title: root tip region 2 after 48 h water-stress, biological rep1

city: Columbia

first: Babu

last: Valliyodan

state: Missouri

address: 1-31 Ag Building

department: Plant Sciences

institute: University of Missouri

description: Gene expression data from soybean root tip water-stress

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

scan_protocol: The arrays were scanned with a GeneChip 7G Plus high-resolution scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Glycine max

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Soybean (cv.Magellan) seeds were surface sterilized in 1% NaClO solution for 2 min, rinsed in deionized water for 30 min and germinated between sheets of germination paper moistened with a solution containing 5 mm CaCl2 and 5 mm Ca(NO3)2 for 36 h at 29 °C and near-saturation humidity in the dark.

extract_protocol: Total RNA was isolated from the root tissues using TRIZOL reagent (Invitrogen, Carlsbad, CA, USA). Genomic DNA was eliminated by digesting the RNA with Turbo DNA-free DNaseI (Ambion) according to the manufacturer’s instructions. After DNaseI treatment, RNA concentration was determined and checked the quality using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA). Total RNA was used for Affymetrix Soybean Genome GeneChip analysis following the manufacturer's recommended protocols (Affymetrix, CA). The cDNA synthesis, cRNA amplification, and synthesis of sense strand cDNAs were carried out using the Ambion WT expression kit.

treatment_protocol: Seedlings with primary roots approximately 15 mm in length were transplanted against the interior surface of Plexiglas cylinders (14.5 cm diameter) filled with a 1:1 (v/v) mixture of vermiculite (no. 2A, Therm-ORock East Inc., New Eagle, PA, USA) and Turface (Profile Products LLC, Buffalo Grove, IL, USA) at water potentials of -0.1 MPa (well-watered treatment, moistened to the drip point) or -1.6 MPa (water-stressed treatment). Totally around 300 roots for each sample with three biological replicates were collected and the root tips were sectioned into regions 1–2 (water stressed) and 1–3 (well-watered controls) after 5h and 48h respectively. The root samples were immediately frozen with liquid nitrogen and then stored at −80 °C.

tag: cultivar

tag: treatment group

value: water-stressed treatment

value: root tip


title: HAP1_WT-T18-A

status: Public on Aug 15 2020

type: SRA

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: gRNA amplicon

library_source: genomic

data_processing:
Library strategy: CRISPR-seq
FASTQ files were pre-processed to extract Cas9 guide sequence using a bespoke Perl script.
The Cas9 guide sequence was extracted from read1 files as the 20 bases preceeding 'CGGTGTTT'.
Trimmed FASTQ files were then aligned to the TKOv3 FASTA file using bowtie v0.12.1 using the following command line parameters:   -p 16 -v 3 -l 18 --chunkmbs 256 -t <library_file> --un unmapped.fastq --al mapped.fastq -1 <trimmed_read1.fastq> aligned.sam
The number of reads aligning to each guide sequence was enumerated for each aligned .sam file, and alignment statistics were recorded.  Guide IDs and counts were written to individual count files.
All individual count files were merged along with library annotations in R.
Supplementary_files_format_and_content: tab-delimited read count matrix

molecule: genomic DNA

organism: Homo sapiens

source_name: HAP1 cell line

growth_protocol:
During generation and clonal expansion, H1-iCas9 cells were cultured on Matrigel (Corning; 0.5mg per 6-well plate) in E8 medium (Life Technologies), passaged using GCDR (STEMCELL) and cryopreserved in mFreSR medium (STEMCELL)
MEF culture: culture on irradiated mouse embryonic fibroblasts (MEFs) in human embryonic stem cell (hESC) medium as described (Ditadi and Sturgeon, 2016). hESC medium consists of DMEM/F12 (50:50; ThermoFisher) supplemented with 20% knockout serum replacement (KOSR) (GIBCO), 1% penicillin/streptomycin (ThermoFisher). 2mM L-glutamine (ThermoFisher), 1% non-essential amino acids (NEAA) (ThermoFisher) and 55uM beta-mercaptoethanol (Sigma). Immediately prior to use, hESC media was supplemented with 15ng/ml human basic fibroblast growth factor (hbFGF) (R&D Systems). Cells were passaged every 4-5 days using TrypLE Express (GIBCO), and plated in presence of 10uM ROCK inhibitor Y-27632 (ROCKi) (Tocris) for 24 hours. Cells were cryopreserved in freezing medium containing 50% hESC medium plus 40% FCS plus 10% DMSO.
Feeder-free conditions: H1-iCas9 cells were maintained on tissue culture plates coated with recombinant human laminin at a concentration of 0.5ug/cm^2 (rhLaminin-521, ThermoFisher; doluted in DBPS with Ca^2+ and Mg^2+, GIBCO) or vitronectin at a concentration of 1.05ug/cm^2 (STEMCELL, diluted in PBS) in mTeSR1 complete medium (STEMCELL). Cells were passaged every 4-5 days using ReLeSR enzyme-free dissociation reagent (STEMCELL) in the absence of ROCKi (only used for thawing and transduction), and cryopreserved in mFreSR medium (STEMCELL). H1 and H1-iCas9 cells were maintained in culture plates of 24-well to 10-cm size at individually optimized cell numbers. Growth media were changed daily with occasional "double-feeds" over two days.
HAP1 cells were obtained from Horizon (clone C631, sex: male with lost Y chromosome, RRID: CVCL_Y019) and HAP1-Cas9 cells were generated analagous to described protocols (Hart et al., 2015). HAP1 cells were cultured in DMEM without sodium pyruvate, with sodium bicarbonate, 1.982g/L glucose and 0.161g/L L-glutamine (Wisent Bioproducts) with 10% FBS (GIBCO) and 1% penicillin/streptomycin (ThermoFisher).

extract_protocol:
Genomic DNA was extracted from screen cell pellets using the Wizard Genomic DNA Purification kit (Promega) according to manufacturer's instructions.
Sequencing libraries were preparaed by amplifying gRNA inserts via a 2-step PCR using primers that include Illumina TruSeq adaptors with i5 and i7 indices.

treatment_protocol:
Cells grown on MEFs: 48 hours prior to infection with the lentiviral pLCKO-TKOv3 library, H1-iCas9 cells were treated with DOX (1.5ug/ml, Sigma). Approximately 6x10^7 cells were infection in suspension (MOI~0.44, 370-fold library coverage) before being plated onto MEFs. 24 hours post infection, hESC medium was repalced with fresh medium containing puromycin (0.5ug/ml) and cells were incubated for 48 hours. After selection, cells were harvested, split into three replicates containing 1.5x10^7 cells each and exposed to another 24 hours of DOX. Cells were counted and passaged every 4 days in presence of ROCKi.
Cells grown on laminin: 48 hours prior to infection with the lentiviral pLCKO-TKOv3 library, H1-iCas9 cells were treated with DOX (1.5ug/ml, Sigma) with a fraction of cells left untreated. 24 hours prior to infection, cells were dissociated using ReLeSR and plated at a density of 1.5x10^6 cells/10cm dish with 10um ROCKi with and without DOX (1.5ug/ml). Approximately 8x10^7 adherent DOX-treated cells and 4x10^7 cells without DOX were infected with pLCKO-TKOv3 library and ROCKi (MOI~0.17 and ~0.42 respectively). 24 hours post infection, mTeSR1 medium was replaced with fresh medium containing puromycin (0.5ug/ml) and cells were incubated for 48 hours. Following selection, cells without DOX were harvested and collected for genomic DNA extraction, and DOX-treated cells were split into three replicates containing 1.5x10^7 cells each.

tag: culture substrate

value: Tissue culture plastic

tag: crispr library

tag: timepoint


title: root tip region 1 after 48 h water-stress, biological rep3

type: RNA

country: USA

molecule: total RNA

tag: tissue


title: root tip region 1 after 48 h water-stress, biological rep2


title: root tip region 2 after 48 h water-stress, biological rep3


title: root tip region 2 after 48 h well-water, biological rep3

description: Gene expression data from soybean root tip well-water

source_name: root tip region 2 after 48 h well-water

value: well-watered controls


title: L1CT-4-4D

city: Zurich

first: Frederic

middle: Francois

last: Guillaume

address: Winterthurerstrasse 190

department: Evolutionary Biology and Environmental Studies

country: Switzerland

institute: University of Zurich

library_source: transcriptomic

data_processing:
reads were mapped against the reference genome(ftp://ftp.ensemblgenomes.org/pub/release30/metazoa/gtf/tribolium_castaneum/Tribolium_castaneum.Tcas3.30.gtf.gz) with STAR v.2.5  (adaptors were trimmed and  the first 10 bases were hard trimmed, minimum average quality Q10, minimum tail quality 10, minimum read length 20).
Number of reads per gene were counted with FeatureCounts (gtfFeatureType: exon, featureLevel: gene, allowMultiOverlap=TRUE, minFeatureOverlap=10, minMapQuality=10)
Genome_build: Tcas3.30
Supplementary_files_format_and_content: tab-delimited text files: raw read counts data for each sample

organism: Tribolium castaneum

source_name: females, whole body

growth_protocol: Beetles were kept in 24h darkness on sterilised organic wheat flour mixed with 10% organic baker's yeast. We sequenced adult reproducing females from different replicate selection lines (seven Control-lines, four Dry-lines, five Hot-lines, seven Hot-Dry lines) under different climate conditions (control, dry, hot, hot-dry). Selection lines had lived under these conditions for 20 generations. Before testing for adaptation, all lines stayed for one generation in control condition. Sequenced individuals were transferred to the respective condition in the egg stage and developed completely in treatment conditions.

extract_protocol:
RNA Mini Prep kit (Zimo Research, California, USA)
LEXOGEN mRNA-Seq Library Kit (LEXOGEN GmbH, Vienne, Austria)

treatment_protocol: Beetles were kept in climate chambers that could control temperature and air humidity. Conditions were: Control: 33°C, 70% relative humidity; Dry : 33°C and 30% r. h.; Hot : 37°C and 70% r. h.; Hot-Dry: 37°C and 30% r. h.

tag: strain

tag: selection regime

value: Control

tag: treatment

value: Dry


title: root tip region 2 after 48 h well-water, biological rep2


title: root tip region 2 after 48 h water-stress, biological rep2


title: root tip region 1 after 48 h water-stress, biological rep1


title: root tip region 2 after 5 h water-stress, biological rep3


title: root tip region 3 after 48 h well-water, biological rep3

source_name: root tip region 3 after 48 h well-water


title: root tip region 3 after 48 h well-water, biological rep1


title: root tip region 2 after 48 h well-water, biological rep1


title: L1CT-4-3D


title: root tip region 1 after 48 h well-water, biological rep1

source_name: root tip region 1 after 48 h well-water


title: L1CT-4-3CT


title: HAP1_WT-T0-B Plasmid

description: plasmid amplicon

source_name: Plasmid pool


title: root tip region 1 after 48 h well-water, biological rep3


title: root tip region 2 after 5 h water-stress, biological rep2


title: HAP1_WT-T0-A Plasmid

description: plasmid amplicon


title: L1CT-4-2HD

value: Hot-Dry


title: L1HD-3-4HD


title: L1CT-4-2H

value: Hot


title: HAP1_WT-T14-C

description: gRNA amplicon


title: HAP1_WT-T14-B

description: gRNA amplicon


title: L1CT-4-2D


title: HAP1_WT-T14-A

description: gRNA amplicon


title: rrp6_bio2_lib2

city: Heidelberg

first: Wu

last: Wei

address: EMBL Heidelberg,Meyerhofstraße 1

department: Genome Biology Unit

country: Germany

institute: EMBL Heidelberg

description: Sample 12

data_processing:
Library strategy: TIF-Seq
Base-calling was performed using Illumina CASAVA pipeline and standard parameters.
5' and 3' sequences were extracted from paired-end sequences
5' and 3' sequences were aligned to the S288c reference R64 genome assembly using novoalign V2.07.10 with default parameters
Transcript isoforms (TIFs) were identified by exact identical 5' and 3' positions
Genome_build: Saccharomyces cerevisiae S288C reference genome R64 downloaded from SGD (http://www.yeastgenome.org/)
Supplementary_files_format_and_content: tab-delimited text files include number of TIFs of each sample (abundance measurements)

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown to mid-log phase (OD1) using either YPAD (1% yeast extract, 2% peptone, 1% glucose) or YPGal (1% yeast extract, 2% peptone, 1% galactose).

extract_protocol: Total RNA was isolated by a standard hot phenol method and contaminant DNA was removed by DNase I treatment. The sample was subject to TIF-Seq protocol (Transcript IsoForm Sequencing) for the unambiguous identification of overlapping transcripts by sequencing both 5’ and 3’ ends of the each mRNA molecule. Briefly, full-length cDNA molecules for capped and polyadenylated mRNAs is produced. After that, they are subject to intramolecular ligation, fragmentation and capture of the 5’-3’ junctions. Finally paired end sequencing of those tags give information to reconstruct the transcriptome architecture.

value: FSY3636 (MATa  delta rrp6::kanMX4, S288c background)

tag: media

value: YPAD media

tag: cell type

value: mid-log phase cells, OD 1

tag: genotype/variation

value: delta rrp6 mutant


title: rrp6_bio1_lib2

description: Sample 11


title: root tip region 3 after 48 h well-water, biological rep2


title: root tip region 2 after 5 h water-stress, biological rep1


title: HAP1_WT-T10-C

description: gRNA amplicon


title: HAP1_WT-T10-B

description: gRNA amplicon


title: rrp6_bio1_lib1

description: Sample 5


title: root tip region 1 after 5 h water-stress, biological rep3


title: root tip region 1 after 48 h well-water, biological rep2


title: root tip region 1 after 5 h water-stress, biological rep1


title: root tip region 1 after 5 h well-water, biological rep2

source_name: root tip region 1 after 5 h well-water


title: HAP1_WT-T10-A

description: gRNA amplicon


title: Microarray OCM1a

city: Shanghai

first: Peiwei

last: Chai

state: Shanghai

address: No.833 Zhizaoju Road

department: Opthalmology

country: China

institute: Shanghai Ninth people's hospital

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

source_name: melanoma cells

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

value: ocular melanoma cells

tag: development state

value: embryos in slow phase of cellularisation.


title: HAP1_WT-T6-C

description: gRNA amplicon


title: Microarray OCM1 decoyCTCF

value: embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.


title: root tip region 1 after 5 h well-water, biological rep1


title: Microarray OCM1a decoyCTCF


title: root tip region 2 after 5 h well-water, biological rep2

source_name: root tip region 2 after 5 h well-water


title: root tip region 2 after 5 h well-water, biological rep1


title: root tip region 1 after 5 h water-stress, biological rep2


title: L1CT-4-2CT


title: root tip region 2 after 5 h well-water, biological rep3


title: L1CT-4-1HD


title: L1CT-4-1D


title: CD44+ CD4+ T cells in T-bet-/- STAT6-/-2

city: Chiba

first: Sohei

last: Makita

state: Chiba

address: 1-8-1 inohana chuo-ku

country: Japan

institute: Chiba university

data_processing:
Illumina Casava1.8.2 software used for basecalling.
RNA-seq libraries were prepared using a SureSelect Strand Specific RNA Library Preparation kit (Agilent).
Sequencing was performed on an Illumina HiSeq1500 using a HiSeq Rapid SBSkit v2 (Illumina) in a 50-base single-end mode.
mRNA profiles were calculated with a Cufflinks software and expressed as FPKM (fragments per kilobase of exon model per million mapped fragments).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Mus musculus

source_name: CD44+ CD4+ T cells

extract_protocol:
Total RNA was isolated by using an RNeasy Mini Kit (Qiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD44+ CD4+ T cells from skin-draining LNs were stimulated with PMA and ionomycin for 2 hours

value: BALB/cAJcl

tag: genotype

value: T-bet-/- STAT6-/-

value: CD44+ CD4+ T cells


title: L1CT-4-1CT


title: Microarray OCM1


title: L1CT-4-1H


title: root tip region 1 after 5 h well-water, biological rep3

value: root tip


title: rrp6_bio2_lib1

description: Sample 6


title: CD44+ CD4+ T cells in STAT6-/-1


title: CD44+ CD4+ T cells in T-bet-/-2

value: T-bet-/-


title: HAP1_WT-T6-B

description: gRNA amplicon

value: Tissue culture plastic


title: HAP1_WT-T6-A

description: gRNA amplicon


title: CD44+ CD4+ T cells in T-bet-/- STAT6-/-1


title: zinc supplemented drinking water + PBS injection,  rep2 [liver_ZP-2]

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
Pre-processing to remove adpater sequences and low quality reads: Trimmomatic; version: 0.33; parameters:ILLUMINACLIP:/TruSeq3-SE.fa:2:30:10 AVGQUAL:20 TRAILING:20 MINLEN:33
Data were mapped to the mm10 reference genome with hisat2 v2.0.4 with Ensembl release 85 derived splice sites (--known-splicesite-infile) and strandedness 'R'
mapped read were stired as position sorted bam files by diretly piping hisat output through samtools (| samtools view -bu - | samtools sort -@ 4 -o out.bam )
read counting was performed with featurecounts (-a Ensemb85.gtf -s 2 -T 6 --primary *.bam)
Differential expressed genes were obtained with DESeq2 with standard analysis settings
Genome_build: mm10
Supplementary_files_format_and_content: processed files are a count matrix containg the counts output from featurecouts for all samples
Supplementary_files_format_and_content: featurecounts read counts

source_name: liver

extract_protocol:
liver was isolated, washed with PBS and stored in RNAlater for RNA extraction with RNeasy Mini Kit (Qiagen)
Illumina truseq RNA stranded library protocol (for single end sequencing)

treatment_protocol: mice recieved 7 days of normal dinking water or drinking water with 25 mM ZnSO4, aftwards an injection of 200 µg DEX in 200 ml PBS OR just 200 ml of PBS was given. Sampeling occured 2 hours after the injections

value: 7 days of 25 mM ZNSO4, 200ml PBS 2h before sampling


title: zinc supplemented drinking water + PBS injection,  rep3 [liver_ZP-3]


title: CD44+ CD4+ T cells in STAT6-/-2


title: CD44+ CD4+ T cells in T-bet-/-1


title: CD44+ CD4+ T cells in WT2

value: wildtype


title: zinc supplemented drinking water + PBS injection, rep1 [liver_ZP-1]


title: CD44+ CD4+ T cells in WT1


title: HAP1_WT-T3-B

description: gRNA amplicon


title: zinc supplemented drinking water + DEX injection, rep3 [liver_ZD-3]

value: 7 days of 25 mM ZNSO4, 200 µg (in 200ml PBS) DEX 2h before sampling


title: HAP1_WT-T3-A

description: gRNA amplicon


title: zinc supplemented drinking water + DEX injection, rep2 [liver_ZD-2]


title: lowfa 8: moderate FA WT 4

city: Boulder

first: David

last: Engelhardt

state: CO

address: 347 UCB

department: MCDB

institute: CU Boulder

data_processing:
Illumina 1.9 encoding
Sample quality evaluated using FastQC v.0.11.5
Alignment using tophat2 v.2.1.1
Indexing using samtools v.1.8
Counts generated by HTSeq v.0.9.1
Abundance and differential expression calculated by DESeq2 v.1.22.2
Genome_build: mm10
Supplementary_files_format_and_content: htseq count files

source_name: F3 E8.5 Mouse Head Tissue

growth_protocol: Mice were maintained on a 2ppm (moderate) or 10ppm (enriched) folic acid diet for three generations

extract_protocol:
F3 E8.5 embryo tissue was collected from the first brachial arch to just above the otic vesicle. Tissue was frozen using liquid nitrogen until RNA was collected using a QIAGEN AllPrep DNA/RNA Micro Kit (Cat. # 80284). Barcoded RNA-seq libraries were made from 1 µg of RNA using the Illumina TruSeq RNA Sample Preparation Kit, v2, Set A (Cat. #RS-122-2001).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: F3 E8.5 embryo

tag: diet

value: 2 ppm FA (moderate)

value: WT

tag: gender

value: F


title: zinc supplemented drinking water + DEX injection, rep1 [liver_ZD-1]


title: lowfa 7: moderate FA WT 3

value: M


title: lowfa 5: moderate FA WT 1


title: ESC_Laminin- H1 iCas9 c4-T12-B

description: gRNA amplicon

source_name: H1-iCas9 cell line

value: Laminin


title: lowfa 4: moderate FA mutant 4

value: homozygous IFT88-NULL


title: ESC_Laminin- H1 iCas9 c4-T12-A

description: gRNA amplicon


title: ESC_Laminin- H1 iCas9 c4-T9-C

description: gRNA amplicon


title: normal drinking water + DEX injection, rep3 [liver_HD-3]

value: 7 days water, 200 µg (in 200ml PBS) DEX 2h before sampling


title: normal drinking water + PBS injection,(control)  rep2 [liver_HP-2]

value: 7 days water, 200ml PBS 2h before sampling


title: normal drinking water + PBS injection,(control) rep1 [liver_HP-1]


title: ESC_Laminin- H1 iCas9 c4-T9-B

description: gRNA amplicon


title: lowfa 3: moderate FA mutant 3


title: HAP1_WT-T3-C

description: gRNA amplicon


title: ESC_Laminin- H1 iCas9 c4-T12-C

description: gRNA amplicon


title: normal drinking water + PBS injection,(control)  rep3 [liver_HP-3]


title: normal drinking water + DEX injection, rep2 [liver_HD-2]


title: lowfa 2: moderate FA mutant 2


title: ESC_Laminin- H1 iCas9 c4-T9-A

description: gRNA amplicon


title: arrested.C12-70min.rep2

city: changsha

first: xiaoyun

last: lei

state: hunan

address: kaifu district, xiangya road

department: xiangya hospital

institute: central south university

data_processing:
CASAVA1.4
We first cleaned the raw reads using trim_galore (version TrimGalore-0.6.0): trim_galore –paired ${sample}_1.fq.gz ${sample}_2.fq.gz --gzip -o trim
Then, reads from each RNA-Seq sample were mapped to the reference D. melanogaster genome (dm6; version BDGP6) downloaded from Ensembl using STAR (version STAR-2.5.3a); key alignment parameters were as follows: “--outFilterMismatchNoverLmax 0.04 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 --outMultimapperOrder Random --outSAMmultNmax 1”.
Finally, transcripts abundance for annotated RNAs were called by featureCounts of Subread package (version subread-1.6.0-Linux-x86_64), and only uniquely aligned reads were included.
To quantify the transcripts abundance, we used the function “fpm” in R package DEseq2 to calculate CPM (Counts Per Million mapped fragments) for each gene in all the samples, and then we transformed the CPM to Log2 scale (CPM+1 was used to avoid Log2 0).
Genome_build: dm6
Supplementary_files_format_and_content: Matrix table with normalized abundance measurements with Log2(CPM+1) for every gene for every stage

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: embryos

extract_protocol:
The RNA extraction from single embryos was done with TRIzol (Life Technologies #87804) according to the manufacturer’s protocol and a previous report.
We obtained 80 to 150 ng of total RNA from each embryo. Total RNA was made into libraries for sequencing using the mRNA-Seq Sample Preparation Kit (Illumina), and sequenced on an Illumina Hiseq platform (Novagene).

value: embryos

tag: Stage

value: cyclin RNAi

tag: group

value: arrested


title: ESC_Laminin- H1 iCas9 c4-T4-C

description: gRNA amplicon


title: ESC_Laminin- H1 iCas9 c4-T4-B

description: gRNA amplicon


title: lowfa 1: moderate FA mutant 1


title: normal drinking water + DEX injection, rep1 [liver_HD-1]


title: highfa 8: enriched FA WT 4

value: 10 ppm FA (enriched)


title: arrested.C12-70min.rep1


title: lowfa 6: moderate FA WT 2


title: mdx/miR-133b-/- [GRL16032-DM4]

city: Blacksburg

first: Robert

last: Settlage

state: VA

address: 1 Washington St

department: Advanced Research Computing

institute: Virginia Tech

data_processing:
ea-utils clipping of sequencing adaptor from sequencing reads
btrim quality trimming of reads
map data to genome using hisat2
count reads mapping to genes using htseq
Genome_build: NCBI Mus musculus GRCm38, annotation build 93
Supplementary_files_format_and_content: sequencing reads from Illumina

source_name: mdx/miR-133b-/-_tibialis anterior

extract_protocol: TheAurum RNA Isolation Kit (Bio-Rad) was used for RNA isolation from skeletal muscle tissue and Dnase treatment of RNA.

tag: age

value: Whole skeletal muscle


title: ESC_Laminin- H1 iCas9 c4-T4-A

description: gRNA amplicon

tag: culture substrate


title: arrested.C12-50min.rep1


title: mdx [GRL16024-D4]

source_name: mdx_tibialis anterior

value: mdx-/-


title: ESC_Laminin- H1 iCas9 c4-T0

description: gRNA amplicon

tag: crispr library


title: highfa 7: enriched FA WT 3


title: arrested.C12-30min.rep2


title: miR-133b-/- [GRL16028-M4]

source_name: miR-133b-/-_tibialis anterior


title: arrested.C12-30min.rep1


title: highfa 6: enriched FA WT 2


title: Control [GRL16020-C4]

source_name: Control_tibialis anterior

value: Wild Type


title: ESC_Laminin- H1 iCas9 c4-T0-No dox

description: gRNA amplicon

value: Uninduced control laminin

tag: timepoint


title: highfa 4: enriched FA mutant 4

tag: tissue

value: F3 E8.5 embryo


title: arrested.C12-15min.rep1


title: highfa 5: enriched FA WT 1


title: ESC_MEF- H1 iCas9 c4-T12-Oct4 high-C

description: gRNA amplicon

value: MEFs


title: arrested.C12-15min.rep2


title: mdx/miR-133b-/- [GRL16031-DM3]


title: highfa 3: enriched FA mutant 3


title: mdx [GRL16023-D3]


title: miR-133b-/- [GRL16027-M3]


title: control.C14L.rep2

value: no injection

value: control


title: arrested.C12-50min.rep2


title: Control [GRL16019-C3]


title: ESC_MEF- H1 iCas9 c4-T12-Oct4 low-C

description: gRNA amplicon


title: ESC_MEF- H1 iCas9 c4-T12-Oct4 high-A

description: gRNA amplicon


title: ESC_MEF- H1 iCas9 c4-T12-Oct4 low-B

description: gRNA amplicon


title: mdx/miR-133b-/- [GRL16030-DM2]


title: control.C14E.rep3


title: 1572874946_3976_P

city: Philadelphia

first: Danielle

middle: R

last: Reed

state: PA

address: 3500 Market St

department: Not applicable

institute: Monell Chemical Senses Center

data_processing: cell ranger 3.02

source_name: surgical biopsy nasal polyps

extract_protocol: Dataset consists of a total of four single-cell datasets generated using    the 10x Genomics Chromium platform. Prior to GEM generation, tissue sample    was taken fresh from OR rinses 3x in phosphate buffered saline, cut into    1-3mm sized pieces and gently digested in Liberase TL solution for 1-hr at    37C. The reaction was quenched with serum and digested cell suspension were    filtered through a 70micron filter centrifuged  gently at 4C and rinsed x2    with pbs followed by lysis of red blood cells with an rbc lysis solution.    This was followed by 2 rinses with phosphate buffered saline. Viability was    assessed by trypan blue of a small aliquot and at this point cells were    used for the Next-generation sequencing libraries that were prepared    following the 10X Single Cell v2 protocol without modification. Sample    quality was evaluated using Agilentâ€™s Bioanalyzer High Sensitivity reagent    kit following cDNA amplification and library construction. The completed    libraries were quantified using the Kapa Library Quantification Kit and the    Life Technologies Viia7 Real-time PCR instrument. Libraries were sequenced    in a paired-end, single-indexed format on the Illumina. Cells were    sequenced to target a depth of at least 27,000 reads per cell

value: surgical biopsy nasal polyps

tag: diagnosis

value: CRSwNP

tag: race

value: America African

value: Female


title: control.C14E.rep2

tag: treatment


title: ESC_MEF- H1 iCas9 c4-T12-Oct4 high-B

description: gRNA amplicon


title: 1572874946_3976_IT

source_name: surgical biopsy  inferior turbinate

value: surgical biopsy  inferior turbinate


title: highfa1: enriched FA mutant 1

value: homozygous IFT88-NULL

value: F


title: UWB1.289_Input

city: Los Angeles

first: Michelle

middle: Renee

last: Jones

state: CA

address: 8720 Alden Dv

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

data_processing:
ChIP-Seq peaks were generated with the AQUAS pipeline.
Reads were aligned with BWA to the reference human genome hg38.
Peak calling was performed with MACS2, with pooled replicate peaks that overlap 50% or more of each individual replicate selected for the final peak set. When replicates were not available (HEYA8, ES2 and RMG-II) pseudo replicates were formed and pooled peaks selected in the same manner from these pseudo replicates. Narrowpeaks were retained for downstream analysis.
Peaks sets were lifted into hg19 using the LiftOver tool.
Genome_build: hg19
Supplementary_files_format_and_content: Narrowpeak files were created in hg38 and then lifted to hg19 and converted to bed files. These files contain the co-ordinates of peaks enriched for H3K27Ac.

source_name: UWB1.289 Cell Line

extract_protocol:
Four 15-cm dishes of confluent cells were fixed in formaldehyde for 10 min, before quenching the fixation with glycine. Cells were collected, lysed in a sarkosyl-containing lysis buffer and sonicated  to yield 100- to 300-bp genomic DNA fragments. Five micrograms of an antibody raised against H3K27ac was incubated with blocked magnetic Dynabeads (Life Technologies) at 4 °C for 4 h. Antibody–bead conjugates were incubated with 100 μg of chromatin at 4 °C overnight, with constant agitation. Beads were washed extensively with RIPA buffer and then treated with RNase and proteinase K (both Qiagen). DNA was then eluted from the beads in TE buffer and cleaned up using the QIAquick PCR Purification kit (Qiagen).
ChIP libraries were constructed using the Kapa Hyper Library Preparation kit, according to the manufacturer's instructions. Library construction was carried out according to the manufacturer's instructions using Bio NextFLex adaptors diluted 1:50. Final PCR on a portion of the adaptor ligation was performed for 12 cycles. Products were evaluated on an Agilent Bioanalyzer, using high-sensitivity DNA chips. ChIP libraries were quantified using the Kapa Biosystems Illumina library quantification kit, before pooling for sequencing.

value: Model of High Grade Serous Ovarian Cancer

tag: cell line


title: miR-133b-/- [GRL16026-M2]


title: highfa 2: enriched FA mutant 2

value: 10 ppm FA (enriched)

value: M


title: control.C14E.rep1

value: embryos


title: control.C13.rep3


title: ESC_MEF- H1 iCas9 c4-T8-B

description: gRNA amplicon


title: Control [GRL16018-C2]

value: Wild Type

value: Whole skeletal muscle


title: UWB1.289_H3K27ac

description: Two biological replicates; Rep A and Rep B. Paired End Sequencing (R1/R2) files available.


title: control.C13.rep2


title: mdx/miR-133b-/- [GRL16029-DM1]


title: control.C14L.rep1


title: A431_Case2

city: Tianjin

first: Peitao

last: Zhang

address: Qixiangtai Road 22

institute: Tianjin Medical University

data_processing:
We use  Bowtie2  to map clean reads to reference gene and use  HISAT to reference genome.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using   Bowtie2  parameters for SE reads: -q --phred64 --sensitive --dpad 0 --gbar,HISTA parameters for SE reads: -p 8 --phred64 --sensitive -I 1 -X 1000
The FPKM is calculated by RSEM, which is the quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model, including the modeling of paired-end (PE) and variable-length reads, fragment length distributions, and quality scores, to determine which transcripts are isoforms of the same gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: cSCC

growth_protocol: A431s were cultured in spheroid medium for spheroid formation

extract_protocol:
RNA was harvested using Trizol reagent. First Strand cDNA Synthesis Kit (04 896 866 001, Roche) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A431s were transfected with control and sgRNA targeting miR-22

tag: cell type

value: skin squamous cell carcinoma

value: sgRNA targeting miR-22


title: ESC_MEF- H1 iCas9 c4-T8-A

description: gRNA amplicon

value: MEFs


title: mdx [GRL16021-D1]

tag: genotype/variation

value: mdx-/-


title: ESC_MEF- H1 iCas9 c4-T4-C

description: gRNA amplicon


title: control.C13.rep1

value: no injection

value: control


title: ESC_MEF- H1 iCas9 c4-T4-B

description: gRNA amplicon


title: control.C12.rep3


title: A431_Control2

value: control sgRNA


title: ESC_MEF- H1 iCas9 c4-T12-Oct4 low-A

description: gRNA amplicon


title: A431_Case1


title: mdx [GRL16022-D2]


title: ESC_MEF- H1 iCas9 c4-T4-A

description: gRNA amplicon


title: ESC_MEF- H1 iCas9 c4-T8-C

description: gRNA amplicon


title: Control [GRL16017-C1]


title: control.C12.rep2


title: A431_Control1


title: ESC_MEF- H1 iCas9 c4-T0

description: gRNA amplicon


title: control.C12.rep1


title: HeLa-S3 cells, CTCF ChIP-seq (BHLHE40 shRNA, rep2)

status: Public on Aug 14 2020

city: guangzhou

first: gongcheng

last: Hu

state: guangdong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
ChIP-seq raw reads were first assessed with FastQC tool and trimmed with trim galore if  they contained adaptors.
Reads were aligned to hg19 genome using bowtie2 with parameters "--very-sensitive --end-to-end --no-unal". Any reads overlapped with hg19 blacklist regions were removed using bedtools. Proper-aligned and high-quality (MAPQ >30) reads were extracted using samtools. Duplicated reads were removed using Picard tools.
Peaks were called using MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak files were generated from MACS2. Normalized bigwig files were generated by using bamCoverage with parameter "--normalizeUsing RPGC".

source_name: Human cervical carcinoma cell line

growth_protocol: HeLa-S3  cells were cultured in DMEM (Hyclone) supplemented with 10% fetal bovine serum. Cultured cells were maintained at 37°C in a 5% CO2 incubator.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: HeLa-S3 cells were infected with lentivirus, and 48h after infection, puromycin (2μg.ml-1) was added to the medium to select positively infected cells.

value: HeLa-S3 cells

tag: chip antibody

value: CTCF(Active motif, 61311)


title: HeLa-S3 cells, CTCF ChIP-seq (control shRNA, rep2)


title: CTCF_shcontrol_HiChIP_rep2

data_processing:
CTCF HiChIP replicates were combined. Paired-end HiChIP raw data were subjected to Trim Galore to remove adaptors. Trimmed reads were aligned to the hg19 genome using the HiC-Pro software, with default settings except that reads were assigned to MboI restriction fragments.
Valid reads from HiC-Pro results were further processed to call loops with hichipper.
Genome_build: hg19
Supplementary_files_format_and_content: Mango correction were performed with CTCF loops and loops with FDR <0.05 were kept.

growth_protocol: HeLa-S3  cells were cultured in DMEM (Hyclone) supplemented with 10% fetal bovine serum. The cells were maintained at 37°C in a 5% CO2 incubator.

extract_protocol:
In brief, up to 15 million crosslinked cells were resuspended in 500 μl of ice-cold Hi-C lysis buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 0.2% NP-40, 1 × Roche protease inhibitors) twice. The nuclei pellet was resuspended in 100 μl of 0.5% SDS and incubated at 62°C for 10 min with no shaking or rotation and then the reaction was quenched with Triton X-100 at 37°C for 15 min. Mbo I restriction enzyme (NEB, R0147) were added at 37°C for 2 hr to digest the nuclei, and heat inactivated at 62°C for 20 min. After filling in the restriction fragment overhangs and marking the DNA ends with biotin, in situ contact was generated with proximity ligation. The nuclei with in situ generated contacts were pelleted at 2,500 × g for 5 min at room temperature and nuclear pellet was resuspended in nuclear lysis buffer (50 mM Tris (pH7.5), 10 mM EDTA, 1% SDS, 1 × Roche protease inhibitor) for sonication and clarified by centrifugation at 16,100 × g at 4°C for 15 min. Clarified samples were transferred to a new tube and diluted with ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris (pH 7.5), 167 mM NaCl) for ChIP procedures. ChIPed DNA was quantified by Qubit (Thermo Fisher) to estimate the amount of Tn5 (Illumina) needed to generate libraries at the correct size distribution. 150 ng of ChIPed DNA was taken into the biotin capture step and tagmented with Tn5.
Tagmented DNA containing beads was PCR amplified and size selected with AMPure XP beads (Beckman). After size selection, libraries were quantified with qPCR against Illumina primers and/or bioanalyzer. Libraries were paired-end sequenced with read lengths of 150.

tag: genotype

value: control shRNA


title: CTCF_shBHLHE40_HiChIP_rep2

value: BHLHE40 shRNA


title: HeLa-S3 cells, Control shRNA_RNA-Seq_rep2

data_processing:
Raw reads were firstly trimmed adaptors and low quality reads using Trim Galore, then mapped to human female genome (hg19 sourced from UCSC genome browser) using STAR (v2.5.2a).
Gene expression levels were quantified as read counts generated by RSEM (v1.2.22) with default settings. Raw tag counts were normalized for GC content using EDASeq (v2.8.0)
Genome_build: hg19
Supplementary_files_format_and_content: Tsv file generated from normalized RNAseq data.

extract_protocol:
Total RNA was extracted from cells by using TriZol, and purified with an RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HeLa-S3 cells were infected with lentivirus. 48 hr after infection, puromycin (2μg.ml-1) was added to the medium to select the positively infected cells.


title: HeLa-S3 cells, Control shRNA_RNA-Seq_rep1


title: HeLa-S3 cells, CTCF_shBHLHE40_HiChIP

value: CTCF (Active motif, 61311)


title: HeLa-S3 cells, BIOTIN ChIP-seq for Biotin tagged BHLHE40

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Biotin-tagged BHLHE40

value: Dynabeads M-280 Streptavidin  (Thermo Fisher Scientific, cat. no.11205D)


title: HeLa-S3 cells, CTCF_shcontrol_HiChIP


title: HeLa-S3 cells, BHLHE40 ChIP-seq (BHLHE40 shRNA, rep2)


title: HeLa-S3 cells, BHLHE40 ChIP-seq (control shRNA, rep2)


title: HeLa-S3 cells, BHLHE40 ChIP-seq (control shRNA, rep1)


title: miR-133b-/- [GRL16025-M1]


title: HeLa-S3 cells, BHLHE40 shRNA_RNA-Seq_rep1


title: HeLa-S3 cells, BHLHE40 ChIP-seq (BHLHE40 shRNA, rep1)


title: HeLa-S3 cells, CTCF ChIP-seq (control shRNA, rep1)


title: HeLa-S3 cells, CTCF ChIP-seq (BHLHE40 shRNA, rep1)


title: Control_2

first: Shuo

last: Chen

state: California

address: 2250 Alcazar Street, Clinical Science Annex, Room 103, CLINICAL SCIENCE ANNEX ROOM 103

institute: Center for Craniofacial Molecular Biology, University of Southern California

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome and transcriptome using STAR 2.6.1d, and normalized
Lognormal with shrinkage mean value were calculated using Gene-specific analysis by Partek flow (Partek Inc., USA).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-delimited text files include lognormal with shrinkage mean value for each feature in individual sample.

source_name: molar

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
RNA isolation with an RNeasy Micro Kit (QIAGEN).
The cDNA library preparation and sequencing were performed at UCLA Technology Center for Genomics & Bioinformatics. Single-end reads with 75 cycles were performed on Illumina Nextseq 500 platform for 3 pairs of samples.

treatment_protocol: Not applicable

tag: strain

value: Wild type

value: 4.5 days

value: Laser capture dissected apical part of furcation


title: Control_1


title: Lhx6-/-_mutant_3


title: Lhx6-/-_mutant_1


title: Control_3


title: Lhx6-/-_mutant_2


title: HeLa-S3 cells, BHLHE40 shRNA_RNA-Seq_rep2


title: FLT3LcDC2_PGPC_F06

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 45 Carleton St.

department: Institute of Medical Engineering and Science

institute: MIT

data_processing:
Following sequencing, runs were demultiplexed using bcl2fastq v2.2
then aligned with HISAT24 against GRCm38 and quantified with RSEM5
generating a gene by sample count matrix further analyzed with Seuratv36 and DESeq27
Genome_build: GRCm38
Supplementary_files_format_and_content: The processed data matrix contains RSEM's expected counts metrics for each sample,  ensemble annotations were mapped to gene symbols using biomaRt and summed when duplicate symbols were found.

source_name: bone marrow

extract_protocol:
RNA was extracted using RNeasy Plus Micro kit
cDNA was produced from isolated RNA with the Smart-Seq2 reverse-transcription protocol as described by Picelli et al.3 with the following modifications: 1) Concentrations of input RNA was normalized to ~2,000 cells-worth of input RNA per reaction. 2) The Superscript II reverse-transcription enzyme was replaced with Superscript III (ThermoFisher, #18080-085) which was applied according to manufacturer's instructions.
Paired-end sequencing libraries were generated from cDNA with the Nextera XT DNA sample Prep Kit (Illumina, #FC-131) according to the manufacturer's instructions. Libraries were pooled at an equimolar ratio and sequenced on a NextSeq500/550 sequencer (Illumina) using a 75 cycle v2.5 sequencing kit with a paired end read structure.

value: PGPC


title: FLT3LcDC2_Nothing_A06

value: Nothing


title: FLT3LcDC2_PGPC_F04


title: HeLa-S3 cells, Input


title: FLT3LcDC2_PGPC_F05


title: FLT3LcDC2_Nothing_A05


title: FLT3LcDC2_LPS_PGPC_C05

value: LPS


title: FLT3LcDC2_Alum_G06

value: Alum


title: FLT3LcDC2_LPS_Alum_E06


title: FLT3LcDC2_LPS_PGPC_C04


title: FLT3LcDC2_Alum_G05


title: FLT3LcDC2_LPS_B04


title: FLT3LcDC1_PGPC_F01


title: FLT3LcDC2_LPS_Alum_E05


title: FLT3LcDC2_LPS_Alum_E04


title: FLT3LcDC2_Alum_G04


title: FLT3LcDC1_PGPC_F03


title: FLT3LcDC2_LPS_B05


title: FLT3LcDC1_Nothing_A03


title: FLT3LcDC1_PGPC_F02


title: FLT3LcDC1_LPS_PGPC_C01


title: FLT3LcDC1_Nothing_A02


title: FLT3LcDC1_LPS_PGPC_C03


title: FLT3LcDC1_Nothing_A01


title: FLT3LcDC2_LPS_B06


title: FLT3LcDC1_LPS_PGPC_C02


title: FLT3LcDC2_Nothing_A04


title: FLT3LcDC1_LPS_Alum_E03


title: FLT3LcDC2_LPS_PGPC_C06


title: FLT3LcDC1_LPS_B03


title: FLT3LcDC1_LPS_Alum_E01


title: FLT3LcDC1_LPS_B02


title: FLT3LcDC1_LPS_B01


title: FLT3LcDC1_Alum_G03


title: FLT3LcDC1_Alum_G02


title: FLT3LcDC1_Alum_G01


title: EWFxr1_1

first: Martin

last: Beaulieu

state: Ontario

address: 1 king's college circle room 4336

department: Pharmacology and Toxicology

data_processing:
The raw sequence data, in the form of FASTQ files, was aligned to the mouse genome (GRCm38, Mus_musculus.GRCm38.84.gtf definition file) using the HISAT2 (v2.1.0)
Accessory programs for the alignment stage include SAMTOOLS (v1.9).
Transcript assembly was done using StringTie (v1.3.4d).
In order to identify differentially expressed genes between groups, the stringtie results were loaded into the ballgown software (2.14.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv file that contains FKPM values of transcripts for all samples

source_name: mPFC neurons

extract_protocol:
RNA was extracted by RiboTag immunoprecipitation
Sample library preparation using Illumina TruSeq Stranded total RNA Sample Preparation kit.

tag: developmental stage

value: adult

value: mPFC

tag: sample type


title: EWFxr1_3


title: EW_3

value: control enforced wake


title: EWFxr1_2


title: S_2

value: control sleep


title: WT2_NT

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome using STAR  v2.4.2a (using options outFilterMismatchNmax 2 and alignEndsType EndToEnd)
Counting proceeded over genes annotated in Ensembl release 83, using htseq-count
Normalization was performed using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file includes the normalized counts

source_name: HeLa WT non treated 2

growth_protocol: Cells were grown using 10% DMEM media

extract_protocol:
RNA samples were extracted using the 5prime RNA extraction kit.
Inhouse poly A based RNA seq

treatment_protocol: Cells were not treated.

value: HeLa

value: Cervical cencer epithelial cells

value: WT

tag: passage


title: EW_2


title: EW_1


title: S_3


title: WT1_NT

source_name: HeLa WT non treated 1


title: WT2_T

source_name: HeLa WT treated 2

treatment_protocol: Cells were treated for 16h with 2nM IFNβ


title: Gsk3D2_3

data_processing:
The raw sequence data, in the form of FASTQ files, was aligned to the mouse genome (GRCm38, Mus_musculus.GRCm38.84.gtf definition file) using the HISAT2 (v2.1.0)
Accessory programs for the alignment stage include SAMTOOLS (v1.9).
Transcript assembly was done using StringTie (v1.3.4d).
In order to identify differentially expressed genes between groups, the stringtie results were loaded into the ballgown software (2.14.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv file that contains FKPM values of transcripts for all 6 samples

source_name: mPFC D2 neurons


title: WT1_T

source_name: HeLa WT treated 1


title: CtrlD2_3

value: control


title: CtrlD2_2


title: FLT3LcDC1_LPS_Alum_E02


title: Gsk3D2_2


title: Gsk3D2_1


title: STAT2_KO_T

source_name: STAT2 KO treated


title: HeLa-S3 cells, Input for Biotin tagged BHLHE40

value: HeLa-S3 cells

value: Biotin-tagged BHLHE40


title: CtrlD2_1


title: STAT1_KO_NT

source_name: STAT1 KO non treated

value: STAT1 -/-


title: STAT1_KO_T

source_name: STAT1 KO treated


title: R2_KO_NT

source_name: IFNAR2 KO non treated


title: S_1


title: PRMT1_NesCre_Cerebellum_(ffCre)_#2

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

description: WT (cerebellum) vs. KO (cerebellum).xlsx

data_processing:
Reads were mapped on mm10 mouse reference genome and quantified using CLC Genomics Workbench version 12.0 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: prmt1 knockout cerebellum

extract_protocol:
Prmt1flox/flox; Nes-Cre mice were generated as previously described (Hashimoto M. et al., J. Biol. Chem. 2016, doi: 10.1074/jbc.M115.684514). Whole brains, cortices or cerebella were frozen in liquid nitrogen and were crushed into powder with a Multi-beads Shocker (Yasui Kikai Co.). Total RNA was extracted using ISOGEN II reagent (Nippon Gene). 500 ng of total RNA were ribosomal RNA-depleted using NEBNext rRNA Depletion Kit (New England Biolabs), and then converted to Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). Reads were mapped on GRCm38 (mm10) mouse reference genome and quantified using CLC Genomics Workbench version 12.0 (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain, Cerebellum

tag: age

value: Postnatal day 0

tag: Sex

value: female

value: prmt1 knockout


title: PRMT1_NesCre_Cerebellum_(ffCre)_#3


title: PRMT1_NesCre_Cerebellum_(ffCre)_#1


title: R2_KO_T

source_name: IFNAR2 KO treated


title: R1_KO_T

source_name: IFNAR1 KO treated


title: PRMT1_NesCre_Cerebellum_(ff-)_#1

source_name: Wild type cerebellum

value: wild type


title: PRMT1_NesCre_Cerebellum_(ff-)_#2


title: PRMT1_NesCre_Cerebellum_(ff-)_#3


title: STAT2_KO_NT

source_name: STAT2 KO non treated


title: KPPC 2

city: philadelphia

first: suraj

last: peri

address: 333 cottman ave

department: biostatistics and bioinformatics

institute: Fox chase cancer center

data_processing: Single-cell RNA-seq data for each replicate were processed using CellRanger 2.1.0 (10x Genomics) to allign and quantify sequencing reads using a mouse reference genome (GRCm38). Individual count tables were merged using CellRanger aggr function. Subsequent data analysis was carried out in R 3.5.1 and the Seurat package (v 3.0.2).

source_name: Pancreatic adenocarcinoma tumor

extract_protocol: For single-cell sequencing, KPPC and KPPCN mice with advanced tumors, 3 of each genotype, were sacrificed 7-8 weeks of age. Single-cell suspensions were isolated from minced tumors using Miltenyi Biotec GentleMacs dissociator in gentleMACS C Tubes (#130-093-23) and mouse tumor tissue dissociation kit (#130-096-730) as per the manufacturer’s instructions. Dead cells were removed by use of Dead Cell removal microbeads (#130-090-101), hematopoeitic cells were depleted by CD45 MicroBeads (#130-052-30). The Chromium controller was used to make single-cell droplet with GEM bead. Single-cell suspensions were converted to barcoded scRNA-seq libraries by using the Chromium Single Cell 3′ Library, Gel Bead & Multiplex Kit and Chip Kit V3 (10X Genomics, #PN-1000092) loading an estimated 6,000 cells per library and following the manufacturer’s instructions. Samples were processed using kits pertaining to the V3 barcoding chemistry of 10x Genomics. For each replicate, all tumor samples were processed in parallel in the same thermal cycler. The final libraries were profiled using the Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies) and quantified using the Qubit 2.0 (Thermal Fisher, #Q32851). Each single-cell RNA-seq library  was sequenced twice in two lanes of HiSeq 4000 (Illumina) to obtain single-end, 98 bp, approximately 500 million reads per library.

value: Pancreatic tumor from 7-8 week old mouse


title: KPPC 3


title: KPPCN 1


title: KPPCN 2


title: PRMT1_NesCre_Cortex_(ff-)_#2

description: WT (cortex) vs. KO (cortex).xlsx

source_name: Wild type cortex

value: Brain, Cortex


title: PRMT1_NesCre_Cortex_(ff-)_#3

description: WT (cortex) vs. KO (cortex).xlsx


title: PRMT1_NesCre_Cortex_(ffCre)_#1

description: WT (cortex) vs. KO (cortex).xlsx

source_name: prmt1 knockout cortex


title: PRMT1_NesCre_Cortex_(ff-)_#1

description: WT (cortex) vs. KO (cortex).xlsx

value: male


title: PRMT1_NesCre_Whole brain_(ffCre)_#3

description: WT (whole brain) vs. KO (whole brain).xlsx

source_name: prmt1 knockout whole brain

value: Whole brain


title: PRMT1_NesCre_Whole brain_(ffCre)_#2


title: PRMT1_NesCre_Whole brain_(ffCre)_#1


title: Glucagon Treatment Lower Band Replicate 2 IP

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Fastq files were trimmed for adapters using cutadapt
Trimmed reads were aligned to the mouse genome build mm10 using STAR aligner
Binding region peaks were identified based on read pileup densities (Clipper)
Reproducible peaks were identified by comparing replicate read pileups along binding regions
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files
Supplementary_files_format_and_content: peak text files

source_name: Glucagon Treatment Lower Band, IP

growth_protocol: Freshly isolated mouse primary hepatocytes were cultured in maintenance medium (high glucose) in 15cm dishes.

extract_protocol:
Cells were subjected to UV cross-linking (254 nm at 400 mJ/cm2) to generate protein-nucleic acid cross-links.
seCLIP-seq

treatment_protocol: Cells were cultured overnight in stravation medium and then stimulated with glucagon (200nM) for 3 hours.

value: Liver

value: Mouse primary hepatocytes

value: Glucagon

tag: rip antibody

value: PGC-1a IP


title: Glucagon Treatment Upper Band Replicate 2 IP

source_name: Glucagon Treatment Upper Band, IP


title: Glucagon Treatment Lower Band Replicate 1 IP


title: Control Upper Band Replicate 2 IP

source_name: Control Upper Band, IP

value: untreated


title: PRMT1_NesCre_Whole brain_(ff-)_#3

source_name: Wild type whole brain


title: Glucagon Treatment Upper Band Replicate 1 IP


title: PRMT1_NesCre_Cortex_(ffCre)_#3

description: WT (cortex) vs. KO (cortex).xlsx


title: PRMT1_NesCre_Whole brain_(ff-)_#2


title: R1_KO_NT

source_name: IFNAR1 KO non treated

value: HeLa

value: Cervical cencer epithelial cells


title: PRMT1_NesCre_Whole brain_(ff-)_#1


title: Control Upper Band  Replicate 1 IP


title: PRMT1_NesCre_Cortex_(ffCre)_#2

description: WT (cortex) vs. KO (cortex).xlsx


title: Control Lower Band Replicate 2 IP

source_name: Control Lower Band, IP


title: KPPC 1


title: Control Lower Band Replicate 1 IP


title: U2OS_ISO_PolII-5SP

city: Ann Arbor

first: Pushpinder

middle: Singh

last: Bawa

state: Michigan

address: 1500 East Medical Center Drive

department: Pathology

institute: University of Michigan

data_processing:
ChIP-Seq reads were aligned to the human reference genome (GRC h38/hg38) with BWA. The SAM file obtained after aliment was converted into BAM format using SAMTools
Using deepTools bamCoverage a coverage file (bigWig format) for each sample was created. The coverage is calculated as the number of reads per bin, where bins are short consecutive counting windows.
While creating the coverage file, the data was normalized with respect to each library size. DeepTools computeMatrix was used to calculate scores per genome regions.
We used PolyASite 2.0 to determine the locations of polyA sites on terminal exons across the human genome. These locations were used as the genome regions while running computeMatrix and calculating scores for each sample across these sites and a 1-kb window up- and downstream from these regions.
To create a profile plot for scores over these polyA sites, we used deepTools plotProfile. The score matrix generated using computeMatrix was the input for plotting the score profile.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig

source_name: U2OS-GFP-DCP1a cell line treated with isotonic media

growth_protocol: Cells were propagated in McCoy’s 5A medium supplemented with 10% fetal bovine serum and Penicillin-Streptomycin (GIBCO, #15140), and were kept under positive selection for GFP-DCP1A expression with 100 μg/mL G418.

extract_protocol:
ChIP-seq experiments were carried out using the HighCell# ChIP-Protein G kit (Diagenode, Cat#:  C01010063) following the manufacturer’s protocol. Chromatin from five million cells was used per ChIP reaction with 6.5 μg of the target protein antibody. In brief, cells were introduced to isotonic (150 mM Na+) or hypertonic (300 mM Na+) conditions for 30 mins, trypsinized in solutions that maintained tonicity and washed twice with 1x PBS (isotonic) or 2 x PBS (hypertonic). This was followed by cross-linking for 12 min in 1% formaldehyde solution in iso or hyper-osmotic PBS (Sigma-Aldrich, Cat#: F8775-25ML). Crosslinking was terminated by the addition of 1/10 volume 1.25 M glycine for 5 min at room temperature. This was followed by cell lysis and sonication (Bioruptor, Diagenode) resulting in an average chromatin fragment size of 200 bp. Fragmented chromatin was used for immunoprecipitation using various antibodies with an overnight incubation at 4 °C. Immunoprecipitated DNA was de-crosslinked and purified using the iPure Kit V2 (Diagenode, Cat#: C03010015) using the manufacturer’s protocol.
Purified DNA was quantified using Qubit-3 (Invitrogen) and 10-100 ng of total DNA was used for library preparation using the KAPA Hyper Prep kit (KAPABiosystems, Cat#: KK8500) as per the protocol. Briefly, DNA was first converted to blunt-ended fragments via end-repair and a single ‘A’ nucleotide was added to fragment ends. This was immediately followed by ligation of Illumina adaptors and PCR amplification (for 9-12 cycles) using Illumina barcoding primers and Phusion DNA polymerase (NEB, Cat# M0530S). PCR products were double size-selected using the KAPA Pure beads (Roche, Cat#: 07983280001) to remove fragments larger than 500 bp (0.65X beads:sample ratio) and primer dimers (0.9X beads:sample ratio). In the end, all libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (paired-end, 50-nucleotide read length) to roughly 30-40 million total reads.

treatment_protocol: Hypertonic medium (300 mM Na+) was prepared by supplementing regular growth medium with 10x PBS such that the appropriate sodium concentration was achieved. Isotonic medium (150 mM Na+) was prepared by mock supplementing regular growth medium with 1x PBS, whose volumes matched that of 10x PBS in hypertonic medium.

value: U2OS-GFP-DCP1a cell line

value: Osteosarcoma

value: isotonic media

value: RNA polymerase II CTD repeat YSPTSPS (phospho S5) Abcam(Cat#:ab5131)


title: Glucagon Treatment Upper Band Replicate 2 Input

source_name: Glucagon Treatment Upper Band, Input


title: U2OS_ISO_PolII-2SP

value: RNA polymerase II CTD repeat YSPTSPS (phospho S2) Abcam(Cat#:ab5095)


title: Glucagon Treatment Lower Band Replicate 2 Input

source_name: Glucagon Treatment Lower Band, Input


title: Glucagon Treatment Upper Band Replicate 1 Input


title: Glucagon Treatment Lower Band Replicate 1 Input


title: Control Upper Band Replicate 2 Input

source_name: Control Upper Band, Input


title: U2OS_ISO_CPSF6

value: CPSF6 Abcam (Cat#:ab175237)


title: Control Lower Band Replicate 2 Input

source_name: Control Lower Band, Input


title: U2OS_ISO_IgG

value: Normal Rabbit IgG Millipore EMD(Cat#:12-370)


title: U2OS_ISO_CPSF73

value: CPSF73 Abcam (Cat#:ab72295)


title: U2OS_HYPER_PolII-5SP

source_name: U2OS-GFP-DCP1a cell line treated with hypertonic media

value: hypertonic media


title: Control Upper Band  Replicate 1 Input


title: U2OS_HYPER_PolII-2SP


title: U2OS_ISO_CPSF1

value: CPSF1 Abcam (Cat#:ab81552)


title: Control Lower Band Replicate 1 Input

value: Liver


title: U2OS_HYPER_CPSF73


title: Cop1 KO rep2

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech

data_processing:
Illumina v1.8 software used for basecalling
Single-cell RNA sequencing data were processed with our in-house pipeline. Briefly, reads were first demultiplexed followed by alignment to mouse reference genome (GRCm38) using GSNAP (version 2013-11-10). A gene-barcode matrix was then generated for each sample. Samples were filtered to remove cells that are either empty droplets or possible doublets/multiplets and if cells had higher percentage of reads mapping to mitochondrial genome. (For both genotypes: cells were included if the number of unique genes detected per cell were between 500 and 3000 and percentage of mitochondrial reads < 0.01%).
After filtering, we detected 918 and 2139 cells in two replicates of Cop1 WT sample and 2446 and 1217 cells in two replicates of Cop1 KO samples.. After scaling and normalizing the data, we performed linear dimensionality reduction using PCA. We ranked the principle components (PCs) by the amount of variance explained by each and found that after the first 15 PCs the explained variance plateaus. To visualize the data in two-dimensional space, Uniform Manifold Approximation and Projection (UMAP) was performed using the first 15 PCs. We then used the UMAP dimensions to determine the nearest neighbor of each cell and perform clustering. All the downstream analysis described above was performed using Seurat v3.0.3 R package (Stuart et al., 2019). Cell type annotation was performed using an unbiased gene marker analysis. We performed differential expression analysis comparing one cluster with all other cells. For a given cluster, genes with adjusted p-value less than 0.05 and log fold change of 0.25 or more were considered as markers for that cluster. Cell type annotation for myeloid cells in the brain was derived from a previous publication (Friedman et al., 2018)
Genome_build: mm10

source_name: brain

extract_protocol:
Microglia were isolated from Copwt/wt Cx3Cr1-CreERT2-eYFP and Copfl/fl Cx3Cr1-CreERT2-eYFP mouse forebrains and quality controlled as previously described (Srinivasan et al., 2016). All steps were carried out at 4°C. Briefly, after perfusion with ice-cold PBS, cortex and hippocampi were dissected and triturated at single cell suspension. After obtaining the cell pellet post Percoll gradient step, cells were washed and resuspended in 4 ml Hibernate A-LF (BrainBits) and stained with Calcein Blue, AM (C1429, ThermoFisher), which served as a viability probe. Filtered cells were then FACS sorted, using eYFP as a microglia marker in addition to Calcein Blue as a viability probe. Animals were always processed in pairs (1 Copwt/wt Cx3Cr1-CreERT2-eYFP and 1 Copfl/fl Cx3Cr1-CreERT2-eYFP) and sorted simultaneously in two BD FACS ARIA sorters. Microglia (Calcein Blue+, eYFP+) were collected directly in 350 μl RNA lysis buffer (RLT buffer from the Qiagen RNeasy Mini kit) and processed for RNA extraction
Sample processing for single-cell RNA-sequencing was done using Chromium Single Cell 3’ Library and Gel bead kit v2 (PN-120237) following manufacturer’s user guide (CG00052, 10x Genomics, Pleasanton, CA). The cell density and viability of the single-cell suspension were determined by Vi-CELL XR cell counter (Beckman Coulter, Pasadena, CA). All of the samples had >80% viable cells. The total cell density was used to impute the volume of single cell suspension needed in the reverse transcription (RT) master mix, aiming to achieve ~ 6,000 cells per sample. cDNAs and libraries were prepared following manufacturer’s user guide (10x Genomics). cDNA amplification and indexed libraries were prepared using 12 and 14 cycles of PCR, respectively. Libraries were profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, Santa Clara, CA) and quantified using Kapa Library Quantification Kit (Kapa Biosystems, Wilmington, MA). Each library was sequenced in one lane of HiSeq4000 (Illumina, San Diego, CA) to achieve ~300 million reads following manufacturer’s sequencing specification (10x Genomics). A balanced design was used for the experiment, where each genotype (Cop1wt/wt and Cop1fl/fl) had cells from one male and one female mouse.

tag: background

value: 6-8 weeks

value: Cop1 KO


title: U2OS_HYPER_CPSF1


title: U2OS_HYPER_IgG


title: SAM24355940 Brain COP1KO

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

source_name: microglia - in vivo, aged mice

extract_protocol:
Total RNA was extracted using a RNeasy kit with on-column DNase digestion (Qiagen)
and 0.5ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina).
The libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million
single end 50 bp reads.

value: Brain


title: Cop1 KO rep1


title: Cop1 WT rep2

value: wild type


title: U2OS-GFP-Dcp1a_Treatment2

data_processing:
Strand-specific paired-end reads were then inspected for sequencing and data quality (for example, insert size, sequencing adaptor contamination, rRNA content, sequencing error rate).
Libraries passing quality control were trimmed of sequencing adaptors and aligned to the human reference genome, GRCh38. Sample were demultiplexed into paired end reads using Illumina's bcl2fastq conversion software v2.20.
Reads were mapped onto hg38 human reference genome using TopHat2. First the reference genome was indexed using bowtie2- build.
Paired end reads were then aligned to the reference genome using TopHat2 with strand specificity and allowing only for the best match for each read.
Aligned file was used to calculate strand specific read count for each gene using bedtools multicov with -s option.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw read count

source_name: U2OS-GFP-DCP1a cell line treated with hypertonic media - Replicate 2

extract_protocol:
Cells were treated with isotinic medium, hypertonic medium or resuced with isotonic medium after hypertonic treatment. Cells were harvested by scraping in RIPA buffer (Thermo-Fisher, PI89900). Total RNA was then extracted with QIAGEN RNeasy midi kit (Cat. No. 75144).
RiboErase
Beginning with at least 5 μg of total RNA, we first applied the Ribo-Zero rRNA Removal Kit (Illumina) to remove ribosomal RNA, and then proceeded with fragmentation, first- and second-strand synthesis, end repair, A-tailing, adaptor ligation, size selection, and uridine digestion. RNA integrity was measured on an Agilent 2100 Bioanalyzer using RNA Nano reagents (Agilent Technologies). Each sample was sequenced in duplicates using the Illumina HiSeq 2000 (with a 100-nt read length).


title: U2OS-GFP-Dcp1a_Rescue2

source_name: U2OS-GFP-DCP1a cell line treated with hypertonic media followed by rescue in isotonic media - Replicate 2


title: SAM24355936 Brain WT

value: WT


title: Cop1 WT rep1


title: U2OS-GFP-Dcp1a_Treatment1

source_name: U2OS-GFP-DCP1a cell line treated with hypertonic media - Replicate 1


title: SAM24355941 Brain COP1KO


title: SAM24355938 Brain WT


title: SAM24355937 Brain WT


title: U2OS-GFP-Dcp1a_Rescue1

source_name: U2OS-GFP-DCP1a cell line treated with hypertonic media followed by rescue in isotonic media - Replicate 1


title: SAM24335241 Brain WT

source_name: microglia - in vivo


title: SAM24355939 Brain COP1KO


title: Till_dCAR 14day

city: Beijing

first: Wang

last: Yao

address: No. 28, fuxing street

institute: Chinese general PLA hospital

data_processing:
base calling; bcl2fastq  v2.2.0;
cut adapter; cutadapt v1.15; cutadapt -a AGATCGGAAGAGC -A AGATCGGAAGAGC -m $length -o ${samplename}_1.cutadapt.fq.gz -p ${samplename}_2.cutadapt.fq.gz $read1 $read2
data quality control; fastqc v0.11.5; fastx_toolkit v0.0.14; fastqc -f fastq $read1 -o $outdir;  fastx_quality_stats -i $samplename.1.fastq -o $samplename.1_quality_stat.txt
mapping; STAR  v2.6.1a; "STAR --runThreadN $starThreads --outSAMattributes All --genomeLoad LoadAndKeep --genomeDir $refSTAR --readFilesIn $read1 $read2 --readFilesCommand zcat"
rebuild index; STAR  v2.6.1a; samtools v1.7; star --genomeDir ./ --runMode genomeGenerate --genomeFastaFiles $reffasta --sjdbFileChrStartEnd SJ.out.tab.* --sjdbOverhang `expr $readlength - 1` --runThreadN $starThreads;   samtools index $samplename\_Aligned.sortedByCoord.out.bam
remapping using new genome; STAR  v2.6.1a; star --runThreadN $starThreads --outSAMattributes All --genomeLoad LoadAndKeep --genomeDir ../GenomeForPass2 --readFilesIn $read1 $read2 --outFileNamePrefix ${samplename}_ --chimSegmentMin 20 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --limitBAMsortRAM 200000000000
assemble; StingTie v1.3.3b; stringtie -p $thread -G $refgtf -o $samplename.gtf -l $samplename $bamfile
Genome_build: Homo_sapiens.GRCh38.94
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: T cell

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were collected from patients by leukapheresis. Primary T cells derived from the PBMCs were activated using Dynabeads Human T-Activator CD3/CD28 magnetic beads (Invitrogen) at a 1:1 bead:cell ratio and cultured in X-VIVO 15 medium (Lonza) supplemented with 300 U/ml recombinant human IL-2 (PeproTech). After 2 days, RetroNectin-coated plates (Takara) were loaded with viral supernatants by centrifuging the plates at 2,000 g for 2 h at 32 °C. Activated T cells were added to the plates and centrifuged at 800 g for 10 min, and Polybrene (Sigma) was added to increase infection efficiency. The following day, the transduced cells were collected and transferred to new flasks for further expansion. The Dynabeads were magnetically removed 2 days after initiating T cell transduction, and the cells were cultured at 106 cells per ml in X-VIVO 15 medium supplemented with 300 IU/mL IL-2, with fresh IL-2-containing medium added every 2 days until the cells were harvested on days 8-10.

extract_protocol:
T cells were resuspended in 250ul PBS and placed in 750ul TRIzol LS (Invitrogen). RNA was extracted using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol. Total RNA integrity was checked using the Bioptic Qsep100 (BIOptic) and quantified using a Synergy H1 (BioTek).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: dCAR and CAR T cells were cocultured with Raji cells for 24 h, followed by magnetic selection of CD3+ cells (Miltenyi Biotec).

value: T cell

value: CAR T cell treatment by DNMTi inhibitor collected from tumor site after 14days of cell infusion in vivo


title: Till_CAR 14day

value: Control CAR T cell collected from tumor site after 14days of cell infusion in vivo


title: Till_dCAR 7day

value: CAR T cell treatment by DNMTi inhibitor collected from tumor site after 7day of cell infusion in vivo


title: Till_CAR 7day

value: Control CAR T cell collected from tumor site after 7day of cell infusion in vivo


title: SAM24335245 Brain LoxP

value: LoxP (Cop1 KO microglia)


title: dCAR 2_A

value: CAR T treatment by DNMTi inhibitor coculture with Raij


title: SAM24335242 Brain WT


title: SAM24335240 Brain WT


title: U2OS_HYPER_CPSF6

value: U2OS-GFP-DCP1a cell line

value: Osteosarcoma

value: CPSF6 Abcam (Cat#:ab175237)


title: U2OS-GFP-Dcp1a_Mock2

source_name: U2OS-GFP-DCP1a cell line treated with isotonic media - Replicate 2

value: isotonic media


title: SAM24335244 Brain LoxP


title: CAR 2_A

value: Control CAR after coculture with Raij


title: dCAR 1_A


title: U2OS-GFP-Dcp1a_Mock1

source_name: U2OS-GFP-DCP1a cell line treated with isotonic media - Replicate 1


title: SAM24335239 Brain WT


title: SAM24335246 Brain LoxP


title: CAR 1_A


title: SAM24335243 Brain LoxP


title: dCAR 2

value: CAR T treatment by DNMTi inhibitor


title: dCAR 1


title: SAM24321925 Brain Loxp_untreated

source_name: microglia - in vitro

value: Loxp_untreated (Cop1 KO microglia)


title: CAR 1

value: Control CAR


title: CAR 2


title: 9 HBVPs

city: Guangzhou

first: Weiqiang

last: Li

address: Zhongshan Road 2

institute: Sun Yat-sen university

description: stable cell line

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were filtered those adaptor comtiminated, unpaired, contains N , and  then mapped to hg19 whole genome using tophat 2.0.2 with default parameters
Reads count were calculated by htseq-count(Htseq Frame work v 0.6.0) with parameters  -s no
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell C, Nat. Biotechnol. 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragment falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each sample, each column represents it's expression across all genes whihe each raw show gene abundence in al samples …

source_name: primary human brain vascular pericytes (from ScienCell Research Laboratories)

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions.
RNA sequencing libraries were constructed using the Illumina mRNA-seq Prep Kit as recommended by the manufacturer. The fragmented and randomly primed 150 bp paired-end libraries were sequenced using Illumina HiSeq 2000.

value: HBVPs


title: SAM24321922 Brain WT_LPS

value: Brain


title: SAM24321926 Brain Loxp_untreated


title: 8 H9-NCSC-PCs 2w

description: stable cell line

source_name: H9-NCSC-derived pericytes (differentiation for 2 weeks)

value: H9-NCSC-PCs 2w


title: 6 hiPSC-NCSC-PCs 2w

description: stable cell line

source_name: hiPSC-NCSC-derived pericytes (differentiation for 2 weeks)

value: hiPSC-NCSC-PCs 2w


title: 7 H9-NCSC-PCs 1w

description: stable cell line

source_name: H9-NCSC-derived pericytes (differentiation for 1 week)

value: H9-NCSC-PCs 1w


title: 5 hiPSC-NCSC-PCs 1w

description: stable cell line

source_name: hiPSC-NCSC-derived pericytes (differentiation for 1 week)

value: hiPSC-NCSC-PCs 1w


title: 4 H9-NCSCs

description: stable cell line

source_name: H9-derived neural crest stem cells


title: SAM24321920 Brain WT_untreated


title: DDX5KO Colon rep1

city: San Diego

first: Wendy

last: Huang

address: 9500 Gilman Drive #0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

description:
Epithelial knockout of DDX5
healthy_colon.txt

data_processing:
Sequenced reads were mapped to mm10 using STAR v2.6.1a with parameters "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000".
Uniquely mapped reads overlapping with the exons were counted using featureCounts for each gene in GENCODE.vM19 annotation.
Differential expression analysis were performed by DESeq2(v1.18.1) package
Genome_build: MM10
Supplementary_files_format_and_content: tab-delimited text files include raw counts, normalized counts values log2FoldChange and pvalue for each gene

source_name: Healthy Colon

growth_protocol: Healthy epithelial cells were harvested from small intestine of 8wk adult mice using 5 mM EDTA in PBS containing 1 mM of DTT for 20 min at 37°C. Tumor tissues were excised from large intestine-colon from each mice and processed for total RNA.

extract_protocol:
RNA was harvested using Qiagen Rneasy kit
Ribodepleted RNA Stranded

treatment_protocol: N/A for healthy epithelial cells. To obtain large intestine-colon tumors, mice were injected with Tamoxifen 3 times on day 1, 2, 3 by i.p with 100 ul of tamoxifen at 20 mg/ml in 5% EtOH and 95% corn oil. Tumor tissues were harvested on Day 30, 33, 37 post tamoxifen injection

value: DDX5(fl/fl), Vil1Cre(+)

tag: tissue

value: Large intestine-colon

value: EDTA fractionation


title: 3 hiPSC-NCSCs

description: stable cell line

source_name: hiPSC-derived neural crest stem cells

value: hiPSC-NCSCs


title: WT Colon rep1

description:
wild type
healthy_colon.txt


title: DDX5KO Ileum rep2

description:
Epithelial knockout of DDX5
healthy_Ileum.txt

source_name: Healthy Ileum

value: Small intestine_Ileum


title: WT Colon rep2

description:
wild type
healthy_colon.txt


title: 2 H9

description: stable cell line

source_name: undifferentiated H9 human embryonic stem cells


title: DDX5KO Ileum rep1


title: 1 hiPSC

description: stable cell line

source_name: undifferentiated human induced pluripotent stem cells

value: hiPSC


title: WT Ileum rep2

description:
wild type
healthy_Ileum.txt


title: WT Ileum rep1

description:
wild type
healthy_Ileum.txt


title: SAM24321921 Brain WT_LPS


title: SAM24321919 Brain WT_untreated


title: DDX5KO Colon rep2


title: S108

city: Cleveland

first: Rafick

last: Pierre-Sekaly

state: OH

address: 2103 Cornell Avenue

institute: Case Western Reserve University

data_processing:
Raw reads were trimmed for low quality reads and miscalled nucleotides using Trimmomatic v. 0.36.
Reads that passed the trimming step were aligned to rhesus macaque genome (Ensembl Mmul_8.0.1 release 88) using the STAR aligner (version 2.5.3a).
Aligned reads were counted using HTSeq (version 0.9.1).
Genome_build: Ensembl Mmul_8.0.1 release 88.
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample.

organism: Macaca mulatta

source_name: blood

extract_protocol:
RNA was extracted from PAXgene samples using the PAXgene Blood RNA kit (PreAnalytiX) according to the manufacturer’s instructions.
GLOBINclear kit (Ambion, Austin, TX, USA) was used to remove globin transcript. Libraries were loaded on Illumina Truseq Paired-End stranded mRNA Kits and sequenced in 2 x 51 base paired-end runs on an Illumina HiSeq 2500 sequencer with an average of 20 million reads per sample.

tag: collection

value: paxgene

tag: animal id

tag: boost timepoint

tag: quartile designation

tag: siv status

value: SIVneg


title: S110


title: S111


title: S107


title: LIneA 12 Blood BBA-seq

city: Changchun

first: Yang

last: Han

address: Xi'an road 5333, Jilin University Heping Campus, Changchun, China

institute: Jilin University

data_processing:
Library strategy: barcoded bisulfite amplicon sequencing (BBA-seq)
Fastq files were subjected to adaptor trimming by TrimGalore
FastQC were subsequently applied for quality checking of Fastq files.
To estimate DNAm levels for each CpG based on BBA-seq data we used the Bismark tool
Genome_build: hg19
Supplementary_files_format_and_content: Text files list the beta values for all the targeted CpGs

source_name: Peripheral  blood

extract_protocol:
Genomic DNA was isolated from peripheral blood with the QIAamp DNA Mini Kit (Qiagen),or from buccal swab with NucleoSpin Tissue Kit (Macherey-Nagel). Then was bisulfite converted by the EZ DNA Methylation Kit (Zymo)
10 pM DNA library was diluted with 15% PhiX spike-in control and eventually subjected to 250 bp pair-end sequencing on a MiSeq lane (Illunima, CA, USA) using Miseq reagent V2 Nano kit (Illumina).

value: Peripheral  blood

tag: age (week)

tag: gender

value: f

tag: disease state

value: Healthy


title: LIneA 11 Blood BBA-seq


title: S106


title: LIneA 9 Blood BBA-seq


title: LIneA 8 Blood BBA-seq


title: LIneA 10 Blood BBA-seq


title: LIneA 13 Blood BBA-seq


title: LIneA 14 Blood BBA-seq


title: S105


title: S104


title: LIneA 5 Blood BBA-seq


title: S103


title: LIneA 15 Blood BBA-seq


title: S102


title: LIneA 4 Blood BBA-seq

value: m


title: LIneA 3 Blood BBA-seq


title: LIneA 6 Blood BBA-seq


title: S101


title: S98


title: LIneA 2 Blood BBA-seq


title: S109


title: LIneA 1 Blood BBA-seq


title: S99


title: DBA 33 Blood BBA-seq


title: S96


title: S100


title: DBA 31 Blood BBA-seq


title: LIneA 7 Blood BBA-seq


title: S97


title: S95


title: S93


title: DBA 32 Blood BBA-seq


title: S92


title: DBA 26 Blood BBA-seq


title: DBA 28 Blood BBA-seq


title: DBA 30 Blood BBA-seq


title: S94


title: DBA 27 Blood BBA-seq


title: S91


title: S90


title: DBA 24 Blood BBA-seq


title: S88


title: DBA 25 Blood BBA-seq


title: S89


title: DBA 23 Blood BBA-seq


title: S87


title: DBA 22 Blood BBA-seq


title: DBA 21 Blood BBA-seq


title: S85


title: DBA 20 Blood BBA-seq


title: DBA 19 Blood BBA-seq


title: DBA 29 Blood BBA-seq


title: S84


title: DBA 17 Blood BBA-seq


title: S82


title: DBA 16 Blood BBA-seq


title: S83


title: S80


title: DBA 18 Blood BBA-seq


title: DBA 15 Blood BBA-seq


title: DBA 13 Blood BBA-seq


title: S78


title: S79


title: S81


title: DBA 12 Blood BBA-seq


title: DBA 11 Blood BBA-seq


title: S76


title: S86


title: S75


title: DBA 10 Blood BBA-seq


title: S72


title: S77


title: DBA 7 Blood BBA-seq


title: DBA 9 Blood BBA-seq


title: S63


title: S73


title: S74


title: DBA 8 Blood BBA-seq


title: DBA 6 Blood BBA-seq


title: S61


title: DBA 5 Blood BBA-seq


title: DBA 4 Blood BBA-seq


title: S60


title: S59


title: DBA 14 Blood BBA-seq


title: DBA 1 Blood BBA-seq


title: S62


title: B6 validation 39 Blood BBA-seq


title: S56


title: B6 validation 40 Blood BBA-seq


title: S58


title: S57


title: B6 validation 38 Blood BBA-seq


title: B6 validation 37 Blood BBA-seq


title: S44


title: S46


title: B6 validation 36 Blood BBA-seq


title: S42


title: B6 validation 34 Blood BBA-seq


title: S41


title: B6 validation 33 Blood BBA-seq


title: S40


title: B6 validation 32 Blood BBA-seq


title: S39


title: DBA 2 Blood BBA-seq


title: B6 validation 31 Blood BBA-seq


title: S38


title: DBA 3 Blood BBA-seq


title: S47


title: B6 validation 30 Blood BBA-seq


title: B6 validation 29 Blood BBA-seq


title: S37


title: B6 validation 27 Blood BBA-seq


title: B6 validation 28 Blood BBA-seq


title: S36


title: S35


title: S34


title: S33


title: S43


title: B6 validation 35 Blood BBA-seq


title: S31

value: preBoost


title: S25


title: B6 validation 22 Blood BBA-seq


title: B6 validation 21 Blood BBA-seq


title: S24


title: S23


title: B6 validation 20 Blood BBA-seq


title: S22


title: B6 validation 19 Blood BBA-seq


title: S21


title: S20


title: B6 validation 17 Blood BBA-seq


title: S18


title: B6 validation 26 Blood BBA-seq


title: B6 validation 16 Blood BBA-seq


title: B6 validation 15 Blood BBA-seq


title: S16


title: S32


title: S15


title: B6 validation 23 Blood BBA-seq


title: S17


title: B6 validation 12 Blood BBA-seq


title: S19


title: B6 validation 11 Blood BBA-seq


title: B6 validation 14 Blood BBA-seq


title: B6 validation 9 Blood BBA-seq


title: B6 validation 18 Blood BBA-seq


title: S13


title: S9


title: S12


title: S11


title: B6 validation 25 Blood BBA-seq


title: S10


title: S14


title: B6 validation 5 Blood BBA-seq


title: B6 validation 4 Blood BBA-seq


title: B6 validation 6 Blood BBA-seq


title: B6 validation 3 Blood BBA-seq


title: S6


title: S8


title: S7


title: S5


title: S4


title: B6 validation 1 Blood BBA-seq


title: B6 validation 2 Blood BBA-seq


title: B6 validation 10 Blood BBA-seq


title: S3


title: B6 training 23 Blood BBA-seq


title: S2


title: B6 validation 7 Blood BBA-seq


title: B6 validation 8 Blood BBA-seq


title: B6 training 22 Blood BBA-seq


title: B6 training 21 Blood BBA-seq


title: S1


title: B6 training 20 Blood BBA-seq


title: 26SrRNA_eri1(mg366)_cde1(tm936)_GFPNRDE3_L

city: Hefei

first: Shouhong

last: Guang

state: Anhui

address: 443 HuangShan Road

department: School of Life Sciences

institute: University of Science & Technology of China

data_processing:
Library strategy: 26S PCR product deep sequencing
The Illumina-generated raw reads were first filtered to remove adaptors, low quality tags as well as contaminants to get clean reads at BGI Shenzhen. Clean reads ranging from 17 to 30 nt were mapped to the C. elegans genome and the transcriptome assembly WS243, respectively, using Bowtie2 with default parameters (Langmead and Salzberg Nat Methods 9: 357-359. (2012)). The number of reads targeting each gene was counted by custom Perl scripts and displayed by IGV (Thorvaldsdottir et al. Brief Bioinform 14: 178-192. (2013)). Total mappable reads excluding sense rRNA were used for normalization.
gel purified and then deep sequenced using an Illumina platform, according to the manufacturer′s instructions, by Novogene (Beijing, China). The number of reads with distinct 3′ -end modifications were counted by custom Perl scripts.
Genome_build: WS243
Supplementary_files_format_and_content: .txt files.located in /count content. Basically, the reads were aligned to C. elegans transcriptome WS243 version by Bowtie2 and counted the number of reads targeting each transcript by Perl script.

organism: Caenorhabditis elegans

source_name: L3 stage

growth_protocol: C. elegans strains were cultured on RNAi plates with E. coli HT115 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm concentrated HT115 plate (approximately 3000 L1s per plate).

extract_protocol:
total RNA were extracted from embryos or L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 30 min.
Briefly, total RNA were extracted from embryos or L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 30 min.
3′ RNA linker: 5′-pGATCCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3′ (the underlined sequence served as a barcode for sample labeling).
The RNAs were reverse transcribed with the following primers:
3′ linker RT: 5′-GCTGGAATTCGCGGTTAAATCCTTGGTGCCCGAGTGTGGATC-3′. The cDNAs were PCR amplified with the primers 26S rRNA-F: 5′-CAGATCACTCTGGTTCAATGTC-3′ and 3′ linker RT primers, gel purified and then deep sequenced using an Illumina platform, according to the manufacturer′s instructions, by Novogene (Beijing, China). The number of reads with distinct 3′ -end modifications were counted by custom Perl scripts.

tag: genotype

tag: temperature

value: 20oC on HT115

tag: antibody

tag: molecule subtype

value: 26S rRNA


title: 26SrRNA_eri1(mg366)_cde1(tm936)_GFPNRDE3_cde1mCHERRY_L


title: B6 training 19 Blood BBA-seq


title: B6 training 17 Blood BBA-seq


title: 26SrRNA_eri1(mg366)_GFPNRDE3_L


title: B6 training 18 Blood BBA-seq


title: 26SrRNA_eri1(mg366)_cde1(tm936)_GFPNRDE3_cde1mCHERRY_E

source_name: embryo stage


title: B6 training 16 Blood BBA-seq


title: B6 training 15 Blood BBA-seq


title: 26SrRNA_eri1(mg366)_GFPNRDE3_E


title: 26SrRNA_eri1(mg366)_cde1(tm936)_GFPNRDE3_E


title: WAGO_IP_small_RNA_cde1(tm936)_GFPWAGO1

data_processing:
The Illumina-generated raw reads were first filtered to remove adaptors, low quality tags as well as contaminants to get clean reads at BGI Shenzhen. Clean reads ranging from 17 to 30 nt were mapped to the C. elegans genome and the transcriptome assembly WS243, respectively, using Bowtie2 with default parameters (Langmead and Salzberg Nat Methods 9: 357-359. (2012)). The number of reads targeting each gene was counted by custom Perl scripts and displayed by IGV (Thorvaldsdottir et al. Brief Bioinform 14: 178-192. (2013)). Total mappable reads excluding sense rRNA were used for normalization.
gel purified and then deep sequenced using an Illumina platform, according to the manufacturer′s instructions, by Novogene (Beijing, China). The number of reads with distinct 3′ -end modifications were counted by custom Perl scripts.
Genome_build: WS243
Supplementary_files_format_and_content: .txt files.located in /count content. Basically, the reads were aligned to C. elegans transcriptome WS243 version by Bowtie2 and counted the number of reads targeting each transcript by Perl script.

source_name: young adult stage

growth_protocol: C. elegans strains were cultured on NGM plates with E. coli OP50 as the food source in a temperature controlled incubator. Worms were maintained at 20°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm NGM concentrated OP50 plate (approximately 3000 L1s per plate).

extract_protocol:
Total small RNAs were isolated from young adult stage worms. Briefly, worms were harvested and dounced on ice with pestle B in TRIzol reagent (Invitrogen) followed by isopropanol precipitation. The precipitates were treated with calf intestinal alkaline phosphatase (CIAP, Invitrogen), re-extracted with TRIzol, and treated with T4 polynucleotide kinase (T4 PNK, New England Biolabs) in the presence of 1 mM ATP.
Small RNAs were cloned and deep sequenced using an Illumina platform, according to the manufacturer's instructions, by  Novogene (Beijing, China). sRNAs ranging from 17 to 30 nt were gel-purified and ligated to a 3’ adaptor (5’-pUCGUAUGCCGUCUUCUGCUUGidT-3’; p, phosphate; idT, inverted deoxythymidine) and a 5’ adaptor (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’). The ligation products were gel-purified, reverse transcribed, and amplified using Illumina’s sRNA primer set (5’-CAAGCAGAAGACG GCATACGA-3’; 5’-AATGATACGGCGACCACCGA-3’). The samples were sequenced using an Illumina Hiseq platform.

value: 20oC on OP50

value: anti-FLAG M2 antibody (Sigma)

value: IPed small RNA


title: B6 training 13 Blood BBA-seq


title: B6 training 14 Blood BBA-seq


title: HRDE1_IP_small_RNA_cde1(tm936)_GFPHRDE1


title: B6 training 12 Blood BBA-seq


title: B6 training 11 Blood BBA-seq


title: HRDE1_IP_small_RNA_GFPHRDE1


title: NRDE3_IP_small_RNA_eri1(mg366)_cde1(tm939)_GFPNRDE3

extract_protocol:
Total small RNAs were isolated from L3 stage worms. Briefly, worms were harvested and dounced on ice with pestle B in TRIzol reagent (Invitrogen) followed by isopropanol precipitation. The precipitates were treated with calf intestinal alkaline phosphatase (CIAP, Invitrogen), re-extracted with TRIzol, and treated with T4 polynucleotide kinase (T4 PNK, New England Biolabs) in the presence of 1 mM ATP.
Small RNAs were cloned and deep sequenced using an Illumina platform, according to the manufacturer's instructions, by  Novogene (Beijing, China). sRNAs ranging from 17 to 30 nt were gel-purified and ligated to a 3’ adaptor (5’-pUCGUAUGCCGUCUUCUGCUUGidT-3’; p, phosphate; idT, inverted deoxythymidine) and a 5’ adaptor (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’). The ligation products were gel-purified, reverse transcribed, and amplified using Illumina’s sRNA primer set (5’-CAAGCAGAAGACG GCATACGA-3’; 5’-AATGATACGGCGACCACCGA-3’). The samples were sequenced using an Illumina Hiseq platform.


title: NRDE3_IP_small_RNA_ eri1(mg366)_GFPNRDE3


title: B6 training 9 Blood BBA-seq


title: NRDE3_IP_small_RNA_ cde-1(tm936)_GFPNRDE3

extract_protocol:
Total small RNAs were isolated from embryo stage worms. Briefly, worms were harvested and dounced on ice with pestle B in TRIzol reagent (Invitrogen) followed by isopropanol precipitation. The precipitates were treated with calf intestinal alkaline phosphatase (CIAP, Invitrogen), re-extracted with TRIzol, and treated with T4 polynucleotide kinase (T4 PNK, New England Biolabs) in the presence of 1 mM ATP.
Small RNAs were cloned and deep sequenced using an Illumina platform, according to the manufacturer's instructions, by  Novogene (Beijing, China). sRNAs ranging from 17 to 30 nt were gel-purified and ligated to a 3’ adaptor (5’-pUCGUAUGCCGUCUUCUGCUUGidT-3’; p, phosphate; idT, inverted deoxythymidine) and a 5’ adaptor (5’-GUUCAGAGUUCUACAGUCCGACGAUC-3’). The ligation products were gel-purified, reverse transcribed, and amplified using Illumina’s sRNA primer set (5’-CAAGCAGAAGACG GCATACGA-3’; 5’-AATGATACGGCGACCACCGA-3’). The samples were sequenced using an Illumina Hiseq platform.


title: B6 training 8 Blood BBA-seq


title: NRDE3_IP_small_RNA_ GFPNRDE3


title: B6 training 6 Blood BBA-seq


title: B6 training 5 Blood BBA-seq


title: B6 training 7 Blood BBA-seq


title: Total_ small_RNA_cde1(tm936)

value: total small RNA


title: B6 training 4 Blood BBA-seq


title: WAGO1_IP_small_RNA_GFPWAGO1


title: set-2 F4 fertile replicate 1

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

data_processing:
TopHat2 was used to align the RNA-seq reads to the C. elegans transcriptome (WS220). Only reads with one unique mapping were allowed, otherwise default arguments were used. Reads mapping to ribosomal RNAs were then removed.
HTSeq was used to obtain read counts per transcript.
Normalization of read counts per transcript and differential expression analysis with no consideration for lineage-dependent relations were done with DESeq2 in R using HTSeq counts. P-values were adjusted for multiple testing using the Benjamini–Hochberg method as implemented in DESeq2.
Genome_build: WS220
Supplementary_files_format_and_content: Text files for each sample with HTSeq counts per transcript (tab delimited). And one text file with DESeq output for normalized read counts per gene for each sample and the differential expression analyses performed (comma delimited).

source_name: dissected gonads from young adults day 1

growth_protocol: C. elegans strains were maintained at 15° or 20° C on OP50 bacteria as described (Brenner 1974). For experiments, set-2 worms were upshifted to 25° C.

extract_protocol:
Total RNA was extracted using Trizol reagent and ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (Cat. #E6310).
Libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina sequencing (Cat. #E7530). Libraries were sequenced at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley using the Illumina HiSeq 2500 or 4000 platforms.

treatment_protocol: Each lineage was initially started from twenty five set-2(bn129)/+ animals grown at 25° C . Subsequent generations of set-2 animals resulting from these 25 worms were assessed for sterility and gonads were isolated at F2 and F4 generations on Day 1 of adulthood. Fertility/sterility was assessed by the presence of progeny and/or eggs in the uterus. Each lineage contains 1 sample of gonads from P0 set-2(bn129)/+ animals, 1 sample of gonads from fertile F2 set-2(bn129) animals, 1 sample of gonads from fertile F4 set-2(bn129) animals and 1 sample of  gonads from sterile F4 set-2 (bn129) animals.

tag: strain


title: B6 training 3 Blood BBA-seq


title: set-2 F4 sterile replicate 1


title: R_deltaXrn1_control_RNAseq

city: Edinburgh

first: Stefan

last: Bresson

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Demultiplexing. Command: pyBarcodeFilter.py -f raw_file.fastq -b barcodes_file.txt
Adapter stripping and quality control. Command: flexbar -r file.fastq -a adapters.txt -ao 4 -m 11 -at RIGHT -u 2 -q TAIL -qf i1.8
Collapsing. Command: pyFastqDuplicateRemover.py -f file.fastq (Note that this step was used only for the CRAC analysis. RNAseq files were not collapsed)
Removal of low-complexity reads. Command: bbduk.sh in=file.fasta entropy=0.5 entropywindow=10 entropyk=6
Alignment. Command: novoalign -f file.fasta -r Random -o SAM -d genome.novoindex
samtools view -bS file.sam
samtools sort file.bam
Bedgraph files (+ strand). Command: bedtools genomecov -split -strand + -ibam sorted_file.bam -bg -scale variable > file_plus_strand.bedgraph
Bedgraph files (- strand). Command: bedtools genomecov -split -strand - -ibam sorted_file.bam -bg -scale variable > file_minus_strand.bedgraph
Read counting. Command: pyReadCounters.py -f file.bam --file_type=bam --sense --gtf=annotation_file.gtf
Genome_build: Saccharomyces cerevisiae EF4.74 with the introns artificially removed to improve mapping
Supplementary_files_format_and_content: The .txt files (generated using pyReadCounters.py) contain information on the number of reads mapping to each transcript. The bedgraph files show the distribution of reads across the genome. Individual replicates were merged into a single file to generate the bedgraph files.

growth_protocol: For CRAC experiments (07-99), cells were cultured in SC -TRP medium containing 2% glucose to 0.4 OD. For the 'control', cells were then subjected to 100 mJ of 254nm UV-crosslinking (4-6 seconds), collected by filtration, resuspended in 50 mL of ice cold PBS, centrifuged to pellet, and frozen at -80°C. For all other conditions,  cells at 0.4 OD were first collected by filtration,  then transferred to the appropriate medium and cultured for either 30 seconds or 16 minutes prior to UV-crosslinking. All subsequent harvesting steps were identical to the control. For RNAseq experiments (A-S), we used the same approach as for CRAC but without the crosslinking step.

extract_protocol: The CRAC protocol is based on Tuck and Tollervey, 2013. Modifications are described in Bresson and Tollervey, 2020.

tag: genotype/variation

tag: cell/ploidy type

value: haploid cells

tag: treatment

value: control


title: Q_deltaSki2_42C_16min_RNAseq


title: P_deltaSki2_control_RNAseq


title: B6 training 1 Blood BBA-seq

tag: tissue


title: B6 training 10 Blood BBA-seq


title: O_wt_42C_CHX_16min_RNAseq

value: wt