtain viable single cell suspensions. Fast-cycling cells were identified by low CFSE intensity at 4 dpi. Hb9::GFP+ at 8 dpi and 14 dpi cells were identified relative to Hb9::GFP negative control.

extract_protocol:
RNA from lysed cells was barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne Silane Beads (Invitrogen, 37002D).
Single-cell RNA-seq libraries were prepared using Single Cell 3′ Library Gel Bead Kit V2 (10x Genomics, 120237).
Sequencing was performed with using multiple NextSeq 500/550 High Output Kit v2 on an Illumina NextSeq with pair end 150bp (PE150). On average, sequencing generated 100-200K reads per cell on average over the libraries.

treatment_protocol: Cell suspensions were loaded into a chip and processed with the Chromium Single Cell Controller (10x Genomics). To generate single-cell gel beads in emulsion (GEMs), individual populations were assigned individual libraries using Single Cell 3′ Library and Gel Bead Kit V2 (10x Genomics, 120237). For each population, the target population size was between 1000-1500 cells. Cell suspensions were calibrated to capture the target number of cells. Fewer cells were captured at 8 dpi due to limited Hb9::GFP+ cells in 6F condition.


title: 6F_8dpi (Single Cell)

source_name: Hb9::GFP+ cell in 6FD conditions at 8 dpi

value: 6F 8dpi


title: 6FDDRR_8dpi (Single Cell)

source_name: Hb9::GFP+ cell in 6FDDRR conditions at 8 dpi

value: 6FDDRR 8dpi


title: 6FDDRR+Top1-iMN-1 (Single Cell)

source_name: Induced motor neurons with 6FDDRR


title: 6F-iMN-1 (Single Cell)


title: CJ20_Control_MDBK_H3K9me3

description: CL4_CJ20_USDA_C30RTACXX_ACTTGA_L004_R1_001

value: Control


title: 6F_4dpi (Single Cell)

source_name: Hyperproliferative cells (e.g. CFSE-Lo population) in 6FD conditions at 4 dpi

value: 6F 4dpi


title: CJ19_Control_MDBK_RNA pol II

description: CL4_CJ19_USDA_C30RTACXX_CAGATC_L004_R1_001

source_name: Control_MDBK_RNA pol II


title: CJ18_Control_MDBK_H3K27ac

description: CL4_CJ18_USDA_C30RTACXX_GCCAAT_L004_R1_001


title: 6FDDRR_4dpi (Single Cell)

source_name: Hyperproliferative cells (e.g. CFSE-Lo population) in 6FDDRR conditions at 4 dpi

value: 6FDDRR 4dpi


title: MEFs-2 (iMIN)

data_processing:
Sequencing reads from triplicate replicates were trimmed and aligned to mm10 reference transcriptome with STAR aligner 2.5.3a.
Gene counts quantified using annotation model (Partek E/M). Differentially expressed genes were identified using DEseq2 for with genome wide false discovery rate (FDR) of less than 0.05 and log2 fold change greater than 1. Comparison of MEFs with all MN samples generated 1186 DEGs.
Genome_build: mm10

source_name: Mouse embryonic fibroblasts

growth_protocol: For cultures at 17 dpi, cells were harvest by DNase/papain (Worthington Chemical) treatment to dissociate cells. Cells were washed three times in DMEM-F12 media and resuspended in N3 neuronal media for sorting. Cells in replicates of 50K were collected based on gates set to identify viable, single Hb9::GFP+ cells.

extract_protocol:
Following sorting, cells were spun and resuspended in 100 uL RLT buffer from the RNAeasy micro kit (Qiagen). RNA in RLT and RNA extracted via RNAeasy kit.
Libraries were constructed and sequenced by Amaryllis (Emryville, CA) via single-end sequencing to generate 30M reads per sample.
Single-end sequencing was used to generate 30M reads per sample.

value: MEFs


title: 6FDDRR-iMN-2 (iMIN)

treatment_protocol: For cultures at 17 dpi, cells were harvest by DNase/papain (Worthington Chemical) treatment to dissociate cells. Cells were washed three times in DMEM-F12 media and resuspended in N3 neuronal media for sorting. Cells in replicates of 50K were collected based on gates set to identify viable, single Hb9::GFP+ cells.


title: MEFs-1 (iMIN)


title: 6FDDRR-iMN-1 (iMIN)


title: 6FDDRR-iMN-3 (iMIN)


title: CJ15_RNA pol II

source_name: Butyrate treatment_RNA pol II

tag: tissue/cell type

value: Rumen


title: CJ26_MDBK_Input_background

description: CL5_CJ26_USDA_C30RTACXX_CGATGT_L005_R1_001


title: CJ13_H3K9ac

source_name: Butyrate treatment_H3K9ac


title: CJ14_H3K27ac

source_name: Butyrate treatment_H3K27ac


title: CJ16_H3K9me3

source_name: Butyrate treatment_H3K9me3


title: 6FDD-iMN-2 (iMIN)

source_name: Induced motor neurons with 6FDD


title: CJ17_Control_MDBK_H3K9ac

description: CL4_CJ17_USDA_C30RTACXX_ACAGTG_L004_R1_001


title: CJ11_RNA pol II

source_name: Control_RNA pol II


title: CJ12_H3K9me3


title: 6FDD-iMN-1 (iMIN)


title: CJ10_H3K27ac


title: 6F-iMN-3 (iMIN)


title: CJ9_H3K9ac


title: 6F-iMN-2 (iMIN)


title: 6F-iMN-1 (iMIN)


title: 6FDDRR_D4_rep1 (ChIP)

data_processing:
Libraries were mapped to the mm10 genome using the BWA algorithm with default settings.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition,  duplicate reads (“PCR duplicates”) are removed.
Since the 5´-ends of the aligned reads (= “tags”) represent the  end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´-  ends to a length of 150-250 bp, depending on the average fragment length in the size selected  library (normally 200 bp). To identify the density of fragments (extended tags) along the genome,  the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This  information (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can be  visualized in genome browsers.
Genome_build: mm10

growth_protocol: Retroviral transduction was performed using Plat-E retroviral packaging cells (Cell Biolabs, Inc., RV-101). MEFs were transduced twice with Ascl1, Brn2, Isl1, Lhx3, Myt1l, and Ngn2 at 48 and 72 hours after transfection. Media was changed 24 hrs following second transduction (1 dpi) with fresh DMEM+10% FBS. Media was changed to glia media at 2 dpi. At 3 dpi, the day after glia media addition, medium was switched to complete N3 neuronal medium (DMEM/F-12 (VWR) with N2 and B27 (ThermoFisher) supplements and 1% glutamax (ThermoFisher)). Medium was supplemented with neurotrophics, GDNF, BDNF, and CNTF (R&D Systems) and FGF-Basic (Peprotech), each at 10 ng/ml. When included for reprogramming, RepSox (Selleck) was added to N3 media at a final concentration of 7.5uM.

extract_protocol:
Cells were processed by Active Motif via a standard ChIPseq protocol to enrich for RNAPII bound regions of DNA.  Replicate RNA Pol II ChIP reactions were performed using 25 μg of primary MEF, 6F, and DDRR chromatin and 4 μg of Abflex RNAPII antibody (Active Motif, cat # 91151).
Libraries were generated via standard Illumina protocols (using NextSeq 500) and sequenced to generate 30M reads per sample.

treatment_protocol: One day after addition of N3 media (and without addition of glial cultures), cells were fixed by adding fresh formaldehyde to culture media at a 1:10 volume (11% final concentration) and fixed for 15 minutes at room temperature with agitation. Formaldehyde was quenched with by adding glycine solution to cells at 1:20 volume (2.5M final concentration) and incubated at room temperature for 5 minutes. Cells were then scraped from cell dish, collected into 1.5mL Eppendorf tubes, and kept on ice for the remainder of processing. Cells were spun down at 800xg for 10 minutes at 4°C. After pelleting, supernatant was removed and cells were resuspended in 1mL chilled 0.5% Igepal in PBS, triturating each cell sample by pipetting up and down several times. Samples were then spun down for 10 minutes at 800xg at 4°C. After spinning down, cells were again resuspended in 1mL 0.5% Igepal in PBS and 1uL PMSF was added (final concentration of 100mM). Cell pellets were then snap-frozen and stored at -80°C.

value: 6FDDRR D4

value: RNAPII  (Active Motif, cat # 91151)


title: CJ6_H3K27ac

source_name: After Weaning_Rumen_H3K27ac

extract_protocol:
Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
Rumen tissues were collected from Holstein calves before and after weaning. DNA recovered from a conventional ChIP procedure was quantified using the QuantiFluor fluorometer (Promega, Madison, WI). The DNA integrity was verified using the Agilent Bioanalyzer 2100 (Agilent; Palo Alto, CA, USA). The DNA was then processed, including end repair, adaptor ligation, and size selection, using an Illumina sample prep kit following the manufacturer’s instructions (Illumina, San Diego, CA, USA). Final DNA libraries were validated and sequenced at 75-nt per sequence read, using an Illumina HiSeq 2500 platform.

value: Hostein

tag: time point

value: After Weaning

tag: tissue

value: rumen epithelial tissue


title: CJ25_input


title: CJ7_RNA pol II

source_name: After Weaning_Rumen_RNA pol II


title: CJ8_H3K9me3

source_name: After Weaning_Rumen_H3K9me3

value: Mouse monoclonal to H3K9me3


title: CJ25_Input_background


title: 6F_D4_rep2 (ChIP)

value: 6F D4


title: 6FDD-iMN-3 (iMIN)


title: MEFs_D4_rep2 (ChIP)


title: CJ3_RNA pol II

source_name: Before Weaning_Rumen_RNA pol II

value: Before Weaning

value: Mouse monoclonalto RNApolyII

value: Abcam


title: 6F_D4_rep1 (ChIP)


title: CJ4_H3K9me3

source_name: Before Weaning_Rumen_H3K9me3


title: MEFs_D4_rep1 (ChIP)


title: 6FDDRR_D4_CFSE-Lo-3 (CNN)

data_processing:
Sequencing reads from triplicate or more replicates were trimmed and aligned to mm10 reference transcriptome with STAR aligner 2.5.3a.
Gene counts quantified using annotation model (Partek E/M).
Samples were aligned to ERCC spike-in reference to quantify total spike-in reads per sample.
Sample reads were normalized by spike-in reads to generate cell number normalized reads per sample.
Genome_build: mm10

source_name: MEFs

growth_protocol: For cultures at 4 dpi, cells were harvest by trypsin treatment to dissociate cells. Cells were washed three times in DMEM-F12 media and resuspended in N3 neuronal media for sorting. Cells in replicates of 50K were collected based on gates set to identify viable, fast-cycling cells (e.g. CFSE-lo) or each condition (e.g. 6F and DDRR).

extract_protocol:
RNA in RLT and RNA extracted via RNAeasy kit.
Libraries were prepared by DNAlink (San Diego, CA) using SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian (Clontech)
Libraries were sequenced using NextSeq 500 Mid-output 75PE (Illumina) to generate 30M reads per sample.

treatment_protocol: Following sorting, cells were spun and resuspended in 100 uL RLT buffer from the RNAeasy micro kit (Qiagen). To normalize to a standard number of cells, ERCC spike-in mix (Thermo-Fisher, 1ul at 1:100 dilution) was added to 50K cells in RLT.

value: 6FDDRR D4 CFSE


title: 6FDDRR_D4_CFSE-Lo-2 (CNN)


title: CJ1_H3K9ac

source_name: Before Weaning_Rumen_H3K9ac

value: Rabbit polyclonal to H3K9ac


title: 6FDDRR_D4_CFSE-Lo-1 (CNN)


title: 6F_D4_CFSE-Lo-3 (CNN)

value: 6F D4 CFSE


title: CO3_WGBS

data_processing:
we removed contaminating adapter molecules, reads containing ploy-N, and low-quality reads using Trim_Galore (version 0.4.1)
We then mapped the clean reads to the cattle reference genome UMD3.1.1 using bismark (version v0.14.4; default options)
Genome_build: UMD 3.1.1
Supplementary_files_format_and_content: txt

extract_protocol:
Briefly, DNA from REPC culture was isolated by phenol/chloroform extraction
DNA (100 ng) was bisulfite-converted and subjected to library preparation using the Pico Methyl-Seq™ Library Prep Kit (Zymo) following the instructions of the supplier. High-Sensitivity DNA chips were used to assess libraries for quality on the Agilent Bioanalyzer and quantified with Qubit fluorometer. Libraries were sequenced on an Illumina HiSeq2500 (100-bp single-end sequencing).

tag: treatmnet

value: Control

value: Rumen Epithelial Primary Cells (REPC)

tag: replicate


title: BT3_WGBS

value: 24h post-Butyrate treatment


title: input DNA (ChIP)

description: input DNA

source_name: pooled

value: pooled


title: 6F_D4_CFSE-Lo-2 (CNN)


title: 6FDDRR_D4_rep2 (ChIP)

value: 6FDDRR D4


title: CJ5_H3K9ac

source_name: After Weaning_Rumen_H3K9ac


title: BT2_WGBS


title: BT1_WGBS


title: 6F_D4_CFSE-Lo-1 (CNN)


title: 6FDDRR_D4-3 (CNN)


title: CO2_RNA-seq

data_processing:
we removed contaminating adapter molecules, reads containing ploy-N, and low-quality reads using Trim_Galore (version 0.4.1)
We then mapped the clean reads to the cattle reference genome UMD3.1.1 using STAR (version 020201)
We used Ensembl genes as the gene annotation file, including 24,616 genes, and the gene expression levels were then determined by FPKM values for accounting for differences in sequence depth and gene length. The FPKM of genes were quantified using Cufflinks
Genome_build: UMD 3.1.1
Supplementary_files_format_and_content: txt

extract_protocol:
Total RNA from 6 rumen epithelial cell samples was extracted using Trizol (Invitrogen, Carlsbad, CA, USA) followed by DNase digestion and Qiagen RNeasy column purification (Qiagen, Valencia, CA, USA). RNA integrity was verified using Agilent Bioanalyzer 2100 (Agilent, Palo Alto, CA, USA). High-quality RNA (RNA integrity number [RIN]: 9.0) was processed using an Illumina TruSeq RNA sample prep kit following the manufacturer’s instruction (Illumina, San Diego, CA, USA).
After quality control (QC) procedures, individual RNA-seq libraries were pooled based on their respective sample-specific 6-bp (base pairs) adaptors and pair-end sequenced at 150 bp/sequence read (PE150) using an Illumina HiSeq 2500 sequencer (Illumina, Inc. San Diego, CA).


title: 6FDDRR_D4-2 (CNN)


title: CO1_RNA-seq


title: CO3_RNA-seq


title: CJ2_H3K27ac

source_name: Before Weaning_Rumen_H3K27ac

value: Rabbit polyclonal to H3K27ac


title: 6FDDRR_D4-1 (CNN)


title: CO2_WGBS

value: Hostein


title: BT2_RNA-seq


title: BT3_RNA-seq


title: CO1_WGBS


title: RA015

city: NewYork

first: Zhaoqi

state: New York

address: ICRC Building 8th Floor, Office 803B 1130 St. Nicholas Ave

department: Systems Biology

institute: Columbia university

data_processing:
Raw data were aligned to hg19 using the STAR alignment package
Unique junction counts as determined by STAR are output to a tabular file
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: Raw junction counts for each sample as output by STAR. Column headers, as follows:
column 1: chromosome
column 2: first base of the intron (1-based)
column 3: last base of the intron (1-based)
column 4: strand (0: undefined, 1: +, 2: -)
column 5: intron motif: 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT
column 6: 0: unannotated, 1: annotated (only if splice junctions database is used) 10
column 7: number of uniquely mapping reads crossing the junction
column 8: number of multi-mapping reads crossing the junction
column 9: maximum spliced alignment overhang

source_name: bone marrow mono nuclear cells

extract_protocol:
Poly-A pulldown from total RNA isolated using Qiagen's RNAeasy kit (Samples lysed in Trizol).
Illumina TruSeq RNA prep kit

value: myelodysplastic syndromes (MDS)

value: bone marrow

value: mono nuclear cells

tag: genotype


title: BT1_RNA-seq

tag: cell type


title: KEB7

city: Belmont

first: Nikolaos

last: Daskalakis

address: Oaks Building 328, Mailstop 212, 115 Mill Street

department: Department of Psychiatry

institute: McLean Hospital/ Harvard Medical School

description:
TRAP polysomonal RNA
pool of 3 animals

data_processing:
Tuxedo/DESeq
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample.

source_name: DRD2 TRAPSeq

extract_protocol:
TRAP polysomonal RNA isolation: TRAP procedure was completed as described in Heintz et al. (2014). Adult Drd2-TRAP mice were anesthetized; their brains removed and snap frozen. Bilateral 1mm punches were collected and pooled from from 3 animals per sample. 2 samples were used from the home-cage (HC) group, and n=3 samples from fear conditioning (FC) group. Messenger RNA was isolated from eGFP-tagged ribosomes. RNA was assessed for quality using the Bioanalyzer Pico (Agilent, Santa Clara, CA). All samples returned RINs (RNA Integrity Numbers) of 8.5 or greater.
Clonetech Ultralow v. 4: Libraries were generated from 1ng of Total RNA using the SMARTer HV kit (Clonetech), barcoding and sequencing primers were added using NexteraXT DNA kit.

treatment_protocol: Brains were extracted 2 h after fear extinction.  Brains from HC control animals were also extracted during this time.

value: Central Amygdala

tag: group

value: Home Cage


title: KEB6

description:
TRAP polysomonal RNA
pool of 3 animals

tag: strain


title: KEB4

description:
TRAP polysomonal RNA
pool of 3 animals

value: Fear conditioning


title: RA011

tag: diagnosis

value: wild type


title: RA008


title: 6F_D4-2 (CNN)

value: 6F D4


title: KEB2

description:
TRAP polysomonal RNA
pool of 3 animals


title: RA007


title: RA006


title: AA309


title: 6F_D4-1 (CNN)


title: AA308


title: AA307


title: AA306


title: 6F_D4-3 (CNN)


title: AA305


title: AA304


title: AA303


title: RA010


title: AA302


title: KEB3

description:
TRAP polysomonal RNA
pool of 3 animals


title: AA301


title: D2A OGT 3 (Median-Normalized)

type: other

city: Boston

first: Suzanne

last: Walker

address: 4 Blackfan Circle

department: Microbiology and Immunobiology

institute: Harvard Medical School

description:
Array barcode 91418, batch HA20446
D2A_3_MedianNorm
raw data file: D2A_3.gpr

hyb_protocol: The arrays were washed four times with TBST (5 mL × 5 min/wash) and incubated with 200 μL 270 µM iodoacetoamide and 1 µM 2,9-dimethyl-5,6,11,12-tetrahydro-dibenzocyclooctene in PBS buffer under a coverslip for 30 min. After the incubation, the arrays were washed again and incubated with 200 μL 1 µM ADIBO-biotin in PBS buffer under a coverslip for 30 min. The arrays were washed with TBS containing 0.5% SDS three times (5 mL × 5 min/wash) and twice with TBST (5 mL × 5 min/wash). The arrays were incubated with 200 μL 0.5 µg/mL streptavidin-Alexa Fluor 647 for 30 min at 4 °C. Finally, the arrays were washed again as above and dipped in water three times, spin-dried (200 ×g, 5 min), and scanned.

scan_protocol: Arrays were scanned with an axon GenePix 4000B using GenePix 5.0 or a GenePix 4300 scanner using GenePix 7.2.

data_processing: Un-normalized data were read into R using limma with normal-exponential background correction. For activity normalized data, a robust linear fit was obtained of the control series of V5-biotin control proteins on each block of each array was obtained, and the fluorescent values of all protein spots on each block was divided by the slope of the linear fit on the corresponding control block. The OGT-treated arrays (both wild-type and D2A) were then normalized for activity measurement by comparing the median staining-normalized signal for the control Estrogen Receptor alpha spots on every block. All proteins that showed evidence of OGT activity on blocks were scaled based upon the difference in staining-normalized Estrogen Receptor alpha between a given array block and the median of control arrays. Detailed methods are available in the supplemental information of the associated publication. The mean for each protein from each array was calculated for the resulting staining-and-activity normalized data and reported as the ActivityNorm samples, with the control samples being only normalized for staining. For comparisons between control arrays and OGT-treated arrays directly, we further median-normalized the staining and activity normalized groups of OGT-treated arrays (wild-type treated or D2A treated), so that each group of arrays had the same log2-transformed median. Values reported in the MedianNorm samples are these protein-level, median-normalized data, and are compared to the control arrays.

label: Alex Fluor 647 conjugated streptavidin

molecule: other

source_name: OGT enzymatic reaction

label_protocol: Human ProtoArray microarrays were warmed from -20 °C to 4 °C for 20 min and washed twice (5 mL × 5 min/wash) with TBS containing 0.04% Tween 20 (TBST) in a four-well array incubation plate on a circular shaker at 50 rpm. Microarrays were then blocked for 1.5 hours at 4 °C with Microarray Blocking buffer (ArrayIt) and washed again with TBST buffer (5 mL × 5 min/wash) three time. The microarrays were then incubated with 200 μL 3 µM OGT and 290 µM UDP-GlcNAz in PBS buffer under a coverslip for 2 hours at room temperature. Control arrays lacked OGT, while D2A arrays had the mutant enzyme at 3 µM instead of wild-type OGT.

growth_protocol: OGT was produced recombinantly from E. coli as described in the associated publication and purified by metal affinity and size exclusion chromatography. UDP-GlcNAz was synthesized as described by Vocadlo et al. Proc. Natl. Acad. Sci. USA 2003, 100, 9116–21.

extract_protocol: Not applicable- arrays were treated enzymatically with recombinant protein. Label protocol describes treatment of array with sugar donor. hyb protocol describes washing and staining.

treatment_protocol: see associated publication

tag: sugar donor

value: UDP-GlcNAz

tag: ogt variant

value: D2A mutant

tag: detection method

value: Chemoenzymatic Biotin Tagging

tag: normalization

value: Staining, Activity, and Median Normalized


title: D2A OGT 2 (Median-Normalized)

description:
Array barcode 91456, batch HA20446
D2A_2_MedianNorm
raw data file: D2A_2.gpr


title: WT OGT 1 (Median-Normalized)

description:
Array barcode 74602, batch HA20358
WT_1_MedianNorm
raw data file: WT_1.gpr

value: wild-type


title: WT OGT 2 (Median-Normalized)

description:
Array barcode 91406, batch HA20446
WT_2_MedianNorm
raw data file: WT_2.gpr


title: D2A OGT 2 (Activity-Normalized)

description:
Array barcode 91456, batch HA20446
D2A_2_ActivityNorm
raw data file: D2A_2.gpr

value: Staining and Activity Normalized


title: Macrophages in a co-culture system with BMSCs, MSR1 WT_1

city: Nanjing

first: Shujie

last: Zhao

address: longmian street

institute: Department of Orthopedic, The First Affiliated Hospital of Nanjing Medical University

data_processing:
fastp version 0.17.1
HISAT2 version 2.1.0
String Tie v1.3.4d
DESEQ2 v1.18.1
R version 3.4.3
Genome_build: gencode v27
Supplementary_files_format_and_content: comma-delimited text file including RPKM values and counts for each Sample

source_name: Macrophages

growth_protocol: To obtain primary bone marrow-derived macrophages, bone marrow cells first underwent lysis of red blood cells and were then resuspended in complete RPMI-1640 medium consisting of 25 ng/ml macrophage colony-stimulating factor (M-CSF) and cultured for 7 days.

extract_protocol:
Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) .  RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA).
Quality RNA samples were converted into cDNA libraries using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (NR601, Vazyme, NanJing, China). VAHTSTM DNA Clean Beads (Vazyme #N411) in this study was used to purify the fragments during the process of library constructing. The purified products were enriched with 12-15 cycles of PCR to create the final cDNA library. Finally, libraries were sequenced on the Illumina Hiseq X Ten according the manufacturer's protocols.

treatment_protocol: Further, macrophages from MSR1 KO or WT mice were co-cultured with BMSCs via a transwell system for 48h.

value: BMM derived macrophages

value: MSR1 WT


title: Macrophages in a co-culture system with BMSCs, MSR1 WT_2


title: Macrophages in a co-culture system with BMSCs, MSR1 KO_1

value: MSR1 KO


title: Macrophages in a co-culture system with BMSCs, MSR1 KO_2


title: WT OGT 3 (Median-Normalized)

description:
Array barcode 91400, batch HA20446
WT_3_MedianNorm
raw data file: WT_3.gpr


title: D2A OGT 3 (Activity-Normalized)

description:
Array barcode 91418, batch HA20446
D2A_3_ActivityNorm
raw data file: D2A_3.gpr


title: D2A OGT 1 (Median-Normalized)

description:
Array barcode 74603, batch HA20358
D2A_1_MedianNorm
raw data file: D2A_1.gpr


title: Bcl11b biallelic trial 1

city: Seattle

first: Nicholas

last: Pease

state: WA

address: 3720 15th Ave NE

institute: University of Washington

description: primary cells

data_processing:
Library strategy: CUT&RUN
Paired-end sequencing reads were aligned separately to mouse (NCBI37/mm9) and yeast (SacCer_Apr2011/sacCer3)  genomes using Bowtie2 (Langmead and Salzberg, 2012) with the following setting: --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700 as suggested for mapping CUT&RUN sequencing data (Skene et al., 2018).
The resulting alignments were converted to BAM files with SAMtools and then converted to BED files with BEDTools.
Reads were sorted and filtered to remove random chromosomes using custom python script, see supplementary files.
BEDTools genomecov was used to generate histograms for the mapped reads using a scaling factor that is the product of the number of spiked-in yeast reads and the number of input cells.
Genome_build: mm9, yeast
Supplementary_files_format_and_content: bedgraph

source_name: cKit enriched bone marrow hematopoietic progenitor cells

growth_protocol: Cultured on OP9-DL1 stromal cells with 5ng/mL of IL-7 and Flt3l

extract_protocol:
CUT&RUN experiments were carried out as previously described (Skene et al, 2018) with the following modifications: 1-2.5x10^5 cells were isolated by FACS as described in sections above, bound to Concanavalin A coated magnetic beads (Bangs Laboratories), and  permeabilized with 0.025% (wt/vol) digitonin. Permeabilized cells were incubated overnight at 4C with 5ug of anti-H3K27me3 (Active Motif 39156) and then washed before incubating with protein A-MNase fusion protein (a gift from Steven Henikoff) for 15 minutes at room temperature. After washing, cells were incubated in CaCl2 to induce MNase cleavage activity for 30 minutes at 0oC. The reaction was stopped with 2XSTOP buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 mg/mL RNase A and 40 mg/mL glycogen) with 2pg of yeast spike-in DNA per sample. Histone-DNA complexes were isolated from insoluble nuclear chromatin by centrifugation and DNA was extracted with a NucleoSpin PCR Clean-up kit (Macherey-Nagel).
Library preparation from CUT&RUN products was completed with KAPA Hyper Prep Kit (KAPA Biosystems) following standard protocol with PCR amplification settings adjusted so that annealing and extension steps are combined into one step at 60oC for 10s. Library products were size selected to be within 200 - 300 bp range using AMPure beads (Agencourt). Libraries were sequenced using an Illumina MiSeq system with paired-end 25 bp sequencing read length and TruSeq primer standard for approximately 5 millions reads per sample.

tag: bcl11b expression

value: biallelic Bcl11b expression

tag: days in culture

tag: antibody

value: H3K27me3 (Active Motif, 39425)

tag: number of cells


title: Bcl11b biallelic trial 2

description: primary cells

value: cKit enriched bone marrow hematopoietic progenitor cells


title: WT OGT 3 (Activity-Normalized)

description:
Array barcode 91400, batch HA20446
WT_3_ActivityNorm
raw data file: WT_3.gpr


title: D2A OGT 1 (Activity-Normalized)

description:
Array barcode 74603, batch HA20358
D2A_1_ActivityNorm
raw data file: D2A_1.gpr


title: WT OGT 2 (Activity-Normalized)

description:
Array barcode 91406, batch HA20446
WT_2_ActivityNorm
raw data file: WT_2.gpr


title: WT OGT 1 (Activity-Normalized)

description:
Array barcode 74602, batch HA20358
WT_1_ActivityNorm
raw data file: WT_1.gpr