title: S133, 1st sample set (scRNA-seq)


title: MuSC_d0_Young_Pax7_bulkRNAseq_Rep3

status: Public on Oct 26 2019

type: SRA

city: Boston

first: Sundari

last: Chetty

state: MA

address: 185 Cambridge Street

department: Harvard Medical School

country: USA

institute: Massachusetts General Hospital, Harvard University

description:
SE RNA-seq
bulkRNAseq.FPKM.tsv
bulkRNAseq.TPM.tsv
bulkRNAseq.expected_count.tsv

library_source: transcriptomic

data_processing:
In according with the NextSeq500 analysis, protocol, base calling and quality scoring are performed by an updated implementation of Real-Time Analysis (RTA), called RTA v2
FASTQ reads are processed with the ENCODE-DCC ATAC-seq pipeline, v 1.0
A merged ATAC-seq peak set across samples was generated by applying the bedtools merge command across the sample naive overlap optimal peak sets
Read counts for each peak for each sample were obtained with the bedtools coverage command over the merged ATAC-seq peak set
Technical replicates with pearson correlation < 0.9 across peak CPM values were excluded from analysis
Genome_build: mm10
Supplementary_files_format_and_content: tagAlign files, bigWig files, and peak calls files (narrowPeak) were generated for each technical replicate via the ENCODE ATAC-seq data processing pipeline ()
Reads were aligned to mm10 reference genome using STAR (v 2.5.0a)
Transcript and gene abundance was quantified via RSEM (v 1.3.0)
Technical replicates with pearson correlation < 0.9 across gene TPM values were excluded from analysis
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimeted text file include FPKM, TPM, and expected read count values for each technical replicate

molecule: total RNA

organism: Mus musculus

source_name: MuSCs, Pre-injury, Young, Pax7+

extract_protocol:
Hind limb muscles (tibialis anterior and gastrocnemius) of control and experimental mice were dissected using sterile surgical tools,  tissues were minced and transferred into 50 mL conical tubes containing 20 mL of digest solution. Cell sorting was done using a BD FACSAria III Cell Sorter.
Chromatin Accessibility Assay and Sequencing Library Preparation.
At least 10,000 MuSCs were centrifuged at 500xg for 5 min at 4˚C in a fixed angle centrifuge. After removing the supernatant, the cell pellets were re-suspended in 50uL ATAC-Resuspension Buffer (RSB) (500uL 1M Tris-HCl, 100uL 5M NaCl, 150uL 1M MgCl2 in 49.25mL sterile water) with 0.1% NP40, 0.1% tween-20, and 0.01% Digitonin. Samples were pipetted up and down three times to mix, incubated 3 minutes on ice, then diluted in 1mL of ice-cold ATAC-RSB containing 0.1% Tween-20 and centrifuged at 500xg for 10 min at 4˚C to pellet the nuclei. The supernatants were carefully removed and the pellets were re-suspended in 25 µL of transposase reaction mix (12.5 µL 2x TD buffer, 1.25 µL TN5 transposase (Illumina) and 11.25 µL nuclease-free water). Transposase reactions were carried out by incubating samples at 37˚C for 30 min under mild agitation (300 rpm on a Thermo-mixer C, Eppendorf). Once the incubation was completed, sample tubes were placed on ice and the transposed DNA fragments from each sample were purified using a Qiagen MinElute PCR Purification Kit following manufacture’s protocol. Purified DNA fragments were then amplified for 13 cycles using barcoded PCR primers and NEB Next High Fidelity 2x PCR Master Mix (New England Bio Labs) on a thermal cycler. Double concentrated Ampure beads were used to purify transposed DNA amplicons. The molarity of each DNA library was determined (Agilent 2100 Bioanalyzer), pooled into a single tube and sequenced on a NextSeq (Illumina) using 76-bp paired-end reads.
Bulk mRNA Isolation and Sequencing Library Preparation.
MuSCs sorted directly into Trizol were thawed at room temperature, and RNA was extracted using a Qiagen miRNeasy Micro Kit as per manufacturer’s instructions. RNA concentration and integrity were measured with a Nanodrop spectrophotometer (Nanodrop 2000c) and Bioanalyzer (Agilent 2100). 1-10 ng of high-quality RNA (RIN>8) was used to produce cDNA libraries using the SmartSeq v4 protocol (Clontech) as per the manufacturer’s instructions. cDNAs were prepared into sequencing libraries using 150 pg of full-length cDNA amplicons (Nextera XT DNA Library Preparation Kit, Illumina) with dual index barcodes as per manufacturer’s instructions. Barcoded cDNA libraries were pooled into a single tube and sequenced on a NextSeq (Illumina) using 76-bp single-ended reads.

tag: cell type

value: Flow sorted muscle stem cells (Pax7+ Muscle stem cells)

tag: age

value: Young

tag: timecourse


title: MuSC_d0_Young_Pax7_bulkRNAseq_Rep2


title: MuSC_d0_Young_Pax7_bulkRNAseq_Rep1


title: MuSC_d1_Aged_bulkRNAseq_Rep2

source_name: MuSCs, Post-injury Day 1, Aged

value: Flow sorted muscle stem cells

value: Aged


title: MuSC_d0_Aged_bulkRNAseq_Rep3

source_name: MuSCs, Pre-injury, Aged


title: S82, 1st sample set (scRNA-seq)

city: PALO ALTO

first: YUAN

last: GUAN

state: CA

address: 1701 Page Mill Road

institute: Stanford University

data_processing:
Adapter sequences and low-quality bases at the end of the reads were then removed using the Cutadapt software
The reads were then aligned to human exon sequences (Build GRCh38) using STAR
The expression level of each gene for each cell were then quantified using the FeatureCounts tool
Fragments Per Kilobase of Exon Per Million (FPKM) were generated using scater package in R
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-delimited file containing the log2-transformed FPKM values

organism: Homo sapiens

source_name: GM

growth_protocol: For production of HO1, iPSCs were dissociated to single cells in buffer with 5 mM EDTA and 10 mM Y-27632 (Santa Cruz Biotechnology, Dallas, Texas), and were re-aggregated in low-cell-adhesion 60 mm dishes (Corning) in endoderm differentiation medium (10e5 cells/dish) containing 10 mM Y-27632. The endoderm differentiation medium consisted of DMEM/F12 + ITS (GIBCO) supplemented with 0.1 mM nonessential amino acids and 1 mM pyruvate. On days 0 to 3, Activin-A (100 ng/ml) and BMP4 (10 ng/ml) were added the definitive endoderm differentiation medium. For endoderm patterning and for the generation of foregut spheroids, Matrigel (BD Biosciences, GFR) was added to RPMI + B27 medium to a final v/v concentration of 2% from days 3 to 9. From days 3 to 6, 50 ng/ml FGF10 (Peprotech) was added to the medium. From days 6 to 9, 10 ng/ml FGF10 and 10 ng/ml BMP4 were added to the medium. After day 9, Matrigel (final 1% v/v concentration) was added to the organoid growth and differentiation medium (HCM, Lonza), which was supplemented with HGF (50 ng/ml), 50-ng/ml oncostatin M and 10 uM Dexamethasone (Sigma, St. Louis MO).  On day 20, the organoids were collected and re-seeded for further differentiation and characterization.

extract_protocol:
Single cells from iPSC (day 0), day 9 HB, and day 30 HO cultures, and PHHs were prepared using the C1 Single-Cell Auto Prep System (Fluidigm, South San Francisco, CA). The captured cells across the 96 wells were manually inspected as a quality control measure to remove empty wells, doublets or debris-containing wells. For quality control (normalization and estimation of technical noise), 0.05 ul of 1:200,000 dilution of External RNA Controls Consortium (ERCC) RNA spike-in Mix1 (Ambion, AM1780) was added to lysis buffer.
High-quality cDNA libraries for single cell transcriptome analysis were prepared using the SMART-Seq v4 Ultra Low RNA Kit for the Fluidigm C1 System (Takara Bio USA, 635025). The size distribution and the concentration of single-cell cDNA were assessed using a Agilent 2100 Bioanalyzer with the high sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA, 5067). Sequencing libraries were constructed in 96-well plates using the Nextera XT DNA Sample Preparation kit according to the manufacturer's protocol (Illumina, San Diego, CA, FC-131-1096) with 96 dual barcoded indices (Illumina; FC-131-1002). Library cleanup and pooling was performed using AMPure XP beads (Agencourt Biosciences; A63880). Up to 200 quantified single-cell libraries were pooled, and these were sequenced 150 bp paired-end on one lane of Illumina HiSeq 4000 to a depth of 2.1 million reads per cell.

tag: differentiation stage

value: GM

tag: cell id at each stage

tag: subject

tag: qc

value: TRUE


title: MuSC_d3_Young_bulkRNAseq_Rep1

source_name: MuSCs, Post-injury Day 3, Young


title: S65, 1st sample set (scRNA-seq)

value: FALSE


title: S48, 1st sample set (scRNA-seq)


title: MuSC_d0_Aged_bulkRNAseq_Rep2


title: MuSC_d0_Young_bulkRNAseq_Rep5

source_name: MuSCs, Pre-injury, Young


title: S99, 1st sample set (scRNA-seq)


title: s3, 2nd sample set (scRNA-seq)

source_name: HB

value: HB


title: MuSC_d0_Aged_bulkRNAseq_Rep1


title: S184, 1st sample set (scRNA-seq)

source_name: DM

value: DM


title: MuSC_d0_Young_bulkRNAseq_Rep4


title: S150, 1st sample set (scRNA-seq)


title: MuSC_d0_Young_bulkRNAseq_Rep3


title: S14, 1st sample set (scRNA-seq)


title: MuSC_d0_Young_bulkRNAseq_Rep2


title: S201, 1st sample set (scRNA-seq)


title: S31, 1st sample set (scRNA-seq)


title: S116, 1st sample set (scRNA-seq)


title: S218, 1st sample set (scRNA-seq)

source_name: PHH

value: PHH


title: MuSC_d0_Aged_bulkRNAseq_Rep4


title: S122, 1st sample set (scRNA-seq)


title: S37, 1st sample set (scRNA-seq)

source_name: phLO

value: phLO


title: S71, 1st sample set (scRNA-seq)


title: S88, 1st sample set (scRNA-seq)


title: MuSC_d0_Young_bulkRNAseq_Rep6


title: S167, 1st sample set (scRNA-seq)


title: S54, 1st sample set (scRNA-seq)


title: S139, 1st sample set (scRNA-seq)

source_name: iPSC

value: iPSC


title: S156, 1st sample set (scRNA-seq)


title: S173, 1st sample set (scRNA-seq)


title: S3, 1st sample set (scRNA-seq)


title: S20, 1st sample set (scRNA-seq)


title: S190, 1st sample set (scRNA-seq)


title: MuSC_d0_Young_bulkRNAseq_Rep1


title: S134, 1st sample set (scRNA-seq)


title: S207, 1st sample set (scRNA-seq)


title: S49, 1st sample set (scRNA-seq)


title: S83, 1st sample set (scRNA-seq)


title: Glioblastoma 27

type: RNA

city: Ottawa

first: Martin

last: Roffe

state: ON

address: 401 Smyth Rd

country: Canada

institute: CHEO Research Institute

description: RSK1 protein groups were defined based on RSK1 protein levels and survival

hyb_protocol: SensationPlus™ FFPE Amplification and WT Labeling Kit

scan_protocol: GeneChip® Expression Wash, Stain and Scan

data_processing: Primary processing (matrix submitted to GEO): The CEL files were normalized and summarized at the gene level using SST-RMA algorithm from the Transcriptome Analysis Console software (Thermo). Further processing: Normalized expression and DABG (detection above background) values were retrieved from the CHP files using the affxparser package. Five of the 30 FFPE-blocks were newer and a batch effect was observed for them. Thus, ComBat algorithm was used to remove batch effects (Leek et al., 2012). Transcript clusters with DABG ≥ 0.05 for all of the samples were excluded. Data were annotated according to the hta20transcriptcluster.db package in R. Only transcript clusters with a corresponding RefSeq ID for protein (“NP”) were kept, and transcript clusters for the same gene were collapsed (based on max intensity) using the WGCNA package (Langfelder and Horvath, 2008).

label: 3' IVT

source_name: Glioblastoma 27

label_protocol: 3' IVT Labeling Kit (Thermo)

growth_protocol: glioblastoma samples

extract_protocol: mRNA from the 30 glioblastoma (GBM) samples from the A.C.Camargo Cancer Center (ACCCC) cohort was extracted from formalin-fixed, paraffin-embedded (FFPE) slices using the ReliaPrep™ FFPE Total RNA Miniprep System (Promega)

tag: tissue

value: brain

tag: tumor type

value: glioblastoma

tag: rsk1 protein group

value: lo

tag: batch

value: old


title: S105, 1st sample set (scRNA-seq)


title: Glioblastoma 24

description: RSK1 protein groups were defined based on RSK1 protein levels and survival; *clustering based on transcriptome slightly different from the assigned RSK1 protein group

source_name: Glioblastoma 24

value: lo*


title: S66, 1st sample set (scRNA-seq)


title: Glioblastoma 21

source_name: Glioblastoma 21

value: hi


title: Glioblastoma 25

source_name: Glioblastoma 25

value: hi*


title: Glioblastoma 23

source_name: Glioblastoma 23


title: Glioblastoma 28

source_name: Glioblastoma 28


title: Glioblastoma 30

source_name: Glioblastoma 30

value: new


title: Glioblastoma 17

source_name: Glioblastoma 17


title: Glioblastoma 13

source_name: Glioblastoma 13


title: S168, 1st sample set (scRNA-seq)


title: S185, 1st sample set (scRNA-seq)


title: Glioblastoma 29

source_name: Glioblastoma 29


title: Glioblastoma 16

source_name: Glioblastoma 16


title: Glioblastoma 20

source_name: Glioblastoma 20


title: S151, 1st sample set (scRNA-seq)


title: Glioblastoma 18

source_name: Glioblastoma 18


title: Glioblastoma 19

source_name: Glioblastoma 19


title: Glioblastoma 14

source_name: Glioblastoma 14


title: S15, 1st sample set (scRNA-seq)

source_name: DM


title: Glioblastoma 11

source_name: Glioblastoma 11


title: Glioblastoma 26

source_name: Glioblastoma 26


title: Glioblastoma 22

source_name: Glioblastoma 22


title: Glioblastoma 15

source_name: Glioblastoma 15


title: S117, 1st sample set (scRNA-seq)


title: S100, 1st sample set (scRNA-seq)


title: Heart of mouse treated with ETX, biological rep6

city: Chongqing

first: Yu

last: Shi

state: Chongqing

address: 10 Changjiang Branch Road

department: Cardiology

country: China

institute: Military Medical University

hyb_protocol: The GeneChip® WT Terminal Labeling Kit (Affymetrix) was used for the fragmentation and labeling of the cDNA. Then, hybridizations for cartridge arrays were set up by using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: The probe arrays were washed, stained and scanned to generate the data.

data_processing: Expression data were generated by Affymetrix Expression Console Software and normalized by RMA(Robust Multi-chip Average) method.

label: biotin

source_name: Heart of mouse treated with ETX

label_protocol: The total RNA (20-50 ng) was reverse transcribed to synthesize first-strand cDNA containing a T7 promoter sequence.

growth_protocol: The hearts tissue were extracted from P14 mice.

extract_protocol: Using the Ambion® Whole Transcript (WT) Expression Kit ((Affymetrix, Thermo Fisher Scientific),extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The total RNA was extracted from P14 heart tissue after treatment with vehicle (PBS) or ETX for 1 week.

tag: strain background

tag: treatment

value: ETX

value: Heart


title: Heart of mouse treated with ETX, biological rep7


title: Glioblastoma 10

source_name: Glioblastoma 10


title: Glioblastoma 9

source_name: Glioblastoma 9


title: Glioblastoma 8

source_name: Glioblastoma 8


title: Kii-20

city: Shinjuku-ku

first: Mitsuru

last: Ishikawa

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with  [RMA normalization (85th percentile), Low signal cutoff (cut off value: 100), Log transformation (Base 2), Ratio to control samples (mean)] by using the transcriptome data analysis software Subio Platform (Subio, Kagoshima, Japan)

source_name: ALS_Frontal lobe

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: clinical phenotypes

value: ALS

tag: gender

value: Female

value: Human Postmortem Brain

tag: tissue subtype

value: Frontal lobe


title: Kii-21

source_name: PDC_Temporal lobe

value: PDC

value: Temporal lobe


title: S32, 1st sample set (scRNA-seq)

value: DM

value: TRUE


title: Kii-18

source_name: PDC_Frontal lobe

value: Male


title: S219, 1st sample set (scRNA-seq)

value: PHH


title: Heart of mouse treated with PBS, biological rep3

source_name: Heart of mouse treated with PBS

value: PBS


title: Heart of mouse treated with PBS, biological rep12


title: Kii-19


title: Heart of mouse treated with PBS, biological rep9


title: S130, 1st sample set (scRNA-seq)

source_name: PHH

value: FALSE


title: Kii-17


title: Glioblastoma 6

source_name: Glioblastoma 6

value: brain

value: glioblastoma

value: hi

value: old


title: Glioblastoma 7

source_name: Glioblastoma 7

value: lo


title: Kii-16

source_name: ALS+D_Frontal lobe

value: ALS+D


title: S202, 1st sample set (scRNA-seq)

source_name: DM


title: Kii-15

value: ALS

value: Female


title: Kii-14

value: Human Postmortem Brain

value: Frontal lobe


title: S45, 1st sample set (scRNA-seq)

source_name: phLO

value: phLO


title: Glioblastoma 4

source_name: Glioblastoma 4

value: new


title: S79, 1st sample set (scRNA-seq)

source_name: GM

value: GM

value: TRUE


title: Kii-12


title: Kii-11


title: Kii-13

value: PDC


title: Glioblastoma 5

source_name: Glioblastoma 5


title: Kii-10

value: Male


title: Glioblastoma 2

source_name: Glioblastoma 2


title: k562_polyA2

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description: RNAlevels.csv

data_processing:
For RNA-seq poly-A data: Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome hg38 with TopHat v2.0.13 , with “–library-type fr-firststrand” , using annotation gene models. FPKM values were generated using Cufflinks v2.2.1 with “-u –max-bundle-frags 100000000”. Read counts were generated using HTSeq-count with “-m intersection-nonempty”.
For quant-seq: the gene quantification CPM were generated with the slam-dunk pipeline http://t-neumann.github.io/slamdunk/
Supplementary_files_format_and_content: RNAlevels.csv

extract_protocol: RNA-seq with poly-A selection

treatment_protocol: the cells are wt K562 cells, without 4sU treatment, we want to see, if QuantSeq could works to measure RNA level, and also we want to compare with 4sU treated K562 cells, to make sure 4sU itself doesn't influence gene expression.

tag: cell line

value: untreated


title: S96, 1st sample set (scRNA-seq)


title: k562_polyA1

description: RNAlevels.csv


title: S62, 1st sample set (scRNA-seq)


title: k562slam2

description: RNAlevels.csv

extract_protocol: mRNA 3′ end sequencing was performed using the Quant-seq mRNA 3′ end library preparation kit (Lexogen) according to the instructions of the manufacturer


title: Glioblastoma 12

source_name: Glioblastoma 12

value: brain


title: S181, 1st sample set (scRNA-seq)


title: Kii-8

source_name: PDC+A_Frontal lobe

value: PDC+A


title: k562slam1

description: RNAlevels.csv


title: Kii-9


title: S164, 1st sample set (scRNA-seq)

source_name: HB

value: HB


title: Glioblastoma 1

source_name: Glioblastoma 1

value: glioblastoma


title: S147, 1st sample set (scRNA-seq)

source_name: iPSC

value: iPSC


title: Kii-7


title: YAPKO2_TRAM_REP3

city: Los Angeles

first: Miller

last: Huang

address: 4650 Sunset Blvd, #57

department: Pediatrics

institute: Children's Hospital Los Angeles

description: YAP1 sgRNA sequence: (5’-GTGCACGATCTGATGCCCGG-3’)

data_processing:
Sequences were aligned to the full hg19 transcriptome and gene counts generated using STAR 2.4.2_a
Expression values (FPKM) were determined using RSEM 1.3.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file of gene FPKMs

source_name: NLF, neuroblastoma-derived cell line

growth_protocol:
RPMI 1640, 10% FBS, 1% Penicillin/Streptomycin, 2mM L-Glutamine
Cells were thawed and grown in 150mm plates to 60-80% confluency before being detached and pelleted for RNA extraction.

extract_protocol:
RNA was extracted using the Qiagen miRNeasy Mini kit (Cat 217004) following the manufacturer's protocol.
Libraries were constructed using Illumina's TruSeq Stranded Total RNA Library Prep kit with RiboZero

treatment_protocol: Cells were treated with either 0.01% DMSO or 20 nM trametinib dissolved in DMSO. Cells were treated 24 hours after plating and samples were collected after 72 hours of treatment.

tag: cell type

value: NLF, neuroblastoma-derived cell line

tag: genetic alteration

value: YAP1 gene knockout

value: 20 nM Trametinib


title: YAPKO2_TRAM_REP2


title: Kii-5

value: Female

tag: age

value: Human Postmortem Brain


title: Kii-4

source_name: ALS_Frontal lobe

value: ALS

value: Frontal lobe


title: Kii-2

value: ALS+D


title: Kii-3


title: Kii-1


title: S113, 1st sample set (scRNA-seq)

tag: differentiation stage

value: DM

value: TRUE


title: YAPKO2_TRAM_REP1


title: YAPKO2_DMSO_REP3


title: Heart of mouse treated with ETX, biological rep10

source_name: Heart of mouse treated with ETX

value: ETX

value: Heart


title: YAPKO2_DMSO_REP2


title: S28, 1st sample set (scRNA-seq)

tag: cell id at each stage


title: S215, 1st sample set (scRNA-seq)

value: phLO

tag: subject

value: FALSE


title: YAPKO2_DMSO_REP1


title: rna_4A2KO_rep2

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

institute: RIKEN

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: hg38
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

extract_protocol:
Truseq stranded mRNA library prep
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling) or TruSeq (illumina) (for mRNA-seq)

tag: genetic background


title: S11, 1st sample set (scRNA-seq)

value: HB

tag: qc


title: rna_4A2KO_rep1


title: YAPKO1_TRAM_REP3

description: YAP1 sgRNA sequence: (5’-CGCCGTCATGAACCCCAAGA-3’)


title: AD3_F

source_name: Alzheimer`s Disease_Frontal lobe

tag: subject id

value: Alzheimer`s Disease

value: Male

tag: tissue


title: AD3_T

source_name: Alzheimer`s Disease_Temporal lobe

value: Temporal lobe


title: AD2_T


title: rna_naive_rep2

value: WT


title: S198, 1st sample set (scRNA-seq)


title: AD1_T


title: Kii-6

source_name: PDC+A_Temporal lobe

value: PDC+A


title: AD2_F


title: YAPKO1_TRAM_REP2

value: NLF, neuroblastoma-derived cell line

value: YAP1 gene knockout

value: 20 nM Trametinib


title: rna_naive_rep1


title: AD1_F

value: Human Postmortem Brain

value: Frontal lobe


title: CT3_F

source_name: Healthy Control_Frontal lobe

value: Healthy Control


title: CT3_T

source_name: Healthy Control_Temporal lobe


title: YAPKO1_DMSO_REP3


title: YAPKO1_TRAM_REP1


title: CT2_T


title: YAPKO1_DMSO_REP2


title: ribo_4A2KO_rep2

data_processing:
Library strategy: Ribosome Profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: hg38
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

extract_protocol:
Rnase I footprinting, ribosome pelleting, RNA extraction
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling) or TruSeq (illumina) (for mRNA-seq)


title: Glioblastoma 3

source_name: Glioblastoma 3

value: brain

tag: tumor type

value: glioblastoma

tag: rsk1 protein group

value: hi

tag: batch

value: new


title: sgCON_TRAM_REP3

description: Scrambled sgRNA sequence: (5'-GCACTCACATCGCTACATCA-3')

value: scrambled sgRNA

tag: treatment


title: ribo_4A2KO_rep1


title: ribo_naive_rep2


title: sgCON_TRAM_REP2


title: YAPKO1_DMSO_REP1


title: sgCON_TRAM_REP1


title: sgCON_DMSO_REP3


title: CT1_F

tag: clinical phenotypes

tag: gender


title: CT1_T

tag: tissue subtype


title: CT2_F


title: BJAB small RNA-Seq replicate 3

city: Ames

first: Walter

last: Moss

state: IA

address: Pammel Dr

institute: Iowa State University

description: small RNA fraction 15-200 nt

data_processing:
The quality of the paired-end, raw sequences as well as the adapters used was checked by FastQC
Illumina TruSeq small RNA 5' and 3' adapters were trimmed using Trim Galore that utilizes Cutadapt to trim adapters. The trimmed sequences were reexamined for quality and trimming efficiency with FastQC.
The ‘new Tuxedo’ package comprised of HISAT2, StringTie, and Ballgown was used to align reads to the human genome, assemble non-micro small RNA transcripts, and compute the abundance of transcripts and differential expression (DE) of these transcripts between BJAB-B1 and BJAB cell lines.
Transcript abundances were estimated, and table counts were created for DE analysis between BJAB-B1 and BJAB samples via Ballgown.
DE analysis was carried out using R packages Ballgown and genefilter; low-abundance genes were filtered out by removing all transcripts with a variance across samples less than one.
DE of miRNAs was performed using an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA)
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Excel file showing DE small ncRNAs

source_name: B cell lymphoma

growth_protocol: Cell lines were grown in RPMI 1640 media, supplemented with 2 mM L-glutamine, 10% fetal bovine serum (FBS), and 1% penicillin-streptomycin, at 37 °C in a 5% CO2 environment.

extract_protocol:
Total RNA was isolated via TRIzol extraction and further purified using the miRNeasy Mini Kit (Qiagen).
Small RNA enrichment was done by excision of the 15 to 200 nt fraction from a polyacrylamide gel. Approximately 1 ug of enriched RNA was used to prepare a small RNA library according to the TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, USA) protocol. Paired-end sequencing (150 bp) on an Illumina Hiseq 2500 was carried out following the vendor's recommended protocol.

tag: cell type

value: B cell lymphoma

tag: cell line

value: BJAB

tag: disease state

value: Burkitt lymphoma


title: BJAB small RNA-Seq replicate 2

description: small RNA fraction 15-200 nt


title: SAMPLE 33: genomic DNA from Lung non smorker2

type: genomic

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

source_name: lung with non-smoker

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cell lines or clinical samples using QIAquick DNA mini kit according to standard instructions

value: Female

tag: sample type

value: clinical sample

value: normal

value: surrounding normal lung


title: sgCON_DMSO_REP2

value: NLF, neuroblastoma-derived cell line

tag: genetic alteration


title: SAMPLE 29: genomic DNA from Lung nonIPF3

source_name: lung without idiopathic pulmonary fibrosis

value: Male


title: SAMPLE 30: genomic DNA from Lung nonIPF4


title: SAMPLE 28: genomic DNA from Lung nonIPF2


title: Vocal fold, 8w_5

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from Sprague-Dawley Rat‘s vocal fold 8 weeks after vocal fold injury

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix rat Clariom S. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

organism: Rattus norvegicus

source_name: Sprague-Dawley Rat 8 weeks after vocal fold injury

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: All animals were kept at least 1 wk at 22°C and 55% relative humidity in a 12-h day/night lighting environment with free access to food and water.

extract_protocol: For microarray profiling, the rat vocal fold total RNA was harvested using TRIzol reagent (Invitrogen, Carlsbad, Canada) and purified using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. The amount and quality of RNA were determined using UV-Vis Spectrophotometer (Thermo, NanoDrop 2000, USA) at the absorbance of 260 nm. The mRNA expression profiling was measured using Affymetrix ClariomTM D rat Array (Affymetrix GeneChip, Santa Clara CA, USA).

treatment_protocol: The vocal fold was injured by separating and removing the lamina propria from the thyroarytenoid muscle.

tag: strain

value: Sprague-Dawley

value: vocal fold

value: vocal fold injury

tag: time

value: 8 weeks after vocal fold injury


title: BJAB small RNA-Seq replicate 1

description: small RNA fraction 15-200 nt


title: SAMPLE 32: genomic DNA from Lung non smorker1


title: SAMPLE 31: genomic DNA from Lung nonIPF5


title: ribo_naive_rep1

tag: genetic background

value: WT


title: SAMPLE 27: genomic DNA from Lung nonIPF1


title: NLF_REP3

value: Parental cell line


title: sgCON_DMSO_REP1


title: NLF_REP2


title: BJAB-B1 small RNA-Seq replicate 2

description: small RNA fraction 15-200 nt


title: BJAB-B1 small RNA-Seq replicate 1

description: small RNA fraction 15-200 nt


title: BJAB-B1 small RNA-Seq replicate 3

description: small RNA fraction 15-200 nt


title: Vocal fold, 8w_3


title: HO_CD47 treatedreplicate4

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

description:
HO_CD47treated_Markers
A partial-thickness scald burn injury was administered to animals according to a previously described protocol by a single surgeon.3,57 Briefly, mice were anesthetized with inhaled isoflurane. Dorsal hair was closely clipped, and an aluminum block heated to 60°C was exposed to the dorsal region over 30% of the total body surface area for 18 s to achieve a partial-thickness burn injury. Each mouse then received a concurrent sterile dorsal hind limb tendon transection at the midpoint of the Achilles tendon (Achilles tenotomy) with placement of a single 5-0 vicryl suture to close the skin. Pain management was achieved with subcutaneous injections of buprenorphine (Buprenex, Reckitt Benckiser Pharmaceuticals) every 12 hr for 2 days.
Post injury harvested tissue samples were digested for 45 minutes in 0.3% Type 1 Collagenase and 0.4% Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37°C under constant agitation at 120rpm. Digestions were subsequently quenched with 10% FBS RPMI and filtered through 40μm sterile strainers. Cells were then washed in PBS with 0.04% BSA, counted and resuspended at a concentration of ~1000 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were processed for further sequencing.
Libraries were sequenced on a HiSeq 4000,  (Illumina, San Diego, CA, USA) using a HiSeq 4000 PE Cluster Kit (PN PE-410-1001) with HiSeq 4000 SBS Kit (100 cycles, PN FC-410-1002)reagents, loaded at 200 pM following Illumina’s denaturing and dilution recommendations.   The run configuration was 26 x 8 x 98 cycles for Read 1, Index and Read 2, respectively.

data_processing:
Cell Ranger Single Cell Software Suite 1.3 was used to perform sample de-multiplexing, barcode processing, and single cell gene counting (Alignment, Barcoding and UMI Count) at the University of Michigan Biomedical Core Facilities DNA Sequencing Core
Genome_build: mm10
Seurat R package was used to perform unsupervised clustering and identification of cell-type specific markers.
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, and matrix.mtx files

source_name: CD47 treated

extract_protocol: Single-cell 3’ library generation was performed on the 10x Genomics Chromium Controller following the manufacturers protocol for the v2 reagent kit (10X Genomics, Pleasanton, CA, USA). Cell suspensions were loaded onto a Chromium Single-Cell A chip along with reverse transcription (RT) master mix and single cell 3’ gel beads, aiming for 2000-6000 cells per channel. In this experiment, 8700 cells were encapsulated into emulsion droplets at a concentration of 700-1200 cells/ul which targets 5000 single cells with an expected multiplet rate of 3.9%. Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed and the resulting Post GEM-RT product was cleaned up using DynaBeads MyOne Silane beads (ThermoFisher Scientific, Waltham, MA, USA).  The cDNA was amplified, SPRIselect (Beckman Coulter, Brea, CA, USA) cleaned and quantified then enzymatically fragmented and size selected using SPRIselect beads to optimize the cDNA amplicon size prior to library construction. An additional round of double-sided SPRI bead cleanup is performed after end repair and A-tailing.  Another single-sided cleanup is done after adapter ligation.  Indexes were added during PCR amplification and a final double-sided SPRI cleanup was performed. Libraries were quantified by Kapa qPCR for Illumina Adapters (Roche) and size was determined by Agilent tapestation D1000 tapes. Read 1 primer sequence are added to the molecules during GEM incubation. P5, P7 and sample index and read 2 primer sequence are added during library construction via end repair, A-tailing, adaptor ligation and PCR. Libraries were generated with unique sample indices (SI) for each sample.

value: cells recruited to injury site

value: A partial-thickness scald burn injury was administered to animals; CD47 activating peptide (10mg/kg i.p. daily) treated 3 days prior to injury and 3 days after injury.

tag: biosource

value: HO model (30% body surface area dorsal burn and Achilles tenotomy) was used in C57 and LysmCre/Tgfb1fx/fx mice


title: HODay21replicate4

description:
HO_Day21_Markers
A partial-thickness scald burn injury was administered to animals according to a previously described protocol by a single surgeon.3,57 Briefly, mice were anesthetized with inhaled isoflurane. Dorsal hair was closely clipped, and an aluminum block heated to 60°C was exposed to the dorsal region over 30% of the total body surface area for 18 s to achieve a partial-thickness burn injury. Each mouse then received a concurrent sterile dorsal hind limb tendon transection at the midpoint of the Achilles tendon (Achilles tenotomy) with placement of a single 5-0 vicryl suture to close the skin. Pain management was achieved with subcutaneous injections of buprenorphine (Buprenex, Reckitt Benckiser Pharmaceuticals) every 12 hr for 2 days.
Post injury harvested tissue samples were digested for 45 minutes in 0.3% Type 1 Collagenase and 0.4% Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37°C under constant agitation at 120rpm. Digestions were subsequently quenched with 10% FBS RPMI and filtered through 40μm sterile strainers. Cells were then washed in PBS with 0.04% BSA, counted and resuspended at a concentration of ~1000 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were processed for further sequencing.
Libraries were sequenced on a HiSeq 4000,  (Illumina, San Diego, CA, USA) using a HiSeq 4000 PE Cluster Kit (PN PE-410-1001) with HiSeq 4000 SBS Kit (100 cycles, PN FC-410-1002)reagents, loaded at 200 pM following Illumina’s denaturing and dilution recommendations.   The run configuration was 26 x 8 x 98 cycles for Read 1, Index and Read 2, respectively.

source_name: Day 21

value: cells recruited to injury site at day 21


title: Vocal fold, 4w_4

description: Gene expression data from Sprague-Dawley Rat‘s vocal fold 4 weeks after vocal fold injury

source_name: Sprague-Dawley Rat 4 weeks after vocal fold injury

tag: tissue

value: 4 weeks after vocal fold injury


title: Vocal fold, 8w_1


title: PC9_SIX4_rep2

city: Luzhou

first: xu

last: liu

address: 25th Taiping Street

institute: The Affiliated Hospital of Southwest Medical University

description:
PolyA RNA
processed data file: count_matrix.txt

data_processing:
Illumina bcl2fastq 2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRch37.p13 whole genome using HISAT2 (version 2.1.0) with default parameters.
Read counts are aggregated at the gene level using HTseq (version 0.9.1) and then identified DEGs using R package DESeq2.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: count_matrix.txt: Tab-delimited text file includes raw counts for each Sample.

source_name: Lung cancer cells

extract_protocol:
Total RNA of stably infected cells was isolated with Trizol and the polyadenylated mRNAs were extracted using Dynabeads Oligo (dT) 25 beads.
RNA libraries were constructed with NEBNext ® Ultra™ Directional RNA Library Prep Kit for Illumina ® (NEB, USA) with 3 independent replicates following the manufacturer’s instructions. One hundred and fifty bp paired-end sequencing was performing using Illumina HiSeq XTen.

treatment_protocol: The SIX4 gene was stably transfected into two human NSCLC cell lines (A549 and PC9) using the lentiviral system.

value: non-small cell lung cancer cells

value: Stable overexpression SIX4


title: PC9_SIX4_rep3


title: Vocal fold, 8w_4


title: Vocal fold, 4w_5


title: Vocal fold, 8w_2


title: Vocal fold, 4w_2


title: SAMPLE 24: genomic DNA from Lung IPF4

source_name: lung with idiopathic pulmonary fibrosis

value: clinical sample

value: normal


title: HODay0replicate4

description:
HO_Day0_Markers
A partial-thickness scald burn injury was administered to animals according to a previously described protocol by a single surgeon.3,57 Briefly, mice were anesthetized with inhaled isoflurane. Dorsal hair was closely clipped, and an aluminum block heated to 60°C was exposed to the dorsal region over 30% of the total body surface area for 18 s to achieve a partial-thickness burn injury. Each mouse then received a concurrent sterile dorsal hind limb tendon transection at the midpoint of the Achilles tendon (Achilles tenotomy) with placement of a single 5-0 vicryl suture to close the skin. Pain management was achieved with subcutaneous injections of buprenorphine (Buprenex, Reckitt Benckiser Pharmaceuticals) every 12 hr for 2 days.
Post injury harvested tissue samples were digested for 45 minutes in 0.3% Type 1 Collagenase and 0.4% Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37°C under constant agitation at 120rpm. Digestions were subsequently quenched with 10% FBS RPMI and filtered through 40μm sterile strainers. Cells were then washed in PBS with 0.04% BSA, counted and resuspended at a concentration of ~1000 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were processed for further sequencing.
Libraries were sequenced on a HiSeq 4000,  (Illumina, San Diego, CA, USA) using a HiSeq 4000 PE Cluster Kit (PN PE-410-1001) with HiSeq 4000 SBS Kit (100 cycles, PN FC-410-1002)reagents, loaded at 200 pM following Illumina’s denaturing and dilution recommendations.   The run configuration was 26 x 8 x 98 cycles for Read 1, Index and Read 2, respectively.

source_name: Day 0

value: cells recruited to injury site at day 0


title: Vocal fold, 4w_1


title: PC9_SIX4_rep1


title: SAMPLE 25: genomic DNA from Lung IPF5

value: Male

value: surrounding normal lung


title: KrTB85TON

city: New York

first: Kristian

last: Laursen

state: NY

address: 1300 York Ave.

department: Pharmacology

institute: Weill Cornell Medicine

description: processed data file: Bmi1OE_Tongue_Abundance_RNA-seq.xlsx

data_processing:
Raw sequencing reads were aligned to the reference genome (mouse mm9) with the Tophat2 software.
Raw read counts were calculated with the HTseq-count software.
Differential expression analysis was done with the DEseq2 package.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Bmi1OE_Tongue_Abundance_RNA-seq.xlsx: Excel file includes normalized gene expression and differential expression values.

source_name: Mouse Tongue Tissue

extract_protocol:
RNeasy plus mini kit (Qiagen; #74134).
cDNA libraries were created with the Illumina TruSeq Stranded mRNA Library Prep kit and sequenced with single-end 50bps on the Illumina HiSeq4000 instrument.

treatment_protocol: ~6-week-old K14-rtTA only and K14-rtTA; TREFLBmi-1 mice were treated with 2mg/mL doxycycline, added to the drinking water.

tag: strain/background

value: C57/Bl6 crossed with FVB/NJ

tag: genotype/variation

value: K14-rtTA; TREFLBmi-1

value: Tongue

tag: age

value: ~6 weeks

value: 2mg/mL Doxycycline for 1 week


title: KrTB82TON

tag: treatment


title: PC9_NEO_rep2

value: Control


title: PC9_NEO_rep3


title: SAMPLE 21: genomic DNA from Lung IPF1


title: SAMPLE 26: genomic DNA from Lung IPF6


title: A549_SIX4_rep1


title: SAMPLE 23: genomic DNA from Lung IPF3


title: Vocal fold, 1w_5

description: Gene expression data from Sprague-Dawley Rat‘s vocal fold 1 weeks after vocal fold injury

source_name: Sprague-Dawley Rat 1 weeks after vocal fold injury

value: Sprague-Dawley

value: vocal fold

value: vocal fold injury

value: 1 week after vocal fold injury


title: PC9_NEO_rep1

value: non-small cell lung cancer cells


title: KrTB70TON


title: KrTB67TON

value: K14-rtTA ONLY


title: Vocal fold, 4w_3

value: 4 weeks after vocal fold injury


title: Vocal fold, 1w_2


title: Vocal fold, 1w_4


title: Vocal fold, 1w_3


title: KrTB72TON


title: Vocal fold, 1w_1


title: KrTB65TON


title: A549_NEO_rep2


title: A549_NEO_rep1


title: KrTB78TON


title: Vocal fold, control_3

description: Gene expression data from Sprague-Dawley Rat‘s vocal fold without treatment

source_name: Sprague-Dawley Rat without treatment

value: control


title: KrTB52TON


title: Vocal fold, control_4


title: Vocal fold, control_2


title: pitx2-Mut_2: pitx2c_mutant_hearts_pool2

status: Public on Oct 25 2019

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides (Davis et al., Kraken: A set of tools for quality control and analysis of high-throughput sequence data). Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus Ensembl Zebrafish genome version DanRer10 (GRCz10.87) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: DanRer10 (GRCz10.87)
Supplementary_files_format_and_content: tab-delimited text files include library size normlized counts per peak

organism: Danio rerio

source_name: pools of 56 hpf hearts

growth_protocol: Embryos were grown at 28C until 56 hpf

extract_protocol:
Hearts were dissected from embryos in HBSS.  RNA was isolated using miRNeasy micro kit (QIAGEN) with on-column DNase digestion
5ng of total RNA was used as input for SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian (Takara Clontech).

value: embryonic heart

tag: Stage

value: 56 hpf

value: pitx2c mutant


title: A549_NEO_rep3


title: pitx2-Mut_1: pitx2c_mutant_hearts_pool1


title: pitx2-OE_1: Tg(myl7:pitx2c-P2A-H2B-GFP)_hearts_pool1

value: pitx2c gain-of-function (OE)


title: Vocal fold, control_5


title: WT_1: wild-type

value: wild-type


title: KrTB53TON

value: C57/Bl6 crossed with FVB/NJ

value: K14-rtTA; TREFLBmi-1

value: Tongue


title: WT_2: wild-type


title: pitx2-OE_2: Tg(myl7:pitx2c-P2A-H2B-GFP)_hearts_pool2


title: SAMPLE 22: genomic DNA from Lung IPF2

tag: gender

value: Male

value: clinical sample

value: normal

value: surrounding normal lung


title: Cord_Blood_TD_male_44

city: Davis

first: Charles

middle: E

last: Mordaunt

address: 3318 Tupper Hall, One Shields Ave

department: Medical Microbiology and Immunology

institute: University of California, Davis

hyb_protocol: Biotin-labeled cRNA was hybridized to Human Gene 2.0 array (Affymetrix) at the John's Hopkins Sequencing and Microarray core using the manufacturer's protocol

scan_protocol: Hybridized arrays were scanned at the John's Hopkins Sequencing and Microarray core. EARLI and MARBLES samples were measured separately and in multiple batches within each study. The manufacturer’s protocol was followed for all washing, staining and scanning procedures.

data_processing: The raw fluorescence data (in Affymetrix CEL file format) with one perfect match and one mismatched probe in each set were analyzed using oligo package in R. Within each study, signal distribution was first assessed in perfect-match probe intensity and Robust multi-Chip Average (RMA) normalized data. During the quality control step, we identified outliers, overly noisy experiments and experimental design problems using the arrayQualityMetrics and oligo R packages. Outliers were excluded based on loading in principle component 1, the Kolmogorov-Smirnov test, median normalized unscaled standard error, and the sum of the distances to all other arrays. For the MARBLES study, 3 outliers were identified and excluded, then 162 samples were normalized using RMA. For the EARLI study, 6 outliers were identified and excluded, then 109 samples were normalized using RMA. We used surrogate variable analysis (SVA) to control for unmeasured environmental, demographic and technical factors that may have substantial effects on gene expression using the SVA R package. Differential expression was determined using the limma package in R with diagnosis and surrogate variables included in the linear model. Expression was compared between ASD and TD subjects, and also Non-TD and TD subjects. Fold change and standard error from each study were input into the METAL command-line tool for meta-analysis. Shared data was limited to those subjects who gave consent.

source_name: Umbilical cord blood from TD male subject

label_protocol: Total RNA with RIN > 7 was converted cDNA and in vitro transcribed to biotin-labeled cRNA at the John's Hopkins Sequencing and Microarray core using the manufacturer's protocol (Affymetrix)

extract_protocol: Umbilical cord blood was collected at the time of birth in PAXgene Blood RNA Tubes with the RNA stabilization reagent (BD Biosciences) and stored at -80C. RNA isolation was performed with the PAXgene Blood RNA Kit (Qiagen) following the manufacturer’s protocol.

tag: diagnosis

value: TD

tag: Sex

value: male

tag: study

value: EARLI

tag: array batch


title: Cord_Blood_TD_male_45


title: Cord_Blood_TD_male_40


title: Cord_Blood_TD_male_39


title: Cord_Blood_TD_male_38


title: Cord_Blood_TD_male_37


title: Cord_Blood_TD_male_34


title: Cord_Blood_TD_male_35


title: Cord_Blood_TD_male_31


title: Cord_Blood_TD_male_25

value: MARBLES


title: Cord_Blood_TD_male_36


title: Cord_Blood_TD_male_29


title: Cord_Blood_TD_male_41


title: Cord_Blood_TD_male_33


title: Cord_Blood_TD_male_28


title: Cord_Blood_TD_male_24


title: Cord_Blood_TD_male_46


title: Cord_Blood_TD_male_30


title: Cord_Blood_TD_male_27


title: Vocal fold, control_1

value: Sprague-Dawley

value: vocal fold

value: control


title: Cord_Blood_TD_male_32


title: Cord_Blood_TD_male_22


title: Cord_Blood_TD_male_42


title: A549_SIX4_rep3

tag: cell line

tag: cell type

value: non-small cell lung cancer cells

value: Stable overexpression SIX4


title: Cord_Blood_TD_male_23


title: Cord_Blood_TD_male_26


title: Cord_Blood_TD_male_18


title: Cord_Blood_TD_male_21


title: Cord_Blood_TD_male_13


title: Cord_Blood_TD_male_19


title: Cord_Blood_TD_male_16


title: Cord_Blood_TD_male_14


title: Cord_Blood_TD_male_11


title: Cord_Blood_TD_male_12


title: Cord_Blood_TD_male_17


title: Cord_Blood_TD_male_8


title: Cord_Blood_TD_male_9


title: Cord_Blood_TD_male_15


title: Cord_Blood_TD_male_7


title: Cord_Blood_TD_male_2


title: NLF_REP1

source_name: NLF, neuroblastoma-derived cell line

value: NLF, neuroblastoma-derived cell line

tag: genetic alteration

value: Parental cell line


title: Cord_Blood_TD_female_45

source_name: Umbilical cord blood from TD female subject

value: female


title: Cord_Blood_TD_male_20


title: Cord_Blood_TD_male_5


title: Cord_Blood_TD_male_4


title: Cord_Blood_TD_male_6


title: Cord_Blood_TD_male_10


title: Cord_Blood_TD_male_3


title: Cord_Blood_TD_male_1


title: A549_SIX4_rep2


title: Cord_Blood_TD_male_43


title: B16-F1ΔFOXC2 Replicate #3

city: Hampden-Sydney

middle: Michael

last: Hargadon

state: VA

address: Brown Student Center, Box 837

department: Biology

institute: Hampden-Sydney College

description: RNA isolated after 24 hours of cell culture in normal growth media

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
Sequence quality was examined using the FastQC software, and raw sequencing data that passed the Illumina chastity filter were used for analysis.
Fragments were 5’, 3’-adaptor trimmed and filtered ≤ 20 bp reads with cutadapt  software. The trimmed reads were aligned to reference genome GRCm38 with Hisat 2 software.
Transcript abundances for each sample were estimated with StringTie, and the normalized expression level (FPKM value) of known genes was calculated with the R package Ballgown.  The number of identified genes per group was calculated based on the mean of FPKM in group ≥ 0.5.
Genome_build: GRCm38
Supplementary_files_format_and_content: The Matrix Table of Processed Data is an Excel (.xlsx) file of the normalized FPKM expression values for known genes from each sample.

source_name: Cell line

growth_protocol: 1e6 B16-F1 or B16-F1ΔFOXC2 melanoma cells in 3ml of normal growth media (RPMI-1640 supplemented with 10% FBS) were seeded into 60mm x 15 mm cell culture dishes and grown for 24 hours at 37° C in 5% CO2.

extract_protocol:
After 24 hours of culture, media was removed from cultures and cells were lysed with Buffer RLT containing b-ME for RNA extraction using an RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's recommendations.  During extraction, on-column DNase-digestion was performed using Qiagen's RNase-free DNase Set.  RNA was quantified using an Epoch Spectrophotometer (BioTek, Winooski, VT).  RNA samples were diluted to 500 ng/ml and stored at -80° C.  Upon completion of all replicate experiments, ~10 mg of RNA from each sample was shipped overnight on dry ice to Arraystar, Inc. (Rockville, MD) for analysis using the company's 6G RNA-sequencing service.  A260/280 and A260/230 ratios were both ≥ 2.0 for all samples.  RNA integrity and genomic DNA contamination were examined by standard denaturing agarose gel electrophoresis, and all samples passed this quality control assessment.
Total RNA from each sample was quantified using a NanoDrop ND-1000 instrument.  ~1-2  µg total RNA  was used to prepare the sequencing library in the following steps: 1. Total RNA was enriched by oligo (dT)  magnetic beads (rRNA removed); 2. RNA-seq library was prepared using KAPA Stranded RNA-Seq Library  Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library  strand-specific. The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute  quantification qPCR method. To sequence the libraries on the Illumina HiSeq 4000 instrument, the barcoded  libraries were mixed, denatured to single stranded DNA in NaOH, captured on Illumina flow cell, amplified  in situ, and subsequently sequenced for 150 cycles for both ends on Illumina HiSeq instrument.

tag: background strain

value: Melanoma

tag: genotype

value: delta FOXC2

tag: cell culture confluence

tag: passages


title: B16-F1ΔFOXC2 Replicate #2


title: WT B16-F1 Replicate #3

value: WT


title: WT B16-F1 Replicate #5


title: B16-F1ΔFOXC2 Replicate #1


title: B16-F1ΔFOXC2 Replicate #4


title: WT B16-F1 Replicate #4


title: Cord_Blood_TD_female_42


title: Identification of miR-28-5p target genes in T24

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 10.7.3.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: mock

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

value: bladder cancer

tag: transfection

value: no transfection

source_name: miR-28-5p transfected cell line


title: Cord_Blood_TD_female_41

value: TD


title: Identification of miR-34c-5p target genes in SBC

value: SBC

value: lung cancer

source_name: miR-34c-5p transfected cell line


title: Cord_Blood_TD_female_40

value: EARLI


title: Cord_Blood_TD_female_44


title: Cord_Blood_TD_female_43


title: Identification of miR-28-3p target genes in T24

source_name: miR-28-3p transfected cell line


title: Cord_Blood_TD_female_36


title: Identification of miR-30a-5p target genes in SBC

source_name: miR-30a-5p transfected cell line


title: Cord_Blood_TD_female_39


title: Cord_Blood_TD_female_38


title: Cord_Blood_TD_female_37


title: Identification of miR-34b-3p target genes in SBC

source_name: miR-34b-3p transfected cell line


title: Cord_Blood_TD_female_34


title: Identification of miR-30a-3p target genes in SBC

source_name: miR-30a-3p transfected cell line


title: Cord_Blood_TD_female_35


title: Cord_Blood_TD_female_32


title: Identification of miR-34b-5p target genes in SBC

source_name: miR-34b-5p transfected cell line


title: Cord_Blood_TD_female_33


title: B16-F1ΔFOXC2 Replicate #5


title: Identification of miR-34c-3p target genes in SBC

source_name: miR-34c-3p transfected cell line


title: Cord_Blood_TD_female_31


title: WT B16-F1 Replicate #1


title: WT B16-F1 Replicate #2


title: MLN_RFP_neg_2: RNA-seq in MLN T-bet- cDC2, rep1

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

data_processing:
RNA-seq: Mouse genome assembly mm10.GRCm38 was used for bulk RNA-seq read alignments. Gene annotations from GENCODE vM17 were used for all analysis. Analysis was done using custom scripts in R v3.4.0 (2017-04-21). Reads were aligned to the mouse genome assembly mm10.GRCm38 using HISAT2 v2.1.0 with default parameters including splice sites obtained from gene annotations. Uniquely aligned reads were extracted using grep with parameters “-v 'NH:i:[2-9]'” and SAMtools v1.9 with parameters “view -h -F 4 -q 20 -b” and sorted and indexed using SAMtools. For analysis of RNA-seq samples in cDC1s, T-bet- cDC2s, T-bet+ cDC2s in the spleen and the lymph node, reads aligned to genes from the GENCODE gene annotation were counted using Rsubread v1.28.1.
ATAC-seq: Mouse genome assembly mm10.GRCm38 was used for ATAC-seq read alignments. Gene annotations from GENCODE vM17 were used for all analysis. Analysis was done using R v3.4.0 (2017-04-21) and custom scripts. Reads were aligned to the mouse genome using Bowtie2 v2.2.5 with parameters “--no-unal -X 1000 --no-mixed --no-discordant”. Uniquely aligned reads were extracted using SAMtools v1.9 with parameters “view -h -bS -F 4 -q 20” and sorted and indexed using SAMtools. For peak calling, MACS2 v2.1.1.20160309 was used with parameters “-g hs --nomodel --shift 0 --extsize 76 --name merged -p 0.1 -B --SPMR --keep-dup 'auto' --call-summits”. Before peak calling, all uniquely aligned reads on strand “+” were shifted by 4bp, and on strand “-” by -5bp. Peak calling was run on all replicates together to obtain a universal list of putative peaks, with peak summits. For each individual replicate, peak calling was run separately with the same parameters. Then IDR [implementation from https://github.com/nboley/idr , v2.0.3] was used to determine reproducible peaks in each of the three conditions (cDC1s, T-bet- cDC2s, T-bet+ cDC2s in the spleen). For this, putative peaks from the universal list were used as the oracle set of peaks (parameter “--peak-list”), and lists of peak p-values as detected in each individual replicate were used as scores. Peaks at IDR < 0.05 for any pair of replicates of the same condition were called reproducible. Peaks of size 76bp or lower and peaks outside standard chromosomes (chr1-chr19, chrX, chrY) were removed. This resulted in the atlas of 74217 reproducible peaks that contained 177956 peak summits. Reads in peaks and in 150bp windows centered around summits  were counted using Rsubread v1.22.1.
Genome_build: mm10.GRCm38
Supplementary_files_format_and_content: peaks-dendritic.bed: Reproducible ATAC-seq peaks (BED format). summits-dendritic.bed: 150bp windows centered at summits of reproducible ATAC-seq peaks (BED format). peaks-dendritic-counts.txt: ATAC-seq read counts in reproducible peaks (tab-delimited text file). summits-dendritic-counts.txt: ATAC-seq read counts in 150bp windows around summits (tab-delimited text file). gene-counts.txt: RNA-seq read counts in genes (tab-delimited text file).

source_name: T-bet- cDC2s from pooled mesenteric lymph nodes

growth_protocol: Mice were bred and housed in the pathogen-free animal facility at Memorial Sloan-Kettering Cancer Center and were used in accordance with institutional guidelines. Mouse experiments were approved by the Institutional Animal Care and Use Committee of Memorial Sloan-Kettering Cancer Center. Unless otherwise noted, 6- to 10-week-old male and female sex-matched mice were used for all experiments. No blinding was performed during the mouse experiments.

extract_protocol:
Single cell suspensions of cells were prepared from spleen or mesenteric lymph nodes. Cells were then stained for 30 min on ice in FACS buffer (PBS, 2% FBS, 2 mM EDTA) with antibodies against cell surface proteins. For exclusion of dead cells, samples were stained with Sytox Blue cell viability reagent immediately prior to cell sorting. Stained cells were sorted using a FACSAria II (BD). For RNA-seq, cells were sorted into Trizol LS.
RNA-seq: RFP+ (T-bet+) or RFP- (T-bet-) cDC2s or cDC1s were were FACS- sorted from Tbx21RFP-Cre mice directly into Trizol-LS (ThermoFisher) and volume was adjusted post-sort. Samples were stored at −80°C prior to RNA extraction. Total RNA was extracted and assessed for nucleic acid quantity and quality on the Agilent BioAnalyzer. SMARTer amplification was followed by Illumina TruSeq paired- end library preparation following manufacturer’s protocols. Samples were sequenced on the Illumina HiSeq 2500 to an average depth of 30 million 50-bp read pairs per sample.  ATAC-seq: FACS-sorted cell populations (50,000 cells) were washed with PBS and cell pellets were resuspended in 50ul of cold lysis buffer followed by centrifugation. Cell pellets were resuspended in 50ul of Tn5 transposase mixture: 1x Tagment DNA Buffer, 2.5ul Tagment DNA Enzyme (Nextera DNA Library Preparation Kit, Illumina). Cells were incubated at 42°C for 45 minutes with agitation followed by DNA isolation using the MinElute Reaction Cleanup Kit (QIAGEN, Hilden, Germany). Construction of ATAC-seq libraries included an initial round of PCR in a total volume of 50uL using the NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, MA, USA) with primers (1.25M each) from (Buenrostro et al., 2015) with the following thermal cycles: 5 minutes at 72°C, 30 s at 98°C, followed by 5 cycles [98°C for 10 s, 63°C for 30 s and 72°C for 60 s]. To avoid over amplification of libraries which result in GC bias, 5uL of the PCR-amplified DNA were subjected to qPCR (BioRad Real-Time PCR System) in a volume of 15uL using SYBR Green dye (final 0.6x SYBR Green I, Life Technologies) and with the respective primers (1.25M each). Following qPCR [30 s at 98°C, followed by 30 cycles (98°C for 10 s, 63°C for 30 s and 72°C for 60 s)], amplification curves were analyzed and the optimal number of PCR cycles for each sample were estimated with cycle thresholds reaching 1/3 of the maximum. Upon selecting the cycle threshold, the remaining 45uL of the initial PCR mix was subjected to a second round of PCR with the following thermal cycles: 30s at 98°C, followed by n cycles [98°C for 10 s, 63°C for 30 s and 72°C for 60 s]. The libraries were purified by Agencourt AMPure XP beads (x1.8 vol.). Samples were quantified and prepared for sequencing by the Integrated Genomics Core at Memorial Sloan Kettering Cancer Center.  After PicoGreen quantification and quality control by Agilent BioAnalyzer, libraries were pooled equimolar and run on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina). The average number of read pairs per sample was 122 million.

value: T-bet- cDC2

tag: tissue

value: pooled mesenteric lymph nodes

tag: strain


title: MLN_RFP_neg_3: RNA-seq in MLN T-bet- cDC2, rep2


title: MLN_RFP_pos_1: RNA-seq in MLN T-bet+ cDC2, rep1

source_name: T-bet+ cDC2s from pooled mesenteric lymph nodes

value: T-bet+ cDC2


title: MLN_XCR1_2: RNA-seq in MLN cDC1, rep2

source_name: cDC1s from pooled mesenteric lymph node

value: pooled mesenteric lymph node


title: MLN_RFP_pos_2: RNA-seq in MLN T-bet+ cDC2, rep2


title: MLN_XCR1_3: RNA-seq in MLN cDC1, rep3


title: Spleen_RFP_neg_3: RNA-seq in spleen T-bet- cDC2, rep3

source_name: T-bet- cDC2s from pooled spleen

value: pooled spleen


title: MLN_XCR1_1: RNA-seq in MLN cDC1, rep1


title: Cord_Blood_TD_female_29


title: Cord_Blood_TD_female_25


title: Cord_Blood_TD_female_27


title: Spleen_RFP_neg_2: RNA-seq in spleen T-bet- cDC2, rep2


title: Cord_Blood_TD_female_24


title: Cord_Blood_TD_female_28


title: Cord_Blood_TD_female_30


title: Spleen_RFP_neg_1: RNA-seq in spleen T-bet- cDC2, rep1


title: Cord_Blood_TD_female_22


title: Cord_Blood_TD_female_20

value: MARBLES


title: Spleen_RFP_pos_1: RNA-seq in spleen T-bet+ cDC2, rep1

source_name: T-bet+ cDC2s from pooled spleen


title: Spleen_RFP_pos_2: RNA-seq in spleen T-bet+ cDC2, rep2


title: Spleen_XCR1_3: RNA-seq in spleen cDC1, rep3

source_name: cDC1s from pooled spleen


title: Spleen_XCR1_2: RNA-seq in spleen cDC1, rep2


title: Spleen_XCR1_1: RNA-seq in spleen cDC1, rep1


title: RFP_neg_2: ATAC-seq in T-bet- cDC2, rep2

library_source: genomic


title: RFP_neg_1: ATAC-seq in T-bet- cDC2, rep1


title: Spleen_RFP_pos_3: RNA-seq in spleen T-bet+ cDC2, rep3


title: Cord_Blood_TD_female_19

source_name: Umbilical cord blood from TD female subject


title: Cord_Blood_TD_female_17


title: Cord_Blood_TD_female_21


title: Cord_Blood_TD_female_26


title: Cord_Blood_TD_female_15


title: Cord_Blood_TD_female_14


title: Cord_Blood_TD_female_13


title: Cord_Blood_TD_female_12


title: XCR1_2: ATAC-seq in cDC1, rep2


title: RFP_pos_1: ATAC-seq in T-bet+ cDC2, rep1


title: Cord_Blood_TD_female_11


title: XCR1_1: ATAC-seq in cDC1, rep1


title: Cord_Blood_TD_female_18


title: RFP_pos_2: ATAC-seq in T-bet+ cDC2, rep2


title: Cord_Blood_TD_female_16


title: Cord_Blood_TD_female_23


title: Cord_Blood_TD_female_9


title: siDDX5-DDX17 replicat 3

city: Lyon

first: jean-baptiste

last: claude

address: 46, allée d’Italie

country: France

institute: [CNRS/ENS Lyon/UCBL/HCL] Laboratoire de Biologie Moléculaire de la Cellule UMR5239

description: replicat 3

data_processing:
Data generated with an Illumina HiSeq, 2x150 configuration (strand-specific)
Filtering & Trimming with Cutadapt (1.13) & Prinseq (lite-0.20.4)
Mapping & QC-mapped with Tophat2 (2.0.13) & Samtools (0.1.19)
Splicing analysis with FARLINE pipeline ( doi: 10.1038/s41598-018-21770-7 )
Genome_build: hg19
Supplementary_files_format_and_content: excel files containing splicing events differentially observed (events : acceptor, donor, mutually exclusive, multi exon skipping)

source_name: Breast cancer cell line

growth_protocol: Cells were maintained under 12 passages and were not allowed to reach more than 75% confluency. Growth conditions : DMEM + 10%serum, 37°C, 5% CO2

extract_protocol:
48h after transfection, cells were 2x washed with ice-cold PBS and total RNA extraction was performed using Tri-Reagent, following the manufacturer's instructions.
Library were made by the sequencing provider (Genewiz) : strand-specific RNA library preparation with rRNA depletion.

treatment_protocol: Cells were plated at 25% confluency and reverse-transfected with final 30nM siRNAs with Lipofectamin RNAiMAX transfection reagent (ThermoFishcer) following the manufacturer's instructions. After 24h, medium were changed for fresh medium.

tag: transfected sirna

value: transfected with siPP targetting DDX5 and DDX17

tag: extract

value: Tri-Reagent


title: Cord_Blood_TD_female_8

value: female


title: Cord_Blood_TD_female_7


title: Cord_Blood_TD_female_6


title: siDDX5-DDX17 replicat 2

description: replicat 2


title: Cord_Blood_TD_female_5


title: Cord_Blood_TD_female_10


title: Cord_Blood_TD_female_4


title: siDDX5-DDX17 replicat 1

description: replicat 1


title: siHNRNPK

description: simplicat

value: transfected with siHNRNPK


title: siFUS

description: simplicat

value: transfected with siFUS


title: siControl replicat 2

description: replicat 2

value: Negative Control siRNA


title: siHNRNPH1

description: simplicat

value: transfected with siHNRNPH1


title: siControl replicat 1

description: replicat 1


title: siHNRNPC

description: simplicat

value: transfected with siHNRNPC


title: HCC78 dox minus parental rep 1 RNA-seq

city: Stanford

first: Mohammad

last: Shahrokh Esfahani

state: California

address: 265 Campus Drive

institute: Stanford University

description:
FLAG; 6xHA; taggged U2AF1
S34F:WT (32:68)
Associated with each replicate of conditions (Dox Plus / Minus of Mutant / Wildtype and Parental Cell line) there are two columns, one for Fragments Per Kilobase of transcript per Million mapped reads, in the gene expression matrix (HCC78_U2AF1_S34F_allsamples_matrix.txt)

data_processing:
FASTQ files corresponding to each end are first trimmed to 100 base pairs using FASTX toolkit 0.0.14. The trimmed RNA-seq fastq files are then mapped using STAR 2.3.0.
RSEM-1.2.29 was then used for individual expression calculation using the STAR bam files.
BAM files of replicates of each condition (except for dox minus mutant where only one reliable sequencing file was achieved) were then merged for alternative splicing analysis. The resulting bam files are then used as input to the MISO for each individual sample. Before running the MISO, we used the pe_utils function to extract the mean and standard deviation of insert sizes for merged BAM files with minimum exon size of 200 and Homo.sapiens.GRCh37.65 as the GFF file.
MISO compare is then used for comparing the outputs of MISO on each individual sample where we identify differentially spliced events as those with at least 10% increase or decrease in PSI value, a Bayes factor of at least 5 and minimum supporting reads of 10.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files of the gene expressions of replicates and the MISO outputs.

source_name: HCC78-derived cell line

growth_protocol: All HCC78-derived cell lines were cultured and passaged every 3d at 2.5 x 10^6 cells in 10cm2 culture dishes with RPMI-1640 with 10% Fetal Bovine Serum, penicillin (100 U/mL) and streptomycin (100ug/mL).

extract_protocol:
RNA was extracted using the QIAGEN RNEasy kit for RNASeq. For iCLIP, whole-cell lysates were generated in iCLIP lysis buffer (50 mM HEPES, 200 mM NaCl, 1 mM EDTA, 10% glycerol, 0.1% 467 NP-40, 0.2% Triton X-100, 0.5% N-lauroylsarcosine) and briefly sonicated using a probe-tip Branson sonicator to solubilize chromatin before pull down with antibodies.
RNA was processed and prepared using the SMARTer® 543 Stranded Total RNA-Seq Kit (Clontech) 544 according to the manufacturer’s protocol. iCLIP was preparing according to the protocol in Zarnegar et al (2016) in Nat Methods.

value: HCC78-derived cell line

tag: tissue type

value: Lung adenocarcinoma

tag: genotype/variation

value: U2AF1 Parental (Dox-)


title: siGL2

description: simplicat


title: Cord_Blood_TD_female_3

tag: diagnosis

value: TD

tag: Sex


title: siControl replicat 3

description: replicat 3


title: HCC78 dox minus parental rep 2 RNA-seq


title: Cord_Blood_NonTD_male_43

source_name: Umbilical cord blood from Non-TD male subject

value: Non-TD

value: male

tag: study

value: EARLI

tag: array batch


title: Cord_Blood_TD_female_1


title: Cord_Blood_NonTD_male_41


title: Cord_Blood_NonTD_male_39


title: Cord_Blood_TD_female_2


title: Cord_Blood_NonTD_male_40


title: Cord_Blood_NonTD_male_42


title: Cord_Blood_NonTD_male_37


title: HCC78 dox minus wild-type rep 2 RNA-seq

description:
FLAG; 6xHA; taggged U2AF1
S34F:WT (33:67)
Associated with each replicate of conditions (Dox Plus / Minus of Mutant / Wildtype and Parental Cell line) there are two columns, one for Fragments Per Kilobase of transcript per Million mapped reads, in the gene expression matrix (HCC78_U2AF1_S34F_allsamples_matrix.txt)

tag: cell line

value: U2AF1 WT (Dox-)


title: HCC78 dox minus mutant rep 2 RNA-seq

description:
FLAG; 6xHA; taggged U2AF1
S34F:WT (28:72)
Associated with each replicate of conditions (Dox Plus / Minus of Mutant / Wildtype and Parental Cell line) there are two columns, one for Fragments Per Kilobase of transcript per Million mapped reads, in the gene expression matrix (HCC78_U2AF1_S34F_allsamples_matrix.txt)

value: U2AF1 Mut (Dox-)


title: siTRA2A-B

description: simplicat

value: transfected with siTRA2A and siTRA2B


title: HCC78 dox plus wild-type rep 1 RNA-seq

description:
FLAG; 6xHA; taggged U2AF1
S34F:WT (12:88)
Associated with each replicate of conditions (Dox Plus / Minus of Mutant / Wildtype and Parental Cell line) there are two columns, one for Fragments Per Kilobase of transcript per Million mapped reads, in the gene expression matrix (HCC78_U2AF1_S34F_allsamples_matrix.txt)

value: U2AF1 WT (Dox+)


title: HCC78 dox plus mutant rep 2 RNA-seq

description:
FLAG; 6xHA; taggged U2AF1
S34F:WT (65:35)
Associated with each replicate of conditions (Dox Plus / Minus of Mutant / Wildtype and Parental Cell line) there are two columns, one for Fragments Per Kilobase of transcript per Million mapped reads, in the gene expression matrix (HCC78_U2AF1_S34F_allsamples_matrix.txt)

value: U2AF1 Mut (Dox+)


title: Cord_Blood_NonTD_male_38


title: HCC78 dox plus mutant rep 1 RNA-seq

description:
FLAG; 6xHA; taggged U2AF1
S34F:WT (62:38)
Associated with each replicate of conditions (Dox Plus / Minus of Mutant / Wildtype and Parental Cell line) there are two columns, one for Fragments Per Kilobase of transcript per Million mapped reads, in the gene expression matrix (HCC78_U2AF1_S34F_allsamples_matrix.txt)


title: Cord_Blood_NonTD_male_35


title: HCC78 dox minus wild-type rep 1 RNA-seq


title: HCC78 dox plus wild-type rep 2 RNA-seq

description:
FLAG; 6xHA; taggged U2AF1
S34F:WT (14:86)
Associated with each replicate of conditions (Dox Plus / Minus of Mutant / Wildtype and Parental Cell line) there are two columns, one for Fragments Per Kilobase of transcript per Million mapped reads, in the gene expression matrix (HCC78_U2AF1_S34F_allsamples_matrix.txt)


title: RNA_CRC2_C_R3

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

institute: Peking University

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling
scRNA-Seq:Read 2 was used to abtain the cell barcodes to further split the reads according to the cell IDs(barcode) and the same time recorded the UMI sequences;Read 1 was picked in each cell according to the cell ID in read2 and the UMI information was aligned to it,and then these raw reads were trimmed to remove TSO or polyA sequence;Adaptor contamination and low-quality reads were discarded from the trimmed Read 1 raw data;TopHat(version 2.0.14) with default settings were used for sequence alignment and uniquely mapped reads were kept.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each single cell RNA samples

molecule: polyA RNA

source_name: non-FAP patient2 carcinoma region3

extract_protocol:
Single cells were picked into scRNA-seq lysis buffer or into scMALBAC lysis buffer by using mouth pipette. Then the cells in scRNA-seq lysis buffer were vortexed for 45 second and heated at 72℃for 3min to release RNA. And the cells in scMALBAC lysis buffer were centrifuge for 1min at 7,000 rpm and then incubate at 50℃ for 3 hours to release genomic DNA from nucleosome. The remaining cells were used to extract genomic DNA according to the manufacturer protocol of DNeasy Blood & Tissue Kit (QIAGEN).
Modified STRT-Seq protocol: we modified the STRT-Seq protocol for application to a large number of cells. Briefly, the 8bp barcodes was used to label individual cells. So the cDNA of cells with different barcodes can be pooled together for library constructions. And we also enrich the 3’ cDNA by the affinity interaction between biotin and Dynabeads® MyOne™ Streptavidin C1 beads. Then the fragmented DNA inserts were library constructed according to the manufacturer procedures of KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series (KAPA, KK8054) and sequencing on Illumina 4000.  DNA library construction protocol: The extracted genomic DNA was fragmented by sonication into 300bp and then library constructed according to the manufacturer procedures of KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series (KAPA, KK8054) and sequencing on Illumina 4000.
single cell RNA-Seq; Single cell whole genomic sequencing

treatment_protocol: The adenomatous polyposis, adenocarcinoma, adjacent normal colon tissue from four adenomatous polyposis patients and a lymphatic metastasis site in one of the four patients were dissected and washed by PBS for several times. Then the tissues were cut into small pieces by surgical scissors. Then the 2mg/mL Collagenase/Dispase was used to digest the tissues into single cells at 37℃ for 30-40 min after which the cell suspension was centrifuged at 800g  at 4℃ for 5min. The supernate was discarded and 1% HSA was used to re-suspended the cell pellet.

tag: patient id

value: CRC Patient2

value: carcinorma


title: Cord_Blood_NonTD_male_30


title: RNA_CRC2_N_B2

source_name: non-FAP patient1 adjacent normal tissue batch2

value: Adjacent Normal tissue


title: RNA_CRC2_C_R2

source_name: non-FAP patient2 carcinoma region2


title: Cord_Blood_NonTD_male_32


title: Cord_Blood_NonTD_male_29


title: Cord_Blood_NonTD_male_36


title: RNA_CRC2_C_R1

source_name: non-FAP patient2 carcinoma region1


title: Cord_Blood_NonTD_male_31


title: RNA_CRC2_N_B1

source_name: non-FAP patient1 adjacent normal tissue batch1


title: RNA_CRC1_SI_N_B1

source_name: non-FAP patient1 small intestine normal tissue batch1

value: CRC Patient1


title: RNA_CRC1_LI_N_B2

source_name: non-FAP patient1 adjacent normal tissue battch2


title: RNA_CRC1_SI_N_B2

source_name: non-FAP patient1 small intestine normal tissue batch2


title: Cord_Blood_NonTD_male_27


title: Cord_Blood_NonTD_male_33


title: Cord_Blood_NonTD_male_26


title: Cord_Blood_NonTD_male_28


title: RNA_CRC1_LI_N_B1

source_name: non-FAP patient1 adjacent normal tissue battch1


title: RNA_CRC1_C_R3_B1

source_name: non-FAP patient1 carcinoma region3 batch1


title: RNA_CRC1_C_R2_B1

source_name: non-FAP patient1 carcinoma region2 batch1


title: RNA_CRC1_C_R1_B2

source_name: non-FAP patient1 carcinoma region1 batch2


title: RNA_FAP1_SI_A

source_name: Patient 1 small intestine normal tissue

value: FAP Patient 1

value: adenoma


title: Cord_Blood_NonTD_male_21


title: RNA_CRC1_C_R1_B1

source_name: non-FAP patient1 carcinoma region1 batch1


title: Cord_Blood_NonTD_male_22


title: Cord_Blood_NonTD_male_20

value: MARBLES


title: RNA_FAP1_LI_N

source_name: Patient 1 large intestine adjacent normal tissue


title: Cord_Blood_NonTD_male_25


title: RNA_FAP1_C_R4

source_name: Patient 1 carcinoma region4


title: Cord_Blood_NonTD_male_19

source_name: Umbilical cord blood from Non-TD male subject


title: RNA_FAP1_C_R3

source_name: Patient 1 carcinoma region3


title: Cord_Blood_NonTD_male_18


title: Cord_Blood_NonTD_male_16


title: RNA_FAP1_C_R1

source_name: Patient 1 carcinoma region1


title: RNA_FAP1_A3

source_name: Patient 1 third adenoma


title: RNA_FAP1_A1_R3

source_name: Patient 1 first adenoma region3


title: Cord_Blood_NonTD_male_17


title: RNA_FAP1_A1_R2

source_name: Patient 1 first adenoma region2


title: Cord_Blood_NonTD_male_14


title: Cord_Blood_NonTD_male_15


title: Cord_Blood_NonTD_male_12


title: Cord_Blood_NonTD_male_13


title: Cord_Blood_NonTD_male_10


title: Cord_Blood_NonTD_male_9


title: RNA_FAP1_C_R2

source_name: Patient 1 carcinoma region2


title: RNA_FAP4_SI_N_B1

source_name: Patient 4 small intestine normal tissue batch1

value: FAP Patient 4


title: RNA_FAP4_SI_N_B2

source_name: Patient 4 small intestine normal tissue batch2


title: RNA_FAP1_A1_R1

source_name: Patient 1 first adenoma region1


title: RNA_FAP4_LI_N2_B2

source_name: Patient 4 second adjacent normal tissue batch2


title: RNA_FAP4_A7_R3

source_name: Patient 4 seventh adenoma region3


title: RNA_FAP4_A7_R2

source_name: Patient 4 seventh adenoma region2


title: Cord_Blood_NonTD_male_5


title: Cord_Blood_NonTD_male_6


title: RNA_FAP4_LI_N1_B1

source_name: Patient 4 first adjacent normal tissue batch1


title: RNA_FAP4_A7_R1

source_name: Patient 4 seventh adenoma region1


title: Cord_Blood_NonTD_male_3


title: Cord_Blood_NonTD_male_4


title: Cord_Blood_NonTD_male_7


title: Cord_Blood_NonTD_male_2


title: Cord_Blood_NonTD_male_1


title: Cord_Blood_NonTD_male_8


title: RNA_FAP4_A6_R2

source_name: Patient 4 sixth adenoma region2


title: Cord_Blood_NonTD_female_37

source_name: Umbilical cord blood from Non-TD female subject

value: female


title: Cord_Blood_NonTD_male_11

source_name: Umbilical cord blood from Non-TD male subject

value: Non-TD


title: RNA_FAP4_A6_R1

source_name: Patient 4 sixth adenoma region1


title: RNA_FAP4_A5_R2

source_name: Patient 4 fifth adenoma region2


title: RNA_FAP4_A4

source_name: Patient 4 fourth adenoma


title: RNA_FAP4_A3

source_name: Patient 4 third adenoma


title: RNA_FAP4_A2

source_name: Patient 4 second adenoma


title: RNA_FAP4_A6_R3

source_name: Patient 4 sixth adenoma region3


title: RNA_FAP4_A1

source_name: Patient 4 first adenoma


title: RNA_FAP5_LI_N2_B2

source_name: Patient 5 second adjacent normal tissue batch2

value: FAP Patient 5


title: RNA_FAP5_LI_N2_B1

source_name: Patient 5 second adjacent normal tissue batch1


title: Cord_Blood_NonTD_female_36

value: EARLI


title: Cord_Blood_NonTD_female_35


title: RNA_FAP5_LI_N1_B1

source_name: Patient 5 first adjacent normal tissue batch1


title: Cord_Blood_NonTD_female_33


title: Cord_Blood_NonTD_female_32


title: Cord_Blood_NonTD_female_34


title: Cord_Blood_NonTD_female_31


title: RNA_FAP5_A8_R2

source_name: Patient 5 eighth adenoma region2


title: RNA_FAP5_A8_R3

source_name: Patient 5 eighth adenoma region3


title: Cord_Blood_NonTD_female_30


title: RNA_FAP5_A8_R1

source_name: Patient 5 eighth adenoma region1


title: RNA_FAP5_A7_R2

source_name: Patient 5 seventh adenoma rergion2


title: RNA_FAP5_A7_R1

source_name: Patient 5 seventh adenoma rergion1


title: Cord_Blood_NonTD_female_28

source_name: Umbilical cord blood from Non-TD female subject


title: RNA_FAP5_A6_R2

source_name: Patient 5 sixth adenoma region2


title: Cord_Blood_NonTD_female_27


title: RNA_FAP5_A5_R1

source_name: Patient 5 fifth adenoma region1


title: RNA_FAP5_A4_B1

source_name: Patient 5 fourth adenoma batch1


title: RNA_FAP5_A4_B2

source_name: Patient 5 fourth adenoma batch2


title: Cord_Blood_NonTD_female_26


title: RNA_FAP5_A7_R3

source_name: Patient 5 seventh adenoma rergion3


title: RNA_FAP5_A3_B1

source_name: Patient 5 third adenoma batch1


title: Cord_Blood_NonTD_female_25


title: Cord_Blood_NonTD_female_23


title: Cord_Blood_NonTD_female_22


title: Cord_Blood_NonTD_female_18


title: Cord_Blood_NonTD_female_24


title: Cord_Blood_NonTD_female_13


title: Cord_Blood_NonTD_male_34

source_name: Umbilical cord blood from Non-TD male subject

value: male


title: Cord_Blood_NonTD_female_29


title: RNA_FAP5_A6_R1

source_name: Patient 5 sixth adenoma region1


title: Cord_Blood_NonTD_female_20


title: Cord_Blood_NonTD_female_21


title: Cord_Blood_NonTD_female_19


title: Cord_Blood_NonTD_female_16


title: RNA_FAP5_A1

source_name: Patient 5 first adenoma


title: RNA_FAP5_A3_B2

source_name: Patient 5 third adenoma batch2


title: RNA_FAP5_A2

source_name: Patient 5 second adenoma


title: siILF3 + poly(I:C) Polysome pool 3

city: Aarhus C

first: Samir

last: Watson

state: Midtjylland

address: Universitetsbyen 83

department: Institute of Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description:
processed data (pairwise comparison):
poly_MP_MnP_polyseq_EdgeR.set.pc.tbl
poly_SnP_MnP_polyseq_EdgeR.set.pc.tbl
poly_SP_MnP_polyseq_EdgeR.set.pc.tbl
poly_SP_MP_polyseq_EdgeR.set.pc.tbl

data_processing:
adapter contamination removed from the original reads with the cutadapt v0.9.4 software (http://code.google.com/p/cutadapt/).  Reads shorter than 25bp after adapter trimming and quality filtering were discarded
; quantification of transcript and gene level abundances per sample were performed with Salmon v0.9.1 (parameters: --seqBias -g) over the Gencode v24 reference human transcriptome. Estimated counts were retrieved as input for differential expression analyses
reads over the 500nts at the 3' end of transcripts were used to generate read-count tables for all samples. Only genes that had at least an average of 10 read counts were analyzed for evidence of differential abundance
full-quantile normalization with the EDA package
Genome_build: hg38

source_name: HeLa_siILF3 transfected_poly(IC) +

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% FBS

extract_protocol:
Cytoplasmic lysates of HeLa cells treated with siRNAs and transfected with or without poly(I:C) were fractionated on a sucrose gradient into 10 fractions. Fractions 1-5 were pooled and fractions 6-to 10 were pooled to form subpolysomal and polysomal pools. RNA was extracted by first precipitating the RNA overnight in ethanol and finally exctacted using Trizol LS.
The libraries were enriched for polyA tailed RNA libraries were prepared using the Illumina Truseq protocol (Illumina)

treatment_protocol: HeLa cells were transfected with siRNAs targetting ILF3 (siILF3) or with non-targetting siRNAs(Mock) for 72h. The cells were then transfected with or without poly(I:C) for 4 hours

value: HeLa

tag: cell type

value: cervix adenocarcinoma cells

tag: treatment

value: siILF3 transfected, poly(IC) +

tag: polysome pools

value: Polysomal

tag: molecule subtype

value: Polysome profile associated  RNA


title: siMock - poly(I:C) Polysome pool 3

source_name: HeLa_Mock transfected_poly(IC) -

value: Mock transfected, poly(IC) -


title: siMock + poly(I:C) Polysome pool 3

source_name: HeLa_Mock transfected_poly(IC) +

value: Mock transfected, poly(IC) +


title: Cord_Blood_NonTD_female_15


title: Cord_Blood_NonTD_female_14


title: siILF3 - poly(I:C) Polysome pool 3

data_processing:
adapter contamination removed from the original reads with the cutadapt v0.9.4 software (http://code.google.com/p/cutadapt/).  Reads shorter than 25bp after adapter trimming and quality filtering were discarded
; quantification of transcript and gene level abundances per sample were performed with Salmon v0.9.1 (parameters: --seqBias -g) over the Gencode v24 reference human transcriptome. Estimated counts were retrieved as input for differential expression analyses. Reads over the 500nts at the 3' end of transcripts were used to generate read-count tables for all samples. Only genes that had at least an average of 10 read counts were analyzed for evidence of differential abundance
full-quantile normalization with the EDA package
Genome_build: hg38

source_name: HeLa_siILF3 transfected_poly(IC) -

value: siILF3 transfected, poly(IC) -


title: Cord_Blood_NonTD_female_17


title: siILF3 - poly(I:C) Polysome pool 2


title: siILF3 + poly(I:C) Polysome pool 2


title: Cord_Blood_NonTD_female_11


title: Cord_Blood_NonTD_female_12


title: siILF3 + poly(I:C) Polysome pool 1


title: siMock + poly(I:C) Polysome pool 2


title: siILF3 - poly(I:C) Polysome pool 1


title: siMock - poly(I:C) Polysome pool 2


title: Cord_Blood_NonTD_female_7


title: Cord_Blood_NonTD_female_9


title: Cord_Blood_NonTD_female_6


title: Cord_Blood_NonTD_female_8


title: siMock - poly(I:C) Polysome pool 1


title: Total RNA siILF3 + poly(I:C) 3

data_processing:
adapter contamination removed from the original reads with the cutadapt v0.9.4 software (http://code.google.com/p/cutadapt/).  Reads shorter than 25bp after adapter trimming and quality filtering were discarded
; quantification of transcript and gene level abundances per sample were performed with Salmon v0.9.1 (parameters: --seqBias -g) over the Gencode v24 reference human transcriptome. Estimated counts were retrieved as input for differential expression analyses
reads over the 500nts at the 3' end of transcripts were used to generate read-count tables for all samples. Only genes that had at least an average of 10 read counts were analyzed for evidence of differential abundance
full-quantile normalization with the EDA package
Genome_build: hg38
Supplementary_files_format_and_content: normalized read counts

source_name: HeLa

extract_protocol:
RNA was extracted using Trizol
The libraries were depleted of Ribosomes using the Ribo-zero rRNA depletion kit (Illumina) and strand-specific libraries were prepared using the Illumina Truseq protocol (Illumina)

value: HeLa, cervix adenocarcinoma cells


title: siMock + poly(I:C) Polysome pool 1


title: Total RNA siILF3 + poly(I:C) 1


title: Cord_Blood_NonTD_female_5

source_name: Umbilical cord blood from Non-TD female subject


title: Cord_Blood_NonTD_female_10


title: Cord_Blood_NonTD_female_4


title: Total RNA siILF3 - poly(I:C) 3


title: Cord_Blood_NonTD_male_23


title: Cord_Blood_NonTD_female_2


title: Cord_Blood_NonTD_female_3


title: Cord_Blood_ASD_male_36

source_name: Umbilical cord blood from ASD male subject

value: ASD


title: Cord_Blood_NonTD_male_24


title: Cord_Blood_ASD_male_37


title: Total RNA siILF3 - poly(I:C) 2


title: Cord_Blood_ASD_male_34


title: Total RNA siILF3 - poly(I:C) 1


title: Total RNA siMock + poly(I:C) 3


title: Total RNA siMock + poly(I:C) 1


title: Total RNA siILF3 + poly(I:C) 2


title: Cord_Blood_ASD_male_33


title: Cord_Blood_ASD_male_31


title: Total RNA siMock - poly(I:C) 2


title: Total RNA siMock - poly(I:C) 3


title: Cord_Blood_NonTD_female_1

value: MARBLES


title: Cord_Blood_ASD_male_32


title: Cord_Blood_ASD_male_35


title: Cord_Blood_ASD_male_30


title: Cord_Blood_ASD_male_28


title: Cord_Blood_ASD_male_29


title: Total RNA siMock - poly(I:C) 1


title: Cord_Blood_ASD_male_26


title: Cord_Blood_ASD_male_27


title: Total RNA siMock + poly(I:C) 2


title: RNA_FAP7_A_B2

description:
processed data file:
Colon_FAP_TPM_new2.txt

data_processing:
library strategy: single cell RNA-Seq
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling
scRNA-Seq:Read 2 was used to abtain the cell barcodes to further split the reads according to the cell IDs(barcode) and the same time recorded the UMI sequences;Read 1 was picked in each cell according to the cell ID in read2 and the UMI information was aligned to it,and then these raw reads were trimmed to remove TSO or polyA sequence;Adaptor contamination and low-quality reads were discarded from the trimmed Read 1 raw data;TopHat(version 2.0.14) with default settings were used for sequence alignment and uniquely mapped reads were kept.
Whole genome sequencing: Quality control pipeline was firstly performed on paired-end sequencing data to remove low quality reads. The cleaned reads were mapped to human genome (hg19) by BWA. The total sequence reads of each 10M window were calculated and normalized by the total read depth of each samples. For each 10M window, they were normalized by dividing the average reads depth of all samples. Finally, the CNV values were visualized by ggplot2 package.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each single cell RNA samples; tab-delimited text files include reads number per 10M windows of each bulk DNA samples.

source_name: Patient 4 adenoma batch2

value: Patient 4

value: adenoma


title: RNA_FAP7_N

source_name: Patient 4 adjacent normal tissue

value: adjacent normal tissue


title: Cord_Blood_ASD_male_25


title: RNA_FAP7_A_B1

source_name: Patient 4 adenoma batch1


title: Cord_Blood_ASD_male_24


title: RNA_FAP2_C_R4

source_name: Patient 3 third adenocarcinoma region4

value: Patient 3

value: adenocarcinoma


title: RNA_FAP2_C_R3

source_name: Patient 3 third adenocarcinoma region3


title: RNA_FAP2_C_R1

source_name: Patient 3 third adenocarcinoma region1


title: RNA_FAP2_C_R2

source_name: Patient 3 third adenocarcinoma region2


title: RNA_FAP2_A1_R2

source_name: Patient 3 small adenoma region2


title: Cord_Blood_ASD_male_20

value: male


title: Cord_Blood_ASD_male_21


title: Cord_Blood_ASD_male_22


title: RNA_FAP2_A1_R1

source_name: Patient 3 small adenoma region1


title: Cord_Blood_ASD_male_19


title: RNA_FAP2_N_B2

source_name: Patient 3 adjacent normal tissue batch2


title: RNA_FAP2_N_B1

source_name: Patient 3 adjacent normal tissue batch1


title: RNA_FAP2_A2_R2

source_name: Patient 3 medium adenoma region2


title: RNA_FAP2_C_R5

source_name: Patient 3 third adenocarcinoma region5


title: Cord_Blood_ASD_male_23


title: Cord_Blood_ASD_male_17


title: RNA_FAP2_LM_R2

source_name: Patient 3 first lymphatic metastasis region2


title: RNA_FAP2_A2_R1

source_name: Patient 3 medium adenoma region1


title: Cord_Blood_ASD_male_16


title: Cord_Blood_ASD_male_18


title: RNA_FAP2_C2_R3

source_name: Patient 3 second adenocarcinoma region 3


title: Cord_Blood_ASD_male_14

source_name: Umbilical cord blood from ASD male subject


title: RNA_FAP2_LM_R1

source_name: Patient 3 first lymphatic metastasis region1


title: Cord_Blood_ASD_male_13


title: Cord_Blood_ASD_male_10


title: Cord_Blood_ASD_male_12


title: Cord_Blood_ASD_male_11


title: RNA_FAP2_C2_R2

source_name: Patient 3 second adenocarcinoma region 2


title: Cord_Blood_ASD_male_15


title: RNA_FAP2_C2_R1

source_name: Patient 3 second adenocarcinoma region 1


title: RNA_FAP2_C1_R3

source_name: Patient 3 first adenocarcinoma region 3


title: Cord_Blood_ASD_male_7


title: RNA_FAP2_C1_R2

source_name: Patient 3 first adenocarcinoma region 2


title: RNA_FAP2_C1_R1

source_name: Patient 3 first adenocarcinoma region 1


title: RNA_FAP6_C2_B2

source_name: Patient 2 descending colon adenocarcinoma batch 2

value: Patient 2


title: Cord_Blood_ASD_male_8


title: Cord_Blood_ASD_male_9


title: RNA_FAP6_A5

source_name: Patient 2 second descending colon adenoma


title: RNA_FAP6_C2_B1

source_name: Patient 2 descending colon adenocarcinoma batch 1


title: RNA_FAP6_C1_B2

source_name: Patient 2 ascending colon adenocarcinoma batch 2


title: Cord_Blood_ASD_male_4


title: Cord_Blood_ASD_male_5


title: Cord_Blood_ASD_male_3


title: RNA_FAP6_C1_B1

source_name: Patient 2 ascending colon adenocarcinoma batch 1


title: Cord_Blood_ASD_female_15

source_name: Umbilical cord blood from ASD female subject

value: female

value: EARLI


title: Cord_Blood_ASD_female_16


title: RNA_FAP6_N1

source_name: Patient 2 ascending colon adjacent normal tissue


title: Cord_Blood_ASD_male_1


title: RNA_FAP6_C3

source_name: Patient 2 fourth ascending colon adenoma


title: Cord_Blood_ASD_female_14


title: RNA_FAP6_A3

source_name: Patient 2 third ascending colon adenoma


title: Cord_Blood_ASD_male_6


title: RNA_FAP6_A2

source_name: Patient 2 second ascending colon adenoma


title: RNA_FAP6_A1

source_name: Patient 2 first ascending colon adenoma


title: Cord_Blood_ASD_female_12


title: Cord_Blood_ASD_female_10


title: RNA_FAP6_N2

source_name: Patient 2 descending colon adjacent normal tissue


title: Cord_Blood_ASD_male_2

source_name: Umbilical cord blood from ASD male subject


title: Cord_Blood_ASD_female_11


title: Cord_Blood_ASD_female_6


title: Cord_Blood_ASD_female_8


title: Cord_Blood_ASD_female_9


title: Cord_Blood_ASD_female_13


title: RNA_FAP3_A1_R1

source_name: Patient 1 small adenoma region 1

value: Patient 1


title: RNA_FAP3_N_B1

source_name: Patient 1 adjacent normal tissue batch1


title: RNA_FAP3_A1_R2

source_name: Patient 1 small adenoma region 2


title: RNA_FAP3_C_R1

source_name: Patient 1 adenocarcinoma region 1


title: RNA_FAP3_A2_R2

source_name: Patient 1 large adenoma region 2


title: RNA_FAP3_N_B2

source_name: Patient 1 adjacent normal tissue batch2


title: RNA_FAP3_A2_R1

source_name: Patient 1 large adenoma region 1


title: RNA_FAP3_C_R2

source_name: Patient 1 adenocarcinoma region 2


title: Sulf2-TTR Gli1 KO replicate 3

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

description:
1647-liver_tumor
processed data file: GeneCount.tsv

data_processing:
Base calling was performed with the Illumina bcl2fastq.
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/).
The paired end reads were aligned by TopHat 2.0.6.
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: GeneCount.tsv: Tab-delimited text file includes raw counts and RPKM values for each gene per sample.

source_name: Liver tumor

extract_protocol:
Standard Trizol-based extraction protocol.
cDNA libraries were generated in accord with the Illumina RNA-Seq preparation protocol.

value: SULF2 overexpression with Gli1 KO

value: Liver tumor


title: Sulf2-TTR Gli1 KO replicate 1

description:
1767-liver-tumor
processed data file: GeneCount.tsv


title: Sulf2-TTR Gli1 KO replicate 2

description:
4206-liver_tumor
processed data file: GeneCount.tsv


title: Sulf2-TTR Gli1 WT replicate 3

description:
3981-liver_tumor
processed data file: GeneCount.tsv

value: SULF2 overexpression with WT Gli1


title: Sulf2-TTR Gli1 WT replicate 2

description:
4204-liver_tumor
processed data file: GeneCount.tsv