title: Pt. 1229BAL [iRepertoire]

city: Aurora

first: Andrew

middle: P

last: Fontenot

state: Colorado

department: Dept. of Medicine

institute: University of Colorado Denver

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1229_BAL_a_output.txt
beta: 1229_BAL_b_output.txt

data_processing:
Library strategy: Amplicon sequencing
All processed files contain the identified TCRs and frequencies for each TCR sequence. The sample source as well as the patient ID are included in the file names.
Paired-end runs were performed, but only the Read 1 files were used for analyses, as they encompassed all bases necessary for the TCR readout. Read 1 was reverse complemented, trimmed by 3 base pairs from the 3' end, and then split by the iRepertoire barcodes for alpha and beta files to be exported separately.
Sequences were then processed using miTCR to (1) identify the V, J, and CDR3 and (2) compute frequency values for individual TCRs.
Genome_build: IMGT TCR database
Supplementary_files_format_and_content: *txt: All processed data files contain the identified TCRs and frequencies for each TCR sequence. The sample source as well as the patient ID are included in the file names.

organism: Homo sapiens

source_name: Bronchoalveolar lavage

extract_protocol:
RNA was purified from CD4+ T cells according to the manufacturer’s instructions in the Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany). Two rounds of PCR using the iRepertoire human TCR alpha and beta kits (iRepertoire, Huntsville, AL) were performed according to the manufacturer’s instructions. Separate reactions were performed for alpha and for beta for each sample.
PCR amplicons were generated using primers in the commercial iRepertoire TCR alpha and beta kits, with each patients' alpha and beta TCR products uniquely barcoded after subsequent PCRs.

treatment_protocol: Bronchoalveolar lavage (BAL) cells were incubated in 6 or 12 well plates for 20 minutes at 37°C to remove alveolar macrophages. CD4+ T cells were obtained after positive selection cell sorting from BAL or blood and incubated overnight in media supplemented with 30 U/ml IL-2.

tag: disease

value: None (healthy control)

tag: hla type

tag: irepertoire commercial primers

tag: cell type isolated

value: CD4+ T cells

tag: patient


title: LD_G6_T5_A

status: Public on Jul 21 2017

type: SRA

city: Urbana

first: Yoshie

last: Hanzawa

state: IL

address: 1201 West Gregory Drive

department: Cropsciences

country: USA

institute: University of illinois at Urbana Chammpaign, USA

description: Read_counts: 8454777

library_source: transcriptomic

data_processing:
The quality-scores line in fastq files processed with Casava1.8 using an ASCII offset of 33 (known as Sanger scores) instead of the previous 64 offset. (pools 1-2-3 run 160, HiSeq#1 with an error rate of 0.84 %, pools 4-5 run 162, HiSeq#1 with an error rate of 0.54% pools 6 through 12, run 226 HiSeq#2error rate: 0.88%).
Adapter Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG
Reads were aligned onto soybean transcriptome (williams 82) obtained from Phytozome database (Schmutz et al, 2010) using Bowtie aligner (Langmead et al, 2009) with following parameters;  -S -q  -k 1 --best -p 4 --phred33-quals
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample.

molecule: total RNA

organism: Glycine max

source_name: First trifoliate

growth_protocol: Plants were grown under long-day (16L:8D) or short-day (10L:14D) conditions for 26 days. For the shift experiment, plants were grown under long-day for three weeks were treated with short-day for 5 days. Sampling was carried out at three time points every 8 hours over a 24 hour period with 3 biological replicates.

extract_protocol:
Plant samples were ground and RNAs were extracted using the RNeasy® Plant Mini Kit (Qiagen®).
The RNAseq libraries were prepared with Illumina's 'TruSeq RNAseq Sample Prep kit. The libraries were pooled and quantitated by qPCR, and sequenced for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3 and analyzed with Casava-1.8 (pipeline 1.9), following the manufacturer's instructions (Illumina, San Diego, CA).

treatment_protocol: For LD treatment, plants were exposed to 16 hours of light from 6:45 until 22:45. For SD treatment, plants were exposed to 10 hours of light from 6:45 until 16:45.  For shift treatment, plants were grown under LD for 21 days and shifted to SD for 5 days. Sampling was carried out 26 DAP (days after planting) at three time points every 8 hours over a 24 hour period with 3 biological replicates.

tag: cultivar

tag: treatment

value: Long Day (16L:8D)

tag: timepoint

value: evening 10:30 pm

tag: age at rna extraction

value: 26 DAP


title: Pt. 1180BAL [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1180_BAL_a_output.txt
beta: 1180_BAL_b_output.txt

value: Non-LS sarcoidosis

value: Other (DR3-/DRB3-)


title: SD_G1_T1_A

description: Read_counts: 5587611

value: Clark

value: Short Day (10L:14D)

value: morning 6:30 am


title: SD_G4_T1_C

description: Read_counts: 8771705


title: SD_G1_T1_C

description: Read_counts: 14135270


title: LD_G6_T1_C

description: Read_counts: 9780640


title: LD_G6_T1_A

description: Read_counts: 12726024


title: LD_G5_T5_C

description: Read_counts: 11041647


title: LD_G6_T1_B

description: Read_counts: 12957444


title: Pt. 1215BAL [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1215_BAL_a_output.txt
beta: 1215_BAL_b_output.txt

value: Lofgren's syndrome (LS) sarcoidosis


title: Pt. 1177BAL [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1177_BAL_a_output.txt
beta: 1177_BAL_b_output.txt


title: LD_G5_T5_A

description: Read_counts: 12253695


title: Pt. 1162BAL [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1162_BAL_a_output.txt
beta: 1162_BAL_b_output.txt


title: LD_G5_T3_B

description: Read_counts: 9371306

value: afternoon 2:30 pm


title: Pt. 1162 Blood [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1162_PBMC_a_output.txt
beta: 1162_PBMC_b_output.txt

source_name: Peripheral blood lymphocytes


title: LD_G5_T5_B

description: Read_counts: 16577244


title: Pt. 1147BAL [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1147_BAL_a_output.txt
beta: 1147_BAL_b_output.txt


title: LD_G6_T3_A

description: Read_counts: 8318483


title: LD_G5_T1_C

description: Read_counts: 10676548


title: LD_G5_T3_A

description: Read_counts: 9681215


title: LD_G5_T1_B

description: Read_counts: 13637399


title: LD_G4_T5_B

description: Read_counts: 7660463


title: LD_G4_T5_C

description: Read_counts: 12050054


title: LD_G5_T1_A

description: Read_counts: 11774959


title: LD_G4_T3_C

description: Read_counts: 11458505


title: Pt. 1127BAL [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1127_BAL_a_output.txt
beta: 1127_BAL_b_output.txt


title: LD_G4_T5_A

description: Read_counts: 20862913


title: Pt. 1124 Blood [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1124_PBMC_a_output.txt
beta: 1124_PBMC_b_output.txt


title: Pt. 1124BAL [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1124_BAL_a_output.txt
beta: 1124_BAL_b_output.txt


title: LD_G4_T3_A

description: Read_counts: 11590706


title: LD_G4_T1_B

description: Read_counts: 9215452


title: LD_G5_T3_C

description: Read_counts: 16715606


title: LD_G4_T1_C

description: Read_counts: 11144166


title: Pt. 1103 Blood [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1103_PBMC_a_output.txt
beta: 1103_PBMC_b_output.txt

value: Fibrosis (non-sarcoidosis)


title: LD_G4_T3_B

description: Read_counts: 10314857


title: Pt. 1127 Blood [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1127_PBMC_a_output.txt
beta: 1127_PBMC_b_output.txt


title: LD_G4_T1_A

description: Read_counts: 10025782


title: LD_G3_T5_B

description: Read_counts: 11213293


title: LD_G3_T5_C

description: Read_counts: 11657784


title: Pt. 1103BAL [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1103_BAL_a_output.txt
beta: 1103_BAL_b_output.txt


title: LD_G3_T5_A

description: Read_counts: 9871527


title: LD_G3_T3_B

description: Read_counts: 11125826


title: LD_G3_T3_C

description: Read_counts: 13090954


title: Pt. 1102 Blood [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1102_PBMC_a_output.txt
beta: 1102_PBMC_b_output.txt


title: Pt. 1102BAL [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1102_BAL_a_output.txt
beta: 1102_BAL_b_output.txt


title: Pt. 1088BAL [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1088_BAL_a_output.txt
beta: 1088_BAL_b_output.txt


title: LD_G3_T1_B

description: Read_counts: 8340264


title: LD_G3_T3_A

description: Read_counts: 9720660


title: LD_G3_T1_C

description: Read_counts: 14647619


title: LD_G2_T5_B

description: Read_counts: 10004107

value: Williams 82


title: LD_G2_T5_C

description: Read_counts: 18647878


title: LD_G2_T5_A

description: Read_counts: 10620243


title: Pt. 1025BAL [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1025_BAL_a_output.txt
beta: 1025_BAL_b_output.txt


title: Pt. 1079BAL [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1079_BAL_a_output.txt
beta: 1079_BAL_b_output.txt


title: LD_G2_T3_C

description: Read_counts: 12532620


title: Pt. 1000 Blood [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1000_PBMC_a_output.txt
beta: 1000_PBMC_b_output.txt


title: Pt. 1146BAL [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1146_BAL_a_output.txt
beta: 1146_BAL_b_output.txt


title: LD_G2_T3_B

description: Read_counts: 11300327


title: LD_G2_T3_A

description: Read_counts: 10430609


title: LD_G2_T1_B

description: Read_counts: 9000047


title: Pt. 1000BAL [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 1000_BAL_a_output.txt
beta: 1000_BAL_b_output.txt


title: LD_G2_T1_C

description: Read_counts: 11708337


title: LD_G1_T5_A

description: Read_counts: 8532235


title: LD_G2_T1_A

description: Read_counts: 12930031


title: LD_G1_T3_C

description: Read_counts: 10787849


title: LD_G1_T5_C

description: Read_counts: 12983196


title: Pt. 989BAL [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 989_BAL_a_output.txt
beta: 989_BAL_b_output.txt


title: LD_G1_T3_B

description: Read_counts: 9777404


title: LD_G1_T5_B

description: Read_counts: 10755893


title: HUVEC-GRO-Seq-Notx

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

description:
nascent RNA
HUVEC-GRO-Seq-Notx

data_processing:
Library strategy: GRO-Seq
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
GRO-Seq results were trimmed to remove A-stretches originating from the library preparation using the Homer software (homerTools trim) and from resulting sequences those shorter than 25 bp were discarded. Sequence reads were further quality filtered with the FASTX software (-q 10 -p 97)
GRO-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.9 (-v 2 -k 3 -m 1 --best)
http://homer.salk.edu/homer/
Genome_build: hg19
Supplementary_files_format_and_content: bedGraphs

source_name: Human umbilical vein endothelial cell

growth_protocol: Cells were purchased from ATCC and cultures according to the instructions provided.

extract_protocol:
Nuclei were extracted from 5-10 million cells and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol-LS.
The RNA was base-hydrolyzed, dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 10 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

tag: cell line

value: HUVEC


title: MPRA_Distal_Doxorubicin_Rep1

city: Kansas City

first: Scott

middle: T

last: Younger

state: MO

address: 2401 Gillham Road

institute: Children's Mercy Kansas City

data_processing:
Library strategy: MPRA
MPRA Read Alignment: First 10 bases of each read matched to MPRA oligonucleotide barcode
MPRA Differential Expression: DESeq2 with default options
processed data files format and content: TXT files are normalized read counts from amplicon sequencing for each sample (MPRA) and statistics comparing untreated and Doxorubicin-treated samples.

source_name: Fetal skin fibroblasts

extract_protocol:
RNA: TriZol
Amplicon sequencing

value: 500 nM Doxorubicin 6 hours

tag: cell type

value: Fetal skin fibroblasts


title: Pt. 989 Blood [iRepertoire]

description:
Alpha [A] and beta [B] PCRs were performed in separate reactions for each patient sample.
TCR specific primers were used from a commercially available kit (iRepertoire human TCR alpha and beta kits [iRepertoire, Huntsville, AL]) to amplify only TCRs from RNA derived from CD4 T cells.
Amplicon sequencing following RT-PCR of a specific gene(s).
alpha: 989_PBMC_a_output.txt
beta: 989_PBMC_b_output.txt


title: MPRA_Distal_Untreated_Rep1


title: LD_G3_T1_A

description: Read_counts: 10044360


title: hCOs day30

city: New Haven

first: Yangfei

last: Xiang

state: CT

address: 10 Amistad St. Room 214J

department: Genetics

institute: Yale University

description: Gene expression in hCO

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Tophat2 (v2.0.12) with SAMtools (v1.3.1) and Bowtie2 (v2.2.9).
RPKM value was calculated Cufflinks (v1.2.1) by using RefSeq genes as reference annotation with "-G" option
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include RefSeq gene id, gene symbol, chromosome and RPKM value for each sample

source_name: human cortex organoids

growth_protocol: ESCs were cultured on Matrigel coated cell culture dish with mTeSR1 media. hMGEOs and hCOs were cultured in each established condition.

extract_protocol:
RNeasy Mini Kit
Tru-Seq RNA library preparation kits

tag: tissue

value: human cortex organoids

tag: status

value: differentiated


title: hCOs day72

description: Gene expression in hCO


title: hMGEOs day72

description: Gene expression in hMGEO

source_name: human MGE organoids

value: human MGE organoids


title: LD_G1_T1_C

description: Read_counts: 14153427

value: Long Day (16L:8D)


title: LD_G1_T1_A

description: Read_counts: 9261535

value: 26 DAP


title: LD_G1_T1_B

description: Read_counts: 10284103


title: GmEM-Input_br1

city: Davis

first: John

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California

library_source: genomic

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Peaks were identified for each biological replicates using MACS2, using default parameters and a q value threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2.

molecule: genomic DNA

source_name: GmEM-Input

growth_protocol: Soybean cv Williams 82 plants were grown in 2 gallon pots containing Ron’s mix (1 part coarse sand, 1 part compost, 1 part peat moss, 3 pounds/yard Dolomite) in UC Davis greenhouses at temperatures ranging 22-30°C and under 16 hour-days.

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 3 ug of an antibody raised against the peptide CPEPRYQIRRTSSASF corresponding to the amino acids 302-316 of GLYMA.06G314400, or 2 ug of an antibody raised against the peptide MSLQQPNQEVPLQEPC corresponding to the amino acids 1-15 of GLYMA.13G317000 .  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol: Early maturation stage embryos were dissected from 6 to 7 mm seeds.  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.

tag: developmental stage

value: early maturation stage

value: embryos

tag: antibody


title: GmEM_GLYMA.13G317000-ChIP_br2

value: anti-peptide GLYMA.13G317000


title: GmEM-Input_br2


title: GmEM_GLYMA.13G317000-ChIP_br1


title: hMGEOs day30

description: Gene expression in hMGEO


title: LCC9_A7(NSC31303).2_RNA-seq

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

data_processing:
Sequencing was performed on the Illumina HiSeq 2500 (Rapid run, Illumina, CA USA) with chemistry v1.0 and using the 2×106bp paired-end read mode and original chemistry from Illumina according to the manufacturer's instructions.
The initial data analysis was HiSeq 2500. The HiSeq Control Software 2.0.5 in combination with RTA 1.17.20.0 (real time analysis) performed the initial image analysis and base calling.
CASAVA-1.8.2 generated and reported run statistics and the final FASTQ files. Sequences were de-multiplexed according to the 6bp index code with 1 mismatch allowed.
FASTQ output was aligned with TopHat and quantified/normalized to the RefSeq GRCh37 transcriptome using the Cufflinks (v2.2.1) pipeline (with frag bias correction)
Genome_build: GRCh37
Supplementary_files_format_and_content: Gene-level FPKM

source_name: Breast Lumen

growth_protocol: LCC9  were grown in phenol red-free IMEM (Corning Cellgro, Manassas, VA) plus 5% charcoal-stripped serum (CSS).

extract_protocol:
Total RNA was extracted from Control and A7 treated LCC9 cells  using miRNeasy Mini Kit (Qiagen), and submitted to Otogenetics Corporation (Norcross, GA USA) for RNA-Seq assays.  Briefly, the integrity and purity of total RNA were assessed using Agilent Bioanalyzer or Tapestation and OD260/280. cDNA was generated from high quality total RNA using SMARTer PCR cDNA Synthesis kit (Clontech Laboratories, Inc., Mountain View, CA USA, catalog# 634926).
The resulting cDNA was fragmented using Bioruptor (Diagenode, Inc., Denville, NJ USA), profiled using Agilent Tapestation, and subjected to Beckman Biomek FXp (Biomek 6000, Beckman Coulter) fully automatic workstation and a Beckman HT library kit (SPRIworks HT, Beckman Coulter, Inc. CA USA; PN B09855AA) to generate fragment libraries. The instructions were strictly followed to perform library construction. Briefly, after fragmentation the ends were repaired and 'A' bases were added to the 3' end of the fragments. Adapters were then ligated to both ends. The adaptor-ligated templates were further purified using Agencourt AMPure SPRI beads (Beckman Coulter, Inc. CA USA). The adaptor-ligated library was amplified by ligation-mediated PCR which consisted of 11 cycles of amplification, and the PCR product was purified using Agencourt AMPure SPRI beads again. After the library construction procedure was completed, QC was performed using Nanodrop 2000 (Thermo Scientific, USA) and an Agilent TapeStation (Agilent, USA) to ensure the library quality and quantity.

treatment_protocol: Subconfluent proliferating cells were seeded into 6-well dishes at 1 x 105 cells/well on Day 0 and allowed to attach for 24-hr. The cells were treated with vehicle or BRCA1 mimetic compound A7 for 24 hrs before harvesting

value: LCC9  Tam resistant

value: Breast Lumen

tag: hormone status

value: Eralpha positive  wt


title: LD_G1_T3_A

description: Read_counts: 16366724

value: Clark

value: afternoon 2:30 pm


title: GmEM_GLYMA.06G314400-ChIP_br2

value: Williams 82

value: anti-peptide GLYMA.06G314400


title: hESC

description: Gene expression in hESC

source_name: human embryonic stem cells

value: human embryonic stem cells

value: undifferentiated


title: LCC9_Control1_RNA_seq


title: LCC9_A7(NSC31303).1_RNA-seq


title: LCC9_Control2_RNA_seq


title: R_AG_TMSC_rep2

city: Beijing

first: Jingyi

last: Li

address: Yiheyuan Road, No.5, Haidian District

country: China

institute: Peking University

description: TMSCs-NRF2 AG/AG

data_processing:
Illumina sequencing platform and low-quality reads (reads with high percentage of N bases and with low phred33) were removed.
The remaining reads were aligned to the human reference (hg19 from UCSC genome browser) by TopHat.
The transcripts were assembled with Cufflinks.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include the FPKM information of each RNA-Seq sample.

source_name: Transformed mesenchymal stem cells, AG

growth_protocol: Human H9 ESCs (WiCell Research) and their genetic modified derivatives were maintained on mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder in human ESC medium or on Matrigel (BD Biosciences) in mTeSR medium. All hMSCs were cultured in hMSC culture medium (MEM (Gibco), 10% fetal bovine serum (FBS, Hyclone), 1% penicillin/streptomycin (Gibco) and 10 ng/mL bFGF (Joint Protein Central)). TMSCs were cultured in hMSC medium without bFGF.

extract_protocol:
Total RNA was isolated with the RNeasy Mini Kit (Qiagen) from 10^6 cells per duplicate following the manuals.
The quality of RNA was checked with Fragment Analyzer (Advanced Analytical), following by RNA library construction by NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB) according to the manufacturer's protocol.

treatment_protocol: We generated homozygous NRF2 A245G mutation knock-in hESCs via homologous recombination-based gene editing and differentiated them into hMSCs. Moreover, we adapted the multi-hits system for human cell transformation via serial transduction of hTERT, SV40 T antigens, p53 shRNA and hRasV12, and named these transformed hMSCs as hTMSCs.

tag: originating cell line

tag: genotype/variation

value: Transformed mesenchymal stem cells

tag: passage

value: Yes


title: GmEM_GLYMA.06G314400-ChIP_br1


title: R_AG_TMSC_rep1

description: TMSCs-NRF2 AG/AG

tag: multi-hits system for human cell transformation


title: BS4

city: Huhhot

first: Bei

address: Zhaowuda Rd.306

institute: Inner Mongolia Agriculture University

data_processing:
Illumina Hiseq 2500 platform
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: equCab2

organism: Equus caballus

source_name: tissue

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The Six libraries were constructed. Three immature testes libraries were named BSM1, BSM2 and BSM3. Three mature testes libraries were named ASM1, ASM2 and ASM3. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer （5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNaseH-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB，USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: mature testis

tag: breed

value: Mongolian horse


title: BS6


title: BS5


title: BS3

value: immature testis


title: R_AG_MSC_LP_rep2

description: MSCs-NRF2 AG/AG_LP

source_name: Mesenchymal stem cells, AG, late passage

value: Mesenchymal stem cells

value: late

value: No


title: BS2


title: R_AG_MSC_LP_rep1

description: MSCs-NRF2 AG/AG_LP


title: BS1


title: R_WT_MSC_LP_rep1

description: MSCs-NRF2 +/+_LP

source_name: Mesenchymal stem cells, WT, late passage


title: ATAC_Doxorubicin_Rep3

data_processing:
Library strategy: ATAC-seq
ATAC-Seq/ChIP-Seq Read Alignment: Bowtie 2.0 with default options using hg19 as reference genome
ATAC-Seq/ChIP-Seq general peak calling: Scripture using hg19 as reference genome
ATAC-Seq/ChIP-Seq significant peak calling: Cuffdiff 2.0 using Scripture output as peak reference
genome build: hg19
processed data files format and content: BED file contains coordinates for p53-bound pioneering sites (ATAC-seq), the peaks identified that were different between the untreated and Doxorubicin-treated samples.

extract_protocol:
column purification
Amplicon sequencing

value: 500 nM Doxorubicin 12 hours

value: Fetal skin fibroblasts


title: R_WT_MSC_LP_rep2

description: MSCs-NRF2 +/+_LP


title: HUVEC-GRO-Seq-Notx-2h

description:
nascent RNA
HUVEC-GRO-Seq-Notx-2h

value: HUVEC


title: ATAC_Doxorubicin_Rep1


title: HUVEC-GRO-Seq-VEGFA-2h

description:
nascent RNA
HUVEC-GRO-Seq-VEGFA-2h


title: U87_GRO-Seq

description:
nascent RNA
U87_GRO-Seq

source_name: Glioblastoma cell line


title: ATAC_Untreated_Rep3


title: THP1_GRO-Seq

description:
nascent RNA
THP1_GRO-Seq

source_name: Leukemic monocyte


title: R_WT_TMSC_rep1

description: TMSCs-NRF2 +/+

source_name: Transformed mesenchymal stem cells, WT


title: T98G_GRO-Seq

description:
nascent RNA
T98G_GRO-Seq


title: ATAC_Untreated_Rep2


title: R_WT_TMSC_rep2

description: TMSCs-NRF2 +/+


title: ATAC_Untreated_Rep1


title: MPRA_Distal_Doxorubicin_Rep2

value: 500 nM Doxorubicin 6 hours


title: SKOV3_GRO-Seq

description:
nascent RNA
SKOV3_GRO-Seq

source_name: Ovarian carcinoma cell line


title: MPRA_Distal_Untreated_Rep2


title: NHA_GRO-Seq_rep1

description:
nascent RNA
NHA_GRO-Seq_rep1

source_name: Normal Human Astrocytes

value: NHA


title: hESC9_GRO-Seq

description:
nascent RNA
hESC9_GRO-Seq
This Sample contains fastq runs from Illumina HiSeq 2000 and Illumina Genome Analyzer II

source_name: Human embryonic stem cell line 9


title: HepG2_GRO-Seq

description:
nascent RNA
HepG2_GRO-Seq

source_name: Hepatocellular carcinoma cell line


title: NHA_GRO-Seq_rep2

description:
nascent RNA
NHA_GRO-Seq_rep2


title: MRC5_GRO-Seq

description:
nascent RNA
MRC5_GRO-Seq

source_name: Lung fibroblast cell line


title: A549_GRO-Seq

description:
nascent RNA
A549_GRO-Seq

source_name: Adenocarcinomic alveolar basal epithelial cell line


title: 293T_GRO-Seq_rep1

description:
nascent RNA
293T_GRO-Seq_rep1

source_name: Human embryonic kidney cell line 293 transformed with large T antigen


title: ARPE_GRO-Seq

description:
nascent RNA
ARPE_GRO-Seq

source_name: Retinal pigment epithelium cell line

value: ARPE


title: 293T_GRO-Seq_rep2

description:
nascent RNA
293T_GRO-Seq_rep2


title: ATAC_Doxorubicin_Rep2

source_name: Fetal skin fibroblasts


title: HeLa_GRO-Seq

description:
nascent RNA
HeLa_GRO-Seq

source_name: Cervical cancer cell line

value: HeLa


title: BRD4 OE rep2

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

data_processing:
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using Bowtie2 (v2.2.9) with parameters -k 2 -p 6
Peak calling was performed using MASC2 (v2.0.10)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated from bedGraph files that generated from MACS, Scores represent reads coverage siganl

source_name: Prostate cells

growth_protocol: C4-2 stable cells were routinely generated by regular cultures (typically 5 × 106 cells into a T75 flask) on uncoated plastic in RPMI1640 medium (Gibco, USA) supplemented with Charcoal stripped serum (Gibco, USA).

extract_protocol:
ChIP DNAs were extracted as as described previously (PMID: 27068475).
Libraries were prepared according to Illumina's instructions accompanying the ChIP-seq Sample Kit.

treatment_protocol: C4-2 stable cells were treated with 1 µm JQ1 for 24 hours.

value: DMSO

tag: chip antibody


title: F133V_DMSO rep1


title: F133V_JQ1 rep1


title: EV_DMSO rep2


title: F133V_JQ1 rep2


title: F133V_DMSO rep2


title: EV_JQ1 rep2


title: BRD4 OE rep1


title: EV_JQ1 rep1


title: R_AG_MSC_EP_rep1

description: MSCs-NRF2 AG/AG_EP

source_name: Mesenchymal stem cells, AG, early passage

value: early


title: R_WT_MSC_EP_rep2

description: MSCs-NRF2 +/+_EP

source_name: Mesenchymal stem cells, WT, early passage


title: EV_DMSO rep1


title: MPRA_Proximal_Doxorubicin_Rep1


title: R_AG_MSC_EP_rep2

description: MSCs-NRF2 AG/AG_EP


title: MPRA_Proximal_Doxorubicin_Rep2


title: MPRA_Proximal_Untreated_Rep1


title: MPRA_Proximal_Untreated_Rep2


title: R_WT_MSC_EP_rep1

description: MSCs-NRF2 +/+_EP


title: F133V JQ1 RNASeq rep1

data_processing:
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Clinic sequence core using the pipeline Cassava 1.7
Reads aligned to human reference genome (hg19) using Tophat (v2.0.6) with default parameters
Raw count and RPKM were calcualted using RSeQC (v2.3.6) with parameters "-d '1+-,1-+,2++,2--' -r hg19.refseq.bed12"
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigWig file

source_name: Prostate cells_F133V_JQ1

growth_protocol: C4-2 stable cells were routinely generated by regular cultures (typically 2–3 × 10^6 cells into a T75 flask) on uncoated plastic in RPMI1640 medium (Gibco, USA) supplemented with Charcoal stripped serum (Gibco, USA).

extract_protocol:
RNAs were extracted using RNeasy Mini Kit.
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit.

tag: genotype

value: SPOP F133V

tag: passages


title: F133V JQ1 RNASeq rep2


title: F133V DMSO RNASeq rep2

source_name: Prostate cells_F133V_DMSO


title: F133V JQ1 RNASeq rep3


title: EV JQ1 RNASeq rep2

source_name: Prostate cells_EV_JQ1

value: wildtype


title: EV JQ1 RNASeq rep1


title: EV DMSO RNASeq rep3

source_name: Prostate cells_EV_DMSO


title: EV JQ1 RNASeq rep3


title: F133V DMSO RNASeq rep1


title: EV DMSO RNASeq rep2


title: EV DMSO RNASeq rep1


title: C8_control

city: Bethesda

first: Yanqin

last: Yang

state: Maryland

address: 10 Center Dr.

institute: NIH

data_processing:
Sequenced paired-end reads were mapped to the mouse genome (mm10, GRCm38) by Tophat v2.1.0 (bowtie v2.2.6.0, samtools v1.3) allowing 2 mismatches and 1 best hit
Mapped reads were counted in Mus_musculus.GRCm38.79.gtf gene region of each sample using HTseq 0.6.1p1 with default setting.  The R Bioconductor edgeR package was used to normalize raw reads and compare the difference.
Genome_build: mm10, GRCm38

organism: Mus musculus

source_name: Explant Culture

growth_protocol: Explants is cultured on 1% collagen gel.

extract_protocol:
RNA is extracted using the RNeasy Mini plus Kit (Qiagen) and quantified by Qubit Fluorometer
Ovation RNA-Seq System V2 kit (NuGen, Inc., San Carlos, CA) and Nextera XT DNA library preparation kit (Illumina, Inc., San Diego, CA)

treatment_protocol: 20mm Blebbistain is added to inhibit nonmuscle myosin II.

value: Epicardial cells

tag: mouse strain

value: Primary explants

tag: treatment

value: Control-No Blebbistatin


title: C4_control


title: C6_control


title: C5_control


title: C2_control


title: C1_control


title: B8_treated

value: Blebbistatin Treated


title: B7_treated


title: hMGEOs day79 rep2 [version 2]

description: Gene expression in hMGEO

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Cellranger (v1.3.0).
Raw count matrix was merged by CellrangerRkit (v1.1.0) and and formatted by writeMM function in Matrix (v1.2-10)
Genome_build: hg19
Supplementary_files_format_and_content: Raw count matrix was formatted by mtx, and barcode and gene information was with tsv format.

source_name: human MGE organoids

extract_protocol: Chromium™ Single Cell 3’ Reagent Kits v1 and v2

value: MGE organoids

value: differentiated

tag: reagent version

value: version 2


title: B5_treated

tag: cell type


title: B6_treated


title: hCOs day30 rep2 [version 1]

description: Gene expression in hCO

source_name: human cortex organoids

value: cortex organoids

value: version 1


title: B4_treated


title: hCOs day79 rep2 [version 2]

description: Gene expression in hCO


title: hMGEOs day 30 rep2 [version 1]

description: Gene expression in hMGEO


title: F133V DMSO RNASeq rep3

tag: cell line


title: B2_treated


title: hMGEOs day72 rep1

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Cellranger (v1.3.0).
Raw count matrix was merged by CellrangerRkit (v1.1.0) and and formatted by writeMM function in Matrix (v1.2-10)
genome build: hg19
processed data files format and content: Raw count matrix was formatted by mtx, and barcode and gene information was with tsv format.

tag: status

value: hMGEO

tag: day


title: B1_treated


title: hMGEOs day30 rep1


title: hCOs day72 rep1

value: hCO


title: B3_treated


title: Adult Run 2

city: New York

first: Donna

middle: L

last: Farber

state: NY

address: 650 West 168th Street, BB1701

department: Surgery

institute: Columbia University

data_processing:
RTA (Illumina) was used for base calling
bcl2fastq (version 1.8.4) was used for converting BCL to fastq format, coupled with adaptor trimming
Tophat (version 2.0.4) was used with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10) to map reads to the reference genome
Relative abundance of genes measured as raw counts were calculated using featureCounts (Bioinformatics, 30:923-30)
Genome_build: mm9
Supplementary_files_format_and_content: Processed files contain gene counts in tab-separated value text format

source_name: Lung CD4+ Thy1.1+ T cells

extract_protocol:
Sorted cells were immediatelly pelleted and flash-frozen at -80°C until RNA extraction. RNA from sorted cells was isolated using the Qiagen RNeasy Mini Kit, flash frozen and stored at -80°C prior to quality analysis and library generation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Naïve (CD44lo) CD4+ T cells were isolated by magnetic separation from the spleens of infant (10-14 days old) or adult (8-16 week old) TS1 mice and 1.5-5x10^5 purified cells were transferred i.p. injection into naïve, congenic adult recipients. Recipient mice were infected 24 hours later with 10-13 TCID50 PR8 influenza/g body weight. Mice were sacrificed at day 13 post-infection and transferred cells were sorted from lungs.

tag: age

value: adult-derived (8-16 week old)

tag: tissue

value: lung

value: CD4+ Thy1.1+ T cells


title: Adult Run 1


title: C7_control


title: Infant Run 3

value: infant-derived (10-14 days old)


title: C3_control


title: Sh_G7_T5_C

description: Read_counts: 9210976

organism: Glycine soja

source_name: First trifoliate

value: Shift (LD 3 weeks -> SD 5 days)

tag: timepoint

value: evening 10:30 pm

tag: age at rna extraction

value: 26 DAP


title: Infant Run 1


title: hESC

description: Chromatin organization in hESC

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Bowtie2 (v2.2.9).
Peak calling was performed by findPeak in HOMER software (v4.9) with “-localSize 50000 -size 100 -minDist 50 -fragLength 0 -o auto”
Genome_build: hg19
Supplementary_files_format_and_content: bed format

source_name: human embryonic stem cells

extract_protocol: Buenrostro et al., 2013

value: undifferentiated


title: KO hMeDIP

city: Hangzhou

first: Lin-Yu

last: Lu

state: Zhejiang

address: 268 Kaixuan Road, North Central Building, Room 536

institute: Zhejiang University

data_processing:
Library strategy: hMeDIP-Seq
The resulted 50 bp single-ended short reads were mapped to mouse genome (mm10) using Bowtie2 (version 2.1.0) with default parameters.
5mC/5hmC peaks were called using MACS2 with FDR < 0.001.
For each consensus peak region, read counts were extracted from both MeDIP/hMeDIP and input samples. Normalization factors were calculated for each sample using PePr. The normalized WT and KO signals for each window were defined as normalized MeDIP/hMeDIP read counts subtracted by normalized input read counts.
Window of significant difference between normalized WT and Uhrf2 KO signals was identified based on a Poisson test of p-value < 1e-5.
HOMER (Hypergeometric Optimization of Motif EnRichmert) Suite (v4.6) was applied to annotate the significant peak regions.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: BigWig files were generated after MACS2 peak calling using default parameters.

source_name: brain, Uhrf2 KO, hMeDIP

extract_protocol:
DNA was extracted from brains using PureLink Genomic DNA Mini Kit (Life Technologies) and sonicated to 200-500 bp. DNA was denatured at 95ºC for 5 minutes and quickly chilled on ice water for 10 minutes. MeDIP and hMeDIP were performed using standard protocols. Each MeDIP reaction contains 1μg DNA, 3μg anti-5-methylcytosine antibody, 3μg rabbit-anti-mouse IgG (Jackson ImmunoResearch), and 50μL protein A beads. Each hMeDIP reaction contains 1μg DNA, 3μl anti-5-hydroxymethylcytosine antibody, and 50μL protein A beads.
Methylated/hydroxymethylated DNA and input DNA were end processed using Quick Blunting Kit and dA-Tailing Module, and ligated to Illumina-compatible adaptors. The DNA was then amplified by PCR using barcode-containing primers.

tag: strain/background

tag: genotype/variation

value: Uhrf2 KO

value: brain

tag: antibody


title: Sh_G7_T3_C

description: Read_counts: 14437113

data_processing:
The quality-scores line in fastq files processed with Casava1.8 using an ASCII offset of 33 (known as Sanger scores) instead of the previous 64 offset. (pools 1-2-3 run 160, HiSeq#1 with an error rate of 0.84 %, pools 4-5 run 162, HiSeq#1 with an error rate of 0.54% pools 6 through 12, run 226 HiSeq#2error rate: 0.88%).
Adapter Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG
Reads were aligned onto soybean transcriptome (williams 82) obtained from Phytozome database (Schmutz et al, 2010) using Bowtie aligner (Langmead et al, 2009) with following parameters;  -S -q  -k 1 --best -p 4 --phred33-quals
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample.

value: afternoon 2:30 pm


title: KO MeDIP

data_processing:
The resulted 50 bp single-ended short reads were mapped to mouse genome (mm10) using Bowtie2 (version 2.1.0) with default parameters.
5mC/5hmC peaks were called using MACS2 with FDR < 0.001.
For each consensus peak region, read counts were extracted from both MeDIP/hMeDIP and input samples. Normalization factors were calculated for each sample using PePr. The normalized WT and KO signals for each window were defined as normalized MeDIP/hMeDIP read counts subtracted by normalized input read counts.
Window of significant difference between normalized WT and Uhrf2 KO signals was identified based on a Poisson test of p-value < 1e-5.
HOMER (Hypergeometric Optimization of Motif EnRichmert) Suite (v4.6) was applied to annotate the significant peak regions.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: BigWig files were generated after MACS2 peak calling using default parameters.

source_name: brain, Uhrf2 KO, MeDIP


title: Sh_G7_T5_B

description: Read_counts: 11183695


title: WT hMeDIP

source_name: brain, WT, hMeDIP

value: wild type


title: hCOs day30 rep1

value: differentiated


title: Sh_G7_T3_A

description: Read_counts: 8259402


title: hCOs day72

description: Chromatin organization in hCO


title: Sh_G7_T1_C

description: Read_counts: 7441300

value: morning 6:30 am


title: Sh_G7_T3_B

description: Read_counts: 9556015


title: Sh_G7_T5_A

description: Read_counts: 11951221


title: Sh_G7_T1_B

description: Read_counts: 13915456


title: KO rep4

description:
KO4
PolyA RNA
Processed data file: WT_UHRF2_read_counts.txt

data_processing:
The resulted 50 bp single-ended short reads were firstly trimmed for adaptor sequence and then filtered to delete low-quality reads.
Then the processed short reads were mapped to mouse genome (mm10) using Tophat (v 2.0.9) with default parameters.
Raw read counts were firstly extracted from the aligned bam files, and then were utilized for differentially expressed gene calling using the Bioconductor package edgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: WT_UHRF2_read_counts.txt: Tab-delimited text file contains the read counts of each sample.

source_name: brain, Uhrf2 KO

extract_protocol:
RNA was extracted from brains by Trizol and purified by RNeasy Mini Kit (QIAGEN).
Library was constructed using TruSeq Stranded mRNA Library Prep Kit.


title: KO Input

source_name: brain, Uhrf2 KO, input


title: Adult Run 3


title: WT Input

source_name: brain, WT, input


title: SD_G7_T5_C

description: Read_counts: 9152754

extract_protocol:
Plant samples were ground and RNAs were extracted using the RNeasy® Plant Mini Kit (Qiagen®).
The RNAseq libraries were prepared with Illumina's 'TruSeq RNAseq Sample Prep kit. The libraries were pooled and quantitated by qPCR, and sequenced for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3 and analyzed with Casava-1.8 (pipeline 1.9), following the manufacturer's instructions (Illumina, San Diego, CA).

value: Short Day (10L:14D)


title: SD_G7_T5_B

description: Read_counts: 9216889


title: hMGEOs day72

description: Chromatin organization in hMGEO


title: WT rep4

description:
WT4
PolyA RNA
Processed data file: WT_UHRF2_read_counts.txt

source_name: brain, WT


title: Infant Run 2


title: KO rep1

description:
KO1
PolyA RNA
Processed data file: WT_UHRF2_read_counts.txt


title: SD_G7_T5_A

description: Read_counts: 8231552


title: WT rep3

description:
WT3
PolyA RNA
Processed data file: WT_UHRF2_read_counts.txt


title: WT MeDIP

source_name: brain, WT, MeDIP


title: WT rep2

description:
WT2
PolyA RNA
Processed data file: WT_UHRF2_read_counts.txt


title: SD_G7_T3_B

description: Read_counts: 14381512


title: SD_G7_T3_A

description: Read_counts: 9144596


title: SD_G7_T1_C

description: Read_counts: 12641385


title: SD_G7_T1_B

description: Read_counts: 11380001


title: Sh_G7_T1_A

description: Read_counts: 12501344


title: LD_G7_T5_C

description: Read_counts: 10101725

value: Long Day (16L:8D)


title: SD_G7_T1_A

description: Read_counts: 11185415


title: Adult 3

city: Nanjing

first: Caifang

last: Ren

state: Jiangsu

address: 1 Weigang

institute: Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University

data_processing:
Clusters were generated on the acBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS (Illumia) according to the manufacturer’s instructions and further sequenced on an Illumina HiseqX Ten platform. Reads that passed the quality control were then mapped to the Ovis Aries reference genome (Oar_v3.1). Based on it, the transcripts were assembled with Cufflinks (version 2.1.1) and Scripture
The Coding Potential Calculator, the Coding-Non-Coding Index, the Protein Families Database and the Coding-Potential Assessment Tool, which have the power to sort lncRNAs from putative protein-coding RNAs were combined to screen the lncRNAs. The transcripts from the intersection of the four methods with fragments per kilo base of exon per million fragments mapped (FPKM) greater than 0.1 were kept and predicted to be lncRNA transcripts.
Transcript abundance was measured by FPKM using Cuffdiff. Differential expression analysis of the groups was performed using the DESeq packages (1.10.1) . LncRNAs or protein-coding genes with a false discovery rate (FDR) < 5% and an absolute value of log2 (fold change) > 1 were assigned as differentially expressed.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: Excel files include lncRNA FPKM values in each Sample and differential analysis results of lncRNA and genes in each comparison, and a fastq file include lncRNA sequence information .

organism: Ovis aries

source_name: longissimus dorsi muscle

extract_protocol:
muscle samples were collected and immediately frozen in liquid nitrogen, then total RNA was isolated with TRIzol reagent.
The strand-specific sequencing libraries were separately prepared using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) according to the manufacturer’s instructions.

tag: breed

value: Hu sheep

tag: developmental stage

value: 2-year-old adult

value: longissimus dorsi muscle


title: RKO-PRDM1β-OE-rep2

city: Shanghai

first: Changlong

last: Liu

state: Shanghai

address: 518 Ziyue Road, Minhang

institute: Shanghai Veterinary Research Institute

description: PRDM1-beta overexpressed colon cancer RKO cells

data_processing:
Sequencing reads were mapped to the human genome (hg19) using Tophat (Bowtie2). Uniquely mapped reads were assembled into transcripts guided by the UCSC Homo sapiens hg19 RefSeq&Gencode gene annotation
Reads Per Kilobase of exon per Megabase of library size (RPKM) of reference genes and transcirpts were estimated using Cufflinks 2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and raw counts for each sample

molecule: polyA RNA

source_name: RKO cells

growth_protocol: Human colon cancer RKO cells and its derivatives were maintained at 37 °C, 5% CO2 in McCoy's 5A media supplemented with 10% FBS and 100U/ml penicillin & 100 µg/ml streptomycin. Cells were passaged every 3 to 4 days to maintain sub-confluence.

extract_protocol:
RNA was extracted from RKO derivatives using Qiagen miRNeasy Mini Kit according to manufacture's protocol
RNA-seq libraries were constructed using Illumina TruSeq® Stranded mRNA LT kit according to manufacture's standard portocols

value: RKO

value: colon epithelial carcinoma


title: RKO-PRDM1β-OE-rep1


title: KO rep3

description:
KO3
PolyA RNA
Processed data file: WT_UHRF2_read_counts.txt


title: RKO-GFP-OE-rep2

description: GFP overexpressed colon cancer RKO cells


title: KO rep2

description:
KO2
PolyA RNA
Processed data file: WT_UHRF2_read_counts.txt


title: LD_G7_T5_A

description: Read_counts: 13985036


title: LD_G7_T5_B

description: Read_counts: 14489086


title: RKO-PRDM1α-OE-rep1

description: PRDM1-alpha overexpressed colon cancer RKO cells


title: Adult 2


title: RKO-GFP-OE-rep1


title: LD_G7_T3_C

description: Read_counts: 9954602


title: RKO-PRDM1α-OE-rep2


title: SD_G7_T3_C

description: Read_counts: 11858227


title: Adult 1


title: Lamb 3

value: 5-day lamb


title: LD_G7_T3_B

description: Read_counts: 12687198


title: RKO-PRDM1-KO5-rep2

description: PRDM1 knockout colon cancer RKO cells


title: RKO-PRDM1-KO5-rep1

description: PRDM1 knockout colon cancer RKO cells


title: Lamb 2


title: LD_G7_T3_A

description: Read_counts: 9064567


title: RKO-PRDM1-KO2-rep2

description: PRDM1 knockout colon cancer RKO cells


title: Lamb 1


title: Fetus 3

value: 110-day fetus


title: RKO-PRDM1-KO2-rep1

description: PRDM1 knockout colon cancer RKO cells


title: LD_G7_T1_B

description: Read_counts: 9446440

value: 26 DAP


title: RKO-WT-rep1

description: PRDM1 wild type colon cancer RKO cells


title: Fetus 1


title: LD_G7_T1_A

description: Read_counts: 7480667


title: RKO-WT-rep2

description: PRDM1 wild type colon cancer RKO cells


title: MCF_7_IgG

status: Public on Jul 20 2017

first: Mai

last: Sanyue

address: 27 Taiping Rd, Haidian District

institute: Beijing Institute of Biotechnology

data_processing:
Raw reads were discarded if they contained more than 2-N bases. A FASTX-Toolkit (Version 0.0.13) was used to obtain clean reads, and the raw sequencing data were also evaluated using FAST-QC.
The splicing-junction mapper from RNA-Seq TopHat (v2.0.6) was employed for RNA-seq alignment. Based on gene annotation of the genome, aligned reads with more than one genome location were discarded due to their ambiguous locations.
Uniquely localized reads were used to calculate the read number and the reads per kilobase and per million reads (RPKM) value for each gene.
RNA-protein interactions were assessed by AbLife or Piranha analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: peak information

source_name: MCF-7 cells

growth_protocol: wild-type MCF-7 cells were grown in Dulbecco’s modified Eagle’s medium (GIBCO Thermo Fisher) containing 10% heat-inactivated fetal bovine serum, 2 mM L-glutamine, 100 units/ml penicillin, and 100 mg/ml streptomycin.

extract_protocol:
The cross-linked cells were lysed for 30 min in cold wash buffer (1× PBS, 1% sodium dodecyl sulfate (SDS), 0.5% Nonidet P-40 (NP-40) and 5% sodium deoxycholate) supplemented with a 1% RNase inhibitor (Takara) and 2% protease inhibitor cocktail (Roche). The cell supernatants were subjected to DNase digestion by RQ1 (Promega) at a final concentration of 1 U/μl for 3 min at 37°C. For immunoprecipitation, 300 μl of lysate was incubated overnight with 10 μg of an anti-RBM39 antibody (Bethyl Laboratories) or control rabbit IgG (Sigma) at 4°C and then incubated for an additional 3 h with Protein A Dynabeads (Thermo Fisher) at 4°C. Next, the beads were applied to a magnet, the supernatant was removed, and the beads were sequentially washed with wash buffer, high-salt buffer (5× PBS, 1% SDS, 0.5% NP-40 and 5% sodium deoxycholate), and polynucleotide kinase (PNK) buffer (50 mM Tris pH=7.4, 10 mM MgCl2 and 0.5% NP-40). Protective on-bead digestion was performed by adding MNase (Thermo Fisher) to a final concentration of 1 U/mL, followed by incubation at 37°C for 15 min. The beads were washed with PNK buffer as described above. Then, dephosphorylation and phosphorylation were performed using calf intestinal alkaline phosphatase (CIAP, NEB) and polynucleotide kinase (PNK, NEB), respectively. The immunoprecipitated protein-RNA complexes were eluted from the beads by heat denaturation and then resolved on a Novex Bis-Tris 4-12% (Thermo Fisher) precast polyacrylamide gel. The protein-RNA complexes were cut from the gel, and RNA was extracted with TRIzol (Thermo Fisher).
The recovered RNA was used to generate a paired-end sequencing library using a Truseq Small RNA Library Preparation Kit (genomegen). Libraries corresponding to 150-250 bps were purified, quantified and stored at -80°C for sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer’s instructions and applied to an Illumina Nextseq 500 system by ABlife Inc. (Wuhan, China) for 151-nt paired-end sequencing.

treatment_protocol: Cells were washed 3 times with ice-cold phosphate-buffered saline (PBS) and irradiated with type C (254 nm) UV at 400 mJ/cm2 for cross-linking.

value: human breast adenocarcinoma

value: control rabbit IgG (Sigma)


title: Fetus 2


title: MCF_7_RBM39

value: anti-RBM39 antibody (Bethyl Laboratories)


title: SP5_2

city: London

first: Michalis

last: Barkoulas

address: South Kensington Campus

department: Life Sciences

country: United Kingdom

institute: Imperial College London

data_processing:
Reads aligned to a custom transcriptome dataset having built this as a genome using bowtie2 in paired end mode
The alignments were converted to count files using bedtools coverageBed module using the options -s and -counts.
Genome_build: WS190
Supplementary_files_format_and_content: tab-delimited text file with raw counts
Supplementary_files_format_and_content: tab-delimited text file with DESeq normalized counts

organism: Caenorhabditis elegans

source_name: L3 larvae

growth_protocol: The strains used in this study were cultured and handled according to standard protocols (Brenner, 1974). The JR667 strain containing the scm::GFP transgene (wIs51) is used as a reference on standard NGM plates with OP50 as a food source. Larvae were synchronized to L3 stage (31hr post hatching)

extract_protocol:
Total RNA was extracted using TRIzol (Ambion) reagent. RNA quality was determined using the Agilent® RNA ScreenType System on an Agilent 2100 Bioanalyzer.
The library preparation was done using the Illumina TruSeq RNA stranded mRNA library prep kit.

tag: Stage

value: L3 (31hr post hatching)

tag: strain

tag: mutation

value: icb38 (2371 bp upstream of the lin-22 ATG deletion)


title: dropseq_1_S1

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

description: We analyzed single-cells, which were sorted to 384-wells in total.

data_processing:
BCL files generated by Illumina NextSeq500 were converted to fastq files by bcl2fastq2 (v2.17.1.14) with demultiplexing pool barcodes.
Data for Quartz-Seq2 was processed by Quartz-Seq2 pipeline. Data for Drop-seq was processed by Drop-seq pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI counts for each gene for each cell

source_name: a mixture of mouse ES cells and the ES-derived primitive endoderm (PrE) cells

extract_protocol:
We performed two single-cell RNA-seq methods (Drop-seq and Quartz-Seq2). Drop-seq was performed as reported previously [Cell. 2015;161:1202–14]. Moreover, we established Quartz-Seq2 (a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads). We used two sets of RT primer for Quartz-Seq2. The set of v3.1 RT primers has 384 kinds of unique cell barcodes, with a length of 14 nucleotides (OPC purification, FASMAC). The set of v3.2 RT primers has 1,536 kinds of unique cell barcodes, with a length of 15 nucleotides (OPC purification, Sigma). The set of v3.1 RT primers corresponds to one set of the 384-well PCR plate with lysis buffer, the wells of which have unique barcodes. The set of v3.2 RT primers corresponds to four sets of the 384-well PCR plate with lysis buffer. Single cells were isolated in the 384-well PCR plate with 1 µL of lysis buffer (0.1111 µM respective RT primers, 0.12 mM dNTP mix, 0.3% NP-40, 1 unit/µL RNasin plus) containing ERCC spike mix I.
For Quartz-Seq2, cryopreserved 384-well plates with single-cell lysate were centrifuged at 10,000 g and 4ºC for 1 min. Subsequently, we denatured total RNA in each 384 plate at 70ºC for 90 s and hybridized the RT primer to poly-adenylated RNA at 35ºC for 15 s using the C1000/S1000 thermal cycler. The resulting plates were again centrifuged at 10,000 g and 4ºC for 1 min. Next, the plates were placed on the 384 aluminum plate at 0ºC. We peeled away the seal and added 1 µL of RT premix (2x Thermopol buffer, 5 units/µL SuperScript III, 0.55 units/µL RNasin plus) to 1 µL of lysis buffer for each well using a Mantis microfluidic dispensing system (Formulatrix) or a 384 Transfer Plate system (1859-384S, Watson). The above RT solution was used for the RT25 condition. For the RT100 condition, we used the following RT solution: 2x Thermopol buffer, 20 units/µL SuperScript III, and 2.2 units/µL RNasin plus. We sealed the plates again and agitated them at 2,600 rpm and 4ºC for 1 min. The plates were then centrifuged at 10,000 g and 4ºC for 1 min. We then performed reverse transcription at 35ºC for 5 min and 50ºC for 50 min. The reverse transcription was stopped at 70ºC for 15 min. Then, the plates were placed on a prechilled aluminum block, after which we peeled off their seals. Subsequently, we turned the plates upside down on the assembled collector type A or type B (supplemental figure). We mainly used type A. We centrifuged the plates with an assemble collector at 3,010 g and 4ºC for 3 min with swing-bucket rotors. Subsequently, we collected the cDNA solution into a disposable reservoir. Typically, we obtained 650–700 µL of cDNA solution from one 384-well PCR plate. We purified and concentrated the cDNA solution using the DNA Clean & Concentrator™-5 kit (Zymo Research). We used three purification columns for one 384-well PCR plate in the case of the v3.1 RT primer system (384-cell barcode). Purified cDNA was extracted into 20 µL of nuclease-free water from one column purification and transferred into an eight-linked PCR tube (TaKaRa). The PCR tubes were placed on an aluminum PCR stand at 0ºC. We added 25 µL of TdT solution [1x Thermopol buffer, 2.4 mM dATP, 0.0384 units/µL RNase H (Invitrogen), 26.88 units/µL terminal transferase (Roche)] into 20 µL of extracted cDNA using a pipette at 0ºC. The resulting 45 µL of TdT solution was mixed with a pipette at 0ºC or ThermoMixer at 2,000 g and 0ºC for 1 min. Immediately thereafter, the PCR tubes were centrifuged at 10,000 g and 0ºC for 1 min. We used a C1000/S1000 thermal cycler equipped with the 96-Deep Well Reaction Module for the following steps. The PCR tubes were placed on the block of the thermal cycler, which had been prechilled to 0ºC. We then performed a poly-A tailing reaction at 37ºC for 75 s. The solution was inactivated at 65ºC for 10 min. The PCR tubes were placed on an aluminum PCR stand at 0ºC. We then dispensed approximately 11 µL of solution into four wells from 45 µL of TdT solution. We added 46.16 µL of PCR I premix (1.08492x MightyAmp Buffer version 2, 0.06932 µM Tagging primer, 0.05415 units/µL MightyAmp DNA polymerase) to 11 µL of TdT solution for the respective wells of the PCR tube. We performed gentle inversion mixing on the resulting solution in the PCR tube. The tubes were then centrifuged at 10,000 g and 4ºC for 1 min. Subsequently, the solution was mixed with ThermoMixer at 2,000 rpm and 4ºC for 2 min. Then, we spun down the tube again. Next, we denatured the solution at 98ºC for 130 s and hybridized Tagging primer to poly-A-tailed cDNA at 40ºC for 1 min. After that, we performed the “Increment step” by heating to 68ºC at 0.2ºC every second and performed second-strand synthesis at 68ºC for 5 min. The tubes were placed on an aluminum PCR stand at 0ºC. We added 50.232 µL of PCR II premix (0.99697x MightyAmp Buffer version.2, 1.8952 µM gM primer) to 56.16 µL of PCR I solution. We performed gentle inversion mixing on the resulting solution in the PCR tube. The tubes were then centrifuged at 10,000 g and 4ºC for 1 min. Subsequently, the solution was mixed with ThermoMixer at 2,000 rpm and 4ºC for 2 min, after which we spun down the tube again. We then placed it on the block of the thermal cycler at 68ºC. Subsequently, we amplified the cDNA for 11 cycles under the following conditions: 98ºC for 10 s, 65ºC for 15 s, and 68ºC 5 min. We then incubated the tube at 68ºC for an additional 5 min. Finally, we transferred all of the PCR solution, derived from one 384-well PCR plate, to a 50-mL Polypropylene Centrifuge Tube (Watson). Typically, we obtained approximately 1.2 mL of PCR solution per 384-well PCR plate. We added 32 µL of 3 M sodium acetate (pH 5.2) and 6420 µL PB-Buffer (Qiagen) to the PCR solution. The mixture was then purified using a MinElute Spin Column (Qiagen). Purified cDNA was extracted into 40 µL of nuclease-free water. We additionally purified the cDNA with 32 µL of Ampure XP beads. Finally, we obtained 32 µL of purified cDNA. We checked the length distribution of amplified cDNA with an Agilent High Sensitivity DNA Kit (Agilent). The typical average size of the amplified cDNA in Quartz-Seq2 was approximately 1,400 bp.   In the case of the usage of the v3.2 RT primer in Quartz-Seq2, we modified the above steps as follows. After reverse transcription, we collected cDNA solution into a disposable reservoir from four sets of 384-well plates, which corresponded to 1,536 wells. We purified and concentrated the cDNA solution using eight purification columns for four 384-well PCR plates in the case of the v3.2 RT primer system. In the PCR step, we amplified cDNA for nine cycles with the following conditions: 98ºC for 10 s, 65ºC for 15 s, and 68ºC for 5 min. Finally, we transferred all of the PCR solution derived from four 384-well plates to a 50-mL Polypropylene Centrifuge Tube (Watson). Typically, we obtained approximately 3.5 mL of PCR solution per four 384-well PCR plates. We added 88 µL of 3 M sodium acetate (pH 5.2) and 17.6 mL of PB-Buffer (Qiagen) to the PCR solution. The mixture was purified using the MinElute Spin Column (Qiagen). Subsequently, cDNA was again purified using Ampure XP magnetic beads.   For the Quartz-Seq1-like reaction, we performed the following procedure in accordance with our previous study. We added 1 µL of RT premix (2x PCR buffer, 5 units/µL SuperScript III, 0.55 units/µL RNasin plus) to 1 µL of lysis buffer. We then performed reverse transcription at 35ºC for 5 min and 45ºC for 20 min. This reverse transcription was stopped at 70ºC for 15 min. We added 5 µL of ExoIB solution (1.6x Exonuclease I buffer, 3.2x PCR buffer, 16 mM DTT) and 20 µL of TdT solution [1x PCR buffer, 3 mM dATP, 0.0384 units/µL RNase H (Invitrogen), 33.6 units/µL terminal transferase (Roche)] into 20 µL of extracted cDNA using a pipette at 0ºC. The PCR tubes were placed on the block of the thermal cycle

value: ES single-cells and PrE single-cells

tag: Sex

value: male

tag: the number of single-cell/well contained in each data

tag: method name of single-cell rna-seq

value: Drop-seq

tag: type of sequence library preparation

value: Nextera

tag: sequencer

tag: the number of fastq reads for dge-matrix (in million)

tag: read2 length for dge-matrix (nt)


title: OH4271_3

value: ot269 (C to T at -4940 from ATG)


title: SP5_1


title: EScellcyclep2_126M

source_name: ES cells

tag: cell type

value: ES single-cells

tag: cell line

value: Quartz-Seq2 (v3.1, RT100)

value: Ligation


title: ESPrEp5_S2

description: We analyzed 384 wells with averaged lysis sample.

source_name: Averaged lysis sample from a mixture of mouse ES cells and the ES-derived primitive endoderm (PrE) cells

value: Averaged sample with ES single-cell and PrE single-cell


title: OH4271_1


title: OH4271_2


title: HTX_SS3_20minM_01_S1

description: We analyzed 384 wells with 10 pg total RNA.

source_name: Purified total RNA from ES cells

value: 10pg total RNA from ES cells

value: Quartz-Seq1 like with UMI


title: ESPrEp2_S1


title: OH4265_3

value: ot267 (W62STOP)


title: LD_G7_T1_C

first: Yoshie

institute: University of illinois at Urbana Chammpaign, USA

description: Read_counts: 10461269

source_name: First trifoliate

tag: treatment

value: Long Day (16L:8D)

tag: timepoint

value: morning 6:30 am

tag: age at rna extraction

value: 26 DAP


title: MxHligation_01_S3

value: prototype 2 of Quartz-Seq2


title: GmMM_GLYMA.13G317000-Input_br2

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Peaks were identified for each biological replicates using MACS2, using default parameters and a q value threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2.

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 2ug of an an antibody raised against the peptide MSLQQPNQEVPLQEPC, corresponding to the amino acids 1-15 of GLYMA.13G317000.  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

treatment_protocol: Mid-maturation stage embryos were dissected from seeds weighing between 200 and 250 mg .  Tissues were crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes.  Tissues were rinsed twice with deionized water and stored at -80C until use.

tag: cultivar

value: Williams 82

value: mid-maturation stage

tag: tissue

value: embryos

tag: antibody


title: GmMM_GLYMA.13G317000-Input_br1

tag: developmental stage


title: MxHligation_S2

tag: strain

value: male

value: prototype 3 of Quartz-Seq2


title: OH4265_1

tag: Stage

value: L3 (31hr post hatching)

tag: mutation


title: SP5_3

value: icb38 (2371 bp upstream of the lin-22 ATG deletion)


title: WT rep1

description:
WT1
PolyA RNA
Processed data file: WT_UHRF2_read_counts.txt

tag: strain/background

tag: genotype/variation

value: wild type

value: brain


title: GmMM_GLYMA.13G317000-ChIP_br1

value: anti-peptide GLYMA.13G317000


title: JR667_3

value: wt


title: NJCMS5B

city: nanjing

first: yanwei

last: li

state: jiangsu

address: No. 1 Weigang Street, Xuanwu Region, Nanjing City

department: College of Agriculture

institute: Nanjing Agricultural University

data_processing:
Basecalls performed using illumina HiSeqTM2500/MiSeq
Sequencing reads were filtered to remove adapters, Ns and low quality reads. The remaining reads called clean reads were stored in FASTQ format.
The clean reads were aligned to the reference genome of soybean (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Gmax) using Bismark software (version 0.12.5) with the default parameters.
With window size w = 3,000 bp, step size = 600 bp [76] and sequencing depth ≥ 5, q-value ≤ 0.05, the sum of methylated and unmethylated counts in every window were calculated.
DMRs were identified using the swDMR software (http://122.228.158.106/swDMR/), which uses a sliding-window approach. The window is set to 1000bp and step length is 100bp. Fisher test is implemented to detect the DMRs with “FDR ≤ 0.05 and coverage changes ≥ 5”.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: tab-delimited excel files include P-values for each Sample

source_name: flower bud

growth_protocol: Both NJCMS5A and NJCMS5B were planted in the summer at the Jiangpu Experimental Station

extract_protocol:
Genomic DNA was extracted from the flower buds of NJCMS5A and NJCMS5B using a DNeasy Plant Mini Kit (Qiagen Valencia, CA, USA)
DNA libraries were prepared for sequencing using standard Illumina protocols.First, the quality of samples was monitored by agarose gels, and the concentration was measured using UV-Vis Spectrophotometer (Thermo Scientific, Waltham, MA, USA). Subsequently, the DNA samples were randomly sonicated to 200-300 bp using Covaris S220. After end repair and adenylation, the sonicated DNA fragments were ligated to cytosine-methylated barcodes as per manufacturer’s instructions. And these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM kit (Zymo Research). After that, the DNA libraries were constructed by PCR amplification.

treatment_protocol: During flowering period, the flower buds in different sizes were collected and pooled from NJCMS5A and NJCMS5B plants respectively, then immediately frozen in liquid nitrogen and stored at -80°C for further use.

value: flower bud

tag: developmental age

value: full-bloom stage

tag: genotype

value: the maintainer line


title: NBF40ExoM_S4

value: 10pg total RNA from ES cells

tag: Sex

tag: the number of single-cell/well contained in each data

tag: method name of single-cell rna-seq

value: prototype 5 of Quartz-Seq2

tag: type of sequence library preparation

value: Ligation

tag: sequencer

tag: the number of fastq reads for dge-matrix (in million)

tag: read2 length for dge-matrix (nt)


title: GmMM_GLYMA.13G317000-ChIP_br2

tag: cultivar

value: Williams 82

tag: tissue


title: NJCMS5A

value: the cytoplasmic male sterility line


title: GmEM_GLYMA.08G357600-Input_br2

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 1 ug of an an antibody raised against the peptide QNQGSDPHARMGGDNC, corresponding to the amino acids 487-502 of GLYMA.08G357600.  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

tag: developmental stage

value: early maturation stage

value: embryo

tag: antibody


title: GmEM_GLYMA.08G357600-Input_br1


title: GmEM_GLYMA.08G357600-ChIP_br2

value: anti-peptide GLYMA.08G357600


title: plate1cat_S1

tag: cell type

value: ES single-cells and PrE single-cells

tag: strain

tag: cell line

value: male

value: Quartz-Seq2 (v3.1, RT100)


title: plate25_S2

value: Averaged lysis sample with ES single-cell and PrE single-cell


title: plate14_S2


title: dropseq_2_S2

value: Drop-seq

value: Nextera


title: mlf 3

city: Toulouse

first: Lucas

last: Waltzer

address: 118 route de Narbonne

department: Centre de Biologie du Développement

country: France

institute: CNRS UMR5547

data_processing:
Basecalling was performed with Casava (v1.7).
Quality score trimming and filtering were performed with Trimmomatic (v0.32).
Trimmed reads were aligned to Drosophila melanogaster rRNA gene sequences using Bowtie2 (v2.1.0) to filter out reads originating from rRNA
rRNA filtered reads were aligned to the annotated Dm genome (build BDGP5, Ensembl release 70) using TopHat (v2.0.10)
Per gene read counts were calculated from the TopHat output using htseq-count (v0.5.4p5)
RPKM (Reads Per Kilobase of exon per Megabase of library size)  were caclulated using Cufflinks (2.1.1)
Differential gene expression was analyzed using the R package DESeq2 (v1.2.8)
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: tab-delimited text files include FBGN number and RPKM values for each sample.

organism: Drosophila melanogaster

source_name: Crystal cells

extract_protocol:
GFP+ cells were flash frozen on dry ice, and RNA was exctracted using Arcturus PicoPure RNA isolation kit. Samples were then processed with NuGEN Ovation UltraLow system mRNA-Seq Protocol.
Library preparation was performed using the Illumina TruSeq RNA-Seq library preparation kit following the manufacturers protocol. Samples were multiplexed using the following barcodes: wt1 (CGATGT), wt2 ( TGACCA), wt3 (ACAGTG), mlf1 (GCCAAT), mlf2 (CAGATC), mlf3 (CTTGTA)

treatment_protocol: Blood cells were collected in ice cold PBS from larval bleed and GFP+ cells were sorted by FACS.

value: Blood

tag: age

value: third instar larvae


title: OH4265_2

tag: Stage

value: L3 (31hr post hatching)

tag: mutation

value: ot267 (W62STOP)


title: GmMM_GLYMA.08G357600-Input_br2.1

data_processing:
Basecalls performed using RTA version 1.12.4.2
Sequenced reads passing Illumina quality filter were aligned to the Glycine max genome (Wm82.a2.v1) using Bowtie v0.12.7 with parameters -v 2 -5 0 -3 0 -m 1 --best --strata
Reads from technical replicates were combined and peaks were identified for each biological replicates using MACS2, using default parameters and a q value threshold of 0.01.
Genome_build: Wm82.a2.v1
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2.

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp.  Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 3ug of an an antibody raised against the peptide QNQGSDPHARMGGDNC, corresponding to the amino acids 487-502 of GLYMA.08G35760.  Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow DR Multiplex System, following the manufaturer's instructions and enriched by PCR using 15 cycles.  Libraries were size-selected by electrophoresis and purified using Qiagen MinElute gel purification kit

value: mid-maturation stage


title: GmMM_GLYMA.08G357600-Input_br1.2


title: mlf 2

tag: genotype


title: GmMM_GLYMA.08G357600-ChIP_br2.2

description:
MM-08G357600-P2-2.RB78
processed data file:MM-GLYMA.08G357600-P2-2_catTR_peaks.narrowPeak


title: NBF40ExoP_S3

value: 10pg total RNA from ES cells

tag: Sex

tag: the number of single-cell/well contained in each data

value: prototype 6 of Quartz-Seq2

value: Ligation


title: GmEM_GLYMA.08G357600-ChIP_br1

value: Williams 82

value: early maturation stage


title: JR667_2

value: wt


title: GmMM_GLYMA.08G357600-Input_br1.1

value: embryo


title: GmMM_GLYMA.08G357600-ChIP_br2.1

description:
MM-08G357600-P2-2.JP80
processed data file:MM-GLYMA.08G357600-P2-2_catTR_peaks.narrowPeak

value: anti-peptide GLYMA.08G357600


title: GmMM_GLYMA.08G357600-ChIP_br1.2

description:
MM-08G357600-P2-1.RB78
processed data file:MM-GLYMA.08G357600-P2-1_catTR_peaks.narrowPeak


title: RT100p01_S3

value: male

tag: method name of single-cell rna-seq

value: Quartz-Seq2 (v3.1, RT100)

tag: type of sequence library preparation


title: GmMM_GLYMA.08G357600-ChIP_br1.1

description:
MM-08G357600-P2-1.JP80
processed data file:MM-GLYMA.08G357600-P2-1_catTR_peaks.narrowPeak


title: JR667_1


title: Depodding4.3

city: West Lafayette

first: Karen

middle: A

last: Hudson

state: IN

address: 915 West State Street

department: Crop Production and Pest Control

institute: USDA-ARS

data_processing:
Aligned to Gmax275 primary transcriptome using Bowtie2
removed reads that aligned multiple transcripts
removed genes with <10 hits per stage/experiment
Normalization using DESeq2.0
Genome_build: Glycine max 275
Supplementary_files_format_and_content: .csv files with RPKM values for each sample

source_name: Line Williams 82_Depodding4

extract_protocol:
RNA was extracted from trifoliate leaves using Phenol-cholorform method.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: line

value: Line Williams 82

tag: time point

value: 76 days after planting

value: Leaf

tag: sample group

value: Depodded


title: wt 2

tag: tissue

value: Blood

value: third instar larvae


title: Depodding4.2


title: wt 3


title: GmMM_GLYMA.08G357600-Input_br2.2

first: John

institute: University of California

tag: cultivar

tag: developmental stage

value: mid-maturation stage


title: RT100p02_S4

tag: cell type

value: 10pg total RNA from ES cells

tag: sequencer

tag: the number of fastq reads for dge-matrix (in million)

tag: read2 length for dge-matrix (nt)


title: plate4cat_S1

value: ES single-cells and PrE single-cells

tag: strain

tag: cell line


title: mlf 1

tag: genotype

tag: age


title: Depodding4.1


title: wt 1


title: RT100RNAp06_S3

tag: Sex

tag: the number of single-cell/well contained in each data

value: Ligation


title: Depodding_Control5.2

source_name: Line Williams 82_Depodding_Control5

value: Control


title: RT25Cellp06_S2

tag: method name of single-cell rna-seq

value: Quartz-Seq2 (v3.1, RT25)

tag: type of sequence library preparation


title: Depodding5.3

source_name: Line Williams 82_Depodding5

tag: line

tag: time point

value: 64 days after planting


title: Depodding_Control5.1

tag: tissue

tag: sample group


title: RT25p01_S1


title: A229T12-EB_SPENrep3

city: Paris

first: Maheva

last: Andriatsilavo

address: 11-13 rue Pierre et Marie Curie

department: Génétique et biologie du développement / Institut Curie / UMR 3215 CNRS / U934 Inserm

institute: Institut Curie

description:
FPKM_Read-count_gene.csv
FPKM_Read-count_Exon-bin.csv
DEseq2-analysis_SPEN-EBvsWT-EB.csv
DEXseq-analysis_SPEN-EBvsWT-EB.csv

data_processing:
Read mapping — Sequencing resulted in about 50 million 100bp paired-reads from each library, which were then aligned against the Drosophila melanogaster r5.54 genome reference using TopHat (version 2.0.6) in a fr-firstrand library type mode with the following parameters (-N 3 --read-edit-dist 3 -p 2 -g 1) (Trapnell et al, 2009). Unmapped reads were discarded.
Read count (FPKM) — Mapped reads were counted on gene using SummarizOverlaps method from the GenomicAlignments package (version 1.8.0) (Lawrence et al, 2013) with a “Union” mode and the following parameters (singleEnd=FALSE, ignore.strand=FALSE, fragments=TRUE), based on the ENSEMBL GENES 75, BDGP5 genome reference. The parameter (inter.feature = FALSE) was added for the read count on exon bin.
PCA analysis — Principal component analysis was performed using the PCAplot function from DEseq2 package on transformed data (rlog function) from all samples, considering a number of 300 top genes (ntop=300) selected by highest row variance. From this analysis, sample A229T8 (EB-WT) was excluded.
Differential gene expression analysis was performed using DEseq2 (version 1.12.2) (Love et al, 2014) with following parameters: DESeq(minReplicatesForReplace=Inf) and results(cooksCutoff=FALSE).
Differential exon usage was analyzed using DEXseq (version 1.18.4) (Anders et al, 2012) with the default parameters.
Genome_build: Drosophila melanogaster r5.54
Supplementary_files_format_and_content: "Read count on gene" file is a semicolon-delimited .csv including FPKM values for each Sample and  mean of FPKM values for each condition
Supplementary_files_format_and_content: "Read count on Exon bin" file is a semicolon-delimited .csv including FPKM values for each Sample and  mean of FPKM values for each condition
Supplementary_files_format_and_content: "DESeq2 analysis" files are semicolon-delimited .csv files including the following columns. [1]"FlyBase gene identifier" ; [2]"gene name" ; [3]"(baseMean) intermediate mean of normalized counts for all samples" ; [4]"log2FoldChange" ; [5]"(lfcSE) standard error" ; [6]"(stat) Wald statistic" ; [7]"(padj) BH adjusted p-values".
Supplementary_files_format_and_content: "DEXseq analysis files are semicolon-delimited .csv files including the following columns. [1]"FlyBase gene identifier" ; [2]"gene name" ; [3]"Feature ID" ; [4]"Exon_ID" ; [5]"mean of the counts across samples in each feature/exon" ; [6]"exon dispersion estimate" ; [7]"LRT statistic: full vs reduced" ; [8]"LRT p-value: full vs reduced" ; [9]"BH adjusted p-values" ; [10]"exon usage coefficient" ; [11]"exon usage coefficient" ; [12]"relative exon usage fold change" ; [13-17]"GRanges object of the coordinates of the exon/feature" ; [18-22]"matrix of integer counts, of each column containing a sample" ; [23]"list of transcripts overlapping with the exon".

source_name: FACS sorted Enteroblast

extract_protocol:
Gut dissociation step was performed as described in (Dutta et al., 2013) using PBS Elastase (final concentration 1mg/ml) solution and mechanic pipetting. Dissociated cells were resuspended in PBS, 1% BSA and FACS sorted (FACS Aria BD Biosciences) using the following parametters : 20psi, 100µm nozzle. Diploid RFP+ positive fractions (ISCs) were separated from the diploid RFP+ GFP+ double positive fractions (EBs). Cells were directly collected in TRIzol (Life Technologies). RNAs was extracted by performing two series of Phenol-Chloroform extractions at 4°C, followed by DNase treatment according to the manufacturer’s instructions. Around 100ng total RNA were collected from 100 000 sorted cells. Total RNA quality and quantification were assessed on an Agilent Bioanalyzer using the Agilent RNA 6000 nano kit.
A classical Illumina TruSeq Stranded RNA (LS) protocol was used to build the libraries, from poly(A)+-enriched mRNA (by Ribo-Zero rRNA removal Illumina kit). Three biological replicates were sequenced per conditions on the Illumina HiSeq 2500.

treatment_protocol: RNAi expression was induced by a 2 days themperature shift of the flies from 18°C to 29°C. Entire midguts were dissected and collected in cold PBS.

value: Intestine

value: 5 days old adult

value: UAS-spen RNAi,  esg>GAL4, tubGAL80.ts, UAS-RFP, nre-GFP

tag: marker

value: RFP, GFP

tag: gender

value: female


title: Depodding_Control5.3

value: Line Williams 82

value: 76 days after planting


title: A229T11-EB_SPENrep2


title: Depodding5.2

value: Leaf

value: Depodded


title: Depodding5.1


title: RT100Cellp03_S4

tag: cell type

value: male

value: Quartz-Seq2 (v3.1, RT100)

tag: sequencer


title: Depodding_Control4.3

source_name: Line Williams 82_Depodding_Control4


title: Depodding_Control4.2


title: RT25p02_S2

value: 10pg total RNA from ES cells

tag: the number of fastq reads for dge-matrix (in million)

tag: read2 length for dge-matrix (nt)


title: A229T9-EB_WTrep3

description:
FPKM_Read-count_gene.csv
FPKM_Read-count_Exon-bin.csv
DEseq2-analysis_WT-ISCvsWT-EB.csv
DEseq2-analysis_SPEN-EBvsWT-EB.csv
DEXseq-analysis_WT-ISCvsWT-EB.csv
DEXseq-analysis_SPEN-EBvsWT-EB.csv

value: wild-type,  esg>GAL4, tubGAL80.ts, UAS-RFP, nre-GFP


title: RT25RNAp07_S1

tag: strain

tag: cell line

value: Ligation


title: Depodding3.2

source_name: Line Williams 82_Depodding3

value: 54 days after planting


title: Depodding_Control4.1

value: Control


title: A229T7-EB_WTrep1

tag: age

tag: genotype


title: Depodding3.1


title: Depodding3.3


title: Depodding_Control3.1

source_name: Line Williams 82_Depodding_Control3


title: Depodding_Control3.2


title: SS3ligation_01_S2

tag: Sex

tag: the number of single-cell/well contained in each data

value: Quartz-Seq1 like with UMI


title: set2_cat_S3

description: We analyzed single-cells, which were sorted to 1,536-wells in total.

value: ES single-cells and PrE single-cells

tag: method name of single-cell rna-seq

value: Quartz-Seq2 (v3.2, RT25)

tag: type of sequence library preparation


title: Depodding_Control3.3

tag: line

tag: time point


title: A229T5-ISC_SPENrep2

description:
FPKM_Read-count_gene.csv
FPKM_Read-count_Exon-bin.csv
DEseq2-analysis_SPEN-ISCvsWT-ISC.csv
DEXseq-analysis_SPEN-ISCvsWT-ISC.csv

source_name: FACS sorted Intestinal stem cell

tag: tissue

value: Intestine

value: 5 days old adult

value: UAS-spen RNAi,  esg>GAL4, tubGAL80.ts, UAS-RFP, nre-GFP

value: RFP


title: Depodding2.3

source_name: Line Williams 82_Depodding2

value: Line Williams 82

value: 45 days after planting

tag: sample group


title: set4_cat_S1


title: SS3ligation_S1


title: A229T4-ISC_SPENrep1

tag: marker

tag: gender

value: female


title: Depodding_Control2.3

source_name: Line Williams 82_Depodding_Control2

value: Leaf


title: Depodding2.1

value: Depodded


title: SS3ligation_S3

tag: cell type

value: 10pg total RNA from ES cells

value: male

tag: sequencer


title: A229T3-ISC_WTrep3

description:
FPKM_Read-count_gene.csv
FPKM_Read-count_Exon-bin.csv
DEseq2-analysis_WT-ISCvsWT-EB.csv
DEseq2-analysis_SPEN-ISCvsWT-ISC.csv
DEXseq-analysis_WT-ISCvsWT-EB.csv
DEXseq-analysis_SPEN-ISCvsWT-ISC.csv

value: wild-type,  esg>GAL4, tubGAL80.ts, UAS-RFP, nre-GFP


title: SS4ligation_03_S4

value: prototype 3 of Quartz-Seq2

value: Ligation

tag: the number of fastq reads for dge-matrix (in million)

tag: read2 length for dge-matrix (nt)


title: SS4ligation_S4

tag: strain

tag: cell line

value: prototype 2 of Quartz-Seq2


title: A229T2-ISC_WTrep2

tag: age

tag: genotype


title: AP1.3

source_name: Line Williams 82_AP1

value: 38 days after planting (R2 growth stage)

value: Initial timepoint


title: Depodding_Control2.1

value: Control


title: A229T1-ISC_WTrep1

value: Intestine

value: 5 days old adult


title: A229T6-ISC_SPENrep3

value: UAS-spen RNAi,  esg>GAL4, tubGAL80.ts, UAS-RFP, nre-GFP

value: RFP


title: S. pombe Set2D cells_BRL112

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
2 X100 bp paired end stranded sequencing was performed on an Illumina HiSeq 2500. Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (cutadapt) and mapped to the S. Pombe  genome by STAR
Bams are sorted by samtools by name and mapped reads were counted with HTSEQ
Genome_build: Schizosaccharomyces_pombe. ASM294v2.29
Supplementary_files_format_and_content: count files are txt format files that contain raw read counts that map  to  transcripts for each defined gene.

organism: Schizosaccharomyces pombe

source_name: S. pombe Set2D cells

growth_protocol: Cultures were grown overnight in YES at 25°C to a density of 2.5 x 106 cells/ml in a 25mL culture.

extract_protocol:
The cells were pelleted by centrifugation and washed in DEPC H2O. The pellet was resuspended in 750ul TES Buffer [50mM Tris-HCl pH 7.5, 10mM EDTA, 100mM NaCl, 0.5% SDS made in DEPC H2O] along with an equal volume of 5:1 phenol:chloroform pH 4.7 and incubated at 65°C for one hour with vortexing for 10 seconds every 10 minutes. The samples were then cooled on ice and centrifuged for five minutes at 13,000 RPM. The aqueous phase was transferred to a 2mL phase lock tube and an additional phenol:chloroform extraction was performed. After centrifugation, the aqueous phase was transferred to a new tube and an equal volume of chloroform was added. To precipitate the RNA, the aqueous phase was transferred to a 2mL microcentrifuge tube and three volumes of ice cold ethanol and 3M NaOAc pH 5.2 were added and the samples were kept at -20°C to precipitate the RNA. The next day, samples were centrifuged at 14,000 RPM and 4°C for 15 minutes to pellet the RNA. The pellet was washed with ice cold 70% ethanol and air dried for 30 minutes. A Turbo DNAse (Ambion) reaction was set up with 100ug of RNA in a 150ul reaction containing 5ul of Turbo DNAse. The reaction was incubated at 37°C for 30 minutes and another 5ul of Turbo DNAse was added and incubated for an additional 30 minutes prior to the removal of the DNAse using 50ul of inactivation beads. An RNeasy Mini kit (Sigma) was used to further clean up and concentrate the RNA which was eluted in a final volume of 30ul of DEPC H2O.
Libraries were prepared from 2ug of RNA. Ribosomal RNA was removed from the samples using Ribo-Zero Gold rRNA Removal Kit (Yeast) following manufacturer instructions (Illumina). Libraries were prepared using the TruSeq Strand Total RNA Library Prep Kit, beginning at Elution 2 – Fragment – Prime step immediately preceding cDNA synthesis according to the manufacturer instructions (Illumina) with the following modifications; the 94 C Elution 2 – Fragment – Prime incubation was reduced to five minutes and the PCR was reduced to 11 cycles.

treatment_protocol: Not applicable

tag: genotype/variation

value: H3 WT Set2D mutant


title: AP1.1

value: Line Williams 82


title: Sterile3.3

source_name: Line T295H_Sterile3

value: Line T295H

value: 63 days after planting

value: Leaf

value: Sterile


title: svf_p04_S1

source_name: stromal vascular fraction (SVF)

value: Single-cells from stromal vascular fraction (SVF)

tag: Sex

value: male

tag: the number of single-cell/well contained in each data

tag: method name of single-cell rna-seq

value: Quartz-Seq2 (v3.1, RT25)


title: svf_p03_S4

tag: type of sequence library preparation

value: Ligation


title: A229T10-EB_SPENrep1

tag: tissue

value: RFP, GFP

value: female


title: svf_p10_S5


title: Sterile3.2

tag: line

tag: time point

tag: sample group


title: Sterile_Control3.3

source_name: Line T295H_Sterile_Control3

value: Control


title: Sterile3.1