title: Input CMS rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Removed the low quality reads; Bsmap was used to map the CMS-IP sequences to hg19;
Macs2 was used to call CMS-IP peaks with default parameters;
DESeq2 was used to call differential 5hmC peaks.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file for CMS-IP data and bed file for 5hmC peaks

extract_protocol:
Genomic DNA was isolated using Qiagen DNeasy Blood and Tissue kit.
CMS-IP library construction: DNA was sheared using Covaris Adaptive Focused Acoustic to the center at 200 bp. DNA fragments were size selected and ligated with methylated adaptors and treated with sodium bisulfite (invitrogen). The extra adapters were removed by AmpurXP (Beckman). The DNA was then denatured for 10 minutes at 95 °C (0.4 M NaOH, 10 mM EDTA), neutralized by the addition of cold 2M ammonium acetate (pH 7.0) for 10 min on ice. Then denatured DNA fragments were incubated with 1 μl anti-CMS antiserum in 1x IP buffer (10 mM sodium phosphate pH 7.0, 140 mM NaCl, 0.05% Triton X-100) for 2 h at 4 °C, and then precipitated with protein A/G beads. Precipitated DNA was eluted with proteinase K, purified with phenol chloroform, amplified and enriched by 10-12 cycles PCR using Kapa HiFi uracil polymerase. RNA-seq library construction is followed standard illumina library construction protocols. MethylC-seq: DNA was sheared using Covaris Adaptive Focused Acoustic to the center at 300 bp. DNA fragments were size selected and ligated with methylated adaptors and treated with sodium bisulfite (invitrogen). Libraries were enriched by 4-6 cycles PCR using Kapa HiFi uracil polymerase.


title: cPS1_51

status: Public on Apr 18 2018

type: SRA

city: Madison

first: David

last: Vereide

state: WI

address: 330 North Orchard Street

department: Regenerative Biology

country: USA

institute: Morgridge Institute for Research

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Some samples were discarded because they failed quality control (SinQC analysis, 19 cells, not included here)
Sequencing reads were mapped to Galgal4 using Bowtie 0.12.9.
Gene expected counts were calculated using RSEM 1.2.3
Genome_build: Galgal4

molecule: total RNA

organism: Gallus gallus

source_name: Chicken primitive streak

growth_protocol: Fertilized White Leghorn chicken eggs were incubated for 20-27 hours to reach Hamburger-Hamilton Stage 4.

extract_protocol:
Hamburger-Hamilton Stage 4 chicken embryos were collected in Ringer's solution. The primitive streak was dissected out using a fine tungsten needle, and the remaining surrounding tissue (rest of the area pellucida) was collected separately.
Diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina).
scRNA-seq with ~40x multiplexing

tag: breed

value: White Leghorn

tag: cell type

value: Chicken primitive streak cell

tag: Stage

value: Hamburger-Hamilton Stage 4


title: Input CMS rep1

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: human ES cells

growth_protocol: Human embryonic stem cells (H1) was cultured in hESC culture media (mTeSR1, Stem Cell Technologies) following manufactures instruction. Every 3-4 days, cells were passaged using AccutaseTM (Innovative Cell Technologies) supplied with 10% (vol/vol) human AB serum (Valley Biomedical) included in the hESC media the day of passage.

treatment_protocol: Pancreatic differentiation was following previous published protocol (Schulz et al., 2012; Xie et al., 2013). Differentiation employed a suspension-based format using rotational culture. Aggregates of undifferentiated hESC were generated by resuspending dissociated cells in hESC media at 1 × 106 cells/mL and culturing them overnight in six-well ultra-low attachment plates (Costar) with 5.5ml per well on an orbital rotator (Innova2000, New Brunswick Scientific) at 95 rpm. The following day undifferentiated aggregates were washed in RPMI media and then differentiated using a multi-step protocol with daily media feeding except on day 10 and continued orbital rotation at either 95 rpm or at 105 rpm on days 4 to 8. In addition to GlutaMAX™ and penicillin/streptomycin, RPMI media (Mediatech) was supplemented with 0.2% (vol/vol) FBS (HyClone) and DMEM High Glucose media (HyClone) was supplemented with 0.5X B-27® supplement (Life Technologies). Human activin, mouse Wnt3a, human KGF, human Noggin, and human EGF were purchased from R&D systems. Other media components included TGFb R1 kinase inhibitor IV (EMD Bioscience), KAAD-Cyclopamine (Toronto Research Chemicals), the retinoid analog TTNPB (Sigma Aldrich), and Insulin-Transferrin-Selenium (ITS; Life Technologies). For some differentiations, 50ng/mL Noggin was also included on days 8 to 12.

tag: strain

value: H1 ES differentiate


title: cPS1_49


title: PE CMS rep1


title: cPS1_50


title: PE CMS rep2


title: cPS1_48


title: cPS1_44


title: GT ATAC

data_processing:
Illumina Casava1.7 software used for basecalling.
Removed the low quality reads;Bowtie2 was used to map ATAC-seq to hg19 with --very sensitive parameter.
Macs2 was used to call ATAC peaks;
Genome_build: hg19

extract_protocol:
Genomic DNA was isolated using Qiagen DNeasy Blood and Tissue kit.
ATAC-seq library preparation was performed as described in Nat Methods. 2013;10(12):1213-8


title: FG CMS rep2


title: cPS1_46


title: FG CMS rep1


title: cPS1_42


title: GT CMS rep1


title: DE CMS rep2


title: DE CMS rep1


title: cPS2_55


title: GT CMS rep2


title: cPS1_41


title: cSR_13

source_name: Chicken surrounding region (area pellucida without primitive streak)

value: Chicken surrounding region cell


title: cPS1_40


title: ES CMS rep1

value: H1 ES


title: ES CMS rep2


title: cPS1_36


title: cPS1_32


title: cPS1_34


title: cPS1_37


title: cPS1_31


title: cPS1_35


title: cPS1_30


title: cPS1_45


title: cPS1_26


title: cPS1_23


title: cPS1_17


title: cPS1_43


title: cPS1_14


title: cPS1_16


title: cPS1_38


title: ATAC_NPC_rep2

city: Kyoto

first: Takashi

last: Ikeda

address: 53 Shogoin Kawahara-cho Sakyo-ku

country: Japan

institute: Kyoto Univ.

data_processing:
The low-quality bases at the 3' read ends and the adaptors were trimmed using cutadapt-1.9.1.
Untrimmed and trimmed reads of 20 bp or longer were mapped to mouse genome (mm9) with BWA 0.7.12 using the default parameters.
The reads with high mapping quality (MAPQ>=20) were used for further analysis. The duplicate reads were removed with the Picard tool. The reads mapping to the mitochondrial DNA (chrM) were excluded for further analysis.
Peak detection was performed using MACS ver. 1.3.7.1, with parameters --mfold=8 --gsize=2.43e+09 --pvalue 1e-5.
Peaks falling within blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were excluded from further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bw (bigwig) *The data were normalized as RPM (reads per million)

organism: Mus musculus

source_name: Neural progenitor cells

growth_protocol: Neural progenitor cells were maintained on a gelatin-coated culture plate in a NPC medium N2B27consisting of a 1:1 mixture of Neurobasal (Thermo Fisher Scientific) and DMEM/F12 (1:1) with L-glutamine and sodium bicarbonate (Thermo Fisher Scientific) supplemented with 1× N2 supplement (Thermo Fisher Scientific), 1× B-27 supplement (Thermo Fisher Scientific), additional 500 µM L-glutamine (Thermo Fisher Scientific), 10 µg/ml insulin (Wako) and 37.5 µg/ml bovine serum albumin (BSA) fraction V (Sigma-Aldrich) supplemented with 10 ng/ml EGF (Peprotech) and 10 ng/ml bFGF (Peprotech).

extract_protocol:
The ATAC-seq was performed as described previously (Buenrostro JD et. al., 2013, Nature Methods 10, 1213-8) with slight modifications. Five thousands of cells were isolated from each sample and lysed in 5 to 10 μl of ice-cold ATAC lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1 % IGEPAL CA-630) for 10 minutes.
Nuclear extraction step was skipped, and Illumina’s adaptors were ligated using transposase reaction mix of Nextera DNA Sample Preparation kit (Illumina), with incubation for 30 minutes at 37 ˚C. Indices were incorporated using Nextera Index Kit (Illumina) in amplification step. The libraries were purified using Ampure XP beads (Beckman Coulter Genomics) to remove remaining adapters

value: In vitro differentiated neural progenitor cells


title: ATAC_NPC_rep1


title: cPS1_22


title: cPS1_12


title: cPS1_10


title: cPS1_11


title: cPS1_13


title: B6_MK4

city: Cambridge

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options. Estimated counts from rsem were upper-quartile normalized where the 75th percentile was set to 1000.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample; Supplementary data file includes normalized counts.
Supplementary_files_format_and_content: LL_RNAseq_2017_rsem_est_counts_mm9.xlsx: estimated counts
Supplementary_files_format_and_content: LL_RNAseq_2017_normalized_counts_mm9.xlsx: normalized counts

molecule: polyA RNA

source_name: mouse pancreatic neuroendocrine tumor from C57Bl/6 (B6) strain background, treated with MK801

extract_protocol:
Total RNA was isolated using the miRNeasy kit from Qiagen
RNA libraries were prepared for sequencing with the Illumina TruSeq kit according to the manufacturer's instructions.

treatment_protocol: mPanNETs were collected from RIP1Tag2 mice ranging from 14-16 weeks old (end stage). Control mice were either not treated, or treated with normal saline for 3 days prior to sacrifice; MK801-treated mice were treated for 3 days prior to sacrifice (at 1mg/kg, i.p. once daily).

tag: genotype


title: B6_MK3


title: B6_MK2


title: B6_MK5


title: B6_MK1


title: cPS1_09


title: C3H_Ctr4

source_name: mouse pancreatic neuroendocrine tumor from C3HeB/Fe (C3H) strain background, without treatment/treated with normal saline

value: C3HeB/Fe (C3H)


title: C3H_Ctr3


title: cPS1_08


title: cPS1_29


title: cPS1_06


title: cPS1_04


title: cPS1_21


title: C3H_Ctr2


title: cPS1_01


title: C3H_Ctr1


title: cPS3_165


title: B6_Ctr6

source_name: mouse pancreatic neuroendocrine tumor from C57Bl/6 (B6) strain background, without treatment/treated with normal saline


title: B6_Ctr5


title: cPS3_164


title: cPS3_162


title: cPS3_161


title: cPS3_163


title: B6_Ctr4


title: B6_Ctr1


title: B6_Ctr2


title: cPS3_160


title: cPS1_05


title: cPS3_159


title: cPS3_156


title: cPS3_157


title: cPS3_158


title: Hi-C_NPC_SrfOE_rep2

data_processing:
Hi-C data mapping and bias correction:  Hi-C read pairs were individually mapped to the mouse genome (UCSC mm9) using the HiC-Pro pipeline (Servant et al. 2015) as the default parameter. After read mapping, each side of the mapped reads was applied to the hiclib pipeline (Imakaev et al. 2012) in the following steps (1. fragment level filtering, 2. binning at 200-kb non-overlapping genomic intervals, 3. bin level filtering, 4. bais correction (iterative correction)). In the hiclib pipeline, default parameter (in the tutorial) was applied to the each steps except for diagonal removal in step 3 as removing only the first diagonal(“removeDiagonal(0)” command). The biological replicates were merged after the fragment level filtering (step 1) as the merged data, and then the latter steps were applied.
A/B compartment analysis:  To generate A/B compartment profile of bias corrected Hi-C heatmap at 200-kb bins, "doCisPCADomains(domainFunction=”lieberman-”)” command as described previously (Lieberman, 2009) in the hiclib pipeline was used with removing only the first diagonal during the analysis. The first eigenvalues were used to identify A/B compartments. Positive or negative eigenvalues are arbitrary, so the correlation with GC contents was used to assign the positive eigenvalue as ‘A compartment’ and negative eigenvalues as ‘B compartment’.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

growth_protocol: Neural progenitor cells were maintained on a gelatin-coated culture plate in a NPC medium consisting of a NPC medium, N2B27 medium prepared as a 1:1 mixture of Neurobasal (Thermo Fisher Scientific) and DMEM/F12 (1:1) with L-glutamine and sodium bicarbonate (Thermo Fisher Scientific) supplemented with 1× N2 supplement (Thermo Fisher Scientific), 1× B-27 supplement (Thermo Fisher Scientific), an additional 500 µM L-glutamine (Thermo Fisher Scientific), 10 µg/ml insulin (Wako) and 37.5 µg/ml bovine serum albumin  (BSA) fraction V (Sigma-Aldrich) supplemented with 10 ng/ml epidermal growth factor (EGF) (Peprotech) and 10 ng/ml human basic fibroblast growth factor  (bFGF) (Peprotech).

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature. Glycine was added to 125 mM final concentration and incubated for 5 min at room temperature. Tubes were placed on ice for 15 min. Cells were washed in ice-cold PBS, and 1–2 × 106 fixed cell pellets were used for the following steps. Cell pellets were resuspended in 3C lysis buffer (10 mM Tris-HCl, 10 mM NaCl and 0.2% NP-40, pH 8.0) with 1× protease inhibitor cocktail (Roche) and incubated on ice for 20 min. After centrifugation, pellets were resuspended in 1.2× NEBuffer 2 (New England Biolabs) with 0.3% SDS and incubated for 1 h at 37 °C with constant shaking. Triton X-100 was subsequently added to a 2% final concentration, and samples were incubated for 1 h at 37 °C.  Samples were further incubated overnight at 37 °C with shaking after the addition of HindIII. After centrifugation, pellets were sequentially incubated in 1× NEBuffer 2 with 300 U HindIII for over 8 h at 37 °C with constant shaking in “Fill-in Mix” (1 × NEBuffer 2, 15 µM each of dATP, dGTP, dTTP and 15 µM Biotin-14-dCTP (Thermo Fisher Scientific) with 25 U Klenow (New England Biolabs)) for 45 min at 37 °C and in “Ligation Mix”  (1× T4 DNA ligase buffer (New England Biolabs) with 60 U/l of T4 DNA ligase (Thermo Fisher Scientific)) overnight at 16 °C. After Tris-HCl (pH 7.5) was added at 10 mM, samples were treated with 100 µg/ml RNase A for 30 min at 37 °C, subjected to reverse-crosslinking and proteinase K treatment overnight at 65 °C in the presence of 400 µg/ml proteinase K followed by incubation in 800 µg/ml proteinase K for an additional 2 h.  DNA was extracted by ethanol precipitation after treatment with phenol/chloroform twice and with chloroform once, and resolved in 10 mM Tris-HCl (pH 7.5) (Hi-C DNA). Hi-C DNAs were checked for quantity and quality by Qubit dsDNA HS Assay Kits (Thermo Fisher Scientific) and electrophoresis, respectively. To generate next generation sequencing libraries, Hi-C DNAs were mixed with “T4 DNA pol mix” (1× NEBuffer 2, 1× BSA, 100 µM dATP, 100 µM dGTP and 2.5 U of T4 DNA polymerase (New England Biolabs)) and incubated for 2 h at 12 °C. These DNAs were purified by ethanol precipitation after treatment with phenol/chloroform twice and with chloroform once, and resolved in nuclease-free water. DNAs were next sheared (300–500 bp) using the DNA Shearing System S220 (Covaris) and subjected to size selection using AMPure XP beads (Beckman Coulter). The size-selected DNAs were subjected to biotin pull-down using Dynabeads MyOne Streptavidin C1 (Thermo Fisher Scientific). The sequencing libraries were prepared using Nextera Mate Pair Sample Prep Kit (Illumina) and KAPA Real-Time Library Amplification Kit (KAPA Biosystems), and purification was done with AMPure XP beads.
10 ng of Hi-C DNA was used for construction of a library. To remove biotin from unligated ends, Hi-C DNA was mixed with 50 µl of “T4 DNA pol mix” (1× NEBuffer 2, 1x BSA, 100 µM dATP, 100 µM dGTP, 2.5 U of T4 DNA polymerase (NEB, M0203S)) and incubated for 2 h at 12°C. The sample volumes were brought up to 100 µl by adding 10 mM Tris-HCl (pH 7.5). Samples were extracted once each with phenol/chloroform and chloroform. After EtOH precipitation, the DNA pellets were resuspended in 130 µl of nuclease-free water. DNA samples were sheared (300–500 bp) using the following settings in Covaris S220 (Duty Factor: 5.0, Peak incident power: 175 W, Cycles per burst: 200, Treatment time: 120 sec) using microTUBE with snap cap (Covaris, 520045). After DNA shearing, DNA size selection was performed using AMPure XP beads (Beckman Coulter). Using the size-selected DNA samples, Biotin pull-down and sequencing library preparations were performed using 30 µl of Dynabeads MyOne Streptavidin C1 (Invitrogen, 65001) and a part of Nextera Mate Pair Sample Preparation kit (Illumina, FC-132-1001) following the kit’s protocol at half scale. For library amplification, KAPA Real-Time Amplification Kits (KAPA BIOSYSTEMS, KK2701) were used to determine the optimal PCR cycles (9–12 cycles) and the final PCR products were purified by AMPure XP beads. The quality of “Hi-C DNA” NGS libraries were measured by a Bioanalyzer High Sensitivity DNA chip. DNA was ligated with adaptors of Illumina TruSeq Library Preparation Kit (illumina).

value: Srf overexpression


title: cPS3_154


title: cPS3_155


title: B6_Ctr7


title: Hi-C_NPC_ActbKO2_rep1

value: Actb knockout


title: cPS3_153


title: Hi-C_NPC_control_rep1

value: control


title: Hi-C_NPC_ActbKO2_rep2


title: cPS3_152

extract_protocol:
Hamburger-Hamilton Stage 4 chicken embryos were collected in Ringer's solution. The primitive streak was dissected out using a fine tungsten needle, and the surrounding tissue (rest of the area pellucida) was collected separately.
Diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina).
scRNA-seq with ~40x multiplexing


title: Hi-C_NPC_ActbKO1_rep2


title: Hi-C_NPC_ActbKO1_rep1


title: cPS3_150


title: B6_Ctr3


title: cPS3_148


title: Hi-C_NPC_SrfOE_rep1


title: cPS3_149


title: cPS3_151


title: cPS3_146


title: cPS3_147


title: Hi-C_NPC_control_rep2


title: cPS3_144


title: cPS3_145


title: cPS3_143


title: cPS3_142


title: fvb-12wk-ERRBS-rep3

city: bronx

first: ying

last: cai

state: New York

address: 1300 morris park ave

institute: Albert Einstein College of Medicine

data_processing:
The reads were aligned to the mouse genome(mm10) with Bismark
Loci with at least 10* coverage and >20 qulity score (given by a customized script) was used
Genome_build: mm10
Supplementary_files_format_and_content: frequence of C or T at CpG loci in txt file

source_name: fvb-mammary-gland

extract_protocol:
Mammary tissue was snap-froze, later geonmic DNA was extracted using a phenol-chloroform method
Libraries were prepared according to Illumina's instructions.

tag: tissue

value: mammary gland

value: FVB

tag: disease state

value: healthy


title: pymt-10wk-ERRBS-rep3

source_name: pymt-early-carcinoma-tumor

value: PyMT

value: carcinoma

tag: tumor stage

value: early carcinoma at week 10


title: pymt-8wk-ERRBS-rep3

source_name: pymt-adenoma/MIN-tumor

value: adenoma/MIN at week 8


title: pymt-12wk-ERRBS-rep3

source_name: pymt-late-carcinoma-tumor

value: late carcinoma with lung metastasis at week 12


title: fvb-12wk-ERRBS-rep2


title: fvb-8wk-ERRBS-rep3


title: fvb-10wk-ERRBS-rep3


title: fvb-6wk-ERRBS-rep3


title: cPS3_141

data_processing:
Basecalls performed using CASAVA version 1.8.2
Some samples were discarded because they failed quality control (SinQC analysis, 19 cells, not included here)
Sequencing reads were mapped to Galgal4 using bowtie 0.12.9.
Gene expected counts were calculated using RSEM 1.2.3
Genome_build: Galgal4

value: White Leghorn

value: Chicken primitive streak cell

value: Hamburger-Hamilton Stage 4


title: fvb-8wk-ERRBS-rep2


title: cPS3_138


title: pymt-10wk-ERRBS-rep2


title: cPS3_140


title: fvb-12wk-ERRBS-rep1


title: fvb-10wk-ERRBS-rep1


title: cPS3_134


title: cPS3_135


title: cPS3_139


title: pymt-8wk-ERRBS-rep2


title: cPS3_137


title: cPS3_136


title: pymt-10wk-ERRBS-rep1


title: fvb-10wk-ERRBS-rep2


title: cPS3_132


title: fvb-8wk-ERRBS-rep1


title: cPS3_131


title: fvb-6wk-ERRBS-rep2


title: cPS3_133


title: pymt-12wk-ERRBS-rep1


title: cPS3_130


title: cPS3_129


title: fvb-6wk-ERRBS-rep1


title: cPS3_127


title: pymt-6wk-ERRBS-rep1

source_name: pymt-hyperplasia-mammary-gland

value: hyperplasia at week 6


title: cPS3_126


title: cPS3_121


title: cPS3_123


title: cPS3_122


title: cPS3_124


title: pymt-6wk-ERRBS-rep2


title: cPS3_125


title: cPS3_117


title: pymt-8wk-ERRBS-rep1


title: cPS3_118


title: cPS3_119


title: cPS3_116


title: cPS2_107


title: cPS2_110


title: cPS3_114


title: cPS2_111


title: cPS3_113


title: cPS2_105


title: cPS2_109


title: cPS2_108


title: cPS2_106


title: cPS2_103


title: cPS2_102


title: cPS2_101


title: cPS3_120


title: cPS2_99


title: cPS2_98


title: cPS2_96


title: cPS2_95


title: cPS2_94


title: cPS2_92


title: cPS2_93


title: cPS2_91


title: cPS3_115


title: cPS2_104


title: cPS_20


title: cPS2_85


title: cPS2_84


title: cPS2_90


title: cPS_23


title: cPS_21


title: cPS2_88


title: cPS2_89


title: cPS2_100


title: cPS2_86


title: cPS2_87


title: cPS_19


title: cPS_22


title: cPS_12


title: cPS_10


title: cPS_09


title: cPS2_97


title: Hfq mut exp RPF

city: Oxford

first: Irina

last: Chelysheva

address: Roosevelt Dr

department: NDM

country: United Kingdom

institute: University of Oxford

description: Ribosome protected RNA

data_processing:
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10
Adapter cutting using cutadapt, version 1.8.3, parameters -e 0.1 -O 1 -m 12
Genome mapping using Bowtie, version 1.1.2, parameters for samples 1-2: -v 2 --best --strata -m 1
Read counting using bedtools, version 2.17.0, parameter: -s, the middle nucleotide of each read was taken
Genome_build: U00096.3
Supplementary_files_format_and_content: Read counts were normalized by the length of the unique CDS per kilobase (RPKM) and the total mapped reads per million (RPM)

organism: Escherichia coli

source_name: E. coli CMA540(MG1693 ∆hfq::cat)

growth_protocol: Strains were grown in LB medium (Difco) supplemented with thymine (50 µg/ml) at 37ºC, unless otherwise stated. Overnight cultures of single fresh grown colonies were diluted to an initial OD600 appr. 0.03. Cultures were collected at exponential phase (OD600 appr. 0.5).

extract_protocol:
Total RNA was extracted using TRI Reagent (Sigma Aldrich), enriched by depleting small RNAs with GeneJET Purification Kit (Fermentas) and rRNA with MICROBExpres Bacterial mRNA Enrichment Kit (Ambion) and fragmented in alkaline solution (2 mM EDTA and 100 mM Na2CO3 pH 9.2 for 40 min at 95°C) to fragments with size of 24-35 nts. For RPFS, cells were lysed by freeze-rupturing (Retch Mill) and 100 A260 units of ribosome-bound mRNA fraction were directly used for polysomal analysis or subjected to nucleolytic digestion with 10 units/µl micrococcal nuclease (Fermentas) for 10 min at room temperature in buffer with pH 9.2 (10 mM Tris pH 11 containing 50 mM NH4Cl, 10 mM MgCl2, 0.2% triton X-100, 100 µg/ml chloramphenicol and 20 mM CaCl2) to obtain the monosomal fraction. Separation was obtained by sucrose density gradient (15-50% w/v). Subsequently, 20-35-nt RNA fragments from the monosomal fraction were size selected on a denaturing 15% polyacrylamide gel.
RNA-size selection and generation of the cDNA libraries was performed as described {Ingolia, 2009}

value: CMA540(MG1693 delta_hfq::cat)

tag: growth phase

value: Exponential


title: WT exp RPF

description: Ribosome protected RNA

source_name: E. coli MG1693


title: cPS_08


title: cPS_07


title: Hfq mut exp mRNA

description: total RNA


title: FP_45

city: Easter Bush

first: Jason

last: Ioannidis

state: Midlothian

address: Easter Bush Veterinary Campus

department: Developmental Biology

institute: The Roslin Institute

data_processing:
sRNAbench, v05/14
sRNAbench adapter trimming, v05/14, adapter = TGGAATTCTCGGGTGCCAAGG
sRNA bench mapping, v05/14, bowtie v0.12.9, 1 mismatch allowed, seed length 19, -n, -m 40 (bowtie parameter)
sRNAbench, v05/14, standard data normalisation (RPMM)
Genome_build: Btau_4.0
Supplementary_files_format_and_content: A single processed data file is provided, "processed_data.xlsx". The file consists of two spreadsheets, "Raw reads" which includes the raw reads obtained after analysis using sRNAbench , and "Normalised reads" which includes the normalised data (reads per million mapped, RPMM).

organism: Bos taurus

source_name: Plasma

extract_protocol:
RNA was extracted from 0.7 mL of plasma using TRIzol LS (Life Technologies, USA), following the manufacturer’s protocol. During the RNA extraction protocol, glycogen (40 μg; Sigma-Aldrich, USA) was added to each sample to facilitate the precipitation of RNA, and an exogenous miRNA control, syn-cel-miR-39-3p (5.6 x 108 copies per sample; Qiagen, NL), was spiked into each sample. RNA was re-suspended in 20 μL of RNase-free water and used immediately or frozen at -80 °C. 250 μL of whole blood cell suspension were homogenised using three volumes of TRIzol LS (Life Technologies, USA). The RNA extraction protocol provided by the manufacturer was followed for the remaining steps. RNA pellets were re-suspended in 10 μL of RNase-free water (Qiagen, NL) and frozen at -80 °C until further use.
Small-RNA libraries were prepared using the Illumina TruSeq small-RNA sample preparation kit (Illumina, USA) following the manufacturer’s protocol. Libraries were submitted to 36-base single-end sequencing using the Illumina HiSeq 2000 platform.

tag: subject id

value: Plasma

tag: Sex

value: female


title: cPS_28


title: FP_46


title: WT exp mRNA

description: total RNA


title: cPS_29


title: cPS_27


title: cPS_11


title: cPS_18


title: cPS_25


title: BC_46

source_name: Blood cells

value: Blood cells


title: FP_47


title: BC_45


title: cPS_17


title: BC_47


title: BC_44


title: cPS_15


title: cPS_14


title: cPS_13


title: cPS_26


title: FP_44


title: RpoB ∆crp 2

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

data_processing:
ChIP-exo reads were aligned to the ASM584v2 genome reference sequence using using bowtie v1.0.0 with parameters  -S
MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping.
Read count was calculated for each genomic position from sequence alignment, and 95% strongest intensity was used as background intensity.
For each peak detected with MACE, binding intensity was calculated by averaging read counts from two biological replicates and dividing by background intensity.
Genome_build: ASM584v2
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

source_name: acetate

growth_protocol: E. coli K-12 MG1655 cra-8myc tagged strains was grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate.

extract_protocol:
Crosslinked cells were then resuspended in 500 ul of lysis buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl and 1 mM EDTA) with 40 ul of protease inhibitor cocktail (50 mg in 0.25 ml of DMSO and 0.75 ml of TDW). Cells were lyzed with 1 ul of lysozyme for 30 min at 37oC on a rocker. 0.55 ml of 2X IP buffer (100 mM Tris-HCl (pH 7.5), 200 mM NaCl, 2% Triton X-100 and 1 mM EDTA) were added to the sample, and then was sonicated to fragmentize genomic DNA. 0.3 ml of Wash buffer I (50 mM Tris-HCl (pH 7.5), 140 mM NaCl, 1% Triton X-100 and 1mM EDTA) was added to make the volume up to 1.4 ml. Only 0.7 ml was taken and transfered to a new tube, and 10 ul of Anti-rpoB mouse antibody was added, and the sample was incubated overnight at 4 oC to make Antibody-TF complex. 50 ul of Dynabeads Pan mouse IgG were washed 3 times with bead washing solution (250 mg BSA in 50 ml of PBS), and were added to the sample. Cell lysate with beads were incubated for 6 hours or overnight at 4oC to make Dynabead-antibody-TF complex. The beads were pulled down on a magnet stand, and washed 2 times with wash buffer I and with wash buffer II (50 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1% Triton X-100 and 1mM EDTA), wash buffer III (10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1% Triton X-100 and 1mM EDTA), and wash buffer IV (10 mM Tris-HCl (pH 8.0), 1mM EDTA). The bead-bound TF-DNA complex was then end-repaired, dA-tailed, and ligated to the first adapter. Adapter-ligated sample was then treated with nick-repair reagent, and was treated with lambda exonuclease and RecJ exonuclease. Then DNA was eluted away from Dynabeads by incubating in 200 ul of elution buffer (50 mM Tris-HCl (pH 8.0), 1% SDS and 1 mM EDTA) at 65oC overnight. Protein was removed by treating 4 ul of protease K and being incubated at 55 oC for 2 hours, and by Phenol-Chloroform-IAA extraction. Purified DNA was used to bulid the second strand synthesis, followed by another dA-tailing, second strand ligation, and 3' overhang removal stpes. Then the sequencing library was amplified with PCR enrichment.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: E. coli cells were crosslinked in 1% formaldehyde for 25 minutes at RT on a rocker, then washed 3 times with 50 ml of ice-cold TBS (Tris buffered saline) each time.

value: delta-crp Knock-out strain

tag: chip antibody

value: anti-rpoB (Santa Cruz Biotech, sc-56766)


title: cPS_16

source_name: Chicken primitive streak


title: RpoB ∆crp 1


title: RpoB ∆cra 1

value: delta-cra Knock-out strain


title: RpoB ∆cra 2


title: cPS_03


title: RpoB WT 1

value: Wildtype


title: RpoB WT 2


title: cPS_01


title: cPS_02


title: Δcra glucose 2

data_processing:
Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0
Genome_build: NC_000913
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample.

growth_protocol: E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

tag: genotype/variation

tag: carbon source

value: glucose


title: Δcra acetate 1

value: acetate


title: Δcra fructose 1

value: fructose


title: Δcra fructose 2


title: Δcra acetate 2


title: Δcra glucose 1


title: WT acetate 1

value: WT


title: cPS_06

value: White Leghorn


title: WT fructose 2


title: WT fructose 1


title: WT glucose 1


title: DBZ treatment rep3

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilian University

data_processing:
Basecalling was done by RTA1.18.64
Truseq adapter and polyA were removed
reads were aligned to the human genome by STAR RNAseq read mapper
reads overlapping with annotated genes were counted with HTseq count
rlog transformation was done by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: raw count table from HTseq count and rlog tranformed expression values from DEseq2

growth_protocol: SW480 cells were suspended in 100 μl of a 1:1 mixture of PBS and growth factor-depleted Matrigel (Corning), and injected subcutaneously into 6-8 week old NOD/SCID mice (NOD.CB17-Prkdcscid, The Jackson Laboratory) for xenograft formation. Mice were randomly assigned to control or treatment groups when tumor volumes reached 100 mm3.

extract_protocol:
RNA was isolated from tumor xenografts using TRIzol (Invitrogen)
500ng of total RNA were used for library generation using mRNA SENSE kit from Lexogen strictly following the manufacturer's protocol

treatment_protocol: mice were treated daily with 1.25 mg selumetinib (AZD6244, Selleckchem) p.o. or 0.35 mg dibenzazepine (DBZ, Axon Medchem) i.p. for 5 days.

tag: agent

value: DBZ

value: xenograft


title: DBZ treatment rep2


title: DBZ treatment rep1


title: cPS_05

value: Chicken primitive streak cell

value: Hamburger-Hamilton Stage 4


title: Cra fructose 2

description: Immunoprecipitated DNA

source_name: cra-8myc tagged strain_fructose

extract_protocol:
E. coli cells were crosslinked in 1% formaldehyde for 25 minutes at RT on a rocker, then washed 3 times with 50 ml of ice-cold TBS (Tris buffered saline) each time.
Crosslinked cells were then resuspended in 500 ul of lysis buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl and 1 mM EDTA) with 40 ul of protease inhibitor cocktail (50 mg in 0.25 ml of DMSO and 0.75 ml of TDW). Cells were lyzed with 1 ul of lysozyme for 30 min at 37C on a rocker. 0.55 ml of 2X IP buffer (100 mM Tris-HCl (pH 7.5), 200 mM NaCl, 2% Triton X-100 and 1 mM EDTA) were added to the sample, and then was sonicated to fragmentize genomic DNA. 0.3 ml of Wash buffer I (50 mM Tris-HCl (pH 7.5), 140 mM NaCl, 1% Triton X-100 and 1mM EDTA) was added to make the volume up to 1.4 ml. Only 0.7 ml was taken and transfered to a new tube, and 15 ul of Anti-c-myc mouse antibody was added, and the sample was incubated overnight at 4C to make Antibody-TF complex. 50 ul of Dynabeads Pan mouse IgG were washed 3 times with bead washing solution (250 mg BSA in 50 ml of PBS), and were added to the sample. Cell lysate with beads were incubated for 6 hours or overnight at 4C to make Dynabead-antibody-TF complex. The beads were pulled down on a magnet stand, and washed 2 times with wash buffer I and with wash buffer II (50 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1% Triton X-100 and 1mM EDTA), wash buffer III (10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1% Triton X-100 and 1mM EDTA), and wash buffer IV (10 mM Tris-HCl (pH 8.0), 1mM EDTA). The bead-bound TF-DNA complex was then end-repaired, dA-tailed, and ligated to the first adapter. Adapter-ligated sample was then treated with nick-repair reagent, and was treated with lambda exonuclease and RecJ exonuclease. Then DNA was eluted away from Dynabeads by incubating in 200 ul of elution buffer (50 mM Tris-HCl (pH 8.0), 1% SDS and 1 mM EDTA) at 65C overnight. Protein was removed by treating 4 ul of protease K and being incubated at 55C for 2 hours, and by Phenol-Chloroform-IAA extraction. Purified DNA was used to bulid the second strand synthesis, followed by another dA-tailing, second strand ligation, and 3' overhang removal stpes. Then the sequencing library was amplified with PCR enrichment.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

tag: cultured in

value: M9 minimal media with 0.2% fructose

value: mid-log

value: anti-myc

tag: chip antibody vendor

value: Santa Cruz Biotech

tag: chip antibody cat. #


title: Cra acetate 1

description: Immunoprecipitated DNA

source_name: cra-8myc tagged strain_acetate

value: M9 minimal media with 0.2% acetate


title: WT glucose 2


title: Cra acetate 2

description: Immunoprecipitated DNA


title: Cra glucose 2

description: Immunoprecipitated DNA

source_name: cra-8myc tagged strain_glucose

value: M9 minimal media with 0.2% glucose


title: Cra fructose 1

description: Immunoprecipitated DNA


title: AZD treatment rep3

value: AZD


title: AZD treatment rep2


title: AZD treatment rep1


title: vehicle treatment rep3

value: vehicle


title: vehicle treatment rep1


title: Cra glucose 1

description: Immunoprecipitated DNA


title: WT acetate 2


title: Batch 3 EUI  NH4

city: Durham

first: Louis

middle: S

last: Tisa

state: NH

address: 46 College Rd

department: MCBS

institute: University of New Hampshire

data_processing:
Illumina Casava1.8.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to Frankia whole genome using CLC workstation
Genome_build: Frankia sp. strain EAN1pec; Frankia sp. strain EUN1f; Frankia sp. strain EuI1c
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Pseudofrankia inefficax

source_name: EuI1c_Nitrogen replete

growth_protocol: 2 days 28C in MP growth medium

extract_protocol:
Rneasy kit
Stable bacterial RNA removal via the Microbexppress kit.   RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Growth under nitrogen replete or nitrogen deficient condition

value: Frankia EuI1c

tag: culture condition

value: Nitrogen replete

tag: temperature

tag: days incubation

value: 2 days


title: Batch 4 EUI  NH4

tag: strain


title: Batch 3 EUI N2

source_name: EuI1c_Nitrogen stressed

value: Nitrogen stressed


title: Batch 4 EUI  N2


title: Batch 1 EUI  N2


title: Batch 1 EUI  NH4


title: Batch 4 EUN  NH4

organism: Parafrankia sp. EUN1f

source_name: EUN1f_Nitrogen replete

value: Frankia EUN1f


title: Batch 3 EUN  N2

source_name: EUN1f_Nitrogen stressed


title: Batch 4 EUN  N2


title: Batch 4 EAN  NH4

organism: Parafrankia sp. EAN1pec

source_name: EAN1pec_Nitrogen replete

value: Frankia EAN1pec


title: Batch 3 EAN  N2

source_name: EAN1pec_Nitrogen stressed


title: Batch 1 EAN  N2


title: vehicle treatment rep2

tag: tissue

value: xenograft


title: Batch 3 EUN  NH4


title: Batch 1 EAN  NH4


title: Batch 4 EAN  N2


title: Batch 3 EAN  NH4


title: Batch 1 EUN  N2


title: ZF4-18-30d rep2

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

country: China

institute: Zhejiang University

description:
Cold_FPKM
4_1

data_processing:
Illumina Casava1.8 software used for basecalling.
Clean RNA-seq reads for each sample were aligned by HISAT2 (2.1.0) with default setting to the zebrafish genome assembly (GRCz10)
Transcripts were assembled by StringTie (1.3.3) with parameter “-G Danio_rerio.GRCz10.88.gtf”
all assemblies were merged together utilizing StringTie’s “merge” function
CPC (Coding Potential Calculator), CNCI (Coding Non-Coding Index) and Pfam were used to delete transcripts with coding potential
The  genes expression levels were estimated by FPKM (fragments per kilobase of exon per million fragments mapped) and assessed using StringTie
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for novel lncRNAs

organism: Danio rerio

growth_protocol: The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection (ATCC CRL 2050; Driever and Rangini, 1993).  The cells were grown at 28 °C, 5% CO2, in Dulbecco's modified Eagle's medium/F12 nutrient mix (DMEM/F12) supplemented with 10% FBS, 1% l-glutamine, 100 u/ml penicillin, 100 μg/ml streptomycin.  For cold treatment, cells were grown at 18 °C, 5% CO2, in the same medium for up to 30 days.  All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd (USA).

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (217004, Qiagen) and purified by RNAClean XP Kit (A63987, Beckman Coulter) and RNase-Free DNase Set (79254, Qiagen).
Libraries were constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero (RS-122-2301/ RS-122-2302, Illumina). Libraries were pooled and sequenced using the Illumina HiSeq machine as 150-bp paired-end sequencing reads.

tag: cell line

tag: cell type

value: embryonic fibroblast cell line

tag: cultured at

value: 18°C for 30 days

tag: sample group

value: cold treatment for 30 days


title: ZF4-18-30d rep3

description:
Cold_FPKM
6_1

treatment_protocol: For cold treatment, cells were grown at 18 °C, 5% CO2, in the same medium for up to 30 days.


title: JNA-019649

city: Kansas City

first: Sufi

middle: Mary

last: Thomas

state: Kansas

address: 3901 Rainbow Blvd. Mail Stop 4031

department: Otolaryngology-Head & Neck Surgery

institute: University of Kansas Medical Center

data_processing:
The mRNA fraction is enriched with oligo dT capture, sized, reverse transcribed into complementary DNA (cDNA) and ligated with the appropriate indexed adaptors using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina RS-122-2101/2102)
Following Agilent Bioanalyzer QC of the library preparation and library quantification using the Roche Lightcycler96 with KAPA SYBR Fast Universal quantitative polymerase chain reaction (qPCR) kit (KAPA Biosystems KK4601), the RNA-Seq libraries were adjusted to a 4nM concentration and pooled for multiplexed sequencing
Libraries were denatured and diluted to the appropriate pM concentration (based on qPCR results) followed by clonal clustering onto the sequencing flow cell using the TruSeq Paired-End (PE) Cluster Kit v3-cBot-HS (Illumina PE401-3001)
The clonal clustering procedure is automated using the Illumina cBOT Cluster Station.  The clustered flow cell was sequenced on the Illumina HiSeq 2500 Sequencing System using the TruSeq SBS Kit v3-HS (Illumina FC401-3002).
Following collection, sequence data was converted and de-multiplexed (if required) into individual sequenced reads, which were mapped to the human genome (assembly GRCh38.rel77) using the STAR software.
Transcript abundance estimates were generated using the Cufflinks software and measured in fragments per kilo base per million reads (FPKM). Differential gene expression estimates were calculated using the Cuffdiff software
The statistical significance of the fold-changes was adjusted for multiple hypothesis testing by the Benjamini & Hochberg method. A false discovery rate (FDR) of 0.05 or less was set as the significance cutoff.
Ingenuity Pathway Analysis (IPA) software (Ingenuity Systems, Redwood City, CA) was used to examine upstream regulators, biological functions, and signaling pathways limited to the data set of differentially expressed genes with a FDR ≤ .05 and fold change of ±1.5.
Genome_build: Human genome assembly GRCh38.rel77
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for gene expression, fold changes, p-value, and false discovery rate (q-value) for junvenile nasopharyngeal angiofibroma fibroblasts (JNA) compared to normal adult tonsillar fibroblasts (NF)

source_name: juvenile nasopharyngeal angiofibroma

growth_protocol: Tumor and tonsil fibroblast cells were cultured in Dulbecco modified Eagle medium to confluence.

extract_protocol:
RNA was harvested using the Trizol method. Stranded mRNA-sequencing was performed using the Illumina HiSeq2500 Sequencing System.
Total RNA (0.5ug) was used to initiate the TruSeq Stranded mRNA-Seq library preparation protocol.

treatment_protocol: Tumor and tonsil explants were minced with collagenase and incubated at 37°C for 5 minutes. Collagenase was removed by centrifugation and tissue was resuspended and plated at 37°C in a 5% CO2 incubator in Dulbecco modified Eagle medium (DMEM) containing 10% heat-inactivated fetal bovine serum (FBS) and a penicillin/streptomycin/ampohotericin B antibiotic cocktail. Seeded cells were grown to confluence, and maintained in DMEM with 10% FBS without antibiotic cocktail.

value: fibroblast

value: juvenile nasopharyngeal angiofibroma

tag: passage #


title: NF-010209-2

source_name: adult tonsil

value: tonsil


title: JNA-019296


title: ZF4-28 rep2

description:
Con_FPKM
3_1

value: normal condition (28°C)

value: control


title: ZF4-28 rep3

description:
Con_FPKM
5_1


title: ZF4-28 rep1

description:
Con_FPKM
1_1


title: virE3_induced

city: Leiden

first: Paul

last: van Heusden

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

data_processing:
Raw sequencing data were processed using CLC Genomic Workbench version 4.6.
Genome_build: Processed reads were aligned to the A. thaliana annotated coding sequences (TAIR v10; www.arabidopsis.org).
Supplementary_files_format_and_content: text file

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana, containing T-DNA with virE3 under control of a tamoxifen-inducible promoter.

growth_protocol: Seedlings were transferred to a 50 ml polypropylene tube containing 10 ml liquid ½ MS medium  without antibiotics. Tubes were incubated at 21 °C at 120 rpm for four additional days.

extract_protocol:
For RNA isolation, the frozen plantlets were ground under liquid nitrogen in a TissueLyser II (Qiagen). RNA was isolated with the RNeasy Mini Kit (Qiagen), using the optional on-column DNAse treatment.
mRNA was used as input for the Illumina TruSeq RNA sample preparation kit v2 with adaptations. The mRNA fraction was purified from total RNA by polyA capture, fragmented and converted to double-stranded cDNA using random hexamers. DNA adapters including sample-specific barcodes were ligated to both ends of the DNA fragments and subjected to PCR amplification.

treatment_protocol: Treatments with tamoxifen were performed by adding 10 µl of 10 µM tamoxifen dissolved in DMSO. In control incubations 10 µl of DMSO was added. Four hours after the addition of tamoxifen or of DMSO the plantlets were rapidly frozen in liquid nitrogen.

tag: line

value: expressing virE3

tag: sample type

value: induced plantlets


title: Control_induced

source_name: Arabidopsis thaliana, containing T-DNA with tamoxifen-inducible promoter.


title: Control_non-induced

value: non-induced plantlets


title: virE3_non-induced


title: Batch 1 EUN  NH4

value: Nitrogen replete


title: Non-stressed WT plants

city: Wuhan

first: Xiaoming

last: Sun

state: Hubei

address: Lumo road, No. 1

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

data_processing:
RNA-Seq data analysis was performed on the AIR platform (www.transcriptomics.cloud). More specifically, the quality of the raw reads was checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and then a trimming step was performed to remove low quality bases and sequencing adapters with the tool BBDuk (https://sourceforge.net/projects/bbmap/). A minimum Phred-like score of 25 was set and a minimum length of the reads of 25 nt.
High quality reads were then mapped on the reference genome (TAIR10) of Arabidopsis with STAR (https://github.com/alexdobin/STAR). Based on the distribution of samples in a first PCA plot, the two most similar replicates per condition were considered for further statistical analyses.
Read summarization was then performed with featureCounts (http://bioinf.wehi.edu.au/featureCounts/) using only the reads with a mapping quality higher than 30. The statistical analysis was performed with R. Specifically, lowly expressed genes were removed with the package HTSFilter (http://www.bioconductor.org/packages/release/bioc/html/HTSFilter.html), selecting "TMM" as the normalization method.
Then, the filtered genes were used to perform a differential analysis with EdgeR. Genes were considered statistically differentially expressed if the corrected p-value was lower than 0.05.
Genome_build: Arabidopsis thaliana Col-0 TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample.

source_name: Whole plants

growth_protocol: Seeds of Arabidopsis thaliana (ecotype Columbia-0) were surface-sterilized with 6% sodium hypochlorite for 5 min followed by three washes with sterile water and then plated on 1/2 MS solid medium containing 0.7% agar. One-week-old seedlings were transferred from plates into pots filled with peat moss in a greenhouse under controlled environmental conditions, at 22 °C, under 50%–60% relative humidity, and under 130 µmol photons m−2 s−1 with a 16 h/8 h light/dark cycle.

extract_protocol:
The 3-week old wild-type and VaAQUILO-overexpressing Arabidopsis growing under normal condition were used to construct mRNA libraries. Total RNA was extracted from collected samples using Column Plant RNAOUT 2.0 kit (Tiandz, Beijing, China), following the instructions of the manufacturer. RNA concentration and quality were detected using Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: RNA-Seq analysis was performed using 3-week-old transgenic Arabidopsis mixture and WT plants under normal and cold stress (treated at 4°C for 3 days) conditions.

value: Whole plants

tag: age

value: 3-week old

tag: genotype

value: Wild type

tag: condition

value: non-stressed


title: Non-stressed VaAQUILO-overexpressing plants

value: VaAQUILO-overexpressing


title: NF-010209-3


title: Stressed WT plants

value: stressed


title: ZF4-18-30d rep1

description:
Cold_FPKM
2_1

value: embryonic fibroblast cell line

value: 18°C for 30 days


title: ssrp1 WT EM BS-seq

status: Public on Apr 17 2018

city: Berkeley

first: Jennifer

middle: M

last: Frost

state: CA

address: 231 Koshland Hall

department: Plant and Microbial Biology

institute: University of California, Berkeley

data_processing:
We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts
Converted reads were aligned to the converted Col and Ler scaffolds, allowing up to two mismatches per read.
100 base reads were divided into the first 50 and the last 50 bases. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Reads that aligned to either Col or Ler with fewer mismatches were assigned to that ecotype.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
Genome_build: TAIR8 and TAIR10
Supplementary_files_format_and_content: All files are in GFF format. Files contain fractional methylation data either for individual cytosines (single-c) or in 50 bp windows.

source_name: ssrp1 WT EM BS-seq

growth_protocol: Arabidopsis thaliana were grown in controlled long-day (16 hours light, 8 hours dark) conditions in a greenhouse at UC Berkeley

extract_protocol:
Arabidopsis flower buds were emasculated at flower stage 12-13 using fine forceps and pollinated with Ler pollen 48 hours later. Eight to ten days after pollination (DAP) developing F1 seeds (torpedo to bending cotyledon stage) were immersed in dissection solution (filter-sterilized 0.3 M sorbitol and 5 mM pH 5.7 MES) on sticky tape and dissected by hand under a stereo-microscope using fine forceps (Fine Science Tools, Inox Dumont #5) and insect mounting pins. The seed coat was discarded, and debris removed by washing collected embryos or endosperm five to six times with dissection solution under the microscope.  For ssrp1-3 and spt16-3 mutant normal and delayed sibling seed collection, seeds were divided into fractions according to embryo development. At 8 DAP, delayed seeds tended to be at the torpedo to early-linear cotyledon stages, whereas normally developing seeds were late-linear cotyledon to bending cotyledon stages.  Seeds with an intermediate developmental stage were discarded. Vegetative cell and sperm nuclei were extracted from mature pollen and fractionated by fluorescence activated cell sorting as described previously.
50 ng of genomic DNA was fragmented by sonication, end repaired and ligated to custom-synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer's instructions for gDNA library construction (Illumina).  Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen) as outlined in the manufacturer's instructions. The bisulfite-converted library was split between two 50 ul reactions and PCR amplified using the following conditions: 2.5 U of ExTaq DNA polymerase (Takara Bio), 5 _l of 10X Extaq reaction buffer, 25 _M dNTPs, 1 _l Primer 1.1 and 1 _l multiplexed indexing primer.  PCR reactions were carried out as follows: 95¼C for 3 minutes, then 14-16 cycles of 95 ¼C 30 s, 65 ¼C 30 s and 72 ¼C 60 s. Enriched libraries were purified twice with AMPure beads (Beckman Coulter) prior to quantification with the Qubit fluorometer (Thermo Scientific) and quality assessment using the DNA Bioanalyzer high sensitivity DNA assay (Agilent)

tag: maternal genotype

value: ssrp1/+ Col

tag: paternal genotype

value: Wild-type Ler

tag: f1 genotype

value: wild-type Col/Ler hybrid

tag: tissue/cell type

value: Embryo


title: E17 rep2

city: Bordeaux

first: Katarzyna

middle: B

last: Hooks

address: 146, rue Léo Saignat

department: CBIB

country: France

institute: Univ. Bordeaux

data_processing:
Real time analysis (RTA) software used for basecalling.The reads were demultiplexed with bcl2fastq and quality checked with FastQC.
For each sample all resulting reads were mapped to both human (GRCh38) and chicken (GalGal4) genomes plus transcripts by hisat2 (2.0.3-beta) with default settings. Reads or read pairs that simultaneously mapped to both genomes were excluded.
Only those reads that mapped uniquely to either human or chicken genome were summed-up at the gene level (Ensembl 82) by featureCounts.
Genome_build: GRCh38, Gallus_gallus-4.0
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts per Sample

source_name: Chorioallantoic membrane (CAM)

growth_protocol: Huh6 cells were grown at 37°C in a humidified atmosphere of 5% CO2 in D-MEM Glutamax, 1g/L D-glucose (Gibco) supplemented with 10% fetal calf serum (FCS, Sigma), 100 U/ml of penicillin and 100 μg/ml streptomycin (Gibco). The identity of the cells was verified once a year by Short Tandem Repeat (STR) profiling (LGC Standards) and found to be identical to original Huh6 markers. Fertilized chick embryos were handled as described in Hagedorn et al. (2005) PNAS. For implantation 1x10^6 cells were included in 40μL Matrigel® (50% culture medium/50% Matrigel®, growth factor reduced, Corning), incubated 45 minutes at 37°C for polymerization and then deposited on the CAM after mild laceration of the membrane.

extract_protocol:
At indicated days tumors or non-implanted CAMs were isolated, washed in PBS and snap frozen in liquid nitrogen. RNA extraction was carried out using the mirVanaTM Isolation Kit (Ambion) according to the manufacturer's protocol (see Fig. 1). RNAs of Huh6 cells in culture were also extracted with the same kit according to the manufacturer's protocol. RNA quality was verified using Agilent RNA 6000 Nano kit on an Agilent 2100 Bioanalyzer (Agilent Technologies).
Four μg of RNA were used to generate sequencing library using the TruSeq Stranded mRNA Sample Preparation kit (Illumina) according to the standard protocol. Library preparation and sequencing were performed by the MGX-Montpellier GenomiX platform.

value: CAM derived cells

tag: developmental day


title: E17 rep3


title: ssrp1/+ ES BS-seq rep1

source_name: ssrp1/+ ES BS-seq

value: ssrp1/+ Col/Ler hybrid

value: Endosperm


title: ssrp1 WT ES BS-seq rep1

source_name: ssrp1 WT ES BS-seq


title: E14 rep3


title: E17 rep1


title: E14 rep2


title: E11 rep2


title: E14 rep1


title: ssrp1/+ EM BS-seq

source_name: ssrp1/+ EM BS-seq


title: E11 rep3


title: E11 rep1


title: T7 rep2

description:
counts_mapped2GR38.txt
counts_mapped2galgal.txt

source_name: Hepatoblastoma cell line

value: HuH6 hepatoblastoma cell line on CAM

tag: passages


title: T4 rep1


title: T7 rep1


title: T4 rep2


title: T4 rep3


title: T7 rep3


title: Stressed VaAQUILO-overexpressing plants

tag: tissue


title: T1 rep3


title: Pol2-SETD7-WT_rep2

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

description: Pol2 ChIP-seq

data_processing:
For Illumina ChIP-seq: ChIP-seq: bowtie -p 4 -q -m 1 -v 3 --sam --best --strata /data/bowtie_index/hg19
For RNA-seq: STAR --genomeDir hg19_gencodev19_ERCC --readFilesIn H7CM_D0_rep1_R1.fastq.gz H7CM_D0_rep1_R2.fastq.gz --readFilesCommand zcat --runThreadN 4
For RNA-seq: featureCounts -T ${CORES} -t exon -g gene_name -s 1 -a hg19.GTF -o mRNA_counts.txt
Genome_build: hg19
Supplementary_files_format_and_content: Text. RNA-seq: DESeq normalized expression. ChIP-seq: DESeq normalized enrichment levels at genebodies.

source_name: SETD7 WT Mesoderm stage cells differentiated from HES3

growth_protocol: hESCs were maintained in chemically defined medium Essential 8 (E8 medium) (Life Technologies) on Matrigel-coated (BD Bioscience, San Jose, CA) plates at 37°C with 5% (vol/vol) CO2.

extract_protocol:
(RNA-seq) iPSC-CMs were detached from cell culture plates and RNA was extracted using a microRNeasy kit (QIAGEN). (ChIP-seq) Lysates were clarified from sonicated nuclei and Protein-DNA complexes were isolated with antibody.
(RNA-seq) RNA libraries were prepared for sequencing using standard Illumina protocols. (ChIP-seq) ChIP-seq libraries were prepared for sequencing using The Ion Proton™ System protocols or NEBNext DNA Library Prep Master Mix Set for Illumina kit (E6040S).

treatment_protocol: hESCs were grown to 90% confluence and subsequently differentiated into beating cardiomyocytes, using a small-molecule-based monolayer method described previously (Cell Stem Cell. 2015 Jul 2;17(1):89-100).

tag: chip antibody cat#

tag: chip antibody vender

value: BioLegend


title: H3K36me3-KO

description: H3K36me3 ChIP-seq

source_name: SETD7 KO Mesoderm stage cells differentiated from HES3

tag: cell type

value: Active Motif


title: H3K36me3-WT

description: H3K36me3 ChIP-seq

value: SETD7 WT Mesoderm stage cells differentiated from HES3


title: T1 rep1


title: Pol2-SETD7-WT_rep1

description: Pol2 ChIP-seq


title: T1 rep2


title: 10T12_Input_repII

city: Berlin

first: Cornelius

last: Fischer

state: Berlin

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine (MDC)

data_processing:
Basecalling was performed using Illumina's CASAVA pipeline version 1.8
Reads from the same sample from different lanes were merged
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2
Low quality reads were removed using smatools with the following configuration: samtools view -b -h -q 42 -F 1024
Reads were removed if aligned to simple repeat regions using intersectBed from bedtools
Peak calling was done using MACS2 with the following configuration: macs2 callpeak -t treatment -c [control/input] -g mm -q 0.01 -f BAM
Only peak intervals that overlepped in replicates constituded the final peak dataset.
Genome_build: mm10

growth_protocol: C3H10T1/2 and 3T3-L1 cells (ATCC) were cultured according to the provider's instructions.

extract_protocol:
ChIP analyses in 3T3-L1 and C3H10T1/2 cells were performed as described previously (Schupp, M. et al. Retinol saturase promotes adipogenesis and is downregulated in obesity. Proc. Natl. Acad. Sci. U.S.A. 106, 1105–1110 (2009)). Approx. 100 µg of sonicated chromatin extracts were used for each IP and incubated with 10 µg of a GATA2 antibody (sc-9008x, Santa Cruz) overnight.
For deep sequencing ChIP samples (100-150ng of pooled DNA derived from individual CHIP experiments) were first amplified using the ChIP-Seq Sample Prep Kit (Illumina) according to the manufacturers instructions.

tag: cell line

tag: chip antibody


title: 10T12_ChIPseq_repI

value: GATA2 (sc-9008x, Santa Cruz)


title: 10T12_Input_repI


title: 3T3-L1_Input_repII

value: 3T3-L1 (ATTC)


title: 3T3-L1_Input_repI


title: 3T3-L1_ChIPseq_repII


title: Pol2-SETD7-MT-1_rep1

description: Pol2 ChIP-seq

value: SETD7 KO Mesoderm stage cells differentiated from HES3


title: 10T12_ChIPseq_repII


title: Pol2S2P-SETD7-WT_rep1

description: Pol2-S2P ChIP-seq

value: Abcam


title: Pol2S2P-SETD7-WT_rep2

description: Pol2-S2P ChIP-seq


title: Pol2S2P-SETD7-MT-1_rep2

description: Pol2-S2P ChIP-seq


title: 3T3-L1_ChIPseq_repI


title: Pol2S2P-SETD7-MT-1_rep1

description: Pol2-S2P ChIP-seq


title: NR_DNA_F1i

city: Taipei

first: Hsien-Sung

last: Huang

address: Rm: 1547, 15th Floor, No.1, Sec.1, Ren-ai Rd.

country: Taiwan

institute: National Taiwan University

description: DNA was extracted from normal light-reared mouse tails with B6/CAST mixture background

data_processing:
ConDeTri was implemented to trim or remove the reads according to the quality score. Qualified reads after filtering low-quality data were analyzed using TopHat/Cufflinks for gene expression estimation. The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads). For differential expression analysis, CummeRbund was employed to perform statistical analyses of gene expression profiles.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene ID, Associated gene name, Description, Gene Biotype, Locus, FPKM
Supplementary_files_format_and_content: Three sets of processed data files for each RNA-Seq data;  The ASE (allele-specific expression), gene expression, and gene isoform expression analysis

extract_protocol:
RNA was extracted using a NucleoSpin miRNAKit (Macherey-Nagel, 740971). Genomic DNA was extracted using NucleoSpin Tissue (Macherey-Nagel, 740952)
Library for RNA-Seq was built up using a SureSelect Strand-Specific RNA Library Prep Kit (Agilent Technologies, G9691A).

tag: strain background

value: hybrid of B6 and CAST

tag: strain

value: F1i; offspring from female CAST and male B6 mating

value: Postnatal day 28

tag: sample group

value: normal-reard

value: Tail

tag: ngs id

tag: date


title: DR_MC_F1i

description:
processed data file:
103821_1223_ASE.xlsx
103821_1223_gene.xlsx
103821_1223_isoform.xlsx

tag: age

value: dark-reard

value: Motor cortex


title: DR_SCN_F1i

value: SCN


title: DR_MC_F1r

value: F1r; offspring from female B6 and male CAST mating


title: DR_SCN_F1r


title: DR_VC_F1r_2

value: Visual cortex


title: DR_Retina_F1i

value: Retina


title: DR_VC_F1r_1


title: DR_VC_F1i


title: NR_SCN_F1i

description:
processed data file:
103961_retina_SCN_ASE103961.xlsx
103961_retina_SCN_gene.xlsx
103961_retina_SCN_isoform.xlsx


title: NR_Retina_F1r

description:
processed data file:
103888_retina_SCN_ASE.xlsx
103888_1230_gene.xlsx
10388_1230_isoform.xlsx


title: NR_SCN_F1r


title: Pol2-SETD7-MT-1_rep2

description: Pol2 ChIP-seq

value: BioLegend


title: NR_MC_F1r

description:
processed data file:
103251_103407_ASE_FOR_REV.xlsx
103251_103407_gene_expression.xlsx
103251_103407_isoform_expression.xlsx


title: NR_MC_F1i


title: NR_VC_F1r


title: DR_Retina_F1r


title: Dentate gyrus_DBS_HZ5177

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

description: Whole-genome bisulfite-Seq

data_processing:
Read alignment using bismark with parameters -n 1 -l 50 --bowtie2 -N 0 and -L 25
Extract context-dependent (CpG/CHG/CHH) methylation using bismark_methylation_extractor with parameters -p --comprehensive --no_overlap
CpG, CHG, CHH specific cytosine reports are genarated using coverage2cytosine script from bismark with 10 minimum read cutoff.
Genome_build: mm10
Supplementary_files_format_and_content: Text file summarizing number of methylated and un-methylated cytosines.

source_name: Dentate gyrus, DBS

growth_protocol: They were group-housed with up to five mice per cage prior to surgery and individually housed with nesting material in the cage after surgery. They were maintained on a 14h light:10h dark cycle (light on at 06:00) with standard mouse chow and water ad libitum in our AAALAS-accredited facility. All experimental procedures and tests were conducted during the light cycle.

extract_protocol:
Genomic DNA was extracted from two wildtype sham and two wildtype DBS mice using the Quick-DNATM Universal Kit (ZymoResearch catalog #: D4068) according to the kit instructions for solid tissues.
Library generation from bisulfite treated DNA was performed using the Illumina TruSeq DNA Methylation Kit (Illumina, San Diego, CA) according to the manufacturer's instructions.

treatment_protocol: Mice were unilaterally implanted at 6 weeks of age with a bipolar stimulating electrode directed to the fimbria-fornix (FF) and a recording electrode placed in the CA1 and dentate gyrus regions of the hippocampus, respectively. After a two-week recovery period, the mice were assigned to either the DBS group or the sham group, and acute DBS or sham treatment was performed in 8-9 weeks old mice. Both groups were exposed to identical conditions except the sham group did not receive electrical stimulation. DBS parameters used were 45 minutes of DBS (130 Hz, 60μs, 50μA) with a 20-minute recovery period prior to euthanasia.

tag: genotype

value: wild type

tag: treatment

value: DBS

value: Dentate gyrus


title: NR_VC_F1i


title: Dentate gyrus_SHAM_HZ5176

description: Whole-genome bisulfite-Seq

source_name: Dentate gyrus, SHAM

value: SHAM


title: HZ42229

city: Cambridge

first: Ayush

middle: T

last: Raman

address: 75 Ames St

department: Epigenomics Program

institute: Broad Institute of MIT and Harvard

data_processing:
The quality of raw reads was assessed using FastQC (Andrews S. 2010). The average per base quality score across all the files were greater than 34 and had passed all the major tests.
The raw reads were aligned to the Mus musculus genome (Gencode Version M10 -- Ensembl 85) using STAR v2.4.2a (Dorbin et al. 2013). The mappability of unique reads for each sample was approximately 92%. The raw counts were computed using quantMode function in STAR. The obtained read counts are analogous to the expression level of each gene across all the samples. RNA libraries were prepared in two batches, and sequencing was performed in three batches. Therefore, we used batch as a covariate in our model for differential expression analysis using DESeq2 (Love et al. 2014).
Genes with raw mean reads greater than 40 (i.e., ~15,568 genes) were used for normalization and differential gene expression analysis using DESeq2 package in R. Wald test defined in the DESeq function of the package was used for differential expression analysis and shrunken log fold-changes (i.e., obtaining reliable variance estimates by pooling information across all the genes) were used for further analysis.
Genome_build: mm10 (Gencode Version M10 -- Ensembl 85)

source_name: Dentate gyrus

extract_protocol:
RNA extraction and purification was performed using the Aurum™ Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad 7326830) per the kit instructions, and genomic DNA was eliminated using an on-column DNase digestion step.
The TruSeq RNA Library Prep Kit v2 (Illumina RS-122-2001) and 250ng of total RNA was used to make each library, and ERCC RNA Spike-In Mix 1 or 2 (Thermo Fisher 4456740) was added to the samples prior to library preparation. Samples were paired end sequenced (PE100) on a HiSeq2500 in high-output mode using the v4 sequencing kit (Illumina; SBS: FC-401-4003, paired-end flow cell: PE-401-4001).

value: KO

tag: batch


title: HZ42239


title: HZ42315

value: WT

value: Batch 2


title: HZ42241


title: Dentate gyrus_DBS_HZ5175

description: Whole-genome bisulfite-Seq


title: HZ42226


title: HZ42231


title: HZ42225

value: Batch 1


title: HZ42233

value: Sham


title: HZ42230


title: Dentate gyrus_SHAM_HZ5174

description: Whole-genome bisulfite-Seq


title: HZ42222_1

description:
WT_Sample1_sham
HZ42222 sample was sequenced on two separate occasions, that’s why we named it as HZ42222_1 and HZ42222_2. HZ42222_2 has more reads as compared to HZ42222_1


title: HZ42234


title: HZ42222_2

description:
WT_Sample3_sham
HZ42222 sample was sequenced on two separate occasions, that’s why we named it as HZ42222_1 and HZ42222_2. HZ42222_2 has more reads as compared to HZ42222_1

value: Batch 3


title: pancreas_388

city: Stony Brook

first: Agnieszka

middle: B.

last: Bialkowska

address: HSC-T17 Room 090

department: Dept. of Medicine

institute: Stony Brook University

data_processing:
The reads were aligned with STAR (version 2.4.0c) to GRCm38.p3, and genes annotated in Gencode vM5 were quantified with featureCounts (v1.4.3-p1).
Normalization and differential expression was done with the Bioconductor package DESeq2.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: tab-delimited text files include counts of reads of each aligned transcript in each sample

source_name: pancreas

extract_protocol:
total RNA was extracted using PureLink RNA Extraction Kit (ThermoFisher)
RNA sequencing libraries were prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (kapabiosystems) in accordance with the manufacturer’s instructions.

treatment_protocol: To induce Cre recombinase activity in both spontaneous PanIN formation study and pancreatitis-induced PanIN formation study, 3 injections of tamoxifen (3 mg/injection) dissolved in corn oil or corn oil control was injected intraperitoneally on alternating days. To induce pancreatitis 48 hours after last tamoxifen injection in pancreatitis-induced PanIN formation study, mice were injected with 100µl of cerulein at 50µg/ml concentration in PBS hourly for 6 hours on 2 consecutive days.

value: 3 Tam, 2 Cer, 2 days post

value: pancreas


title: pancreas_342


title: NR_Retina_F1i

value: hybrid of B6 and CAST

value: F1i; offspring from female CAST and male B6 mating

value: Postnatal day 28

value: normal-reard


title: pancreas_329


title: pancreas_386


title: pancreas_356


title: pancreas_319


title: pancreas_328


title: pancreas_308


title: HZ42223


title: HZ42236


title: HCN3+ sample 2

city: Toronto

first: Norman

last: Rosenblum

state: ON

address: 686 bay st

country: Canada

institute: Hospital for sick children

data_processing:
Sequencing platform: Illumina HiSeq 2500 1 lane
sequencing data is in FASTQ format generated using bcl2fastq2 v2.17. The quality of the data is assessed using FastQC v.0.11.2
Adaptors are trimmed using using Trim Galore V0.40 running Cutadapt V. 1.8 with the following parameters: -q 20 – the reads are trimmed from the 3' end base by base, trimming stops if the quality of the base is greater then 20;--illumina – 13 bases universal to the Illumina primers are recognized and the reads are trimmed from the point of encountering of the primer fragment on;   --stringency 5 – at least 5 nucleotides overlap with the Illumina primer sequence are needed for trimming;  --length 40 – any read that is shorter then 40 nucleotides as a result of trimming is discarded;  --paired – only pairs of reads are retained (for paired-end reads only, not for single reads).The quality of the trimmed reads is re-assessed with FastQC.
The trimmed reads are also screened for presence of rRNA and mtRNA/DNA sequences using FastQ-Screen v.0.4.3The raw trimmed reads are aligned to the reference genome using Tophat v. 2.0.11
Tophat alignments are processed to extract raw read counts for genes using htseq-count v.0.6.1p2. Assigning reads to genes by htseq-count is done in the mode “intersection_nonempty”
Two-condition differential gene expression is performed with DESeq v.1.18.0 package
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample (samples in different columns)
Supplementary_files_format_and_content: abundance measurments, log 2 fold change (-ve compared to +ve)

source_name: FACS isolated urinary tract pacemaker cells

growth_protocol: WT B6 mice were mated and embryonic days were timed by checking for a vaginal plug, the presense of which was set at E0.5

extract_protocol:
At E18.5 pregnant dams were sacrificed using CO2, pelvis kidney junctions (PKJs) were dissected out of all embryos and pooled together, PKJs were dispersed using collagenase, incubated with anti-HCN3 antibody, incubated  with secondary antibody, HCN3+ and HCN3- cells were purified using FACS , RNA was extracted  using the micro Qiagen RNA  extraction kit
Library prep was done using the Clontech cDNA conversion kit followed by Nextera XT library prep

tag: developmental stage


title: HCN3- sample 2

source_name: FACS isolated HCN3- pelvic kidney junction cells


title: HCN3+ sample 1


title: HCN3- sample 1


title: HCN3- sample 3


title: Wild type, replicate 2

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

data_processing:
Basecalling and demultiplexing of the samples was done using the Illumina software “BCL to FASTQ file converter v2.17.1.14”
Demultiplexed fastq files were mapped to the Mouse genome (ENSEMBL, version 87) using rna-STAR.
The “ --quantMode GeneCounts” option in STAR was used to retrieve raw read counts per gene.
Genome_build: GRCm38
Supplementary_files_format_and_content: Each processed data file contains 2 columns: in the first column are the ENSEMBL gene Ids, and in the second column are the raw counts corresponding to each gene.

source_name: Wild type, Adenoma

growth_protocol: Cells were split approximately twice a week, and seeded in MatrigelⓇ (Corning) drops in a 24-well plate. After polymerization, 500 μl of complete medium [(DMEM/F12, Biological Industries) with penicillin (100 U/ml) and streptomycin (100 μg/ml) (Biological Industries) supplemented with N2 and B27 (Invitrogen) containing 140 nM ROCK inhibitor (Y27632, Sigma), 100 ng/ml Noggin (Peprotech), 100 ng/ml R-spondin (R&D Systems), 50 ng/ml EGF (Sigma) and 20 ng/ml basic FGF (Peprotech)] was added and cultures maintained at 37°C in 5% CO2.

extract_protocol:
Total RNA from three biological replicates per condition was extracted following RNeasy Micro Kit (Qiagen) protocol
TruSeq stranded mRNA protocol with polyA selection.

value: APC min/+; Villin-Cre; IKKa +/+

value: Intestinal Adenoma cells


title: Knock out, replicate 2

source_name: Knock out, Adenoma

value: APC min/+; Villin-Cre; IKKa FL/FL


title: Knock out, replicate 1


title: Knock out, replicate 3


title: H3K27ac_D0

description: H3K27ac ChIP-seq

source_name: H7 hESC

value: H7 hESC

value: Active Motif


title: H3K27ac_D5

description: H3K27ac ChIP-seq

source_name: Cardiac progenitor stage cells differentiated from H7


title: H3K27ac_D2

description: H3K27ac ChIP-seq

source_name: Mesoderm stage cells differentiated from H7


title: NHD13HSC1

city: New York

first: Haiming

last: Xu

state: NY

address: 1275 York Avenue

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

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 mm9 whole genome
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Genome_build: mm9
Supplementary_files_format_and_content: text file with raw read count for genes

source_name: bone marrow

extract_protocol:
Trizol was used to extract RNA from FACS sorted CD150+CD34–Flt3–LSK viable cells. Total RNA was used for quality controls and for normalization of starting material. cDNA-libraries were generated with 10 ng of total RNA using the SMARTer Ultra Low RNA Kit for Illumina Sequencing according to the manufacturer’s indications. Sequencing was done using the Illumina Next-Gen Sequencing HiSeq platform with 30-45 million 75bp, paired-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

value: post natal 4 months

value: HSC

tag: cell markers


title: H3K27ac_D9

description: H3K27ac ChIP-seq

source_name: Cardiomyocytes stage differentiated from H7


title: WTHSC2

tag: tissue

value: wild type


title: DNA_Input_D5

description: DNA input

value: Cardiac progenitor stage cells differentiated from H7

tag: chip antibody cat#


title: DNA_Input_D2

description: DNA input

value: Mesoderm stage cells differentiated from H7

tag: chip antibody vender


title: NHD13HSC2

tag: cell type


title: DNA_Input_D0

description: DNA input


title: DNA_Input_D9

description: DNA input

value: Cardiomyocytes stage differentiated from H7


title: SETD7_D9_rep1

description:
SETD7 ChIP-seq
SETD7_ChIPseq_vsd_enrichment.txt

value: Abcam


title: SETD7_D9_rep2


title: SETD7_D5_rep2


title: SETD7_D5_rep1


title: Wild type, replicate 3


title: Wild type, replicate 1


title: SETD7_D2_rep2


title: SETD7_D2_rep1


title: H7CM_D9_rep2

description:
Cardiomyocytes differentiated from H7
RNA-seq_vsd_exp.txt


title: SETD7_D0_rep2


title: H7CM_D9_rep1


title: H7CM_D5_rep2

description:
Cardiac progenitor cells differentiated from H7
RNA-seq_vsd_exp.txt


title: SETD7_D0_rep1


title: H7CM_D0_rep2

description:
H7 ESC
RNA-seq_vsd_exp.txt


title: H7CM_D5_rep1


title: H7CM_D2_rep2

description:
Mesoderm cells differentiated from H7
RNA-seq_vsd_exp.txt


title: Huh6 rep1

value: HuH6 hepatoblastoma cell line

tag: passages


title: WTHSC1


title: OSCC

city: HsinChu

first: Hsien-Da

address: 1001 University Road

department: Biological Science and Technology

institute: National Chiao Tung University

data_processing:
Reads of small RNA-seq were trimmed 3’adapter and quality pre-processed using cutadapt v1.9.1 and FASTX-Toolkit v0.0.13.2, respectively.
The reads with Phred quality score ≥ 20 and longer than 18 nucleotides were retained.
The UCSC reference genome (hg19) and miRBase v21 were employed for annotation of reads that could be mapped to genome.
Genome_build: hg38
Supplementary_files_format_and_content: raw count sample matrix file

source_name: plasma

extract_protocol:
Blood was centrifuged at 3000 rpm for 10 min to separate plasma and stored at −80°C. For small RNA sequencing, total RNA was extracted from 3 ml of pooled plasma using a combined version of phenol–chloroform extraction followed by column purification.
Library was constructed by TruSeq Small RNA Preparation Kits (Illumina Inc, CA,  USA) according to the manufacturer’s instructions.

tag: number of pooling samples

tag: diagnosis

value: Oral squamous cell carcinoma


title: Huh6 rep2

source_name: Hepatoblastoma cell line


title: H7CM_D0_rep1

description:
H7 ESC
RNA-seq_vsd_exp.txt


title: OL

value: Oral leukoplakia


title: Normal

value: Healthy control


title: XRN2_MUT_B

city: Warszawa

first: Tomasz

middle: M.

last: Kuliński

state: Mazowieckie

address: ul. Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

description: endogenous XRN2 repleced with catalytically inactive XRN2(D233AD235A-EGFP fusion

data_processing:
Basecalls performed using CASAVA v1.8.2
Aligment STAR v 2.5.2b
Quality control, read processing and filtering, visualization of the results and counting of reads for the Genecode v22 comprehensive annotation were performed using custom scripts using elements of the RSeQC, BWtools, BEDtools and SAMtools packages.
de novo transcriptome assembly snd abbundance estimation StringTie v1.2.4
Genome_build: GRCh38

source_name: transgenic Flp-In T-REx-293 cell line

extract_protocol:
Total RNA was isolated with the TRI Reagent (T9424, Sigma) according to the manufacturer’s instructions. RNA was subjected to TURBO DNase (AM2238, Ambion) treatment and rRNA was depleted using Ribo-Zero Gold rRNA Removal Kit (MRZG12324, Human/Mouse/Rat, Illumina) according to the manufacturer’s protocol. Prior to rRNA depletion, to provide an internal performance control for further steps, 1 µg of RNA was mixed with 4 µl of 1:99 diluted ERCC RNA Spike-In Control Mix 1 (4456740, Ambion).
Libraries were constructed as previously described in Sultan et al., 2012 (PMID: 2609201) with minor modifications. Fragmentation and first strand cDNA synthesis were performed as in TruSeq RNA Library Prep kit v2 protocol (Illumina, RS-122-2001, instruction number 15026495 Rev. D), using SuperScript III reverse transcriptase (18080-085, Thermo Fisher Scientific). Enriched library quality was verified using 2100 Bioanalyzer and High Sensitivity DNA kit (5067-4626, Agilent). The libraries’ concentration was estimated by qPCR means with KAPA Universal Library Quantification Kit (KK4824, Kapa Biosystems), according to the supplied protocol. Sequencing was carried out on an Illumina NextSeq 500 sequencing platform, using NextSeq 500 High Output Kit (150 cycles) (FC-404-1002, Illumina) and standard libraries denaturation and pair-end sequencing procedures (Instructions: 15048776 Rev. D, 15046563 Rev. F) of 2x75 cycles.

value: embrionic kidney (PubMed ID:886304)

tag: parental cell line

value: 294 - ATCC  number CRL-1573

tag: xrn2 ribonuclelytic acitvity

value: impaired


title: XRN2_MUT_C

value: 295 - ATCC  number CRL-1573


title: XRN2_WT_B

description: endogenous XRN2 repleced with catalytically active XRN2-EGFP fusion

value: wild-type


title: XRN2_WT_C


title: XRN2_MUT_A

value: 293 - ATCC  number CRL-1573


title: XRN2_WT_A


title: H7CM_D2_rep1


title: h1 ES BS-seq

source_name: h1 ES BS-seq

tag: maternal genotype

value: ssrp1/+ h1.1 h1.2 Col

tag: paternal genotype

value: Wild-type Ler

tag: f1 genotype

value: h1 Col/Ler hybrid

tag: tissue/cell type

value: Endosperm


title: ssrp1/+ BCEM BS-seq

source_name: ssrp1/+ BCEM BS-seq

value: Wild-type Col

value: wild-type Col/Ler hybrid

value: Embryo


title: WT vegetative cell BS-seq

description: FACS sorted cells

source_name: WT vegetative cell BS-seq

value: ssrp1/+ Col

value: Vegetative cell


title: WT ES BS-seq

source_name: WT ES BS-seq


title: ssrp1/+ h1 ES BS-seq

source_name: ssrp1/+ h1 ES BS-seq

value: ssrp1/+ h1 Col/Ler hybrid


title: WT EM BS-seq

source_name: WT EM BS-seq


title: WT sperm BS-seq

description: FACS sorted cells

source_name: WT sperm BS-seq

value: Sperm


title: Huh6 rep3

value: HuH6 hepatoblastoma cell line


title: spt16 WT ES BS-seq

source_name: spt16 WT ES BS-seq

value: spt16/+ Col


title: Huh6 rep4


title: ssrp1/+ sperm BS-seq

description: FACS sorted cells

source_name: ssrp1/+ sperm BS-seq


title: ssrp1/+ vegetative cell BS-seq

description: FACS sorted cells

source_name: ssrp1/+ vegetative cell BS-seq


title: spt16/+ ES BS-seq

source_name: spt16/+ ES BS-seq

value: spt16/+ Col/Ler hybrid


title: spt16 WT EM BS-seq

source_name: spt16 WT EM BS-seq


title: ssrp1 WT ES BS-seq rep2

source_name: ssrp1 WT ES BS-seq


title: 24_6 [re-analysis]

city: Panajim

first: vishal

last: gupta

state: Goa

address: Dona Paula

department: Biological Oceanography

country: India

institute: CSIR-National Institute of Oceanography

data_processing:
FASTQ quality check through base quality score distribution, average base content per read and GC distribution in the read
Illumina adapters were removed, reads with average quality score less than 20 were fileterd, removed non-coding RNAs and mtRNA and 5' end were trimmed by Cutadapt, Sickle and Bowtie2
Reads were assembeled by Trinity2.0.6
Transcripts with FPKM>1 weer take into account for differential expression studies
Reads were aligned to assembled transcriptome using Bowtie2 and differential gene expression analysis was carried out using DESeq
Genome_build: RNA-seq
Supplementary_files_format_and_content: tab delimited format and contain fold change, p value and read count for individual sample

organism: Ulva lactuca

source_name: Ulva lactuca thalli

growth_protocol: The algal thalli were desiccated for 24 h, 36 h and 72 h at a moisture condition of 20%.

extract_protocol:
RNA was extracted following the protocol of commercial kit from SIGMA for Plant RNA extraction
Library were constructed by True-seq kit

treatment_protocol: Desiccation

value: thalli

tag: treatment

value: Control (Always submerge)


title: 36_0 [re-analysis]

value: Desiccation for 36 h


title: Picked doublets or triplets, JC68

status: Public on Apr 16 2018

city: Utrecht

first: Jean-Charles

last: Boisset

address: Uppsalalaan 8

institute: Hubrecht Institute

data_processing:
Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases).
Genome_build: mm10
Supplementary_files_format_and_content: *.gene.coutt.csv: Tab separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicate the cell number of the experiment, separated by a space. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: Small intestinal crypts

extract_protocol:
Cells were mouth pipetted or sorted directly into 384-well plates containing 0.02 μL of 1:50,000 ERCC Spike-in RNA (Ambion), 0.015 µL of 1% IGEPAL (Sigma), 0.035 µL of RNAse inhibitor (Clonetech), and 0.020 µL of 10 mM dNTPs and water to a total volume of 100 nL, covered with 5µL of mineral oil
RNA was processed using the previously described CEL-seq2 technique (with modifications as described in Muraro et al., Cell Systems, 2016). Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

tag: strain

value: Small intestinal crypts


title: 72_0 [re-analysis]

value: Desiccation for 72 h


title: ssrp1/+ ES BS-seq rep2

source_name: ssrp1/+ ES BS-seq

value: Wild-type Ler

value: ssrp1/+ Col/Ler hybrid


title: sorted single cells, Gk5b-L


title: sorted single cells, GK5b-G


title: sorted single cells, GK5a-M2-1


title: sorted single cells, GK5a-M2-5


title: sorted single cells, GK5a-M2-3


title: sorted single cells, GK5a-M2-2


title: spt16/+ EM BS-seq

source_name: spt16/+ EM BS-seq


title: Picked doublets or triplets, JC72


title: 24_0 [re-analysis]

value: Desiccation for 24 h


title: CS24 BAL_Control

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

data_processing:
Raw sequence data in FASTQ format were assessed for Per Base Sequence Quality (Phred average score =33, ribosomal RNA content <2%) using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
NovoAlign (Novocraft, http://novocraft.com) was used to align reads to a set of transcript sequences and also to the reference genome (hg19).
Raw read counts were mapped on UCSC mRNA transcript human database based on the GRCh37/hg19 human genome version. NovoAlign parameters were set to allow multiple alignments to the transcriptome set to allow for isoforms, but only unique alignments to the genome.
The raw counts per transcript were then aggregated onto unique UCSC gene symbols of protein-coding mRNAs, to obtain a final table with non-normalized expression levels (counts) for 19723 unique gene symbol IDs. These  data are contained in the file processed_data_matrix_counts.txt
Raw non-normalized data were fed into the R-Bioconductor tool edgeR to assemble differentially expressed gene lists.
Genome_build: hg19
Supplementary_files_format_and_content: raw read counts aggregated on UCSC mRNA transcripts database based on the GRCh37/hg19 human genome

source_name: lung bronchoalveolar lavage(BAL)

extract_protocol:
Fiberoptic bronchoscopy (FOB) and bronchoalveolar lavage(BAL) were carried out at first evaluation of IPF patients and control subjects. All FOBs and BALs were carried out following established procedures recommended by international guidelines, by instillation of 100 ml of room temperature normal saline solution per lobe in one to three lung lobes (right middle lobe, lingula or left lower lobe). Portions of BAL samples remaining after aliquots for diagnostic exams were taken, then used to generate the RNA sample bank, after informed consent was obtained. Lavage samples were maintained on ice and processed for RNA extraction within one hour of the endoscopic procedure. Total RNA from BAL cells (5x106) was obtained using the RNA/DNA/Protein Purification Kit (Norgen Biotech Corp., Thorold, ON, Canada). For the purpose of RNA analysis, study samples were selected based upon alveolar macrophage differential counts ( >80%), cell viability ( >95%),  epithelial cells counts (<5%).  Samples of BAL differential cell counts were done on Diff Quick (Bio-Optica, Milan, Italy) stained cytopreps (Cytospin Shandon 4, Thermo Scientific, Waltham, MA, USA). Samples were further selected after RNA quality assessment based upon RNA integrity (R.I.N.> 6.0) analyzed by Agilent 2100 Bioanalyzer with the Total RNA pico kit (Agilent Technologies, SantaClara CA).
For library preparation and high-throughput sequencing (Cofactor Genomics, Saint Louis, MO), cDNA was synthesized by random priming using the NuGEN Ovation FFPE RNA-seq system (NuGEN Technologies, San Carlos, CA), as recommended for clinical samples potentially affected by low RNA integrity [35],  and fragmented to an average size of 200 bp using the Covaris S2 (Covaris, Woburn, MA). Fragmented cDNA was end repaired, A-tailed and ligated with barcoded Illumina adapters. Ligated DNA was treated with NuGEN mouse Insert Dependent Adaptor Cleavage (InDA-C) reagent to deplete cDNA corresponding to ribosomal RNA, and PCR amplified. Final library yield was measured using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific, Waltham, MA)  and library size assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: BAL macrophages

tag: age

tag: Sex

value: female

tag: disease

value: Control

tag: smoker

value: Yes


title: CS12 BAL_IPF

tag: tissue

value: Idiopathic pulmonary fibrosis

value: No


title: CS13 BAL_IPF

value: Yes [ex]


title: CS25 BAL_Control


title: CS19 BAL_IPF

value: male

value: Smoking


title: CS17 BAL_IPF


title: CS20 BAL_IPF


title: CS6 BAL_IPF


title: Picked doublets or triplets, JC71


title: sorted single cells, GK5a-M2-4


title: CS22 BAL_IPF


title: CS10 BAL_IPF


title: CS11 BAL_IPF


title: CS 9 BAL_IPF


title: CS15 BAL_IPF


title: CS8 BAL_IPF


title: CS2 BAL_Control


title: CS4 BAL_Control


title: CS5 BAL_Control


title: CS7 BAL_IPF


title: CS23 BAL_Control


title: LS_EBL9

city: Houston

first: Eduardo

last: Vilar

address: 1515 Holcombe Blvd., Unit 1360

department: Clinical Cancer Prevention

institute: The University of Texas MD Anderson Cancer Center

description: colonic tubular adenoma from patient with Lynch Syndrome (LS)

data_processing:
mRNA sequences were aligned with Bowtie 1.1.2 on hg19 and quantified with RSEM 1.2.21 using default settings. RSEM expected counts were used for analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited RSEM output with expected counts, TPM, FPKM values

source_name: RNA

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) and the RNeasy kit (Qiagen). RNA was quantified using Qubit (Life Technologies) and RNA quality was assessed with the Agilent 2100 Bioanalyzer to select samples with RNA integrity numbers (RIN) ≥8 for analysis.
Sample preparation, library construction, and sequencing was performed at the DNA Analysis Facility Core at MD Anderson

value: tubular adenoma

tag: size


title: LS_EBL7

value: tubular adenoma with HGD


title: LS_EBL5

description: colonic hyperplastic polyp from patient with Lynch Syndrome (LS)

value: hyperplastic polyp


title: LS_EBL3


title: LS_EBL26


title: LS_EBL11


title: LS_EBL20


title: FAP_G67

description: colonic tubular adenoma from patient with Familial Adenomatous Polyposis (FAP)


title: LS_EBL1


title: FAP_G55


title: LS_EBL23


title: FAP_G48


title: LS_EBL18


title: LS_EBL13


title: FAP_G47


title: FAP_G61


title: FAP_G6


title: CS3 BAL_IPF

value: Yes [Ex smoker]


title: FAP_G53


title: FAP_G29


title: FAP_G25


title: CS1 BAL_Control


title: FAP_G2


title: FAP_G15


title: FAP_G13


title: Gro-seq-siCTL-CTL-MCF7

city: Ganzhou

first: Wenjuan

last: Zhang

state: Jiangxi

address: No. 23, Qingnian Road

department: First Affiliated Hospital

institute: Gannan Medical University

description: Nascent RNA sequencing

data_processing:
Library strategy: Gro-seq
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.1.
The bigwig files were generated by using Homer v4.7, in which the total tags are normalized to 1.00e+07.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

growth_protocol: MCF7 cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
MCF7 cells were washed 3 times with cold 1X phosphate buffered saline (PBS) buffer and then incubated in swelling buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5min on ice and harvested. Cells were first re-suspended and lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol). The resultant nuclei were washed once again with 10 ml lysis buffer and then re-suspended in 100ml of freezing buffer (50mM Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA).
For run-on assay, resuspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of SUPERase In, 1% sarkosyl, 500mM ATP, GTP, and Br-UTP, 2mM CTP) and incubated for 5 min at 30°C. The nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol LS reagent (Invitogen) following manufacturer’s instructions. NRO-RNA was then subjected to base hydrolysis on ice for 40 min and followed by treatment with DNase I and antarctic phosphatase. To purify the Br-UTP labeled nascent RNA, the NRO-RNA was immunoprecipitated with an anti-BrdU agarose beads (Santa Cruz Biotech) in binding buffer (0.5XSSPE, 1mM EDTA, 0.05% tween-20) for 1h at 4°C while rotating.  To repair the end, the immunoprecipitated BrU-RNA was re-suspended in 50mL reaction (43mL DEPC water, 5.2mL T4 PNK buffer, 1mL SUPERase In and 1mL T4 PNK (New England BioLabs)) and incubated at 37°C for 1h. RNA was then extracted, precipitated using acidic phenol-chloroform (Ambion) and subjected to poly-A tailing reaction by using poly-A polymerase (New England BioLabs) for 30 min at 37°C. Subsequently, reverse transcription was performed using oNTI223- primers (5’- pGATCGTCGGACTGTAGAACTCT; CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN-3’) where the p indicates 5’ phosphorylation, ‘;’ indicates the abasic dSpacer furan and VN indicates degenerate nucleotides. Specifically, tailed RNA (8.0mL) was subjected to reverse transcription using superscript III (Invitrogen), after which the cDNA products were separated on a 10% polyacrylamide TBE-urea gel. The extended first-strand product (100-500bp) was excised and recovered by gel extraction. After that, the first-strand cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1 (New England BioLabs). Re-linearized single strand cDNA (sscDNA) was separated in a 10% polyacrylamide TBE gel as described above and the product of needed size was excised (~170-400bp) for gel extraction. Finally, sscDNA template was amplified by PCR using the Phusion High-Fidelity enzyme (NEB) according to the manufacturer’s instructions. Primers oNTI200 (5’-CAAGCAGAAGACGGCATA-3’) and oNTI201 (5’- AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACG-3’) were used to generate DNAs for deep sequencing.

treatment_protocol: MCF7 cells were maintained in stripping medium (phenol red free) for three days before treating with or without estrogen (E2, 10-7 M) for 1h.

tag: sirna

value: siCTL

tag: cell line

value: Michigan Cancer Foundation-7 cells(MCF-7 cells)


title: Gro-seq-siJMJD6-CTL-MCF7

description: Nascent RNA sequencing


title: Gro-seq-siCTL-E2-MCF7

description: Nascent RNA sequencing


title: Med12-siCTL-CTL-MCF7

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.1.
The bigwig files were generated by using Homer v4.7, in which the total tags are normalized to 1.00e+07.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells were then fixed with 1% formaldehyde (Sigma) for 10 mins at room temperature (RT) (for MED12 and Pol II ChIP), or fixed with disuccinimidyl glutarate (DSG) (2mM) (Proteochem) for 45 min at RT, washed twice with PBS and then double-fixed with 1% formaldehyde for another 10 min at RT (for JMJD6 ChIP). Fixation was stopped by adding glycine (0.125M) and incubated for 5 mins at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300~500 bp average in size through sonication. Resultant was immunoprecipitated with anti-MED12, anti-Pol II or anti-JMJD6 antibody overnight at 4°C, followed by incubation with protein G magnetic beads (Invitrogen) for an additional 2 hrs. After washing and elution, the protein-DNA complex was reversed by heating at 65°C overnight. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) and subjected to high throughput sequencing.
The libraries were constructed following Illumina’s Chip-Seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

tag: antibody

tag: antibody catalog/vendor

value: A300-774A(Bethyl Laboratory)


title: PolII-siJMJD6-CTL-MCF7

value: PolII

value: SC-899(Santa Cruz Biotechnology)


title: PolII-siJMJD6-E2-MCF7


title: Med12-siCTL-E2-MCF7


title: JMJD6-E2-MCF7


title: JMJD6-CTL-MCF7


title: Med12-siJMJD6-CTL-MCF7


title: Med12-siJMJD6-E2-MCF7


title: PolII-siCTL-CTL-MCF7