title: S50_Individual15_TissueNormal_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATddhE

description:
S50
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA3_rep3 T1

status: Public on Feb 05 2021

type: SRA

city: Modena

first: Andrea

last: Cossarizza

state: Modena

address: Via Campi 287

country: Italy

institute: University of Modena and Reggio Emilia

library_source: transcriptomic

data_processing:
Fastq generation, alignment to the human genome and gene quantification were performed with Generate FASTQ v 1.0.0 and SureCell RNA Single-Cell v 1.1.0 respectively.
The UMI count matrix was used for downstream analysis with Seurat v3 and Monocle2 R packages.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with UMI counts for every gene and every cell

molecule: polyA RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cell

extract_protocol:
Cryopreserved PBMC were thawed in R10 supplemented with 20 μg/ml DNase I from bovine pancreas (Sigma-Aldrich). After washing with phosphate buffer saline (PBS), cells were stained with the Red Live Dead Fixable Viability kit (ThermoFisher) for 15 min at room temperature. PBMC were washed with PBS and stained with mAb anti-CD3-PE and -CD8-FITC (Biolegend). Viable CD3+, CD8+ T cells were sorted by using eS3 sorter. Cell sorting was performed with 96-99% purity. Cell suspension were then visualized and counted with trypan blue using Bio-Rad T20 Automated Cell Counter to get a precise estimation of total number of sorted cells and of cells concentration. Cells were then pelletted and resuspended in the appropriate volume of cold 1X PBS + 0.1% BSA until reached the final concentration of 3000 cells/μl. Afterwards we loaded about 54.000 cells of each sample into one cartrige of the ddseq system.
Following capture and lysis, cDNA was synthesized and amplified for 15 cycles following the Illumina® Bio-Rad® SureCellTM WTA 3′Library Prep for Peripheral Blood Mononuclear Cells (PBMC) protocol. 50 ng of the amplified cDNA were then used for each sample to construct Illumina sequencing libraries. Sequencing was performed on the NextSeq550 Illumina sequencing platform following Illumina® Bio-Rad® instruction for read generation, reaching at least 50000 reads as mean reads per cell.

tag: time-point

tag: donor

value: Melanoma patients

tag: disease state

value: Not-Responders

tag: tissue

value: Blood

tag: cell type

value: CD8 T lymphocytes

tag: treatment

value: Nivolumab


title: MELA5_rep1 T1

value: Pembrolizumab


title: S53_Individual18_TissueNormal_DietHFD_InterventionLIR_BatchF18FTSEUHT1008_RATddhE

city: Dublin

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

country: Ireland

institute: St. Vincent's University Hospital

description:
S53
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata

data_processing:
See https://github.com/brucemoran/rdl_RNAseq for full reproducible pipeline.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: rdl_RNAseq.sleuthObject.Rdata: sleuth object containing raw counts, filtered transcript and gene level counts and scaled values (TPM, scaled reads per base).
Supplementary_files_format_and_content: rdl_RNAseq.sleuthObject.obs_raw.tsv: Tab-separated text file containing TPM.

molecule: total RNA

organism: Rattus norvegicus

source_name: Endometrium

growth_protocol: Rats were age-matched and housed in spacious ventilated cages with hard floors in groups of 3-4 rats. They had 24 hour access to ad-lib food and water. Enrichment, in the form of cardboard and Perspex tunnels were provided in all cages. Ample saw dust was used as bedding and this was changed, along with the cage on a weekly basis. Weekly weights and food intakes were recorded prospectively and all animals were inspected daily for any welfare concerns. All animals were formally scored weekly using the rat grimace scale with any welfare concerns immediately reported to the departmental vet (DV). Animal handling training provided by the BMF staff as well as the professional qualification TEARAP were both mandatory requirements prior to commencing this study. High fat diet with 60%kCal fat, 20%kCal carbohydrate and 20%kCal protein was sourced from Research Diets, NJ, USA and was used as diet in the HFD, LG and DRG groups respectively. This calorie rich research diet, D12492, was chosen as it has an established safety and efficacy in causing diet-induced-obesity in research rats. Normal chow with 3%kCal fat content was used as the chosen diet in the NCD group as it is generally accepted as the standard diet for research rats. The normal chow was sourced from Tekland Global Diets, WI, USA. Rats in the validation study and the LG group of rats from the intervention study were fed ‘ad lib’ amounts of their respective diets from their cage hoppers and had access to the food 24 hours a day. As stated, rats in the DRG had ‘ad lib’ access to HFD from 3 to 12 months of age and restricted access to HFD from 12 to 15 months of age in order to achieve the desired amount of weight loss.

extract_protocol:
RNA was isolated from normal and endometrial tumour tissue using EZ-RNA Total RNA Isolation Kit according to the manufacturer’s protocol (Omega Bio-Tek). RNA quantity and quality were determined using a Nanodrop spectrophotometer ND-1000 (Nanodrop Technologies, DE, USA), and Agilent Bioanalyzer 2100 (Agilent Technologies, UK).
Next-generation sequencing libraries were prepared using the NeoPrep Automated Library Prep System and Illumina TruSeq stranded mRNA library prep kit using the manufacturer's instructions (Illumina, San Diego, CA, USA).
After quality control procedures, individual RNAseq libraries were pooled based on their respective sample-specific- 7 bp adapters and sequenced at 2 x 75bp paired end read length using an Illumina NextSeq 500 sequencer.

treatment_protocol: Victoza, the tradename for Liraglutide was sourced from the college pharmacy. Liraglutide is a long acting GLP-1 agonist developed by NovoNordisk, which shares 97% homology with GLP-1 and has a circulating half-life of 10-14 hours. Liraglutide was approved for use in type 2 diabetes in Europe in 2009 and the USA in 2010 and is administered as a once daily subcutaneous injection either as a monotherapy or in combination with other antidiabetic agents in humans. In this context it was used as a monotherapy with the sole aim of inducing weight loss. It is commercially available as a pre-made solution in a calibrated 3ml syringe in a concentration of 6mg/ml. Liraglutide was dose-titrated daily over an eight-day period commencing at a dose of .01mg/kg/day to 0.24mg/kg/rat/day. Water intake was monitored twice daily in the two days prior to commencing injections in order to ascertain the average daily water intake per rat. Sub-cutaneous injection sites were altered daily in order to avoid injection site inflammation or ulceration. The sites used included the scruff of the neck, both flanks and the abdomen. Injections were given between 0600 and 1100 am in order to facilitate proper monitoring of water intake. Twice daily intake of water was monitored until adypsia was out-ruled and maintenance dose liraglutide was reached which was typically for 10 days. The rats also had daily welfare scores using the ‘rat grimace scale’ during this period until the maintenance dose of liraglutide had been reached and fears regarding adypsia had ceased (Appendix 6). Rats showing signs of adypsia were given a bolus injection of 4mls of normal saline and subjected to twice daily welfare scores. Any rat scoring greater than or equal to five on the welfare score card was subjected to a review by the departmental vet. At 12 months of age this group of rats were subjected to the intervention of weight loss via diet restriction. Having previously had ad lib access to HFD this group of rats now had rationed access to food each morning (between 1000-1200) in order to achieve the desired weight loss. The estimated daily intake of food per rat was calculated in the month leading up to the commencement of diet restriction. This daily intake was slowly tapered down over a four-week period in order to achieve the desired weight loss. The weight loss was then maintained for the remainder of the study. In order to accurately and safely achieve this weight loss each rat was individually housed for meal times and given the required amount of time to consume its meal. This avoided the emergence of a ‘dominant’ or ‘runt’ rat in each cage. Once the food had been consumed by each rat they were then returned to group housing where there was no access to food but ad lib access to water. The rats were scored daily for the duration of this intervention using the rat grimace scale. Any rat scoring greater than or equal to five on the welfare score card was subjected to a review by the departmental vet.

tag: individual

tag: strain

value: BDII/Han

value: Normal endometrium

tag: diet

value: HFD

tag: intervention

value: LIR

tag: batch


title: S47_Individual12_TissueNormal_DietHFD_InterventionRES_BatchF18FTSEUHT1008_RATddhE

description:
S47
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata

value: RES


title: MELA3_rep1 T1


title: MELA3_rep2 T1


title: MELA3_rep4 T1


title: MELA5_rep3 T1


title: S48_Individual13_TissueNormal_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATddhE

description:
S48
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata

value: NO


title: S41_Individual8_TissueNormal_DietHFD_InterventionRES_BatchF18FTSEUHT1008_RATddhE

description:
S41
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA31_rep2 T0


title: S46_Individual11_TissueNormal_DietHFD_InterventionRES_BatchF18FTSEUHT1008_RATddhE

description:
S46
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA31_rep3 T0


title: S43_Individual9_TissueTumour_DietHFD_InterventionRES_BatchF18FTSEUHT1008_RATddhE

description:
S43
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata

value: Endometrial tumor


title: S40_Individual6_TissueNormal_DietHFD_InterventionRES_BatchF18FTSEUHT1008_RATddhE

description:
S40
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S42_Individual9_TissueTumour_DietHFD_InterventionRES_BatchF18FTSEUHT1008_RATddhE

description:
S42
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S45_Individual10_TissueNormal_DietHFD_InterventionRES_BatchF18FTSEUHT1008_RATddhE

description:
S45
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA31_rep4 T0


title: MELA31_rep1 T0


title: S39_Individual4_TissueNormal_DietHFD_InterventionRES_BatchF18FTSEUHT1008_RATddhE

description:
S39
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA30_rep4 T0


title: S38_Individual3_TissueNormal_DietHFD_InterventionRES_BatchF18FTSEUHT1008_RATddhE

description:
S38
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA30_rep2 T0


title: S44_Individual9_TissueNormal_DietHFD_InterventionRES_BatchF18FTSEUHT1008_RATddhE

description:
S44
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S37_Individual2_TissueNormal_DietHFD_InterventionRES_BatchF18FTSEUHT1008_RATddhE

description:
S37
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA29_rep4 T0

value: Responders


title: MELA29_rep1 T0


title: MELA29_rep3 T0


title: MELA29_rep2 T0


title: S35_Individual22_TissueNormal_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S35
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S34_Individual22_TissueTumour_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S34
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA28_rep4 T0


title: S33_Individual22_TissueTumour_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S33
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S32_Individual22_TissueTumour_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S32
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S28_Individual12_TissueTumour_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S28
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S27_Individual12_TissueTumour_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S27
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA27_rep4 T0


title: MELA28_rep1 T0


title: S29_Individual12_TissueTumour_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S29
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S30_Individual13_TissueNormal_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S30
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA27_rep2 T0


title: S26_Individual12_TissueTumour_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S26
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA26_rep4 T0


title: S36_Individual2_TissueTumour_DietHFD_InterventionRES_BatchF18FTSEUHT1008_RATddhE

description:
S36
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA27_rep3 T0


title: S31_Individual21_TissueTumour_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S31
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA26_rep3 T0


title: MELA27_rep1 T0


title: S25_Individual11_TissueTumour_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S25
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA25_rep4 T0


title: S23_Individual11_TissueTumour_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S23
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S24_Individual11_TissueTumour_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S24
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA25_rep3 T0


title: MELA28_rep2 T0


title: MELA25_rep1 T0


title: MELA25_rep2 T0


title: S21_Individual8_TissueNormal_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S21
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S19_Individual7_TissueTumour_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S19
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata

value: NC


title: S20_Individual7_TissueNormal_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S20
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA24_rep2 T0


title: S18_Individual7_TissueTumour_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S18
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S17_Individual7_TissueTumour_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S17
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA23_rep3 T0


title: S15_Individual6_TissueTumour_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S15
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA23_rep1 T0


title: S14_Individual6_TissueTumour_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S14
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA23_rep2 T0


title: S16_Individual6_TissueTumour_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S16
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S13_Individual6_TissueTumour_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S13
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA21_rep4 T0


title: S12_Individual5_TissueNormal_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S12
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA26_rep1 T0


title: MELA21_rep2 T0


title: S22_Individual10_TissueNormal_DietHFD_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S22
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA21_rep1 T0


title: S10_Individual5_TissueTumour_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S10
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S9_Individual5_TissueTumour_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S9
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA20_rep4 T0


title: S8_Individual4_TissueTumour_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S8
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA12_rep4 T1


title: MELA20_rep3 T0


title: MELA24_rep1 T0


title: MELA20_rep1 T0


title: MELA20_rep2 T0


title: S5_Individual2_TissueNormal_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S5
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S7_Individual4_TissueTumour_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S7
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S6_Individual3_TissueNormal_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S6
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: S1_Individual1_TissueNormal_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S1
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA16_rep2 T0


title: MELA17_rep3 T0


title: MELA21_rep3 T0


title: S4_Individual1_TissueTumour_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S4
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA13_rep3 T0


title: S3_Individual1_TissueTumour_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S3
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA17_rep1 T0


title: MELA16_rep4 T0


title: MELA12_rep1 T0


title: S2_Individual1_TissueTumour_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S2
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: MELA16_rep3 T0


title: MELA13_rep4 T0


title: S11_Individual5_TissueTumour_DietNC_InterventionNO_BatchF18FTSEUHT1008_RATetsE

description:
S11
PolyA RNA
processed data file: rdl_RNAseq.sleuthObject.Rdata


title: 4xPolD pol delta (repeat 2)

city: Brighton

first: Robert

last: Zach

address: Science Park Road, GDSC

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

description: Experiment 2 (1 sequencing run)

library_source: genomic

data_processing:
Library strategy: Pu-Seq
Strand-specific mapping by bowtie2 (f - forward strand; r - reverse strand).
Binning (300 bp).
Genome_build: Schizosaccharomyces pombe 972h- RefSeq Genome (assembly ASM294v2).
Supplementary_files_format_and_content: *.count.csv: Comma-separated text files containing binned counts. 3 columns: chro - chromosome; pos - position; count - number of reads.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: exponentially growing culture

growth_protocol: Cells grown in YES.

extract_protocol:
Standard DNA extraction procedure.
Standard Pu-Seq procedure (Daigaku et al., 2015) or a modified version.

treatment_protocol: No treatment.

value: untreated

tag: medium

value: YES


title: 4xPolD pol delta (repeat 1, tech 2)

description: Experiment 1 (second of 2 sequencing runs)


title: MELA12_rep4 T0

value: Melanoma patients


title: MELA11_rep2 T0

value: Not-Responders


title: MELA12_rep3 T0

value: Blood


title: 4xPolD pol alpha (repeat 1, tech 2)


title: 4xPolD pol epsilon (repeat 1, tech 1)

description: Experiment 1 (first of 2 sequencing runs)


title: 4xPolD pol epsilon (repeat 1, tech 2)


title: MELA10_rep4 T0

value: CD8 T lymphocytes


title: MELA10_rep3 T0

value: Nivolumab


title: MELA10_rep2 T0


title: 2xPolD pol epsilon (repeat 2)

description: Experiment 2 (1 sequencing run)


title: MELA17_rep4 T0


title: MELA12_rep2 T0


title: 4xPolD pol alpha (repeat 1, tech 1)


title: MELA11_rep4 T0


title: MELA7_rep4 T0


title: 2xPolD pol epsilon (repeat 1, tech 1)


title: 2xPolD pol delta (repeat 2)

description: Experiment 2 (1 sequencing run)


title: MELA11_rep1 T0


title: MELA7_rep1 T0


title: MELA11_rep3 T0


title: 2xPolD pol delta (repeat 1, tech 2)


title: 4xPolD pol delta (repeat 1, tech 1)


title: 4xPolD pol epsilon (repeat 2)

description: Experiment 2 (1 sequencing run)


title: 2xPolD pol alpha (repeat 1, tech 2)


title: 2xPolD pol alpha (repeat 2)

description: Experiment 2 (1 sequencing run)


title: 2xPolD pol alpha (repeat 1, tech 1)


title: MELA5_rep1 T0

value: Pembrolizumab


title: WT pol alpha (repeat 1, tech 2)


title: WT pol delta (repeat 1, tech 2)


title: MELA3_rep3 T0


title: WT pol delta (repeat 2)

description: Experiment 2 (1 sequencing run)


title: MELA3_rep1 T0


title: WT pol delta (repeat 1, tech 1)


title: 2xPolD pol epsilon (repeat 1, tech 2)


title: MELA7_rep3 T0


title: WT pol epsilon (repeat 2)

description: Experiment 2 (1 sequencing run)


title: MELA7_rep2 T0


title: 2xPolD pol delta (repeat 1, tech 1)


title: MELA5_rep4 T0


title: Group3-2

city: Seoul

first: Sungwoon

last: Choi

state: Gwanak-gu

address: 1. Gwanak-ro

department: Veterinary Medicine

country: South Korea

institute: Seoul National University

description:
fecal PCR(+), ELISA(-), Clinical sign(-)
Small RNA
miRNA_expression_norm.txt

data_processing:
Low quality bases or reads were trimmed using the Cutadapt tool (Marcel Martin, 2011).
Filtered reads were mapped to the reference genome of the related species using the aligner Bowtie.
The expression estimation find by mirdeep2 tool.
The variant calling was performed by the GATK to search variants in the miRNA seed region.
miRNA level count data were generated using mirdeep2.
Genome_build: UMD3.1.83
Supplementary_files_format_and_content: miRNA_expression_norm.txt: Tab-delimited text file includes abundance measurements.

organism: Bos taurus

source_name: Bovine serum

extract_protocol:
Small RNA was extracted from bovine serum using the miRNeasy Serum/Plasma Kit (Qiagen, Germany) according to the manufacturer's instruction.
The libraries were prepared for 50bp single-end sequencing using the NEXTflex Small RNA-Seq Kit (Bioo Scientific Corp.).

tag: breed

value: Holstein

value: Whole blood

tag: condition

value: MAP infection

tag: fecal pcr

value: Positive

tag: elisa

value: Negative

tag: clinical sign


title: WT pol alpha (repeat 2)

description: Experiment 2 (1 sequencing run)


title: MELA3_rep4 T0

tag: time-point


title: Group4-2

description:
fecal PCR(-), ELISA(-), Clinical sign(-)
Small RNA
miRNA_expression_norm.txt

value: Uninfected


title: 1639_ZB

type: genomic

city: Los Angeles

first: Darryl

last: Shibata

state: CA

address: 1441 Eastlake Ave NOR2424

country: USA

institute: USC Keck School of Medicine

description: colorectal tumor sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing:
Minfi R package, 'noob' method
Normalized (minfi noob method) Beta value
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: genomic DNA from colorectal tumor Z, side B

label_protocol: Standard Illumina Protocol

extract_protocol: Qiagen DNeasy Blood and Tissue Kit

value: colorectal tumor bulk

tag: tumor type (stage)

value: Carcinoma (3)

tag: patient age

tag: patient sex

value: M


title: 1639_ZA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor Z, side A

tag: tissue


title: MELA5_rep3 T0

tag: donor

tag: disease state

tag: cell type

tag: treatment


title: WT pol alpha (repeat 1, tech 1)

value: untreated

tag: strain


title: Group2-1

description:
fecal PCR(+), ELISA(+), Clinical sign(-)
Small RNA
miRNA_expression_norm.txt


title: Group1-2

description:
fecal PCR(+), ELISA(+), Clinical sign(+)
Small RNA
miRNA_expression_norm.txt


title: Group1-1


title: 1639_NB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor N, side B

value: Carcinoma (1)


title: Group4-1


title: WT pol epsilon (repeat 1, tech 2)

value: YES


title: 1639_NA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor N, side A


title: 1639_GA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor G, side A

value: F


title: Group2-2


title: 1639_GB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor G, side B


title: siCCT4-3

city: kunming

first: Gan

last: Wang

address: jiaochang dobg lu 32#

country: China

institute: Kunming Institute of Zoology

data_processing:
Sequenced reads were mapped to human reference genome (hg38) using STAR (2.5.2a) with default parameters.
Aligned reads were summarized into gene counts using the featureCounts (v1.5.0) command of the Subread package with default parameters in conjunction with the human gencode annotation file (hg38 release 85).
Genome_build: hg38
tab-delimited text file containing raw read counts for all samples
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: MG63 cells were cultured in regular growth medium (DMEM + 10% FBS + 1%P/S)

extract_protocol:
The TruSeq stranded RNA sample prep kit was used for library generation according to Illumina's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For samples 1-6, cells were treated with either 1 µM anticarin-β or vehicle. After 18 hours, the cells were collected for RNA-Seq.For samples 7-12, cells were transfected with either Allstar control siRNA or CCT4-specific siRNA. After two days, the cells were collected for RNA-Seq.

tag: cell line

value: human osteosarcoma cell

tag: sirna

value: CCT4-specific siRNA


title: 1639_AB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor A, side B

value: Adenoma


title: 1586_IB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor I, side B

value: Carcinoma (4)


title: siCCT4-2


title: Group3-1

tag: breed

value: Holstein


title: siCK3

value: Allstar control siRNA


title: 1586_IA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor I, side A


title: siCK2


title: WT pol epsilon (repeat 1, tech 1)

tag: medium


title: 1387_UB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor U, side B

value: Carcinoma (2)


title: siCK1


title: 1387_UA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor U, side A


title: 1387_DB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor D, side B


title: 1387_DA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor D, side A


title: ab2

tag: agent

value: Anticarin-Beta


title: ab1


title: ck2

value: Vehicle


title: ck3


title: ab3


title: 1378_FA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor F, side A


title: 1378_FB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor F, side B


title: ck1


title: siCCT4-1


title: 1639_AA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor A, side A


title: 1357_OA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor O, side A


title: 1350_JA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor J, side A


title: 1350_PB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor P, side B


title: 1350_PA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor P, side A


title: 4xPolD pol alpha (repeat 2)

description: Experiment 2 (1 sequencing run)

source_name: exponentially growing culture


title: 1350_CB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor C, side B


title: 1350_CA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor C, side A


title: 1350_MB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor M, side B


title: H9N

city: Qingdao

first: Lei

last: Sun

state: Shandong

address: Shandong street

institute: Shandong University

description: transcriptome

data_processing:
Library strategy: icSHAPE
remove duplicete reads as icshape pipeline
trimmed reads adaptor as icshape pipeline
mapping reads to human hg38 or mouse mm10 reference genome with STAR as default parameters
calculate rpkm as icshape pipeline
calulate reverse transcript stop sites as icshape-pipe
calculate icSHAPE score as icshape-pipe
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: tab-delimited text files for icshape files. First column is the Ensemble ID, second is gene length, third is *, then every column is the nucleotide resolution icSHAPE score. NULL means no confident score.

source_name: human ES H9 cells

growth_protocol: HeLa, HEK293 and HepG2 cells were cultured in DMEM medium supplemented with 10% FBS at 37 °C with 5% CO2 in 15 cm plates to approximately 80–90% confluency. K562 cells were cultured in RPMI 1640 medium supplemented with 10% FBS at 37 °C with 5% CO2 in 15 cm plates to approximately 2 * 107 cells. mES E14T cells were cultured as described previously(Shen et al., 2008). In brief, cells were grown at 37 °C with 5% CO2 in 10 cm plates in complete ESC culture medium (DMEM supplemented with 15% heat-inactivated FCS (fetal calf serum), 1% of nucleoside mix (Millipore), 0.1 mM nonessential amino acid, 2 mM Glutamax, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF)). hES cells were cultured as described previously(Jung et al., 2017). Briefly, cells were grown at 37 °C with 5% CO2 in 10 cm plates in knockout serum replacer (KSR) plus bFGF medium (knockout DMEM, supplemented with 20% knockout serum replacer, 0.1 mM nonessential amino acids, 0.1 mM β-mercaptoethanol,1 mM L-glutamine, and 4 ng ml-1 recombinant human bFGF (bFGF, R&D systems)).

extract_protocol:
All cells were incubated with NAI-N3 at 37°C for 5min.
100 µg of RNA from each samples was depleted of ribosomal RNA (rRNA) using DynabeadsTM mRNA DIRECTTM kit (invitrogen). To sequence the libraries on the Hiseq X system, we designed new linker, reverse transcription (RT) primer and P5, P7 amplification PCR primer. The experimental barcodes for different libraries located on PCR primers rather than on RT primers. The linker of NAI-N3 modification samples: /5rApp/AGATCGGAAGAGCACACGTCT/3ddC/; the linker of DMSO control samples: /5rApp/AGATCGGAAGAGCACACGTCT/3Biotin/; RT primer: /5phos/DDDNNNNNNNNNNAGATCGGAAGAGCGTCGTGGA/iSp18/GGATCC/iSp18/CAGACGTGTGC, D = A/G/T and N = A/T/G/C are used to discriminate PCR duplicates; P5-Solexa PCR primer: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCC-3’; P7-Solexa PCR primer: 5’-CAAGCAGAAGACGGCATACGAGAT CGAGGCTGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’. The underline “CGAGGCTG” is the specific experimental barcode to distinguish different libraries. Libraries of all cell lines were sequenced on Hiseq X system to approximately 200 million reads per replicate.

treatment_protocol: For in vivo treatment, cells was incubated with NAI-N3 at 37°C for 5min, then subcellular fractionation was performed. For in vitro treatment, RNA was extracted by RNeasy mini columns (Qiagen) after subcellular fractionation. For refolding, purified RNA was first denatured at 95°C for 1 min, quickly cooled to 4°C, and then incubated for 5 min in the folding buffer with 100 mM HEPES, 6 mM MgCl2, and 100 mM NaCl. Samples were then respectively modified for 5 minutes at 37°C with the NAI-N3 reagent and DMSO as control. For irCLIP, cells were initially washed with ice-cold PBS, then crosslinked on ice with UV-C (254 nm) at 0.3 J/cm2 in a Stratalinker, washed again with ice-cold PBS (+10 mM EDTA) for 5 minutes, and removed from the plate. Immunoprecipitation of crosslinked protein-RNA complexes was performed with anti-LIN28 antibody (Abcam ab46030), the control samples with anti-GFP antibody (Abcam).

value: human ES H9 cells


title: 1350_CN

description: normal colon sample

source_name: genomic DNA from matching normal C

value: normal colon bulk

value: Normal tissue


title: H9D

description: transcriptome

value: DMSO


title: EpCAMhi MDA-MB-231 UPF2 siRNA 1

city: Boston

first: Judy

last: Lieberman

state: MA

address: 200 Longwood Ave

department: PCMM

institute: Boston Children's Hospital

data_processing:
RNA-Seq reads were aligned to the ENSEMBL GRCh38 (build 98) genome assembly using Hisat version 2.2.0  with the following configurations: -dta --rna-strandness RF
Per sample read counts of exons were generated via bam files sorted by name and DEXSeq wrapper functions of HTSeq (dexseq_count.py) using the  -p yes -s reverse -f bam options.
Novel transcripts assembly per sample was performed via stringTie 2.1.2 using the following options: --rf -G.
stringTie GTF files for all samples were merge via stringTie --merge -G function.  stringTie Fasta file was generate using gffread function.
Kallisto V0.46 index for novel transcripts was build using stringTie Fasta file using --make-unique option.
Kallisto abundances for novel transctipts were generate via kallisto quant function using the  --rf-stranded --plaintext options.
Abundance estimates for novel transcript assembly was combined and normalized using importIsoformExpression function from IsoformSwitchAnalyzeR package default options.
Abundance estimates for standard GRCh38 (98) transcriptome was generated using kallisto quant and kallisto index for GRCh38.cdna.all (98)
Genome_build: ENSEMBL human genome GRCh38 (98)
Supplementary_files_format_and_content: abundance_stringTie: CSV with novel transcripts and normalized TPM for each sample in each row
Supplementary_files_format_and_content: abundance_standard_genome: CSV with  standard GRCh38 transcripts and TPM for each sample in each row
Supplementary_files_format_and_content: HTSeq_exon_counts: CSV with genes, exons,  and read counts in each row
Supplementary_files_format_and_content: stringtie_merged: GTF file of novel transcriptome assembly via stringTie

source_name: EpCAMhi MDA-MB-231 breast cancer cell line

extract_protocol:
Total RNA was extracted from each sample using TRIzol and Direct-zol RNA miniprep kit. The RNA integrity number (RIN) of all samples was determined by an Agilent 2100 Bioanalyzer in the Harvard Medical School Biopolymers Facility. All RNA samples had RINs greater than 9.
Standard mRNA libraries were prepared with NEBNext® Ultra™ II Directional RNA Library Prep Kit after polyA-mRNA isolation (New England BioLabs). Libraries for negative control and UPF2 siRNA transfected samples were pooled separately and each pool was run on one lane of an Illumina Hiseq X10 system, yielding around 120 million mapped paired-end reads (150bp X 2) per sample.

treatment_protocol: EpCAMhiMDA-MB-231 cells were transfected with 100 nM of negative control siRNA or ON-TARGETplus human UPF2 siRNA-SMARTpool (both from Dharmacon) for 72 hour.

value: UPF2 siRNA transfection for 72 hours


title: HepG2N

description: transcriptome

source_name: HepG2 cell line

value: HepG2 cell line


title: EpCAMhi MDA-MB-231 UPF2 siRNA 3

value: EpCAMhi MDA-MB-231 breast cancer cell line


title: 1357_OB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor O, side B

value: colorectal tumor bulk

value: Carcinoma (3)

value: M


title: 1345_JB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor J, side B

value: F


title: HepG2D

description: transcriptome


title: 1345_SA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor S, side A

value: Adenoma


title: 1345_SB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor S, side B


title: 1345_TB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor T, side B


title: K562N

description: transcriptome

source_name: K562 cell line

value: K562 cell line


title: EpCAMhi MDA-MB-231 UPF2 siRNA 2


title: EpCAMhi MDA-MB-231 Negative siRNA 3

value: Negative siRNA transfection for 72 hours


title: EpCAMhi MDA-MB-231 Negative siRNA 1


title: EpCAMhi MDA-MB-231 Negative siRNA 2


title: K562D

description: transcriptome


title: HeLaN

description: transcriptome

source_name: HeLa cell line

value: HeLa cell line


title: HeLaD

description: transcriptome


title: 1345_TA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor T, side A


title: HEK293N

description: transcriptome

source_name: HEK293 cell line

value: HEK293 cell line


title: 1345_WB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor W, side B

value: Carcinoma (1)


title: 1350_MA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor M, side A

value: Carcinoma (2)


title: 1345_WA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor W, side A


title: 1345_WN

description: normal colon sample

source_name: genomic DNA from matching normal W

value: normal colon bulk


title: 1345_XB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor X, side B


title: CHD4_delta-6.7kb_ZNF410-Rep3

first: Divya

last: Vinjamur

address: 1 Blackfan Circle

data_processing:
Sequenced reads were aligned to the UCSC hg19 reference genome assembly and gene counts were quantified.
Differential expression testing was performed by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 csv file with log2 fold change, p-values and adjusted p-values for each gene.

source_name: CHD4 6.7 kb element deletion HUDEP-2 cells

growth_protocol: HUDEP-2 cells were cultured in expansion phase medium for 6 days after transduction or electroporation with Cas9 and sgRNA.

extract_protocol:
RNA was isolated using Trizol according to the manufacturer’s protocol (Thermo Fisher #15596026). Purified RNA was treated with DNase I.
mRNA libraries were prepared using standard Illumina protocols.

tag: culture condition

value: Expansion phase culture

value: ZNF410 sgRNA


title: CHD4_delta-6.7kb_ZNF410-Rep1


title: CHD4_delta-6.7kb_ZNF410-Rep2


title: 1345_XA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor X, side A


title: CHD4_delta-6.7kb_AAVS1-Rep2

value: AAVS1 sgRNA


title: 1345_KN2

description: normal colon sample

source_name: genomic DNA from matching normal K2

value: Normal tissue


title: 1345_EB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor E, side B


title: CHD4_delta-6.7kb_AAVS1-Rep1


title: 1345_KA2

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor K2, side A


title: 1345_KB2

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor K2, side B


title: HUDEP-2_ZNF410-Rep3

source_name: HUDEP-2 cells


title: 1337_JN

description: normal colon sample

source_name: genomic DNA from matching normal J


title: HUDEP-2_ZNF410-Rep1


title: CHD4_delta-6.7kb_AAVS1-Rep3


title: HUDEP-2_AAVS1-Rep3


title: 1345_EA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor E, side A


title: HUDEP-2_AAVS1-Rep1


title: 1337_HB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor H, side B

value: Carcinoma (4)


title: 1345_EN

description: normal colon sample

source_name: genomic DNA from matching normal E


title: HUDEP-2_ZNF410-Rep2


title: HUDEP-2_AAVS1-Rep2


title: 1337_HA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor H, side A

value: colorectal tumor bulk


title: HEK293D

description: transcriptome

source_name: HEK293 cell line

value: DMSO


title: 1337_HN

description: normal colon sample

source_name: genomic DNA from matching normal H

value: M


title: CD34_ZNF410_Rep-2

data_processing:
Adapter sequences were trimmed with Trimmomatic.
Trimmed reads were aligned to either the human reference genome hg19 or the mouse reference genome mm10 using bowtie2.
The alignment files (.sam) were converted to sorted, indexed bam files and marked for duplicates using Picard.
Reads were filtered using an alignment score cutoff of 10 with samtools
Peak calling was performed using macs2. Genomic regions annotated as part of the ENCODE project blacklist as problematic regions for alignment of high-throughput functional genomics data were excluded from analysis.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Excel spreadsheet containing genome-wide regions of ZNF410 chromatin occupancy. Data for each cell type is on a separate sheet of the workbook.

source_name: CD34+ HSPCs

extract_protocol:
Genomic DNA was isolated and prepared following the CUT&RUN protocol from Skene PJ, et al. Nat Protoc. 2018, PMID: 29651053.
Libraries were prepared using the NEBNext Ultra™ II DNA Library Prep Kit for Illumina following the protocol from Liu N, et al. Cell 2018, PMID: 29606353.
CUT&RUN, Paired-end 42bp sequencing.

tag: antibody

value: CUT&RUN with ZNF410 antibody


title: 1337_KB

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor K, side B

value: Adenoma


title: 1337_KA

description: colorectal tumor sample

source_name: genomic DNA from colorectal tumor K, side A


title: CD34_IgG_Rep-2

value: CUT&RUN with IgG antibody


title: CD34_IgG_Rep-1


title: CD34_ZNF410_Rep-1


title: HUDEP-2_IgG


title: HUDEP-2_ZNF410


title: ZNF_IgG_Rep-4

source_name: HUDEP-2 cells with overexpression of HA tagged ZNF410


title: ZNF_IgG_Rep-3


title: ZNF_IgG_Rep-1


title: Border zone cells cryoinjured mice hearts P7

city: Durham

first: Ravi

last: Karra

state: NC

address: 247A CARL Building

department: Department of Medicine

institute: Duke University

data_processing:
Sequenced reads were trimmed, aligned and binned into cell barcodes, using the Drop-seq pipeline v1.13.3
Genome_build: NCBIM37.67
Supplementary_files_format_and_content: Raw_gene_UMI_counts_matrix.txt.gz: The processed txt file is tab-delimited UMI count data for each gene of each single cell.

organism: Mus musculus

source_name: Border zones from cryoinjured hearts

extract_protocol:
Border zones of 3 cryoinjured hearts were collected at P7 and then dissociated into single cells.
Single cells were captured into droplets using microfluidics followed by preparation of single-cell cDNA libraries with the Drop-seq protocol.

value: hearts

tag: age

value: post natal day 7

tag: genotype

value: wild type

value: cryoinjury


title: ZNF_HA_Rep-4

value: CUT&RUN with HA antibody


title: ZNF_HA_Rep-3


title: ZNF_HA_Rep-2


title: E15 Ebf2-EGFP pos cells rep2

city: Shanghai

first: Jia

last: Li

address: No.67 chifeng road, yangpu district

institute: Tongji University

data_processing:
Average 60 million paired-end reads for each sample were obtained by HiSeq2000, then were mapped to the mouse genome build mm10 using Tophat v2.0.8b with about 85% mapping ratio (Kim D, et al., 2013).
To measure gene or lncRNA expression level, we calculated fragment per kilobase per million (FPKM) using Cufflinks v2.2.0 (Trapnell C, et al., 2010) based on the annotations for protein-coding genes (downloaded from UCSC, mm10, archive-2013-03-06-15-06-02) and known lncRNAs (lincRNAs and antisense lncRNAs, downloaded from ENSEMBL Release M6, 201507) (Mudge JM, et al., 2015)
Cuffdiff was used to identify differentially expressed genes between every two conditions (with 2 biological replicates) (FDR < 0.05 and fold change > 2 as cutoff) (Trapnell C, et al., 2013)
Genome_build: mm10
Supplementary_files_format_and_content: csv files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cerebral cortex

extract_protocol:
Ebf2-EGFP positive and negative cells at E11.5, E13.5, E15.5 were dissociated, resuspended and purified by FACS. Total RNA was extracted using QIAGEN RNeasy Mini Kits and processed by Sera-Mag Oligo (dT) beads (Thermo Scientific), libraries were prepared using the NEB Next mRNA Sample PreP Master Mix Set 1.
RNA libraries were prepared using the NEB Next mRNA Sample PreP Master Mix Set 1 and were performed according to the manufacturer’s instruction.

value: Ebf2-EGFP positive

value: cerebral cortex

tag: developmental stage


title: E15 Ebf2-EGFP pos cells rep1


title: E15 Ebf2-EGFP neg cells rep1

value: Ebf2-EGFP negative


title: E15 Ebf2-EGFP neg cells rep2


title: E13 Ebf2-EGFP neg cells rep1


title: WT-3: wild type BCG

city: Guang zhou

first: siyuan

last: feng

address: 74 zhongshan 2nd road

institute: Sun Yat-Sen University

data_processing:
All raw sequence reads by RNA-Seq were initially pre-processed by Trimmomatic (v0.36) to trim the adaptor sequences and remove low-quality sequences.
The alignment results were input into Cufflinks (v2.2.1). Unless otherwise stated, the unit of expression level in our analyses is FPKM.
Cuffdiff (v2.2.1) was used to test for differential expression. We defined genes as differentially expressed using the following criteria: FPKM > 10 and FDR < 0.001. The data for visualization was generated by R (R Development Core Team, Vienna, Austria).
Supplementary_files_format_and_content: Table S2 Differential gene expression between wild type and the ΔTCR mutant

organism: Mycobacterium tuberculosis variant bovis

source_name: bacteria

growth_protocol: Exponentially growing bacterial cultures (OD600 0.4-0.6) were pelleted and washed once with 7H9/Tween-80

extract_protocol:
Total RNA was prepared from wild-type and mutant strains using TRIzol reagent (Invitrogen), followed by DNase I treatment.
Approximately 1-μg total RNA samples were treated by the Ribo-Zero rRNA removal procedure (Illumina) to enrichment for mRNA.
Approximately 1μg of RNA was used for library preparation using a ScriptSeq (v2) RNA-seq kit and high-throughput sequencing on an Illumina NextSeq platform.

value: Exponentially growing bacterial culture

value: Wild type


title: TCR-1: deletion of TCR

value: deletion of TCR


title: TCR-2: deletion of TCR


title: WT-2: wild type BCG


title: HeLa_NHS_siZNF451_Slam-seq_REP2

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Library strategy: Slam-seq
3'UTR annotations were taken from Gencode annotation release 31 and merged on a gene level. Adapters and polyA stretches were trimmed from raw reads using fastp. Trimmed reads were further processed with SlamDunk v0.3.4. "Slamdunk all" command was executed with default parameters except '-5 12 -n 100 -t 20 -m -rl 100 --skip-sam'.  Differential gene expression was done with DESeq2 using raw read counts with at least 2 T>C conversions. Size factors were calculated based on corresponding total read counts for global normalization.
Genome_build: hg38
Supplementary_files_format_and_content: slamdunk_mapped_filtered_tcount.tsv

source_name: HeLa

growth_protocol: HeLa cells were plated, and after 24 hours for experiment (1) NELF-A Wildtype was knocked down using Lipofectamine RNAiMAX with concurrent transfection with either NELF-A WT or NELF-A ΔIDR using Lipofectamine 3000, for experiment (2) scr siRNA and siZNF451 was used with Lipofectamine RNAiMAX all per manufacturers instructions. Media was changed 24 hours after transfection and/or knockdown.

extract_protocol:
RNA was extracted using Trizol per manufactures protocol, with addition of DTT, and protection from light during the procedure to prevent S-S cross-binding.
5 ug of RNA was used for SLAMseq modifications, as described in Herzog et. al. 2017. Briefly, Iodoacetamide (Sigma I1149) was conjugated to 4SU in a 50mM pH 8.0 phosphate buffer in DMSO/Water (1:1), the reaction was quenched with DTT and RNA was reprecipitated using Ethanol and NaOAc. Libraries were prepared using Quantseq 3’ mRNA-Seq Library Prep Kit (Lexogen).

treatment_protocol: Heat-shock and labeling was carried out 24 hours after the change of media (48 hours after transfection and/or knockdown) in the following manner: Cells were subject to heat shock at 43 degrees Celsius for 30 minutes, with labeling beginning 15 minutes into heat-shock with 200uM 4SU (Caymen Chemical 16373), after a total of thirty minutes of heat-shock, cells were returned to 37 degrees Celsius for 90 minutes of recovery. The total labeling time was 105 minutes.

value: HeLa

tag: condition

value: Non Heat-Shock


title: ZNF_HA_Rep-1


title: E13 Ebf2-EGFP pos cells rep2

tag: tissue


title: WT-1: wild type BCG


title: E13 Ebf2-EGFP pos cells rep1


title: HeLa_NHS_siSCR_Slam-seq_REP3

value: siSCR


title: HeLa_NHS_siZNF451_Slam-seq_REP1


title: TCR-3: deletion of TCR


title: HeLa_NHS_siSCR_Slam-seq_REP1


city: Beijing

first: Junyang

address: 1 Beichen West Road, Chaoyang District, Beijing,

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Global gene expression profile of Geobacillus thermoglucosidasius DSM2542 at 8 h with 1% xylose

data_processing:
For RNA-seq raw reads of fastq format were firstly processed to remove low quality reads and those containing adapter.
The clean reads were mapped against predicted transcripts of the Geobacillus thermoglucosidasius DSM2542 genome (https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP012712.1) by using SOAPaligner/SOAP2.
HTSeq v0.6.1 was used to count the read numbers mapped to each gene, and then the FPKM was calculated based on the gene length and mapped read counts.
Genome_build: https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP012712.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample of RNA_seq.

organism: Parageobacillus thermoglucosidasius

source_name: Cells of Geobacillus thermoglucosidasius DSM2542 harvested at 8 h after fermentation

growth_protocol: Geobacillus thermoglucosidasius DSM2542 were cultivated in 250 mL shake flask with 50 mL USYE medium containing 40 mM each (final concentrations) of Bis-Tris, PIPES, and HEPES at pH 7.0 at 60 °C, 250 rpm.

extract_protocol:
RNA was harvested using Trizol reagent. 3 ug of total RNA was used for RNA-seq
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell pellets were quickly harvested by fast filtration and flash frozen in liquid nitrogen, and then ground into powder

tag: synonymn

value: Geobacillus thermoglucosidasius

value: treated with 1% xylose

tag: timepoint


title: ZNF_IgG_Rep-2

value: CUT&RUN with IgG antibody


title: E13 Ebf2-EGFP neg cells rep2

tag: cell type


title: E11 Ebf2-EGFP neg cells rep2


title: HeLa_HS_siZNF451_Slam-seq_REP3

tag: treatment

value: Heat-Shock + Recovery


title: HeLa_HS_siZNF451_Slam-seq_REP2


description: Global gene expression profile of Geobacillus thermoglucosidasius DSM2542 at 8 h without xylose

tag: strain

value: untreated


title: HeLa_NHS_siZNF451_Slam-seq_REP3

tag: cell line


title: HeLa_HS_siZNF451_Slam-seq_REP1


title: E11 Ebf2-EGFP neg cells rep1


description: Global gene expression profile of Geobacillus thermoglucosidasius DSM2542 at 6 h with 1% xylose

source_name: Cells of Geobacillus thermoglucosidasius DSM2542 harvested at 6 h after fermentation

value: wild type


title: E11 Ebf2-EGFP pos cells rep2


title: HeLa_HS_siSCR_Slam-seq_REP2


title: HeLa_HS_siSCR_Slam-seq_REP1


title: E11 Ebf2-EGFP pos cells rep1


title: HeLa_HS_siSCR_Slam-seq_REP3


title: VCaP: Input

data_processing:
ChIP-seq reads were aligned to the human genome build hg38 using Bowtie2. Duplicate and discordant reads were removed.  Gene annotations and transcript start site (TSS) information for human genes were from taken from Gencode annotation release 26.
Genome_build: hg38

source_name: VCaP

extract_protocol: VCaP cells were grown in DMEM medium supplemented with 10% feta bovine serum and 1% penicillin/streptomycin antibiotics at 37 degree C temperature incubator with 5% CO2. Nuclei from approximately 10 million formaldehyde crosslinked (1%; 10min at room temperature) cells were isolated and chromatin was fragmented using sonicator (bioruptor). Lysates were cleared and protein-DNA complexes were isolated using target specific antibodies and protein-A/G magnetic beads. DNA fragments were purified and libraries were prepared accorcing to standard Illumina protocol.

treatment_protocol: Heat shock for ChIP-seq samples was done at 43 degree C incubator for 30min. Silencing for VCaP cells was done by transfecting siRNA for UBE2I (siUBE2I samples) or non-targeting control siRNA (siNON samples) using lipofectamine RNAiMAX transfection reagent (life technologies).

value: VCaP

tag: chip antibody

value: none (input)


title: VCaP: Pol2_siUBC9_HS2

description: resequencing of sample previously submitted to GEO as GSM1777596

growth_protocol: VCaP cells were grown in DMEM medium supplemented with 10% feta bovine serum and 1% penicillin/streptomycin antibiotics at 37 degree C temperature incubator with 5% CO2.

value: anti-Pol2, clone:8WG16 (Covance, catalog# MMS-126R, lot# E12CF00481)

value: siUBE2I transfected

value: Heat-Shock


description: Global gene expression profile of Geobacillus thermoglucosidasius DSM2542 at 4 h with 1% xylose

source_name: Cells of Geobacillus thermoglucosidasius DSM2542 harvested at 4 h after fermentation


description: Global gene expression profile of Geobacillus thermoglucosidasius DSM2542 at 4 h without xylose


title: Apo E3, male, 21 days post injury

city: New York

first: Jens

last: Hansen

state: NY

address: 1425 Madison Ave

department: Department of Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Random read removal to remove read imbalances between samples
Read alignment with Star 2.5.4b, bowtie2 2.1.10, samtools 0.1.7
Identification of DEGs using Cuffdiff 1.3.0

source_name: Incomplete spinal cord injury

extract_protocol:
TRIzol reagent (ThermoFisher)
TruSeq RNA Sample Prep Kit v2 protocol (Illumina),

treatment_protocol: Incomplete spical cord injury after induction of anesthesia by inhalation of 3% isoflurane (50 kdyne contusion spinal cord injury)

value: Human ApoE3 Targeted Replacement Mice


title: VCaP: Pol2_siUBC9_Ctrl1

description: resequencing of sample previously submitted to GEO as GSM1777593


title: HeLa_NHS_siSCR_Slam-seq_REP2


title: VCaP: Pol2_siUBC9_HS1

description: resequencing of sample previously submitted to GEO as GSM1777595


title: VCaP: Pol2_siCtrl_HS1

description: resequencing of sample previously submitted to GEO as GSM1777590

value: control siRNA transfected


title: VCaP: Pol2_siCtrl_HS2

description: resequencing of sample previously submitted to GEO as GSM1777591


title: VCaP: Pol2_siCtrl_Ctrl1

description: resequencing of sample previously submitted to GEO as GSM1777588


title: OEgal2detalgalK-Gal-2

city: Tianjin

first: Jingen

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Myceliophthora thermophila ATCC 42464 genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
Genome_build: Myceliophthora thermophila ATCC 42464(https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html)
Supplementary_files_format_and_content: tab-delimited text files including Reads count and RPKM for each sample.

organism: Thermothelomyces thermophilus

source_name: Myceliophthora thermophila ATCC 42464

growth_protocol: M. thermophila strains were inoculated into 1×Vogel’s salt with 2% glucose and cultivated at 45 °C for 18h. Mycelia were collected and washed three times with 1×Vogel’s salt, and then transferred into the medium with 2% glucose or galactose as the carbon source for an additional 4 h of cultivation.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: carbon

value: Gal


title: OEgal2deltagalK-Gal-1


title: Apo E4, male, 7 days post injury

value: Human ApoE4 Targeted Replacement Mice


title: Apo E3, male, 7 days post injury


title: VCaP: Pol2_siCtrl_Ctrl2

description: resequencing of sample previously submitted to GEO as GSM1777589

value: Non Heat-Shock


title: OEgal2-Gal-1


title: E12.5_FetalLiver_Rep2_P06H_iX16

city: Paris

first: Laina

last: Freyer

address: 25-28 rue du Dr Roux

department: Developmental and Stem Cell Biology

country: France

institute: Institut Pasteur

data_processing:
Demultiplexing and generation of UMI count tables was performed using the pipeline described in Jaitin et al. 2014 (10.1126/science.1247651). Read 1 was used for mapping to the mouse genome whereas Read 2 was used to identify UMI and cell barcodes.
Supplementary_files_format_and_content: Txt files containing raw counts (UMI) per feature.

source_name: erythro-myeloid progenitors

growth_protocol: Timed matings were performed to determine embryonic day E0.5 as the date of vaginal plug. Then embryos were isolated at E9.5, E10.5 or E12.5 days of embryonic development.

extract_protocol:
Embryos were isolated from euthanized females and dissected in PBS to remove the fetal liver and/or yolk sac.
MARS-Seq

treatment_protocol: For Csf1r-MeriCreMer;Rosa26-eYFP samples, 4-hydroxytamoxifen (OHT) was injected at embryonc day E8.5.

tag: embryonic stage

value: fetal liver


title: E12.5_FetalLiver_Rep2_P06A_iX08


title: OEgal2-Gal-2


title: WTdeltagalK-Gal-2

value: WTdeltagalK


title: E12.5_FetalLiver_Rep2_P04A_iX06


description: Global gene expression profile of Geobacillus thermoglucosidasius DSM2542 at 6 h without xylose

value: Geobacillus thermoglucosidasius


title: E12.5_FetalLiver_Rep2_P04H_iX14


title: E12.5_FetalLiver_Rep2_P05H_iX15


title: WTdeltagalK-Gal-1


title: 3T9_MycER_HEA_ER

city: Milano

first: Mattia

last: Dalsass

state: MI

address: Via Adamello, 16

institute: IEO

description: 5% Hela Chromatin spiked in

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_masker -Q33 -q 20 -r -N -v -i
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile -fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Removing duplicate reads: samtools rmdup -sS bamfile
Peak calling with MACS version 2.0.10; macs2 -t samplebam -c inputbam --mfold=7 30 -g mm -p 0.00001 or macs2 -t samplebam -c inputbam -f BAMPE --mfold=7 30 -g mm -p 0.00001
Genome_build: mm9
Supplementary_files_format_and_content: bed files with enriched regions

source_name: immortalized fibroblasts

growth_protocol: All the cell lines used in this work were grown in DMEM, supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 1% penicillin/streptomycin. For the cb9Δmyc and the cb9-mycHEA cell lines, medium was also complemented with doxycycline (1 µg/ml) to keep the tet-Myc transgene expressed, unless otherwise specified.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies.
Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection with AMPure beads and PCR with index primers.

value: 3T9 fibroblastst

value: infected with BP-MycER-HEA

value: OHT 4h

value: ER-alpha 06-935 Santa Cruz


title: E12.5_FetalLiver_Rep2_P05A_iX07


title: VCaP: Pol2_siUBC9_Ctrl2

description: resequencing of sample previously submitted to GEO as GSM1777594

value: VCaP


title: E12.5_FetalLiver_Rep2_P03H_iX13


title: 3T9_MycER_WT_ER

description: 5% Hela Chromatin spiked in

value: infected with BP-MycER-WT


title: 3T9_EV_ER

description: 5% Hela Chromatin spiked in

value: infected with empty vector


title: 3T9_MycER_RA_ER

description: 5% Hela Chromatin spiked in

value: infected with BP-MycER-RA


title: WT-Gal-2

value: WT


title: E12.5_FetalLiver_Rep1_P01H_iX02


title: E12.5_FetalLiver_Rep2_P03A_iX05


title: E10.5_FetalLiver_Rep6_P06H_iX12


title: 3T9_MycER_HEA_Myc

description: 5% Hela Chromatin spiked in

value: c-Myc N262 (Santa Cruz sc764)


title: WT-Gal-1


title: E10.5_FetalLiver_Rep6_P06A_iX11


title: 3T9_MycER_WT_Myc

description: 5% Hela Chromatin spiked in


title: E12.5_FetalLiver_Rep1_P01A_iX01


title: E10.5_FetalLiver_Rep5_P05A_iX09


title: WT-Glu-2

value: Glu


title: WT-Glu-1


title: E10.5_FetalLiver_Rep4_P04H_iX08


title: 3T9_EV_Myc

description: 5% Hela Chromatin spiked in


title: 3T9_MycER_RA_Myc

description: 5% Hela Chromatin spiked in


title: E10.5_FetalLiver_Rep4_P04A_iX07


title: E10.5_FetalLiver_Rep3_P15H_iX30


title: 3T9_input


title: E10.5_FetalLiver_Rep3_P15A_iX29


title: WT-NoC-2


title: WT-NoC-1


title: E10.5_FetalLiver_Rep3_P14H_iX28


title: E10.5_FetalLiver_Rep2_P10H_iX20


title: mESN

description: transcriptome

source_name: mouse ES cells

value: mouse ES cells


title: mESD

description: transcriptome

value: DMSO


title: E10.5_FetalLiver_Rep1_P08A_iX10


title: E10.5_FetalLiver_Rep5_P05H_iX10


title: E10.5_YolkSac_Rep6_P03H_iX06

value: yolk sac


title: E10.5_FetalLiver_Rep1_P08H_iX18

value: fetal liver


title: E10.5_FetalLiver_Rep2_P10A_iX12


title: MycER_RA_8h_rep1

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v -i
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Genome_build: Genome_build: mm9
Supplementary_files_format_and_content: txt file reporting the eRPKM, log2FC and padj from DESEq2 output

growth_protocol: All the cell lines used in this work were grown in DMEM, supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was purified from cell lysates onto Quick-RNA Miniprep columns (Zymo, #R1054) and treated on-column with DNaseI
For RNA-seq experiments, total RNA was purified as above, and RNA quality checked with the Agilent 2100 Bioanalyzer (Agilent Technologies). 0.5-1 g of RNA were used to prepare libraries for RNA-seq with the TruSeq stranded total RNA Sample Prep Kit (Illumina, #20020596) following the manufacturer’s instructions.

value: OHT 8h


title: E10.5_YolkSac_Rep5_P16H_iX32


title: MycER_RA_8h_rep3


title: MycER_HEA_8h_rep3


title: E10.5_YolkSac_Rep6_P03A_iX05


title: E10.5_YolkSac_Rep5_P16A_iX31


title: E10.5_YolkSac_Rep3_P09H_iX19


title: E10.5_YolkSac_Rep3_P09A_iX11


title: MycER_HEA_8h_rep2


title: E10.5_YolkSac_Rep2_P07H_iX17


title: E10.5_YolkSac_Rep2_P07A_iX09


title: MycER_HEA_8h_rep1


title: MycER_WT_8h_rep3


title: MycER_RA_8h_rep2


title: X-PUT-2

city: Atlanta

first: Ken

last: Moberg

state: Georgia

address: 615 Michael Street

department: Cell Biology

institute: Emory University School of Medicine

description: A fraction of initial head lysate volumes were isolated to generate Input samples; the remainder underwent IP protocols. Thus, PUT samples are derived from this isolate, 20% of the initial head lysate volumes.

data_processing:
Many of the data processing steps detailed below were conducted on the Galaxy web platform, specifically using the public server at usegalaxy.org. For each Galaxy tool described, exact parameters and version numbers used are also detailed in a Supplemental Table of the Rounds et al. submission associated with this accession.
To start on Galaxy, for each sample, reads from across all four NextSeq flow cell lanes were concatenated using the “Concatenate datasets tail-to-head” tool (Galaxy Version 1.0.0).
Reads were mapped using RNA STAR (Dobin et al. 2013), Galaxy Version 2.6.0b-1 and default parameters with the following exceptions: read type—paired (as individual datasets), reference genome—from history (using the BDGP6.22, Ensembl 97 FASTA and GTF), and length of the genomic sequence around annotated junctions—74.
Mapped reads were assigned to exons/genes and tallied using featureCounts (Liao et al. 2014), Galaxy Version 1.6.3+galaxy2 and default parameters with the following exceptions: specify strand information—Stranded(Reverse), gene annotation file—history (using the BDGP6.22, Ensembl 97 GTF), create gene-length file—true, count fragments instead of reads—enabled, GFF gene identifier—gene_name.
To enable inter-sample read count comparisons, count normalization and differential expression analysis was conducted using DESeq2 (Love et al. 2014), Galaxy Version 2.11.40.2 and default parameters with the following exceptions: factors—3 levels, each a dataset collection of four biological replicates, output normalized counts table—true, output all levels vs all levels—true. Importantly, DESeq2 analysis was performed twice, once on the 12 IP samples and once on the 12 Input samples; for discussion of this sample separation method see the Supplementary Materials and Methods of the Rounds et al. submission associated with this accession.
To identify Nab2-associated and Atx2-associated RNAs, we calculated IP/Input (i.e. “percent input” or “percent recovery”) (Zhao et al. 2010; Aguilo et al. 2015; Li et al. 2019) values for each of a “testable” set of 5,760 genes with 1)detectable expression in all twelve Inputs and 2)an average normalized Nab2 or Atx2 RIP read count greater than 10. These criteria were based on those used in (Lu et al. 2014; Malmevik et al. 2015). Fold enrichment differences were statistically tested by performing gene-by-gene one-way ANOVAs (Li et al. 2019), applying Dunnett’s post-hoc test (Dunnett 1955), and calculating adjusted p-values corrected for multiple hypothesis testing within each gene-by-gene ANOVA. We identify a small, focused set of statistically significantly enriched RNAs using this approach, arguing type I (i.e. false positive) error is sufficiently controlled and additional corrections between genes are not necessary (Rothman 1990). See Methods of the Rounds et al. submission associated with this accession for more detail.
Genome_build: BDGP6.22 (downloaded from release 97 of the Ensembl database)
Supplementary_files_format_and_content: The "Percent_Input_..." file is a tab-delimited text file containing results of RBP-RNA ASSOCIATION SIGNIFICANCE TESTING for all 5,760 genes in the TESTABLE SET (see data processing steps for set definition). The essential values to identify SIGNIFICANTLY RBP-ASSOCIATED TRANSCRIPTS are listed in the first 6 columns; these values are gene name, properly normalized % Input values per genotype, and the results of RBP-RNA association statistical significance testing. Later columns give further details or illustrate calculations used to arrive at the final results in the first 6 columns. Genes are ordered first by Nab2-FLAG fold enrichment ("% Input F Norm AVG"); then, all genes with a value in that field greater than 1 are ordered, smallest to largest, by adjusted Dunnet's post-hoc test p-value (FvsW DunAdjp). In all, for all testable genes, IP/Input (i.e. % input or fold enrichment) values are reported at both the level of overall genotype (e.g. elav>Nab2-FLAG or "F") and individual sample pair (e.g. elav>Nab2-FLAG RIP and PUT sample #2). This report also includes gene-level results of gene-by-gene one-way ANOVAs (for association significance testing) along with averages of DESeq2-normalized counts per genotype and RIP or PUT sample type combination (e.g. W.RIP). Where appropriate, standard deviation (SD) and standard error of the mean (SEM) values are also reported.
Supplementary_files_format_and_content: The DESeq2-normalized read counts file ("DESeq2_Normalized_Counts-combined...") is a tab-delimited text file containing a matrix of NORMALIZED READ COUNTS for all 24 samples. Normalized counts were generated by two independent DESeq2 analyses, one on the 12 RIP samples and one on the 12 PUT samples, and then combined into this matrix. See "data processing step" text for further detail. DESeq2 normalization accounts for library size and composition, enabling accurate comparison of relative RNA abundance for a given gene between samples. FPKM and similar methods do not account for library composition. Critically though, DESeq2-normalized counts should not be directly compared between different genes—instead, genes should be compared by comparing relative fold changes or enrichment values. The inclusion of "Parametric" in the file name refers to the "fit type" setting used when running DESeq2.
Supplementary_files_format_and_content: All "…[featureCounts…" files are .tabular files that contain, for a single sample, unedited, non-normalized RAW COUNTS per gene as assigned by featureCounts analysis of the appropriate .bam read mapping/alignment file produced by STAR. These files are may be opened by text editors and Microsoft Excel.

organism: Drosophila melanogaster

source_name: Input lysate, Heads

extract_protocol:
Following immunoprecipitation, RNA was isolated from IP and Input samples using a TRIzol-column hybrid approach adapted from (Rodriguez-Lanetty). To account for volume differences, samples were vigorously homogenized in TRIzol reagent (15596018, Thermo Fisher) at a ratio of either 1:10 (IP sample:TRIzol) or 1:3 (Input sample:TRIzol) and then incubated for 5 minutes at room temperature. All homogenized samples were clarified by centrifugation at 12,000×g at 4°C for 5 minutes, IP samples were magnetized to collect beads, and supernatant was isolated from all samples. After adding chloroform at a ratio of 0.2:1 (choloroform:TRIzol), samples were manually shaken and incubated at room temperature for 3 minutes. Samples were phase separated by centrifugation at 12,000×g at 4°C for 15 minutes, after which the aqueous layer was carefully isolated and mixed with an equal volume of 100% ethanol. RNA was further purified using an RNeasy Mini Kit (74106, QIAGEN) according to the manufacturer’s instructions (RNeasy Mini Handbook, 4th Ed., June 2012) with the following deviations: for each sample, a final 30 µL elution was performed twice, isolating 60 µL of RNA in total into each collection tube. An on-column DNase digestion step was also performed under the same instructions using an RNase-Free DNase Set (79254, QIAGEN). Final RNA concentration and sample purity were determined via a NanoDrop 1000 spectrophotometer (Thermo Fisher).
Once obtained, RNA samples were transferred on dry ice to the Georgia Genomics and Bioinformatics Core at UGA for library preparation and sequencing. There, IP samples were first concentrated using solid phase reversible immobilization (SPRI) beads. Then, the TruSeq Stranded Total RNA Library Prep Gold kit (20020598, Illumina) was used to deplete rRNA and prepare stranded cDNA libraries from all twenty-four samples. These uniquely barcoded cDNA libraries were then pooled by sample type, forming one IP library pool and one Input library pool. Each pool was sequenced on a separate NextSeq High Output Flow Cell (Illumina) for 150 cycles to generate paired-end, 75 base-pair (bp) reads.

treatment_protocol: 300 female Drosophila heads each of the genotypes elav>Gal4 alone, elav>Nab2-FLAG, and elav>Atx2-3xFLAG, previously isolated in bulk (see Supplementary Materials and Methods in the Rounds et al. submission associated with this accession), were fixed in 1% formaldehyde, 0.1% NP-40 in PBS for 30 minutes at 4°C. Fixation was quenched by adding glycine to a final concentration of 250 mM and rocking for 10 minutes at 4°C. Heads were washed in 0.1% NP-40 in PBS and then manually homogenized with a smooth Teflon pestle for 5 minutes in 250 µL of NIB in a size AA glass tissue grinder at 4°C (3431D70, Thomas Scientific). Homogenates were spun through 35 µm cell strainer caps into round-bottom tubes (352235, Falcon) to remove exoskeletal debris, transferred, and then centrifuged for 5 minutes at 500×g at 4°C to separate an insoluble fraction. Twenty percent of the soluble supernatant volume was isolated and defined as Input; the remaining eighty percent was used for immunoprecipitation. Both Input and IP samples were diluted to final concentrations of 0.8x IP Buffer to ensure comparable and efficient sample lysis. IP samples were transferred onto the α-FLAG-conjugated magnetic Dynabeads, and both sample types were incubated, rotating, for 10 minutes at room temperature. Next, IP sample supernatant was collected as the Unbound fraction, and IP sample beads were washed three times in IP Buffer. Finally, IP sample beads were resuspended in IP Buffer, transferred to clean tubes, and stored along with Input samples overnight at 4°C to allow passive hydrolysis to partially reverse formaldehyde crosslinks. For RNA immunoprecipitation, harsh elution of RNA from IP sample beads was accomplished the next day with Trizol—both IP and Input samples were subjected to the RNA extraction protocol detailed below.

tag: genotype (shorthand)

value: X

tag: sample/treatment type and description

value: PUT; RNA from Input samples

value: decapitated adult female heads, isolated in bulk protocol

tag: tissue amount

value: 300 heads

tag: control or experimental?

value: Experimental


title: X-PUT-3

tag: genotype


title: E10.5_YolkSac_Rep1_P02H_iX04


title: X-PUT-4


title: MycER_WT_8h_rep2

value: 3T9 fibroblastst


title: F-PUT-4

value: F


title: X-PUT-1


title: E9.5_YolkSac_Rep2_P02A_iX03


title: MycER_WT_8h_rep1

value: infected with BP-MycER-WT


title: E9.5_YolkSac_Rep2_P01H_iX02


title: E9.5_YolkSac_Rep2_P01A_iX01


title: E9.5_YolkSac_Rep1_P11A_iX21


title: E9.5_YolkSac_Rep1_P11H_iX22


title: F-PUT-3


title: F-PUT-2


title: EV_8h_rep2

value: infected with empty vector


title: EV_8h_rep3


title: E10.5_YolkSac_Rep1_P02A_iX03


title: MEL_IgG_Rep-3

source_name: MEL cells

tag: antibody

value: CUT&RUN with IgG antibody


title: F-PUT-1


title: W-PUT-4

value: W

value: Control


title: MEL_ZNF410_Rep-2

value: CUT&RUN with ZNF410 antibody


title: MEL_ZNF410_Rep-3


title: MEL_IgG_Rep-1


title: MEL_ZNF410_Rep-1


title: W-PUT-3


title: MycER_RA_4h_rep3

value: infected with BP-MycER-RA

value: OHT 4h


title: E9.5_YolkSac_Rep2_P02H_iX04

value: yolk sac


title: MycER_RA_4h_rep2


title: MycER_RA_4h_rep1


title: W-PUT-1


title: X-RIP-4

description: A fraction of initial head lysate volumes were isolated to generate Input samples; the remainder underwent IP protocols. Thus, RIP samples are derived from this remainder, 80% of the initial head lysate volumes.

source_name: anti-FLAG immunoprecipitate, Heads

value: RIP; RNA from anti-FLAG immunoprecipitate


title: WT_1

first: Jaehyung

last: Kim

address: 46, Gaeunsa 2-gil, Seongbuk-gu, Seoul, Korea

institute: KoreaUniversity

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: read count values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: strain background

tag: age

value: 5 months of age

tag: genotype/variation

value: willd type

value: skin


title: WT_2

tag: tissue


title: EV_8h_rep1

tag: cell type

value: OHT 8h


title: WT_5


title: MEL_IgG_Rep-2


title: WT_4


title: WT_3


title: MycER_HEA_4h_rep2

value: infected with BP-MycER-HEA

tag: treatment


title: STAT3cKO_1

value: keratinocyte-specific ablation of STAT3


title: MyHSC_6_week_single-cell

city: San Diego

first: Pura

last: Muñoz-Cánoves

address: 5510 Morehouse Dr

institute: Altos Labs

description: single-cell RNA-seq

data_processing:
Total RNA sequenced reads were pseudoaligned to the mm10 reference cDNA using Salmon v1.4.0.
Single Cell RNA sequenced reads were aligned to the mm10 reference genome using 10X Genomics Cell Ranger v5.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: Tar files with the output of Salmon, including quant.sf containing the TPM values
Supplementary_files_format_and_content: Tar files with raw and filtered gene matrices, features, and barcodes

source_name: myeloid biased HSC

extract_protocol:
Total RNA was extracted by using MagMax96 total RNA isolation kit (Ambion, AM1830) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using Nextera XT DNA Library Preparation Kit

tag: strain

value: myeloid biased HSC

value: WT

value: 6 weeks


title: W-PUT-2

value: PUT; RNA from Input samples

value: decapitated adult female heads, isolated in bulk protocol

value: 300 heads


title: MycER_WT_4h_rep3

value: 3T9 fibroblastst

value: infected with BP-MycER-WT


title: STAT3cKO_3


title: X-RIP-3

value: X

value: Experimental


title: STAT3cKO_5


title: X-RIP-1

value: RIP; RNA from anti-FLAG immunoprecipitate


title: STAT3cKO_2

value: 5 months of age


title: STAT3cKO_4


title: F-RIP-4

value: F


title: MycER_WT_4h_rep2

value: OHT 4h


title: MycER_HEA_4h_rep3


title: sgAMBRA1#2 c2

city: Stanford

first: Andrea

middle: Christine

last: Chaikovsky

state: California

address: 265 Campus Drive

institute: Stanford University

data_processing:
RNA qunatification done by salmon version 0.8.2
Differential expression analysis with DESeq2 version 1.22.2
Genome_build: human GRCh38
Supplementary_files_format_and_content: quant.sf files are tab delimited text files

source_name: Cell line

growth_protocol: U937 cells were cultured in RPMI-1640 medium supplemented with 10% bovine growth serum and 1% penicillin-streptomycin-glutamine. Cells were plated at equal density and cultured for 48 hours prior to RNA extraction.

extract_protocol:
Cells were flash frozen on dry ice and sent to Novogene for total RNA isolation and quality control.
Library preparation and sequencing were performed by Novogene using Illumina’s sequencing platform.

tag: cell line

tag: cancer type

value: lymphoma

value: AMBRA1 knockout


title: sgAMBRA1#2 c1


title: MycER_WT_4h_rep1


title: sgAMBRA1#1 c2


title: EV_4h_rep3

value: infected with empty vector


title: SUB07865: Control_vs_AsiC_treatment_CD45pso_cell_comparision

first: Ying

last: Zhang

address: 200 Longwood Avenue, Warren Alpert Building Room 260

description: mRNA from single cells

data_processing:
Raw data were processed using the InDrops pipeline in Python (https://github.com/indrops/indrops)  for version 3 libraries with default parameters
reads were aligned to a reference mouse transcriptome (Ensembl GRCm38 release 85)
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Tab Separated Values files include UMI s for each sample
Supplementary_files_format_and_content: SUB07865-I21.SUB.counts.tsv: Biological sample: EpCAM aptamer Control treatment 1
Supplementary_files_format_and_content: SUB07865-I22.SUB.counts.tsv: Biological sample: Combined EpCAM-AsiCs treatment 1
Supplementary_files_format_and_content: SUB07865-I23.SUB.counts.tsv: Biological sample: Combined EpCAM-AsiCs treatment 2
Supplementary_files_format_and_content: SUB07865-I24.SUB.counts.tsv: Biological sample: EpCAM aptamer Control treatment 2

source_name: CD45+ tumor-infiltrating lymphocytes

growth_protocol: 6-8 week old BALB/c mice were orthotopically implanted with ~105 4T1E breast tumor cells/mouse.

extract_protocol:
On day 14, tumors were harvested, incubated at 37°C for 15 min with 100 mg/ml Liberase TL (Roche) diluted in Ca2+ and Mg2+-free RPMI (ThermoFisher), followed by shaking at 37°C for 10 min. Samples were then filtered twice through 40 mM strainers. Dead cells were removed and CD45+ cells were enriched with CD45 microbeads at 4°C. More than 95% of cells were CD45+ as verified by flow cytometry. The enriched cells were diluted to 200,000 cells/ml in Ca2+ and Mg2+-free RPMI medium containing 1% FBS and kept on ice until the cells were flowed into the microfluidic device. 6,000 cells per sample were encapsulated using the inDrop technology (Klein et al., Cell, 2015)
Single-cell transcriptomes were barcoded within the microfluidic droplets. After within droplet reverse transcription, emulsions of approximately 3,000 cells were broken and used for library preparation as described (Klein et al., Cell, 2015; Zilionis et al., Nature Protocols, 2017),. Libraries were indexed with V3 sequencing adaptors, pooled from different samples at equimolar ratios, and sequenced on an Illumina NextSeq 500 system using the NextSeq 75 High Output Kits and standard Illumina sequencing primers and 61 cycles for read 1 and 14 cycles for read 2, 8 cycles each for index read 1 and index read 2.

treatment_protocol: Mice bearing palpable 4T1E tumors were treated with either EpCAM aptamer or EpCAM-AsiCs cocktail targeting Upf2, Parp1, Cd47 and Mcl1 by s.c. injection every third day.

value: BALB/cJ

value: 4T1E breast tumor


title: EV_4h_rep2


title: sgCtrl c1

value: wild-type


title: MycER_HEA_4h_rep1

value: infected with BP-MycER-HEA


title: sgCtrl c2


title: X-RIP-2

value: decapitated adult female heads, isolated in bulk protocol


title: EV_4h_rep1


title: F-RIP-2

value: 300 heads


title: W-RIP-4

value: W

value: Control


title: F-RIP-1


title: F-RIP-3


title: W-RIP-2


title: W-RIP-3


title: PARP-1 KD_GRO-seq_E2 rep1

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: GROseq libraries under  PARP-1 KD E2 rep1

data_processing:
Library strategy: GRO-Seq
The GRO--seq reads were aligned to the hg19 human reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were further converted to (1) “bed” files for later Metagene and read-density analyses and (2) “wiggle” files counting reads in non-overlapping 200-bp windows across the genome for presentation as genome browser tracks by using the BEDTools software package  (Quinlan et al, 2010).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

growth_protocol: MCF-7 cell lines were obtained from the ATCC used for GRO-seq and proliferation assays described herein. MCF-7 cells were maintained in Minimum Essential Medium Eagle supplemented with 5% calf serum.

extract_protocol:
MCF-7 cells were washed three times with ice-cold PBS and then resuspended for swelling in ice-cold Hypotonic Lysis Buffer [10 mM Tris•HCl, pH 7.4, 0.5% NP-40, 10% Glycerol, 3 mM CaCl2, 2 mM MgCl2, and 1 mM DTT containing 1x protease inhibitor cocktail (Sigma-Aldrich) and 4 units/mL SUPERase-In (Ambion)]. The swollen cells were collected by centrifugation at 1000 RCF for 10 min at 4°C and then resuspended in 1.5 ml of lysis buffer and pipetted up and down through a narrow opening tip 30 to 50 times to lyse the cells and release the nuclei. The nuclei were collected by centrifugation and washed once with 1 mL of Hypotonic Lysis Buffer. After a final collection by centrifugation, the resulting pellets of nuclei were resuspended in 500 µL of Freezing Buffer (50 mM Tris•HCl, pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, and 4 units/mL of SUPERase-In per mL), counted, frozen in liquid nitrogen in 100 µL aliquots containing 5 x 106 nuclei, and stored at -80°C until use. (PMID: 7256882)
GRO-seq libraries were prepared as described previously with some minor modifications (PMID: 24564208).

treatment_protocol: Prior to all experiments, MCF-7 cells were grown for 3 days in phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum (CDCS). For experiments, cells were treated with 100 nM E2 or vehicle (ethanol) for 40 minutes.

value: human Estrogen receptor alpha+ breast cancer cells

tag: biological replicate


title: Luc KD_GRO-seq_E2 rep2

description: GROseq libraries under  Luc KD E2 rep2

value: LucKD


title: W-RIP-1

value: RIP; RNA from anti-FLAG immunoprecipitate


title: Y_WT_653

value: myeloid biased HSC

value: Igf2bp2 WT

value: 3 Months


title: Luc KD_GRO-seq_E2 rep1

description: GROseq libraries under Luc KD E2 rep1


title: Y_WT_652


title: PARP-1 KD_GRO-seq_E2 rep2

description: GROseq libraries under  PARP-1 E2 rep2


title: with DEX pretreatment, reoxygenation time is 0 h

type: RNA

city: Urayasu

first: Yui

last: Yamane

state: Chiba

address: 2-1-1 Tomioka

country: Japan

institute: Juntendo University Urayasu Hospital

description:
Gene expression data from human astrocytes with DEX pretreatment and reoxygenated for 0 h
HAD 0 h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Gene Spring v14.9.1 (Agilent) using Affymetrix default analysis settings and global scaling as normalization method. A given gene was analyzed if its normalized intensity was more than 0.2.

label: biotin

source_name: human astrocytes after DEX pretreatment, OGD exposure and reoxygenation for 0h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HA were  maintained in astrocyte medium (ScienCell Research), calculated the number and disseminated in 6 well plate with 5×103 cells/cm2 each well.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HA were incubated with or without 5 nM DEX for 1h. After washing with PBS, cells were resuspended in glucose-free DMEM and placed in an anaerobic chamber. Anoxia was initiated by transferring cell cultures to a modular incubator chamber  MIC-101 (Billups-Rothenberg) and flushing with a preanalysed gas mixture 95 % N2 / 5 % CO2 (Nippon Megacare Co.) for 15 min along with bubbling the cell culture with the same gas at a flow rate of 3 L/min. Then, the cells were further incubated in the anaerobic chamber for 4h at 37 ℃. After incubation, the cells were resuspended in the astrocyte medium, and further incubated in the normal atmosphere during 0, 2, 6, 12, 24 h. Total RNA was prepared from the HA by extraction with TRIzol reagent (Invitrogen)

value: astrocyte

value: brain


title: without DEX pretreatment, reoxygenation time is 12 h

description:
Gene expression data from human astrocytes without DEX pretreatment and reoxygenated for 12 h
HAC 12 h

source_name: human astrocytes after no DEX pretreatment, OGD exposure and reoxygenation for 12h


title: control

description:
Gene expression data from human astrocytes without stress
resting

source_name: human astrocytes without DEX pretreatment nor OGD/R

value: without stress


title: 515-10 hours

first: Lihua

last: Ding

address: 27th Taiping Rd, Haidian District

institute: Beijing Institute of Biotechnology

description: Breast cancer tissue of 69 aged female

data_processing:
Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Hisat2 v2.0.5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MCF7 cells

extract_protocol:
Total RNA was extracted with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Breast cancer tissue

value: Treated with hypoxia for 10 hours


title: 515-16 hours

description: Breast cancer tissue of 69 aged female

value: Treated with hypoxia for 16 hours


title: Y_WT_618


title: with DEX pretreatment, reoxygenation time is 6 h

description:
Gene expression data from human astrocytes with DEX pretreatment and reoxygenated for 6 h
HAD 6 h

source_name: human astrocytes after DEX pretreatment, OGD exposure and reoxygenation for 6h


title: without DEX pretreatment, reoxygenation time is 24 h

description:
Gene expression data from human astrocytes without DEX pretreatment and reoxygenated for 24 h
HAC 24 h

source_name: human astrocytes after no DEX pretreatment, OGD exposure and reoxygenation for 24h


title: 515-5 hours

description: Breast cancer tissue of 69 aged female

value: Treated with hypoxia for 5 hours


title: Y_KO_657

value: Igf2bp2 KO


title: Y_WT_615


title: with DEX pretreatment, reoxygenation time is 12 h

description:
Gene expression data from human astrocytes with DEX pretreatment and reoxygenated for 12 h
HAD 12 h

source_name: human astrocytes after DEX pretreatment, OGD exposure and reoxygenation for 12h


title: with DEX pretreatment, reoxygenation time is 2 h

description:
Gene expression data from human astrocytes with DEX pretreatment and reoxygenated for 2 h
HAD 2 h

source_name: human astrocytes after DEX pretreatment, OGD exposure and reoxygenation for 2h


title: without DEX pretreatment, reoxygenation time is 6 h

description:
Gene expression data from human astrocytes without DEX pretreatment and reoxygenated for 6 h
HAC 6 h

source_name: human astrocytes after no DEX pretreatment, OGD exposure and reoxygenation for 6h


title: without DEX pretreatment, reoxygenation time is 2 h

description:
Gene expression data from human astrocytes without DEX pretreatment and reoxygenated for 2 h
HAC 2 h

source_name: human astrocytes after no DEX pretreatment, OGD exposure and reoxygenation for 2h


title: without DEX pretreatment, reoxygenation time is 0 h

description:
Gene expression data from human astrocytes without DEX pretreatment and reoxygenated for 0 h
HAC 0 h

source_name: human astrocytes after no DEX pretreatment, OGD exposure and reoxygenation for 0h


title: 515-Control 2

description: Breast cancer tissue of 69 aged female

value: Treated with hypoxia for 0 hours


title: 4T1 OX

city: Guangzhou

first: Li

last: Liang

state: China

address: guangzhoudadaobei street NO.1838

institute: Southern medical university

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Genome_build: Ensembl release 90
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: 4T1 cells

growth_protocol: 4T1 cells were maintained at 37 °C and 5% CO2 for 48 hours

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA).
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeq2500 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: 5,000,000 4T1 cells were treated with PBS or potassium oxalate (20mM) for 48 hours

value: potassium oxalate (20 microM)

value: breast cancer cells


title: Y_KO_648


title: HUVEC_BMP9_10stimulated, biological rep1

city: Bad Nauheim

first: Thomas

last: Boettger

state: Hessen

address: Ludwigstr. 43

department: Cardiac Development

institute: MPI for Heart and Lung Research

description: Gene expression data from HUVEC stimulated with BMP9 and BMP10

hyb_protocol: Nucleic acid hybridization was performed following Affymetrix instructions.

scan_protocol: Array scanning was performed using a GeneChip Scanner 3000 7G.

data_processing: Data were processed using the GeneChip™ Expression Console Software. Summarization and Normalization were performed usng the RMA algorithm of Arraystar software

source_name: human umbilical vein endothelial cells

label_protocol: RNA was labelled using the Affymetrix GeneChip WT protocol following the manufacturer's instructions.

growth_protocol: Human Umbilical Vein Endothelial Cell (HUVECs) obtained from Lonza (CC-2519) were cultured in Endothelial Basal Medium (CC-3121) combined with 10% FCS and EGM (CC-4133). Cells were plated in T75 cell culture flasks for maintenance at 37°C and 5 % CO2.

extract_protocol: RNA was isolated using TRIZOL (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: HUVECs were starved by switching the medium to Endothelial Basal Medium without FCS and the EGM but just containing 0.1 % BSA for 6 h. After starvation for 6 hours, HUVECs were stimulated using BMP9 (R&D 5566-BP-010) and BMP10 (R&D 6038-BP), at a concentration of 1 ng/mL and 5 ng/mL respectively. Cells were stimulated for 6 hours before the isolation of RNA.

value: stimulated with BMP9 and BMP10

value: umbilical vein endothelial cells


title: HUVEC_not_stimulated, biological rep1

description: Gene expression data from unstimulated HUVEC

value: unstimulated HUVEC


title: HUVEC_not_stimulated, biological rep2


title: HUVEC_BMP9_10stimulated, biological rep2


title: Ebf2-EGFP E15pos cells scRNA-seq rep7

first: Jia

address: No.67 chifeng road, yangpu district

institute: Tongji University

description: single cell RNA

data_processing:
Samples were sequenced on Illumina HiSeq2500 platform using 150 base paired-end reads. Sequencing reads were analyzed by Cell Ranger (v2.0.0).
The gene expression datasets were analyzed by Seurat (v2.0) and Monocle package.
Genome_build: mm10
Supplementary_files_format_and_content: csv files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cerebral cortex

extract_protocol:
Ebf2-EGFP positive cells at E15.5 were dissociated, resuspended and purified by FACS, about eight embryos from two timed-pregnant mice were used in the experiments.
Approximately 3000 cells were processed for downstream reverse transcription, cDNA synthesis and library preparation according to 10× Genomics Chromium Single Cell protocol.

value: cortical Ebf2-EGFP+ cells

value: cerebral cortex

tag: developmental stage


title: Ebf2-EGFP E15pos cells scRNA-seq rep8

description: single cell RNA


title: Ebf2-EGFP E15pos cells scRNA-seq rep6

description: single cell RNA


title: Ebf2-EGFP E15pos cells scRNA-seq rep5

description: single cell RNA


title: 4T1 NC

value: PBS


title: Ebf2-EGFP E15pos cells scRNA-seq rep4

description: single cell RNA


title: Y_KO_640

source_name: myeloid biased HSC

value: myeloid biased HSC

value: 3 Months