title: ATAC_EAE_cMaf_flfl _3

tag: background strain

value: c-Maf flfl


title: highfat_smRNA1

status: Public on Feb 08 2018

type: SRA

city: West Lafayette

first: Theresa

middle: M

last: Casey

state: Indiana

address: 175 S. University Street

department: Animal Sciences

country: USA

institute: Purdue University

description:
highfat diet
Sample name: HF62

library_source: transcriptomic

data_processing:
Raw Sequenced reads were trimmed for the adaptor sequence, followed by the clipping of 4 bases from either ends (as specified by  the Bioo Scientific kit “NEXTflex Illumina Small RNA Sequencing Kit v3”) and quality trimming through cutadapt software version 1.9.1
Preprocessing of trimmed reads through the mapper.pl script from miRDeep2 which performs steps such as adapter clipping, discarding the reads shorter than 18 bp and reads collapsing.
Quantification and expression profiling of known miRNA was performed by the quantifier.pl script from miRDeep2 using the collapsed reads and miRBase database as a reference.
The quantifier script generated the read counts against the known miRNAs from each sample.
The read counts from the different sample were collated using the custom scripts to generate a single file representing the read counts against known miRNA from all the samples.
Genome_build: Mus musculus GRCm38 (Release 85) downloaded from Ensembl website. Mus musculus miRNAs (Release 21) downloaded from the miRBase website.
Supplementary_files_format_and_content: Tab delimited text file containing read counts for each known miRNA from each sample.

molecule: total RNA

organism: Mus musculus

source_name: milk fat

extract_protocol:
Milk fat layer was isolated by centrifugation (1000-g for 5 min) at 4 °C from lactation day 10 samples, and transferred to a new microfuge.  An equal volume of PBS was added and mixed with milk fat by vortexing. Milk-fat PBS mixture was centrifuged for 5 min in 4 °C at 3000 rpm to remove cells and other debris that may have been trapped in fat. The miRNeasy Mini Kit (cat. No. 217004, company: QIAGEN) was used to isolate total RNA following manufacturer’s directions using these specifications; Lysis Reagent was added to sample at a 1:3.5 ratio (200ul milk sample to 700ul QIAzol) followed by disruption and homogenization using vortex. Total RNA was eluted from final column with 20 µl of RNase-Free water and stored at -80° C, until sequencing.
NEXTflexTM –Small RNA-Seq Kit v3 (Bioo Scientific) was used to generate small RNA libraries directly from total RNA. Libraries were sequenced on an Illumina HiSeq2500 platform

treatment_protocol: Nine 4-week old female ICR (CD1; Envigo) mice were matched by weight and divided into two treatment groups: control (n=5) and high fat (HF; n=4) diet. Mice were exposed to a 12h light: 12h dark cycle throughout entire study.  For the 4 weeks prior to mating, female mice were housed in pairs within treatment and fed a high fat diet (HF; Research Diets #D12492, 60% of total kcal energy is fat and 7% of total kcal is sucrose; 5.24kcal/gm; Brunswick, NJ) or control diet that was matched for sucrose (C; Research Diets #D12450J, 10% of total kcal energy is fat and  7% of total kcal is sucrose; 3.85 kcal/gm). Dams remained on respective diets throughout pregnancy and lactation. Milk was collected from each dam on post-natal day 10.

tag: biological replicate

tag: tissue

value: milk fat

tag: strain

value: ICR

tag: age

value: primiparous

tag: developmental stage

value: lactation day 10

tag: Sex

value: female


title: control_smRNA5

description:
control diet
Sample name: C74


title: highfat_smRNA2

description:
highfat diet
Sample name: HF68


title: control_smRNA2

description:
control diet
Sample name: C64


title: control_smRNA4

description:
control diet
Sample name: C73


title: control_smRNA1

description:
control diet
Sample name: C63


title: control_smRNA3

description:
control diet
Sample name: C67


title: WT_BMDM

city: Boston

first: Xu

last: Zhou

state: MA

address: 300 Longwood Ave

department: Pediatrics

institute: Boston Children's Hospital

description: total RNA isolated from wild type murine bone marrow derived macrophages

data_processing:
RNA-seq library was sequenced with Next-seq 500
Fastq files were downloaded from Basespace and were aligned with Kallisto v0.43.1 against all cDNA transcripts from mouse genome assembly GRCm38, with 100 rounds of boostrap method.
ESEMBL id of each aligned transrpt was matched to the offical gene symbols through BioaRt in R
The expression of a gene is calculated by summing the TPM of all ESEMBL transcripts matching that gene.
Genome_build: GRCm38
Supplementary_files_format_and_content: The processed csv file contain the final processed gene expresion in TPM. The first column is the official gene symbol, the second column is the gene description, the third column is the TPM expression in murine embyronic fibroblasts, and the fourth column is the TPM expression in murine bone marrow  derived macrophages.

source_name: bone marrow derived macrophage

growth_protocol:
Bone marrow derived macrophages (BMDMs) were differentiated from whole bone marrow in the presence of L929-conditioned media. Femurs and tibias were removed from C57BL/6J mice, flushed, and exposed to hypotonic lysis to remove red blood cells. Cells were plated in macrophage growth media (MGM) overnight (RPMI + 2mM L-glutamine, 1mM sodium pyruvate, 10mM HEPES, 200U/mL penicillin/streptomycin, 10% FBS, and 30% L929-conditioned media). The next day (day 1), nonadherent cells were harvested, washed, and replated in 15cm petri dishes in 20mL of MGM. On day 4, 15mL of MGM was added to the plate. On Day 6, cells were lifted with 3mM cold EDTA in PBS for 15 min and plated at 750,000 in 12-well tissue treated plate.
All cell cultures were in their growth medium as descrbied in a 37° C incubator at 5% CO2.
After overnight culture, adherent cells were washed twice with ice-cold PBS and collected with RLT buffer (Qiagen RNeasy kit).

extract_protocol:
RNA was purified from cells using Qiagen RNeasy columns with on-column DNAse digestion according to the manufacturer’s instructions.
Sequencing libraries were constructed following Illumina Tru-seq stranded mRNA protocol. Paired-end sequencing was performed with Next-seq 500 with 76 bp from each end.

tag: cell type

value: bone marrow derived macrophage

tag: culture medium

value: MGM

tag: cell number


title: WT_MEF

description: total RNA isolated from wild type murine embryonic fibroblast

source_name: embryonic fibroblast

growth_protocol:
Mouse embryonic fibroblasts (MEFs) were harvested from E13.5-E14.4 embryos and sorted for purity. Staged embryos were removed from a pregnant female by removing the uterus and separating each embryo from its amniotic sac. The head and “red tissue,” including fetal liver, were removed and discarded. The remaining portion of each embryo was minced using razor blades in 0.05% trypsin + EDTA and placed in a 37° C incubator for 30 min. After digestion, the tissue was transferred into a conical tube, washed with complete DMEM (DMEM + 2mM L-glutamine, 1mM sodium pyruvate, 10mM HEPES, 200U/mL penicillin/streptomycin, 10% FBS; Gibco) and resuspended in complete DMEM in 15cm tissue culture plates overnight. The following day, cells and undigested tissue debris were lifted from the plates using 0.05% trypsin + EDTA, spun down, resuspended, and filtered over a 70 um filter. These cells were expanded for 1-2 passages and then sorted for CD45-, CD11b-, and F4/80-negativity to exclude contaminating macrophages. The sorted MEFs were split once after sorting to allow for recovery and used for experiments at p4-p7.
All cell cultures were in their growth medium as descrbied in a 37° C incubator at 5% CO2.
After overnight culture, adherent cells were washed twice with ice-cold PBS and collected with RLT buffer (Qiagen RNeasy kit).

value: embryonic fibroblast

value: Complete DMEM


title: RN-Root-T2

city: College Station

first: Cecilia

last: Tamborindeguy

address: Heep Center

institute: Texas A&M University

data_processing:
analyses was performed on CyVerse.org
The pre-filtered reads were quality-filtered using FASTQC tools.
The RNA-seq reads that passed the quality filters were mapped to the potato reference genome (PGSC_DM_v3.4 gene models ensemblv19-preinstalled in iplantcollaborative.org) using the Tuxedo RNA-seq pipeline (Trapnell et al., 2013, Trapnell et al., 2009, Trapnell et al., 2010).
The Tuxedo pipeline comprised TopHat2 (mapping), Cufflinks2 (transcript assembly), and Cuffmerge2 (transcript merging).
Identification of differential gene expression was conducted using Cuffdiff2, following the defaults parameters in CyVerse.
Genome_build: PGSC_DM_v3.4
Supplementary_files_format_and_content: .gtf file

organism: Solanum tuberosum

source_name: Russet Norkotah

growth_protocol: Tubers were planted in Springlake, TX and plant were grown on commercial field

extract_protocol:
Plant Sample were collected in the field place in RNA-later, kept on ice till brought back in the lab and Frozen.   and removed, flash frozen on dry ice, and RNA was harvested using Qiagen Plant RNeasy. TruSeq RNA Library Preparation Kit v2 was used on poly(A) RNA enriched.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Root

value: 84 day old

tag: selection

value: Russet Norkotah


title: TXNS278-Leaf-T2

value: Leaf


title: TXNS278-Root-T2


title: ATAC_HDM_cMaf_flfl_1

city: London

first: Leona

last: Gabrysova

address: 1 Midland Road

country: United Kingdom

institute: The Crick Institute

library_source: genomic

data_processing:
sequencing quality control done with Skewer 0.2.2
sequencing reads mapped to mm10 with BWA-MEM
Duplicates were removed using Picard
alignment QC, discarded alignments with a mapQ below 30 using SAMtools 1.3.1
Discarded alignemnts done to mitochondrial DNA, shifted Reads to represent the Tn5 insertion, and remove fragments spanning nucleosomes (size >99 bp) using awk and BEDTools 2.4.2. Fragments spanning nucleosomes were not removed for the one untreated sample
MACS2 2.1.1 (parameters --keep-dup all, --nomodel, --shift -100, --extsize 200) was used to call peaks (q-value < 0.01)
To retrieve bigwig files we used DeepTools 2.4.2, bamCoverage command to retrieve RPKM normalised coverage
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are provided for ATAC-seq data normalised to RPKMs (fragments spanning nucleosomes excluded), for peaks called bed files are provided

molecule: genomic DNA

source_name: CD4+ T cells (Th2 HDM allergy model)

growth_protocol: On day 25, CD4+ T cells were enriched from perfused lungs (pooled) following a Percoll gradient separation by positive selection using anti-CD4 microbeads (Miltenyi Biotech). After staining in PBS with 5% FCS for 20 min at 4C with anti-CD3-APC, anti-CD8 FITC, anti-CD4-eFluor450 and and anti-CD44-PE (eBioscience), CD3+CD8-CD4+CD44+ T cells were sorted on MoFloTM XDP (Beckman Coulter) cytometer.

extract_protocol: Cells sorting was followed by a transposition reaction and purification, prepared as in Buenrostro et al. Curr Protoc Mol Biol. 2015 with the transposition reaction carried out for 1h and 30 minutes at 37 °C and subsequent PCR amplification for 12 cycles

treatment_protocol: c-Maf flfl mice were sensitized with 10 mg HDM (Greer) or PBS and 2mg Imject Alum (Thermo Scientific) by intraperitoneal injections on days 0 and 14, and challenged intratracheally with 10 mg HDM or PBS on days 21 and 24.

tag: genotype

value: Lung

value: CD4+ T cell

tag: time point

value: day 25 of HDM induced allergy


title: TXNS278-Leaf-T1

value: 66 day old


title: RN-Leaf-T1


title: RN-Root-T1


title: TXNS278-Root-T1


title: WAT_ZT08

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Raw sequencing reads were aligned to the baboon PapAnu2.0 genome with STAR
Read counts per gene were calculated using FeatureCounts
DESeq2 was used to generate FPKM values
Genome_build: PapAnu2.0
Supplementary_files_format_and_content: comma-separated values containing FPKM quantification for all samples
Supplementary_files_format_and_content: gene-level quantification (FPKM normalization)

molecule: polyA RNA

organism: Papio anubis

source_name: White adipose tissue

extract_protocol:
Twelve male Papio anubis hamadryas (age 5-6 yrs, 7-11 kg) were maintained in a 12hr light-12 hr dark cycle. Animals were fed twice a day (at 9:00 and 15:00) with fruits and primate meal pellets, with access to water ad libitum. Timed biosamples were collected every 2 hrs from ZT0 to ZT22, one primate at each sample time. The Institute veterinary services administered animals a lethal dose of sodium pentobarbital, after which blood (centrifuged for plasma), urine and CSF samples collected. Animals were perfused through the left ventricle with 4 liters of ice cold (2°C) buffered, oxygenated Ame's solution. Collection of brain sections used standardized procedures for NHPs (Davenport et al., 2013). The brain and eyes were rapidly removed (less than 5 min) and kept at 4°C on ice. Tissue collections were made simultaneously in three stations. In Station 1, the brain was cut into serial sections using a specifically built baboon brain matrix. Sections were placed on individual ice cold plates, each section photographed and punches obtained from selected brain structures. Sections were packaged in individual sterilized plastic pouches (Nasco) then frozen in dry ice and stored at -80°C. At the same time (Station 2), samples were taken from the eyes (retina, RPE, vitreous, lens, cornea, iris, optic nerve), divided into aliquots and frozen in dry ice. During the night-time periods, the head and eyes were covered with opaque plastic prior to perfusion and dissections of the eye and retina were performed in the dark using infrared viewers. Station 3 collected various body tissues and organs. All tissues were distributed into individual aliquots with certain larger tissues stored in bulk samples (liver, muscle, etc.), frozen in dry ice, and then stored at -80°C. The whole procedure, from collection to storage lasted no more than 30-40 min.
Libraries were prepped using Illumina’s TruSeq Stranded mRNA HT kit according to manufacturer’s instructions.  In brief, total RNA starting with 1ug was poly-A selected, fragmented by metal-ion hydrolysis and then converted to cDNA using SuperScript II.  The cDNA was then end-repaired, adenylated and ligated with Illumina sequencing adapters.  Finally, the libraries were enriched by PCR amplification.  Libraries were pooled and sequenced using an Illumina HiSeq 2500 with 50-bp single-read chemistry.

value: White adipose tissue

tag: time


title: WAT_ZT20


title: WAT_ZT22


title: WAT_ZT18


title: WAT_ZT10


title: WAT_ZT16


title: WAT_ZT14


title: WAT_ZT04


title: WAT_ZT02


title: WAS_ZT22

source_name: White adipose subcutaneous

value: White adipose subcutaneous


title: WAT_ZT00


title: WAS_ZT08


title: WAS_ZT10


title: WAS_ZT04


title: WAS_ZT18


title: WAS_ZT16


title: WAS_ZT02


title: WAR_ZT22

source_name: White adipose perirenal

value: White adipose perirenal


title: WAR_ZT18


title: WAR_ZT14


title: WAR_ZT16


title: WAS_ZT00


title: WAR_ZT12


title: WAS_ZT20


title: WAR_ZT10


title: WAS_ZT12


title: WAR_ZT04


title: WAS_ZT06


title: WAR_ZT06


title: WAR_ZT00


title: WAP_ZT22

source_name: White adipose pericardial

value: White adipose pericardial


title: WAR_ZT08


title: WAP_ZT20


title: WAP_ZT14


title: WAP_ZT16


title: WAP_ZT10


title: WAP_ZT08


title: WAP_ZT12


title: WAP_ZT06


title: WAP_ZT18


title: WAP_ZT04


title: WAP_ZT02


title: WAP_ZT00


title: WAM_ZT18

source_name: White adipose mesenteric

value: White adipose mesenteric


title: WAM_ZT16


title: WAM_ZT14


title: WAM_ZT12


title: WAM_ZT10


title: WAM_ZT08


title: WAM_ZT02


title: WAM_ZT06


title: WAM_ZT04


title: VMH_ZT18

source_name: Ventromedial hypothalamus

value: Ventromedial hypothalamus


title: VMH_ZT20


title: WAM_ZT00


title: VMH_ZT14


title: VMH_ZT22


title: WAM_ZT22


title: VMH_ZT16


title: WAM_ZT20


title: VMH_ZT10


title: VMH_ZT04


title: VMH_ZT08


title: VMH_ZT00


title: VIC_ZT22

source_name: Visual cortex

value: Visual cortex


title: WAR_ZT20


title: VIC_ZT20


title: VIC_ZT18


title: VIC_ZT14


title: VIC_ZT12


title: VMH_ZT12


title: VIC_ZT10


title: VIC_ZT08


title: VMH_ZT06


title: VIC_ZT06


title: VIC_ZT04


title: THR_ZT20

source_name: Thyroid

value: Thyroid


title: THR_ZT22


title: THR_ZT16


title: THR_ZT18


title: VIC_ZT02


title: THR_ZT14


title: THR_ZT12


title: THR_ZT04


title: THR_ZT06


title: THR_ZT02


title: VMH_ZT02


title: THR_ZT10


title: THR_ZT08


title: VIC_ZT16


title: THR_ZT00


title: THA_ZT20

source_name: Thalamus

value: Thalamus


title: THA_ZT18


title: THA_ZT16


title: VIC_ZT00


title: THA_ZT14


title: THA_ZT12


title: THA_ZT08


title: THA_ZT06


title: THA_ZT02


title: THA_ZT04


title: TES_ZT22

source_name: Testicles

value: Testicles


title: TES_ZT20


title: THA_ZT00


title: TES_ZT14


title: TES_ZT08


title: TES_ZT12


title: TES_ZT06


title: TES_ZT04


title: TES_ZT16


title: THA_ZT22


title: TES_ZT00


title: SUN_ZT20

source_name: Substantia nigra

value: Substantia nigra


title: SUN_ZT22


title: SUN_ZT18


title: THA_ZT10


title: SUN_ZT16


title: TES_ZT02


title: SUN_ZT14


title: SUN_ZT10


title: SUN_ZT12


title: TES_ZT18


title: SUN_ZT06


title: WAR_ZT02


title: TES_ZT10


title: SUN_ZT08


title: SUN_ZT00


title: SUN_ZT04


title: STF_ZT18

source_name: Stomach fundus

value: Stomach fundus


title: STF_ZT22


title: STF_ZT14


title: STF_ZT20


title: STF_ZT12


title: SUN_ZT02


title: STF_ZT16


title: STF_ZT04


title: STF_ZT02


title: STF_ZT10


title: STF_ZT00


title: STF_ZT06


title: WAS_ZT14


title: SPL_ZT16

source_name: Spleen

value: Spleen


title: SPL_ZT20


title: SPL_ZT22


title: SPL_ZT18


title: SPL_ZT14


title: SPL_ZT12


title: SPL_ZT04


title: SPL_ZT08


title: SPL_ZT10


title: SPL_ZT06


title: SPL_ZT02


title: SPL_ZT00


title: SON_ZT20

source_name: Supraoptic nucleus

value: Supraoptic nucleus


title: SON_ZT16


title: SON_ZT18


title: SON_ZT22


title: SON_ZT14


title: SON_ZT10


title: SON_ZT12


title: SON_ZT08


title: SON_ZT04


title: SON_ZT00


title: WAT_ZT12


title: SON_ZT06


title: SMM_ZT22

source_name: Smooth muscle

value: Smooth muscle


title: SMM_ZT20


title: SMM_ZT16


title: SMM_ZT14


title: SMM_ZT08


title: SMM_ZT10


title: SMM_ZT12


title: SMM_ZT06


title: SKI_ZT22

source_name: Skin

value: Skin


title: SMM_ZT00


title: SKI_ZT20


title: SMM_ZT02


title: SKI_ZT18


title: SKI_ZT14


title: SMM_ZT04


title: SKI_ZT10


title: SON_ZT02


title: SKI_ZT12


title: SKI_ZT08


title: SKI_ZT06


title: SKI_ZT02


title: SCN_ZT22

source_name: Suprachiasmatic nuclei

value: Suprachiasmatic nuclei


title: SKI_ZT16


title: SMM_ZT18


title: SCN_ZT18


title: SKI_ZT00


title: WAT_ZT06

source_name: White adipose tissue

value: White adipose tissue


title: STF_ZT08


title: SCN_ZT16


title: SCN_ZT20


title: SCN_ZT14


title: SCN_ZT10


title: SCN_ZT12


title: SCN_ZT04


title: SCN_ZT08


title: SCN_ZT02


title: RPE_ZT22

source_name: Retinal pigment epithelium

value: Retinal pigment epithelium


title: SCN_ZT00


title: RPE_ZT20


title: RPE_ZT18


title: RPE_ZT16


title: SKI_ZT04


title: RPE_ZT12


title: RPE_ZT10


title: RPE_ZT08


title: RPE_ZT06


title: RPE_ZT02


title: RPE_ZT04


title: RET_ZT10

source_name: Retina

value: Retina


title: RET_ZT20


title: RET_ZT16


title: RET_ZT18


title: RET_ZT22


title: RET_ZT12


title: RET_ZT14


title: RPE_ZT00


title: RET_ZT06


title: SCN_ZT06


title: RET_ZT04


title: RET_ZT08


title: RET_ZT00


title: RET_ZT02


title: PVN_ZT20

source_name: Paraventricular nuclei

value: Paraventricular nuclei


title: PVN_ZT22


title: PVN_ZT18


title: PVN_ZT16


title: RPE_ZT14


title: PVN_ZT14


title: PVN_ZT12


title: PVN_ZT02


title: PVN_ZT04


title: PVN_ZT08


title: PVN_ZT10


title: PVN_ZT00


title: PUT_ZT22

source_name: Putamen

value: Putamen


title: PVN_ZT06


title: PUT_ZT20


title: PUT_ZT10


title: PUT_ZT14


title: PUT_ZT02


title: PUT_ZT04


title: PUT_ZT06


title: PUT_ZT00


title: PRO_ZT18

source_name: Prostate

value: Prostate


title: PRO_ZT22


title: PRO_ZT20


title: PRO_ZT14


title: PRO_ZT12


title: PRO_ZT10


title: PRO_ZT08


title: PRO_ZT04


title: PRO_ZT06


title: PRO_ZT00


title: PRC_ZT20

source_name: Prefontal cortex

value: Prefontal cortex


title: PRC_ZT22


title: PUT_ZT18


title: PRC_ZT18


title: PRC_ZT16


title: PRC_ZT14


title: PRC_ZT12


title: PUT_ZT08


title: PUT_ZT16


title: PRC_ZT08


title: PRC_ZT10


title: PUT_ZT12


title: PRO_ZT16


title: PRC_ZT06


title: PRC_ZT02


title: PRO_ZT02


title: PRC_ZT00


title: PRA_ZT16

source_name: Preoptic area

value: Preoptic area


title: PRA_ZT12


title: PRA_ZT10


title: PRA_ZT08


title: PRA_ZT18


title: PRA_ZT14


title: PRA_ZT04


title: PRA_ZT06


title: PRA_ZT02


title: PRA_ZT00


title: PON_ZT20

source_name: Pons

value: Pons


title: PON_ZT22


title: PON_ZT18


title: PON_ZT10


title: PON_ZT12


title: PON_ZT16


title: PON_ZT08


title: PON_ZT14


title: PON_ZT04


title: PRC_ZT04


title: PON_ZT06


title: PON_ZT02


title: PRA_ZT22


title: PRA_ZT20


title: PIT_ZT22

source_name: Pituitary

value: Pituitary


title: PON_ZT00


title: PIT_ZT20


title: PIT_ZT12


title: PIT_ZT10


title: PIT_ZT14


title: PIT_ZT18


title: PIT_ZT02


title: PIT_ZT16


title: PIT_ZT04


title: PIT_ZT08


title: PIT_ZT00


title: PIN_ZT16

source_name: Pineal gland

value: Pineal gland


title: PIN_ZT18


title: PIN_ZT14


title: PIN_ZT20


title: PIN_ZT12


title: PIN_ZT08


title: PIN_ZT06


title: PIN_ZT02


title: PIN_ZT04


title: PAN_ZT22

source_name: Pancreas

value: Pancreas


title: PAN_ZT20


title: PIN_ZT00


title: PAN_ZT18


title: PAN_ZT16


title: PAN_ZT14


title: PAN_ZT10


title: PAN_ZT12


title: PAN_ZT08


title: PIT_ZT06


title: PIN_ZT22


title: PAN_ZT02


title: PAN_ZT06


title: PAN_ZT04


title: ONH_ZT20

source_name: Optic nerve head

value: Optic nerve head


title: ONH_ZT14


title: ONH_ZT16


title: ONH_ZT22


title: ONH_ZT08


title: ONH_ZT10


title: ONH_ZT04


title: ONH_ZT00


title: OMF_ZT20

source_name: Omental fat

value: Omental fat


title: OMF_ZT16


title: ONH_ZT02


title: OMF_ZT14


title: OMF_ZT22


title: OMF_ZT18


title: OMF_ZT10


title: ONH_ZT06


title: OMF_ZT12


title: OMF_ZT08


title: OMF_ZT02


title: OMF_ZT04


title: OMF_ZT06


title: PAN_ZT00


title: OMF_ZT00


title: ONH_ZT18


title: OLB_ZT22

source_name: Olfactory bulb

value: Olfactory bulb


title: ONH_ZT12


title: OLB_ZT16


title: OLB_ZT14


title: OLB_ZT20


title: OLB_ZT18


title: OLB_ZT08


title: OLB_ZT12


title: OLB_ZT10


title: OLB_ZT06


title: OLB_ZT04


title: OLB_ZT02


title: OES_ZT18

source_name: Oesophagus

value: Oesophagus


title: OES_ZT14


title: OES_ZT12


title: OES_ZT22


title: OES_ZT20


title: OES_ZT06


title: OES_ZT10


title: OES_ZT04


title: OES_ZT02


title: MUG_ZT18

source_name: Muscle gastrocnemian

value: Muscle gastrocnemian


title: OES_ZT00


title: MUG_ZT20


title: MUG_ZT16


title: MUG_ZT22


title: MUG_ZT14


title: MUG_ZT12


title: MUG_ZT08


title: MUG_ZT10


title: MUG_ZT04


title: MUG_ZT02


title: MUG_ZT00


title: OLB_ZT00


title: MUA_ZT16

source_name: Muscle abdominal

value: Muscle abdominal


title: PIN_ZT10


title: MUA_ZT18


title: OES_ZT08


title: OES_ZT16


title: MUA_ZT20


title: MUA_ZT14


title: MUA_ZT10


title: MUA_ZT04


title: MUA_ZT12


title: MUA_ZT06


title: MUA_ZT08


title: MMB_ZT22

source_name: Mammilliary body

value: Mammilliary body


title: MMB_ZT20


title: MUA_ZT02


title: MUA_ZT00


title: MMB_ZT14


title: MMB_ZT16


title: MMB_ZT18


title: MMB_ZT10


title: MMB_ZT08


title: MMB_ZT12


title: MUA_ZT22


title: MUG_ZT06


title: MMB_ZT02


title: MGP_ZT22

source_name: Medial globus pallidus

value: Medial globus pallidus


title: MMB_ZT06


title: MGP_ZT20


title: MGP_ZT18


title: MGP_ZT10


title: MGP_ZT12


title: MGP_ZT04


title: MGP_ZT02


title: MGP_ZT06


title: MEL_ZT20

source_name: Mesenteric lymphonodes

value: Mesenteric lymphonodes


title: MEL_ZT18


title: MEL_ZT14


title: MEL_ZT12


title: MEL_ZT10


title: MEL_ZT16


title: MEL_ZT06


title: MEL_ZT22


title: MEL_ZT00


title: MMB_ZT04


title: MEL_ZT08


title: MMB_ZT00


title: MEL_ZT04


title: MEL_ZT02


title: LUN_ZT18

source_name: Lungs

value: Lungs


title: MGP_ZT14


title: LUN_ZT20


title: LUN_ZT22


title: MGP_ZT08


title: MGP_ZT16


title: LUN_ZT14


title: LUN_ZT16


title: MGP_ZT00


title: LUN_ZT10


title: LUN_ZT12


title: LUN_ZT06


title: LUN_ZT00


title: LUN_ZT08


title: LIV_ZT22

source_name: Liver

value: Liver


title: LUN_ZT04


title: LUN_ZT02


title: LIV_ZT18


title: LIV_ZT20


title: LIV_ZT12


title: LIV_ZT08


title: LIV_ZT16


title: LIV_ZT06


title: LIV_ZT10


title: LIV_ZT04


title: LIV_ZT14


title: LIV_ZT00


title: LH_ZT22

source_name: Lateral hypothalamus

value: Lateral hypothalamus


title: LH_ZT20


title: LH_ZT16


title: LH_ZT18


title: LH_ZT10


title: LH_ZT12


title: LH_ZT14


title: LIV_ZT02


title: LH_ZT04


title: LH_ZT06


title: LH_ZT00


title: LGP_ZT22

source_name: Lateral globus pallidus

value: Lateral globus pallidus


title: LGP_ZT20


title: LH_ZT08


title: Sample 23_Arabidopsis Col-0 dry seeds

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

country: China

institute: SUSTC (current, may different with previous institution )

data_processing:
Bowtie for alignment, v1, default parameter
Cufflink for expression profiling, v2.1.0, default paremeter
Genome_build: TAIR10
Supplementary_files_format_and_content: "cuffdiff" output text file containing the normalized value and fold-changes

organism: Arabidopsis thaliana

source_name: Arabidopsis Col-0 dry seeds

growth_protocol: Ripened seeds (8-weeks) of Col-0, csn5a-1, and csn1-10 that were collected on the same day from plants grown side-by-side at the same time were used. The 2-day germinating seeds, prepared with the same volume of dry seeds as above, were sterilized and incubate on cell culture wells with 0.5X liquid GM medium at 22oC under constant light for 2 days.

extract_protocol:
RNAeasy Kit
stander Illumina mRNA-seq protocol

treatment_protocol: No treatment

tag: ecotype background

tag: genotype/variation

value: wild type

value: dry seeds


title: LGP_ZT14


title: Sample 22_Arabidopsis Col-0 dry seeds


title: Sample 24_Arabidopsis Col-0 dry seeds


title: LH_ZT02


title: LGP_ZT08


title: Sample 19_Arabidopsis csn5b-1 dry seeds

source_name: Arabidopsis csn5b-1 dry seeds


title: Sample 18_Arabidopsis csn5a-1 dry seeds

source_name: Arabidopsis csn5a-1 dry seeds


title: LGP_ZT10


title: LGP_ZT06


title: LGP_ZT04


title: Sample 17_Arabidopsis csn5a-1 dry seeds


title: LGP_ZT02


title: Sample 16_Arabidopsis csn5a-1 dry seeds


title: Sample 15_Arabidopsis csn1-10 dry seeds

source_name: Arabidopsis csn1-10 dry seeds


title: Sample 14_Arabidopsis csn1-10 dry seeds


title: Sample 20_Arabidopsis csn5b-1 dry seeds


title: KIM_ZT22

source_name: Kidney medulla

value: Kidney medulla


title: Sample 21_Arabidopsis csn5b-1 dry seeds


title: LGP_ZT00


title: LGP_ZT18


title: KIM_ZT20


title: KIM_ZT18


title: Sample 13_Arabidopsis csn1-10 dry seeds


title: KIM_ZT16


title: Sample 11_Arabidopsis Col-0 2day seeds

source_name: Arabidopsis Col-0 2day seeds

value: 2-day germinating seeds


title: KIM_ZT14


title: Sample 12_Arabidopsis Col-0 2day seeds


title: Sample 10_Arabidopsis Col-0 2day seeds


title: LGP_ZT16


title: Sample 9_Arabidopsis csn5b-1 2day seeds

source_name: Arabidopsis csn5b-1 2day seeds


title: KIM_ZT10


title: Sample 8_Arabidopsis csn5b-1 2day seeds


title: KIM_ZT08


title: Sample 7_Arabidopsis csn5b-1 2day seeds


title: KIM_ZT06


title: Sample 6_Arabidopsis csn5a-1 2day seeds

source_name: Arabidopsis csn5a-1 2day seeds


title: Sample 4_Arabidopsis csn5a-1 2day seeds


title: Sample 5_Arabidopsis csn5a-1 2day seeds


title: KIM_ZT04


title: KIM_ZT02


title: KIM_ZT00


title: Sample 2_Arabidopsis csn1-10 2day seeds

source_name: Arabidopsis csn1-10 2day seeds


title: Sample 3_Arabidopsis csn1-10 2day seeds


title: KIC_ZT22

source_name: Kidney cortex

value: Kidney cortex


title: Sample 1_Arabidopsis csn1-10 2day seeds


title: KIC_ZT20


title: KIC_ZT16


title: ATH+VDA_24h_n=3

city: Jena

first: Sandra

middle: S

last: Scholz

address: Dornburger Straße 159

department: Plantphysiology

country: Germany

institute: Friedrich-Schiller-University Jena

data_processing:
The removal of low quality reads and Illumina adapters was performed using Trimmomatic.
The remaining reads were then aligned to the A. thaliana (TAIR10.33) and V. dahliae (ASM15067v2.37) reference genome using the RNA-seq aligner STAR.
Differential gene expression analysis was performed using DESeq2 with the raw counts obtained from FeatureCounts.
Genome_build: A. thaliana (TAIR10.33) and V. dahliae (ASM15067v2.37)
Supplementary_files_format_and_content: RawCounts_featureCounts.xlsx
DEGs_DualRNASeq_ATH-VDA.xlsx with normalized expressions of DEG (average of 3 replicates each)

source_name: roots & hyphae

growth_protocol: For short time co-cultivation assays 9 day-old A. thaliana seedlings of equal sizes were used. Co-cultivation of A. thaliana and the fungi was performed under in vitro culture conditions on a nylon membrane on PNM media (Johnson et al., 2011). Two days prior to use, 100 μl of the generated spore solutions or an equal amount of water were plated on 6 sterile membrane stripes (4 cm x 1 cm) placed on PDA plates and incubated at RT.

extract_protocol:
Both, RNA of plant and fungus, was isolated from 100 mg root material (≈ 120 seedlings per replicate). The frozen roots were finely ground with mortar and pistil and weighted. The RNA from the samples was extracted with peqGOLD TriFast™ FL (VWR, Darmstadt, Germany) according to the manufacturer’s protocol.  The RNA was further processed by use of the PureLink™ RNA Mini Kit (Thermo Fisher Scientific, Dreieich, Germany) with on-column DNAse treatment. RNA was dissolved in water and checked for quality.
The isolated RNA was shipped to GeneCore (Heidelberg, Germany) where library construction was performed using the mRNA sequencing Sample Preparation Guide (Illumina, Cat#RS-930-1001), followed by a validation of the library and RNA sequencing (Hi Seq 2000, single-end 75 bp, ~50 Mill. reads/sample).

treatment_protocol: For the co-cultivation the membrane stripes with fungus or water were placed on the PNM plates together with 2 plants per membrane. The plants were placed in the way that the roots were in contact with the fungus while the leaves were not. Plates were sealed with 3M™ Micropore tape and incubated for 24 h at 80 μmol m-2 sec-1 with light from one side (leaves directed to light). Roots were harvested for RNA extraction. All experiments were performed 3 times independently.

tag: host ecotype

tag: co-cultivation

value: Arabidopsis thaliana & Verticillium dahliae

tag: replicate


title: ATH_24h_n=3

source_name: roots


title: ATH+VDA_24h_n=2


title: KIC_ZT10

tag: tissue


title: ATH+VDA_24h_n=1


title: ATH_24h_n=2


title: KIM_ZT12


title: KIC_ZT12


title: KIC_ZT08


title: KIC_ZT04


title: ATH_24h_n=1


title: KIC_ZT00


title: IRI_ZT20

source_name: Iris

value: Iris


title: IRI_ZT16


title: IRI_ZT18


title: KIC_ZT18


title: IRI_ZT14


title: KIC_ZT14


title: IRI_ZT12


title: IRI_ZT06


title: KIC_ZT02


title: IRI_ZT08


title: IRI_ZT02


title: IRI_ZT04


title: IRI_ZT10


title: KIC_ZT06


title: ILE_ZT14

source_name: Ileum

value: Ileum


title: ILE_ZT16


title: ILE_ZT22


title: ILE_ZT18


title: ILE_ZT20


title: ILE_ZT08


title: IRI_ZT00


title: ILE_ZT04


title: ILE_ZT06


title: ILE_ZT10


title: ILE_ZT02


title: HIP_ZT22

source_name: Hippocampus

value: Hippocampus


title: ILE_ZT00


title: LGP_ZT12


title: HIP_ZT18


title: HIP_ZT12


title: HIP_ZT16


title: HIP_ZT06


title: HIP_ZT10


title: HIP_ZT08


title: HIP_ZT04


title: HIP_ZT00


title: ILE_ZT12


title: HEA_ZT20

source_name: Heart

value: Heart


title: HEA_ZT18


title: HEA_ZT22


title: HEA_ZT16


title: HEA_ZT14


title: HEA_ZT04


title: 7W_husband_blood

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

institute: Liangzhu Laboratory

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
All sequencing reads were first trimmed to remove adaptors and low quality bases using trim_galore (RefXXX) (parameters: --quality 20 --phred33 –length 50 --paired).
Next, reads passed quality control were mapped to human or mouse reference genome (version: hg19 or mm9) using bismark (version: 0.7.6) for bisulfite sequencing reads with paired-end alignment mode (parameters: --non-directional --fastq) and tophat for RNA-seq reads. To rescue more bisulfite sequencing reads, unmapped reads were realigned to the same reference genome in single-end alignment mode.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: For bisulfite sequencing samples, the processed files include the DNA methylation levels of cytosines in CpG, CHH and CHG context, in bed format. Processed data of RNA-seq samples were gene expression tables obtained from cufflinks.

organism: Homo sapiens

source_name: Peripheral Blood

extract_protocol:
single cell or small amounts of cells were seeded into the lysis buffer using the mouth pipette, and DNAs were released after proteinase treatment at 50C and then bisulfite converted.
After purification, DNAs were complemented with the biotinated random primer (5’-biotin-CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) and 50 units of klenow polymerase (3’ to 5’exo-, New England Biolabs). This random priming was repeated 5 times in total. The second strands were synthesized using another random primer (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’) and the final libraries were generated after 8-12 cycles PCR amplification with the Illumina universal PCR primer and Illumina indexed primer. For RNA-Seq, transcriptome of single cells or low amount of cells were amplified using a modified Smart-seq2. We reversely transcribed RNA molecules using a oligo (dT) primer anchored with 8bp unique molecular identifiers (UMI). Amplified cDNAs were fragmented into around 300 bp using a Covaris S2 and the sequencing libraries were constructed using a Kapa Hyper Prep Kit (Kapa Biosystems).

value: Peripheral Blood

tag: gender

tag: bulk or single cell

value: bulk cells


title: HEA_ZT06


title: HEA_ZT10


title: HEA_ZT08


title: HEA_ZT02


title: 7W_wife_blood


title: HIP_ZT14


title: 11W_husband_blood


title: 9W-PBAT-villus-2

source_name: Villus

value: Villus


title: HAB_ZT20

source_name: Habenula

value: Habenula


title: HIP_ZT02


title: 9W-PBAT-heart-2


title: HAB_ZT14


title: HAB_ZT18


title: HAB_ZT12


title: 9W-PBAT-villus-1


title: HEA_ZT12


title: HAB_ZT16


title: HEA_ZT00


title: HAB_ZT08


title: HAB_ZT10


title: HAB_ZT06


title: HAB_ZT04


title: HIP_ZT20


title: DUO_ZT12

source_name: Duodenum

value: Duodenum


title: DUO_ZT10


title: HAB_ZT02


title: HAB_ZT00


title: HAB_ZT22


title: DUO_ZT18


title: DUO_ZT20


title: 11W_wife_blood


title: DUO_ZT22


title: DUO_ZT16


title: DUO_ZT08


title: DUO_ZT06


title: DUO_ZT14


title: 9W-PBAT-heart-1


title: DUO_ZT02


title: DUO_ZT04


title: DMH_ZT20

source_name: Dorsomedial hypothalamus

value: Dorsomedial hypothalamus


title: DMH_ZT18


title: DMH_ZT22


title: DMH_ZT12


title: DMH_ZT14


title: DUO_ZT00


title: DMH_ZT10


title: DMH_ZT08


title: DMH_ZT06


title: DMH_ZT04


title: DEC_ZT22

source_name: Descending colon

value: Descending colon


title: DMH_ZT00


title: DEC_ZT20


title: DEC_ZT16


title: DEC_ZT14


title: DEC_ZT18


title: DEC_ZT12


title: DEC_ZT06


title: DEC_ZT00


title: DEC_ZT02


title: COR_ZT22

source_name: Cornea

value: Cornea


title: DEC_ZT10


title: DEC_ZT04


title: COR_ZT18


title: COR_ZT20


title: COR_ZT16


title: COR_ZT10


title: COR_ZT08


title: COR_ZT12


title: COR_ZT06


title: COR_ZT00


title: COR_ZT02


title: CER_ZT22

source_name: Cerebellum

value: Cerebellum


title: CER_ZT20


title: CER_ZT16


title: DEC_ZT08


title: CER_ZT18


title: CER_ZT14


title: CER_ZT08


title: CER_ZT10


title: CER_ZT00


title: CER_ZT02


title: CEC_ZT22

source_name: Cecum

value: Cecum


title: CER_ZT04


title: CEC_ZT20


title: CEC_ZT16


title: DMH_ZT16


title: COR_ZT14


title: CEC_ZT18


title: CER_ZT12


title: COR_ZT04


title: CEC_ZT14


title: CEC_ZT12


title: CEC_ZT10


title: CEC_ZT06


title: CEC_ZT00


title: CEC_ZT08


title: CEC_ZT04


title: BOM_ZT22

source_name: Bone marrow

value: Bone marrow


title: BOM_ZT20


title: CER_ZT06


title: BOM_ZT10


title: BOM_ZT14


title: BOM_ZT06


title: CEC_ZT02


title: BLA_ZT22

source_name: Bladder

value: Bladder


title: BOM_ZT16


title: BLA_ZT20


title: BOM_ZT02


title: BOM_ZT18


title: BLA_ZT12


title: BLA_ZT16


title: BOM_ZT04


title: BOM_ZT00


title: BLA_ZT10


title: BLA_ZT08


title: BLA_ZT06


title: BLA_ZT14


title: BLA_ZT02


title: BLA_ZT04


title: AXL_ZT20

source_name: Axillary lymphonodes

value: Axillary lymphonodes


title: AXL_ZT22


title: AXL_ZT18


title: BLA_ZT00


title: BOM_ZT12


title: BOM_ZT08


title: BLA_ZT18


title: AXL_ZT12


title: AXL_ZT14


title: AXL_ZT16


title: AXL_ZT08


title: AXL_ZT02


title: AXL_ZT00


title: AXL_ZT04


title: ASC_ZT18

source_name: Ascending colon

value: Ascending colon


title: ASC_ZT20


title: ASC_ZT22


title: DMH_ZT02


title: ASC_ZT08


title: ASC_ZT16


title: ASC_ZT12


title: ASC_ZT14


title: ASC_ZT02


title: ASC_ZT04


title: ARC_ZT22

source_name: Arcuate nucleus

value: Arcuate nucleus


title: ASC_ZT00


title: ARC_ZT20


title: AXL_ZT10


title: ASC_ZT06


title: AXL_ZT06


title: ARC_ZT12


title: ARC_ZT16


title: ARC_ZT10


title: ARC_ZT08


title: Islets

city: Miami

first: Juan

last: Domínguez-Bendala

state: FL

address: 1450 NW 10th Ave Miami

department: Department of Surgery

institute: Diabetes Research Institute, University of Miami, Miller School of Medicine

description: Pancreatic Islet equivalents

data_processing:
Real time image analysis and base calling were performed on the instrument using the HiSeq Sequencing Control Software version 2.2.58
The raw FASTQ files were split into files containing 4,000,000 reads and checked for quality using the FASTX-Toolkit. The reads were filtered (removing sequences that did not pass Illumina’s quality filter) and trimmed based on the quality results (5 nucleotides at the left end of both the R1 and R2 reads).
Sequence alignment was performed using TopHat v2.1.0 with the following settings: tophat2 -p 2 -o [OUTPUT FOLDER] --library-type fr-firststrand –r [Dx] –mate-std-dev [Ds] [hg38 BOWTIE2 GENOME INDEX] [FASTQ 1] [FASTQ 2]. Where Dx and Ds represent sample-specific values for the mean and standard deviation, respectively, of the inner distance between reads, as determined by non-gapped alignment to human mRNA. FASTQ1 and FASTQ2 represent two files containing matched pairs of reads. The hg38 genome, hg38.fa.gz, was downloaded from ftp://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/  and the BOWTIE2 index generated using the following command: bowtie2-build hg38.fa hg38. In practice split FASTQs with 4 million reads each were aligned separately to the genome to accelerate processing. An example execution command of an alignment of a single FASTQ file is given here: tophat2 -p 2 -o SL253780_CB602ANXX_L006_000 --library-type fr-secondstrand -r 112 --mate-std-dev 108 bowtie2_index/hg38 SL253780_CB602ANXX_L006_R1_000.fastq SL253780_CB602ANXX_L006_R2_000.fastq. Following the alignment BAM files were merged on a per-sample basis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
RPKM values were then normalised against 10 selected house keeping genes.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include mRNA RPKM values for each sample.

source_name: Pancreas

growth_protocol: hNEPT was obtained as a byproduct of human islet isolation. The tissue pellet was washed 5 times using starting medium (10%FBS+RPMI+100ug/ml Soyabean Trypsin Inhibitor) at an rcf of 300g. 0.5ml of tissue pellet was resuspended in 30 ml of starting medium in a 175 cm2 cell culture flask (Corning, cat. 431080, Corning, NY). Cells were cultured at 8% oxygen, 95% humidity and 5% Carbon dioxide for 2 consecutive days without handling. After 48h, the flasks were washed with DPBS (ThermoFisher, cat. D8537) + 10% FBS (ThermoFisher, cat. 10437028) 3 times and the medium changed to StemPro (ThermoFischer, Cat. A1000701). Sorted cells were plated in starting medium + 10μM ROCK inhibitor Y-27632 (Millipore, cat. SCM075) for 2-3 days allowing for cells to attach. The media was then changed to StemPro for the duration of the culture experiment. For differentiation, cells were cultured at 21% Oxygen, 95% humidity and 5% Carbon dioxide.

extract_protocol:
RNA harvested from ~150,000 cells using Trizol reagent. (RNA processing, cDNA library construction and NGS sequencing were all performed at Ocean Ridge biosciences FL. USA) Total RNA was isolated from the tissue samples using the TRI Reagent® (Molecular Research Center; Part #: TR118) method. Following isolation, RNA was pooled from 3 human samples, quantified by O.D. measurement, and then digested with RNase free DNase I (Epicentre; Part # D9905K) and re-purified using RNeasy MinElute columns (Qiagen; Part #: 74204). The newly digested RNA samples were then quantified by O.D. measurement and checked for quality by chip-based capillary electrophoresis using an Agilent 2100 Bioanalyzer.
Amplified cDNA libraries suitable for sequencing were prepared from 8 nanograms (ng) of DNA-free total RNA using the Clontech SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Clontech/Takara; Part # 634411). The quality and size distribution of the amplified libraries were determined by chip-based capillary electrophoresis (Agilent 2100 Bioanalyzer; Agilent Technologies). Libraries were quantified using the KAPA Library Quantification Kit (Kapa Biosystems, Boston, MA).
The libraries were pooled at equimolar concentrations and diluted prior to loading onto the flow cell of the Illumina cBot cluster station. The libraries were extended and bridge amplified to create sequence clusters using the Illumina HiSeq PE Cluster Kit v4 and sequenced on an Illumina HiSeq Flow Cell v4 with 50 nt paired-end reads plus dual index reads using the Illumina HiSeq SBS Kit v4.

treatment_protocol: Cells treated with BMP7 were supplemented with 100ng/ml recombinant BMP7 (PeproTech, Cat# 120-03)

tag: donor samples

value: Pancreatic Islets

tag: patient type

value: Non diabetic human


title: ALK3Bright_P2RY1+_differentiated

description: ALK3Bright/P2RY1+  cells differentiated by BMP7 removal

value: Human Non-Endocrine Pancreatic Tissue


title: ASC_ZT10


title: ALK3Bright_P2RY1+_BMP7treated

description: ALK3Bright/P2RY1+  cells treated with BMP7


title: ALK3Bright_P2RY1+

description: ALK3Bright/P2RY1+  cells sorted via FACS


title: ARC_ZT06


title: ARC_ZT04


title: ventralH_Restraint_repl5

city: Zurich

first: Johannes

last: Bohacek

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich/ ETH Zurich

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, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: ventral hippocampus

extract_protocol:
Samples were homogenized at 4°C in a tissue lyser bead mill (Qiagen, Germany) for 2 min in 1 ml TrisureTM (Bioline USA Inc., MA), and RNA was extracted according to manufacturer's recommendations. Library was constructed using Illumina TruSeq RNA library preparation using poly(A)-enrichment according to manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: ventral hippocampus

tag: age

value: post natal day 105

value: wild type


title: ARC_ZT00


title: ARC_ZT02


title: ARC_ZT18


title: ventralH_Restraint_repl2


title: ventralH_Restraint_repl1


title: ARC_ZT14


title: AOR_ZT20

source_name: Aorta

value: Aorta


title: AOR_ZT18


title: ventralH_Swim_repl4


title: AOR_ZT14


title: ventralH_Swim_repl5


title: AOR_ZT16


title: ventralH_Swim_repl2


title: AOR_ZT12


title: ventralH_Swim_repl3


title: AOR_ZT10


title: ventralH_Swim_repl1


title: ventralH_Handling_repl5


title: AOR_ZT04


title: AOR_ZT06


title: ventralH_Handling_repl4


title: ventralH_Handling_repl3


title: ventralH_Restraint_repl4


title: ventralH_Restraint_repl3


title: AOR_ZT02


title: ventralH_Handling_repl2


title: AOR_ZT22


title: ventralH_Handling_repl1


title: AOR_ZT00


title: ANT_ZT22

source_name: Antrum

value: Antrum


title: ventralH_Homecage_repl5


title: ANT_ZT20


title: ventralH_Homecage_repl3


title: ventralH_Homecage_repl4


title: ANT_ZT16


title: ventralH_Homecage_repl1


title: dorsalH_Restraint_repl4

source_name: dorsal hippocampus

value: dorsal hippocampus


title: dorsalH_Restraint_repl5


title: dorsalH_Restraint_repl3


title: ANT_ZT10


title: ANT_ZT14


title: ANT_ZT08


title: dorsalH_Swim_repl5


title: dorsalH_Restraint_repl1


title: ANT_ZT04


title: ANT_ZT00


title: ANT_ZT06


title: ANT_ZT02


title: dorsalH_Swim_repl4


title: dorsalH_Swim_repl2


title: dorsalH_Swim_repl3


title: ANT_ZT18


title: AMY_ZT22

source_name: Amygdala

value: Amygdala


title: AMY_ZT20


title: AMY_ZT18


title: dorsalH_Swim_repl1


title: dorsalH_Handling_repl5


title: ANT_ZT12


title: AMY_ZT16


title: ventralH_Homecage_repl2


title: AMY_ZT14


title: dorsalH_Restraint_repl2


title: dorsalH_Handling_repl2


title: dorsalH_Handling_repl3


title: dorsalH_Handling_repl4


title: dorsalH_Homecage_repl5


title: dorsalH_Handling_repl1


title: dorsalH_Homecage_repl4


title: AMY_ZT08


title: dorsalH_Homecage_repl3


title: AMY_ZT10


title: AMY_ZT06


title: AMY_ZT02


title: AMY_ZT00


title: AMY_ZT04


title: dorsalH_Homecage_repl2


title: dorsalH_Homecage_repl1


title: ADM_ZT20

source_name: Adrenal medulla

value: Adrenal medulla


title: ADM_ZT22


title: ADM_ZT18


title: ADM_ZT16


title: wholeH_Restraint_repl3

source_name: whole hippocampus

value: whole hippocampus


title: wholeH_Restraint_repl5


title: wholeH_Restraint_repl2


title: wholeH_Restraint_repl4


title: ADM_ZT12


title: ADM_ZT14


title: AMY_ZT12


title: wholeH_Swim_repl5


title: wholeH_Swim_repl4


title: wholeH_Swim_repl3


title: ADM_ZT08


title: ADM_ZT10


title: ADM_ZT06


title: wholeH_Swim_repl1


title: wholeH_Handling_repl5


title: wholeH_Handling_repl3


title: wholeH_Handling_repl2


title: ADM_ZT02


title: ADC_ZT22

source_name: Adrenal cortex

value: Adrenal cortex


title: ADM_ZT04


title: ADC_ZT18


title: ADC_ZT20


title: wholeH_Handling_repl4


title: wholeH_Homecage_repl3


title: wholeH_Handling_repl1


title: wholeH_Homecage_repl5


title: wholeH_Homecage_repl2


title: wholeH_Restraint_repl1


title: ADC_ZT14


title: ADC_ZT12


title: wholeH_Homecage_repl4


title: wholeH_Homecage_repl1


title: ADC_ZT16


title: ADC_ZT06


title: ADC_ZT10


title: VDA_24h_n=3

organism: Verticillium dahliae

source_name: hyphae


title: ADC_ZT08


title: wholeH_Swim_repl2


title: ADM_ZT00


title: VDA_24h_n=2


title: VDA_24h_n=1


title: ADC_ZT00


title: ADC_ZT02


title: ADC_ZT04


title: AOR_ZT08


title: SV40 BSC40 PA-m6A-seq late mutant validation

city: Taipei

first: Kevin

last: Tsai

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

description: Aligned to the SV40 genome (RefSeq NC_001669.1)

data_processing:
Library strategy: PA-m6A-seq
CASAVA 1.8.2
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the SV40 genome using Bowtie 0.12.7: bowtie -m 9 -v 1 -a --best --strata --chunkmbs 2048
Filtered out all reads that lack a TC mutation
Awk script to generate bed file, columns are "chromosome, start, end, score, strand": BEGIN{FS=OFS="\t"} { chromosome=$3; startC=$4+1; endC=(length($5) + $4); strand=$2; split($1,sc,"-"); name=sc[1]; score= (sc[2] / [Total 15nt+ read count of each run]); if($2!="") print(chromosome"\t"startC"\t"endC"\t"score"\t"strand); }
Genome_build: RefSeq NC_001669.1
Supplementary_files_format_and_content: bed files, aligned to SV40 NC_001669.1; score = counts per million total reads. Total reads only include reads that has a fastq quality score >33, contain a piece of the Illumina sequencing index, and is longer then 15nt. Repetitive Bed entries are due to that fact that each of those entries has a T-C mutation in a different position. T-C mutations are from the UV crosslinking of CLIP (crosslink and immunoprecipitation) techniques, and provide us with validation that our pulled down reads are indeed interacting with our protein of interest.

organism: Betapolyomavirus macacae

source_name: BSC40 infected with SV40 776 mutant VPm

extract_protocol:
PAR-CLIP
All samples were processed with the Illumina Tru-seq small RNA-seq kit

tag: virus strain

tag: virus genotype

value: mutant "VPm"

tag: host cell line

value: Cercopithecus aethiops cell line BSC40

tag: technique

tag: antibody

value: anti-m6A, Synaptic Systems, Cat No 202111, Lot No, 202111/4


title: GFPneg2_2

city: Moscow

first: Deborah

middle: Lynn

last: Stenkamp

state: Idaho

address: 875 Perimeter Drive, MS 3051

department: Biological Sciences

institute: University of Idaho

data_processing:
Quality trimmed with Sickle (https://github.com/najoshi/sickle)
Paired reads were overlapped with FLASH (https://ccb.jhu.edu/software/FLASH/)
Overlapped reads were against the Danio rerio reference using BWA (http://bio-bwa.sourceforge.net/)
BAMs were sorted using SAMtools (http://samtools.sourceforge.net/)
Reads were counted by feature using htseq-count (http://www-huber.embl.de/HTSeq/doc/count.html)
Counts were analyzed and differentially expressed genes were identified with R and edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html)
Genome_build: Zv9.75
Supplementary_files_format_and_content: Read count data from HTSeq; EdgeR analysis results with annotation

organism: Danio rerio

source_name: Zebrafish retinal cells, not rods

growth_protocol: Zebrafish (XOPS:eGFP transgenic line) were on a 14:10 light:dark cycle in recirculating, monitored system water, housed and propagated according to The Zebrafish Book (Westerfield).

extract_protocol:
RNA was extracted from tissue samples using the NucleoSpin® RNA kit (Macherey-Nagel) using the manufacturer’s protocol, quantified and quality-checked on a Nanodrop spectrophotometer. Both quantity and quality were assessed by using an Agilent 2100 Bioanalyzer. All samples used for RNA-seq had an RNA integrity number (RIN) > 8.0, and experimental design was such that GFP+ cells, or GFP- cells derived from the two retinas of a single fish constituted each RNA sample as a biological replicate. At least 5 ng of RNA was available per sample, and provided to the University of Idaho’s Institute for Bioinformatics and Evolutionary Studies (IBEST) Genomics Core for RNA amplification and the generation of cDNA.
Quality and quantity of cDNA were verified by Bioanalyzer. All sample preparation was achieved with Ovation® RNA-Seq System V2 (NuGEN), and sequencing performed on an Illumina (San Diego, CA) MiSeq. Four replicates (from four different fish) were sequenced (Fig. 1A). Mapping percentages ranged from 97.0% to 97.4% per sample, and sequencing depth ranged from 2,781,516 to 3,480,515 reads per sample.

treatment_protocol: Whole retinas were dissociated into cell suspensions by incubating with 0.225% trypsin (Fisher ThermoScientific) and 0.001% papain (Sigma) for 10 minutes at 37°C. Dissociation was stopped by the addition of fetal bovine serum (10% v/v final concentration). Suspended cells were pelleted and incubated with DNAseI at room temperature for 15 min. Cells were pelleted and resuspended in 100 µL phosphate-buffered (pH 6.5) saline (PBS) and immediately FACS-sorted. GFP+ vs. GFP- retinal cells were sorted using a FACSAria flow cytometer, using the 488 nm laser and FITC fluorescence filter, and the 70 µm nozzle. Some cells were collected for fluorescence microscopy, or for post-sort FACS analysis. For RNA-seq or qPCR, GFP+ and GFP- cells were collected separately in a final volume of 100 µL of the FACS sheath fluid, and RNA was immediately extracted.

tag: cell type

value: non-rod retinal cells

value: GFP-; FACS-sorted non-rods from retina


title: GFPpos2_2

source_name: Zebrafish retinal rod photoreceptors

value: rod photoreceptors

tag: genotype/variation

value: GFP+; FACS-sorted rods


title: GFPpos5_2


title: GFPneg5_2


title: T2

city: New York

first: Jeremy

last: Dasen

state: NY

address: 522 First Avenue

department: Neuroscience Program

institute: NYU School of Medicine

data_processing:
Reads were cleaned with Trimmomatic v0.33 to remove sequencing primers and trim low quality bases from 3' and 5' ends until the final 4-base window had an average Q30 ≥ 15
All RNA-seq data files were combined and de novo assembled into one set of transcripts with Trinity r2013-02-25
The resulting transcriptome assembly contained 82,429 contigs, of which 19,244 were similar to annotated zebrafish genes (BLAST e-value < 10e-4)
Gene expression was quantified in each RNA-seq sample by quasi-mapping to the set of transcriptome contigs with Salmon (v0.8.2).
Differential expression between spinal cord (T) and pectoral fin (P) groups was computed using the Bioconductor package edgeR (v3.18.1)
Genome_build: de novo assembled
Supplementary_files_format_and_content: ExpressionTable.xlsx is the final output of edgeR analysis of P vs T samples, including log2 fold change and FDR corrected p-value, annotated with additional columns for the matching zebrafish gene (GenBank ID) and a brief description of gene function, if known.
Supplementary_files_format_and_content: Spades_transcripts.fasta is the output of Trininity assembly of all RNA-seq reads from P and T samples

organism: Leucoraja erinaceus

source_name: Tail spinal cord cells

extract_protocol:
Total RNA from manually sorted cells was extracted using Arcturus Picopure RNA isolation kit from Applied biosystems.
Illumina TruSeq stranded mRNA

value: Spinal cord

value: stage 30-31

tag: genotype

value: Tail spinal cord cells


title: GFPneg2


title: GFPneg1


title: SV40 BSC40 PA-m6A-seq late mutant validation WT control

source_name: BSC40 infected with SV40 776

value: wildtype


title: T4

value: wild type


title: P3

source_name: Pectoral fin motor neurons

value: Pectoral fin motor neurons


title: GFPpos2


title: SV40 BSC40 FLAG-YTHDF3 PAR-CLIP

data_processing:
CASAVA 1.8.2
fastx toolkit: fastq_quality_filter -Q33| fastx_clipper -Q33 -v -a [index_sequence] -l 15 -c | fastq_to_fasta -Q33
Aligned to the SV40 genome using Bowtie 0.12.7: bowtie -m 9 -v 1 -a --best --strata --chunkmbs 2048
Filtered out all reads that lack a TC mutation
Awk script to generate bed file, columns are "chromosome, start, end, score, strand": BEGIN{FS=OFS="\t"} { chromosome=$3; startC=$4+1; endC=(length($5) + $4); strand=$2; split($1,sc,"-"); name=sc[1]; score= (sc[2] / [Total 15nt+ read count of each run]); if($2!="") print(chromosome"\t"startC"\t"endC"\t"score"\t"strand); }
Genome_build: RefSeq NC_001669.1
Supplementary_files_format_and_content: bed files, aligned to SV40 NC_001669.1; score = counts per million total reads. Total reads only include reads that has a fastq quality score >33, contain a piece of the Illumina sequencing index, and is longer then 15nt. Repetitive Bed entries are due to that fact that each of those entries has a T-C mutation in a different position. T-C mutations are from the UV crosslinking of CLIP (crosslink and immunoprecipitation) techniques, and provide us with validation that our pulled down reads are indeed interacting with our protein of interest.

value: Cercopithecus aethiops cell line BSC40 clonally expressing FLAG-YTHDF3

value: PAR-CLIP

value: anti-Flag, Sigma, Cat No F1804, Lot No SLBQ6349V


title: P1


title: GFPpos1


title: SV40 BSC40 FLAG-YTHDF2 PAR-CLIP

value: Cercopithecus aethiops cell lineBSC40 clonally expressing FLAG-YTHDF2


title: T1


title: SV40 BSC40 FLAG-GFP PAR-CLIP

value: Cercopithecus aethiops cell line BSC40 clonally expressing FLAG-GFP


title: SV40 BSC40 PA-m6A-seq early mutant validation WT control

value: Cercopithecus aethiops cell line BSC40


title: 1321N1

status: Public on Feb 07 2018

city: Tempe

first: Joshua

last: LaBaer

state: AZ

address: 1001 S McAllister Ave

department: Biodesign Institute

institute: ASU

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to the Ensembl release 75 (GRch37) genome sequences using TopHat version 2.0.8 with defualt options
Uniquely mapped reads were extracted with samtools version 1.0 with "view -F 256" command
FPKM values for known transcripts were calculated with Cufflink 2.2.1 with an option -G
Entrez gene annotation was added by using 'gene2ensembl' file downloaded from NCBI FTP site
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files with Ensenbl Gene ID, Entrez Gene ID, Gene Symbol, and FPKM

source_name: human Glial cells from brain astrocytoma

growth_protocol: All cells were grown and maintained in growth conditions specified by the vendor

extract_protocol:
RNA  from  Ibrutinib-responsive  and  Ibrutinib  non-responsive  cell  lines was  extracted  with RNA  easy  kit (Qiagen) and checked for high quality before sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were cultured in 6 well plates for 48 hours before RNA extraction.

tag: cell line

value: Glial

tag: disease

value: brain astrocytoma

tag: passage number


title: COV318

source_name: ovarian cancer cells

tag: tissue

value: ovarian

value: ovarian epithelial-serous carcinoma


title: H146

source_name: lung cancer cells from small cell lung cancer

value: lung

value: small cell lung cancer


title: HEC59

source_name: cells from endometrial carcinoma

value: endometrial

value: endometrial carcinoma


title: H716

source_name: cells from cecum/colorectal adenocarcinoma

value: cecum

value: colorectal adenocarcinoma


title: KLE

source_name: uterus/endometrium cancer cells

value: KLE

value: endometrial adenocarcinoma


title: H522

source_name: lung cancer cells from non-small cell lung cancer

value: non-small cell lung cancer


title: P2

value: Spinal cord

value: stage 30-31

value: wild type

value: Pectoral fin motor neurons


title: H661

source_name: lung cancer cells from large cell lung cancer

value: large cell lung cancer


title: Input_Chipseq

city: Houston

first: Dongyu

last: Zhao

state: TX

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNA-seq reads were mapped to the human reference genome version hg19 using TopHat (version 2.1.0). We downloaded the human reference gene set (Refseq gene) from https://www.ncbi.nlm.nih.gov/refseq/rsg/. The number of fragments that originated from each gene in each sample is estimated using cuffdiff in the software Cufflinks (version 2.2.1) with classic-fpkm normalization method. The differentially expressed genes based on read counts are inferred using edgeR R package v3.12 after library-size factor normalization. MEV version 4.8.1 was used to plot heat maps.
All ChIP-seq sequencing reads were mapped to the version hg19 of the human genome using Bowtie (version 1.1.2) . The Dregion function in DANPOS (version 2.2.3) was used to calculate read density and define enrichment peaks. Briefly, we extended each read at the 3′ end to be 200 bp long and then calculated read density as the number of reads covering each base pair in the genome. For each sample, the total number of mapped reads was normalized to 25 million. For AR and BMI1 data, we used Poisson test P value 1 × 10−35 for read density cutoff to define seed peaks. We then used Poisson test P value 1 × 10−15 for read density cutoff to extend each seed peak. DANPOS subtracted input background signal from the ChIP signal. To further reduce the input background effect, we removed any ChIP-Seq peaks that overlap with a peak in the input data. For input data, we used Poisson test P value 1 × 10−15 for read density cutoff to define seed peaks. We then used Poisson test P value 1 × 10−10 for read density cutoff to extend each seed peak. The selector function in DANPOS was used to map the peak regions to TSSs. The overlap function in DANPOS was used to calculate the number of overlapped peak regions.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-Seq data, tab-delimited text files contian normalized count values for each gene of each sample. For ChIP-Seq data, wig files showing the average singnal density acocross genome are generated using DANPOS2 v2.2.3.

source_name: Castration-resistant prostate cancer

growth_protocol: Cells were seeded in 96-well plates and treated with the two single drugs, and the combination of both at concentration gradients for 96 hours. Bioluminescence was measured to quantify cell survival by using CellTiter-Glo® Luminescent Cell Viability Assay Kit and was read on Synergy 2 Multi-Mode Reader.

extract_protocol:
ChIP was performed using the ChIP Assay kit with the procedure provided by the manufacturer.
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

value: Prostate

tag: chip antibody

value: Input


title: SV40 BSC40 PA-m6A-seq repeat 1

value: wildtype

value: Cercopithecus aethiops cell line BSC40

value: anti-m6A, Synaptic Systems, Cat No 202111, Lot No, 202111/4


title: Hoxb5_Pro/pre-B_rep7

city: chengdu

first: Yong

last: Dong

state: sichuan

address: Xindu road 783, Xindu district

department: Immunology

institute: Chengdu medical college

data_processing:
Bcl2fastq convert .bcl files into fastq files
Fastq files were aligned to mm10 genome.*.bt2 files to generate accepted_hits.bam file by tophat, and the used cuffquant scripts (cufflinks-2.2.1) to calculated genes expression level.
Gene expression levels of different samples were normalized by cuffnorm scripts (cufflinks-2.2.1), and finally generated genes.fpkm_table
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_table was generated by cuffnorm; gene expression value

growth_protocol: All mice in this study were kept in C57BL/6J backgroud. B220+ enriched cells  from bone marrow, and then transduced with Hoxb5 virus or GFP control virus in vitro.

extract_protocol:
The procedure of RNA extraction and reverse transcription into double-stranded DNA is based on published methods(PMID:20203668).
Libraries were prepared according to Illumina's instructions accompanying the  illumina Nextera XT DNA Sample Preparation Kit (FC-131-1096).

treatment_protocol: 1000 Hoxb5 or control transduced Pro-/pre-B cells were  sorted for RNAseq  analysis.

tag: strain background

value: Bone marrow

value: B220+ enriched cells

tag: transduced with

value: Hoxb5 virus

value: Pro/pre-B cells


title: Hoxb5_Pro/pre-B_rep6


title: BMI1_Chipseq

value: BMI1 antibody


title: AR_Chipseq

value: AR antibody


title: Control_RNAseq_Rep1

growth_protocol: C4-2 cells were cultured in 5% CO2 and maintained in vitro in RPMI 1640 medium supplemented with 10% FBS, 2 mmol/L glutamines, 100 Units/mL penicillin, and 100 mg/mL streptomycin.

extract_protocol:
Total RNA was isolated from cells using the RNA MiniPrep kit (Direct-zol, R2052, ZYMO Research) with the procedure provided by the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 0.3 million cells were plated in six-well plates, grown without antibiotics to  80% confluence, and then transfected with siRNA sequences or their corresponding mock sequences using a Lipofectamine 2000 kit (Invitrogen, Cat.11668-019) with the procedure  provided by the manufacturer


title: Control_RNAseq_Rep2


title: Hoxb5_Pro/pre-B_rep8


title: Hoxb5_Pro/pre-B_rep3


title: control_Pro/pre-B_rep7

value: GFP control virus


title: control_Pro/pre-B_rep6


title: control_Pro/pre-B_rep8


title: Hoxb5_Pro/pre-B_rep2


title: control_Pro/pre-B_rep3


title: control_Pro/pre-B_rep2


title: control_Pro/pre-B_rep5


title: control_Pro/pre-B_rep4


title: control_Pro/pre-B_rep1


title: iCD8_SP rep4

description: iCD8_SP rep4

data_processing:
Bcl2fastq convert .bcl files into fastq files
Fastq files were aligned to NCBIM37 genome.*.bt2 files to generate accepted_hits.bam file by tophat, and the used cuffquant scripts (cufflinks-2.2.1) to calculated genes expression level.
Gene expression levels of different samples were normalized by cuffnorm scripts (cufflinks-2.2.1), and finally generated genes.fpkm_table
Genome_build: NCBIM37
Supplementary_files_format_and_content: fpkm_table was generated by cuffnorm

source_name: Induced CD8 single positive cells

growth_protocol: All mice in this study were kept in C57BL/6J backgroud. Pro-/pre B cells were sorted from bone marrow, and then infected with Hoxb5 virus in vitro. After the infection, Hoxb5 transduced Pro-/pre-B cells were  sorted and transplanted into sublethal irradiation recipients.

treatment_protocol: Target cells were sorted from the bone marrow or the thymus of recipients.

tag: strain

value: Thymus


title: BMI1_Knockdown_RNAseq_Rep2


title: RNF2_Knockdown_RNAseq_Rep2

treatment_protocol: 0.3 million cells were plated in six-well plates, grown without antibiotics to  80% confluence, and then transfected with siRNA sequences or their corresponding mock sequences using a Lipofectamine 2000 kit with the procedure  provided by the manufacturer


title: iCD8_SP rep2

description: iCD8_SP rep2


title: Hoxb5_Pro/pre-B_rep5


title: BMI1_Knockdown_RNAseq_Rep1


title: Hoxb5_Pro/pre-B_rep4


title: iCD8_SP rep1

description: iCD8_SP rep1


title: Hoxb5_Pro/pre-B_rep1


title: iCD4_SP rep3

description: iCD4_SP rep3

source_name: Induced CD4 single positive cells


title: iDN4 rep3

description: iDN4 rep3

source_name: Induced Double negative cells_phase4


title: iDN4 rep4

description: iDN4 rep4


title: iCD4_SP rep4

description: iCD4_SP rep4


title: iCD4_SP rep2

description: iCD4_SP rep2


title: iCD4_SP rep1

description: iCD4_SP rep1


title: iDP rep3

description: iDP rep3

source_name: Induced double positve cells


title: iDP rep2

description: iDP rep2


title: iDP rep1

description: iDP rep1


title: iDN4 rep2

description: iDN4 rep2


title: iDN3 rep3

description: iDN3 rep3

source_name: Induced Double negative cells_phase3


title: iDN4 rep1

description: iDN4 rep1


title: iDN3 rep1

description: iDN3 rep1


title: iDN3 rep2

description: iDN3 rep2


title: iDN2 rep1

description: iDN2 rep1

source_name: Induced Double negative cells_phase2


title: iCD8_SP rep3

description: iCD8_SP rep3


title: iDN1 rep3

description: iDN1 rep3

source_name: Induced Double negative cells_phase1


title: iDN1 rep2

description: iDN1 rep2


title: iDN1 rep4

description: iDN1 rep4


title: iDN2 rep2

description: iDN2 rep2


title: iDN1 rep1

description: iDN1 rep1


title: CD8_SP rep3

description: CD8_SP rep3

source_name: CD8 single positive cells


title: CD8_SP rep2

description: CD8_SP rep2


title: CD4_SP rep1

description: CD4_SP rep1

source_name: CD4 single positive cells


title: DP rep1

description: DP rep1

source_name: Double positve cells


title: CD8_SP rep1

description: CD8_SP rep1


title: DP rep4

description: DP rep4


title: DN4 rep3

description: DN4 rep3

source_name: Double negative cells_phase4


title: CD4_SP rep3

description: CD4_SP rep3


title: DN4 rep1

description: DN4 rep1


title: DP rep3

description: DP rep3


title: CD4_SP rep2

description: CD4_SP rep2


title: DP rep2

description: DP rep2


title: DN2 rep1

description: DN2 rep1

source_name: Double negative cells_phase2


title: DN1 rep2

description: DN1 rep2

source_name: Double negative cells_phase1


title: DN2 rep3

description: DN2 rep3


title: DN3 rep1

description: DN3 rep1

source_name: Double negative cells_phase3


title: DN2 rep2

description: DN2 rep2


title: DN4 rep2

description: DN4 rep2


title: Thy_iETPs rep2

description: Thy_iETPs rep2

source_name: Induced early T progenitors from thymus


title: Thy_iETPs rep1

description: Thy_iETPs rep1


title: DN1 rep1

description: DN1 rep1


title: Thy_iETPs rep3

description: Thy_iETPs rep3


title: Thy_ETPs rep1

description: Thy_ETPs rep1

source_name: Early T progenitors from thymus


title: BM_iETPs rep2

description: BM_iETPs rep2

source_name: Induced early T progenitors from bone marrow


title: BM_ETPs rep2

description: BM_ETPs rep2

source_name: Early T progenitors from bone marrow


title: BM_iETPs rep1

description: BM_iETPs rep1


title: Thy_ETPs rep2

description: Thy_ETPs rep2


title: BM_ETPs rep1

description: BM_ETPs rep1


title: DN3 rep2

description: DN3 rep2


title: Mature lineage cells 8

description: Mature lineage cells 8

source_name: Myeloid cells


title: Mature lineage cells 6

description: Mature lineage cells 6

source_name: B cells


title: Mature lineage cells 9

description: Mature lineage cells 9


title: Mature lineage cells 7

description: Mature lineage cells 7


title: NCMD4

city: Rochester

first: Xuewei

last: Wang

address: 200 1st street

institute: Mayo Clinic

data_processing:
Base calling by CASAVA
Alignment by Tophat2
Gene count by featureCount
Normalization by edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tsv file for gene count

source_name: LLC1 cells

growth_protocol: Conditioned medium was obtained from LLC 1 cells.  To this conditioned medium was added either vehicle or calcitriol.  Conditioned medium was used to treat  primary human skeletal muscle cells for period of 24 hours .  LLC1 cells were grown as described ATCC.  Human skeletal muscle cells were  grown using re-agents obtained from Lonza.

extract_protocol:
RNA was prepared using RNA/protein spin columns (Clontech, Mountain View, CA).  Lysis solution was added to cells in 6-well plates and cells were solubilized by passage of tissue successively through 21 and 27 gauge needles.  Individual cell lysates were applied to RNA spin columns for purification.  RNAs eluted into nuclease-free water were quantitated by UV spectroscopy, quality assessed by 260nm/280nm ratio then frozen at -80 0C.  Before library construction, RNA quality was assessed by capillary electrophoresis against a known size standard.
Poly-A containing mRNA was purified using poly-T oligo attached magnetic beads. The purified mRNA was fragmented and ethanol precipitated. The RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis was performed using DNA polymerase I and RNase H. The cDNA was purified ends were repaired and phosphorylated using Klenow, T4 polymerase, and T4 polynucleotide kinase, after which an “A” base was added to the 3’ ends of double-stranded DNA using Klenow exo- (3’ to 5’ exo minus).  Paired end DNA adaptors (Illumina) with a single “T” base overhang at the 3’ end were ligated. DNA fragments of approximately 250-300 bp were purified on, and excised from agarose gels.  The adapter-modified DNA fragments were enriched by PCR using primers PE 1.0 and PE 2.0 (Illumina). The concentration and size distribution of the libraries was determined on an Agilent Bioanalyzer DNA 1000 chip.
cDNA libraries were loaded onto Illumina TruSeq v3 paired end flow cells at concentrations of 9 pM to generate cluster densities of 600,000-800,000/mm2 following Illumina’s standard protocol using the Illumina cBot and Hi-Seq 3000/4000 PE cluster kit.  The flow cells were sequenced as 100 X 2 paired end reads on an Illumina HiSeq 3000/4000 sequencing kit and HCS v 3.3.20 collection software. Base-calling is performed using Illumina’s RTA version 2.5.2.

treatment_protocol: Human skeletal muscle cells were treated with LLC1 conditioned medium for a period of 24 hours prior to the isolation of RNA.

tag: treatment

value: Non-conditioned medium + Calcitriol


title: Mature lineage cells 4

description: Mature lineage cells 4


title: DN1 rep3

description: DN1 rep3


title: NCMD3


title: NCMD2


title: NCMD1


title: Mature lineage cells 5

description: Mature lineage cells 5


title: BM_ETPs rep3

description: BM_ETPs rep3


title: Mature lineage cells 2

description: Mature lineage cells 2

source_name: T cells


title: NCM4

value: Non-conditioned medium


title: Pro-_Pre-B rep4

description: Pro-_Pre-B rep4

source_name: Pro-_pre-B cells


title: HL60_KO-3_rep2

city: Marburg

first: Uta

middle: Maria

last: Bauer

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research

institute: Philipps University Marburg

description:
CRISPR/Cas9-mediated deletion of SKI in HL60 cells.
Processed data file: HL60_raw_countFeatures.txt
Processed data file: HL60_deseq_norm_countFeatures.txt

data_processing:
Illumina RTA 1.8.66.4 software used for basecalling.
Sequenced reads were trimmed for adaptor using Illumina bcl2fastq, then mapped to hg19 whole genome using Tophat2.
Exon counts were aggregated for each gene to build a read count table using SubRead function featureCount.
Counts for each gene were normalized by DESeq2 according to instructions by authors.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: HL60_raw_countFeatures.txt: Tab-delimited text file includes raw counts.
Supplementary_files_format_and_content: HL60_deseq_norm_countFeatures.txt: Tab-delimited text file includes DESeq norm count for each Sample.

source_name: immortalized cell line

growth_protocol: HL60 cells were cultured in RPMI supplemented with 10% FCS.

extract_protocol:
RNA was prepared using RNA-Mini-Kit (Seqlab, Göttingen, Germany).
Library preparation was done with Illumina TruSeq stranded mRNA Kit.

value: acute myeloid leukemia

value: CRISPR/Cas9-mediated deletion of SKI


title: Mature lineage cells 3

description: Mature lineage cells 3


title: Pro-_Pre-B rep3

description: Pro-_Pre-B rep3


title: Mature lineage cells 1

description: Mature lineage cells 1


title: HL60_KO-3_rep3


title: HL60_CTR-1_rep2

description:
CRISPR/Cas9 control HL60 cells.
Processed data file: HL60_raw_countFeatures.txt
Processed data file: HL60_deseq_norm_countFeatures.txt

value: CRISPR/Cas9 control


title: NCM3


title: Pro-_Pre-B rep2

description: Pro-_Pre-B rep2


title: NCM2


title: HL60_CTR-1_rep3


title: NCM1


title: Pro-_Pre-B rep1

description: Pro-_Pre-B rep1


title: HL60_CTR-1_rep1


title: CMD4

value: Conditioned medium + Calcitriol


title: HL602_KO-1_SKI

description: CRISPR/Cas9-mediated deletion of SKI in HL60 cells.

data_processing:
Illumina RTA 1.8.66.4 software used for basecalling.
Sequenced reads were trimmed for adaptor using Illumina bcl2fastq, then mapped to hg19 whole genome using bowtie2.
Aligned files (bam) were filtered for duplicated aligned reads.
MACS 1.4 was used to perform the peak calling.
Peaks were filtered using criteria; minimum 35 tags and 2 fold above IgG; peak length/tag count <= 15.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigwig files generated using deeptools2 bamCoverage function.
Supplementary_files_format_and_content: Peak files incorporate the number of peaks after filtering for given sample.

extract_protocol:
Cells were crosslinked in the presence of 1% formaldehyde. Cell lysates were sonicated and Protein-DNA complexes were enriched by immunoprecipitation with mentioned antibodies.
Libraries were prepared according to the manufacturer’s protocol (Diagenode, MicroPlex Library Preparation Kit).

value: anti-SKI (sc-9140, Santa Cruz)


title: HL60_WT_CEBPB

description: Unmodified HL60 cells.

value: WT

value: anti-CEBPbeta (sc-150, Santa Cruz)


title: HL60_KO-3_rep1


title: HL602_KO-3_SKI


title: HL60_CTR-1_H3K4me3

description: CRISPR/Cas9 control HL60 cells.

value: anti-H3K4me3 (07-473, Millipore)


title: MPP rep3

description: MPP rep3

source_name: Multipotent progenitors

value: Bone marrow


title: HL60_WT_RUNX1

description: Unmodified HL60 cells.

value: anti-RUNX1 (ab23980, Abcam)


title: HL60_WT_1_SKI

description: Unmodified HL60 cells.


title: CMD2


title: CMD1


title: HL60_CTR-1_SKI

description: CRISPR/Cas9 control HL60 cells.


title: HL60_WT_2_SKI

description: Unmodified HL60 cells.


title: CM4

value: Conditioned medium


title: CM3


title: MPP rep1

description: MPP rep1


title: MPP rep2

description: MPP rep2


title: HL60_KO-3_IgG

value: rabbit IgG (I5006, Sigma)


title: HL60_KO-3_H3K27ac

value: anti-H3K27ac (39133, Active Motif)


title: HL60_KO-3_H3K4me3


title: HSC rep2

description: HSC rep2

source_name: Hematopoietic stem cells


title: HL60_WT_IgG

description: Unmodified HL60 cells.


title: CMD3


title: CM2


title: MPP rep4

description: MPP rep4


title: CM1


title: HSC rep1

description: HSC rep1


title: HL60_CTR-1_H3K27ac

description: CRISPR/Cas9 control HL60 cells.


title: With Asparagine A

city: Cold Spring Harbor

first: Simon

middle: Robert Vincent

last: Knott

address: 1 Bungtown Rd

department: Biology

institute: Cold Spring Harbor Laboratory

description: Sample 3

data_processing:
Map to mm10 genome with Bowtie2
Count transcripts per gene with HT-seq
Genome_build: mm10
Supplementary_files_format_and_content: Counts per gene for each biological replicate. Column sample matchings are: 1)Without Asparagine A 2)Without Asparagine B 3)With Asparagine A C)With Asparagine B

source_name: With Asparagine A

growth_protocol: Grown in DMEM +/- Asparagine

extract_protocol:
Qiagen RNAeasy
Nugen Ovation RNAseq V2
mRNA squencing

value: Grown with Asparagine


title: With Asparagine B

description: Sample 4

source_name: With Asparagine B


title: Without Asparagine B

description: Sample 2

source_name: Without Asparagine B

value: Grown without Asparagine


title: HSC rep3

description: HSC rep3


title: HSC rep4

description: HSC rep4


title: Without Asparagine A

description: Sample 1

source_name: Without Asparagine A


title: HL60_CTR-1_IgG

description: CRISPR/Cas9 control HL60 cells.


title: RNASEQ_RAW_WT_UT_R3_B

city: Milano

first: Viviana

last: Piccolo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

data_processing:
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm10 genome and transcripts using TopHat v2.1.0  (PMID: 23618408),  option --b2-very-sensitive
Transcripts abundance were quantified using HTSeq (PMID: 25260700), option -s no
Differentially expressed genes were called using edgeR (PMID: 19910308)
Genome_build: mm10 (Genome Reference Consortium GRCm38), transcripts from Mus Musculus UCSC iGenome
Supplementary_files_format_and_content: Counts per million (CPM) mapped reads obtained with edgeR

source_name: Macrophages

growth_protocol: RAW 264.7 mouse macrophage cell line was purchased from the American Type Culture Collection (ATCC). Cells were grown in Dulbecco minimal essential medium (DMEM) containing 10% fetal bovine serum (FBS) and 2 mM glutamine.

extract_protocol:
Total RNA was extracted using Maxwell® 16 LEV Simply RNA cells kit (Promega).
mRNA-seq library preparation from 1 μg of total RNA was performed with TruSeq RNA Sample Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Cells were treated or not, for 4h, with LPS

value: RAW 264.7 Macrophages

value: wild type

value: BALB/c

value: untreated


title: RNASEQ_RAW_WT_LPS_4h_R2_B

value: 4h LPS


title: RNASEQ_RAW_WT_LPS_4h_R1_B


title: MLE3

data_processing:
Base calling by CASAVA
Alignment by Tophat2
Gene count by featureCount
Normalization by edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tsv file for gene count

source_name: ATCC

growth_protocol: Cells were grown in appropriate growth medium to approximately 80% confluence.

treatment_protocol: Cells were not  treated with any reagents.


title: RNASEQ_RAW_KO_UT_R2

description: CPM.TABLE.READS

treatment_protocol: Cells were treated or not, for 2h, with LPS alone, Jak inhibitor alone or LPS plus Jak inhibitor.


title: MLE4


title: shRenilla Replicate A

description: Sample 5

data_processing:
Map to mm10 genome with Bowtie2
Count transcripts per gene with HT-seq
Supplementary_files_format_and_content: Counts per gene for each biological replicate. Columns correspond to the following samples: 1)shRenilla Replicate A 2)shRenilla Replicate B 3)shAsns-1 Replicate A 4)shAsns-1 Replicate B 5)shAsns-2 Replicate A 6)shAsns-2 Replicate B

source_name: shRenilla Replicate A

growth_protocol: Grown in DMEM + Non Essential Amino Acids

extract_protocol:
Trizol
Nugen Ovation RNAseq V2
mRNA squencing

treatment_protocol: shRNA Knockdown

value: shRNA Infected


title: MLE1


title: shRenilla Replicate B

description: Sample 6

source_name: shRenilla Replicate B


title: RNASEQ_RAW_WT_UT_R1_B


title: RNASEQ_RAW_WT_LPS_2h_Jack-i_R2

description: CPM.TABLE.READS

value: 2h LPS plus Jak inhibitor


title: MLE2


title: RNASEQ_RAW_WT_LPS_4h_R3_B


title: shAsns-2 Replicate B

description: Sample 4

source_name: shAsns-2 Replicate B


title: shAsns-2 Replicate A

description: Sample 3

source_name: shAsns-2 Replicate A


title: RNASEQ_RAW_WT_Jak-i_R2

description: CPM.TABLE.READS

value: Jak inhibitor


title: LLC4


title: RNASEQ_RAW_WT_LPS_2h_R2

description: CPM.TABLE.READS

value: 2h LPS


title: RNASEQ_RAW_WT_UT_R2_B


title: LLC3


title: shAsns-1 Replicate B

description: Sample 2

source_name: shAsns-1 Replicate B


title: Lung shRenilla Replicate D

description: Sample 24

data_processing:
Map to mm10 genome with Bowtie2
Count transcripts per gene with HT-seq
Supplementary_files_format_and_content: Counts per gene for each biological replicate. Columns correspond to the following samples: 1)Tumor shRenilla A 2)Tumor shRenilla B 3)Tumor shRenilla C 4)Tumor shRenilla D 5)Tumor shASNS-1 A 6)Tumor shASNS-1 B 7)Tumor shASNS-1 C 8)Tumor shASNS-1 D 9)Tumor shASNS 2 A 10)Tumor shASNS 2 B 11)Tumor shASNS-2 C 12)Tumor shASNS-2 D 13)Lung shRenilla A 14)Lung shRenilla B 15)Lung shRenilla C 16)Lung shRenilla D 17)Lung shASNS-1 A 18)Lung shASNS-1 B 19)Lung shASNS-1 C 20)Lung shASNS-1 D 21)Lung shASNS-2  22)Lung shASNS-2 B 23)Lung shASNS-2 C 24)Lung shASNS-2 D

source_name: Lung shRenilla Replicate D

tag: sample type

value: 6TG Selected


title: RNASEQ_RAW_KO_LPS_2h_R2

description: CPM.TABLE.READS


title: RNASEQ_RAW_WT_UT_R2

description: CPM.TABLE.READS


title: RNF2_Knockdown_RNAseq_Rep1

source_name: Castration-resistant prostate cancer

value: Prostate


title: shAsns-1 Replicate A

description: Sample 1

source_name: shAsns-1 Replicate A


title: RNASEQ_RAW_KO_LPS_2h_R1

description: CPM.TABLE.READS


title: LLC2


title: Lung shAsns-2 Replicate  C

description: Sample 19

source_name: Lung shAsns-2 Replicate  C


title: RNASEQ_RAW_WT_Jak-i_R1

description: CPM.TABLE.READS


title: Lung shRenilla Replicate B

description: Sample 22

source_name: Lung shRenilla Replicate B


title: Lung shAsns-2 Replicate A

description: Sample 17

source_name: Lung shAsns-2 Replicate A


title: RNASEQ_RAW_WT_UT_R1

description: CPM.TABLE.READS


title: Lung shRenilla Replicate C

description: Sample 23

source_name: Lung shRenilla Replicate C


title: Lung shRenilla Replicate A

description: Sample 21

source_name: Lung shRenilla Replicate A


title: Lung shAsns-2 Replicate D

description: Sample 20

source_name: Lung shAsns-2 Replicate D


title: H3K27ac_RAW_KO_1h

description: Chromatin IP against H3K27ac

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the UCSC mm10 reference genome using Bowtie2  v.2.2.6 (PMID: 22388286)  with "--very-sensitive" parameter. Subsequently, only uniquely mapping reads were considered in the analysis.
Peaks were called using using SICER v1.1  (PMID: 24743992) using a redundancy threshold of 1,  a window size of 200 bp, a gap size of 600 bp and a False Discovery Rate (FDR)  cutoff of 1 × 10−3. Fragment size was set to 150 and the effective genome fraction to 0.80.
Genome_build: mm10 (Genome Reference Consortium GRCm38)
Supplementary_files_format_and_content: Regions that overlap with the blacklists  identified  by  the  ENCODE  consortia were filtered out (PMID: 2955616).
Supplementary_files_format_and_content: Summary file of significant islands (FDR<=0.01) detected with SICER (PMID: 24743992) in a bed format with the end position included : chrom, start, end, ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, FDR_threshold

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with specific antibody.
DNA libraries were prepared for HiSeq2000 sequencing as previously described (Ostuni, 2013).

treatment_protocol: Cells were left untreated or treated for 1h and 2h, with LPS.

value: H3K27ac (abcam, ab4729)

value: treated 1h LPS


title: RNASEQ_RAW_WT_LPS_2h_Jack-i_R1

description: CPM.TABLE.READS


title: RNASEQ_RAW_KO_UT_R1

description: CPM.TABLE.READS


title: RNASEQ_RAW_WT_LPS_2h_R1

description: CPM.TABLE.READS


title: H3K27ac_RAW_KO_UT

description: Chromatin IP against H3K27ac


title: Lung shAsns-1 Replicate B

description: Sample 14

source_name: Lung shAsns-1 Replicate B


title: H3K27ac_RAW_WT_2h

description: Chromatin IP against H3K27ac

source_name: Macrophages

value: 2h with LPS


title: H3K27ac_RAW_KO_2h

description: Chromatin IP against H3K27ac

value: treated 2h LPS


title: Lung shAsns-1 Replicate D

description: Sample 16

source_name: Lung shAsns-1 Replicate D


title: Lung shAsns-1 Replicate A

description: Sample 13

source_name: Lung shAsns-1 Replicate A


title: Lung shAsns-1 Replicate  C

description: Sample 15

source_name: Lung shAsns-1 Replicate  C


title: H3K27ac_RAW_WT_1h

description: Chromatin IP against H3K27ac

value: 1h with LPS


title: H3K27ac_RAW_WT_UT

description: Chromatin IP against H3K27ac


title: Tumor shRenilla Replicate D

description: Sample 12

source_name: Tumor shRenilla Replicate D


title: Tumor shRenilla Replicate C

description: Sample 11

source_name: Tumor shRenilla Replicate C


title: Tumor shRenilla Replicate B

description: Sample 10

source_name: Tumor shRenilla Replicate B


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Tcf7l2, 8 day, rep 1

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

data_processing:
Reads for both shScr and shTcf7l2 cells at 0, 2, 4, 6, and 8 days of differentiation were mapped against the Gencode M1 transcriptome using Tophat version 2.0.13 (with underlying Bowtie version 2.2.3.0), summarized as gene-level read counts in R using summarizeOverlaps from GenomicAlignments package in union mode, and annotated using attributes extracted from the Gencode M1 transcriptome .gtf file.
Conversion to sorted BAM format using samtools
Differential expression was analyzed in R using DESeq2 version 1.10.1 with Wald statistic. Per time point, a significant differentially expressed gene (DEG) was required to have a FDR < 0.05 when comparing the shTcf7l2 against shScr cells.
For uses outside DESeq2, the data were vst-normalized using varianceStabilizingTransformation of the DESeq2 package in the 'blind' mode.
Genome_build: mm9
Supplementary_files_format_and_content: differential expression:  tab-delimited data matrix with genes as rows, and annotation and statistical and descriptive data as columns, including vst-normalized gene-wise counts per sample

source_name: 3T3-L1 cells

growth_protocol: Early passage 3T3L1 cells were purchased from ATCC and routinely cultured in low glucose DMEM with 10% Fetal Bovine Serum (FBS). Prior to differentiation cells were cultured at low density (< 50%) and used up to passage 8 only. Differentiation was performed using procedures described elsewhere (Zebisch et al., 2012), with the exception that a thiazolidinedione (TZD) was not routinely added to differentiation media.

extract_protocol:
RNA was extracted standard procedures.
Illumina sequencing libraries were prepared using the TruSeq RNA Sample Prep Kit V2, essentially as described previously (Norton et al., 2014).

treatment_protocol: Stable silencing of Tcf7l2 was performed in very low passage (passage 2) 3T3-L1 fibroblasts using SMARTvector (Dharmacon, USA) lentiviral shRNAs (shScr: scrambled control; shTcf7l2: specific silencing of Tcf7l2). Puromycin selection was used to isolate a heterogeneous cell population post-infection. Results obtained using a single shRNA were validated using multiple shRNA sequences in the same and alternate plasmid backbones (i.e. MISSION shRNA lentivirus, Sigma, USA).

value: shRNA - Tcf7l2

tag: time point

value: 8 d


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Tcf7l2, 8 day, rep 2


title: LLC1

source_name: ATCC


title: Input_RAW_S12288

description: Chromatin IP against H3K27ac

value: RAW 264.7 Macrophages

value: wild type


title: Lung shAsns-2 Replicate B

description: Sample 18

source_name: Lung shAsns-2 Replicate B


title: Tumor shRenilla Replicate A

description: Sample 9

source_name: Tumor shRenilla Replicate A


title: Hoxb5

description: Hoxb5 antibody enriched DNA (Chip DNA)

data_processing:
Chipseq fastq files were aligned to mm10 genome by bowtie2.
The generated bam files werer used as the input files for Homer packages. Finding Hoxb5 binding peaks and annotation information procedure was according to the Homer user manual with default parameters for transcription factor. Bigwig (.bw) files were generated by homer software packages.
Genome_build: mm10
Supplementary_files_format_and_content: bw

source_name: Pro-/Pre-B

growth_protocol: All mice in this study were kept in C57BL/6J backgroud. Pro-/pre B cells were sorted from Rosa26BirA/BirA transgenic mice transduced with virus over-expressing bio-tagged Hoxb5 gene (day 3).

extract_protocol:
Sonication and Chromatin Immunprecipitation (Chip) by dynabeads M-280 Streptavidin antibody (Thermo Fisher, catalog is 11205D,2 mL, lot:00381796), and  genomic DNA was extracted by Phenol chloroform method.
Chipseq libraries were constructed using VAHTSTM Universal DNA library Prep Kit for illumina (ND604) and libraries sequence procedure performed on HiSeq X Ten system.

treatment_protocol: Target cells were sorted from the infected Pro-/preB cells.

value: Bone marrow

value: M-280 Streptavidin


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Tcf7l2, 6 day, rep 2

value: 6 d


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Scrambled, 6 day, rep 2

value: shRNA - Scrambled


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Tcf7l2, 6 day, rep 1


title: Tumor shAsns-2 Replicate D

description: Sample 8

source_name: Tumor shAsns-2 Replicate D

value: shRNA Infected


title: Tumor shAsns-2 Replicate  C

description: Sample 7

source_name: Tumor shAsns-2 Replicate  C


title: Tumor shAsns-2 Replicate A

description: Sample 5

source_name: Tumor shAsns-2 Replicate A


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Scrambled, 8 day, rep 1


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Scrambled, 6 day, rep 1


title: Tumor shAsns-1 Replicate D

description: Sample 4

source_name: Tumor shAsns-1 Replicate D


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Tcf7l2, 4 day, rep 2

value: 4 d


title: Tumor shAsns-1 Replicate B

description: Sample 2

source_name: Tumor shAsns-1 Replicate B

value: 6TG Selected


title: Tumor shAsns-2 Replicate B

description: Sample 6

source_name: Tumor shAsns-2 Replicate B


title: Tumor shAsns-1 Replicate  C

description: Sample 3

source_name: Tumor shAsns-1 Replicate  C


title: Hoxb5_input

description: Sonication input DNA


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Tcf7l2, 4 day, rep 1


title: Tumor shAsns-1 Replicate A

description: Sample 1

source_name: Tumor shAsns-1 Replicate A


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Scrambled, 4 day, rep 1


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Scrambled, 8 day, rep 2


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Tcf7l2, 2 day, rep 2

value: 2 d


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Scrambled, 4 day, rep 2


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Tcf7l2, 2 day, rep 1


title: MUT-IP-biological rep1

city: Beijing

first: Guifang

last: Jia

address: college of chemistry and molecular engineering, Peking University

institute: Peking University

description: processed data file: Mut-peaks.txt

data_processing:
Sequencing reads were aligned to the reference genome (TAIR10) using Tophat (v2.0.14). If one read could be mapped to multiple locations, a random read will be chosen. Gene structure annotations were downloaded from TAIR. The longest isoform was used if multiple isoforms were detected. Aligned reads were extended to 150bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates, in order to eliminate the interference from intron in peak calling.
The peak calling method was modified from D. Dominissini et al (Dominissini et al. 2012). To call m6A peaks, the longest isoform of each TAIR10 gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with reads counts less than 1/20 of the top window in both m6A-IP and input sample were excluded. For each gene, the reads count in each window was normalized by the median count of all windows of that gene. A negative binomial model was used to identify the differential windows between IP and input samples by using the edgeR package(Robinson et al. 2010), combining information from all replicates in the two groups. The window was called as positive if the FDR < 1% and log2(Enrichment Score) >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP sample in the current peak/window (a), median reads count of the IP sample in all 100bp windows on the current mRNA (b), reads count of the input sample in the current peak/window (c) and median reads count of the input sample in all 100bp windows on the current mRNA (d). The enrichment score of each window was calculated as (a×d)/(b×c).
Genome_build: TAIR10
Supplementary_files_format_and_content: peaks enrichment and location are present in tab-delimited plain text files

extract_protocol:
Total RNA was extracted with modified CTAB method. Briefly, well ground materials were suspended in five volume of 65°C pre-heated extracting buffer (100 mM Tris-HCl pH 7.9, 2% CTAB, 2% PVP-30, 2 M NaCl, 25 mM EDTA, 0.05% spermidine, and fresh 2% β-ME). The mixture was heated at 65°C for 10 minutes, and extracted with chloroform/isoamyl alcohol (24:1) twice. The upper layer was precipitated with 1/2 volume 8 M LiCl for 2 hours to yield >200 nt RNA. Total RNA was treated with RNase-free DNase I (New England BioLab) in order to remove DNA contamination for reverse transcription, or directly used for mRNA isolation. Poly(A) RNA was isolated from total RNA using the Dynabeads Oligo dT (Invitrogen). The mRNA was quantified by Agilent 2100 Bioanalyzer.
RNA was randomly fragmented to ~100 nt by RNA Fragmentation Reagents (New England Biolab), and incubated with 5 μg m6A-specific antibody (Synaptic Systems) overnight at 4 °C. The m6A-containing fragments were pulled down with BSA pre-blocked Dynabeads Protein A (invitrogen), and eluted with 6.7mM m6A-containing buffer. Eluted RNA was precipitated by 75% ethanol. NEBNext Ultra RNA Library Prep Kit (E7530) was used for library building on input and IP sample.

tag: ecotype

value: atalkbh10b -/-

tag: ip antibody

value: m6A antibody (Synaptic Systems, catalog# 202003, lot# 202003/53)

tag: age

value: seedling


title: MUT-INPUT-biological rep2

description: processed data file: Mut-peaks.txt


title: MUT-IP-biological rep2

description: processed data file: Mut-peaks.txt


title: MUT-INPUT-biological rep1

description: processed data file: Mut-peaks.txt


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Scrambled, 2 day, rep 1


title: WT-IP-biological rep2

description: processed data file: WT-peaks.txt


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Scrambled, 2 day, rep 2


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Tcf7l2, 0 day, rep 2

value: 0 d


title: WT-IP-biological rep1

description: processed data file: WT-peaks.txt


title: WT-INPUT-biological rep2

description: processed data file: WT-peaks.txt


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Tcf7l2, 0 day, rep 1


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Scrambled, 0 day, rep 1


title: WT-INPUT-biological rep1

description: processed data file: WT-peaks.txt


title: RNA-seq sample for timecourse of shRNA knock-down of Tcf7l2: shRNA - Scrambled, 0 day, rep 2