title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_6

value: Eed -/-

value: Male


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_7

status: Public on May 11 2022

type: SRA

city: Taipei

first: Pao-Yang

last: Chen

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

library_source: transcriptomic

data_processing:
The RNA-seq reads were aligned using HISAT2
Genes that are expressed (read counts > 0) in at least one replicate in both control and ECKO are included for analysis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using edgeR
WGBS reads were aligned with BS Seeker 2.  CG sites with read depth >= 4 are preserved in the Cgmap.gz file.
Genome_build: mm9
Supplementary_files_format_and_content: Excel files includes RPKM values for each sample.

molecule: polyA RNA

organism: Mus musculus

source_name: Primordial germ cells

growth_protocol: Control and ECKO male and female embryos were obtained from crosses between OG; Eedfl/fl (Lengner et al., 2007; Yu et al., 2009) homozygous females and BC; Eedf/l+ heterozygous males (Ohinata et al., 2005) at E10.5, E11.5 and E13.5. Embryos were staged by the detection of a vaginal plug on the morning after time-mating pairs were established E0.5.

extract_protocol:
Female E12.5 gonads were extracted and digested in 0.05% trypsin. GFP positive single mPGCs were sorted into a 96 well skirtless plate, each well containing 3 µL of 0.2% Triton X-100 and 2U/µL RNaseOUT (Thermo Fisher Scientific).
Single Cell RNA sequencing libraries were prepared according to the Smart Seq 2 single cell sequencing protocol (Picelli et al., 2014). The RNA was converted to cDNA in each well using Superscript II (Invitrogen). The cDNA was amplified in each well using a KAPA HiFI HotStart polymerase (KAPA Biosystems) in a PCR run for 18 cycles. cDNA was tagged via the Nextera Tagmentation kit (Illumina) using libraries A and C (Illumina). Indexed cDNA was pooled and run on a 2% agarose gel and the smear between 200-500 bp was extracted. Gel extract was cleaned with the Qiagen Gel Extraction Kit (Qiagen) and sent for sequencing.

tag: cell type

value: Primordial germ cells

tag: strain

tag: developmental stage

tag: genotype

tag: gender


title: scRNA-seq_E12-5_XY_ECKO_Embryo_2_Rep_8


title: mRNA-seq PFC Oxycodone Rep1

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

country: USA

institute: University of California, San Diego (UCSD)

description: mRNA transcripts from PFC Oxycodone Rep1

data_processing:
csRNA-seq: Sequencing reads were trimmed for 3’ adapter sequences using HOMER (“homerTools trim −3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20”) and aligned to the rat mRatBN7.2/rn7 genome assembly using STAR (Dobin et al., 2013) with default parameters. Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. Furthermore, reads with spliced or soft clipped alignments were discarded (the latter often removes erroneous alignments from abundant snRNA species). Transcription Start Regions (TSRs), representing 150 bp sized loci with significant transcription initiation activity (i.e. ‘peaks’ in csRNA-seq), were defined using HOMER’s findPeaks tool using the ‘-style tss’ option, which uses short input RNA-seq to eliminate loci with csRNA-seq signal arising from non-initiating, high abundance RNAs that nonetheless are captured and sequenced by the method (full description is available in Duttke et al. (Duttke et al., 2019)). To lessen the impact of outlier samples across the data collected for this study, csRNA-seq samples were first pooled into a single META-experiment per brain tissue region to collectively identify TSRs in each tissue.
Hi-C: Sequencing reads were first trimmed for sequences downstream of the restriction/ligation site (“GATCGATC”) and aligned to the rat genome using STAR with default parameters. Normalized interaction contact maps were then generated using HOMER. Juicer_tools was then used to generate the hic file.
snATAC-seq: Sequencing reads were processed using Cell Ranger ATAC 2.0 with a custom reference for Rattus norvegicus, built from the Ensembl Rnor 6.0 release 103 genome and annotation. The filtered results were subsequently analyzed using Signac 1.4.0 (Stuart et al., 2021).
RNA-seq: Sequencing reads were aligned to the rat mRatBN7.2/rn7 genome assembly using STAR (Dobin et al., 2013) with default parameters. Gene expression counts were calculated using featureCounts.
Assembly: rn7 (csRNA-seq, RNA-seq, Hi-C), rn6 (snATAC-seq)
Supplementary files format and content: BED (genomic locations of transcription start regions - TSRs), gene_counts.txt (tab-delimited text file with counts per gene from RNA-seq experiments), H5 (compressed sparse matrix file), TSV (tab delimited), CSV (comma separated file), hic (chromatin contact binary file)

organism: Rattus norvegicus

source_name: prefrontal cortex (PFC)

growth_protocol: Male Heterogenous Stock (HS) rats were trained to self-administer drugs in short access conditions (2 h/day for 4 days for oxycodone or 2 h/day for 10 days for cocaine) followed by long access conditions (12 h/day for oxycodone and 6 h /day for cocaine) for 14 days to develop escalation of drug intake. Age-matched naive male rats that were not exposed to any drug were used as control. Lastly, brain punches of PFC and NAc tissues were collected after 5 weeks of abstinence.

extract_protocol:
Brain punches of PFC and NAc tissues were extracted and snap-frozen (at -30°C). Cryosections of approximately 500 microns were used to dissect PFC and NAc punches on a –20°C frozen stage. Total RNA was extracted using the TRIZOL protocol.
csRNA-seq: csRNA-seq was performed as described previously (Duttke et al., 2019). Briefly, small RNAs of 15–60 nt were size selected from 0.3–1.0 microgram of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside, and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by Terminator 5’-phosphate-dependent exonuclease (Lucigen). Subsequent 5’ dephosphorylation by quickCIP (NEB) followed by decapping with RppH (NEB) augments Cap-specific 5’ adapter ligation by T4 RNA ligase 1 (NEB)(Hetzel et al., 2016). Thermostable quickCIP was used instead of rSAP and hence the bead clean-up step was skipped before heat denaturation prior to the second round of CIP treatment. The 3’ adapter was ligated using truncated T4 RNA ligase 2 (NEB) prior 3’ repair to select against degraded RNA fragments. Following cDNA synthesis, libraries were amplified for 11–14 cycles and sequenced SE75 on the Illumina NextSeq 500 sequencer.   RNA-seq: RNA sequencing libraries were generated using the Illumina Stranded mRNA Prep (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End reads (PE100) to a depth of approximately 25 million reads per sample on an Illumina NovaSeq 6000.  Hi-C: PFC tissue as pulverized in liquid nitrogen. The Arima-Hi-C kit was used to construct the Hi-C libraries (#A410231, Arima Genomics). Sequencing of the libraries was conducted on an Illumina Novaseq S4 instrument.   snATAC-seq: Nuclei were isolated from brain tissue as previously described (Corces et al., 2018). Briefly, frozen tissue was homogenized using a 2 ml glass dounce with 1 ml cold 1x Homogenization Buffer (HB). Cell suspension was filtered using a 70 µm Flowmi strainer (BAH136800070, Millipore Sigma) and centrifuged at 350g for 5 min at 4°C. Nuclei were isolated by iodixanol (D1556, Millipore Sigma) density gradient. The nuclei iodixanol solution (25%) was layered on top of 40% and 30% iodixanol solutions. Samples were centrifuged in a swinging bucket centrifuge at 3,000g for 20 min at 4°C. Nuclei were isolated from the 30%-40% interface. Library preparation targeting the capture of ~6000 nuclei was carried out as detailed in the Chromium Next GEM Single Cell ATAC v1.1 manual (10x Genomics). Library sequencing was performed using the Illumina NovaSeq.

value: heterogeneous stock (HS)

tag: treatment

value: prolonged abstinence after oxycodone intravenous self-administration

tag: tissue

value: prefrontal cortex (PFC)


title: mIMCD-3 WT cells, treatment 48 h dark + DMSO (1:1000) during last hour, experiment number e1994

city: Bonn

first: Jan

middle: N.

last: Hansen

address: Venusberg Campus 1

country: Germany

institute: University of Bonn

data_processing:
Sequencing data was demultiplexed and converted into fastq format using bcl2fastq2 v2.20
Kallisto version 0.44.0 was used to quantify abundances of transcripts from RNA-seq data.
Genome_build: Mus musculus, Release M16 (GRCm38.p5)
Supplementary_files_format_and_content: Count table (csv file) showing the pseudo-counts determined by kallisto. Rows reveal different transcripts, Columns reveal the different samples.

molecule: total RNA

source_name: immortalized kidney cell line (mIMCD-3)

growth_protocol: mIMCD-3 (CRL-2123) WT cells were obtained and authenticated from American Type Culture Collection (ATCC). Cyto-bPAC cells were described in Hansen et al., eLife, 2020. Cilia-bPAC cells were generated as folllows: WT mIMCD-3 cells were transfected with pc3.1-mNPHP3(201)-bPAC-mCherry (Hansen et al., 2020) and selected with 1.2 mg/ml Geneticin™ (G418 Sulfate, Gibco, #11811031) until cell clones could be picked, analyzed, and maintained as monoclonal cell lines. All cells have been tested and are free from mycoplasma and other microorganisms. All cells were maintained in DMEM/F12 (1:1) medium, supplemented with GlutaMax (Gibco, #31331-028) and 10 % FCS at 37°C and 5 % CO2. For Cilia-bPAC and Cyto-bPAC cells, growth medium during maintenance was additionally supplemented with 0.8 mg/ml G418. During the experiment, no G418 was supplemented. For the experiment, cells were seeded in triplicates in 6-well plates (2.46 x 105 cells/well, Greiner CELLSTAR, #657160) and kept in the dark during the entire experiment (except for specific light stimulations in some conditions, see treatment column). 24 h after seeding, cells were starved (starvation medium: reduced growth medium with 0.5 % FCS).

extract_protocol:
Cell lysis was performed under dim red light only to prevent activation of bPAC: Cells were washed ones with PBS and next directly lysed from the plates by addition of 400 µl / well of Trizol (Thermo Fisher Scientific, #15596026). Triplicates were pooled into one tube. RNA was extracted using the miRNeasy micro kit (Qiagen). Total RNA quantity and quality were determined via RNA assay on a Tapestation 4200 system (Agilent).
5 ng total RNA were used as an input for NGS library preparation following the SMART-Seq2 protocol (Picelli et al., 2014). Final libraries were quantified by HS dsDNA assay on a Qubit (Invitrogen) and fragment size distribution was checked via D5000 assay on a Tapestation 4200 system (Agilent). Libraries were equimolarly pooled and clustered at 1.4 pM and sequenced SR 75 cycles on a NextSeq500 instrument with High Output v2 chemistry (Illumina) to ~10 million raw reads per sample.

treatment_protocol: Either 24 h or 47 h after starting the starvation, cells were stimulated for 1 h with light (465 nm, 38.8 µW/cm²), or, alternatively, they were kept in the dark during the entire time. WT cells in the dark were stimulated also with DMSO or 10 mM Forskolin for 1 h (see characteristics for individual samples).

tag: experimentid

value: WT

tag: cell line

value: immortalized kidney cell line (mIMCD-3)


title: mRNA-seq PFC Naïve Rep1

description: mRNA transcripts from PFC Naïve Rep1

value: Naïve control


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_10

value: wild type

value: Female


title: invitro_DART-seq-APOBEC1-YTH-D422N Replicate 3

city: Durham

first: Huanyu

last: Zhu

state: NC

address: 307 Research Drive

department: Biochemistry

institute: Duke University

description:
Bed files were first generated for sites found in each replicate. Processed bed file are high confidence sites that were then found by further filtering for sites found in at least 2 of 3 replicates
processed data file:
inVitro_APO1-DF2_D422N-YTHmut.bed
inVitro_APO1-DF2_D422N-YTHblock.bed

data_processing:
library strategy: DART-Seq (deamination adjacent to RNA modification targets)
Trimming of adaptor sequences (Flexbar 3.0.3)
Alignment to hg19 using NovoAlign
Deduplication using SAMtools
YTHmut or YTHblock samples: Bam files were mered using SAMtools
Identification of m6A sites usin Bullseye
Genome_build: hg19
Supplementary_files_format_and_content: Bed files are lists of m6A sites identified within each replicate using Bullseye. High confidence m6A sites in paper were a result of keeping only these sites that occur in at least 2 of 3 replicates.

organism: Homo sapiens

source_name: Kidney

growth_protocol: HEK293T cells expressing DART or ADAR variants through transient transfection were cultured in DMEM + 10% FBS with penicillin/streptomycin.

extract_protocol:
Cellular DART-seq: Trizol was used to extract total RNA from cells expressing DART protein variants. The UltraII Directional RNA Library Prep Kit (NEB, E7760) with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, 7490) was used to generate sequencing libraries using 1000ng of input RNA. In vitro DART-seq: Trizol was used to extract total RNA from HEK293T cells. After in vitro DART treatment, edited RNA was isolated using RNeasy MiElute Cleanup Kit (Qiagen 74204).
Cellular DART-seq: The UltraII Directional RNA Library Prep Kit (NEB, E7760) with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, 7490) was used to generate sequencing libraries using 1µg of input RNA. In vitro DART-seq: The NEBNext Single Cell/Low Input RNA Library Prep Kit (NEB, E6420) was used to enerate sequencin libraries using the full 50ng of total RNA used during in vitro DART incubation.

treatment_protocol: STM2457 treatment: When cells were ~40% confluent. HEK293T cells were treated with 10µM of STM2457 for 72hrs. After 48hrs, ADAR-YTH, ADAR-YTH_D422N, ADAR-YTHmut, or ADAR were transiently transfected into treated cells.

value: 4hr, 37C, 50ng RNA, 250ng APOBEC1-YTH-D422N


title: mIMCD-3 Cilia-bPAC cells, treatment 24 h dark + 1 h light + 23 h dark, experiment number e1994

value: Cilia-bPAC

value: 24 h dark + 1 h light + 23 h dark


title: invitro_DART-seq-APOBEC1-YTH-D422N Replicate 2


title: mIMCD-3 Cyto-bPAC cells, treatment 47 h dark + 1 h light, experiment number e1994

value: Cyto-bPAC

value: 47 h dark + 1 h light


title: invitro_DART-seq-APOBEC1-YTH-D422N Replicate 1


title: snATAC-seq PFC

description: genomic DNA

library_source: genomic

data_processing:
csRNA-seq: Sequencing reads were trimmed for 3’ adapter sequences using HOMER (“homerTools trim −3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20”) and aligned to the rat mRatBN7.2/rn7 genome assembly using STAR (Dobin et al., 2013) with default parameters. Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. Furthermore, reads with spliced or soft clipped alignments were discarded (the latter often removes erroneous alignments from abundant snRNA species). Transcription Start Regions (TSRs), representing 150 bp sized loci with significant transcription initiation activity (i.e. ‘peaks’ in csRNA-seq), were defined using HOMER’s findPeaks tool using the ‘-style tss’ option, which uses short input RNA-seq to eliminate loci with csRNA-seq signal arising from non-initiating, high abundance RNAs that nonetheless are captured and sequenced by the method (full description is available in Duttke et al. (Duttke et al., 2019)). To lessen the impact of outlier samples across the data collected for this study, csRNA-seq samples were first pooled into a single META-experiment per brain tissue region to collectively identify TSRs in each tissue.
Hi-C: Sequencing reads were first trimmed for sequences downstream of the restriction/ligation site (“GATCGATC”) and aligned to the rat genome using STAR with default parameters. Normalized interaction contact maps were then generated using HOMER. Juicer_tools was then used to generate the hic file.
snATAC-seq: Sequencing reads were processed using Cell Ranger ATAC 2.0 with a custom reference for Rattus norvegicus, built from the Ensembl Rnor 6.0 release 103 genome and annotation. The filtered results were subsequently analyzed using Signac 1.4.0 (Stuart et al., 2021).
Genome_build: rn7 (csRNA-seq, Hi-C), rn6 (snATAC-seq)
Supplementary_files_format_and_content: BED (genomic locations of transcription start regions - TSRs), H5 (compressed sparse matrix file), TSV (tab delimited), CSV (comma separated file), hic (chromatin contact binary file)

molecule: genomic DNA

source_name: Single cell open chromatin sites from PFC

extract_protocol:
Brain punches of PFC and NAc tissues were extracted and snap-frozen (at -30°C). Cryosections of approximately 500 microns were used to dissect PFC and NAc punches on a –20°C frozen stage. Total RNA was extracted using the TRIZOL protocol.
csRNA-seq: csRNA-seq was performed as described previously (Duttke et al., 2019). Briefly, small RNAs of 15–60 nt were size selected from 0.3–1.0 microgram of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside, and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by Terminator 5’-phosphate-dependent exonuclease (Lucigen). Subsequent 5’ dephosphorylation by quickCIP (NEB) followed by decapping with RppH (NEB) augments Cap-specific 5’ adapter ligation by T4 RNA ligase 1 (NEB)(Hetzel et al., 2016). Thermostable quickCIP was used instead of rSAP and hence the bead clean-up step was skipped before heat denaturation prior to the second round of CIP treatment. The 3’ adapter was ligated using truncated T4 RNA ligase 2 (NEB) prior 3’ repair to select against degraded RNA fragments. Following cDNA synthesis, libraries were amplified for 11–14 cycles and sequenced SE75 on the Illumina NextSeq 500 sequencer.   Hi-C: PFC tissue as pulverized in liquid nitrogen. The Arima-Hi-C kit was used to construct the Hi-C libraries (#A410231, Arima Genomics). Sequencing of the libraries was conducted on an Illumina Novaseq S4 instrument.   snATAC-seq: Nuclei were isolated from brain tissue as previously described (Corces et al., 2018). Briefly, frozen tissue was homogenized using a 2 ml glass dounce with 1 ml cold 1x Homogenization Buffer (HB). Cell suspension was filtered using a 70 µm Flowmi strainer (BAH136800070, Millipore Sigma) and centrifuged at 350g for 5 min at 4°C. Nuclei were isolated by iodixanol (D1556, Millipore Sigma) density gradient. The nuclei iodixanol solution (25%) was layered on top of 40% and 30% iodixanol solutions. Samples were centrifuged in a swinging bucket centrifuge at 3,000g for 20 min at 4°C. Nuclei were isolated from the 30%-40% interface. Library preparation targeting the capture of ~6000 nuclei was carried out as detailed in the Chromium Next GEM Single Cell ATAC v1.1 manual (10x Genomics). Library sequencing was performed using the Illumina NovaSeq.


title: mIMCD-3 Cyto-bPAC cells, treatment 24 h dark + 1 h light + 23 h dark, experiment number e1994


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_9


title: invitro_DART-seq-APOBEC1-YTH Replicate 3

description:
Bed files were first generated for sites found in each replicate. Processed bed file are high confidence sites that were then found by further filtering for sites found in at least 2 of 3 replicates
processed data file:
inVitro_APO1-DF2YTH-YTHmut.bed
inVitro_APO1-DF2YTH-YTHblock.bed

value: 4hr, 37C, 50ng RNA, 250ng APOBEC1-YTH


title: Hi-C PFC

description: genomic DNA

source_name: 3D chromatin structure from PFC

value: SHR/OlaIpcv


title: invitro_DART-seq-APOBEC1-YTH Replicate 2


title: mRNA-seq PFC Cocaine Rep2

description: mRNA transcripts from PFC Cocaine Rep1

value: prolonged abstinence after cocaine intravenous self-administration


title: mIMCD-3 Cyto-bPAC cells, treatment 48 h dark, experiment number e1994

value: 48 h dark


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_11

value: Primordial germ cells


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_12


title: GOCA2_CELLS_RNASEQ_REP1

city: Doha

first: Najeeb

last: Halabi

address: Education City

country: Qatar

institute: Weill Cornell Medicine in Qatar

data_processing:
STAR_2.3.0e.Linux_x86_64
Rsubread 1.12.6
edgeR
Assembly: not provided
Supplementary files format and content: excel file with RPKM values

extract_protocol:
Qiagen mini RNA/DNA extraction kit
Nugen ovation single-cell RNA sequencing

value: OVARIAN CANCER


title: invitro_DART-seq-APOBEC1-YTH Replicate 1


title: mIMCD-3 WT cells, treatment 47 h dark + 1 h light, experiment number e1994


title: mIMCD-3 WT cells, treatment 24 h dark + 1 h light + 23 h dark, experiment number e1994


title: mIMCD-3 WT cells, treatment 48 h dark, experiment number e1994


title: APOCC_CELLS_RNASEQ_REP2

source_name: APOCC

value: APOCC


title: Cellular_DART-seq-ADAR Replicate 1

description:
processed data file:
cell_ADAR-DF2_D422N.bed
cell_ADAR-DF2_D422N-STM.bed

tag: transgene

value: ADAR


title: Cellular_DART-seq-ADAR Replicate 2


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_13


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_15


title: APOCC_CELLS_RNASEQ_REP1


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_14


title: scRNA-seq_E12-5_XX_Control_Embryo_2_Rep_16


title: mIMCD-3 WT cells, treatment 48 h dark + Forskolin 10 µM during last hour, experiment number e1989

value: WT

value: immortalized kidney cell line (mIMCD-3)


title: Cellular_DART-seq-ADAR-YTH-D422N-STM2457 Replicate 3

description:
Bed files were first generated for sites found in each replicate. Processed bed file are high confidence sites that were then found by further filtering for sites found in at least 2 of 3 replicates
processed data file:
cell_ADAR-DF2_D422N-STM.bed

value: cells were treated for 72hrs with 10µM of STM2459


title: A549, normoxia, ATRA (IA14)

city: Middletown

first: Nikolaos

last: Tsotakos

state: PENNSYLVANIA

address: 777 W Harrisburg Pike

institute: Penn State Harrisburg

data_processing:
Adapter sequences were trimmed and low length reads (<50nt) were discarded with Trimmomatic (v.0.38)
Alignment of the filtered reads to the human genome (hg38) was performed using hisat2 and features were counted with htseq
[20, 21]. Genes that were differentially expressed between groups were acquired with DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each sample

growth_protocol: A549 human lung epithelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNA-Bee (Tel-Test).
Stranded indexed cDNA libraries were prepared with the NEXTFLEX® Rapid Directional RNA-Seq Library Prep Kit (Perkin Elmer) following manufacturer's protocols.

treatment_protocol:
Cells were treated with 10^-5 mM ATRA or vehicle (ethanol) for 24 hours.
Cells were then exposed to either hyperoxia (95% O2) or normoxia (21% O2) for 72 hours.

value: adenocarcinoma, human alveolar basal epithelial cells

value: 10-5 mM ATRA, normoxia

tag: time


title: Cellular_DART-seq-ADAR-YTH-D422N-STM2457 Replicate 2

value: cells were treated for 72hrs with 10µM of STM2458


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_9

value: Eed -/-

value: Male


title: mIMCD-3 Cilia-bPAC cells, treatment 47 h dark + 1 h light, experiment number e1989

value: Cilia-bPAC

value: 47 h dark + 1 h light


title: mIMCD-3 WT cells, treatment 48 h dark + Forskolin 10 µM during last hour, experiment number e19115


title: GOCA2_CELLS_RNASEQ_REP2


title: Cellular_DART-seq-ADAR-YTH-D422N-STM2457 Replicate 1

value: cells were treated for 72hrs with 10µM of STM2457


title: A549, normoxia (IA13)

value: normoxia


title: A549, hyperoxia, vehicle (IA12)

value: ethanol (vehicle), hyperoxia


title: Cellular_DART-seq-ADAR-YTHmut Replicate 2

value: ADAR-YTHmut


title: A549, normoxia, vehicle (IA15)

value: ethanol (vehicle), normoxia


title: mIMCD-3 Cilia-bPAC cells, treatment 48 h dark, experiment number e1989

value: 48 h dark


title: mIMCD-3 Cilia-bPAC cells, treatment 24 h dark + 1 h light + 23 h dark, experiment number e1989

value: 24 h dark + 1 h light + 23 h dark


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_12

value: Primordial germ cells


title: mIMCD-3 Cyto-bPAC cells, treatment 47 h dark + 1 h light, experiment number e1989

value: Cyto-bPAC

value: immortalized kidney cell line (mIMCD-3)


title: Cellular_DART-seq-ADAR-YTH-D422N Replicate 3

description:
Bed files were first generated for sites found in each replicate. Processed bed file are high confidence sites that were then found by further filtering for sites found in at least 2 of 3 replicates
processed data file:
cell_ADAR-DF2_D422N.bed


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_13


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_10


title: mIMCD-3 Cyto-bPAC cells, treatment 24 h dark + 1 h light + 23 h dark, experiment number e1989


title: mIMCD-3 WT cells, treatment 48 h dark + DMSO (1:1000) during last hour, experiment number e1989

value: WT


title: A549, hyperoxia, ATRA (IA11)

value: adenocarcinoma, human alveolar basal epithelial cells

value: 10-5 mM ATRA, hyperoxia


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_14

value: Eed -/-


title: A549, hyperoxia (IA10)

value: adipogenic differentiation


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_11

value: Male


title: Cellular_DART-seq-ADAR-YTHmut Replicate 1


title: Cellular_DART-seq-ADAR-YTH-D422N Replicate 2


title: A549, normoxia, ATRA (IA09)

value: 10-5 mM ATRA, normoxia


title: mIMCD-3 WT cells, treatment 24 h dark + 1 h light + 23 h dark, experiment number e1989


title: A549, normoxia (IA07)


title: mIMCD-3 WT cells, treatment 48 h dark, experiment number e1989


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_15


title: scRNA-seq_E12-5_XY_ECKO_Embryo_1_Rep_16


title: Cellular_DART-seq-APOBEC1-YTHmut Replicate 3

description:
processed data file:
cell_APO1-DF2YTH.bed
cell_APO1-DF2_D422N.bed
cell_APO1-DF1YTH.bed
cell_APO1-DF1_D401N.bed


title: A549, normoxia, vehicle (IA08)


title: Cellular_DART-seq-APOBEC1-YTHmut Replicate 4


title: A549, hyperoxia, vehicle (IA06)


title: Cellular_DART-seq-APOBEC1-YTHmut Replicate 1


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_20

value: Female


title: A549, hyperoxia (IA04)

value: hyperoxia


title: Cellular_DART-seq-APOBEC1-YTHmut Replicate 2


title: A549, hyperoxia, ATRA (IA05)


title: A549, normoxia, ATRA (IA03)


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_18


title: Leaves infiltrated with X. citri 48 hpi, replicate2

city: Campinas

first: Celso

middle: Eduardo

last: Benedetti

state: SP

address: R. Giuseppe Maximo Scolfaro 10000

country: Brazil

institute: Laboratorio Nacional de Biociencias

description:
Sample_XC48_2
H2O_x_XC48.txt

data_processing:
The expression value of each transcript (FPKM) was calculated using RSEM according to Mortazavi et al. (2008)
Assembly: Reads of each sample (28.000.000 on average) were aligned with the Citrus sinensis transcripts of the Phytozome database using the RSEM program (Li and Dewey, 2011)
Supplementary files format and content: RPKMs

organism: Citrus sinensis

source_name: leaves

growth_protocol: Citrus plants were grown under green-house conditions

extract_protocol:
Infiltrated leaf sectors collected at 24 and 48 h post inoculation were frozen in liquid nitrogen and total RNA was extracted from three independent leaves using Trizol reagent.
The RNA samples were treated with DNase I to remove traces of DNA and subjected to HISEQ2500 Illumina sequencing at the LaCTAD facility of the State University of Campinas, Brazil

treatment_protocol: Plant leaves of similar size and age were infiltrated with water suspensions of Xc or Xa (OD600nm = 0.1), or water as control

value: leaves

tag: cultivar

value: Natal

tag: infection

value: XC infection 48 hpi


title: mIMCD-3 WT cells, treatment 47 h dark + 1 h light, experiment number e1989

value: 47 h dark + 1 h light


title: Leaves infiltrated with X. citri 48 hpi, replicate3

description:
Sample_XC48_3
H2O_x_XC48.txt


title: Leaves infiltrated with X. citri 48 hpi, replicate1

description:
Sample_XC48_1
H2O_x_XC48.txt


title: Leaves infiltrated with X. citri 24 hpi, replicate3

description:
Sample_XC_24_3
H2O_x_XC24.txt

value: XC infection 24 hpi


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_19

value: Primordial germ cells


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_17


title: Cellular_DART-seq-APOBEC1-DF1-D401N Replicate 2

description:
Bed files were first generated for sites found in each replicate. Processed bed file are high confidence sites that were then found by further filtering for sites found in at least 2 of 3 replicates
processed data file:
cell_APO1-DF1_D401N.bed


title: A549, hyperoxia (IA01)


title: Leaves infiltrated with X. citri 24 hpi, replicate2

description:
Sample_XC_24_2
H2O_x_XC24.txt


title: Cellular_DART-seq-ADAR-YTH-D422N Replicate 1


title: pcYY2-3

city: Chongqing

first: Yanjun

middle: Chongqing

last: Li

state: Chongqing

address: 174 Shazheng Street

country: China

institute: Chongqing University

data_processing:
illumina Hiseq 2000/2500 used for basecalling
Sequenced reads were filtered for Seqtk, and get clean Reads that can be used for data analysis, using the bowtie2 (version: 2-2.0.5), the Genome mapping was performed on post-pretreatment reads, which was more suitable for the sequencing data of the prokaryotic transcriptome. The comparison result generated by Mapping is the BAM file
Fragments Per Kilobase of exon model per Million mapped reads.We first apply HTSeq in TopHat than after each gene Fragments could count to count, and then use TMM (trimmed mean of M values) normalization method, finally calculated using perl script FPKM value of each gene.
Supplementary_files_format_and_content: count and FPKM

source_name: Human colon cancer cells

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
The cDNA fragments afterwards through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.


title: Cellular_DART-seq-APOBEC1-DF1-D401N Replicate 1


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_21


title: Cellular_DART-seq-APOBEC1-DF1YTH Replicate 3

description:
Bed files were first generated for sites found in each replicate. Processed bed file are high confidence sites that were then found by further filtering for sites found in at least 2 of 3 replicates
processed data file:
cell_APO1-DF1YTH.bed


title: A549, hyperoxia, ATRA (IA02)


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_23


title: Cellular_DART-seq-APOBEC1-DF1YTH Replicate 2


title: Cellular_DART-seq-APOBEC1-DF1YTH Replicate 1


title: pcCon-3


title: pcYY2-2


title: Leaves infiltrated with X. citri 24 hpi, replicate1

description:
Sample_XC_24_1
H2O_x_XC24.txt


title: Leaves infiltrated with X. aurantifolii 48 hpi, replicate2

description:
Sample_XA_48_2
H2O_x_XA48.txt

value: XA infection 48 hpi


title: pcCon-2


title: Cellular_DART-seq-APOBEC1-DF1-D401N Replicate 3


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_18

value: wild type


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_22


title: Cellular_DART-seq-APOBEC1-YTH-D422N Replicate 2

description:
Bed files were first generated for sites found in each replicate. Processed bed file are high confidence sites that were then found by further filtering for sites found in at least 2 of 3 replicates
processed data file:
cell_APO1-DF2_D422N.bed


title: Leaves infiltrated with X. aurantifolii 24 hpi, replicate3

description:
Sample_XA_24_3
H2O_x_XA24.txt

value: XA infection 24 hpi


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_20


title: Leaves infiltrated with X. aurantifolii 48 hpi, replicate1

description:
Sample_XA_48_1
H2O_x_XA48.txt


title: pcCon-1


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_17


title: pcYY2-1


title: Cellular_DART-seq-APOBEC1-YTH-D422N Replicate 1


title: Leaves infiltrated with water, replicate3

description:
Sample_H2O_3
H2O_x_XA24.txt
H2O_x_XA48.txt
H2O_x_XC24.txt
H2O_x_XC48.txt

value: Control, no infection


title: Leaves infiltrated with X. aurantifolii 48 hpi, replicate3

description:
Sample_XA_48_3
H2O_x_XA48.txt


title: scRNA-seq_E12-5_XX_ECKO_Embryo_1_Rep_24


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_19


title: Leaves infiltrated with X. aurantifolii 24 hpi, replicate1

description:
Sample_XA_24_1
H2O_x_XA24.txt


title: Cellular_DART-seq-APOBEC1-YTH-D422N Replicate 3


title: Cellular_DART-seq-APOBEC1-YTH Replicate 3

description:
Bed files were first generated for sites found in each replicate. Processed bed file are high confidence sites that were then found by further filtering for sites found in at least 2 of 3 replicates
processed data file:
cell_APO1-DF2YTH.bed


title: Leaves infiltrated with water, replicate2

description:
Sample_H2O_2
H2O_x_XA24.txt
H2O_x_XA48.txt
H2O_x_XC24.txt
H2O_x_XC48.txt


title: Leaves infiltrated with X. aurantifolii 24 hpi, replicate2

description:
Sample_XA_24_2
H2O_x_XA24.txt


title: Leaves infiltrated with water, replicate1

description:
Sample_H2O_1
H2O_x_XA24.txt
H2O_x_XA48.txt
H2O_x_XC24.txt
H2O_x_XC48.txt


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_22


title: Cellular_DART-seq-APOBEC1-YTH Replicate 2


title: WGBS_E10.5_XX_ECKO_Rep_2

extract_protocol:
Female E10.5 gonads were extracted and digested in 0.05% trypsin. GFP positive single mPGCs were sorted into a 96 well skirtless plate, each well containing 3 µL of 0.2% Triton X-100 and 2U/µL RNaseOUT (Thermo Fisher Scientific).
Cells were sorted into lysis buffer from Zymo MethylDirect Kit and bisulfite converted, and then constructed libraries with Zymo Pico Methylation Kit.


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_23


title: X-linked IE2-GFP DFF-ChIP

city: Iowa City

first: David

middle: H

last: Price

state: IA

address: 431 Newton Road

department: Department of Biochemistry and Molecular Biology

institute: University of Iowa

data_processing:
Adapter trimming using trim_galore 0.6.
Alignment of trimmed reads to hg38 using bowtie 1.2.2 (ChIP-Seq) or hisat2 (RNA-Seq)
Deduplication of fragments based on their unique molecular index tags using awk and bash.
Conversion of deduped bed files into bedGraph and bigwig using bedtools genomecov and kentUtils bedGraphToBigWig programs.
Genome_build: hg38 (human), KF297339.1 (HCMV TB40/E), FJ616285.1 (HCMV Towne)
Supplementary_files_format_and_content: bigwig files containing pileup of normalized RNA-Seq data and ChIP data

source_name: Human Foreskin Fibroblast

growth_protocol: HFF cells were maintained in DMEM (Gibco 11965-092) supplemented with 10% FBS.

extract_protocol:
For RNA-Seq, cells were directly lysed in Trizol, and extracted and DNase treated prior to quality control analysis as described in the text. For standard ChIP-Seq, cells were fixed in 1% formaldehyde, harvested, and frozen as described in the text. Chromatin was sheared and ChIP was performed as detailed in the methods. For DFF-ChIP, native isolated nuclei or crosslinked cells were harvested as described in the methods, and chromatin was digested with DFF for 1 hour at 37° C. Soluble chromatin was extracted and ChIP was carried out as described in the methods.
Details of library construction for each type of assay are provided in the methods.

treatment_protocol: HFF were infected at an MOI of 3 with the indicated virus for the indicated times. DMSO vehicle control or dTAG treatments were carried out for 6 or 12 h as previously described.

value: Human Foreskin Fibroblast

value: Untreated

value: HCMV TB40/E IE2-GFP 48 h

tag: chip antibody

value: GFP-Trap agarose (Chromotek gta-10)


title: Native IE2-GFP DFF-ChIP


title: IE2-GFP-Standard ChIP Rep 2


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_21


title: scRNA-seq_E12-5_XX_Control_Embryo_1_Rep_24


title: Cellular_DART-seq-APOBEC1-YTH Replicate 1


title: MD_007 RNA, biological

type: RNA

city: Yangsan

first: Jae-Hwan

last: Choi

address: Kumo-ro 20, Beomo-ri, Mulgum-eup

department: Neurology

country: South Korea

institute: Pusan National University Yangsan Hospital

description: Gene expression data from MD

hyb_protocol: Approximately 5.5 μg of the labeled cDNAs were hybridized onto the Affymetrix GeneChip Array at 45℃ for 16 hours.

scan_protocol: After washing, the arrays were stained on a GeneChip Fluidics Station 450 and scanned on the GeneChip Scanner 3000.

data_processing:
Raw data were analyzed using Affymetrix GeneChip Command Console Software (AGCC). The raw data were summarized and normalized with Robust Multi-array Average (RMA) module implemented in Affymetrix Power Tools.
The differentially expressed genes (DEGs) between MD and normal control samples were screened by fold-change (fc) filtering combined with student’s t-test. False discovery rate (FDR) was controlled by adjusted p-value using Benjamini-Hochberg algorithm. Genes were considered differentially expressed at |fold changes| > 2.0 and adjusted p-value < 0.05.

label: biotin

source_name: peripheral whole blood

label_protocol: Purified RNA sample was transcribed to double-strand cDNA using the GeneChip Whole Transcript (WT) Amplication kit. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

extract_protocol: The samples were incubated for a minimum of 2 hours at room temperature (15-25℃) to achieve complete lysis of blood cells. And then, the samples were centrifuged for 10 minutes at 5000 x g using a swing-out rotor. The supernatant was decanted, and 4 mL of RNase-free water was added to the pellet. The samples were vortexed until the pellet was visibly dissolved, and centrifuged for 10 minutes at 5000 x g. After the entire supernatant was removed, the remaining pellet was resuspended in 350 μL of buffer BR1 and transferred to microcentrifuge tube, followed by automated RNA purification using QIAcube. The purity and quantity of RNA were measured using a NanoDrop ND-1000 (Thermo Fisher Scientiﬁc, Wilmington, DE, USA). The quality of RNA was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) with an RNA Integrity Number.

treatment_protocol: Peripheral whole blood (2.5 ml) was collected from the patients andhealthy normal controls. The samples immediately placed into PAXgene Blood RNA Tubes (QIAGEN), and were stored under refrigerated conditions (2-8℃) before RNA extraction.

value: Whole blood

tag: disease

value: Meniere's disease (MD)


title: MD_008 RNA, biological

description: Gene expression data from MD


title: WGBS_E10.5_XX_ECKO_Rep_1

value: Eed -/-

value: Female


title: MD_009 RNA, biological

description: Gene expression data from MD


title: IE2-GFP Standard ChIP Rep 1


title: WGBS_E10.5_XX_Control_Rep_2


title: WGBS_E10.5_XX_Control_Rep_3


title: High, 1048_L

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

data_processing:
FASTQC software (v0.11.8) was used to check the quality of the raw sequencing reads.
Sequencing indexing adapters were removed using Cutadapt (v2.6)
Input reads were then aligned to the bovine reference genome (UMD3.1) using STAR (v2.6.1), incorporating the quantmode function to determine the number of mapped reads.
The R (v3.4) Bioconductor package, EdgeR (v3.5), was applied to identify statistically significant differentially expressed genes.
A false discovery rate (FDR) of <0.1 was applied as a threshold to call genes with differential expression levels.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: Tab delimited txt file of merged gene read counts

organism: Bos taurus

source_name: Liver

growth_protocol: Angus X Holstein-Friesian heifer calves were fed differentially either a High plane of nutrition (n=15) or a Moderate plane of nutrition (n=15)  from 2-21 weeks of age. Calves on the High plane of nutrition were expected to grow at 1.2 kg/day, with the Moderate plane of nutrition expected to gain 0.5 kg/day.

extract_protocol:
RNA was  precipitated and purified from hypothalamus samples using the Qiagen RNeasy Plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
cDNA libraries were prepared from high quality RNA  using the Illumina TruSeq stranded RNA sample prep kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.

treatment_protocol: Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates during the calf phase. During the subsequent post-weaning phase this group were then offered concentrates ad libitum and hay to appetite. During the calf phase the Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 1 kg of concentrates, subsequently receiving 1kg of concentrates and hay to appetite during the post-weaning phase. The calf phase lasted for 8 weeks and was followed by the post-weaning phase which lasted for 11 weeks.

tag: diet

value: High-plane of nutrition

value: Liver

tag: breed

value: Holstein-Friesian X Angus


title: Pol II Standard ChIP

tag: cell type

value: POLR2A mouse mAb (Santa Cruz sc-55492)


title: WGBS_E10.5_XX_Control_Rep_1

value: Primordial germ cells

tag: strain


title: RNA-seq_E11.5_XY_ECKO_Rep_4

extract_protocol:
Male and female E11.5 and male E13.5 gonads were extracted and digested in 0.05% trypsin. GFP positive mPGCs were sorted into 300 µL RLT buffer and RNA extracted using the Rneasy Micro Kit (Qiagen)
Following cleanup, the samples were converted to cDNA following the Ovation RNA-seq System V2 protocol (Nugen). cDNA was indexed using the Ovation Rapid DR Multiplex System (Nugen).

tag: developmental stage

value: Male


title: Moderate, 2532_L

value: Moderate-plane of nutrition


title: High, 2528_L


title: Moderate, 2537_L


title: 12 h dTAG RNA-Seq Rep 2

value: 12 h dTAG

value: HCMV Towne IE2-FKBP 96 h


title: 12 h dTAG RNA-Seq Rep 3

value: Human Foreskin Fibroblast


title: High, 2535_L


title: High, 2120_L


title: RNA-seq_E11.5_XY_ECKO_Rep_3

tag: genotype


title: MD_006 RNA, biological

description: Gene expression data from MD


title: MD_003 RNA, biological

description: Gene expression data from MD


title: MD_005 RNA, biological

description: Gene expression data from MD


title: 6 h dTAG RNA-Seq Rep 3

value: 6 h dTAG


title: Control_009 RNA, biological

description: Gene expression data from control

value: Control


title: MD_002 RNA, biological

description: Gene expression data from MD


title: 6 h dTAG RNA-Seq Rep 2


title: MD_004 RNA, biological

description: Gene expression data from MD


title: Moderate, 1690_L


title: Control_008 RNA, biological

description: Gene expression data from control


title: RNA-seq_E11.5_XY_ECKO_Rep_2

tag: gender


title: MD_001 RNA, biological

description: Gene expression data from MD


title: 6 h dTAG RNA-Seq Rep 1

tag: treatment


title: 12 h dTAG RNA-Seq Rep 1


title: Moderate, 2346_L

tag: tissue


title: 6 h DMSO RNA-Seq Rep 3

value: 6 h DMSO


title: High, 1707_L


title: Control_007 RNA, biological

description: Gene expression data from control

value: Whole blood


title: RNA-seq_E11.5_XY_Control_Rep_4

value: wild type


title: High, 1531_L


title: RNA-seq_E11.5_XY_Control_Rep_2


title: RNA-seq_E11.5_XY_ECKO_Rep_1

value: Eed -/-


title: Moderate, 1392_L


title: RNA-seq_E11.5_XY_Control_Rep_1


title: mIMCD-3 Cyto-bPAC cells, treatment 48 h dark, experiment number e1989

tag: experimentid

value: Cyto-bPAC

value: immortalized kidney cell line (mIMCD-3)

value: 48 h dark


title: Input 2

city: Wuhan

first: Dong

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After aligning the reads to the human reference genome GRCH38 with TopHat 2, we only kept those reads that mapped uniquely for downstream analysis. The “ABLIRC” strategy was used to identify the genomic regions of IGF2BP2 binding.
We finally determined the IP target genes by the peaks and used the HOMER software to call the IP binding motifs
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.

source_name: KGN cells, Input

growth_protocol: KGN cells were irradiated once for 400 mJ/cm2, ground in liquid nitrogen and lysed in ice-cold wash buffer. Cells lysis was performed in cold wash buffer (1× PBS, 0.1% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate) supplemented with a 200 U/mL RNase inhibitor (Takara, Japan) and protease inhibitor cocktail (Roche) and incubated on ice for 30 min. We cleared the cell lysate by centrifugation at 10,000 rpm for 10 min at 4°C. We then added RQ I (1 U/μl, Promega, England) to a final concentration of 1 U/μl and incubated it in a water bath for 30 min at 37°C. Immediately afterwards, we added a stop solution to the lysates in order to quench DNase. The mixture was then vibrated vigorously and centrifuged at 13,000 × g at 4℃ for 20 min to remove cell debris. RNA digestion was then performed by MNase (EN0181, Thermo Scientific, Germany).

extract_protocol:
The immunoprecipitates were further incubated with protein A /G Dynabeads for 2h at 4 °C. After applying the magnet and removing the supernatant, we sequentially washed the beads with lysis buffer, high-salt buffer (250 mM Tris 7.4, 750 mM NaCl, 10 mM EDTA, 0.1% SDS, 0.5% NP-40 and 0.5% deoxycholate), and PNK buffer (50 mM Tris, 20 mM EGTA and 0.5% NP-40) twice. The beads were then resuspended in Elution buffer (50 nM Tris 8.0, 10 mM EDTA and 1% SDS) and the suspension was incubated for 20 min in a heat block at 70°C to release the immunoprecipitated RBP with crosslinked RNA before vortex. The magnetic beads were removed from the separator and the supernatant was transferred to a clean 1.5 ml microfuge tube. Proteinase K (Roche) was added to the 1% input (without immunoprecipitated）and the immunoprecipitated RBP with crosslinked RNA to a final concentration of 1.2 mg/ml, and the mixture was incubated for 120 min at 55°C.
The RNA was purified with the Trizol reagent (Life technologies, USA).  cDNA libraries were prepared with the KAPA RNA Hyper Prep Kit (KK8541, KAPA, Boston, USA) according to the manufacturer’s protocol. We prepared high-throughput sequencing libraries following the manufacturer's instructions for the Illumina NovaSeq 6000 system with 150 nt paired-end sequencing.

treatment_protocol: For immunoprecipitation, the supernatant was incubated overnight at 4 °C with 10μg IGF2BP-antibody (11601-1-AP, Proteintech, Chicago, USA) and control IgG-antibody (2729S, CST, USA).

tag: cell line

value: KGN

tag: rip antibody

value: IgG-antibody (2729S, CST, USA)


title: 6 h DMSO RNA-Seq Rep 1


title: Moderate, 1689_L

value: Liver

value: Holstein-Friesian X Angus


title: RNA-seq_E11.5_XY_Control_Rep_3

value: Primordial germ cells

value: Male


title: Control_005 RNA, biological

description: Gene expression data from control


title: TN-wt-3

city: Seoul

first: Jae Bum

last: Kim

address: Bldg 105-Rm. 333, Seoul National University, San 56-1, Sillim Dong, Kwanak-Gu

department: Biological Sciences

institute: Seoul National University

data_processing:
Raw sequenced reads were trimmed and performed quality control using TrimGalore (version 0.4.4)
The trimmed reads were mapped to the mouse genome GRCm38/mm10 by STAR aligner (version 2.6.1d)
Raw read counts per gene were computed with HTSeq-count (version 0.13.5)
Statistical test for differentially expressed genes (DEG) was performed by DESeq2 (version 1.30.0)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files inclues raw gene counts for every gene and every sample

source_name: inguinal adipose tissue

growth_protocol: 10 week old male mice

extract_protocol:
inguinal adipose tissues were isolated from mice
mRNA libraries were prepared for sequencing using standard protocols.

treatment_protocol: Thermoneutral (30℃) 1 week or cold (4-6℃) 3 days

value: inguinal adipose tissue

tag: age

value: HIF2a loxP/loxP

value: Thermoneutral (30℃) 1 week


title: Control_002 RNA, biological

description: Gene expression data from control

value: Control


title: High, 1388_L

value: High-plane of nutrition


title: TN-wt-2


title: Moderate, 1395_L

value: Moderate-plane of nutrition


title: IGF2BP2 IP 2

source_name: KGN cells, IGF2BP2 IP

value: IGF2BP-antibody (11601-1-AP, Proteintech, Chicago, USA)


title: IGF2BP2 IP 1


title: Control_004 RNA, biological

description: Gene expression data from control

value: Whole blood


title: High, 1089_L


title: High, 1360_L


title: Control_003 RNA, biological

description: Gene expression data from control


title: Moderate, 1057_L


title: Input 1


title: MPRA-pDNA-rep2

city: Kansas City

first: Scott

middle: T

last: Younger

state: MO

address: 2401 Gillham Road

institute: Children's Mercy Kansas City

data_processing:
MPRA Read Alignment: First 12 bases of each read matched to MPRA oligonucleotide barcode
MPRA Differential Expression: DESeq2 with default options
RNA-Seq Read Alignment: STAR with default options and pre-alignment adapter trimming
RNA-Seq Gene Abundance Determination: featureCounts using Gencode v38 as reference transcriptome
RNA-Seq Differential Expression: DESeq2 with default options
Genome_build: hg38
Supplementary_files_format_and_content: TXT files are expression matrices with normalized read counts for each library element (MPRA) or abundance determinations for each gene (RNA-Seq)

molecule: other

organism: other sequences

source_name: Plasmid

extract_protocol:
TRiZol (Thermo Fisher) / RNEasy mini kit (Qiagen)
Amplicon Sequencing / TruSeq DNA PCR-Free High Throughput Library Prep Kit

tag: molecule type

value: plasmid DNA


title: TN-2KO-1

value: Adipoq-Cre HIF2a loxP/loxP


title: Control_006 RNA, biological

description: Gene expression data from control


title: Control_001 RNA, biological

description: Gene expression data from control


title: Moderate, 1082_L


title: MPRA-pDNA-rep1


title: Azole Resistant Progeny Pool BC6 rep3 [S6BCR3]

city: Nottingham

first: Fei

last: Sang

address: QMC

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

description:
S18
S6BCR.filtered.pass.snpEff.protein_coding.vcf.gz

data_processing:
Raw PE reads were trimmed against adaptor sequences by scythe (v0.981), and quality trimmed by sickle (v1.33) using default settings.
Trimmed reads were aligned to the reference using bwa (v0.7.17) with default settings.
Uniquely and correctly mapped reads were extracted for the downstream analysis. GATK (v2.4-9) was used to detect variants
SnpEff was used to annotate variants
Genome_build: Aspergillus fumigatus A1163 (JGI Build Aspfu_A1163_1)
Supplementary_files_format_and_content: NOT PROVIDED

organism: Aspergillus fumigatus

source_name: DNA from 40 pooled azole resistant progeny from sixth back cross (BC6) to isolate 47-51

growth_protocol: Isolates were cultured on Aspergillus complete medium and grown for 7 days at 28 ˚C before use.

extract_protocol:
DNA was extracted using a Qiagen Plant DNA extraction kit following the manufacturer’s instructions for adaptation for filamentous fungi. DNA quality and quantity for genome sequencing was then assessed by gel electrophoresis, Nanodrop and Qubit methodologies.
Libraries were prepared from 100 ng to 1 ug of input DNA using the NEBNext Ultra kit (NEB, UK) following the manufacturer’s standard protocol. Libraries were then pooled and sequenced using the MiSeq instrument with the MiSeq Reagent Kit v3 (600 cycles) (Illumina, USA) to generate 2 x 300bp paired end reads

treatment_protocol: Azole sensitivity or resistance of parental A. fumigatus isolates and subsequent progeny were determined using the ETEST® method in accordance with manufacturer’s instructions (Biomerieux).

tag: genotype/phenotyp

value: azole resistant

tag: strain/isolate background


title: Azole Sensitive Progeny Pool BC6 rep2 [S6BCS2]

description:
S14
S6BCS.filtered.pass.snpEff.protein_coding.vcf.gz

source_name: DNA from 40 pooled azole sensitive progeny from sixth back cross (BC6) to isolate 47-51

value: wild type azole sensitive


title: KGN cells, OE IGF2BP2 2

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
The dataset containing the clean reads was aligned to the GRch38 genome by tophat2 allowing 4 mismatches.
Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped)
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified using the ABLas pipeline.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: KGN cells, IGF2BP2 over-expression

growth_protocol: KGN cells were cultured at 37 ℃ in DMEM/F-12 with 10% fetal bovine serum (FBS, Gibco, USA), 1% penicillin-streptomycin (5,000 U/mL, Gibco, USA). KGN cells were transfected with pIRES-hrGFP-1a-IGF2BP2 and empty vectors (control) by Lipofectamine 2000 (11668019, Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48h for RT-qPCR analysis.

extract_protocol:
The KGN cells were ground into a fine powder before RNA extraction. Total RNA was treated with RQ1 DNase (Promega) to remove DNA. For each sample, 0.5μg of total RNA was used for RNA-seq library preparation using the KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (KK8544). Polyadenylated mRNAs were purified, fragmented and converted into double strand cDNA. Following the end repair and A tailing, the DNA fragments were ligated to the Diluted Roche Adaptor (KK8726). After purifying and size fractioning to 300-500bps, the ligated products were amplified and purified, quantified and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) was not amplified, allowing for strand-specific sequencing.
The libraries were prepared for high-throughput sequencing following the manufacturer's instructions for the Illumina NovaSeq 6000 system with 150 nt paired-end sequencing.

treatment_protocol: The overexpression of IGF2BP2 in KGN cells via plasmid transfection was verified RT-qPCR. Briefly, standard procedures were followed to obtain the cDNA and RT-qPCR was performed on the Bio-Rad S1000 with Bestar SYBR Green RT-PCR Master Mix (DBI Bioscience, Shanghai, China). The expression of GAPDH (glyceraldehyde-3-phosphate dehydrogenase) was used as an internal control. The concentration of each transcript was normalized to GAPDH mRNA level using 2- ΔΔCT method (Livak & Schmittgen 2001). Paired Student’s t-test was performed via GraphPad Prism software (San Diego, CA) to compare the differences.

value: KGN

value: IGF2BP2 overexpression


title: KGN cells, OE IGF2BP2 3


title: TN 2KO 3


title: High, 1050_L

value: Liver

value: Holstein-Friesian X Angus


title: Azole Sensitive Progeny Pool BC6 rep1 [S6BCS1]

description:
S13
S6BCS.filtered.pass.snpEff.protein_coding.vcf.gz

value: pooled azole sensitive progeny from sixth back cross (BC6) to isolate 47-51


title: Azole Resistant Progeny Pool BC6 rep2 [S6BCR2]

description:
S17
S6BCR.filtered.pass.snpEff.protein_coding.vcf.gz

value: pooled azole resistant progeny from sixth back cross (BC6) to isolate 47-51


title: Azole Resistant Progeny Pool BC6 rep1 [S6BCR1]

description:
S16
S6BCR.filtered.pass.snpEff.protein_coding.vcf.gz


title: KGN cells, OE IGF2BP2 1


title: Azole Sensitive Progeny Pool BC6 rep3 [S6BCS3]

description:
S15
S6BCS.filtered.pass.snpEff.protein_coding.vcf.gz


title: Moderate, 991_L


title: KGN cells, NC 3

source_name: KGN cells, control plasmid

value: control


title: Moderate, 981_L


title: cold-wt-1

value: inguinal adipose tissue

value: HIF2a loxP/loxP

value: Cold (4-6℃) 3 days


title: cold-wt-3


title: TN 2KO 2

value: Thermoneutral (30℃) 1 week


title: cold-wt-2


title: Azole Resistant Progeny Pool BC2 rep3 [S2BCR3]

description:
S12
S2BCR.filtered.pass.snpEff.protein_coding.vcf.gz

source_name: DNA from 60 pooled azole resistant progeny from second back cross (BC2) to isolate 47-51


title: KGN cells, NC 2


title: cold-2KO-3


title: Moderate, 975_L

value: Moderate-plane of nutrition


title: sgKDM5B-rep2

value: sgRNA pool targeting KDM5B

value: mRNA


title: High, 986_L

value: High-plane of nutrition


title: Moderate, 911_L


title: cold-2KO-2

value: Adipoq-Cre HIF2a loxP/loxP


title: Azole Resistant Progeny Pool BC2 rep1 [S2BCR1]

description:
S10
S2BCR.filtered.pass.snpEff.protein_coding.vcf.gz

value: azole resistant

value: pooled azole resistant progeny from second back cross (BC2) to isolate 47-51


title: Azole Resistant Progeny Pool BC2 rep2 [S2BCR2]

description:
S11
S2BCR.filtered.pass.snpEff.protein_coding.vcf.gz


title: High, 553_L


title: sgKDM5B-rep1


title: Azole Sensitive Progeny Pool BC2 rep3 [S2BCS3]

description:
S9
S2BCS.filtered.pass.snpEff.protein_coding.vcf.gz

source_name: DNA from 60 pooled azole sensitive progeny from second back cross (BC2) to isolate 47-51

value: wild type azole sensitive


title: KGN cells, NC 1

value: KGN


title: cold-2KO-1


title: Moderate, 3622_L

value: Liver

value: Holstein-Friesian X Angus


title: Azole Sensitive Progeny Pool BC2 rep2 [S2BCS2]

description:
S8
S2BCS.filtered.pass.snpEff.protein_coding.vcf.gz

value: pooled azole sensitive progeny from second back cross (BC2) to isolate 47-51


title: sgVariant-rep2

value: sgRNA pool targeting Variant Site


title: High, 3148_L


title: sgVariant-rep1


title: High, 3620_L


title: sgNT-rep1

value: Nontargeting sgRNA pool


title: sgNT-rep2


title: Azole Sensitive Progeny Pool BC2 rep1 [S2BCS1]

description:
S7
S2BCS.filtered.pass.snpEff.protein_coding.vcf.gz


title: Azole Resistant Parent  rep3 [S1711C]

description:
S6
S1711.filtered.pass.snpEff.protein_coding.vcf.gz

source_name: Isolate 47-308

value: Isolate 47-308


title: Learned_Motor Learning_Scramble

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University School of Medicine

description:
processed data file: Fgfr2_KO_aggr_filtered_feature_bc_matrix.h5
M_HK-Sc-D3_S4_L001

data_processing:
Raw sequencing reads were examined by quality metrics and analyzed using the Cell Ranger pipeline (10X Genomics).
Given that the single-nuclei RNA-seq assay captures unspliced pre-mRNA with introns as well as mature mRNA, a custom reference is not appropriate for alignment that only counts reads aligned to exons. Therefore, we created a new "pre-mRNA" GTF with listing each gene transcript locus as an exon and then run cellranger mkref command to generate a genome reference. Next, the cellranger count command was used to generate raw feature-barcode matrices aligned to the newly generated reference (mm10) above.
To ensure PCR amplified transcripts were counted only once, only single UMIs were counted for gene expression level.
To minimize batch effects in combining the different samples, we used cellranger aggr pipeline to equalize the read depth between samples and recomputes the matrices. In this way, the combined cell x UMI count matrix was generated for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: A H5 file of combined cell x UMI count matrix for all samples

source_name: Single nuceli

extract_protocol:
Whole cerebellum  microdissected from mice upon accelerating motor learning (Baseline, learned) under Scramble and Fgfr2 KO conditions were rapidly transferred to a chilled dounce homogenizer and dounced in 1.5 ml homogenization buffer containing 0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitor to release nuclei. Each sample were mixed with 1.5 ml 50% iodixanol (Sigma) and layered onto 29% iodixanol. The gradient was centrifuged at 10,000 g for 30 mins at 4°C. Nuclei were diluted in 10% BSA with Dyecycle Ruby for FACS. Dyecycle Ruby was used for singlet and GFP for positive was sorted for Purkinje nuclei. After counting and analyzing nuclei integrity, all samples were subjected to library construction by using Chromium Single Cell 3’ Reagent Kit V3 (10X Genomics).
Single nuclei RNA seq: Single nuclei libraries were prepared for sequencing using standard protocols

tag: genotype/variation

value: Scramble

value: Cerebellum


title: High, 2570_L

tag: diet


title: MPRA-cDNA-rep2

value: MPRA Library


title: Azole Resistant Parent  rep2 [S1711B]

description:
S5
S1711.filtered.pass.snpEff.protein_coding.vcf.gz


title: Learned_Associative Learning Paradigm Rep2

description: All_samples_rep2_combined_aggr_filtered_feature_bc_matrix.h5

extract_protocol:
Whole cerebellum or anterior lobules (anterior dorsal cerebellar vermis, ADCV) microdissected from mice upon different training conditions (Activation rotarod (baseline, activation), accelerating motor learning (Baseline, learning, learned), and associated motor learning (Baseline, learning and learned) were rapidly transferred to a chilled dounce homogenizer and dounced in 1.5 ml homogenization buffer containing 0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitor to release nuclei. Each sample were mixed with 1.5 ml 50% iodixanol (Sigma) and layered onto 29% iodixanol. The gradient was centrifuged at 10,000 g for 30 mins at 4°C. Nuclei were diluted in 10% BSA with Dyecycle Ruby for FACS. Dyecycle Ruby was used for singlet and GFP for positive was sorted for Purkinje nuclei. After counting and analyzing nuclei integrity, all samples were subjected to library construction by using Chromium Single Cell 3’ Reagent Kit V3 (10X Genomics).
Single nuclei libraries were prepared for sequencing using standard protocols

tag: group


title: Baseline_Motor Learning_Scramble

description:
processed data file: Fgfr2_KO_aggr_filtered_feature_bc_matrix.h5
M_HK-Sc-Base_S3_L001


title: MPRA-cDNA-rep1


title: Azole Resistant Parent  rep1 [S1711A]

description:
S4
S1711.filtered.pass.snpEff.protein_coding.vcf.gz


title: Learned_Motor Learning_Fgfr2_KO

description:
processed data file: Fgfr2_KO_aggr_filtered_feature_bc_matrix.h5
M_HK-KO-D3-Tfg_S3_L001

value: Fgfr2 KO


title: RB05_mRNA

city: Guangzhou

first: Cheng

last: Wu

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen University

data_processing:
Illumina BCL files were converted to fastq files by using 10X Genomics Cell Ranger pipeline mkfastq function (v 2.1.0; https://support.10xgenomics.com/)
Cellranger count function was used to generate Gene-Barcode matrices from the FASTQ files, which uses the STAR algorithm to map high-quality reads to the human reference genome (GRCh38), then performs UMI counting.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene-cell counts for every sample

source_name: Retiboblastoma

extract_protocol:
Single cells of RB tumor tissues were isolated by using Neuronal Isolation Enzyme (with papain)(Thermo Fisher,#88285)
The libraries were constructed using the Chromium platform and Chromium Single Cell 3′ v2 chemistry. Briefly, cellular suspensions were loaded on a Chromium Single Cell Instrument (10x Genomics, Pleasanton, CA) for GEMs Generation and Barcoding. Single cell RNA-Seq libraries were prepared using the Chromium Single Cell  Library Kit (10x Genomics, Pleasanton, CA).

value: Tumor tissue

tag: celltype

value: malignant and immune cells

tag: blood mut (rb1)

value: No

value: 1Y 9M

tag: invasivenes

value: Invasive

tag: Sex

value: female


title: Azole Sensitive Parent  rep2 [S4751B]

description:
S2
S4751.filtered.pass.snpEff.protein_coding.vcf.gz

source_name: Isolate 47-51

value: wild type azole sensitive

value: Isolate 47-51


title: RB03_mRNA_rep2

value: 2Y 3M

value: Non-Invasive


title: Learning_Associative Learning Paradigm Rep2

tag: strain


title: MIA PaCa-2 rhCYGB 3

city: Osaka

first: Hoang

middle: Viet

last: Dinh

state: Osaka-fu

address: 1-4-3 Asahimachi - Abeno-ku

department: Hepatology

country: Japan

institute: Osaka city university

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated using FastQC v0.11.7
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed
Trimmed reads are mapped to reference genome with HISAT2 version 2.1.0, splice-aware aligner
Transcript is assembled by StringTie version 2.1.3b with aligned reads
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage. The FPKM value or the RPKM is used as a normalization value.
In groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypothesis testing
In case of known gene annotation, functional annotation and gene-set enrichment analysis are performed using GO and KEGG database on differentially expressed genes
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: MIA PaCa-2 rhCYGB

growth_protocol: MIA PaCa-2 were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% heat-inactivated FBS and 2.5% horse serum in a humidified atmosphere, at 37oC and 5% CO2.

extract_protocol:
1 μg of total RNA was subjected to library synthesis using TruSeq Stranded mRNA LT Sample Prep Kit. The resulting mRNA was fragmented, reverse transcribed using random primers into cDNA, and ligated adapters onto both ends of the cDNA fragments. After amplifying fragments using PCR, select fragments with insert sizes between 200-400 bp. For paired-end sequencing, both ends of the cDNA is sequenced by the read length
TruSeq Stranded mRNA Sample Preparation Guide.

treatment_protocol: MIA PaCa-2 cells were seeded into 24-well plates at 0.5 ×105 cells/well and incubated for 24 hours. The next day, culture medium was changed to DMEM supplemented with 1% FBS and the following day cells were treated with rhCYGB 4µM for 48 hours.

value: MIA PaCa-2

tag: cell type

value: Human pancreatic cancer cell line

tag: disease

value: Carcinoma

tag: treatment

value: rhCYGB


title: Azole Sensitive Parent  rep3 [S4751C]

description:
S3
S4751.filtered.pass.snpEff.protein_coding.vcf.gz


title: Baseline_Motor Learning_Fgfr2_KO

description:
processed data file: Fgfr2_KO_aggr_filtered_feature_bc_matrix.h5
M_HK-KO-Base-Tfg_S2_L001

tag: tissue

value: Cerebellum


title: Moderate, 2551_L

value: Moderate-plane of nutrition

value: Liver

tag: breed

value: Holstein-Friesian X Angus


title: Baseline_Associative Learning Paradigm Rep2


title: MIA PaCa-2 rhCYGB 2

tag: cell line


title: Azole Sensitive Parent  rep1 [S4751A]

description:
S1
S4751.filtered.pass.snpEff.protein_coding.vcf.gz


title: RB03_mRNA_rep1

value: Tumor tissue

value: malignant and immune cells

tag: age

value: Non- Invasive


title: MIA PaCa-2 rhCYGB 1


title: Learning_Motor Learning Paradigm Rep2

value: Learning_Motor Learning Paradigm Rep2


title: Learned_Motor Learning Paradigm Rep2

value: Learned_Motor Learning Paradigm


title: 6 h DMSO RNA-Seq Rep 2

source_name: Human Foreskin Fibroblast

value: Human Foreskin Fibroblast

value: 6 h DMSO

tag: infection

value: HCMV Towne IE2-FKBP 96 h


title: RB02_mRNA_rep2

value: No

value: 3Y 5M

value: Non-Invasive

value: female


title: RB02_mRNA_rep1


title: PG10, stationary phase, rep. #3

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description: Ribo- RNA

data_processing:
Genes deleted in PG10 were removed from the dataset.
Fastq files were mapped to the B. subtilis 168 reference genome using Bowtie (parameters: -a -l 28 -n 2 -m 7 --best --strata).
Counts per gene were calculated using featureCounts and the latest RefSeq annotation  (parameters: -t gene -g locus_tag -O -M --fraction).
Differentially expressed genes were identified using DESeq2, selecting genes with an absolute log2(fold-change) ≥ 0.5 and FDR-adjusted p-value < 0.05.
Genome_build: B. subtilis str. 168 (accession: NC_000964.3)
Supplementary_files_format_and_content: BEDGRAPH

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Bacterial

growth_protocol: Bacterial cells were grown were grown in LB broth at 37 degrees celsius and 220 rpm

extract_protocol:
Cell were lysed using glassbeads and totRNA was isolated using TRIzol/chloroform
rRNA depletion and cDNA library preparation was performed using Zymo-Seq RiboFree Total RNA-Seq Library Kit (Zymo Research, cat. 3003)

value: miniBacillus PG10 (ReuBeta et al. 2017; PMID:27965289)

tag: growth phase

value: stationary


title: MIA PaCa-2 Control 3

source_name: MIA PaCa-2 Control

value: MIA PaCa-2

value: Human pancreatic cancer cell line

value: Carcinoma

value: Control


title: PG10, stationary phase, rep. #2

description: Ribo- RNA


title: RB01_mRNA_rep2

value: Tumor tissue

value: malignant and immune cells

value: 7 Y


title: Activity_Activity Paradigm Rep2

value: Cerebellum

value: Activity_Activity Paradigm


title: MIA PaCa-2 Control 1


title: Baseline_Motor Learning Paradigm Rep2

value: Baseline_Motor Learning Paradigm


title: PG10, stationary phase, rep. #1

description: Ribo- RNA


title: MIA PaCa-2 Control 2


title: PG10, exponential phase, rep. #3

description: Ribo- RNA

value: mid-to-late exponential


title: RB01_mRNA_rep1

value: No


title: RB06_mRNA

value: 1Y 8M

value: Invasive

value: male


title: RB07_mRNA

value: 2 Y

value: female


title: Learned_Associative Learning Paradigm

description: All_samples_combined_aggr_filtered_feature_bc_matrix.h5


title: PG10, exponential phase, rep. #2

description: Ribo- RNA

value: miniBacillus PG10 (ReuBeta et al. 2017; PMID:27965289)


title: Learning_Associative Learning Paradigm


title: PG10, exponential phase, rep. #1

description: Ribo- RNA


title: Islet 5 mock

city: Worcester

first: Athma

middle: A

last: Pai

state: MA

address: 368 Plantation Street, ASC5-2057

department: RNA Therapeutics Institute

institute: University of Massachusetts Medical School

description: total RNA (ribo -)

data_processing:
Adapter trimming was carried out using trimmomatic/0.3.2
Transcript quantification was carried out using kallisto/0.4.0 with default parameters
FASTQs were mapped to ENSEMBL hg38 v95 using STAR/2.7.0e with default parameters
Genome_build: hg38 v95 (ENSEMBL)
Supplementary_files_format_and_content: "paired.fq.gz" trimmed paired output from trimmommatic (see vignette); ".tsv" abundance files from kallisto quant; ".bam"; mapped bam files output from STAR alignment

source_name: pancreatic islet

extract_protocol:
Total RNA was extracted using Trizol. Ribosomal RNA was depleted using Ribo Zero Gold kit (Illumina).
Each rRNA depleted sample was then split into two, with one aliquot digested with RNase R and the other aliquot mock digested according to Pandey et al. 2019
PE libraries were constructed using TruSeq Stranded Illumina Total RNA Preparation Kit

value: frozen pancreatic islet


title: TN-wt-1

source_name: inguinal adipose tissue

value: inguinal adipose tissue

tag: genotype

value: HIF2a loxP/loxP

value: Thermoneutral (30℃) 1 week


title: RB04_mRNA

value: Tumor tissue

value: malignant and immune cells

value: 3 Y

value: Non-Invasion


title: Islet 3 mock

description: total RNA (ribo -)


title: Islet 4 mock

description: total RNA (ribo -)


title: Baseline_Associative Learning Paradigm

value: Cerebellum


title: B. subtilis 168, stationary phase, rep. #3

description: Ribo- RNA

value: stationary


title: Islet 2 mock

description: total RNA (ribo -)


title: Islet 5 RNase R

description: circRNA enriched RNA (ribo -)


title: ATAC-Seq E5 RPE 2

city: Baltimore

first: Seth

last: Blackshaw

state: MD

address: 733 N Broadway

department: Neuroscience

institute: Johns Hopkins University

data_processing:
Reads were trimmed using cut adapt and trim galore with the trimming parameters --clip_R1 16 --clip_R2 18 --three_prime_clip_R1 6 --three_prime_clip_R2 4.
Alignment of raw reads to chicken genome GRCg6a was performed with Bowtie2 (Langmead and Salzberg, 2012) using the parameters --very-sensitive -k 5 -p 40.
Aligned reads were deduplicated using Picard tools (Broad Institute, Picard Toolkit).
Peaks were called for samples individually with HMMRATAC (Tarbell and Liu, 2019). HMMRATAC defined open regions were unified across all samples into a consensus peak file using BEDtools merge -d 10 -I (Quinlan and Hall, 2010).
Peaks aligning to the mitochondrial chromosome were discarded, and peak counts were determined using featureCounts with parameters -F SAF -s 0 -T 10 (Liao et al., 2014).
Differential expression testing of peak regions and peak summits was performed with DESeq2.
Genome_build: GRCg6a
Supplementary_files_format_and_content: Normalized peak count matrix from DESeq2.

organism: Gallus gallus

source_name: Retinal pigment epithelium

growth_protocol: White Leghorn chicken eggs obtained from Michigan State University were used. Eggs were incubated in a humidified, rotating incubator at 38 °C before performing experiments at Hamburger Hamilton stage 24 (E4) or 26 (E5).

extract_protocol:
RPE was isolated in cold PBS and two isolated sheets of RPE were collected per biological sample and placed on ice. RPE cells were lysed in cold ATAC-Seq Kit lysis buffer (Active Motif cat. 53150) and nuclei were counted with a hemocytometer.
Approximately 100,000 RPE nuclei from 2 embryos were aliquoted for Tn5 tagmentation per sample and ATAC-seq library preparation was performed using ATAC-Seq Kit (Active Motif cat. 53150) per manufacturer’s instructions.

treatment_protocol: For treated conditions, surgical retinectomy was performed and FGF2-containing heparain beads were delivered to the eye cup at the time of injury.

value: Development

tag: Stage


title: Learned_Motor Learning Paradigm


title: Learning_Motor Learning Paradigm


title: Baseline_Activity Paradigm Rep2

tag: group

value: Baseline_Activity Paradigm


title: B. subtilis 168, stationary phase, rep. #1

description: Ribo- RNA


title: Baseline_Motor Learning Paradigm


title: B. subtilis 168, stationary phase, rep. #2

description: Ribo- RNA


title: ATAC-Seq E4 RPE 2


title: Activity_Activity Paradigm


title: B. subtilis 168, exponential phase, rep. #3

description: Ribo- RNA

value: mid-to-late exponential


title: B. subtilis 168, exponential phase, rep. #2

description: Ribo- RNA


title: Islet 4 RNase R

description: circRNA enriched RNA (ribo -)


title: Islet 3 RNase R

description: circRNA enriched RNA (ribo -)


title: Islet 2 RNase R

description: circRNA enriched RNA (ribo -)


title: Baseline_Activity Paradigm


title: Islet 1 RNase R

description: circRNA enriched RNA (ribo -)


title: Sample_WT_FG_3

status: Public on May 10 2022

first: Binbin

last: Tao

address: No. 7 Donghu South Road

institute: Institute of Hydrobiology

data_processing:
Then these libraries were sequenced on the Illumina sequencing platform (Illumina HiSeq X Ten) and 150bp paired-end reads were generated.
Raw data (raw reads) were processed using Trimmomatic.
The reads containing poly-N and the low-quality reads were removed to obtain the clean reads. These clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Genome_build: GRCz11
Supplementary_files_format_and_content: Txt file includes gene ID,  gene name and FPKM values for each Sample

organism: Danio rerio

source_name: follicles

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Ovary

tag: stage of follicles

value: FG

value: wild type


title: ATAC-Seq E5 RPE 1


title: Islet 1 mock

description: total RNA (ribo -)


title: GM12878_Fiber-seq

city: Seattle

first: Andrew

middle: Ben

last: Stergachis

state: WA

address: 1959 NE Pacific St

department: Medical Genetics

institute: University of Washington

description: Single-molecule chromatin fiber-sequencing (Fiber-seq) of GM12878 cells using a complete reference genome

data_processing:
Library strategy: Fiber-seq
PacBio subreads bam
Concensus HiFi sequence: raw subreads of 3 SMRT cells were processed with ccs to obtain consensus sequences using pbccs (v6.0.0) with the --chunk flag.
Alignment: CCS reads were aligned to CHM13 v1.0 using pbmm2 (v1.2.0) with the -N 1, --preset CCS and --sort flags.
ipdRatio identification:  we ran ipdSummary v 3.0 with the CCS-specific extracted genomic sequence as the --reference with flags --pvalue 0.001 --identify m6A
m6A identification:  We trained a Gaussian Mixture Model (GMM) from Adenine ipdRatios gathered from a subsample of 5,000 fibers by running python3 faster_GMM.py --slurm input.csv
Genome_build: chm13.draft_v1.0
Supplementary_files_format_and_content: BED12 (Browser Extensible Data) format, representing the following genomic features: location of methylation of the adenosine base at the nitrogen-6 position(m6a); position of nucleosomes; and position of actuated cis-regulatory elements

source_name: GM12878 cell line from Homo sapiens

growth_protocol: AmnioMax C-100 Basal Medium with AmnioMAX™ C-100 Supplement and 1% PenStrep

extract_protocol:
Promega Wizard® HMW DNA Extraction Kit followed by Megaruptor 3 Shearing and size selection
PacBio SMRTbell Express Template Prep Kit 2.0

treatment_protocol: 1 million GM12878  nuclei treated with 200 units of Hia5 m6A-MTase for 10 minutes at 25°C

value: lymphoblastoid cell

value: Fiber-seq


title: Sample_WT_FG_4


title: Sample_WT_EGG_2

value: mature egg


title: CHM13_Fiber-seq

description: Single-molecule chromatin fiber-sequencing (Fiber-seq) of CHM13 cells using a complete reference genome

data_processing:
Library strategy: Fiber-seq
Concensous HiFi sequence: raw subreads of 3 SMRT cells were processed with ccs to obtain consensus sequences using pbccs (v6.0.0) with the --chunk flag.
Alignment: CCS reads were aligned to CHM13 v1.0 using pbmm2 (v1.2.0) with the -N 1, --preset CCS and --sort flags.
ipdRatio identification:  we ran ipdSummary v 3.0 with the CCS-specific extracted genomic sequence as the --reference with flags --pvalue 0.001 --identify m6A
m6A identification:  We trained a Gaussian Mixture Model (GMM) from Adenine ipdRatios gathered from a subsample of 5,000 fibers by running python3 faster_GMM.py --slurm input.csv
Genome_build: chm13.draft_v1.0
Supplementary_files_format_and_content: BED12 (Browser Extensible Data) format, representing the following genomic features: location of methylation of the adenosine base at the nitrogen-6 position(m6a); position of nucleosomes; and position of actuated cis-regulatory elements

source_name: CHM13hTERT cell line from Homo sapiens

treatment_protocol: 1 million CHM13 nuclei treated with 200 units of Hia5 m6A-MTase for 10 minutes at 25°C

value: Hydatidiform mole


title: Sample_WT_EGG_5


title: Sample_WT_FG_2


title: ATAC-Seq E4 RPE 1


title: Sample_WT_EGG_1


title: Sample_WT_EGG_3


title: Sample_WT_FG_1


title: Sample_KO_FG_3

value: sinhcaf-/-


title: Sample_KO_EGG_4


title: Sample_KO_FG_1


title: Sample_KO_FG_4


title: Sample_KO_FG_2


title: B. subtilis 168, exponential phase, rep. #1

description: Ribo- RNA


title: Sample_KO_EGG_3


title: Sample_KO_EGG_5


title: Sample_KO_EGG_2


title: Sample_KO_EGG_1


title: Alysiella filiformis in BSTSY+FBS stationary (OD600=1), replicate2

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

data_processing:
Reads adapter-trimmed and filtered using trimmomativ v0.39 (ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 MINLEN:80 SLIDINGWINDOW:4:15) and prinseq-lite v0.20.4 (-min_qual_mean 30 -min_len 25). PhiX contaminant sequences were removed using bbduk.sh of bbmap v38.90 (k=31 hdist=1), as well as further contaminants (human, animal, plant, fungi) removed against repeat-masked references (minid=0.95 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 qtrim=rl trimq=10 untrim). Reads mapping to rRNA were removed using sortmerna v4.1.0 against the pre-built sortmerna rRNA databases and the organism-specific rRNA sequences. Reads were mapped against the reference genomes (XXX upload Csteedae) using bowtie2 v2.4.4, and Q>30 filtered and index-sorted using samtools v1.9. Reads were counted using featureCounts of the subread-package v2.0.0 in single-end mode (-s 2)  against the ”gene” features of the reference genomes’ gff-file (see supplementary file).
Genome_build: NZ_CP083931.1
Supplementary_files_format_and_content: raw counts

organism: Alysiella filiformis DSM 16848

source_name: bacterial cells

growth_protocol: Cells grown in modified PY-medium or BSTSY+FBS 37°C 350 rpm

extract_protocol:
500 µl liquid culture were fixed with 1 ml RNAprotect Bacteria Reagent (Qiagen), and cells grown on solid medium scraped off and resuspended in 1 ml thereof, and stored at -70°C until the next day. Total RNA was extracted using the RNeasy® Mini Kit (Qiagen) for low cell numbers, including the on-column DNA digestion. Eluted RNA (30 ul) was treated with 2 U of DNase for 30 min using the TURBO DNA-free kit (Invitrogen). RNA was cleaned up using the RNA Clean & Concentrator-25 kit (Zymo) including the on-column DNA digestion. Absence of DNA was checked via PCR (35 cycles) against a ~200 bp fragment of gyrB.
RNA was quality checked (all samples had a RIN > 9), rRNA depleted using an in-facility developed protocol, and reverse-stranded sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).

tag: sample type

value: cells


title: Alysiella filiformis in BSTSY+FBS stationary (OD600=1), replicate3


title: Alysiella filiformis in BSTSY+FBS stationary (OD600=1), replicate1


title: Sample_WT_EGG_4


title: Alysiella filiformis in BSTSY+FBS exponential (OD600=0.2), replicate2


title: Alysiella filiformis in BSTSY+FBS exponential (OD600=0.2), replicate1


title: Alysiella filiformis in mod. PY medium stationary (OD600=1), replicate 3


title: Alysiella filiformis in mod. PY medium + 25 ug/ml rifampicin exponential (OD600=0.2), replicate 1


title: Alysiella filiformis in mod. PY medium + 25 ug/ml rifampicin exponential (OD600=0.2), replicate 3


title: Alysiella filiformis in mod. PY medium stationary (OD600=1), replicate 1


title: Alysiella filiformis in mod. PY medium + 25 ug/ml rifampicin exponential (OD600=0.2), replicate 2


title: Alysiella filiformis in mod. PY medium stationary (OD600=1), replicate 2


title: Alysiella filiformis on mod. PY plate 24h, replicate 3


title: Alysiella filiformis on mod. PY plate 24h, replicate 1


title: Alysiella filiformis in mod. PY medium exponential (OD600=0.2), replicate3


title: Alysiella filiformis in mod. PY medium exponential (OD600=0.2), replicate2


title: Alysiella filiformis on mod. PY plate 24h, replicate 2


title: Alysiella filiformis in mod. PY medium late exponential

data_processing:
Reads adapter-trimmed and filtered using trimmomativ v0.39 (ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 MINLEN:80 SLIDINGWINDOW:4:15) and prinseq-lite v0.20.4 (-min_qual_mean 30 -min_len 25). PhiX contaminant sequences were removed using bbduk.sh of bbmap v38.90 (k=31 hdist=1), as well as further contaminants (human, animal, plant, fungi) removed against repeat-masked references (minid=0.95 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 qtrim=rl trimq=10 untrim). Reads were mapped against the reference genomes using bowtie2 v2.4.4, and index-sorted using samtools v1.9. Reads were counted using the bamCoverage program of deeptools v3.5.1 (Ramírez et al. 2016) in non-overlapping 1kb windows and the resulting bigwig file converted to human-readable format using the bigWigToWig of UCSC v391.
Genome_build: NZ_CP083931.1
Supplementary_files_format_and_content: Read counts in 1kb non-overlapping windows

growth_protocol: Cells grown in modified PY medium 37°C 350 rpm

extract_protocol:
Cells were lysed using lysozyme and Proteinase K, DNA extracted using Phenol-Chloform and precipitated using ammonium acetate (2.5M final concentration), 2X 100% ice-cold Ethanol, and 5 ug/ml glycogen. RNA was degraded by incubation with 10 mg/ml RNase A for 30 min at 37°C, and DNA cleaned up using DNA Clean & Concentrator-5 (Zymo).
Enzymatic shearing; NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina, 150 bp PE sequenced on NovaSeq 6000 S4
WGS


title: Alysiella filiformis in mod. PY medium early exponential


title: Alysiella filiformis in mod. PY medium stationary


title: Alysiella filiformis in mod. PY medium exponential (OD600=0.2), replicate1


title: Alysiella filiformis in BSTSY+FBS exponential (OD600=0.2), replicate3


title: CT10

city: Majadahonda

first: Francisco

last: Díez-Fuertes

address: Carretera Majadahonda - Pozuelo Km 2.2

country: Spain

institute: Instituto de Salud Carlos III

description: PBMCs from non-affected relative

data_processing:
fastQC tool to evaluate sequence yield, base quality, GC profile, k-mer distribution, overrepresented sequences, and primer contamination.
The Trimmomatic tool is used to trim the adapter and/or primer sequences from the ends of the fastq generated.
The reference index files required by Bowtie2 mapping program and the transcript- specific reference sequences are generated from the reference fasta file and the corresponding annotation gtf file.
The ‘rsem-calculate-expression’ command from the RSEM expression analysis software is used to map single-end reads to the reference transcripts. The RNA expression values at gene and isoform levels are calculated using the expectation-maximization (EM) algorithm as implemented by the RSEM program. Multiple threads of eight or more are used to generate alignments mapped to genomic coordinates, while tagging reads with nonunique alignments (--tag), calculating 95% credibility intervals (--calc-ci) and posterior mean estimates (--calc-pme) and allowing insertions in the range of 1–500 bases (--fragment-length-min/max).
The number of fragments that are derived from a given isoform or gene using RSEM´s approximate maximum likelihood estimates was employed for differential expression between samples from LGMD1F patients and healthy controls. An R package called EBSeq for differential expression analysis using RNA-Seq data was used
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with TPM values for each library
Supplementary_files_format_and_content: Matrix table with fold changes and p-values of the differential expression between LGMDD2 and controls

source_name: PBMCs

growth_protocol: PBMCs from LGMDD2 patients and healthy controls were isolated by centrifugation using Ficoll-Hypaque gradient (GE Healthcare). PBMCs were cultured in RPMI 1640 medium (Bio Whittaker) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 µg/ml streptomycin, 100 units/ml penicillin (Bio Whittaker).

extract_protocol:
Total RNA from activated PBMCs was isolated from 5x106 cells of each samples using RNeasy Mini Kit (Qiagen)
ScriptSeqTM v2 RNA-Seq Library Preparation Kit (Illumina, San Diego, Ca, USA),

treatment_protocol: PBMCs were then activated with purified antihuman CD3 (clone OKT3), CD28 (clone CD28.2) (Biosciences) and 300 U/ml interleukin-2 (IL-2) (Chiron) for 3 days.

tag: pathology

value: Control


title: CT3

description: PBMCs from non-affected relative


title: CT7

description: PBMCs from non-affected relative


title: CT4

description: PBMCs from non-affected relative


title: CT5

description: PBMCs from non-affected relative


title: CT1

description: PBMCs from non-affected relative


title: CT2

description: PBMCs from non-affected relative


title: P8

description: PBMCs from LGMDD2 patient


title: CT8

description: PBMCs from non-affected relative


title: P7

description: PBMCs from LGMDD2 patient


title: iPSC-201B7 n1

city: Kyoto

first: Mio

last: Iwasaki

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

description:
Human pluripotent stem cell line in feeder free condition
MI001_010

hyb_protocol: Manufature's protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

source_name: Pluripotent stem cell line in feeder free condition (201B7, P22)

label_protocol: Manufature's protocol

growth_protocol: Two types of human induced pluripotent stem cells (iPSC-1, 201B7; and iPSC-2, 1418E1) and embryonic stem cells (ESC; H9) were maintained under feeder-free conditions on iMatrix-511 (Nippi) with StemFit AK03N medium (Ajinomoto). A Rock inhibitor (Y-27632, final concentration, 10 µM) was used only on the day of plating (Nakagawa et al., 2014). Two types of human dermal fibroblasts (HDF-1, HDF1388; and HDF-2, Tig120) were cultured in Dulbecco’s modiﬁed Eagle’s medium (DMEM; Nacalai Tesque) with 10% fetal bovine serum (FBS, Thermo Fisher Scientific) and 0.5% penicillin and streptomycin (gibco).

extract_protocol: RNA was prepared using the miReasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: Human induced pluripotent stem cell line


title: iPSC-1418E1 n2

description:
Human pluripotent stem cell line in feeder free condition
MI001_008

source_name: Pluripotent stem cell line in feeder free condition (1418E1, P12)


title: ESC-H9 n2

description:
Human embryonic stem cell line in feeder free condition
MI001_005

source_name: Embryonic stem cell line in feeder free condition (H9, P44)

value: Human embryonic stem cell line


title: iPSC-1418E1 n3

description:
Human pluripotent stem cell line in feeder free condition
MI001_009

source_name: Pluripotent stem cell line in feeder free condition (1418E1, P13)


title: P9

description: PBMCs from LGMDD2 patient


title: CT6

description: PBMCs from non-affected relative


title: iPSC-1418E1 n1

description:
Human pluripotent stem cell line in feeder free condition
MI001_007

source_name: Pluripotent stem cell line in feeder free condition (1418E1, P11)


title: Tig120 n3

description:
Human dermal fibroblast cell line
MI001_015

source_name: Human dermal fibroblast (Tig120, P11)

value: Human dermal fibroblast cell line


title: iPSC-201B7 n2

description:
Human pluripotent stem cell line in feeder free condition
MI001_011

source_name: Pluripotent stem cell line in feeder free condition (201B7, P23)


title: ESC-H9 n3

description:
Human embryonic stem cell line in feeder free condition
MI001_006


title: Tig120 n1

description:
Human dermal fibroblast cell line
MI001_013

source_name: Human dermal fibroblast (Tig120, P9)


title: HDF1388 n1

description:
Human dermal fibroblast cell line
MI001_001

source_name: Human dermal fibroblast (HDF1388, P11)


title: HDF1388 n3

description:
Human dermal fibroblast cell line
MI001_003

source_name: Human dermal fibroblast (HDF1388, P8)


title: Tig120 n2

description:
Human dermal fibroblast cell line
MI001_014

source_name: Human dermal fibroblast (Tig120, P10)


title: iPSC-201B7 n3

description:
Human pluripotent stem cell line in feeder free condition
MI001_012

source_name: Pluripotent stem cell line in feeder free condition (201B7, P24)


title: P10

description: PBMCs from LGMDD2 patient


title: HDF1388 n2

description:
Human dermal fibroblast cell line
MI001_002


title: CT9

description: PBMCs from non-affected relative


title: P5

description: PBMCs from LGMDD2 patient


title: ESC-H9 n1

description:
Human embryonic stem cell line in feeder free condition
MI001_004


title: P6

description: PBMCs from LGMDD2 patient


title: P2

description: PBMCs from LGMDD2 patient


title: ATAC_HEC_KO_Rep2

city: Beijing

first: Jie

address: Qing Hua Yuan

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

description: cultured cells

data_processing:
for ATAC-seq and ChIP-seq, all of the paired-end raw reads were processed using TrimGalore to trim adaptor and low-quality reads. Adaptor-trimmed paired-end reads from ATAC-seq and ChIP-seq were aligned to hg38 by bowtie2 (version 2.3.5) with the parameters: --t --q --N 1 --L 25. PCR duplicates and multiple mapped reads were removed. The replicate BAM files for each time point were merged and removed reads aligning to blacklisted genomic regions before calling peaks with MACS2 (version 2.2.6) and the enriched TF motifs were analyzed by Homer (version 4.10.4, findMotifsGenome).
Genome_build: GRCh38

source_name: cultured cells

growth_protocol: Undifferentiated hPSCs were cultured in E8 medium without feeders.

extract_protocol: For ATAC-seq, ATAC-seq library was prepared followed the omini-ATAC-seq protocol.

value: Embryonic stem cells

value: human embryonic stem cell line H1


title: ATAC_HEC_KO_Rep1

description: cultured cells


title: ATAC_HEC_WT_Rep1

description: cultured cells


title: U87-shGPR17_RNF2

city: Fujian Province, China

first: huiqing

last: Liu

address: State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen ,Fujian Province, China

institute: Xiamen University

data_processing:
FASTQ data were processed with Trimmomatic v0.39 to remove low-quality reads
reads of ChIP-seq data were aligned to the hg19 genome using Bowtie v2.3.5.
Peak calling was performed using MACS2 with a p value cutoff of 0.01.
For the differential binding peaks of RNF2 ChIP-seq, MAnorm was used with cutoff P<0.05 and fold change>2.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using deepTools 3.1.3 and visualized by IGV 2.4.16

growth_protocol: U87-SCR and U87-shGPR17 were cultured in DMEM (BasalMedia, Cat# L110KJ) supplemented with 10%FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and RNF2-DNA complexes were isolated with antibody.
The libraries were constructed following NEB’s Chip-seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an ‘A’ base so the adaptors from NEB with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are double-selected and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: U87 cells were transfected with scramble or GPR17 shRNA(pLKO1 vector), and screened by  2ug/ml puromycin treatment until monoclonal cell line was obtained.

value: human gliobastoma cell line

tag: chip antibody


title: U87-GPR17-1

data_processing:
Differential expressed genes were identified using DESeq2 with fold change>1.5 and p<0.05.
Supplementary_files_format_and_content: tab-delimited text files include raw gene count for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
U87 cells were collected,and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: U87-GPR17-2


title: U87-SCR_RNF2