title: KO : AOMDSS : V29_5


title: hFLCs-2

status: Public on Sep 02 2019

type: SRA

city: Beijing

first: Bingqing

last: Xie

address: Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R.China

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
The transcriptome reads were mapped using STAR.
The read counts for each gene were calculated using featureCounts. For microRNA, clean fasta format sequencing reads generated from the sequencer mapped against the human genome build hg19 and calculated read counts by miRDeep2.
Gene expression was normalized by DESeq2, and low expression genes with total counts across all samples less than 1 were excluded.
Genome_build: hg19 for human
Supplementary_files_format_and_content: CSV files include the expression values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: human fetal liver cells

extract_protocol:
Total RNA from each sample was isolated using Direct-zol RNA Miniprep kit (ZYMO RESEARCH) or TRNzol Universal (TIANGEN).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.For microRNAs, RNA sequencing libraries were prepared using the NEB Next® Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) following the manufacturer’s recommendations.

treatment_protocol: hHPLCs  were cultured in HEM and collected from RNA extraction at indicated passages. hiHeps derived from hHPLCs of different passages were cultured in 2C medium for 10 days and then collected from RNA extraction. Primary huaman hepatocytes were fresh isolated.

tag: batch number

value: batch 2

tag: treatment

value: HEM

tag: cell type

value: human fetal liver cells


title: anlr-hsc_27

city: Ulm

first: Johannes

last: Pospiech

address: Albert-Einstein Allee 11

country: Germany

institute: Ulm University

data_processing:
Barcodes and adaptors were trimmed from raw reads.
Alignment to mm10 with UCSC annotations using a proprietary Burrow-Wheeler Transform alignment (COBWeb). Reads that aligned to more than one location or exhibited an alignment quality of <30 were removed.
Generation of FPKM counts using an EM algorithm. Normalization using the DESeq algorithm and baselining to the median of all samples.
Differential expression analysis was performed using a moderated t-test with significance set at p<0.05 and FC>3.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files contain DESeq-normalized and baselined log(FPKM) counts for each sample. Row names show ENTREZ gene IDs, column names indicate samples.

molecule: polyA RNA

organism: Mus musculus

source_name: Non Label retaining LT-HSCs

extract_protocol:
Bone marrow was flushed from femora and tibiae of SCL-TAxH2B-GFP double heterozygous mice. Hematopoietic mononuclear cells were isolated by low-density centrifugation and depleted of lineage cells using magnetic separation. Lineage depleted cells were sorted as single LT-HSCs (LSK CD34-/low Flk2- CD48- CD150+) based on GFP expression (positive and negative). Cells were cultured overnight without growth factors at 3% O2 and washed twice with PBS before processing. RNA was isolated using Clontech's SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing. Amplified cDNA was purified using Beckman Coulter's Agencourt AMPure XP beads.
Libraries were manually prepared using Illumina's Nextera XT DNA Library preparation kit. Manual library normalization was performed after quantification using Agilent's Bioanalyzer.

tag: strain

tag: age

value: > 20 months

tag: tissue

value: Bone marrow (flushed from femora and tibiae)

value: Hematopoietic mononuclear cells

tag: replicate

tag: gfp expression


title: HEFs-3

source_name: human embryonic fibroblast

value: HEF medium

value: human embryonic fibroblast


title: KO : AOMDSS : V32_2

type: RNA

city: Salt Lake City

first: Jordan

middle: A

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

department: Biochemistry

country: USA

institute: University of Utah

description: Loss of the mitochondrial pyruvate carrier promotes stem cell gene expression in AOMDSS colon adenomas, though loss of Apc promotes a more unified pehnotype.

hyb_protocol: RNA was hybridized to probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol (below). Probes were based on manufacturer's  fourescent barcode system.

scan_protocol: Scanning was carried out on the NanoString Elements platform according to manufacturer's protocols at the University of Utah Molecular Diagnostics Core.

data_processing: We scaled the raw data by generating a geometric mean scaling factor per sample to normalize the dataset. This was performed using NanoString nSolver 4

label: Manufacturer designed probes with flourescent tag barcodes

source_name: colon adenoma

extract_protocol: if tumors, at least 8-10 section of 8um thick sections were stained with aniline blue and microdissected for tumors over normal crypts or microdissected upon animal sacrifice and snap frozen. if crypts, crypts were isolated from the colon (Schell et al 2017), washed and snap frozen. Whole crypt RNA was extracted using the QIAGEN RNeasy kit. Tumor tissue RNA was extracted using the QIAGEN FFPE RNeasy kit or the QIAGEN RNeasy kit (please refer to associated manuscript for full details).

treatment_protocol: colon epithelial tumors were induced spontaneously in mice by either chemical treatment (AOMDSS) or genetic recombination (loss of Apc).

value: colon adenoma

tag: genetic mouse model

value: AOMDSS

tag: sample prep

value: FFPE

tag: days post tamoxifen

tag: Sex

value: Female

tag: genotype

tag: grade

value: low grade


title: HEFs-2


title: KO : AOMDSS : APC AJ01_1

label_protocol: Manufacturer designed probes with flourescent tag barcodes


title: anlr-hsc_25


title: hiHeps (hHPLCs-1 P40)

source_name: human induced hepatocytes

value: 2C medium

value: human induced hepatocytes


title: hiHeps (hHPLCs-1 P30)


title: KO : AOMDSS : AN08_1

value: Male

value: high grade


title: capture-C-seq, het, rep2

city: Los Angeles

first: Wange

last: Lu

state: CA

address: 1425 San Pablo Street, BCC 409

institute: University of Southern California

library_source: genomic

data_processing:
RIP-seq reads were aligned to the mm9 genome assembly using TopHat2 version 2.1.0. Duplicates were removed using Picard MarkDuplicates version 1.141. HTSeq version 0.6.0 was used to quantitate the filtered reads mapped to each gene. Read counts were further normalized and compared between conditions using DESeq2 version 1.14.1.
4C-seq reads were aligned to the mm9 genome assembly using BWA version 0.7.15.
Adaptor sequences were trimmed off from raw reads using Trim Galore version 0.4.2. Read pairs with central overlap were reconstructed into single reads using FLASH version 1.2.11. In silico resctriction enzyme digestion was performed to identify junctions formed by distally interacting sub-fragment and "viewpoint" sub-fragment. Sub-fragments were aligned to the mm9 genome assembly using bowtie2 version 2.2.9.
RNA-seq reads were aligned to the mm9 genome assembly using TopHat2 version 2.1.0. HTSeq version 0.6.0 was used to quantitate the filtered reads mapped to each gene. Read counts were further normalized and compared between conditions using DESeq2 version 1.14.1.
Genome_build: mm9
Supplementary_files_format_and_content: For RIP-seq and capture-C, bedgraph files were generated with the score in the 4th column representing intensity. For 4C-seq, bed files were generated including significant interacting regions for each replicate. For RNA-seq, txt files were generated including regularized log transformed counts over the gene*sample matrix.

molecule: genomic DNA

source_name: ESC

growth_protocol: Mouse ESCs were cultured in growth medium consisting of 85% GMEM (Gibico), 15% FBS (Hyclone), 2 mM L-glutamine, 5000 units/ml penicillin and streptomycin, 0.1 mM non-essential amino acids (Invitrogen), 0.1 mM 2-mercaptoethanol (Sigma), 1 mM Sodium Pyruvate (Thermo), and 1000 units/ml LIF (ESGRO).

extract_protocol:
RIP-seq: RIP library was constructed with EZ-Magna Nuclear RIP™ (Cross-Linked) Nuclear RNA-Binding Protein Immunoprecipitation KitMillipore Kit (Millipore), using antibodies of Klf4 (R&D) and FLAG(Sigma). Libraries were then constructed and indexed with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB). The size and concentration of library was examined with the DNA bioanalyzer.  4C-seq: 10e7 cells were resuspended and fixed in 2% formaldehyde in culture medium for 10 min at room temperature and then quenched by 0.125M ice-cold glycine. Cells were centrifuged for 8 min at 320 g at 4°C and washed once in 10 ml of cold PBS. All the supernatant was removed and then the cell pellet was resuspended in 5 ml cold lysis buffer (10 mM Tris, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 1×protease inhibitors, 0.2% NP-40) and incubated for 10 min on ice. Cells were centrifuged for 5 min at 600 g at 4°C and the supernatant was removed. The cell pellet was resuspended once with 10 ml of cold PBS. After centrifugation for 5 min at 600g at 4°C, the supernatant was discarded. The cell pellet was resuspended in 440 μl Milli-Q, 60 μl of 10*RE buffer and 7.5 μl of 20% SDS and incubated for 1 h at 37°C while shaking at 900 RPM. 50 μl of 20% Triton X-100 was added followed by incubation for 1 h at 37°C while shaking at 900 RPM. 400 U restriction enzyme HindIII (NEB) was added followed by incubation o/n at 37°C while shaking at 900 RPM. Another 200 U DpnII was added followed by incubation for 6 hours at 37°C while shaking at 900 RPM. Then 40 μl of 20% SDS was added followed by incubation for 20 min at 65°C to inactivate the enzyme. The samples were transferred (~600 μl) to a 50-ml Falcon tube with addition of 700 μl of 10×ligation buffer and 5.7 ml Milli-Q to 7 ml. 375 μl of 20% Triton X-100 was added followed by incubation for 1 h at 37°C while shaking gently. 100U T4 ligase (Clontech) was added followed by incubation o/n at 4°C. 15 μl Prot K (20 mg/ml, 300 μg) was added and samples were de-crosslinked o/n at 65°C. 30 μl RNase A (10 mg/ml, 300μg) was added followed by incubation for 45 min at 37°C. DNA was then extracted with phenol–chloroform and 3C library was quantified by NanoDrop. Then the 3C library was digested in 500 μl reaction with 50 U DpnII followed by incubation o/n at 37°C. Then the library was ligated in 14 ml reaction with 100 U Ligase at 16 C o/n followed by purification with phenol-chloroform. The samples were purified with the QIAquick PCR purification kit (Qiagen) and quantified with NanoDrop. 3.2 μg 4C templates were pre-mixed with 160 μl of 5×PCR buffer, 40 μl dNTP (10 mM), 19.2 μl forward primer (50 uM), 19.2 μl Reverse primer (50 uM), 11.2 μl Expand Long Template Polymerase (Roche), and ddH2O to 800 μl in total. The library was separated into 16 reactions of 50 μl for each. Then PCR was conducted with the program: 2 min 94°C, 10 sec 94°C, 1 min 55°C, 3 min 68°C, 29 repeats, 5 min 68°C, and 4°C forever. The samples were purified with QIAquick PCR purification kit and run on Agarose-gel (2%) for 10 min. The gel excision (150 bp-800 bp) and extraction were performed with QIAquick Gel Extraction Kit (Qiagen). Then the 4C library was purified with QIAquick PCR purification kit. The quality and concentration of 4C library were examined with bio-analyzer.   capture-C: 10e7 cells were resuspended and fixed in 2% formaldehyde in culture medium for 10 min at room temperature and then quenched by 0.125M ice-cold glycine. Cells were centrifuged for 8 min at 320 g at 4°C and washed once in 10 ml of cold PBS. All the supernatant was removed and then the cell pellet was resuspended in 5 ml cold lysis buffer (10 mM Tris, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 1×protease inhibitors, 0.2% NP-40) and incubated for 10 min on ice. Cells were centrifuged for 5 min at 600 g at 4°C and the supernatant was removed. The cell pellet was resuspended once with 10 ml of cold PBS. After centrifugation for 5 min at 600g at 4°C, the supernatant was discarded. The cell pellet was resuspended in 440 μl Milli-Q, 60 μl of 10*RE buffer and 7.5 μl of 20% SDS and incubated for 1 h at 37°C while shaking at 900 RPM. 50 μl of 20% Triton X-100 was added followed by incubation for 1 h at 37°C while shaking at 900 RPM. 400 U restriction enzyme DpnII (NEB) was added followed by incubation o/n at 37°C while shaking at 900 RPM. Another 200 U DpnII was added followed by incubation for 6 hours at 37°C while shaking at 900 RPM. Then 40 μl of 20% SDS was added followed by incubation for 20 min at 65°C to inactivate the enzyme. The samples were transferred (~600 μl) to a 50-ml Falcon tube with addition of 700 μl of 10×ligation buffer and 5.7 ml Milli-Q to 7 ml. 375 μl of 20% Triton X-100 was added followed by incubation for 1 h at 37°C while shaking gently. 100U T4 ligase (Clontech) was added followed by incubation o/n at 4°C. 15 μl Prot K (20 mg/ml, 300 μg) was added and samples were de-crosslinked o/n at 65°C. 30 μl RNase A (10 mg/ml, 300μg) was added followed by incubation for 45 min at 37°C. DNA was then extracted with phenol–chloroform and 3C library was quantified by NanoDrop. The 3C library was then sonicated to 100-300bp. The library was constructed and indexed with NEBNext DNA Library Prep Master Mix Set for Illumina (NEB). Then 1 μg from each indexed library was pooled together and then captured with two biotin-labeled probes using the SeqCap EZ Hybridization and Wash Kit (Roche). After amplification with P5&P7 primers, a second capture step was performed with the same probes. Then Capture-C library was amplified with P5&P7 primers followed by the purification with AMPure XP system (Beckman). The size and concentration of library were examined with DNA bio-analyzer.  RNA-seq: RNA library was constructed with the TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat (Illumina).
RIP-seq, 4C-seq, capture-C, RNA-seq


title: KO : AOMDSS : AN08_2


title: KO : APC : L35_p4APC

value: Apc

value: Frozen


title: anlr-hsc_24


title: mRNA 48h-M3

status: Public on Sep 03 2019

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
RNA-seq: was performed using TopHat v2.1.0 and Cufflinks v2.2.1
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCA_000004515.4
Supplementary_files_format_and_content: FPKM

organism: Glycine max

source_name: root hair cells_312 hrs after sowing

growth_protocol: The soybean plants were growth with an ultrasound aeroponic system (Qiao et al., 2013) under controlled conditions.

extract_protocol: Truseq RNA-seq v2 (Illumina)

value: willam 82

value: 312 hours after sowing

value: root hair cells


title: hiHeps (hHPLCs-1 P20)

value: batch 2


title: anlr-hsc_23

value: > 20 months

value: Bone marrow (flushed from femora and tibiae)

value: Hematopoietic mononuclear cells


title: ChIP-seq_GcrA

city: Namur

first: Xavier

last: De Bolle

address: 61 rue de Bruxelles

country: Belgium

institute: University of Namur

data_processing:
Fastq reads were aligned to the chromosomes I (NC_007618) and chromosome II (NC_007624) of Brucella abortus 2308, using Galaxy website (https://usegalaxy.org/) using Bowtie2, and result file in BAM format was converted to tabular format
Genome_build: NC_007618 and NC_007624
Supplementary_files_format_and_content: One text file for each chromosome, with the number of reads aligned every 5 bp, and one excel file with the proposed peaks:
[ChIP-seq_GcrA_chr1.txt] ChIP-seq profile on chromosome 1
[ChIP-seq_GcrA_chr2.txt] ChIP-seq profile on chromosome 2
[ChIP-seq_all_peaks_Z_4_GcrA.xlsx] binding sites on chromosomes 1 and 2

organism: Brucella abortus

source_name: culture in rich medium until late exponential phase (OD600 = 0.8)

growth_protocol: Growth in rich (2YT) medium until late exponential phase (OD600 = 0.8)

extract_protocol:
Bacteria resuspended in lysis buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl, 2.2 mg/ml lysozyme, 20 ml protease inhibitor solution from Roche). Bacteria were lysed with 0.1 and 0.5 mm diameter Zirconia/Silica beads (Biospec Products) in the cell Disruptor Genie from Scientific Industries at maximal amplitude (2800) for 25 min at 4°C
Illuminy MiSeq

treatment_protocol: 10 mM sodium phosphate buffer (pH 7.6) and 1% (v/v) formaldehyde for 10 min at RT and 30 min on ice

tag: chip antibody

value: Homemade rabbit antiserum against recombinant His6-GcrA


title: hiHeps (hHPLCs-1 P10)


title: anlr-hsc_21


title: KO : APC : L35_p3APC

value: colon adenoma


title: hHPLCs-1 P40

source_name: human hepatic progenitor-like cells

value: HEM

value: human hepatic progenitor-like cells


title: anlr-hsc_22


title: hiHeps (hHPLCs-1 P4)

value: 2C medium


title: WT : AOMDSS : AD14_AOMDSS

source_name: colon crypts

value: colon crypts

value: AOMDSS

value: Control

value: non pathologic


title: anlr-hsc_26


title: hHPLCs-1 P30


title: asexual_sort_invitro3

city: Philadelphia

first: Boris

last: Striepen

state: PA

address: 380 S University Ave

department: Department of Pathobiology

institute: University of Pennsylvania

data_processing:
fastq files were pseudoaligned to the Cryptosporidium parvum reference transcriptome (ASM16534v1) using kallisto v0.44.0
transcripts were collapsed to gene symbols in R using Bioconductor tximport and a transcript-to-gene key generated from the C. parvum Iowa II TSV file available for download from EnsemblProtists (ASM15634v1.37)
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³ 2-fold and p-value £ 0.01) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: Cryptosporidium parvum reference transcriptome Iowa II (ASM16534v1)
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

organism: Cryptosporidium parvum

source_name: sorted Cryptosporidium parvum infected HCT8 cells

growth_protocol: 80% confluent monolayers of HCT-8 cells in 6-well plates were infected with 300,000 oocysts per well for 24 hours at 5% CO2 and 37 ℃

extract_protocol:
For sorted cells RNA was isolated using the RNeasy Micro Kit (Qiagen) and processed as per manufacturer’s instructions. For bulk infections, RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer's instructions.
cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA Inc) for the sorted cells, and all libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina), according to the manufacturer’s instructions.

treatment_protocol: For sorted cells, infected cells were sorted directly into RLT buffer from the RNeasy Micro Kit (Qiagen)

tag: oocyst source

value: Bunchgrass Farms

tag: parasite strain

value: eno tdNeon

tag: in vitro/in vivo

value: in vitro

tag: host

value: Human cell line HCT8


title: KO : AOMDSS : N43A_3

value: FFPE

value: Female

value: low grade


title: alr-hsc_37

source_name: Label retaining LT-HSCs

value: > 20 months

value: Bone marrow (flushed from femora and tibiae)

tag: cell type

value: Hematopoietic mononuclear cells


title: WT : AOMDSS : AO22_AOMDSS

value: Frozen

value: Male


title: WT : AOMDSS : AD12_AOMDSS


title: hHPLCs-1 P20

tag: batch number

value: batch 2

tag: treatment

value: HEM

value: human hepatic progenitor-like cells


title: KO : Norm : AR38_60

tag: tissue

value: colon crypts

value: Normal


title: alr-hsc_36

tag: strain

tag: age

tag: replicate


title: hHPLCs-1 P10


title: KO : Norm : AZ27_60

tag: genetic mouse model

tag: sample prep

value: non pathologic


title: alr-hsc_35

tag: gfp expression


title: alr-hsc_34


title: hHPLCs-1 P3


title: alr-hsc_33


title: alr-hsc_32


title: anlr-hsc_19


title: WT : AOMDSS : AH03_AOMDSS

value: AOMDSS

tag: days post tamoxifen

tag: Sex

tag: genotype

value: Control


title: KO : Norm : G29_60

tag: grade


title: anlr-hsc_20


title: WT : Norm : G30_60


title: WT : Norm : AZ26_60


title: alr-hsc_31


title: alr-hsc_30


title: WT : Norm : AR37_60


title: anlr-hsc_18


title: KO : APC : L35_p5APC

value: colon adenoma

value: Apc


title: hiHeps(hHPLCs-2-P9) (miRNA-seq)

value: 2C medium

value: human induced hepatocytes


title: hiHeps(hHPLCs-3-P10) (miRNA-seq)


title: anlr-hsc_17

value: > 20 months


title: hiHeps(hHPLCs-2-P29) (miRNA-seq)


title: KO : APC : L30_p4APC

value: Female

value: low grade


title: hiHeps(hHPLCs-5-P7) (miRNA-seq)


title: KO : APC : L30_p3APC

value: Frozen


title: hiHeps(hHPLCs-1-P28) (miRNA-seq)


title: alr-hsc_29

value: Bone marrow (flushed from femora and tibiae)

value: Hematopoietic mononuclear cells


title: anlr-hsc_16


title: anlr-hsc_14


title: HepG2 cells (miRNA-seq)

source_name: human hepatocarcinoma

value: HEF medium

value: human hepatocarcinoma


title: hiHeps(hHPLCs-1-P11) (miRNA-seq)


title: anlr-hsc_15


title: KO : AOMDSS : AH03_p1AOMDSS

value: Male


title: WT : AOMDSS : AD14_p2AOMDSS


title: hiHeps(hHPLCs-4-P9) (miRNA-seq)


title: WT : AOMDSS : AO22_p3AOMDSS


title: HEFs-1

value: batch 1

value: human embryonic fibroblast


title: WT : APC : AD14_p3AOMDSS

value: AOMDSS


title: F-PHHs-2# (miRNA-seq)

source_name: primary human hepatocyte

value: fresh isolated

value: primary human hepatocyte


title: alr-hsc_28


title: WT : AOMDSS : AO22_p1AOMDSS

value: colon adenoma

value: Control


title: alr-hsc_27


title: WT : AOMDSS : AO22_p2AOMDSS


title: anlr-hsc_13


title: WT : AOMDSS : AD14_p1AOMDSS


title: F-PHHs-1* (miRNA-seq)


title: AL2# (miRNA-seq)

source_name: human adult liver

value: human adult liver


title: alr-hsc_26

value: > 20 months


title: alr-hsc_25


title: AL1* (miRNA-seq)


title: HEFs-2 (miRNA-seq)


title: alr-hsc_24


title: HEFs-1 (miRNA-seq)


title: KO : APC : L35_p2APC

value: Apc


title: alr-hsc_23


title: KO : APC : L35_p1APC

value: low grade


title: HEFs-4 (miRNA-seq)


title: hiHeps-6 (donor 4)

value: 2C medium

value: human induced hepatocytes


title: KO : APC : L30_p2APC

value: Frozen

value: Female


title: hiHeps-5 (donor 3)


title: alr-hsc_22

value: Bone marrow (flushed from femora and tibiae)

value: Hematopoietic mononuclear cells


title: alr-hsc_21


title: hiHeps-4 (donor 2)


title: KO : APC : L30_p1APC


title: alr-hsc_19


title: hiHeps-3(CRL-2097)


title: KO : APC : M15_p2APC


title: anlr-hsc_11


title: alr-hsc_20


title: F-PHHs-5*


title: KO : APC : M15_p1APC


title: anlr-hsc_12


title: WT : AOMDSS : AD12_p2AOMDSS

value: Male


title: WT : AOMDSS : AD12_p1AOMDSS


title: AL3*


title: KO : APC : N19_p1APC


title: KO : APC : N22_p1APC


title: anlr-hsc_10


title: anlr-hsc_9


title: AL1


title: alr-hsc_18


title: WT : APC : K19_p3APC


title: WT : APC : K23_p2APC


title: alr-hsc_17


title: WT : APC : K23_p1APC


title: shGFP [GFP_2]

city: New York

first: Dylan

last: McNally

state: NY

institute: Weill Cornell Medicine

data_processing:
reads were aligned to mm10 using STAR (v2.5.3a) with standard input parameters
aligned reads were sorted by position with standard input parameterts of sambamba sort (v0.6.6)
transcript counts were produced using htseq-count (v0.8.0) with parameters -f bam -r pos -s no against the enseble gencode.v28 annotation set
counts were read into DEseq2 (v1.18.1) and lowly expressed genes were filtered out (mean raw counts < 0.67 across all samples)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file including matrix of samples and raw counts

source_name: breast epithelial cells

growth_protocol: MCF10A cells were maintained in DMEM:F12 media supplemented with 5% Horse serum, 10 µg/ml Insulin, 100 ng/ml cholera toxin, 20 ng/ml EGF, 0.5 mg/ml hydrocortizone and penicillin-streptomycin. Cells were split every other day.

extract_protocol:
Total RNA was isolated using the PureLink RNA isolation kit (Life Technologies) and contaminant DNA was digested with DNAse I (Amplification grade, Sigma-Aldrich)
The TruSeq RNA Sample Preparation v2 Guide protocol was followed (Illumina, Part # 15026495 Rev. F) as per the manufacturer indications.

treatment_protocol: Cells were transduced with lentiviral particles, 24 hours later were selected with 2 μg/mL puromycin, total RNA was collected 3 days after infection.

tag: cell line

tag: genetic modification

tag: trc#


title: shCHAF1B-#2 [Chaf22_2]


title: alr-hsc_14

tag: cell type


title: shCHAF1B-#2 [Chaf22_1]


title: AL2

tag: batch number


title: shGFP [GFP_1]


title: alr-hsc_16


title: shGFP [GFP_3]


title: shCHAF1B-#1 [Chaf16_2]


title: alr-hsc_15


title: shCHAF1B-#2 [Chaf22_3]


title: WT : APC : K19_p2APC


title: shCHAF1B-#1 [Chaf16_3]


title: alr-hsc_13


title: alr-hsc_12


title: KO : APC : S06_p1APC


title: WT : APC : S01_p1APC


title: alr-hsc_11


title: KO : APC : S02_p1APC


title: KO : APC : S02_p2APC


title: WT : APC : K17_p1APC


title: WT : APC : K19_p1APC


title: shCHAF1B-#1 [Chaf16_1]


title: anlr-hsc_8


title: anlr-hsc_7


title: WT : APC : K16_p1APC


title: WT : APC : K16_p3APC


title: anlr-hsc_6


title: WT : APC : K16_p2APC


title: WT : APC : K30_p2APC


title: anlr-hsc_4


title: WT : APC : K30_p1APC


title: KO : APC : M15_APC

value: colon crypts

value: non pathologic


title: anlr-hsc_1


title: anlr-hsc_3


title: anlr-hsc_2


title: alr-hsc_10


title: KO : APC : N19_APC


title: alr-hsc_9


title: KO : APC : N22_APC


title: WT : APC : K28_p1APC


title: anlr-hsc_5


title: alr-hsc_8


title: KO : APC : S02_APC


title: KO : APC : S06_APC


title: RNA-seq, RA, PG, hom, rep3

description: RNA-Seq_rld_transformed_normalized_counts_of_PG_samples.txt


title: alr-hsc_7


title: alr-hsc_6


title: Melanocyte stem cell KO P21, Biological rep4

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description:
Gene expression data from melanocyte stem cells isolated from the skin of 21-days old B-raf and C-raf knock-out mice
P21_KO_557-6

hyb_protocol: 2,5 ug of the biotin labeled cDNA were hybridized for 5min at 45°C (GeneChip® Hybridization, Wash, and Stain Kit, Affymetrix) on GeneChip Mouse Gene 2.0 ST Array

scan_protocol: GeneChip Mouse Gene 2.0 ST Array  were scanned using the GeneChip Scanner 3000 7G from Affymetrix

data_processing: Data were normalized using Expression Console from Affymetrix (RMA-GENE analysis)

label: biotin

source_name: Melanocyte stem cell KO P21

label_protocol: Biotinylated cDNA were prepared from 5 ug of cDNA with the Encore Biotin Module kit (Nugen)

growth_protocol: Double B-raff/f;C-raff/f conditional knockout mice (Galabova-Kovacs et al., 2006; Jesenberger et al., 200)1 were crossed to the Tyr::Cre transgenic mice (Delmas et al., 2003) and to the Z/EG mice (Novak et al., 2000). The resulting B-raff/f;C-raff/f;Tyr::Cre/°;Z/EG/° mice were named mutant animals and compared to the B-raf+/+;C-raf+/+;Tyr::Cre/°;Z/EG/° mice. Tyr::Cre and Z/EG strains were initially on a C57Bl/6 background, whereas the B-raff/f;C-raff/f mice were on a 129/Sv background.

extract_protocol: Total RNA were extracted using the Nucleospin RNA XS kit (Macherey-Nagel). Then, cDNA were synthesized and amplified with the Ovation PicoSL WTA system V2 (Nugen).

treatment_protocol: Whole skin was removed from 4-day or 21-day old B-raff/f;C-raff/f;Tyr::Cre/°;Z/EG/° and B-raf+/+;C-raf+/+;Tyr::Cre/°;Z/EG/° mice. The skin was digested in a mixture of collagenaseIV and dispase for 2hours at 37°C and then mechanically dissociated with forceps followed by multiple passages trough an 18-G needle. After washing (HBSS 1X, EDTA 2mM, 20% fetal bovine serum) and centrifugation, samples were resuspended (RPMI, 5% fetal bovine serum, 1% Penicillin/Streptomycin, 2mM EDTA) and strained in order to obtain single-cell suspensions. This suspension was stained with an anti-NGFRp75 antibody for 30min at 4°C, then with an Alexa647 as secondary antibody. GFP+/p75- cells (corresponding to melanoblasts or melanocyte stem cell depending of the animal age) was sorted on a FACS-AriaIII (BD Biosciences, San Jose, CA).

tag: strain background

tag: genotype/variation

value: B-raf fl/fl; C-raf fl/fl; TyrCre/°;Z/EG

value: 21 days

value: skin

value: melanocyte stem cell population


title: WT : APC : K19_APC

tag: tissue


title: Melanocyte stem cell WT P21, Biological rep2

description:
Gene expression data from melanocyte stem cells isolated from the skin of 21-days old wild-type mice
P21_WT_536-8

source_name: Melanocyte stem cell WT P21

value: B-raf +/+; C-raf +/+; TyrCre/°;Z/EG

tag: age


title: Melanocyte stem cell WT P21, Biological rep1

description:
Gene expression data from melanocyte stem cells isolated from the skin of 21-days old wild-type mice
P21_WT_573-1


title: Melanocyte stem cell KO P21, Biological rep3

description:
Gene expression data from melanocyte stem cells isolated from the skin of 21-days old B-raf and C-raf knock-out mice
P21_KO_557-2


title: RNA-seq, RA, PG, hom, rep2

tag: strain


title: RNA-seq, RA, PG, het, rep3


title: RNA-seq, RA, PG, hom, rep1


title: Melanocyte stem cell KO P21, Biological rep1

description:
Gene expression data from melanocyte stem cells isolated from the skin of 21-days old B-raf and C-raf knock-out mice
P21_KO_560-4


title: Melanocyte stem cell KO P21, Biological rep2

description:
Gene expression data from melanocyte stem cells isolated from the skin of 21-days old B-raf and C-raf knock-out mice
P21_KO_557-3


title: Melanoblast P4, Biological rep1

description:
Gene expression data from melanoblasts isolated from the skin of 4-days old wild-type mice
P4_WT_538-3

source_name: Melanoblast P4

value: 4 days

value: melanoblast cell population


title: WT : APC : K17_APC

tag: genetic mouse model

value: Apc


title: Melanoblast P4, Biological rep2

description:
Gene expression data from melanoblasts isolated from the skin of 4-days old wild-type mice
P4_WT_566-8


title: alr-hsc_5

value: > 20 months

tag: replicate


title: alr-hsc_4

tag: gfp expression


title: alr-hsc_3


title: RNA-seq, RA, PG, het, rep2


title: RNA-seq, RA, G, hom, rep3

description: RNA-Seq_rld_transformed_normalized_counts_of_G_samples.txt


title: alr-hsc_1


title: WT : APC : K16_APC

tag: sample prep

tag: days post tamoxifen


title: WT : APC : K30_APC

tag: Sex

tag: genotype


title: alr-hsc_2


title: WT : APC : S01_APC

tag: grade


title: WT : APC : K23_APC


title: RNA-seq, RA, G, hom, rep1


title: RNA-seq, RA, PG, het, rep1


title: RNA-seq, RA, G, het, rep3


title: RNA-seq, RA, G, het, rep2


title: RNA-seq, ES, PG, hom, rep3


title: WT : APC : Tantin_9

value: colon adenoma

value: FFPE

value: unknown


title: RNA-seq, RA, G, het, rep1


title: WT : APC : Tantin_7

value: Female


title: WT : APC : Tantin_10


title: WT : APC : Tantin_6


title: RNA-seq, RA, G, hom, rep2


title: RNA-seq, ES, PG, hom, rep1


title: WT : AOMDSS : Tantin_5

value: AOMDSS

value: Control


title: RNA-seq, ES, PG, het, rep3


title: WT : APC : Tantin_11


title: WT : AOMDSS : Tantin_3

value: Male


title: WT : APC : K28_APC

value: colon crypts

value: Frozen

value: non pathologic


title: RNA-seq, ES, PG, het, rep2


title: WT : AOMDSS : Tantin_2


title: RNA-seq, ES, PG, hom, rep2


title: RNA-seq, ES, PG, het, rep1


title: H.pylori vs. naïve 2

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: Whole mouse genome 4x44k microarrays were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range (XDR)  using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware). Intra-array data were normalized with the GE2_1105_Oct12 extraction protocol and interarray normalization was done by the mean of trimmed positive non-flagged/non-control reporters.

label_protocol: RNA labeling was performed with the Quick-Amp Labeling Kit  (Agilent Technologies) according supplier's instructions.

growth_protocol: AGS cells  were cultivated in RPMI medium (Gibco) supplemented with 10% heat inactivated fetal calf serum, 2 mM L-glutamate. Cultures were kept at 37°C in a humidified atmosphere of 95% air and 5% CO2.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method according the manufacturer´s protocol.

treatment_protocol: AGS cells were transfected with 20 nM siRNAs in 12 well plates or infected for 45 min with H. pylori (MOI 100) under serum-free conditions.

tag: cell line

value: AGS (gastric adenocarcinoma)

tag: infection

value: H.pylori infected

tag: transfection

source_name: naive

value: naive uninfected


title: WT : AOMDSS : Tantin_1

source_name: colon adenoma


title: RNA-seq, ES, G, hom, rep3


title: naive vs. H.pylori 2


title: WT : AOMDSS : Tantin_4


title: naive vs. H.pylori 1


title: H.pylori all* control vs. H.pylori IKK KD 2

source_name: H.pylori all* control

value: all star control

source_name: H.pylori IKK KD

value: IKK siRNA knock down


title: RNA-seq, ES, G, hom, rep2

source_name: ESC


title: H.pylori vs. naïve 1


title: H.pylori IKK KD vs. H.pylori all* control 2


title: H.pylori IKK KD vs. H.pylori all* control 1


title: H.pylori all* control vs. H.pylori IKK KD 1


title: WT : APC : Tantin_15

value: Apc


title: WT : APC : Tantin_19


title: RNA-seq, ES, G, hom, rep1


title: RNA-seq, ES, G, het, rep3


title: WT : APC : Tantin_14


title: H.pylori all* control vs. H.pylori ALPK1 KD 2

source_name: H.pylori ALPK1 KD

value: ALPK1 siRNA knock down


title: RNA-seq, ES, G, het, rep2


title: RNA-seq, ES, G, het, rep1


title: WT : APC : Tantin_13

value: colon adenoma


title: H.pylori ALPK1 KD vs. H.pylori all* control 2


title: WT : AOMDSS : APC M-24_2

value: FFPE

value: low grade


title: H.pylori ALPK1 KD vs. H.pylori all* control 1


title: HDM Tfr 2

city: Boston

first: Peter

last: Sage

address: 221 Longwood Ave

department: Medicine/Renal

institute: Brigham and Women's Hospital

data_processing:
Basecalling was performed using Illumina Software
Reads were aligned to the mouse genome mm10 using CLC Genomics software suite
Reads per million were generated for each sample
Genome_build: mm10
Supplementary_files_format_and_content: Tab-deliminated file

source_name: Ex Vivo Sorted Lymph Node Cells

extract_protocol:
Lymph nodes were mashed through 70micron filters and cells were sorted
RNA libraries were constructed using previously published protocols using Illumina adaptors (Sage Nature Immunology 2016)

treatment_protocol: Ex Vivo Sorting

tag: cell type

value: T Follicular Regulatory Cell

tag: immunization/treatment

value: House Dust Mite Challenge


title: WT : AOMDSS : APC P-36_1

value: AOMDSS

value: Control


title: RIP-seq, Input-3F, rep3

description: nuclear RNA


title: WT : AOMDSS : APC M-24_1

value: Female

value: high grade


title: WT : AOMDSS : APC Y-07_2


title: Transverse aortic constriction

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
Read2 was aligned with bowtie2-2.2.7 using the -k 1 option
The aligned reads were tagged with their corresponding UMI and barcode from read1
Each aligned read was tagged with its gene name
An expression matrix was generated by counting the number of unique UMIs per gene per cell
Reads were normalized by dividing the read count of each gene by the total number of reads per cell and multiplying by 10000
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text

source_name: Heart tissue

extract_protocol:
Transverse aortic constriction (TAC) was performed on C57BL6/J wild type (WT) 8-10-week-old male mice (The Jackson Laboratories and confirmed via echocardiographic analysis, similar to previously described (Duan et al., 2017). Mice with an estimated pressure gradient across the aortic constriction below 40 mmHg were not included in the experiments. Hearts (n=4, pooled) were collected at 14 days post-TAC, perfused with ice-cold PBS to remove red blood cells followed by perfusion with 50 mM KCl to arrest the heart in diastole and then fixed for 4 hours in freshly prepared 4% PFA at 4 °C, rinsed with PBS and cryoprotected in 30% sucrose/PBS overnight before embedding in OCT (Tissue-Tek).
The quantity and quality of cDNA was measured using an Agilent Bioanalyzer hsDNA chip. To generate a library cDNA was fragmented and amplified (12 cycles) using the Nextera XT DNA Sample prep kit with three separate reactions of 600, 1,200 and 1,800 pg input cDNA. The libraries were pooled and purified twice using 0.7X volume of SPRIselect beads. The purified libraries were quantified using an hsDNA chip and were sequenced on an Illumina HiSeq 2500 using the sequencing parameters described in the DropSeq protocol.
DropSeq was performed as previously described (Macosko et al., 2015).

value: Heart tissue

value: male


title: HDM Tfr 1


title: HDM Tfh 1

value: T Follicular Helper Cell


title: OVA Tfr 2


title: RIP-seq, Input-3F, rep2

description: nuclear RNA


title: WT : AOMDSS : APC U-30_1

value: Male


title: RIP-seq, Input-3F, rep1

description: nuclear RNA


title: RIP-seq, Flag-3F, rep3

description: nuclear RNA


title: WT : AOMDSS : APC X-09_1


title: OVA Tfh 2


title: RIP-seq, Flag-3F, rep2

description: nuclear RNA


title: H.pylori all* control vs. H.pylori ALPK1 KD 1

value: AGS (gastric adenocarcinoma)

value: H.pylori infected

value: all star control


title: OVA Tcon 2

value: T Conventional Cell


title: HDM Tfh 2


title: WT : AOMDSS : APC Y07_2

value: colon adenoma


title: WT : AOMDSS : W27_2

value: FFPE


title: RIP-seq, Flag-3F, rep1

description: nuclear RNA


title: Peripheral blood from normal patients, biological rep1

city: Shanghai

first: Bingbing

last: Zha

address: 801Heqing   Rd

institute: Fifth People's Hospital of Shanghai Fudan University

description:
Peripheral blood was obtained from normal patients
CD52_NS

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

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

data_processing: The chip data were analyzed, including data preprocessing, gene expression analysis, transcript expression analysis, variable shear analysis, differential gene analysis, differential gene GO/KEGG enrichment analysis and lncRNA analysis.

source_name: Peripheral blood of normal patiernts

label_protocol: Total RNA was amplified, labeled and purified by Affymetrix WT PLUS Reagent Kit(Cat#902280， Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions to obtain biotin labeled cDNA.

growth_protocol: Peripheral blood was obtained from newly diagnosed GD patients and age matched healthy individuals,and were resuspended in phosphate buffered saline (PBS) containing 2% fetal bovine serum (FBS).

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Isolation of peripheral blood mononuclear cells (PBMCs)，Then human CD19 B cells were isolated by positive selection,RNA was extracted from the purified CD19 B cells, then LncRNA and mRNA microarray expression profiling

tag: disease state

value: control

value: peripheral blood

value: CD19 B cells


title: WT : AOMDSS : W25_2

tag: tissue

value: AOMDSS

value: low grade


title: RIP-seq, Klf4-3F, rep3

description: nuclear RNA


title: OVA Tfr 1

value: T Follicular Regulatory Cell


title: WT : AOMDSS : APC AJ-08_4

value: Control

value: high grade


title: RIP-seq, Klf4-3F, rep2

description: nuclear RNA


title: Late carcinoma_D8_12weeks

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description:
fibroblast FACS sorting
Gene expression

hyb_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip Expression Wash, Stain and Scan protocol (Affymetrix, Santa Clara, CA, USA)

scan_protocol: GeneChips were scanned using the Affymetrix   3000 7G scanner according to the instruction manual.

data_processing: RMA normalization, summarization by mean, all were done on CEL files by Partek Genomics suite (version 6.5)(Partek, St Louis, MO, USA).

source_name: FVB/n mice, mammary tissue

label_protocol: RNA was converted to cDNA using iScriptTM reverse transcriptase (Bio-Rad).

extract_protocol:
cell growth protocol: Mammary tumors isolated from MMTV-PyMT female mice or normal mammary tissue isolated from 8- weeks old FVB/n female mice were disassociated into single cell suspensions and fibroblasts were isolated using FACS sorting as CD140+ F4/80- EpCAM- cells.  female mice. Tissue dissociation and preparation of single cell suspension was performed as previously  described (Sharon, Y., Alon, L., Glanz, S., Servais, C. & Erez, N. Isolation of normal and cancerassociated  fibroblasts from fresh tissues by Fluorescence Activated Cell Sorting (FACS).  Journal of visualized experiments : JoVE, e4425, doi:10.3791/4425 (2013)).
RNA was prepared using Nucleuspin RNA II Kit (MACHERY-NAGEL). RNA concentration and purity was analyzed using NanoDrop 2000c Spectrophotometer.

value: MMTV-PyMT

value: mammary tumor

tag: tumor stage

value: Late carcinoma

value: fibroblasts

tag: gender

value: female


title: Late carcinoma_D9_12weeks

description:
fibroblast FACS sorting
Gene expression

tag: strain


title: RIP-seq, Klf4-3F, rep1

description: nuclear RNA


title: WT : AOMDSS : APC AJ-08_2

tag: genetic mouse model

value: Male


title: WT : AOMDSS : APC AJ-08_3


title: Peripheral blood from GD patients, biological rep1

description:
Peripheral blood was obtained from GD patients
mix_3_NS

source_name: Peripheral blood of Graves' patiernts

value: Graves' disease


title: Late carcinoma_D11_12weeks

description:
fibroblast FACS sorting
Gene expression


title: WT : AOMDSS : W27_1

value: colon adenoma


title: WT : AOMDSS : APC AJ-04_1

value: FFPE


title: RIP-seq, Input-WT, rep2

description: nuclear RNA


title: RIP-seq, Input-WT, rep3

description: nuclear RNA


title: WT : AOMDSS : W26_1


title: Carcinoma_D4_9weeks

description:
fibroblast FACS sorting
Gene expression

value: Carcinoma


title: RIP-seq, Klf4-WT, rep2

description: nuclear RNA


title: RIP-seq, Klf4-WT, rep1

description: nuclear RNA


title: RIP-seq, Input-WT, rep1

description: nuclear RNA


title: RIP-seq, Klf4-WT, rep3

description: nuclear RNA


title: OVA Tcon 1

value: T Conventional Cell


title: OVA Tfh 1

value: T Follicular Helper Cell


title: WT : AOMDSS : W23_1

value: AOMDSS

value: Female


title: WT : AOMDSS : W-25_1

value: low grade


title: Carcinoma_D3_9weeks

description:
fibroblast FACS sorting
Gene expression


title: WT : AOMDSS : APC AJ-08_1

value: Control


title: Hyperplasia_D12_4weeks

description:
fibroblast FACS sorting
Gene expression

value: Hyperplasia


title: YL-STAG2-743-R1-T1_HiC

city: Worcester

first: Job

last: Dekker

state: MA

address: 368 Plantation Street, AS5-1049

department: Program in Systems Biology

institute: University of Massachusetts Medical School

data_processing:
Mapping onto mm9 genome using cMapping pipeline (cMapping : https://github.com/dekkerlab/cMapping)
contact matrix files were generated using cWorld pipeline (cworlds-dekker : https://github.com/dekkerlab/cworld-dekker)
Genome_build: mm9
Supplementary_files_format_and_content: Insulation score calling, heatmap generation and compartment calling using cWorld pipeline (cworlds-dekker : https://github.com/dekkerlab/cworld-dekker)

source_name: Hematopoietic progenitor cells

extract_protocol:
Murine bone marrow cells were negatively selected for lineage markers using antibodies conjugated to magnetic beads and separated using EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit (STEMCELL Technologies).
Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. PMID: 28435001

tag: protocol

value: HiC 2.0

tag: enzyme

value: DpnII

value: Hematopoietic progenitor cells

tag: genotype/variation

value: Stag2 knock-out


title: Normal_D5_Normal

description:
fibroblast FACS sorting
Gene expression

value: FVB/n

value: mammary

value: fibroblasts

value: female


title: Hyperplasia_D7_4weeks

description:
fibroblast FACS sorting
Gene expression

value: MMTV-PyMT

value: mammary tumor


title: Control

city: Vilnius

first: Rapolas

last: Zilionis

state: LT

address: Sauletekis av 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

description:
Control
PolyA RNA
Single cell RNAseq

data_processing:
Raw sequencing data were processed for initial QC analysis and alignment by the sequencing core of the Institute of Human Genetics (UCSF) using Cell Ranger pipeline.
Cells with fewer than 1000 total counts or more than 10% of counts from mitochondrial genes were excluded, leaving 3,173 and 4,645 high-quality transcriptomes for control and injury recovery, respectively.
Upon initial visualization of the two conditions individually, a fraction of cells (824 in control and 301 in recovery) forming well-separated clusters and characterized by distinct expression of either immune genes or mesenchymal cell markers was identified and excluded from further analysis.
Normalization: count data rescaled to 10,000 total counts per cell.
See also https://github.com/rapolaszilionis/Sharir_et_al_2019
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: control_matrix.mtx – mtx file with raw expression counts (cells x genes).
Supplementary_files_format_and_content: control_genes.tsv – tsv file with gene list, gene order as in control_matrix.mtx.
Supplementary_files_format_and_content: control_barcodes.tsv – tsv file with cell barcodes, barcode order as in control_matrix.mtx.
Supplementary_files_format_and_content: control_loom.loom.hdf5 – loom file containing spliced and unspliced transcript counts. Used for calculating RNA velocity vectors.
Supplementary_files_format_and_content: injury_matrix.mtx – mtx file with raw expression counts (cells x genes).
Supplementary_files_format_and_content: injury_genes.tsv – tsv file with gene list, gene order as in injury_matrix.mtx.
Supplementary_files_format_and_content: injury_barcodes.tsv – tsv file with cell barcodes, barcode order as in injury_matrix.mtx.
Supplementary_files_format_and_content: injury_loom.loom.hdf5 – loom file containing spliced and unspliced transcript counts. Used for calculating RNA velocity vectors.
Supplementary_files_format_and_content: cell_info_8594x25.tsv – tsv file with per-cell information (e.g. cluster labels, xy coordinates), cells x features.
Supplementary_files_format_and_content: raw_counts_8594x27998.mtx – mtx file combining all count data.
Supplementary_files_format_and_content: gene_names_alphabetically.txt – tsv file with gene list, gene order alphabetical and as in raw_counts_8594x27998.mtx.
Supplementary_files_format_and_content: average_gene_expression_per_population.tsv – tsv file with average gene expression per population, genes x populations.

source_name: Incisor growth region

growth_protocol: Mice were maintained in the University of California San Francisco (UCSF) specific pathogen-free animal facility in accordance with the guidelines established by the Institutional Animal Care and Use Committee and Laboratory Animal Resource Center. All experimental procedures were approved by the Laboratory Animal Resource Center at UCSF. Incisor injury was performed according to the Swiss Animal Welfare Law and in compliance with the regulations of the Cantonal Veterinary Office, Zurich. Male mice aged 8–12 weeks were used for all experiments.

extract_protocol:
Proximal incisors (roughly 3 mm in length) were first severed away using a pair of scissors after removal of the surrounding jaw bones. The bulbous portion, as well as the lateral wing-shaped epithelium, and the surrounding mesenchyme were subsequently dissected from the rest of the incisor and collected in cold HBSS (pH 8.0) and digested enzymatically at 37°C in collagenase type II at concentration 2 mg/ml (Gibco/BRL type II in DMEM) for 30 min, followed by collagenase inactivation with 2% FBS. The digested tissue was mechanically disrupted using 1 ml pipette tip and centrifuged at 400 x g for 3 min. Cells were resuspended in HBSS (pH 8.0) containing 2% FBS. To isolate epithelial cells by fluorescence-activated cell sorting, proximal incisor cell suspension was stained with mAb specifically recognizing CD326 (G8.8, AF647 conjugate, Biolegend) for 30 min on ice followed by centrifugation at 400 x g for 3 min. Prior to fluorescence-activated cell sorting (BD FACSAria2 SORP), cells were filtered through 40 μm mesh (BD Falcon) and stained with DAPI.
Epithelial cells from 5 controls and 5 5FU-treated mice were isolated as described above. The resulting cell suspensions (~20,000 cells each) were submitted as separate samples with targeted cell recovery of 3,000 per sample to be barcoded for single-cell RNAseq using the Chromium Controller (10X Genomics) and the Single Cell 3’ Library Kit v2 (PN-120236/37/62). Resulting libraries were sequenced on a HiSeq 4000 (Illumina) using HiSeq 4000 PE Cluster Kit (PN PE-410-1001) with HiSeq 4000 SBS Kit (150 cycles, PN FC-410-1002), one sample being loaded per sequencing lane.

treatment_protocol: Either no treatment or 5FU-induced injury.

tag: strain/background

value: wild type

tag: Sex

value: male

tag: age

value: 8-12 weeks

value: incisor growth region epithelium

tag: antibody

tag: perturbation


title: Hyperplasia_D6_4weeks

description:
fibroblast FACS sorting
Gene expression


title: Injured

description:
3-days post injury by 5FU.
PolyA RNA
Single cell RNAseq

value: CD326 (G8.8, AF647 conjugate, Biolegend)

value: 5-fluorouracil induced injury


title: KO : AOMDSS : APC-AJ-01_2

value: colon adenoma

value: AOMDSS

tag: sample prep

value: FFPE

tag: days post tamoxifen

value: Female

tag: genotype

tag: grade

value: high grade


title: KO : AOMDSS : MPC-Lrig V29_3

tag: tissue


title: Carcinoma_D10_9weeks

description:
fibroblast FACS sorting
Gene expression

tag: tumor stage

value: Carcinoma

tag: cell type


title: YL-STAG2-740-R1_HiC

value: HiC 2.0

value: DpnII

value: Hematopoietic progenitor cells

value: Stag2 knock-out


title: YL-STAG2-742-R1_HiC

value: Stag2 wildtype


title: KO : AOMDSS : MPC-Lrig V-32_3


title: Normal_D2_Normal

description:
fibroblast FACS sorting
Gene expression

tag: strain

value: FVB/n

value: mammary

value: fibroblasts

tag: gender

value: female


title: KO : AOMDSS : X-11_1

tag: genetic mouse model

value: Male


title: KO : AOMDSS : AN-08_4


title: shPLCG1-1_Rep4

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Hannover Medical School

description: Gene expression data from Kasumi-1 transduced with PLCG1 shRNA

hyb_protocol: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.For each sample the gProcessedSignal was extracted from the Agilent Feature Extraction Files and the log2 values were quantile normalized using the LIMMA package from R/Bioconductor

source_name: KASUMI-1 AML cell line

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into Cy3-labeled fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method(Arraystar Flash RNA Labeling Kit, Arraystar).  The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was  fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

growth_protocol: Kasumi-1 cells were transduced with a lentviral vector expressing validated human PLCG1 shRNA or non-targeting control (scrambled). Target cells were infected twice (8 hours gap in between) by spinfection at 33°C. 48 hours post-infection, puromycin (1 μg/ml) was added to select for transduced cells. Three days post-infection (24h puromycin selection) total RNA of 2x106 cells was isolated.

extract_protocol: TRIzol-Chloroform according to manufacturers instructions. RNA quality was assessed using the Agilent 2100 Bioanalyzer.

value: human t(8;21) AML cell line

tag: cell line

tag: treatment

value: transduced with PLCG1 shRNA


title: shPLCG1-1_Rep3


title: shPLCG1-1_Rep2


title: shPLCG1-1_Rep1


title: S Lycopersicum, IL, rep2

status: Public on Sep 01 2019

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

country: United Kingdom

institute: University of East Anglia

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapters and HD signatures, for the HD samples, were trimmed and the files were converted from redundant to non-redundant format [Beckers et al 2017]
the reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change, offset = 20
Genome_build: S Lycopersicum v 3.2
Supplementary_files_format_and_content: csv, raw abundances

organism: Solanum lycopersicum

source_name: leaf

growth_protocol: the plants were grown in Panasonic Plant Growth Chambers set at 25 and 18°C ( day and night, respectively) with 16 hours of light

extract_protocol:
Leaf tissue was used for RNA extraction before small RNA library construction
Illumina compatible method using standard Illumina adapters

treatment_protocol: the RNA was not treated with TAP prior to library construction

tag: adapter

value: standard


title: YL-STAG2-746-R1-T1_HiC

tag: protocol

tag: enzyme

tag: genotype/variation


title: S Lycopersicum, IL, rep1


title: Rxra-KO rep2

first: Maria

last: Casanova Acebes

state: New York

address: 1470 Madison Ave

department: Oncological Sciences

institute: Mount Sinai School of Medicine

data_processing:
Transcript abundances were summarized to gene level using tximport.
The expression matrix was filtered for only transcripts with greater than 5 TPM in replicates.
Only genes with at least 1 count per million in the 2 replicates were considered for statistical analysis.
Differential expression statistics between different macrophage subsets were generated using limma with TMM normalization.
Genes with a Benjamini-Hochberg adjusted p-value < 0.05 and a cut-off of 0.6 in logFC were considered differentially expressed (DEGs).
Genome_build: Transcript abundances were quantified with the Ensembl GRCh38 cDNA reference using Kallisto version 0.43.0.
Supplementary_files_format_and_content: Excel file include TPMs values for each sample

source_name: Peritoneal cavity

extract_protocol:
Cells were lysed in RLT buffer and RNA was extracted according to the protocol provided by the RNeasy Mini Kit (Qiagen, USA).
cDNA synthesis and library preparation were performed using the SMART-Seq v4 Ultra Low Input RNA Kit and Low Input Library Prep Kit v2 (Clontech), respectively.

treatment_protocol: LPMs were double-sorted in phenol-red free DMEM, 0.1% azide, 10 mM HEPES, 2% FCS, which resulted in a 99% pure LPMs population.

value: Peritoneal cavity

tag: age

value: 8 weeks old

value: Rxra-/-


title: S Lycopersicum, HD, rep2

value: HD


title: Jurkat cells treated with Tamoxifen

city: Colima

first: Ivan

last: Delgado-Enciso

state: Colima

address: Av Universidad 333

department: School of Medicine

country: Mexico

institute: Universidad de Colima

description: Cell line was purchased from ATCC. Jurkat, clone E6-1, from 14 years male  (ATCC®TIB™)

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

scan_protocol: Acquisition and quantification of array images was performed in GenePix 4100A with its accompanying software GenePix from Molecular Devices. All images were captured using 10µm resolution.

data_processing:
For each spot the Alexa555 and Alexa647 density mean value and background mean value were calculated with software ArrayPro Analyzer from Media Cibernetics. Microarray data analysis was performed with genArise, developed in the Computing Unit of Cellular Physiology Institute of UNAM (http://www.ifc.unam.mx/genarise/). GenArise carry out a number of transformations: background correction, lowess normalization, intensity filter, replicates analysis and selecting differentially expressed genes.
GenArise software identified differential expressed genes by calculating an intensity-dependent z-score between samples and reference (HDF).

source_name: Cell line derived from a T-cell Acute Lymphoblastic Leukaemia with no treatment (control)

label_protocol: 10 µg of total RNA was used for cDNA synthesis, incorporating dUTP-Alexa555 or dUTP-Alexa647 employing the Firs-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647.

growth_protocol: The cells were cultured in suspension in Advanced RPMI 1640 Medium supplemented with 5% (v/v) heat-inactivated fetal bovine serum (FBS), 2mM GlutaMAX, 10 mM HEPES and 100 U/ml penicillin/100 mg/ml streptomycin (all from Gibco, Thermo Fisher Scientific).

extract_protocol: Total RNA extacted using Trizol followed by DNAse treatment and column clean-up

treatment_protocol: Jurkat cells were treated with 7.5 µM Tamoxifen for 24 hours. In controls, the corresponding concentration of vehicle (ethanol) was used.

value: Jurkat cells

source_name: Cell line derived from a T-cell Acute Lymphoblastic Leukaemia treated with 7.5 µM Tamoxifen for 24 hours


title: WT rep1

value: wild type


title: WT rep2


title: RBPJ 6 days induced

city: Toronto

first: Juan Carlos

last: Zuniga-Pflucker

state: Ontario

address: 2075 Bayview Avenue

department: Immunology

country: Canada

institute: University of Toronto

data_processing:
Filtering (Seurat using R software)
Normalization (Seurat using R software)
Scaling (Seurat using R software)
Sample Barcode: I1
Cell Barcode and UMI: R1
Biological Read: R2
Genome_build: mm10
Supplementary_files_format_and_content: Text file containing matrix of individual cells (marked by unique bardocodes) and their expression values for genes.

source_name: BM LMPPS

growth_protocol: All mice were maintained in specific pathogen free conditions.

extract_protocol:
BM LMPPs were FACS sorted.
10X Genomics Illumina NextSeq 500

treatment_protocol: To induce expression of RBPJ in otherwise RBPJ deficient mice, 2mg/ml of doxycycline was first IP injected and then treated with 1mg/ml of doxycycline drinking water.

tag: group

value: RBPJ 6 days induced


title: Rxra-KO rep1


title: RBPJ 3 days induced

value: RBPJ 3 days induced


title: shSCR_Rep3

description: Gene expression data from Kasumi-1 transduced with scrambled shRNA

value: transduced with scrambled shRNA


title: RBPJ 6 days induced 2

data_processing:
Mouse genome alignment (HISAT2)
Transcript assembly (StringTie)
Obtain raw read counts (HTSeq)
Genome_build: mm10
Supplementary_files_format_and_content: Text file containing read counts for genes.

source_name: Thymus DN1a/b cells

extract_protocol:
Thymus DN1a/b cells were FACS sorted.
NextSeq


title: RBPJ uninduced

value: RBPJ uninduced


title: Control

value: Control


title: shSCR_Rep4


title: RBPJ 6 days induced 1


title: S Lycopersicum, HD, rep1


title: T2: Leaf Alternaria brassicae treated after 24 hpi, biological rep2

city: New Delhi

first: Senthil-Kumar

last: Muthappa

address: Aruna Asaf Ali Road

country: India

institute: National Institute of Plant Genome Research

description: Leaf tissue infected with Alternaria brassicae, sample of 24 hpi, biological replicate 2

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Genotypic designed Chickpea GXP_8X60K (AMADID: 037094). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65°C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327) and scanned using the Agilent Microarray Scanner (AgilentTechnologies, Part Number G2600D).

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the quantile normalization method . Gene based analysis was performed.

organism: Cicer arietinum

source_name: 25-das-old Chickpea plants spray inoculated with Alternaria brassicae, at 24 hpi

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: The seeds were sown in soil mixture of agropeat (Prakruthi Agro Tech, Karnataka, India): vermiculite (Keltech Energies Ltd, Maharashtra, India) mix (3:1 volume/volume, pre-weighed. Plants were grown in short-day conditions with 8 h of light, 16 h of dark, 200 µE m-2s-1 light intensity, 75% humidity, and 21 °C constant temperature in growth chamber (PGR15, Conviron, Winnipeg, Canada). The bottom irrigation was done by water and  Hogland solution (Cat # TS1094, Himedia Laboratories, Mumbai, India) thrice a week till the start of treatment.

extract_protocol: The total RNA for the samples was isolated by using TriZol reagent (Cat# 15596026 Invitrogen, Carlsbad, CA, USA) following manufacturers’ protocol. Then, RNA was cleaned by using RNeasy minikit (Cat#74104, Qiagen, Valencia, CA, USA) and further quantified by using NanoDrop ND-1000 spectrophotometer (Thermo Scientific, MA, USA). The RNA quality was examined by the Bioanalyzer (Agilent, Palo Alto, CA, USA).

treatment_protocol: The leaves of 25 days after sowing (DAS) old chickpea plants were spray-inoculated with A. brassicae spore suspension at the concentration of 5 X 10^6, containing the 0.05% Tween-20 (Cat # MB067, Himedia Laboratories, Mumbai). The spray was performed till the whole plant is fully drenched with the spore suspension. The Control plants for chickpea were spray inoculated with sterile water containing 0.05% Tween-20. Leaf samples were harvested at 24 hpi and 48 hpi after pathogen infection.

tag: variety

value: PUSA 372

value: Leaf

value: 25-Days after sowing


title: C3: leaf water treated as mock control,  biological rep3

description: Mock control, leaf tissue infiltrated with water, biological replicate 3

source_name: 25-das-old Chickpea plants spray inoculated with water (Mock control)


title: C2: leaf water treated as mock control,  biological rep2

description: Mock control, leaf tissue infiltrated with water, biological replicate 2


title: T3: Leaf Alternaria brassicae treated after 24 hpi, biological rep3

description: Leaf tissue infected with Alternaria brassicae, sample of 24 hpi, biological replicate 3


title: RBPJ uninduced 2


title: T4: Leaf Alternaria brassicae treated after 48 hpi, biological rep1

description: Leaf tissue infected with Alternaria brassicae, sample of 48 hpi, biological replicate 1

source_name: 25-das-old Chickpea plants spray inoculated with Alternaria brassicae, at 48 hpi


title: shSCR_Rep1

value: human t(8;21) AML cell line


title: T5: Leaf Alternaria brassicae treated after 48 hpi, biological rep2

description: Leaf tissue infected with Alternaria brassicae, sample of 48 hpi, biological replicate 2


title: C1: leaf water treated as mock control,  biological rep1

description: Mock control, leaf tissue infiltrated with water, biological replicate 1


title: Control 1


title: Control 2


title: Input

city: Newark

first: Maha

last: Abdellatif

state: NJ

address: 185 S. Orange Ave.

department: Cell Biology and Molecular Medicine

institute: Rutgers-University

data_processing:
Sequence Analysis: The 75-nt sequence reads generated by Illumina sequencing (using NextSeq  500) are mapped to the genome using the BWA algorithm with default settings. Alignment  information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter,  align with no more than 2 mismatches, and map uniquely to the genome are used in the  subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are  removed.
Determination of Fragment Density: Since the 5´-ends of the aligned reads (= “tags”) represent the  end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´-  ends to a length of 150-250 bp, depending on the average fragment length in the size selected  library (normally 200 bp). To identify the density of fragments (extended tags) along the genome,  the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This  information (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can be  visualized in genome browsers. bigWig files also provide the peak metrics in the  Active Motif analysis program described below.
“Peak Finding”: MACS v.1.4.2 was used to identify the binding sites of ACAA2 and OGDH. Normalization: The tag number of all samples (within a comparison group) is reduced by random sampling to the number of tags present in the smallest sample. This normalization method works well for most assays and can detect site-specific as well as most global differences in target enrichments between samples.
Merged Region Analysis: To compare peak metrics between 2 or more samples, overlapping  Intervals are grouped into “Merged Regions”, which are defined by the start coordinate of the most  upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping  Intervals; “merged peaks”). In locations where only one sample has an Interval, this Interval defines  the Merged Region. The use of Merged Regions is necessary because the locations and lengths of  Intervals are rarely exactly the same when comparing different samples.  6. Annotations: After defining the Intervals and Merged Regions, their genomic locations along with  their proximities to gene annotations and other genomic features are determined and presented in  Excel spreadsheets. In addition, average and peak (i.e. at “summit”) fragment densities within  Intervals and Merged Regions are compiled.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files show peak shapes in the form of a signal histogram and cand be visualized in the UCSC browser

source_name: hear tissue

extract_protocol:
Heart were surgically removed and snap frozen and shipped to Active Motif for ChIP-Seq (a pool of 3 for each condition)
Library was constructed by Active Motif (https://www.activemotif.com/)
ChIP using anti-ACAA2 and anti-OGDH

treatment_protocol: Wild type C57BL/6J male mice were subjected to a sham or a transverse aortic constriction surgery. Hearts were removed 7 days post-surgery

tag: phenotype

tag: surgical procedure

value: DNA pooled from sham and TAC hearts

tag: days post-surgery


title: RBPJ uninduced 1


title: OGDH_ChIP_Seq Sham

value: Normal heart / 12wk old mice subjected to Sham operation

tag: antibody

value: anti-OGDH (Cell Signalling Technologies 26865)


title: ACAA2_ChIP-Seq Sham

value: anti-ACAA2 (Origene Technologies  TA506126)


title: OGDH_ChIP-Seq TAC

value: Hypertrophied heart / 12wk old mice subjected to Transaortic coarctation (TAC) for 7 days


title: ACAA2_ChIP-Seq TAC


title: 12B2_S2

city: Oxford

first: Cristina

last: Di Genua

address: Headley Way

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

data_processing:
Short reads (76-bp) were aligned to the mouse genome using STAR
Gene expression levels were quantified as read counts using the featureCounts function from the Subread package
The read counts were used for the identification of global differential gene expression between specified populations using the edgeR package
Reads per kilobase of transcript per million (RPKM) values were also generated using the edgeR package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow cells of transplanted mice

extract_protocol:
cDNA libraries were synthesized from 50 sorted cells using a modified Smart-Seq2 method
Illumina sequencing libraries were prepared using the Illumina Nextera XT DNA kit, using one fourth of the standard volume recommended by Illumina
Samples were sequenced on Illumina NextSeq Instrument

treatment_protocol: CD45.2 HSCs (Lin-cKit+Sca1+CD150+Flt3-) cells were isolated by initial cKit enrichment by Flourescent Activated Cell Sortting from bone marrow cells of transplanted mice

tag: strain background

tag: transplanted with

value: Aml1ETO/+ fetal liver cells

tag: tissue

value: bone marrow

tag: cell type

value: bulk LSKCD150+Flt3-CD45.2+ cells

tag: batch


title: 3B2_S17


title: 7B2_S6

value: KrasG12D/+ fetal liver cells


title: 5B2_S5

value: WT fetal liver cells


title: 6B2_S22


title: 51B1_S18


title: 46B1_S11

value: Aml1ETO/+;KrasG12D/+ fetal liver cells


title: 8B2_S10


title: 45B1_S8


title: 44B1_S12


title: 50B1_S4


title: 2B2_S1


title: 10B2_S20


title: 11B2_S21


title: 9B2_S15


title: 47B1_S14


title: 41B1_S19


title: 1B2_S16


title: 49B1_S7


title: 48B1_S23


title: 4B2_S3


title: 42B1_S9


title: Pre-6

city: Bloomington

first: Jason

last: Tennessen

state: IN

address: 1001 E. Third St

department: Department of Biology

institute: Indiana University

data_processing:
Illumina Casava software used for basecalling.
All files where trimmed using Trimmomatic v0.32 using these settings: "ILLUMINACLIP:~/bin/Trimmomatic-0.32/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30".
Reads were mapped against Flybase r6.03 using Tophat2 v2.0.13 (Bowtie2 v2.2.4). The parameters used were:--library-type fr-secondstrand --b2-very-sensitive --read-edit-dist 2 --max-multihits 100.
Gene counts were produced using HTseq-Count v0.6.1p1.
DESeq2 was used to perform fold change analysis.
Genome_build: Flybase r6.03
Supplementary_files_format_and_content: Gene counts

organism: Drosophila melanogaster

source_name: mid-L2 larvae

growth_protocol: Synchronized populations of larvae were grown on molasses agar plates covered with yeast paste for 60 hours at 25ºC.

extract_protocol: Larvae were homogenized in trizol reagent following the manufacturers protocol

tag: genotype

value: w[1118]; Ldh[precise]

tag: developmental stage

value: whole larvae


title: Pre-2


title: Pre-5


title: Pre-1


title: 43B1_S13


title: T1: Leaf Alternaria brassicae treated after 24 hpi, biological rep1

description: Leaf tissue infected with Alternaria brassicae, sample of 24 hpi, biological replicate 1

value: PUSA 372


title: Delter-3


title: Delter-2


title: LOX-PP-2

city: Chennai

first: Karunakaran

last: Coral

state: Tamilnadu

address: 41, College road

department: R S Mehta Jain Department of Biochemistry and Cell Biology,

institute: Vision Research Foundation, Chennai

description:
Tissue culture
RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with Affymetrix HTA2.0 array using an affymetrix hybridisation kit

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The raw data was analyzed using TAC 4.0 software, which allows for the identification of differentially expressed genes in the sample. Gene level analysis was performed and data was normalized using quantile normalization. Background noise was deducted using detection above background algorithm (DABG). Only the probe sets characterized by a DABG p-value <0.05 in at least 50 % of the samples were considered for statistical analysis. We performed an unpaired Student’s t-test to compare gene intensities between LOX-PP transfected vs EV transfected cells.

source_name: Y79 cell lysate

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Y79 cell is suspention cell line, supplemented with RPMI-1640, 10% FBS and antibiotic solution containing penecillin and streptomycin with 5% CO2 in 37˚C

extract_protocol: RNA was extracted using Trizol reagent, followed by DNASE I treatment with prescribed protocol provided with Kit

treatment_protocol: Y79 cells were treated with optimised LOX-PP clone concentration complexed with HP Xtreme DNA transfection reagent using manufacturer's protocol. After 48 hours incubation in CO2 incubator with 5% CO2. The cells were removed and  washed with 1x PBS.

tag: cell line

value: LOX-PP overexpressed


title: Huh7 Sorafenib-resistant Pool 3

city: Columbus

first: Kelly

last: Regan

state: Ohio

address: 1800 Cannon Drive

institute: The Ohio State Univ

description:
treatment_Sorafenib-Resistant-Pool
Gene expression data of a pool of sorafenib-resistant Huh7 hepatocellular carcinoma cells

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50 mg/ml), Eukarytic Hybridization Controls (Affymetrix). Hear 65oC for 5 mins, 99oC for 5 mins, 45oC for 5 mins, centrifuge top speed for 5 mins. Hybridize 16 hours at 45oC at 60 rpm. Fluidics washing is FS450_0001.

scan_protocol: Affymetrix Gene Chip Scanner 3000 7G using AGCC (Affymetrix GeneChip Command Console)

data_processing: Signal intensities were generated using Affymetrix Expression Console software. Gene expression levels were RMA-normalized and log2-transformed

source_name: Huh7, sorafenib resistant pool

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: All cells were maintained in Minimum Essential Media supplemented with L-glutamine (2 mM), 10% FBS, sodium pyruvate (0.11 g/L) and penicillin/streptomycin (100 U/mL).  Cell media for sorafenib resistant cell lines was also supplemented with sorafenib (6µM and 0.1% DMSO).  Sorafenib was withdrawn from the cell media of resistant Huh7 cells for 5-7 days prior performing all experiments.

extract_protocol: RNA was extracted using Trizol reagent (invitrogen) and purified using RNeasy Mini kit (Qiagen)

treatment_protocol: Sorafenib resistant pool (Huh7-R) and resistant clone (Huh7-R-A7) cells were derived from parental Huh7 (Huh7-S) cells. To generate the resistant cell lines, parental cells were initially pulsed with high concentration of sorafenib (10 µM) in MEM media for 4 hours once a week for 6 weeks. These cells were then continuously exposed to sorafenib gradually increasing to 6 µM. The resistant clone Huh7-R-A7 was isolated from an individual colony of Huh7-R cells. Sorafenib was withdrawn from the cells one week prior to harvesting for microarray analysis.

value: Hepatocellular carcinoma


title: Huh7 Sorafenib-resistant Clone A7 3

description:
treatment_Sorafenib-Resistant-CloneA9
Gene expression data of a clone (A7) of sorafenib-resistant Huh7 hepatocellular carcinoma cells

source_name: Huh7, sorafenib resistant clone


title: Delter-1


title: Huh7 Parental 1

description:
treatment_Parental-Untreated
Gene expression data of parental (untreated) Huh7 hepatocellular carcinoma cells

source_name: Huh7, parental untreated


title: Delter-6


title: Huh7 Parental 3


title: Empty vector-1

value: empty vector


title: Empty vector-2


title: Huh7 Sorafenib-resistant Clone A7 1

description:
treatment_Sorafenib-Resistant-CloneA7
Gene expression data of a clone (A7) of sorafenib-resistant Huh7 hepatocellular carcinoma cells


title: Huh7 Sorafenib-resistant Pool 1


title: Huh7 Sorafenib-resistant Clone A7 2

description:
treatment_Sorafenib-Resistant-CloneA8
Gene expression data of a clone (A7) of sorafenib-resistant Huh7 hepatocellular carcinoma cells


title: Huh7 Parental 2


title: Huh7 Sorafenib-resistant Pool 2


title: UM-UC-3_DANCR siRNA2

city: Guangzhou

first: Xu

last: Chen

state: Guangdong

address: 107. W. Yanjiang Road

department: Department of Urology

institute: Sun Yat-sen Memorial Hospital

hyb_protocol: Hybridization was performed at 45℃ with rotation for 16 h (Affymetrix GeneChip Hybridization Oven 640). The GeneChip arrays were washed and then stained (streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The hybridization data were analyzed using GeneChip Operating software (GCOS 1.4). The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4. An invariant set normalization procedure was performed to normalize the different arrays using DNA-chip analyzer [dChip].

source_name: Bladder cancer cell line UM-UC-3

label_protocol: An aliquot of 0.1 µg of total RNA was used to synthesize double-stranded cDNA, then produce biotin-tagged cRNA using the MessageAmpTM Premier RNA Amplification Kit. The resulting bio-tagged cRNA were fragmented to strands of 35–200 bases in length according to the protocols from Affymetrix.

growth_protocol: UM-UC-3 cells were cultured in DMEM containing 10% FBS (Shanghai ExCell Biology, China) supplemented with 1% penicillin/streptomycin. Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufacturers’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.

treatment_protocol: siRNA transfections were done with 75 nM siRNA and Lipofectamine RNAimax (Life Technologies) following manufacturer's instructions.

value: Bladder cancer cell line

tag: sirna

value: DANCR siRNA2

tag: sirna target point on wdr5 cds

tag: sirna sequence

value: GAGCUAGAGCAGUGACAAUTT

tag: inhibition rate (relative to control sirna)


title: UM-UC-3_DANCR NC

value: Negative control

value: UUCUCCGAACGUGUCACGUTT


title: shSCR_Rep2

source_name: KASUMI-1 AML cell line

value: human t(8;21) AML cell line

tag: treatment

value: transduced with scrambled shRNA


title: LOX-PP-1

source_name: Y79 cell Lysate

tag: genotype/variation


title: MEL_WT1

city: Hangzhou

first: Caiyong

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat2.
Reads per kilobase of exon per megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. Breifly, 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: mm10
Supplementary_files_format_and_content: Excel file include RPKM values for all samples

source_name: mouse erythroleukemia cells

growth_protocol: MEL cells were maintained in a complete medium composed of Dulbecco’s Modified Eagle Medium (DMEM), 10% fetal bovine serum (FBS), 1% penicillin-streptomycin (PS), 1% sodium pyruvate, 1% glutamine, and 1% non-essential amino acid (NEAA). Dimethyl sulfoxide (DMSO, 1.5%) was supplemented to the medium to induce the erythroid-like differentiation of MEL cells.

extract_protocol:
RNA was extracted using Trizol reagent. The mRNA was enriched by depleting ribosomal RNA using Epicentre Ribo-Zero removal kit (Illumina) and fragmented.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: wild type


title: UM-UC-3_DANCR siRNA1

value: DANCR siRNA1

value: GCGUACUAACUUGUAGCAATT


title: MEL_Wdr26KO2


title: MEL_WT2


title: MEL_Wdr26KO1


title: Digenic rep1 (MFC-225)

city: Rochester

first: Rory

last: Olson

state: MN

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
TopHat2 (Kim et al 2013) with the Bowtie (Li et al. 2009) option was used to align each sample's reads to the mm10 reference genome.
Gene counts were generated by FeatureCounts (Liao et al. 2014) using Ensembl's mm10 gene definition file.
RSeqQC (Wang et al. 2012) was used to create quality control metrics.
EdgeR (Robinson et al. 2010) was used to for differential expression analysis across group comparisons.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes raw expression, normalized expression, FC

source_name: Kidney tissue

extract_protocol:
Kidneys were removed, flash frozen by liquid nitrogen, and RNA was harvested using RNAeasy Mini Kit (Qiagen, Cat#74104). 150bp paired-end reads were sequenced on Illumina HiSeq4000 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: whole kidney

tag: age

value: post natal day 12

value: Digenic


title: Digenic rep3 (MFC-251)


title: Digenic rep2 (MFC-250)


title: Pkd1-RC/RC rep3 (MFC-356)


title: WT rep3 (MFC-344)

value: WT


title: Pkhd1-/- rep1 (MFC-245)


title: Pkd1-RC/RC rep2 (MFC-333)


title: Digenic rep3 (MFC-355)

value: post natal day 3


title: Pkhd1-/- rep3 (MFC-319)


title: Digenic rep2 (MFC-316)


title: WT rep2 (MFC-343)


title: Pkd1-RC/RC rep1 (MFC-254)


title: WT rep1 (MFC-262)


title: Pkd1-RC/RC rep3 (MFC-326)


title: Pkhd1-/- rep1 (MFC-223)


title: Pkhd1-/- rep2 (MFC-300)


title: KO : AOMDSS : MPC-APC-Lrig N-43A_2

city: Salt Lake City

first: Jordan

last: Berg

state: UT

address: 15 N Medical Drive East, Rm 5520

department: Biochemistry

institute: University of Utah

description: Loss of the mitochondrial pyruvate carrier promotes stem cell gene expression in AOMDSS colon adenomas, though loss of Apc promotes a more unified pehnotype.

data_processing: We scaled the raw data by generating a geometric mean scaling factor per sample to normalize the dataset. This was performed using NanoString nSolver 4

source_name: colon adenoma

extract_protocol: if tumors, at least 8-10 section of 8um thick sections were stained with aniline blue and microdissected for tumors over normal crypts or microdissected upon animal sacrifice and snap frozen. if crypts, crypts were isolated from the colon (Schell et al 2017), washed and snap frozen. Whole crypt RNA was extracted using the QIAGEN RNeasy kit. Tumor tissue RNA was extracted using the QIAGEN FFPE RNeasy kit or the QIAGEN RNeasy kit (please refer to associated manuscript for full details).

treatment_protocol: colon epithelial tumors were induced spontaneously in mice by either chemical treatment (AOMDSS) or genetic recombination (loss of Apc).

value: colon adenoma

tag: genetic mouse model

value: AOMDSS

tag: sample prep

value: FFPE

tag: days post tamoxifen

tag: Sex

value: Female

tag: grade

value: high grade


title: Sample 6; Mature; miRNA-Seq

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

institute: Klinikum rechts der Isar – Technical University Munich

description:
processed immediately after sorting
small RNA

data_processing:
System suite 2.2.0; RTA version 2.4.11
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37 whole genome using Bowtie2 using the following parameters: --local -p 8 -q --phred33 -D 20 -R 3 -N 0 -L 8 -i S,1,0.50
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: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include HTSeq count values for each Sample

source_name: Platelets

extract_protocol:
Platelet were sorted and pelleted.  RNA was harvested using Trizol (Qiazol) reagent.
Small-RNA-seq library preparation was performed starting from 1 ng of small-RNA with the SMART-Seq Stranded Kit (Clontech-Takara).

tag: tissue

value: Platelets

tag: Stage

value: Mature


title: Pkhd1-/- rep2 (MFC-246)

tag: genotype


title: Sample 5; Immature; miRNA-Seq

value: Immature


title: Pkhd1-/- rep3 (MFC-339)


title: Pkd1-RC/RC rep2 (MFC-282)


title: WT rep3 (MFC-359)


title: WT rep2 (MFC-324)


title: Sample 1; Immature; miRNA-Seq


title: Sample 3; Immature; miRNA-Seq


title: Sample 4; Mature; miRNA-Seq


title: Digenic rep1 (MFC-305)


title: Sample 2; Mature; miRNA-Seq


title: Sample 8; Mature

description: processed immediately after sorting

data_processing:
System suite 2.2.0; RTA version 2.4.11
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37 whole genome using TopHat-2.0.1 with default parameters
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: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include HTSeq count values for each Sample

extract_protocol:
Platelet were sorted and pelleted.  RNA was harvested using Trizol (Qiazol) reagent.
Total-RNA-seq library preparation was performed starting from 0.5 ng of total-RNA with the SMART-Seq Stranded Kit (Clontech-Takara).


title: Sample 6; Mature

description: processed immediately after sorting


title: WT rep1 (MFC-286)


title: Pkhd1-/- rep1 (MFC-387)

value: post natal day 0


title: Digenic rep3 (MFC-381)


title: Digenic rep1 (MFC-369)


title: Digenic rep2 (MFC-379)


title: Sample 4; Mature

description: processed immediately after sorting


title: Sample 2; Mature

description: processed immediately after sorting


title: Pkhd1-/- rep2 (MFC-394)


title: Pkd1-RC/RC rep2 (MFC-365)


title: Sample 1; Immature

description: processed immediately after sorting


title: Pkd1-RC/RC rep1 (MFC-360)


title: Sample 7; Immature

description: processed immediately after sorting


title: Sample 3; Immature

description: processed immediately after sorting


title: Pkd1-RC/RC rep3 (MFC-397)


title: Pkd1-RC/RC rep1 (MFC-281)


title: WT rep3 (MFC-409)


title: WT rep2 (MFC-383)


title: UO9-3 (re-analyzed)

city: Boston

first: Rachel

last: Flynn

address: 72 East Concord Street, K-712D

department: Department of Pharmacology

institute: Boston University School of Medicine

description: ribo-depleted RNA

data_processing:
Bases were called with the Illumina CASAVA 1.7 pipeline
Read library quality was assessed using fastqc (FastQC 2016) and multiqc (Ewels 2016) packages.
Illumina adapters were removed (R1: TACACTCTTTCCCTACACGACGCTCTTCCGATCT, R2: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) and leading and trailing low quality bases (below quality 30) were trimmed using Trimmomatic (Bolger 2014).  Reads which were less than 36 bases long after these steps were dropped.
The expression of the genes was quantified using Salmon (Patro, Duggal, Love, Irizarry, & Kingsford, 2017) with index built from the GENCODE v27 transcriptome.
The counts matrix was then normalized using in-house bioinformatics software package de_toolkit’s deseq2 method.
The counts of the genes were extracted and plotted with ggplot2 package (Wickham, 2016).
Genome_build: hg38
Supplementary_files_format_and_content: A table of the normalized counts of ATRX, DAXX, H3F3A, SMARCAL1, SLX4IP, TERT genes in the 60 samples (including all three batches of each cell line and patient derived osteosarcoma xenograft sample) and their correspnding ATL statuc and full source name.

source_name: in vitro cells

extract_protocol:
QIAzol, Qiagen Rneasy kit
Kapa RNA HyperPrep kit with Riboerase. Sequenced on a Illumina NextSeq 500.

tag: cell line

tag: alt status

value: ALT+


title: U2-1 (re-analyzed)

description: ribo-depleted RNA


title: Sample 5; Immature

description: processed immediately after sorting


title: Pkhd1-/- rep3 (MFC-399)


title: SJ-1 (re-analyzed)

description: ribo-depleted RNA

value: SJ

value: ALT-


title: SRF-KO-LPS Treated_BMDMs 3

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus_musculus/Ensembl/GRCm38.PatchesSkipped
Supplementary_files_format_and_content: raw counts

source_name: SRF-KO-LPS Treated_BMDMs

growth_protocol: Isolated BM cells were seeded in 60 mm non-treated plastic dishes for 7 days at 37 oC and 5% CO2 conditions.

extract_protocol:
RNA was isolated with Qiagen RNA Isolation Kit as per the manufacturer’s protocol.
TruSeq RNA stranded protocol

treatment_protocol: Cells were activated with LPS for 6 h.

value: SRF-KO

value: bone marrow

tag: cell type

value: primary macrophage

value: LPS for 6 h


title: SRF-KO-LPS Treated_BMDMs 2


title: Control_LPS Treated_BMDMs 3

source_name: Control_LPS Treated_BMDMs

value: wild type


title: Control_LPS Treated_BMDMs 1


title: RF-UO9-2 (re-analyzed)

description: ribo-depleted RNA


title: Control_Untreated_BMDMS 2

value: none (untreated)


title: Control_LPS Treated_BMDMs 2


title: SRF-KO-LPS Treated_BMDMs 1


title: WT rep1 (MFC-375)

value: whole kidney

value: WT


title: RF-SJ-2 (re-analyzed)

description: ribo-depleted RNA


title: UO9-1 (re-analyzed)

description: ribo-depleted RNA


title: RF-MG-2 (re-analyzed)

description: ribo-depleted RNA

value: MG


title: Conditional deletion of Prmt1 2

city: Los Angeles

first: Jian

last: Xu

state: CA

address: 2250 Alcazar Street, CSA 106

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

data_processing:
Image analysis and base calling was carried out using RTA 1.13.48.0.  Final file formatting, demultiplexing and fastq generation were carried out using CASAVA v 1.8.2.
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genome mm10 using STAR version 2.4.1d with default parameter settings
Gencode M12 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.
Read counts per gene/transcript in all samples were normalized using Upper Quartile normalization (before adding 1 raw read as offset) and analyzed for differential expression using Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Genome_build: mm10
Supplementary_files_format_and_content: .txt file of gene counts data

source_name: Palatal shelve lysates

growth_protocol: C57BL mice were raised in animal facilities according to protocol.

extract_protocol:
Total RNA isolated from E14.5 palatal shelves was extracted using TRIzol (Thermo Fisher Scientific)
Total RNA was enriched for poly(A) RNA and fragmented for library construction. RNA fragments were reverse transcribed followed by A-tailing and index adapter ligation, then denatured and amplified on cBot. Library analysis and quality checks were performed on a LabChip GX.

treatment_protocol: Embryos were harvest at E14.5 forgenotyping, palatal shelves dissection and RNA extraction. .

tag: developmental stage

value: Wnt1-Cre; PRMT1 fl/fl

value: embryo


title: RF-G2-2 (re-analyzed)

description: ribo-depleted RNA


title: SA-3 (re-analyzed)

description: ribo-depleted RNA

value: SA


title: Control_Untreated_BMDMS 3


title: RF-U2-2 (re-analyzed)

description: ribo-depleted RNA


title: SA-1 (re-analyzed)

description: ribo-depleted RNA


title: RF-SA-2 (re-analyzed)

description: ribo-depleted RNA


title: Control 3

value: PRMT1 fl/fl


title: RF-FOB-2 (re-analyzed)

description: ribo-depleted RNA

value: FOB


title: RF-NY-2 (re-analyzed)

description: ribo-depleted RNA

value: NY

value: ALT+


title: Control 2


title: Control_Untreated_BMDMS 1


title: SJ-3 (re-analyzed)

description: ribo-depleted RNA

value: SJ

value: ALT-


title: U2-3 (re-analyzed)

description: ribo-depleted RNA


title: Control 1


title: Conditional deletion of Prmt1 1


title: Conditional deletion of Prmt1 3


title: RF-NOS-2 (re-analyzed)

description: ribo-depleted RNA

value: NOS


title: RF-HOS-2 (re-analyzed)

description: ribo-depleted RNA

value: HOS


title: NY-3 (re-analyzed)

description: ribo-depleted RNA


title: NOS-3 (re-analyzed)

description: ribo-depleted RNA


title: RF-3N1-2 (re-analyzed)

description: ribo-depleted RNA