title: WDT-3

city: Harbin

first: Ning

last: Li

address: No.600 Changjiang Road

department: College of Agriculture

institute: Northeast Agricultural University

data_processing:
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 Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time
Genome_build: http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa

growth_protocol: The seeds were surface sterilized with 2% sodium hypochlorite for 45 min and immersed in reverse osmosis (RO) water in the dark, and the uniformly germinated seeds were sown in 96-well plates supported by a plastic container in a culture room (14 h light/10 h dark at 28 ± 1 °C).

extract_protocol:
Rice leaves were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fourteen days after germination, the seedlings of WD20342 and Caidao were subjected to control and alkaline stress treatment (marked as WDT and CDT, respectively). The seedlings of WD20342 and Caidao were kept grown on RO water served as controls (marked as WD and CD, respectively). For alkaline stress treatment, seedlings were transferred on their 96-well plates into containers filled with 0.5 % Na2CO3 solution for 36 h.

tag: cultivar

tag: cultivar background

value: Indica

tag: alkaline sensitivity

value: alkaline-tolerant

tag: developmental stage

value: Seedling stage

tag: treated with

value: 0.5 % Na2CO3 solution for 36 h

value: leaves


title: WDT-2

status: Public on Jul 12 2018

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: CD4_stimulated_FOSL_ChIP-seq

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

country: USA

institute: NHLBI,NIH

library_source: genomic

data_processing:
Basecalls performed using CASAVA
Reads were aligned to hg18 genome using Bowtie2
Redudant reads or PETs were removed from further analysis
For Capture-C datasets, only PETs with bait at promoter of IL2RA were reteined. Reads from replicates were combined. Normalized read count mean value in 21 running window (500 bp) were calucated.
Normalized read count were calculated and uploaded to UCSC genome browser.
Genome_build: hg18
Supplementary_files_format_and_content: HiC/Capture-C Interaction file: A is the first anchor and B is the second anchor, each row is one interaction event detected by paired-end tag (PET); bedgraph file: First 3 columns indicate genomic coordinate, Column 4 indicates RPBM value.

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

growth_protocol: Human CD4+ T cells were purified from human blood using human CD4 T cell enrichment Kit from Stemcell Technologies (cat# 19052) according to the manufactures manual. The cells were used directly as resting T cells or activated using anti-CD3/CD28 beads (Invitrogen Dynabeads Human T-Activator CD3/CD28, Cat# 11131D) for 16 hours at 37°C.

extract_protocol:
The anti-FOSL1 antibody (Santa Cruz Biotechnoloy, Inc. The Cat# is sc-183)-immunoprecipetated chromatin on beads were added with 100ul EB buffer, 3 ul  of 10% SDS and 5 ul  of 20 mg/ml proteinase K. Incubate at 65C overnight. Extract 1x with 200 ul  of phenol/chloroform (PCI) for DNA. Add 1 ul  of 20 mg/ml glycogen, final 0.2M NaCl and final 70% Ethanol to precipitate. Incubate at -80°C for 1 hour. Spin at max speed for 30 min. Wash pellet once with 1 ml 70% ethanol, then spin for 10 min. at 4°C. Air dry and resuspend ChIP DNA in 40 ul  1xTE.
ChIP DNA is subjected to DN Aend repair using the Epicentre DNA END-Repair kit (Cat. No. ER0720, Epicentre Biotechnologies) according to the manufacturer instruction. Repair DNA was cleaned with the MinElute column using MinElute Reaction Cleanup protocol (Qiagen, pgs 28-29 of MinElute Handbook) and eluted with 40ul EB. Add 5 ul  10x NEB Buffer #2. 1 ul  10 mM dATP and 3 ul  5 U/ul  Klenow Fragment (3´→5´ exo–). Incubate for 30 min at 37°C. Purify the reaction again as above and elute the DNA in 22 ul  of EB. Add 3 μl 10x T4 DNA ligase buffer, 2 μl adapter (15uM,  annealed from primer: multiplexing    adapter-top with multiplexing adapter-bottom that is the same as Illumina’s InPE adaptor), mix then add 3 μl T4 DNA ligase (400 units/μl). Incubate for 30 min at room temperature. Add 6 ul H2O and load 18ul per lane on E-gel. Run 10 min. Gel purify the fragments from 200-400 bp. Elute DNA in 22ul EB. Add 25 μl of master mix (HF fusion), 1 μl of 10uM Multiplexing PCR Primer 1.0, 1 μl of 10uM one of the indexed primer2: PCR Primer2- IndexM1-64, or PCR Primer2- IndexM2-64, till PCR Primer2- IndexM12-64 (M stands for Modified, -64 means it is 64bp long). PCR Conditions:   98°C for 30 sec. 17 cycles of 98°C, 10”; 65°C, 30”; 72°C, 30”, 72°C for 5 min. 4°C hold. Gel purify the 250-450 bp fragments for sequencing.

treatment_protocol: The resting CD4+ T cells were activated using anti-CD3/CD28 beads (Invitrogen Dynabeads Human T-Activator CD3/CD28, Cat# 11131D) for 16 hours at 37°C.

value: blood

tag: cell type

value: CD4+ T cells

tag: treatment

value: stimulated

tag: fixation

value: fixed

tag: antibody

value: anti-FOSL1 antibody (Santa Cruz Biotechnoloy, catalog# sc-183, lot# 12314)


title: CD4_stimulated_FOSL_ChIP-seq_rep


title: WDT-1


title: CD4_resting_FOSL_ChIP-seq_rep

value: resting


title: CD4_resting_input_ChIP-seq


title: CD4_resting_FOSL_ChIP-seq


title: WD-1

value: none (control)


title: WD-3


title: WD-2


title: CDT-3

value: Caidao (CD)

value: Japonica

value: alkaline-sensitive


title: CD4_resting_rep2_RNA-seq

description: RNA-seq

data_processing:
Basecalls performed using CASAVA
Reads were aligned to hg18/hg19 genome using Bowtie2
Read of PETs <1Kb were used for peakcalling for getting the HSs
The EPTs >1Kb were used for identify interaction among the HSs
Calculated the p value of interaction based on hypergeometric distribution
Genome_build: hg18
Supplementary_files_format_and_content: TrAC-looping Interaction file: A is the first anchor and B is the second anchor, each row is one interaction event; RPKM file: column 1  (Gene Symbol), column 2( RPKM)

source_name: Blood

extract_protocol:
Human CD4+ T cells were purified from human blood using human CD4 T cell enrichment Kit from Stemcell Technologies (cat# 19052) according to the manufactures manual.
The eluted DNA was purified by phenol-chloroform extraction and ethanol precipitation. For intramolecular circulization, the DNA was incubated in the presence of T7 DNA ligase in 50ml of ligation buffer (66 mM Tris-HCl pH 7.4,  10 mM MgCl2, 1 mM ATP, 1 mM DTT, 7.5% Polyethylene glycol (PEG 6000) at room temperature for overnight. The ligated DNA was precipitated by ethanol and then resuspended in 55μl sampling buffer from templify100 kit (GE Hearlthcare cat# 25-6400-10).  The DNA was denatured at 97°C for 3min and then chilled on ice. RCA was performed by adding 50μl Reactions buffer +2μl enzyme mix to the denatured DNA mix and incubated at 30°C for overnight. Use 1μl of RCA product for PCR by mixing with 25μl NEB Phusion HF master mix, 23μl H2O, 1μl 10μM PCR primer N501, 1 μl 10μM  PCR primer N701 with the cycling conditions: 98 °C for 30 s; 11 cycle of 98 °C for 10 s, 65 °C for 30 s and 72 °C for 8 s; 72 °C for 5 min; 4C hold. The PCR products were resolved on E-gel and the DNA with a size range of 250-650bp was isolated and sequenced by paired-end sequencing on Illumina Hiseq 2500.

treatment_protocol: The resting CD4+ T cells were  activated using anti-CD3/CD28 beads (Invitrogen Dynabeads Human T-Activator CD3/CD28, Cat# 11131D) for 16 hours at 37°C.

value: Resting CD4+ T cells


title: CD4_Activated_rep1_RNA-seq

description: RNA-seq

value: Activated CD4+ T cells


title: CD4_Activated_rep2_RNA-seq

description: RNA-seq


title: CDT-2


title: CD4_resting_rep1_RNA-seq

description: RNA-seq


title: CD4_ Activated_rep1-tech1_TrAC-loop

description: TrAC-looping

data_processing:
Library strategy: TrAC-loop
Basecalls performed using CASAVA
Reads were aligned to hg18/hg19 genome using Bowtie2
Read of PETs <1Kb were used for peakcalling for getting the HSs
The EPTs >1Kb were used for identify interaction among the HSs
Calculated the p value of interaction based on hypergeometric distribution
Genome_build: hg18
Supplementary_files_format_and_content: TrAC-looping Interaction file: A is the first anchor and B is the second anchor, each row is one interaction event; RPKM file: column 1  (Gene Symbol), column 2( RPKM)


title: CD4_stimulated_input_ChIP-seq


title: CDT-1


title: CD-1


title: CD4_Activated_rep1-tech2_TrAC-loop

description: TrAC-looping


title: CD4_Activated_rep2_TrAC-loop

description: TrAC-looping


title: IGTB979_activated T cells_RNA-seq

city: San Francisco

first: Rachel

last: Gate

state: CA

address: 533 Parnassus Ave

institute: UCSF

data_processing:
Used RSEM for alignment to hg19 transcriptome and quantification of isoforms and gene expected counts
Genome_build: hg19 transcriptome
Supplementary_files_format_and_content: Read abundances were calculated using RSEM for gene expression counts

source_name: activated T cells

growth_protocol: Briefly, CD4+ T cells were isolated from whole blood by negative selection using RosetteSep human CD4+ T cell enrichment cocktail (STEMCELL Technologies Inc., Vancouver, BC) and RosetteSep density medium gradient centrifugation. Isolated CD4+ T cells were placed in freezing container at -80°C for overnight, and then moved into a liquid nitrogen tank for long-term storage. On the day of activation, CD4+ T cells were thawed in a 37°C water bath, counted and resuspended in RPMI- 1640 supplemented with 10% FCS, and plated at 50,000 cells per well in a 96 well round-bottom plate.

extract_protocol: RNA was isolated using Qiagen RNeasy Plus Mini Kit and RNA integrity was quantified by Agilent RNA 6000 Nano Kit using the Agilent Bioanalyzer. Purified RNA were converted to RNA-seq libraries using a previously published protocol in Satija  et.al, where reverse transcription was carried out based on the SMART template switching method and the resulting cDNA was further tagmented and PCR amplified using Nextera XT DNA Sample kit (Illumina) to add the Illumina sequencing adaptors. Samples were sequenced on Illumina HiSeq 2500 to an average depth of 16.9 million reads per sample (+/- 8.7 million).

treatment_protocol: Cells were either left untreated or stimulated for 48 hours with beads conjugated with anti-CD3 and anti-CD28 antibodies (Dynabeads, Invitrogen #11131D, Life Technologies) at a cell:bead ratio of 1:1. At each time point, cells were further purified by a second step positive selection with CD4+ Dynabeads (Invitrogen #11145D, Life Technologies).

tag: activation

value: anti-CD3 and anti-CD28

tag: Sex

value: Male

tag: age

tag: race

value: Caucasian

tag: ethnicity

value: Non-Hispanic

tag: bmi

tag: systolic

tag: diastolic


title: CD-3

tag: cultivar

tag: cultivar background

value: Seedling stage

value: leaves


title: IGTB950_activated T cells_RNA-seq

value: blood

value: Female


title: IGTB920_activated T cells_RNA-seq


title: IGTB867_activated T cells_RNA-seq


title: CD-2

tag: alkaline sensitivity

tag: developmental stage


title: CD4_resting_rep2_TrAC-loop

description: TrAC-looping

tag: tissue


title: CD4_resting_rep1-rech2_TrAC-loop

description: TrAC-looping

tag: cell type


title: IGTB965_activated T cells_RNA-seq


title: IGTB713_activated T cells_RNA-seq


title: IGTB853_activated T cells_RNA-seq


title: IGTB677_activated T cells_RNA-seq


title: IGTB707_activated T cells_RNA-seq


title: IGTB694_activated T cells_RNA-seq


title: IGTB843_activated T cells_RNA-seq


title: IGTB661_activated T cells_RNA-seq


title: IGTB507_activated T cells_RNA-seq


title: IGTB655_activated T cells_RNA-seq


title: IGTB529_activated T cells_RNA-seq


title: IGTB572_activated T cells_RNA-seq


title: IGTB494_activated T cells_RNA-seq


title: IGTB467_activated T cells_RNA-seq


title: CD4_resting_rep1-tech1_TrAC-loop

description: TrAC-looping


title: IGTB95_activated T cells_RNA-seq


title: IGTB190_activated T cells_RNA-seq


title: IGTB836_activated T cells_RNA-seq


title: IGTB178_activated T cells_RNA-seq


title: IGTB980_activated T cells_RNA-seq


title: IGTB1140_activated T cells_RNA-seq


title: IGTB874_activated T cells_RNA-seq


title: IGTB863_activated T cells_RNA-seq


title: IGTB780_activated T cells_RNA-seq


title: IGTB719_activated T cells_RNA-seq


title: IGTB638_activated T cells_RNA-seq


title: IGTB731_activated T cells_RNA-seq


title: IGTB576_activated T cells_RNA-seq


title: IGTB619_activated T cells_RNA-seq


title: IGTB330_activated T cells_RNA-seq


title: IGTB195_activated T cells_RNA-seq


title: IGTB1576_activated T cells_RNA-seq


title: IGTB374_activated T cells_RNA-seq


title: IGTB1591_activated T cells_RNA-seq


title: IGTB1569_activated T cells_RNA-seq


title: IGTB1586_activated T cells_RNA-seq


title: IGTB1563_activated T cells_RNA-seq


title: IGTB1506_activated T cells_RNA-seq


title: IGTB1587_activated T cells_RNA-seq


title: IGTB1538_activated T cells_RNA-seq


title: IGTB1502_activated T cells_RNA-seq


title: IGTB839_activated T cells_RNA-seq


title: IGTB1553_activated T cells_RNA-seq


title: IGTB1487_activated T cells_RNA-seq


title: IGTB1505_activated T cells_RNA-seq


title: IGTB1282_activated T cells_RNA-seq


title: IGTB1436_activated T cells_RNA-seq


title: IGTB1312_activated T cells_RNA-seq


title: IGTB1411_activated T cells_RNA-seq


title: IGTB1248_activated T cells_RNA-seq


title: IGTB1164_activated T cells_RNA-seq


title: IGTB865_activated T cells_RNA-seq


title: IGTB824_activated T cells_RNA-seq


title: IGTB838_activated T cells_RNA-seq


title: IGTB501_activated T cells_RNA-seq


title: IGTB712_activated T cells_RNA-seq


title: IGTB70_activated T cells_RNA-seq


title: IGTB688_activated T cells_RNA-seq


title: IGTB611_activated T cells_RNA-seq


title: IGTB506_activated T cells_RNA-seq


title: IGTB350_activated T cells_RNA-seq


title: IGTB234_activated T cells_RNA-seq


title: IGTB218_activated T cells_RNA-seq


title: IGTB231_activated T cells_RNA-seq


title: IGTB1547_activated T cells_RNA-seq


title: IGTB1589_activated T cells_RNA-seq


title: IGTB1571_activated T cells_RNA-seq


title: IGTB1483_activated T cells_RNA-seq


title: IGTB1458_activated T cells_RNA-seq


title: IGTB1424_activated T cells_RNA-seq


title: IGTB1432_activated T cells_RNA-seq


title: IGTB1415_activated T cells_RNA-seq


title: IGTB1372_activated T cells_RNA-seq


title: IGTB1324_activated T cells_RNA-seq


title: IGTB1393_activated T cells_RNA-seq


title: IGTB737_activated T cells_RNA-seq


title: IGTB1365_activated T cells_RNA-seq


title: IGTB1305_activated T cells_RNA-seq


title: IGTB1279_activated T cells_RNA-seq


title: IGTB1321_activated T cells_RNA-seq


title: IGTB621_activated T cells_RNA-seq


title: IGTB1227_activated T cells_RNA-seq


title: IGTB1275_activated T cells_RNA-seq


title: IGTB1236_activated T cells_RNA-seq


title: IGTB496_activated T cells_RNA-seq


title: IGTB1198_activated T cells_RNA-seq


title: IGTB1216_activated T cells_RNA-seq


title: IGTB1212_activated T cells_RNA-seq


title: IGTB1193_activated T cells_RNA-seq


title: IGTB1191_activated T cells_RNA-seq


title: IGTB1219_0hr_unstimulated T cells_ATAC-Seq

data_processing:
library strategy: ATAC-seq
Paired-end reads were aligned using BWA
Reads were filtered for mitochondrial contamination and multiply-mapped reads
Pilot samples were merged and peaks were called on the merged samples for activated and stimulated samples
Coverage for each sample was caluclated for the called activated and stimulated peaks
Genome_build: hg19
Supplementary_files_format_and_content: peaks were called using MASC2 and the coverage of each sample in called peaks was quantified using BEDtools

source_name: unstimulated T cells

extract_protocol: We performed ATAC-seq as previously described Buenrostro et.al.

value: no stimulation

value: African American


title: IGTB1190_activated T cells_RNA-seq


title: IGTB1133_0hr_Atac13_rep1_unstimulated T cells_ATAC-Seq


title: IGTB1219_48hr_Atac13_activated T cells_ATAC-Seq


title: IGTB1130_0hr_unstimulated T cells_ATAC-Seq

value: East Asian - Korea


title: IGTB1218_48hr_Atac13_activated T cells_ATAC-Seq


title: IGTB1077_0hr_unstimulated T cells_ATAC-Seq

value: East Asian- China


title: IGTB1130_48hr_Atac13_activated T cells_ATAC-Seq


title: IGTB1133_0hr_Atac13_rep2_unstimulated T cells_ATAC-Seq


title: IGTB1133_48hr_Atac13_rep2_activated T cells_ATAC-Seq


title: IGTB979_activated T cells_ATAC-Seq


title: IGTB965_activated T cells_ATAC-Seq


title: IGTB1077_48hr_Atac13_activated T cells_ATAC-Seq


title: IGTB950_activated T cells_ATAC-Seq


title: IGTB95_activated T cells_ATAC-Seq


title: IGTB929_activated T cells_ATAC-Seq


title: IGTB874_activated T cells_ATAC-Seq


title: IGTB920_activated T cells_ATAC-Seq


title: IGTB867_activated T cells_ATAC-Seq


title: IGTB1240_activated T cells_RNA-seq


title: IGTB863_activated T cells_ATAC-Seq


title: IGTB865_activated T cells_ATAC-Seq


title: IGTB1218_0hr_unstimulated T cells_ATAC-Seq


title: IGTB853_activated T cells_ATAC-Seq


title: IGTB839_activated T cells_ATAC-Seq


title: IGTB836_activated T cells_ATAC-Seq


title: IGTB824_activated T cells_ATAC-Seq


title: IGTB803_activated T cells_ATAC-Seq


title: IGTB1133_48hr_Atac13_rep1_activated T cells_ATAC-Seq


title: IGTB980_activated T cells_ATAC-Seq


title: IGTB780_activated T cells_ATAC-Seq


title: IGTB731_activated T cells_ATAC-Seq


title: IGTB70_activated T cells_ATAC-Seq


title: IGTB719_activated T cells_ATAC-Seq


title: IGTB737_activated T cells_ATAC-Seq


title: IGTB713_activated T cells_ATAC-Seq


title: IGTB911_activated T cells_ATAC-Seq


title: IGTB677_activated T cells_ATAC-Seq


title: IGTB712_activated T cells_ATAC-Seq


title: IGTB688_activated T cells_ATAC-Seq


title: IGTB661_activated T cells_ATAC-Seq


title: IGTB694_activated T cells_ATAC-Seq


title: IGTB655_activated T cells_ATAC-Seq


title: IGTB707_activated T cells_ATAC-Seq


title: IGTB843_activated T cells_ATAC-Seq


title: IGTB619_activated T cells_ATAC-Seq


title: IGTB576_activated T cells_ATAC-Seq


title: IGTB611_activated T cells_ATAC-Seq


title: IGTB529_activated T cells_ATAC-Seq


title: IGTB572_activated T cells_ATAC-Seq


title: IGTB507_activated T cells_ATAC-Seq


title: IGTB501_activated T cells_ATAC-Seq


title: IGTB496_activated T cells_ATAC-Seq


title: IGTB481_activated T cells_ATAC-Seq


title: IGTB494_activated T cells_ATAC-Seq


title: IGTB398_activated T cells_ATAC-Seq


title: IGTB467_activated T cells_ATAC-Seq


title: IGTB374_activated T cells_ATAC-Seq


title: IGTB621_activated T cells_ATAC-Seq


title: IGTB638_activated T cells_ATAC-Seq


title: IGTB330_activated T cells_ATAC-Seq


title: eSox17_OKM_1neg

city: Munster

first: Veeramohan

last: Veerapandian

state: North Rhine-Westphalia

address: Röntgenstr. 20

department: Department Tissue Morphogenesis

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description:
DERBYseq_eSox17_Processed.txt
Amplicon sequencing
genome integrated DNA

data_processing:
fastqc
Reads were demultiplexed based on custom barcode used by custom Python script
Relevant positions of randomised codons were extracted, translated and tri-peptides were counted to construct count matrices where rows are variants and columns are biological sample types
DESeq2 for differential variant enrichment analysis
Genome_build: N/A
Supplementary_files_format_and_content: Tab delimited text files.

organism: Mus musculus

source_name: Synthesized DNA (Sox17)

growth_protocol: OG2MEF cells were transduced twice by pMX-Oct4,pMX-Klf4,(with(OKM) or without pMX-cMyc (OK)) along with pMX-eSox2 or pMX-eSox17 library. After second viral transduction, the cells were cultured under Serum + LIF + Vitamin C (MEs) reprogramming medium.

extract_protocol:
Exogenously introduced genomic DNA was isolated Quick gDNA micro prep kit (Zymo research)
Custom barcodes and Illumina adapters was used for library constructions.

value: OG2 MEF

tag: protocol

value: reprogramming cells


title: eSox17_OKM_2neg


title: eSox17_OKM_3neg


title: IGTB231_activated T cells_ATAC-Seq


title: eSox17_OKM_3pos


title: eSox17_OK_3neg


title: IGTB1591_activated T cells_ATAC-Seq


title: eSox17_OK_2neg


title: IGTB190_activated T cells_ATAC-Seq


title: IGTB1589_activated T cells_ATAC-Seq


title: IGTB506_activated T cells_ATAC-Seq


title: eSox17_OKM_1pos


title: IGTB1587_activated T cells_ATAC-Seq


title: eSox17_OK_3pos


title: eSox17_OK_2pos


title: IGTB1576_activated T cells_ATAC-Seq


title: IGTB234_activated T cells_ATAC-Seq


title: eSox17_Input_3

description:
DERBYseq_eSox17_Processed.txt
Amplicon sequencing
pMX eSox17 library plasmid DNA


title: IGTB350_activated T cells_ATAC-Seq


title: IGTB1569_activated T cells_ATAC-Seq


title: eSox17_OK_1pos


title: eSox17_OK_1neg


title: eSox17_Input_2


title: eSox2_Input_30_10KFD2

description:
DERBYseq_eSox2_Processed.txt
Amplicon sequencing
pMX eSox2 library plasmid DNA

source_name: Synthesized DNA (Sox2)


title: eSox2_Input_30_10KFD1


title: IGTB1553_activated T cells_ATAC-Seq


title: IGTB1563_activated T cells_ATAC-Seq


title: IGTB1547_activated T cells_ATAC-Seq


title: eSox17_Input_1


title: eSox2_Input_30_1000FD2


title: IGTB1506_activated T cells_ATAC-Seq


title: eSox17_OKM_2pos


title: IGTB195_activated T cells_ATAC-Seq


title: IGTB1586_activated T cells_ATAC-Seq


title: IGTB1502_activated T cells_ATAC-Seq


title: IGTB1505_activated T cells_ATAC-Seq


title: IGTB1487_activated T cells_ATAC-Seq


title: eSox2_Input_30_1000FD1


title: eSox2_Input_30_ND2


title: eSox2_Input_30_100FD1


title: IGTB1458_activated T cells_ATAC-Seq


title: IGTB1538_activated T cells_ATAC-Seq


title: eSox2_Input_30_100FD2


title: eSox2_Input_15_10KFD2


title: eSox2_Input_30_ND1


title: eSox2_Input_15_10KFD1


title: IGTB1436_activated T cells_ATAC-Seq


title: eSox2_Input_15_1000FD2


title: IGTB1483_activated T cells_ATAC-Seq


title: eSox2_Input_15_1000FD1


title: IGTB1415_activated T cells_ATAC-Seq


title: IGTB1424_activated T cells_ATAC-Seq


title: IGTB1411_activated T cells_ATAC-Seq


title: eSox2_Input_15_100FD2


title: IGTB1432_activated T cells_ATAC-Seq


title: IGTB1394_activated T cells_ATAC-Seq


title: eSox2_Input_15_100FD1


title: eSox2_Input_15_ND2


title: IGTB1393_activated T cells_ATAC-Seq


title: eSox2_Input_15_ND1


title: IGTB1365_activated T cells_ATAC-Seq


title: eSox2_OK_3negB

description:
DERBYseq_eSox2_Processed.txt
Amplicon sequencing
genome integrated DNA


title: IGTB1372_activated T cells_ATAC-Seq


title: eSox2_OK_3negA


title: IGTB1324_activated T cells_ATAC-Seq


title: IGTB1359_activated T cells_ATAC-Seq


title: eSox2_OK_2negA


title: IGTB1323_activated T cells_ATAC-Seq


title: IGTB1321_activated T cells_ATAC-Seq


title: eSox2_OK_1negB


title: eSox2_OK_2negB


title: eSox2_OK_1negA


title: IGTB1312_activated T cells_ATAC-Seq


title: WT DRC EpiC SMC1 rep2

city: Stanford

first: Amy

last: Chen

address: 279 Campus Drive West

institute: Stanford University

data_processing:
Fastq files were mapped to the genome using Bowtie2 with the following setting: -p 4 -q -D 15 -R 10 -L 22 -i S,1,1.15
Mapped reads were filtered to keep only uniquely mapping, deduplicated reads
MACS2 was used for peak finding using the following settings: --nomodel --extsize 200 -s 50 --bw 200 -f BAM -g mm -B -q 0.05
Genome_build: mm10
Supplementary_files_format_and_content: bigwig format after combining replicates for each condition

source_name: epiblast cells

growth_protocol: All cells were grown in Knockout DMEM with 15%FBS, Pen/Strep, L-glutamine and Non-essential amino acids. ESCs were also grown in Lif and 2i (GSKi and MEKi).

extract_protocol:
DNA was extracted using a standard ChIP protocol
Library was constructed using a standard Illumina protocol
ChIP-seq, ATAC-seq

treatment_protocol: Doxycycline was added at 0.5ug/ml for 24hrs

value: EpiCs

tag: cell line of origin

value: dual miRNA reporter V6.5 ESCs

tag: chip antibody

tag: treatment

value: -Lif -2i day 3


title: WT DRC EpiC SMC1 rep1


title: WT DRC EpiC IgG rep2

value: IgG (normal rabbit)


title: IGTB1305_activated T cells_ATAC-Seq

tag: activation

value: anti-CD3 and anti-CD28

tag: Sex

value: Male


title: IGTB1294_activated T cells_ATAC-Seq

tag: race

value: Caucasian

value: Non-Hispanic


title: WT DRC EpiC IgG rep1


title: eSox2_OK_3posB


title: eSox2_OK_2posB


title: WT DRC ESC SMC1 rep2

source_name: embryonic stem cells

value: ESCs

value: Lif 2i


title: IGTB178_activated T cells_ATAC-Seq

value: blood

value: Female

tag: ethnicity


title: WT DRC ESC SMC1 rep1


title: IGTB1279_activated T cells_ATAC-Seq

tag: bmi


title: IGTB1282_activated T cells_ATAC-Seq

tag: systolic


title: eSox2_OK_2posA


title: IGTB1275_activated T cells_ATAC-Seq

tag: diastolic


title: WT DRC ESC IgG rep2


title: WT DRC ESC IgG rep1


title: eSox2_OK_1posA


title: eSox2_OK_1posB


title: IGTB1243_activated T cells_ATAC-Seq


title: MCM_sWAT [Sample 8]

city: Shenyang

first: Zhe

last: Wang

address: 120 Dongling Road

institute: Shenyang Agricultural University

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The filtered reads were mapped to known reference genomes
Gene annotation were performed using Ensembl mouse gene ID
Abundances of mRNA-Seq reads were reported in FPKM
Genome_build: Reference genome (ftp://ftp.ensembl.org/pub/release-74/fasta/mus_musculus/dna/)
Supplementary_files_format_and_content: The txt file, GeneCounts_FPKM.txt, includes the normalized gene counts of the 20 samples.

source_name: Subcutaneous white adipose tissue

extract_protocol:
Total RNA of adipose tissues was extracted using RNeasy Lipid Tissue Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The bats and mice were treated under 30°C and 10°C for 7 days

tag: strain background

value: ICR

value: 10°C for 1 week

tag: gender

value: Subcutaneous white adipose tissue (sWAT)


title: IGTB1248_activated T cells_ATAC-Seq


title: eSox2_OKM_3negB

value: OG2 MEF


title: MCF_sWAT [Sample 7]


title: IGTB1240_activated T cells_ATAC-Seq


title: eSox2_OKM_3negA

value: reprogramming cells


title: MHM_sWAT [Sample 6]

value: 30°C for 1 week


title: eSox2_OK_3posA


title: IGTB1236_activated T cells_ATAC-Seq


title: IGTB1227_activated T cells_ATAC-Seq


title: eSox2_OKM_2negA


title: MCF_iBAT [Sample 3]

source_name: Brown adipose tissue

value: interscapular brown adipose tissue (iBAT)


title: eSox2_OKM_1negB


title: IGTB1216_activated T cells_ATAC-Seq


title: IGTB1212_activated T cells_ATAC-Seq


title: eSox2_OKM_1negA


title: MCM_iBAT [Sample 4]


title: MHM_iBAT [Sample 2]


title: MHF_iBAT [Sample 1]


title: eSox2_OKM_3posB


title: eSox2_OKM_3posA


title: eSox2_OKM_2posB


title: IGTB1198_activated T cells_ATAC-Seq


title: eSox2_OKM_2posA


title: IGTB1197_activated T cells_ATAC-Seq


title: IGTB1193_activated T cells_ATAC-Seq


title: MHF_sWAT [Sample 5]


title: eSox2_OKM_1posB


title: IGTB1191_activated T cells_ATAC-Seq


title: IGTB1164_activated T cells_ATAC-Seq


title: IGTB1190_activated T cells_ATAC-Seq


title: IGTB1140_activated T cells_ATAC-Seq


title: eSox2_OKM_2negB


title: PDlC-D14 miRNA

status: Public on Jul 11 2018

city: Beijing

first: Yunfei

last: Zheng

state: Beijing

address: 22 Zhongguancun Avenue South, Haidian District

department: Oral and Maxillofacial Surgery

institute: Peking University School and Hospital of Stomatology

description:
Small RNA
Processed data file: miRNA.All.Counts.exp.txt

data_processing:
mRNA: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15 b) 13% base quality <20.
mRNA: Hisat2 2.0.4 mapping to reference genome.
mRNA: Count counting.
miRNA: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15 b) 13% base quality <20 c) 15bp < read length < 30bp.
miRNA: Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo sapiens miRNA database and GRCH38.p10 genome.
miRNA: Count counting.
Genome_build: hg19_GRCh38 / miRBase 21.0
Supplementary_files_format_and_content: all.counts.exp.txt: Tab-delimited text file contains counts for each mRNA sample.
Supplementary_files_format_and_content: miRNA.All.Counts.exp.txt: Tab-delimited text file contains counts for each miRNA sample.

source_name: periodontal ligament stem cells, osteogenic differentiation, D14

growth_protocol: PDL tissue was collected from the middle third root of healthy premolars, cut into pieces, and digested in equal volumes of type I collagenase and dispase. Next, the isolated cells were cultured in α-Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. The cells were passaged using 0.25% trypsin and further expanded until passage 4 before they were used in the experiments.

extract_protocol:
mRNA: Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Agilent) and kept at -80℃. The RNA with RIN >8.0 is right for cDNA library construction.
miRNA: Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Agilent) and kept at -80℃. The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by gel electrophoresis.
RNA-Seq: RNA libraries were prepared for sequencing using standard Illumina protocols.
miRNA-Seq: RNA libraries were prepared for sequencing using standard Ion Proton protocols.

treatment_protocol: For osteogenic induction, PDLSCs were cultured in α-MEM supplemented with 10% FBS, 100 nM dexamethasone, 200 µM L-ascorbic acid, and 10 mM β-glycerophosphate. The medium was changed every 2 days, and cells were harvested at the indicated time points.

value: Stem cells isolated from periodontal ligament

tag: passage

value: Osteogenic induction

tag: time point

value: Day 14


title: PDlC-D7 miRNA

source_name: periodontal ligament stem cells, osteogenic differentiation, D7

value: Day 7


title: anti-Qk6 iCLIP, C2C12 myoblasts (MiSeq)

city: Galveston

first: W.

middle: Samuel

last: Fagg

state: TX

address: 301 University Blvd, Department of Surgery, MRB5.150, L21875

department: Surgery/Biochemistry and Molecular Biology

institute: University of Texas Medical Branch

description:
UUUTTAGUU bp 1 to 9 of read1 is UMI
c2c12_qk6b_ls056

data_processing:
Library strategy: iCLIP-Seq
iCLIP 1: based on random bases of internal barcode positions 1-9 of each read, the readIDs were divided into classes (for later use in duplicate removal). Note: positions 4-7 comprised fixed values for each sample
iCLIP 2: each read was searched for the presence of adaptor sequence AGATCGGA and trimmed from that point on. Reads shorter than 30bp after trimming (including internal barcode positions 1-9) were discarded.
iCLIP 3: internal barcode positions 1-9 were trimmed before mapping
iCLIP 4: reads mapping (by Bowtie2) to mouse repeatMasker elements were discarded
iCLIP 5:  reads were mapped to mm9 by Tophat, aided by a gtf file based on UCSC Knowngenes, and with parameters --no-novel-juncs, --no-coverage-search
iCLIP 6: for each class of internal random barcode bases from step (1), duplicate read mappings of the same length and position were discarded
iCLIP 7: peaks were called on the dup-removed bam files from step (6) by Clipper (Yeo et al) using default parameters for mm9 and --premRNA.
Genome_build: mm9
Supplementary_files_format_and_content: SupplementalTable_QK_CLIPper_Data.xlsx is an Excel spreadsheet file with one worksheet contaiing peak calls for each sample analyzed by Clipper.

source_name: myoblast

growth_protocol: C2C12 cells were maintained in DMEM (high glucose) supplemented with 10% FBS; for myotube differentiation, C2C12 myoblasts were allowed to reach ~90% confluence then media were changed to DMEM (high glucose) supplemented with 2% horse serum and cultured an additional 72h with daily media change

extract_protocol:
following immunoprecipitation and radiolabeling, protein:RNA complexes were separated by SDS-PAGE then transferred to nitrocellulose where they were extracted from a region corresponding to protein:RNA then extracted with phenol:chloroform:isoamyl alcohol after proteinase digestion
All libraries prepared according to Konig et al J Vis Exp. 2011 30;50 and Huppertz et al Methods. 2014 Feb; 65(3):274-87.

treatment_protocol: crosslinking was performed by irradiating cells with UV light with 400 mJ in an Aglient Stratalinker

value: myoblast

tag: cell line


title: anti-HA iCLIP, C2C12 myoblasts (MiSeq + HiSeq)

description:
UUUAACCUU bp 1 to 9 of read1 is UMI
c2c12_ctrl_ls053

tag: cell type


title: anti-PanQk iCLIP 72h differentiated C2C12 myotubes (MiSeq + HiSeq)

description:
UUUCGGAUU bp 1 to 9 of read1 is UMI
c2c12_pqkd_ls055

source_name: myotube

value: myotube


title: C2C12 Qk6/7 depletion replicate 3

data_processing:
RNAseq 1: the 100x100bp pairedEnd reads were trimmed at the 3' ends to 90x90. Fastq files from 2 runs of the same replicate were concatenated.
RNAseq 2: reads mapping (by Bowtie2) to repeatMasker elements in mouse were discarded.
RNAseq 3:  reads were mapped by Tophat2 to mm9 assisted by gtf files of UCSC Known Genes. Duplicate mappings were removed with Samtools rmdup.
RNAseq 4: The final set of mappings was converted to coverage using bedTools genomeCoverageBed.
RNAseq 5: The coverage summed over all exonic positions of a gene was divided by 180 (90+90) to determine the read per gene for a sample. This was done for all UCSC KnownGenes.
RNAseq 6: For input to DESeq all genes with non-zero counts in any sample were considered. Replicates were combined per the DESeq methodology.
RNAseq 7: The set of UCSC Known Genes was parsed into a set of exonic parts for DEXseq with the supplied script dexseq_prepare_annotation.py
RNAseq 8: For input to DEXseq, the coverage of each exonic part was divided by 180 (90+90) to determine the reads per exonic part for a sample. Replicates were combined per the DESeq methodology.
Genome_build: mm9
Supplementary_files_format_and_content: SupplementalTable_Expression_and_SplicingChanges.xlsx contains 3 worksheets, one for DESeq, one for DEXseq containing all exonic parts, and one for DEXseq containing only significant exonic parts.

growth_protocol: C2C12 cells were maintained in DMEM (high glucose) supplemented with 10% FBS

extract_protocol:
RNA was extracted using TRIzol
All libraries prepared according to Jacobs et al. Nature 516:242-245, with ribosome depletion using RiboZero kit

treatment_protocol: Transient transfection using Lipofectamine 2000 according to the manufacturer's specifications


title: eSox2_OKM_1posA

tag: protocol


title: IGTB1203_activated T cells_ATAC-Seq

tag: tissue

value: anti-CD3 and anti-CD28

value: Caucasian

value: Non-Hispanic


title: PDlC-D3 miRNA

source_name: periodontal ligament stem cells, osteogenic differentiation, D3

value: Day 3


title: anti-PanQk iCLIP, C2C12 myoblasts (MiSeq + HiSeq)

description:
UUUGGTTUU bp 1 to 9 of read1 is UMI
c2c12_pqku_ls054


title: anti-Qk7 iCLIP, C2C12 myoblasts (MiSeq pilot)

description:
UUUCAANUU bp 1 to 9 of read1 is UMI
c2c12_qk7b_ls041


title: anti-PanQk iCLIP, 72h differentiated C2C12 myotubes (MiSeq pilot)

description:
UUUTTGNUU bp 1 to 9 of read1 is UMI
c2c12_pqkd_ls040


title: C2C12 Qk6/7 depletion replicate 2


title: C2C12 Qk5 depletion replicate 2


title: PDlC miRNA

source_name: periodontal ligament stem cells, osteogenic differentiation, D0

value: Day 0


title: C2C12 Qk6/7 depletion replicate 1 run2


title: C2C12 Qk5 depletion replicate 3


title: C2C12 Qk5 depletion replicate 1 run1


title: C2C12 panQk depletion replicate 1 run2


title: C2C12 panQk depletion replicate 1 run1


title: Lilium_8mm_mRNA-seq

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: Lilium maculatum L-8, 8 mm anthers

data_processing:
Sequenced reads were trimmed to remove adapters and converted to flat file format using the pre-processing script described in Mathioni et al. (DOI: 10.1002/cppb.20043). SMRT sequencing libraries were processed using SMRT Analysis software (version 2.3) from Pacific Biosciences with recommended settings.
Genome_build: Data from mRNA-seq and SMRT-seq were used for de novo transcriptome assemblies, so as to compensate for the lack of Lilium genome.  These assemblies were then used along with sRNA data to identify phased-siRNA precursor transcripts and other protein factors that play a role in reproductive phasiRNA pathways. mRNA-seq assembly was performed using “Trinity RNA-Seq assembler”, full-length transcript assembly was prepared using “SMRT-tools” (v3) provided by Pacific Biosciences. Phased siRNA precursors were identified using “PHASIS suite” (https://github.com/atulkakrana/PHASIS/wiki), and transcripts for protein-coding genes were identified using “Trinotate” (https://trinotate.github.io/).
Supplementary_files_format_and_content: Flat file with tab separated reads and abundance counts for sRNAs, FASTA files for SMRT-seq.

organism: Lilium maculatum

source_name: Lilium maculatum - Meiotic anther

growth_protocol: Flowering Lilium plants were purchased from Home Depot (Newark, Delaware)

extract_protocol:
Anthers were dissected using a 2 mm stage micrometer in a stereo microscope, and immediately frozen in liquid nitrogen until total RNA isolation was performed. Total RNA was isolated using the PureLink Plant RNA Reagent following the manufacturer’s instructions. Total RNA quality and quantity were assessed before proceeding to the next step.
Small RNAs (20 to 30 nt) were size selected in a 15% polyacrylamide/urea gel and libraries were constructed using the TruSeq Small RNA Prep Kit (Illumina, cat. # RS-200-0012). Small RNA libraries containing different index tags were pooled and sequenced on an Illumina HiSeq 2500 instrument at the Delaware Biotechnology Institute. The complete protocol for sRNA library preparation is described in Mathioni et al. (DOI: 10.1002/cppb.20043). RNA-seq libraries (for mRNA) were constructed using the TruSeq Stranded Total RNA Library Preparation Kit with Ribo-Zero Plant (Illumina, cat # RS-122-2401), and RNA was treated with DNase I (NEB, cat # M0303S) and then cleaned using the RNA Clean & Concentrator™-5 (Zymo Research, cat # R1015). Single Molecule Real Time (SMRT) sequencing libraries were prepared using protocol recommended by Pacific Biosciences for Isoform Sequencing using SageELF size selection system
Small RNA sequencing using Illumina single-end (1x50 bp) reads. Messenger RNA sequencing using Illumina single-end (2x150 bp) reads and Single Molecule Real Time (SMRT) sequencing of full length (cDNA) transcripts.

value: anther


title: C2C12 control replicate 1 run2


title: C2C12 control replicate 2


title: Lilium_10mm_mRNA-seq

description: Lilium maculatum L-10, 10 mm anthers

source_name: Lilium maculatum anther


title: Lilium_6mm_sRNA-seq

description: Lilium maculatum L-6, 6 mm anthers


title: C2C12 control replicate 1 run1


title: IGTB109_activated T cells_ATAC-Seq

value: blood

value: Male


title: C2C12 Qk5 depletion replicate 1 run2


title: C2C12 control replicate 3


title: PDlC mRNA

description: Processed data file: all.counts.exp.txt


title: Lilium_4mm_sRNA-seq

description: Lilium maculatum L-4, 4 mm anthers

source_name: Lilium maculatum - Premeiotic anther


title: Lilium.4kb.3cells.SMRT

description: Lilium maculatum L-4-6, 4-6 mm anthers

data_processing:
Library strategy: Single Molecule Real Time (SMRT) sequencing of full length (cDNA) transcripts
Sequenced reads were trimmed to remove adapters and converted to flat file format using the pre-processing script described in Mathioni et al. (DOI: 10.1002/cppb.20043). SMRT sequencing libraries were processed using SMRT Analysis software (version 2.3) from Pacific Biosciences with recommended settings.
Genome_build: Data from mRNA-seq and SMRT-seq were used for de novo transcriptome assemblies, so as to compensate for the lack of Lilium genome.  These assemblies were then used along with sRNA data to identify phased-siRNA precursor transcripts and other protein factors that play a role in reproductive phasiRNA pathways. mRNA-seq assembly was performed using “Trinity RNA-Seq assembler”, full-length transcript assembly was prepared using “SMRT-tools” (v3) provided by Pacific Biosciences. Phased siRNA precursors were identified using “PHASIS suite” (https://github.com/atulkakrana/PHASIS/wiki), and transcripts for protein-coding genes were identified using “Trinotate” (https://trinotate.github.io/).
Supplementary_files_format_and_content: Flat file with tab separated reads and abundance counts for sRNAs, FASTA files for SMRT-seq.


title: Lilium_leaf_mRNA-seq

description: Lilium maculatum leaf

source_name: Lilium maculatum leaf

value: leaf


title: Lilium_5mm_mRNA-seq

description: Lilium maculatum L-5, 5 mm anthers


title: Lilium_5mm_sRNA-seq

description: Lilium maculatum L-5, 5 mm anthers


title: Lilium.2-3kb.3cells.SMRT

description: Lilium maculatum L-4-6, 4-6 mm anthers


title: Lilium_4mm_mRNA-seq

description: Lilium maculatum L-4, 4 mm anthers


title: Lilium_8mm_sRNA-seq

description: Lilium maculatum L-8, 8 mm anthers


title: PDlC-D7 mRNA

description: Processed data file: all.counts.exp.txt


title: PDlC-D14 mRNA

description: Processed data file: all.counts.exp.txt


title: Lilium.2kb.5cells.SMRT

description: Lilium maculatum L-4-6, 4-6 mm anthers


title: F3 testis chlordecone 1mg 3

status: Public on Jul 10 2018

city: rennes

first: Chunxiang

last: HAO

address: 263, ave du Général Leclerc

country: France

institute: Université de Rennes 1

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
The reads in FASTQ format were processed for quality control using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). For the analysis of differentially expressed genes, the quality-checked reads for each condition were processed using the TopHat version 2.0.12 package (Kim et al. 2013). The reads were mapped to the reference genome [Mus musculus Ensembl mm10 sequence], and the alignment files were generated as BAM files. These files were used as the input for Cufflinks, a complement method used to generate assembled transcripts for each condition; the abundance was evaluated using read data. The assembled transcripts were compared and annotated using Cuffmerge against the Ensembl (mm10) gene annotations (Trapnell et al. 2012). These assemblies are used in Cuffquant and Cuffnorm from the Cufflinks 2.2.1 package to calculate the expression levels. To identify transcripts differentially expressed between chlordecone- and control-derived samples, we first selected the cases for which we obtained values greater than the 50th quantile of all values in at least one condition, and then we filtered transcripts which are more than a 2-fold different between chlordecone and control -derived samples. Finally, we employed a statistical test implemented in the R package, Limma, with the false-discovery rate set at less than 5% (Ritchie et al. 2015). RNA-Seq data were visualized using the Integrated Genomics Viewer (version 2.3.36) (Thorvaldsdottir et al. 2013).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

molecule: polyA RNA

source_name: testes

growth_protocol: We treated adult female mice with chlordecone with doses 0 (control),  100 Xg/kg/day and 1 mg/kg/day during gestation period E6- E15. Male born from Chlordecone- treated mice were crossed for a three generations. The testes from F3 generations were taken for mRNA extraction. For mRNA extraction we used columb. Three biological replicates used for each condition . We hypothesize that chlordecone cause changes in mRNA due to transgenerational effect of pesticides (Skinner et al, Science 2005).

extract_protocol:
For RNA-seq 10 mkg of total RNA was used. Total RNA was extracted using Trizol reagent
A strand-specific library preparation protocol for RNA sequencing was performed using the sequencing technological platform at IGBMC, Strasbourg, France. Paired end, 50-bp sequencing stranded RNA-seq

tag: strain

value: testes


title: Lilium_leaf_sRNA-seq

description: Lilium maculatum leaf


title: F3 testis chlordecone 1mg 2


title: C2C12 Qk6/7 depletion replicate 1 run1


title: F3 testis chlordecone 100ug 3


title: F3 testis chlordecone 100ug 1


title: F3 testis control 3


title: F3 testis control 2


title: PDlC-D3 mRNA

description: Processed data file: all.counts.exp.txt

tag: treatment


title: C2C12-50000-1

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: 50,000 cells

data_processing:
Alignment: bowtie2 (version 2.2.1), parameters -X 2000
Mark PCR duplicate reads: Picard MarkDuplicates (version 1.1)
Filter reads: unmapped, mate unmapped, not primary alignment, reads failing platforms, reads marked as PCR duplicates
Peak calling with MACS2 (version 2.1), parameters --nomodel --shift 75 --extsize 150 --keep-dup all -p 0.01
Filter peaks: peaks present in both replicates, FDR q-value < 0.01
Bigwig files: filtered read coverage for each sample
Peak files: filtered peaks
genome build: UCSC mm9

source_name: C2C12 cells

growth_protocol: MEFs and C2C12 cells were cultured in DMEM containing 10% FBS, penicillin, and streptomycin. Xenopus oocytes, into which MEFs were transplanted, were cultured in MBS medium.

extract_protocol:
Cultured cells were harvested, washed with PBS, and then transferred to cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3mM MgCl2, 0.1% IGEPAL, 0.5% Triton X-100). Triton X-100 was needed especially for permeabilizing cells after nuclear transfer.
Cells in lysis buffer were collected by centrifugation and the cell pellet was resuspended in the transposon reaction mix (25 μl 2x TD Buffer [Illumina, FC-121-1030], 2.5 μl Tn5 Transposes [Illumina, FC-121-1030], 22.5 μl Nuclease Free H2O). A total of 50 μl of the transposon reaction was used for 50,000 cells while 3,000 cells were incubated in 10 μl of the transposon reaction. Transposition reaction was performed at 37oC for 30 min. After the transposition reaction, transposed DNA was purified using a QIAGEN MinElute kit and used for the subsequent PCR amplification. Cultured cells with 1,000 were directly subjected to PCR amplification without using the purification kit. Transposed DNA was amplified by two rounds of PCR using NEB Next High Fidelity Master Mix (New England Labs, M0541) and the Customized Nextera PCR primers totaling 50 μl (Buenrostro et al., 2013). The first PCR cycles varied from 5 to 15 cycles depending on the starting cell numbers. The number of second PCR cycles was determined by qPCR using the 10% of the total PCR reaction in order to amplify the DNA in the exponential growth phase. The amplified DNA was purified using QIAGEN PCR Cleanup kit and finally resuspended in 20 μl of elution buffer. The quality of library was checked on polyacrylamide gels and quantified using the KAPA library quantification kit for Illumina sequencing platforms (KAPA Biosystems).

treatment_protocol: Xenopus oocytes were overexpressed with or without Toca1 to see the effect of enhanced nuclear actin polymerization on open chromatin formation.

value: Cultured cells, myoblast

tag: library strategy

value: ATAC-seq


title: F3 testis chlordecone 100ug 2


title: C2C12-1000-1

description: 1,000 cells


title: KK1 JQ1 Treated BRD4

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: No additional information.

data_processing:
ChIP-Seq Analysis - NextSeq
Calculation Method: Sequencing of ChIP-seq samples was performed on a NextSeq 500 sequencer (Illumina), with single reads of 76 bp length. Reads were aligned to human genome build 36 (hg18) with Bowtie software. Redundant reads were removed and reads uniquely mapping to reference genome were used for further analysis. To perform peak calling, the genome was divided into "bins" of 25 bp. Each sequencing tag was associated with the bin of its start site and an additional extension of seven bins (for a total of 200 bp) along the direction of its read to match the average library size. For a given experiment, the number of "hits" in a bin was defined as the number of extended tags associated with that bin. Bins with fewer than three hits were removed. Peaks were formed by merging consecutive significant bins. The height of the peak was defined as the largest number of hits in any of the bins forming the peak. The "apex" of the peak was defined as the bin that had this largest number of hits. In the case of ties, the earliest such peak was chosen as the apex.
Supplementary_files_format_and_content: wig file
Genome_build: hg18

source_name: KK1 JQ1 Treated BRD4

extract_protocol:
BRD4 Antibody Extraction
Other: 20 million exponentially growing cells were collected per sample and cross-linked with 1% formaldehyde for 10 min at room temperature. The cross-linked cells were resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% sodium deoxycholate) to a final concentration of 4 million cells/ml. DNA was sheared with a Misonix XL sonicator. For each immune precipitation reaction, the chromatins were incubated overnight with 100 ug (1 mg/ml) of BRD4 antibody (Bethyl, Cat No. A301-985A100). The following day, chromatin/antibody complexes were incubated with Protein G Dynabeads (50 ul; Thermo Fisher Scientific) for 4 h at 4 C, washed 3 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNase A (0.2 ug/ul). Reverse crosslinking was performed overnight at 65 C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50 C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN).
ChIP DNA was used to generate ChIP-seq libraries with the NEXTflex Illumina ChIP-seq Library Prep Kit (Bio Scientific) according to manufacturer's instructions.

treatment_protocol:
Treatment type: compound
Agent: JQ1
Treatment dose: 500 nM
Treatment time: 24 hours
In-vitro treatment: KK1 cells were treated with JQ1 (Constellation Pharmaceuticals) for 24 hours.

tag: disease state

value: Adult T-cell Leukemia/Lymphoma (ATLL)


title: KK1 JQ1 Treated H3K27ac

description: No additional information.

source_name: KK1 JQ1 Treated H3K27ac

extract_protocol:
H3K27ac Antibody Extraction
Other: 20 million exponentially growing cells were collected per sample and cross-linked with 1% formaldehyde for 10 min at room temperature. The cross-linked cells were resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% sodium deoxycholate) to a final concentration of 4 million cells/ml. DNA was sheared with a Misonix XL sonicator. For each immune precipitation reaction, the chromatins were incubated overnight with 5 ug of H3K27ac antibody (Abcam, ab4729). The following day, chromatin/antibody complexes were incubated with Protein G Dynabeads (50 ul; Thermo Fisher Scientific) for 4 h at 4 C, washed 3 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNase A (0.2 ug/ul). Reverse crosslinking was performed overnight at 65 C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50 C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN).
ChIP DNA was used to generate ChIP-seq libraries with the NEXTflex Illumina ChIP-seq Library Prep Kit (Bio Scientific) according to manufacturer's instructions.


title: ST1 JQ1 Treated BRD4

description: No additional information.

source_name: ST1 JQ1 Treated BRD4

treatment_protocol:
Treatment type: compound
Agent: JQ1
Treatment dose: 250 nM
Treatment time: 24 hours
In-vitro treatment: ST1 cells were treated with JQ1 (Constellation Pharmaceuticals) for 24 hours.


title: KK1 BirA BATF3

description: No additional information.

source_name: KK1 BirA BATF3

extract_protocol:
Streptavidin DynaBeads
Other: 20 million exponentially growing cells were collected per sample and cross-linked with 1% formaldehyde for 10 min at room temperature. The cross-linked cells were resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% sodium deoxycholate) to a final concentration of 4 million cells/ml. DNA was sheared with a Misonix XL sonicator. Chromatin was incubated with MyOne Streptavidin T1 Dynabeads (Thermo Fisher Scientific), washed 3 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNase A (0.2 ug/ul). Reverse crosslinking was performed overnight at 65 C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50 C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN).
ChIP DNA was used to generate ChIP-seq libraries with the NEXTflex Illumina ChIP-seq Library Prep Kit (Bio Scientific) according to manufacturer's instructions.

treatment_protocol:
Treatment type: Transduction
In-vitro treatment: KK1 and ST1 cells that stably expressed the BirA enzyme were transduced with N-terminally tagged BATF3 (pRCMV/TO-flag-BIOTIN-BATF3-puro). Selection was carried out with puromycin and expression was induced with Doxycycline.


title: Muscle_AE_1h_07

city: Phoenix

first: Jared

middle: M

last: Dickinson

address: 425 N 5th St

institute: Arizona State University

description: Gene expression 1 h post acute aerobic exercise

data_processing:
Illumina BCL2fastq
Sequencing alignment using STAR
HTSeq-count
DESeq for normalization
Genome_build: hg19
Supplementary_files_format_and_content: tab-deliminted text files counts table normalized with DESeq2

source_name: vastus lateralis, AE 1h

extract_protocol:
TRI Reagent followed by Clontech’s SMARTer Universal Low Input RNA kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Acute aerobic and resistance exercise

tag: Sex

tag: age

value: Young

tag: exercise

value: Acute Aerobic Exercise

tag: time

value: 1h Post


title: ST1 DMSO Treated H3K27ac

description: No additional information.

source_name: ST1 DMSO Treated H3K27ac

treatment_protocol:
Treatment type: compound
Agent: DMSO (Dimethyl sulfoxide)
Treatment time: 24 hours
In-vitro treatment: Cells were treated with DMSO.


title: C2C12-50000-2

description: 50,000 cells


title: RD1.R3

city: London

first: Masahiro

last: Ono

address: Sir Alexander Fleming Building

department: Life Sciences

institute: Imperial College London

data_processing:
Basecalls performed using CASAVA-1.8.2
Sequenced reads were demultiplexed and trimmed for adaptor sequence
Read quality was chacked by FastQC ver 0.11.2.
High-quality reads were aligned to the mm10 genome using tophat2 ver 2.0.9.
GenomicAlignments was used to count reads, and DESeq2 was used to perform regularized-log transformation.
Genome_build: mm10
Supplementary_files_format_and_content: Count data (regularized-log transformed)

source_name: CD4+ T-cells

extract_protocol:
RNA was extracted from FACS sorted T-cells (100-250K) using the Arcuturs Picopure RNA extraction kit according to the protocol for RNA extraction for cell pellets
Library constructed using Illumina's TruSeq Stranded mRNA LT kit set a (RS-122-2101) according to manufacturer's isntructions. Clusters were generated on the Illumina HiSeq platform

treatment_protocol: 3 % Oxazolone applied to abdominal skin, T-cells then isolated by FACS from draining LN 5 days after treatment

value: C57/BL6 Foxp3Timer Foxp3-IRES-GFP

value: female

value: CD4+ T-cells

tag: t-cell subset

value: CD4+GFP+ mature Foxp3 expressers


title: Muscle_AE_4h_07

description: Gene expression 4 h post acute aerobic exercise

source_name: vastus lateralis, AE 4h

value: 4h post


title: RD2.R3

value: CD4+GFP+ decaying Foxp3 expressers


title: Muscle_RE_1h_07

description: Gene expression 1 h post acute resistance exercise

source_name: vastus lateralis, RE 1h

value: Acute Resistance Exercise


title: ST1 JQ1 Treated H3K27ac

description: No additional information.

source_name: ST1 JQ1 Treated H3K27ac


title: Lilium_6mm_mRNA-seq

description: Lilium maculatum L-6, 6 mm anthers

value: anther


title: ST1 DMSO Treated BRD4

description: No additional information.

source_name: ST1 DMSO Treated BRD4


title: Muscle_RE_4h_07

description: Gene expression 4 h post acute resistance exercise

source_name: vastus lateralis, RE 4h

value: Male


title: C2C12-1000-2

description: 1,000 cells


title: KK1 DMSO Treated BRD4

description: No additional information.

source_name: KK1 DMSO Treated BRD4


title: F3 testis chlordecone 1mg 1


title: BL2.R3

value: CD4+GFP+ maturing Foxp3 expressers


title: F3 testis control 1

value: testes


title: KK1 BirA Empty Control - repeat 2

description: No additional information.

source_name: KK1 BirA Empty Control

treatment_protocol:
Treatment type: Transduction
In-vitro treatment: KK1 and ST1 cells that stably expressed the BirA enzyme were transduced with the empty BioTag vector. Selection was carried out with puromycin and expression was induced with Doxycycline.


title: Muscle_Baseline_07

description: Gene expression baseline, prior to acute exercise

source_name: vastus lateralis, baseline

value: Baseline

value: Pre Exercise


title: CD44LO.R3

value: CD44loGFP-Foxp3Timer- (Naive  T-cells)


title: BL1.R3

value: CD4+GFP+ de novo Foxp3 expressers


title: KK1 DMSO Treated H3K27ac

description: No additional information.

source_name: KK1 DMSO Treated H3K27ac

value: Adult T-cell Leukemia/Lymphoma (ATLL)


title: Muscle_RE_4h_05

value: Young


title: ST1 BirA HBZ

description: No additional information.

source_name: ST1 BirA HBZ

treatment_protocol:
Treatment type: Transduction
In-vitro treatment: KK1 and ST1 cells that stably expressed the BirA enzyme were transduced with N-terminally tagged HBZ (pRCMV/TO-flag-BIOTIN-HBZ-puro). Selection was carried out with puromycin and expression was induced with Doxycycline.


title: KK1 BirA HBZ

description: No additional information.

source_name: KK1 BirA HBZ


title: CD44HI.R3

value: C57/BL6 Foxp3Timer Foxp3-IRES-GFP

value: CD44hiGFP-Foxp3Timer- (Activated effector T-cells)


title: KK1 BirA Empty Control - repeat 1

description: No additional information.


title: RD2.R2

value: female

value: CD4+ T-cells


title: Muscle_AE_4h_05

value: Acute Aerobic Exercise

value: 4h post


title: ST1 BirA Empty Control - repeat 2

description: No additional information.

source_name: ST1 BirA Empty Control


title: Muscle_RE_4h_04

value: Acute Resistance Exercise


title: Muscle_Baseline_05


title: BL2.R2


title: Muscle_AE_1h_04

value: 1h Post


title: Muscle_AE_1h_05

value: Male


title: RD1.R2

value: CD4+GFP+ mature Foxp3 expressers


title: Muscle_RE_1h_04


title: BL1.R2


title: ST1 BATF3

description: No additional information.

source_name: ST1 BATF3

extract_protocol:
BATF3 Antibody Extraction
Other: 20 million exponentially growing cells were collected per sample and cross-linked with 1% formaldehyde for 10 min at room temperature. The cross-linked cells were resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% sodium deoxycholate) to a final concentration of 4 million cells/ml. DNA was sheared with a Misonix XL sonicator. For each immune precipitation reaction, the chromatins were incubated overnight with 5 ug of BATF3 antibody (R&D, AF7437).The following day, chromatin/antibody complexes were incubated with Protein G Dynabeads (50 ul; Thermo Fisher Scientific) for 4 h at 4 C, washed 3 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNase A (0.2 ug/ul). Reverse crosslinking was performed overnight at 65 C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50 C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN).
ChIP DNA was used to generate ChIP-seq libraries with the NEXTflex Illumina ChIP-seq Library Prep Kit (Bio Scientific) according to manufacturer's instructions.


title: ST1 IgG Negative Control

description: No additional information.

source_name: ST1 IgG Negative Control

extract_protocol:
IgG Negative Control Extraction
Other: 20 million exponentially growing cells were collected per sample and cross-linked with 1% formaldehyde for 10 min at room temperature. The cross-linked cells were resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% sodium deoxycholate) to a final concentration of 4 million cells/ml. DNA was sheared with a Misonix XL sonicator. For each immune precipitation reaction, the chromatins were incubated overnight with 5 ug of normal rabbit IgG (Santa Cruz Biotechnology, sc2027) as a negative control. The following day, chromatin/antibody complexes were incubated with Protein G Dynabeads (50 ul; Thermo Fisher Scientific) for 4 h at 4 C, washed 3 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNase A (0.2 ug/ul). Reverse crosslinking was performed overnight at 65 C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50 C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN).
ChIP DNA was used to generate ChIP-seq libraries with the NEXTflex Illumina ChIP-seq Library Prep Kit (Bio Scientific) according to manufacturer's instructions.


title: CD44HI.R2


title: CD44LO.R2


title: RD2.R1

value: CD4+GFP+ decaying Foxp3 expressers


title: Muscle_RE_1h_05


title: KK1 BATF3

description: No additional information.

source_name: KK1 BATF3


title: Muscle_Baseline_04

value: Baseline


title: Muscle_RE_1h_03


title: Muscle_RE_4h_03


title: KK1 IgG Negative Control

description: No additional information.

source_name: KK1 IgG Negative Control


title: ST1 IRF4

description: No additional information.

source_name: ST1 IRF4

extract_protocol:
IRF4 Antibody Extraction
Other: 20 million exponentially growing cells were collected per sample and cross-linked with 1% formaldehyde for 10 min at room temperature. The cross-linked cells were resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% sodium deoxycholate) to a final concentration of 4 million cells/ml. DNA was sheared with a Misonix XL sonicator. For each immune precipitation reaction, the chromatins were incubated overnight with 5 ug of IRF4 antibody (Santa Cruz Biotechnology, sc6059 and sc11450 (1:1 mix)). The following day, chromatin/antibody complexes were incubated with Protein G Dynabeads (50 ul; Thermo Fisher Scientific) for 4 h at 4 C, washed 3 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNase A (0.2 ug/ul). Reverse crosslinking was performed overnight at 65 C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50 C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN).
ChIP DNA was used to generate ChIP-seq libraries with the NEXTflex Illumina ChIP-seq Library Prep Kit (Bio Scientific) according to manufacturer's instructions.


title: BL1.R1

source_name: CD4+ T-cells


title: CD44LO.R1


title: ST1 IgG Control

description: No additional information.

source_name: ST1 IgG Control


title: Muscle_RE_1h_02

source_name: vastus lateralis, RE 1h


title: Muscle_RE_4h_01


title: Muscle_RE_4h_02


title: Muscle_AE_1h_03

source_name: vastus lateralis, AE 1h


title: Muscle_AE_1h_01


title: ST1 BirA BATF3

description: No additional information.

source_name: ST1 BirA BATF3


title: ST1 BirA Empty Control - repeat 1

description: No additional information.


title: BL2.R1

value: CD4+GFP+ maturing Foxp3 expressers


title: Muscle_AE_1h_02


title: Muscle_AE_4h_01

source_name: vastus lateralis, AE 4h


title: CD44HI.R1


title: Muscle_Baseline_02

value: Pre Exercise


title: siLOC-test-2

city: Bangalore

first: Manchanahalli

middle: Rangaswamy

last: Satyanarayana Rao

state: Karnataka

address: Jakkur, Bengaluru, Karnataka

department: Molecular Biology and Genetics Unit (MBGU)

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

description: sample_11 in the *gene_exp_filtered.txt files linked at the foot of the GSE101050 record.

data_processing:
Raw paired-end sequence data for the two replicates of each of the two samples (Control and LOC-silenced) were checked for quality analysis using FASTQC. Low-quality reads were then removed from the analysis and after trimming (based on quality of sequenced reads) from the trimmed paired-end reads the unwanted sequences (mitochondrial genome sequence, ribosomal RNAs, transfer RNAs, adapter sequences and non-poly A tailed RNAs) were also removed using in-house perl-scripts and pi card tools (1.119)
After quality control analysis validated reads were aligned against the Hg19 genome assembly using TopHat with default parameters.
Then the differential gene expression analysis was done using Cufflinks (2.2.1) for the reads aligned with reference gene model and the list of differentially expressed genes were produced which were further used for GO.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM tracking files, list of upregulated and downregulated genes (all are in .txt format)

growth_protocol: Human embryonic kidney cell line HEK293T was cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin at 37 ºC and 5% CO2

extract_protocol:
Total RNA was extracted using Trizol reagent and DNase I digested to remove genomic DNA.
Libraries are produced by generating cDNA from RNA and then adding adapters to the cDNA. The libraries are then sequenced in Immunia HiSeq-2500 platform

treatment_protocol: Expression of LOC284454 was downregualted with small interfering RNAs (siRNA), HEK293T cells were transfected with a pool of two individual siRNAs from Dharmacon (Thermo Scientific) targeting LOC284454 or scrambled silencing siRNA, according to the manufacturer’s transfection protocol.

value: Human Embryonic Kidney cells

tag: genotype/variation

value: LOC-silenced


title: Muscle_AE_4h_03

value: Young


title: Muscle_RE_1h_01


title: Muscle_Baseline_01


title: Muscle_AE_4h_02


title: Muscle_Baseline_03


title: MEF_48h_after_NT_Toca1

description: 3,000 cells

organism: Mus musculus musculus x Mus musculus castaneus

source_name: MEFs

value: Permeabilized MEFs were transplanted into Xenopus oocytes

value: ATAC-seq

value: MEFs were established using embryos derived from Musculus musculus crossed with Mus musculus castaneus


title: pYA-ECP100

city: Ames

first: Angelica

middle: G

last: Van Goor

state: Iowa

address: 1221 Kildee Hall

institute: USDA-NIFA

description: PolyA mRNA

data_processing:
Clipped barcode adapter sequences Version 0.0.13 Discard sequences shorter than: 30 bp, minimum quality score: 30, and minimum percent of bases that must have this quality: 80. FASTX Clipper Version 0.0.13 Discard sequences shorter than: 30 bp, minimum quality score: 30, and minimum percent of bases that must have this quality: 80.
Mapped reads to GalGal 4.0  Version 2.0.9 Bowtie version: 2.1.0 TopHat  Version 2.0.9 Bowtie version: 2.1.0
Count reads to chicken genome Version 0.6.1 Use acceptedhits.bam from tophat2 output, Minimum mapping quality 0 because of only high quality data phred 30 going in, Bed file for overlap is output from tophat junctions.bed, GFF file was downloaded from NCBI Gallus_gallus.Galgal4.78.gtf, Mode: intersection-nonempty for stringency, Strandspecificity: none because sequencing wasn’t strand specific, Minimum quality: default 0, Feature type: exon, Feature attribute: gene_id, Feature counts output file: name of samplefeaturecounts.txt HTSeq  Version 0.6.1 Use acceptedhits.bam from tophat2 output, Minimum mapping quality 0 because of only high quality data phred 30 going in, Bed file for overlap is output from tophat junctions.bed, GFF file was downloaded from NCBI Gallus_gallus.Galgal4.78.gtf, Mode: intersection-nonempty for stringency, Strandspecificity: none because sequencing wasn’t strand specific, Minimum quality: default 0, Feature type: exon, Feature attribute: gene_id, Feature counts output file: name of samplefeaturecounts.txt

organism: Gallus gallus

source_name: Chicken splenic tissue

growth_protocol: Chickens were raised with ad libitim access to feed and water that met all NRC requirements.

extract_protocol:
The total RNA was isolated from 4 chicken spleens per treatment group (8 birds total) with the RNAqueous kit (Ambion) using all manufacturers recommendations as previously described (Cheeseman et al. 2007).
Only samples with an RNA Integrity Number (RIN) greater than 9 were used for cDNA library construction using the TruSeq RNA Library preparation kit v2 (Illumina) that preferentially amplifies PolyA mRNA. The cDNA libraries created from the spleen of 8 chickens were run on the HiSeq 3000 machine (Illumina) with the option of 150 bp single end reads at the Iowa State University DNA Facility. One lane was used for sequencing with 8 multiplexed samples per lane.
Individually barcoded samples with 8 different bar codes per lane for multiplexing.

treatment_protocol: Four-day-old chicks were orally given 20 ml of PBS (unvaccinated) or 10^9 CFU of RASV c8025(pYA4428) containing genes for ecp

tag: breed

value: White Leghorn

value: Vaccinated

value: Four-week-old


title: siLOC-test-1

description: sample_10 in the *gene_exp_filtered.txt files linked at the foot of the GSE101050 record.

tag: passage


title: ScSi-control-2

description: sample_8 in the *gene_exp_filtered.txt files linked at the foot of the GSE101050 record.

value: control


title: pYA-ECP-62

description: PolyA mRNA


title: RD1.R1

value: C57/BL6 Foxp3Timer Foxp3-IRES-GFP

value: female

value: CD4+ T-cells


title: ScSi-control-1

description: sample_7 in the *gene_exp_filtered.txt files linked at the foot of the GSE101050 record.


title: MEF_48h_after_NT-2

description: 3,000 cells


title: pYA-ECP-99

description: PolyA mRNA


title: MEF_48h_after_NT-1

description: 3,000 cells


title: PBS-11

description: PolyA mRNA

value: Non-vaccinated


title: MEF_before_NT

description: 3,000 cells

value: Cultured mouse embryonic fibroblasts were permeabilized  for nuclear transfer


title: PBS-22

description: PolyA mRNA


title: PBS-23

description: PolyA mRNA


title: KK1 IgG Control

description: No additional information.

data_processing:
ChIP-Seq Analysis - GA2x
Calculation Method: Sequencing of ChIP-seq samples was performed on a GA2x sequencer (Illumina), with single reads of 36 bp length. Reads were aligned to human genome build 36 (hg18) with Bowtie software. Redundant reads were removed and reads uniquely mapping to reference genome were used for further analysis. To perform peak calling, the genome was divided into "bins" of 25 bp. Each sequencing tag was associated with the bin of its start site and an additional extension of seven bins (for a total of 200 bp) along the direction of its read to match the average library size. For a given experiment, the number of "hits" in a bin was defined as the number of extended tags associated with that bin. Bins with fewer than three hits were removed. Peaks were formed by merging consecutive significant bins. The height of the peak was defined as the largest number of hits in any of the bins forming the peak. The "apex" of the peak was defined as the bin that had this largest number of hits. In the case of ties, the earliest such peak was chosen as the apex.
Supplementary_files_format_and_content: wig file
Genome_build: hg18

source_name: KK1 IgG Control

value: Adult T-cell Leukemia/Lymphoma (ATLL)


title: KK1 IRF4

description: No additional information.

source_name: KK1 IRF4


title: PBS-10

description: PolyA mRNA


title: TruSeq.Lab3.SynthB

status: Public on Jul 09 2018

city: Ann Arbor

first: Muneesh

last: Tewari

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

data_processing:
All FASTQ files were processed through the exceRpt small RNA-seq pipeline using the Genboree Workbench tools (http://genboree.org/java-bin/workbench.jsp). Default parameters were used, except for changing "minimum read length" to 15, and uploading the FASTQ file with the synthetic pool sequences as a "Spike-in". For the subset of "4N" libraries, the "Random Barcodes Present in Samples" option was checked, and the corresponding default subsettings were used (barcode length = 4; barcode location -5p and -3p).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_fastq.clipped.trimmed.filtered.calibratormapped.counts.txt: Tab-delimited text files contain the name of the synthetic RNA in column 1, and mapped read counts in the second. The sequence ID contains the equimolar and ratiometric pool IDs, if present in both pools; an "NA", if not. The ratiometric pool ID contains the name of the sequence, relative concentration in pool A and relative concentration in pool B, delimited by "|".

molecule: other

organism: synthetic construct

source_name: Synthetic smallRNA; Ratiometric Pool B

extract_protocol:
The RNA sample was provided as a single aliquot containing all the synthetic RNAs. 10 femtomoles of the RNA pool was used as input for each library.
Library construction protocols varied by sample (See lib.method.simple and lib.method.detail sample characteristics). TruSeq, CleanTag, NEBNext and 4N_NEXTflex protocols use the commercial kits and were optimized for sequencing of small RNAs from low-input biosamples. 4N_A, _B, _C and _D are in-house protocols using 5' and 3' adapters with 4N randomized terminal nucleotides.

tag: lab

value: TruSeq

tag: pool

value: SynthB


title: TruSeq.Lab6.SynthB


title: TruSeq.Lab2.SynthB


title: TruSeq.Lab6.SynthA

source_name: Synthetic smallRNA; Ratiometric Pool A

value: SynthA


title: TruSeq.Lab5.PlasmaPool

data_processing:
All FASTQ files were processed through the exceRpt small RNA-seq pipeline using the Genboree Workbench tools (http://genboree.org/java-bin/workbench.jsp). Default parameters were used, except for changing "minimum read length" to 15. No spike-in sequences were provided for plasma pool samples. For the subset of "4N" libraries, the "Random Barcodes Present in Samples" option was checked, and the corresponding default subsettings were used (barcode length = 4; barcode location -5p and -3p).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_fastq_readCounts_miRNAmature_sense.txt: Processed data files are tab-delimited text files that contain counts for genomic alignments to known human miRNAs, including only reads mapping in the same orientation as the indicated miRNA. For each miRNA, counts are provided to indicate i) number of unique reads, ii) total reads and iii) total reads, adjusted for ambiguous mapping to other genomic loci. Libraries generated using 4N adapters have an additional column that includes the number of unique random barcodes, also adjusted for multi-mapping. Our study used the "multimapAdjustedReadCount" column for all our calculations.

source_name: Human Plasma Pool; 11 healthy individuals

extract_protocol:
Whole blood was collected from 11 healthy male participants, and was processed to separate and collect the plasma. Blood was collected in K2EDTA vacutainer tubes, inverted 8-10 times and centrifuged at 500xg for 10 minutes at room temperature. The plasma layer was then transferred to a fresh 15ml tube and centrifuged at 2500 xg for 10 minutes at room temperature. The top 80% of the plasma was transferred to a fresh 15ml tube. 5x volumes of QIAzol Lysis reagent was added to 1.2 ml of the plasma. RNA was extracted using the miRNeasy kit.
Library construction protocols varied by sample (See lib.method.simple and lib.method.detail sample characteristics). TruSeq, CleanTag, NEBNext and 4N_NEXTflex protocols use the commercial kits and were optimized for sequencing of small RNAs from low-input biosamples. 4N_A, _B, _C and _D are in-house protocols using 5' and 3' adapters with 4N randomized terminal nucleotides.

value: Plasma

tag: disease status

value: Healthy

value: Male

tag: age range

value: 21-45 years

value: TRUSEQ

value: PlasmaPool


title: 4N_B.Lab2.SynthA


title: 4N_Xu.Lab5.PlasmaPool

tag: tissue


title: 4N_B.Lab2.SynthB


title: 4N_C.Lab6.SynthB


title: 4N_A.Lab5.PlasmaPool


title: pYA-ECP-61

description: PolyA mRNA

value: White Leghorn

value: Vaccinated

value: Four-week-old


title: NEBNext.Lab3.SynthA

value: NEBNext


title: TruSeq.Lab3.SynthEQ

data_processing:
All FASTQ files were processed through the exceRpt small RNA-seq pipeline using the Genboree Workbench tools (http://genboree.org/java-bin/workbench.jsp). Default parameters were used, except for changing "minimum read length" to 15, and uploading the FASTQ file with the synthetic pool sequences as a "Spike-in". For the subset of "4N" libraries, the "Random Barcodes Present in Samples" option was checked, and the corresponding default subsettings were used (barcode length = 4; barcode location -5p and -3p).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_fastq_readCounts_miRNAmature_sense.txt: Mature miRNA Read Counts: Tab-delimited text files contain counts for genomic alignments to known human miRNAs, including only reads mapping in the same orientation as the indicated miRNA. For each miRNA, counts are provided to indicate i) number of unique reads, ii) total reads and iii) total reads, adjusted for ambiguous mapping to other genomic loci. Libraries generated using 4N adapters have an additional column that includes the number of unique random barcodes, also adjusted for multi-mapping. Our study used the "multimapAdjustedReadCount" column for all our calculations.
Supplementary_files_format_and_content: *_fastq.clipped.trimmed.filtered.calibratormapped.counts.txt: Mapped Calibrator Counts: Tab-delimited text files contain the name of the synthetic RNA in column 1, and mapped read counts in the second. The sequence ID contains the equimolar and ratiometric pool IDs, if present in both pools; an "NA", if not. The ratiometric pool ID contains the name of the sequence, relative concentration in pool A and relative concentration in pool B, delimited by "|".

source_name: Synthetic smallRNA; Equimolar Pool

value: SynthEQ


title: CleanTag.Lab5.PlasmaPool

value: CleanTag


title: TruSeq.Lab3.SynthA


title: TruSeq.Lab2.SynthEQ


title: TruSeq.Lab6.SynthEQ


title: 4N_B.Lab2.SynthEQ


title: NEBNext.Lab3.SynthEQ


title: 4N_C.Lab6.SynthEQ


title: NEBNext.Lab3.SynthB


title: TruSeq.Lab2.SynthA


title: 4N_C.Lab6.SynthA


title: AB1 CeHR Reversion Rep3

city: Newark

first: Irem

last: Celen

state: DE

address: 15 Innovation Way

institute: University of Delaware

data_processing:
Quality control was implemented on the raw sequence data with FASTQC software (version 0.11.2).
The raw reads were mapped to the reference genome (WBCel235), obtained from Ensembl along with the annotation file, by using TopHat.
The Tuxedo pipeline was employed to find differential gene expressions with default parameters.
Genome_build: WBCel235
Supplementary_files_format_and_content: format: cuffdiff; output: fold changes for the gene expressions among the generations and environmental conditions.

organism: Caenorhabditis elegans

source_name: AB1 CeHR Reversion

growth_protocol: P0 generation animals were grown in bacteria-seeded agar plates (OP50 NGM), F1 generation animals of both the N2 and AB1 strain were cultured in CeHR. F1 generation of the N2 strain was also cultured in S-Medium. F2 generation animals were placed back to OP50 NGM. All animals were grown at 21°C

extract_protocol:
Total RNA from young adult C. elegans (4 hours post L4) were isolated with a modified TRIzol protocol and recovered by alcohol precipitation. Total RNA was further purified by PureLink ™ RNA Mini Kit (Life Technologies).
Two micrograms of total RNA were used for library preparations using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina).

tag: strain

tag: generation

tag: developmental stage

value: Young adult


title: Lilium_10mm_sRNA-seq

description: Lilium maculatum L-10, 10 mm anthers

source_name: Lilium maculatum anther

value: anther


title: AB1 CeHR Rep2

source_name: AB1 CeHR


title: AB1 CeHR Rep3


title: AB1 CeHR Rep1


title: N2 S-Medium Reversion Rep3

source_name: N2 S-Medium Reversion


title: AB1 CeHR Reversion Rep2


title: AB1 OP50 NGM Rep3

source_name: AB1 OP50 NGM


title: N2 S-Medium Rep3

source_name: N2 S-Medium


title: AB1 OP50 NGM Rep1


title: N2 S-Medium Reversion Rep2


title: N2 CeHR Reversion Rep2

source_name: N2 CeHR Reversion


title: N2 CeHR Reversion Rep3


title: N2 S-Medium Rep1


title: N2 CeHR Reversion Rep1


title: N2 CeHR Rep3

source_name: N2 CeHR


title: N2 CeHR Rep2


title: AB1 CeHR Reversion Rep1


title: N2 CeHR Rep1


title: N2 OP50 NGM Rep3

source_name: N2 OP50 NGM


title: N2 OP50 NGM Rep2


title: N2 OP50 NGM Rep1


title: TruSeq.Lab9.SynthB

value: TruSeq


title: AB1 OP50 NGM Rep2


title: TruSeq.Lab8.SynthB

value: SynthB


title: TruSeq.Lab5.SynthB


title: N2 S-Medium Rep2


title: CleanTag.Lab5.SynthB


title: NEBNext.Lab9.SynthB


title: 4N_NEXTflex.Lab8.SynthB


title: 4N_Xu.Lab5.SynthB


title: N2 S-Medium Reversion Rep1


title: NEBNext.Lab9.SynthA

value: SynthA


title: 4N_Xu.Lab5.SynthA


title: 4N_NEXTflex.Lab8.SynthA


title: TruSeq.Lab5.SynthA


title: TruSeq.Lab9.SynthA


title: 4N_A.Lab5.SynthA


title: TruSeq.Lab9.SynthEQ


title: CleanTag.Lab5.SynthA


title: TruSeq.Lab5.SynthEQ


title: YAP/TAZ-dKO_40kPa_Rep3

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
Illumina Casava1.8 software was used for basecalling.
Reads were aligned to the hg19 reference genome using STAR 2.4.2a with default parameters.
Only uniquely mapped reads were kept for further analysis.
FPKM values for each gene were computed using cufflinks v2.2.1 with default parameters according to Gencode human annotation release 24.
Genome_build: hg19
Supplementary_files_format_and_content: *txt: Tab-delimited text files include FPKM values.

source_name: HEK293A cells, YAP/TAZ-dKO, 40kPa

growth_protocol: Cells were cultured in DMEM containing 10% FBS and antibotics.

extract_protocol:
Total RNAs were extracted by TRIzol (Thermo Fisher Scientific) from HEK293A cells seeded on high and low stiffness fibronectin-coated hydrogels.
The resulting RNA was then used to prepare libraries using Illumina TruSeq Stranded mRNA Library Prep Kit Set A (Illumina, RS- 122-2101) or Set B (Illumina, RS-122-2102).

treatment_protocol: Cells were seeded onto high or low stiffness hydrogels coated with fibronectin. No other treatments.

tag: cell line

value: YAP/TAZ-dKO

tag: matrices


title: YAP/TAZ-dKO_40kPa_Rep2


title: NEBNext.Lab9.SynthEQ


title: YAP/TAZ-dKO_1kPa_Rep3

source_name: HEK293A cells, YAP/TAZ-dKO, 1kPa


title: YAP/TAZ-dKO_40kPa_Rep1


title: CleanTag.Lab5.SynthEQ


title: 4N_NEXTflex.Lab8.SynthEQ


title: YAP/TAZ-dKO_1kPa_Rep2


title: YAP/TAZ-dKO_1kPa_Rep1


title: 4N_A.Lab5.SynthB


title: TruSeq.Lab8.SynthA


title: LATS1/2-dKO_40kPa_Rep3

source_name: HEK293A cells, LATS1/2-dKO, 40kPa


title: LATS1/2-dKO_40kPa_Rep1


title: LATS1/2-dKO_40kPa_Rep2


title: TruSeq.Lab8.SynthEQ


title: LATS1/2-dKO_1kPa_Rep3

source_name: HEK293A cells, LATS1/2-dKO, 1kPa


title: 4N_Xu.Lab5.SynthEQ


title: RAP2A/B/C-tKO_1kPa_Rep2

source_name: HEK293A cells, RAP2A/B/C-tKO, 1kPa


title: RAP2A/B/C-tKO_1kPa_Rep1


title: WT_40kPa_Rep1

source_name: HEK293A cells, WT, 40kPa

value: WT


title: LATS1/2-dKO_1kPa_Rep2


title: LATS1/2-dKO_1kPa_Rep1


title: 4N_A.Lab5.SynthEQ


title: RAP2A/B/C-tKO_40kPa_Rep2

source_name: HEK293A cells, RAP2A/B/C-tKO, 40kPa


title: RAP2A/B/C-tKO_40kPa_Rep3


title: WT_40kPa_Rep3


title: WT_40kPa_Rep2


title: RAP2A/B/C-tKO_40kPa_Rep1


title: RAP2A/B/C-tKO_1kPa_Rep3


title: TruSeq.Lab4.PlasmaPool

source_name: Human Plasma Pool; 11 healthy individuals

value: Plasma

value: Healthy

tag: Sex

value: Male


title: WT_1kPa_Rep2

source_name: HEK293A cells, WT, 1kPa


title: TruSeq.Lab1.PlasmaPool

value: 21-45 years

value: TRUSEQ

value: PlasmaPool


title: 4N_D.Lab1.PlasmaPool


title: NEBNext.Lab4.PlasmaPool

value: NebNext


title: WT_1kPa_Rep1


title: TruSeq.Lab6.PlasmaPool


title: TruSeq.Lab3.PlasmaPool


title: TruSeq.Lab2.PlasmaPool


title: 4N_B.Lab4.PlasmaPool


title: NEBNext.Lab3.PlasmaPool

value: NEBNext


title: ref6C, rep3

city: Berlin

first: Dijun

address: Philippstr. 13 (House 22)

department: Plant Cell and Molecular Biology

institute: Humboldt University

description: Processed data file: RNAseq.xlsx

data_processing:
RNA-seq reads were mapped to A. thaliana reference genome (TAIR10) using STAR (version 020201).
Expression levels (in terms of FPKM, fragments per kilobase of transcript per million mapped reads) of all annotated protein-coding genes were estimated by RSEM (version 1.2.22).
Differentially expressed genes between mutants and wild type were identified by DESeq2.
Genome_build: TAIR10
Supplementary_files_format_and_content: RNAseq.xlsx: Excel file includes counts and FPKMs.

organism: Arabidopsis thaliana

source_name: flowers, ref6C

growth_protocol: Plants were grown in a climatized greenhouse under long day conditions (22°C daytime, 20°C at night).

extract_protocol:
Total RNAs from 5-week-old flowers of wild-type, ref6-3, ref6C, elf6-3ref6C and elf6-3ref6Cjmj13G were isolated by using the RNeasy Plant Mini Kit (Qiagen, Germany) according to manufacturer.
2 μg total RNA was used to produce libraries using TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina, USA). Pooled libraries were submitted to a NextSeq®550 sequencing platform (Illumina, USA) for sequencing.

treatment_protocol: No treatment.

tag: ecotype/background

value: flower

value: un-open flowers of 5-week-old plants


title: 4N_C.Lab6.PlasmaPool


title: ref6C, rep2

description: Processed data file: RNAseq.xlsx


title: ref6C, rep1

description: Processed data file: RNAseq.xlsx


title: WT_1kPa_Rep3


title: ref6-3, rep2

description: Processed data file: RNAseq.xlsx

source_name: flowers, ref6-3


title: ref6-3, rep3

description: Processed data file: RNAseq.xlsx


title: elf6-3ref6C, rep3

description: Processed data file: RNAseq.xlsx

source_name: flowers, elf6-3ref6C


title: elf6-3ref6C, rep2

description: Processed data file: RNAseq.xlsx


title: ref6-3, rep1

description: Processed data file: RNAseq.xlsx


title: 4N_B.Lab2.PlasmaPool


title: elf6-3ref6C, rep1

description: Processed data file: RNAseq.xlsx


title: elf6-3ref6Cjmj13G, rep3

description: Processed data file: RNAseq.xlsx

source_name: flowers, elf6-3ref6Cjmj13G


title: SAM24326082 Intestine Small SAM24326082 dFz7-21_6h_1 6h dFz7-21

city: South San Francisco

first: Robert

last: Piskol

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: intestinal primary mouse organoids

extract_protocol: RNA was extracted from samples using the RNeasy Micro kit (cat # 74004; Qiagen) according to the manufacturerâ??s instructions and resuspended in a volume of 14ul. RNA quality was evaluated using Bioanalyzer.

value: Intestine Small

tag: time

tag: treatment


title: SAM24326087 Intestine Small SAM24326087 Fz7-21S_6h_2 6h Fz7-21S


title: SAM24326100 Intestine Small SAM24326100 Fz7-21S_24h_3 24h Fz7-21S


title: SAM24326099 Intestine Small SAM24326099 Fz7-21S_24h_2 24h Fz7-21S


title: SAM24326091 Intestine Small SAM24326091 DMSO 24h_2 24h DMSO

value: DMSO


title: SAM24326081 Intestine Small SAM24326081 DMSO 6h_4 6h DMSO


title: SAM24326088 Intestine Small SAM24326088 Fz7-21S_6h_3 6h Fz7-21S


title: SAM24326079 Intestine Small SAM24326079 DMSO 6h_2 6h DMSO


title: elf6-3ref6Cjmj13G, rep2

description: Processed data file: RNAseq.xlsx

tag: genotype/variation


title: SAM24326096 Intestine Small SAM24326096 dFz7-21_24h_3 24h dFz7-21


title: WT, rep3

description: Processed data file: RNAseq.xlsx

source_name: flowers, WT

value: wild type


title: WT, rep2

description: Processed data file: RNAseq.xlsx


title: elf6-3ref6Cjmj13G, rep1

description: Processed data file: RNAseq.xlsx


title: SAM24326084 Intestine Small SAM24326084 dFz7-21_6h_3 6h dFz7-21


title: WT, rep1

description: Processed data file: RNAseq.xlsx


title: SAM24326090 Intestine Small SAM24326090 DMSO 24h_1 24h DMSO


title: SAM24326089 Intestine Small SAM24326089 Fz7-21S_6h_4 6h Fz7-21S


title: triple H3, rep1

description: Processed data file: H3_triple.rpkm.bw

data_processing:
Reads were mapped to the A. thaliana genome (TAIR10) using Bowtie (version 1.1.2) with parameters “--threads 8 -n 2 -m 3 -k 1 --best --chunkmbs 256 -q”.
Redundant reads were removed using Picard tools (v2.60; http://broadinstitute.github.io/picard/). Peak-calling was performed using MACS2 (version 2.1.0). Duplicated reads were not considered (--keep-dup=1) during peak calling in order to achieve a better specificity.
The “--mfold” parameter was set as “2-20” to build the model. The parameter “-broad” was used in the calling of H3K27me3-enriched regions (broad peaks), whereas ‘--call-summits’ was used in the calling of narrow peaks for REF6 ChIP-seq data.
Peaks across replicates with an IDR ≤ 0.05 (https://sites.google.com/site/anshulkundaje/projects/idr) were retained.
Wiggle tracks were generated by DeepTools with the command “bamCoverage”; read coverage was normalized as RPKM (Reads Per Kilobase per Million reads).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

source_name: flowers, H3 ChIP

extract_protocol:
Chromatin immunoprecipitation for H3K27me3 modification was performed according to a published protocol with minor modifications (Kaufmann et al. 2010; doi:10.1038/nprot.2009.244) while for REF6 ChIP, magnetic GFP beads (Miltenyi, Germany) was used by following the procedures described (van Mourik et al. 2015. Book Chapter. Methods in Molecular Biology: Plant Functional Genomics. 1284:93-1210.)
ChIP-seq libraries as well as control libraries that were based on “input” DNA were prepared using ThruPLEX DNA-seq kit (RUBICON GENOMICS, USA) following the manufacturer.

tag: chip antibody

value: anti-H3 (Abcam, ab1791)


title: WT H3, rep2

description: Processed data file: H3_WT.rpkm.bw


title: SAM24326085 Intestine Small SAM24326085 dFz7-21_6h_4 6h dFz7-21


title: triple H3, rep2

description: Processed data file: H3_triple.rpkm.bw


title: SAM24326093 Intestine Small SAM24326093 DMSO 24h_4 24h DMSO


title: SAM24326086 Intestine Small SAM24326086 Fz7-21S_6h_1 6h Fz7-21S


title: SAM24326095 Intestine Small SAM24326095 dFz7-21_24h_2 24h dFz7-21


title: SAM24326083 Intestine Small SAM24326083 dFz7-21_6h_2 6h dFz7-21


title: triple H3K27me3, rep2

description:
Processed data file: H3K27me3_triple.rpkm.bw
Processed data file: H3K27me3_triple.broadPeak.bed.gz

source_name: flowers, H3K27me3 ChIP

value: anti-H3K27me3 (Millipore, Catalog 07-449)


title: WT H3, rep1

description: Processed data file: H3_WT.rpkm.bw


title: triple H3K27me3, rep1


title: SAM24326078 Intestine Small SAM24326078 DMSO 6h_1 6h DMSO


title: SAM24326101 Intestine Small SAM24326101 Fz7-21S_24h_4 24h Fz7-21S


title: Input DNA for DSG samples, rep2

description: Processed data file: DSG_input.rpkm.bw

source_name: flowers, with DSG, input

value: UBQ10p::GFP Col-0


title: WT H3K27me3, rep1

description:
Processed data file: H3K27me3_WT.rpkm.bw
Processed data file: H3K27me3_WT.broadPeak.bed.gz


title: Input DNA for NO-DSG samples, rep2

description: Processed data file: NODSG_input.rpkm.bw

source_name: flowers, input


title: SAM24326094 Intestine Small SAM24326094 dFz7-21_24h_1 24h dFz7-21


title: SAM24326092 Intestine Small SAM24326092 DMSO 24h_3 24h DMSO


title: Input DNA for NO-DSG samples, rep1


title: WT H3K27me3, rep2


title: SAM24326098 Intestine Small SAM24326098 Fz7-21S_24h_1 24h Fz7-21S


title: triple REF6-ZnF-GFP with DSG, rep1

description:
Processed data file: REF6_DSG_triple.rpkm.bw
Processed data file: REF6_DSG_triple.narrowPeak.bed.gz

source_name: flowers, with DSG, REF6-ZnF-GFP ChIP

value: REF6p::REF6-ZnF-GFP elf6-3ref6Cjmj13G

value: GFP


title: SAM24326080 Intestine Small SAM24326080 DMSO 6h_3 6h DMSO


title: ref6 REF6-ZnF-GFP with DSG, rep3

description:
Processed data file: REF6_DSG_ref6.rpkm.bw
Processed data file: REF6_DSG_ref6.narrowPeak.bed.gz

value: REF6p::REF6-GFP ref6-3


title: Input DNA for DSG samples, rep1

description: Processed data file: DSG_input.rpkm.bw


title: SAM24326097 Intestine Small SAM24326097 dFz7-21_24h_4 24h dFz7-21


title: triple REF6-ZnF-GFP with DSG, rep2


title: ref6 REF6-ZnF-GFP with DSG, rep1


title: REF6-GFP with DSG, rep2

description:
Processed data file: REF6_DSG.rpkm.bw
Processed data file: REF6_DSG.narrowPeak.bed.gz

source_name: flowers, with DSG, REF6-GFP ChIP

value: REF6-GFP, ref6-3


title: REF6-GFP with DSG, rep3


title: REF6-GFP with DSG, rep1


title: mtr4-KD2

city: Shanghai

first: Hong

last: Cheng

address: 320 YueYang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences

description:
processed data-2.txt
rRNA-depleted RNA

data_processing:
Basecalls performed using TopHat2.0,fastx_toolkit-0.0.13.2 (Q33)
RNA-seq reads were cleaned and mapped the human genome (hg19 version) TopHat2.0. Reads mapping to multiple independent genomic locations were assigned to the most abundant biotype of the locations. Genome annotations from RefSeq and ENSEMBL were downloaded from the UCSC genome browser website, and supplemented with published datasets.
To compare the expression of individual RNAs, we calculated the corrected reads per million (RPM) of each transcript. Fold changes were computed from the average normalized read coverage per million bases for ensemble gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited .txt files include RPM values for each Sample

source_name: uterine cervix

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS (Biochrom).

extract_protocol:
RNA was isolated from HeLa with TRIzol (Invitrogen). 5 mg of total RNA was depleted with rRNA and constructed sequencing libraries.
Libraries were generated with TruSeq Stranded Total RNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: For RNAi, siRNA transfections were carried out with  Lipofectamine RNAiMax(Invitrogen) for 72 hr.

value: HeLa cell

value: uterine cervix

value: mtr4 knockdown


title: rrp40-KD3

description:
processed data-3.txt
rRNA-depleted RNA

value: rrp40 knockdown


title: mtr4-KD3

description:
processed data-3.txt
rRNA-depleted RNA


title: rrp40-KD2

description:
processed data-2.txt
rRNA-depleted RNA


title: rrp40-KD1

description:
processed data-1.txt
rRNA-depleted RNA


title: luciferase-KD1

description:
processed data-1.txt
rRNA-depleted RNA

value: control


title: REF6-GFP w/o DSG, rep1

last: Chen

description:
Processed data file: REF6_NODSG.rpkm.bw
Processed data file: REF6_NODSG.narrowPeak.bed.gz

source_name: flowers, REF6-GFP ChIP

value: flower


title: luciferase-KD3

description:
processed data-3.txt
rRNA-depleted RNA


title: REF6-GFP w/o DSG, rep3

value: un-open flowers of 5-week-old plants


title: REF6-GFP w/o DSG, rep2


title: mtr4-KD1

description:
processed data-1.txt
rRNA-depleted RNA


title: 4N_D.Lab1.SynthB

source_name: Synthetic smallRNA; Ratiometric Pool B

value: SynthB


title: TruSeq.Lab4.SynthA

source_name: Synthetic smallRNA; Ratiometric Pool A

value: TruSeq

value: SynthA


title: NEBNext.Lab4.SynthA

value: NEBNext


title: 4N_B.Lab4.SynthA


title: TruSeq.Lab1.SynthA


title: TruSeq.Lab1.SynthB


title: TruSeq.Lab1.SynthEQ

source_name: Synthetic smallRNA; Equimolar Pool

value: SynthEQ


title: ref6 REF6-ZnF-GFP with DSG, rep2


title: TruSeq.Lab4.SynthEQ


title: NEBNext.Lab4.SynthEQ


title: 4N_NEXTflex.Lab7.SynthB


title: 4N_NEXTflex.Lab7.SynthA


title: 4N_D.Lab1.SynthEQ


title: luciferase-KD2

description:
processed data-2.txt
rRNA-depleted RNA


title: TruSeq.Lab4.SynthB


title: NEBNext.Lab4.SynthB


title: 4N_NEXTflex.Lab7.SynthEQ