title: Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in WT cells

status: Public on Apr 21 2018

city: San Francisco

first: Yan

last: Zhang

state: CA

address: 600 16th Street

department: Microbiology and Immunology

institute: UC San Francisco

data_processing:
Basecalls performed using Casava versions 1.6 or 1.7.
Sequenced reads were trimmed for adaptor sequence.
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded.
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1.
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read.
Genome_build: NC000913.2
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).

organism: Escherichia coli

growth_protocol: All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker.

extract_protocol:
Extraction was performed as described in detail previously (Li et al., 2012; Oh et al., 2011; Rouskin et al., 2014). For ribosome profiling, 200 ml of cell culture was rapidly filtered by passing through a nitrocellulose filter. Cell pellets was were rapidly collected using a pre-warmed metal table crumber, flash frozen in liquid nitrogen, and combined with frozen droplets of lysis buffer. Cells and lysis buffer were pulverized in 10 ml canisters (Retsch) pre-chilled in liquid nitrogen using Qiagen TissueLyser II. Pulverized lysate was thawed on ice and clarified by centrifugation at 4°C. Lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of micrococcal nuclease (Roche) at 25°C. The ribosome-protected RNA fragments were isolated using a sucrose gradient followed by hot acid phenol extraction.
mRNA fragments were size selected via gel purification, and ligated to 5' adenylated DNA oligo. After reverse transcription, the single stranded DNA was circularized, and PCR amplified (Oh et al., 2011; Li et al., 2014; Rouskin et al., 2014).

treatment_protocol: For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion).

tag: strain background

value: Before rifampicin treatment

tag: temperature

tag: molecule subtype

value: Total RNA


title: Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in ∆rnr cells

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

source_name: MG1655 ∆rnr

tag: genotype/variation

value: {delta}rnr

tag: treatment


title: Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in ∆rnr cells

value: After 250 µg/mL rifampicin treatment for 2 hr


title: Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in WT cells

value: wild type


title: Total RNA-seq 20 min after shift to 10°C in ∆rnr cells


title: BPH H745

status: Public on Apr 22 2018

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data from Homo sapiens were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: hg19). Reference genome index was built by using bowtie2-build component of Bowtie2 (ver. 2.0, http://bowtie-bio.sourceforge.net/bowtie2) and SAMtools (ver. 0.1.18, http://samtools.sourceforge.net/).
Tophat2 was applied to tissue samples for mapping reads to reference genome. The fragments
per
kilobase
 of
transcript
 per
million
 fragments
mapped (FPKM) of each sample was estimated by Cufflinks software (V2.0.2).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text format with FPKM values of transcripts

organism: Homo sapiens

source_name: BPH

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.

tag: biopsy site

value: prostate

tag: progression step

value: BPH

tag: normal/tumor

value: nomal


title: Total RNA-seq 4 hr after shift to 10°C in ∆rnr cells


title: Total RNA-seq 8 hr after shift to 10°C in WT cells


title: Total RNA-seq 20 min after shift to 10°C in WT cells


title: Total RNA-seq 4 hr after shift to 10°C in WT cells


title: T16R2

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

country: Australia

institute: The University of Queensland

data_processing:
The quality of raw data from each library was controlled by CLC Genomic Workbench version 7.5.1.  Raw data were stripped of adapters and reads with quality score above 0.05 and less than 2 ambiguous nucleotides were retained. Reads without 3’ adapters and also reads with less than 16 nt were discarded from the libraries. Clean data considered as mappable reads for further analysis.
Tab separated files with the read sequences and their counts were used as input file for homologous miRNA analysis CLC genomic workbench.

organism: Plutella xylostella

source_name: Low dose- 6 hrs Expossed - Replicate 2

growth_protocol: We obtained an insecticide susceptible population of DBM from the Waite campus at the University of Adelaide.

extract_protocol: Total RNA was extracted from larvae using Triazol® following the manufacturer’s protocol (Life Technologies). RNA concentrations were measured using a spectrophotometer and integrity was ensured through analysis of RNA on a 1% (w/v) agarose gel. The small RNA libraries were generated from all samples with three biological replicates using the Illumina Truseq small RNA preparation kit at the Australian Genome Research Facility (AGRF-Melbourne, Australia). The purified cDNA libraries were sequenced on Illumina HiSeq and raw sequencing reads (50 nt) were obtained using Illumina’s Sequencing Control Studio software.

treatment_protocol: To determine P. xylostella miRNA responses to a xenobiotic stress, we exposed the susceptible DBM larvae to two doses of Chlorantraniliprole (0.01 and 0.1 ppm). Total RNA samples were collected from surviving larvae 6 and 24 h post-treatment. This included 16 samples (three replicates for each time and dose of treatment plus two replicates of control larvae at both times).

tag: strain

value: Waite

tag: tissue

value: Whole body

tag: developmental stage

value: 3rd Instar larvae


title: Total RNA-seq 8 hr after shift to 10°C in ∆rnr cells


title: DMS-seq 8 hr after shift to 10°C in ∆cspBG cells

source_name: MG1655 ∆cspBG

value: {delta}cspBG

value: DMS-modified mRNA


title: E17.5Srg170dcKOVeh_V_2

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

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

country: Germany

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

data_processing:
Base calling and fastq conversion were performed using Illumina pipeline scripts.
Reads were mapped to mouse genome mm10.
In ChIP-Seq reads were filtered leaving only high quality reads (MAPQ != (0, 2, 3, 4)).
In RNA-Seq reads were counted using FeaturesCount. In ChIP-Seq peaks were called using MACS2 with q-value < 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files and count files.

organism: Mus musculus

source_name: embryonic cortex

extract_protocol:
RNA was isolated using Rneasy kit from Qiagen. Chromatin immunoprecipitation was performed using home-made protocol.
Libraries for ChIP-Seq were prepared using NEBNext Ultra DNA Library Preparation Kit for Illumina. Libraries for RNA-Seq were prepared using Illumina TruSeq RNA Sample Preparation v2 Kit.

tag: age

value: BAF dcKO_hGFAP-Cre

value: Vehicle


title: DMS-seq 8 hr after shift to 10°C in ∆cspABEG cells

source_name: MG1655 ∆cspABEG

value: {delta}cspABEG


title: T16R1

source_name: Low dose- 6 hrs Expossed - Replicate 1


title: T124R3

source_name: Low dose- 24 hrs Expossed - Replicate 3


title: DMS-seq 8 hr after shift to 10°C in WT cells


title: DMS-seq 6 hr after shift to 10°C in WT cells


title: mRNA-seq at 37°C in ∆cspABCEG cells

source_name: MG1655 ∆cspABCEG

value: {delta}cspABCEG

value: mRNA


title: mRNA-seq 8 hr after shift to 10°C in WT cells


title: mRNA-seq at 37°C in WT cells_2


title: mRNA-seq 8 hr after shift to 10°C in ∆cspABEG cells


title: Ribosome profiling at 37°C in ∆cspABCEG cells

value: Ribosome protected mRNA


title: Ribosome profiling 8 hr after shift to 10°C in ∆cspABEG cells


title: Ribosome profiling 15 min after shift to 10°C in WT cells


title: Ribosome profiling 8 hr after shift to 10°C in WT cells


title: Ribosome profiling 10 min after shift to 10°C in WT cells_2


title: Ribosome profiling 5 min after shift to 10°C in WT cells


title: DMS-MaPSeq of purified cspA mRNA at 10°C, rep2

description: DMS-modified mRNA purified from in vitro transcription reaction

data_processing:
Basecalls performed using Casava versions 1.6 or 1.7.
Sequenced reads were trimmed for adaptor sequence.
Trimmed reads were sequentially aligned using Bowtie v0.12.7 to E. coli rRNA and noncoding RNA allowing one mismatch. Reads aligning to any of these indices were discarded.
The remaining reads were aligned using Bowtie v0.12.7 against E. coli MG1655 genome using parameters -v1 -m2 -k1.
Bowtie alignments against the E. coli genome were converted to wiggle files. For ribosome footprints and mRNA-seq, the position of each alignment is distributed into several nucleotides in the center of each read. For each read, the center residues that are at least 10 nucleotides away from either ends were given the same score, which is weighted by the length of the fragment [Oh et al,. Cell 147, 1295 (2011)]. Scores therefore represent the number of read alignments attributed to each genomic position under each scoring scheme. For DMS-seq, the position of each alignment was the position immediately 5' of the 5' end of the read.
For DMS-MaPSeq, reads were aligned to the 5’UTR of cspA using bowtie2 and an alignment seed of 12nt.  Low sequence quality bases (Q score < 20%) and missing bases due to truncated reads were set to question marks. Reads that consisted of more than 20% question marks were filtered out. Only mutations that agreed between the forward and the reverse read were considered true mutations. Mutation rate per base was calculated as number of reads with a mutation at the base divided by total number of reads covering the base.
Genome_build: NC000913.2
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position (see publication for details).
Supplementary_files_format_and_content: Txt files are processed data for DMS-MaPseq with two columns: first column containing chromosome positions (relative to transcription start site (1) of cspA) and second column containing the mutation rate.

organism: Escherichia coli str. K-12 substr. MG1655


title: DMS-MaPSeq of purified cspA mRNA at 37°C, rep1


title: DMS-MaPSeq of purified cspA mRNA at 10°C, rep1


title: DMS-MaPSeq of purified cspA mRNA at 10°C with 0.1mM CspA protein, rep1

value: 0.1mM CspA protein


title: DMS-seq 30 min after shift to 10°C in WT cells


title: Ribosome profiling at 37°C in WT cells_2


title: Ctrl_KO_rep1

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
Second mate was used for sample demultiplexing.
Individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All.
Gene expression was obtained via ht-seq and DESeq2 for differential expression.
Gene expression was obtained using in-house scripts bassed on MACS and HTSeq (https://github.com/ctlab/quant3p).
Genome_build: mm10
Supplementary_files_format_and_content: text file with read counts

molecule: polyA RNA

source_name: Bone marrow-derived macrophages

growth_protocol: Nrf2-/- mice were purchased from Jackson Laboratory (Stock No:  017009).

extract_protocol:
mRNA was extracted from cell lysates using oligo-dT beads (Invitrogen).
For cDNA synthesis, we used custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). After first-strand synthesis, samples were pooled together based on Actb qPCR values and RNA-DNA hybrids were degraded with consecutive acid-alkali treatment. Subsequently, a second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated with T4 ligase (NEB) followed by SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) clean-up. The mixture was enriched by PCR for 12 cycles and SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) purified to yield final strand-specific RNA-seq libraries.

treatment_protocol: Bone marrow-derived macrophages (BMDMs) from WT and Nrf2–/– mice were derived in 7 days in MCSF supplemented complete RPMI. Some samples cells were stimulated with 250 uM DimethylItaconate(DI) for 12 hours prior to collection.

value: bone marrow

tag: cell type

value: macrophages

tag: genotype

value: Ctrl


title: DMS-seq of WT cells after kasugamycin treatment at 10°C

description: DMS-modified mRNA

value: After 10 mg/mL kasugamycin treatment for 40 min


title: Ctrl_WT_rep2

value: WT


title: DI_WT_rep1

value: Demethyl Itaconate


title: DI_KO_rep1


title: Ctrl_KO_rep2


title: DI_WT_rep2


title: DMS-seq of purified mRNA in vitro at 10°C, rep2

description: DMS-modified mRNA purified from WT cells


title: 5-hmC siCtrl

city: La jolla

first: Hong

address: 9500 Gilman Dr.

institute: University of California, Sand diego

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
reads were aligned to the mm9 genome assembly using Bowtie version 2.0.1.

molecule: genomic DNA

source_name: ESC

growth_protocol: 46c cells were prepared in feeder free condition with DMEM-KO supplemented with 15% ESC qualified-fetal bovine serum, 2 mM nonessential amino acids, glutamx, penicillin/streptomycin, 2-mercaptoethanol and 1000u/ml LIF. Peritoneal macrophage is obtained from 6-8 weeks of female C57BL/6J mice obtained from Jackson laboratory. Mice are injected with thiogycollate 3-4 days before collecting day, and cultured in RPMI supplemented with 10% FBS and penicillin/streptomycin for overnight before it is used

extract_protocol: Genomic DNA was isolated and sonicated. 100~300bp of fragmented DNA were ligated to barcoded adaptor, purified and immunoprecipitated with 5-hmC antibody followed by washing and purification. Purified hydroxy methylated DNA was processed with NEBNext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: Cells were transfected with siRNA for 48hrs

tag: cell line


title: 5-hmC siEsrrb


title: DMS-seq of purified mRNA in vitro at 10°C, rep1


title: ChIP-Seq Rad21

extract_protocol:
For ChIP-seq, cells were fixed with 2mM disuccinimidyl glutarate (DSG) for 45 mins and 1% formaldehyde for 10mins, and followed by glycine for 5 mins. Chromatin DNA was sheared to 200–500 bp average in size by sonication and chromatin was immunoprecipitated with antibodies. Protein G dynabeads (Invitrogen) were added and incubated overnight at 4°C. After washing and elution, the protein–DNA complex was reverse-crosslinked by heating at 65°C, and immunoprecipitated DNA was purified by using QIAquick Spin column.
the libraries were constructed following Illumina’s Chip-Seq Sample prep kit.

treatment_protocol: Peritoneal macrophage is treated with KLA for either 1hr or 6hrs.

tag: chip antibody

value: Rad21, abcam ab992


title: Pro-cap ESC

description: Transcription start site

data_processing:
Library strategy: Pro-cap
Basecalls performed using CASAVA version 1.4
Gro-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.0.1.

extract_protocol:
ESC and macrophage were incubated in swellinig buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) , and Cells were lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol). The resultant nuclei were washed once again with lysis buffer and then re-suspended in 100ml of freezing buffer (50mM Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA).
The cDNA products were separated on a 10% polyacrylamide TBE-urea gel and only those fragments migrating between 100-300bp were excised and recovered by gel extraction. Next, the first-strand cDNA was circularized by CircLigase (Epicenter, Cat# CL4115K) and relinearized by APE1 (NEB, Cat# M0282L). Finally, cDNA template was amplified by PCR using the Phusion High-Fidelity enzyme (NEB, Cat# M0530L) according to the manufacturer’s instructions. The oligonucleotide primers oNTI200 and oNTI201 were used to generate DNA library for deep sequencing and the primer sequences were described in previous paper.

value: ESC


title: Rad21_mESC (#2)

data_processing:
Basecalls performed using CASAVA version 1.4
reads were aligned to the mm9 genome assembly using Bowtie version 2.0.1.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

growth_protocol: ESCs were prepared cultured in Serum medium. Serum cultured ESCs were in feeder free condition with DMEM-KO supplemented with 15% ESC qualified-fetal bovine serum, 2 mM nonessential amino acids, glutamx, penicillin/streptomycin, 2-mercaptoethanol and 1000u/ml LIF.


title: ChIP-seq Rad21 Macrophage

source_name: Peritoneal macropahge

value: Peritoneal macrophage


title: ChIP-Seq H3K4me2

value: H3K4me2, Millipore 07-030


title: Pro-cap Macrophage

description: Transcription start site

source_name: peritoneal macrophage

value: peritoneal macrophage


title: DMS-MaPSeq of purified cspA mRNA at 10°C with 0.025mM CspA protein

value: 0.025mM CspA protein


title: Rad21_mESC (#3)


title: ATAC macrophage

data_processing:
Library strategy: ATAC-seq
Basecalls performed using CASAVA version 1.4
reads were aligned to the mm9 genome assembly using Bowtie version 2.0.1.

extract_protocol: Nuclei were prepared from 50,000 cells and transpose reaction was performed for 30mins at 37°C. DNA fragments were amplified by PCR, purified for deep sequencing


title: ATAC ESC


title: Ctrl_WT_rep1


title: DI_KO_rep2


title: 4C-seq Tnfaip3 in macrophage + KLA

data_processing:
Library strategy: 4C-Seq
Basecalls performed using CASAVA version 1.4
4C-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.0.1.

extract_protocol: cells were fixed using 1% formaldehyde and stopped by adding Glycine (0.125M). After lysis, soluble chromatin was subjected to restriction endonuclease digestion: First digestion with HindII, second digestion with DpnII. Intra-molecular ligations were performed using T4 DNA ligase (NEB), reverse crosslinked and purified. The purified chromatin was subjected to RNase digestion and further purified. PCR reactions were performed with a first primer designed on the viewpoint and a second outer primer designed beside the DpnII site. Both primers contained illumina sequencing adapters and Barcodes for multiplexing. Approximately 16 reactions were performed for each viewpoint to generate complex libraries.

treatment_protocol: Peritoneal macrophage is treated with KLA for 1hr.


title: 4C-seq Il1a in ESC


title: 4C-seq Il1a in macrophage + KLA


title: mRNA-seq 4 hr after shift to 10°C in WT cells

value: wild type


title: mRNA-seq 6 hr after shift to 10°C in WT cells


title: mRNA-seq 3 hr after shift to 10°C in WT cells


title: mRNA-seq 30 min after shift to 10°C in WT cells


title: mRNA-seq at 37°C in WT cells_1


title: mRNA-seq 10 min after shift to 10°C in WT cells


title: Ribosome profiling 6 hr after shift to 10°C in WT cells


title: Ribosome profiling 4 hr after shift to 10°C in WT cells


title: Ribosome profiling 2 hr after shift to 10°C in WT cells


title: mRNA-seq 2 hr after shift to 10°C in WT cells


title: Ribosome profiling 3 hr after shift to 10°C in WT cells


title: Ribosome profiling 30 min after shift to 10°C in WT cells


title: RNA-macrophage

description: RNA-seq Macrophage

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.0.1.

growth_protocol: ESCs were prepared in feeder free condition with DMEM-KO supplemented with 15% ESC qualified-fetal bovine serum, 2 mM nonessential amino acids, glutamx, penicillin/streptomycin, 2-mercaptoethanol and 1000u/ml LIF. Peritoneal macrophage is obtained from 6-8 weeks of female C57BL/6J mice obtained from Jackson laboratory. Mice are injected with thiogycollate 3-4 days before collecting day, and cultured in RPMI supplemented with 10% FBS and penicillin/streptomycin for overnight before it is used

extract_protocol:
RNA was isolated using Rnease kit (Qiagen) according to instructions.
100ng of Dnase-treated total RNA samples were processed using Trueseq stranded mRNA Library Prep Kit (Illumina, RS-122-2101, RS-122-2102) according to the manufacturer's instructions.

value: Mus musculus


title: RNA-seq mutant #14

description: RNA-seq mutant #14


title: RNA-seq mutant #10

description: RNA-seq mutant #10


title: Ribosome profiling 10 min after shift to 10°C in WT cells_1


title: ATAC ESC Serum

growth_protocol: ESCs were prepared either 2i medium or Serum medium. Serum cultured ESCs were in feeder free condition with DMEM-KO supplemented with 15% ESC qualified-fetal bovine serum, 2 mM nonessential amino acids, glutamx, penicillin/streptomycin, 2-mercaptoethanol and 1000u/ml LIF. 2i cultured ESCs were in feeder free condition in N2/B27 media with 50% Neurobasal and 50% DMEM/F12, 2 mM nonessential amino acids, glutamax, penicillin/streptomycin, 2-mercaptoethanol, N2 supplement, B27, 1000 U/ml LIF and 2i.

tag: medium

value: serum medium


title: ChIP-Seq H3K27Ac_2i

value: H3K27Ac, abcam ab4729


title: ChIP-Seq H3K4me2_Serum


title: RNA-seq ESC

description: RNA-seq ESC


title: ATAC ESC 2i

value: 2i medium


title: Ribosome profiling at 37°C in WT cells_1

tag: strain background

value: Ribosome protected mRNA


title: 4C-seq Tnfaip3 in ESC


title: RNA-seq WT

description: RNA-seq WT


title: ChIP-Seq H3K27Ac_Serum


title: ChIP-Seq H3K4me2_2i


title: scATAC-seq_RA_D4_S96

status: Public on Apr 20 2018

city: Stanford

first: Mahdi

last: Zamanighomi

address: 390 Serra Mall

department: Statistics

institute: Stanford University

data_processing:
Reads are mapped to mm9 using the ATAC-seq pipeline described in https://github.com/kundajelab/atac_dnase_pipelines.
We used MACS2 to perfom peak calling on aligned sequencing reads aggregated across all cells.
Genome_build: mm9
Supplementary_files_format_and_content: xlsx file showing read counts across peaks and cells

source_name: mouse embryonic stem cell

growth_protocol: mESC cells R1 were grown in mESC medium supplemented with 15% Knockout Serum Replacement and 1,000 U/ml of LIF. mESCs were differentiated using the handing drop method for 48 hours. Then, embryoid bodies (EBs) were collected for further treatment.

extract_protocol:
Single cells were captured and transposed with Tn5 using C1 fluidigm
scATAC-seq library were constructed by additional 13 cycles of PCR with dual index primers, followed by MinElute PCR purification.

treatment_protocol: EBs were placed in the well of a 6-well ultra-low attachment plate with fresh differentiation medium containing 0.5 mM retinoic acid (RA) for 4 days, with the medium being changed daily.

tag: agent

value: RA

tag: time

value: day 4

tag: protocol

value: Retinoic-acid induction


title: scATAC-seq_RA_D4_S94


title: scATAC-seq_RA_D4_S92


title: scATAC-seq_RA_D4_S90


title: scATAC-seq_RA_D4_S91


title: scATAC-seq_RA_D4_S93


title: scATAC-seq_RA_D4_S89


title: scATAC-seq_RA_D4_S87


title: scATAC-seq_RA_D4_S86


title: scATAC-seq_RA_D4_S84


title: scATAC-seq_RA_D4_S85


title: scATAC-seq_RA_D4_S82


title: scATAC-seq_RA_D4_S83


title: scATAC-seq_RA_D4_S81


title: scATAC-seq_RA_D4_S79


title: scATAC-seq_RA_D4_S78


title: scATAC-seq_RA_D4_S80


title: scATAC-seq_RA_D4_S74


title: scATAC-seq_RA_D4_S77


title: scATAC-seq_RA_D4_S76


title: scATAC-seq_RA_D4_S73


title: scATAC-seq_RA_D4_S75


title: scATAC-seq_RA_D4_S71


title: scATAC-seq_RA_D4_S88


title: scATAC-seq_RA_D4_S95


title: scATAC-seq_RA_D4_S66


title: scATAC-seq_RA_D4_S68


title: scATAC-seq_RA_D4_S70


title: scATAC-seq_RA_D4_S64


title: scATAC-seq_RA_D4_S65


title: scATAC-seq_RA_D4_S67


title: scATAC-seq_RA_D4_S63


title: scATAC-seq_RA_D4_S62


title: scATAC-seq_RA_D4_S69


title: scATAC-seq_RA_D4_S61


title: scATAC-seq_RA_D4_S60


title: scATAC-seq_RA_D4_S59


title: scATAC-seq_RA_D4_S58


title: scATAC-seq_RA_D4_S57


title: scATAC-seq_RA_D4_S54


title: scATAC-seq_RA_D4_S55


title: scATAC-seq_RA_D4_S50


title: scATAC-seq_RA_D4_S52


title: scATAC-seq_RA_D4_S49


title: scATAC-seq_RA_D4_S47


title: scATAC-seq_RA_D4_S44


title: scATAC-seq_RA_D4_S46


title: scATAC-seq_RA_D4_S45


title: scATAC-seq_RA_D4_S43


title: scATAC-seq_RA_D4_S40


title: scATAC-seq_RA_D4_S42


title: scATAC-seq_RA_D4_S41


title: scATAC-seq_RA_D4_S38


title: scATAC-seq_RA_D4_S37


title: scATAC-seq_RA_D4_S35


title: scATAC-seq_RA_D4_S36


title: scATAC-seq_RA_D4_S32


title: scATAC-seq_RA_D4_S33


title: scATAC-seq_RA_D4_S34


title: scATAC-seq_RA_D4_S39


title: scATAC-seq_RA_D4_S53


title: scATAC-seq_RA_D4_S31


title: scATAC-seq_RA_D4_S56


title: scATAC-seq_RA_D4_S30


title: scATAC-seq_RA_D4_S51


title: scATAC-seq_RA_D4_S26


title: scATAC-seq_RA_D4_S28


title: scATAC-seq_RA_D4_S27


title: scATAC-seq_RA_D4_S72


title: scATAC-seq_RA_D4_S25


title: scATAC-seq_RA_D4_S24


title: scATAC-seq_RA_D4_S48


title: scATAC-seq_RA_D4_S23


title: scATAC-seq_RA_D4_S22


title: scATAC-seq_RA_D4_S21


title: scATAC-seq_RA_D4_S19


title: scATAC-seq_RA_D4_S17


title: scATAC-seq_RA_D4_S18


title: scATAC-seq_RA_D4_S16


title: scATAC-seq_RA_D4_S10


title: scATAC-seq_RA_D4_S14


title: scATAC-seq_RA_D4_S13


title: scATAC-seq_RA_D4_S8


title: scATAC-seq_RA_D4_S29


title: scATAC-seq_RA_D4_S15


title: scATAC-seq_RA_D4_S12


title: scATAC-seq_RA_D4_S6


title: scATAC-seq_RA_D4_S7


title: scATAC-seq_RA_D4_S2


title: scATAC-seq_RA_D4_S5


title: scATAC-seq_RA_D4_S11


title: scATAC-seq_RA_D4_S4


title: scATAC-seq_RA_D4_S1


title: scATAC-seq_RA_D4_S9


title: scATAC-seq_RA_D4_S3


title: scATAC-seq_RA_D4_S20


title: Control 24 hour

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description: RNA-seq on Control (untreated) cells

data_processing:
5 bases were trimmed from reads' 5'-end, using FastX toolkit. Reads were aligned to the mm9 reference genome using TopHat with parameters "--bowtie1 -a 5".
Genome_build: mm9
Bedgraph files were generated using the Wiggles tool included in the TopHat suite.
Supplementary_files_format_and_content: BEDGRAPH

source_name: GT1-7 cells

growth_protocol: GT1-7 cells, an immortalized line derived from highly differentiated mouse gonadotropin-hormone releasing hormone (GnRH) neurons (generously donated by Prof. P.L. Mellon), were maintained in Dulbecco’s Modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Lonza), gentamycin (50 µg mL-1), and glutamine (2 mM) at 37°C, in a humidified atmosphere of 5% CO2 in air.

extract_protocol:
Cells were washed twice in PBS, then 1 ml of ice-cold TRIzol was added directly to cells. Cells were scraped using a P1000 pipette, and solution was pipetted up-and-down to homogeneity. RNA extraction was performed following manufacturer instructions.
Libraries were prepared using Illumina TruSeq RNA Sample Prep Kit v2, following manufacturer instructions.

treatment_protocol: NPs, stored in a stock solution (1 mg mL-1 in water) were sonicated for 20 min before final dilution. For all protocols except patch clamp, the NPs were administered by substituting the extracellular solution (either culture medium or Tyrode) with an identical one containing a stable suspension of NPs at the final desired concentration.

value: GT1-7 cells

tag: treatment

value: Control (untreated)

value: 24 hour


title: NP 6 hour

description: RNA-seq on NP-treated cells

value: NP

value: 6 hour


title: Control 6 hour

description: RNA-seq on Control (untreated) cells


title: NP 30 minutes

description: RNA-seq on NP-treated cells

value: 30 minutes


title: Control 30 minutes

description: RNA-seq on Control (untreated) cells


title: Control 1 hour

description: RNA-seq on Control (untreated) cells

value: 1 hour


title: NP 24 hour

description: RNA-seq on NP-treated cells


title: mus-52_highPi_II

city: Ribeirão Preto

first: Pablo

middle: Rodrigo

last: Sanches

state: SP

address: Av. Bandeirantes, 3900

department: Genetics

country: Brazil

institute: University of São Paulo

data_processing:
FastQC v0.11.2 was used to visualize the libraries quality before and after trimming.
FASTX-Tookit (fastq_quality_filter) was used to remove poor quality sequences, such that remaining sequences had a minimum quality score of 20 with a minimum of 50% of bases within a read meeting this quality score requirement.
Filtered reads were mapped onto the N. crassa genome using the Bowtie2 v2.1.0.
Reads were assigned to annotated genes and counted using the "summarizeOverlaps" function from the GenomicRanges Bioconductor package.
The data were analyzed using the R package DESeq version 1.28.0. The samples were normalized, and the dispersions were estimated using the default DESeq settings. DESeq was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.05 and a log2(foldchange) > 1.5 (upregulation) or < -1.5 (downregulation) were called as differentially expressed.
Genome_build: Broad NC12
Supplementary_files_format_and_content: tab-delimited text files include reads count values for each sample and DESeq output in CSV format containing mean expression, fold changes and p value.

organism: Neurospora crassa

source_name: Δmus-52 in high-Pi, replicate II

growth_protocol: All strains were maintained on solid Vogel’s minimal (VM) medium, pH 5.8 containing 2% sucrose at 30°C.

extract_protocol:
Approximately 100 mg of frozen mycelia from both N. crassa strains were harvested on Millipore filters (pore size 0.22 µm), and rinsed 3 times with 5–10 ml aliquots of distilled water. Total RNA was isolated using a TRIzol RNA kit and treated with RNAse-free DNAse I. RNA concentrations were determined using a NanoDrop ND-1000 spectrophotometer, and RNA integrity was verified using both agarose electrophoresis and the Agilent Bioanalyser platform 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Conidia from 6 day-cultures of each N. crassa strain (approximately 106 cells ml−1) were germinated for 5 h at 30°C in an orbital shaker (200 rpm), in low- and high-Pi media (final concentrations, 10 μM or 10 mM Pi, respectively). Media were supplemented with 44 mM sucrose as the carbon source, and the pH was adjusted to 5.4 (buffered with 50 mM sodium citrate).

value: mus-52 deletion

value: high inorganic phosphate


title: mus-52_lowPi_III

source_name: Δmus-52 in low-Pi, replicate III

value: low inorganic phosphate


title: mus-52_lowPi_II

source_name: Δmus-52 in low-Pi, replicate II


title: mus-52_highPi_III

source_name: Δmus-52 in high-Pi, replicate III


title: 74A_highPi_I

source_name: 74A [wt] in high-Pi, replicate I

value: wild type


title: mus-52_lowPi_I

source_name: Δmus-52 in low-Pi, replicate I


title: 74A_highPi_II

source_name: 74A [wt] in high-Pi, replicate II


title: 74A_highPi_III

source_name: 74A [wt] in high-Pi, replicate III


title: NP 1 hour

description: RNA-seq on NP-treated cells


title: 74A_lowPi_III

source_name: 74A [wt] in low-Pi, replicate III


title: 74A_lowPi_I

source_name: 74A [wt] in low-Pi, replicate I


title: 74A_lowPi_II

source_name: 74A [wt] in low-Pi, replicate II


title: mus-52_highPi_I

source_name: Δmus-52 in high-Pi, replicate I


title: Prop3.24h.1

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

country: Belgium

institute: Ghent University

description: 24 hours of exposure

data_processing:
Adapter removal and dynamic trimming to achieve 99.9% base call accuracy was done with Trim Galore version 0.3.2.
Reads were alignmed using bowtie2 version 2.1.0 to the XinB3 transcriptome (BioProject PRJNA284518)
Aligned reads were processed to htseq resulting in read counts per gene
Read counts were normalized using a trimmed-mean of M-values in R using edgeR
A quasi-likelihood negative binomial generalized log-linear model was fitted to the data to determine differential expression. Benjamini-Hochberg method was applied to adjust for multiple testing
Genome_build: BioProject PRJNA284518
Supplementary_files_format_and_content: Matrix with normalized cpm values using edgeR per gene. Samples are listed by their title

organism: Daphnia magna

source_name: whole body tissue

growth_protocol: 20 individuals of 5 days old D. magna were exposed to different 35 ml chemical solutions separately and were harvested at 1, 6, and 24 hours of exposure

extract_protocol:
Total RNA was extracted from the body sample using the RNeasy kit and Qiashredder (Qiagen,Venlo, The Netherlands) following manufacturer’s protocol.
An Illumina mRNA sequencing library was made from 500 ng of total RNA using the 'Truseq stranded mRNA library prep kit' (Illumina, San Diego, CA, US)

treatment_protocol: Animals were exposed to 1mg/L propranolol (Prop), 4mg/L propranolol (Prop3), 100 mg/L isoprenaline (Iso), and a mixture of the two: 1mg/L propranolol and 100 mg/L isoprenaline (IP)

value: 5 day-old

tag: Sex

value: female

value: whole body


title: Prop.24h.1

description: 24 hours of exposure


title: Prop.24h.2

description: 24 hours of exposure


title: Prop3.24h.2

description: 24 hours of exposure


title: Cont.24h.2

description: 24 hours of exposure


title: Cont.24h.3

description: 24 hours of exposure


title: Prop.24h.3

description: 24 hours of exposure


title: Prop3.24h.3

description: 24 hours of exposure


title: Prop3.6h.1

description: 6 hours of exposure


title: Prop3.6h.2

description: 6 hours of exposure


title: Cont.24h.1

description: 24 hours of exposure


title: Iso.6h.2

description: 6 hours of exposure


title: IP.6h.3

description: 6 hours of exposure


title: IP.6h.2

description: 6 hours of exposure


title: IP.6h.1

description: 6 hours of exposure


title: GAL-V5-Psd1_rep5

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
HiSeq2000 using v3 chemistry. Control software version 2.0.12.0, RTA version 1.17.21.3, BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
map to ensemble sacCer3 assembly with STAR 2.5.3a
quantify transcripts with rsem 1.3.0 and samtools 1.3
Genome_build: sacCer3 with Ensembl annotation
Supplementary_files_format_and_content: weidberg_counts.txt.gz is parsed integer counts for samples from rsem genes.results files
Supplementary_files_format_and_content: weidberg_l2fpkm.txt.gz is parsed fpkm for samples from rsem genes.results files with 1 added to each fpkm value prior to transformation to log2 space

organism: Saccharomyces cerevisiae

source_name: GAL-V5-PSD1 W303

growth_protocol: YPR (1% yeast extract, 2% peptone, 2% raffinose)

extract_protocol:
RNeasy mini-kit (Qiagen)
Neoprep

treatment_protocol: induction of GAL-PSD1 (+/-) with 2% galactose for 4h

tag: genotype/variation

value: carrying a 2u plasmid to express V5-PSD1 from the GAL1-10  promoter


title: Iso.6h.1

description: 6 hours of exposure


title: Prop.6h.3

description: 6 hours of exposure


title: GAL-V5-Psd1_rep3


title: GAL-V5-Psd1_rep2


title: Prop.6h.2

description: 6 hours of exposure


title: GAL-V5-Psd1_rep4


title: Prop.6h.1

description: 6 hours of exposure


title: GAL-V5-Psd1_rep1


title: Cont.6h.3

description: 6 hours of exposure


title: Cont.6h.2

description: 6 hours of exposure


title: GAL-Psd1_oe_Pdr3_ko_rep5

source_name: pdr3∆ GAL-PSD1 W303

value: deletion of PDR3 background carrying a 2u plasmid to express PSD1 from the GAL1-10  promoter


title: GAL-Psd1_oe_Pdr3_ko_rep6


title: Iso.6h.3

description: 6 hours of exposure


title: GAL-Psd1_oe_Pdr3_ko_rep4


title: GAL-Psd1_oe_Pdr3_ko_rep2


title: GAL-Psd1_oe_Pdr3_ko_rep3


title: GAL-Psd1_oe_Pdr3_ko_rep1


title: GAL-Psd1_oe_rep6

source_name: GAL-PSD1 W303

value: carrying a 2u plasmid to express PSD1 from the GAL1-10 promoter


title: Cont.3h.3

description: 3 hours of exposure


title: Prop.3h.2

description: 3 hours of exposure


title: Prop.3h.3

description: 3 hours of exposure


title: GAL-Psd1_oe_rep4


title: GAL-Psd1_oe_rep5


title: Cont.3h.1

description: 3 hours of exposure


title: Prop3.1h.2

description: 1 hour of exposure


title: Prop3.1h.1

description: 1 hour of exposure


title: Empty_rep5

source_name: Empty Vector W303

value: carrying a 2u empty plasmid


title: Empty_rep4


title: IP.1h.3

description: 1 hour of exposure


title: IP.1h.2

description: 1 hour of exposure


title: Empty_rep3


title: Iso.1h.3

description: 1 hour of exposure


title: Empty_rep2


title: Iso.1h.2

description: 1 hour of exposure


title: Prop.3h.1

description: 3 hours of exposure


title: Empty_rep1


title: Iso.1h.1

description: 1 hour of exposure


title: GAL-Psd1_oe_rep3


title: Prop3.1h.3

description: 1 hour of exposure


title: Cont.6h.1

description: 6 hours of exposure


title: Prop.1h.2

description: 1 hour of exposure


title: Prop.1h.3

description: 1 hour of exposure


title: Prop.1h.1

description: 1 hour of exposure


title: GAL-Psd1_oe_rep2


title: Cont.1h.2

description: 1 hour of exposure


title: Cont.1h.3

description: 1 hour of exposure


title: Cont.0h.1

description: 0 hours of exposure


title: Blood_Fed 2

status: Public on Apr 19 2018

data_processing:
The quality of raw data from each library was controlled by CLC Genomic Workbench version 7.5.1.  Raw data were stripped of adapters and reads with quality score above 0.05 and less than 2 ambiguous nucleotides were retained. Reads without 3’ adapters and also reads with less than 16 nt were discarded from the libraries. Clean data considered as mappable reads for further analysis.
Tab separated files with the read sequences and their counts were used as input file for homologous miRNA analysis CLC genomic workbench.
Genome_build: Aedes aegypti genome (GCA_000004015.1) was used
Supplementary_files_format_and_content: text file, miRNA copy number

organism: Aedes aegypti

source_name: Corpora allata

growth_protocol: Female mosquitoes were reared at 28◦C and 80% relative humidityunder a photoperiod of 16-h light:8-h dark. Female adults were offered a cotton pad soaked in sucrose 3% solution. We will refer to the cotton wool pad sucrose-fed females as “sugar-fed.” Four days old females were fed pig blood. We will refer to those as "blood-fed".

extract_protocol:
Total RNA was extracted from 50 CAs from each developmental stage in triplicate using Norgen Biotek’s total RNA purification kit.
The small RNA libraries were generated using the Illumina Truseq™ Small RNA Preparation kit according to Illumina’s TruSeq™ Small RNA Sample Preparation Guide at LC Sciences facility (Texas, USA).

treatment_protocol: No Treatment

value: Rockefeller

value: corpora allata - corpora cardiaca complex

tag: gender

value: 24h Blood fed adult


title: Blood_Fed 1

tag: strain


title: Adult 3

tag: tissue

value: 24h sugar fed adult


title: Cont.1h.1

description: 1 hour of exposure


title: IP.1h.1

description: 1 hour of exposure


title: Blood_Fed 3

tag: developmental stage


title: Adult 1


title: Cont.3h.2

description: 3 hours of exposure

tag: age


title: Adult 2


title: Pupa 1

value: 24h pupa


title: GAL-Psd1_oe_rep1


title: Low_iron_medium_2

city: Dunedin

first: Christopher

middle: Michael

last: Brown

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

data_processing:
Adapter sequences were trimmed using Skewer v0.2.2 (-n -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -y AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA)
Reads were aligned to non-coding RNAs using STAR 2.5.2b (--outStd SAM --outReadsUnmapped Fastx --seedSearchLmax 10 --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 255 --outFilterMismatchNmax 1 --outFilterIntronMotifs RemoveNoncanonical > /dev/null)
Unmapped reads were aligned to genome with GENCODE v19 annotation (using parameter --seedSearchLmax 10 --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 255 --outFilterMismatchNmax 1 --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate)
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files of uniquely mapped reads were generated using STAR (--runMode inputAlignmentsFromBAM –outWigType bedGraph --outWigStrand Unstranded).

source_name: Liver tumor

growth_protocol: DMEM supplemented with 10% Fetal Bovine Serum, and 1% antibiotic-antimycotic cocktail (streptomycin, amphotericin B and Penicillin)

extract_protocol:
Total RNA was isolated using Rneasy kit.
Ribosomal RNA depletion using Ribo-Zero kit; random selection by shearing; paired-end

treatment_protocol: DMEM for SILAC supplemented with or without SILAC amino acid labels for 3 passages (heavy, 0.5 mM of Arg10 and Lys8; medium, 0.5 mM of Arg6 and Lys4; low, 0.5 mM of unlabelled Arg and Lys)

value: Liver tumor

tag: disease state

value: hepatocellular carcinoma

tag: passage


title: Ctrl_iron_2

tag: cell line


title: High_iron_heavy_2


title: Pupa 3


title: Ctrl_iron_1


title: Low_iron_medium_1


title: Leicester_with_progressor_longitudinal_Sample177

city: London

first: Akul

last: Singhania

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Raw paired-end RNA-seq data obtained for Berry London, Berry South Africa and Leicester cohorts was processed separately and subjected to quality control using FastQC (Babraham Bioinformatics) and MultiQC. Trimmomatic v0.36 was used to remove adapters and filter raw reads below the 36 bases long and leading and trailing bases below quality 25. Filtered reads were aligned to the Homo sapiens genome Ensembl GRCh38 (release 86) using HISAT2 v2.0.4 with default settings and RF rna-strandedness including unpaired read reads resulting from Trimmomatic. Mapped and aligned reads were quantified to obtain gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness. Raw counts were processed using the bioconductor package edgeR v3.14.0 in R. Genes expressed with counts per million (CPM) >2 in at least 5 samples were considered and normalised using trimmed mean of M- values (TMM) to remove library-specific artefacts.
Genome_build: Homo sapiens genome Ensembl GRCh38 (release 86)
Supplementary_files_format_and_content: Raw_counts_Leicester_with_progressor_longitudinal.xlsx: Raw counts generated from paired-end RNA-seq fastq files, aligned using HISAT2 and quantified using HtSeq
Supplementary_files_format_and_content: edgeR_normalized_Leicester_with_progressor_longitudinal.xlsx: Log2 expression values generated from edgeR, filtered using counts per million (CPM) >2 in at least 5 samples and normalised using trimmed mean of M- values (TMM) to remove library-specific artefacts

extract_protocol:
Total RNA was isolated from 1 ml whole blood using the MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit (Applied Biosystems/Thermo Fisher Scientific) according to the manufacturer’s instructions. Globin RNA was depleted from total RNA (1.5–2 µg) using the human GLOBINclear kit (Thermo Fisher Scientific) according to manufacturer’s instructions. RNA yield of total and globin-reduced RNA was assessed using a NanoDrop™ 8000 spectrophotometer (Thermo Fisher Scientific). Quality and integrity of total and globin-reduced RNA were assessed with the HT RNA Assay reagent kit (Perkin Elmer) using a LabChip GX bioanalyser (Caliper Life Sciences/Perkin Elmer) and assigned an RNA Quality Score (RQS).
Samples (200 ng) with an RQS > 6 were used to prepare a cDNA library using the TruSeq Stranded mRNA HT Library Preparation Kit (Illumina). The tagged libraries were sized and quantitated in duplicate (Agilent TapeStation system), using D1000 ScreenTape and reagents (Agilent), normalised, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million paired end reads (75 bp) per sample.

value: Whole blood

tag: group

tag: outlier

value: No

value: Negative

tag: ethnicity

value: British

value: M

value: Baseline


title: Leicester_with_progressor_longitudinal_Sample183

value: F


title: Leicester_with_progressor_longitudinal_Sample176

value: LTBI


title: Leicester_with_progressor_longitudinal_Sample174


title: Leicester_with_progressor_longitudinal_Sample175

value: Pulmonary


title: Leicester_with_progressor_longitudinal_Sample184


title: Leicester_with_progressor_longitudinal_Sample182

value: Yes


title: Pupa 2

value: Rockefeller

value: female


title: Leicester_with_progressor_longitudinal_Sample170


title: Leicester_with_progressor_longitudinal_Sample179


title: Leicester_with_progressor_longitudinal_Sample172


title: Leicester_with_progressor_longitudinal_Sample181

value: Positive


title: Leicester_with_progressor_longitudinal_Sample173


title: Leicester_with_progressor_longitudinal_Sample178


title: Leicester_with_progressor_longitudinal_Sample180


title: Leicester_with_progressor_longitudinal_Sample171


title: Leicester_with_progressor_longitudinal_Sample166


title: Leicester_with_progressor_longitudinal_Sample164


title: Leicester_with_progressor_longitudinal_Sample161


title: Leicester_with_progressor_longitudinal_Sample163


title: Leicester_with_progressor_longitudinal_Sample167


title: Leicester_with_progressor_longitudinal_Sample162


title: Leicester_with_progressor_longitudinal_Sample159


title: Leicester_with_progressor_longitudinal_Sample160

value: Non-Pulmonary


title: Leicester_with_progressor_longitudinal_Sample158


title: Leicester_with_progressor_longitudinal_Sample157


title: Leicester_with_progressor_longitudinal_Sample155


title: Leicester_with_progressor_longitudinal_Sample156


title: Leicester_with_progressor_longitudinal_Sample165


title: Leicester_with_progressor_longitudinal_Sample151


title: Leicester_with_progressor_longitudinal_Sample148


title: Leicester_with_progressor_longitudinal_Sample147


title: Leicester_with_progressor_longitudinal_Sample149


title: Leicester_with_progressor_longitudinal_Sample146


title: Leicester_with_progressor_longitudinal_Sample154


title: Leicester_with_progressor_longitudinal_Sample152


title: Leicester_with_progressor_longitudinal_Sample153


title: Leicester_with_progressor_longitudinal_Sample140


title: Leicester_with_progressor_longitudinal_Sample137

value: Control


title: Leicester_with_progressor_longitudinal_Sample143


title: Leicester_with_progressor_longitudinal_Sample138


title: Leicester_with_progressor_longitudinal_Sample144


title: High_iron_heavy_1

value: Liver tumor


title: Leicester_with_progressor_longitudinal_Sample135


title: Leicester_with_progressor_longitudinal_Sample134


title: Leicester_with_progressor_longitudinal_Sample133


title: Leicester_with_progressor_longitudinal_Sample132


title: Leicester_with_progressor_longitudinal_Sample127


title: Leicester_with_progressor_longitudinal_Sample130


title: Leicester_with_progressor_longitudinal_Sample131


title: Leicester_with_progressor_longitudinal_Sample126


title: Leicester_with_progressor_longitudinal_Sample142


title: Leicester_with_progressor_longitudinal_Sample145


title: Leicester_with_progressor_longitudinal_Sample141


title: Leicester_with_progressor_longitudinal_Sample139


title: Leicester_with_progressor_longitudinal_Sample150


title: Leicester_with_progressor_longitudinal_Sample125


title: Leicester_with_progressor_longitudinal_Sample136


title: Leicester_with_progressor_longitudinal_Sample123


title: Leicester_with_progressor_longitudinal_Sample115


title: Leicester_with_progressor_longitudinal_Sample117


title: Leicester_with_progressor_longitudinal_Sample119


title: Leicester_with_progressor_longitudinal_Sample121


title: Leicester_with_progressor_longitudinal_Sample120


title: Leicester_with_progressor_longitudinal_Sample114


title: Leicester_with_progressor_longitudinal_Sample124


title: Leicester_with_progressor_longitudinal_Sample122


title: Leicester_with_progressor_longitudinal_Sample113


title: Leicester_with_progressor_longitudinal_Sample118


title: Leicester_with_progressor_longitudinal_Sample109


title: Leicester_with_progressor_longitudinal_Sample116


title: Leicester_with_progressor_longitudinal_Sample112


title: Leicester_with_progressor_longitudinal_Sample111


title: Leicester_with_progressor_longitudinal_Sample129


title: Leicester_with_progressor_longitudinal_Sample128


title: Leicester_with_progressor_longitudinal_Sample108


title: Leicester_with_progressor_longitudinal_Sample107


title: Leicester_with_progressor_longitudinal_Sample105


title: Leicester_with_progressor_longitudinal_Sample104


title: Leicester_with_progressor_longitudinal_Sample103


title: Leicester_with_progressor_longitudinal_Sample100


title: Leicester_with_progressor_longitudinal_Sample101


title: Leicester_with_progressor_longitudinal_Sample99


title: Leicester_with_progressor_longitudinal_Sample98


title: Leicester_with_progressor_longitudinal_Sample97


title: Leicester_with_progressor_longitudinal_Sample110


title: Leicester_with_progressor_longitudinal_Sample95


title: Leicester_with_progressor_longitudinal_Sample93


title: Leicester_with_progressor_longitudinal_Sample89


title: Leicester_with_progressor_longitudinal_Sample90


title: Leicester_with_progressor_longitudinal_Sample92


title: Leicester_with_progressor_longitudinal_Sample86


title: Leicester_with_progressor_longitudinal_Sample84


title: Leicester_with_progressor_longitudinal_Sample85


title: Leicester_with_progressor_longitudinal_Sample102


title: Leicester_with_progressor_longitudinal_Sample96


title: Leicester_with_progressor_longitudinal_Sample83


title: Leicester_with_progressor_longitudinal_Sample80


title: Leicester_with_progressor_longitudinal_Sample82


title: Leicester_with_progressor_longitudinal_Sample79


title: Leicester_with_progressor_longitudinal_Sample87


title: Leicester_with_progressor_longitudinal_Sample91


title: Leicester_with_progressor_longitudinal_Sample81


title: Leicester_with_progressor_longitudinal_Sample106


title: Leicester_with_progressor_longitudinal_Sample78


title: Leicester_with_progressor_longitudinal_Sample72


title: Leicester_with_progressor_longitudinal_Sample73


title: Leicester_with_progressor_longitudinal_Sample94


title: Leicester_with_progressor_longitudinal_Sample70


title: Leicester_with_progressor_longitudinal_Sample69


title: Leicester_with_progressor_longitudinal_Sample88


title: Leicester_with_progressor_longitudinal_Sample75


title: Leicester_with_progressor_longitudinal_Sample67


title: Leicester_with_progressor_longitudinal_Sample77


title: Leicester_with_progressor_longitudinal_Sample71


title: Leicester_with_progressor_longitudinal_Sample66


title: Leicester_with_progressor_longitudinal_Sample62


title: Leicester_with_progressor_longitudinal_Sample74


title: Leicester_with_progressor_longitudinal_Sample76


title: Leicester_with_progressor_longitudinal_Sample63


title: Leicester_with_progressor_longitudinal_Sample68


title: Leicester_with_progressor_longitudinal_Sample59


title: Leicester_with_progressor_longitudinal_Sample60


title: Leicester_with_progressor_longitudinal_Sample56


title: Leicester_with_progressor_longitudinal_Sample53


title: Leicester_with_progressor_longitudinal_Sample52


title: Leicester_with_progressor_longitudinal_Sample51


title: Leicester_with_progressor_longitudinal_Sample57


title: Leicester_with_progressor_longitudinal_Sample50


title: Leicester_with_progressor_longitudinal_Sample49


title: Leicester_with_progressor_longitudinal_Sample46


title: Leicester_with_progressor_longitudinal_Sample44


title: Leicester_with_progressor_longitudinal_Sample48


title: Leicester_with_progressor_longitudinal_Sample47


title: Leicester_with_progressor_longitudinal_Sample64


title: Leicester_with_progressor_longitudinal_Sample65


title: Leicester_with_progressor_longitudinal_Sample43


title: Leicester_with_progressor_longitudinal_Sample45


title: Leicester_with_progressor_longitudinal_Sample61


title: Leicester_with_progressor_longitudinal_Sample42


title: Leicester_with_progressor_longitudinal_Sample41


title: Leicester_with_progressor_longitudinal_Sample40


title: Leicester_with_progressor_longitudinal_Sample33


title: Leicester_with_progressor_longitudinal_Sample22


title: Leicester_with_progressor_longitudinal_Sample23


title: Leicester_with_progressor_longitudinal_Sample39


title: Leicester_with_progressor_longitudinal_Sample24


title: Leicester_with_progressor_longitudinal_Sample34


title: Leicester_with_progressor_longitudinal_Sample21


title: Leicester_with_progressor_longitudinal_Sample36


title: Leicester_with_progressor_longitudinal_Sample35


title: Leicester_with_progressor_longitudinal_Sample37


title: Leicester_with_progressor_longitudinal_Sample18


title: Leicester_with_progressor_longitudinal_Sample15


title: Leicester_with_progressor_longitudinal_Sample38


title: Leicester_with_progressor_longitudinal_Sample13


title: Leicester_with_progressor_longitudinal_Sample32


title: Leicester_with_progressor_longitudinal_Sample55


title: Leicester_with_progressor_longitudinal_Sample30


title: Leicester_with_progressor_longitudinal_Sample31


title: Leicester_with_progressor_longitudinal_Sample20


title: Leicester_with_progressor_longitudinal_Sample17


title: Leicester_with_progressor_longitudinal_Sample14


title: Leicester_with_progressor_longitudinal_Sample16


title: Leicester_with_progressor_longitudinal_Sample19


title: Leicester_with_progressor_longitudinal_Sample54


title: Leicester_with_progressor_longitudinal_Sample11


title: Leicester_with_progressor_longitudinal_Sample8


title: Leicester_with_progressor_longitudinal_Sample12


title: Leicester_with_progressor_longitudinal_Sample10


title: Leicester_non_progressor_longitudnal_only_Sample160

data_processing:
Raw paired-end RNA-seq data obtained for Berry London, Berry South Africa and Leicester cohorts was processed separately and subjected to quality control using FastQC (Babraham Bioinformatics) and MultiQC. Trimmomatic v0.36 was used to remove adapters and filter raw reads below the 36 bases long and leading and trailing bases below quality 25. Filtered reads were aligned to the Homo sapiens genome Ensembl GRCh38 (release 86) using HISAT2 v2.0.4 with default settings and RF rna-strandedness including unpaired read reads resulting from Trimmomatic. Mapped and aligned reads were quantified to obtain gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness. Raw counts were processed using the bioconductor package edgeR v3.14.0 in R. Genes expressed with counts per million (CPM) >2 in at least 5 samples were considered and normalised using trimmed mean of M- values (TMM) to remove library-specific artefacts.
Genome_build: Homo sapiens genome Ensembl GRCh38 (release 86)
Supplementary_files_format_and_content: Raw_counts_Leicester_non_progressor_longitudnal_only.xlsx: Raw counts generated from paired-end RNA-seq fastq files, aligned using HISAT2 and quantified using HtSeq
Supplementary_files_format_and_content: edgeR_normalized_Leicester_non_progressor_longitudnal_only.xlsx: Log2 expression values generated from edgeR, filtered using counts per million (CPM) >2 in at least 5 samples and normalised using trimmed mean of M- values (TMM) to remove library-specific artefacts


title: Leicester_with_progressor_longitudinal_Sample4


title: Leicester_with_progressor_longitudinal_Sample3


title: Leicester_with_progressor_longitudinal_Sample6


title: Leicester_non_progressor_longitudnal_only_Sample158


title: Leicester_with_progressor_longitudinal_Sample5


title: Leicester_non_progressor_longitudnal_only_Sample159


title: Leicester_non_progressor_longitudnal_only_Sample157


title: Leicester_non_progressor_longitudnal_only_Sample156


title: Leicester_non_progressor_longitudnal_only_Sample153


title: Leicester_non_progressor_longitudnal_only_Sample155


title: Leicester_non_progressor_longitudnal_only_Sample154


title: Leicester_non_progressor_longitudnal_only_Sample151


title: Leicester_non_progressor_longitudnal_only_Sample150


title: Leicester_non_progressor_longitudnal_only_Sample152


title: Leicester_non_progressor_longitudnal_only_Sample161


title: Leicester_non_progressor_longitudnal_only_Sample146


title: Leicester_non_progressor_longitudnal_only_Sample145


title: Leicester_non_progressor_longitudnal_only_Sample143


title: Leicester_non_progressor_longitudnal_only_Sample141


title: Leicester_non_progressor_longitudnal_only_Sample140


title: Leicester_with_progressor_longitudinal_Sample7


title: Leicester_with_progressor_longitudinal_Sample2


title: Leicester_with_progressor_longitudinal_Sample1


title: Leicester_non_progressor_longitudnal_only_Sample142


title: Leicester_non_progressor_longitudnal_only_Sample144


title: Leicester_non_progressor_longitudnal_only_Sample137


title: Leicester_non_progressor_longitudnal_only_Sample136


title: Leicester_non_progressor_longitudnal_only_Sample134


title: Leicester_non_progressor_longitudnal_only_Sample133


title: Leicester_non_progressor_longitudnal_only_Sample132


title: Leicester_non_progressor_longitudnal_only_Sample131


title: Leicester_non_progressor_longitudnal_only_Sample127


title: Leicester_non_progressor_longitudnal_only_Sample126


title: Leicester_non_progressor_longitudnal_only_Sample129


title: Leicester_non_progressor_longitudnal_only_Sample123


title: Leicester_non_progressor_longitudnal_only_Sample130


title: Leicester_non_progressor_longitudnal_only_Sample125


title: Leicester_non_progressor_longitudnal_only_Sample121


title: Leicester_non_progressor_longitudnal_only_Sample117


title: Leicester_non_progressor_longitudnal_only_Sample116


title: Leicester_non_progressor_longitudnal_only_Sample120


title: Leicester_non_progressor_longitudnal_only_Sample118


title: Leicester_non_progressor_longitudnal_only_Sample115


title: Leicester_non_progressor_longitudnal_only_Sample114


title: Leicester_non_progressor_longitudnal_only_Sample113


title: Leicester_non_progressor_longitudnal_only_Sample112


title: Leicester_non_progressor_longitudnal_only_Sample122


title: Leicester_non_progressor_longitudnal_only_Sample108


title: Leicester_non_progressor_longitudnal_only_Sample111


title: Leicester_non_progressor_longitudnal_only_Sample109


title: Leicester_non_progressor_longitudnal_only_Sample104


title: Leicester_non_progressor_longitudnal_only_Sample102


title: Leicester_non_progressor_longitudnal_only_Sample107


title: Leicester_non_progressor_longitudnal_only_Sample103


title: Leicester_non_progressor_longitudnal_only_Sample110


title: Leicester_non_progressor_longitudnal_only_Sample100


title: Leicester_non_progressor_longitudnal_only_Sample101


title: Leicester_non_progressor_longitudnal_only_Sample135


title: Leicester_non_progressor_longitudnal_only_Sample98


title: Leicester_non_progressor_longitudnal_only_Sample97


title: Leicester_non_progressor_longitudnal_only_Sample96


title: Leicester_non_progressor_longitudnal_only_Sample95


title: Leicester_non_progressor_longitudnal_only_Sample94


title: Leicester_non_progressor_longitudnal_only_Sample87


title: Leicester_non_progressor_longitudnal_only_Sample93


title: Leicester_non_progressor_longitudnal_only_Sample78


title: Leicester_non_progressor_longitudnal_only_Sample84


title: Leicester_non_progressor_longitudnal_only_Sample71


title: Leicester_non_progressor_longitudnal_only_Sample85


title: Leicester_non_progressor_longitudnal_only_Sample79


title: Leicester_non_progressor_longitudnal_only_Sample86


title: Leicester_non_progressor_longitudnal_only_Sample80


title: Leicester_non_progressor_longitudnal_only_Sample83


title: Leicester_non_progressor_longitudnal_only_Sample77


title: Leicester_non_progressor_longitudnal_only_Sample73


title: Leicester_non_progressor_longitudnal_only_Sample81


title: Leicester_non_progressor_longitudnal_only_Sample69


title: Leicester_non_progressor_longitudnal_only_Sample99


title: Leicester_non_progressor_longitudnal_only_Sample67


title: Leicester_non_progressor_longitudnal_only_Sample70


title: Leicester_non_progressor_longitudnal_only_Sample68


title: Leicester_non_progressor_longitudnal_only_Sample66


title: Leicester_non_progressor_longitudnal_only_Sample65


title: Leicester_non_progressor_longitudnal_only_Sample64


title: Leicester_non_progressor_longitudnal_only_Sample63


title: Leicester_non_progressor_longitudnal_only_Sample88


title: Leicester_non_progressor_longitudnal_only_Sample61


title: Leicester_non_progressor_longitudnal_only_Sample92


title: Leicester_non_progressor_longitudnal_only_Sample62


title: Leicester_non_progressor_longitudnal_only_Sample57


title: Leicester_non_progressor_longitudnal_only_Sample55


title: Leicester_non_progressor_longitudnal_only_Sample56


title: Leicester_non_progressor_longitudnal_only_Sample54


title: Leicester_non_progressor_longitudnal_only_Sample72


title: Leicester_non_progressor_longitudnal_only_Sample52


title: Leicester_non_progressor_longitudnal_only_Sample53


title: Leicester_non_progressor_longitudnal_only_Sample44


title: Leicester_non_progressor_longitudnal_only_Sample43


title: Leicester_non_progressor_longitudnal_only_Sample50


title: Leicester_non_progressor_longitudnal_only_Sample40


title: Leicester_non_progressor_longitudnal_only_Sample48


title: Leicester_non_progressor_longitudnal_only_Sample47


title: Leicester_non_progressor_longitudnal_only_Sample41


title: Leicester_non_progressor_longitudnal_only_Sample38


title: Leicester_non_progressor_longitudnal_only_Sample51


title: Leicester_non_progressor_longitudnal_only_Sample42


title: Leicester_non_progressor_longitudnal_only_Sample45


title: Leicester_non_progressor_longitudnal_only_Sample49


title: Leicester_non_progressor_longitudnal_only_Sample39


title: Leicester_non_progressor_longitudnal_only_Sample37


title: Leicester_non_progressor_longitudnal_only_Sample36


title: Leicester_non_progressor_longitudnal_only_Sample58


title: Leicester_non_progressor_longitudnal_only_Sample35


title: Leicester_non_progressor_longitudnal_only_Sample34


title: Leicester_non_progressor_longitudnal_only_Sample28


title: Leicester_non_progressor_longitudnal_only_Sample30


title: Leicester_non_progressor_longitudnal_only_Sample29


title: Leicester_non_progressor_longitudnal_only_Sample33


title: Leicester_non_progressor_longitudnal_only_Sample26


title: Leicester_non_progressor_longitudnal_only_Sample25


title: Leicester_non_progressor_longitudnal_only_Sample32


title: Leicester_non_progressor_longitudnal_only_Sample24


title: Leicester_non_progressor_longitudnal_only_Sample27


title: Leicester_non_progressor_longitudnal_only_Sample20


title: Leicester_non_progressor_longitudnal_only_Sample22


title: Leicester_non_progressor_longitudnal_only_Sample21


title: Leicester_non_progressor_longitudnal_only_Sample18


title: Leicester_non_progressor_longitudnal_only_Sample17


title: Leicester_non_progressor_longitudnal_only_Sample15


title: Leicester_non_progressor_longitudnal_only_Sample13


title: Leicester_non_progressor_longitudnal_only_Sample14


title: Leicester_non_progressor_longitudnal_only_Sample16


title: Leicester_non_progressor_longitudnal_only_Sample31


title: Leicester_non_progressor_longitudnal_only_Sample11


title: Leicester_non_progressor_longitudnal_only_Sample19


title: Leicester_non_progressor_longitudnal_only_Sample6


title: Leicester_non_progressor_longitudnal_only_Sample3


title: Leicester_non_progressor_longitudnal_only_Sample2


title: Leicester_non_progressor_longitudnal_only_Sample4


title: Berry_SouthAfrica_Sample51

data_processing:
Raw paired-end RNA-seq data obtained for Berry London, Berry South Africa and Leicester cohorts was processed separately and subjected to quality control using FastQC (Babraham Bioinformatics) and MultiQC. Trimmomatic v0.36 was used to remove adapters and filter raw reads below the 36 bases long and leading and trailing bases below quality 25. Filtered reads were aligned to the Homo sapiens genome Ensembl GRCh38 (release 86) using HISAT2 v2.0.4 with default settings and RF rna-strandedness including unpaired read reads resulting from Trimmomatic. Mapped and aligned reads were quantified to obtain gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness. Raw counts were processed using the bioconductor package edgeR v3.14.0 in R. Genes expressed with counts per million (CPM) >2 in at least 5 samples were considered and normalised using trimmed mean of M- values (TMM) to remove library-specific artefacts.
Genome_build: Homo sapiens genome Ensembl GRCh38 (release 86)
Supplementary_files_format_and_content: Raw_counts_Berry_SouthAfrica.xlsx: Raw counts generated from paired-end RNA-seq fastq files, aligned using HISAT2 and quantified using HtSeq
Supplementary_files_format_and_content: edgeR_normalized_Berry_SouthAfrica.xlsx: Log2 expression values generated from edgeR, filtered using counts per million (CPM) >2 in at least 5 samples and normalised using trimmed mean of M- values (TMM) to remove library-specific artefacts

value: whole blood


title: Berry_SouthAfrica_Sample50


title: Berry_SouthAfrica_Sample47


title: Berry_SouthAfrica_Sample46


title: Leicester_non_progressor_longitudnal_only_Sample10

value: Whole blood


title: Berry_SouthAfrica_Sample45

value: No


title: Berry_SouthAfrica_Sample41


title: Berry_SouthAfrica_Sample43


title: Berry_SouthAfrica_Sample42


title: Leicester_non_progressor_longitudnal_only_Sample23


title: Berry_SouthAfrica_Sample49


title: Leicester_non_progressor_longitudnal_only_Sample12

value: Negative


title: Leicester_non_progressor_longitudnal_only_Sample7


title: Leicester_non_progressor_longitudnal_only_Sample5


title: Berry_SouthAfrica_Sample38


title: Berry_SouthAfrica_Sample40


title: Berry_SouthAfrica_Sample36


title: Berry_SouthAfrica_Sample37


title: Berry_SouthAfrica_Sample39


title: Berry_SouthAfrica_Sample34


title: Berry_SouthAfrica_Sample35


title: Berry_SouthAfrica_Sample30


title: Berry_SouthAfrica_Sample29


title: Berry_SouthAfrica_Sample32


title: Berry_SouthAfrica_Sample33


title: Berry_SouthAfrica_Sample26


title: Berry_SouthAfrica_Sample27


title: Berry_SouthAfrica_Sample24


title: Berry_SouthAfrica_Sample25


title: Berry_SouthAfrica_Sample22


title: Berry_SouthAfrica_Sample19


title: Berry_SouthAfrica_Sample23


title: Berry_SouthAfrica_Sample21


title: Berry_SouthAfrica_Sample18


title: Berry_SouthAfrica_Sample16


title: Berry_SouthAfrica_Sample14


title: Berry_SouthAfrica_Sample13


title: Berry_SouthAfrica_Sample15


title: Berry_SouthAfrica_Sample11


title: Berry_SouthAfrica_Sample12


title: Berry_SouthAfrica_Sample9


title: Berry_SouthAfrica_Sample10


title: Berry_SouthAfrica_Sample8


title: Berry_SouthAfrica_Sample4


title: Berry_SouthAfrica_Sample7


title: Berry_SouthAfrica_Sample6


title: Berry_SouthAfrica_Sample3


title: Berry_SouthAfrica_Sample1


title: Berry_SouthAfrica_Sample28


title: Berry_London_Sample53

data_processing:
Raw paired-end RNA-seq data obtained for Berry London, Berry South Africa and Leicester cohorts was processed separately and subjected to quality control using FastQC (Babraham Bioinformatics) and MultiQC. Trimmomatic v0.36 was used to remove adapters and filter raw reads below the 36 bases long and leading and trailing bases below quality 25. Filtered reads were aligned to the Homo sapiens genome Ensembl GRCh38 (release 86) using HISAT2 v2.0.4 with default settings and RF rna-strandedness including unpaired read reads resulting from Trimmomatic. Mapped and aligned reads were quantified to obtain gene-level counts using HtSeq v0.6.1 with default settings and reverse strandedness. Raw counts were processed using the bioconductor package edgeR v3.14.0 in R. Genes expressed with counts per million (CPM) >2 in at least 5 samples were considered and normalised using trimmed mean of M- values (TMM) to remove library-specific artefacts.
Genome_build: Homo sapiens genome Ensembl GRCh38 (release 86)
Supplementary_files_format_and_content: Raw_counts_Berry_London.xlsx: Raw counts generated from paired-end RNA-seq fastq files, aligned using HISAT2 and quantified using HtSeq
Supplementary_files_format_and_content: edgeR_normalized_Berry_London.xlsx: Log2 expression values generated from edgeR, filtered using counts per million (CPM) >2 in at least 5 samples and normalised using trimmed mean of M- values (TMM) to remove library-specific artefacts


title: Berry_SouthAfrica_Sample20


title: Berry_London_Sample54


title: Berry_London_Sample51


title: Berry_London_Sample50


title: Berry_SouthAfrica_Sample17


title: Berry_London_Sample49


title: Berry_London_Sample47


title: Berry_London_Sample44


title: Berry_London_Sample46


title: Berry_London_Sample42


title: Berry_London_Sample43


title: Berry_London_Sample41


title: Berry_London_Sample39


title: Berry_London_Sample37


title: Berry_London_Sample38


title: Berry_SouthAfrica_Sample2


title: Berry_London_Sample36


title: Berry_London_Sample33


title: Berry_London_Sample35


title: Berry_London_Sample31


title: Berry_London_Sample34


title: Berry_London_Sample52


title: Berry_London_Sample29


title: Berry_London_Sample30


title: Berry_London_Sample48


title: Berry_London_Sample28


title: Berry_London_Sample26


title: Berry_London_Sample45


title: Berry_London_Sample25


title: Berry_London_Sample22


title: Berry_London_Sample24


title: Berry_London_Sample23


title: Berry_London_Sample20


title: Berry_London_Sample21


title: Berry_London_Sample19


title: Berry_London_Sample40


title: Berry_London_Sample17


title: Berry_London_Sample18


title: Berry_London_Sample15


title: Berry_London_Sample14


title: Berry_London_Sample13


title: Berry_London_Sample32


title: Berry_London_Sample11


title: Berry_London_Sample12


title: Berry_London_Sample10


title: Berry_London_Sample27


title: Berry_London_Sample5


title: Berry_London_Sample6


title: Berry_London_Sample3


title: Berry_London_Sample7


title: Berry_London_Sample8


title: Berry_London_Sample1


title: FAS43 L1 replicate 2

city: Geneva

first: Florian

last: Steiner

address: 30, Quai Ernest-Ansermet

department: Department of Molecular and Cellular Biology

country: Switzerland

institute: University of Geneva

description:
N2_FAS43_L1.txt
Sample_F43_ld

data_processing:
The reads (length=50 bp) were mapped with the TopHat v2.0.13 (default parameters) software to the C. elegans reference genome.
Read counts representing the total number of reads aligning to each genomic feature were produced from aligned reads by the Python software htseq-count (-- mode=union, with HTSeq v.0.6.1) with the reference .gtf file.
The normalization and differential expression analysis between N2 and FAS43 samples was performed with the R/Bioconductor package edgeR v.3.10.5, for the genes annotated in the reference genome. Briefly, very lowly expressed genes were filtered out, and the data were normalized according to the library size.
Differentially expressed genes were estimated using a GLM approach (General Linear Model), negative binomial distribution and a quasi-likelihood F-test.
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include raw counts and normalized abundance measurements (by edgeR) and significance values for each gene.

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: Nematodes were cultured using standard procedures at 20°C.

extract_protocol:
RNA was isolated from N2 and FAS43 mixed-stage embryos and L1 larvae grown at 20°C using Trizol, in duplicates for all samples.
The TruSeq mRNA stranded kit from Illumina was used for the library preparation with 1000 ng of total RNA as input. Reads of 50 bases were generated using the TruSeq SBS HS v3 chemistry on an Illumina HiSeq 2500 sequencer.

tag: genotype

value: L1 larvae


title: Berry_London_Sample9


title: FAS43 L1 replicate 1

description:
N2_FAS43_L1.txt
Sample_F43_l


title: N2 L1 replicate 2

description:
N2_FAS43_L1.txt
Sample_N2_ld

value: wildtype


title: FAS43 embryos replicate 2

description:
N2_FAS43_emb.txt
Sample_F43_ed

source_name: Mixed stage embryos

value: Mixed stage embryos


title: Berry_London_Sample2


title: N2 L1 replicate 1

description:
N2_FAS43_L1.txt
Sample_N2_l


title: Berry_London_Sample4


title: N2 embryos replicate 2

description:
N2_FAS43_emb.txt
Sample_N2_ed


title: N2 embryos replicate 1

description:
N2_FAS43_emb.txt
Sample_N2_e


title: FAS43 embryos replicate 1

description:
N2_FAS43_emb.txt
Sample_F43_e


title: Berry_London_Sample16


title: YbeY-HTF replicate 1

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

institute: University of New South Wales

description: RNA-YbeY complexes

data_processing:
Library strategy: CRAC
The analysis pipeline is described in Sy et al Methods in Molecular Biology 2017 in press. Briefly,
trimming, quality filtering, alignment, and read mapping were performed using CRAC_pipeline_SE.py available at https://bitbucket.org/sgrann/pycrac and decribed in Sy et al (Methods in Molecular Biology 2017 in press)
peak calling was performed using blockbuster (Langenberger et al Bioinformatics 2009 25:2298)
statistically signficant peaks for identified using pyCalclulateFDR available in the pyCRAC package ( https://bitbucket.org/sgrann/pycrac )
Genome_build: NC_002695.1, NC_002127.1, NC_002128.1
Supplementary_files_format_and_content: File type: mapped reads (pyReadCounters GTF output)  Format: GTF Content: reads mapped to genome
Supplementary_files_format_and_content: File type: mapped reads (bedgraph) Format: bedGraph Content: reads mapped to genome
Supplementary_files_format_and_content: File type: mapped deletions (bedgraph) Format: bedGraph Content: contact-dependant deletions mapped to genome
Supplementary_files_format_and_content: File type: mapped reads (GTF output) Format: GTF Content: reads mapped to genome with 6/7 rRNA operons masked
Supplementary_files_format_and_content: File type: mapped reads (all but one rRNA operon masked) (bedgraph output) Format: bedGraph Content: reads mapped to genome with 6/7 rRNA operons masked
Supplementary_files_format_and_content: File type: mapped deletions (all but one rRNA operon masked) (bedgraph output) Format: bedGraph Content: contact-dependant deletions mapped to genome with 6/7 rRNA operons masked

organism: Escherichia coli O157:H7

source_name: E. coli O157:H7 str. ZAP193 ybeY-HTF

growth_protocol: Cell were grown in MEM-HEPES + 0.1% glucose + 250nM Fe(NO3)3 to an OD600 of 0.8

extract_protocol:
as per Tree et al Molecular Cell 2014
CRAC (as per Tree et al Molecular Cell 2014)

treatment_protocol: Cells were UV-crosslinked with 1800mJ of UV-C (254nM)

value: ybeY-HTF

tag: growth media


title: x1 control

city: Copenhagen

first: Mireya

last: Plass

address: Robert-Rössle Str. 10

institute: MDC-Berlin

data_processing:
Paired-end reads, one containing the cellular and the molecular barcodes and the other containing an RNA fragment, were joined in a bam file using picard-tools v 1.95.
Reads were then sorted using samtools 1.3.
Reads were then tagged with the cell and the molecular barcodes (UMIs), trimmed at the 5’end to remove adapter sequences and at the 3’end to remove polyA tails using Dropseq tools v 1.12
Reads were mapped to the S. mediterranea dd_Smed_v6 transcriptome assembly using STAR v 2.5 1b
Reads mapped to different transcripts were aggregated and assigned to the corresponding gene, counting reads mapping to different transcripts only once.
Dropseq tools v 1.12 were used to correct synthesis errors affecting the last position of the cell barcode and assign mapped reads to genes included in the transcriptome
To define the number of cells, we plotted the cumulative fraction of reads assigned to each cellular barcoded for each of the barcodes sequenced ordered decreasingly and identified the inflection point of the curve using the R package dropbead (https://github.com/rajewsky-lab/dropbead)
The final DGE for each of the samples was obtained using DigitalExpression from drop-seq tools using all mapped reads and counting the number of unique UMIs assigned to each gene in each of the selected cells
Genome_build: Schmidtea mediterranea dd_Smed_v6 transcriptome assembly
Supplementary_files_format_and_content: DGE files contain a matrix in which columns are cells and rows are genes, and in each position it contains the amount of UMIs assigned to each gene in each cell of the sample

organism: Schmidtea mediterranea

source_name: bulk population whole cells

growth_protocol: 20ºC Artificial Montjuic Water

extract_protocol:
trypsin dissociation and cell filtering, whole cells selected by hoechst and calcein content
Macosko et al. 2015 Cell. Online Dropseq Protocol-v 3.1
Drop-seq

treatment_protocol: RNAi (dsRNA injected 5 days prior to sample collection) or wild type

tag: run name

tag: condition

value: wild type

tag: fixation method

value: adult


title: untagged control

description: RNA (background)

source_name: E. coli O157:H7 str.  ZAP193

value: MEM-HEPES + 0.1% glucose + 250nM Fe(NO3)3


title: YbeY-HTF replicate 2

description: RNA-YbeY complexes

source_name: E. coli O157:H7 str.  ZAP193 ybeY-HTF


title: fix 2

value: methanol


title: SynII_S

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

description: Genome assembly used for mapping sequencing reads.

data_processing:
Reads were mapped to the references genome sequence (using the Stampy package).
Samtools view was used to filter reads, retaining uniquely mapped reads with each segment properly aligned according to the aligner (-f 2) and with high mapping quality (-q 50).
Replication timing profile was generated by normalizing the replicating (S phase) sample to the non-replicating (G2) sample in 1 kb windows.
Windows where fewer than 250 reads were mapped in either sample were excluded.
The resulting absolute ratios reflect the read numbers; therefore data was normalized by dividing by an empirically determined factor.
Genome_build: SynII_genome_complete.fa
Supplementary_files_format_and_content: Processed files (*.wig) are available as Series supplementary files.

source_name: genomic DNA from S phase cells enriched by FACS  from asynchronous culture

growth_protocol: Cells were harvested from mid-log phase cultures grown in YPD media.

extract_protocol:
Cells obtained from FACS were resuspended in 500 µL of 1.2 M sorbitol, 200 mM Tris-HCl (pH7.5), 20 mM EDTA, 0.1% b-mercaptoethanol. Cells were spheroplasted with Zymolyase and then treated with SDS, Proteinase K and RNase A. DNA was purified by phenol chloroform extraction.
Library preparation and sequencing was carried out according to Illumina instructions.

treatment_protocol: Cells were sorted by DNA content, selecting S phase and G2 phase cells

tag: relevant genotype

value: his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 SynII-Y::URA3


title: x1

source_name: X1 sorted whole cells


title: gfp(RNAi)

value: gfp(RNAi)


title: RNA-seq_NPC_shSrf_12kPa

status: Public on Apr 18 2018

city: Kyoto

first: Takashi

last: Ikeda

address: 53 Shogoin Kawahara-cho Sakyo-ku

country: Japan

institute: Kyoto Univ.

description: From cells cultured on a 12kPa extracellular matrix

data_processing:
The low-quality bases at the 3' read ends and the adaptors were trimmed using cutadapt-1.9.1.
Untrimmed and trimmed reads of 20 bp or longer were mapped to mouse genome (mm10) using tophat-2.1.0 with the GENCODE version M14 annotation gtf file and the aligner Bowtie2-2.2.8.
The reads with high mapping quality (MAPQ>=20) were used for further analyses.
The expression level of each gene was calculated as reads per kilobase per million mapped reads (RPKM) by cufflinks-2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include gene names and FPKM values for each Sample

source_name: Neural progenitor cells

growth_protocol: Neural progenitor cells were maintained on a type I collagen-coated culture plate in a NPC medium consisting of a NPC medium, N2B27 medium prepared as a 1:1 mixture of Neurobasal (Thermo Fisher Scientific) and DMEM/F12 (1:1) with L-glutamine and sodium bicarbonate (Thermo Fisher Scientific) supplemented with 1× N2 supplement (Thermo Fisher Scientific), 1× B-27 supplement (Thermo Fisher Scientific), an additional 500 µM L-glutamine (Thermo Fisher Scientific), 10 µg/ml insulin (Wako) and 37.5 µg/ml bovine serum albumin (BSA) fraction V (Sigma-Aldrich). To analyze the effect of extracellular matrix stiffness on gene expression, NPCs were maintained in a NPC medium without EGF and bFGF on a matrix (12 kPa) lied over culture dishes coated with type I collagen (Matrigen).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
One hundred nanograms of each total RNA was used for construction of the library using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). Libraries were assessed for quality and quantity using Agilent Bioanalyzer 2100 and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).

treatment_protocol: An shSrf-expressing gene was introduced retrovirally

tag: protocol

tag: cell type

value: In vitro differentiated neural progenitor cells


title: RNA-seq_NPC_control_0.5kPa

description: From cells cultured on a 0.5-kPa extracellular matrix

growth_protocol: Neural progenitor cells were maintained on a type I collagen-coated culture plate in a NPC medium consisting of a NPC medium, N2B27 medium prepared as a 1:1 mixture of Neurobasal (Thermo Fisher Scientific) and DMEM/F12 (1:1) with L-glutamine and sodium bicarbonate (Thermo Fisher Scientific) supplemented with 1× N2 supplement (Thermo Fisher Scientific), 1× B-27 supplement (Thermo Fisher Scientific), an additional 500 µM L-glutamine (Thermo Fisher Scientific), 10 µg/ml insulin (Wako) and 37.5 µg/ml bovine serum albumin (BSA) fraction V (Sigma-Aldrich). To analyze the effect of extracellular matrix stiffness on gene expression, NPCs were maintained in a NPC medium without EGF and bFGF on a matrix (0.5 kPa) lied over culture dishes coated with type I collagen (Matrigen).


title: dmso

value: ds25_planaria frozen

value: cryopreserved in DMSO


title: RNA-seq_NPC_shSrf_0.5kPa


title: live

value: ds25_planaria live


title: cSR_29

city: Madison

first: David

last: Vereide

state: WI

address: 330 North Orchard Street

department: Regenerative Biology

institute: Morgridge Institute for Research

data_processing:
Basecalls performed using CASAVA version 1.8.2
Some samples were discarded because they failed quality control (SinQC analysis, 19 cells, not included here)
Sequencing reads were mapped to Galgal4 using Bowtie 0.12.9.
Gene expected counts were calculated using RSEM 1.2.3
Genome_build: Galgal4

organism: Gallus gallus

source_name: Chicken surrounding region (area pellucida without primitive streak)

growth_protocol: Fertilized White Leghorn chicken eggs were incubated for 20-27 hours to reach Hamburger-Hamilton Stage 4.

extract_protocol:
Hamburger-Hamilton Stage 4 chicken embryos were collected in Ringer's solution. The primitive streak was dissected out using a fine tungsten needle, and the remaining surrounding tissue (rest of the area pellucida) was collected separately.
Diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina).
scRNA-seq with ~40x multiplexing

tag: breed

value: White Leghorn

value: Chicken surrounding region cell

tag: Stage

value: Hamburger-Hamilton Stage 4


title: RNA-seq_NPC_control_12kPa


title: cSR_27


title: SynII_G2

description: In the processed data file the values for each chromosome were generated by dividing by 2.7

source_name: genomic DNA from G2 cells enriched by FACS  from asynchronous culture

tag: strain


title: cSR_30


title: h2b(RNAi)

tag: developmental stage


title: cSR_17


title: cSR_16


title: cSR_26


title: ZR3

city: Houston

first: Li

last: Ma

state: TX

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

description: transfected with ZRANB1 siRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Pair-ended reads were mapped to human hg19 genome using Tophat V2.1.1, along with the human reference annotation file from RefSeq.
Uniquely mapped reads were extracted using SAMtools. Cufflinks V2.2.1 was used to assemble the transcriptome and quantitate the gene expression level with fragments per kb of transcripts per million mapped reads (FPKM).
Differentially Express Genes(DEGs) were identified using Cuffdiff V2.2.1 with corrected P-value <= 0.05 and absolute log2 fold change (log2FC) >= 0.7.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: transfected with ZRANB1 siRNA

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% FBS and 1% penicillin and streptomycin.

extract_protocol:
RNA was isolated from LM2-scramble siRNA, LM2-ZRANB1 siRNA, LM2-scramble shRNA, and LM2-EZH2 shRNA cells using the RNeasy Mini Kit (Qiagen, 74104), according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Breast cancer cell line


title: cSR_14


title: ZR2

description: transfected with ZRANB1 siRNA


title: fix 1


title: ZR1

description: transfected with ZRANB1 siRNA


title: SC3

description: transfected with scramble siRNA

source_name: transfected with scramble siRNA


title: SC2

description: transfected with scramble siRNA


title: cSR_07


title: cSR_04


title: SC1

description: transfected with scramble siRNA


title: cSR_15


title: cSR_18


title: cSR_05

source_name: Chicken epiblast


title: cSR_19


title: cSR_28


title: cSR_03

value: Chicken epiblast cell


title: EZ3

description: transduced with EZH2 shRNA

source_name: transduced with EZH2 shRNA


title: cSR_02


title: EZ2

description: transduced with EZH2 shRNA


title: cSR_25


title: CT2

description: transduced with scramble shRNA

source_name: transduced with scramble shRNA


title: cSR_06


title: cSR_24


title: CT3

description: transduced with scramble shRNA


title: EZ1

description: transduced with EZH2 shRNA


title: smallRNASeq sample K10

city: Ljubljana

first: Anja

last: Kovanda

address: Jamova 39

department: Dept. of Biotechnology

country: Slovenia

institute: Institute Jozef Stefan

description:
NG-133-0022_S21
NG-0022_S26

data_processing:
trimming, adaptor removal with CLC Genomics Workbench 8.5.1
annotation using human miRBase 21 and Ensemble Non coding RNA (GRCh38ncrna)- Annotate and Merge from CLC Genomics Workbench 8.5.1
Statistics using Baggerley's test with Benjamini and Hochberg FDR
Supplementary_files_format_and_content: K vs. ALS_annotated_all.xlsx: trimming, adaptor removal with CLC Genomics Workbench 8.5.1 / annotation using human miRBase 21 and Ensemble Non coding RNA (GRCh38ncrna)- Annotate and Merge from CLC Genomics Workbench 8.5.1 / Statistics using Baggerley's test with Benjamini and Hochberg FDR --> output .xlsx file
Supplementary_files_format_and_content: K vs. ALS_unannotated_all.xlsx: trimming, adaptor removal with CLC Genomics Workbench 8.5.1 / annotation using human miRBase 21 and Ensemble Non coding RNA (GRCh38ncrna)- Annotate and Merge from CLC Genomics Workbench 8.5.1 / Statistics using Baggerley's test with Benjamini and Hochberg FDR --> output .xlsx file

source_name: healthy control

extract_protocol:
muscle biopsy procedure
Illumina® TruSeq® small RNA library Prep
Small RNA Seq on NextSeq 500

value: healthy control


title: CT1

description: transduced with scramble shRNA


title: cSR_23


title: cSR_20


title: cSR_21


title: smallRNASeq sample K8

description:
NG-133-0020_S19
NG-0020_S24


title: smallRNASeq sample K9

description:
NG-133-0021_S20
NG-0021_S25


title: cSR_10


title: cSR_12


title: cSR_11


title: smallRNASeq sample K7

description:
NG-133-0019_S18
NG-0019_S23


title: smallRNASeq sample K5

description:
NG-133-0017_S16
NG-0017_S21


title: cSR_09


title: cSR_22


title: smallRNASeq sample K4

description:
NG-133-0016_S15
NG-0016_S20


title: smallRNASeq sample K6

description:
NG-133-0018_S17
NG-0018_S22


title: cSR_08


title: cSR_01


title: cPS2_83

source_name: Chicken primitive streak

value: Chicken primitive streak cell


title: smallRNASeq sample K2

description:
NG-133-0014_S13
NG-0014_S18


title: smallRNASeq sample K1

description:
NG-133-0013_S12
NG-0013_S17


title: smallRNASeq sample K11

description:
NG-133-0023_S22
NG-0023_S27


title: cPS2_81


title: cPS2_79


title: smallRNASeq sample ALS11

description:
NG-133-0011_S10
NG-0011_S15

source_name: ALS patient

value: ALS patient


title: smallRNASeq sample ALS12

description:
NG-133-0012_S11
NG-0012_S16


title: cPS2_78


title: cPS2_77


title: cPS2_76


title: smallRNASeq sample ALS9

description:
NG-133-0009_S8
NG-0009_S13


title: smallRNASeq sample ALS8

description:
NG-133-0008_S7
NG-0008_S12


title: smallRNASeq sample ALS7

description:
NG-133-0007_S6
NG-0007_S11


title: cPS2_75


title: smallRNASeq sample ALS6

description:
NG-133-0006_S5
NG-0006_S10


title: cPS2_74


title: cPS2_72


title: cPS2_73


title: smallRNASeq sample K3

description:
NG-133-0015_S14
NG-0015_S19


title: cPS2_70


title: cPS2_69


title: cPS2_71


title: smallRNASeq sample ALS1

description:
NG-133-0001_S1
NG-0001_S6


title: cPS2_82


title: cPS2_68


title: cPS2_67


title: cPS2_66


title: cPS2_65


title: FG WGBS

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Removed the low quality reads; Bsmap was used to map the Whole Genome Bisulfite Sequences to hg19;
MOABS was used to call methylation ratios for each CpG site; RPKM was calculated to measure the genes expression level.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file for WGBS data; bed files for CMS-IP peaks ; Tab-delimited text file include the RPKM for each gene in each sample

source_name: human ES cells

growth_protocol: Human embryonic stem cells (H1) was cultured in hESC culture media (mTeSR1, Stem Cell Technologies) following manufactures instruction. Every 3-4 days, cells were passaged using AccutaseTM (Innovative Cell Technologies) supplied with 10% (vol/vol) human AB serum (Valley Biomedical) included in the hESC media the day of passage.

extract_protocol:
Genomic DNA was isolated using Qiagen DNeasy Blood and Tissue kit.
Purified genomic DNA was sonicated into ~300 bp using Covaris focused ultrasonicators following manufacture’s instruction. Sheared DNA was ligated with methylated adaptors using a TruSeq DNA library preparation kit (Illumina) followed by sodium bisulfite treatment (Zymo Research, EZ DNA methylation-lightning kit). Whole genome-wide bisulfite sequencing (WGBS) were performed by following previous publication (18). DNA libraries with methylated adapters were amplified using KAPA HiFi Uracil+ (Kapa Biosystems) polymerase   with   4   PCR   cycles. Amplified DNA fragments were purified by AmpuXP beads and sequenced using illumina NextSeq instrument (150 cycle, pair-ended).

treatment_protocol: Pancreatic differentiation was following previous published protocol (Schulz et al., 2012; Xie et al., 2013). Differentiation employed a suspension-based format using rotational culture. Aggregates of undifferentiated hESC were generated by resuspending dissociated cells in hESC media at 1 × 106 cells/mL and culturing them overnight in six-well ultra-low attachment plates (Costar) with 5.5ml per well on an orbital rotator (Innova2000, New Brunswick Scientific) at 95 rpm. The following day undifferentiated aggregates were washed in RPMI media and then differentiated using a multi-step protocol with daily media feeding except on day 10 and continued orbital rotation at either 95 rpm or at 105 rpm on days 4 to 8. In addition to GlutaMAX™ and penicillin/streptomycin, RPMI media (Mediatech) was supplemented with 0.2% (vol/vol) FBS (HyClone) and DMEM High Glucose media (HyClone) was supplemented with 0.5X B-27® supplement (Life Technologies). Human activin, mouse Wnt3a, human KGF, human Noggin, and human EGF were purchased from R&D systems. Other media components included TGFb R1 kinase inhibitor IV (EMD Bioscience), KAAD-Cyclopamine (Toronto Research Chemicals), the retinoid analog TTNPB (Sigma Aldrich), and Insulin-Transferrin-Selenium (ITS; Life Technologies). For some differentiations, 50ng/mL Noggin was also included on days 8 to 12.

value: H1 ES differentiate


title: GT WGBS


title: PE WGBS


title: DE WGBS


title: PE RNA rep1

data_processing:
Illumina Casava1.7 software used for basecalling.
Removed the low quality reads; Bowtie2 was used to map RNAseq to hg19 with default parameters.
DESeq2 was used to count the raw reads number fail in genes and call differential expressed genes
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include the RPKM for each gene in each sample

extract_protocol:
RNA was isolated using Qiagen RNeasy mini kit.
RNA library was constructed according to illumina Trueseq kit protocol


title: cPS2_64


title: smallRNASeq sample ALS10

description:
NG-133-0010_S9
NG-0010_S14


title: GT RNA rep2


title: GT RNA rep1


title: DE RNA rep2


title: cPS2_62


title: smallRNASeq sample ALS4

description:
NG-133-0004_S4
NG-0004_S9


title: DE RNA rep1


title: PE RNA rep2


title: cPS2_60


title: cPS2_58


title: cPS2_61


title: cPS2_59


title: smallRNASeq sample ALS3

description:
NG-133-0003_S3
NG-0003_S8


title: smallRNASeq sample ALS2

description:
NG-133-0002_S2
NG-0002_S7


title: cPS2_56

data_processing:
Basecalls performed using CASAVA version 1.8.2
Some samples were discarded because they failed quality control (SinQC analysis, 19 cells, not included here)
Sequencing reads were mapped to Galgal4 using bowtie 0.12.8.
Gene expected counts were calculated using RSEM 1.2.3
Genome_build: Galgal4

growth_protocol: Fertilized White Leghorn chicken eggs were incubated for 22-24 hours to reach Hamburger-Hamilton Stage 4.

extract_protocol:
Hamburger-Hamilton Stage 4 chicken embryos were collected in Ringer's solution. The primitive streak was dissected out using a fine tungsten needle, and the remaining epiblast (area pellucida) was collected separately.
Diluted single-cell cDNA libraries were fragmented and amplified using the Nextera XT DNA Sample Preparation Kit and the Nextera XT DNA Sample Preparation Index Kit (Illumina).
scRNA-seq with ~40x multiplexing


title: cPS2_57


title: cPS2_63


title: ES RNA rep2

value: H1 ES


title: PE ATAC

data_processing:
Illumina Casava1.7 software used for basecalling.
Removed the low quality reads;Bowtie2 was used to map ATAC-seq to hg19 with --very sensitive parameter.
Macs2 was used to call ATAC peaks;
Genome_build: hg19

extract_protocol:
Genomic DNA was isolated using Qiagen DNeasy Blood and Tissue kit.
ATAC-seq library preparation was performed as described in Nat Methods. 2013;10(12):1213-8


title: ES RNA rep1


title: FG ATAC


title: cPS2_53


title: cPS2_52


title: cPS2_54


title: ES ATAC


title: DE ATAC