title: tail_DNA-HU-1256A.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1256A

value: pump

value: HU


title: sir2 (i.e. mutant) strain without terminator, MCM2-ChEC, G1, calcium-treated

status: Public on May 08 2019

type: SRA

city: Seattle

first: Eric

middle: Jan

last: Foss

state: WA

address: 1100 Fairview Ave N

department: Clinical Research Division

country: USA

institute: Fred Hutchinson Cancer Research Center

library_source: genomic

data_processing:
align paired-end fastq files with GSNAP
sort bam files with Picard's SortSam
annotate bam files with Picard's AddOrReplaceReadGroups
count per-base pair read depths with BedTools' genomecov
Genome_build: sacCer3 for all files, except chrXII replaced with chrXIIrDtH.fa for strains with terminator downstream of c-pro (16818, 16851, 16907, 16920) and with chrXII replaced with chrXIIrDHYGdel.fa for "no terminator" control strains (16833, 16849, 16855, 16905)
Supplementary_files_format_and_content: processed_files_for_Foss_et_al_042219_1.txt: text; this file contains read depths for base pairs 458000-460000 on chrXII for all raw fastq files after they have been aligned to the appropriate genomes with the gsnap alignment algorithm
Supplementary_files_format_and_content: chrXIIrDtH.fa: fasta:  this file contains the chrXII sequence for strains with a terminator inserted immediately downstream from c-pro; all other chromosomes are the same as for sacCer3 genome build
Supplementary_files_format_and_content: chrXIIrDHYGdel.fa: fasta:  this file contains the chrXII sequence for "no terminator control" strains, i.e. controls for strains with a terminator inserted immediately downstream from c-pro; all other chromosomes are the same as for sacCer3 genome build

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast experiments were carried out using standard YPD (yeast peptone dextrose) medium [2% (wt/vol) glucose, 1% yeast extract, 2% (wt/vol) peptone].

extract_protocol:
as described:  Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S. Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A. 2011;108(45):18318-23. Epub 2011/10/26. doi: 1110731108 [pii]10.1073/pnas.1110731108. PubMed PMID: 22025700; PubMed Central PMCID: PMC3215028.
as described:  Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S. Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A. 2011;108(45):18318-23. Epub 2011/10/26. doi: 1110731108 [pii]10.1073/pnas.1110731108. PubMed PMID: 22025700; PubMed Central PMCID: PMC3215028.
paired-end

treatment_protocol: sonication (replication profiling), MNase (MNase-seq), calcium (MCM2-ChEC), details in manuscript

tag: sample type

value: calcium-treated DNA (ChEC)

tag: cell type

value: alpha factor-arrested cells


title: sir2 (i.e. mutant), G2, MNase-seq

description: sir2 (i.e. mutant), G2, MNase-seq

value: MNase-seq

value: nocodazole-arrested cells


title: tail_DNA-HU-1254.pump

type: genomic

city: Ann Arbor

first: Thomas

middle: E.

last: Wilson

state: MI

address: 2065 BSRB, 109 Zina Pitcher

department: Department of Pathology

institute: University of Michigan

description: test F1 pup from the pump experiment

hyb_protocol: DNA was hybridized to Nimblegen mouse MM9 whole genome tiling UX3 microarrays using manufacturer’s instructions. We used a single female C57BL/6 x C3H/HeJ hybrid animal for reference DNA for all hybridizations.

scan_protocol: Arrays were scanned on a NimbleGen MS 200 scanner per manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 data extraction.

organism: Mus musculus

source_name: pump HU sample 1254

label_protocol: DNA was labeled for hybridization to Nimblegen mouse MM9 whole genome tiling UX3 microarrays using manufacturer’s instructions.

extract_protocol: DNA was isolated from tail snips of selected pups using the Qiagen Blood & Cell Culture DNA Mini Kit using manufacturer’s protocol (https://www.qiagen.com/us/resources/resourcedetail?id=28375699-647d-4b6b-a6a3-6a2715f7d46f&lang=en).

treatment_protocol: hydroxyurea administered to sire by peristaltic pump

tag: route

tag: type

tag: strain

value: C57BL/6J (sire) x C3H/HeJ (dam)

tag: sire

tag: dam

tag: tissue

value: tail snip genomic DNA from F1 pup

source_name: common C57BL/6J x C3H/HeJ female aCGH reference mouse

value: Ref

value: C57BL/6J x C3H/HeJ


title: LIV-148

city: East Lansing

first: Timothy

last: Zacharewski

state: Michigan

address: 603 Wilson Road

department: BMB

institute: Michigan State University

library_source: transcriptomic

data_processing:
[Quality control] FASTQC v0.11.3
[Removal of artifacts] FASTX v0.0.14
[Alignment] TopHat2 v2.1.0
[Conversion to SAM format] SAMTools v1.2
[Abundance measurement] HTSeq v0.6.1
[Count transformation] DESeq
[Normalization and analysis] Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: GRCm38 release 81
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene (raw counts)

molecule: total RNA

source_name: Liver

extract_protocol:
Livers were homogenized in TRIzol (Ambion, Waltham, MA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions with an additional phenol:chloroform extraction and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified using a Nano-drop spectrophotometer (Thermo Scientific, Wilmington, DE) at 260 nm and purity was assessed by calculating the A260/A280 ratio. RNA quality was analyzed using the Caliper LabChip GX (Perkin Elmer, Waltham, MA).
Libraries were were prepared using the Illumina TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA). Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions.

treatment_protocol: Male C57BL/6 mice were gavaged with sesame oil vehicle or 30 ug/kg TCDD every  4 days for 28 days.

tag: Sex

value: Male

tag: age

value: 9-10 weeks old

value: Liver

tag: treatment

value: 30 µg/kg TCDD

tag: duration of treatment

value: 28 Days

tag: frequency of treatment

value: Mice dosed every 4 days for 28 days

tag: timepoint


title: Donor 2 : CD11c+ [AH9_3]

city: Westmead

first: J

middle: Dinny

last: Graham

state: NSW

address: 176 Hawkesbury Rd

department: Westmead Institute for Medical Research

country: Australia

institute: University of Sydney

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH9_3

data_processing:
Reads were aligned using STAR v2.5.3 to the GRCh38 genome and were summarized to gene counts as annotated by GENCODE v26.
Gene counts were normalized using TMM and variance stabilized using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file containing read counts for each lane of sequencing data for each sample. Each biological sample has 4 lanes of raw sequence data.

molecule: polyA RNA

organism: Homo sapiens

source_name: Abdominal skin epidermal tissue

extract_protocol:
Primary cell populations isolated by flow cytometry (n=200 cells per population) were captured directly into lysis buffer containing 0.1% triton X-100, 1U RNaseOUT RNase inhibitor, 2.5mM each dNTP mix, 2.5uM anchored oligo-dT primer (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’) in a total volume of 20ul. Full-length mRNA was reverse transcribed and amplified using the Smart-seq2 protocol of Picelli et al (Nature Methods. 2013;10(11):1096-8).
Sequencing libraries were prepared from 1ng cDNA product using Illumina Nextera XT reagents, in accordance with the supplier’s protocol, except that PCR was limited to 8 cycles to minimize read duplicates, and final library elution was performed using 17.5μl elution buffer EB.  All libraries were pooled and sequenced on four lanes of an Illumina HiSeq 2500 sequencer, using a HiSeq Rapid Cluster Kit v2.

value: Abdominal skin epidermal tissue

value: Epidermal CD11c+

tag: biological replicate/donor number

tag: sample number


title: sir2 fob1 MCM2-ChEC, G1, calcium-treated, replicate


title: tail_DNA-HU-1253.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1253

value: pump

value: HU


title: LIV-147


title: Donor 2 : CD11c+ [AH9_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH9_2


title: tail_DNA-HU-1251.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1251


title: LIV-144

value: Sesame Oil Control


title: Donor 2 : CD11c+ [AH9_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH9_1


title: tail_DNA-HU-1238.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1238


title: LIV-143


title: sir2 (i.e. mutant) strain with terminator, flow-sorted cells, S phase, sonicated DNA

value: sonicated DNA

value: flow-sorted log phase cells, S phase


title: Donor 2 : LC [AH8_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH8_3

value: Langerhans cell


title: fob1 G1 MCM2-ChEC, calcium-treated, replicate (this strain is WT for SIR2, even though the file name says "sir2")

description: fob1 G1 MCM2-ChEC, calcium-treated, replicate (NOTE!!!!!!! This strain is WT for SIR2, even though the file name says "sir2")

value: calcium-treated DNA (ChEC)

value: alpha factor-arrested cells


title: tail_DNA-HU-1232.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1232

value: C57BL/6J (sire) x C3H/HeJ (dam)

value: tail snip genomic DNA from F1 pup

value: Ref

value: C57BL/6J x C3H/HeJ


title: LIV-142

value: Male

value: 9-10 weeks old

value: Liver


title: SIR2 (i.e. WT) strain without terminator, MCM2-ChEC, G1, calcium-treated, replicate


title: Donor 2 : LC [AH8_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH8_1

value: Abdominal skin epidermal tissue


title: tail_DNA-HU-1233b.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1233b


title: sir2 (i.e. mutant) strain with terminator, flow-sorted cells, G1, sonicated DNA

value: flow-sorted log phase cells, G1


title: tail_DNA-HU-1227.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1227

value: pump


title: LIV-133

value: 28 Days

value: Mice dosed every 4 days for 28 days


title: sir2 fob1 MCM2-ChEC, G1, calcium-treated


title: Donor 2 : LC [AH8_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH8_4


title: LIV-187

value: 30 µg/kg TCDD


title: SIR2 (i.e. WT) strain without terminator, MCM2-ChEC, G1, calcium-treated


title: LIV-190


title: tail_DNA-HU-M707.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M707

treatment_protocol: hydroxyurea administered to sire by oral gavage

value: gavage

value: HU


title: tail_DNA-HU-1228.pump

description: test F1 pup from the pump experiment

source_name: pump HU sample 1228


title: Donor 2 : LC [AH8_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH8_2

value: Langerhans cell


title: sir2 MCM2-ChEC G1, calcium-treated

description: sir2 MCM2-ChEC G1, calcium-treated

value: calcium-treated DNA (ChEC)

value: alpha factor-arrested cells


title: Donor 1 : LC [AH7_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH7_4


title: Donor 1 : LC [AH7_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH7_3


title: sir2 (i.e. mutant) strain with terminator, MCM2-ChEC, G1, calcium-treated


title: LIV-186


title: tail_DNA-HU-M569.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M569

value: C57BL/6J (sire) x C3H/HeJ (dam)

value: tail snip genomic DNA from F1 pup


title: Donor 1 : LC [AH7_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH7_2


title: Donor 1 : LC [AH7_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH7_1


title: tail_DNA-HU-F656.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F656

value: Ref

value: C57BL/6J x C3H/HeJ


title: sir2 (i.e. mutant) strain without terminator, flow-sorted cells, S phase, sonicated DNA

value: sonicated DNA

value: flow-sorted log phase cells, S phase


title: Donor 1 : CD11c+ [AH6_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH6_4

value: Abdominal skin epidermal tissue

value: Epidermal CD11c+


title: tail_DNA-HU-M319xF410.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M319xF410


title: tail_DNA-HU-M689.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M689


title: tail_DNA-HU-F565.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F565


title: LIV-132

value: Male

value: 9-10 weeks old

value: Liver

value: Sesame Oil Control


title: cdc6-1, MNase-seq, G1, 37 degrees (restrictive temperature)

source_name: yeast

value: MNase-seq


title: tail_DNA-HU-M561.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M561

value: gavage

value: HU

source_name: common C57BL/6J x C3H/HeJ female aCGH reference mouse


title: Donor 1 : CD11c+ [AH6_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH6_2

source_name: Abdominal skin epidermal tissue


title: fob1 G1 MCM2-ChEC, calcium-treated

description: fob1 G1 MCM2-ChEC, calcium-treated

value: calcium-treated DNA (ChEC)


title: tail_DNA-HU-M687.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M687


title: LIV-128

source_name: Liver

value: 30 µg/kg TCDD

value: 28 Days

value: Mice dosed every 4 days for 28 days


title: sir2 (i.e. mutant) strain without terminator, flow-sorted cells, G1, sonicated DNA

value: flow-sorted log phase cells, G1


title: LIV-123


title: Donor 1 : CD11c+ [AH6_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH6_1


title: SIR2 (i.e. WT) strain with terminator, MCM2-ChEC, G1, calcium-treated

value: alpha factor-arrested cells


title: tail_DNA-HU-F686.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F686

value: C57BL/6J (sire) x C3H/HeJ (dam)

value: tail snip genomic DNA from F1 pup

value: Ref

value: C57BL/6J x C3H/HeJ


title: Donor 1 : CD33 Low [AH5_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH5_3

value: Abdominal skin epidermal tissue

value: Epidermal CD33 low


title: SIR2 (i.e. WT) strain with terminator, MCM2-ChEC, G1, calcium-treated, replicate


title: tail_DNA-HU-F559.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F559


title: LIV-180

value: Male

value: 9-10 weeks old

value: Liver


title: LIV-120


title: Donor 1 : CD33 Low [AH5_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH5_2


title: Donor 1 : CD11c+ [AH6_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH6_3

value: Epidermal CD11c+


title: LIV-126


title: LIV-119


title: SIR2 (i.e. WT) strain, MCM2-ChEC, G1, calcium-treated, replicate


title: Donor 1 : CD33 Low [AH5_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH5_1


title: tail_DNA-HU-M652.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M652

value: gavage

value: HU


title: LIV-122

value: Sesame Oil Control


title: tail_DNA-HU-M648.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M648


title: SIR2 (i.e. WT) strain without terminator, flow-sorted cells, G1, sonicated DNA

value: sonicated DNA


title: LIV-121

value: 28 Days

value: Mice dosed every 4 days for 28 days


title: cdc6-1, MNase-seq, G1, 23 degrees (permissive temperature)

value: MNase-seq

value: alpha factor-arrested cells


title: LIV-115


title: tail_DNA-HU-F649.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F649

value: C57BL/6J (sire) x C3H/HeJ (dam)

value: tail snip genomic DNA from F1 pup


title: LIV-116

value: 30 µg/kg TCDD


title: Donor 1 : CD33 Low [AH5_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH5_4

value: Abdominal skin epidermal tissue


title: Donor 1 : CDC1 [AH4_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH4_4

source_name: Abdominal skin dermal tissue

value: Abdominal skin dermal tissue

value: Dermal cDC1


title: tail_DNA-HU-M304xF426.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M304xF426

value: Ref

value: C57BL/6J x C3H/HeJ


title: LIV-114

value: Male

value: 9-10 weeks old

value: Liver


title: Donor 1 : CDC1 [AH4_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH4_3


title: Donor 1 : CDC1 [AH4_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH4_2


title: SIR2 (i.e. WT) strain with terminator, flow-sorted cells, S phase, sonicated DNA

value: flow-sorted log phase cells, S phase


title: tail_DNA-HU-M701.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M701

value: gavage

value: HU


title: SIR2 (i.e. WT) strain without terminator, flow-sorted cells, S phase, sonicated DNA

value: sonicated DNA


title: LIV-113

value: Sesame Oil Control

value: 28 Days

value: Mice dosed every 4 days for 28 days


title: SIR2 (i.e. WT) strain with terminator, flow-sorted cells, G1, sonicated DNA

value: flow-sorted log phase cells, G1


title: Donor 1 : CDC1 [AH4_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH4_1


title: Donor 1 : Lang+ [AH3_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH3_4

value: Dermal cDC2 (lang+)


title: LIV-110

value: 30 µg/kg TCDD


title: tail_DNA-HU-F646.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F646

value: C57BL/6J (sire) x C3H/HeJ (dam)

value: tail snip genomic DNA from F1 pup


title: SIR2 (i.e. WT) strain, MCM2-ChEC, G1, calcium-treated

value: calcium-treated DNA (ChEC)

value: alpha factor-arrested cells


title: LIV-107

value: Male


title: Donor 1 : Lang+ [AH3_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH3_3

value: Abdominal skin dermal tissue


title: LIV-108

value: 9-10 weeks old

value: Liver


title: 4_DAT_Heat_4 [degradome]

city: Ottawa

first: Sylvie

last: Cloutier

state: Ontario

address: 960 Carling Avenue

country: Canada

institute: Agriculture and Agri-Food Canada

data_processing:
Library strategy: degradome-seq
Raw reads were quality-checked and adapter sequences were removed using a custom Perl script.
Reads ranging from 19-21 nt were extracted using Geneious (Biomatters Ltd, Auckland, NZ) and were converted to distinct tags using Tally (Davis et al., 2013; Methods, 63, 41-49)
The distinct tags were mapped to the coding sequences of wheat (IWGSC RefSeq v1.0, 2017) using sPARTA (Kakrana et al., 2014; Nucleic Acid Research, 42, e139. The previously annotated miRNA sequences were queried for target prediction using the sPARTA’s miRferno target prediction module.
miRNA targets with a threshold P-value <0.05 and read abundance >4 were retained for further analysis
Genome_build: Wheat IWGSC RefSeq v1.0., 2017; The assembly and corresponding annotations were downloaded from the International Wheat Genome Sequencing Consortium (IWGSC) sequence repository hosted by URGI-INRA https://wheat-urgi.versailles.inra.fr/Seq-Repository/Assemblies and https://wheat-urgi.versailles.inra.fr/Seq-Repository/Annotations
Supplementary_files_format_and_content: miRNA_targets_identified_by_degradome_sequencing.xlsx

organism: Triticum aestivum

growth_protocol: A total of 144 Triticum aestivum cv Chinese Spring wheat plants were grown in a PG-40 growth cabinet under long-day conditions of 16 hours of light (300 μmol m−2 s−1) at 18°C and 8 hours of darkness at 16°C. To minimize variation sources, all seeds used in this experiment came from the self-pollination of a single Chinese Spring individual.

extract_protocol:
Leaf tissue was collected from all heat-stressed and control individual plants immediately at the end of the stress period, i.e., time point zero day after treatment (0 DAT), and at one and four days after treatment (1 and 4 DAT). Total RNA was isolated from all 432 leaf tissue samples using TRI-reagent (Ambion, Naugatuck, CT) as previously described (Ragupathy et al., 2016; Scientific Reports, 6, 39373).
Degradome libraries were constructed from 75 µg of total RNA as described in Zhai et al. (2014) in Methods, 67, 84-90.  Twelve random libraries were pooled in equimolar amounts and two HiSeq2000 single end 50-bp reads were obtained by the McGill University and Genome Quebec Innovation Centre.
Degradome (also known as Parallel Ananlysis of RNA Ends) sequencing

treatment_protocol: At the boot stage, a set of 72 plants were exposed to a 37°C heat stress for 5 days while the other 72 plants remained under the control conditions mentioned above. The heat stressed plants were amply watered twice per day during the 5-day stress period to avoid a confounding effect with drought stress.

tag: cultivar

value: cv Chinese Spring

tag: exposed to

value: 37°C heat stress for 5 days

tag: time point

value: 4 day after treatment (DAT)

value: leaf tissues


title: 4_DAT_Heat_3 [degradome]


title: 4_DAT_Heat_2 [degradome]


title: tail_DNA-HU-F730.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F730

tag: route

value: gavage

value: HU

value: Ref

value: C57BL/6J x C3H/HeJ


title: tail_DNA-HU-M301xF420.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M301xF420

tag: type


title: Donor 1 : CD14 MDM [AH2_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH2_4

tag: cell type

value: Dermal CD14 MDM


title: LIV-103

tag: strain

value: Sesame Oil Control

value: 28 Days

value: Mice dosed every 4 days for 28 days


title: Donor 1 : Lang+ [AH3_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH3_2

value: Dermal cDC2 (lang+)


title: 4_DAT_Control_3 [degradome]

value: Control condition


title: LIV-104

value: Male


title: 4_DAT_Heat_1 [degradome]


title: LIV-101

value: 9-10 weeks old


title: tail_DNA-HU-M554.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M554

value: C57BL/6J (sire) x C3H/HeJ (dam)

tag: sire

tag: dam

value: tail snip genomic DNA from F1 pup


title: tail_DNA-HU-M644.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M644

tag: tissue


title: Donor 1 : CD14 MDM [AH2_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH2_2

value: Abdominal skin dermal tissue


title: NIH3T3 cells expressing FOXP2-CPED1-4

city: Beijing

first: Yanyang

last: Zhao

state: Not required for this country

address: No.1, Dahua Road,Dongdan

country: China

institute: Genetics Medicine

description: NIH3T3 cells expressing FOXP2-CPED1-4

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads of low quality, polluted by adaptors were filtered out with NGSQC, and then, the well quality data were aligned to mouse reference genome (version of mm9) using HISAT2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using StringTie(Pertea et al., Nature Biotechnology, 2015, doi:10.1038/nbt.3122). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and the total amount of the sequencing reads
Genome_build: mm9
Supplementary_files_format_and_content: .txt file includes RPKM values for each Sample

source_name: NIH3T3 cells stably overexpressing FOXP2-CPED1, clone4

extract_protocol:
RNA was harvested from cells using Trizol reagent. NEBNext Ultra RNA Library Prep Kit (Cat#E7530) for Illumina was used with 1 ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: embryo

tag: cell line

value: fibroblast

tag: genotype

value: stably overexpressing FOXP2-CPED1

tag: clone


title: Donor 1 : CD14 MDM [AH2_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH2_3


title: tail_DNA-HU-F555.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F555

value: gavage

value: HU

source_name: common C57BL/6J x C3H/HeJ female aCGH reference mouse


title: NIH3T3 cells expressing FOXP2-CPED1-3

description: NIH3T3 cells expressing FOXP2-CPED1-3

source_name: NIH3T3 cells stably overexpressing FOXP2-CPED1, clone3


title: tail_DNA-HU-M297xF414.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M297xF414

value: Ref

value: C57BL/6J x C3H/HeJ


title: Donor 1 : CD14 MDM [AH2_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH2_1

value: Dermal CD14 MDM


title: 4_DAT_Control_4 [degradome]

value: cv Chinese Spring

value: 4 day after treatment (DAT)

value: leaf tissues


title: Donor 1 : Lang+ [AH3_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH3_1

value: Dermal cDC2 (lang+)


title: NIH3T3 cells expressing FOXP2-CPED1-2

description: NIH3T3 cells expressing FOXP2-CPED1-2

source_name: NIH3T3 cells stably overexpressing FOXP2-CPED1, clone2


title: tail_DNA-HU-F724.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F724

value: FUnk


title: tail_DNA-HU-F721.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F721


title: 4_DAT_Control_1 [degradome]

value: Control condition


title: Donor 1 : Mac [AH1_4]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 4
sample name in processed data file:
AH1_4

value: Dermal macrophage


title: tail_DNA-HU-M711.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M711

value: C57BL/6J (sire) x C3H/HeJ (dam)

value: tail snip genomic DNA from F1 pup


title: 1_DAT_Heat_4 [degradome]

value: 37°C heat stress for 5 days

value: 1 day after treatment (DAT)


title: NIH3T3 cells expressing FOXP2-4

description: NIH3T3 cells expressing FOXP2-4

source_name: NIH3T3 cells stably overexpressing FOXP2, clone4

value: embryo

value: fibroblast

value: stably overexpressing FOXP2


title: 1_DAT_Heat_2 [degradome]


title: Donor 1 : Mac [AH1_3]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 3
sample name in processed data file:
AH1_3

source_name: Abdominal skin dermal tissue

value: Abdominal skin dermal tissue


title: 1_DAT_Heat_3 [degradome]


title: NIH3T3 cells expressing FOXP2-3

description: NIH3T3 cells expressing FOXP2-3

source_name: NIH3T3 cells stably overexpressing FOXP2, clone3


title: tail_DNA-HU-F712.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F712

value: gavage

value: HU

value: Ref

value: C57BL/6J x C3H/HeJ


title: Donor 1 : Mac [AH1_2]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 2
sample name in processed data file:
AH1_2


title: tail_DNA-HU-M294xF408.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M294xF408


title: 4_DAT_Control_2 [degradome]

value: cv Chinese Spring

value: 4 day after treatment (DAT)

value: leaf tissues


title: NIH3T3 cells expressing FOXP2-CPED1-1

description: NIH3T3 cells expressing FOXP2-CPED1-1

source_name: NIH3T3 cells stably overexpressing FOXP2-CPED1, clone1

value: stably overexpressing FOXP2-CPED1


title: LIV-131

source_name: Liver

tag: Sex

value: Male

tag: age

value: 9-10 weeks old

value: Liver

tag: treatment

value: Sesame Oil Control

tag: duration of treatment

value: 28 Days

tag: frequency of treatment

value: Mice dosed every 4 days for 28 days

tag: timepoint


title: tail_DNA-HU-F549.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F549

tag: route

value: C57BL/6J (sire) x C3H/HeJ (dam)

value: tail snip genomic DNA from F1 pup


title: NIH3T3 cells expressing FOXP2-2

description: NIH3T3 cells expressing FOXP2-2

source_name: NIH3T3 cells stably overexpressing FOXP2, clone2

value: embryo

value: fibroblast

value: stably overexpressing FOXP2


title: Donor 1 : Mac [AH1_1]

description:
Each sample was sequenced across 4 HiSeq lanes, this is lane 1
sample name in processed data file:
AH1_1

value: Abdominal skin dermal tissue

value: Dermal macrophage

tag: biological replicate/donor number

tag: sample number


title: 1_DAT_Control_4 [degradome]

tag: cultivar

value: cv Chinese Spring

tag: exposed to

value: Control condition

tag: time point

value: 1 day after treatment (DAT)


title: COLO205_PIWIL1_SH3_3

city: Bethesda

first: Pavol

last: Genzor

state: MD

address: 6720A Rockledge Drive, Suite 100

department: ACESO

institute: Henry M Jackson Foundation

description: GeneQuantitationTPM; TEQuantificationCOUNTS

data_processing:
When applicable, raw data with multiple sequencing runs for the same sample were concatenated in termianl using 'cat' command
Trimming 5' (GTTCAGAGTTCTACAGTCCGACGATC) and 3' Adapters and barcode splitting for small RNA was performed with Cutadapt v1.16
Mapping to tRNA and rRNA (UCSC) for removal of contaminating fragemnts in small RNA was performed using STAR v2.5.2b
Genome mapping to hg38 for transposon quantitation and small RNA analysis was performed using STAR v2.5.2b
Genome mapping to hg38 for differential gene expression was performed using Hisat  v2.2.1.0
Gene quantiation was performed using Stringtie v1.3.4d
Transposon quantitation was performed using Tetoolkit v2.0.3
Immunoprecipitated RNAs (RIP) and small RNAs (sRNA) were further processed and normalized in R environment with custom scripts provided upon request.
Genome_build: hg38
Supplementary_files_format_and_content: xlsx files: (1) GeneQuantificationTPM, (2) TEQuantificationCOUNTS, (3) SizeDistributionAllCOUNTS, (4) ReadAnnotationNormCOUNTS

growth_protocol: COLO205 cells were grown according to the standard procedures outlined on ATCC website

extract_protocol:
total RNA: extracted RNA was used to prepare libraries using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®
Extraction was performed using Zymo Direct-Zol RNA Miniprep Kit and associated procedures

treatment_protocol: No treatements of cells were performed

tag: cell type

value: colon adenocarcinoma

value: retroviral shRNA3 PIWIL1


title: NIH3T3 cells expressing FOXP2-1

description: NIH3T3 cells expressing FOXP2-1

source_name: NIH3T3 cells stably overexpressing FOXP2, clone1

tag: developmental stage


title: tail_DNA-HU-M546.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M546

value: gavage

tag: type

value: HU

tag: strain

tag: sire

tag: dam

tag: tissue

source_name: common C57BL/6J x C3H/HeJ female aCGH reference mouse

value: Ref

value: C57BL/6J x C3H/HeJ


title: 1_DAT_Control_3 [degradome]

value: leaf tissues


title: COLO205_PIWIL1_SH3_2

tag: genotype

tag: cell line


title: tail_DNA-HU-M290xF402.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M290xF402

value: C57BL/6J (sire) x C3H/HeJ (dam)


title: NIH3T3 parent cells

description: NIH3T3 parent cells

source_name: NIH3T3 parent cells

value: parent


title: 1_DAT_Heat_1 [degradome]

value: 37°C heat stress for 5 days


title: COLO205_PIWIL1_SH3_1


title: tail_DNA-HU-F545.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F545

value: tail snip genomic DNA from F1 pup


title: 1_DAT_Control_2 [degradome]


title: NIH3T3 cells expressing vector

description: NIH3T3 cells expressing vector

source_name: NIH3T3 cells stably overexpressing vector

value: embryo

value: fibroblast

value: stably overexpressing vector


title: 1_DAT_Control_1 [degradome]

value: cv Chinese Spring


title: tail_DNA-HU-M638.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M638


title: 0_DAT_Heat_4 [degradome]

value: 0 day after treatment (DAT)


title: COLO205_PIWIL1_SH2_3

value: retroviral shRNA2 PIWIL1


title: 0_DAT_Heat_3 [degradome]


title: tail_DNA-HU-F637.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F637


title: tail_DNA-HU-F726.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F726


title: D2_5-GV

first: Uros

last: Midic

address: 474 S. Shaw Lane

department: Animal Sciences

data_processing:
Illumina Real Time Analysis (RTA) v1.18.6
HiSAT2 alignment to NCBI GRCm38.p4 (Mus Musculus) assembly
Trimming 8 bases from 5' end of unaligned reads (from first alignment); alignment of trimmed reads
Merging accepted_hits.bam from three alignment step (samtools merge)
featureCounts (Subread 1.5.1)
DESeq2 1.16.1
Genome_build: GRCm38.p4 (Mus Musculus)
Supplementary_files_format_and_content: read_count.txt (Per-gene read count, tab-delimited)

source_name: D2 GV oocytes

growth_protocol: Female mice of B6, D2, and B6xD2 F1 genotypes were obtained from Jackson Laboratories at 7 weeks age and used from 8 to 12 weeks age. Both GV and MII oocytes were collected into room temperature HEPES-buffered M2 media. During GV oocyte collection, M2 medium was supplemented with 0.225M 3-Isobutyl-1-methylxanthine (IBMX) (Sigma: I7018) to prevent GVBD. Immediately after collection, MII or GV oocytes isolated from a single mother were pooled, constituting a single biological replicate. The zonae pellucidae were removed by treating in acidified Tyrode’s buffer (TYRODE 1910) for approximately 30 sec followed by immediate washing through M2 media for 1 min.

extract_protocol:
RNA was extracted from pools of GV or MII oocytes (n=9-20) collected from a single mother, using the ARCTURUS PicoPure RNA Isolation kit (ThermoFisher #12204-01). Per the protocol oocytes were heat treated in 20 μL PicoPure extraction buffer at 40oC for 30 minutes and then processed immediately or stored at -80oC. During the RNA isolation, the optional DNase treatment was done for 15 minutes at RT (Qiagen #79254). Isolated RNA was eluted into 11 μl of the PicoPure elution buffer and was immediately used or stored at -80oC.
Five microliters of the isolated RNA was processed and amplified with SPIA technology using the Ovation RNAseq System V2 (NUGEN #7102-32). Libraries were purified using a Qiagen MinElute Cleanup Kit (Qiagen #28204) and eluted into 22 μl of the provided elution buffer. Purified library concentrations were quantified on a Nanodrop (Thermo Fisher NanoDrop Lite) or Biodrop (uLite) and stored at -80oC. Approximately 1μg of SPIA library sample was diluted into 1X TE for a total volume of 130 μL and was fragmented to an average fragment length of 300 bp on a Covaris shearer. 20 μl of each fragmented SPIA library were then mixed with 14 μl H2O, 4 μl 10X S1 nuclease buffer, and 2 μl S1 nuclease for a 40 μL total reaction volume that was incubated for 30 minutes at RT (Promega # M5761). Starting with an additional bead purification, SPIA libraries were taken through the Ovation Ultralow System V2 1-16 (Nugen #0344-32). Samples were randomized for barcode ligation. Library amplification proceeded for 12 cycles. After the last bead purification, amplified-barcoded libraries were eluted in 30 μL of 1X TE. The first batch of libraries were sequenced on an Illumina HiSeq 2500 system; these libraries were loaded at 65% of standard concentration with PhiX library added up to 10% of the input. The second batch of libraries was sequenced on the HiSeq 4000 system where the input was not decreased and PhiX was loaded only to the standard 1%.
50bp single-end RNAseq

tag: Stage

value: GV

tag: batch


title: COLO205_PIWIL1_SH2_2

value: colon adenocarcinoma


title: D2_4-MII

source_name: D2 MII oocytes

value: MII


title: D2_4-GV


title: tail_DNA-HU-M288xF397.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M288xF397

tag: route

value: gavage

value: HU


title: 0_DAT_Heat_1 [degradome]


title: COLO205_PIWIL1_SH2_1


title: COLO205_PIWIL1_SH1_3

value: retroviral shRNA1 PIWIL1


title: 0_DAT_Heat_2 [degradome]

value: leaf tissues


title: D2_3-MII


title: COLO205_PIWIL1_SH1_2


title: D2_3-GV


title: tail_DNA-HU-F538.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F538

value: C57BL/6J (sire) x C3H/HeJ (dam)

value: Ref

value: C57BL/6J x C3H/HeJ


title: 0_DAT_Control_4 [degradome]

value: Control condition


title: COLO205_PIWIL1_SH1_1


title: tail_DNA-HU-M634.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M634

value: tail snip genomic DNA from F1 pup


title: D2_2-MII


title: 0_DAT_Control_3 [degradome]


title: COLO205_PIWIL1_CTRL_3

value: retroviral control shRNA


title: 0_DAT_Control_2 [degradome]


title: tail_DNA-HU-F685.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F685


title: tail_DNA-HU-F633.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F633


title: COLO205_PIWIL1_CTRL_2


title: BDF1_5-MII

source_name: B6xD2 F1 MII oocytes

value: B6xD2 F1


title: BDF1_5-GV

source_name: B6xD2 F1 GV oocytes


title: COLO205_PIWIL1_CTRL_1


title: tail_DNA-HU-M699.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M699

source_name: common C57BL/6J x C3H/HeJ female aCGH reference mouse


title: CdH-Hep

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

data_processing:
Basecalls performed using BCL2Fastq version 1.8.4
Sequenced reads were trimmed for low-quality sequence by using Sickle (V1.33).
After preprocessing, the sequenced reads were mapped to hg19 human reference genome using RSEM (v.1.2.31) with STAR (v2.5.2b)
Merged expression level from paired end reads and orphan read and calculate merged transcript per million (TPM) by using in-house script.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file which contains gene & transcript ID, transcript size, effective size, count, and TPM.

source_name: Human hepatocyte like cells derived form CdH

growth_protocol: Liver tissue samples were perfused via portal vein with a solution A containing 0.19 g/L EDTA (Gibco BRL Co, NY, USA), 8 g/L NaCl, 0.4 g/L KCl, 0.078 g/L NaH2PO4·2H2O, 0.151 g/L Na2HPO4·12H2O, and 0.19 g/L HEPES for 5 min at 37°C, followed by a solution B containing 0.3 g/L collagenase (Sigma, C5138USA), 0.56 g/L CaCl2, 8 g/L NaCl, 0.4 g/L KCl, 0.078 g/L NaH2PO4·2H2O, 0.151 g/L Na2HPO4·12H2O, 0.19 g/L HEPES for 8 min at 37°C. Viable hepatocytes were selected by isodensity centrifugation in Percoll (GE Healthcare, Little Chalfont, United Kingdom). Viability was 80-90% as judged by 0.4% trypan blue exclusion assay. CdH: Hepatocytes were seeded on collagen-coated dishes (STEMCELL Technologies, BC, Canada) at 5000 cells/cm2 in basic High Glucose DMEM/F-12 media (Gibco, CA, USA) containing 1% FBS (Gibco), 10 mM nicotinamide (Sigma-Aldrich, MO, USA), 0.1 μM dexamethasone (Sigma-Aldrich), 1% insulin-transferrin-selenium (ITS) (Gibco), 1% penicillin/streptomycin (Gibco), and 20 ng/ml epidermal growth factor (EGF) (Peprotech, NJ, USA). After overnight incubation, the basic medium was supplemented with 4 μM A83-01 (Gibco) and 3 μM CHIR99021 (STEMCELL Technologies), and 20 ng/ml of hepatocyte growth factor (Peprotech), designated reprogramming medium.

extract_protocol:
Total RNAs were isolated using Trizol Reagent (Gibco). 1-μg RNA samples were reverse transcribed using a Transcriptor First Strand cDNA Synthesis Kit (Roche, PA, USA).
A library was independently prepared with 1 µg of total RNA for each sample using an Illumina TruSeq Stranded mRNA Sample Prep Kit (#RS-122-2101, Illumina, Inc., San Diego, CA, USA). The initial step of library preparation involved purifying poly‐A containing mRNA molecules using poly‐T-attached magnetic beads. After this step, the purified mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved mRNA fragments were copied to the top strand of cDNA using SuperScript II reverse transcriptase (Invitrogen, #18064014) and random primers, and the reverse complement strand of cDNA was synthesized using DNA polymerase I, RNase H, and dUTP. These cDNA fragments underwent the ends repair process including the addition of a single ‘A’ base and adapter ligation. After these steps, the final cDNA libraries were created, purified, and enriched with PCR

value: hepatocyte like cells derived form CdH


title: tail_DNA-HU-M286xF393.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M286xF393


title: G6710

city: Yangling

first: Cunling

last: Jia

state: Shaanxi

address: Xinong road 22#

department: Animal science

institute: Northwest A&F University

data_processing:
Basecalls performed using CASAVA version 1.8
Reads passed filtering were mapped to the Gallus_gallus-4.0 reference genome using TopHat v2.1.1. incorporates the Bowtie v2.0.6 algorithm.
The analyses were conducted within R using packages GenomicFeatures for computing overlaps, and GenomicAlignments for counting short reads mapped within genomic regions on Gallus gallus genome GTF file. Differentially expressed genes (DEGs) were identified by using the edgeR package.
Genome_build: Gallus_gallus-4.0
Supplementary_files_format_and_content: tab-delimited text files include counts of reads values for each Sample

organism: Gallus gallus

source_name: Liver

growth_protocol: Arbor Acres (AA) broiler breeder chicks were reared according to AA Breeder Management Guide specifications to reach target body weight until 21 wk of age.

extract_protocol:
Liver, abdominal fat and ovary were collected at necropsy. Tissue samples were frozen immediately in liquid nitrogen.  Total RNA was extracted from adipose, liver and ovary samples by TRIzol reagent. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: From 22 wk of age, forty chicks were divided into two groups and transferred into individual laying cages. One group was fed ad libitum with the ration 11.74 MJ/kg metabolizable energy and 17 g crude protein/100 g feed (ad libitum group), and the other group was fed continually on the above guide (restricted group).

value: Arbor Acres

value: Liver

tag: feeding

value: restricted

tag: age

value: 30 weeks


title: tail_DNA-HU-F700.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F700


title: G1724


title: BDF1_3-GV

value: GV


title: BDF1_3-MII

value: MII


title: CdH2

source_name: Human chemically derived hepatic progenitor cells replicate #2


title: ATAC-seq

city: Memphis

first: Jinghui

last: Zhang

state: TN

address: 262 Danny Thomas PL, Mail stop 1135

institute: St. Jude Children's Research Hospital

description: The Nalm6 cell line was established from the peripheral blood of a 19-year-old man with acute lymphoblastic leukemia (ALL) in relapse in 1976.

data_processing:
BWA (version 0.5.9-r26-dev, default parameter) to align the ATAC-seq reads to human genome hg19 (GRCh37), Picard (version 1.65(1160)) then have been used for marking duplicated reads.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Nalm6_ATACseq.bw: bigWig file

source_name: B cell precursor leukemia

growth_protocol: For ATAC sequencing, we follow the protocol established by Buenrostro et al. (Buenrostro, J.D., Wu, B., Chang, H.Y. & Greenleaf, W.J. Curr Protoc Mol Biol 109, 21 29 21-29 (2015)).

extract_protocol: Briefly, around 50,000 Nalm6 cells were used for nuclei preparation. Chromatin tagmentation and library construction were carried out using the Nextera DNA sample preparation kit (Illumina, Cat# FC-121-1030). DNA library sequencing was done on an Illumina HiSeq 2500 with 75 bp pair-end reads.

value: B cell precursor leukemia cell line


title: tail_DNA-HU-M718.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M718

value: gavage

value: HU


title: BDF1_2-GV


title: G1725

value: ad libitum


title: G6709


title: 0_DAT_Control_1 [degradome]

tag: cultivar

value: cv Chinese Spring

value: 0 day after treatment (DAT)

value: leaf tissues


title: tail_DNA-HU-M535.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M535

value: C57BL/6J (sire) x C3H/HeJ (dam)

value: tail snip genomic DNA from F1 pup

value: Ref

value: C57BL/6J x C3H/HeJ


title: B6_5-GV

source_name: B6 GV oocytes


title: G1723

value: Arbor Acres


title: Fetal hepatocyte

source_name: Human fetal hepatocytes

value: fetal hepatocytes


title: B6_4-GV


title: BDF1_4-MII

value: B6xD2 F1


title: tail_DNA-HU-F534.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F534


title: B6_3-MII

source_name: B6 MII oocytes


title: H-fibroblast

source_name: Human fibroblasts

value: fibroblasts


title: G1721

value: Liver

value: 30 weeks


title: tail_DNA-HU-F629.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F629


title: M6709

source_name: Ovary

value: Ovary

value: restricted


title: M6710


title: tail_DNA-HU-M631.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M631

value: gavage

value: HU


title: B6_2-MII

value: MII


title: M1723

value: ad libitum


title: B6_2-GV

value: GV


title: tail_DNA-HU-M277xF379.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M277xF379

value: C57BL/6J (sire) x C3H/HeJ (dam)

source_name: common C57BL/6J x C3H/HeJ female aCGH reference mouse


title: M1724


title: Mut-3

city: New Orleans

first: Yiping

last: Chen

state: LA

address: 6400 Freret

department: CMB

institute: Tulane University

data_processing:
cDNA library preparation and sequencing were performed at the Translational Research Center of Tulane University. A total of 260 million 150bp pair-end reads were obtained on Illumina NextSeq 550 equipment for three pairs of samples
Using "Terminal" to merge four lanes Fastq data into one at both ends (R1 and R2).
Data were uploaded in Galaxy platform in fastq
Fastq to Fasta converter
Run Hisat2 (output: BAM)
Run Feature Counts with uploaded mm10 genome
Run DEseq2
Genome_build: mm10

source_name: Tooth germ

extract_protocol:
Tooth germs were removed, flash frozen on dry ice, and RNA was harvested using RNeasy Mini Kit (cat.74134; Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Mut-2


title: B6_1-MII


title: tail_DNA-HU-M530.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M530

value: tail snip genomic DNA from F1 pup


title: VB1-2

city: harbin

first: Ningning

last: Song

address: No.678. Haping Road

institute: Harbin Veterinary Research Institute

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 BCG_str_Tokyo_172 whole genome using bowtie2(version: 2-2.0.5)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mycobacterium bovis BCG_str_Tokyo_172

organism: Mycobacterium tuberculosis variant bovis

source_name: BCG culture

growth_protocol: Mycobacterium bovis BCG str. Tokyo 172 strain was grown in Middlebrook 7H9 medium Becton Dickinson supplemented with 0.05% Tween 80(V/V), 10% ADC (Albumin-Dextrose-Catalase, BD) and 0.2% (V/V) glycerol. The bacteria were incubated at 100 rpm 37℃ until the culture reached an exponential phase.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat#74106, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: VB1 was added at a final concentration of 8 mM in 7H9 liquid medium.

tag: treatment

value: Vitamin B1


title: VB1-3


title: tail_DNA-HU-F529.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F529

value: Ref

value: C57BL/6J x C3H/HeJ


title: M1721

value: Arbor Acres


title: Con-3

value: Wildtype


title: tail_DNA-HU-M526.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M526


title: Con-2


title: F6710

source_name: Adipose

value: Adipose


title: tail_DNA-HU-F528.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F528


title: control 3

value: control


title: F6709

value: 30 weeks


title: tail_DNA-HU-F679.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F679


title: Con-1


title: F1724


title: tail_DNA-HU-M675.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M675


title: control 2


title: M1725

value: Ovary


title: Mut-1


title: 4_DAT_Heat_4 [RNA-seq]

data_processing:
Adapter sequences were removed using Trimmomatic (Bolger et al., 2014; Bioinformatics, 30, 2114-2120) with parameters ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:55. Adapter-trimmed reads longer than 55 nucleotides were retained.
Reads were mapped to the coding sequences of wheat (IWGSC RefSeq v1.0., 2017) using kallisto (Bray et al., 2016; Nature Biotechnology, 34, 525-527) with default parameters.
Transcripts representing read counts higher than five RPM in at least one library were used for differential expression analysis
Genome_build: Wheat IWGSC RefSeq v1.0., 2017; The assembly and corresponding annotations were downloaded from the International Wheat Genome Sequencing Consortium (IWGSC) sequence repository hosted by URGI-INRA https://wheat-urgi.versailles.inra.fr/Seq-Repository/Assemblies and https://wheat-urgi.versailles.inra.fr/Seq-Repository/Annotations
Supplementary_files_format_and_content: Transcript_estimated_read_counts.xlsx

extract_protocol:
Leaf tissue was collected from all heat-stressed and control individual plants immediately at the end of the stress period, i.e., time point zero day after treatment (0 DAT), and at one and four days after treatment (1 and 4 DAT). Total RNA was isolated from all 432 leaf tissue samples using TRI-reagent (Ambion, Naugatuck, CT) as previously described (Ragupathy et al., 2016; Scientific Reports, 6, 39373).
mRNA enrichment, library construction and sequencing were performed by the McGill University and Genome Quebec Innovation Centre (Montreal, QC, Canada). The clustering was done on an Illumina cBot and the flowcell was run on a HiSeq 4000 for 2x100 cycles (paired-end mode) following the manufacturer's instructions.

value: cv Chinese Spring

tag: exposed to

value: 37°C heat stress for 5 days

tag: time point

value: 4 day after treatment (DAT)

value: leaf tissues


title: 4_DAT_Heat_3 [RNA-seq]


title: 4_DAT_Heat_4 [small RNA]

data_processing:
Adapter sequences were trimmed using a custom Perl script and quality assessment was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads ranging from 18 to 24 bp were filtered and exported as fasta files using Geneious (Biomatters Ltd, Auckland, New Zealand)
Redundant reads from each dataset were grouped as distinct tags and were used to query the Rfam (version 11) and wheat chloroplast (http://www.ncbi.nlm.nih.gov/nuccore/NC_002762.1) databases to remove rRNAs, tRNAs, snRNAs, snoRNAs, other long non-coding RNAs and chloroplast sequences
Distinct tags represented by ≥10 reads per million (RPM) in at least one library were mapped to miRNA coding loci previously identified from the hexaploid bread wheat assembly (International Wheat Genome Sequencing Consortium, 2017) using Bowtie2. Distinct tags with 0 mismatch were extracted for hairpin structure prediction using RNAfold (Lorenz et al. Algorithms Mol Biol 2011).
The distinct tags with secondary hairpin structure with <-0.2 kcal/mol/nt were filtered for prediction of star sequence in the opposite strand with a 2bp offset on the 3’-strand of the hairpin.
The read counts of miRNAs annotated with strong evidence for biosynthesis were chosen for differential expression ananysis.
Genome_build: Wheat IWGSC RefSeq v1.0., 2017; The assembly and corresponding annotations were downloaded from the International Wheat Genome Sequencing Consortium (IWGSC) sequence repository hosted by URGI-INRA https://wheat-urgi.versailles.inra.fr/Seq-Repository/Assemblies and https://wheat-urgi.versailles.inra.fr/Seq-Repository/Annotations
Supplementary_files_format_and_content: Raw_read_counts_of_annotated_miRNAs.xlsx

extract_protocol:
Leaf tissue was collected from all heat-stressed and control individual plants immediately at the end of the stress period, i.e., time point zero day after treatment (0 DAT), and at one and four days after treatment (1 and 4 DAT). Total RNA was isolated from all 432 leaf tissue samples using TRI-reagent (Ambion, Naugatuck, CT) as previously described (Ragupathy et al., 2016; Scientific Reports, 6, 39373).
sRNA libraries were constructed from low molecular weight (LMW) RNA isolated from 72 µg of total RNA as described by Lu and Souret (2010) in Methods and protocols (eds. B.C. Meyers & P.J. Green), pp. 107-125. Humana Press, New York. libraries were constructed using Illumina TruSeq® small RNA kit following the manufacturer’s instructions. Six pools, each containing equimolar amounts of 12 random libraries and where each library was present in three different pools. The library pools were normalized to 2 nM and sequenced on a MiSeq for 50 cycles using a MiSeq Reagent Kit v2 (Illumina). A total of six runs were performed to sequence the six pools where each library was sequenced in three separate runs.


title: tail_DNA-HU-M628.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M628

value: gavage

value: HU


title: 4_DAT_Heat_2 [RNA-seq]


title: F1725

value: ad libitum


title: tail_DNA-HU-F627.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F627

value: C57BL/6J (sire) x C3H/HeJ (dam)

value: tail snip genomic DNA from F1 pup


title: control 1


title: 4_DAT_Heat_1 [RNA-seq]


title: F1723


title: tail_DNA-HU-F703.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample F703

value: Ref


title: 4_DAT_Heat_3 [small RNA]


title: 4_DAT_Heat_2 [small RNA]


title: CdH1

source_name: Human chemically derived hepatic progenitor cells replicate #1

tag: cell type


title: F1721


title: Capture-C for IGHM enhancer

data_processing:
Library strategy: Capture-C
The data was analyzed using the pipeline captureC. In order to avoid much high reads coverage at the oligos region when visualizing the signals, the reads at the extended 500 bp region of the fragment were filtered.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Nalm6-IGHMenh_CaptureC.bw: bigWig file

source_name: B cell precursor leukemia

extract_protocol: Three oligos were designed near the cutting sites to capture IGH enhancer (Eμ). Nalm6 was cultured to about 80% confluence and resuspended 10^7 cells in 10 ml of medium. Cells were crosslinked with 2% formaldehyde and quenched by 0.125M glycine. After lysis, cells on ice for 20 min, digested with 500 units of DpnII, then perform the proximity ligation. After reverse crosslinking, ligated DNA was purified, then sheared to 200bp and prepared as general indexed Illumina libraries. 2ug of different indexed samples were captured twice by specific biotinylated oligos, then PCR amplified streptavidin beads pulled down libraries. The NG capture-C libraries were sequenced on MiSeq V2 paired-end 100 cycles.

value: B cell precursor leukemia cell line


title: 4_DAT_Control_4 [RNA-seq]

value: Control condition


title: tail_DNA-Ctl-F693.gavage

description: control F1 pup from the gavage experiment

source_name: gavage Ctl sample F693

treatment_protocol: untreated

tag: type

value: Ctl

value: C57BL/6J x C3H/HeJ


title: 4_DAT_Heat_1 [small RNA]


title: tail_DNA-HU-M274xF373.gavage

description: test F1 pup from the gavage experiment

source_name: gavage HU sample M274xF373

tag: strain


title: tail_DNA-Ctl-M611.gavage

source_name: gavage Ctl sample M611

tag: sire

source_name: common C57BL/6J x C3H/HeJ female aCGH reference mouse


title: 4_DAT_Control_4 [small RNA]


title: 4_DAT_Control_3 [small RNA]


title: tail_DNA-Ctl-M664.gavage

source_name: gavage Ctl sample M664

tag: dam


title: 4_DAT_Control_3 [RNA-seq]

tag: tissue


title: 4_DAT_Control_1 [RNA-seq]


title: 4_DAT_Control_2 [RNA-seq]


title: 4_DAT_Control_2 [small RNA]


title: tail_DNA-Ctl-M621.gavage

source_name: gavage Ctl sample M621


title: 1_DAT_Heat_4 [RNA-seq]

value: 1 day after treatment (DAT)


title: 4_DAT_Control_1 [small RNA]


title: 1_DAT_Heat_4 [small RNA]


title: 1_DAT_Heat_3 [RNA-seq]


title: tail_DNA-Ctl-F617.gavage

source_name: gavage Ctl sample F617


title: 1_DAT_Heat_2 [RNA-seq]


title: 1_DAT_Heat_3 [small RNA]


title: 1_DAT_Heat_1 [RNA-seq]


title: 1_DAT_Heat_2 [small RNA]


title: VB1-1

source_name: BCG culture

value: Vitamin B1


title: TCF3 at 100nM concentration

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to 200 or 100 nM in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated antibody was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least two different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple Alexa 488 scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the Alexa 488 signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. Next, the Seed-and-wobble algorithm was applied to compute enrichment scores (E-scores) and median intensities for all possible 8-mers.

label: Alexa 488

molecule: protein

source_name: Human TCF3

label_protocol: Proteins were tagged with N-terminal GST (EGR1, GATA1, TCF3), N-terminal 6xHis (E2F7, Stat3, MITF), or C-terminal Flag (FOXO3) by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated antibody (to GST: Invitrogen A11131, to 6xHis: Qiagen 35310, to Flag: Fisher 50-193-003).

growth_protocol: GATA1, TCF3: Gateway-compatible clones containing the full-length genes were purchased from GeneCopoeia and the genes were transferred into pDEST15 using the LR Clonase reaction (Life Technologies). This vector enables the production of N-terminally GST-tagged proteins. Cells were grown in LB broth to an OD600 of 0.4 to 0.6 and then expression was induced with IPTG at 30° to 37° C. Pelleted cells were frozen, stored at -20 C, and thawed cells were lysed with lysozyme. The DBD of E2F7 was a kind gift from the Nevins lab (Duke University), where it was expressed and purified as described in Liu et al. 2003 (DOI: 10.1074/jbc.M113.467506). The DBD of EGR1 was a kind gift from the Iwahara lab (University of Texas Medical Branch), where it was expressed and purified as described in Chattopadhyay et al. 2016 (DOI: 10.1021/acs.biochem.6b00757). FOXO3 was a kind gift from the Nevins lab (Duke University), where it was expressed in human 293 cells, as described in Shats et al. 2013 (DOI: 10.1158/0008-5472.CAN-13-0453). MITF was a kind gift from the Young lab (MIT), where it was expressed and purified as described in Lin et al. 2013 (DOI: 10.1016/j.cell.2012.08.026). The DBD of mouse Stat3 was a kind gift from the Arbely lab (Ben Gurion University) where it was expressed and purified as described in Belo et al. 2018 (DOI: https://doi.org/10.1101/537696).

extract_protocol: GST-tagged GATA1 and TCF3 were purified from the soluble portion of the lysate using GST resin (GE Healthcare) according to manufacturer’s instructions. The DBD of E2F7 (from the Nevins lab) was purified as described in Liu et al. 2003 (DOI: 10.1074/jbc.M113.467506). The DBD of EGR1 (from the Iwahara lab) was purified as described in Chattopadhyay et al. 2016 (DOI: 10.1021/acs.biochem.6b00757. FOXO3 (cell lysates from the Nevins lab) was purified by immunoprecipitation using anti-Flag M2-agarose affinity gels (Sigma) according to manufacturer's instructions. MITF (from the Young lab) was purified as described in Lin et al. 2013 (DOI: 10.1016/j.cell.2012.08.026). The DBD of mouse Stat3 (from the Arbely lab) was purified as described in Belo et al. 2018 (DOI: https://doi.org/10.1101/537696).

tag: transcription factor

tag: protein concentration

value: Protein concentration:100nM


title: TBP at 240nM concentration

organism: Arabidopsis thaliana

source_name: A.thaliana TBP (DBD)

label_protocol: The protein was tagged with N-terminal His-6 tag. Protein-bound array was incubated with Alexa-488-conjugated antibody (Qiagen 35310).

growth_protocol: The protein was a kind gift from the Al-Hashimi lab (Duke University). E. coli C41(DE3) cells were transformed with a pET15b plasmid encoding the (Genscript) Arabidopsis thaliana. TATA box binding protein (TBP) DNA binding domain gene with a His-6 tag on the N-terminus. Cells were induced at 15 ºC with 0.5 mM ITPG overnight and pelleted the next day (4 ºC, 4000 rpm). The cell pellets were reconstituted with buffer A (5% glycerol, 4 mM MgCl, 600 mM NaCl, 40 mM MES pH 7.2) and lysed via sonication (4 times at 80% amplitude for 30 sec. for a volume of ~35 mL) and pelleted (40 min, 4 ºC, 16,000 rpm).

extract_protocol: The supernatant was bound to Ni-NTA beads (Qiagen) and the column was washed with increasing concentrations of imidazole in the buffer A. TBP was eluted in buffer A containing between 100 and 1000 mM imidazole, and BME (5 to 10 mM) was added to these fractions directly after elution to avoid oxidizing the Ni beads. TBP was concentrated via centrifugation with a 10K cutoff filter (Amicon) and stored at ~0.5 mM at -80 ºC in either buffer A or 20 mM HEPES-KOH (pH 8), 100 mM KCl, 20% glycerol, 1 mM MgCl2, 1 mM CaCl. Protein yields were typically 2 to 5 mg/L. Concentrations were determined by UV-vis using a calculated molar absorption coefficient of 10.5 mM-1 cm-1.

value: TBP (DBD)

value: Protein concentration:240nM


title: 1_DAT_Control_4 [RNA-seq]

value: cv Chinese Spring


title: Stat3 at 400nM concentration

source_name: Mouse Stat3 (DBD, phosphorylated)

value: Protein concentration:400nM


title: MITF at 100nM concentration

source_name: Human MITF

value: MITF


title: 1_DAT_Heat_1 [small RNA]

value: 37°C heat stress for 5 days

value: leaf tissues


title: 1_DAT_Control_3 [RNA-seq]


title: tail_DNA-Ctl-F523.gavage

source_name: gavage Ctl sample F523

extract_protocol: DNA was isolated from tail snips of selected pups using the Qiagen Blood & Cell Culture DNA Mini Kit using manufacturer’s protocol (https://www.qiagen.com/us/resources/resourcedetail?id=28375699-647d-4b6b-a6a3-6a2715f7d46f&lang=en).

value: gavage

value: C57BL/6J (sire) x C3H/HeJ (dam)


title: tail_DNA-Ctl-M671.gavage

source_name: gavage Ctl sample M671

value: tail snip genomic DNA from F1 pup

value: Ref


title: tail_DNA-Ctl-M519.gavage

source_name: gavage Ctl sample M519


title: 1_DAT_Control_4 [small RNA]

value: Control condition


title: 1_DAT_Control_3 [small RNA]


title: 1_DAT_Control_1 [RNA-seq]


title: FOXO3 at 100nM concentraion

source_name: Human FOXO3


title: EGR1 at 300nM concentration

source_name: Human EGR1 (DBD)

value: Protein concentration:300nM


title: tail_DNA-Ctl-M614.gavage

source_name: gavage Ctl sample M614

value: Ctl

value: C57BL/6J x C3H/HeJ


title: 0_DAT_Heat_4 [RNA-seq]

value: 0 day after treatment (DAT)


title: tail_DNA-Ctl-F667.gavage

source_name: gavage Ctl sample F667


title: 1_DAT_Control_2 [small RNA]

value: 1 day after treatment (DAT)


title: tail_DNA-Ctl-F515.gavage

source_name: gavage Ctl sample F515


title: 1_DAT_Control_2 [RNA-seq]


title: tail_DNA-Ctl-F607.gavage

source_name: gavage Ctl sample F607

source_name: common C57BL/6J x C3H/HeJ female aCGH reference mouse


title: 1_DAT_Control_1 [small RNA]


title: 0_DAT_Heat_3 [RNA-seq]


title: 0_DAT_Heat_4 [small RNA]


title: E2F7 at 500 nM concentration

source_name: Human E2F7 (DBD)

value: Protein concentration:500nM


title: 0_DAT_Heat_2 [RNA-seq]


title: tail_DNA-Ctl-M510.gavage

source_name: gavage Ctl sample M510


title: tail_DNA-Ctl-M603.gavage

source_name: gavage Ctl sample M603


title: GATA1 at 65nM concentration

source_name: Human GATA1

value: Protein concentration:65nM


title: 0_DAT_Heat_3 [small RNA]

value: cv Chinese Spring


title: A375 siCDK11 replicate 3

type: RNA

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

hyb_protocol: Sample hybridization, purification and immobilization were performed according to the manufacturer’s protocol (NanoString Technologies).

scan_protocol: Sample imaging was performed according to the manufacturer’s protocol (NanoString Technologies).

data_processing: Digital analyzer output reporter code count (RCC) files were analyzed using two R software packages: the NanoStringQCPro package to assess quality and to obtain a normalized data matrix for visualization purposes and the NanoStringDiff package for differential gene expression testing. The raw count data was background subtracted, base 2 log transformed, centered and scaled. Sample group comparisons between siCDK11 and siControl were made using the general linear model method employed in the NanoStringDiff R package.

label: NanoString capture and reporter probe mix

source_name: A375 malignant melanoma cell line

label_protocol: Samples were not specifically labeled, but prepared according to the manufacturer’s protocol (NanoString Technologies).

growth_protocol: A375 growth conditions were DMEM high glucose (HyClone SH30243.01), 10% FBS, 1% Pen/Strep. All cell lines were grown in an incubator at 37 ºC with 5% CO2.

extract_protocol: Total RNA was isolated from frozen cell pellets using the RNeasy mini kit (Qiagen), including the on-column DNase digestion according to the manufacturer’s protocol, and quantitated using a NanoDrop spectrophotometer.

treatment_protocol: Standard chemistry siRNAs were obtained from Dharmacon (Lafayette, CO). The sense strand sequence for siCDK11: 5'-gagcgagcagcagcgugugdTdT-3'. The control siRNA (siControl) used was siNon-targeting #2 (Dharmacon; D-001810-02). SiRNA transfection complexes were formed by combining 30 nM siRNA with 10 µL Dharmafect 1 and OPTI-MEM in total volume of 400 µL. After a 20 min incubation, 1.6 mL of antibiotic-free media containing 5% FBS was mixed in and the total volume was added to cells at 50% confluence on 60 mm plates after the previous growth media was removed. After 5 h of incubation at 37 C 5% CO2, an additional 2 mL of complete media was added to each plate. At 48 hr post-transfection, the cells were harvested for RNA.

tag: cell line

value: A375 malignant melanoma cell line

tag: sirna target

value: siCDK11A and siCDK11B

tag: run cartridge

tag: run lane

tag: run date


title: 0_DAT_Heat_1 [RNA-seq]

tag: cultivar

value: 37°C heat stress for 5 days


title: tail_DNA-Ctl-F506.gavage

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 data extraction.

source_name: gavage Ctl sample F506

tag: route


title: tail_DNA-Ctl-F579.gavage

source_name: gavage Ctl sample F579


title: 0_DAT_Control_4 [RNA-seq]

tag: exposed to

value: leaf tissues


title: A375 siNonTargeting replicate 3

value: siNonTargeting NT


title: tail_DNA-Ctl-M660.gavage

source_name: gavage Ctl sample M660

value: gavage

value: C57BL/6J (sire) x C3H/HeJ (dam)


title: 0_DAT_Control_4 [small RNA]

tag: time point


title: 0_DAT_Heat_1 [small RNA]


title: A375 siCDK11 replicate 2


title: 0_DAT_Control_3 [small RNA]


title: tail_DNA-Ctl-F511.gavage

source_name: gavage Ctl sample F511

value: tail snip genomic DNA from F1 pup

value: Ref


title: 0_DAT_Control_1 [RNA-seq]

value: Control condition


title: A375 siCDK11 replicate 1


title: tail_DNA-Ctl-M714.gavage

source_name: gavage Ctl sample M714

value: Ctl


title: A375 siNonTargeting replicate 2


title: A375 siNonTargeting replicate 1


title: NR3C1 at 800 nM concentration

source_name: Human NR3C (also known as GR) (DBD)

label_protocol: Protein was tagged with N-terminal 6xHis. Protein-bound arrays were incubated with Alexa-488-conjugated antibody (Qiagen 35310).

growth_protocol: The protein (DBD of human GR, amino acids 418-506) was a kind gift from the Pufall lab (University of Iowa), where it was expressed and purified as described in Zhang et al. 2018 (DOI: 10.1101/gr.222844.117).

extract_protocol: The protein was purified as described in Zhang et al. 2018 (DOI: 10.1101/gr.222844.117)

value: Protein concentration:800nM


title: tail_DNA-Ctl-F502.gavage

source_name: gavage Ctl sample F502

value: C57BL/6J x C3H/HeJ


title: TFAP2A at 100nM concentration

source_name: Human TFAP2A

label_protocol: Proteins were tagged with N-terminal GST during cloning. Protein-bound arrays were incubated with anti-GST Alexa-488-conjugated antibody (Invitrogen A11131).

growth_protocol: Gateway-compatible clones containing the full-length genes were purchased from GeneCopoeia and the genes were transferred into pDEST15 using the LR Clonase reaction (Life Technologies). This vector enables the production of N-terminally GST-tagged proteins. Cells were grown in LB broth to an OD600 of 0.4 to 0.6 and then expression was induced with IPTG at 30° to 37° C. Pelleted cells were frozen, stored at -20 C, and thawed cells were lysed with lysozyme.

extract_protocol: GST-tagged SIX6 and TFAP2A were purified from the soluble portion of the lysate using GST resin (GE Healthcare) according to manufacturer’s instructions.

value: Protein concentration:100nM


title: tail_DNA-Ctl-M575.gavage

source_name: gavage Ctl sample M575


title: Zfp24 at 100nM concentration

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to 200 or 100 nM in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-647-conjugated antibody was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned at 635nm wavelength to detect the Alexa-647-conjugated antibody using at least two different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the fluorescent signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. Next, the Seed-and-wobble algorithm was applied to compute enrichment scores (E-scores) and median intensities for all possible 8-mers.

source_name: Mouse Zfp24

label_protocol: Protein was recognized with a primary antibody (Sigma-Aldrich) followed by a secondary, Alexa-647-conjugated antibody (Life Technologies).

growth_protocol: The protein was a kind gift from the Popko lab (University of Chicago) where it was expressed and purified as described in Elbaz et al. 2018 (DOI: 10.1016/j.celrep.2018.04.089).


title: 0_DAT_Control_1 [small RNA]

value: 0 day after treatment (DAT)


title: 0_DAT_Control_2 [small RNA]


title: 0_DAT_Control_3 [RNA-seq]


title: 0_DAT_Control_2 [RNA-seq]


title: SIX6 at 100nM concentration

source_name: Human SIX6


title: tail_DNA-Ctl-M571.gavage

source_name: gavage Ctl sample M571

source_name: common C57BL/6J x C3H/HeJ female aCGH reference mouse


title: siERK1n2_17 [WGC100713R]

status: Public on May 07 2019

city: new haven

first: Nicolas

last: Ricard

state: CT

address: 300 george street

department: internal medicine

institute: yale university

data_processing:
Bases were called in real-time on the Illumina HiSeq X
Paired-end reads were aligned to hg38 (GRCh38) using STAR 2.5.1b aligner with a custom-built index in two-pass mode.  The first pass parameters were: --twopassMode Basic --outFilterType BySJout --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.66 --outFilterIntronMotifs None --outSJfilterReads All --outSAMstrandField intronMotif --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 0 --chimScoreDropMax 20 --chimScoreSeparation 10 --chimScoreJunctionNonGTAG -1 --quantMode TranscriptomeSAM. The second pass genome index was created from the first pass SJ.out.tab file with an --sjdbOverhang 149.  The second pass alignment was run against the new index, with the same initial alignment parameters.
Expression quantification was performed using RSEM v1.2.28 with GENCODE release 24 annotation using the following parameters: --bam --no-bam-output --estimate-rspd --append-names --paired-end --forward-prob 0.5
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file including RSEM counts for each sample

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVEC) were purchased from Lonza and cultivated in EBM-2 MV medium (Lonza)

extract_protocol:
RNA extractions were done using RNeasy mini kit (Qiagen) with DNAse digestion (Qiagen).
Paired-end sequencing library was prepared using Illumina Truseq v1 library prep kit.

treatment_protocol: siRNAs were purchased from Qiagen: siRNA MAPK1_10 and MAPK3_6, and siSCR  #1027281.  siRNA transfetions were done in OptiMem medium (ThermoFisher) with the lipofectamine RNAimax transfection agent (ThermoFisher).

tag: cell type

value: Human umbilical vein endothelial cells (HUVEC)

tag: genotype/variation


title: siERK1n2_24 [WGC100718R]


title: siERK1n2_19 [WGC100715R]


title: siERK1n2_22 [WGC100717R]


title: siERK1n2_21 [WGC100716R]


title: siERK1n2_18 [WGC100714R]


title: siERK1n2_16 [WGC100712R]


title: siERK1n2_15 [WGC100711R]


title: siERK1n2_9 [WGC100706R]


title: siERK1n2_14 [WGC100710R]


title: siERK1n2_10 [WGC100707R]


title: siERK1n2_6 [WGC100704R]


title: siERK1n2_5 [WGC100703R]


title: siERK1n2_3 [WGC100701R]


title: siERK1n2_11 [WGC100708R]


title: siSCR_24 [WGC100698R]

value: siSCR


title: siSCR_23 [WGC100697R]


title: siSCR_22 [WGC100696R]


title: siERK1n2_1 [WGC100699R]


title: siERK1n2_8 [WGC100705R]


title: siSCR_19 [WGC100693R]


title: siSCR_17 [WGC100691R]


title: siSCR_16 [WGC100690R]


title: siSCR_14 [WGC100688R]


title: siSCR_12 [WGC100686R]


title: siSCR_15 [WGC100689R]


title: genomic DNA from pancreatic tumor [M_18_3]

city: Asahikawa

first: Yusuke

last: Mizukami

state: Hokkaido

address: 2-1 Modorigaoka Higashi

department: Medicine

country: Japan

institute: Asahikawa Medical University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip kits (Illumina, Inc., San Diego, CA) using standard Illumina protocol.

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing:
Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles.
Background intensity computed from a set of negative controls was subtracted from each analytical data point.
The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100).
The ß-value reflects the methylation level of each CpG site.
A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.
The non_normalized.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: IPMN

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from formalin-fixed paraffin-embedded samples using GeneRead DNA FFPE Kit (Qiagen, Hilden, Germany) according to standard instructions

tag: gender

value: Male

tag: tumor type/grade

value: intraductal papillary mucinous neoplasm; KRAS G12D & GNAS R201H

tag: sample type

value: formalin-fixed paraffin-embedded sample


title: genomic DNA from pancreatic tumor [M_18_2]


title: siSCR_9 [WGC100685R]


title: siSCR_20 [WGC100694R]


title: siSCR_21 [WGC100695R]


title: siSCR_4 [WGC100682R]


title: siSCR_1 [WGC100679R]


title: siSCR_3 [WGC100681R]


title: siSCR_13 [WGC100687R]


title: HiC_wbc_rep1

city: Chicagp

first: Yaping

last: Liu

state: IL

address: 303 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Hi-C data processing: Raw fastq files from various Hi-C experiments were uniformly processed using Juicer command line tools v1.5.6 and  aligned to the human genome (GRCh38 with decoys, alt contigs, and HLA contigs). Only results after filtering reads with mapping quality score > 30 were used to generate a Pearson correlation matrix and compartment A/B eigenvector. PCA was performed using the PCA function in scikit-learn 0.19.1 in Python 3.6. The first principal component was used to segment the compartments. For each chromosome, compartments were split into two groups based on their sign. After excluding regions with mappability less than 0.75, the group of compartments with the lower mean gene density (based on Ensembl v84 annotations) was defined as compartment B; the other group was defined as compartment A. HiCCUPS loops were called by hiccups command line in Juicer with parameters “-k KR -m 512 -r 5000,10000,25000 -f .1,.1,.1 -p 4,2,1 -i 7,5,3 -t 0.02,1.5,1.75,2 -d 20000,20000,50000”.
Genome_build: hg38
Supplementary_files_format_and_content: hic

source_name: white blood cells

extract_protocol:
WBCs are freshly isolated from whole blood, purified neutrophils are obtained frozen from a commercial source (Astarte Biologics Inc) and then thawed
Hi-C library preparation on white blood cells and neutrophils was performed using the Arima-HiC kit (Arima Genomics, Inc.; Cat # A510008), according to the manufacturer’s protocols. Briefly, WBCs (freshly isolated from whole blood) or purified neutrophils (obtained frozen from a commercial source and then thawed) were crosslinked using formaldehyde. Crosslinked cells were then subject to the Arima-HiC protocol, which utilizes multiple restriction enzymes to digest chromatin. Arima-HiC sequencing libraries were prepared by first shearing purified proximally-ligated DNA and then size-selecting 200-600 bp DNA fragments using SPRI beads. The size-selected fragments were then enriched using Enrichment Beads (provided in Arima-HiC kit), and then converted into Illumina-compatible sequencing libraries with TruSeq adapters using the KAPA Hyper Prep kit. The purified, PCR-amplified DNA underwent standard QC (qPCR and Bioanalyzer) and was sequenced with unique dual indexes on the Illumina HiSeq X (WBC) or NovaSeq 6000 (neutrophils) Sequencing System at 2x151 base pairs.

value: primary cell

tag: restriction enzyme

value: Arima (multi-enzyme)


title: HiC_wbc_rep2

description: Hi-C library preparation on white blood cells and neutrophils was performed using the Arima-HiC kit (Arima Genomics, Inc.; Cat # A510008), according to the manufacturer’s protocols. Briefly, WBCs (freshly isolated from whole blood) or purified neutrophils (obtained frozen from a commercial source and then thawed) were crosslinked using formaldehyde. Crosslinked cells were then subject to the Arima-HiC protocol, which utilizes multiple restriction enzymes to digest chromatin. Arima-HiC sequencing libraries were prepared by first shearing purified proximally-ligated DNA and then size-selecting 200-600 bp DNA fragments using SPRI beads. The size-selected fragments were then enriched using Enrichment Beads (provided in Arima-HiC kit), and then converted into Illumina-compatible sequencing libraries with TruSeq adapters using the KAPA Hyper Prep kit. The purified, PCR-amplified DNA underwent standard QC (qPCR and Bioanalyzer) and was sequenced with unique dual indexes on the Illumina HiSeq X (WBC) or NovaSeq 6000 (neutrophils) Sequencing System at 2x151 base pairs.


title: siSCR_18 [WGC100692R]


title: genomic DNA from pancreatic tumor [M_18_1]

source_name: INV

value: invasive pancreatic ductal adenocarcinoma; KRAS G12D


title: genomic DNA from pancreatic tumor [M_18_5]

source_name: PanIN

value: pancreatic intraepithelial  neoplasia; KRAS G12D


title: siSCR_7 [WGC100683R]


title: Exp180G

city: Pleasanton

first: Maeve

last: Ohuallachain

state: CALIFORNIA

address: 4300 Hacienda Drive

institute: ROCHE SEQUENCING SOLUTIONS INC

data_processing:
FLASH-1.2.11 was used to merge the paired end reads.
seqtk-v1.2 was used to convert merged fastq file to fasta format.
The reads were then parsed to identify cell-id and marker-id based on the white-list info in the associated qdata folder, deduplicated based on cell-id and marker-ids and finally chimeric reads were filtered out.
Expression counts were then used to remove putative debris and doublets cells based on the criteria listed in Singlet_settings.txt in the corresponding qdata folder.
Expression counts matrix was then normalized by scaling the counts by row-means and multiplying by a factor of 10.
Genome_build: A github repository for the software used to process the raw-fastqs is available at the following location: https://github.com/bioinform/QBC_Single_Cell_Analysis_NGS
Supplementary_files_format_and_content: Tab separated text files containing jittered expression counts (both normalized and un-normalized) for different markers for each individual cell
The *tar.gz contains various files containing white-list information for cell-barcode ids, anchor-sequence info, marker-sequence info and settings information for removal of cell-debris and cell-doublets. The files in this folder is used to process the raw fastqs for each of the experiment.

source_name: primary spleen cells

growth_protocol: Spleen cells were obtained from C57/Blk6 mice, between 6-8 weeks of age. 16% formaldehyde solution (Thermo Scientific, 28908) was added directly to cells to a final concentration of 1.6% and incubated for 10 min at room temperature to fix the cells. Cells to be analyzed for only protein expression were stored in 1X PBS with 10% DMSO at -80°C until antibody staining.

extract_protocol:
QIAquick Gel Extraction Kit (Qiagen, 28704).
PCR with Illumina dual index primers
Single cell barcoding by split-pool synthesis via ligation

tag: strain

value: primary spleen cells

tag: molecule type

value: various proteins


title: Exp180M


title: exp213B


title: exp211-a1


title: 0_DAT_Heat_2 [small RNA]

value: cv Chinese Spring

value: 37°C heat stress for 5 days

tag: tissue

value: leaf tissues


title: genomic DNA from pancreatic tumor [M_18_4]

source_name: CIS

value: carcinoma in situ; KRAS G12D


title: exp185T


title: KO cells adipogenic sample 3

city: Abu Dhabi

first: Mohamed

last: Al-Sayegh

address: Saadiyaat Island - 1st floor ERB, Room 136, P.O. Box 129188

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

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 the Mus musculus GRCm38.p4 genome using tophat2 v2.1.0 with the parameters “–no-novel-junctions” and “–G” when specifying the genome file
Raw counts of mapped reads of each genes were derived using HTseq count
DESeq2 was used for differential expression analysis.
Genome_build: Mus musculus GRCm38.p4 genome version
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: connective tissue - MEFs

growth_protocol: The  β-actin−/− MEFs (KO) and wild-type (WT) from Dr. Christophe Ampe, University of Gent, Belgium, were cultured in DMEM with high glucose, 10% fetal bovine serum, and 100 U/ml penicillin and 100 µg/ml streptomycin (all from Millipore-Sigma), in a humidified incubator with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using combination of TriZol LS and RNeasy Mini Kit (Qiagen) according to the manufacturer protocol.
Total RNA was used for library construction at the Center for Genomics and Systems Biology, New York University Abu Dhabi, using TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: The  β-actin−/− MEFs (KO) and wild-type (WT) were induced to adipocyte differentiation media including growth medium supplemented with 10mg/ml Insulin (Ins), 2mM Dexamethasone (Dex), 0.5mM 3-isobutyl-1-methylxanthine (IBMX) and 25mg/ml Ascorbic Acid (AsA).

value: BALB/c

tag: age

value: 10.5 day old embryos

tag: genotype

value: beta-actin knockout

value: Mouse Embryonic Fibroblast (MEFs)

tag: treatment

value: Incubated with adipocyte differentiation media for 6 days


title: KOTS_H3K4me3_ChIP_rep2

city: Fukuoka

first: Takashi

last: Ishiuchi

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

department: Medical Institute of Bioregulation

institute: Kyushu University

data_processing:
For RNA-seq, reads were aligned using TopHat (v2.1.1) with the option ‘--segment-length 34 --library-type fr-secondstrand’, and the Cufflinks program (v2.2.1) with the option ‘-u --library-type fr-secondstrand’ was used to calculate the fragments per kilobase of exon per million mapped fragments (fpkm) value.
For H3K4 ChIP-seq, reads were aligned to the mouse genome (mm9) using Bowtie2 (v2.2.9) with the option ‘-N 1’after removing adaptor sequences and low quality reads by TrimGalore. The enrichment of H3K4me3 was analyzed through the normalization with input samples.
ATAC-seq reads were aligned  aligned to the mouse genome (mm9) using Bowtie2 (v2.2.9) with the option ‘-N 1 -L 25’.
Genome_build: mm9, hg38
Supplementary_files_format_and_content: Text files include FPKM values for each sample. BigWig files include the information of genomic distributions of ChIP or ATAC reads.

source_name: TS cells

growth_protocol: Mouse TS cells were cultured in RPMI medium containing 70% feeder-consitioned medium, FGF4, heparin and Activin A (Peprotech). Human TS cells were cultured as described previously (Okae et al, Cell Stem Cell, 2018).

extract_protocol:
Total RNA was extracted with RNeasy Mini kit (QIAGEN). For ChIP-seq, chromatin was sonicated with Covaris S2. ATAC-seq was carried out with a standard protocol.
150 ng of total RNA from each sample was used for library preparation. mRNA was purified with NEBnext poly(A) mRNA magnetic isolation module (NEB), and sequence libraries were prepared with NEBnext Ultra II Directional RNA library prep kit (NEB) following the manufacturer’s protocol. ChIPmentation was carried out for H3K4me3 ChIP-seq library construction with 7 min incubation with a Tn5 tagmentation enzyme solution (Schmidl et al., 2015). ATAC-seq was carried out as described previously (Buenrostro et al., 2013).

value: trophoblast stem (TS) cells

value: Zfp281 knockout

tag: chip antibody

value: H3K4me3 (Millipore, catalog# MC315, lot# 2965110)


title: KO cells adipogenic sample 1


title: WT cells adipogenic sample 1

value: wild-type


title: WT cells adipogenic sample 3


title: KOTS_H3K4me3_ChIP_rep1


title: 3113-XQ-4_mutant rep1

city: Nashville

first: Xianghu

last: Qu

address: 2213 Garland Ave

institute: Vanderbilt medical center

data_processing:
Raw data quality control was performed with QC3 (https://github.com/slzhao/QC3)
Alignment was done using Tophat v2.0.9.
FPKM and cuffdiff were generated using Cufflinks v2.2.1.
Read counts were generated using HTSeq and processed using MultiRankSeq.
Genome_build: mm10
Supplementary_files_format_and_content: Baldwin_Qu_TIE2_FPKM_table is a tab delimited text file containing Ensemble gene ID, Gene name, and reads for each control and mutant replicate.   Differential Gene Expression (Baldwin_Qu_TIE2_Gene_exp) is a diff file with Ensembl Gene ID, Gene name, Gene Chromosomal location, normalized FPKM read count data, and statistical comparisons between controls and mutants.

source_name: conditional knockout (Nfatc1Cre:Tie2 flox/flox)_hearts

extract_protocol:
RNA was isolated from whole hearts using Trizol, n= 18 per genotype, and then divided into three replicates.
Libraries were prepared using Illumina Tru-seq RNA sample prep kit.

tag: strain background

tag: developmental stage

value: embryonic day 11.5

value: Nfatc1Cre:Tie2 fl/fl

value: heart


title: WTTS_K4me3_Input


title: 3113-XQ-5_mutant rep2


title: 3113-XQ-2_control rep2

source_name: control (Tie2 flox/wild-type)_hearts

value: Tie2 flox/wild-type


title: WTTS_H3K4me3_ChIP_rep1


title: 3113-XQ-1_control rep1


title: 3113-XQ-3_control rep3


title: KOTS_K4me3_Input


title: WT cells adipogenic sample 2


title: KOmTS2_RNA

description:
processed data file: mTS_FPKM.txt
TSKO2_FPKM


title: KOmTS1_RNA

description:
processed data file: mTS_FPKM.txt
TSKO1_FPKM


title: BE2C_NCT503c

city: Birmingham

first: Han-Fei

last: Ding

state: Alabama

address: WTI 602D, 1824 6th Avenue South

department: Pathology

institute: University of Alabama at Birmingham

description: RNA expression value

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were normalized, significance determined by ANOVA, and fold change calculated with the Partek Genomics Suite (Partek Inc., St. Louis, MO).

label: biotin

label_protocol: TdT-labled cRNA were prepared with an Affymetrix GeneChip WT Terminal labeling kit

growth_protocol: BE(2)-C cells were cultured in DME/F-12 1:1 (HyClone SH30023, Thermo Scientific) supplemented with 10% FBS (Atlanta Biologicals S11050).

extract_protocol: Total RNA was isolated from the cell samples using Trizol (Invitrogen), and RNA quality and quantity was assessed using a Agilent BioAnalyzer and a Nanodrop Spectrophotometer.

treatment_protocol: BE(2)-C cells were treated with DMSO or 10 µM NCT-503 for 2 days.

value: Neuroblastoma

tag: cell line


title: KO cells adipogenic sample 2


title: BE2C_DMSOc

description: RNA expression value


title: 3113-XQ-6_mutant rep3


title: WTmTS1_RNA

description:
processed data file: mTS_FPKM.txt
TSWT1_FPKM


title: WTTS_H3K4me3_ChIP_rep2


title: BE2C_NCT503b

description: RNA expression value


title: BE2C_DMSOa

description: RNA expression value


title: WTmTS2_RNA

description:
processed data file: mTS_FPKM.txt
TSWT2_FPKM


title: BE2C_DMSOb

description: RNA expression value


title: BE2C_NCT503a

description: RNA expression value


title: siERK1n2_4 [WGC100702R]

value: Human umbilical vein endothelial cells (HUVEC)


title: 99k_HiSeq

source_name: K562 cell line

growth_protocol: K562 cells and SK-MEL-2 cells were obtained from America Type Tissue Collection (ATCC). K562 cells were grown in IMDM media (from Invitrogen) with 10% FBS and 1% Pen Strep Glut. SK-MEL-2 were grown in EMEM (from ATCC) with 10% FBA and 1% PenStrep Glut. Cells to be analyzed for only mRNA expression or both protein and mRNA expression were stored in methanol at -80°C until staining.

value: cell line

value: CD33 protein and various targeted RNA transcripts


title: cbfs treated with 24 h, rep 1 [cbf24_1]

city: Beijing

first: Yuxin

address: No. 2 Yuanmingyuan west road, Haidian district

institute: China Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Arabidopsis TAIR10 genome using TOPHAT v.2.1.0
CUFFLINKS v.2.2.1 was used to assemble the new transcripts
HTSEQ v.0.6.0 was used to calculate the raw read counts for each gene.
Gene expression normalization among samples was performed by using DESEQ2.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: cbfs treated with 24 h

growth_protocol: The plants were grown on 1/2 MS mediam under long day condition at 22 degree  for 14 d

extract_protocol:
The total RNA extraction was performed following the protocol of Tiangen RNAprep pure Plant Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 14-day-old plants were treated with 4 degree for indicated time: 0, 3 and 24 h

value: cbfs-1 mutant

value: seedling

value: under 4 degree for 24h


title: cbfs treated with 24 h, rep 2 [cbf24_2]