title: 16_T0c_LE6

city: Cologne

first: Ludwig

last: Eichinger

address: Joseph-Stelzmann-Str. 52

department: Biochemistry Medical Faculty

institute: Centre for Biochemistry Medical Faculty University of Cologne

description:
ATG16‾ mutant
processed data: FPKM_2.txt

data_processing:
Illumina Casava software used for basecalling.
RNA-Seq data were processed through the QuickNGS analysis pipeline version 1.2.7, based on Ensembl release 33.
Sequenced reads mapped to Dictyostelium_discoideum.
Fragment Per Kilobase of exon per Million (FPKM) were calculated using Cufflinks.
Genome_build: Ensembl Version 33 Dictyostelium_discoideum (http://protists.ensembl.org/Dictyostelium_discoideum/Info/Index)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.

organism: Dictyostelium discoideum

source_name: D. discoideum cells 16_T0c_LE6

growth_protocol: D. discoideum cells were grown to log phase and 1 x 10e7 cells were harvested (500 x g, 5 min, 4°C), followed by two washing steps with 10 ml Soerensen’s phosphate buffer.

extract_protocol:
Total RNA extraction was carried out using the Qiagen RNeasy® Mini Kit according to the manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Total RNA from either vegetative or 3 h starved (in Soerensen’s phosphate buffer) D. discoideum cells was isolated.

tag: strain/background

tag: genotype/variation

tag: condition

value: vegetative


title: control siRNA vehicle 2

status: Public on Jan 15 2019

type: SRA

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

country: USA

institute: ROSWELL PARK CANCER INSTITUTE

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE annotation (p7) using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using HTSeq v0.6.1 using intersect-strict option
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

molecule: total RNA

organism: Homo sapiens

source_name: LNCaP prostate cancer cells

extract_protocol: RNA Libraries are prepared using the Illumina NextSeq RNA Exome protocol and kit reagents.

tag: cell type

value: LNCaP prostate cancer cells

tag: sirna

value: OTPC

tag: treatment

value: ETOH


title: plateA1.positionC3.single.cell

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

country: China

institute: Chinese Academy of Sciences

description:
all.single.cell.gene.counts.txt
A1-C3

data_processing:
Reads were mapped to the mouse GRCm38 genome assemblies by HISAT2 using default settings
Uniquely aligned reads were counted using the ‘htseq-count’ tool of HTSeq
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes counts values for each single cell

organism: Mus musculus

source_name: BASCs-Tracer

extract_protocol:
Lungs were digest with Collagenase, Dispase and Elastase sollution, Single epithelial cell was sorted by BD AriaII. Cell was lysed by single cell RNA lysis buffer containing 0.45% (vol/vol) NP40, followed by reverse transcription using SuperScript II reverse transcriptase (Invitrogen) and whole transcription amplification using KAPA HiFi HotStart ReadyMix (2X; KAPA Biosystems). PCR product was purified using AMPure XP beads (Agencourt) and quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher).
Libraries were constructed using illumina Nextera XT DNA sample preparation kit

tag: tissue

value: Lung

value: epithelial cell

tag: genotype

tag: cell sub-type

value: Club cell


title: 12_T0c_LE6

state: NRW

country: Germany

description:
ATG12‾ mutant
processed data: FPKM_2.txt

source_name: D. discoideum cells 12_T0c_LE6


title: 12_16_T0c_LE6

description:
ATG12‾/16‾ mutant
processed data: FPKM_2.txt

source_name: D. discoideum cells 12_16_T0c_LE6


title: AX2T0c_LE6

description:
AX2 wild-type
processed data: FPKM_2.txt

source_name: D. discoideum cells AX2T0c_LE6

value: wild-type


title: plateA1.positionB3.single.cell

description:
all.single.cell.gene.counts.txt
A1-B3


title: plateA1.positionH2.single.cell

description:
all.single.cell.gene.counts.txt
A1-H2

value: BASCs


title: 12_16_T0b_LE6

source_name: D. discoideum cells 12_16_T0b_LE6


title: Bay Scallop PA-treated Gills

city: nanjing

first: Cheng

last: Chi

address: weigang road

institute: Nanjing Agricultural University

data_processing:
The library preparation and Illumina sequencing were performed by Beijing Genomics Institute (BGI) (Hongkong, China). For cluster generation, the qualified and quantified libraries were firstly amplified within the flow cell on the cBot instrument (HiSeq® 4000 PE Cluster Kit, Illumina). For paired-end sequencing, the clustered flow cell was then loaded onto the HiSeq 4000 Sequencer (HiSeq® 4000 SBS Kit, Illumina) with 100bp which was recommended read lengths.
The resulting sequences assembled using Trinity (version: v2.0.6; parameters: --min_contig_length 150  --CPU 8 --min_kmer_cov 3 --min_glue 3 --bfly_opts '-V 5 --edge-thr=0.1 --stder) was referred to as transcripts.
Gene family clustering was then carried out using TGICL (version: v2.0.6; parameters: -l 40 -c 10 -v 25 -O '-repeat_stringency 0.90 -minmatch 35 -minscore 35') to obtain the final unigenes.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Supplementary_files_format_and_content: Excel files includes RPKM values and fasta files include unigene sequences for each group.

organism: Argopecten irradians

source_name: pooled tissues of 18 individuals

extract_protocol:
Gills were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA integrity was measured using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gill


title: Bay Scallop Control Gills


title: plateA1.positionA3.single.cell

description:
all.single.cell.gene.counts.txt
A1-A3


title: plateA1.positionF2.single.cell

description:
all.single.cell.gene.counts.txt
A1-F2


title: 12_T0b_LE6

source_name: D. discoideum cells 12_T0b_LE6


title: 16_T0b_LE6

source_name: D. discoideum cells 16_T0b_LE6


title: plateA1.positionE2.single.cell

description:
all.single.cell.gene.counts.txt
A1-E2


title: DHCA sample 6

city: Seattle

first: Vishal

last: Nigam

state: WA

address: 1900 9th Ave

department: Pediatrics

institute: Seattle Childrens Research Institute

description:
33
DHCA experimental group
processed data file: 0618_striatum.feature_counts.all_samples.txt
processed data file: sham_DHCA_striatum_mRNA_seq.txt

data_processing:
RNA sequencing reads were aligned to the Pig genome (Sscrofa11.1) using Star.
featureCounts was used to map the reads to the exons of genes.
DESeq2 was used to normalize the data using regularized-logarithm.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: 0618_striatum.feature_counts.all_samples.txt includes the counts.
Supplementary_files_format_and_content: sham_DHCA_striatum_mRNA_seq.txt includes the fold changes and statistics.

organism: Sus scrofa

source_name: striatum region

growth_protocol: Newborn piglets were used. For the sham control group, the piglets were kept under anesthesia with 4% isoflurane.

extract_protocol:
RNeasy (Qiagen) was used to isolate the RNA.
Illumina TruSeq kit was used to generate the cDNA libraries.
The libraries were sequenced on a HiSeq 1500 (Illumina).

treatment_protocol: Bypass DHCA group: After induction of anesthesia with 4% isoflurane, the piglets were cannulated for bypass via a median sternotomy and maintained on CPB at 1500/ml/kg/min while they were cooled to 18oC over 20-30 min. Then, the piglets were exposed to 30 min of DHCA after which CPB was resumed during rewarming to 37oC. These piglets were recovered for 6h.

value: Striatum region

tag: developmental stage

value: Neonatal

value: Deep hypothermic cardiac arrest


title: AX2T0b_LE6

source_name: D. discoideum cells AX2T0b_LE6


title: plateA1.positionH6.single.cell

description:
all.single.cell.gene.counts.txt
A1-H6


title: RPMI.8402_NVS.ZP7.3_1

type: RNA

city: Cambridge

first: Joseph

last: Loureiro

state: MA

address: 181 Massachusetts Ave

department: CBT

institute: Novartis

hyb_protocol: An amount of biotin-labelled cRNA of approximately 10 μg for each sample was hybridized for approximately 16 to 18 hours at 45°C on an array.

scan_protocol: The array was washed and stained using Affymetrix Fluidics Workstation 450 and scanned using an Affymetrix Scanner 3000 according to the manufacturer’s technical manual.

data_processing: R/Bioconductor - affy -> gcrma -> limma

label: biotin

molecule: polyA RNA

label_protocol: Affymetrix 3' Plus protocol to make biotin-labelled cRNA

growth_protocol: 10 million cells were plated in 10mls of growth media for each compound treatment.

extract_protocol: RNA was isolated using the Qiagen Rneasy Mini Kit. RNA quality and concentration was measured using the NanoDrop ND-1000 (Thermo Scientific).

treatment_protocol: Cells were plated and treated with compound on the same day. 16hr compound treatment. DMSO final concentration for all treatment conditions maintained at 0.5%.

tag: cell line


title: RPMI.8402_DMSO_3

value: DMSO


title: RPMI.8402_DMSO_2


title: RPMI.8402_NVS.ZP7.3_3


title: 16_T0a_LE6

source_name: D. discoideum cells 16_T0a_LE6


title: DHCA sample 5

description:
27
DHCA experimental group
processed data file: 0618_striatum.feature_counts.all_samples.txt
processed data file: sham_DHCA_striatum_mRNA_seq.txt


title: RPMI.8402_DMSO_1


title: P12.ICHIKAWA_NVS.ZP7.3_3


title: plateA1.positionB7.single.cell

description:
all.single.cell.gene.counts.txt
A1-B7


title: 12_16_T0a_LE6

source_name: D. discoideum cells 12_16_T0a_LE6


title: RMDB_27

city: Leeds

first: Chulin

last: Sha

address: Woodhouse Lane

department: School of Mole&Cell Biology

country: United Kingdom

institute: University of Leeds

description: REMoDLB trial

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Arrays were scanned on a BeadArray reader

data_processing: The data were normalised using lumi package in R

label: Biotin

label_protocol: Standard Illumina label protocol

extract_protocol: Total RNA was extracted from 5mm paraffin sections using the Ambion RecoverAll kit standard protocol, with the exception of a 16-hour protease digestion. These were routinely collected tissue samples and no attempt was made to standardise fixation or processing protocols

tag: clinic diagnosis

value: Diffuse Large B-cell Lymphoma

tag: molecular subtype

value: MHG

tag: molecular coo subtype

value: GCB


title: P12.ICHIKAWA_NVS.ZP7.3_1


title: P12.ICHIKAWA_DMSO_3


title: P12.ICHIKAWA_NVS.ZP7.3_2


title: 12_T0a_LE6

source_name: D. discoideum cells 12_T0a_LE6

value: vegetative


title: plateA1.positionD2.single.cell

description:
all.single.cell.gene.counts.txt
A1-D2


title: plateA1.positionA2.single.cell

description:
all.single.cell.gene.counts.txt
A1-A2


title: plateA1.positionG2.single.cell

description:
all.single.cell.gene.counts.txt
A1-G2


title: plateA1.positionC2.single.cell

description:
all.single.cell.gene.counts.txt
A1-C2


title: DHCA sample 3

description:
15
DHCA experimental group
processed data file: 0618_striatum.feature_counts.all_samples.txt
processed data file: sham_DHCA_striatum_mRNA_seq.txt


title: plateA1.positionB2.single.cell

description:
all.single.cell.gene.counts.txt
A1-B2


title: 12_16_T0c

description:
ATG12‾/16‾ mutant
processed data: FPKM_1.txt

source_name: D. discoideum cells 12_16_T0c


title: DHCA sample 2

description:
9
DHCA experimental group
processed data file: 0618_striatum.feature_counts.all_samples.txt
processed data file: sham_DHCA_striatum_mRNA_seq.txt


title: AX2T0a_LE6

source_name: D. discoideum cells AX2T0a_LE6


title: DHCA sample 1

description:
3
DHCA experimental group
processed data file: 0618_striatum.feature_counts.all_samples.txt
processed data file: sham_DHCA_striatum_mRNA_seq.txt


title: RPMI.8402_NVS.ZP7.3_2


title: plateA1.positionH1.single.cell

description:
all.single.cell.gene.counts.txt
A1-H1


title: SUPT11_NVS.ZP7.3_3


title: P12.ICHIKAWA_DMSO_1


title: 16_T3c

description:
ATG16‾ mutant
processed data: FPKM_1.txt

source_name: D. discoideum cells 16_T3c

value: 3h starved


title: plateA1.positionG1.single.cell

description:
all.single.cell.gene.counts.txt
A1-G1


title: plateA1.positionF1.single.cell

description:
all.single.cell.gene.counts.txt
A1-F1


title: 16_T0c

source_name: D. discoideum cells 16_T0c


title: plateA1.positionE1.single.cell

description:
all.single.cell.gene.counts.txt
A1-E1

source_name: BASCs-Tracer


title: 12_16_T3c

source_name: D. discoideum cells 12_16_T3c


title: plateA1.positionD1.single.cell

description:
all.single.cell.gene.counts.txt
A1-D1


title: Sham sample 4

description:
19
Sham control
processed data file: 0618_striatum.feature_counts.all_samples.txt
processed data file: sham_DHCA_striatum_mRNA_seq.txt

value: Sham


title: Sham sample 3

description:
13
Sham control
processed data file: 0618_striatum.feature_counts.all_samples.txt
processed data file: sham_DHCA_striatum_mRNA_seq.txt


title: Sham sample 6

description:
31
Sham control
processed data file: 0618_striatum.feature_counts.all_samples.txt
processed data file: sham_DHCA_striatum_mRNA_seq.txt


title: 12_T0c

description:
ATG12‾ mutant
processed data: FPKM_1.txt

source_name: D. discoideum cells 12_T0c


title: Sham sample 2

description:
7
Sham control
processed data file: 0618_striatum.feature_counts.all_samples.txt
processed data file: sham_DHCA_striatum_mRNA_seq.txt


title: Sham sample 1

description:
1
Sham control
processed data file: 0618_striatum.feature_counts.all_samples.txt
processed data file: sham_DHCA_striatum_mRNA_seq.txt


title: plateA1.positionC1.single.cell

description:
all.single.cell.gene.counts.txt
A1-C1


title: SUPT11_NVS.ZP7.3_2


title: Sham sample 5

description:
25
Sham control
processed data file: 0618_striatum.feature_counts.all_samples.txt
processed data file: sham_DHCA_striatum_mRNA_seq.txt


title: AX2T3c

description:
AX2 wild-type
processed data: FPKM_1.txt

source_name: D. discoideum cells AX2T3c


title: SUPT11_NVS.ZP7.3_1


title: DHCA sample 4

description:
21
DHCA experimental group
processed data file: 0618_striatum.feature_counts.all_samples.txt
processed data file: sham_DHCA_striatum_mRNA_seq.txt


title: P12.ICHIKAWA_DMSO_2


title: SUPT11_DMSO_3


title: plateA1.positionB1.single.cell

description:
all.single.cell.gene.counts.txt
A1-B1


title: AX2T0c

source_name: D. discoideum cells AX2T0c


title: degradome of NECS

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

data_processing:
Library strategy: degradome-seq
Remove low quality reads with nucleotides of scores lower than 30 in the first 25 nucleotides
Cut the first 20 nucleotides in the remaining reads
Sort and remove repetitive sequences
Calculate the counts of unique sequences
Genome_build: JCVI.Medtr.v4 and medsa.CADL_HM342.v0.95P
Supplementary_files_format_and_content: sequences and count values

organism: Medicago sativa

source_name: genotypes NECS of Alfalfa

growth_protocol: Rooted stem cuttings were cultured on Murashige and Skoog media and grown in a Conviron growth room, Noble Research Institute, Ardmore, OK.

extract_protocol:
Total RNA was isolated from selected tissues using TRIzol reagent with the manufacture's protocol.
Degradome or PARE library was prepared by following the protocol reported in Li et al. 2010 (The Plant Journal 2010, 62:742-759).

value: NECS

value: roots and shoots


title: 12_T3c

source_name: D. discoideum cells 12_T3c


title: 16_T3b

source_name: D. discoideum cells 16_T3b


title: degradome of Altet

source_name: genotypes Altet of Alfalfa

value: Altet


title: plateA1.positionA1.single.cell

description:
all.single.cell.gene.counts.txt
A1-A1

value: Lung

value: epithelial cell


title: degradome of NF08ALF06

source_name: genotypes NF08ALF06 of Alfalfa


title: 12_16_T0b

source_name: D. discoideum cells 12_16_T0b


title: 16_T0b

source_name: D. discoideum cells 16_T0b


title: SUPT11_DMSO_2


title: TALL1_NVS.ZP7.3_3


title: SUPT11_DMSO_1


title: WT_plus replicate 3

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

institute: Technische Universität Braunschweig

data_processing:
library quality assessment using FastQC
alignment vs. reference genome using Bowtie2 with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq) and subsequent RPKM normalization
Detection of differentially expressed genes using DESEQ2 with raw count data and default parametrization
Genome_build: Chromosome: NC_009089.1, Plasmid: NC_008226.1
Supplementary_files_format_and_content: *.txt files: TAB format with RPKM normalized read counts per gene

organism: Clostridioides difficile 630

growth_protocol: C. difficile was grown anaerobically up to an optical density of 0.4

extract_protocol:
Total bacterial RNA was isolated from bacterial cell pellets, from three independent experiments, using acid phenol and glass beads. DNA was digested using TURBO DNase (Ambion) and the DNA-free RNA was purified with phenol:chloroform:isoamylalcohol (25:24:1). Remaining traces of phenol were removed by washing the samples twice with chloroform:isoamylalcohol (24:1). RNA integrity was assessed using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer. To 2 µg of total RNA 1 µL of 1:10 diluted ERCC ExFold RNA Spike-In Mix 1 or 2 (Ambion) was added. rRNA was depleted using the Ribo-Zero rRNA Removal Kit (Gram-Positive Bacteria) as recommended by the manufacturer (Epicentre).
Strand-specific barcoded cDNA libraries were prepared using the ScriptSeq v2 RNA-Seq Library Preparation Kit as recommended by the manufacturer (Epicentre). Library quality was validated using Agilent 2100 Bioanalyzer (Agilent Technologies) following the manufacturer’s instruction.

treatment_protocol: Samples were grown under iron limiting conditions or under iron saturation

value: exponentially growing cells

value: wildtype

value: iron saturation (15 uM)


title: TALL1_NVS.ZP7.3_2


title: TALL1_NVS.ZP7.3_1


title: TALL1_DMSO_2


title: TALL1_DMSO_1


title: WT_plus replicate 2


title: TALL1_DMSO_3


title: 12_T0b

source_name: D. discoideum cells 12_T0b


title: 12_16_T3b

source_name: D. discoideum cells 12_16_T3b


title: WT_plus replicate 1


title: AX2T3b

source_name: D. discoideum cells AX2T3b

value: wild-type


title: ET1_1 [miRNA-Seq]

city: Beijing

first: Su-Ren

last: Chen

address: 1Beichen West Road, Chaoyang District

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description: Total RNA (including small RNA)

data_processing:
Experiment Pipeline Steps for Small RNA Sequencing: 1) Filter small RNA: separate 18-30nt RNA segment by PAGE gel. 2) 3' adaptor ligation: link 5-adenylated, 3-blocked single-stranded DNA adapter to 3'  end of selected small RNAs from step 1. 3) Reverse primer annealing: the RT primer is added to the solution from step 2, and is cross-linked to the 3' adapter of RNAs and excessive free 3' adapter. 4) 5' adaptor ligation: the 5' adaptor is linked to the 5' end of the product from step 3. The connection (5鈥 adaptor) will be attached to the 5鈥 end only, but it is not c onnected to the 3' adaptor or RT primer hybrid chain. This greatly reduces self-ligation. 5) Strand cDNA synthesis: reverse extend the RT primer in step 3 to synthetize strand cDNA. 6) PCR amplification: use high-ping polymerase to amplify cDNA, enrich cDNA with both 3' and 5' adaptor. 7) Library fragment selection: separate the PCR product of 100~120bp by PAGE gel to eliminate primer-dimer and other byproducts. 8) Library quantitative and pooling cyclization.
Bioinformatics Analysis Pipeline for Small RNA Sequencing: 1. Eliminate the low-quality reads, adaptors and other contaminants to get clean reads 2. Summarize the length distribution of the clean tags, common and specific sequences between samples 3. Annotate the clean tags into different categories 4. Predict the novel miRNA 5. Function annotation of known miRNAs
Data Filtering: 1) Remove low quality tags 2) Remove tags with 5' primer contaminants 3) Remove tags without 3' primer 4) Remove tags without insertion 5) Remove tags with poly A 6) Remove tags shorter than 18nt 7) Summarize the length distribution of the clean tags. After filtering, the remaining tags are called 'clean tags' and stored in FASTQ format.
Reads Mapping: Bowtie2 : -q -L 16 --phred64 -p 6 cmsearch: --cpu 6 --noali
sRNA Classification: MiRbase > pirnabank > snoRNA(human/plant) > Rfam > other sRNA. sRNA Prediction: miRDeep2, Piano,
DEGseq: Fold Change >= 2 and Adjusted Pvalue <= 0.001
Genome_build: mm10
Supplementary_files_format_and_content: Including RPKM values for each sample

source_name: Mouse testicular peritubular myoid (PTM) cells

growth_protocol: The isolated PTM cells were cultured in DMEM/F12 containing 10% fetal bovine serum (FBS) at 37°C with 5% CO2.

extract_protocol:
Total RNA (including small RNA) was extracted from the untreated PTM cells (PTM_1, _2, _3) and ET1-treated PTM cells (ET1_1, _2, _3) using TRNzol (Tiangen, Beijing, China).
Small RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: PTM cells were treated with or without 50 nM ET1 in DMEM/F12 for 5 min at 37°C incubator.

value: 50 nM ET1, 5min

tag: passage

value: Primary

tag: strain


title: ET1_2 [miRNA-Seq]

description: Total RNA (including small RNA)

value: Mouse testicular peritubular myoid (PTM) cells


title: WT_minus replicate 3

value: iron limiting conditions (0.2 uM)


title: 12_T3b

source_name: D. discoideum cells 12_T3b


title: ET1_3 [miRNA-Seq]

description: Total RNA (including small RNA)


title: WT_minus replicate 2


title: AX2T0b

source_name: D. discoideum cells AX2T0b


title: PTM_3 [miRNA-Seq]

description: Total RNA (including small RNA)


title: 12_16_T3a

source_name: D. discoideum cells 12_16_T3a


title: PTM_2 [miRNA-Seq]

description: Total RNA (including small RNA)


title: PTM_1 [miRNA-Seq]

description: Total RNA (including small RNA)


title: WT_minus replicate 1


title: ET1_3 [RNA-Seq]

data_processing:
SOAPnuke: v1.5.2, -l 15 -q 0.2 -n 0.05
HISAT2: v2.0.4, --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Bowtie2: v2.2.5, -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
RSEM: v1.2.12, default
DEGseq: Fold Change >= 2 and Adjusted Pvalue <= 0.001
Genome_build: mm10
Supplementary_files_format_and_content: Including RPKM values for each sample

extract_protocol:
Total RNA was extracted from the untreated PTM cells (PTM_1, _2, _3) and ET1-treated PTM cells (ET1_1, _2, _3) using TRNzol (Tiangen, Beijing, China).
RNA libraries were prepared for sequencing using standard BGI protocols


title: ET1_2 [RNA-Seq]


title: PTM_3 [RNA-Seq]


title: Fur_plus replicate 1

value: fur mutant


title: 16_T3a

source_name: D. discoideum cells 16_T3a


title: 16_T0a

source_name: D. discoideum cells 16_T0a

value: vegetative


title: Fur_plus replicate 3


title: 12_T0a

source_name: D. discoideum cells 12_T0a


title: Fur_plus replicate 2


title: PTM_2 [RNA-Seq]


title: ET1_1 [RNA-Seq]


title: Fur_minus replicate 3


title: Fur_minus replicate 2


title: 12_16_T0a

source_name: D. discoideum cells 12_16_T0a


title: AX2T3a

source_name: D. discoideum cells AX2T3a

value: 3h starved


title: PTM_1 [RNA-Seq]


title: Fur_minus replicate 1


title: AX2T0a

source_name: D. discoideum cells AX2T0a


title: ATF6b-OE, biological rep2

city: Cincinnati

first: Vikram

last: Prasad

state: OH

address: 240, Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: 3.0 ug of fragmented cDNA were hybridized to Clariom S Arrays, Mouse (Applied Biosystems). Probe arrays were incubated at 45°C for 17 hrs in the Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Probe arrays were washed and stained using the Fluidics Station 450 (Affymetrix), utilizing the fluidics protocol FS450-0007. The Stain and Antibody solutions are produced by Applied Biosystems and contained in the Genechip Hybridization Wash and Stain Kit.

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

data_processing: The .cel were created by Command Console (Affymetrix). The .cel files were analyzed by Expression Console (Affymetrix) to create .sst-rma-gene-full.chp files.

source_name: ventricles harvested from aMHC-tTA/;ATF6b-cn (experimental) mice

label_protocol: The GeneChip 3’ IVT Pico Reagent Kit is used to create biotin – labeled double -strand cDNA targets for hybridization to the Clariom S Arrays, Mouse.

extract_protocol:
[cell isolation protocol] Ventricles from control and experimental mice were flash-frozen and processed for total RNA isolation.
Total RNA was isolated using the RNeasy kit (Qiagen)

value: ventricles


title: ATF6a-OE, biological rep2

source_name: ventricles harvested from aMHC-tTA/;ATF6α-cn (experimental) mice


title: ATF6b-OE, biological rep1


title: ATF6a-OE, biological rep1


title: 12_T3a

source_name: D. discoideum cells 12_T3a


title: Control, biological rep2

source_name: ventricles harvested from aMHC-tTA (control) mice

value: aMHC-tTA


title: Control, biological rep1


title: CD271+ sample 1

status: Public on Jan 14 2019

city: Kanazawa

first: Oto

last: Inoue

address: 13-1 Takaramachi

department: System biology

country: Japan

institute: Kanazawa University

description:
Gene expression profile from CD271-positive ADSCs obtained from patient 1
EA1719_05

hyb_protocol: Following fragmentation, 15ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were calculated by Microarray Suite version 5.0 (MAS5.0) with Thermo Fisher Scientific default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Sorted ADSCs were cultured in standard conditions (5% carbon dioxide, 37°C) in DMEM / F12 (Thermo Fisher Scientific) supplemented with 10% FBS and 1% antibiotic-antimycotic solution. At 24 hours after seeding, non-adherent cells were removed by washing the plates, and then medium was changed every 3 days. ADSCs at passage 6 were used for analysis.

extract_protocol: Total RNA was extracted from cultured ADSCs using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: cd271 expression

value: positive

value: cultured adipose-derived stem cells


title: CD271+ sample 4

description:
Gene expression profile from CD271-positive ADSCs obtained from patient 4
EA1719_08


title: CD271+ sample 3

description:
Gene expression profile from CD271-positive ADSCs obtained from patient 3
EA1719_07


title: CD271+ sample 2

description:
Gene expression profile from CD271-positive ADSCs obtained from patient 2
EA1719_06


title: CD271- sample 3

description:
Gene expression profile from CD271-negative ADSCs obtained from patient 3
EA1719_03

value: negative


title: HM 199 treated with SBS_biological replicate #1

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Rat GE 4*44K V3 Microarray  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters .  Data treatment was performed with bioconductor and Limma library. Background substraction was performed using the Normexp correction with offset =50. Quantile normalization was then applied.  Features flagged in Feature Extraction as control, as Feature Non-uniform outliers, saturating or too weak were excluded.

source_name: human skeletal muscle cells_SBS

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp labeling One color : Cy3 (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was extracted with Trizol (Life Technologies) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: fully differentiated human myotubes

tag: treated with

value: summer bear serum for 48hrs


title: WilEx-dDG4

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

data_processing:
BAM files were converted to FASTQ with Picard Tools
Reads were aligned to the mouse genome with STAR
Reads counts per gene were calculated with STAR
Genome_build: mm10
Supplementary_files_format_and_content: Ensembl gene Ids and read counts, tab delimited

source_name: Dorsal dentate gyrus

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Dorsal dentate gyrus

value: Wildtype

tag: environment

value: Exercise


title: WilEx-Vis4

source_name: Visual cortex

value: Visual cortex


title: WilEx-dDG2


title: WilEx-Vis5


title: WilEx-dDG5


title: WilEx-Vis1


title: WilEx-vDG2

source_name: Ventral dentate gyrus

value: Ventral dentate gyrus


title: CD271- sample 1

description:
Gene expression profile from CD271-negative ADSCs obtained from patient 1
EA1719_01


title: HM 305 treated with WBS_biological replicate #3

source_name: human skeletal muscle cells_WBS

value: winter bear serum for 48hrs


title: HM 305 treated with SBS_biological replicate #3


title: WilEx-vDG5


title: WilEx-Vis2


title: WilEx-vDG1


title: HM 199 treated with WBS_biological replicate #1


title: CD271- sample 4

description:
Gene expression profile from CD271-negative ADSCs obtained from patient 4
EA1719_04


title: HM 305 treated with WBS_biological replicate #2


title: HM 258 treated with SBS_biological replicate #4


title: HM 258 treated with WBS_biological replicate #4


title: WilE-Vis4

value: Enriched


title: HM 305 treated with SBS_biological replicate #2


title: WilEx-vDG4


title: WilEx-dDG1


title: CD271- sample 2

description:
Gene expression profile from CD271-negative ADSCs obtained from patient 2
EA1719_02


title: WilE-Vis3


title: WilE-Vis2


title: WilE-Vis1


title: WilE-vDG4


title: WilE-dDG2


title: WilC-Vis2

value: Control


title: WilE-dDG31


title: WilE-dDG4


title: WilC-Vis3


title: WilC-vDG1


title: WilC-dDG4


title: WilE-vDG3


title: WilE-vDG1


title: WilE-vDG31


title: WilC-dDG2


title: WilC-Vis1


title: WilE-vDG2


title: WilE-dDG1


title: WilE-dDG3


title: WilC-vDG2


title: WilC-dDG3


title: WilC-vDG4


title: WilC-vDG3


title: WilC-Vis4


title: WilE-Vis31


title: WilC-dDG1


title: HomEx-Vis4

value: CREB -/-


title: HomEx-Vis5


title: HomEx-Vis3


title: HomEx-Vis2


title: HomEx-vDG5


title: HomEx-Vis1


title: HomEx-vDG4


title: HomE-Vis4


title: HomEx-dDG2


title: HomE-Vis5


title: HomEx-dDG4


title: HomEx-dDG1


title: HomE-Vis2


title: HomE-vDG1


title: HomEx-vDG2


title: HomEx-vDG1


title: HomEx-dDG3


title: HomE-vDG2


title: HomE-vDG4


title: HomE-dDG5


title: HomEx-dDG5


title: HomE-vDG3


title: HomE-dDG2


title: HomE-Vis3


title: HomE-vDG5


title: HomE-dDG4


title: HomE-dDG3


title: HomC-Vis5


title: HomC-Vis4


title: HomC-Vis3


title: HomC-Vis2


title: HomEx-vDG3


title: HomE-dDG1


title: HomC-Vis1


title: siCntl_nascent_rep1_NacentRNA

city: Newark

first: Bin

last: Tian

state: NJ

address: 205 South Orange Ave.

department: Department of Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers New Jersey Medical School

description: Analysis of nasent RNA under siNXF1

data_processing:
Library strategy: ChATT-seq
Adpter trimming performed using Cutadapt
3'READs reads were aligned to hg19 using bowtie2. Reads with a mapping quality score (MAPQ) >=10 were kept for further analysis. Reads with >=2 non-genomic 5’Ts after alignment were called polyA site supporting (PASS) reads. pAs within 24 nt of each other were clustered. pAs with less than 5 PASS reads in all the samples were first trimmed.
RNAseq of nacent RNA reads were aligned to hg19 using STAR. Only mapped reads without any soft clipping at the 5’ end of read were used for further analysis. The genomic position corresponding to the 5’ end of each read was identified by a Python script using the HTSeq software package (Anders et al., 2015). The 5’ positions of the remaining reads were used to reflect Pol II positions, the reads mapped to the same region were uniqued
ChIP-seq reads reads were mapped to the hg19 genome assembly using BWA-MEM (0.7.15). The reads mapped to the same region were uniqued, and the unique reads count of each position was then normorlized to one million (UPM).
Raw reads from RNA-seq of total RNA were first mapped to the hg19 genome assembly using STAR (v2.5.2) (Dobin et al., 2013) with default parameters. The read count of the coding sequence (CDS) of each gene was summed and then normalized by the median ratio method in DESeq (Dobin et al., 2013). Only genes with more than five reads in all samples were used for further gene expression analysis.  Alternative splicing (AS) was analyzed using rMATS (v4.0.2) (Shen et al., 2014) with default parameters. Significant AS events were those with a delta PSI >5% and P-value <0.05. Only AS events with at least five reads mapped on splice junctions were used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads count for each pAs/pol2/nascent RNA loci/gene

source_name: cervical cancer cells

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Biochrom).

extract_protocol: See extract_protocols.xls linked at the foot of the GSE117701 record.

treatment_protocol: See the "protocol" column in the SAMPLES section. For untreated samples, cells were cultured in normal medium; Sodium Arsenite treatment: 250 µM. For RNAi, siRNAs were transfected with Lipofectamine® RNAiMAX (Invitrogen) following the manufacture’s procedure.

value: HeLa

value: Untreated, with 4sU labeling

tag: protocol

value: chATT-seq

tag: molecule subtype

value: chromatin associated 4sU-labeled nascent RNA


title: HomE-Vis1


title: siNXF1_nascent_rep1_NacentRNA

description: Analysis of nasent RNA under siNXF1

value: siNXF1, with 4sU labeling


title: HomC-vDG2


title: HomC-dDG1


title: siNXF1_N_rep1_3READ

description: Analysis of differential cytopalsmic/nuclear distribution of APA isoforms

data_processing:
Adpter trimming performed using Cutadapt
3'READs reads were aligned to hg19 using bowtie2. Reads with a mapping quality score (MAPQ) >=10 were kept for further analysis. Reads with >=2 non-genomic 5’Ts after alignment were called polyA site supporting (PASS) reads. pAs within 24 nt of each other were clustered. pAs with less than 5 PASS reads in all the samples were first trimmed.
RNAseq of nacent RNA reads were aligned to hg19 using STAR. Only mapped reads without any soft clipping at the 5’ end of read were used for further analysis. The genomic position corresponding to the 5’ end of each read was identified by a Python script using the HTSeq software package (Anders et al., 2015). The 5’ positions of the remaining reads were used to reflect Pol II positions, the reads mapped to the same region were uniqued
ChIP-seq reads reads were mapped to the hg19 genome assembly using BWA-MEM (0.7.15). The reads mapped to the same region were uniqued, and the unique reads count of each position was then normorlized to one million (UPM).
Raw reads from RNA-seq of total RNA were first mapped to the hg19 genome assembly using STAR (v2.5.2) (Dobin et al., 2013) with default parameters. The read count of the coding sequence (CDS) of each gene was summed and then normalized by the median ratio method in DESeq (Dobin et al., 2013). Only genes with more than five reads in all samples were used for further gene expression analysis.  Alternative splicing (AS) was analyzed using rMATS (v4.0.2) (Shen et al., 2014) with default parameters. Significant AS events were those with a delta PSI >5% and P-value <0.05. Only AS events with at least five reads mapped on splice junctions were used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads count for each pAs/pol2/nascent RNA loci/gene

value: nucleus


title: siCntl_N_rep2_3READ

value: Untreated


title: HomC-dDG5


title: HomC-vDG4


title: HomC-vDG5


title: HomC-dDG2


title: siCntl_N_rep1_3READ


title: HomC-dDG4


title: siCntl_C_rep1_3READ

value: cytoplasm


title: HomC-dDG3

value: Dorsal dentate gyrus


title: HetEx-Vis4

value: CREB +/-


title: siCFI68_rep2_3READ

description: Analysis of APA under KD of export factors


title: HetEx-Vis5

value: Exercise


title: HetEx-Vis3

value: Visual cortex


title: siCFI68_C_rep2_3READ


title: siCFI68_N_rep2_3READ


title: siNXF1_rep2_3READ


title: siCntl_rep2_3READ


title: HetEx-Vis11


title: siCntl_C_rep2_3READ


title: HetEx-Vis1


title: siTHOC2_rep1_3READ


title: siCntl_rep1_3READ


title: 22RV-1_input DNA

city: Shanghai

first: Ni

last: Li

state: Shanghai

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: Institute of Health Sciences, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

library_source: genomic

data_processing:
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) were mapped to the genome using the BWA algorithm with default settings.
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome were used in the subsequent analysis
Tags were extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp). To identify the density of fragments (extended tags) along the genome, the genome was divided into 32-nt bins and the number of fragments in each bin was determined.
Peaks were called using MACS2.
Tag Normalization: tag number of all samples was reduced (by random sampling) to the number of tags present in the smallest sample.
Genome_build: hg38
Supplementary_files_format_and_content: The number of fragments in each bin is stored in a bigWig file.

molecule: genomic DNA

source_name: cell line

growth_protocol: RPMI1640 supplied with 10% fetal bovine serum.

extract_protocol:
The chromatin was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against BRG1 (abcam, ab110641).
Libraries were prepared for sequencing using standard Illumina protocols.

value: prostate cancer

tag: genotype/variation

tag: antibody


title: siNXF1_C_rep1_3READ

tag: treatment


title: HomC-vDG3

tag: tissue

value: Ventral dentate gyrus

tag: genotype


title: siNXF1_rep1_3READ


title: HomC-vDG1


title: 22RV-1_PTEN-KD_BRG1_ChIPSeq

value: PTEN knockdown

value: BRG1 (abcam, ab110641)


title: HetEx-vDG4


title: HetEx-vDG3


title: 22RV-1_control_BRG1_ChIPSeq

value: control


title: HetEx-dDG11


title: HetEx-vDG1


title: HetEx-dDG3


title: HetEx-dDG5


title: HetEx-dDG4


title: HetE-Vis5

value: Enriched


title: HetE-Vis4


title: HetEx-vDG5


title: HetEx-vDG11


title: ATAC-seq; WT MEF cells; Rep1

city: Boston

first: Jeannie

middle: T

last: Lee

address: 185 Cambridge Street

department: Molecular Biology

institute: Harvard University / MGH

description:
DNA extracted by Qiagen Kit.
ATAC-seq Library.
processed data file: AccessibilityClass_Monoallelic.bed
processed data file: AccessibilityClass_Biallelic.bed
processed data file: AccessibilityClass_XiRestored.bed

data_processing:
Base-calling was performed with Illumina real time analysis (RTA) basecaller v1.17.21.3.
For ATAC-seq: Adaptor sequences were trimmed with Trim Galore! V0.4.1 (stringency 12 and allowed error rate 0.2). Identical genomic sequences (PCR duplicates) were removed by custom program prior to alignment. To account for the M. mus (mus) / M. castaneus (cas) hybrid character of mouse dermal fibroblast lines that were employed in a ChIP-seq studies, reads were first aligned to custom mus/129 and cas genomes, and then mapped back to the reference mm10 genome. All alignments were performed by utilizing bowtie2 (v2.2.7) in paired-end mode. Post-processing of alignments was performed with custom scripts using SAMtools, and BEDtools (v2.25.0). These included accounting, alignment file-type conversion, extracting and reads sorting (SAMtools), and obtaining wig coverage files (SAMtools depth). To increase available read depth, we pooled together two biological replicates of ATAC-seq performed in wild-type cells, and separately pooled two biological replicates of ATAC-seq performed in XaWT XiΔXist cells. We also pooled two ATAC-seq biological replicates performed in a second XaWT XiΔXist cell line that served us as an independent biological system showing highly concordant results with those obtained by our main cell system. In each of these cases, pooled replicates were highly correlated to each other (r2 > 0.9), indicating strong data reproducibility. For visualizing ATAC-seq binding signal, we generated fragments per million (fpm)-normalized bigWig files from the raw ATAC read counts for all reads (comp), mus-specific (mus), and cas-specific reads, separately. Uniquely aligned wig files were scaled to total number of fragments per million in each library (determined by SAMtools flagstat combining reads ‘‘with itself and mate mapped’’ and ‘‘singletons’’). ATAC-seq tag density bigWig files were viewed in Integrative Genomics Viewer (IGV). To quantify reproducibility between two biological replicates of ATAC-seq generated in WT cells (or XaWT XiΔXist cells), we first counted per each two replicates the number of uniquely aligned neutral/cas/mus (comp) reads, per sample, and performed random downsampling without replacement of the larger sample in order to equalize reads number within two replicates (in general, all of our replicate samples had very similar numbers of reads also prior to downsampling). Next, we called MACS2 peaks (by employing –BAMPE (paired-end mode), and pvalue=0.005) in individual replicates. Peak sets called in individual replicates were then combined, and overlapping peaks were merged to form a union peak set. By applying Homer suit’s makeTagDirectory and annotatePeaks algorithms we obtained a read count matrix of two biological replicates over union peak set, and normalized these values per each library’s reads size by using edgeR. Log2 of ATAC-seq peaks’ signal within autosomes was plotted (≥10 reads per peak), and Pearson correlation coefficient of two biological replicates was calculated. In both cell lines, WT and XaWT XiΔXist, correlation coefficients of biological replicates of ATAC-seq were high (r2>0.94, 0.95, respectively), indicating strong data reproducibility. Similarly, high correlation coefficients were also obtained when comparing two biological replicates of ATAC-seq performed in WT cells treated with siControl, or with siBRG1 (r2 >0.92, 0.9, respectively), and in XaWT XiΔXist cells treated with siControl, or with siBRG1 (r2 >0.96, in both).
Genome_build: mm10
Supplementary_files_format_and_content: AccessibilityClass_Monoallelic.bed
Supplementary_files_format_and_content: AccessibilityClass_Biallelic.bed
Supplementary_files_format_and_content: AccessibilityClass_XiRestored.bed

source_name: Mouse embryonic female fibroblasts (WT)

growth_protocol: Differentiated mouse fibroblast cells were cultured in regular fibroblast medium, 1% Pen/Strep, high-glucose DMEM+GlutaMax with 10% FBS.

extract_protocol:
50,000 cells were washed briefly in cold PBS and permeabilized with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) containing proteinase inhibitor cocktail (Roche). Nuclei were resuspended in 1X TD Buffer (Illumina FC-121-1030), and 2.5uL of Tn5 Transposase (Illumina FC-121-1030) were added. Transposition reaction was performed at 37°C for 30 min, and DNA was purified using a Qiagen MinElute Kit.
DNA libraries were amplified for a total of 8 cycles. Libraries were assessed for quality control on the BioAnalyzer 2100 (Agilent) to ensure nucleosomal phasing and complexity. Sequencing was performed on the HiSeq 2500 (Illumina), using 50 bp paired-end reads. Sequencing Nextera adapters: F: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, R: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG

value: CAST/Ei x 129/Sv/Jae

tag: cell type

value: Mouse embryonic female fibroblasts

tag: Sex

value: Female


title: ATAC-seq; WT MEF cells; Rep2


title: RNA-seq; WT cells; Rep1

description:
WT_rep1
processed data file: AnalyzeRNA_GenesExons_noadj_comps_WTrep1_WTrep2_KO1rep1_KO1rep2_KO2rep1_KO2rep2.txt
processed data file: RNAseq_gene_expression_classes.txt

data_processing:
Base-calling was performed with Illumina real time analysis (RTA) basecaller v1.17.21.3.
For RNA-seq: RNA-seq libraries were subjected to high-throughput sequencing using Illumina HiSeq 2500 apparatus according to manufacturer instructions. On average, approximately 60 million paired-end 50 bp reads were generated per every RNA-seq sample (Supplementary Table 1). Adaptor sequences were trimmed with Trim Galore! V0.4.1 (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (stringency 12 and allowed error rate 0.2). Identical genomic sequences (PCR duplicates) were removed by custom program prior to alignment. To account for the M. mus (mus) / M. castaneus (cas) hybrid character of mouse dermal fibroblast lines that were employed in a ATAC-seq studies, reads were first aligned to custom mus/129 and cas genomes, and then mapped back to the reference mm10 genome. All alignments were performed by utilizing tophat2 in paired-end mode. Post-processing of alignments was performed with custom scripts using SAMtools, and BEDtools (v2.25.0). These included accounting, alignment file-type conversion, extracting and reads sorting (SAMtools), and obtaining wig coverage files (SAMtools depth). After elimination of PCR duplicates, all aligned unique allelic reads were mapped to the exons of each gene and quantified using the Homer software [analyzeRNA.pl rna mm10 -count exons -noadj]. To classify expressed genes based on their allelic transcriptional signals we applied a machine learning model trained on the set of ATAC-seq peaks of three accessibility classes as described in the manuscript. We paired each of the two XaWT XiΔXist cell lines with WT cell line and generated per each of the biological replicates a matrix of transcription signals per gene (allelic reads >10). Each of the four RNA-seq matrices was then used as an input for calling our svm model, and genes with svm decision.values > 0.65 were classified into either one of three clusters, Monoallelic, Bi-allelic, or Xi-restored. Per each of the biological replicates we then generated a common matrix presenting each gene’s predicted classification along with its allelic transcriptional signals in WT cells and in two XaWT XiΔXist cell lines. Finally, we created a combined matrix of genes that were reproducibly classified in two biological replicates (RNAseq_gene_expression_classes.txt).
Genome_build: mm10
Supplementary_files_format_and_content: AnalyzeRNA_GenesExons_noadj_comps_WTrep1_WTrep2_KO1rep1_KO1rep2_KO2rep1_KO2rep2.txt
Supplementary_files_format_and_content: RNAseq_gene_expression_classes.txt

source_name: Dermal female fibroblasts (WT)

extract_protocol:
Total RNA was extracted using TRIzol (15596018, Thermo Fisher Scientific), depleted of ribosomal RNA with RiboMinus™ Eukaryote Kit v2 (A15020, Thermo Fisher Scientific) and of genomic DNA with TURBO DNase (AM2239, Thermo Fisher Scientific), and then purified using an RNeasy minelute cleanup kit (Qiagen). 30-100ng ribosomal RNA-depleted RNA were fragmented in 6mM MgCl2 Buffer at 94°C for 10 minutes, followed by random-primed first strand cDNA synthesis with SuperScript III Reverse Transcriptase (18080085, Thermo Fisher Scientific) in the presence of actinomycin D (11805017, Thermo Fisher Scientific) at 50°C for 30 minutes. Secondary strand synthesis was performed using NEBNext Ultra Directional RNA second strand synthesis module (New England Biolabs). Adaptor oligos were ligated to the cDNA library using NEBNext Chip-seq library master mix (New England Biolabs).
Libraries were amplified with multiplexing barcodes (NEBNext Multiplex Oligos for Illumina, New England Biolabs) and quantified using KAPA library quantification kit (Kapa Biosystems). RNA-seq was performed in two biological replicates. Sequencing was performed on the HiSeq 2500 (Illumina), using 50 bp paired-end reads.

value: Differentiated dermal female fibroblast cells


title: HetE-Vis6


title: HetE-vDG6


title: HetE-Vis21


title: HetEx-dDG1


title: HetE-vDG5


title: HetE-vDG4


title: HetE-vDG3


title: RNA-seq; XaWT XiΔXist cells; Rep1

description:
KO_1_rep1
processed data file: AnalyzeRNA_GenesExons_noadj_comps_WTrep1_WTrep2_KO1rep1_KO1rep2_KO2rep1_KO2rep2.txt
processed data file: RNAseq_gene_expression_classes.txt

source_name: Dermal female fibroblasts (XaWT XiΔXist)


title: RNA-seq; XaWT XiΔXist cells; Rep2

description:
KO_1_rep2
processed data file: AnalyzeRNA_GenesExons_noadj_comps_WTrep1_WTrep2_KO1rep1_KO1rep2_KO2rep1_KO2rep2.txt
processed data file: RNAseq_gene_expression_classes.txt


title: RNA-seq; WT cells; Rep2

description:
WT_rep2
processed data file: AnalyzeRNA_GenesExons_noadj_comps_WTrep1_WTrep2_KO1rep1_KO1rep2_KO2rep1_KO2rep2.txt
processed data file: RNAseq_gene_expression_classes.txt


title: RNA-seq; XaWT XiΔXist #2 cells; Rep1

description:
KO_2_rep1
processed data file: AnalyzeRNA_GenesExons_noadj_comps_WTrep1_WTrep2_KO1rep1_KO1rep2_KO2rep1_KO2rep2.txt
processed data file: RNAseq_gene_expression_classes.txt

source_name: Dermal female fibroblasts (XaWT XiΔXist) 2nd cell line


title: siCntl_input_rep1_ChIPseq

description: Analysis of po2 pausing under siNXF1

tag: cell line

value: HeLa

value: ChIP-seq


title: siNXF1_input_rep1_ChIPseq

description: Analysis of po2 pausing under siNXF1


title: siCntl_pol2_IP_rep1_ChIPseq

description: Analysis of po2 pausing under siNXF1

value: Untreated


title: HetE-Vis3


title: siNXF1_pol2_IP_rep1_ChIPseq

description: Analysis of po2 pausing under siNXF1


title: RNA-seq; XaWT XiΔXist #2 cells; Rep2

description:
KO_2_rep2
processed data file: AnalyzeRNA_GenesExons_noadj_comps_WTrep1_WTrep2_KO1rep1_KO1rep2_KO2rep1_KO2rep2.txt
processed data file: RNAseq_gene_expression_classes.txt


title: HetE-Vis2


title: HetE-vDG21


title: HetE-vDG2


title: HetE-dDG6

value: Dorsal dentate gyrus


title: Input_E1

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

institute: Institut Pasteur

data_processing:
basecalls performed using CASAVA 1.8
ChIP-Seq: Reads aligned with bowtie2 to mm9 genome with options “-k 10”, those with mapping quality 255 and edit distance less that 4 were retained. For H3K27me3 samples macs2 was used to call broad peaks options “--broad -q 0.2 -g mm” against inputs. H3K27me3 domains were identified by merging all peaks within 3kb and taking those present in at least 8 samples.
Bigwig File generation: For all ChIP-seq samples, reads were extended to a fragment length of 150 bp to generate bigwigs, for ATAC-seq +/-5bp surrounding the cutsites at the ends of each paired-end fragment (11bp total) were marked.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files

source_name: ES Cell

growth_protocol: ES cells (E14Tg2a and derivatives) were cultured at 37°C in 7% CO2 on 0.1% gelatine (SIGMA, G1890-100G) in DMEM+GlutaMax-I (Gibco 31966-021), 10% FCS (Sigma F7524), 100 μM 2- mercaptoethanol (Gibco 31350-010), 1× MEM non-essential amino acids (Gibco 1140-035) and 10 ng/ml recombinant LIF (MILTENYI BIOTEC, 130-099-895). Cells were passaged 1:10 every 2–3 days with 1X trypsin-EDTA 0.05% (Thermo 25300062). Only when mentioned cells were cultured in 2i medium containing 0.5X DMEM/F12 (Gibco 31331093), 0.5X Neurobasal (Gibco 21103049), 0.5% N2 supplement 100X (Gibco 17502048), 1% B27 supplement 50X (Gibco 17504044), 10µg/mL Insulin (Sigma I1882-100MG), 2 mM L-Glutamine (Invitrogen 91139), 0.05% BSA (Sigma A3311-10G), 100 μM 2-mercaptoethanol (Gibco, 31350-010), 10 ng/ml recombinant LIF (MILTENYI BIOTEC, 130-099-895), 1 µM PD0325901 (Axon Medchem Bv Axon-1408), 3 µM CHIR99021 (Axon Medchem Bv Axon-1386). When specified cells were treated with 1 µg/mL of Doxycycline (Sigma D3072-1ML), 1 µg/mL Puromycin (Sigma P9620- 10ML), 400 µg/mL Hygromycin B (Sigma H3274-50MG), 0.2 mg/mL G418 (Sigma G8168- 10ML), 1µM Tamoxifen (Sigma H7904-5MG).

extract_protocol:
Chromatin: cells were resuspended in 3 ml PBS and crosslinked for 10 min at room temperature with 1% formaldehyde (Sigma F8775). Crosslinking was stopped with 0.125 mM glycine for 5 min at room temperature. 44iN cells (3.107 ) used for TF binding profiling were crosslinked in 3 ml of freshly prepared PBS-DSG 7/17 2 mM at pH 7.0 (Sigma, 80424-5 mg) for 50 min at room temperature with occasional shaking. After pelleting and washing in PBS, cells were incubated for 10 min in 3 ml PBS 1% formaldehyde (Sigma F8775), quenched with 0.125 MM glycine. After fixation, cells were pelleted, washed twice with ice-cold PBS and resuspended in 6 ml of swelling buffer (25 mM Hepes pH 7.95, 10 mM KCl, 10 mM EDTA) freshly supplemented with 1X protease inhibitor cocktail (PIC-Roche, 04 693 116 001) and 0.5% NP-40. After 30 min on ice with occasional shaking, the suspension was centrifuged and resuspended in 450 μl of TSE150 (0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris-HCl pH8, 150 mM NaCl) buffer, freshly supplemented with 1X PIC. Samples were split in 3 (150µL) and sonicated in 1.5 mL tubes (Diagenode) using a Bioruptor Pico (Diagenode) for 7 cycles divided into 30 s ON - 30 s OFF sub-cycles at maximum power, in circulating ice-cold water. After centrifugation (10 min, full speed, 4 °C), the supernatant was stored at −80 °C. Five microlitres was used to quantify the chromatin concentration and check DNA size (typically 200–500 bp).
ChIP-seq: Chiped DNA was end repair in a total volume of 50µL (sample 37.5 µL, 10mM dNTPs 2 µL, NEB T4 ligase buffer 5 µL, NEB T4 polymerase 2.5 µL, NEB Klenow polymerase 0.5 µL, NEB T4 PNK 2.5 µL) and incubated for 30min at 20°C. After DNA purification (see below), A-tailing was subsequently performed in a total volume of 25 µL (sample 20 µL, NEB Buffer 2 2.5 µL, 5mM dATP 1 µL, NEB Klenow 3'-5' exo minus 1.5 µL) at 37°C for 30min. Illumina TruSeq adapters were used for libraries indexing, ordered from IDT Company with 5’ phosphate modification. Illumina adapters’ compatibility was checked with the online tool checkmyindex (checkmyindex.pasteur.fr) for multiplexing. Truseq adapters were annealed with Illumina Universal adapter at 20µM each in 1X NEB Buffer 2 on a TM 100 Thermal Cycler (Biorad). Adapters ligation was performed in a total volume of 25 µL (sample 19.25 µL, NEB 10x T4 ligase buffer 2.5 µL, 0.2µM adapter 1.25 µL, NEB T4 ligase 2 µL) at 16°C overnight. After DNA purification, DNA was amplified in a total volume of 50 µL (sample 19.5 µL, Pico green 1 µL – 9/17 1:10 in water; Life Technologies P7589 –, 25 µL of KAPA HiFi HOTSTART Ready mix – NC0295239 –, PCR 1.0 10µM 1 µL, PCR 2.0, 10µM 1 µL) on a LightCycler 480 (Roche). PCR primers are listed in Table S4. Any sample reaching an absolute fluorescence value of 6 was taken out from the plate at the end of the last extension. Any library requiring more than 16 cycles of amplification to reach this level was discarded and reprepared. DNA was finally purified and the concentration was measured with a Qubit 4 Fluorometer (Thermo Q33226). Libraries quality check and size estimation were then performed on an Agilent 2200 Tape Station with High Sensitivity D5000 ScreenTape (Agilent Technologies, 5067-5592) and High Sensitivity D1000 Reagents (Agilent Technologies, 5067-5585) using 1-2ng of material. Libraries were subsequently adjusted to equimolar concentration of 2nM according to fragments average size and concentration prior mixing them for subsequent sequencing on the HiSeq 2500 sequencer (Illumina) in 65 bases V4 single-end mode

value: SunTag-Nanog

tag: parental

tag: lif

value: -Dox

tag: chip target

value: Input


title: HetE-dDG4

value: CREB +/-


title: siALYREF_rep1_3READ

value: siALYREF


title: HetE-dDG3


title: H3K27me3_E1N4_pL_pD_2

value: +Dox


title: Input_A1


title: H3K27me3_E1N4_pL_pD_1


title: ATAC_44iN_pD_1

data_processing:
basecalls performed using CASAVA 1.8
ATAC-seq: Paired end 65bp reads were trimmed by aligning read pairs to discover regions of reverse complementarity surrounded by Nextera sequencing adapters. Reads were aligned to mm9 genome using bowtie2 with options “-k 10 -I 0 -X 1000 --no-discordant --no-mixed”, and filtered for pairs with mapping quality 255 and mean edit distance < 4 between read pairs
Bigwig File generation: For all ChIP-seq samples, reads were extended to a fragment length of 150 bp to generate bigwigs, for ATAC-seq +/-5bp surrounding the cutsites at the ends of each paired-end fragment (11bp total) were marked.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files

extract_protocol:
Chromatin: cells were resuspended in 3 ml PBS and crosslinked for 10 min at room temperature with 1% formaldehyde (Sigma F8775). Crosslinking was stopped with 0.125 mM glycine for 5 min at room temperature. 44iN cells (3.107 ) used for TF binding profiling were crosslinked in 3 ml of freshly prepared PBS-DSG 7/17 2 mM at pH 7.0 (Sigma, 80424-5 mg) for 50 min at room temperature with occasional shaking. After pelleting and washing in PBS, cells were incubated for 10 min in 3 ml PBS 1% formaldehyde (Sigma F8775), quenched with 0.125 MM glycine. After fixation, cells were pelleted, washed twice with ice-cold PBS and resuspended in 6 ml of swelling buffer (25 mM Hepes pH 7.95, 10 mM KCl, 10 mM EDTA) freshly supplemented with 1X protease inhibitor cocktail (PIC-Roche, 04 693 116 001) and 0.5% NP-40. After 30 min on ice with occasional shaking, the suspension was centrifuged and resuspended in 450 μl of TSE150 (0.1% SDS, 1% Triton, 2 mM EDTA, 20 mM Tris-HCl pH8, 150 mM NaCl) buffer, freshly supplemented with 1X PIC. Samples were split in 3 (150µL) and sonicated in 1.5 mL tubes (Diagenode) using a Bioruptor Pico (Diagenode) for 7 cycles divided into 30 s ON - 30 s OFF sub-cycles at maximum power, in circulating ice-cold water. After centrifugation (10 min, full speed, 4 °C), the supernatant was stored at −80 °C. Five microlitres was used to quantify the chromatin concentration and check DNA size (typically 200–500 bp).
ATAC-seq: 50,000 viable cells were washed with cold 1X PBS, pelleted by centrifugation for 5 min at 500g at 4°C, resuspended in 50 μl of transposition reaction mix (25 μl of Tagmentation DNA buffer, 2.5 μl Tagment DNA enzyme (Illumina) and 22.5 μl nuclease-free H2O) and incubated for 30 min at 37 °C. DNA was purified with a MinElute PCR purification kit (Qiagen). Libraries were prepared as described (Buenrostro et al., 2015) but replacing NEB Next HighFidelity 2X PCR Master Mix, by KAPA HiFi HotStart (KapaBiosystems KM2602) for PCR amplification, after determining the number of cycles needed by qPCR. The concentration and quality of the libraries were assessed as described above. Libraries were sequenced on the HiSeq 2500 sequencer (Illumina) in 65 bases V4 paired-end mode.


title: HetE-dDG2


title: HetE-dDG21


title: ATAC_44iN_mD_1


title: ATAC_44iN_mD_2


title: ATAC_44iN_pD_2


title: siUAP56_rep1_3READ


title: siCFI68_rep1_3READ


title: HetC-Vis4

value: Visual cortex

value: Control


title: HetC-Vis3


title: HetC-Vis5


title: HetC-Vis1


title: HetC-Vis2


title: HetE-dDG5

value: Enriched


title: H3K27me3_A1N2_mL_mD_2


title: H3K27me3_A1N2_mL_pD_1


title: H3K27me3_A1N2_pL_mD_2


title: H3K27me3_A1N2_pL_mD_1


title: H3K27me3_E1N4_mL_pD_1


title: H3K27me3_E1N4_mL_mD_2


title: H3K27me3_A1N2_pL_pD_1


title: H3K27me3_A1N2_mL_pD_2


title: H3K27me3_E1N4_pL_mD_2


title: HetC-vDG6

value: Ventral dentate gyrus


title: H3K27me3_E1N4_mL_mD_1


title: HetC-vDG5


title: HetC-Vis6


title: H3K27me3_A1N2_mL_mD_1


title: HetC-vDG4


title: HetC-vDG3


title: HetC-vDG2


title: IN44Sox2plus2


title: IN44Input


title: IN44Sox2minus2


title: HetC-vDG1


title: IN44Sox2plus1


title: HetC-dDG6


title: IN44Sox2minus1


title: IN44Oct4plus2


title: HetC-dDG4


title: IN44Oct4minus2


title: IN44Oct4plus1


title: HetC-dDG5


title: HetC-dDG3


title: IN44Oct4minus1


title: HetC-dDG2


title: HetC-dDG1


title: SGBS_adipocyte_rep2

city: Chapel Hill

first: Karen

middle: L

last: Mohlke

state: NC

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Mate-pair fastq files were merged and samples were processed as single-end
Reads containing sequencing adapters were removed using TagDust version 1.12 with parameters -f 0.001
Reads with low base quality were removed with fastq_quality_filter (FASTX Toolkit version 0.0.13.2) with parameters -Q 33 -q 20 -p 90
Filtered reads were aligned to the hg19 human genome using bowtie2 version 2.3.4.1 in single-end mode with parameters --np 6 -S <sam_file>
Nuclear chromosome alignments with high mapping uniqueness were selected using samtools version 1.6 with parameters -q 20 and each nuclear chromosome
Alignments overlapping Duke excluded and Dac blacklisted regions were removed using bedtools version 2.25.0
Alignments were shifted by +4 on the + strand and -5 on the - strand using awk
Peaks were called with MACS2 version 2.1.0.20140616 with parameters callpeak -q 0.05 --nomodel --shift -100 --extsize 200 --bdg --keep-dup 1
Representative peaks were determined by: (1) Peaks were called on individual replicates (replicate peaks) and on reads merged across replicates (merged peaks). (2) Merged peaks that shared at least one base with a replicate peak in 2 or more replicates were considered representative peaks.
Fimo version 4.11.2 was used to scan the hg19 genome for JASPAR core 2016 vertebrate motifs with parameters --max-stored-scores 100000000 --parse-genomic-coord
Footprints were identified for 17 transcription factors using centipede. Please see the accompanying manuscript for detailed footprinting methods. Note that footprints were only reported for the SGBS sample with 400k cells due to excessive duplication in the SGBS sample with 800k cells.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were generated by MACS2 and contain ATAC-seq peak genomic coordinates, fold change over background, p-value, q-value, and peak summit position. Enrichment bigWig files represent ATAC-seq signal fold change over background and were calculated by dividing ATAC-seq signal calculated by MACS2 by the background estimated by MACS2.

source_name: adipocyte

growth_protocol: SGBS preadipocytes were maintained at 37º with 5% CO2 in DMEM:F12 supplemented with 10% FBS and 5% 3.3 mM biotin/1.7 mM panthotenate solution

extract_protocol:
SGBS cells were rinsed with DPBS, and lysed in nuclei isolation buffer containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin as detergent.
Omni ATAC-seq was performed with 50k cells and 25 ul 2x TD buffer, 2.5 ul transposase, 16.5 ul PBS, 0.5 ul 1% digitonin, 5.5 ul H2O per reaction

treatment_protocol: SGBS adipocytes were differentiated from preadipocytes in DMEM:F12 supplemented with 5% 3.3 mM biotin/1.7 mM panthotenate solution, 0.01 mg/mL transferrin, 20 nM insulin, 200 nM cortisol, 0.4 nM triiodothyronine, 50 nM dexamethasone, 500 uM IBMX, and 2 uM rosiglitazone. After four days, differentiated SGBS cells were maintained a further 10 days in DMEM:F12 supplemented with 5% 3.3 mM biotin/1.7 mM panthotenate solution, 0.01 mg/mL transferrin, 20 nM insulin, 200 nM cortisol, 0.4 nM triiodothyronine.

value: SGBS adipocyte

tag: number cells


title: SGBS_adipocyte_rep3


title: SunTag_C2ON3_Nanog/Otx_-LIF_+Dox_2

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
B426-sample14

data_processing:
basecalls performed using CASAVA 1.8
RNA-seq: Reads were aligned to mm9 genome STAR and quantified by RSEM using the RSEM-STAR pipeline, with additional options “--seed 1618 --calc-pme --calc-ci --estimate-rspd --forward-prob 0.0”.  Rounded expected counts were normalised with DEseq2.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited files

extract_protocol:
RNA: Cells were lysed with 1mL TRIzol (ThermoFisher) and RNAs extracted according to manufacturer’s protocol. To eliminate any genomic DNA contamination, this was followed by an additional DNAse I treatment (Qiagen 79254) for 20min at 37°C followed by phenol:chloroform purification. RNAs were resuspended in Ultrapure DNAse/Rnase Free Distilled Water (Thermo 10977035)
RNA-seq: We used 0.5 μg of total RNA to purify polyadenylated mRNAs and to build an RNA library, using TruSeq Stranded mRNA Sample Prep Kit (Illumina, #RS-122-9004DOC), as recommended by the manufacturer. Directional libraries were checked for concentration and quality on DNA chips with the Bioanalyser (Agilent). More precise and accurate quantification were performed with sensitive fluorescent-based quantitation assays ("Quant-It" assays kit and QuBit fluorometer, Invitrogen). Samples were normalized to 2nM and multiplexed. After denaturation using 0.1N NaOH (5’ at room temperature), the samples were diluted to 9pM and loaded on the flowcell. Sequencing was performed on the HiSeq 2500 sequencer (Illumina) in 65 bases V4 single-end mode

value: SunTag-NanogOtx


title: IN44Brg1minus1


title: SunTag_C2ON3_Nanog/Otx_-LIF_+Dox_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
B426-sample6


title: IN44Brg1plus1


title: IN44Brg1plus2


title: SunTag_C1ON3_Nanog/Otx_-LIF_-Dox_2

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
B426-sample9


title: IN44Esrrbminus2

value: Esrrb


title: IN44Esrrbminus1


title: SunTag_C1ON3_Nanog/Otx_-LIF_+Dox_2

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
B426-sample10


title: SunTag_C2ON3_Nanog/Otx_+LIF_+Dox_2

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
B426-sample16


title: SunTag_C2ON3_Nanog/Otx_-LIF_-Dox_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
B426-sample5


title: IN44Esrrbplus2


title: SunTag_C2ON3_Nanog/Otx_-LIF_-Dox_2

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
B426-sample13


title: SGBS_preadipocyte_rep2

source_name: preadipocyte

value: SGBS preadipocyte


title: IN44Esrrbplus1


title: SGBS_adipocyte_rep1


title: SunTag_C2ON3_Nanog/Otx_+LIF_+Dox_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
B426-sample8


title: IN44Brg1minus2


title: SGBS_preadipocyte_rep1


title: SunTag_C1ON3_Nanog/Otx_-LIF_+Dox_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
B426-sample2


title: SunTag_C1ON3_Nanog/Otx_+LIF_+Dox_2

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
B426-sample12


title: SunTag_C1ON3_Nanog/Otx_-LIF_-Dox_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
B426-sample1


title: SunTag_C2ON3_Nanog/Otx_+LIF_-Dox_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
B426-sample15


title: Sample92

city: La Jolla

first: Sheng

last: Zhong

state: California

address: 9500 Gilman Drive MC 0412

department: Bioengineering

institute: University of California, San Diego

data_processing:
Alignment STAR (v2.5.4b) with default parameters
Called for fusion candidates with STAR-Fusion (v0.8.0) using default parameters
Expression data was calculated with Cufflinks (v2.2.1)
Genome_build: hg38
Supplementary_files_format_and_content: gene fpkm, isoform fpkm, STAR-fusion candidates

source_name: lung tissue biopsy

extract_protocol:
Lung cancer biopsies were obtained flash frozen in dry ice, and RNA was harvested using Trizol reagent. RNA quality and quantity was analyzed using High Sensitivity D1000 ScreenTape.
Libraries were prepared according to Illumina's instructions accompanying the TruSight RNA Pan-Cancer Panel (Part# RS-303-1002).

value: lung tissue biopsy

tag: patient diagnosis

value: LUAD

tag: tumor stage

tag: age

tag: gender

value: F


title: Sample95

value: T2aN0M0 IB

value: M


title: Sample90

value: LUAD/LUSC

value: T2N0M0 IB


title: Sample96


title: Sample89

value: T3N2M0 IIIA


title: Sample84

value: T1bN0M0G3 R0 IB


title: SunTag_C1ON3_Nanog/Otx_+LIF_-Dox_2

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
B426-sample11

value: -Dox


title: SunTag_C1ON3_Nanog/Otx_+LIF_-Dox_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
B426-sample3


title: Sample87

description: No fusions detected in this sample.

value: T1bN0M0 IA


title: SunTag_C2_Nanog_-LIF_-Dox_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_H5

value: SunTag-Nanog


title: SunTag_C1_Nanog_-LIF_-Dox_2

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_H3


title: SunTag_C1_Nanog_-LIF_+Dox_1 (HV_H4)

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_H4

value: +Dox


title: SunTag_C1ON3_Nanog/Otx_+LIF_+Dox_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
B426-sample4


title: Sample81

value: BRCA


title: Sample78

value: LUSC


title: Sample83

value: T2N1M0 IIB


title: SunTag_C1_Nanog_-LIF_+Dox_1 (HV_H2)

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_H2


title: SunTag_C1_Nanog_-LIF_-Dox_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_H1


title: Sample82

value: pT2aN0M0 IB


title: SunTag_C2_Nanog_+LIF_-Dox_2

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_G7


title: Sample91

value: lung tissue biopsy


title: Sample80


title: Sample79

value: IF


title: SunTag_C2_Nanog_+LIF_-Dox_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_G5


title: SunTag_C2_Nanog_+LIF_+Dox_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_G6


title: Sample77

value: LUAD

value: pT2aN1M0 IIb


title: SunTag_C2_Nanog_-LIF_+Dox_2

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_H6


title: SunTag_C1_Nanog_+LIF_+Dox_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_G4


title: Sample76

value: pT2bN0M0 IIA

value: M


title: Tg2a_2i_3

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_F3


title: Sample88


title: SunTag_C1_Nanog_+LIF_-Dox_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_G1


title: Tg2a_2i_2

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_F2


title: Sample73

value: F


title: Sample75

value: T1bN1M0 I


title: Sample62


title: Sample64

value: T2N0M0 IIA


title: Tg2a_2i_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_F1


title: Tg2a_FCS_3

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_E3

value: FCS


title: Sample61


title: 44iN_-Dox_LT_2

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_D3

value: -Dox (LT)


title: 44iN_+Dox_2

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_C4


title: 44iN_-Dox_LT_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_D1


title: Tg2a_FCS_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_E1


title: Tg2a_FCS_2

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_E2


title: Sample56


title: Sample59

value: T2aN1M0 IIA


title: Sample57


title: Sample58

value: pT4N0M0 IIIA


title: 44iN_-Dox_24h_2

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_C3


title: 44iN_+Dox_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_C2

value: +Dox


title: Sample53

value: T1bN0M0 IA


title: 44iN_-Dox_24h_1

description:
rnaseq_counts_raw.tsv.gz
rnaseq_counts_deseqnorm.tsv.gz
HV_C1


title: Sample74

value: T2aN2M0 IIIA


title: Sample52


title: Sample51

value: T2N0M0 IB


title: Sample50

value: lung tissue biopsy


title: Sample49

description: No fusions detected in this sample.

value: LUSC


title: let7KO_litter number1_library number35

first: Areum

last: Han

address: Karp Family Building, 7th Floor. 300 Longwood Ave.

institute: Boston Children's Hospital

data_processing:
Raw reads were extracted and adaptors were removed using cutadapt tool(-n 1 -e 0.05 -O 20).
Then trimmed reads were mapped to mouse genome using tophat2(tophat-2.0.9, bowtie-2.0.6, samtools_0.1.19, --library-type=fr-unstranded --GTF= /Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --min-intron-length=10 --coverage-search --microexon-search --min-isoform-fraction=0).
From the aligned bamfiles, we counted how many reads were mapped to each gene using the htseq-count tool.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph, bw = read density information for visualization on genome browsers
Supplementary_files_format_and_content: txt = tab-delimited text files include count values for each gene in each sample.

source_name: whole kidney

extract_protocol:
RNA from each kidney was isolated using Trizol and treated with DNase.
Sequencing libraries were generated using a SMARTer Ultra Low RNA kit (V3) and sequenced on the HiSeq 2500 machine (Illumina).

tag: strain

value: Mixed (CD1 and C57BL/6)


title: let7KO_litter number1_library number34

tag: genotype/variation


title: let7KO_litter number2_library number36


title: wild type_litter number1_library number32

value: WT


title: Sample47

value: LUAD


title: Sample48

value: T2aN0M0 IB


title: wild type_litter number2_library number33


title: Sample60

value: PT4N2M0 IIIB

value: M


title: Sample55

value: pT2aN2M0 IIIA


title: wild type_litter number1_library number31


title: Sample44

value: T2bN1M1 IV


title: LIN28OE_litter number1_library number26


title: Sample43

value: F


title: Sample46


title: Sample42

value: T2aN0M0 IIA


title: Sample45

value: pT2aN0M0 Ⅱa


title: Sample41


title: wild type_litter number1_library number28


title: wild type_litter number2_library number29


title: LIN28OE_litter number1_library number27


title: Sample40

value: T1aN0M0 IA


title: MethylC-seq_NPC_21d

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
MethylC-seq reads were mapped to mm9 reference genome using MethylPy (https://bitbucket.org/schultzmattd/methylpy/wiki/Home). To ensure the correct calling of mCG and mCH, we removed cytosine positions with potential single nucleotide variants located at cytosines or immediately downstream of cytosines.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)

growth_protocol: Homozygous TauEGFP knock-in mice (Tucker et al., 2001) were bred with C57BL/6 mice (Jackson Labs) to generate heterozygous embryos. Only the limbs were isolated from E13.5 embryos, chopped into small pieces, trypsinized and plated in MEF media, containing 10% cosmic calf serum (Hyclone), 0.008% Beta mercaptoethanol (Sigma), MEM non-essential amino acids, Sodium Pyruvate, and Penicillin/Streptomycin (Pen/Strep) (all from Invitrogen), to derive fibroblast cultures (called TauEGFP MEFs). For homozygous Dnmt3a/3bfl/fl MEFs, Dnmt3afl/fl and Dnmt3bfl/fl mice on a C57BL/6 background were crossed to generate Dnmt3a/3bfl/fl mice15–17 . Whole body MEFs were harvested from E13.5 embryos by removing the head, spinal cord and red organs, minced into small pieces, trypsinized and plated in MEF media on gelatinized flasks to derive fibroblast cultures. Both MEFs were expanded for three passages prior to experiments. Lentivirus was produced, and TauEGFP MEFs were co-infected with reverse tetracyclin transactivator (rtTA) and doxycycline (dox) inducible TetO-Ascl1 alone or with TetO-Brn2 and TetO-Mytl1 as previously described19. Dox was added with fresh MEF media 16-20hrs post lentiviral infection, and cultures were switched to N3 media containing DMEM/F12, N2 and B27 supplements, 20ug/ml Insulin, Pen/Strep (all from Invitrogen) with dox after 2 days. Cells were harvested at 48 hours, 5d and 22d post-dox induction. Control MEFs were not infected and harvested 48hr after addition of dox. For 5d and 22d, cells were FAC (Fluorescence-activated cell)-sorted for TauEGFP+ cells to select for cells that were reprogramming. To ensure that reprogramming efficiencies are comparable, immunofluorescence staining for Tuj1 was performed for each batch of cells at day 14, and only samples that average at least 20 Tuj1+ neurons per 10X field of view were used. In addition for FAC-sorted samples, only samples containing >5% TauEGFP+ cells was used.

extract_protocol: A detailed protocol for MethylC-seq libraries preparation can be found in Urich et al., (2015). MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat Protoc 10, 475-483.

value: Neural progenitor cells differentiated for 21 days


title: Sample39


title: Sample38


title: MethylC-seq_NPC_7d_B

value: Neural progenitor cells differentiated for 7 days


title: MethylC-seq_NPC_7d_A


title: Sample36

description: No fusions detected in this sample.


title: MethylC-seq_NPC_14d

value: Neural progenitor cells differentiated for 14 days


title: Sample33

value: lung tissue biopsy


title: LIN28OE_litter number2_library number30


title: MethylC-seq_BAM_22d_B

value: Direct reprogramming from fibroblast to neuron induced with BAM for 22 days


title: Sample35

value: LUSC


title: Sample32

value: T4N0M0 IIIA


title: MethylC-seq_BAM_22d_A


title: Sample31

value: LUAD


title: MethylC-seq_BAM_5d_C

value: Direct reprogramming from fibroblast to neuron induced with BAM for 5 days


title: MethylC-seq_BAM_5d_B


title: Sample30


title: wild type_litter number1_library number25

value: WT


title: MethylC-seq_Ascl1_5d_B

value: Direct reprogramming from fibroblast to neuron induced with Ascl1 for 5 days


title: Sample28


title: Sample24

value: T3N0M0 IIB

value: M


title: MethylC-seq_Ascl1_5d_A


title: Sample26

value: IF

value: F


title: MethylC-seq_Ascl1_22d_A

value: Direct reprogramming from fibroblast to neuron induced with Ascl1 for 22 days


title: MethylC-seq_Ascl1_22d_B


title: Sample25


title: Sample23


title: Sample22


title: MethylC-seq_NPC_A

value: Neural progenitor cells


title: MethylC-seq_Ascl1_2d_A

value: Direct reprogramming from fibroblast to neuron induced with Ascl1 for 2 days


title: MethylC-seq_MEF_B

value: Mouse embryonic fibroblast


title: Sample21


title: Sample19

value: PT2N2M0 IIIA


title: MethylC-seq_MEF_A


title: MethylC-seq_NPC_B


title: ChIP-seq; XaWT Xi[delta]Xist cells; IgG Rep1

description:
ChIP-IgG_Xidel.comp.bw
ChIP-IgG_Xidel.mus.bw
ChIP-IgG_Xidel.cas.bw

data_processing:
Base-calling was performed with Illumina real time analysis (RTA) basecaller v1.17.21.3
For ATAC-seq: Adaptor sequences were trimmed with Trim Galore! V0.4.1 (stringency 12 and allowed error rate 0.2). Identical genomic sequences (PCR duplicates) were removed by custom program prior to alignment. To account for the M. mus (mus) / M. castaneus (cas) hybrid character of mouse dermal fibroblast lines that were employed in a ChIP-seq studies, reads were first aligned to custom mus/129 and cas genomes, and then mapped back to the reference mm10 genome. All alignments were performed by utilizing bowtie2 (v2.2.7) in paired-end mode. Post-processing of alignments was performed with custom scripts using SAMtools, and BEDtools (v2.25.0). These included accounting, alignment file-type conversion, extracting and reads sorting (SAMtools), and obtaining wig coverage files (SAMtools depth). To increase available read depth, we pooled together two biological replicates of ATAC-seq performed in wild-type cells, and separately pooled two biological replicates of ATAC-seq performed in XaWT Xi[delta]Xist cells. We also pooled two ATAC-seq biological replicates performed in a second XaWT Xi[delta]Xist cell line that served us as an independent biological system showing highly concordant results with those obtained by our main cell system. In each of these cases, pooled replicates were highly correlated to each other (r2 > 0.9), indicating strong data reproducibility. For visualizing ATAC-seq binding signal, we generated fragments per million (fpm)-normalized bigWig files from the raw ATAC read counts for all reads (comp), mus-specific (mus), and cas-specific reads, separately. Uniquely aligned wig files were scaled to total number of fragments per million in each library (determined by SAMtools flagstat combining reads ‘‘with itself and mate mapped’’ and ‘‘singletons’’). ATAC-seq tag density bigWig files were viewed in Integrative Genomics Viewer (IGV). To quantify reproducibility between two biological replicates of ATAC-seq generated in WT cells (or XaWT Xi[delta]Xist cells), we first counted per each two replicates the number of uniquely aligned neutral/cas/mus (comp) reads, per sample, and performed random downsampling without replacement of the larger sample in order to equalize reads number within two replicates (in general, all of our replicate samples had very similar numbers of reads also prior to downsampling). Next, we called MACS2 peaks (by employing –BAMPE (paired-end mode), and pvalue=0.005) in individual replicates. Peak sets called in individual replicates were then combined, and overlapping peaks were merged to form a union peak set. By applying Homer suit’s makeTagDirectory and annotatePeaks algorithms we obtained a read count matrix of two biological replicates over union peak set, and normalized these values per each library’s reads size by using edgeR. Log2 of ATAC-seq peaks’ signal within autosomes was plotted (≥10 reads per peak), and Pearson correlation coefficient of two biological replicates was calculated. In both cell lines, WT and XaWT Xi[delta]Xist, correlation coefficients of biological replicates of ATAC-seq were high (r2>0.94, 0.95, respectively), indicating strong data reproducibility. Similarly, high correlation coefficients were also obtained when comparing two biological replicates of ATAC-seq performed in WT cells treated with siControl, or with siBRG1 (r2 >0.92, 0.9, respectively), and in XaWT Xi[delta]Xist cells treated with siControl, or with siBRG1 (r2 >0.96, in both).
For ChIP-seq: Adaptor sequences were trimmed with Trim Galore! V0.4.1 (stringency 12 and allowed error rate 0.2). Identical genomic sequences (PCR duplicates) were removed by custom program prior to alignment. To account for the M. mus (mus) / M. castaneus (cas) hybrid character of mouse dermal fibroblast lines that were employed in a ATAC-seq and ChIP-seq studies, reads were first aligned to custom mus/129 and cas genomes, and then mapped back to the reference mm10 genome. All alignments were performed by utilizing novoalign (v3.00.02) in paired-end mode (Novocraft Technology, Selangor, Malaysia). Post-processing of alignments was performed with custom scripts using SAMtools v0.1.18, and BEDtools (v2.25.0). These included accounting, alignment file-type conversion, extracting and reads sorting (SAMtools), and obtaining wig coverage files (SAMtools depth).  In each of these cases, pooled replicates were highly correlated to each other (r2 > 0.91), indicating strong data reproducibility (for details about calculation of correlation coefficients between two replicates see the following section). For visualizing ChIP binding signal, we generated fragments per million (fpm)-normalized bigWig files from the raw ChIP read counts for all reads (comp), mus-specific (mus), and cas-specific reads separately. Uniquely aligned wig files were scaled to total number of fragments per million in each library (determined by SAMtools flagstat combining reads ‘‘with itself and mate mapped’’ and ‘‘singletons’’). ChIP-seq tag density bigWig files were viewed in Integrative Genomics Viewer (IGV). To quantify reproducibility between two biological replicates of BRG1 ChIP-seq generated in WT cells (or XaWT Xi[delta]Xist cells), we first called MACS2 peaks (by employing –BAMPE (paired-end mode), qvalue=0.005, and –bdg) in individual replicates, by contrasting each sample (uniquely aligned comp reads) against its corresponding control sample (prepared in the same cell line). Fold-enrichment signal (FE; IP sample’s signal over its corresponding Input sample’s signal) was calculated per each sample by executing MACS2 bdgcmp using –method FE. Peak sets called in individual replicates were then pooled, and overlapping peaks were merged to form a union peak set. By applying Homer suit’s makeTagDirectory and annotatePeaks algorithms we obtained a read counts matrix of two biological replicates over union peak set, and normalized these values per each library’s reads size using edgeR. Log2 fold-enrichment peak signal was plotted, and Pearson correlation coefficient of two biological replicates was calculated. In both cell lines, WT and XaWT Xi[delta]Xist, BRG1 ChIP-seq correlation coefficients of biological replicates were high (r2 >0.97, 0.91, respectively), indicating strong data reproducibility.
Genome_build: mm10

source_name: Dermal female fibroblasts (XaWT Xi[delta]Xist). Genetic manipulation: Post XCI deletion of Xist on inactive X-chromosome

growth_protocol: Differentiated mouse fibroblast cells were cultured in regular fibroblast medium, 1% Pen/Strep, high-glucose DMEM+GlutaMax with 10% FBS

extract_protocol:
Approximately 50 × 106 cells were washed in PBS, scraped in lysis buffer (10 mM Tris-HCl pH7.5, 30 mM NaCl, 0.1% NP40, 3 mM MgCl2 and proteinase inhibitor cocktail (Roche)) and incubated for 10 min on ice. After centrifugation, nuclei pellets were resuspended in benzonase buffer (50 mM Tris pH 7.5, 300mM NaCl, 0.5% NP40, 2.5mM MgCl2 and proteinase inhibitor cocktail). Chromatin was digested by adding 125 units of benzonase (Sigma) for 30 min on ice and was spun at 16,000g at 4ºC. Benzonase digestion was stopped by diluting twice the supernatants in 50 mM Tris pH 7.5, 100mM NaCl, 0.5% NP40, 15mM EDTA containing proteinase inhibitor cocktail. After pre-clearing step using 100 uL Dynabeads protein G magnetic beads (Invitrogen), the chromatin was incubated with 4 ug of either anti-BRG1 (ab110641) or anti-IgG (Cell signaling, 2729S) antibodies pre-bound to 50 ul Dynabeads protein-G magnetic beads (Invitrogen) rotating for 4 hr at 4C. An aliquot of untreated chromatin was processed in parallel and used as the total input DNA control. Beads were washed 3 times in 50 mM Tris pH 7.5, 150 mM NaCl, 0.5% NP40, 5mM EDTA, followed by 3 times in 50 mM Tris pH 7.5, 500 mM NaCl, 0.5% NP40, 5mM EDTA. DNA was eluted twice by incubation in elution buffer (1% SDS, 0.1M NaHCO3) for 15 min. DNA was subjeced to RNase and proteinase K digestion and then purified.
For sequencing, 10 ng of IP or input DNA was used for ChIP-seq library construction using NEBNext Ultra DNA Library Prep Kit for Illumina. Libraries were assessed for quality control on the BioAnalyzer 2100 (Aglient). Sequencing was performed on the HiSeq 2500 (Illumina), using 50 bp paired-end reads. NEBNext adapters F: GATCGGAAGAGCACACGTCTGAACTCCAGTC, R: ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: CAST/Ei x 129/Sv/Jae

tag: cells

value: Differentiated dermal female fibroblast cells

value: Female


title: Sample18

value: lung tissue biopsy

value: LUSC/SCLC

value: p T1bNxM0 1A


title: Sample17

value: Carcinoid


title: HCT116 Drosha KO_Doxo_2

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

data_processing:
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the hg19 genome using TopHat
The miRNA normalized counts was generated as in Farazi et al., Cancer research 2011 (GEO accession number GSE28884)
Genome_build: hg19
Supplementary_files_format_and_content: format: xlsx content: Normalized counts

growth_protocol: HeyA8 cells are cultured in RPMI1640 medium supplemented with 10% FBS and 1% L-Glutamine. HCT116 cell lines were cultured in McCoy's 5A medium, supplemented with 10% FBS and 1% L-Glutamine.

extract_protocol:
AGO1-4 were pulled down from whole cell lysate (Hauptmann et al., 2015 PNAS).  The RNA was isolated using Trizol.
Preadenylated, barcoded 3´adapter oligonucleotide was ligated followed by ligation of a 5´adapter. Ligation products were reverse transcribed and amplified by PCR.

treatment_protocol: cells were treated where indicated with Doxorubicin (doxo) for 20h, 40h or 80h

value: treated with Doxorubicin

tag: passages

tag: pull down

value: Pull down with Pan-AGO peptide (Hauptmann et al., 2015 PNAS


title: Sample27

tag: tissue

value: LUAD

value: pT2aN0M0 IB


title: HCT116 Drosha KO_Doxo_1


title: Sample15

description: No fusions detected in this sample.

value: angioma

value: F


title: HCT116 Drosha KO_Ctrl_2

value: control cells


title: HCT116 Drosha KO_Ctrl_1


title: ChIP-seq; XaWT Xi[delta]Xist cells; Input Rep1

description:
BRG1DepositionClass_Monoallelic.bed
BRG1DepositionClass_Biallelic.bed
BRG1DepositionClass_XiRestored.bed
ChIP-Input_Xidel.comp.bw
ChIP-Input_Xidel.mus.bw
ChIP-Input_Xidel.cas.bw


title: Sample14

value: SCLC

value: PT3N0M0 IIB

value: M


title: HCT116_Doxo_1


title: Sample11


title: Sample13

value: LUSC

value: T2N0M0 IB


title: HCT116_Doxo_2


title: ChIP-seq; WT cells; Input Rep1

description:
BRG1DepositionClass_Monoallelic.bed
BRG1DepositionClass_Biallelic.bed
BRG1DepositionClass_XiRestored.bed
ChIP-Input_WT.comp.bw
ChIP-Input_WT.mus.bw
ChIP-Input_WT.cas.bw

value: CAST/Ei x 129/Sv/Jae

value: Differentiated dermal female fibroblast cells

value: Female


title: MethylC-seq_Ascl1_2d_B

first: Joseph

tag: cell type

value: Direct reprogramming from fibroblast to neuron induced with Ascl1 for 2 days


title: ChIP-seq; WT cells; IgG Rep1

description:
ChIP-IgG_WT.comp.bw
ChIP-IgG_WT.mus.bw
ChIP-IgG_WT.cas.bw

tag: Sex


title: ChIP-seq; XaWT Xi[delta]Xist cells; BRG1 Rep2

description:
BRG1DepositionClass_Monoallelic.bed
BRG1DepositionClass_Biallelic.bed
BRG1DepositionClass_XiRestored.bed
ChIP-BRG1_Xidel.merged.comp.bw
ChIP-BRG1_Xidel.merged.mus.bw
ChIP-BRG1_Xidel.merged.cas.bw


title: HCT116_CTrl_2


title: Sample10

value: lung tissue biopsy

value: T3N0M0 IIB


title: ChIP-seq; XaWT Xi[delta]Xist cells; BRG1 Rep1


title: Sample3

value: T2aN0M0 IB


title: Snap25_1_CAATTCG_TRAP_RF

city: St Louis

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

data_processing:
Quality check using using FastQC (version 0.11.2)
Trim low-quality bases from the ends of reads and to remove adapter sequences using Trimmomatic (version 0.32). Only fragments 25-35 nt in length were retained for subsequent analysis
Reads aligning to the mouse rRNA were removed using STAR (version 2.3.1z8)
Surviving reads were then aligned to non-degenerate mouse transcriptome using Bowtie2 (version 2.2.2), retaining both uniquely mapped and multi-mapped reads
For Readthrough identification: In order to count reads aligning to non-overlapping regions for readthrough analysis in culture (deposited in GSE77076) and TRAP-RF data, we used the BEDTools intersect command. Then, similar to prior work (Dunn et al 2013), we removed reads aligning to the following positions: 12 nts after the start codon; 15 nts before and 9 nts after the first stop codon, and 15 nts after the second stop codon. This resulted in four remaining transcriptomic regions: 5’UTR, CDS, readthrough region, and distal 3’UTR. Reads were counted in each of these regions using the uniq Unix utility. Readthrough analysis was performed in R. Transcripts were filtered based on CDS counts as follows: in culture RF, transcripts with ≥ 320 CDS counts across all samples were retained, and in TRAP RF, transcripts with ≥ 128 CDS counts across replicates in either the Aldh1l1 or Snap25 samples were retained. Subsequently, to avoid false positive identification of readthrough events because of alternative splicing, if a gene was annotated as having multiple isoforms with stop codons at different genomic locations, only the transcript with the downstream-most stop codon was retained. Using edgeR, counts were normalized to RPKM, and readthrough rate was defined for each transcript as the ratio of readthrough region RPKM to coding sequence RPKM. Next, for readthrough identification in culture RF and brain TRAP-RF datasets, transcripts with ≥ 32 readthrough region counts across samples were retained. In each dataset, surviving transcripts with ≥ 1% readthrough rate in at least 2 samples were retained for readthrough analysis. Genes with ≥ 100% readthrough or with RPKM(distal 3’UTR) ≥ RPKM(readthrough region), for any transcript isoform or in any sample, were labeled false positives and eliminated.
Genome_build: Ensembl 75 (mouse) transcriptome with degenerate sequences removed
Supplementary_files_format_and_content: txt files with counts of certain transcript region for each sample [For annotation on transcript region: "a": 5' untranslated region [5'UTR]; "b": Coding Sequence[CDS]; "c": readthrough region; "d": distal 3'UTR]

source_name: brain

extract_protocol:
TRAP-RF-in-vivo: P21 Snap25::eGFP-RpL10a, Aldh1l1:: eGFP-RpL10a, along with their eGFP-negative littermates were euthanized, and their brains frozen in liquid nitrogen and stored at -80C until use. Two brains were pooled per sample, and replicate experiments were done. TRAP was  performed as described (Heiman et al 2008) with a few modifications. Briefly, the brains were homogenized in ice in a buffer (20 mM pH 7.4 HEPES, 150 mM KCl, 5 mM MgCl2, 0.5 mM dithiothreitol, 100 μg/ml CHX, Turbo DNAse, protease inhibitors, and RNase inhibitors). The lysates were cleared by centrifuging at 2000 xg for 10 m at 40C and then treated with DHPC (to 30mM, Avanti) and NP-40 (to 1%, Ipgal-ca630, Sigma) for 5 min in ice. Lysates were then further cleared by centrifuging at 20,000 xg for 15 m at 40C and then mixed with protein L-coated magnetic beads (Invitrogen), previously conjugated with a mix of two monoclonal anti-GFP antibodies  (Doyle et al 2008), and incubated with rotation for 4 h at 4°C. Beads were washed 5 times with a high-salt buffer (20 mM pH7.4 HEPES, 350 mM KCl, 5 mM MgCl2, 1% NP-40, 0.5 mM dithiothreitol, and 100 μg/ml CHX) and then resuspended in normal-salt buffer (150 mM KCl, otherwise as above). To couple to RF, on-bead RNA digestion was performed with RNAse I (Invitrogen) for 1 h with end-to-end rotation, followed by washing three times with normal-salt buffer. Small ribosomal subunits with the mRNA fragments were eluted with ribosome dissociation buffer as described (20 mM pH7.3 Tris-HCl, 250 mM NaCl, 0.5% Triton X-100, 50mM EDTA) (Gonzalez et al 2014). RNA was extracted with phenol-chloroform, quality-tested with Agilent BioAnalyzer, and then subjected to dephosphorylation and subsequent library preparation as described for RF (Ingolia et al 2011). Briefly, the cell lysates were treated with RNAseI and subjected to sucrose-cushion ultracentrifugation for pelleting monosomes. mRNA fragments were isolated from the monosomes, size-selected in a polyacrylamide, ligated to cloning linkers, and converted to cDNAs.
The cDNAs were then circularized, depleted of rRNAs, PCRed and size-selected and finally deep-sequenced on Illumina Hiseq 2000 (50 bp, single end).

tag: footpring method

value: TRAP RF

tag: condition

value: in vivo

value: neuron

tag: molecule

value: ribomsome protected RNA fragment


title: Snap25_2_TGGTCTG_TRAP_RF


title: ChIP-seq; WT cells; BRG1 Rep1

description:
BRG1DepositionClass_Monoallelic.bed
BRG1DepositionClass_Biallelic.bed
BRG1DepositionClass_XiRestored.bed
ChIP-BRG1_WT.merged.comp.bw
ChIP-BRG1_WT.merged.mus.bw
ChIP-BRG1_WT.merged.cas.bw


title: ChIP-seq; WT cells; BRG1 Rep2


title: Sample1

value: LUAD


title: Aldh1_1_CGTCGGT_TRAP_RF

value: astrocyte