title: E8 rep3

city: Suita

first: Kouichi

last: Hasegawa

state: Osaka

address: 6F Techno Alliance Bldg. 2-8 Yamadaoka

department: StemRIM Institute of Regeneration-Inducing Medicine

institute: Osaka University

data_processing:
HCS version 2.0.12.0 and RTA version 1.17.21.3 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and  mapped to hg19/GRCh37 whole genome using QuasR  with parameters -m 1 --best --strata -v 2
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: embryonic stem cells

growth_protocol: KhES-1human ES cells in Essential 8 (E8) culture media on 0.5µg/cm2 Laminin-E8 fragment-coated dishes.

extract_protocol:
Total RNAs were purified with RNAeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: embryonic stem cells

tag: cell line

tag: medium


title: Line4_control ASO (4VB_BC_D702_D506)

status: Public on Sep 12 2017

type: SRA

city: La Jolla

first: Cristiano

last: Sacchetti

state: CA

address: 9420 Athena Circle

country: USA

institute: La Jolla Institute for Allergy and Immunology

library_source: transcriptomic

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the human hg19 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: hg19
Supplementary_files_format_and_content: count matrix with rows as genes and columns as samples

molecule: total RNA

organism: Homo sapiens

source_name: Dermal fibroblasts isolated from healthy human skin biopsies

growth_protocol: 150,000 dermal fibroblasts for each donor were seeded on a 6-well plate in triplicate for each ASO treatment. Complete DMEM with 10% FBS used as media.

extract_protocol:
Cells were washed in ice-cold DPBS to stop RNA transcription. Total RNA was extracted with a RNeasy Micro kit from QIAGEN. 500 nanograms of total RNA was used to generate libraries.
3 NHDF lines were plated in triplicate, incubated with control or PTP4A1 ASOs and serum-starved for 24 hours prior the experiment. RNA was extracted using micro RNeasy kits from Qiagen and 500 ng of total RNA for each condition were used to generate mRNA-focused libraries on a Biomek FXP automation platform from Beckman Coulter (Carlsbad, CA) with the TruSeq Stranded mRNA HT Sample Prep Kit from Illumina (San Diego, CA).

treatment_protocol: After 24 hours, cells were incubated 7 days with 2.5 micromolar PTP4A1 or control ASOs. Media and ASOs were replaced after 3 days. After 6 days of ASOs treatment cell were incubated in starvation media (DMEM complete with 0.1% FBS and ASOs). 24 hours later cell were lysed.

tag: treatment

value: control ASO

value: NHDF Line 4


title: Line4_control ASO (4VC_BC_D702_D507)

value: Dermal fibroblasts isolated from healthy human skin biopsies


title: Line2_anti-PTP4A1 ASO (APB_BC_D701_D505)

value: anti-PTP4A1 ASO

value: NHDF Line 2


title: Line4_control ASO (4VA_BC_D702_D505)


title: Line4_anti-PTP4A1 ASO (4PB_BC_D703_D501)


title: 12C_72_plus_3_off

city: Heidelberg

first: Tatsiana

last: Ryl

address: Im Neuenheimer Feld 280

department: Theoretical Systems Biology

country: Germany

institute: German Cancer Research Center

data_processing:
RTA 1.17.21.3
Raw reads were aligned to hg19 genome by STAR (v2.4.0h1)
counts of genes were generated by Htseq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with counts for each samples

molecule: polyA RNA

source_name: cell line

growth_protocol: MYCN-high (without doxycycline) and MCN-low cells (with doxycycline) were grown in RPMI1640 media supplemented with 100 U/ml Penicillin and 10% FCS in 10cm2 dishes.

extract_protocol:
RNA was extracted from 106 cells using RNeasy mini kit (Qiagen) with a separate step for DNAse I digestion (Qiagen). ERCC Spike-in control mix-1 (Life technologies) was added to each sample prior to processing (1 μl of a 1:10 dilution of mix-1). RNA from each sample was processed using the RiboGold kit (Epicentre) to remove rRNA
The rRNA-depleted was used to prepare libraries for sequencing using ScriptSeq Complete Gold Kit low input  (Epicenter).

treatment_protocol: Cells were treated with 0.1µg/ml Doxorubicin for 72 hours. After treatment the medium with DOX was washed out and replaced with a normal growth medium.

tag: time

tag: mycn level

value: mycnLow


title: Line4_anti-PTP4A1 ASO (4PA_BC_D702_D508)


title: 13B_72_plus_8_on

value: mycnHigh


title: Line4_anti-PTP4A1 ASO (4PC_BC_D703_D502)


title: Line3_control ASO (3VC_BC_D702_D501)

value: NHDF Line 3


title: 11C_72_plus_3_on


title: 8C_72h_Doxo_off


title: 10B_72_plus_3_off


title: Line3_control ASO (3VB_BC_D701_D508)


title: 9B_72_plus_3_on


title: 7C_72h_Doxo_on


title: Line3_control ASO (3VA_BC_D701_D507)


title: 6B_72h_Doxo_off


title: Line3_anti-PTP4A1 ASO (3PC_BC_D702_D504)


title: 5B_72h_Doxo_on


title: Line3_anti-PTP4A1 ASO (3PB_BC_D702_D503)


title: 4C_control_off


title: Line3_anti-PTP4A1 ASO (3PA_BC_D702_D502)


title: Line2_control ASO (2VC_BC_D701_D503)


title: 2B_control_off


title: 1B_control_on


title: Line2_control ASO (2VB_BC_D701_D502)


title: 3C_control_on


title: Line2_control ASO (2VA_BC_D701_D501)


title: 22h_Tet-_ACTGAT_L006

first: Chunxuan

last: Shao

data_processing:
RTA 1.17.21.3
Raw reads were aligned to hg19 genome by Tophat (v2.0.5)
counts of genes were generated by Htseq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with counts for each samples

extract_protocol:
RNA was extracted from 10e6 cells using RNeasy mini kit (Qiagen) with a separate step for DNAse I digestion (Qiagen). ERCC Spike-in control mix-1 (Life technologies) was added to each sample prior to processing (1 μl of a 1:10 dilution of mix-1). RNA from each sample was processed using the RiboGold kit (Epicentre) to remove rRNA.
rRNA-depleted RNA was used to prepare libraries with the Ultra directional RNA library prep kit for Illumina (New England Bioscience) according to manufacturer's instructions.

value: IMR5/75 neuroblastoma cells with tetracycline-inducible MYCN shRNA

tag: time point

tag: tet treatment

value: minus


title: 46_CCGTCC_L004

value: plus


title: 20h_Tet-_GTTTCG_L006


title: male control 2

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

description: male control 2

data_processing:
Illumina Casava1.7 software used for basecalling.
Alignment was performed with STAR 2.5.2b against the mm10 mouse transcriptome
feature quantification with HTSeq 0.9.1
Differential expression analysis was performed on the mapped reads using the DESeq package in R.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: tab-delimited text containing feature counts, Excel workbook containing differential expression results

organism: Mus musculus

source_name: quadriceps

extract_protocol:
Quadriceps were removed  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: quadriceps

tag: age

value: 20 weeks

tag: genotype

value: wildtype

tag: Sex

value: male


title: Line2_anti-PTP4A1 ASO (2PA_BC_D701_D504)


title: 44_GATCAG_L004


title: 42_ACAGTG_L004


title: male MERKO 3

description: male MERKO 3

value: muscle-specific Er_alpha-/-


title: male MERKO 2

description: male MERKO 2


title: male control 3

description: male control 3


title: Line2_anti-PTP4A1 ASO (2PC_BC_D701_D506)


title: 40_CGATGT_L004


title: 18h_Tet-_GTCCGC_L006


title: male control 1

description: male control 1


title: 14h_Tet-_TGACCA_L006


title: 10h_Tet-_GCCAAT_L005


title: 12h_Tet_plus__ATGTCA_L005


title: 12h_Tet-_GATCAG_L005


title: male MERKO 1

description: male MERKO 1


title: 10h_Tet_plus__CAGATC_L005


title: 14h_Tet_plus__ACAGTG_L006


title: 8h_Tet-_CGATGT_L005


title: 8h_Tet_plus__TTAGGC_L005


title: 6h_Tet-_GATCAG_L004


title: 6h_Tet_plus__GTGGCC_L004


title: 18h_Thy-0h-_Tet_plus__TGACCA_L004


title: 16h_Tet-_CAGATC_L006


title: 3h_Tet_plus__CAGATC_L004


title: 3h_Tet-_ACAGTG_L004


title: c9_PGCLC_0R3B_1

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: 3'-RNAseq amplified from 1ng RNA

data_processing:
Adaptor removal, mapping and abundance measurement were performed as described in GSE63266. All SOLiD reads were processed by cutadapt v1.11 with the "-c -e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -g CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -a AAAAAAAAAAAAAAAAAAAA" option. Illuina reads were processed by cutadapt v1.11 with the "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT" option.
Reads with 30 bases and longer were mapped onto mouse mm10 genome and reference genes using  tophat v1.4.1/bowtie 1.0.1 with the "--no-coverage-search" option. Abundance measurement was performed using cufflinks-2.2.0 using the “--compatible-hits-norm”, “--no-length-correction” and “--library-type fr-secondstrand” options and mm10 reference gene annotations with extended TTSs.
Abundance of ERCC spike-in transcripts were counted separately from bam files produced by tophat.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each Sample

source_name: PGC like cells

growth_protocol:
The ESC culture and PGCLC induction were performed as described previously with a few modifications.  ESCs were maintained under a 2i+LIF condition on a dish coated with poly-L-ornithine (0.01%; Sigma) and Laminin (300 ng/ml; BD Biosciences) or on mouse embryonic fibroblasts (MEF).  EpiLCs were induced by plating 1.0 × 105 ESCs on wells of a 12-well plate coated with human plasma fibronectin (16.7 ug/ml; Millipore) in N2B27 medium containing activin A (20 ng/ml; Peprotech), bFGF (12 ng/ml; Life Technology) and KSR (1%; Thermo Fisher).  42-46 hrs after the EpiLC induction, PGCLCs were induced under a floating condition by plating 2.0 × 103 EpiLCs in wells of a low-cell-binding 96-well Lipidure-coat plate (Thermo Fisher) in 200 ml of GK15 medium with BMP4 (500 ng/ml; R&D Systems), LIF (1000 u/ml; Merck Millipore), SCF (100 ng/ml; R&D Systems), and EGF (50 ng/ml; R&D Systems).  The GK15 medium was composed of GMEM (Thermo Fisher) with 15% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin and 2 mM L-glutamine. The PGC/PGCLC culture was performed as described previously.  Briefly, d4 PGCLC aggregates were collected, washed with PBS, and dissociated with TrypLE Express (Thermo Fisher).  They were then washed with DMEM+0.1%BSA (Gibco) and filtered by a cell strainer (BD Bioscience) to remove large clumps of cells.  Next, the samples were centrifuged, resuspended in 0.1% BSA-PBS and sorted by FACS (Aria lll; BD Bioscience).  The BV (+) cells were plated onto mitomycin C (MMC)-treated m220 feeder cells in the PGC/PGCLC-expansion medium.  The PGC/PGCLC-expansion medium was composed of GMEM with 10% KSR, 2.5% FBS, 0.1 mM NEAA, 1 mM sodium pyruvate, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 10 mM Forskolin and 10 mM Rolipram.  The entire medium was changed every 2 days from c3.  The cytokines/chemicals for the induction of the female fate were provided from c3 to the end of the culture.  The concentrations of RA and BMP used were 100 nM and 300 ng/mL, respectively, unless otherwise specified.
To obtain PGCs and male and female germ cells, ICR female mice were mated with Dppa3-EGFP male mice or Ddx4-RFP male mice.

extract_protocol:
Total RNAs from collected cells were extracted with an RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
cDNA synthesis and amplification from isolated RNAs/single cells were perfomed essentially as reported in [Kurimoto, K.et.al., Nucleic Acids Research, 34(5), e42.]. Library constructions for NextSeq500 (illumina) System were performed according to the procedure described in [Nakamura et.al., Nuceic Acids Res. (2015)] with a few modifications.

treatment_protocol: E9.5 to E13.5 germ cells were sorted as GFP(+) cells by FACS, E14.5 and E15.5 germ cells as RFP(+) cells, d4PGCLCs as BV(+) cells, and cultured PGCLCs as SC(+) cells.

value: germ cells derived from ESCs

tag: developmental stage

value: culture day9

value: Prdm1-mVenusTg/0; Dppa3-ECFPTg/0


title: 22_CCGTCC_L008


title: DH55 Root expressing acdS under RolD promoter after salt treatment rep3

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

data_processing:
The tagged libraries were sequenced using a HiSeq 2500 (Illumina Inc.).
Trimmomatic (Bolger et al., 2014) was used to discard low-quality reads, trim adaptor sequences, trim low quality nucleotides at the beginning or end of the read (PHRED33 quality score of less than 3), and discard short reads (under 21 nt).
The retained high-quality reads were mapped to the C. sativa reference genome and transcripts available in the NCBI C. sativa release 100 (JFZQ00000000.1, Kagale et al., 2014) using STAR (Dobin et al, 2012)
For each gene, normailization for library size was performed by dividing the counts by the library size following the method described by Anders and Huber, 2010 to yield CPM
Further normalization was performed using DESeq to approximate a negative binomial distribution.
The differential expression analysis of digital gene expression data software (edgeR) was used to calculate expression changes between libraries (Chen et al., 2014).  The Biological Coefficient of Variation (BCV) value was set to 2 according to the software's instructions.  Expression changes were said to be significant if the multiple test corrected p-value and the false discovery rate (FDR) were ≤ 0.05 and the absolute value of  log 2 CPM was higher than 1.
Genome_build: C. sativa release 100 (JFZQ00000000.1)
Supplementary_files_format_and_content: MS Excel spreadsheet with the genes as rows and the samples as columns.  Each replicate is it's own column.

organism: Camelina sativa

source_name: Root

growth_protocol: Camelina sativa cv. DH55 seeds were sown in soil-less potting mixture (Stringham, 1971) in 10 x 10 x 8 cm square pots.  Plants were grown in a controlled growth chamber (16 h light/8 h dark, 20/17°C) supplemented with halogen lights.   Bacteria were cultured for 24 h in tryptic soy broth (TSB) containing 100 μg ml−1 ampicillin for wild-type strains or 100 μg ml−1 ampicillin and 10 μg ml−1 tetracycline for the acdS mutant strains (Ali et al., 2012). Bacterial cultures were centrifuged at 4,000 x g and re-suspended to an OD600nm = 0.50 ± 0.02 in 0.03 M MgSO4.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen Inc.)
cDNA libraries were prepared using the TruSeq Stranded mRNA and Total RNA Library Prep kits with TruSeq LT indexed adaptors (Illumina Inc.).

treatment_protocol: Salt Treatment:  NaCl solutions at 192 mM were prepared to obtain a solution with an electrical conductivitie (EC) of 15 dSm-1 at 20°C. 50 ml of tap water (EC 1,248 µSm-1) was applied daily to each pot and replaced with 50 ml of saline solution (EC 15 dSm-1) 7 days after sowing.  The accumulation of salt in the pots was controlled by draining and the EC of the drained water was measured weekly.  Bacterial Treatment: Soil was inoculated with either 2 ml of PGPB or 2 ml of 0.03 M MgSO4 (control and transgenic plants) at the time of sowing and again one week after sowing.  Root matter was harvested 21 days after the initial salt treatment just before the plants began to bolt.

tag: infraspecific name

value: 28 days after planting


title: 20h_Tet-_GGCTAC_L003


title: 22h_Tet-_CTTGTA_L003


title: DH55 Root after 8R6 exposure and salt treatment rep1


title: DH55 Root after 8R6 exposure and salt treatment rep3


title: DH55 Root after salt treatment rep3


title: 14h_Tet-_ATCACG_L003


title: DH55 Root expressing acdS under 35S promoter after salt treatment rep3


title: 16_ACAGTG_L008


title: 16h_Tet-_ACTTGA_L003


title: DH55 Root expressing acdS under 35S promoter after salt treatment rep1


title: DH55 Root expressing acdS under RolD promoter after salt treatment rep1


title: 18_TAGCTT_L008


title: DH55 Root after 8R6 exposure and salt treatment rep2


title: 14h_Tet_plus__GCCAAT_L003


title: DH55 Root after salt treatment rep2


title: 18h_Thy-0h-_Tet-_CGATGT_L004


title: DH55 Root after salt treatment rep1


title: 12h_Tet_plus__CTTGTA_L002


title: 10h_Tet_plus__GCCAAT_L002


title: 10h_Tet-_ACAGTG_L002


title: 20_GGCTAC_L008


title: 8h_Tet-_CGATGT_L002


title: H3K79me3_WT_2

city: Baltimore

first: Wahid

middle: A

last: Mulla

state: MD

address: 855 North Wolfe Street

institute: Johns Hopkins University

library_source: genomic

data_processing:
Reads were mapped to the sacCer3 reference genome using bowtie with parameters: --best –strata -v2 -m 1
Data were filtered
Peaks were called by MACS2 using default settings (Zhang, Liu et al. 2008), mapped to the closest gene, and kept only if they occurred within 600 bases of the transcription start site.
Peak scores, defined as the -log10 transformed q-values, normalized to chromosome copy number, were converted to Z-scores for comparison across strains and plotted as the difference between disome X and WT haploid strains
Genome_build: sacCer3
Supplementary_files_format_and_content: Peak scores, defined as the -log10 transformed q-values, normalized to chromosome copy number, were converted to Z-scores for comparison across strains and plotted as the difference between disome X and WT haploid strains

molecule: genomic DNA

organism: Saccharomyces cerevisiae S288C

source_name: Yeast cells

extract_protocol:
Chromatin immunoprecipitation was performed as previously described (Aparicio, Geisberg et al. 2005). Briefly, yeast cells were grown in 500 ml of SC medium to an OD600 of 0.8–0.9 and were crosslinked with 1% formaldehyde (Sigma-Aldrich, Saint Louis, MO) for 20 minutes before the chromatin was extracted. The chromatin was sonicated using Bioruptor (Diagenode, Denville, NJ) at the high setting for ten cycles of 30 sec on/off to yield an average DNA fragment size of 500 bp. Chromatin extracts were diluted in immunoprecipitation (IP) buffer and centrifuged to pellet debris; the resulting supernatant, containing the chromatin solution, was aliquoted for immunoprecipitation as follows. Chromatin was first incubated overnight with antibody at 4°C, then with Dynabeads® protein G beads (Thermo Fisher Scientific, Waltham, MA). Beads were washed several times, and DNA was recovered in elution buffer (1% SDS, 0.1 M NaHCO3). Crosslinking was reversed by incubating samples at 65°C overnight, followed by protease treatment, phenol/chloroform extraction, and ethanol precipitation of the recovered DNA.
Sequence libraries were constructed and validated using the Illumina library protocol and sequenced using the Illumina HiSeq 2000 system as 50 bp single-end reads.

value: wt

tag: replicate

value: Second

tag: chip antibody

value: anti-H3K79me3, Abcam


title: DH55 Root expressing acdS under 35S promoter after salt treatment rep2


title: H3K4me3_Disome10_2

value: disome X

value: anti-H3K4me3, EMD Millipore


title: NAB_WT_2


title: H3K4me3_WT_2


title: NAB_Disome10_2


title: 6h_Tet-_CAGATC_L008

value: IMR5/75 neuroblastoma cells with tetracycline-inducible MYCN shRNA


title: H3K79me3_WT_1

value: First


title: 3h_Tet-_ACAGTG_L008

value: minus


title: DH55 Root expressing acdS under RolD promoter after salt treatment rep2


title: H3K79me3_Disome10_1


title: Foxf1fl/+ EC RNAseq

city: Cincinnati

first: Craig

middle: Steven

last: Bolte

state: Ohio

address: 3333 Burnett Ave

department: Center for Lung Regenerative Medicine

institute: Cincinnati Children's Research Foundation

description:
BioWardrobe ID: 4062
processed data file: Foxf1 RNA Seq updated.xlsx
RNA-Seq analysis of endothelial cells from regenerating control lungs

data_processing:
ChIP-Seq data analysis was performed using the BioWardrobe (PMID: 26248465 ). Briefly, for ChIP-Seq fastq files from Illumina pipeline were aligned by bowtie (version 1.1.1 PMID: 19261174) with maximum one mismatch. Only unique alignments were used.   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. To visualize the data it were uploaded to UCSC genome browser and fragment coverage were used with estimated fragment size determined by MACS2.
RNA-Seq analysis : Differentially expressed genes were identified using DESeq
Genome_build: mm10
Supplementary_files_format_and_content: For ChIP-seq: the tab separated file lists the islands identified by MACS2.
Supplementary_files_format_and_content: For RNA-seq excel file lists FPKM  for genes in wt and FoxF1het.

organism: Mus

growth_protocol: ChIPseq: MFLM-91U cells were maintained in DMEM + 10% FBS; RNAseq: FACS-sorted endothelial cells (CD45-CD31+CD326-) from PDGFb-iCre Foxf1fl/+ and Foxf1fl/+ cells 4 days after pneumonectomy surgery

extract_protocol:
ChIPseq: Formaldehyde cross-linked chromatin was sonicated using Covaris S220 to 200-300 bp and ChIP was performed using SX-8G IP-STAR robot (Diagenode) using anti-FOXF1 antibody (R&D Systems, AF4798, lot # CAHH0316081).; RNAseq: total RNA was extracted from FACS-sorted endothelial cells using the Qiagen QIAquick RNA isolation kit.
Chipmentation procedure was used to create ChIP-Seq libraries PMID:    26280331
RNAseq:Total RNA was amplified using the Ovation RNA-Seq System v2 (NuGEN) according to the manufacturer’s protocol. The libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies). 1 ng of cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Amplicon Tagment Mix), incubating at 55C for 10 min. NT Buffer was then added to neutralize the samples. RNA-Seq libraries were prepared by PCR with the Nextera PCR Master Mix, and 2 Nextera Indexes (N7XX, and N5XX) according to the following program: one cycle of 72C for 3min, one cycle of 98C for 30s, 12 cycles of 95C for 10s, 55C for 30s, and 72C for 1min, and one cycle of 72C for 5min.  The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocol.

treatment_protocol: ChiPseq performed on untreated, non-conlfuent cells; RNAseq was performed on cells isolated 4 days after pneumonectomy surgery.

tag: strain background

tag: genotype/variation

value: control

value: lungs

tag: cell type


title: PDGFb-Foxf1fl/+ EC RNAseq

description:
BioWardrobe ID: 4077
processed data file: Foxf1 RNA Seq updated.xlsx
RNA-Seq analysis of endothelial cells from regenerating Foxf1-deficient lungs

source_name: FACS-sorted endothelial cells (CD45-CD31+CD326-)


title: H3K4me3_WT_1


title: 3h_Tet_plus__GCCAAT_L008

tag: cell line

value: plus


title: 18h_Tet-_TAGCTT_L003


title: 18_h_Thy_-0h-_Tet_plus__TGACCA_L008


title: FOXF1 ChIPseq

description:
BioWardrobe ID: 2738
FoxF1 ChIP-Seq in murine-derived lung mesenchymal cell line

source_name: MFLM-91U cell line

value: FVB/N

tag: chip-seq antibody

value: FoxF1 (R&D Systems, AF4798, lot # CAHH0316081)


title: NAB_WT_1


title: H3K79me3_Disome10_2


title: 15110402-tub-uBcd-NC14-12

status: Public on Sep 11 2017

city: Evanston

first: Shelby

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

description:
uniform Bcd (high) ATAC-seq
processed data file:
tub-uBcd.open.10.bp.cpm.bc.wig.gz
tub-uBcd.nucleoatac_signal.smooth.bedgraph.gz
tub-uBcd.nucmap_combined.bed.txt.gz

data_processing:
library Strategy: ATAC-seq
ChIP-seq: Sequenced reads were barcode-split.
Barcode-split reads were mapped to the Drosophila melanogaster genome (dm3) using Bowtie2 with default parameters.
Peaks were called on the alignments in .bam format for each replicate of the wild-type and uniform Bcd samples using MACS2.
Top reproducible peaks were identified by sorting by the -log10(p.value) from MACS2 and using an irreproducibile discovery rate (IDR) of 1%.
Peaks for each genotype were filtered by the ratio of ChIP-seq read counts to ATAC-seq read counts, using a ratio of ATAC/ChIP ≤ 5.4 as the cutoff.
Peaks common to wild-type and uniform Bcd embryos were used as the final peaks list. The peaks are provided as a tab-delimited table with annotations.
BAM formatted files for individual replicates were merged for each genotype. For wild-type, samples C, D, and G were excluded as outliers.
Genome coverage was calculated from the merged BAM files in 10 bp windows across the genome and normalized to counts per million reads.

ATAC-Seq: Sequenced reads were barcode-split and adapters were removed using TrimGalore.
Trimmed reads were mapped to the Drosophila melanogaster genome (dm3) using BWA with default parameters.
Alignments were converted to .bam format, duplicates were marked with Picard MarkDuplicates, and reads were filtered for quality score (>= 30), duplication, and were required to be mapped, properly paired, and non secondary alignments.
Only reads corresponding to chr2L, chr2R, chr3L, chr3R, chr4, and chrX were considered for further analysis.
Paired end read fragments <= 100 bp were considered to have originated from 'open' chromatin. Replicates were pooled, and average coverage over open regions was calculated over 10 bp discrete windows. These data are provided as .wig formatted files in the processed data file deposit.
Peaks were called with Zinba on pooled biological replicates. The peaks are provided as a tab-delimited table with annotations.
Nucleosomes within 2500bp regions flanking the maximum open position as called by Zinba were called using NucleoATAC. Both smoothed nucleosome profiles and dyad position/occupancy scores are provided in the processed data file deposit.
Genome coverage was calculated in 10 bp windows across the genome and normalized to counts per million reads.
Genome_build: dm3
Supplementary_files_format_and_content: ChIP Peaks are provided as a tab-delimited text file with additional logical indexers that indicate categories of peak as determined by analysis. Coverage of reads are provided as .wig files for each genotype.
Supplementary_files_format_and_content: ATAC Peaks are provided as a tab-delimited text file with additional logical indexers that indicate categories of peak as determined by analysis. Coverage of reads originating from open chromatin are provided as .wig files for each genotype. Predicted nucleosome positions are provided in two formats: smoothed nucleosome profiles from NucleoATAC are provided in bedgraph format, and dyad positions and estimated occupancy are provided in a .bed.txt format.

organism: Drosophila melanogaster

source_name: uniform Bcd (high) ATAC-seq

growth_protocol: Adults were allowed to lay eggs on yeasted apple juice agar plates. Adults were between 4 and 12 days old for embryo collection.

extract_protocol:
Embryos were observed under a fluorescent microscope until they reached the desired timepoint. Embryos were dechorionated in 4% bleach for 1 minute, washed extensively with water, and macerated in a small volume of extraction buffer. Nuclear pellets were collected and briefly frozen on dry ice.
Frozen nuclear pellets were thawed and fragmented using the Nextera Tn5 transposase solution (Illumina), 2.5 ul per 10 ul reaction. Fragmentation was for 30 minutes at 37 degrees with shaking. Samples were cleaned up with a Qiagen minelute kit and subjected to limited PCR amplification with barcoded primers.

tag: maternal genetic info.

value: w; {alphaTub75c>GFP-bcd-sqh3'UTR}attP40/+; p{His2Av-GFP} bcd[E1]/bcd[E1]

tag: timepoint

value: NC14+12 minutes

value: embryo

tag: number of embryos


title: 15110401-tub-uBcd-NC14-12


title: 16060604-mtrm-uBcd-NC14-12

description:
uniform Bcd (medium) ATAC-seq
processed data file:
mtrm-uBcd.open.10.bp.cpm.bc.wig.gz
mtrm-uBcd.nucleoatac_signal.smooth.bedgraph.gz
mtrm-uBcd.nucmap_combined.bed.txt.gz

source_name: uniform Bcd (medium) ATAC-seq

value: w; {mtrm>GFP-bcd-sqh3'UTR}attP40/+; p{His2Av-GFP} bcd[E1]/bcd[E1]


title: 16060606-mtrm-uBcd-NC14-12


title: 16060603-mtrm-uBcd-NC14-12


title: 6h_Tet_plus__CTTGTA_L008

tag: time point

tag: tet treatment


title: 15110302-tub-uBcd-NC14-12

tag: tissue


title: NAB_Disome10_1

tag: strain

tag: genotype


title: 16060602-mtrm-uBcd-NC14-12


title: 16060601-mtrm-uBcd-NC14-12


title: H3K4me3_Disome10_1


title: 15110303-tub-uBcd-NC14-12


title: 16051006-bcd-uBcd-NC14-12

description:
uniform Bcd (low) ATAC-seq
processed data file:
bcd-uBcd.open.10.bp.cpm.bc.wig.gz
bcd-uBcd.nucleoatac_signal.smooth.bedgraph.gz
bcd-uBcd.nucmap_combined.bed.txt.gz

source_name: uniform Bcd (low) ATAC-seq

value: w; {bcd>GFP-bcd-sqh3'UTR}attP40/+; p{His2Av-GFP} bcd[E1]/bcd[E1]


title: 16051005-bcd-uBcd-NC14-12


title: 16050903-bcd-uBcd-NC14-12


title: 15110304-tub-uBcd-NC14-12


title: 18_h_Thy_-0h-_Tet-_CGATGT_L008


title: 16051004-bcd-uBcd-NC14-12


title: 16050902-bcd-uBcd-NC14-12


title: 8h_Tet_plus__TGACCA_L002


title: 16033008-zld-NC14-12

description:
zelda germline clone ATAC-seq
processed data file:
zld.open.10.bp.cpm.bc.wig.gz
zld.nucleoatac_signal.smooth.bedgraph.gz
zld.nucmap_combined.bed.txt.gz

source_name: zelda germline clone ATAC-seq

value: w p{His2Av-RFP} zld[294] FRT19A


title: 16050901-bcd-uBcd-NC14-12


title: 16032803-zld-NC14-12


title: 16032802-zld-NC14-12


title: 16032801-zld-NC14-12


title: 15072901--bnt-E-NC14-12

description:
bcd nanos torsolike ATAC-seq
processed data file:

source_name: bcd nanos torsolike ATAC-seq

value: w; p{His2Av-GFP} bcd[E1] nos[L7] tsl[4]/bcd[E1] nos[L7] tsl[4]


title: 15072801--bnt-D-NC14-12


title: 15072603--bnt-C-NC14-12


title: 15072602--bnt-B-NC14-12


title: 15072601--bnt-A-NC14-12


title: 15110201-bcdE1-NC14-12

description:
bcd mutant ATAC-seq
processed data file:
e1.open.10.bp.cpm.bc.wig.gz
bcdE1.nucleoatac_signal.smooth.bedgraph.gz
bcdE1.nucmap_combined.bed.txt.gz

source_name: bcd mutant ATAC-seq

value: w; p{His2Av-GFP} bcd[E1]/bcd[E1]


title: 15110301-bcdE1-NC14-12


title: 15072902--bnt-F-NC14-12


title: 15072704--WT-D-NC14-12

description:
wild type ATAC-seq
processed data file:
wt.open.10.bp.cpm.bc.wig.gz
WT.nucleoatac_signal.smooth.bedgraph.gz
WT.nucmap_combined.bed.txt.gz
Annotated_ATAC_Peaks.gz

source_name: wild type ATAC-seq

value: w; p{His2Av-GFP}


title: 15110101-bcdE1-NC14-12


title: 15073002--WT-F-NC14-12


title: 15073001--WT-E-NC14-12


title: 16032904-zld-NC14-12


title: 15110202-bcdE1-NC14-12


title: 15072702--WT-B-NC14-12


title: 15072701--WT-A-NC14-12


title: GFP-Bcd_bnt_Bcd_ChIP_C

description:
nanos torsolike (graded bcd only) Chromatin Immunoprecipitation
processed data file:
bnt.10bp.cpm.bc.wig.gz

data_processing:
ChIP-seq: Sequenced reads were barcode-split.
Barcode-split reads were mapped to the Drosophila melanogaster genome (dm3) using Bowtie2 with default parameters.
Peaks were called on the alignments in .bam format for each replicate of the wild-type and uniform Bcd samples using MACS2.
Top reproducible peaks were identified by sorting by the -log10(p.value) from MACS2 and using an irreproducibile discovery rate (IDR) of 1%.
Peaks for each genotype were filtered by the ratio of ChIP-seq read counts to ATAC-seq read counts, using a ratio of ATAC/ChIP ≤ 5.4 as the cutoff.
Peaks common to wild-type and uniform Bcd embryos were used as the final peaks list. The peaks are provided as a tab-delimited table with annotations.
BAM formatted files for individual replicates were merged for each genotype. For wild-type, samples C, D, and G were excluded as outliers.
Genome coverage was calculated from the merged BAM files in 10 bp windows across the genome and normalized to counts per million reads.

ATAC-Seq: Sequenced reads were barcode-split and adapters were removed using TrimGalore.
Trimmed reads were mapped to the Drosophila melanogaster genome (dm3) using BWA with default parameters.
Alignments were converted to .bam format, duplicates were marked with Picard MarkDuplicates, and reads were filtered for quality score (>= 30), duplication, and were required to be mapped, properly paired, and non secondary alignments.
Only reads corresponding to chr2L, chr2R, chr3L, chr3R, chr4, and chrX were considered for further analysis.
Paired end read fragments <= 100 bp were considered to have originated from 'open' chromatin. Replicates were pooled, and average coverage over open regions was calculated over 10 bp discrete windows. These data are provided as .wig formatted files in the processed data file deposit.
Peaks were called with Zinba on pooled biological replicates. The peaks are provided as a tab-delimited table with annotations.
Nucleosomes within 2500bp regions flanking the maximum open position as called by Zinba were called using NucleoATAC. Both smoothed nucleosome profiles and dyad position/occupancy scores are provided in the processed data file deposit.
Genome coverage was calculated in 10 bp windows across the genome and normalized to counts per million reads.
Genome_build: dm3
Supplementary_files_format_and_content: ChIP Peaks are provided as a tab-delimited text file with additional logical indexers that indicate categories of peak as determined by analysis. Coverage of reads are provided as .wig files for each genotype.
Supplementary_files_format_and_content: ATAC Peaks are provided as a tab-delimited text file with additional logical indexers that indicate categories of peak as determined by analysis. Coverage of reads originating from open chromatin are provided as .wig files for each genotype. Predicted nucleosome positions are provided in two formats: smoothed nucleosome profiles from NucleoATAC are provided in bedgraph format, and dyad positions and estimated occupancy are provided in a .bed.txt format.

extract_protocol:
Embryos from a 0-4 hour collection were crosslinked in formaldehyde for 15 minutes prior to quenching with glycine and 3 1x PBS washes. Embryos were hand sorted under a dissecting scope in order to collect NC14 stage only. Collected embryos were frozen at -80° until sufficient numbers were collected. To perform ChIP, collected embryos were thawed and homogenized prior to sonication in RIPA buffer. Sheared chromatin was subjected to overnight immunoprecipitation with an anti-GFP antibody and immunocomplexes were precipitated with protein-G dynambeads. Pellets were washed extensively prior to elution and crosslink reversal.
ChIP samples were subjected to library preparation using the NEB Next Library Mastermix Kit following the manufacturer's instructions.

value: y w p{GFP-Bcd}; bcd[E1] nos[L7] tsl[4]


title: 15072703--WT-C-NC14-12


title: Bcd085_Bcd_ChIP_B

description:
truncated Bcd (graded) Chromatin Immunoprecipitation
processed data file:
bcd085.10bp.cpm.bc.wig.gz

value: w; {GFP-bcd[085]}attP40; bcd[E1]


title: GFP-Bcd_bnt_Bcd_ChIP_B

source_name: nanos torsolike (graded bcd only) Chromatin Immunoprecipitation


title: Bcd085_Bcd_ChIP_C

source_name: truncated Bcd (graded) Chromatin Immunoprecipitation


title: tub_uBcd_Bcd_ChIP_C

description:
uniform Bcd (high) Chromatin Immunoprecipitation
processed data file:
tub-uBcd.10bp.cpm.bc.wig.gz
Annotated_Bcd_ChIP_Peaks.gz


title: tub-uBcd_Bcd_ChIP_A

source_name: uniform Bcd (high) Chromatin Immunoprecipitation


title: 16033007-zld-NC14-12


title: Bcd085_Bcd_ChIP_A


title: tub_uBcd_Bcd_ChIP_B


title: mtrm-uBcd_Bcd_ChIP_B

description:
uniform Bcd (medium) Chromatin Immunoprecipitation
processed data file:
mtrm-uBcd.10bp.cpm.bc.wig.gz
Annotated_Bcd_ChIP_Peaks.gz


title: mtrm-uBcd_Bcd_ChIP_A

source_name: uniform Bcd (medium) Chromatin Immunoprecipitation


title: 15110102-bcdE1-NC14-12


title: bcd-uBcd_Bcd_ChIP_A

description:
uniform Bcd (low) Chromatin Immunoprecipitation
processed data file:
bcd-uBcd.10bp.cpm.bc.wig.gz
Annotated_Bcd_ChIP_Peaks.gz


title: bcd-uBcd_Bcd_ChIP_B

source_name: uniform Bcd (low) Chromatin Immunoprecipitation


title: bcd-uBcd_Bcd_ChIP_C


title: WT_Bcd_ChIP_H

description:
wild-type (graded) Bcd Chromatin Immunoprecipitation
processed data file:
wt.10bp.cpm.bc.wig.gz
Annotated_Bcd_ChIP_Peaks.gz

value: y w p{GFP-Bcd}; bcd[E1]


title: WT_Bcd_ChIP_E

source_name: wild-type (graded) Bcd Chromatin Immunoprecipitation


title: WT_Bcd_ChIP_F


title: WT_Bcd_ChIP_C

description:
wild-type (graded) Bcd Chromatin Immunoprecipitation
processed data file:
Annotated_Bcd_ChIP_Peaks.gz


title: WT_Bcd_ChIP_B


title: WT_Bcd_ChIP_G


title: WT_Bcd_ChIP_D


title: WT_Bcd_ChIP_A


title: 15110403-tub-uBcd-NC14-12


title: mtrm-uBcd_Bcd_ChIP_C


title: DJ1 KO rep 3 [rat-KO4_S21_L004]

city: Bethesda

first: Mark

middle: R

last: Cookson

address: NIHBC 35 - PNRC I BG RM 1A-116

institute: National Institutue on Aging, NIH

data_processing:
Basecalls performed using CASAVA version 1.7.1
Tophat v.2.0.6/ Bowtie v2.0.2.0
HTSeq v0.5.3p9
DESeq2 v1.8.1
Genome_build: rn5
Supplementary_files_format_and_content: We have included two processed data files.  The raw counts are the output of HTSeq, and the normalized abundance measurements are the output from DESeq2.

organism: Rattus rattus

source_name: DJ1 KO_hemibrain

growth_protocol: Frozen rat brains from 6-month-old male rats were a gift from the Michael J Fox Foundation. These rats are described in PMID: 24969022.

extract_protocol:
Frozen hemibrains were homogenized in TriZol reagent and RNA was extracted according to the Invitrogen TriZol protocol.
TruSeq RNA Sample Preparation Kits (v2, Illumina)

value: Long Evans

value: DJ-1 Knockout

tag: age

value: 6 months

tag: gender

value: male

value: Hemibrain (Half cerebrum + half cerebellum + half brainstem)


title: WT rep 6 [rat-wt6_S20_L004]

value: Wildtype


title: WT rep 8 [rat-wt8_S25_L005]


title: DJ1 KO rep 4 [rat-KO5_S22_L004]


title: DJ1 KO rep 6 [rat-KO8_S27_L005]


title: WT rep 5 [rat-wt5_S19_L004]


title: DJ1 KO rep 2 [rat-KO3_S17_L003]


title: WT rep 3 [rat-wt3_S15_L003]


title: DJ1 KO rep 1 [rat-KO1_S16_L003]


title: WT rep 1 [rat-wt1_S13_L003]


title: WT rep 4 [rat-wt4_S18_L004]


title: WT rep 7 [rat-wt7_S24_L005]


title: WT rep 2 [rat-wt2_S14_L003]


title: Bystander macrophages donor 3

city: Montreal

first: Eric

last: Cohen

state: Quebec

address: 110 Ave des Pins Ouest

institute: IRCM

data_processing:
Basecalls performed using CASAVA version 1.8
Adaptor sequences and poor quality bases were trimmed with Cutadapt
Alignment of reads was performed using miRDeep2 (mapper.pl) on the GRCh37 human genome
Quantification of individual microRNAs were performed using miRDeep2
Differential expression measurements were performed with DESeq2 v1.4.5
Genome_build: GRCh37
Supplementary_files_format_and_content: Diff files with differential expression

source_name: Macrophages derived from blood monocytes

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from leukapheresis samples (obtained from consenting healthy adults) by Ficoll-Paque; washed in phosphate-buffered solution (PBS) and monocytes separated by adhesion to cell culture plates (cultured in RPMI at 37 °C at 5% CO2). Non-adherent cells were washed out and monocytes cultured in RPMI supplemented with 5% corresponding blood donor plasma for 7 days in order to differentiate into macrophages. Macrophages were maintained in culture with RPMI supplemented with 5% fetal bovine serum (FBS).

extract_protocol:
RNA was extracted from macrophages using the QIAGEN Rneasy Plus kit using the Total RNA Containing Small RNAs from Cells (Appendix D of 12/2014 Handbook)
Illumina TruSeq Small RNA system; sequencing using PE50 on a HiSeq 2000 sequencer (Illumina technologies)

treatment_protocol: Macrophages were either left uninfected (mock) or infected 6 days with a modified HIV-1 expressing GFP (NL4.3ADA-GFP) also initially harboring vesicular stomatitis virus glycoproteins (VSV-G) at an multiplicity of infection (MOI) of 1. Cells were recovered by Accutase/PBS-EDTA (1:1) treatment and gentle scraping, washed, and GFP-positive/GFP-negative cells separated using an Influx (BD Biosciences) cell sorter in a biosafety level 3 laboratory. Cells were directly recovered in RNAlater (Qiagen), centrifuged, and RNA extracted.

tag: status

value: bystander


title: Productively infected macrophages donor 3

value: Macrophages derived from blood monocytes

value: HIV-1 infected


title: Bystander macrophages donor 1


title: Productively infected macrophages donor 2


title: Uninfected macrophages donor 2

value: uninfected


title: Uninfected macrophages donor 1


title: Uninfected macrophages donor 3


title: DJ1 KO rep 5 [rat-KO7_S26_L005]


title: 14263X23

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: 15 N Medical Dr.

institute: University of Utah

data_processing:
Reads were aligned to mouse genome from Ensembl release 87 using STAR.
Reads mapping uniquely to features in the Ensembl mouse GTF were counted using featureCounts.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2
Genome_build: GRCm38 (mouse)
Supplementary_files_format_and_content: FeatureCount output files

source_name: 155 Flox CD4cre CD4+ICB_002

growth_protocol: B16f10-OVA tumors were grown in cell culture before injecting 1 x 10^6 cells per mouse subcutaneously in the hind flank.  Tumors were grown for 12 days.  Tumors were then removed and digested with Accumax and flow sorted based on the above mentioned strategy.

extract_protocol: Cells were flow sorted, RNA was isolated with miRneasy micro kit, library was prepped.

treatment_protocol: Select mice were treated with anti-PD-1/PD-L1 and anti-CTLA-4 antibodies injected IP on days 3, 6, and 9 in a volume of 250 ul in concentrations of 1mg/mL, 1mg/mL and 0.4mg/ml respectively


title: 14263X24

source_name: 155 Flox CD4cre CD4+ICB_003


title: 14263X21

source_name: 155 Flox CD4cre CD4_003


title: 14263X19

source_name: 155 Flox CD4cre CD4_001


title: 14263X20

source_name: 155 Flox CD4cre CD4_002


title: 14263X22

source_name: 155 Flox CD4cre CD4+ICB_001


title: 14263X11

source_name: 155 Flox CD4cre CD8+ICB_002


title: 14263X8

source_name: 155 Flox CD4cre CD8_002


title: 14263X10

source_name: 155 Flox CD4cre CD8+ICB_001


title: 14263X12

source_name: 155 Flox CD4cre CD8+ICB_003


title: 14263X13


title: 14263X9

source_name: 155 Flox CD4cre CD8_003


title: Bystander macrophages donor 2


title: crelKO aTreg 2

city: Lyon

first: Yenkel

last: Grinberg-Bleyer

address: 28 rue Laennec

department: Immunity, viruses and inflammation

country: France

institute: Cancer Research Center of Lyon

description: DATASET 2

data_processing:
raw FASTQ files were aligned on the mm10 genome using STAR aligner with default parameters
Aligned fragments were then counted and annotated using Rsamtools v3.2 and the TxDb.Mmusculus.UCSC.mm10.knownGene’ version 3.1.2  transcript database
Normalized FPKM (fragments per kilobase per million mapped reads) were obtained using the robust FPKM estimate function of DeSeq2 v1.10.1 after removing the batch effect using the ComBat function of the sva package v3.18.0
Differentially expressed genes were obtained using the DESeqResults function of the same package
All p-values were adjusted for mutliple comparison using the Benjamini & Hochberg FDR algorithm
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: c-RelKO CD62Llo CD44lhi aTreg

extract_protocol:
RNA was prepared using the Qiagen Rneasy  Mini Kit reagents and protocol.
RNA libraries were prepared for sequencing using the TruSeq Sample Prepr Kit v2

value: Foxp3-CRE-YFP+ Treg cells

value: C57Bl/6 Foxp3-CRE-YFP*c-Rel F/F


title: p65KO aTreg 2

description: DATASET 2

source_name: p65KO CD62Llo CD44lhi aTreg

value: C57Bl/6 Foxp3-CRE-YFP*p65 F/F


title: 14263X14


title: 14263X15


title: WT aTreg 3

description: DATASET 2

source_name: WT CD62Llo CD44lhi aTreg

value: C57Bl/6 Foxp3-CRE-YFP


title: crelKO aTreg 3

description: DATASET 2


title: WT aTreg 2

description: DATASET 2


title: WT aTreg 1

description: DATASET 2


title: crelko rTreg 1

description: DATASET 2

source_name: c-RelKO CD62Lhi CD44lo rTreg


title: WT rTreg 2

description: DATASET 2

source_name: WT CD62Lhi CD44lo rTreg

growth_protocol: Cells were FACS-sorted and RNA was extracted immediatedly

treatment_protocol: No treatment


title: p65KO rTreg 1

description: DATASET 2

source_name: p65KO CD62Lhi CD44lo rTreg


title: c-Rel-/- Treg rep2

description: DATASET 1 YS006

source_name: c-Rel-/- Treg

growth_protocol: Cells were stimulated in complete RPMI medium, in 12-well tissue culture plates coated with 5 ug/ml anti-mCD3, in the presence of 1ug/mL soluble anti-mCD28 and 10 ng/mL murine IL-2, at 37°C for 16 hours.


title: WT rTreg 1

description: DATASET 2


title: p65KO rTreg 2

description: DATASET 2


title: 14263X3


title: 14263X7

source_name: 155 Flox CD4cre CD8_001


title: 14263X2


title: 14263X1


title: LIB98722_SAM24318642: uncrushed dlki

city: South San Francisco

first: Josh

last: Kaminker

address: 1 DNA Way

department: Bioinformatics and Computational Biology

institute: Genentech

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

source_name: RNA from mouse retinas following optic nerve crush

extract_protocol: RNA-seq was performed from a separate cohort of animals to compare gene expression changes in eye retina three days post acute injury (optic nerve crush) from mice treated with vehicle (MCT, n=5) or with (n=5) the DLK inhibitor GNE-3511 (75mg/kg dosed 60 and 68 hr post-injury). A total of four experimental groups were included as follows: vehicle-treated 1) uncrushed retina, 2) vehicle-treated crushed retina, 3) GNE-3511-treated uncrushed retina, and 4) GNE-3511-treated crushed retina. Total RNA was extracted using Qiagen RNeasy kit as per manufacturerâs protocol including the on-column DNase digestion. Quality control of samples was done to determine RNA quantity and quality prior to their processing by RNA-seq. The concentration of RNA samples was determined using NanoDrop 8000 (Thermo Scientific) and the integrity of RNA was determined by Fragment Analyzer (Advanced Analytical Technologies). 0.5 Âµg of total RNA was used as an input material for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). Size of the libraries was confirmed using Fragment Analyzer (Advanced Analytical Technologies) and their concentration was determined by qPCR based method using Library quantification kit (KAPA). The libraries were multiplexed then sequenced on Illumina HiSeq4000 (Illumina) to generate 30M of single end 50 base pair reads.

value: retina

tag: eye treatment

value: uncrushed

tag: drug treatment

value: DLKi


title: WT Treg + H2O rep1

description: DATASET 1 YS001

source_name: WT Treg + H2O

treatment_protocol: In some conditions cells were stimulated in the presence of 500ug/mL Pentoxifylline (pre-diluted in H2O), or its H2O diluent.


title: c-Rel-/- Treg rep1

description: DATASET 1 YS003


title: WT Treg + PTXF rep1

description: DATASET 1 YS002

source_name: WT Treg + PTXF


title: p65KO aTreg 1

description: DATASET 2


title: LIB98728_SAM24318648: uncrushed dlki


title: LIB98724_SAM24318644: uncrushed dlki


title: LIB98721_SAM24318641: crushed dlki

value: crushed


title: crelKO rTreg 2

description: DATASET 2


title: LIB98718_SAM24318638: uncrushed control

value: control


title: LIB98730_SAM24318650: uncrushed dlki


title: LIB98719_SAM24318639: crushed control


title: Liver_SREBP1c_KO_2

city: Seoul

first: Jae Bum

last: Kim

department: Biology

country: South Korea

institute: Seoul National University

data_processing:
Sanger / Illumina 1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSC mm10 whole genome using bowtie and TopHat
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinkds. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

source_name: Liver tissue

growth_protocol: 12-week-old C57BL/6 male mice

extract_protocol:
Liver lysates were extracted using Trizol. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 12 hour refeeding after 24 hour fasting

value: Liver

value: SREBP1c KO


title: Liver_SREBP1c_KO_1


title: LIB98723_SAM24318643: crushed dlki


title: WT Treg + PTXF rep2

description: DATASET 1 YS005


title: Liver_WT_2

value: SREBP1c WT


title: Liver_WT_1


title: EGFP_1

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description:
GFP_1
TCCTGAGC-TATCCTCT

data_processing:
Fastq files were align to the mm9 reference genome using STAR and default parameters
Ensmebl v67 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method
Genome_build: mm9
Supplementary_files_format_and_content: Voom transformed abundance measurements

source_name: lung mesenchyme

extract_protocol:
RNA was extracted and purified using Trizol from adult Axin2CreERT2:tdT:PdgfraEGFP and Wnt2CreERT2:R26REFYP  FACS sorted mouse lungs
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung mesenchyme

tag: lineage

value: GFP

tag: developmental stage

value: adult


title: LIB98729_SAM24318649: crushed dlki


title: LIB98720_SAM24318640: uncrushed control


title: Axin2:Pdgfra Rep2

description:
G_T_2
TAGGCATG-ACTGCATA


title: WT Treg + H2O rep2

description: DATASET 1 YS004

tag: cell type


title: Negative Rep2

description:
neg_2
TAAGGCGA-TATCCTCT

value: neg


title: Wnt2 Rep1

description:
Wnt2_1
GGACTCCT-ACTGCATA


title: LIB98727_SAM24318647: crushed dlki


title: LIB98732_SAM24318658: uncrushed control


title: Axin2 Rep2

description:
tdt_2
GCTACGCT-ACTGCATA

value: tdt


title: Wnt2 Rep2

description:
Wnt2_2
CGTACTAG-TATCCTCT


title: Pdgfra Rep2

description:
GFP_2
CTCTCTAC-ACTGCATA


title: LIB98726_SAM24318646: uncrushed dlki


title: LREXJQ1_rep3_RNASeq

city: Bronx

first: Deyou

last: Zheng

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
For ChIPSeq, reads were aligned to the human genome (hg19) using Bowtie (v1.1.1) with default parameters and the results were converted to bam files by Samtools. Reads mapped to a single genomic location were kept and redundant ones were filtered out.
For ChemSeq, reads were aligned to the human genome (hg19) using Bowtie (v1.1.1) with default parameters and the results were converted to bam files by Samtools. Reads mapped to a single genomic location were kept and redundant ones were filtered out.
For RNASeq, reads were aligned to the human genome (hg19) using STAR (v2.4.2a). The number of RNA-seq fragments mapped to each gene was determined for all genes in the GENCODE database (v19) using the HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIPSeq and ChemSeq, Tdf files were generated from the bam files by Igvtools with default parameters for visualization in IGV. For RNASeq, counts were generated by HTSeq.

growth_protocol: Standard growth conditions as outlined in methods of paper

extract_protocol:
ChIP protocol outlined in methods of paper; Tumors harvested and flash frozen in liquid nitrogen, RNA was extracted via lysing in MP Biomedical Lysing Matrix tubes in homogenizer, then Trizol extraction, followed by cleanup using Qiagen RNEasy columns
ChIP-seq and RNA-seq libraries prepared using standard KAPA Hyper Library and Illumina protocols

tag: cell line

value: LREX' tumor

tag: treatment


title: LREXJQ1_rep4_RNASeq


title: LREXJQ1_rep2_RNASeq


title: LIB98725_SAM24318645: crushed dlki


title: Axin2 Rep1

description:
tdt_1
CAGAGAGG-ACTGCATA


title: Negative_0

description:
neg_0
AAGAGGCA-ACTGCATA


title: Axin2:Pdgfra Rep1

description:
G_T_1
AGGCAGAA-TATCCTCT


title: S48-2

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
FastQC (Read Quality Assessment)
TrimGalore (Adapter and Quality Trimming)
Tophat (Read Alignment)
Cuffdiff (Differential Expression)
Genome_build: rn6 (UCSC)
Supplementary_files_format_and_content: Cuffdiff Gene FPKM Table

organism: Rattus norvegicus

source_name: NRVM

growth_protocol: NRVM was cultured from Day 2 pups of SD rats. They were cultured initially in plating medium containing 10% serum and then switched to no serum maintainance medium (containing ITS) for 24 hours before the start of pretreatment.

extract_protocol:
Total RNA was extracted using Trizol followed with miRNAeasy Kit from Qiagen following manufacturer's instructions.
Illumina TruSeq stranded mRNA

treatment_protocol: NRVM was pretreated with SR9009 or Vehicle for 24hours, then given PE (phenylephrine) for the indicated time.

value: Sprague-Dawley

value: NRVM

value: heart

tag: time after phenylephrine (pe)

tag: pretreatment


title: LREXJQ1_rep1_RNASeq


title: S48-1


title: LIB98717_SAM24318637: crushed control

value: retina


title: LREXveh_rep4_RNASeq

source_name: LREXveh

value: veh


title: S48-0


title: V48-0

value: Vehicle


title: LREXveh_rep3_RNASeq


title: V48-2


title: S4-2


title: LREXveh_rep2_RNASeq


title: S4-1


title: LIB98731_SAM24318657: crushed control

value: crushed


title: S4-0


title: V4-2


title: 227_KS2_CD31

city: London

first: Diana

last: Passaro

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
The RSEM package (version 1.2.29) in conjunction with the STAR alignment algorithm (version 2.5.1b)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to mm10 Ensembl genes downloaded from the UCSC Table Browser 15 on 14th April 2016
The “--forward-prob” parameter was set to “0” and all other parameters were kept as default
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.2.3)
Genome_build: mm10 Ensembl
Supplementary_files_format_and_content: Tab delimited text files containing TMM normalised data. Rows represent Ensembl mouse genes and columns represent individual samples.

growth_protocol: Umbilical Cord Blood (CB) samples were obtained from normal full-term deliveries after signed informed consent. AML samples used for xenografts were obtained after informed consent at St Bartholomew’s Hospital (London, UK).

extract_protocol:
bones were dissected in small pieces of 2-3 mm diameter and incubated 30 min at 37 degrees in a HBSS digestion solution containing 2% FBS, DNase I (10 μg/ml, Sigma), Collagenase (1 mg/ml, Sigma), Dispase II (5 mg/ml, Sigma) and Heparin (20 U/ml, Sigma). Bone pieces were next crashed with mortar and pestle in the same digestion solution and incubated at 37 degrees for 30 min. Cell suspension was then homogenized with a micropipette and filtered with a 100 micron cell strainer. Human and Murine hematopoietic cells were eliminated using magnetic beads isolation kits, and CD31+ labelled endothelial cells were isolated via FACS in RNA extraction buffer.
Total RNA from sorted cell samples was isolated using the RNeasy Mini Kit (Qiagen, Crawley, UK). The quality and concentration of total RNA were determined on Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Pico Assay. 3.5 ng of Total RNA in 5 μl volume was used to generate cDNA synthesis with Nugen Ovation® RNA‑Seq System V2 kit (part No. 7102). The resulting SPIA-cDNA were normalized to 100 ng in 15 μl based on Qubit DNA HS assay. Fragmentation was done using 8 microTUBE-15 AFA Beads Strip V2 (PN 520159) on Covaris E-series at setting 20%DF, 18W, 200 burst, 20C tempt, 120s treatment time and no Intensifier.
Only 10-30 ng in 10 μl of fragmented cDNA was used starting from the End Repair step of the Ovation® Ultralow Library Systems V2 (part No. 0344NB) protocol, with 10 cycles PCR. The RNAseq libraries were quality checked on Qubit DNA HS assay, Bioanalyser and Illumina Ecoreal QPCR followed by Illumina PE51 sequencing on Hiseq 2500 V3 reagents.

treatment_protocol: AML patient-derived samples and CB were transplanted into 8- to 12-week old unconditioned NSG mice (Jackson Laboratory, BarHarbor, Maine, USA). Human bone marrow engraftment was assessed by tibia pucture.

tag: sample type

value: engrafted with AML patient-derived cells

value: bone marrow-derived endothelial


title: V4-0


title: LREXveh_rep1_RNASeq


title: LNARJQ1_rep4_RNASeq


title: 102_GD_CD31


title: V4-1


title: S0-2


title: 228_KS2_CD31


title: 229_KS2_CD31


title: S0-1


title: V0-2


title: 230_KS2_CD31


title: LNARJQ1_rep2_RNASeq

value: LNAR' tumor


title: V0-1


title: 100_SW2_CD31


title: 16060605-mtrm-uBcd-NC14-12

source_name: uniform Bcd (medium) ATAC-seq

tag: maternal genetic info.

value: w; {mtrm>GFP-bcd-sqh3'UTR}attP40/+; p{His2Av-GFP} bcd[E1]/bcd[E1]

tag: timepoint

value: NC14+12 minutes

value: embryo

tag: number of embryos


title: V0-0

tag: strain

tag: tissue


title: LNARJQ1_rep1_RNASeq


title: LNARveh_rep4_RNASeq

source_name: LNARveh


title: 99_SW2_CD31


title: 79_MS_CD31


title: 98_SW2_CD31


title: V48-1


title: LNARveh_rep3_RNASeq


title: 74_MS_CD31


title: LNARJQ1_rep3_RNASeq


title: LNARveh_rep2_RNASeq


title: 73_RC_CD31


title: LNARveh_rep1_RNASeq


title: 67_RC_CD31


title: LREX_BRD4_ChIPSeq

value: LREX'

tag: chip antibody

value: Sigma HPA015055


title: LREXEnz_BRD4_ChIPSeq

value: Enz


title: 70_RC_CD31


title: 72_RC_CD31


title: S0-0


title: LNAREnz_BRD4_ChIPSeq

value: LNAR'


title: 86_hCB_CD31

value: engrafted with control human CB cells


title: LNAR_BRD4_ChIPSeq


title: 85_hCB_CD31


title: Productively infected macrophages donor 1

source_name: Macrophages derived from blood monocytes

tag: status

value: HIV-1 infected


title: 180_ctrl_CD31

value: unengrafted


title: LREX_input_ChemSeq

data_processing:
Library strategy: Chem-seq
For ChIPSeq, reads were aligned to the human genome (hg19) using Bowtie (v1.1.1) with default parameters and the results were converted to bam files by Samtools. Reads mapped to a single genomic location were kept and redundant ones were filtered out.
For ChemSeq, reads were aligned to the human genome (hg19) using Bowtie (v1.1.1) with default parameters and the results were converted to bam files by Samtools. Reads mapped to a single genomic location were kept and redundant ones were filtered out.
For RNASeq, reads were aligned to the human genome (hg19) using STAR (v2.4.2a). The number of RNA-seq fragments mapped to each gene was determined for all genes in the GENCODE database (v19) using the HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIPSeq and ChemSeq, Tdf files were generated from the bam files by Igvtools with default parameters for visualization in IGV. For RNASeq, counts were generated by HTSeq.


title: 95_ctrl_CD31


title: LREXEnz_bioJQ1_ChemSeq


title: LREXEnz_input_ChemSeq


title: LREX_bioJQ1_ChemSeq


title: 83_hCB_CD31


title: 96_ctrl_CD31


title: 84_hCB_CD31


title: 87_ctrl_CD31


title: 94_ctrl_CD31


title: LNAR_input_ChemSeq


title: LNAREnz_bioJQ1_ChemSeq


title: LNAREnz_input_ChemSeq


title: LREX_H3K27me3_ChIPSeq

value: Millipore 07-449


title: LNAR_bioJQ1_ChemSeq


title: LNAREnz_H3K27me3_ChIPSeq


title: LREXEnz_H3K27me3_ChIPSeq


title: LNAR_H3K27me3_ChIPSeq


title: Bulk lung mesenchyme

data_processing:
The Cell Ranger Single Cell Software Suite was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome). 5bp UMI tags were extracted from Read2.
Genome_build: mm10
Supplementary_files_format_and_content: mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample

extract_protocol: Cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single cell GEMs. Approximately ~1200 to 2800 cells were loaded per channel. Two biological replicates were generated per sample. Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) following the protocols outlined in Zheng et. al. Sequencing libraries were loaded at 2.1pM on an Illumina NextSeq500 with 2 × 75 paired-end kits using the following read length: 98bp Read1, 14bp I7 Index, 8bp I5 Index and 5bp Read2.

tag: genotype

tag: age

value: adult, 6 weeks of age


title: RNA-seq_HT29_LDN-193189

city: Wakayama

first: Shogo

last: Ehata

state: Wakayama

address: Kimiidera 811-1

department: School of Medicine

institute: Wakayama Medical University

description: HT29 cells treated woth LDN-193189

data_processing:
Ion Proton
Reads per kilobase of exon permMegabase of library size (RPKM) were calculated by CLC Genomics Workbench (Qiagen).
Genome_build: hg19
Supplementary_files_format_and_content: Expression data of the four samples were summarized into two processed files.

growth_protocol: HT29 and DLD-1 were obtained from the Japanese Cancer Research Resource Bank and cultured in RPMI containing 10% FBS, penicillin, and streptomycin.

extract_protocol:
Total RNA was isolated with RNeasy (Qiagen).
cDNA libraries were prepared using Dynabeads mRNA DIRECT Purification Kit (Life Technologies) and Ion Total RNA-Seq Kit v.2 (Life Technologies).

treatment_protocol: Cells were seeded in 6-well plates. On the following day, cells were deprived of serum and cultured with DMSO or 0.2–0.3 µM LDN-193189 for 3 days.

tag: histology

value: colon adenocarcinoma


title: RNA-seq_DLD-1_DMSO

description: untreated DLD-1 cells

value: DMSO


title: RNA-seq_DLD-1_LDN-193189

description: DLD-1 cells treated woth LDN-193189


title: RNA-seq_HT29_DMSO

description: untreated HT29 cells


title: LREX_H3K4me3_ChIPSeq

value: Abcam ab8580


title: rna.shPAF1_THP1_rep2

city: Chicago

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description:
total RNA
RNA-seq in cells treated with PAF1 shRNA

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: THP1 cells

growth_protocol: HCT116 and DLD1 cells were grown in DMEM supplemented with 10% FBS. THP1 cells were grown in RPMI-1640 supplemented with 10% FBS and 55 µM 2-mercaptoethanol.

extract_protocol:
For ChIP-seq, cells were crosslinked with 1% paraformaldehyde for 10 minutes at room temperature with gentle rotation, and then quenched by 0.125 M glycine solution. After washing, nuclei were sonicated using Covaris Sonicator, and the supernatant was used for immunoprecipitation with the indicated antibody. ChIP-sequencing libraries were prepared with Illumina’s Tru-seq DNA sample prep kit. Total RNA was extracted from cells using RNeasy mini Kit (Qiagen) followed by ribosomal RNA depletion with the RiboZero kit (Epicenter). Poly(A) depleted and Poly(A)-enriched RNA were separated by 3 rounds of Oligo(dT) magnetic beads (Thermo). For sequencing, 2 μg of resulting RNA was used for ribosomal RNA depletion with the RiboZero kit (Epicenter) and libraries were made with the TruSeq RNA sample Prep Kit (Illumina).
ChIP-sequencing libraries were prepared with Illumina’s Tru-seq DNA sample prep kit using standard protocols. RNA-seq libraries were prepared with Illumina’s TruSeq RNA sample Prep Kit using standard protocols.

value: AML leukemia cell line

tag: shRNA

value: PAF1 shRNA replicate 2


title: LREXEnz_H3K4me3_ChIPSeq


title: 82_hCB_CD31

tag: cell type

value: bone marrow-derived endothelial


title: rna.NONT_THP1_rep2

description:
total RNA
RNA-seq in cells treated with non-targeting shRNA

tag: cell line

value: non-targeting shRNA replicate 2


title: rna.NONT_THP1_rep1

value: non-targeting shRNA replicate 1


title: LREXEnz_H3K4me1_ChIPSeq

value: LREX'

value: Abcam ab8895

tag: treatment


title: LNAR_H3K4me1_ChIPSeq


title: LREX_H3K4me1_ChIPSeq


title: rna.shPAF1_THP1_rep1

value: PAF1 shRNA replicate 1


title: LREXEnz_H3K27ac_ChIPSeq

value: Abcam ab4729

value: Enz


title: pol2.shPAF1_THP1_rep1

description:
fragmented genomic DNA
Chromatin IP of Total Pol II in cells treated with PAF1 shRNA

value: PAF1 shRNA


title: LNAR_H3K27ac_ChIPSeq

value: LNAR'


title: YOH

status: Public on Sep 10 2017

city: Zhenjiang

first: Xiangfeng

state: Jiangsu

address: 301, Xuefu Road

department: Food school

country: China

institute: Jiangsu university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase Million was the value of expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced.TPM means transcripts per million,using the formula of R1*1000*1000000/(L1*Rtoatl),R1: The count value of the gene;L1: The length of the gene;Rtotal: the sum value of all the corrected count value .
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and TPM for each Sample

organism: Meyerozyma caribbica

source_name: Fungus

growth_protocol: Pichia caribbica was cultured in NYDB medium at 28℃ in dark for 20h and on a rotary shaker at 180 rpm.

extract_protocol:
The medium was removed,Pichia caribbica was collected and ground to powder, and RNA was extracted 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.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The sample of Pichia caribbica was treated with or without H2O2 in NYDB medium at 28℃ in dark for 40 minutes and on a rotary shaker at 180 rpm.

value: Pichia caribbica cultured in NYDB medium  H2O2

tag: incubation time

value: 40 mins treated with H2O2

tag: incubation conditions

value: 28℃ in dark and on a rotary shaker at 180 rpm


title: Y

value: Pichia caribbica cultured in NYDB medium without H2O2

value: 40 mins treated with distill water


title: pol2.shPAF1_THP1_rep2

value: AML leukemia cell line


title: pol2.NONT_THP1_rep2

description:
fragmented genomic DNA
Chromatin IP of Total Pol II in cells treated with non-targeting shRNA

value: non-targeting shRNA


title: LREX_H3K27ac_ChIPSeq


title: S3, donor 4

status: Public on Sep 09 2017

city: Kuopio

first: Suvi

last: Kuosmanen

address: Neulaniementie 2

country: Finland

institute: University of Eastern Finland

description: Sample 15

data_processing:
RNA-seq libraries were sequenced on Illumina NextSeq 500 system
RNA-seq data was mapped using  Bowtie2 (2.2.2)
CountTable was created using in-house software of Exiqon
Genome_build: GRCh37 and miRBase version is 20
Supplementary_files_format_and_content: text file (tab separated) includes raw counts for all samples

source_name: Vascular endothelial cells

extract_protocol:
Standard RNA extraction protocol
RNA library preparation is described in the publication

value: HUVEC


title: pol2.NONT_THP1_rep1


title: S3, donor 1

description: Sample 12


title: S3, donor 3

description: Sample 14


title: S2, donor 1

description: Sample 8


title: S1, donor 4

description: Sample 7


title: S2, donor 3

description: Sample 10


title: S2, donor 2

description: Sample 9


title: S1, donor 1

description: Sample 4


title: S1, donor 3

description: Sample 6


title: S1, donor 2

description: Sample 5


title: S0, donor 2

description: Sample 2


title: LNAR_H3K4me3_ChIPSeq

value: Abcam ab8580


title: S0, donor 3

description: Sample 3


title: S0, donor 1

description: Sample 1


title: S2, donor 4

description: Sample 11


title: FET cells treated with TGFβ1 replicate 3

city: Omaha

first: Jing

last: Wang

address: S 42 St and Emile St

institute: University of Nebraska Medical Center

data_processing:
The raw counts were then normalized using trimmed mean of M values (TMM) method  and compared using Bioconductor package “edgeR”.
The average coverage for each gene was calculated using the normalized read counts from “edgeR.”
Differentially expressed genes were identified if the average coverage ≥1 in at least one sample, log2 based fold change ≥1 or ≤ -1 and FDR < 0.05.
Supplementary_files_format_and_content: RPKM

source_name: FET

extract_protocol:
FET cells in triplicates were treated with RSPO1 or TGFβ1 for 4 hours. RNA was isolated using RNeasy Mini kit (47104, Qiagen Germantown, MD, USA). RNA sequencing was performed by the City of Hope Integrative Genomics Core facility. Poly(A) RNA-seq libraries were constructed using TruSeq mRNA Library Preparation Kit (RS-122, Illumia, San Diego, CA, USA). Purified libraries were validated using Bioanalyzer 2100 system with DNA High Sensitivity Chip (Agilent, Santa Clara, CA, USA) and quantified with Qubit Flourometer (Invitrogen). All libraries were sequenced on the Illumina Hiseq 2500 with single read 51 bp reads following the manufacturer's recommendations. The 51-bp-long single-ended sequence reads were mapped to human genome (hg19) using TopHat, and the frequency of Refseq genes was counted with customized R scripts. The raw counts were then normalized using trimmed mean of M values (TMM) method and compared using Bioconductor package “edgeR”. The average coverage for each gene was calculated using the normalized read counts from “edgeR.” Differentially expressed genes were identified if the average coverage ≥1 in at least one sample, log2 based fold change ≥1 or ≤ -1 and FDR < 0.05.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human colon carcinoma cell lines

tag: passage

value: passage 5-6


title: S3, donor 2

description: Sample 13


title: FET cells treated with RSOP1 replicate 2


title: FET cells treated with TGFβ1 replicate 2


title: FET cells treated with RSOP1 replicate 3


title: FET cells treated with control buffer replicate 2


title: drb24 sRNA dataset

city: Callaghan

first: Kate

last: Hutcheon

state: New South Wales

address: University Drive

country: Australia

institute: University of Newcastle

data_processing:
Sequencing adapters were removed using the FASTX toolkit. Reads greater than 35nt, less than 16nt in length, or which contained invalid bases were discarded using the UEA small RNA workbench filter tool.
Genome_build: TAIR10
Supplementary_files_format_and_content: Processed data contains the read count of filtered sRNA sequences present in each dataset

organism: Arabidopsis thaliana

source_name: inflorescence tissue

growth_protocol: Seeds were sown directly to soil and stratified at 4°C for 48 hours. Plants were transferred to growth cabinets under long day (16h light, 8h dark) conditions. Temperature conditions were 23°C day / 18°C night.

extract_protocol:
Total RNA was isolated from inflorescence tissue using TRIzol reagent according to the protocol provided by the manufacturer.
size fractionation

value: drb2-1 drb4-1


title: Wild-type sRNA dataset


title: drb2 sRNA dataset


title: drb35 sRNA dataset

value: drb3-1 drb5-1


title: Input DNA2

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

data_processing:
ChIP-Seq reads were aligned to the mm10 mouse genome using the BWA short read aligner 58 (version 0.7.12).
The aligned reads were filtered to keep only uniquely mapping reads.
A cross-correlation analysis was performed to assess quality metrics (Phantompeakqualtools package).
Peaks of enriched Satb2 binding were called using MACS2 (version 2.1.0),  by allowing only one tag at the same location and setting the false discovery rate to 0.01 and the fold-enrichment cutoff to 2
Genome_build: mm10
Supplementary_files_format_and_content: narrow peak file (extended bed format) was generated using MACS2

source_name: Primary hippocampal neurons

growth_protocol: Hippocampi were dissected from newborn C57BL/6J mice at postnatal day P0 to P1. Hippocampal tissue was trypsinized and dissociated by trituration. Neurons were plated on 100 mm tissue culture dishes , previously coated with poly-L-ornithine and laminin, at a density of 8 x 104 cells/cm2. Cells were cultured in Neurobasal medium containing B-27 supplement and antibiotics  for 11 days.

extract_protocol:
Hippocampal neurons were cross-linked with formaldehyde at 1% final concentration for 10 min at room temperature, and chromatin was prepared using the Zymo-Spin ChIP kit (Zymo Research) following manufacturer’s instructions. Sonication was performed at high power setting for 40 cycles (30 s ON, 30 s OFF) using a Bioruptor Plus (Diagenode Inc., Denville, NJ), yielding fragment size range of 200-700 bp. ChIP assays were performed in triplicates using 20 μg of chromatin and 10 μg of anti-V5 tag antibody (ab15828). IgG (12-370, Millipore) was included as a negative control. ChIP DNA was purified using ChIP DNA Clean and Concentrator (Zymo Research) and the relative abundance of a control region in V5-immunoprecipitated DNA was quantified by qPCR with sequence-specific primers.
DNA libraries (Satb2-ChIP and Input control DNA) were prepared and sequenced on a HiSeq 2000 sequencer (Illumina)

treatment_protocol: Hippocampal neurons were transduced with AAV8-hSyn-Satb2-V5 at multiplicity of infection 1.5 × 105 at DIV4 and used for ChIP-seq analysis at DIV11.

value: hippocampal neuron

tag: passages

value: transduced with AAV8-hSyn-Satb2-V5 at DIV4

tag: antibody


title: drb1 sRNA dataset


title: drb14 sRNA dataset

value: drb1-1 drb4-1


title: drb12 sRNA dataset

value: drb1-1 drb2-1


title: drb4 sRNA dataset


title: FET cells treated with TGFβ1 replicate 1


title: FET cells treated with control buffer replicate 3


title: FET cells treated with control buffer replicate 1


title: Satb2_ChIPSeq2

value: anti-V5 tag antibody (Abcam, catalog# 15828)


title: small RNAs in the dicer-2[null] rescued by the transgenic Dicer-2 [DCdsRBD]

status: Public on Sep 08 2017

city: BALTIMORE

first: Ryuya

last: Fukunaga

address: 725 N. Wolfe St. 521A Physiology Bldg

department: Department of Biological Chemistry

institute: Johns Hopkins University School of Medicine

description: small RNAs in fly heads

data_processing:
Basecalls performed using bcl2fastq version 2.16
Sequenced reads were trimmed for adaptor sequence.
Genome_build: dm3
Supplementary_files_format_and_content: [.txt] Tab-delimited text file. Length of the read, Number of the read, Sequence of the read.

source_name: Female fly heads

extract_protocol:
Female fly heads were hand-dissected and RNAs were prepared using miRVana.
Libraries were prepared as previously described (Fukunaga et al, 2014 and Han et al, 2015).

tag: genotype/variation

value: wIR; dicer-2[null], Act5C-Gal4/dicer-2[null] ; UAST-HA-Dicer-2[DCdsRBS]/+

tag: sample type

value: in vivo


title: small RNAs in the dicer-2[null] rescued by the transgenic Dicer-2 [DHelicase]

description: small RNAs in fly heads

value: wIR; dicer-2[null], Act5C-Gal4/dicer-2[null] ; UAST-HA-Dicer-2[DHelicase]/+


title: control  zebrafish endothelial cells rep2

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

data_processing:
Reads were aligned to the zv9 genome assembly using TopHat v2.0.9
For each sample, reads counts of all genes were computed using HTSeq v0.5.3p9
Genome_build: zv9
Supplementary_files_format_and_content: reads_count_HTSeq.xls: Reads count for each gene of all samples

organism: Danio rerio

source_name: zebrafish embryos

extract_protocol: For RNA-seq, RNA was isolated from endothelial cells of control, mettl3 and ythdf2 morphant zebrafish embryos using the QIAGEN RNeasy Micro kit by following the company manual and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 101 bp.

value: normal

value: endothelial cells

tag: tissue

value: trunk


title: ythdf2 morphant  zebrafish endothelial cells rep2


title: ythdf2 morphant  zebrafish endothelial cells rep1


title: control  zebrafish endothelial cells rep1


title: mettl3 morphant  zebrafish endothelial cells rep1


title: mettl3 morphant  zebrafish endothelial cells rep2


title: FET cells treated with RSOP1 replicate 1


title: PLK_pH7

first: Kami

state: New York

address: 1300 Morris Park Avenue

department: Medicine

description: Small RNA

data_processing:
Read trimming (Cutadapt)
Alignment with Bowtie2
Conversion to BigWig (deeptools)
Read counts were obtained using HTSeq count using 'union' and 'intersection-strict' modes
Genome_build: Toxoplasma gondii strain ME49 version 25
Supplementary_files_format_and_content: BigWig format containing read density
Supplementary_files_format_and_content: raw_counts2.txt: All_sample_read_counts

organism: Toxoplasma gondii

source_name: Cultured parasites

extract_protocol:
Small RNAs gel extracted before library construction
RNA 6000 Nano Kit and a Small RNA Chip kit

tag: strain

value: PLK

tag: growth condition

value: tachyzoite (pH7)


title: PLK_pH8

description: Small RNA

value: bradyzoite (pH8)


title: CTG_pH7

description: Small RNA

value: CTG


title: RH_pH8

description: Small RNA

value: RH


title: RH_pH7

description: Small RNA


title: CTG_pH8

description: Small RNA


title: ΔphcA 2

city: Madison

first: Caitilyn

last: Allen

state: Wisconsin

address: 1630 Linden Drive

department: Department of Plant Pathology

institute: UW-Madison

data_processing:
The raw sequence reads were mapped to the combined genome (tomato+Ralstonia solanacearum) using Subjunc aligner from Subread
The alignment bam files were compared against Ralstonia solanacearum gene annotation GFF file,  raw counts for each gene were generated using the featureCounts tool from subread
The raw counts data were normalized using voom method from the R Limma package, then used for differential expression analysis using limma
Genome_build: The tomato genome is from ITAG2.4(S_lycopersicum_chromosomes.2.50.fa). The tomato mitochondrion and chloroplast sequences are download from http://www.mitochondrialgenome.org/downloads. The Ralstonia solanacearum genome and megaplasmid sequences used is from GMI1000 (GenBank NC_003295.1 and NC_003296.1).
Supplementary_files_format_and_content: Ralstonia solanacearum genes and normalized counts

organism: Ralstonia solanacearum

source_name: Bacteria

extract_protocol:
Hot phenol method was used to extract RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Homogenate containing bacteria and plant tissues was centrifuged for 7 min in pre-chilled 1.5 ml tubes at 20,817 x g, the supernatant was discarded, and the pellet was frozen in in liquid nitrogen and stored at -80°C freezer for RNA extraction

value: Infected tomato plants

tag: sample collection time

value: 72 hour post infection


title: ΔphcA 1


title: ΔphcA 3


title: Wild-type 3


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 44

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: Bone marrow

extract_protocol:
Bone marrow cells were collected from the femurs and tibiae of 7 week old mice.
Cells were stained with antibodies and single cells sorted using a FACS Influx5 (BD Biosciences)
Cells were sorted directly into individual wells of 96-well PCR plate containing lysis buffer.
Single-cell RNA-sequencing was performed as previously described (Picelli et al (2014) Nat. protocols 9:171)
Pooled libraries were run on an Illumina HiSeq 4000 sequencer.
RNA libraries were prepared for sequencing using Illumina XT DNA preparation kit

value: Lymphoid-primed multipotent progenitor (LMPP, Lin- Sca-1+ c-Kit+ Flt3hi IL-7Ra- B220-)

tag: age

value: 7 weeks

tag: genotype


title: Wild-type 1


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 48


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 47


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 43


title: E4165 miRNA-Seq

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

description:
small RNA
endometrium_edgeR.txt

data_processing:
Raw FASTQ files were adapter trimmed and 5' poly-G tail artifacts were removed using cutadapt (version 1.11) at the core facility (University of Missouri DNA Core)
Reads were quality trimmed to a sliding window quality score of 30 and a minimum length of 17 bp with fqtrim (version 0.9.4, doi:10.5281/zenodo.20552)
Trimmed reads were mapped to the Ovis aries genome assembly (Oar_v3.1) with using miRDeep2.0.0.8 with miRBase (release 21) miRNAs downloaded for sheep and Bos taurus, Mus musculus, and Homo sapiens as related species
Novel miRNAs with a score ≥4 and no RFAM alerts were promoted and added to the Ovis aries miRbase file.
MiRNA expression was calculated with miRDeep2.0.0.8 using the quantifier.pl script
Model based DE analysis was completed using the edgeR-robust method with raw read counts
Genes without evidence of expression (CPM rowSum = 0) were filtered out and false discovery rate (FDR) was set at 0.05 for differential expression (DE) analysis
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: miRNA ID, miRNA ID from related species with same seed sequence for novel miRNAs, fold change, edgeR-robust FDR P-value and CPM for each sample in tab-delimited text format

organism: Ovis aries

source_name: endometrium

extract_protocol:
Endometrium was physically dissected from the uterus at collection and snap frozen in liquid nitrogen. Total RNA was isolated from tissue homogenzied in TRIzol reagent. The uterine lumen was flushed with 10 ml sterile PBS. Recovered uterine flush was clarified by centrifugation, filtered through a 0.22 µm PVDF syringe filter and concentrated by ultrafiltration. Extracellular vesicles (EVs) were isolated from concentrated flush by size exclusion chromatography (SEC) using qEVoriginal columns (Izon Science Ltd, Oxford, United Kingdom). Total RNA was isolated from EVs with the miRNeasy kit including on-column DNase digestion.
Illumina TruSeq small RNA

treatment_protocol: Ovariectomized ewes were injected daily with 50 mg P4 for 14 days (n = 5) or 50 mg P4 for 7 days and 50 mg P4 + 50 mg RU486 from days 8 to 14 (n = 5).

tag: group


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 42

tag: cell type


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 41


title: E4139 miRNA-Seq

description:
small RNA
endometrium_edgeR.txt


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 40


title: E4120 miRNA-Seq

description:
small RNA
endometrium_edgeR.txt


title: E4132 miRNA-Seq

description:
small RNA
endometrium_edgeR.txt


title: E4144 miRNA-Seq

description:
small RNA
endometrium_edgeR.txt


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 39


title: E4111 miRNA-Seq

description:
small RNA
endometrium_edgeR.txt


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 38


title: E4146 miRNA-Seq

description:
small RNA
endometrium_edgeR.txt


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 46


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 45


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 35


title: Wild-type 2


title: E4071 miRNA-Seq

description:
small RNA
endometrium_edgeR.txt


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 34


title: E4053 miRNA-Seq

description:
small RNA
endometrium_edgeR.txt


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 36


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 37


title: 4132 miRNA-Seq

description:
small RNA
extracellularVesicles_edgeR.txt

source_name: uterine lumen extracellular vesicles


title: 4144 miRNA-Seq


title: 4139 miRNA-Seq


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 33


title: E4169 miRNA-Seq

description:
small RNA
endometrium_edgeR.txt


title: 4146 miRNA-Seq


title: 4169 miRNA-Seq


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 32


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 31


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 30


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 29


title: E4169 RNA-Seq

data_processing:
Raw FASTQ files were adapter trimmed using cutadapt (version 1.11) at the core facility (University of Missouri DNA Core)
Reads were quality trimmed to a sliding window quality score of 30 and a minimum length of 20 bp with fqtrim (version 0.9.4, doi:10.5281/zenodo.20552)
Trimmed reads were mapped to the Ovis aries genome assembly (Oar_v3.1) with using hisat2 (version 2.0.3)
Reads overlapping annotations (ensembl version 84) were quantified with featureCounts (version 1.5.0)
Model based DE analysis was completed using the edgeR-robust method with raw read counts
Genes without evidence of expression (CPM rowSum < 1) were filtered out and false discovery rate (FDR) was set at 0.05 for differential expression (DE) analysis
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: ensembl gene ID, edgeR-robust FDR P-value, and RPKM for each sample in tab-delimited text format

extract_protocol:
Endometrium was physically dissected from the uterus at collection and snap frozen in liquid nitrogen. Total RNA was isolated from tissue homogenzied in TRIzol reagent.
Illumina TruSeq stranded mRNA


title: 4120 miRNA-Seq


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 28


title: 4111 miRNA-Seq


title: E4165 RNA-Seq


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 26


title: E4120 RNA-Seq


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 22


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 23


title: 4165 miRNA-Seq


title: E4111 RNA-Seq


title: E4146 RNA-Seq


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 25


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 19


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 21


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 24


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 17


title: E4053 RNA-Seq


title: E4144 RNA-Seq


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 18


title: E4139 RNA-Seq


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 16


title: 46hpi_P9

first: Daniel

middle: E.

last: Neafsey

state: MA

address: 415 Main St.

institute: Broad Institute

description:
TAGGCATG_P9
46hpi.raw.tsv
46hpi.normalized.tsv

data_processing:
Illumina NextSeq standard basecalling platform
Well barcode demultiplexing. Custom python script. Separates wells in 384-well plate
Unique molecular identifier demultiplexing. Custom python script. Counts reads from same mRNA molecule as only 1
Transcript alignment with bwa aln v0.7.10 allowing 4 mismatches in seed sequence and rest of sequence.
Discard reads with polyA tails (> 20 As in a row)
Additional filtering: Filter reads for rRNA. Remove samples with fewer than 300 reads. Remove genes that were found in <20 samples.
Generate normalized abundances with edgeR v3.14.0
Genome_build: PlasmoDB Plasmodium falciparum 3D7 transcript v29
Supplementary_files_format_and_content: 38hpi.raw.tsv - 38hpi raw read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 42hpi.raw.tsv - 42hpi raw read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 46hpi.raw.tsv - 46hpi raw read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 38hpi.filtered.tsv - 38hpi filtered read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 42hpi.filtered.tsv - 42hpi filtered read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 46hpi.filtered.tsv - 46hpi filtered read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 38hpi.normalized.tsv - 38hpi normalized read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 42hpi.normalized.tsv - 42hpi normalized read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: 46hpi.normalized.tsv - 46hpi normalized read counts in matrix format, where rows are samples and columns are genes
Supplementary_files_format_and_content: all.normalized.tsv - all normalized read counts from all time points in matrix forrmat, where rows are samples and columns are genes

organism: Plasmodium falciparum NF54

source_name: Single cell sorted Plasmodium infected human erythrocytes

growth_protocol: P.falciparum cell culture was performed as described previously (REF). Culture media consisted of RPMI-1640 supplemented with 25 mM HEPES, 100 μM hypoxanthine, 24 mM sodium bicarbonate, and gentamicin (all from Sigma-Aldrich). Serum media was generated by additional supplementation of 10% O+ human serum (The Interstate Companies) while serum-free medium was generated by additional supplementation of 0.39% fatty acid-free BSA, 30 μM oleic acid, and 30 μM palmitic acid (all from Sigma-Aldrich). To generate serum-free media supplemented with 20 μM LysoPC, LysoPC (Avanti Polar Lipids) was dissolved in ethanol and dried on culture dishes prior to culture addition. All cell cultures were maintained in a 5% CO2/1 % O2 and 95 % N2 gas mixture (Med-Tech Gases). All experiments used a clone of the Pf2004/164TdTomato P.falciparum line 14, which requires addition of 4 nM WR99210 (Jacobus Pharmaceuticals).

extract_protocol:
We used an optimized version of Single Cell RNA Barcoding and Sequencing 7 (SCRB-seq; Soumillon et al, 2014), further reducing the reverse transcriptase reaction volume. In brief, poly(A)+ mRNA from flow-sorted single Plasmodium infected erythrocytes were converted to cDNA, decorated with universal adapters, well barcodes, and unique molecular identifiers (UMIs), using a template-switching reverse transcriptase. Then, cDNA from multiple cells was pooled, amplified, and prepped for multiplexed sequencing using a transposon-based fragmentation method, enriching for 3’ ends and preserving strand information.
Nextera XT

treatment_protocol: Parasite cultures were sorbitol-synchronized (Sigma-Aldrich) as described previously 21 to a 4-hour cycle window using 4 consecutive treatments across two growth cycles. At 28-32 hour post invasion, parasites were washed in RPMI/mFA media and plated with or without LysoPC. At 4, 8, and 12 hours post induction, cells were stained with Vybrant DyeCycle Violet (Life Technologies) in HBSS (Thermo Fisher Scientific). Stained cells were pelleted and resuspended in phenol red-free PBS supplemented with 0.3% RNaseOUT (Life Technologies). Collection Twin.tec PCR 384-well plates (Eppendorf) were prepared by addition of cell lysis buffer to each well; lysis buffer consisted of nuclease-free water (Thermo Fisher Scientific) supplemented with 0.2% HF buffer (New England Biolabs). Single Vybrant Dye Cycle Violet-positive cells were sorted using a Beckman Coulter MoFlo Astrios EQ. At each time point, 48 cells from the non-induced culture (+LysoPC) and 336 cells from the induced culture (-LysoPC) were sorted into the collection plate and snap frozen on dry ice. Cultures were maintained for an additional two cycles for parasitemia and gametocytemia measurement. The media of both non-induced and induced cultures was replaced with RPMI/serum 12 hours post induction and daily thereafter.

tag: time point

tag: induced

value: Uninduced


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 15


title: 46hpi_P8

description:
TAGGCATG_P8
46hpi.raw.tsv
46hpi.normalized.tsv


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 27


title: 46hpi_P7

description:
TAGGCATG_P7
46hpi.raw.tsv
46hpi.normalized.tsv


title: 46hpi_P6

description:
TAGGCATG_P6
46hpi.raw.tsv
46hpi.normalized.tsv


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 14


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 13


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 12


title: 46hpi_P5

description:
TAGGCATG_P5
46hpi.raw.tsv
46hpi.normalized.tsv


title: 46hpi_P4

description:
TAGGCATG_P4
46hpi.raw.tsv
46hpi.normalized.tsv


title: 46hpi_unknown

description:
TAGGCATG_unknown
46hpi.raw.tsv
46hpi.normalized.tsv


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 11


title: E4071 RNA-Seq


title: 46hpi_P24

description:
TAGGCATG_P24
46hpi.raw.tsv
46hpi.normalized.tsv


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 10


title: E4132 RNA-Seq


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 08


title: 46hpi_P3

description:
TAGGCATG_P3
46hpi.raw.tsv
46hpi.normalized.tsv


title: 46hpi_P21

description:
TAGGCATG_P21
46hpi.raw.tsv
46hpi.normalized.tsv


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 09


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 20


title: 46hpi_P22

description:
TAGGCATG_P22
46hpi.raw.tsv
46hpi.normalized.tsv


title: 46hpi_P2

description:
TAGGCATG_P2
46hpi.raw.tsv
46hpi.normalized.tsv


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 07


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 05


title: 46hpi_P20

description:
TAGGCATG_P20
46hpi.raw.tsv
46hpi.normalized.tsv


title: 46hpi_P23

description:
TAGGCATG_P23
46hpi.raw.tsv
46hpi.normalized.tsv


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 03


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 04


title: 46hpi_P18

description:
TAGGCATG_P18
46hpi.raw.tsv
46hpi.normalized.tsv


title: Lymphoid-primed multipotent progenitor (LMPP) Mbd3del/del mouse 18219 cell 06


title: 46hpi_P19

description:
TAGGCATG_P19
46hpi.raw.tsv
46hpi.normalized.tsv