title: w1118_dpse_dvir_HD_m_r4.ERCC

description: ERCC SetA

tag: Sex

tag: age post eclosion (days)

value: ATTACTCG-ATAGAGGC


title: dwil_WB_f_r4

status: Public on Oct 18 2017

type: SRA

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

country: USA

institute: NIDDK, NIH

description: mixed-species (D. willistoni, D. ananassae, and D. yakuba) RNA preparation

library_source: transcriptomic

data_processing:
De-multiplexed reads (Chastity > 0.6) were generated by Illumina CASAVA (v.1.8.2) as fastq files.  For the single-species samples (i.e., D. melanogaster genitalia samples), we provided the raw de-multiplexed fastq files without processing.  For the multi-species samples, we first made merged genome and annotation of appropriate Drosophila species plus corrected ERCC standards (Lee et al., Journal of Genomics, 2016, PMID 27512518).  Additionally, we added a four-letter prefix for each chromosome or scaffold in the merged genome or annotation (e.g., 2L => dmel_2L).  ERCC names were unchanged due to their specific prefix.  The de-multiplexed reads from the multi-species samples were then mapped to the appropriate merged genome and annotation using STAR (v2.4.2a) (Doblin et al., Bioinformatics, 2012, PMID 23104886) with default parameters.  We used an in-house python script to fetch the prefix of read names in the bam alignments, and obtained all uniquely-mapped and multi-hit (2-10 hits) reads (in bam format) that were mapped exclusively to a single species or exclusively to ERCC.  We converted the bam reads to fastq reads by BEDTools (2.25.0; bamtofastq) (Quinlan and Hall, 2010, Bioinformatics, PMID 20110278).  After this step, reads of each multi-species sample were split into five categories – species 1, species 2, species 3, ERCC, and leftover, which includes unmapped reads and reads mapped to multiple species (or multiple species plus ERCC).  For multi-species samples, the original fastq file can be restored by merging the reads of appropriate three species as well as the ERCC and leftover reads.
We provide both STAR (SRR5639* and SRR6181*) and HiSAT2 (SRR724*) fastq and associated matrices of raw gene-level read counts in this GEO entry. For STAR read count files, we used the FlyBase (FB) annotations (version 2017_03). For HiSAT2 read count files, we used both FB and updated (YO) annotations (data in Supplementary Files of this GEO). For the latter one, we also provide two extra columns in the expression matrix, showing the maximum exon-level Jaccard index overlap between our YO annotation gene IDs and FlyBase ones. In addition, we provided bigWig tracks for all samples (replicated merged), YO annotation files (in both gtf and gff3 format), ortholog look up table (among YO gene ID, FlyBase gene ID, and dmel gene), gene-level normalized read counts based on either YO or FlyBase annotation, and transcript-level transcripts per million (TPM) based on YO or FlyBase annotation.
Supplementary_files_format_and_content: counts

molecule: polyA RNA

organism: Drosophila willistoni

source_name: whole body

growth_protocol: D. melanogaster stocks were obtained from the Drosophila Stock Center (Bloomington IN, NIH P40OD018537, http://fly.bio.indiana.edu), and were reared at the NIH (Bethesda MD).  Fly food for D. melanogaster was a medium of water (8.5 L), agar (79 g), torumel yeast (275 g), cornmeal (520 g), granulated sugar (1,100 g), p-hydroxy-benzoic acid methyl ester (23.8 g), and 95% ethanol (91.8 mL) (LabExpress, Ann Arbor MI). All non-melanogaster flies were reared and dissected at the Drosophila Species Stock Center (San Diego CA, NSF CSBR 1351502, https://stockcenter.ucsd.edu).  D. yakuba, D. ananassae, D. pseudoobscura, D. willistoni, and D. virilis were grown on a medium of de-ionized water (28 L), agar (300 g), soy flour (700 g), cornmeal (2,940 g), molasses (2,230 g), yeast (860 g), propionate (135 g), and nipogen (200 g) (https://stockcenter.ucsd.edu/info/food_cornmeal.php). D. persimilis and D. mojavensis were grown on a medium of agar (85 g), yeast (165 g), methylparaben (13.4 g), blended bananas (825 g), syrup (570 g), liquid malt extract (180 g), and 100% ethanol (134 mL) (https://stockcenter.ucsd.edu/info/food_banana_Opuntia.php).  All flies were reared at 23-25 oC.

extract_protocol:
Flies were anesthetized using CO2, and all samples were dissected in phosphate buffered saline solution (PH 7.4, Life Technologies, Carlsbad CA) and transferred to 56 or 112 μL of RNAlater (Life Technologies, Carlsbad CA) in 96-well 1.5 mL plates at room temperature after being macerated with forceps. Plates were stored at -80 oC at the NIH after dissection (melanogaster samples) or after dissection and shipping (non-melanogaster samples).  For RNA extraction, we added 20-30 1.0 mm glass beads (BioSpec Products, Bartlesville OK) to each sample and added RLT buffer from the RNeasy 96 kit (Qiagen, Valencia CA) to 712 μL (final volume).  We homogenized the samples three times for 60 seconds each with a mini-beadbeater (Biospec Products, Bartlesville OK). Extraction of total RNA was performed using the RNeasy 96 kit (spin version), except that we used 712 μL of 70% ethanol due to the increased volumes of RNAlater/RLT mixture.  RNA was quantified using Quant-iT RiboGreen (Life Technologies, Carlsbad CA).  We spot checked RNA integrity by capillary electrophoresis on a TapeStation 2200 (Agilent Technologies, Santa Clara CA) and found that the rRNA bands were distinct. We used 33 ng aliquots of RNA of three genetically distant species for each library, except for thorax, where we used 17 ng due to lower yield. The mixing of RNA was performed using a pipetting robot (Andrew Alliance, Vernier CH). RNA from D. melanogaster genitalia was not mixed with tissues of the other species.
We used 100 ng of total RNA as input (except thorax samples: 50 ng), and followed the TruSeq PolyA+ stranded mRNA kit protocol with half volume reactions (Illumina, San Diego CA).  For each sample, we also added 10 pg Standard Reference Material 2374 beta (Pool 78A or 78B) ERCC spike-ins (Lee et al., Journal of Genomics, 2016, PMID 27512518) to the Fragment-Prime-Finish Mix during the mRNA fragmentation step.  We used 96-plex molecular barcoding (Kozarewa and Turner, Methods in Molecular Biology, 2011, PMID 21431778) from the Illumina TruSeq kit for all samples. Libraries were quantified with Quant-iT PicoGreen (Life Technologies, Carlsbad CA). For each sample, we conducted RNA-seq for the three libraries with the highest DNA concentration out of four libraries. The quality (i.e., no overt primer dimers or low complexity) of all selected libraries were confirmed by capillary electrophoresis on a TapeStation 2200 (Agilent Technologies, Santa Clara CA). We performed single-end 76 bp PolyA+ sequencing on the HiSeq2000 Sequencing System (Illumina, San Diego CA).

tag: flybase species id

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: developmental stage

value: adult

tag: tissue

value: whole body

value: Female

tag: fly culture temperature (oc)

tag: replicate

tag: illumina barcode

value: TCTCGCGC-TATAGCCT

tag: plate and well id

tag: ercc infomation

value: without ERCC


title: Vγ2+ F rep2

city: Copenhagen

first: Terkild

middle: Brink

last: Buus

address: Blegdamsvej 3

department: ISIM

country: Denmark

institute: University of Copenhagen

description:
V2F_2
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: ATCACG

data_processing:
Standard Illumina Casava software used for basecalling.
Sequenced reads were pseudoaligned to the mouse transcriptome (ENSEMBL, GRCm38 release 79) using the Kallisto pipeline
Kallisto abundance matrices imported to R with tximport
Normalized Expression values were calculated by DEseq2 taking transcript lengths into account
Genome_build: GRCm38 release 79 (ENSEMBL)
Supplementary_files_format_and_content: Expression_Matrix.csv (semicolon separated)

organism: Mus musculus

source_name: Thymus, γδT, TCRVγ2+CD73+CD117-CD24+

extract_protocol:
TRI Reagent (ThermoFisher) and 1-Bromo-3-chloropropane (BCP). Extracted upper phase and precipitated with 99.9% ethanol.
SMARTer Ultra Low Input RNA v4 (cDNA synthesis and amplification) and SMARTer Low Input Library Prep Kit V2 (library prep from cDNA) using vendor provided protocols.

tag: gender

value: female

tag: age

value: 8 weeks

value: Thymus

tag: strain

tag: cell type

value: TCRdelta+ thymocytes

tag: cell population


title: Thy1_KO_rep2

city: Cincinnati

first: So

last: Maezawa

address: 3333 Burnet Ave.

department: Reproductive Sciences

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic

data_processing:
Data analysis was performed using the BioWardrobe (PMID: 26248465 )
Fastq files from Illumina pipeline were aligned by bowtie (version 1.1.1 PMID: 19261174) with maximum one allowed error in a sequence and no more than one number of hits was allowed. MACS2 (version 2.1.0.20140616 PMID: 18798982) were used to estimate fragment size and to find islands of enrichment. MACS2 were used with q-value threshold less than 0.2.
Genome_build: mm10

molecule: genomic DNA

source_name: Thy1+ spermatogonia

extract_protocol: The ATAC-seq libraries were prepared as previously described (Buenrostro et al. 2013). Around 500,000 of Thy1+ or c-Kit+ spermatogonia, 250,000 of pachytene spermatocytes, and 1,000,000 of round spermatids were used. Briefly, samples were lysed in 50 μl of lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40). Immediately after lysis, nuclei were spun at 500g for 5 min to remove the supernatant. Nuclei were then incubated with the Tn5 transposes and tagmentation buffer at 37 °C for 30 min (Illumina). After the tagmentation, the transposed DNA was purified by MinElute kit (Qiagen). PCR was performed to amplify the library using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min; following by 72 °C 5 min. qPCR was used to estimate of the number of additional cycles needed to generate products at 25% saturation. Typically, two to five additional PCR cycles were added to the initial set of five cycles. The library was purified by AMPure XP beads (Beckman). Size selection of library pools were achieved by running on agrose gel electrophoresis and excising gel slices in the 250- to 500-bp size range. The pool purified from the gel slices was analyzed on an Agilent Bioanalyzer, and 75-bp single-read sequencing was performed using an Illumina HiSeq 2500 platform according to standard oper¬ating procedures.

value: testis

tag: genotype

tag: biowardrobe ides


title: dwil_TX_m_r4

source_name: thorax without digestive system

value: thorax without digestive system

tag: Sex

value: Male

tag: age post eclosion (days)

value: TCCGCGAA-GGCTCTGA


title: Vγ2+ B rep1

description:
V2B_1
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: CTTGTA

source_name: Thymus, γδT, TCRVγ2+CD25-CD371+CD73-


title: w1118_dpse_dvir_GO_m_r4.ERCC

description: ERCC SetA

organism: synthetic construct

source_name: ERCC that merged to the multi-species sample (Drosophila melanogaster; Drosophila pseudoobscura; Drosophila virilis)

tag: flybase species id

value: not applicable

tag: strain (strain name or flybase id or drosophila species stock center id)

value: ATTACTCG-AGGCGAAG

value: ERCC SetA


title: w1118_dpse_dvir_GO_f_r4.ERCC

description: ERCC SetA

tag: developmental stage

tag: tissue

value: GAATTCGT-AGGCGAAG


title: w1118_dpse_dvir_RE_f_r4.ERCC

description: ERCC SetA

tag: fly culture temperature (oc)

tag: replicate

value: GAATTCGT-TAATCTTA


title: dwil_RE_m_r4

source_name: reproductive system without gonad

value: adult

value: reproductive system without gonad

tag: illumina barcode

value: CGGCTATG-CAGGACGT

tag: plate and well id


title: orgR_dmoj_dper_TX_m_r4.ERCC

description: ERCC SetA

source_name: ERCC that merged to the multi-species sample (Drosophila melanogaster; Drosophila mojavensis; Drosophila persimilis)

value: ATTACTCG-CCTATCCT

tag: ercc infomation


title: dwil_RE_f_r4

value: Female

value: TCCGCGAA-CAGGACGT

value: without ERCC


title: w1118_dpse_dvir_AC_m_r4.ERCC

description: ERCC SetA

value: TCCGGAGA-GGCTCTGA


title: Vγ2+ A rep2

description:
V2A_2
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: ACTTGA

source_name: Thymus, γδT, TCRVγ2+CD25+CD73-

tag: gender

value: female

tag: age

value: 8 weeks

value: Thymus

value: TCRdelta+ thymocytes


title: Vγ2+ E rep2

description:
V2E_2
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: CTTGTA

source_name: Thymus, γδT, TCRVγ2+CD73+CD200+CD117+

tag: strain

tag: cell type


title: dwil_WB_m_r4

value: whole body

value: Male

value: AGCGATAG-TATAGCCT


title: w1118_dpse_dvir_AC_f_r4.ERCC

description: ERCC SetB

value: not applicable

value: TAATGCGC-GGCTCTGA

value: ERCC SetB


title: Vγ2+ C rep1

description:
V2C_1
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: ATCACG

tag: cell population


title: orgR_dmoj_dper_WB_m_r4.ERCC

description: ERCC SetB

value: CGCTCATT-TATAGCCT


title: Vγ2+ B rep2

description:
V2B_2
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: GATCAG


title: Vγ1.1+ G rep2

description:
V1G_2
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: CAGATC

source_name: Thymus, γδT, TCRVγ1.1+CD73+CD117-CD24-


title: dwil_TX_f_r4

value: adult

value: thorax without digestive system

value: AGCGATAG-GGCTCTGA


title: orgR_dmoj_dper_WB_f_r4.ERCC

description: ERCC SetA

value: GAATTCGT-TATAGCCT

value: ERCC SetA


title: orgR_dmoj_dper_RE_f_r4.ERCC

description: ERCC SetB

value: CTGAAGCT-TAATCTTA


title: Vγ1.1+ G rep1

description:
V1G_1
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: TAGCTT

value: female


title: dwil_HD_m_r4

source_name: head

value: head

value: TCTCGCGC-ATAGAGGC

value: without ERCC


title: Vγ2+ A rep1

description:
V2A_1
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: GGCTAC

value: 8 weeks

value: Thymus

value: TCRdelta+ thymocytes


title: orgR_dmoj_dper_TX_f_r4.ERCC

description: ERCC SetA

value: not applicable

value: GAATTCGT-CCTATCCT


title: dwil_GO_m_r4

source_name: gonad

value: gonad

value: Male

value: TCTCGCGC-TAATCTTA


title: dwil_GO_f_r4

value: adult

value: Female

value: TCCGCGAA-TAATCTTA


title: orgR_dmoj_dper_RE_m_r4.ERCC

description: ERCC SetA

value: TCCGGAGA-TAATCTTA

value: ERCC SetA


title: w1118_dpse_dvir_TX_f_r4.leftover

description: mixed-species [D. melanogaster (w1118), D. pseudoobscura, and D. virilis] RNA preparation

organism:
Drosophila melanogaster
Drosophila pseudoobscura
Drosophila virilis

value: thorax without digestive system

value: ATTCAGAA-CCTATCCT


title: orgR_dmoj_dper_GO_m_r4.ERCC

description: ERCC SetA

value: ATTACTCG-AGGCGAAG


title: orgR_dmoj_dper_HD_m_r4.ERCC

description: ERCC SetA

value: TCCGGAGA-ATAGAGGC


title: dwil_DG_m_r4

source_name: digestive plus excretory system

value: digestive plus excretory system

value: TCCGCGAA-GTACTGAC

value: without ERCC


title: Vγ1.1+ E rep2

description:
V1E_2
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: ACAGTG

source_name: Thymus, γδT, TCRVγ1.1+CD73+CD200+CD117+

value: female

value: 8 weeks

value: Thymus

value: TCRdelta+ thymocytes


title: dwil_AC_m_r4

source_name: abdomen without digestive or reproductive system

value: Male

value: TCTCGCGC-AGGCGAAG


title: dwil_AC_f_r4

value: adult

value: abdomen without digestive or reproductive system

value: Female


title: Vγ1.1+ F rep2

description:
V1F_2
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: GCCAAT

source_name: Thymus, γδT, TCRVγ1.1+CD73+CD117-CD24+


title: w1118_dpse_dvir_WB_m_r4.leftover

source_name: whole body

value: whole body

value: GAGATTCC-TATAGCCT


title: Vγ1.1+ D rep2

description:
V1D_2
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: TGACCA


title: dwil_HD_f_r4

value: head

value: TCTCGCGC-ATAGAGGC


title: w1118_dpse_dvir_GO_f_r4.leftover

value: gonad

value: GAATTCGT-AGGCGAAG


title: w1118_dpse_dvir_WB_f_r4.leftover

value: CTGAAGCT-TATAGCCT


title: w1118_dpse_dvir_DG_f_r4.leftover

value: digestive plus excretory system

value: ATTCAGAA-GTACTGAC

value: without ERCC


title: orgR_dmoj_dper_HD_f_r4.ERCC

description: ERCC SetB

value: not applicable

value: TAATGCGC-ATAGAGGC

value: ERCC SetB


title: orgR_dmoj_dper_AC_m_r4.ERCC

description: ERCC SetA

value: TCCGGAGA-GGCTCTGA

value: ERCC SetA


title: w1118_dpse_dvir_TX_m_r4.leftover

value: adult

value: thorax without digestive system

value: Male

value: TCCGGAGA-CCTATCCT


title: Vγ1.1+ C rep1

description:
V1C_1
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: GCCAAT

value: female

value: 8 weeks

value: Thymus

value: TCRdelta+ thymocytes


title: Vγ1.1+ F rep1

description:
V1F_1
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: GATCAG


title: w1118_dpse_dvir_RE_m_r4.leftover

source_name: reproductive system without gonad and genitalia; reproductive system without gonad

value: GAGATTCC-TAATCTTA


title: orgR_dmoj_dper_AC_f_r4.ERCC

description: ERCC SetA

value: GAATTCGT-GGCTCTGA


title: Vγ1.1+ E rep1

description:
V1E_1
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: ACTTGA


title: orgR_dmoj_dper_GO_f_r4.ERCC

description: ERCC SetB

value: CTGAAGCT-AGGCGAAG


title: dwil_DG_f_r4

description: mixed-species (D. willistoni, D. ananassae, and D. yakuba) RNA preparation

value: digestive plus excretory system

value: Female

value: TCCGCGAA-GTACTGAC

value: without ERCC


title: w1118_dpse_dvir_RE_f_r4.leftover

value: reproductive system without gonad and genitalia; reproductive system without gonad

value: GAATTCGT-TAATCTTA


title: orgR_dmoj_dper_DG_m_r4.ERCC

description: ERCC SetA

value: not applicable

value: ATTACTCG-GTACTGAC

value: ERCC SetA


title: w1118_dpse_dvir_GO_m_r4.leftover

value: adult

value: gonad

value: Male

value: ATTACTCG-AGGCGAAG


title: orgR_dmoj_dper_DG_f_r4.ERCC

description: ERCC SetB

value: CTGAAGCT-GTACTGAC

value: ERCC SetB


title: Vγ1.1+ D rep1

description:
V1D_1
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: CAGATC

value: female

value: 8 weeks

value: Thymus

value: TCRdelta+ thymocytes


title: w1118_dpse_dvir_DG_m_r4.leftover

value: digestive plus excretory system

value: GAGATTCC-GTACTGAC


title: dwil_dana_dyak_RE_f_r4.ERCC

description: ERCC SetA

source_name: ERCC that merged to the multi-species sample (Drosophila willistoni; Drosophila ananassae; Drosophila yakuba)

value: TCCGCGAA-CAGGACGT


title: w1118_dpse_dvir_AC_f_r4.leftover

value: abdomen without digestive or reproductive system

value: Female

value: TAATGCGC-GGCTCTGA

value: without ERCC


title: w1118_dpse_dvir_HD_m_r4.leftover

value: adult

value: head

value: ATTACTCG-ATAGAGGC


title: w1118_dpse_dvir_HD_f_r4.leftover

value: GAATTCGT-ATAGAGGC


title: Vγ1.1+ C rep2

description:
V1C_2
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: TTAGGC


title: dwil_dana_dyak_HD_m_r4.ERCC

description: ERCC SetB

value: not applicable

value: TCTCGCGC-ATAGAGGC


title: dpse_WB_f_r4

organism: Drosophila pseudoobscura

value: whole body

value: CTGAAGCT-TATAGCCT


title: Vγ1.1+ B rep2

description:
V1B_2
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: CGATGT

source_name: Thymus, γδT, TCRVγ1.1+CD25-CD371+CD73-

value: female

value: 8 weeks

value: Thymus


title: dwil_dana_dyak_WB_f_r4.ERCC

description: ERCC SetB

value: TCTCGCGC-TATAGCCT

value: ERCC SetB


title: dwil_dana_dyak_WB_m_r4.ERCC

description: ERCC SetB

value: AGCGATAG-TATAGCCT


title: dwil_dana_dyak_HD_f_r4.ERCC

description: ERCC SetB


title: dwil_dana_dyak_TX_m_r4.ERCC

description: ERCC SetA

value: TCCGCGAA-GGCTCTGA

value: ERCC SetA


title: Vγ1.1+ A rep2

description:
V1A_2
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: ATCACG

source_name: Thymus, γδT, TCRVγ1.1+CD25+CD73-

value: TCRdelta+ thymocytes


title: dpse_RE_m_r4

value: adult

value: reproductive system without gonad

value: Male

value: GAGATTCC-TAATCTTA

value: without ERCC


title: dwil_dana_dyak_TX_f_r4.ERCC

description: ERCC SetB

value: not applicable

value: AGCGATAG-GGCTCTGA


title: dwil_dana_dyak_GO_f_r4.ERCC

description: ERCC SetA

value: TCCGCGAA-TAATCTTA


title: Vγ1.1+ A rep1

description:
V1A_1
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: TGACCA

value: female


title: dpse_WB_m_r4

value: whole body

value: GAGATTCC-TATAGCCT


title: w1118_dpse_dvir_AC_m_r4.leftover

value: abdomen without digestive or reproductive system

value: TCCGGAGA-GGCTCTGA


title: Vγ1.1+ B rep1

description:
V1B_1
Viable CD19-CD4-CD8-TCRdelta+ thymocytes sorted into TRI Reagent
Barcode: ACAGTG

value: 8 weeks

value: Thymus


title: dwil_dana_dyak_GO_m_r4.ERCC

description: ERCC SetB

value: TCTCGCGC-TAATCTTA

value: ERCC SetB


title: dpse_TX_f_r4

source_name: thorax without digestive system

value: adult

value: thorax without digestive system

value: Female

value: ATTCAGAA-CCTATCCT


title: dpse_RE_f_r4

source_name: reproductive system without gonad

value: reproductive system without gonad

value: GAATTCGT-TAATCTTA

value: without ERCC


title: dwil_dana_dyak_AC_f_r4.ERCC

description: ERCC SetB

value: not applicable

value: TCTCGCGC-AGGCGAAG


title: dwil_dana_dyak_AC_m_r4.ERCC

description: ERCC SetB


title: dwil_dana_dyak_DG_m_r4.ERCC

description: ERCC SetA

value: TCCGCGAA-GTACTGAC

value: ERCC SetA


title: dpse_TX_m_r4

value: Male

value: TCCGGAGA-CCTATCCT


title: dwil_dana_dyak_RE_m_r4.ERCC

description: ERCC SetA

value: CGGCTATG-CAGGACGT


title: 7d-CD8

city: Shanghai

first: Wei

last: Guisheng

address: Chifeng road 65

country: China

institute: shanghaitech

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to human reference genome (hg19 version) using STAR
Read counts were calculated by using htseq-count
Differential gene expression analysis was done using R package DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: file generated by Deseq2. gene_id,baseMean, log2FoldChange,lfcSE,stat,pvalue,padj

molecule: total RNA

organism: Homo sapiens

source_name: CD8 T cells

growth_protocol: The separation of decidual tissues and mononuclear cells was performed according to the procedure of nonenzymatic leukocytes separation. Briefly, vacuum-aspirated abortion tissues were washed in sterile PBS, and decidual tissue was macroscopically separated from fetal tissue and placenta, which was then cut into small pieces using ocular scissors and filtered by a 74-μm nylon mesh filter to obtain a single cell suspension. Both decidual mononuclear cells (DMCs) and peripheral blood mononuclear cells (PBMCs) were isolated and purified by density gradient centrifugation using LymphoprepTM.

extract_protocol:
Total RNA was extracted by using Trizol Reagent, and was purified by RNeasy Micro Kit.
Library preparation was performed as previously described (Zhang et al., 2014). We used 200 ng RNA per sample as input material for the RNA sample preparations. cDNA libraries were constructed by using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s instruction, and the products were purified by AMPure XP system and library quality was determined on the Agilent Bioanalyzer 2100 system.

tag: tissues

value: decidual tissues

value: early pregnancy


title: dpse_GO_m_r4

value: gonad

tag: Sex

value: ATTACTCG-AGGCGAAG


title: dpse_HD_m_r4

value: adult

value: head

tag: age post eclosion (days)

value: ATTACTCG-ATAGAGGC


title: dyak_TX_f_r4

organism: Drosophila yakuba

tag: flybase species id

value: thorax without digestive system

value: Female

value: AGCGATAG-GGCTCTGA


title: dyak_WB_f_r4

tag: strain (strain name or flybase id or drosophila species stock center id)

value: whole body

value: TCTCGCGC-TATAGCCT

value: without ERCC


title: dpse_DG_m_r4

tag: developmental stage

value: digestive plus excretory system

value: GAGATTCC-GTACTGAC


title: dyak_WB_m_r4

tag: tissue

value: Male

value: AGCGATAG-TATAGCCT


title: dyak_RE_m_r4

value: reproductive system without gonad

tag: fly culture temperature (oc)

value: CGGCTATG-CAGGACGT


title: dpse_HD_f_r4

tag: replicate

value: GAATTCGT-ATAGAGGC


title: dpse_GO_f_r4

value: gonad

tag: illumina barcode

value: GAATTCGT-AGGCGAAG


title: DA-2-CD8

value: decidual tissues

value: early pregnancy


title: dyak_TX_m_r4

value: adult

value: thorax without digestive system

value: TCCGCGAA-GGCTCTGA

tag: plate and well id


title: dwil_dana_dyak_DG_f_r4.ERCC

description: ERCC SetA

value: not applicable

value: TCCGCGAA-GTACTGAC

tag: ercc infomation

value: ERCC SetA


title: dpse_DG_f_r4

value: digestive plus excretory system

value: Female

value: ATTCAGAA-GTACTGAC

value: without ERCC


title: 6d-CD8


title: BA-2-CD8

value: peripheral blood


title: dyak_HD_m_r4

value: head

value: Male

value: TCTCGCGC-ATAGAGGC


title: dpse_AC_m_r4

value: abdomen without digestive or reproductive system

value: TCCGGAGA-GGCTCTGA


title: dyak_HD_f_r4


title: dyak_GO_m_r4

value: gonad

value: TCTCGCGC-TAATCTTA


title: dpse_AC_f_r4

value: adult

value: TAATGCGC-GGCTCTGA


title: dyak_DG_m_r4


title: 6xue-CD8

value: early pregnancy


title: dyak_DG_f_r4

value: TCCGCGAA-GTACTGAC


title: dana_WB_m_r4

organism: Drosophila ananassae

value: whole body

value: AGCGATAG-TATAGCCT


title: dyak_AC_m_r4

value: TCTCGCGC-AGGCGAAG


title: dyak_RE_f_r4

value: reproductive system without gonad

value: Female

value: TCCGCGAA-CAGGACGT


title: dana_WB_f_r4

value: TCTCGCGC-TATAGCCT

value: without ERCC


title: HiC_dCas9VP64/p65_Sox4gRNA_rep2

city: Montpellier

first: Boyan

last: Bonev

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics - CNRS

data_processing:
Hi-C data was processed using the Cwalks pipeline (http://compgenomics.weizmann.ac.il/tanay/?page_id=690). In brief, raw sequencing reads were mapped independently to the mm10 reference genome using Bowtie2 in local alignment mode. The uniquely mapped (MAPQ > 36) reads were translated into a pair of fragment-ends (fends) by associating each read with its downstream fend. PCR duplicates and reads mapping to the same restriction fragment were excluded.
Genome_build: mm10
Supplementary_files_format_and_content: Each processed file represent pairwise information of the observed genome contacts and can be further analyzed using the "Shaman" pipeline (https://bitbucket.org/tanaylab/shaman).

source_name: embryonic stem cells (ES)

growth_protocol: E14Tg2a cell lines were maintained as described in (Gaspard et. al., 2009). In brief, cells were cultured in DMEM (ThermoFished, Cat.N:21969-035), suppelemented with 15% FBS (ES-qualified, ThermoFished, Cat.N:16141-079) 1,000 U ml of LIF (Millipore, Cat.N: ESG1106), 0.1 mM of non-essential amino acids (ThermoFished, Cat.N: 11140-035), 1 mM of glutamax (ThermoFisher, Cat.N: 35050-038), 50U of penicillin and streptomycin (ThermoFirsher, Cat.N: 15070-063) and 0.1 mM of 2-mercaptoethanol (ThermoFisher, Cat.N: 31350-010). Media was changed every day and cells were passaged every two days using StemPro Accutase (ThermoFisher, Cat.N: A11105-01).

extract_protocol:
HiC and library preparation was carried out using the in-situ method as described previously (Rao et. al., 2014) with minor modifications.  In brief, cells were digested overnight at 37C using 500U of DpnII. After biotin filling, proximity ligation was carried out for 4 hours at 18C with 2000U T4 DNA Ligase. After reverse-crosslinking, DNA was purified using ethanol precipitation and sheared to 300-400bp fragments using Covaris S220 sonicator.
Ligation fragments containing biotin were immobilized on MyOne Streptavidin T1 beads (ThermoFished Cat.N: 65602), end-repaired and a-tailed as described (Rao et al., 2014). NEXTflex adaptors (Bioo Scientific, Cat.N: 514101) were then ligated and fragments were PCR amplified using KAPA HiFi Library Ampification Kit (Kapa Biosystems, Cat.N: KK2620) for 6-8 cycles. DNA was then double-size selected using AMPure XP beads (Agencourt, Cat.N: A63881) in order to isolate fragments between 300 and 800bp.

treatment_protocol: E14Tg2a cells were infected by a lentivirus contain dCas9-VP64 (Addgene, Cat.N 61425) or empty dCas9 (generating by removing the VP64 from the dCas9-VP64). Four days after infection cells were selected by adding 15ug/ml of basticidine ( Gibco, Cat.N A11139-03) during one week. To generate dCas9-VP64/p65-Hsf1 cell line, dCas9-VP64 positive cells were then additionally infected by lentivirus contain MS2-P65-HSF1 helper protein (Addgene, Cat.N 61426). Four days after infection positive cells were selected by adding hygromycine at 1mg/ml (Gibco, Cat.N 10687010). Guide RNAs (Zfp604 – AGAAAGCGGAATGAGAAGTT and Sox4 - TTGCTCTGTAAATTGGAATG) were designed and cloned in lenti sgRNA(MS2) zeo backbone (Addgene, Cat.N 61427) according to Zhang lab protocol (http://sam.genome-engineering.org/). The above mentioned CRISPR-dCas9 cell lines (plus the original E14Tg2a cell line as control) were infected by the sgRNA lentivirus and selected with 250ug/ml of zeocin (Invitrogen Cat.N R250-01) for 5 days. The first biological Hi-C/RNA replicate was collected one week after the original infection date, while the second was done one passage later (9 days post-infection).

tag: strain/cell line

value: E14Tg2a + dCas9_VP64 + p65/Hsf1

tag: grna


title: 61B-OE-Mock-2

city: Hangzhou

first: Xushen

last: Xiong

state: Zhejiang

address: Wenyi Road West

department: Medical Center

institute: Zhejiang University

description: The corresponding mock control

data_processing:
Raw sequencing reads produced were firstly subjected to Trim_galore (version 0.3.7. http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for quality control and adaptor trimming. The minimum quality threshold was set to 20, and the minimum length required for reads after trimming was 30 nt. The remaining reads were further processed by removing the first 10 nt random barcode in the 5’ end.
Processed reads were mapped to mitochondrial genome using BWA-MEM with default parameters (version 0.7.15-r1140).
Reads mapping to an identical position of reference were considered as PCR duplications if their 10 nt random barcodes were the same, and only one of these reads was kept; The mapped reads mapped to heavy strand and light strand were separated.
Samtools mpileup (1.2) was used to extract the reads mapping of every nucleotide in the mitochondrial genome.
Mismatch rate was calculated using in-house scripts.
Genome_build: hg19
Supplementary_files_format_and_content: Mismatch rate file in tab-delimited format; containing the mismatch rate for every nucleotide in the mt-genome. The mismatch rate was calculated for both heavy strand and light strand.

source_name: HEK293T Mock control

growth_protocol: cells was maintained in DMEM with 10% FBS and penicillin/streptomycin.

extract_protocol:
Total RNA was isolated from cell lines by Trizol(invitrogen).mRNA was enriched from total RNA with size selection using Megaclear kit (invitrogen) followed by two rounds of polyA selection using Dynabeads Oligo(dT)25 (invitrogen); RNA fraction under 200nt was collected from the flow through of Megaclear kit.
RNA samples were dephosphorylated with PNK (NEB) and ligated to 3’ RNA linker using T4 RNA ligase2, truncated KQ (NEB). Reverse transcription was carried using different reverse transcriptase for different samples.  5’ adaptor was ligated to cDNA and then amplified by PCR. PCR products were purified by 8% TBE gel

tag: cell line

value: human embryonic kidney cells

tag: enrichment

value: No antibody enriched


title: dyak_AC_f_r4

value: abdomen without digestive or reproductive system


title: HiC_dCas9VP64_Sox4gRNA_rep2

value: E14Tg2a + dCas9_VP64


title: dana_TX_m_r4

value: adult

value: thorax without digestive system

value: Male

value: TCCGCGAA-GGCTCTGA


title: 61B-OE-2

source_name: TRMT61B OE in HEK293T

tag: cell type


title: HiC_dCas9_Sox4gRNA_rep2

value: E14Tg2a + dCas9


title: HiC_E14_Sox4gRNA_rep2


title: HiC_dCas9VP64_Sox4gRNA_rep1


title: HiC_dCas9VP64/p65_Sox4gRNA_rep1


title: dana_TX_f_r4

value: AGCGATAG-GGCTCTGA


title: dana_RE_m_r4

value: CGGCTATG-CAGGACGT


title: dana_RE_f_r4

value: reproductive system without gonad


title: HiC_E14_Sox4gRNA_rep1


title: NOS3_PS

city: La Jolla

first: Shu

last: Chien

state: CA

address: 9500 Gilman Drive

department: Institute of Engineering In Medicine

institute: University of California, San Diego

description: NOS3 viewpoint of HUVECs treated with pulsatile shear

data_processing:
Library strategy: 4C-seq
raw Fastq files are aligned to human genome build hg19 with bowtie
samtools are used to generate sorted bam files
bedGraph files were generated by bedtool genomecov method
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

source_name: Human umbilical cord vein endothelial cells, subjected to PS

growth_protocol: HUVECs were seeded to glass slides coated with Collagen I, and maintained in medium M199 supplemented with 10% Endothelial Cell Growth Medium (Cell Application), 10% FBS, 1% sodium pyruvate, 1% L-glutamine, and 1% penicillin-streptomycin

extract_protocol:
ECs were crosslinked with 2% formaldehyde, followed by 0.1 M glycine quanching and nuclei pelleting
The cross-linked DNA underwent two rounds of digestion respectively by DpnII and CviQI recognizing 4 bp restriction sites. Each digestion was followed by a reaction with T4 DNA ligase for proximity ligation. The resulting 4C template was used for the subsequent PCR reactions, of which 16 reactions were pooled and purified for next-generation sequencing

treatment_protocol: HUVECs were subjected to PS (12±4 dyn/cm2), OS (0.5±4 dyn/cm2)

tag: treatment

value: pulsatile shear

value: HUVEC

tag: viewpoint


title: HiC_dCas9_Sox4gRNA_rep1


title: 7xue-CD8

tag: tissues

value: peripheral blood

value: early pregnancy


title: dana_HD_m_r4

source_name: head

tag: flybase species id

value: head

tag: Sex

tag: age post eclosion (days)

value: TCTCGCGC-ATAGAGGC

value: without ERCC


title: dyak_GO_f_r4

source_name: gonad

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: developmental stage

tag: tissue

value: gonad

value: Female

value: TCCGCGAA-TAATCTTA


title: HiC_dCas9VP64/p65_Zfp608gRNA_rep2

value: E14Tg2a + dCas9_VP64 + p65/Hsf1


title: HiC_dCas9VP64_Zfp608gRNA_rep2

value: E14Tg2a + dCas9_VP64


title: HiC_dCas9_Zfp608gRNA_rep2


title: dana_HD_f_r4

value: adult

tag: fly culture temperature (oc)

tag: replicate

tag: illumina barcode


title: KM1234

city: Ilsan

first: Jinyeong

last: Lim

address: Ilsan

country: South Korea

institute: National Cancer Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2 v2.2.3 with default parameters
Transcript is assembled by Cufflinks v2.2.1 with aligned reads that contain paired-end information.
Expression profiles (FPKM) of assembled transcripts for each sample are calculated by Cufflinks. Expression profiles are represented as normalization value which is based on transcript length and depth of coverage as FPKM values (Fragments Per Kilobase of transcript per Million Mapped reads).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: MCSs

growth_protocol: GCTB stromal cells in DMEM medium supplemented with 10% fetal bovine serum (FBS) and 5ug/ml of Gentamycin at 37C in a 5% CO2 pressure.

extract_protocol:
We collected the cultured GCTB cell with 0.25 % EDTA-trypsin and extract the RNA used QIAGEN Rneasy mini kit followed the standard protocol. QIAshredder spin columns and Dnase I digestion step was included
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: h3f3a status

value: WT

value: stem cells


title: 61B-OE-1

value: human embryonic kidney cells

value: No antibody enriched


title: GCTB12

source_name: stromal cell

value: male

tag: disease

value: GCTB


title: HiC_E14_Zfp608gRNA_rep2

tag: strain/cell line

tag: grna


title: NOS3_OS

description: NOS3 viewpoint of HUVECs treated with oscillitory shear

source_name: Human umbilical cord vein endothelial cells, subjected to OS

value: oscillatory shear

tag: cell type

value: HUVEC


title: GCTB11


title: GCTB10

value: female


title: dana_GO_f_r4

tag: plate and well id

tag: ercc infomation


title: HiC_dCas9VP64/p65_Zfp608gRNA_rep1


title: dana_GO_m_r4

value: Male

value: TCTCGCGC-TAATCTTA


title: HiC_dCas9VP64_Zfp608gRNA_rep1


title: HiC_dCas9_Zfp608gRNA_rep1

value: E14Tg2a + dCas9


title: dana_DG_f_r4

source_name: digestive plus excretory system

value: digestive plus excretory system

value: Female

value: TCCGCGAA-GTACTGAC

value: without ERCC


title: ChIP_CN_Input_1

description: Processed data files: CN_Input.bw

data_processing:
Fastq files were aligned to the mm10 reference genome, PCR duplicates were removed using Samtools and normalized genome coverage tracks were generated from uniquely mapping reads (mapq>30) using deepTools2.  In order to avoid double counting for paired-end data, reads with mates were extended to match the fragment size defined by the two read mates, and the second read mate was discarded. Single-end reads, unmated reads, mate reads that map too far apart (>4x fragment length) were extended by 200bp. Biological replicates were pooled and coverage was then calculated as reads per million of mapped reads (RPM) in 10bp bins.To determine the peaks for ChIPs with narrow binding profiles (CTCF, Ring1B, H3K4me3, H3K27ac, Pax6, NeuroD2), datasets were uniformly processed using the AQUAS Transcription Factor pipeline (based off the Encode (phase-3) specifications) with default parameters (IDR=5%).
supplementary_files_format_and_content:bigWig file represents the average (from two replicates) genome coverage in Reads per Million in 10bp bins. Peak files are in compressed narrowPeak format
assembly: mm10

source_name: in-vitro differentiated cortical neurons (CN)

growth_protocol: Cells were differentiated into neuronal progenitors and cortical neurons as described in (Gaspard et. al., 2009) with minor changes. In brief, cells were plated at low density (2.5x105) on gelatin-coated 10cm dishes in ES media and after 12h cultured in DDM media (DMEM/F12 + GlutaMAX (ThermoFisher, Cat.N: 31331-028), supplemented with 1x N2 (ThermoFisher, Cat.N: 17502-048), 1 mM of sodium pyruvate (ThermoFisher, Cat.N: 11360-070), 500 ug/ml BSA Fraction V (ThermoFisher, Cat.N:15260-037), 0.1mM of 2-mercaptoethanol and 50U of penicillin and streptomycin) for a total of 12 days. Cyclopamine (Merck – 239803) was added from day 2 to day 10 of differentiation. Media was changed every two days. After 12 days of differentiation, neural progenitors were dissociated using StemPro Accutase, plated on poly-lysine (Sigma, Cat.N: P2636) /laminin (Sigma, Cat.N: 11243217001) and cultured in 1:1 mixture of DDM and Neurobasal/N27 media (ThermoFisher, Cat.N: 21103-049, supplemented with 1x B27 without retinoic acid (ThermoFisher, Cat.N: 12587-010) and 2mM GlutaMax) for either additional 2 days (D12+2) to obtain neural progenitors (NPC), or additional 9 days (D12+9) to obtain cortical neurons (CN).

extract_protocol:
Cells were processed for FACS as described for HiC, except for permeabilization or fxCycle addition. GFP+ purified cells were immediately pelleted, frozen in liquid nitrogen and stored at -80C until further use. 1x10^6 cells per IP for chromatin marks, or 2.5x10^6 cells for CTCF/Ring1B were then thawed on ice, resuspended in cold cell lysis buffer (10mM Tris pH 8, 10mM NaCl, 0.2% NP-40) + 1xEDTA-free Protease Inhibitors. 10mM sodium butyrate was added if H3K27ac was examined. Cells were lysed for 20min, washed once with cold PBS and resuspended in 50ul per IP cold nuclei lysis buffer (50mM Tris pH8, 10mM EDTA, 1% SDS) + 1xProtease Inhibitors / Sodium Butyrate. Nuclei were lysed for 10min at 4C with rotation and then sonicated for 16-18 cycles using Bioruptor (Diagenode). After sonication, 5x volumes of IP dilution buffer (20mM Tris pH8, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.01% SDS + protease inhibitors) was added, chromatin was precleared using 25ul Protein A dynabeads (ThermoFisher, Cat.N: 10002D) / 1mL for 1hrs at 4C with rotation.  Meanwhile, 25ul beads / IP were washed once with cold 0.5% BSA in PBS, and incubated with the antibody for 4-5hrs at 4C in 0.5ml 0.5% BSA in PBS). Beads were then washed once with 0.5% BSA in PBS, added to the precleared chromatin and incubated overnight at 4C with rotation. Beads were then washed once with cold IP wash buffer 1 (20mM Tris pH8, 2mM EDTA, 50mM NaCl, 1% Triton X-100, 0.1% SDS), twice with high salt wash buffer (20mM Tris pH8, 2mM EDTA, 500mM NaCl, 1% Triton X-100,0.1% SDS), once with cold IP wash buffer 2 (10mM Tris pH8,1mM EDTA,250mM LiCl,1% NP-40,1% sodium deoxycholate) and twice with cold TE buffer (1mM Tris pH8, 1mM EDTA). DNA:protein complexes were then eluted twice for 15min at 65C in 100ul elution buffer (100mM NaHCO3, 1%SDS) each time. 16ul 5M NaCl was then added and samples + inputs were reverse cross-linked at 65C, RNase A and proteinase K treated and purified using ultrapure phenol/chloroform (ThermoFisher, Cat.N: 15593-049).
Libraries were prepared using Illumina’s TruSeq ChIP Sample Preparation Kit, according to the manufacturer’s instructions with minor modifications. In brief, 5-10ng of ChIP DNA was end repaired, 3' Ends were adenylated and Illumina adapters were ligated. Libraries were then PCR amplified using KAPA HiFi Library Ampification Kit for 10-12 cycles to maximize complexity and the gel-based size-selection was performed after PCR amplification.

tag: strain/genotype

value: Tau-GFP

tag: sorting

value: GFP+


title: dana_DG_m_r4

tag: flybase species id

value: adult

tag: Sex


title: HiC_E14_Zfp608gRNA_rep1


title: ChIP_CN_Input_2

description: Processed data files: CN_Input.bw

value: in-vitro differentiated cortical neurons (CN)


title: dana_AC_m_r4

source_name: abdomen without digestive or reproductive system

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: age post eclosion (days)

value: TCTCGCGC-AGGCGAAG


title: 61B-OE-Mock-1

description: The corresponding mock control

tag: cell line

value: human embryonic kidney cells

tag: enrichment

value: No antibody enriched


title: GCTB09

value: WT

value: GCTB


title: ChIP_CN_H3K36me3_2

description: Processed data files: CN_H3K36me3.bw

tag: tissue


title: ChIP_CN_H3K36me3_1

description: Processed data files: CN_H3K36me3.bw


title: ChIP_CN_H3K27me3_2

description: Processed data files: CN_H3K27me3.bw


title: ChIP_CN_H3K4me3_2

description: Processed data files: CN_H3K4me3.bw CN_H3K4me3.IDR0.05.filt.narrowPeak.gz


title: ChIP_CN_H3K9me3_2

description: Processed data files: CN_H3K9me3.bw


title: GCTB08

value: male


title: dmoj_WB_m_r4

description: mixed-species [D. melanogaster (Oregon-R), D. mojavensis, and D. persimilis] RNA preparation

organism: Drosophila mojavensis

source_name: whole body

tag: developmental stage

value: whole body

value: Male

tag: fly culture temperature (oc)

tag: replicate

tag: illumina barcode

value: CGCTCATT-TATAGCCT


title: ChIP_CN_H3K27me3_1

description: Processed data files: CN_H3K27me3.bw


title: ChIP_CN_H3K4me3_1


title: ChIP_CN_H3K27ac_2

description: Processed data files: CN_H3K27ac.bw CN_H3K27ac.IDR0.05.filt.narrowPeak.gz


title: ChIP_CN_H3K27ac_1


title: dmoj_TX_m_r4

value: thorax without digestive system

value: ATTACTCG-CCTATCCT


title: ChIP_CN_H3K4me1_2

description: Processed data files: CN_H3K4me1.bw


title: dana_AC_f_r4

value: abdomen without digestive or reproductive system

value: Female


title: Mock_under200nt_fraction_RNA

description: Smal RNA-seq (fraction below 200nt)

data_processing:
Raw sequencing reads produced from m1A-MAP were firstly subjected to Trim_galore (version 0.3.7. http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for quality control and adaptor trimming. The minimum quality threshold was set to 20, and the minimum length required for reads after trimming was 30 nt. The remaining reads were further processed by removing the first 10 nt random barcode in the 5’ end. As for the ribosome profiling (Ribo-seq) data and the corresponding RNA-seq data, reads with a quality lower than 20 were discarded, and the adaptor in 3’ end was trimmed. Processed reads with a length ranging from 25 nt to 35 nt in the ribosome profiling sample were kept for further analysis.
Processed reads were mapped to human transcriptome or mitochondrial genome using BWA-MEM with default parameters (version 0.7.15-r1140).
Reads mapping to an identical position of reference were considered as PCR duplications if their 10 nt random barcodes were the same, and only one of these reads was kept.
Samtools mpileup (1.2) was used to extract the reads mapping of every nucleotide in the transcriptome and mitochondrial genome.
Mismatch rate was calculated using in-house scripts. RPKM was calculated using in-house scripts following the definition of RPKM.
Genome_build: hg19
Supplementary_files_format_and_content: Mismatch rate file in xls format; containing the mismatch rate for every nucleotide in the transcriptome.

value: human embryonic kindey cells

tag: further treatment

tag: reverse transcription condition

value: TGIRT; pH 8.3; 3mM MgCl2

tag: molecule subtype

value: RNA fraction under 200 nt


title: ChIP_CN_H3K9me3_1

description: Processed data files: CN_H3K9me3.bw

value: in-vitro differentiated cortical neurons (CN)

value: Tau-GFP

value: GFP+


title: ChIP_CN_H3K4me1_1

description: Processed data files: CN_H3K4me1.bw


title: dmoj_TX_f_r4

value: adult

value: GAATTCGT-CCTATCCT

tag: plate and well id

tag: ercc infomation

value: without ERCC


title: TRMT6_61A_KD_under200nt_fraction_RNA

description: Smal RNA-seq (fraction below 200nt)

tag: cell type

tag: genotype/variation

value: TRMT6/61A KD


title: ChIP_CN_Ring1B_1

description: Processed data files: CN_Ring1B.bw CN_Ring1B.IDR0.05.filt.narrowPeak.gz

tag: strain/genotype

tag: sorting


title: GCTB07

tag: Sex

value: female

tag: h3f3a status

tag: disease

value: GCTB


title: dmoj_WB_f_r4

tag: flybase species id

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: tissue

value: whole body

tag: age post eclosion (days)

value: GAATTCGT-TATAGCCT


title: ChIP_CN_CTCF_2

description: Processed data files: CN_CTCF.bw CN_CTCF.IDR0.05.filt.narrowPeak.gz


title: m1A_IP_demethylase_TGIRT_rep2

tag: cell line

tag: enrichment

value: Immunoprecipation with anti-m1A antibody  (MBL; D345-3 lot 002) followed by demethylase treatment

value: Demethylation using purified AlkB

value: poly-A RNA


title: HEK293T_Ribo-seq

description: Ribosome profiling

value: human embryonic kindey cells

tag: further treatment

tag: reverse transcription condition

value: SS III; pH 8.3; 3mM MgCl2

value: Ribosome protected RNA


title: HEK293T_RNA-seq

tag: molecule subtype

value: rRNA depleted fraction


title: ChIP_NPC_Input_2

description: Processed data files: NPC_Input.bw

source_name: in-vitro differentiated neural progenitor cells (NPC)


title: m1A_IP_demethylase_TGIRT_rep1

value: TGIRT; pH 8.3; 3mM MgCl2


title: dmoj_RE_f_r4

tag: developmental stage

value: reproductive system without gonad

value: Female

tag: fly culture temperature (oc)

tag: replicate

tag: illumina barcode

value: CTGAAGCT-TAATCTTA

tag: plate and well id

tag: ercc infomation


title: dmoj_RE_m_r4

value: adult

tag: Sex

value: Male

value: TCCGGAGA-TAATCTTA

value: without ERCC


title: ChIP_CN_Ring1B_2

value: in-vitro differentiated cortical neurons (CN)

tag: strain/genotype

value: Tau-GFP

tag: sorting

value: GFP+


title: dmoj_HD_m_r4

tag: flybase species id

tag: strain (strain name or flybase id or drosophila species stock center id)

value: head

value: TCCGGAGA-ATAGAGGC


title: ChIP_CN_CTCF_1

tag: tissue


title: ChIP_NPC_H3K36me3_2

description: Processed data files: NPC_H3K36me3.bw

value: in-vitro differentiated neural progenitor cells (NPC)


title: m1A_IP_TGIRT_rep2

tag: cell line

tag: cell type

value: human embryonic kindey cells

value: Immunoprecipation with anti-m1A antibody  (MBL; D345-3 lot 002)

value: poly-A RNA


title: m1A_IP_TGIRT_rep1

tag: enrichment

tag: further treatment

value: TGIRT; pH 8.3; 3mM MgCl2


title: ChIP_NPC_H3K27ac_1

description: Processed data files: NPC_H3K27ac.bw NPC_H3K27ac.IDR0.05.filt.narrowPeak.gz


title: dmoj_HD_f_r4

tag: age post eclosion (days)

value: TAATGCGC-ATAGAGGC


title: m1A_input_TGIRT_rep1

tag: reverse transcription condition

tag: molecule subtype


title: ChIP_NPC_H3K27me3_2

description: Processed data files: NPC_H3K27me3.bw


title: ChIP_NPC_H3K9me3_1

description: Processed data files: NPC_H3K9me3.bw


title: RT-10

value: SS II; pH 8.0; 6mM MnCl2

value: Total RNA


title: ChIP_NPC_H3K36me3_1

description: Processed data files: NPC_H3K36me3.bw


title: ChIP_NPC_H3K27me3_1

description: Processed data files: NPC_H3K27me3.bw


title: ChIP_NPC_H3K27ac_2


title: ChIP_NPC_H3K4me1_1

description: Processed data files: NPC_H3K4me1.bw


title: m1A_input_TGIRT_rep2


title: dmoj_GO_m_r4

tag: developmental stage

value: adult

value: gonad

tag: fly culture temperature (oc)

tag: replicate

value: ATTACTCG-AGGCGAAG


title: dmoj_GO_f_r4

value: Female

tag: illumina barcode

value: CTGAAGCT-AGGCGAAG

tag: plate and well id

tag: ercc infomation

value: without ERCC


title: ChIP_NPC_H3K4me3_2

description: Processed data files: NPC_H3K4me3.bw NPC_H3K4me3.IDR0.05.filt.narrowPeak.gz

tag: strain/genotype

tag: sorting

value: GFP+


title: RT-8

value: SS III; pH 8.0; 6mM MnCl2


title: ChIP_NPC_H3K4me3_1


title: ChIP_NPC_CTCF_2

description: Processed data files: NPC_CTCF.bw NPC_CTCF.IDR0.05.filt.narrowPeak.gz


title: dmoj_DG_m_r4

tag: flybase species id

tag: strain (strain name or flybase id or drosophila species stock center id)

value: digestive plus excretory system

tag: Sex

value: Male

value: ATTACTCG-GTACTGAC


title: ChIP_NPC_H3K9me3_2

description: Processed data files: NPC_H3K9me3.bw

tag: tissue

value: in-vitro differentiated neural progenitor cells (NPC)


title: dmoj_DG_f_r4

value: CTGAAGCT-GTACTGAC


title: Day22_RNAseq

first: yuanyuan

last: li

state: Shanghai

address: Yue yang 320

institute: sibcb

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat2 v2.0.4 program
fragment per kilobase per million (FPKM) as expression level using Cufflinks v2.0.2 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: neuronal cells

extract_protocol:
Human ES cells and human ES-derived neuronal cells were removed, 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 1 ug of total RNA for the construction of sequencing libraries.

tag: cell type

value: ES-derived neuronal cells

tag: passages

tag: strain


title: ChIP_NPC_H3K4me1_2

description: Processed data files: NPC_H3K4me1.bw


title: ChIP_NPC_Input_1

description: Processed data files: NPC_Input.bw


title: ChIP_ES_CTCF_1

description: Processed data files: ES_CTCF.bw ES_CTCF.IDR0.05.filt.narrowPeak.gz

growth_protocol: Oct4-GFP  feeder-free cell line were maintained as described in (Gaspard et. al., 2009). In brief, cells were cultured in DMEM (ThermoFished, Cat.N:21969-035), suppelemented with 15% FBS (ES-qualified, ThermoFished, Cat.N:16141-079) 1,000 U ml of LIF (Millipore, Cat.N: ESG1106), 0.1 mM of non-essential amino acids (ThermoFished, Cat.N: 11140-035), 1 mM of glutamax (ThermoFisher, Cat.N: 35050-038), 50U of penicillin and streptomycin (ThermoFirsher, Cat.N: 15070-063) and 0.1 mM of 2-mercaptoethanol (ThermoFisher, Cat.N: 31350-010). Media was changed every day and cells were passaged every two days using StemPro Accutase (ThermoFisher, Cat.N: A11105-01).

value: embryonic stem cells (ES)


title: ChIP_ES_CTCF_2


title: RT-9

tag: cell line

value: human embryonic kindey cells

tag: enrichment

tag: further treatment

tag: reverse transcription condition

value: SS II; pH 7.0; 6mM MnCl2


title: ChIP_ES_Ring1B_1

description: Processed data files: ES_Ring1B.bw ES_Ring1B.IDR0.05.filt.narrowPeak.gz


title: dmoj_AC_m_r4

tag: developmental stage

value: adult

value: abdomen without digestive or reproductive system

tag: age post eclosion (days)

tag: fly culture temperature (oc)

tag: replicate

value: TCCGGAGA-GGCTCTGA


title: ChIP_NPC_Ring1B_2

description: Processed data files: NPC_Ring1B.bw NPC_Ring1B.IDR0.05.filt.narrowPeak.gz

tag: strain/genotype


title: Day16_RNAseq


title: ChIP_NPC_Ring1B_1

tag: sorting


title: dmoj_AC_f_r4

tag: flybase species id

value: Female

tag: illumina barcode

value: GAATTCGT-GGCTCTGA

tag: plate and well id

tag: ercc infomation


title: RNAseq_ncx_CN_1

data_processing:
Fastq files were aligned to the mm10 reference genome using STAR version 2.5.0b in basic twoPass mode using the “Encode” options as specified in the manual. PCR duplicates were removed and RPM normalized strand-specific coverage tracks based on uniquely aligned reads were also produced using STAR in  “inputAlignmentsFromBAM” runMode.Reads overlapping with annotated genes (Ensembl build GRCm38.p4) were counted using the summarizeOverlaps function from the R package “GenomicAlignments” in strand-specific, paired –end mode. FPKM (Fragments per kilobase per million mapped fragments) counts and differential expression was estimated using DeSeq2 (Love et. al., 2014).
supplementary_files_format_and_content:text file with 3 columns - ENSEMBL gene ID, fpkm counts per gene, Official Gene Symbol
assembly: mm10

source_name: CN purified in-vivo from E14.5 neocortex

extract_protocol:
Cells were processed for FACS as described for HiC, except without fixation, permeabilization or fxCycle addition. GFP+ purified cells were immediately pelleted and resuspended in TRIzol (ThermoFisher, Cat.N: 15596026). After 5min at room temperature samples were vortexed for 20s, 0.2x volumes of chloroform was added, tubes were mixed by inverting and samples were centrifuged at 13,000 rpm at 4C for 15min. The aqueous phase was then processed using the RNeasy Mini Kit (Qiagen, Cat.N: 74104) according to the manufacturer’s instructions.
Purified RNA (maximum of 1ug) was then used for library generation using the TruSeq Stranded Total RNA Library Kit (Illumina, RS-122-2301). In brief, rRNA was depleted using RiboZero Gold, RNA was fragmented and first strand cDNA was synthesized in the presence of actinoMycin D. Second strand cDNA was then synthesised in the presence of dUTP and dsDNA was selected using AMPure XP beads. DNA was then 3'-adenylated, ligated to Illumina adapters and PCR-amplified for 10-12 cycles.

tag: tissue

value: cortical neurons purified in-vivo from E14.5 neocortex

value: C57BL/6J Hes5-GFP+/- dcx-mRFP+/-

value: GFP-/mRFP+


title: ChIP_NPC_CTCF_1

value: GFP+


title: RT-7

tag: cell type

value: SS III; pH 7.0; 6mM MnCl2

tag: molecule subtype

value: Total RNA


title: Day20_RNAseq

tag: passages

tag: strain


title: RT-3

tag: cell line

tag: enrichment

tag: further treatment

value: SS III; pH 7.0; 6mM MgCl2


title: RT-2

tag: reverse transcription condition

value: AMV; pH 8.3; 10mM MgCl2


title: RT-5

value: SS III; pH 7.0; 3mM MgCl2


title: RT-6

value: SS III; pH 8.3; 3mM MgCl2


title: RT-1

value: human embryonic kindey cells

value: AMV; pH 7.0; 10mM MgCl2


title: RT-4

value: SS III; pH 8.3; 6mM MgCl2


title: RNAseq_ncx_NPC_2

source_name: NPC purified in-vivo from E14.5 neocortex

value: neural progenitor cells purified in-vivo from E14.5 neocortex

value: GFP+/mRFP-


title: Day14_RNAseq

value: ES-derived neuronal cells


title: RNAseq_CN_2

value: in-vitro differentiated cortical neurons (CN)

value: Tau-GFP


title: RNAseq_NPC_2

value: in-vitro differentiated neural progenitor cells (NPC)


title: ChIP_ES_Input_1

description: Processed data files: ES_Input.bw

source_name: embryonic stem cells (ES)

value: embryonic stem cells (ES)


title: RNAseq_ES_2

value: GFP+


title: ChIP_ES_Ring1B_2


title: Day6_RNAseq


title: RNAseq_ncx_NPC_1

value: C57BL/6J Hes5-GFP+/- dcx-mRFP+/-


title: RNAseq_ncx_CN_2

value: cortical neurons purified in-vivo from E14.5 neocortex

value: GFP-/mRFP+


title: Day10_RNAseq


title: Day18_RNAseq


title: Day2_RNAseq


title: Day12_RNAseq


title: RNAseq_NPC_1


title: Day0_RNAseq

source_name: human embryonic stem cells

value: human embryonic stem cells


title: RNAseq_CN_1


title: HiC_unsorted

data_processing:
Library strategy: HiC
Hi-C data was processed using the Cwalks pipeline (http://compgenomics.weizmann.ac.il/tanay/?page_id=690). In brief, raw sequencing reads were mapped independently to the mm10 reference genome using Bowtie2 in local alignment mode. The uniquely mapped (MAPQ > 36) reads were translated into a pair of fragment-ends (fends) by associating each read with its downstream fend. PCR duplicates and reads mapping to the same restriction fragment were excluded.
supplementary_files_format_and_content:Each processed file represent pairwise information of the observed genome contacts and can be further analyzed using the "Shaman" pipeline (https://bitbucket.org/tanaylab/shaman).
assembly: mm10

growth_protocol: E14Tg2a, Oct4-GFP and Sox1-GFP feeder-free or Tau-GFP (grown on irradiated CF-1 MEF feeders (Tebu-Bio, Cat.N: GSC-6001G)) cell lines were maintained as described in (Gaspard et. al., 2009). In brief, cells were cultured in DMEM (ThermoFished, Cat.N:21969-035), suppelemented with 15% FBS (ES-qualified, ThermoFished, Cat.N:16141-079) 1,000 U ml of LIF (Millipore, Cat.N: ESG1106), 0.1 mM of non-essential amino acids (ThermoFished, Cat.N: 11140-035), 1 mM of glutamax (ThermoFisher, Cat.N: 35050-038), 50U of penicillin and streptomycin (ThermoFirsher, Cat.N: 15070-063) and 0.1 mM of 2-mercaptoethanol (ThermoFisher, Cat.N: 31350-010). Media was changed every day and cells were passaged every two days using StemPro Accutase (ThermoFisher, Cat.N: A11105-01).

extract_protocol:
HiC and library preparation was carried out using the in-situ method as described previously (Rao et. al., 2014) with minor modifications. In order to maximize library complexity, FACS-purified samples were split into batches of 1x10^6 cells and processed separately. In brief, cells were digested overnight at 37C using 500U of DpnII. After biotin filling, proximity ligation was carried out for 4 hours at 18C with 2000U T4 DNA Ligase. After reverse-crosslinking, DNA was purified using ethanol precipitation and sheared to 300-400bp fragments using Covaris S220 sonicator.
Ligation fragments containing biotin were immobilized on MyOne Streptavidin T1 beads (ThermoFished Cat.N: 65602), end-repaired and a-tailed as described. NEXTflex adaptors (Bioo Scientific, Cat.N: 514101) were then ligated and fragments were PCR amplified using KAPA HiFi Library Ampification Kit (Kapa Biosystems, Cat.N: KK2620) for 6-8 cycles. DNA was then double-size selected using AMPure XP beads (Agencourt, Cat.N: A63881) in order to isolate fragments between 300 and 800bp.


title: Day8_RNAseq


title: ChIP-seq from CD14-positive monocyte (ENCLB008QBO)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR065SKV/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq
experiment encode accession: ENCSR065SKV
assay title: ChIP-seq
encode release date: 2017-10-12
lab: Manuel Garber, UMass
library encode accession: ENCLB008QBO
size range: 150-400

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens CD14-positive monocyte primary cell

extract_protocol: not provided

tag: antibody

value: CD14-positive monocyte

value: primary cell

tag: biosample encode accession

tag: Sex

value: not collected

tag: lab

value: Manuel Garber, UMass

tag: age

value: unknown

tag: dev stage

tag: link

value: ENCBS812XJL at ENCODE; https://www.encodeproject.org/ENCBS812XJL/

value: derived from ENCODE donor ENCDO984LDA; https://www.encodeproject.org/ENCDO984LDA/


title: HiC_GFP

tag: strain/genotype

tag: sorting


title: RNAseq_ES_1

tag: tissue


city: Neuherberg

first: Dmitry

last: Shaposhnikov

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Center Munich

data_processing:
FASTQ files were aligned to hg19(UCSC) using bowtie (default parameters but -m 1).
Calculation of genomic coverage vectors was performed for each sample after 200 bp read extension.
Coverages were exported in BEDGRAPH format.
Genome_build: hg19
Supplementary_files_format_and_content: BEDGRAPH

source_name: trophoblast progenitors at day 3_Input DNA for samples TFAP2A_10, GATA3_7, GATA2_4

growth_protocol: H9 cell line was grown on Geltrex-coated plates in mTESR1 medium

extract_protocol:
ChIP'ed DNA fragments were prepared using High Sensitivity ChIP kit (Active Motif, #53040) according to manufacturer's instrcutions using aforementioned antibodies
Libraries were prepared using NEBNext® ChIP-Seq Library Prep kit for Illumina (New England Biolabs, #E6200) according to manufacturer's instructions

treatment_protocol: For trophoblast differentiation, cells were seeded at 100% confluency on Matrigel-coated plates containing KSR-based differentiation medium and 50 ng/ml BMP4. During the time course, medium was changed every 24 hours.

tag: source cell type

value: Human embryonic stem cells (hESC)

tag: treated with

value: BMP4 for 3 day

tag: cell type

value: trophoblast progenitors at day 3

tag: chip antibody


title: HiC_CN_4

value: in-vitro differentiated cortical neurons (CN)

value: Tau-GFP


title: ChIP-seq from CD14-positive monocyte (ENCLB709FWW)

description:
https://www.encodeproject.org/experiments/ENCSR102GGG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq
experiment encode accession: ENCSR102GGG
assay title: ChIP-seq
encode release date: 2017-10-12
lab: Manuel Garber, UMass
library encode accession: ENCLB709FWW
size range: 150-400

value: ENCBS724NLM at ENCODE; https://www.encodeproject.org/ENCBS724NLM/

value: derived from ENCODE donor ENCDO456UXD; https://www.encodeproject.org/ENCDO456UXD/


title: Input DNA for samples  GATA3_9, GATA2_6

source_name: trophoblast progenitors at day 3_Input DNA for samples GATA3_9, GATA2_6

tag: cell line


title: HiC_FACS

value: embryonic stem cells (ES)

value: passed through FACS only


title: HiC_CN_2


title: Input DNA for samples TFAP2C_6

source_name: trophoblast progenitors at day 3_Input DNA for samples TFAP2C_6


title: Day4_RNAseq

value: ES-derived neuronal cells

tag: passages

tag: strain


title: HiC_NPC_3

value: in-vitro differentiated neural progenitor cells (NPC)


title: HiC_NPC_4


title: HiC_CN_3


title: HiC_NPC_2


title: Input DNA for sample  TFAP2A_13

source_name: trophoblast progenitors at day 3_Input DNA for sample TFAP2A_13


source_name: trophoblast progenitors at day 3_Input DNA for samples GATA3_8, GATA3_9, GATA2_5


source_name: trophoblast progenitors at day 3_Input DNA for samples TFAP2A_1 and TFAP2C_2


title: HiC_CN_6


title: Control_45

city: Valencia

first: Marta

last: Seco-Cervera

address: Av Blasco Ibañez, 15

country: Spain

institute: University of Valencia

data_processing:
Sequenced reads were trimmed for adaptor sequence and filtered by size and quality using Cutadapt
The remaining sequences were aligned to the human genome reference (Hg38) from the UCSC Genome Browser using the Subread package in Linux
The expression of every miRNA per sample was measured using the annotation file with mature miRNAs from miRBase (v21) and the R package Rsubread.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes raw counts of sequencing reads of every miRNA per sample

source_name: Plasma

extract_protocol:
blood samples were collected in EDTA tubes and centrifuged at 2500 rpm for 10 minutes. Once plasma was obtained, each sample was stored at −80°C until RNA extraction. 500 µL of plasma were used to isolate cell-free total RNA (including miRNAs) using the miRNeasy Serum/Plasma kit (Qiagen, Valencia, CA, USA) following the manufacturer’s protocol.
RNA libraries were prepared with NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 1&2), and they were sequenced using standard Illumina protocols.

value: FEMALE

tag: neuropathy (yes

tag: cardiopathy (yes

tag: diabetes (yes

tag: gaa repetitions (allele1/allele2)

value: Not referred to


title: Control_11

tag: Sex

tag: age


title: Control_44

value: MALE


title: TFAP2C ChIP, biological replicate 3

source_name: trophoblast progenitors at day 3_TFAP2C ChIP

value: anti-TFAP2C (#sc-12762, Santa Cruz)


title: TFAP2C ChIP, biological replicate 2


title: Control_50


title: HiC_NPC_1


title: Control_9


title: TFAP2A ChIP, biological replicate 3

source_name: trophoblast progenitors at day 3_TFAP2A ChIP

value: anti-TFAP2A (#sc-184, Santa Cruz)


title: TFAP2C ChIP, biological replicate 1


title: vcS5, replicate 1

city: Vienna

first: Richard

last: Moriggl

address: Waehringer Strasse 13A

country: Austria

institute: Ludwig Boltzmann Institute for Cancer Research LBI-CR

description:
line1-36-SPL
expression profile of vcS5 transgenic splenocytes, replicate 1

data_processing:
Alignments to genome version mm10 and the corresponding Ensgene annotation were accomplished with Bowtie2 (v2.1.0) and Tophat2 (v2.0.9), using a seed length of 15nt, maximal 4% error and maximal 100 hits per read.
Expression level estimation and differential expression analysis was performed by Cufflinks/Cuffdiff (v2.1.1) with default parameters except for --frag-bias-correct.
Low expressed (FPKM sum<2) and highly variable (coefficient of variation>1.2 within replicates) genes were removed in order to retain a reliable set of expression values.
Genome_build: mm10
Supplementary_files_format_and_content: wt-SPL_line1-SPL_annotated.txt reports FPKMs

source_name: splenocytes

extract_protocol:
Spleens were isolated and kept on ice, single-cell suspensions were flash-frozen, RNA was harvested using Trizol reagent.
2µg of total RNA per sample was taken for cDNA library synthesis using TruSeq RNA Sample Prep kit v2 (Illumina, San Diego, CA) according to the manufacturers recommendations.
50 bp single-end RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: splenocyte

tag: genotype/variation

value: vcS5 +/T


title: Control_21


title: TFAP2A ChIP, biological replicate 2

value: Human embryonic stem cells (hESC)

value: BMP4 for 3 day

value: trophoblast progenitors at day 3


title: vcS5, replicate 2

description:
line1-46-SPL
expression profile of vcS5 transgenic splenocytes, replicate 2


title: GATA2 ChIP, biological replicate 3

source_name: trophoblast progenitors at day 3_GATA2 ChIP

value: anti-GATA2 (H116, sc-9008, Santa Cruz)


title: wild-type, replicate 1

description:
wt-56-SPL
expression profile of wt splenocytes, replicate 1

value: wt


title: Control_10


title: HiC_CN_1

source_name: in-vitro differentiated cortical neurons (CN)

tag: strain/genotype

value: Tau-GFP


title: HiC_CN_5

value: in-vitro differentiated cortical neurons (CN)

tag: sorting


title: Control_22


title: GATA2 ChIP, biological replicate 2


title: wild-type, replicate 2

description:
wt-57-SPL
expression profile of wt splenocytes, replicate 2

tag: tissue


title: Control_35


title: EX4-Treated-3

city: HUNTSVILLE

first: NRIPESH

last: PRASAD

state: AL

address: 601 GENOME WAY

department: GENOMIC SERVICES LABORATORY

institute: HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY

description: Human islet grafts + mouse kidney tissue contaminated

data_processing:
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Raw reads were mapped to the reference hg19 using TopHat v2.0. The alignment metrics of the mapped reads were estimated using SAMtools. Aligned reads were imported to the commercial data analysis platform AvadisNGS (Strand Scientifics, CA, USA). After quality inspection, the aligned reads were filtered on the basis of read quality metrics; reads with a base quality score of less than 30, alignment score of less than 95, and mapping quality of less than 40 were removed. Remaining reads were then filtered on the basis of their read statistics; missing mates, translocated, unaligned, and flipped reads were removed. The reads list was then filtered to remove duplicates. Samples were grouped and transcript abundance was quantified for this final read list using Trimmed Means of M-values (TMM) as the normalization method. Output data utilized for all subsequent comparisons were summarized as normalized signal values generated by AvadisNGS. Differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions, and the p-value of the differentially expressed gene list was estimated by ANOVA using Benjamini Hochberg corrections of 0.05 for false-discovery rate.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

organism:
Homo sapiens
Mus musculus

source_name: transplanted human juvenile islet grafts

extract_protocol:
Norgen Total RNA Purification Kit
Five hundred nanograms of total RNA was required for downstream RNA-seq applications. Polyadenylated RNAs were isolated using NEBNext Magnetic Oligo d(T)25 Beads. The NEBNext mRNA Library Prep Reagent Set for Illumina (New England BioLabs Inc., Ipswich, MA, USA) was then used to prepare individually bar-coded next-generation sequencing expression libraries as per manufacturer's recommended protocol. Library quality was assessed using the Qubit 2.0 Fluorometer, and the library concentration was estimated by utilizing a DNA 1000 Chip on an Agilent 2100 Bioanalyzer. Accurate quantification for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA). Paired-end sequencing (100 million, 100-bp, paired-end reads) was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc., San Diego, CA, USA).

treatment_protocol: Two weeks after human islet transplantation, Ex-4 or PBS was delivered by micro-osmotic pumps implanted in recepient mice for 4 weeks.

value: Recipient - NSG mice

value: Human islet grafts with some mouse kidney tissue

value: Donor - 6 years old

tag: genotype

value: recipient mice - immunodeficiency

tag: treatment


title: GATA2 ChIP, biological replicate 1

tag: source cell type

tag: treated with

tag: cell type


title: Control_31

value: FEMALE

value: Not referred to


title: GATA3 ChIP, biological replicate 3

source_name: trophoblast progenitors at day 3_GATA3 ChIP

tag: cell line

tag: chip antibody

value: anti-GATA3 (#CM405A, Biocare Medical)


title: PBS-Control-3

tag: strain

value: PBS


title: Control_20

value: MALE

tag: neuropathy (yes

tag: cardiopathy (yes


title: Control_47

tag: diabetes (yes

tag: gaa repetitions (allele1/allele2)


title: Control_46

tag: Sex

tag: age


title: TFAP2A ChIP, biological replicate 1

value: anti-TFAP2A (#sc-184, Santa Cruz)


title: Control_49


title: Control_7


title: EX4-Treated-1


title: GATA3 ChIP, biological replicate 1

value: Human embryonic stem cells (hESC)


title: HEK mRNA 8.5cycle OED rep3

city: Chicago

first: Chuan

last: He

state: ILLINOIS

address: 929 E 57th St., GCIS E319

department: Department of Chemistry

institute: The University of Chicago

description:
processed data file:
HEKmRNA.Nm.genome.bed.txt

data_processing:
Sequencing reads from Illumina NextSeq-500 were pre-processed by removing standard adapters “AGATCGGAAGAGCACACGTCT” using Cutadapt (v1.9.1)
A customized script was further used to filter reads carrying the correct in-line barcode sequence in the most 3’ of sequencing reads, according to the principle of the experimental design to avoid mis-priming. Another 5-nt from the most 5’ and most 3’ of the remaining reads were further chopped and sequences were recorded as barcode to distinguish PCR duplicates.
We performed Chi-squared test on each base of RNA molecular and computed the enrichment of OED-treated library over the average depth of the same transcript and the depth of the same position in the input library.
Genome_build: hg38
Supplementary_files_format_and_content: txt files with the putative Nm modification sites

source_name: HEK mRNA 8.5cycle OED

growth_protocol: The Hela cells and HEK293t cells were cultured in medium containing DMEM medium (Gibco Invitrogen, Carlsbad, CA) supplemented with 5% (v/v) fetal bovine serum (FBS), 1 mM L-glutamine. Fresh medium is changed very day and cells are harvest when they are near 90% confluent.

extract_protocol:
Total RNA was harvested using Trizol reagent followed by iso-propanol precipitation. mRNA was then purified by the standard Aldrich mRNA extraction protocol.
mRNA was fragmented by alkaline hydrolysis and  then eight rounds of oxidation/elimination/dephosphorylation (OED) were conducted, followed by 5?-phosphorylation and the last oxidation/elimination (OE) to block the fragments without Nm at the 3'-end. RNA libraries were then prepared for sequencing using standard NEB small RNA library protocols except using the new 3'- and 5'-adaptors.

treatment_protocol: The cells were cultered until the appropriate stage. The culture medium were thrown out and washed with PBS. The cells were then treated with Trizol (Invirtrogen).

value: HEK

value: Enriched


title: PBS-Control-1


title: Control_34


title: HEK mRNA 8.5cycle OED rep2


title: Patient_28


title: HEK mRNA 8.5cycle OED rep1


title: 45_24h_RG7834

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

description:
differentiated HepaRG
VEIpolyA-HBV_counts.gct
VEIpolyA-HBV_rpkms.gct
VEIpolyA-human_counts.gct
VEIpolyA-human_rpkms.gct

data_processing:
Basecalling with CASAVA
Read quality check with FASTQC
Read mapping onto human genome hg19 with bowtie2
Read mapping onto HBV genome AB267090 with bowtie2
Gene quantification with RefSeq mRNA annotations
Genome_build: hg19
Genome_build: AB267090
Supplementary_files_format_and_content: Read counts and normalized read counts (rpkms) per EntrezGene gene and HBV transcript in gct format

organism:
Homo sapiens
Hepatitis B virus

source_name: HepRG cells

growth_protocol: HepaRG cells (Biopredic International, Saint-Gregoire, France) were cultured in Williams E medium (supplemented with 10% HepaRG growth supplement (Biopredic)) and differentiated using 1.8% DMSO for at least 2 weeks before infection. Afterwards differentiated HepaRG were replated in 24 well format and cultured for one more week before infection

extract_protocol:
Total RNA extraction was performed using the QIAGEN RNeasy 96 kit with DNase digestion as per the manufacturer’s instructions. All samples used for analysis had an RNA integrity number >8. The quantity and quality of total RNA were assessed by spectrophotometric analysis and by Agilent Tapestation 2200. Total RNA samples were normalized and randomized for further processing.
Sequencing libraries were generated from 150ng total RNA using the Illumina TruSeq Stranded Total RNA sample preparation kit with Ribo Zero Gold as per manufacturer’s instructions, quantified using the Kapa Library Quantification kit (Kapa Biosystems), normalized to 2nM and pooled as per the randomization plan. Pooled libraries were sequenced on a Illumina HiSeq 2500 sequencer for 2 × 50 cycles using the TruSeq PE Cluster Kit and TruSeq SBS Kit sequencing reagents (Illumina). Each lane was spiked with the PhiX Control library (Illumina) at a final concentration of 1 % (v/v) as a sequencing control

treatment_protocol: Differentiated HepaRG (dHepaRG) cells in 24 well plates were infected with HBV at an MOI of 20 for 20 h, before the cells were washed 4 times with PBS to remove the HBV inoculum. At day 7 post-infection, cells were treated with either 100nM of RG7834 ("RG7834") or DMSO ("vehicle").

tag: timepoint

tag: dose

tag: transfection

value: HBV


title: HEK mRNA 8cycle OED

source_name: HEK mRNA 8cycle OED

value: input


title: Patient_37


title: GATA3 ChIP, biological replicate 2

value: BMP4 for 3 day

value: trophoblast progenitors at day 3


title: 44_24h_RG7834


title: Patitnt_43


title: 42_24h_NT

value: vehicle


title: Patient_40


title: HEK mRNA

source_name: HEK mRNA


title: 41_24h_NT


title: PBS-Control-2

value: Recipient - NSG mice

tag: tissue

value: Human islet grafts with some mouse kidney tissue

tag: genotype


title: HeLa mRNA 8.5cycle OED rep3

description:
processed data file:
HeLamRNA.Nm.genome.bed.txt

source_name: HeLa mRNA 8.5cycle OED

value: HeLa

tag: treatment


title: Patient_26

value: FEMALE


title: HeLa mRNA 8.5cycle OED rep2


title: Patient_3


title: 33_12h_RG7834


title: HeLa mRNA 8.5cycle OED rep1


title: Patient_16


title: 32_12h_RG7834


title: 40_24h_NT


title: HeLa mRNA

source_name: HeLa mRNA


title: HeLa mRNA 8cycle OED

source_name: HeLa mRNA 8cycle OED


title: Patient_15


title: 43_24h_RG7834


title: Patient_39


title: Mixed adult females and males

city: Sainte-Anne-de-Bellevue

first: Lucienne

last: Tritten

state: QC

address: 21111 Lakeshore Road

department: Institute of Parasitology

country: Canada

institute: McGill University

description: microRNA

data_processing:
Basecall with Real Time Analysis v1.18.54
The 3' adaptor was removed from raw reads and reads with the length less than 10 were excluded to constitute the mappable reads.
The mappable reads were aligned against the H. p. bakeri genome, the mouse genome and miRbase using Bowtie.
Only mature miRNA sequences between 18-24 nt were retained.
Genome_build: http://nematodes.org/genomes/heligmosomoides_polygyrus/nHp_1_0.fna.gz; miRbase v21; Mus musculus mm9
Supplementary_files_format_and_content: H. p. bakeri miRNAs.xls and mouse miRNAs.xls: counts  of miRNA candidates identified in H. p. bakeri and mouse host

organism:
Mus musculus
Heligmosomoides polygyrus bakeri

source_name: Worm secretions, culture media

growth_protocol: Live whole worms in culture

extract_protocol:
RNA extraction kit: SeraMir RNA kit (System Biosciences) from pelletted microvesicles
Illumina MiSeq using v3 reagent kit, paired-end (2x75 bp)

treatment_protocol: Culture media subjected to ExoQuick-TC (System Biosciences) for microvesicle precipitation

tag: sample type

value: live worms


title: 29_12h_NT


title: dwil_dana_dyak_WB_m_r4.leftover

first: Brian

last: Oliver

address: 50 South Drive

institute: NIDDK, NIH

description: mixed-species (D. willistoni, D. ananassae, and D. yakuba) RNA preparation

data_processing:
De-multiplexed reads (Chastity > 0.6) were generated by Illumina CASAVA (v.1.8.2) as fastq files.  For the single-species samples (i.e., D. melanogaster genitalia samples), we provided the raw de-multiplexed fastq files without processing.  For the multi-species samples, we first made merged genome and annotation of appropriate Drosophila species plus corrected ERCC standards (Lee et al., Journal of Genomics, 2016, PMID 27512518).  Additionally, we added a four-letter prefix for each chromosome or scaffold in the merged genome or annotation (e.g., 2L => dmel_2L).  ERCC names were unchanged due to their specific prefix.  The de-multiplexed reads from the multi-species samples were then mapped to the appropriate merged genome and annotation using STAR (v2.4.2a) (Doblin et al., Bioinformatics, 2012, PMID 23104886) with default parameters.  We used an in-house python script to fetch the prefix of read names in the bam alignments, and obtained all uniquely-mapped and multi-hit (2-10 hits) reads (in bam format) that were mapped exclusively to a single species or exclusively to ERCC.  We converted the bam reads to fastq reads by BEDTools (2.25.0; bamtofastq) (Quinlan and Hall, 2010, Bioinformatics, PMID 20110278).  After this step, reads of each multi-species sample were split into five categories – species 1, species 2, species 3, ERCC, and leftover, which includes unmapped reads and reads mapped to multiple species (or multiple species plus ERCC).  For multi-species samples, the original fastq file can be restored by merging the reads of appropriate three species as well as the ERCC and leftover reads.
We provide both STAR (SRR5639* and SRR6181*) and HiSAT2 (SRR724*) fastq and associated matrices of raw gene-level read counts in this GEO entry. For STAR read count files, we used the FlyBase (FB) annotations (version 2017_03). For HiSAT2 read count files, we used both FB and updated (YO) annotations (data in Supplementary Files of this GEO). For the latter one, we also provide two extra columns in the expression matrix, showing the maximum exon-level Jaccard index overlap between our YO annotation gene IDs and FlyBase ones. In addition, we provided bigWig tracks for all samples (replicated merged), YO annotation files (in both gtf and gff3 format), ortholog look up table (among YO gene ID, FlyBase gene ID, and dmel gene), gene-level normalized read counts based on either YO or FlyBase annotation, and transcript-level transcripts per million (TPM) based on YO or FlyBase annotation.
Supplementary_files_format_and_content: counts

organism:
Drosophila ananassae
Drosophila yakuba
Drosophila willistoni

source_name: whole body

extract_protocol:
Flies were anesthetized using CO2, and all samples were dissected in phosphate buffered saline solution (PH 7.4, Life Technologies, Carlsbad CA) and transferred to 56 or 112 μL of RNAlater (Life Technologies, Carlsbad CA) in 96-well 1.5 mL plates at room temperature after being macerated with forceps. Plates were stored at -80 oC at the NIH after dissection (melanogaster samples) or after dissection and shipping (non-melanogaster samples).  For RNA extraction, we added 20-30 1.0 mm glass beads (BioSpec Products, Bartlesville OK) to each sample and added RLT buffer from the RNeasy 96 kit (Qiagen, Valencia CA) to 712 μL (final volume).  We homogenized the samples three times for 60 seconds each with a mini-beadbeater (Biospec Products, Bartlesville OK). Extraction of total RNA was performed using the RNeasy 96 kit (spin version), except that we used 712 μL of 70% ethanol due to the increased volumes of RNAlater/RLT mixture.  RNA was quantified using Quant-iT RiboGreen (Life Technologies, Carlsbad CA).  We spot checked RNA integrity by capillary electrophoresis on a TapeStation 2200 (Agilent Technologies, Santa Clara CA) and found that the rRNA bands were distinct. We used 33 ng aliquots of RNA of three genetically distant species for each library, except for thorax, where we used 17 ng due to lower yield. The mixing of RNA was performed using a pipetting robot (Andrew Alliance, Vernier CH). RNA from D. melanogaster genitalia was not mixed with tissues of the other species.
We used 100 ng of total RNA as input (except thorax samples: 50 ng), and followed the TruSeq PolyA+ stranded mRNA kit protocol with half volume reactions (Illumina, San Diego CA).  For each sample, we also added 10 pg Standard Reference Material 2374 beta (Pool 78A or 78B) ERCC spike-ins (Lee et al., Journal of Genomics, 2016, PMID 27512518) to the Fragment-Prime-Finish Mix during the mRNA fragmentation step.  We used 96-plex molecular barcoding (Kozarewa and Turner, Methods in Molecular Biology, 2011, PMID 21431778) from the Illumina TruSeq kit for all samples. Libraries were quantified with Quant-iT PicoGreen (Life Technologies, Carlsbad CA). For each sample, we conducted RNA-seq for the three libraries with the highest DNA concentration out of four libraries. The quality (i.e., no overt primer dimers or low complexity) of all selected libraries were confirmed by capillary electrophoresis on a TapeStation 2200 (Agilent Technologies, Santa Clara CA). We performed single-end 76 bp PolyA+ sequencing on the HiSeq2000 Sequencing System (Illumina, San Diego CA).

tag: flybase species id

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: developmental stage

value: adult

value: whole body

value: Male

tag: age post eclosion (days)

tag: fly culture temperature (oc)

tag: replicate

tag: illumina barcode

value: AGCGATAG-TATAGCCT

tag: plate and well id

tag: ercc infomation

value: without ERCC


title: 30_12h_NT


title: 28_12h_NT


title: EX4-Treated-2

tag: strain

tag: age

value: Donor - 6 years old

value: recipient mice - immunodeficiency


title: dwil_dana_dyak_WB_f_r4.leftover

tag: Sex

value: Female

value: TCTCGCGC-TATAGCCT


title: 21_9h_RG7834

tag: timepoint

tag: dose

tag: transfection

value: HBV


title: Patient_30

source_name: Plasma

value: MALE

tag: neuropathy (yes

tag: cardiopathy (yes

tag: diabetes (yes

tag: gaa repetitions (allele1/allele2)


title: dwil_dana_dyak_TX_m_r4.leftover

source_name: thorax without digestive system

tag: flybase species id

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: developmental stage

tag: tissue

value: thorax without digestive system

value: TCCGCGAA-GGCTCTGA


title: Patients_13


title: dwil_dana_dyak_RE_m_r4.leftover

source_name: reproductive system without gonad

value: reproductive system without gonad

tag: age post eclosion (days)

tag: fly culture temperature (oc)

tag: replicate

tag: illumina barcode

value: CGGCTATG-CAGGACGT


title: 20_9h_RG7834

tag: treatment


title: 18_9h_NT

value: vehicle


title: 19_9h_RG7834


title: dwil_dana_dyak_RE_f_r4.leftover

tag: Sex

value: TCCGCGAA-CAGGACGT

tag: plate and well id

tag: ercc infomation


title: dwil_dana_dyak_HD_m_r4.leftover

source_name: head

value: adult

value: head

value: TCTCGCGC-ATAGAGGC


title: Patient_29

tag: age


title: 31_12h_RG7834

tag: timepoint

tag: dose

tag: transfection


title: 17_9h_NT


title: Patient_17

tag: neuropathy (yes

tag: cardiopathy (yes

tag: diabetes (yes

tag: gaa repetitions (allele1/allele2)


title: dwil_dana_dyak_HD_f_r4.leftover

tag: flybase species id

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: developmental stage

tag: tissue


title: 16_9h_NT


title: dwil_dana_dyak_GO_m_r4.leftover

source_name: gonad

value: gonad

value: Male

tag: age post eclosion (days)

tag: fly culture temperature (oc)

tag: replicate

tag: illumina barcode

value: TCTCGCGC-TAATCTTA


title: Patient_1

tag: Sex


title: Patient_18

value: FEMALE

tag: age


title: Patient_5


title: Patient_14


title: Patient_6


title: dwil_dana_dyak_DG_m_r4.leftover

source_name: digestive plus excretory system

value: digestive plus excretory system

value: TCCGCGAA-GTACTGAC

tag: plate and well id

tag: ercc infomation

value: without ERCC


title: dwil_dana_dyak_TX_f_r4.leftover

value: Female

value: AGCGATAG-GGCTCTGA


title: 08_6h_RG7834

tag: timepoint

tag: treatment

tag: dose

tag: transfection

value: HBV


title: dwil_dana_dyak_GO_f_r4.leftover

value: TCCGCGAA-TAATCTTA


title: Patient_4

value: MALE

tag: neuropathy (yes

tag: cardiopathy (yes

tag: diabetes (yes

tag: gaa repetitions (allele1/allele2)


title: Patient_2


title: dwil_dana_dyak_AC_m_r4.leftover

source_name: abdomen without digestive or reproductive system

tag: flybase species id

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: developmental stage

tag: tissue

value: TCTCGCGC-AGGCGAAG


title: 07_6h_RG7834


title: Patient_41


title: 06_6h_NT

value: vehicle


title: Patient_42


title: 04_6h_NT


title: Patient_25


title: dwil_dana_dyak_AC_f_r4.leftover

value: adult

value: abdomen without digestive or reproductive system

tag: age post eclosion (days)

tag: fly culture temperature (oc)

tag: replicate

tag: illumina barcode


title: Patient_38

tag: Sex

tag: age


title: orgR_dmoj_dper_WB_f_r4.leftover

description: mixed-species [D. melanogaster (Oregon-R), D. mojavensis, and D. persimilis] RNA preparation

organism:
Drosophila melanogaster
Drosophila mojavensis
Drosophila persimilis

value: whole body

value: GAATTCGT-TATAGCCT

tag: plate and well id

tag: ercc infomation


title: 09_6h_RG7834

tag: timepoint

tag: treatment

tag: dose

tag: transfection


title: dper_WB_m_r4

organism: Drosophila persimilis

value: Male

value: CGCTCATT-TATAGCCT


title: Patient_27

value: FEMALE

tag: neuropathy (yes

tag: cardiopathy (yes

tag: diabetes (yes

tag: gaa repetitions (allele1/allele2)


title: dper_WB_f_r4

tag: flybase species id

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: developmental stage

tag: tissue


title: orgR_dmoj_dper_TX_m_r4.leftover

value: thorax without digestive system

tag: age post eclosion (days)

tag: fly culture temperature (oc)

tag: replicate

tag: illumina barcode

value: ATTACTCG-CCTATCCT


title: dwil_dana_dyak_DG_f_r4.leftover

value: digestive plus excretory system

tag: Sex

value: TCCGCGAA-GTACTGAC

tag: plate and well id

tag: ercc infomation

value: without ERCC


title: orgR_dmoj_dper_TX_f_r4.leftover

value: Female

value: GAATTCGT-CCTATCCT


title: orgR_dmoj_dper_RE_m_r4.leftover

source_name: reproductive system without gonad and genitalia; reproductive system without gonad

value: TCCGGAGA-TAATCTTA


title: dper_TX_f_r4


title: orgR_dmoj_dper_RE_f_r4.leftover

value: reproductive system without gonad and genitalia; reproductive system without gonad

value: CTGAAGCT-TAATCTTA


title: dper_RE_m_r4

value: adult

value: reproductive system without gonad


title: dper_RE_f_r4


title: orgR_dmoj_dper_HD_m_r4.leftover

value: head

value: TCCGGAGA-ATAGAGGC


title: dper_HD_m_r4

value: Male


title: dper_GO_m_r4

value: gonad

value: ATTACTCG-AGGCGAAG


title: orgR_dmoj_dper_GO_m_r4.leftover


title: orgR_dmoj_dper_WB_m_r4.leftover

value: whole body

value: CGCTCATT-TATAGCCT


title: dper_DG_m_r4

value: digestive plus excretory system

value: ATTACTCG-GTACTGAC


title: orgR_dmoj_dper_GO_f_r4.leftover

value: CTGAAGCT-AGGCGAAG

value: without ERCC


title: dper_HD_f_r4

value: Female

value: TAATGCGC-ATAGAGGC


title: orgR_dmoj_dper_HD_f_r4.leftover


title: orgR_dmoj_dper_DG_m_r4.leftover


title: dper_DG_f_r4

value: CTGAAGCT-GTACTGAC


title: dper_GO_f_r4


title: dper_TX_m_r4

value: thorax without digestive system

value: ATTACTCG-CCTATCCT


title: orgR_dmoj_dper_DG_f_r4.leftover

value: adult


title: orgR_dmoj_dper_AC_m_r4.leftover

value: abdomen without digestive or reproductive system

value: TCCGGAGA-GGCTCTGA


title: dper_AC_m_r4

value: Male


title: orgR_dmoj_dper_AC_f_r4.leftover

value: GAATTCGT-GGCTCTGA


title: dper_AC_f_r4


title: s02_170602_T6E_shMafB_H3K27ac_27656648_S2

status: Public on Oct 17 2017

city: Philadelphia

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

department: Pathology

institute: University of Pennsylvania

data_processing:
bcl2fastq for creation of fastq files
trimming adaptors with trim_galore
alignment with bwa aln
removing unmapped, reads not maped on propare pair, and low quality reads
remove black list and duplicate reads
Genome_build: GRCm38
Supplementary_files_format_and_content: bigwig

source_name: T6E cell line

growth_protocol: T6E cells (Pear et al., 1996) were grown in RPMI 1640 (Corning cellgro) supplemented with penicillin/streptomycin, 20% fetal bovine serum, 2mM L-glutamine,  nonessential amino acids, 1 mM sodium pyruvate, and 5 uM 2-mercaptoethanol under standard culture conditions and were maintained in the culture until reaching passage 10.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10min and fixation was quenched with 0.125M glycin for 5min, fixed cells were washed with PBS and nuclear extracts were lysed and DNA was sonicated to 200- 400 bp fragments. Antibodies were incubated with lysates overnight at 4℃. Antibody-chromatin complexes were captured with protein G–conjugated beads, washed, and eluted. After RNase (37℃) and proteinase K (56℃) treatments, cross-links were reversed overnight and DNA was purified using Qiagen PCR purification kit.
Libraries were prepared using NEBNext® Ultra II DNA Library Prep Kit

treatment_protocol: T6E cells were retrovirally transduced with either MigR1-scrambled shRNA or MigR1-MafB shRNA and were sorted for expression of GFP at day3 and were fixed for ChIP assay.

tag: cell line

tag: transduction

value: MafB shRNA

tag: condition

value: knockdown

tag: chip andibody

value: ab4729, Abcam


title: s01_170602_T6E_shCtrl_H3K27ac_27656648_S1

value: scrambled shRNA

value: wildtype


title: 05_6h_NT

source_name: HepRG cells

tag: timepoint

tag: treatment

value: vehicle

tag: dose

tag: transfection

value: HBV


title: Flag-empty_1_RNA_seq

city: Seoul

first: Ui-Hyun

last: Park

address: 209 Neungdong-ro Gwangjin-gu

department: Division of Integrative Bioscience and Biotechnology

institute: Sejong Univ.

data_processing:
Library prep: TruSeq RNA Sample Prep Kit v2 for mRNA prep
Sequencing: RNA samples were transferred to Macrogen (Seoul, Korea) for the preparation of mRNA-seq library, sequencing of library, and isolation of differentially expressed genes (DEG)
Genome_build: mm10

source_name: 3T3-L1 cells

growth_protocol: Murine 3T3-L1 preadipocytes were incubated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% heat inactivated bovine serum (BS) and antibiotic-antimycotic mix

extract_protocol:
Total RNA was extracted from 3T3-L1 cells using Trizol reagent after differentiation for 8 days.
RNA samples were transferred to Macrogen (Seoul, Korea) for the preparation of mRNA-seq library, sequencing of library, and isolation of differentially expressed genes (DEG)

treatment_protocol: 3T3-L1 cells  were grown to 100% confluency and then were cultured in adipogenesis initiation media containing 5 μg/ml insulin, 1 μg/ml dexamethasone, 0.5 mM IBMX, with 5 μM Rosiglitazone in 10% FBS DMEM. At day 2 (on day 0), 10% FBS DMEM media containing 5 μg/ml insulin were added every 2 days.

tag: adipognesis

value: differentiation for 8 days

tag: cell type

value: preadipocyte

tag: stable cell line

value: Stable expression of Flag-empty


title: Flag-CAC1_1_RNA_seq

value: Stable expression of Flag-CACUL1


title: sh-Luci_1_RNA_seq

value: Stable expression of Sh-Luciferase


title: 140409_I266_FCC4E1TACXX_L8_RHUMuweNWURBAPEI-115

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

institute: Regeneron

data_processing:
Alignment STAR version STAR_2.3.1d
Sequenced reads were filtered for low-quality sequence and the presence of 'N's, then mapped to hg19 whole genome using star STAR_2.3.1d
Gene counts were calculated by using HTSeq count
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including the raw gene counts for all the detected genes in the Tcells and Monocytes

source_name: Monocytes

extract_protocol:
Paxgene RNA
GlobinClear Globin transcript reduction followed by Illumina mRNA-Seq

value: Monocytes

tag: stimulation

value: mTb

tag: subjectid

value: IC

tag: bin

tag: group

value: case

tag: age

tag: gender

value: female

tag: previousdiagnosisoftb

value: No

tag: tst

tag: qft


title: 140409_I266_FCC4E1TACXX_L8_RHUMuweNXYRAAPEI-95

value: male


title: 140409_I266_FCC4E1TACXX_L8_RHUMuweNZLRAAPEI-15

value: unstim

value: control


title: 140409_I266_FCC4E1TACXX_L8_RHUMuweNYYRAAPEI-84


title: 140409_I266_FCC4E1TACXX_L8_RHUMuweNYURAAPEI-53

value: positive


title: 140409_I266_FCC4E1TACXX_L8_RHUMuweNYVRAAPEI-56


title: 140409_I266_FCC4E1TACXX_L8_RHUMuweNYWRAAPEI-74


title: 140409_I266_FCC4E1TACXX_L8_RHUMuweNYJRAAPEI-19


title: 140409_I266_FCC4E1TACXX_L8_RHUMuweNZMRAAPEI-16


title: 140409_I266_FCC4E1TACXX_L8_RHUMuweNZTRAAPEI-36


title: 140409_I266_FCC4E1TACXX_L8_RHUMuweNWVRAAPEI-122


title: 140409_I266_FCC4E1TACXX_L7_RHUMuweNXWRAAPEI-90


title: 140409_I266_FCC4E1TACXX_L8_RHUMuweNZRRAAPEI-30


title: 140409_I266_FCC4E1TACXX_L7_RHUMuweNZPRAAPEI-19


title: 140409_I266_FCC4E1TACXX_L7_RHUMuweNZKRAAPEI-14


title: 140409_I266_FCC4E1TACXX_L7_RHUMuweNYARAAPEI-115


title: 140409_I266_FCC4E1TACXX_L7_RHUMuweNAACRAAPEI-74

value: Yes


title: 140409_I266_FCC4E1TACXX_L7_RHUMuweNSIRAAPEI-122

source_name: T cells

value: Tcells


title: 140409_I266_FCC4E1TACXX_L7_RHUMuweNZYRAAPEI-46


title: 140409_I266_FCC4E1TACXX_L7_RHUMuweNYNRAAPEI-36


title: 140409_I266_FCC4E1TACXX_L7_RHUMuweNZSRAAPEI-33


title: sh-CAC1_1_RNA_seq

value: differentiation for 8 days

value: Stable expression of sh-CACUL1


title: 140409_I266_FCC4E1TACXX_L7_RHUMuweNZIRAAPEI-129


title: Control_33

tag: Sex

value: FEMALE

tag: neuropathy (yes

tag: cardiopathy (yes

tag: diabetes (yes

tag: gaa repetitions (allele1/allele2)

value: Not referred to


title: 140409_I266_FCC4E1TACXX_L8_RHUMuweNSJRAAPEI-129

tag: timepoint


title: 140409_I266_FCC4E1TACXX_L7_RHUMuweNYRRAAPEI-45

tag: cell type


title: 140409_I266_FCC4E1TACXX_L7_RHUMuweNYQRAAPEI-44


title: 140409_I266_FCC4E1TACXX_L6_RHUMuweNAAHRAAPEI-89


title: 140409_I266_FCC4E1TACXX_L6_RHUMuweNRKRBAPEI-90